diff --git a/.github/workflows/tagbot.py b/.github/workflows/tagbot.py new file mode 100644 index 00000000000..26472f8bcbd --- /dev/null +++ b/.github/workflows/tagbot.py @@ -0,0 +1,182 @@ +# NOTE: In order to write comment and edit labels, this script requires workflows with write permissions. +# It should not use any untrusted third party code, or any code checked into the repository itself +# as that could indirectly grant PRs the ability to edit labels and comments on PRs. + +import os +import git +import requests +import json +from pathlib import Path + + +def get_first_commit_date(repo, file_path): + commits = list(repo.iter_commits(paths=file_path)) + if commits: + return commits[-1].committed_date + else: + raise ValueError(f'{file_path} has no commit info, this should not happen') + + +def sort_by_added_date(repo, file_paths): + files_with_dates = [(get_first_commit_date(repo, file_path), file_path) for file_path in file_paths] + sorted_files = sorted(files_with_dates, reverse=True) + return [file for date, file in sorted_files] + + +def similar_easyconfigs(repo, new_file): + possible_neighbours = [x for x in new_file.parent.glob('*.eb') if x != new_file] + return sort_by_added_date(repo, possible_neighbours) + + +def pr_ecs(pr_diff): + new_ecs = [] + changed_ecs = [] + for item in pr_diff: + if item.a_path.endswith('.eb'): + if item.change_type == 'A': + new_ecs.append(Path(item.a_path)) + else: + changed_ecs.append(Path(item.a_path)) + return new_ecs, changed_ecs + + +GITHUB_API_URL = 'https://api.github.com' +event_path = os.getenv('GITHUB_EVENT_PATH') +token = os.getenv('GH_TOKEN') +repo = os.getenv('GITHUB_REPOSITORY') +base_branch_name = os.getenv('GITHUB_BASE_REF') + +with open(event_path) as f: + data = json.load(f) + +pr_number = data['pull_request']['number'] +# Can't rely on merge_commit_sha for pull_request_target as it might be outdated +# merge_commit_sha = data['pull_request']['merge_commit_sha'] + +print("PR number:", pr_number) +print("Base branch name:", base_branch_name) + +# Change into "pr" checkout directory to allow diffs and glob to work on the same content +os.chdir('pr') +gitrepo = git.Repo('.') + +target_commit = gitrepo.commit('origin/' + base_branch_name) +print("Target commit ref:", target_commit) +merge_commit = gitrepo.head.commit +print("Merge commit:", merge_commit) +pr_diff = target_commit.diff(merge_commit) + +new_ecs, changed_ecs = pr_ecs(pr_diff) +modified_workflow = any(item.a_path.startswith('.github/workflows/') for item in pr_diff) + + +print("Changed ECs:", ', '.join(str(p) for p in changed_ecs)) +print("Newly added ECs:", ', '.join(str(p) for p in new_ecs)) +print("Modified workflow:", modified_workflow) + +new_software = 0 +updated_software = 0 +to_diff = dict() +for new_file in new_ecs: + neighbours = similar_easyconfigs(gitrepo, new_file) + print(f"Found {len(neighbours)} neighbours for {new_file}") + if neighbours: + updated_software += 1 + to_diff[new_file] = neighbours + else: + new_software += 1 + +print(f"Generating comment for {len(to_diff)} updates softwares") +# Limit comment size for large PRs: +if len(to_diff) > 20: # Too much, either bad PR or some broad change. Not diffing. + max_diffs_per_software = 0 +elif len(to_diff) > 10: + max_diffs_per_software = 1 +elif len(to_diff) > 5: + max_diffs_per_software = 2 +else: + max_diffs_per_software = 3 + +comment = '' +if max_diffs_per_software > 0: + for new_file, neighbours in to_diff.items(): + compare_neighbours = neighbours[:max_diffs_per_software] + if compare_neighbours: + print(f"Diffs for {new_file}") + comment += f'#### Updated software `{new_file.name}`\n\n' + + for neighbour in compare_neighbours: + print(f"against {neighbour}") + comment += '
\n' + comment += f'Diff against {neighbour.name}\n\n' + comment += f'[{neighbour}](https://github.com/{repo}/blob/{base_branch_name}/{neighbour})\n\n' + comment += '```diff\n' + comment += gitrepo.git.diff(f'HEAD:{neighbour}', f'HEAD:{new_file}') + comment += '\n```\n
\n\n' + +print("Adjusting labels") +current_labels = [label['name'] for label in data['pull_request']['labels']] + +label_checks = [(changed_ecs, 'change'), + (new_software, 'new'), + (updated_software, 'update'), + (modified_workflow, 'workflow')] + +labels_add = [] +labels_del = [] +for condition, label in label_checks: + if condition and label not in current_labels: + labels_add.append(label) + elif not condition and label in current_labels: + labels_del.append(label) + +url = f"{GITHUB_API_URL}/repos/{repo}/issues/{pr_number}/labels" + +headers = { + "Accept": "application/vnd.github+json", + "Authorization": f"Bearer {token}", + "X-GitHub-Api-Version": "2022-11-28", +} + +if labels_add: + print(f"Setting labels: {labels_add} at {url}") + response = requests.post(url, headers=headers, json={"labels": labels_add}) + if response.status_code == 200: + print(f"Labels {labels_add} added successfully.") + else: + print(f"Failed to add labels: {response.status_code}, {response.text}") + +for label in labels_del: + print(f"Removing label: {label} at {url}") + response = requests.delete(f'{url}/{label}', headers=headers) + if response.status_code == 200: + print(f"Label {label} removed successfully.") + else: + print(f"Failed to delete label: {response.status_code}, {response.text}") + +# Write comment with diff +if updated_software: + # Search for comment by bot to potentially replace + url = f"{GITHUB_API_URL}/repos/{repo}/issues/{pr_number}/comments" + response = requests.get(url, headers=headers) + comment_id = None + for existing_comment in response.json(): + if existing_comment["user"]["login"] == "github-actions[bot]": # Bot username in GitHub Actions + comment_id = existing_comment["id"] + + if comment_id: + # Update existing comment + url = f"{GITHUB_API_URL}/repos/{repo}/issues/comments/{comment_id}" + response = requests.patch(url, headers=headers, json={"body": comment}) + if response.status_code == 200: + print("Comment updated successfully.") + else: + print(f"Failed to update comment: {response.status_code}, {response.text}") + else: + # Post a new comment + url = f"{GITHUB_API_URL}/repos/{repo}/issues/{pr_number}/comments" + response = requests.post(url, headers=headers, json={"body": comment}) + if response.status_code == 201: + print("Comment posted successfully.") + else: + print(f"Failed to post comment: {response.status_code}, {response.text}") diff --git a/.github/workflows/tagbot.yml b/.github/workflows/tagbot.yml new file mode 100644 index 00000000000..8c0fa06294b --- /dev/null +++ b/.github/workflows/tagbot.yml @@ -0,0 +1,54 @@ +name: Tagbot +on: [pull_request_target] + +concurrency: + group: "${{ github.workflow }}-${{ github.event.pull_request.number }}" + cancel-in-progress: true + +jobs: + tagbot: + # Note: can't rely on github.event.pull_request.merge_commit_sha because pull_request_target + # does not wait for github mergability check, and the value is outdated. + # Instead we merge manually in a temporary subdir "pr" + runs-on: ubuntu-24.04 + permissions: + pull-requests: write + steps: + - name: Checkout base branch for workflow scripts + uses: actions/checkout@v4 + + - name: Checkout PR for computing diff into "pr" subdirectory + uses: actions/checkout@v4 + with: + ref: "${{ github.event.pull_request.head.sha }}" + path: 'pr' + fetch-depth: 0 + + - name: Attempt test merge + id: merge + run: | + git config user.name "github-workflow" + git config user.email "github-workflow@github.com" + git merge --no-edit --no-ff origin/${{ github.event.pull_request.base.ref }} + continue-on-error: true + working-directory: pr + + - name: Abort if merge failed + if: steps.merge.outcome == 'failure' + run: | + echo "Merge conflict detected, failing job." + exit 1 + + - name: set up Python + uses: actions/setup-python@v5 + with: + python-version: 3.12 + + - name: Get packages + run: pip install gitpython requests + + - name: Tag and comment + env: + GH_TOKEN: ${{ secrets.GITHUB_TOKEN }} + run: python .github/workflows/tagbot.py + diff --git a/.gitignore b/.gitignore index c667a41e000..c2974194435 100644 --- a/.gitignore +++ b/.gitignore @@ -1,12 +1,15 @@ .pydevproject .project LICENSE_HEADER +*.eb.bak_* *.pyc *.pyo *.nja +*.out build/ dist/ *egg-info/ +.venv/ *.swp *.ropeproject/ eb-*.log diff --git a/RELEASE_NOTES b/RELEASE_NOTES index 45d27a2e696..af2e74ae887 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -3,8 +3,298 @@ For more detailed information, please see the git log. These release notes can also be consulted at https://docs.easybuild.io/en/latest/Release_notes.html. -The latest version of easybuild-easyconfig provides 19,487 easyconfig files, for 3,470 different software packages, -incl. 40 different (compiler) toolchains. +The latest version of easybuild-easyconfig provides 20,670 easyconfig files, for 3,670 different software packages, +incl. 41 different (compiler) toolchains. + + +v4.9.4 (22 September 2024) +-------------------------- + +update/bugfix release + +- added example easyconfig files for 14 new software packages: + - Biotite (#21026), chopper (#21418), CLUMPP (#21329), cramino (#21382), dub (#21378), ESM3 (#21026), GOMC (#21008), + MOKIT (#21352), nanoQC (#21371), phasius (#21389), PyBullet (#21356), rnamotif (#21336), versioningit (#21424), + xskillscore (#21351) +- added additional easyconfigs for various supported software packages, including: + - awscli 2.17.54, BiG-SCAPE-1.1.9, ccache 4.10.2, CLHEP 2.4.7.1, CREST 3.0.2, decona 1.4-2024073, dftd4 3.7.0, + GATE 9.4, Gdk-Pixbuf 2.42.11, Geant4 11.2.2, Geant4-data 11.2, Ghostscript 10.03.1, GitPython 3.1.43, + GObject-Introspection 1.80.1, HarfBuzz 9.0.0, ImageMagick 7.1.1-38, JasPer 4.2.4, joypy 0.2.6, Julia 1.10.4, + LDC 1.39.0, Leptonica 1.84.1, Markdown 3.7, MPICH 4.2.2, NanoComp 1.24.0, nanoget 1.19.3, nanomath 1.4.0, + NanoPlot 1.43.0, Pango 1.54.0, PCAngsd 1.2, Pillow 10.4.0, python-isal 1.7.0, pocl 6.0, PROJ 9.4.1, protobuf 28.0, + protobuf-python 5.28.0, R-tesseract 5.2.1, RepeatMasker 4.1.7-p1, RHEIA 1.1.11, RMBlast 2.14.1, + scikit-build-core 0.10.6, sleuth 0.30.1, SNAP-ESA 10.0.0, tesseract 5.3.4, Triton 2.1.0, TurboVNC 3.1.2, + VirtualGL 3.1.1, zlib-ng 2.2.1 +- minor enhancements, including: + - enable support for Apache ORC to Arrow v14.0.1 and v16.1.0 (#21056) + - use proper dependency for tensorboard in easyconfigs for TensorFlow v2.15.1 (#21337) +- various bug fixes, including: + - account for crates for easyconfigs using Cargo-based easyblock when determining checksums for patches in easyconfigs test suite (#21419) + - avoid missing symbol in mclust extension of R-4.0.3 w/ foss/2020b (#21429) + - fix build of librosa 0.10.1 in some environments by removing "python -m build" for soxr extension (#21434) + - fix repeated sanity check runs in manta easyconfigs (#21435) + - fix test_easyconfig_locations when easyconfigs index is present (#21394) + - use proper dependency for libnsl in git-annex (#21441) + - avoid writing into ~/.stack directory during build for git-annex (#21452) +- other changes: + - remove exts_default_options from TensorFlow 2.3.1 (#21290) + + +v4.9.3 (14 September 2024) +-------------------------- + +update/bugfix release + +- added easyconfigs for foss/2024a (#21100) and intel/2024a (#21101) common toolchains +- new toolchain: gmpflf/2024.06 (#20882) +- added example easyconfig files for 107 new software packages: + - absl-py (#21039), accelerate (#21107), affogato (#20636), APOST3D (#21133), bayesian-optimization (#21301), + BayesOpt (#21261), BGEN-enkre (#15752), bitsandbytes (#21248), bliss (#21206), cfgrib (#21113), CLANS (#21099), + colorize (#20964), CORSIKA (#20693), COSTA (#20989), coxeter (#21254), Critic2 (#20833), crypt4gh (#20870), + dblatex (#21207), dictys (#21166), DL_POLY_Classic_GUI (#20819), EGA-QuickView (#20870, #20888), EMMAX (#21174), + empanada-dl (#20454), empanada-napari (#20454), ESIpy (#21006), fastfilters (#21003), fish (#21345, #21381), + flash-attention (#21083), Flax (#21039), fonttools (#21363), fsm-lite (#20503), GDMA (#21171), GeoDict (#20650), + GPflow (#21172), gtk-doc (#21207), Gubbins (#20413), Gymnasium (#20420), HERRO (#21252), IEntropy (#20808), + ilastik-napari (#21003), IMAGE (#20994), junos-eznc (#21166), jupyter-collaboration (#20741), + jupyter-vscode-proxy (#20876), langchain-mistralai (#20759), langchain-openai (#20711), LRBinner (#21310), + lrcalc (#21339), MAGIC (#20900), mallard-ducktype (#21127), MATES (#21229), MBX (#21155), mcqd (#21283), + MeshLab (#20806), meteogrid (#20921), micro-sam (#20636), miniprot (#21157), napari-denoiseg (#20934), + NECAT (#21359), nellie (#21267), NextPolish (#21265), nifty (#20636), ome-types (#21256), openai-python (#20711), + OpenForceField-Toolkit (#20852), orjson (#20880), PEcAn (#21227), PretextMap (#20790), PyBEL (#20953), + pyMBE (#21034), pystencils (#20889), python-blosc (#20636), python-elf (#20636), rankwidth (#20788), Rasqal (#21207), + Redland (#21227), Regenie (#15752), rMATS-long (#20916), Sagemath (#21365), scCustomize (#20907), SCENICplus (#21085), + scFEA (#20777), sdsl-lite (#20503), SharedMeatAxe (#21303), Single-cell-python-bundle (#20116), SIRIUS (#20989), + sirocco (#21304), SKA2 (#20411), SpFFT (#20989), spla (#11607), Stable-Baselines3 (#20884), submitit (#21103), + SVDSS2 (#20855), tdlib (#21305), torch-em (#20636), Umpire (#20989), Uni-Core (#21182), vigra (#20636), + Visit (#20981), weblogo (#20800), wradlib (#21110), xtb-IFF (#20783), yell (#20964), yelp-tools (#21127), + yelp-xsl (#21127), z5py (#20636), Zoltan (#21324) +- added additional easyconfigs for various supported software packages, including: + - AGAT 1.4.0, ASE 3.23.0, Abseil 20240722.0, Albumentations 1.4.0, AlphaPulldown 2.0.0b4, AlphaPulldown 2.0.0b4, + AmberTools 26.3, Arrow 16.1.0, alsa-lib 1.2.11, archspec 0.2.4, attr 2.5.2, BayesTraits 4.1.2, BeautifulSoup 4.12.3, + Biopython 1.84, Boost.MPI 1.83.0, bcl-convert 4.2.7-2, beagle-lib 4.0.1, biom-format 2.1.16, byacc 2.0.20240109, + CDO 2.3.0, CFITSIO 4.4.1, CUDA-Samples 12.2, CUDA 12.5.0 + 12.6.0, CUTLASS 3.4.0, Catch2 2.13.10, CellOracle 0.18.0, + Clang 18.1.8, Coreutils 9.5, chewBBACA 3.3.9, code-server 4.90.2, connected-components-3d 3.14.1, cooler 0.10.2, + cryptography 42.0.8, cutadapt 4.9, cyvcf2 0.31.1, dorado 0.7.3, dtcmp 1.1.5, ESMF 8.6.1, EvidentialGene 2023.07.15, + Extrae 4.2.0, ecBuild 3.8.5, elfutils 0.191, FFmpeg 7.0.2, FLAC 1.4.3, FUSE 3.16.2, Flask 3.0.3, Flye 2.9.4, + FriBidi 1.0.15, ffnvcodec 12.2.72.0, flatbuffers-python 24.3.25, flatbuffers 24.3.25, fmt 10.2.1, fpylll 0.6.1, + GCC 14.2.0, GDAL 3.9.0, GEOS 3.12.1, GHC 9.10.1, GLM 1.0.1, GLib 2.80.4, GLibmm 2.72.1 + 2.75.0 + 2.77.0 + 2.78.1, + GPAW 24.6.0, GetOrganelle 1.7.7.1, Guile 2.0.14 + 3.0.10, Gurobi 11.0.2, gap 4.13.0, genomepy 0.16.1, gensim 4.3.2, + gffutils 0.13, gh 2.52.0, git-annex 10.20240731, gmpy2 2.2.0, googletest 1.15.2, graph-tool 2.59, HDBSCAN 0.8.38.post1, + HOMER 4.11.1, HTSeq 2.0.7, HiCMatrix 17.2, Highway 1.2.0, Hypre 2.31.0, hatchling 1.24.2, histolab 0.7.0, + hypothesis 6.103.1, IQ-TREE 2.3.5, ImageMagick 7.1.1-34, Imath 3.1.11, IsoQuant 3.5.0, igraph 0.10.12, imageio 2.34.1, + imbalanced-learn 0.12.3, inferCNV 1.21.0, intervaltree 0.1, JsonCpp 1.9.5, Julia 1.10.4, jax 0.4.25, json-fortran 8.5.2, + Kent_tools 468, LLVM 18.1.8, LittleCMS 2.16, libdrm 2.4.122, libdwarf 0.10.1, libedit 20240517, libgeotiff 1.7.3, + libgit2 1.8.1, libopus 1.5.2, libsigc++ 3.6.0, libspatialindex 2.0.0, libunistring 1.2, libunwind 1.8.1, libwebp 1.4.0, + libxslt 1.1.42, libzip 1.10.1, lwgrp 1.0.6, lxml 5.3.0, MCR R2024a, MPICH 4.2.1, MUMPS 5.7.2, MariaDB 11.6.0, + Maven 3.9.7, Mercurial 6.8.1, Mesa 24.1.3, Miniconda3 23.10.0-1, MultiQC 1.22.3, makedepend 1.0.9, matplotlib 3.9.2, + maturin 1.6.0, medaka 1.12.1, meshio 5.3.5, meson-python 0.16.0, mm-common 1.0.6, NanoCaller 3.6.0, Normaliz 3.10.3, + n2v 0.3.3, nano 8.1, ncbi-vdb 3.1.1, nettle 3.10, nsync 1.29.2, numexpr 2.9.0, ORCA 6.0.0, OpenEXR 3.2.4, OpenFOAM 12, + OpenFOAM v2406, OpenJPEG 2.5.2, Optax 0.2.2, Optuna 3.6.1, PaStiX 6.3.2, Perl-bundle-CPAN 5.38.2, Pillow-SIMD 10.4.0, + Pint 0.24, Platypus-Opt 1.2.0, PostgreSQL 16.4, PyAEDT 0.9.9, PyCharm 2024.1.6, PyRosetta 4.release-384, + PyWavelets 1.7.0, PyYAML 6.0.2, Pygments 2.18.0, Pylint 3.2.5, Pyomo 6.7.3, Python-bundle-PyPI 2024.06, packmol 20.14.4, + pagmo 2.19.0, parallel 20240722, pixman 0.43.4, pod5-file-format 0.3.10, poetry 1.8.3, popt 1.19, pretty-yaml 24.7.0, + primecount 7.14, psycopg 3.2.1, pyGenomeTracks 3.9, pybind11 2.12.0, pycocotools 2.0.7, pydantic 2.7.4, pygmo 2.19.5, + pyperf 2.7.0, pyseer 1.3.12, pysteps 1.10.0, QuantumESPRESSO 7.3.1, Qwt 6.3.0, R-bundle-CRAN 2024.06, R 4.4.1, + RDKit 2024.03.3, RapidJSON 1.1.0-20240409, Ray-project 2.9.1, ReFrame 4.6.2, Rust 1.79.0, redis-py 5.0.9, + regionmask 0.12.1, rjags 4-15, rpmrebuild 2.18, SDL2 2.30.6, SHAP 0.43.0, SIP 6.8.3, SRA-Toolkit 3.1.1, + STAR 2.7.11b_alpha_2024-02-09, STRUMPACK 7.1.0, SVDSS2 2.0.0-alpha.3, Safetensors 0.4.3, Salmon 1.10.3, + SciPy-bundle 2024.05, SeqKit 2.8.2, SingleM 0.16.0, Sphinx-RTD-Theme 2.0.0, Stack 3.1.1, SuiteSparse 7.7.0, + SuperLU 6.0.1, SuperLU_DIST 8.2.1, scArches 0.6.1, scib-metrics 0.5.1, scvi-tools 1.1.2, sdsl-lite 2.0.3, + setuptools-rust 1.9.0, sirocco 2.1.0, slepc4py 3.20.2, smafa 0.8.0, snpEff 5.2c, spaCy 3.7.4, spektral 1.2.0, + spglib-python 2.5.0, spglib 2.5.0, TELEMAC-MASCARET 8p5r0, Tk 8.6.14, Tkinter 3.12.3, Trycycler 0.5.5, tiktoken 0.7.0, + timm 1.0.8, UCX-CUDA 1.16.0, unixODBC 2.3.12, utf8proc 2.9.0, VSEARCH 2.28.1, virtualenv 20.26.2, WRF 4.5.1, + Wayland 1.23.0, X11 20240607, XGBoost 2.1.1, XML-LibXML 2.0210, x264 20240513, x265 3.6, xarray 2024.5.0, xtb-IFF 1.1, + xtb 6.7.1, xtensor 0.24.7, yelp-xsl 42.1 +- minor enhancements, including: + - add internal CUDA header patch for PSM2 v12.0.1 (#20804) + - add patch for JupyterHub support to recent tensorboard easyconfigs (#20823) + - make sure that recent ImageMagick versions pick up the right pkgconf + improve sanity check for ImageMagick (#20900) + - also install utilities for recent versions of FUSE 3.x (#20918) + - add RISC-V support to x264 v20231019 (#20968) + - add RISC-v support to recent LAME easyconfigs by removing workaround for finding libncurses (#20970) + - enable PIC in recent x265 easyconfigs to solve compilation errors on RISC-V (#20971) + - add extensions to R-bundle-CRAN: missmDA (#21167, #21183). insight (#21260), performance + datwizard + bayestestR (#21272, #21285) + - add Qt support to VTK 9.3.0 (#21221) + - add `helper_scripts` to `$PATH` in easyconfig for ProteinMPNN v1.0.1-20230627 (#21289) + - also build & install the plugins with OpenFOAM v2406 (#21332) +- various bug fixes, including: + - fix easyconfigs for recent versions of QuantumESPRESSO (#20070) + - add wrapper for Julia with linking safeguards and delegate environment setup to JuliaPackage (#20103) + - fix typo in description of SuiteSparse v7.7.0 (#20567) + - add 'pic' flag to IML (#20789) + - add patch to recent SciPy-bundle easyconfigs to fix build error with numpy with some Fortran compilers (#20817) + - rename unpacked sources for components of EasyBuild v4.9.2, to ensure that '`--install-latest-eb-release`' works with older EasyBuild versions (#20818) + - fix build of OpenBLAS 0.3.24 on A64FX (#20820) + - remove maturin build dependency from langchain-antropic (#20825) + - add GMP and MPFR as dependencies to OpenFOAM v2306 and v2312 (#20841) + - add patch to SciPy-bundle 2024.05 that fixes numpy test failures on RISC-V (#20847) + - skip unreliable memory leak test in PyTorch 2.1.2 (#20874) + - use PyYAML 6.0.1 instead of 6.0 for recent ReFrame versions to fix problem with Cython 3.x (#20879) + - use PyPI source tarball and gfbf/2023a toolchain for pyBigWig (#20881) + - add fix for failing test on zen4 to Highway 1.0.4 (#20942) + - add patch to fix implicit function declaration in OpenMPI 4.1.4 (#20949) + - only use libxsmm as dependency for CP2K 2023.1 w/ `foss/2023a` on x86_64 (#20951) + - copy missing `rsem_perl_utils.pm` in DETONATE, since it's required by `rsem-eval-calculate-score` command (#20956) + - set `$SATSUMA2_PATH` so Satsuma2 can locate executables (#20957) + - disable auto-vectorizer (`-ftree-vectorize`) for OpenFOAM v10 + v11 when using toolchain that with GCC >= 11 (#20958) + - disable test step for WIEN2k 23.2 because files required by it can no longer be downloaded (#20969) + - add patch to fix Qt6 issues with ParaView v5.12.0, e.g. representation selection (#21002) + - update homepage in phonopy easyconfigs (#21014) + - make libunwind dependency architecture specific in Extrae 4.2.0 easyconfig (#21017) + - add `OPENSSL_ENABLE_SHA1_SIGNATURES` for building `ansys-pythonnet` (#21028) + - fix download URLs for old Intel software (2018-2023) by using `IRC_NAS` instead of `irc_nas` (#21108) + - update source and homepage URLs in Szip easyconfigs (#21129) + - rename source URL in HDF v4.2.16-2 easyconfig (#21130) + - consistently fix homeage + source URL for `HDF` + `h4toh5` (#21134) + - ensure that recent BioPerl easyconfigs use `Bundle` easyblock (#21136) + - fix checksum checks for easyconfigs using a `Bundle`-like easyblock in easyconfigs test suite (#21143) + - add pkgconf build dependency to scikit-misc v0.3.1 (#21144) + - explicitly disable use of MySQL in recent GDAL easyconfigs (#21156) + - fix easyconfig tensorflow-probability v0.20.0 to pass `pip check` (#21172) + - stop RStudio-Server 2023.09 from installing R packages (+ move to `foss/2023a` toolchain) (#21175) + - remove `Time::HiRes` from `Perl-bundle-CPAN` since there's newer version in `Perl` (#21198) + - fix build of STAR 2.7.11a + 2.7.11b on non-x86 architectures by avoiding use of `-maxv2` + add missing `xxd` build dependency (#21200) + - add missing cairo dependency for python-igraph v0.10.6 (#21211) + - add patch for xtb 6.7.0 to fix build failure due to changes in tblite (#21255) + - add patch for HDF5 v1.14.3 to suppress fp exceptions (#21280) + - update easyconfig for dorado 0.7.3 to properly use provided OpenSSL dependency, and not install external libraries into its own lib directory (#21297) + - use proper Python dependency for OTF2 (#21325) + - use source tarballs from GitHub for recent libdap easyconfigs (#21334) + - remove Highway build dependency in Brunsli easyconfigs, since it's not actually required at all (#21366) + - add alternative checksum for bold 1.3.0 extension in R-bundle-CRAN (#21370) +- other changes: + - archive outdated example easyconfigs for Fujitsu toolchain (#20781) + - upgrade rpmrebuild build dependency to version 2.18 in bcl-convert 4.2.7 easyconfig (#20861) + - use proper dependency for Safetensors in easyconfig for Transformers v4.39.3 (#20864) + - remove CMake Arrow flag as there is no Arrow dependency in recent GDAL easyconfigs (#20905) + - whitelist `ConfigureMakePythonPackage` for `sanity_check_paths` CI check (#20963) + - rename `gubbins-2.4.0.eb` to `Gubbins-2.4.0.eb` (#20995) + - make pytest v7.4.2 independent of Python-bundle-PyPI (#21004) + - reorganize Flax/JAX stack in 2023a: move `jax` + `Optax` to `gfbf/2023a` toolchain + use standalone `Flax` + `absl-py` as dependencies (#21038) + - use stand-alone absl-py as dependency for jax w/ `gfbf/2023a` (#21039) + - remove Cython dependency from Python-bundle-PyPI 2024.06 + add standalone easyconfig for Cython 3.0.10 (#21233) + - add Cython build dependency for SciPy-bundle v2024.05 (#21235) + - use top-level parameters for `use_pip` & co instead of `exts_default_options` for `PythonBundle` easyconfigs (#21292) + + +v4.9.2 (12 June 2024) +--------------------- + +update/bugfix release + +- added easyconfigs for foss/2024.05 toolchain (candidate for foss/2024a) (#20646) +- added example easyconfig files for 82 new software packages: + - AEDT (#20357), amdahl (#20346), AMGX (#20255), assembly-stats (#20281), Bio-FeatureIO (#20461), + bitshuffle (#20661), Cassiopeia (#20289), CCCL (#20255), charm-gems (#20327), CheckM2 (#20399), + chromVARmotifs (#20402), cmph (#20278), COMEBin (#20717), Compass (#20500), ctffind5 (#20669), currentNe (#20791), + CVX (#20231), deepfold (#20247), dotNET-Core (#20256), EasyMocap (#20446), ensmallen (#20485), EVcouplings (#20744), + Faiss (#19669), FDMNES (#20321), gnupg-bundle (#20406), grpcio (#20191), hatch-jupyter-builder (#20606), + hevea (#20597), HiGHS (#20186), hmmcopy_utils (#20472), HOMER (#20590), ICON (#20573), jiter (#20746), + LangChain (#20746), langchain-anthropic (#20746), libabigail (#20539), libbraiding (#20655), libhomfly (#20482), + libsupermesh (#20470), LIBSVM-MATLAB (#20752), Lightning (#19964), lil-aretomo (#20696), makefun (#20619), + MetalWalls (#20403), MICOM (#20186), ml-collections (#20247), ml_dtypes (#20707), mlpack (#20485), MOFA2 (#20538), + mumott (#20719), nvitop (#20512), ocamlbuild (#20552), optiSLang (#20320), orthAgogue (#20278), pdf2docx (#20416), + planarity (#20753), plantri (#20467), plmc (#20744), PortAudio (#20307), premailer (#20348), ProteinMPNN (#20705), + PRRTE (#20698), PSM2 (#20496), PyAEDT (#20357), pybind11-stubgen (#20518), PyEXR (#19983), pyGAM (#20385), + PyHMMER (#20544), pyseer (#20502), PyVista (#20649), qmflows (#20384), SciTools-Iris (#20767), SCReadCounts (#20455), + SDL2_gfx (#20466), subunit (#20412), TF-COMB (#20666), tiktoken (#20336), TorchIO (#20648), t-SNE-CUDA (#19669), + VAMPIRE-ASM (#20368), wfdb (#20521), WGDgc (#20367) +- added additional easyconfigs for various supported software packages, including: + - 4ti2 1.6.10, AFNI 24.0.02, Autoconf 2.72, Autotools 20231222, adjustText 1.1.1, aiohttp 3.9.5, alevin-fry 0.9.0, + alsa-lib 1.2.9, atropos 1.1.32, autopep8 2.2.0, BCFtools 1.19, BLIS 1.0, BWA 0.7.18, Boost 1.85.0, bcrypt 4.1.3, + binutils 2.42, bokeh 3.4.1, CGAL 5.6.1, CREST 3.0.1, CellRanger-ARC 2.0.2, CellRanger 8.0.1, CellRank 2.0.2, + Clang 17.0.6, CoCoALib 0.99850, Cython 3.0.10, cURL 8.7.1, cffi 1.16.0, code-server 4.89.1, + configurable-http-proxy 4.6.1, coverage 7.4.4, cpio 2.15, cppyy 3.1.2, cysignals 1.11.4, Doxygen 1.11.0, + dask-labextension 7.0.0, dask 2024.5.1, deal.II 9.5.2, dorado 0.5.3, dotNET-Core 8.0.203, E-ANTIC 2.0.2, + ECL 24.5.10, ESPResSo 4.2.2, eclib 20240408, expat 2.6.2, FLTK 1.3.9, FMM3D 1.0.4, FlexiBLAS 3.4.4, f90wrap 0.2.13, + fgbio 2.2.1, fontconfig 2.15.0, freetype-py 2.4.0, GAMESS-US 20220930-R2 + 20230930-R2, GCC 13.3.0 + 14.1.0, + GDB 14.2, GDRCopy 2.4.1, GOATOOLS 1.4.5, GTDB-Tk 2.4.0, Giza 1.4.1, gc 8.2.6, gcloud 472.0.0, gemmi 0.6.5, + gettext 0.22.5, giac 1.9.0-99, git 2.45.1, gmsh 4.12.2, gsutil 5.29, HDDM 0.9.9, HTSlib 1.19.1, HyPhy 2.5.60, + h5py 3.11.0, hwloc 2.10.0, ICU 75.1, IOR 4.0.0, imagecodecs 2024.1.1, imgaug 0.4.1, ipympl 0.9.4, + Jupyter-bundle 20240522, JupyterHub 4.1.5, JupyterLab 4.2.0, JupyterNotebook 7.2.0, jupyter-matlab-proxy 0.12.2, + jupyter-resource-usage 1.0.2, jupyter-rsession-proxy 2.2.0, jupyter-server-proxy 4.1.2, jupyter-server 2.14.0, + Kalign 3.4.0, KrakenUniq 1.0.4, kallisto 0.50.1, LAPACK 3.12.0, libarchive 3.7.4, libde265 1.0.15, libdeflate 1.20, + libdwarf 0.9.2, libfabric 1.21.0, libffi 3.4.5, libgcrypt 1.10.3, libgpg-error 1.48, libheif 1.17.6, libidn2 2.3.7, + libnsl 2.0.1, libpciaccess 0.18.1, libpng 1.6.43, libuv 1.48.0, libxml2 2.12.7, line_profiler 4.1.2, MATSim 15.0, + MDTraj 1.9.9, Mako 1.3.5, Meson 1.4.0, MetaMorpheus 1.0.5, Molpro 2024.1.0, MuJoCo 3.1.4, matlab-proxy 0.18.1, + mold 2.31.0, mpmath 1.3.0, NASM 2.16.03, NanoPlot 1.42.0, Nextflow 24.04.2, Ninja 1.12.1, nanoget 1.19.1, + napari 0.4.19.post1, nauty 2.8.8, ncurses 6.5, nghttp2 1.58.0, nghttp3 1.3.0, nglview 3.1.2, ngtcp2 1.2.0, + nodejs 20.13.1, numactl 2.0.18, nvtop 3.1.0, OCaml 5.1.1, OSU-Micro-Benchmarks 7.4, OpenBLAS 0.3.27, OpenMPI 5.0.3, + PARI-GP 2.15.5, PCRE2 10.43, PMIx 5.0.2, Perl 5.38.2, PhyML 3.3.20220408, PnetCDF 1.13.0, PyAMG 5.1.0, + PyQtGraph 0.13.7, PyTorch-Geometric 2.5.0, PyTorch-bundle 2.1.2, PycURL 7.45.3, Pysam 0.22.0, Python 3.12.3, + p11-kit 0.25.3, p4est 2.8.6, parallel 20240322, pauvre 0.2.3, petsc4py 3.20.3, pkgconf 2.2.0, plc 3.10, polars 0.20.2, + poppler 24.04.0, psutil 5.9.8, py3Dmol 2.1.0, pybedtools 0.9.1, pygame 2.5.2, pyiron 0.5.1, pyro-ppl 1.9.0, + python-mujoco 3.1.4, ROOT 6.30.06, RPostgreSQL 0.7-6, RStudio-Server 2023.12.1+402, Rtree 1.2.0, Rust 1.78.0, + SAMtools 1.19.2, SCOTCH 7.0.4, SDL2_image 2.8.2, SDL2_mixer 2.8.0, SDL2_ttf 2.22.0, SQLite 3.45.3, SWIG 4.2.1, + SentencePiece 0.2.0, Seurat 5.1.0, SeuratDisk 20231104, SimNIBS 4.0.1, Singular 4.4.0, Spack 0.21.2, Squidpy 1.4.1, + SymEngine-python 0.11.0, SymEngine 0.11.2, sbt 1.6.2, scikit-build-core 0.9.3, scikit-learn 1.4.2, TOBIAS 0.16.1, + Tcl 8.6.14, TensorFlow 2.15.1, Transformers 4.39.3, texlive 20230313, tmux 3.4, tokenizers 0.15.2, 0.2.5.20231120, + tornado 6.4, UCC 1.3.0, UCX 1.16.0, util-linux 2.40, VSCode 1.88.1, Valgrind 3.23.0, VisPy 0.14.1, wget 1.24.5, + XZ 5.4.5, xorg-macros 1.20.1, xprop 1.2.7, xtb 6.7.0, xxd 9.1.0307, yaml-cpp 0.8.0, zarr 2.17.1, zfp 1.0.1, + zlib-ng 2.1.6, zlib 1.3.1, zstd 1.5.6 +- minor enhancements, including: + - add missing (optional) dependency pyproject-metadata to scikit-build-core (#20391) + - add hatch-requirements-txt extension to hatchling easyconfigs (#20389) + - install pkg-config files for ncurses 6.4 when using GCCcore toolchain (#20405) + - use regular 'configure' instead of wrapper script for recent UCX easyconfigs (#20428) + - add RISC-V support to UCX 1.15.0 (#20429), UCC 1.2.0 (#20432), BLIS 0.9.0 (#20468), PAPI 7.1.0 (20659) + - add extensions to R-bundle-CRAN v2023.12: cmna (#20445), rhandsontable (#20614), XBRL (#20506) + - add checksum for RISC-V version to easyconfig for Java 21.0.2 (#20495) + - remove 'TORCHVISION_INCLUDE' from PyTorch-bundle easyconfigs, now handled by custom easyblock for torchvision (#20504) + - add dependencies required for GUI in Cellpose 2.2.2 easyconfigs (#20620) + - add 'build_info_msg' about kernel modules to GDRCopy (#20641) + - build both static and shared libs for Brotli 1.1.0 (#20757) +- various bug fixes, including: + - add missing dependencies for funannotate (#17690) + - fix path to SuiteSparse include/lib in easyconfig for CVXopt v1.3.1 (#20232) + - fix Highway 1.0.3 on some systems by disabling 'AVX3_DL' (#20298) + - replace incorrect scikit-bio 0.5.9 with scikit-bio 0.6.0 as dependency for scCODA (#20300) + - add alternate checksum to OpenMolcas v23.06 (#20301) + - change arrow-R dependency of Bioconductor v3.18 to v14.0.1 (which depends on required matching Arrow v14.0.1) (#20324) + - fix hardcoded '/bin/mv' path in Rhdf5lib extension included in R-bundle-Bioconductor v3.16 + v3.18 (#20378) + - remove dependency on HDF5 in recent Bioconductor easyconfigs (#20379) + - make sure that libjpeg-turbo libraries are installed in 'lib' subdirectory (#20386) + - add patch for Libint 2.7.2 to fix compiler error with glibc >= 2.34 (#20396) + - use 'bash' rather than 'sh' to run PLINK-2.00a3.7 tests (#20404) + - add patch to fix 'UNPACK-OPAL-VALUE: UNSUPPORTED TYPE 33 FOR KEY' error in OpenMPI 4.1.5 (#20422) + - add patch to increase compatibility with AVX512 platforms for bwa-mem2 v2.2.1 (#20434) + - add patch for GROMACS 2024.1 to fix filesystem race in tests (#20439) + - demote poetry to build dependency for nanocompore (#20453) + - add patch to fix CVE-2024-27322 in R v3.6.x (#20464), v4.0.x (#20463), and v4.1.x + v4.2.x + v4.3.x (#20462) + - disable test that fetches from the web for torchtext extension in PyTorch-bundle v2.1.2 (#20484) + - fix sanity check paths for JupyterLab 4.0.5 (#20514) + - fix detection of CC/CXX compilers for 'wmake' in OpenFOAM v2306 + v2312 (#20517) + - use the included gmxapi for GROMACS 2024.1 (#20522) + - add new checksum for signal_1.8-0 to R-bundle-CRAN-2023.12 (#20527) + - fix test in Cwd extension of Perl-bundle-CPAN 5.36.1 (#20536) + - fix patch name in easyconfig for Perl-bundle-CPAN 5.36.1 + add also use it for Perl-bundle-CPAN 5.38.0 (#20540) + - fix cwd_enoent test in Perl (#20541) + - move dependency on BeasutifulSoup in IPython v8.14.0 to jupyter-server (#20547) + - remove dependency on BeasutifulSoup from IPython v8.17.2 (#20548) + - add alternative checksum for source tarball of MONAI 1.3.0 (#20618) + - add cpio as build dependency to recent BLAST+ versions (#20674) + - add --disable-htmlpages to recent FFmpeg easyconfigs (#20686) + - remove duplicate crates from easyconfig for timm-0.9.7 (#20687) + - add missing HDF5 dependency in recent Armadillo easyconfigs (>= 11.4.3) (#20710) + - add patches for failing LAPACK tests and RISC-V test segfaults to OpenBLAS 0.3.27 (#20745) + - move all easyconfigs for libavif to GCCcore toolchain + fix dependencies (#20747) + - make sure mummerplot can use gnuplot if available for recent MUMmer (#20749) + - prevent configure script of recent BLAST+ versions from prepending system paths to $PATH (#20751) + - fix fastparquet v2023.4.0 using CargoPythonBundle easyblock (#20775) + - remove --with-64 from configopts for recent BLAST+ versions (#20784) + - add patch to fix build of pdsh 2.34 with Slurm 23.x (#20795) +- other changes: + - move 'build' from extensions to dependencies in easyconfig for napari 0.4.18 (#20433) + - update version of fsspec extension in easyconfig for Squidpy 1.4.1 to be compatible with s3fs provided via PyTorch-bundle (#20477) + - add commented out PSM2 dependency, relevant for x86_64 systems with OmniPath, to recent libfabric easyconfigs (#20501, #20585, #20794) + - replace SQLAlchemy extension with regular dependency in easyconfig for Optuna v3.5.0 (#20510) + - replace SQLAlchemy extension in JupyterHub v4.0.2 easyconfig with regular dependency (#20511) + - bump Cython to v3.0.8 in Cartopy v0.22.0 easyconfig for foss/2023a toolchain, to avoid dependency version conflict with sckit-learn v1.4.2, which requires Cython >= v3.0.8 (#20525) + - change dependency on hatchling of BeautifulSoup v4.12.2 to a build dependency (#20546) + - bump async-timeout to 4.0.3 in aiohttp 3.8.5 (#20553) + - stick to gfbf/2023a as toolchain for ipympl v0.9.3 (#20586) + - rename tornado-timeouts.patch to tornado-6.1_increase-default-timeouts.patch + add missing authorship (#20587) + - remove easyconfigs for CellBender v0.3.1, since this version has been redacted due to a serious bug (#20722) v4.9.1 (5 April 2024) diff --git a/easybuild/easyconfigs/0/4ti2/4ti2-1.6.10-GCC-13.2.0.eb b/easybuild/easyconfigs/0/4ti2/4ti2-1.6.10-GCC-13.2.0.eb new file mode 100644 index 00000000000..5bfd73b4635 --- /dev/null +++ b/easybuild/easyconfigs/0/4ti2/4ti2-1.6.10-GCC-13.2.0.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = '4ti2' +version = '1.6.10' + +homepage = 'https://4ti2.github.io/' +description = """A software package for algebraic, geometric and combinatorial problems on linear spaces""" + +toolchain = {'name': 'GCC', 'version': '13.2.0'} + +github_account = '4ti2' +source_urls = [GITHUB_SOURCE] +sources = ['Release_%s.tar.gz' % '_'.join(version.split('.'))] +checksums = ['2f1bce3203da65b651d68cbd0ace0f89a16d1f436cf5f24e22bc15ec22df936a'] + +dependencies = [ + ('GMP', '6.3.0'), + ('GLPK', '5.0'), +] + +builddependencies = [('Autotools', '20220317')] + +preconfigopts = './autogen.sh && ' + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['4ti2gmp', '4ti2int32', '4ti2int64']], + 'dirs': ['include/4ti2', 'lib', 'share'] +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.71-FCC-4.5.0.eb b/easybuild/easyconfigs/__archive__/a/Autoconf/Autoconf-2.71-FCC-4.5.0.eb similarity index 100% rename from easybuild/easyconfigs/a/Autoconf/Autoconf-2.71-FCC-4.5.0.eb rename to easybuild/easyconfigs/__archive__/a/Autoconf/Autoconf-2.71-FCC-4.5.0.eb diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.16.3-FCC-4.5.0.eb b/easybuild/easyconfigs/__archive__/a/Automake/Automake-1.16.3-FCC-4.5.0.eb similarity index 100% rename from easybuild/easyconfigs/a/Automake/Automake-1.16.3-FCC-4.5.0.eb rename to easybuild/easyconfigs/__archive__/a/Automake/Automake-1.16.3-FCC-4.5.0.eb diff --git a/easybuild/easyconfigs/a/Autotools/Autotools-20210128-FCC-4.5.0.eb b/easybuild/easyconfigs/__archive__/a/Autotools/Autotools-20210128-FCC-4.5.0.eb similarity index 100% rename from easybuild/easyconfigs/a/Autotools/Autotools-20210128-FCC-4.5.0.eb rename to easybuild/easyconfigs/__archive__/a/Autotools/Autotools-20210128-FCC-4.5.0.eb diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.7.6-FCC-4.5.0.eb b/easybuild/easyconfigs/__archive__/b/Bison/Bison-3.7.6-FCC-4.5.0.eb similarity index 100% rename from easybuild/easyconfigs/b/Bison/Bison-3.7.6-FCC-4.5.0.eb rename to easybuild/easyconfigs/__archive__/b/Bison/Bison-3.7.6-FCC-4.5.0.eb diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.36.1-FCC-4.5.0.eb b/easybuild/easyconfigs/__archive__/b/binutils/binutils-2.36.1-FCC-4.5.0.eb similarity index 100% rename from easybuild/easyconfigs/b/binutils/binutils-2.36.1-FCC-4.5.0.eb rename to easybuild/easyconfigs/__archive__/b/binutils/binutils-2.36.1-FCC-4.5.0.eb diff --git a/easybuild/easyconfigs/b/buildenv/buildenv-default-FCC-4.5.0.eb b/easybuild/easyconfigs/__archive__/b/buildenv/buildenv-default-FCC-4.5.0.eb similarity index 100% rename from easybuild/easyconfigs/b/buildenv/buildenv-default-FCC-4.5.0.eb rename to easybuild/easyconfigs/__archive__/b/buildenv/buildenv-default-FCC-4.5.0.eb diff --git a/easybuild/easyconfigs/b/buildenv/buildenv-default-Fujitsu-21.05.eb b/easybuild/easyconfigs/__archive__/b/buildenv/buildenv-default-Fujitsu-21.05.eb similarity index 100% rename from easybuild/easyconfigs/b/buildenv/buildenv-default-Fujitsu-21.05.eb rename to easybuild/easyconfigs/__archive__/b/buildenv/buildenv-default-Fujitsu-21.05.eb diff --git a/easybuild/easyconfigs/d/DB/DB-18.1.40-FCC-4.5.0.eb b/easybuild/easyconfigs/__archive__/d/DB/DB-18.1.40-FCC-4.5.0.eb similarity index 100% rename from easybuild/easyconfigs/d/DB/DB-18.1.40-FCC-4.5.0.eb rename to easybuild/easyconfigs/__archive__/d/DB/DB-18.1.40-FCC-4.5.0.eb diff --git a/easybuild/easyconfigs/e/expat/expat-2.2.9-FCC-4.5.0.eb b/easybuild/easyconfigs/__archive__/e/expat/expat-2.2.9-FCC-4.5.0.eb similarity index 100% rename from easybuild/easyconfigs/e/expat/expat-2.2.9-FCC-4.5.0.eb rename to easybuild/easyconfigs/__archive__/e/expat/expat-2.2.9-FCC-4.5.0.eb diff --git a/easybuild/easyconfigs/f/FCC/FCC-4.5.0.eb b/easybuild/easyconfigs/__archive__/f/FCC/FCC-4.5.0.eb similarity index 100% rename from easybuild/easyconfigs/f/FCC/FCC-4.5.0.eb rename to easybuild/easyconfigs/__archive__/f/FCC/FCC-4.5.0.eb diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-1.0.0-FCC-4.5.0-fujitsu.eb b/easybuild/easyconfigs/__archive__/f/FFTW/FFTW-1.0.0-FCC-4.5.0-fujitsu.eb similarity index 100% rename from easybuild/easyconfigs/f/FFTW/FFTW-1.0.0-FCC-4.5.0-fujitsu.eb rename to easybuild/easyconfigs/__archive__/f/FFTW/FFTW-1.0.0-FCC-4.5.0-fujitsu.eb diff --git a/easybuild/easyconfigs/f/Fujitsu/Fujitsu-21.05.eb b/easybuild/easyconfigs/__archive__/f/Fujitsu/Fujitsu-21.05.eb similarity index 100% rename from easybuild/easyconfigs/f/Fujitsu/Fujitsu-21.05.eb rename to easybuild/easyconfigs/__archive__/f/Fujitsu/Fujitsu-21.05.eb diff --git a/easybuild/easyconfigs/f/ffmpi/ffmpi-4.5.0.eb b/easybuild/easyconfigs/__archive__/f/ffmpi/ffmpi-4.5.0.eb similarity index 100% rename from easybuild/easyconfigs/f/ffmpi/ffmpi-4.5.0.eb rename to easybuild/easyconfigs/__archive__/f/ffmpi/ffmpi-4.5.0.eb diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.4-FCC-4.5.0.eb b/easybuild/easyconfigs/__archive__/f/flex/flex-2.6.4-FCC-4.5.0.eb similarity index 100% rename from easybuild/easyconfigs/f/flex/flex-2.6.4-FCC-4.5.0.eb rename to easybuild/easyconfigs/__archive__/f/flex/flex-2.6.4-FCC-4.5.0.eb diff --git a/easybuild/easyconfigs/g/groff/groff-1.22.4-FCC-4.5.0.eb b/easybuild/easyconfigs/__archive__/g/groff/groff-1.22.4-FCC-4.5.0.eb similarity index 100% rename from easybuild/easyconfigs/g/groff/groff-1.22.4-FCC-4.5.0.eb rename to easybuild/easyconfigs/__archive__/g/groff/groff-1.22.4-FCC-4.5.0.eb diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.3-Fujitsu-21.05.eb b/easybuild/easyconfigs/__archive__/h/HPL/HPL-2.3-Fujitsu-21.05.eb similarity index 100% rename from easybuild/easyconfigs/h/HPL/HPL-2.3-Fujitsu-21.05.eb rename to easybuild/easyconfigs/__archive__/h/HPL/HPL-2.3-Fujitsu-21.05.eb diff --git a/easybuild/easyconfigs/h/help2man/help2man-1.48.3-FCC-4.5.0.eb b/easybuild/easyconfigs/__archive__/h/help2man/help2man-1.48.3-FCC-4.5.0.eb similarity index 100% rename from easybuild/easyconfigs/h/help2man/help2man-1.48.3-FCC-4.5.0.eb rename to easybuild/easyconfigs/__archive__/h/help2man/help2man-1.48.3-FCC-4.5.0.eb diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-8.1-FCC-4.5.0.eb b/easybuild/easyconfigs/__archive__/l/libreadline/libreadline-8.1-FCC-4.5.0.eb similarity index 100% rename from easybuild/easyconfigs/l/libreadline/libreadline-8.1-FCC-4.5.0.eb rename to easybuild/easyconfigs/__archive__/l/libreadline/libreadline-8.1-FCC-4.5.0.eb diff --git a/easybuild/easyconfigs/l/libtool/libtool-2.4.6-FCC-4.5.0.eb b/easybuild/easyconfigs/__archive__/l/libtool/libtool-2.4.6-FCC-4.5.0.eb similarity index 100% rename from easybuild/easyconfigs/l/libtool/libtool-2.4.6-FCC-4.5.0.eb rename to easybuild/easyconfigs/__archive__/l/libtool/libtool-2.4.6-FCC-4.5.0.eb diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-FCC-4.5.0.eb b/easybuild/easyconfigs/__archive__/m/M4/M4-1.4.18-FCC-4.5.0.eb similarity index 100% rename from easybuild/easyconfigs/m/M4/M4-1.4.18-FCC-4.5.0.eb rename to easybuild/easyconfigs/__archive__/m/M4/M4-1.4.18-FCC-4.5.0.eb diff --git a/easybuild/easyconfigs/m/makeinfo/makeinfo-6.7-FCC-4.5.0.eb b/easybuild/easyconfigs/__archive__/m/makeinfo/makeinfo-6.7-FCC-4.5.0.eb similarity index 100% rename from easybuild/easyconfigs/m/makeinfo/makeinfo-6.7-FCC-4.5.0.eb rename to easybuild/easyconfigs/__archive__/m/makeinfo/makeinfo-6.7-FCC-4.5.0.eb diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-6.2-FCC-4.5.0.eb b/easybuild/easyconfigs/__archive__/n/ncurses/ncurses-6.2-FCC-4.5.0.eb similarity index 100% rename from easybuild/easyconfigs/n/ncurses/ncurses-6.2-FCC-4.5.0.eb rename to easybuild/easyconfigs/__archive__/n/ncurses/ncurses-6.2-FCC-4.5.0.eb diff --git a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7.1-ffmpi-4.5.0.eb b/easybuild/easyconfigs/__archive__/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7.1-ffmpi-4.5.0.eb similarity index 100% rename from easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7.1-ffmpi-4.5.0.eb rename to easybuild/easyconfigs/__archive__/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7.1-ffmpi-4.5.0.eb diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.32.1-FCC-4.5.0.eb b/easybuild/easyconfigs/__archive__/p/Perl/Perl-5.32.1-FCC-4.5.0.eb similarity index 99% rename from easybuild/easyconfigs/p/Perl/Perl-5.32.1-FCC-4.5.0.eb rename to easybuild/easyconfigs/__archive__/p/Perl/Perl-5.32.1-FCC-4.5.0.eb index 7081ac17a66..d70fd1c84b2 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.32.1-FCC-4.5.0.eb +++ b/easybuild/easyconfigs/__archive__/p/Perl/Perl-5.32.1-FCC-4.5.0.eb @@ -236,7 +236,12 @@ exts_list = [ ('File::Spec', '3.75', { 'source_tmpl': 'PathTools-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/X/XS/XSAWYERX'], - 'checksums': ['a558503aa6b1f8c727c0073339081a77888606aa701ada1ad62dd9d8c3f945a2'], + 'patches': ['PathTools-3.75_fix-cwd_enoent-test.patch'], + 'checksums': [ + 'a558503aa6b1f8c727c0073339081a77888606aa701ada1ad62dd9d8c3f945a2', + {'PathTools-3.75_fix-cwd_enoent-test.patch': + '7a456a99d9b04a36359f3623f0deef8fe7f472c742f99cdcf0215c50afbbe7b1'}, + ], }), ('Test::Simple', '1.302183', { 'source_tmpl': 'Test-Simple-%(version)s.tar.gz', @@ -1667,7 +1672,12 @@ exts_list = [ ('Cwd', '3.75', { 'source_tmpl': 'PathTools-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/X/XS/XSAWYERX'], - 'checksums': ['a558503aa6b1f8c727c0073339081a77888606aa701ada1ad62dd9d8c3f945a2'], + 'patches': ['PathTools-3.75_fix-cwd_enoent-test.patch'], + 'checksums': [ + 'a558503aa6b1f8c727c0073339081a77888606aa701ada1ad62dd9d8c3f945a2', + {'PathTools-3.75_fix-cwd_enoent-test.patch': + '7a456a99d9b04a36359f3623f0deef8fe7f472c742f99cdcf0215c50afbbe7b1'}, + ], }), ('MIME::Base64', '3.16', { 'source_tmpl': 'MIME-Base64-%(version)s.tar.gz', diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.11-FCC-4.5.0.eb b/easybuild/easyconfigs/__archive__/z/zlib/zlib-1.2.11-FCC-4.5.0.eb similarity index 100% rename from easybuild/easyconfigs/z/zlib/zlib-1.2.11-FCC-4.5.0.eb rename to easybuild/easyconfigs/__archive__/z/zlib/zlib-1.2.11-FCC-4.5.0.eb diff --git a/easybuild/easyconfigs/a/ABRicate/ABRicate-1.0.0-gompi-2023a.eb b/easybuild/easyconfigs/a/ABRicate/ABRicate-1.0.0-gompi-2023a.eb new file mode 100644 index 00000000000..b21e8fda565 --- /dev/null +++ b/easybuild/easyconfigs/a/ABRicate/ABRicate-1.0.0-gompi-2023a.eb @@ -0,0 +1,41 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 + +easyblock = 'Tarball' + +name = 'ABRicate' +version = '1.0.0' + +homepage = 'https://github.com/tseemann/abricate' +description = "Mass screening of contigs for antimicrobial and virulence genes" + +toolchain = {'name': 'gompi', 'version': '2023a'} + +# https://github.com/tseemann/abricate +github_account = 'tseemann' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.zip'] +checksums = ['e7e2af45e47b887c4dba754af87a24014dcb5552eb3fe2a3fd66bb5359a0daf9'] + +dependencies = [ + ('Perl', '5.36.1'), + ('any2fasta', '0.4.2'), + ('BioPerl', '1.7.8'), + ('BLAST+', '2.14.1'), +] + +postinstallcmds = ['%(installdir)s/bin/abricate --setupdb'] + +sanity_check_paths = { + 'files': ['bin/abricate', 'bin/abricate-get_db'], + 'dirs': ['db'], +} + +sanity_check_commands = [ + "abricate --help", + "abricate --list", +] + +modloadmsg = "abricate databases are located in $EBROOTABRICATE/db\n" + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/a/AGAT/AGAT-1.4.0-GCC-12.3.0.eb b/easybuild/easyconfigs/a/AGAT/AGAT-1.4.0-GCC-12.3.0.eb new file mode 100644 index 00000000000..2677e62fda1 --- /dev/null +++ b/easybuild/easyconfigs/a/AGAT/AGAT-1.4.0-GCC-12.3.0.eb @@ -0,0 +1,70 @@ +# easybuild easyconfig +# +# John Dey Fred Hutchinson Cancer Center +# Thomas Eylenbosch - Gluo NV +# Update: Petr Král (INUITS) +# +easyblock = 'Bundle' + +name = 'AGAT' +version = '1.4.0' + +homepage = 'https://agat.readthedocs.io/en/latest/' +description = """AGAT: Another GTF/GFF Analysis Toolkit. Suite of tools to handle gene annotations + in any GTF/GFF format.""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +builddependencies = [('binutils', '2.40')] + +dependencies = [ + ('Perl', '5.36.1'), + ('BioPerl', '1.7.8'), +] + +exts_defaultclass = 'PerlModule' +exts_filter = ("perl -e 'require %(ext_name)s'", '') + +exts_list = [ + ('Set::Object', '1.42', { + 'source_tmpl': 'Set-Object-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RU/RURBAN'], + 'checksums': ['d18c5a8a233eabbd0206cf3da5b00fcdd7b37febf12a93dcc3d1c026e6fdec45'], + }), + ('File::Share', '0.27', { + 'source_tmpl': 'File-Share-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IN/INGY'], + 'checksums': ['d6e8f4b55ebd38e0bb45e44392e3fa27dc1fde16abc5d1ff53e157e19a5755be'], + }), + ('Sort::Naturally', '1.03', { + 'source_tmpl': 'Sort-Naturally-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + 'checksums': ['eaab1c5c87575a7826089304ab1f8ffa7f18e6cd8b3937623e998e865ec1e746'], + }), + ('Class::MethodMaker', '2.24', { + 'source_tmpl': 'Class-MethodMaker-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SC/SCHWIGON/class-methodmaker'], + 'checksums': ['5eef58ccb27ebd01bcde5b14bcc553b5347a0699e5c3e921c7780c3526890328'], + }), + ('Term::ProgressBar', '2.23', { + 'source_tmpl': 'Term-ProgressBar-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MANWAR'], + 'checksums': ['defc03fb9f4ac1c9df1359d312bff3c0865ddefbf3aba64cd42a69a86215d49d'], + }), + (name, version, { + 'modulename': 'AGAT::Utilities', + 'source_urls': ['https://github.com/NBISweden/AGAT/archive/refs/tags'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['d5e30db44b5d05ed51c606a823894c01c85c1ed85580148ad5473cb2f2b2ac77'], + }), +] + +modextrapaths = {'PERL5LIB': 'lib/perl5/site_perl/%(perlver)s/'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['bin', 'lib/perl5/site_perl/%(perlver)s/%(name)s'], +} + +sanity_check_commands = ['agat_convert_bed2gff.pl --help'] +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/a/ALL/ALL-0.9.2-foss-2023b.eb b/easybuild/easyconfigs/a/ALL/ALL-0.9.2-foss-2023b.eb new file mode 100644 index 00000000000..eb1a53ff8da --- /dev/null +++ b/easybuild/easyconfigs/a/ALL/ALL-0.9.2-foss-2023b.eb @@ -0,0 +1,41 @@ +easyblock = 'CMakeMake' + +name = 'ALL' +version = '0.9.2' + +homepage = 'https://gitlab.jsc.fz-juelich.de/SLMS/loadbalancing' +description = """A Load Balancing Library (ALL) aims to provide an easy way to include dynamic +domain-based load balancing into particle based simulation codes. The library +is developed in the Simulation Laboratory Molecular Systems of the Jülich +Supercomputing Centre at Forschungszentrum Jülich.""" + +toolchain = {'name': 'foss', 'version': '2023b'} +toolchainopts = {'usempi': True} + +source_urls = ["https://gitlab.jsc.fz-juelich.de/SLMS/loadbalancing/-/archive/v%(version)s/"] +sources = ['loadbalancing-v%(version)s.tar.gz'] +checksums = ['2b4ef52c604c3c0c467712d0912a33c82177610b67edc14df1e034779c6ddb71'] + +builddependencies = [ + ('CMake', '3.27.6'), + ('Boost', '1.83.0'), # only needed for tests +] + +dependencies = [ + ('VTK', '9.3.0'), +] + +configopts = '-DCM_ALL_FORTRAN=ON -DCM_ALL_USE_F08=ON -DCM_ALL_VORONOI=ON -DCM_ALL_VTK_OUTPUT=ON ' +configopts += '-DCM_ALL_TESTS=ON -DCM_ALL_AUTO_DOC=OFF -DVTK_DIR=$EBROOTVTK ' + +runtest = 'test' + +sanity_check_paths = { + 'files': [ + 'include/ALL.hpp', 'include/ALL_Voronoi.hpp', 'lib/all_module.mod', + 'lib/libALL.a', 'lib/libALL_fortran.a' + ], + 'dirs': ['lib/cmake'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/a/AMRFinderPlus/AMRFinderPlus-3.12.8-gompi-2023a.eb b/easybuild/easyconfigs/a/AMRFinderPlus/AMRFinderPlus-3.12.8-gompi-2023a.eb new file mode 100644 index 00000000000..cc4de6c8fb0 --- /dev/null +++ b/easybuild/easyconfigs/a/AMRFinderPlus/AMRFinderPlus-3.12.8-gompi-2023a.eb @@ -0,0 +1,41 @@ +easyblock = 'MakeCp' + +name = 'AMRFinderPlus' +version = '3.12.8' + +homepage = 'https://github.com/ncbi/amr' +description = """This software and the accompanying database are designed to find acquired antimicrobial + resistance genes and some point mutations in protein or assembled nucleotide sequences.""" + +toolchain = {'name': 'gompi', 'version': '2023a'} + +github_account = 'ncbi' +source_urls = ['https://github.com/ncbi/amr/archive/'] +sources = ['amrfinder_v%(version)s.tar.gz'] +checksums = ['a199bc332877bad9033a7620bc5e8e849db1f19a9ba8b7357ec5451a6a283aa0'] + +dependencies = [ + ('BLAST+', '2.14.1'), + ('HMMER', '3.4'), + ('cURL', '8.0.1') +] + +# Binaries are installed to the root of the installation, so add that root to the PATH: +modextrapaths = {'PATH': ''} + +# a list of binary files that will be produced +local_binaries = ['amr_report', 'amrfinder', 'amrfinder_update', 'dna_mutation', 'fasta2parts', 'fasta_check', + 'fasta_extract', 'gff_check'] + +files_to_copy = local_binaries + +sanity_check_paths = { + 'files': local_binaries, + 'dirs': [], +} + +sanity_check_commands = [ + ('amrfinder', '-h') +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-GCCcore-12.3.0-Java-11.eb b/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-GCCcore-12.3.0-Java-11.eb new file mode 100644 index 00000000000..4f76242d899 --- /dev/null +++ b/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-GCCcore-12.3.0-Java-11.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'ANTLR' +version = '2.7.7' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'https://www.antlr2.org/' +description = """ANTLR, ANother Tool for Language Recognition, (formerly PCCTS) + is a language tool that provides a framework for constructing recognizers, + compilers, and translators from grammatical descriptions containing + Java, C#, C++, or Python actions.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://www.antlr2.org/download/'] +sources = [SOURCELOWER_TAR_GZ] +patches = ['%(name)s-%(version)s_includes.patch'] +checksums = [ + '853aeb021aef7586bda29e74a6b03006bcb565a755c86b66032d8ec31b67dbb9', # antlr-2.7.7.tar.gz + 'd167d3248a03301bc93efcb37d5df959aae6794968e42231af0b0dd26d6a2e66', # ANTLR-2.7.7_includes.patch +] + +builddependencies = [('binutils', '2.40')] + +dependencies = [('Java', '11', '', SYSTEM)] + +configopts = '--disable-examples --disable-csharp --disable-python' + +sanity_check_paths = { + 'files': ['bin/antlr', 'bin/antlr-config'], + 'dirs': ['include'], +} + +sanity_check_commands = ["antlr --help"] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-GCCcore-13.3.0-Java-21.0.2.eb b/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-GCCcore-13.3.0-Java-21.0.2.eb new file mode 100644 index 00000000000..333a0374279 --- /dev/null +++ b/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-GCCcore-13.3.0-Java-21.0.2.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'ANTLR' +version = '2.7.7' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'https://www.antlr2.org/' +description = """ANTLR, ANother Tool for Language Recognition, (formerly PCCTS) + is a language tool that provides a framework for constructing recognizers, + compilers, and translators from grammatical descriptions containing + Java, C#, C++, or Python actions.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://www.antlr2.org/download/'] +sources = [SOURCELOWER_TAR_GZ] +patches = ['%(name)s-%(version)s_includes.patch'] +checksums = [ + '853aeb021aef7586bda29e74a6b03006bcb565a755c86b66032d8ec31b67dbb9', # antlr-2.7.7.tar.gz + 'd167d3248a03301bc93efcb37d5df959aae6794968e42231af0b0dd26d6a2e66', # ANTLR-2.7.7_includes.patch +] + +builddependencies = [('binutils', '2.42')] + +dependencies = [('Java', '21.0.2', '', SYSTEM)] + +configopts = '--disable-examples --disable-csharp --disable-python' + +sanity_check_paths = { + 'files': ['bin/antlr', 'bin/antlr-config'], + 'dirs': ['include'], +} + +sanity_check_commands = ["antlr --help"] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/a/AOCC/AOCC-4.2.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/a/AOCC/AOCC-4.2.0-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..b88337b09b4 --- /dev/null +++ b/easybuild/easyconfigs/a/AOCC/AOCC-4.2.0-GCCcore-13.3.0.eb @@ -0,0 +1,29 @@ +name = 'AOCC' +version = '4.2.0' + +homepage = 'https://developer.amd.com/amd-aocc/' +description = """AOCC is a high-performance x86 CPU compiler for C, C++, and Fortran programming languages. + It supports target-dependent and target-independent optimizations. It is highly optimized for x86 targets, + especially for AMD “Zen”-based processors giving a performance edge for time critical HPC and other + applications over other compilers.""" + +# Clang also depends on libstdc++ during runtime, but this dependency is +# already specified as the toolchain. +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = [ + 'https://download.amd.com/developer/eula/%(namelower)s/%(namelower)s-%(version_major)s-%(version_minor)s' +] +sources = ['%(namelower)s-compiler-%(version)s.tar'] +checksums = ['ed5a560ec745b24dc0685ccdcbde914843fb2f2dfbfce1ba592de4ffbce1ccab'] + +dependencies = [ + ('binutils', '2.42'), + ('ncurses', '6.5'), + ('zlib', '1.3.1'), + ('libxml2', '2.12.7'), +] + +clangversion = '16.0.3' + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/a/AOCC/AOCC-5.0.0-GCCcore-14.2.0.eb b/easybuild/easyconfigs/a/AOCC/AOCC-5.0.0-GCCcore-14.2.0.eb new file mode 100644 index 00000000000..36d359a6469 --- /dev/null +++ b/easybuild/easyconfigs/a/AOCC/AOCC-5.0.0-GCCcore-14.2.0.eb @@ -0,0 +1,24 @@ +name = 'AOCC' +version = '5.0.0' + +homepage = 'https://developer.amd.com/amd-aocc/' +description = "AMD Optimized C/C++ & Fortran compilers (AOCC) based on LLVM 13.0" + +# Clang also depends on libstdc++ during runtime, but this dependency is +# already specified as the toolchain. +toolchain = {'name': 'GCCcore', 'version': '14.2.0'} + +source_urls = ['https://download.amd.com/developer/eula/aocc/aocc-5-0/'] +sources = ['aocc-compiler-%(version)s.tar'] +checksums = ['966fac2d2c759e9de6e969c10ada7a7b306c113f7f1e07ea376829ec86380daa'] + +clangversion = '17.0.6' + +dependencies = [ + ('binutils', '2.42'), + ('ncurses', '6.5'), + ('zlib', '1.3.1'), + ('libxml2', '2.13.4'), +] + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/a/APOST3D/APOST3D-20240527-intel-compilers-2023.1.0.eb b/easybuild/easyconfigs/a/APOST3D/APOST3D-20240527-intel-compilers-2023.1.0.eb new file mode 100644 index 00000000000..c5c4c40ac5b --- /dev/null +++ b/easybuild/easyconfigs/a/APOST3D/APOST3D-20240527-intel-compilers-2023.1.0.eb @@ -0,0 +1,51 @@ +easyblock = 'CmdCp' + +name = 'APOST3D' +version = '20240527' +local_commit = 'e06c8b0' + +description = """ +Open-source APOST-3D software features a large number of wavefunction analysis tools developed +over the past 20 years, aiming at connecting classical chemical concepts with the electronic +structure of molecules. APOST-3D relies on the identification of the atom in the molecule +(AIM), and several analysis tools are implemented in the most general way so that they can be +used in combination with any chosen AIM. +A Fortran-based code developed at the Universitat de Girona (UdG) by P. Salvador and collaborators. +""" +homepage = 'https://github.com/mgimferrer/APOST3D' + +toolchain = {'name': 'intel-compilers', 'version': '2023.1.0'} + +builddependencies = [ + ('make', '4.4.1'), +] + +source_urls = ['https://github.com/mgimferrer/APOST3D/archive'] +sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}] +checksums = ['1eb9a0f97b4dd135b782b96cadc37b3acfc27c69521cf3aab6cc10d4fc9292af'] + +local_cmds = ' export APOST3D_PATH=%(start_dir)s && ' +# Compile provided Libxc version 4.2.3 +# (it is not possible to couple APOST-3D with newer Libxc libraries): +local_cmds += 'bash compile_libxc.sh && ' +# Compile +local_cmds += 'make -f Makefile_profgen && ' +# Run test calculations on single-processor: +local_cmds += 'bash compiler-runtest && ' +# Recompile using info geneated in previous step +local_cmds += 'make -f Makefile_profuse && ' +# Run test calculations in parallel: +local_cmds += 'bash compiler-runtest2' + +cmds_map = [('.*', local_cmds)] + +local_bin_files = ['apost3d', 'apost3d-eos', 'eos_aom'] + +files_to_copy = [(local_bin_files, 'bin')] + +sanity_check_paths = { + 'files': ['bin/%s' % f for f in local_bin_files], + 'dirs': [''], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/a/APR-util/APR-util-1.6.3-GCCcore-13.3.0.eb b/easybuild/easyconfigs/a/APR-util/APR-util-1.6.3-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..fc5f92c2b70 --- /dev/null +++ b/easybuild/easyconfigs/a/APR-util/APR-util-1.6.3-GCCcore-13.3.0.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'APR-util' +version = '1.6.3' + +homepage = 'https://apr.apache.org/' +description = "Apache Portable Runtime (APR) util libraries." + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://archive.apache.org/dist/apr/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['2b74d8932703826862ca305b094eef2983c27b39d5c9414442e9976a9acf1983'] + +builddependencies = [('binutils', '2.42')] + +dependencies = [ + ('APR', '1.7.4'), + ('SQLite', '3.45.3'), + ('expat', '2.6.2'), +] + +configopts = "--with-apr=$EBROOTAPR/bin/apr-1-config --with-sqlite3=$EBROOTSQLITE --with-expat=$EBROOTEXPAT " + +sanity_check_paths = { + 'files': ["bin/apu-1-config", "lib/libaprutil-1.%s" % SHLIB_EXT, "lib/libaprutil-1.a"], + 'dirs': ["include/apr-1"], +} + +parallel = 1 + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/a/APR/APR-1.7.4-GCCcore-13.3.0.eb b/easybuild/easyconfigs/a/APR/APR-1.7.4-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..8ac5ed02a98 --- /dev/null +++ b/easybuild/easyconfigs/a/APR/APR-1.7.4-GCCcore-13.3.0.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'APR' +version = '1.7.4' + +homepage = 'https://apr.apache.org/' +description = "Apache Portable Runtime (APR) libraries." + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://archive.apache.org/dist/apr/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['a4137dd82a185076fa50ba54232d920a17c6469c30b0876569e1c2a05ff311d9'] + +builddependencies = [('binutils', '2.42')] + +sanity_check_paths = { + 'files': ["bin/apr-1-config", "lib/libapr-1.%s" % SHLIB_EXT, "lib/libapr-1.a"], + 'dirs': ["include/apr-1"], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/a/ASE/ASE-3.23.0-gfbf-2023a.eb b/easybuild/easyconfigs/a/ASE/ASE-3.23.0-gfbf-2023a.eb new file mode 100644 index 00000000000..554779e99cc --- /dev/null +++ b/easybuild/easyconfigs/a/ASE/ASE-3.23.0-gfbf-2023a.eb @@ -0,0 +1,48 @@ +easyblock = 'PythonBundle' + +name = 'ASE' +version = '3.23.0' + +homepage = 'https://wiki.fysik.dtu.dk/ase' +description = """ASE is a python package providing an open source Atomic Simulation Environment + in the Python scripting language. + +From version 3.20.1 we also include the ase-ext package, it contains optional reimplementations +in C of functions in ASE. ASE uses it automatically when installed.""" + +toolchain = {'name': 'gfbf', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('SciPy-bundle', '2023.07'), + ('Flask', '2.3.3'), + ('matplotlib', '3.7.2'), + ('Tkinter', '%(pyver)s'), # Needed by GUI of ASE + ('spglib-python', '2.1.0'), # optional +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('pytest-mock', '3.11.1', { + 'checksums': ['7f6b125602ac6d743e523ae0bfa71e1a697a2f5534064528c6ff84c2f7c2fc7f'], + }), + ('ase', version, { + 'checksums': ['91a2aa31d89bd90b0efdfe4a7e84264f32828b2abfc9f38e65e041ad76fec8ae'], + }), + ('ase-ext', '20.9.0', { + 'checksums': ['a348b0e42cf9fdd11f04b3df002b0bf150002c8df2698ff08d3c8fc7a1223aed'], + }), +] + +sanity_check_paths = { + 'files': ['bin/ase'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +# make sure Tkinter is available, otherwise 'ase gui' will not work +sanity_check_commands = ["python -c 'import tkinter' "] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/a/ASE/ASE-3.23.0-gfbf-2023b.eb b/easybuild/easyconfigs/a/ASE/ASE-3.23.0-gfbf-2023b.eb new file mode 100644 index 00000000000..07ad1ecc555 --- /dev/null +++ b/easybuild/easyconfigs/a/ASE/ASE-3.23.0-gfbf-2023b.eb @@ -0,0 +1,48 @@ +easyblock = 'PythonBundle' + +name = 'ASE' +version = '3.23.0' + +homepage = 'https://wiki.fysik.dtu.dk/ase' +description = """ASE is a python package providing an open source Atomic Simulation Environment + in the Python scripting language. + +From version 3.20.1 we also include the ase-ext package, it contains optional reimplementations +in C of functions in ASE. ASE uses it automatically when installed.""" + +toolchain = {'name': 'gfbf', 'version': '2023b'} + +dependencies = [ + ('Python', '3.11.5'), + ('Python-bundle-PyPI', '2023.10'), + ('SciPy-bundle', '2023.11'), + ('Flask', '3.0.0'), + ('matplotlib', '3.8.2'), + ('Tkinter', '%(pyver)s'), # Needed by GUI of ASE + ('spglib-python', '2.5.0'), # optional +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('pytest-mock', '3.14.0', { + 'checksums': ['2719255a1efeceadbc056d6bf3df3d1c5015530fb40cf347c0f9afac88410bd0'], + }), + ('ase', version, { + 'checksums': ['91a2aa31d89bd90b0efdfe4a7e84264f32828b2abfc9f38e65e041ad76fec8ae'], + }), + ('ase-ext', '20.9.0', { + 'checksums': ['a348b0e42cf9fdd11f04b3df002b0bf150002c8df2698ff08d3c8fc7a1223aed'], + }), +] + +sanity_check_paths = { + 'files': ['bin/ase'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +# make sure Tkinter is available, otherwise 'ase gui' will not work +sanity_check_commands = ["python -c 'import tkinter' "] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/a/ASE/ASE-3.23.0-gfbf-2024a.eb b/easybuild/easyconfigs/a/ASE/ASE-3.23.0-gfbf-2024a.eb new file mode 100644 index 00000000000..472ebbb24b2 --- /dev/null +++ b/easybuild/easyconfigs/a/ASE/ASE-3.23.0-gfbf-2024a.eb @@ -0,0 +1,48 @@ +easyblock = 'PythonBundle' + +name = 'ASE' +version = '3.23.0' + +homepage = 'https://wiki.fysik.dtu.dk/ase' +description = """ASE is a python package providing an open source Atomic Simulation Environment + in the Python scripting language. + +From version 3.20.1 we also include the ase-ext package, it contains optional reimplementations +in C of functions in ASE. ASE uses it automatically when installed.""" + +toolchain = {'name': 'gfbf', 'version': '2024a'} + +dependencies = [ + ('Python', '3.12.3'), + ('Python-bundle-PyPI', '2024.06'), + ('SciPy-bundle', '2024.05'), + ('Flask', '3.0.3'), + ('matplotlib', '3.9.2'), + ('Tkinter', '%(pyver)s'), # Needed by GUI of ASE + ('spglib-python', '2.5.0'), # optional +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('pytest-mock', '3.14.0', { + 'checksums': ['2719255a1efeceadbc056d6bf3df3d1c5015530fb40cf347c0f9afac88410bd0'], + }), + ('ase', version, { + 'checksums': ['91a2aa31d89bd90b0efdfe4a7e84264f32828b2abfc9f38e65e041ad76fec8ae'], + }), + ('ase-ext', '20.9.0', { + 'checksums': ['a348b0e42cf9fdd11f04b3df002b0bf150002c8df2698ff08d3c8fc7a1223aed'], + }), +] + +sanity_check_paths = { + 'files': ['bin/ase'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +# make sure Tkinter is available, otherwise 'ase gui' will not work +sanity_check_commands = ["python -c 'import tkinter' "] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/a/ASE/ASE-3.23.0-iimkl-2023a.eb b/easybuild/easyconfigs/a/ASE/ASE-3.23.0-iimkl-2023a.eb new file mode 100644 index 00000000000..f8bbed9f583 --- /dev/null +++ b/easybuild/easyconfigs/a/ASE/ASE-3.23.0-iimkl-2023a.eb @@ -0,0 +1,48 @@ +easyblock = 'PythonBundle' + +name = 'ASE' +version = '3.23.0' + +homepage = 'https://wiki.fysik.dtu.dk/ase' +description = """ASE is a python package providing an open source Atomic Simulation Environment + in the Python scripting language. + +From version 3.20.1 we also include the ase-ext package, it contains optional reimplementations +in C of functions in ASE. ASE uses it automatically when installed.""" + +toolchain = {'name': 'iimkl', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('SciPy-bundle', '2023.07'), + ('Flask', '2.3.3'), + ('matplotlib', '3.7.2'), + ('Tkinter', '%(pyver)s'), # Needed by GUI of ASE + ('spglib-python', '2.1.0'), # optional +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('pytest-mock', '3.11.1', { + 'checksums': ['7f6b125602ac6d743e523ae0bfa71e1a697a2f5534064528c6ff84c2f7c2fc7f'], + }), + ('ase', version, { + 'checksums': ['91a2aa31d89bd90b0efdfe4a7e84264f32828b2abfc9f38e65e041ad76fec8ae'], + }), + ('ase-ext', '20.9.0', { + 'checksums': ['a348b0e42cf9fdd11f04b3df002b0bf150002c8df2698ff08d3c8fc7a1223aed'], + }), +] + +sanity_check_paths = { + 'files': ['bin/ase'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +# make sure Tkinter is available, otherwise 'ase gui' will not work +sanity_check_commands = ["python -c 'import tkinter' "] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/a/ATK/ATK-2.38.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/a/ATK/ATK-2.38.0-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..506079ce98c --- /dev/null +++ b/easybuild/easyconfigs/a/ATK/ATK-2.38.0-GCCcore-13.3.0.eb @@ -0,0 +1,39 @@ +easyblock = 'MesonNinja' + +name = 'ATK' +version = '2.38.0' + +homepage = 'https://developer.gnome.org/atk/' +description = """ + ATK provides the set of accessibility interfaces that are implemented by other + toolkits and applications. Using the ATK interfaces, accessibility tools have + full access to view and control running applications. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['ac4de2a4ef4bd5665052952fe169657e65e895c5057dffb3c2a810f6191a0c36'] + +builddependencies = [ + ('binutils', '2.42'), + ('Meson', '1.4.0'), + ('Ninja', '1.12.1'), + ('pkgconf', '2.2.0'), + ('GObject-Introspection', '1.80.1'), +] + +dependencies = [ + ('GLib', '2.80.4'), +] + +configopts = "--buildtype=release --default-library=both " +configopts += "-Dintrospection=true " + +sanity_check_paths = { + 'files': ['lib/libatk-1.0.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.5.0-foss-2023a.eb b/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.5.0-foss-2023a.eb new file mode 100644 index 00000000000..2c31ade2eb0 --- /dev/null +++ b/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.5.0-foss-2023a.eb @@ -0,0 +1,74 @@ +# Updated by: Pavel Grochal (INUITS) +# License: GPLv2 +# Update: Petr Král (INUITS) + +easyblock = 'ConfigureMake' + +name = 'AUGUSTUS' +version = '3.5.0' + +homepage = 'https://bioinf.uni-greifswald.de/augustus/' +description = "AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences" + +toolchain = {'name': 'foss', 'version': '2023a'} + +github_account = 'Gaius-Augustus' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['5ed6ce6106303b800c5e91d37a250baff43b20824657b853ae04d11ad8bdd686'] + +builddependencies = [ + ('Python', '3.11.3'), +] + +dependencies = [ + ('zlib', '1.2.13'), + ('Boost', '1.82.0'), + ('GSL', '2.7'), + ('SAMtools', '1.18'), + ('HTSlib', '1.18'), # also provides tabix + ('BCFtools', '1.18'), + ('lpsolve', '5.5.2.11'), + ('SuiteSparse', '7.1.0'), + ('BamTools', '2.5.2'), + ('SQLite', '3.42.0'), +] + +skipsteps = ['configure'] + +# run "make clean" to avoid using binaries included with the source tarball +prebuildopts = "make clean && " + +_tmpl = 'INCLUDE_PATH_{dep}=-I{root}{incl} LIBRARY_PATH_{dep}="-L{root}{lib} -Wl,-rpath,{root}{lib}"' + +buildopts = ' '.join([ + 'COMPGENEPRED=true SQLITE=true ZIPINPUT=true MYSQL=false CXX="$CXX" ', + _tmpl.format(dep='ZLIB', root='$EBROOTZLIB', incl='/include', lib='/lib'), + _tmpl.format(dep='BOOST', root='$EBROOTBOOST', incl='/include', lib='/lib'), + _tmpl.format(dep='LPSOLVE', root='$EBROOTLPSOLVE', incl='/include', lib='/lib'), + _tmpl.format(dep='SUITESPARSE', root='$EBROOTSUITESPARSE', incl='/include', lib='/lib'), + _tmpl.format(dep='GSL', root='$EBROOTGSL', incl='/include', lib='/lib'), + _tmpl.format(dep='SQLITE', root='$EBROOTSQLITE', incl='/include', lib='/lib'), + _tmpl.format(dep='BAMTOOLS', root='$EBROOTBAMTOOLS', incl='/include/bamtools', lib='/lib'), + _tmpl.format(dep='HTSLIB', root='$EBROOTHTSLIB', incl='/include/htslib', lib='/lib'), +]) + +preinstallopts = "sed -i '/ln -sf/d' Makefile && " +installopts = 'INSTALLDIR=%(installdir)s ' + +sanity_check_paths = { + 'files': ['bin/augustus', 'bin/bam2hints', 'bin/etraining', 'bin/fastBlockSearch', + 'bin/filterBam', 'bin/getSeq', 'bin/homGeneMapping', 'bin/joingenes', + 'bin/load2sqlitedb', 'bin/prepareAlign'], + 'dirs': ['config', 'scripts'], +} +sanity_check_commands = ['augustus --help'] + +modextrapaths = {'PATH': 'scripts'} +modextravars = { + 'AUGUSTUS_BIN_PATH': '%(installdir)s/bin', + 'AUGUSTUS_CONFIG_PATH': '%(installdir)s/config', + 'AUGUSTUS_SCRIPTS_PATH': '%(installdir)s/scripts', +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/a/Abseil/Abseil-20240722.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/a/Abseil/Abseil-20240722.0-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..24951c68814 --- /dev/null +++ b/easybuild/easyconfigs/a/Abseil/Abseil-20240722.0-GCCcore-13.3.0.eb @@ -0,0 +1,34 @@ +easyblock = 'CMakeMake' + +name = 'Abseil' +version = '20240722.0' + +homepage = 'https://abseil.io/' +description = """Abseil is an open-source collection of C++ library code designed to augment the +C++ standard library. The Abseil library code is collected from Google's own +C++ code base, has been extensively tested and used in production, and is the +same code we depend on in our daily coding lives.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +source_urls = [ + 'https://github.com/%(namelower)s/%(namelower)s-cpp/archive/refs/tags'] +sources = ['%(version)s.tar.gz'] +checksums = ['f50e5ac311a81382da7fa75b97310e4b9006474f9560ac46f54a9967f07d4ae3'] + +builddependencies = [ + ('binutils', '2.42'), + ('CMake', '3.29.3'), +] + +configopts = "-DABSL_PROPAGATE_CXX_STD=ON " + +build_shared_libs = True + +sanity_check_paths = { + 'files': ['lib/libabsl_base.' + SHLIB_EXT], + 'dirs': ['include/absl'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/a/Advisor/Advisor-2019_update2.eb b/easybuild/easyconfigs/a/Advisor/Advisor-2019_update2.eb index 24ce3fe1c31..2e121781a46 100644 --- a/easybuild/easyconfigs/a/Advisor/Advisor-2019_update2.eb +++ b/easybuild/easyconfigs/a/Advisor/Advisor-2019_update2.eb @@ -10,7 +10,7 @@ description = """Vectorization Optimization and Thread Prototyping toolchain = SYSTEM -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15084/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/15084/'] sources = ['advisor_%(version)s.tar.gz'] checksums = ['b63e11b0601013ad21789869ad76be5a836da566ee47c125dcda19ff8277de77'] diff --git a/easybuild/easyconfigs/a/Advisor/Advisor-2019_update3.eb b/easybuild/easyconfigs/a/Advisor/Advisor-2019_update3.eb index a9f9a888154..7b025287362 100644 --- a/easybuild/easyconfigs/a/Advisor/Advisor-2019_update3.eb +++ b/easybuild/easyconfigs/a/Advisor/Advisor-2019_update3.eb @@ -10,7 +10,7 @@ description = """Vectorization Optimization and Thread Prototyping toolchain = SYSTEM -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15206/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/15206/'] sources = ['advisor_%(version)s.tar.gz'] checksums = ['6597f165dee3c6444eb0f38a9069327d10584b09555f5d2c4ed86b8f84d980bb'] diff --git a/easybuild/easyconfigs/a/Advisor/Advisor-2019_update5.eb b/easybuild/easyconfigs/a/Advisor/Advisor-2019_update5.eb index 6a0d2fa4ece..cbcdab88d6e 100644 --- a/easybuild/easyconfigs/a/Advisor/Advisor-2019_update5.eb +++ b/easybuild/easyconfigs/a/Advisor/Advisor-2019_update5.eb @@ -10,7 +10,7 @@ description = """Vectorization Optimization and Thread Prototyping toolchain = SYSTEM -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15825/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/15825/'] sources = ['advisor_%(version)s.tar.gz'] checksums = ['3f203ee63df37e87423fdd4cbeb5ec027b3d11e50c9121935f8b323dd635e866'] diff --git a/easybuild/easyconfigs/a/Advisor/Advisor-2021.2.0.eb b/easybuild/easyconfigs/a/Advisor/Advisor-2021.2.0.eb index 2a7de357e47..144362e2eb7 100644 --- a/easybuild/easyconfigs/a/Advisor/Advisor-2021.2.0.eb +++ b/easybuild/easyconfigs/a/Advisor/Advisor-2021.2.0.eb @@ -13,7 +13,7 @@ description = """Vectorization Optimization and Thread Prototyping toolchain = SYSTEM -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/17730/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/17730/'] sources = ['l_oneapi_advisor_p_%(version)s.189_offline.sh'] checksums = ['9d9e9aa11819e6422f732de0e29e70a164e576254504857713cfec90b6b78664'] diff --git a/easybuild/easyconfigs/a/Advisor/Advisor-2021.4.0.eb b/easybuild/easyconfigs/a/Advisor/Advisor-2021.4.0.eb index 55354cc6e25..ec07e00e07e 100644 --- a/easybuild/easyconfigs/a/Advisor/Advisor-2021.4.0.eb +++ b/easybuild/easyconfigs/a/Advisor/Advisor-2021.4.0.eb @@ -13,7 +13,7 @@ description = """Vectorization Optimization and Thread Prototyping toolchain = SYSTEM -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18220/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18220/'] sources = ['l_oneapi_advisor_p_%(version)s.389_offline.sh'] checksums = ['dd948f7312629d9975e12a57664f736b8e011de948771b4c05ad444438532be8'] diff --git a/easybuild/easyconfigs/a/Advisor/Advisor-2022.1.0.eb b/easybuild/easyconfigs/a/Advisor/Advisor-2022.1.0.eb index 58235ccff90..34a2115a37c 100644 --- a/easybuild/easyconfigs/a/Advisor/Advisor-2022.1.0.eb +++ b/easybuild/easyconfigs/a/Advisor/Advisor-2022.1.0.eb @@ -13,7 +13,7 @@ description = """Vectorization Optimization and Thread Prototyping toolchain = SYSTEM -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18730/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18730/'] sources = ['l_oneapi_advisor_p_%(version)s.171_offline.sh'] checksums = ['b627dbfefa779b44e7ab40dfa37614e56caa6e245feaed402d51826e6a7cb73b'] diff --git a/easybuild/easyconfigs/a/Advisor/Advisor-2023.0.0.eb b/easybuild/easyconfigs/a/Advisor/Advisor-2023.0.0.eb index 187fcafa180..e6d811a03a0 100644 --- a/easybuild/easyconfigs/a/Advisor/Advisor-2023.0.0.eb +++ b/easybuild/easyconfigs/a/Advisor/Advisor-2023.0.0.eb @@ -11,7 +11,7 @@ description = """Vectorization Optimization and Thread Prototyping toolchain = SYSTEM source_urls = [ - 'https://registrationcenter-download.intel.com/akdlm/irc_nas/19094/'] + 'https://registrationcenter-download.intel.com/akdlm/IRC_NAS/19094/'] sources = ['l_oneapi_advisor_p_%(version)s.25338_offline.sh'] checksums = ['5d8ef163f70ee3dc42b13642f321d974f49915d55914ba1ca9177ed29b100b9d'] diff --git a/easybuild/easyconfigs/a/Advisor/Advisor-2025.0.0.eb b/easybuild/easyconfigs/a/Advisor/Advisor-2025.0.0.eb new file mode 100644 index 00000000000..1f057b7f100 --- /dev/null +++ b/easybuild/easyconfigs/a/Advisor/Advisor-2025.0.0.eb @@ -0,0 +1,27 @@ +name = 'Advisor' +version = '2025.0.0' + +homepage = 'https://software.intel.com/content/www/us/en/develop/tools/oneapi/components/advisor.html' +description = """Vectorization Optimization and Thread Prototyping + - Vectorize & thread code or performance “dies” + - Easy workflow + data + tips = faster code faster + - Prioritize, Prototype & Predict performance gain + """ + +toolchain = SYSTEM + +source_urls = [ + 'https://registrationcenter-download.intel.com/akdlm/IRC_NAS/fe95ae4a-3692-4e31-919d-3e7bdf5832f1/'] +sources = ['intel-advisor-%(version)s.798_offline.sh'] +checksums = ['bf85d4b0bd199a2babdff6b4bd3885ce569a3ad0e992b99b2e14dbb30af88cd4'] + +dontcreateinstalldir = True + +sanity_check_paths = { + 'files': ['%(namelower)s/%(version_major_minor)s/bin64/advisor'], + 'dirs': ['%(namelower)s/%(version_major_minor)s/bin64', + '%(namelower)s/%(version_major_minor)s/lib64', + '%(namelower)s/%(version_major_minor)s/include/intel64'] +} + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/a/Albumentations/Albumentations-1.4.0-foss-2023a.eb b/easybuild/easyconfigs/a/Albumentations/Albumentations-1.4.0-foss-2023a.eb new file mode 100644 index 00000000000..36b765ffdc8 --- /dev/null +++ b/easybuild/easyconfigs/a/Albumentations/Albumentations-1.4.0-foss-2023a.eb @@ -0,0 +1,36 @@ +easyblock = 'PythonBundle' + +name = 'Albumentations' +version = '1.4.0' + +homepage = 'https://albumentations.ai' +description = "Albumentations is a Python library for fast and flexible image augmentations" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('SciPy-bundle', '2023.07'), + ('PyYAML', '6.0'), + ('scikit-image', '0.22.0'), + ('scikit-learn', '1.3.1'), + ('OpenCV', '4.8.1', '-contrib'), +] + +preinstallopts = "sed -i 's|CHOOSE_INSTALL_REQUIRES),|[]),|g' setup.py && " + +use_pip = True + +exts_list = [ + ('qudida', '0.0.4', { + 'checksums': ['db198e2887ab0c9aa0023e565afbff41dfb76b361f85fd5e13f780d75ba18cc8'], + }), + ('albumentations', version, { + 'checksums': ['649f8a14896f788b356ecc70083c4fb91bedab4ff4e2b39ad217a824e189ded0'], + }), +] + +sanity_pip_check = True + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.2-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.2-foss-2023a-CUDA-12.1.1.eb new file mode 100644 index 00000000000..3fe9e6719f6 --- /dev/null +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.2-foss-2023a-CUDA-12.1.1.eb @@ -0,0 +1,167 @@ +easyblock = 'PythonBundle' + +name = 'AlphaFold' +version = '2.3.2' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://deepmind.com/research/case-studies/alphafold' +description = "AlphaFold can predict protein structures with atomic accuracy even where no similar structure is known" + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [ + ('poetry', '1.5.1') +] + +dependencies = [ + ('Python', '3.11.3'), + ('CUDA', '12.1.1', '', SYSTEM), + ('SciPy-bundle', '2023.07'), + ('PyYAML', '6.0'), + ('TensorFlow', '2.13.0'), # doesn't require TF-gpu + ('Biopython', '1.83'), + ('HH-suite', '3.3.0'), + ('HMMER', '3.4'), + ('Kalign', '3.4.0'), + ('jax', '0.4.25', versionsuffix), # also provides absl-py # requirement is ==0.3.25! + ('UCX-CUDA', '1.14.1', versionsuffix), + ('cuDNN', '8.9.2.26', versionsuffix, SYSTEM), + ('NCCL', '2.18.3', versionsuffix), + ('OpenMM', '8.0.0', versionsuffix), + ('dm-tree', '0.1.8'), + ('dm-haiku', '0.0.12', versionsuffix), +] + +# commit to use for downloading stereo_chemical_props.txt and copy to alphafold/common, +# see docker/Dockerfile in AlphaFold repository +local_scp_commit = '7102c6' + +components = [ + ('stereo_chemical_props.txt', local_scp_commit, { + 'easyblock': 'Binary', + 'source_urls': [ + 'https://git.scicore.unibas.ch/schwede/openstructure/-/raw/%s/modules/mol/alg/src/' % local_scp_commit, + ], + 'sources': [ + { + 'download_filename': 'stereo_chemical_props.txt', + 'filename': 'stereo_chemical_props-%s.txt' % local_scp_commit, + 'extract_cmd': "cp %s ./stereo_chemical_props.txt", + } + ], + 'checksums': [ + '24510899eeb49167cffedec8fa45363a4d08279c0c637a403b452f7d0ac09451', # stereo_chemical_props-7102c6.txt + ] + }) +] + +use_pip = True + +exts_list = [ + ('PDBFixer', '1.9', { + 'source_urls': ['https://github.com/openmm/pdbfixer/archive/refs/tags/'], + 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}], + 'checksums': ['88b9a77e50655f89d0eb2075093773e82c27a4cef842cb7d735c877b20cd39fb'], + }), + ('tabulate', '0.9.0', { + 'checksums': ['0095b12bf5966de529c0feb1fa08671671b3368eec77d7ef7ab114be2c068b3c'], + }), + ('websocket-client', '1.5.1', { + 'modulename': 'websocket', + 'checksums': ['3f09e6d8230892547132177f575a4e3e73cfdf06526e20cc02aa1c3b47184d40'], + }), + ('docker', '7.0.0', { + 'checksums': ['323736fb92cd9418fc5e7133bc953e11a9da04f4483f828b527db553f1e7e5a3'], + }), + ('immutabledict', '4.1.0', { + 'checksums': ['93d100ccd2cd09a1fd3f136b9328c6e59529ba341de8bb499437f6819159fe8a'], + }), + ('contextlib2', '21.6.0', { + 'checksums': ['ab1e2bfe1d01d968e1b7e8d9023bc51ef3509bba217bb730cee3827e1ee82869'], + }), + ('ml_collections', '0.1.1', { + 'preinstallopts': "touch requirements.txt && touch requirements-test.txt && ", + 'checksums': ['3fefcc72ec433aa1e5d32307a3e474bbb67f405be814ea52a2166bfc9dbe68cc'], + }), + (name, version, { + 'patches': [ + 'AlphaFold-2.0.0_fix-packages.patch', + 'AlphaFold-2.3.2_data-dep-paths-shebang-UniRef30.patch', + 'AlphaFold-2.0.0_n-cpu.patch', + 'AlphaFold-2.0.1_setup_rm_tfcpu.patch', + 'AlphaFold-2.3.2_use_openmm_8.0.0.patch', + 'AlphaFold-2.3.2_BioPythonPDBData.patch', + ], + 'source_urls': ['https://github.com/deepmind/alphafold/archive/refs/tags/'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}], + 'checksums': [ + {'AlphaFold-2.3.2.tar.gz': '4ea8005ba1b573fa1585e4c29b7d188c5cbfa59b4e4761c9f0c15c9db9584a8e'}, + {'AlphaFold-2.0.0_fix-packages.patch': '826d2d1a5d6ac52c51a60ba210e1947d5631a1e2d76f8815305b5d23f74458db'}, + {'AlphaFold-2.3.2_data-dep-paths-shebang-UniRef30.patch': + '58cd0ce4094afe76909649abe68034c4fbdb500967f5c818f49b530356dc012b'}, + {'AlphaFold-2.0.0_n-cpu.patch': 'dfda4dd5f9aba19fe2b6eb9a0ec583d12dcefdfee8ab8803fc57ad48d582db04'}, + {'AlphaFold-2.0.1_setup_rm_tfcpu.patch': + '1a2e4e843bd9a4d15ee39e6c37cc63ba281311cc7a0a5610f0e43b52ef93faac'}, + {'AlphaFold-2.3.2_use_openmm_8.0.0.patch': + 'bbef940c0c959040aaf3984ec47777a229c164517b54616a2688d58fae636d84'}, + {'AlphaFold-2.3.2_BioPythonPDBData.patch': + 'e4483a525ae5c4dc5a5f633bed8cf5337c329e64b603ab7b684a9d18cd26a22f'}, + ], + }), +] + +local_pylibdir = '%(installdir)s/lib/python%(pyshortver)s/site-packages' +local_link_scp = 'ln -s %%(installdir)s/stereo_chemical_props.txt %s/alphafold/common' % local_pylibdir + +postinstallcmds = [ + 'cp %(builddir)s/AlphaFold/alphafold-%(version)s/run_alphafold*.py %(installdir)s/bin', + 'cp -rpP %(builddir)s/AlphaFold/alphafold-%(version)s/scripts %(installdir)s', + 'cd %(installdir)s/bin && ln -s run_alphafold.py alphafold', + 'chmod a+x %(installdir)s/bin/run_alphafold.py', + local_link_scp, +] + +sanity_check_paths = { + 'files': ['bin/alphafold', 'bin/pdbfixer', 'bin/run_alphafold.py', 'stereo_chemical_props.txt'], + 'dirs': ['lib/python%(pyshortver)s/site-packages', 'scripts'], +} + +sanity_check_commands = [ + "pdbfixer --help", + "python -m openmm.testInstallation", + "python -c 'import alphafold'", + "alphafold --help 2>&1 | grep 'Full AlphaFold protein structure prediction script'", + "python %(installdir)s/bin/run_alphafold_test.py", +] + +sanity_pip_check = True + +# these allow to make predictions on proteins that would typically be too long to fit into GPU memory; +# see https://github.com/deepmind/alphafold/blob/main/docker/run_docker.py +modextravars = { + # these allow to make predictions on proteins that would typically be too long to fit into GPU memory; + # see https://github.com/deepmind/alphafold/blob/main/docker/run_docker.py + 'TF_FORCE_UNIFIED_MEMORY': '1', + # jaxlib 0.4.1: https://jax.readthedocs.io/en/latest/changelog.html#jaxlib-0-4-1-dec-13-2022 + # "The behavior of XLA_PYTHON_CLIENT_MEM_FRACTION=.XX has been changed to allocate XX% of the total GPU memory + # instead of the previous behavior of using currently available GPU memory to calculate preallocation. Please refer + # to GPU memory allocation for more details." + # https://jax.readthedocs.io/en/latest/gpu_memory_allocation.html + 'XLA_PYTHON_CLIENT_MEM_FRACTION': '2.5', + # + # Download with $EBROOTALPHAFOLD/scripts/download_all_data.sh /path/to/AlphaFold_DBs/$EBVERSIONALPHAFOLD + 'ALPHAFOLD_DATA_DIR': '/path/to/AlphaFold_DBs/%(versions)s', # please adapt + # Adapt in order to use a different version of UniRef30 by default, + # e.g., v2023_02 from https://wwwuser.gwdg.de/~compbiol/uniclust/2023_02/UniRef30_2023_02_hhsuite.tar.gz: + 'ALPHAFOLD_UNIREF30_VER': '2021_03', + 'OPENMM_RELAX': 'CUDA' # unset or set to 'CPU' in order not to run the energy minimization on GPU; PR#189 +} + +postinstallmsgs = [ + "A newer version of UniRef30 (2023_02) is available at: " + "https://wwwuser.gwdg.de/~compbiol/uniclust/2023_02/UniRef30_2023_02_hhsuite.tar.gz. " + "Untar to $ALPHAFOLD_DATA_DIR/uniref30/ and set the default version accordingly by changing " + "modextravars:ALPHAFOLD_UNIREF30_VER." +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.2_BioPythonPDBData.patch b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.2_BioPythonPDBData.patch new file mode 100644 index 00000000000..df73873cb1c --- /dev/null +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.2_BioPythonPDBData.patch @@ -0,0 +1,14 @@ +# Thomas Hoffmann, EMBL Heidelberg, structures-it@embl.de, 2024/10 +# BioPython 1.83 does not provide protein_letters_3to1 in Bio.Data.SCOPdata but in Bio.Data.PDBData (and Bio.Data.IUPACData) +diff -ru -ru alphafold-2.3.2/alphafold/data/mmcif_parsing.py alphafold-2.3.2_BioPythonSCOPData/alphafold/data/mmcif_parsing.py +--- alphafold-2.3.2/alphafold/data/mmcif_parsing.py 2024-02-19 09:55:16.359778490 +0100 ++++ alphafold-2.3.2_BioPythonSCOPData/alphafold/data/mmcif_parsing.py 2023-03-27 13:50:49.000000000 +0200 +@@ -21,7 +21,7 @@ + + from absl import logging + from Bio import PDB +-from Bio.Data import SCOPData ++from Bio.Data import PDBData as SCOPData + + # Type aliases: + ChainId = str diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.2_data-dep-paths-shebang-UniRef30.patch b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.2_data-dep-paths-shebang-UniRef30.patch new file mode 100644 index 00000000000..c7bbd59ac0c --- /dev/null +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.2_data-dep-paths-shebang-UniRef30.patch @@ -0,0 +1,164 @@ +pick up on $ALPHAFOLD_DATA_DIR to specify location to downloaded data +(see https://github.com/deepmind/alphafold/blob/main/docker/run_docker.py); +pick up on HH-suite, HHMER, Kalign dependencies provided via EasyBuild +author: Kenneth Hoste (HPC-UGent) +update 2.0.1 -> 2.1.0/2.1.2/2.3.0/2.3.2: Thomas Hoffmann (EMBL); +uniref30 version env. variable (THEMBL) + +diff -ru alphafold-2.3.2/run_alphafold.py alphafold-2.3.2_data-dep-paths-shebang-UniRef30/run_alphafold.py +--- alphafold-2.3.2/run_alphafold.py 2023-03-27 13:50:49.000000000 +0200 ++++ alphafold-2.3.2_data-dep-paths-shebang-UniRef30/run_alphafold.py 2024-10-11 11:34:06.330278962 +0200 +@@ -1,3 +1,4 @@ ++#!/usr/bin/env python + # Copyright 2021 DeepMind Technologies Limited + # + # Licensed under the Apache License, Version 2.0 (the "License"); +@@ -42,6 +43,48 @@ + import numpy as np + + # Internal import (7716). ++use_reduced_dbs = any("--db_preset=reduced_dbs" in s for s in sys.argv[1:]) ++use_monomer_preset = not any("--model_preset=multimer" in s for s in sys.argv[1:]) ++ ++data_dir = os.getenv('ALPHAFOLD_DATA_DIR') ++use_gpu_relax = os.getenv('OPENMM_RELAX')=='CUDA' ++uniref30_ver = os.getenv('ALPHAFOLD_UNIREF30_VER') ++if not uniref30_ver: uniref30_ver = '2021_03' ++ ++if data_dir: ++ mgnify_database_path = os.path.join(data_dir, 'mgnify', 'mgy_clusters_2022_05.fa') ++ uniref90_database_path = os.path.join(data_dir, 'uniref90', 'uniref90.fasta') ++ template_mmcif_dir = os.path.join(data_dir, 'pdb_mmcif', 'mmcif_files') ++ obsolete_pdbs_path = os.path.join(data_dir, 'pdb_mmcif', 'obsolete.dat') ++ if use_monomer_preset: ++ pdb_seqres_database_path = None ++ uniprot_database_path = None ++ pdb70_database_path = os.path.join(data_dir, 'pdb70', 'pdb70') ++ else: ++ pdb_seqres_database_path = os.path.join(data_dir, 'pdb_seqres', 'pdb_seqres.txt') ++ uniprot_database_path = os.path.join(data_dir, 'uniprot', 'uniprot.fasta') ++ pdb70_database_path = None ++ if use_reduced_dbs: ++ small_bfd_database_path = os.path.join(data_dir, 'small_bfd','bfd-first_non_consensus_sequences.fasta') ++ uniref30_database_path = None ++ bfd_database_path = None ++ else: ++ small_bfd_database_path = None ++ bfd_database_path = os.path.join(data_dir, 'bfd', 'bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt') ++ uniref30_database_path = os.path.join(data_dir, 'uniref30', 'UniRef30_%s' % uniref30_ver) ++else: ++ sys.stderr.write("$ALPHAFOLD_DATA_DIR is not defined!") ++ uniref90_database_path = None ++ mgnify_database_path = None ++ bfd_database_path = None ++ uniref30_database_path = None ++ pdb70_database_path = None ++ template_mmcif_dir = None ++ obsolete_pdbs_path = None ++ small_bfd_database_path = None ++ uniprot_database_path = None ++ pdb_seqres_database_path = None ++ use_gpu_relax = None + + logging.set_verbosity(logging.INFO) + +@@ -59,7 +102,7 @@ + 'separated by commas. All FASTA paths must have a unique basename as the ' + 'basename is used to name the output directories for each prediction.') + +-flags.DEFINE_string('data_dir', None, 'Path to directory of supporting data.') ++flags.DEFINE_string('data_dir', data_dir, 'Path to directory of supporting data.') + flags.DEFINE_string('output_dir', None, 'Path to a directory that will ' + 'store the results.') + flags.DEFINE_string('jackhmmer_binary_path', shutil.which('jackhmmer'), +@@ -71,32 +114,32 @@ + flags.DEFINE_string('hmmsearch_binary_path', shutil.which('hmmsearch'), + 'Path to the hmmsearch executable.') + flags.DEFINE_string('hmmbuild_binary_path', shutil.which('hmmbuild'), +- 'Path to the hmmbuild executable.') ++ 'Path to the hmmbuild executable.') + flags.DEFINE_string('kalign_binary_path', shutil.which('kalign'), +- 'Path to the Kalign executable.') +-flags.DEFINE_string('uniref90_database_path', None, 'Path to the Uniref90 ' +- 'database for use by JackHMMER.') +-flags.DEFINE_string('mgnify_database_path', None, 'Path to the MGnify ' +- 'database for use by JackHMMER.') +-flags.DEFINE_string('bfd_database_path', None, 'Path to the BFD ' +- 'database for use by HHblits.') +-flags.DEFINE_string('small_bfd_database_path', None, 'Path to the small ' +- 'version of BFD used with the "reduced_dbs" preset.') +-flags.DEFINE_string('uniref30_database_path', None, 'Path to the UniRef30 ' +- 'database for use by HHblits.') +-flags.DEFINE_string('uniprot_database_path', None, 'Path to the Uniprot ' +- 'database for use by JackHMMer.') +-flags.DEFINE_string('pdb70_database_path', None, 'Path to the PDB70 ' +- 'database for use by HHsearch.') +-flags.DEFINE_string('pdb_seqres_database_path', None, 'Path to the PDB ' +- 'seqres database for use by hmmsearch.') +-flags.DEFINE_string('template_mmcif_dir', None, 'Path to a directory with ' +- 'template mmCIF structures, each named .cif') ++ 'Path to the Kalign executable.') ++flags.DEFINE_string('uniref90_database_path', uniref90_database_path, 'Path to the Uniref90 ' ++ 'database for use by JackHMMER.') ++flags.DEFINE_string('mgnify_database_path', mgnify_database_path, 'Path to the MGnify ' ++ 'database for use by JackHMMER.') ++flags.DEFINE_string('bfd_database_path', bfd_database_path, 'Path to the BFD ' ++ 'database for use by HHblits.') ++flags.DEFINE_string('small_bfd_database_path', small_bfd_database_path, 'Path to the small ' ++ 'version of BFD used with the "reduced_dbs" preset.') ++flags.DEFINE_string('uniref30_database_path', uniref30_database_path, 'Path to the UniRef30 ' ++ 'database for use by HHblits.') ++flags.DEFINE_string('uniprot_database_path', uniprot_database_path, 'Path to the Uniprot ' ++ 'database for use by JackHMMer.') ++flags.DEFINE_string('pdb70_database_path', pdb70_database_path, 'Path to the PDB70 ' ++ 'database for use by HHsearch.') ++flags.DEFINE_string('pdb_seqres_database_path', pdb_seqres_database_path, 'Path to the PDB ' ++ 'seqres database for use by hmmsearch.') ++flags.DEFINE_string('template_mmcif_dir', template_mmcif_dir, 'Path to a directory with ' ++ 'template mmCIF structures, each named .cif') + flags.DEFINE_string('max_template_date', None, 'Maximum template release date ' +- 'to consider. Important if folding historical test sets.') +-flags.DEFINE_string('obsolete_pdbs_path', None, 'Path to file containing a ' +- 'mapping from obsolete PDB IDs to the PDB IDs of their ' +- 'replacements.') ++ 'to consider. Important if folding historical test sets.') ++flags.DEFINE_string('obsolete_pdbs_path', obsolete_pdbs_path, 'Path to file containing a ' ++ 'mapping from obsolete PDB IDs to the PDB IDs of their ' ++ 'replacements.') + flags.DEFINE_enum('db_preset', 'full_dbs', + ['full_dbs', 'reduced_dbs'], + 'Choose preset MSA database configuration - ' +@@ -137,7 +180,7 @@ + 'distracting stereochemical violations but might help ' + 'in case you are having issues with the relaxation ' + 'stage.') +-flags.DEFINE_boolean('use_gpu_relax', None, 'Whether to relax on GPU. ' ++flags.DEFINE_boolean('use_gpu_relax', use_gpu_relax, 'Whether to relax on GPU. ' + 'Relax on GPU can be much faster than CPU, so it is ' + 'recommended to enable if possible. GPUs must be available' + ' if this setting is enabled.') +@@ -334,6 +377,10 @@ + 'sure it is installed on your system.') + + use_small_bfd = FLAGS.db_preset == 'reduced_dbs' ++ if use_small_bfd and data_dir: ++ bfd_database_path = None ++ uniref30_database_path = None ++ + _check_flag('small_bfd_database_path', 'db_preset', + should_be_set=use_small_bfd) + _check_flag('bfd_database_path', 'db_preset', +@@ -456,13 +503,7 @@ + flags.mark_flags_as_required([ + 'fasta_paths', + 'output_dir', +- 'data_dir', +- 'uniref90_database_path', +- 'mgnify_database_path', +- 'template_mmcif_dir', + 'max_template_date', +- 'obsolete_pdbs_path', +- 'use_gpu_relax', + ]) + + app.run(main) diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.2_use_openmm_8.0.0.patch b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.2_use_openmm_8.0.0.patch new file mode 100644 index 00000000000..765fdb3c4d6 --- /dev/null +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.2_use_openmm_8.0.0.patch @@ -0,0 +1,243 @@ +# Add compatibility with OpenMM-8.0.0 +# The patch is based on the recipe from https://github.com/deepmind/alphafold/issues/404 +# Author: maxim-masterov (SURF) (7.7.0) +# update 8.0.0: THEMBL +diff -ru alphafold-2.3.2/alphafold/relax/amber_minimize.py alphafold-2.3.2_use_openmm_7.7.0/alphafold/relax/amber_minimize.py +--- alphafold-2.3.2/alphafold/relax/amber_minimize.py 2023-03-27 13:50:49.000000000 +0200 ++++ alphafold-2.3.2_use_openmm_7.7.0/alphafold/relax/amber_minimize.py 2023-04-06 10:38:33.512754033 +0200 +@@ -27,10 +27,10 @@ + import ml_collections + import numpy as np + import jax +-from simtk import openmm +-from simtk import unit +-from simtk.openmm import app as openmm_app +-from simtk.openmm.app.internal.pdbstructure import PdbStructure ++from openmm import * ++from openmm import unit ++from openmm import app as openmm_app ++from openmm.app.internal.pdbstructure import PdbStructure + + + ENERGY = unit.kilocalories_per_mole +@@ -47,7 +47,7 @@ + + + def _add_restraints( +- system: openmm.System, ++ system: System, + reference_pdb: openmm_app.PDBFile, + stiffness: unit.Unit, + rset: str, +diff -ru alphafold-2.3.2/alphafold/relax/cleanup.py alphafold-2.3.2_use_openmm_7.7.0/alphafold/relax/cleanup.py +--- alphafold-2.3.2/alphafold/relax/cleanup.py 2023-03-27 13:50:49.000000000 +0200 ++++ alphafold-2.3.2_use_openmm_7.7.0/alphafold/relax/cleanup.py 2023-04-06 10:39:25.224888763 +0200 +@@ -20,8 +20,8 @@ + import io + + import pdbfixer +-from simtk.openmm import app +-from simtk.openmm.app import element ++from openmm import app ++from openmm.app import element + + + def fix_pdb(pdbfile, alterations_info): +diff -ru alphafold-2.3.2/alphafold/relax/cleanup_test.py alphafold-2.3.2_use_openmm_7.7.0/alphafold/relax/cleanup_test.py +--- alphafold-2.3.2/alphafold/relax/cleanup_test.py 2023-03-27 13:50:49.000000000 +0200 ++++ alphafold-2.3.2_use_openmm_7.7.0/alphafold/relax/cleanup_test.py 2023-04-06 10:39:58.409616942 +0200 +@@ -17,7 +17,7 @@ + + from absl.testing import absltest + from alphafold.relax import cleanup +-from simtk.openmm.app.internal import pdbstructure ++from openmm.app.internal import pdbstructure + + + def _pdb_to_structure(pdb_str): +diff -ru alphafold-2.3.2/docker/Dockerfile alphafold-2.3.2_use_openmm_7.7.0/docker/Dockerfile +--- alphafold-2.3.2/docker/Dockerfile 2023-03-27 13:50:49.000000000 +0200 ++++ alphafold-2.3.2_use_openmm_7.7.0/docker/Dockerfile 2023-04-06 10:41:10.315194781 +0200 +@@ -76,7 +76,6 @@ + + # Apply OpenMM patch. + WORKDIR /opt/conda/lib/python3.8/site-packages +-RUN patch -p0 < /app/alphafold/docker/openmm.patch + + # Add SETUID bit to the ldconfig binary so that non-root users can run it. + RUN chmod u+s /sbin/ldconfig.real +diff -ru alphafold-2.3.2/notebooks/AlphaFold.ipynb alphafold-2.3.2_use_openmm_7.7.0/notebooks/AlphaFold.ipynb +--- alphafold-2.3.2/notebooks/AlphaFold.ipynb 2023-03-27 13:50:49.000000000 +0200 ++++ alphafold-2.3.2_use_openmm_7.7.0/notebooks/AlphaFold.ipynb 2023-04-06 10:50:41.351746867 +0200 +@@ -103,16 +103,17 @@ + " %shell rm -rf /opt/conda\n", + " %shell wget -q -P /tmp \\\n", + " https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh \\\n", +- " \u0026\u0026 bash /tmp/Miniconda3-latest-Linux-x86_64.sh -b -p /opt/conda \\\n", +- " \u0026\u0026 rm /tmp/Miniconda3-latest-Linux-x86_64.sh\n", ++ " && bash /tmp/Miniconda3-latest-Linux-x86_64.sh -b -p /opt/conda \\\n", ++ " && rm /tmp/Miniconda3-latest-Linux-x86_64.sh\n", ++ + " pbar.update(9)\n", + "\n", + " PATH=%env PATH\n", + " %env PATH=/opt/conda/bin:{PATH}\n", + " %shell conda install -qy conda==4.13.0 \\\n", +- " \u0026\u0026 conda install -qy -c conda-forge \\\n", ++ " && conda install -qy -c conda-forge \\\n", + " python=3.9 \\\n", +- " openmm=7.5.1 \\\n", ++ " openmm=8.0.0 \\\n", + " pdbfixer\n", + " pbar.update(80)\n", + "\n", +@@ -164,8 +165,8 @@ + " pbar.update(10)\n", + "\n", + " # Apply OpenMM patch.\n", +- " %shell pushd /opt/conda/lib/python3.9/site-packages/ \u0026\u0026 \\\n", +- " patch -p0 \u003c /content/alphafold/docker/openmm.patch \u0026\u0026 \\\n", ++ " %shell pushd /opt/conda/lib/python3.8/site-packages/ && \\\n", ++ + " popd\n", + "\n", + " # Make sure stereo_chemical_props.txt is in all locations where it could be searched for.\n", +@@ -189,9 +190,10 @@ + "\n", + "import jax\n", + "if jax.local_devices()[0].platform == 'tpu':\n", +- " raise RuntimeError('Colab TPU runtime not supported. Change it to GPU via Runtime -\u003e Change Runtime Type -\u003e Hardware accelerator -\u003e GPU.')\n", ++ " raise RuntimeError('Colab TPU runtime not supported. Change it to GPU via Runtime -> Change Runtime Type -> Hardware accelerator -> GPU.')\n", + "elif jax.local_devices()[0].platform == 'cpu':\n", +- " raise RuntimeError('Colab CPU runtime not supported. Change it to GPU via Runtime -\u003e Change Runtime Type -\u003e Hardware accelerator -\u003e GPU.')\n", ++ " raise RuntimeError('Colab CPU runtime not supported. Change it to GPU via Runtime -> Change Runtime Type -> Hardware accelerator -> GPU.')\n", ++ + "else:\n", + " print(f'Running with {jax.local_devices()[0].device_kind} GPU')\n", + "\n", +@@ -211,7 +213,7 @@ + "source": [ + "## Making a prediction\n", + "\n", +- "Please paste the sequence of your protein in the text box below, then run the remaining cells via _Runtime_ \u003e _Run after_. You can also run the cells individually by pressing the _Play_ button on the left.\n", ++ "Please paste the sequence of your protein in the text box below, then run the remaining cells via _Runtime_ > _Run after_. You can also run the cells individually by pressing the _Play_ button on the left.\n", + "\n", + "Note that the search against databases and the actual prediction can take some time, from minutes to hours, depending on the length of the protein and what type of GPU you are allocated by Colab (see FAQ below)." + ] +@@ -306,21 +308,21 @@ + "\n", + "# Check whether total length exceeds limit.\n", + "total_sequence_length = sum([len(seq) for seq in sequences])\n", +- "if total_sequence_length \u003e MAX_LENGTH:\n", ++ "if total_sequence_length > MAX_LENGTH:\n", + " raise ValueError('The total sequence length is too long: '\n", + " f'{total_sequence_length}, while the maximum is '\n", + " f'{MAX_LENGTH}.')\n", + "\n", + "# Check whether we exceed the monomer limit.\n", + "if model_type_to_use == ModelType.MONOMER:\n", +- " if len(sequences[0]) \u003e MAX_MONOMER_MODEL_LENGTH:\n", ++ " if len(sequences[0]) > MAX_MONOMER_MODEL_LENGTH:\n", + " raise ValueError(\n", + " f'Input sequence is too long: {len(sequences[0])} amino acids, while '\n", + " f'the maximum for the monomer model is {MAX_MONOMER_MODEL_LENGTH}. You may '\n", + " 'be able to run this sequence with the multimer model by selecting the '\n", + " 'use_multimer_model_for_monomers checkbox above.')\n", + " \n", +- "if total_sequence_length \u003e MAX_VALIDATED_LENGTH:\n", ++ "if total_sequence_length > MAX_VALIDATED_LENGTH:\n", + " print('WARNING: The accuracy of the system has not been fully validated '\n", + " 'above 3000 residues, and you may experience long running times or '\n", + " f'run out of memory. Total sequence length is {total_sequence_length} '\n", +@@ -421,7 +423,7 @@ + "]\n", + "\n", + "# Search UniProt and construct the all_seq features only for heteromers, not homomers.\n", +- "if model_type_to_use == ModelType.MULTIMER and len(set(sequences)) \u003e 1:\n", ++ "if model_type_to_use == ModelType.MULTIMER and len(set(sequences)) > 1:\n", + " MSA_DATABASES.extend([\n", + " # Swiss-Prot and TrEMBL are concatenated together as UniProt.\n", + " {'db_name': 'uniprot',\n", +@@ -455,7 +457,7 @@ + " for sequence_index, sequence in enumerate(sorted(set(sequences)), 1):\n", + " fasta_path = f'target_{sequence_index:02d}.fasta'\n", + " with open(fasta_path, 'wt') as f:\n", +- " f.write(f'\u003equery\\n{sequence}')\n", ++ " f.write(f'>query\\n{sequence}')\n", + " sequence_to_fasta_path[sequence] = fasta_path\n", + "\n", + " # Run the search against chunks of genetic databases (since the genetic\n", +@@ -516,7 +518,7 @@ + " num_templates=0, num_res=len(sequence)))\n", + "\n", + " # Construct the all_seq features only for heteromers, not homomers.\n", +- " if model_type_to_use == ModelType.MULTIMER and len(set(sequences)) \u003e 1:\n", ++ " if model_type_to_use == ModelType.MULTIMER and len(set(sequences)) > 1:\n", + " valid_feats = msa_pairing.MSA_FEATURES + (\n", + " 'msa_species_identifiers',\n", + " )\n", +@@ -680,7 +682,7 @@ + "banded_b_factors = []\n", + "for plddt in plddts[best_model_name]:\n", + " for idx, (min_val, max_val, _) in enumerate(PLDDT_BANDS):\n", +- " if plddt \u003e= min_val and plddt \u003c= max_val:\n", ++ " if plddt >= min_val and plddt <= max_val:\n", + " banded_b_factors.append(idx)\n", + " break\n", + "banded_b_factors = np.array(banded_b_factors)[:, None] * final_atom_mask\n", +@@ -693,14 +695,14 @@ + " f.write(relaxed_pdb)\n", + "\n", + "\n", +- "# --- Visualise the prediction \u0026 confidence ---\n", ++ "# --- Visualise the prediction & confidence ---\n", + "show_sidechains = True\n", + "def plot_plddt_legend():\n", + " \"\"\"Plots the legend for pLDDT.\"\"\"\n", +- " thresh = ['Very low (pLDDT \u003c 50)',\n", +- " 'Low (70 \u003e pLDDT \u003e 50)',\n", +- " 'Confident (90 \u003e pLDDT \u003e 70)',\n", +- " 'Very high (pLDDT \u003e 90)']\n", ++ " thresh = ['Very low (pLDDT < 50)',\n", ++ " 'Low (70 > pLDDT > 50)',\n", ++ " 'Confident (90 > pLDDT > 70)',\n", ++ " 'Very high (pLDDT > 90)']\n", + "\n", + " colors = [x[2] for x in PLDDT_BANDS]\n", + "\n", +@@ -816,13 +818,13 @@ + "id": "jeb2z8DIA4om" + }, + "source": [ +- "## FAQ \u0026 Troubleshooting\n", ++ "## FAQ & Troubleshooting\n", + "\n", + "\n", + "* How do I get a predicted protein structure for my protein?\n", + " * Click on the _Connect_ button on the top right to get started.\n", + " * Paste the amino acid sequence of your protein (without any headers) into the “Enter the amino acid sequence to fold”.\n", +- " * Run all cells in the Colab, either by running them individually (with the play button on the left side) or via _Runtime_ \u003e _Run all._ Make sure you run all 5 cells in order.\n", ++ " * Run all cells in the Colab, either by running them individually (with the play button on the left side) or via _Runtime_ > _Run all._ Make sure you run all 5 cells in order.\n", + " * The predicted protein structure will be downloaded once all cells have been executed. Note: This can take minutes to hours - see below.\n", + "* How long will this take?\n", + " * Downloading the AlphaFold source code can take up to a few minutes.\n", +@@ -831,8 +833,8 @@ + " * Running AlphaFold and generating the prediction can take minutes to hours, depending on the length of your protein and on which GPU-type Colab has assigned you.\n", + "* My Colab no longer seems to be doing anything, what should I do?\n", + " * Some steps may take minutes to hours to complete.\n", +- " * If nothing happens or if you receive an error message, try restarting your Colab runtime via _Runtime_ \u003e _Restart runtime_.\n", +- " * If this doesn’t help, try resetting your Colab runtime via _Runtime_ \u003e _Factory reset runtime_.\n", ++ " * If nothing happens or if you receive an error message, try restarting your Colab runtime via _Runtime_ > _Restart runtime_.\n", ++ " * If this doesn’t help, try resetting your Colab runtime via _Runtime_ > _Factory reset runtime_.\n", + "* How does this compare to the open-source version of AlphaFold?\n", + " * This Colab version of AlphaFold searches a selected portion of the BFD dataset and currently doesn’t use templates, so its accuracy is reduced in comparison to the full version of AlphaFold that is described in the [AlphaFold paper](https://doi.org/10.1038/s41586-021-03819-2) and [Github repo](https://github.com/deepmind/alphafold/) (the full version is available via the inference script).\n", + "* What is a Colab?\n", +@@ -841,7 +843,7 @@ + " * The resources allocated to your Colab vary. See the [Colab FAQ](https://research.google.com/colaboratory/faq.html) for more details.\n", + " * You can execute the Colab nonetheless.\n", + "* I received an error “Colab CPU runtime not supported” or “No GPU/TPU found”, what do I do?\n", +- " * Colab CPU runtime is not supported. Try changing your runtime via _Runtime_ \u003e _Change runtime type_ \u003e _Hardware accelerator_ \u003e _GPU_.\n", ++ " * Colab CPU runtime is not supported. Try changing your runtime via _Runtime_ > _Change runtime type_ > _Hardware accelerator_ > _GPU_.\n", + " * The type of GPU allocated to your Colab varies. See the [Colab FAQ](https://research.google.com/colaboratory/faq.html) for more details.\n", + " * If you receive “Cannot connect to GPU backend”, you can try again later to see if Colab allocates you a GPU.\n", + " * [Colab Pro](https://colab.research.google.com/signup) offers priority access to GPUs.\n", diff --git a/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-2.0.0b2_fix-import-protein_letters_3to1.patch b/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-2.0.0b2_fix-import-protein_letters_3to1.patch new file mode 100644 index 00000000000..34994664f80 --- /dev/null +++ b/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-2.0.0b2_fix-import-protein_letters_3to1.patch @@ -0,0 +1,13 @@ +fix import of protein_letters_3to1 from Biopython +author: Kenneth Hoste (HPC-UGent) +--- AlphaPulldown/alphapulldown/utils/remove_clashes_low_plddt.py.orig 2024-06-05 09:30:16.114746286 +0200 ++++ AlphaPulldown/alphapulldown/utils/remove_clashes_low_plddt.py 2024-06-05 09:30:35.242665615 +0200 +@@ -4,7 +4,7 @@ + from alphafold.data.mmcif_parsing import parse + from alphafold.common.residue_constants import residue_atoms, atom_types + from Bio.PDB import NeighborSearch, PDBIO, MMCIFIO +-from Bio.PDB.Polypeptide import protein_letters_3to1 ++from Bio.Data.SCOPData import protein_letters_3to1 + from Bio import SeqIO + from colabfold.batch import convert_pdb_to_mmcif + from Bio.PDB import Structure, Model, Chain, Residue diff --git a/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-2.0.0b4-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-2.0.0b4-foss-2022a-CUDA-11.7.0.eb new file mode 100644 index 00000000000..492a787c919 --- /dev/null +++ b/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-2.0.0b4-foss-2022a-CUDA-11.7.0.eb @@ -0,0 +1,106 @@ +# created by Denis Kristak (Inuits) +easyblock = 'PythonBundle' + +name = 'AlphaPulldown' +version = '2.0.0b4' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/KosinskiLab/AlphaPulldown' +description = """AlphaPulldown is a Python package that streamlines protein-protein +interaction screens and high-throughput modelling of higher-order oligomers using AlphaFold-Multimer""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('CUDA', '11.7.0', '', SYSTEM), + ('Python', '3.10.4'), + ('OpenMM', '8.0.0'), + ('Kalign', '3.3.5'), + ('PyYAML', '6.0'), + ('jax', '0.3.25', versionsuffix), # also provides absl-py + ('Biopython', '1.79'), + ('h5py', '3.7.0'), + ('IPython', '8.5.0'), + ('JupyterLab', '3.5.0'), + ('matplotlib', '3.5.2'), + ('TensorFlow', '2.11.0', versionsuffix), + ('PyTorch', '1.12.0', versionsuffix), + ('tqdm', '4.64.0'), + ('dm-tree', '0.1.8'), + ('py3Dmol', '2.0.1.post1'), + ('HMMER', '3.3.2'), + ('HH-suite', '3.3.0'), + ('Uni-Core', '0.0.3', versionsuffix), +] + +use_pip = True + +exts_list = [ + ('importlib-resources', '5.13.0', { + 'modulename': 'importlib_resources', + 'source_tmpl': 'importlib_resources-%(version)s.tar.gz', + 'checksums': ['82d5c6cca930697dbbd86c93333bb2c2e72861d4789a11c2662b933e5ad2b528'], + }), + ('jmp', '0.0.4', { + 'checksums': ['5dfeb0fd7c7a9f72a70fff0aab9d0cbfae32a809c02f4037ff3485ceb33e1730'], + }), + ('dm-haiku', '0.0.9', { + 'modulename': 'haiku', + 'source_urls': ['https://github.com/deepmind/dm-haiku/archive/refs/tags/'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['d550f07f5891ede30ada5faafde98f549ed1b8ceadb7a601cca3d81db7d82414'], + }), + ('contextlib2', '21.6.0', { + 'checksums': ['ab1e2bfe1d01d968e1b7e8d9023bc51ef3509bba217bb730cee3827e1ee82869'], + }), + ('ml-collections', '0.1.1', { + 'preinstallopts': "touch requirements.txt && touch requirements-test.txt && ", + 'sources': ['ml_collections-%(version)s.tar.gz'], + 'checksums': ['3fefcc72ec433aa1e5d32307a3e474bbb67f405be814ea52a2166bfc9dbe68cc'], + }), + ('PDBFixer', '1.9', { + 'source_urls': ['https://github.com/openmm/pdbfixer/archive/'], + 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['88b9a77e50655f89d0eb2075093773e82c27a4cef842cb7d735c877b20cd39fb'], + }), + ('ihm', '1.3', { + 'checksums': ['09f69809fd81509cc26b60253c55b02ce79fc01fc8f4a068bca2953a7dfd33be'], + }), + ('modelcif', '1.0', { + 'checksums': ['e8375bc502a73dcfab0b7fbdd454d67d393bbb8969981eb52199d77192a3de56'], + }), + (name, version, { + 'sources': [{ + 'filename': SOURCE_TAR_GZ, + 'git_config': { + 'url': 'https://github.com/KosinskiLab', + 'repo_name': 'AlphaPulldown', + 'tag': version, + 'recursive': True, + }, + }], + 'patches': ['AlphaPulldown-2.0.0b2_fix-import-protein_letters_3to1.patch'], + 'checksums': [ + None, + 'd41247cd12f6ef8579adbc893f6c1af5fba051167ee838449974365f4bdccf06', + ], + # remove strict version requirements for Python dependencies + 'preinstallopts': "sed -i 's/[>=]=.*//g' setup.cfg && ", + }), +] + +fix_python_shebang_for = ['bin/*.py'] + +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/run_multimer_jobs.py', 'bin/rename_colab_search_a3m.py'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/alphapulldown'], +} + +sanity_check_commands = [ + "run_multimer_jobs.py --help | grep 'A script to perform structure prediction'", + "convert_to_modelcif.py --help | grep 'turn it into a ModelCIF'", +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-2.0.0b4-foss-2022a.eb b/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-2.0.0b4-foss-2022a.eb new file mode 100644 index 00000000000..f410c438e23 --- /dev/null +++ b/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-2.0.0b4-foss-2022a.eb @@ -0,0 +1,104 @@ +# created by Denis Kristak (Inuits) +easyblock = 'PythonBundle' + +name = 'AlphaPulldown' +version = '2.0.0b4' + +homepage = 'https://github.com/KosinskiLab/AlphaPulldown' +description = """AlphaPulldown is a Python package that streamlines protein-protein +interaction screens and high-throughput modelling of higher-order oligomers using AlphaFold-Multimer""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('OpenMM', '8.0.0'), + ('Kalign', '3.3.5'), + ('PyYAML', '6.0'), + ('jax', '0.3.25'), # also provides absl-py + ('Biopython', '1.79'), + ('h5py', '3.7.0'), + ('IPython', '8.5.0'), + ('JupyterLab', '3.5.0'), + ('matplotlib', '3.5.2'), + ('TensorFlow', '2.11.0'), + ('PyTorch', '1.12.0'), + ('tqdm', '4.64.0'), + ('dm-tree', '0.1.8'), + ('py3Dmol', '2.0.1.post1'), + ('HMMER', '3.3.2'), + ('HH-suite', '3.3.0'), + ('Uni-Core', '0.0.3'), +] + +use_pip = True + +exts_list = [ + ('importlib-resources', '5.13.0', { + 'modulename': 'importlib_resources', + 'source_tmpl': 'importlib_resources-%(version)s.tar.gz', + 'checksums': ['82d5c6cca930697dbbd86c93333bb2c2e72861d4789a11c2662b933e5ad2b528'], + }), + ('jmp', '0.0.4', { + 'checksums': ['5dfeb0fd7c7a9f72a70fff0aab9d0cbfae32a809c02f4037ff3485ceb33e1730'], + }), + ('dm-haiku', '0.0.9', { + 'modulename': 'haiku', + 'source_urls': ['https://github.com/deepmind/dm-haiku/archive/refs/tags/'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['d550f07f5891ede30ada5faafde98f549ed1b8ceadb7a601cca3d81db7d82414'], + }), + ('contextlib2', '21.6.0', { + 'checksums': ['ab1e2bfe1d01d968e1b7e8d9023bc51ef3509bba217bb730cee3827e1ee82869'], + }), + ('ml-collections', '0.1.1', { + 'preinstallopts': "touch requirements.txt && touch requirements-test.txt && ", + 'sources': ['ml_collections-%(version)s.tar.gz'], + 'checksums': ['3fefcc72ec433aa1e5d32307a3e474bbb67f405be814ea52a2166bfc9dbe68cc'], + }), + ('PDBFixer', '1.9', { + 'source_urls': ['https://github.com/openmm/pdbfixer/archive/'], + 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['88b9a77e50655f89d0eb2075093773e82c27a4cef842cb7d735c877b20cd39fb'], + }), + ('ihm', '1.3', { + 'checksums': ['09f69809fd81509cc26b60253c55b02ce79fc01fc8f4a068bca2953a7dfd33be'], + }), + ('modelcif', '1.0', { + 'checksums': ['e8375bc502a73dcfab0b7fbdd454d67d393bbb8969981eb52199d77192a3de56'], + }), + (name, version, { + 'sources': [{ + 'filename': SOURCE_TAR_GZ, + 'git_config': { + 'url': 'https://github.com/KosinskiLab', + 'repo_name': 'AlphaPulldown', + 'tag': version, + 'recursive': True, + }, + }], + 'patches': ['AlphaPulldown-2.0.0b2_fix-import-protein_letters_3to1.patch'], + 'checksums': [ + None, + 'd41247cd12f6ef8579adbc893f6c1af5fba051167ee838449974365f4bdccf06', + ], + # remove strict version requirements for Python dependencies + 'preinstallopts': "sed -i 's/[>=]=.*//g' setup.cfg && ", + }), +] + +fix_python_shebang_for = ['bin/*.py'] + +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/run_multimer_jobs.py', 'bin/rename_colab_search_a3m.py'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/alphapulldown'], +} + +sanity_check_commands = [ + "run_multimer_jobs.py --help | grep 'A script to perform structure prediction'", + "convert_to_modelcif.py --help | grep 'turn it into a ModelCIF'", +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/a/AmberTools/AmberTools-23.6-foss-2023a.eb b/easybuild/easyconfigs/a/AmberTools/AmberTools-23.6-foss-2023a.eb new file mode 100644 index 00000000000..ca7d8074aab --- /dev/null +++ b/easybuild/easyconfigs/a/AmberTools/AmberTools-23.6-foss-2023a.eb @@ -0,0 +1,86 @@ +easyblock = 'EB_Amber' + +name = 'AmberTools' +local_ambertools_ver = 23 +# Patch levels from http://ambermd.org/AmberPatches.php and http://ambermd.org/ATPatches.php +patchlevels = (6, 0) # (AmberTools, Amber) +version = '%s.%s' % (local_ambertools_ver, patchlevels[0]) + +homepage = 'https://ambermd.org/' +description = """AmberTools consists of several independently developed packages that work well by themselves, + and with Amber itself. The suite can also be used to carry out complete molecular dynamics simulations, + with either explicit water or generalized Born solvent models.""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'usempi': True} + +# download requires registration +local_download_credentials = '?Name=Easybuild&Institution=Easybuild&City=Internet&State=Other&Country=Belgium' +source_urls = ['https://ambermd.org/cgi-bin/AmberTools%s-get.pl' % local_ambertools_ver] +sources = [{ + 'download_filename': local_download_credentials, + 'filename': 'AmberTools%s.tar.bz2' % local_ambertools_ver, +}] +patches = [ + 'AmberTools-20_cmake-locate-netcdf.patch', + 'AmberTools-20_fix_missing_MPI_LIBRARY_error.patch', + 'AmberTools-20_fix_xblas_missing_make_dependency.patch', + 'AmberTools-21_CMake-FlexiBLAS.patch', + 'AmberTools-21_fix_incorrect_dvout_call.patch', + 'AmberTools-21_fix_more_blas_argument_problems.patch', + 'AmberTools-21_fix_potential_use_before_init.patch', + 'AmberTools-21_fix_rism_argument_mismatch.patch', + 'AmberTools-21_fix_xray_fftpack_arg_mismatch.patch', + 'AmberTools-22_fix_test_missing_cuda_dir.patch', +] +checksums = [ + {'AmberTools23.tar.bz2': 'debb52e6ef2e1b4eaa917a8b4d4934bd2388659c660501a81ea044903bf9ee9d'}, + {'AmberTools-20_cmake-locate-netcdf.patch': '473e07c53b6f641d96d333974a6af2e03413fecef79f879d3fdecf7fecaab4d0'}, + {'AmberTools-20_fix_missing_MPI_LIBRARY_error.patch': + '0b89a0624167bc23876bcdefcb1055f591e38e3bd559a71d5749e342bd311acc'}, + {'AmberTools-20_fix_xblas_missing_make_dependency.patch': + 'ff25e91fdc72347a778c3837b581e174d6a8c71efa5b46e11391b18bca84fd65'}, + {'AmberTools-21_CMake-FlexiBLAS.patch': '9543812c24c4b7842f64f1f8abaf2c92b5c4c0fadcdbd9811e76b81a778f0d36'}, + {'AmberTools-21_fix_incorrect_dvout_call.patch': + '1054d4007f5c79126a41582e1e80514267cf406416ed6c471574cd708b16319b'}, + {'AmberTools-21_fix_more_blas_argument_problems.patch': + 'c6279b57752239184b942d37f760749494ae0eff95236f3368c76ac0d2726a7c'}, + {'AmberTools-21_fix_potential_use_before_init.patch': + '377e645b5bd2c91ebb4d0b6fbca0407a94289e5ddc5b1e7ed0cb0b0724ad2139'}, + {'AmberTools-21_fix_rism_argument_mismatch.patch': + '14255e5739cec39303df570f06820c7532f7395e1b73b1e4104377984e2c9fc1'}, + {'AmberTools-21_fix_xray_fftpack_arg_mismatch.patch': + '99c954e693659efc2a1d121f91510f56408006f0751d91595f45a34b03364e2f'}, + {'AmberTools-22_fix_test_missing_cuda_dir.patch': + 'fb1ab74314d7816169bb9f3f527b78085654aae2825c52cebf50a5760401b737'}, +] + +builddependencies = [ + ('CMake', '3.26.3'), + ('pkgconf', '1.9.5'), + ('Bison', '3.8.2'), + ('flex', '2.6.4'), + ('make', '4.4.1'), +] + +dependencies = [ + ('zlib', '1.2.13'), + ('bzip2', '1.0.8'), + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('Perl', '5.36.1'), + ('Perl-bundle-CPAN', '5.36.1'), + ('Boost', '1.82.0'), + ('libreadline', '8.2'), + ('matplotlib', '3.7.2'), + ('netCDF', '4.9.2'), + ('netCDF-Fortran', '4.6.1'), + ('PnetCDF', '1.12.3'), + ('Tkinter', '%(pyver)s'), + ('X11', '20230603'), + ('mpi4py', '3.1.4'), +] + +runtest = True + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/a/Arcade-Learning-Environment/Arcade-Learning-Environment-0.8.1-foss-2023a.eb b/easybuild/easyconfigs/a/Arcade-Learning-Environment/Arcade-Learning-Environment-0.8.1-foss-2023a.eb new file mode 100644 index 00000000000..aca8f2dca72 --- /dev/null +++ b/easybuild/easyconfigs/a/Arcade-Learning-Environment/Arcade-Learning-Environment-0.8.1-foss-2023a.eb @@ -0,0 +1,63 @@ +easyblock = 'CMakeMake' + +name = 'Arcade-Learning-Environment' +version = '0.8.1' + +homepage = 'https://github.com/mgbellemare/Arcade-Learning-Environment' +description = """The Arcade Learning Environment (ALE) is a simple framework that allows +researchers and hobbyists to develop AI agents for Atari 2600 games. It is +built on top of the Atari 2600 emulator Stella and separates the details of +emulation from agent design. This video depicts over 50 games currently +supported in the ALE.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +github_account = 'mgbellemare' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['28960616cd89c18925ced7bbdeec01ab0b2ebd2d8ce5b7c88930e97381b4c3b5'] + +builddependencies = [ + ('CMake', '3.26.3'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('pybind11', '2.11.1'), + ('SciPy-bundle', '2023.07'), + ('SDL2', '2.28.2'), + ('zlib', '1.2.13'), +] + +# main build of C++ libraries +configopts = "-DBUILD_PYTHON_LIB=OFF" + +# install Python bindings and its dependencies +exts_defaultclass = 'PythonPackage' +exts_default_options = { + 'download_dep_fail': True, + 'use_pip': True, + 'sanity_pip_check': True, +} +exts_list = [ + ('ale-py', version, { + 'patches': ['%(name)s-%(version)s_fix_version.patch'], + 'preinstallopts': 'ALE_BUILD_VERSION=%(version)s', + 'source_tmpl': 'v%(version)s.tar.gz', + 'checksums': [ + {'v0.8.1.tar.gz': '28960616cd89c18925ced7bbdeec01ab0b2ebd2d8ce5b7c88930e97381b4c3b5'}, + {'ale-py-0.8.1_fix_version.patch': '3ad39a05eb82c3aacf34a6de562ad2d76c254a906963bdef6a810f0b5ce0d22f'}, + ], + }), +] + +sanity_check_paths = { + 'files': ['bin/ale-import-roms', 'lib64/libale.a'], + 'dirs': ['include/ale', 'lib/python%(pyshortver)s/site-packages/'], +} + +sanity_check_commands = ["ale-import-roms --help"] + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/a/Archive-Zip/Archive-Zip-1.68-GCCcore-13.2.0.eb b/easybuild/easyconfigs/a/Archive-Zip/Archive-Zip-1.68-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..389e96b3d06 --- /dev/null +++ b/easybuild/easyconfigs/a/Archive-Zip/Archive-Zip-1.68-GCCcore-13.2.0.eb @@ -0,0 +1,31 @@ +easyblock = 'PerlModule' + +name = 'Archive-Zip' +version = '1.68' + +homepage = 'https://metacpan.org/pod/Archive::Zip' +description = "Provide an interface to ZIP archive files." + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://cpan.metacpan.org/authors/id/P/PH/PHRED/'] +sources = [SOURCE_TAR_GZ] +checksums = ['984e185d785baf6129c6e75f8eb44411745ac00bf6122fb1c8e822a3861ec650'] + +builddependencies = [ + ('binutils', '2.40'), +] +dependencies = [ + ('Perl', '5.38.0'), + ('UnZip', '6.0'), + ('Zip', '3.0'), +] + +options = {'modulename': 'Archive::Zip'} + +sanity_check_paths = { + 'files': ['bin/crc32'], + 'dirs': ['lib/perl5/site_perl/%(perlver)s/Archive/Zip'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/a/Archive-Zip/Archive-Zip-1.68-GCCcore-13.3.0.eb b/easybuild/easyconfigs/a/Archive-Zip/Archive-Zip-1.68-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..9656cf84761 --- /dev/null +++ b/easybuild/easyconfigs/a/Archive-Zip/Archive-Zip-1.68-GCCcore-13.3.0.eb @@ -0,0 +1,31 @@ +easyblock = 'PerlModule' + +name = 'Archive-Zip' +version = '1.68' + +homepage = 'https://metacpan.org/pod/Archive::Zip' +description = "Provide an interface to ZIP archive files." + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://cpan.metacpan.org/authors/id/P/PH/PHRED/'] +sources = [SOURCE_TAR_GZ] +checksums = ['984e185d785baf6129c6e75f8eb44411745ac00bf6122fb1c8e822a3861ec650'] + +builddependencies = [ + ('binutils', '2.42'), +] +dependencies = [ + ('Perl', '5.38.2'), + ('UnZip', '6.0'), + ('Zip', '3.0'), +] + +options = {'modulename': 'Archive::Zip'} + +sanity_check_paths = { + 'files': ['bin/crc32'], + 'dirs': ['lib/perl5/site_perl/%(perlver)s/Archive/Zip'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/a/Armadillo/Armadillo-11.4.3-foss-2022a.eb b/easybuild/easyconfigs/a/Armadillo/Armadillo-11.4.3-foss-2022a.eb index 261ecca60bb..c8c874dba00 100644 --- a/easybuild/easyconfigs/a/Armadillo/Armadillo-11.4.3-foss-2022a.eb +++ b/easybuild/easyconfigs/a/Armadillo/Armadillo-11.4.3-foss-2022a.eb @@ -12,10 +12,13 @@ source_urls = ['https://sourceforge.net/projects/arma/files'] sources = [SOURCELOWER_TAR_XZ] checksums = ['87603263664988af41da2ca4f36205e36ea47a9281fa6cfd463115f3797a1da2'] -builddependencies = [('CMake', '3.24.3')] +builddependencies = [ + ('CMake', '3.24.3'), +] dependencies = [ ('Boost', '1.79.0'), + ('HDF5', '1.12.2'), ('arpack-ng', '3.8.0'), ] diff --git a/easybuild/easyconfigs/a/Armadillo/Armadillo-11.4.3-foss-2022b.eb b/easybuild/easyconfigs/a/Armadillo/Armadillo-11.4.3-foss-2022b.eb index f5eb6f67b05..1be96397544 100644 --- a/easybuild/easyconfigs/a/Armadillo/Armadillo-11.4.3-foss-2022b.eb +++ b/easybuild/easyconfigs/a/Armadillo/Armadillo-11.4.3-foss-2022b.eb @@ -12,10 +12,13 @@ source_urls = ['https://sourceforge.net/projects/arma/files'] sources = [SOURCELOWER_TAR_XZ] checksums = ['87603263664988af41da2ca4f36205e36ea47a9281fa6cfd463115f3797a1da2'] -builddependencies = [('CMake', '3.24.3')] +builddependencies = [ + ('CMake', '3.24.3'), +] dependencies = [ ('Boost', '1.81.0'), + ('HDF5', '1.14.0'), ('arpack-ng', '3.8.0'), ] diff --git a/easybuild/easyconfigs/a/Armadillo/Armadillo-12.6.2-foss-2023a.eb b/easybuild/easyconfigs/a/Armadillo/Armadillo-12.6.2-foss-2023a.eb index 2ca4adac034..9b6d74fe58b 100644 --- a/easybuild/easyconfigs/a/Armadillo/Armadillo-12.6.2-foss-2023a.eb +++ b/easybuild/easyconfigs/a/Armadillo/Armadillo-12.6.2-foss-2023a.eb @@ -18,6 +18,7 @@ builddependencies = [ dependencies = [ ('Boost', '1.82.0'), + ('HDF5', '1.14.0'), ('arpack-ng', '3.9.0'), ] diff --git a/easybuild/easyconfigs/a/Armadillo/Armadillo-12.8.0-foss-2023b.eb b/easybuild/easyconfigs/a/Armadillo/Armadillo-12.8.0-foss-2023b.eb index cde4b18960c..2ca0b7de51d 100644 --- a/easybuild/easyconfigs/a/Armadillo/Armadillo-12.8.0-foss-2023b.eb +++ b/easybuild/easyconfigs/a/Armadillo/Armadillo-12.8.0-foss-2023b.eb @@ -17,6 +17,7 @@ builddependencies = [ ] dependencies = [ ('Boost', '1.83.0'), + ('HDF5', '1.14.3'), ('arpack-ng', '3.9.0'), ] diff --git a/easybuild/easyconfigs/a/Arrow/Arrow-14.0.1-gfbf-2023a.eb b/easybuild/easyconfigs/a/Arrow/Arrow-14.0.1-gfbf-2023a.eb index 85715fef495..0c588b9f16b 100644 --- a/easybuild/easyconfigs/a/Arrow/Arrow-14.0.1-gfbf-2023a.eb +++ b/easybuild/easyconfigs/a/Arrow/Arrow-14.0.1-gfbf-2023a.eb @@ -39,10 +39,10 @@ dependencies = [ start_dir = 'cpp' # see https://arrow.apache.org/docs/developers/python.html -configopts = "-DARROW_DATASET=on -DARROW_PYTHON=on -DARROW_PARQUET=ON -DARROW_WITH_SNAPPY=ON " +configopts = "-DARROW_DATASET=on -DARROW_PYTHON=on -DARROW_PARQUET=ON -DARROW_ORC=ON " configopts += "-DCMAKE_INSTALL_LIBDIR=lib -DPython3_ROOT_DIR=$EBROOTPYTHON " -configopts += "-DARROW_WITH_ZLIB=ON -DARROW_WITH_BZ2=ON -DARROW_WITH_ZSTD=ON -DARROW_WITH_LZ4=ON " -configopts += "-DZSTD_ROOT=$EBROOTZSTD " +configopts += "-DARROW_WITH_ZLIB=ON -DARROW_WITH_BZ2=ON -DARROW_WITH_LZ4=ON -DARROW_WITH_SNAPPY=ON " +configopts += "-DARROW_WITH_ZSTD=ON -DZSTD_ROOT=$EBROOTZSTD " # install Python bindings _pyarrow_preinstall_opts = "export PKG_CONFIG_PATH=%(installdir)s/lib/pkgconfig:$PKG_CONFIG_PATH && " @@ -52,7 +52,7 @@ _pyarrow_preinstall_opts += "export XDG_CACHE_HOME=$TMPDIR && " _pyarrow_preinstall_opts += "sed -i 's/numpy==[0-9.]*/numpy/g' pyproject.toml && " _pyarrow_preinstall_opts += "Python3_ROOT_DIR=$EBROOTPYTHON " _pyarrow_preinstall_opts += "PYARROW_CMAKE_OPTIONS='-DZSTD_LIB=$EBROOTZSTD/lib/libzstd.%s ' " % SHLIB_EXT -_pyarrow_preinstall_opts += "PYARROW_WITH_DATASET=1 PYARROW_WITH_PARQUET=1 " +_pyarrow_preinstall_opts += "PYARROW_WITH_DATASET=1 PYARROW_WITH_PARQUET=1 PYARROW_WITH_ORC=1 " exts_defaultclass = 'PythonPackage' exts_default_options = { @@ -81,6 +81,7 @@ sanity_check_commands = [ "python -c 'import pyarrow'", "python -c 'import pyarrow.dataset'", "python -c 'import pyarrow.parquet'", + "python -c 'import pyarrow.orc'", ] moduleclass = 'data' diff --git a/easybuild/easyconfigs/a/Arrow/Arrow-16.1.0-gfbf-2023b.eb b/easybuild/easyconfigs/a/Arrow/Arrow-16.1.0-gfbf-2023b.eb new file mode 100644 index 00000000000..5219bd9c54f --- /dev/null +++ b/easybuild/easyconfigs/a/Arrow/Arrow-16.1.0-gfbf-2023b.eb @@ -0,0 +1,87 @@ +easyblock = 'CMakeMake' + +name = 'Arrow' +version = '16.1.0' + +homepage = 'https://arrow.apache.org' +description = """Apache Arrow (incl. PyArrow Python bindings), a cross-language development platform + for in-memory data.""" + +toolchain = {'name': 'gfbf', 'version': '2023b'} + +source_urls = ['https://archive.apache.org/dist/%(namelower)s/%(namelower)s-%(version)s'] +sources = ['apache-arrow-%(version)s.tar.gz'] +checksums = ['c9e60c7e87e59383d21b20dc874b17153729ee153264af6d21654b7dff2c60d7'] + +builddependencies = [ + ('CMake', '3.27.6'), + ('Autotools', '20220317'), + ('flex', '2.6.4'), + ('Bison', '3.8.2'), + ('pkgconf', '2.0.3'), +] + +# Arrow strongly prefers included jemalloc, so not including it as a dependency +dependencies = [ + ('Python', '3.11.5'), + ('SciPy-bundle', '2023.11'), # for numpy + ('Boost', '1.83.0'), + ('lz4', '1.9.4'), + ('zlib', '1.2.13'), + ('bzip2', '1.0.8'), + ('zstd', '1.5.5'), + ('snappy', '1.1.10'), + ('RapidJSON', '1.1.0-20240409'), + ('RE2', '2024-03-01'), + ('utf8proc', '2.9.0'), +] + +start_dir = 'cpp' + +# see https://arrow.apache.org/docs/developers/python.html +configopts = "-DARROW_DATASET=on -DARROW_PYTHON=on -DARROW_PARQUET=ON -DARROW_ORC=ON " +configopts += "-DCMAKE_INSTALL_LIBDIR=lib -DPython3_ROOT_DIR=$EBROOTPYTHON " +configopts += "-DARROW_WITH_ZLIB=ON -DARROW_WITH_BZ2=ON -DARROW_WITH_LZ4=ON -DARROW_WITH_SNAPPY=ON " +configopts += "-DARROW_WITH_ZSTD=ON -DZSTD_ROOT=$EBROOTZSTD " + +# install Python bindings +_pyarrow_preinstall_opts = "export PKG_CONFIG_PATH=%(installdir)s/lib/pkgconfig:$PKG_CONFIG_PATH && " +_pyarrow_preinstall_opts += "export Arrow_DIR=%(installdir)s && export ArrowDataset_DIR=%(installdir)s && " +_pyarrow_preinstall_opts += "export ArrowAcero_DIR=%(installdir)s && export Parquet_DIR=%(installdir)s && " +_pyarrow_preinstall_opts += "export XDG_CACHE_HOME=$TMPDIR && " +_pyarrow_preinstall_opts += "sed -i 's/numpy==[0-9.]*/numpy/g' pyproject.toml && " +_pyarrow_preinstall_opts += "Python3_ROOT_DIR=$EBROOTPYTHON " +_pyarrow_preinstall_opts += "PYARROW_CMAKE_OPTIONS='-DZSTD_LIB=$EBROOTZSTD/lib/libzstd.%s ' " % SHLIB_EXT +_pyarrow_preinstall_opts += "PYARROW_WITH_DATASET=1 PYARROW_WITH_PARQUET=1 PYARROW_WITH_ORC=1 " + +exts_defaultclass = 'PythonPackage' +exts_default_options = { + 'download_dep_fail': True, + 'use_pip': True, + 'sanity_pip_check': True, +} +exts_list = [ + ('pyarrow', version, { + 'sources': ['apache-arrow-%(version)s.tar.gz'], + 'checksums': ['c9e60c7e87e59383d21b20dc874b17153729ee153264af6d21654b7dff2c60d7'], + 'start_dir': '%(builddir)s/apache-arrow-%(version)s/python', + 'preinstallopts': _pyarrow_preinstall_opts, + }), +] + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +sanity_check_paths = { + 'files': ['lib/libarrow.a', 'lib/libarrow.%s' % SHLIB_EXT, + 'lib/python%%(pyshortver)s/site-packages/pyarrow/libarrow_python.%s' % SHLIB_EXT], + 'dirs': ['include/arrow', 'lib/cmake/Arrow', 'lib/pkgconfig', 'lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "python -c 'import pyarrow'", + "python -c 'import pyarrow.dataset'", + "python -c 'import pyarrow.parquet'", + "python -c 'import pyarrow.orc'", +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/a/Arrow/Arrow-17.0.0-gfbf-2024a.eb b/easybuild/easyconfigs/a/Arrow/Arrow-17.0.0-gfbf-2024a.eb new file mode 100644 index 00000000000..76dcfd2cc40 --- /dev/null +++ b/easybuild/easyconfigs/a/Arrow/Arrow-17.0.0-gfbf-2024a.eb @@ -0,0 +1,96 @@ +easyblock = 'CMakeMake' + +name = 'Arrow' +version = '17.0.0' + +homepage = 'https://arrow.apache.org' +description = """Apache Arrow (incl. PyArrow Python bindings), a cross-language development platform + for in-memory data.""" + +toolchain = {'name': 'gfbf', 'version': '2024a'} + +source_urls = ['https://archive.apache.org/dist/%(namelower)s/%(namelower)s-%(version)s'] +sources = ['apache-arrow-%(version)s.tar.gz'] +checksums = ['9d280d8042e7cf526f8c28d170d93bfab65e50f94569f6a790982a878d8d898d'] + +builddependencies = [ + ('CMake', '3.29.3'), + ('Cython', '3.0.10'), + ('Autotools', '20231222'), + ('flex', '2.6.4'), + ('Bison', '3.8.2'), + ('pkgconf', '2.2.0'), +] + +# Arrow strongly prefers included jemalloc, so not including it as a dependency +dependencies = [ + ('Python', '3.12.3'), + ('Python-bundle-PyPI', '2024.06'), + ('SciPy-bundle', '2024.05'), # for numpy + ('Boost', '1.85.0'), + ('lz4', '1.9.4'), + ('zlib', '1.3.1'), + ('bzip2', '1.0.8'), + ('zstd', '1.5.6'), + ('snappy', '1.1.10'), + ('RapidJSON', '1.1.0-20240815'), + ('RE2', '2024-07-02'), + ('utf8proc', '2.9.0'), +] + +start_dir = 'cpp' + +# see https://arrow.apache.org/docs/developers/python.html +configopts = "-DARROW_DATASET=on -DARROW_PYTHON=on -DARROW_PARQUET=ON -DARROW_ORC=ON " +configopts += "-DCMAKE_INSTALL_LIBDIR=lib -DPython3_ROOT_DIR=$EBROOTPYTHON " +configopts += "-DARROW_WITH_ZLIB=ON -DARROW_WITH_BZ2=ON -DARROW_WITH_LZ4=ON -DARROW_WITH_SNAPPY=ON " +configopts += "-DARROW_WITH_ZSTD=ON -DZSTD_ROOT=$EBROOTZSTD " + +# install Python bindings +_pyarrow_preinstall_opts = "export PKG_CONFIG_PATH=%(installdir)s/lib/pkgconfig:$PKG_CONFIG_PATH && " +_pyarrow_preinstall_opts += "export Arrow_DIR=%(installdir)s && export ArrowDataset_DIR=%(installdir)s && " +_pyarrow_preinstall_opts += "export ArrowAcero_DIR=%(installdir)s && export Parquet_DIR=%(installdir)s && " +_pyarrow_preinstall_opts += "export XDG_CACHE_HOME=$TMPDIR && " +_pyarrow_preinstall_opts += "sed -i 's/numpy==[0-9.]*/numpy/g' pyproject.toml && " +_pyarrow_preinstall_opts += "Python3_ROOT_DIR=$EBROOTPYTHON " +_pyarrow_preinstall_opts += "PYARROW_CMAKE_OPTIONS='-DZSTD_LIB=$EBROOTZSTD/lib/libzstd.%s ' " % SHLIB_EXT +_pyarrow_preinstall_opts += "PYARROW_WITH_DATASET=1 PYARROW_WITH_PARQUET=1 PYARROW_WITH_ORC=1 " + +exts_defaultclass = 'PythonPackage' +exts_default_options = { + 'download_dep_fail': True, + 'use_pip': True, + 'sanity_pip_check': True, +} +exts_list = [ + ('pyarrow', version, { + 'preinstallopts': ( + "export PKG_CONFIG_PATH=%(installdir)s/lib/pkgconfig:$PKG_CONFIG_PATH" + " && export Arrow_DIR=%(installdir)s && export ArrowDataset_DIR=%(installdir)s" + " && export ArrowAcero_DIR=%(installdir)s && export Parquet_DIR=%(installdir)s" + " && export XDG_CACHE_HOME=$TMPDIR && sed -i 's/numpy==[0-9.]*/numpy/g' pyproject.toml" + " && Python3_ROOT_DIR=$EBROOTPYTHON PYARROW_CMAKE_OPTIONS='-DZSTD_LIB=$EBROOTZSTD/lib/libzstd.so" + " ' PYARROW_WITH_DATASET=1 PYARROW_WITH_PARQUET=1 PYARROW_WITH_ORC=1 " + ), + 'sources': ['apache-arrow-%(version)s.tar.gz'], + 'start_dir': '%(builddir)s/apache-arrow-%(version)s/python', + 'checksums': ['9d280d8042e7cf526f8c28d170d93bfab65e50f94569f6a790982a878d8d898d'], + }), +] + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +sanity_check_paths = { + 'files': ['lib/libarrow.a', 'lib/libarrow.%s' % SHLIB_EXT, + 'lib/python%%(pyshortver)s/site-packages/pyarrow/libarrow_python.%s' % SHLIB_EXT], + 'dirs': ['include/arrow', 'lib/cmake/Arrow', 'lib/pkgconfig', 'lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "python -c 'import pyarrow'", + "python -c 'import pyarrow.dataset'", + "python -c 'import pyarrow.parquet'", + "python -c 'import pyarrow.orc'", +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/a/Austin/Austin-3.2.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/a/Austin/Austin-3.2.0-GCCcore-11.2.0.eb index d4f3285a8fd..b2d0fe9046a 100644 --- a/easybuild/easyconfigs/a/Austin/Austin-3.2.0-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/a/Austin/Austin-3.2.0-GCCcore-11.2.0.eb @@ -53,7 +53,7 @@ sanity_check_paths = { sanity_check_commands = [ "austin --help", "austin-tui --help", - "pip check", + "PIP_DISABLE_PIP_VERSION_CHECK=true python -s -m pip check", ] modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} diff --git a/easybuild/easyconfigs/a/Auto-WEKA/Auto-WEKA-2.6-WEKA-3.8.5-Java-11.eb b/easybuild/easyconfigs/a/Auto-WEKA/Auto-WEKA-2.6-WEKA-3.8.5-Java-11.eb new file mode 100644 index 00000000000..165bfe50d5a --- /dev/null +++ b/easybuild/easyconfigs/a/Auto-WEKA/Auto-WEKA-2.6-WEKA-3.8.5-Java-11.eb @@ -0,0 +1,42 @@ +easyblock = "Tarball" + +name = 'Auto-WEKA' +version = '2.6' +local_weka_version = '3.8.5' +versionsuffix = '-WEKA-%s-Java-%%(javaver)s' % local_weka_version + +homepage = 'http://www.cs.ubc.ca/labs/beta/Projects/autoweka/' +description = """ +Auto-WEKA considers the problem of simultaneously selecting a learning +algorithm and setting its hyperparameters, going beyond previous methods that +address these issues in isolation. Auto-WEKA does this using a fully automated +approach, leveraging recent innovations in Bayesian optimization. Our hope is +that Auto-WEKA will help non-expert users to more effectively identify machine +learning algorithms and hyperparameter settings appropriate to their +applications, and hence to achieve improved performance.""" + +toolchain = SYSTEM + +source_urls = ['http://www.cs.ubc.ca/labs/beta/Projects/autoweka/'] +sources = ['autoweka-%(version)s.zip'] +checksums = ['8fba8835f6326a9fd621ffe9f119921adae00dcef97ffad5357362b155374840'] + +dependencies = [ + ('Java', '11'), + ('WEKA', local_weka_version, '-Java-%(javaver)s'), +] + +sanity_check_paths = { + 'files': ['autoweka.jar'], + 'dirs': [] +} + +sanity_check_commands = [ + "java weka.Run -no-scan weka.classifiers.meta.AutoWEKAClassifier -h" +] + +modloadmsg = """Run %(name)s classifiers with: +java weka.Run -no-scan weka.classifiers.meta.AutoWEKAClassifier -h +""" + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/a/Autoconf-archive/Autoconf-archive-2023.02.20-GCCcore-12.2.0.eb b/easybuild/easyconfigs/a/Autoconf-archive/Autoconf-archive-2023.02.20-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..73e0608725b --- /dev/null +++ b/easybuild/easyconfigs/a/Autoconf-archive/Autoconf-archive-2023.02.20-GCCcore-12.2.0.eb @@ -0,0 +1,53 @@ +## +# This is a contribution from DeepThought HPC Service, Flinders University, Adelaide, Australia +# Homepage: https://staff.flinders.edu.au/research/deep-thought +# +# Authors:: Robert Qiao +# License:: GNU Free Documentation License +# +# Notes:: +## + +easyblock = 'ConfigureMake' + +name = 'Autoconf-archive' +version = '2023.02.20' + +homepage = "https://www.gnu.org/software/autoconf-archive" + +description = """ +The GNU Autoconf Archive is a collection of more than 500 macros for GNU Autoconf +that have been contributed as free software by friendly supporters of the cause from +all over the Internet. Every single one of those macros can be re-used without +imposing any restrictions whatsoever on the licensing of the generated configure script. +In particular, it is possible to use all those macros in configure scripts that +are meant for non-free software. This policy is unusual for a Free Software Foundation +project. The FSF firmly believes that software ought to be free, and software licenses +like the GPL are specifically designed to ensure that derivative work based on free +software must be free as well. In case of Autoconf, however, an exception has been made, +because Autoconf is at such a pivotal position in the software development tool chain +that the benefits from having this tool available as widely as possible outweigh the +disadvantage that some authors may choose to use it, too, for proprietary software. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['71d4048479ae28f1f5794619c3d72df9c01df49b1c628ef85fde37596dc31a33'] + +builddependencies = [ + ('binutils', '2.39'), + ('Autotools', '20220317'), + ('makeinfo', '7.0.3'), +] + +preconfigopts = 'autoreconf -i -f &&' + +sanity_check_paths = { + 'files': [], + 'dirs': ['share/%s' % x for x in + ['aclocal', 'doc', 'info']], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.72-GCCcore-13.3.0.eb b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.72-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..8cbff6d13b2 --- /dev/null +++ b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.72-GCCcore-13.3.0.eb @@ -0,0 +1,48 @@ +easyblock = 'ConfigureMake' + +name = 'Autoconf' +version = '2.72' + +homepage = 'https://www.gnu.org/software/autoconf/' + +description = """ + Autoconf is an extensible package of M4 macros that produce shell scripts + to automatically configure software source code packages. These scripts can + adapt the packages to many kinds of UNIX-like systems without manual user + intervention. Autoconf creates a configuration script for a package from a + template file that lists the operating system features that the package can + use, in the form of M4 macro calls. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['afb181a76e1ee72832f6581c0eddf8df032b83e2e0239ef79ebedc4467d92d6e'] + +builddependencies = [ + ('binutils', '2.42'), +] + +dependencies = [ + ('M4', '1.4.19'), + # non-standard Perl modules are required, + # see https://github.com/easybuilders/easybuild-easyconfigs/issues/1822 + ('Perl', '5.38.2'), +] + +preconfigopts = "export PERL='/usr/bin/env perl' && " + +sanity_check_paths = { + 'files': ["bin/%s" % x + for x in ["autoconf", "autoheader", "autom4te", "autoreconf", + "autoscan", "autoupdate", "ifnames"]], + 'dirs': [], +} + +sanity_check_commands = [ + "autoconf --help", + "autom4te --help", +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.16.5-GCCcore-13.3.0.eb b/easybuild/easyconfigs/a/Automake/Automake-1.16.5-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..f22a104b063 --- /dev/null +++ b/easybuild/easyconfigs/a/Automake/Automake-1.16.5-GCCcore-13.3.0.eb @@ -0,0 +1,39 @@ +easyblock = 'ConfigureMake' + +name = 'Automake' +version = '1.16.5' + +homepage = 'https://www.gnu.org/software/automake/automake.html' + +description = "Automake: GNU Standards-compliant Makefile generator" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['07bd24ad08a64bc17250ce09ec56e921d6343903943e99ccf63bbf0705e34605'] + +builddependencies = [ + ('binutils', '2.42'), +] + +dependencies = [ + ('Autoconf', '2.72'), + # non-standard Perl modules are required, + # see https://github.com/easybuilders/easybuild-easyconfigs/issues/1822 + ('Perl', '5.38.2'), +] + +preconfigopts = "export PERL='/usr/bin/env perl' && " + +sanity_check_paths = { + 'files': ['bin/aclocal', 'bin/automake'], + 'dirs': [] +} + +sanity_check_commands = [ + "aclocal --help", + "automake --help", +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/a/Autotools/Autotools-20231222-GCCcore-13.3.0.eb b/easybuild/easyconfigs/a/Autotools/Autotools-20231222-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..4c0c23dd0b1 --- /dev/null +++ b/easybuild/easyconfigs/a/Autotools/Autotools-20231222-GCCcore-13.3.0.eb @@ -0,0 +1,24 @@ +easyblock = 'Bundle' + +name = 'Autotools' +version = '20231222' # date of the most recent change + +homepage = 'https://autotools.io' + +description = """ + This bundle collect the standard GNU build tools: Autoconf, Automake + and libtool +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +dependencies = [ + ('Autoconf', '2.72'), # 20231222 + ('Automake', '1.16.5'), # 20211003 + ('libtool', '2.4.7'), # 20220317 +] + +# Pure bundle -- no need to specify 'binutils' used when building GCCcore +# toolchain as build dependency + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/a/absl-py/absl-py-2.1.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/a/absl-py/absl-py-2.1.0-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..faadde2a51d --- /dev/null +++ b/easybuild/easyconfigs/a/absl-py/absl-py-2.1.0-GCCcore-12.3.0.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonBundle' + +name = 'absl-py' +version = '2.1.0' + +homepage = 'https://github.com/abseil/abseil-py' +description = """absl-py is a collection of Python library code for building Python +applications. The code is collected from Google's own Python code base, and has +been extensively tested and used in production.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +builddependencies = [('binutils', '2.40')] + +dependencies = [('Python', '3.11.3')] + +use_pip = True + +exts_list = [ + ('absl-py', version, { + 'modulename': 'absl', + 'checksums': ['7820790efbb316739cde8b4e19357243fc3608a152024288513dd968d7d959ff'], + }), +] + +sanity_pip_check = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/a/absl-py/absl-py-2.1.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/a/absl-py/absl-py-2.1.0-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..fb76611558b --- /dev/null +++ b/easybuild/easyconfigs/a/absl-py/absl-py-2.1.0-GCCcore-13.3.0.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonBundle' + +name = 'absl-py' +version = '2.1.0' + +homepage = 'https://github.com/abseil/abseil-py' +description = """absl-py is a collection of Python library code for building Python +applications. The code is collected from Google's own Python code base, and has +been extensively tested and used in production.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +builddependencies = [('binutils', '2.42')] + +dependencies = [('Python', '3.12.3')] + +use_pip = True + +exts_list = [ + ('absl-py', version, { + 'modulename': 'absl', + 'checksums': ['7820790efbb316739cde8b4e19357243fc3608a152024288513dd968d7d959ff'], + }), +] + +sanity_pip_check = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/a/accelerate/accelerate-0.33.0-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/a/accelerate/accelerate-0.33.0-foss-2023a-CUDA-12.1.1.eb new file mode 100644 index 00000000000..7f6d595a7c5 --- /dev/null +++ b/easybuild/easyconfigs/a/accelerate/accelerate-0.33.0-foss-2023a-CUDA-12.1.1.eb @@ -0,0 +1,39 @@ +easyblock = 'PythonBundle' + +name = 'accelerate' +version = '0.33.0' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/huggingface/accelerate' +description = """A simple way to launch, train, and use PyTorch models on almost any device and +distributed configuration, automatic mixed precision (including fp8), +and easy-to-configure FSDP and DeepSpeed support.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('SciPy-bundle', '2023.07'), + ('CUDA', '12.1.1', '', SYSTEM), + ('PyTorch-bundle', '2.1.2', versionsuffix), + ('PyYAML', '6.0'), + ('Safetensors', '0.4.3'), +] + +sanity_pip_check = True +use_pip = True + +exts_list = [ + ('huggingface-hub', '0.24.5', { + 'sources': ['huggingface_hub-%(version)s.tar.gz'], + 'checksums': ['7b45d6744dd53ce9cbf9880957de00e9d10a9ae837f1c9b7255fc8fa4e8264f3'], + }), + (name, version, { + 'checksums': ['11ba481ed6ea09191775df55ce464aeeba67a024bd0261a44b77b30fb439e26a'], + }), +] + +sanity_check_commands = ['accelerate test'] + +moduleclass = 'ai' diff --git a/easybuild/easyconfigs/a/adjustText/adjustText-0.7.3-foss-2022b.eb b/easybuild/easyconfigs/a/adjustText/adjustText-0.7.3-foss-2022b.eb new file mode 100644 index 00000000000..4c13c121047 --- /dev/null +++ b/easybuild/easyconfigs/a/adjustText/adjustText-0.7.3-foss-2022b.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'adjustText' +version = '0.7.3' + +homepage = 'https://github.com/Phlya/adjustText' +description = "A small library for automatically adjustment of text position in matplotlib plots to minimize overlaps." + +toolchain = {'name': 'foss', 'version': '2022b'} + +sources = [SOURCE_TAR_GZ] +checksums = ['b90e275a95b4d980cbbac7967914b8d66477c09bc346a0b3c9e2125bba664b06'] + +dependencies = [ + ('Python', '3.10.8'), + ('matplotlib', '3.7.0'), + ('SciPy-bundle', '2023.02'), +] + +download_dep_fail = True +use_pip = True + +sanity_pip_check = True + +options = {'modulename': 'adjustText'} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/a/adjustText/adjustText-0.7.3-foss-2023a.eb b/easybuild/easyconfigs/a/adjustText/adjustText-0.7.3-foss-2023a.eb new file mode 100644 index 00000000000..70ad0961c47 --- /dev/null +++ b/easybuild/easyconfigs/a/adjustText/adjustText-0.7.3-foss-2023a.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'adjustText' +version = '0.7.3' + +homepage = 'https://github.com/Phlya/adjustText' +description = "A small library for automatically adjustment of text position in matplotlib plots to minimize overlaps." + +toolchain = {'name': 'foss', 'version': '2023a'} + +sources = [SOURCE_TAR_GZ] +checksums = ['b90e275a95b4d980cbbac7967914b8d66477c09bc346a0b3c9e2125bba664b06'] + +dependencies = [ + ('Python', '3.11.3'), + ('matplotlib', '3.7.2'), + ('SciPy-bundle', '2023.07'), +] + +download_dep_fail = True +use_pip = True + +sanity_pip_check = True + +options = {'modulename': 'adjustText'} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/a/adjustText/adjustText-1.1.1-foss-2023a.eb b/easybuild/easyconfigs/a/adjustText/adjustText-1.1.1-foss-2023a.eb new file mode 100644 index 00000000000..f109d19d3aa --- /dev/null +++ b/easybuild/easyconfigs/a/adjustText/adjustText-1.1.1-foss-2023a.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonBundle' + +name = 'adjustText' +version = '1.1.1' + +homepage = 'https://github.com/Phlya/adjustText' +description = "A small library for automatically adjustment of text position in matplotlib plots to minimize overlaps." + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('matplotlib', '3.7.2'), + ('SciPy-bundle', '2023.07'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + (name, version, { + 'modulename': 'adjustText', + 'checksums': ['e2c0975ef2c642478e60f4c03c5e9afbdeda7764336907ef69a9205bfa2d9896'], + }), +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/a/affogato/affogato-0.3.3-foss-2023a.eb b/easybuild/easyconfigs/a/affogato/affogato-0.3.3-foss-2023a.eb new file mode 100644 index 00000000000..391f9d95eda --- /dev/null +++ b/easybuild/easyconfigs/a/affogato/affogato-0.3.3-foss-2023a.eb @@ -0,0 +1,40 @@ +easyblock = 'CMakeMakeCp' + +name = 'affogato' +version = '0.3.3' + +homepage = 'https://github.com/constantinpape/affogato/' +description = """Affinity based segmentation algorithms and tools.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['https://github.com/constantinpape/affogato/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['ad3bb1aca50ce9311d4e88e97e701237bce94faa6e79460f0bc2d2061f1484d2'] + +builddependencies = [('CMake', '3.26.3')] + +dependencies = [ + ('Python', '3.11.3'), + ('Boost', '1.82.0'), + ('SciPy-bundle', '2023.07'), + ('vigra', '1.11.2'), + ('xtensor', '0.24.7'), + ('h5py', '3.9.0'), +] + +configopts = '-DBUILD_PYTHON=ON ' +# Fix path to python executable - it finds v3.6.8 from /usr/bin/ without this fix +configopts += '-DPYTHON_EXECUTABLE="$EBROOTPYTHON/bin/python" ' + +files_to_copy = [(['python/affogato'], 'lib/python%(pyshortver)s/site-packages')] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/affogato'], +} +sanity_check_commands = ["python -c 'import affogato'"] + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/a/aiohttp/aiohttp-3.10.10-GCCcore-13.3.0.eb b/easybuild/easyconfigs/a/aiohttp/aiohttp-3.10.10-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..c6b30e2d82e --- /dev/null +++ b/easybuild/easyconfigs/a/aiohttp/aiohttp-3.10.10-GCCcore-13.3.0.eb @@ -0,0 +1,72 @@ +easyblock = 'PythonBundle' + +name = 'aiohttp' +version = '3.10.10' + +homepage = 'https://github.com/aio-libs/aiohttp' +description = "Asynchronous HTTP client/server framework for asyncio and Python." + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +builddependencies = [ + ('binutils', '2.42'), + ('poetry', '1.8.3'), + ('Cython', '3.0.10'), +] + +dependencies = [ + ('Python', '3.12.3'), + ('Python-bundle-PyPI', '2024.06'), +] + +use_pip = True + +# aioredis and aiosignal do not depend on aiohttp, but are commonly used together and share dependencies +exts_list = [ + ('botocore', '1.35.36', { + 'checksums': ['354ec1b766f0029b5d6ff0c45d1a0f9e5007b7d2f3ec89bcdd755b208c5bc797'], + }), + ('jmespath', '1.0.1', { + 'checksums': ['90261b206d6defd58fdd5e85f478bf633a2901798906be2ad389150c5c60edbe'], + }), + ('multidict', '6.1.0', { + 'checksums': ['22ae2ebf9b0c69d206c003e2f6a914ea33f0a932d4aa16f236afc049d9958f4a'], + }), + ('expandvars', '0.12.0', { + 'checksums': ['7d1adfa55728cf4b5d812ece3d087703faea953e0c0a1a78415de9df5024d844'], + }), + ('propcache', '0.2.0', { + 'checksums': ['df81779732feb9d01e5d513fad0122efb3d53bbc75f61b2a4f29a020bc985e70'], + }), + ('yarl', '1.15.4', { + 'checksums': ['a0c5e271058d148d730219ca4f33c5d841c6bd46e05b0da60fea7b516906ccd3'], + }), + ('frozenlist', '1.4.1', { + 'checksums': ['c037a86e8513059a2613aaba4d817bb90b9d9b6b69aace3ce9c877e8c8ed402b'], + }), + ('async-timeout', '4.0.3', { + 'checksums': ['4640d96be84d82d02ed59ea2b7105a0f7b33abe8703703cd0ab0bf87c427522f'], + }), + ('aiosignal', '1.3.1', { + 'checksums': ['54cd96e15e1649b75d6c87526a6ff0b6c1b0dd3459f43d9ca11d48c339b68cfc'], + }), + ('aiohappyeyeballs', '2.4.3', { + 'checksums': ['75cf88a15106a5002a8eb1dab212525c00d1f4c0fa96e551c9fbe6f09a621586'], + }), + (name, version, { + 'checksums': ['0631dd7c9f0822cc61c88586ca76d5b5ada26538097d0f1df510b082bad3411a'], + }), + ('aioitertools', '0.12.0', { + 'checksums': ['c2a9055b4fbb7705f561b9d86053e8af5d10cc845d22c32008c43490b2d8dd6b'], + }), + ('wrapt', '1.16.0', { + 'checksums': ['5f370f952971e7d17c7d1ead40e49f32345a7f7a5373571ef44d800d06b1899d'], + }), + ('aiobotocore', '2.15.2', { + 'checksums': ['9ac1cfcaccccc80602968174aa032bf978abe36bd4e55e6781d6500909af1375'], + }), +] + +sanity_pip_check = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/a/aiohttp/aiohttp-3.8.5-GCCcore-12.3.0.eb b/easybuild/easyconfigs/a/aiohttp/aiohttp-3.8.5-GCCcore-12.3.0.eb index 3c96a3e7458..d5eec66b4ab 100644 --- a/easybuild/easyconfigs/a/aiohttp/aiohttp-3.8.5-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/a/aiohttp/aiohttp-3.8.5-GCCcore-12.3.0.eb @@ -30,8 +30,8 @@ exts_list = [ ('frozenlist', '1.4.0', { 'checksums': ['09163bdf0b2907454042edb19f887c6d33806adc71fbd54afc14908bfdc22251'], }), - ('async-timeout', '4.0.2', { - 'checksums': ['2163e1640ddb52b7a8c80d0a67a08587e5d245cc9c553a74a847056bc2976b15'], + ('async-timeout', '4.0.3', { + 'checksums': ['4640d96be84d82d02ed59ea2b7105a0f7b33abe8703703cd0ab0bf87c427522f'], }), (name, version, { 'checksums': ['b9552ec52cc147dbf1944ac7ac98af7602e51ea2dcd076ed194ca3c0d1c7d0bc'], diff --git a/easybuild/easyconfigs/a/aiohttp/aiohttp-3.9.5-GCCcore-13.2.0.eb b/easybuild/easyconfigs/a/aiohttp/aiohttp-3.9.5-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..550b4aebf60 --- /dev/null +++ b/easybuild/easyconfigs/a/aiohttp/aiohttp-3.9.5-GCCcore-13.2.0.eb @@ -0,0 +1,53 @@ +easyblock = 'PythonBundle' + +name = 'aiohttp' +version = '3.9.5' + +homepage = 'https://github.com/aio-libs/aiohttp' +description = "Asynchronous HTTP client/server framework for asyncio and Python." + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +builddependencies = [ + ('binutils', '2.40'), + ('poetry', '1.6.1'), +] + +dependencies = [ + ('Python', '3.11.5'), + ('Python-bundle-PyPI', '2023.10'), +] + +use_pip = True + +# aioredis and aiosignal do not depend on aiohttp, but are commonly used together and share dependencies +exts_list = [ + ('multidict', '6.0.5', { + 'checksums': ['f7e301075edaf50500f0b341543c41194d8df3ae5caf4702f2095f3ca73dd8da'], + }), + ('expandvars', '0.12.0', { + 'checksums': ['7d1adfa55728cf4b5d812ece3d087703faea953e0c0a1a78415de9df5024d844'], + }), + ('yarl', '1.9.4', { + 'checksums': ['566db86717cf8080b99b58b083b773a908ae40f06681e87e589a976faf8246bf'], + }), + ('frozenlist', '1.4.1', { + 'checksums': ['c037a86e8513059a2613aaba4d817bb90b9d9b6b69aace3ce9c877e8c8ed402b'], + }), + ('async-timeout', '4.0.3', { + 'checksums': ['4640d96be84d82d02ed59ea2b7105a0f7b33abe8703703cd0ab0bf87c427522f'], + }), + ('aiosignal', '1.3.1', { + 'checksums': ['54cd96e15e1649b75d6c87526a6ff0b6c1b0dd3459f43d9ca11d48c339b68cfc'], + }), + ('aiohappyeyeballs', '2.3.2', { + 'checksums': ['77e15a733090547a1f5369a1287ddfc944bd30df0eb8993f585259c34b405f4e'], + }), + (name, version, { + 'checksums': ['edea7d15772ceeb29db4aff55e482d4bcfb6ae160ce144f2682de02f6d693551'], + }), +] + +sanity_pip_check = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/a/alevin-fry/alevin-fry-0.9.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/a/alevin-fry/alevin-fry-0.9.0-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..50f776e14a3 --- /dev/null +++ b/easybuild/easyconfigs/a/alevin-fry/alevin-fry-0.9.0-GCCcore-13.2.0.eb @@ -0,0 +1,470 @@ +easyblock = 'Cargo' + +name = 'alevin-fry' +version = '0.9.0' + +homepage = 'https://github.com/COMBINE-lab/alevin-fry' +description = """alevin-fry is an efficient and flexible tool for processing single-cell sequencing data, + currently focused on single-cell transcriptomics and feature barcoding.""" +# software_license = 'LicenseBSD3' + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +crates = [ + (name, version), + ('adler', '1.0.2'), + ('ahash', '0.8.11'), + ('aho-corasick', '1.1.2'), + ('alga', '0.9.3'), + ('android-tzdata', '0.1.1'), + ('android_system_properties', '0.1.5'), + ('anstream', '0.6.13'), + ('anstyle', '1.0.6'), + ('anstyle-parse', '0.2.3'), + ('anstyle-query', '1.0.2'), + ('anstyle-wincon', '3.0.2'), + ('anyhow', '1.0.80'), + ('approx', '0.3.2'), + ('approx', '0.5.1'), + ('arrayvec', '0.7.4'), + ('autocfg', '1.1.0'), + ('bincode', '1.3.3'), + ('bio-types', '1.0.1'), + ('bit-vec', '0.6.3'), + ('bitflags', '1.3.2'), + ('bitflags', '2.4.2'), + ('block-buffer', '0.10.4'), + ('bstr', '1.9.1'), + ('buffer-redux', '1.0.1'), + ('bumpalo', '3.15.4'), + ('bytecount', '0.6.7'), + ('bytemuck', '1.14.3'), + ('byteorder', '1.5.0'), + ('bytes', '1.5.0'), + ('bzip2', '0.4.4'), + ('bzip2-sys', '0.1.11+1.0.8'), + ('cc', '1.0.90'), + ('cfg-if', '1.0.0'), + ('chrono', '0.4.35'), + ('clap', '4.5.2'), + ('clap_builder', '4.5.2'), + ('clap_derive', '4.5.0'), + ('clap_lex', '0.7.0'), + ('colorchoice', '1.0.0'), + ('console', '0.15.8'), + ('core-foundation-sys', '0.8.6'), + ('crc32fast', '1.4.0'), + ('crossbeam-channel', '0.5.12'), + ('crossbeam-deque', '0.8.5'), + ('crossbeam-epoch', '0.9.18'), + ('crossbeam-queue', '0.3.11'), + ('crossbeam-utils', '0.8.19'), + ('crypto-common', '0.1.6'), + ('csv', '1.3.0'), + ('csv-core', '0.1.11'), + ('dashmap', '5.5.3'), + ('deranged', '0.3.11'), + ('derive-new', '0.5.9'), + ('digest', '0.10.7'), + ('dirs-next', '2.0.0'), + ('dirs-sys-next', '0.1.2'), + ('either', '1.10.0'), + ('encode_unicode', '0.3.6'), + ('equivalent', '1.0.1'), + ('errno', '0.3.8'), + ('fixedbitset', '0.4.2'), + ('flate2', '1.0.28'), + ('generic-array', '0.14.7'), + ('getrandom', '0.2.12'), + ('hashbrown', '0.14.3'), + ('heck', '0.4.1'), + ('hermit-abi', '0.3.9'), + ('iana-time-zone', '0.1.60'), + ('iana-time-zone-haiku', '0.1.2'), + ('indexmap', '2.2.5'), + ('indicatif', '0.17.8'), + ('instant', '0.1.12'), + ('is-terminal', '0.4.12'), + ('itertools', '0.12.1'), + ('itoa', '1.0.10'), + ('js-sys', '0.3.69'), + ('lazy_static', '1.4.0'), + ('lexical-core', '0.8.5'), + ('lexical-parse-float', '0.8.5'), + ('lexical-parse-integer', '0.8.6'), + ('lexical-util', '0.8.5'), + ('lexical-write-float', '0.8.5'), + ('lexical-write-integer', '0.8.5'), + ('libc', '0.2.153'), + ('libm', '0.2.8'), + ('libmimalloc-sys', '0.1.35'), + ('libradicl', '0.8.2'), + ('libredox', '0.0.1'), + ('linux-raw-sys', '0.4.13'), + ('lock_api', '0.4.11'), + ('log', '0.4.21'), + ('lzma-sys', '0.1.20'), + ('matrixmultiply', '0.3.8'), + ('md-5', '0.10.6'), + ('memchr', '2.7.1'), + ('mimalloc', '0.1.39'), + ('miniz_oxide', '0.7.2'), + ('nalgebra', '0.29.0'), + ('nalgebra-macros', '0.1.0'), + ('ndarray', '0.15.6'), + ('needletail', '0.5.1'), + ('noodles', '0.65.0'), + ('noodles-bam', '0.56.0'), + ('noodles-bgzf', '0.26.0'), + ('noodles-core', '0.14.0'), + ('noodles-cram', '0.56.0'), + ('noodles-csi', '0.30.0'), + ('noodles-fasta', '0.33.0'), + ('noodles-sam', '0.53.0'), + ('noodles-util', '0.37.0'), + ('num', '0.4.1'), + ('num-bigint', '0.4.4'), + ('num-complex', '0.2.4'), + ('num-complex', '0.4.5'), + ('num-conv', '0.1.0'), + ('num-format', '0.4.4'), + ('num-integer', '0.1.46'), + ('num-iter', '0.1.44'), + ('num-rational', '0.4.1'), + ('num-traits', '0.2.18'), + ('num_cpus', '1.16.0'), + ('number_prefix', '0.4.0'), + ('once_cell', '1.19.0'), + ('parking_lot_core', '0.9.9'), + ('paste', '1.0.14'), + ('petgraph', '0.6.4'), + ('pkg-config', '0.3.30'), + ('portable-atomic', '1.6.0'), + ('powerfmt', '0.2.0'), + ('ppv-lite86', '0.2.17'), + ('proc-macro2', '1.0.78'), + ('quote', '1.0.35'), + ('rand', '0.8.5'), + ('rand_chacha', '0.3.1'), + ('rand_core', '0.6.4'), + ('rand_distr', '0.4.3'), + ('rawpointer', '0.2.1'), + ('rayon', '1.9.0'), + ('rayon-core', '1.12.1'), + ('redox_syscall', '0.4.1'), + ('redox_users', '0.4.4'), + ('regex', '1.10.3'), + ('regex-automata', '0.4.6'), + ('regex-syntax', '0.8.2'), + ('rustix', '0.38.31'), + ('rustversion', '1.0.14'), + ('ryu', '1.0.17'), + ('safe_arch', '0.7.1'), + ('sce', '0.2.0'), + ('scopeguard', '1.2.0'), + ('scroll', '0.12.0'), + ('serde', '1.0.197'), + ('serde_derive', '1.0.197'), + ('serde_json', '1.0.114'), + ('simba', '0.6.0'), + ('slog', '2.7.0'), + ('slog-async', '2.8.0'), + ('slog-term', '2.9.1'), + ('smallvec', '1.13.1'), + ('snap', '1.1.1'), + ('sprs', '0.11.1'), + ('static_assertions', '1.1.0'), + ('statrs', '0.16.0'), + ('strsim', '0.11.0'), + ('strum_macros', '0.25.3'), + ('syn', '1.0.109'), + ('syn', '2.0.52'), + ('take_mut', '0.2.2'), + ('term', '0.7.0'), + ('terminal_size', '0.3.0'), + ('thiserror', '1.0.57'), + ('thiserror-impl', '1.0.57'), + ('thread_local', '1.1.8'), + ('time', '0.3.34'), + ('time-core', '0.1.2'), + ('time-macros', '0.2.17'), + ('trait-set', '0.3.0'), + ('typed-builder', '0.18.1'), + ('typed-builder-macro', '0.18.1'), + ('typenum', '1.17.0'), + ('unicode-ident', '1.0.12'), + ('unicode-width', '0.1.11'), + ('utf8parse', '0.2.1'), + ('version_check', '0.9.4'), + ('wasi', '0.11.0+wasi-snapshot-preview1'), + ('wasm-bindgen', '0.2.92'), + ('wasm-bindgen-backend', '0.2.92'), + ('wasm-bindgen-macro', '0.2.92'), + ('wasm-bindgen-macro-support', '0.2.92'), + ('wasm-bindgen-shared', '0.2.92'), + ('wide', '0.7.15'), + ('winapi', '0.3.9'), + ('winapi-i686-pc-windows-gnu', '0.4.0'), + ('winapi-x86_64-pc-windows-gnu', '0.4.0'), + ('windows-core', '0.52.0'), + ('windows-sys', '0.48.0'), + ('windows-sys', '0.52.0'), + ('windows-targets', '0.48.5'), + 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'89beec544f246e679fc25490e3f8e08003bc4bf612068f325120dad4cea02c1c'}, + {'winapi-0.3.9.tar.gz': '5c839a674fcd7a98952e593242ea400abe93992746761e38641405d28b00f419'}, + {'winapi-i686-pc-windows-gnu-0.4.0.tar.gz': 'ac3b87c63620426dd9b991e5ce0329eff545bccbbb34f3be09ff6fb6ab51b7b6'}, + {'winapi-x86_64-pc-windows-gnu-0.4.0.tar.gz': '712e227841d057c1ee1cd2fb22fa7e5a5461ae8e48fa2ca79ec42cfc1931183f'}, + {'windows-core-0.52.0.tar.gz': '33ab640c8d7e35bf8ba19b884ba838ceb4fba93a4e8c65a9059d08afcfc683d9'}, + {'windows-sys-0.48.0.tar.gz': '677d2418bec65e3338edb076e806bc1ec15693c5d0104683f2efe857f61056a9'}, + {'windows-sys-0.52.0.tar.gz': '282be5f36a8ce781fad8c8ae18fa3f9beff57ec1b52cb3de0789201425d9a33d'}, + {'windows-targets-0.48.5.tar.gz': '9a2fa6e2155d7247be68c096456083145c183cbbbc2764150dda45a87197940c'}, + {'windows-targets-0.52.4.tar.gz': '7dd37b7e5ab9018759f893a1952c9420d060016fc19a472b4bb20d1bdd694d1b'}, + {'windows_aarch64_gnullvm-0.48.5.tar.gz': '2b38e32f0abccf9987a4e3079dfb67dcd799fb61361e53e2882c3cbaf0d905d8'}, + {'windows_aarch64_gnullvm-0.52.4.tar.gz': 'bcf46cf4c365c6f2d1cc93ce535f2c8b244591df96ceee75d8e83deb70a9cac9'}, + {'windows_aarch64_msvc-0.48.5.tar.gz': 'dc35310971f3b2dbbf3f0690a219f40e2d9afcf64f9ab7cc1be722937c26b4bc'}, + {'windows_aarch64_msvc-0.52.4.tar.gz': 'da9f259dd3bcf6990b55bffd094c4f7235817ba4ceebde8e6d11cd0c5633b675'}, + {'windows_i686_gnu-0.48.5.tar.gz': 'a75915e7def60c94dcef72200b9a8e58e5091744960da64ec734a6c6e9b3743e'}, + {'windows_i686_gnu-0.52.4.tar.gz': 'b474d8268f99e0995f25b9f095bc7434632601028cf86590aea5c8a5cb7801d3'}, + {'windows_i686_msvc-0.48.5.tar.gz': '8f55c233f70c4b27f66c523580f78f1004e8b5a8b659e05a4eb49d4166cca406'}, + {'windows_i686_msvc-0.52.4.tar.gz': '1515e9a29e5bed743cb4415a9ecf5dfca648ce85ee42e15873c3cd8610ff8e02'}, + {'windows_x86_64_gnu-0.48.5.tar.gz': '53d40abd2583d23e4718fddf1ebec84dbff8381c07cae67ff7768bbf19c6718e'}, + {'windows_x86_64_gnu-0.52.4.tar.gz': '5eee091590e89cc02ad514ffe3ead9eb6b660aedca2183455434b93546371a03'}, + {'windows_x86_64_gnullvm-0.48.5.tar.gz': '0b7b52767868a23d5bab768e390dc5f5c55825b6d30b86c844ff2dc7414044cc'}, + {'windows_x86_64_gnullvm-0.52.4.tar.gz': '77ca79f2451b49fa9e2af39f0747fe999fcda4f5e241b2898624dca97a1f2177'}, + {'windows_x86_64_msvc-0.48.5.tar.gz': 'ed94fce61571a4006852b7389a063ab983c02eb1bb37b47f8272ce92d06d9538'}, + {'windows_x86_64_msvc-0.52.4.tar.gz': '32b752e52a2da0ddfbdbcc6fceadfeede4c939ed16d13e648833a61dfb611ed8'}, + {'xz2-0.1.7.tar.gz': '388c44dc09d76f1536602ead6d325eb532f5c122f17782bd57fb47baeeb767e2'}, + {'zerocopy-0.7.32.tar.gz': '74d4d3961e53fa4c9a25a8637fc2bfaf2595b3d3ae34875568a5cf64787716be'}, + {'zerocopy-derive-0.7.32.tar.gz': '9ce1b18ccd8e73a9321186f97e46f9f04b778851177567b1975109d26a08d2a6'}, +] + +builddependencies = [ + ('binutils', '2.40'), + ('Rust', '1.76.0'), + ('CMake', '3.27.6'), +] + +dependencies = [ + ('bzip2', '1.0.8'), +] + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': [], +} + +sanity_check_commands = ["%(namelower)s --help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/a/alsa-lib/alsa-lib-1.2.11-GCCcore-13.2.0.eb b/easybuild/easyconfigs/a/alsa-lib/alsa-lib-1.2.11-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..fd05a43146f --- /dev/null +++ b/easybuild/easyconfigs/a/alsa-lib/alsa-lib-1.2.11-GCCcore-13.2.0.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'alsa-lib' +version = '1.2.11' + +homepage = 'https://www.alsa-project.org' +description = """The Advanced Linux Sound Architecture (ALSA) provides audio and MIDI functionality + to the Linux operating system.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://www.alsa-project.org/files/pub/lib/'] +sources = [SOURCE_TAR_BZ2] +checksums = ['9f3f2f69b995f9ad37359072fbc69a3a88bfba081fc83e9be30e14662795bb4d'] + +dependencies = [('binutils', '2.40')] + +configopts = ['--disable-shared --enable-static', '--enable-shared'] + +sanity_check_paths = { + 'files': ['bin/aserver', 'include/asoundlib.h', + 'lib64/libatopology.%s' % SHLIB_EXT, 'lib64/libasound.%s' % SHLIB_EXT, 'lib64/libasound.a'], + 'dirs': ['include/alsa', 'lib/pkgconfig', 'share'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/a/alsa-lib/alsa-lib-1.2.11-GCCcore-13.3.0.eb b/easybuild/easyconfigs/a/alsa-lib/alsa-lib-1.2.11-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..4333348a741 --- /dev/null +++ b/easybuild/easyconfigs/a/alsa-lib/alsa-lib-1.2.11-GCCcore-13.3.0.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'alsa-lib' +version = '1.2.11' + +homepage = 'https://www.alsa-project.org' +description = """The Advanced Linux Sound Architecture (ALSA) provides audio and MIDI functionality + to the Linux operating system.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://www.alsa-project.org/files/pub/lib/'] +sources = [SOURCE_TAR_BZ2] +checksums = ['9f3f2f69b995f9ad37359072fbc69a3a88bfba081fc83e9be30e14662795bb4d'] + +dependencies = [('binutils', '2.42')] + +configopts = ['--disable-shared --enable-static', '--enable-shared'] + +sanity_check_paths = { + 'files': ['bin/aserver', 'include/asoundlib.h', + 'lib64/libatopology.%s' % SHLIB_EXT, 'lib64/libasound.%s' % SHLIB_EXT, 'lib64/libasound.a'], + 'dirs': ['include/alsa', 'lib/pkgconfig', 'share'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/a/amdahl/amdahl-0.3.1-gompi-2023a.eb b/easybuild/easyconfigs/a/amdahl/amdahl-0.3.1-gompi-2023a.eb new file mode 100644 index 00000000000..03df4c86664 --- /dev/null +++ b/easybuild/easyconfigs/a/amdahl/amdahl-0.3.1-gompi-2023a.eb @@ -0,0 +1,35 @@ +easyblock = 'PythonPackage' + +name = 'amdahl' +version = '0.3.1' + +homepage = "https://github.com/hpc-carpentry/amdahl" +description = """This Python module contains a pseudo-application that can be used as a black +box to reproduce Amdahl's Law. It does not do real calculations, nor any real +communication, so can easily be overloaded. +""" + +toolchain = {'name': 'gompi', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('mpi4py', '3.1.4'), +] + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['b2e0f13fbfc082c83871583d6254ba6c1abc0033ee9cf8a5d018c5541c32ff74'] + +download_dep_fail = True +sanity_pip_check = True +use_pip = True + +sanity_check_paths = { + 'files': ['bin/amdahl'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "amdahl --help", +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/a/anndata/anndata-0.10.5.post1-foss-2023a.eb b/easybuild/easyconfigs/a/anndata/anndata-0.10.5.post1-foss-2023a.eb index b49190c6e5a..8c520bf7d04 100644 --- a/easybuild/easyconfigs/a/anndata/anndata-0.10.5.post1-foss-2023a.eb +++ b/easybuild/easyconfigs/a/anndata/anndata-0.10.5.post1-foss-2023a.eb @@ -9,11 +9,14 @@ description = """anndata is a Python package for handling annotated data matrice toolchain = {'name': 'foss', 'version': '2023a'} +builddependencies = [ + ('hatchling', '1.18.0'), +] + dependencies = [ ('Python', '3.11.3'), ('SciPy-bundle', '2023.07'), ('h5py', '3.9.0'), - ('hatchling', '1.18.0'), ] use_pip = True diff --git a/easybuild/easyconfigs/a/anndata/anndata-0.11.1-foss-2023b.eb b/easybuild/easyconfigs/a/anndata/anndata-0.11.1-foss-2023b.eb new file mode 100644 index 00000000000..cb2317d16cc --- /dev/null +++ b/easybuild/easyconfigs/a/anndata/anndata-0.11.1-foss-2023b.eb @@ -0,0 +1,45 @@ +easyblock = 'PythonBundle' + +name = 'anndata' +version = '0.11.1' + +homepage = 'https://github.com/scverse/anndata' +description = """anndata is a Python package for handling annotated data matrices in memory and on disk, + positioned between pandas and xarray""" + +toolchain = {'name': 'foss', 'version': '2023b'} + +builddependencies = [ + ('hatchling', '1.18.0'), +] + +dependencies = [ + ('Python', '3.11.5'), + ('Python-bundle-PyPI', '2023.10'), + ('SciPy-bundle', '2023.11'), + ('h5py', '3.11.0'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('array_api_compat', '1.9.1', { + 'checksums': ['17bab828c93c79a5bb8b867145b71fcb889686607c5672b060aef437e0359ea8'], + }), + ('natsort', '8.4.0', { + 'checksums': ['45312c4a0e5507593da193dedd04abb1469253b601ecaf63445ad80f0a1ea581'], + }), + (name, version, { + 'checksums': ['36bff9a85276fc5f1b9fd01f15aff9aa49408129985f42e0fca4e2c5b7fa909f'], + }), +] + +sanity_check_paths = { + 'files': ['bin/natsort'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["natsort --help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/a/anndata/anndata-0.9.2-foss-2021b.eb b/easybuild/easyconfigs/a/anndata/anndata-0.9.2-foss-2021b.eb new file mode 100644 index 00000000000..f5f7d79dadf --- /dev/null +++ b/easybuild/easyconfigs/a/anndata/anndata-0.9.2-foss-2021b.eb @@ -0,0 +1,37 @@ +easyblock = 'PythonBundle' + +name = 'anndata' +version = '0.9.2' + +homepage = 'https://github.com/scverse/anndata' +description = """anndata is a Python package for handling annotated data matrices in memory and on disk, + positioned between pandas and xarray""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), + ('h5py', '3.6.0'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('natsort', '8.4.0', { + 'checksums': ['45312c4a0e5507593da193dedd04abb1469253b601ecaf63445ad80f0a1ea581'], + }), + (name, version, { + 'checksums': ['e5b8383d09723af674cae7ad0c2ef53eb1f8c73949b7f4c182a6e30f42196327'], + }), +] + +sanity_check_paths = { + 'files': ['bin/natsort'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["natsort --help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/a/any2fasta/any2fasta-0.4.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/a/any2fasta/any2fasta-0.4.2-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..3f96b328b6a --- /dev/null +++ b/easybuild/easyconfigs/a/any2fasta/any2fasta-0.4.2-GCCcore-12.3.0.eb @@ -0,0 +1,35 @@ +# Author: Pavel Grochal (INUITS) +# Updated by: Denis Kristak (INUITS) +# License: GPLv2 + +easyblock = 'Tarball' + +name = 'any2fasta' +version = '0.4.2' + +homepage = 'https://github.com/tseemann/any2fasta' +description = "Convert various sequence formats to FASTA" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +# https://github.com/tseemann/any2fasta +github_account = 'tseemann' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.zip'] +checksums = ['3faa738ab409c7073afe3769e9d32dd5b28a2c12e72c2e4ac6f4e9946ee9a22f'] + +dependencies = [('Perl', '5.36.1')] + +modextrapaths = {'PATH': ''} + +sanity_check_paths = { + 'files': ['any2fasta'], + 'dirs': [], +} + +sanity_check_commands = [ + 'any2fasta -h', + 'any2fasta -q %(builddir)s/%(name)s-%(version)s/test.fq', +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/a/archspec/archspec-0.2.4-GCCcore-13.3.0.eb b/easybuild/easyconfigs/a/archspec/archspec-0.2.4-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..5a4f3a288e9 --- /dev/null +++ b/easybuild/easyconfigs/a/archspec/archspec-0.2.4-GCCcore-13.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'archspec' +version = '0.2.4' + +homepage = 'https://github.com/archspec/archspec' +description = "A library for detecting, labeling, and reasoning about microarchitectures" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['eabbae22f315d24cc2ce786a092478ec8e245208c9877fb213c2172a6ecb9302'] + +builddependencies = [ + ('binutils', '2.42'), + ('poetry', '1.8.3'), +] + +dependencies = [('Python', '3.12.3')] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +sanity_check_commands = ["python -c 'from archspec.cpu import host; print(host())'"] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/a/argtable/argtable-2.13-GCCcore-12.3.0.eb b/easybuild/easyconfigs/a/argtable/argtable-2.13-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..8a411de3fd2 --- /dev/null +++ b/easybuild/easyconfigs/a/argtable/argtable-2.13-GCCcore-12.3.0.eb @@ -0,0 +1,30 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel +# Modified by: Adam Huffman +# The Francis Crick Institute + +easyblock = 'ConfigureMake' + +name = 'argtable' +version = '2.13' + +homepage = 'https://argtable.sourceforge.io/' +description = """ Argtable is an ANSI C library for parsing GNU style + command line options with a minimum of fuss. """ + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%s%s.tar.gz' % (name, version.replace('.', '-'))] +checksums = ['8f77e8a7ced5301af6e22f47302fdbc3b1ff41f2b83c43c77ae5ca041771ddbf'] + +builddependencies = [('binutils', '2.40')] + +sanity_check_paths = { + 'files': ['include/argtable2.h', 'lib/libargtable2.%s' % SHLIB_EXT, 'lib/libargtable2.a'], + 'dirs': ['share'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/a/arrow-R/arrow-R-16.1.0-foss-2023b-R-4.4.1.eb b/easybuild/easyconfigs/a/arrow-R/arrow-R-16.1.0-foss-2023b-R-4.4.1.eb new file mode 100644 index 00000000000..dd2e4260145 --- /dev/null +++ b/easybuild/easyconfigs/a/arrow-R/arrow-R-16.1.0-foss-2023b-R-4.4.1.eb @@ -0,0 +1,35 @@ +easyblock = 'RPackage' + +name = 'arrow-R' +version = '16.1.0' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://cran.r-project.org/web/packages/arrow' +description = "R interface to the Apache Arrow C++ library" + +toolchain = {'name': 'foss', 'version': '2023b'} + +source_urls = [ + 'https://cran.r-project.org/src/contrib/Archive/arrow', # package archive + 'https://cran.r-project.org/src/contrib/', # current version of packages + 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages +] +sources = ['arrow_%(version)s.tar.gz'] +checksums = ['66c1586ee7becd65b4d21b11ffcd157dc19f75c3c10ff5c5b3610689aadce7ef'] + +dependencies = [ + ('R', '4.4.1'), + ('R-bundle-CRAN', '2024.06'), + ('Arrow', '16.1.0'), # arrow-R x.y.z[.N] only works with Arrow x.y.z +] + +preinstallopts = "export LIBARROW_BINARY=true && " + +sanity_check_paths = { + 'files': [], + 'dirs': ['arrow'], +} + +options = {'modulename': 'arrow'} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/a/assimp/assimp-5.4.3-GCCcore-13.3.0.eb b/easybuild/easyconfigs/a/assimp/assimp-5.4.3-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..3f0dfef4b64 --- /dev/null +++ b/easybuild/easyconfigs/a/assimp/assimp-5.4.3-GCCcore-13.3.0.eb @@ -0,0 +1,36 @@ +# Authors:: Richard Lawrence - TAMU HPRC - https://hprc.tamu.edu + +easyblock = 'CMakeMake' + +name = 'assimp' +version = '5.4.3' + +homepage = 'https://github.com/assimp/assimp' +description = """ + Open Asset Import Library (assimp) is a library to import and export various + 3d-model-formats including scene-post-processing to generate missing render data. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://github.com/%(name)s/%(name)s/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['66dfbaee288f2bc43172440a55d0235dfc7bf885dda6435c038e8000e79582cb'] + +builddependencies = [ + ('binutils', '2.42'), + ('pkgconf', '2.2.0'), + ('CMake', '3.29.3'), + ('zlib', '1.3.1'), +] + +# workaround bug with GCC13 https://github.com/assimp/assimp/issues/5315 +configopts = "-DASSIMP_WARNINGS_AS_ERRORS=OFF " + + +sanity_check_paths = { + 'files': ['include/%(name)s/types.h', 'lib/libassimp.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/a/at-spi2-atk/at-spi2-atk-2.38.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/a/at-spi2-atk/at-spi2-atk-2.38.0-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..6efc7996fd0 --- /dev/null +++ b/easybuild/easyconfigs/a/at-spi2-atk/at-spi2-atk-2.38.0-GCCcore-13.3.0.eb @@ -0,0 +1,37 @@ +easyblock = 'MesonNinja' + +name = 'at-spi2-atk' +version = '2.38.0' + +homepage = 'https://wiki.gnome.org/Accessibility' +description = "AT-SPI 2 toolkit bridge" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['cfa008a5af822b36ae6287f18182c40c91dd699c55faa38605881ed175ca464f'] + +builddependencies = [ + ('binutils', '2.42'), + ('Meson', '1.4.0'), + ('Ninja', '1.12.1'), + ('pkgconf', '2.2.0'), +] + +dependencies = [ + ('GLib', '2.80.4'), + ('DBus', '1.15.8'), + ('at-spi2-core', '2.54.0'), + ('libxml2', '2.12.7'), + ('ATK', '2.38.0'), +] + +configopts = "--libdir lib " + +sanity_check_paths = { + 'files': ['lib/libatk-bridge-2.0.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/a/at-spi2-core/at-spi2-core-2.54.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/a/at-spi2-core/at-spi2-core-2.54.0-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..b1a1a4c863f --- /dev/null +++ b/easybuild/easyconfigs/a/at-spi2-core/at-spi2-core-2.54.0-GCCcore-13.3.0.eb @@ -0,0 +1,40 @@ +easyblock = 'MesonNinja' + +name = 'at-spi2-core' +version = '2.54.0' + +homepage = 'https://wiki.gnome.org/Accessibility' +description = """ + Assistive Technology Service Provider Interface. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['d7eee7e75beddcc272cedc2b60535600f3aae6e481589ebc667afc437c0a6079'] + +builddependencies = [ + ('binutils', '2.42'), + ('Meson', '1.4.0'), + ('Ninja', '1.12.1'), + ('GObject-Introspection', '1.80.1'), + ('gettext', '0.22.5'), + ('pkgconf', '2.2.0'), +] + +dependencies = [ + ('GLib', '2.80.4'), + ('DBus', '1.15.8'), + ('X11', '20240607'), +] + +# Hard disable Dbus broker detection and (potential) use of systemd +configopts = "--libdir lib -Duse_systemd=false -Ddefault_bus=dbus-daemon" + +sanity_check_paths = { + 'files': ['lib/libatspi.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/a/atropos/atropos-1.1.32-gompi-2023a.eb b/easybuild/easyconfigs/a/atropos/atropos-1.1.32-gompi-2023a.eb new file mode 100644 index 00000000000..dddac86e727 --- /dev/null +++ b/easybuild/easyconfigs/a/atropos/atropos-1.1.32-gompi-2023a.eb @@ -0,0 +1,57 @@ +easyblock = 'PythonBundle' + +name = 'atropos' +version = '1.1.32' + +homepage = 'https://atropos.readthedocs.io' +description = "Atropos is tool for specific, sensitive, and speedy trimming of NGS reads." + +toolchain = {'name': 'gompi', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('tqdm', '4.66.1'), + ('Pysam', '0.22.0'), + ('pytest', '7.4.2'), + ('SRA-Toolkit', '3.0.10'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('versioneer', '0.29', { + 'checksums': ['5ab283b9857211d61b53318b7c792cf68e798e765ee17c27ade9f6c924235731'], + }), + ('screed', '1.1.3', { + 'checksums': ['37e81697c7dba95a053554e5b5a86aff329705e1cf5dfc5e7b8da586dee072b8'], + }), + ('bz2file', '0.98', { + 'checksums': ['64c1f811e31556ba9931953c8ec7b397488726c63e09a4c67004f43bdd28da88'], + }), + ('khmer', '2.1.1', { + 'checksums': ['a709606910bb8679bd8525e9d2bf6d1421996272e343b54cc18090feb2fdbe24'], + }), + ('pokrok', '0.2.0', { + 'checksums': ['cfe7956602d8bbc142a07bcb259e0d1d939f96d7b074e00dceea3cb5e39244e8'], + }), + ('xphyle', '4.0.5', { + 'checksums': ['b744723a3c88d81318c7291c32682b8715a046f70d0a1db729bda783fd5e08bd'], + }), + ('srastream', '0.1.3', { + 'checksums': ['7f2cfd76ae988349ad5407a952cd4c133ae5dff7cf12c76072c53d82b50c2634'], + }), + (name, version, { + 'checksums': ['17e9dc3d76d7a2ca607a12da191a6d7ba1cfbd1a8c924215870417f85858fd83'], + }), +] + +sanity_check_paths = { + 'files': ['bin/atropos'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["atropos detect --help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/a/attr/attr-2.5.2-GCCcore-13.3.0.eb b/easybuild/easyconfigs/a/attr/attr-2.5.2-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..fcd6d723f16 --- /dev/null +++ b/easybuild/easyconfigs/a/attr/attr-2.5.2-GCCcore-13.3.0.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'attr' +version = '2.5.2' + +homepage = 'https://savannah.nongnu.org/projects/attr' + +description = """Commands for Manipulating Filesystem Extended Attributes""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = [GNU_SAVANNAH_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['39bf67452fa41d0948c2197601053f48b3d78a029389734332a6309a680c6c87'] + +builddependencies = [('binutils', '2.42')] + +sanity_check_paths = { + 'files': ['bin/attr', 'bin/getfattr', 'bin/setfattr', + 'include/%(name)s/attributes.h', 'include/%(name)s/error_context.h', + 'include/%(name)s/libattr.h', 'lib/libattr.a', + 'lib/libattr.%s' % SHLIB_EXT], + 'dirs': ['share'], +} + +sanity_check_commands = ["getfattr --help"] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/a/autopep8/autopep8-2.2.0-foss-2023a.eb b/easybuild/easyconfigs/a/autopep8/autopep8-2.2.0-foss-2023a.eb new file mode 100644 index 00000000000..63f57b621be --- /dev/null +++ b/easybuild/easyconfigs/a/autopep8/autopep8-2.2.0-foss-2023a.eb @@ -0,0 +1,23 @@ +easyblock = 'PythonPackage' + +name = 'autopep8' +version = '2.2.0' + +homepage = "https://github.com/hhatto/autopep8" +description = """A tool that automatically formats Python code to conform to the PEP 8 style guide.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +sources = [SOURCE_WHL] +checksums = ['05418a981f038969d8bdcd5636bf15948db7555ae944b9f79b5a34b35f1370d4'] + +dependencies = [ + ('Python', '3.11.3'), + ('pycodestyle', '2.11.1'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/a/awscli/awscli-2.17.54-GCCcore-13.2.0.eb b/easybuild/easyconfigs/a/awscli/awscli-2.17.54-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..9b70b1a9008 --- /dev/null +++ b/easybuild/easyconfigs/a/awscli/awscli-2.17.54-GCCcore-13.2.0.eb @@ -0,0 +1,73 @@ +easyblock = 'PythonBundle' + +name = 'awscli' +version = '2.17.54' + +homepage = 'https://pypi.python.org/pypi/awscli' +description = 'Universal Command Line Environment for AWS' + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.27.6'), # required for awscrt +] + +dependencies = [ + ('Python', '3.11.5'), + ('PyYAML', '6.0.1'), + ('ruamel.yaml', '0.18.6'), +] + +use_pip = True + +exts_list = [ + ('jmespath', '1.0.1', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['02e2e4cc71b5bcab88332eebf907519190dd9e6e82107fa7f83b1003a6252980'], + }), + ('botocore', '1.35.22', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['d9bc656e7dde0b3e3f3080fc54bacff6a97fd7806b98acbcc21c7f9d4d0102b9'], + }), + ('s3transfer', '0.10.2', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['eca1c20de70a39daee580aef4986996620f365c4e0fda6a86100231d62f1bf69'], + }), + ('prompt_toolkit', '3.0.47', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['0d7bfa67001d5e39d02c224b663abc33687405033a8c422d0d675a5a13361d10'], + }), + ('distro', '1.9.0', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['7bffd925d65168f85027d8da9af6bddab658135b840670a223589bc0c8ef02b2'], + }), + ('awscrt', '0.21.5', { + 'preinstallopts': "export AWS_CRT_BUILD_USE_SYSTEM_LIBCRYPTO=1 && ", + 'checksums': ['7ec2a67af30fbf386494df00bbdf996f7024000df6b01ab160014afef2b91005'], + }), + # older version of `urllib3` to avoid `ImportError: cannot import name 'DEFAULT_CIPHERS' from 'urllib3.util.ssl_'` + # see https://github.com/aws/aws-cli/issues/7905#issuecomment-1559817550 + ('urllib3', '1.26.20', { + 'source_tmpl': SOURCE_WHL, + 'checksums': ['0ed14ccfbf1c30a9072c7ca157e4319b70d65f623e91e7b32fadb2853431016e'], + }), + (name, version, { + # version requirements are too strict + 'preinstallopts': """sed -i 's/>[^"]*//g' pyproject.toml && """, + 'source_tmpl': '%(version)s.tar.gz', + 'source_urls': ['https://github.com/aws/aws-cli/archive/'], + 'checksums': ['c0a37eeb52b7df336e117667b67a275929701e9f6dad0ddb7de59a6f834e5b48'], + }), +] + +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/aws'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/'], +} + +sanity_check_commands = ["aws help"] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/BCFtools/BCFtools-1.21-GCC-13.3.0.eb b/easybuild/easyconfigs/b/BCFtools/BCFtools-1.21-GCC-13.3.0.eb new file mode 100644 index 00000000000..ad508758ba5 --- /dev/null +++ b/easybuild/easyconfigs/b/BCFtools/BCFtools-1.21-GCC-13.3.0.eb @@ -0,0 +1,40 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Author: Jonas Demeulemeester +# The Francis Crick Insitute, London, UK +# Updated to 1.21 jpecar / EMBL + +easyblock = 'ConfigureMake' + +name = 'BCFtools' +version = '1.21' + +homepage = 'https://www.htslib.org/' +description = """Samtools is a suite of programs for interacting with high-throughput sequencing data. + BCFtools - Reading/writing BCF2/VCF/gVCF files and calling/filtering/summarising SNP and short indel sequence + variants""" + +toolchain = {'name': 'GCC', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['528a4cc1d3555368db75a700b22a3c95da893fd1827f6d304716dfd45ea4e282'] + +dependencies = [ + ('zlib', '1.3.1'), + ('HTSlib', '1.21'), + ('bzip2', '1.0.8'), + ('XZ', '5.4.5'), + ('GSL', '2.8'), +] + +configopts = "--with-htslib=$EBROOTHTSLIB --enable-libgsl" + + +sanity_check_paths = { + 'files': ['bin/%(namelower)s', 'bin/plot-vcfstats', 'bin/vcfutils.pl'], + 'dirs': ['libexec/%(namelower)s'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/BEDTools/BEDTools-2.31.1-GCC-13.2.0.eb b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.31.1-GCC-13.2.0.eb new file mode 100644 index 00000000000..ee6ee7885ea --- /dev/null +++ b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.31.1-GCC-13.2.0.eb @@ -0,0 +1,46 @@ +# Author: Maxime Schmitt, University of Luxembourg +# Author: Adam Huffman, The Francis Crick Institute +# +# Based on the work of: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics (SIB) +# Biozentrum - University of Basel + +easyblock = 'MakeCp' + +name = 'BEDTools' +version = '2.31.1' + +homepage = 'https://bedtools.readthedocs.io/' +description = """BEDTools: a powerful toolset for genome arithmetic. +The BEDTools utilities allow one to address common genomics tasks such as finding feature overlaps and +computing coverage. +The utilities are largely based on four widely-used file formats: BED, GFF/GTF, VCF, and SAM/BAM.""" + +toolchain = {'name': 'GCC', 'version': '13.2.0'} + +source_urls = ['https://github.com/arq5x/bedtools2/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['79a1ba318d309f4e74bfa74258b73ef578dccb1045e270998d7fe9da9f43a50e'] + +builddependencies = [ + ('Python', '3.11.5'), +] +dependencies = [ + ('XZ', '5.4.4'), + ('zlib', '1.2.13'), + ('bzip2', '1.0.8'), + ('BamTools', '2.5.2'), +] + +buildopts = 'CXX="$CXX"' + +files_to_copy = ['bin', 'docs', 'data', 'genomes', 'scripts', 'test'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['bedtools', 'pairToBed', 'mergeBed', 'bedToBam', 'fastaFromBed']], + 'dirs': files_to_copy, +} + +sanity_check_commands = ['%(namelower)s --help'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/BEDTools/BEDTools-2.31.1-GCC-13.3.0.eb b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.31.1-GCC-13.3.0.eb new file mode 100644 index 00000000000..8503277b570 --- /dev/null +++ b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.31.1-GCC-13.3.0.eb @@ -0,0 +1,53 @@ +# Author: Maxime Schmitt, University of Luxembourg +# Author: Adam Huffman, The Francis Crick Institute +# +# Based on the work of: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics (SIB) +# Biozentrum - University of Basel + +easyblock = 'MakeCp' + +name = 'BEDTools' +version = '2.31.1' + +homepage = 'https://bedtools.readthedocs.io/' +description = """BEDTools: a powerful toolset for genome arithmetic. +The BEDTools utilities allow one to address common genomics tasks such as finding feature overlaps and +computing coverage. +The utilities are largely based on four widely-used file formats: BED, GFF/GTF, VCF, and SAM/BAM.""" + +toolchain = {'name': 'GCC', 'version': '13.3.0'} + +source_urls = ['https://github.com/arq5x/bedtools2/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['79a1ba318d309f4e74bfa74258b73ef578dccb1045e270998d7fe9da9f43a50e'] + +builddependencies = [ + ('Python', '3.12.3'), +] +dependencies = [ + ('XZ', '5.4.5'), + ('zlib', '1.3.1'), + ('bzip2', '1.0.8'), + ('BamTools', '2.5.2'), +] + +buildopts = 'CXX="$CXX"' + +files_to_copy = [ + 'bin', + 'docs', + 'data', + 'genomes', + 'scripts', + 'test', +] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['bedtools', 'pairToBed', 'mergeBed', 'bedToBam', 'fastaFromBed']], + 'dirs': files_to_copy, +} + +sanity_check_commands = ['%(namelower)s --help'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/BGEN-enkre/3rd-party-removal.patch b/easybuild/easyconfigs/b/BGEN-enkre/3rd-party-removal.patch new file mode 100644 index 00000000000..83f35651997 --- /dev/null +++ b/easybuild/easyconfigs/b/BGEN-enkre/3rd-party-removal.patch @@ -0,0 +1,176 @@ +Removal of sqlite3, boost and zstd from 3-party modules +Author: J. Sassmannshausen +diff --git a/bgen.tgz.orig/3rd_party/wscript b/bgen.tgz/3rd_party/wscript +index 220728a..e69de29 100644 +--- a/bgen.tgz.orig/3rd_party/wscript ++++ b/bgen.tgz/3rd_party/wscript +@@ -1,2 +0,0 @@ +-def build( bld ): +- bld.recurse( [ 'boost_1_55_0', 'sqlite3', 'zstd-1.1.0' ] ) +diff --git a/bgen.tgz.orig/Makefile b/bgen.tgz/Makefile +index a7b0ac8..c62ac16 100644 +--- a/bgen.tgz.orig/Makefile ++++ b/bgen.tgz/Makefile +@@ -1,14 +1,9 @@ + FLAGS = -g -std=c++11 -lz \ + -I genfile/include \ + -I db/include \ +--I 3rd_party/boost_1_55_0 \ +--I 3rd_party/zstd-1.1.0 \ +--I 3rd_party/zstd-1.1.0/lib \ +--I 3rd_party/zstd-1.1.0/lib/common \ +--I 3rd_party/zstd-1.1.0/lib/compress \ +--I 3rd_party/zstd-1.1.0/lib/decompress \ +--I 3rd_party/sqlite3 \ +--I include/3rd_party/sqlite3 \ ++-I ${EBBOST}/include \ ++-I ${EBDEVELZSTD}/include \ ++-I ${EBSQLITE3}/include \ + -D SQLITE_ENABLE_COLUMN_METADATA \ + -D SQLITE_ENABLE_STAT4 \ + -D SQLITE_MAX_EXPR_DEPTH=10000 \ +diff --git a/bgen.tgz.orig/db/include/db/SQLStatement.hpp b/bgen.tgz/db/include/db/SQLStatement.hpp +index e107bd2..fca5957 100644 +--- a/bgen.tgz.orig/db/include/db/SQLStatement.hpp ++++ b/bgen.tgz/db/include/db/SQLStatement.hpp +@@ -12,7 +12,7 @@ + #include + #include + #include +-#include "sqlite3/sqlite3.h" ++#include "sqlite3.h" + #include "db/SQLite3Connection.hpp" + + namespace db { +diff --git a/bgen.tgz.orig/db/include/db/SQLite3Connection.hpp b/bgen.tgz/db/include/db/SQLite3Connection.hpp +index b4bd219..cfbbd3a 100644 +--- a/bgen.tgz.orig/db/include/db/SQLite3Connection.hpp ++++ b/bgen.tgz/db/include/db/SQLite3Connection.hpp +@@ -10,7 +10,7 @@ + #include + #include + #include +-#include "sqlite3/sqlite3.h" ++#include "sqlite3.h" + #include "db/Connection.hpp" + #include "db/Transaction.hpp" + #include "db/Error.hpp" +diff --git a/bgen.tgz.orig/db/include/db/SQLite3Statement.hpp b/bgen.tgz/db/include/db/SQLite3Statement.hpp +index d41a710..76dbfb6 100644 +--- a/bgen.tgz.orig/db/include/db/SQLite3Statement.hpp ++++ b/bgen.tgz/db/include/db/SQLite3Statement.hpp +@@ -11,7 +11,7 @@ + #include + #include + +-#include "sqlite3/sqlite3.h" ++#include "sqlite3.h" + #include "db/SQLite3Connection.hpp" + #include "db/SQLStatement.hpp" + +diff --git a/bgen.tgz.orig/db/src/SQLStatement.cpp b/bgen.tgz/db/src/SQLStatement.cpp +index 60168c6..32576ca 100644 +--- a/bgen.tgz.orig/db/src/SQLStatement.cpp ++++ b/bgen.tgz/db/src/SQLStatement.cpp +@@ -7,7 +7,7 @@ + #include + #include + #include +-#include "sqlite3/sqlite3.h" ++#include "sqlite3.h" + #include "db/SQLStatement.hpp" + + namespace db { +diff --git a/bgen.tgz.orig/db/src/SQLite3Statement.cpp b/bgen.tgz/db/src/SQLite3Statement.cpp +index 84e0658..03b3d5e 100644 +--- a/bgen.tgz.orig/db/src/SQLite3Statement.cpp ++++ b/bgen.tgz/db/src/SQLite3Statement.cpp +@@ -9,7 +9,7 @@ + #include + #include + #include +-#include "sqlite3/sqlite3.h" ++#include "sqlite3.h" + #include "db/SQLite3Connection.hpp" + #include "db/SQLStatement.hpp" + #include "db/SQLite3Statement.hpp" +diff --git a/bgen.tgz.orig/db/wscript b/bgen.tgz/db/wscript +index 7b0b617..a3861f0 100644 +--- a/bgen.tgz.orig/db/wscript ++++ b/bgen.tgz/db/wscript +@@ -5,8 +5,8 @@ def build( bld ): + bld.stlib( + target = 'db', + source = sources, +- includes='./include', ++ includes='${EBSQLITE}/include ./include', + cxxflags = [], + use = 'boost sqlite3', +- export_includes = './include' ++ export_includes = '${EBSQLITE}/include ./include' + ) +diff --git a/bgen.tgz.orig/wscript b/bgen.tgz/wscript +index a6385d9..47b9fc9 100644 +--- a/bgen.tgz.orig/wscript ++++ b/bgen.tgz/wscript +@@ -63,7 +63,7 @@ def build( bld ): + use = 'zlib zstd sqlite3 db', + export_includes = 'genfile/include' + ) +- bld.recurse( [ '3rd_party', 'appcontext', 'genfile', 'db', 'apps', 'example', 'test', 'R' ] ) ++ bld.recurse( [ 'appcontext', 'genfile', 'db', 'apps', 'example', 'test', 'R' ] ) + # Copy files into rbgen package directory + for source in bgen_sources: + bld( rule = 'cp ${SRC} ${TGT}', source = source, target = 'R/rbgen/src/bgen/' + os.path.basename( source.abspath() ), always = True ) +@@ -126,12 +126,12 @@ class ReleaseBuilder: + shutil.copytree( 'R/package/', rbgen_dir ) + os.makedirs( os.path.join( rbgen_dir, "src", "include" )) + os.makedirs( os.path.join( rbgen_dir, "src", "include", "boost" )) +- os.makedirs( os.path.join( rbgen_dir, "src", "include", "zstd-1.1.0" )) ++ os.makedirs( os.path.join( rbgen_dir, "src", "include", "zstd" )) + os.makedirs( os.path.join( rbgen_dir, "src", "db" )) + os.makedirs( os.path.join( rbgen_dir, "src", "bgen" )) + os.makedirs( os.path.join( rbgen_dir, "src", "boost" )) + os.makedirs( os.path.join( rbgen_dir, "src", "sqlite3" )) +- os.makedirs( os.path.join( rbgen_dir, "src", "zstd-1.1.0" )) ++ os.makedirs( os.path.join( rbgen_dir, "src", "zstd" )) + + # Copy source files in + from glob import glob +@@ -141,11 +141,11 @@ class ReleaseBuilder: + for filename in glob( 'db/src/*.cpp' ): + shutil.copy( filename, os.path.join( rbgen_dir, "src", "db", os.path.basename( filename ) ) ) + +- for filename in glob( '3rd_party/sqlite3/sqlite3/sqlite3.c' ): +- shutil.copy( filename, os.path.join( rbgen_dir, "src", "sqlite3", os.path.basename( filename ) ) ) ++# for filename in glob( '3rd_party/sqlite3/sqlite3/sqlite3.c' ): ++# shutil.copy( filename, os.path.join( rbgen_dir, "src", "sqlite3", os.path.basename( filename ) ) ) + +- for filename in glob( '3rd_party/zstd-1.1.0/lib/common/*.c' ) + glob( '3rd_party/zstd-1.1.0/lib/compress/*.c' ) + glob( '3rd_party/zstd-1.1.0/lib/decompress/*.c' ): +- shutil.copy( filename, os.path.join( rbgen_dir, "src", "zstd-1.1.0", os.path.basename( filename ) ) ) ++# for filename in glob( '3rd_party/zstd-1.1.0/lib/common/*.c' ) + glob( '3rd_party/zstd-1.1.0/lib/compress/*.c' ) + glob( '3rd_party/zstd-1.1.0/lib/decompress/*.c' ): ++# shutil.copy( filename, os.path.join( rbgen_dir, "src", "zstd-1.1.0", os.path.basename( filename ) ) ) + + boostGlobs = [ + 'libs/system/src/*.cpp', +@@ -160,14 +160,14 @@ class ReleaseBuilder: + 'libs/chrono/src/*.cpp', + ] + +- for pattern in boostGlobs: +- for filename in glob( '3rd_party/boost_1_55_0/%s' % pattern ): +- shutil.copy( filename, os.path.join( rbgen_dir, "src", "boost", os.path.basename( filename ) ) ) ++# for pattern in boostGlobs: ++# for filename in glob( '3rd_party/boost_1_55_0/%s' % pattern ): ++# shutil.copy( filename, os.path.join( rbgen_dir, "src", "boost", os.path.basename( filename ) ) ) + + include_paths = [ +- "3rd_party/boost_1_55_0/boost/", +- "3rd_party/zstd-1.1.0/", +- "3rd_party/sqlite3/", ++ "${EBBOOST}", ++ "${EBROOTZSTD}", ++ "${EBROOTSQLITE}", + "genfile/include/genfile", + "db/include/db" + ] diff --git a/easybuild/easyconfigs/b/BGEN-enkre/BGEN-enkre-1.1.7-GCC-11.2.0.eb b/easybuild/easyconfigs/b/BGEN-enkre/BGEN-enkre-1.1.7-GCC-11.2.0.eb new file mode 100644 index 00000000000..b0c0bc1be02 --- /dev/null +++ b/easybuild/easyconfigs/b/BGEN-enkre/BGEN-enkre-1.1.7-GCC-11.2.0.eb @@ -0,0 +1,74 @@ +# Contribution from the NIHR Biomedical Research Centre +# Guy's and St Thomas' NHS Foundation Trust and King's College London +# uploaded by J. Sassmannshausen +# we recommend to use --download-timeout=1000 when fetching the files + +easyblock = 'CmdCp' + +name = 'BGEN-enkre' +version = '1.1.7' + +homepage = 'https://enkre.net/cgi-bin/code/bgen/dir?ci=trunk' +description = """This repository contains a reference implementation +of the BGEN format, written in C++. The library can be used as the +basis for BGEN support in other software, or as a reference for +developers writing their own implementations of the BGEN format. +Please cite: +Band, G. and Marchini, J., "BGEN: a binary file format for imputed genotype and haplotype data", +bioArxiv 308296; doi: https://doi.org/10.1101/308296 +""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +source_urls = ['https://code.enkre.net/bgen/tarball/v%(version)s/'] +sources = ['v%(version)s.tgz'] +patches = [ + '3rd-party-removal.patch', + 'BGEN-enkre_streampos.patch', +] + +checksums = [ + ('6476b077af6c8e98e85fd7e09f58cb3fdf143ff91850c984248fd4dc2d74a8c3', # v1.1.7.tgz + 'b922ac22c1c0e365d0de6054f6ce2ad911bc81db5bcd8ca915bae750f57bd0a7'), + '0269b91d21976f38a9cf9bf7811375d16bf35be587d903ab1d846b2001b7d767', # 3rd-party-removal.patch + '61c05ae5f7363d5b7b6015f0a015b93f149dbda4b23b9f48f9517a6ce93d5869', # BGEN-enkre_streampos.patch +] + +builddependencies = [ + ('binutils', '2.37'), + ('Python', '3.9.6'), +] + +dependencies = [ + ('SQLite', '3.36'), + ('zstd', '1.5.0'), + ('Boost', '1.55.0'), +] + +cmds_map = [ + ('.*', "./waf configure && echo LIB_zstd = [\\'zstd\\'] >> build/c4che/_cache.py &&" + " echo LIB_sqlite3 = [\\'sqlite3\\'] >> build/c4che/_cache.py &&" + "echo LIB_boost = [\\'boost_system\\', \\'boost_filesystem\\', \\'boost_thread\\', \\'boost_timer\\'] " + " >> build/c4che/_cache.py && ./waf"), +] + +files_to_copy = [ + (['build/apps/edit-bgen', 'build/apps/bgenix', 'build/apps/cat-bgen'], 'bin'), + (['build/db/libdb.a', 'build/libbgen.a'], 'lib'), + (['genfile/include/*', 'db/include/*'], 'include'), +] + +postinstallcmds = ['./build/test/unit/test_bgen'] + +sanity_check_paths = { + 'files': ['bin/edit-bgen', 'bin/bgenix', 'bin/cat-bgen'], + 'dirs': ['bin', 'lib', 'include'], +} + +sanity_check_commands = [ + 'bgenix -help', + 'cat-bgen -help', + 'edit-bgen -help', +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/BGEN-enkre/BGEN-enkre-1.1.7-GCC-12.3.0.eb b/easybuild/easyconfigs/b/BGEN-enkre/BGEN-enkre-1.1.7-GCC-12.3.0.eb new file mode 100644 index 00000000000..bf5a35b052b --- /dev/null +++ b/easybuild/easyconfigs/b/BGEN-enkre/BGEN-enkre-1.1.7-GCC-12.3.0.eb @@ -0,0 +1,73 @@ +# Contribution from the NIHR Biomedical Research Centre +# Guy's and St Thomas' NHS Foundation Trust and King's College London +# uploaded by J. Sassmannshausen +# we recommend to use --download-timeout=1000 when fetching the files + +easyblock = 'CmdCp' + +name = 'BGEN-enkre' +version = '1.1.7' + +homepage = 'https://enkre.net/cgi-bin/code/bgen/dir?ci=trunk' +description = """This repository contains a reference implementation +of the BGEN format, written in C++. The library can be used as the +basis for BGEN support in other software, or as a reference for +developers writing their own implementations of the BGEN format. +Please cite: +Band, G. and Marchini, J., "BGEN: a binary file format for imputed genotype and haplotype data", +bioArxiv 308296; doi: https://doi.org/10.1101/308296 +""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +source_urls = ['https://code.enkre.net/bgen/tarball/v%(version)s/'] +sources = ['v%(version)s.tgz'] +patches = [ + '3rd-party-removal.patch', + 'BGEN-enkre_streampos.patch', +] + +checksums = [ + ('6476b077af6c8e98e85fd7e09f58cb3fdf143ff91850c984248fd4dc2d74a8c3', # v1.1.7.tgz + 'b922ac22c1c0e365d0de6054f6ce2ad911bc81db5bcd8ca915bae750f57bd0a7'), + '0269b91d21976f38a9cf9bf7811375d16bf35be587d903ab1d846b2001b7d767', # 3rd-party-removal.patch + '61c05ae5f7363d5b7b6015f0a015b93f149dbda4b23b9f48f9517a6ce93d5869', # BGEN-enkre_streampos.patch +] + +builddependencies = [ + ('Python', '3.11.3'), +] + +dependencies = [ + ('SQLite', '3.42.0'), + ('zstd', '1.5.5'), + ('Boost', '1.55.0'), +] + +cmds_map = [ + ('.*', "./waf configure && echo LIB_zstd = [\\'zstd\\'] >> build/c4che/_cache.py &&" + " echo LIB_sqlite3 = [\\'sqlite3\\'] >> build/c4che/_cache.py &&" + "echo LIB_boost = [\\'boost_system\\', \\'boost_filesystem\\', \\'boost_thread\\', \\'boost_timer\\'] " + " >> build/c4che/_cache.py && ./waf"), +] + +files_to_copy = [ + (['build/apps/edit-bgen', 'build/apps/bgenix', 'build/apps/cat-bgen'], 'bin'), + (['build/db/libdb.a', 'build/libbgen.a'], 'lib'), + (['genfile/include/*', 'db/include/*'], 'include'), +] + +postinstallcmds = ['./build/test/unit/test_bgen'] + +sanity_check_paths = { + 'files': ['bin/edit-bgen', 'bin/bgenix', 'bin/cat-bgen'], + 'dirs': ['bin', 'lib', 'include'], +} + +sanity_check_commands = [ + 'bgenix -help', + 'cat-bgen -help', + 'edit-bgen -help', +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/BGEN-enkre/BGEN-enkre_streampos.patch b/easybuild/easyconfigs/b/BGEN-enkre/BGEN-enkre_streampos.patch new file mode 100644 index 00000000000..5d7c0e471c3 --- /dev/null +++ b/easybuild/easyconfigs/b/BGEN-enkre/BGEN-enkre_streampos.patch @@ -0,0 +1,12 @@ +diff -ruN 1.1.7.tgz.orig/src/View.cpp 1.1.7.tgz/src/View.cpp +--- 1.1.7.tgz.orig/src/View.cpp 2020-06-29 01:19:43.000000000 -0700 ++++ 1.1.7.tgz/src/View.cpp 2022-06-06 18:05:10.650577000 -0700 +@@ -177,7 +177,7 @@ + + // get file size + { +- std::ios::streampos origin = m_stream->tellg() ; ++ std::streampos origin = m_stream->tellg() ; + m_stream->seekg( 0, std::ios::end ) ; + m_file_metadata.size = m_stream->tellg() - origin ; + m_stream->seekg( 0, std::ios::beg ) ; diff --git a/easybuild/easyconfigs/b/BLAST+/BLAST+-2.13.0-gompi-2022a.eb b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.13.0-gompi-2022a.eb index fb96f2a9897..4e9e9d4d83e 100644 --- a/easybuild/easyconfigs/b/BLAST+/BLAST+-2.13.0-gompi-2022a.eb +++ b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.13.0-gompi-2022a.eb @@ -27,6 +27,8 @@ source_urls = ['https://ftp.ncbi.nlm.nih.gov/blast/executables/%(namelower)s/%(v sources = ['ncbi-blast-%(version)s+-src.tar.gz'] checksums = ['89553714d133daf28c477f83d333794b3c62e4148408c072a1b4620e5ec4feb2'] +builddependencies = [('cpio', '2.14')] + dependencies = [ ('zlib', '1.2.12'), ('bzip2', '1.0.8'), @@ -38,7 +40,10 @@ dependencies = [ ('LMDB', '0.9.29'), ] -configopts = "--with-64 --with-z=$EBROOTZLIB --with-bz2=$EBROOTBZIP2 " +# remove line that prepends system paths to $PATH from configure script +preconfigopts = r'sed -i "s|^PATH=\(.*\)$|#PATH=\1 |" %(start_dir)s/src/build-system/configure && ' + +configopts = "--with-z=$EBROOTZLIB --with-bz2=$EBROOTBZIP2 " configopts += "--with-pcre=$EBROOTPCRE --with-boost=$EBROOTBOOST " configopts += "--with-gmp=$EBROOTGMP --with-png=$EBROOTLIBPNG " configopts += "--with-jpeg=$EBROOTLIBJPEGMINTURBO --with-lmdb=$EBROOTLMDB" diff --git a/easybuild/easyconfigs/b/BLAST+/BLAST+-2.14.0-gompi-2022b.eb b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.14.0-gompi-2022b.eb index 142ad4eb6aa..a4033efcdde 100644 --- a/easybuild/easyconfigs/b/BLAST+/BLAST+-2.14.0-gompi-2022b.eb +++ b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.14.0-gompi-2022b.eb @@ -27,6 +27,8 @@ source_urls = ['https://ftp.ncbi.nlm.nih.gov/blast/executables/%(namelower)s/%(v sources = ['ncbi-blast-%(version)s+-src.tar.gz'] checksums = ['bf477f1b0c3b82f0b7a7094bf003a9a83e37e3b0716c1df799060c4feab17500'] +builddependencies = [('cpio', '2.15')] + dependencies = [ ('zlib', '1.2.12'), ('bzip2', '1.0.8'), @@ -38,7 +40,10 @@ dependencies = [ ('LMDB', '0.9.29'), ] -configopts = "--with-64 --with-z=$EBROOTZLIB --with-bz2=$EBROOTBZIP2 " +# remove line that prepends system paths to $PATH from configure script +preconfigopts = r'sed -i "s|^PATH=\(.*\)$|#PATH=\1 |" %(start_dir)s/src/build-system/configure && ' + +configopts = "--with-z=$EBROOTZLIB --with-bz2=$EBROOTBZIP2 " configopts += "--with-pcre=$EBROOTPCRE --with-boost=$EBROOTBOOST " configopts += "--with-gmp=$EBROOTGMP --with-png=$EBROOTLIBPNG " configopts += "--with-jpeg=$EBROOTLIBJPEGMINTURBO --with-lmdb=$EBROOTLMDB" diff --git a/easybuild/easyconfigs/b/BLAST+/BLAST+-2.14.1-gompi-2023a.eb b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.14.1-gompi-2023a.eb index 47c8e2d2ef6..844a9854825 100644 --- a/easybuild/easyconfigs/b/BLAST+/BLAST+-2.14.1-gompi-2023a.eb +++ b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.14.1-gompi-2023a.eb @@ -27,6 +27,8 @@ source_urls = ['https://ftp.ncbi.nlm.nih.gov/blast/executables/%(namelower)s/%(v sources = ['ncbi-blast-%(version)s+-src.tar.gz'] checksums = ['712c2dbdf0fb13cc1c2d4f4ef5dd1ce4b06c3b57e96dfea8f23e6e99f5b1650e'] +builddependencies = [('cpio', '2.15')] + dependencies = [ ('zlib', '1.2.13'), ('bzip2', '1.0.8'), @@ -38,7 +40,10 @@ dependencies = [ ('LMDB', '0.9.31'), ] -configopts = "--with-64 --with-z=$EBROOTZLIB --with-bz2=$EBROOTBZIP2 " +# remove line that prepends system paths to $PATH from configure script +preconfigopts = r'sed -i "s|^PATH=\(.*\)$|#PATH=\1 |" %(start_dir)s/src/build-system/configure && ' + +configopts = "--with-z=$EBROOTZLIB --with-bz2=$EBROOTBZIP2 " configopts += "--with-pcre=$EBROOTPCRE --with-boost=$EBROOTBOOST " configopts += "--with-gmp=$EBROOTGMP --with-png=$EBROOTLIBPNG " configopts += "--with-jpeg=$EBROOTLIBJPEGMINTURBO --with-lmdb=$EBROOTLMDB" diff --git a/easybuild/easyconfigs/b/BLAT/BLAT-3.7-GCC-12.3.0.eb b/easybuild/easyconfigs/b/BLAT/BLAT-3.7-GCC-12.3.0.eb new file mode 100644 index 00000000000..ba6cac7d238 --- /dev/null +++ b/easybuild/easyconfigs/b/BLAT/BLAT-3.7-GCC-12.3.0.eb @@ -0,0 +1,55 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2013 The Cyprus Institute +# Authors:: Andreas Panteli , Thekla Loizou +# Contributors:: Alex Domingo (Vrije Universiteit Brussel) +# License:: MIT/GPL +# +## + +name = 'BLAT' +version = '3.7' + +homepage = 'https://genome.ucsc.edu/goldenPath/help/blatSpec.html' +description = """BLAT on DNA is designed to quickly find sequences of 95% and +greater similarity of length 25 bases or more.""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://genome-test.gi.ucsc.edu/~kent/src/'] +sources = ['%%(namelower)sSrc%s.zip' % ''.join(version.split('.'))] +patches = ['BLAT-%(version)s_mend-tests.patch'] +checksums = [ + {'blatSrc37.zip': '88ee2b272d42ab77687c61d200b11f1d58443951069feb7e10226a2509f84cf2'}, + {'BLAT-3.7_mend-tests.patch': '1f42c7fadf7676a5cc3a2016f70089c3541aa1d53816cf86072682c44cf311a6'}, +] + +# BLAT relies on a bundled old version of HTSlib. We use the bundled library +# because it is statically linked and the newer HTSlib in this toolchain is not +# API compatible with it. +dependencies = [ + ('freetype', '2.13.0'), + ('libiconv', '1.17'), + ('libpng', '1.6.39'), + ('MariaDB', '11.6.0'), + ('OpenSSL', '1.1', '', SYSTEM), + ('util-linux', '2.39'), + ('zlib', '1.2.13'), +] + +pretestopts = 'PATH="%(builddir)s/blatSrc/bin:$PATH"' +runtest = 'test' + +_blat_bins = ["blat", "faToNib", "faToTwoBit", "gfClient", "gfServer", "nibFrag", "pslPretty", + "pslReps", "pslSort", "twoBitInfo", "twoBitToFa"] + +files_to_copy = [(["bin/%s" % x for x in _blat_bins] + ["webBlat/webBlat"], 'bin')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in _blat_bins + ["webBlat"]], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/BLIS/BLIS-1.0-GCC-13.3.0.eb b/easybuild/easyconfigs/b/BLIS/BLIS-1.0-GCC-13.3.0.eb new file mode 100644 index 00000000000..18d8ec6c887 --- /dev/null +++ b/easybuild/easyconfigs/b/BLIS/BLIS-1.0-GCC-13.3.0.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'BLIS' +version = '1.0' + +homepage = 'https://github.com/flame/blis/' +description = """BLIS is a portable software framework for instantiating high-performance +BLAS-like dense linear algebra libraries.""" + +toolchain = {'name': 'GCC', 'version': '13.3.0'} + +source_urls = ['https://github.com/flame/blis/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['9c12972aa1e50f64ca61684eba6828f2f3dd509384b1e41a1e8a9aedea4b16a6'] + +builddependencies = [ + ('Python', '3.12.3'), + ('Perl', '5.38.2'), +] + +configopts = '--enable-cblas --enable-threading=openmp --enable-shared CC="$CC" auto' + +runtest = 'check' + +sanity_check_paths = { + 'files': ['include/blis/cblas.h', 'include/blis/blis.h', + 'lib/libblis.a', 'lib/libblis.%s' % SHLIB_EXT], + 'dirs': [], +} + +modextrapaths = {'CPATH': 'include/blis'} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/b/BRAKER/BRAKER-3.0.8-foss-2023a.eb b/easybuild/easyconfigs/b/BRAKER/BRAKER-3.0.8-foss-2023a.eb new file mode 100644 index 00000000000..7a87a70ddb1 --- /dev/null +++ b/easybuild/easyconfigs/b/BRAKER/BRAKER-3.0.8-foss-2023a.eb @@ -0,0 +1,55 @@ +# updated: Denis Kristak (INUITS) +# Update: Petr Král (INUITS) +easyblock = 'Tarball' + +name = 'BRAKER' +version = '3.0.8' + +homepage = 'https://github.com/Gaius-Augustus/BRAKER' +description = """BRAKER is a pipeline for fully automated prediction of protein coding genes with GeneMark-ES/ET + and AUGUSTUS in novel eukaryotic genomes.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['https://github.com/Gaius-Augustus/BRAKER/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['f2623290c3007a3e42719a0bb2713bec7226db222bfef742895a9d5d0b4ee526'] + +dependencies = [ + ('Perl', '5.36.1'), + ('Python', '3.11.3'), + ('AUGUSTUS', '3.5.0'), + ('GeneMark-ET', '4.72'), + ('BamTools', '2.5.2'), + ('SAMtools', '1.18'), + ('GenomeThreader', '1.7.3', '-Linux_x86_64-64bit', SYSTEM), + ('spaln', '3.0.6b'), + ('Exonerate', '2.4.0'), + ('BLAST+', '2.14.1'), + ('Biopython', '1.83'), + ('DIAMOND', '2.1.8'), + ('CDBtools', '0.99'), +] + +fix_perl_shebang_for = ['scripts/*.pl'] +fix_python_shebang_for = ['scripts/*.py'] + +sanity_check_paths = { + 'files': [ + 'scripts/braker.pl', + 'scripts/compare_intervals_exact.pl', + 'scripts/compute_accuracies.sh', + 'scripts/compute_accuracies.sh', + 'scripts/filterGenemark.pl', + 'scripts/findGenesInIntrons.pl', + 'scripts/gatech_pmp2hints.pl', + 'scripts/sortGeneMark.py', + ], + 'dirs': ['docs', 'example'], +} + +sanity_check_commands = ["braker.pl --help"] + +modextrapaths = {'PATH': 'scripts'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/BRiAl/BRiAl-1.2.12-GCC-13.2.0.eb b/easybuild/easyconfigs/b/BRiAl/BRiAl-1.2.12-GCC-13.2.0.eb new file mode 100644 index 00000000000..50bbeea16ee --- /dev/null +++ b/easybuild/easyconfigs/b/BRiAl/BRiAl-1.2.12-GCC-13.2.0.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'BRiAl' +version = '1.2.12' + +homepage = 'https://github.com/BRiAl/BRiAl' +description = """BRiAl is the legacy version of PolyBoRi maintained by sagemath developers.""" + +toolchain = {'name': 'GCC', 'version': '13.2.0'} + +source_urls = ['https://github.com/BRiAl/BRiAl/releases/download/%(version)s'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['ca009e3722dd3f0a60d15501caed1413146c80abced57423e32ae0116f407494'] + +dependencies = [ + ('Boost', '1.83.0'), + ('m4ri', '20200125'), + ('CUDD', '3.0.0'), +] + +configopts = "--with-boost=$EBROOTBOOST " + +runtest = 'check' + +sanity_check_paths = { + 'files': ['include/polybori.h'] + + ['lib/libbrial.%s' % e for e in ['a', SHLIB_EXT]], + 'dirs': [], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/b/BWA/BWA-0.7.18-GCCcore-12.3.0.eb b/easybuild/easyconfigs/b/BWA/BWA-0.7.18-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..a5599e37642 --- /dev/null +++ b/easybuild/easyconfigs/b/BWA/BWA-0.7.18-GCCcore-12.3.0.eb @@ -0,0 +1,52 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Cyprus Institute / CaSToRC, Uni.Lu/LCSB, NTUA +# Authors:: George Tsouloupas , Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +# +# Version >= 0.7.15 +# Author: Adam Huffman +# The Francis Crick Institute +# +# Note that upstream development is mainly at: https://github.com/lh3/bwa +# +# 0.7.18 +# Erica Bianco (HPCNow!) +## + +name = 'BWA' +version = '0.7.18' + +homepage = 'http://bio-bwa.sourceforge.net/' +description = """ + Burrows-Wheeler Aligner (BWA) is an efficient program that aligns relatively + short nucleotide sequences against a long reference sequence such as the human + genome. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/lh3/%(name)s/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['194788087f7b9a77c0114aa481b2ef21439f6abab72488c83917302e8d0e7870'] + +builddependencies = [('binutils', '2.40')] + +dependencies = [ + ('Perl', '5.36.1'), + ('zlib', '1.2.13'), +] + +# Allow use of x86 intrinsics on PPC +prebuildopts = 'export CFLAGS="$CFLAGS -fcommon -DNO_WARN_X86_INTRINSICS" && ' +prebuildopts += "sed -i 's|^CC=|#CC=|g' Makefile && " +prebuildopts += "sed -i 's|^CFLAGS=|#CFLAGS=|g' Makefile && " +prebuildopts += "sed -i 's|^LIBS=|LIBS= $(LDFLAGS) |g' Makefile && " + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/BamTools/BamTools-2.5.2-GCC-13.2.0.eb b/easybuild/easyconfigs/b/BamTools/BamTools-2.5.2-GCC-13.2.0.eb new file mode 100644 index 00000000000..a8e5449e98c --- /dev/null +++ b/easybuild/easyconfigs/b/BamTools/BamTools-2.5.2-GCC-13.2.0.eb @@ -0,0 +1,22 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +name = 'BamTools' +version = '2.5.2' + +homepage = 'https://github.com/pezmaster31/bamtools' +description = "BamTools provides both a programmer's API and an end-user's toolkit for handling BAM files." + +toolchain = {'name': 'GCC', 'version': '13.2.0'} +toolchainopts = {'pic': True} + +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['4d8b84bd07b673d0ed41031348f10ca98dd6fa6a4460f9b9668d6f1d4084dfc8'] + +builddependencies = [ + ('CMake', '3.27.6'), +] + +# https://github.com/pezmaster31/bamtools +github_account = 'pezmaster31' + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/BamTools/BamTools-2.5.2-GCC-13.3.0.eb b/easybuild/easyconfigs/b/BamTools/BamTools-2.5.2-GCC-13.3.0.eb new file mode 100644 index 00000000000..23e1ad0e743 --- /dev/null +++ b/easybuild/easyconfigs/b/BamTools/BamTools-2.5.2-GCC-13.3.0.eb @@ -0,0 +1,22 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +name = 'BamTools' +version = '2.5.2' + +homepage = 'https://github.com/pezmaster31/bamtools' +description = "BamTools provides both a programmer's API and an end-user's toolkit for handling BAM files." + +toolchain = {'name': 'GCC', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['4d8b84bd07b673d0ed41031348f10ca98dd6fa6a4460f9b9668d6f1d4084dfc8'] + +builddependencies = [ + ('CMake', '3.29.3'), +] + +# https://github.com/pezmaster31/bamtools +github_account = 'pezmaster31' + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/Bandage/Bandage-0.9.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/b/Bandage/Bandage-0.9.0-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..acdc093c96d --- /dev/null +++ b/easybuild/easyconfigs/b/Bandage/Bandage-0.9.0-GCCcore-12.3.0.eb @@ -0,0 +1,30 @@ +easyblock = 'MakeCp' + +name = 'Bandage' +version = '0.9.0' + +homepage = 'http://rrwick.github.io/Bandage' +description = "Bandage is a program for visualising de novo assembly graphs" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://github.com/rrwick/Bandage/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['04de8152d8bf5e5aa32b41a63cf1c23e1fee7b67ccd9f1407db8dc2824ca4e30'] + +builddependencies = [('binutils', '2.40')] + +dependencies = [('Qt5', '5.15.10')] + +prebuildopts = "qmake Bandage.pro && " + +files_to_copy = [(['Bandage'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/Bandage'], + 'dirs': [], +} + +sanity_check_commands = ["Bandage --help && ldd $(which Bandage)"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/BayesOpt/BayesOpt-0.9-GCC-12.3.0.eb b/easybuild/easyconfigs/b/BayesOpt/BayesOpt-0.9-GCC-12.3.0.eb new file mode 100644 index 00000000000..2e20ceba904 --- /dev/null +++ b/easybuild/easyconfigs/b/BayesOpt/BayesOpt-0.9-GCC-12.3.0.eb @@ -0,0 +1,33 @@ +easyblock = 'CMakeMake' + +name = 'BayesOpt' +version = '0.9' + +homepage = 'https://rmcantin.github.io/bayesopt' +description = """BayesOpt is an efficient implementation of the Bayesian optimization methodology for +nonlinear-optimization, experimental design, stochastic bandits and hyperparameter tunning""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +source_urls = ['https://github.com/rmcantin/bayesopt/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['f4e60cfac380eccd2d1adc805b752b5bd22a1d8a27dc6aeb630c403adc04f28c'] + +builddependencies = [ + ('CMake', '3.26.3'), +] + +dependencies = [ + ('Boost', '1.82.0'), + ('NLopt', '2.7.1'), +] + +# don't build included version of NLopt (use provided dependency) +configopts = "-DNLOPT_BUILD=OFF" + +sanity_check_paths = { + 'files': ['lib/libbayesopt.a'], + 'dirs': ['include/bayesopt'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/b/BayesTraits/BayesTraits-4.1.2-Linux.eb b/easybuild/easyconfigs/b/BayesTraits/BayesTraits-4.1.2-Linux.eb new file mode 100644 index 00000000000..541dedf129e --- /dev/null +++ b/easybuild/easyconfigs/b/BayesTraits/BayesTraits-4.1.2-Linux.eb @@ -0,0 +1,40 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel + +# Updated by +# Author: Alex Salois +# Research Cyberinfrastructure +# Montana State University + +easyblock = "Tarball" + +name = 'BayesTraits' +version = '4.1.2' +versionsuffix = '-Linux' + +homepage = 'https://www.evolution.reading.ac.uk/SoftwareMain.html' +description = """ BayesTraits is a computer package for performing analyses of trait + evolution among groups of species for which a phylogeny or sample of phylogenies is + available. This new package incoporates our earlier and separate programes Multistate, + Discrete and Continuous. BayesTraits can be applied to the analysis of traits that adopt + a finite number of discrete states, or to the analysis of continuously varying traits. + Hypotheses can be tested about models of evolution, about ancestral states and about + correlations among pairs of traits. """ + +toolchain = SYSTEM + +source_urls = ['https://www.evolution.reading.ac.uk/BayesTraitsV%(version)s/Files/'] +sources = ['BayesTraitsV%(version)s%(versionsuffix)s.tar.gz'] +checksums = ['d5251c2b256405fc63c55caf8371b267530a3c4ebd11cbfd3ebd4013c9d49db0'] + +sanity_check_paths = { + 'files': ['BayesTraitsV4', 'Artiodactyl.trees', 'Bird.trees', 'Mammal.trees', + 'Marsupials.trees', 'NortheastBantu.trees', 'Primates.trees'], + 'dirs': [], +} + +modextrapaths = {'PATH': ''} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/Bazel/Bazel-6.1.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/b/Bazel/Bazel-6.1.0-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..1bacc7b9363 --- /dev/null +++ b/easybuild/easyconfigs/b/Bazel/Bazel-6.1.0-GCCcore-12.3.0.eb @@ -0,0 +1,29 @@ +name = 'Bazel' +version = '6.1.0' + +homepage = 'https://bazel.io/' +description = """Bazel is a build tool that builds code quickly and reliably. +It is used to build the majority of Google's software.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://github.com/bazelbuild/%(namelower)s/releases/download/%(version)s'] +sources = ['%(namelower)s-%(version)s-dist.zip'] +patches = ['Bazel-6.3.1_add-symlinks-in-runfiles.patch'] +checksums = [ + {'bazel-6.1.0-dist.zip': 'c4b85675541cf66ee7cb71514097fdd6c5fc0e02527243617a4f20ca6b4f2932'}, + {'Bazel-6.3.1_add-symlinks-in-runfiles.patch': '81db53aa87229557480b6f719c99a0f1af9c69dfec12185451e520b0128c3ae2'}, +] + +builddependencies = [ + ('binutils', '2.40'), + ('Python', '3.11.3'), + ('Zip', '3.0'), +] + +dependencies = [('Java', '11', '', SYSTEM)] + +runtest = True +testopts = "-- //examples/cpp:hello-success_test //examples/py/... //examples/py_native:test //examples/shell/..." + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/Bazel/Bazel-7.4.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/b/Bazel/Bazel-7.4.1-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..1fc72e512e2 --- /dev/null +++ b/easybuild/easyconfigs/b/Bazel/Bazel-7.4.1-GCCcore-13.3.0.eb @@ -0,0 +1,26 @@ +name = 'Bazel' +version = '7.4.1' + +homepage = 'https://bazel.io/' +description = """Bazel is a build tool that builds code quickly and reliably. +It is used to build the majority of Google's software.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://github.com/bazelbuild/%(namelower)s/releases/download/%(version)s'] +sources = ['%(namelower)s-%(version)s-dist.zip'] +checksums = ['83386618bc489f4da36266ef2620ec64a526c686cf07041332caff7c953afaf5'] + +builddependencies = [ + ('binutils', '2.42'), + ('Python', '3.12.3'), + ('Zip', '3.0'), +] +dependencies = [ + ('Java', '21.0.2', '', SYSTEM), +] + +runtest = True +testopts = "-- //examples/cpp:hello-success_test //examples/py/... //examples/py_native:test //examples/shell/..." + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/BeautifulSoup/BeautifulSoup-4.12.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/b/BeautifulSoup/BeautifulSoup-4.12.2-GCCcore-12.3.0.eb index cc388eeb4ca..8d4556012b6 100644 --- a/easybuild/easyconfigs/b/BeautifulSoup/BeautifulSoup-4.12.2-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/b/BeautifulSoup/BeautifulSoup-4.12.2-GCCcore-12.3.0.eb @@ -9,12 +9,12 @@ description = "Beautiful Soup is a Python library designed for quick turnaround toolchain = {'name': 'GCCcore', 'version': '12.3.0'} builddependencies = [ - ('binutils', '2.40') + ('binutils', '2.40'), + ('hatchling', '1.18.0'), ] dependencies = [ ('Python', '3.11.3'), - ('hatchling', '1.18.0'), ] use_pip = True diff --git a/easybuild/easyconfigs/b/BeautifulSoup/BeautifulSoup-4.12.2-GCCcore-13.2.0.eb b/easybuild/easyconfigs/b/BeautifulSoup/BeautifulSoup-4.12.2-GCCcore-13.2.0.eb index 4aeb23721ad..bbf74453cfd 100644 --- a/easybuild/easyconfigs/b/BeautifulSoup/BeautifulSoup-4.12.2-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/b/BeautifulSoup/BeautifulSoup-4.12.2-GCCcore-13.2.0.eb @@ -9,12 +9,12 @@ description = "Beautiful Soup is a Python library designed for quick turnaround toolchain = {'name': 'GCCcore', 'version': '13.2.0'} builddependencies = [ - ('binutils', '2.40') + ('binutils', '2.40'), + ('hatchling', '1.18.0'), ] dependencies = [ ('Python', '3.11.5'), - ('hatchling', '1.18.0'), ] use_pip = True diff --git a/easybuild/easyconfigs/b/BeautifulSoup/BeautifulSoup-4.12.3-GCCcore-13.3.0.eb b/easybuild/easyconfigs/b/BeautifulSoup/BeautifulSoup-4.12.3-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..95cb6cf3228 --- /dev/null +++ b/easybuild/easyconfigs/b/BeautifulSoup/BeautifulSoup-4.12.3-GCCcore-13.3.0.eb @@ -0,0 +1,35 @@ +easyblock = 'PythonBundle' + +name = 'BeautifulSoup' +version = '4.12.3' + +homepage = 'https://www.crummy.com/software/BeautifulSoup' +description = "Beautiful Soup is a Python library designed for quick turnaround projects like screen-scraping." + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +builddependencies = [ + ('binutils', '2.42'), + ('hatchling', '1.24.2'), +] + +dependencies = [ + ('Python', '3.12.3'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('soupsieve', '2.5', { + 'checksums': ['5663d5a7b3bfaeee0bc4372e7fc48f9cff4940b3eec54a6451cc5299f1097690'], + }), + (name, version, { + 'modulename': 'bs4', + 'source_tmpl': 'beautifulsoup4-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/b/beautifulsoup4'], + 'checksums': ['74e3d1928edc070d21748185c46e3fb33490f22f52a3addee9aee0f4f7781051'], + }), +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/b/BiG-SCAPE/BiG-SCAPE-1.1.9-foss-2023b.eb b/easybuild/easyconfigs/b/BiG-SCAPE/BiG-SCAPE-1.1.9-foss-2023b.eb new file mode 100644 index 00000000000..59f7c1a7cd5 --- /dev/null +++ b/easybuild/easyconfigs/b/BiG-SCAPE/BiG-SCAPE-1.1.9-foss-2023b.eb @@ -0,0 +1,68 @@ +easyblock = 'PythonPackage' + +name = 'BiG-SCAPE' +version = '1.1.9' + +homepage = 'https://bigscape-corason.secondarymetabolites.org/index.html' +description = """BiG-SCAPE and CORASON provide a set of tools to explore the diversity of biosynthetic gene clusters +(BGCs) across large numbers of genomes, by constructing BGC sequence similarity networks, grouping BGCs into gene +cluster families, and exploring gene cluster diversity linked to enzyme phylogenies.""" + +toolchain = {'name': 'foss', 'version': '2023b'} + +github_account = 'medema-group' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +patches = [ + 'BiG-SCAPE-1.1.5_use_env_var_for_html.patch', + 'BiG-SCAPE-1.1.5_use_correct_name_for_FastTree.patch', +] +checksums = [ + {'v1.1.9.tar.gz': 'ef0ddb5b433e0b1467ae5f96037fd6d23ebcba6bc08201d1421eba35d072e534'}, + {'BiG-SCAPE-1.1.5_use_env_var_for_html.patch': '540be22396ab982c2aeaaed4ce5acdb8ccb8ce2b31d36bc69d37be7a29c7c42a'}, + {'BiG-SCAPE-1.1.5_use_correct_name_for_FastTree.patch': + 'e1572e4134c6163a3927ac32bd2a39b7f87cf01109f7913b3c55126e2381a771'}, +] + +dependencies = [ + ('Python', '3.11.5'), + ('SciPy-bundle', '2023.11'), + ('Biopython', '1.84'), + ('scikit-learn', '1.4.0'), + ('networkx', '3.2.1'), + ('HMMER', '3.4'), + ('FastTree', '2.1.11'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +options = {'modulename': 'bigscape'} + +local_lib_py_bigscape_path = 'lib/python%(pyshortver)s/site-packages/bigscape' + +sanity_check_paths = { + 'files': ['bin/bigscape'], + 'dirs': [local_lib_py_bigscape_path], +} + +sanity_check_commands = [ + 'bigscape --help', +] + +modextravars = { + 'BIG_SCAPE_HTML_PATH': '%(installdir)s/' + local_lib_py_bigscape_path, +} + +modloadmsg = "%(name)s needs processed Pfam database to work properly.\n" +modloadmsg += "For this, download the latest 'Pfam-A.hmm.gz' file from the Pfam website " +modloadmsg += "(http://ftp.ebi.ac.uk/pub/databases/Pfam/releases/), " +modloadmsg += "uncompress it and process it using the `hmmpress` command.\n" +modloadmsg += "For data files, like the domains_color_file.tsv and domain_includelist.txt, " +modloadmsg += "one can set the environment variable BIG_SCAPE_DATA_PATH, if that is not set " +modloadmsg += "it will use the directory where the bigscape command is started from.\n" +modloadmsg += "One can copy the domains_color_file.tsv from " +modloadmsg += "%(installdir)s/lib/python%(pyshortver)s/site-packages/BiG-SCAPE/domains_color_file.tsv\n" + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/BindCraft/BindCraft-1.1.0-foss-2023a.eb b/easybuild/easyconfigs/b/BindCraft/BindCraft-1.1.0-foss-2023a.eb new file mode 100644 index 00000000000..49345e486d8 --- /dev/null +++ b/easybuild/easyconfigs/b/BindCraft/BindCraft-1.1.0-foss-2023a.eb @@ -0,0 +1,89 @@ +easyblock = 'Tarball' + +name = 'BindCraft' +version = '1.1.0' + +homepage = 'https://github.com/martinpacesa/BindCraft' +description = """Simple binder design pipeline using AlphaFold2 backpropagation, MPNN, and PyRosetta. + Select your target and let the script do the rest of the work and finish once you have enough designs to order!""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['https://github.com/martinpacesa/BindCraft/archive/refs/tags/'] +sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}] +checksums = ['c682f59501f0bcfbb8289fd066362dcea37ed8553cdff5c794a2baa6d4149ce7'] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('Biopython', '1.83'), + ('Seaborn', '0.13.2'), + ('tqdm', '4.66.1'), + ('OpenMM', '8.0.0'), + ('FFmpeg', '6.0'), + ('matplotlib', '3.7.2'), + ('PyRosetta', '4.release-387'), + ('jax', '0.4.25'), + ('dm-haiku', '0.0.13'), + ('dm-tree', '0.1.8'), + ('ml-collections', '0.1.1'), + ('Optax', '0.2.2'), + ('py3Dmol', '2.1.0'), + ('JupyterLab', '4.0.5'), + ('hatchling', '1.18.0'), + ('Flax', '0.8.4'), +] + +exts_defaultclass = 'PythonPackage' +exts_default_options = { + 'source_urls': [PYPI_SOURCE], + 'download_dep_fail': True, + 'use_pip': True, + 'sanity_pip_check': True, +} +exts_list = [ + ('PDBFixer', '1.9', { + 'source_urls': ['https://github.com/openmm/pdbfixer/archive/'], + 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['88b9a77e50655f89d0eb2075093773e82c27a4cef842cb7d735c877b20cd39fb'], + }), + ('jupyter_console', '6.6.3', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['309d33409fcc92ffdad25f0bcdf9a4a9daa61b6f341177570fdac03de5352485'], + }), + # older version compatible with `jupyterlab-4.0.5` + ('notebook', '7.0.8', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['7f421b3fd46a17d91830e724b94e8e9ae922af152ebfd48b1e13ae4a07d8193c'], + }), + ('jupyter', '1.1.1', { + 'source_tmpl': SOURCE_WHL, + 'checksums': ['7a59533c22af65439b24bbe60373a4e95af8f16ac65a6c00820ad378e3f7cc83'], + }), + ('immutabledict', '4.2.0', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['d728b2c2410d698d95e6200237feb50a695584d20289ad3379a439aa3d90baba'], + }), + ('colabdesign', '1.1.1', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['8f556fb575d2bbef79fa1789698d55221f2cc51df38f2cc054f38cb6ecc08e27'], + }), +] + +fix_python_shebang_for = ['bindcraft.py'] + +postinstallcmds = ['chmod a+x %(installdir)s/bindcraft.py'] + +modextrapaths = { + 'PATH': '', + 'PYTHONPATH': ['', 'lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_paths = { + 'files': ['bindcraft.py'], + 'dirs': [], +} + +sanity_check_commands = ["bindcraft.py --help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/Bio-DB-HTS/Bio-DB-HTS-3.01-GCC-13.3.0.eb b/easybuild/easyconfigs/b/Bio-DB-HTS/Bio-DB-HTS-3.01-GCC-13.3.0.eb new file mode 100644 index 00000000000..490e86bfb7a --- /dev/null +++ b/easybuild/easyconfigs/b/Bio-DB-HTS/Bio-DB-HTS-3.01-GCC-13.3.0.eb @@ -0,0 +1,32 @@ +easyblock = 'PerlModule' + +name = 'Bio-DB-HTS' +version = '3.01' + +homepage = 'https://metacpan.org/release/Bio-DB-HTS' +description = "Read files using HTSlib including BAM/CRAM, Tabix and BCF database files" + +toolchain = {'name': 'GCC', 'version': '13.3.0'} + +source_urls = ['https://cpan.metacpan.org/authors/id/A/AV/AVULLO/'] +sources = ['Bio-DB-HTS-%(version)s.tar.gz'] +checksums = ['12a6bc1f579513cac8b9167cce4e363655cc8eba26b7d9fe1170dfe95e044f42'] + +builddependencies = [('pkgconf', '2.2.0')] + +dependencies = [ + ('Perl', '5.38.2'), + ('BioPerl', '1.7.8'), + ('HTSlib', '1.21'), +] + +preconfigopts = "env HTSLIB_DIR=$EBROOTHTSLIB" + +options = {'modulename': 'Bio::DB::HTS'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/perl5/site_perl/%(perlver)s', 'man/man3'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.8-GCCcore-12.2.0.eb b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.8-GCCcore-12.2.0.eb index 8caddd5df22..e8e52099b07 100644 --- a/easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.8-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.8-GCCcore-12.2.0.eb @@ -5,7 +5,7 @@ # Fred Hutchinson Cancer Research Center # Thomas Eylenbosch - Gluo NV -easyblock = 'PerlModule' +easyblock = 'Bundle' name = 'BioPerl' version = '1.7.8' diff --git a/easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.8-GCCcore-12.3.0.eb b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.8-GCCcore-12.3.0.eb index b47216124f8..4212570abb1 100644 --- a/easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.8-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.8-GCCcore-12.3.0.eb @@ -5,7 +5,7 @@ # Fred Hutchinson Cancer Research Center # Thomas Eylenbosch - Gluo NV -easyblock = 'PerlModule' +easyblock = 'Bundle' name = 'BioPerl' version = '1.7.8' diff --git a/easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.8-GCCcore-13.3.0.eb b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.8-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..ba3029a6a41 --- /dev/null +++ b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.8-GCCcore-13.3.0.eb @@ -0,0 +1,58 @@ +# easybuild easyconfig +# +# John Dey jfdey@fredhutch.org +# +# Fred Hutchinson Cancer Research Center +# Thomas Eylenbosch - Gluo NV + +easyblock = 'Bundle' + +name = 'BioPerl' +version = '1.7.8' + +homepage = 'https://bioperl.org/' +description = """Bioperl is the product of a community effort to produce Perl code which is useful in biology. + Examples include Sequence objects, Alignment objects and database searching objects.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +builddependencies = [('binutils', '2.42')] + +dependencies = [ + ('Perl', '5.38.2'), + ('Perl-bundle-CPAN', '5.38.2'), + ('XML-LibXML', '2.0210'), + ('DB_File', '1.859'), +] + +exts_defaultclass = 'PerlModule' +exts_filter = ("perldoc -lm %(ext_name)s ", "") + +exts_list = [ + ('XML::Writer', '0.900', { + 'source_tmpl': 'XML-Writer-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JO/JOSEPHW'], + 'checksums': ['73c8f5bd3ecf2b350f4adae6d6676d52e08ecc2d7df4a9f089fa68360d400d1f'], + }), + (name, version, { + 'source_tmpl': '%(name)s-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CJ/CJFIELDS/'], + 'checksums': ['c490a3be7715ea6e4305efd9710e5edab82dabc55fd786b6505b550a30d71738'], + }), + ('Bio::Procedural', '1.7.4', { + 'source_tmpl': 'Bio-Procedural-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CJ/CJFIELDS/'], + 'checksums': ['d2bd9cfbb091eee2d80ed6cf812ac3813b1c8a1aaca20671037f5f225d31d1da'], + }), +] + +modextrapaths = { + 'PERL5LIB': 'lib/perl5/site_perl/%(perlver)s/', +} + +sanity_check_paths = { + 'files': [], + 'dirs': ['bin', 'lib/perl5/site_perl/%(perlver)s/Bio'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/Biopython/Biopython-1.84-foss-2023b.eb b/easybuild/easyconfigs/b/Biopython/Biopython-1.84-foss-2023b.eb new file mode 100644 index 00000000000..03c23f41186 --- /dev/null +++ b/easybuild/easyconfigs/b/Biopython/Biopython-1.84-foss-2023b.eb @@ -0,0 +1,46 @@ +# Updated from previous easyconfig +# Author: Robert Mijakovic +# Update: Pavel Tománek (INUITS) + +easyblock = 'PythonPackage' + +name = 'Biopython' +version = '1.84' + +homepage = 'https://www.biopython.org' +description = """Biopython is a set of freely available tools for biological + computation written in Python by an international team of developers. It is + a distributed collaborative effort to develop Python libraries and + applications which address the needs of current and future work in + bioinformatics. """ + +toolchain = {'name': 'foss', 'version': '2023b'} + +source_urls = ['https://biopython.org/DIST'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['60fbe6f996e8a6866a42698c17e552127d99a9aab3259d6249fbaabd0e0cc7b4'] + +dependencies = [ + ('Python', '3.11.5'), + ('SciPy-bundle', '2023.11'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +# Run only tests that don't require internet connection +runtest = 'python setup.py test --offline' + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/Bio', + 'lib/python%(pyshortver)s/site-packages/BioSQL'] +} + +# extra check to ensure numpy dependency is available +sanity_check_commands = ["python -c 'import Bio.MarkovModel'"] + +options = {'modulename': 'Bio'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/Biotite/Biotite-0.41.0-gfbf-2023a.eb b/easybuild/easyconfigs/b/Biotite/Biotite-0.41.0-gfbf-2023a.eb new file mode 100644 index 00000000000..8d4385e45f5 --- /dev/null +++ b/easybuild/easyconfigs/b/Biotite/Biotite-0.41.0-gfbf-2023a.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonBundle' + +name = 'Biotite' +version = '0.41.0' + +homepage = 'https://www.biotite-python.org/' +description = """Biotite is your Swiss army knife for bioinformatics. Whether you want to +identify homologous sequence regions in a protein family or you would like to +find disulfide bonds in a protein structure: Biotite has the right tool for +you. This package bundles popular tasks in computational molecular biology into +a uniform Python library.""" + +toolchain = {'name': 'gfbf', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('SciPy-bundle', '2023.07'), + ('networkx', '3.1'), +] + +use_pip = True + +exts_list = [ + ('biotite', version, { + 'checksums': ['a5fddb4d738291772735cf04dfa8b642e0bdd6b4c2c0c71e2db727c0a66bd106'], + }), +] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.8.2-GCCcore-13.3.0.eb b/easybuild/easyconfigs/b/Bison/Bison-3.8.2-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..168af69373e --- /dev/null +++ b/easybuild/easyconfigs/b/Bison/Bison-3.8.2-GCCcore-13.3.0.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'Bison' +version = '3.8.2' + +homepage = 'https://www.gnu.org/software/bison' +description = """Bison is a general-purpose parser generator that converts an annotated context-free grammar + into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['06c9e13bdf7eb24d4ceb6b59205a4f67c2c7e7213119644430fe82fbd14a0abb'] + +builddependencies = [ + ('M4', '1.4.19'), + # use same binutils version that was used when building GCCcore toolchain + ('binutils', '2.42', '', SYSTEM), +] + + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['bison', 'yacc']] + [('lib/liby.a', 'lib64/liby.a')], + 'dirs': [], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.8.2-GCCcore-14.2.0.eb b/easybuild/easyconfigs/b/Bison/Bison-3.8.2-GCCcore-14.2.0.eb new file mode 100644 index 00000000000..427ebbbe2b7 --- /dev/null +++ b/easybuild/easyconfigs/b/Bison/Bison-3.8.2-GCCcore-14.2.0.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'Bison' +version = '3.8.2' + +homepage = 'https://www.gnu.org/software/bison' +description = """Bison is a general-purpose parser generator that converts an annotated context-free grammar + into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables.""" + +toolchain = {'name': 'GCCcore', 'version': '14.2.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['06c9e13bdf7eb24d4ceb6b59205a4f67c2c7e7213119644430fe82fbd14a0abb'] + +builddependencies = [ + ('M4', '1.4.19'), + # use same binutils version that was used when building GCCcore toolchain + ('binutils', '2.42', '', SYSTEM), +] + + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['bison', 'yacc']] + [('lib/liby.a', 'lib64/liby.a')], + 'dirs': [], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/b/Block/Block-1.5.3-20200525-foss-2023a.eb b/easybuild/easyconfigs/b/Block/Block-1.5.3-20200525-foss-2023a.eb new file mode 100644 index 00000000000..da1316c8aa6 --- /dev/null +++ b/easybuild/easyconfigs/b/Block/Block-1.5.3-20200525-foss-2023a.eb @@ -0,0 +1,56 @@ +easyblock = 'MakeCp' + +name = 'Block' +version = '1.5.3-20200525' +_commit = 'f95317b08043b7c531289576d59ad74a6d920741' + +homepage = 'https://sanshar.github.io/Block/' +description = """Block implements the density matrix renormalization group (DMRG) algorithm for +quantum chemistry.""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'cstd': 'c++11', 'pic': True} + +# Version 1.5 is a major rewrite of Block that was named at some point StackBlock +# sources are available in sanshar/StackBlock +# sources at sanshar/Block@b0e3671aad and pyscf/Block@db27636b76 correspond to version 1.1.1 +source_urls = ['https://github.com/sanshar/StackBlock/archive'] +sources = [{'download_filename': '%s.tar.gz' % _commit, 'filename': '%(version)s.tar.gz'}] +patches = [ + 'Block-1.5.3_use-eb-environment.patch', + 'Block-1.5.3_replace_mpi_cxx_binds_with_boost_mpi.patch', + 'Block-1.5.3_resolve_deprecated_Bind_placeholder.patch' +] +checksums = [ + {'1.5.3-20200525.tar.gz': '8d793c5e460d7747a0adcb06ce4b457c6750cf2d42cead1d060db8b44643c3b1'}, + {'Block-1.5.3_use-eb-environment.patch': '7f3e8a52f28d251441d20dfde1f9cb8cdc0c34216defab61cc6980e540a6cf60'}, + {'Block-1.5.3_replace_mpi_cxx_binds_with_boost_mpi.patch': + 'f53f1f88cb7b12ab38d1313f93a9bbd31c745dca1beca7a8d51d00e0ae4e762f'}, + {'Block-1.5.3_resolve_deprecated_Bind_placeholder.patch': + '51d692f294e800e0a9e027ef35bf761612ecb9efe77ddb378ec973b55e39a1e8'}, +] + +dependencies = [ + ('Boost.MPI', '1.82.0'), +] + +buildopts = [ + # Multi-threaded build (block.spin_adapted-serial) + 'OPENMP="yes" EXECUTABLE="block.spin_adapted-serial"', + # MPI build (block.spin_adapted) + 'USE_MPI="yes"', +] + +files_to_copy = [(['block.spin_adapted*'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/block.spin_adapted', 'bin/block.spin_adapted-serial'], + 'dirs': [], +} + +sanity_check_commands = [ + "block.spin_adapted-serial --version", + "%(mpi_cmd_prefix)s block.spin_adapted --version", +] + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/b/Boost.MPI/Boost.MPI-1.83.0-gompi-2023b.eb b/easybuild/easyconfigs/b/Boost.MPI/Boost.MPI-1.83.0-gompi-2023b.eb new file mode 100644 index 00000000000..2378bf71abb --- /dev/null +++ b/easybuild/easyconfigs/b/Boost.MPI/Boost.MPI-1.83.0-gompi-2023b.eb @@ -0,0 +1,29 @@ +easyblock = 'EB_Boost' + +name = 'Boost.MPI' +version = '1.83.0' + +homepage = 'https://www.boost.org/' +description = """Boost provides free peer-reviewed portable C++ source libraries.""" + +toolchain = {'name': 'gompi', 'version': '2023b'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://boostorg.jfrog.io/artifactory/main/release/%(version)s/source/'] +sources = ['boost_%s.tar.gz' % '_'.join(version.split('.'))] +checksums = ['c0685b68dd44cc46574cce86c4e17c0f611b15e195be9848dfd0769a0a207628'] + +dependencies = [ + ('bzip2', '1.0.8'), + ('zlib', '1.2.13'), + ('XZ', '5.4.4'), + ('zstd', '1.5.5'), + ('ICU', '74.1'), +] + +configopts = '--without-libraries=python' + +boost_mpi = True +tagged_layout = True + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/Boost.Python/Boost.Python-1.82.0-GCC-12.3.0.eb b/easybuild/easyconfigs/b/Boost.Python/Boost.Python-1.82.0-GCC-12.3.0.eb new file mode 100644 index 00000000000..ee38c6983cd --- /dev/null +++ b/easybuild/easyconfigs/b/Boost.Python/Boost.Python-1.82.0-GCC-12.3.0.eb @@ -0,0 +1,24 @@ +easyblock = 'EB_Boost' + +name = 'Boost.Python' +version = '1.82.0' + +homepage = 'https://boostorg.github.io/python' +description = """Boost.Python is a C++ library which enables seamless interoperability between C++ + and the Python programming language.""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://boostorg.jfrog.io/artifactory/main/release/%(version)s/source/'] +sources = ['boost_1_82_0.tar.gz'] +checksums = ['66a469b6e608a51f8347236f4912e27dc5c60c60d7d53ae9bfe4683316c6f04c'] + +dependencies = [ + ('Boost', version), + ('Python', '3.11.3'), +] + +only_python_bindings = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.55.0-GCC-11.2.0.eb b/easybuild/easyconfigs/b/Boost/Boost-1.55.0-GCC-11.2.0.eb new file mode 100644 index 00000000000..1814c8648e9 --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.55.0-GCC-11.2.0.eb @@ -0,0 +1,21 @@ +name = 'Boost' +version = '1.55.0' + +homepage = 'http://www.boost.org/' +description = """Boost provides free peer-reviewed portable C++ source libraries.""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] +checksums = ['19c4305cd6669f2216260258802a7abc73c1624758294b2cad209d45cc13a767'] + +dependencies = [ + ('bzip2', '1.0.8'), + ('zlib', '1.2.11'), +] + +configopts = '--without-libraries=python' + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.55.0-GCC-12.3.0.eb b/easybuild/easyconfigs/b/Boost/Boost-1.55.0-GCC-12.3.0.eb new file mode 100644 index 00000000000..e7cdaf16fbd --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.55.0-GCC-12.3.0.eb @@ -0,0 +1,21 @@ +name = 'Boost' +version = '1.55.0' + +homepage = 'http://www.boost.org/' +description = """Boost provides free peer-reviewed portable C++ source libraries.""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] +checksums = ['19c4305cd6669f2216260258802a7abc73c1624758294b2cad209d45cc13a767'] + +dependencies = [ + ('bzip2', '1.0.8'), + ('zlib', '1.2.13'), +] + +configopts = '--without-libraries=python' + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.75.0-GCC-12.3.0.eb b/easybuild/easyconfigs/b/Boost/Boost-1.75.0-GCC-12.3.0.eb new file mode 100644 index 00000000000..9e6080cae87 --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.75.0-GCC-12.3.0.eb @@ -0,0 +1,28 @@ +name = 'Boost' +version = '1.75.0' + +homepage = 'https://www.boost.org/' +description = """Boost provides free peer-reviewed portable C++ source libraries.""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://boostorg.jfrog.io/artifactory/main/release/%(version)s/source/'] +sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] +checksums = ['aeb26f80e80945e82ee93e5939baebdca47b9dee80a07d3144be1e1a6a66dd6a'] + +dependencies = [ + ('bzip2', '1.0.8'), + ('zlib', '1.2.13'), + ('XZ', '5.4.2'), + ('zstd', '1.5.5'), + ('ICU', '73.2'), +] + +configopts = '--without-libraries=python,mpi' + +# disable MPI, build Boost libraries with tagged layout +boost_mpi = False +tagged_layout = True + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.85.0-GCC-13.3.0.eb b/easybuild/easyconfigs/b/Boost/Boost-1.85.0-GCC-13.3.0.eb new file mode 100644 index 00000000000..10518dc36a3 --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.85.0-GCC-13.3.0.eb @@ -0,0 +1,31 @@ +## +# Authors:: Denis Kristak +## +name = 'Boost' +version = '1.85.0' + +homepage = 'https://www.boost.org/' +description = """Boost provides free peer-reviewed portable C++ source libraries.""" + +toolchain = {'name': 'GCC', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://boostorg.jfrog.io/artifactory/main/release/%(version)s/source/'] +sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] +checksums = ['be0d91732d5b0cc6fbb275c7939974457e79b54d6f07ce2e3dfdd68bef883b0b'] + +dependencies = [ + ('bzip2', '1.0.8'), + ('zlib', '1.3.1'), + ('XZ', '5.4.5'), + ('zstd', '1.5.6'), + ('ICU', '75.1'), +] + +configopts = '--without-libraries=python,mpi' + +# disable MPI, build Boost libraries with tagged layout +boost_mpi = False +tagged_layout = True + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/Bowtie/Bowtie-1.3.1-GCC-12.2.0.eb b/easybuild/easyconfigs/b/Bowtie/Bowtie-1.3.1-GCC-12.2.0.eb new file mode 100644 index 00000000000..202b84a2953 --- /dev/null +++ b/easybuild/easyconfigs/b/Bowtie/Bowtie-1.3.1-GCC-12.2.0.eb @@ -0,0 +1,30 @@ +## +# This is a contribution from DeepThought HPC Service, Flinders University, Adelaide, Australia +# Homepage: https://staff.flinders.edu.au/research/deep-thought +# +# Authors:: Robert Qiao +# License:: Artistic v2.0 +# +# Notes:: +## + +name = 'Bowtie' +version = '1.3.1' + +homepage = 'http://bowtie-bio.sourceforge.net/index.shtml' +description = """Bowtie is an ultrafast, memory-efficient short read aligner. + It aligns short DNA sequences (reads) to the human genome.""" + +toolchain = {'name': 'GCC', 'version': '12.2.0'} +toolchainopts = {'pic': True, 'cstd': 'gnu++98'} + +source_urls = ['https://sourceforge.net/projects/bowtie-bio/files/bowtie/%(version)s/'] +sources = ['%(namelower)s-%(version)s-src.zip'] +checksums = ['e23517aa53846ef828172be911750cd05748522117efcbbe5a36f3241fb40761'] + +dependencies = [ + ('tbb', '2021.9.0'), + ('zlib', '1.2.12'), +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/Bowtie/Bowtie-1.3.1-GCC-12.3.0.eb b/easybuild/easyconfigs/b/Bowtie/Bowtie-1.3.1-GCC-12.3.0.eb new file mode 100644 index 00000000000..9617ba2e343 --- /dev/null +++ b/easybuild/easyconfigs/b/Bowtie/Bowtie-1.3.1-GCC-12.3.0.eb @@ -0,0 +1,30 @@ +## +# This is a contribution from DeepThought HPC Service, Flinders University, Adelaide, Australia +# Homepage: https://staff.flinders.edu.au/research/deep-thought +# +# Authors:: Robert Qiao +# License:: Artistic v2.0 +# +# Notes:: +## + +name = 'Bowtie' +version = '1.3.1' + +homepage = 'http://bowtie-bio.sourceforge.net/index.shtml' +description = """Bowtie is an ultrafast, memory-efficient short read aligner. + It aligns short DNA sequences (reads) to the human genome.""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} +toolchainopts = {'pic': True, 'cstd': 'gnu++98'} + +source_urls = ['https://sourceforge.net/projects/bowtie-bio/files/bowtie/%(version)s/'] +sources = ['%(namelower)s-%(version)s-src.zip'] +checksums = ['e23517aa53846ef828172be911750cd05748522117efcbbe5a36f3241fb40761'] + +dependencies = [ + ('tbb', '2021.11.0'), + ('zlib', '1.2.13'), +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/Braindecode/Braindecode-0.8.1-foss-2023a-PyTorch-2.1.2-CUDA-12.1.1.eb b/easybuild/easyconfigs/b/Braindecode/Braindecode-0.8.1-foss-2023a-PyTorch-2.1.2-CUDA-12.1.1.eb new file mode 100644 index 00000000000..80012266f49 --- /dev/null +++ b/easybuild/easyconfigs/b/Braindecode/Braindecode-0.8.1-foss-2023a-PyTorch-2.1.2-CUDA-12.1.1.eb @@ -0,0 +1,47 @@ +easyblock = 'PythonBundle' + +name = 'Braindecode' +version = '0.8.1' +local_torch_version = '2.1.2' +versionsuffix = '-PyTorch-' + local_torch_version + '-CUDA-%(cudaver)s' + +homepage = 'https://braindecode.org/' +description = """Braindecode is an open-source Python toolbox for decoding raw +electrophysiological brain data with deep learning models. It includes dataset +fetchers, data preprocessing and visualization tools, as well as +implementations of several deep learning architectures and data augmentations +for analysis of EEG, ECoG and MEG.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('CUDA', '12.1.1', '', SYSTEM), + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('einops', '0.7.0'), + ('h5py', '3.9.0'), + ('matplotlib', '3.7.2'), + ('MNE-Python', '1.6.1'), + ('MOABB', '1.0.0'), + ('skorch', '0.15.0', versionsuffix), +] + +use_pip = True + +exts_list = [ + ('docstring-inheritance', '2.1.2', { + 'modulename': 'docstring_inheritance', + 'checksums': ['ac9af95a7b06a305d43720274d0e62523d23f835bf94ce2bb814687e6fe3957b'], + }), + ('torchinfo', '1.8.0', { + 'checksums': ['72e94b0e9a3e64dc583a8e5b7940b8938a1ac0f033f795457f27e6f4e7afa2e9'], + }), + ('braindecode', version, { + 'use_pip_extras': 'moabb', + 'checksums': ['e80515c3d20a80f16800770936d1eb0012de15830a8175dce376256bdaf928e7'], + }), +] + +sanity_pip_check = True + +moduleclass = 'ai' diff --git a/easybuild/easyconfigs/b/Brotli-python/Brotli-python-1.0.9-GCCcore-12.3.0.eb b/easybuild/easyconfigs/b/Brotli-python/Brotli-python-1.0.9-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..48f717c030a --- /dev/null +++ b/easybuild/easyconfigs/b/Brotli-python/Brotli-python-1.0.9-GCCcore-12.3.0.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonPackage' + +name = 'Brotli-python' +version = '1.0.9' + +homepage = 'https://github.com/google/brotli' +description = """Brotli is a generic-purpose lossless compression algorithm that compresses data using a combination + of a modern variant of the LZ77 algorithm, Huffman coding and 2nd order context modeling, with a compression ratio + comparable to the best currently available general-purpose compression methods. It is similar in speed with deflate + but offers more dense compression. +The specification of the Brotli Compressed Data Format is defined in RFC 7932.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://pypi.python.org/packages/source/B/Brotli'] +sources = ['Brotli-%(version)s.zip'] +checksums = ['4d1b810aa0ed773f81dceda2cc7b403d01057458730e309856356d4ef4188438'] + +builddependencies = [ + ('binutils', '2.40'), +] + +dependencies = [ + ('Brotli', '1.0.9'), + ('Python', '3.11.3'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +options = {'modulename': 'brotli'} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/Brotli/Brotli-1.1.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/b/Brotli/Brotli-1.1.0-GCCcore-13.2.0.eb index eeacd739652..2e194e0d508 100644 --- a/easybuild/easyconfigs/b/Brotli/Brotli-1.1.0-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/b/Brotli/Brotli-1.1.0-GCCcore-13.2.0.eb @@ -21,8 +21,11 @@ builddependencies = [ ('CMake', '3.27.6'), ] +configopts = ['-DBUILD_SHARED_LIBS=ON', '-DBUILD_SHARED_LIBS=OFF'] + sanity_check_paths = { - 'files': ['bin/brotli', 'lib/libbrotlidec.%s' % SHLIB_EXT, 'lib/libbrotlienc.%s' % SHLIB_EXT], + 'files': ['bin/brotli', 'lib/libbrotlidec.%s' % SHLIB_EXT, 'lib/libbrotlienc.%s' % SHLIB_EXT, + 'lib/libbrotlidec.a', 'lib/libbrotlienc.a'], 'dirs': [], } diff --git a/easybuild/easyconfigs/b/Brotli/Brotli-1.1.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/b/Brotli/Brotli-1.1.0-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..fe7258a493f --- /dev/null +++ b/easybuild/easyconfigs/b/Brotli/Brotli-1.1.0-GCCcore-13.3.0.eb @@ -0,0 +1,34 @@ +easyblock = 'CMakeMake' + +name = 'Brotli' +version = '1.1.0' + +homepage = 'https://github.com/google/brotli' +description = """Brotli is a generic-purpose lossless compression algorithm that compresses data using a combination + of a modern variant of the LZ77 algorithm, Huffman coding and 2nd order context modeling, with a compression ratio + comparable to the best currently available general-purpose compression methods. It is similar in speed with deflate + but offers more dense compression. +The specification of the Brotli Compressed Data Format is defined in RFC 7932.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://github.com/google/brotli/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['e720a6ca29428b803f4ad165371771f5398faba397edf6778837a18599ea13ff'] + +builddependencies = [ + ('binutils', '2.42'), + ('CMake', '3.29.3'), +] + +configopts = ['-DBUILD_SHARED_LIBS=ON', '-DBUILD_SHARED_LIBS=OFF'] + +sanity_check_paths = { + 'files': ['bin/brotli', 'lib/libbrotlidec.%s' % SHLIB_EXT, 'lib/libbrotlienc.%s' % SHLIB_EXT, + 'lib/libbrotlidec.a', 'lib/libbrotlienc.a'], + 'dirs': [], +} + +sanity_check_commands = ["brotli --help"] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-10.2.0.eb index 22f38cbf5f9..9e505b4df5e 100644 --- a/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-10.2.0.eb @@ -21,7 +21,6 @@ builddependencies = [ dependencies = [ ('Brotli', '1.0.9'), - ('Highway', '0.12.2'), ] # skip use of third_party directory, since we provide Brotli via a proper dependency diff --git a/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-10.3.0.eb b/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-10.3.0.eb index 301194a32a4..0661abf0609 100644 --- a/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-10.3.0.eb @@ -22,7 +22,6 @@ builddependencies = [ dependencies = [ ('Brotli', '1.0.9'), - ('Highway', '0.12.2'), ] # skip use of third_party directory, since we provide Brotli via a proper dependency diff --git a/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-11.3.0.eb index 7522f1025e3..57bba400bde 100644 --- a/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-11.3.0.eb @@ -22,7 +22,6 @@ builddependencies = [ dependencies = [ ('Brotli', '1.0.9'), - ('Highway', '1.0.3'), ] # skip use of third_party directory, since we provide Brotli via a proper dependency diff --git a/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-12.2.0.eb index cc914cae6cd..df29a7bda20 100644 --- a/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-12.2.0.eb @@ -22,7 +22,6 @@ builddependencies = [ dependencies = [ ('Brotli', '1.0.9'), - ('Highway', '1.0.3'), ] # skip use of third_party directory, since we provide Brotli via a proper dependency diff --git a/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-12.3.0.eb index 22917f651e9..42e15bb4356 100644 --- a/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-12.3.0.eb @@ -22,7 +22,6 @@ builddependencies = [ dependencies = [ ('Brotli', '1.0.9'), - ('Highway', '1.0.4'), ] # skip use of third_party directory, since we provide Brotli via a proper dependency diff --git a/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-13.2.0.eb b/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..6481ba231cd --- /dev/null +++ b/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-13.2.0.eb @@ -0,0 +1,53 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +# update: Thomas Hoffmann (EMBL) +easyblock = 'CMakeMake' + +name = 'Brunsli' +version = '0.1' + +homepage = 'https://github.com/google/brunsli/' +description = """Brunsli is a lossless JPEG repacking library.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://github.com/google/brunsli/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['62762dc740f9fcc9706449c078f12c2a366416486d2882be50a9f201f99ac0bc'] + +builddependencies = [ + ('CMake', '3.27.6'), + ('binutils', '2.40'), +] + +dependencies = [ + ('Brotli', '1.1.0'), +] + +# skip use of third_party directory, since we provide Brotli via a proper dependency +preconfigopts = "sed -i 's/add_subdirectory(third_party)//g' ../brunsli-%(version)s/CMakeLists.txt && " +preconfigopts += "sed -i 's/\\(brotli...\\)-static/\\1/g' ../brunsli-%(version)s/brunsli.cmake && " + +configopts = '-DCMAKE_CXX_FLAGS="$CXXFLAGS -lbrotlienc -lbrotlidec -lbrotlicommon" ' + +# make sure that libraries end up in /lib (not lib64) +configopts += "-DCMAKE_INSTALL_LIBDIR=lib " + +buildopts = "BROTLI_DIR=$EBROOTBROTLI BROTLI_INCLUDE=$EBROOTBROTLI/include" + +# also install dbrunsli binary and missing libraries +postinstallcmds = [ + "mkdir %(installdir)s/bin", + "cp dbrunsli %(installdir)s/bin/", + "cp libbrunsli*.a %(installdir)s/lib/", + "cp libbrunsli*.%s %%(installdir)s/lib/" % SHLIB_EXT, +] + +sanity_check_paths = { + 'files': ['bin/dbrunsli'], + 'dirs': ['include/brunsli', 'lib'], +} + +sanity_check_commands = ['dbrunsli 2>&1 | grep Usage'] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..3afc7fffd75 --- /dev/null +++ b/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-13.3.0.eb @@ -0,0 +1,53 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +# update: Thomas Hoffmann (EMBL) +easyblock = 'CMakeMake' + +name = 'Brunsli' +version = '0.1' + +homepage = 'https://github.com/google/brunsli/' +description = """Brunsli is a lossless JPEG repacking library.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://github.com/google/brunsli/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['62762dc740f9fcc9706449c078f12c2a366416486d2882be50a9f201f99ac0bc'] + +builddependencies = [ + ('CMake', '3.29.3'), + ('binutils', '2.42'), +] + +dependencies = [ + ('Brotli', '1.1.0'), +] + +# skip use of third_party directory, since we provide Brotli via a proper dependency +preconfigopts = "sed -i 's/add_subdirectory(third_party)//g' ../brunsli-%(version)s/CMakeLists.txt && " +preconfigopts += "sed -i 's/\\(brotli...\\)-static/\\1/g' ../brunsli-%(version)s/brunsli.cmake && " + +configopts = '-DCMAKE_CXX_FLAGS="$CXXFLAGS -lbrotlienc -lbrotlidec -lbrotlicommon" ' + +# make sure that libraries end up in /lib (not lib64) +configopts += "-DCMAKE_INSTALL_LIBDIR=lib " + +buildopts = "BROTLI_DIR=$EBROOTBROTLI BROTLI_INCLUDE=$EBROOTBROTLI/include" + +# also install dbrunsli binary and missing libraries +postinstallcmds = [ + "mkdir %(installdir)s/bin", + "cp dbrunsli %(installdir)s/bin/", + "cp libbrunsli*.a %(installdir)s/lib/", + "cp libbrunsli*.%s %%(installdir)s/lib/" % SHLIB_EXT, +] + +sanity_check_paths = { + 'files': ['bin/dbrunsli'], + 'dirs': ['include/brunsli', 'lib'], +} + +sanity_check_commands = ['dbrunsli 2>&1 | grep Usage'] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/b/bakta/bakta-1.10.1-foss-2023b.eb b/easybuild/easyconfigs/b/bakta/bakta-1.10.1-foss-2023b.eb new file mode 100644 index 00000000000..89703e6caf7 --- /dev/null +++ b/easybuild/easyconfigs/b/bakta/bakta-1.10.1-foss-2023b.eb @@ -0,0 +1,69 @@ +easyblock = 'PythonBundle' + +name = 'bakta' +version = '1.10.1' + +homepage = "https://github.com/oschwengers/bakta" +description = """Bakta is a tool for the rapid & standardized annotation of bacterial genomes and plasmids + from both isolates and MAGs. It provides dbxref-rich, sORF-including and taxon-independent annotations + in machine-readable JSON & bioinformatics standard file formats for automated downstream analysis.""" + +toolchain = {'name': 'foss', 'version': '2023b'} + +builddependencies = [ + ('scikit-build-core', '0.9.3'), +] + +dependencies = [ + ('Python', '3.11.5'), + ('Biopython', '1.84'), + ('PyYAML', '6.0.1'), + ('PyHMMER', '0.10.15'), + ('matplotlib', '3.8.2'), + ('python-isal', '1.6.1'), + ('zlib-ng', '2.2.2'), + ('archspec', '0.2.2'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('about_time', '4.2.1', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['8bbf4c75fe13cbd3d72f49a03b02c5c7dca32169b6d49117c257e7eb3eaee341'], + }), + ('grapheme', '0.6.0', { + 'checksums': ['44c2b9f21bbe77cfb05835fec230bd435954275267fea1858013b102f8603cca'], + }), + ('alive_progress', '3.2.0', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['0677929f8d3202572e9d142f08170b34dbbe256cc6d2afbf75ef187c7da964a8'], + }), + ('pyCirclize', '1.7.1', { + 'source_tmpl': SOURCELOWER_PY3_WHL, + 'checksums': ['e0c049877b1ee47245866cc9968f2aded5fe3ead8a3333841536dc29fd14bc90'], + }), + ('pyrodigal', '3.6.3', { + 'checksums': ['3e226f743c960d4d30c46ae6868aff7e2a6b98f8d837cfbd2637568569b21f78'], + }), + ('xopen', '2.0.2', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['74e7f7fb7e7f42bd843c798595fa5a52086d7d1bf3de0e8513c6615516431313'], + }), + (name, version, { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['82967b4eefd2a1084743211fe955fa394972c2d2c878c6682e00b13dabc5a445'], + }), +] + +local_bins = ['bakta', 'bakta_db', 'bakta_io', 'bakta_plot', 'bakta_proteins'] + +sanity_check_paths = { + 'files': ['bin/%s' % bin for bin in local_bins], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ['%s --help' % bin for bin in local_bins] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/bamtofastq/bamtofastq-1.4.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/b/bamtofastq/bamtofastq-1.4.1-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..8759374058b --- /dev/null +++ b/easybuild/easyconfigs/b/bamtofastq/bamtofastq-1.4.1-GCCcore-12.3.0.eb @@ -0,0 +1,220 @@ +easyblock = 'Cargo' + +name = 'bamtofastq' +version = '1.4.1' + +homepage = 'https://github.com/10XGenomics/bamtofastq' +description = """Convert 10x BAM files to the original FASTQs compatible with 10x pipelines.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://github.com/10XGenomics/bamtofastq/archive/refs/tags'] +sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}] + +builddependencies = [ + ('binutils', '2.40'), + ('Rust', '1.75.0'), + ('CMake', '3.26.3'), +] + +dependencies = [('bzip2', '1.0.8')] + +crates = [ + ('addr2line', '0.17.0'), + ('adler', '1.0.2'), + ('aho-corasick', '0.7.18'), + ('anyhow', '1.0.53'), + ('autocfg', '1.0.1'), + ('backtrace', '0.3.63'), + ('bincode', '1.3.3'), 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b/easybuild/easyconfigs/b/bayesian-optimization/bayesian-optimization-1.5.1-foss-2023a.eb new file mode 100644 index 00000000000..8215f2c822a --- /dev/null +++ b/easybuild/easyconfigs/b/bayesian-optimization/bayesian-optimization-1.5.1-foss-2023a.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonBundle' + +name = 'bayesian-optimization' +version = '1.5.1' + +homepage = 'https://bayesian-optimization.github.io/BayesianOptimization/index.html' +description = "Pure Python implementation of bayesian global optimization with gaussian processes." + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('scikit-learn', '1.3.1'), + ('SciPy-bundle', '2023.07'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('colorama', '0.4.6', { + 'source_tmpl': SOURCE_WHL, + 'checksums': ['4f1d9991f5acc0ca119f9d443620b77f9d6b33703e51011c16baf57afb285fc6'], + }), + ('bayesian_optimization', version, { + 'source_tmpl': SOURCE_PY3_WHL, + 'modulename': 'bayes_opt', + 'checksums': ['098946c933d6039073b7ccb0c9f1b4c73ac6e39350043b02e5243b08583c4c5c'], + }), +] + +sanity_check_commands = ["python -c 'from bayes_opt import BayesianOptimization'"] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/b/bcl-convert/bcl-convert-4.2.7-2el7.x86_64.eb b/easybuild/easyconfigs/b/bcl-convert/bcl-convert-4.2.7-2el7.x86_64.eb new file mode 100644 index 00000000000..dfed34de942 --- /dev/null +++ b/easybuild/easyconfigs/b/bcl-convert/bcl-convert-4.2.7-2el7.x86_64.eb @@ -0,0 +1,26 @@ +easyblock = 'Rpm' + +name = 'bcl-convert' +version = '4.2.7-2' +versionsuffix = 'el7.x86_64' + +homepage = 'https://support.illumina.com/sequencing/sequencing_software/bcl-convert.html' +description = """The Illumina BCL Convert v4.0 is a standalone local software app that converts the + Binary Base Call (BCL) files produced by Illumina sequencing systems to FASTQ files.""" + +toolchain = SYSTEM + +builddependencies = [('rpmrebuild', '2.18')] + +source_urls = ['https://webdata.illumina.com/downloads/software/bcl-convert/'] +sources = ['bcl-convert-%(version)s.%(versionsuffix)s.rpm'] +checksums = ['ea508d763dc27d30d1a34f6a38d8da31ea67797d7b4971e8c10677bc48539565'] + +sanity_check_paths = { + 'files': ['usr/bin/bcl-convert'], + 'dirs': [], +} + +sanity_check_commands = ["bcl-convert --help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/bcrypt/bcrypt-4.1.3-GCCcore-13.2.0.eb b/easybuild/easyconfigs/b/bcrypt/bcrypt-4.1.3-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..cbada951cfd --- /dev/null +++ b/easybuild/easyconfigs/b/bcrypt/bcrypt-4.1.3-GCCcore-13.2.0.eb @@ -0,0 +1,147 @@ +easyblock = 'CargoPythonPackage' + +name = 'bcrypt' +version = '4.1.3' + +homepage = 'https://github.com/pyca/bcrypt/' +description = """Acceptable password hashing for your software and your servers (but you should +really use argon2id or scrypt) +""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} +toolchainopts = {'pic': True} + + 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{'unicode-ident-1.0.12.tar.gz': '3354b9ac3fae1ff6755cb6db53683adb661634f67557942dea4facebec0fee4b'}, + {'unindent-0.2.3.tar.gz': 'c7de7d73e1754487cb58364ee906a499937a0dfabd86bcb980fa99ec8c8fa2ce'}, + {'version_check-0.9.4.tar.gz': '49874b5167b65d7193b8aba1567f5c7d93d001cafc34600cee003eda787e483f'}, + {'wasi-0.11.0+wasi-snapshot-preview1.tar.gz': '9c8d87e72b64a3b4db28d11ce29237c246188f4f51057d65a7eab63b7987e423'}, + {'windows-targets-0.52.5.tar.gz': '6f0713a46559409d202e70e28227288446bf7841d3211583a4b53e3f6d96e7eb'}, + {'windows_aarch64_gnullvm-0.52.5.tar.gz': '7088eed71e8b8dda258ecc8bac5fb1153c5cffaf2578fc8ff5d61e23578d3263'}, + {'windows_aarch64_msvc-0.52.5.tar.gz': '9985fd1504e250c615ca5f281c3f7a6da76213ebd5ccc9561496568a2752afb6'}, + {'windows_i686_gnu-0.52.5.tar.gz': '88ba073cf16d5372720ec942a8ccbf61626074c6d4dd2e745299726ce8b89670'}, + {'windows_i686_gnullvm-0.52.5.tar.gz': '87f4261229030a858f36b459e748ae97545d6f1ec60e5e0d6a3d32e0dc232ee9'}, + {'windows_i686_msvc-0.52.5.tar.gz': 'db3c2bf3d13d5b658be73463284eaf12830ac9a26a90c717b7f771dfe97487bf'}, + {'windows_x86_64_gnu-0.52.5.tar.gz': '4e4246f76bdeff09eb48875a0fd3e2af6aada79d409d33011886d3e1581517d9'}, + {'windows_x86_64_gnullvm-0.52.5.tar.gz': '852298e482cd67c356ddd9570386e2862b5673c85bd5f88df9ab6802b334c596'}, + {'windows_x86_64_msvc-0.52.5.tar.gz': 'bec47e5bfd1bff0eeaf6d8b485cc1074891a197ab4225d504cb7a1ab88b02bf0'}, + {'zeroize-1.7.0.tar.gz': '525b4ec142c6b68a2d10f01f7bbf6755599ca3f81ea53b8431b7dd348f5fdb2d'}, +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/beagle-lib/beagle-lib-4.0.1-GCC-12.3.0-CUDA-12.1.1.eb b/easybuild/easyconfigs/b/beagle-lib/beagle-lib-4.0.1-GCC-12.3.0-CUDA-12.1.1.eb new file mode 100644 index 00000000000..2c2bbf6705b --- /dev/null +++ b/easybuild/easyconfigs/b/beagle-lib/beagle-lib-4.0.1-GCC-12.3.0-CUDA-12.1.1.eb @@ -0,0 +1,35 @@ +easyblock = 'CMakeMake' + +name = 'beagle-lib' +version = '4.0.1' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/beagle-dev/beagle-lib' +description = """beagle-lib is a high-performance library that can perform the core calculations at the heart of most + Bayesian and Maximum Likelihood phylogenetics packages.""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +source_urls = ['https://github.com/beagle-dev/beagle-lib/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['9d258cd9bedd86d7c28b91587acd1132f4e01d4f095c657ad4dc93bd83d4f120'] + +dependencies = [ + ('Java', '11', '', SYSTEM), + ('CUDA', '12.1.1', '', SYSTEM), +] + +builddependencies = [ + ('CMake', '3.26.3'), + ('pkgconf', '1.9.5'), +] + +configopts = '-DBUILD_CUDA=ON ' + +sanity_check_paths = { + 'files': ["include/libhmsbeagle-1/libhmsbeagle/%s" % x for x in ["beagle.h", "platform.h"]] + + ["lib/libhmsbeagle%s.%s" % (x, SHLIB_EXT) for x in ["-cpu", "-cpu-sse", "-jni", ""]], + 'dirs': [] +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.42-GCCcore-13.3.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.42-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..7a10c5ed2bc --- /dev/null +++ b/easybuild/easyconfigs/b/binutils/binutils-2.42-GCCcore-13.3.0.eb @@ -0,0 +1,31 @@ +name = 'binutils' +version = '2.42' + +homepage = 'https://directory.fsf.org/project/binutils/' +description = "binutils: GNU binary utilities" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['5d2a6c1d49686a557869caae08b6c2e83699775efd27505e01b2f4db1a024ffc'] + +builddependencies = [ + ('flex', '2.6.4'), + ('Bison', '3.8.2'), + # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils + ('binutils', version, '', SYSTEM) +] + +dependencies = [ + # zlib is a runtime dep to avoid that it gets embedded in libbfd.so, + # see https://github.com/easybuilders/easybuild-easyblocks/issues/1350 + ('zlib', '1.3.1'), +] + +# avoid build failure when makeinfo command is not available +# see https://sourceware.org/bugzilla/show_bug.cgi?id=15345 +buildopts = 'MAKEINFO=true' +installopts = buildopts + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.42-GCCcore-14.2.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.42-GCCcore-14.2.0.eb new file mode 100644 index 00000000000..94b762d7803 --- /dev/null +++ b/easybuild/easyconfigs/b/binutils/binutils-2.42-GCCcore-14.2.0.eb @@ -0,0 +1,31 @@ +name = 'binutils' +version = '2.42' + +homepage = 'https://directory.fsf.org/project/binutils/' +description = "binutils: GNU binary utilities" + +toolchain = {'name': 'GCCcore', 'version': '14.2.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['5d2a6c1d49686a557869caae08b6c2e83699775efd27505e01b2f4db1a024ffc'] + +builddependencies = [ + ('flex', '2.6.4'), + ('Bison', '3.8.2'), + # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils + ('binutils', version, '', SYSTEM) +] + +dependencies = [ + # zlib is a runtime dep to avoid that it gets embedded in libbfd.so, + # see https://github.com/easybuilders/easybuild-easyblocks/issues/1350 + ('zlib', '1.3.1'), +] + +# avoid build failure when makeinfo command is not available +# see https://sourceware.org/bugzilla/show_bug.cgi?id=15345 +buildopts = 'MAKEINFO=true' +installopts = buildopts + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/biom-format/biom-format-2.1.16-foss-2023b.eb b/easybuild/easyconfigs/b/biom-format/biom-format-2.1.16-foss-2023b.eb new file mode 100644 index 00000000000..91d9cecbd99 --- /dev/null +++ b/easybuild/easyconfigs/b/biom-format/biom-format-2.1.16-foss-2023b.eb @@ -0,0 +1,49 @@ +## +# This is a contribution from DeepThought HPC Service, Flinders University, Adelaide, Australia +# Homepage: https://staff.flinders.edu.au/research/deep-thought +# +# Authors:: Robert Qiao +# License:: Revised BSD +# +# Notes:: updated by Kenneth Hoste (HPC-UGent) for foss/2021b +## +# Updated: Petr Král (INUITS) +# Updated: Lara Peeters (Ghent University) + +easyblock = 'PythonPackage' + +name = 'biom-format' +version = '2.1.16' + +homepage = 'https://biom-format.org' +description = """ +The BIOM file format (canonically pronounced biome) is designed to be + a general-use format for representing biological sample by observation + contingency tables. BIOM is a recognized standard for the Earth Microbiome + Project and is a Genomics Standards Consortium supported project. +""" + +toolchain = {'name': 'foss', 'version': '2023b'} +toolchainopts = {'usempi': True} + +sources = [SOURCE_TAR_GZ] +checksums = ['47f88d57a94ecaa4d06f3578ca394e78db6d12e46ab0886634743181e67dcfc9'] + +dependencies = [ + ('Python', '3.11.5'), + ('SciPy-bundle', '2023.11'), + ('h5py', '3.11.0'), +] + +use_pip = True +sanity_pip_check = True +download_dep_fail = True + +sanity_check_paths = { + 'files': ['bin/biom'], + 'dirs': ['lib'], +} + +options = {'modulename': 'biom'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/bitsandbytes/bitsandbytes-0.43.3-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/b/bitsandbytes/bitsandbytes-0.43.3-foss-2023a-CUDA-12.1.1.eb new file mode 100644 index 00000000000..8127a86c558 --- /dev/null +++ b/easybuild/easyconfigs/b/bitsandbytes/bitsandbytes-0.43.3-foss-2023a-CUDA-12.1.1.eb @@ -0,0 +1,49 @@ +easyblock = 'CMakeMake' + +name = 'bitsandbytes' +version = '0.43.3' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://huggingface.co/docs/bitsandbytes/main/en/index' +description = "bitsandbytes enables accessible large language models via k-bit quantization for PyTorch." +github_account = 'bitsandbytes-foundation' + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['7a468bc977da19c176cc578954bfd7a3c64182f387a6849e9f0a38d5cba1b4df'] + +builddependencies = [ + ('CMake', '3.26.3'), + ('pkgconf', '1.9.5'), +] + +dependencies = [ + ('CUDA', '12.1.1', '', SYSTEM), + ('Python', '3.11.3'), + ('PyTorch', '2.1.2', versionsuffix), + ('SciPy-bundle', '2023.07'), +] + +configopts = '-DCOMPUTE_BACKEND=cuda' +skipsteps = ['install'] + +postinstallcmds = [ + 'pip install --prefix=%(installdir)s --no-deps --ignore-installed --no-index --no-build-isolation %(start_dir)s', +] + +sanity_check_paths = { + 'files': ['lib/python%%(pyshortver)s/site-packages/bitsandbytes/libbitsandbytes_cuda121.%s' % SHLIB_EXT], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "python -c 'import bitsandbytes'", +] + +modextrapaths = { + 'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages'] +} + +moduleclass = 'ai' diff --git a/easybuild/easyconfigs/b/bitsandbytes/bitsandbytes-0.43.3-foss-2023a.eb b/easybuild/easyconfigs/b/bitsandbytes/bitsandbytes-0.43.3-foss-2023a.eb new file mode 100644 index 00000000000..8b360bb263b --- /dev/null +++ b/easybuild/easyconfigs/b/bitsandbytes/bitsandbytes-0.43.3-foss-2023a.eb @@ -0,0 +1,46 @@ +easyblock = 'CMakeMake' + +name = 'bitsandbytes' +version = '0.43.3' + +homepage = 'https://huggingface.co/docs/bitsandbytes/main/en/index' +description = "bitsandbytes enables accessible large language models via k-bit quantization for PyTorch." +github_account = 'bitsandbytes-foundation' + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['7a468bc977da19c176cc578954bfd7a3c64182f387a6849e9f0a38d5cba1b4df'] + +builddependencies = [ + ('CMake', '3.26.3'), + ('pkgconf', '1.9.5'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('PyTorch', '2.1.2'), + ('SciPy-bundle', '2023.07'), +] + +skipsteps = ['install'] + +postinstallcmds = [ + 'pip install --prefix=%(installdir)s --no-deps --ignore-installed --no-index --no-build-isolation %(start_dir)s', +] + +sanity_check_paths = { + 'files': ['lib/python%%(pyshortver)s/site-packages/bitsandbytes/libbitsandbytes_cpu.%s' % SHLIB_EXT], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "python -c 'import bitsandbytes'", +] + +modextrapaths = { + 'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages'] +} + +moduleclass = 'ai' diff --git a/easybuild/easyconfigs/b/bitshuffle/bitshuffle-0.5.1-foss-2023a.eb b/easybuild/easyconfigs/b/bitshuffle/bitshuffle-0.5.1-foss-2023a.eb new file mode 100644 index 00000000000..3faf7d3a1ee --- /dev/null +++ b/easybuild/easyconfigs/b/bitshuffle/bitshuffle-0.5.1-foss-2023a.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonBundle' + +name = 'bitshuffle' +version = '0.5.1' + +homepage = 'https://github.com/kiyo-masui/bitshuffle' +description = """ +Filter for improving compression of typed binary data. +Bitshuffle is an algorithm that rearranges typed, binary data for improving compression, as +well as a python/C package that implements this algorithm within the Numpy framework. +The library can be used along side HDF5 to compress and decompress datasets and is integrated +through the dynamically loaded filters framework. Bitshuffle is HDF5 filter number 32008. +""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('h5py', '3.9.0'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + (name, version, { + 'checksums': ['988f224739aa6858475a4c59172968c7b51cc657d2249580c8f96848708fbae3'], + }), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/b/bliss/bliss-0.77-GCC-13.2.0.eb b/easybuild/easyconfigs/b/bliss/bliss-0.77-GCC-13.2.0.eb new file mode 100644 index 00000000000..ec9a99bc306 --- /dev/null +++ b/easybuild/easyconfigs/b/bliss/bliss-0.77-GCC-13.2.0.eb @@ -0,0 +1,41 @@ +easyblock = 'CMakeMake' + +name = 'bliss' +version = '0.77' + +homepage = 'https://users.aalto.fi/~tjunttil/bliss/' +description = """Bliss is an open-source tool for computing canonical labelings and automorphism groups of graphs.""" + +toolchain = {'name': 'GCC', 'version': '13.2.0'} + +source_urls = ['https://users.aalto.fi/~tjunttil/bliss/downloads/'] +sources = [SOURCE_ZIP] +patches = ['bliss-0.77_install_fix.patch'] +checksums = [ + {'bliss-0.77.zip': 'acc8b98034f30fad24c897f365abd866c13d9f1bb207e398d0caf136875972a4'}, + {'bliss-0.77_install_fix.patch': '1550b6c7f8208f56093c0b6bf0d2e3df42afab81cd69eb70303515c9923e9513'}, +] + +builddependencies = [ + ('CMake', '3.27.6'), +] + +dependencies = [ + ('GMP', '6.3.0'), +] + +configopts = "-DUSE_GMP=ON " + +sanity_check_paths = { + 'files': [ + 'bin/bliss', + 'lib/libbliss.%s' % SHLIB_EXT, + ], + 'dirs': [ + 'include/%(name)s', + ], +} + +sanity_check_commands = ["bliss -help"] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/b/bliss/bliss-0.77_install_fix.patch b/easybuild/easyconfigs/b/bliss/bliss-0.77_install_fix.patch new file mode 100644 index 00000000000..faea2ad4daf --- /dev/null +++ b/easybuild/easyconfigs/b/bliss/bliss-0.77_install_fix.patch @@ -0,0 +1,33 @@ +Adds install commands to CMakeLists.txt +Source: https://gitlab.archlinux.org/archlinux/packaging/packages/bliss/-/blob/0.77-3/make-install.patch +diff -u CMakeLists.txt.orig CMakeLists.txt +--- CMakeLists.txt.orig 2021-02-18 11:59:34.000000000 +0100 ++++ CMakeLists.txt 2024-08-15 15:04:21.293765655 +0200 +@@ -62,3 +62,27 @@ + target_link_libraries(bliss-executable ${GMP_LIBRARIES}) + endif(USE_GMP) + set_target_properties(bliss-executable PROPERTIES OUTPUT_NAME bliss) ++ ++include(GNUInstallDirs) ++ ++set( ++ BLISS_HEADERS ++ src/bliss_C.h ++ src/uintseqhash.hh ++ src/abstractgraph.hh ++ src/stats.hh ++ src/digraph.hh ++ src/defs.hh ++ src/heap.hh ++ src/graph.hh ++ src/partition.hh ++ src/kqueue.hh ++ src/utils.hh ++ src/orbit.hh ++ src/timer.hh ++ src/bignum.hh ++) ++ ++install(TARGETS bliss-executable RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR}) ++install(TARGETS bliss LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR}) ++install(FILES ${BLISS_HEADERS} DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}/bliss) diff --git a/easybuild/easyconfigs/b/bokeh/bokeh-3.4.1-gfbf-2023b.eb b/easybuild/easyconfigs/b/bokeh/bokeh-3.4.1-gfbf-2023b.eb new file mode 100644 index 00000000000..58f15fcf3e9 --- /dev/null +++ b/easybuild/easyconfigs/b/bokeh/bokeh-3.4.1-gfbf-2023b.eb @@ -0,0 +1,50 @@ +easyblock = 'PythonBundle' + +name = 'bokeh' +version = '3.4.1' + +homepage = 'https://github.com/bokeh/bokeh' +description = "Statistical and novel interactive HTML plots for Python" + +toolchain = {'name': 'gfbf', 'version': '2023b'} + +builddependencies = [ + ('meson-python', '0.15.0'), +] + +dependencies = [ + ('Python', '3.11.5'), + ('Python-bundle-PyPI', '2023.10'), + ('SciPy-bundle', '2023.11'), + ('matplotlib', '3.8.2'), + ('PyYAML', '6.0.1'), + ('Pillow', '10.2.0'), + ('tornado', '6.4'), +] + +use_pip = True + +exts_list = [ + ('contourpy', '1.2.1', { + 'checksums': ['4d8908b3bee1c889e547867ca4cdc54e5ab6be6d3e078556814a22457f49423c'], + }), + ('xyzservices', '2024.4.0', { + 'checksums': ['6a04f11487a6fb77d92a98984cd107fbd9157fd5e65f929add9c3d6e604ee88c'], + }), + (name, version, { + # bokeh uses git tags to get version, so we'll instead inject the version into setup.py + 'preinstallopts': """sed -i 's/setup(/setup(version="%(version)s",/g' setup.py && """, + 'checksums': ['d824961e4265367b0750ce58b07e564ad0b83ca64b335521cd3421e9b9f10d89'], + }), +] + +sanity_check_paths = { + 'files': ['bin/bokeh'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["bokeh --help"] + +sanity_pip_check = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/bokeh/bokeh-3.6.0-gfbf-2024a.eb b/easybuild/easyconfigs/b/bokeh/bokeh-3.6.0-gfbf-2024a.eb new file mode 100644 index 00000000000..fadc3d201b6 --- /dev/null +++ b/easybuild/easyconfigs/b/bokeh/bokeh-3.6.0-gfbf-2024a.eb @@ -0,0 +1,49 @@ +easyblock = 'PythonBundle' + +name = 'bokeh' +version = '3.6.0' + +homepage = 'https://github.com/bokeh/bokeh' +description = "Statistical and novel interactive HTML plots for Python" + +toolchain = {'name': 'gfbf', 'version': '2024a'} + +builddependencies = [ + ('meson-python', '0.16.0'), +] + +dependencies = [ + ('Python', '3.12.3'), + ('Python-bundle-PyPI', '2024.06'), + ('SciPy-bundle', '2024.05'), + ('matplotlib', '3.9.2'), + ('PyYAML', '6.0.2'), + ('Pillow', '10.4.0'), + ('tornado', '6.4.1'), +] + +use_pip = True + +exts_list = [ + ('contourpy', '1.2.1', { + 'checksums': ['4d8908b3bee1c889e547867ca4cdc54e5ab6be6d3e078556814a22457f49423c'], + }), + ('xyzservices', '2024.4.0', { + 'checksums': ['6a04f11487a6fb77d92a98984cd107fbd9157fd5e65f929add9c3d6e604ee88c'], + }), + (name, version, { + 'preinstallopts': """sed -i 's/setup(/setup(version="%(version)s",/g' setup.py && """, + 'checksums': ['0032dc1e76ad097b07626e51584685ff48c65481fbaaad105663b1046165867a'], + }), +] + +sanity_check_paths = { + 'files': ['bin/bokeh'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["bokeh --help"] + +sanity_pip_check = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/boto3/boto3-1.35.36-GCCcore-13.3.0.eb b/easybuild/easyconfigs/b/boto3/boto3-1.35.36-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..4f327430573 --- /dev/null +++ b/easybuild/easyconfigs/b/boto3/boto3-1.35.36-GCCcore-13.3.0.eb @@ -0,0 +1,40 @@ +easyblock = 'PythonBundle' + +name = 'boto3' +version = '1.35.36' + +homepage = 'https://github.com/boto/boto3' +description = """Boto3 is the Amazon Web Services (AWS) Software Development Kit +(SDK) for Python, which allows Python developers to write software that makes +use of services like Amazon S3 and Amazon EC2.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +builddependencies = [ + ('binutils', '2.42'), +] + +dependencies = [ + ('Python', '3.12.3'), + ('Python-bundle-PyPI', '2024.06'), +] + +exts_list = [ + ('botocore', version, { + 'checksums': ['354ec1b766f0029b5d6ff0c45d1a0f9e5007b7d2f3ec89bcdd755b208c5bc797'], + }), + ('jmespath', '1.0.1', { + 'checksums': ['90261b206d6defd58fdd5e85f478bf633a2901798906be2ad389150c5c60edbe'], + }), + ('s3transfer', '0.10.3', { + 'checksums': ['4f50ed74ab84d474ce614475e0b8d5047ff080810aac5d01ea25231cfc944b0c'], + }), + (name, version, { + 'checksums': ['586524b623e4fbbebe28b604c6205eb12f263cc4746bccb011562d07e217a4cb'], + }), +] + +use_pip = True +sanity_pip_check = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/b/bwa-mem2/bwa-mem2-2.2.1-intel-compilers-2023.1.0.eb b/easybuild/easyconfigs/b/bwa-mem2/bwa-mem2-2.2.1-intel-compilers-2023.1.0.eb index 74c175b5994..e4edd8be316 100644 --- a/easybuild/easyconfigs/b/bwa-mem2/bwa-mem2-2.2.1-intel-compilers-2023.1.0.eb +++ b/easybuild/easyconfigs/b/bwa-mem2/bwa-mem2-2.2.1-intel-compilers-2023.1.0.eb @@ -15,10 +15,14 @@ toolchainopts = {'pic': True, 'oneapi': False} github_account = 'bwa-mem2' source_urls = [GITHUB_SOURCE] sources = ['v%(version)s.tar.gz'] -patches = ['%(name)s-%(version)s_use_external_deps.patch'] +patches = [ + 'bwa-mem2-%(version)s_use_external_deps.patch', + 'bwa-mem2-%(version)s_common_avx512_flags.patch', +] checksums = [ {'v2.2.1.tar.gz': '36ddd28ce7020d5a036ddeffa00e692296fd40c80380671bd4ea5757bd28841b'}, {'bwa-mem2-2.2.1_use_external_deps.patch': '0a9d7f7b3289029e19cf7dbab1778448097b9e0f92fa41a74a8cf81c9e114967'}, + {'bwa-mem2-2.2.1_common_avx512_flags.patch': '1a784bca167c6e3576a83c11715cbf6f8dced09d46021c0d283f7a1b185d6569'}, ] dependencies = [('safestringlib', '20240228')] diff --git a/easybuild/easyconfigs/b/bwa-mem2/bwa-mem2-2.2.1_common_avx512_flags.patch b/easybuild/easyconfigs/b/bwa-mem2/bwa-mem2-2.2.1_common_avx512_flags.patch new file mode 100644 index 00000000000..b7e55ecf1f1 --- /dev/null +++ b/easybuild/easyconfigs/b/bwa-mem2/bwa-mem2-2.2.1_common_avx512_flags.patch @@ -0,0 +1,15 @@ +Use common AVX512 flagset to increase compatibility of bwa-mem2.avx512bw binary +across platforms supporting AVX512 +see https://github.com/bwa-mem2/bwa-mem2/issues/236 +author: Alex Domingo (Vrije Universiteit Brussel) +--- Makefile.orig 2024-04-29 14:52:21.634066000 +0200 ++++ Makefile 2024-04-29 14:52:48.590282000 +0200 +@@ -76,7 +76,7 @@ + endif + else ifeq ($(arch),avx512) + ifeq ($(CXX), icpc) +- ARCH_FLAGS=-xCORE-AVX512 ++ ARCH_FLAGS=-march=common-avx512 #-xCORE-AVX512 + else + ARCH_FLAGS=-mavx512bw + endif diff --git a/easybuild/easyconfigs/b/byacc/byacc-2.0.20240109-GCCcore-13.3.0.eb b/easybuild/easyconfigs/b/byacc/byacc-2.0.20240109-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..fa57e4306e6 --- /dev/null +++ b/easybuild/easyconfigs/b/byacc/byacc-2.0.20240109-GCCcore-13.3.0.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'byacc' +version = '2.0.20240109' + +homepage = 'http://invisible-island.net/byacc/byacc.html' +description = """Berkeley Yacc (byacc) is generally conceded to be the best yacc variant available. + In contrast to bison, it is written to avoid dependencies upon a particular compiler. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://invisible-island.net/archives/byacc/'] +sources = ['byacc-%s.tgz' % version.split('.')[2]] +checksums = ['f2897779017189f1a94757705ef6f6e15dc9208ef079eea7f28abec577e08446'] + +builddependencies = [('binutils', '2.42')] + +sanity_check_paths = { + 'files': ["bin/yacc"], + 'dirs': [] +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.8-GCCcore-13.3.0.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.8-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..adb4b34a9bb --- /dev/null +++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.8-GCCcore-13.3.0.eb @@ -0,0 +1,27 @@ +name = 'bzip2' +version = '1.0.8' + +homepage = 'https://sourceware.org/bzip2' +description = """ + bzip2 is a freely available, patent free, high-quality data compressor. It + typically compresses files to within 10% to 15% of the best available + techniques (the PPM family of statistical compressors), whilst being around + twice as fast at compression and six times faster at decompression. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://sourceware.org/pub/%(name)s/'] +sources = [SOURCE_TAR_GZ] +patches = ['bzip2-%(version)s-pkgconfig.patch'] +checksums = [ + 'ab5a03176ee106d3f0fa90e381da478ddae405918153cca248e682cd0c4a2269', # bzip2-1.0.8.tar.gz + '9299e8ee4d014ea973777b6ea90661fe329dfa991f822add4c763ea9ddb9aab1', # bzip2-1.0.8-pkgconfig.patch +] + +builddependencies = [ + ('binutils', '2.42'), +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/c/CAMPARI/CAMPARI-4.0-foss-2023a.eb b/easybuild/easyconfigs/c/CAMPARI/CAMPARI-4.0-foss-2023a.eb new file mode 100644 index 00000000000..af659719245 --- /dev/null +++ b/easybuild/easyconfigs/c/CAMPARI/CAMPARI-4.0-foss-2023a.eb @@ -0,0 +1,54 @@ +easyblock = 'ConfigureMake' + +name = 'CAMPARI' +version = '4.0' +_date = '12202020' + +homepage = 'http://campari.sourceforge.net/V4/index.html' +description = """ +CAMPARI is a joint package for performing and analyzing molecular simulations, in particular of systems of biological +relevance. It focuses on a wide availability of algorithms for (advanced) sampling and is capable of combining Monte +Carlo and molecular dynamics in seamless fashion.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['campari_v%s_%s.zip' % (version.split('.')[0], _date)] +checksums = ['bc627fb286b5461a5c68aa3e1a551ecd81016495163685800163c734f7c4f1bd'] + +builddependencies = [ + ('Autotools', '20220317'), +] + +dependencies = [ + ('netCDF-Fortran', '4.6.1'), + ('libtirpc', '1.3.3'), +] + +start_dir = 'source' + +# remove hardcoded paths in configure script +preconfigopts = 'sed -i "s|/usr/share|$EBROOTAUTOMAKE/share|" configure &&' +# ignore default compiler settings and use EB build environment +local_fcflags = '$FCFLAGS -fallow-argument-mismatch $CPPFLAGS' +configopts = '--enable-compiler=ignore --with-trailing-user-fcflags="%s" ' % local_fcflags +configopts += '--enable-mpi=auto ' +configopts += 'LIBS="$LIBS $LIBFFT $LIBBLAS -ltirpc"' + +buildopts = 'all' + +maxparallel = 10 + +postinstallcmds = ['cp -a %(builddir)s/campari/{data,doc,examples,params,tools,LICENSE} %(installdir)s/'] + +_binaries = ['campari', 'campari_mpi', 'campari_mpi_threads', 'campari_threads', 'camp_ncminer', 'camp_ncminer_threads'] +_libraries = ['lcampari.a', 'lcampari_mpi.a', 'lcampari_mpi_threads.a', 'lcampari_threads.a', 'libxdrf.a'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in _binaries] + ['lib/%s' % x for x in _libraries], + 'dirs': [], +} + +sanity_check_commands = ['campari -h | grep "USAGE: CAMPARI"'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/CAMPARI/CAMPARI-4.0-intel-2023a.eb b/easybuild/easyconfigs/c/CAMPARI/CAMPARI-4.0-intel-2023a.eb index 203b4e4cd9f..743bf47a462 100644 --- a/easybuild/easyconfigs/c/CAMPARI/CAMPARI-4.0-intel-2023a.eb +++ b/easybuild/easyconfigs/c/CAMPARI/CAMPARI-4.0-intel-2023a.eb @@ -30,9 +30,10 @@ start_dir = 'source' # remove hardcoded paths in configure script preconfigopts = 'sed -i "s|/usr/share|$EBROOTAUTOMAKE/share|" configure &&' # ignore default compiler settings and use EB build environment -configopts = '--enable-compiler=ignore --with-trailing-user-fcflags="$FCFLAGS" ' +local_fcflags = '$FCFLAGS -fallow-argument-mismatch $CPPFLAGS' +configopts = '--enable-compiler=ignore --with-trailing-user-fcflags="%s" ' % local_fcflags configopts += '--enable-mpi=auto ' -configopts += 'LIBS="$LIBS $LIBFFT -ltirpc"' +configopts += 'LIBS="$LIBS $LIBFFT $LIBBLAS -ltirpc"' buildopts = 'all' diff --git a/easybuild/easyconfigs/c/CASTEP/CASTEP-24.1-foss-2023b.eb b/easybuild/easyconfigs/c/CASTEP/CASTEP-24.1-foss-2023b.eb new file mode 100644 index 00000000000..678f4e7df25 --- /dev/null +++ b/easybuild/easyconfigs/c/CASTEP/CASTEP-24.1-foss-2023b.eb @@ -0,0 +1,49 @@ +easyblock = 'ConfigureMake' + +name = 'CASTEP' +version = '24.1' + +homepage = 'http://www.castep.org' +description = """ +CASTEP is an electronic structure materials modelling code based on density +functional theory (DFT), with functionality including geometry optimization +molecular dynamics, phonons, NMR chemical shifts and much more. +""" + +toolchain = {'name': 'foss', 'version': '2023b'} + +download_instructions = """CASTEP is proprietary software, available under a free-of-charge license for academic use +only. Visit http://www.castep.org and navigate to "Getting Castep" to apply for a license.""" + +sources = [SOURCE_TAR_GZ] +checksums = ['97d77a4f3ce3f5c5b87e812f15a2c2cb23918acd7034c91a872b6d66ea0f7dbb'] + +dependencies = [ + ('Perl', '5.38.0'), + ('Python', '3.11.5'), + ('SciPy-bundle', '2023.11'), # for elastic constants and castepconv utility +] + +skipsteps = ['configure'] + +_generic_opts = ' COMMS_ARCH=mpi FFT=fftw3 MATH_LIBS="-lflexiblas" ' + +buildopts = _generic_opts + 'FFTLIBDIR=$FFT_LIB_DIR MATHLIBDIR=$BLAS_LIB_DIR' +buildopts += ' castep tools utilities' + +preinstallopts = 'mkdir -p %(installdir)s/bin &&' +installopts = _generic_opts + 'INSTALL_DIR="%(installdir)s/bin"' +installopts += ' install-castep install-tools install-utilities' + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['castep.mpi', 'optados.mpi', 'orbitals2bands', 'dispersion.pl', + 'elastics.py', 'ceteprouts.pm']], + 'dirs': [], +} + +sanity_check_commands = [ + 'castep.mpi --help', + 'optados.mpi --help', +] + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.8.1-GCC-12.3.0.eb b/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.8.1-GCC-12.3.0.eb new file mode 100644 index 00000000000..bd59609605c --- /dev/null +++ b/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.8.1-GCC-12.3.0.eb @@ -0,0 +1,41 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# changed toolchain and Perl version +# Updated by: Thomas Eylenbosch(Gluo N.V.), Pavel Tománek (Inuits) + +easyblock = 'MakeCp' + +name = 'CD-HIT' +version = '4.8.1' + +homepage = 'http://weizhongli-lab.org/cd-hit/' +description = """ CD-HIT is a very widely used program for clustering and + comparing protein or nucleotide sequences.""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} +toolchainopts = {'openmp': True} + +source_urls = ['https://github.com/weizhongli/cdhit/releases/download/V%(version)s/'] +sources = ['%(namelower)s-v%(version)s-2019-0228.tar.gz'] +checksums = ['26172dba3040d1ae5c73ff0ac6c3be8c8e60cc49fc7379e434cdf9cb1e7415de'] + +dependencies = [ + ('Perl', '5.36.1'), + ('zlib', '1.2.13'), +] + +buildopts = ' CC="$CXX" CCFLAGS="$CPPFLAGS $CXXFLAGS"' + +local_list_of_executables = ['cd-hit', 'cd-hit-est', 'cd-hit-2d', 'cd-hit-est-2d', 'cd-hit-div', 'cd-hit-454'] + +files_to_copy = [(local_list_of_executables, 'bin'), (['*.pl'], 'bin'), 'README', 'doc', 'license.txt'] + +fix_perl_shebang_for = ['bin/*.pl'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_list_of_executables], + 'dirs': [], +} + +sanity_check_commands = ["cd-hit -h | grep 'CD-HIT version %(version)s'"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.8.1-GCC-13.2.0.eb b/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.8.1-GCC-13.2.0.eb new file mode 100644 index 00000000000..c1a0cf57158 --- /dev/null +++ b/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.8.1-GCC-13.2.0.eb @@ -0,0 +1,41 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# changed toolchain and Perl version +# Updated by: Thomas Eylenbosch(Gluo N.V.), Pavel Tománek (Inuits) +# Update: Petr Král (INUITS) +easyblock = 'MakeCp' + +name = 'CD-HIT' +version = '4.8.1' + +homepage = 'http://weizhongli-lab.org/cd-hit/' +description = """ CD-HIT is a very widely used program for clustering and + comparing protein or nucleotide sequences.""" + +toolchain = {'name': 'GCC', 'version': '13.2.0'} +toolchainopts = {'openmp': True} + +source_urls = ['https://github.com/weizhongli/cdhit/releases/download/V%(version)s/'] +sources = ['%(namelower)s-v%(version)s-2019-0228.tar.gz'] +checksums = ['26172dba3040d1ae5c73ff0ac6c3be8c8e60cc49fc7379e434cdf9cb1e7415de'] + +dependencies = [ + ('Perl', '5.38.0'), + ('zlib', '1.2.13'), +] + +buildopts = ' CC="$CXX" CCFLAGS="$CPPFLAGS $CXXFLAGS"' + +local_list_of_executables = ['cd-hit', 'cd-hit-est', 'cd-hit-2d', 'cd-hit-est-2d', 'cd-hit-div', 'cd-hit-454'] + +files_to_copy = [(local_list_of_executables, 'bin'), (['*.pl'], 'bin'), 'README', 'doc', 'license.txt'] + +fix_perl_shebang_for = ['bin/*.pl'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_list_of_executables], + 'dirs': [], +} + +sanity_check_commands = ["cd-hit -h | grep 'CD-HIT version %(version)s'"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/CDBtools/CDBtools-0.99-GCC-12.3.0.eb b/easybuild/easyconfigs/c/CDBtools/CDBtools-0.99-GCC-12.3.0.eb new file mode 100644 index 00000000000..8266bd8155c --- /dev/null +++ b/easybuild/easyconfigs/c/CDBtools/CDBtools-0.99-GCC-12.3.0.eb @@ -0,0 +1,29 @@ +easyblock = 'MakeCp' + +name = 'CDBtools' +version = '0.99' + +homepage = 'http://compbio.dfci.harvard.edu/tgi' +description = "CDB (Constant DataBase) indexing and retrieval tools for FASTA files" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +source_urls = ['ftp://occams.dfci.harvard.edu/pub/bio/tgi/software/cdbfasta'] +sources = [{'download_filename': 'cdbfasta.tar.gz', 'filename': SOURCE_TAR_GZ}] +checksums = ['68767e8b2fb9de5a6d68ee16df73293f65e02f05cf2f747a9dd6b8854766722c'] + +buildopts = 'CC="$CXX" DBGFLAGS="$CXXFLAGS"' + +files_to_copy = [(['cdbfasta', 'cdbyank'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/cdbfasta', 'bin/cdbyank'], + 'dirs': [], +} + +sanity_check_commands = [ + "cdbfasta -v", + "cdbyank -v", +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/CDO/CDO-2.3.0-iimpi-2022a.eb b/easybuild/easyconfigs/c/CDO/CDO-2.3.0-iimpi-2022a.eb new file mode 100644 index 00000000000..58cf406d164 --- /dev/null +++ b/easybuild/easyconfigs/c/CDO/CDO-2.3.0-iimpi-2022a.eb @@ -0,0 +1,58 @@ +# updated to version 2.0.6, based on the previous 2.0.5 version +# J. Sassmannshausen (Imperial College London, UK) +# Alex Domingo (Vrije Universiteit Brussel, BE) +# Maxim Masterov (SURF, NL) + +easyblock = 'ConfigureMake' + +name = 'CDO' +version = '2.3.0' + +homepage = 'https://code.zmaw.de/projects/cdo' +description = """CDO is a collection of command line Operators to manipulate and analyse Climate and NWP model Data.""" + +toolchain = {'name': 'iimpi', 'version': '2022a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://code.mpimet.mpg.de/attachments/download/29019/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['10c878227baf718a6917837527d4426c2d0022cfac4457c65155b9c57f091f6b'] + +builddependencies = [ + ('pkgconf', '1.8.0'), +] + +dependencies = [ + ('cURL', '7.83.0'), + ('ecCodes', '2.27.0'), + ('FFTW', '3.3.10'), + ('HDF5', '1.12.2'), + ('libxml2', '2.9.13'), + ('netCDF', '4.9.0'), + ('PROJ', '9.0.0'), + ('Szip', '2.1.1'), + ('UDUNITS', '2.2.28'), + ('util-linux', '2.38'), +] + +# Build libcdi +configopts = "--enable-cdi-lib " + +# Use dependencies from EasyBuild +configopts += "--with-curl=$EBROOTCURL --with-eccodes=$EBROOTECCODES --with-fftw3 --with-hdf5=$EBROOTHDF5 " +configopts += "--with-netcdf=$EBROOTNETCDF --with-proj=$EBROOTPROJ --with-szlib=$EBROOTSZIP " +configopts += "--with-udunits2=$EBROOTUDUNITS --with-util-linux-uuid=$EBROOTUTILMINLINUX " + +# Make sure that right Fortran compiler is used, also on non-x86_64 architectures +configopts += 'CPPFLAGS="$CPPFLAGS -DgFortran" ' + +buildopts = "V=1" + +sanity_check_paths = { + 'files': ['bin/cdo', 'lib/libcdi.a', 'lib/libcdi.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +sanity_check_commands = ["cdo --version 2>&1 | grep 'CDI library version : %(version)s'"] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/c/CDO/CDO-2.4.4-gompi-2024a.eb b/easybuild/easyconfigs/c/CDO/CDO-2.4.4-gompi-2024a.eb new file mode 100644 index 00000000000..57b6de8e609 --- /dev/null +++ b/easybuild/easyconfigs/c/CDO/CDO-2.4.4-gompi-2024a.eb @@ -0,0 +1,57 @@ +# updated to version 2.0.6, based on the previous 2.0.5 version +# J. Sassmannshausen (Imperial College London, UK) +# Alex Domingo (Vrije Universiteit Brussel, BE) +# Maxim Masterov (SURF, NL) + +easyblock = 'ConfigureMake' + +name = 'CDO' +version = '2.4.4' + + +homepage = 'https://code.zmaw.de/projects/cdo' +description = """CDO is a collection of command line Operators to manipulate and analyse Climate and NWP model Data.""" + +toolchain = {'name': 'gompi', 'version': '2024a'} +toolchainopts = {'cstd': 'c++20', 'usempi': True} + +source_urls = ['https://code.mpimet.mpg.de/attachments/download/29649/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['49f50bd18dacd585e9518cfd4f55548f692426edfb3b27ddcd1c653eab53d063'] + +builddependencies = [ + ('pkgconf', '2.2.0'), +] + +dependencies = [ + ('cURL', '8.7.1'), + ('ecCodes', '2.38.3'), + ('FFTW', '3.3.10'), + ('HDF5', '1.14.5'), + ('libxml2', '2.12.7'), + ('netCDF', '4.9.2'), + ('PROJ', '9.4.1'), + ('Szip', '2.1.1'), + ('UDUNITS', '2.2.28'), + ('util-linux', '2.40'), +] + +# Build libcdi +configopts = "--enable-cdi-lib " + +# Use dependencies from EasyBuild +configopts += "--with-curl=$EBROOTCURL --with-eccodes=$EBROOTECCODES --with-fftw3 --with-hdf5=$EBROOTHDF5 " +configopts += "--with-netcdf=$EBROOTNETCDF --with-proj=$EBROOTPROJ --with-szlib=$EBROOTSZIP " +configopts += "--with-udunits2=$EBROOTUDUNITS --with-util-linux-uuid=$EBROOTUTILMINLINUX " + +# Make sure that right Fortran compiler is used, also on non-x86_64 architectures +configopts += 'CPPFLAGS="$CPPFLAGS -DgFortran" ' + +sanity_check_paths = { + 'files': ['bin/cdo', 'lib/libcdi.a', 'lib/libcdi.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +sanity_check_commands = ["cdo --version 2>&1 | grep 'Climate Data Operators version %(version)s'"] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/c/CESM-deps/CESM-deps-2-foss-2023a.eb b/easybuild/easyconfigs/c/CESM-deps/CESM-deps-2-foss-2023a.eb new file mode 100644 index 00000000000..1144c2b34cc --- /dev/null +++ b/easybuild/easyconfigs/c/CESM-deps/CESM-deps-2-foss-2023a.eb @@ -0,0 +1,51 @@ +easyblock = 'Bundle' + +name = 'CESM-deps' +version = '2' + +homepage = 'https://www.cesm.ucar.edu/models/cesm2/' +description = """CESM is a fully-coupled, community, global climate model that +provides state-of-the-art computer simulations of the Earth's past, present, +and future climate states.""" + +# The following environment is suitable for CESM >= 2.2.2 and CTSM >= 5.2.0 +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('CMake', '3.26.3'), + ('Python', '3.11.3'), + ('lxml', '4.9.2'), + ('Perl', '5.36.1'), + ('XML-LibXML', '2.0209'), + ('ESMF', '8.6.0'), + ('netCDF', '4.9.2'), + ('netCDF-Fortran', '4.6.1'), + ('netCDF-C++4', '4.3.1'), + ('PnetCDF', '1.12.3'), + ('git', '2.41.0', '-nodocs'), + ('git-lfs', '3.5.1', '', SYSTEM), +] + +components = [ + # install extra configuration tools and files for VSC clusters + ('cesm-config', '1.7.0', { + 'easyblock': 'Tarball', + 'source_urls': ['https://github.com/vub-hpc/%(name)s/archive'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}], + 'checksums': ['c5aeb50595ca4d342a5024d593c2549acf16e72dadc5f39d9a7915d3dc8f3c13'], + 'start_dir': '%(name)s-%(version)s', + }), +] + +sanity_check_paths = { + 'files': ['bin/update-cesm-machines', 'scripts/case.pbs', 'scripts/case.slurm'], + 'dirs': ['machines', 'irods'], +} + +usage = """Environment to build and run CESM v2 simulations + 1. Download a release of CESM v2: `git clone -b release-cesm2.2.2 https://github.com/ESCOMP/cesm.git cesm-2.2.2` + 2. Add external programs for CESM: `cd cesm-2.2.2; ./manage_externals/checkout_externals` + 3. Update config files: `update-cesm-machines cime/config/cesm/machines/ $EBROOTCESMMINDEPS/machines/` + 4. Create case: `cd cime/scripts && ./create_newcase --machine ...`""" + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/c/CFITSIO/CFITSIO-4.4.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/c/CFITSIO/CFITSIO-4.4.1-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..eaa1b0866ac --- /dev/null +++ b/easybuild/easyconfigs/c/CFITSIO/CFITSIO-4.4.1-GCCcore-13.3.0.eb @@ -0,0 +1,43 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +easyblock = 'ConfigureMake' + +name = 'CFITSIO' +version = '4.4.1' + +homepage = 'https://heasarc.gsfc.nasa.gov/fitsio/' +description = """CFITSIO is a library of C and Fortran subroutines for reading and writing data files in +FITS (Flexible Image Transport System) data format.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://heasarc.gsfc.nasa.gov/FTP/software/fitsio/c/'] +sources = [SOURCELOWER_TAR_GZ] +patches = ['%(name)s-3.48_install_test_data.patch'] +checksums = [ + {'cfitsio-4.4.1.tar.gz': '66a1dc3f21800f9eeabd9eac577b91fcdd9aabba678fbba3b8527319110d1d25'}, + {'CFITSIO-3.48_install_test_data.patch': 'dbf16f857f133468fc1e6a793c6e89fca66d54796593e03606f2722a2a980c0c'}, +] + +builddependencies = [ + ('binutils', '2.42'), +] +# curl for HTTPs support +dependencies = [ + ('cURL', '8.7.1'), +] + +# make would create just static libcfitsio.a. +# Let's create dynamic lib and testprog too. +buildopts = "&& make shared && make testprog" + + +sanity_check_paths = { + 'files': ['lib/libcfitsio.a', 'lib/libcfitsio.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +sanity_check_commands = ['cd %(installdir)s/share && testprog'] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-5.6.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/c/CGAL/CGAL-5.6.1-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..01aa21c6311 --- /dev/null +++ b/easybuild/easyconfigs/c/CGAL/CGAL-5.6.1-GCCcore-13.3.0.eb @@ -0,0 +1,26 @@ +easyblock = 'CMakeMake' +name = 'CGAL' +version = '5.6.1' + +homepage = 'https://www.cgal.org/' +description = """The goal of the CGAL Open Source Project is to provide easy access to efficient + and reliable geometric algorithms in the form of a C++ library.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'strict': True} + +source_urls = ['https://github.com/CGAL/cgal/releases/download/v%(version)s/'] +sources = [SOURCE_TAR_XZ] +checksums = ['cdb15e7ee31e0663589d3107a79988a37b7b1719df3d24f2058545d1bcdd5837'] + +builddependencies = [ + ('CMake', '3.29.3'), + ('binutils', '2.42'), +] + +sanity_check_paths = { + 'files': ['include/CGAL/Simple_cartesian.h'], + 'dirs': ['include/CGAL', 'lib/cmake/CGAL'], +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/c/CIRCE/CIRCE-0.3.4-foss-2023a.eb b/easybuild/easyconfigs/c/CIRCE/CIRCE-0.3.4-foss-2023a.eb new file mode 100644 index 00000000000..6a41b512096 --- /dev/null +++ b/easybuild/easyconfigs/c/CIRCE/CIRCE-0.3.4-foss-2023a.eb @@ -0,0 +1,55 @@ +easyblock = 'PythonBundle' + +name = 'CIRCE' +version = '0.3.4' + +homepage = 'https://github.com/cantinilab/Circe' +description = """This repo contains a python package for inferring co-accessibility networks + from single-cell ATAC-seq data, using skggm for the graphical lasso and scanpy for data processing.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [ + ('poetry', '1.5.1'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('scikit-learn', '1.3.1'), + ('scanpy', '1.9.8'), +] + +use_pip = True +sanity_pip_check = True + +# Some requirements are too strict. +local_preinstallopts = """sed -i 's/pandas = "[^"]*"/pandas = "*"/g' pyproject.toml && """ +local_preinstallopts += """sed -i "s/'pandas>=[^']*'/'pandas'/g" setup.py && """ + +# build the C components linking `flexiblas` instead of `lapack` and `blas` +local_preinstallopts += """sed -i "s/lapack/flexiblas/g;s/, 'blas'//g" setup.py && """ +local_preinstallopts += """sed -i "s/lapack/flexiblas/g;/blas/d" pyquic_ext/pyquic.cpp && """ + +exts_list = [ + ('joblib', '1.4.2', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['06d478d5674cbc267e7496a410ee875abd68e4340feff4490bcb7afb88060ae6'], + }), + ('rich', '13.9.2', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['8c82a3d3f8dcfe9e734771313e606b39d8247bb6b826e196f4914b333b743cf1'], + }), + ('circe_py', version, { + 'preinstallopts': local_preinstallopts, + 'modulename': 'circe', + 'checksums': ['279004948dff84816361e857ee3fb383cdb17587f376c6f10f82a66810cba16c'], + }), +] + +# NOTE This has been tested manually using the following script: +# https://github.com/cantinilab/Circe/blob/a70e031f9de4760739eb3c7571277678d5e80c8a/Examples/Minimal_example.ipynb +# with a small modification: +# https://github.com/cantinilab/Circe/issues/5#issuecomment-2419821380 + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/CLANS/CLANS-2.0.8-foss-2023a.eb b/easybuild/easyconfigs/c/CLANS/CLANS-2.0.8-foss-2023a.eb new file mode 100644 index 00000000000..e1ce2f2a9e1 --- /dev/null +++ b/easybuild/easyconfigs/c/CLANS/CLANS-2.0.8-foss-2023a.eb @@ -0,0 +1,38 @@ +easyblock = "PythonBundle" + +name = 'CLANS' +version = '2.0.8' + +homepage = 'https://github.com/inbalpaz/CLANS' +description = """ +CLANS 2.0 is a Python-based program for clustering sequences in the 2D or 3D space, based on +their sequence similarities. CLANS visualizes the dynamic clustering process and enables the +user to interactively control it and explore the cluster map in various ways. +""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('numba', '0.58.1'), + ('VisPy', '0.12.2'), + ('Biopython', '1.83'), + ('Pillow', '10.0.0'), + ('PyQt5', '5.15.10'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + (name, version, { + 'source_urls': ['https://github.com/inbalpaz/CLANS/archive/refs/tags/'], + 'sources': ['%(version)s.tar.gz'], + 'checksums': ['7b856ec3b13c420dbe30169e8cdd7d6899acb79042ca66920eafd05adf4d2815'], + }), +] + +sanity_check_commands = ['python -m clans -h'] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/c/CLHEP/CLHEP-2.4.7.1-GCC-12.3.0.eb b/easybuild/easyconfigs/c/CLHEP/CLHEP-2.4.7.1-GCC-12.3.0.eb new file mode 100644 index 00000000000..4bf02eab9a1 --- /dev/null +++ b/easybuild/easyconfigs/c/CLHEP/CLHEP-2.4.7.1-GCC-12.3.0.eb @@ -0,0 +1,29 @@ +easyblock = 'CMakeMake' + +name = 'CLHEP' +version = '2.4.7.1' + +homepage = 'https://proj-clhep.web.cern.ch/proj-clhep/' +description = """The CLHEP project is intended to be a set of HEP-specific foundation and + utility classes such as random generators, physics vectors, geometry and linear algebra. + CLHEP is structured in a set of packages independent of any external package.""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://proj-clhep.web.cern.ch/proj-clhep/dist1/'] +sources = [SOURCELOWER_TGZ] +checksums = ['1c8304a7772ac6b99195f1300378c6e3ddf4ad07c85d64a04505652abb8a55f9'] + +builddependencies = [ + ('CMake', '3.26.3'), +] + +sanity_check_paths = { + 'files': ['bin/clhep-config', 'lib/libCLHEP.a', 'lib/libCLHEP.%s' % SHLIB_EXT], + 'dirs': ['include/CLHEP'], +} + +sanity_check_commands = ["clhep-config --help"] + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/c/CLUMPP/CLUMPP-1.1.2-Linux64.eb b/easybuild/easyconfigs/c/CLUMPP/CLUMPP-1.1.2-Linux64.eb new file mode 100644 index 00000000000..3b42e01a2be --- /dev/null +++ b/easybuild/easyconfigs/c/CLUMPP/CLUMPP-1.1.2-Linux64.eb @@ -0,0 +1,38 @@ +easyblock = 'Tarball' + +name = 'CLUMPP' +version = '1.1.2' +versionsuffix = '-Linux64' + +homepage = 'https://rosenberglab.stanford.edu/clumpp.html' +description = """ +CLUMPP is a program that deals with label switching and multimodality problems +in population-genetic cluster analyses.""" + +toolchain = SYSTEM + +source_urls = ['https://rosenberglab.stanford.edu/software/'] +sources = ['%(name)s_Linux64.%(version)s.tar.gz'] +checksums = ['58cf3fe9e37f890621a76a244362256ffe4dde5e409346ae811d56af26cfe724'] + +postinstallcmds = [ + 'cd %(installdir)s && mkdir bin && mv CLUMPP bin/' +] + +sanity_check_paths = { + 'files': ['bin/CLUMPP'], + 'dirs': [], +} + +_clumpp_test_cmd = [ + "tmpdir=$(mktemp -d)", + "cp %(installdir)s/{paramfile,arabid.popfile,arabid.permutationfile} $tmpdir", + "cd $tmpdir", + "CLUMPP", +] + +sanity_check_commands = [ + " && ".join(_clumpp_test_cmd), +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.29.3-GCCcore-13.3.0.eb b/easybuild/easyconfigs/c/CMake/CMake-3.29.3-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..d8c9cce51ca --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.29.3-GCCcore-13.3.0.eb @@ -0,0 +1,30 @@ +name = 'CMake' +version = '3.29.3' + +homepage = 'https://www.cmake.org' + +description = """ + CMake, the cross-platform, open-source build system. CMake is a family of + tools designed to build, test and package software. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://www.cmake.org/files/v%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['252aee1448d49caa04954fd5e27d189dd51570557313e7b281636716a238bccb'] + +builddependencies = [ + ('binutils', '2.42'), +] + +dependencies = [ + ('ncurses', '6.5'), + ('zlib', '1.3.1'), + ('bzip2', '1.0.8'), + ('cURL', '8.7.1'), + ('libarchive', '3.7.4'), + ('OpenSSL', '3', '', SYSTEM), +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/c/COLMAP/COLMAP-3.8-foss-2022b.eb b/easybuild/easyconfigs/c/COLMAP/COLMAP-3.8-foss-2022b.eb new file mode 100644 index 00000000000..1da3b634c94 --- /dev/null +++ b/easybuild/easyconfigs/c/COLMAP/COLMAP-3.8-foss-2022b.eb @@ -0,0 +1,45 @@ +easyblock = 'CMakeNinja' + +name = 'COLMAP' +version = '3.8' + +homepage = 'https://colmap.github.io' +description = """COLMAP is a general-purpose Structure-from-Motion (SfM) and Multi-View Stereo (MVS) pipeline +with a graphical and command-line interface""" + +source_urls = ['https://github.com/colmap/colmap/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['02288f8f61692fe38049d65608ed832b31246e7792692376afb712fa4cef8775'] + +toolchain = {'name': 'foss', 'version': '2022b'} + +builddependencies = [ + ('CMake', '3.24.3'), + ('Ninja', '1.11.1'), + ('Eigen', '3.4.0'), + ('googletest', '1.12.1'), +] + +dependencies = [ + ('Boost', '1.81.0'), + ('Qt5', '5.15.7'), + ('FLANN', '1.9.2'), + ('FreeImage', '3.18.0'), + ('METIS', '5.1.0'), + ('glog', '0.6.0'), + ('SQLite', '3.39.4'), + ('glew', '2.2.0', '-egl'), + ('CGAL', '5.5.2'), + ('Ceres-Solver', '2.2.0'), +] + +configopts = "-DCMAKE_CXX_STANDARD=17" + +sanity_check_paths = { + 'files': ['bin/colmap', 'lib/colmap/libcolmap.a', 'lib/colmap/libpba.a', 'lib/colmap/libvlfeat.a'], + 'dirs': ['include/colmap'], +} + +sanity_check_commands = ["colmap -h"] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/c/COMEBin/COMEBin-1.0.3-20240310-foss-2022a.eb b/easybuild/easyconfigs/c/COMEBin/COMEBin-1.0.3-20240310-foss-2022a.eb new file mode 100644 index 00000000000..4bc881dc9c1 --- /dev/null +++ b/easybuild/easyconfigs/c/COMEBin/COMEBin-1.0.3-20240310-foss-2022a.eb @@ -0,0 +1,77 @@ +easyblock = 'Tarball' + +name = 'COMEBin' +local_commit = '987db95' +version = '1.0.3-20240310' + +homepage = 'https://github.com/ziyewang/COMEBin' +description = "Effective binning of metagenomic contigs using COntrastive Multi-viEw representation learning" + +toolchain = {'name': 'foss', 'version': '2022a'} + +source_urls = ['https://github.com/ziyewang/COMEBin/archive/'] +sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}] +patches = ['COMEBin-1.0.3_fix-run-script.patch'] +checksums = [ + {'COMEBin-1.0.3-20240310.tar.gz': 'aa9c9e98d0cd121b2be60cae85d735527f510ad07df1a84ed6405cbc66eea684'}, + {'COMEBin-1.0.3_fix-run-script.patch': 'e9ac578667d4f7233cf716cc98b134b8bd7cb7bcc70a06322500319d84b67773'}, +] + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('matplotlib', '3.5.2'), + ('PyTorch', '1.12.0'), + ('tensorboard', '2.10.0'), + ('Biopython', '1.79'), + ('scikit-learn', '1.1.2'), + ('tqdm', '4.64.0'), + ('leidenalg', '0.9.1'), + ('BEDTools', '2.30.0'), + ('BWA', '0.7.17'), + ('CheckM', '1.2.2'), + ('FragGeneScan', '1.31'), + ('HMMER', '3.3.2'), + ('pplacer', '1.1.alpha19', '', SYSTEM), + ('prodigal', '2.6.3'), + ('SAMtools', '1.16.1'), + ('python-igraph', '0.10.3'), + ('PyYAML', '6.0'), +] + +exts_defaultclass = 'PythonPackage' + +exts_default_options = { + 'source_urls': [PYPI_SOURCE], + 'use_pip': True, + 'download_dep_fail': True, + 'sanity_pip_check': True, +} + +exts_list = [ + ('fastjsonschema', '2.19.1', { + 'checksums': ['e3126a94bdc4623d3de4485f8d468a12f02a67921315ddc87836d6e456dc789d'], + }), + ('hnswlib', '0.8.0', { + 'checksums': ['cb6d037eedebb34a7134e7dc78966441dfd04c9cf5ee93911be911ced951c44c'], + }), + ('biolib', '0.1.9', { + 'checksums': ['bc9ae68c6d76d46e4295fe0b1df5a48b575fe96374bd96d624c3330feb94856f'], + }), +] + +postinstallcmds = ["chmod a+x %(installdir)s/bin/run_comebin.sh"] + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +sanity_check_paths = { + 'files': ['bin/run_comebin.sh', 'COMEBin/main.py'], + 'dirs': ['COMEBin/models', 'COMEBin/scripts'], +} + +sanity_check_commands = [ + "run_comebin.sh | grep '^Usage: bash run_comebin.sh'" + "python %(installdir)s/COMEBin/main.py --help", +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/COMEBin/COMEBin-1.0.3_fix-run-script.patch b/easybuild/easyconfigs/c/COMEBin/COMEBin-1.0.3_fix-run-script.patch new file mode 100644 index 00000000000..1752260e69b --- /dev/null +++ b/easybuild/easyconfigs/c/COMEBin/COMEBin-1.0.3_fix-run-script.patch @@ -0,0 +1,12 @@ +fix determining path to top-level directory, +since run_comebin.sh is located in bin/run_comebin.sh +--- bin/run_comebin.sh.orig 2024-06-04 16:27:24.373968000 +0200 ++++ bin/run_comebin.sh 2024-06-04 16:27:38.413830000 +0200 +@@ -25,6 +25,7 @@ + echo "";} + + run_file_path=$(dirname $(which run_comebin.sh)) ++run_file_path=$(dirname $(dirname $(which run_comebin.sh))) + + if [[ $? -ne 0 ]]; then + echo "cannot find run_comebin.sh file - something went wrong with the installation!" diff --git a/easybuild/easyconfigs/c/CORSIKA/CORSIKA-77550-foss-2023a.eb b/easybuild/easyconfigs/c/CORSIKA/CORSIKA-77550-foss-2023a.eb new file mode 100644 index 00000000000..c6f619d9d75 --- /dev/null +++ b/easybuild/easyconfigs/c/CORSIKA/CORSIKA-77550-foss-2023a.eb @@ -0,0 +1,49 @@ +easyblock = "ConfigureMake" + +name = 'CORSIKA' +version = '77550' + +homepage = "https://www.iap.kit.edu/corsika" +description = """CORSIKA (COsmic Ray SImulations for KAscade) is a program for detailed +simulation of extensive air showers initiated by high energy cosmic ray +particles. Protons, light nuclei up to iron, photons, and many other particles +may be treated as primaries.""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'usempi': True} + +download_instructions = "Sources have to be requested to the developers" +sources = [SOURCELOWER_TAR_GZ] +patches = ['%(name)s-%(version)s_fix_include.patch'] +checksums = [ + {'corsika-77550.tar.gz': 'fed74c144e22deb5a7c1d2dc1f04f0100eb2732cb48665a3da49ce471a3775ee'}, + {'CORSIKA-77550_fix_include.patch': 'e858fc4c1fa33d31d050b2fca50e130c23b2d3e4b81b851af34dc3f39e9c709e'}, +] + +dependencies = [ + ("ROOT", "6.30.06"), +] + +# custom coconut script does not recognize -j +parallel = False + +# execute ./coconut manually with your own options and extract configure command from top of config.log +_mpi_opts = "--enable-PARALLEL --with-mpirunner-lib=src/parallel --enable-PARALLELIB " +configopts = "CORDETECTOR=HORIZONTAL CORTIMELIB=TIMEAUTO CORHEMODEL=QGSJETII CORLEMODEL=URQMD " +configopts += "--enable-UPWARD --enable-SLANT --enable-THIN --enable-COREAS " +configopts += _mpi_opts + +build_cmd = "./coconut" +buildopts = "--batch " + _mpi_opts + +install_cmd = ' && '.join([ + 'mkdir -p %(installdir)s/bin', + 'cp %(builddir)s/%(namelower)s-%(version)s/run/* %(installdir)s/bin/', +]) + +sanity_check_paths = { + 'files': ['bin/mpi_corsika77550Linux_QGSII_urqmd_thin_coreas_parallel_runner'], + 'dirs': [], +} + +moduleclass = "phys" diff --git a/easybuild/easyconfigs/c/CORSIKA/CORSIKA-77550_fix_include.patch b/easybuild/easyconfigs/c/CORSIKA/CORSIKA-77550_fix_include.patch new file mode 100644 index 00000000000..e7bc3863fae --- /dev/null +++ b/easybuild/easyconfigs/c/CORSIKA/CORSIKA-77550_fix_include.patch @@ -0,0 +1,22 @@ +Move include out of function to avoid error: +/usr/include/sys/stat.h:453:1: error: nested function ‘stat’ declared ‘extern’ +Author: Samuel Moors (Vrije Universiteit Brussel) +diff -Nur corsika-77550.orig/src/parallel/mpi_runner.c corsika-77550/src/parallel/mpi_runner.c +--- corsika-77550.orig/src/parallel/mpi_runner.c 2024-04-18 18:30:39.000000000 +0200 ++++ corsika-77550/src/parallel/mpi_runner.c 2024-08-09 16:15:39.969688000 +0200 +@@ -99,6 +99,7 @@ + #include + #include + #include "config.h" ++#include + + /////////////////////initializing parameters/////////////////// + //the number of data type block in the MPI message +@@ -1023,7 +1024,6 @@ + strcpy(str2, strtmp); + } + strcpy(statdir,str2); +- #include + struct stat sb; + if (stat(statdir, &sb) == 0 && S_ISDIR(sb.st_mode)) + { diff --git a/easybuild/easyconfigs/c/COSTA/COSTA-2.2.2-foss-2023a.eb b/easybuild/easyconfigs/c/COSTA/COSTA-2.2.2-foss-2023a.eb new file mode 100644 index 00000000000..0f347ce481e --- /dev/null +++ b/easybuild/easyconfigs/c/COSTA/COSTA-2.2.2-foss-2023a.eb @@ -0,0 +1,27 @@ +easyblock = 'CMakeMake' + +name = 'COSTA' +version = '2.2.2' + +homepage = 'https://github.com/eth-cscs/COSTA' +description = """OSTA is a communication-optimal, highly-optimised algorithm for data redistribution +accross multiple processors, using MPI and OpenMP and offering the possibility +to transpose and scale some or all data.""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'openmp': True} + +source_urls = ['https://github.com/eth-cscs/COSTA/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['e87bc37aad14ac0c5922237be5d5390145c9ac6aef0350ed17d86cb2d994e67c'] + +builddependencies = [ + ('CMake', '3.26.3'), +] + +sanity_check_paths = { + 'files': ['lib/libcosta.a'], + 'dirs': ['include/costa'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-2023.1-foss-2023a.eb b/easybuild/easyconfigs/c/CP2K/CP2K-2023.1-foss-2023a.eb index d16e202463a..d9ace4b896b 100644 --- a/easybuild/easyconfigs/c/CP2K/CP2K-2023.1-foss-2023a.eb +++ b/easybuild/easyconfigs/c/CP2K/CP2K-2023.1-foss-2023a.eb @@ -25,11 +25,16 @@ builddependencies = [ dependencies = [ ('Libint', '2.7.2', '-lmax-6-cp2k'), ('libxc', '6.2.2'), - ('libxsmm', '1.17'), ('libvori', '220621'), ('FFTW', '3.3.10'), ('PLUMED', '2.9.0'), ] +if ARCH == 'x86_64': + # LIBXSMM is not supported supported on ARM with GCC 12.2.0 and 12.3.0 + # see https://www.cp2k.org/dev:compiler_support + dependencies += [ + ('libxsmm', '1.17'), + ] type = 'psmp' diff --git a/easybuild/easyconfigs/c/CPPE/CPPE-0.3.1-GCC-12.3.0.eb b/easybuild/easyconfigs/c/CPPE/CPPE-0.3.1-GCC-12.3.0.eb new file mode 100644 index 00000000000..06b34618eb5 --- /dev/null +++ b/easybuild/easyconfigs/c/CPPE/CPPE-0.3.1-GCC-12.3.0.eb @@ -0,0 +1,49 @@ +easyblock = 'CMakeMake' + +name = 'CPPE' +version = '0.3.1' + +homepage = 'https://github.com/maxscheurer/cppe' +description = """CPPE is an open-source, light-weight C++ and Python library for Polarizable +Embedding (PE)1,2 calculations. It provides an easy-to-use API to implement PE +for ground-state self-consistent field (SCF) calculations and post-SCF methods. +A convenient Python interface is also available.""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +github_account = 'maxscheurer' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['38d4230ba3ace78936049c23ad4b1fe9e704fd250ec57cc9733cb3904b62cf7c'] + +builddependencies = [ + ('CMake', '3.26.3'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('pybind11', '2.11.1'), +] + +exts_defaultclass = 'PythonPackage' +exts_default_options = { + 'source_urls': [PYPI_SOURCE], + 'download_dep_fail': True, + 'use_pip': True, + 'sanity_pip_check': True, +} + +exts_list = [ + ('cppe', version, { + 'checksums': ['b0aef578d6919f8c103d4d4a9fcd3db481bd73c59c157985f52bf62477425d6c'], + }), +] + +sanity_check_paths = { + 'files': ['lib/libcppe.%s' % SHLIB_EXT], + 'dirs': ['include/cppe', 'lib/python%(pyshortver)s/site-packages', 'share/cmake'], +} + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/c/CREST/CREST-20240319-gfbf-2023a.eb b/easybuild/easyconfigs/c/CREST/CREST-2.12-gfbf-2023b.eb similarity index 59% rename from easybuild/easyconfigs/c/CREST/CREST-20240319-gfbf-2023a.eb rename to easybuild/easyconfigs/c/CREST/CREST-2.12-gfbf-2023b.eb index 7649571fc62..87ae95876bf 100644 --- a/easybuild/easyconfigs/c/CREST/CREST-20240319-gfbf-2023a.eb +++ b/easybuild/easyconfigs/c/CREST/CREST-2.12-gfbf-2023b.eb @@ -5,8 +5,7 @@ easyblock = 'CMakeMake' name = 'CREST' -version = '20240319' -_commit = '2719412edf8bb606cebdd4cd6bbb4cdbd249e1e5' +version = '2.12' homepage = 'https://xtb-docs.readthedocs.io/en/latest/crest.html' description = """CREST is an utility/driver program for the xtb program. Originally it was designed @@ -16,23 +15,24 @@ description = """CREST is an utility/driver program for the xtb program. Origina program) and tool for the creation and analysation of structure ensembles. """ -toolchain = {'name': 'gfbf', 'version': '2023a'} -toolchainopts = {'opt': True, 'optarch': True, 'extra_fflags': '-ffree-line-length-none'} - -separate_build_dir = False +toolchain = {'name': 'gfbf', 'version': '2023b'} github_account = 'grimme-lab' source_urls = [GITHUB_LOWER_SOURCE] -sources = [{'download_filename': '%s.tar.gz' % _commit, 'filename': SOURCE_TAR_GZ}] -checksums = ['770b7ca72bc47bc4e1ffd8ca56566df7b03f4d3b702b04ec6b83bad9a125884d'] +sources = ['v%(version)s.tar.gz'] +patches = ['CREST-2.12-longline.patch'] +checksums = [ + {'v2.12.tar.gz': '390f0ac0aedafbd6bb75974fcffefe7e0232ad6c4ea0ab4f1a77e656a3ce263d'}, + {'CREST-2.12-longline.patch': '596ca2bcce3bbdfe99a3849934f41b388fb763a4898240091593b9b6a454fea9'}, +] -builddependencies = [('CMake', '3.26.3')] +builddependencies = [('CMake', '3.27.6')] -dependencies = [('xtb', '6.6.1')] # required to run the program +dependencies = [('xtb', '6.7.1')] # required to run the program # Simple test command just to check if the program is working: -test_cmd = 'export PATH=%%(builddir)s/%%(namelower)s-%s:$PATH && ' % _commit -test_cmd += 'cd %%(builddir)s/%%(namelower)s-%s/examples/expl-0/ && ./run.sh ' % _commit +test_cmd = 'export PATH=%(builddir)s/easybuild_obj:$PATH && ' +test_cmd += 'cd %(builddir)s/%(namelower)s-%(version)s/examples/expl-0/ && ./run.sh ' sanity_check_paths = { 'files': ['bin/%s' % name.lower()], diff --git a/easybuild/easyconfigs/c/CREST/CREST-2.12-longline.patch b/easybuild/easyconfigs/c/CREST/CREST-2.12-longline.patch new file mode 100644 index 00000000000..c3b84785f5f --- /dev/null +++ b/easybuild/easyconfigs/c/CREST/CREST-2.12-longline.patch @@ -0,0 +1,16 @@ +Dealing with a long line, which gfortran does not like +Author: J. Sassmannshausen (Imperial College London/UK) +diff --git a/crest-2.12.orig/src/qcg/solvtool.f90 b/crest-2.12/src/qcg/solvtool.f90 +index cec514c..f38b576 100644 +--- a/crest-2.12.orig/src/qcg/solvtool.f90 ++++ b/crest-2.12/src/qcg/solvtool.f90 +@@ -3158,7 +3158,8 @@ subroutine check_prog_path_iff(env) + str=trim(str) + open(unit=27, file=str, iostat=ios) + read(27,'(a)',iostat=ios) path +- if(ios .ne. 0) error stop 'No xtb-IFF found. This is currently required for QCG and available at https:/github.com/grimme-lab/xtbiff/releases/tag/v1.1' ++ if(ios .ne. 0) error stop 'No xtb-IFF found. This is currently required for QCG and available at & ++ https:/github.com/grimme-lab/xtbiff/releases/tag/v1.1' + + end subroutine check_prog_path_iff + diff --git a/easybuild/easyconfigs/c/CREST/CREST-3.0.2-foss-2023a.eb b/easybuild/easyconfigs/c/CREST/CREST-3.0.2-foss-2023a.eb new file mode 100644 index 00000000000..38fc051e0fb --- /dev/null +++ b/easybuild/easyconfigs/c/CREST/CREST-3.0.2-foss-2023a.eb @@ -0,0 +1,47 @@ +easyblock = 'CMakeMake' + +name = 'CREST' +version = '3.0.2' + +homepage = 'https://xtb-docs.readthedocs.io/en/latest/crest.html' +description = """CREST is an utility/driver program for the xtb program. Originally it was designed + as conformer sampling program, hence the abbreviation Conformer–Rotamer Ensemble Sampling Tool, + but now offers also some utility functions for calculations with the GFNn–xTB methods. Generally + the program functions as an IO based OMP scheduler (i.e., calculations are performed by the xtb + program) and tool for the creation and analysation of structure ensembles. +""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'opt': True} + +sources = [{ + 'filename': SOURCE_TAR_GZ, + 'git_config': { + 'url': 'https://github.com/crest-lab', + 'repo_name': 'crest', + 'tag': 'v%s' % version, + 'recursive': True, + }, +}] +checksums = [None] + +builddependencies = [('CMake', '3.26.3')] + +dependencies = [ + ('dftd4', '3.7.0'), + ('mctc-lib', '0.3.1'), + ('mstore', '0.3.0'), + ('multicharge', '0.3.0'), + ('xtb', '6.6.1'), +] + +runtest = "test" + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': [], +} + +sanity_check_commands = ["crest -h", "crest --cite"] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/c/CREST/CREST-3.0.2-gfbf-2023b.eb b/easybuild/easyconfigs/c/CREST/CREST-3.0.2-gfbf-2023b.eb new file mode 100644 index 00000000000..9b7dd90fcf7 --- /dev/null +++ b/easybuild/easyconfigs/c/CREST/CREST-3.0.2-gfbf-2023b.eb @@ -0,0 +1,47 @@ +easyblock = 'CMakeMake' + +name = 'CREST' +version = '3.0.2' + +homepage = 'https://xtb-docs.readthedocs.io/en/latest/crest.html' +description = """CREST is an utility/driver program for the xtb program. Originally it was designed + as conformer sampling program, hence the abbreviation Conformer–Rotamer Ensemble Sampling Tool, + but now offers also some utility functions for calculations with the GFNn–xTB methods. Generally + the program functions as an IO based OMP scheduler (i.e., calculations are performed by the xtb + program) and tool for the creation and analysation of structure ensembles. +""" + +toolchain = {'name': 'gfbf', 'version': '2023b'} +toolchainopts = {'opt': True} + +sources = [{ + 'filename': SOURCE_TAR_GZ, + 'git_config': { + 'url': 'https://github.com/crest-lab', + 'repo_name': 'crest', + 'tag': 'v%s' % version, + 'recursive': True, + }, +}] +checksums = [None] + +builddependencies = [('CMake', '3.27.6')] + +dependencies = [ + ('dftd4', '3.7.0'), + ('mctc-lib', '0.3.1'), + ('mstore', '0.3.0'), + ('multicharge', '0.3.0'), + ('xtb', '6.7.1'), +] + +runtest = "test" + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': [], +} + +sanity_check_commands = ["crest -h", "crest --cite"] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/c/CSBDeep/CSBDeep-0.7.4-foss-2023a.eb b/easybuild/easyconfigs/c/CSBDeep/CSBDeep-0.7.4-foss-2023a.eb new file mode 100644 index 00000000000..3b3b0f37650 --- /dev/null +++ b/easybuild/easyconfigs/c/CSBDeep/CSBDeep-0.7.4-foss-2023a.eb @@ -0,0 +1,37 @@ +# This easyconfig was created by the BEAR Software team at the University of Birmingham. +# Update: Petr Král (INUITS) +easyblock = 'PythonBundle' + +name = 'CSBDeep' +version = '0.7.4' + +homepage = "https://csbdeep.bioimagecomputing.com/" +description = """CSBDeep is a toolbox for Content-aware Image Restoration (CARE).""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('TensorFlow', '2.13.0'), + ('matplotlib', '3.7.2'), + ('tqdm', '4.66.1'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('tifffile', '2024.6.18', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['67299c0445fc47463bbc71f3cb4676da2ab0242b0c6c6542a0680801b4b97d8a'], + }), + ('%(namelower)s', version, { + 'source_tmpl': SOURCE_WHL, + 'checksums': ['155d61827439373dc9c2a730a1ef621f7e373fea16599d583e0a70f1e48bd6db'], + }), +] + +sanity_check_commands = ['care_predict'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/CUDA-Python/CUDA-Python-12.1.0-gfbf-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/c/CUDA-Python/CUDA-Python-12.1.0-gfbf-2023a-CUDA-12.1.1.eb new file mode 100644 index 00000000000..f58021c3a9a --- /dev/null +++ b/easybuild/easyconfigs/c/CUDA-Python/CUDA-Python-12.1.0-gfbf-2023a-CUDA-12.1.1.eb @@ -0,0 +1,38 @@ +easyblock = 'PythonBundle' + +name = 'CUDA-Python' +# Warning: major and minor versions of CUDA and CUDA-Python are tied +version = '12.1.0' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://nvidia.github.io/cuda-python/' +description = "Python bindings for CUDA" +github_account = 'NVIDIA' + +toolchain = {'name': 'gfbf', 'version': '2023a'} + +dependencies = [ + ('CUDA', '%(version_major)s.%(version_minor)s.1', '', SYSTEM), + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), +] + +use_pip = True + +exts_list = [ + ('pyclibrary', '0.2.2', { + 'checksums': ['9902fffe361bb86f57ab62aa4195ec4dd382b63c5c6892be6d9784ec0a3575f7'], + }), + ('cuda-python', version, { + 'modulename': 'cuda', + 'source_urls': ['https://github.com/%(github_account)s/%(namelower)s/archive'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(namelower)s-%(version)s.tar.gz'}], + 'checksums': ['6fdfacaabbd6bc7f5dddec3ecf6bb0968e4a6b5151896d6352703ff5e0fc4abb'], + }), +] + +sanity_pip_check = True + +sanity_check_commands = ["python -c 'from cuda import cuda, nvrtc'"] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-11.3-GCC-10.3.0-CUDA-11.3.1.eb b/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-11.3-GCC-10.3.0-CUDA-11.3.1.eb index b71d2bfad4d..ad7b6aba80b 100644 --- a/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-11.3-GCC-10.3.0-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-11.3-GCC-10.3.0-CUDA-11.3.1.eb @@ -11,7 +11,11 @@ toolchain = {'name': 'GCC', 'version': '10.3.0'} source_urls = ['https://github.com/NVIDIA/cuda-samples/archive/'] sources = ['v%(version)s.tar.gz'] -checksums = ['2bee5f7c89347259aaab75aa6df6e10375059bdbbaf04cc7936f5db7d54fa3ac'] +patches = ['cuda-samples-11.3_multiple-sms.patch'] +checksums = [ + {'v11.3.tar.gz': '2bee5f7c89347259aaab75aa6df6e10375059bdbbaf04cc7936f5db7d54fa3ac'}, + {'cuda-samples-11.3_multiple-sms.patch': 'b31613f4160456f0d0abf82999c7fb7eee781f0efadc8b9bbb5a02ef0f37e21d'}, +] dependencies = [ ('CUDA', '11.3.1', '', SYSTEM), @@ -32,7 +36,7 @@ local_filters += "Samples/simpleVulkan/Makefile " local_filters += "Samples/simpleVulkanMMAP/Makefile " local_filters += "Samples/streamOrderedAllocationIPC/Makefile " local_filters += "Samples/vulkanImageCUDA/Makefile" -buildopts = "HOST_COMPILER=g++ FILTER_OUT='%s'" % local_filters +buildopts = "HOST_COMPILER=g++ SMS='%%(cuda_cc_space_sep_no_period)s' FILTER_OUT='%s'" % local_filters files_to_copy = [ (['bin/%s/linux/release/*' % ARCH], 'bin'), diff --git a/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-11.6-GCC-11.3.0-CUDA-11.7.0.eb b/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-11.6-GCC-11.3.0-CUDA-11.7.0.eb index d4240930bd1..ea78eae4061 100644 --- a/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-11.6-GCC-11.3.0-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-11.6-GCC-11.3.0-CUDA-11.7.0.eb @@ -11,7 +11,11 @@ toolchain = {'name': 'GCC', 'version': '11.3.0'} source_urls = ['https://github.com/NVIDIA/cuda-samples/archive/'] sources = ['v%(version)s.tar.gz'] -checksums = ['75b858bcf9e534eaa0f129c418e661b83872d743de218df8a5278cc429f9ea98'] +patches = ['cuda-samples-11.6_multiple-sms.patch'] +checksums = [ + {'v11.6.tar.gz': '75b858bcf9e534eaa0f129c418e661b83872d743de218df8a5278cc429f9ea98'}, + {'cuda-samples-11.6_multiple-sms.patch': '8849e4882d797d155d6ebb71377fa1409205361776ade8da699452a4ecb94a0a'}, +] dependencies = [ ('CUDA', '11.7.0', '', SYSTEM), @@ -33,7 +37,7 @@ local_filters += "Samples/simpleVulkanMMAP/Makefile " local_filters += "Samples/streamOrderedAllocationIPC/Makefile " local_filters += "Samples/vulkanImageCUDA/Makefile" -buildopts = "HOST_COMPILER=g++ FILTER_OUT='%s'" % local_filters +buildopts = "HOST_COMPILER=g++ SMS='%%(cuda_cc_space_sep_no_period)s' FILTER_OUT='%s'" % local_filters files_to_copy = [ (['bin/%s/linux/release/*' % ARCH], 'bin'), diff --git a/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-11.8-GCC-11.3.0-CUDA-11.7.0.eb b/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-11.8-GCC-11.3.0-CUDA-11.7.0.eb new file mode 100644 index 00000000000..be16c76f3be --- /dev/null +++ b/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-11.8-GCC-11.3.0-CUDA-11.7.0.eb @@ -0,0 +1,59 @@ +easyblock = 'MakeCp' + +name = 'CUDA-Samples' +version = '11.8' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/NVIDIA/cuda-samples' +description = "Samples for CUDA Developers which demonstrates features in CUDA Toolkit" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +source_urls = ['https://github.com/NVIDIA/cuda-samples/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = ['cuda-samples-11.6_multiple-sms.patch'] +checksums = [ + {'v11.8.tar.gz': '1bc02c0ca42a323f3c7a05b5682eae703681a91e95b135bfe81f848b2d6a2c51'}, + {'cuda-samples-11.6_multiple-sms.patch': '8849e4882d797d155d6ebb71377fa1409205361776ade8da699452a4ecb94a0a'}, +] + +dependencies = [ + ('CUDA', '11.7.0', '', SYSTEM), +] + +# Get rid of pre-built Windows DLLs and only build deviceQuery for now. +prebuildopts = "rm -r bin/win64 && " + +# Filter out samples that require extensive dependencies. +local_filters = "Samples/2_Concepts_and_Techniques/EGLStream_CUDA_Interop/Makefile " +local_filters += "Samples/4_CUDA_Libraries/boxFilterNPP/Makefile " +local_filters += "Samples/4_CUDA_Libraries/cannyEdgeDetectorNPP/Makefile " +local_filters += "Samples/4_CUDA_Libraries/cudaNvSci/Makefile " +local_filters += "Samples/4_CUDA_Libraries/cudaNvSciNvMedia/Makefile " +local_filters += "Samples/5_Domain_Specific/simpleGL/Makefile " +local_filters += "Samples/3_CUDA_Features/warpAggregatedAtomicsCG/Makefile " +local_filters += "Samples/5_Domain_Specific/simpleVulkan/Makefile " +local_filters += "Samples/5_Domain_Specific/simpleVulkanMMAP/Makefile " +local_filters += "Samples/2_Concepts_and_Techniques/streamOrderedAllocationIPC/Makefile " +local_filters += "Samples/5_Domain_Specific/vulkanImageCUDA/Makefile " +local_filters += "Samples/6_Performance/LargeKernelParameter/Makefile " + +buildopts = "HOST_COMPILER=g++ SMS='%%(cuda_cc_space_sep_no_period)s' FILTER_OUT='%s'" % local_filters + +files_to_copy = [ + (['bin/%s/linux/release/*' % ARCH], 'bin'), + 'LICENSE', +] + +local_binaries = ['deviceQuery', 'matrixMul', 'bandwidthTest', 'cudaOpenMP'] + +# Only paths are used for sanity checks. +# Commands may fail due to missing compatibility libraries that might be needed +# to be able to use this specific CUDA version in combination with the available +# NVIDIA drivers. +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_binaries], + 'dirs': [], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-12.1-GCC-12.3.0-CUDA-12.1.1.eb b/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-12.1-GCC-12.3.0-CUDA-12.1.1.eb index 3e7ffe79da0..5a886ca74d4 100644 --- a/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-12.1-GCC-12.3.0-CUDA-12.1.1.eb +++ b/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-12.1-GCC-12.3.0-CUDA-12.1.1.eb @@ -11,7 +11,11 @@ toolchain = {'name': 'GCC', 'version': '12.3.0'} source_urls = ['https://github.com/NVIDIA/cuda-samples/archive/'] sources = ['v%(version)s.tar.gz'] -checksums = ['f758160645b366d79c2638d8dfd389f01029b8d179ab0c11726b9ef58aecebd9'] +patches = ['cuda-samples-11.6_multiple-sms.patch'] +checksums = [ + {'v12.1.tar.gz': 'f758160645b366d79c2638d8dfd389f01029b8d179ab0c11726b9ef58aecebd9'}, + {'cuda-samples-11.6_multiple-sms.patch': '8849e4882d797d155d6ebb71377fa1409205361776ade8da699452a4ecb94a0a'}, +] dependencies = [ ('CUDA', '12.1.1', '', SYSTEM), @@ -58,7 +62,7 @@ if ARCH == 'aarch64': local_filters += "Samples/3_CUDA_Features/cdpQuadtree/Makefile " local_filters += "Samples/3_CUDA_Features/cdpAdvancedQuicksort/Makefile " -buildopts = "HOST_COMPILER=g++ FILTER_OUT='%s'" % local_filters +buildopts = "HOST_COMPILER=g++ SMS='%%(cuda_cc_space_sep_no_period)s' FILTER_OUT='%s'" % local_filters # Remove libraries in the bin dir after a successful 'make' buildopts += " && rm bin/*/linux/release/lib*.so.*" diff --git a/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-12.2-GCC-11.3.0-CUDA-12.2.0.eb b/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-12.2-GCC-11.3.0-CUDA-12.2.0.eb new file mode 100644 index 00000000000..89e1c6fc87b --- /dev/null +++ b/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-12.2-GCC-11.3.0-CUDA-12.2.0.eb @@ -0,0 +1,63 @@ +easyblock = 'MakeCp' + +name = 'CUDA-Samples' +version = '12.2' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/NVIDIA/cuda-samples' +description = "Samples for CUDA Developers which demonstrates features in CUDA Toolkit" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +source_urls = ['https://github.com/NVIDIA/cuda-samples/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = ['cuda-samples-11.6_multiple-sms.patch'] +checksums = [ + {'v12.2.tar.gz': '1823cfe28e97a9230107aa72b231f78952c0f178b71a920f036d360518480bdc'}, + {'cuda-samples-11.6_multiple-sms.patch': '8849e4882d797d155d6ebb71377fa1409205361776ade8da699452a4ecb94a0a'}, +] + +builddependencies = [ + ('CMake', '3.24.3'), +] + +dependencies = [ + ('CUDA', '12.2.0', '', SYSTEM), +] + +# Get rid of pre-built Windows DLLs and only build deviceQuery for now. +prebuildopts = "rm -r bin/win64 && " + +# Filter out samples that require extensive dependencies. +local_filters = "Samples/2_Concepts_and_Techniques/EGLStream_CUDA_Interop/Makefile " +local_filters += "Samples/4_CUDA_Libraries/boxFilterNPP/Makefile " +local_filters += "Samples/4_CUDA_Libraries/cannyEdgeDetectorNPP/Makefile " +local_filters += "Samples/4_CUDA_Libraries/cudaNvSci/Makefile " +local_filters += "Samples/4_CUDA_Libraries/cudaNvSciNvMedia/Makefile " +local_filters += "Samples/5_Domain_Specific/simpleGL/Makefile " +local_filters += "Samples/3_CUDA_Features/warpAggregatedAtomicsCG/Makefile " +local_filters += "Samples/5_Domain_Specific/simpleVulkan/Makefile " +local_filters += "Samples/5_Domain_Specific/simpleVulkanMMAP/Makefile " +local_filters += "Samples/2_Concepts_and_Techniques/streamOrderedAllocationIPC/Makefile " +local_filters += "Samples/5_Domain_Specific/vulkanImageCUDA/Makefile " +local_filters += "Samples/6_Performance/LargeKernelParameter/Makefile " + +buildopts = "HOST_COMPILER=g++ SMS='%%(cuda_cc_space_sep_no_period)s' FILTER_OUT='%s'" % local_filters + +files_to_copy = [ + (['bin/%s/linux/release/*' % ARCH], 'bin'), + 'LICENSE', +] + +local_binaries = ['deviceQuery', 'matrixMul', 'bandwidthTest', 'cudaOpenMP'] + +# Only paths are used for sanity checks. +# Commands may fail due to missing compatibility libraries that might be needed +# to be able to use this specific CUDA version in combination with the available +# NVIDIA drivers. +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_binaries], + 'dirs': [], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/c/CUDA-Samples/cuda-samples-11.3_multiple-sms.patch b/easybuild/easyconfigs/c/CUDA-Samples/cuda-samples-11.3_multiple-sms.patch new file mode 100644 index 00000000000..b6613f6a3c4 --- /dev/null +++ b/easybuild/easyconfigs/c/CUDA-Samples/cuda-samples-11.3_multiple-sms.patch @@ -0,0 +1,31 @@ +# Fixes "nvcc fatal: Option '--ptx (-ptx)' is not allowed when compiling for multiple GPU architectures" +# fatal compilation issue when building for multiple SM architectures +# More info, see https://github.com/NVIDIA/cuda-samples/issues/289 + +# Author: Caspar van Leeuwen + +diff -Nru cuda-samples-11.3.orig/Samples/memMapIPCDrv/Makefile cuda-samples-11.3/Samples/memMapIPCDrv/Makefile +--- cuda-samples-11.3.orig/Samples/memMapIPCDrv/Makefile 2024-07-29 13:17:10.330743000 +0200 ++++ cuda-samples-11.3/Samples/memMapIPCDrv/Makefile 2024-07-29 13:19:13.158507504 +0200 +@@ -321,6 +321,12 @@ + ifneq ($(HIGHEST_SM),) + GENCODE_FLAGS += -gencode arch=compute_$(HIGHEST_SM),code=compute_$(HIGHEST_SM) + endif ++ ++# Generate the explicit PTX file for the lowest SM architecture in $(SMS), so it works on all SMS listed there ++LOWEST_SM := $(firstword $(sort $(SMS))) ++ifneq ($(LOWEST_SM),) ++GENCODE_FLAGS_LOWEST_SM += -gencode arch=compute_$(LOWEST_SM),code=compute_$(LOWEST_SM) ++endif + endif + + ifeq ($(TARGET_OS),darwin) +@@ -401,7 +407,7 @@ + endif + + $(PTX_FILE): memMapIpc_kernel.cu +- $(EXEC) $(NVCC) $(INCLUDES) $(ALL_CCFLAGS) $(GENCODE_FLAGS) -o $@ -ptx $< ++ $(EXEC) $(NVCC) $(INCLUDES) $(ALL_CCFLAGS) $(GENCODE_FLAGS_LOWEST_SM) -o $@ -ptx $< + $(EXEC) mkdir -p data + $(EXEC) cp -f $@ ./data + $(EXEC) mkdir -p ../../bin/$(TARGET_ARCH)/$(TARGET_OS)/$(BUILD_TYPE) diff --git a/easybuild/easyconfigs/c/CUDA-Samples/cuda-samples-11.6_multiple-sms.patch b/easybuild/easyconfigs/c/CUDA-Samples/cuda-samples-11.6_multiple-sms.patch new file mode 100644 index 00000000000..8c4e36f7e74 --- /dev/null +++ b/easybuild/easyconfigs/c/CUDA-Samples/cuda-samples-11.6_multiple-sms.patch @@ -0,0 +1,56 @@ +# Fixes "nvcc fatal: Option '--ptx (-ptx)' is not allowed when compiling for multiple GPU architectures" +# fatal compilation issue when building for multiple SM architectures +# More info, see https://github.com/NVIDIA/cuda-samples/issues/289 + +# Author: Caspar van Leeuwen + +diff -Nru cuda-samples-12.2.orig/Samples/3_CUDA_Features/memMapIPCDrv/Makefile cuda-samples-12.2/Samples/3_CUDA_Features/memMapIPCDrv/Makefile +--- cuda-samples-12.2.orig/Samples/3_CUDA_Features/memMapIPCDrv/Makefile 2024-07-29 12:14:28.538848000 +0200 ++++ cuda-samples-12.2/Samples/3_CUDA_Features/memMapIPCDrv/Makefile 2024-07-29 13:02:45.134261829 +0200 +@@ -313,6 +313,12 @@ + ifneq ($(HIGHEST_SM),) + GENCODE_FLAGS += -gencode arch=compute_$(HIGHEST_SM),code=compute_$(HIGHEST_SM) + endif ++ ++# Generate the explicit PTX file for the lowest SM architecture in $(SMS), so it works on all SMS listed there ++LOWEST_SM := $(firstword $(sort $(SMS))) ++ifneq ($(LOWEST_SM),) ++GENCODE_FLAGS_LOWEST_SM += -gencode arch=compute_$(LOWEST_SM),code=compute_$(LOWEST_SM) ++endif + endif + + ifeq ($(TARGET_OS),darwin) +@@ -394,7 +400,7 @@ + endif + + $(PTX_FILE): memMapIpc_kernel.cu +- $(EXEC) $(NVCC) $(INCLUDES) $(ALL_CCFLAGS) $(GENCODE_FLAGS) -o $@ -ptx $< ++ $(EXEC) $(NVCC) $(INCLUDES) $(ALL_CCFLAGS) $(GENCODE_FLAGS_LOWEST_SM) -o $@ -ptx $< + $(EXEC) mkdir -p data + $(EXEC) cp -f $@ ./data + $(EXEC) mkdir -p ../../../bin/$(TARGET_ARCH)/$(TARGET_OS)/$(BUILD_TYPE) +diff -Nru cuda-samples-12.2.orig/Samples/3_CUDA_Features/ptxjit/Makefile cuda-samples-12.2/Samples/3_CUDA_Features/ptxjit/Makefile +--- cuda-samples-12.2.orig/Samples/3_CUDA_Features/ptxjit/Makefile 2024-07-29 12:14:28.546771000 +0200 ++++ cuda-samples-12.2/Samples/3_CUDA_Features/ptxjit/Makefile 2024-07-29 13:02:38.741961008 +0200 +@@ -307,6 +307,12 @@ + ifneq ($(HIGHEST_SM),) + GENCODE_FLAGS += -gencode arch=compute_$(HIGHEST_SM),code=compute_$(HIGHEST_SM) + endif ++ ++# Generate the explicit PTX file for the lowest SM architecture in $(SMS), so it works on all SMS listed there ++LOWEST_SM := $(firstword $(sort $(SMS))) ++ifneq ($(LOWEST_SM),) ++GENCODE_FLAGS_LOWEST_SM += -gencode arch=compute_$(LOWEST_SM),code=compute_$(LOWEST_SM) ++endif + endif + + ifeq ($(TARGET_OS),darwin) +@@ -390,7 +396,7 @@ + endif + + $(PTX_FILE): ptxjit_kernel.cu +- $(EXEC) $(NVCC) $(INCLUDES) $(ALL_CCFLAGS) $(GENCODE_FLAGS) -o $@ -ptx $< ++ $(EXEC) $(NVCC) $(INCLUDES) $(ALL_CCFLAGS) $(GENCODE_FLAGS_LOWEST_SM) -o $@ -ptx $< + $(EXEC) mkdir -p data + $(EXEC) cp -f $@ ./data + $(EXEC) mkdir -p ../../../bin/$(TARGET_ARCH)/$(TARGET_OS)/$(BUILD_TYPE) diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-12.5.0.eb b/easybuild/easyconfigs/c/CUDA/CUDA-12.5.0.eb new file mode 100644 index 00000000000..0a81b7bd4c1 --- /dev/null +++ b/easybuild/easyconfigs/c/CUDA/CUDA-12.5.0.eb @@ -0,0 +1,24 @@ +name = 'CUDA' +version = '12.5.0' +local_nv_version = '555.42.02' + +homepage = 'https://developer.nvidia.com/cuda-toolkit' +description = """CUDA (formerly Compute Unified Device Architecture) is a parallel + computing platform and programming model created by NVIDIA and implemented by the + graphics processing units (GPUs) that they produce. CUDA gives developers access + to the virtual instruction set and memory of the parallel computational elements in CUDA GPUs.""" + +toolchain = SYSTEM + +source_urls = ['https://developer.download.nvidia.com/compute/cuda/%(version)s/local_installers/'] +sources = ['cuda_%%(version)s_%s_linux%%(cudaarch)s.run' % local_nv_version] +checksums = [{ + 'cuda_%%(version)s_%s_linux.run' % local_nv_version: + '90fcc7df48226434065ff12a4372136b40b9a4cbf0c8602bb763b745f22b7a99', + 'cuda_%%(version)s_%s_linux_ppc64le.run' % local_nv_version: + '33f39ad7bc624d5c8e59938990358cec80b9966431e34d1ab2d6115d78a3f264', + 'cuda_%%(version)s_%s_linux_sbsa.run' % local_nv_version: + 'e7b864c9ae27cef77cafc78614ec33cbb0a27606af9375deffa09c4269a07f04' +}] + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-12.6.0.eb b/easybuild/easyconfigs/c/CUDA/CUDA-12.6.0.eb new file mode 100644 index 00000000000..24c7b5f5c90 --- /dev/null +++ b/easybuild/easyconfigs/c/CUDA/CUDA-12.6.0.eb @@ -0,0 +1,22 @@ +name = 'CUDA' +version = '12.6.0' +local_nv_version = '560.28.03' + +homepage = 'https://developer.nvidia.com/cuda-toolkit' +description = """CUDA (formerly Compute Unified Device Architecture) is a parallel + computing platform and programming model created by NVIDIA and implemented by the + graphics processing units (GPUs) that they produce. CUDA gives developers access + to the virtual instruction set and memory of the parallel computational elements in CUDA GPUs.""" + +toolchain = SYSTEM + +source_urls = ['https://developer.download.nvidia.com/compute/cuda/%(version)s/local_installers/'] +sources = ['cuda_%%(version)s_%s_linux%%(cudaarch)s.run' % local_nv_version] +checksums = [{ + 'cuda_%%(version)s_%s_linux.run' % local_nv_version: + '31ab04394e69b14dd8656e2b44c2877db1a0e898dff8a7546a4c628438101b94', + 'cuda_%%(version)s_%s_linux_sbsa.run' % local_nv_version: + '398db7baca17d51ad5035c606714c96380c965fd1742478c743bc6bbb1d8f63c' +}] + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/c/CUDD/CUDD-3.0.0-GCC-13.2.0.eb b/easybuild/easyconfigs/c/CUDD/CUDD-3.0.0-GCC-13.2.0.eb new file mode 100644 index 00000000000..c1f83cad099 --- /dev/null +++ b/easybuild/easyconfigs/c/CUDD/CUDD-3.0.0-GCC-13.2.0.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'CUDD' +version = '3.0.0' + +homepage = 'https://github.com/ivmai/cudd' +description = """The CUDD package is a package written in C for the manipulation of + decision diagrams. It supports binary decision diagrams (BDDs), algebraic decision + diagrams (ADDs), and Zero-Suppressed BDDs (ZDDs).""" + +toolchain = {'name': 'GCC', 'version': '13.2.0'} + +source_urls = ['https://github.com/ivmai/cudd/archive/refs/tags'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['5fe145041c594689e6e7cf4cd623d5f2b7c36261708be8c9a72aed72cf67acce'] + +sanity_check_paths = { + 'files': ['include/cudd.h', 'lib/libcudd.a'], + 'dirs': [], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/c/CUTLASS/CUTLASS-3.4.0-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/c/CUTLASS/CUTLASS-3.4.0-foss-2023a-CUDA-12.1.1.eb new file mode 100644 index 00000000000..3322e6b4b56 --- /dev/null +++ b/easybuild/easyconfigs/c/CUTLASS/CUTLASS-3.4.0-foss-2023a-CUDA-12.1.1.eb @@ -0,0 +1,49 @@ +easyblock = 'CMakeMake' + +name = 'CUTLASS' +version = '3.4.0' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/NVIDIA/cutlass' +description = """CUTLASS is a collection of CUDA C++ template +abstractions for implementing high-performance matrix-matrix +multiplication (GEMM) and related computations at all levels and scales +within CUDA. It incorporates strategies for hierarchical decomposition +and data movement similar to those used to implement cuBLAS and cuDNN. +CUTLASS decomposes these "moving parts" into reusable, modular software +components abstracted by C++ template classes. Primitives for different +levels of a conceptual parallelization hierarchy can be specialized and +tuned via custom tiling sizes, data types, and other algorithmic policy. +The resulting flexibility simplifies their use as building blocks within +custom kernels and applications.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +github_account = 'NVIDIA' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['49f4b854acc2a520126ceefe4f701cfe8c2b039045873e311b1f10a8ca5d5de1'] + +builddependencies = [ + ('CMake', '3.26.3'), + ('Python', '3.11.3'), +] + +dependencies = [ + ('CUDA', '12.1.1', '', SYSTEM), + ('cuDNN', '8.9.2.26', versionsuffix, SYSTEM), +] + +_copts = [ + '-DCUTLASS_NVCC_ARCHS="%(cuda_cc_cmake)s"', + '-DCUTLASS_ENABLE_CUBLAS=1', + '-DCUTLASS_ENABLE_CUDNN=1', +] +configopts = ' '.join(_copts) + +sanity_check_paths = { + 'files': ['include/cutlass/cutlass.h', 'lib/libcutlass.%s' % SHLIB_EXT], + 'dirs': ['lib/cmake'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/c/CUnit/CUnit-2.1-3-GCCcore-12.3.0.eb b/easybuild/easyconfigs/c/CUnit/CUnit-2.1-3-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..827f7ea4e80 --- /dev/null +++ b/easybuild/easyconfigs/c/CUnit/CUnit-2.1-3-GCCcore-12.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'CUnit' +version = '2.1-3' + +homepage = 'https://sourceforge.net/projects/cunit/' +description = "Automated testing framework for C." + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCE_TAR_BZ2] +checksums = ['f5b29137f845bb08b77ec60584fdb728b4e58f1023e6f249a464efa49a40f214'] + +builddependencies = [ + ('binutils', '2.40'), + ('Autotools', '20220317'), +] + +preconfigopts = "autoreconf -i && " + +sanity_check_paths = { + 'files': ['lib/libcunit.a', 'lib/libcunit.%s' % SHLIB_EXT], + 'dirs': ['include/CUnit', 'lib/pkgconfig', 'share'], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/c/CVX/CVX-2.2-MATLAB-2023a.eb b/easybuild/easyconfigs/c/CVX/CVX-2.2-MATLAB-2023a.eb new file mode 100644 index 00000000000..b3c3ec1b113 --- /dev/null +++ b/easybuild/easyconfigs/c/CVX/CVX-2.2-MATLAB-2023a.eb @@ -0,0 +1,36 @@ +easyblock = 'Tarball' + +name = 'CVX' +version = '2.2' +_matlab_ver = '2023a' +versionsuffix = '-MATLAB-%s' % _matlab_ver + +homepage = 'https://cvxr.com/cvx/' +description = """CVX is a Matlab-based modeling system for convex optimization. + CVX turns Matlab into a modeling language, allowing constraints and objectives + to be specified using standard Matlab expression syntax. +""" + +toolchain = SYSTEM + +source_urls = ['https://web.cvxr.com/cvx/'] +sources = ['%(namelower)s-a64.tar.gz'] +checksums = ['16e4622c80f2bf63152aaee59db4fe42afa4d2282179e5d216358953c7f9ea4d'] + +dependencies = [ + ('MATLAB', _matlab_ver), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib', 'commands', 'sedumi', 'sdpt3'], +} + +modloadmsg = "IMPORTANT: You need to run `cvx_setup` once inside MATLAB before using CVX." + +modextrapaths = { + 'MATLABPATH': ['', 'functions/vec_', 'structures', 'lib', 'functions', + 'commands', 'builtins'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/c/CVXOPT/CVXOPT-1.3.1-foss-2022a.eb b/easybuild/easyconfigs/c/CVXOPT/CVXOPT-1.3.1-foss-2022a.eb index 9bac0454227..2c32ff36414 100644 --- a/easybuild/easyconfigs/c/CVXOPT/CVXOPT-1.3.1-foss-2022a.eb +++ b/easybuild/easyconfigs/c/CVXOPT/CVXOPT-1.3.1-foss-2022a.eb @@ -32,8 +32,15 @@ use_pip = True sanity_pip_check = True download_dep_fail = True -preinstallopts = 'CVXOPT_BUILD_FFTW=1 CVXOPT_BUILD_GSL=1 CVXOPT_BLAS_EXTRA_LINK_ARGS="$LIBLAPACK" ' -preinstallopts += 'CVXOPT_FFTW_EXTRA_LINK_ARGS="$LIBFFT" CVXOPT_SUITESPARSE_SRC_DIR=$EBROOTSUITESPARSE' +preinstallopts = " ".join([ + 'CVXOPT_BUILD_FFTW=1', + 'CVXOPT_BUILD_GSL=1', + 'CVXOPT_BLAS_EXTRA_LINK_ARGS="$LIBBLAS"', + 'CVXOPT_LAPACK_EXTRA_LINK_ARGS="$LIBLAPACK"', + 'CVXOPT_FFTW_EXTRA_LINK_ARGS="$LIBFFT"', + 'CVXOPT_SUITESPARSE_LIB_DIR=$EBROOTSUITESPARSE/lib', + 'CVXOPT_SUITESPARSE_INC_DIR=$EBROOTSUITESPARSE/include', +]) installopts = ' --no-binary cvxopt' diff --git a/easybuild/easyconfigs/c/CVXOPT/CVXOPT-1.3.2-foss-2023a.eb b/easybuild/easyconfigs/c/CVXOPT/CVXOPT-1.3.2-foss-2023a.eb new file mode 100644 index 00000000000..d6793ad49bb --- /dev/null +++ b/easybuild/easyconfigs/c/CVXOPT/CVXOPT-1.3.2-foss-2023a.eb @@ -0,0 +1,49 @@ +easyblock = 'PythonPackage' + +name = 'CVXOPT' +version = '1.3.2' + +homepage = 'https://cvxopt.org' +description = """CVXOPT is a free software package for convex optimization based on the Python programming language. + Its main purpose is to make the development of software for convex optimization applications straightforward by + building on Python's extensive standard library and on the strengths of Python as a high-level programming language. +""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'pic': True} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +patches = ['CVXOPT-1.3.1_fix-setup-py.patch'] + +checksums = [ + '3461fa42c1b2240ba4da1d985ca73503914157fc4c77417327ed6d7d85acdbe6', # cvxopt-1.3.2.tar.gz + '350904c0427d4652fc73b95b7e0d78a17c917cb94ed6c356dbbbfb07f2173849', # CVXOPT-1.3.1_fix-setup-py.patch +] + +dependencies = [ + ('Python', '3.11.3'), + ('SuiteSparse', '7.1.0'), + ('GSL', '2.7'), +] + +use_pip = True +sanity_pip_check = True +download_dep_fail = True + +preinstallopts = " ".join([ + 'CVXOPT_BUILD_FFTW=1', + 'CVXOPT_BUILD_GSL=1', + 'CVXOPT_BLAS_EXTRA_LINK_ARGS="$LIBBLAS"', + 'CVXOPT_LAPACK_EXTRA_LINK_ARGS="$LIBLAPACK"', + 'CVXOPT_FFTW_EXTRA_LINK_ARGS="$LIBFFT"', + 'CVXOPT_SUITESPARSE_LIB_DIR=$EBROOTSUITESPARSE/lib', + 'CVXOPT_SUITESPARSE_INC_DIR=$EBROOTSUITESPARSE/include', +]) + +installopts = ' --no-binary cvxopt' + +sanity_check_commands = ['cd %(builddir)s/%(namelower)s-%(version)s && python -m unittest discover -s tests'] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/c/Cassiopeia/Cassiopeia-2.0.0-foss-2023a.eb b/easybuild/easyconfigs/c/Cassiopeia/Cassiopeia-2.0.0-foss-2023a.eb index 69b70834b9b..bdcee918b8b 100644 --- a/easybuild/easyconfigs/c/Cassiopeia/Cassiopeia-2.0.0-foss-2023a.eb +++ b/easybuild/easyconfigs/c/Cassiopeia/Cassiopeia-2.0.0-foss-2023a.eb @@ -11,6 +11,8 @@ toolchain = {'name': 'foss', 'version': '2023a'} builddependencies = [ ('CMake', '3.26.3'), ('poetry', '1.5.1'), + ('hatchling', '1.18.0'), + ('hatch-jupyter-builder', '0.9.1'), ] dependencies = [ @@ -27,7 +29,6 @@ dependencies = [ ('PyYAML', '6.0'), ('typing-extensions', '4.9.0'), ('tqdm', '4.66.1'), - ('hatchling', '1.18.0'), ('BeautifulSoup', '4.12.2'), ('statsmodels', '0.14.1'), ('Seaborn', '0.13.2'), @@ -39,12 +40,6 @@ use_pip = True sanity_pip_check = True exts_list = [ - ('hatch_jupyter_builder', '0.9.1', { - 'checksums': ['79278198d124c646b799c5e8dca8504aed9dcaaa88d071a09eb0b5c2009a58ad'], - }), - ('hatch_nodejs_version', '0.3.2', { - 'checksums': ['8a7828d817b71e50bbbbb01c9bfc0b329657b7900c56846489b9c958de15b54c'], - }), ('deprecation', '2.1.0', { 'checksums': ['72b3bde64e5d778694b0cf68178aed03d15e15477116add3fb773e581f9518ff'], }), diff --git a/easybuild/easyconfigs/c/Catch2/Catch2-2.13.10-GCCcore-13.3.0.eb b/easybuild/easyconfigs/c/Catch2/Catch2-2.13.10-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..00abfac39c8 --- /dev/null +++ b/easybuild/easyconfigs/c/Catch2/Catch2-2.13.10-GCCcore-13.3.0.eb @@ -0,0 +1,30 @@ +easyblock = 'CMakeMake' + +name = 'Catch2' +version = '2.13.10' + +homepage = 'https://github.com/catchorg/Catch2' +description = """A modern, C++-native, header-only, + test framework for unit-tests, TDD and BDD + - using C++11, C++14, C++17 and later +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://github.com/catchorg/Catch2/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['d54a712b7b1d7708bc7a819a8e6e47b2fde9536f487b89ccbca295072a7d9943'] + +builddependencies = [ + ('binutils', '2.42'), # to make CMake compiler health check pass on old systems + ('CMake', '3.29.3'), +] + +separate_build_dir = True + +sanity_check_paths = { + 'files': ['include/catch2/catch.hpp'], + 'dirs': ['lib/cmake'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/c/CellBender/CellBender-0.3.0-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/c/CellBender/CellBender-0.3.0-foss-2023a-CUDA-12.1.1.eb new file mode 100644 index 00000000000..94c6fc2c609 --- /dev/null +++ b/easybuild/easyconfigs/c/CellBender/CellBender-0.3.0-foss-2023a-CUDA-12.1.1.eb @@ -0,0 +1,72 @@ +easyblock = 'PythonBundle' + +name = 'CellBender' +version = '0.3.0' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'http://github.com/broadinstitute/CellBender' +description = """ +CellBender is a software package for eliminating technical artifacts from +high-throughput single-cell RNA sequencing (scRNA-seq) data. +""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('CUDA', '12.1.1', '', SYSTEM), + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('matplotlib', '3.7.2'), + ('PyTorch', '2.1.2', versionsuffix), + ('IPython', '8.14.0'), + ('anndata', '0.10.5.post1'), + ('jupyter-contrib-nbextensions', '0.7.0'), + ('pyro-ppl', '1.9.0', versionsuffix), + ('loompy', '3.0.7'), + ('PyTables', '3.8.0'), + ('Qtconsole', '5.5.1'), +] + +use_pip = True + +exts_list = [ + ('async-timeout', '4.0.3', { + 'checksums': ['4640d96be84d82d02ed59ea2b7105a0f7b33abe8703703cd0ab0bf87c427522f'], + }), + ('traitlets', '5.14.1', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['2e5a030e6eff91737c643231bfcf04a65b0132078dad75e4936700b213652e74'], + }), + ('jupyter_console', '6.6.3', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['309d33409fcc92ffdad25f0bcdf9a4a9daa61b6f341177570fdac03de5352485'], + }), + ('jupyter', '1.0.0', { + 'checksums': ['d9dc4b3318f310e34c82951ea5d6683f67bed7def4b259fafbfe4f1beb1d8e5f'], + }), + ('notebook', '6.5.7', { + 'checksums': ['04eb9011dfac634fbd4442adaf0a8c27cd26beef831fe1d19faf930c327768e4'], + }), + ('mistune', '0.8.4', { + 'checksums': ['59a3429db53c50b5c6bcc8a07f8848cb00d7dc8bdb431a4ab41920d201d4756e'], + }), + ('nbconvert', '6.5.4', { + 'checksums': ['9e3c7c6d491374cbdd5f35d268c05809357716d346f4573186bbeab32ee50bc1'], + }), + ('cellbender', version, { + 'checksums': ['94a46fb2b5921414ea86213cfdebca267b9ba6ba02df854cbd353980ab3aff42'], + }), +] + +sanity_check_paths = { + 'files': ['bin/cellbender'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "cellbender --help", +] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/CellBender/CellBender-0.3.0-foss-2023a.eb b/easybuild/easyconfigs/c/CellBender/CellBender-0.3.0-foss-2023a.eb new file mode 100644 index 00000000000..5fb9920fb70 --- /dev/null +++ b/easybuild/easyconfigs/c/CellBender/CellBender-0.3.0-foss-2023a.eb @@ -0,0 +1,70 @@ +easyblock = 'PythonBundle' + +name = 'CellBender' +version = '0.3.0' + +homepage = 'http://github.com/broadinstitute/CellBender' +description = """ +CellBender is a software package for eliminating technical artifacts from +high-throughput single-cell RNA sequencing (scRNA-seq) data. +""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('matplotlib', '3.7.2'), + ('PyTorch', '2.1.2'), + ('IPython', '8.14.0'), + ('anndata', '0.10.5.post1'), + ('jupyter-contrib-nbextensions', '0.7.0'), + ('pyro-ppl', '1.9.0'), + ('loompy', '3.0.7'), + ('PyTables', '3.8.0'), + ('Qtconsole', '5.5.1'), +] + +use_pip = True + +exts_list = [ + ('async-timeout', '4.0.3', { + 'checksums': ['4640d96be84d82d02ed59ea2b7105a0f7b33abe8703703cd0ab0bf87c427522f'], + }), + ('traitlets', '5.14.1', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['2e5a030e6eff91737c643231bfcf04a65b0132078dad75e4936700b213652e74'], + }), + ('jupyter_console', '6.6.3', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['309d33409fcc92ffdad25f0bcdf9a4a9daa61b6f341177570fdac03de5352485'], + }), + ('jupyter', '1.0.0', { + 'checksums': ['d9dc4b3318f310e34c82951ea5d6683f67bed7def4b259fafbfe4f1beb1d8e5f'], + }), + ('notebook', '6.5.7', { + 'checksums': ['04eb9011dfac634fbd4442adaf0a8c27cd26beef831fe1d19faf930c327768e4'], + }), + ('mistune', '0.8.4', { + 'checksums': ['59a3429db53c50b5c6bcc8a07f8848cb00d7dc8bdb431a4ab41920d201d4756e'], + }), + ('nbconvert', '6.5.4', { + 'checksums': ['9e3c7c6d491374cbdd5f35d268c05809357716d346f4573186bbeab32ee50bc1'], + }), + ('cellbender', version, { + 'checksums': ['94a46fb2b5921414ea86213cfdebca267b9ba6ba02df854cbd353980ab3aff42'], + }), +] + +sanity_check_paths = { + 'files': ['bin/cellbender'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "cellbender --help", +] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/CellBender/CellBender-0.3.1-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/c/CellBender/CellBender-0.3.1-foss-2022a-CUDA-11.7.0.eb deleted file mode 100644 index 88f92ec75ab..00000000000 --- a/easybuild/easyconfigs/c/CellBender/CellBender-0.3.1-foss-2022a-CUDA-11.7.0.eb +++ /dev/null @@ -1,85 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'CellBender' -local_commit = 'e2fb597' -version = '0.3.1' -versionsuffix = '-CUDA-%(cudaver)s' - -homepage = 'http://github.com/broadinstitute/CellBender' -description = """ -CellBender is a software package for eliminating technical artifacts from -high-throughput single-cell RNA sequencing (scRNA-seq) data. -""" - -toolchain = {'name': 'foss', 'version': '2022a'} - -dependencies = [ - ('CUDA', '11.7.0', '', SYSTEM), - ('Python', '3.10.4'), - ('SciPy-bundle', '2022.05'), - ('matplotlib', '3.5.2'), - ('PyTorch', '1.12.0', versionsuffix), - ('IPython', '8.5.0'), - ('anndata', '0.8.0'), - ('jupyter-contrib-nbextensions', '0.7.0'), - ('pyro-ppl', '1.8.4', versionsuffix), - ('loompy', '3.0.7'), - ('PyTables', '3.8.0'), - ('Qtconsole', '5.4.0'), -] - -use_pip = True - -local_comm_preinstallopts = """sed -i -e 's/^requires.*hatchling.*/requires = ["setuptools"]/g' """ -local_comm_preinstallopts += """-e 's/^build-backend.*/build-backend = "setuptools.build_meta"/g' """ -local_comm_preinstallopts += """-e 's/^dynamic = .*version.*/version = "%(version)s"/g' pyproject.toml && """ - -exts_list = [ - ('setuptools', '69.0.3', { - 'checksums': ['be1af57fc409f93647f2e8e4573a142ed38724b8cdd389706a867bb4efcf1e78'], - }), - ('comm', '0.2.1', { - 'checksums': ['0bc91edae1344d39d3661dcbc36937181fdaddb304790458f8b044dbc064b89a'], - 'preinstallopts': local_comm_preinstallopts, - }), - # jupyter-console 6.6.3 requires ipykernel>=6.14 - ('ipykernel', '6.20.2', { - 'source_tmpl': SOURCE_PY3_WHL, - 'checksums': ['5d0675d5f48bf6a95fd517d7b70bcb3b2c5631b2069949b5c2d6e1d7477fb5a0'], - }), - # jupyter-console 6.6.3 requires jupyter-core!=5.0.*,>=4.12 - ('jupyter_core', '4.12.0', { - 'source_tmpl': SOURCE_PY3_WHL, - 'checksums': ['a54672c539333258495579f6964144924e0aa7b07f7069947bef76d7ea5cb4c1'], - }), - # jupyter-console 6.6.3 requires traitlets>=5.4 - ('traitlets', '5.14.1', { - 'source_tmpl': SOURCE_PY3_WHL, - 'checksums': ['2e5a030e6eff91737c643231bfcf04a65b0132078dad75e4936700b213652e74'], - }), - ('jupyter_console', '6.6.3', { - 'source_tmpl': SOURCE_PY3_WHL, - 'checksums': ['309d33409fcc92ffdad25f0bcdf9a4a9daa61b6f341177570fdac03de5352485'], - }), - ('jupyter', '1.0.0', { - 'checksums': ['d9dc4b3318f310e34c82951ea5d6683f67bed7def4b259fafbfe4f1beb1d8e5f'], - }), - ('cellbender', version, { - 'source_urls': ['https://github.com/broadinstitute/CellBender/archive'], - 'sources': [{'download_filename': '%s.tar.gz' % local_commit, 'filename': '%(name)s-%(version)s.tar.gz'}], - 'checksums': ['7eb67837d28495adb82147e80a2ab58eeb406c5d91aa69dd0cc120d9cb3d6396'], - }), -] - -sanity_check_paths = { - 'files': ['bin/cellbender'], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -sanity_check_commands = [ - "cellbender --help", -] - -sanity_pip_check = True - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/CellBender/CellBender-0.3.1-foss-2022a.eb b/easybuild/easyconfigs/c/CellBender/CellBender-0.3.1-foss-2022a.eb deleted file mode 100644 index 798e18442ab..00000000000 --- a/easybuild/easyconfigs/c/CellBender/CellBender-0.3.1-foss-2022a.eb +++ /dev/null @@ -1,83 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'CellBender' -local_commit = 'e2fb597' -version = '0.3.1' - -homepage = 'http://github.com/broadinstitute/CellBender' -description = """ -CellBender is a software package for eliminating technical artifacts from -high-throughput single-cell RNA sequencing (scRNA-seq) data. -""" - -toolchain = {'name': 'foss', 'version': '2022a'} - -dependencies = [ - ('Python', '3.10.4'), - ('SciPy-bundle', '2022.05'), - ('matplotlib', '3.5.2'), - ('PyTorch', '1.12.0'), - ('IPython', '8.5.0'), - ('anndata', '0.8.0'), - ('jupyter-contrib-nbextensions', '0.7.0'), - ('pyro-ppl', '1.8.4'), - ('loompy', '3.0.7'), - ('PyTables', '3.8.0'), - ('Qtconsole', '5.4.0'), -] - -use_pip = True - -local_comm_preinstallopts = """sed -i -e 's/^requires.*hatchling.*/requires = ["setuptools"]/g' """ -local_comm_preinstallopts += """-e 's/^build-backend.*/build-backend = "setuptools.build_meta"/g' """ -local_comm_preinstallopts += """-e 's/^dynamic = .*version.*/version = "%(version)s"/g' pyproject.toml && """ - -exts_list = [ - ('setuptools', '69.0.3', { - 'checksums': ['be1af57fc409f93647f2e8e4573a142ed38724b8cdd389706a867bb4efcf1e78'], - }), - ('comm', '0.2.1', { - 'checksums': ['0bc91edae1344d39d3661dcbc36937181fdaddb304790458f8b044dbc064b89a'], - 'preinstallopts': local_comm_preinstallopts, - }), - # jupyter-console 6.6.3 requires ipykernel>=6.14 - ('ipykernel', '6.20.2', { - 'source_tmpl': SOURCE_PY3_WHL, - 'checksums': ['5d0675d5f48bf6a95fd517d7b70bcb3b2c5631b2069949b5c2d6e1d7477fb5a0'], - }), - # jupyter-console 6.6.3 requires jupyter-core!=5.0.*,>=4.12 - ('jupyter_core', '4.12.0', { - 'source_tmpl': SOURCE_PY3_WHL, - 'checksums': ['a54672c539333258495579f6964144924e0aa7b07f7069947bef76d7ea5cb4c1'], - }), - # jupyter-console 6.6.3 requires traitlets>=5.4 - ('traitlets', '5.14.1', { - 'source_tmpl': SOURCE_PY3_WHL, - 'checksums': ['2e5a030e6eff91737c643231bfcf04a65b0132078dad75e4936700b213652e74'], - }), - ('jupyter_console', '6.6.3', { - 'source_tmpl': SOURCE_PY3_WHL, - 'checksums': ['309d33409fcc92ffdad25f0bcdf9a4a9daa61b6f341177570fdac03de5352485'], - }), - ('jupyter', '1.0.0', { - 'checksums': ['d9dc4b3318f310e34c82951ea5d6683f67bed7def4b259fafbfe4f1beb1d8e5f'], - }), - ('cellbender', version, { - 'source_urls': ['https://github.com/broadinstitute/CellBender/archive'], - 'sources': [{'download_filename': '%s.tar.gz' % local_commit, 'filename': '%(name)s-%(version)s.tar.gz'}], - 'checksums': ['7eb67837d28495adb82147e80a2ab58eeb406c5d91aa69dd0cc120d9cb3d6396'], - }), -] - -sanity_check_paths = { - 'files': ['bin/cellbender'], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -sanity_check_commands = [ - "cellbender --help", -] - -sanity_pip_check = True - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/CellOracle/CellOracle-0.18.0-foss-2023a.eb b/easybuild/easyconfigs/c/CellOracle/CellOracle-0.18.0-foss-2023a.eb new file mode 100644 index 00000000000..d6eb8f4cead --- /dev/null +++ b/easybuild/easyconfigs/c/CellOracle/CellOracle-0.18.0-foss-2023a.eb @@ -0,0 +1,66 @@ +easyblock = 'PythonBundle' + +name = 'CellOracle' +version = '0.18.0' + +homepage = 'https://github.com/morris-lab/CellOracle' +description = """CellOracle is a Python library for in silico gene perturbation analyses using single-cell omics data +and Gene Regulatory Network models.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('R', '4.3.2'), + ('SciPy-bundle', '2023.07'), + ('Python-bundle-PyPI', '2023.06'), + ('numba', '0.58.1'), + ('matplotlib', '3.7.2'), + ('Seaborn', '0.13.2'), + ('scikit-learn', '1.3.1'), + ('h5py', '3.9.0'), + ('velocyto', '0.17.17'), + ('umap-learn', '0.5.5'), + ('Arrow', '14.0.1'), + ('tqdm', '4.66.1'), + ('python-igraph', '0.11.4'), + ('IPython', '8.14.0'), + ('scanpy', '1.9.8'), + ('GOATOOLS', '1.4.5'), + ('genomepy', '0.16.1'), + ('GimmeMotifs', '0.17.2'), + ('anndata', '0.10.5.post1'), + ('python-louvain', '0.16'), + ('jupyter-contrib-nbextensions', '0.7.0'), + ('Qtconsole', '5.5.1'), +] + +use_pip = True + +# remove louvain from requirements, since CellOracle doesn't actually use it at all +local_preinstallopts = "sed -i '/louvain/d' requirements.txt && " +# drop strict version requirement for matplotlib dependency +local_preinstallopts += "sed -i 's/matplotlib.*/matplotlib/g' requirements.txt && " +# drop strict version requirement for pandas dependency +local_preinstallopts += "sed -i 's/pandas.*/pandas/g' requirements.txt && " + + +exts_list = [ + ('jupyter_console', '6.6.3', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['309d33409fcc92ffdad25f0bcdf9a4a9daa61b6f341177570fdac03de5352485'], + }), + ('jupyter', '1.0.0', { + 'checksums': ['d9dc4b3318f310e34c82951ea5d6683f67bed7def4b259fafbfe4f1beb1d8e5f'], + }), + ('celloracle', version, { + 'preinstallopts': local_preinstallopts, + 'checksums': ['a73bbdae36289748051e073409d853489a233bda90f50ab5031131b92dda2133'], + }), +] + +sanity_check_commands = ["python -c 'import celloracle; celloracle.check_python_requirements()'"] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/CellRanger-ARC/CellRanger-ARC-2.0.2.eb b/easybuild/easyconfigs/c/CellRanger-ARC/CellRanger-ARC-2.0.2.eb new file mode 100644 index 00000000000..fc7d6955925 --- /dev/null +++ b/easybuild/easyconfigs/c/CellRanger-ARC/CellRanger-ARC-2.0.2.eb @@ -0,0 +1,37 @@ +# The STAR binary included in this version has been vectorized with AVX +# hence it is not recommended for systems that do not support it. + +easyblock = 'Tarball' + +name = 'CellRanger-ARC' +version = '2.0.2' + +homepage = 'https://support.10xgenomics.com/single-cell-multiome-atac-gex/software/pipelines/latest/' +homepage += 'what-is-cell-ranger-arc' +description = """Cell Ranger ARC is a set of analysis pipelines that process + Chromium Single Cell Multiome ATAC + Gene Expression sequencing data to generate a + variety of analyses pertaining to gene expression, chromatin accessibility and + their linkage. Furthermore, since the ATAC and gene expression measurements are on + the very same cell, we are able to perform analyses that link chromatin + accessibility and gene expression.""" + +toolchain = SYSTEM + +download_instructions = """ +Download manually from: +https://www.10xgenomics.com/support/software/cell-ranger-arc/downloads +""" + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['02a02457938dcf8dcb418b6c65effac06b210282d167437bfa8b2f10023dacae'] + +keepsymlinks = True + +sanity_check_paths = { + 'files': ["bin/cellranger-arc"], + 'dirs': ["bin/rna", "bin/tenkit"], +} + +sanity_check_commands = ['cellranger-arc -h'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/CellRanger/CellRanger-8.0.1.eb b/easybuild/easyconfigs/c/CellRanger/CellRanger-8.0.1.eb new file mode 100644 index 00000000000..baa6b095438 --- /dev/null +++ b/easybuild/easyconfigs/c/CellRanger/CellRanger-8.0.1.eb @@ -0,0 +1,31 @@ +# The STAR binary included in this version has been vectorized with AVX +# hence it is not recommended for systems that do not support it. + +easyblock = 'Tarball' + +name = 'CellRanger' +version = '8.0.1' + +homepage = 'https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger' +description = """Cell Ranger is a set of analysis pipelines that process Chromium + single-cell RNA-seq output to align reads, generate gene-cell matrices and perform + clustering and gene expression analysis.""" + +toolchain = SYSTEM + +download_instructions = """ +Download manually from https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest +""" +sources = [SOURCELOWER_TAR_GZ] +checksums = ['ea2a35ac0f03961bab2ea485565d60cc6709a981c833a5e6c2b13a8fef641e81'] + +keepsymlinks = True + +sanity_check_paths = { + 'files': ['bin/cellranger'], + 'dirs': ['bin/rna', 'bin/tenkit'], +} + +sanity_check_commands = ['cellranger testrun --id=tiny'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/CellRanger/CellRanger-9.0.0.eb b/easybuild/easyconfigs/c/CellRanger/CellRanger-9.0.0.eb new file mode 100644 index 00000000000..b25f6cc0d72 --- /dev/null +++ b/easybuild/easyconfigs/c/CellRanger/CellRanger-9.0.0.eb @@ -0,0 +1,31 @@ +# The STAR binary included in this version has been vectorized with AVX +# hence it is not recommended for systems that do not support it. + +easyblock = 'Tarball' + +name = 'CellRanger' +version = '9.0.0' + +homepage = 'https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger' +description = """Cell Ranger is a set of analysis pipelines that process Chromium + single-cell RNA-seq output to align reads, generate gene-cell matrices and perform + clustering and gene expression analysis.""" + +toolchain = SYSTEM + +download_instructions = """ +Download manually from https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest +""" +sources = [SOURCELOWER_TAR_GZ] +checksums = ['d57e574630bc0871299ba0e3e3b9a770b572cd35a819c52bfd58403ccd72035d'] + +keepsymlinks = True + +sanity_check_paths = { + 'files': ['bin/cellranger'], + 'dirs': ['bin/rna', 'bin/tenkit'], +} + +sanity_check_commands = ['cellranger testrun --id=tiny'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/CellRank/CellRank-2.0.2-foss-2022a.eb b/easybuild/easyconfigs/c/CellRank/CellRank-2.0.2-foss-2022a.eb new file mode 100644 index 00000000000..1bd10280160 --- /dev/null +++ b/easybuild/easyconfigs/c/CellRank/CellRank-2.0.2-foss-2022a.eb @@ -0,0 +1,67 @@ +easyblock = 'PythonBundle' + +name = 'CellRank' +version = '2.0.2' + +homepage = 'https://cellrank.readthedocs.io/en/stable/' +description = """CellRank is a toolkit to uncover cellular dynamics based on + Markov state modeling of single-cell data. It contains two main modules: +kernels compute cell-cell transition probabilities and estimators generate +hypothesis based on these. """ + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('petsc4py', '3.17.4'), + ('slepc4py', '3.17.2'), + ('scikit-learn', '1.1.2'), + ('scVelo', '0.2.5'), + ('scanpy', '1.9.1'), # also provides anndata + ('numba', '0.56.4'), + ('networkx', '2.8.4'), + ('matplotlib', '3.5.2'), + ('Seaborn', '0.12.1'), + ('wrapt', '1.15.0'), +] + +use_pip = True + +_preinstallopts_pygam = """sed -i -e 's/numpy = .*/numpy = "^1.22.3"/g' """ +_preinstallopts_pygam += """-e 's/scipy = .*/scipy = "^1.8.1"/g' pyproject.toml && """ + +exts_list = [ + ('docrep', '0.3.2', { + 'checksums': ['ed8a17e201abd829ef8da78a0b6f4d51fb99a4cbd0554adbed3309297f964314'], + }), + ('python-utils', '3.8.1', { + 'checksums': ['ec3a672465efb6c673845a43afcfafaa23d2594c24324a40ec18a0c59478dc0b'], + }), + ('progressbar2', '4.3.2', { + 'modulename': 'progressbar', + 'checksums': ['c37e6e1b4e57ab43f95c3d0e8d90061bec140e4fed56b8343183db3aa1e19a52'], + }), + ('pygam', '0.9.0', { + 'patches': ['pygam-0.9.0_fix-poetry.patch'], + 'checksums': [ + {'pygam-0.9.0.tar.gz': 'dba62285a275cdd15a6adf764f6717b3cd077502f01cf1bcee5ce7cbda221956'}, + {'pygam-0.9.0_fix-poetry.patch': '90460a5416167f146f5bf2c55e46c23d1e7a8f864652e24665354a1b39d7e3d0'}, + ], + 'preinstallopts': _preinstallopts_pygam, + }), + ('pygpcca', '1.0.4', { + 'checksums': ['5e3b49279abc62d25133811daeee050715f995ff02042c46e2a2034331d090d1'], + 'preinstallopts': "sed -i 's/jinja2==/jinja2>=/g' requirements.txt && ", + }), + ('cellrank', version, { + 'checksums': ['47c1d2e953ac91f572937d816142b4ac5f0c876174c60f857562de76a9f8aa61'], + # strip away too strict version requirements for pandas + anndata + 'preinstallopts': "sed -i -e 's/pandas>=1.5.0/pandas/g' -e 's/anndata>=0.9/anndata/g' pyproject.toml && ", + }), +] + +sanity_pip_check = True + +sanity_check_commands = ["python -c 'import cellrank as cr'"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/CellRank/CellRank-2.0.2-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/c/CellRank/CellRank-2.0.2-foss-2023a-CUDA-12.1.1.eb new file mode 100644 index 00000000000..3ec16f6ab04 --- /dev/null +++ b/easybuild/easyconfigs/c/CellRank/CellRank-2.0.2-foss-2023a-CUDA-12.1.1.eb @@ -0,0 +1,78 @@ +easyblock = 'PythonBundle' + +name = 'CellRank' +version = '2.0.2' +versionsuffix = '-CUDA-12.1.1' + +homepage = 'https://cellrank.readthedocs.io/en/stable/' +description = """CellRank is a toolkit to uncover cellular dynamics based on + Markov state modeling of single-cell data. It contains two main modules: +kernels compute cell-cell transition probabilities and estimators generate +hypothesis based on these. """ + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [('poetry', '1.5.1')] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('anndata', '0.10.5.post1'), + ('matplotlib', '3.7.2'), + ('networkx', '3.1'), + ('numba', '0.58.1'), + ('scanpy', '1.9.8'), + ('scikit-learn', '1.3.1'), + ('scVelo', '0.3.1'), + ('Seaborn', '0.13.2'), + ('wrapt', '1.15.0'), + ('PyTorch', '2.1.2', versionsuffix), + ('wandb', '0.16.1'), + ('PyTorch-Lightning', '2.2.1', versionsuffix), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('loguru', '0.7.2', { + 'checksums': ['e671a53522515f34fd406340ee968cb9ecafbc4b36c679da03c18fd8d0bd51ac'], + }), + ('nam', '0.0.3', { + 'checksums': ['48400d12b5f29fdd1671aebdf78d7f41bcac4f5c8ab7ed48770ee0c4fbc0673b'], + }), + ('python-utils', '3.8.2', { + 'checksums': ['c5d161e4ca58ce3f8c540f035e018850b261a41e7cb98f6ccf8e1deb7174a1f1'], + }), + ('progressbar2', '4.4.1', { + 'modulename': 'progressbar', + 'checksums': ['97d323ba03ad3d017a4d047fd0b2d3e733c5a360c07f87d269f96641c3de729f'], + }), + ('dunamai', '1.19.2', { + 'checksums': ['3be4049890763e19b8df1d52960dbea60b3e263eb0c96144a677ae0633734d2e'], + }), + ('poetry_dynamic_versioning', '1.2.0', { + 'checksums': ['1a7bbdba2530499e73dfc6ac0af19de29020ab4aaa3e507573877114e6b71ed6'], + }), + ('pygpcca', '1.0.4', { + 'preinstallopts': "sed -i 's/jinja2==3.0.3/jinja2>=3.0.3/' requirements.txt && ", + 'checksums': ['5e3b49279abc62d25133811daeee050715f995ff02042c46e2a2034331d090d1'], + }), + ('pygam', '0.9.1', { + 'checksums': ['a321a017bf485ed93fc6233e02621f8e7eab3d4f8971371c9ae9e079c55be01d'], + }), + ('joblib', '1.3.2', { + 'checksums': ['92f865e621e17784e7955080b6d042489e3b8e294949cc44c6eac304f59772b1'], + }), + ('docrep', '0.3.2', { + 'checksums': ['ed8a17e201abd829ef8da78a0b6f4d51fb99a4cbd0554adbed3309297f964314'], + }), + (name, version, { + 'modulename': 'cellrank', + 'preinstallopts': "sed -i 's/matplotlib>=3.5.0,<3.7.2/matplotlib>=3.5.0/' pyproject.toml && ", + 'source_tmpl': '%(namelower)s-%(version)s.tar.gz', + 'checksums': ['47c1d2e953ac91f572937d816142b4ac5f0c876174c60f857562de76a9f8aa61'], + }), +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/CellRank/pygam-0.9.0_fix-poetry.patch b/easybuild/easyconfigs/c/CellRank/pygam-0.9.0_fix-poetry.patch new file mode 100644 index 00000000000..cc463d4ea64 --- /dev/null +++ b/easybuild/easyconfigs/c/CellRank/pygam-0.9.0_fix-poetry.patch @@ -0,0 +1,26 @@ +workaround for: + RuntimeError: The Poetry configuration is invalid: + - Additional properties are not allowed ('group' was unexpected) +author: Kenneth Hoste (HPC-UGent) +--- pygam-0.9.0/pyproject.toml.orig 2024-01-05 22:13:47.399107878 +0100 ++++ pygam-0.9.0/pyproject.toml 2024-01-05 22:13:52.323119792 +0100 +@@ -12,19 +12,6 @@ + scipy = "^1.10.1" + progressbar2 = "^4.2.0" + +-[tool.poetry.group.dev.dependencies] +-pytest = "^7.2.2" +-flake8 = "^6.0.0" +-codecov = "^2.1.12" +-pytest-cov = "^4.0.0" +-mock = "^5.0.1" +-nbsphinx = "^0.9.0" +-sphinx-rtd-theme = "^1.2.0" +-sphinxcontrib-napoleon = "^0.7" +-ipython = "^8.11.0" +-pandas = "^1.5.3" +-black = "^23.1.0" +- + [tool.black] + line-length = 88 + skip-string-normalization = true diff --git a/easybuild/easyconfigs/c/Cellformer/Cellformer-20240917-foss-2023a-R-4.3.2.eb b/easybuild/easyconfigs/c/Cellformer/Cellformer-20240917-foss-2023a-R-4.3.2.eb new file mode 100644 index 00000000000..67df72c221f --- /dev/null +++ b/easybuild/easyconfigs/c/Cellformer/Cellformer-20240917-foss-2023a-R-4.3.2.eb @@ -0,0 +1,186 @@ +easyblock = 'Tarball' + +name = 'Cellformer' +version = '20240917' +versionsuffix = '-R-%(rver)s' +local_commit = '99a1165' + +homepage = 'https://github.com/elo-nsrb/Cellformer' +description = '''An implementation of Cellformer from our publication: Berson et al. + "Whole genome deconvolution unveils Alzheimer’s resilient epigenetic signature"''' + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['https://github.com/elo-nsrb/Cellformer/archive/'] +sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': '%(name)s-%(version)s.tar.gz'}] +checksums = ['7cbddad75a4d47dfc0a39cd660ef20fe4e3cb755631b1b96136c1c3d5226c914'] + +dependencies = [ + ('Python', '3.11.3'), + ('PyTorch', '2.1.2'), + ('PyTorch-bundle', '2.1.2'), + ('scikit-learn', '1.3.1'), + ('PyTorch-Lightning', '2.2.1'), + ('anndata', '0.10.5.post1'), + ('h5py', '3.9.0'), + ('SciPy-bundle', '2023.07'), + ('Seaborn', '0.13.2'), + ('tensorboard', '2.15.1'), + ('tensorboardX', '2.6.2.2'), + ('torchvision', '0.16.0'), + ('tqdm', '4.66.1'), + ('scanpy', '1.9.8'), + ('pretty-yaml', '24.7.0'), + ('Arrow', '14.0.1'), + ('R', '4.3.2'), + ('R-bundle-CRAN', '2023.12'), + ('R-bundle-Bioconductor', '3.18', versionsuffix), + ('ArchR', '1.0.2', versionsuffix), + ('typing-extensions', '4.9.0'), + ('einops', '0.7.0'), +] + +exts_defaultclass = 'PythonPackage' +exts_default_options = { + 'source_urls': [PYPI_SOURCE], + 'download_dep_fail': True, + 'use_pip': True, + 'sanity_pip_check': True, + 'installopts': '', +} + +exts_list = [ + ('asteroid_filterbanks', '0.4.0', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['4932ac8b6acc6e08fb87cbe8ece84215b5a74eee284fe83acf3540a72a02eaf5'], + }), + ('huggingface_hub', '0.25.2', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['1897caf88ce7f97fe0110603d8f66ac264e3ba6accdf30cd66cc0fed5282ad25'], + }), + ('julius', '0.2.7', { + 'checksums': ['3c0f5f5306d7d6016fcc95196b274cae6f07e2c9596eed314e4e7641554fbb08'], + }), + ('cached_property', '1.5.2', { + 'source_tmpl': SOURCE_WHL, + 'checksums': ['df4f613cf7ad9a588cc381aaf4a512d26265ecebd5eb9e1ba12f1319eb85a6a0'], + }), + ('mir_eval', '0.7', { + 'checksums': ['e1febaa5766c65a7545c2a170b241490f47a98987370b1e06742424c5debe65e'], + }), + ('pesq', '0.0.4', { + 'checksums': ['b724b28f73fb638522982bd68e8c3c0957e2f45210639a460233b17aa7fc890b'], + }), + ('pb_bss_eval', '0.0.2', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['a72c2fd04c9f4a4e734cf615029c3877e6e4536225eeaaae05bb0cf014b3af1b'], + }), + ('soundfile', '0.12.1', { + 'source_tmpl': SOURCE_WHL, + 'checksums': ['828a79c2e75abab5359f780c81dccd4953c45a2c4cd4f05ba3e233ddf984b882'], + }), + ('pytorch_ranger', '0.1.1', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['1e69156c9cc8439185cb8ba4725b18c91947fbe72743e25aca937da8aeb0c8ec'], + }), + ('torch_optimizer', '0.1.0', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['b7adaed38b66a5c5105a59b30a71c4ab7c9954baf0acabd969fee3dac954657d'], + }), + ('pystoi', '0.4.1', { + 'source_tmpl': SOURCE_WHL, + 'checksums': ['e277b671663d26d35a2416c9c8010a74084e6c3970354506398051a554896939'], + }), + ('torch_stoi', '0.2.3', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['6eee85e33b42fe843a2150de46000f72e7b87cbeb19ae6ab9bbd94b6ec6b3cd2'], + }), + ('torchmetrics', '1.4.3', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['76e67490231acef7f70cf36ab129df72fb2b0256dada7051001ab3b9f8699bf4'], + }), + ('asteroid', '0.7.0', { + # requirement too strict + 'preinstallopts': "sed -i 's/torchmetrics<=0.11.4/torchmetrics/g' setup.py && ", + 'checksums': ['0326f28c5342495cb08ba0520efd0e21e39435dfd78854837fdd5a6c9c9ca410'], + }), + ('everett', '3.1.0', { + 'source_tmpl': SOURCE_WHL, + 'checksums': ['db13891b849e45e54faea93ee79881d12458c5378f5b9b7f806eeff03ce1de3c'], + }), + ('configobj', '5.0.9', { + 'checksums': ['03c881bbf23aa07bccf1b837005975993c4ab4427ba57f959afdd9d1a2386848'], + }), + ('python_box', '6.1.0', { + 'modulename': 'box', + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['bdec0a5f5a17b01fc538d292602a077aa8c641fb121e1900dff0591791af80e8'], + }), + ('sentry_sdk', '2.15.0', { + 'source_tmpl': SOURCE_WHL, + 'checksums': ['8fb0d1a4e1a640172f31502e4503543765a1fe8a9209779134a4ac52d4677303'], + }), + ('wurlitzer', '3.1.1', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['0b2749c2cde3ef640bf314a9f94b24d929fe1ca476974719a6909dfc568c3aac'], + }), + ('comet_ml', '3.47.0', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['81062bbef2d0758c8e77d8a469824d2c20ec13b09855c78b51b078203628b8c2'], + }), + ('fast_histogram', '0.14', { + 'checksums': ['390973b98af22bda85c29dcf6f008ba0d626321e9bd3f5a9d7a43e5690ea69ea'], + }), + ('mpl_scatter_density', '0.7', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['721b4efeafcbc0ba4a5c1ecd8f401dc2d1aa6a372445c5b49e1da34e70a95ead'], + }), + ('tensorboard_data_server', '0.7.0', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['753d4214799b31da7b6d93837959abebbc6afa86e69eacf1e9a317a48daa31eb'], + }), + ('tensorboard_plugin_wit', '1.8.1', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['ff26bdd583d155aa951ee3b152b3d0cffae8005dc697f72b44a8e8c2a77a8cbe'], + }), + ('torchmetrics', '1.4.2', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['87b9eca51ff6f93985a0f9db509f646cb45425b016f4d2f383d8c28d40dde5b6'], + }), + ('torchmetrics', '0.11.4', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['45f892f3534e91f3ad9e2488d1b05a93b7cb76b7d037969435a41a1f24750d9a'], + }), +] + +modextrapaths = { + 'PATH': '', + 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', +} + +fix_python_shebang_for = [ + 'src/*/*.py', + 'src/*/*/*.py', + 'src/*/*/*/*.py', +] + +local_scripts = [ + 'createPeakMatrix.sh', + 'createDataset.sh', + 'deconvolution.sh', + 'trainModel.sh', + 'validation.sh', +] + +postinstallcmds = [ + "sed -i 's|python |python %(installdir)s/|g' %(installdir)s/*.sh" +] + ['chmod a+rx %%(installdir)s/%s' % script for script in local_scripts] + +sanity_check_paths = { + 'files': local_scripts, + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["%s --help | grep '^Usage:'" % script for script in local_scripts] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/Cellpose/Cellpose-2.2.2-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/c/Cellpose/Cellpose-2.2.2-foss-2022a-CUDA-11.7.0.eb index d0f93dfe418..feace92583f 100644 --- a/easybuild/easyconfigs/c/Cellpose/Cellpose-2.2.2-foss-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/c/Cellpose/Cellpose-2.2.2-foss-2022a-CUDA-11.7.0.eb @@ -27,10 +27,17 @@ dependencies = [ ('tqdm', '4.64.0'), ('imagecodecs', '2022.9.26'), ('scikit-build', '0.15.0'), + ('QtPy', '2.3.0'), ] use_pip = True +# avoid hatchling requirement to install +# (since installing it introduces conflicting version requirements with poetry included with Python) +_preinstallopts_no_hatchling = """sed -i -e 's/^build-backend = .*/build-backend = "setuptools.build_meta"/g' """ +_preinstallopts_no_hatchling += """-e 's/^requires = .*/requires = ["setuptools"]/g' """ +_preinstallopts_no_hatchling += r"""-e 's/dynamic = \["version"\]/version = "%(version)s"/g' pyproject.toml && """ + exts_list = [ ('tifffile', '2023.4.12', { 'checksums': ['2fa99f9890caab919d932a0acaa9d0f5843dc2ef3594e212963932e20713badd'], @@ -47,6 +54,10 @@ exts_list = [ ('roifile', '2023.5.12', { 'checksums': ['32eeba0d9ad52cc249d6a234b737c1808a6c5d7d9baae6453709eb74222b3433'], }), + ('superqt', '0.6.6', { + 'preinstallopts': _preinstallopts_no_hatchling, + 'checksums': ['792e09165c8a788ee245bdb784e018f9077fb309253354d86793cdf1d092f99f'], + }), (name, version, { # OpenCV dependency provides opencv-contrib-python (equivalent to opencv-python-headless) 'preinstallopts': "sed -i 's/opencv-python-headless/opencv-contrib-python/g' setup.py && ", diff --git a/easybuild/easyconfigs/c/Cellpose/Cellpose-2.2.2-foss-2022a.eb b/easybuild/easyconfigs/c/Cellpose/Cellpose-2.2.2-foss-2022a.eb index ccb478c890b..90f73c6aef8 100644 --- a/easybuild/easyconfigs/c/Cellpose/Cellpose-2.2.2-foss-2022a.eb +++ b/easybuild/easyconfigs/c/Cellpose/Cellpose-2.2.2-foss-2022a.eb @@ -25,10 +25,17 @@ dependencies = [ ('tqdm', '4.64.0'), ('imagecodecs', '2022.9.26'), ('scikit-build', '0.15.0'), + ('QtPy', '2.3.0'), ] use_pip = True +# avoid hatchling requirement to install +# (since installing it introduces conflicting version requirements with poetry included with Python) +_preinstallopts_no_hatchling = """sed -i -e 's/^build-backend = .*/build-backend = "setuptools.build_meta"/g' """ +_preinstallopts_no_hatchling += """-e 's/^requires = .*/requires = ["setuptools"]/g' """ +_preinstallopts_no_hatchling += r"""-e 's/dynamic = \["version"\]/version = "%(version)s"/g' pyproject.toml && """ + exts_list = [ ('tifffile', '2023.4.12', { 'checksums': ['2fa99f9890caab919d932a0acaa9d0f5843dc2ef3594e212963932e20713badd'], @@ -45,6 +52,10 @@ exts_list = [ ('roifile', '2023.5.12', { 'checksums': ['32eeba0d9ad52cc249d6a234b737c1808a6c5d7d9baae6453709eb74222b3433'], }), + ('superqt', '0.6.6', { + 'preinstallopts': _preinstallopts_no_hatchling, + 'checksums': ['792e09165c8a788ee245bdb784e018f9077fb309253354d86793cdf1d092f99f'], + }), (name, version, { # OpenCV dependency provides opencv-contrib-python (equivalent to opencv-python-headless) 'preinstallopts': "sed -i 's/opencv-python-headless/opencv-contrib-python/g' setup.py && ", diff --git a/easybuild/easyconfigs/c/Ceres-Solver/Ceres-Solver-2.2.0-foss-2022b.eb b/easybuild/easyconfigs/c/Ceres-Solver/Ceres-Solver-2.2.0-foss-2022b.eb new file mode 100644 index 00000000000..e0adc9dd257 --- /dev/null +++ b/easybuild/easyconfigs/c/Ceres-Solver/Ceres-Solver-2.2.0-foss-2022b.eb @@ -0,0 +1,32 @@ +easyblock = 'CMakeMake' + +name = 'Ceres-Solver' +version = '2.2.0' + +homepage = 'http://ceres-solver.org' +description = """Ceres Solver is an open source C++ library for modeling and solving large, complicated optimization +problems""" + +source_urls = ['http://ceres-solver.org/'] +sources = ['ceres-solver-%(version)s.tar.gz'] +checksums = ['48b2302a7986ece172898477c3bcd6deb8fb5cf19b3327bc49969aad4cede82d'] + +toolchain = {'name': 'foss', 'version': '2022b'} + +builddependencies = [ + ('CMake', '3.24.3'), + ('Eigen', '3.4.0'), +] + +dependencies = [ + ('glog', '0.6.0'), + ('gflags', '2.2.2'), + ('SuiteSparse', '5.13.0', '-METIS-5.1.0'), +] + +sanity_check_paths = { + 'files': ['lib/libceres.a'], + 'dirs': ['include/ceres', 'lib/cmake/Ceres'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/c/CharLS/CharLS-2.4.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/c/CharLS/CharLS-2.4.2-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..9d814bdfc23 --- /dev/null +++ b/easybuild/easyconfigs/c/CharLS/CharLS-2.4.2-GCCcore-12.3.0.eb @@ -0,0 +1,30 @@ +easyblock = 'CMakeMake' + +name = 'CharLS' +version = '2.4.2' + +homepage = 'https://github.com/team-charls/charls' +description = """CharLS is a C++ implementation of the JPEG-LS standard for lossless and near-lossless image +compression and decompression. JPEG-LS is a low-complexity image compression standard that matches JPEG 2000 +compression ratios.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/team-charls/charls/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['d1c2c35664976f1e43fec7764d72755e6a50a80f38eca70fcc7553cad4fe19d9'] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.26.3') +] + +configopts = '-DBUILD_SHARED_LIBS=ON ' + +sanity_check_paths = { + 'files': ['lib/libcharls.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/c/CheMPS2/CheMPS2-1.8.12-foss-2023a.eb b/easybuild/easyconfigs/c/CheMPS2/CheMPS2-1.8.12-foss-2023a.eb new file mode 100644 index 00000000000..fb8dea8412b --- /dev/null +++ b/easybuild/easyconfigs/c/CheMPS2/CheMPS2-1.8.12-foss-2023a.eb @@ -0,0 +1,32 @@ +easyblock = 'CMakeMake' + +name = 'CheMPS2' +version = '1.8.12' + +homepage = 'https://github.com/SebWouters/CheMPS2' +description = """CheMPS2 is a scientific library which contains a spin-adapted implementation of the +density matrix renormalization group (DMRG) for ab initio quantum chemistry.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['https://github.com/SebWouters/CheMPS2/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['eef1b92d74ac07fde58c043f64e8cac02b5400c209c44dcbb51641f86e0c7c83'] + +builddependencies = [ + ('CMake', '3.26.3'), +] + +dependencies = [ + ('HDF5', '1.14.0') +] + +pretestopts = 'export OMP_NUM_THREADS=1 && ' +runtest = 'test' + +sanity_check_paths = { + 'files': ['bin/chemps2', 'lib64/libchemps2.%s' % SHLIB_EXT, 'lib64/libchemps2.a'], + 'dirs': ['include/chemps2'] +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/c/Check/Check-0.15.2-GCCcore-13.3.0.eb b/easybuild/easyconfigs/c/Check/Check-0.15.2-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..1e0764bfb44 --- /dev/null +++ b/easybuild/easyconfigs/c/Check/Check-0.15.2-GCCcore-13.3.0.eb @@ -0,0 +1,37 @@ +easyblock = 'ConfigureMake' + +name = 'Check' +version = '0.15.2' + +homepage = 'https://libcheck.github.io/check/' +description = """ +Check is a unit testing framework for C. It features a simple interface for +defining unit tests, putting little in the way of the developer. Tests are +run in a separate address space, so both assertion failures and code errors +that cause segmentation faults or other signals can be caught. Test results +are reportable in the following: Subunit, TAP, XML, and a generic logging +format.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +github_account = 'libcheck' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['998d355294bb94072f40584272cf4424571c396c631620ce463f6ea97aa67d2e'] + +builddependencies = [ + ('binutils', '2.42'), + ('Autotools', '20231222'), + ('pkgconf', '2.2.0'), +] + +preconfigopts = "autoreconf -f -i && " +configopts = "--disable-build-docs" + +sanity_check_paths = { + 'files': ['bin/checkmk', 'lib/libcheck.a', 'lib/libcheck.%s' % SHLIB_EXT], + 'dirs': ['include', 'share'] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/c/CheckM2/CheckM2-1.0.2-foss-2022b.eb b/easybuild/easyconfigs/c/CheckM2/CheckM2-1.0.2-foss-2022b.eb new file mode 100644 index 00000000000..9f834b1a38f --- /dev/null +++ b/easybuild/easyconfigs/c/CheckM2/CheckM2-1.0.2-foss-2022b.eb @@ -0,0 +1,64 @@ +easyblock = 'PythonBundle' + +name = 'CheckM2' +version = '1.0.2' + +homepage = 'https://github.com/chklovski/CheckM2/' +description = "Assessing the quality of metagenome-derived genome bins using machine learning" + +toolchain = {'name': 'foss', 'version': '2022b'} + +builddependencies = [('CMake', '3.24.3')] +dependencies = [ + ('Python', '3.10.8'), + ('SciPy-bundle', '2023.02'), + ('DIAMOND', '2.1.8'), + ('TensorFlow', '2.13.0'), + ('prodigal', '2.6.3'), + ('h5py', '3.8.0'), + ('tqdm', '4.64.1'), +] + +exts_list = [ + ('scikit-learn', '0.23.2', { + 'modulename': 'sklearn', + 'checksums': ['20766f515e6cd6f954554387dfae705d93c7b544ec0e6c6a5d8e006f6f7ef480'], + }), + ('lightgbm', '3.2.1', { + 'checksums': ['bd98e3b501b4c24dc127f4ad93e467f42923fe3eefa99e143b5b93158f024395'], + }), + (name, version, { + 'patches': ['%(name)s-%(version)s_fileManager.py-database-fix.patch'], + 'source_urls': ['https://github.com/chklovski/CheckM2/archive/'], + 'sources': ['%(version)s.tar.gz'], + 'checksums': [ + {'1.0.2.tar.gz': '9d3129e4d0b53acc38519a259cc1e20a215dff0cbce51cef874545ca2fff005a'}, + {'CheckM2-1.0.2_fileManager.py-database-fix.patch': + '953f0eeef49ea537c0cb97c173a2488c29f09b58cd10800c60078b436a7ea2c7'}, + ], + }), +] + +postinstallcmds = [ + # np.float is depreciated in newer numpy + 'sed -i "s/np.float/float/g" %(installdir)s/lib/python%(pyshortver)s/site-packages/checkm2/predictQuality.py', + # update DB_LOCATION_DEFINITION in defaultValues.py to env CHECKM2DB + "cd %(installdir)s/lib/python%(pyshortver)s/site-packages/checkm2 && " + r"sed -i 's/\(DB_LOCATION_DEFINITION\) = .*/\1 = os.environ.get(\"CHECKM2DB\", \"Not Set\")/' defaultValues.py", +] + +modloadmsg = """You need download a diamond database now and setup a path to this db: +First you need to setup $CHECKM2DB as: +$ export CHECKM2DB="path/to/database/CheckM2_database/uniref100.KO.1.dmnd" +Next, download the database (/CheckM2_database/uniref100.KO.1.dmnd will be created): +$ checkm2 database --download --path path/to/database +You can check path to the database by: +$ checkm2 database --current +You can either test if everything is setup properly by: +$ checkm2 testrun +""" + +use_pip = True +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/CheckM2/CheckM2-1.0.2_fileManager.py-database-fix.patch b/easybuild/easyconfigs/c/CheckM2/CheckM2-1.0.2_fileManager.py-database-fix.patch new file mode 100644 index 00000000000..5c64bd20738 --- /dev/null +++ b/easybuild/easyconfigs/c/CheckM2/CheckM2-1.0.2_fileManager.py-database-fix.patch @@ -0,0 +1,126 @@ +Author: Pavel Tomanek (Inuits) + Kenneth Hoste (HPC-UGent) +This patch changes the way a path to the diamond database is set. It used to be stored in install dir in +diamond_path.json, but since this is unmodifiable file for user, the path is stored in env variable CHECKM2DB. +The patch needs to change whole file - there was a problem with dos style endings (CRLF). +diff -ruZ CheckM2-1.0.2.orig/checkm2/fileManager.py CheckM2-1.0.2/checkm2/fileManager.py +--- CheckM2-1.0.2.orig/checkm2/fileManager.py 2023-05-19 01:56:46.000000000 +0200 ++++ CheckM2-1.0.2/checkm2/fileManager.py 2024-05-30 22:13:45.230761282 +0200 +@@ -22,62 +22,34 @@ + + diamond_definition = self.__get_db_file() + +- if diamond_definition['DBPATH'] == 'Not Set': ++ if diamond_definition == 'Not Set': + self.DATABASE_DIR = 'Not Set' + else: +- self.DATABASE_DIR = diamond_definition['DBPATH'] ++ self.DATABASE_DIR = diamond_definition + else: + diamond_definition = self.__get_db_file() + +- if diamond_definition['DBPATH'] == 'Not Set': ++ if diamond_definition == 'Not Set': + self.DATABASE_DIR = 'Not Set' + else: +- self.DATABASE_DIR = diamond_definition['DBPATH'] ++ self.DATABASE_DIR = diamond_definition + + + def __get_db_file(self): +- diamond_location = DefaultValues.DB_LOCATION_DEFINITION +- try: +- with open(diamond_location) as f: +- diamond_definition = json.load(f) +- return diamond_definition +- except: +- logging.warning('Could not open DIAMOND location definition file. Creating new file.') +- db_ref_file = {"Type": "DIAMONDDB", "DBPATH": "Not Set"} +- with open(diamond_location, 'w') as dl: +- json.dump(db_ref_file, dl) +- try: +- with open(diamond_location) as f: +- diamond_definition = json.load(f) +- return diamond_definition +- except Exception as e: +- logging.error('Could not create new file: {}'.format(e)) +- sys.exit(1) +- ++ return DefaultValues.DB_LOCATION_DEFINITION + + def get_DB_location(self): + if self.DATABASE_DIR == 'Not Set': +- logging.error('DIAMOND database not found. Please download database using ') ++ logging.error( ++ 'DIAMOND database not found. Please download database using $ checkm2 database --download --path /path/to/database ' ++ + ',but FIRST set CHECKM2DB to PATH by $ export CHECKM2DB=\"/path/to/database/CheckM2_database/uniref100.KO.1.dmnd\"' ++ ) + sys.exit(1) + else: + return self.DATABASE_DIR + + def set_DB_location(self, provided_location): +- logging.info('Checking provided DIAMOND database location') +- if versionControl.VersionControl().checksum_version_validate_DIAMOND(provided_location): +- #great - let's set it +- diamond_definition = self.__get_db_file() +- +- diamond_definition['DBPATH'] = os.path.abspath(provided_location) +- with open(DefaultValues.DB_LOCATION_DEFINITION, 'w') as dd: +- json.dump(diamond_definition, dd) +- +- logging.info("Database check successful! Database path successfully added.") +- +- else: +- logging.error("Checksum in CheckM2 reference doesn't match provided database. Please check your files.") +- sys.exit(1) +- ++ logging.info("Set path to database location by: $ export CHECKM2DB=path/to/database/CheckM2_database/uniref100.KO.1.dmnd") + + def download_database(self, download_location): + +@@ -87,32 +59,11 @@ + + diamond_location = DefaultValues.DB_LOCATION_DEFINITION + +- try: +- with open(diamond_location) as f: +- diamond_definition = json.load(f) +- except: +- logging.warning('Could not open DIAMOND location definition file. Creating new file.') +- x = {"Type": "DIAMONDDB", "DBPATH": "Not Set"} +- with open(diamond_location, 'w') as dl: +- json.dump(x, dl) +- try: +- with open(diamond_location) as f: +- diamond_definition = json.load(f) +- except Exception as e: +- logging.error('Could not create new file: {}'.format(e)) +- sys.exit(1) +- if diamond_definition['DBPATH'] != 'Not Set': +- logging.warning('DIAMOND database found at {}. Overwriting previous database.'.format(diamond_definition['DBPATH'])) +- +- + make_sure_path_exists(os.path.join(download_location, 'CheckM2_database')) + + backpack_downloader = zenodo_backpack.zenodo_backpack_downloader('INFO') + highest_compatible_version, DOI = versionControl.VersionControl().return_highest_compatible_DB_version() + +- +- diamond_loc_final = os.path.join(download_location, 'CheckM2_database', 'uniref100.KO.1.dmnd') +- + if download_location is not None: + #check we have writing permission + try: +@@ -126,12 +77,6 @@ + + backpack_downloader.download_and_extract(download_location, DOI, progress_bar=True, no_check_version=False) + +- diamond_definition['DBPATH'] = os.path.abspath(diamond_loc_final) +- +- with open(diamond_location, 'w') as dd: +- json.dump(diamond_definition, dd) +- +- + else: + logging.info('Failed to determine download location') + sys.exit(1) diff --git a/easybuild/easyconfigs/c/Circuitscape/Circuitscape-5.12.3-Julia-1.9.2.eb b/easybuild/easyconfigs/c/Circuitscape/Circuitscape-5.12.3-Julia-1.9.2.eb index a6649359df9..8e8e7e2f86b 100644 --- a/easybuild/easyconfigs/c/Circuitscape/Circuitscape-5.12.3-Julia-1.9.2.eb +++ b/easybuild/easyconfigs/c/Circuitscape/Circuitscape-5.12.3-Julia-1.9.2.eb @@ -403,6 +403,10 @@ exts_list = [ }), ] -sanity_check_commands = ["julia -e 'using Pkg;Pkg.test(\"Circuitscape\")'"] +_julia_env = "%(installdir)s/environments/v" + '.'.join(_julia_ver.split('.')[:2]) + +sanity_check_commands = [ + """julia -e 'using Pkg; Pkg.activate("%s"); Pkg.test("%%(name)s")'""" % _julia_env, +] moduleclass = 'lib' diff --git a/easybuild/easyconfigs/c/Clang/Clang-17.0.0_20230515-GCCcore-12.3.0-CUDA-12.1.1.eb b/easybuild/easyconfigs/c/Clang/Clang-17.0.0_20230515-GCCcore-12.3.0-CUDA-12.1.1.eb new file mode 100644 index 00000000000..947a6afdad5 --- /dev/null +++ b/easybuild/easyconfigs/c/Clang/Clang-17.0.0_20230515-GCCcore-12.3.0-CUDA-12.1.1.eb @@ -0,0 +1,61 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2013-2015 Dmitri Gribenko, Ward Poelmans +# Authors:: Dmitri Gribenko +# Authors:: Ward Poelmans +# License:: GPLv2 or later, MIT, three-clause BSD. +# $Id$ +## + +name = 'Clang' +version = '17.0.0_20230515' +versionsuffix = '-CUDA-%(cudaver)s' +_commit = 'c5dede880d17' + +homepage = 'https://clang.llvm.org/' +description = """C, C++, Objective-C compiler, based on LLVM. Does not + include C++ standard library -- use libstdc++ from GCC.""" + +# Clang also depends on libstdc++ during runtime, but this dependency is +# already specified as the toolchain. +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +sources = [{ + 'source_urls': ["https://github.com/llvm/llvm-project/archive"], + 'download_filename': '%s.tar.gz' % _commit, + 'filename': 'llvm-project-%s.tar.gz' % version, +}] +checksums = ['6f371f9ac208b8e9dc57fc117b1a9c8565d7ea2bbb49a2768cb9c3c0fee0291d'] + +builddependencies = [ + ('CMake', '3.26.3'), + ('Perl', '5.36.1'), + # Including Python bindings would require this as a runtime dep + ('Python', '3.11.3'), +] +dependencies = [ + # since Clang is a compiler, binutils is a runtime dependency too + ('binutils', '2.40'), + ('hwloc', '2.9.1'), + ('libxml2', '2.11.4'), + ('ncurses', '6.4'), + ('GMP', '6.2.1'), + ('Z3', '4.12.2'), + ('CUDA', '12.1.1', '', SYSTEM), +] + +# enabling RTTI makes the flang compiler need to link to libc++ so instead of +# flang-new -flang-experimental-exec -fopenmp hello_openmp.f90 +# you would need +# flang-new -flang-experimental-exec -fopenmp hello_openmp.f90 -l c++ +enable_rtti = False + +assertions = True +python_bindings = False +skip_all_tests = True + +llvm_runtimes = ['libunwind', 'libcxx', 'libcxxabi'] +llvm_projects = ['polly', 'lld', 'lldb', 'clang-tools-extra', 'flang'] + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/c/Clang/Clang-17.0.6-GCCcore-13.2.0.eb b/easybuild/easyconfigs/c/Clang/Clang-17.0.6-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..1cb99d62d99 --- /dev/null +++ b/easybuild/easyconfigs/c/Clang/Clang-17.0.6-GCCcore-13.2.0.eb @@ -0,0 +1,55 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2013-2015 Dmitri Gribenko, Ward Poelmans +# Authors:: Dmitri Gribenko +# Authors:: Ward Poelmans +# License:: GPLv2 or later, MIT, three-clause BSD. +# $Id$ +## + +name = 'Clang' +version = '17.0.6' + +homepage = 'https://clang.llvm.org/' +description = """C, C++, Objective-C compiler, based on LLVM. Does not + include C++ standard library -- use libstdc++ from GCC.""" + +# Clang also depends on libstdc++ during runtime, but this dependency is +# already specified as the toolchain. +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ["https://github.com/llvm/llvm-project/releases/download/llvmorg-%(version)s"] +sources = [ + 'llvm-project-%(version)s.src.tar.xz', +] +checksums = ['58a8818c60e6627064f312dbf46c02d9949956558340938b71cf731ad8bc0813'] + +builddependencies = [ + ('CMake', '3.27.6'), + ('Perl', '5.38.0'), + # Including Python bindings would require this as a runtime dep + # and SWIG as an additional build dep + ('Python', '3.11.5'), +] +dependencies = [ + # since Clang is a compiler, binutils is a runtime dependency too + ('binutils', '2.40'), + ('hwloc', '2.9.2'), + ('libxml2', '2.11.5'), + ('ncurses', '6.4'), + ('GMP', '6.3.0'), + ('Z3', '4.13.0'), +] + +# If True, Flang does not currently support building with LLVM exceptions enabled. +enable_rtti = False + +assertions = True +python_bindings = False +skip_all_tests = True + +llvm_runtimes = ['libunwind', 'libcxx', 'libcxxabi'] +llvm_projects = ['polly', 'lld', 'lldb', 'clang-tools-extra', 'flang'] + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/c/Clang/Clang-18.1.8-GCCcore-13.3.0.eb b/easybuild/easyconfigs/c/Clang/Clang-18.1.8-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..8b096078c89 --- /dev/null +++ b/easybuild/easyconfigs/c/Clang/Clang-18.1.8-GCCcore-13.3.0.eb @@ -0,0 +1,55 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2013-2015 Dmitri Gribenko, Ward Poelmans +# Authors:: Dmitri Gribenko +# Authors:: Ward Poelmans +# License:: GPLv2 or later, MIT, three-clause BSD. +# $Id$ +## + +name = 'Clang' +version = '18.1.8' + +homepage = 'https://clang.llvm.org/' +description = """C, C++, Objective-C compiler, based on LLVM. Does not + include C++ standard library -- use libstdc++ from GCC.""" + +# Clang also depends on libstdc++ during runtime, but this dependency is +# already specified as the toolchain. +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ["https://github.com/llvm/llvm-project/releases/download/llvmorg-%(version)s"] +sources = [ + 'llvm-project-%(version)s.src.tar.xz', +] +checksums = ['0b58557a6d32ceee97c8d533a59b9212d87e0fc4d2833924eb6c611247db2f2a'] + +builddependencies = [ + ('CMake', '3.29.3'), + ('Perl', '5.38.2'), + # Including Python bindings would require this as a runtime dep + # and SWIG as an additional build dep + ('Python', '3.12.3'), +] +dependencies = [ + # since Clang is a compiler, binutils is a runtime dependency too + ('binutils', '2.42'), + ('hwloc', '2.10.0'), + ('libxml2', '2.12.7'), + ('ncurses', '6.5'), + ('GMP', '6.3.0'), + ('Z3', '4.13.0'), +] + +# If True, Flang does not currently support building with LLVM exceptions enabled. +enable_rtti = False + +assertions = True +python_bindings = False +skip_all_tests = True + +llvm_runtimes = ['libunwind', 'libcxx', 'libcxxabi'] +llvm_projects = ['polly', 'lld', 'lldb', 'clang-tools-extra', 'flang'] + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/c/Clustal-Omega/Clustal-Omega-1.2.4-GCC-12.3.0.eb b/easybuild/easyconfigs/c/Clustal-Omega/Clustal-Omega-1.2.4-GCC-12.3.0.eb new file mode 100644 index 00000000000..04f5b0991d1 --- /dev/null +++ b/easybuild/easyconfigs/c/Clustal-Omega/Clustal-Omega-1.2.4-GCC-12.3.0.eb @@ -0,0 +1,35 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel +# Modified by Adam Huffman +# Francis Crick Institute + +easyblock = 'ConfigureMake' + +name = 'Clustal-Omega' +version = '1.2.4' + +homepage = 'http://www.clustal.org/omega/' +description = """ Clustal Omega is a multiple sequence alignment + program for proteins. It produces biologically meaningful multiple + sequence alignments of divergent sequences. Evolutionary relationships + can be seen via viewing Cladograms or Phylograms """ + +toolchain = {'name': 'GCC', 'version': '12.3.0'} +toolchainopts = {'openmp': True} + +source_urls = [homepage] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['8683d2286d663a46412c12a0c789e755e7fd77088fb3bc0342bb71667f05a3ee'] + +dependencies = [('argtable', '2.13')] + +sanity_check_paths = { + 'files': ['bin/clustalo'], + 'dirs': [], +} + +sanity_check_commands = ["clustalo --help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/Cluster-Buster/Cluster-Buster-20240927-GCC-12.3.0.eb b/easybuild/easyconfigs/c/Cluster-Buster/Cluster-Buster-20240927-GCC-12.3.0.eb new file mode 100644 index 00000000000..752cc55bb94 --- /dev/null +++ b/easybuild/easyconfigs/c/Cluster-Buster/Cluster-Buster-20240927-GCC-12.3.0.eb @@ -0,0 +1,26 @@ +easyblock = 'MakeCp' + +name = 'Cluster-Buster' +version = '20240927' +local_commit = '06fee8b' + +homepage = 'https://github.com/weng-lab/cluster-buster' +description = """Cluster-Buster is a program for finding interesting functional regions, + such as transcriptional enhancers, in DNA sequences.""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +source_urls = ['https://github.com/weng-lab/cluster-buster/archive/'] +sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCELOWER_TAR_GZ}] +checksums = ['a77583ae1f38cc08af551932e5f6b35185fde78db330270bb2eb32ecb4d926cc'] + +files_to_copy = [(['cbust'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/cbust'], + 'dirs': [], +} + +sanity_check_commands = ['cbust -h'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/CoCoALib/CoCoALib-0.99850-GCC-13.2.0.eb b/easybuild/easyconfigs/c/CoCoALib/CoCoALib-0.99850-GCC-13.2.0.eb new file mode 100644 index 00000000000..f85edd9ec85 --- /dev/null +++ b/easybuild/easyconfigs/c/CoCoALib/CoCoALib-0.99850-GCC-13.2.0.eb @@ -0,0 +1,42 @@ +easyblock = 'ConfigureMake' + +name = 'CoCoALib' +version = '0.99850' + +homepage = 'https://cocoa.dima.unige.it/cocoa/cocoalib/' +description = "CoCoALib is a free GPL3 C++ library for doing Computations in Commutative Algebra." + +toolchain = {'name': 'GCC', 'version': '13.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://cocoa.dima.unige.it/cocoa/cocoalib/tgz'] +sources = [SOURCE_TGZ] +checksums = ['d3e7af0153c6950f83f4e3556540f0177fedf5179f0f7667b7d6d670268fd445'] + +dependencies = [ + ('GMP', '6.3.0'), + ('cddlib', '0.94m'), # optional +] + +# libreadline only needed for CoCoA-5 +configopts = "--only-cocoalib --no-readline --threadsafe-hack " +# Use cddlib and GMP from EB +configopts += "--with-libcddgmp=${EBROOTCDDLIB}/lib/libcddgmp.a --with-libgmp=$EBROOTGMP/lib/libgmp.a " + +buildopts = 'CXX="$CXX" CXXFLAGS="$CXXFLAGS"' + +# Makefile is not smart enough to create missing directories +preinstallopts = "mkdir %(installdir)s/{include,lib} && " + +# Move doc and examples from include to share +postinstallcmds = [ + "mkdir %(installdir)s/share", + "mv %(installdir)s/include/CoCoA-%(version)s/{doc,examples} %(installdir)s/share/", +] + +sanity_check_paths = { + 'files': ['lib/libcocoa.a'], + 'dirs': ['include/CoCoA-%(version)s', 'share/doc', 'share/examples'] +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/c/CodingQuarry/CodingQuarry-2.0-foss-2023a.eb b/easybuild/easyconfigs/c/CodingQuarry/CodingQuarry-2.0-foss-2023a.eb new file mode 100644 index 00000000000..4757b9125f2 --- /dev/null +++ b/easybuild/easyconfigs/c/CodingQuarry/CodingQuarry-2.0-foss-2023a.eb @@ -0,0 +1,51 @@ +easyblock = 'MakeCp' + +name = 'CodingQuarry' +version = '2.0' + +homepage = 'https://sourceforge.net/p/codingquarry' +description = "Highly accurate hidden Markov model gene prediction in fungal genomes using RNA-seq transcripts" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'openmp': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['CodingQuarry_v%(version)s.tar.gz'] +patches = ['CodingQuarry-2.0_python3.patch'] +checksums = [ + {'CodingQuarry_v2.0.tar.gz': '1198afbf7cebcf0975c5b20d92b7a2dd6d956072fcde6e86fdce6aeae4842504'}, + {'CodingQuarry-2.0_python3.patch': '8e1b117431d8b104f2114875d8f751aa91c1c3c1b0ddd5a4f85251605c2ab9df'}, +] + +dependencies = [ + ('Python', '3.11.3'), + ('Biopython', '1.83'), +] + +buildopts = 'CFLAGS="$CFLAGS"' + +files_to_copy = [ + (['CodingQuarry', 'CufflinksGTF_to_CodingQuarryGFF3.py'], 'bin'), + 'QuarryFiles', + 'TESTING', +] + +fix_python_shebang_for = [ + 'bin/CufflinksGTF_to_CodingQuarryGFF3.py', + 'QuarryFiles/scripts/*.py', +] + +sanity_check_paths = { + 'files': ['bin/CodingQuarry', 'bin/CufflinksGTF_to_CodingQuarryGFF3.py'], + 'dirs': ['QuarryFiles/scripts', 'QuarryFiles/self_train', 'QuarryFiles/species', 'TESTING'], +} + +sanity_check_commands = [ + "CodingQuarry --help | grep '^CodingQuarry v. %(version)s'", + "mkdir -p %(builddir)s && cp -a %(installdir)s/TESTING %(builddir)s/TESTING", + "cd %(builddir)s/TESTING && CufflinksGTF_to_CodingQuarryGFF3.py Sp_transcripts.gtf > test.gff3", +] + +modextravars = {'QUARRY_PATH': '%(installdir)s/QuarryFiles'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/Compass/Compass-2024.04-foss-2021b.eb b/easybuild/easyconfigs/c/Compass/Compass-2024.04-foss-2021b.eb new file mode 100644 index 00000000000..0ff4a4f9bdb --- /dev/null +++ b/easybuild/easyconfigs/c/Compass/Compass-2024.04-foss-2021b.eb @@ -0,0 +1,42 @@ +easyblock = 'PythonBundle' + +name = 'Compass' +version = '2024.04' + +homepage = 'https://github.com/YosefLab/Compass' +description = """In-Silico Modeling of Metabolic Heterogeneity using Single-Cell Transcriptomes.""" +local_commit = "7664cb0" + +toolchain = {'name': 'foss', 'version': '2021b'} + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), + ('tqdm', '4.62.3'), + ('python-libsbml', '5.20.2'), + ('scikit-learn', '1.0.1'), + ('python-igraph', '0.9.8'), + ('leidenalg', '0.8.8'), + ('anndata', '0.9.2'), + ('CPLEX', '22.1.1'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('compass', version, { + 'source_urls': ['https://github.com/YosefLab/Compass/archive/'], + 'sources': [{'download_filename': '7664cb0.tar.gz', 'filename': '%(name)s-%(version)s-7664cb0.tar.gz'}], + 'checksums': ['87529c5fae108fa2a8e3e35438d3b25874faa78af670a2349228c76fa0843376'], + 'preinstallopts': "sed -i '/python-igraph/d' setup.py && ", + }), +] + +sanity_check_commands = [ + "compass -h", + "python -c 'import cplex'", + "python -c 'import igraph'", +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/Compress-Raw-Zlib/Compress-Raw-Zlib-2.213-GCCcore-13.3.0.eb b/easybuild/easyconfigs/c/Compress-Raw-Zlib/Compress-Raw-Zlib-2.213-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..13ea1eaab8d --- /dev/null +++ b/easybuild/easyconfigs/c/Compress-Raw-Zlib/Compress-Raw-Zlib-2.213-GCCcore-13.3.0.eb @@ -0,0 +1,31 @@ +easyblock = 'PerlModule' + +name = 'Compress-Raw-Zlib' +version = '2.213' + +homepage = 'https://metacpan.org/pod/Compress::Raw::Zlib' +description = "Low-Level Interface to zlib or zlib-ng compression library" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://cpan.metacpan.org/authors/id/P/PM/PMQS/'] +sources = ['%(name)s-%(version)s.tar.gz'] +checksums = ['56b21c99cb3a3a7f7876a74dd05daa3f41fc9143ddd4dc98f8e46710a106af45'] + +builddependencies = [ + ('binutils', '2.42'), +] + +dependencies = [ + ('Perl', '5.38.2'), + ('zlib', '1.3.1'), +] + +options = {'modulename': 'Compress::Raw::Zlib'} + +sanity_check_paths = { + 'files': ['lib/perl5/site_perl/%(perlver)s/%(arch)s-linux-thread-multi/Compress/Raw/Zlib.pm'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/c/ConcurrentVersionsSystem/ConcurrentVersionsSystem-1.11.23-GCCcore-13.3.0.eb b/easybuild/easyconfigs/c/ConcurrentVersionsSystem/ConcurrentVersionsSystem-1.11.23-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..b43a426454f --- /dev/null +++ b/easybuild/easyconfigs/c/ConcurrentVersionsSystem/ConcurrentVersionsSystem-1.11.23-GCCcore-13.3.0.eb @@ -0,0 +1,45 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +## + +easyblock = 'ConfigureMake' + +name = 'ConcurrentVersionsSystem' +version = '1.11.23' + +homepage = 'https://savannah.nongnu.org/projects/cvs' +description = """CVS is a version control system, an important component of +Source Configuration Management (SCM). +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = [' https://ftp.gnu.org/non-gnu/cvs/source/stable/%(version)s/'] +sources = ['cvs-%(version)s.tar.bz2'] +patches = [ + 'CVS-1.11.23-zlib-1.patch', + 'CVS-1.11.23-getline.patch', +] +checksums = [ + '400f51b59d85116e79b844f2d5dbbad4759442a789b401a94aa5052c3d7a4aa9', # cvs-1.11.23.tar.bz2 + # CVS-1.11.23-zlib-1.patch + '3c0ee6509c4622778c093316437a5b047c51820e11cee3ed3a405c2a590a9ff4', + # CVS-1.11.23-getline.patch + '6a1aa65acfbb41b7639adc70248d908981f172c2529bb52d84359713f9541874', +] + +builddependencies = [ + ('binutils', '2.42') +] + +dependencies = [ + ('zlib', '1.3.1') +] + +sanity_check_paths = { + 'files': ['bin/cvs', 'bin/cvsbug', 'bin/rcs2log'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/c/Coreutils/Coreutils-9.5-GCCcore-13.3.0.eb b/easybuild/easyconfigs/c/Coreutils/Coreutils-9.5-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..60e5009dc91 --- /dev/null +++ b/easybuild/easyconfigs/c/Coreutils/Coreutils-9.5-GCCcore-13.3.0.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = "Coreutils" +version = "9.5" + +homepage = 'https://www.gnu.org/software/coreutils/' +description = """The GNU Core Utilities are the basic file, shell and text +manipulation utilities of the GNU operating system. These are +the core utilities which are expected to exist on every +operating system. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_XZ] + +checksums = ['cd328edeac92f6a665de9f323c93b712af1858bc2e0d88f3f7100469470a1b8a'] + +builddependencies = [('binutils', '2.42')] + +sanity_check_paths = { + 'files': ['bin/sort', 'bin/echo', 'bin/du', 'bin/date', 'bin/true'], + 'dirs': [] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/c/Critic2/Critic2-1.2-foss-2023a.eb b/easybuild/easyconfigs/c/Critic2/Critic2-1.2-foss-2023a.eb new file mode 100644 index 00000000000..9d1605b7366 --- /dev/null +++ b/easybuild/easyconfigs/c/Critic2/Critic2-1.2-foss-2023a.eb @@ -0,0 +1,37 @@ +easyblock = 'CMakeMake' + +name = 'Critic2' +version = '1.2' + +homepage = 'https://aoterodelaroza.github.io/critic2/' +description = """Critic2 is a program for the analysis of quantum mechanical +calculation results in molecules and periodic solids.""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'extra_fflags': '-ffree-line-length-none'} + +source_urls = ['https://github.com/aoterodelaroza/critic2/archive/refs/tags/'] +sources = ['%(version)s.tar.gz'] +checksums = ['b59ecffd83405dbcc4b5d157d4a94bf2756916f72e83e09a94d277d54d0f2225'] + +configopts = '-DLIBCINT_INCLUDE_DIRS=$EBROOTLIBCINT/include/ ' +configopts += '-DLIBCINT_LIBRARY=$EBROOTLIBCINT/lib64/libcint.so ' + +builddependencies = [ + ('CMake', '3.26.3'), +] + +dependencies = [ + ('libxc', '6.2.2'), + ('libcint', '5.4.0'), + ('libreadline', '8.2'), +] + +sanity_check_paths = { + 'files': ["bin/critic2"], + 'dirs': ["bin"], +} + +sanity_check_commands = ['critic2 -h'] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/c/CubeLib/CubeLib-4.8.2-GCCcore-13.3.0.eb b/easybuild/easyconfigs/c/CubeLib/CubeLib-4.8.2-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..6b2414be446 --- /dev/null +++ b/easybuild/easyconfigs/c/CubeLib/CubeLib-4.8.2-GCCcore-13.3.0.eb @@ -0,0 +1,52 @@ +# Copyright 2019-2024 Juelich Supercomputing Centre, Germany +# Copyright 2023-2024 TU Dresden, Germany +# Authors:: Markus Geimer +# Alexander Grund +# Jan André Reuter +# License:: 3-clause BSD +# +# This work is based on experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ + +easyblock = 'EB_Score_minus_P' + +name = 'CubeLib' +version = '4.8.2' + +homepage = 'https://www.scalasca.org/software/cube-4.x/download.html' +description = """ + Cube, which is used as performance report explorer for Scalasca and Score-P, + is a generic tool for displaying a multi-dimensional performance space + consisting of the dimensions (i) performance metric, (ii) call path, and + (iii) system resource. Each dimension can be represented as a tree, where + non-leaf nodes of the tree can be collapsed or expanded to achieve the + desired level of granularity. + + This module provides the Cube general purpose C++ library component and + command-line tools. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://apps.fz-juelich.de/scalasca/releases/cube/%(version_major_minor)s/dist'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['d6fdef57b1bc9594f1450ba46cf08f431dd0d4ae595c47e2f3454e17e4ae74f4'] + +builddependencies = [ + # use same binutils version that was used when building GCCcore + ('binutils', '2.42'), + ('pkgconf', '2.2.0'), +] +dependencies = [ + ('zlib', '1.3.1'), +] + +configopts = '--enable-shared' + +sanity_check_paths = { + 'files': ['bin/cubelib-config', + 'lib/libcube4.a', 'lib/libcube4.%s' % SHLIB_EXT], + 'dirs': ['include/cubelib'], +} + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/c/CubeWriter/CubeWriter-4.8.2-GCCcore-13.3.0.eb b/easybuild/easyconfigs/c/CubeWriter/CubeWriter-4.8.2-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..e030f21ba6c --- /dev/null +++ b/easybuild/easyconfigs/c/CubeWriter/CubeWriter-4.8.2-GCCcore-13.3.0.eb @@ -0,0 +1,52 @@ +# Copyright:: Copyright 2019-2024 Juelich Supercomputing Centre, Germany +# Copyright 2023-2024 TU Dresden, Germany +# Authors:: Markus Geimer +# Alexander Grund +# Jan André Reuter +# License:: 3-clause BSD +# +# This work is based on experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ + +easyblock = 'EB_Score_minus_P' + +name = 'CubeWriter' +version = '4.8.2' + +homepage = 'https://www.scalasca.org/software/cube-4.x/download.html' +description = """ + Cube, which is used as performance report explorer for Scalasca and Score-P, + is a generic tool for displaying a multi-dimensional performance space + consisting of the dimensions (i) performance metric, (ii) call path, and + (iii) system resource. Each dimension can be represented as a tree, where + non-leaf nodes of the tree can be collapsed or expanded to achieve the + desired level of granularity. + + This module provides the Cube high-performance C writer library component. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://apps.fz-juelich.de/scalasca/releases/cube/%(version_major_minor)s/dist'] +sources = ['cubew-%(version)s.tar.gz'] +checksums = ['4f3bcf0622c2429b8972b5eb3f14d79ec89b8161e3c1cc5862ceda417d7975d2'] + +builddependencies = [ + # use same binutils version that was used when building GCCcore + ('binutils', '2.42'), + ('pkgconf', '2.2.0'), +] + +dependencies = [ + ('zlib', '1.3.1'), +] + +configopts = '--enable-shared' + +sanity_check_paths = { + 'files': ['bin/cubew-config', + 'lib/libcube4w.a', 'lib/libcube4w.%s' % SHLIB_EXT], + 'dirs': ['include/cubew'], +} + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/c/Cufflinks/Cufflinks-20190706-GCC-12.3.0.eb b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-20190706-GCC-12.3.0.eb new file mode 100644 index 00000000000..3f087e541cb --- /dev/null +++ b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-20190706-GCC-12.3.0.eb @@ -0,0 +1,49 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild + +name = 'Cufflinks' +version = '20190706' +local_commit = 'dc3b0cb' + +homepage = 'http://cole-trapnell-lab.github.io/%(namelower)s/' +description = "Transcript assembly, differential expression, and differential regulation for RNA-Seq" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +github_account = 'cole-trapnell-lab' +source_urls = [GITHUB_LOWER_SOURCE] +sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}] +patches = ['Cufflinks-20190706_fix-automake.patch'] +checksums = [ + {'Cufflinks-20190706.tar.gz': '444c632083a473fe4fd99ff189cef5bbd95daee0912e8eefe79534bf225fbcb6'}, + {'Cufflinks-20190706_fix-automake.patch': '4eb2eb9e8e549eb6c2e17493801c36554dbfb009d9af86e28195e898a350b3a6'}, +] + +builddependencies = [ + ('Eigen', '3.4.0'), + ('Autotools', '20220317'), + ('SAMtools', '1.18'), + ('Boost', '1.75.0'), +] + +dependencies = [ + ('zlib', '1.2.13'), + ('HTSlib', '1.18'), +] + +preconfigopts = 'autoreconf -i && export LIBS="${LIBS} -lhts" && export CFLAGS="$CFLAGS -fcommon" && ' +configopts = '--with-boost=${EBROOTBOOST} --with-bam=${EBROOTSAMTOOLS}' + +buildopts = "BOOST_FILESYSTEM_LIB=$EBROOTBOOST/lib/libboost_filesystem.a " +buildopts += "BOOST_SERIALIZATION_LIB=$EBROOTBOOST/lib/libboost_serialization.a " +buildopts += "BOOST_SYSTEM_LIB=$EBROOTBOOST/lib/libboost_system.a " +buildopts += "BOOST_THREAD_LIB=$EBROOTBOOST/lib/libboost_thread.a " + +sanity_check_paths = { + 'files': ['bin/cufflinks'], + 'dirs': [] +} + +sanity_check_commands = ["cufflinks 2>&1 | grep 'Usage:.* cufflinks'"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/Cufflinks/Cufflinks-20190706_fix-automake.patch b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-20190706_fix-automake.patch new file mode 100644 index 00000000000..332b4c724e4 --- /dev/null +++ b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-20190706_fix-automake.patch @@ -0,0 +1,14 @@ +fix for: +error: AM_INIT_AUTOMAKE expanded multiple times +author: Kenneth Hoste (HPC-UGent) +--- cufflinks-dc3b0cb72a4ac2b6bbc887099e71fc0c21e107b7/configure.ac.orig 2019-07-06 18:28:01.000000000 +0200 ++++ cufflinks-dc3b0cb72a4ac2b6bbc887099e71fc0c21e107b7/configure.ac 2024-09-27 13:39:13.512597490 +0200 +@@ -14,7 +14,7 @@ + AC_CONFIG_SRCDIR([config.h.in]) + AC_CONFIG_HEADERS([config.h]) + AC_CONFIG_AUX_DIR([build-aux]) +-AM_INIT_AUTOMAKE ++#AM_INIT_AUTOMAKE + + #AM_PATH_CPPUNIT(1.10.2) + diff --git a/easybuild/easyconfigs/c/Cython/Cython-3.0.10-GCCcore-13.2.0.eb b/easybuild/easyconfigs/c/Cython/Cython-3.0.10-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..194048d611d --- /dev/null +++ b/easybuild/easyconfigs/c/Cython/Cython-3.0.10-GCCcore-13.2.0.eb @@ -0,0 +1,40 @@ +easyblock = 'PythonPackage' + +name = 'Cython' +version = '3.0.10' + +homepage = 'https://cython.org/' +description = """ +Cython is an optimising static compiler for both the Python programming +language and the extended Cython programming language (based on Pyrex). +""" +docurls = [ + 'https://cython.org/#documentation', + 'https://github.com/cython/cython', +] + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['dcc96739331fb854dcf503f94607576cfe8488066c61ca50dfd55836f132de99'] + +builddependencies = [ + ('binutils', '2.40'), +] + +dependencies = [ + ('Python', '3.11.5'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/cygdb', 'bin/cython', 'bin/cythonize'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["cython --version"] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/c/Cython/Cython-3.0.10-GCCcore-13.3.0.eb b/easybuild/easyconfigs/c/Cython/Cython-3.0.10-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..c9e419d570a --- /dev/null +++ b/easybuild/easyconfigs/c/Cython/Cython-3.0.10-GCCcore-13.3.0.eb @@ -0,0 +1,40 @@ +easyblock = 'PythonPackage' + +name = 'Cython' +version = '3.0.10' + +homepage = 'https://cython.org/' +description = """ +Cython is an optimising static compiler for both the Python programming +language and the extended Cython programming language (based on Pyrex). +""" +docurls = [ + 'https://cython.org/#documentation', + 'https://github.com/cython/cython', +] + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['dcc96739331fb854dcf503f94607576cfe8488066c61ca50dfd55836f132de99'] + +builddependencies = [ + ('binutils', '2.42'), +] + +dependencies = [ + ('Python', '3.12.3'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/cygdb', 'bin/cython', 'bin/cythonize'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["cython --version"] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/c/cURL/cURL-8.7.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/c/cURL/cURL-8.7.1-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..02470220971 --- /dev/null +++ b/easybuild/easyconfigs/c/cURL/cURL-8.7.1-GCCcore-13.3.0.eb @@ -0,0 +1,43 @@ +easyblock = 'ConfigureMake' + +name = 'cURL' +version = '8.7.1' + +homepage = 'https://curl.haxx.se' + +description = """ + libcurl is a free and easy-to-use client-side URL transfer library, + supporting DICT, FILE, FTP, FTPS, Gopher, HTTP, HTTPS, IMAP, IMAPS, LDAP, + LDAPS, POP3, POP3S, RTMP, RTSP, SCP, SFTP, SMTP, SMTPS, Telnet and TFTP. + libcurl supports SSL certificates, HTTP POST, HTTP PUT, FTP uploading, HTTP + form based upload, proxies, cookies, user+password authentication (Basic, + Digest, NTLM, Negotiate, Kerberos), file transfer resume, http proxy tunneling + and more. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://curl.haxx.se/download/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['f91249c87f68ea00cf27c44fdfa5a78423e41e71b7d408e5901a9896d905c495'] + +builddependencies = [ + ('binutils', '2.42'), +] + +dependencies = [ + ('zlib', '1.3.1'), + ('OpenSSL', '3', '', SYSTEM), +] + +configopts = '--with-zlib ' +configopts += '--with-ssl=$EBROOTOPENSSL ' + +modextravars = {'CURL_INCLUDES': '%(installdir)s/include'} + +sanity_check_paths = { + 'files': ['bin/curl', 'lib/libcurl.a', 'lib/libcurl.%s' % SHLIB_EXT], + 'dirs': ['lib/pkgconfig', 'include/curl'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/c/cairo/cairo-1.18.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/c/cairo/cairo-1.18.0-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..2622f010126 --- /dev/null +++ b/easybuild/easyconfigs/c/cairo/cairo-1.18.0-GCCcore-13.3.0.eb @@ -0,0 +1,51 @@ +easyblock = 'MesonNinja' + + +name = 'cairo' +version = '1.18.0' + +homepage = 'https://cairographics.org' +description = """Cairo is a 2D graphics library with support for multiple output devices. + Currently supported output targets include the X Window System (via both Xlib and XCB), Quartz, Win32, image buffers, + PostScript, PDF, and SVG file output. Experimental backends include OpenGL, BeOS, OS/2, and DirectFB""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = [ + 'https://cairographics.org/releases/', + 'https://cairographics.org/snapshots/' +] +sources = [SOURCE_TAR_XZ] +checksums = ['243a0736b978a33dee29f9cca7521733b78a65b5418206fef7bd1c3d4cf10b64'] + +builddependencies = [ + ('binutils', '2.42'), + ('pkgconf', '2.2.0'), + ('Ninja', '1.12.1'), + ('Meson', '1.4.0'), +] +dependencies = [ + ('bzip2', '1.0.8'), + ('zlib', '1.3.1'), + ('libpng', '1.6.43'), + ('freetype', '2.13.2'), + ('pixman', '0.43.4'), + ('expat', '2.6.2'), + ('GLib', '2.80.4'), + ('X11', '20240607'), +] + +configopts = "--default-library=both" # static and shared library + +sanity_check_paths = { + 'files': ['bin/cairo-trace', 'lib/cairo/libcairo-trace.%s' % SHLIB_EXT, 'lib/cairo/libcairo-trace.a', + 'lib/libcairo.a', 'lib/libcairo-gobject.a', 'lib/libcairo-script-interpreter.a', + 'lib/libcairo.%s' % SHLIB_EXT, 'lib/libcairo-gobject.%s' % SHLIB_EXT, + 'lib/libcairo-script-interpreter.%s' % SHLIB_EXT] + + ['include/cairo/cairo%s.h' % x for x in ['', '-deprecated', '-features', '-ft', '-gobject', '-pdf', '-ps', + '-script', '-script-interpreter', '-svg', '-version', '-xcb', + '-xlib', '-xlib-xrender']], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/c/cairomm/cairomm-1.16.2-GCC-12.3.0.eb b/easybuild/easyconfigs/c/cairomm/cairomm-1.16.2-GCC-12.3.0.eb new file mode 100644 index 00000000000..286c56e1bbb --- /dev/null +++ b/easybuild/easyconfigs/c/cairomm/cairomm-1.16.2-GCC-12.3.0.eb @@ -0,0 +1,39 @@ +# Updated to MesonNinja as the autogen.sh complained. +# Author: J. Sassmannshausen (Imperial College London) + +easyblock = 'MesonNinja' + +name = 'cairomm' +version = '1.16.2' + +homepage = 'http://cairographics.org' +description = "The Cairomm package provides a C++ interface to Cairo." + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +source_urls = ['http://cairographics.org/releases/'] +sources = [SOURCE_TAR_XZ] +checksums = ['6a63bf98a97dda2b0f55e34d1b5f3fb909ef8b70f9b8d382cb1ff3978e7dc13f'] + +builddependencies = [ + ('Meson', '1.1.1'), + ('Ninja', '1.11.1'), + ('Doxygen', '1.9.7'), + ('M4', '1.4.19'), +] + +dependencies = [ + ('cairo', '1.17.8'), + ('libsigc++', '3.6.0'), + ('mm-common', '1.0.6'), + ('Boost', '1.82.0'), +] + +runtest = 'ninja test' + +sanity_check_paths = { + 'files': ['lib/libcairomm-1.16.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/c/ccache/ccache-4.10.2-GCCcore-13.3.0.eb b/easybuild/easyconfigs/c/ccache/ccache-4.10.2-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..5a6b4ee2256 --- /dev/null +++ b/easybuild/easyconfigs/c/ccache/ccache-4.10.2-GCCcore-13.3.0.eb @@ -0,0 +1,49 @@ +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL + +easyblock = 'CMakeNinja' + +name = 'ccache' +version = '4.10.2' + +homepage = 'https://ccache.dev/' +description = """Ccache (or “ccache”) is a compiler cache. It speeds up recompilation by +caching previous compilations and detecting when the same compilation is being done again""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = [GITHUB_RELEASE] +sources = [SOURCE_TAR_GZ] +checksums = ['108100960bb7e64573ea925af2ee7611701241abb36ce0aae3354528403a7d87'] + +builddependencies = [ + ('binutils', '2.42'), + ('CMake', '3.29.3'), + ('Ninja', '1.12.1'), + ('zstd', '1.5.6'), + ('pkgconf', '2.2.0'), +] + +dependencies = [ + ('hiredis', '1.2.0'), +] + +# use BFD linker rather than default ld.gold (required on CentOS 8) +preconfigopts = 'LDFLAGS="-fuse-ld=bfd"' +configopts = ' '.join([ + '-DENABLE_DOCUMENTATION=OFF', + '-DENABLE_IPO=ON', + # Link most libraries statically + '-DSTATIC_LINK=ON', + # Disable downloading dependencies + '-DZSTD_FROM_INTERNET=OFF -DHIREDIS_FROM_INTERNET=OFF', +]) + +sanity_check_paths = { + 'files': ['bin/ccache'], + 'dirs': [] +} +sanity_check_commands = ['ccache --help'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/c/cddlib/cddlib-0.94m-GCCcore-13.2.0.eb b/easybuild/easyconfigs/c/cddlib/cddlib-0.94m-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..c747475d137 --- /dev/null +++ b/easybuild/easyconfigs/c/cddlib/cddlib-0.94m-GCCcore-13.2.0.eb @@ -0,0 +1,38 @@ +easyblock = 'ConfigureMake' + +name = 'cddlib' +version = '0.94m' + +homepage = 'https://github.com/cddlib/cddlib' +description = "An efficient implementation of the Double Description Method" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} +toolchainopts = {'pic': True} + +github_account = 'cddlib' +source_urls = [GITHUB_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['766d8ec2135989830748e5e2fe57f307ed0706431c135541c3c081cbec0bc34f'] + +builddependencies = [ + ('Autotools', '20220317'), + ('binutils', '2.40'), +] + +dependencies = [('GMP', '6.3.0')] + +preconfigopts = "autoreconf -f -i && " + +buildopts = "SUBDIRS='lib-src src'" # build sources but spare the documentation in latex +installopts = buildopts + +local_exes = ['adjacency', 'allfaces', 'cddexec', 'fourier', 'lcdd', 'projection', 'redcheck', 'scdd', 'testcdd1', + 'testcdd2', 'testlp1', 'testlp2', 'testlp3', 'testshoot'] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_exes] + ['bin/%s_gmp' % x for x in local_exes] + + ['lib/%s.%s' % (l, e) for l in ['libcdd', 'libcddgmp'] for e in ['a', SHLIB_EXT]] + + ['include/cddlib/%s.h' % h for h in ['cdd', 'cddmp', 'cddtypes', 'setoper', 'splitmix64']], + 'dirs': ['share/doc'] +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/c/cell2location/cell2location-0.05-alpha-fosscuda-2020b.eb b/easybuild/easyconfigs/c/cell2location/cell2location-0.05-alpha-fosscuda-2020b.eb index 9a0eeba1628..1556b0f9dad 100644 --- a/easybuild/easyconfigs/c/cell2location/cell2location-0.05-alpha-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/c/cell2location/cell2location-0.05-alpha-fosscuda-2020b.eb @@ -45,12 +45,6 @@ preinstallopts = "sed -i 's/theano/Theano-PyMC/g' setup.py && " use_pip = True -exts_default_options = { - 'download_dep_fail': True, - 'sanity_pip_check': True, - 'use_pip': True, -} - exts_list = [ ('opt-einsum', '3.3.0', { 'source_tmpl': 'opt_einsum-%(version)s.tar.gz', diff --git a/easybuild/easyconfigs/c/cffi/cffi-1.16.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/c/cffi/cffi-1.16.0-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..94a734e98da --- /dev/null +++ b/easybuild/easyconfigs/c/cffi/cffi-1.16.0-GCCcore-13.3.0.eb @@ -0,0 +1,38 @@ +easyblock = "PythonBundle" + +name = 'cffi' +version = '1.16.0' + +homepage = 'https://cffi.readthedocs.io/en/latest/' +description = """C Foreign Function Interface for Python. Interact with almost any C code from +Python, based on C-like declarations that you can often copy-paste from header +files or documentation. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +builddependencies = [ + ('binutils', '2.42'), +] + +dependencies = [ + ('Python', '3.12.3'), +] + +exts_default_options = { + 'download_dep_fail': True, + 'sanity_pip_check': True, + 'use_pip': True, +} + +exts_list = [ + ('pycparser', '2.22', { + 'checksums': ['491c8be9c040f5390f5bf44a5b07752bd07f56edf992381b05c701439eec10f6'], + }), + (name, version, { + 'checksums': ['bcb3ef43e58665bbda2fb198698fcae6776483e0c4a631aa5647806c25e02cc0'], + }), +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/c/cfgrib/cfgrib-0.9.14.0-foss-2023a.eb b/easybuild/easyconfigs/c/cfgrib/cfgrib-0.9.14.0-foss-2023a.eb new file mode 100644 index 00000000000..b6b2b66159c --- /dev/null +++ b/easybuild/easyconfigs/c/cfgrib/cfgrib-0.9.14.0-foss-2023a.eb @@ -0,0 +1,41 @@ +easyblock = "PythonBundle" + +name = 'cfgrib' +version = '0.9.14.0' + +homepage = 'https://github.com/ecmwf/cfgrib/' +description = """ +A Python interface to map GRIB files to the NetCDF Common Data Model following the CF +Convention using ecCodes. +""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [ + ('poetry', '1.7.1'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('ecCodes', '2.31.0'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('findlibs', '0.0.5', { + 'checksums': ['7a801571e999d0ee83f9b92cbb598c21f861ee26ca9dba74cea8958ba4335e7e'], + }), + ('eccodes', '1.7.1', { + 'checksums': ['d3c7e9bab779d35b624cfd7b3331de111602cba6a6f6368efcc12407f30b2697'], + }), + (name, version, { + 'checksums': ['2b9a1e6bd47397e585f878ffd8aaac5969f6c9a448da767c700917b89c275bb2'], + }), +] + +sanity_check_commands = ['python -m cfgrib selfcheck'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/c/chewBBACA/chewBBACA-3.3.9-foss-2022b.eb b/easybuild/easyconfigs/c/chewBBACA/chewBBACA-3.3.9-foss-2022b.eb new file mode 100644 index 00000000000..b9964db690a --- /dev/null +++ b/easybuild/easyconfigs/c/chewBBACA/chewBBACA-3.3.9-foss-2022b.eb @@ -0,0 +1,66 @@ +easyblock = 'PythonBundle' + +name = 'chewBBACA' +version = '3.3.9' + +homepage = 'https://github.com/B-UMMI/chewBBACA' +description = """chewBBACA is a software suite for the creation and evaluation of core genome and whole genome +MultiLocus Sequence Typing (cg/wgMLST) schemas and results. The "BBACA" stands for "BSR-Based Allele Calling Algorithm". +BSR stands for BLAST Score Ratio as proposed by Rasko DA et al. The "chew" part adds extra coolness to the name and +could be thought of as "Comprehensive and Highly Efficient Workflow".""" + +toolchain = {'name': 'foss', 'version': '2022b'} + +dependencies = [ + ('Python', '3.10.8'), + ('SciPy-bundle', '2023.02'), + # Cython 3 is required, see https://github.com/althonos/pyrodigal/issues/40 + # Cython included with Python-bundle-PyPI (0.29.35) is too old + ('Cython', '3.0.8'), + ('Biopython', '1.81'), + ('plotly.py', '5.13.1'), + ('BLAST+', '2.14.0'), + ('prodigal', '2.6.3'), + ('MAFFT', '7.505', '-with-extensions'), + ('FastTree', '2.1.11'), + ('archspec', '0.2.0'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('pyrodigal', '3.5.1', { + 'checksums': ['20af59a6d968c88910b99d5f647bb7dd22d49e440ead95fe715cdd2c49f36e9f'], + }), + ('isodate', '0.6.1', { + 'checksums': ['48c5881de7e8b0a0d648cb024c8062dc84e7b840ed81e864c7614fd3c127bde9'], + }), + ('rdflib', '7.0.0', { + 'checksums': ['9995eb8569428059b8c1affd26b25eac510d64f5043d9ce8c84e0d0036e995ae'], + }), + ('SPARQLWrapper', '2.0.0', { + 'modulename': 'SPARQLWrapper', + 'checksums': ['3fed3ebcc77617a4a74d2644b86fd88e0f32e7f7003ac7b2b334c026201731f1'], + }), + (name, version, { + 'modulename': 'CHEWBBACA', + # relax numpy version requirement + 'preinstallopts': "sed -i 's/numpy~=1.24.3/numpy~=1.24.2/g' pyproject.toml && ", + 'runtest': "python setup.py test", + 'sources': ['%(namelower)s-%(version)s.tar.gz'], + 'checksums': ['4bf0792b8cdd1783b50340ac713748ef2a351209cacb50ad4c9e2fe2e7fba772'], + }), +] + +sanity_check_paths = { + 'files': ['bin/chewBBACA.py', 'bin/chewie'], + 'dirs': [], +} + +sanity_check_commands = [ + 'chewBBACA.py --help', + 'chewie --help', +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/chopper/chopper-0.9.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/c/chopper/chopper-0.9.0-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..b1788fb34f9 --- /dev/null +++ b/easybuild/easyconfigs/c/chopper/chopper-0.9.0-GCCcore-12.3.0.eb @@ -0,0 +1,315 @@ +easyblock = 'Cargo' + +name = 'chopper' +version = '0.9.0' + +homepage = 'https://github.com/wdecoster/chopper' +description = """Rust implementation of NanoFilt+NanoLyse, both +originally written in Python. This tool, intended for long read +sequencing such as PacBio or ONT, filters and trims a fastq file. +Filtering is done on average read quality and minimal or maximal read +length, and applying a headcrop (start of read) and tailcrop (end of +read) while printing the reads passing the filter.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +github_account = 'wdecoster' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +patches = [ + 'chopper-0.9.0_fix_incorrect_version.patch', +] +checksums = [ + {'v0.9.0.tar.gz': 'ae5b6f8f5ffde45582998b63cb45b4221b25ee37a9fde7a256e653c7f3f12075'}, + {'adler-1.0.2.tar.gz': 'f26201604c87b1e01bd3d98f8d5d9a8fcbb815e8cedb41ffccbeb4bf593a35fe'}, + {'aho-corasick-1.1.3.tar.gz': '8e60d3430d3a69478ad0993f19238d2df97c507009a52b3c10addcd7f6bcb916'}, + {'anstream-0.6.13.tar.gz': 'd96bd03f33fe50a863e394ee9718a706f988b9079b20c3784fb726e7678b62fb'}, + {'anstyle-1.0.6.tar.gz': 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'0.1.11+1.0.8'), + ('cc', '1.0.94'), + ('cfg-if', '1.0.0'), + ('clap', '4.5.4'), + ('clap_builder', '4.5.2'), + ('clap_derive', '4.5.4'), + ('clap_lex', '0.7.0'), + ('cmake', '0.1.50'), + ('colorchoice', '1.0.0'), + ('crc32fast', '1.4.0'), + ('crossbeam-deque', '0.8.5'), + ('crossbeam-epoch', '0.9.18'), + ('crossbeam-utils', '0.8.19'), + ('csv', '1.3.0'), + ('csv-core', '0.1.11'), + ('custom_derive', '0.1.7'), + ('derive-new', '0.5.9'), + ('editdistancek', '1.0.2'), + ('either', '1.11.0'), + ('enum-map', '2.7.3'), + ('enum-map-derive', '0.17.0'), + ('equivalent', '1.0.1'), + ('feature-probe', '0.1.1'), + ('fixedbitset', '0.4.2'), + ('flate2', '1.0.28'), + ('fxhash', '0.2.1'), + ('getrandom', '0.2.14'), + ('hashbrown', '0.14.3'), + ('heck', '0.4.1'), + ('heck', '0.5.0'), + ('hermit-abi', '0.1.19'), + ('indexmap', '2.2.6'), + ('itertools', '0.11.0'), + ('itertools-num', '0.1.3'), + ('itoa', '1.0.11'), + ('lazy_static', '1.4.0'), + ('libc', '0.2.153'), + ('libm', '0.2.8'), + ('libz-ng-sys', '1.1.15'), + ('libz-sys', '1.1.16'), + ('lzma-sys', '0.1.20'), + ('matrixmultiply', '0.3.8'), + ('memchr', '2.7.2'), + ('minimap2', '0.1.17+minimap2.2.27'), + ('minimap2-sys', '0.1.18+minimap2.2.27'), + ('miniz_oxide', '0.7.2'), + ('multimap', '0.9.1'), + ('nalgebra', '0.29.0'), + ('nalgebra-macros', '0.1.0'), + ('ndarray', '0.15.6'), + ('needletail', '0.5.1'), + ('newtype_derive', '0.1.6'), + ('num-complex', '0.4.5'), + ('num-integer', '0.1.46'), + ('num-rational', '0.4.1'), + ('num-traits', '0.2.18'), + ('ordered-float', '3.9.2'), + ('paste', '1.0.14'), + ('petgraph', '0.6.4'), + ('pkg-config', '0.3.30'), + ('ppv-lite86', '0.2.17'), + ('proc-macro2', '1.0.81'), + ('quote', '1.0.36'), + ('rand', '0.8.5'), + ('rand_chacha', '0.3.1'), + ('rand_core', '0.6.4'), + ('rand_distr', '0.4.3'), + ('rawpointer', '0.2.1'), + ('rayon', '1.10.0'), + ('rayon-core', '1.12.1'), + ('regex', '1.10.4'), + ('regex-automata', '0.4.6'), + ('regex-syntax', '0.8.3'), + ('rustc_version', '0.1.7'), + ('rustversion', '1.0.15'), + ('ryu', '1.0.17'), + ('safe_arch', '0.7.1'), + ('semver', '0.1.20'), + ('serde', '1.0.198'), + ('serde_derive', '1.0.198'), + ('simba', '0.6.0'), + ('simdutf8', '0.1.4'), + ('statrs', '0.16.0'), + ('strsim', '0.11.1'), + ('strum', '0.25.0'), + ('strum_macros', '0.25.3'), + ('syn', '1.0.109'), + ('syn', '2.0.60'), + ('thiserror', '1.0.58'), + ('thiserror-impl', '1.0.58'), + ('triple_accel', '0.4.0'), + ('typenum', '1.17.0'), + ('unicode-ident', '1.0.12'), + ('utf8parse', '0.2.1'), + ('vcpkg', '0.2.15'), + ('vec_map', '0.8.2'), + ('wasi', '0.11.0+wasi-snapshot-preview1'), + ('wide', '0.7.16'), + ('winapi', '0.3.9'), + ('winapi-i686-pc-windows-gnu', '0.4.0'), + ('winapi-x86_64-pc-windows-gnu', '0.4.0'), + ('windows-sys', '0.52.0'), + ('windows-targets', '0.52.5'), + ('windows_aarch64_gnullvm', '0.52.5'), + ('windows_aarch64_msvc', '0.52.5'), + ('windows_i686_gnu', '0.52.5'), + ('windows_i686_gnullvm', '0.52.5'), + ('windows_i686_msvc', '0.52.5'), + ('windows_x86_64_gnu', '0.52.5'), + ('windows_x86_64_gnullvm', '0.52.5'), + ('windows_x86_64_msvc', '0.52.5'), + ('xz2', '0.1.7'), +] +sanity_check_paths = { + 'files': ['bin/chopper'], + 'dirs': [], +} + +sanity_check_commands = [ + 'chopper --help', +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/chopper/chopper-0.9.0_fix_incorrect_version.patch b/easybuild/easyconfigs/c/chopper/chopper-0.9.0_fix_incorrect_version.patch new file mode 100644 index 00000000000..57c15b94db4 --- /dev/null +++ b/easybuild/easyconfigs/c/chopper/chopper-0.9.0_fix_incorrect_version.patch @@ -0,0 +1,28 @@ +Fix incorrect version number in the 0.9.0 tar file. + +Åke Sandgren, 2024-09-16 +diff --git a/Cargo.lock b/Cargo.lock +index 3e8f1fe..53fa5da 100644 +--- a/Cargo.lock ++++ b/Cargo.lock +@@ -236,7 +236,7 @@ checksum = "baf1de4339761588bc0619e3cbc0120ee582ebb74b53b4efbf79117bd2da40fd" + + [[package]] + name = "chopper" +-version = "0.8.0" ++version = "0.9.0" + dependencies = [ + "approx", + "atty", +diff --git a/Cargo.toml b/Cargo.toml +index f268dce..7f7277a 100644 +--- a/Cargo.toml ++++ b/Cargo.toml +@@ -1,6 +1,6 @@ + [package] + name = "chopper" +-version = "0.8.0" ++version = "0.9.0" + authors = ["wdecoster "] + edition = "2021" + diff --git a/easybuild/easyconfigs/c/cisDIVERSITY/cisDIVERSITY-1.1-foss-2023a-Python-2.7.18.eb b/easybuild/easyconfigs/c/cisDIVERSITY/cisDIVERSITY-1.1-foss-2023a-Python-2.7.18.eb new file mode 100644 index 00000000000..76a00927a51 --- /dev/null +++ b/easybuild/easyconfigs/c/cisDIVERSITY/cisDIVERSITY-1.1-foss-2023a-Python-2.7.18.eb @@ -0,0 +1,56 @@ +easyblock = 'MakeCp' + +name = 'cisDIVERSITY' +version = '1.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/NarlikarLab/cisDIVERSITY/' +description = """A module discovery tool used for finding diverse sequence architectures, +each one characterized by presence or absence of de novo motifs.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['https://github.com/NarlikarLab/cisDIVERSITY/releases/download/v%(version)s/'] +sources = [{ + 'download_filename': '%(name)s_v%(version)s.tar.gz', + 'filename': SOURCE_TAR_GZ, +}] +checksums = ['4ba5967fa754ec78b9dd6b6dc9d2ee5de87dbb4d7906d47e57e73aec87897725'] + +dependencies = [ + ('Python', '2.7.18'), + ('R', '4.3.2'), + ('numpy', '1.16.6', versionsuffix), +] + +exts_defaultclass = 'RPackage' +exts_default_options = { + 'source_urls': [ + 'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'https://cran.r-project.org/src/contrib/', # current version of packages + 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + ], + 'source_tmpl': '%(name)s_%(version)s.tar.gz', +} + +exts_list = [ + ('corrplot', '0.95', { + 'checksums': ['84a31f675041e589201b4d640753302abc10ccc2c0ca0a409b5153861989d776'], + }), +] + +files_to_copy = [(['learnDiverseModules'], 'bin')] + +modextrapaths = {'R_LIBS_SITE': ''} + +sanity_check_paths = { + 'files': ['bin/learnDiverseModules'], + 'dirs': ['corrplot'], +} + +sanity_check_commands = [ + 'learnDiverseModules -h', + 'Rscript -e "library(corrplot)"', +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/cliquer/cliquer-1.21-GCCcore-13.2.0.eb b/easybuild/easyconfigs/c/cliquer/cliquer-1.21-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..3fa7d597761 --- /dev/null +++ b/easybuild/easyconfigs/c/cliquer/cliquer-1.21-GCCcore-13.2.0.eb @@ -0,0 +1,42 @@ +easyblock = 'MakeCp' + +name = 'cliquer' +version = '1.21' + +homepage = 'https://users.aalto.fi/~pat/cliquer.html' +description = """Cliquer is a set of C routines for finding cliques in an arbitrary weighted graph. + It uses an exact branch-and-bound algorithm developed by Patric Ostergard. It is designed with + the aim of being efficient while still being flexible and easy to use.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['http://users.aalto.fi/~pat/cliquer/'] +sources = [SOURCE_TAR_GZ] +checksums = ['ff306d27eda82383c0257065e3ffab028415ac9af73bccfdd9c2405b797ed1f1'] + +builddependencies = [('binutils', '2.40')] + +local_sharedlib = 'libcliquer.%s' % SHLIB_EXT + +prebuildopts = 'sed -i "s/^CFLAGS=/CFLAGS=$CFLAGS /" Makefile && ' + +buildopts = ' && $CC -shared $CFLAGS $LDFLAGS -o %s *.o' % local_sharedlib + +local_headers = ['cliquer', 'set', 'graph', 'misc', 'reorder', 'cliquerconf'] + +files_to_copy = [ + (['cl'], 'bin'), + ([local_sharedlib], 'lib'), + (['%s.h' % h for h in local_headers], 'include/cliquer'), +] + +sanity_check_paths = { + 'files': ['bin/cl', 'lib/%s' % local_sharedlib] + + ['include/cliquer/%s.h' % h for h in local_headers], + 'dirs': [], +} + +sanity_check_commands = ["cl --help"] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/c/cmcrameri/cmcrameri-1.9-gfbf-2023a.eb b/easybuild/easyconfigs/c/cmcrameri/cmcrameri-1.9-gfbf-2023a.eb new file mode 100644 index 00000000000..81e043144e9 --- /dev/null +++ b/easybuild/easyconfigs/c/cmcrameri/cmcrameri-1.9-gfbf-2023a.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonBundle' + +name = 'cmcrameri' +version = '1.9' + +homepage = 'https://github.com/callumrollo/cmcrameri' +description = "Python wrapper around Fabio Crameri's perceptually uniform colormaps." + +toolchain = {'name': 'gfbf', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('matplotlib', '3.7.2'), +] + +use_pip = True + +exts_list = [ + (name, version, { + 'checksums': ['56faf9b7f53eb03fed450137bec7dc25c1854929d7b841b9c75616fc2c357640'], + }), +] + +sanity_pip_check = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/c/code-cli/code-cli-1.93.1-x64.eb b/easybuild/easyconfigs/c/code-cli/code-cli-1.93.1-x64.eb new file mode 100644 index 00000000000..48e53c03e62 --- /dev/null +++ b/easybuild/easyconfigs/c/code-cli/code-cli-1.93.1-x64.eb @@ -0,0 +1,35 @@ +easyblock = 'Tarball' + +name = 'code-cli' +version = '1.93.1' +versionsuffix = '-x64' + +homepage = 'https://code.visualstudio.com/' +description = ''' + Visual Studio Code is a lightweight but powerful source code editor + which runs on your desktop and is available for Windows, macOS and + Linux. It comes with built-in support for JavaScript, TypeScript and + Node.js and has a rich ecosystem of extensions for other languages + and runtimes (such as C++, C#, Java, Python, PHP, Go, .NET). Begin + your journey with VS Code with these introductory videos. +''' + +toolchain = {'name': 'system', 'version': 'system'} + +source_urls = ['https://update.code.visualstudio.com/%(version)s/cli-alpine-x64/stable#'] +sources = [{ + 'download_filename': 'vscode_cli_alpine_x64_cli.tar.gz', + 'filename': 'vscode-%(version)s%(versionsuffix)s.tar.gz', +}] +checksums = ['1fd27b23ca8c6f4b55922de3181b312a094d8aa18ad6e0a716b7b94224064288'] + +modextrapaths = {'PATH': ''} + +sanity_check_paths = { + 'files': ['code'], + 'dirs': [] +} + +sanity_check_commands = ["code --help"] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/c/code-server/code-server-4.89.1.eb b/easybuild/easyconfigs/c/code-server/code-server-4.89.1.eb new file mode 100644 index 00000000000..dfd586cb4fc --- /dev/null +++ b/easybuild/easyconfigs/c/code-server/code-server-4.89.1.eb @@ -0,0 +1,20 @@ +name = 'code-server' +version = '4.89.1' + +homepage = 'https://github.com/coder/code-server' +description = """Run VS Code on any machine anywhere and access it in the browser.""" + +toolchain = SYSTEM + +source_urls = ['https://github.com/coder/code-server/releases/download/v%(version)s/'] +sources = ['code-server-%(version)s-linux-%(mapped_arch)s.tar.gz'] +checksums = [ + { + 'code-server-%(version)s-linux-amd64.tar.gz': + '5c3769b1ab5cbb2eceb092524dc46f558905e4260155b477d3a313f9ea25ca33', + 'code-server-%(version)s-linux-arm64.tar.gz': + '69d3d1f7158d6e2125bd2f831611ab959a2aa80d5a7d96422a44070eb2b8645b', + } +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/c/code-server/code-server-4.90.2.eb b/easybuild/easyconfigs/c/code-server/code-server-4.90.2.eb new file mode 100644 index 00000000000..d85b34c752c --- /dev/null +++ b/easybuild/easyconfigs/c/code-server/code-server-4.90.2.eb @@ -0,0 +1,20 @@ +name = 'code-server' +version = '4.90.2' + +homepage = 'https://github.com/coder/code-server' +description = """Run VS Code on any machine anywhere and access it in the browser.""" + +toolchain = SYSTEM + +source_urls = ['https://github.com/coder/code-server/releases/download/v%(version)s/'] +sources = ['code-server-%(version)s-linux-%(mapped_arch)s.tar.gz'] +checksums = [ + { + 'code-server-%(version)s-linux-amd64.tar.gz': + 'c66b57759e41c66c28577eaefa4cce106f7b5ad5fb3ab394baea5eaa5b604cce', + 'code-server-%(version)s-linux-arm64.tar.gz': + '12e51e3575069c438aa4dee93bddfc221e7850192a7745b84fc77b420cedf205', + } +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/c/code-server/code-server-4.93.1.eb b/easybuild/easyconfigs/c/code-server/code-server-4.93.1.eb new file mode 100644 index 00000000000..3217ab284bf --- /dev/null +++ b/easybuild/easyconfigs/c/code-server/code-server-4.93.1.eb @@ -0,0 +1,20 @@ +name = 'code-server' +version = '4.93.1' + +homepage = 'https://github.com/coder/code-server' +description = """Run VS Code on any machine anywhere and access it in the browser.""" + +toolchain = SYSTEM + +source_urls = ['https://github.com/coder/code-server/releases/download/v%(version)s/'] +sources = ['code-server-%(version)s-linux-%(mapped_arch)s.tar.gz'] +checksums = [ + { + 'code-server-%(version)s-linux-amd64.tar.gz': + '8c001f865cf082e914375e8f28e9e15b25faa1f3de455ddc30158d54fc2326d3', + 'code-server-%(version)s-linux-arm64.tar.gz': + '1e29278529d0d8376d1344ed816b37f4e88a5ba16ce74cb1173fe437c8519852', + } +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/c/colorize/colorize-0.7.7-GCC-12.3.0.eb b/easybuild/easyconfigs/c/colorize/colorize-0.7.7-GCC-12.3.0.eb new file mode 100644 index 00000000000..35921013c3e --- /dev/null +++ b/easybuild/easyconfigs/c/colorize/colorize-0.7.7-GCC-12.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'RubyGem' + +name = 'colorize' +version = '0.7.7' + +homepage = 'https://github.com/fazibear/colorize' +description = """Ruby gem for colorizing text using ANSI escape sequences. +Extends String class or add a ColorizedString with methods to set the text color, background color and text effects.""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +source_urls = ['https://rubygems.org/downloads/'] +sources = ['%(name)s-%(version)s.gem'] +checksums = ['d6ab95a5fcdea3c36c3327d38c1e79e2950ee1788506d8489ae35db330937a99'] + +gem_file = '%(name)s-%(version)s.gem' + +dependencies = [ + ('Ruby', '3.3.0'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['gems/%(namelower)s-%(version)s'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/c/columba/columba-1.2-20240326-GCC-13.3.0.eb b/easybuild/easyconfigs/c/columba/columba-1.2-20240326-GCC-13.3.0.eb new file mode 100644 index 00000000000..bbdb6d884b8 --- /dev/null +++ b/easybuild/easyconfigs/c/columba/columba-1.2-20240326-GCC-13.3.0.eb @@ -0,0 +1,29 @@ +easyblock = 'CMakeMake' + +name = 'columba' +local_commit = '526b0a0' +version = '1.2-20240326' + +homepage = 'https://github.com/biointec/columba' +description = "Fast Approximate Pattern Matching using Search Schemes" + +toolchain = {'name': 'GCC', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/biointec/columba/archive'] +sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}] +checksums = ['018898cf6ba93a974a141b397b68a7df13457e80bf92b1747f7b30c4a0d756f1'] + +builddependencies = [ + ('CMake', '3.29.3'), + ('sparsehash', '2.0.4'), +] + +sanity_check_paths = { + 'files': ['bin/columba', 'bin/columba_build'], + 'dirs': [], +} + +sanity_check_commands = ["columba --help"] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/c/configurable-http-proxy/configurable-http-proxy-4.6.1-GCCcore-13.2.0.eb b/easybuild/easyconfigs/c/configurable-http-proxy/configurable-http-proxy-4.6.1-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..c8aae63595d --- /dev/null +++ b/easybuild/easyconfigs/c/configurable-http-proxy/configurable-http-proxy-4.6.1-GCCcore-13.2.0.eb @@ -0,0 +1,32 @@ +easyblock = 'Binary' + +name = 'configurable-http-proxy' +version = '4.6.1' + +homepage = 'https://github.com/jupyterhub/configurable-http-proxy' +description = """HTTP proxy for node.js including a REST API for updating the routing table. + Developed as a part of the Jupyter Hub multi-user server.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://github.com/jupyterhub/%(name)s/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['52bac444b1a0629e7817102949f685bdb719d0cbfd0abbaeaa91d42f1ed60852'] + +builddependencies = [ + ('binutils', '2.40'), +] +dependencies = [ + ('nodejs', '20.9.0'), +] + +install_cmd = "npm install --no-package-lock -g --prefix %(installdir)s %(version)s.tar.gz" + +sanity_check_paths = { + 'files': ['bin/%(name)s'], + 'dirs': [], +} + +sanity_check_commands = ['%(name)s --version'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/c/connected-components-3d/connected-components-3d-3.14.1-foss-2023a.eb b/easybuild/easyconfigs/c/connected-components-3d/connected-components-3d-3.14.1-foss-2023a.eb new file mode 100644 index 00000000000..5a366beb6d0 --- /dev/null +++ b/easybuild/easyconfigs/c/connected-components-3d/connected-components-3d-3.14.1-foss-2023a.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonPackage' + +name = 'connected-components-3d' +version = '3.14.1' + +homepage = 'https://github.com/seung-lab/connected-components-3d/' +description = """cc3d is an implementation of connected components in three dimensions using a 26, 18, + or 6-connected neighborhood in 3D or 4 and 8-connected in 2D.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +sources = [SOURCE_TAR_GZ] +checksums = ['fdc4099508b734b266a42ee12534ee42e29467c28506b137e8c1edc8c7513c92'] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +options = {'modulename': 'cc3d'} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/c/cooler/cooler-0.10.2-foss-2023a.eb b/easybuild/easyconfigs/c/cooler/cooler-0.10.2-foss-2023a.eb new file mode 100644 index 00000000000..57091228de3 --- /dev/null +++ b/easybuild/easyconfigs/c/cooler/cooler-0.10.2-foss-2023a.eb @@ -0,0 +1,49 @@ +easyblock = 'PythonBundle' + +name = 'cooler' +version = '0.10.2' + +homepage = 'https://open2c.github.io/cooler' +description = """Cooler is a support library for a storage format, also called cooler, used to store + genomic interaction data of any size, such as Hi-C contact matrices.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [ + ('hatchling', '1.18.0'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('h5py', '3.9.0'), + ('PyYAML', '6.0'), + ('pyfaidx', '0.8.1.1'), +] + +use_pip = True + +exts_list = [ + ('asciitree', '0.3.3', { + 'checksums': ['4aa4b9b649f85e3fcb343363d97564aa1fb62e249677f2e18a96765145cc0f6e'], + }), + ('toolz', '0.12.0', { + 'checksums': ['88c570861c440ee3f2f6037c4654613228ff40c93a6c25e0eba70d17282c6194'], + }), + ('cytoolz', '0.12.3', { + 'checksums': ['4503dc59f4ced53a54643272c61dc305d1dbbfbd7d6bdf296948de9f34c3a282'], + }), + ('dill', '0.3.8', { + 'checksums': ['3ebe3c479ad625c4553aca177444d89b486b1d84982eeacded644afc0cf797ca'], + }), + ('multiprocess', '0.70.16', { + 'checksums': ['161af703d4652a0e1410be6abccecde4a7ddffd19341be0a7011b94aeb171ac1'], + }), + (name, version, { + 'checksums': ['3780a2e69b2ec89882dfc2775de5d9b54ccb79569dc5f042b4851599388112dc'], + }), +] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/cooler/cooler-0.10.2-foss-2023b.eb b/easybuild/easyconfigs/c/cooler/cooler-0.10.2-foss-2023b.eb new file mode 100644 index 00000000000..f092666e99d --- /dev/null +++ b/easybuild/easyconfigs/c/cooler/cooler-0.10.2-foss-2023b.eb @@ -0,0 +1,46 @@ +easyblock = 'PythonBundle' + +name = 'cooler' +version = '0.10.2' + +homepage = 'https://open2c.github.io/cooler' +description = """Cooler is a support library for a storage format, also called cooler, used to store + genomic interaction data of any size, such as Hi-C contact matrices.""" + +toolchain = {'name': 'foss', 'version': '2023b'} + +builddependencies = [ + ('hatchling', '1.18.0'), +] + +dependencies = [ + ('Python', '3.11.5'), + ('Python-bundle-PyPI', '2023.10'), + ('SciPy-bundle', '2023.11'), + ('h5py', '3.11.0'), + ('PyYAML', '6.0.1'), + ('pyfaidx', '0.8.1.1'), + ('dill', '0.3.8'), + ('multiprocess', '0.70.16'), +] + +use_pip = True + +exts_list = [ + ('asciitree', '0.3.3', { + 'checksums': ['4aa4b9b649f85e3fcb343363d97564aa1fb62e249677f2e18a96765145cc0f6e'], + }), + ('toolz', '1.0.0', { + 'checksums': ['2c86e3d9a04798ac556793bced838816296a2f085017664e4995cb40a1047a02'], + }), + ('cytoolz', '1.0.0', { + 'checksums': ['eb453b30182152f9917a5189b7d99046b6ce90cdf8aeb0feff4b2683e600defd'], + }), + (name, version, { + 'checksums': ['3780a2e69b2ec89882dfc2775de5d9b54ccb79569dc5f042b4851599388112dc'], + }), +] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/coxeter/coxeter-20180226-GCCcore-13.2.0.eb b/easybuild/easyconfigs/c/coxeter/coxeter-20180226-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..247bb5ac24d --- /dev/null +++ b/easybuild/easyconfigs/c/coxeter/coxeter-20180226-GCCcore-13.2.0.eb @@ -0,0 +1,45 @@ +easyblock = 'ConfigureMake' + +name = 'coxeter' +version = '20180226' +local_commit = '7b5a1f0' + +homepage = 'https://github.com/tscrim/coxeter' +description = """A library for the study of combinatorial aspects of Coxeter group theory""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://github.com/tscrim/coxeter/archive/%s/' % local_commit] +sources = [SOURCE_TAR_GZ] +patches = [ + 'coxeter-20180226_makefile.patch', + ('coxeter-20180226_sage_interface.patch', 0), +] +checksums = [ + {'coxeter-20180226.tar.gz': '5e0668c40b29c03c438a6ebc0f49f13aaf155b4bcbff56303a753390e6fce3aa'}, + {'coxeter-20180226_makefile.patch': '229ed201e41bae0ae7b22aa21d5007127aeb52fd158543dd5fff2e89797e211f'}, + {'coxeter-20180226_sage_interface.patch': '18ba75e51a944ffccb7fa440b823f68a0aad9066e8edcdd2b52bac6b43404bd3'}, +] + +builddependencies = [('binutils', '2.40')] + +skipsteps = ['configure'] + +buildopts = 'CC="$CC" CFLAGS="$CFLAGS"' +preinstallopts = 'mkdir -p "%(installdir)s/bin" "%(installdir)s/lib" && ' +installopts = 'SAGE_LOCAL="%(installdir)s"' + +sanity_check_paths = { + 'files': [ + 'bin/%(name)s', + 'lib/lib%%(name)s3.%s' % SHLIB_EXT, + ], + 'dirs': [ + 'include/%(name)s', + 'share/%(name)s', + ] +} + +sanity_check_commands = ['echo "qq" | coxeter'] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/c/coxeter/coxeter-20180226_makefile.patch b/easybuild/easyconfigs/c/coxeter/coxeter-20180226_makefile.patch new file mode 100644 index 00000000000..d00d6860689 --- /dev/null +++ b/easybuild/easyconfigs/c/coxeter/coxeter-20180226_makefile.patch @@ -0,0 +1,101 @@ +Allows installation of files needed for Sagemath +Source: https://gitlab.archlinux.org/archlinux/packaging/packages/coxeter/-/blob/main/coxeter-makefile.patch +diff -u makefile.orig makefile +--- makefile.orig 2018-02-26 13:57:36.000000000 +0100 ++++ makefile 2024-08-16 14:15:51.889503570 +0200 +@@ -12,6 +12,7 @@ + gflags = -c $(includedirs) -g + + cflags = $(gflags) # the default setting ++cflags = -c $(includedirs) $(CPPFLAGS) $(CXXFLAGS) -fPIC + + ifdef optimize + NDEBUG = true +@@ -22,18 +23,74 @@ + cflags = $(pflags) + endif + +-cc = g++ ++EXENAME = coxeter ++LIBNAME = coxeter3 ++ifeq ($(UNAME),Darwin) ++ EXEEXT = ++ LIBPREFIX = lib ++ LIBEXT = .dylib ++ LIBDIR = lib ++ LINKFLAGS = -dynamiclib -Wl,-headerpad_max_install_names,-undefined,dynamic_lookup,-compatibility_version,3.0,-current_version,3.0,-install_name,$(SAGE_LOCAL)/lib/$(LIBPREFIX)$(LIBNAME)$(LIBEXT) ++ LINKLIBS = ++else ++ifeq ($(UNAME),CYGWIN) ++ EXEEXT = .exe ++ LIBPREFIX = cyg ++ LIBEXT = .dll ++ LIBDIR = bin ++ IMPLIB = lib$(LIBNAME).dll.a ++ LINKFLAGS = -shared -Wl,--out-implib=$(IMPLIB) -Wl,--export-all-symbols ++ LINKLIBS = -lc ++else ++ EXEEXT = ++ LIBPREFIX = lib ++ LIBEXT = .so ++ LIBDIR = lib ++ LINKFLAGS = $(LDFLAGS) -shared -Wl,-soname,libcoxeter3.so ++ LINKLIBS = -lc ++endif ++endif ++LIBRARY = $(LIBPREFIX)$(LIBNAME)$(LIBEXT) + +-all: coxeter #clean ++all: coxeter executable + + coxeter: $(objects) +- $(cc) -o coxeter $(objects) ++ $(CXX) $(LINKFLAGS) -o $(LIBRARY) $(objects) $(LINKLIBS) ++ ++executable: $(objects) ++ $(CXX) $(LDFLAGS) -o $(EXENAME)$(EXEEXT) $(objects) ++ ++DATADIR="$$SAGE_LOCAL/share/coxeter/" ++INCLUDEDIR="$$SAGE_LOCAL/include/coxeter/" ++LIBRARYDIR="$$SAGE_LOCAL/$(LIBDIR)" ++ ++install: coxeter executable ++ cp $(EXENAME)$(EXEEXT) "$$SAGE_LOCAL/bin/" ++ cp $(LIBRARY) $(LIBRARYDIR) ++ if [ $(UNAME) = "CYGWIN" ]; then \ ++ cp $(IMPLIB) "$$SAGE_LOCAL/lib/"; \ ++ fi ++ ++ mkdir -p $(DATADIR) ++ cp -r coxeter_matrices headers messages $(DATADIR) ++ mkdir -p $(INCLUDEDIR) ++ cp -r *.h *.hpp $(INCLUDEDIR) ++ ++check: coxeter executable ++ $(EXENAME)$(EXEEXT) < test.input > test.output ++ ++ if ! diff test.output.expected test.output > /dev/null; then \ ++ echo >&2 "Error testing coxeter on test.input:"; \ ++ diff test.output.expected test.output; \ ++ exit 1; \ ++ fi ++ rm -f test.output + + clean: + rm -f $(objects) + + %.o:%.cpp +- $(cc) $(cflags) $*.cpp ++ $(CXX) $(cflags) $*.cpp + + # dependencies --- these were generated automatically by make depend on my + # system; they are explicitly copied for portability. Only local dependencies +@@ -43,7 +100,7 @@ + # contents of tmp in lieu of the dependencies listed here. + + %.d:%.cpp +- @$(cc) -MM $*.cpp ++ @$(CXX) -MM $*.cpp + depend: $(dependencies) + + affine.o: affine.cpp affine.h globals.h coxgroup.h coxtypes.h io.h list.h \ diff --git a/easybuild/easyconfigs/c/coxeter/coxeter-20180226_sage_interface.patch b/easybuild/easyconfigs/c/coxeter/coxeter-20180226_sage_interface.patch new file mode 100644 index 00000000000..2b4cd427ca9 --- /dev/null +++ b/easybuild/easyconfigs/c/coxeter/coxeter-20180226_sage_interface.patch @@ -0,0 +1,89 @@ +Adds sage interface. See https://github.com/tscrim/coxeter/pull/14 +Source: https://gitlab.archlinux.org/archlinux/packaging/packages/coxeter/-/blob/git.20180226-4/coxeter-sage.patch +diff -u /dev/null sage.h +--- /dev/null 2024-08-27 08:29:37.672016778 +0200 ++++ sage.h 2024-08-27 12:17:23.716096310 +0200 +@@ -0,0 +1,23 @@ ++/* ++ Coxeter version 3.0 Copyright (C) 2009 Mike Hansen ++ See file main.cpp for full copyright notice ++*/ ++ ++#ifndef SAGE_H /* guard against multiple inclusions */ ++#define SAGE_H ++ ++#include "globals.h" ++#include "coxgroup.h" ++#include "coxtypes.h" ++#include "schubert.h" ++#include "list.h" ++ ++namespace sage { ++ using namespace coxeter; ++ using namespace coxtypes; ++ using namespace list; ++ ++ void interval(List& result, CoxGroup& W, const CoxWord& g, const CoxWord& h); ++} ++ ++#endif +diff -u /dev/null sage.cpp +--- /dev/null 2024-08-27 08:29:37.672016778 +0200 ++++ sage.cpp 2024-08-27 12:17:23.716096310 +0200 +@@ -0,0 +1,56 @@ ++/* ++ Coxeter version 3.0 Copyright (C) 2009 Mike Hansen ++ See file main.cpp for full copyright notice ++*/ ++ ++#include "sage.h" ++ ++namespace sage { ++ ++ void interval(List& list, CoxGroup& W, const CoxWord& g, const CoxWord& h) ++ ++ /* ++ Returns a list of the elements in the Bruhat interval between g and h. ++ Note that this assumes that g and h are in order. ++ */ ++ { ++ if (not W.inOrder(g,h)) { ++ return; ++ } ++ ++ W.extendContext(h); ++ ++ CoxNbr x = W.contextNumber(g); ++ CoxNbr y = W.contextNumber(h); ++ ++ BitMap b(W.contextSize()); ++ W.extractClosure(b,y); ++ ++ BitMap::ReverseIterator b_rend = b.rend(); ++ List res(0); ++ ++ for (BitMap::ReverseIterator i = b.rbegin(); i != b_rend; ++i) ++ if (not W.inOrder(x,*i)) { ++ BitMap bi(W.contextSize()); ++ W.extractClosure(bi,*i); ++ CoxNbr z = *i; // andnot will invalidate iterator ++ b.andnot(bi); ++ b.setBit(z); // otherwise the decrement will not be correct ++ } else ++ res.append(*i); ++ ++ schubert::NFCompare nfc(W.schubert(),W.ordering()); ++ Permutation a(res.size()); ++ sortI(res,nfc,a); ++ ++ list.setSize(0); ++ for (size_t j = 0; j < res.size(); ++j) { ++ CoxWord w(0); ++ W.schubert().append(w, res[a[j]]); ++ list.append(w); ++ } ++ ++ return; ++ } ++ ++} diff --git a/easybuild/easyconfigs/c/cp2k-input-tools/cp2k-input-tools-0.9.1-foss-2023a.eb b/easybuild/easyconfigs/c/cp2k-input-tools/cp2k-input-tools-0.9.1-foss-2023a.eb new file mode 100644 index 00000000000..6e8baed0be5 --- /dev/null +++ b/easybuild/easyconfigs/c/cp2k-input-tools/cp2k-input-tools-0.9.1-foss-2023a.eb @@ -0,0 +1,45 @@ +easyblock = 'PythonBundle' + +name = 'cp2k-input-tools' +version = '0.9.1' + +homepage = 'https://github.com/cp2k/cp2k-input-tools' +description = "Fully validating pure-python CP2K input file parsers including preprocessing capabilities" + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [ + ('poetry', '1.5.1'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('Pint', '0.23'), + ('pydantic', '2.5.3'), +] + +use_pip = True + +exts_list = [ + ('transitions', '0.9.2', { + 'checksums': ['2f8490dbdbd419366cef1516032ab06d07ccb5839ef54905e842a472692d4204'], + }), + (name, version, { + 'sources': ['cp2k_input_tools-%(version)s.tar.gz'], + 'checksums': ['bf7d229bbcfa41b1caaa32e7eb3c1c689d56bd1cbd4de674bd2fde8de4efb27c'], + }), +] + +sanity_check_paths = { + 'files': ['bin/fromcp2k'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "fromcp2k --help", +] + +sanity_pip_check = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/c/cpio/cpio-2.15-GCCcore-12.2.0.eb b/easybuild/easyconfigs/c/cpio/cpio-2.15-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..f97452acc3d --- /dev/null +++ b/easybuild/easyconfigs/c/cpio/cpio-2.15-GCCcore-12.2.0.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' +name = 'cpio' +version = '2.15' + +homepage = "https://savannah.gnu.org/projects/cpio/" +description = """The cpio package contains tools for archiving.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_BZ2] +checksums = ['937610b97c329a1ec9268553fb780037bcfff0dcffe9725ebc4fd9c1aa9075db'] + +builddependencies = [ + ('binutils', '2.39'), + ('makeinfo', '7.0.3'), +] + +postinstallcmds = ['makeinfo --plaintext -o %(installdir)s/doc/cpio.txt doc/cpio.texi'] + +sanity_check_paths = { + 'files': ['bin/cpio'], + 'dirs': [] +} + +sanity_check_commands = ['cpio --help'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/c/cpio/cpio-2.15-GCCcore-12.3.0.eb b/easybuild/easyconfigs/c/cpio/cpio-2.15-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..88be666ec15 --- /dev/null +++ b/easybuild/easyconfigs/c/cpio/cpio-2.15-GCCcore-12.3.0.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' +name = 'cpio' +version = '2.15' + +homepage = "https://savannah.gnu.org/projects/cpio/" +description = """The cpio package contains tools for archiving.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_BZ2] +checksums = ['937610b97c329a1ec9268553fb780037bcfff0dcffe9725ebc4fd9c1aa9075db'] + +builddependencies = [ + ('binutils', '2.40'), + ('makeinfo', '7.0.3'), +] + +postinstallcmds = ['makeinfo --plaintext -o %(installdir)s/doc/cpio.txt doc/cpio.texi'] + +sanity_check_paths = { + 'files': ['bin/cpio'], + 'dirs': [] +} + +sanity_check_commands = ['cpio --help'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/c/cpio/cpio-2.15-GCCcore-13.2.0.eb b/easybuild/easyconfigs/c/cpio/cpio-2.15-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..43cc1783368 --- /dev/null +++ b/easybuild/easyconfigs/c/cpio/cpio-2.15-GCCcore-13.2.0.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' +name = 'cpio' +version = '2.15' + +homepage = "https://savannah.gnu.org/projects/cpio/" +description = """The cpio package contains tools for archiving.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_BZ2] +checksums = ['937610b97c329a1ec9268553fb780037bcfff0dcffe9725ebc4fd9c1aa9075db'] + +builddependencies = [ + ('binutils', '2.40'), + ('makeinfo', '7.1'), +] + +postinstallcmds = ['makeinfo --plaintext -o %(installdir)s/doc/cpio.txt doc/cpio.texi'] + +sanity_check_paths = { + 'files': ['bin/cpio'], + 'dirs': [] +} + +sanity_check_commands = ['cpio --help'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/c/cpio/cpio-2.15-GCCcore-13.3.0.eb b/easybuild/easyconfigs/c/cpio/cpio-2.15-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..3640f333607 --- /dev/null +++ b/easybuild/easyconfigs/c/cpio/cpio-2.15-GCCcore-13.3.0.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' +name = 'cpio' +version = '2.15' + +homepage = "https://savannah.gnu.org/projects/cpio/" +description = """The cpio package contains tools for archiving.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_BZ2] +checksums = ['937610b97c329a1ec9268553fb780037bcfff0dcffe9725ebc4fd9c1aa9075db'] + +builddependencies = [ + ('binutils', '2.42'), + ('makeinfo', '7.1'), +] + +postinstallcmds = ['makeinfo --plaintext -o %(installdir)s/doc/cpio.txt doc/cpio.texi'] + +sanity_check_paths = { + 'files': ['bin/cpio'], + 'dirs': [] +} + +sanity_check_commands = ['cpio --help'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/c/cppy/cppy-1.2.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/c/cppy/cppy-1.2.1-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..3043857d925 --- /dev/null +++ b/easybuild/easyconfigs/c/cppy/cppy-1.2.1-GCCcore-13.3.0.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonPackage' + +name = 'cppy' +version = '1.2.1' + +homepage = "https://github.com/nucleic/cppy" +description = """A small C++ header library which makes it easier to write +Python extension modules. The primary feature is a PyObject smart pointer +which automatically handles reference counting and provides convenience +methods for performing common object operations.""" + + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +builddependencies = [('binutils', '2.42')] + +dependencies = [ + ('Python', '3.12.3'), +] + +sources = ['%(name)s-%(version)s.tar.gz'] +patches = ['cppy-1.2.1-manual_version.patch'] +checksums = [ + {'cppy-1.2.1.tar.gz': '83b43bf17b1085ac15c5debdb42154f138b928234b21447358981f69d0d6fe1b'}, + {'cppy-1.2.1-manual_version.patch': '048aa0a86fd2e99c6896443b07ec83eaa369724297f639ef74c65c404b8f288f'}, +] + +download_dep_fail = True +sanity_pip_check = True +use_pip = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/c/cppyy/cppyy-3.1.2-GCCcore-13.2.0.eb b/easybuild/easyconfigs/c/cppyy/cppyy-3.1.2-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..89c6bc40e3d --- /dev/null +++ b/easybuild/easyconfigs/c/cppyy/cppyy-3.1.2-GCCcore-13.2.0.eb @@ -0,0 +1,46 @@ +easyblock = 'PythonBundle' + +name = 'cppyy' +version = '3.1.2' + +homepage = "https://cppyy.readthedocs.io" +description = """cppyy is an automatic, run-time, Python-C++ bindings generator, + for calling C++ from Python and Python from C++.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.27.6'), +] + +dependencies = [ + ('Python', '3.11.5'), +] + +exts_list = [ + ('cppyy-cling', '6.30.0', { + 'modulename': False, + 'preinstallopts': 'MAKE_NPROCS=%(parallel)s', + 'checksums': ['5d9e0551a4cb618eb3392001b3dc2c6294f02257f02fcd4d868999ba04f92af1'], + }), + ('cppyy-backend', '1.15.2', { + 'checksums': ['8d0ec169f6ea40d26999a61b274ce2ac880082e8d16aace6a0702933d3d835fc'], + }), + ('CPyCppyy', '1.12.16', { + 'modulename': False, + 'checksums': ['09a845652ac1a82777ec499dda862f54493c1560e9df4cadecda09ecde9e4202'], + }), + (name, version, { + 'checksums': ['7937d184af02e1510f44d5655e0bcc3c6a7888ef5b3f06c3dd09ba93d1c1f19b'], + }), + ('cppyythonizations', '1.2.3', { + 'source_tmpl': 'cppyythonizations-%(version)s-py3-none-any.whl', + 'checksums': ['a08bb4fbaf0fc6b980211e7b549b06869f5b9f9cb835b3ab6224cae5905fd8c2'], + }), +] + +use_pip = True +sanity_pip_check = True + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/c/cramino/cramino-0.14.5-GCC-12.3.0.eb b/easybuild/easyconfigs/c/cramino/cramino-0.14.5-GCC-12.3.0.eb new file mode 100644 index 00000000000..49c61ff64fb --- /dev/null +++ b/easybuild/easyconfigs/c/cramino/cramino-0.14.5-GCC-12.3.0.eb @@ -0,0 +1,351 @@ +easyblock = 'Cargo' + +name = 'cramino' +version = '0.14.5' + +homepage = 'https://github.com/wdecoster/cramino' +description = """A tool for quick quality assessment of cram and bam files, intended for long read sequencing.""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +source_urls = ['https://github.com/wdecoster/cramino/archive/'] +sources = 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'9ce1b18ccd8e73a9321186f97e46f9f04b778851177567b1975109d26a08d2a6'}, +] + +crates = [ + ('ahash', '0.8.9'), + ('aho-corasick', '1.1.2'), + ('android-tzdata', '0.1.1'), + ('android_system_properties', '0.1.5'), + ('anstream', '0.6.12'), + ('anstyle', '1.0.6'), + ('anstyle-parse', '0.2.3'), + ('anstyle-query', '1.0.2'), + ('anstyle-wincon', '3.0.2'), + ('arrow', '50.0.0'), + ('arrow-arith', '50.0.0'), + ('arrow-array', '50.0.0'), + ('arrow-buffer', '50.0.0'), + ('arrow-cast', '50.0.0'), + ('arrow-csv', '50.0.0'), + ('arrow-data', '50.0.0'), + ('arrow-ipc', '50.0.0'), + ('arrow-json', '50.0.0'), + ('arrow-ord', '50.0.0'), + ('arrow-row', '50.0.0'), + ('arrow-schema', '50.0.0'), + ('arrow-select', '50.0.0'), + ('arrow-string', '50.0.0'), + ('autocfg', '1.1.0'), + ('base64', '0.21.7'), + ('bio-types', '1.0.1'), + ('bitflags', '1.3.2'), + ('bumpalo', '3.15.1'), + ('byteorder', '1.5.0'), + ('bytes', '1.5.0'), + ('bzip2-sys', '0.1.11+1.0.8'), + ('cc', '1.0.86'), + ('cfg-if', '1.0.0'), + 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+ ('wasm-bindgen-macro', '0.2.91'), + ('wasm-bindgen-macro-support', '0.2.91'), + ('wasm-bindgen-shared', '0.2.91'), + ('windows-core', '0.52.0'), + ('windows-sys', '0.52.0'), + ('windows-targets', '0.52.0'), + ('windows_aarch64_gnullvm', '0.52.0'), + ('windows_aarch64_msvc', '0.52.0'), + ('windows_i686_gnu', '0.52.0'), + ('windows_i686_msvc', '0.52.0'), + ('windows_x86_64_gnu', '0.52.0'), + ('windows_x86_64_gnullvm', '0.52.0'), + ('windows_x86_64_msvc', '0.52.0'), + ('zerocopy', '0.7.32'), + ('zerocopy-derive', '0.7.32'), +] + +builddependencies = [ + ('Rust', '1.75.0'), + ('CMake', '3.26.3'), +] + +dependencies = [ + ('bzip2', '1.0.8'), + ('OpenSSL', '1.1', '', SYSTEM), + ('Perl', '5.36.1'), + ('Perl-bundle-CPAN', '5.36.1'), +] + +sanity_check_paths = { + 'files': ['bin/%(name)s'], + 'dirs': [], +} + +sanity_check_commands = ["%(name)s --help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/crb-blast/crb-blast-0.6.9-GCC-12.3.0.eb b/easybuild/easyconfigs/c/crb-blast/crb-blast-0.6.9-GCC-12.3.0.eb new file mode 100644 index 00000000000..c9e4de852a5 --- /dev/null +++ b/easybuild/easyconfigs/c/crb-blast/crb-blast-0.6.9-GCC-12.3.0.eb @@ -0,0 +1,58 @@ +easyblock = 'Bundle' + +name = 'crb-blast' +version = '0.6.9' + +homepage = 'https://github.com/cboursnell/crb-blast' +description = """Conditional Reciprocal Best BLAST - high confidence ortholog assignment.""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +dependencies = [ + ('Ruby', '3.3.0'), +] + +exts_default_options = { + 'source_urls': ['https://rubygems.org/downloads/'], + 'source_tmpl': '%(name)s-%(version)s.gem', +} + +exts_defaultclass = 'RubyGem' + +exts_list = [ + ('facade', '1.2.1', { + 'checksums': ['0764de5519088227675a2a67da23322500c3c507b89486d91296e031d87d036e'], + }), + ('pathname2', '1.8.4', { + 'checksums': ['1711264f3f7c1b380f96e1f0383b135d9703488f7b1acf66346a176efc257b7a'], + }), + ('fixwhich', '1.0.2', { + 'checksums': ['c6a8f796a7eb60ffbc29f0d2af85461761a36c2864d25e445ff18bfbd1657078'], + }), + ('bindeps', '1.2.1', { + 'checksums': ['3c11d75aa722bed67246852bb430a182361a128910d384b664b91f3e65bc34b5'], + }), + ('bio', '1.6.0.pre.20181210', { + 'checksums': ['c4114aeb99b012f90660b92ead4ca88c1578fd58252ed3ec46eb45dc4a2c6cc9'], + }), + ('threach', '0.2.0', { + 'checksums': ['432cbf3569bf9b09e26f93d0959fd6fb911c71e790e8a4cc4d1110e139a2ffca'], + }), + ('trollop', '2.9.10', { + 'checksums': ['ceca2d91f349163d6ee3e792d356d4ded7472e6da31ac6dcc5956d1b03607bf7'], + }), + (name, version, { + 'checksums': ['69c346e7d83efe9b9a383a39b57e7cce186a82b7074f275b14906f8f05678e3e'], + }), +] + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': ['gems/%(namelower)s-%(version)s'], +} + +sanity_check_commands = ["%(namelower)s --help"] + +modextrapaths = {'GEM_PATH': ['']} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/crypt4gh/crypt4gh-1.7-GCC-12.3.0.eb b/easybuild/easyconfigs/c/crypt4gh/crypt4gh-1.7-GCC-12.3.0.eb new file mode 100644 index 00000000000..c52d7b3d83d --- /dev/null +++ b/easybuild/easyconfigs/c/crypt4gh/crypt4gh-1.7-GCC-12.3.0.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonBundle' + +name = 'crypt4gh' +version = '1.7' + +homepage = 'https://github.com/EGA-archive/crypt4gh' +description = """crypt4gh is a Python tool to encrypt, decrypt or re-encrypt files, +according to the GA4GH encryption file format.""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('PyYAML', '6.0'), + ('cryptography', '41.0.1'), + ('bcrypt', '4.0.1'), +] + +use_pip = True + +exts_list = [ + (name, version, { + 'checksums': ['1569bc4ff9b689c8852e3892ac3f6fea4b31948ca0b1e5bc28d0d2f80def2a28'], + }), +] + +sanity_pip_check = True + +sanity_check_commands = ['crypt4gh -h'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/c/cryptography/cryptography-42.0.8-GCCcore-13.3.0.eb b/easybuild/easyconfigs/c/cryptography/cryptography-42.0.8-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..be6bff8c478 --- /dev/null +++ b/easybuild/easyconfigs/c/cryptography/cryptography-42.0.8-GCCcore-13.3.0.eb @@ -0,0 +1,131 @@ +easyblock = 'CargoPythonPackage' + +name = 'cryptography' +version = '42.0.8' + +homepage = 'https://github.com/pyca/cryptography' +description = "cryptography is a package designed to expose cryptographic primitives and recipes to Python developers." + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +builddependencies = [ + ('binutils', '2.42'), + ('pkgconf', '2.2.0'), + ('Rust', '1.78.0'), # required for cryptography + ('hatchling', '1.24.2'), + ('setuptools-rust', '1.9.0'), +] + +dependencies = [ + ('Python', '3.12.3'), + ('cffi', '1.16.0'), +] +crates = [ + ('asn1', '0.15.5'), + ('asn1_derive', '0.15.5'), + ('autocfg', '1.1.0'), + ('base64', '0.21.7'), + ('bitflags', '1.3.2'), + ('bitflags', '2.4.2'), + ('cc', '1.0.83'), + ('cfg-if', '1.0.0'), + ('foreign-types', '0.3.2'), + ('foreign-types-shared', '0.1.1'), + ('heck', '0.4.1'), + ('indoc', '2.0.4'), + ('libc', '0.2.152'), + ('lock_api', '0.4.11'), + ('memoffset', '0.9.0'), + ('once_cell', '1.19.0'), + ('openssl', '0.10.64'), + ('openssl-macros', '0.1.1'), + ('openssl-sys', '0.9.102'), + ('parking_lot', '0.12.1'), + ('parking_lot_core', '0.9.9'), + ('pem', '3.0.3'), + ('pkg-config', '0.3.29'), + ('portable-atomic', '1.6.0'), + ('proc-macro2', '1.0.78'), + ('pyo3', '0.20.3'), + ('pyo3-build-config', '0.20.3'), + ('pyo3-ffi', '0.20.3'), + ('pyo3-macros', '0.20.3'), + ('pyo3-macros-backend', '0.20.3'), + ('quote', '1.0.35'), + ('redox_syscall', '0.4.1'), + ('scopeguard', '1.2.0'), + ('self_cell', '1.0.3'), + ('smallvec', '1.13.1'), + ('syn', '2.0.48'), + ('target-lexicon', '0.12.13'), + ('unicode-ident', '1.0.12'), + ('unindent', '0.2.3'), + ('vcpkg', '0.2.15'), + ('windows-targets', '0.48.5'), + ('windows_aarch64_gnullvm', '0.48.5'), + ('windows_aarch64_msvc', '0.48.5'), + ('windows_i686_gnu', '0.48.5'), + ('windows_i686_msvc', '0.48.5'), + ('windows_x86_64_gnu', '0.48.5'), + ('windows_x86_64_gnullvm', '0.48.5'), + ('windows_x86_64_msvc', '0.48.5'), +] +sources = [SOURCE_TAR_GZ] +checksums = [ + {'cryptography-42.0.8.tar.gz': '8d09d05439ce7baa8e9e95b07ec5b6c886f548deb7e0f69ef25f64b3bce842f2'}, + {'asn1-0.15.5.tar.gz': 'ae3ecbce89a22627b5e8e6e11d69715617138290289e385cde773b1fe50befdb'}, + {'asn1_derive-0.15.5.tar.gz': '861af988fac460ac69a09f41e6217a8fb9178797b76fcc9478444be6a59be19c'}, + {'autocfg-1.1.0.tar.gz': 'd468802bab17cbc0cc575e9b053f41e72aa36bfa6b7f55e3529ffa43161b97fa'}, + {'base64-0.21.7.tar.gz': '9d297deb1925b89f2ccc13d7635fa0714f12c87adce1c75356b39ca9b7178567'}, + {'bitflags-1.3.2.tar.gz': 'bef38d45163c2f1dde094a7dfd33ccf595c92905c8f8f4fdc18d06fb1037718a'}, + {'bitflags-2.4.2.tar.gz': 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'3fdb12b2476b595f9358c5161aa467c2438859caa136dec86c26fdd2efe17b92'}, + {'openssl-0.10.64.tar.gz': '95a0481286a310808298130d22dd1fef0fa571e05a8f44ec801801e84b216b1f'}, + {'openssl-macros-0.1.1.tar.gz': 'a948666b637a0f465e8564c73e89d4dde00d72d4d473cc972f390fc3dcee7d9c'}, + {'openssl-sys-0.9.102.tar.gz': 'c597637d56fbc83893a35eb0dd04b2b8e7a50c91e64e9493e398b5df4fb45fa2'}, + {'parking_lot-0.12.1.tar.gz': '3742b2c103b9f06bc9fff0a37ff4912935851bee6d36f3c02bcc755bcfec228f'}, + {'parking_lot_core-0.9.9.tar.gz': '4c42a9226546d68acdd9c0a280d17ce19bfe27a46bf68784e4066115788d008e'}, + {'pem-3.0.3.tar.gz': '1b8fcc794035347fb64beda2d3b462595dd2753e3f268d89c5aae77e8cf2c310'}, + {'pkg-config-0.3.29.tar.gz': '2900ede94e305130c13ddd391e0ab7cbaeb783945ae07a279c268cb05109c6cb'}, + {'portable-atomic-1.6.0.tar.gz': '7170ef9988bc169ba16dd36a7fa041e5c4cbeb6a35b76d4c03daded371eae7c0'}, + {'proc-macro2-1.0.78.tar.gz': 'e2422ad645d89c99f8f3e6b88a9fdeca7fabeac836b1002371c4367c8f984aae'}, + {'pyo3-0.20.3.tar.gz': '53bdbb96d49157e65d45cc287af5f32ffadd5f4761438b527b055fb0d4bb8233'}, + {'pyo3-build-config-0.20.3.tar.gz': 'deaa5745de3f5231ce10517a1f5dd97d53e5a2fd77aa6b5842292085831d48d7'}, + {'pyo3-ffi-0.20.3.tar.gz': '62b42531d03e08d4ef1f6e85a2ed422eb678b8cd62b762e53891c05faf0d4afa'}, + {'pyo3-macros-0.20.3.tar.gz': '7305c720fa01b8055ec95e484a6eca7a83c841267f0dd5280f0c8b8551d2c158'}, + {'pyo3-macros-backend-0.20.3.tar.gz': '7c7e9b68bb9c3149c5b0cade5d07f953d6d125eb4337723c4ccdb665f1f96185'}, + {'quote-1.0.35.tar.gz': '291ec9ab5efd934aaf503a6466c5d5251535d108ee747472c3977cc5acc868ef'}, + {'redox_syscall-0.4.1.tar.gz': '4722d768eff46b75989dd134e5c353f0d6296e5aaa3132e776cbdb56be7731aa'}, + {'scopeguard-1.2.0.tar.gz': '94143f37725109f92c262ed2cf5e59bce7498c01bcc1502d7b9afe439a4e9f49'}, + {'self_cell-1.0.3.tar.gz': '58bf37232d3bb9a2c4e641ca2a11d83b5062066f88df7fed36c28772046d65ba'}, + {'smallvec-1.13.1.tar.gz': 'e6ecd384b10a64542d77071bd64bd7b231f4ed5940fba55e98c3de13824cf3d7'}, + {'syn-2.0.48.tar.gz': '0f3531638e407dfc0814761abb7c00a5b54992b849452a0646b7f65c9f770f3f'}, + {'target-lexicon-0.12.13.tar.gz': '69758bda2e78f098e4ccb393021a0963bb3442eac05f135c30f61b7370bbafae'}, + {'unicode-ident-1.0.12.tar.gz': '3354b9ac3fae1ff6755cb6db53683adb661634f67557942dea4facebec0fee4b'}, + {'unindent-0.2.3.tar.gz': 'c7de7d73e1754487cb58364ee906a499937a0dfabd86bcb980fa99ec8c8fa2ce'}, + {'vcpkg-0.2.15.tar.gz': 'accd4ea62f7bb7a82fe23066fb0957d48ef677f6eeb8215f372f52e48bb32426'}, + {'windows-targets-0.48.5.tar.gz': '9a2fa6e2155d7247be68c096456083145c183cbbbc2764150dda45a87197940c'}, + {'windows_aarch64_gnullvm-0.48.5.tar.gz': '2b38e32f0abccf9987a4e3079dfb67dcd799fb61361e53e2882c3cbaf0d905d8'}, + {'windows_aarch64_msvc-0.48.5.tar.gz': 'dc35310971f3b2dbbf3f0690a219f40e2d9afcf64f9ab7cc1be722937c26b4bc'}, + {'windows_i686_gnu-0.48.5.tar.gz': 'a75915e7def60c94dcef72200b9a8e58e5091744960da64ec734a6c6e9b3743e'}, + {'windows_i686_msvc-0.48.5.tar.gz': '8f55c233f70c4b27f66c523580f78f1004e8b5a8b659e05a4eb49d4166cca406'}, + {'windows_x86_64_gnu-0.48.5.tar.gz': '53d40abd2583d23e4718fddf1ebec84dbff8381c07cae67ff7768bbf19c6718e'}, + {'windows_x86_64_gnullvm-0.48.5.tar.gz': '0b7b52767868a23d5bab768e390dc5f5c55825b6d30b86c844ff2dc7414044cc'}, + {'windows_x86_64_msvc-0.48.5.tar.gz': 'ed94fce61571a4006852b7389a063ab983c02eb1bb37b47f8272ce92d06d9538'}, +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/c/ctffind5/ctffind5-5.0.2-foss-2023a.eb b/easybuild/easyconfigs/c/ctffind5/ctffind5-5.0.2-foss-2023a.eb new file mode 100644 index 00000000000..29cb349d816 --- /dev/null +++ b/easybuild/easyconfigs/c/ctffind5/ctffind5-5.0.2-foss-2023a.eb @@ -0,0 +1,83 @@ +# Thomas Hoffmann, EMBL Heidelberg, structures-it@embl.de, 2024/05 +easyblock = 'ConfigureMake' + +name = 'ctffind5' +version = '5.0.2' + +local_commit = 'b21db55a91366fe4f75301c56091d213bbd326eb' +local_branch = 'ctffind5_merge' + +homepage = 'https://grigoriefflab.umassmed.edu/ctf_estimation_ctffind_ctftilt' +description = """Program for finding CTFs of electron micrographs.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +# Use git_config in order to allow setting CISTEM_CURRENT_BRANCH and CISTEM_VERSION_TEXT by configure +sources = [{ + 'download_filename': '%s.tar.gz' % local_commit, + 'filename': 'cisTEM-ctffind5-%s.tar.gz' % local_commit[:7], + 'git_config': { + 'url': 'https://github.com/timothygrant80', + 'repo_name': 'cisTEM', + 'commit': local_commit, + 'keep_git_dir': True, + } +}] + +# no checksume, due to git_config +checksums = [None] + +# Alternative source: +# https://grigoriefflab.umassmed.edu/sites/default/files/cisTEM-ctffind5-b21db55.tar.gz + +# switch branch in order to inject proper branch name into binary: +preconfigopts = 'git switch --create %s &&' % local_branch + +# disable all targets except for ctffind and applyctf (do not build any other cisTEM tool): +local_remove_targets = """sed -i "s/^bin_PROGRAMS/""" +local_remove_targets += """bin_PROGRAMS=ctffind applyctf\\nnoinst_PROGRAMS/g" """ +local_remove_targets += """ src/Makefile.am &&""" +preconfigopts += local_remove_targets + +# run autotools +preconfigopts += './regenerate_project.b &&' + + +local_configureopts = [ + # '--enable-latest-instruction-set', # don't use; managed by CFLAGS + '--enable-shared', + '--with-gnu-ld', + '--with-wx-config=$EBROOTWXWIDGETS/bin/wx-config', + '--disable-silent-rules', + '--enable-openmp', + '--disable-debugmode' + '--disable-staticmode', + '--enable-experimental', + '--without-cuda', +] + +configopts = ' '.join(local_configureopts) + +builddependencies = [ + ('Autotools', '20220317'), + ('git', '2.41.0', '-nodocs') +] + +dependencies = [ + ('wxWidgets', '3.2.2.1') +] + +sanity_check_paths = { + 'files': ['bin/ctffind', 'bin/applyctf'], + 'dirs': ['bin'], +} + +sanity_check_commands = [ + # ctffind command expects filename of input image via stdin, + # so we pipe in a newline via 'echo' to make it exit + 'echo | ctffind | grep Version | grep %(version)s', + 'echo | ctffind | grep "Library Version" | grep %s' % local_commit[:7], + 'echo | ctffind | grep "Branch" | grep %s' % local_branch, +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/cuDNN/cuDNN-9.5.0.50-CUDA-12.6.0.eb b/easybuild/easyconfigs/c/cuDNN/cuDNN-9.5.0.50-CUDA-12.6.0.eb new file mode 100644 index 00000000000..76340a4e654 --- /dev/null +++ b/easybuild/easyconfigs/c/cuDNN/cuDNN-9.5.0.50-CUDA-12.6.0.eb @@ -0,0 +1,37 @@ +name = 'cuDNN' +version = '9.5.0.50' +versionsuffix = '-CUDA-%(cudaver)s' +homepage = 'https://developer.nvidia.com/cudnn' +description = """The NVIDIA CUDA Deep Neural Network library (cuDNN) is +a GPU-accelerated library of primitives for deep neural networks.""" + +toolchain = SYSTEM + +# note: cuDNN is tied to specific to CUDA versions, +# see also https://docs.nvidia.com/deeplearning/cudnn/support-matrix/index.html#cudnn-cuda-hardware-versions +local_short_ver = '.'.join(version.split('.')[:3]) +local_cuda_major = '12' + +source_urls = [ + 'https://developer.download.nvidia.com/compute/cudnn/redist/cudnn/linux-%(cudnnarch)s/' +] +sources = ['%%(namelower)s-linux-%%(cudnnarch)s-%%(version)s_cuda%s-archive.tar.xz' % local_cuda_major] +checksums = [{ + '%%(namelower)s-linux-sbsa-%%(version)s_cuda%s-archive.tar.xz' % local_cuda_major: + '494b640a69feb40ce806a726aa63a1de6b2ec459acbe6a116ef6fe3e6b27877d', + '%%(namelower)s-linux-x86_64-%%(version)s_cuda%s-archive.tar.xz' % local_cuda_major: + '86e4e4f4c09b31d3850b402d94ea52741a2f94c2f717ddc8899a14aca96e032d', +}] + +dependencies = [('CUDA', '12.6.0')] + +sanity_check_paths = { + 'files': [ + 'include/cudnn.h', 'lib64/libcudnn_adv_static.a', 'lib64/libcudnn_cnn_static.a', + 'lib64/libcudnn_engines_precompiled_static.a', 'lib64/libcudnn_engines_runtime_compiled_static.a', + 'lib64/libcudnn_graph_static.a', 'lib64/libcudnn_heuristic_static.a', 'lib64/libcudnn_ops_static.a', + ], + 'dirs': ['include', 'lib64'], +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/c/cuQuantum/cuQuantum-24.08.0.5-CUDA-12.1.1.eb b/easybuild/easyconfigs/c/cuQuantum/cuQuantum-24.08.0.5-CUDA-12.1.1.eb new file mode 100644 index 00000000000..f2437f12613 --- /dev/null +++ b/easybuild/easyconfigs/c/cuQuantum/cuQuantum-24.08.0.5-CUDA-12.1.1.eb @@ -0,0 +1,27 @@ +easyblock = 'Tarball' + +name = 'cuQuantum' +local_shortver = '24.08.0' +version = local_shortver + '.5' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://developer.nvidia.com/cuquantum-sdk' +description = """NVIDIA cuQuantum is an SDK of libraries and tools for quantum computing workflows.""" + +toolchain = SYSTEM + +source_urls = ['https://developer.download.nvidia.com/compute/cuquantum/redist/cuquantum/linux-x86_64/'] +sources = ['cuquantum-linux-x86_64-%(version)s_cuda%(cudamajver)s-archive.tar.xz'] +checksums = ['485968734706eeffcd3adc3b2d2086e59be7ff3ddd907e96f1eb97335beb344a'] + +local_cudamajver = '12' +dependencies = [('CUDA', local_cudamajver + '.1.1')] + +sanity_check_paths = { + 'files': ['include/custatevec.h', 'include/cutensornet/types.h', + 'lib/libcutensornet.%s' % SHLIB_EXT, + 'lib/libcutensornet_static.a'], + 'dirs': ['distributed_interfaces'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/c/cuTENSOR/cuTENSOR-2.0.2.5-CUDA-12.6.0.eb b/easybuild/easyconfigs/c/cuTENSOR/cuTENSOR-2.0.2.5-CUDA-12.6.0.eb new file mode 100644 index 00000000000..fe7b69ac9b0 --- /dev/null +++ b/easybuild/easyconfigs/c/cuTENSOR/cuTENSOR-2.0.2.5-CUDA-12.6.0.eb @@ -0,0 +1,40 @@ +easyblock = 'Tarball' + +name = 'cuTENSOR' +version = '2.0.2.5' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://developer.nvidia.com/cutensor' +description = """The cuTENSOR Library is a GPU-accelerated tensor linear algebra library providing tensor contraction, + reduction and elementwise operations.""" + +toolchain = SYSTEM + +source_urls = [ + 'https://developer.download.nvidia.com/compute/cutensor/redist/libcutensor/linux-%(arch)s/' +] +sources = ['libcutensor-linux-%(arch)s-%(version)s-archive.tar.xz'] + +checksums = [{ + 'libcutensor-linux-sbsa-%(version)s-archive.tar.xz': + '5163dd40f11f328e469a6d9b0056c8346f5d59ed538c18d6b954e4ae657c69cc', + 'libcutensor-linux-x86_64-%(version)s-archive.tar.xz': + '0e957ae7b352f599de34b6fa1ba999b0617887f885d7436ac5737d71a6b83baa', +}] + +local_cudamajver = '12' +dependencies = [('CUDA', '12.6.0')] + +sanity_check_paths = { + 'files': ['include/cutensor.h', 'include/cutensor/types.h', + 'lib/%s/libcutensor.%s' % (local_cudamajver, SHLIB_EXT), + 'lib/%s/libcutensor_static.a' % local_cudamajver], + 'dirs': [], +} + +modextrapaths = { + 'LD_LIBRARY_PATH': ['lib/%s' % local_cudamajver], + 'LIBRARY_PATH': ['lib/%s' % local_cudamajver], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/c/currentNe/currentNe-1.0.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/c/currentNe/currentNe-1.0.0-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..d90b8442fa5 --- /dev/null +++ b/easybuild/easyconfigs/c/currentNe/currentNe-1.0.0-GCCcore-12.3.0.eb @@ -0,0 +1,38 @@ +easyblock = 'MakeCp' + +name = 'currentNe' +version = '1.0.0' +local_commit = '37daed5' + +homepage = 'https://github.com/esrud/currentNe' +description = """Estimation of current effective population using artificial neural networks.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +github_account = 'esrud' +source_urls = [GITHUB_SOURCE] +sources = [{ + "download_filename": "%s.tar.gz" % local_commit, + "filename": "%(name)s-%(version)s.tar.gz", +}] +checksums = ['77aab8e7403b726b30f34474d3177a3b118afb4b0dc57636dc0b2b93274c6bca'] + +builddependencies = [ + ('binutils', '2.40'), + ('make', '4.4.1'), +] + +files_to_copy = [ + 'lib', + (['currentNe.cpp'], 'lib'), + (['currentNe'], 'bin'), +] + +sanity_check_paths = { + 'files': ['lib/currentNe.cpp'], + 'dirs': ['bin', 'lib'] +} + +sanity_check_commands = ['currentNe -h 2>&1 | grep "USAGE"'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-4.9-GCCcore-12.3.0.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-4.9-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..1f54c552c2e --- /dev/null +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-4.9-GCCcore-12.3.0.eb @@ -0,0 +1,60 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics (SIB) +# Biozentrum - University of Basel +# Modified by: Adam Huffman, Jonas Demeulemeester +# The Francis Crick Institute +# Modified by: Albert Bogdanowicz +# Institute of Biochemistry and Biophysics PAS +# Modified by: Jasper Grimm +# University of York + +easyblock = 'PythonBundle' + +name = 'cutadapt' +version = '4.9' + +homepage = 'https://opensource.scilifelab.se/projects/cutadapt/' +description = """Cutadapt finds and removes adapter sequences, primers, poly-A tails and + other types of unwanted sequence from your high-throughput sequencing reads.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +builddependencies = [ + ('binutils', '2.40'), + ('Cython', '3.0.8'), # required for dnaio +] + +dependencies = [ + ('pigz', '2.8'), + ('Python', '3.11.3'), + ('python-isal', '1.1.0'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + # note: newer xopen versions require newer python-isal + ('xopen', '1.7.0', { + 'checksums': ['901f9c8298e95ed74767a4bd76d9f4cf71d8de27b8cf296ac3e7bc1c11520d9f'], + }), + ('dnaio', '1.2.1', { + 'checksums': ['4786dc63614b9f3011463d9ea9d981723dd38d1091a415a557f71d8c74400f38'], + }), + (name, version, { + 'checksums': ['da3b45775b07334d2e2580a7b154d19ea7e872f0da813bb1ac2a4da712bfc223'], + }), +] + +sanity_check_paths = { + 'files': ['bin/cutadapt'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "cutadapt --help", + "cutadapt --version", +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/cysignals/cysignals-1.11.4-GCCcore-13.2.0.eb b/easybuild/easyconfigs/c/cysignals/cysignals-1.11.4-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..08a87d938bb --- /dev/null +++ b/easybuild/easyconfigs/c/cysignals/cysignals-1.11.4-GCCcore-13.2.0.eb @@ -0,0 +1,41 @@ +# +# Author: Fenglai Liu +# fenglai@accre.vanderbilt.edu +# Vanderbilt University +# +# Update: Petr Král (INUITS) +# +easyblock = 'PythonPackage' + +name = 'cysignals' +version = '1.11.4' + +homepage = 'https://pypi.org/project/cysignals/' +description = """The cysignals package provides mechanisms to handle +interrupts (and other signals and errors) in Cython code.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['0f1e321e55a07f901c86a36a1e4497f6ff9dfe700681d0130a38c36e4eb238c3'] + +builddependencies = [ + ('Autotools', '20220317'), + ('binutils', '2.40'), + ('Cython', '3.0.10'), +] + +dependencies = [ + ('Python', '3.11.5'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/cysignals-CSI'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/c/cyvcf2/cyvcf2-0.31.1-gfbf-2023a.eb b/easybuild/easyconfigs/c/cyvcf2/cyvcf2-0.31.1-gfbf-2023a.eb new file mode 100644 index 00000000000..6604fb2a1af --- /dev/null +++ b/easybuild/easyconfigs/c/cyvcf2/cyvcf2-0.31.1-gfbf-2023a.eb @@ -0,0 +1,45 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 +easyblock = 'PythonBundle' + +name = 'cyvcf2' +version = '0.31.1' + +homepage = 'https://github.com/brentp/cyvcf2' +description = "cyvcf2 is a cython wrapper around htslib built for fast parsing of Variant Call Format (VCF) files." + +toolchain = {'name': 'gfbf', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('HTSlib', '1.18'), +] + +fix_python_shebang_for = ['bin/*'] + +use_pip = True + +exts_list = [ + ('humanfriendly', '10.0', { + 'checksums': ['6b0b831ce8f15f7300721aa49829fc4e83921a9a301cc7f606be6686a2288ddc'], + }), + ('coloredlogs', '15.0.1', { + 'checksums': ['7c991aa71a4577af2f82600d8f8f3a89f936baeaf9b50a9c197da014e5bf16b0'], + }), + (name, version, { + 'preinstallopts': 'CYVCF2_HTSLIB_MODE=EXTERNAL', + 'checksums': ['00bd0e09a3719d29fbc02bc8a40a690ac2c475e91744648750907d1816558fc5'], + }), +] + +sanity_check_paths = { + 'files': ['bin/cyvcf2'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["cyvcf2 --help"] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-13.3.0.eb b/easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..64022827805 --- /dev/null +++ b/easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-13.3.0.eb @@ -0,0 +1,33 @@ +name = 'DB' +version = '18.1.40' + +homepage = 'https://www.oracle.com/technetwork/products/berkeleydb' + +description = """Berkeley DB enables the development of custom data management + solutions, without the overhead traditionally associated with such custom + projects.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +# use http to allow auto-downloading... +source_urls = ['http://download.oracle.com/berkeley-db/'] +sources = [SOURCELOWER_TAR_GZ] +patches = ['%(name)s-%(version)s_fix_doc_install.patch'] +checksums = [ + '0cecb2ef0c67b166de93732769abdeba0555086d51de1090df325e18ee8da9c8', # db-18.1.40.tar.gz + '441f48568156f72f02a8662998d293cc7edad687604b4f8af722f21c6db2a52d', # DB-18.1.40_fix_doc_install.patch +] + +builddependencies = [('binutils', '2.42')] + +dependencies = [('OpenSSL', '3', '', SYSTEM)] + +sanity_check_paths = { + 'files': ['bin/db_%s' % x for x in ['archive', 'checkpoint', 'convert', 'deadlock', 'dump', 'hotbackup', + 'load', 'log_verify', 'printlog', 'recover', 'replicate', 'stat', + 'tuner', 'upgrade', 'verify']] + + ['include/db.h', 'lib/libdb.a', 'lib/libdb.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/d/DBD-mysql/DBD-mysql-4.050-GCC-12.3.0.eb b/easybuild/easyconfigs/d/DBD-mysql/DBD-mysql-4.050-GCC-12.3.0.eb new file mode 100644 index 00000000000..eec33081a4c --- /dev/null +++ b/easybuild/easyconfigs/d/DBD-mysql/DBD-mysql-4.050-GCC-12.3.0.eb @@ -0,0 +1,30 @@ +easyblock = 'PerlModule' + +name = 'DBD-mysql' +version = '4.050' + +homepage = 'https://metacpan.org/pod/distribution/DBD-mysql/lib/DBD/mysql.pm' +description = "Perl binding for MySQL" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +source_urls = ['https://cpan.metacpan.org/authors/id/D/DV/DVEEDEN'] +sources = [SOURCE_TAR_GZ] +checksums = ['4f48541ff15a0a7405f76adc10f81627c33996fbf56c95c26c094444c0928d78'] + +dependencies = [ + ('Perl', '5.36.1'), + ('Perl-bundle-CPAN', '5.36.1'), + ('MariaDB', '11.6.0'), + ('zlib', '1.2.13'), + ('OpenSSL', '1.1', '', SYSTEM), +] + +options = {'modulename': 'DBD::mysql'} + +sanity_check_paths = { + 'files': ['lib/perl5/site_perl/%%(perlver)s/%s-linux-thread-multi/DBD/mysql.pm' % ARCH], + 'dirs': ['lib/perl5/site_perl/%%(perlver)s/%s-linux-thread-multi/DBD/mysql' % ARCH], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/d/DBD-mysql/DBD-mysql-4.051-GCC-13.3.0.eb b/easybuild/easyconfigs/d/DBD-mysql/DBD-mysql-4.051-GCC-13.3.0.eb new file mode 100644 index 00000000000..f8f26485760 --- /dev/null +++ b/easybuild/easyconfigs/d/DBD-mysql/DBD-mysql-4.051-GCC-13.3.0.eb @@ -0,0 +1,30 @@ +easyblock = 'PerlModule' + +name = 'DBD-mysql' +version = '4.051' + +homepage = 'https://metacpan.org/pod/distribution/DBD-mysql/lib/DBD/mysql.pm' +description = "Perl binding for MySQL" + +toolchain = {'name': 'GCC', 'version': '13.3.0'} + +source_urls = ['https://cpan.metacpan.org/authors/id/D/DV/DVEEDEN'] +sources = [SOURCE_TAR_GZ] +checksums = ['16969bfae7a080384167be3fb1803450fde87f7b0e2682276b3f6469fa147864'] + +dependencies = [ + ('Perl', '5.38.2'), + ('Perl-bundle-CPAN', '5.38.2'), + ('MariaDB', '11.7.0'), + ('zlib', '1.3.1'), + ('OpenSSL', '3', '', SYSTEM), +] + +options = {'modulename': 'DBD::mysql'} + +sanity_check_paths = { + 'files': ['lib/perl5/site_perl/%%(perlver)s/%s-linux-thread-multi/DBD/mysql.pm' % ARCH], + 'dirs': ['lib/perl5/site_perl/%%(perlver)s/%s-linux-thread-multi/DBD/mysql' % ARCH], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/d/DB_File/DB_File-1.859-GCCcore-13.3.0.eb b/easybuild/easyconfigs/d/DB_File/DB_File-1.859-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..e7120c9c13e --- /dev/null +++ b/easybuild/easyconfigs/d/DB_File/DB_File-1.859-GCCcore-13.3.0.eb @@ -0,0 +1,31 @@ +easyblock = 'PerlModule' + +name = 'DB_File' +version = '1.859' + +homepage = 'https://perldoc.perl.org/DB_File.html' +description = """Perl5 access to Berkeley DB version 1.x.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://www.cpan.org/modules/by-module/DB_File/PMQS'] +sources = [SOURCE_TAR_GZ] +checksums = ['5674e0d2cd0b060c4d1253670ea022c64d842a55257f9eb8edb19c0f53e2565c'] + +builddependencies = [ + ('binutils', '2.42'), +] + +dependencies = [ + ('Perl', '5.38.2'), + ('DB', '18.1.40'), +] + +preconfigopts = 'env DB_FILE_INCLUDE="$EBROOTDB/include" DB_FILE_LIB="$EBROOTDB/lib" ' + +sanity_check_paths = { + 'files': ['lib/perl5/site_perl/%(perlver)s/%(arch)s-linux-thread-multi/DB_File.pm'], + 'dirs': [], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/d/DBus/DBus-1.15.8-GCCcore-13.3.0.eb b/easybuild/easyconfigs/d/DBus/DBus-1.15.8-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..ca182becfcd --- /dev/null +++ b/easybuild/easyconfigs/d/DBus/DBus-1.15.8-GCCcore-13.3.0.eb @@ -0,0 +1,45 @@ +easyblock = 'CMakeMake' + +name = 'DBus' +version = '1.15.8' + +homepage = 'https://dbus.freedesktop.org/' + +description = """ + D-Bus is a message bus system, a simple way for applications to talk + to one another. In addition to interprocess communication, D-Bus helps + coordinate process lifecycle; it makes it simple and reliable to code + a "single instance" application or daemon, and to launch applications + and daemons on demand when their services are needed. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://dbus.freedesktop.org/releases/dbus'] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['84fc597e6ec82f05dc18a7d12c17046f95bad7be99fc03c15bc254c4701ed204'] + +builddependencies = [ + ('binutils', '2.42'), + ('CMake', '3.29.3'), + ('pkgconf', '2.2.0'), +] + +dependencies = [ + ('expat', '2.6.2'), +] + +configopts = '-DENABLE_SYSTEMD=OFF ' +# disable documentation +configopts += '-DDBUS_ENABLE_XML_DOCS=OFF -DDBUS_ENABLE_QTHELP_DOCS=OFF -DDBUS_ENABLE_DOXYGEN_DOCS=OFF ' + +sanity_check_paths = { + 'files': ['bin/dbus-%s' % x for x in + ['cleanup-sockets', 'daemon', 'launch', 'monitor', + 'run-session', 'send', 'uuidgen']] + + ['lib/libdbus-1.%s' % SHLIB_EXT], + 'dirs': ['include', 'share'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/d/DETONATE/DETONATE-1.11-GCC-12.3.0.eb b/easybuild/easyconfigs/d/DETONATE/DETONATE-1.11-GCC-12.3.0.eb index c1457cc041c..24a8b13835c 100644 --- a/easybuild/easyconfigs/d/DETONATE/DETONATE-1.11-GCC-12.3.0.eb +++ b/easybuild/easyconfigs/d/DETONATE/DETONATE-1.11-GCC-12.3.0.eb @@ -33,6 +33,7 @@ builddependencies = [ ] dependencies = [ + ('Perl', '5.36.1'), ('Boost', '1.82.0'), ('sparsehash', '2.0.4'), ('BamTools', '2.5.2'), @@ -45,16 +46,20 @@ buildopts = 'CXX="$CXX" CXXFLAGS="$CXXFLAGS -fopenmp" && cd ../rsem-eval && make runtest = 'test' -files_to_copy = [(['ref-eval', 'ref-eval-estimate-true-assembly', '../rsem-eval/rsem-*'], 'bin')] +files_to_copy = [ + (['ref-eval', 'ref-eval-estimate-true-assembly', '../rsem-eval/rsem-*', '../rsem-eval/*.pm'], 'bin'), +] sanity_check_paths = { 'files': ['bin/%s' % x for x in ['ref-eval', 'ref-eval-estimate-true-assembly', 'rsem-build-read-index', 'rsem-eval-calculate-score', 'rsem-eval-estimate-transcript-length-distribution', 'rsem-eval-run-em', 'rsem-extract-reference-transcripts', - 'rsem-parse-alignments', 'rsem-plot-model', 'rsem-preref', 'rsem-sam-validator', - 'rsem-scan-for-paired-end-reads', 'rsem-simulate-reads', + 'rsem-parse-alignments', 'rsem_perl_utils.pm', 'rsem-plot-model', 'rsem-preref', + 'rsem-sam-validator', 'rsem-scan-for-paired-end-reads', 'rsem-simulate-reads', 'rsem-synthesis-reference-transcripts']], 'dirs': [], } +sanity_check_commands = [r"rsem-eval-calculate-score --help 2>&1 | grep 'rsem-eval-calculate-score \[options\]'"] + moduleclass = 'bio' diff --git a/easybuild/easyconfigs/d/DFT-D4/DFT-D4-3.7.0-gomkl-2023b.eb b/easybuild/easyconfigs/d/DFT-D4/DFT-D4-3.7.0-gomkl-2023b.eb new file mode 100644 index 00000000000..02f10d2d9dc --- /dev/null +++ b/easybuild/easyconfigs/d/DFT-D4/DFT-D4-3.7.0-gomkl-2023b.eb @@ -0,0 +1,45 @@ +easyblock = 'MesonNinja' + +name = 'DFT-D4' +version = '3.7.0' + +homepage = 'https://www.chemie.uni-bonn.de/pctc/mulliken-center/software/dftd4' +description = """Generally Applicable Atomic-Charge Dependent London Dispersion Correction.""" + +toolchain = {'name': 'gomkl', 'version': '2023b'} + +source_urls = ['https://github.com/dftd4/dftd4/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] +patches = ['DFT-D4-3.2.0-remove_module_id.patch'] +checksums = [ + {'v3.7.0.tar.gz': 'f00b244759eff2c4f54b80a40673440ce951b6ddfa5eee1f46124297e056f69c'}, + {'DFT-D4-3.2.0-remove_module_id.patch': '8c3c81338cb57972580e4cf3db307aa2e44b8b3f6d1ba7ae24fa9d807490a93b'}, +] + +builddependencies = [ + ('CMake', '3.27.6'), + ('Ninja', '1.11.1'), + ('Meson', '1.2.3'), + ('pkgconf', '2.0.3'), +] + +dependencies = [ + ('Python', '3.11.5'), + ('cffi', '1.15.1'), + ('mstore', '0.3.0'), + ('mctc-lib', '0.3.1'), + ('multicharge', '0.3.0'), +] + +configopts = '-Dpython=true -Dapi_v2=true ' +# if not intel compiler used, lapack mkl is not found. +configopts += '-Dlapack=mkl ' + +sanity_check_paths = { + 'files': ['bin/dftd4', 'lib/libdftd4.a', 'lib/libdftd4.%s' % SHLIB_EXT, 'include/dftd4.mod'], + 'dirs': [], +} + +sanity_check_commands = ["dftd4 --version"] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/d/DFTB+/DFTB+-24.1-foss-2023a.eb b/easybuild/easyconfigs/d/DFTB+/DFTB+-24.1-foss-2023a.eb new file mode 100644 index 00000000000..c862fcea552 --- /dev/null +++ b/easybuild/easyconfigs/d/DFTB+/DFTB+-24.1-foss-2023a.eb @@ -0,0 +1,93 @@ +easyblock = 'CMakeMake' + +name = 'DFTB+' +version = '24.1' + +homepage = 'https://www.dftb-plus.info' +description = """DFTB+ is a fast and efficient versatile quantum mechanical simulation package. +It is based on the Density Functional Tight Binding (DFTB) method, containing +almost all of the useful extensions which have been developed for the DFTB +framework so far. Using DFTB+ you can carry out quantum mechanical simulations +like with ab-initio density functional theory based packages, but in an +approximate way gaining typically around two order of magnitude in speed.""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'usempi': True, 'openmp': True, 'pic': True} + +_external_dir = '%%(builddir)s/dftbplus-%%(version)s/external/%s/origin/' +_external_extract = 'mkdir -p %s && tar -C %s' % (_external_dir, _external_dir) +_external_extract += ' --strip-components=1 -xzf %%s' + +source_urls = ['https://github.com/dftbplus/dftbplus/releases/download/%(version)s'] +sources = [ + 'dftbplus-%(version)s.tar.xz', + { + # Slater-Koster (slakos) data for testing + 'source_urls': ['https://github.com/dftbplus/testparams/archive'], + 'download_filename': 'fbe3d62127d86bd8e49ad25a1e5793e6a095e8e7.tar.gz', + 'filename': 'slakos-data-%(version)s.tar.gz', + 'extract_cmd': _external_extract % ('slakos', 'slakos'), + }, + { + # GBSA (gbsa) data for testing + 'source_urls': ['https://github.com/grimme-lab/gbsa-parameters/archive'], + 'download_filename': '6836c4d997e4135e418cfbe273c96b1a3adb13e2.tar.gz', + 'filename': 'gbsa-data-%(version)s.tar.gz', + 'extract_cmd': _external_extract % ('gbsa', 'gbsa'), + }, +] +checksums = [ + {'dftbplus-24.1.tar.xz': '3bc405d1ab834b6b145ca671fb44565ec50a6f576e9e18e7a1ae2c613a311321'}, + {'slakos-data-24.1.tar.gz': '78a0494c2ff9216d6a9199ba07d632b18b809e0198f43905c044b5748bde488d'}, + {'gbsa-data-24.1.tar.gz': 'd464f9f7b1883d1353b433d0c7eae2f5606af092d9b51d38e9ed15e072610a79'}, +] + +builddependencies = [ + ('CMake', '3.26.3'), + ('pkgconf', '1.9.5'), + ('git', '2.41.0', '-nodocs'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('dftd4', '3.7.0'), + ('ELSI', '2.11.0', '-PEXSI'), + ('libmbd', '0.12.6'), +] + +# Prefer dependencies from EB than bundled sources +configopts = '-DHYBRID_CONFIG_METHODS="Find;Submodule;Fetch" ' +configopts += '-DWITH_MPI=1 -DWITH_OMP=1 -DWITH_SDFTD3=1 -DWITH_ELSI=1 -DWITH_MBD=1 -DWITH_UNIT_TESTS=1 ' +configopts += '-DBUILD_SHARED_LIBS=1 -DWITH_API=1 -DWITH_PYTHON=0 ' # Python bindings installed as extension +configopts += '-DSCALAPACK_LIBRARY="$LIBSCALAPACK" ' + +runtest = 'test' + +exts_defaultclass = 'PythonPackage' +exts_default_options = { + 'download_dep_fail': True, + 'use_pip': True, + 'runtest': False, +} +exts_list = [ + ('dptools', version, { + 'source_tmpl': 'dftbplus-%(version)s.tar.xz', + 'source_urls': ['https://github.com/dftbplus/dftbplus/releases/download/%(version)s'], + 'start_dir': 'tools/dptools', + 'checksums': ['3bc405d1ab834b6b145ca671fb44565ec50a6f576e9e18e7a1ae2c613a311321'], + }), +] + +sanity_check_paths = { + 'files': ['bin/' + x for x in ['dftb+', 'dp_bands', 'dp_dos', 'gen2cif', 'gen2xyz', 'makecube', + 'modes', 'repeatgen', 'straingen', 'waveplot', 'xyz2gen']] + + ['lib/libdftbplus.%s' % SHLIB_EXT, 'lib/libmpifx.%s' % SHLIB_EXT], + 'dirs': ['include/dftbplus', 'lib/cmake', 'lib/pkgconfig', 'lib/python%(pyshortver)s/site-packages'] +} + +sanity_check_commands = ["python -c 'import dptools'"] + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/d/DL_POLY_4/DL_POLY_4-5.1.0-foss-2023a.eb b/easybuild/easyconfigs/d/DL_POLY_4/DL_POLY_4-5.1.0-foss-2023a.eb new file mode 100644 index 00000000000..1d47dce62d0 --- /dev/null +++ b/easybuild/easyconfigs/d/DL_POLY_4/DL_POLY_4-5.1.0-foss-2023a.eb @@ -0,0 +1,24 @@ +easyblock = 'CMakeMake' + +name = "DL_POLY_4" +version = "5.1.0" + +homepage = "https://www.scd.stfc.ac.uk/Pages/DL_POLY.aspx" +description = "DL_POLY is a general purpose classical molecular dynamics (MD) simulation software" + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['https://gitlab.com/ccp5/dl-poly/-/archive/%(version)s/'] +sources = ['dl_poly_%(version)s.tar.bz2'] +checksums = ['da5364986cd71e047e080753f6ca75135bf19bd5607770b839dea3734c2fdfaa'] + +builddependencies = [('CMake', '3.26.3')] + +sanity_check_paths = { + 'files': ['bin/DLPOLY.Z'], + 'dirs': [] +} + +sanity_check_commands = ['DLPOLY.Z -h'] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/d/DL_POLY_Classic_GUI/DL_POLY_Classic_GUI-1.10.eb b/easybuild/easyconfigs/d/DL_POLY_Classic_GUI/DL_POLY_Classic_GUI-1.10.eb new file mode 100644 index 00000000000..84de0bbf36a --- /dev/null +++ b/easybuild/easyconfigs/d/DL_POLY_Classic_GUI/DL_POLY_Classic_GUI-1.10.eb @@ -0,0 +1,34 @@ +easyblock = 'JAR' + +name = 'DL_POLY_Classic_GUI' +version = '1.10' + +homepage = 'https://gitlab.com/DL_POLY_Classic/dl_poly' +description = """ +The DL_POLY Graphical User Interface (or GUI) is a program written in the +Java language and is intended for use with the DL_POLY molecular +simulation program. +This is the GUI for DL_POLY Classic, it can also be used for DL_POLY_4. +""" + +toolchain = SYSTEM + +source_urls = ['https://gitlab.com/DL_POLY_Classic/dl_poly/-/raw/RELEASE-%(version_major)s-%(version_minor)s/java/'] +sources = ['GUI.jar'] +checksums = ['8d3a5ed75d5ee8eb2e4403d8ed9355cd214c7e5b7afc8161c89a50edbc0a481d'] + +dependencies = [ + ('Java', '17', '', SYSTEM), +] + + +sanity_check_paths = { + 'files': ['GUI.jar'], + 'dirs': [''], +} + +modloadmsg = """ +To execute this Graphical User Interface run: java GUI +""" + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/d/DMTCP/DMTCP-3.0.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/d/DMTCP/DMTCP-3.0.0-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..0474c5e8f88 --- /dev/null +++ b/easybuild/easyconfigs/d/DMTCP/DMTCP-3.0.0-GCCcore-12.2.0.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'DMTCP' +version = '3.0.0' + +homepage = 'http://dmtcp.sourceforge.net/index.html' +description = """DMTCP is a tool to transparently checkpoint the state of multiple +simultaneous applications, including multi-threaded and distributed applications. +It operates directly on the user binary executable, without any Linux kernel modules +or other kernel modifications.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://github.com/dmtcp/dmtcp/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['2c7e95e1dbc55db33433bfee48a65f274298e98f246a36ab6dad1e0694750d37'] + +builddependencies = [('binutils', '2.39')] + +sanity_check_paths = { + 'files': ['bin/dmtcp_command', 'bin/dmtcp_discover_rm', 'bin/dmtcp_nocheckpoint', 'bin/dmtcp_srun_helper', + 'bin/dmtcp_sshd', 'bin/dmtcp_coordinator', 'bin/dmtcp_launch', 'bin/dmtcp_restart', 'bin/dmtcp_ssh'], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/d/DMTCP/DMTCP-3.0.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/d/DMTCP/DMTCP-3.0.0-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..9947d4f758d --- /dev/null +++ b/easybuild/easyconfigs/d/DMTCP/DMTCP-3.0.0-GCCcore-12.3.0.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'DMTCP' +version = '3.0.0' + +homepage = 'http://dmtcp.sourceforge.net/index.html' +description = """DMTCP is a tool to transparently checkpoint the state of multiple +simultaneous applications, including multi-threaded and distributed applications. +It operates directly on the user binary executable, without any Linux kernel modules +or other kernel modifications.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://github.com/dmtcp/dmtcp/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['2c7e95e1dbc55db33433bfee48a65f274298e98f246a36ab6dad1e0694750d37'] + +builddependencies = [('binutils', '2.40')] + +sanity_check_paths = { + 'files': ['bin/dmtcp_command', 'bin/dmtcp_discover_rm', 'bin/dmtcp_nocheckpoint', 'bin/dmtcp_srun_helper', + 'bin/dmtcp_sshd', 'bin/dmtcp_coordinator', 'bin/dmtcp_launch', 'bin/dmtcp_restart', 'bin/dmtcp_ssh'], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/d/DMTCP/DMTCP-3.0.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/d/DMTCP/DMTCP-3.0.0-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..9721668c208 --- /dev/null +++ b/easybuild/easyconfigs/d/DMTCP/DMTCP-3.0.0-GCCcore-13.2.0.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'DMTCP' +version = '3.0.0' + +homepage = 'http://dmtcp.sourceforge.net/index.html' +description = """DMTCP is a tool to transparently checkpoint the state of multiple +simultaneous applications, including multi-threaded and distributed applications. +It operates directly on the user binary executable, without any Linux kernel modules +or other kernel modifications.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://github.com/dmtcp/dmtcp/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['2c7e95e1dbc55db33433bfee48a65f274298e98f246a36ab6dad1e0694750d37'] + +builddependencies = [('binutils', '2.40')] + +sanity_check_paths = { + 'files': ['bin/dmtcp_command', 'bin/dmtcp_discover_rm', 'bin/dmtcp_nocheckpoint', 'bin/dmtcp_srun_helper', + 'bin/dmtcp_sshd', 'bin/dmtcp_coordinator', 'bin/dmtcp_launch', 'bin/dmtcp_restart', 'bin/dmtcp_ssh'], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/d/Dask-ML/Dask-ML-2022.5.27-foss-2022a.eb b/easybuild/easyconfigs/d/Dask-ML/Dask-ML-2022.5.27-foss-2022a.eb new file mode 100644 index 00000000000..12884bd5e3a --- /dev/null +++ b/easybuild/easyconfigs/d/Dask-ML/Dask-ML-2022.5.27-foss-2022a.eb @@ -0,0 +1,51 @@ +easyblock = 'PythonBundle' + +name = 'Dask-ML' +version = '2022.5.27' + +homepage = 'http://ml.dask.org/' +description = """ +Dask-ML provides scalable machine learning in Python using Dask alongside popular machine +learning libraries like Scikit-Learn, XGBoost, and others. +""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('scikit-learn', '1.1.2'), + ('dask', '2022.10.0'), + ('numba', '0.56.4'), + ('SciPy-bundle', '2022.05'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('sparse', '0.14.0', { + 'checksums': ['5f5827a37f6cd6f6730a541f994c95c60a3ae2329e01f4ba21ced5339aea0098'], + }), + ('dask-glm', '0.3.2', { + 'checksums': ['c947a566866698a01d79978ae73233cb5e838ad5ead6085143582c5e930b9a4a'], + }), + ('versioneer', '0.29', { + 'checksums': ['5ab283b9857211d61b53318b7c792cf68e798e765ee17c27ade9f6c924235731'], + }), + ('distributed', '2022.10.0', { + 'checksums': ['dcfbc9c528bcd9e4f9686e673956a90172826395ac5b258039e580777d50782f'], + }), + ('multipledispatch', '1.0.0', { + 'checksums': ['5c839915465c68206c3e9c473357908216c28383b425361e5d144594bf85a7e0'], + }), + ('packaging', '20.4', { + 'checksums': ['4357f74f47b9c12db93624a82154e9b120fa8293699949152b22065d556079f8'], + }), + (name, version, { + 'modulename': 'dask_ml', + 'sources': ['dask-ml-%(version)s.tar.gz'], + 'checksums': ['6369d3934192bcc1923fcee84c3fb8fbcceca102137901070ba3f1d9e386cce4'], + }), +] + +moduleclass = 'ai' diff --git a/easybuild/easyconfigs/d/Dask-ML/Dask-ML-2024.4.4-foss-2023a.eb b/easybuild/easyconfigs/d/Dask-ML/Dask-ML-2024.4.4-foss-2023a.eb new file mode 100644 index 00000000000..f4bdf4425ae --- /dev/null +++ b/easybuild/easyconfigs/d/Dask-ML/Dask-ML-2024.4.4-foss-2023a.eb @@ -0,0 +1,50 @@ +easyblock = 'PythonBundle' + +name = 'Dask-ML' +version = '2024.4.4' + +homepage = 'http://ml.dask.org/' +description = """ +Dask-ML provides scalable machine learning in Python using Dask alongside popular machine +learning libraries like Scikit-Learn, XGBoost, and others. +""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [('hatchling', '1.18.0')] + +dependencies = [ + ('Python', '3.11.3'), + ('scikit-learn', '1.3.1'), + ('dask', '2023.9.2'), + ('numba', '0.58.1'), + ('SciPy-bundle', '2023.07'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('sparse', '0.15.4', { + # replace use of 'version_file' (which requires setuptools-scm >= 8.0) with 'write_to' + 'preinstallopts': "sed -i 's/^version_file/write_to/' pyproject.toml && ", + 'checksums': ['d4b1c57d24ff0f64f2fd5b5a95b49b7fb84ed207a26d7d58ce2764dcc5c72b84'], + }), + ('dask-glm', '0.3.2', { + 'checksums': ['c947a566866698a01d79978ae73233cb5e838ad5ead6085143582c5e930b9a4a'], + }), + ('distributed', '2023.9.2', { + 'checksums': ['b76b43be6a297c6cc6dc4eac7f5a05a8c6834aaf025ed37395d1d830448d540e'], + }), + ('multipledispatch', '1.0.0', { + 'checksums': ['5c839915465c68206c3e9c473357908216c28383b425361e5d144594bf85a7e0'], + }), + ('packaging', '24.1', { + 'checksums': ['026ed72c8ed3fcce5bf8950572258698927fd1dbda10a5e981cdf0ac37f4f002'], + }), + ('dask_ml', version, { + 'checksums': ['7956910a49e1e31944280fdb311adf245da11ef410d67deb7a05c67c7d0c4498'], + }), +] + +moduleclass = 'ai' diff --git a/easybuild/easyconfigs/d/DeepDRR/DeepDRR-1.1.3-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/d/DeepDRR/DeepDRR-1.1.3-foss-2022a-CUDA-11.7.0.eb new file mode 100644 index 00000000000..9191c43123a --- /dev/null +++ b/easybuild/easyconfigs/d/DeepDRR/DeepDRR-1.1.3-foss-2022a-CUDA-11.7.0.eb @@ -0,0 +1,49 @@ +easyblock = 'PythonBundle' + +name = 'DeepDRR' +version = '1.1.3' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://deepdrr.readthedocs.io/' +description = """ +DeepDRR provides state-of-the-art tools to generate realistic radiographs and +fluoroscopy from 3D CTs on a training set scale.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('CUDA', '11.7.0', '', SYSTEM), + ('Python', '3.10.4'), + ('scikit-image', '0.19.3'), + ('PyTorch', '1.12.1', versionsuffix), + ('PyTorch-bundle', '1.12.1', versionsuffix), + ('NiBabel', '4.0.2'), + ('pydicom', '2.3.0'), + ('PyVista', '0.43.8'), + ('PyCUDA', '2024.1', versionsuffix), + ('OpenCV', '4.6.0', versionsuffix + '-contrib'), + ('Seaborn', '0.12.1'), +] + +use_pip = True + +exts_list = [ + ('colorlog', '6.8.2', { + 'checksums': ['3e3e079a41feb5a1b64f978b5ea4f46040a94f11f0e8bbb8261e3dbbeca64d44'], + }), + ('nptyping', '2.5.0', { + 'checksums': ['e3d35b53af967e6fb407c3016ff9abae954d3a0568f7cc13a461084224e8e20a'], + }), + ('pynrrd', '1.0.0', { + 'modulename': 'nrrd', + 'checksums': ['4eb4caba03fbca1b832114515e748336cb67bce70c7f3ae36bfa2e135fc990d2'], + }), + ('deepdrr', version, { + 'preinstallopts': "sed -i 's/opencv-python/opencv-contrib-python/g' setup.py && ", + 'checksums': ['aa75571e2382b408051fb95b302a63f584781a35441b9969c293e54e5f69b484'], + }), +] + +sanity_pip_check = True + +moduleclass = 'ai' diff --git a/easybuild/easyconfigs/d/DeepLoc/DeepLoc-2.0-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/d/DeepLoc/DeepLoc-2.0-foss-2023a-CUDA-12.1.1.eb new file mode 100644 index 00000000000..379eb0439bb --- /dev/null +++ b/easybuild/easyconfigs/d/DeepLoc/DeepLoc-2.0-foss-2023a-CUDA-12.1.1.eb @@ -0,0 +1,61 @@ +easyblock = 'PythonBundle' + +name = 'DeepLoc' +version = '2.0' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://services.healthtech.dtu.dk/services/DeepLoc-2.0' +description = "DeepLoc 2.0 predicts the subcellular localization(s) of eukaryotic proteins" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('CUDA', '12.1.1', '', SYSTEM), + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('matplotlib', '3.7.2'), + ('Biopython', '1.83'), + ('ONNX-Runtime', '1.19.2', versionsuffix), + ('ESM-2', '2.0.0', versionsuffix), # for fair-esm + ('PyTorch', '2.1.2', versionsuffix), + ('PyTorch-Lightning', '2.2.1', versionsuffix), + ('Transformers', '4.39.3'), + ('SentencePiece', '0.2.0'), + ('mygene', '3.2.2'), # required by bio +] + +use_pip = True + +local_deeploc_download_url = 'https://services.healthtech.dtu.dk/cgi-bin/sw_request?' +local_deeploc_download_url += 'software=deeploc&version=2.0&packageversion=2.0&platform=All' + +exts_list = [ + ('gprofiler-official', '1.0.0', { + 'checksums': ['5015b47f10fbdcb59c57e342e815c9c07afbe57cd3984154f75b845ddef2445d'], + 'modulename': 'gprofiler', + }), + ('bio', '1.7.1', { + 'sources': ['bio-%(version)s-py%(pymajver)s-none-any.whl'], + 'checksums': ['851545804b08413a3f27fd5131edefc30acfdee513919eebabb29678d8632218'], + 'modulename': 'biorun', + }), + (name, version, { + 'download_instructions': "Download via %s" % local_deeploc_download_url, + 'sources': ['deeploc-%(version)s.All.tar.gz'], + 'checksums': ['1741cf61cc38bba6307f1838c08ff9dd01386da09b8939610d15c27f98173651'], + 'modulename': 'DeepLoc2', + }), +] + +sanity_check_paths = { + 'files': ['bin/deeploc2'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "deeploc2 --help", +] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/d/DeepLoc/DeepLoc-2.0-foss-2023a.eb b/easybuild/easyconfigs/d/DeepLoc/DeepLoc-2.0-foss-2023a.eb new file mode 100644 index 00000000000..558d3f61871 --- /dev/null +++ b/easybuild/easyconfigs/d/DeepLoc/DeepLoc-2.0-foss-2023a.eb @@ -0,0 +1,59 @@ +easyblock = 'PythonBundle' + +name = 'DeepLoc' +version = '2.0' + +homepage = 'https://services.healthtech.dtu.dk/services/DeepLoc-2.0' +description = "DeepLoc 2.0 predicts the subcellular localization(s) of eukaryotic proteins" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('matplotlib', '3.7.2'), + ('Biopython', '1.83'), + ('ONNX-Runtime', '1.19.2'), + ('ESM-2', '2.0.0'), # for fair-esm + ('PyTorch', '2.1.2'), + ('PyTorch-Lightning', '2.2.1'), + ('Transformers', '4.39.3'), + ('SentencePiece', '0.2.0'), + ('mygene', '3.2.2'), # required by bio +] + +use_pip = True + +local_deeploc_download_url = 'https://services.healthtech.dtu.dk/cgi-bin/sw_request?' +local_deeploc_download_url += 'software=deeploc&version=2.0&packageversion=2.0&platform=All' + +exts_list = [ + ('gprofiler-official', '1.0.0', { + 'checksums': ['5015b47f10fbdcb59c57e342e815c9c07afbe57cd3984154f75b845ddef2445d'], + 'modulename': 'gprofiler', + }), + ('bio', '1.7.1', { + 'sources': ['bio-%(version)s-py%(pymajver)s-none-any.whl'], + 'checksums': ['851545804b08413a3f27fd5131edefc30acfdee513919eebabb29678d8632218'], + 'modulename': 'biorun', + }), + (name, version, { + 'download_instructions': "Download via %s" % local_deeploc_download_url, + 'sources': ['deeploc-%(version)s.All.tar.gz'], + 'checksums': ['1741cf61cc38bba6307f1838c08ff9dd01386da09b8939610d15c27f98173651'], + 'modulename': 'DeepLoc2', + }), +] + +sanity_check_paths = { + 'files': ['bin/deeploc2'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "deeploc2 --help", +] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/d/Dice/Dice-20240702-foss-2023a.eb b/easybuild/easyconfigs/d/Dice/Dice-20240702-foss-2023a.eb new file mode 100644 index 00000000000..56756b3f99f --- /dev/null +++ b/easybuild/easyconfigs/d/Dice/Dice-20240702-foss-2023a.eb @@ -0,0 +1,51 @@ +easyblock = 'MakeCp' + +name = 'Dice' +version = '20240702' +_commit = '0f52b62' + +homepage = 'https://github.com/sanshar/Dice' +description = """Dice contains code for performing SHCI, VMC, GFMC, DMC, FCIQMC, stochastic MRCI +and SC-NEVPT2, and AFQMC calculations with a focus on ab initio systems.""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'cstd': 'c++14', 'pic': True} + +github_account = 'sanshar' +source_urls = [GITHUB_SOURCE] +sources = [{'download_filename': '%s.tar.gz' % _commit, 'filename': SOURCE_TAR_GZ}] +patches = ['Dice-20240101_deprecated-global-placeholders.patch'] +checksums = [ + {'Dice-20240702.tar.gz': '3fe36938642ebf7886231290655c1a2d1fdd256e2bc7e9375669c574c406fc23'}, + {'Dice-20240101_deprecated-global-placeholders.patch': + 'fbf4037e928a57e737faed95dc7d6e1e5cdb8cee8db48503268d250a34c12ccc'}, +] + +builddependencies = [ + ('Eigen', '3.4.0'), + ('git', '2.41.0', '-nodocs'), +] + +dependencies = [ + ('Boost.MPI', '1.82.0'), + ('HDF5', '1.14.0'), +] + +# Use build environment defined by EB +prebuildopts = "sed -i 's/^FLAGS_BASE =.*/FLAGS_BASE=$(CXXFLAGS) -g -w -I. $(CPPFLAGS)/' Makefile && " +buildopts = 'CXX="$MPICXX" USE_INTEL="no" HAS_AVX2="no" ' # avoid changes to -march +buildopts += 'INCLUDE_MKL="-I${EBROOTFLEXIBLAS}/include" LIB_MKL="${LIBBLAS}" ' # use FlexiBLAS +buildopts += 'GIT_BRANCH="master" GIT_HASH="%s"' % _commit +buildopts += 'BOOST="${EBROOTBOOSTMPI}" ' +buildopts += 'EIGEN="${EBROOTEIGEN}/include" ' +buildopts += 'HDF5="${EBROOTHDF5}" ' + +files_to_copy = ['bin'] + +_binaries = ['Dice', 'DQMC', 'GFMC', 'ICPT', 'VMC', 'ZDice2', 'ZSHCI'] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in _binaries], + 'dirs': [], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.11.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.11.0-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..da8dc7f5808 --- /dev/null +++ b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.11.0-GCCcore-13.3.0.eb @@ -0,0 +1,41 @@ +easyblock = 'CMakeMake' + +name = 'Doxygen' +version = '1.11.0' + +homepage = 'https://www.doxygen.org' +description = """ + Doxygen is a documentation system for C++, C, Java, Objective-C, Python, + IDL (Corba and Microsoft flavors), Fortran, VHDL, PHP, C#, and to some + extent D. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%(namelower)s-%(version)s.src.tar.gz'] +checksums = ['c9edfdf8c5f3e8bee0c4c967850caead27099883ee7ff8b11044e6d63faf3607'] + +builddependencies = [ + ('binutils', '2.42'), + ('Bison', '3.8.2'), + ('CMake', '3.29.3'), + ('flex', '2.6.4'), + ('pkgconf', '2.2.0'), + ('Python', '3.12.3'), +] + +dependencies = [ + ('libiconv', '1.17'), +] + +configopts = "-DICONV_DIR=$EBROOTLIBICONV -DICONV_IN_GLIBC=OFF" + +sanity_check_paths = { + 'files': ["bin/doxygen"], + 'dirs': [], +} + +sanity_check_commands = ["doxygen --help"] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/d/dask-labextension/dask-labextension-7.0.0-foss-2023a.eb b/easybuild/easyconfigs/d/dask-labextension/dask-labextension-7.0.0-foss-2023a.eb new file mode 100644 index 00000000000..a0baf17a0ae --- /dev/null +++ b/easybuild/easyconfigs/d/dask-labextension/dask-labextension-7.0.0-foss-2023a.eb @@ -0,0 +1,37 @@ +easyblock = 'PythonBundle' + +name = 'dask-labextension' +version = '7.0.0' + +homepage = 'https://github.com/dask/dask-labextension' +description = """This package provides a JupyterLab extension to manage Dask clusters, as well +as embed Dask's dashboard plots directly into JupyterLab panes.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('JupyterLab', '4.0.5'), + ('jupyter-server-proxy', '4.0.0'), + ('dask', '2023.9.2'), +] + +use_pip = True + +exts_list = [ + ('dask_labextension', version, { + 'sources': ['%(name)s-%(version)s-py3-none-any.whl'], + 'checksums': ['34fd1ee80a7259dc292a789cc82e4563d7cd1f5a26eb2ee8b434517482f82027'], + }), +] + +sanity_pip_check = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/dask_labextension', 'etc/jupyter', 'share/jupyter'], +} + +modextrapaths = {'EB_ENV_JUPYTER_ROOT': ''} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/d/dask-labextension/dask-labextension-7.0.0-gfbf-2023b.eb b/easybuild/easyconfigs/d/dask-labextension/dask-labextension-7.0.0-gfbf-2023b.eb new file mode 100644 index 00000000000..7ff6ec31bf7 --- /dev/null +++ b/easybuild/easyconfigs/d/dask-labextension/dask-labextension-7.0.0-gfbf-2023b.eb @@ -0,0 +1,37 @@ +easyblock = 'PythonBundle' + +name = 'dask-labextension' +version = '7.0.0' + +homepage = 'https://github.com/dask/dask-labextension' +description = """This package provides a JupyterLab extension to manage Dask clusters, as well +as embed Dask's dashboard plots directly into JupyterLab panes.""" + +toolchain = {'name': 'gfbf', 'version': '2023b'} + +dependencies = [ + ('Python', '3.11.5'), + ('JupyterLab', '4.2.0'), + ('jupyter-server-proxy', '4.1.2'), + ('dask', '2024.5.1'), +] + +use_pip = True + +exts_list = [ + ('dask_labextension', version, { + 'sources': ['%(name)s-%(version)s-py3-none-any.whl'], + 'checksums': ['34fd1ee80a7259dc292a789cc82e4563d7cd1f5a26eb2ee8b434517482f82027'], + }), +] + +sanity_pip_check = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/dask_labextension', 'etc/jupyter', 'share/jupyter'], +} + +modextrapaths = {'EB_ENV_JUPYTER_ROOT': ''} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/d/dask/dask-2024.5.1-gfbf-2023b.eb b/easybuild/easyconfigs/d/dask/dask-2024.5.1-gfbf-2023b.eb new file mode 100644 index 00000000000..36229e3f967 --- /dev/null +++ b/easybuild/easyconfigs/d/dask/dask-2024.5.1-gfbf-2023b.eb @@ -0,0 +1,67 @@ +easyblock = 'PythonBundle' + +name = 'dask' +version = '2024.5.1' + +homepage = 'https://dask.org/' +description = """ Dask natively scales Python. Dask provides advanced parallelism for analytics, +enabling performance at scale for the tools you love.""" + +toolchain = {'name': 'gfbf', 'version': '2023b'} + +dependencies = [ + ('Python', '3.11.5'), + ('Python-bundle-PyPI', '2023.10'), + ('SciPy-bundle', '2023.11'), + ('PyYAML', '6.0.1'), + ('bokeh', '3.4.1'), +] + +use_pip = True + +exts_list = [ + ('toolz', '0.12.1', { + 'checksums': ['ecca342664893f177a13dac0e6b41cbd8ac25a358e5f215316d43e2100224f4d'], + }), + ('locket', '1.0.0', { + 'checksums': ['5c0d4c052a8bbbf750e056a8e65ccd309086f4f0f18a2eac306a8dfa4112a632'], + }), + ('partd', '1.4.2', { + 'checksums': ['d022c33afbdc8405c226621b015e8067888173d85f7f5ecebb3cafed9a20f02c'], + }), + ('HeapDict', '1.0.1', { + 'checksums': ['8495f57b3e03d8e46d5f1b2cc62ca881aca392fd5cc048dc0aa2e1a6d23ecdb6'], + }), + ('zict', '3.0.0', { + 'checksums': ['e321e263b6a97aafc0790c3cfb3c04656b7066e6738c37fffcca95d803c9fba5'], + }), + ('tblib', '3.0.0', { + 'checksums': ['93622790a0a29e04f0346458face1e144dc4d32f493714c6c3dff82a4adb77e6'], + }), + (name, version, { + 'checksums': ['e071fda67031c314569e37ca70b3e88bb30f1d91ff8ee4122b541845847cc264'], + }), + ('distributed', version, { + 'checksums': ['c4e641e5fc014de3b43c584c70f703a7d44557b51b1143db812b8bc861aa84e2'], + }), + ('dask-mpi', '2022.4.0', { + 'checksums': ['0a04f1d7d35a06cdff506593330d4414ea242c9172498ce191f5742eac499e17'], + }), + ('docrep', '0.3.2', { + 'checksums': ['ed8a17e201abd829ef8da78a0b6f4d51fb99a4cbd0554adbed3309297f964314'], + }), + ('dask-jobqueue', '0.8.5', { + 'checksums': ['f6923f9d7ff894b96efbf706118b2cd37fd37751d567e91c22dfd3e2eaa93202'], + }), +] + +sanity_check_paths = { + 'files': ['bin/dask-%s' % x for x in ['mpi', 'scheduler', 'ssh', 'worker']], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["dask-scheduler --help"] + +sanity_pip_check = True + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/d/dask/dask-2024.9.1-gfbf-2024a.eb b/easybuild/easyconfigs/d/dask/dask-2024.9.1-gfbf-2024a.eb new file mode 100644 index 00000000000..93df8dc002f --- /dev/null +++ b/easybuild/easyconfigs/d/dask/dask-2024.9.1-gfbf-2024a.eb @@ -0,0 +1,64 @@ +easyblock = 'PythonBundle' + +name = 'dask' +version = '2024.9.1' + +homepage = 'https://dask.org/' +description = """ Dask natively scales Python. Dask provides advanced parallelism for analytics, +enabling performance at scale for the tools you love.""" + +toolchain = {'name': 'gfbf', 'version': '2024a'} + +dependencies = [ + ('Python', '3.12.3'), + ('Python-bundle-PyPI', '2024.06'), + ('SciPy-bundle', '2024.05'), + ('PyYAML', '6.0.2'), + ('bokeh', '3.6.0'), +] + +use_pip = True + +exts_list = [ + ('toolz', '0.12.1', { + 'checksums': ['ecca342664893f177a13dac0e6b41cbd8ac25a358e5f215316d43e2100224f4d'], + }), + ('locket', '1.0.0', { + 'checksums': ['5c0d4c052a8bbbf750e056a8e65ccd309086f4f0f18a2eac306a8dfa4112a632'], + }), + ('partd', '1.4.2', { + 'checksums': ['d022c33afbdc8405c226621b015e8067888173d85f7f5ecebb3cafed9a20f02c'], + }), + ('HeapDict', '1.0.1', { + 'checksums': ['8495f57b3e03d8e46d5f1b2cc62ca881aca392fd5cc048dc0aa2e1a6d23ecdb6'], + }), + ('zict', '3.0.0', { + 'checksums': ['e321e263b6a97aafc0790c3cfb3c04656b7066e6738c37fffcca95d803c9fba5'], + }), + ('tblib', '3.0.0', { + 'checksums': ['93622790a0a29e04f0346458face1e144dc4d32f493714c6c3dff82a4adb77e6'], + }), + (name, version, { + 'checksums': ['06eccc6a68d2882bcd9de24548fa96e8d0da7fbfff0baed3f3c2a526b73dfbb4'], + }), + ('distributed', version, { + 'checksums': ['4d573d89ff4fdde0dd96ad5cfdb843ce8ecef8caf002435bc60d14414dc1e819'], + }), + ('docrep', '0.3.2', { + 'checksums': ['ed8a17e201abd829ef8da78a0b6f4d51fb99a4cbd0554adbed3309297f964314'], + }), + ('dask-jobqueue', '0.8.5', { + 'checksums': ['f6923f9d7ff894b96efbf706118b2cd37fd37751d567e91c22dfd3e2eaa93202'], + }), +] + +sanity_check_paths = { + 'files': ['bin/dask-%s' % x for x in ['scheduler', 'ssh', 'worker']], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["dask-scheduler --help"] + +sanity_pip_check = True + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/d/datalad/datalad-1.1.3-GCCcore-13.3.0.eb b/easybuild/easyconfigs/d/datalad/datalad-1.1.3-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..66b0e738846 --- /dev/null +++ b/easybuild/easyconfigs/d/datalad/datalad-1.1.3-GCCcore-13.3.0.eb @@ -0,0 +1,84 @@ +easyblock = 'PythonBundle' + +name = 'datalad' +version = "1.1.3" + +homepage = 'https://www.datalad.org/' +description = "DataLad is a free and open source distributed data management system that keeps track of your data, \ +creates structure, ensures reproducibility, supports collaboration, \ +and integrates with widely used data infrastructure." + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +builddependencies = [ + ('binutils', '2.42'), + ('hatchling', '1.24.2'), + ('poetry', '1.8.3') +] + +dependencies = [ + ('git-annex', '10.20240731'), + ('Python', '3.12.3'), + ('Python-bundle-PyPI', '2024.06'), + ('tqdm', '4.66.5'), + ('PLY', '3.11'), + ('scikit-build', '0.17.6'), +] + +use_pip = True + +exts_list = [ + ('humanize', '4.10.0', { + 'checksums': ['06b6eb0293e4b85e8d385397c5868926820db32b9b654b932f57fa41c23c9978'], + }), + ('fasteners', '0.19', { + 'checksums': ['b4f37c3ac52d8a445af3a66bce57b33b5e90b97c696b7b984f530cf8f0ded09c'], + }), + ('patool', '2.3.0', { + 'modulename': 'patoolib', + 'checksums': ['498e294fd8c7d50889d65019d431c6867bf3fb1fec5ea2d39d1d39d1215002f8'], + }), + ('annexremote', '1.6.5', { + 'checksums': ['ad0ccdd84a8771ad58922d172ee68b225ece77bf464abe4d24ff91a4896a423e'], + }), + ('looseversion', '1.3.0', { + 'checksums': ['ebde65f3f6bb9531a81016c6fef3eb95a61181adc47b7f949e9c0ea47911669e'], + }), + ('botocore', '1.35.0', { + 'checksums': ['6ab2f5a5cbdaa639599e3478c65462c6d6a10173dc8b941bfc69b0c9eb548f45'], + }), + ('jmespath', '1.0.1', { + 'checksums': ['90261b206d6defd58fdd5e85f478bf633a2901798906be2ad389150c5c60edbe'], + }), + ('s3transfer', '0.10.2', { + 'checksums': ['0711534e9356d3cc692fdde846b4a1e4b0cb6519971860796e6bc4c7aea00ef6'], + }), + ('boto3', '1.35.0', { + 'checksums': ['bdc242e3ea81decc6ea551b04b2c122f088c29269d8e093b55862946aa0fcfc6'], + }), + ('python_gitlab', '4.8.0', { + 'modulename': 'gitlab', + 'checksums': ['c2c4d7b1cd503d905afe5dfc0f3f6619934361f76ae855c6cec9a666864d37cf'], + }), + ('iso8601', '2.1.0', { + 'checksums': ['6b1d3829ee8921c4301998c909f7829fa9ed3cbdac0d3b16af2d743aed1ba8df'], + }), + (name, version, { + 'checksums': ['7b3a39419ac457df94552214ca64092297d544e15576c0be57f5d7ee35fba7ab'], + }), +] + +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/datalad'], + 'dirs': [], +} + +sanity_check_commands = [ + "datalad --help", + "datalad --version", +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/d/dblatex/dblatex-0.3.12-foss-2023a.eb b/easybuild/easyconfigs/d/dblatex/dblatex-0.3.12-foss-2023a.eb new file mode 100644 index 00000000000..db41d0c240f --- /dev/null +++ b/easybuild/easyconfigs/d/dblatex/dblatex-0.3.12-foss-2023a.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonPackage' + +name = 'dblatex' +version = '0.3.12' + +homepage = 'https://dblatex.sourceforge.net/' +description = """dblatex is a program that transforms your SGML/XML DocBook documents to DVI, + PostScript or PDF by translating them into pure LaTeX as a first process. + MathML 2.0 markups are supported, too. It started as a clone of DB2LaTeX.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['https://master.dl.sourceforge.net/project/dblatex/dblatex/dblatex-%(version)s/'] +sources = ['%(name)s3-%(version)s.tar.bz2'] +checksums = ['16e82786272ed1806a079d37914d7ba7a594db792dc4cc34c1c3737dbd4da079'] + +dependencies = [ + ('Python', '3.11.3'), + ('libxslt', '1.1.38'), + ('texlive', '20230313'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +options = {'modulename': 'dbtexmf.dblatex'} + +postinstallcmds = ["cp -r %(builddir)s/%(name)s3-%(version)s/scripts %(installdir)s/bin"] + +sanity_check_commands = ['dblatex --help'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/d/decona/decona-1.4-20240731-foss-2023a.eb b/easybuild/easyconfigs/d/decona/decona-1.4-20240731-foss-2023a.eb new file mode 100644 index 00000000000..3e1eb388a12 --- /dev/null +++ b/easybuild/easyconfigs/d/decona/decona-1.4-20240731-foss-2023a.eb @@ -0,0 +1,41 @@ +easyblock = 'Tarball' + +name = 'decona' +version = '1.4-20240731' +local_commit = 'f7488ad' + +homepage = 'https://github.com/Saskia-Oosterbroek/decona' +description = "fastq to polished sequenses: pipeline suitable for mixed samples and long (Nanopore) reads" + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['https://github.com/Saskia-Oosterbroek/decona/archive'] +sources = ['%s.tar.gz' % local_commit] +checksums = ['7504160481ccdd3410fc79348c01a9a3bf0795ad73679cc305e1dcdf3e395962'] + +dependencies = [ + ('Python', '3.11.3'), + ('NanoFilt', '2.8.0'), + ('qcat', '1.1.0'), + ('CD-HIT', '4.8.1'), + ('minimap2', '2.26'), + ('Racon', '1.5.0'), + ('medaka', '1.11.3'), + ('BLAST+', '2.14.1'), +] + +fix_python_shebang_for = ['decona'] + +modextrapaths = { + 'PATH': '', + 'PYTHONPATH': '', +} + +sanity_check_paths = { + 'files': ['decona'], + 'dirs': [], +} + +sanity_check_commands = ["decona -v | grep 'This is Decona %s'" % version.split('-')[0]] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/d/deepTools/deepTools-3.5.5-gfbf-2023a.eb b/easybuild/easyconfigs/d/deepTools/deepTools-3.5.5-gfbf-2023a.eb new file mode 100644 index 00000000000..88204ce2678 --- /dev/null +++ b/easybuild/easyconfigs/d/deepTools/deepTools-3.5.5-gfbf-2023a.eb @@ -0,0 +1,53 @@ +easyblock = 'PythonBundle' + +name = 'deepTools' +version = '3.5.5' + +homepage = 'https://deeptools.readthedocs.io/' +description = """deepTools is a suite of python tools particularly developed for the efficient analysis of + high-throughput sequencing data, such as ChIP-seq, RNA-seq or MNase-seq.""" + +toolchain = {'name': 'gfbf', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('matplotlib', '3.7.2'), + ('plotly.py', '5.16.0'), + ('Pysam', '0.22.0'), + ('pyBigWig', '0.3.22'), +] + +use_pip = True + +exts_list = [ + ('py2bit', '0.3.0', { + 'checksums': ['450555c40cba66957ac8c9a4b6afb625fb34c4bb41638de78c87661ff8b682ef'], + }), + ('deeptoolsintervals', '0.1.9', { + 'checksums': ['7d94c36fd2b6f10d8b99e536d2672e8228971f1fc810497d33527bba2c40d4f6'], + }), + ('numpydoc', '1.5.0', { + 'checksums': ['b0db7b75a32367a0e25c23b397842c65e344a1206524d16c8069f0a1c91b5f4c'], + }), + (name, version, { + 'checksums': ['1c04870187117fa42eb11de95e7ff136f1445965b49ad5dae46099c3ed273f7b'], + }), +] + +sanity_check_paths = { + 'files': ['bin/bamCompare', 'bin/bamCoverage', 'bin/bamPEFragmentSize', 'bin/computeGCBias', 'bin/computeMatrix', + 'bin/correctGCBias', 'bin/multiBamSummary', 'bin/plotCorrelation', 'bin/plotCoverage', + 'bin/plotHeatmap', 'bin/plotProfile'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "bamCompare --help", + "multiBamSummary --help", + "plotHeatmap --help", +] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/d/dftd3-lib/dftd3-lib-0.10-GCC-11.3.0.eb b/easybuild/easyconfigs/d/dftd3-lib/dftd3-lib-0.10-GCC-11.3.0.eb new file mode 100644 index 00000000000..d788355e010 --- /dev/null +++ b/easybuild/easyconfigs/d/dftd3-lib/dftd3-lib-0.10-GCC-11.3.0.eb @@ -0,0 +1,34 @@ +easyblock = 'CMakeMake' + +name = 'dftd3-lib' +version = '0.10' + +homepage = 'https://github.com/dftbplus/dftd3-lib' +description = """This is a repackaged version of the DFTD3 program by S. Grimme and his coworkers. +The original program (V3.1 Rev 1) was downloaded at 2016-04-03. It has been +converted to free format and encapsulated into modules.""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +github_account = 'dftbplus' +source_urls = [GITHUB_SOURCE] +sources = ['%(version)s.tar.gz'] +patches = ['dftd3-lib-0.9_fix-extras-syntax.patch'] +checksums = [ + {'0.10.tar.gz': 'db61bc6c7c699628e8c5bf2018ea38de03a53eac38014e06845829d765caf6bb'}, + {'dftd3-lib-0.9_fix-extras-syntax.patch': '717e719170258544555bfc33390a70c2573d971c6548d8f2c951a5606ec77f74'}, +] + +builddependencies = [ + ('CMake', '3.23.1'), +] + +configopts = '-DCMAKE_INSTALL_INCLUDEDIR="%(installdir)s/include" ' + +sanity_check_paths = { + 'files': ['bin/dftd3', 'lib/libdftd3.a'], + 'dirs': ['include/dftd3/modfiles'], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/d/dftd4/dftd4-3.7.0-foss-2023a.eb b/easybuild/easyconfigs/d/dftd4/dftd4-3.7.0-foss-2023a.eb new file mode 100644 index 00000000000..912ed2baf4a --- /dev/null +++ b/easybuild/easyconfigs/d/dftd4/dftd4-3.7.0-foss-2023a.eb @@ -0,0 +1,50 @@ +# A. Domingo (Vrije Universiteit Brussel) +# J. Sassmannshausen (Imperial College London/UK) +# C. Willemyns (Vrije Universiteit Brussel) + +easyblock = 'CMakeNinja' + +name = 'dftd4' +version = '3.7.0' + +homepage = 'https://dftd4.readthedocs.io' +description = """ +The dftd4 project provides an implementation of the generally applicable, charge dependent +London-dispersion correction, termed DFT-D4. +""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'usempi': False, 'openmp': True, 'pic': True} + +github_account = 'dftd4' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['f00b244759eff2c4f54b80a40673440ce951b6ddfa5eee1f46124297e056f69c'] + +builddependencies = [ + ('CMake', '3.26.3'), + ('Ninja', '1.11.1'), +] + +dependencies = [ + ('mctc-lib', '0.3.1'), + ('mstore', '0.3.0'), + ('multicharge', '0.3.0'), +] + +build_shared_libs = True + +configopts = '-DWITH_BLAS=1 -DWITH_OpenMP=1' + +# run suite of tests with ctest +test_cmd = 'ctest' +runtest = '' + +sanity_check_paths = { + 'files': ['bin/dftd4', 'lib/libdftd4.%s' % SHLIB_EXT, 'include/dftd4.h'], + 'dirs': ['include/dftd4', 'lib/cmake', 'lib/pkgconfig'], +} + +sanity_check_commands = ["dftd4 --help"] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/d/dftd4/dftd4-3.7.0-gfbf-2023b.eb b/easybuild/easyconfigs/d/dftd4/dftd4-3.7.0-gfbf-2023b.eb new file mode 100644 index 00000000000..2f5ef00ad89 --- /dev/null +++ b/easybuild/easyconfigs/d/dftd4/dftd4-3.7.0-gfbf-2023b.eb @@ -0,0 +1,50 @@ +# A. Domingo (Vrije Universiteit Brussel) +# J. Sassmannshausen (Imperial College London/UK) +# C. Willemyns (Vrije Universiteit Brussel) + +easyblock = 'CMakeNinja' + +name = 'dftd4' +version = '3.7.0' + +homepage = 'https://dftd4.readthedocs.io' +description = """ +The dftd4 project provides an implementation of the generally applicable, charge dependent +London-dispersion correction, termed DFT-D4. +""" + +toolchain = {'name': 'gfbf', 'version': '2023b'} +toolchainopts = {'openmp': True} + +github_account = 'dftd4' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['f00b244759eff2c4f54b80a40673440ce951b6ddfa5eee1f46124297e056f69c'] + +builddependencies = [ + ('CMake', '3.27.6'), + ('Ninja', '1.11.1'), +] + +dependencies = [ + ('mctc-lib', '0.3.1'), + ('mstore', '0.3.0'), + ('multicharge', '0.3.0'), +] + +build_shared_libs = True + +configopts = '-DWITH_BLAS=1 -DWITH_OpenMP=1' + +# run suite of tests with ctest +test_cmd = 'ctest' +runtest = '' + +sanity_check_paths = { + 'files': ['bin/dftd4', 'lib/libdftd4.%s' % SHLIB_EXT, 'include/dftd4.h'], + 'dirs': ['include/dftd4', 'lib/cmake', 'lib/pkgconfig'], +} + +sanity_check_commands = ["dftd4 --help"] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/d/dictys/dictys-1.1.0-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/d/dictys/dictys-1.1.0-foss-2023a-CUDA-12.1.1.eb new file mode 100644 index 00000000000..f04774b1b55 --- /dev/null +++ b/easybuild/easyconfigs/d/dictys/dictys-1.1.0-foss-2023a-CUDA-12.1.1.eb @@ -0,0 +1,83 @@ +easyblock = 'PythonBundle' + +name = 'dictys' +version = '1.1.0' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/pinellolab/dictys' +description = "Context specific and dynamic gene regulatory network reconstruction and analysis." + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [('poetry', '1.5.1')] +dependencies = [ + ('Python', '3.11.3'), + ('CUDA', '12.1.1', '', SYSTEM), + ('PyTorch-bundle', '2.1.2', versionsuffix), + ('pybedtools', '0.9.1'), + ('SAMtools', '1.18'), + ('MACS2', '2.2.9.1'), + ('FFmpeg', '6.0'), + ('matplotlib', '3.7.2'), + ('Python-bundle-PyPI', '2023.06'), + ('SciPy-bundle', '2023.07'), + ('networkx', '3.1'), + ('h5py', '3.9.0'), + ('pyro-ppl', '1.9.0', versionsuffix), + ('adjustText', '0.7.3'), + ('Pysam', '0.22.0'), + ('paramiko', '3.2.0'), + ('Jupyter-bundle', '20230823'), + ('Qtconsole', '5.5.1'), + ('junos-eznc', '2.7.1'), +] + +# regenerate WellingtonC.c to works with python 3.11 + unpin matplotlib version +local_pyDNase_preinstallopts = ( + "cd pyDNase/footprinting && rm WellingtonC.c && cythonize -i WellingtonC.pyx && cd .. && cd .. && " + "sed -i 's/matplotlib < 2.0.0/matplotlib/' setup.py && " +) + +exts_list = [ + ('jupyter_console', '6.6.3', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['309d33409fcc92ffdad25f0bcdf9a4a9daa61b6f341177570fdac03de5352485'], + }), + ('jupyter', '1.0.0', { + 'checksums': ['d9dc4b3318f310e34c82951ea5d6683f67bed7def4b259fafbfe4f1beb1d8e5f'], + }), + ('args', '0.1.0', { + 'checksums': ['a785b8d837625e9b61c39108532d95b85274acd679693b71ebb5156848fcf814'], + }), + ('clint', '0.5.1', { + 'checksums': ['05224c32b1075563d0b16d0015faaf9da43aa214e4a2140e51f08789e7a4c5aa'], + }), + ('pynetbox', '7.4.0', { + 'checksums': ['fd0b1f197b3880048408ff5ed84422dd599bcd9389e32cb06a09b9b0d55c1636'], + }), + ('absl-py', '1.4.0', { + 'modulename': 'absl', + 'checksums': ['d2c244d01048ba476e7c080bd2c6df5e141d211de80223460d5b3b8a2a58433d'], + }), + ('aerleon', '1.9.0', { + 'checksums': ['850cd621dda750263db313d4473302b48b82adaaa9220e6fd0677cb7900f95f6'], + }), + ('homer', '0.7.0', { + 'checksums': ['efaf9b3948f6aecdf88cc87c0296a18aed77c152489a7f85c571965fb16f9e57'], + }), + ('pyDNase', '0.3.0', { + 'preinstallopts': local_pyDNase_preinstallopts, + 'modulename': 'pyDNase', + 'checksums': ['dba03cadca37929a1cc41545e962136f29efc41f8e3c6de042c51c47ee04d558'], + }), + (name, version, { + 'checksums': ['59610a8c57e9fc525ec5d13b69efc8b513c78a85a595e0e2b0138da62a035978'], + }), +] + +use_pip = True +sanity_pip_check = True + +sanity_check_commands = ["dictys --help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/d/dictys/dictys-1.1.0-foss-2023a.eb b/easybuild/easyconfigs/d/dictys/dictys-1.1.0-foss-2023a.eb new file mode 100644 index 00000000000..0b97a82cfde --- /dev/null +++ b/easybuild/easyconfigs/d/dictys/dictys-1.1.0-foss-2023a.eb @@ -0,0 +1,81 @@ +easyblock = 'PythonBundle' + +name = 'dictys' +version = '1.1.0' + +homepage = 'https://github.com/pinellolab/dictys' +description = "Context specific and dynamic gene regulatory network reconstruction and analysis." + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [('poetry', '1.5.1')] +dependencies = [ + ('Python', '3.11.3'), + ('PyTorch-bundle', '2.1.2'), + ('pybedtools', '0.9.1'), + ('SAMtools', '1.18'), + ('MACS2', '2.2.9.1'), + ('FFmpeg', '6.0'), + ('matplotlib', '3.7.2'), + ('Python-bundle-PyPI', '2023.06'), + ('SciPy-bundle', '2023.07'), + ('networkx', '3.1'), + ('h5py', '3.9.0'), + ('pyro-ppl', '1.9.0'), + ('adjustText', '0.7.3'), + ('Pysam', '0.22.0'), + ('paramiko', '3.2.0'), + ('Jupyter-bundle', '20230823'), + ('Qtconsole', '5.5.1'), + ('junos-eznc', '2.7.1'), +] + +# regenerate WellingtonC.c to works with python 3.11 + unpin matplotlib version +local_pyDNase_preinstallopts = ( + "cd pyDNase/footprinting && rm WellingtonC.c && cythonize -i WellingtonC.pyx && cd .. && cd .. && " + "sed -i 's/matplotlib < 2.0.0/matplotlib/' setup.py && " +) + +exts_list = [ + ('jupyter_console', '6.6.3', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['309d33409fcc92ffdad25f0bcdf9a4a9daa61b6f341177570fdac03de5352485'], + }), + ('jupyter', '1.0.0', { + 'checksums': ['d9dc4b3318f310e34c82951ea5d6683f67bed7def4b259fafbfe4f1beb1d8e5f'], + }), + ('args', '0.1.0', { + 'checksums': ['a785b8d837625e9b61c39108532d95b85274acd679693b71ebb5156848fcf814'], + }), + ('clint', '0.5.1', { + 'checksums': ['05224c32b1075563d0b16d0015faaf9da43aa214e4a2140e51f08789e7a4c5aa'], + }), + ('pynetbox', '7.4.0', { + 'checksums': ['fd0b1f197b3880048408ff5ed84422dd599bcd9389e32cb06a09b9b0d55c1636'], + }), + ('absl-py', '1.4.0', { + 'modulename': 'absl', + 'checksums': ['d2c244d01048ba476e7c080bd2c6df5e141d211de80223460d5b3b8a2a58433d'], + }), + ('aerleon', '1.9.0', { + 'checksums': ['850cd621dda750263db313d4473302b48b82adaaa9220e6fd0677cb7900f95f6'], + }), + ('homer', '0.7.0', { + 'checksums': ['efaf9b3948f6aecdf88cc87c0296a18aed77c152489a7f85c571965fb16f9e57'], + }), + ('pyDNase', '0.3.0', { + 'preinstallopts': local_pyDNase_preinstallopts, + 'modulename': 'pyDNase', + 'checksums': ['dba03cadca37929a1cc41545e962136f29efc41f8e3c6de042c51c47ee04d558'], + }), + (name, version, { + 'checksums': ['59610a8c57e9fc525ec5d13b69efc8b513c78a85a595e0e2b0138da62a035978'], + }), +] + +use_pip = True +sanity_pip_check = True + +sanity_check_commands = ["dictys --help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/d/dill/dill-0.3.8-GCCcore-13.2.0.eb b/easybuild/easyconfigs/d/dill/dill-0.3.8-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..0cc0fb8820c --- /dev/null +++ b/easybuild/easyconfigs/d/dill/dill-0.3.8-GCCcore-13.2.0.eb @@ -0,0 +1,27 @@ +# This easyconfig was created by Simon Branford of the BEAR Software team at the University of Birmingham. +easyblock = 'PythonPackage' + +name = 'dill' +version = '0.3.8' + +homepage = 'https://pypi.org/project/dill/' +description = """dill extends python's pickle module for serializing and de-serializing python objects to the majority + of the built-in python types. Serialization is the process of converting an object to a byte stream, and the inverse + of which is converting a byte stream back to on python object hierarchy.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['3ebe3c479ad625c4553aca177444d89b486b1d84982eeacded644afc0cf797ca'] + +builddependencies = [('binutils', '2.40')] + +dependencies = [ + ('Python', '3.11.5'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/d/dlib/dlib-19.24.6-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/d/dlib/dlib-19.24.6-foss-2023a-CUDA-12.1.1.eb new file mode 100644 index 00000000000..c3ffb7be647 --- /dev/null +++ b/easybuild/easyconfigs/d/dlib/dlib-19.24.6-foss-2023a-CUDA-12.1.1.eb @@ -0,0 +1,50 @@ +easyblock = 'PythonPackage' + +name = 'dlib' +version = '19.24.6' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/davisking/dlib' +description = """Dlib is a modern C++ toolkit containing machine learning +algorithms and tools for creating complex software in C++ to solve real world +problems. It is used in both industry and academia in a wide range of domains +including robotics, embedded devices, mobile phones, and large high performance +computing environments.""" + +# dlib can use BLAS/LAPACK, so using full toolchain +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'pic': True} + +sources = [SOURCE_TAR_GZ] +patches = ['dlib-19.24.6_FlexiBLAS.patch'] +checksums = [ + {'dlib-19.24.6.tar.gz': '77e3c28ac2c66141514b07cbb74b7c7f80381c019ce5fec99007980bc6490d7d'}, + {'dlib-19.24.6_FlexiBLAS.patch': '47fb348d5f1cd064a135d33cf49fdef56ade24a64218311743076cb6b313738b'}, +] + +builddependencies = [ + ('CMake', '3.26.3'), + ('pkgconf', '1.9.5'), +] +dependencies = [ + ('CUDA', '12.1.1', '', SYSTEM), + ('cuDNN', '8.9.2.26', versionsuffix, SYSTEM), + ('Python', '3.11.3'), + ('libjxl', '0.8.2'), + ('X11', '20230603'), +] + +download_dep_fail = True +use_pip = True + +preinstallopts = "export CMAKE_BUILD_PARALLEL_LEVEL=%(parallel)s && " +preinstallopts += "sed -i 's/BLAS_REFERENCE cblas/BLAS_REFERENCE flexiblas/g' dlib/cmake_utils/find_blas.cmake && " + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_pip_check = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/d/dlib/dlib-19.24.6_FlexiBLAS.patch b/easybuild/easyconfigs/d/dlib/dlib-19.24.6_FlexiBLAS.patch new file mode 100644 index 00000000000..bb12f35adbc --- /dev/null +++ b/easybuild/easyconfigs/d/dlib/dlib-19.24.6_FlexiBLAS.patch @@ -0,0 +1,25 @@ +use FlexiBLAS as BLAS/LAPACK library +author: Kenneth Hoste (HPC-UGent) +diff -ru dlib-19.24.6.orig/dlib/cmake_utils/find_blas.cmake dlib-19.24.6/dlib/cmake_utils/find_blas.cmake +--- dlib-19.24.6.orig/dlib/cmake_utils/find_blas.cmake 2024-02-18 14:43:31.000000000 +0100 ++++ dlib-19.24.6/dlib/cmake_utils/find_blas.cmake 2024-09-20 20:35:35.927348475 +0200 +@@ -66,17 +66,15 @@ + + # First, search for libraries via pkg-config, which is the cleanest path + find_package(PkgConfig) +- pkg_check_modules(BLAS_REFERENCE cblas) +- pkg_check_modules(LAPACK_REFERENCE lapack) ++ pkg_check_modules(BLAS_REFERENCE flexiblas) + # Make sure the cblas found by pkgconfig actually has cblas symbols. + SET(CMAKE_REQUIRED_LIBRARIES "${BLAS_REFERENCE_LDFLAGS}") + CHECK_FUNCTION_EXISTS(cblas_ddot PKGCFG_HAVE_CBLAS) + if (BLAS_REFERENCE_FOUND AND LAPACK_REFERENCE_FOUND AND PKGCFG_HAVE_CBLAS) + set(blas_libraries "${BLAS_REFERENCE_LDFLAGS}") +- set(lapack_libraries "${LAPACK_REFERENCE_LDFLAGS}") + set(blas_found 1) + set(lapack_found 1) +- set(REQUIRES_LIBS "${REQUIRES_LIBS} cblas lapack") ++ set(REQUIRES_LIBS "${REQUIRES_LIBS} flexiblas") + message(STATUS "Found BLAS and LAPACK via pkg-config") + return() + endif() diff --git a/easybuild/easyconfigs/d/dm-haiku/dm-haiku-0.0.12-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/d/dm-haiku/dm-haiku-0.0.12-foss-2023a-CUDA-12.1.1.eb new file mode 100644 index 00000000000..f66f10ec557 --- /dev/null +++ b/easybuild/easyconfigs/d/dm-haiku/dm-haiku-0.0.12-foss-2023a-CUDA-12.1.1.eb @@ -0,0 +1,50 @@ +# update 0.0.12: Thomas Hoffmann (EMBL) +easyblock = 'PythonBundle' + +name = 'dm-haiku' +version = '0.0.12' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/deepmind/dm-haiku' +description = """Haiku is a simple neural network library for JAX developed by some of the authors of Sonnet, a neural +network library for TensorFlow.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('jax', '0.4.25', versionsuffix), # required by jmp, also provides absl-py + ('PyYAML', '6.0'), + ('CUDA', '12.1.1', '', SYSTEM), + ('tensorstore', '0.1.65'), + ('protobuf-python', '4.24.0'), + ('Optax', '0.2.2', versionsuffix), +] + +use_pip = True + +exts_list = [ + ('jmp', '0.0.4', { + 'checksums': ['5dfeb0fd7c7a9f72a70fff0aab9d0cbfae32a809c02f4037ff3485ceb33e1730'], + }), + ('flax', '0.8.4', { + 'checksums': ['968683f850198e1aa5eb2d9d1e20bead880ef7423c14f042db9d60848cb1c90b'], + }), + ('nest_asyncio', '1.6.0', { + 'checksums': ['6f172d5449aca15afd6c646851f4e31e02c598d553a667e38cafa997cfec55fe'], + }), + ('orbax_checkpoint', '0.5.18', { + 'modulename': 'orbax.checkpoint', + 'preinstallopts': """sed -i 's/jax >= 0.4.25/&\\*/g' pyproject.toml &&""", + 'checksums': ['29f5d311b412760bd6a2fecab3bdbf75407bc00dc6d0457d19478258ecc8fa6d'], + }), + (name, version, { + 'modulename': 'haiku', + 'checksums': ['ba0b3acf71433156737fe342c486da11727e5e6c9e054245f4f9b8f0b53eb608'], + }), +] + +sanity_pip_check = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/d/dm-haiku/dm-haiku-0.0.13-foss-2023a.eb b/easybuild/easyconfigs/d/dm-haiku/dm-haiku-0.0.13-foss-2023a.eb new file mode 100644 index 00000000000..532f9092e79 --- /dev/null +++ b/easybuild/easyconfigs/d/dm-haiku/dm-haiku-0.0.13-foss-2023a.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonBundle' + +name = 'dm-haiku' +version = '0.0.13' + +homepage = 'https://github.com/deepmind/dm-haiku' +description = """Haiku is a simple neural network library for JAX developed by some of the authors of Sonnet, a neural +network library for TensorFlow.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('jax', '0.4.25'), # required by jmp, also provides absl-py +] + +use_pip = True + +exts_list = [ + ('jmp', '0.0.4', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['6aa7adbddf2bd574b28c7faf6e81a735eb11f53386447896909c6968dc36807d'], + }), + ('dm_haiku', version, { + 'modulename': 'haiku', + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['ee9562c68a059f146ad07f555ca591cb8c11ef751afecc38353863562bd23f43'], + }), +] + +sanity_pip_check = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/d/dorado/dorado-0.6.1-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/d/dorado/dorado-0.6.1-foss-2023a-CUDA-12.1.1.eb new file mode 100644 index 00000000000..378a9deec6b --- /dev/null +++ b/easybuild/easyconfigs/d/dorado/dorado-0.6.1-foss-2023a-CUDA-12.1.1.eb @@ -0,0 +1,97 @@ +easyblock = 'CMakeMake' + +name = 'dorado' +version = '0.6.1' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/nanoporetech/dorado' +description = """Dorado is a high-performance, easy-to-use, open source basecaller for Oxford Nanopore reads.""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://github.com/nanoporetech/dorado/archive/'] +sources = [{ + 'git_config': { + 'url': 'https://github.com/nanoporetech', + 'repo_name': name, + 'tag': 'v%(version)s', + 'recursive': True, + }, + 'filename': SOURCE_TAR_GZ, +}] +patches = ['dorado-0.6.1_include-fstream.patch'] +checksums = [ + None, + 'a7692a2d67422d808b3b81f3a297b7b89299ab0091e5d01f0b8a9aee9b942377', +] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.26.3'), + ('patchelf', '0.18.0'), +] + +dependencies = [ + ('CUDA', '12.1.1', '', SYSTEM), + ('OpenSSL', '1.1', '', SYSTEM), + ('PyTorch', '2.1.2', '-CUDA-%(cudaver)s'), + ('HDF5', '1.14.0'), + ('zstd', '1.5.5'), + ('HTSlib', '1.18'), + ('kineto', '0.4.0'), + ('libaec', '1.0.6'), +] + +# don't link to OpenSSL static libraries +# fix for CMake Error "missing: OPENSSL_CRYPTO_LIBRARY" (if only shared OpenSSL libraries are available) +preconfigopts = "sed -i '/OPENSSL_USE_STATIC_LIBS TRUE/d' ../dorado/cmake/OpenSSL.cmake && " +preconfigopts += "export OPENSSL_ROOT_DIR=$EBROOTOPENSSL && " +# link in the ssl and crypto libs, to fix: +# undefined reference to symbol 'SSL_get_peer_certificate@@OPENSSL_1_1_0' +preconfigopts += "sed -i 's/OpenSSL::SSL/ssl\\n crypto/g' ../dorado/dorado/utils/CMakeLists.txt && " + +# don't use vendored HTSlib, use provided HTSlib dependency +preconfigopts += "rm -r ../dorado/dorado/3rdparty/htslib/ && " +preconfigopts += "sed -i '/add_dependencies.*htslib_project/d' ../dorado/CMakeLists.txt && " +preconfigopts += "sed -i '/add_dependencies.*htslib_project/d' ../dorado/dorado/utils/CMakeLists.txt && " +preconfigopts += "sed -i '/Htslib.cmake/d' ../dorado/CMakeLists.txt && " +# link with -lhts, not -lhtslib +preconfigopts += "sed -i 's/htslib/hts/g' ../dorado/CMakeLists.txt && " +preconfigopts += "sed -i 's/htslib/hts/g' ../dorado/dorado/utils/CMakeLists.txt && " + +# disable treating warnings like errors by stripping out -Werror +# cfr. https://github.com/nanoporetech/dorado/issues/779 +preconfigopts += "sed -i 's/-Werror//g' ../dorado/cmake/Warnings.cmake && " + +configopts = "-DDORADO_INSTALL_PATH=%(installdir)s " +configopts += "-DCUDA_TOOLKIT_ROOT_DIR=$EBROOTCUDA -DCMAKE_CUDA_COMPILER=$EBROOTCUDA/bin/nvcc " +configopts += "-DDORADO_LIBTORCH_DIR=$EBROOTPYTORCH/lib " +# add -pthread flag (in addition to -lpthread) to avoid linking error: +# in function `_GLOBAL__sub_I_mutex.cc': mutex.cc:(.text.startup+0x17): undefined reference to `pthread_atfork' +configopts += '-DCMAKE_C_FLAGS="$CFLAGS -pthread" ' + +# disable CMake fiddling with RPATH when EasyBuild is configured to use RPATH linking +configopts += "$(if %(rpath_enabled)s; then " +configopts += "echo '-DCMAKE_SKIP_INSTALL_RPATH=YES -DCMAKE_SKIP_RPATH=YES'; fi) " + +# CUDA libraries that are copied to installdir need to be patched to have an RPATH section +# when EasyBuild is configured to use RPATH linking (required to pass RPATH sanity check); +# by default, CMake sets RUNPATH to '$ORIGIN' rather than RPATH (but that's disabled above) +postinstallcmds = [ + "if %(rpath_enabled)s; then " + " for lib in $(ls %(installdir)s/lib/lib{cu,nv}*.so*); do " + " echo setting RPATH in $lib;" + " patchelf --force-rpath --set-rpath '$ORIGIN' $lib;" + " done;" + "fi", +] + +sanity_check_paths = { + 'files': ['bin/dorado'], + 'dirs': [], +} + +sanity_check_commands = ["dorado basecaller --help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/d/dorado/dorado-0.6.1_include-fstream.patch b/easybuild/easyconfigs/d/dorado/dorado-0.6.1_include-fstream.patch new file mode 100644 index 00000000000..c1165f3fe5c --- /dev/null +++ b/easybuild/easyconfigs/d/dorado/dorado-0.6.1_include-fstream.patch @@ -0,0 +1,27 @@ +add missing include to fix compiler errors like: + + error: variable std::ofstream summary_out has initializer but incomplete type + +see also https://github.com/nanoporetech/dorado/pull/780 + +author: Kenneth Hoste (HPC-UGent) +--- dorado/dorado/cli/duplex.cpp.orig 2024-04-30 17:59:15.483935823 +0200 ++++ dorado/dorado/cli/duplex.cpp 2024-04-30 17:59:34.658694274 +0200 +@@ -39,6 +39,7 @@ + #include + #include + #include ++#include + #include + #include + #include +--- dorado/dorado/cli/demux.cpp.orig 2024-04-30 18:13:40.327122548 +0200 ++++ dorado/dorado/cli/demux.cpp 2024-04-30 18:15:37.576760942 +0200 +@@ -17,6 +17,7 @@ + #include + + #include ++#include + #include + #include + #include diff --git a/easybuild/easyconfigs/d/dorado/dorado-0.7.3-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/d/dorado/dorado-0.7.3-foss-2023a-CUDA-12.1.1.eb new file mode 100644 index 00000000000..9927f0492b4 --- /dev/null +++ b/easybuild/easyconfigs/d/dorado/dorado-0.7.3-foss-2023a-CUDA-12.1.1.eb @@ -0,0 +1,106 @@ +easyblock = 'CMakeMake' + +name = 'dorado' +version = '0.7.3' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/nanoporetech/dorado' +description = """Dorado is a high-performance, easy-to-use, open source basecaller for Oxford Nanopore reads.""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://github.com/nanoporetech/dorado/archive/'] +sources = [{ + 'git_config': { + 'url': 'https://github.com/nanoporetech', + 'repo_name': name, + 'tag': 'v%(version)s', + 'recursive': True, + }, + 'filename': SOURCE_TAR_GZ, +}] +patches = [ + '%(name)s-%(version)s_include-fstream.patch', + '%(name)s-%(version)s_dont_install_external_libraries.patch', +] + +checksums = [ + None, + 'a32cbd34185bcc5ae3d552a072e396825aa7184187cd11c70a4380618387a530', + '2a250d606c0ae17f47d99981309fa204a1394ddd81851a1d530dcd0aea2306ac', +] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.26.3'), + ('patchelf', '0.18.0'), +] + +dependencies = [ + ('CUDA', '12.1.1', '', SYSTEM), + ('OpenSSL', '1.1', '', SYSTEM), + ('PyTorch', '2.1.2', '-CUDA-%(cudaver)s'), + ('HDF5', '1.14.0'), + ('zstd', '1.5.5'), + ('HTSlib', '1.18'), + ('kineto', '0.4.0'), + ('libaec', '1.0.6'), +] + +# don't link to OpenSSL static libraries +# fix for CMake Error "missing: OPENSSL_CRYPTO_LIBRARY" (if only shared OpenSSL libraries are available) +preconfigopts = "sed -i '/OPENSSL_USE_STATIC_LIBS TRUE/d' ../dorado/cmake/OpenSSL.cmake && " +# link in the ssl and crypto libs, to fix: +# undefined reference to symbol 'SSL_get_peer_certificate@@OPENSSL_1_1_0' +preconfigopts += "sed -i 's/OpenSSL::SSL/ssl\\n crypto/g' ../dorado/dorado/utils/CMakeLists.txt && " + +# don't use vendored HTSlib, use provided HTSlib dependency +preconfigopts += "rm -r ../dorado/dorado/3rdparty/htslib/ && " +preconfigopts += "sed -i '/add_dependencies.*htslib_project/d' ../dorado/CMakeLists.txt && " +preconfigopts += "sed -i '/add_dependencies.*htslib_project/d' ../dorado/dorado/utils/CMakeLists.txt && " +preconfigopts += "sed -i '/Htslib.cmake/d' ../dorado/CMakeLists.txt && " +# link with -lhts, not -lhtslib +preconfigopts += "sed -i 's/htslib/hts/g' ../dorado/CMakeLists.txt && " +preconfigopts += "sed -i 's/htslib/hts/g' ../dorado/dorado/utils/CMakeLists.txt && " + +# disable treating warnings like errors by stripping out -Werror +# cfr. https://github.com/nanoporetech/dorado/issues/779 +preconfigopts += "sed -i 's/-Werror//g' ../dorado/cmake/Warnings.cmake && " + +_copts = [ + "-DCUDA_TOOLKIT_ROOT_DIR=$EBROOTCUDA", + "-DCMAKE_CUDA_COMPILER=$EBROOTCUDA/bin/nvcc", + '-DOPENSSL_ROOT_DIR=$EBROOTOPENSSL', + "-DDORADO_LIBTORCH_DIR=$EBROOTPYTORCH/lib", + # add -pthread flag (in addition to -lpthread) to avoid linking error: + # in function `_GLOBAL__sub_I_mutex.cc': mutex.cc:(.text.startup+0x17): undefined reference to `pthread_atfork' + '-DCMAKE_C_FLAGS="$CFLAGS -pthread"', +] + +configopts = ' '.join(_copts) + ' ' + +# disable CMake fiddling with RPATH when EasyBuild is configured to use RPATH linking +configopts += "$(if %(rpath_enabled)s; then " +configopts += "echo '-DCMAKE_SKIP_INSTALL_RPATH=YES -DCMAKE_SKIP_RPATH=YES'; fi) " + +# CUDA libraries that are copied to installdir need to be patched to have an RPATH section +# when EasyBuild is configured to use RPATH linking (required to pass RPATH sanity check); +# by default, CMake sets RUNPATH to '$ORIGIN' rather than RPATH (but that's disabled above) +postinstallcmds = [ + "if %(rpath_enabled)s; then " + " for lib in $(ls %(installdir)s/lib/lib{cu,nv}*.so*); do " + " echo setting RPATH in $lib;" + " patchelf --force-rpath --set-rpath '$ORIGIN' $lib;" + " done;" + "fi", +] + +sanity_check_paths = { + 'files': ['bin/dorado'], + 'dirs': [], +} + +sanity_check_commands = ["dorado basecaller --help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/d/dorado/dorado-0.7.3_dont_install_external_libraries.patch b/easybuild/easyconfigs/d/dorado/dorado-0.7.3_dont_install_external_libraries.patch new file mode 100644 index 00000000000..67bd9efee78 --- /dev/null +++ b/easybuild/easyconfigs/d/dorado/dorado-0.7.3_dont_install_external_libraries.patch @@ -0,0 +1,54 @@ +Don't install external libraries in Dorado's lib directory. + +Åke Sandgren, 2024-09-02 +diff --git a/CMakeLists.txt b/CMakeLists.txt +index a84c7524..0791dda8 100755 +--- a/CMakeLists.txt ++++ b/CMakeLists.txt +@@ -431,7 +431,7 @@ if(CMAKE_SYSTEM_NAME STREQUAL "Linux") + else() + # bundle the libraries from the cuda toolkit + file(GLOB NATIVE_CUDA_LIBS "${CUDAToolkit_TARGET_DIR}/targets/${CMAKE_SYSTEM_PROCESSOR}-linux/lib/${LIB}") +- install(FILES ${NATIVE_CUDA_LIBS} DESTINATION lib COMPONENT redist_libs) ++ #install(FILES ${NATIVE_CUDA_LIBS} DESTINATION lib COMPONENT redist_libs) + endif() + endforeach() + +@@ -444,14 +444,14 @@ if(CMAKE_SYSTEM_NAME STREQUAL "Linux") + RESOLVE_SYMLINKS("${DEBUG_LIBRARIES}" NEW_HDF_DEBUG_LIBRARIES) + foreach(HDF_LIB IN LISTS NEW_HDF_DEBUG_LIBRARIES) + if(${HDF_LIB} MATCHES "hdf5") +- install(FILES ${HDF_LIB} DESTINATION lib COMPONENT redist_libs CONFIGURATIONS Debug) ++ #install(FILES ${HDF_LIB} DESTINATION lib COMPONENT redist_libs CONFIGURATIONS Debug) + endif() + endforeach() + FILTER_LIST("${HDF5_C_LIBRARIES}" RELEASE_LIBRARIES optimized debug ${SHARED_LIB_EXT}) + RESOLVE_SYMLINKS("${RELEASE_LIBRARIES}" NEW_HDF_RELEASE_LIBRARIES) + foreach(HDF_LIB IN LISTS NEW_HDF_RELEASE_LIBRARIES) + if(${HDF_LIB} MATCHES "hdf5") +- install(FILES ${HDF_LIB} DESTINATION lib COMPONENT redist_libs CONFIGURATIONS Release ReleaseWithDebInfo) ++ #install(FILES ${HDF_LIB} DESTINATION lib COMPONENT redist_libs CONFIGURATIONS Release ReleaseWithDebInfo) + endif() + endforeach() + endif() +@@ -459,17 +459,17 @@ if(CMAKE_SYSTEM_NAME STREQUAL "Linux") + find_library(SZ_DLL sz REQUIRED) + get_filename_component(SZ_DLL_PATH ${SZ_DLL} DIRECTORY) + file(GLOB SZ_DLLS "${SZ_DLL_PATH}/libsz.so*") +- install(FILES ${SZ_DLLS} DESTINATION lib COMPONENT redist_libs) ++ #install(FILES ${SZ_DLLS} DESTINATION lib COMPONENT redist_libs) + + find_library(AEC_DLL aec REQUIRED) + get_filename_component(AEC_DLL_PATH ${AEC_DLL} DIRECTORY) + file(GLOB AEC_DLLS "${AEC_DLL_PATH}/libaec.so*") +- install(FILES ${AEC_DLLS} DESTINATION lib COMPONENT redist_libs) ++ #install(FILES ${AEC_DLLS} DESTINATION lib COMPONENT redist_libs) + + # If zstd has been dynamically linked, add the .so to the package + get_filename_component(ZSTD_LIBRARY_PATH ${ZSTD_LIBRARY_RELEASE} DIRECTORY) + file(GLOB ZSTD_DLLS "${ZSTD_LIBRARY_PATH}/*zstd.so*") +- install(FILES ${ZSTD_DLLS} DESTINATION lib COMPONENT redist_libs) ++ #install(FILES ${ZSTD_DLLS} DESTINATION lib COMPONENT redist_libs) + + elseif(WIN32) + file(GLOB TORCH_DLLS "${TORCH_LIB}/lib/*.dll") diff --git a/easybuild/easyconfigs/d/dorado/dorado-0.7.3_include-fstream.patch b/easybuild/easyconfigs/d/dorado/dorado-0.7.3_include-fstream.patch new file mode 100644 index 00000000000..bf8d2346e5d --- /dev/null +++ b/easybuild/easyconfigs/d/dorado/dorado-0.7.3_include-fstream.patch @@ -0,0 +1,27 @@ +add missing include to fix compiler errors like: + + error: variable std::ofstream summary_out has initializer but incomplete type + +see also https://github.com/nanoporetech/dorado/pull/780 + +author: Kenneth Hoste (HPC-UGent) +--- dorado/dorado/cli/duplex.cpp.orig 2024-04-30 17:59:15.483935823 +0200 ++++ dorado/dorado/cli/duplex.cpp 2024-04-30 17:59:34.658694274 +0200 +@@ -39,6 +39,7 @@ + #include + #include + #include ++#include + #include + #include + #include +--- dorado/dorado/cli/demux.cpp.orig 2024-04-30 18:13:40.327122548 +0200 ++++ dorado/dorado/cli/demux.cpp 2024-04-30 18:15:37.576760942 +0200 +@@ -17,6 +17,7 @@ + #include + + #include ++#include + #include + #include + #include \ No newline at end of file diff --git a/easybuild/easyconfigs/d/dorado/dorado-0.8.0-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/d/dorado/dorado-0.8.0-foss-2023a-CUDA-12.1.1.eb new file mode 100644 index 00000000000..778c00e0d6e --- /dev/null +++ b/easybuild/easyconfigs/d/dorado/dorado-0.8.0-foss-2023a-CUDA-12.1.1.eb @@ -0,0 +1,105 @@ +easyblock = 'CMakeMake' + +name = 'dorado' +version = '0.8.0' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/nanoporetech/dorado' +description = """Dorado is a high-performance, easy-to-use, open source basecaller for Oxford Nanopore reads.""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://github.com/nanoporetech/dorado/archive/'] +sources = [{ + 'git_config': { + 'url': 'https://github.com/nanoporetech', + 'repo_name': name, + 'tag': 'v%(version)s', + 'recursive': True, + }, + 'filename': SOURCE_TAR_GZ, +}] +patches = [ + '%(name)s-%(version)s_dont_install_external_libraries.patch', +] + +checksums = [ + None, + '28942b7057af00c574a5e70d33a58b4036fd09ae0b041f45b67581c8dda832b1', +] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.26.3'), + ('patchelf', '0.18.0'), +] + +dependencies = [ + ('CUDA', '12.1.1', '', SYSTEM), + ('OpenSSL', '1.1', '', SYSTEM), + ('PyTorch', '2.1.2', '-CUDA-%(cudaver)s'), + ('HDF5', '1.14.0'), + ('zstd', '1.5.5'), + ('HTSlib', '1.18'), + ('kineto', '0.4.0'), + ('libaec', '1.0.6'), +] + +# don't link to OpenSSL static libraries +# fix for CMake Error "missing: OPENSSL_CRYPTO_LIBRARY" (if only shared OpenSSL libraries are available) +preconfigopts = "sed -i '/OPENSSL_USE_STATIC_LIBS TRUE/d' ../dorado/cmake/OpenSSL.cmake && " +# link in the ssl and crypto libs, to fix: +# undefined reference to symbol 'SSL_get_peer_certificate@@OPENSSL_1_1_0' +preconfigopts += "sed -i 's/OpenSSL::SSL/ssl\\n crypto/g' ../dorado/dorado/utils/CMakeLists.txt && " + +# don't use vendored HTSlib, use provided HTSlib dependency +preconfigopts += "rm -r ../dorado/dorado/3rdparty/htslib/ && " +preconfigopts += "sed -i '/add_dependencies.*htslib_project/d' ../dorado/CMakeLists.txt && " +preconfigopts += "sed -i '/add_dependencies.*htslib_project/d' ../dorado/dorado/utils/CMakeLists.txt && " +preconfigopts += "sed -i '/Htslib.cmake/d' ../dorado/CMakeLists.txt && " +# link with -lhts, not -lhtslib +preconfigopts += "sed -i 's/htslib/hts/g' ../dorado/CMakeLists.txt && " +preconfigopts += "sed -i 's/htslib/hts/g' ../dorado/dorado/utils/CMakeLists.txt && " +preconfigopts += "sed -i 's/htslib/hts/g' ../dorado/dorado/torch_utils/CMakeLists.txt && " + +# disable treating warnings like errors by stripping out -Werror +# cfr. https://github.com/nanoporetech/dorado/issues/779 +preconfigopts += "sed -i 's/-Werror//g' ../dorado/cmake/Warnings.cmake && " + +_copts = [ + "-DCUDA_TOOLKIT_ROOT_DIR=$EBROOTCUDA", + "-DCMAKE_CUDA_COMPILER=$EBROOTCUDA/bin/nvcc", + '-DOPENSSL_ROOT_DIR=$EBROOTOPENSSL', + "-DDORADO_LIBTORCH_DIR=$EBROOTPYTORCH/lib", + # add -pthread flag (in addition to -lpthread) to avoid linking error: + # in function `_GLOBAL__sub_I_mutex.cc': mutex.cc:(.text.startup+0x17): undefined reference to `pthread_atfork' + '-DCMAKE_C_FLAGS="$CFLAGS -pthread"', +] + +configopts = ' '.join(_copts) + ' ' + +# disable CMake fiddling with RPATH when EasyBuild is configured to use RPATH linking +configopts += "$(if %(rpath_enabled)s; then " +configopts += "echo '-DCMAKE_SKIP_INSTALL_RPATH=YES -DCMAKE_SKIP_RPATH=YES'; fi) " + +# CUDA libraries that are copied to installdir need to be patched to have an RPATH section +# when EasyBuild is configured to use RPATH linking (required to pass RPATH sanity check); +# by default, CMake sets RUNPATH to '$ORIGIN' rather than RPATH (but that's disabled above) +postinstallcmds = [ + "if %(rpath_enabled)s; then " + " for lib in $(ls %(installdir)s/lib/lib{cu,nv}*.so*); do " + " echo setting RPATH in $lib;" + " patchelf --force-rpath --set-rpath '$ORIGIN' $lib;" + " done;" + "fi", +] + +sanity_check_paths = { + 'files': ['bin/dorado'], + 'dirs': [], +} + +sanity_check_commands = ["dorado basecaller --help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/d/dorado/dorado-0.8.0_dont_install_external_libraries.patch b/easybuild/easyconfigs/d/dorado/dorado-0.8.0_dont_install_external_libraries.patch new file mode 100644 index 00000000000..cd205c1cbb7 --- /dev/null +++ b/easybuild/easyconfigs/d/dorado/dorado-0.8.0_dont_install_external_libraries.patch @@ -0,0 +1,51 @@ +Don't install external libraries in Dorado's lib directory. +Simon Branford (University of Birmingham) +--- cmake/InstallRedistLibs.cmake.orig 2024-09-27 13:43:56.612497000 +0100 ++++ cmake/InstallRedistLibs.cmake 2024-09-27 13:44:31.683753000 +0100 +@@ -46,7 +46,7 @@ + else() + # bundle the libraries from the cuda toolkit + file(GLOB NATIVE_CUDA_LIBS "${CUDAToolkit_TARGET_DIR}/targets/${CMAKE_SYSTEM_PROCESSOR}-linux/lib/${LIB}") +- install(FILES ${NATIVE_CUDA_LIBS} DESTINATION lib COMPONENT redist_libs) ++ #install(FILES ${NATIVE_CUDA_LIBS} DESTINATION lib COMPONENT redist_libs) + endif() + endforeach() + +@@ -59,14 +59,14 @@ + RESOLVE_SYMLINKS("${DEBUG_LIBRARIES}" NEW_HDF_DEBUG_LIBRARIES) + foreach(HDF_LIB IN LISTS NEW_HDF_DEBUG_LIBRARIES) + if(${HDF_LIB} MATCHES "hdf5") +- install(FILES ${HDF_LIB} DESTINATION lib COMPONENT redist_libs CONFIGURATIONS Debug) ++ #install(FILES ${HDF_LIB} DESTINATION lib COMPONENT redist_libs CONFIGURATIONS Debug) + endif() + endforeach() + FILTER_LIST("${HDF5_C_LIBRARIES}" RELEASE_LIBRARIES optimized debug ${SHARED_LIB_EXT}) + RESOLVE_SYMLINKS("${RELEASE_LIBRARIES}" NEW_HDF_RELEASE_LIBRARIES) + foreach(HDF_LIB IN LISTS NEW_HDF_RELEASE_LIBRARIES) + if(${HDF_LIB} MATCHES "hdf5") +- install(FILES ${HDF_LIB} DESTINATION lib COMPONENT redist_libs CONFIGURATIONS Release ReleaseWithDebInfo) ++ #install(FILES ${HDF_LIB} DESTINATION lib COMPONENT redist_libs CONFIGURATIONS Release ReleaseWithDebInfo) + endif() + endforeach() + endif() +@@ -74,17 +74,17 @@ + find_library(SZ_DLL sz REQUIRED) + get_filename_component(SZ_DLL_PATH ${SZ_DLL} DIRECTORY) + file(GLOB SZ_DLLS "${SZ_DLL_PATH}/libsz.so*") +- install(FILES ${SZ_DLLS} DESTINATION lib COMPONENT redist_libs) ++ #install(FILES ${SZ_DLLS} DESTINATION lib COMPONENT redist_libs) + + find_library(AEC_DLL aec REQUIRED) + get_filename_component(AEC_DLL_PATH ${AEC_DLL} DIRECTORY) + file(GLOB AEC_DLLS "${AEC_DLL_PATH}/libaec.so*") +- install(FILES ${AEC_DLLS} DESTINATION lib COMPONENT redist_libs) ++ #install(FILES ${AEC_DLLS} DESTINATION lib COMPONENT redist_libs) + + # If zstd has been dynamically linked, add the .so to the package + get_filename_component(ZSTD_LIBRARY_PATH ${ZSTD_LIBRARY_RELEASE} DIRECTORY) + file(GLOB ZSTD_DLLS "${ZSTD_LIBRARY_PATH}/*zstd.so*") +- install(FILES ${ZSTD_DLLS} DESTINATION lib COMPONENT redist_libs) ++ #install(FILES ${ZSTD_DLLS} DESTINATION lib COMPONENT redist_libs) + + elseif(WIN32) + file(GLOB TORCH_DLLS "${TORCH_LIB}/lib/*.dll") diff --git a/easybuild/easyconfigs/d/double-conversion/double-conversion-3.3.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/d/double-conversion/double-conversion-3.3.0-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..c4b5780f6ee --- /dev/null +++ b/easybuild/easyconfigs/d/double-conversion/double-conversion-3.3.0-GCCcore-13.3.0.eb @@ -0,0 +1,36 @@ + +easyblock = 'CMakeMake' + +name = 'double-conversion' +version = '3.3.0' + +homepage = 'https://github.com/google/double-conversion' +description = "Efficient binary-decimal and decimal-binary conversion routines for IEEE doubles." + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://github.com/google/%(name)s/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['04ec44461850abbf33824da84978043b22554896b552c5fd11a9c5ae4b4d296e'] + +builddependencies = [ + ('binutils', '2.42'), + ('CMake', '3.29.3'), +] + +# Build static lib, static lib with -fPIC and shared lib +configopts = [ + '', + "-DCMAKE_POSITION_INDEPENDENT_CODE=ON -DCMAKE_STATIC_LIBRARY_SUFFIX_CXX=_pic.a", + '-DBUILD_SHARED_LIBS=ON', +] + + +sanity_check_paths = { + 'files': ['include/double-conversion/%s.h' % h for h in ['bignum', 'cached-powers', 'diy-fp', 'double-conversion', + 'fast-dtoa', 'fixed-dtoa', 'ieee', 'strtod', 'utils']] + + ['lib/libdouble-conversion.%s' % e for e in ['a', SHLIB_EXT]] + ['lib/libdouble-conversion_pic.a'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/d/dtcmp/dtcmp-1.1.5-gompi-2024a.eb b/easybuild/easyconfigs/d/dtcmp/dtcmp-1.1.5-gompi-2024a.eb new file mode 100644 index 00000000000..5143b629849 --- /dev/null +++ b/easybuild/easyconfigs/d/dtcmp/dtcmp-1.1.5-gompi-2024a.eb @@ -0,0 +1,39 @@ +# +# Author: Robert Mijakovic +# +easyblock = 'ConfigureMake' + +name = 'dtcmp' +version = '1.1.5' + +homepage = 'https://github.com/LLNL/dtcmp' +description = """The Datatype Comparison (DTCMP) Library provides pre-defined and user-defined +comparison operations to compare the values of two items which can be arbitrary MPI datatypes. +Using these comparison operations, the library provides various routines for manipulating data, +which may be distributed over the processes of an MPI communicator.""" + +toolchain = {'name': 'gompi', 'version': '2024a'} + +github_account = 'LLNL' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['5c3d672fcf1be81e9afb65ef3f860a7dfe0f1bd79360ac63848acfe4d44439c9'] + +builddependencies = [ + ('Autotools', '20231222'), + ('pkgconf', '2.2.0'), +] + +dependencies = [ + ('lwgrp', '1.0.6'), +] + +preconfigopts = './autogen.sh && ' +configopts = '--with-lwgrp=$EBROOTLWGRP' + +sanity_check_paths = { + 'files': ['include/%(name)s.h', 'lib/lib%%(name)s.%s' % SHLIB_EXT, 'share/%(name)s/README.md'], + 'dirs': [] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/d/dub/dub-1.38.1-GCCcore-13.2.0.eb b/easybuild/easyconfigs/d/dub/dub-1.38.1-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..cfd077260fb --- /dev/null +++ b/easybuild/easyconfigs/d/dub/dub-1.38.1-GCCcore-13.2.0.eb @@ -0,0 +1,31 @@ +easyblock = 'CmdCp' + +name = 'dub' +version = '1.38.1' + +homepage = 'https://github.com/dlang/dub' +description = "Package and build manager for D applications and libraries" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://github.com/dlang/dub/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['a7c9a2f819fdea7359f298cba76e81a24ca1536d756c3b4b98c2480463c37907'] + +builddependencies = [ + ('binutils', '2.40'), + ('LDC', '1.39.0'), +] + +cmds_map = [('.*', "ldmd2 -v -run build.d")] + +files_to_copy = [(['bin/dub'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/dub'], + 'dirs': [], +} + +sanity_check_commands = ["dub --help"] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/d/duplex-tools/duplex-tools-0.3.3-foss-2023a.eb b/easybuild/easyconfigs/d/duplex-tools/duplex-tools-0.3.3-foss-2023a.eb new file mode 100644 index 00000000000..fb67d050e02 --- /dev/null +++ b/easybuild/easyconfigs/d/duplex-tools/duplex-tools-0.3.3-foss-2023a.eb @@ -0,0 +1,68 @@ +# Author: Jasper Grimm (UoY) +# Updated: Petr Král, Pavel Tománek (INUITS) +easyblock = 'PythonBundle' + +name = 'duplex-tools' +version = '0.3.3' + +homepage = 'https://github.com/nanoporetech/duplex-tools' +description = """ +Duplex Tools contains a set of utilities for dealing with Duplex sequencing data. Tools are provided + to identify and prepare duplex pairs for basecalling by Dorado (recommended) and Guppy, and for + recovering simplex basecalls from incorrectly concatenated pairs. +""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +_minimap2_ver = '2.26' +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('matplotlib', '3.7.2'), + ('edlib', '1.3.9'), + ('minimap2', _minimap2_ver), + ('python-parasail', '1.3.4'), + ('Pysam', '0.22.0'), + ('tqdm', '4.66.1'), + ('Arrow', '14.0.1'), + ('h5py', '3.9.0'), + ('pod5-file-format', '0.3.10'), + ('parasail', '2.6.2'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('mappy', _minimap2_ver, { + 'checksums': ['e53fbe9a3ea8762a64b8103f4f779c9fb16d418eaa0a731f45cebc83867a9b71'], + }), + ('natsort', '8.4.0', { + 'checksums': ['45312c4a0e5507593da193dedd04abb1469253b601ecaf63445ad80f0a1ea581'], + }), + ('pyfastx', '2.0.1', { + # PYPI source tarball is incomplete, causes ImportErrors + # see https://github.com/lmdu/pyfastx/issues/60 + 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}], + 'source_urls': ['https://github.com/lmdu/%(name)s/archive'], + 'checksums': ['93aff63ce88bc5cfe7152d8dcb3f2164356bcd8f95a68fb20af107e59a7f9b55'], + }), + (name, version, { + 'sources': [{'download_filename': 'duplex_tools-%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}], + 'checksums': ['883e0a6610d14328a640b6a31eaef90592d2967cda68db0547a4d99924281300'], + }), +] + +_bins = ['dorado_stereo.sh', 'duplex_tools', 'minimap2.py', 'natsort', 'pyfastx'] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in _bins], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + 'dorado_stereo.sh -h', + 'duplex_tools --help', + 'pyfastx --help', +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/e/E-ANTIC/E-ANTIC-2.0.2-gfbf-2023b.eb b/easybuild/easyconfigs/e/E-ANTIC/E-ANTIC-2.0.2-gfbf-2023b.eb new file mode 100644 index 00000000000..fcb851f1091 --- /dev/null +++ b/easybuild/easyconfigs/e/E-ANTIC/E-ANTIC-2.0.2-gfbf-2023b.eb @@ -0,0 +1,38 @@ +easyblock = 'ConfigureMake' + +name = 'E-ANTIC' +version = '2.0.2' + +homepage = 'https://github.com/flatsurf/e-antic' +description = """E-ANTIC is a C/C++ library to deal with real embedded number fields built on +top of ANTIC (https://github.com/wbhart/antic). Its aim is to have as fast as +possible exact arithmetic operations and comparisons.""" + +toolchain = {'name': 'gfbf', 'version': '2023b'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/flatsurf/e-antic/releases/download/%(version)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['8328e6490129dfec7f4aa478ebd54dc07686bd5e5e7f5f30dcf20c0f11b67f60'] + +dependencies = [ + ('FLINT', '3.1.1'), + ('Boost', '1.83.0'), + ('Python', '3.11.5'), + ('cppyy', '3.1.2'), +] + +configopts = '--without-benchmark --without-byexample --without-pytest --without-doc' + +sanity_check_paths = { + 'files': ['lib/lib%s.%s' % (lib, ext) for lib in ['eantic', 'eanticxx'] for ext in ['a', SHLIB_EXT]] + + ['include/e-antic/%s.h' % h for h in ['e-antic', 'fmpq_poly_extra', 'renf', + 'renf_elem', 'renfxx']], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["python -c 'import pyeantic'"] + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/e/ECL/ECL-24.5.10-GCCcore-13.2.0.eb b/easybuild/easyconfigs/e/ECL/ECL-24.5.10-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..cb4390c3499 --- /dev/null +++ b/easybuild/easyconfigs/e/ECL/ECL-24.5.10-GCCcore-13.2.0.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'ECL' +version = '24.5.10' + +homepage = 'https://ecl.common-lisp.dev/' +description = """ECL (Embeddable Common-Lisp) is an interpreter of the Common-Lisp language + as described in the X3J13 Ansi specification, featuring CLOS (Common-Lisp Object System), + conditions, loops, etc, plus a translator to C, which can produce standalone executables.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://common-lisp.net/project/ecl/static/files/release'] +sources = [SOURCELOWER_TGZ] +checksums = ['e4ea65bb1861e0e495386bfa8bc673bd014e96d3cf9d91e9038f91435cbe622b'] + +builddependencies = [('binutils', '2.40')] + +dependencies = [ + ('GMP', '6.3.0'), +] + +configopts = "--enable-manual=no " + +sanity_check_paths = { + 'files': ['bin/ecl', 'bin/ecl-config', 'include/ecl/ecl.h', 'lib/libecl.%s' % SHLIB_EXT], + 'dirs': ['share'], +} + +sanity_check_commands = ["ecl --help"] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/e/EGA-QuickView/EGA-QuickView-20240620-GCC-12.3.0.eb b/easybuild/easyconfigs/e/EGA-QuickView/EGA-QuickView-20240620-GCC-12.3.0.eb new file mode 100644 index 00000000000..24e7302367a --- /dev/null +++ b/easybuild/easyconfigs/e/EGA-QuickView/EGA-QuickView-20240620-GCC-12.3.0.eb @@ -0,0 +1,43 @@ +easyblock = 'ConfigureMake' + +name = 'EGA-QuickView' +version = '20240620' +local_commit = 'fe2034d' + +homepage = 'https://github.com/EGA-archive/ega-quickview' +description = """EGA-QuickView is a FUSE file system to access EGA files remotely.""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +github_account = 'EGA-archive' +source_urls = [GITHUB_SOURCE] +sources = [{ + 'download_filename': '%s.tar.gz' % local_commit, + 'filename': '%(name)s-%(version)s.tar.gz', +}] +checksums = ['90836e42009736a8e20a2569918638f3cb2b53574265ca4f4bed7abd81a5e887'] + +builddependencies = [ + ('make', '4.4.1'), + ('Autotools', '20220317'), + ('pkgconf', '1.9.5'), +] + +dependencies = [ + ('libsodium', '1.0.18'), + ('FUSE', '3.16.2'), + ('GLib', '2.77.1'), +] + +preconfigopts = "autoreconf -i && " +# fix Makefile to create /bin in installdir +preinstallopts = "sed -i 's/install: $(TARGET)/install: $(TARGET) $(bindir)/' Makefile && " + +sanity_check_paths = { + 'files': ['bin/ega-qv'], + 'dirs': [], +} + +sanity_check_commands = ['ega-qv -h'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/e/ELPA/ELPA-2024.05.001-foss-2024a.eb b/easybuild/easyconfigs/e/ELPA/ELPA-2024.05.001-foss-2024a.eb new file mode 100644 index 00000000000..8dcbc6ed3f2 --- /dev/null +++ b/easybuild/easyconfigs/e/ELPA/ELPA-2024.05.001-foss-2024a.eb @@ -0,0 +1,46 @@ +# # +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Authors:: Inge Gutheil , Alan O'Cais +# License:: MIT/GPL +# +# # + +name = 'ELPA' +version = '2024.05.001' +local_version = version.replace('.', '_') + +homepage = 'https://elpa.mpcdf.mpg.de/' +description = "Eigenvalue SoLvers for Petaflop-Applications." + +toolchain = {'name': 'foss', 'version': '2024a'} +toolchainopts = {'openmp': True, 'usempi': True} + +source_urls = ['https://gitlab.mpcdf.mpg.de/elpa/elpa/-/archive/release_%s/' % local_version] +sources = ['{}-release_{}.tar.gz'.format('%(namelower)s', local_version)] +patches = [ + '%(name)s-2023.05.001_fix_hardcoded_perl_path.patch', + '%(name)s-2023.05.001_fix_AVX512_support.patch', +] +checksums = [ + {'elpa-release_2024_05_001.tar.gz': '5e0c685536869bb91c230d70cac5e779ff418575681836f240b3e64e10b23f3e'}, + {'ELPA-2023.05.001_fix_hardcoded_perl_path.patch': + '0548105065777a2ed07dde306636251c4f96e555a801647564de37d1ddd7b0b5'}, + {'ELPA-2023.05.001_fix_AVX512_support.patch': 'ecf08b64fe1da432a218040fa45d4ecfbb3269d58cb018b12da5a2d854bf96be'}, +] + +builddependencies = [ + ('Autotools', '20231222'), + ('Python', '3.12.3'), + ('Perl', '5.38.2'), +] + +preconfigopts = './autogen.sh && export LDFLAGS="-lm $LDFLAGS" && autoreconf && ' + +# When building in parallel, the file test_setup_mpi.mod is sometimes +# used before it is built, leading to an error. This must be a bug in +# the makefile affecting parallel builds. +maxparallel = 1 + + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/e/ELSI/ELSI-2.11.0-foss-2023a-PEXSI.eb b/easybuild/easyconfigs/e/ELSI/ELSI-2.11.0-foss-2023a-PEXSI.eb new file mode 100644 index 00000000000..a1be84f6de9 --- /dev/null +++ b/easybuild/easyconfigs/e/ELSI/ELSI-2.11.0-foss-2023a-PEXSI.eb @@ -0,0 +1,47 @@ +name = 'ELSI' +version = '2.11.0' +versionsuffix = '-PEXSI' + +homepage = 'https://wordpress.elsi-interchange.org/' +description = """ELSI provides and enhances scalable, open-source software library solutions for + electronic structure calculations in materials science, condensed matter physics, chemistry, and many other fields. + ELSI focuses on methods that solve or circumvent eigenvalue problems in electronic structure theory. + The ELSI infrastructure should also be useful for other challenging eigenvalue problems. +""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'usempi': True, 'pic': True, 'cstd': 'c++11', 'extra_fflags': '-fallow-argument-mismatch'} + +source_urls = ['https://gitlab.com/elsi_project/elsi_interface/-/archive/v2.11.0/'] +sources = ['elsi_interface-v%(version)s.tar.gz'] +patches = [ + 'ELSI-2.11.0_bison_3.8_compat.patch', +] +checksums = [ + {'elsi_interface-v2.11.0.tar.gz': '2e6929827ed9c99a32381ed9da40482e862c28608d59d4f27db7dcbcaed1520d'}, + {'ELSI-2.11.0_bison_3.8_compat.patch': 'a1284f5c0f442129610aa0fb463cc2b54450e3511a2fd6c871fadc21a16e9504'}, +] + +builddependencies = [ + ('flex', '2.6.4'), + ('Bison', '3.8.2'), + ('CMake', '3.26.3'), +] + +dependencies = [ + ('ELPA', '2023.05.001'), + ('NTPoly', '3.1.0'), +] + +abs_path_compilers = True +build_internal_pexsi = True + +configopts = '-DENABLE_BSEPACK=ON ' + +# Tests use 4 MPI ranks, they require a minimum of 4 cores +# Map each MPI process to a single CPU core to avoid tests fails +pretestopts = "export OMPI_MCA_rmaps_base_mapping_policy=slot:PE=1 && " + +runtest = True + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/e/ELSI/ELSI-2.11.0_bison_3.8_compat.patch b/easybuild/easyconfigs/e/ELSI/ELSI-2.11.0_bison_3.8_compat.patch new file mode 100644 index 00000000000..255ed4a5575 --- /dev/null +++ b/easybuild/easyconfigs/e/ELSI/ELSI-2.11.0_bison_3.8_compat.patch @@ -0,0 +1,14 @@ +Make it compatible with Bison 3.7 +Author: Åke Sandgren, 20211020 +Update: Cintia Willemyns (Vrije Universiteit Brussel) +--- elsi_interface-v2.11.0.orig/external/SCOTCH/CMakeLists.txt 2024-09-10 19:01:11.447551000 +0200 ++++ elsi_interface-v2.11.0/external/SCOTCH/CMakeLists.txt 2024-09-10 19:08:44.913993743 +0200 +@@ -56,7 +56,7 @@ + COMMAND mv ${PROJECT_BINARY_DIR}/generated/tmp2.c ${PROJECT_BINARY_DIR}/generated/parser_yy.c + # Versions of bison > 2.X insert a '#include tmp2.h' in tmp2.c. A simple 'mv' will not work. + # The file needs to remain in the directory with the old name. Hence the 'cp' +- COMMAND cp ${PROJECT_BINARY_DIR}/generated/tmp2.h ${PROJECT_BINARY_DIR}/generated/parser_ly.h ++ COMMAND ln -s ${PROJECT_BINARY_DIR}/generated/tmp2.h ${PROJECT_BINARY_DIR}/generated/parser_ly.h + COMMAND flex -Pscotchyy -o${PROJECT_BINARY_DIR}/generated/tmp1.c ${SCOTCH_DIR}/parser_ll.l + COMMAND mv ${PROJECT_BINARY_DIR}/generated/tmp1.c ${PROJECT_BINARY_DIR}/generated/parser_ll.c + DEPENDS ${SCOTCH_DIR}/parser_yy.y ${SCOTCH_DIR}/parser_ll.l ${SCOTCH_DIR}/parser_yy.h ${SCOTCH_DIR}/parser_ll.h diff --git a/easybuild/easyconfigs/e/ELSI/ELSI-2.9.1-foss-2022a-PEXSI.eb b/easybuild/easyconfigs/e/ELSI/ELSI-2.9.1-foss-2022a-PEXSI.eb new file mode 100644 index 00000000000..d5ef7e3da14 --- /dev/null +++ b/easybuild/easyconfigs/e/ELSI/ELSI-2.9.1-foss-2022a-PEXSI.eb @@ -0,0 +1,45 @@ +name = 'ELSI' +version = '2.9.1' +versionsuffix = '-PEXSI' + +homepage = 'https://wordpress.elsi-interchange.org/' +description = """ELSI provides and enhances scalable, open-source software library solutions for + electronic structure calculations in materials science, condensed matter physics, chemistry, and many other fields. + ELSI focuses on methods that solve or circumvent eigenvalue problems in electronic structure theory. + The ELSI infrastructure should also be useful for other challenging eigenvalue problems. +""" + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'usempi': True, 'pic': True, 'cstd': 'c++11', 'extra_fflags': '-fallow-argument-mismatch'} + +source_urls = ['https://wordpress.elsi-interchange.org/wp-content/uploads/2022/05'] +sources = ['elsi_interface-v%(version)s.tar.gz'] +patches = [ + 'pexsi-1.2.0-mpi30.patch', + 'ELSI-2.7.1_bison_3.7_compat.patch', +] +checksums = [ + {'elsi_interface-v2.9.1.tar.gz': 'ad3dc163159a79f7a83f360265f2446920c151ecce9c294136e630fe424f1d29'}, + {'pexsi-1.2.0-mpi30.patch': 'd5580de710cee652c27622f167a10933f792546481d9c08d62f452885cb63abb'}, + {'ELSI-2.7.1_bison_3.7_compat.patch': '986f95c2eb22c8a8bef13357a10242dcf0a0fac562c88bdc9bdf46cc6e7a1edb'}, +] + +builddependencies = [ + ('flex', '2.6.4'), + ('Bison', '3.8.2'), + ('CMake', '3.23.1'), +] + +dependencies = [ + ('ELPA', '2021.11.001'), + ('NTPoly', '2.7.1'), +] + +abs_path_compilers = True +build_internal_pexsi = True + +configopts = '-DENABLE_BSEPACK=ON ' + +runtest = True + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/e/EMMAX/EMMAX-20100310-foss-2023a.eb b/easybuild/easyconfigs/e/EMMAX/EMMAX-20100310-foss-2023a.eb new file mode 100644 index 00000000000..c68628823fb --- /dev/null +++ b/easybuild/easyconfigs/e/EMMAX/EMMAX-20100310-foss-2023a.eb @@ -0,0 +1,40 @@ +easyblock = 'MakeCp' + +name = 'EMMAX' +# version is based on datestamp of files in emmax-beta-src.tar.gz +# (last checked on 13 Aug 2024) +version = '20100310' + +homepage = 'https://csg.sph.umich.edu//kang/emmax' +description = """EMMAX is a statistical test for large scale human or model organism + association mapping accounting for the sample structure""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['https://csg.sph.umich.edu//kang/emmax/download/'] +sources = [{'download_filename': 'emmax-beta-src.tar.gz', 'filename': SOURCE_TAR_GZ}] +patches = ['EMMAX-20100310_fix-build.patch'] +checksums = [ + {'EMMAX-20100310.tar.gz': '79670917a0ac74ff1899fb27361e2e07b0f3a7911a9d9c6e0c18cf066b8987ea'}, + {'EMMAX-20100310_fix-build.patch': 'fae62d1f9f7bd4b94c81cdeb01d5134cc2825bcab050ddbfa89ce232eca8497e'}, +] + +dependencies = [ + ('zlib', '1.2.13'), +] + +buildopts = 'CC="$CC $CFLAGS" CLIBS="-lflexiblas -lm -lz"' + +files_to_copy = [(['emmax', 'emmax-kin'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/emmax', 'bin/emmax-kin'], + 'dirs': [], +} + +sanity_check_commands = [ + "emmax 2>&1 | grep '^Usage: emmax'", + "emmax-kin 2>&1 | grep '^Usage: emmax_IBS_kin'", +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/e/EMMAX/EMMAX-20100310_fix-build.patch b/easybuild/easyconfigs/e/EMMAX/EMMAX-20100310_fix-build.patch new file mode 100644 index 00000000000..c2827ab10a9 --- /dev/null +++ b/easybuild/easyconfigs/e/EMMAX/EMMAX-20100310_fix-build.patch @@ -0,0 +1,88 @@ +fix build with recent compiler & BLAS/LAPACK library +author: Kenneth Hoste (HPC-UGent) + +--- emmax-beta-src/emmax.c.orig 2024-08-13 16:28:41.536119000 +0200 ++++ emmax-beta-src/emmax.c 2024-08-13 16:54:06.856501202 +0200 +@@ -7,7 +7,8 @@ + #include + #include + #include +-#include ++#include ++#include + #include + //#include "lapack_wrapper.h" + +@@ -1621,15 +1622,13 @@ + double *W, + double *WORK, int LWORK, int *IWORK, int LIWORK) + { +- extern void dsyevd_ (char *JOBZp, char *UPLOp, int *Np, +- double *A, int *LDAp, +- double *W, +- double *WORK, int *LWORKp, int *IWORK, int *LIWORKp, +- int *INFOp); + int INFO; +- dsyevd_ (&JOBZ, &UPLO, &N, A, &LDA, ++ int32_t N32 = N; ++ int32_t LDA32 = LDA; ++ int32_t LWORK32 = LWORK; ++ dsyevd_ (&JOBZ, &UPLO, &N32, A, &LDA32, + W, +- WORK, &LWORK, IWORK, &LIWORK, &INFO); ++ WORK, &LWORK32, IWORK, &LIWORK, &INFO, 1, 1); + + return INFO; + } +@@ -1640,16 +1639,11 @@ + double *W, double *Z, int LDZ, int *ISUPPZ, + double *WORK, int LWORK, int *IWORK, int LIWORK) + { +- extern void dsyevr_ (char *JOBZp, char *RANGEp, char *UPLOp, int *Np, +- double *A, int *LDAp, double *VLp, double *VUp, +- int *ILp, int *IUp, double *ABSTOLp, int *Mp, +- double *W, double *Z, int *LDZp, int *ISUPPZ, +- double *WORK, int *LWORKp, int *IWORK, int *LIWORKp, +- int *INFOp); + int INFO; +- dsyevr_ (&JOBZ, &RANGE, &UPLO, &N, A, &LDA, &VL, &VU, +- &IL, &IU, &ABSTOL, M, W, Z, &LDZ, ISUPPZ, +- WORK, &LWORK, IWORK, &LIWORK, &INFO); ++ int32_t N32 = N, LDA32 = LDA, IL32 = IL, IU32 = IU, LDZ32 = LDZ, LWORK32 = LWORK, LIWORK32 = LIWORK; ++ dsyevr_ (&JOBZ, &RANGE, &UPLO, &N32, A, &LDA32, &VL, &VU, ++ &IL32, &IU32, &ABSTOL, M, W, Z, &LDZ32, ISUPPZ, ++ WORK, &LWORK32, IWORK, &LIWORK32, &INFO, 1, 1, 1); + + return INFO; + } +@@ -1739,16 +1733,27 @@ + } + + /* Turn Y into its LU form, store pivot matrix */ +- info = clapack_dgetrf (CblasColMajor, n, n, Y, n, ipiv); ++ dgetrf_(&n, &n, Y, &n, ipiv, &info); + + /* Don't bother continuing when illegal argument (info<0) or singularity (info>0) occurs */ +- if (info!=0) return info; ++ if (info != 0) { ++ free(ipiv); ++ return info; ++ } + + /* Feed this to the lapack inversion routine. */ +- info = clapack_dgetri (CblasColMajor, n, Y, n, ipiv); ++ int lwork = n * n; ++ double *work = malloc(lwork * sizeof(double)); ++ if (work == NULL) { ++ printf("malloc failed for work array in matrix_invert\n"); ++ free(ipiv); ++ return 2; ++ } ++ dgetri_(&n, Y, &n, ipiv, work, &lwork, &info); + + /* Cleanup and exit */ + free(ipiv); ++ free(work); + return info; + } + diff --git a/easybuild/easyconfigs/e/ESIpy/ESIpy-20240731-foss-2022a.eb b/easybuild/easyconfigs/e/ESIpy/ESIpy-20240731-foss-2022a.eb new file mode 100644 index 00000000000..290a85e008e --- /dev/null +++ b/easybuild/easyconfigs/e/ESIpy/ESIpy-20240731-foss-2022a.eb @@ -0,0 +1,40 @@ +easyblock = 'Tarball' + +name = 'ESIpy' +version = '20240731' +_commit = '25ff61c' + +homepage = 'https://github.com/jgrebol/ESIpy' +description = """Program aimed at the calculation of population analysis and aromaticity +indicators from different Hilbert space partitions.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +sources = [ + { + 'source_urls': ['https://github.com/jgrebol/ESIpy/archive'], + 'download_filename': '%s.tar.gz' % _commit, + 'filename': SOURCE_TAR_GZ, + }, +] +checksums = ['d8b7bf723ea37426ba6a3d4ddc07c2e969c75afd1ff4843c7d21b2faa1f035b0'] + +dependencies = [ + ('Python', '3.10.4'), + ('PySCF', '2.1.1'), +] + +sanity_check_paths = { + 'files': ['esi.py'], + 'dirs': ['utils', 'examples'], +} + +sanity_check_commands = [ + "python -c 'import esi'", +] + +modextrapaths = { + 'PYTHONPATH': '', +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/e/ESM-2/ESM-2-2.0.0-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/e/ESM-2/ESM-2-2.0.0-foss-2023a-CUDA-12.1.1.eb new file mode 100644 index 00000000000..eae9330bcdb --- /dev/null +++ b/easybuild/easyconfigs/e/ESM-2/ESM-2-2.0.0-foss-2023a-CUDA-12.1.1.eb @@ -0,0 +1,42 @@ +easyblock = 'PythonBundle' + +name = 'ESM-2' +version = '2.0.0' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/facebookresearch/esm' +description = """ESM-2 outperforms all tested single-sequence protein language models + across a range of structure prediction tasks. ESMFold harnesses the ESM-2 language model to generate + accurate structure predictions end to end directly from the sequence of a protein.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [ + ('Java', '11', '', SYSTEM), # needed by ANTLR4 runtime +] + +dependencies = [ + ('CUDA', '12.1.1', '', SYSTEM), + ('Python', '3.11.3'), + ('PyTorch', '2.1.2', versionsuffix), +] + +use_pip = True +sanity_pip_check = True + +# omegaconf is required for esmfold (in addition to OpenFold-1.0.1) +exts_list = [ + ('antlr4-python3-runtime', '4.9.3', { + 'modulename': 'antlr4', + 'checksums': ['f224469b4168294902bb1efa80a8bf7855f24c99aef99cbefc1bcd3cce77881b'], + }), + ('omegaconf', '2.3.0', { + 'checksums': ['d5d4b6d29955cc50ad50c46dc269bcd92c6e00f5f90d23ab5fee7bfca4ba4cc7'], + }), + ('fair-esm', version, { + 'modulename': "esm, esm.pretrained", + 'checksums': ['4ed34d4598ec75ed6550a4e581d023bf8d4a8375317ecba6269bb68135f80c85'], + }), +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/e/ESM-2/ESM-2-2.0.0-foss-2023a.eb b/easybuild/easyconfigs/e/ESM-2/ESM-2-2.0.0-foss-2023a.eb new file mode 100644 index 00000000000..8b461b544cc --- /dev/null +++ b/easybuild/easyconfigs/e/ESM-2/ESM-2-2.0.0-foss-2023a.eb @@ -0,0 +1,40 @@ +easyblock = 'PythonBundle' + +name = 'ESM-2' +version = '2.0.0' + +homepage = 'https://github.com/facebookresearch/esm' +description = """ESM-2 outperforms all tested single-sequence protein language models + across a range of structure prediction tasks. ESMFold harnesses the ESM-2 language model to generate + accurate structure predictions end to end directly from the sequence of a protein.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [ + ('Java', '11', '', SYSTEM), # needed by ANTLR4 runtime +] + +dependencies = [ + ('Python', '3.11.3'), + ('PyTorch', '2.1.2'), +] + +use_pip = True +sanity_pip_check = True + +# omegaconf is required for esmfold (in addition to OpenFold-1.0.1) +exts_list = [ + ('antlr4-python3-runtime', '4.9.3', { + 'modulename': 'antlr4', + 'checksums': ['f224469b4168294902bb1efa80a8bf7855f24c99aef99cbefc1bcd3cce77881b'], + }), + ('omegaconf', '2.3.0', { + 'checksums': ['d5d4b6d29955cc50ad50c46dc269bcd92c6e00f5f90d23ab5fee7bfca4ba4cc7'], + }), + ('fair-esm', version, { + 'modulename': "esm, esm.pretrained", + 'checksums': ['4ed34d4598ec75ed6550a4e581d023bf8d4a8375317ecba6269bb68135f80c85'], + }), +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/e/ESM3/ESM3-3.0.0.post2-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/e/ESM3/ESM3-3.0.0.post2-foss-2023a-CUDA-12.1.1.eb new file mode 100644 index 00000000000..1382c12efc6 --- /dev/null +++ b/easybuild/easyconfigs/e/ESM3/ESM3-3.0.0.post2-foss-2023a-CUDA-12.1.1.eb @@ -0,0 +1,53 @@ +easyblock = 'PythonBundle' + +name = 'ESM3' +version = '3.0.0.post2' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://www.evolutionaryscale.ai/' +description = """ESM3 is a frontier generative model for biology, able to jointly reason across +three fundamental biological properties of proteins: sequence, structure, and +function. These three data modalities are represented as tracks of discrete +tokens at the input and output of ESM3. You can present the model with a +combination of partial inputs across the tracks, and ESM3 will provide output +predictions for all the tracks. +""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('CUDA', '12.1.1', '', SYSTEM), + ('Python', '3.11.3'), + ('PyTorch-bundle', '2.1.2', versionsuffix), + ('Transformers', '4.39.3'), + ('Biopython', '1.83'), + ('Biotite', '0.41.0'), + ('Brotli-python', '1.0.9'), + ('einops', '0.7.0'), + ('IPython', '8.14.0'), + ('scikit-learn', '1.3.1'), +] + +use_pip = True + +exts_list = [ + ('msgpack-numpy', '0.4.8', { + 'checksums': ['c667d3180513422f9c7545be5eec5d296dcbb357e06f72ed39cc683797556e69'], + }), + ('cloudpathlib', '0.16.0', { + 'checksums': ['cdfcd35d46d529587d744154a0bdf962aca953b725c8784cd2ec478354ea63a3'], + }), + ('esm', version, { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['5544b6974945d791205226408100429c2ea6e49b30265aea1d359caabe20bb14'], + }), +] + +sanity_pip_check = True + +sanity_check_commands = [ + "python -c 'import esm'", + "python -c 'from esm.models.esm3 import ESM3'", +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/e/ESM3/ESM3-3.0.0.post2-foss-2023a.eb b/easybuild/easyconfigs/e/ESM3/ESM3-3.0.0.post2-foss-2023a.eb new file mode 100644 index 00000000000..60125c1af46 --- /dev/null +++ b/easybuild/easyconfigs/e/ESM3/ESM3-3.0.0.post2-foss-2023a.eb @@ -0,0 +1,51 @@ +easyblock = 'PythonBundle' + +name = 'ESM3' +version = '3.0.0.post2' + +homepage = 'https://www.evolutionaryscale.ai/' +description = """ESM3 is a frontier generative model for biology, able to jointly reason across +three fundamental biological properties of proteins: sequence, structure, and +function. These three data modalities are represented as tracks of discrete +tokens at the input and output of ESM3. You can present the model with a +combination of partial inputs across the tracks, and ESM3 will provide output +predictions for all the tracks. +""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('PyTorch-bundle', '2.1.2'), + ('Transformers', '4.39.3'), + ('Biopython', '1.83'), + ('Biotite', '0.41.0'), + ('Brotli-python', '1.0.9'), + ('einops', '0.7.0'), + ('IPython', '8.14.0'), + ('scikit-learn', '1.3.1'), +] + +use_pip = True + +exts_list = [ + ('msgpack-numpy', '0.4.8', { + 'checksums': ['c667d3180513422f9c7545be5eec5d296dcbb357e06f72ed39cc683797556e69'], + }), + ('cloudpathlib', '0.16.0', { + 'checksums': ['cdfcd35d46d529587d744154a0bdf962aca953b725c8784cd2ec478354ea63a3'], + }), + ('esm', version, { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['5544b6974945d791205226408100429c2ea6e49b30265aea1d359caabe20bb14'], + }), +] + +sanity_pip_check = True + +sanity_check_commands = [ + "python -c 'import esm'", + "python -c 'from esm.models.esm3 import ESM3'", +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/e/ESMF/ESMF-8.6.0-foss-2023a.eb b/easybuild/easyconfigs/e/ESMF/ESMF-8.6.0-foss-2023a.eb new file mode 100644 index 00000000000..356f3864756 --- /dev/null +++ b/easybuild/easyconfigs/e/ESMF/ESMF-8.6.0-foss-2023a.eb @@ -0,0 +1,37 @@ +name = 'ESMF' +version = '8.6.0' + +homepage = 'https://www.earthsystemcog.org/projects/esmf/' +description = """The Earth System Modeling Framework (ESMF) is a suite of software tools for developing + high-performance, multi-component Earth science modeling applications.""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'usempi': True, 'openmp': True, 'cstd': 'c++11', 'pic': True} + +source_urls = ['https://github.com/esmf-org/esmf/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = ['ESMF-6.1.1_libopts.patch'] +checksums = [ + 'ed057eaddb158a3cce2afc0712b49353b7038b45b29aee86180f381457c0ebe7', # v8.6.0.tar.gz + '3851627f07c32a7da55d99072d619942bd3a1d9dd002e1557716158e7aacdaf4', # ESMF-6.1.1_libopts.patch +] + +builddependencies = [('CMake', '3.26.3')] + +dependencies = [ + ('netCDF', '4.9.2'), + ('netCDF-Fortran', '4.6.1'), + ('netCDF-C++4', '4.3.1'), + ('libarchive', '3.6.2'), +] + +# disable errors from GCC 10 on mismatches between actual and dummy argument lists (GCC 9 behaviour) +prebuildopts = 'ESMF_F90COMPILEOPTS="${ESMF_F90COMPILEOPTS} -fallow-argument-mismatch"' + +buildopts = 'ESMF_NETCDF_INCLUDE=$EBROOTNETCDFMINFORTRAN/include ' +buildopts += 'ESMF_NETCDF_LIBS="`nc-config --libs` `nf-config --flibs` `ncxx4-config --libs`"' + +# too parallel causes the build to become really slow +maxparallel = 8 + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/e/ESMF/ESMF-8.6.1-foss-2023b.eb b/easybuild/easyconfigs/e/ESMF/ESMF-8.6.1-foss-2023b.eb new file mode 100644 index 00000000000..d8471ef09d1 --- /dev/null +++ b/easybuild/easyconfigs/e/ESMF/ESMF-8.6.1-foss-2023b.eb @@ -0,0 +1,37 @@ +name = 'ESMF' +version = '8.6.1' + +homepage = 'https://www.earthsystemcog.org/projects/esmf/' +description = """The Earth System Modeling Framework (ESMF) is a suite of software tools for developing + high-performance, multi-component Earth science modeling applications.""" + +toolchain = {'name': 'foss', 'version': '2023b'} +toolchainopts = {'usempi': True, 'openmp': True, 'cstd': 'c++11', 'pic': True} + +source_urls = ['https://github.com/esmf-org/esmf/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = ['ESMF-6.1.1_libopts.patch'] +checksums = [ + {'v8.6.1.tar.gz': 'dc270dcba1c0b317f5c9c6a32ab334cb79468dda283d1e395d98ed2a22866364'}, + {'ESMF-6.1.1_libopts.patch': '3851627f07c32a7da55d99072d619942bd3a1d9dd002e1557716158e7aacdaf4'}, +] + +builddependencies = [('CMake', '3.27.6')] + +dependencies = [ + ('netCDF', '4.9.2'), + ('netCDF-Fortran', '4.6.1'), + ('netCDF-C++4', '4.3.1'), + ('libarchive', '3.7.2'), +] + +# disable errors from GCC 10 on mismatches between actual and dummy argument lists (GCC 9 behaviour) +prebuildopts = 'ESMF_F90COMPILEOPTS="${ESMF_F90COMPILEOPTS} -fallow-argument-mismatch"' + +buildopts = 'ESMF_NETCDF_INCLUDE=$EBROOTNETCDFMINFORTRAN/include ' +buildopts += 'ESMF_NETCDF_LIBS="`nc-config --libs` `nf-config --flibs` `ncxx4-config --libs`"' + +# too parallel causes the build to become really slow +maxparallel = 8 + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/e/ESMF/ESMF-8.7.0-foss-2024a.eb b/easybuild/easyconfigs/e/ESMF/ESMF-8.7.0-foss-2024a.eb new file mode 100644 index 00000000000..a659656f754 --- /dev/null +++ b/easybuild/easyconfigs/e/ESMF/ESMF-8.7.0-foss-2024a.eb @@ -0,0 +1,37 @@ +name = 'ESMF' +version = '8.7.0' + +homepage = 'https://www.earthsystemcog.org/projects/esmf/' +description = """The Earth System Modeling Framework (ESMF) is a suite of software tools for developing + high-performance, multi-component Earth science modeling applications.""" + +toolchain = {'name': 'foss', 'version': '2024a'} +toolchainopts = {'usempi': True, 'openmp': True, 'cstd': 'c++11', 'pic': True} + +source_urls = ['https://github.com/esmf-org/esmf/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = ['ESMF-6.1.1_libopts.patch'] +checksums = [ + {'v8.7.0.tar.gz': 'd7ab266e2af8c8b230721d4df59e61aa03c612a95cc39c07a2d5695746f21f56'}, + {'ESMF-6.1.1_libopts.patch': '3851627f07c32a7da55d99072d619942bd3a1d9dd002e1557716158e7aacdaf4'}, +] + +builddependencies = [('CMake', '3.29.3')] + +dependencies = [ + ('netCDF', '4.9.2'), + ('netCDF-Fortran', '4.6.1'), + ('netCDF-C++4', '4.3.1'), + ('libarchive', '3.7.4'), +] + +# disable errors from GCC 10 on mismatches between actual and dummy argument lists (GCC 9 behaviour) +prebuildopts = 'ESMF_F90COMPILEOPTS="${ESMF_F90COMPILEOPTS} -fallow-argument-mismatch"' + +buildopts = 'ESMF_NETCDF_INCLUDE=$EBROOTNETCDFMINFORTRAN/include ' +buildopts += 'ESMF_NETCDF_LIBS="`nc-config --libs` `nf-config --flibs` `ncxx4-config --libs`"' + +# too parallel causes the build to become really slow +maxparallel = 8 + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/e/ESMPy/ESMPy-8.6.0-foss-2023a.eb b/easybuild/easyconfigs/e/ESMPy/ESMPy-8.6.0-foss-2023a.eb new file mode 100644 index 00000000000..8510ec6f7c2 --- /dev/null +++ b/easybuild/easyconfigs/e/ESMPy/ESMPy-8.6.0-foss-2023a.eb @@ -0,0 +1,59 @@ +easyblock = 'PythonBundle' + +name = 'ESMPy' +version = '8.6.0' + +homepage = 'https://earthsystemmodeling.org/esmpy' +description = "Earth System Modeling Framework (ESMF) Python Interface" + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [ + ('pytest', '7.4.2'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('ESMF', version), +] + +use_pip = True + +# downloads of data files from data.earthsystemmodeling.org are failing at the +# time of writting, switch to github.com: +_switch_data_url_regex = r"s/^\(DATA_URL.*earthsystemmodeling.org\)/# \1/;s/# \(DATA_URL.*github.com\)/\1/" + +_pre_test_cmds = [ + "sed -i '%s' src/esmpy/util/cache_data.py" % _switch_data_url_regex, + "unset ESMPY_DATA_DIR", + "export ESMPY_DATA_NEW_DIR=/tmp", + "", +] + +exts_list = [ + ('esmpy', version, { + 'patches': ['ESMPy-%(version)s_use-static-version.patch'], + 'source_urls': ['https://github.com/esmf-org/esmf/archive/'], + 'sources': ['v%(version)s.tar.gz'], + 'checksums': [ + {'v8.6.0.tar.gz': + 'ed057eaddb158a3cce2afc0712b49353b7038b45b29aee86180f381457c0ebe7'}, + {'ESMPy-8.6.0_use-static-version.patch': + '4878e0066593c993e7fc16638ab8e671693c402263b13d1c903b5c5b717f6468'}, + ], + 'start_dir': 'src/addon/%(name)s', + 'preinstallopts': "sed -i 's/EB_ESMPY_VERSION/%(version)s/' pyproject.toml && ", + 'pretestopts': " && ".join(_pre_test_cmds), + 'runtest': 'pytest', + 'testinstall': True, + }), +] + +sanity_pip_check = True + +# set data directory to a user-writable directory +# default: %(installdir)s/lib/python%(pyshortver)s/site-packages/esmpy/data +modextravars = {'ESMPY_DATA_DIR': '/tmp'} + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/e/ESMPy/ESMPy-8.6.0_use-static-version.patch b/easybuild/easyconfigs/e/ESMPy/ESMPy-8.6.0_use-static-version.patch new file mode 100644 index 00000000000..1a81dbd6151 --- /dev/null +++ b/easybuild/easyconfigs/e/ESMPy/ESMPy-8.6.0_use-static-version.patch @@ -0,0 +1,49 @@ +Replace dynamic versioning with a plain static version string. Tarballs of +ESMPy downloaded from github lack git repository data required by +setuptools-git-versioning. +author: Alex Domingo (Vrije Universiteit Brussel) +diff --git a/pyproject.toml.orig b/pyproject.toml +index b3da4b6..e0e207d 100644 +--- a/src/addon/esmpy/pyproject.toml.orig ++++ b/src/addon/esmpy/pyproject.toml +@@ -1,5 +1,5 @@ + [build-system] +-requires = [ "setuptools>=41", "wheel", "setuptools-git-versioning" ] ++requires = [ "setuptools>=41", "wheel" ] + build-backend = "setuptools.build_meta" + + [project] +@@ -12,15 +12,8 @@ license = { text = "University of Illinois-NCSA" } + dependencies = [ + "numpy", + 'importlib-metadata; python_version < "3.8"', +- # setuptools-git-versioning shouldn't be needed here, but is +- # included as a workaround for problems with the build-time +- # installation of this package with python 3.10 (given by the +- # build-system section above). By including it here, we at least +- # ensure that this package will be available for a second or +- # subsequent pip install of esmpy. +- 'setuptools-git-versioning; python_version >= "3.10"', + ] +-dynamic = [ "version" ] ++version = "EB_ESMPY_VERSION" + + [project.optional-dependencies] + testing = [ +@@ -28,16 +21,6 @@ testing = [ + "pytest-json-report", + ] + +-[tool.setuptools-git-versioning] +-enabled = true +-template = "{tag}" +-dev_template = "{tag}" +-dirty_template = "{tag}" +-starting_version = "8.6.0" # this is a backup for pip <= 22.0 where git-versioning doesn't work +- +-[tool.dynamic] +-version = "placeholder" # this is a placeholder for the version pulled with git-versioning +- + [tool.setuptools.packages.find] + where = [ "src" ] + exclude = [ "doc*" ] diff --git a/easybuild/easyconfigs/e/ESPResSo/ESPResSo-4.2.2-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/e/ESPResSo/ESPResSo-4.2.2-foss-2023a-CUDA-12.1.1.eb new file mode 100644 index 00000000000..eb37f56eb35 --- /dev/null +++ b/easybuild/easyconfigs/e/ESPResSo/ESPResSo-4.2.2-foss-2023a-CUDA-12.1.1.eb @@ -0,0 +1,60 @@ +easyblock = 'CMakeMake' + +name = 'ESPResSo' +version = '4.2.2' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://espressomd.org/wordpress' +description = """A software package for performing and analyzing scientific Molecular Dynamics simulations.""" + +source_urls = ['https://github.com/espressomd/espresso/releases/download/%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['2bc02f91632b0030f1203759768bd718bd8a0005f72696980b12331b4bfa0d76'] + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'usempi': True, 'pic': True} + +builddependencies = [('CMake', '3.26.3')] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('Boost.MPI', '1.82.0'), + ('HDF5', '1.14.0'), + ('Mesa', '23.1.4'), + ('GSL', '2.7'), + ('IPython', '8.14.0'), + ('Pint', '0.23'), + ('CUDA', '12.1.1', '', SYSTEM), +] + +# default CUDA compute capabilities to use (override via --cuda-compute-capabilities) +cuda_compute_capabilities = ['5.2', '6.0', '7.0', '7.5', '8.0', '8.6', '9.0'] + +configopts = ' -DCMAKE_SKIP_RPATH=OFF -DWITH_TESTS=ON -DWITH_CUDA=ON' +# make sure the right Python is used (note: -DPython3_EXECUTABLE or -DPython_EXECUTABLE does not work!) +configopts += ' -DPYTHON_EXECUTABLE=$EBROOTPYTHON/bin/python ' + +runtest = 'check_unit_tests && make check_python' + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +_binaries = ['ipypresso', 'pypresso'] +_libs = [ + 'Espresso_config', 'Espresso_core', 'Espresso_script_interface', 'Espresso_shapes', + '_init', 'analyze', 'code_info', 'electrokinetics', 'galilei', + 'integrate', 'interactions', 'lb', 'particle_data', 'polymer', 'profiler', + 'script_interface', 'system', 'thermostat', 'utils', 'version', +] + +_lib_path = 'lib/python%(pyshortver)s/site-packages/espressomd' + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in _binaries] + + [_lib_path + '/%s.' % x + SHLIB_EXT for x in _libs], + 'dirs': ['bin', 'lib'] +} + +sanity_check_commands = ['pypresso -h', 'ipypresso -h'] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/e/ESPResSo/ESPResSo-4.2.2-foss-2023a.eb b/easybuild/easyconfigs/e/ESPResSo/ESPResSo-4.2.2-foss-2023a.eb new file mode 100644 index 00000000000..eb16f7546f5 --- /dev/null +++ b/easybuild/easyconfigs/e/ESPResSo/ESPResSo-4.2.2-foss-2023a.eb @@ -0,0 +1,55 @@ +easyblock = 'CMakeMake' + +name = 'ESPResSo' +version = '4.2.2' + +homepage = 'https://espressomd.org/wordpress' +description = """A software package for performing and analyzing scientific Molecular Dynamics simulations.""" + +source_urls = ['https://github.com/espressomd/espresso/releases/download/%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['2bc02f91632b0030f1203759768bd718bd8a0005f72696980b12331b4bfa0d76'] + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'usempi': True, 'pic': True} + +builddependencies = [('CMake', '3.26.3')] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('Boost.MPI', '1.82.0'), + ('HDF5', '1.14.0'), + ('Mesa', '23.1.4'), + ('GSL', '2.7'), + ('IPython', '8.14.0'), + ('Pint', '0.23'), +] + +configopts = ' -DCMAKE_SKIP_RPATH=OFF -DWITH_TESTS=ON -DWITH_CUDA=OFF' +# make sure the right Python is used (note: -DPython3_EXECUTABLE or -DPython_EXECUTABLE does not work!) +configopts += ' -DPYTHON_EXECUTABLE=$EBROOTPYTHON/bin/python ' + +runtest = 'check_unit_tests && make check_python' + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +_binaries = ['ipypresso', 'pypresso'] +_libs = [ + 'Espresso_config', 'Espresso_core', 'Espresso_script_interface', 'Espresso_shapes', + '_init', 'analyze', 'code_info', 'electrokinetics', 'galilei', + 'integrate', 'interactions', 'lb', 'particle_data', 'polymer', 'profiler', + 'script_interface', 'system', 'thermostat', 'utils', 'version', +] + +_lib_path = 'lib/python%(pyshortver)s/site-packages/espressomd' + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in _binaries] + + [_lib_path + '/%s.' % x + SHLIB_EXT for x in _libs], + 'dirs': ['bin', 'lib'] +} + +sanity_check_commands = ['pypresso -h', 'ipypresso -h'] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/e/ESPResSo/ESPResSo-4.2.2-foss-2023b.eb b/easybuild/easyconfigs/e/ESPResSo/ESPResSo-4.2.2-foss-2023b.eb new file mode 100644 index 00000000000..950f31dba26 --- /dev/null +++ b/easybuild/easyconfigs/e/ESPResSo/ESPResSo-4.2.2-foss-2023b.eb @@ -0,0 +1,55 @@ +easyblock = 'CMakeMake' + +name = 'ESPResSo' +version = '4.2.2' + +homepage = 'https://espressomd.org/wordpress' +description = """A software package for performing and analyzing scientific Molecular Dynamics simulations.""" + +source_urls = ['https://github.com/espressomd/espresso/releases/download/%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['2bc02f91632b0030f1203759768bd718bd8a0005f72696980b12331b4bfa0d76'] + +toolchain = {'name': 'foss', 'version': '2023b'} +toolchainopts = {'usempi': True, 'pic': True} + +builddependencies = [('CMake', '3.27.6')] + +dependencies = [ + ('Python', '3.11.5'), + ('SciPy-bundle', '2023.11'), + ('Boost.MPI', '1.83.0'), + ('HDF5', '1.14.3'), + ('Mesa', '23.1.9'), + ('GSL', '2.7'), + ('IPython', '8.17.2'), + ('Pint', '0.24'), +] + +configopts = ' -DCMAKE_SKIP_RPATH=OFF -DWITH_TESTS=ON -DWITH_CUDA=OFF' +# make sure the right Python is used (note: -DPython3_EXECUTABLE or -DPython_EXECUTABLE does not work!) +configopts += ' -DPYTHON_EXECUTABLE=$EBROOTPYTHON/bin/python ' + +runtest = 'check_unit_tests && make check_python' + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +_binaries = ['ipypresso', 'pypresso'] +_libs = [ + 'Espresso_config', 'Espresso_core', 'Espresso_script_interface', 'Espresso_shapes', + '_init', 'analyze', 'code_info', 'electrokinetics', 'galilei', + 'integrate', 'interactions', 'lb', 'particle_data', 'polymer', 'profiler', + 'script_interface', 'system', 'thermostat', 'utils', 'version', +] + +_lib_path = 'lib/python%(pyshortver)s/site-packages/espressomd' + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in _binaries] + + [_lib_path + '/%s.' % x + SHLIB_EXT for x in _libs], + 'dirs': ['bin', 'lib'] +} + +sanity_check_commands = ['pypresso -h', 'ipypresso -h'] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/e/EVcouplings/EVcouplings-0.1.1-foss-2023a.eb b/easybuild/easyconfigs/e/EVcouplings/EVcouplings-0.1.1-foss-2023a.eb new file mode 100644 index 00000000000..cc4bc9b90bc --- /dev/null +++ b/easybuild/easyconfigs/e/EVcouplings/EVcouplings-0.1.1-foss-2023a.eb @@ -0,0 +1,61 @@ +easyblock = 'PythonBundle' + +name = 'EVcouplings' +version = '0.1.1' + +homepage = 'https://github.com/debbiemarkslab/EVcouplings' +description = """ +Predict protein structure, function and mutations using evolutionary sequence covariation. +""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [ + ('hatchling', '1.18.0'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('numba', '0.58.1'), + ('SciPy-bundle', '2023.07'), + ('ruamel.yaml', '0.17.32'), + ('matplotlib', '3.7.2'), + ('bokeh', '3.2.2'), + ('Biopython', '1.83'), + ('Seaborn', '0.13.2'), + ('scikit-learn', '1.3.1'), + ('HMMER', '3.4'), + # Needs plmc installed with single precision + ('plmc', '20230121', '-32bit'), +] + +exts_list = [ + ('mmtf-python', '1.1.3', { + 'modulename': 'mmtf', + 'checksums': ['12a02fe1b7131f0a2b8ce45b46f1e0cdd28b9818fe4499554c26884987ea0c32'], + }), + ('filelock', '3.13.4', { + 'checksums': ['d13f466618bfde72bd2c18255e269f72542c6e70e7bac83a0232d6b1cc5c8cf4'], + }), + ('billiard', '4.2.0', { + 'checksums': ['9a3c3184cb275aa17a732f93f65b20c525d3d9f253722d26a82194803ade5a2c'], + }), + ('evcouplings', version, { + 'patches': ['EVcouplings-%(version)s_fix-import-Iterable-Mapping.patch'], + 'sources': ['%(name)s-%(version)s.zip'], + 'checksums': [ + {'evcouplings-0.1.1.zip': 'aba07acdc39a0da73f39f48a8cac915d5b671abc008c123bbe30e6759a2499d2'}, + {'EVcouplings-0.1.1_fix-import-Iterable-Mapping.patch': + 'db2cff1de3488baaa1f0ac186c02c61432c27a3e5221525f1c773817722e7ba9'}, + ], + }), +] + +sanity_check_commands = [ + "evcouplings --help", +] + +use_pip = True +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/e/EVcouplings/EVcouplings-0.1.1_fix-import-Iterable-Mapping.patch b/easybuild/easyconfigs/e/EVcouplings/EVcouplings-0.1.1_fix-import-Iterable-Mapping.patch new file mode 100644 index 00000000000..59caa949d96 --- /dev/null +++ b/easybuild/easyconfigs/e/EVcouplings/EVcouplings-0.1.1_fix-import-Iterable-Mapping.patch @@ -0,0 +1,77 @@ +The Iterable and Mapping were removed from collections in Python 3.10 +Import Iterable and Mapping from collections.abc +Author: Cintia Willemyns (Vrije Universiteit Brussel) +diff -Naru evcouplings-0.1.1.orig/evcouplings/align/protocol.py evcouplings-0.1.1/evcouplings/align/protocol.py +--- evcouplings-0.1.1.orig/evcouplings/align/protocol.py 2024-06-04 17:15:24.409905000 +0200 ++++ evcouplings-0.1.1/evcouplings/align/protocol.py 2024-06-04 17:16:54.492901448 +0200 +@@ -8,7 +8,8 @@ + + """ + +-from collections import OrderedDict, Iterable ++from collections import OrderedDict ++from collections.abc import Iterable + import re + from shutil import copy + import os +diff -Naru evcouplings-0.1.1.orig/evcouplings/compare/pdb.py evcouplings-0.1.1/evcouplings/compare/pdb.py +--- evcouplings-0.1.1.orig/evcouplings/compare/pdb.py 2024-06-04 17:15:24.419850000 +0200 ++++ evcouplings-0.1.1/evcouplings/compare/pdb.py 2024-06-04 17:52:31.882593767 +0200 +@@ -5,7 +5,8 @@ + Thomas A. Hopf + """ + +-from collections import OrderedDict, Iterable ++from collections import OrderedDict ++from collections.abc import Iterable + from os import path + from urllib.error import HTTPError + +diff -Naru evcouplings-0.1.1.orig/evcouplings/couplings/mapping.py evcouplings-0.1.1/evcouplings/couplings/mapping.py +--- evcouplings-0.1.1.orig/evcouplings/couplings/mapping.py 2024-06-04 17:15:24.405238000 +0200 ++++ evcouplings-0.1.1/evcouplings/couplings/mapping.py 2024-06-04 17:52:59.165312780 +0200 +@@ -7,7 +7,7 @@ + Anna G. Green (MultiSegmentCouplingsModel) + """ + +-from collections import Iterable ++from collections.abc import Iterable + from copy import deepcopy + from evcouplings.couplings.model import CouplingsModel + import pandas as pd +diff -Naru evcouplings-0.1.1.orig/evcouplings/couplings/model.py evcouplings-0.1.1/evcouplings/couplings/model.py +--- evcouplings-0.1.1.orig/evcouplings/couplings/model.py 2024-06-04 17:15:24.407628000 +0200 ++++ evcouplings-0.1.1/evcouplings/couplings/model.py 2024-06-04 17:53:16.476317130 +0200 +@@ -6,7 +6,7 @@ + Authors: + Thomas A. Hopf + """ +-from collections import Iterable ++from collections.abc import Iterable + from copy import deepcopy + + from numba import jit +diff -Naru evcouplings-0.1.1.orig/evcouplings/utils/app.py evcouplings-0.1.1/evcouplings/utils/app.py +--- evcouplings-0.1.1.orig/evcouplings/utils/app.py 2024-06-04 17:15:24.424719000 +0200 ++++ evcouplings-0.1.1/evcouplings/utils/app.py 2024-06-04 17:53:56.971793813 +0200 +@@ -14,7 +14,7 @@ + import re + from copy import deepcopy + from os import path, environ +-from collections import Mapping ++from collections.abc import Mapping + + import click + +diff -Naru evcouplings-0.1.1.orig/evcouplings/utils/tracker/mongodb.py evcouplings-0.1.1/evcouplings/utils/tracker/mongodb.py +--- evcouplings-0.1.1.orig/evcouplings/utils/tracker/mongodb.py 2024-06-04 17:15:24.421959000 +0200 ++++ evcouplings-0.1.1/evcouplings/utils/tracker/mongodb.py 2024-06-04 17:54:25.411050098 +0200 +@@ -16,7 +16,7 @@ + + import os + from datetime import datetime +-from collections import Mapping ++from collections.abc import Mapping + + from pymongo import MongoClient, errors + import gridfs diff --git a/easybuild/easyconfigs/e/EVidenceModeler/EVidenceModeler-2.0.0_set-correct-CFlags-for-ParaFly.patch b/easybuild/easyconfigs/e/EVidenceModeler/EVidenceModeler-2.0.0_set-correct-CFlags-for-ParaFly.patch new file mode 100644 index 00000000000..3920012f0c7 --- /dev/null +++ b/easybuild/easyconfigs/e/EVidenceModeler/EVidenceModeler-2.0.0_set-correct-CFlags-for-ParaFly.patch @@ -0,0 +1,14 @@ +take into account $CFLAGS and $CXXFLAGS set in build environment when building ParaFly +author: Lara Peeters (HPC-UGent) +diff -ru EVidenceModeler.orig/Makefile EVidenceModeler/Makefile +--- EVidenceModeler.orig/Makefile 2024-10-10 09:25:20.000000000 +0200 ++++ EVidenceModeler/Makefile 2024-10-16 10:58:57.509308850 +0200 +@@ -6,7 +6,7 @@ + CC = gcc + + parafly: +- cd plugins/ParaFly && sh ./configure --prefix=`pwd` CXX=$(CXX) CC=$(CC) CFLAGS="-fopenmp" CXXFLAGS="-fopenmp" && $(MAKE) install ++ cd plugins/ParaFly && sh ./configure --prefix=`pwd` CXX=$(CXX) CC=$(CC) CFLAGS="$(CFLAGS) -fopenmp" CXXFLAGS="$(CXXFLAGS) -fopenmp" && $(MAKE) install + + + diff --git a/easybuild/easyconfigs/e/EVidenceModeler/EVidenceModeler-2.1.0-foss-2023a.eb b/easybuild/easyconfigs/e/EVidenceModeler/EVidenceModeler-2.1.0-foss-2023a.eb new file mode 100644 index 00000000000..62454399723 --- /dev/null +++ b/easybuild/easyconfigs/e/EVidenceModeler/EVidenceModeler-2.1.0-foss-2023a.eb @@ -0,0 +1,47 @@ +easyblock = 'Tarball' + +name = 'EVidenceModeler' +version = '2.1.0' + +homepage = 'https://github.com/EVidenceModeler/EVidenceModeler' +description = """ EVM provides a flexible and intuitive framework for +combining diverse evidence types into a single automated gene structure annotation system.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +sources = [{ + 'filename': '%(name)s-v%(version)s.tar.gz', + 'git_config': { + 'url': 'https://github.com/EVidenceModeler', + 'repo_name': '%(name)s', + 'tag': '%(name)s-v%(version)s', + 'recursive': True, + } +}] +patches = ['EVidenceModeler-2.0.0_set-correct-CFlags-for-ParaFly.patch'] +checksums = [ + None, # EVidenceModeler-v2.1.0.tar.gz + '619fc54db10fad3638daa177373c19c9ba4b69dcb80585822bfa9b2500f57d13', + # EVidenceModeler-2.0.0_set-correct-CFlags-for-ParaFly.patch +] + +dependencies = [ + ('PASA', '2.5.3',), +] + +# Install ParaFly +postinstallcmds = ["cd %(installdir)s && rm plugins/ParaFly/bin/ParaFly && make"] + +sanity_check_paths = { + 'files': ['EVidenceModeler', 'plugins/ParaFly/bin/ParaFly'], + 'dirs': ['plugins/ParaFly', 'testing'], +} + +modextrapaths = { + 'EVM_HOME': '', + 'PATH': '', +} + +sanity_check_commands = ["EVidenceModeler -h 2>&1 | grep 'Evidence Modeler'"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.9.2.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.9.2.eb new file mode 100644 index 00000000000..cb476c53d7f --- /dev/null +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.9.2.eb @@ -0,0 +1,56 @@ +easyblock = 'EB_EasyBuildMeta' + +name = 'EasyBuild' +version = '4.9.2' + +homepage = 'https://easybuilders.github.io/easybuild' +description = """EasyBuild is a software build and installation framework + written in Python that allows you to install software in a structured, + repeatable and robust way.""" + +toolchain = SYSTEM + +source_urls = [ + # easybuild-framework + 'https://files.pythonhosted.org/packages/cc/1f/676fc9e29c68e9c39c6dadf150ab4e5bf4907de4b9afd2bc6e0afd24ab7c/', + # easybuild-easyblocks + 'https://files.pythonhosted.org/packages/5d/85/e8593ceeb00c61253204e74d2a8360076ce016f42d83d33841f8e7de57a1/', + # easybuild-easyconfigs + 'https://files.pythonhosted.org/packages/99/b2/d899b4310bc54a10e0fb46995a2abc333857db16d116f22a53b0313d13d7/', +] +# note: subdirectory for each unpacked source tarball is renamed because custom easyblock in older EasyBuild version +# that is used for installing EasyBuild with EasyBuild expects subdirectories with '-' rather than '_'; +# see also https://github.com/easybuilders/easybuild-easyblocks/pull/3358 +sources = [ + { + 'filename': 'easybuild_framework-%(version)s.tar.gz', + 'extract_cmd': "tar xfvz %s && mv easybuild_framework-%(version)s easybuild-framework-%(version)s", + }, + { + 'filename': 'easybuild_easyblocks-%(version)s.tar.gz', + 'extract_cmd': "tar xfvz %s && mv easybuild_easyblocks-%(version)s easybuild-easyblocks-%(version)s", + }, + { + 'filename': 'easybuild_easyconfigs-%(version)s.tar.gz', + 'extract_cmd': "tar xfvz %s && mv easybuild_easyconfigs-%(version)s easybuild-easyconfigs-%(version)s", + }, +] +checksums = [ + {'easybuild_framework-4.9.2.tar.gz': 'cc6e0fe7bab2a96d424656ed70bf33e3b083eef5ceaa5d5fed88aa7b91dd3d63'}, + {'easybuild_easyblocks-4.9.2.tar.gz': '48202a89995a3d0a19228a35e409228bb6aa190ec7d7a7560e449303954953df'}, + {'easybuild_easyconfigs-4.9.2.tar.gz': '52d6f6378fc331cda8a94ff196d5bd6bb74c8029c973ee6a92763c256571eec7'}, +] + +# order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?) +# EasyBuild is a (set of) Python packages, so it depends on Python +# usually, we want to use the system Python, so no actual Python dependency is listed +allow_system_deps = [('Python', SYS_PYTHON_VERSION)] + +local_pyshortver = '.'.join(SYS_PYTHON_VERSION.split('.')[:2]) + +sanity_check_paths = { + 'files': ['bin/eb'], + 'dirs': ['lib/python%s/site-packages' % local_pyshortver], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.9.3.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.9.3.eb new file mode 100644 index 00000000000..4059b342213 --- /dev/null +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.9.3.eb @@ -0,0 +1,56 @@ +easyblock = 'EB_EasyBuildMeta' + +name = 'EasyBuild' +version = '4.9.3' + +homepage = 'https://easybuilders.github.io/easybuild' +description = """EasyBuild is a software build and installation framework + written in Python that allows you to install software in a structured, + repeatable and robust way.""" + +toolchain = SYSTEM + +source_urls = [ + # easybuild-framework + 'https://files.pythonhosted.org/packages/10/a0/e5484d4078f7450042cd7b7a1af24fd3f8d0cb4818f4578e4c322ba488d8/', + # easybuild-easyblocks + 'https://files.pythonhosted.org/packages/ee/40/4f6412917f83429f9389b977903c8905f216cb211c8bf3111f28c3017677/', + # easybuild-easyconfigs + 'https://files.pythonhosted.org/packages/13/95/44d1e10ceaaf08219ef50d1d97d500ba3b6b34f2d76dd1ff64def71612dc/', +] +# note: subdirectory for each unpacked source tarball is renamed because custom easyblock in older EasyBuild version +# that is used for installing EasyBuild with EasyBuild expects subdirectories with '-' rather than '_'; +# see also https://github.com/easybuilders/easybuild-easyblocks/pull/3358 +sources = [ + { + 'filename': 'easybuild_framework-%(version)s.tar.gz', + 'extract_cmd': "tar xfvz %s && mv easybuild_framework-%(version)s easybuild-framework-%(version)s", + }, + { + 'filename': 'easybuild_easyblocks-%(version)s.tar.gz', + 'extract_cmd': "tar xfvz %s && mv easybuild_easyblocks-%(version)s easybuild-easyblocks-%(version)s", + }, + { + 'filename': 'easybuild_easyconfigs-%(version)s.tar.gz', + 'extract_cmd': "tar xfvz %s && mv easybuild_easyconfigs-%(version)s easybuild-easyconfigs-%(version)s", + }, +] +checksums = [ + {'easybuild_framework-4.9.3.tar.gz': '43bbcaa0a7b075eb6483054428ef4b1279a9fc850301171688f86899eaebfff8'}, + {'easybuild_easyblocks-4.9.3.tar.gz': '4f036be918f88fe2dadba87f15d696e9b4d3f8f06986c675b9fafc77b591649d'}, + {'easybuild_easyconfigs-4.9.3.tar.gz': 'f7f501c87cb16a8eb393f5e98cb3cd5f8e84314901e81ff50f8140681b415676'}, +] + +# order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?) +# EasyBuild is a (set of) Python packages, so it depends on Python +# usually, we want to use the system Python, so no actual Python dependency is listed +allow_system_deps = [('Python', SYS_PYTHON_VERSION)] + +local_pyshortver = '.'.join(SYS_PYTHON_VERSION.split('.')[:2]) + +sanity_check_paths = { + 'files': ['bin/eb'], + 'dirs': ['lib/python%s/site-packages' % local_pyshortver], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.9.4.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.9.4.eb new file mode 100644 index 00000000000..064536bb936 --- /dev/null +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.9.4.eb @@ -0,0 +1,59 @@ +easyblock = 'EB_EasyBuildMeta' + +name = 'EasyBuild' +version = '4.9.4' + +homepage = 'https://easybuilders.github.io/easybuild' +description = """EasyBuild is a software build and installation framework + written in Python that allows you to install software in a structured, + repeatable and robust way.""" + +toolchain = SYSTEM + +source_urls = [ + # easybuild-framework + 'https://files.pythonhosted.org/packages/bd/25/512d9e895a86f4df198274e8a5f6868406d97cc75da9acc5797f78139b52/', + # easybuild-easyblocks + 'https://files.pythonhosted.org/packages/d7/b0/b9289c78fafc21c5c01b225aeee89c69914166742e5f80955d49ed8f9722/', + # easybuild-easyconfigs + 'https://files.pythonhosted.org/packages/ed/2c/7b2b22235ffe9310a93cbfef06fb3723466aa8ccc4aca4888b59433e55a6/', +] +# note: subdirectory for each unpacked source tarball is renamed because custom easyblock in older EasyBuild version +# that is used for installing EasyBuild with EasyBuild expects subdirectories with '-' rather than '_'; +# see also https://github.com/easybuilders/easybuild-easyblocks/pull/3358 +sources = [ + { + 'filename': 'easybuild_framework-%(version)s.tar.gz', + 'extract_cmd': "tar xfvz %s && mv easybuild_framework-%(version)s easybuild-framework-%(version)s", + }, + { + 'filename': 'easybuild_easyblocks-%(version)s.tar.gz', + 'extract_cmd': "tar xfvz %s && mv easybuild_easyblocks-%(version)s easybuild-easyblocks-%(version)s", + }, + { + 'filename': 'easybuild_easyconfigs-%(version)s.tar.gz', + 'extract_cmd': "tar xfvz %s && mv easybuild_easyconfigs-%(version)s easybuild-easyconfigs-%(version)s", + }, +] +patches = ['EasyBuild-4.9.4_fix-riscv-toolchain-opts-typo.patch'] +checksums = [ + {'easybuild_framework-4.9.4.tar.gz': '5b380a2e3a359f64f06789c390200b922a840f6b10b441e5163696a34bd9bc27'}, + {'easybuild_easyblocks-4.9.4.tar.gz': '1272f1e294090caafde8cbda72ae344ef400fdd161163781f67b3cffe761dd62'}, + {'easybuild_easyconfigs-4.9.4.tar.gz': 'beee4e098f5fee18f2029d6a0b893549aba26e075b147cc0008cb16fd4c8d982'}, + {'EasyBuild-4.9.4_fix-riscv-toolchain-opts-typo.patch': + '602d9abfdd90f435bdc877b1d2710a17ae577c790914e7bf61428dc7073ad1b6'}, +] + +# order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?) +# EasyBuild is a (set of) Python packages, so it depends on Python +# usually, we want to use the system Python, so no actual Python dependency is listed +allow_system_deps = [('Python', SYS_PYTHON_VERSION)] + +local_pyshortver = '.'.join(SYS_PYTHON_VERSION.split('.')[:2]) + +sanity_check_paths = { + 'files': ['bin/eb'], + 'dirs': ['lib/python%s/site-packages' % local_pyshortver], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.9.4_fix-riscv-toolchain-opts-typo.patch b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.9.4_fix-riscv-toolchain-opts-typo.patch new file mode 100644 index 00000000000..f93ba6247c4 --- /dev/null +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.9.4_fix-riscv-toolchain-opts-typo.patch @@ -0,0 +1,23 @@ +https://github.com/easybuilders/easybuild-framework/pull/4668 +From 688c6709504c4b54f881b9a674c3c5dfd6acd241 Mon Sep 17 00:00:00 2001 +From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= +Date: Fri, 4 Oct 2024 16:35:35 +0200 +Subject: [PATCH] fix typo in veryloose toolchain option + +--- + easybuild/toolchains/compiler/gcc.py | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/easybuild/toolchains/compiler/gcc.py b/easybuild/toolchains/compiler/gcc.py +index e9748f3bda..fd50ad2c03 100644 +--- a/easybuild/toolchains/compiler/gcc.py ++++ b/easybuild/toolchains/compiler/gcc.py +@@ -85,7 +85,7 @@ class Gcc(Compiler): + COMPILER_UNIQUE_OPTION_MAP['strict'] = [] + COMPILER_UNIQUE_OPTION_MAP['precise'] = [] + COMPILER_UNIQUE_OPTION_MAP['loose'] = ['fno-math-errno'] +- COMPILER_UNIQUE_OPTION_MAP['verloose'] = ['fno-math-errno'] ++ COMPILER_UNIQUE_OPTION_MAP['veryloose'] = ['fno-math-errno'] + + # used when 'optarch' toolchain option is enabled (and --optarch is not specified) + COMPILER_OPTIMAL_ARCHITECTURE_OPTION = { diff --git a/easybuild/easyconfigs/e/EasyMocap/EasyMocap-0.2-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/e/EasyMocap/EasyMocap-0.2-foss-2022a-CUDA-11.7.0.eb new file mode 100644 index 00000000000..f5a93adc6f7 --- /dev/null +++ b/easybuild/easyconfigs/e/EasyMocap/EasyMocap-0.2-foss-2022a-CUDA-11.7.0.eb @@ -0,0 +1,81 @@ +easyblock = 'PythonBundle' + +name = 'EasyMocap' +version = '0.2' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://chingswy.github.io/easymocap-public-doc/' +description = """EasyMoCap is an open-source toolbox designed for markerless + human motion capture from RGB videos. This project offers a wide range of motion + capture methods across various settings.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('CUDA', '11.7.0', '', SYSTEM), + ('Python', '3.10.4'), + ('PyTorch', '1.12.0', versionsuffix), + ('torchvision', '0.13.1', versionsuffix), + ('tqdm', '4.64.0'), + ('OpenCV', '4.6.0', '-CUDA-%(cudaver)s-contrib'), + ('flatbuffers', '2.0.7'), + ('matplotlib', '3.5.2'), + ('PortAudio', '19.7.0'), + # for pyrender + ('freetype-py', '2.4.0'), + ('imageio', '2.22.2'), + ('networkx', '2.8.4'), + ('PyOpenGL', '3.1.6'), + ('trimesh', '3.17.1'), + # for ipdb + ('IPython', '8.5.0'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('chumpy', '0.70', { + 'checksums': ['a0275c2018784ca1302875567dc81761f5fd469fab9f3ac0f3e7c39e9180350a'], + }), + ('func_timeout', '4.3.5', { + 'checksums': ['74cd3c428ec94f4edfba81f9b2f14904846d5ffccc27c92433b8b5939b5575dd'], + }), + ('ipdb', '0.13.13', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['45529994741c4ab6d2388bfa5d7b725c2cf7fe9deffabdb8a6113aa5ed449ed4'], + }), + ('termcolor', '2.4.0', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['9297c0df9c99445c2412e832e882a7884038a25617c60cea2ad69488d4040d63'], + }), + ('yacs', '0.1.8', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['99f893e30497a4b66842821bac316386f7bd5c4f47ad35c9073ef089aa33af32'], + }), + ('pyglet', '2.0.15', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['9e4cc16efc308106fd3a9ff8f04e7a6f4f6a807c6ac8a331375efbbac8be85af'], + }), + ('pyrender', '0.1.45', { + # PyOpenGL requirement is too strict + 'preinstallopts': "sed -i 's/PyOpenGL==3.1.0/PyOpenGL>=3.1.0/g' setup.py && ", + 'checksums': ['284b2432bf6832f05c5216c4b979ceb514ea78163bf53b8ce2bdf0069cb3b92e'], + }), + # Building from source fails. See https://github.com/google/mediapipe/issues/5247 + ('mediapipe', '0.10.11', { + 'sources': ['mediapipe-%(version)s-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl'], + 'checksums': ['fc5283a50227a93d7755fd0f83d0d6daeb0f1c841df1ac9101e96e32e7e03ba1'], + }), + ('sounddevice', '0.4.6', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['5de768ba6fe56ad2b5aaa2eea794b76b73e427961c95acad2ee2ed7f866a4b20'], + }), + (name, version, { + 'source_urls': ['https://github.com/zju3dv/EasyMocap/archive'], + 'sources': ['v%(version)s.tar.gz'], + 'checksums': ['d4c42b82ea8a53662354ff70b775e505c654ca4fd51524029214acbc16aa9773'], + }), +] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.4.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.4.0-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..f6a47336ef1 --- /dev/null +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.4.0-GCCcore-13.3.0.eb @@ -0,0 +1,21 @@ +name = 'Eigen' +version = '3.4.0' + +homepage = 'https://eigen.tuxfamily.org' +description = """Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, + and related algorithms.""" + +# only includes header files, but requires CMake so using non-system toolchain +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://gitlab.com/libeigen/eigen/-/archive/%(version)s'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['b4c198460eba6f28d34894e3a5710998818515104d6e74e5cc331ce31e46e626'] + +# using CMake built with GCCcore to avoid relying on the system compiler to build it +builddependencies = [ + ('binutils', '2.42'), # to make CMake compiler health check pass on old systems + ('CMake', '3.29.3'), +] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/e/EvidentialGene/EvidentialGene-2018.01.01-gompi-2023a.eb b/easybuild/easyconfigs/e/EvidentialGene/EvidentialGene-2018.01.01-gompi-2023a.eb new file mode 100644 index 00000000000..15d8b4dc07c --- /dev/null +++ b/easybuild/easyconfigs/e/EvidentialGene/EvidentialGene-2018.01.01-gompi-2023a.eb @@ -0,0 +1,40 @@ +easyblock = "PackedBinary" + +name = "EvidentialGene" +version = '2018.01.01' +local_month = ['', 'jan', 'feb', 'mar', 'apr', 'may', 'jun', 'jul', 'aug', 'sep', 'oct', 'nov', 'dec'] +local_dlver = version.split('.')[0][-2:] + local_month[int(version.split('.')[1])] + version.split('.')[2] + +homepage = 'http://arthropods.eugenes.org/EvidentialGene/' +description = """EvidentialGene is a genome informatics project for + "Evidence Directed Gene Construction for Eukaryotes", + for constructing high quality, accurate gene sets for + animals and plants (any eukaryotes), being developed by + Don Gilbert at Indiana University, gilbertd at indiana edu.""" + +toolchain = {'name': 'gompi', 'version': '2023a'} + +source_urls = [ + 'http://arthropods.eugenes.org/EvidentialGene/other/evigene_old/', + 'http://arthropods.eugenes.org/EvidentialGene/other/evigene_old/evigene_older/', +] +sources = ['evigene%s.tar' % local_dlver] +checksums = ['6972108112cdb1fb106da11321d06b09f518b544e4739d0bf19da1984131e221'] + +dependencies = [ + ('Perl', '5.36.1'), + ('Exonerate', '2.4.0'), + ('CD-HIT', '4.8.1'), + ('BLAST+', '2.14.1'), +] + +fix_perl_shebang_for = ['scripts/*.pl', 'scripts/*/*.pl', 'scripts/*/*/*.pl'] + +sanity_check_paths = { + 'files': [], + 'dirs': ['scripts/'], +} + +modextravars = {'evigene': '%(installdir)s'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/e/EvidentialGene/EvidentialGene-2023.07.15-gompi-2023a.eb b/easybuild/easyconfigs/e/EvidentialGene/EvidentialGene-2023.07.15-gompi-2023a.eb new file mode 100644 index 00000000000..c4ae0c4e12d --- /dev/null +++ b/easybuild/easyconfigs/e/EvidentialGene/EvidentialGene-2023.07.15-gompi-2023a.eb @@ -0,0 +1,40 @@ +easyblock = "PackedBinary" + +name = "EvidentialGene" +version = '2023.07.15' +local_month = ['', 'jan', 'feb', 'mar', 'apr', 'may', 'jun', 'jul', 'aug', 'sep', 'oct', 'nov', 'dec'] +local_dlver = version.split('.')[0][-2:] + local_month[int(version.split('.')[1])] + version.split('.')[2] + +homepage = 'http://arthropods.eugenes.org/EvidentialGene/' +description = """EvidentialGene is a genome informatics project for + "Evidence Directed Gene Construction for Eukaryotes", + for constructing high quality, accurate gene sets for + animals and plants (any eukaryotes), being developed by + Don Gilbert at Indiana University, gilbertd at indiana edu.""" + +toolchain = {'name': 'gompi', 'version': '2023a'} + +source_urls = [ + 'http://arthropods.eugenes.org/EvidentialGene/other/evigene_old/', + 'http://arthropods.eugenes.org/EvidentialGene/other/evigene_old/evigene_older/', +] +sources = ['evigene%s.tar' % local_dlver] +checksums = ['8fe8e5c21ac3f8b7134d8e26593fe66647eb8b7ba2c1cd1c158fc811769b9539'] + +dependencies = [ + ('Perl', '5.36.1'), + ('Exonerate', '2.4.0'), + ('CD-HIT', '4.8.1'), + ('BLAST+', '2.14.1'), +] + +fix_perl_shebang_for = ['scripts/*.pl', 'scripts/*/*.pl', 'scripts/*/*/*.pl'] + +sanity_check_paths = { + 'files': [], + 'dirs': ['scripts/'], +} + +modextravars = {'evigene': '%(installdir)s'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/e/Exonerate/Exonerate-2.4.0-GCC-12.3.0.eb b/easybuild/easyconfigs/e/Exonerate/Exonerate-2.4.0-GCC-12.3.0.eb new file mode 100644 index 00000000000..4e57e85a280 --- /dev/null +++ b/easybuild/easyconfigs/e/Exonerate/Exonerate-2.4.0-GCC-12.3.0.eb @@ -0,0 +1,47 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel +# foss-2016b modified by: +# Adam Huffman +# The Francis Crick Institute + +easyblock = 'ConfigureMake' + +name = 'Exonerate' +version = '2.4.0' + +homepage = 'https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate' +# also https://github.com/nathanweeks/exonerate +description = """ Exonerate is a generic tool for pairwise sequence comparison. + It allows you to align sequences using a many alignment models, using either + exhaustive dynamic programming, or a variety of heuristics. """ + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +source_urls = ['https://ftp.ebi.ac.uk/pub/software/vertebrategenomics/%(namelower)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['f849261dc7c97ef1f15f222e955b0d3daf994ec13c9db7766f1ac7e77baa4042'] + +builddependencies = [ + ('pkgconf', '1.9.5'), +] +dependencies = [ + ('GLib', '2.77.1'), +] + +# parallel build fails +parallel = 1 + +runtest = 'check' + +_bins = ['exonerate', 'fastaclip', 'fastacomposition', 'fastafetch', 'fastaoverlap', 'ipcress'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in _bins], + 'dirs': ['share'], +} + +sanity_check_commands = ['%s -h | grep "from exonerate version %%(version)s"' % x for x in _bins] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/e/Extrae/Extrae-4.2.0-debug_add_event.patch b/easybuild/easyconfigs/e/Extrae/Extrae-4.2.0-debug_add_event.patch new file mode 100644 index 00000000000..bd5c925f69f --- /dev/null +++ b/easybuild/easyconfigs/e/Extrae/Extrae-4.2.0-debug_add_event.patch @@ -0,0 +1,12 @@ +diff -Nru extrae-4.2.0.orig/src/tracer/hwc/papi_hwc.c extrae-4.2.0/src/tracer/hwc/papi_hwc.c +--- extrae-4.2.0.orig/src/tracer/hwc/papi_hwc.c 2024-07-01 16:12:04.562957639 +0200 ++++ extrae-4.2.0/src/tracer/hwc/papi_hwc.c 2024-07-02 17:21:19.783586061 +0200 +@@ -615,7 +615,7 @@ + char EventName[PAPI_MAX_STR_LEN]; + + PAPI_event_code_to_name (HWC_sets[i].counters[j], EventName); +- fprintf (stderr, PACKAGE_NAME": Error! Hardware counter %s (0x%08x) cannot be added in set %d (task %d, thread %d)\n", EventName, HWC_sets[i].counters[j], i+1, TASKID, threadid); ++ fprintf (stderr, PACKAGE_NAME": Error! Hardware counter %s (0x%08x) cannot be added in set %d (task %d, thread %d) because of %d\n", EventName, HWC_sets[i].counters[j], i+1, TASKID, threadid, rc); + HWC_sets[i].counters[j] = NO_COUNTER; + /* break; */ + } diff --git a/easybuild/easyconfigs/e/Extrae/Extrae-4.2.0-detect_binutils.patch b/easybuild/easyconfigs/e/Extrae/Extrae-4.2.0-detect_binutils.patch new file mode 100644 index 00000000000..ae5847ad80e --- /dev/null +++ b/easybuild/easyconfigs/e/Extrae/Extrae-4.2.0-detect_binutils.patch @@ -0,0 +1,42 @@ +diff -Nru extrae-4.2.0.orig/config/macros.m4 extrae-4.2.0/config/macros.m4 +--- extrae-4.2.0.orig/config/macros.m4 2024-07-01 16:12:03.689962036 +0200 ++++ extrae-4.2.0/config/macros.m4 2024-07-01 16:13:05.811649165 +0200 +@@ -779,6 +779,8 @@ + elif test -r "${binutils_home_dir}/lib/libbfd.a" -a \ + "${binutils_require_shared}" = "no" ; then + BFD_LIBSDIR="${binutils_home_dir}/lib" ++ elif test -r "${binutils_home_dir}/libbfd.so" ; then ++ BFD_LIBSDIR="${binutils_home_dir}" + else + dnl Try something more automatic using find command + libbfd_lib="" +@@ -814,6 +816,8 @@ + LIBERTY_LIBSDIR="${binutils_home_dir}/lib" + elif test -r "${binutils_home_dir}/lib/libiberty.a" ; then + LIBERTY_LIBSDIR="${binutils_home_dir}/lib" ++ elif test -r "${binutils_home_dir}/libiberty.a" ; then ++ LIBERTY_LIBSDIR="${binutils_home_dir}" + else + dnl Try something more automatic using find command + libiberty_lib="" +diff -Nru extrae-4.2.0.orig/configure extrae-4.2.0/configure +--- extrae-4.2.0.orig/configure 2024-07-01 16:12:03.308963954 +0200 ++++ extrae-4.2.0/configure 2024-07-01 16:17:00.458465744 +0200 +@@ -35074,6 +35074,8 @@ + elif test -r "${binutils_home_dir}/lib/libbfd.a" -a \ + "${binutils_require_shared}" = "no" ; then + BFD_LIBSDIR="${binutils_home_dir}/lib" ++ elif test -r "${binutils_home_dir}/libbfd.so" ; then ++ BFD_LIBSDIR="${binutils_home_dir}" + else + libbfd_lib="" + +@@ -35108,6 +35110,8 @@ + LIBERTY_LIBSDIR="${binutils_home_dir}/lib" + elif test -r "${binutils_home_dir}/lib/libiberty.a" ; then + LIBERTY_LIBSDIR="${binutils_home_dir}/lib" ++ elif test -r "${binutils_home_dir}/libiberty.a" ; then ++ LIBERTY_LIBSDIR="${binutils_home_dir}" + else + libiberty_lib="" + diff --git a/easybuild/easyconfigs/e/Extrae/Extrae-4.2.0-fix-hw-counters-checks.patch b/easybuild/easyconfigs/e/Extrae/Extrae-4.2.0-fix-hw-counters-checks.patch new file mode 100644 index 00000000000..2d588694b4c --- /dev/null +++ b/easybuild/easyconfigs/e/Extrae/Extrae-4.2.0-fix-hw-counters-checks.patch @@ -0,0 +1,137 @@ +diff -Nru extrae-4.2.0.orig/tests/functional/hw-counters/check_Extrae_PAPI_TOT_CYC.sh extrae-4.2.0/tests/functional/hw-counters/check_Extrae_PAPI_TOT_CYC.sh +--- extrae-4.2.0.orig/tests/functional/hw-counters/check_Extrae_PAPI_TOT_CYC.sh 2024-07-01 16:12:03.454963219 +0200 ++++ extrae-4.2.0/tests/functional/hw-counters/check_Extrae_PAPI_TOT_CYC.sh 2024-07-03 16:51:00.533542188 +0200 +@@ -10,7 +10,29 @@ + EXTRAE_CONFIG_FILE=extrae-PAPI_TOT_CYC.xml ./check_Extrae_counters_xml + ../../../src/merger/mpi2prv -f TRACE.mpits -o ${TRACE}.prv + +-# Check ++# Check PAPI availability ++if ! command -v papi_avail &> /dev/null ++then ++ echo "papi_avail could not be found" ++ exit 0 ++fi ++ ++# Check COUNTER availability ++PAPI_TOT_CYC_available=`papi_avail | grep PAPI_TOT_CYC | awk '{print $3}'` ++if [[ "$PAPI_TOT_CYC_available" == No ]] ++then ++ echo "PAPI_TOT_CYC is not available" ++ exit 0 ++fi ++ ++# Check that HW counters are accessible ++ACCESS_LEVEL=`sysctl kernel.perf_event_paranoid |awk '{print $3}'` ++if [ $ACCESS_LEVEL \> 1 ] ++then ++ echo "perf_event_paranoid configuration does not allow access to HW counters" ++ exit 0 ++fi ++ + CheckEntryInPCF ${TRACE}.pcf PAPI_TOT_CYC + + rm -fr TRACE* set-0 ${TRACE}.??? +diff -Nru extrae-4.2.0.orig/tests/functional/hw-counters/check_Extrae_PAPI_TOT_INS_CYC.sh extrae-4.2.0/tests/functional/hw-counters/check_Extrae_PAPI_TOT_INS_CYC.sh +--- extrae-4.2.0.orig/tests/functional/hw-counters/check_Extrae_PAPI_TOT_INS_CYC.sh 2024-07-01 16:12:03.448963249 +0200 ++++ extrae-4.2.0/tests/functional/hw-counters/check_Extrae_PAPI_TOT_INS_CYC.sh 2024-07-03 16:52:55.509932826 +0200 +@@ -10,7 +10,30 @@ + EXTRAE_CONFIG_FILE=extrae-PAPI_TOT_INS_CYC.xml ./check_Extrae_counters_xml + ../../../src/merger/mpi2prv -f TRACE.mpits -o ${TRACE}.prv + +-# Check ++# Check PAPI availability ++if ! command -v papi_avail &> /dev/null ++then ++ echo "papi_avail could not be found" ++ exit 0 ++fi ++ ++# Check COUNTER availability ++PAPI_TOT_CYC_available=`papi_avail | grep PAPI_TOT_CYC | awk '{print $3}'` ++if [[ "$PAPI_TOT_CYC_available" == No ]] ++then ++ echo "PAPI_TOT_CYC is not available" ++ exit 0 ++fi ++ ++# Check counters accessibility level ++ACCESS_LEVEL=`sysctl kernel.perf_event_paranoid |awk '{print $3}'` ++if [ $ACCESS_LEVEL \> 1 ] ++then ++ echo "perf_event_paranoid configuration does not allow access to HW counters" ++ exit 0 ++fi ++ ++ + CheckEntryInPCF ${TRACE}.pcf PAPI_TOT_INS + CheckEntryInPCF ${TRACE}.pcf PAPI_TOT_CYC + +diff -Nru extrae-4.2.0.orig/tests/functional/hw-counters/check_Extrae_PAPI_TOT_INS.sh extrae-4.2.0/tests/functional/hw-counters/check_Extrae_PAPI_TOT_INS.sh +--- extrae-4.2.0.orig/tests/functional/hw-counters/check_Extrae_PAPI_TOT_INS.sh 2024-07-01 16:12:03.455963214 +0200 ++++ extrae-4.2.0/tests/functional/hw-counters/check_Extrae_PAPI_TOT_INS.sh 2024-07-03 16:54:17.878497036 +0200 +@@ -10,7 +10,29 @@ + EXTRAE_CONFIG_FILE=extrae-PAPI_TOT_INS.xml ./check_Extrae_counters_xml + ../../../src/merger/mpi2prv -f TRACE.mpits -o ${TRACE}.prv + +-# Check ++# Check PAPI availability ++if ! command -v papi_avail &> /dev/null ++then ++ echo "papi_avail could not be found" ++ exit 0 ++fi ++ ++# Check COUNTERS availability ++PAPI_TOT_INS_available=`papi_avail | grep PAPI_TOT_INS | awk '{print $3}'` ++if [[ "$PAPI_TOT_INS_available" == No ]] ++then ++ echo "PAPI_TOT_INS is not available" ++ exit 0 ++fi ++ ++# Check COUNTERS accessibility level ++ACCESS_LEVEL=`sysctl kernel.perf_event_paranoid |awk '{print $3}'` ++if [ $ACCESS_LEVEL \> 1 ] ++then ++ echo "perf_event_paranoid configuration does not allow access to HW counters" ++ exit 0 ++fi ++ + CheckEntryInPCF ${TRACE}.pcf PAPI_TOT_INS + + rm -fr TRACE* set-0 ${TRACE}.??? +diff -Nru extrae-4.2.0.orig/tests/functional/xml/check_Extrae_xml_envvar_counters.sh extrae-4.2.0/tests/functional/xml/check_Extrae_xml_envvar_counters.sh +--- extrae-4.2.0.orig/tests/functional/xml/check_Extrae_xml_envvar_counters.sh 2024-07-01 16:12:03.484963068 +0200 ++++ extrae-4.2.0/tests/functional/xml/check_Extrae_xml_envvar_counters.sh 2024-07-03 16:56:41.975736132 +0200 +@@ -10,7 +10,29 @@ + COUNTERS=PAPI_TOT_INS EXTRAE_CONFIG_FILE=extrae_envvar_counters.xml ./check_Extrae_xml + ../../../src/merger/mpi2prv -f TRACE.mpits -o ${TRACE}.prv + +-# Check ++# Check PAPI availability ++if ! command -v papi_avail &> /dev/null ++then ++ echo "papi_avail could not be found" ++ exit 0 ++fi ++ ++# Check COUNTER availability ++PAPI_TOT_INS_available=`papi_avail | grep PAPI_TOT_INS | awk '{print $3}'` ++if [[ "$PAPI_TOT_INS_available" == No ]] ++then ++ echo "PAPI_TOT_INS is not available" ++ exit 0 ++fi ++ ++# Check COUNTERS accessibility level ++ACCESS_LEVEL=`sysctl kernel.perf_event_paranoid |awk '{print $3}'` ++if [ $ACCESS_LEVEL \> 1 ] ++then ++ echo "perf_event_paranoid configuration does not allow access to HW counters" ++ exit 0 ++fi ++ + CheckEntryInPCF ${TRACE}.pcf PAPI_TOT_INS + + rm -fr TRACE* set-0 ${TRACE}.??? diff --git a/easybuild/easyconfigs/e/Extrae/Extrae-4.2.0-gompi-2023b.eb b/easybuild/easyconfigs/e/Extrae/Extrae-4.2.0-gompi-2023b.eb new file mode 100644 index 00000000000..4fca4663aca --- /dev/null +++ b/easybuild/easyconfigs/e/Extrae/Extrae-4.2.0-gompi-2023b.eb @@ -0,0 +1,54 @@ +name = 'Extrae' +version = '4.2.0' + +homepage = 'https://tools.bsc.es/extrae' +description = """Extrae is the package devoted to generate Paraver trace-files for a post-mortem analysis. +Extrae is a tool that uses different interposition mechanisms to inject probes into the target application +so as to gather information regarding the application performance.""" + +toolchain = {'name': 'gompi', 'version': '2023b'} + +toolchainopts = {'usempi': True} + +source_urls = ['https://ftp.tools.bsc.es/%(namelower)s'] + +sources = ['%(namelower)s-%(version)s-src.tar.bz2'] + +patches = [ + 'Extrae-4.2.0-detect_binutils.patch', + 'Extrae-4.2.0-fix-hw-counters-checks.patch', + 'Extrae-4.2.0-debug_add_event.patch', +] + +checksums = [ + # extrae-4.2.0-src.tar.bz2 + '7b83a1ed008440bbc1bda88297d2d0e9256780db1cf8401b3c12718451f8919a', + '1c7bf9d97405c5c2f9dba3604faf141c1563c70958e942822aab521eb7ea0c9e', # Extrae-4.2.0-detect_binutils.patch + '147d897a5a9ba6ebb1b5de32c964b2cd73534f31a540125a94fd37f2ceb1edfe', # Extrae-4.2.0-fix-hw-counters-checks.patch + '9c3541b16f1acf6ff56ab44a24d44c2ec91f9415be217c39f9c0a32e2093ccca', # Extrae-4.2.0-debug_add_event.patch +] + +builddependencies = [ + ('Automake', '1.16.5'), +] + +dependencies = [ + ('zlib', '1.2.13'), + ('Boost', '1.83.0'), + ('libxml2', '2.11.5'), + ('libdwarf', '0.9.2'), + ('PAPI', '7.1.0'), +] + +# libunwind causes segv errors on aarch64 +if ARCH != 'aarch64': + dependencies.append( + ('libunwind', '1.6.2'), + ) + +# Disable dynamic memory instrumentation for this release, has been seen to sometimes cause MPI test failures +configopts = '--disable-instrument-dynamic-memory' + +runtest = 'check' + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/e/e3nn/e3nn-0.3.3-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/e/e3nn/e3nn-0.3.3-foss-2023a-CUDA-12.1.1.eb new file mode 100644 index 00000000000..8c30352e396 --- /dev/null +++ b/easybuild/easyconfigs/e/e3nn/e3nn-0.3.3-foss-2023a-CUDA-12.1.1.eb @@ -0,0 +1,40 @@ +easyblock = 'PythonBundle' + +name = 'e3nn' +version = '0.3.3' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://e3nn.org/' +description = """ +Euclidean neural networks (e3nn) is a python library based on pytorch to create equivariant +neural networks for the group O(3). +""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('CUDA', '12.1.1', '', SYSTEM), + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('PyTorch', '2.1.2', versionsuffix), + ('sympy', '1.12'), +] + +use_pip = True + +exts_list = [ + ('opt-einsum', '3.3.0', { + 'source_tmpl': 'opt_einsum-%(version)s.tar.gz', + 'checksums': ['59f6475f77bbc37dcf7cd748519c0ec60722e91e63ca114e68821c0c54a46549'], + }), + ('opt_einsum_fx', '0.1.4', { + 'checksums': ['7eeb7f91ecb70be65e6179c106ea7f64fc1db6319e3d1289a4518b384f81e74f'], + }), + (name, version, { + 'checksums': ['532b34a5644153659253c59943fe4224cd9c3c46ce8a79f1dc7c00afccb44ecb'], + }), +] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/e/ecBuild/ecBuild-3.8.5-GCCcore-13.3.0.eb b/easybuild/easyconfigs/e/ecBuild/ecBuild-3.8.5-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..97c3992ce77 --- /dev/null +++ b/easybuild/easyconfigs/e/ecBuild/ecBuild-3.8.5-GCCcore-13.3.0.eb @@ -0,0 +1,37 @@ +easyblock = 'Tarball' + +name = 'ecBuild' +version = '3.8.5' + +homepage = 'https://ecbuild.readthedocs.io/' + +description = """ +A CMake-based build system, consisting of a collection of CMake macros and +functions that ease the managing of software build systems """ + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +github_account = 'ecmwf' +sources = [ + { + 'source_urls': [GITHUB_SOURCE], + 'filename': '%(version)s.tar.gz', + 'extract_cmd': 'tar -xzf %s --strip-components=1', + }, +] +checksums = ['aa0c44cab0fffec4c0b3542e91ebcc736b3d41b68a068d30c023ec0df5f93425'] + +builddependencies = [('binutils', '2.42')] + +buildininstalldir = True + +skipsteps = ['install'] + +sanity_check_paths = { + 'files': ['bin/ecbuild', 'cmake/ecbuild-config.cmake'], + 'dirs': ['bin', 'lib', 'share', 'cmake'], +} + +sanity_check_commands = ['ecbuild --help'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/e/ecCodes/ecCodes-2.27.0-iimpi-2022a.eb b/easybuild/easyconfigs/e/ecCodes/ecCodes-2.27.0-iimpi-2022a.eb new file mode 100644 index 00000000000..33fddc6886a --- /dev/null +++ b/easybuild/easyconfigs/e/ecCodes/ecCodes-2.27.0-iimpi-2022a.eb @@ -0,0 +1,47 @@ +easyblock = 'CMakeMake' + +name = 'ecCodes' +version = '2.27.0' + +homepage = 'https://software.ecmwf.int/wiki/display/ECC/ecCodes+Home' +description = """ecCodes is a package developed by ECMWF which provides an application programming interface and + a set of tools for decoding and encoding messages in the following formats: WMO FM-92 GRIB edition 1 and edition 2, + WMO FM-94 BUFR edition 3 and edition 4, WMO GTS abbreviated header (only decoding).""" + +toolchain = {'name': 'iimpi', 'version': '2022a'} +toolchainopts = {'usempi': False} + +source_urls = ['https://confluence.ecmwf.int/download/attachments/45757960/'] +sources = ['eccodes-%(version)s-Source.tar.gz'] +checksums = ['ede5b3ffd503967a5eac89100e8ead5e16a881b7585d02f033584ed0c4269c99'] + +builddependencies = [('CMake', '3.23.1')] + +dependencies = [ + ('netCDF', '4.9.0'), + ('JasPer', '2.0.33'), + ('libjpeg-turbo', '2.1.3'), + ('libpng', '1.6.37'), + ('zlib', '1.2.12'), + ('libaec', '1.0.6'), +] + +# Python bindings are provided by a separate package 'eccodes-python' +configopts = "-DENABLE_NETCDF=ON -DENABLE_PNG=ON -DENABLE_PYTHON=OFF " +configopts += "-DENABLE_JPG=ON -DENABLE_JPG_LIBJASPER=ON " +configopts += "-DENABLE_ECCODES_THREADS=ON" # multi-threading with pthreads + +local_exes = ['%s_%s' % (a, b) + for a in ['bufr', 'grib', 'gts', 'metar'] + for b in ['compare', 'copy', 'dump', 'filter', 'get', 'ls']] +local_exes += ['codes_%s' % c for c in ['count', 'info', 'split_file']] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_exes] + + ['lib/libeccodes_f90.%s' % SHLIB_EXT, 'lib/libeccodes.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +sanity_check_commands = ['%s -V' % x for x in local_exes if not x.startswith('codes_')] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/e/ecCodes/ecCodes-2.38.3-gompi-2024a.eb b/easybuild/easyconfigs/e/ecCodes/ecCodes-2.38.3-gompi-2024a.eb new file mode 100644 index 00000000000..2aa0915ea2e --- /dev/null +++ b/easybuild/easyconfigs/e/ecCodes/ecCodes-2.38.3-gompi-2024a.eb @@ -0,0 +1,46 @@ +easyblock = 'CMakeMake' + +name = 'ecCodes' +version = '2.38.3' + +homepage = 'https://software.ecmwf.int/wiki/display/ECC/ecCodes+Home' +description = """ecCodes is a package developed by ECMWF which provides an application programming interface and + a set of tools for decoding and encoding messages in the following formats: WMO FM-92 GRIB edition 1 and edition 2, + WMO FM-94 BUFR edition 3 and edition 4, WMO GTS abbreviated header (only decoding).""" + +toolchain = {'name': 'gompi', 'version': '2024a'} +toolchainopts = {'usempi': False} + +source_urls = ['https://github.com/ecmwf/eccodes/archive/refs/tags/'] +sources = [{'download_filename': '%(version)s.tar.gz', 'filename': '%(namelower)s-%(version)s.tar.gz'}] +checksums = ['2f13adc4fbdfa3ea11f75ce4ed8937bf40a8fcedd760a519b15e4e17dedc9424'] + +builddependencies = [ + ('CMake', '3.29.3'), + ('ecBuild', '3.8.5'), +] +dependencies = [ + ('netCDF', '4.9.2'), + ('JasPer', '4.2.4'), + ('libjpeg-turbo', '3.0.1'), + ('libpng', '1.6.43'), + ('zlib', '1.3.1'), + ('libaec', '1.1.3'), +] + +# Python bindings are provided by a separate package 'eccodes-python' +configopts = "-DENABLE_NETCDF=ON -DENABLE_PNG=ON -DENABLE_PYTHON=OFF -DENABLE_JPG=ON " +configopts += "-DENABLE_JPG_LIBJASPER=ON -DENABLE_ECCODES_THREADS=ON" + + +sanity_check_paths = { + 'files': ['bin/bufr_compare', 'bin/bufr_copy', 'bin/bufr_dump', 'bin/bufr_filter', 'bin/bufr_get', 'bin/bufr_ls', + 'bin/grib_compare', 'bin/grib_copy', 'bin/grib_dump', 'bin/grib_filter', 'bin/grib_get', 'bin/grib_ls', + 'bin/gts_compare', 'bin/gts_copy', 'bin/gts_dump', 'bin/gts_filter', 'bin/gts_get', 'bin/gts_ls', + 'bin/metar_compare', 'bin/metar_copy', 'bin/metar_dump', 'bin/metar_filter', 'bin/metar_get', + 'bin/metar_ls', 'bin/codes_count', 'bin/codes_info', 'bin/codes_split_file', + 'lib/libeccodes_f90.%s' % SHLIB_EXT, 'lib/libeccodes.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/e/edlib/edlib-1.3.9.post1-GCC-13.3.0.eb b/easybuild/easyconfigs/e/edlib/edlib-1.3.9.post1-GCC-13.3.0.eb new file mode 100644 index 00000000000..96672c2751b --- /dev/null +++ b/easybuild/easyconfigs/e/edlib/edlib-1.3.9.post1-GCC-13.3.0.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonBundle' + +name = 'edlib' +version = '1.3.9.post1' + +homepage = 'https://martinsos.github.io/edlib' +description = "Lightweight, super fast library for sequence alignment using edit (Levenshtein) distance." + +toolchain = {'name': 'GCC', 'version': '13.3.0'} + +dependencies = [ + ('Python', '3.12.3'), + ('Python-bundle-PyPI', '2024.06'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('cogapp', '3.4.1', { + 'checksums': ['a806d5db9e318a1a2d3fce988008179168e7db13e5e55b19b79763f9bb9d2982'], + }), + (name, version, { + 'checksums': ['b0fb6e85882cab02208ccd6daa46f80cb9ff1d05764e91bf22920a01d7a6fbfa'], + }), +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/e/eggnog-mapper/eggnog-mapper-2.1.12-foss-2023a.eb b/easybuild/easyconfigs/e/eggnog-mapper/eggnog-mapper-2.1.12-foss-2023a.eb new file mode 100644 index 00000000000..4937c8bba74 --- /dev/null +++ b/easybuild/easyconfigs/e/eggnog-mapper/eggnog-mapper-2.1.12-foss-2023a.eb @@ -0,0 +1,56 @@ +# Eggnog DB installation instructions: +# 1. 'export EGGNOG_DATA_DIR=//eggnog-mapper-data' +# 2. run 'download_eggnog_data.py' +# 3. Check the expected DB version with 'emapper.py --version' + +easyblock = 'PythonPackage' + +name = 'eggnog-mapper' +version = '2.1.12' + +homepage = 'https://github.com/eggnogdb/eggnog-mapper' +description = """EggNOG-mapper is a tool for fast functional annotation of novel +sequences. It uses precomputed orthologous groups and phylogenies from the +eggNOG database (http://eggnog5.embl.de) to transfer functional information from +fine-grained orthologs only. Common uses of eggNOG-mapper include the annotation +of novel genomes, transcriptomes or even metagenomic gene catalogs.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +github_account = 'eggnogdb' +source_urls = [GITHUB_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['b3c53fb0e606a5cfec75cbc84f7c215f57f43ce00d8e50f449513acdad76da73'] + +dependencies = [ + ('Python', '3.11.3'), + ('Biopython', '1.83'), + ('HMMER', '3.4'), + ('DIAMOND', '2.1.8'), + ('prodigal', '2.6.3'), + ('wget', '1.24.5'), + ('MMseqs2', '14-7e284'), + ('XlsxWriter', '3.1.3'), +] + +# strip out (too) strict version requirements for dependencies +preinstallopts = "sed -i 's/==[0-9.]*//g' setup.cfg && " + +use_pip = True +sanity_pip_check = True +download_dep_fail = True + +sanity_check_paths = { + 'files': ['bin/create_dbs.py', 'bin/download_eggnog_data.py', 'bin/emapper.py'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + 'download_eggnog_data.py --help', + 'create_dbs.py --help', + 'emapper.py --version | grep %(version)s', +] + +options = {'modulename': 'eggnogmapper'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/e/einops/einops-0.7.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/e/einops/einops-0.7.0-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..7af581e455f --- /dev/null +++ b/easybuild/easyconfigs/e/einops/einops-0.7.0-GCCcore-12.2.0.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonPackage' + +name = 'einops' +version = '0.7.0' + +homepage = 'https://einops.rocks/' +description = """ +Flexible and powerful tensor operations for readable and reliable code. +Supports numpy, pytorch, tensorflow, jax, and others.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['b2b04ad6081a3b227080c9bf5e3ace7160357ff03043cd66cc5b2319eb7031d1'] + +builddependencies = [ + ('binutils', '2.39'), +] + +dependencies = [ + ('Python', '3.10.8'), +] + +download_dep_fail = True +use_pip = True + +sanity_pip_check = True + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/e/elfutils/elfutils-0.191-GCCcore-13.3.0.eb b/easybuild/easyconfigs/e/elfutils/elfutils-0.191-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..e5eb4ef3c7d --- /dev/null +++ b/easybuild/easyconfigs/e/elfutils/elfutils-0.191-GCCcore-13.3.0.eb @@ -0,0 +1,41 @@ +easyblock = 'ConfigureMake' + +name = 'elfutils' +version = '0.191' + +homepage = 'https://elfutils.org/' + +description = """ + The elfutils project provides libraries and tools for ELF files + and DWARF data. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://sourceware.org/elfutils/ftp/%(version)s/'] +sources = [SOURCE_TAR_BZ2] +checksums = ['df76db71366d1d708365fc7a6c60ca48398f14367eb2b8954efc8897147ad871'] + +builddependencies = [ + ('M4', '1.4.19'), + ('pkgconf', '2.2.0'), +] + +dependencies = [ + ('binutils', '2.42'), + ('bzip2', '1.0.8'), + ('libarchive', '3.7.4'), + ('XZ', '5.4.5'), + ('zstd', '1.5.6'), +] + +configopts = "--disable-debuginfod --disable-libdebuginfod" + +sanity_check_paths = { + 'files': ['bin/eu-elfcmp', 'include/dwarf.h', 'lib/libelf.%s' % SHLIB_EXT], + 'dirs': [] +} + +sanity_check_commands = ["eu-elfcmp --help"] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/e/empanada-dl/empanada-dl-0.1.7-foss-2023a.eb b/easybuild/easyconfigs/e/empanada-dl/empanada-dl-0.1.7-foss-2023a.eb new file mode 100644 index 00000000000..168c3e3c751 --- /dev/null +++ b/easybuild/easyconfigs/e/empanada-dl/empanada-dl-0.1.7-foss-2023a.eb @@ -0,0 +1,43 @@ +easyblock = 'PythonBundle' + +name = 'empanada-dl' +version = '0.1.7' + +homepage = 'https://empanada.readthedocs.io/' +description = "Tool for panoptic segmentation of organelles in 2D and 3D electron microscopy (EM) images." + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('SciPy-bundle', '2023.07'), + ('numba', '0.58.1'), + ('OpenCV', '4.8.1', '-contrib'), + ('PyYAML', '6.0'), + ('zarr', '2.17.1'), + ('torchvision', '0.16.0'), + ('Albumentations', '1.4.0'), + ('dask', '2023.9.2'), + ('connected-components-3d', '3.14.1'), + ('matplotlib', '3.7.2'), + ('imagecodecs', '2024.1.1'), +] + +use_pip = True + +exts_list = [ + ('cztile', '0.1.2', { + 'checksums': ['3e42c4a93fd7b2df985b42e66dc3c585b3ebd9c1167e9f7e7d5c34c57697b929'], + }), + (name, version, { + # fix requirements - numpy version and opencv-python>=4.5.3 - pip is not aware of cv2 in OpenCV from EB + 'preinstallopts': "sed -i 's/numpy==1.22/numpy>=1.22/g' setup.cfg && sed -i '34d' setup.cfg && ", + 'modulename': 'empanada', + 'checksums': ['4289e69842242203be77cdb656a12fb2be4ed83816969b24a0b4eab1d67c3b91'], + }), +] + +sanity_pip_check = True + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/e/empanada-napari/empanada-napari-1.1.0-foss-2023a.eb b/easybuild/easyconfigs/e/empanada-napari/empanada-napari-1.1.0-foss-2023a.eb new file mode 100644 index 00000000000..e429617f718 --- /dev/null +++ b/easybuild/easyconfigs/e/empanada-napari/empanada-napari-1.1.0-foss-2023a.eb @@ -0,0 +1,38 @@ +easyblock = 'PythonBundle' + +name = 'empanada-napari' +version = '1.1.0' + +homepage = 'https://empanada.readthedocs.io/' +description = "Panoptic segmentation algorithms for 2D and 3D electron microscopy in napari." + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('SciPy-bundle', '2023.07'), + ('napari', '0.4.18'), + ('MLflow', '2.10.2'), + ('openpyxl', '3.1.2'), + ('SimpleITK', '2.3.1'), + ('imagecodecs', '2024.1.1'), + ('Albumentations', '1.4.0'), + ('connected-components-3d', '3.14.1'), + ('empanada-dl', '0.1.7'), +] + +exts_list = [ + ('ImageHash', '4.3.1', { + 'checksums': ['7038d1b7f9e0585beb3dd8c0a956f02b95a346c0b5f24a9e8cc03ebadaf0aa70'], + }), + (name, version, { + 'preinstallopts': "sed -i 's/numpy==1.22/numpy>=1.22/g' setup.cfg && ", + 'checksums': ['f4890cb6f20689933e28903dd7d43238aeae32afb53fa225bdf41d4bdcfc2c71'], + }), +] + +use_pip = True +sanity_pip_check = True + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/e/enchant-2/enchant-2-2.6.5-GCCcore-12.3.0.eb b/easybuild/easyconfigs/e/enchant-2/enchant-2-2.6.5-GCCcore-12.3.0.eb index af01c621328..9f66e2f8724 100644 --- a/easybuild/easyconfigs/e/enchant-2/enchant-2-2.6.5-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/e/enchant-2/enchant-2-2.6.5-GCCcore-12.3.0.eb @@ -6,7 +6,7 @@ easyblock = 'ConfigureMake' name = 'enchant-2' version = '2.6.5' -homepage = 'https://github.com/AbiWord/enchant' +homepage = 'http://rrthomas.github.io/enchant/' description = """Enchant aims to provide a simple but comprehensive abstraction for dealing with different spell checking libraries in a consistent way. A client, such as a text editor or word processor, need not know anything about a specific @@ -15,7 +15,7 @@ be added without needing any change to the program using Enchant.""" toolchain = {'name': 'GCCcore', 'version': '12.3.0'} -source_urls = ['https://github.com/AbiWord/enchant/releases/download/v%(version)s'] +source_urls = ['https://github.com/rrthomas/enchant/releases/download/v%(version)s'] sources = ['enchant-%(version)s.tar.gz'] checksums = ['9e8fd28cb65a7b6da3545878a5c2f52a15f03c04933a5ff48db89fe86845728e'] diff --git a/easybuild/easyconfigs/e/epiScanpy/epiScanpy-0.4.0-foss-2023a.eb b/easybuild/easyconfigs/e/epiScanpy/epiScanpy-0.4.0-foss-2023a.eb index 552e826a3a2..45d4f74af79 100644 --- a/easybuild/easyconfigs/e/epiScanpy/epiScanpy-0.4.0-foss-2023a.eb +++ b/easybuild/easyconfigs/e/epiScanpy/epiScanpy-0.4.0-foss-2023a.eb @@ -11,6 +11,10 @@ analysis tool Scanpy (Genome Biology, 2018) [Wolf18].""" toolchain = {'name': 'foss', 'version': '2023a'} +builddependencies = [ + ('hatchling', '1.18.0'), +] + dependencies = [ ('Python', '3.11.3'), ('SciPy-bundle', '2023.07'), diff --git a/easybuild/easyconfigs/e/exiv2/exiv2-0.28.3-GCCcore-13.3.0.eb b/easybuild/easyconfigs/e/exiv2/exiv2-0.28.3-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..fba04816180 --- /dev/null +++ b/easybuild/easyconfigs/e/exiv2/exiv2-0.28.3-GCCcore-13.3.0.eb @@ -0,0 +1,38 @@ +easyblock = 'CMakeMake' + +name = 'exiv2' +version = '0.28.3' + +homepage = 'http://www.exiv2.org' +description = """ + Exiv2 is a C++ library and a command line utility to manage image metadata. It provides fast and easy read and write + access to the Exif, IPTC and XMP metadata of digital images in various formats. Exiv2 is available as free software and + with a commercial license, and is used in many projects. +""" + + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://github.com/Exiv2/exiv2/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['1315e17d454bf4da3cc0edb857b1d2c143670f3485b537d0f946d9ed31d87b70'] + +builddependencies = [ + ('binutils', '2.42'), + ('CMake', '3.29.3'), +] + +dependencies = [ + ('expat', '2.6.2'), + ('Brotli', '1.1.0'), + ('inih', '58'), +] + +sanity_check_paths = { + 'files': ['bin/exiv2', 'lib/libexiv2.%s' % SHLIB_EXT], + 'dirs': [] +} + +sanity_check_commands = ["exiv2 --help"] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/e/expat/expat-2.6.2-GCCcore-13.3.0.eb b/easybuild/easyconfigs/e/expat/expat-2.6.2-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..41b5a1340fb --- /dev/null +++ b/easybuild/easyconfigs/e/expat/expat-2.6.2-GCCcore-13.3.0.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'expat' +version = '2.6.2' + +homepage = 'https://libexpat.github.io' + +description = """Expat is an XML parser library written in C. It is a stream-oriented parser +in which an application registers handlers for things the parser might find +in the XML document (like start tags).""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/libexpat/libexpat/releases/download/R_%s/' % version.replace('.', '_')] +sources = [SOURCE_TAR_BZ2] +checksums = ['9c7c1b5dcbc3c237c500a8fb1493e14d9582146dd9b42aa8d3ffb856a3b927e0'] + +builddependencies = [('binutils', '2.42')] + +# Since expat 2.2.6, docbook2X is needed to produce manpage of xmlwf. +# Docbook2X needs XML-Parser and XML-Parser needs expat. +# -> circular dependency. "--without-docbook" breaks this circle. +configopts = ['--without-docbook'] + +sanity_check_paths = { + 'files': ['include/expat.h', 'lib/libexpat.a', 'lib/libexpat.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/e/expecttest/expecttest-0.2.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/e/expecttest/expecttest-0.2.1-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..a70bf3973ca --- /dev/null +++ b/easybuild/easyconfigs/e/expecttest/expecttest-0.2.1-GCCcore-13.3.0.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonPackage' + +name = 'expecttest' +version = '0.2.1' + +homepage = 'https://github.com/ezyang/expecttest' +description = """This library implements expect tests (also known as "golden" tests). Expect tests are a method of + writing tests where instead of hard-coding the expected output of a test, you run the test to get the output, and + the test framework automatically populates the expected output. If the output of the test changes, you can rerun + the test with the environment variable EXPECTTEST_ACCEPT=1 to automatically update the expected output.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['e52b1cf8a6f84506e6962a0bbdd248ea442124d826e849f263ec1c322ebb73f5'] + +builddependencies = [ + ('binutils', '2.42'), + ('poetry', '1.8.3'), +] +dependencies = [ + ('Python', '3.12.3'), +] + +download_dep_fail = True +sanity_pip_check = True +use_pip = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/f/FASTA/FASTA-36.3.8i-GCC-12.3.0.eb b/easybuild/easyconfigs/f/FASTA/FASTA-36.3.8i-GCC-12.3.0.eb new file mode 100644 index 00000000000..58fd687455a --- /dev/null +++ b/easybuild/easyconfigs/f/FASTA/FASTA-36.3.8i-GCC-12.3.0.eb @@ -0,0 +1,36 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild + +easyblock = 'MakeCp' + +name = "FASTA" +version = "36.3.8i" +local_version_date = '14-Nov-2020' + +homepage = 'https://fasta.bioch.virginia.edu/fasta_www2/fasta_list2.shtml' +description = """The FASTA programs find regions of local or global (new) similarity between +protein or DNA sequences, either by searching Protein or DNA databases, or by identifying +local duplications within a sequence.""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +source_urls = ['https://github.com/wrpearson/fasta36/archive/'] +sources = ['v%%(version)s_%s.tar.gz' % local_version_date] +checksums = ['b4b1c3c9be6beebcbaf4215368e159d69255e34c0bdbc84affa10cdb473ce008'] + +buildopts = '-C ./src -f ../make/Makefile.linux_sse2 all' + +files_to_copy = ["bin", "conf", "data", "doc", "FASTA_LIST", "misc", "README", "seq", "sql", "test"] + +postinstallcmds = ["cd %(installdir)s/bin && ln -s fasta%(version_major)s fasta"] + +sanity_check_paths = { + 'files': ["FASTA_LIST", "README"] + ['bin/%s' % x for x in ['map_db']] + + ['bin/%s%%(version_major)s' % x for x in ['fasta', 'fastm', 'fastx', 'ggsearch', 'lalign', 'tfastf', + 'tfasts', 'tfasty', 'fastf', 'fasts', 'fasty', 'glsearch', + 'ssearch', 'tfastm', 'tfastx']], + 'dirs': ["conf", "data", "doc", "misc", "seq", "sql", "test"] +} + +sanity_check_commands = ["fasta --help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/f/FFTW.MPI/FFTW.MPI-3.3.10-gmpich-2024.06.eb b/easybuild/easyconfigs/f/FFTW.MPI/FFTW.MPI-3.3.10-gmpich-2024.06.eb new file mode 100644 index 00000000000..4b79e9e7c27 --- /dev/null +++ b/easybuild/easyconfigs/f/FFTW.MPI/FFTW.MPI-3.3.10-gmpich-2024.06.eb @@ -0,0 +1,19 @@ +name = 'FFTW.MPI' +version = '3.3.10' + +homepage = 'https://www.fftw.org' +description = """FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) +in one or more dimensions, of arbitrary input size, and of both real and complex data.""" + +toolchain = {'name': 'gmpich', 'version': '2024.06'} +toolchainopts = {'pic': True} + +source_urls = [homepage] +sources = ['fftw-%(version)s.tar.gz'] +checksums = ['56c932549852cddcfafdab3820b0200c7742675be92179e59e6215b340e26467'] + +dependencies = [('FFTW', '3.3.10')] + +runtest = 'check' + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/f/FFTW.MPI/FFTW.MPI-3.3.10-gompi-2024.05.eb b/easybuild/easyconfigs/f/FFTW.MPI/FFTW.MPI-3.3.10-gompi-2024.05.eb new file mode 100644 index 00000000000..b6ab2a2d4f0 --- /dev/null +++ b/easybuild/easyconfigs/f/FFTW.MPI/FFTW.MPI-3.3.10-gompi-2024.05.eb @@ -0,0 +1,19 @@ +name = 'FFTW.MPI' +version = '3.3.10' + +homepage = 'https://www.fftw.org' +description = """FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) +in one or more dimensions, of arbitrary input size, and of both real and complex data.""" + +toolchain = {'name': 'gompi', 'version': '2024.05'} +toolchainopts = {'pic': True} + +source_urls = [homepage] +sources = ['fftw-%(version)s.tar.gz'] +checksums = ['56c932549852cddcfafdab3820b0200c7742675be92179e59e6215b340e26467'] + +dependencies = [('FFTW', '3.3.10')] + +runtest = 'check' + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/f/FFTW.MPI/FFTW.MPI-3.3.10-gompi-2024a.eb b/easybuild/easyconfigs/f/FFTW.MPI/FFTW.MPI-3.3.10-gompi-2024a.eb new file mode 100644 index 00000000000..2ed420c412f --- /dev/null +++ b/easybuild/easyconfigs/f/FFTW.MPI/FFTW.MPI-3.3.10-gompi-2024a.eb @@ -0,0 +1,19 @@ +name = 'FFTW.MPI' +version = '3.3.10' + +homepage = 'https://www.fftw.org' +description = """FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) +in one or more dimensions, of arbitrary input size, and of both real and complex data.""" + +toolchain = {'name': 'gompi', 'version': '2024a'} +toolchainopts = {'pic': True} + +source_urls = [homepage] +sources = ['fftw-%(version)s.tar.gz'] +checksums = ['56c932549852cddcfafdab3820b0200c7742675be92179e59e6215b340e26467'] + +dependencies = [('FFTW', '3.3.10')] + +runtest = 'check' + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.10-GCC-13.3.0.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.10-GCC-13.3.0.eb new file mode 100644 index 00000000000..bf18544e701 --- /dev/null +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.10-GCC-13.3.0.eb @@ -0,0 +1,17 @@ +name = 'FFTW' +version = '3.3.10' + +homepage = 'https://www.fftw.org' +description = """FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) +in one or more dimensions, of arbitrary input size, and of both real and complex data.""" + +toolchain = {'name': 'GCC', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +source_urls = [homepage] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['56c932549852cddcfafdab3820b0200c7742675be92179e59e6215b340e26467'] + +runtest = 'check' + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/f/FFmpeg/FFmpeg-5.0.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-5.0.1-GCCcore-11.3.0.eb index 5f6462eec21..6a468c1f81d 100644 --- a/easybuild/easyconfigs/f/FFmpeg/FFmpeg-5.0.1-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-5.0.1-GCCcore-11.3.0.eb @@ -33,7 +33,7 @@ dependencies = [ configopts = '--enable-pic --enable-shared --enable-gpl --enable-version3 --enable-nonfree --cc="$CC" --cxx="$CXX" ' configopts += '--enable-libx264 --enable-libx265 --enable-libmp3lame --enable-libfreetype --enable-fontconfig ' -configopts += '--enable-libfribidi --enable-sdl2' +configopts += '--enable-libfribidi --enable-sdl2 --disable-htmlpages' sanity_check_paths = { 'files': ['bin/ff%s' % x for x in ['mpeg', 'probe', 'play']] + diff --git a/easybuild/easyconfigs/f/FFmpeg/FFmpeg-5.1.2-GCCcore-12.2.0.eb b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-5.1.2-GCCcore-12.2.0.eb index b06aee26953..dfe40032efc 100644 --- a/easybuild/easyconfigs/f/FFmpeg/FFmpeg-5.1.2-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-5.1.2-GCCcore-12.2.0.eb @@ -33,7 +33,7 @@ dependencies = [ configopts = '--enable-pic --enable-shared --enable-gpl --enable-version3 --enable-nonfree --cc="$CC" --cxx="$CXX" ' configopts += '--enable-libx264 --enable-libx265 --enable-libmp3lame --enable-libfreetype --enable-fontconfig ' -configopts += '--enable-libfribidi --enable-sdl2' +configopts += '--enable-libfribidi --enable-sdl2 --disable-htmlpages' sanity_check_paths = { 'files': ['bin/ff%s' % x for x in ['mpeg', 'probe', 'play']] + diff --git a/easybuild/easyconfigs/f/FFmpeg/FFmpeg-6.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-6.0-GCCcore-12.3.0.eb index 4f5fb4a0bc5..caa80fed59d 100644 --- a/easybuild/easyconfigs/f/FFmpeg/FFmpeg-6.0-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-6.0-GCCcore-12.3.0.eb @@ -33,7 +33,7 @@ dependencies = [ configopts = '--enable-pic --enable-shared --enable-gpl --enable-version3 --enable-nonfree --cc="$CC" --cxx="$CXX" ' configopts += '--enable-libx264 --enable-libx265 --enable-libmp3lame --enable-libfreetype --enable-fontconfig ' -configopts += '--enable-libfribidi --enable-sdl2' +configopts += '--enable-libfribidi --enable-sdl2 --disable-htmlpages' sanity_check_paths = { 'files': ['bin/ff%s' % x for x in ['mpeg', 'probe', 'play']] + diff --git a/easybuild/easyconfigs/f/FFmpeg/FFmpeg-6.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-6.0-GCCcore-13.2.0.eb index fab8972c089..c75695951f6 100644 --- a/easybuild/easyconfigs/f/FFmpeg/FFmpeg-6.0-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-6.0-GCCcore-13.2.0.eb @@ -33,7 +33,7 @@ dependencies = [ configopts = '--enable-pic --enable-shared --enable-gpl --enable-version3 --enable-nonfree --cc="$CC" --cxx="$CXX" ' configopts += '--enable-libx264 --enable-libx265 --enable-libmp3lame --enable-libfreetype --enable-fontconfig ' -configopts += '--enable-libfribidi --enable-sdl2' +configopts += '--enable-libfribidi --enable-sdl2 --disable-htmlpages' sanity_check_paths = { 'files': ['bin/ff%s' % x for x in ['mpeg', 'probe', 'play']] + diff --git a/easybuild/easyconfigs/f/FFmpeg/FFmpeg-7.0.2-GCCcore-13.3.0.eb b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-7.0.2-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..246a8306b76 --- /dev/null +++ b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-7.0.2-GCCcore-13.3.0.eb @@ -0,0 +1,45 @@ +easyblock = 'ConfigureMake' + +name = 'FFmpeg' +version = '7.0.2' + +homepage = 'https://www.ffmpeg.org/' +description = "A complete, cross-platform solution to record, convert and stream audio and video." + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://%(namelower)s.org/releases/'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['1ed250407ea8f955cca2f1139da3229fbc13032a0802e4b744be195865ff1541'] + +builddependencies = [ + ('binutils', '2.42'), + ('pkgconf', '2.2.0'), + ('ffnvcodec', '12.2.72.0', '', SYSTEM), # optional nvenc/dec support +] +dependencies = [ + ('NASM', '2.16.03'), + ('zlib', '1.3.1'), + ('bzip2', '1.0.8'), + ('x264', '20240513'), + ('LAME', '3.100'), + ('x265', '3.6'), + ('X11', '20240607'), + ('freetype', '2.13.2'), + ('fontconfig', '2.15.0'), + ('FriBidi', '1.0.15'), + ('SDL2', '2.30.6'), +] + +configopts = '--enable-pic --enable-shared --enable-gpl --enable-version3 --enable-nonfree --cc="$CC" --cxx="$CXX" ' +configopts += '--enable-libx264 --enable-libx265 --enable-libmp3lame --enable-libfreetype --enable-fontconfig ' +configopts += '--enable-libfribidi --enable-sdl2 --disable-htmlpages' + +sanity_check_paths = { + 'files': ['bin/ff%s' % x for x in ['mpeg', 'probe', 'play']] + + ['lib/lib%s.%s' % (x, y) for x in ['avdevice', 'avfilter', 'avformat', 'avcodec', 'postproc', + 'swresample', 'swscale', 'avutil'] for y in [SHLIB_EXT, 'a']], + 'dirs': ['include'] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/f/FLAC/FLAC-1.4.3-GCCcore-13.2.0.eb b/easybuild/easyconfigs/f/FLAC/FLAC-1.4.3-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..a0abaac6ca9 --- /dev/null +++ b/easybuild/easyconfigs/f/FLAC/FLAC-1.4.3-GCCcore-13.2.0.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'FLAC' +version = '1.4.3' + +homepage = 'https://xiph.org/flac/' +description = """FLAC stands for Free Lossless Audio Codec, an audio format similar to MP3, but lossless, meaning +that audio is compressed in FLAC without any loss in quality.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://ftp.osuosl.org/pub/xiph/releases/flac/'] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['6c58e69cd22348f441b861092b825e591d0b822e106de6eb0ee4d05d27205b70'] + +builddependencies = [('binutils', '2.40')] + +dependencies = [('libogg', '1.3.5')] + +configopts = '--enable-static --enable-shared' + +sanity_check_paths = { + 'files': ['bin/flac', 'lib/libFLAC.a', 'lib/libFLAC++.a', + 'lib/libFLAC.%s' % SHLIB_EXT, 'lib/libFLAC++.%s' % SHLIB_EXT], + 'dirs': ['include/FLAC', 'include/FLAC++'], +} + +sanity_check_commands = ["flac --help"] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/f/FLAC/FLAC-1.4.3-GCCcore-13.3.0.eb b/easybuild/easyconfigs/f/FLAC/FLAC-1.4.3-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..f767483f7cd --- /dev/null +++ b/easybuild/easyconfigs/f/FLAC/FLAC-1.4.3-GCCcore-13.3.0.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'FLAC' +version = '1.4.3' + +homepage = 'https://xiph.org/flac/' +description = """FLAC stands for Free Lossless Audio Codec, an audio format similar to MP3, but lossless, meaning +that audio is compressed in FLAC without any loss in quality.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://ftp.osuosl.org/pub/xiph/releases/flac/'] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['6c58e69cd22348f441b861092b825e591d0b822e106de6eb0ee4d05d27205b70'] + +builddependencies = [('binutils', '2.42')] + +dependencies = [('libogg', '1.3.5')] + +configopts = '--enable-static --enable-shared' + +sanity_check_paths = { + 'files': ['bin/flac', 'lib/libFLAC.a', 'lib/libFLAC++.a', + 'lib/libFLAC.%s' % SHLIB_EXT, 'lib/libFLAC++.%s' % SHLIB_EXT], + 'dirs': ['include/FLAC', 'include/FLAC++'], +} + +sanity_check_commands = ["flac --help"] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/f/FLANN/FLANN-1.9.2-foss-2022b.eb b/easybuild/easyconfigs/f/FLANN/FLANN-1.9.2-foss-2022b.eb new file mode 100644 index 00000000000..ce4946fff26 --- /dev/null +++ b/easybuild/easyconfigs/f/FLANN/FLANN-1.9.2-foss-2022b.eb @@ -0,0 +1,42 @@ +# Contribution from the NIHR Biomedical Research Centre +# Guy's and St Thomas' NHS Foundation Trust and King's College London +# uploaded by J. Sassmannshausen + +easyblock = 'CMakeMake' + +name = 'FLANN' +version = '1.9.2' + +homepage = 'https://github.com/mariusmuja/flann/' +description = "FLANN is a library for performing fast approximate nearest neighbor searches in high dimensional spaces." + +toolchain = {'name': 'foss', 'version': '2022b'} +toolchainopts = {'openmp': True} + +source_urls = ['https://github.com/mariusmuja/flann/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['e26829bb0017f317d9cc45ab83ddcb8b16d75ada1ae07157006c1e7d601c8824'] + +builddependencies = [ + ('CMake', '3.24.3'), +] + +dependencies = [ + ('Python', '3.10.8'), + ('SciPy-bundle', '2023.02'), + ('lz4', '1.9.4'), +] + +configopts = "-DUSE_OPENMP=ON -DUSE_MPI=ON -DBUILD_PYTHON_BINDINGS=ON -DBUILD_C_BINDINGS=ON" + +modextrapaths = {'PYTHONPATH': ['share/flann/python']} + +sanity_check_paths = { + 'files': ['lib/libflann_cpp_s.a', 'lib/libflann_s.a', + 'lib/libflann_cpp.%s' % SHLIB_EXT, 'lib/libflann.%s' % SHLIB_EXT], + 'dirs': ['include/flann', 'lib/pkgconfig', 'share/flann/python'], +} + +sanity_check_commands = ["python -c 'import pyflann'"] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/f/FLANN/FLANN-1.9.2-foss-2023a.eb b/easybuild/easyconfigs/f/FLANN/FLANN-1.9.2-foss-2023a.eb new file mode 100644 index 00000000000..37143785fe1 --- /dev/null +++ b/easybuild/easyconfigs/f/FLANN/FLANN-1.9.2-foss-2023a.eb @@ -0,0 +1,40 @@ +# Contribution from the NIHR Biomedical Research Centre +# Guy's and St Thomas' NHS Foundation Trust and King's College London +# uploaded by J. Sassmannshausen + +easyblock = 'CMakeMake' + +name = 'FLANN' +version = '1.9.2' + +homepage = 'https://github.com/mariusmuja/flann/' +description = "FLANN is a library for performing fast approximate nearest neighbor searches in high dimensional spaces." + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'openmp': True} + +source_urls = ['https://github.com/mariusmuja/flann/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['e26829bb0017f317d9cc45ab83ddcb8b16d75ada1ae07157006c1e7d601c8824'] + +builddependencies = [('CMake', '3.26.3')] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('lz4', '1.9.4'), +] + +configopts = "-DUSE_OPENMP=ON -DUSE_MPI=ON -DBUILD_PYTHON_BINDINGS=ON -DBUILD_C_BINDINGS=ON" + +modextrapaths = {'PYTHONPATH': ['share/flann/python']} + +sanity_check_paths = { + 'files': ['lib/libflann_cpp_s.a', 'lib/libflann_s.a', + 'lib/libflann_cpp.%s' % SHLIB_EXT, 'lib/libflann.%s' % SHLIB_EXT], + 'dirs': ['include/flann', 'lib/pkgconfig', 'share/flann/python'], +} + +sanity_check_commands = ["python -c 'import pyflann'"] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/f/FLINT/FLINT-3.1.2-gfbf-2024a.eb b/easybuild/easyconfigs/f/FLINT/FLINT-3.1.2-gfbf-2024a.eb new file mode 100644 index 00000000000..970496a35d0 --- /dev/null +++ b/easybuild/easyconfigs/f/FLINT/FLINT-3.1.2-gfbf-2024a.eb @@ -0,0 +1,45 @@ +easyblock = 'CMakeMake' + +name = 'FLINT' +version = '3.1.2' + +homepage = 'https://www.flintlib.org/' + +description = """FLINT (Fast Library for Number Theory) is a C library in support of computations + in number theory. Operations that can be performed include conversions, arithmetic, computing GCDs, + factoring, solving linear systems, and evaluating special functions. In addition, FLINT provides + various low-level routines for fast arithmetic. FLINT is extensively documented and tested.""" + +toolchain = {'name': 'gfbf', 'version': '2024a'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.flintlib.org'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['fdb3a431a37464834acff3bdc145f4fe8d0f951dd5327c4c6f93f4cbac5c2700'] + +builddependencies = [ + ('CMake', '3.29.3'), + ('Python', '3.12.3'), +] + +dependencies = [ + ('GMP', '6.3.0'), + ('MPFR', '4.2.1'), + ('NTL', '11.5.1'), +] + +# Make flexiblas the first to be found and used to avoid linking openblas. +preconfigopts = 'sed -i "s/PATH_SUFFIXES openblas/PATH_SUFFIXES flexiblas openblas/g;' +preconfigopts += 's/accelerate openblas/accelerate flexiblas openblas/g" ' +preconfigopts += '%(builddir)s/%(namelower)s-%(version)s/CMake/FindCBLAS.cmake && ' + +configopts = '-DWITH_NTL=on -DBUILD_TESTING=yes' + +runtest = 'test' + +sanity_check_paths = { + 'files': ['lib/lib%%(namelower)s.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/f/FLTK/FLTK-1.3.9-GCCcore-13.2.0.eb b/easybuild/easyconfigs/f/FLTK/FLTK-1.3.9-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..3afeffc0a2c --- /dev/null +++ b/easybuild/easyconfigs/f/FLTK/FLTK-1.3.9-GCCcore-13.2.0.eb @@ -0,0 +1,43 @@ +easyblock = 'ConfigureMake' + +name = 'FLTK' +version = '1.3.9' + +homepage = 'https://www.fltk.org' +description = """FLTK is a cross-platform C++ GUI toolkit for UNIX/Linux (X11), Microsoft Windows, + and MacOS X. FLTK provides modern GUI functionality without the bloat and supports 3D graphics via OpenGL + and its built-in GLUT emulation.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://fltk.org/pub/%(namelower)s/%(version)s/'] +sources = ['%(namelower)s-%(version)s-source.tar.gz'] +patches = ['FLTK-1.3.6_fix-LDFLAGS.patch'] +checksums = [ + {'fltk-1.3.9-source.tar.gz': 'd736b0445c50d607432c03d5ba5e82f3fba2660b10bc1618db8e077a42d9511b'}, + {'FLTK-1.3.6_fix-LDFLAGS.patch': 'f8af2414a1ee193a186b0d98d1e3567add0ee003f44ec64dce2ce2dfd6d95ebf'}, +] + +configopts = '--enable-shared --enable-threads --enable-xft' + +builddependencies = [ + ('binutils', '2.40'), + ('groff', '1.23.0'), +] + +dependencies = [ + ('Mesa', '23.1.9'), + ('libGLU', '9.0.3'), + ('libpng', '1.6.40'), + ('libjpeg-turbo', '3.0.1'), + ('xprop', '1.2.7'), + ('zlib', '1.2.13'), +] + +sanity_check_paths = { + 'files': ['bin/fltk-config', 'bin/fluid', 'lib/libfltk.a', 'lib/libfltk.%s' % SHLIB_EXT], + 'dirs': ['lib'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/f/FUSE/FUSE-3.14.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/f/FUSE/FUSE-3.14.1-GCCcore-11.3.0.eb index 856159422b1..f82d2647ceb 100644 --- a/easybuild/easyconfigs/f/FUSE/FUSE-3.14.1-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/f/FUSE/FUSE-3.14.1-GCCcore-11.3.0.eb @@ -18,13 +18,15 @@ builddependencies = [ ('binutils', '2.38'), ] -# -Dutils=True only works as root -configopts = '-Dutils=False' +# avoid that root permissions are required when installing utils (like fusermount) +configopts = "-Dinitscriptdir=%(installdir)s/etc/init.d -Dudevrulesdir=%(installdir)s/udev/rules.d -Duseroot=false" sanity_check_paths = { - 'files': ['lib64/libfuse%%(version_major)s.%s' % SHLIB_EXT, - 'lib64/pkgconfig/fuse%(version_major)s.pc'], - 'dirs': ['include/fuse%(version_major)s'], + 'files': ['bin/fusermount3', 'etc/fuse.conf', 'lib/libfuse%%(version_major)s.%s' % SHLIB_EXT, + 'lib/pkgconfig/fuse%(version_major)s.pc'], + 'dirs': ['include/fuse%(version_major)s', 'share/man'], } +sanity_check_commands = ["fusermount3 -h | grep '^fusermount3'"] + moduleclass = 'lib' diff --git a/easybuild/easyconfigs/f/FUSE/FUSE-3.14.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/f/FUSE/FUSE-3.14.1-GCCcore-12.2.0.eb index 1be42749206..b16a0debad6 100644 --- a/easybuild/easyconfigs/f/FUSE/FUSE-3.14.1-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/f/FUSE/FUSE-3.14.1-GCCcore-12.2.0.eb @@ -18,13 +18,15 @@ builddependencies = [ ('binutils', '2.39') ] -# -Dutils=True only works as root -configopts = '-Dutils=False' +# avoid that root permissions are required when installing utils (like fusermount) +configopts = "-Dinitscriptdir=%(installdir)s/etc/init.d -Dudevrulesdir=%(installdir)s/udev/rules.d -Duseroot=false" sanity_check_paths = { - 'files': ['lib64/libfuse%%(version_major)s.%s' % SHLIB_EXT, - 'lib64/pkgconfig/fuse%(version_major)s.pc'], - 'dirs': ['include/fuse%(version_major)s'], + 'files': ['bin/fusermount3', 'etc/fuse.conf', 'lib/libfuse%%(version_major)s.%s' % SHLIB_EXT, + 'lib/pkgconfig/fuse%(version_major)s.pc'], + 'dirs': ['include/fuse%(version_major)s', 'share/man'], } +sanity_check_commands = ["fusermount3 -h | grep '^fusermount3'"] + moduleclass = 'lib' diff --git a/easybuild/easyconfigs/f/FUSE/FUSE-3.16.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/f/FUSE/FUSE-3.16.2-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..341358950aa --- /dev/null +++ b/easybuild/easyconfigs/f/FUSE/FUSE-3.16.2-GCCcore-12.3.0.eb @@ -0,0 +1,32 @@ +easyblock = 'MesonNinja' + +name = 'FUSE' +version = '3.16.2' + +homepage = 'https://github.com/libfuse/libfuse' +description = "The reference implementation of the Linux FUSE (Filesystem in Userspace) interface" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://github.com/libfuse/libfuse/archive/'] +sources = ['fuse-%(version)s.tar.gz'] +checksums = ['1bc306be1a1f4f6c8965fbdd79c9ccca021fdc4b277d501483a711cbd7dbcd6c'] + +builddependencies = [ + ('Meson', '1.1.1'), + ('Ninja', '1.11.1'), + ('binutils', '2.40'), +] + +# avoid that root permissions are required when installing utils (like fusermount) +configopts = "-Dinitscriptdir=%(installdir)s/etc/init.d -Dudevrulesdir=%(installdir)s/udev/rules.d -Duseroot=false" + +sanity_check_paths = { + 'files': ['bin/fusermount3', 'etc/fuse.conf', 'lib/libfuse%%(version_major)s.%s' % SHLIB_EXT, + 'lib/pkgconfig/fuse%(version_major)s.pc'], + 'dirs': ['include/fuse%(version_major)s', 'share/man'], +} + +sanity_check_commands = ["fusermount3 -h | grep '^fusermount3'"] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/f/Faiss/Faiss-1.7.4-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/f/Faiss/Faiss-1.7.4-foss-2023a-CUDA-12.1.1.eb new file mode 100644 index 00000000000..1a9b1727bba --- /dev/null +++ b/easybuild/easyconfigs/f/Faiss/Faiss-1.7.4-foss-2023a-CUDA-12.1.1.eb @@ -0,0 +1,70 @@ +# Author: Jasper Grimm (UoY) +easyblock = 'CMakePythonPackage' + +name = 'Faiss' +version = '1.7.4' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/facebookresearch/faiss' +description = """ +Faiss is a library for efficient similarity search and clustering of dense + vectors. It contains algorithms that search in sets of vectors of any size, up + to ones that possibly do not fit in RAM. It also contains supporting code for + evaluation and parameter tuning. Faiss is written in C++ with complete + wrappers for Python/numpy. Some of the most useful algorithms are implemented + on the GPU. It is developed primarily at Meta's Fundamental AI Research group. +""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +github_account = 'facebookresearch' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['d9a7b31bf7fd6eb32c10b7ea7ff918160eed5be04fe63bb7b4b4b5f2bbde01ad'] + +builddependencies = [ + ('CMake', '3.26.3'), + ('SWIG', '4.1.1'), +] + +dependencies = [ + ('CUDA', '12.1.1', '', SYSTEM), + ('Python', '3.11.3'), + ('PyTorch', '2.1.2', versionsuffix), + ('SciPy-bundle', '2023.07'), +] + +_copts = [ + '-DFAISS_ENABLE_GPU=ON', + '-DFAISS_ENABLE_PYTHON=ON', + '-DFAISS_ENABLE_C_API=ON', + '-DBUILD_TESTING=ON', + '-DBUILD_SHARED_LIBS=ON', + '-DPython_EXECUTABLE="${EBROOTPYTHON}/bin/python"', + '-DCUDAToolkit_ROOT="${CUDA_ROOT}"', + '-DCMAKE_CUDA_ARCHITECTURES="%(cuda_cc_cmake)s"', + '-DCMAKE_INSTALL_LIBDIR=%(installdir)s/lib', +] + +configopts = ' '.join(_copts) + +buildopts = 'faiss swigfaiss' + +postinstallcmds = [ + ' && '.join([ + # run a pip install in the 'faiss/python' subdir + 'cd ../easybuild_obj/%(namelower)s/python', + 'python -m pip install --prefix=%(installdir)s --no-build-isolation .', + # for some reason, 'libfaiss_python_callbacks.so' doesn't get installed, so copy this manually + 'cp libfaiss_python_callbacks.%s %%(installdir)s/lib/python%%(pyshortver)s/site-packages/faiss' % SHLIB_EXT + ]) +] + +modextrapaths = {'LD_LIBRARY_PATH': "lib/python%(pyshortver)s/site-packages/faiss"} + +sanity_check_paths = { + 'files': ['lib/lib%%(namelower)s.%s' % SHLIB_EXT], + 'dirs': ['include/%(namelower)s', 'lib/python%(pyshortver)s/site-packages/%(namelower)s'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/f/FastTree/FastTree-2.1.11-GCCcore-12.2.0.eb b/easybuild/easyconfigs/f/FastTree/FastTree-2.1.11-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..abb4f293128 --- /dev/null +++ b/easybuild/easyconfigs/f/FastTree/FastTree-2.1.11-GCCcore-12.2.0.eb @@ -0,0 +1,42 @@ +# Updated from previous config +# Author: Pavel Grochal (INUITS) +# License: GPLv2 + +easyblock = 'CmdCp' + +name = 'FastTree' +version = '2.1.11' + +homepage = 'http://www.microbesonline.org/fasttree/' +description = """FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide + or protein sequences. FastTree can handle alignments with up to a million of sequences in a reasonable amount of + time and memory. """ + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'openmp': True} + +# HTTPS cert error: +# hostname 'www.microbesonline.org' doesn't match either of 'genomics.lbl.gov', 'mojave.qb3.berkeley.edu', ... +source_urls = ['http://www.microbesonline.org/fasttree/'] +sources = [{'filename': '%(name)s-%(version)s.c', 'extract_cmd': 'cp %s FastTree.c'}] +checksums = ['9026ae550307374be92913d3098f8d44187d30bea07902b9dcbfb123eaa2050f'] + +builddependencies = [('binutils', '2.39')] + +cmds_map = [('%(name)s-%(version)s.c', '$CC -DOPENMP $CFLAGS $LIBS %%(source)s -o %(name)s')] + +files_to_copy = [(['FastTree'], 'bin')] + +# as FastTree is built with OpenMP, the correct binary is FastTreeMP +# the FastTree binary should normally be built without OpenMP, but let’s keep it as is for backward compatibility +# see http://www.microbesonline.org/fasttree/#OpenMP +postinstallcmds = ['cd %(installdir)s/bin && ln -s FastTree FastTreeMP'] + +sanity_check_paths = { + 'files': ['bin/FastTree'], + 'dirs': [], +} + +sanity_check_commands = ['FastTree 2>&1 | grep "FastTree Version %(version)s"'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/f/FastTree/FastTree-2.1.11-GCCcore-13.2.0.eb b/easybuild/easyconfigs/f/FastTree/FastTree-2.1.11-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..b44229828a4 --- /dev/null +++ b/easybuild/easyconfigs/f/FastTree/FastTree-2.1.11-GCCcore-13.2.0.eb @@ -0,0 +1,42 @@ +# Updated from previous config +# Author: Pavel Grochal (INUITS) +# License: GPLv2 + +easyblock = 'CmdCp' + +name = 'FastTree' +version = '2.1.11' + +homepage = 'http://www.microbesonline.org/fasttree/' +description = """FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide + or protein sequences. FastTree can handle alignments with up to a million of sequences in a reasonable amount of + time and memory. """ + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} +toolchainopts = {'openmp': True} + +# HTTPS cert error: +# hostname 'www.microbesonline.org' doesn't match either of 'genomics.lbl.gov', 'mojave.qb3.berkeley.edu', ... +source_urls = ['http://www.microbesonline.org/fasttree/'] +sources = [{'filename': '%(name)s-%(version)s.c', 'extract_cmd': 'cp %s FastTree.c'}] +checksums = ['9026ae550307374be92913d3098f8d44187d30bea07902b9dcbfb123eaa2050f'] + +builddependencies = [('binutils', '2.40')] + +cmds_map = [('%(name)s-%(version)s.c', '$CC -DOPENMP $CFLAGS $LIBS %%(source)s -o %(name)s')] + +files_to_copy = [(['FastTree'], 'bin')] + +# as FastTree is built with OpenMP, the correct binary is FastTreeMP +# the FastTree binary should normally be built without OpenMP, but let’s keep it as is for backward compatibility +# see http://www.microbesonline.org/fasttree/#OpenMP +postinstallcmds = ['cd %(installdir)s/bin && ln -s FastTree FastTreeMP'] + +sanity_check_paths = { + 'files': ['bin/FastTree'], + 'dirs': [], +} + +sanity_check_commands = ['FastTree 2>&1 | grep "FastTree Version %(version)s"'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/f/Filtlong/Filtlong-0.2.1-GCC-12.3.0.eb b/easybuild/easyconfigs/f/Filtlong/Filtlong-0.2.1-GCC-12.3.0.eb new file mode 100644 index 00000000000..25bf2c570f0 --- /dev/null +++ b/easybuild/easyconfigs/f/Filtlong/Filtlong-0.2.1-GCC-12.3.0.eb @@ -0,0 +1,39 @@ +# This file is an EasyBuild reciPY as per https://easybuilders.github.io/easybuild/ +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'MakeCp' + +name = 'Filtlong' +version = '0.2.1' + +homepage = 'https://github.com/rrwick/Filtlong' +description = """Filtlong is a tool for filtering long reads by quality. It can take a set + of long reads and produce a smaller, better subset. It uses both read length (longer is better) + and read identity (higher is better) when choosing which reads pass the filter""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +source_urls = ['https://github.com/rrwick/Filtlong/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['e6f47675e87f98cf2481a60bef5cad38396f1e4db653a5c1673139f37770273a'] + +unpack_options = '--strip-components=1' + +parallel = 1 + +dependencies = [ + ('zlib', '1.2.13'), +] + +files_to_copy = ["*"] + +sanity_check_paths = { + 'files': ['bin/filtlong'], + 'dirs': [] +} + +sanity_check_commands = ["filtlong --help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/f/Flask/Flask-3.0.3-GCCcore-13.3.0.eb b/easybuild/easyconfigs/f/Flask/Flask-3.0.3-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..46b9452f48b --- /dev/null +++ b/easybuild/easyconfigs/f/Flask/Flask-3.0.3-GCCcore-13.3.0.eb @@ -0,0 +1,65 @@ +easyblock = 'PythonBundle' + +name = 'Flask' +version = '3.0.3' + +homepage = 'https://flask.palletsprojects.com/' +description = """ +Flask is a lightweight WSGI web application framework. It is designed to make +getting started quick and easy, with the ability to scale up to complex +applications. +This module includes the Flask extensions: Flask-Cors""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +builddependencies = [ + ('binutils', '2.42'), +] +dependencies = [ + ('Python', '3.12.3'), + ('Python-bundle-PyPI', '2024.06'), +] + +sanity_pip_check = True +use_pip = True + +exts_list = [ + ('itsdangerous', '2.2.0', { + 'checksums': ['e0050c0b7da1eea53ffaf149c0cfbb5c6e2e2b69c4bef22c81fa6eb73e5f6173'], + }), + ('werkzeug', '3.0.4', { + 'checksums': ['34f2371506b250df4d4f84bfe7b0921e4762525762bbd936614909fe25cd7306'], + }), + ('asgiref', '3.7.2', { + 'checksums': ['9e0ce3aa93a819ba5b45120216b23878cf6e8525eb3848653452b4192b92afed'], + }), + ('blinker', '1.8.2', { + 'checksums': ['8f77b09d3bf7c795e969e9486f39c2c5e9c39d4ee07424be2bc594ece9642d83'], + }), + ('flask', version, { + 'checksums': ['ceb27b0af3823ea2737928a4d99d125a06175b8512c445cbd9a9ce200ef76842'], + }), + ('msgspec', '0.18.6', { + 'checksums': ['a59fc3b4fcdb972d09138cb516dbde600c99d07c38fd9372a6ef500d2d031b4e'], + }), + ('Flask-Cors', '5.0.0', { + 'sources': ['flask_cors-%(version)s.tar.gz'], + 'checksums': ['5aadb4b950c4e93745034594d9f3ea6591f734bb3662e16e255ffbf5e89c88ef'], + }), + ('cachelib', '0.13.0', { + 'checksums': ['209d8996e3c57595bee274ff97116d1d73c4980b2fd9a34c7846cd07fd2e1a48'], + }), + ('Flask-Session', '0.8.0', { + 'sources': ['flask_session-%(version)s.tar.gz'], + 'checksums': ['20e045eb01103694e70be4a49f3a80dbb1b57296a22dc6f44bbf3f83ef0742ff'], + }), +] + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ['%(namelower)s --version'] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/f/Flax/Flax-0.8.4-gfbf-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/f/Flax/Flax-0.8.4-gfbf-2023a-CUDA-12.1.1.eb new file mode 100644 index 00000000000..4aeb0c7d815 --- /dev/null +++ b/easybuild/easyconfigs/f/Flax/Flax-0.8.4-gfbf-2023a-CUDA-12.1.1.eb @@ -0,0 +1,44 @@ +easyblock = 'PythonBundle' + +name = 'Flax' +version = '0.8.4' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://flax.readthedocs.io' +description = """Flax is a high-performance neural network library and ecosystem for JAX that is +designed for flexibility: Try new forms of training by forking an example and +by modifying the training loop, not by adding features to a framework.""" + +toolchain = {'name': 'gfbf', 'version': '2023a'} + +dependencies = [ + ('CUDA', '12.1.1', '', SYSTEM), + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('jax', '0.4.25', versionsuffix), + ('Optax', '0.2.2', versionsuffix), + ('protobuf-python', '4.24.0'), + ('PyYAML', '6.0'), +] + +use_pip = True + +exts_list = [ + ('nest_asyncio', '1.6.0', { + 'checksums': ['6f172d5449aca15afd6c646851f4e31e02c598d553a667e38cafa997cfec55fe'], + }), + ('orbax_checkpoint', '0.5.15', { + 'modulename': 'orbax.checkpoint', + 'checksums': ['15195e8d1b381b56f23a62a25599a3644f5d08655fa64f60bb1b938b8ffe7ef3'], + }), + ('tensorstore', '0.1.60', { + 'checksums': ['88da8f1978982101b8dbb144fd29ee362e4e8c97fc595c4992d555f80ce62a79'], + }), + ('flax', '0.8.4', { + 'checksums': ['968683f850198e1aa5eb2d9d1e20bead880ef7423c14f042db9d60848cb1c90b'], + }), +] + +sanity_pip_check = True + +moduleclass = 'ai' diff --git a/easybuild/easyconfigs/f/Flax/Flax-0.8.4-gfbf-2023a.eb b/easybuild/easyconfigs/f/Flax/Flax-0.8.4-gfbf-2023a.eb new file mode 100644 index 00000000000..dedc08531c3 --- /dev/null +++ b/easybuild/easyconfigs/f/Flax/Flax-0.8.4-gfbf-2023a.eb @@ -0,0 +1,42 @@ +easyblock = 'PythonBundle' + +name = 'Flax' +version = '0.8.4' + +homepage = 'https://flax.readthedocs.io' +description = """Flax is a high-performance neural network library and ecosystem for JAX that is +designed for flexibility: Try new forms of training by forking an example and +by modifying the training loop, not by adding features to a framework.""" + +toolchain = {'name': 'gfbf', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('jax', '0.4.25'), + ('Optax', '0.2.2'), + ('protobuf-python', '4.24.0'), + ('PyYAML', '6.0'), +] + +use_pip = True + +exts_list = [ + ('nest_asyncio', '1.6.0', { + 'checksums': ['6f172d5449aca15afd6c646851f4e31e02c598d553a667e38cafa997cfec55fe'], + }), + ('orbax_checkpoint', '0.5.15', { + 'modulename': 'orbax.checkpoint', + 'checksums': ['15195e8d1b381b56f23a62a25599a3644f5d08655fa64f60bb1b938b8ffe7ef3'], + }), + ('tensorstore', '0.1.60', { + 'checksums': ['88da8f1978982101b8dbb144fd29ee362e4e8c97fc595c4992d555f80ce62a79'], + }), + ('flax', '0.8.4', { + 'checksums': ['968683f850198e1aa5eb2d9d1e20bead880ef7423c14f042db9d60848cb1c90b'], + }), +] + +sanity_pip_check = True + +moduleclass = 'ai' diff --git a/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.4.4-GCC-13.3.0.eb b/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.4.4-GCC-13.3.0.eb new file mode 100644 index 00000000000..9b9f5e8edb2 --- /dev/null +++ b/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.4.4-GCC-13.3.0.eb @@ -0,0 +1,59 @@ +easyblock = 'Bundle' + +name = 'FlexiBLAS' +version = '3.4.4' + +homepage = 'https://gitlab.mpi-magdeburg.mpg.de/software/flexiblas-release' +description = """FlexiBLAS is a wrapper library that enables the exchange of the BLAS and LAPACK implementation +used by a program without recompiling or relinking it.""" + +toolchain = {'name': 'GCC', 'version': '13.3.0'} +local_extra_flags = "-fstack-protector-strong -fstack-clash-protection" +toolchainopts = {'pic': True, 'extra_cflags': local_extra_flags, 'extra_fflags': local_extra_flags} + +builddependencies = [ + ('CMake', '3.29.3'), + ('Python', '3.12.3'), # required for running the tests + ('BLIS', '1.0'), +] + +dependencies = [ + ('OpenBLAS', '0.3.27'), +] + +# note: first listed backend will be used as default by FlexiBLAS, +# unless otherwise specified via easyconfig parameter flexiblas_default +local_backends = ['OpenBLAS', 'BLIS'] + +# imkl supplies its backend via the imkl module, not as a dependency +if ARCH == 'x86_64': + local_backends.append('imkl') + +default_component_specs = {'start_dir': '%(namelower)s-%(version)s'} +sanity_check_all_components = True + +# Also build and install LAPACKE, which FlexiBLAS does not support yet +components = [ + (name, version, { + 'source_urls': + ['https://gitlab.mpi-magdeburg.mpg.de/api/v4/projects/386/packages/generic/flexiblas-source/v3.4.4/'], + 'sources': [SOURCELOWER_TAR_GZ], + 'checksums': ['05040ae092142dd0bf38d1bb9ce33f6b475d9f9bb455e33be997932ae855c22b'], + 'backends': local_backends, + }), + ('LAPACK', '3.12.0', { + 'easyblock': 'CMakeMake', + 'source_urls': ['https://github.com/Reference-LAPACK/lapack/archive/'], + 'sources': ['v%(version)s.tar.gz'], + 'checksums': ['eac9570f8e0ad6f30ce4b963f4f033f0f643e7c3912fc9ee6cd99120675ad48b'], + 'configopts': ('-DBUILD_SHARED_LIBS=ON -DUSE_OPTIMIZED_BLAS=ON -DLAPACKE=ON ' + '-DUSE_OPTIMIZED_LAPACK=ON -DBUILD_DEPRECATED=ON ' + '-DCMAKE_INSTALL_INCLUDEDIR=%(installdir)s/include/flexiblas'), + 'sanity_check_paths': { + 'files': ['lib/liblapacke.%s' % SHLIB_EXT, 'include/flexiblas/lapacke.h'], + 'dirs': [], + }, + }), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/f/FloPy/FloPy-3.8.2-gfbf-2023a.eb b/easybuild/easyconfigs/f/FloPy/FloPy-3.8.2-gfbf-2023a.eb new file mode 100644 index 00000000000..50f72e07c0d --- /dev/null +++ b/easybuild/easyconfigs/f/FloPy/FloPy-3.8.2-gfbf-2023a.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonBundle' + +name = 'FloPy' +version = '3.8.2' +homepage = 'https://flopy.readthedocs.io' + +description = "FloPy is a Python package to create, run, and post-process MODFLOW-based models" + +toolchain = {'name': 'gfbf', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('matplotlib', '3.7.2'), +] + +exts_list = [ + ('flopy', version, { + 'checksums': ['0ce2941f4095df2ca1d510f28df57224bdeb90636a3f3beeb199f09f635ddc62'], + }), +] + +use_pip = True +sanity_pip_check = True + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/f/Flye/Flye-2.9.4-GCC-13.2.0.eb b/easybuild/easyconfigs/f/Flye/Flye-2.9.4-GCC-13.2.0.eb new file mode 100644 index 00000000000..c11373f69a1 --- /dev/null +++ b/easybuild/easyconfigs/f/Flye/Flye-2.9.4-GCC-13.2.0.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonPackage' + +name = 'Flye' +version = '2.9.4' + +homepage = 'https://github.com/fenderglass/Flye' +description = """Flye is a de novo assembler for long and noisy reads, such as those produced by PacBio + and Oxford Nanopore Technologies.""" + +toolchain = {'name': 'GCC', 'version': '13.2.0'} + +source_urls = ['https://github.com/fenderglass/Flye/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['197a2dfe39fc324a39d8e1901af4f539609159c4a64a578ec8e60f73f5ea4696'] + +dependencies = [('Python', '3.11.5')] + +download_dep_fail = True +use_pip = True + +if ARCH == "aarch64": + preinstallopts = 'export arm_neon=1 && export aarch64=1 && ' + +sanity_check_paths = { + 'files': ['bin/flye'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ['%(namelower)s --help'] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/f/FragGeneScan/FragGeneScan-1.31-GCCcore-12.3.0.eb b/easybuild/easyconfigs/f/FragGeneScan/FragGeneScan-1.31-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..8466e596a3d --- /dev/null +++ b/easybuild/easyconfigs/f/FragGeneScan/FragGeneScan-1.31-GCCcore-12.3.0.eb @@ -0,0 +1,38 @@ +easyblock = 'MakeCp' + +name = 'FragGeneScan' +version = '1.31' + +homepage = 'https://omics.informatics.indiana.edu/FragGeneScan/' +description = "FragGeneScan is an application for finding (fragmented) genes in short reads." + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%(name)s%(version)s.tar.gz'] +checksums = ['cd3212d0f148218eb3b17d24fcd1fc897fb9fee9b2c902682edde29f895f426c'] + +builddependencies = [('binutils', '2.40')] + +dependencies = [('Perl', '5.36.1')] + +fix_perl_shebang_for = ['*.pl'] + +prebuildopts = "make clean && " +buildopts = 'CC="$CC" CFLAG="$CFLAGS" fgs && chmod -R go+rx *.pl train example' + +files_to_copy = ['FragGeneScan', 'run_FragGeneScan.pl', 'example', 'train'] + +modextrapaths = {'PATH': ['']} + +sanity_check_paths = { + 'files': ['FragGeneScan', 'run_FragGeneScan.pl'], + 'dirs': ['example', 'train'], +} + +sanity_check_commands = [ + "run_FragGeneScan.pl help", + "run_FragGeneScan.pl -genome=./example/NC_000913.fna -out=./example/NC_000913-fgs -complete=1 -train=complete", +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/f/FriBidi/FriBidi-1.0.15-GCCcore-13.3.0.eb b/easybuild/easyconfigs/f/FriBidi/FriBidi-1.0.15-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..a31f21a37dd --- /dev/null +++ b/easybuild/easyconfigs/f/FriBidi/FriBidi-1.0.15-GCCcore-13.3.0.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'FriBidi' +version = '1.0.15' + +homepage = 'https://github.com/fribidi/fribidi' + +description = """ + The Free Implementation of the Unicode Bidirectional Algorithm. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://github.com/fribidi/fribidi/releases/download/v%(version)s'] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['0bbc7ff633bfa208ae32d7e369cf5a7d20d5d2557a0b067c9aa98bcbf9967587'] + +builddependencies = [ + ('binutils', '2.42'), + ('pkgconf', '2.2.0'), + ('Autotools', '20231222'), +] + +sanity_check_paths = { + 'files': ['bin/%(namelower)s', 'include/%(namelower)s/%(namelower)s.h', + 'lib/lib%%(namelower)s.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/face-recognition/face-recognition-1.3.0-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/f/face-recognition/face-recognition-1.3.0-foss-2023a-CUDA-12.1.1.eb new file mode 100644 index 00000000000..d06d8172e1d --- /dev/null +++ b/easybuild/easyconfigs/f/face-recognition/face-recognition-1.3.0-foss-2023a-CUDA-12.1.1.eb @@ -0,0 +1,45 @@ +easyblock = 'PythonBundle' + +name = 'face-recognition' +version = '1.3.0' +versionsuffix = '-CUDA-12.1.1' + +homepage = 'https://github.com/ageitgey/face_recognition' +description = """Recognize and manipulate faces from Python or from the command line with + the world’s simplest face recognition library.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('Pillow', '10.0.0'), + ('dlib', '19.24.6', versionsuffix), +] + +use_pip = True + +exts_list = [ + ('face-recognition-models', '0.3.0', { + 'sources': ['face_recognition_models-%(version)s.tar.gz'], + 'checksums': ['b79bd200a88c87c9a9d446c990ae71c5a626d1f3730174e6d570157ff1d896cf'], + }), + (name, version, { + 'sources': ['face_recognition-%(version)s.tar.gz'], + 'checksums': ['5e5efdd1686aa566af0d3cc1313b131e4b197657a8ffd03669e6d3fad92705ec'], + }), +] + +sanity_check_paths = { + 'files': ['bin/face_detection', 'bin/face_recognition'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "face_detection --help", + "face_recognition --help", +] + +sanity_pip_check = True + +moduleclass = 'ai' diff --git a/easybuild/easyconfigs/f/fastahack/fastahack-1.0.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/f/fastahack/fastahack-1.0.0-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..2d430c8a5f2 --- /dev/null +++ b/easybuild/easyconfigs/f/fastahack/fastahack-1.0.0-GCCcore-12.2.0.eb @@ -0,0 +1,36 @@ +# Updated: Denis Kristak (INUITS) +# Updated: Petr Král (INUITS) + +easyblock = 'ConfigureMake' + +name = 'fastahack' +version = '1.0.0' + +homepage = 'https://github.com/ekg/fastahack' +description = """Utilities for indexing and sequence extraction from FASTA files.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +github_account = 'ekg' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +patches = ['%(name)s-%(version)s_build-libs.patch'] +checksums = [ + 'cc1c04729b0c8ba3647cbb7e15e2b490ce701d73773f30f5892d68c36a1dceae', # v1.0.0.tar.gz + '7f804486c6bafd9b1572cb5f86ff28dbebb4d6da551bde1091d6ff8f82748bf4', # fastahack-1.0.0_build-libs.patch +] + +builddependencies = [('binutils', '2.39')] + +skipsteps = ['configure'] + +installopts = 'PREFIX=%(installdir)s ' + +sanity_check_paths = { + 'files': ['bin/%(name)s', 'lib/libfastahack.%s' % SHLIB_EXT], + 'dirs': [], +} + +sanity_check_commands = ['%(name)s --help'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/f/fastfilters/fastfilters-0.3-foss-2023a.eb b/easybuild/easyconfigs/f/fastfilters/fastfilters-0.3-foss-2023a.eb new file mode 100644 index 00000000000..a9d67a03798 --- /dev/null +++ b/easybuild/easyconfigs/f/fastfilters/fastfilters-0.3-foss-2023a.eb @@ -0,0 +1,46 @@ +easyblock = 'CMakeMake' + +name = 'fastfilters' +version = '0.3' + +homepage = 'https://github.com/ilastik/fastfilters/' +description = """Fast gaussian and derivative convolutional filters.""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'optarch': False} + +sources = [{ + 'filename': 'v%(version)s.tar.gz', + 'git_config': { + 'url': 'https://github.com/ilastik', + 'repo_name': 'fastfilters', + 'tag': 'v%(version)s', + 'recursive': True, + 'keep_git_dir': True, + } +}] +checksums = [None] + +builddependencies = [ + ('CMake', '3.26.3'), +] +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('SciPy-bundle', '2023.07'), + ('pybind11', '2.11.1'), +] + +configopts = '-DFF_INSTALL_DIR="%(installdir)s/lib/python%(pyshortver)s/site-packages/" ' +configopts += '-DPYTHON_EXECUTABLE="$EBROOTPYTHON/bin/python"' + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib', 'include'], +} + +sanity_check_commands = ["python -c 'import fastfilters'"] + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/f/fastp/fastp-0.23.4-GCC-13.2.0.eb b/easybuild/easyconfigs/f/fastp/fastp-0.23.4-GCC-13.2.0.eb new file mode 100644 index 00000000000..49b2a29c4f9 --- /dev/null +++ b/easybuild/easyconfigs/f/fastp/fastp-0.23.4-GCC-13.2.0.eb @@ -0,0 +1,38 @@ +easyblock = 'ConfigureMake' + +name = 'fastp' +version = '0.23.4' + +homepage = 'https://github.com/OpenGene/fastp' +description = """A tool designed to provide fast all-in-one preprocessing for FastQ files. + This tool is developed in C++ with multithreading supported to afford high performance.""" + +toolchain = {'name': 'GCC', 'version': '13.2.0'} + +github_account = 'OpenGene' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['4fad6db156e769d46071add8a778a13a5cb5186bc1e1a5f9b1ffd499d84d72b5'] + +dependencies = [ + ('zlib', '1.2.13'), + ('libdeflate', '1.19'), + ('ISA-L', '2.31.0'), +] + +skipsteps = ['configure'] + +buildopts = ' CXX=${CXX}' + +preinstallopts = 'mkdir -p %(installdir)s/bin && ' + +installopts = 'PREFIX=%(installdir)s' + +sanity_check_paths = { + 'files': ['bin/fastp'], + 'dirs': [], +} + +sanity_check_commands = [('fastp', '--help')] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/f/fastparquet/fastparquet-2023.4.0-gfbf-2022b.eb b/easybuild/easyconfigs/f/fastparquet/fastparquet-2023.4.0-gfbf-2022b.eb index 2320c4b7539..95fbef237e5 100644 --- a/easybuild/easyconfigs/f/fastparquet/fastparquet-2023.4.0-gfbf-2022b.eb +++ b/easybuild/easyconfigs/f/fastparquet/fastparquet-2023.4.0-gfbf-2022b.eb @@ -1,4 +1,4 @@ -easyblock = 'PythonBundle' +easyblock = 'CargoPythonBundle' name = 'fastparquet' version = '2023.4.0' @@ -12,12 +12,77 @@ toolchain = {'name': 'gfbf', 'version': '2022b'} builddependencies = [ ('patchelf', '0.17.2'), + ('maturin', '1.1.0'), # for cramjam ] dependencies = [ ('Python', '3.10.8'), ('SciPy-bundle', '2023.02'), - ('maturin', '1.1.0'), +] + +crates = [ + ('adler', '1.0.2'), + ('ahash', '0.7.6'), + ('alloc-no-stdlib', '2.0.4'), + ('alloc-stdlib', '0.2.2'), + ('autocfg', '1.1.0'), + ('bitflags', '1.3.2'), + ('brotli', '3.3.4'), + ('brotli-decompressor', '2.3.2'), + ('bzip2', '0.4.3'), + ('bzip2-sys', '0.1.11+1.0.8'), + ('cc', '1.0.73'), + ('cfg-if', '1.0.0'), + ('crc32fast', '1.3.2'), + ('flate2', '1.0.23'), + ('getrandom', '0.2.8'), + ('indoc', '1.0.6'), + ('jobserver', '0.1.24'), + ('libc', '0.2.126'), + ('libmimalloc-sys', '0.1.25'), + ('lock_api', '0.4.7'), + ('lz4', '1.23.3'), + ('lz4-sys', '1.9.4'), + ('matrixmultiply', '0.3.2'), + ('memoffset', '0.6.5'), + ('mimalloc', '0.1.29'), + ('miniz_oxide', '0.5.1'), + ('ndarray', '0.15.4'), + ('num-complex', '0.4.1'), + ('num-integer', '0.1.45'), + ('num-traits', '0.2.15'), + ('numpy', '0.17.2'), + ('once_cell', '1.10.0'), + ('parking_lot', '0.12.0'), + ('parking_lot_core', '0.9.3'), + ('pkg-config', '0.3.25'), + ('proc-macro2', '1.0.39'), + ('pyo3', '0.17.3'), + ('pyo3-build-config', '0.17.3'), + ('pyo3-ffi', '0.17.3'), + ('pyo3-macros', '0.17.3'), + ('pyo3-macros-backend', '0.17.3'), + ('quote', '1.0.18'), + ('rawpointer', '0.2.1'), + ('redox_syscall', '0.2.13'), + ('scopeguard', '1.1.0'), + ('smallvec', '1.8.0'), + ('snap', '1.0.5'), + ('syn', '1.0.95'), + ('target-lexicon', '0.12.3'), + ('unicode-ident', '1.0.0'), + ('unindent', '0.1.9'), + ('version_check', '0.9.4'), + ('wasi', '0.11.0+wasi-snapshot-preview1'), + ('windows-sys', '0.36.1'), + ('windows_aarch64_msvc', '0.36.1'), + ('windows_i686_gnu', '0.36.1'), + ('windows_i686_msvc', '0.36.1'), + ('windows_x86_64_gnu', '0.36.1'), + ('windows_x86_64_msvc', '0.36.1'), + ('zstd', '0.11.2+zstd.1.5.2'), + ('zstd-safe', '5.0.2+zstd.1.5.2'), + ('zstd-sys', '2.0.1+zstd.1.5.2'), ] use_pip = True diff --git a/easybuild/easyconfigs/f/ffnvcodec/ffnvcodec-12.2.72.0.eb b/easybuild/easyconfigs/f/ffnvcodec/ffnvcodec-12.2.72.0.eb new file mode 100644 index 00000000000..cc4461c3a8b --- /dev/null +++ b/easybuild/easyconfigs/f/ffnvcodec/ffnvcodec-12.2.72.0.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'ffnvcodec' +version = '12.2.72.0' + +homepage = 'https://git.videolan.org/?p=ffmpeg/nv-codec-headers.git' + +description = """FFmpeg nvidia headers. Adds support for nvenc and nvdec. Requires Nvidia GPU and drivers to be present +(picked up dynamically).""" + +toolchain = SYSTEM + +sources = [{ + 'git_config': { + 'url': 'https://git.videolan.org/git/ffmpeg/', + 'repo_name': 'nv-codec-headers', + 'tag': 'n%(version)s', + }, + 'filename': SOURCE_TAR_GZ, +}] +checksums = [None] + +skipsteps = ['configure'] + +preinstallopts = 'sed -i "s|PREFIX =.*|PREFIX ?= %(installdir)s|" Makefile && ' + +sanity_check_paths = { + 'files': ['include/ffnvcodec/nvEncodeAPI.h', 'lib/pkgconfig/ffnvcodec.pc'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/f/file/file-5.43-GCCcore-13.2.0.eb b/easybuild/easyconfigs/f/file/file-5.43-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..dcd8b7cbfa0 --- /dev/null +++ b/easybuild/easyconfigs/f/file/file-5.43-GCCcore-13.2.0.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'file' +version = '5.43' + +homepage = 'https://www.darwinsys.com/file/' +description = """The file command is 'a file type guesser', that is, a command-line tool + that tells you in words what kind of data a file contains.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['ftp://ftp.astron.com/pub/file/'] +sources = [SOURCE_TAR_GZ] +checksums = ['8c8015e91ae0e8d0321d94c78239892ef9dbc70c4ade0008c0e95894abfb1991'] + +builddependencies = [ + ('Autotools', '20220317'), + ('binutils', '2.40'), +] + +preconfigopts = "autoreconf -f -i && " + +sanity_check_paths = { + 'files': ['bin/file', 'include/magic.h', 'lib/libmagic.%s' % SHLIB_EXT], + 'dirs': ['share'] +} + +sanity_check_commands = ['%(name)s --help'] + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/f/filevercmp/filevercmp-20191210-GCCcore-12.2.0.eb b/easybuild/easyconfigs/f/filevercmp/filevercmp-20191210-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..f9acad2dfe3 --- /dev/null +++ b/easybuild/easyconfigs/f/filevercmp/filevercmp-20191210-GCCcore-12.2.0.eb @@ -0,0 +1,37 @@ +# Updated: Denis Kristak (INUITS) +# Updated: Petr Král (INUITS) + +easyblock = 'ConfigureMake' + +name = 'filevercmp' +version = '20191210' +local_commit = 'df20dcc' + +homepage = 'https://github.com/ekg/filevercmp' +description = """filevercmp function as in sort --version-sort.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +github_account = 'ekg' +source_urls = [GITHUB_SOURCE] +sources = ['%s.tar.gz' % local_commit] +patches = ['%(name)s-%(version)s_build-libs.patch'] +checksums = [ + '89835829a7829f7a25783b2cf9d482f1e3c794703343c9214c15c66a8c7f4aae', # df20dcc.tar.gz + '051438f76dd04219abfb283f61101c04d748407031e180b7ae3841344416ec4f', # filevercmp-20191210_build-libs.patch +] + +builddependencies = [('binutils', '2.39')] + +skipsteps = ['configure'] + +installopts = 'DESTDIR="" PREFIX=%(installdir)s ' + +sanity_check_paths = { + 'files': ['bin/%(name)s', 'lib/libfilevercmp.%s' % SHLIB_EXT], + 'dirs': [], +} + +sanity_check_commands = ['%(name)s abca bcac'] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/f/fish/fish-3.7.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/f/fish/fish-3.7.1-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..0c7e084ac23 --- /dev/null +++ b/easybuild/easyconfigs/f/fish/fish-3.7.1-GCCcore-13.3.0.eb @@ -0,0 +1,36 @@ +easyblock = 'CMakeMake' + +name = 'fish' + +version = '3.7.1' + +homepage = 'https://fishshell.com/' +description = """ +fish is a smart and user-friendly command line shell for Linux, macOS, and the rest of the family. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://github.com/fish-shell/fish-shell/releases/download/%(version)s/'] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['614c9f5643cd0799df391395fa6bbc3649427bb839722ce3b114d3bbc1a3b250'] + +builddependencies = [ + ('binutils', '2.42'), + ('CMake', '3.29.3') +] + +dependencies = [ + ('ncurses', '6.5'), +] + +configopts = '-DBUILD_DOCS=off ' + +sanity_check_paths = { + 'files': ['bin/fish'], + 'dirs': [], +} + +sanity_check_commands = ['fish --version'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/f/flash-attention/flash-attention-2.6.3-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/f/flash-attention/flash-attention-2.6.3-foss-2023a-CUDA-12.1.1.eb new file mode 100644 index 00000000000..754eef2c70e --- /dev/null +++ b/easybuild/easyconfigs/f/flash-attention/flash-attention-2.6.3-foss-2023a-CUDA-12.1.1.eb @@ -0,0 +1,41 @@ +easyblock = 'PythonBundle' + +name = 'flash-attention' +version = '2.6.3' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/Dao-AILab/flash-attention' +description = """Fast and memory-efficient exact attention.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [('Ninja', '1.11.1')] +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('CUDA', '12.1.1', '', SYSTEM), + ('PyTorch-bundle', '2.1.2', versionsuffix), + ('einops', '0.7.0'), + ('CUTLASS', '3.4.0', versionsuffix), +] + +sanity_pip_check = True +use_pip = True + +exts_list = [ + (name, version, { + 'modulename': 'flash_attn', + # solves Invalid cross-device link error + # https://github.com/Dao-AILab/flash-attention/issues/875 + 'preinstallopts': "sed -i 's/os.rename/shutil.move/' setup.py && ", + 'source_urls': ['https://github.com/Dao-AILab/flash-attention/archive/'], + 'sources': ['v%(version)s.tar.gz'], + 'checksums': ['136e149165d4c8c67273d16daa957b5cd5e6fc629061ffd39fa5a25224454d6c'], + }), +] + +sanity_check_commands = [ + "python -c 'from flash_attn import flash_attn_qkvpacked_func, flash_attn_func'", +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/f/flatbuffers-python/flatbuffers-python-24.3.25-GCCcore-13.3.0.eb b/easybuild/easyconfigs/f/flatbuffers-python/flatbuffers-python-24.3.25-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..6e3bd315965 --- /dev/null +++ b/easybuild/easyconfigs/f/flatbuffers-python/flatbuffers-python-24.3.25-GCCcore-13.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'flatbuffers-python' +version = '24.3.25' + +homepage = 'https://github.com/google/flatbuffers/' +description = """Python Flatbuffers runtime library.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://pypi.python.org/packages/source/f/flatbuffers'] +sources = [{'download_filename': 'flatbuffers-%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}] +checksums = ['de2ec5b203f21441716617f38443e0a8ebf3d25bf0d9c0bb0ce68fa00ad546a4'] + +dependencies = [ + ('binutils', '2.42'), + ('Python', '3.12.3'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +preinstallopts = 'VERSION=%(version)s ' +options = {'modulename': 'flatbuffers'} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/f/flatbuffers/flatbuffers-24.3.25-GCCcore-13.3.0.eb b/easybuild/easyconfigs/f/flatbuffers/flatbuffers-24.3.25-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..42c0b9a28f1 --- /dev/null +++ b/easybuild/easyconfigs/f/flatbuffers/flatbuffers-24.3.25-GCCcore-13.3.0.eb @@ -0,0 +1,33 @@ +## +# Author: Robert Mijakovic +## +easyblock = 'CMakeNinja' + +name = 'flatbuffers' +version = '24.3.25' + +homepage = 'https://github.com/google/flatbuffers/' +description = """FlatBuffers: Memory Efficient Serialization Library""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/google/flatbuffers/archive/v%(version)s/'] +sources = [SOURCE_TAR_GZ] +checksums = ['4157c5cacdb59737c5d627e47ac26b140e9ee28b1102f812b36068aab728c1ed'] + +builddependencies = [ + ('binutils', '2.42'), + ('CMake', '3.29.3'), + ('Ninja', '1.12.1'), + ('Python', '3.12.3'), +] + +configopts = '-DFLATBUFFERS_ENABLE_PCH=ON ' + +sanity_check_paths = { + 'files': ['include/flatbuffers/flatbuffers.h', 'bin/flatc', 'lib/libflatbuffers.a'], + 'dirs': ['lib/cmake'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-13.3.0.eb b/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..dda9307eaea --- /dev/null +++ b/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-13.3.0.eb @@ -0,0 +1,34 @@ +name = 'flex' +version = '2.6.4' + +homepage = 'https://github.com/westes/flex' + +description = """ + Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner, + sometimes called a tokenizer, is a program which recognizes lexical patterns + in text. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/westes/flex/releases/download/v%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['e87aae032bf07c26f85ac0ed3250998c37621d95f8bd748b31f15b33c45ee995'] + +builddependencies = [ + ('Bison', '3.8.2'), + ('help2man', '1.49.3'), + # use same binutils version that was used when building GCC toolchain + ('binutils', '2.42', '', SYSTEM), +] + +dependencies = [ + ('M4', '1.4.19'), +] + +# glibc 2.26 requires _GNU_SOURCE defined to expose reallocarray in the correct +# header, see https://github.com/westes/flex/issues/241 +preconfigopts = 'export CPPFLAGS="$CPPFLAGS -D_GNU_SOURCE" && ' + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-14.2.0.eb b/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-14.2.0.eb new file mode 100644 index 00000000000..d91f13aa5d0 --- /dev/null +++ b/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-14.2.0.eb @@ -0,0 +1,34 @@ +name = 'flex' +version = '2.6.4' + +homepage = 'https://github.com/westes/flex' + +description = """ + Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner, + sometimes called a tokenizer, is a program which recognizes lexical patterns + in text. +""" + +toolchain = {'name': 'GCCcore', 'version': '14.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/westes/flex/releases/download/v%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['e87aae032bf07c26f85ac0ed3250998c37621d95f8bd748b31f15b33c45ee995'] + +builddependencies = [ + ('Bison', '3.8.2'), + ('help2man', '1.49.3'), + # use same binutils version that was used when building GCC toolchain + ('binutils', '2.42', '', SYSTEM), +] + +dependencies = [ + ('M4', '1.4.19'), +] + +# glibc 2.26 requires _GNU_SOURCE defined to expose reallocarray in the correct +# header, see https://github.com/westes/flex/issues/241 +preconfigopts = 'export CPPFLAGS="$CPPFLAGS -D_GNU_SOURCE" && ' + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flit/flit-3.9.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/f/flit/flit-3.9.0-GCCcore-12.3.0.eb index 15b9ad83d78..a19ba324250 100644 --- a/easybuild/easyconfigs/f/flit/flit-3.9.0-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/f/flit/flit-3.9.0-GCCcore-12.3.0.eb @@ -17,11 +17,8 @@ dependencies = [ ('Python', '3.11.3'), ] -exts_default_options = { - 'download_dep_fail': True, - 'sanity_pip_check': True, - 'use_pip': True, -} +sanity_pip_check = True +use_pip = True exts_list = [ ('idna', '3.4', { diff --git a/easybuild/easyconfigs/f/flit/flit-3.9.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/f/flit/flit-3.9.0-GCCcore-13.2.0.eb index 79b1a625e7e..9ef1de6c8b7 100644 --- a/easybuild/easyconfigs/f/flit/flit-3.9.0-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/f/flit/flit-3.9.0-GCCcore-13.2.0.eb @@ -18,11 +18,8 @@ dependencies = [ ('Python', '3.11.5'), ] -exts_default_options = { - 'download_dep_fail': True, - 'sanity_pip_check': True, - 'use_pip': True, -} +sanity_pip_check = True +use_pip = True exts_list = [ ('idna', '3.4', { diff --git a/easybuild/easyconfigs/f/flit/flit-3.9.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/f/flit/flit-3.9.0-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..650b15edaa5 --- /dev/null +++ b/easybuild/easyconfigs/f/flit/flit-3.9.0-GCCcore-13.3.0.eb @@ -0,0 +1,72 @@ +easyblock = 'PythonBundle' + +name = 'flit' +version = '3.9.0' + +homepage = 'https://github.com/pypa/flit' +description = "A simple packaging tool for simple packages." + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +builddependencies = [ + ('binutils', '2.42'), + ('hatchling', '1.24.2'), +] + +dependencies = [ + ('Python', '3.12.3'), +] + +sanity_pip_check = True +use_pip = True + +exts_list = [ + ('idna', '3.7', { + 'checksums': ['028ff3aadf0609c1fd278d8ea3089299412a7a8b9bd005dd08b9f8285bcb5cfc'], + }), + ('certifi', '2024.6.2', { + 'checksums': ['3cd43f1c6fa7dedc5899d69d3ad0398fd018ad1a17fba83ddaf78aa46c747516'], + }), + ('urllib3', '2.2.1', { + 'checksums': ['d0570876c61ab9e520d776c38acbbb5b05a776d3f9ff98a5c8fd5162a444cf19'], + }), + ('charset-normalizer', '3.3.2', { + 'checksums': ['f30c3cb33b24454a82faecaf01b19c18562b1e89558fb6c56de4d9118a032fd5'], + }), + ('packaging', '24.1', { + 'checksums': ['026ed72c8ed3fcce5bf8950572258698927fd1dbda10a5e981cdf0ac37f4f002'], + }), + ('setuptools-scm', '8.1.0', { + 'sources': ['setuptools_scm-%(version)s.tar.gz'], + 'checksums': ['42dea1b65771cba93b7a515d65a65d8246e560768a66b9106a592c8e7f26c8a7'], + }), + ('typing-extensions', '4.12.2', { + 'sources': ['typing_extensions-%(version)s.tar.gz'], + 'checksums': ['1a7ead55c7e559dd4dee8856e3a88b41225abfe1ce8df57b7c13915fe121ffb8'], + }), + ('flit-scm', '1.7.0', { + 'sources': ['flit_scm-%(version)s.tar.gz'], + 'checksums': ['961bd6fb24f31bba75333c234145fff88e6de0a90fc0f7e5e7c79deca69f6bb2'], + }), + ('requests', '2.32.3', { + 'checksums': ['55365417734eb18255590a9ff9eb97e9e1da868d4ccd6402399eaf68af20a760'], + }), + ('docutils', '0.21.2', { + 'checksums': ['3a6b18732edf182daa3cd12775bbb338cf5691468f91eeeb109deff6ebfa986f'], + }), + ('tomli-w', '1.0.0', { + 'sources': ['tomli_w-%(version)s.tar.gz'], + 'checksums': ['f463434305e0336248cac9c2dc8076b707d8a12d019dd349f5c1e382dd1ae1b9'], + }), + (name, version, { + 'checksums': ['d75edf5eb324da20d53570a6a6f87f51e606eee8384925cd66a90611140844c7'], + }), +] + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(namelower)s'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/f/fmt/fmt-10.2.1-GCCcore-13.2.0.eb b/easybuild/easyconfigs/f/fmt/fmt-10.2.1-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..45cfe72e73f --- /dev/null +++ b/easybuild/easyconfigs/f/fmt/fmt-10.2.1-GCCcore-13.2.0.eb @@ -0,0 +1,27 @@ +easyblock = 'CMakeMake' + +name = 'fmt' +version = '10.2.1' + +homepage = 'http://fmtlib.net/' +description = "fmt (formerly cppformat) is an open-source formatting library." + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/fmtlib/fmt/releases/download/%(version)s/'] +sources = ['fmt-%(version)s.zip'] +checksums = ['312151a2d13c8327f5c9c586ac6cf7cddc1658e8f53edae0ec56509c8fa516c9'] + + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.27.6'), +] + +sanity_check_paths = { + 'files': ['lib/libfmt.a'], + 'dirs': ['include/fmt', 'lib/cmake'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/f/fmt/fmt-11.0.2-GCCcore-13.3.0.eb b/easybuild/easyconfigs/f/fmt/fmt-11.0.2-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..cfb38383787 --- /dev/null +++ b/easybuild/easyconfigs/f/fmt/fmt-11.0.2-GCCcore-13.3.0.eb @@ -0,0 +1,26 @@ +easyblock = 'CMakeMake' + +name = 'fmt' +version = '11.0.2' + +homepage = 'http://fmtlib.net/' +description = "fmt (formerly cppformat) is an open-source formatting library." + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/fmtlib/fmt/releases/download/%(version)s/'] +sources = ['fmt-%(version)s.zip'] +checksums = ['40fc58bebcf38c759e11a7bd8fdc163507d2423ef5058bba7f26280c5b9c5465'] + +builddependencies = [ + ('binutils', '2.42'), + ('CMake', '3.29.3'), +] + +sanity_check_paths = { + 'files': ['lib/libfmt.a'], + 'dirs': ['include/fmt', 'lib/cmake'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/f/fontconfig/fontconfig-2.15.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.15.0-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..e2586c86e8c --- /dev/null +++ b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.15.0-GCCcore-13.3.0.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'fontconfig' +version = '2.15.0' + +homepage = 'https://www.freedesktop.org/wiki/Software/fontconfig/' + +description = """ + Fontconfig is a library designed to provide system-wide font configuration, + customization and application access. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.freedesktop.org/software/fontconfig/release/'] +sources = [SOURCE_TAR_GZ] +checksums = ['f5f359d6332861bd497570848fcb42520964a9e83d5e3abe397b6b6db9bcaaf4'] + +builddependencies = [ + ('binutils', '2.42'), + ('gperf', '3.1'), + ('pkgconf', '2.2.0'), + ('Python', '3.12.3'), +] + +dependencies = [ + ('expat', '2.6.2'), + ('freetype', '2.13.2'), + ('util-linux', '2.40'), +] + +configopts = '--disable-docs ' + +sanity_check_paths = { + 'files': ['include/fontconfig/fontconfig.h', 'lib/libfontconfig.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/f/fonttools/fonttools-4.53.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/f/fonttools/fonttools-4.53.1-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..8453a35a695 --- /dev/null +++ b/easybuild/easyconfigs/f/fonttools/fonttools-4.53.1-GCCcore-11.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'fonttools' +version = '4.53.1' + +homepage = 'https://python-markdown.github.io/' +description = """ +fontTools is a library for manipulating fonts, written in Python. +The project includes the TTX tool, that can convert TrueType and OpenType fonts to and from an XML text format, +which is also called TTX. +It supports TrueType, OpenType, AFM and to an extent Type 1 and some Mac-specific formats.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['e128778a8e9bc11159ce5447f76766cefbd876f44bd79aff030287254e4752c4'] + +builddependencies = [('binutils', '2.38')] +dependencies = [('Python', '3.10.4')] + +download_dep_fail = True +sanity_pip_check = True +use_pip = True + +options = {'modulename': 'fontTools'} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/f/fonttools/fonttools-4.53.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/f/fonttools/fonttools-4.53.1-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..cfaada6dee8 --- /dev/null +++ b/easybuild/easyconfigs/f/fonttools/fonttools-4.53.1-GCCcore-12.2.0.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'fonttools' +version = '4.53.1' + +homepage = 'https://python-markdown.github.io/' +description = """ +fontTools is a library for manipulating fonts, written in Python. +The project includes the TTX tool, that can convert TrueType and OpenType fonts to and from an XML text format, +which is also called TTX. +It supports TrueType, OpenType, AFM and to an extent Type 1 and some Mac-specific formats.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['e128778a8e9bc11159ce5447f76766cefbd876f44bd79aff030287254e4752c4'] + +builddependencies = [('binutils', '2.39')] +dependencies = [('Python', '3.10.8')] + +download_dep_fail = True +sanity_pip_check = True +use_pip = True + +options = {'modulename': 'fontTools'} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/f/fonttools/fonttools-4.53.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/f/fonttools/fonttools-4.53.1-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..bf71a8f341f --- /dev/null +++ b/easybuild/easyconfigs/f/fonttools/fonttools-4.53.1-GCCcore-12.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'fonttools' +version = '4.53.1' + +homepage = 'https://python-markdown.github.io/' +description = """ +fontTools is a library for manipulating fonts, written in Python. +The project includes the TTX tool, that can convert TrueType and OpenType fonts to and from an XML text format, +which is also called TTX. +It supports TrueType, OpenType, AFM and to an extent Type 1 and some Mac-specific formats.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['e128778a8e9bc11159ce5447f76766cefbd876f44bd79aff030287254e4752c4'] + +builddependencies = [('binutils', '2.40')] +dependencies = [('Python', '3.11.3')] + +download_dep_fail = True +sanity_pip_check = True +use_pip = True + +options = {'modulename': 'fontTools'} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/f/fonttools/fonttools-4.53.1-GCCcore-13.2.0.eb b/easybuild/easyconfigs/f/fonttools/fonttools-4.53.1-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..0e8a62e088b --- /dev/null +++ b/easybuild/easyconfigs/f/fonttools/fonttools-4.53.1-GCCcore-13.2.0.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'fonttools' +version = '4.53.1' + +homepage = 'https://python-markdown.github.io/' +description = """ +fontTools is a library for manipulating fonts, written in Python. +The project includes the TTX tool, that can convert TrueType and OpenType fonts to and from an XML text format, +which is also called TTX. +It supports TrueType, OpenType, AFM and to an extent Type 1 and some Mac-specific formats.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['e128778a8e9bc11159ce5447f76766cefbd876f44bd79aff030287254e4752c4'] + +builddependencies = [('binutils', '2.40')] +dependencies = [('Python', '3.11.5')] + +download_dep_fail = True +sanity_pip_check = True +use_pip = True + +options = {'modulename': 'fontTools'} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/f/fonttools/fonttools-4.53.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/f/fonttools/fonttools-4.53.1-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..ed395cfd0ee --- /dev/null +++ b/easybuild/easyconfigs/f/fonttools/fonttools-4.53.1-GCCcore-13.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'fonttools' +version = '4.53.1' + +homepage = 'https://python-markdown.github.io/' +description = """ +fontTools is a library for manipulating fonts, written in Python. +The project includes the TTX tool, that can convert TrueType and OpenType fonts to and from an XML text format, +which is also called TTX. +It supports TrueType, OpenType, AFM and to an extent Type 1 and some Mac-specific formats.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['e128778a8e9bc11159ce5447f76766cefbd876f44bd79aff030287254e4752c4'] + +builddependencies = [('binutils', '2.42')] +dependencies = [('Python', '3.12.3')] + +download_dep_fail = True +sanity_pip_check = True +use_pip = True + +options = {'modulename': 'fontTools'} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/f/foss/foss-2024.05.eb b/easybuild/easyconfigs/f/foss/foss-2024.05.eb new file mode 100644 index 00000000000..0d3f8fac41a --- /dev/null +++ b/easybuild/easyconfigs/f/foss/foss-2024.05.eb @@ -0,0 +1,28 @@ +easyblock = 'Toolchain' + +name = 'foss' +version = '2024.05' + +homepage = 'https://easybuild.readthedocs.io/en/master/Common-toolchains.html#foss-toolchain' +description = """GNU Compiler Collection (GCC) based compiler toolchain, including + OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.""" + +toolchain = SYSTEM + +local_gccver = '13.3.0' + +# toolchain used to build foss dependencies +local_comp_mpi_tc = ('gompi', version) + +# we need GCC and OpenMPI as explicit dependencies instead of gompi toolchain +# because of toolchain preparation functions +dependencies = [ + ('GCC', local_gccver), + ('OpenMPI', '5.0.3', '', ('GCC', local_gccver)), + ('FlexiBLAS', '3.4.4', '', ('GCC', local_gccver)), + ('FFTW', '3.3.10', '', ('GCC', local_gccver)), + ('FFTW.MPI', '3.3.10', '', local_comp_mpi_tc), + ('ScaLAPACK', '2.2.0', '-fb', local_comp_mpi_tc), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/f/foss/foss-2024a.eb b/easybuild/easyconfigs/f/foss/foss-2024a.eb new file mode 100644 index 00000000000..7e9a4ba5112 --- /dev/null +++ b/easybuild/easyconfigs/f/foss/foss-2024a.eb @@ -0,0 +1,28 @@ +easyblock = 'Toolchain' + +name = 'foss' +version = '2024a' + +homepage = 'https://easybuild.readthedocs.io/en/master/Common-toolchains.html#foss-toolchain' +description = """GNU Compiler Collection (GCC) based compiler toolchain, including + OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.""" + +toolchain = SYSTEM + +local_gccver = '13.3.0' + +# toolchain used to build foss dependencies +local_comp_mpi_tc = ('gompi', version) + +# we need GCC and OpenMPI as explicit dependencies instead of gompi toolchain +# because of toolchain preparation functions +dependencies = [ + ('GCC', local_gccver), + ('OpenMPI', '5.0.3', '', ('GCC', local_gccver)), + ('FlexiBLAS', '3.4.4', '', ('GCC', local_gccver)), + ('FFTW', '3.3.10', '', ('GCC', local_gccver)), + ('FFTW.MPI', '3.3.10', '', local_comp_mpi_tc), + ('ScaLAPACK', '2.2.0', '-fb', local_comp_mpi_tc), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/f/fplll/fplll-5.4.5-GCCcore-13.2.0.eb b/easybuild/easyconfigs/f/fplll/fplll-5.4.5-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..5184f1f3c1e --- /dev/null +++ b/easybuild/easyconfigs/f/fplll/fplll-5.4.5-GCCcore-13.2.0.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'fplll' +version = '5.4.5' + +homepage = 'https://github.com/fplll/fplll' +description = """fplll contains implementations of several lattice algorithms. + The implementation relies on floating-point orthogonalization, and the 1982 paper from +Lenstra, Lenstra Jr. and Lovasz (LLL) is central to the code, hence the name.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://github.com/fplll/fplll/releases/download/%(version)s'] +sources = [SOURCE_TAR_GZ] +checksums = ['76d3778f0326597ed7505bab19493a9bf6b73a5c5ca614e8fb82f42105c57d00'] + +builddependencies = [ + ('binutils', '2.40'), +] + +dependencies = [ + ('MPFR', '4.2.1'), +] + +sanity_check_paths = { + 'files': ['bin/fplll', 'lib/libfplll.%s' % SHLIB_EXT, 'include/fplll.h'], + 'dirs': ['share'] +} + +sanity_check_commands = ["fplll --help"] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/f/fpylll/fpylll-0.6.1-foss-2023b.eb b/easybuild/easyconfigs/f/fpylll/fpylll-0.6.1-foss-2023b.eb new file mode 100644 index 00000000000..5361252deb7 --- /dev/null +++ b/easybuild/easyconfigs/f/fpylll/fpylll-0.6.1-foss-2023b.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonPackage' + +name = 'fpylll' +version = '0.6.1' + +homepage = 'https://pypi.org/project/fpylll' +description = "A Python wrapper for fplll." + +# can be moved down to gfbf in more recent toolchain versions +toolchain = {'name': 'foss', 'version': '2023b'} + +sources = [SOURCE_TAR_GZ] +checksums = ['dfd9529a26c50993a2a716177debd7994312219070574cad31b35b4f0c040a19'] + +dependencies = [ + ('Python', '3.11.5'), + ('SciPy-bundle', '2023.11'), + ('cysignals', '1.11.4'), + ('fplll', '5.4.5'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.13.2-GCCcore-13.3.0.eb b/easybuild/easyconfigs/f/freetype/freetype-2.13.2-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..1c6fa03dfa0 --- /dev/null +++ b/easybuild/easyconfigs/f/freetype/freetype-2.13.2-GCCcore-13.3.0.eb @@ -0,0 +1,43 @@ +name = 'freetype' +version = '2.13.2' + +homepage = 'https://www.freetype.org' + +description = """ + FreeType 2 is a software font engine that is designed to be small, efficient, + highly customizable, and portable while capable of producing high-quality + output (glyph images). It can be used in graphics libraries, display servers, + font conversion tools, text image generation tools, and many other products + as well. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +source_urls = [ + GNU_SAVANNAH_SOURCE, + SOURCEFORGE_SOURCE, +] +sources = [SOURCE_TAR_GZ] +checksums = ['1ac27e16c134a7f2ccea177faba19801131116fd682efc1f5737037c5db224b5'] + +builddependencies = [('binutils', '2.42')] + +dependencies = [ + ('bzip2', '1.0.8'), + ('libpng', '1.6.43'), + ('zlib', '1.3.1'), + ('Brotli', '1.1.0'), +] + +configopts = '--enable-freetype-config --with-harfbuzz=no' + +sanity_check_paths = { + 'files': ['bin/freetype-config', 'lib/libfreetype.a', + 'lib/libfreetype.%s' % SHLIB_EXT, 'lib/pkgconfig/freetype2.pc'], + 'dirs': ['include/freetype2'], +} + +sanity_check_commands = ["freetype-config --help"] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/f/freud-analysis/freud-analysis-2.6.2-foss-2021a.eb b/easybuild/easyconfigs/f/freud-analysis/freud-analysis-2.6.2-foss-2021a.eb new file mode 100644 index 00000000000..8274a709f9f --- /dev/null +++ b/easybuild/easyconfigs/f/freud-analysis/freud-analysis-2.6.2-foss-2021a.eb @@ -0,0 +1,46 @@ +## +# Author: Robert Mijakovic +## +easyblock = 'PythonBundle' + +name = 'freud-analysis' +version = '2.6.2' + +homepage = 'https://github.com/glotzerlab/freud' +description = """The freud Python library provides a simple, flexible, powerful set of tools for analyzing trajectories +obtained from molecular dynamics or Monte Carlo simulations. High performance, parallelized C++ is used to compute +standard tools such as radial distribution functions, correlation functions, order parameters, and clusters, as well as +original analysis methods including potentials of mean force and torque (PMFTs) and local environment matching. The +freud library supports many input formats and outputs NumPy arrays, enabling integration with the scientific Python +ecosystem for many typical materials science workflows.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +builddependencies = [ + ('pkg-config', '0.29.2'), + ('CMake', '3.20.1'), + ('scikit-build', '0.11.1'), +] + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('tbb', '2020.3'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('rowan', '1.3.0.post1', { + 'source_urls': ['https://pypi.python.org/packages/source/r/rowan'], + 'checksums': ['8f1d0e3279f80c6ae1ee68a90955301853b5586f64e42ba4c27d85504d525e4f'], + }), + (name, version, { + 'modulename': 'freud', + 'source_urls': ['https://pypi.python.org/packages/source/f/freud-analysis'], + 'checksums': ['1cc1b95a8a386e0ac7162246b42be800cfdaf335684a614aae02841aa4df6614'], + }), +] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/f/fsm-lite/fsm-lite-1.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/f/fsm-lite/fsm-lite-1.0-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..65a1167d998 --- /dev/null +++ b/easybuild/easyconfigs/f/fsm-lite/fsm-lite-1.0-GCCcore-12.2.0.eb @@ -0,0 +1,36 @@ +# This easyconfig was created by the BEAR Software team at the University of Birmingham. +easyblock = "MakeCp" + +name = 'fsm-lite' +version = '1.0' + +homepage = "https://github.com/nvalimak/fsm-lite" +description = """A singe-core implemetation of frequency-based substring mining.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://github.com/nvalimak/%(name)s/archive/'] +sources = ['v%(version)s-stable.tar.gz'] +checksums = ['f781a9fbab5265bd09b3b5b7e1cba904582ec201c3d30baed36e28a03de3ac61'] + +builddependencies = [ + ('CMake', '3.24.3'), + ('binutils', '2.39'), +] + +dependencies = [ + ('sdsl-lite', '2.0.3'), +] + +prebuildopts = "sed -i '1s/.*/SDSL_INSTALL_PREFIX=${EBROOTSDSLMINLITE}/' Makefile && make depend &&" + +files_to_copy = [(['fsm-lite'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/fsm-lite'], + 'dirs': [], +} + +sanity_check_commands = ["fsm-lite --help 2>&1 | grep usage"] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/f/fsom/fsom-20151117-GCCcore-12.2.0.eb b/easybuild/easyconfigs/f/fsom/fsom-20151117-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..b9de5b70eff --- /dev/null +++ b/easybuild/easyconfigs/f/fsom/fsom-20151117-GCCcore-12.2.0.eb @@ -0,0 +1,43 @@ +# Updated: Denis Kristak (INUITS) +# Updated: Petr Král (INUITS) + +easyblock = 'ConfigureMake' + +name = 'fsom' +version = '20151117' +local_commit = '56695e1' + +homepage = 'https://github.com/ekg/fsom' +description = """A tiny C library for managing SOM (Self-Organizing Maps) neural networks.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +github_account = 'ekg' + +source_urls = [GITHUB_SOURCE] +sources = ['%s.tar.gz' % local_commit] + +patches = [ + '%(name)s-%(version)s_build-libs.patch', + '%(name)s-20141119_fix-abs-overload.patch' +] + +checksums = [ + '1ba3360985be781bb9f79d974705c86e7bb0719cb83638955e113b5dd83ec8dd', # 56695e1.tar.gz + 'd4e19b2db054cc5d3153ceba88ad2b11e5143e3a3c243103ce1e6994a83c43fe', # fsom-20151117_build-libs.patch + '54dd6ae76033535fe1b0231142d8bd41a815950dc3fd269dc321f698d4973639', # fsom-20141119_fix-abs-overload.patch +] + +builddependencies = [('binutils', '2.39')] + +skipsteps = ['configure'] + +installopts = 'PREFIX=%(installdir)s ' + +sanity_check_paths = { + 'files': ['bin/%(name)s', 'lib/libfsom.%s' % SHLIB_EXT], + 'dirs': [], +} +sanity_check_commands = ["%(name)s --help"] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/f/funannotate/funannotate-1.8.13-foss-2021b.eb b/easybuild/easyconfigs/f/funannotate/funannotate-1.8.13-foss-2021b.eb index 78068a53cc2..18991c61de3 100644 --- a/easybuild/easyconfigs/f/funannotate/funannotate-1.8.13-foss-2021b.eb +++ b/easybuild/easyconfigs/f/funannotate/funannotate-1.8.13-foss-2021b.eb @@ -9,6 +9,7 @@ description = """funannotate is a pipeline for genome annotation (built specific toolchain = {'name': 'foss', 'version': '2021b'} +# see also https://github.com/nextgenusfs/funannotate/blob/master/docs/dependencies.rst dependencies = [ ('Python', '3.9.6'), ('SciPy-bundle', '2021.10'), @@ -17,6 +18,41 @@ dependencies = [ ('matplotlib', '3.4.3'), ('scikit-learn', '1.0.1'), ('Seaborn', '0.11.2'), + ('tbl2asn', '20220427', '-linux64', SYSTEM), + ('DBD-mysql', '4.050'), + ('CodingQuarry', '2.0'), + ('Trinity', '2.15.1'), + ('AUGUSTUS', '3.4.0'), + ('BamTools', '2.5.2'), + ('BEDTools', '2.30.0'), + ('BLAST+', '2.12.0'), # provides makeblastdb, tblastn + ('BLAT', '3.7'), + ('DIAMOND', '2.0.13'), + ('eggnog-mapper', '2.1.7'), + ('ETE', '3.1.2'), + ('Exonerate', '2.4.0'), + ('FASTA', '36.3.8i'), + ('GlimmerHMM', '3.0.4c'), + ('GMAP-GSNAP', '2021-12-17'), # provides gmap + ('GeneMark-ET', '4.71'), # provides gmes_petap.pl + ('HISAT2', '2.2.1'), + ('HMMER', '3.3.2'), # provides hmmscan, hmmsearch + ('kallisto', '0.48.0'), + ('MAFFT', '7.490', '-with-extensions'), + ('minimap2', '2.22'), + ('pigz', '2.6'), + ('Proteinortho', '6.2.3'), + ('Kent_tools', '422'), # provides pslCDnaFilter + ('Salmon', '1.4.0'), + ('SAMtools', '1.14'), + ('SignalP', '6.0g', '-fast'), + ('SNAP', '2.0.1'), + ('StringTie', '2.2.1'), + ('tRNAscan-SE', '2.0.12'), + ('tantan', '40'), + ('trimAl', '1.4.1'), + ('Trimmomatic', '0.39', '-Java-11', SYSTEM), + ('BioPerl', '1.7.8'), ] use_pip = True @@ -38,7 +74,10 @@ sanity_check_paths = { 'dirs': [], } -sanity_check_commands = ["funannotate --help 2>&1 | grep 'Usage:[ ]*funannotate'"] +sanity_check_commands = [ + "funannotate --help 2>&1 | grep 'Usage:[ ]*funannotate'", + "funannotate check --show-versions", +] sanity_pip_check = True diff --git a/easybuild/easyconfigs/f/funannotate/funannotate-1.8.17-foss-2023a.eb b/easybuild/easyconfigs/f/funannotate/funannotate-1.8.17-foss-2023a.eb new file mode 100644 index 00000000000..ed9d5580415 --- /dev/null +++ b/easybuild/easyconfigs/f/funannotate/funannotate-1.8.17-foss-2023a.eb @@ -0,0 +1,94 @@ +easyblock = 'PythonBundle' + +name = 'funannotate' +version = '1.8.17' + +homepage = 'https://funannotate.readthedocs.io' +description = """funannotate is a pipeline for genome annotation (built specifically for fungi, but will also work + with higher eukaryotes)""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +# see also https://github.com/nextgenusfs/funannotate/blob/master/docs/dependencies.rst +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('Biopython', '1.83'), + ('GOATOOLS', '1.4.5'), + ('matplotlib', '3.7.2'), + ('scikit-learn', '1.3.1'), + ('Seaborn', '0.13.2'), + ('tbl2asn', '20230713'), + ('DBD-mysql', '4.050'), + ('CodingQuarry', '2.0'), + ('Trinity', '2.15.2'), + ('AUGUSTUS', '3.5.0'), + ('BamTools', '2.5.2'), + ('BEDTools', '2.31.0'), + ('BLAST+', '2.14.1'), # provides makeblastdb, tblastn + ('BLAT', '3.7'), + ('DIAMOND', '2.1.8'), + ('eggnog-mapper', '2.1.12'), + ('ETE', '3.1.3'), + ('Exonerate', '2.4.0'), + ('FASTA', '36.3.8i'), + ('GlimmerHMM', '3.0.4c'), + ('GMAP-GSNAP', '2023-04-20'), # provides gmap + ('GeneMark-ET', '4.72'), # provides gmes_petap.pl + ('HISAT2', '2.2.1'), + ('HMMER', '3.4'), # provides hmmscan, hmmsearch + ('kallisto', '0.51.1'), + ('MAFFT', '7.520', '-with-extensions'), + ('minimap2', '2.26'), + ('pigz', '2.8'), + ('Proteinortho', '6.3.2'), + ('Kent_tools', '468'), # provides pslCDnaFilter + ('Salmon', '1.10.3'), + ('SAMtools', '1.18'), + ('SignalP', '6.0h', '-fast'), + ('SNAP-HMM', '20221022'), + ('StringTie', '2.2.3'), + ('tRNAscan-SE', '2.0.12'), + ('tantan', '50'), + ('trimAl', '1.4.1'), + ('Trimmomatic', '0.39', '-Java-11', SYSTEM), + ('BioPerl', '1.7.8'), + ('EVidenceModeler', '2.1.0'), +] + +use_pip = True + +exts_list = [ + ('distro', '1.9.0', { + 'checksums': ['2fa77c6fd8940f116ee1d6b94a2f90b13b5ea8d019b98bc8bafdcabcdd9bdbed'], + }), + ('natsort', '8.4.0', { + 'checksums': ['45312c4a0e5507593da193dedd04abb1469253b601ecaf63445ad80f0a1ea581'], + }), + (name, version, { + 'checksums': ['bdadfd7a5636383c1c40c26dab37c5908a77e8c4064adced84f1ba9e86187a04'], + 'preinstallopts': ( + """sed -i 's|REQUIRES_PYTHON = ">=3.6.0, <3.10"|REQUIRES_PYTHON = ">=3.6.0"|' setup.py && """ + """sed -i 's|"biopython<1.80",|"biopython",|' setup.py && """ + ) + }), +] + +sanity_check_paths = { + 'files': ['bin/funannotate'], + 'dirs': [], +} + +modextrapaths = { + 'GENEMARK_PATH': '$EBROOTGENEMARKMINET', +} + +sanity_check_commands = [ + "funannotate --help 2>&1 | grep 'Usage:[ ]*funannotate'", + "funannotate check --show-versions", +] + + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GATE/GATE-9.4-foss-2023a.eb b/easybuild/easyconfigs/g/GATE/GATE-9.4-foss-2023a.eb new file mode 100644 index 00000000000..6fd245d2079 --- /dev/null +++ b/easybuild/easyconfigs/g/GATE/GATE-9.4-foss-2023a.eb @@ -0,0 +1,29 @@ +name = 'GATE' +version = '9.4' + +homepage = 'http://www.opengatecollaboration.org/' +description = """GATE is an advanced opensource software developed by the international OpenGATE collaboration and + dedicated to the numerical simulations in medical imaging. It currently supports simulations of Emission Tomography + (Positron Emission Tomography - PET and Single Photon Emission Computed Tomography - SPECT), and Computed Tomography""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['https://github.com/OpenGATE/Gate/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['96c53f6ab1b25c0e540d8f9564bce0049371b378de80a7118a0ff8834c6c117c'] + +builddependencies = [ + ('CMake', '3.26.3'), +] +dependencies = [ + ('Geant4', '11.2.2'), + ('CLHEP', '2.4.7.1'), + ('ROOT', '6.30.06'), +] + +preinstallopts = "sed -i 's|/usr/local/bin|%(installdir)s/bin|g' Makefile &&" + +# enable extra capabilities (Davis requires Geant4 10.04 or newer) +configopts = "-DGATE_USE_OPTICAL=1 -DGATE_USE_DAVIS=1" + +moduleclass = 'cae' diff --git a/easybuild/easyconfigs/g/GATK/GATK-4.3.0.0-GCCcore-12.3.0-Java-11.eb b/easybuild/easyconfigs/g/GATK/GATK-4.3.0.0-GCCcore-12.3.0-Java-11.eb new file mode 100644 index 00000000000..c5247c1cf5a --- /dev/null +++ b/easybuild/easyconfigs/g/GATK/GATK-4.3.0.0-GCCcore-12.3.0-Java-11.eb @@ -0,0 +1,55 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2013 Cyprus Institute / CaSToRC, University of Luxembourg / LCSB +# Authors:: George Tsouloupas , Fotis Georgatos , +# Kenneth Hoste (UGent) +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +# Modified by: Adam Huffman, Jonas Demeulemeester +# The Francis Crick Institute +# Modified for version 4.0.5.1 by: Ruben van Dijk, University of Groningen +# Modified for version 4.2.3.0 by: J. Sassmannshausen / GSTT +# Modified for version 4.4.0.0 by: Thomas Eylenbosch / Gluo NV +## + +easyblock = 'Tarball' + +name = 'GATK' +version = '4.3.0.0' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'https://www.broadinstitute.org/gatk/' +description = """The Genome Analysis Toolkit or GATK is a software package developed at the Broad Institute + to analyse next-generation resequencing data. The toolkit offers a wide variety of tools, + with a primary focus on variant discovery and genotyping as well as strong emphasis on + data quality assurance. Its robust architecture, powerful processing engine and + high-performance computing features make it capable of taking on projects of any size.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://github.com/broadinstitute/gatk/releases/download/%(version)s/'] +sources = ['gatk-%(version)s.zip'] +checksums = ['e2c27229b34c3e22445964adf00639a0909887bbfcc040f6910079177bc6e2dd'] + +dependencies = [ + ('Java', '11', '', SYSTEM), + ('Python', '3.11.3'), +] + +modextrapaths = {'PATH': ''} + +sanity_check_paths = { + 'files': ['gatk'], + 'dirs': [], +} + +sanity_check_commands = [ + "gatk --help", + "gatk --list", +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GATK/GATK-4.6.0.0-GCCcore-13.2.0-Java-17.eb b/easybuild/easyconfigs/g/GATK/GATK-4.6.0.0-GCCcore-13.2.0-Java-17.eb new file mode 100644 index 00000000000..1c700e8eab0 --- /dev/null +++ b/easybuild/easyconfigs/g/GATK/GATK-4.6.0.0-GCCcore-13.2.0-Java-17.eb @@ -0,0 +1,55 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2013 Cyprus Institute / CaSToRC, University of Luxembourg / LCSB +# Authors:: George Tsouloupas , Fotis Georgatos , +# Kenneth Hoste (UGent) +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +# Modified by: Adam Huffman, Jonas Demeulemeester +# The Francis Crick Institute +# Modified for version 4.0.5.1 by: Ruben van Dijk, University of Groningen +# Modified for version 4.2.3.0 by: J. Sassmannshausen / GSTT +# Modified for version 4.4.0.0 by: Thomas Eylenbosch / Gluo NV +## + +easyblock = 'Tarball' + +name = 'GATK' +version = '4.6.0.0' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'https://www.broadinstitute.org/gatk/' +description = """The Genome Analysis Toolkit or GATK is a software package developed at the Broad Institute + to analyse next-generation resequencing data. The toolkit offers a wide variety of tools, + with a primary focus on variant discovery and genotyping as well as strong emphasis on + data quality assurance. Its robust architecture, powerful processing engine and + high-performance computing features make it capable of taking on projects of any size.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://github.com/broadinstitute/gatk/releases/download/%(version)s/'] +sources = ['gatk-%(version)s.zip'] +checksums = ['a5d31e34630f355e5a119894f2587fec47049fedff04300f6633c31ef14c3a66'] + +dependencies = [ + ('Java', '17', '', SYSTEM), + ('Python', '3.11.5'), +] + +modextrapaths = {'PATH': ''} + +sanity_check_paths = { + 'files': ['gatk'], + 'dirs': [], +} + +sanity_check_commands = [ + "gatk --help", + "gatk --list", +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GCC/GCC-13.3.0.eb b/easybuild/easyconfigs/g/GCC/GCC-13.3.0.eb new file mode 100644 index 00000000000..3428422c0b9 --- /dev/null +++ b/easybuild/easyconfigs/g/GCC/GCC-13.3.0.eb @@ -0,0 +1,22 @@ +easyblock = 'Bundle' + +name = 'GCC' +version = '13.3.0' + +homepage = 'https://gcc.gnu.org/' +description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, + as well as libraries for these languages (libstdc++, libgcj,...).""" + +toolchain = SYSTEM + +dependencies = [ + ('GCCcore', version), + # binutils built on top of GCCcore, which was built on top of binutils (built with system toolchain) + ('binutils', '2.42', '', ('GCCcore', version)), +] + +altroot = 'GCCcore' +altversion = 'GCCcore' + +# this bundle serves as a compiler-only toolchain, so it should be marked as compiler (important for HMNS) +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/g/GCC/GCC-14.2.0.eb b/easybuild/easyconfigs/g/GCC/GCC-14.2.0.eb new file mode 100644 index 00000000000..7126db6c52d --- /dev/null +++ b/easybuild/easyconfigs/g/GCC/GCC-14.2.0.eb @@ -0,0 +1,22 @@ +easyblock = 'Bundle' + +name = 'GCC' +version = '14.2.0' + +homepage = 'https://gcc.gnu.org/' +description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, + as well as libraries for these languages (libstdc++, libgcj,...).""" + +toolchain = SYSTEM + +dependencies = [ + ('GCCcore', version), + # binutils built on top of GCCcore, which was built on top of binutils (built with system toolchain) + ('binutils', '2.42', '', ('GCCcore', version)), +] + +altroot = 'GCCcore' +altversion = 'GCCcore' + +# this bundle serves as a compiler-only toolchain, so it should be marked as compiler (important for HMNS) +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-13.3.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-13.3.0.eb new file mode 100644 index 00000000000..77acc578454 --- /dev/null +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-13.3.0.eb @@ -0,0 +1,65 @@ +easyblock = 'EB_GCC' + +name = 'GCCcore' +version = '13.3.0' + +homepage = 'https://gcc.gnu.org/' +description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, + as well as libraries for these languages (libstdc++, libgcj,...).""" + +toolchain = SYSTEM + +source_urls = [ + 'https://ftpmirror.gnu.org/gnu/gcc/gcc-%(version)s', # GCC auto-resolving HTTP mirror + 'https://sourceware.org/pub/gcc/releases/gcc-%(version)s', # fallback URL for GCC + 'https://ftpmirror.gnu.org/gnu/gmp', # idem for GMP + 'https://ftpmirror.gnu.org/gnu/mpfr', # idem for MPFR + 'https://ftpmirror.gnu.org/gnu/mpc', # idem for MPC + 'ftp://gcc.gnu.org/pub/gcc/infrastructure/', # GCC dependencies + 'https://gcc.gnu.org/pub/gcc/infrastructure/', # HTTPS mirror for GCC dependencies + 'https://libisl.sourceforge.io/', # fallback URL for isl + 'https://sourceware.org/pub/newlib/', # for newlib + 'https://github.com/MentorEmbedded/nvptx-tools/archive', # for nvptx-tools +] +sources = [ + 'gcc-%(version)s.tar.gz', + 'gmp-6.3.0.tar.bz2', + 'mpfr-4.2.1.tar.bz2', + 'mpc-1.3.1.tar.gz', + 'isl-0.26.tar.bz2', + 'newlib-4.4.0.20231231.tar.gz', + {'download_filename': '9962793.tar.gz', 'filename': 'nvptx-tools-20240419.tar.gz'}, +] +patches = [ + 'GCCcore-6.2.0-fix-find-isl.patch', + 'GCCcore-9.3.0_gmp-c99.patch', + 'GCCcore-12.x_riscv_multiarch_support.patch', +] +checksums = [ + {'gcc-13.3.0.tar.gz': '3a2b10cab86e32358fdac871546d57e2700e9bdb5875ef33fff5b601265b9e32'}, + {'gmp-6.3.0.tar.bz2': 'ac28211a7cfb609bae2e2c8d6058d66c8fe96434f740cf6fe2e47b000d1c20cb'}, + {'mpfr-4.2.1.tar.bz2': 'b9df93635b20e4089c29623b19420c4ac848a1b29df1cfd59f26cab0d2666aa0'}, + {'mpc-1.3.1.tar.gz': 'ab642492f5cf882b74aa0cb730cd410a81edcdbec895183ce930e706c1c759b8'}, + {'isl-0.26.tar.bz2': '5eac8664e9d67be6bd0bee5085d6840b8baf738c06814df47eaf4166d9776436'}, + {'newlib-4.4.0.20231231.tar.gz': '0c166a39e1bf0951dfafcd68949fe0e4b6d3658081d6282f39aeefc6310f2f13'}, + {'nvptx-tools-20240419.tar.gz': 'a4f65efe0ba960d75a18741faf2b93dbf51c2492a53b734d590ce5da4bd3f237'}, + {'GCCcore-6.2.0-fix-find-isl.patch': '5ad909606d17d851c6ad629b4fddb6c1621844218b8d139fed18c502a7696c68'}, + {'GCCcore-9.3.0_gmp-c99.patch': '0e135e1cc7cec701beea9d7d17a61bab34cfd496b4b555930016b98db99f922e'}, + {'GCCcore-12.x_riscv_multiarch_support.patch': '92fc2b17b6943611a657904500fbf3db8160eddbcea320828d4a50a885e2778f'}, +] + +builddependencies = [ + ('M4', '1.4.19'), + ('binutils', '2.42'), +] + +languages = ['c', 'c++', 'fortran'] + +withisl = True +withnvptx = True + +# Perl is only required when building with NVPTX support +if withnvptx: + osdependencies = ['perl'] + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-14.2.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-14.2.0.eb new file mode 100644 index 00000000000..438a848145f --- /dev/null +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-14.2.0.eb @@ -0,0 +1,63 @@ +easyblock = 'EB_GCC' + +name = 'GCCcore' +version = '14.2.0' + +homepage = 'https://gcc.gnu.org/' +description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, + as well as libraries for these languages (libstdc++, libgcj,...).""" + +toolchain = SYSTEM + +source_urls = [ + 'https://ftpmirror.gnu.org/gnu/gcc/gcc-%(version)s', # GCC auto-resolving HTTP mirror + 'https://sourceware.org/pub/gcc/releases/gcc-%(version)s', # fallback URL for GCC + 'https://ftpmirror.gnu.org/gnu/gmp', # idem for GMP + 'https://ftpmirror.gnu.org/gnu/mpfr', # idem for MPFR + 'https://ftpmirror.gnu.org/gnu/mpc', # idem for MPC + 'ftp://gcc.gnu.org/pub/gcc/infrastructure/', # GCC dependencies + 'https://gcc.gnu.org/pub/gcc/infrastructure/', # HTTPS mirror for GCC dependencies + 'https://libisl.sourceforge.io/', # fallback URL for isl + 'https://sourceware.org/pub/newlib/', # for newlib + 'https://github.com/MentorEmbedded/nvptx-tools/archive', # for nvptx-tools +] +sources = [ + 'gcc-%(version)s.tar.gz', + 'gmp-6.3.0.tar.bz2', + 'mpfr-4.2.1.tar.bz2', + 'mpc-1.3.1.tar.gz', + 'isl-0.26.tar.bz2', + 'newlib-4.4.0.20231231.tar.gz', + {'download_filename': '3136cf9.tar.gz', 'filename': 'nvptx-tools-20240801.tar.gz'}, +] +patches = [ + 'GCCcore-6.2.0-fix-find-isl.patch', + 'GCCcore-9.3.0_gmp-c99.patch', +] +checksums = [ + {'gcc-14.2.0.tar.gz': '7d376d445f93126dc545e2c0086d0f647c3094aae081cdb78f42ce2bc25e7293'}, + {'gmp-6.3.0.tar.bz2': 'ac28211a7cfb609bae2e2c8d6058d66c8fe96434f740cf6fe2e47b000d1c20cb'}, + {'mpfr-4.2.1.tar.bz2': 'b9df93635b20e4089c29623b19420c4ac848a1b29df1cfd59f26cab0d2666aa0'}, + {'mpc-1.3.1.tar.gz': 'ab642492f5cf882b74aa0cb730cd410a81edcdbec895183ce930e706c1c759b8'}, + {'isl-0.26.tar.bz2': '5eac8664e9d67be6bd0bee5085d6840b8baf738c06814df47eaf4166d9776436'}, + {'newlib-4.4.0.20231231.tar.gz': '0c166a39e1bf0951dfafcd68949fe0e4b6d3658081d6282f39aeefc6310f2f13'}, + {'nvptx-tools-20240801.tar.gz': 'a1106bf11b66d12e67194d8aa37196bb96996b614f44b3d3bc1b5854eefec03c'}, + {'GCCcore-6.2.0-fix-find-isl.patch': '5ad909606d17d851c6ad629b4fddb6c1621844218b8d139fed18c502a7696c68'}, + {'GCCcore-9.3.0_gmp-c99.patch': '0e135e1cc7cec701beea9d7d17a61bab34cfd496b4b555930016b98db99f922e'}, +] + +builddependencies = [ + ('M4', '1.4.19'), + ('binutils', '2.42'), +] + +languages = ['c', 'c++', 'fortran'] + +withisl = True +withnvptx = True + +# Perl is only required when building with NVPTX support +if withnvptx: + osdependencies = ['perl'] + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-3.6.2-foss-2022b.eb b/easybuild/easyconfigs/g/GDAL/GDAL-3.6.2-foss-2022b.eb index c293d01731d..576d90e74d6 100644 --- a/easybuild/easyconfigs/g/GDAL/GDAL-3.6.2-foss-2022b.eb +++ b/easybuild/easyconfigs/g/GDAL/GDAL-3.6.2-foss-2022b.eb @@ -61,9 +61,9 @@ dependencies = [ # common configopts for static, shared library builds _base_configopts = ' '.join([ '-DGDAL_USE_INTERNAL_LIBS=OFF', - '-DArrow_DIR=$EBROOTARROW', '-DGEOTIFF_INCLUDE_DIR=$EBROOTLIBGEOTIFF/include', '-DPython_ROOT=$EBROOTPYTHON', + '-DGDAL_USE_MYSQL=OFF', ]) # iterative build for both static and shared libraries diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-3.7.1-foss-2023a.eb b/easybuild/easyconfigs/g/GDAL/GDAL-3.7.1-foss-2023a.eb index 92bfe549e74..88e35cd4db4 100644 --- a/easybuild/easyconfigs/g/GDAL/GDAL-3.7.1-foss-2023a.eb +++ b/easybuild/easyconfigs/g/GDAL/GDAL-3.7.1-foss-2023a.eb @@ -61,7 +61,7 @@ dependencies = [ ] # iterative build for both static and shared libraries -local_configopts_common = "-DGDAL_USE_INTERNAL_LIBS=OFF -DArrow_DIR=$EBROOTARROW " +local_configopts_common = "-DGDAL_USE_INTERNAL_LIBS=OFF -DGDAL_USE_MYSQL=OFF " local_configopts_common += "-DGEOTIFF_INCLUDE_DIR=$EBROOTLIBGEOTIFF/include -DPython_ROOT=$EBROOTPYTHON " configopts = [ diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-3.9.0-foss-2023b.eb b/easybuild/easyconfigs/g/GDAL/GDAL-3.9.0-foss-2023b.eb new file mode 100644 index 00000000000..21299457516 --- /dev/null +++ b/easybuild/easyconfigs/g/GDAL/GDAL-3.9.0-foss-2023b.eb @@ -0,0 +1,81 @@ +easyblock = 'CMakeMake' + +name = 'GDAL' +version = '3.9.0' + +homepage = 'https://www.gdal.org' +description = """GDAL is a translator library for raster geospatial data formats that is released under an X/MIT style + Open Source license by the Open Source Geospatial Foundation. As a library, it presents a single abstract data model + to the calling application for all supported formats. It also comes with a variety of useful commandline utilities for + data translation and processing.""" + +toolchain = {'name': 'foss', 'version': '2023b'} +toolchainopts = {'usempi': True} + +source_urls = ['https://download.osgeo.org/%(namelower)s/%(version)s/'] +sources = [SOURCELOWER_TAR_XZ] +patches = ['%(name)s-3.6.2_fix-python-CC-CXX.patch'] +checksums = [ + {'gdal-3.9.0.tar.xz': '577f80e9d14ff7c90b6bfbc34201652b4546700c01543efb4f4c3050e0b3fda2'}, + {'GDAL-3.6.2_fix-python-CC-CXX.patch': '859b874b0c8ff7626a76d51f008bf05b7f89a35b325bdd1d126d2364154acc63'}, +] + +builddependencies = [ + ('CMake', '3.27.6'), + ('pkgconf', '2.0.3'), + ('Bison', '3.8.2'), +] +dependencies = [ + ('Python', '3.11.5'), + ('netCDF', '4.9.2'), + ('expat', '2.5.0'), + ('GEOS', '3.12.1'), + ('SQLite', '3.43.1'), + ('libarchive', '3.7.2'), + ('libxml2', '2.11.5'), + ('libpng', '1.6.40'), + ('libjpeg-turbo', '3.0.1'), + ('LibTIFF', '4.6.0'), + ('zlib', '1.2.13'), + ('cURL', '8.3.0'), + ('PCRE', '8.45'), + ('PROJ', '9.3.1'), + ('libgeotiff', '1.7.3'), + ('SciPy-bundle', '2023.11'), + ('HDF5', '1.14.3'), + ('HDF', '4.2.16-2'), + ('Armadillo', '12.8.0'), + ('CFITSIO', '4.3.1'), + ('zstd', '1.5.5'), + ('giflib', '5.2.1'), + ('json-c', '0.17'), + ('Xerces-C++', '3.2.5'), + ('PCRE2', '10.42'), + ('OpenEXR', '3.2.0'), + ('Brunsli', '0.1'), + ('Qhull', '2020.2'), + ('LERC', '4.0.0'), + ('OpenJPEG', '2.5.0'), + ('SWIG', '4.1.1'), +] + +# iterative build for both static and shared libraries +local_configopts_common = "-DGDAL_USE_INTERNAL_LIBS=OFF -DGDAL_USE_MYSQL=OFF " +local_configopts_common += "-DGEOTIFF_INCLUDE_DIR=$EBROOTLIBGEOTIFF/include -DPython_ROOT=$EBROOTPYTHON " + +configopts = [ + local_configopts_common + "-DBUILD_SHARED_LIBS=OFF", + local_configopts_common +] + + +sanity_check_paths = { + 'files': ['lib/libgdal.a', 'lib/libgdal.%s' % SHLIB_EXT], + 'dirs': ['bin', 'include', 'lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["python -c 'import osgeo.%(namelower)s'"] + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/g/GDB/GDB-14.2-GCCcore-13.3.0.eb b/easybuild/easyconfigs/g/GDB/GDB-14.2-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..7cb65516ac9 --- /dev/null +++ b/easybuild/easyconfigs/g/GDB/GDB-14.2-GCCcore-13.3.0.eb @@ -0,0 +1,49 @@ +easyblock = 'ConfigureMake' + +name = 'GDB' +version = '14.2' + +homepage = 'https://www.gnu.org/software/gdb/gdb.html' +description = "The GNU Project Debugger" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['2d4dd8061d8ded12b6c63f55e45344881e8226105f4d2a9b234040efa5ce7772'] + +builddependencies = [ + ('binutils', '2.42'), + ('makeinfo', '7.1'), +] + +dependencies = [ + ('zlib', '1.3.1'), + ('libreadline', '8.2'), + ('ncurses', '6.5'), + ('expat', '2.6.2'), + ('Python', '3.12.3'), + ('ISL', '0.26'), + ('MPC', '1.3.1'), +] + +preconfigopts = "mkdir obj && cd obj && " +configure_cmd_prefix = '../' +prebuildopts = "cd obj && " +preinstallopts = prebuildopts + +configopts = '--with-system-zlib --with-system-readline --with-expat=$EBROOTEXPAT ' +configopts += '--with-python=$EBROOTPYTHON/bin/python --with-isl=$EBROOTISL --with-mpc=$EBROOTMPC ' +configopts += '--enable-tui --enable-plugins --disable-install-libbfd ' + +sanity_check_paths = { + 'files': ['bin/gdb', 'bin/gdbserver'], + 'dirs': [], +} + +sanity_check_commands = [ + 'gdb --help', + 'gdbserver --help', +] + +moduleclass = 'debugger' diff --git a/easybuild/easyconfigs/g/GDMA/GDMA-2.3.3_20230603-GCC-12.3.0.eb b/easybuild/easyconfigs/g/GDMA/GDMA-2.3.3_20230603-GCC-12.3.0.eb new file mode 100644 index 00000000000..d22b6d74689 --- /dev/null +++ b/easybuild/easyconfigs/g/GDMA/GDMA-2.3.3_20230603-GCC-12.3.0.eb @@ -0,0 +1,42 @@ +easyblock = 'ConfigureMake' + +name = 'GDMA' +version = '2.3.3_20230603' +_commit = '6b8e81ec' + +homepage = 'https://gitlab.com/anthonyjs/gdma' +description = """ +The GDMA program carries out Distributed Multipole Analysis of wavefunctions +calculated by the Gaussian system of programs or the Psi4 package, using the +formatted checkpoint files that they can produce. The result is a set of +multipole moments at sites defined by the user (usually at the positions of the +atomic nuclei) which, given an accurate wavefunction, provide an accurate +description of the electrostatic field of the molecule.""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +sources = [{ + 'source_urls': ['https://gitlab.com/anthonyjs/gdma/-/archive/'], + 'download_filename': '%s.tar.gz' % _commit, + 'filename': SOURCE_TAR_GZ, +}] +checksums = ['cc008932ae8768e6cbd444337a998e02b2100c123492c260d6020590e76bec1e'] + +parallel = 1 + +skipsteps = ['configure'] + +# avoid using git to obtain the commit: not a cloned repo +prebuildopts = """sed -i "/^log =/,/^commit =/c commit = '%s'" src/version.py && """ % _commit + +preinstallopts = 'mkdir -p %(installdir)s/bin && ' +installopts = 'INSTALL_DIR=%(installdir)s/bin' + +sanity_check_paths = { + 'files': ['bin/gdma'], + 'dirs': [], +} + +sanity_check_commands = ['echo|gdma'] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.1-GCCcore-10.2.0-CUDA-11.1.1.eb b/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.1-GCCcore-10.2.0-CUDA-11.1.1.eb index c99c15a13e4..915d01b254a 100644 --- a/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.1-GCCcore-10.2.0-CUDA-11.1.1.eb +++ b/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.1-GCCcore-10.2.0-CUDA-11.1.1.eb @@ -27,21 +27,21 @@ dependencies = [ ('Check', '0.15.2'), ] -# This easyconfig only installs the library and binaries of GDRCopy. Please -# keep in mind that GDRCopy also needs the following kernel modules at runtime: -# -# 1. Kernel module for GDRCopy: improves Host to GPU communication -# https://github.com/NVIDIA/gdrcopy -# RPM: 'gdrcopy-kmod', DEB: 'gdrdrv-dkms' -# Requirements: version of GDRCopy kernel module (gdrdrv.ko) >= 2.0 -# -# 2. (optional) Kernel module for GPUDirect RDMA: improves GPU to GPU communication -# https://github.com/Mellanox/nv_peer_memory -# RPM: 'nvidia_peer_memory' -# Requirements: Mellanox HCA with MLNX_OFED 2.1 -# -# These kernel modules are not listed as system dependencies to lower the system -# requirements to build this easyconfig, as they are not needed for the build. +build_info_msg = """This easyconfig only installs the library and binaries of GDRCopy. Please +keep in mind that GDRCopy also needs the following kernel modules at runtime: + +1. Kernel module for GDRCopy: improves Host to GPU communication + https://github.com/NVIDIA/gdrcopy + RPM: 'gdrcopy-kmod', DEB: 'gdrdrv-dkms' + Requirements: version of GDRCopy kernel module (gdrdrv.ko) >= 2.0 + +2. (optional) Kernel module for GPUDirect RDMA: improves GPU to GPU communication + https://github.com/Mellanox/nv_peer_memory + RPM: 'nvidia_peer_memory' + Requirements: Mellanox HCA with MLNX_OFED 2.1 + +These kernel modules are not listed as system dependencies to lower the system +requirements to build this easyconfig, as they are not needed for the build.""" skipsteps = ['configure'] diff --git a/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.1-GCCcore-10.2.0-CUDA-11.2.1.eb b/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.1-GCCcore-10.2.0-CUDA-11.2.1.eb index accc04a5bde..443bbdd4af7 100644 --- a/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.1-GCCcore-10.2.0-CUDA-11.2.1.eb +++ b/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.1-GCCcore-10.2.0-CUDA-11.2.1.eb @@ -27,21 +27,21 @@ dependencies = [ ('Check', '0.15.2'), ] -# This easyconfig only installs the library and binaries of GDRCopy. Please -# keep in mind that GDRCopy also needs the following kernel modules at runtime: -# -# 1. Kernel module for GDRCopy: improves Host to GPU communication -# https://github.com/NVIDIA/gdrcopy -# RPM: 'gdrcopy-kmod', DEB: 'gdrdrv-dkms' -# Requirements: version of GDRCopy kernel module (gdrdrv.ko) >= 2.0 -# -# 2. (optional) Kernel module for GPUDirect RDMA: improves GPU to GPU communication -# https://github.com/Mellanox/nv_peer_memory -# RPM: 'nvidia_peer_memory' -# Requirements: Mellanox HCA with MLNX_OFED 2.1 -# -# These kernel modules are not listed as system dependencies to lower the system -# requirements to build this easyconfig, as they are not needed for the build. +build_info_msg = """This easyconfig only installs the library and binaries of GDRCopy. Please +keep in mind that GDRCopy also needs the following kernel modules at runtime: + +1. Kernel module for GDRCopy: improves Host to GPU communication + https://github.com/NVIDIA/gdrcopy + RPM: 'gdrcopy-kmod', DEB: 'gdrdrv-dkms' + Requirements: version of GDRCopy kernel module (gdrdrv.ko) >= 2.0 + +2. (optional) Kernel module for GPUDirect RDMA: improves GPU to GPU communication + https://github.com/Mellanox/nv_peer_memory + RPM: 'nvidia_peer_memory' + Requirements: Mellanox HCA with MLNX_OFED 2.1 + +These kernel modules are not listed as system dependencies to lower the system +requirements to build this easyconfig, as they are not needed for the build.""" skipsteps = ['configure'] diff --git a/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.1-GCCcore-9.3.0-CUDA-11.0.2.eb b/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.1-GCCcore-9.3.0-CUDA-11.0.2.eb index 864159cc441..3c02c5d5c02 100644 --- a/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.1-GCCcore-9.3.0-CUDA-11.0.2.eb +++ b/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.1-GCCcore-9.3.0-CUDA-11.0.2.eb @@ -27,21 +27,21 @@ dependencies = [ ('Check', '0.15.2'), ] -# This easyconfig only installs the library and binaries of GDRCopy. Please -# keep in mind that GDRCopy also needs the following kernel modules at runtime: -# -# 1. Kernel module for GDRCopy: improves Host to GPU communication -# https://github.com/NVIDIA/gdrcopy -# RPM: 'gdrcopy-kmod', DEB: 'gdrdrv-dkms' -# Requirements: version of GDRCopy kernel module (gdrdrv.ko) >= 2.0 -# -# 2. (optional) Kernel module for GPUDirect RDMA: improves GPU to GPU communication -# https://github.com/Mellanox/nv_peer_memory -# RPM: 'nvidia_peer_memory' -# Requirements: Mellanox HCA with MLNX_OFED 2.1 -# -# These kernel modules are not listed as system dependencies to lower the system -# requirements to build this easyconfig, as they are not needed for the build. +build_info_msg = """This easyconfig only installs the library and binaries of GDRCopy. Please +keep in mind that GDRCopy also needs the following kernel modules at runtime: + +1. Kernel module for GDRCopy: improves Host to GPU communication + https://github.com/NVIDIA/gdrcopy + RPM: 'gdrcopy-kmod', DEB: 'gdrdrv-dkms' + Requirements: version of GDRCopy kernel module (gdrdrv.ko) >= 2.0 + +2. (optional) Kernel module for GPUDirect RDMA: improves GPU to GPU communication + https://github.com/Mellanox/nv_peer_memory + RPM: 'nvidia_peer_memory' + Requirements: Mellanox HCA with MLNX_OFED 2.1 + +These kernel modules are not listed as system dependencies to lower the system +requirements to build this easyconfig, as they are not needed for the build.""" skipsteps = ['configure'] diff --git a/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.2-GCCcore-10.2.0.eb index 85810e2394d..f6498b61ef3 100644 --- a/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.2-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.2-GCCcore-10.2.0.eb @@ -20,21 +20,21 @@ builddependencies = [ ('pkg-config', '0.29.2'), ] -# This easyconfig only installs the library of GDRCopy. Please keep in mind -# that GDRCopy also needs the following kernel modules at runtime: -# -# 1. Kernel module for GDRCopy: improves Host to GPU communication -# https://github.com/NVIDIA/gdrcopy -# RPM: 'gdrcopy-kmod', DEB: 'gdrdrv-dkms' -# Requirements: version of GDRCopy kernel module (gdrdrv.ko) >= 2.0 -# -# 2. (optional) Kernel module for GPUDirect RDMA: improves GPU to GPU communication -# https://github.com/Mellanox/nv_peer_memory -# RPM: 'nvidia_peer_memory' -# Requirements: Mellanox HCA with MLNX_OFED 2.1 -# -# These kernel modules are not listed as system dependencies to lower the system -# requirements to build this easyconfig, as they are not needed for the build. +build_info_msg = """This easyconfig only installs the library of GDRCopy. Please keep in mind +that GDRCopy also needs the following kernel modules at runtime: + +1. Kernel module for GDRCopy: improves Host to GPU communication + https://github.com/NVIDIA/gdrcopy + RPM: 'gdrcopy-kmod', DEB: 'gdrdrv-dkms' + Requirements: version of GDRCopy kernel module (gdrdrv.ko) >= 2.0 + +2. (optional) Kernel module for GPUDirect RDMA: improves GPU to GPU communication + https://github.com/Mellanox/nv_peer_memory + RPM: 'nvidia_peer_memory' + Requirements: Mellanox HCA with MLNX_OFED 2.1 + +These kernel modules are not listed as system dependencies to lower the system +requirements to build this easyconfig, as they are not needed for the build.""" skipsteps = ['configure'] diff --git a/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.2-GCCcore-10.3.0.eb b/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.2-GCCcore-10.3.0.eb index e9750d55747..cd3d0ee01c6 100644 --- a/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.2-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.2-GCCcore-10.3.0.eb @@ -20,21 +20,21 @@ builddependencies = [ ('pkg-config', '0.29.2'), ] -# This easyconfig only installs the library of GDRCopy. Please keep in mind -# that GDRCopy also needs the following kernel modules at runtime: -# -# 1. Kernel module for GDRCopy: improves Host to GPU communication -# https://github.com/NVIDIA/gdrcopy -# RPM: 'gdrcopy-kmod', DEB: 'gdrdrv-dkms' -# Requirements: version of GDRCopy kernel module (gdrdrv.ko) >= 2.0 -# -# 2. (optional) Kernel module for GPUDirect RDMA: improves GPU to GPU communication -# https://github.com/Mellanox/nv_peer_memory -# RPM: 'nvidia_peer_memory' -# Requirements: Mellanox HCA with MLNX_OFED 2.1 -# -# These kernel modules are not listed as system dependencies to lower the system -# requirements to build this easyconfig, as they are not needed for the build. +build_info_msg = """This easyconfig only installs the library of GDRCopy. Please keep in mind +that GDRCopy also needs the following kernel modules at runtime: + +1. Kernel module for GDRCopy: improves Host to GPU communication + https://github.com/NVIDIA/gdrcopy + RPM: 'gdrcopy-kmod', DEB: 'gdrdrv-dkms' + Requirements: version of GDRCopy kernel module (gdrdrv.ko) >= 2.0 + +2. (optional) Kernel module for GPUDirect RDMA: improves GPU to GPU communication + https://github.com/Mellanox/nv_peer_memory + RPM: 'nvidia_peer_memory' + Requirements: Mellanox HCA with MLNX_OFED 2.1 + +These kernel modules are not listed as system dependencies to lower the system +requirements to build this easyconfig, as they are not needed for the build.""" skipsteps = ['configure'] diff --git a/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.3-GCCcore-11.2.0.eb b/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.3-GCCcore-11.2.0.eb index 7074317643e..b6d234c96b7 100644 --- a/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.3-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.3-GCCcore-11.2.0.eb @@ -20,21 +20,21 @@ builddependencies = [ ('pkg-config', '0.29.2'), ] -# This easyconfig only installs the library of GDRCopy. Please keep in mind -# that GDRCopy also needs the following kernel modules at runtime: -# -# 1. Kernel module for GDRCopy: improves Host to GPU communication -# https://github.com/NVIDIA/gdrcopy -# RPM: 'gdrcopy-kmod', DEB: 'gdrdrv-dkms' -# Requirements: version of GDRCopy kernel module (gdrdrv.ko) >= 2.0 -# -# 2. (optional) Kernel module for GPUDirect RDMA: improves GPU to GPU communication -# https://github.com/Mellanox/nv_peer_memory -# RPM: 'nvidia_peer_memory' -# Requirements: Mellanox HCA with MLNX_OFED 2.1 -# -# These kernel modules are not listed as system dependencies to lower the system -# requirements to build this easyconfig, as they are not needed for the build. +build_info_msg = """This easyconfig only installs the library of GDRCopy. Please keep in mind +that GDRCopy also needs the following kernel modules at runtime: + +1. Kernel module for GDRCopy: improves Host to GPU communication + https://github.com/NVIDIA/gdrcopy + RPM: 'gdrcopy-kmod', DEB: 'gdrdrv-dkms' + Requirements: version of GDRCopy kernel module (gdrdrv.ko) >= 2.0 + +2. (optional) Kernel module for GPUDirect RDMA: improves GPU to GPU communication + https://github.com/Mellanox/nv_peer_memory + RPM: 'nvidia_peer_memory' + Requirements: Mellanox HCA with MLNX_OFED 2.1 + +These kernel modules are not listed as system dependencies to lower the system +requirements to build this easyconfig, as they are not needed for the build.""" skipsteps = ['configure'] diff --git a/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.3-GCCcore-11.3.0.eb b/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.3-GCCcore-11.3.0.eb index 43ffd95b310..d155d8ae274 100644 --- a/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.3-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.3-GCCcore-11.3.0.eb @@ -20,21 +20,21 @@ builddependencies = [ ('pkgconf', '1.8.0'), ] -# This easyconfig only installs the library of GDRCopy. Please keep in mind -# that GDRCopy also needs the following kernel modules at runtime: -# -# 1. Kernel module for GDRCopy: improves Host to GPU communication -# https://github.com/NVIDIA/gdrcopy -# RPM: 'gdrcopy-kmod', DEB: 'gdrdrv-dkms' -# Requirements: version of GDRCopy kernel module (gdrdrv.ko) >= 2.0 -# -# 2. (optional) Kernel module for GPUDirect RDMA: improves GPU to GPU communication -# https://github.com/Mellanox/nv_peer_memory -# RPM: 'nvidia_peer_memory' -# Requirements: Mellanox HCA with MLNX_OFED 2.1 -# -# These kernel modules are not listed as system dependencies to lower the system -# requirements to build this easyconfig, as they are not needed for the build. +build_info_msg = """This easyconfig only installs the library of GDRCopy. Please keep in mind +that GDRCopy also needs the following kernel modules at runtime: + +1. Kernel module for GDRCopy: improves Host to GPU communication + https://github.com/NVIDIA/gdrcopy + RPM: 'gdrcopy-kmod', DEB: 'gdrdrv-dkms' + Requirements: version of GDRCopy kernel module (gdrdrv.ko) >= 2.0 + +2. (optional) Kernel module for GPUDirect RDMA: improves GPU to GPU communication + https://github.com/Mellanox/nv_peer_memory + RPM: 'nvidia_peer_memory' + Requirements: Mellanox HCA with MLNX_OFED 2.1 + +These kernel modules are not listed as system dependencies to lower the system +requirements to build this easyconfig, as they are not needed for the build.""" skipsteps = ['configure'] diff --git a/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.3-GCCcore-12.2.0.eb b/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.3-GCCcore-12.2.0.eb index c9c58812cf5..44973308cfc 100644 --- a/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.3-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.3-GCCcore-12.2.0.eb @@ -20,21 +20,21 @@ builddependencies = [ ('pkgconf', '1.9.3'), ] -# This easyconfig only installs the library of GDRCopy. Please keep in mind -# that GDRCopy also needs the following kernel modules at runtime: -# -# 1. Kernel module for GDRCopy: improves Host to GPU communication -# https://github.com/NVIDIA/gdrcopy -# RPM: 'gdrcopy-kmod', DEB: 'gdrdrv-dkms' -# Requirements: version of GDRCopy kernel module (gdrdrv.ko) >= 2.0 -# -# 2. (optional) Kernel module for GPUDirect RDMA: improves GPU to GPU communication -# https://github.com/Mellanox/nv_peer_memory -# RPM: 'nvidia_peer_memory' -# Requirements: Mellanox HCA with MLNX_OFED 2.1 -# -# These kernel modules are not listed as system dependencies to lower the system -# requirements to build this easyconfig, as they are not needed for the build. +build_info_msg = """This easyconfig only installs the library of GDRCopy. Please keep in mind +that GDRCopy also needs the following kernel modules at runtime: + +1. Kernel module for GDRCopy: improves Host to GPU communication + https://github.com/NVIDIA/gdrcopy + RPM: 'gdrcopy-kmod', DEB: 'gdrdrv-dkms' + Requirements: version of GDRCopy kernel module (gdrdrv.ko) >= 2.0 + +2. (optional) Kernel module for GPUDirect RDMA: improves GPU to GPU communication + https://github.com/Mellanox/nv_peer_memory + RPM: 'nvidia_peer_memory' + Requirements: Mellanox HCA with MLNX_OFED 2.1 + +These kernel modules are not listed as system dependencies to lower the system +requirements to build this easyconfig, as they are not needed for the build.""" skipsteps = ['configure'] diff --git a/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.3.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.3.1-GCCcore-12.3.0.eb index 9eb358afb3f..b0c0227e952 100644 --- a/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.3.1-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.3.1-GCCcore-12.3.0.eb @@ -20,21 +20,21 @@ builddependencies = [ ('pkgconf', '1.9.5'), ] -# This easyconfig only installs the library of GDRCopy. Please keep in mind -# that GDRCopy also needs the following kernel modules at runtime: -# -# 1. Kernel module for GDRCopy: improves Host to GPU communication -# https://github.com/NVIDIA/gdrcopy -# RPM: 'gdrcopy-kmod', DEB: 'gdrdrv-dkms' -# Requirements: version of GDRCopy kernel module (gdrdrv.ko) >= 2.0 -# -# 2. (optional) Kernel module for GPUDirect RDMA: improves GPU to GPU communication -# https://github.com/Mellanox/nv_peer_memory -# RPM: 'nvidia_peer_memory' -# Requirements: Mellanox HCA with MLNX_OFED 2.1 -# -# These kernel modules are not listed as system dependencies to lower the system -# requirements to build this easyconfig, as they are not needed for the build. +build_info_msg = """This easyconfig only installs the library of GDRCopy. Please keep in mind +that GDRCopy also needs the following kernel modules at runtime: + +1. Kernel module for GDRCopy: improves Host to GPU communication + https://github.com/NVIDIA/gdrcopy + RPM: 'gdrcopy-kmod', DEB: 'gdrdrv-dkms' + Requirements: version of GDRCopy kernel module (gdrdrv.ko) >= 2.0 + +2. (optional) Kernel module for GPUDirect RDMA: improves GPU to GPU communication + https://github.com/Mellanox/nv_peer_memory + RPM: 'nvidia_peer_memory' + Requirements: Mellanox HCA with MLNX_OFED 2.1 + +These kernel modules are not listed as system dependencies to lower the system +requirements to build this easyconfig, as they are not needed for the build.""" skipsteps = ['configure'] diff --git a/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.4-GCCcore-13.2.0.eb b/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.4-GCCcore-13.2.0.eb index d871eaf60d3..56d6902c8a7 100644 --- a/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.4-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.4-GCCcore-13.2.0.eb @@ -20,21 +20,21 @@ builddependencies = [ ('pkgconf', '2.0.3'), ] -# This easyconfig only installs the library of GDRCopy. Please keep in mind -# that GDRCopy also needs the following kernel modules at runtime: -# -# 1. Kernel module for GDRCopy: improves Host to GPU communication -# https://github.com/NVIDIA/gdrcopy -# RPM: 'gdrcopy-kmod', DEB: 'gdrdrv-dkms' -# Requirements: version of GDRCopy kernel module (gdrdrv.ko) >= 2.0 -# -# 2. (optional) Kernel module for GPUDirect RDMA: improves GPU to GPU communication -# https://github.com/Mellanox/nv_peer_memory -# RPM: 'nvidia_peer_memory' -# Requirements: Mellanox HCA with MLNX_OFED 2.1 -# -# These kernel modules are not listed as system dependencies to lower the system -# requirements to build this easyconfig, as they are not needed for the build. +build_info_msg = """This easyconfig only installs the library of GDRCopy. Please keep in mind +that GDRCopy also needs the following kernel modules at runtime: + +1. Kernel module for GDRCopy: improves Host to GPU communication + https://github.com/NVIDIA/gdrcopy + RPM: 'gdrcopy-kmod', DEB: 'gdrdrv-dkms' + Requirements: version of GDRCopy kernel module (gdrdrv.ko) >= 2.0 + +2. (optional) Kernel module for GPUDirect RDMA: improves GPU to GPU communication + https://github.com/Mellanox/nv_peer_memory + RPM: 'nvidia_peer_memory' + Requirements: Mellanox HCA with MLNX_OFED 2.1 + +These kernel modules are not listed as system dependencies to lower the system +requirements to build this easyconfig, as they are not needed for the build.""" skipsteps = ['configure'] diff --git a/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.4.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.4.1-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..f8e2370943b --- /dev/null +++ b/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.4.1-GCCcore-13.3.0.eb @@ -0,0 +1,52 @@ +easyblock = 'ConfigureMake' + +name = 'GDRCopy' +version = '2.4.1' + +homepage = 'https://github.com/NVIDIA/gdrcopy' +description = "A low-latency GPU memory copy library based on NVIDIA GPUDirect RDMA technology." + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +github_account = 'NVIDIA' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['faa7e816e9bad3301e53d6721457f7ef5ab42b7aa3b01ffda51f8e5620bb20ed'] + +builddependencies = [ + ('binutils', '2.42'), + ('Autotools', '20231222'), + ('pkgconf', '2.2.0'), +] + +build_info_msg = """This easyconfig only installs the library of GDRCopy. Please keep in mind +that GDRCopy also needs the following kernel modules at runtime: + +1. Kernel module for GDRCopy: improves Host to GPU communication + https://github.com/NVIDIA/gdrcopy + RPM: 'gdrcopy-kmod', DEB: 'gdrdrv-dkms' + Requirements: version of GDRCopy kernel module (gdrdrv.ko) >= 2.0 + +2. (optional) Kernel module for GPUDirect RDMA: improves GPU to GPU communication + https://github.com/Mellanox/nv_peer_memory + RPM: 'nvidia_peer_memory' + Requirements: Mellanox HCA with MLNX_OFED 2.1 + +These kernel modules are not listed as system dependencies to lower the system +requirements to build this easyconfig, as they are not needed for the build.""" + +skipsteps = ['configure'] + +local_envopts = "prefix=%(installdir)s" +prebuildopts = "PATH=$PATH:/sbin " # ensures that ldconfig is found +buildopts = "config lib %s" % local_envopts +install_cmd = "make lib_install" +installopts = local_envopts + +sanity_check_paths = { + 'files': ['lib/libgdrapi.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/g/GEOS/GEOS-3.12.1-GCC-13.2.0.eb b/easybuild/easyconfigs/g/GEOS/GEOS-3.12.1-GCC-13.2.0.eb new file mode 100644 index 00000000000..8dc235ab95c --- /dev/null +++ b/easybuild/easyconfigs/g/GEOS/GEOS-3.12.1-GCC-13.2.0.eb @@ -0,0 +1,26 @@ +easyblock = 'CMakeMake' + +name = 'GEOS' +version = '3.12.1' + +homepage = 'https://trac.osgeo.org/geos' +description = """GEOS (Geometry Engine - Open Source) is a C++ port of the Java Topology Suite (JTS)""" + +toolchain = {'name': 'GCC', 'version': '13.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://download.osgeo.org/geos/'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['d6ea7e492224b51193e8244fe3ec17c4d44d0777f3c32ca4fb171140549a0d03'] + +builddependencies = [('CMake', '3.27.6')] + +# Build static and shared libraries +configopts = ['', '-DBUILD_SHARED_LIBS=OFF'] + +sanity_check_paths = { + 'files': ['bin/geos-config', 'lib/libgeos.%s' % SHLIB_EXT, 'lib/libgeos.a', 'include/geos.h'], + 'dirs': [], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/g/GEOS/GEOS-3.12.2-GCC-13.3.0.eb b/easybuild/easyconfigs/g/GEOS/GEOS-3.12.2-GCC-13.3.0.eb new file mode 100644 index 00000000000..6b174f0bf8a --- /dev/null +++ b/easybuild/easyconfigs/g/GEOS/GEOS-3.12.2-GCC-13.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'CMakeMake' + +name = 'GEOS' +version = '3.12.2' + +homepage = 'https://trac.osgeo.org/geos' +description = """GEOS (Geometry Engine - Open Source) is a C++ port of the Java Topology Suite (JTS)""" + +toolchain = {'name': 'GCC', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://download.osgeo.org/geos/'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['34c7770bf0090ee88488af98767d08e779f124fa33437e0aabec8abd4609fec6'] + +builddependencies = [('CMake', '3.29.3')] + +# Build static and shared libraries +configopts = ['', '-DBUILD_SHARED_LIBS=OFF'] + +sanity_check_paths = { + 'files': ['bin/geos-config', 'lib/libgeos.%s' % SHLIB_EXT, 'lib/libgeos.a', 'lib/libgeos_c.%s' % SHLIB_EXT, + 'include/geos.h'], + 'dirs': [], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/g/GHC/GHC-9.10.1-x86_64.eb b/easybuild/easyconfigs/g/GHC/GHC-9.10.1-x86_64.eb new file mode 100644 index 00000000000..2074b920ebd --- /dev/null +++ b/easybuild/easyconfigs/g/GHC/GHC-9.10.1-x86_64.eb @@ -0,0 +1,82 @@ +# This is a binary install that requires a './configure' and 'make install' steps for GHC. +# We pull the centos7 binary tarball as is the one built against oldest system libs, +# making it upwards compatible with newer distros. +# +# To get a functional 'ghc' binary on the SYSTEM toolchain we need +# gmp headers and ncurses libtinfo.so.5, to avoid requiring extra OS deps for them +# we include them in this bundle. +# Binaries obtained with ghc do not require them, so it should be possible to use this bundle +# just as builddep among different toolchains. +# +# For details, see the PR discussion: +# https://github.com/easybuilders/easybuild-easyconfigs/pull/11310 + +easyblock = 'Bundle' + +name = 'GHC' +version = '9.10.1' +versionsuffix = '-x86_64' + +homepage = 'https://haskell.org/ghc/' +description = """The Glorious/Glasgow Haskell Compiler""" + +toolchain = SYSTEM + +builddependencies = [ + ('binutils', '2.42'), + ('M4', '1.4.19'), +] + +default_easyblock = 'ConfigureMake' + +local_distro_tarball = 'centos7' + +components = [ + ('GMP', '6.3.0', { + 'source_urls': [GNU_SOURCE], + 'sources': [SOURCELOWER_TAR_BZ2], + 'checksums': ['ac28211a7cfb609bae2e2c8d6058d66c8fe96434f740cf6fe2e47b000d1c20cb'], + 'configopts': ' --enable-cxx', + 'start_dir': '%(namelower)s-%(version)s', + }), + ('ncurses', '5.9', { + 'source_urls': [GNU_SOURCE], + 'sources': [SOURCE_TAR_GZ], + 'patches': [ + 'ncurses-%(version)s_configure_darwin.patch', + 'ncurses-%(version)s_fix-missing-const.patch', + ], + 'checksums': [ + '9046298fb440324c9d4135ecea7879ffed8546dd1b58e59430ea07a4633f563b', + '8c471fc2b1961a6e6e5981b7f7b3512e7fe58fcb04461aa4520157d4c1159998', + '027f7bd5876b761b48db624ddbdd106fa1c535dfb2752ef5a0eddeb2a8896cfd', + ], + 'preconfigopts': "export CPPFLAGS='-P -std=c++14' && ", + 'configopts': ' --with-shared --enable-overwrite --with-termlib=tinfo', + 'start_dir': '%(namelower)s-%(version)s', + }), + (name, version, { + 'source_urls': ['https://downloads.haskell.org/~ghc/%(version)s/'], + 'sources': ['%%(namelower)s-%%(version)s-x86_64-%s-linux.tar.xz' % local_distro_tarball], + 'checksums': ['fab143f10f845629cb1b373309b5680667cbaab298cf49827e383ee8a9ddf683'], + # ghc-8.6.5-x86_64-centos7-linux.tar.xz + 'skipsteps': ['build'], + 'preinstallopts': 'LD_LIBRARY_PATH="%(installdir)s/lib:$LD_LIBRARY_PATH" ', + 'start_dir': '%(namelower)s-%(version)s-x86_64-unknown-linux', + }), +] + +local_ncurses_libs = ["form", "menu", "ncurses", "panel", "tinfo"] + +sanity_check_paths = { + 'files': ['lib/lib%s.%s' % (x, y) for x in ['gmp', 'gmpxx'] for y in [SHLIB_EXT, 'a']] + + ['include/gmp.h', 'include/gmpxx.h'] + + ['lib/lib%s%s.a' % (x, y) for x in local_ncurses_libs for y in ['', '_g']] + + ['lib/lib%s.%s' % (x, y) for x in local_ncurses_libs for y in [SHLIB_EXT]] + + ['bin/ghc', 'bin/ghci', 'bin/ghc-pkg', 'bin/runghc', 'bin/runhaskell'], + 'dirs': ['bin', 'lib', 'share', 'include'], +} + +sanity_check_commands = ['ghc --version'] + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/g/GI-DocGen/GI-DocGen-2023.3-GCCcore-12.3.0.eb b/easybuild/easyconfigs/g/GI-DocGen/GI-DocGen-2023.3-GCCcore-12.3.0.eb index d098c3c3cbc..4fae7c08b54 100644 --- a/easybuild/easyconfigs/g/GI-DocGen/GI-DocGen-2023.3-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/g/GI-DocGen/GI-DocGen-2023.3-GCCcore-12.3.0.eb @@ -21,11 +21,8 @@ dependencies = [ ('Python-bundle-PyPI', '2023.06'), ] -exts_default_options = { - 'download_dep_fail': True, - 'sanity_pip_check': True, - 'use_pip': True, -} +sanity_pip_check = True +use_pip = True exts_list = [ ('Markdown', '3.5.2', { diff --git a/easybuild/easyconfigs/g/GL2PS/GL2PS-1.4.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/g/GL2PS/GL2PS-1.4.2-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..55df4c13600 --- /dev/null +++ b/easybuild/easyconfigs/g/GL2PS/GL2PS-1.4.2-GCCcore-12.3.0.eb @@ -0,0 +1,34 @@ +easyblock = 'CMakeMake' + +name = 'GL2PS' +version = '1.4.2' + +homepage = 'https://www.geuz.org/gl2ps/' +description = """GL2PS: an OpenGL to PostScript printing library""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://geuz.org/gl2ps/src/'] +sources = [SOURCELOWER_TGZ] +checksums = ['8d1c00c1018f96b4b97655482e57dcb0ce42ae2f1d349cd6d4191e7848d9ffe9'] + +builddependencies = [ + ('CMake', '3.26.3'), + ('binutils', '2.40'), +] + +dependencies = [ + ('X11', '20230603'), + ('Mesa', '23.1.4'), + ('libGLU', '9.0.3'), + ('freeglut', '3.4.0'), + ('libpng', '1.6.39'), + ('zlib', '1.2.13'), +] + +sanity_check_paths = { + 'files': ['include/gl2ps.h', 'lib/libgl2ps.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GLM/GLM-1.0.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/g/GLM/GLM-1.0.1-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..e57a89d030a --- /dev/null +++ b/easybuild/easyconfigs/g/GLM/GLM-1.0.1-GCCcore-13.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'CMakeMake' + +name = 'GLM' +version = '1.0.1' + +homepage = 'https://github.com/g-truc/glm' +description = """ +OpenGL Mathematics (GLM) is a header only C++ mathematics library for graphics +software based on the OpenGL Shading Language (GLSL) specifications.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://github.com/g-truc/glm/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['9f3174561fd26904b23f0db5e560971cbf9b3cbda0b280f04d5c379d03bf234c'] + +builddependencies = [ + ('binutils', '2.42'), + ('CMake', '3.29.3'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['include/glm/gtc', 'include/glm/gtx'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/g/GLPK/GLPK-5.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/g/GLPK/GLPK-5.0-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..ad96183a02b --- /dev/null +++ b/easybuild/easyconfigs/g/GLPK/GLPK-5.0-GCCcore-13.3.0.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'GLPK' +version = '5.0' + +homepage = 'https://www.gnu.org/software/glpk/' +description = """The GLPK (GNU Linear Programming Kit) package is intended for + solving large-scale linear programming (LP), + mixed integer programming (MIP), and other related problems. + It is a set of routines written in ANSI C + and organized in the form of a callable library.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['4a1013eebb50f728fc601bdd833b0b2870333c3b3e5a816eeba921d95bec6f15'] + +builddependencies = [ + ('binutils', '2.42'), +] +dependencies = [ + ('GMP', '6.3.0'), +] + +configopts = '--with-gmp' + + +sanity_check_paths = { + 'files': ['bin/glpsol', 'include/%(namelower)s.h', 'lib/libglpk.a', 'lib/libglpk.%s' % SHLIB_EXT], + 'dirs': [], +} + +sanity_check_commands = ["glpsol --help"] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.80.4-GCCcore-13.3.0.eb b/easybuild/easyconfigs/g/GLib/GLib-2.80.4-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..f95eacd4a7b --- /dev/null +++ b/easybuild/easyconfigs/g/GLib/GLib-2.80.4-GCCcore-13.3.0.eb @@ -0,0 +1,53 @@ +easyblock = 'MesonNinja' + +name = 'GLib' +version = '2.80.4' + +homepage = 'https://www.gtk.org/' +description = """GLib is one of the base libraries of the GTK+ project""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['24e029c5dfc9b44e4573697adf33078a9827c48938555004b3b9096fa4ea034f'] + +builddependencies = [ + # Python is required for building against GLib, at least when + # gdbus-codegen or one of the other python scripts are used. + # Since Meson 0.50 and later are Python >=3.5 only we can't build + # Python specific versions of GLib that uses Python 2.x + # thus Python should not be a runtime dependency for GLib. + # Packages that use GLib should either have an explicit + # (build)dependency on Python or it will use the system version + # EasyBuild itself uses. + ('Python', '3.12.3'), + ('Meson', '1.4.0'), + ('Ninja', '1.12.1'), + ('binutils', '2.42'), + ('pkgconf', '2.2.0'), +] + +dependencies = [ + ('libffi', '3.4.5'), + ('gettext', '0.22.5'), + ('libxml2', '2.12.7'), + ('PCRE2', '10.43'), + ('util-linux', '2.40'), +] + +# avoid using hardcoded path to Python binary in build step +preconfigopts = "export PYTHON=python && " + +configopts = "--buildtype=release --default-library=both " + +fix_python_shebang_for = ['bin/*'] + +sanity_check_paths = { + 'files': ['lib/libglib-%(version_major)s.0.a', 'lib/libglib-%%(version_major)s.0.%s' % SHLIB_EXT], + 'dirs': ['bin', 'include'], +} + + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GLibmm/GLibmm-2.72.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/g/GLibmm/GLibmm-2.72.1-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..728b2ec6a20 --- /dev/null +++ b/easybuild/easyconfigs/g/GLibmm/GLibmm-2.72.1-GCCcore-11.3.0.eb @@ -0,0 +1,34 @@ +easyblock = 'MesonNinja' + +name = 'GLibmm' +version = '2.72.1' + +homepage = 'https://www.gtk.org/' +description = """C++ bindings for Glib""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://ftp.gnome.org/pub/gnome/sources/glibmm/%(version_major_minor)s/'] +sources = ['%(namelower)s-%(version)s.tar.xz'] +checksums = ['2a7649a28ab5dc53ac4dabb76c9f61599fbc628923ab6a7dd74bf675d9155cd8'] + +builddependencies = [ + ('binutils', '2.38'), + ('pkgconf', '1.8.0'), + ('Meson', '0.62.1'), + ('Ninja', '1.10.2'), +] + +dependencies = [ + ('GLib', '2.72.1'), + ('libsigc++', '3.4.0'), +] + +sanity_check_paths = { + 'files': ['lib/libglibmm-2.68.%s' % SHLIB_EXT, 'lib/libgiomm-2.68.%s' % SHLIB_EXT, + 'include/glibmm-2.68/glibmm.h', 'include/giomm-2.68/giomm.h'], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GLibmm/GLibmm-2.75.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/g/GLibmm/GLibmm-2.75.0-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..ba2c86f4057 --- /dev/null +++ b/easybuild/easyconfigs/g/GLibmm/GLibmm-2.75.0-GCCcore-12.2.0.eb @@ -0,0 +1,34 @@ +easyblock = 'MesonNinja' + +name = 'GLibmm' +version = '2.75.0' + +homepage = 'https://www.gtk.org/' +description = """C++ bindings for Glib""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://ftp.gnome.org/pub/gnome/sources/glibmm/%(version_major_minor)s/'] +sources = ['%(namelower)s-%(version)s.tar.xz'] +checksums = ['60bb12e66488aa8ce41f0eb2f3612f89f5ddc887e3e4d45498524bf60b266b3d'] + +builddependencies = [ + ('binutils', '2.39'), + ('pkgconf', '1.9.3'), + ('Meson', '0.64.0'), + ('Ninja', '1.11.1'), +] + +dependencies = [ + ('GLib', '2.75.0'), + ('libsigc++', '3.6.0'), +] + +sanity_check_paths = { + 'files': ['lib/libglibmm-2.68.%s' % SHLIB_EXT, 'lib/libgiomm-2.68.%s' % SHLIB_EXT, + 'include/glibmm-2.68/glibmm.h', 'include/giomm-2.68/giomm.h'], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GLibmm/GLibmm-2.77.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/g/GLibmm/GLibmm-2.77.0-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..768bdcbb2ed --- /dev/null +++ b/easybuild/easyconfigs/g/GLibmm/GLibmm-2.77.0-GCCcore-12.3.0.eb @@ -0,0 +1,34 @@ +easyblock = 'MesonNinja' + +name = 'GLibmm' +version = '2.77.0' + +homepage = 'https://www.gtk.org/' +description = """C++ bindings for Glib""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://ftp.gnome.org/pub/gnome/sources/glibmm/%(version_major_minor)s/'] +sources = ['%(namelower)s-%(version)s.tar.xz'] +checksums = ['7cb34684e7ac6dfbf83492a52dff3f919e2fff63eb7810613bf71eb272d5450e'] + +builddependencies = [ + ('binutils', '2.40'), + ('pkgconf', '1.9.5'), + ('Meson', '1.1.1'), + ('Ninja', '1.11.1'), +] + +dependencies = [ + ('GLib', '2.77.1'), + ('libsigc++', '3.6.0'), +] + +sanity_check_paths = { + 'files': ['lib/libglibmm-2.68.%s' % SHLIB_EXT, 'lib/libgiomm-2.68.%s' % SHLIB_EXT, + 'include/glibmm-2.68/glibmm.h', 'include/giomm-2.68/giomm.h'], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GLibmm/GLibmm-2.78.1-GCCcore-13.2.0.eb b/easybuild/easyconfigs/g/GLibmm/GLibmm-2.78.1-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..1cfbeec1c85 --- /dev/null +++ b/easybuild/easyconfigs/g/GLibmm/GLibmm-2.78.1-GCCcore-13.2.0.eb @@ -0,0 +1,34 @@ +easyblock = 'MesonNinja' + +name = 'GLibmm' +version = '2.78.1' + +homepage = 'https://www.gtk.org/' +description = """C++ bindings for Glib""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://ftp.gnome.org/pub/gnome/sources/glibmm/%(version_major_minor)s/'] +sources = ['%(namelower)s-%(version)s.tar.xz'] +checksums = ['f473f2975d26c3409e112ed11ed36406fb3843fa975df575c22d4cb843085f61'] + +builddependencies = [ + ('binutils', '2.40'), + ('pkgconf', '2.0.3'), + ('Meson', '1.2.3'), + ('Ninja', '1.11.1'), +] + +dependencies = [ + ('GLib', '2.78.1'), + ('libsigc++', '3.6.0'), +] + +sanity_check_paths = { + 'files': ['lib/libglibmm-2.68.%s' % SHLIB_EXT, 'lib/libgiomm-2.68.%s' % SHLIB_EXT, + 'include/glibmm-2.68/glibmm.h', 'include/giomm-2.68/giomm.h'], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2023-04-20-GCC-12.3.0.eb b/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2023-04-20-GCC-12.3.0.eb new file mode 100644 index 00000000000..bdd355aef6b --- /dev/null +++ b/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2023-04-20-GCC-12.3.0.eb @@ -0,0 +1,55 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel +# 2016-11-07 modified by: +# Adam Huffman +# The Francis Crick Institute + +easyblock = 'ConfigureMake' + +name = 'GMAP-GSNAP' +version = '2023-04-20' + +homepage = 'http://research-pub.gene.com/gmap/' +description = """GMAP: A Genomic Mapping and Alignment Program for mRNA and EST Sequences + GSNAP: Genomic Short-read Nucleotide Alignment Program""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +source_urls = ['http://research-pub.gene.com/gmap/src/'] +sources = [SOURCELOWER_TAR_GZ] +patches = [ + 'GMAP-GSNAP-2023-02-17_cleanup-headers.patch', + 'GMAP-GSNAP-2023-02-17_fix-typecast.patch', +] +checksums = [ + {'gmap-gsnap-2023-04-20.tar.gz': 'f858bc699cbcc9b3f06751ace55c86bfc21e4ca821a90b10681feac2172b725e'}, + {'GMAP-GSNAP-2023-02-17_cleanup-headers.patch': '7d17d4cbc717556e3a64475eb931b692e9d564b486acf6c9dbf4c2bf29853832'}, + {'GMAP-GSNAP-2023-02-17_fix-typecast.patch': 'eafe728cf00cf52320bbf4b710ef76b662df92533d22fa67dc273855c180296f'}, +] + +# with these deps you can use standard compressed files +# details in http://research-pub.gene.com/gmap/src/README +dependencies = [ + ('bzip2', '1.0.8'), + ('zlib', '1.2.13'), +] + +# GSNAP uses MAX_STACK_READLENGTH to control the use of stack or heap memory depending on the read length +# details in http://research-pub.gene.com/gmap/src/README +# configopts = 'MAX_STACK_READLENGTH=300' + +runtest = 'check' + +sanity_check_paths = { + 'files': ['bin/gmap', 'bin/gsnap'], + 'dirs': [], +} + +sanity_check_commands = [ + "gmap --help", + "gsnap --help", +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2024-09-18-GCC-13.3.0.eb b/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2024-09-18-GCC-13.3.0.eb new file mode 100644 index 00000000000..25bc1f03a06 --- /dev/null +++ b/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2024-09-18-GCC-13.3.0.eb @@ -0,0 +1,54 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel +# 2016-11-07 modified by: +# Adam Huffman +# The Francis Crick Institute + +easyblock = 'ConfigureMake' + +name = 'GMAP-GSNAP' +version = '2024-09-18' + +homepage = 'http://research-pub.gene.com/gmap/' +description = """GMAP: A Genomic Mapping and Alignment Program for mRNA and EST Sequences + GSNAP: Genomic Short-read Nucleotide Alignment Program""" + +toolchain = {'name': 'GCC', 'version': '13.3.0'} + +source_urls = ['http://research-pub.gene.com/gmap/src/'] +sources = [SOURCELOWER_TAR_GZ] +patches = [ + 'GMAP-GSNAP-2024-09-18_fix-source-files-for-haswell.patch', +] +checksums = [ + {'gmap-gsnap-2024-09-18.tar.gz': '00d28c1a8c95295c8edd006cc0d1b5154cabe185de1f5a5dd8ccdb01fab38a18'}, + {'GMAP-GSNAP-2024-09-18_fix-source-files-for-haswell.patch': + 'a7ce5bbc83c16d7d4b5f79cf9d96311943fecb114ecab7c6a45e85e95ba54748'}, +] + +# with these deps you can use standard compressed files +# details in http://research-pub.gene.com/gmap/src/README +dependencies = [ + ('bzip2', '1.0.8'), + ('zlib', '1.3.1'), +] + +# GSNAP uses MAX_STACK_READLENGTH to control the use of stack or heap memory depending on the read length +# details in http://research-pub.gene.com/gmap/src/README +# configopts = 'MAX_STACK_READLENGTH=300' + +runtest = 'check' + +sanity_check_paths = { + 'files': ['bin/gmap', 'bin/gsnap'], + 'dirs': [], +} + +sanity_check_commands = [ + "gmap --help", + "gsnap --help", +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2024-09-18_fix-source-files-for-haswell.patch b/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2024-09-18_fix-source-files-for-haswell.patch new file mode 100644 index 00000000000..05112c3e4b5 --- /dev/null +++ b/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2024-09-18_fix-source-files-for-haswell.patch @@ -0,0 +1,13 @@ +Fix source files for Haswell architecture +diff -ru gmap-2024-09-18.orig/src/select64-common.h gmap-2024-09-18/src/select64-common.h +--- gmap-2024-09-18.orig/src/select64-common.h 2023-10-26 02:31:15.000000000 +0200 ++++ gmap-2024-09-18/src/select64-common.h 2024-10-15 16:51:04.695772640 +0200 +@@ -67,7 +67,7 @@ + return place + kSelectInByte[((x >> place) & 0xFF) | (byteRank << 8)]; + #elif defined(__GNUC__) || defined(__clang__) + // GCC and Clang won't inline the intrinsics. +- uint64_t result = uint64_t(1) << k; ++ uint64_t result = (uint64_t)1 << k; + + asm("pdep %1, %0, %0\n\t" + "tzcnt %0, %0" diff --git a/easybuild/easyconfigs/g/GMP-ECM/GMP-ECM-7.0.5-GCCcore-13.2.0.eb b/easybuild/easyconfigs/g/GMP-ECM/GMP-ECM-7.0.5-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..41f00635646 --- /dev/null +++ b/easybuild/easyconfigs/g/GMP-ECM/GMP-ECM-7.0.5-GCCcore-13.2.0.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'GMP-ECM' +version = '7.0.5' + +homepage = 'https://gitlab.inria.fr/zimmerma/ecm' +description = "Yet another implementation of the Elliptic Curve Method." + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://gitlab.inria.fr/zimmerma/ecm/uploads/89f6f0d65d3e980cef33dc922004e4b2'] +sources = ['ecm-%(version)s.tar.gz'] +checksums = ['c721dd22e557c4a5dac9ac7e156a400cd2298812dd1f9b56e89966de01471ba8'] + +builddependencies = [ + ('M4', '1.4.19'), + ('binutils', '2.40'), +] + +dependencies = [('GMP', '6.3.0')] + +configopts = "--with-gmp=$EBROOTGMP --enable-shared " + +sanity_check_paths = { + 'files': ['bin/ecm', 'include/ecm.h'] + ['lib/libecm.%s' % e for e in ['a', SHLIB_EXT]], + 'dirs': [], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/g/GMP/GMP-6.3.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/g/GMP/GMP-6.3.0-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..29f69f73299 --- /dev/null +++ b/easybuild/easyconfigs/g/GMP/GMP-6.3.0-GCCcore-13.3.0.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'GMP' +version = '6.3.0' + +homepage = 'https://gmplib.org/' +description = """ + GMP is a free library for arbitrary precision arithmetic, operating on signed + integers, rational numbers, and floating point numbers. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'precise': True, 'pic': True} + +source_urls = ['https://ftp.gnu.org/gnu/%(namelower)s'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['ac28211a7cfb609bae2e2c8d6058d66c8fe96434f740cf6fe2e47b000d1c20cb'] + +builddependencies = [ + ('Autotools', '20231222'), + ('binutils', '2.42'), +] + +# enable C++ interface +configopts = '--enable-cxx' + +# copy libgmp.so* to /lib to make sure that it is picked up by tests +# when EasyBuild is configured with --rpath, and clean up afterwards (let 'make install' do its job) +pretestopts = "mkdir -p %%(installdir)s/lib && cp -a .libs/libgmp.%s* %%(installdir)s/lib && " % SHLIB_EXT +testopts = " && rm -r %(installdir)s/lib" + +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/lib%s.%s' % (l, e) for l in ['gmp', 'gmpxx'] for e in [SHLIB_EXT, 'a']] + + ['include/gmp.h', 'include/gmpxx.h'], + 'dirs': ['share'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/g/GOATOOLS/GOATOOLS-1.4.5-foss-2022b.eb b/easybuild/easyconfigs/g/GOATOOLS/GOATOOLS-1.4.5-foss-2022b.eb new file mode 100644 index 00000000000..46728a39e63 --- /dev/null +++ b/easybuild/easyconfigs/g/GOATOOLS/GOATOOLS-1.4.5-foss-2022b.eb @@ -0,0 +1,73 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +# Update: Pavel Tománek (Inuits) +easyblock = 'PythonPackage' + +name = 'GOATOOLS' +version = '1.4.5' + +homepage = 'https://github.com/tanghaibao/goatools' +description = "A Python library for Gene Ontology analyses" + +toolchain = {'name': 'foss', 'version': '2022b'} + +# must download sources via git to preserve .git directory, +# since setuptools-scm is used to determine version +sources = [{ + 'git_config': { + 'url': 'https://github.com/tanghaibao', + 'repo_name': 'goatools', + 'tag': 'v%(version)s', + 'keep_git_dir': True, + }, + 'filename': SOURCE_TAR_GZ, +}] +checksums = [None] + +builddependencies = [('cURL', '7.86.0')] + +dependencies = [ + ('Python', '3.10.8'), + ('SciPy-bundle', '2023.02'), + ('XlsxWriter', '3.1.2'), + ('statsmodels', '0.14.0'), + ('pydot', '2.0.0'), + ('openpyxl', '3.1.2'), +] + +exts_defaultclass = 'PythonPackage' +exts_default_options = { + 'source_urls': [PYPI_SOURCE], + 'download_dep_fail': True, + 'use_pip': True, + 'sanity_pip_check': True, +} + +exts_list = [ + ('ftpretty', '0.4.0', { + 'checksums': ['61233b9212f2cceec96ee2c972738fa31cae7248e92d0874c99c04ee739bb5a9'], + }), +] + +download_dep_fail = True +use_pip = True + +postinstallcmds = ["cp -a %(builddir)s/goatools/data/ %(installdir)s/"] + +sanity_check_paths = { + 'files': ['bin/find_enrichment.py'], + 'dirs': ['data', 'lib/python%(pyshortver)s/site-packages'], +} + +# example test run, see https://github.com/tanghaibao/goatools/blob/master/run.sh +sanity_check_commands = [ + "mkdir -p %(builddir)s", + "cd %(builddir)s && curl -OL http://geneontology.org/ontology/go-basic.obo", + "cd %(builddir)s && curl -OL http://www.geneontology.org/ontology/subsets/goslim_generic.obo", + "cd %(builddir)s && cp -a %(installdir)s/data .", + "cd %(builddir)s && find_enrichment.py --pval=0.05 --indent data/study data/population data/association", +] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GOATOOLS/GOATOOLS-1.4.5-foss-2023a.eb b/easybuild/easyconfigs/g/GOATOOLS/GOATOOLS-1.4.5-foss-2023a.eb new file mode 100644 index 00000000000..02e35cba627 --- /dev/null +++ b/easybuild/easyconfigs/g/GOATOOLS/GOATOOLS-1.4.5-foss-2023a.eb @@ -0,0 +1,72 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +# Update: Pavel Tománek (Inuits) + +easyblock = 'PythonPackage' + +name = 'GOATOOLS' +version = '1.4.5' + +homepage = 'https://github.com/tanghaibao/goatools' +description = "A Python library for Gene Ontology analyses" + +toolchain = {'name': 'foss', 'version': '2023a'} + +sources = [{ + 'git_config': { + 'url': 'https://github.com/tanghaibao', + 'repo_name': 'goatools', + 'tag': 'v%(version)s', + 'keep_git_dir': True, + }, + 'filename': SOURCE_TAR_GZ, +}] +checksums = [None] + +builddependencies = [('cURL', '8.0.1')] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('XlsxWriter', '3.1.3'), + ('statsmodels', '0.14.1'), + ('pydot', '2.0.0'), + ('openpyxl', '3.1.2'), +] + +exts_defaultclass = 'PythonPackage' +exts_default_options = { + 'source_urls': [PYPI_SOURCE], + 'download_dep_fail': True, + 'use_pip': True, + 'sanity_pip_check': True, +} + +exts_list = [ + ('ftpretty', '0.4.0', { + 'checksums': ['61233b9212f2cceec96ee2c972738fa31cae7248e92d0874c99c04ee739bb5a9'], + }), +] + +download_dep_fail = True +use_pip = True + +postinstallcmds = ["cp -a %(builddir)s/goatools/data/ %(installdir)s/"] + +sanity_check_paths = { + 'files': ['bin/find_enrichment.py'], + 'dirs': ['data', 'lib/python%(pyshortver)s/site-packages'], +} + +# example test run, see https://github.com/tanghaibao/goatools/blob/master/run.sh +sanity_check_commands = [ + "mkdir -p %(builddir)s", + "cd %(builddir)s && curl -OL http://geneontology.org/ontology/go-basic.obo", + "cd %(builddir)s && curl -OL http://www.geneontology.org/ontology/subsets/goslim_generic.obo", + "cd %(builddir)s && cp -a %(installdir)s/data .", + "cd %(builddir)s && find_enrichment.py --pval=0.05 --indent data/study data/population data/association", +] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GOMC/GOMC-2.76-20230613-GCC-11.3.0-CUDA-11.7.0.eb b/easybuild/easyconfigs/g/GOMC/GOMC-2.76-20230613-GCC-11.3.0-CUDA-11.7.0.eb new file mode 100644 index 00000000000..fbe1458a01a --- /dev/null +++ b/easybuild/easyconfigs/g/GOMC/GOMC-2.76-20230613-GCC-11.3.0-CUDA-11.7.0.eb @@ -0,0 +1,49 @@ +easyblock = 'CMakeMake' + +name = 'GOMC' +version = '2.76-20230613' +versionsuffix = '-CUDA-%(cudaver)s' +_commit = '9fc85fb' + +homepage = 'https://gomc-wsu.org/' +description = """GPU Optimized Monte Carlo (GOMC) is a parallel molecular +simulation code designed for high-performance simulation of large systems.""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +sources = [ + { + 'source_urls': ['https://github.com/GOMC-WSU/GOMC/archive'], + 'download_filename': '%s.tar.gz' % _commit, + 'filename': SOURCE_TAR_GZ, + }, +] +checksums = ['14725836707e4525cc7daea219a6eb47a8aeb675d01ef6d16ad60a9986dd3c1e'] + +builddependencies = [ + ('CMake', '3.23.1'), +] +dependencies = [ + ('CUDA', '11.7.0', '', SYSTEM), + ('UCX-CUDA', '1.12.1', versionsuffix), +] + +# default CUDA compute capabilities to use (override via --cuda-compute-capabilities) +cuda_compute_capabilities = ['6.0', '7.0', '7.5', '8.0', '8.6'] +configopts = '-DCMAKE_CUDA_ARCHITECTURES="%(cuda_cc_cmake)s" ' + +preinstallopts = 'mkdir %(installdir)s/bin &&' +install_cmd = 'cp' +installopts = '%(builddir)s/easybuild_obj/%(name)s_{CPU,GPU}_* %(installdir)s/bin' + +_gomc_exe = ['GOMC_CPU_GCMC', 'GOMC_CPU_GEMC', 'GOMC_CPU_NPT', 'GOMC_CPU_NVT', 'GOMC_GPU_GCMC', + 'GOMC_GPU_GEMC', 'GOMC_GPU_NPT', 'GOMC_GPU_NVT'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in _gomc_exe], + 'dirs': [], +} + +sanity_check_commands = ['%s | grep "Info: GOMC"' % x for x in _gomc_exe] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/g/GOTCHA/GOTCHA-1.0.7-GCCcore-13.3.0.eb b/easybuild/easyconfigs/g/GOTCHA/GOTCHA-1.0.7-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..4810ca2d6d3 --- /dev/null +++ b/easybuild/easyconfigs/g/GOTCHA/GOTCHA-1.0.7-GCCcore-13.3.0.eb @@ -0,0 +1,37 @@ +easyblock = "CMakeMake" + +name = "GOTCHA" +version = "1.0.7" + +homepage = "https://gotcha.readthedocs.io/en/latest/" +description = """Gotcha is a library that wraps functions. Tools can use gotcha to install hooks into other +libraries, for example putting a wrapper function around libc's malloc. It is similar to LD_PRELOAD, but +operates via a programmable API. This enables easy methods of accomplishing tasks like code instrumentation +or wholesale replacement of mechanisms in programs without disrupting their source code.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/LLNL/GOTCHA/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['1ecc1917a46ba0a63b75f0668b280e447afcb7623ad171caa35c596355d986f7'] + +builddependencies = [ + ('binutils', '2.42'), + ('CMake', '3.29.3'), + ('Check', '0.15.2') +] + +configopts = [ + "-DGOTCHA_ENABLE_TESTS=ON", + "-DDEPENDENCIES_PREINSTALLED=ON" +] + +sanity_check_paths = { + 'files': [('lib/libgotcha.%s' % SHLIB_EXT, 'lib64/libgotcha.%s' % SHLIB_EXT), + 'lib/cmake/gotcha/gotcha-config.cmake', + 'include/gotcha/gotcha.h'], + 'dirs': [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.80.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.80.1-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..83ab6981ae3 --- /dev/null +++ b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.80.1-GCCcore-13.3.0.eb @@ -0,0 +1,51 @@ +easyblock = 'MesonNinja' + +name = 'GObject-Introspection' +version = '1.80.1' + +homepage = 'https://gi.readthedocs.io/en/latest/' +description = """GObject introspection is a middleware layer between C libraries + (using GObject) and language bindings. The C library can be scanned at + compile time and generate a metadata file, in addition to the actual + native C library. Then at runtime, language bindings can read this + metadata and automatically provide bindings to call into the C library.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +patches = ['GObject-Introspection-1.80.1_install-GLib-GIR-files.patch'] +checksums = [ + {'gobject-introspection-1.80.1.tar.xz': 'a1df7c424e15bda1ab639c00e9051b9adf5cea1a9e512f8a603b53cd199bc6d8'}, + {'GObject-Introspection-1.80.1_install-GLib-GIR-files.patch': + 'c1909f1b7fd30784ae789ac0b5e45e0ca3dd2456890b864efa86a2f8c2e563aa'}, +] + +builddependencies = [ + ('binutils', '2.42'), + ('pkgconf', '2.2.0'), + ('CMake', '3.29.3'), + ('Meson', '1.4.0'), + ('Ninja', '1.12.1'), + ('Python', '3.12.3'), + ('Bison', '3.8.2'), + ('cairo', '1.18.0'), + ('flex', '2.6.4'), +] + +dependencies = [ + ('GLib', '2.80.4'), + ('libffi', '3.4.5'), + ('util-linux', '2.40'), +] + +preconfigopts = "env GI_SCANNER_DISABLE_CACHE=true " +configopts = "-Dcairo=enabled" + +sanity_check_paths = { + 'files': ['bin/g-ir-%s' % x for x in ['annotation-tool', 'compiler', 'generate', 'scanner']] + + ['lib/libgirepository-1.0.' + SHLIB_EXT], + 'dirs': ['include', 'share'] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.80.1_install-GLib-GIR-files.patch b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.80.1_install-GLib-GIR-files.patch new file mode 100644 index 00000000000..5c09ded1cb2 --- /dev/null +++ b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.80.1_install-GLib-GIR-files.patch @@ -0,0 +1,52 @@ +This reverts a commit from upstream +> build: Do not install generated GLib GIR files +> +> GLib 2.79 ships its own introspection data. + +However GObject-Introspection requires (optionally) Cairo, which requires GLib +which requires GLib-Introspection for generating the introspection data. + +So there is a cyclic dependency, see https://gitlab.gnome.org/GNOME/gobject-introspection/-/issues/517 + +Author: Alexander Grund (TU Dresden) + +diff --git a/gir/meson.build b/gir/meson.build +index 3a016831..312aa886 100644 +--- a/gir/meson.build ++++ b/gir/meson.build +@@ -241,6 +241,8 @@ glib_gir = custom_target('gir-glib', + output: 'GLib-2.0.gir', + depends: [gir_giscanner_pymod, glib_gir_dep, gdump], + depend_files: gir_giscanner_built_files, ++ install: true, ++ install_dir: girdir, + env: g_ir_scanner_env, + command: glib_command + [ + '--cflags-begin'] + glib_includes + extra_giscanner_cflags + [ +@@ -308,6 +310,8 @@ gobject_gir = custom_target('gir-gobject', + output: 'GObject-2.0.gir', + depends: [glib_gir, gir_giscanner_pymod, gobject_gir_dep, gdump], + depend_files: gir_giscanner_built_files, ++ install: true, ++ install_dir: girdir, + env: g_ir_scanner_env, + command: gobject_command + [ + '--include-uninstalled=' + glib_gir.full_path(), +@@ -360,6 +364,8 @@ uninstalled_gir_files += custom_target('gir-gmodule', + output: 'GModule-2.0.gir', + depends: [glib_gir, gir_giscanner_pymod, gmodule_gir_dep, gdump], + depend_files: gir_giscanner_built_files, ++ install: true, ++ install_dir: girdir, + env: g_ir_scanner_env, + command: gmodule_command + [ + '--include-uninstalled=' + glib_gir.full_path(), +@@ -455,6 +461,8 @@ gio_gir = custom_target('gir-gio', + output: 'Gio-2.0.gir', + depends: [gobject_gir, gir_giscanner_pymod, gio_gir_dep, gdump], + depend_files: gir_giscanner_built_files, ++ install: true, ++ install_dir: girdir, + env: g_ir_scanner_env, + command: gio_command + [ + '--include-uninstalled=' + gobject_gir.full_path(), diff --git a/easybuild/easyconfigs/g/GPAW/GPAW-24.6.0-foss-2023a-ASE-3.23.0.eb b/easybuild/easyconfigs/g/GPAW/GPAW-24.6.0-foss-2023a-ASE-3.23.0.eb new file mode 100644 index 00000000000..62db4b69440 --- /dev/null +++ b/easybuild/easyconfigs/g/GPAW/GPAW-24.6.0-foss-2023a-ASE-3.23.0.eb @@ -0,0 +1,52 @@ +easyblock = "PythonPackage" + +name = 'GPAW' +version = '24.6.0' +_aseversion = '3.23.0' +versionsuffix = '-ASE-' + _aseversion + +homepage = 'https://wiki.fysik.dtu.dk/gpaw/' +description = """GPAW is a density-functional theory (DFT) Python code based on the projector-augmented wave (PAW) + method and the atomic simulation environment (ASE). It uses real-space uniform grids and multigrid methods or + atom-centered basis-functions.""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'usempi': True, 'openmp': False} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +patches = [ + ('GPAW-20.1.0-Add-Easybuild-configuration-files.patch', 1), +] +checksums = [ + {'gpaw-24.6.0.tar.gz': 'fb48ef0db48c0e321ce5967126a47900bba20c7efb420d6e7b5459983bd8f6f6'}, + {'GPAW-20.1.0-Add-Easybuild-configuration-files.patch': + '2b337399479bf018a86156ed073dd7a78ec8c0df1f28b015f9284c6bf9fa5f15'}, +] + +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('SciPy-bundle', '2023.07'), + ('ASE', _aseversion), + ('libxc', '6.2.2'), + ('libvdwxc', '0.4.0'), + ('ELPA', '2023.05.001'), + ('PyYAML', '6.0'), + ('GPAW-setups', '24.1.0', '', SYSTEM), +] + +prebuildopts = 'GPAW_CONFIG=doc/platforms/Linux/EasyBuild/config_foss.py' +preinstallopts = prebuildopts + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/gpaw%s' % x for x in ['', '-analyse-basis', '-basis', '-plot-parallel-timings', + '-runscript', '-setup', '-upfplot']], + 'dirs': ['lib/python%(pyshortver)s/site-packages'] +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/g/GPAW/GPAW-24.6.0-foss-2024a.eb b/easybuild/easyconfigs/g/GPAW/GPAW-24.6.0-foss-2024a.eb new file mode 100644 index 00000000000..9b8721280c8 --- /dev/null +++ b/easybuild/easyconfigs/g/GPAW/GPAW-24.6.0-foss-2024a.eb @@ -0,0 +1,50 @@ +easyblock = "PythonPackage" + +name = 'GPAW' +version = '24.6.0' + +homepage = 'https://wiki.fysik.dtu.dk/gpaw/' +description = """GPAW is a density-functional theory (DFT) Python code based on the projector-augmented wave (PAW) + method and the atomic simulation environment (ASE). It uses real-space uniform grids and multigrid methods or + atom-centered basis-functions.""" + +toolchain = {'name': 'foss', 'version': '2024a'} +toolchainopts = {'usempi': True, 'openmp': False} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +patches = [ + ('GPAW-20.1.0-Add-Easybuild-configuration-files.patch', 1), +] +checksums = [ + {'gpaw-24.6.0.tar.gz': 'fb48ef0db48c0e321ce5967126a47900bba20c7efb420d6e7b5459983bd8f6f6'}, + {'GPAW-20.1.0-Add-Easybuild-configuration-files.patch': + '2b337399479bf018a86156ed073dd7a78ec8c0df1f28b015f9284c6bf9fa5f15'}, +] + +dependencies = [ + ('Python', '3.12.3'), + ('Python-bundle-PyPI', '2024.06'), + ('SciPy-bundle', '2024.05'), + ('ASE', '3.23.0'), + ('libxc', '6.2.2'), + ('libvdwxc', '0.4.0'), + ('ELPA', '2024.05.001'), + ('PyYAML', '6.0.2'), + ('GPAW-setups', '24.1.0', '', SYSTEM), +] + +prebuildopts = 'GPAW_CONFIG=doc/platforms/Linux/EasyBuild/config_foss.py' +preinstallopts = prebuildopts + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/gpaw%s' % x for x in ['', '-analyse-basis', '-basis', '-plot-parallel-timings', + '-runscript', '-setup', '-upfplot']], + 'dirs': ['lib/python%(pyshortver)s/site-packages'] +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/g/GPAW/GPAW-24.6.0-intel-2023a-ASE-3.23.0.eb b/easybuild/easyconfigs/g/GPAW/GPAW-24.6.0-intel-2023a-ASE-3.23.0.eb new file mode 100644 index 00000000000..dc4091af2d3 --- /dev/null +++ b/easybuild/easyconfigs/g/GPAW/GPAW-24.6.0-intel-2023a-ASE-3.23.0.eb @@ -0,0 +1,51 @@ +easyblock = "PythonPackage" + +name = 'GPAW' +version = '24.6.0' +_aseversion = '3.23.0' +versionsuffix = '-ASE-' + _aseversion + +homepage = 'https://wiki.fysik.dtu.dk/gpaw/' +description = """GPAW is a density-functional theory (DFT) Python code based on the projector-augmented wave (PAW) + method and the atomic simulation environment (ASE). It uses real-space uniform grids and multigrid methods or + atom-centered basis-functions.""" + +toolchain = {'name': 'intel', 'version': '2023a'} +toolchainopts = {'usempi': True, 'openmp': False} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +patches = [ + ('GPAW-20.1.0-Add-Easybuild-configuration-files.patch', 1), +] +checksums = [ + {'gpaw-24.6.0.tar.gz': 'fb48ef0db48c0e321ce5967126a47900bba20c7efb420d6e7b5459983bd8f6f6'}, + {'GPAW-20.1.0-Add-Easybuild-configuration-files.patch': + '2b337399479bf018a86156ed073dd7a78ec8c0df1f28b015f9284c6bf9fa5f15'}, +] + +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('SciPy-bundle', '2023.07'), + ('ASE', _aseversion), + ('libxc', '6.2.2'), + ('ELPA', '2023.05.001'), + ('PyYAML', '6.0'), + ('GPAW-setups', '24.1.0', '', SYSTEM), +] + +prebuildopts = 'GPAW_CONFIG=doc/platforms/Linux/EasyBuild/config_intel.py' +preinstallopts = prebuildopts + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/gpaw%s' % x for x in ['', '-analyse-basis', '-basis', '-plot-parallel-timings', + '-runscript', '-setup', '-upfplot']], + 'dirs': ['lib/python%(pyshortver)s/site-packages'] +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/g/GPflow/GPflow-2.9.2-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/g/GPflow/GPflow-2.9.2-foss-2022a-CUDA-11.7.0.eb new file mode 100644 index 00000000000..8838542f89b --- /dev/null +++ b/easybuild/easyconfigs/g/GPflow/GPflow-2.9.2-foss-2022a-CUDA-11.7.0.eb @@ -0,0 +1,49 @@ +easyblock = 'PythonBundle' + +name = 'GPflow' +version = '2.9.2' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://gpflow.github.io' +description = """GPflow is a package for building Gaussian process models in Python. It +implements modern Gaussian process inference for composable kernels and +likelihoods.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('CUDA', '11.7.0', '', SYSTEM), + ('Python', '3.10.4'), + ('TensorFlow', '2.11.0', versionsuffix), + ('tensorflow-probability', '0.19.0', versionsuffix), +] + +use_pip = True + +exts_list = [ + ('Deprecated', '1.2.14', { + 'checksums': ['e5323eb936458dccc2582dc6f9c322c852a775a27065ff2b0c4970b9d53d01b3'], + }), + ('dropstackframe', '0.1.0', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['d619c7f87d144660f4569d447648830932f7920d570fd14f0dec552c81a0eb22'], + }), + ('lark', '1.1.9', { + 'checksums': ['15fa5236490824c2c4aba0e22d2d6d823575dcaf4cdd1848e34b6ad836240fba'], + }), + ('check_shapes', '1.1.1', { + 'checksums': ['b699fcb1e60bb17e2c97007e444b89eeeea2a9102ff11d61fb52454af5348403'], + }), + ('multipledispatch', '1.0.0', { + 'checksums': ['5c839915465c68206c3e9c473357908216c28383b425361e5d144594bf85a7e0'], + }), + ('gpflow', version, { + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/GPflow/GPflow/archive/'], + 'checksums': ['a32914c2b581b1dd2ac9a6f40352adb5f6f2c32f53028382e542014dd829553e'], + }), +] + +sanity_pip_check = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/g/GPflow/GPflow-2.9.2-foss-2022a.eb b/easybuild/easyconfigs/g/GPflow/GPflow-2.9.2-foss-2022a.eb new file mode 100644 index 00000000000..b94a4e3bc29 --- /dev/null +++ b/easybuild/easyconfigs/g/GPflow/GPflow-2.9.2-foss-2022a.eb @@ -0,0 +1,47 @@ +easyblock = 'PythonBundle' + +name = 'GPflow' +version = '2.9.2' + +homepage = 'https://gpflow.github.io' +description = """GPflow is a package for building Gaussian process models in Python. It +implements modern Gaussian process inference for composable kernels and +likelihoods.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('TensorFlow', '2.11.0'), + ('tensorflow-probability', '0.19.0'), +] + +use_pip = True + +exts_list = [ + ('Deprecated', '1.2.14', { + 'checksums': ['e5323eb936458dccc2582dc6f9c322c852a775a27065ff2b0c4970b9d53d01b3'], + }), + ('dropstackframe', '0.1.0', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['d619c7f87d144660f4569d447648830932f7920d570fd14f0dec552c81a0eb22'], + }), + ('lark', '1.1.9', { + 'checksums': ['15fa5236490824c2c4aba0e22d2d6d823575dcaf4cdd1848e34b6ad836240fba'], + }), + ('check_shapes', '1.1.1', { + 'checksums': ['b699fcb1e60bb17e2c97007e444b89eeeea2a9102ff11d61fb52454af5348403'], + }), + ('multipledispatch', '1.0.0', { + 'checksums': ['5c839915465c68206c3e9c473357908216c28383b425361e5d144594bf85a7e0'], + }), + ('gpflow', version, { + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/GPflow/GPflow/archive/'], + 'checksums': ['a32914c2b581b1dd2ac9a6f40352adb5f6f2c32f53028382e542014dd829553e'], + }), +] + +sanity_pip_check = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/g/GPflow/GPflow-2.9.2-foss-2023a.eb b/easybuild/easyconfigs/g/GPflow/GPflow-2.9.2-foss-2023a.eb new file mode 100644 index 00000000000..a2a0f0a5adc --- /dev/null +++ b/easybuild/easyconfigs/g/GPflow/GPflow-2.9.2-foss-2023a.eb @@ -0,0 +1,51 @@ +easyblock = 'PythonBundle' + +name = 'GPflow' +version = '2.9.2' + +homepage = 'https://gpflow.github.io' +description = """GPflow is a package for building Gaussian process models in Python. It +implements modern Gaussian process inference for composable kernels and +likelihoods.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [ + ('poetry', '1.7.1'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('TensorFlow', '2.13.0'), + ('tensorflow-probability', '0.20.0'), +] + +use_pip = True + +exts_list = [ + ('Deprecated', '1.2.14', { + 'checksums': ['e5323eb936458dccc2582dc6f9c322c852a775a27065ff2b0c4970b9d53d01b3'], + }), + ('dropstackframe', '0.1.0', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['d619c7f87d144660f4569d447648830932f7920d570fd14f0dec552c81a0eb22'], + }), + ('lark', '1.1.9', { + 'checksums': ['15fa5236490824c2c4aba0e22d2d6d823575dcaf4cdd1848e34b6ad836240fba'], + }), + ('check_shapes', '1.1.1', { + 'checksums': ['b699fcb1e60bb17e2c97007e444b89eeeea2a9102ff11d61fb52454af5348403'], + }), + ('multipledispatch', '1.0.0', { + 'checksums': ['5c839915465c68206c3e9c473357908216c28383b425361e5d144594bf85a7e0'], + }), + ('gpflow', version, { + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/GPflow/GPflow/archive/'], + 'checksums': ['a32914c2b581b1dd2ac9a6f40352adb5f6f2c32f53028382e542014dd829553e'], + }), +] + +sanity_pip_check = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/g/GPyOpt/GPyOpt-1.2.6-foss-2023a.eb b/easybuild/easyconfigs/g/GPyOpt/GPyOpt-1.2.6-foss-2023a.eb new file mode 100644 index 00000000000..ca08a08a88c --- /dev/null +++ b/easybuild/easyconfigs/g/GPyOpt/GPyOpt-1.2.6-foss-2023a.eb @@ -0,0 +1,63 @@ +easyblock = 'PythonBundle' + +name = 'GPyOpt' +version = '1.2.6' + +homepage = 'https://sheffieldml.github.io/GPyOpt' +description = "GPyOpt is a Python open-source library for Bayesian Optimization" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('matplotlib', '3.7.2'), +] + +use_pip = True + +exts_list = [ + ('paramz', '0.9.6', { + 'sources': ['%(name)s-%(version)s-py3-none-any.whl'], + 'checksums': ['4916be6f77f457316bcac8460be9c226026aed81fe7be302b32c0ba74e2ac6dd'], + }), + ('GPy', '1.13.2', { + 'modulename': 'GPy', + 'checksums': ['a38256b4dda536a5b5e6134a3924b42d454e987ee801fb6fc8b55a922da27920'], + }), + ('python-dateutil', '2.9.0.post0', { + 'modulename': 'dateutil', + 'checksums': ['37dd54208da7e1cd875388217d5e00ebd4179249f90fb72437e91a35459a0ad3'], + }), + ('pyDOE', '0.3.8', { + 'modulename': '%(name)s', + 'sources': ['%(name)s-%(version)s.zip'], + 'checksums': ['cbd6f14ae26d3c9f736013205f53ea1191add4567033c3ee77b7dd356566c4b6'], + }), + ('sobol-seq', '0.2.0', { + 'sources': ['sobol_seq-%(version)s.tar.gz'], + 'checksums': ['e16e701bd7b03ec6ce65b3a64c9205799f6a2d00c2054dd8c4ff4343f3981172'], + }), + ('emcee', '2.2.1', { + 'checksums': ['b83551e342b37311897906b3b8acf32979f4c5542e0a25786ada862d26241172'], + }), + (name, version, { + 'modulename': 'GPyOpt', + 'checksums': ['e714daa035bb529a6db23c53665a762a4ab3456b9329c19ad3b03983f94c9b2a'], + }), +] + +local_GPy_file = '%(installdir)s/lib/python%(pyshortver)s/site-packages/GPy/plotting/matplot_dep/plot_definitions.py' + +# Fix GPy with matplotlib>=3.4.0 +# see issue 953 and fix from https://github.com/SheffieldML/GPy/pull/960 +postinstallcmds = [ + 'sed -i ' + '''-e 's|ax._process_unit_info(xdata=X, ydata=y1)|ax._process_unit_info([("x", X), ("y", y1)], convert=False)|' ''' + '''-e 's|ax._process_unit_info(ydata=y2)|ax._process_unit_info([("y", y2)], convert=False)|' %s''' % local_GPy_file, +] + + +sanity_pip_check = True + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/g/GROMACS-LS/GROMACS-LS-2016.3-foss-2023a.eb b/easybuild/easyconfigs/g/GROMACS-LS/GROMACS-LS-2016.3-foss-2023a.eb new file mode 100644 index 00000000000..e47a07b97f8 --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS-LS/GROMACS-LS-2016.3-foss-2023a.eb @@ -0,0 +1,49 @@ +easyblock = 'EB_GROMACS' + +name = 'GROMACS-LS' +version = '2016.3' + +homepage = 'https://vanegaslab.org/software' +description = """ +GROMACS-LS and the MDStress library enable the calculation of local +stress fields from molecular dynamics simulations. + +This is a double precision only CPU only build. +""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'openmp': True, 'usempi': True} + +source_urls = ['https://vanegaslab.org/files'] +sources = ['gromacs-ls-2016.3-12282019.tar.gz'] +patches = [ + 'GROMACS-LS-2016.3_fix_typo.patch', +] +checksums = [ + {'gromacs-ls-2016.3-12282019.tar.gz': '20f4d4f255800432be188abe41b7fec923cacc5fc895914b3beac0808ddf1919'}, + {'GROMACS-LS-2016.3_fix_typo.patch': '4b9945476405a358bc64784984c51f08ab1aa3a598fb981b2dad8e0c61665fe0'}, +] + +builddependencies = [ + ('CMake', '3.26.3'), +] + +dependencies = [ + ('MDStress', '20191228'), +] + +# GROMACS-LS can only be built with double precision +single_precision = False + +# GROMACS-LS can only handle hwloc version < 2 +configopts = '-DGMX_HWLOC=OFF' + +# The tests have not been rewritten to handle the mdstress changes +skipsteps = ['test'] + +sanity_check_paths = { + 'files': ['bin/gmx_LS', 'lib/libgromacs_LS.a'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GROMACS-LS/GROMACS-LS-2016.3_fix_typo.patch b/easybuild/easyconfigs/g/GROMACS-LS/GROMACS-LS-2016.3_fix_typo.patch new file mode 100644 index 00000000000..2529da617ed --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS-LS/GROMACS-LS-2016.3_fix_typo.patch @@ -0,0 +1,38 @@ +Fix a couple of smaller problems + +Åke Sandgren, 2024-11-07 +diff -ru gromacs-ls-2016.3.orig/cmake/gmxTestCXX11.cmake gromacs-ls-2016.3/cmake/gmxTestCXX11.cmake +--- gromacs-ls-2016.3.orig/cmake/gmxTestCXX11.cmake 2019-12-28 15:42:21.000000000 +0100 ++++ gromacs-ls-2016.3/cmake/gmxTestCXX11.cmake 2024-11-07 10:45:40.060210373 +0100 +@@ -49,7 +49,7 @@ + elseif(CYGWIN) + set(CXX11_CXX_FLAG "-std=gnu++0x") #required for strdup + else() +- set(CXX11_CXX_FLAG "-std=c++0x") ++ set(CXX11_CXX_FLAG "-std=c++11") + endif() + CHECK_CXX_COMPILER_FLAG("${CXX11_CXX_FLAG}" CXXFLAG_STD_CXX0X) + if(NOT CXXFLAG_STD_CXX0X) +diff -ru gromacs-ls-2016.3.orig/src/gromacs/mdlib/minimize.cpp gromacs-ls-2016.3/src/gromacs/mdlib/minimize.cpp +--- gromacs-ls-2016.3.orig/src/gromacs/mdlib/minimize.cpp 2019-12-28 15:42:28.000000000 +0100 ++++ gromacs-ls-2016.3/src/gromacs/mdlib/minimize.cpp 2024-11-07 10:55:06.668206192 +0100 +@@ -54,6 +54,7 @@ + + #include + #include ++#include + + #include "gromacs/commandline/filenm.h" + #include "gromacs/domdec/domdec.h" +diff -ru gromacs-ls-2016.3.orig/src/programs/mdrun/runner.cpp gromacs-ls-2016.3/src/programs/mdrun/runner.cpp +--- gromacs-ls-2016.3.orig/src/programs/mdrun/runner.cpp 2019-12-28 15:42:30.000000000 +0100 ++++ gromacs-ls-2016.3/src/programs/mdrun/runner.cpp 2024-11-07 10:33:22.588969615 +0100 +@@ -175,7 +175,7 @@ + int localsspatialatom; + int localsdispcor; + int localspbc; +- real localsmindihang; ++ real localsmindihangle; + unsigned long Flags; + }; + diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2023.3-foss-2023a-PLUMED-2.9.0.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2023.3-foss-2023a-PLUMED-2.9.0.eb new file mode 100644 index 00000000000..943aa4ac839 --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2023.3-foss-2023a-PLUMED-2.9.0.eb @@ -0,0 +1,100 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2016 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC, +# Ghent University / The Francis Crick Institute +# Authors:: +# * Wiktor Jurkowski +# * Fotis Georgatos +# * George Tsouloupas +# * Kenneth Hoste +# * Adam Huffman +# * Ake Sandgren +# * J. Sassmannshausen +# * Dugan Witherick +# * Christoph Siegert +# License:: MIT/GPL + +name = 'GROMACS' +version = '2023.3' +_plumedver = '2.9.0' +versionsuffix = '-PLUMED-%s' % _plumedver + +homepage = 'https://www.gromacs.org' +description = """ +GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the +Newtonian equations of motion for systems with hundreds to millions of +particles. + +This is a CPU only build, containing both MPI and threadMPI binaries +for both single and double precision. + +It also contains the gmxapi extension for the single precision MPI build +next to PLUMED.""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'openmp': True, 'usempi': True} + +source_urls = [ + 'https://ftp.gromacs.org/pub/gromacs/', + 'ftp://ftp.gromacs.org/pub/gromacs/', +] +sources = [SOURCELOWER_TAR_GZ] +patches = [ + 'GROMACS-2023.1_set_omp_num_threads_env_for_ntomp_tests.patch', + 'GROMACS-2023.1_fix_tests_for_gmx_thread_mpi.patch', + '%(name)s-%(version)s_skip_test_for_plumed.patch', +] +checksums = [ + {'gromacs-2023.3.tar.gz': '4ec8f8d0c7af76b13f8fd16db8e2c120e749de439ae9554d9f653f812d78d1cb'}, + {'GROMACS-2023.1_set_omp_num_threads_env_for_ntomp_tests.patch': + '7f41bda16c9c2837624265dda4be252f655d1288ddc4486b1a2422af30d5d199'}, + {'GROMACS-2023.1_fix_tests_for_gmx_thread_mpi.patch': + '6df844bb3bbc51180446a3595c61a4ef195e5f975533a04cef76841aa763aec1'}, + {'GROMACS-2023.3_skip_test_for_plumed.patch': + '6c541ee74f71f6a63950134d9d0e3afb176a2e25e76e017b4d1986a59163c083'}, +] + +builddependencies = [ + ('CMake', '3.26.3'), + ('scikit-build', '0.17.6'), + ('Doxygen', '1.9.7'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('networkx', '3.1'), + ('mpi4py', '3.1.4'), + ('PLUMED', _plumedver), +] + + +configopts = '-DCMAKE_CXX_FLAGS="$CXXFLAGS -fpermissive" ' + +# PLUMED 2.9.0 is compatible with GROMACS 2023; 2023.3 seems to work fine too +ignore_plumed_version_check = True + +exts_defaultclass = 'PythonPackage' + +exts_default_options = { + 'source_urls': [PYPI_SOURCE], + 'use_pip': True, + 'download_dep_fail': True, + 'sanity_pip_check': True, +} + +exts_list = [ + ('gmxapi', '0.4.2', { + 'preinstallopts': 'export CMAKE_ARGS="-Dgmxapi_ROOT=%(installdir)s ' + + '-C %(installdir)s/share/cmake/gromacs_mpi/gromacs-hints_mpi.cmake" && ', + 'source_tmpl': 'gromacs-2023.3.tar.gz', + 'start_dir': 'python_packaging/gmxapi', + 'checksums': ['4ec8f8d0c7af76b13f8fd16db8e2c120e749de439ae9554d9f653f812d78d1cb'], + }), +] + +modextrapaths = { + 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2023.4-foss-2023a.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2023.4-foss-2023a.eb new file mode 100644 index 00000000000..e8c0d929bd9 --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2023.4-foss-2023a.eb @@ -0,0 +1,87 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2016 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC, +# Ghent University / The Francis Crick Institute +# Authors:: +# * Wiktor Jurkowski +# * Fotis Georgatos +# * George Tsouloupas +# * Kenneth Hoste +# * Adam Huffman +# * Ake Sandgren +# * J. Sassmannshausen +# * Dugan Witherick +# * Christoph Siegert +# License:: MIT/GPL + +name = 'GROMACS' +version = '2023.4' + +homepage = 'https://www.gromacs.org' +description = """ +GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the +Newtonian equations of motion for systems with hundreds to millions of +particles. + +This is a CPU only build, containing both MPI and threadMPI binaries +for both single and double precision. + +It also contains the gmxapi extension for the single precision MPI build. +""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'openmp': True, 'usempi': True} + +source_urls = [ + 'https://ftp.gromacs.org/pub/gromacs/', + 'ftp://ftp.gromacs.org/pub/gromacs/', +] +sources = [SOURCELOWER_TAR_GZ] +patches = [ + 'GROMACS-2023.1_set_omp_num_threads_env_for_ntomp_tests.patch', + 'GROMACS-2023.1_fix_tests_for_gmx_thread_mpi.patch', +] +checksums = [ + {'gromacs-2023.4.tar.gz': 'e5d6c4d9e7ccacfaccb0888619bd21b5ea8911f82b410e68d6db5d40f695f231'}, + {'GROMACS-2023.1_set_omp_num_threads_env_for_ntomp_tests.patch': + '7f41bda16c9c2837624265dda4be252f655d1288ddc4486b1a2422af30d5d199'}, + {'GROMACS-2023.1_fix_tests_for_gmx_thread_mpi.patch': + '6df844bb3bbc51180446a3595c61a4ef195e5f975533a04cef76841aa763aec1'}, +] + +builddependencies = [ + ('CMake', '3.26.3'), + ('scikit-build', '0.17.6'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('networkx', '3.1'), + ('mpi4py', '3.1.4'), +] + +exts_defaultclass = 'PythonPackage' + +exts_default_options = { + 'source_urls': [PYPI_SOURCE], + 'use_pip': True, + 'download_dep_fail': True, + 'sanity_pip_check': True, +} + +exts_list = [ + ('gmxapi', '0.4.2', { + 'preinstallopts': 'export CMAKE_ARGS="-Dgmxapi_ROOT=%(installdir)s ' + + '-C %(installdir)s/share/cmake/gromacs_mpi/gromacs-hints_mpi.cmake" && ', + 'source_tmpl': 'gromacs-2023.4.tar.gz', + 'start_dir': 'python_packaging/gmxapi', + 'checksums': ['e5d6c4d9e7ccacfaccb0888619bd21b5ea8911f82b410e68d6db5d40f695f231'], + }), +] + +modextrapaths = { + 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2024.3-foss-2023b-PLUMED-2.9.2.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2024.3-foss-2023b-PLUMED-2.9.2.eb new file mode 100644 index 00000000000..9743e8a09a2 --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2024.3-foss-2023b-PLUMED-2.9.2.eb @@ -0,0 +1,93 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2016 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC, +# Ghent University / The Francis Crick Institute +# Authors:: +# * Wiktor Jurkowski +# * Fotis Georgatos +# * George Tsouloupas +# * Kenneth Hoste +# * Adam Huffman +# * Ake Sandgren +# * J. Sassmannshausen +# * Dugan Witherick +# * Christoph Siegert +# License:: MIT/GPL + +name = 'GROMACS' +version = '2024.3' +_plumedver = '2.9.2' +versionsuffix = '-PLUMED-%s' % _plumedver + +homepage = 'https://www.gromacs.org' +description = """ +GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the +Newtonian equations of motion for systems with hundreds to millions of +particles. + +This is a CPU only build, containing both MPI and threadMPI binaries +for both single and double precision. + +It also contains the gmxapi extension for the single precision MPI build. +""" + +toolchain = {'name': 'foss', 'version': '2023b'} +toolchainopts = {'openmp': True, 'usempi': True} + +source_urls = [ + 'https://ftp.gromacs.org/pub/gromacs/', + 'ftp://ftp.gromacs.org/pub/gromacs/', +] +sources = [SOURCELOWER_TAR_GZ] +patches = [ + 'GROMACS-2023.1_set_omp_num_threads_env_for_ntomp_tests.patch', + 'GROMACS-2023.1_fix_tests_for_gmx_thread_mpi.patch', + 'GROMACS-2023.3_skip_test_for_plumed.patch', +] +checksums = [ + {'gromacs-2024.3.tar.gz': 'bbda056ee59390be7d58d84c13a9ec0d4e3635617adf2eb747034922cba1f029'}, + {'GROMACS-2023.1_set_omp_num_threads_env_for_ntomp_tests.patch': + '7f41bda16c9c2837624265dda4be252f655d1288ddc4486b1a2422af30d5d199'}, + {'GROMACS-2023.1_fix_tests_for_gmx_thread_mpi.patch': + '6df844bb3bbc51180446a3595c61a4ef195e5f975533a04cef76841aa763aec1'}, + {'GROMACS-2023.3_skip_test_for_plumed.patch': '6c541ee74f71f6a63950134d9d0e3afb176a2e25e76e017b4d1986a59163c083'}, +] + +builddependencies = [ + ('CMake', '3.27.6'), + ('scikit-build-core', '0.9.3'), +] + +dependencies = [ + ('Python', '3.11.5'), + ('SciPy-bundle', '2023.11'), + ('networkx', '3.2.1'), + ('mpi4py', '3.1.5'), + ('PLUMED', _plumedver), +] + +# PLUMED 2.9.2 is compatible with GROMACS 2024.2; 2024.3 seems to work fine too +ignore_plumed_version_check = True + +exts_defaultclass = 'PythonPackage' + +exts_default_options = { + 'source_urls': [PYPI_SOURCE], + 'use_pip': True, + 'download_dep_fail': True, + 'sanity_pip_check': True, +} + +exts_list = [ + ('gmxapi', '0.4.2', { + 'preinstallopts': 'export CMAKE_ARGS="-Dgmxapi_ROOT=%(installdir)s ' + + '-C %(installdir)s/share/cmake/gromacs_mpi/gromacs-hints_mpi.cmake" && ', + 'checksums': ['c746c6498c73a75913d7fcb01c13cc001d4bcb82999e9bf91d63578565ed1a1f'], + }), +] + +modextrapaths = { + 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2024.3-foss-2023b.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2024.3-foss-2023b.eb new file mode 100644 index 00000000000..a5ece3769bb --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2024.3-foss-2023b.eb @@ -0,0 +1,85 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2016 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC, +# Ghent University / The Francis Crick Institute +# Authors:: +# * Wiktor Jurkowski +# * Fotis Georgatos +# * George Tsouloupas +# * Kenneth Hoste +# * Adam Huffman +# * Ake Sandgren +# * J. Sassmannshausen +# * Dugan Witherick +# * Christoph Siegert +# License:: MIT/GPL + +name = 'GROMACS' +version = '2024.3' + +homepage = 'https://www.gromacs.org' +description = """ +GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the +Newtonian equations of motion for systems with hundreds to millions of +particles. + +This is a CPU only build, containing both MPI and threadMPI binaries +for both single and double precision. + +It also contains the gmxapi extension for the single precision MPI build. +""" + +toolchain = {'name': 'foss', 'version': '2023b'} +toolchainopts = {'openmp': True, 'usempi': True} + +source_urls = [ + 'https://ftp.gromacs.org/pub/gromacs/', + 'ftp://ftp.gromacs.org/pub/gromacs/', +] +sources = [SOURCELOWER_TAR_GZ] +patches = [ + 'GROMACS-2023.1_set_omp_num_threads_env_for_ntomp_tests.patch', + 'GROMACS-2023.1_fix_tests_for_gmx_thread_mpi.patch', +] +checksums = [ + {'gromacs-2024.3.tar.gz': 'bbda056ee59390be7d58d84c13a9ec0d4e3635617adf2eb747034922cba1f029'}, + {'GROMACS-2023.1_set_omp_num_threads_env_for_ntomp_tests.patch': + '7f41bda16c9c2837624265dda4be252f655d1288ddc4486b1a2422af30d5d199'}, + {'GROMACS-2023.1_fix_tests_for_gmx_thread_mpi.patch': + '6df844bb3bbc51180446a3595c61a4ef195e5f975533a04cef76841aa763aec1'}, +] + +builddependencies = [ + ('CMake', '3.27.6'), + ('scikit-build-core', '0.9.3'), +] + +dependencies = [ + ('Python', '3.11.5'), + ('SciPy-bundle', '2023.11'), + ('networkx', '3.2.1'), + ('mpi4py', '3.1.5'), +] + +exts_defaultclass = 'PythonPackage' + +exts_default_options = { + 'source_urls': [PYPI_SOURCE], + 'use_pip': True, + 'download_dep_fail': True, + 'sanity_pip_check': True, +} + +exts_list = [ + ('gmxapi', '0.4.2', { + 'preinstallopts': 'export CMAKE_ARGS="-Dgmxapi_ROOT=%(installdir)s ' + + '-C %(installdir)s/share/cmake/gromacs_mpi/gromacs-hints_mpi.cmake" && ', + 'checksums': ['c746c6498c73a75913d7fcb01c13cc001d4bcb82999e9bf91d63578565ed1a1f'], + }), +] + +modextrapaths = { + 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2024.4-foss-2023b-CUDA-12.4.0-PLUMED-2.9.2.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2024.4-foss-2023b-CUDA-12.4.0-PLUMED-2.9.2.eb new file mode 100644 index 00000000000..1fc7764f5a7 --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2024.4-foss-2023b-CUDA-12.4.0-PLUMED-2.9.2.eb @@ -0,0 +1,98 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2016 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC, +# Ghent University / The Francis Crick Institute +# Authors:: +# * Wiktor Jurkowski +# * Fotis Georgatos +# * George Tsouloupas +# * Kenneth Hoste +# * Adam Huffman +# * Ake Sandgren +# * J. Sassmannshausen +# * Dugan Witherick +# * Christoph Siegert +# License:: MIT/GPL + +name = 'GROMACS' +version = '2024.4' +local_plumedver = '2.9.2' +versionsuffix = '-CUDA-%%(cudaver)s-PLUMED-%s' % local_plumedver + +homepage = 'https://www.gromacs.org' +description = """ +GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the +Newtonian equations of motion for systems with hundreds to millions of +particles. + +This is a GPU enabled build, containing both MPI and threadMPI binaries. + +It also contains the gmxapi extension for the single precision MPI build. +""" + +toolchain = {'name': 'foss', 'version': '2023b'} +toolchainopts = {'openmp': True, 'usempi': True} + +source_urls = [ + 'https://ftp.gromacs.org/pub/gromacs/', + 'ftp://ftp.gromacs.org/pub/gromacs/', +] +sources = [SOURCELOWER_TAR_GZ] +patches = [ + 'GROMACS-2023.1_set_omp_num_threads_env_for_ntomp_tests.patch', + 'GROMACS-2023.1_fix_tests_for_gmx_thread_mpi.patch', + 'GROMACS-2023.3_skip_test_for_plumed.patch', +] +checksums = [ + {'gromacs-2024.4.tar.gz': 'ac618ece2e58afa86b536c5a2c4fcb937f0760318f12d18f10346b6bdebd86a8'}, + {'GROMACS-2023.1_set_omp_num_threads_env_for_ntomp_tests.patch': + '7f41bda16c9c2837624265dda4be252f655d1288ddc4486b1a2422af30d5d199'}, + {'GROMACS-2023.1_fix_tests_for_gmx_thread_mpi.patch': + '6df844bb3bbc51180446a3595c61a4ef195e5f975533a04cef76841aa763aec1'}, + {'GROMACS-2023.3_skip_test_for_plumed.patch': '6c541ee74f71f6a63950134d9d0e3afb176a2e25e76e017b4d1986a59163c083'}, +] + +builddependencies = [ + ('CMake', '3.27.6'), + ('scikit-build-core', '0.9.3'), +] + +dependencies = [ + ('CUDA', '12.4.0', '', SYSTEM), + ('UCX-CUDA', '1.15.0', '-CUDA-%(cudaver)s'), + ('Python', '3.11.5'), + ('SciPy-bundle', '2023.11'), + ('networkx', '3.2.1'), + ('mpi4py', '3.1.5'), + ('PLUMED', local_plumedver), +] + +# be a bit more forgiving w.r.t. timeouts for GROMACS test suite, +# see also https://gitlab.com/gromacs/gromacs/-/issues/5062 +configopts = "-DGMX_TEST_TIMEOUT_FACTOR=3" + +# PLUMED 2.9.2 is compatible with GROMACS 2024.2; 2024.4 seems to work fine too +ignore_plumed_version_check = True + +exts_defaultclass = 'PythonPackage' + +exts_default_options = { + 'source_urls': [PYPI_SOURCE], + 'use_pip': True, + 'download_dep_fail': True, + 'sanity_pip_check': True, +} + +exts_list = [ + ('gmxapi', '0.4.2', { + 'preinstallopts': 'export CMAKE_ARGS="-Dgmxapi_ROOT=%(installdir)s ' + + '-C %(installdir)s/share/cmake/gromacs_mpi/gromacs-hints_mpi.cmake" && ', + 'checksums': ['c746c6498c73a75913d7fcb01c13cc001d4bcb82999e9bf91d63578565ed1a1f'], + }), +] + +modextrapaths = { + 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2024.4-foss-2023b-CUDA-12.4.0.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2024.4-foss-2023b-CUDA-12.4.0.eb new file mode 100644 index 00000000000..d93065bbed6 --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2024.4-foss-2023b-CUDA-12.4.0.eb @@ -0,0 +1,91 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2016 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC, +# Ghent University / The Francis Crick Institute +# Authors:: +# * Wiktor Jurkowski +# * Fotis Georgatos +# * George Tsouloupas +# * Kenneth Hoste +# * Adam Huffman +# * Ake Sandgren +# * J. Sassmannshausen +# * Dugan Witherick +# * Christoph Siegert +# License:: MIT/GPL + +name = 'GROMACS' +version = '2024.4' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://www.gromacs.org' +description = """ +GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the +Newtonian equations of motion for systems with hundreds to millions of +particles. + +This is a GPU enabled build, containing both MPI and threadMPI binaries. + +It also contains the gmxapi extension for the single precision MPI build. +""" + +toolchain = {'name': 'foss', 'version': '2023b'} +toolchainopts = {'openmp': True, 'usempi': True} + +source_urls = [ + 'https://ftp.gromacs.org/pub/gromacs/', + 'ftp://ftp.gromacs.org/pub/gromacs/', +] +sources = [SOURCELOWER_TAR_GZ] +patches = [ + 'GROMACS-2023.1_set_omp_num_threads_env_for_ntomp_tests.patch', + 'GROMACS-2023.1_fix_tests_for_gmx_thread_mpi.patch', +] +checksums = [ + {'gromacs-2024.4.tar.gz': 'ac618ece2e58afa86b536c5a2c4fcb937f0760318f12d18f10346b6bdebd86a8'}, + {'GROMACS-2023.1_set_omp_num_threads_env_for_ntomp_tests.patch': + '7f41bda16c9c2837624265dda4be252f655d1288ddc4486b1a2422af30d5d199'}, + {'GROMACS-2023.1_fix_tests_for_gmx_thread_mpi.patch': + '6df844bb3bbc51180446a3595c61a4ef195e5f975533a04cef76841aa763aec1'}, +] + +builddependencies = [ + ('CMake', '3.27.6'), + ('scikit-build-core', '0.9.3'), +] + +dependencies = [ + ('CUDA', '12.4.0', '', SYSTEM), + ('UCX-CUDA', '1.15.0', versionsuffix), + ('Python', '3.11.5'), + ('SciPy-bundle', '2023.11'), + ('networkx', '3.2.1'), + ('mpi4py', '3.1.5'), +] + +# be a bit more forgiving w.r.t. timeouts for GROMACS test suite, +# see also https://gitlab.com/gromacs/gromacs/-/issues/5062 +configopts = "-DGMX_TEST_TIMEOUT_FACTOR=3" + +exts_defaultclass = 'PythonPackage' + +exts_default_options = { + 'source_urls': [PYPI_SOURCE], + 'use_pip': True, + 'download_dep_fail': True, + 'sanity_pip_check': True, +} + +exts_list = [ + ('gmxapi', '0.4.2', { + 'preinstallopts': 'export CMAKE_ARGS="-Dgmxapi_ROOT=%(installdir)s ' + + '-C %(installdir)s/share/cmake/gromacs_mpi/gromacs-hints_mpi.cmake" && ', + 'checksums': ['c746c6498c73a75913d7fcb01c13cc001d4bcb82999e9bf91d63578565ed1a1f'], + }), +] + +modextrapaths = { + 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2024.4-foss-2023b-PLUMED-2.9.2.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2024.4-foss-2023b-PLUMED-2.9.2.eb new file mode 100644 index 00000000000..5920405282c --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2024.4-foss-2023b-PLUMED-2.9.2.eb @@ -0,0 +1,97 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2016 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC, +# Ghent University / The Francis Crick Institute +# Authors:: +# * Wiktor Jurkowski +# * Fotis Georgatos +# * George Tsouloupas +# * Kenneth Hoste +# * Adam Huffman +# * Ake Sandgren +# * J. Sassmannshausen +# * Dugan Witherick +# * Christoph Siegert +# License:: MIT/GPL + +name = 'GROMACS' +version = '2024.4' +local_plumedver = '2.9.2' +versionsuffix = '-PLUMED-%s' % local_plumedver + +homepage = 'https://www.gromacs.org' +description = """ +GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the +Newtonian equations of motion for systems with hundreds to millions of +particles. + +This is a CPU only build, containing both MPI and threadMPI binaries +for both single and double precision. + +It also contains the gmxapi extension for the single precision MPI build. +""" + +toolchain = {'name': 'foss', 'version': '2023b'} +toolchainopts = {'openmp': True, 'usempi': True} + +source_urls = [ + 'https://ftp.gromacs.org/pub/gromacs/', + 'ftp://ftp.gromacs.org/pub/gromacs/', +] +sources = [SOURCELOWER_TAR_GZ] +patches = [ + 'GROMACS-2023.1_set_omp_num_threads_env_for_ntomp_tests.patch', + 'GROMACS-2023.1_fix_tests_for_gmx_thread_mpi.patch', + 'GROMACS-2023.3_skip_test_for_plumed.patch', +] +checksums = [ + {'gromacs-2024.4.tar.gz': 'ac618ece2e58afa86b536c5a2c4fcb937f0760318f12d18f10346b6bdebd86a8'}, + {'GROMACS-2023.1_set_omp_num_threads_env_for_ntomp_tests.patch': + '7f41bda16c9c2837624265dda4be252f655d1288ddc4486b1a2422af30d5d199'}, + {'GROMACS-2023.1_fix_tests_for_gmx_thread_mpi.patch': + '6df844bb3bbc51180446a3595c61a4ef195e5f975533a04cef76841aa763aec1'}, + {'GROMACS-2023.3_skip_test_for_plumed.patch': '6c541ee74f71f6a63950134d9d0e3afb176a2e25e76e017b4d1986a59163c083'}, +] + +builddependencies = [ + ('CMake', '3.27.6'), + ('scikit-build-core', '0.9.3'), +] + +dependencies = [ + ('Python', '3.11.5'), + ('SciPy-bundle', '2023.11'), + ('networkx', '3.2.1'), + ('mpi4py', '3.1.5'), + ('PLUMED', local_plumedver), +] + +# PLUMED 2.9.2 is compatible with GROMACS 2024.2; 2024.4 seems to work fine too +ignore_plumed_version_check = True + +# be a bit more forgiving w.r.t. timeouts for GROMACS test suite, +# see also https://gitlab.com/gromacs/gromacs/-/issues/5062 +configopts = "-DGMX_TEST_TIMEOUT_FACTOR=3" + +exts_defaultclass = 'PythonPackage' + +exts_default_options = { + 'source_urls': [PYPI_SOURCE], + 'use_pip': True, + 'download_dep_fail': True, + 'sanity_pip_check': True, +} + +exts_list = [ + ('gmxapi', '0.4.2', { + 'preinstallopts': 'export CMAKE_ARGS="-Dgmxapi_ROOT=%(installdir)s ' + + '-C %(installdir)s/share/cmake/gromacs_mpi/gromacs-hints_mpi.cmake" && ', + 'checksums': ['c746c6498c73a75913d7fcb01c13cc001d4bcb82999e9bf91d63578565ed1a1f'], + }), +] + +modextrapaths = { + 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2024.4-foss-2023b.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2024.4-foss-2023b.eb new file mode 100644 index 00000000000..778af16ba08 --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2024.4-foss-2023b.eb @@ -0,0 +1,89 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2016 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC, +# Ghent University / The Francis Crick Institute +# Authors:: +# * Wiktor Jurkowski +# * Fotis Georgatos +# * George Tsouloupas +# * Kenneth Hoste +# * Adam Huffman +# * Ake Sandgren +# * J. Sassmannshausen +# * Dugan Witherick +# * Christoph Siegert +# License:: MIT/GPL + +name = 'GROMACS' +version = '2024.4' + +homepage = 'https://www.gromacs.org' +description = """ +GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the +Newtonian equations of motion for systems with hundreds to millions of +particles. + +This is a CPU only build, containing both MPI and threadMPI binaries +for both single and double precision. + +It also contains the gmxapi extension for the single precision MPI build. +""" + +toolchain = {'name': 'foss', 'version': '2023b'} +toolchainopts = {'openmp': True, 'usempi': True} + +source_urls = [ + 'https://ftp.gromacs.org/pub/gromacs/', + 'ftp://ftp.gromacs.org/pub/gromacs/', +] +sources = [SOURCELOWER_TAR_GZ] +patches = [ + 'GROMACS-2023.1_set_omp_num_threads_env_for_ntomp_tests.patch', + 'GROMACS-2023.1_fix_tests_for_gmx_thread_mpi.patch', +] +checksums = [ + {'gromacs-2024.4.tar.gz': 'ac618ece2e58afa86b536c5a2c4fcb937f0760318f12d18f10346b6bdebd86a8'}, + {'GROMACS-2023.1_set_omp_num_threads_env_for_ntomp_tests.patch': + '7f41bda16c9c2837624265dda4be252f655d1288ddc4486b1a2422af30d5d199'}, + {'GROMACS-2023.1_fix_tests_for_gmx_thread_mpi.patch': + '6df844bb3bbc51180446a3595c61a4ef195e5f975533a04cef76841aa763aec1'}, +] + +builddependencies = [ + ('CMake', '3.27.6'), + ('scikit-build-core', '0.9.3'), +] + +dependencies = [ + ('Python', '3.11.5'), + ('SciPy-bundle', '2023.11'), + ('networkx', '3.2.1'), + ('mpi4py', '3.1.5'), +] + +# be a bit more forgiving w.r.t. timeouts for GROMACS test suite, +# see also https://gitlab.com/gromacs/gromacs/-/issues/5062 +configopts = "-DGMX_TEST_TIMEOUT_FACTOR=3" + +exts_defaultclass = 'PythonPackage' + +exts_default_options = { + 'source_urls': [PYPI_SOURCE], + 'use_pip': True, + 'download_dep_fail': True, + 'sanity_pip_check': True, +} + +exts_list = [ + ('gmxapi', '0.4.2', { + 'preinstallopts': 'export CMAKE_ARGS="-Dgmxapi_ROOT=%(installdir)s ' + + '-C %(installdir)s/share/cmake/gromacs_mpi/gromacs-hints_mpi.cmake" && ', + 'checksums': ['c746c6498c73a75913d7fcb01c13cc001d4bcb82999e9bf91d63578565ed1a1f'], + }), +] + +modextrapaths = { + 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GSL/GSL-2.8-GCC-13.3.0.eb b/easybuild/easyconfigs/g/GSL/GSL-2.8-GCC-13.3.0.eb new file mode 100644 index 00000000000..251304ed936 --- /dev/null +++ b/easybuild/easyconfigs/g/GSL/GSL-2.8-GCC-13.3.0.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'GSL' +version = '2.8' + +homepage = 'https://www.gnu.org/software/gsl/' +description = """The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. + The library provides a wide range of mathematical routines such as random number generators, special functions + and least-squares fitting.""" + +toolchain = {'name': 'GCC', 'version': '13.3.0'} +toolchainopts = {'unroll': True, 'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['6a99eeed15632c6354895b1dd542ed5a855c0f15d9ad1326c6fe2b2c9e423190'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['gsl-config', 'gsl-histogram', 'gsl-randist']] + + ['include/gsl/gsl_types.h'] + + ['lib/lib%s.%s' % (x, SHLIB_EXT) for x in ['gsl', 'gslcblas']], + 'dirs': [], +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.24.8-GCC-13.3.0.eb b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.24.8-GCC-13.3.0.eb new file mode 100644 index 00000000000..13311a9a434 --- /dev/null +++ b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.24.8-GCC-13.3.0.eb @@ -0,0 +1,43 @@ +easyblock = 'MesonNinja' + +name = 'GST-plugins-base' +version = '1.24.8' + +homepage = 'https://gstreamer.freedesktop.org/' +description = """GStreamer is a library for constructing graphs of media-handling + components. The applications it supports range from simple + Ogg/Vorbis playback, audio/video streaming to complex audio + (mixing) and video (non-linear editing) processing.""" + +toolchain = {'name': 'GCC', 'version': '13.3.0'} + +source_urls = ['https://gstreamer.freedesktop.org/src/gst-plugins-base'] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['10fb31743750ccd498d3933e8aaecda563ebc65596a6ab875b47ee936e4b9599'] + +builddependencies = [ + ('Meson', '1.4.0'), + ('Ninja', '1.12.1'), + ('GObject-Introspection', '1.80.1'), + ('gettext', '0.22.5'), + ('pkgconf', '2.2.0'), + ('Bison', '3.8.2'), +] + +dependencies = [ + ('zlib', '1.3.1'), + ('GLib', '2.80.4'), + ('GStreamer', '1.24.8'), + ('Gdk-Pixbuf', '2.42.11'), + ('X11', '20240607'), + ('Mesa', '24.1.3'), + ('Graphene', '1.10.8'), +] + +sanity_check_paths = { + 'files': ['bin/gst-%s-1.0' % x for x in ['discoverer', 'play', 'device-monitor']] + + ['lib/libgst%s-1.0.%s' % (x, SHLIB_EXT) for x in ['app', 'audio', 'video']], + 'dirs': ['include', 'share'] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GStreamer/GStreamer-1.24.8-GCC-13.3.0.eb b/easybuild/easyconfigs/g/GStreamer/GStreamer-1.24.8-GCC-13.3.0.eb new file mode 100644 index 00000000000..5c3ef3f7b45 --- /dev/null +++ b/easybuild/easyconfigs/g/GStreamer/GStreamer-1.24.8-GCC-13.3.0.eb @@ -0,0 +1,47 @@ +easyblock = 'MesonNinja' + +name = 'GStreamer' +version = '1.24.8' + +homepage = 'https://gstreamer.freedesktop.org/' +description = """GStreamer is a library for constructing graphs of media-handling + components. The applications it supports range from simple + Ogg/Vorbis playback, audio/video streaming to complex audio + (mixing) and video (non-linear editing) processing.""" + +toolchain = {'name': 'GCC', 'version': '13.3.0'} + +source_urls = ['https://%(namelower)s.freedesktop.org/src/%(namelower)s'] +sources = [SOURCELOWER_TAR_XZ] +patches = ['%(name)s-1.24_fix_bad_suid.patch'] +checksums = ['b807dbf36c5d2b3ce1c604133ed0c737350f9523ce4d8d644a1177c5f9d6ded3', # gstreamer-1.24.8.tar.xz + 'e40c8b195cc9d44f2d9b92e57608e097ef8dac6fa761c5610fcb836f88610cb1', # %(name)s-1.24_fix_bad_suid.patch + ] + +builddependencies = [ + ('Meson', '1.4.0'), + ('Ninja', '1.12.1'), + ('Perl', '5.38.2'), + ('Bison', '3.8.2'), + ('flex', '2.6.4'), + ('GObject-Introspection', '1.80.1'), + ('gettext', '0.22.5'), + ('pkgconf', '2.2.0'), +] +dependencies = [ + ('Python', '3.12.3'), + ('zlib', '1.3.1'), + ('GMP', '6.3.0'), + ('GSL', '2.8'), + ('GLib', '2.80.4'), + ('libunwind', '1.8.1'), + ('elfutils', '0.191'), +] + + +sanity_check_paths = { + 'files': [], + 'dirs': ['include', 'share', 'libexec'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GStreamer/GStreamer-1.24_fix_bad_suid.patch b/easybuild/easyconfigs/g/GStreamer/GStreamer-1.24_fix_bad_suid.patch new file mode 100644 index 00000000000..c7497079889 --- /dev/null +++ b/easybuild/easyconfigs/g/GStreamer/GStreamer-1.24_fix_bad_suid.patch @@ -0,0 +1,22 @@ +Do NOT make files setuid or try to do setcap. +That's a recipe for disaster. +Åke Sandgren, 20221031 +Stefan Wolfsheimer, upated to version 1.24.8 + +--- gstreamer-1.24.8.orig/libs/gst/helpers/ptp/ptp_helper_post_install.sh 2024-09-19 12:01:21.000000000 +0200 ++++ gstreamer-1.24.8/libs/gst/helpers/ptp/ptp_helper_post_install.sh 2024-10-22 17:43:55.971711002 +0200 +@@ -11,14 +11,10 @@ + setuid-root) + echo "$0: permissions before: " + ls -l "$ptp_helper" +- chown root "$ptp_helper" || true +- chmod u+s "$ptp_helper" || true + echo "$0: permissions after: " + ls -l "$ptp_helper" + ;; + capabilities) +- echo "Calling $setcap cap_sys_nice,cap_net_bind_service,cap_net_admin+ep $ptp_helper" +- $setcap cap_sys_nice,cap_net_bind_service,cap_net_admin+ep "$ptp_helper" || true + ;; + none) + echo "No perms/caps to set for $ptp_helper" diff --git a/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-2.4.0-foss-2023a.eb b/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-2.4.0-foss-2023a.eb new file mode 100644 index 00000000000..a8f48c5966b --- /dev/null +++ b/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-2.4.0-foss-2023a.eb @@ -0,0 +1,46 @@ +# Updated from previous config +# Author: Pavel Grochal (INUITS) +# License: GPLv2 + +easyblock = 'PythonBundle' + +name = 'GTDB-Tk' +version = '2.4.0' + +homepage = 'https://github.com/Ecogenomics/GTDBTk' +description = "A toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes." + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('DendroPy', '4.6.1'), + ('matplotlib', '3.7.2'), + ('prodigal', '2.6.3'), + ('HMMER', '3.4'), + ('pplacer', '1.1.alpha19', '', SYSTEM), + ('skani', '0.2.2'), + ('FastTree', '2.1.11'), + ('Mash', '2.3'), + ('tqdm', '4.66.1'), + ('pydantic', '1.10.13'), +] + +use_pip = True + +exts_list = [ + ('gtdbtk', version, { + 'checksums': ['e67bab2c8f3e47c7242c70236c78e85bb9dc4721636bbf5044b171f18f22b1f7'], + }), +] + +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/gtdbtk'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["gtdbtk --help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GTK3/GTK3-3.24.42-GCCcore-13.3.0.eb b/easybuild/easyconfigs/g/GTK3/GTK3-3.24.42-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..2df9a346d4a --- /dev/null +++ b/easybuild/easyconfigs/g/GTK3/GTK3-3.24.42-GCCcore-13.3.0.eb @@ -0,0 +1,72 @@ +easyblock = 'Bundle' + +name = 'GTK3' +version = '3.24.42' + +homepage = 'https://developer.gnome.org/gtk3/stable/' +description = """GTK+ is the primary library used to construct user interfaces in GNOME. It + provides all the user interface controls, or widgets, used in a common + graphical application. Its object-oriented API allows you to construct + user interfaces without dealing with the low-level details of drawing and + device interaction. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +builddependencies = [ + ('binutils', '2.42'), + ('Autotools', '20231222'), + ('Meson', '1.4.0'), + ('Ninja', '1.12.1'), + ('pkgconf', '2.2.0'), + ('GObject-Introspection', '1.80.1'), +] + +dependencies = [ + ('ATK', '2.38.0'), + ('at-spi2-atk', '2.38.0'), + ('cairo', '1.18.0'), + ('Gdk-Pixbuf', '2.42.11'), + ('GLib', '2.80.4'), + ('Pango', '1.54.0'), + ('libepoxy', '1.5.10'), + ('X11', '20240607'), + ('FriBidi', '1.0.15'), + ('Wayland', '1.23.0'), +] + +default_easyblock = 'MesonNinja' + +default_component_specs = { + 'sources': [SOURCELOWER_TAR_XZ], + 'start_dir': '%(namelower)s-%(version)s', +} + +components = [ + ('GTK+', version, { + 'source_urls': [FTPGNOME_SOURCE], + 'checksums': ['50f89f615092d4dd01bbd759719f8bd380e5f149f6fd78a94725e2de112377e2'], + }), + ('hicolor-icon-theme', '0.18', { + 'easyblock': 'MesonNinja', + 'source_urls': ['https://icon-theme.freedesktop.org/releases/'], + 'checksums': ['db0e50a80aa3bf64bb45cbca5cf9f75efd9348cf2ac690b907435238c3cf81d7'], + }), + ('adwaita-icon-theme', '47.0', { + 'source_urls': ['https://ftp.gnome.org/pub/GNOME/sources/%(namelower)s/%(version_major)s'], + 'checksums': ['ad088a22958cb8469e41d9f1bba0efb27e586a2102213cd89cc26db2e002bdfe'], + }), +] + +postinstallcmds = ['gtk-update-icon-cache'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['gtk3-demo', 'gtk3-demo-application', 'gtk3-icon-browser', 'gtk3-widget-factory', + 'gtk-builder-tool', 'gtk-launch', 'gtk-query-immodules-3.0', 'gtk-query-settings', + 'gtk-update-icon-cache']] + + ['lib/%s-%%(version_major)s.%s' % (x, SHLIB_EXT) for x in ['libgailutil', 'libgdk', 'libgtk']], + 'dirs': ['include/%s-%%(version_major)s.0' % x for x in ['gail', 'gtk']] + + ['share/icons/hicolor', 'share/icons/Adwaita'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GTS/GTS-0.7.6-GCCcore-13.3.0.eb b/easybuild/easyconfigs/g/GTS/GTS-0.7.6-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..dd36868a20d --- /dev/null +++ b/easybuild/easyconfigs/g/GTS/GTS-0.7.6-GCCcore-13.3.0.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'GTS' +version = '0.7.6' + +homepage = 'http://gts.sourceforge.net/' +description = """GTS stands for the GNU Triangulated Surface Library. +It is an Open Source Free Software Library intended to provide a set of useful +functions to deal with 3D surfaces meshed with interconnected triangles.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['059c3e13e3e3b796d775ec9f96abdce8f2b3b5144df8514eda0cc12e13e8b81e'] + +builddependencies = [ + ('pkgconf', '2.2.0'), + ('binutils', '2.42'), +] +dependencies = [ + ('GLib', '2.80.4'), +] + +sanity_check_paths = { + 'files': ['lib/libgts.%s' % SHLIB_EXT, 'bin/gts2oogl', 'bin/gtscheck'], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.42.11-GCCcore-13.3.0.eb b/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.42.11-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..2ac4237f4c0 --- /dev/null +++ b/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.42.11-GCCcore-13.3.0.eb @@ -0,0 +1,46 @@ +easyblock = 'MesonNinja' + +name = 'Gdk-Pixbuf' +version = '2.42.11' + +homepage = 'https://docs.gtk.org/gdk-pixbuf/' +description = """ + The Gdk Pixbuf is a toolkit for image loading and pixel buffer manipulation. + It is used by GTK+ 2 and GTK+ 3 to load and manipulate images. In the past it + was distributed as part of GTK+ 2 but it was split off into a separate package + in preparation for the change to GTK+ 3. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['49dcb402388708647e8c321d56b6fb30f21e51e515d0c5a942268d23052a2f00'] + +builddependencies = [ + ('binutils', '2.42'), + ('Meson', '1.4.0'), + ('Ninja', '1.12.1'), + ('pkgconf', '2.2.0'), + ('GObject-Introspection', '1.80.1'), +] + +dependencies = [ + ('GLib', '2.80.4'), + ('libjpeg-turbo', '3.0.1'), + ('libpng', '1.6.43'), + ('LibTIFF', '4.6.0'), + ('X11', '20240607'), +] + +configopts = "--buildtype=release --default-library=both " +configopts += "-Dgio_sniffing=false -Dintrospection=enabled -Dman=false" + +sanity_check_paths = { + 'files': ['lib/libgdk_pixbuf-%(version_major)s.0.a', 'lib/libgdk_pixbuf-%%(version_major)s.0.%s' % SHLIB_EXT], + 'dirs': ['bin', 'include/gdk-pixbuf-%(version_major)s.0', 'lib/gdk-pixbuf-%(version_major)s.0', 'share'], +} + +sanity_check_commands = ["gdk-pixbuf-pixdata --help"] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/Geant4-data/Geant4-data-11.2.eb b/easybuild/easyconfigs/g/Geant4-data/Geant4-data-11.2.eb new file mode 100644 index 00000000000..a085843d7d2 --- /dev/null +++ b/easybuild/easyconfigs/g/Geant4-data/Geant4-data-11.2.eb @@ -0,0 +1,54 @@ +easyblock = 'Tarball' +name = 'Geant4-data' +version = '11.2' # version should somewhat match the Geant4 version it should be used in + +homepage = 'https://geant4.web.cern.ch/' +description = """Datasets for Geant4.""" + +toolchain = SYSTEM + +# Pick up the correct sets and versions from cmake/Modules/G4DatasetDefinitions.cmake +# in the Geant source, +# see also https://github.com/Geant4/geant4/blob/v11.2.2/cmake/Modules/G4DatasetDefinitions.cmake +local_datasets = [ + ('G4NDL', '4.7.1', 'G4NDL', 'G4NEUTRONHPDATA'), # NDL + ('G4EMLOW', '8.5', 'G4EMLOW', 'G4LEDATA'), # Low energy electromagnetics + ('PhotonEvaporation', '5.7', 'G4PhotonEvaporation', 'G4LEVELGAMMADATA'), # Photon evaporation + ('RadioactiveDecay', '5.6', 'G4RadioactiveDecay', 'G4RADIOACTIVEDATA'), # Radioisotopes + ('G4SAIDDATA', '2.0', 'G4SAIDDATA', 'G4SAIDXSDATA'), # SAID + ('G4PARTICLEXS', '4.0', 'G4PARTICLEXS', 'G4PARTICLEXSDATA'), # Particle XS - replaces Neutron XS + ('G4PII', '1.3', 'G4PII', 'G4PIIDATA'), # PII + ('RealSurface', '2.2', 'G4RealSurface', 'G4REALSURFACEDATA'), # Optical Surfaces + ('G4ABLA', '3.3', 'G4ABLA', 'G4ABLADATA'), # ABLA + ('G4INCL', '1.2', 'G4INCL', 'G4INCLDATA'), # INCL + ('G4ENSDFSTATE', '2.3', 'G4ENSDFSTATE', 'G4ENSDFSTATEDATA'), # ENSDFSTATE + ('G4TENDL', '1.4', 'G4TENDL', 'G4PARTICLEHPDATA'), # TENDL +] + +source_urls = ['https://cern.ch/geant4-data/datasets'] +sources = ['%s.%s.tar.gz' % (x[2], x[1]) for x in local_datasets] +checksums = [ + {'G4NDL.4.7.1.tar.gz': 'd3acae48622118d2579de24a54d533fb2416bf0da9dd288f1724df1485a46c7c'}, + {'G4EMLOW.8.5.tar.gz': '66baca49ac5d45e2ac10c125b4fb266225e511803e66981909ce9cd3e9bcef73'}, + {'G4PhotonEvaporation.5.7.tar.gz': '761e42e56ffdde3d9839f9f9d8102607c6b4c0329151ee518206f4ee9e77e7e5'}, + {'G4RadioactiveDecay.5.6.tar.gz': '3886077c9c8e5a98783e6718e1c32567899eeb2dbb33e402d4476bc2fe4f0df1'}, + {'G4SAIDDATA.2.0.tar.gz': '1d26a8e79baa71e44d5759b9f55a67e8b7ede31751316a9e9037d80090c72e91'}, + {'G4PARTICLEXS.4.0.tar.gz': '9381039703c3f2b0fd36ab4999362a2c8b4ff9080c322f90b4e319281133ca95'}, + {'G4PII.1.3.tar.gz': '6225ad902675f4381c98c6ba25fc5a06ce87549aa979634d3d03491d6616e926'}, + {'G4RealSurface.2.2.tar.gz': '9954dee0012f5331267f783690e912e72db5bf52ea9babecd12ea22282176820'}, + {'G4ABLA.3.3.tar.gz': '1e041b3252ee9cef886d624f753e693303aa32d7e5ef3bba87b34f36d92ea2b1'}, + {'G4INCL.1.2.tar.gz': 'f880b16073ee0a92d7494f3276a6d52d4de1d3677a0d4c7c58700396ed0e1a7e'}, + {'G4ENSDFSTATE.2.3.tar.gz': '9444c5e0820791abd3ccaace105b0e47790fadce286e11149834e79c4a8e9203'}, + {'G4TENDL.1.4.tar.gz': '4b7274020cc8b4ed569b892ef18c2e088edcdb6b66f39d25585ccee25d9721e0'}, +] + +start_dir = '..' + +modextrapaths = {x[3]: x[0] + x[1] for x in local_datasets} + +sanity_check_paths = { + 'files': [], + 'dirs': [x[0] + x[1] for x in local_datasets], +} + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/g/Geant4/Geant4-11.2.2-GCC-12.3.0.eb b/easybuild/easyconfigs/g/Geant4/Geant4-11.2.2-GCC-12.3.0.eb new file mode 100644 index 00000000000..d4cdf6c78cb --- /dev/null +++ b/easybuild/easyconfigs/g/Geant4/Geant4-11.2.2-GCC-12.3.0.eb @@ -0,0 +1,48 @@ +name = 'Geant4' +version = '11.2.2' + +homepage = 'https://geant4.web.cern.ch/' +description = """Geant4 is a toolkit for the simulation of the passage of particles through matter. + Its areas of application include high energy, nuclear and accelerator physics, + as well as studies in medical and space science.""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +github_account = 'Geant4' +source_urls = [GITHUB_SOURCE] +sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCELOWER_TAR_GZ}] +patches = [ + 'Geant4-11.1.2_use_data_env_vars_from_Geant4-data_module.patch', +] +checksums = [ + {'geant4-11.2.2.tar.gz': '0b0cfce14e9143079c4440d27ee21f889c4c4172ac5ee7586746b940ffcf812a'}, + {'Geant4-11.1.2_use_data_env_vars_from_Geant4-data_module.patch': + '822265b7cbcaacdffd28b1094786a3c94122aff63338e514d5d3810cdf9218a6'}, +] + +builddependencies = [ + ('CMake', '3.26.3'), +] + +dependencies = [ + ('expat', '2.5.0'), + # recommended CLHEP version, see https://geant4.web.cern.ch/download/release-notes/notes-v11.1.0.html + ('CLHEP', '2.4.7.1'), + ('Xerces-C++', '3.2.4'), + ('Qt5', '5.15.10'), + ('Geant4-data', '11.2', '', SYSTEM), +] + +_copts = [ + "-DGEANT4_INSTALL_DATA=OFF", + "-DGEANT4_USE_SYSTEM_ZLIB=ON", + "-DGEANT4_USE_SYSTEM_EXPAT=ON", + "-DGEANT4_USE_SYSTEM_CLHEP=ON", + "-DGEANT4_USE_QT=ON", + "-DGEANT4_USE_GDML=ON", + "-DGEANT4_USE_OPENGL_X11=ON", + "-DGEANT4_USE_RAYTRACER_X11=ON", +] +configopts = ' '.join(_copts) + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/g/GeneMark-ET/GeneMark-ET-4.72-GCCcore-12.3.0.eb b/easybuild/easyconfigs/g/GeneMark-ET/GeneMark-ET-4.72-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..75ffcc9f5f7 --- /dev/null +++ b/easybuild/easyconfigs/g/GeneMark-ET/GeneMark-ET-4.72-GCCcore-12.3.0.eb @@ -0,0 +1,43 @@ +# updated: Denis Kristak (INUITS) +# Update: Petr Král (INUITS) +easyblock = 'Tarball' + +name = 'GeneMark-ET' +version = '4.72' + +homepage = 'http://exon.gatech.edu/GeneMark' +description = "Eukaryotic gene prediction suite with automatic training" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +sources = ['gmes_linux_64-%(version)s.tar.gz'] +checksums = ['629f430e7262bdb5df8f24413e65d26e35eb10ea34212145b692ee4689591e54'] + +download_instructions = """ +1. complete the license form: http://exon.gatech.edu/GeneMark/license_download.cgi +2. rename the tarball: `mv gmes_linux_64.tar.gz gmes_linux_64-%(version)s.tar.gz` +""" + +# To run this code, install the key: copy key "gm_key" into user's home directory as: +# gunzip gm_key.gz +# cp gm_key_64 ~/.gm_key + +dependencies = [ + ('Perl', '5.36.1'), + ('Perl-bundle-CPAN', '5.36.1'), +] + +fix_perl_shebang_for = ['*.pl'] + +sanity_check_paths = { + 'files': ['gmes.cfg', 'gmes_petap.pl'], + 'dirs': ['lib'], +} + +sanity_check_commands = [ + "gmes_petap.pl | grep 'Usage:'", +] + +modextrapaths = {'PATH': ''} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GeoDict/GeoDict-2024.SP2-gmpich-2024.06.eb b/easybuild/easyconfigs/g/GeoDict/GeoDict-2024.SP2-gmpich-2024.06.eb new file mode 100644 index 00000000000..42186eafddb --- /dev/null +++ b/easybuild/easyconfigs/g/GeoDict/GeoDict-2024.SP2-gmpich-2024.06.eb @@ -0,0 +1,41 @@ +easyblock = 'Tarball' + +name = 'GeoDict' +version = '2024.SP2' + +homepage = 'https://www.math2market.com/geodict-software/geodict-applications.html' +description = """ +The innovative and easy-to-use material simulator GeoDict is the most complete software +solution for multi-scale 3D image processing, modeling of materials, visualization, material +property characterization, simulation-based material development, and optimization of +processes. +""" + +toolchain = {'name': 'gmpich', 'version': '2024.06'} + +source_urls = [ + 'https://www.gddownload.de/Releases' +] +sources = [ + '%(name)s2024-3-4-Linux-x86_64-ServicePack2.tar.gz', + '%(name)s2024-3-4-Linux-x86_64-ServicePack2-Tools.tar.gz' +] +checksums = [ + {'GeoDict2024-3-4-Linux-x86_64-ServicePack2.tar.gz': + '049401063d892eac65696d7d1ed8d4b915c9a81bb13e325cc0657c60ce8aeb28'}, + {'GeoDict2024-3-4-Linux-x86_64-ServicePack2-Tools.tar.gz': + '1b50fb840e8e78c225c748d73eaca60faedd822de33f20c716b1e98b15492eac'}, +] + +dependencies = [ + ('X11', '20230603'), +] + +modextrapaths = {'PATH': '.'} + +sanity_check_paths = { + 'files': ['geodict2024'], + 'dirs': ['Python', 'Tools'], +} + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/g/GetOrganelle/GetOrganelle-1.7.7.1-foss-2023a.eb b/easybuild/easyconfigs/g/GetOrganelle/GetOrganelle-1.7.7.1-foss-2023a.eb new file mode 100644 index 00000000000..4c6746689d9 --- /dev/null +++ b/easybuild/easyconfigs/g/GetOrganelle/GetOrganelle-1.7.7.1-foss-2023a.eb @@ -0,0 +1,43 @@ +easyblock = 'PythonPackage' + +name = 'GetOrganelle' +version = '1.7.7.1' + +homepage = 'https://github.com/Kinggerm/GetOrganelle' +description = """This toolkit assemblies organelle genome from genomic skimming data.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['https://github.com/Kinggerm/GetOrganelle/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['cf8e14766de43967182be839de20c9d1709b60fae38a0b3d175742dfad7a5d44'] + +dependencies = [ + ('Python', '3.11.3'), + ('Bandage', '0.9.0'), + ('SciPy-bundle', '2023.07'), + ('sympy', '1.12'), + ('SPAdes', '3.15.4'), + ('Bowtie2', '2.5.1'), + ('BLAST+', '2.14.1'), + ('Perl', '5.36.1'), + ('matplotlib', '3.7.2') +] + +download_dep_fail = True +use_pip = True + +options = {'modulename': False} + +fix_python_shebang_for = ['bin/*.py'] + +sanity_pip_check = True + +sanity_check_commands = ["get_organelle_from_reads.py -h"] + +sanity_check_paths = { + 'files': ['bin/check_annotations.py', 'bin/get_organelle_from_reads.py', 'bin/slim_graph.py'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/Ghostscript/Ghostscript-10.03.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-10.03.1-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..174aec3f515 --- /dev/null +++ b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-10.03.1-GCCcore-13.3.0.eb @@ -0,0 +1,58 @@ +easyblock = 'ConfigureMake' + +name = 'Ghostscript' +version = '10.03.1' + +homepage = 'https://ghostscript.com' +description = """Ghostscript is a versatile processor for PostScript data with the ability to render PostScript to + different targets. It used to be part of the cups printing stack, but is no longer used for that.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +source_urls = [ + 'https://github.com/ArtifexSoftware/ghostpdl-downloads/releases/download/gs%s/' % version.replace('.', ''), +] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['31cd01682ad23a801cc3bbc222a55f07c4ea3e068bdfb447792d54db21a2e8ad'] + +builddependencies = [ + ('binutils', '2.42'), + ('pkgconf', '2.2.0'), +] + +dependencies = [ + ('zlib', '1.3.1'), + ('libpng', '1.6.43'), + ('freetype', '2.13.2'), + ('libjpeg-turbo', '3.0.1'), + ('expat', '2.6.2'), + ('GLib', '2.80.4'), + ('cairo', '1.18.0'), + ('LibTIFF', '4.6.0'), +] + +# Do not use local copies of zlib, jpeg, freetype, and png +preconfigopts = 'mv zlib zlib.no && mv jpeg jpeg.no && mv freetype freetype.no && ' +preconfigopts += 'mv libpng libpng.no && export LIBS="$LIBS -L$EBROOTZLIB/lib -lz" && ' +configopts = "--with-system-libtiff --enable-dynamic --disable-hidden-visibility" + +# also build and install shared libs +build_cmd_targets = ['', 'so'] +installopts = 'soinstall' + +postinstallcmds = [ + # install header files + "mkdir -p %(installdir)s/include/%(namelower)s", + "install -v -m644 base/*.h %(installdir)s/include/%(namelower)s", + "install -v -m644 psi/*.h %(installdir)s/include/%(namelower)s", +] + +sanity_check_paths = { + 'files': ['bin/gs', 'lib/libgs.%s' % SHLIB_EXT], + 'dirs': ['lib/%(namelower)s', 'include/%(namelower)s', 'share/man'], +} + +sanity_check_commands = ["gs --help"] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/g/GimmeMotifs/GimmeMotifs-0.17.2-foss-2023a.eb b/easybuild/easyconfigs/g/GimmeMotifs/GimmeMotifs-0.17.2-foss-2023a.eb new file mode 100644 index 00000000000..64b42485b8f --- /dev/null +++ b/easybuild/easyconfigs/g/GimmeMotifs/GimmeMotifs-0.17.2-foss-2023a.eb @@ -0,0 +1,81 @@ +easyblock = 'PythonBundle' + +name = 'GimmeMotifs' +version = '0.17.2' + +homepage = 'https://github.com/vanheeringen-lab/gimmemotifs' +description = "Suite of motif tools, including a motif prediction pipeline for ChIP-seq experiments" + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [('poetry', '1.5.1')] +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('SciPy-bundle', '2023.07'), + ('matplotlib', '3.7.2'), + ('pybedtools', '0.9.1'), + ('Pysam', '0.22.0'), + ('scikit-learn', '1.3.1'), + ('Seaborn', '0.13.2'), + ('statsmodels', '0.14.1'), + ('tqdm', '4.66.1'), + ('genomepy', '0.16.1'), + ('qnorm', '0.8.1'), + ('Arrow', '14.0.1'), # provides pyarrow, required by feather-format + ('HTSeq', '2.0.7'), # required by biofluff + ('pyBigWig', '0.3.22'), # required by biofluff +] + +use_pip = True + +exts_list = [ + ('palettable', '3.3.3', { + 'checksums': ['094dd7d9a5fc1cca4854773e5c1fc6a315b33bd5b3a8f47064928facaf0490a8'], + }), + ('biofluff', '3.0.4', { + 'modulename': 'fluff', + # remove pyBigWig dependency - pip_check fails with "import pybigwig" + 'preinstallopts': "sed -i '/pyBigWig/d' setup.py && ", + 'checksums': ['ef7b0a54103a830f197f21aa3d1ade8bdcddf613b437ea38c95260bb45324d6b'], + }), + ('diskcache', '5.6.3', { + 'checksums': ['2c3a3fa2743d8535d832ec61c2054a1641f41775aa7c556758a109941e33e4fc'], + }), + ('feather-format', '0.4.1', { + 'modulename': 'feather', + 'checksums': ['45f67e3745d394d4f160ca6d636bbfd4f8b68d01199dc1649b6e487d3e878903'], + }), + ('iteround', '1.0.4', { + 'source_urls': ['https://github.com/cgdeboer/iteround/archive/'], + 'sources': ['v%(version)s.tar.gz'], + 'checksums': ['445e4f0c793ae558e4db3cdee7e23d77459b9c586e8021667aa60c14ba7ff45f'], + }), + ('logomaker', '0.8', { + 'checksums': ['d8c7501a7d6d7961cd68e5a44e939000ebf1b0c4197a0c9198351e1d681d3f6d'], + }), + ('loguru', '0.7.2', { + 'checksums': ['e671a53522515f34fd406340ee968cb9ecafbc4b36c679da03c18fd8d0bd51ac'], + }), + ('xxhash', '3.4.1', { + 'checksums': ['0379d6cf1ff987cd421609a264ce025e74f346e3e145dd106c0cc2e3ec3f99a9'], + }), + ('xdg', '6.0.0', { + 'checksums': ['24278094f2d45e846d1eb28a2ebb92d7b67fc0cab5249ee3ce88c95f649a1c92'], + }), + ('gimmemotifs', version, { + 'preinstallopts': """sed -i '/"configparser"/d' setup.py && """, + 'checksums': ['fbf70997abce6a75451c10b96994f8dbc03152b01df5cf30bf4397c98a9b54d2'], + }), +] + +sanity_check_paths = { + 'files': ['bin/gimme'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["gimme --help"] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GitPython/GitPython-3.1.43-GCCcore-13.3.0.eb b/easybuild/easyconfigs/g/GitPython/GitPython-3.1.43-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..e6ca0d7b0aa --- /dev/null +++ b/easybuild/easyconfigs/g/GitPython/GitPython-3.1.43-GCCcore-13.3.0.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonBundle' + +name = 'GitPython' +version = '3.1.43' + +homepage = 'https://gitpython.readthedocs.org' +description = """ GitPython is a python library used to interact with Git repositories """ + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +builddependencies = [('binutils', '2.42')] +dependencies = [ + ('Python', '3.12.3'), + ('git', '2.45.1'), +] + +sanity_pip_check = True +use_pip = True + +exts_list = [ + ('smmap', '5.0.1', {'checksums': ['dceeb6c0028fdb6734471eb07c0cd2aae706ccaecab45965ee83f11c8d3b1f62']}), + ('gitdb', '4.0.11', {'checksums': ['bf5421126136d6d0af55bc1e7c1af1c397a34f5b7bd79e776cd3e89785c2b04b']}), + (name, version, { + 'modulename': 'git', + 'checksums': ['35f314a9f878467f5453cc1fee295c3e18e52f1b99f10f6cf5b1682e968a9e7c'], + }), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/g/GlimmerHMM/GlimmerHMM-3.0.4c-GCC-12.3.0.eb b/easybuild/easyconfigs/g/GlimmerHMM/GlimmerHMM-3.0.4c-GCC-12.3.0.eb new file mode 100644 index 00000000000..ad435033f81 --- /dev/null +++ b/easybuild/easyconfigs/g/GlimmerHMM/GlimmerHMM-3.0.4c-GCC-12.3.0.eb @@ -0,0 +1,57 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild + +easyblock = 'MakeCp' + +name = 'GlimmerHMM' +version = '3.0.4c' + +homepage = 'https://ccb.jhu.edu/software/glimmerhmm' +description = """GlimmerHMM is a new gene finder based on a Generalized Hidden Markov Model. + Although the gene finder conforms to the overall mathematical framework of a GHMM, additionally + it incorporates splice site models adapted from the GeneSplicer program and a decision tree adapted + from GlimmerM. It also utilizes Interpolated Markov Models for the coding and noncoding models.""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://ccb.jhu.edu/software/%(namelower)s/dl'] +sources = [SOURCE_TAR_GZ] +checksums = ['31ee2ceb8f31338205b2de626d83d0f92d2cd55a04d48a6803193a2d0ad1b4a3'] + +dependencies = [ + ('Perl', '5.36.1'), +] + +start_dir = 'sources' + +# make sure -O0 is not used as compiler option +prebuildopts = "ls makefile train/makefile | xargs sed -i 's/-O0 .*//g' && " + +# also build in 'train' subdirectory to overwrite pre-compiled binaries +buildopts = "&& cd ../train && make" + +local_train_files = ['build1', 'build2', 'build-icm', 'build-icm-noframe', 'erfapp', 'falsecomp', + 'findsites', 'karlin', 'score', 'score2', 'scoreATG', 'scoreATG2', 'scoreSTOP', + 'scoreSTOP2', 'splicescore', 'trainGlimmerHMM'] +files_to_copy = [ + (['sources/%(namelower)s'], 'bin'), + (['train/%s' % x for x in local_train_files], 'bin'), + (['train/*.pm'], 'lib/perl%(perlmajver)s'), + 'trained_dir', 'README', 'train/readme.train', +] + +fix_perl_shebang_for = ['bin/trainGlimmerHMM'] + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': ['trained_dir'], +} + +sanity_check_commands = [ + "%(namelower)s -h", + r"trainGlimmerHMM -h 2>&1 | grep '^[ ]*Train GlimmerHMM module'", +] + +modextrapaths = {'PERL5LIB': 'lib/perl%(perlmajver)s'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GlobalArrays/GlobalArrays-5.8.2-intel-2024a.eb b/easybuild/easyconfigs/g/GlobalArrays/GlobalArrays-5.8.2-intel-2024a.eb new file mode 100644 index 00000000000..40829149482 --- /dev/null +++ b/easybuild/easyconfigs/g/GlobalArrays/GlobalArrays-5.8.2-intel-2024a.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'GlobalArrays' +version = '5.8.2' + +homepage = 'https://hpc.pnl.gov/globalarrays' +description = "Global Arrays (GA) is a Partitioned Global Address Space (PGAS) programming model" + +toolchain = {'name': 'intel', 'version': '2024a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://github.com/%(name)s/ga/releases/download/'] +sources = ['v%(version)s/ga-%(version)s.tar.gz'] +checksums = ['51599e4abfe36f05cecfaffa33be19efbe9e9fa42d035fd3f866469b663c22a2'] + +configopts = ' --with-mpi --enable-i8' +configopts += ' --with-blas8="-L$MKLROOT/lib/intel64 -lmkl_sequential -lmkl_intel_ilp64"' +configopts += ' --with-scalapack="-L$MKLROOT/lib/intel64 -lmkl_scalapack_ilp64 -lmkl_intel_ilp64 ' +configopts += '-lmkl_sequential -lmkl_core -lmkl_blacs_intelmpi_ilp64 -lpthread -lm -ldl"' + +# select armci network as (Comex) MPI-1 two-sided +configopts += ' --with-mpi-ts' + +sanity_check_paths = { + 'files': ['bin/adjust.x', 'bin/collisions.x', 'bin/ga-config', 'lib/libarmci.a', + 'lib/libcomex.a', 'lib/libga.a'], + 'dirs': ['include'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/g/GnuTLS/GnuTLS-3.7.8-GCCcore-12.3.0.eb b/easybuild/easyconfigs/g/GnuTLS/GnuTLS-3.7.8-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..320c4782a22 --- /dev/null +++ b/easybuild/easyconfigs/g/GnuTLS/GnuTLS-3.7.8-GCCcore-12.3.0.eb @@ -0,0 +1,48 @@ +easyblock = 'ConfigureMake' + +name = 'GnuTLS' +version = '3.7.8' + +homepage = 'https://www.gnutls.org' +description = """GnuTLS is a secure communications library implementing the SSL, TLS + and DTLS protocols and technologies around them. It provides a simple + C language application programming interface (API) to access the secure + communications protocols as well as APIs to parse and write X.509, PKCS #12, + OpenPGP and other required structures. It is aimed to be portable + and efficient with focus on security and interoperability.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://www.gnupg.org/ftp/gcrypt/gnutls/v%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['c58ad39af0670efe6a8aee5e3a8b2331a1200418b64b7c51977fb396d4617114'] + +builddependencies = [ + ('binutils', '2.40'), + ('pkgconf', '1.9.5'), +] + +dependencies = [ + ('GMP', '6.2.1'), + ('nettle', '3.9.1'), + ('Guile', '3.0.9'), + ('libtasn1', '4.19.0'), + ('libidn2', '2.3.7'), + ('p11-kit', '0.25.3'), + ('zlib', '1.2.13'), + ('zstd', '1.5.5'), +] + +configopts = "--with-guile-site-dir=%(installdir)s/lib/guile --enable-openssl-compatibility " +configopts += "--with-guile-site-ccache-dir=%(installdir)s/lib/guile/site-ccache " +configopts += "--with-guile-extension-dir=%(installdir)s/lib/guile/extensions " +configopts += "--with-idn --with-p11-kit --with-zlib --with-zstd --without-brotli --without-tpm --without-tpm2" + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['certtool', 'gnutls-cli', 'gnutls-cli-debug', + 'gnutls-serv', 'ocsptool', 'psktool', 'srptool']] + + ['lib/libgnutls%s' % x for x in ['.%s' % SHLIB_EXT, 'xx.%s' % SHLIB_EXT, '-openssl.%s' % SHLIB_EXT]], + 'dirs': ['include/gnutls', 'lib/guile'], +} + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/g/Gradio/Gradio-4.19.0-gfbf-2023a.eb b/easybuild/easyconfigs/g/Gradio/Gradio-4.19.0-gfbf-2023a.eb new file mode 100644 index 00000000000..3f949981b52 --- /dev/null +++ b/easybuild/easyconfigs/g/Gradio/Gradio-4.19.0-gfbf-2023a.eb @@ -0,0 +1,119 @@ +easyblock = 'PythonBundle' + +name = 'Gradio' +version = '4.19.0' + +homepage = "https://www.gradio.app" +description = """ +Gradio is an open-source Python package that allows you to quickly build a demo or web +application for your machine learning model, API, or any arbitrary Python function. +""" + +toolchain = {'name': 'gfbf', 'version': '2023a'} + +builddependencies = [ + ('binutils', '2.40'), + ('Rust', '1.75.0'), + ('maturin', '1.4.0', '-Rust-1.75.0'), + ('hatchling', '1.18.0'), + ('poetry', '1.5.1'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('PyYAML', '6.0'), + ('pydantic', '2.5.3'), + ('matplotlib', '3.7.2'), + ('Pillow', '10.0.0'), + ('tqdm', '4.66.1'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('aiofiles', '23.2.1', { + 'checksums': ['84ec2218d8419404abcb9f0c02df3f34c6e0a68ed41072acfb1cef5cbc29051a'], + }), + ('toolz', '0.12.1', { + 'checksums': ['ecca342664893f177a13dac0e6b41cbd8ac25a358e5f215316d43e2100224f4d'], + }), + ('altair', '5.2.0', { + 'checksums': ['2ad7f0c8010ebbc46319cc30febfb8e59ccf84969a201541c207bc3a4fa6cf81'], + }), + ('starlette', '0.36.3', { + 'checksums': ['90a671733cfb35771d8cc605e0b679d23b992f8dcfad48cc60b38cb29aeb7080'], + }), + ('typing-extensions', '4.8.0', { + 'source_tmpl': 'typing_extensions-%(version)s.tar.gz', + 'checksums': ['df8e4339e9cb77357558cbdbceca33c303714cf861d1eef15e1070055ae8b7ef'], + }), + ('fastapi', '0.109.2', { + 'checksums': ['f3817eac96fe4f65a2ebb4baa000f394e55f5fccdaf7f75250804bc58f354f73'], + }), + ('ffmpy', '0.3.2', { + 'checksums': ['475ebfff1044661b8d969349dbcd2db9bf56d3ee78c0627e324769b49a27a78f'], + }), + ('websockets', '11.0.3', { + 'checksums': ['88fc51d9a26b10fc331be344f1781224a375b78488fc343620184e95a4b27016'], + }), + ('gradio-client', '0.10.0', { + 'source_tmpl': 'gradio_client-%(version)s.tar.gz', + 'checksums': ['feaee70f18363d76f81a7d25fc3456f40ed5f92417e642c8f1bf86dc65e3a981'], + }), + ('huggingface-hub', '0.20.3', { + 'source_tmpl': 'huggingface_hub-%(version)s.tar.gz', + 'checksums': ['94e7f8e074475fbc67d6a71957b678e1b4a74ff1b64a644fd6cbb83da962d05d'], + }), + ('orjson', '3.9.14', { + 'checksums': ['06fb40f8e49088ecaa02f1162581d39e2cf3fd9dbbfe411eb2284147c99bad79'], + }), + ('pydub', '0.25.1', { + 'checksums': ['980a33ce9949cab2a569606b65674d748ecbca4f0796887fd6f46173a7b0d30f'], + }), + ('python-multipart', '0.0.9', { + 'modulename': 'multipart', + 'source_tmpl': 'python_multipart-%(version)s.tar.gz', + 'checksums': ['03f54688c663f1b7977105f021043b0793151e4cb1c1a9d4a11fc13d622c4026'], + }), + ('ruff', '0.2.1', { + 'checksums': ['3b42b5d8677cd0c72b99fcaf068ffc62abb5a19e71b4a3b9cfa50658a0af02f1'], + }), + ('typer', '0.9.0', { + 'checksums': ['50922fd79aea2f4751a8e0408ff10d2662bd0c8bbfa84755a699f3bada2978b2'], + }), + ('h11', '0.14.0', { + 'checksums': ['8f19fbbe99e72420ff35c00b27a34cb9937e902a8b810e2c88300c6f0a3b699d'], + }), + ('uvicorn', '0.27.1', { + 'checksums': ['3d9a267296243532db80c83a959a3400502165ade2c1338dea4e67915fd4745a'], + }), + ('anyio', '4.2.0', { + 'checksums': ['e1875bb4b4e2de1669f4bc7869b6d3f54231cdced71605e6e64c9be77e3be50f'], + }), + ('httpcore', '1.0.3', { + 'checksums': ['5c0f9546ad17dac4d0772b0808856eb616eb8b48ce94f49ed819fd6982a8a544'], + }), + ('sniffio', '1.3.0', { + 'checksums': ['e60305c5e5d314f5389259b7f22aaa33d8f7dee49763119234af3755c55b9101'], + }), + ('httpx', '0.26.0', { + 'checksums': ['451b55c30d5185ea6b23c2c793abf9bb237d2a7dfb901ced6ff69ad37ec1dfaf'], + }), + ('importlib-resources', '6.1.1', { + 'source_tmpl': 'importlib_resources-%(version)s.tar.gz', + 'checksums': ['3893a00122eafde6894c59914446a512f728a0c1a45f9bb9b63721b6bacf0b4a'], + }), + ('Jinja2', '3.1.3', { + 'checksums': ['ac8bd6544d4bb2c9792bf3a159e80bba8fda7f07e81bc3aed565432d5925ba90'], + }), + ('tomlkit', '0.12.0', { + 'checksums': ['01f0477981119c7d8ee0f67ebe0297a7c95b14cf9f4b102b45486deb77018716'], + }), + ('gradio', version, { + 'checksums': ['e77e3ce8a4113865abd1dcf92cc9426d9da4896e0a6fd2824a0c90ec751dd442'], + }), +] + +moduleclass = 'ai' diff --git a/easybuild/easyconfigs/g/Graphene/Graphene-1.10.8-GCCcore-13.3.0.eb b/easybuild/easyconfigs/g/Graphene/Graphene-1.10.8-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..d2ff38adec0 --- /dev/null +++ b/easybuild/easyconfigs/g/Graphene/Graphene-1.10.8-GCCcore-13.3.0.eb @@ -0,0 +1,32 @@ +easyblock = 'MesonNinja' + +name = 'Graphene' +version = '1.10.8' + +homepage = 'https://ebassi.github.io/graphene/' +description = "Graphene is a thin layer of types for graphic libraries" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +github_account = 'ebassi' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['922dc109d2dc5dc56617a29bd716c79dd84db31721a8493a13a5f79109a4a4ed'] + +builddependencies = [ + ('Meson', '1.4.0'), + ('Ninja', '1.12.1'), + ('pkgconf', '2.2.0'), + ('GObject-Introspection', '1.80.1'), + ('binutils', '2.42'), +] +dependencies = [('GLib', '2.80.4')] + +configopts = "-Dgobject_types=true -Dintrospection=enabled" + +sanity_check_paths = { + 'files': ['lib/libgraphene-1.0.%s' % SHLIB_EXT, 'share/gir-1.0/Graphene-1.0.gir'], + 'dirs': ['include/graphene-1.0', 'lib/pkgconfig'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/g/GraphicsMagick/GraphicsMagick-1.3.45-GCCcore-13.3.0.eb b/easybuild/easyconfigs/g/GraphicsMagick/GraphicsMagick-1.3.45-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..63340e41506 --- /dev/null +++ b/easybuild/easyconfigs/g/GraphicsMagick/GraphicsMagick-1.3.45-GCCcore-13.3.0.eb @@ -0,0 +1,51 @@ +easyblock = 'ConfigureMake' + +name = 'GraphicsMagick' +version = '1.3.45' + +homepage = 'http://www.graphicsmagick.org/' +description = """GraphicsMagick is the swiss army knife of image processing.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +source_urls = [ + SOURCEFORGE_SOURCE, + 'ftp://ftp.graphicsmagick.org/pub/GraphicsMagick/%(version_major_minor)s/', +] +sources = [SOURCE_TAR_XZ] +patches = [ + 'GraphicsMagick_pkgconfig_libtiff.patch' +] +checksums = [ + {'GraphicsMagick-1.3.45.tar.xz': 'dcea5167414f7c805557de2d7a47a9b3147bcbf617b91f5f0f4afe5e6543026b'}, + {'GraphicsMagick_pkgconfig_libtiff.patch': '25b4c5361f30e23c809a078ac4b26e670d2b8341496323480037e2095d969294'}, +] + +builddependencies = [ + ('binutils', '2.42'), + ('Autotools', '20231222'), +] + +dependencies = [ + ('X11', '20240607'), + ('bzip2', '1.0.8'), + ('freetype', '2.13.2'), + ('libpng', '1.6.43'), + ('libjpeg-turbo', '3.0.1'), + ('LibTIFF', '4.6.0'), + ('libxml2', '2.12.7'), + ('XZ', '5.4.5'), + ('zlib', '1.3.1'), + ('Ghostscript', '10.03.1'), +] + +modextrapaths = {'CPATH': ['include/GraphicsMagick']} + +sanity_check_paths = { + 'files': ['bin/gm', 'lib/libGraphicsMagick.a', 'lib/libGraphicsMagick++.a', + 'lib/libGraphicsMagickWand.a'], + 'dirs': ['include/GraphicsMagick', 'lib/pkgconfig'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/Greenlet/Greenlet-3.1.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/g/Greenlet/Greenlet-3.1.1-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..b54b7ecfcc3 --- /dev/null +++ b/easybuild/easyconfigs/g/Greenlet/Greenlet-3.1.1-GCCcore-13.3.0.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonPackage' + +name = 'Greenlet' +version = '3.1.1' + +homepage = 'https://github.com/python-greenlet/greenlet' + +description = """The greenlet package is a spin-off of Stackless, a version of CPython that +supports micro-threads called "tasklets". Tasklets run pseudo-concurrently (typically in a single +or a few OS-level threads) and are synchronized with data exchanges on "channels". +A "greenlet", on the other hand, is a still more primitive notion of micro-thread with no implicit +scheduling; coroutines, in other words. This is useful when you want to control exactly when your code runs. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +builddependencies = [('binutils', '2.42')] +dependencies = [('Python', '3.12.3')] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['4ce3ac6cdb6adf7946475d7ef31777c26d94bccc377e070a7986bd2d5c515467'] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/g/gubbins/gubbins-2.4.0.eb b/easybuild/easyconfigs/g/Gubbins/Gubbins-2.4.0.eb similarity index 98% rename from easybuild/easyconfigs/g/gubbins/gubbins-2.4.0.eb rename to easybuild/easyconfigs/g/Gubbins/Gubbins-2.4.0.eb index c209965f2eb..7b9bbd1be45 100644 --- a/easybuild/easyconfigs/g/gubbins/gubbins-2.4.0.eb +++ b/easybuild/easyconfigs/g/Gubbins/Gubbins-2.4.0.eb @@ -10,7 +10,7 @@ easyblock = 'Conda' -name = 'gubbins' +name = 'Gubbins' version = '2.4.0' homepage = 'https://sanger-pathogens.github.io/gubbins' diff --git a/easybuild/easyconfigs/g/Gubbins/Gubbins-3.3.5-foss-2022b.eb b/easybuild/easyconfigs/g/Gubbins/Gubbins-3.3.5-foss-2022b.eb new file mode 100644 index 00000000000..99c52d785fd --- /dev/null +++ b/easybuild/easyconfigs/g/Gubbins/Gubbins-3.3.5-foss-2022b.eb @@ -0,0 +1,65 @@ +# This easyconfig was created by the BEAR Software team at the University of Birmingham. +easyblock = 'ConfigureMake' + +name = 'Gubbins' +version = '3.3.5' + +homepage = "https://nickjcroucher.github.io/gubbins/" +description = """Gubbins (Genealogies Unbiased By recomBinations In Nucleotide Sequences) is an algorithm that + iteratively identifies loci containing elevated densities of base substitutions, which are marked as recombinations, + while concurrently constructing a phylogeny based on the putative point mutations outside of these regions. + Simulations demonstrate the algorithm generates highly accurate reconstructions under realistic models of short-term + bacterial evolution, and can be run in only a few hours on alignments of hundreds of bacterial genome sequences.""" + +toolchain = {'name': 'foss', 'version': '2022b'} + +source_urls = ['https://github.com/nickjcroucher/gubbins/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['4ee363f82708bdda0c00d1c6c334cf20127bd852ee488619f61140771a279774'] + +builddependencies = [ + ('Autotools', '20220317'), + ('Autoconf-archive', '2023.02.20'), + ('pkgconf', '1.9.3'), + ('Check', '0.15.2'), + ('subunit', '1.4.3'), +] + +dependencies = [ + ('Python', '3.10.8'), + ('Biopython', '1.81'), + ('DendroPy', '4.5.2'), + ('numba', '0.58.1'), + ('SciPy-bundle', '2023.02'), + ('FastTree', '2.1.11'), + ('IQ-TREE', '2.2.2.6'), + ('rapidNJ', '2.3.3'), + ('RAxML', '8.2.12', '-avx2'), + ('RAxML-NG', '1.2.0'), + ('SKA2', '0.3.7'), + ('dill', '0.3.7'), + ('multiprocess', '0.70.15'), +] + +preconfigopts = "autoreconf -i && " +# runtest = 'check' # runs the Python tests and this causes package to be installed into the Python install +postinstallcmds = [ + """sed -i 's/self.executable = "iqtree"/self.executable = "iqtree2"/' python/gubbins/treebuilders.py""", + "cd python && python -m pip install --prefix %(installdir)s --no-build-isolation . " +] + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +sanity_check_paths = { + 'files': ['bin/gubbins', 'lib/libgubbins.%s' % SHLIB_EXT], + 'dirs': [], +} + +sanity_check_commands = [ + "gubbins --help", + "run_gubbins.py --version", + 'python -s -c "import gubbins"', + 'PIP_DISABLE_PIP_VERSION_CHECK=true python -s -m pip check', +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/Guile/Guile-2.0.14-GCCcore-13.3.0.eb b/easybuild/easyconfigs/g/Guile/Guile-2.0.14-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..06a1dc6a05a --- /dev/null +++ b/easybuild/easyconfigs/g/Guile/Guile-2.0.14-GCCcore-13.3.0.eb @@ -0,0 +1,41 @@ +easyblock = 'ConfigureMake' + +name = 'Guile' +version = '2.0.14' + +homepage = 'http://www.gnu.org/software/guile' +description = """Guile is the GNU Ubiquitous Intelligent Language for Extensions, the official extension language for +the GNU operating system. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['8aeb2f353881282fe01694cce76bb72f7ffdd296a12c7a1a39255c27b0dfe5f1'] + +builddependencies = [ + ('binutils', '2.42'), + ('pkgconf', '2.2.0'), +] + +dependencies = [ + ('gc', '8.2.6'), + ('GMP', '6.3.0'), + ('libffi', '3.4.5'), + ('libunistring', '1.2'), + ('libtool', '2.4.7'), + ('libreadline', '8.2'), + ('XZ', '5.4.5'), +] + +configopts = " --enable-error-on-warning=no" + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["guile", 'guile-config', 'guile-snarf', 'guile-tools']] + + ["lib/libguile-%(version_major_minor)s.a", + "include/guile/%(version_major_minor)s/libguile.h"], + 'dirs': [] +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/g/Guile/Guile-3.0.10-GCCcore-13.3.0.eb b/easybuild/easyconfigs/g/Guile/Guile-3.0.10-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..46917679856 --- /dev/null +++ b/easybuild/easyconfigs/g/Guile/Guile-3.0.10-GCCcore-13.3.0.eb @@ -0,0 +1,46 @@ +easyblock = 'ConfigureMake' + +name = 'Guile' +version = '3.0.10' + +homepage = 'https://www.gnu.org/software/guile/' + +description = """ + Guile is a programming language, designed to help programmers create flexible + applications that can be extended by users or other programmers with plug-ins, + modules, or scripts. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['2dbdbc97598b2faf31013564efb48e4fed44131d28e996c26abe8a5b23b56c2a'] + +builddependencies = [ + ('Autotools', '20231222'), + ('binutils', '2.42'), + ('pkgconf', '2.2.0'), +] + +dependencies = [ + ('gc', '8.2.6'), + ('GMP', '6.3.0'), + ('libffi', '3.4.5'), + ('libunistring', '1.2'), +] + +postinstallcmds = ["cd %(installdir)s/bin && ln -s guile guile%(version_major)s"] + +sanity_check_paths = { + 'files': ['bin/guild', 'bin/guile', 'bin/guile-config', + 'bin/guile-snarf', 'bin/guile-tools', + 'include/guile/%(version_major_minor)s/libguile.h', + 'lib/libguile-%(version_major_minor)s.a', + 'lib/libguile-%%(version_major_minor)s.%s' % SHLIB_EXT], + 'dirs': ['include/guile/%(version_major_minor)s/libguile', + 'lib/guile/%(version_major_minor)s/ccache'], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/g/Gurobi/Gurobi-11.0.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/g/Gurobi/Gurobi-11.0.2-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..0e8c4d8115e --- /dev/null +++ b/easybuild/easyconfigs/g/Gurobi/Gurobi-11.0.2-GCCcore-12.3.0.eb @@ -0,0 +1,63 @@ +name = 'Gurobi' +version = '11.0.2' + +homepage = 'https://www.gurobi.com' +description = """The Gurobi Optimizer is a state-of-the-art solver for mathematical programming. +The solvers in the Gurobi Optimizer were designed from the ground up to exploit modern +architectures and multi-core processors, using the most advanced implementations of the +latest algorithms.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://packages.gurobi.com/%(version_major_minor)s/'] +local_archs = {'aarch64': 'armlinux64', 'x86_64': 'linux64'} +sources = ['gurobi%%(version)s_%s.tar.gz' % local_archs[ARCH]] +patches = ['Gurobi-11.0.0_use-eb-python-gurobi-shell.patch'] +checksums = [ + {'gurobi11.0.2_linux64.tar.gz': 'f43ac8a3edb987b9a0a61452acd9d8dbe9eb37368c6da7ce36e5247cb2a1a368', + 'gurobi11.0.2_armlinux64.tar.gz': '311b38a89717e26f3f829479ef8e6776674b2711c427a90b84ac9978acd19ff2'}, + {'Gurobi-11.0.0_use-eb-python-gurobi-shell.patch': + '566473a3ba4e35b0e74595368f9f4133fc4a3c97cca84154c4b938645786e663'}, +] + +builddependencies = [ + ('binutils', '2.40'), +] + +dependencies = [ + ('Python', '3.11.3'), +] + +exts_defaultclass = 'PythonPackage' + +exts_default_options = { + 'source_urls': [PYPI_SOURCE], + 'download_dep_fail': True, + 'use_pip': True, +} + +exts_list = [ + ('gurobipy', version, { + 'sources': ['gurobipy-%(version)s-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_%(arch)s.whl'], + 'checksums': [{ + 'gurobipy-%(version)s-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_aarch64.whl': + '871e818026c8f288d7440fcd4b842becdf1006f43495fc4f6e3ec6d9b8ba3d7a', + 'gurobipy-%(version)s-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.whl': + '86265b7a9a8f3e531c1bbee6e61c1e7d0b68264e976795b4cf7aec68b9e66eb8', + }], + }), +] + +# remove bundled Python interpreter in favour of the dependency in EB +postinstallcmds = ['rm %(installdir)s/bin/python*'] + +# license is mandatory for installation +# use EB_GUROBI_LICENSE_FILE environment variable, or +# uncomment and modify the following variable: +# license_file = '/path/to/my-license-file' + +modloadmsg = """Gurobi shell based on Python %(pyver)s can be launched with command `gurobi.sh` +Gurobi Python Interface can be loaded in Python %(pyver)s with 'import gurobipy' +""" + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/g/Gymnasium/Gymnasium-0.29.1-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/g/Gymnasium/Gymnasium-0.29.1-foss-2023a-CUDA-12.1.1.eb new file mode 100644 index 00000000000..b9248ab9aac --- /dev/null +++ b/easybuild/easyconfigs/g/Gymnasium/Gymnasium-0.29.1-foss-2023a-CUDA-12.1.1.eb @@ -0,0 +1,54 @@ +easyblock = 'PythonBundle' + +name = 'Gymnasium' +version = '0.29.1' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://gymnasium.farama.org/' +description = """ +Gymnasium is an open source Python library for developing and comparing reinforcement learning +algorithms by providing a standard API to communicate between learning algorithms and +environments, as well as a standard set of environments compliant with that API. +""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [ + ('CMake', '3.26.3'), + ('SWIG', '4.1.1'), +] + +dependencies = [ + ('CUDA', '12.1.1', '', SYSTEM), + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('OpenCV', '4.8.1', versionsuffix + '-contrib'), + ('pygame', '2.5.2'), + ('MuJoCo', '3.1.4'), +] + +use_pip = True + +exts_list = [ + ('cloudpickle', '3.0.0', { + 'checksums': ['996d9a482c6fb4f33c1a35335cf8afd065d2a56e973270364840712d9131a882'], + }), + ('Farama-Notifications', '0.0.4', { + 'checksums': ['13fceff2d14314cf80703c8266462ebf3733c7d165336eee998fc58e545efd18'], + }), + ('box2d-py', '2.3.8', { + 'modulename': 'Box2D', + 'checksums': ['bdacfbbc56079bb317548efe49d3d5a86646885cc27f4a2ee97e4b2960921ab7'], + }), + ('gymnasium', version, { + 'use_pip_extras': 'all', + 'checksums': ['1a532752efcb7590478b1cc7aa04f608eb7a2fdad5570cd217b66b6a35274bb1'], + }), +] + +local_envs = ['box2d', 'classic_control', 'mujoco', 'toy_text'] +sanity_check_commands = ["python -c 'import gymnasium.envs.%s'" % e for e in local_envs] + +sanity_pip_check = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/g/Gymnasium/Gymnasium-0.29.1-foss-2023a.eb b/easybuild/easyconfigs/g/Gymnasium/Gymnasium-0.29.1-foss-2023a.eb new file mode 100644 index 00000000000..e389e3ef7d7 --- /dev/null +++ b/easybuild/easyconfigs/g/Gymnasium/Gymnasium-0.29.1-foss-2023a.eb @@ -0,0 +1,52 @@ +easyblock = 'PythonBundle' + +name = 'Gymnasium' +version = '0.29.1' + +homepage = 'https://gymnasium.farama.org/' +description = """ +Gymnasium is an open source Python library for developing and comparing reinforcement learning +algorithms by providing a standard API to communicate between learning algorithms and +environments, as well as a standard set of environments compliant with that API. +""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [ + ('CMake', '3.26.3'), + ('SWIG', '4.1.1'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('OpenCV', '4.8.1', '-contrib'), + ('pygame', '2.5.2'), + ('MuJoCo', '3.1.4'), +] + +use_pip = True + +exts_list = [ + ('cloudpickle', '3.0.0', { + 'checksums': ['996d9a482c6fb4f33c1a35335cf8afd065d2a56e973270364840712d9131a882'], + }), + ('Farama-Notifications', '0.0.4', { + 'checksums': ['13fceff2d14314cf80703c8266462ebf3733c7d165336eee998fc58e545efd18'], + }), + ('box2d-py', '2.3.8', { + 'modulename': 'Box2D', + 'checksums': ['bdacfbbc56079bb317548efe49d3d5a86646885cc27f4a2ee97e4b2960921ab7'], + }), + ('gymnasium', version, { + 'use_pip_extras': 'all', + 'checksums': ['1a532752efcb7590478b1cc7aa04f608eb7a2fdad5570cd217b66b6a35274bb1'], + }), +] + +local_envs = ['box2d', 'classic_control', 'mujoco', 'toy_text'] +sanity_check_commands = ["python -c 'import gymnasium.envs.%s'" % e for e in local_envs] + +sanity_pip_check = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/g/g2lib/g2lib-3.2.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/g/g2lib/g2lib-3.2.0-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..04674a29ff7 --- /dev/null +++ b/easybuild/easyconfigs/g/g2lib/g2lib-3.2.0-GCCcore-13.2.0.eb @@ -0,0 +1,32 @@ +name = 'g2lib' +version = '3.2.0' + +homepage = 'https://www.nco.ncep.noaa.gov/pmb/codes/GRIB2/' +description = """Library contains GRIB2 encoder/decoder and search/indexing routines.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = [homepage] +sources = ['%(name)s-%(version)s.tar'] +patches = [ + '%(name)s-%(version)s_makefile.patch', +] +checksums = [ + '9d3866de32e13e80798bfb08dbbea9223f32cec3fce3c57b6838e76f27d5a1d3', # g2lib-3.2.0.tar + 'e434394a6ec8bd68dbd57e3fdb44c47372b07380e362ed955bb038b78dd81812', # g2lib-3.2.0_makefile.patch +] + +builddependencies = [('binutils', '2.40')] + +dependencies = [ + ('JasPer', '4.0.0'), + ('libpng', '1.6.40'), +] + +buildopts = 'CFLAGS="$CFLAGS -DLINUXG95 -D__64BIT__" FC=$FC CC=$CC ' +buildopts += 'FFLAGS="$FFLAGS -fno-range-check -fallow-invalid-boz -fallow-argument-mismatch -I."' + +# parallel build tends to fail +parallel = 1 + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/g/gap/gap-4.13.0-foss-2023b.eb b/easybuild/easyconfigs/g/gap/gap-4.13.0-foss-2023b.eb new file mode 100644 index 00000000000..248ab5ded0a --- /dev/null +++ b/easybuild/easyconfigs/g/gap/gap-4.13.0-foss-2023b.eb @@ -0,0 +1,55 @@ +easyblock = 'ConfigureMake' + +name = 'gap' +version = '4.13.0' + +homepage = 'https://www.gap-system.org' +description = """GAP is a system for computational discrete algebra, +with particular emphasis on Computational Group Theory.""" + +toolchain = {'name': 'foss', 'version': '2023b'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.gap-system.org/pub/gap/gap-%(version_major_minor)s/tar.gz/'] +sources = [SOURCE_TAR_GZ] +checksums = ['cc76ecbe33d6719450a593e613fb87e9e4247faa876f632dd0f97c398f92265d'] + +unpack_options = '--strip-components=1' + +builddependencies = [ + ('Perl', '5.38.0'), # needed to install NormalizInterface +] + +dependencies = [ + ('GMP', '6.3.0'), + ('libreadline', '8.2'), + ('zlib', '1.2.13'), + ('4ti2', '1.6.10'), # needed by 4ti2Interface, HeLP + ('cddlib', '0.94m'), # needed by CddInterface + ('cURL', '8.3.0'), # needed by curlInterface + ('lrslib', '7.2'), # needed by HeLP + ('ncurses', '6.4'), # needed by Browse + ('Normaliz', '3.10.3'), # needed by NormalizInterface, HeLP + ('Singular', '4.4.0'), # needed by singular + ('ZeroMQ', '4.3.5'), # needed by ZeroMQInterface +] + +# install target is incomplete and hardcodes the build path +buildininstalldir = True + +# Disable bundled script to download and build Normaliz +prebuildopts = "sed -i 's|./build-normaliz.sh|continue # build-normaliz.sh|' bin/BuildPackages.sh && " +# BuildPackages.sh tries to build any GAP packages that require compilation +# If one fails due to missing dependencies, it's skipped automatically +buildopts = ' && cd pkg && ../bin/BuildPackages.sh' + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['gap', 'gac']] + + ['include/gap/%s.h' % h for h in ['gap', 'system', 'version']] + + ['lib/libgap.%s' % SHLIB_EXT], + 'dirs': ['share/gap'] +} + +sanity_check_commands = ["gap tst/testinstall.g"] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/g/gawk/gawk-5.3.0-GCC-12.3.0.eb b/easybuild/easyconfigs/g/gawk/gawk-5.3.0-GCC-12.3.0.eb new file mode 100644 index 00000000000..8c63821d169 --- /dev/null +++ b/easybuild/easyconfigs/g/gawk/gawk-5.3.0-GCC-12.3.0.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'gawk' +version = '5.3.0' + +homepage = 'https://www.gnu.org/software/gawk' +description = """The awk utility interprets a special-purpose programming language that makes it possible to handle +simple data-reformatting jobs with just a few lines of code.""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['378f8864ec21cfceaa048f7e1869ac9b4597b449087caf1eb55e440d30273336'] + +sanity_check_paths = { + 'files': ['bin/gawk'], + 'dirs': [], +} + +sanity_check_commands = ["gawk --help"] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/g/gc/gc-8.2.6-GCCcore-13.3.0.eb b/easybuild/easyconfigs/g/gc/gc-8.2.6-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..3a120e6a4e9 --- /dev/null +++ b/easybuild/easyconfigs/g/gc/gc-8.2.6-GCCcore-13.3.0.eb @@ -0,0 +1,42 @@ +easyblock = 'ConfigureMake' + +name = 'gc' +version = '8.2.6' +local_libatomic_version = '7.8.2' + +homepage = 'https://hboehm.info/gc/' +description = """The Boehm-Demers-Weiser conservative garbage collector can be used as a +garbage collecting replacement for C malloc or C++ new. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = [ + 'https://github.com/ivmai/bdwgc/releases/download/v%(version)s/', # preferred for gc-%(version)s.tar.gz + 'https://hboehm.info/gc/gc_source/', # alternate for gc-%(version)s.tar.gz + 'https://github.com/ivmai/libatomic_ops/releases/download/v%s/' % local_libatomic_version, +] +sources = [ + SOURCE_TAR_GZ, + 'libatomic_ops-%s.tar.gz' % local_libatomic_version, +] +checksums = [ + {'gc-8.2.6.tar.gz': 'b9183fe49d4c44c7327992f626f8eaa1d8b14de140f243edb1c9dcff7719a7fc'}, + {'libatomic_ops-7.8.2.tar.gz': 'd305207fe207f2b3fb5cb4c019da12b44ce3fcbc593dfd5080d867b1a2419b51'}, +] + +builddependencies = [ + ('binutils', '2.42'), +] + +preconfigopts = 'ln -s %(builddir)s/libatomic_ops*/ libatomic_ops && ' + +configopts = "--enable-static" + +sanity_check_paths = { + 'files': ['include/gc.h', 'lib/libcord.a', 'lib/libcord.%s' % SHLIB_EXT, + 'lib/libgc.a', 'lib/libgc.%s' % SHLIB_EXT], + 'dirs': ['include/gc', 'share'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/g/genomepy/genomepy-0.16.1-foss-2023a.eb b/easybuild/easyconfigs/g/genomepy/genomepy-0.16.1-foss-2023a.eb new file mode 100644 index 00000000000..345af8fe325 --- /dev/null +++ b/easybuild/easyconfigs/g/genomepy/genomepy-0.16.1-foss-2023a.eb @@ -0,0 +1,56 @@ +easyblock = 'PythonBundle' + +name = 'genomepy' +version = '0.16.1' + +homepage = 'https://github.com/vanheeringen-lab/genomepy' +description = "genomepy is designed to provide a simple and straightforward way to download and use genomic data" + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [('hatchling', '1.18.0')] +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('SciPy-bundle', '2023.07'), + ('tqdm', '4.66.1'), + ('Biopython', '1.83'), + ('mygene', '3.2.2'), + ('pyfaidx', '0.8.1.1'), + ('PyYAML', '6.0'), + ('protobuf-python', '4.24.0'), +] + +use_pip = True + +exts_list = [ + ('diskcache', '5.6.3', { + 'checksums': ['2c3a3fa2743d8535d832ec61c2054a1641f41775aa7c556758a109941e33e4fc'], + }), + ('loguru', '0.7.2', { + 'checksums': ['e671a53522515f34fd406340ee968cb9ecafbc4b36c679da03c18fd8d0bd51ac'], + }), + ('mysql-connector-python', '8.4.0', { + 'modulename': 'mysql.connector', + 'sources': ['mysql_connector_python-%(version)s-py2.py3-none-any.whl'], + 'checksums': ['35939c4ff28f395a5550bae67bafa4d1658ea72ea3206f457fff64a0fbec17e4'], + }), + ('norns', '0.1.6', { + 'preinstallopts': "sed -i '/nose/d' setup.py && ", + 'checksums': ['1f3c6ccbe79b2cb3076f66a352cd76462593adbabe9ebb262f879a9d0a6634e4'], + }), + (name, version, { + 'checksums': ['22e81827acfdb4d9e6adda1f8e4cfafbb97f1c1788348e86b930c9daa51088c5'], + }), +] + +sanity_check_paths = { + 'files': ['bin/genomepy'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["genomepy --help"] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/gensim/gensim-4.3.2-foss-2023a.eb b/easybuild/easyconfigs/g/gensim/gensim-4.3.2-foss-2023a.eb new file mode 100644 index 00000000000..cb315af1a31 --- /dev/null +++ b/easybuild/easyconfigs/g/gensim/gensim-4.3.2-foss-2023a.eb @@ -0,0 +1,31 @@ +easyblock = 'PythonBundle' + +name = 'gensim' +version = '4.3.2' + +homepage = 'https://radimrehurek.com/gensim' +description = """Gensim is a Python library for topic modelling, document indexing and similarity retrieval with + large corpora.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('wrapt', '1.15.0'), +] + +use_pip = True + +exts_list = [ + ('smart_open', '7.0.4', { + 'checksums': ['62b65852bdd1d1d516839fcb1f6bc50cd0f16e05b4ec44b52f43d38bcb838524'], + }), + (name, version, { + 'checksums': ['99ac6af6ffd40682e70155ed9f92ecbf4384d59fb50af120d343ea5ee1b308ab'], + }), +] + +sanity_pip_check = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.22.5-GCCcore-13.3.0.eb b/easybuild/easyconfigs/g/gettext/gettext-0.22.5-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..b5e182315e9 --- /dev/null +++ b/easybuild/easyconfigs/g/gettext/gettext-0.22.5-GCCcore-13.3.0.eb @@ -0,0 +1,38 @@ +easyblock = 'ConfigureMake' + +name = 'gettext' +version = '0.22.5' + +homepage = 'https://www.gnu.org/software/gettext/' +description = """GNU 'gettext' is an important step for the GNU Translation Project, as it is an asset on which we may +build many other steps. This package offers to programmers, translators, and even users, a well integrated set of tools +and documentation""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['ec1705b1e969b83a9f073144ec806151db88127f5e40fe5a94cb6c8fa48996a0'] + +builddependencies = [('binutils', '2.42')] + +dependencies = [ + ('libxml2', '2.12.7'), + ('ncurses', '6.5'), + ('libiconv', '1.17'), +] + +configopts = '--without-emacs --with-libxml2-prefix=$EBROOTLIBXML2' + +sanity_check_paths = { + 'files': ['bin/gettext', 'lib/libasprintf.a', 'lib/libasprintf.%s' % SHLIB_EXT, + 'lib/libgettextpo.a', 'lib/libgettextpo.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +sanity_check_commands = [ + "gettext --help", + "msginit --help", +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.22.5.eb b/easybuild/easyconfigs/g/gettext/gettext-0.22.5.eb new file mode 100644 index 00000000000..9c596a9eb89 --- /dev/null +++ b/easybuild/easyconfigs/g/gettext/gettext-0.22.5.eb @@ -0,0 +1,39 @@ +easyblock = 'ConfigureMake' + +name = 'gettext' +version = '0.22.5' + +homepage = 'https://www.gnu.org/software/gettext/' +description = """GNU 'gettext' is an important step for the GNU Translation Project, as it is an asset on which we may +build many other steps. This package offers to programmers, translators, and even users, a well integrated set of tools +and documentation""" + +# This is a basic stripped down version of gettext without any +# dependencies on other packages used as initial builddep for XZ +# It is the first step in the cyclic dependency chain of +# XZ -> libxml2 -> gettext -> XZ + +toolchain = SYSTEM + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['ec1705b1e969b83a9f073144ec806151db88127f5e40fe5a94cb6c8fa48996a0'] + +dependencies = [ + ('ncurses', '6.5'), +] + +configopts = '--without-emacs --with-included-libxml --without-xz --without-bzip2' + +sanity_check_paths = { + 'files': ['bin/gettext', 'lib/libasprintf.a', 'lib/libasprintf.%s' % SHLIB_EXT, + 'lib/libgettextpo.a', 'lib/libgettextpo.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +sanity_check_commands = [ + "gettext --help", + "msginit --help", +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/g/gfbf/gfbf-2024.05.eb b/easybuild/easyconfigs/g/gfbf/gfbf-2024.05.eb new file mode 100644 index 00000000000..f0c1233309a --- /dev/null +++ b/easybuild/easyconfigs/g/gfbf/gfbf-2024.05.eb @@ -0,0 +1,20 @@ +easyblock = 'Toolchain' + +name = 'gfbf' +version = '2024.05' + +homepage = '(none)' +description = """GNU Compiler Collection (GCC) based compiler toolchain, including + FlexiBLAS (BLAS and LAPACK support) and (serial) FFTW.""" + +toolchain = SYSTEM + +local_gccver = '13.3.0' + +dependencies = [ + ('GCC', local_gccver), + ('FlexiBLAS', '3.4.4', '', ('GCC', local_gccver)), + ('FFTW', '3.3.10', '', ('GCC', local_gccver)), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/g/gfbf/gfbf-2024a.eb b/easybuild/easyconfigs/g/gfbf/gfbf-2024a.eb new file mode 100644 index 00000000000..51b74722cb5 --- /dev/null +++ b/easybuild/easyconfigs/g/gfbf/gfbf-2024a.eb @@ -0,0 +1,20 @@ +easyblock = 'Toolchain' + +name = 'gfbf' +version = '2024a' + +homepage = '(none)' +description = """GNU Compiler Collection (GCC) based compiler toolchain, including + FlexiBLAS (BLAS and LAPACK support) and (serial) FFTW.""" + +toolchain = SYSTEM + +local_gccver = '13.3.0' + +dependencies = [ + ('GCC', local_gccver), + ('FlexiBLAS', '3.4.4', '', ('GCC', local_gccver)), + ('FFTW', '3.3.10', '', ('GCC', local_gccver)), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/g/gffread/gffread-0.12.7-GCCcore-12.3.0.eb b/easybuild/easyconfigs/g/gffread/gffread-0.12.7-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..eba4233b57f --- /dev/null +++ b/easybuild/easyconfigs/g/gffread/gffread-0.12.7-GCCcore-12.3.0.eb @@ -0,0 +1,34 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +easyblock = 'MakeCp' + +name = 'gffread' +version = '0.12.7' + +homepage = 'https://ccb.jhu.edu/software/stringtie/gff.shtml#gffread' +description = """GFF/GTF parsing utility providing format conversions, +region filtering, FASTA sequence extraction and more.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/gpertea/%(namelower)s/releases/download/v%(version)s/'] +sources = [SOURCE_TAR_GZ] +checksums = ['bfde1c857495e578f5b3af3c007a9aa40593e69450eafcc6a42c3e8ef08ed1f5'] + +builddependencies = [('binutils', '2.40')] + +buildopts = " release" + +files_to_copy = [ + (['%(name)s'], 'bin'), + 'LICENSE', +] + +sanity_check_paths = { + 'files': ['bin/%(name)s'], + 'dirs': [] +} + +sanity_check_commands = ['%(name)s'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/gffutils/gffutils-0.13-foss-2023a.eb b/easybuild/easyconfigs/g/gffutils/gffutils-0.13-foss-2023a.eb new file mode 100644 index 00000000000..2b52f3965bc --- /dev/null +++ b/easybuild/easyconfigs/g/gffutils/gffutils-0.13-foss-2023a.eb @@ -0,0 +1,47 @@ +easyblock = 'PythonBundle' + +name = 'gffutils' +version = '0.13' + +homepage = 'https://github.com/daler/gffutils' +description = """Gffutils is a Python package for working with and manipulating + the GFF and GTF format files typically used for genomic annotations.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('pyfaidx', '0.8.1.1'), + ('Biopython', '1.83'), + ('pybedtools', '0.9.1'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('six', '1.16.0', { + 'checksums': ['1e61c37477a1626458e36f7b1d82aa5c9b094fa4802892072e49de9c60c4c926'], + }), + ('argh', '0.31.3', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['2edac856ff50126f6e47d884751328c9f466bacbbb6cbfdac322053d94705494'], + }), + ('argcomplete', '3.5.0', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['d4bcf3ff544f51e16e54228a7ac7f486ed70ebf2ecfe49a63a91171c76bf029b'], + }), + ('simplejson', '3.19.3', { + 'checksums': ['8e086896c36210ab6050f2f9f095a5f1e03c83fa0e7f296d6cba425411364680'], + }), + (name, version, { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['58e7bb579796fff70e728380ef2d8ffd4a3bc895e53e6529855a0cf87ba6a77a'], + }), +] + +sanity_check_commands = [ + "python -c 'from gffutils import helpers'" +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/gflags/gflags-2.2.2-GCCcore-12.2.0.eb b/easybuild/easyconfigs/g/gflags/gflags-2.2.2-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..042dd4fdbf0 --- /dev/null +++ b/easybuild/easyconfigs/g/gflags/gflags-2.2.2-GCCcore-12.2.0.eb @@ -0,0 +1,35 @@ +easyblock = 'CMakeMake' + +name = 'gflags' +version = '2.2.2' + +homepage = 'https://github.com/gflags/gflags' +description = """ +The gflags package contains a C++ library that implements commandline flags +processing. It includes built-in support for standard types such as string +and the ability to define flags in the source file in which they are used. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/gflags/gflags/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['34af2f15cf7367513b352bdcd2493ab14ce43692d2dcd9dfc499492966c64dcf'] + +builddependencies = [ + ('binutils', '2.39'), + ('CMake', '3.24.3'), +] + +configopts = '-DBUILD_SHARED_LIBS=ON -DBUILD_STATIC_LIBS=ON' + +sanity_check_paths = { + 'files': ['bin/gflags_completions.sh'] + + ['lib/%s' % x for x in ['libgflags.%s' % SHLIB_EXT, 'libgflags_nothreads.%s' % SHLIB_EXT, + 'libgflags.a', 'libgflags_nothreads.a']] + + ['include/gflags/gflags_completions.h'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/g/gflags/gflags-2.2.2-GCCcore-13.3.0.eb b/easybuild/easyconfigs/g/gflags/gflags-2.2.2-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..de0ad50b22c --- /dev/null +++ b/easybuild/easyconfigs/g/gflags/gflags-2.2.2-GCCcore-13.3.0.eb @@ -0,0 +1,35 @@ +easyblock = 'CMakeMake' + +name = 'gflags' +version = '2.2.2' + +homepage = 'https://github.com/gflags/gflags' +description = """ +The gflags package contains a C++ library that implements commandline flags +processing. It includes built-in support for standard types such as string +and the ability to define flags in the source file in which they are used. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/gflags/gflags/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['34af2f15cf7367513b352bdcd2493ab14ce43692d2dcd9dfc499492966c64dcf'] + +builddependencies = [ + ('binutils', '2.42'), + ('CMake', '3.29.3'), +] + +configopts = '-DBUILD_SHARED_LIBS=ON -DBUILD_STATIC_LIBS=ON' + +sanity_check_paths = { + 'files': ['bin/gflags_completions.sh'] + + ['lib/%s' % x for x in ['libgflags.%s' % SHLIB_EXT, 'libgflags_nothreads.%s' % SHLIB_EXT, + 'libgflags.a', 'libgflags_nothreads.a']] + + ['include/gflags/gflags_completions.h'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/g/gh/gh-2.52.0.eb b/easybuild/easyconfigs/g/gh/gh-2.52.0.eb new file mode 100644 index 00000000000..53a5bb57d66 --- /dev/null +++ b/easybuild/easyconfigs/g/gh/gh-2.52.0.eb @@ -0,0 +1,28 @@ +easyblock = 'GoPackage' + +name = 'gh' +version = '2.52.0' + +homepage = 'https://github.com/cli/' +description = "GitHub’s official command line tool" + +toolchain = SYSTEM + +source_urls = ['https://github.com/cli/cli/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['41de39d0f1bcacb454d9b8a46e5b97ff8b8e803cd26d284e553e45bf025325d9'] + +builddependencies = [ + ('Go', '1.22.1') +] + +installopts = './cmd/%(name)s' + +sanity_check_paths = { + 'files': ['bin/%(name)s'], + 'dirs': [] +} + +sanity_check_commands = ['%(name)s --version'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/g/giac/giac-1.9.0-99-gfbf-2023b.eb b/easybuild/easyconfigs/g/giac/giac-1.9.0-99-gfbf-2023b.eb new file mode 100644 index 00000000000..7680e38cbdb --- /dev/null +++ b/easybuild/easyconfigs/g/giac/giac-1.9.0-99-gfbf-2023b.eb @@ -0,0 +1,43 @@ +easyblock = 'ConfigureMake' + +name = 'giac' +version = '1.9.0-99' + +homepage = 'https://www-fourier.ujf-grenoble.fr/~parisse/giac.html' +description = """Giac is a C++ library, it is the CAS computing kernel. + It may be used inside other C++ programs, and also Python, Java and Javascript programs.""" + +toolchain = {'name': 'gfbf', 'version': '2023b'} +toolchainopts = {'cstd': 'gnu++14'} + +source_urls = ['https://www-fourier.ujf-grenoble.fr/~parisse/debian/dists/stable/main/source/'] +sources = ['giac_%(version)s.tar.gz'] +checksums = ['166775fbf2becd583c6ffa23ca6ca8a0b44dd7790dca8d966da767d3f6647ce4'] + +dependencies = [ + ('FLTK', '1.3.9'), + ('GLPK', '5.0'), + ('GMP-ECM', '7.0.5'), + ('GSL', '2.7'), + ('MPFI', '1.5.4'), + ('NTL', '11.5.1'), + ('PARI-GP', '2.15.5'), + ('CoCoALib', '0.99850'), + ('cURL', '8.3.0'), + ('cliquer', '1.21'), + ('libpng', '1.6.40'), + ('libreadline', '8.2'), + ('nauty', '2.8.8'), + ('hevea', '2.36'), +] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['cas_help', 'hevea2mml', 'icas', 'pgiac', 'xcas']] + + ['lib/libgiac.%s' % e for e in ['a', SHLIB_EXT]] + + ['include/giac/giac.h'], + 'dirs': ['share'], +} + +sanity_check_commands = ["giac <(echo '?findhelp') | grep \"Returns the help about the command\""] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/g/giflib/giflib-5.2.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/g/giflib/giflib-5.2.1-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..66ef70d59ce --- /dev/null +++ b/easybuild/easyconfigs/g/giflib/giflib-5.2.1-GCCcore-13.3.0.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'giflib' +version = '5.2.1' + +homepage = 'http://giflib.sourceforge.net/' +description = """giflib is a library for reading and writing gif images. +It is API and ABI compatible with libungif which was in wide use while +the LZW compression algorithm was patented.""" + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['31da5562f44c5f15d63340a09a4fd62b48c45620cd302f77a6d9acf0077879bd'] + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +builddependencies = [('binutils', '2.42')] + +skipsteps = ['configure'] + +installopts = 'PREFIX=%(installdir)s' + +sanity_check_paths = { + 'files': ['bin/giftool'], + 'dirs': [] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/g/giflib/giflib-5.2.2-GCCcore-13.3.0.eb b/easybuild/easyconfigs/g/giflib/giflib-5.2.2-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..d8db77830fe --- /dev/null +++ b/easybuild/easyconfigs/g/giflib/giflib-5.2.2-GCCcore-13.3.0.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'giflib' +version = '5.2.2' + +homepage = 'http://giflib.sourceforge.net/' +description = """giflib is a library for reading and writing gif images. +It is API and ABI compatible with libungif which was in wide use while +the LZW compression algorithm was patented.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['be7ffbd057cadebe2aa144542fd90c6838c6a083b5e8a9048b8ee3b66b29d5fb'] + +builddependencies = [ + ('binutils', '2.42'), + ('ImageMagick', '7.1.1-38'), +] + +skipsteps = ['configure'] + +installopts = 'PREFIX=%(installdir)s' + +sanity_check_paths = { + 'files': ['bin/giftool'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/g/git-annex/git-annex-10.20230802-GCCcore-12.2.0.eb b/easybuild/easyconfigs/g/git-annex/git-annex-10.20230802-GCCcore-12.2.0.eb index 2e2696826f6..0e64dba099a 100644 --- a/easybuild/easyconfigs/g/git-annex/git-annex-10.20230802-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/g/git-annex/git-annex-10.20230802-GCCcore-12.2.0.eb @@ -16,6 +16,7 @@ dependencies = [ ('GHC', '9.2.2', '-x86_64', SYSTEM), ('Stack', '2.11.1', '-x86_64', SYSTEM), ('git', '2.38.1', '-nodocs'), + ('libnsl', '2.0.0'), ] sources = [{ @@ -29,7 +30,7 @@ sources = [{ checksums = [None] -prebuildopts = "stack setup && stack build && " +prebuildopts = "export STACK_ROOT=$(mktemp -d) && stack setup && stack build && " buildopts = "install-bins BUILDER=stack PREFIX=%(builddir)s" files_to_copy = [ diff --git a/easybuild/easyconfigs/g/git-annex/git-annex-10.20230802-GCCcore-12.3.0.eb b/easybuild/easyconfigs/g/git-annex/git-annex-10.20230802-GCCcore-12.3.0.eb index 6b6af7f9eba..d21f13320b1 100644 --- a/easybuild/easyconfigs/g/git-annex/git-annex-10.20230802-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/g/git-annex/git-annex-10.20230802-GCCcore-12.3.0.eb @@ -18,6 +18,7 @@ dependencies = [ ('GHC', '9.4.6', '-x86_64', SYSTEM), ('Stack', '2.13.1', '-x86_64', SYSTEM), ('git', '2.41.0', '-nodocs'), + ('libnsl', '2.0.1'), ] sources = [{ @@ -31,7 +32,7 @@ sources = [{ checksums = [None] -prebuildopts = "stack setup && stack build && " +prebuildopts = "export STACK_ROOT=$(mktemp -d) && stack setup && stack build && " buildopts = "install-bins BUILDER=stack PREFIX=%(builddir)s" files_to_copy = [ diff --git a/easybuild/easyconfigs/g/git-annex/git-annex-10.20240731-GCCcore-13.3.0.eb b/easybuild/easyconfigs/g/git-annex/git-annex-10.20240731-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..9701f4ce94d --- /dev/null +++ b/easybuild/easyconfigs/g/git-annex/git-annex-10.20240731-GCCcore-13.3.0.eb @@ -0,0 +1,49 @@ +easyblock = 'MakeCp' + +name = 'git-annex' +version = '10.20240731' + +homepage = 'https://git-annex.branchable.com' +description = """git-annex allows managing large files with git, without storing the file contents in git. It can sync, +backup, and archive your data, offline and online. Checksums and encryption keep your data safe and secure. Bring the +power and distributed nature of git to bear on your large files with git-annex.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +builddependencies = [ + ('binutils', '2.42') +] + +dependencies = [ + ('GHC', '9.10.1', '-x86_64', SYSTEM), + ('Stack', '3.1.1', '-x86_64', SYSTEM), + ('git', '2.45.1'), + ('libnsl', '2.0.1'), +] + +sources = [{ + 'git_config': {'url': 'git://git-annex.branchable.com', + 'repo_name': '%(name)s', + 'tag': '%(version)s', + 'clone_into': '%(name)s-%(version)s', + }, + 'filename': '%(name)s-%(version)s.tar.gz', +}] + +checksums = [None] + +prebuildopts = "export STACK_ROOT=$(mktemp -d) && stack setup && stack build && " +buildopts = "install-bins BUILDER=stack PREFIX=%(builddir)s" + +files_to_copy = [ + (['git-annex', 'git-annex-shell'], 'bin'), +] + +sanity_check_paths = { + 'files': ['bin/git-annex', 'bin/git-annex-shell'], + 'dirs': [], +} + +sanity_check_commands = ['git-annex version'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/g/git/git-2.45.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/g/git/git-2.45.1-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..3cd07e7cc61 --- /dev/null +++ b/easybuild/easyconfigs/g/git/git-2.45.1-GCCcore-13.3.0.eb @@ -0,0 +1,42 @@ +easyblock = 'ConfigureMake' + +name = 'git' +version = '2.45.1' + +homepage = 'https://git-scm.com' +description = """Git is a free and open source distributed version control system designed +to handle everything from small to very large projects with speed and efficiency.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://github.com/git/git/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['d98c8f70d58f49f7546d59b25e25f2deae6999eb036a33b0fe6f5d07c33f67c6'] + +builddependencies = [ + ('binutils', '2.42'), + ('Autotools', '20231222'), +] + +dependencies = [ + ('cURL', '8.7.1'), + ('expat', '2.6.2'), + ('gettext', '0.22.5'), + ('Perl', '5.38.2'), + ('OpenSSL', '3', '', SYSTEM), +] + +preconfigopts = 'make configure && ' + +# Work around git build system bug. If LIBS contains -lpthread, then configure +# will not append -lpthread to LDFLAGS, but Makefile ignores LIBS. +configopts = "--with-perl=${EBROOTPERL}/bin/perl --enable-pthreads='-lpthread'" + +postinstallcmds = ['cd contrib/subtree; make install'] + +sanity_check_paths = { + 'files': ['bin/git'], + 'dirs': ['libexec/git-core', 'share'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/g/glew/glew-2.2.0-GCCcore-12.2.0-egl.eb b/easybuild/easyconfigs/g/glew/glew-2.2.0-GCCcore-12.2.0-egl.eb new file mode 100644 index 00000000000..7babe095c23 --- /dev/null +++ b/easybuild/easyconfigs/g/glew/glew-2.2.0-GCCcore-12.2.0-egl.eb @@ -0,0 +1,43 @@ +easyblock = 'ConfigureMake' +versionsuffix = '-egl' +# available: -glx, -osmesa, -egl +# GLEW does support GLX (onscreen or requiring VirtualGL), EGL (technically can do both onscreen and +# offscreen), and OSMESA (offscreen software only). + +name = 'glew' +version = '2.2.0' + +homepage = 'https://github.com/nigels-com/glew' +description = """The OpenGL Extension Wrangler Library (GLEW) is a cross-platform open-source +C/C++ extension loading library. GLEW provides efficient run-time mechanisms +for determining which OpenGL extensions are supported on the target platform.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://github.com/nigels-com/glew/releases/download/%(name)s-%(version)s/'] +sources = ['%(name)s-%(version)s.tgz'] +checksums = ['d4fc82893cfb00109578d0a1a2337fb8ca335b3ceccf97b97e5cc7f08e4353e1'] + +builddependencies = [('binutils', '2.39')] + +dependencies = [ + ('Mesa', '22.2.4'), + ('X11', '20221110'), +] + +local_system = 'SYSTEM=linux`echo %(versionsuffix)s|sed -e "s/-glx//g"`' +buildopts = local_system + +skipsteps = ['configure'] + +preinstallopts = 'GLEW_PREFIX=%(installdir)s GLEW_DEST=%(installdir)s ' +install_cmd = 'make install.all ' + local_system + +sanity_check_paths = { + 'files': ['lib/libGLEW.a', 'lib/libGLEW.%s' % SHLIB_EXT] + + ['bin/glewinfo', 'bin/visualinfo'] + + ['include/GL/%s.h' % h for h in ['glew', 'glxew', 'wglew']], + 'dirs': [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/g/glew/glew-2.2.0-GCCcore-12.3.0-egl.eb b/easybuild/easyconfigs/g/glew/glew-2.2.0-GCCcore-12.3.0-egl.eb new file mode 100644 index 00000000000..81bca17cbb7 --- /dev/null +++ b/easybuild/easyconfigs/g/glew/glew-2.2.0-GCCcore-12.3.0-egl.eb @@ -0,0 +1,43 @@ +easyblock = 'ConfigureMake' +versionsuffix = '-egl' +# available: -glx, -osmesa, -egl +# GLEW does support GLX (onscreen or requiring VirtualGL), EGL (technically can do both onscreen and +# offscreen), and OSMESA (offscreen software only). + +name = 'glew' +version = '2.2.0' + +homepage = 'https://github.com/nigels-com/glew' +description = """The OpenGL Extension Wrangler Library (GLEW) is a cross-platform open-source +C/C++ extension loading library. GLEW provides efficient run-time mechanisms +for determining which OpenGL extensions are supported on the target platform.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://github.com/nigels-com/glew/releases/download/%(name)s-%(version)s/'] +sources = ['%(name)s-%(version)s.tgz'] +checksums = ['d4fc82893cfb00109578d0a1a2337fb8ca335b3ceccf97b97e5cc7f08e4353e1'] + +builddependencies = [('binutils', '2.40')] + +dependencies = [ + ('Mesa', '23.1.4'), + ('X11', '20230603'), +] + +local_system = 'SYSTEM=linux`echo %(versionsuffix)s|sed -e "s/-glx//g"`' +buildopts = local_system + +skipsteps = ['configure'] + +preinstallopts = 'GLEW_PREFIX=%(installdir)s GLEW_DEST=%(installdir)s ' +install_cmd = 'make install.all ' + local_system + +sanity_check_paths = { + 'files': ['lib/libGLEW.a', 'lib/libGLEW.%s' % SHLIB_EXT] + + ['bin/glewinfo', 'bin/visualinfo'] + + ['include/GL/%s.h' % h for h in ['glew', 'glxew', 'wglew']], + 'dirs': [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/g/glog/glog-0.6.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/g/glog/glog-0.6.0-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..e3742d09ea3 --- /dev/null +++ b/easybuild/easyconfigs/g/glog/glog-0.6.0-GCCcore-12.2.0.eb @@ -0,0 +1,33 @@ +easyblock = 'CMakeMake' + +name = 'glog' +version = '0.6.0' + +homepage = 'https://github.com/google/glog' +description = "A C++ implementation of the Google logging module." + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'cstd': 'c++11'} + +source_urls = ['https://github.com/google/glog/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['8a83bf982f37bb70825df71a9709fa90ea9f4447fb3c099e1d720a439d88bad6'] + +builddependencies = [ + ('binutils', '2.39'), + ('CMake', '3.24.3'), +] + +dependencies = [ + ('gflags', '2.2.2'), + ('libunwind', '1.6.2'), +] + +configopts = '-DBUILD_SHARED_LIBS=ON ' + +sanity_check_paths = { + 'files': ['include/glog/logging.h', 'include/glog/raw_logging.h', 'lib/libglog.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/g/gmpflf/gmpflf-2024.06.eb b/easybuild/easyconfigs/g/gmpflf/gmpflf-2024.06.eb new file mode 100644 index 00000000000..bd4f74361b7 --- /dev/null +++ b/easybuild/easyconfigs/g/gmpflf/gmpflf-2024.06.eb @@ -0,0 +1,27 @@ +easyblock = 'Toolchain' + +name = 'gmpflf' +version = '2024.06' + +homepage = '(none)' +description = """GNU Compiler Collection (GCC) based compiler toolchain, including + MPICH for MPI support, FlexiBLAS (OpenBLAS and LAPACK), FFTW and ScaLAPACK.""" + +toolchain = SYSTEM + +local_gccver = '12.3.0' + +# toolchain used to build gmpflf dependencies +local_comp_mpi_tc = ('gmpich', version) + +# we need GCC and MPICH as explicit dependencies instead of gompi toolchain +# because of toolchain preparation functions +dependencies = [ + ('GCC', local_gccver), + ('MPICH', '4.2.1', '', ('GCC', local_gccver)), + ('FlexiBLAS', '3.3.1', '', ('GCC', local_gccver)), + ('FFTW', '3.3.10', '', ('GCC', local_gccver)), + ('FFTW.MPI', '3.3.10', '', local_comp_mpi_tc), + ('ScaLAPACK', '2.2.0', '-fb', local_comp_mpi_tc), +] +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/g/gmpich/gmpich-2024.06.eb b/easybuild/easyconfigs/g/gmpich/gmpich-2024.06.eb new file mode 100644 index 00000000000..14afd408f3d --- /dev/null +++ b/easybuild/easyconfigs/g/gmpich/gmpich-2024.06.eb @@ -0,0 +1,20 @@ +easyblock = 'Toolchain' + +name = 'gmpich' +version = '2024.06' + + +homepage = '(none)' +description = """gcc and GFortran based compiler toolchain, + including MPICH for MPI support.""" + +toolchain = SYSTEM + +local_gccver = '12.3.0' + +dependencies = [ + ('GCC', local_gccver), + ('MPICH', '4.2.1', '', ('GCC', local_gccver)), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/g/gmpy2/gmpy2-2.2.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/g/gmpy2/gmpy2-2.2.0-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..45d90e26d6a --- /dev/null +++ b/easybuild/easyconfigs/g/gmpy2/gmpy2-2.2.0-GCCcore-13.3.0.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonPackage' + +name = 'gmpy2' +version = '2.2.0' + +homepage = 'https://github.com/aleaxit/gmpy' +description = "GMP/MPIR, MPFR, and MPC interface to Python 2.6+ and 3.x" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['e19e62dfeb1e4a57079f0bf51c51dec30633d9fe9e89cb9a083e05e4823afa70'] + +builddependencies = [ + ('binutils', '2.42') +] + +dependencies = [ + ('Python', '3.12.3'), + ('GMP', '6.3.0'), + ('MPFR', '4.2.1'), + ('MPC', '1.3.1'), +] + +download_dep_fail = True +sanity_pip_check = True +use_pip = True + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/g/gnupg-bundle/gnupg-bundle-20240306-GCCcore-13.2.0.eb b/easybuild/easyconfigs/g/gnupg-bundle/gnupg-bundle-20240306-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..67d7657a048 --- /dev/null +++ b/easybuild/easyconfigs/g/gnupg-bundle/gnupg-bundle-20240306-GCCcore-13.2.0.eb @@ -0,0 +1,66 @@ +easyblock = 'Bundle' + +name = 'gnupg-bundle' +version = '20240306' + +homepage = 'https://www.gnupg.org/software/index.html' +description = """GnuPG — The Universal Crypto Engine""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +builddependencies = [('binutils', '2.40')] + +default_easyblock = 'ConfigureMake' + +default_component_specs = { + 'sources': [SOURCE_TAR_BZ2], + 'start_dir': '%(name)s-%(version)s', +} + +components = [ + ('libgpg-error', '1.48', { # 2024-02-23 + 'source_urls': ['https://www.gnupg.org/ftp/gcrypt/libgpg-error/'], + 'checksums': ['89ce1ae893e122924b858de84dc4f67aae29ffa610ebf668d5aa539045663d6f'], + }), + ('libassuan', '2.5.7', { # 2024-03-06 + 'source_urls': ['https://www.gnupg.org/ftp/gcrypt/libassuan/'], + 'checksums': ['0103081ffc27838a2e50479153ca105e873d3d65d8a9593282e9c94c7e6afb76'], + }), + ('libgcrypt', '1.10.3', { # 2023-11-14 + 'source_urls': ['https://www.gnupg.org/ftp/gcrypt/libgcrypt/'], + 'checksums': ['8b0870897ac5ac67ded568dcfadf45969cfa8a6beb0fd60af2a9eadc2a3272aa'], + }), + ('libksba', '1.6.6', { # 2024-02-23 + 'source_urls': ['https://www.gnupg.org/ftp/gcrypt/libksba/'], + 'checksums': ['5dec033d211559338838c0c4957c73dfdc3ee86f73977d6279640c9cd08ce6a4'], + }), + ('npth', '1.7', { # 2024-02-23 + 'source_urls': ['https://www.gnupg.org/ftp/gcrypt/npth/'], + 'checksums': ['8589f56937b75ce33b28d312fccbf302b3b71ec3f3945fde6aaa74027914ad05'], + }), + ('gnupg', '2.4.5', { # 2024-03-07 + 'source_urls': ['https://www.gnupg.org/ftp/gcrypt/gnupg/'], + 'checksums': ['f68f7d75d06cb1635c336d34d844af97436c3f64ea14bcb7c869782f96f44277'], + }), + ('gpgme', '1.23.2', { # 2023-11-28 + 'source_urls': ['https://www.gnupg.org/ftp/gcrypt/gpgme/'], + 'checksums': ['9499e8b1f33cccb6815527a1bc16049d35a6198a6c5fae0185f2bd561bce5224'], + }), +] + +sanity_check_paths = { + 'files': [ + 'bin/gpgrt-config', + 'bin/libassuan-config', + 'bin/libgcrypt-config', + 'include/gpg-error.h', + 'include/gcrypt.h', + 'include/gpgrt.h', + 'include/gpgme.h', + 'include/npth.h', + 'include/assuan.h', + ], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/g/gnuplot/gnuplot-6.0.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/g/gnuplot/gnuplot-6.0.1-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..e27fc37776f --- /dev/null +++ b/easybuild/easyconfigs/g/gnuplot/gnuplot-6.0.1-GCCcore-13.3.0.eb @@ -0,0 +1,51 @@ +easyblock = 'ConfigureMake' + +name = 'gnuplot' +version = '6.0.1' + +homepage = 'http://gnuplot.sourceforge.net' +description = "Portable interactive, function plotting utility" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = [('https://sourceforge.net/projects/%(name)s/files/%(name)s/%(version)s', 'download')] +sources = [SOURCE_TAR_GZ] +checksums = ['e85a660c1a2a1808ff24f7e69981ffcbac66a45c9dcf711b65610b26ea71379a'] + +builddependencies = [ + ('binutils', '2.42'), + ('pkgconf', '2.2.0'), + ('Autotools', '20231222'), +] +dependencies = [ + ('ncurses', '6.5'), + ('cairo', '1.18.0'), + ('libjpeg-turbo', '3.0.1'), + ('libpng', '1.6.43'), + ('libgd', '2.3.3'), + ('Pango', '1.54.0'), + ('libcerf', '2.4'), + ('X11', '20240607'), + ('Qt6', '6.7.2'), + ('Lua', '5.4.7'), +] + +preconfigopts = 'autoreconf && ' + +# make sure that right Lua library is used (bypassing pkg-config) +preconfigopts += 'export LUA_CFLAGS="-I$EBROOTLUA/include" && export LUA_LIBS="$EBROOTLUA/lib/liblua.a" && ' + +# fix undefined reference to symbol 'libiconv_open' +preconfigopts += ' export LDFLAGS="-Wl,--copy-dt-needed-entries" && ' + +configopts = "--without-latex --disable-wxwidgets" + +sanity_check_paths = { + 'files': ['bin/%(name)s'], + 'dirs': [], +} + +# make sure that pdf terminal type is available +sanity_check_commands = ["%(name)s -e 'set terminal pdf'"] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/gomkl/gomkl-2023b.eb b/easybuild/easyconfigs/g/gomkl/gomkl-2023b.eb new file mode 100644 index 00000000000..d5b856a6fe9 --- /dev/null +++ b/easybuild/easyconfigs/g/gomkl/gomkl-2023b.eb @@ -0,0 +1,19 @@ +easyblock = "Toolchain" + +name = 'gomkl' +version = '2023b' + +homepage = '(none)' +description = """GNU Compiler Collection (GCC) based compiler toolchain with OpenMPI and MKL""" + +toolchain = SYSTEM + +local_comp = ('GCC', '13.2.0') + +dependencies = [ + local_comp, + ('OpenMPI', '4.1.6', '', local_comp), + ('imkl', '2023.2.0', '', ('gompi', version)), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/g/gompi/gompi-2024.05.eb b/easybuild/easyconfigs/g/gompi/gompi-2024.05.eb new file mode 100644 index 00000000000..c3f4137cd28 --- /dev/null +++ b/easybuild/easyconfigs/g/gompi/gompi-2024.05.eb @@ -0,0 +1,20 @@ +easyblock = 'Toolchain' + +name = 'gompi' +version = '2024.05' + +homepage = '(none)' +description = """GNU Compiler Collection (GCC) based compiler toolchain, + including OpenMPI for MPI support.""" + +toolchain = SYSTEM + +local_gccver = '13.3.0' + +# compiler toolchain dependencies +dependencies = [ + ('GCC', local_gccver), # includes both GCC and binutils + ('OpenMPI', '5.0.3', '', ('GCC', local_gccver)), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/g/gompi/gompi-2024a.eb b/easybuild/easyconfigs/g/gompi/gompi-2024a.eb new file mode 100644 index 00000000000..c49f4050ff8 --- /dev/null +++ b/easybuild/easyconfigs/g/gompi/gompi-2024a.eb @@ -0,0 +1,20 @@ +easyblock = 'Toolchain' + +name = 'gompi' +version = '2024a' + +homepage = '(none)' +description = """GNU Compiler Collection (GCC) based compiler toolchain, + including OpenMPI for MPI support.""" + +toolchain = SYSTEM + +local_gccver = '13.3.0' + +# compiler toolchain dependencies +dependencies = [ + ('GCC', local_gccver), # includes both GCC and binutils + ('OpenMPI', '5.0.3', '', ('GCC', local_gccver)), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/g/googletest/googletest-1.15.2-GCCcore-13.3.0.eb b/easybuild/easyconfigs/g/googletest/googletest-1.15.2-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..16b74bdae1b --- /dev/null +++ b/easybuild/easyconfigs/g/googletest/googletest-1.15.2-GCCcore-13.3.0.eb @@ -0,0 +1,28 @@ +easyblock = 'CMakeMake' + +name = 'googletest' +version = '1.15.2' + +homepage = 'https://github.com/google/googletest' +description = "Google's framework for writing C++ tests on a variety of platforms" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://github.com/google/googletest/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['7b42b4d6ed48810c5362c265a17faebe90dc2373c885e5216439d37927f02926'] + +builddependencies = [ + ('binutils', '2.42'), + ('CMake', '3.29.3'), +] +# build twice, once for static, once for shared libraries +configopts = ['', ' -DBUILD_SHARED_LIBS=ON '] + +sanity_check_paths = { + 'files': ['lib/lib%s.%s' % (local_lib, local_ext) for local_lib in ['gmock', 'gmock_main', 'gtest', 'gtest_main'] + for local_ext in ['a', SHLIB_EXT]], + 'dirs': ['include/gmock', 'include/gtest'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/g/gperf/gperf-3.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/g/gperf/gperf-3.1-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..0cc2e3debee --- /dev/null +++ b/easybuild/easyconfigs/g/gperf/gperf-3.1-GCCcore-13.3.0.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'gperf' +version = '3.1' + +homepage = 'https://www.gnu.org/software/gperf/' +description = """ + GNU gperf is a perfect hash function generator. For a given list of strings, + it produces a hash function and hash table, in form of C or C++ code, for + looking up a value depending on the input string. The hash function is + perfect, which means that the hash table has no collisions, and the hash + table lookup needs a single string comparison only. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['588546b945bba4b70b6a3a616e80b4ab466e3f33024a352fc2198112cdbb3ae2'] + +builddependencies = [ + ('binutils', '2.42'), +] + +sanity_check_paths = { + 'files': ['bin/gperf'], + 'dirs': [], +} + +sanity_check_commands = ["gperf --help"] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/g/gperftools/gperftools-2.16-GCCcore-13.3.0.eb b/easybuild/easyconfigs/g/gperftools/gperftools-2.16-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..1a31ffabd1b --- /dev/null +++ b/easybuild/easyconfigs/g/gperftools/gperftools-2.16-GCCcore-13.3.0.eb @@ -0,0 +1,37 @@ +easyblock = 'ConfigureMake' + +name = 'gperftools' +version = '2.16' + +homepage = 'https://github.com/gperftools/gperftools' +description = """ +gperftools is a collection of a high-performance multi-threaded malloc() +implementation, plus some pretty nifty performance analysis tools. +Includes TCMalloc, heap-checker, heap-profiler and cpu-profiler. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +github_account = '%(name)s' +source_urls = [GITHUB_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['737be182b4e42f5c7f595da2a7aa59ce0489a73d336d0d16847f2aa52d5221b4'] + +builddependencies = [ + ('Autotools', '20231222'), + ('binutils', '2.42'), +] +dependencies = [ + ('libunwind', '1.8.1'), +] + +preconfigopts = "autoreconf -f -i && " +configopts = '--enable-libunwind' + +sanity_check_paths = { + 'files': ['bin/pprof', 'lib/libprofiler.a', 'lib/libprofiler.%s' % SHLIB_EXT, + 'lib/libtcmalloc.a', 'lib/libtcmalloc.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/g/graph-tool/graph-tool-2.59-foss-2023a.eb b/easybuild/easyconfigs/g/graph-tool/graph-tool-2.59-foss-2023a.eb new file mode 100644 index 00000000000..307e764d139 --- /dev/null +++ b/easybuild/easyconfigs/g/graph-tool/graph-tool-2.59-foss-2023a.eb @@ -0,0 +1,62 @@ +# Author: J. Sassmannshausen (Imperial College London/UK) +# Update: Pavel Tománek (Inuits) + +easyblock = 'ConfigureMake' + +name = 'graph-tool' +version = '2.59' + +homepage = 'https://graph-tool.skewed.de/' +description = """Graph-tool is an efficient Python module for manipulation and + statistical analysis of graphs (a.k.a. networks). Contrary to + most other python modules with similar functionality, the core + data structures and algorithms are implemented in C++, making + extensive use of template metaprogramming, based heavily on + the Boost Graph Library. This confers it a level of + performance that is comparable (both in memory usage and + computation time) to that of a pure C/C++ library.""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'cstd': 'c++17', 'openmp': True} + +source_urls = ['https://downloads.skewed.de/%(name)s/'] +sources = [SOURCE_TAR_BZ2] +checksums = ['cde479c0a7254b72f6e795d03b0273b0a7d81611a6a3364ba649c2c85c99acae'] + +builddependencies = [ + ('gawk', '5.3.0'), + ('pkgconf', '1.9.5'), + ('expat', '2.5.0'), + ('CGAL', '5.6'), + ('GMP', '6.2.1'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('Boost.Python', '1.82.0'), + ('sparsehash', '2.0.4'), + ('matplotlib', '3.7.2'), + ('PyCairo', '1.25.0'), + ('cairomm', '1.16.2'), + ('PyGObject', '3.46.0'), + ('GTK3', '3.24.37'), +] + +configopts = '--enable-openmp --with-cgal=$EBROOTCGAL --with-boost=$EBROOTBOOST ' +configopts += '--with-boost-python=boost_python311 ' +configopts += '--with-python-module-path=%(installdir)s/lib/python%(pyshortver)s/site-packages ' + + +sanity_check_paths = { + 'files': ['lib/python%(pyshortver)s/site-packages/graph_tool/all.py'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/graph_tool/include', 'share'], +} + +sanity_check_commands = [ + "python -c 'from graph_tool.all import Graph, BlockState'", + "python -c 'import graph_tool.inference'", +] + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/g/graphite2/graphite2-1.3.14-GCCcore-13.3.0.eb b/easybuild/easyconfigs/g/graphite2/graphite2-1.3.14-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..7e199ecf26b --- /dev/null +++ b/easybuild/easyconfigs/g/graphite2/graphite2-1.3.14-GCCcore-13.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'CMakeMake' + +name = 'graphite2' +version = '1.3.14' + +homepage = 'https://scripts.sil.org/cms/scripts/page.php?site_id=projects&item_id=graphite_home' +description = """Graphite is a "smart font" system developed specifically to + handle the complexities of lesser-known languages of the world.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://github.com/silnrsi/graphite/archive/'] +sources = ['%(version)s.zip'] +checksums = ['36e15981af3bf7a3ca3daf53295c8ffde04cf7d163e3474e4d0836e2728b4149'] + +builddependencies = [ + ('CMake', '3.29.3'), + ('binutils', '2.42'), +] + +sanity_check_paths = { + 'files': ['bin/gr2fonttest'] + + ['lib/lib%%(name)s.%s' % x for x in [SHLIB_EXT, 'la']], + 'dirs': ['include/%(name)s', 'share'] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/g/groff/groff-1.23.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/g/groff/groff-1.23.0-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..000049dbdda --- /dev/null +++ b/easybuild/easyconfigs/g/groff/groff-1.23.0-GCCcore-13.3.0.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'groff' +version = '1.23.0' + +homepage = 'https://www.gnu.org/software/groff' +description = """Groff (GNU troff) is a typesetting system that reads plain text mixed with formatting commands + and produces formatted output.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://ftp.gnu.org/gnu/groff'] +sources = [SOURCE_TAR_GZ] +checksums = ['6b9757f592b7518b4902eb6af7e54570bdccba37a871fddb2d30ae3863511c13'] + +builddependencies = [ + ('binutils', '2.42'), + ('M4', '1.4.19'), +] + +sanity_check_paths = { + 'files': ['bin/groff', 'bin/nroff', 'bin/troff'], + 'dirs': ['lib/groff', 'share'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/g/grpcio/grpcio-1.57.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/g/grpcio/grpcio-1.57.0-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..27e974c5de0 --- /dev/null +++ b/easybuild/easyconfigs/g/grpcio/grpcio-1.57.0-GCCcore-12.2.0.eb @@ -0,0 +1,54 @@ +easyblock = 'PythonBundle' + +name = 'grpcio' +version = '1.57.0' + +homepage = 'https://grpc.io/' +description = """gRPC is a modern, open source, high-performance remote procedure call (RPC) +framework that can run anywhere. gRPC enables client and server applications to +communicate transparently, and simplifies the building of connected systems.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +use_pip = True +sanity_pip_check = True + +builddependencies = [ + ('binutils', '2.39'), + ('OpenSSL', '1.1', '', SYSTEM), + ('RE2', '2023-03-01'), +] + +dependencies = [ + ('Python', '3.10.8'), + ('protobuf-python', '4.23.0'), + ('Abseil', '20230125.2'), +] + +exts_list = [ + (name, version, { + 'modulename': 'grpc', + 'preinstallopts': ( + # patch hardcoded /usr paths to prefix them with alternate sysroot path (if defined) + "sed -i 's@/usr@%(sysroot)s/usr@g' setup.py && " + "export GRPC_PYTHON_BUILD_EXT_COMPILER_JOBS=%(parallel)s && " + # Required to avoid building with non-default C++ standard but keep other flags, + # see https://github.com/grpc/grpc/issues/34256 + 'export GRPC_PYTHON_CFLAGS="-fvisibility=hidden -fno-wrapv -fno-exceptions" &&' + "GRPC_PYTHON_BUILD_SYSTEM_OPENSSL=True " + "GRPC_PYTHON_BUILD_SYSTEM_ZLIB=True " + "GRPC_PYTHON_BUILD_SYSTEM_RE2=True " + "GRPC_PYTHON_BUILD_SYSTEM_ABSL=True " + ), + 'patches': ['grpcio-1.57.0_use-ebroot.patch'], + 'checksums': [ + {'grpcio-1.57.0.tar.gz': + '4b089f7ad1eb00a104078bab8015b0ed0ebcb3b589e527ab009c53893fd4e613'}, + {'grpcio-1.57.0_use-ebroot.patch': + '5faf822cd817b723ae9361e43656d0ecc7b3333a166bbab2df80b43ae588e510'}, + ], + }), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/g/grpcio/grpcio-1.57.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/g/grpcio/grpcio-1.57.0-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..01d839324bb --- /dev/null +++ b/easybuild/easyconfigs/g/grpcio/grpcio-1.57.0-GCCcore-12.3.0.eb @@ -0,0 +1,54 @@ +easyblock = 'PythonBundle' + +name = 'grpcio' +version = '1.57.0' + +homepage = 'https://grpc.io/' +description = """gRPC is a modern, open source, high-performance remote procedure call (RPC) +framework that can run anywhere. gRPC enables client and server applications to +communicate transparently, and simplifies the building of connected systems.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +use_pip = True +sanity_pip_check = True + +builddependencies = [ + ('binutils', '2.40'), + ('OpenSSL', '1.1', '', SYSTEM), + ('RE2', '2023-08-01'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('protobuf-python', '4.24.0'), + ('Abseil', '20230125.3'), +] + +exts_list = [ + (name, version, { + 'modulename': 'grpc', + 'preinstallopts': ( + # patch hardcoded /usr paths to prefix them with alternate sysroot path (if defined) + "sed -i 's@/usr@%(sysroot)s/usr@g' setup.py && " + "export GRPC_PYTHON_BUILD_EXT_COMPILER_JOBS=%(parallel)s && " + # Required to avoid building with non-default C++ standard but keep other flags, + # see https://github.com/grpc/grpc/issues/34256 + 'export GRPC_PYTHON_CFLAGS="-fvisibility=hidden -fno-wrapv -fno-exceptions" &&' + "GRPC_PYTHON_BUILD_SYSTEM_OPENSSL=True " + "GRPC_PYTHON_BUILD_SYSTEM_ZLIB=True " + "GRPC_PYTHON_BUILD_SYSTEM_RE2=True " + "GRPC_PYTHON_BUILD_SYSTEM_ABSL=True " + ), + 'patches': ['grpcio-1.57.0_use-ebroot.patch'], + 'checksums': [ + {'grpcio-1.57.0.tar.gz': + '4b089f7ad1eb00a104078bab8015b0ed0ebcb3b589e527ab009c53893fd4e613'}, + {'grpcio-1.57.0_use-ebroot.patch': + '5faf822cd817b723ae9361e43656d0ecc7b3333a166bbab2df80b43ae588e510'}, + ], + }), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/g/grpcio/grpcio-1.57.0_use-ebroot.patch b/easybuild/easyconfigs/g/grpcio/grpcio-1.57.0_use-ebroot.patch new file mode 100644 index 00000000000..3a7bc8cc255 --- /dev/null +++ b/easybuild/easyconfigs/g/grpcio/grpcio-1.57.0_use-ebroot.patch @@ -0,0 +1,51 @@ +diff --git a/setup.py b/setup.py +index 97c1dcec54..cc7bc8552e 100644 +--- a/setup.py ++++ b/setup.py +@@ -313,29 +313,33 @@ if "win32" in sys.platform: + CORE_C_FILES = filter(lambda x: "third_party/cares" not in x, CORE_C_FILES) + + if BUILD_WITH_SYSTEM_OPENSSL: ++ EBROOTOPENSSL = os.environ.get('EBROOTOPENSSL') + CORE_C_FILES = filter( + lambda x: "third_party/boringssl" not in x, CORE_C_FILES + ) + CORE_C_FILES = filter(lambda x: "src/boringssl" not in x, CORE_C_FILES) +- SSL_INCLUDE = (os.path.join("/usr", "include", "openssl"),) ++ SSL_INCLUDE = (os.path.join(EBROOTOPENSSL, "include", "openssl"),) + + if BUILD_WITH_SYSTEM_ZLIB: ++ EBROOTZLIB = os.environ.get('EBROOTZLIB') + CORE_C_FILES = filter(lambda x: "third_party/zlib" not in x, CORE_C_FILES) +- ZLIB_INCLUDE = (os.path.join("/usr", "include"),) ++ ZLIB_INCLUDE = (os.path.join(EBROOTZLIB, "include"),) + + if BUILD_WITH_SYSTEM_CARES: + CORE_C_FILES = filter(lambda x: "third_party/cares" not in x, CORE_C_FILES) + CARES_INCLUDE = (os.path.join("/usr", "include"),) + + if BUILD_WITH_SYSTEM_RE2: ++ EBROOTRE2 = os.environ.get('EBROOTRE2') + CORE_C_FILES = filter(lambda x: "third_party/re2" not in x, CORE_C_FILES) +- RE2_INCLUDE = (os.path.join("/usr", "include", "re2"),) ++ RE2_INCLUDE = (os.path.join(EBROOTRE2, "include", "re2"),) + + if BUILD_WITH_SYSTEM_ABSL: ++ EBROOTABSEIL = os.environ.get('EBROOTABSEIL') + CORE_C_FILES = filter( + lambda x: "third_party/abseil-cpp" not in x, CORE_C_FILES + ) +- ABSL_INCLUDE = (os.path.join("/usr", "include"),) ++ ABSL_INCLUDE = (os.path.join(EBROOTABSEIL, "include"),) + + EXTENSION_INCLUDE_DIRECTORIES = ( + (PYTHON_STEM,) +@@ -378,7 +382,7 @@ if BUILD_WITH_SYSTEM_RE2: + EXTENSION_LIBRARIES += ("re2",) + if BUILD_WITH_SYSTEM_ABSL: + EXTENSION_LIBRARIES += tuple( +- lib.stem[3:] for lib in pathlib.Path("/usr").glob("lib*/libabsl_*.so") ++ lib.stem[3:] for lib in pathlib.Path(EBROOTABSEIL).glob("lib*/libabsl_*.so") + ) + + DEFINE_MACROS = (("_WIN32_WINNT", 0x600),) diff --git a/easybuild/easyconfigs/g/gsutil/gsutil-5.29-GCCcore-13.2.0.eb b/easybuild/easyconfigs/g/gsutil/gsutil-5.29-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..209e6e8c1fc --- /dev/null +++ b/easybuild/easyconfigs/g/gsutil/gsutil-5.29-GCCcore-13.2.0.eb @@ -0,0 +1,90 @@ +easyblock = 'PythonBundle' + +name = 'gsutil' +version = '5.29' + +homepage = 'https://cloud.google.com/storage/docs/gsutil' +description = """gsutil is a Python application that lets you access Cloud Storage from the command line.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +builddependencies = [ + ('binutils', '2.40') +] + +dependencies = [ + ('Python', '3.11.5'), + ('Python-bundle-PyPI', '2023.10'), + ('aiohttp', '3.9.5'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('httplib2', '0.20.4', { + 'checksums': ['58a98e45b4b1a48273073f905d2961666ecf0fbac4250ea5b47aef259eb5c585'], + }), + ('argcomplete', '3.3.0', { + 'checksums': ['fd03ff4a5b9e6580569d34b273f741e85cd9e072f3feeeee3eba4891c70eda62'], + }), + ('fasteners', '0.19', { + 'checksums': ['b4f37c3ac52d8a445af3a66bce57b33b5e90b97c696b7b984f530cf8f0ded09c'], + }), + ('google-auth', '2.17.0', { + 'modulename': 'google.auth', + 'checksums': ['f51d26ebb3e5d723b9a7dbd310b6c88654ef1ad1fc35750d1fdba48ca4d82f52'], + }), + ('rsa', '4.7.2', { + 'checksums': ['9d689e6ca1b3038bc82bf8d23e944b6b6037bc02301a574935b2dd946e0353b9'], + }), + ('google-apitools', '0.5.32', { + 'modulename': 'apitools', + 'checksums': ['c3763e52289f61e21c41d5531e20fbda9cc8484a088b8686fd460770db8bad13'], + }), + ('google-auth-httplib2', '0.2.0', { + 'checksums': ['38aa7badf48f974f1eb9861794e9c0cb2a0511a4ec0679b1f886d108f5640e05'], + }), + ('google-reauth', '0.1.1', { + 'checksums': ['f9f6852a55c2c5453d581cd01f3d1278e86147c03d008409800390a834235892'], + }), + ('monotonic', '1.6', { + 'checksums': ['3a55207bcfed53ddd5c5bae174524062935efed17792e9de2ad0205ce9ad63f7'], + }), + ('pyOpenSSL', '24.1.0', { + 'modulename': 'OpenSSL', + 'checksums': ['cabed4bfaa5df9f1a16c0ef64a0cb65318b5cd077a7eda7d6970131ca2f41a6f'], + }), + ('boto', '2.49.0', { + 'checksums': ['ea0d3b40a2d852767be77ca343b58a9e3a4b00d9db440efb8da74b4e58025e5a'], + }), + ('cachetools', '5.3.3', { + 'checksums': ['ba29e2dfa0b8b556606f097407ed1aa62080ee108ab0dc5ec9d6a723a007d105'], + }), + ('oauth2client', '4.1.3', { + 'checksums': ['d486741e451287f69568a4d26d70d9acd73a2bbfa275746c535b4209891cccc6'], + }), + ('pyasn1_modules', '0.4.0', { + 'checksums': ['831dbcea1b177b28c9baddf4c6d1013c24c3accd14a1873fffaa6a2e905f17b6'], + }), + ('pyu2f', '0.1.5', { + 'checksums': ['a3caa3a11842fc7d5746376f37195e6af5f17c0a15737538bb1cebf656fb306b'], + }), + ('crcmod', '1.7', { + 'checksums': ['dc7051a0db5f2bd48665a990d3ec1cc305a466a77358ca4492826f41f283601e'], + }), + ('gcs-oauth2-boto-plugin', '3.2', { + 'checksums': ['a46817f3abed2bc4f6b4b12b0de7c8bf5ff5f1822dc03c45fa1ae6ed7a455843'], + }), + ('retry_decorator', '1.1.1', { + 'checksums': ['e1e8ad02e518fe11073f2ea7d80b6b8be19daa27a60a1838aff7c731ddcf2ebe'], + }), + (name, version, { + 'modulename': 'gslib', + 'checksums': ['0ba61c0ca97a592a2ed9d6eeb74b20434831bc6ceba380138103b24d2d53b921'], + }), +] + +sanity_check_commands = ['gsutil help'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/g/gtk-doc/gtk-doc-1.34.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/g/gtk-doc/gtk-doc-1.34.0-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..dd18263d557 --- /dev/null +++ b/easybuild/easyconfigs/g/gtk-doc/gtk-doc-1.34.0-GCCcore-12.3.0.eb @@ -0,0 +1,51 @@ +easyblock = 'MesonNinja' + +name = 'gtk-doc' +version = '1.34.0' + +homepage = 'https://gitlab.gnome.org/GNOME/gtk-doc' +description = """Documentation tool for public library API""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://gitlab.gnome.org/GNOME/gtk-doc/-/archive/%(version)s/'] +sources = [SOURCE_TAR_GZ] +checksums = ['e1d544fa70ae60014a241b674c9d989f4ad6a96554652ebf73bbe94b4da1aa35'] + +builddependencies = [ + ('binutils', '2.40'), + ('yelp-tools', '42.1'), + ('Ninja', '1.11.1'), + ('Meson', '1.1.1'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('Pygments', '2.18.0'), + ('GLib', '2.77.1'), +] + +sanity_check_paths = { + 'files': [ + 'bin/gtkdoc-depscan', + 'bin/gtkdoc-fixxref', + 'bin/gtkdoc-check', + 'bin/gtkdocize', + 'bin/gtkdoc-mkdb', + 'bin/gtkdoc-mkhtml', + 'bin/gtkdoc-mkhtml2', + 'bin/gtkdoc-mkman', + 'bin/gtkdoc-mkpdf', + 'bin/gtkdoc-rebase', + 'bin/gtkdoc-scan', + 'bin/gtkdoc-scangobj', + ], + 'dirs': [ + 'lib/cmake/GtkDoc', + 'share/%(name)s', + ], +} + +sanity_check_commands = ['gtkdoc-depscan'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/g/gym-pybullet-drones/gym-pybullet-drones-2.0.0-3d7b12e-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/g/gym-pybullet-drones/gym-pybullet-drones-2.0.0-3d7b12e-foss-2023a-CUDA-12.1.1.eb new file mode 100644 index 00000000000..3f1a7405848 --- /dev/null +++ b/easybuild/easyconfigs/g/gym-pybullet-drones/gym-pybullet-drones-2.0.0-3d7b12e-foss-2023a-CUDA-12.1.1.eb @@ -0,0 +1,45 @@ +easyblock = 'PythonBundle' + +name = 'gym-pybullet-drones' +local_commit = '3d7b12edd4915a27e6cec9f2c0eb4b5479f7735e' +version = '2.0.0-%s' % local_commit[:7] +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://utiasdsl.github.io/gym-pybullet-drones/' +description = """PyBullet-based Gym for single and multi-agent +reinforcement learning with nano-quadcopters""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [ + ('poetry', '1.7.1'), + ('pytest', '7.4.2'), +] + +dependencies = [ + ('CUDA', '12.1.1', '', SYSTEM), + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('matplotlib', '3.7.2'), + ('Gymnasium', '0.29.1', versionsuffix), + ('PyBullet', '3.2.6'), + ('Stable-Baselines3', '2.3.2', versionsuffix), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('transforms3d', '0.4.2', { + 'checksums': ['e8b5df30eaedbee556e81c6938e55aab5365894e47d0a17615d7db7fd2393680'], + }), + (name, version, { + 'preinstallopts': """sed -i -e 's/gymnasium.*/gymnasium="*"/' """ + """-e 's/transforms3d.*/transforms3d="*"/' pyproject.toml && """, + 'source_urls': ['https://github.com/utiasDSL/gym-pybullet-drones/archive'], + 'sources': [{'download_filename': '%s.tar.gz' % local_commit, 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['8ff745f590328e2a8fc4701c90d77056d7041f09f28e0ccb821efcc599ae0d8e'], + }), +] + +moduleclass = 'ai' diff --git a/easybuild/easyconfigs/g/gym-pybullet-drones/gym-pybullet-drones-2.0.0-3d7b12e-foss-2023a.eb b/easybuild/easyconfigs/g/gym-pybullet-drones/gym-pybullet-drones-2.0.0-3d7b12e-foss-2023a.eb new file mode 100644 index 00000000000..7f2f12c79bc --- /dev/null +++ b/easybuild/easyconfigs/g/gym-pybullet-drones/gym-pybullet-drones-2.0.0-3d7b12e-foss-2023a.eb @@ -0,0 +1,43 @@ +easyblock = 'PythonBundle' + +name = 'gym-pybullet-drones' +local_commit = '3d7b12edd4915a27e6cec9f2c0eb4b5479f7735e' +version = '2.0.0-%s' % local_commit[:7] + +homepage = 'https://utiasdsl.github.io/gym-pybullet-drones/' +description = """PyBullet-based Gym for single and multi-agent +reinforcement learning with nano-quadcopters""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [ + ('poetry', '1.7.1'), + ('pytest', '7.4.2'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('matplotlib', '3.7.2'), + ('Gymnasium', '0.29.1'), + ('PyBullet', '3.2.6'), + ('Stable-Baselines3', '2.3.2'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('transforms3d', '0.4.2', { + 'checksums': ['e8b5df30eaedbee556e81c6938e55aab5365894e47d0a17615d7db7fd2393680'], + }), + (name, version, { + 'preinstallopts': """sed -i -e 's/gymnasium.*/gymnasium="*"/' """ + """-e 's/transforms3d.*/transforms3d="*"/' pyproject.toml && """, + 'source_urls': ['https://github.com/utiasDSL/gym-pybullet-drones/archive'], + 'sources': [{'download_filename': '%s.tar.gz' % local_commit, 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['8ff745f590328e2a8fc4701c90d77056d7041f09f28e0ccb821efcc599ae0d8e'], + }), +] + +moduleclass = 'ai' diff --git a/easybuild/easyconfigs/g/gzip/gzip-1.13-GCCcore-13.3.0.eb b/easybuild/easyconfigs/g/gzip/gzip-1.13-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..62e179b0998 --- /dev/null +++ b/easybuild/easyconfigs/g/gzip/gzip-1.13-GCCcore-13.3.0.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'gzip' +version = '1.13' + +homepage = 'https://www.gnu.org/software/gzip/' +description = "gzip (GNU zip) is a popular data compression program as a replacement for compress" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['20fc818aeebae87cdbf209d35141ad9d3cf312b35a5e6be61bfcfbf9eddd212a'] + +builddependencies = [('binutils', '2.42')] + +sanity_check_paths = { + 'files': ["bin/gunzip", "bin/gzip", "bin/uncompress"], + 'dirs': [], +} + +sanity_check_commands = [True, ('gzip', '--version')] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/HDBSCAN/HDBSCAN-0.8.38.post1-foss-2023a.eb b/easybuild/easyconfigs/h/HDBSCAN/HDBSCAN-0.8.38.post1-foss-2023a.eb new file mode 100644 index 00000000000..b260708eab8 --- /dev/null +++ b/easybuild/easyconfigs/h/HDBSCAN/HDBSCAN-0.8.38.post1-foss-2023a.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'HDBSCAN' +version = '0.8.38.post1' + +homepage = 'http://hdbscan.readthedocs.io/en/latest/' +description = """The hdbscan library is a suite of tools to use unsupervised learning to find clusters, or dense + regions, of a dataset. The primary algorithm is HDBSCAN* as proposed by Campello, Moulavi, and Sander. The library + provides a high performance implementation of this algorithm, along with tools for analysing the resulting + clustering.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['5fbdba2ffb5a99a8b52fa2915658ced6bed59f4d0d5f40b1c673646c928aac0b'] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('scikit-learn', '1.3.1'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.11-intel-2016a.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.11-intel-2016a.eb index e115932f8ee..3e25fa94133 100644 --- a/easybuild/easyconfigs/h/HDF/HDF-4.2.11-intel-2016a.eb +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.11-intel-2016a.eb @@ -3,15 +3,16 @@ easyblock = 'ConfigureMake' name = 'HDF' version = '4.2.11' -homepage = 'http://www.hdfgroup.org/products/hdf4/' +homepage = 'http://support.hdfgroup.org/products/hdf4/' description = """HDF (also known as HDF4) is a library and multi-object file format for storing and managing data between machines.""" toolchain = {'name': 'intel', 'version': '2016a'} toolchainopts = {'pic': True} +source_urls = ['http://support.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/'] sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/'] +checksums = ['c3f7753b2fb9b27d09eced4d2164605f111f270c9a60b37a578f7de02de86d24'] builddependencies = [ ('flex', '2.6.0'), diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.12-intel-2017a.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.12-intel-2017a.eb index 36b03f18536..5fade2d2248 100644 --- a/easybuild/easyconfigs/h/HDF/HDF-4.2.12-intel-2017a.eb +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.12-intel-2017a.eb @@ -3,15 +3,16 @@ easyblock = 'ConfigureMake' name = 'HDF' version = '4.2.12' -homepage = 'http://www.hdfgroup.org/products/hdf4/' +homepage = 'http://support.hdfgroup.org/products/hdf4/' description = """HDF (also known as HDF4) is a library and multi-object file format for storing and managing data between machines.""" toolchain = {'name': 'intel', 'version': '2017a'} toolchainopts = {'pic': True} +source_urls = ['http://support.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/'] sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/'] +checksums = ['dd419c55e85d1a0e13f3ea5ed35d00710033ccb16c85df088eb7925d486e040c'] builddependencies = [ ('flex', '2.6.3'), diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.13-GCCcore-6.4.0.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.13-GCCcore-6.4.0.eb index f1b4395af48..39dc5507935 100644 --- a/easybuild/easyconfigs/h/HDF/HDF-4.2.13-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.13-GCCcore-6.4.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'HDF' version = '4.2.13' -homepage = 'http://www.hdfgroup.org/products/hdf4/' +homepage = 'http://support.hdfgroup.org/products/hdf4/' description = """ HDF (also known as HDF4) is a library and multi-object file format for @@ -14,7 +14,7 @@ toolchain = {'name': 'GCCcore', 'version': '6.4.0'} toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/'] +source_urls = ['http://support.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/'] checksums = ['be9813c1dc3712c2df977d4960e1f13f20f447dfa8c3ce53331d610c1f470483'] builddependencies = [ diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.13-intel-2017a-no-netcdf.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.13-intel-2017a-no-netcdf.eb index 84bff2749e9..74e44dbfc26 100644 --- a/easybuild/easyconfigs/h/HDF/HDF-4.2.13-intel-2017a-no-netcdf.eb +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.13-intel-2017a-no-netcdf.eb @@ -4,7 +4,7 @@ name = 'HDF' version = '4.2.13' versionsuffix = '-no-netcdf' -homepage = 'http://www.hdfgroup.org/products/hdf4/' +homepage = 'http://support.hdfgroup.org/products/hdf4/' description = """HDF (also known as HDF4) is a library and multi-object file format for storing and managing data between machines. This version suppresses the netcdf api, that gives issues with some applications""" @@ -12,7 +12,7 @@ toolchain = {'name': 'intel', 'version': '2017a'} toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/'] +source_urls = ['http://support.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/'] checksums = ['be9813c1dc3712c2df977d4960e1f13f20f447dfa8c3ce53331d610c1f470483'] builddependencies = [ diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.14-GCCcore-6.4.0.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.14-GCCcore-6.4.0.eb index 1f31e675f7a..56e705f36a2 100644 --- a/easybuild/easyconfigs/h/HDF/HDF-4.2.14-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.14-GCCcore-6.4.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'HDF' version = '4.2.14' -homepage = 'http://www.hdfgroup.org/products/hdf4/' +homepage = 'http://support.hdfgroup.org/products/hdf4/' description = """ HDF (also known as HDF4) is a library and multi-object file format for @@ -13,7 +13,7 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '6.4.0'} toolchainopts = {'pic': True} -source_urls = ['http://www.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/'] +source_urls = ['http://support.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/'] sources = [SOURCELOWER_TAR_GZ] checksums = ['2d383e87c8a0ca6a5352adbd1d5546e6cc43dc21ff7d90f93efa644d85c0b14a'] diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.14-GCCcore-7.3.0.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.14-GCCcore-7.3.0.eb index 204d917a179..51b65acec93 100644 --- a/easybuild/easyconfigs/h/HDF/HDF-4.2.14-GCCcore-7.3.0.eb +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.14-GCCcore-7.3.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'HDF' version = '4.2.14' -homepage = 'https://www.hdfgroup.org/products/hdf4/' +homepage = 'https://support.hdfgroup.org/products/hdf4/' description = """ HDF (also known as HDF4) is a library and multi-object file format for @@ -13,7 +13,7 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '7.3.0'} toolchainopts = {'pic': True} -source_urls = ['https://www.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/'] +source_urls = ['https://support.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/'] sources = [SOURCELOWER_TAR_GZ] checksums = ['2d383e87c8a0ca6a5352adbd1d5546e6cc43dc21ff7d90f93efa644d85c0b14a'] diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.14-GCCcore-8.2.0.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.14-GCCcore-8.2.0.eb index bf3fff366f2..a78efd6cee2 100644 --- a/easybuild/easyconfigs/h/HDF/HDF-4.2.14-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.14-GCCcore-8.2.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'HDF' version = '4.2.14' -homepage = 'https://www.hdfgroup.org/products/hdf4/' +homepage = 'https://support.hdfgroup.org/products/hdf4/' description = """ HDF (also known as HDF4) is a library and multi-object file format for @@ -13,7 +13,7 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '8.2.0'} toolchainopts = {'pic': True} -source_urls = ['http://www.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/'] +source_urls = ['http://support.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/'] sources = [SOURCELOWER_TAR_GZ] checksums = ['2d383e87c8a0ca6a5352adbd1d5546e6cc43dc21ff7d90f93efa644d85c0b14a'] diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.14-GCCcore-8.3.0.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.14-GCCcore-8.3.0.eb index ff08dc71e80..fdee3ff0383 100644 --- a/easybuild/easyconfigs/h/HDF/HDF-4.2.14-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.14-GCCcore-8.3.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'HDF' version = '4.2.14' -homepage = 'https://www.hdfgroup.org/products/hdf4/' +homepage = 'https://support.hdfgroup.org/products/hdf4/' description = """ HDF (also known as HDF4) is a library and multi-object file format for @@ -13,7 +13,7 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '8.3.0'} toolchainopts = {'pic': True} -source_urls = ['http://www.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/'] +source_urls = ['http://support.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/'] sources = [SOURCELOWER_TAR_GZ] checksums = ['2d383e87c8a0ca6a5352adbd1d5546e6cc43dc21ff7d90f93efa644d85c0b14a'] diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-10.2.0.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-10.2.0.eb index bdb2cb878ee..91e084fc238 100644 --- a/easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-10.2.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'HDF' version = '4.2.15' -homepage = 'https://www.hdfgroup.org/products/hdf4/' +homepage = 'https://support.hdfgroup.org/products/hdf4/' description = """ HDF (also known as HDF4) is a library and multi-object file format for @@ -13,7 +13,7 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '10.2.0'} toolchainopts = {'pic': True} -source_urls = ['http://www.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/'] +source_urls = ['http://support.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/'] sources = [SOURCELOWER_TAR_GZ] patches = ['HDF-4.2.15_fix-aarch64.patch'] checksums = [ diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-10.3.0.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-10.3.0.eb index 869a6a796a2..7fff3f348bb 100644 --- a/easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-10.3.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'HDF' version = '4.2.15' -homepage = 'https://www.hdfgroup.org/products/hdf4/' +homepage = 'https://support.hdfgroup.org/products/hdf4/' description = """ HDF (also known as HDF4) is a library and multi-object file format for @@ -13,7 +13,7 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '10.3.0'} toolchainopts = {'pic': True} -source_urls = ['http://www.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/'] +source_urls = ['http://support.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/'] sources = [SOURCELOWER_TAR_GZ] patches = ['HDF-4.2.15_fix-aarch64.patch'] checksums = [ diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-11.2.0.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-11.2.0.eb index fc36bb04673..7acaaafc09d 100644 --- a/easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-11.2.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'HDF' version = '4.2.15' -homepage = 'https://www.hdfgroup.org/products/hdf4/' +homepage = 'https://support.hdfgroup.org/products/hdf4/' description = """ HDF (also known as HDF4) is a library and multi-object file format for @@ -13,7 +13,7 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '11.2.0'} toolchainopts = {'pic': True} -source_urls = ['http://www.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/'] +source_urls = ['http://support.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/'] sources = [SOURCELOWER_TAR_GZ] patches = ['HDF-4.2.15_fix-aarch64.patch'] checksums = [ diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-11.3.0.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-11.3.0.eb index 682e5e20b6c..4af8d274164 100644 --- a/easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-11.3.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'HDF' version = '4.2.15' -homepage = 'https://www.hdfgroup.org/products/hdf4/' +homepage = 'https://support.hdfgroup.org/products/hdf4/' description = """ HDF (also known as HDF4) is a library and multi-object file format for @@ -13,7 +13,7 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '11.3.0'} toolchainopts = {'pic': True} -source_urls = ['http://www.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/'] +source_urls = ['http://support.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/'] sources = [SOURCELOWER_TAR_GZ] patches = ['HDF-4.2.15_fix-aarch64.patch'] checksums = [ diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-12.2.0.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-12.2.0.eb index f0286cd30bd..abab2d962f5 100644 --- a/easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-12.2.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'HDF' version = '4.2.15' -homepage = 'https://www.hdfgroup.org/products/hdf4/' +homepage = 'https://support.hdfgroup.org/products/hdf4/' description = """ HDF (also known as HDF4) is a library and multi-object file format for @@ -13,7 +13,7 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '12.2.0'} toolchainopts = {'pic': True} -source_urls = ['http://www.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/'] +source_urls = ['http://support.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/'] sources = [SOURCELOWER_TAR_GZ] patches = ['HDF-4.2.15_fix-aarch64.patch'] checksums = [ diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-9.3.0.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-9.3.0.eb index fd6e6693977..7e6b5eefbe8 100644 --- a/easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-9.3.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'HDF' version = '4.2.15' -homepage = 'https://www.hdfgroup.org/products/hdf4/' +homepage = 'https://support.hdfgroup.org/products/hdf4/' description = """ HDF (also known as HDF4) is a library and multi-object file format for @@ -13,7 +13,7 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '9.3.0'} toolchainopts = {'pic': True} -source_urls = ['http://www.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/'] +source_urls = ['http://support.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/'] sources = [SOURCELOWER_TAR_GZ] patches = ['HDF-4.2.15_fix-aarch64.patch'] checksums = [ diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.16-2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.16-2-GCCcore-12.3.0.eb index 453ca292d42..175aaba4731 100644 --- a/easybuild/easyconfigs/h/HDF/HDF-4.2.16-2-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.16-2-GCCcore-12.3.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'HDF' version = '4.2.16-2' -homepage = 'https://www.hdfgroup.org/products/hdf4/' +homepage = 'https://support.hdfgroup.org/products/hdf4/' description = """ HDF (also known as HDF4) is a library and multi-object file format for storing and managing data between machines. @@ -12,7 +12,7 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '12.3.0'} toolchainopts = {'pic': True} -source_urls = ['http://www.hdfgroup.org/ftp/%(name)s/releases/%(name)s%(version)s/src/'] +source_urls = ['http://support.hdfgroup.org/ftp/%(name)s/releases/%(name)s%(version)s/src/'] sources = [SOURCELOWER_TAR_GZ] checksums = [ diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.16-2-GCCcore-13.2.0.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.16-2-GCCcore-13.2.0.eb index 6f54f50d488..f2c20e888b9 100644 --- a/easybuild/easyconfigs/h/HDF/HDF-4.2.16-2-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.16-2-GCCcore-13.2.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'HDF' version = '4.2.16-2' -homepage = 'https://www.hdfgroup.org/products/hdf4/' +homepage = 'https://support.hdfgroup.org/products/hdf4/' description = """ HDF (also known as HDF4) is a library and multi-object file format for storing and managing data between machines. @@ -12,7 +12,7 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '13.2.0'} toolchainopts = {'pic': True} -source_urls = ['http://www.hdfgroup.org/ftp/%(name)s/releases/%(name)s%(version)s/src/'] +source_urls = ['http://support.hdfgroup.org/ftp/%(name)s/releases/%(name)s%(version)s/src/'] sources = [SOURCELOWER_TAR_GZ] checksums = [ diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.16-GCCcore-12.3.0.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.16-GCCcore-12.3.0.eb index d24dbfac77e..fd9d8d3d4ea 100644 --- a/easybuild/easyconfigs/h/HDF/HDF-4.2.16-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.16-GCCcore-12.3.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'HDF' version = '4.2.16' -homepage = 'https://www.hdfgroup.org/products/hdf4/' +homepage = 'https://support.hdfgroup.org/products/hdf4/' description = """ HDF (also known as HDF4) is a library and multi-object file format for @@ -13,7 +13,7 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '12.3.0'} toolchainopts = {'pic': True} -source_urls = ['http://www.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/'] +source_urls = ['http://support.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/'] sources = [SOURCELOWER_TAR_GZ] checksums = ['2bd48dcefb5ab4829fba27dca6fad20b842d495dfd64944b2412b2b0968bf167'] diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.3.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/h/HDF/HDF-4.3.0-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..de3ac32380a --- /dev/null +++ b/easybuild/easyconfigs/h/HDF/HDF-4.3.0-GCCcore-13.3.0.eb @@ -0,0 +1,58 @@ +easyblock = 'ConfigureMake' + +name = 'HDF' +version = '4.3.0' + +homepage = 'https://support.hdfgroup.org/products/hdf4/' +description = """ + HDF (also known as HDF4) is a library and multi-object file format for + storing and managing data between machines. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/HDFGroup/hdf4/archive/refs/tags/'] +sources = ['%(namelower)s%(version)s.tar.gz'] +checksums = ['a6639a556650e6ea8632a17b8188a69de844bdff54ce121a1fd5b92c8dd06cb1'] + +builddependencies = [ + ('binutils', '2.42'), + ('Bison', '3.8.2'), + ('flex', '2.6.4'), +] + +dependencies = [ + ('libjpeg-turbo', '3.0.1'), + ('Szip', '2.1.1'), + ('zlib', '1.3.1'), + ('libtirpc', '1.3.5'), +] + +preconfigopts = "LIBS='-ltirpc' " + +local_common_configopts = '--with-szlib=$EBROOTSZIP CFLAGS="$CFLAGS -I$EBROOTLIBTIRPC/include/tirpc" ' +local_common_configopts += '--includedir=%(installdir)s/include/%(namelower)s ' + +configopts = [ + local_common_configopts, + # Cannot build shared libraries and Fortran... + # https://trac.osgeo.org/gdal/wiki/HDF#IncompatibilitywithNetCDFLibraries + # netcdf must be disabled to allow HDF to be used by GDAL + local_common_configopts + "--enable-shared --disable-fortran --disable-netcdf", +] + + +sanity_check_paths = { + 'files': ['bin/h4cc', 'bin/ncdump', 'lib/libdf.a', 'lib/libhdf4.settings', 'lib/libmfhdf.a', 'lib/libmfhdf.so'], + 'dirs': ['include/%(namelower)s'], +} + +sanity_check_commands = [ + "h4cc --help", + "ncdump -V", +] + +modextrapaths = {'CPATH': 'include/%(namelower)s'} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.14.3-gompi-2023b.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.14.3-gompi-2023b.eb index f2aab3663a3..5cb05f4a4a1 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.14.3-gompi-2023b.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.14.3-gompi-2023b.eb @@ -12,7 +12,11 @@ toolchainopts = {'pic': True, 'usempi': True} source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src'] sources = [SOURCELOWER_TAR_GZ] -checksums = ['09cdb287aa7a89148c1638dd20891fdbae08102cf433ef128fd345338aa237c7'] +patches = ['HDF5-1.14.3_suppress_fp_exceptions.patch'] +checksums = [ + {'hdf5-1.14.3.tar.gz': '09cdb287aa7a89148c1638dd20891fdbae08102cf433ef128fd345338aa237c7'}, + {'HDF5-1.14.3_suppress_fp_exceptions.patch': 'bf33e579c93a16043c54b266321bbe95e4a8797f7fe6d096a13ce905ed2ffde7'}, +] # replace src include path with installation dir for $H5BLD_CPPFLAGS _regex = 's, -I[^[:space:]]+H5FDsubfiling , -I%(installdir)s/include ,g' diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.14.3-iimpi-2023b.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.14.3-iimpi-2023b.eb index 77fa0c12ab9..e180d8619ee 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.14.3-iimpi-2023b.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.14.3-iimpi-2023b.eb @@ -12,7 +12,11 @@ toolchainopts = {'pic': True, 'usempi': True} source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src'] sources = [SOURCELOWER_TAR_GZ] -checksums = ['09cdb287aa7a89148c1638dd20891fdbae08102cf433ef128fd345338aa237c7'] +patches = ['HDF5-1.14.3_suppress_fp_exceptions.patch'] +checksums = [ + {'hdf5-1.14.3.tar.gz': '09cdb287aa7a89148c1638dd20891fdbae08102cf433ef128fd345338aa237c7'}, + {'HDF5-1.14.3_suppress_fp_exceptions.patch': 'bf33e579c93a16043c54b266321bbe95e4a8797f7fe6d096a13ce905ed2ffde7'}, +] # replace src include path with installation dir for $H5BLD_CPPFLAGS _regex = 's, -I[^[:space:]]+H5FDsubfiling , -I%(installdir)s/include ,g' diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.14.3_suppress_fp_exceptions.patch b/easybuild/easyconfigs/h/HDF5/HDF5-1.14.3_suppress_fp_exceptions.patch new file mode 100644 index 00000000000..420125db46d --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.14.3_suppress_fp_exceptions.patch @@ -0,0 +1,223 @@ +See: https://github.com/HDFGroup/hdf5/commit/e0d095ebf020706ec7d7c82e6674b18f1a0a2d5b + +Created using +git checkout hdf5-1_14_3 +git cherry-pick e0d095ebf020706ec7d7c82e6674b18f1a0a2d5b + +commit 7c58dd64db0a6c04dea46dee1c7effbe8103ae82 +Author: Dana Robinson <43805+derobins@users.noreply.github.com> +Date: Tue Nov 7 08:13:30 2023 -0800 + + Disable FP exceptions in H5T init code (#3837) + + The H5T floating-point datatype initialization code can raise exceptions when handling signaling NaNs. This change disables FE_INVALID exceptions during initialization. + + Also removes the -ieee=full change for NAG Fortran as that shouldn't be necessary anymore. + + Fixes #3831 + +diff --git a/config/linux-gnulibc1 b/config/linux-gnulibc1 +index 328f8d3cec..079f08d96c 100644 +--- a/config/linux-gnulibc1 ++++ b/config/linux-gnulibc1 +@@ -173,10 +173,7 @@ case $FC_BASENAME in + nagfor) + + F9XSUFFIXFLAG="" +- # NOTE: The default is -ieee=stop, which will cause problems +- # when the H5T module performs floating-point type +- # introspection +- AM_FCFLAGS="$AM_FCFLAGS -ieee=full" ++ AM_FCFLAGS="$AM_FCFLAGS" + FSEARCH_DIRS="" + + # Production +diff --git a/release_docs/RELEASE.txt b/release_docs/RELEASE.txt +index 200576332b..7de2a56974 100644 +--- a/release_docs/RELEASE.txt ++++ b/release_docs/RELEASE.txt +@@ -250,6 +250,29 @@ Bug Fixes since HDF5-1.14.2 release + =================================== + Library + ------- ++ - Suppressed floating-point exceptions in H5T init code ++ ++ The floating-point datatype initialization code in H5Tinit_float.c ++ could raise FE_INVALID exceptions while munging bits and performing ++ comparisons that might involve NaN. This was not a problem when the ++ initialization code was executed in H5detect at compile time (prior ++ to 1.14.3), but now that the code is executed at library startup ++ (1.14.3+), these exceptions can be caught by user code, as is the ++ default in the NAG Fortran compiler. ++ ++ Starting in 1.14.4, we now suppress floating-point exceptions while ++ initializing the floating-point types and clear FE_INVALID before ++ restoring the original environment. ++ ++ Fixes GitHub #3831 ++ ++ - Fixed a file handle leak in the core VFD ++ ++ When opening a file with the core VFD and a file image, if the file ++ already exists, the file check would leak the POSIX file handle. ++ ++ Fixes GitHub issue #635 ++ + - Fixed some issues with chunk index metadata not getting read + collectively when collective metadata reads are enabled + +@@ -619,12 +642,6 @@ Known Problems + this release with link errors. As a result, Windows binaries for this release + will not include Fortran. The problem will be addressed in HDF5 1.14.4. + +- IEEE standard arithmetic enables software to raise exceptions such as overflow, +- division by zero, and other illegal operations without interrupting or halting +- the program flow. The HDF5 C library intentionally performs these exceptions. +- Therefore, the "-ieee=full" nagfor switch is necessary when compiling a program +- to avoid stopping on an exception. +- + CMake files do not behave correctly with paths containing spaces. + Do not use spaces in paths because the required escaping for handling spaces + results in very complex and fragile build files. +diff --git a/src/H5Tinit_float.c b/src/H5Tinit_float.c +index 3b9e127fe4..3213f00fec 100644 +--- a/src/H5Tinit_float.c ++++ b/src/H5Tinit_float.c +@@ -51,19 +51,23 @@ + * Function: DETECT_F + * + * Purpose: This macro takes a floating point type like `double' and +- * a base name like `natd' and detects byte order, mantissa +- * location, exponent location, sign bit location, presence or +- * absence of implicit mantissa bit, and exponent bias and +- * initializes a detected_t structure with those properties. ++ * and detects byte order, mantissa location, exponent location, ++ * sign bit location, presence or absence of implicit mantissa ++ * bit, and exponent bias and initializes a detected_t structure ++ * with those properties. ++ * ++ * Note that these operations can raise floating-point ++ * exceptions and building with some compiler options ++ * (especially Fortran) can cause problems. + *------------------------------------------------------------------------- + */ +-#define DETECT_F(TYPE, VAR, INFO) \ ++#define DETECT_F(TYPE, INFO) \ + do { \ +- TYPE _v1, _v2, _v3; \ +- unsigned char _buf1[sizeof(TYPE)], _buf3[sizeof(TYPE)]; \ +- unsigned char _pad_mask[sizeof(TYPE)]; \ +- unsigned char _byte_mask; \ +- int _i, _j, _last = (-1); \ ++ TYPE _v1, _v2, _v3; \ ++ uint8_t _buf1[sizeof(TYPE)], _buf3[sizeof(TYPE)]; \ ++ uint8_t _pad_mask[sizeof(TYPE)]; \ ++ uint8_t _byte_mask; \ ++ int _i, _j, _last = -1; \ + \ + memset(&INFO, 0, sizeof(INFO)); \ + INFO.size = sizeof(TYPE); \ +@@ -81,7 +85,7 @@ + _v1 = (TYPE)4.0L; \ + H5MM_memcpy(_buf1, (const void *)&_v1, sizeof(TYPE)); \ + for (_i = 0; _i < (int)sizeof(TYPE); _i++) \ +- for (_byte_mask = (unsigned char)1; _byte_mask; _byte_mask = (unsigned char)(_byte_mask << 1)) { \ ++ for (_byte_mask = (uint8_t)1; _byte_mask; _byte_mask = (uint8_t)(_byte_mask << 1)) { \ + _buf1[_i] ^= _byte_mask; \ + H5MM_memcpy((void *)&_v2, (const void *)_buf1, sizeof(TYPE)); \ + H5_GCC_CLANG_DIAG_OFF("float-equal") \ +@@ -118,7 +122,7 @@ + _v1 = (TYPE)1.0L; \ + _v2 = (TYPE)-1.0L; \ + if (H5T__bit_cmp(sizeof(TYPE), INFO.perm, &_v1, &_v2, _pad_mask, &(INFO.sign)) < 0) \ +- HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "failed to detect byte order"); \ ++ HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "failed to determine sign bit"); \ + \ + /* Mantissa */ \ + INFO.mpos = 0; \ +@@ -126,12 +130,11 @@ + _v1 = (TYPE)1.0L; \ + _v2 = (TYPE)1.5L; \ + if (H5T__bit_cmp(sizeof(TYPE), INFO.perm, &_v1, &_v2, _pad_mask, &(INFO.msize)) < 0) \ +- HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "failed to detect byte order"); \ ++ HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "failed to determine mantissa"); \ + INFO.msize += 1 + (unsigned)(INFO.imp ? 0 : 1) - INFO.mpos; \ + \ + /* Exponent */ \ +- INFO.epos = INFO.mpos + INFO.msize; \ +- \ ++ INFO.epos = INFO.mpos + INFO.msize; \ + INFO.esize = INFO.sign - INFO.epos; \ + \ + _v1 = (TYPE)1.0L; \ +@@ -456,17 +459,24 @@ H5T__set_precision(H5T_fpoint_det_t *d) + herr_t H5_NO_UBSAN + H5T__init_native_float_types(void) + { ++ fenv_t saved_fenv; + H5T_fpoint_det_t det; + H5T_t *dt = NULL; + herr_t ret_value = SUCCEED; + + FUNC_ENTER_PACKAGE + ++ /* Turn off floating-point exceptions while initializing to avoid ++ * tripping over signaling NaNs while looking at "don't care" bits. ++ */ ++ if (feholdexcept(&saved_fenv) != 0) ++ HSYS_GOTO_ERROR(H5E_DATATYPE, H5E_CANTSET, FAIL, "can't save floating-point environment"); ++ + /* H5T_NATIVE_FLOAT */ + + /* Get the type's characteristics */ + memset(&det, 0, sizeof(H5T_fpoint_det_t)); +- DETECT_F(float, FLOAT, det); ++ DETECT_F(float, det); + + /* Allocate and fill type structure */ + if (NULL == (dt = H5T__alloc())) +@@ -497,7 +507,7 @@ H5T__init_native_float_types(void) + + /* Get the type's characteristics */ + memset(&det, 0, sizeof(H5T_fpoint_det_t)); +- DETECT_F(double, DOUBLE, det); ++ DETECT_F(double, det); + + /* Allocate and fill type structure */ + if (NULL == (dt = H5T__alloc())) +@@ -528,7 +538,7 @@ H5T__init_native_float_types(void) + + /* Get the type's characteristics */ + memset(&det, 0, sizeof(H5T_fpoint_det_t)); +- DETECT_F(long double, LDOUBLE, det); ++ DETECT_F(long double, det); + + /* Allocate and fill type structure */ + if (NULL == (dt = H5T__alloc())) +@@ -561,6 +571,14 @@ H5T__init_native_float_types(void) + H5T_native_order_g = det.order; + + done: ++ /* Clear any FE_INVALID exceptions from NaN handling */ ++ if (feclearexcept(FE_INVALID) != 0) ++ HSYS_GOTO_ERROR(H5E_DATATYPE, H5E_CANTSET, FAIL, "can't clear floating-point exceptions"); ++ ++ /* Restore the original environment */ ++ if (feupdateenv(&saved_fenv) != 0) ++ HSYS_GOTO_ERROR(H5E_DATATYPE, H5E_CANTSET, FAIL, "can't restore floating-point environment"); ++ + if (ret_value < 0) { + if (dt != NULL) { + dt->shared = H5FL_FREE(H5T_shared_t, dt->shared); +diff --git a/src/H5private.h b/src/H5private.h +index 14a0ac3225..3aaa0d5245 100644 +--- a/src/H5private.h ++++ b/src/H5private.h +@@ -26,6 +26,7 @@ + #include + #include + #include ++#include + #include + #include + #include diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.14.5-gompi-2024a.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.14.5-gompi-2024a.eb new file mode 100644 index 00000000000..59171962924 --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.14.5-gompi-2024a.eb @@ -0,0 +1,27 @@ +name = 'HDF5' +# Note: Odd minor releases are only RCs and should not be used. +version = '1.14.5' + +homepage = 'https://portal.hdfgroup.org/display/support' +description = """HDF5 is a data model, library, and file format for storing and managing data. + It supports an unlimited variety of datatypes, and is designed for flexible + and efficient I/O and for high volume and complex data.""" + +toolchain = {'name': 'gompi', 'version': '2024a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://github.com/HDFGroup/hdf5/archive'] +sources = ['hdf5_%(version)s.tar.gz'] +checksums = ['c83996dc79080a34e7b5244a1d5ea076abfd642ec12d7c25388e2fdd81d26350'] + +dependencies = [ + ('zlib', '1.3.1'), + ('Szip', '2.1.1'), +] + +postinstallcmds = [ + 'sed -i -r "s, -I[^[:space:]]+H5FDsubfiling , -I%(installdir)s/include ,g" %(installdir)s/bin/h5c++', + 'sed -i -r "s, -I[^[:space:]]+H5FDsubfiling , -I%(installdir)s/include ,g" %(installdir)s/bin/h5pcc', +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.14.5-iimpi-2024a.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.14.5-iimpi-2024a.eb new file mode 100644 index 00000000000..153463a2234 --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.14.5-iimpi-2024a.eb @@ -0,0 +1,26 @@ +name = 'HDF5' +# Note: Odd minor releases are only RCs and should not be used. +version = '1.14.5' + +homepage = 'https://portal.hdfgroup.org/display/support' +description = """HDF5 is a data model, library, and file format for storing and managing data. + It supports an unlimited variety of datatypes, and is designed for flexible + and efficient I/O and for high volume and complex data.""" + +toolchain = {'name': 'iimpi', 'version': '2024a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://github.com/HDFGroup/hdf5/archive'] +sources = ['hdf5_%(version)s.tar.gz'] +checksums = ['c83996dc79080a34e7b5244a1d5ea076abfd642ec12d7c25388e2fdd81d26350'] + +# replace src include path with installation dir for $H5BLD_CPPFLAGS +_regex = 's, -I[^[:space:]]+H5FDsubfiling , -I%(installdir)s/include ,g' +postinstallcmds = ['sed -i -r "%s" %%(installdir)s/bin/%s' % (_regex, x) for x in ['h5c++', 'h5pcc']] + +dependencies = [ + ('zlib', '1.3.1'), + ('Szip', '2.1.1'), +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/HERRO/HERRO-0.1.0_20240808-foss-2023a.eb b/easybuild/easyconfigs/h/HERRO/HERRO-0.1.0_20240808-foss-2023a.eb new file mode 100644 index 00000000000..a4057965c49 --- /dev/null +++ b/easybuild/easyconfigs/h/HERRO/HERRO-0.1.0_20240808-foss-2023a.eb @@ -0,0 +1,382 @@ +easyblock = 'Cargo' + +name = 'HERRO' +version = '0.1.0_20240808' +local_commit = 'deccc46' + +homepage = 'https://github.com/lbcb-sci/herro' +description = """ +HERRO is a highly-accurate, haplotype-aware, deep-learning tool for error correction of Nanopore R10.4.1 or +R9.4.1 reads (read length of >= 10 kbps is recommended). +""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['https://github.com/lbcb-sci/herro/archive/'] +sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}] + +builddependencies = [ + ('Rust', '1.75.0'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('bzip2', '1.0.8'), + ('libffi', '3.4.4'), + ('libnsl', '2.0.1'), + ('SQLite', '3.42.0'), + ('util-linux', '2.39'), + ('zlib', '1.2.13'), + ('ncurses', '6.4'), + ('libreadline', '8.2'), + ('SeqKit', '2.3.1', '', SYSTEM), + ('Tk', '8.6.13'), + ('XZ', '5.4.2'), + ('matplotlib', '3.7.2'), + ('edlib', '1.3.9'), + ('h5py', '3.9.0'), + ('duplex-tools', '0.3.3'), + ('PyTorch', '2.1.2'), + ('Pillow', '10.0.0'), + ('zstd', '1.5.5'), + ('parasail', '2.6.2'), +] + +exts_defaultclass = 'PythonPackage' +exts_default_options = { + 'source_urls': [PYPI_SOURCE], + 'download_dep_fail': True, + 'use_pip': True, + 'sanity_pip_check': True, + 'preinstallopts': '', + 'installopts': '', +} + +exts_list = [ + ('zstandard', '0.22.0', { + 'checksums': ['8226a33c542bcb54cd6bd0a366067b610b41713b64c9abec1bc4533d69f51e70'], + }), + ('Porechop', '20240119', { + 'modulename': 'porechop', + 'source_urls': ['https://github.com/dehui333/Porechop/archive/'], + 'sources': [{'download_filename': 'd2e77c6.tar.gz', 'filename': SOURCE_TAR_GZ}], + 'checksums': ['6e5ff3a780fc2855b0101b4a6102437d9a0fc201e40ffabc44c0c67d7c9ad621'], + }), +] + +# use tch version 0.14.0 - compatible with PyTorch 2.1 +local_torch_opts = "sed -i 's/tch = \"0.13.0\"/tch = \"0.14.0\"/' Cargo.toml && " +local_torch_opts += 'export LIBTORCH_BYPASS_VERSION_CHECK=1 && export LIBTORCH_USE_PYTORCH=1 && ' +local_torch_opts += 'export LIBTORCH=$EBROOTPYTORCH/lib && RUSTFLAGS="-Ctarget-cpu=native"' +prebuildopts = pretestopts = preinstallopts = local_torch_opts + +# copy scripts to /bin to be easier to run scripts for users +postinstallcmds = [ + 'cp -a %(start_dir)s/scripts/* %(installdir)s/bin', + 'rm %(installdir)s/bin/herro-env.yml', + "chmod a+rx %(installdir)s/bin/*.sh", + "chmod a-x %(installdir)s/bin/*.py", +] + +_bins = [ + 'herro', + 'porechop', + 'no_split.sh', + 'postprocess_corrected.sh', + 'create_batched_alignments.sh', + 'porechop_with_split.sh', + 'preprocess.sh', + 'batch.py', + 'create_clusters.py', +] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in _bins], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["herro --help"] + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +modloadmsg = """ +To run scripts from /scripts directory just run .sh +Do not run it as scripts/.sh +For example - run preprocess.sh as: + $ preprocess.sh +""" + +crates = [ + ('adler2', '2.0.0'), + ('aes', '0.8.4'), + ('anstream', '0.6.15'), + ('anstyle', '1.0.8'), + ('anstyle-parse', '0.2.5'), + ('anstyle-query', '1.1.1'), + ('anstyle-wincon', '3.0.4'), + ('anyhow', '1.0.86'), + ('approx', '0.5.1'), + ('autocfg', '1.3.0'), + ('base64ct', '1.6.0'), + ('block-buffer', '0.10.4'), + ('buffer-redux', '1.0.2'), + ('bytecount', '0.6.8'), + ('byteorder', '1.5.0'), + ('bzip2', '0.4.4'), + ('bzip2-sys', '0.1.11+1.0.8'), + ('cc', '1.1.13'), + ('cfg-if', '1.0.0'), + ('cipher', '0.4.4'), + ('clap', '4.4.18'), + ('clap_builder', '4.4.18'), + ('clap_derive', '4.4.7'), + ('clap_lex', '0.6.0'), + ('colorchoice', '1.0.2'), + ('console', '0.15.8'), + ('constant_time_eq', '0.1.5'), + ('cpufeatures', '0.2.13'), + ('crc32fast', '1.4.2'), + ('crossbeam-channel', '0.5.13'), + ('crossbeam-utils', '0.8.20'), + ('crunchy', '0.2.2'), + ('crypto-common', '0.1.6'), + ('deranged', '0.3.11'), + ('digest', '0.10.7'), + ('either', '1.13.0'), + ('encode_unicode', '0.3.6'), + ('flate2', '1.0.32'), + ('generic-array', '0.14.7'), + ('getrandom', '0.2.15'), + ('glob', '0.3.1'), + ('half', '2.4.1'), + ('heck', '0.4.1'), + ('hmac', '0.12.1'), + ('indicatif', '0.17.8'), + ('inout', '0.1.3'), + ('instant', '0.1.13'), + ('is_terminal_polyfill', '1.70.1'), + ('itertools', '0.12.1'), + ('itoa', '1.0.11'), + ('jemalloc-sys', '0.5.4+5.3.0-patched'), + ('jemallocator', '0.5.4'), + ('jobserver', '0.1.32'), + ('lazy_static', '1.5.0'), + ('libc', '0.2.158'), + ('lzma-sys', '0.1.20'), + ('matrixmultiply', '0.3.9'), + ('memchr', '2.7.4'), + ('miniz_oxide', '0.8.0'), + ('ndarray', 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('strsim', '0.10.0'), + ('subtle', '2.6.1'), + ('syn', '1.0.109'), + ('syn', '2.0.75'), + ('tch', '0.14.0'), + ('thiserror', '1.0.63'), + ('thiserror-impl', '1.0.63'), + ('time', '0.3.36'), + ('time-core', '0.1.2'), + ('torch-sys', '0.14.0'), + ('typenum', '1.17.0'), + ('ucd-trie', '0.1.6'), + ('unicode-ident', '1.0.12'), + ('unicode-width', '0.1.13'), + ('utf8parse', '0.2.2'), + ('version_check', '0.9.5'), + ('wasi', '0.11.0+wasi-snapshot-preview1'), + ('windows-sys', '0.52.0'), + ('windows-targets', '0.52.6'), + ('windows_aarch64_gnullvm', '0.52.6'), + ('windows_aarch64_msvc', '0.52.6'), + ('windows_i686_gnu', '0.52.6'), + ('windows_i686_gnullvm', '0.52.6'), + ('windows_i686_msvc', '0.52.6'), + ('windows_x86_64_gnu', '0.52.6'), + ('windows_x86_64_gnullvm', '0.52.6'), + ('windows_x86_64_msvc', '0.52.6'), + ('xz2', '0.1.7'), + ('zerocopy', '0.7.35'), + ('zerocopy-derive', '0.7.35'), + ('zip', '0.6.6'), + ('zstd', '0.11.2+zstd.1.5.2'), + ('zstd', '0.13.2'), + ('zstd-safe', '5.0.2+zstd.1.5.2'), + ('zstd-safe', '7.2.1'), + ('zstd-sys', '2.0.13+zstd.1.5.6'), +] + +checksums = [ + {'HERRO-0.1.0_20240808.tar.gz': '885f64ab097c89cf8ec8ec38625c6325271997e89636de756aa12fb68aab7598'}, + {'adler2-2.0.0.tar.gz': '512761e0bb2578dd7380c6baaa0f4ce03e84f95e960231d1dec8bf4d7d6e2627'}, + {'aes-0.8.4.tar.gz': 'b169f7a6d4742236a0a00c541b845991d0ac43e546831af1249753ab4c3aa3a0'}, + {'anstream-0.6.15.tar.gz': '64e15c1ab1f89faffbf04a634d5e1962e9074f2741eef6d97f3c4e322426d526'}, + {'anstyle-1.0.8.tar.gz': '1bec1de6f59aedf83baf9ff929c98f2ad654b97c9510f4e70cf6f661d49fd5b1'}, + {'anstyle-parse-0.2.5.tar.gz': 'eb47de1e80c2b463c735db5b217a0ddc39d612e7ac9e2e96a5aed1f57616c1cb'}, + {'anstyle-query-1.1.1.tar.gz': '6d36fc52c7f6c869915e99412912f22093507da8d9e942ceaf66fe4b7c14422a'}, + {'anstyle-wincon-3.0.4.tar.gz': '5bf74e1b6e971609db8ca7a9ce79fd5768ab6ae46441c572e46cf596f59e57f8'}, + {'anyhow-1.0.86.tar.gz': 'b3d1d046238990b9cf5bcde22a3fb3584ee5cf65fb2765f454ed428c7a0063da'}, + 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'fa4f8080344d4671fb4e831a13ad1e68092748387dfc4f55e356242fae12ce3e'}, + {'zip-0.6.6.tar.gz': '760394e246e4c28189f19d488c058bf16f564016aefac5d32bb1f3b51d5e9261'}, + {'zstd-0.11.2+zstd.1.5.2.tar.gz': '20cc960326ece64f010d2d2107537f26dc589a6573a316bd5b1dba685fa5fde4'}, + {'zstd-0.13.2.tar.gz': 'fcf2b778a664581e31e389454a7072dab1647606d44f7feea22cd5abb9c9f3f9'}, + {'zstd-safe-5.0.2+zstd.1.5.2.tar.gz': '1d2a5585e04f9eea4b2a3d1eca508c4dee9592a89ef6f450c11719da0726f4db'}, + {'zstd-safe-7.2.1.tar.gz': '54a3ab4db68cea366acc5c897c7b4d4d1b8994a9cd6e6f841f8964566a419059'}, + {'zstd-sys-2.0.13+zstd.1.5.6.tar.gz': '38ff0f21cfee8f97d94cef41359e0c89aa6113028ab0291aa8ca0038995a95aa'}, +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/h/HISAT2/HISAT2-2.2.1-gompi-2023a.eb b/easybuild/easyconfigs/h/HISAT2/HISAT2-2.2.1-gompi-2023a.eb new file mode 100644 index 00000000000..89974da79ff --- /dev/null +++ b/easybuild/easyconfigs/h/HISAT2/HISAT2-2.2.1-gompi-2023a.eb @@ -0,0 +1,61 @@ +## +# This is a contribution from DeepThought HPC Service, Flinders University, Adelaide, Australia +# Homepage: https://staff.flinders.edu.au/research/deep-thought +# +# Authors:: Robert Qiao +# License:: GPLv3.0 +# +# Notes:: +# 2.2.1 - changes from Adam Huffman +# Bumped to foss-2021b +# J. Sassmannshausen + +easyblock = 'MakeCp' + +name = 'HISAT2' +version = '2.2.1' + +homepage = 'https://daehwankimlab.github.io/hisat2' +description = """HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads + (both DNA and RNA) against the general human population (as well as against a single reference genome).""" + +toolchain = {'name': 'gompi', 'version': '2023a'} + +sources = [{ + 'source_urls': ['https://cloud.biohpc.swmed.edu/index.php/s/fE9QCsX3NH4QwBi'], + 'download_filename': 'download', + 'filename': '%(namelower)s-%(version)s-source.zip', +}] +patches = [ + 'hisat2-libname-fix.patch', +] +checksums = [ + {'hisat2-2.2.1-source.zip': '48e933330d4d8470d2b3dfe7ec3918f2e98a75f7381891e23b7df1fb4f135eb1'}, + {'hisat2-libname-fix.patch': '8aa91d1dd6455b96c10ce48827f8313b006241d815fbe6382422dbae3b610726'}, +] + +dependencies = [ + ('ncbi-vdb', '3.0.10'), + ('SRA-Toolkit', '3.0.10'), # provides NGS +] + +buildopts = 'CC="$CC" CPP="$CXX" RELEASE_FLAGS="$CFLAGS" ' +buildopts += 'USE_SRA=1 NCBI_NGS_DIR="$EBROOTSRAMINTOOLKIT" NCBI_VDB_DIR="$EBROOTNCBIMINVDB" ' +# add new libncbi-ngs from the NGS merge into SRA-Toolkit v3 +buildopts += 'SRA_LIB="-lncbi-ngs-c++ -lngs-c++ -lncbi-ngs -lncbi-vdb -ldl"' + +local_executables = ['hisat2', 'hisat2-align-l', 'hisat2-align-s', 'hisat2-build', 'hisat2-build-l', 'hisat2-build-s', + 'hisat2-inspect', 'hisat2-inspect-s', 'hisat2-inspect-l', 'hisat2-repeat', 'extract_exons.py', + 'extract_splice_sites.py', 'hisat2_extract_exons.py', 'hisat2_extract_snps_haplotypes_UCSC.py', + 'hisat2_extract_snps_haplotypes_VCF.py', 'hisat2_extract_splice_sites.py', + 'hisat2_read_statistics.py', 'hisat2_simulate_reads.py'] +files_to_copy = [(local_executables, 'bin'), 'scripts', 'example'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_executables], + 'dirs': ['scripts', 'example'], +} + +sanity_check_commands = ["hisat2 --help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/h/HMMER/HMMER-3.4-gompi-2023b.eb b/easybuild/easyconfigs/h/HMMER/HMMER-3.4-gompi-2023b.eb new file mode 100644 index 00000000000..bb76dc1e937 --- /dev/null +++ b/easybuild/easyconfigs/h/HMMER/HMMER-3.4-gompi-2023b.eb @@ -0,0 +1,78 @@ +## +# EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Nils Christian , +# Fotis Georgatos +# Updated by: Filip Kružík (INUITS) +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a +# component of the policy: +# https://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +## + +easyblock = 'ConfigureMake' + +name = 'HMMER' +version = '3.4' + +homepage = 'http://hmmer.org/' +description = """HMMER is used for searching sequence databases for homologs + of protein sequences, and for making protein sequence alignments. It + implements methods using probabilistic models called profile hidden Markov + models (profile HMMs). Compared to BLAST, FASTA, and other sequence + alignment and database search tools based on older scoring methodology, + HMMER aims to be significantly more accurate and more able to detect remote + homologs because of the strength of its underlying mathematical models. In the + past, this strength came at significant computational expense, but in the new + HMMER3 project, HMMER is now essentially as fast as BLAST.""" + +toolchain = {'name': 'gompi', 'version': '2023b'} + +source_urls = [ + 'http://eddylab.org/software/hmmer/', + 'http://eddylab.org/software/hmmer%(version_major)s/%(version)s/', +] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['ca70d94fd0cf271bd7063423aabb116d42de533117343a9b27a65c17ff06fbf3'] + +builddependencies = [ + ('Python', '3.11.5'), + ('Perl', '5.38.0'), +] + +# replace hardcoded /usr/bin/perl shebang lines with '/usr/bin/env perl' across all files +preconfigopts = "grep '/usr/bin/perl' . | cut -f1 -d: | xargs echo sed -i 's@/usr/bin/perl@/usr/bin/env perl@g' && " + +configopts = '--enable-mpi' + +buildopts = ' V=1 ' + +testopts = buildopts +runtest = 'check' + +installopts = ' && cd easel && make install' + +local_bin_files = ['alimask', 'esl-afetch', 'esl-alimanip', 'esl-alimap', 'esl-alimask', + 'esl-alimerge', 'esl-alipid', 'esl-alirev', 'esl-alistat', 'esl-compalign', + 'esl-compstruct', 'esl-construct', 'esl-histplot', 'esl-mask', 'esl-reformat', + 'esl-selectn', 'esl-seqrange', 'esl-seqstat', 'esl-sfetch', 'esl-shuffle', + 'esl-ssdraw', 'esl-translate', 'esl-weight', 'hmmalign', 'hmmbuild', + 'hmmconvert', 'hmmemit', 'hmmfetch', 'hmmlogo', 'hmmpgmd', 'hmmpress', + 'hmmscan', 'hmmsearch', 'hmmsim', 'hmmstat', 'jackhmmer', 'makehmmerdb', + 'nhmmer', 'nhmmscan', 'phmmer'] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in local_bin_files], + 'dirs': ['bin', 'share'], +} + +sanity_check_commands = [ + "esl-construct -h", + "hmmsearch -h", + "nhmmer -h", +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/h/HOLE2/HOLE2-2.3.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/h/HOLE2/HOLE2-2.3.1-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..addf2b3cf87 --- /dev/null +++ b/easybuild/easyconfigs/h/HOLE2/HOLE2-2.3.1-GCCcore-12.3.0.eb @@ -0,0 +1,43 @@ +easyblock = 'ConfigureMake' + +name = 'HOLE2' +version = '2.3.1' + +homepage = 'https://www.holeprogram.org/' +description = """HOLE is a program that allows the analysis and visualisation of +the pore dimensions of the holes through molecular structures of ion channels""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://github.com/osmart/hole2/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['1109dd3d15a63b6c72833314f3ef0fcfdf56341e634fbd2195df7427e6b435ae'] + +builddependencies = [ + ('binutils', '2.40'), +] + +skipsteps = ['configure'] + +prebuildopts = "".join([ + "source source.apache && ", + "cd src && ", +]) + +preinstallopts = prebuildopts +install_cmd = "make install-all PREFIX=%(installdir)s" + +parallel = 1 + +local_binary = [ + 'bln2gnu', 'capost2gnu', 'grd2gnu', 'hole', 'labqpt', 'make_post2gnu', + 'make_post_map', 'qplot', 'qpt_conv', 'sos_triangle', 'sph_process', + 'vdwdot', 'vmd_triangles_to_lines' +] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_binary], + 'dirs': ['bin', 'share/hole2/rad'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/h/HOMER/HOMER-4.11-foss-2023a-R-4.3.2.eb b/easybuild/easyconfigs/h/HOMER/HOMER-4.11-foss-2023a-R-4.3.2.eb new file mode 100644 index 00000000000..49de16a3d99 --- /dev/null +++ b/easybuild/easyconfigs/h/HOMER/HOMER-4.11-foss-2023a-R-4.3.2.eb @@ -0,0 +1,49 @@ +easyblock = 'Binary' + +name = 'HOMER' +version = '4.11' +versionsuffix = '-R-%(rver)s' + +homepage = "http://homer.ucsd.edu/homer/" +description = """HOMER (Hypergeometric Optimization of Motif EnRichment) is a suite of tools for Motif Discovery and + next-gen sequencing analysis. It is a collection of command line programs for unix-style operating systems written + in Perl and C++. HOMER was primarily written as a de novo motif discovery algorithm and is well suited for finding + 8-20 bp motifs in large scale genomics data. HOMER contains many useful tools for analyzing ChIP-Seq, GRO-Seq, + RNA-Seq, DNase-Seq, Hi-C and numerous other types of functional genomics sequencing data sets.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['http://homer.ucsd.edu/homer'] +sources = ['configureHomer.pl'] +checksums = ['ccdaa3004a0e0df0882634671d4a1acc88364761e0e6c7ea329ebbf1eb729537'] + +builddependencies = [ + ('wget', '1.24.5'), + ('Zip', '3.0'), + ('UnZip', '6.0'), +] + +dependencies = [ + ('Perl', '5.36.1'), + ('R', '4.3.2'), + ('SAMtools', '1.18'), + ('R-bundle-Bioconductor', '3.18', versionsuffix) +] + +postinstallcmds = ["cd %(installdir)s && perl ./configureHomer.pl -install homer -version v%(version)s"] + +sanity_check_paths = { + 'files': [ + 'bin/homer', + 'bin/getGenomeTilingPeaks', + 'config.txt', + 'DoughnutDocumentation.pdf', + 'data/accession/homologene.data', + 'motifs/hnf1b.motif', + ], + 'dirs': ['bin', 'data', 'motifs', 'update'], +} + +sanity_check_commands = ["%(namelower)s --help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/h/HOMER/HOMER-4.11.1-foss-2022b.eb b/easybuild/easyconfigs/h/HOMER/HOMER-4.11.1-foss-2022b.eb new file mode 100644 index 00000000000..0131cad9771 --- /dev/null +++ b/easybuild/easyconfigs/h/HOMER/HOMER-4.11.1-foss-2022b.eb @@ -0,0 +1,57 @@ +easyblock = 'Binary' + +name = 'HOMER' +version = '4.11.1' + +homepage = 'http://homer.ucsd.edu/homer/' +description = """HOMER (Hypergeometric Optimization of Motif EnRichment) is a suite of tools for Motif Discovery and +next-gen sequencing analysis. It is a collection of command line programs for unix-style operating systems written +in Perl and C++. HOMER was primarily written as a de novo motif discovery algorithm and is well suited for finding +8-20 bp motifs in large scale genomics data. HOMER contains many useful tools for analyzing ChIP-Seq, GRO-Seq, +RNA-Seq, DNase-Seq, Hi-C and numerous other types of functional genomics sequencing data sets.""" + +toolchain = {'name': 'foss', 'version': '2022b'} + +source_urls = ['http://homer.ucsd.edu/homer/data/software'] +sources = ['homer.v%(version)s.zip'] +checksums = ['80d1cd00616729894017b24a36a2ef81f9cde8bd364e875aead1e0cfb500c82b'] + +extract_sources = True + +builddependencies = [ + ('wget', '1.21.4'), + ('Zip', '3.0'), + ('UnZip', '6.0'), +] + +dependencies = [ + ('Perl', '5.36.0'), + ('weblogo', '2.8.2'), + ('SAMtools', '1.17'), + ('Kent_tools', '461'), + ('R', '4.2.2'), + ('R-bundle-Bioconductor', '3.16', '-R-4.2.2') +] + +buildininstalldir = True +skipsteps = ['install'] + +# This installs the entire suite, to install only base Homer package run : +# cd %(installdir)s; perl ./configureHomer.pl -install homer +postinstallcmds = ['perl ./configureHomer.pl -install -all -keepScript'] + +sanity_check_paths = { + 'dirs': ['bin', 'data', 'motifs', 'update'], + 'files': [ + 'bin/homer', + 'bin/getGenomeTilingPeaks', + 'config.txt', + 'DoughnutDocumentation.pdf', + 'data/accession/homologene.data', + 'motifs/hnf1b.motif', + ], +} + +sanity_check_commands = ["%(namelower)s --help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/h/HPDBSCAN/HPDBSCAN-20210826-foss-2020b.eb b/easybuild/easyconfigs/h/HPDBSCAN/HPDBSCAN-20210826-foss-2020b.eb index b96581acb3c..5a0f068b7d1 100644 --- a/easybuild/easyconfigs/h/HPDBSCAN/HPDBSCAN-20210826-foss-2020b.eb +++ b/easybuild/easyconfigs/h/HPDBSCAN/HPDBSCAN-20210826-foss-2020b.eb @@ -12,7 +12,11 @@ toolchainopts = {'usempi': True} source_urls = ['https://github.com/Markus-Goetz/hpdbscan/archive/'] sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': '%(name)s-%(version)s.tar.gz'}] -checksums = ['52ff343f77aeea5a425a911d88a57314c6bc877c18209eb53819d114421a868d'] +patches = ['HPDBSCAN-20210826_fix-numpy-headers.patch'] +checksums = [ + {'HPDBSCAN-20210826.tar.gz': '52ff343f77aeea5a425a911d88a57314c6bc877c18209eb53819d114421a868d'}, + {'HPDBSCAN-20210826_fix-numpy-headers.patch': 'cceb6a8cc15cb9bfbf92e5944f0398c1ac9db85a04fea3f7b1e0a0595fb530b1'}, +] builddependencies = [ ('CMake', '3.18.4'), diff --git a/easybuild/easyconfigs/h/HPDBSCAN/HPDBSCAN-20210826_fix-numpy-headers.patch b/easybuild/easyconfigs/h/HPDBSCAN/HPDBSCAN-20210826_fix-numpy-headers.patch new file mode 100644 index 00000000000..bbc6f3764ba --- /dev/null +++ b/easybuild/easyconfigs/h/HPDBSCAN/HPDBSCAN-20210826_fix-numpy-headers.patch @@ -0,0 +1,81 @@ +Fix finding numpy includes such as ``. +Fixes failing compilation unless the numpy headers are in the compilers search path (e.g. $CPATH) +See https://github.com/Markus-Goetz/hpdbscan/pull/12 + +Author: Alexander Grund (TU Dresden) + +diff --git a/CMakeLists.txt b/CMakeLists.txt +index 6c3e450..b25c597 100644 +--- a/CMakeLists.txt ++++ b/CMakeLists.txt +@@ -44,7 +44,7 @@ TARGET_COMPILE_OPTIONS(hpdbscan-bin PRIVATE ${OpenMP_CXX_FLAGS}) + + ## hdf5 + FIND_PACKAGE(HDF5 1.8.10 REQUIRED) +-INCLUDE_DIRECTORIES("${HDF5_INCLUDE_DIRS}") ++TARGET_INCLUDE_DIRECTORIES(hpdbscan-bin PRIVATE "${HDF5_INCLUDE_DIRS}") + TARGET_LINK_LIBRARIES(hpdbscan-bin PRIVATE "${HDF5_LIBRARIES}") + + ## swig and python detection for optional bindings +@@ -57,10 +57,9 @@ IF(SWIG_FOUND) + MESSAGE("PYTHON HEADERS NOT FOUND, BUILDING WITHOUT BINDINGS") + MESSAGE("TRY INSTALLING THE python-dev OR python-devel PACKAGE") + ELSE() +- INCLUDE_DIRECTORIES(${PYTHON_INCLUDE_DIRS}) + FIND_PACKAGE(NumPy) +- IF(NUMPY_FOUND) +- EXECUTE_PROCESS(COMMAND swig -c++ -python -I"${PYTHON_INCLUDE_DIRS}" -I"${NUMPY_INCLUDE_DIRS}" -o "${CMAKE_CURRENT_BINARY_DIR}/hpdbscan_wrap.cpp" "${CMAKE_CURRENT_SOURCE_DIR}/swig/hpdbscan.i") ++ IF(NumPy_FOUND) ++ EXECUTE_PROCESS(COMMAND swig -c++ -python -o "${CMAKE_CURRENT_BINARY_DIR}/hpdbscan_wrap.cpp" "${CMAKE_CURRENT_SOURCE_DIR}/swig/hpdbscan.i") + ADD_LIBRARY(hpdbscan-binding SHARED ${CMAKE_CURRENT_BINARY_DIR}/hpdbscan_wrap.cpp) + IF(MPI_FOUND) + FIND_PACKAGE(MPI4PY) +@@ -71,8 +70,10 @@ IF(SWIG_FOUND) + MESSAGE("MPI FOUND, BUT MPI4PY MISSING, BINDING WILL BE BUILT WITHOUT MPI SUPPORT") + ENDIF() + ENDIF() ++ TARGET_INCLUDE_DIRECTORIES(hpdbscan-binding PRIVATE ${PYTHON_INCLUDE_DIRS} ${NUMPY_INCLUDE_DIRS}) + TARGET_LINK_LIBRARIES(hpdbscan-binding PRIVATE ${OpenMP_CXX_FLAGS}) + TARGET_COMPILE_OPTIONS(hpdbscan-binding PRIVATE ${OpenMP_CXX_FLAGS}) ++ TARGET_INCLUDE_DIRECTORIES(hpdbscan-binding PRIVATE "${HDF5_INCLUDE_DIRS}") + TARGET_LINK_LIBRARIES(hpdbscan-binding PRIVATE "${HDF5_LIBRARIES}") + + # rename the library +diff --git a/cmake/FindNumPy.cmake b/cmake/FindNumPy.cmake +index ba0d7fd..8e353b5 100644 +--- a/cmake/FindNumPy.cmake ++++ b/cmake/FindNumPy.cmake +@@ -1,28 +1,15 @@ + # modified from https://github.com/live-clones/xdmf/blob/master/CMake/FindMPI4PY.cmake + +-IF(NOT NUMPY_INCLUDE_DIR) ++IF(NOT NUMPY_INCLUDE_DIRS) + EXECUTE_PROCESS(COMMAND + "${PYTHON_EXECUTABLE}" "-c" "import numpy as np; print(np.get_include())" +- OUTPUT_VARIABLE NUMPY_INCLUDE_DIR ++ OUTPUT_VARIABLE NUMPY_COMMAND_OUTPUT + RESULT_VARIABLE NUMPY_COMMAND_RESULT + OUTPUT_STRIP_TRAILING_WHITESPACE) +- IF(NUMPY_COMMAND_RESULT) +- MESSAGE("numpy not found") +- SET(NUMPY_FOUND FALSE) +- ELSE() +- IF(NUMPY_INCLUDE_DIR MATCHES "Traceback") +- MESSAGE("numpy matches traceback") +- ## Did not successfully include NUMPY +- SET(NUMPY_FOUND FALSE) +- ELSE() +- ## successful +- SET(NUMPY_FOUND TRUE) +- SET(NUMPY_INCLUDE_DIR ${NUMPY_INCLUDE_DIR} CACHE STRING "numpy include path") +- ENDIF() ++ IF(NOT NUMPY_COMMAND_RESULT AND NOT NUMPY_COMMAND_OUTPUT MATCHES "Traceback") ++ SET(NUMPY_INCLUDE_DIRS ${NUMPY_COMMAND_OUTPUT} CACHE STRING "numpy include path") + ENDIF() +-ELSE() +- SET(NUMPY_FOUND TRUE) + ENDIF() + + INCLUDE(FindPackageHandleStandardArgs) +-FIND_PACKAGE_HANDLE_STANDARD_ARGS(NUMPY DEFAULT_MSG NUMPY_INCLUDE_DIR) ++FIND_PACKAGE_HANDLE_STANDARD_ARGS(NumPy DEFAULT_MSG NUMPY_INCLUDE_DIRS) diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.3-foss-2024.05.eb b/easybuild/easyconfigs/h/HPL/HPL-2.3-foss-2024.05.eb new file mode 100644 index 00000000000..8dd7ddcfa9c --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.3-foss-2024.05.eb @@ -0,0 +1,21 @@ +name = 'HPL' +version = '2.3' + +homepage = 'https://www.netlib.org/benchmark/hpl/' +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" + +toolchain = {'name': 'foss', 'version': '2024.05'} +toolchainopts = {'usempi': True} + +source_urls = ['https://www.netlib.org/benchmark/%(namelower)s'] +sources = [SOURCELOWER_TAR_GZ] +# fix Make dependencies, so parallel build also works +patches = ['HPL_parallel-make.patch'] +checksums = [ + '32c5c17d22330e6f2337b681aded51637fb6008d3f0eb7c277b163fadd612830', # hpl-2.3.tar.gz + '2a5bf9c4f328049828ddecec7ba3f05a9e25d236f4212747c53bd22fea80c5e6', # HPL_parallel-make.patch +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.3-foss-2024a.eb b/easybuild/easyconfigs/h/HPL/HPL-2.3-foss-2024a.eb new file mode 100644 index 00000000000..8a70a42bb41 --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.3-foss-2024a.eb @@ -0,0 +1,21 @@ +name = 'HPL' +version = '2.3' + +homepage = 'https://www.netlib.org/benchmark/hpl/' +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" + +toolchain = {'name': 'foss', 'version': '2024a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://www.netlib.org/benchmark/%(namelower)s'] +sources = [SOURCELOWER_TAR_GZ] +# fix Make dependencies, so parallel build also works +patches = ['HPL_parallel-make.patch'] +checksums = [ + '32c5c17d22330e6f2337b681aded51637fb6008d3f0eb7c277b163fadd612830', # hpl-2.3.tar.gz + '2a5bf9c4f328049828ddecec7ba3f05a9e25d236f4212747c53bd22fea80c5e6', # HPL_parallel-make.patch +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.3-gmpflf-2024.06.eb b/easybuild/easyconfigs/h/HPL/HPL-2.3-gmpflf-2024.06.eb new file mode 100644 index 00000000000..a6a7fb49164 --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.3-gmpflf-2024.06.eb @@ -0,0 +1,21 @@ +name = 'HPL' +version = '2.3' + +homepage = 'https://www.netlib.org/benchmark/hpl/' +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" + +toolchain = {'name': 'gmpflf', 'version': '2024.06'} +toolchainopts = {'usempi': True} + +source_urls = ['https://www.netlib.org/benchmark/%(namelower)s'] +sources = [SOURCELOWER_TAR_GZ] +# fix Make dependencies, so parallel build also works +patches = ['HPL_parallel-make.patch'] +checksums = [ + '32c5c17d22330e6f2337b681aded51637fb6008d3f0eb7c277b163fadd612830', # hpl-2.3.tar.gz + '2a5bf9c4f328049828ddecec7ba3f05a9e25d236f4212747c53bd22fea80c5e6', # HPL_parallel-make.patch +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.3-intel-2024a.eb b/easybuild/easyconfigs/h/HPL/HPL-2.3-intel-2024a.eb new file mode 100644 index 00000000000..5544839d177 --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.3-intel-2024a.eb @@ -0,0 +1,21 @@ +name = 'HPL' +version = '2.3' + +homepage = 'https://www.netlib.org/benchmark/hpl/' +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" + +toolchain = {'name': 'intel', 'version': '2024a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://www.netlib.org/benchmark/%(namelower)s'] +sources = [SOURCELOWER_TAR_GZ] +# fix Make dependencies, so parallel build also works +patches = ['HPL_parallel-make.patch'] +checksums = [ + '32c5c17d22330e6f2337b681aded51637fb6008d3f0eb7c277b163fadd612830', # hpl-2.3.tar.gz + '2a5bf9c4f328049828ddecec7ba3f05a9e25d236f4212747c53bd22fea80c5e6', # HPL_parallel-make.patch +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/HPX/HPX-1.10.0-foss-2024a.eb b/easybuild/easyconfigs/h/HPX/HPX-1.10.0-foss-2024a.eb new file mode 100644 index 00000000000..110ca403b7c --- /dev/null +++ b/easybuild/easyconfigs/h/HPX/HPX-1.10.0-foss-2024a.eb @@ -0,0 +1,78 @@ +# # +# Author: Benjamin Czaja (benjamin.czaja@surf.nl) +# Institute: SURF(sara) +# +# # +easyblock = 'CMakeNinja' + +name = 'HPX' +version = '1.10.0' + +homepage = 'http://stellar-group.org/libraries/hpx/' +description = """HPX (High Performance ParalleX) is a general purpose C++ runtime system + for parallel and distributed applications of any scale.""" + +toolchain = {'name': 'foss', 'version': '2024a'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/STEllAR-GROUP/%(namelower)s/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['5720ed7d2460fa0b57bd8cb74fa4f70593fe8675463897678160340526ec3c19'] + +builddependencies = [ + ('CMake', '3.29.3'), + ('Ninja', '1.12.1'), + ('pkgconf', '2.2.0'), +] +dependencies = [ + ('HDF5', '1.14.5'), + ('Boost', '1.85.0'), + ('hwloc', '2.10.0'), + ('gperftools', '2.16'), +] + +configopts = '-DCMAKE_CXX_COMPILER=g++ ' +configopts += '-DHPX_WITH_MALLOC=tcmalloc ' +configopts += '-DHPX_WITH_HWLOC=TRUE ' +configopts += '-DHPX_WITH_GOOGLE_PERFTOOLS=TRUE ' +configopts += '-DHPX_WITH_NETWORKING=TRUE ' +configopts += '-DHPX_WITH_PARCELPORT_TCP=FALSE ' +configopts += '-DHPX_WITH_PARCELPORT_MPI=TRUE ' +configopts += '-DHPX_WITH_TESTS=FALSE ' +configopts += '-DHPX_WITH_EXAMPLES=TRUE ' +# configopts += '-DHPX_WITH_MAX_CPU_COUNT=128' #this should be handled by a hook for the system +# configopts += '-DHPX_WITH_MAX_CPU_COUNT=' + os.cpu_count() +configopts += '-DHPX_WITH_FETCH_ASIO=TRUE ' + +bin_lib_subdirs = ['lib/%(namelower)s/'] + +local_lib_names = [ + 'libhpx_accumulator.%s' % SHLIB_EXT, + 'libhpx_cancelable_action.%s' % SHLIB_EXT, + 'libhpx_component_storage.%s' % SHLIB_EXT, + 'libhpx_core.%s' % SHLIB_EXT, + 'libhpx_iostreams.%s' % SHLIB_EXT, + 'libhpx_jacobi.%s' % SHLIB_EXT, + 'libhpx_nqueen.%s' % SHLIB_EXT, + 'libhpx_partitioned_vector.%s' % SHLIB_EXT, + 'libhpx_process.%s' % SHLIB_EXT, + 'libhpx_random_mem_access.%s' % SHLIB_EXT, + 'libhpx_simple_central_tuplespace.%s' % SHLIB_EXT, + 'libhpx.%s' % SHLIB_EXT, + 'libhpx_startup_shutdown.%s' % SHLIB_EXT, + 'libhpx_template_accumulator.%s' % SHLIB_EXT, + 'libhpx_template_function_accumulator.%s' % SHLIB_EXT, + 'libhpx_throttle.%s' % SHLIB_EXT, + 'libhpx_unordered.%s' % SHLIB_EXT, +] + +sanity_check_paths = { + 'files': ['lib/%s' % lib for lib in local_lib_names] + + ['include/asio.hpp', 'include/hpx/hpx.hpp'] + + ['bin/hpxcxx', 'bin/hpxrun.py'], + 'dirs': ['bin', 'lib'] + bin_lib_subdirs, +} + +modextrapaths = {'LD_LIBRARY_PATH': bin_lib_subdirs} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/h/HTSeq/HTSeq-2.0.7-foss-2023a.eb b/easybuild/easyconfigs/h/HTSeq/HTSeq-2.0.7-foss-2023a.eb new file mode 100644 index 00000000000..60ffab860b4 --- /dev/null +++ b/easybuild/easyconfigs/h/HTSeq/HTSeq-2.0.7-foss-2023a.eb @@ -0,0 +1,43 @@ +# Updated to PythonBundle and latest version from Pypi +# Author: J. Sassmannshausen (Imperial College London/UK) +# Update: P.Tománek (Inuits) + +easyblock = 'PythonBundle' + +name = 'HTSeq' +version = '2.0.7' + +homepage = 'https://github.com/simon-anders/htseq' +description = """HTSeq is a Python library to facilitate processing and analysis + of data from high-throughput sequencing (HTS) experiments.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [('SWIG', '4.1.1')] + +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('Pysam', '0.22.0'), + ('SciPy-bundle', '2023.07'), + ('matplotlib', '3.7.2'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('htseq', version, { + 'modulename': 'HTSeq', + 'checksums': ['c1490cede77fb04c8f3a9efeb44d41399cd466a6082180529e63c1dade203fdd'], + }), +] + +sanity_check_paths = { + 'files': ['bin/%(namelower)s-count', 'bin/%(namelower)s-qa'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(name)s/scripts'], +} + +sanity_check_commands = ['%(namelower)s-count --help'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/h/HTSlib/HTSlib-1.21-GCC-13.3.0.eb b/easybuild/easyconfigs/h/HTSlib/HTSlib-1.21-GCC-13.3.0.eb new file mode 100644 index 00000000000..2f35f9fa5a2 --- /dev/null +++ b/easybuild/easyconfigs/h/HTSlib/HTSlib-1.21-GCC-13.3.0.eb @@ -0,0 +1,41 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel +# 1.4 modified by: +# Adam Huffman, Jonas Demeulemeester +# The Francis Crick Institute +# Updated to 1.14 +# J. Sassmannshausen /GSTT +# Updated to 1.21 jpecar EMBL + +easyblock = 'ConfigureMake' + +name = 'HTSlib' +version = '1.21' + +homepage = 'https://www.htslib.org/' +description = """A C library for reading/writing high-throughput sequencing data. + This package includes the utilities bgzip and tabix""" + +toolchain = {'name': 'GCC', 'version': '13.3.0'} + +source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s/'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['84b510e735f4963641f26fd88c8abdee81ff4cb62168310ae716636aac0f1823'] + +# cURL added for S3 support +dependencies = [ + ('zlib', '1.3.1'), + ('bzip2', '1.0.8'), + ('XZ', '5.4.5'), + ('cURL', '8.7.1'), +] + + +sanity_check_paths = { + 'files': ['bin/bgzip', 'bin/tabix', 'lib/libhts.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/h/HTSplotter/HTSplotter-2.11-foss-2023a.eb b/easybuild/easyconfigs/h/HTSplotter/HTSplotter-2.11-foss-2023a.eb new file mode 100644 index 00000000000..75808cd8e7a --- /dev/null +++ b/easybuild/easyconfigs/h/HTSplotter/HTSplotter-2.11-foss-2023a.eb @@ -0,0 +1,64 @@ +easyblock = 'PythonBundle' + +name = 'HTSplotter' +version = '2.11' + +homepage = 'https://github.com/CBIGR/HTSplotter' +description = """HTSplotter allows an end-to-end data processing and analysis of chemical and genetic in vitro +perturbation screens.""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'pic': True} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('matplotlib', '3.7.2'), + ('h5py', '3.9.0'), + ('Seaborn', '0.13.2'), + ('tqdm', '4.66.1'), +] + +use_pip = True + +exts_list = [ + ('argon2-cffi-bindings', '21.2.0', { + 'modulename': '_argon2_cffi_bindings', + 'checksums': ['bb89ceffa6c791807d1305ceb77dbfacc5aa499891d2c55661c6459651fc39e3'], + }), + ('argon2_cffi', '23.1.0', { + 'modulename': 'argon2', + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['c670642b78ba29641818ab2e68bd4e6a78ba53b7eff7b4c3815ae16abf91c7ea'], + }), + ('minio', '7.2.9', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['fe5523d9c4a4d6cfc07e96905852841bccdb22b22770e1efca4bf5ae8b65774b'], + }), + ('pypdf', '5.0.0', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['67603e2e96cdf70e676564520933c017d450f16075b9966be5fee128812ace8c'], + }), + ('pypdf2', '3.0.1', { + 'modulename': 'PyPDF2', + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['d16e4205cfee272fbdc0568b68d82be796540b1537508cef59388f839c191928'], + }), + ('PyPDF3', '1.0.6', { + 'modulename': 'PyPDF3', + 'checksums': ['c946f3273419e37258e35e72273f49904ab15723d87a761c1115ef99799f8c5f'], + }), + (name, version, { + 'modulename': 'HTSplotter', + # Fixes the following error. + # `TypeError: rv_generic_interval() missing 1 required positional argument: 'confidence'` + # see https://github.com/KatherLab/marugoto/issues/14 + # see also scipy release notes https://docs.scipy.org/doc/scipy/release/1.9.0-notes.html#deprecated-features + 'preinstallopts': "sed -i 's/alpha/confidence/g' HTSplotter/save_hdf5brfiles.py && ", + 'checksums': ['51c0cee4e8eeecfd03f32dd707e0fa433cec91abb9334ec1d28e7f82615dbe29'], + }), +] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-9.0.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-9.0.0-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..40540c3fcdc --- /dev/null +++ b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-9.0.0-GCCcore-13.3.0.eb @@ -0,0 +1,51 @@ +easyblock = 'MesonNinja' + +name = 'HarfBuzz' +version = '9.0.0' + +homepage = 'https://www.freedesktop.org/wiki/Software/HarfBuzz' +description = """HarfBuzz is an OpenType text shaping engine.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +github_account = 'harfbuzz' +source_urls = [GITHUB_SOURCE] +sources = ['%(version)s.tar.gz'] +patches = ['HarfBuzz-9.0.0_fix-subset-test.patch'] +checksums = [ + {'9.0.0.tar.gz': 'b7e481b109d19aefdba31e9f5888aa0cdfbe7608fed9a43494c060ce1f8a34d2'}, + {'HarfBuzz-9.0.0_fix-subset-test.patch': '1635505c27c312dca507863f2a865eb88d42e35ff4cc241cfa0e90c0ade8b790'}, +] + +builddependencies = [ + ('binutils', '2.42'), + ('GObject-Introspection', '1.80.1'), + ('pkgconf', '2.2.0'), + ('Ninja', '1.12.1'), + ('Meson', '1.4.0'), + ('fonttools', '4.53.1'), # For tests +] + +dependencies = [ + ('GLib', '2.80.4'), + ('ICU', '75.1'), + ('cairo', '1.18.0'), + ('freetype', '2.13.2'), +] + +configopts = '--default-library=both' # static and shared library +configopts += ' -Dgobject=enabled -Dintrospection=enabled' +configopts += ' -Dglib=enabled' +configopts += ' -Dicu=enabled' +configopts += ' -Dcairo=enabled' +configopts += ' -Dfreetype=enabled' + +runtest = 'meson' +testopts = 'test -C %(builddir)s/easybuild_obj -t 60' + +sanity_check_paths = { + 'files': ['lib/libharfbuzz.%s' % SHLIB_EXT, 'bin/hb-view'], + 'dirs': [] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-9.0.0_fix-subset-test.patch b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-9.0.0_fix-subset-test.patch new file mode 100644 index 00000000000..25a2b619fc8 --- /dev/null +++ b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-9.0.0_fix-subset-test.patch @@ -0,0 +1,26 @@ +The test "feature_variation_instance_collect_lookups" fails when run in environments +where the decimal separator is not a dot ("."). +Fix this by using the C locale. +See https://github.com/harfbuzz/harfbuzz/pull/4857 + +Author: Alexander Grund (TU Dresden) + +diff --git a/test/subset/run-tests.py b/test/subset/run-tests.py +index 9e09d95d1d9..c0c256d8974 100755 +--- a/test/subset/run-tests.py ++++ b/test/subset/run-tests.py +@@ -135,10 +135,13 @@ def check_ots (path): + + has_ots = has_ots() + ++env = os.environ.copy() ++env['LC_ALL'] = 'C' + process = subprocess.Popen ([hb_subset, '--batch'], + stdin=subprocess.PIPE, + stdout=subprocess.PIPE, +- stderr=sys.stdout) ++ stderr=sys.stdout, ++ env=env) + + fails = 0 + for path in args: diff --git a/easybuild/easyconfigs/h/HeFFTe/HeFFTe-2.4.1-foss-2023b.eb b/easybuild/easyconfigs/h/HeFFTe/HeFFTe-2.4.1-foss-2023b.eb new file mode 100644 index 00000000000..7d38225fc55 --- /dev/null +++ b/easybuild/easyconfigs/h/HeFFTe/HeFFTe-2.4.1-foss-2023b.eb @@ -0,0 +1,33 @@ +easyblock = 'CMakeMake' + +name = 'HeFFTe' +version = '2.4.1' + +homepage = 'https://icl.utk.edu/fft' +description = "Highly Efficient FFT for Exascale (HeFFTe) library" + +toolchain = {'name': 'foss', 'version': '2023b'} + +source_urls = ['https://github.com/icl-utk-edu/heffte/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['de2cf26df5d61baac7841525db3f393cb007f79612ac7534fd4757f154ba3e6c'] + +builddependencies = [ + ('CMake', '3.27.6'), +] + +build_shared_libs = True + +configopts = "-DHeffte_ENABLE_FFTW=ON -DFFTW_ROOT=$EBROOTFFTW -DHeffte_ENABLE_CUDA=OFF -DHeffte_ENABLE_MKL=OFF" + +# allow oversubscription of MPI ranks to cores, tests are hardcoded to use up to 12 MPI ranks +pretestopts = "export OMPI_MCA_rmaps_base_oversubscribe=true && " + +runtest = 'test' + +sanity_check_paths = { + 'files': ['lib/libheffte.%s' % SHLIB_EXT], + 'dirs': ['include', 'lib/cmake/Heffte', 'share/heffte/examples'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/h/HiCMatrix/HiCMatrix-17.2-foss-2023a.eb b/easybuild/easyconfigs/h/HiCMatrix/HiCMatrix-17.2-foss-2023a.eb new file mode 100644 index 00000000000..474b8906ff5 --- /dev/null +++ b/easybuild/easyconfigs/h/HiCMatrix/HiCMatrix-17.2-foss-2023a.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonBundle' + +name = 'HiCMatrix' +version = '17.2' + +homepage = 'https://github.com/deeptools/HiCMatrix' +description = "This library implements the central class of HiCExplorer to manage Hi-C interaction matrices." + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('PyTables', '3.8.0'), + ('cooler', '0.10.2'), +] + +use_pip = True + +exts_list = [ + ('intervaltree', '3.1.0', { + 'checksums': ['902b1b88936918f9b2a19e0e5eb7ccb430ae45cde4f39ea4b36932920d33952d'], + }), + (name, version, { + 'source_tmpl': '%(version)s.tar.gz', + 'source_urls': ['https://github.com/deeptools/HiCMatrix/archive/'], + 'checksums': ['a2428676b5aad014e7b1653e3effe94f7ea8a68cc78be83e4b67f2255f6b4fbb'], + }), +] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/h/Highway/Highway-1.0.3-GCCcore-11.3.0.eb b/easybuild/easyconfigs/h/Highway/Highway-1.0.3-GCCcore-11.3.0.eb index 987a76bd0c1..9202b5b1d43 100644 --- a/easybuild/easyconfigs/h/Highway/Highway-1.0.3-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/h/Highway/Highway-1.0.3-GCCcore-11.3.0.eb @@ -12,7 +12,11 @@ toolchain = {'name': 'GCCcore', 'version': '11.3.0'} source_urls = ['https://github.com/google/highway/archive/refs/tags/'] sources = ['%(version)s.tar.gz'] -checksums = ['566fc77315878473d9a6bd815f7de78c73734acdcb745c3dde8579560ac5440e'] +patches = ['Highway-1.0.3_disable_AVX3_DL.patch'] +checksums = [ + '566fc77315878473d9a6bd815f7de78c73734acdcb745c3dde8579560ac5440e', + {'Highway-1.0.3_disable_AVX3_DL.patch': '5729765a75c42551056f95f24fc81031293066253978548c573d06eb33bf9853'}, +] builddependencies = [ ('binutils', '2.38'), diff --git a/easybuild/easyconfigs/h/Highway/Highway-1.0.3-GCCcore-12.2.0.eb b/easybuild/easyconfigs/h/Highway/Highway-1.0.3-GCCcore-12.2.0.eb index f1833e66b17..198469448b6 100644 --- a/easybuild/easyconfigs/h/Highway/Highway-1.0.3-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/h/Highway/Highway-1.0.3-GCCcore-12.2.0.eb @@ -12,7 +12,11 @@ toolchain = {'name': 'GCCcore', 'version': '12.2.0'} source_urls = ['https://github.com/google/highway/archive/refs/tags/'] sources = ['%(version)s.tar.gz'] -checksums = ['566fc77315878473d9a6bd815f7de78c73734acdcb745c3dde8579560ac5440e'] +patches = ['Highway-1.0.3_disable_AVX3_DL.patch'] +checksums = [ + '566fc77315878473d9a6bd815f7de78c73734acdcb745c3dde8579560ac5440e', + {'Highway-1.0.3_disable_AVX3_DL.patch': '5729765a75c42551056f95f24fc81031293066253978548c573d06eb33bf9853'}, +] builddependencies = [ ('binutils', '2.39'), diff --git a/easybuild/easyconfigs/h/Highway/Highway-1.0.3_disable_AVX3_DL.patch b/easybuild/easyconfigs/h/Highway/Highway-1.0.3_disable_AVX3_DL.patch new file mode 100644 index 00000000000..cbbdc731467 --- /dev/null +++ b/easybuild/easyconfigs/h/Highway/Highway-1.0.3_disable_AVX3_DL.patch @@ -0,0 +1,31 @@ +Using AVX3_DL in the baseline doesn't work in 1.0.3 causing the build to fail with +> #error "Logic error: best baseline should be included in dynamic targets" + +This is caused by using a wrong defined and fixed by +https://github.com/google/highway/commit/f0f688b6d6d1ec94489cc989ccb9729b0342aa58 +However that leads to a test failure: +> HwyConvertTestGroup/HwyConvertTest.TestAllTruncate/AVX3_DL +> u8x16 expect [0+ ->]: +> 0x00,0x01,0x02,0x03,0x04,0x05,0x06, +> u8x16 actual [0+ ->]: +> 0x00,0x1A,0x02,0x1A,0x04,0x1A,0x06, +> Abort at .../hwy/tests/convert_test.cc:386: AVX3_DL, u8x16 lane 1 mismatch: expected '0x01', got '0x1A'. + +Hence AVX3_DL in 1.0.3 seems to be broken and must not be used. +This patch disables it by making the condition always false. + +Author: Alexander Grund (TU Dresden) + +diff --git a/hwy/detect_targets.h b/hwy/detect_targets.h +index 2beca95b..379c4525 100644 +--- a/hwy/detect_targets.h ++++ b/hwy/detect_targets.h +@@ -340,7 +340,7 @@ + #if HWY_BASELINE_AVX3 != 0 && defined(__AVXVNNI__) && defined(__VAES__) && \ + defined(__VPCLMULQDQ__) && defined(__AVX512VBMI__) && \ + defined(__AVX512VBMI2__) && defined(__AVX512VPOPCNTDQ__) && \ +- defined(__AVX512BITALG__) ++ defined(__AVX512BITALG__) && 0 + #define HWY_BASELINE_AVX3_DL HWY_AVX3_DL + #else + #define HWY_BASELINE_AVX3_DL 0 diff --git a/easybuild/easyconfigs/h/Highway/Highway-1.0.4-GCCcore-12.3.0.eb b/easybuild/easyconfigs/h/Highway/Highway-1.0.4-GCCcore-12.3.0.eb index a05239847d3..993087b828c 100644 --- a/easybuild/easyconfigs/h/Highway/Highway-1.0.4-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/h/Highway/Highway-1.0.4-GCCcore-12.3.0.eb @@ -12,7 +12,13 @@ toolchain = {'name': 'GCCcore', 'version': '12.3.0'} source_urls = ['https://github.com/google/highway/archive/refs/tags/'] sources = ['%(version)s.tar.gz'] -checksums = ['faccd343935c9e98afd1016e9d20e0b8b89d908508d1af958496f8c2d3004ac2'] +patches = ['Highway-1.0.4-zen4-fix-TruncateTo-bug.patch'] + +checksums = [ + {'1.0.4.tar.gz': 'faccd343935c9e98afd1016e9d20e0b8b89d908508d1af958496f8c2d3004ac2'}, + {'Highway-1.0.4-zen4-fix-TruncateTo-bug.patch': + 'e571413c290076a729dbb1df105a4bfa106099238d1b438e74a9dfc9557eb4a2'}, +] builddependencies = [ ('binutils', '2.40'), diff --git a/easybuild/easyconfigs/h/Highway/Highway-1.0.4-zen4-fix-TruncateTo-bug.patch b/easybuild/easyconfigs/h/Highway/Highway-1.0.4-zen4-fix-TruncateTo-bug.patch new file mode 100644 index 00000000000..f489a6bd15f --- /dev/null +++ b/easybuild/easyconfigs/h/Highway/Highway-1.0.4-zen4-fix-TruncateTo-bug.patch @@ -0,0 +1,59 @@ +A single test failed when building on AMD Genoa a.k.a Zen4 with the error message +reported in https://github.com/google/highway/issues/1913 + +Building v1.0.5 passed all tests. Hence, this patch uses some of the changes made +in v1.0.5 to let the single failing test succeed. + +Looking at the PRs added by v1.0.5 a promising candidate was identified +(https://github.com/google/highway/pull/1276) and all changed files in the PR +were "studied in detail" (assessed if the changes could be related to the failing +test on Zen4). Luckily, the four changes provided in the patch below were +found to resolve the issue. It was also tested if a subset of these four changes +would resolve the issue, but this did not succeed. + +Author: Thomas Roeblitz (University of Bergen) + +diff --git a/hwy/ops/x86_256-inl.h b/hwy/ops/x86_256-inl.h +index 4e2e83e8..2fbf99c7 100644 +--- a/hwy/ops/x86_256-inl.h ++++ b/hwy/ops/x86_256-inl.h +@@ -4185,7 +4185,7 @@ HWY_INLINE Vec128 LookupAndConcatHalves(Vec256 v) { + #if HWY_TARGET <= HWY_AVX3_DL + alignas(32) static constexpr uint32_t kMap[8] = { + LO, HI, 0x10101010 + LO, 0x10101010 + HI, 0, 0, 0, 0}; +- const auto result = _mm256_permutexvar_epi8(v.raw, Load(d32, kMap).raw); ++ const auto result = _mm256_permutexvar_epi8(Load(d32, kMap).raw, v.raw); + #else + alignas(32) static constexpr uint32_t kMap[8] = {LO, HI, ~0u, ~0u, + ~0u, ~0u, LO, HI}; +@@ -4208,7 +4208,7 @@ HWY_INLINE Vec128 LookupAndConcatQuarters(Vec256 v) { + #if HWY_TARGET <= HWY_AVX3_DL + alignas(32) static constexpr uint16_t kMap[16] = { + LO, HI, 0x1010 + LO, 0x1010 + HI, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}; +- const auto result = _mm256_permutexvar_epi8(v.raw, Load(d16, kMap).raw); ++ const auto result = _mm256_permutexvar_epi8(Load(d16, kMap).raw, v.raw); + return LowerHalf(Vec128{_mm256_castsi256_si128(result)}); + #else + constexpr uint16_t ff = static_cast(~0u); +@@ -4229,7 +4229,7 @@ HWY_API Vec32 TruncateTo(D /* tag */, Vec256 v) { + #if HWY_TARGET <= HWY_AVX3_DL + alignas(32) static constexpr uint32_t kMap[8] = {0x18100800u, 0, 0, 0, + 0, 0, 0, 0}; +- const auto result = _mm256_permutexvar_epi8(v.raw, Load(d32, kMap).raw); ++ const auto result = _mm256_permutexvar_epi8(Load(d32, kMap).raw, v.raw); + return LowerHalf(LowerHalf(LowerHalf(Vec256{result}))); + #else + alignas(32) static constexpr uint32_t kMap[8] = {0xFFFF0800u, ~0u, ~0u, ~0u, +diff --git a/hwy/ops/x86_512-inl.h b/hwy/ops/x86_512-inl.h +index 167922d8..83f2ee67 100644 +--- a/hwy/ops/x86_512-inl.h ++++ b/hwy/ops/x86_512-inl.h +@@ -3497,7 +3497,7 @@ HWY_API Vec128 TruncateTo(D /* tag */, const Vec512 v) { + alignas(16) static constexpr uint8_t k8From32[16] = { + 0, 4, 8, 12, 16, 20, 24, 28, 32, 36, 40, 44, 48, 52, 56, 60}; + const Vec512 bytes{ +- _mm512_permutexvar_epi32(LoadDup128(d8, k8From32).raw, v.raw)}; ++ _mm512_permutexvar_epi8(LoadDup128(d8, k8From32).raw, v.raw)}; + #else + const Full512 d32; + // In each 128 bit block, gather the lower byte of 4 uint32_t lanes into the diff --git a/easybuild/easyconfigs/h/Highway/Highway-1.2.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/h/Highway/Highway-1.2.0-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..27739befe52 --- /dev/null +++ b/easybuild/easyconfigs/h/Highway/Highway-1.2.0-GCCcore-13.3.0.eb @@ -0,0 +1,32 @@ +easyblock = 'CMakeMake' + +name = 'Highway' +version = '1.2.0' + +homepage = 'https://github.com/google/highway' + +description = """Highway is a C++ library for SIMD (Single Instruction, Multiple Data), i.e. applying the same +operation to 'lanes'.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://github.com/google/highway/archive/refs/tags/'] +sources = ['%(version)s.tar.gz'] +checksums = ['7e0be78b8318e8bdbf6fa545d2ecb4c90f947df03f7aadc42c1967f019e63343'] + +builddependencies = [ + ('binutils', '2.42'), + ('CMake', '3.29.3'), + ('googletest', '1.15.2'), +] + +configopts = "-DHWY_SYSTEM_GTEST=ON" + +runtest = "test" + +sanity_check_paths = { + 'files': ['lib/libhwy.a'], + 'dirs': ['include/hwy'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/h/Hypre/Hypre-2.31.0-foss-2023b.eb b/easybuild/easyconfigs/h/Hypre/Hypre-2.31.0-foss-2023b.eb new file mode 100644 index 00000000000..62d72e357a8 --- /dev/null +++ b/easybuild/easyconfigs/h/Hypre/Hypre-2.31.0-foss-2023b.eb @@ -0,0 +1,18 @@ +name = 'Hypre' +version = '2.31.0' + +homepage = 'https://computation.llnl.gov/projects/hypre-scalable-linear-solvers-multigrid-methods' +description = """Hypre is a library for solving large, sparse linear systems of equations on massively + parallel computers. The problems of interest arise in the simulation codes being developed at LLNL + and elsewhere to study physical phenomena in the defense, environmental, energy, and biological sciences.""" + +toolchain = {'name': 'foss', 'version': '2023b'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/hypre-space/hypre/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['9a7916e2ac6615399de5010eb39c604417bb3ea3109ac90e199c5c63b0cb4334'] + +start_dir = 'src' + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/h/h4toh5/h4toh5-2.2.3-foss-2018b.eb b/easybuild/easyconfigs/h/h4toh5/h4toh5-2.2.3-foss-2018b.eb index 0b79b7cfc94..605d20f196f 100644 --- a/easybuild/easyconfigs/h/h4toh5/h4toh5-2.2.3-foss-2018b.eb +++ b/easybuild/easyconfigs/h/h4toh5/h4toh5-2.2.3-foss-2018b.eb @@ -3,13 +3,13 @@ easyblock = 'ConfigureMake' name = 'h4toh5' version = '2.2.3' -homepage = 'http://www.hdfgroup.org/h4toh5/' +homepage = "https://docs.hdfgroup.org/archive/support/products/hdf5_tools/h4toh5/index.html" description = """The h4toh5 software consists of the h4toh5 and h5toh4 command-line utilities, as well as a conversion library for converting between individual HDF4 and HDF5 objects.""" toolchain = {'name': 'foss', 'version': '2018b'} -source_urls = ['http://www.hdfgroup.org/ftp/HDF5/tools/%s/src' % name] +source_urls = ['http://support.hdfgroup.org/ftp/HDF5/tools/%s/src' % name] sources = ['h4h5tools-%(version)s.tar.gz'] checksums = ['ba167d9e5ec1f9014a95e3f5d0621f814caa6e83508e235ce60cfd315e3a9d3f'] diff --git a/easybuild/easyconfigs/h/h4toh5/h4toh5-2.2.3-gompi-2019b.eb b/easybuild/easyconfigs/h/h4toh5/h4toh5-2.2.3-gompi-2019b.eb index 81636ad6de3..079d5eb7de1 100644 --- a/easybuild/easyconfigs/h/h4toh5/h4toh5-2.2.3-gompi-2019b.eb +++ b/easybuild/easyconfigs/h/h4toh5/h4toh5-2.2.3-gompi-2019b.eb @@ -3,13 +3,13 @@ easyblock = 'ConfigureMake' name = 'h4toh5' version = '2.2.3' -homepage = 'http://www.hdfgroup.org/h4toh5/' +homepage = "https://docs.hdfgroup.org/archive/support/products/hdf5_tools/h4toh5/index.html" description = """The h4toh5 software consists of the h4toh5 and h5toh4 command-line utilities, as well as a conversion library for converting between individual HDF4 and HDF5 objects.""" toolchain = {'name': 'gompi', 'version': '2019b'} -source_urls = ['http://www.hdfgroup.org/ftp/HDF5/tools/%s/src' % name] +source_urls = ['http://support.hdfgroup.org/ftp/HDF5/tools/%s/src' % name] sources = ['h4h5tools-%(version)s%(versionsuffix)s.tar.gz'] checksums = ['ba167d9e5ec1f9014a95e3f5d0621f814caa6e83508e235ce60cfd315e3a9d3f'] diff --git a/easybuild/easyconfigs/h/h4toh5/h4toh5-2.2.3-gompi-2020b.eb b/easybuild/easyconfigs/h/h4toh5/h4toh5-2.2.3-gompi-2020b.eb index 8e8e8c7f705..50fe19e455a 100644 --- a/easybuild/easyconfigs/h/h4toh5/h4toh5-2.2.3-gompi-2020b.eb +++ b/easybuild/easyconfigs/h/h4toh5/h4toh5-2.2.3-gompi-2020b.eb @@ -3,13 +3,13 @@ easyblock = 'ConfigureMake' name = 'h4toh5' version = '2.2.3' -homepage = 'http://www.hdfgroup.org/h4toh5/' +homepage = "https://docs.hdfgroup.org/archive/support/products/hdf5_tools/h4toh5/index.html" description = """The h4toh5 software consists of the h4toh5 and h5toh4 command-line utilities, as well as a conversion library for converting between individual HDF4 and HDF5 objects.""" toolchain = {'name': 'gompi', 'version': '2020b'} -source_urls = ['http://www.hdfgroup.org/ftp/HDF5/tools/%s/src' % name] +source_urls = ['http://support.hdfgroup.org/ftp/HDF5/tools/%s/src' % name] sources = ['h4h5tools-%(version)s%(versionsuffix)s.tar.gz'] checksums = ['ba167d9e5ec1f9014a95e3f5d0621f814caa6e83508e235ce60cfd315e3a9d3f'] diff --git a/easybuild/easyconfigs/h/h4toh5/h4toh5-2.2.5-gompi-2022a.eb b/easybuild/easyconfigs/h/h4toh5/h4toh5-2.2.5-gompi-2022a.eb index 1a825bc8ed8..28d67776a1b 100644 --- a/easybuild/easyconfigs/h/h4toh5/h4toh5-2.2.5-gompi-2022a.eb +++ b/easybuild/easyconfigs/h/h4toh5/h4toh5-2.2.5-gompi-2022a.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'h4toh5' version = '2.2.5' -homepage = 'http://www.hdfgroup.org/h4toh5/' +homepage = "https://docs.hdfgroup.org/archive/support/products/hdf5_tools/h4toh5/index.html" description = """The h4toh5 software consists of the h4toh5 and h5toh4 command-line utilities, as well as a conversion library for converting between individual HDF4 and HDF5 objects.""" diff --git a/easybuild/easyconfigs/h/hatch-jupyter-builder/hatch-jupyter-builder-0.9.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/h/hatch-jupyter-builder/hatch-jupyter-builder-0.9.1-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..071c33cd4b1 --- /dev/null +++ b/easybuild/easyconfigs/h/hatch-jupyter-builder/hatch-jupyter-builder-0.9.1-GCCcore-12.3.0.eb @@ -0,0 +1,35 @@ +easyblock = 'PythonBundle' + +name = 'hatch-jupyter-builder' +version = "0.9.1" + +homepage = 'https://hatch-jupyter-builder.readthedocs.io' +description = """Hatch Jupyter Builder is a plugin for the hatchling Python build backend. It is +primarily targeted for package authors who are providing JavaScript as part of +their Python packages. +Typical use cases are Jupyter Lab Extensions and Jupyter Widgets.""" + + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +builddependencies = [ + ('binutils', '2.40'), +] +dependencies = [ + ('Python', '3.11.3'), + ('hatchling', '1.18.0'), +] + +sanity_pip_check = True +use_pip = True + +exts_list = [ + ('hatch_nodejs_version', '0.3.2', { + 'checksums': ['8a7828d817b71e50bbbbb01c9bfc0b329657b7900c56846489b9c958de15b54c'], + }), + ('hatch_jupyter_builder', '0.9.1', { + 'checksums': ['79278198d124c646b799c5e8dca8504aed9dcaaa88d071a09eb0b5c2009a58ad'], + }), +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/hatch-jupyter-builder/hatch-jupyter-builder-0.9.1-GCCcore-13.2.0.eb b/easybuild/easyconfigs/h/hatch-jupyter-builder/hatch-jupyter-builder-0.9.1-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..a1c10cc3b01 --- /dev/null +++ b/easybuild/easyconfigs/h/hatch-jupyter-builder/hatch-jupyter-builder-0.9.1-GCCcore-13.2.0.eb @@ -0,0 +1,35 @@ +easyblock = 'PythonBundle' + +name = 'hatch-jupyter-builder' +version = "0.9.1" + +homepage = 'https://hatch-jupyter-builder.readthedocs.io' +description = """Hatch Jupyter Builder is a plugin for the hatchling Python build backend. It is +primarily targeted for package authors who are providing JavaScript as part of +their Python packages. +Typical use cases are Jupyter Lab Extensions and Jupyter Widgets.""" + + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +builddependencies = [ + ('binutils', '2.40'), +] +dependencies = [ + ('Python', '3.11.5'), + ('hatchling', '1.18.0'), +] + +sanity_pip_check = True +use_pip = True + +exts_list = [ + ('hatch_nodejs_version', '0.3.2', { + 'checksums': ['8a7828d817b71e50bbbbb01c9bfc0b329657b7900c56846489b9c958de15b54c'], + }), + ('hatch_jupyter_builder', '0.9.1', { + 'checksums': ['79278198d124c646b799c5e8dca8504aed9dcaaa88d071a09eb0b5c2009a58ad'], + }), +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/hatch-jupyter-builder/hatch-jupyter-builder-0.9.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/h/hatch-jupyter-builder/hatch-jupyter-builder-0.9.1-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..f4483b94edd --- /dev/null +++ b/easybuild/easyconfigs/h/hatch-jupyter-builder/hatch-jupyter-builder-0.9.1-GCCcore-13.3.0.eb @@ -0,0 +1,35 @@ +easyblock = 'PythonBundle' + +name = 'hatch-jupyter-builder' +version = "0.9.1" + +homepage = 'https://hatch-jupyter-builder.readthedocs.io' +description = """Hatch Jupyter Builder is a plugin for the hatchling Python build backend. It is +primarily targeted for package authors who are providing JavaScript as part of +their Python packages. +Typical use cases are Jupyter Lab Extensions and Jupyter Widgets.""" + + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +builddependencies = [ + ('binutils', '2.42'), +] +dependencies = [ + ('Python', '3.12.3'), + ('hatchling', '1.24.2'), +] + +sanity_pip_check = True +use_pip = True + +exts_list = [ + ('hatch_nodejs_version', '0.3.2', { + 'checksums': ['8a7828d817b71e50bbbbb01c9bfc0b329657b7900c56846489b9c958de15b54c'], + }), + ('hatch_jupyter_builder', version, { + 'checksums': ['79278198d124c646b799c5e8dca8504aed9dcaaa88d071a09eb0b5c2009a58ad'], + }), +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/hatchling/hatchling-1.24.2-GCCcore-13.3.0.eb b/easybuild/easyconfigs/h/hatchling/hatchling-1.24.2-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..d936671cca9 --- /dev/null +++ b/easybuild/easyconfigs/h/hatchling/hatchling-1.24.2-GCCcore-13.3.0.eb @@ -0,0 +1,59 @@ +easyblock = 'PythonBundle' + +name = 'hatchling' +version = '1.24.2' + +homepage = 'https://hatch.pypa.io' +description = """Extensible, standards compliant build backend used by Hatch, +a modern, extensible Python project manager.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +builddependencies = [ + ('binutils', '2.42'), +] + +dependencies = [ + ('Python', '3.12.3'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('pathspec', '0.12.1', { + 'checksums': ['a482d51503a1ab33b1c67a6c3813a26953dbdc71c31dacaef9a838c4e29f5712'], + }), + ('pluggy', '1.5.0', { + 'checksums': ['2cffa88e94fdc978c4c574f15f9e59b7f4201d439195c3715ca9e2486f1d0cf1'], + }), + ('editables', '0.5', { + 'checksums': ['309627d9b5c4adc0e668d8c6fa7bac1ba7c8c5d415c2d27f60f081f8e80d1de2'], + }), + ('trove-classifiers', '2024.5.22', { + 'sources': ['trove_classifiers-%(version)s-py3-none-any.whl'], + 'checksums': ['c43ade18704823e4afa3d9db7083294bc4708a5e02afbcefacd0e9d03a7a24ef'], + }), + (name, version, { + 'checksums': ['41ddc27cdb25db9ef7b68bef075f829c84cb349aa1bff8240797d012510547b0'], + }), + ('hatch-vcs', '0.4.0', { + 'sources': ['hatch_vcs-%(version)s.tar.gz'], + 'checksums': ['093810748fe01db0d451fabcf2c1ac2688caefd232d4ede967090b1c1b07d9f7'], + }), + ('hatch-fancy-pypi-readme', '24.1.0', { + 'sources': ['hatch_fancy_pypi_readme-%(version)s.tar.gz'], + 'checksums': ['44dd239f1a779b9dcf8ebc9401a611fd7f7e3e14578dcf22c265dfaf7c1514b8'], + }), + ('hatch-requirements-txt', '0.4.1', { + 'source_tmpl': 'hatch_requirements_txt-%(version)s.tar.gz', + 'checksums': ['2c686e5758fd05bb55fa7d0c198fdd481f8d3aaa3c693260f5c0d74ce3547d20'], + }), +] + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(namelower)s'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/help2man/help2man-1.49.3-GCCcore-13.3.0.eb b/easybuild/easyconfigs/h/help2man/help2man-1.49.3-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..631d7becc2b --- /dev/null +++ b/easybuild/easyconfigs/h/help2man/help2man-1.49.3-GCCcore-13.3.0.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'help2man' +version = '1.49.3' + +homepage = 'https://www.gnu.org/software/help2man/' +description = """help2man produces simple manual pages from the '--help' and '--version' output of other commands.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_XZ] +checksums = ['4d7e4fdef2eca6afe07a2682151cea78781e0a4e8f9622142d9f70c083a2fd4f'] + +builddependencies = [ + # use same binutils version that was used when building GCC toolchain + ('binutils', '2.42', '', SYSTEM), +] + +sanity_check_paths = { + 'files': ['bin/help2man'], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/help2man/help2man-1.49.3-GCCcore-14.2.0.eb b/easybuild/easyconfigs/h/help2man/help2man-1.49.3-GCCcore-14.2.0.eb new file mode 100644 index 00000000000..2161ee0b1af --- /dev/null +++ b/easybuild/easyconfigs/h/help2man/help2man-1.49.3-GCCcore-14.2.0.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'help2man' +version = '1.49.3' + +homepage = 'https://www.gnu.org/software/help2man/' +description = """help2man produces simple manual pages from the '--help' and '--version' output of other commands.""" + +toolchain = {'name': 'GCCcore', 'version': '14.2.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_XZ] +checksums = ['4d7e4fdef2eca6afe07a2682151cea78781e0a4e8f9622142d9f70c083a2fd4f'] + +builddependencies = [ + # use same binutils version that was used when building GCC toolchain + ('binutils', '2.42', '', SYSTEM), +] + +sanity_check_paths = { + 'files': ['bin/help2man'], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/hevea/hevea-2.36-GCC-13.2.0.eb b/easybuild/easyconfigs/h/hevea/hevea-2.36-GCC-13.2.0.eb new file mode 100644 index 00000000000..8b2f9b128eb --- /dev/null +++ b/easybuild/easyconfigs/h/hevea/hevea-2.36-GCC-13.2.0.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'hevea' +version = '2.36' + +homepage = 'http://pauillac.inria.fr/~maranget/hevea/' +description = """A quite complete and fast LATEX to HTML translator""" + +toolchain = {'name': 'GCC', 'version': '13.2.0'} + +source_urls = ['http://pauillac.inria.fr/~maranget/hevea/distri'] +sources = [SOURCE_TAR_GZ] +checksums = ['5d6759d7702a295c76a12c1b2a1a16754ab0ec1ffed73fc9d0b138b41e720648'] + +builddependencies = [ + ('ocamlbuild', '0.14.3'), +] + +dependencies = [ + ('texlive', '20230313'), +] + +skipsteps = ['configure'] + +buildopts = 'PREFIX="" ' + +installopts = 'DESTDIR="%(installdir)s" ' + +sanity_check_paths = { + 'files': ['bin/%(name)s'], + 'dirs': ['lib/%(name)s'], +} + +sanity_check_commands = ['%(name)s --help'] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/h/hic-straw/hic-straw-1.3.1-foss-2023b.eb b/easybuild/easyconfigs/h/hic-straw/hic-straw-1.3.1-foss-2023b.eb new file mode 100644 index 00000000000..4a9b159e99b --- /dev/null +++ b/easybuild/easyconfigs/h/hic-straw/hic-straw-1.3.1-foss-2023b.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonPackage' + +name = 'hic-straw' +version = '1.3.1' + +homepage = 'https://github.com/aidenlab/straw' +description = "Straw is a library which allows rapid streaming of contact data from .hic files." + +toolchain = {'name': 'foss', 'version': '2023b'} + +sources = [SOURCE_TAR_GZ] +checksums = ['fb0f878127f6b1d096303c67793477c83fddf3f4a1a8e29a9d92952634989876'] + +builddependencies = [('pybind11', '2.11.1')] + +dependencies = [ + ('Python', '3.11.5'), + ('Python-bundle-PyPI', '2023.10'), + ('SciPy-bundle', '2023.11'), + ('cURL', '8.3.0'), +] + +use_pip = True +sanity_pip_check = True +download_dep_fail = True + +options = {'modulename': 'hicstraw'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/h/hiredis/hiredis-1.2.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/h/hiredis/hiredis-1.2.0-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..bc3a5a1c715 --- /dev/null +++ b/easybuild/easyconfigs/h/hiredis/hiredis-1.2.0-GCCcore-13.3.0.eb @@ -0,0 +1,41 @@ +# Author: Alexander Grund (TU Dresden) +# Based on EC by J. Sassmannshausen (Imperial College London) + +easyblock = 'CMakeMake' + +name = 'hiredis' +version = '1.2.0' + +homepage = 'https://github.com/redis/hiredis' +description = """Hiredis is a minimalistic C client library for the Redis database. + +It is minimalistic because it just adds minimal support for the protocol, +but at the same time it uses a high level printf-alike API in order to +make it much higher level than otherwise suggested by its minimal code base +and the lack of explicit bindings for every Redis command.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +github_account = 'redis' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['82ad632d31ee05da13b537c124f819eb88e18851d9cb0c30ae0552084811588c'] + +builddependencies = [ + ('binutils', '2.42'), + ('CMake', '3.29.3'), +] + +dependencies = [ + ('OpenSSL', '3', '', SYSTEM), +] + +configopts = ['-DBUILD_SHARED_LIBS=ON', '-DBUILD_SHARED_LIBS=OFF'] + +sanity_check_paths = { + 'files': ['lib/libhiredis.a', 'lib/libhiredis.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/histolab/histolab-0.6.0-foss-2022a.eb b/easybuild/easyconfigs/h/histolab/histolab-0.6.0-foss-2022a.eb new file mode 100644 index 00000000000..a7dc410e6f0 --- /dev/null +++ b/easybuild/easyconfigs/h/histolab/histolab-0.6.0-foss-2022a.eb @@ -0,0 +1,37 @@ +easyblock = 'PythonBundle' + +name = 'histolab' +version = '0.6.0' + +homepage = 'https://github.com/histolab/histolab' +description = """Library for Digital Pathology Image Processing.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +builddependencies = [('poetry', '1.2.2')] +dependencies = [ + ('Python', '3.10.4'), + ('Pillow', '9.1.1'), + ('scikit-image', '0.19.3'), + ('SciPy-bundle', '2022.05'), + ('openslide-python', '1.2.0'), +] + +use_pip = True + +exts_list = [ + # requires importlib-metadata = ">=4.12,<7.0" + ('importlib_metadata', '6.11.0', { + 'checksums': ['1231cf92d825c9e03cfc4da076a16de6422c863558229ea0b22b675657463443'], + }), + ('certifi', '2024.6.2', { + 'checksums': ['3cd43f1c6fa7dedc5899d69d3ad0398fd018ad1a17fba83ddaf78aa46c747516'], + }), + (name, version, { + 'checksums': ['fcb8cf70fdf32a58e2980905d657ea53a541503a436e8303f0cb0da6e9f2e20f'], + }), +] + +sanity_pip_check = True + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/h/histolab/histolab-0.7.0-foss-2023a.eb b/easybuild/easyconfigs/h/histolab/histolab-0.7.0-foss-2023a.eb new file mode 100644 index 00000000000..3aa69b74e7b --- /dev/null +++ b/easybuild/easyconfigs/h/histolab/histolab-0.7.0-foss-2023a.eb @@ -0,0 +1,38 @@ +easyblock = 'PythonBundle' + +name = 'histolab' +version = '0.7.0' + +homepage = 'https://github.com/histolab/histolab' +description = """Library for Digital Pathology Image Processing.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [('poetry', '1.5.1')] +dependencies = [ + ('Python', '3.11.3'), + ('Pillow', '10.0.0'), + ('scikit-image', '0.22.0'), + ('SciPy-bundle', '2023.07'), + ('openslide-python', '1.3.1'), +] + +use_pip = True + +local_preinstallopts = """sed -i 's/scikit-image = ">=0.19.0,<0.19.4"/scikit-image = ">=0.19.0"/' pyproject.toml && """ +local_preinstallopts += """sed -i 's/numpy = ">=1.23.2,<=1.24.4"/numpy = ">=1.23.2"/' pyproject.toml && """ +local_preinstallopts += """sed -i 's/scipy = ">=1.5.0,<1.10.1"/scipy = ">=1.5.0"/' pyproject.toml && """ + +exts_list = [ + ('certifi', '2024.6.2', { + 'checksums': ['3cd43f1c6fa7dedc5899d69d3ad0398fd018ad1a17fba83ddaf78aa46c747516'], + }), + (name, version, { + 'preinstallopts': local_preinstallopts, + 'checksums': ['c0f6a6d0381f0ca056f524e3b8217b0a8304ea79a0cdc88f76a39b1bf7531031'], + }), +] + +sanity_pip_check = True + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-2.10.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/h/hwloc/hwloc-2.10.0-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..cbe85325933 --- /dev/null +++ b/easybuild/easyconfigs/h/hwloc/hwloc-2.10.0-GCCcore-13.3.0.eb @@ -0,0 +1,44 @@ +easyblock = 'ConfigureMake' + +name = 'hwloc' +version = '2.10.0' + +homepage = 'https://www.open-mpi.org/projects/hwloc/' + +description = """ + The Portable Hardware Locality (hwloc) software package provides a portable + abstraction (across OS, versions, architectures, ...) of the hierarchical + topology of modern architectures, including NUMA memory nodes, sockets, shared + caches, cores and simultaneous multithreading. It also gathers various system + attributes such as cache and memory information as well as the locality of I/O + devices such as network interfaces, InfiniBand HCAs or GPUs. It primarily + aims at helping applications with gathering information about modern computing + hardware so as to exploit it accordingly and efficiently. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] +sources = [SOURCE_TAR_GZ] +checksums = ['c7fd8a1404a9719c76aadc642864b9f77aed1dc1fc8882d6af861a9260ba240d'] + +builddependencies = [ + ('binutils', '2.42'), +] + +dependencies = [ + ('numactl', '2.0.18'), + ('libxml2', '2.12.7'), + ('libpciaccess', '0.18.1'), +] + +configopts = "--disable-cairo --disable-opencl --disable-cuda --disable-nvml --disable-gl --disable-libudev " + +sanity_check_paths = { + 'files': ['bin/lstopo', 'include/hwloc/linux.h', + 'lib/libhwloc.%s' % SHLIB_EXT], + 'dirs': ['share/man/man3'], +} +sanity_check_commands = ['lstopo'] + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/h/hypothesis/hypothesis-6.103.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/h/hypothesis/hypothesis-6.103.1-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..e9bb1d78543 --- /dev/null +++ b/easybuild/easyconfigs/h/hypothesis/hypothesis-6.103.1-GCCcore-13.3.0.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonPackage' + +name = 'hypothesis' +version = '6.103.1' + +homepage = "https://github.com/HypothesisWorks/hypothesis" +description = """Hypothesis is an advanced testing library for Python. It lets you write tests which are parametrized + by a source of examples, and then generates simple and comprehensible examples that make your tests fail. This lets + you find more bugs in your code with less work.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['d299d5c21d6408eab3be670c94c974f3acf0b511c61fe81804b09091e393ee1f'] + +builddependencies = [ + ('binutils', '2.42'), +] + +dependencies = [ + ('Python', '3.12.3'), + ('Python-bundle-PyPI', '2024.06'), # required for attrs, sortedcontainers +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/i/ICU/ICU-75.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/i/ICU/ICU-75.1-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..cb7075fa963 --- /dev/null +++ b/easybuild/easyconfigs/i/ICU/ICU-75.1-GCCcore-13.3.0.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'ICU' +version = '75.1' + +homepage = 'https://icu.unicode.org' +description = """ICU is a mature, widely used set of C/C++ and Java libraries providing Unicode and Globalization + support for software applications.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/unicode-org/icu/releases/download/release-%(version_major)s-%(version_minor)s'] +sources = ['icu4c-%(version_major)s_%(version_minor)s-src.tgz'] +checksums = ['cb968df3e4d2e87e8b11c49a5d01c787bd13b9545280fc6642f826527618caef'] + +builddependencies = [ + ('binutils', '2.42'), + ('Python', '3.12.3'), +] + +start_dir = 'source' + +sanity_check_paths = { + 'files': ['lib/libicu%s.%s' % (x, SHLIB_EXT) for x in ['data', 'i18n', 'io', 'test', 'tu', 'uc']], + 'dirs': ['bin', 'include/unicode', 'share/icu', 'share/man'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/i/IEntropy/IEntropy-2024.06.12-foss-2023a-R-4.3.2.eb b/easybuild/easyconfigs/i/IEntropy/IEntropy-2024.06.12-foss-2023a-R-4.3.2.eb new file mode 100644 index 00000000000..ee26df679bf --- /dev/null +++ b/easybuild/easyconfigs/i/IEntropy/IEntropy-2024.06.12-foss-2023a-R-4.3.2.eb @@ -0,0 +1,36 @@ +easyblock = 'RPackage' + +name = 'IEntropy' +version = '2024.06.12' +local_commit = '3cd58ab' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://github.com/LinLi-0909/IEntropy' +description = """Here, by deriving entropy decomposition formula, we proposed a feature selection method, +intrinsic entropy (IE) model, to identify the informative genes for accurately clustering analysis.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['https://github.com/LinLi-0909/IEntropy/archive/'] +sources = [{ + "download_filename": "%s.tar.gz" % local_commit, + "filename": "%(name)s-%(version)s.tar.gz" +}] +checksums = ['7449340df7218c790dcdff5dbb14ba7d613bd9bdfb0a440296a561bbb742f9c1'] + +dependencies = [ + ('R', '4.3.2'), + ('R-bundle-Bioconductor', '3.18', '-R-%(rver)s'), +] + +unpack_sources = True +start_dir = 'IEntropy' + +sanity_check_paths = { + 'files': [], + 'dirs': ['%(name)s'], +} + +sanity_check_commands = ['Rscript -e "library(IEntropy)"'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/i/IGV/IGV-2.17.4-Java-17.eb b/easybuild/easyconfigs/i/IGV/IGV-2.17.4-Java-17.eb new file mode 100644 index 00000000000..35e427d0ad0 --- /dev/null +++ b/easybuild/easyconfigs/i/IGV/IGV-2.17.4-Java-17.eb @@ -0,0 +1,34 @@ +# EasyBuild easyconfig +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics +# Modified by Adam Huffman +# Big Data Institute, University of Oxford + +easyblock = 'Tarball' + +name = 'IGV' +version = '2.17.4' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'https://www.broadinstitute.org/software/igv/' +description = """This package contains command line utilities for + preprocessing, computing feature count density (coverage), sorting, and + indexing data files.""" + +toolchain = SYSTEM + +source_urls = ['http://data.broadinstitute.org/igv/projects/downloads/%(version_major)s.%(version_minor)s'] +sources = ['%(name)s_%(version)s.zip'] +checksums = ['6a36ae64fa3b74182db654a93f6254256305a8afa6b878f381b5d04fc1e8eaa5'] + +dependencies = [('Java', '17', '', SYSTEM)] + +sanity_check_paths = { + 'files': ['%(namelower)s.sh', 'lib/%(namelower)s.jar'], + 'dirs': [], +} + +modextrapaths = {'PATH': ''} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/i/IJulia/IJulia-1.24.2-Julia-1.10.3.eb b/easybuild/easyconfigs/i/IJulia/IJulia-1.24.2-Julia-1.10.3.eb new file mode 100644 index 00000000000..f2072785aa5 --- /dev/null +++ b/easybuild/easyconfigs/i/IJulia/IJulia-1.24.2-Julia-1.10.3.eb @@ -0,0 +1,84 @@ +easyblock = 'JuliaBundle' + +name = 'IJulia' +version = '1.24.2' +_julia_ver = '1.10.3' +versionsuffix = "-Julia-%s" % _julia_ver + +homepage = 'https://github.com/JuliaLang/IJulia.jl' +description = "Julia kernel for Jupyter" + +toolchain = SYSTEM + +dependencies = [ + ('Julia', _julia_ver, '-linux-%s' % ARCH, SYSTEM), +] + +exts_list = [ + ('Preferences', '1.4.3', { + 'source_urls': ['https://github.com/JuliaPackaging/Preferences.jl/archive/'], + 'checksums': ['02b995891818b91266f98bcb46eefc513dfb66b177b5a6a0d1cff97be3e4582d'], + }), + ('JLLWrappers', '1.5.0', { + 'source_urls': ['https://github.com/JuliaPackaging/JLLWrappers.jl/archive/'], + 'checksums': ['6e83b81afd0c57636e80bcf52ad51f6ba43d98643cac999727b958d9ab3d4a01'], + }), + ('SnoopPrecompile', '2.10.8', { + 'source_urls': ['https://github.com/timholy/SnoopCompile.jl/archive/'], + 'start_dir': '%(name)s', + 'checksums': ['9b3204ce72fa3d0f1a359428e9f2ae43db2ee91f7ba77407056aced39d74d9d6'], + }), + ('PrecompileTools', '1.2.1', { + 'source_urls': ['https://github.com/JuliaLang/PrecompileTools.jl/archive/'], + 'checksums': ['af58b384e08b488b2da5ad19e72817b8b0ddb026997f8cf85f2964cc2c26cd34'], + }), + ('Parsers', '2.8.1', { + 'source_urls': ['https://github.com/JuliaData/Parsers.jl/archive/'], + 'checksums': ['6ea035be48ef5daaecdff62ac8f29c6110aaf20f3349058a4f96e2503f55b693'], + }), + ('JSON', '0.21.4', { + 'source_urls': ['https://github.com/JuliaIO/JSON.jl/archive/'], + 'checksums': ['c6b620ad4150ec5a154367f50c9579af800e3a89a6d8f9cb5dd30215a5d3f552'], + }), + ('MbedTLS', '1.1.9', { + 'source_urls': ['https://github.com/JuliaLang/MbedTLS.jl/archive/'], + 'checksums': ['d421bb36f9eb7f8840bd7108c2c33a9a5532454ac9465861e2f7797f89c1f56b'], + }), + ('VersionParsing', '1.3.0', { + 'source_urls': ['https://github.com/JuliaInterop/VersionParsing.jl/archive/'], + 'checksums': ['f90fe419e1a40ef0eccfaaed1d1b7792d9115a059a82d0c23e3c04c944d0f8ca'], + }), + ('Conda', '1.10.0', { + 'source_urls': ['https://github.com/JuliaPy/Conda.jl/archive/'], + 'checksums': ['2007170cad58d6f27626500abd52bd782023b8ecb7a7d05a678d7aec3c0f9948'], + }), + ('SoftGlobalScope', '1.1.0', { + 'source_urls': ['https://github.com/stevengj/SoftGlobalScope.jl/archive/'], + 'checksums': ['8d4264386c859403938498cd9ddd5e94e10181deba4a3e71d391b16750e3848b'], + }), + ('libsodium_jll', '1.0.20+0', { + 'source_urls': ['https://github.com/JuliaBinaryWrappers/libsodium_jll.jl/archive/'], + 'sources': [{'filename': 'libsodium-v%(version)s.tar.gz'}], + 'checksums': ['f7c3a17acc3a478ec10a4a49a0dd04694140f4483644ec9db638706ea9844aba'], + }), + ('ZeroMQ_jll', '4.3.5+0', { + 'source_urls': ['https://github.com/JuliaBinaryWrappers/ZeroMQ_jll.jl/archive/'], + 'sources': [{'filename': 'ZeroMQ-v%(version)s.tar.gz'}], + 'checksums': ['29d1f35e48c1436743a6da28518cb7aeccb32af4b439c3976df1967c6a252e87'], + }), + ('ZMQ', '1.2.4', { + 'source_urls': ['https://github.com/JuliaInterop/ZMQ.jl/archive/'], + 'checksums': ['a15fe752d2b049ad7521d03909ae8ad6c28e4cf46fc823f666cbc1cc6f5795ba'], + }), + (name, version, { + 'preinstallopts': "mkdir -p %(installdir)s/jupyter && export JUPYTER_DATA_DIR=%(installdir)s/jupyter && ", + 'source_urls': ['https://github.com/JuliaLang/IJulia.jl/archive/'], + 'checksums': ['de215348c7c41e1ca15c0d21f5f9a78bedce77b02ef89d67f38702c4d57ee80d'], + }), +] + +modextrapaths = { + 'JUPYTER_PATH': 'jupyter', +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/i/IMAGE/IMAGE-1.1-foss-2022b.eb b/easybuild/easyconfigs/i/IMAGE/IMAGE-1.1-foss-2022b.eb new file mode 100644 index 00000000000..3b7413af016 --- /dev/null +++ b/easybuild/easyconfigs/i/IMAGE/IMAGE-1.1-foss-2022b.eb @@ -0,0 +1,57 @@ +easyblock = 'Tarball' + +name = 'IMAGE' +version = '1.1' + +homepage = 'https://github.com/JesperGrud/IMAGE' +description = """IMAGE (Motif Activity and Gene Expression changes of transcription factors) is software for +integrated analysis of motif activity and gene expression changes of transcription factors. IMAGE makes prediction +of causal transcription factors based on transcriptome profiling and genome-wide maps of enhancer activity.""" + +toolchain = {'name': 'foss', 'version': '2022b'} + +source_urls = ['https://github.com/JesperGrud/IMAGE/archive/refs/tags'] +sources = ['v%(version)s.tar.gz'] +checksums = ['e286cd5e7eb5aaaf9e103a9651ece39ff4ce260c463facdf1758b6d72a285062'] + +dependencies = [ + ('Perl', '5.36.0'), + ('HOMER', '4.11.1'), + ('R', '4.2.2'), + ('R-bundle-Bioconductor', '3.16', '-R-4.2.2'), +] + +postinstallcmds = [ + 'mkdir %(installdir)s/bin', + 'mv %(installdir)s/IMAGE.pl %(installdir)s/bin/', + 'chmod +x %(installdir)s/bin/IMAGE.pl', + ( + 'sed -i "s|my \\$TMPDIR = \\$INSTALLDIR . \\$TMP;|my \\$TMPDIR = \\$TMP;|g" ' + '%(installdir)s/bin/IMAGE.pl' + ), + ( + 'sed -i "s|my \\$UTILDIR = \\$INSTALLDIR . \\$UTIL;|my \\$UTILDIR = \'%(installdir)s\' . \\$UTIL;|g" ' + '%(installdir)s/bin/IMAGE.pl' + ), +] + +fix_perl_shebang_for = ['bin/*.pl'] + +sanity_check_paths = { + 'dirs': ['bin', 'utils', 'tmp'], + 'files': [ + 'utils/Collection.motif', + 'utils/extractSequence', + 'utils/Genename_Motif.txt', + 'utils/Parallel.sh', + 'utils/Regression.R', + 'utils/SplitMotifLibrary.sh', + 'bin/IMAGE.pl', + ] +} + +sanity_check_commands = [ + "IMAGE.pl", +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/i/IML/IML-1.0.5-gfbf-2023b.eb b/easybuild/easyconfigs/i/IML/IML-1.0.5-gfbf-2023b.eb index d9171489748..29698d8351f 100644 --- a/easybuild/easyconfigs/i/IML/IML-1.0.5-gfbf-2023b.eb +++ b/easybuild/easyconfigs/i/IML/IML-1.0.5-gfbf-2023b.eb @@ -8,6 +8,7 @@ description = """IML is a free library of C source code which implements algorit exact solutions to dense systems of linear equations over the integers.""" toolchain = {'name': 'gfbf', 'version': '2023b'} +toolchainopts = {'pic': True} source_urls = ['http://www.cs.uwaterloo.ca/~astorjoh'] sources = [SOURCELOWER_TAR_BZ2] diff --git a/easybuild/easyconfigs/i/IOR/IOR-4.0.0-gompi-2023b.eb b/easybuild/easyconfigs/i/IOR/IOR-4.0.0-gompi-2023b.eb new file mode 100644 index 00000000000..edc20007c6d --- /dev/null +++ b/easybuild/easyconfigs/i/IOR/IOR-4.0.0-gompi-2023b.eb @@ -0,0 +1,40 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel +# Author: Robert Mijakovic +# DeepThought, Flinders University + +easyblock = 'CMakeMake' + +name = 'IQ-TREE' +version = '2.3.5' + +# HTTPS is not working +homepage = 'http://www.iqtree.org/' +description = """Efficient phylogenomic software by maximum likelihood""" + +toolchain = {'name': 'gompi', 'version': '2023a'} +# Including 'usempi' will take precedence and override IQTREE_FLAGS and produces only 'iqtree-mpi' binary + +source_urls = ['https://github.com/iqtree/iqtree2/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] +patches = [ + 'IQ-TREE-2.3.5_use_EB_LSD2.patch', +] +checksums = [ + {'v2.3.5.tar.gz': '8e323e0b7c46e97901d3500f11e810703e0e5d25848188047eca9602d03fa6b1'}, + {'IQ-TREE-2.3.5_use_EB_LSD2.patch': 'b4578b01f06ae52b94b332622c0f6630497cd29cb61010f58f7c5018c2c32a5f'}, +] + +builddependencies = [ + ('CMake', '3.26.3'), + ('Eigen', '3.4.0'), +] +dependencies = [ + ('zlib', '1.2.13'), + ('Boost', '1.82.0'), + ('LSD2', '2.4.1'), +] + +local_conf_opts = ' -DUSE_LSD2=ON ' +configopts = [ + '-DIQTREE_FLAGS=omp' + local_conf_opts, + '-DIQTREE_FLAGS=mpi -DCMAKE_C_COMPILER="$MPICC" -DCMAKE_CXX_COMPILER="$MPICXX"' + local_conf_opts, +] + +sanity_check_paths = { + 'files': ['bin/iqtree2', 'bin/iqtree2-mpi'], + 'dirs': [], +} + +sanity_check_commands = [ + "iqtree2 --help", + "mkdir -p $TMPDIR/{test-omp,test-mpi}", + "cd $TMPDIR/test-omp && cp -a %(installdir)s/example.phy . && iqtree2 -s example.phy -redo", + "cd $TMPDIR/test-mpi && cp -a %(installdir)s/example.phy . && mpirun -np 1 iqtree2-mpi -s example.phy -redo", +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/i/IQ-TREE/IQ-TREE-2.3.5_use_EB_LSD2.patch b/easybuild/easyconfigs/i/IQ-TREE/IQ-TREE-2.3.5_use_EB_LSD2.patch new file mode 100644 index 00000000000..b567f096fa9 --- /dev/null +++ b/easybuild/easyconfigs/i/IQ-TREE/IQ-TREE-2.3.5_use_EB_LSD2.patch @@ -0,0 +1,36 @@ +diff -ruN iqtree2-2.3.5/CMakeLists.txt iqtree2-2.3.5-orig/CMakeLists.txt +--- iqtree2-2.3.5/CMakeLists.txt 2024-06-26 04:33:33.000000000 +0000 ++++ iqtree2-2.3.5-orig/CMakeLists.txt 2024-07-03 08:23:41.030462539 +0000 +@@ -758,10 +758,6 @@ + add_subdirectory(terracetphast) + endif() + +-if (USE_LSD2) +- add_subdirectory(lsd2) +-endif() +- + add_library(kernelsse tree/phylokernelsse.cpp) + + if (NOT BINARY32 AND NOT IQTREE_FLAGS MATCHES "novx") +@@ -820,9 +816,6 @@ + if (USE_TERRAPHAST) + set_target_properties(terracetphast terraphast PROPERTIES COMPILE_FLAGS "${SSE_FLAGS}") + endif() +- if (USE_LSD2) +- set_target_properties(lsd2 PROPERTIES COMPILE_FLAGS "${SSE_FLAGS}") +- endif() + if (USE_BOOSTER) + set_target_properties(booster PROPERTIES COMPILE_FLAGS "${SSE_FLAGS}") + endif() +diff -ruN iqtree2-2.3.5/main/timetree.cpp iqtree2-2.3.5-orig/main/timetree.cpp +--- iqtree2-2.3.5/main/timetree.cpp 2024-06-26 04:33:33.000000000 +0000 ++++ iqtree2-2.3.5-orig/main/timetree.cpp 2024-07-03 08:24:32.438606710 +0000 +@@ -8,7 +8,7 @@ + #include "timetree.h" + + #ifdef USE_LSD2 +-#include "lsd2/src/lsd.h" ++#include "lsd.h" + #endif + + /** map from taxon name to date */ diff --git a/easybuild/easyconfigs/i/IQ-TREE/IQ-TREE-2.3.6-gompi-2023a.eb b/easybuild/easyconfigs/i/IQ-TREE/IQ-TREE-2.3.6-gompi-2023a.eb new file mode 100644 index 00000000000..7f78472bcea --- /dev/null +++ b/easybuild/easyconfigs/i/IQ-TREE/IQ-TREE-2.3.6-gompi-2023a.eb @@ -0,0 +1,56 @@ +# Updated to v2.1.3 by +# R.QIAO +# DeepThought, Flinders University +# Update: Petr Král (INUITS) + +easyblock = 'CMakeMake' + +name = 'IQ-TREE' +version = '2.3.6' + +# HTTPS is not working +homepage = 'http://www.iqtree.org/' +description = """Efficient phylogenomic software by maximum likelihood""" + +toolchain = {'name': 'gompi', 'version': '2023a'} +# Including 'usempi' will take precedence and override IQTREE_FLAGS and produces only 'iqtree-mpi' binary + +source_urls = ['https://github.com/iqtree/iqtree2/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] +patches = [ + 'IQ-TREE-2.3.5_use_EB_LSD2.patch', +] +checksums = [ + {'v2.3.6.tar.gz': '2d389ea74e19773496363cd68270b341ac7cc47c60e7f32859682403b34744cf'}, + {'IQ-TREE-2.3.5_use_EB_LSD2.patch': 'b4578b01f06ae52b94b332622c0f6630497cd29cb61010f58f7c5018c2c32a5f'}, +] + +builddependencies = [ + ('CMake', '3.26.3'), + ('Eigen', '3.4.0'), +] +dependencies = [ + ('zlib', '1.2.13'), + ('Boost', '1.82.0'), + ('LSD2', '2.4.1'), +] + +local_conf_opts = ' -DUSE_LSD2=ON ' +configopts = [ + '-DIQTREE_FLAGS=omp' + local_conf_opts, + '-DIQTREE_FLAGS=mpi -DCMAKE_C_COMPILER="$MPICC" -DCMAKE_CXX_COMPILER="$MPICXX"' + local_conf_opts, +] + +sanity_check_paths = { + 'files': ['bin/iqtree2', 'bin/iqtree2-mpi'], + 'dirs': [], +} + +sanity_check_commands = [ + "iqtree2 --help", + "mkdir -p $TMPDIR/{test-omp,test-mpi}", + "cd $TMPDIR/test-omp && cp -a %(installdir)s/example.phy . && iqtree2 -s example.phy -redo", + "cd $TMPDIR/test-mpi && cp -a %(installdir)s/example.phy . && mpirun -np 1 iqtree2-mpi -s example.phy -redo", +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/i/IRkernel/IRkernel-1.3.2-gfbf-2023a-R-4.3.2.eb b/easybuild/easyconfigs/i/IRkernel/IRkernel-1.3.2-gfbf-2023a-R-4.3.2.eb new file mode 100644 index 00000000000..43953215612 --- /dev/null +++ b/easybuild/easyconfigs/i/IRkernel/IRkernel-1.3.2-gfbf-2023a-R-4.3.2.eb @@ -0,0 +1,72 @@ +easyblock = 'Bundle' + +name = 'IRkernel' +version = '1.3.2' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://irkernel.github.io' +description = """The R kernel for the 'Jupyter' environment executes R code + which the front-end (Jupyter Notebook or other front-ends) submits to the + kernel via the network.""" + +toolchain = {'name': 'gfbf', 'version': '2023a'} + +dependencies = [ + ('R', '4.3.2'), + ('Python', '3.11.3'), + ('IPython', '8.14.0'), + ('ZeroMQ', '4.3.4'), +] + +exts_defaultclass = 'RPackage' +exts_filter = ("R -q --no-save", "library(%(ext_name)s)") + +exts_default_options = { + 'source_urls': [ + 'https://cran.r-project.org/src/contrib/', + 'https://cran.rstudio.com/src/contrib/', + 'https://cran.r-project.org/src/contrib/Archive/%(name)s/', + ], + 'source_tmpl': '%(name)s_%(version)s.tar.gz', +} + +exts_list = [ + ('uuid', '1.1-1', { + 'checksums': ['1611240eb706e6f53400b25c9cf792ad90f151b72ed0918a1e756997f7abb716'], + }), + ('repr', '1.1.7', { + 'checksums': ['73bd696b4d4211096e0d1e382d5ce6591527d2ff400cc7ae8230f0235eed021b'], + }), + ('IRdisplay', '1.1', { + 'checksums': ['83eb030ff91f546cb647899f8aa3f5dc9fe163a89a981696447ea49cc98e8d2b'], + }), + ('pbdZMQ', '0.3-11', { + 'checksums': ['da7e204d857370201f75a05fbd808a2f409d440cc96855bb8f48f4a5dd75405b'], + }), + (name, version, { + 'checksums': ['e1c6d8bddc23e5039dd9c537feb371f937d60028fb753b90345698c58ae424a6'], + }), +] + +modextrapaths = { + 'R_LIBS_SITE': '', + 'JUPYTER_PATH': '%(name)s' +} + +# IPython notebook looks for the json kernel file in kernels/IRkernel +# We start the kernel with default bitmapType 'cairo'. This is a more sensible default +# for headless nodes. See https://github.com/IRkernel/IRkernel/issues/388 +local_kerneldir = '%(installdir)s/IRkernel' +postinstallcmds = [ + 'mkdir -p %s/kernels/ir' % local_kerneldir, + 'cp %s/kernelspec/* %s/kernels/ir' % (local_kerneldir, local_kerneldir), + ('sed -i \'s/"IRkernel::main()"/"options(bitmapType=\\x27cairo\\x27); IRkernel::main()"/g\'' + ' %s/kernels/ir/kernel.json') % local_kerneldir +] + +sanity_check_paths = { + 'files': ['%s/kernels/ir/kernel.json' % local_kerneldir], + 'dirs': [name], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/i/ISA-L/ISA-L-2.31.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/i/ISA-L/ISA-L-2.31.0-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..1e79d2b10db --- /dev/null +++ b/easybuild/easyconfigs/i/ISA-L/ISA-L-2.31.0-GCCcore-13.3.0.eb @@ -0,0 +1,45 @@ +# Author: Jasper Grimm (UoY) + +easyblock = 'ConfigureMake' + +name = 'ISA-L' +version = '2.31.0' + +homepage = 'https://github.com/intel/isa-l' +description = "Intelligent Storage Acceleration Library" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +github_account = 'intel' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['e218b7b2e241cfb8e8b68f54a6e5eed80968cc387c4b1af03708b54e9fb236f1'] + +builddependencies = [ + ('Autotools', '20231222'), + ('binutils', '2.42'), + ('pkgconf', '2.2.0'), +] +dependencies = [('NASM', '2.16.03')] + +preconfigopts = "autoreconf -i -f &&" + +runtest = 'check' + +local_bins = ['bin/igzip'] +local_includes = ['include/%(namelower)s.h'] +local_includes += ['include/isa-l/%s.h' % i for i in ['crc64', 'crc', 'erasure_code', 'gf_vect_mul', 'igzip_lib', + 'mem_routines', 'raid', 'test']] +local_libs = ['lib/libisal.%s' % k for k in ['a', 'la', SHLIB_EXT]] + +sanity_check_paths = { + 'files': local_bins + local_includes + local_libs, + 'dirs': ['bin', 'include', 'lib', 'share'], +} + +sanity_check_commands = [ + "igzip --help", + "igzip --version", +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/i/ISCE2/ISCE2-2.6.3-foss-2023a.eb b/easybuild/easyconfigs/i/ISCE2/ISCE2-2.6.3-foss-2023a.eb new file mode 100644 index 00000000000..ceae2b31949 --- /dev/null +++ b/easybuild/easyconfigs/i/ISCE2/ISCE2-2.6.3-foss-2023a.eb @@ -0,0 +1,48 @@ +easyblock = 'CMakeMake' + +name = 'ISCE2' +version = '2.6.3' + +homepage = 'https://github.com/isce-framework/isce2' +description = """ISCE is a framework designed for the purpose of processing Interferometric Synthetic + Aperture Radar (InSAR) data. The framework aspects of it have been designed as a general software + development framework. It may have additional utility in a general sense for building other + types of software packages. In its InSAR aspect ISCE supports data from many space-borne + satellites and one air-borne platform.""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'openmp': True} + +source_urls = ['https://github.com/isce-framework/isce2/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['13fd55ffcadcdd723b61053241d5e49905157b0b0ac6ed8532e4faccaa6d77f1'] + +builddependencies = [ + ('CMake', '3.26.3'), + ('FFTW', '3.3.10'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('Cython', '3.0.8'), + ('GDAL', '3.7.1'), + ('motif', '2.3.8'), + ('OpenCV', '4.8.1', '-contrib'), + ('pybind11', '2.11.1'), +] + +fix_python_shebang_for = ['bin/*.py'] + +modextrapaths = {'PYTHONPATH': 'packages'} + +sanity_check_paths = { + 'files': ['bin/stripmapApp.py'], + 'dirs': ['packages'], +} + +sanity_check_commands = [ + "python -c 'import isce'", + "stripmapApp.py --help 2>&1 | grep 'ISCE VERSION = %(version)s'", +] + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/i/ISL/ISL-0.26-GCCcore-13.3.0.eb b/easybuild/easyconfigs/i/ISL/ISL-0.26-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..2f2eb41a3a0 --- /dev/null +++ b/easybuild/easyconfigs/i/ISL/ISL-0.26-GCCcore-13.3.0.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'ISL' +version = '0.26' + +homepage = 'https://libisl.sourceforge.io' +description = "isl is a library for manipulating sets and relations of integer points bounded by linear constraints." + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://libisl.sourceforge.io'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['5eac8664e9d67be6bd0bee5085d6840b8baf738c06814df47eaf4166d9776436'] + +builddependencies = [('binutils', '2.42')] +dependencies = [('GMP', '6.3.0')] + +sanity_check_paths = { + 'files': ['lib/libisl.%s' % SHLIB_EXT, 'lib/libisl.a'], + 'dirs': ['include/isl'] +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/i/ITK/ITK-5.3.0-foss-2022b.eb b/easybuild/easyconfigs/i/ITK/ITK-5.3.0-foss-2022b.eb new file mode 100644 index 00000000000..9ba65978898 --- /dev/null +++ b/easybuild/easyconfigs/i/ITK/ITK-5.3.0-foss-2022b.eb @@ -0,0 +1,78 @@ +# Contributors: +# Fenglai Liu (fenglai@accre.vanderbilt.edu) - Vanderbilt University +# Alex Domingo (alex.domingo.toro@vub.be) - Vrije Universiteit Brussel (VUB) +# Denis Kristak, Pavel Tománek (INUITS) +# +easyblock = 'CMakeMake' + +name = 'ITK' +version = '5.3.0' + +homepage = 'https://itk.org' +description = """Insight Segmentation and Registration Toolkit (ITK) provides + an extensive suite of software tools for registering and segmenting + multidimensional imaging data.""" + +toolchain = {'name': 'foss', 'version': '2022b'} +toolchainopts = {'pic': True, 'cstd': 'c++11'} + +github_account = 'InsightSoftwareConsortium' +source_urls = [GITHUB_SOURCE] +sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}] +patches = [ + 'ITK-5.3.0_vtk-include.patch', + 'ITK-5.3.0_fix-compatibility-swig-4-1.patch', +] +checksums = [ + {'ITK-5.3.0.tar.gz': '64e7e8094a5023c8f68ee042459d6319581fadb35e2fe90a4ae230ce36369db1'}, + {'ITK-5.3.0_vtk-include.patch': '138ebd2e0e7f9001aba5f4a7e8145ffcf0093913d50f109ecff447773fd52a48'}, + {'ITK-5.3.0_fix-compatibility-swig-4-1.patch': '0138878d96e90d6bfdc81fd4f2b5ec413d61c1de666a16842b417c2686ebf506'}, +] + +builddependencies = [ + ('CMake', '3.24.3'), + ('Bison', '3.8.2'), + ('Eigen', '3.4.0'), + ('SWIG', '4.1.1'), + ('Perl', '5.36.0'), +] +dependencies = [ + ('Python', '3.10.8'), + ('double-conversion', '3.2.1'), + ('expat', '2.4.9'), + ('HDF5', '1.14.0'), + ('libjpeg-turbo', '2.1.4'), + ('libpng', '1.6.38'), + ('LibTIFF', '4.4.0'), + ('VTK', '9.2.6'), + ('zlib', '1.2.12'), +] + +# Features +configopts = '-DBUILD_SHARED_LIBS=ON -DBUILD_TESTING=OFF ' +configopts += '-DModule_ITKReview=ON -DModule_ITKVtkGlue=ON -DModule_SimpleITKFilters=ON ' +# Enable Python bindings +configopts += '-DITK_WRAP_PYTHON:BOOL=ON -DPython3_EXECUTABLE=$EBROOTPYTHON/bin/python ' +configopts += '-DSWIG_EXECUTABLE=$EBROOTSWIG/bin/swig -DSWIG_DIR=$EBROOTSWIG ' +configopts += '-DPY_SITE_PACKAGES_PATH=%(installdir)s/lib/python%(pyshortver)s/site-packages ' +# Dependencies from EB +local_sys_deps = ['DOUBLECONVERSION', 'EIGEN', 'EXPAT', 'FFTW', 'HDF5', 'JPEG', 'PNG', 'SWIG', 'TIFF', 'ZLIB'] +local_sys_cmake = ['-DITK_USE_SYSTEM_%s=ON' % d for d in local_sys_deps] +configopts += ' '.join(local_sys_cmake) + +prebuildopts = "LC_ALL=C " + +local_lib_names = ['ITKCommon', 'ITKIOHDF5', 'ITKIOJPEG', 'ITKIOPNG', 'ITKIOTIFF', + 'ITKReview', 'ITKVTK', 'ITKVtkGlue', 'itkSimpleITKFilters'] + +sanity_check_paths = { + 'files': ['bin/itkTestDriver'] + + ['lib/lib%s-%%(version_major)s.%%(version_minor)s.%s' % (l, SHLIB_EXT) for l in local_lib_names], + 'dirs': ['include/ITK-%(version_major)s.%(version_minor)s', 'lib/python%(pyshortver)s/site-packages', 'share'], +} + +sanity_check_commands = ["python -c 'import itk'"] + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/i/ITK/ITK-5.3.0_vtk-include.patch b/easybuild/easyconfigs/i/ITK/ITK-5.3.0_vtk-include.patch new file mode 100644 index 00000000000..f77306c9f8e --- /dev/null +++ b/easybuild/easyconfigs/i/ITK/ITK-5.3.0_vtk-include.patch @@ -0,0 +1,13 @@ +Manually add the include directory of VTK +dirty fix for issue https://github.com/InsightSoftwareConsortium/ITK/issues/4375 +author: Alex Domingo (Vrije Universiteit Brussel) +--- Wrapping/CMakeLists.txt.orig 2023-12-21 13:41:44.845008000 +0100 ++++ Wrapping/CMakeLists.txt 2023-12-21 13:42:14.794328946 +0100 +@@ -112,6 +112,7 @@ + ############################################################################### + # Configure specific wrapper modules + ############################################################################### ++include_directories("$ENV{EBROOTVTK}/include/vtk-9.2/") + + unset(WRAP_ITK_MODULES CACHE) + \ No newline at end of file diff --git a/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.0-37-GCCcore-11.3.0.eb b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.0-37-GCCcore-11.3.0.eb index efff91588b0..6a78cb9c5a9 100644 --- a/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.0-37-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.0-37-GCCcore-11.3.0.eb @@ -30,14 +30,18 @@ builddependencies = [ ('pkgconf', '1.8.0'), ] +preconfigopts = 'PKG_CONFIG=$EBROOTPKGCONF/bin/pkgconf' configopts = "--with-gslib --with-x" sanity_check_paths = { - 'files': [], - 'dirs': ['bin', 'etc/%(name)s-%(version_major)s', - 'include/%(name)s-%(version_major)s', 'lib', 'share'], + 'files': ['bin/magick'], + 'dirs': ['etc/%(name)s-%(version_major)s', 'include/%(name)s-%(version_major)s', 'lib', 'share'], } +sanity_check_commands = [ + 'magick --help', +] + modextravars = {'MAGICK_HOME': '%(installdir)s'} moduleclass = 'vis' diff --git a/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.0-4-GCCcore-11.2.0.eb b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.0-4-GCCcore-11.2.0.eb index c3033c0d080..7d03b87d1d8 100644 --- a/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.0-4-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.0-4-GCCcore-11.2.0.eb @@ -30,14 +30,18 @@ builddependencies = [ ('pkg-config', '0.29.2'), ] +preconfigopts = 'PKG_CONFIG=$EBROOTPKGCONF/bin/pkgconf' configopts = "--with-gslib --with-x" sanity_check_paths = { - 'files': [], - 'dirs': ['bin', 'etc/%(name)s-%(version_major)s', - 'include/%(name)s-%(version_major)s', 'lib', 'share'], + 'files': ['bin/magick'], + 'dirs': ['etc/%(name)s-%(version_major)s', 'include/%(name)s-%(version_major)s', 'lib', 'share'], } +sanity_check_commands = [ + 'magick --help', +] + modextravars = {'MAGICK_HOME': '%(installdir)s'} moduleclass = 'vis' diff --git a/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.0-53-GCCcore-12.2.0.eb b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.0-53-GCCcore-12.2.0.eb index 1ddf40ec50a..e758d987dfa 100644 --- a/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.0-53-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.0-53-GCCcore-12.2.0.eb @@ -30,14 +30,18 @@ builddependencies = [ ('pkgconf', '1.9.3'), ] +preconfigopts = 'PKG_CONFIG=$EBROOTPKGCONF/bin/pkgconf' configopts = "--with-gslib --with-x" sanity_check_paths = { - 'files': [], - 'dirs': ['bin', 'etc/%(name)s-%(version_major)s', - 'include/%(name)s-%(version_major)s', 'lib', 'share'], + 'files': ['bin/magick'], + 'dirs': ['etc/%(name)s-%(version_major)s', 'include/%(name)s-%(version_major)s', 'lib', 'share'], } +sanity_check_commands = [ + 'magick --help', +] + modextravars = {'MAGICK_HOME': '%(installdir)s'} moduleclass = 'vis' diff --git a/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.1-15-GCCcore-12.3.0.eb b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.1-15-GCCcore-12.3.0.eb index 9504c227680..4fe1068022b 100644 --- a/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.1-15-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.1-15-GCCcore-12.3.0.eb @@ -29,14 +29,18 @@ dependencies = [ ('FriBidi', '1.0.12'), ] +preconfigopts = 'PKG_CONFIG=$EBROOTPKGCONF/bin/pkgconf' configopts = "--with-gslib --with-x" - sanity_check_paths = { - 'files': [], - 'dirs': ['bin', 'etc/%(name)s-%(version_major)s', 'include/%(name)s-%(version_major)s', 'lib', 'share'], + 'files': ['bin/magick'], + 'dirs': ['etc/%(name)s-%(version_major)s', 'include/%(name)s-%(version_major)s', 'lib', 'share'], } +sanity_check_commands = [ + 'magick --help', +] + modextravars = {'MAGICK_HOME': '%(installdir)s'} moduleclass = 'vis' diff --git a/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.1-34-GCCcore-13.2.0.eb b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.1-34-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..2ccdcb32a55 --- /dev/null +++ b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.1-34-GCCcore-13.2.0.eb @@ -0,0 +1,46 @@ +easyblock = 'ConfigureMake' + +name = 'ImageMagick' +version = '7.1.1-34' + +homepage = 'https://www.imagemagick.org/' +description = "ImageMagick is a software suite to create, edit, compose, or convert bitmap images" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://github.com/%(name)s/%(name)s/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['19f4303774b56be182c576b266c34bc824fcaef1d1d243192344d015adb0ec28'] + +builddependencies = [ + ('binutils', '2.40'), + ('pkgconf', '2.0.3'), +] +dependencies = [ + ('bzip2', '1.0.8'), + ('X11', '20231019'), + ('Ghostscript', '10.02.1'), + ('JasPer', '4.0.0'), + ('libjpeg-turbo', '3.0.1'), + ('LibTIFF', '4.6.0'), + ('LittleCMS', '2.15'), + ('Pango', '1.51.0'), + ('pixman', '0.42.2'), + ('FriBidi', '1.0.13'), +] + +preconfigopts = 'PKG_CONFIG=$EBROOTPKGCONF/bin/pkgconf' +configopts = "--with-gslib --with-x" + +sanity_check_paths = { + 'files': ['bin/magick'], + 'dirs': ['etc/%(name)s-%(version_major)s', 'include/%(name)s-%(version_major)s', 'lib', 'share'], +} + +sanity_check_commands = [ + 'magick --help', +] + +modextravars = {'MAGICK_HOME': '%(installdir)s'} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.1-38-GCCcore-13.3.0.eb b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.1-38-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..776471b14b2 --- /dev/null +++ b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.1-38-GCCcore-13.3.0.eb @@ -0,0 +1,50 @@ +easyblock = 'ConfigureMake' + +name = 'ImageMagick' +version = '7.1.1-38' + +homepage = 'https://www.imagemagick.org/' +description = "ImageMagick is a software suite to create, edit, compose, or convert bitmap images" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://github.com/%(name)s/%(name)s/archive/'] +sources = ['%(version)s.tar.gz'] +patches = ['ImageMagick-7.1.1-38_fix-linking.patch'] +checksums = [ + {'7.1.1-38.tar.gz': '5e449530ccec8b85ae2bfd1ad773184fb7a4737d40fd9439db8a5d4beee4403e'}, + {'ImageMagick-7.1.1-38_fix-linking.patch': '0fbe8e3b6621e3e0d1efec59949fecb45924bc6e65851b9b6399bb3eff8d55d9'}, +] + +builddependencies = [ + ('binutils', '2.42'), + ('pkgconf', '2.2.0'), +] +dependencies = [ + ('bzip2', '1.0.8'), + ('X11', '20240607'), + ('Ghostscript', '10.03.1'), + ('JasPer', '4.2.4'), + ('libjpeg-turbo', '3.0.1'), + ('LibTIFF', '4.6.0'), + ('LittleCMS', '2.16'), + ('Pango', '1.54.0'), + ('pixman', '0.43.4'), + ('FriBidi', '1.0.15'), +] + +preconfigopts = 'PKG_CONFIG=$EBROOTPKGCONF/bin/pkgconf' +configopts = "--with-gslib --with-x" + +sanity_check_paths = { + 'files': ['bin/magick'], + 'dirs': ['etc/%(name)s-%(version_major)s', 'include/%(name)s-%(version_major)s', 'lib', 'share'], +} + +sanity_check_commands = [ + 'magick --help', +] + +modextravars = {'MAGICK_HOME': '%(installdir)s'} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.1-38_fix-linking.patch b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.1-38_fix-linking.patch new file mode 100644 index 00000000000..2c9d54a4ac0 --- /dev/null +++ b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.1-38_fix-linking.patch @@ -0,0 +1,27 @@ +The configure script sets this to a path inside the install location which is empty during build. +However this path(s) is/are used by the compiler/linker to find libraries. `pkg-config` used during configure assumes this is the same during build as on invocation of itself and omits any path already contained in the variable. + +This combination causes build failures due to dependent libraries not being found in the link step unless there happens to be some other way the paths get pulled in. E.g. if HarfBuzz is built using (the deprecated) configure&make it has `*.la` files which contain the required link flags. If HarfBuzz is built using the new Meson build system those files are no longer present and the linker paths will be missing. + +As there doesn't seem to be a specific reason for the variable to be set to an empty directory in the Makefile just remove it. + +See https://github.com/ImageMagick/ImageMagick/pull/7613 + +Author: Alexander Grund (TU Dresden) + +--- + Makefile.in | 1 - + 1 file changed, 1 deletion(-) + +diff --git a/Makefile.in b/Makefile.in +index 47b78566f0c..3a9761cfd5b 100644 +--- a/Makefile.in ++++ b/Makefile.in +@@ -3288,7 +3288,6 @@ LIBOBJS = @LIBOBJS@ + LIBOPENJP2_CFLAGS = @LIBOPENJP2_CFLAGS@ + LIBOPENJP2_LIBS = @LIBOPENJP2_LIBS@ + LIBRARY_EXTRA_CPPFLAGS = @LIBRARY_EXTRA_CPPFLAGS@ +-LIBRARY_PATH = @LIBRARY_PATH@ + LIBS = @LIBS@ + LIBSTDCLDFLAGS = @LIBSTDCLDFLAGS@ + LIBTOOL = @LIBTOOL@ diff --git a/easybuild/easyconfigs/i/Imath/Imath-3.1.11-GCCcore-13.3.0.eb b/easybuild/easyconfigs/i/Imath/Imath-3.1.11-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..05efb6d6c62 --- /dev/null +++ b/easybuild/easyconfigs/i/Imath/Imath-3.1.11-GCCcore-13.3.0.eb @@ -0,0 +1,28 @@ +easyblock = 'CMakeMake' + +name = 'Imath' +version = '3.1.11' + +homepage = 'https://imath.readthedocs.io/en/latest/' +description = """ +Imath is a C++ and python library of 2D and 3D vector, matrix, and math operations for computer graphics +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/AcademySoftwareFoundation/%(namelower)s/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['9057849585e49b8b85abe7cc1e76e22963b01bfdc3b6d83eac90c499cd760063'] + +builddependencies = [ + ('binutils', '2.42'), + ('CMake', '3.29.3'), +] + +sanity_check_paths = { + 'files': ['lib/libImath.%s' % SHLIB_EXT], + 'dirs': ['include/Imath'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/i/Infernal/Infernal-1.1.5-foss-2023a.eb b/easybuild/easyconfigs/i/Infernal/Infernal-1.1.5-foss-2023a.eb new file mode 100644 index 00000000000..7a89f4503eb --- /dev/null +++ b/easybuild/easyconfigs/i/Infernal/Infernal-1.1.5-foss-2023a.eb @@ -0,0 +1,39 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Cedric Laczny , Fotis Georgatos +# License:: MIT/GPL +# Updated:: Denis Kristak (INUITS) +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +## + +easyblock = 'ConfigureMake' + +name = 'Infernal' +version = "1.1.5" + +homepage = 'http://eddylab.org/infernal/' +description = """Infernal ("INFERence of RNA ALignment") is for searching DNA sequence databases + for RNA structure and sequence similarities.""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'pic': True} + +source_urls = ['http://eddylab.org/%(namelower)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['ad4ddae02f924ca7c85bc8c4a79c9f875af8df96aeb726702fa985cbe752497f'] + +local_bins = ['align', 'build', 'calibrate', 'convert', 'emit', 'fetch', 'press', 'scan', 'search', 'stat'] + +sanity_check_paths = { + 'files': ['bin/cm%s' % x for x in local_bins], + 'dirs': [] +} + +sanity_check_commands = ['cm%s -h' % x for x in local_bins] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/i/Inspector/Inspector-2019_update5.eb b/easybuild/easyconfigs/i/Inspector/Inspector-2019_update5.eb index b27635916ca..179e26005de 100644 --- a/easybuild/easyconfigs/i/Inspector/Inspector-2019_update5.eb +++ b/easybuild/easyconfigs/i/Inspector/Inspector-2019_update5.eb @@ -7,7 +7,7 @@ description = """Intel Inspector XE is an easy to use memory error checker and t toolchain = SYSTEM -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15827/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/15827/'] sources = ['inspector_%(version)s.tar.gz'] checksums = ['676fd0b25a56fba63495c048abf485b08583cbb01eb0cf6e1174ee7b352af6d5'] diff --git a/easybuild/easyconfigs/i/Inspector/Inspector-2021.4.0.eb b/easybuild/easyconfigs/i/Inspector/Inspector-2021.4.0.eb index 11b56c0bc1c..494b031a5e1 100644 --- a/easybuild/easyconfigs/i/Inspector/Inspector-2021.4.0.eb +++ b/easybuild/easyconfigs/i/Inspector/Inspector-2021.4.0.eb @@ -10,7 +10,7 @@ description = """Intel Inspector is a dynamic memory and threading error toolchain = SYSTEM -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18239/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18239/'] sources = ['l_inspector_oneapi_p_%(version)s.266_offline.sh'] checksums = ['c8210cbcd0e07cc75e773249a5e4a02cf34894ec80a213939f3a20e6c5705274'] diff --git a/easybuild/easyconfigs/i/Inspector/Inspector-2022.0.0.eb b/easybuild/easyconfigs/i/Inspector/Inspector-2022.0.0.eb index 430cc62b2d4..22f082dd1f4 100644 --- a/easybuild/easyconfigs/i/Inspector/Inspector-2022.0.0.eb +++ b/easybuild/easyconfigs/i/Inspector/Inspector-2022.0.0.eb @@ -10,7 +10,7 @@ description = """Intel Inspector is a dynamic memory and threading error toolchain = SYSTEM -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18363/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18363/'] sources = ['l_inspector_oneapi_p_%(version)s.56_offline.sh'] checksums = ['79a0eb2ae3f1de1e3456076685680c468702922469c3fda3e074718fb0bea741'] diff --git a/easybuild/easyconfigs/i/Inspector/Inspector-2022.1.0.eb b/easybuild/easyconfigs/i/Inspector/Inspector-2022.1.0.eb index a7772259cc8..33515e7a8e5 100644 --- a/easybuild/easyconfigs/i/Inspector/Inspector-2022.1.0.eb +++ b/easybuild/easyconfigs/i/Inspector/Inspector-2022.1.0.eb @@ -10,7 +10,7 @@ description = """Intel Inspector is a dynamic memory and threading error toolchain = SYSTEM -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18712/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18712/'] sources = ['l_inspector_oneapi_p_%(version)s.123_offline.sh'] checksums = ['8551180aa30be3abea11308fb11ea9a296f0e056ab07d9254585448a0b23333e'] diff --git a/easybuild/easyconfigs/i/Inspector/Inspector-2024.2.0.eb b/easybuild/easyconfigs/i/Inspector/Inspector-2024.2.0.eb new file mode 100644 index 00000000000..0d345bc2c5e --- /dev/null +++ b/easybuild/easyconfigs/i/Inspector/Inspector-2024.2.0.eb @@ -0,0 +1,19 @@ + +name = 'Inspector' +version = '2024.2.0' + +homepage = 'https://software.intel.com/content/www/us/en/develop/tools/oneapi/components/inspector.html' +description = """Intel Inspector is a dynamic memory and threading error + checking tool for users developing serial and parallel applications""" + +toolchain = SYSTEM + +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/1549c5b3-cf23-4595-9593-b5d0460a8dcd/'] +sources = ['l_inspector_oneapi_p_%(version)s.22_offline.sh'] +checksums = ['e2aab9b1b428d0c23184beae8caac55fa3d3f973ac51a6b6908eb38b0d9097ed'] + +dontcreateinstalldir = True + +requires_runtime_license = False + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/i/IntelClusterChecker/IntelClusterChecker-2021.5.0.eb b/easybuild/easyconfigs/i/IntelClusterChecker/IntelClusterChecker-2021.5.0.eb index 55107c33e8a..c0357dea2d0 100644 --- a/easybuild/easyconfigs/i/IntelClusterChecker/IntelClusterChecker-2021.5.0.eb +++ b/easybuild/easyconfigs/i/IntelClusterChecker/IntelClusterChecker-2021.5.0.eb @@ -13,7 +13,7 @@ can be identified and practical resolutions provided. toolchain = SYSTEM -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18359/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18359/'] sources = ['l_clck_p_%(version)s.560_offline.sh'] checksums = ['2b661eff4a87607fd29e21fe29883873c0a7216d7d0a99557dc48b6eae9adeb0'] diff --git a/easybuild/easyconfigs/i/IntelPython/IntelPython-2.7.15-2019.2.066.eb b/easybuild/easyconfigs/i/IntelPython/IntelPython-2.7.15-2019.2.066.eb index c46f42bb81b..48ab0a8f836 100644 --- a/easybuild/easyconfigs/i/IntelPython/IntelPython-2.7.15-2019.2.066.eb +++ b/easybuild/easyconfigs/i/IntelPython/IntelPython-2.7.15-2019.2.066.eb @@ -15,7 +15,7 @@ description = """ Accelerating Python* performance on modern architectures from Intel. """ -source_urls = ['http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15115/'] +source_urls = ['http://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/15115/'] sources = ['l_pythoni%s_p_%s.tar.gz' % (local_pysver, local_relver)] checksums = ['dd0b73db5d0d79c3cdf779d10092eae32780d720b74ed8fde2a2c46e23143de1'] diff --git a/easybuild/easyconfigs/i/IntelPython/IntelPython-3.6.8-2019.2.066.eb b/easybuild/easyconfigs/i/IntelPython/IntelPython-3.6.8-2019.2.066.eb index fd51e3b2082..d0c2dc13c67 100644 --- a/easybuild/easyconfigs/i/IntelPython/IntelPython-3.6.8-2019.2.066.eb +++ b/easybuild/easyconfigs/i/IntelPython/IntelPython-3.6.8-2019.2.066.eb @@ -15,7 +15,7 @@ description = """ Accelerating Python* performance on modern architectures from Intel. """ -source_urls = ['http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15115/'] +source_urls = ['http://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/15115/'] sources = ['l_pythoni%s_p_%s.tar.gz' % (local_pysver, local_relver)] checksums = ['804883fc1413ee72b0ae421a8ac82ab158fc01c8b4631a44a9d2ef1a19324751'] diff --git a/easybuild/easyconfigs/i/IsoQuant/IsoQuant-3.5.0-foss-2023a.eb b/easybuild/easyconfigs/i/IsoQuant/IsoQuant-3.5.0-foss-2023a.eb new file mode 100644 index 00000000000..41248bcbf73 --- /dev/null +++ b/easybuild/easyconfigs/i/IsoQuant/IsoQuant-3.5.0-foss-2023a.eb @@ -0,0 +1,45 @@ +easyblock = 'Tarball' + +name = 'IsoQuant' +version = '3.5.0' + +homepage = 'https://github.com/ablab/IsoQuant' +description = """IsoQuant is a tool for the genome-based analysis of long RNA reads, + such as PacBio or Oxford Nanopores. IsoQuant allows to reconstruct and quantify + transcript models with high precision and decent recall. If the reference annotation is given, + IsoQuant also assigns reads to the annotated isoforms based on their intron and exon structure. + IsoQuant further performs annotated gene, isoform, exon and intron quantification. + If reads are grouped (e.g. according to cell type), counts are reported according to the provided grouping.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['https://github.com/ablab/%(name)s/archive/'] +sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}] +checksums = ['8cbba80b5eb0ed85fe0b519693157eb97820bc1d79ff44435736bf799af85c1f'] + +dependencies = [ + ('Python', '3.11.3'), + ('gffutils', '0.13'), + ('Biopython', '1.83'), + ('SciPy-bundle', '2023.07'), + ('pybedtools', '0.9.1'), + ('Pysam', '0.22.0'), + ('pyfaidx', '0.8.1.1'), + ('minimap2', '2.26'), + ('SAMtools', '1.18'), + ('PyYAML', '6.0'), +] + +modextrapaths = { + 'PATH': '', + 'PYTHONPATH': '', +} + +sanity_check_paths = { + 'files': ['isoquant.py'], + 'dirs': [], +} + +sanity_check_commands = ["mkdir -p %(builddir)s && cd %(builddir)s && isoquant.py --test"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/i/icc/icc-2018.1.163-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/i/icc/icc-2018.1.163-GCC-6.4.0-2.28.eb index ca49a084587..f6eb99cebdc 100644 --- a/easybuild/easyconfigs/i/icc/icc-2018.1.163-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/i/icc/icc-2018.1.163-GCC-6.4.0-2.28.eb @@ -8,7 +8,7 @@ description = "Intel C and C++ compilers" toolchain = SYSTEM -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12382/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/12382/'] sources = ['parallel_studio_xe_%(version_major)s_update%(version_minor)s_composer_edition_for_cpp.tgz'] checksums = ['ddbfdf88eed095817650ec0a226ef3b9c07c41c855d258e80eaade5173fedb6e'] diff --git a/easybuild/easyconfigs/i/icc/icc-2018.3.222-GCC-7.3.0-2.30.eb b/easybuild/easyconfigs/i/icc/icc-2018.3.222-GCC-7.3.0-2.30.eb index 9b3a071f005..c04b1a09909 100644 --- a/easybuild/easyconfigs/i/icc/icc-2018.3.222-GCC-7.3.0-2.30.eb +++ b/easybuild/easyconfigs/i/icc/icc-2018.3.222-GCC-7.3.0-2.30.eb @@ -8,7 +8,7 @@ description = "Intel C and C++ compilers" toolchain = SYSTEM -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13003/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/13003/'] sources = ['parallel_studio_xe_%(version_major)s_update%(version_minor)s_composer_edition_for_cpp.tgz'] checksums = ['d8b7e6633faa2e0b7d4eebf3260cb3a200b951cb2cf7b5db957c5ae71508d34b'] diff --git a/easybuild/easyconfigs/i/icc/icc-2018.5.274-GCC-7.3.0-2.30.eb b/easybuild/easyconfigs/i/icc/icc-2018.5.274-GCC-7.3.0-2.30.eb index 3918ba3f3f1..f2d6c096878 100644 --- a/easybuild/easyconfigs/i/icc/icc-2018.5.274-GCC-7.3.0-2.30.eb +++ b/easybuild/easyconfigs/i/icc/icc-2018.5.274-GCC-7.3.0-2.30.eb @@ -8,7 +8,7 @@ description = "Intel C and C++ compilers" toolchain = SYSTEM -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13723/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/13723/'] # released as "2018 update 4" despite internal version number if 2018.5.274, so can't use %(version_minor)s template sources = ['parallel_studio_xe_%(version_major)s_update4_composer_edition_for_cpp.tgz'] checksums = ['3850ab2a01fe8888af8fed65b7d24e0ddf45a84efe9635ff0f118c38dfc4544b'] diff --git a/easybuild/easyconfigs/i/icc/icc-2019.0.117-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/i/icc/icc-2019.0.117-GCC-8.2.0-2.31.1.eb index b78d2e8e11c..5cf05e6a559 100644 --- a/easybuild/easyconfigs/i/icc/icc-2019.0.117-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/i/icc/icc-2019.0.117-GCC-8.2.0-2.31.1.eb @@ -8,7 +8,7 @@ description = "Intel C and C++ compilers" toolchain = SYSTEM -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13582/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/13582/'] sources = ['parallel_studio_xe_%(version_major)s_composer_edition_for_cpp.tgz'] checksums = ['17932a54a76d04432de16e6db15a6ed80fa80ed20193f3b717fd391f623e23e1'] diff --git a/easybuild/easyconfigs/i/icc/icc-2019.1.144-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/i/icc/icc-2019.1.144-GCC-8.2.0-2.31.1.eb index 7b37d3169dc..f2341a844c3 100644 --- a/easybuild/easyconfigs/i/icc/icc-2019.1.144-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/i/icc/icc-2019.1.144-GCC-8.2.0-2.31.1.eb @@ -8,7 +8,7 @@ description = "Intel C and C++ compilers" toolchain = SYSTEM -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/14865/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/14865/'] sources = ['parallel_studio_xe_%(version_major)s_update%(version_minor)s_composer_edition_for_cpp.tgz'] checksums = ['4a156bbeac9bd8d67e74b33ad6f3ae02d4c24c8444365465db6dc50d3e891946'] diff --git a/easybuild/easyconfigs/i/icc/icc-2019.2.187-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/i/icc/icc-2019.2.187-GCC-8.2.0-2.31.1.eb index f192fd17472..9f9b71a21df 100644 --- a/easybuild/easyconfigs/i/icc/icc-2019.2.187-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/i/icc/icc-2019.2.187-GCC-8.2.0-2.31.1.eb @@ -8,7 +8,7 @@ description = "Intel C and C++ compilers" toolchain = SYSTEM -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15093/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/15093/'] sources = ['parallel_studio_xe_%(version_major)s_update%(version_minor)s_composer_edition_for_cpp.tgz'] checksums = ['fc434a2e005af223f43d258c16f004134def726a8d2a225e830af85d553bee55'] diff --git a/easybuild/easyconfigs/i/icc/icc-2019.3.199-GCC-8.3.0-2.32.eb b/easybuild/easyconfigs/i/icc/icc-2019.3.199-GCC-8.3.0-2.32.eb index 65821a417db..2d194db100a 100644 --- a/easybuild/easyconfigs/i/icc/icc-2019.3.199-GCC-8.3.0-2.32.eb +++ b/easybuild/easyconfigs/i/icc/icc-2019.3.199-GCC-8.3.0-2.32.eb @@ -8,7 +8,7 @@ description = "Intel C and C++ compilers" toolchain = SYSTEM -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15273/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/15273/'] sources = ['parallel_studio_xe_%(version_major)s_update%(version_minor)s_composer_edition_for_cpp.tgz'] checksums = ['969985e83ebf7bfe3c3ac3b771a7d16ba9b5dfbda84e7c2a60ef25fb827b58ae'] diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2019.4.243.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2019.4.243.eb index 5cefbfc2dee..85453f37251 100644 --- a/easybuild/easyconfigs/i/iccifort/iccifort-2019.4.243.eb +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2019.4.243.eb @@ -8,7 +8,7 @@ description = "Intel C, C++ & Fortran compilers" toolchain = SYSTEM -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15537/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/15537/'] sources = ['parallel_studio_xe_%(version_major)s_update%(version_minor)s_composer_edition.tgz'] patches = ['iccifort-%(version)s_no_mpi_rt_dependency.patch'] checksums = [ diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2019.5.281.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2019.5.281.eb index c080762f21d..b4eb6588ec7 100644 --- a/easybuild/easyconfigs/i/iccifort/iccifort-2019.5.281.eb +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2019.5.281.eb @@ -8,7 +8,7 @@ description = "Intel C, C++ & Fortran compilers" toolchain = SYSTEM -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15813/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/15813/'] sources = ['parallel_studio_xe_%(version_major)s_update%(version_minor)s_composer_edition.tgz'] patches = ['iccifort-%(version)s_no_mpi_rt_dependency.patch'] checksums = [ diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2020.0.166-GCC-9.2.0.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2020.0.166-GCC-9.2.0.eb index a8f9c94588f..a21e15527d5 100644 --- a/easybuild/easyconfigs/i/iccifort/iccifort-2020.0.166-GCC-9.2.0.eb +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2020.0.166-GCC-9.2.0.eb @@ -8,7 +8,7 @@ description = "Intel C, C++ & Fortran compilers" toolchain = SYSTEM -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/16229/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/16229/'] sources = ['parallel_studio_xe_%(version_major)s_composer_edition.tgz'] patches = ['iccifort-%(version)s_no_mpi_rt_dependency.patch'] checksums = [ diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2020.0.166.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2020.0.166.eb index 70593480c69..4ad42c13a31 100644 --- a/easybuild/easyconfigs/i/iccifort/iccifort-2020.0.166.eb +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2020.0.166.eb @@ -8,7 +8,7 @@ description = "Intel C, C++ & Fortran compilers" toolchain = SYSTEM -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/16229/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/16229/'] sources = ['parallel_studio_xe_%(version_major)s_composer_edition.tgz'] patches = ['iccifort-%(version)s_no_mpi_rt_dependency.patch'] checksums = [ diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2020.1.217.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2020.1.217.eb index 89d42319787..98e64dff918 100644 --- a/easybuild/easyconfigs/i/iccifort/iccifort-2020.1.217.eb +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2020.1.217.eb @@ -8,7 +8,7 @@ description = "Intel C, C++ & Fortran compilers" toolchain = SYSTEM -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/16530/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/16530/'] sources = ['parallel_studio_xe_%(version_major)s_update%(version_minor)s_composer_edition.tgz'] patches = ['iccifort-%(version)s_no_mpi_rt_dependency.patch'] checksums = [ diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2020.4.304.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2020.4.304.eb index fbd8bc1719b..056539c7f76 100644 --- a/easybuild/easyconfigs/i/iccifort/iccifort-2020.4.304.eb +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2020.4.304.eb @@ -8,7 +8,7 @@ description = "Intel C, C++ & Fortran compilers" toolchain = SYSTEM -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/17117/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/17117/'] sources = ['parallel_studio_xe_%(version_major)s_update%(version_minor)s_composer_edition.tgz'] patches = ['iccifort-%(version)s_no_mpi_rt_dependency.patch'] checksums = [ diff --git a/easybuild/easyconfigs/i/ifort/ifort-2018.1.163-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/i/ifort/ifort-2018.1.163-GCC-6.4.0-2.28.eb index 66cf55bd0c0..2ce7d5ee7f1 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2018.1.163-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2018.1.163-GCC-6.4.0-2.28.eb @@ -8,7 +8,7 @@ description = "Intel Fortran compiler" toolchain = SYSTEM -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12383/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/12383/'] sources = ['parallel_studio_xe_%(version_major)s_update%(version_minor)s_composer_edition_for_fortran.tgz'] patches = ['ifort_%(version)s_no_mpi_mic_dependency.patch'] checksums = [ diff --git a/easybuild/easyconfigs/i/ifort/ifort-2018.3.222-GCC-7.3.0-2.30.eb b/easybuild/easyconfigs/i/ifort/ifort-2018.3.222-GCC-7.3.0-2.30.eb index 8572f079dca..3bdc51210af 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2018.3.222-GCC-7.3.0-2.30.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2018.3.222-GCC-7.3.0-2.30.eb @@ -8,7 +8,7 @@ description = "Intel Fortran compiler" toolchain = SYSTEM -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13004/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/13004/'] sources = ['parallel_studio_xe_%(version_major)s_update%(version_minor)s_composer_edition_for_fortran.tgz'] patches = ['ifort_%(version)s_no_mpi_mic_dependency.patch'] checksums = [ diff --git a/easybuild/easyconfigs/i/ifort/ifort-2018.5.274-GCC-7.3.0-2.30.eb b/easybuild/easyconfigs/i/ifort/ifort-2018.5.274-GCC-7.3.0-2.30.eb index 7668ec76749..3f9f1de0c45 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2018.5.274-GCC-7.3.0-2.30.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2018.5.274-GCC-7.3.0-2.30.eb @@ -8,7 +8,7 @@ description = "Intel Fortran compiler" toolchain = SYSTEM -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13724/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/13724/'] # released as "2018 update 4" despite internal version number if 2018.5.274, so can't use %(version_minor)s template sources = ['parallel_studio_xe_%(version_major)s_update4_composer_edition_for_fortran.tgz'] patches = ['ifort-%(version)s_no_mpi_mic_dependency.patch'] diff --git a/easybuild/easyconfigs/i/ifort/ifort-2019.0.117-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/i/ifort/ifort-2019.0.117-GCC-8.2.0-2.31.1.eb index 3457239087d..453cf476095 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2019.0.117-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2019.0.117-GCC-8.2.0-2.31.1.eb @@ -8,7 +8,7 @@ description = "Intel Fortran compiler" toolchain = SYSTEM -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13583/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/13583/'] sources = ['parallel_studio_xe_%(version_major)s_composer_edition_for_fortran.tgz'] patches = ['ifort-%(version)s_no_mpi_mic_dependency.patch'] checksums = [ diff --git a/easybuild/easyconfigs/i/ifort/ifort-2019.1.144-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/i/ifort/ifort-2019.1.144-GCC-8.2.0-2.31.1.eb index c47117b085b..c6c03d9340f 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2019.1.144-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2019.1.144-GCC-8.2.0-2.31.1.eb @@ -8,7 +8,7 @@ description = "Intel Fortran compiler" toolchain = SYSTEM -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/14866/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/14866/'] sources = ['parallel_studio_xe_%(version_major)s_update%(version_minor)s_composer_edition_for_fortran.tgz'] patches = ['ifort-%(version)s_no_mpi_mic_dependency.patch'] checksums = [ diff --git a/easybuild/easyconfigs/i/ifort/ifort-2019.2.187-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/i/ifort/ifort-2019.2.187-GCC-8.2.0-2.31.1.eb index 924762c6de2..5a043c03822 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2019.2.187-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2019.2.187-GCC-8.2.0-2.31.1.eb @@ -8,7 +8,7 @@ description = "Intel Fortran compiler" toolchain = SYSTEM -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15094/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/15094/'] sources = ['parallel_studio_xe_%(version_major)s_update%(version_minor)s_composer_edition_for_fortran.tgz'] patches = ['ifort-%(version)s_no_mpi_mic_dependency.patch'] checksums = [ diff --git a/easybuild/easyconfigs/i/ifort/ifort-2019.3.199-GCC-8.3.0-2.32.eb b/easybuild/easyconfigs/i/ifort/ifort-2019.3.199-GCC-8.3.0-2.32.eb index b8eb911adc2..b996c679995 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2019.3.199-GCC-8.3.0-2.32.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2019.3.199-GCC-8.3.0-2.32.eb @@ -8,7 +8,7 @@ description = "Intel Fortran compiler" toolchain = SYSTEM -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15274/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/15274/'] sources = ['parallel_studio_xe_%(version_major)s_update%(version_minor)s_composer_edition_for_fortran.tgz'] patches = ['ifort-%(version)s_no_mpi_mic_dependency.patch'] checksums = [ diff --git a/easybuild/easyconfigs/i/igraph/igraph-0.10.12-foss-2023b.eb b/easybuild/easyconfigs/i/igraph/igraph-0.10.12-foss-2023b.eb new file mode 100644 index 00000000000..6e5f77cd3c8 --- /dev/null +++ b/easybuild/easyconfigs/i/igraph/igraph-0.10.12-foss-2023b.eb @@ -0,0 +1,42 @@ +# Author: Denis Krišťák (INUITS) +# Modified: Jasper Grimm (UoY) +# Update: Pavel Tománek (INUITS) +# Update: Petr Král (INUITS) + +easyblock = 'CMakeMake' + +name = 'igraph' +version = '0.10.12' + +homepage = 'https://igraph.org' +description = """igraph is a collection of network analysis tools with the emphasis on +efficiency, portability and ease of use. igraph is open source and free. igraph can be +programmed in R, Python and C/C++.""" + +toolchain = {'name': 'foss', 'version': '2023b'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/igraph/igraph/releases/download/%(version)s'] +sources = [SOURCE_TAR_GZ] +checksums = ['b011f7f9f38a3e59924cc9ff652e6d33105fa03fcaf3792f47d752626a0a4625'] + +builddependencies = [ + ('CMake', '3.27.6'), +] + +dependencies = [ + ('GLPK', '5.0'), + ('libxml2', '2.11.5'), + ('zlib', '1.2.13'), + ('arpack-ng', '3.9.0'), +] + +# Build static and shared libraries +configopts = ["-DBUILD_SHARED_LIBS=OFF", "-DBUILD_SHARED_LIBS=ON"] + +sanity_check_paths = { + 'files': ['include/igraph/igraph.h'] + ['lib/libigraph.%s' % x for x in ['a', SHLIB_EXT]], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/i/iimpi/iimpi-2024a.eb b/easybuild/easyconfigs/i/iimpi/iimpi-2024a.eb new file mode 100644 index 00000000000..d6150133621 --- /dev/null +++ b/easybuild/easyconfigs/i/iimpi/iimpi-2024a.eb @@ -0,0 +1,18 @@ +# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild +easyblock = 'Toolchain' + +name = 'iimpi' +version = '2024a' + +homepage = 'https://software.intel.com/parallel-studio-xe' +description = """Intel C/C++ and Fortran compilers, alongside Intel MPI.""" + +toolchain = SYSTEM + +local_comp_ver = '2024.2.0' +dependencies = [ + ('intel-compilers', local_comp_ver), + ('impi', '2021.13.0', '', ('intel-compilers', local_comp_ver)), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/i/ilastik-napari/ilastik-napari-0.2.4-foss-2023a.eb b/easybuild/easyconfigs/i/ilastik-napari/ilastik-napari-0.2.4-foss-2023a.eb new file mode 100644 index 00000000000..64e20f93f38 --- /dev/null +++ b/easybuild/easyconfigs/i/ilastik-napari/ilastik-napari-0.2.4-foss-2023a.eb @@ -0,0 +1,37 @@ +easyblock = 'PythonBundle' + +name = 'ilastik-napari' +version = '0.2.4' + +homepage = 'https://github.com/ilastik/ilastik-napari/' +description = "Napari plugin for interactive pixel classification." + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('SciPy-bundle', '2023.07'), + ('napari', '0.4.18'), + ('QtPy', '2.4.1'), + ('scikit-learn', '1.3.1'), + ('numba', '0.58.1'), + ('fastfilters', '0.3'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('sparse', '0.15.4', { + 'source_tmpl': '%(name)s-%(version)s-py2.py3-none-any.whl', + 'checksums': ['76ec76fee2aee82a84eb97155dd530a9644e3b1fdea2406bc4b454698b36d938'], + }), + (name, version, { + 'source_tmpl': 'ilastik_napari-%(version)s.tar.gz', + 'modulename': 'ilastik', + 'checksums': ['8e971a70389f9257eaca7561637301f996f316fdff2cb223c5828d162970bec4'], + }), +] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/i/imagecodecs/imagecodecs-2024.1.1-foss-2023a.eb b/easybuild/easyconfigs/i/imagecodecs/imagecodecs-2024.1.1-foss-2023a.eb new file mode 100644 index 00000000000..25c939f0627 --- /dev/null +++ b/easybuild/easyconfigs/i/imagecodecs/imagecodecs-2024.1.1-foss-2023a.eb @@ -0,0 +1,78 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +# update: Thomas Hoffmann (EMBL), Denis Kristak (Inuits), Cintia Willemyns (Vrije Universiteit Brussel) +easyblock = 'PythonBundle' + +name = 'imagecodecs' +version = '2024.1.1' + +homepage = 'https://github.com/cgohlke/imagecodecs' +description = """Imagecodecs is a Python library that provides block-oriented, in-memory buffer transformation, +compression, and decompression functions for use in the tifffile, czifile, zarr, and other +scientific image input/output modules.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +local_openjpeg_maj_min = '2.5' +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('Cython', '3.0.8'), + ('matplotlib', '3.7.2'), + ('Brotli', '1.0.9'), + ('Blosc', '1.21.5'), + ('Blosc2', '2.8.0'), + ('CFITSIO', '4.3.0'), + ('CharLS', '2.4.2'), + ('giflib', '5.2.1'), + ('jxrlib', '1.1'), + ('LittleCMS', '2.15'), + ('LERC', '4.0.0'), + ('libaec', '1.0.6'), + ('libavif', '1.0.4'), + ('libdeflate', '1.18'), + ('libjpeg-turbo', '2.1.5.1'), + ('libjxl', '0.8.2'), + ('LibLZF', '3.6'), + ('libpng', '1.6.39'), + ('LibTIFF', '4.5.0'), + ('libwebp', '1.3.1'), + ('lz4', '1.9.4'), + ('OpenJPEG', local_openjpeg_maj_min + '.0'), + ('snappy', '1.1.10'), + ('zlib-ng', '2.1.6'), + ('Zopfli', '1.0.3'), + ('zfp', '1.0.1'), + ('zstd', '1.5.5'), + ('Brunsli', '0.1'), + ('HDF5', '1.14.0'), + ('h5py', '3.9.0'), + ('libheif', '1.17.6'), + ('bitshuffle', '0.5.1'), # Cannot be as extension because Cython 3.0.8 is too new +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('colorlog', '6.8.2', { + 'checksums': ['3e3e079a41feb5a1b64f978b5ea4f46040a94f11f0e8bbb8261e3dbbeca64d44'], + }), + (name, version, { + 'buildopts': '--global-option="build_ext" --global-option="--lite"', + 'extract_cmd': "tar -xvf %s && find . -type f -print0 | xargs -0 dos2unix", + 'patches': ['imagecodecs-2024.1.1_fix-aec-version.patch'], + 'preinstallopts': "export CPATH=$EBROOTOPENJPEG/include/openjpeg-2.5/:$CPATH && ", + 'source_urls': [ + 'https://github.com/cgohlke/imagecodecs/releases/download/v%(version)s/imagecodecs-2024.1.1.tar.gz' + ], + 'sources': ['%(name)s-%(version)s.tar.gz'], + 'checksums': [ + {'imagecodecs-2024.1.1.tar.gz': 'fde46bd698d008255deef5411c59b35c0e875295e835bf6079f7e2ab22f216eb'}, + {'imagecodecs-2024.1.1_fix-aec-version.patch': + '7feb0a5fe37893d1a186f85c8f6cdb940704605ee2da5ea8e5d555ec5bfa01aa'}, + ], + }), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/i/imagecodecs/imagecodecs-2024.1.1_fix-aec-version.patch b/easybuild/easyconfigs/i/imagecodecs/imagecodecs-2024.1.1_fix-aec-version.patch new file mode 100644 index 00000000000..045dca394d7 --- /dev/null +++ b/easybuild/easyconfigs/i/imagecodecs/imagecodecs-2024.1.1_fix-aec-version.patch @@ -0,0 +1,16 @@ +Determine version of libaec from header does not work and causes error +Author: Cintia Willemyns (Vrije Universiteit Brussel) +--- imagecodecs-2024.1.1.orig/imagecodecs/_aec.pyx 2024-05-27 15:12:24.533724000 +0200 ++++ imagecodecs-2024.1.1/imagecodecs/_aec.pyx 2024-05-27 15:13:02.238325670 +0200 +@@ -76,10 +76,7 @@ + + def aec_version(): + """Return libaec library version string.""" +- return ( +- f'libaec {AEC_VERSION_MAJOR}.{AEC_VERSION_MINOR}.{AEC_VERSION_PATCH}' +- ) +- ++ return 'libaec 1.0.6' + + def aec_check(data): + """Return whether data is AEC encoded.""" diff --git a/easybuild/easyconfigs/i/imageio/imageio-2.34.1-gfbf-2023b.eb b/easybuild/easyconfigs/i/imageio/imageio-2.34.1-gfbf-2023b.eb new file mode 100644 index 00000000000..8f602262f3d --- /dev/null +++ b/easybuild/easyconfigs/i/imageio/imageio-2.34.1-gfbf-2023b.eb @@ -0,0 +1,25 @@ +easyblock = 'PythonPackage' + +name = 'imageio' +version = '2.34.1' + +homepage = 'https://imageio.github.io' +description = """Imageio is a Python library that provides an easy interface to read and write a wide range of + image data, including animated images, video, volumetric data, and scientific formats.""" + +toolchain = {'name': 'gfbf', 'version': '2023b'} + +sources = [SOURCE_TAR_GZ] +checksums = ['f13eb76e4922f936ac4a7fec77ce8a783e63b93543d4ea3e40793a6cabd9ac7d'] + +dependencies = [ + ('Python', '3.11.5'), + ('matplotlib', '3.8.2'), + ('Pillow', '10.2.0'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/i/imbalanced-learn/imbalanced-learn-0.12.3-gfbf-2023a.eb b/easybuild/easyconfigs/i/imbalanced-learn/imbalanced-learn-0.12.3-gfbf-2023a.eb new file mode 100644 index 00000000000..4881e78a0e7 --- /dev/null +++ b/easybuild/easyconfigs/i/imbalanced-learn/imbalanced-learn-0.12.3-gfbf-2023a.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonBundle' + +name = 'imbalanced-learn' +version = '0.12.3' + +homepage = 'https://github.com/scikit-learn-contrib/imbalanced-learn' +description = """imbalanced-learn is a Python package offering a number of re-sampling techniques commonly used in + datasets showing strong between-class imbalance.""" + +toolchain = {'name': 'gfbf', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('scikit-learn', '1.3.1'), +] + +sanity_pip_check = True +use_pip = True + +exts_list = [ + (name, version, { + 'modulename': 'imblearn', + 'checksums': ['5b00796a01419e9102bd425e27c319d58d1f6cf2dfa751e02ed7f4edf67c3c1b'], + }), +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/i/imgaug/imgaug-0.4.1-foss-2023a.eb b/easybuild/easyconfigs/i/imgaug/imgaug-0.4.1-foss-2023a.eb new file mode 100644 index 00000000000..2b1f0c837e5 --- /dev/null +++ b/easybuild/easyconfigs/i/imgaug/imgaug-0.4.1-foss-2023a.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonPackage' + +name = 'imgaug' +version = '0.4.1' + +homepage = 'https://imgaug.readthedocs.io/en/latest/' +description = """ This python library helps you with augmenting images for your machine learning projects. + It converts a set of input images into a new, much larger set of slightly altered images. """ + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('Pillow', '10.0.0'), + ('matplotlib', '3.7.2'), + ('scikit-image', '0.22.0'), + ('OpenCV', '4.8.1', '-contrib'), + ('Shapely', '2.0.1'), + ('imageio', '2.33.1'), +] + +source_urls = ['https://github.com/nsetzer/imgaug/archive/'] +sources = ['%(version)s.tar.gz'] +patches = ['imgaug-0.4.1_openvc_requirement.patch'] +checksums = [ + {'0.4.1.tar.gz': 'dd9655f8d871da35c37cf674ba35c76175a77aeac517e8dafe6673c8f853115f'}, + {'imgaug-0.4.1_openvc_requirement.patch': '0e0993322184c56115ea04262f8eacef4a86a9aa7b26c8cd67258ccaa441d8a7'}, +] + +download_dep_fail = True +sanity_pip_check = True +use_pip = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/i/imkl-FFTW/imkl-FFTW-2024.2.0-iimpi-2024a.eb b/easybuild/easyconfigs/i/imkl-FFTW/imkl-FFTW-2024.2.0-iimpi-2024a.eb new file mode 100644 index 00000000000..b26ab65f452 --- /dev/null +++ b/easybuild/easyconfigs/i/imkl-FFTW/imkl-FFTW-2024.2.0-iimpi-2024a.eb @@ -0,0 +1,11 @@ +name = 'imkl-FFTW' +version = '2024.2.0' + +homepage = 'https://software.intel.com/content/www/us/en/develop/tools/oneapi/components/onemkl.html' +description = "FFTW interfaces using Intel oneAPI Math Kernel Library" + +toolchain = {'name': 'iimpi', 'version': '2024a'} + +dependencies = [('imkl', version, '', SYSTEM)] + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/i/imkl/imkl-2018.1.163-iccifort-2018.1.163-GCC-6.4.0-2.28-serial.eb b/easybuild/easyconfigs/i/imkl/imkl-2018.1.163-iccifort-2018.1.163-GCC-6.4.0-2.28-serial.eb index 65486c1a522..1af220dba70 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2018.1.163-iccifort-2018.1.163-GCC-6.4.0-2.28-serial.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2018.1.163-iccifort-2018.1.163-GCC-6.4.0-2.28-serial.eb @@ -12,7 +12,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'iccifort', 'version': '2018.1.163-GCC-6.4.0-2.28'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12384/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/12384/'] sources = ['l_mkl_%(version)s.tgz'] checksums = ['f6dc263fc6f3c350979740a13de1b1e8745d9ba0d0f067ece503483b9189c2ca'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2018.1.163-iimpi-2018a.eb b/easybuild/easyconfigs/i/imkl/imkl-2018.1.163-iimpi-2018a.eb index 770acb76d87..a90fc9aaaac 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2018.1.163-iimpi-2018a.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2018.1.163-iimpi-2018a.eb @@ -11,7 +11,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'iimpi', 'version': '2018a'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12384/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/12384/'] sources = ['l_mkl_%(version)s.tgz'] checksums = ['f6dc263fc6f3c350979740a13de1b1e8745d9ba0d0f067ece503483b9189c2ca'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2018.3.222-gimpi-2018b.eb b/easybuild/easyconfigs/i/imkl/imkl-2018.3.222-gimpi-2018b.eb index f340d755ee2..c873144967b 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2018.3.222-gimpi-2018b.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2018.3.222-gimpi-2018b.eb @@ -11,7 +11,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'gimpi', 'version': '2018b'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13005/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/13005/'] sources = ['l_mkl_%(version)s.tgz'] checksums = ['108d59c0927e58ce8c314db6c2b48ee331c3798f7102725f425d6884eb6ed241'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2018.3.222-gompi-2018b.eb b/easybuild/easyconfigs/i/imkl/imkl-2018.3.222-gompi-2018b.eb index 6ead35efc9a..89a3f33d184 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2018.3.222-gompi-2018b.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2018.3.222-gompi-2018b.eb @@ -11,7 +11,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'gompi', 'version': '2018b'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13005/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/13005/'] sources = ['l_mkl_%(version)s.tgz'] checksums = ['108d59c0927e58ce8c314db6c2b48ee331c3798f7102725f425d6884eb6ed241'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2018.3.222-iimpi-2018b.eb b/easybuild/easyconfigs/i/imkl/imkl-2018.3.222-iimpi-2018b.eb index 7f53145d6a3..450dc0082e2 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2018.3.222-iimpi-2018b.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2018.3.222-iimpi-2018b.eb @@ -11,7 +11,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'iimpi', 'version': '2018b'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13005/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/13005/'] sources = ['l_mkl_%(version)s.tgz'] checksums = ['108d59c0927e58ce8c314db6c2b48ee331c3798f7102725f425d6884eb6ed241'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2018.3.222-iompi-2018b.eb b/easybuild/easyconfigs/i/imkl/imkl-2018.3.222-iompi-2018b.eb index aeabee4d300..0fcf2f60e8e 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2018.3.222-iompi-2018b.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2018.3.222-iompi-2018b.eb @@ -11,7 +11,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'iompi', 'version': '2018b'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13005/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/13005/'] sources = ['l_mkl_%(version)s.tgz'] checksums = ['108d59c0927e58ce8c314db6c2b48ee331c3798f7102725f425d6884eb6ed241'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2018.4.274-iimpi-2018.04.eb b/easybuild/easyconfigs/i/imkl/imkl-2018.4.274-iimpi-2018.04.eb index 02dba60737e..7d2dc1809af 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2018.4.274-iimpi-2018.04.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2018.4.274-iimpi-2018.04.eb @@ -11,7 +11,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'iimpi', 'version': '2018.04'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13725/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/13725/'] sources = ['l_mkl_%(version)s.tgz'] checksums = ['18eb3cde3e6a61a88f25afff25df762a560013f650aaf363f7d3d516a0d04881'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2019.0.117-iimpi-2019.00.eb b/easybuild/easyconfigs/i/imkl/imkl-2019.0.117-iimpi-2019.00.eb index a382ae20ac7..d222e9cd3b3 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2019.0.117-iimpi-2019.00.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2019.0.117-iimpi-2019.00.eb @@ -11,7 +11,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'iimpi', 'version': '2019.00'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13575/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/13575/'] sources = ['l_mkl_%(version)s.tgz'] checksums = ['4e1fe2c705cfc47050064c0d6c4dee1a8c6740ac1c4f64dde9c7511c4989c7ad'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2019.1.144-gompi-2019a.eb b/easybuild/easyconfigs/i/imkl/imkl-2019.1.144-gompi-2019a.eb index aa6a03a6929..ae7e676174e 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2019.1.144-gompi-2019a.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2019.1.144-gompi-2019a.eb @@ -9,7 +9,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'gompi', 'version': '2019a'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/14895/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/14895/'] sources = ['l_mkl_%(version)s.tgz'] checksums = ['5205a460a9c685f7a442868367389b2d0c25e1455346bc6a37c5b8ff90a20fbb'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2019.1.144-iimpi-2019.01.eb b/easybuild/easyconfigs/i/imkl/imkl-2019.1.144-iimpi-2019.01.eb index e63cc1a2695..15e03750772 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2019.1.144-iimpi-2019.01.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2019.1.144-iimpi-2019.01.eb @@ -11,7 +11,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'iimpi', 'version': '2019.01'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/14895/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/14895/'] sources = ['l_mkl_%(version)s.tgz'] checksums = ['5205a460a9c685f7a442868367389b2d0c25e1455346bc6a37c5b8ff90a20fbb'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2019.1.144-iimpi-2019a.eb b/easybuild/easyconfigs/i/imkl/imkl-2019.1.144-iimpi-2019a.eb index 782473ec9fa..dcd07853ae8 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2019.1.144-iimpi-2019a.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2019.1.144-iimpi-2019a.eb @@ -9,7 +9,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'iimpi', 'version': '2019a'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/14895/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/14895/'] sources = ['l_mkl_%(version)s.tgz'] checksums = ['5205a460a9c685f7a442868367389b2d0c25e1455346bc6a37c5b8ff90a20fbb'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2019.1.144-iimpic-2019a.eb b/easybuild/easyconfigs/i/imkl/imkl-2019.1.144-iimpic-2019a.eb index b8fb1ebef4c..af64b61bfd7 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2019.1.144-iimpic-2019a.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2019.1.144-iimpic-2019a.eb @@ -9,7 +9,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'iimpic', 'version': '2019a'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/14895/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/14895/'] sources = ['l_mkl_%(version)s.tgz'] checksums = ['5205a460a9c685f7a442868367389b2d0c25e1455346bc6a37c5b8ff90a20fbb'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2019.1.144-iompi-2019.01.eb b/easybuild/easyconfigs/i/imkl/imkl-2019.1.144-iompi-2019.01.eb index 3a5e6baedc4..e7a42454f04 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2019.1.144-iompi-2019.01.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2019.1.144-iompi-2019.01.eb @@ -11,7 +11,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'iompi', 'version': '2019.01'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/14895/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/14895/'] sources = ['l_mkl_%(version)s.tgz'] checksums = ['5205a460a9c685f7a442868367389b2d0c25e1455346bc6a37c5b8ff90a20fbb'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2019.2.187-iimpi-2019.02.eb b/easybuild/easyconfigs/i/imkl/imkl-2019.2.187-iimpi-2019.02.eb index 645ffaf31a7..8cd693cc5ec 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2019.2.187-iimpi-2019.02.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2019.2.187-iimpi-2019.02.eb @@ -11,7 +11,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'iimpi', 'version': '2019.02'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15095/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/15095/'] sources = ['l_mkl_%(version)s.tgz'] checksums = ['2bf004e6b5adb4f956993d6c20ea6ce289bb630314dd501db7f2dd5b9978ed1d'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2019.3.199-iimpi-2019.03.eb b/easybuild/easyconfigs/i/imkl/imkl-2019.3.199-iimpi-2019.03.eb index 2c06461ab97..8685b03cc91 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2019.3.199-iimpi-2019.03.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2019.3.199-iimpi-2019.03.eb @@ -11,7 +11,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'iimpi', 'version': '2019.03'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15275/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/15275/'] sources = ['l_mkl_%(version)s.tgz'] checksums = ['06de2b54f4812e7c39a118536259c942029fe1d6d8918ad9df558a83c4162b8f'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2019.5.281-gompi-2019b.eb b/easybuild/easyconfigs/i/imkl/imkl-2019.5.281-gompi-2019b.eb index 3c2759d1539..940151b46dc 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2019.5.281-gompi-2019b.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2019.5.281-gompi-2019b.eb @@ -11,7 +11,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'gompi', 'version': '2019b'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15816/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/15816/'] sources = ['l_mkl_%(version)s.tgz'] checksums = ['9995ea4469b05360d509c9705e9309dc983c0a10edc2ae3a5384bc837326737e'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2019.5.281-gompic-2019b.eb b/easybuild/easyconfigs/i/imkl/imkl-2019.5.281-gompic-2019b.eb index 3421505968c..91ca97f6bc6 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2019.5.281-gompic-2019b.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2019.5.281-gompic-2019b.eb @@ -11,7 +11,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'gompic', 'version': '2019b'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15816/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/15816/'] sources = ['l_mkl_%(version)s.tgz'] checksums = ['9995ea4469b05360d509c9705e9309dc983c0a10edc2ae3a5384bc837326737e'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2019.5.281-iimpi-2019b.eb b/easybuild/easyconfigs/i/imkl/imkl-2019.5.281-iimpi-2019b.eb index d95d740ea28..61489356fe3 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2019.5.281-iimpi-2019b.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2019.5.281-iimpi-2019b.eb @@ -11,7 +11,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'iimpi', 'version': '2019b'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15816/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/15816/'] sources = ['l_mkl_%(version)s.tgz'] checksums = ['9995ea4469b05360d509c9705e9309dc983c0a10edc2ae3a5384bc837326737e'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2019.5.281-iimpic-2019b.eb b/easybuild/easyconfigs/i/imkl/imkl-2019.5.281-iimpic-2019b.eb index 62cf27a5251..b1e88a55dd3 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2019.5.281-iimpic-2019b.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2019.5.281-iimpic-2019b.eb @@ -11,7 +11,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'iimpic', 'version': '2019b'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15816/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/15816/'] sources = ['l_mkl_%(version)s.tgz'] checksums = ['9995ea4469b05360d509c9705e9309dc983c0a10edc2ae3a5384bc837326737e'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2019.5.281-iompi-2019b.eb b/easybuild/easyconfigs/i/imkl/imkl-2019.5.281-iompi-2019b.eb index 906ad9525cd..8e7d6fa5ec2 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2019.5.281-iompi-2019b.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2019.5.281-iompi-2019b.eb @@ -11,7 +11,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'iompi', 'version': '2019b'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15816/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/15816/'] sources = ['l_mkl_%(version)s.tgz'] checksums = ['9995ea4469b05360d509c9705e9309dc983c0a10edc2ae3a5384bc837326737e'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2020.0.166-iimpi-2020.00.eb b/easybuild/easyconfigs/i/imkl/imkl-2020.0.166-iimpi-2020.00.eb index 610ba004009..d27b6e67346 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2020.0.166-iimpi-2020.00.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2020.0.166-iimpi-2020.00.eb @@ -11,7 +11,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'iimpi', 'version': '2020.00'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/16232/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/16232/'] sources = ['l_mkl_%(version)s.tgz'] checksums = ['f6d92deb3ff10b11ba3df26b2c62bb4f0f7ae43e21905a91d553e58f0f5a8ae0'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2020.1.217-gompi-2020a.eb b/easybuild/easyconfigs/i/imkl/imkl-2020.1.217-gompi-2020a.eb index dcb4894a2a4..d662fdae171 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2020.1.217-gompi-2020a.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2020.1.217-gompi-2020a.eb @@ -11,7 +11,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'gompi', 'version': '2020a'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/16533/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/16533/'] sources = ['l_mkl_%(version)s.tgz'] checksums = ['082a4be30bf4f6998e4d6e3da815a77560a5e66a68e254d161ab96f07086066d'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2020.1.217-iimpi-2020.06-impi-18.5.eb b/easybuild/easyconfigs/i/imkl/imkl-2020.1.217-iimpi-2020.06-impi-18.5.eb index 89aac0e1547..a683875dd81 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2020.1.217-iimpi-2020.06-impi-18.5.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2020.1.217-iimpi-2020.06-impi-18.5.eb @@ -11,7 +11,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'iimpi', 'version': '2020.06-impi-18.5'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/16533/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/16533/'] sources = ['l_mkl_%(version)s.tgz'] checksums = ['082a4be30bf4f6998e4d6e3da815a77560a5e66a68e254d161ab96f07086066d'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2020.1.217-iimpi-2020a.eb b/easybuild/easyconfigs/i/imkl/imkl-2020.1.217-iimpi-2020a.eb index 3111a3509b0..aef431b9b6d 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2020.1.217-iimpi-2020a.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2020.1.217-iimpi-2020a.eb @@ -11,7 +11,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'iimpi', 'version': '2020a'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/16533/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/16533/'] sources = ['l_mkl_%(version)s.tgz'] checksums = ['082a4be30bf4f6998e4d6e3da815a77560a5e66a68e254d161ab96f07086066d'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2020.1.217-iimpic-2020a.eb b/easybuild/easyconfigs/i/imkl/imkl-2020.1.217-iimpic-2020a.eb index 3475dab254a..dbfbc356455 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2020.1.217-iimpic-2020a.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2020.1.217-iimpic-2020a.eb @@ -11,7 +11,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'iimpic', 'version': '2020a'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/16533/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/16533/'] sources = ['l_mkl_%(version)s.tgz'] checksums = ['082a4be30bf4f6998e4d6e3da815a77560a5e66a68e254d161ab96f07086066d'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2020.1.217-iompi-2020a.eb b/easybuild/easyconfigs/i/imkl/imkl-2020.1.217-iompi-2020a.eb index 3eca90fc0a2..1f80ac1e253 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2020.1.217-iompi-2020a.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2020.1.217-iompi-2020a.eb @@ -11,7 +11,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'iompi', 'version': '2020a'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/16533/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/16533/'] sources = ['l_mkl_%(version)s.tgz'] checksums = ['082a4be30bf4f6998e4d6e3da815a77560a5e66a68e254d161ab96f07086066d'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-NVHPC-21.2.eb b/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-NVHPC-21.2.eb index 75ac380269e..71a9f0f37b9 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-NVHPC-21.2.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-NVHPC-21.2.eb @@ -11,7 +11,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'NVHPC', 'version': '21.2'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/16917/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/16917/'] sources = ['l_mkl_%(version)s.tgz'] checksums = ['2314d46536974dbd08f2a4e4f9e9a155dc7e79e2798c74e7ddfaad00a5917ea5'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-gompi-2020b.eb b/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-gompi-2020b.eb index 541c3c12aea..1526523c788 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-gompi-2020b.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-gompi-2020b.eb @@ -11,7 +11,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'gompi', 'version': '2020b'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/16917/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/16917/'] sources = ['l_mkl_%(version)s.tgz'] checksums = ['2314d46536974dbd08f2a4e4f9e9a155dc7e79e2798c74e7ddfaad00a5917ea5'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-gompic-2020b.eb b/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-gompic-2020b.eb index e07323d8ee3..570499af77d 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-gompic-2020b.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-gompic-2020b.eb @@ -11,7 +11,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'gompic', 'version': '2020b'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/16917/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/16917/'] sources = ['l_mkl_%(version)s.tgz'] checksums = ['2314d46536974dbd08f2a4e4f9e9a155dc7e79e2798c74e7ddfaad00a5917ea5'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-iimpi-2020b.eb b/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-iimpi-2020b.eb index e1f7dd0c3fd..15ccb6b8c77 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-iimpi-2020b.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-iimpi-2020b.eb @@ -11,7 +11,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'iimpi', 'version': '2020b'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/16917/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/16917/'] sources = ['l_mkl_%(version)s.tgz'] checksums = ['2314d46536974dbd08f2a4e4f9e9a155dc7e79e2798c74e7ddfaad00a5917ea5'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-iimpic-2020b.eb b/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-iimpic-2020b.eb index a350ab4a6ed..73aac3a85e7 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-iimpic-2020b.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-iimpic-2020b.eb @@ -11,7 +11,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'iimpic', 'version': '2020b'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/16917/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/16917/'] sources = ['l_mkl_%(version)s.tgz'] checksums = ['2314d46536974dbd08f2a4e4f9e9a155dc7e79e2798c74e7ddfaad00a5917ea5'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-iompi-2020b.eb b/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-iompi-2020b.eb index 89d0c991d88..68e2a157d3d 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-iompi-2020b.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-iompi-2020b.eb @@ -11,7 +11,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'iompi', 'version': '2020b'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/16917/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/16917/'] sources = ['l_mkl_%(version)s.tgz'] checksums = ['2314d46536974dbd08f2a4e4f9e9a155dc7e79e2798c74e7ddfaad00a5917ea5'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2021.1.1-iimpi-2020.12.eb b/easybuild/easyconfigs/i/imkl/imkl-2021.1.1-iimpi-2020.12.eb index 737f7462d7d..363e95f7dc9 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2021.1.1-iimpi-2020.12.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2021.1.1-iimpi-2020.12.eb @@ -7,7 +7,7 @@ description = "Intel oneAPI Math Kernel Library" toolchain = {'name': 'iimpi', 'version': '2020.12'} # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/17402/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/17402/'] sources = ['l_onemkl_p_%(version)s.52_offline.sh'] checksums = ['818b6bd9a6c116f4578cda3151da0612ec9c3ce8b2c8a64730d625ce5b13cc0c'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2021.2.0-gompi-2021a.eb b/easybuild/easyconfigs/i/imkl/imkl-2021.2.0-gompi-2021a.eb index ff7c13049ea..77a41fb58ed 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2021.2.0-gompi-2021a.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2021.2.0-gompi-2021a.eb @@ -7,7 +7,7 @@ description = "Intel oneAPI Math Kernel Library" toolchain = {'name': 'gompi', 'version': '2021a'} # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/17757/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/17757/'] sources = ['l_onemkl_p_%(version)s.296_offline.sh'] checksums = ['816e9df26ff331d6c0751b86ed5f7d243f9f172e76f14e83b32bf4d1d619dbae'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2021.2.0-iimpi-2021a.eb b/easybuild/easyconfigs/i/imkl/imkl-2021.2.0-iimpi-2021a.eb index aa8f14f2250..741b626f55c 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2021.2.0-iimpi-2021a.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2021.2.0-iimpi-2021a.eb @@ -7,7 +7,7 @@ description = "Intel oneAPI Math Kernel Library" toolchain = {'name': 'iimpi', 'version': '2021a'} # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/17757/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/17757/'] sources = ['l_onemkl_p_%(version)s.296_offline.sh'] checksums = ['816e9df26ff331d6c0751b86ed5f7d243f9f172e76f14e83b32bf4d1d619dbae'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2021.2.0-iompi-2021a.eb b/easybuild/easyconfigs/i/imkl/imkl-2021.2.0-iompi-2021a.eb index 60282631f05..2bb82fd3380 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2021.2.0-iompi-2021a.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2021.2.0-iompi-2021a.eb @@ -7,7 +7,7 @@ description = "Intel oneAPI Math Kernel Library" toolchain = {'name': 'iompi', 'version': '2021a'} # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/17757/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/17757/'] sources = ['l_onemkl_p_%(version)s.296_offline.sh'] checksums = ['816e9df26ff331d6c0751b86ed5f7d243f9f172e76f14e83b32bf4d1d619dbae'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2021.3.0-gompi-2021a.eb b/easybuild/easyconfigs/i/imkl/imkl-2021.3.0-gompi-2021a.eb index 07a876f213e..a4746816d23 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2021.3.0-gompi-2021a.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2021.3.0-gompi-2021a.eb @@ -10,7 +10,7 @@ description = "Intel oneAPI Math Kernel Library" toolchain = {'name': 'gompi', 'version': '2021a'} # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/17901'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/17901'] sources = ['l_onemkl_p_%(version)s.520_offline.sh'] checksums = ['a06e1cdbfd8becc63440b473b153659885f25a6e3c4dcb2907ad9cd0c3ad59ce'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2021.4.0-iompi-2021b.eb b/easybuild/easyconfigs/i/imkl/imkl-2021.4.0-iompi-2021b.eb old mode 100755 new mode 100644 index a6e0651ef64..4f45be5badc --- a/easybuild/easyconfigs/i/imkl/imkl-2021.4.0-iompi-2021b.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2021.4.0-iompi-2021b.eb @@ -7,7 +7,7 @@ description = "Intel oneAPI Math Kernel Library" toolchain = {'name': 'iompi', 'version': '2021b'} # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18222/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18222/'] sources = ['l_onemkl_p_%(version)s.640_offline.sh'] checksums = ['9ad546f05a421b4f439e8557fd0f2d83d5e299b0d9bd84bdd86be6feba0c3915'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2021.4.0.eb b/easybuild/easyconfigs/i/imkl/imkl-2021.4.0.eb index f3e3040b1ee..bacd9ba4607 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2021.4.0.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2021.4.0.eb @@ -7,7 +7,7 @@ description = "Intel oneAPI Math Kernel Library" toolchain = SYSTEM # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18222/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18222/'] sources = ['l_onemkl_p_%(version)s.640_offline.sh'] checksums = ['9ad546f05a421b4f439e8557fd0f2d83d5e299b0d9bd84bdd86be6feba0c3915'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2022.0.1.eb b/easybuild/easyconfigs/i/imkl/imkl-2022.0.1.eb index 67a5563ac0b..c348328e0e4 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2022.0.1.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2022.0.1.eb @@ -7,7 +7,7 @@ description = "Intel oneAPI Math Kernel Library" toolchain = SYSTEM # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18444/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18444/'] sources = ['l_onemkl_p_%(version)s.117_offline.sh'] checksums = ['22afafbe2f3762eca052ac21ec40b845ff2f3646077295c88c2f37f80a0cc160'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2022.1.0-gompi-2022a.eb b/easybuild/easyconfigs/i/imkl/imkl-2022.1.0-gompi-2022a.eb index 2eb923c837e..955038d0fc1 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2022.1.0-gompi-2022a.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2022.1.0-gompi-2022a.eb @@ -10,7 +10,7 @@ description = "Intel oneAPI Math Kernel Library" toolchain = {'name': 'gompi', 'version': '2022a'} # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18721/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18721/'] sources = ['l_onemkl_p_%(version)s.223_offline.sh'] checksums = ['4b325a3c4c56e52f4ce6c8fbb55d7684adc16425000afc860464c0f29ea4563e'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2022.1.0.eb b/easybuild/easyconfigs/i/imkl/imkl-2022.1.0.eb index c34d533cf35..b0653443859 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2022.1.0.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2022.1.0.eb @@ -7,7 +7,7 @@ description = "Intel oneAPI Math Kernel Library" toolchain = SYSTEM # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18721/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18721/'] sources = ['l_onemkl_p_%(version)s.223_offline.sh'] checksums = ['4b325a3c4c56e52f4ce6c8fbb55d7684adc16425000afc860464c0f29ea4563e'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2022.2.0.eb b/easybuild/easyconfigs/i/imkl/imkl-2022.2.0.eb index 82776023871..a3c46807fc6 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2022.2.0.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2022.2.0.eb @@ -7,7 +7,7 @@ description = "Intel oneAPI Math Kernel Library" toolchain = SYSTEM # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18898/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18898/'] sources = ['l_onemkl_p_%(version)s.8748_offline.sh'] checksums = ['07d7caedd4b9f025c6fd439a0d2c2f279b18ecbbb63cadb864f6c63c1ed942db'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2022.2.1.eb b/easybuild/easyconfigs/i/imkl/imkl-2022.2.1.eb index 3daf55958a3..f2a7a15068e 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2022.2.1.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2022.2.1.eb @@ -7,7 +7,7 @@ description = "Intel oneAPI Math Kernel Library" toolchain = SYSTEM # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/19038/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/19038/'] sources = ['l_onemkl_p_%(version)s.16993_offline.sh'] checksums = ['eedd4b795720de776b1fc5f542ae0fac37ec235cdb567f7c2ee3182e73e3e59d'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2023.0.0.eb b/easybuild/easyconfigs/i/imkl/imkl-2023.0.0.eb index 4e6e5afb344..f29032bc3dd 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2023.0.0.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2023.0.0.eb @@ -7,7 +7,7 @@ description = "Intel oneAPI Math Kernel Library" toolchain = SYSTEM # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/19138/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/19138/'] sources = ['l_onemkl_p_%(version)s.25398_offline.sh'] checksums = ['0d61188e91a57bdb575782eb47a05ae99ea8eebefee6b2dfe20c6708e16e9927'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2023.1.0-gompi-2023a.eb b/easybuild/easyconfigs/i/imkl/imkl-2023.1.0-gompi-2023a.eb index 5e4f3cb8b1d..17ed1c0a2aa 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2023.1.0-gompi-2023a.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2023.1.0-gompi-2023a.eb @@ -10,7 +10,7 @@ description = "Intel oneAPI Math Kernel Library" toolchain = {'name': 'gompi', 'version': '2023a'} # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18721/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/cd17b7fe-500e-4305-a89b-bd5b42bfd9f8/'] sources = ['l_onemkl_p_%(version)s.46342_offline.sh'] checksums = ['cc28c94cab23c185520b93c5a04f3979d8da6b4c90cee8c0681dd89819d76167'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2023.2.0-gompi-2023b.eb b/easybuild/easyconfigs/i/imkl/imkl-2023.2.0-gompi-2023b.eb new file mode 100644 index 00000000000..e194f389253 --- /dev/null +++ b/easybuild/easyconfigs/i/imkl/imkl-2023.2.0-gompi-2023b.eb @@ -0,0 +1,18 @@ +name = 'imkl' +version = '2023.2.0' + +homepage = 'https://software.intel.com/content/www/us/en/develop/tools/oneapi/components/onemkl.html' +description = "Intel oneAPI Math Kernel Library" + +toolchain = {'name': 'gompi', 'version': '2023b'} + +# see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/adb8a02c-4ee7-4882-97d6-a524150da358/'] +sources = ['l_onemkl_p_%(version)s.49497_offline.sh'] +checksums = ['4a0d93da85a94d92e0ad35dc0fc3b3ab7f040bd55ad374c4d5ec81a57a2b872b'] + +interfaces = False + +installopts = "--download-cache=%(builddir)s/cache --download-dir=%(builddir)s/download --log-dir=%(builddir)s/log" + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/i/imkl/imkl-2024.2.0.eb b/easybuild/easyconfigs/i/imkl/imkl-2024.2.0.eb new file mode 100644 index 00000000000..30331a8a80a --- /dev/null +++ b/easybuild/easyconfigs/i/imkl/imkl-2024.2.0.eb @@ -0,0 +1,18 @@ +name = 'imkl' +version = '2024.2.0' + +homepage = 'https://software.intel.com/content/www/us/en/develop/tools/oneapi/components/onemkl.html' +description = "Intel oneAPI Math Kernel Library" + +toolchain = SYSTEM + +# see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/cdff21a5-6ac7-4b41-a7ec-351b5f9ce8fd'] +sources = ['l_onemkl_p_%(version)s.664_offline.sh'] +checksums = ['f1f46f5352c197a9840e08fc191a879dad79ebf742fe782e386ba8006f262f7a'] + +interfaces = False + +installopts = "--download-cache=%(builddir)s/cache --download-dir=%(builddir)s/download --log-dir=%(builddir)s/log" + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/i/impi/impi-2018.1.163-iccifort-2018.1.163-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/i/impi/impi-2018.1.163-iccifort-2018.1.163-GCC-6.4.0-2.28.eb index 21ad001e53c..a0341a987d6 100644 --- a/easybuild/easyconfigs/i/impi/impi-2018.1.163-iccifort-2018.1.163-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/i/impi/impi-2018.1.163-iccifort-2018.1.163-GCC-6.4.0-2.28.eb @@ -8,7 +8,7 @@ description = "Intel MPI Library, compatible with MPICH ABI" toolchain = {'name': 'iccifort', 'version': '2018.1.163-GCC-6.4.0-2.28'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12405/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/12405/'] sources = ['l_mpi_%(version)s.tgz'] checksums = ['130b11571c3f71af00a722fa8641db5a1552ac343d770a8304216d8f5d00e75c'] diff --git a/easybuild/easyconfigs/i/impi/impi-2018.3.222-GCC-7.3.0-2.30.eb b/easybuild/easyconfigs/i/impi/impi-2018.3.222-GCC-7.3.0-2.30.eb index e39879ac218..60f2eed4dd9 100644 --- a/easybuild/easyconfigs/i/impi/impi-2018.3.222-GCC-7.3.0-2.30.eb +++ b/easybuild/easyconfigs/i/impi/impi-2018.3.222-GCC-7.3.0-2.30.eb @@ -8,7 +8,7 @@ description = "Intel MPI Library, compatible with MPICH ABI" toolchain = {'name': 'GCC', 'version': '7.3.0-2.30'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13063/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/13063/'] sources = ['l_mpi_%(version)s.tgz'] checksums = ['5021d14b344fc794e89f146e4d53d70184d7048610895d7a6a1e8ac0cf258999'] diff --git a/easybuild/easyconfigs/i/impi/impi-2018.3.222-iccifort-2018.3.222-GCC-7.3.0-2.30.eb b/easybuild/easyconfigs/i/impi/impi-2018.3.222-iccifort-2018.3.222-GCC-7.3.0-2.30.eb index f4e9e1a638f..0fc63f042f8 100644 --- a/easybuild/easyconfigs/i/impi/impi-2018.3.222-iccifort-2018.3.222-GCC-7.3.0-2.30.eb +++ b/easybuild/easyconfigs/i/impi/impi-2018.3.222-iccifort-2018.3.222-GCC-7.3.0-2.30.eb @@ -8,7 +8,7 @@ description = "Intel MPI Library, compatible with MPICH ABI" toolchain = {'name': 'iccifort', 'version': '2018.3.222-GCC-7.3.0-2.30'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13063/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/13063/'] sources = ['l_mpi_%(version)s.tgz'] checksums = ['5021d14b344fc794e89f146e4d53d70184d7048610895d7a6a1e8ac0cf258999'] diff --git a/easybuild/easyconfigs/i/impi/impi-2018.4.274-iccifort-2018.5.274-GCC-7.3.0-2.30.eb b/easybuild/easyconfigs/i/impi/impi-2018.4.274-iccifort-2018.5.274-GCC-7.3.0-2.30.eb index 060befc0a5a..75004db76a8 100644 --- a/easybuild/easyconfigs/i/impi/impi-2018.4.274-iccifort-2018.5.274-GCC-7.3.0-2.30.eb +++ b/easybuild/easyconfigs/i/impi/impi-2018.4.274-iccifort-2018.5.274-GCC-7.3.0-2.30.eb @@ -8,7 +8,7 @@ description = "Intel MPI Library, compatible with MPICH ABI" toolchain = {'name': 'iccifort', 'version': '2018.5.274-GCC-7.3.0-2.30'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13651/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/13651/'] sources = ['l_mpi_%(version)s.tgz'] checksums = ['a1114b3eb4149c2f108964b83cad02150d619e50032059d119ac4ffc9d5dd8e0'] diff --git a/easybuild/easyconfigs/i/impi/impi-2018.4.274-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/i/impi/impi-2018.4.274-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb index e6c3602e1e3..d4574181af9 100644 --- a/easybuild/easyconfigs/i/impi/impi-2018.4.274-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/i/impi/impi-2018.4.274-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb @@ -6,7 +6,7 @@ description = "Intel MPI Library, compatible with MPICH ABI" toolchain = {'name': 'iccifort', 'version': '2019.1.144-GCC-8.2.0-2.31.1'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13651/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/13651/'] sources = ['l_mpi_%(version)s.tgz'] checksums = ['a1114b3eb4149c2f108964b83cad02150d619e50032059d119ac4ffc9d5dd8e0'] diff --git a/easybuild/easyconfigs/i/impi/impi-2018.4.274-iccifortcuda-2019a.eb b/easybuild/easyconfigs/i/impi/impi-2018.4.274-iccifortcuda-2019a.eb index 137bf491a27..c28ff1e7e55 100644 --- a/easybuild/easyconfigs/i/impi/impi-2018.4.274-iccifortcuda-2019a.eb +++ b/easybuild/easyconfigs/i/impi/impi-2018.4.274-iccifortcuda-2019a.eb @@ -6,7 +6,7 @@ description = "Intel MPI Library, compatible with MPICH ABI" toolchain = {'name': 'iccifortcuda', 'version': '2019a'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13651/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/13651/'] sources = ['l_mpi_%(version)s.tgz'] checksums = ['a1114b3eb4149c2f108964b83cad02150d619e50032059d119ac4ffc9d5dd8e0'] diff --git a/easybuild/easyconfigs/i/impi/impi-2018.5.288-iccifort-2019.5.281.eb b/easybuild/easyconfigs/i/impi/impi-2018.5.288-iccifort-2019.5.281.eb index 8f89b212fa4..4cb68a33fc8 100644 --- a/easybuild/easyconfigs/i/impi/impi-2018.5.288-iccifort-2019.5.281.eb +++ b/easybuild/easyconfigs/i/impi/impi-2018.5.288-iccifort-2019.5.281.eb @@ -8,7 +8,7 @@ description = "Intel MPI Library, compatible with MPICH ABI" toolchain = {'name': 'iccifort', 'version': '2019.5.281'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15614/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/15614/'] sources = ['l_mpi_%(version)s.tgz'] checksums = ['3198257c19e82cd327d739b10120933e0547da8cddf8a8005677717326236796'] diff --git a/easybuild/easyconfigs/i/impi/impi-2018.5.288-iccifort-2020.1.217.eb b/easybuild/easyconfigs/i/impi/impi-2018.5.288-iccifort-2020.1.217.eb index 4c7b3a6b0df..e27d2ec5b55 100644 --- a/easybuild/easyconfigs/i/impi/impi-2018.5.288-iccifort-2020.1.217.eb +++ b/easybuild/easyconfigs/i/impi/impi-2018.5.288-iccifort-2020.1.217.eb @@ -8,7 +8,7 @@ description = "Intel MPI Library, compatible with MPICH ABI" toolchain = {'name': 'iccifort', 'version': '2020.1.217'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15614/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/15614/'] sources = ['l_mpi_%(version)s.tgz'] checksums = ['3198257c19e82cd327d739b10120933e0547da8cddf8a8005677717326236796'] diff --git a/easybuild/easyconfigs/i/impi/impi-2018.5.288-iccifortcuda-2019b.eb b/easybuild/easyconfigs/i/impi/impi-2018.5.288-iccifortcuda-2019b.eb index 02e2ace8251..2f959f48e46 100644 --- a/easybuild/easyconfigs/i/impi/impi-2018.5.288-iccifortcuda-2019b.eb +++ b/easybuild/easyconfigs/i/impi/impi-2018.5.288-iccifortcuda-2019b.eb @@ -8,7 +8,7 @@ description = "Intel MPI Library, compatible with MPICH ABI" toolchain = {'name': 'iccifortcuda', 'version': '2019b'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15614/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/15614/'] sources = ['l_mpi_%(version)s.tgz'] checksums = ['3198257c19e82cd327d739b10120933e0547da8cddf8a8005677717326236796'] diff --git a/easybuild/easyconfigs/i/impi/impi-2019.0.117-iccifort-2019.0.117-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/i/impi/impi-2019.0.117-iccifort-2019.0.117-GCC-8.2.0-2.31.1.eb index 2f60b422703..77755c77620 100644 --- a/easybuild/easyconfigs/i/impi/impi-2019.0.117-iccifort-2019.0.117-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/i/impi/impi-2019.0.117-iccifort-2019.0.117-GCC-8.2.0-2.31.1.eb @@ -8,7 +8,7 @@ description = "Intel MPI Library, compatible with MPICH ABI" toolchain = {'name': 'iccifort', 'version': '2019.0.117-GCC-8.2.0-2.31.1'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13584/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/13584/'] sources = ['l_mpi_%(version)s.tgz'] checksums = ['dfb403f49c1af61b337aa952b71289c7548c3a79c32c57865eab0ea0f0e1bc08'] diff --git a/easybuild/easyconfigs/i/impi/impi-2019.1.144-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/i/impi/impi-2019.1.144-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb index 8e2ed0b3980..6a222b3ed18 100644 --- a/easybuild/easyconfigs/i/impi/impi-2019.1.144-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/i/impi/impi-2019.1.144-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb @@ -8,7 +8,7 @@ description = "Intel MPI Library, compatible with MPICH ABI" toolchain = {'name': 'iccifort', 'version': '2019.1.144-GCC-8.2.0-2.31.1'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/14879/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/14879/'] sources = ['l_mpi_%(version)s.tgz'] checksums = ['dac86a5db6b86503313742b17535856a432955604f7103cb4549a9bfc256c3cd'] diff --git a/easybuild/easyconfigs/i/impi/impi-2019.12.320-iccifort-2020.4.304.eb b/easybuild/easyconfigs/i/impi/impi-2019.12.320-iccifort-2020.4.304.eb index a5ba5409ff0..2bf8b19fb29 100644 --- a/easybuild/easyconfigs/i/impi/impi-2019.12.320-iccifort-2020.4.304.eb +++ b/easybuild/easyconfigs/i/impi/impi-2019.12.320-iccifort-2020.4.304.eb @@ -8,7 +8,7 @@ description = "Intel MPI Library, compatible with MPICH ABI" toolchain = {'name': 'iccifort', 'version': '2020.4.304'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/17836/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/17836/'] sources = ['l_mpi_%(version)s.tgz'] checksums = ['8108fbf2353a9f1926036bb67647b65c0e4933a3eb66e1dc933960e5b055f320'] diff --git a/easybuild/easyconfigs/i/impi/impi-2019.2.187-iccifort-2019.2.187-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/i/impi/impi-2019.2.187-iccifort-2019.2.187-GCC-8.2.0-2.31.1.eb index 7cdc6aca429..5f75ad2ec68 100644 --- a/easybuild/easyconfigs/i/impi/impi-2019.2.187-iccifort-2019.2.187-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/i/impi/impi-2019.2.187-iccifort-2019.2.187-GCC-8.2.0-2.31.1.eb @@ -8,7 +8,7 @@ description = "Intel MPI Library, compatible with MPICH ABI" toolchain = {'name': 'iccifort', 'version': '2019.2.187-GCC-8.2.0-2.31.1'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15040/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/15040/'] sources = ['l_mpi_%(version)s.tgz'] checksums = ['6a3305933b5ef9e3f7de969e394c91620f3fa4bb815a4f439577739d04778b20'] diff --git a/easybuild/easyconfigs/i/impi/impi-2019.3.199-iccifort-2019.3.199-GCC-8.3.0-2.32.eb b/easybuild/easyconfigs/i/impi/impi-2019.3.199-iccifort-2019.3.199-GCC-8.3.0-2.32.eb index c0b1f565c0a..cb1ec1f179c 100644 --- a/easybuild/easyconfigs/i/impi/impi-2019.3.199-iccifort-2019.3.199-GCC-8.3.0-2.32.eb +++ b/easybuild/easyconfigs/i/impi/impi-2019.3.199-iccifort-2019.3.199-GCC-8.3.0-2.32.eb @@ -8,7 +8,7 @@ description = "Intel MPI Library, compatible with MPICH ABI" toolchain = {'name': 'iccifort', 'version': '2019.3.199-GCC-8.3.0-2.32'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15260/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/15260/'] sources = ['l_mpi_%(version)s.tgz'] checksums = ['5304346c863f64de797250eeb14f51c5cfc8212ff20813b124f20e7666286990'] diff --git a/easybuild/easyconfigs/i/impi/impi-2019.6.166-iccifort-2020.0.166-GCC-9.2.0.eb b/easybuild/easyconfigs/i/impi/impi-2019.6.166-iccifort-2020.0.166-GCC-9.2.0.eb index e19a15d6e33..49f0fa7a8d7 100644 --- a/easybuild/easyconfigs/i/impi/impi-2019.6.166-iccifort-2020.0.166-GCC-9.2.0.eb +++ b/easybuild/easyconfigs/i/impi/impi-2019.6.166-iccifort-2020.0.166-GCC-9.2.0.eb @@ -8,7 +8,7 @@ description = "Intel MPI Library, compatible with MPICH ABI" toolchain = {'name': 'iccifort', 'version': '2020.0.166-GCC-9.2.0'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/16120/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/16120/'] sources = ['l_mpi_%(version)s.tgz'] checksums = ['119be69f1117c93a9e5e9b8b4643918e55d2a55a78ad9567f77d16cdaf18cd6e'] diff --git a/easybuild/easyconfigs/i/impi/impi-2019.7.217-iccifort-2020.1.217.eb b/easybuild/easyconfigs/i/impi/impi-2019.7.217-iccifort-2020.1.217.eb index d0ad0188c0d..07f8323810c 100644 --- a/easybuild/easyconfigs/i/impi/impi-2019.7.217-iccifort-2020.1.217.eb +++ b/easybuild/easyconfigs/i/impi/impi-2019.7.217-iccifort-2020.1.217.eb @@ -8,7 +8,7 @@ description = "Intel MPI Library, compatible with MPICH ABI" toolchain = {'name': 'iccifort', 'version': '2020.1.217'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/16546/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/16546/'] sources = ['l_mpi_%(version)s.tgz'] checksums = ['90383b0023f84ac003a55d8bb29dbcf0c639f43a25a2d8d8698a16e770ac9c07'] diff --git a/easybuild/easyconfigs/i/impi/impi-2019.7.217-iccifortcuda-2020a.eb b/easybuild/easyconfigs/i/impi/impi-2019.7.217-iccifortcuda-2020a.eb index 557e0a8eab1..8a5646c25c1 100644 --- a/easybuild/easyconfigs/i/impi/impi-2019.7.217-iccifortcuda-2020a.eb +++ b/easybuild/easyconfigs/i/impi/impi-2019.7.217-iccifortcuda-2020a.eb @@ -8,7 +8,7 @@ description = "Intel MPI Library, compatible with MPICH ABI" toolchain = {'name': 'iccifortcuda', 'version': '2020a'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/16546/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/16546/'] sources = ['l_mpi_%(version)s.tgz'] checksums = ['90383b0023f84ac003a55d8bb29dbcf0c639f43a25a2d8d8698a16e770ac9c07'] diff --git a/easybuild/easyconfigs/i/impi/impi-2019.9.304-iccifort-2020.4.304.eb b/easybuild/easyconfigs/i/impi/impi-2019.9.304-iccifort-2020.4.304.eb index d4a9ef76ae4..d723d12dc1c 100644 --- a/easybuild/easyconfigs/i/impi/impi-2019.9.304-iccifort-2020.4.304.eb +++ b/easybuild/easyconfigs/i/impi/impi-2019.9.304-iccifort-2020.4.304.eb @@ -8,7 +8,7 @@ description = "Intel MPI Library, compatible with MPICH ABI" toolchain = {'name': 'iccifort', 'version': '2020.4.304'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/17263/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/17263/'] sources = ['l_mpi_%(version)s.tgz'] checksums = ['618a5dc2de54306645e6428c5eb7d267b54b11b5a83dfbcad7d0f9e0d90bb2e7'] diff --git a/easybuild/easyconfigs/i/impi/impi-2019.9.304-iccifortcuda-2020b.eb b/easybuild/easyconfigs/i/impi/impi-2019.9.304-iccifortcuda-2020b.eb index 3305cf60a8d..7082d103ec8 100644 --- a/easybuild/easyconfigs/i/impi/impi-2019.9.304-iccifortcuda-2020b.eb +++ b/easybuild/easyconfigs/i/impi/impi-2019.9.304-iccifortcuda-2020b.eb @@ -8,7 +8,7 @@ description = "Intel MPI Library, compatible with MPICH ABI" toolchain = {'name': 'iccifortcuda', 'version': '2020b'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/17263/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/17263/'] sources = ['l_mpi_%(version)s.tgz'] checksums = ['618a5dc2de54306645e6428c5eb7d267b54b11b5a83dfbcad7d0f9e0d90bb2e7'] diff --git a/easybuild/easyconfigs/i/impi/impi-2021.1.1-intel-compilers-2021.1.2.eb b/easybuild/easyconfigs/i/impi/impi-2021.1.1-intel-compilers-2021.1.2.eb index 1a0fbe3b035..d8a92d6db7e 100644 --- a/easybuild/easyconfigs/i/impi/impi-2021.1.1-intel-compilers-2021.1.2.eb +++ b/easybuild/easyconfigs/i/impi/impi-2021.1.1-intel-compilers-2021.1.2.eb @@ -7,7 +7,7 @@ description = "Intel MPI Library, compatible with MPICH ABI" toolchain = {'name': 'intel-compilers', 'version': '2021.1.2'} # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/17397/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/17397/'] sources = ['l_mpi_oneapi_p_%(version)s.76_offline.sh'] checksums = ['8b7693a156c6fc6269637bef586a8fd3ea6610cac2aae4e7f48c1fbb601625fe'] diff --git a/easybuild/easyconfigs/i/impi/impi-2021.13.0-intel-compilers-2024.2.0.eb b/easybuild/easyconfigs/i/impi/impi-2021.13.0-intel-compilers-2024.2.0.eb new file mode 100644 index 00000000000..2e99bc6c0d8 --- /dev/null +++ b/easybuild/easyconfigs/i/impi/impi-2021.13.0-intel-compilers-2024.2.0.eb @@ -0,0 +1,16 @@ +name = 'impi' +version = '2021.13.0' + +homepage = 'https://software.intel.com/content/www/us/en/develop/tools/mpi-library.html' +description = "Intel MPI Library, compatible with MPICH ABI" + +toolchain = {'name': 'intel-compilers', 'version': '2024.2.0'} + +# see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/9f84e1e8-11b2-4bd1-8512-3e3343585956'] +sources = ['l_mpi_oneapi_p_%(version)s.719_offline.sh'] +checksums = ['5e23cf495c919e17032577e3059438f632297ee63f2cdb906a2547298823cc64'] + +dependencies = [('UCX', '1.16.0')] + +moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-2021.2.0-intel-compilers-2021.2.0.eb b/easybuild/easyconfigs/i/impi/impi-2021.2.0-intel-compilers-2021.2.0.eb index 345fd82fc3d..ecd3c9521f1 100644 --- a/easybuild/easyconfigs/i/impi/impi-2021.2.0-intel-compilers-2021.2.0.eb +++ b/easybuild/easyconfigs/i/impi/impi-2021.2.0-intel-compilers-2021.2.0.eb @@ -7,7 +7,7 @@ description = "Intel MPI Library, compatible with MPICH ABI" toolchain = {'name': 'intel-compilers', 'version': '2021.2.0'} # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/17729/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/17729/'] sources = ['l_mpi_oneapi_p_%(version)s.215_offline.sh'] checksums = ['d0d4cdd11edaff2e7285e38f537defccff38e37a3067c02f4af43a3629ad4aa3'] diff --git a/easybuild/easyconfigs/i/impi/impi-2021.3.0-intel-compilers-2021.3.0.eb b/easybuild/easyconfigs/i/impi/impi-2021.3.0-intel-compilers-2021.3.0.eb index 8a736821926..1507acd5413 100644 --- a/easybuild/easyconfigs/i/impi/impi-2021.3.0-intel-compilers-2021.3.0.eb +++ b/easybuild/easyconfigs/i/impi/impi-2021.3.0-intel-compilers-2021.3.0.eb @@ -10,7 +10,7 @@ description = "Intel MPI Library, compatible with MPICH ABI" toolchain = {'name': 'intel-compilers', 'version': '2021.3.0'} # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/17947'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/17947'] sources = ['l_mpi_oneapi_p_%(version)s.294_offline.sh'] checksums = ['04c48f864ee4c723b1b4ca62f2bea8c04d5d7e3de19171fd62b17868bc79bc36'] diff --git a/easybuild/easyconfigs/i/impi/impi-2021.4.0-intel-compilers-2021.4.0.eb b/easybuild/easyconfigs/i/impi/impi-2021.4.0-intel-compilers-2021.4.0.eb index a0c8a98edd8..24180258119 100644 --- a/easybuild/easyconfigs/i/impi/impi-2021.4.0-intel-compilers-2021.4.0.eb +++ b/easybuild/easyconfigs/i/impi/impi-2021.4.0-intel-compilers-2021.4.0.eb @@ -7,7 +7,7 @@ description = "Intel MPI Library, compatible with MPICH ABI" toolchain = {'name': 'intel-compilers', 'version': '2021.4.0'} # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18186/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18186/'] sources = ['l_mpi_oneapi_p_%(version)s.441_offline.sh'] checksums = ['cc4b7072c61d0bd02b1c431b22d2ea3b84b967b59d2e587e77a9e7b2c24f2a29'] diff --git a/easybuild/easyconfigs/i/impi/impi-2021.5.0-intel-compilers-2022.0.1.eb b/easybuild/easyconfigs/i/impi/impi-2021.5.0-intel-compilers-2022.0.1.eb index bee00810199..ea941c35ab2 100644 --- a/easybuild/easyconfigs/i/impi/impi-2021.5.0-intel-compilers-2022.0.1.eb +++ b/easybuild/easyconfigs/i/impi/impi-2021.5.0-intel-compilers-2022.0.1.eb @@ -7,7 +7,7 @@ description = "Intel MPI Library, compatible with MPICH ABI" toolchain = {'name': 'intel-compilers', 'version': '2022.0.1'} # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18370/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18370/'] sources = ['l_mpi_oneapi_p_%(version)s.495_offline.sh'] checksums = ['3aae53fe77f7c6aac7a32b299c25d6ca9a00ba4e2d512a26edd90811e59e7471'] diff --git a/easybuild/easyconfigs/i/impi/impi-2021.6.0-intel-compilers-2022.1.0.eb b/easybuild/easyconfigs/i/impi/impi-2021.6.0-intel-compilers-2022.1.0.eb index b1d328caa62..288c103cd03 100644 --- a/easybuild/easyconfigs/i/impi/impi-2021.6.0-intel-compilers-2022.1.0.eb +++ b/easybuild/easyconfigs/i/impi/impi-2021.6.0-intel-compilers-2022.1.0.eb @@ -7,7 +7,7 @@ description = "Intel MPI Library, compatible with MPICH ABI" toolchain = {'name': 'intel-compilers', 'version': '2022.1.0'} # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18714/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18714/'] sources = ['l_mpi_oneapi_p_%(version)s.602_offline.sh'] checksums = ['e85db63788c434d43c1378e5e2bf7927a75d11aee8e6b78ee0d933da920977a6'] diff --git a/easybuild/easyconfigs/i/impi/impi-2021.7.0-intel-compilers-2022.2.0.eb b/easybuild/easyconfigs/i/impi/impi-2021.7.0-intel-compilers-2022.2.0.eb index 8f400fabac4..2df8a69062f 100644 --- a/easybuild/easyconfigs/i/impi/impi-2021.7.0-intel-compilers-2022.2.0.eb +++ b/easybuild/easyconfigs/i/impi/impi-2021.7.0-intel-compilers-2022.2.0.eb @@ -7,7 +7,7 @@ description = "Intel MPI Library, compatible with MPICH ABI" toolchain = {'name': 'intel-compilers', 'version': '2022.2.0'} # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18926/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18926/'] sources = ['l_mpi_oneapi_p_%(version)s.8711_offline.sh'] checksums = ['4eb1e1487b67b98857bc9b7b37bcac4998e0aa6d1b892b2c87b003bf84fb38e9'] diff --git a/easybuild/easyconfigs/i/impi/impi-2021.7.1-intel-compilers-2022.2.1.eb b/easybuild/easyconfigs/i/impi/impi-2021.7.1-intel-compilers-2022.2.1.eb index 68aeb9beb63..aa2976fafaf 100644 --- a/easybuild/easyconfigs/i/impi/impi-2021.7.1-intel-compilers-2022.2.1.eb +++ b/easybuild/easyconfigs/i/impi/impi-2021.7.1-intel-compilers-2022.2.1.eb @@ -7,7 +7,7 @@ description = "Intel MPI Library, compatible with MPICH ABI" toolchain = {'name': 'intel-compilers', 'version': '2022.2.1'} # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/19010/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/19010/'] sources = ['l_mpi_oneapi_p_%(version)s.16815_offline.sh'] checksums = ['90e7804f2367d457cd4cbf7aa29f1c5676287aa9b34f93e7c9a19e4b8583fff7'] diff --git a/easybuild/easyconfigs/i/impi/impi-2021.8.0-intel-compilers-2023.0.0.eb b/easybuild/easyconfigs/i/impi/impi-2021.8.0-intel-compilers-2023.0.0.eb index 86153bb28f5..89dce35e1f2 100644 --- a/easybuild/easyconfigs/i/impi/impi-2021.8.0-intel-compilers-2023.0.0.eb +++ b/easybuild/easyconfigs/i/impi/impi-2021.8.0-intel-compilers-2023.0.0.eb @@ -7,7 +7,7 @@ description = "Intel MPI Library, compatible with MPICH ABI" toolchain = {'name': 'intel-compilers', 'version': '2023.0.0'} # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/19131/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/19131/'] sources = ['l_mpi_oneapi_p_%(version)s.25329_offline.sh'] checksums = ['0fcb1171fc42fd4b2d863ae474c0b0f656b0fa1fdc1df435aa851ccd6d1eaaf7'] diff --git a/easybuild/easyconfigs/i/inferCNV/inferCNV-1.21.0-foss-2023a-R-4.3.2.eb b/easybuild/easyconfigs/i/inferCNV/inferCNV-1.21.0-foss-2023a-R-4.3.2.eb new file mode 100644 index 00000000000..7404bfe1502 --- /dev/null +++ b/easybuild/easyconfigs/i/inferCNV/inferCNV-1.21.0-foss-2023a-R-4.3.2.eb @@ -0,0 +1,59 @@ +easyblock = 'Bundle' + +name = 'inferCNV' +version = '1.21.0' +versionsuffix = '-R-%(rver)s' +local_biocver = '3.18' +local_commit = '124eec089e5d9ab5a2a2352461d03db6cdcf0ea0' +github_account = 'broadinstitute' + +homepage = 'https://github.com/broadinstitute/inferCNV/wiki' +description = """InferCNV is used to explore tumor single cell RNA-Seq data to identify evidence + for somatic large-scale chromosomal copy number alterations, such as gains or + deletions of entire chromosomes or large segments of chromosomes.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('R', '4.3.2'), + ('R-bundle-Bioconductor', local_biocver, '-R-%(rver)s'), + ('rjags', '4-15', '-R-%(rver)s'), +] + +exts_default_options = { + 'source_urls': [ + 'https://bioconductor.org/packages/release/bioc/src/contrib/', # current version of packages + 'https://bioconductor.org/packages/%s/bioc/src/contrib/' % local_biocver, + 'https://bioconductor.org/packages/%s/bioc/src/contrib/Archive/%%(name)s' % local_biocver, + 'https://bioconductor.org/packages/%s/data/annotation/src/contrib/' % local_biocver, + 'https://bioconductor.org/packages/%s/data/experiment/src/contrib/' % local_biocver, + 'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'https://cran.r-project.org/src/contrib/', # current version of packages + 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + ], + 'source_tmpl': '%(name)s_%(version)s.tar.gz' +} + +exts_defaultclass = 'RPackage' + +exts_list = [ + ('phyclust', '0.1-34', { + 'checksums': ['d2047030e9f24c5dc8bbb378867fbcb8e71d1f1c2ab77e9285f79f670568f5f3'], + }), + (name, version, { + 'modulename': '%(namelower)s', + 'source_urls': ['https://github.com/%(github_account)s/%(name)s/archive'], + 'sources': [{'download_filename': '%s.tar.gz' % local_commit, 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['c8886c0a7c292e28a5fb0acaab3ae00eb2b3906aa0a1d146d5931819a37daefb'], + }), +] + +modextrapaths = {'R_LIBS_SITE': ''} + +sanity_check_paths = { + 'files': [], + 'dirs': ['infercnv'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/i/inih/inih-58-GCCcore-13.3.0.eb b/easybuild/easyconfigs/i/inih/inih-58-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..0837277c267 --- /dev/null +++ b/easybuild/easyconfigs/i/inih/inih-58-GCCcore-13.3.0.eb @@ -0,0 +1,30 @@ +easyblock = 'MesonNinja' + +name = 'inih' +version = '58' + +homepage = 'https://dri.freedesktop.org' +description = """Direct Rendering Manager runtime library.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://github.com/benhoyt/inih/archive/refs/tags/'] +sources = ['r%(version)s.tar.gz'] +checksums = ['e79216260d5dffe809bda840be48ab0eec7737b2bb9f02d2275c1b46344ea7b7'] + +builddependencies = [ + ('binutils', '2.42'), + ('pkgconf', '2.2.0'), + ('Meson', '1.4.0'), + ('Ninja', '1.12.1'), +] + +# installing manpages requires an extra build dependency (docbook xsl) +# configopts = '-Dman-pages=disabled' + +sanity_check_paths = { + 'files': ['lib/libinih.%s' % SHLIB_EXT, 'include/ini.h'], + 'dirs': ['include', 'lib'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2021.1.2.eb b/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2021.1.2.eb index 820a237e44d..67a5c1f5701 100644 --- a/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2021.1.2.eb +++ b/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2021.1.2.eb @@ -9,11 +9,11 @@ toolchain = SYSTEM # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html sources = [ { - 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/irc_nas/17513/'], + 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/17513/'], 'filename': 'l_dpcpp-cpp-compiler_p_%(version)s.63_offline.sh', }, { - 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/irc_nas/17508/'], + 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/17508/'], 'filename': 'l_fortran-compiler_p_%(version)s.62_offline.sh', }, ] diff --git a/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2021.2.0.eb b/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2021.2.0.eb index 4fe1af0da99..e4986d623f0 100644 --- a/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2021.2.0.eb +++ b/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2021.2.0.eb @@ -9,11 +9,11 @@ toolchain = SYSTEM # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html sources = [ { - 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/irc_nas/17749/'], + 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/17749/'], 'filename': 'l_dpcpp-cpp-compiler_p_%(version)s.118_offline.sh', }, { - 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/irc_nas/17756/'], + 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/17756/'], 'filename': 'l_fortran-compiler_p_%(version)s.136_offline.sh', }, ] diff --git a/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2021.3.0.eb b/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2021.3.0.eb index efcc5a7498b..cececeebef0 100644 --- a/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2021.3.0.eb +++ b/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2021.3.0.eb @@ -12,11 +12,11 @@ toolchain = SYSTEM # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html sources = [ { - 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/irc_nas/17928/'], + 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/17928/'], 'filename': 'l_dpcpp-cpp-compiler_p_%(version)s.3168_offline.sh', }, { - 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/irc_nas/17959/'], + 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/17959/'], 'filename': 'l_fortran-compiler_p_%(version)s.3168_offline.sh', }, ] diff --git a/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2021.4.0.eb b/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2021.4.0.eb index b12d0b8bb3c..977bf5ced0e 100644 --- a/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2021.4.0.eb +++ b/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2021.4.0.eb @@ -9,11 +9,11 @@ toolchain = SYSTEM # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html sources = [ { - 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18209/'], + 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18209/'], 'filename': 'l_dpcpp-cpp-compiler_p_%(version)s.3201_offline.sh', }, { - 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18210/'], + 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18210/'], 'filename': 'l_fortran-compiler_p_%(version)s.3224_offline.sh', }, ] diff --git a/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2022.0.1.eb b/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2022.0.1.eb index 56c8e9b5da4..967197cdfd7 100644 --- a/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2022.0.1.eb +++ b/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2022.0.1.eb @@ -9,11 +9,11 @@ toolchain = SYSTEM # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html sources = [ { - 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18435/'], + 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18435/'], 'filename': 'l_dpcpp-cpp-compiler_p_%(version)s.71_offline.sh', }, { - 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18436/'], + 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18436/'], 'filename': 'l_fortran-compiler_p_%(version)s.70_offline.sh', }, ] diff --git a/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2022.0.2.eb b/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2022.0.2.eb index b54023cfe84..011509935b0 100644 --- a/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2022.0.2.eb +++ b/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2022.0.2.eb @@ -9,11 +9,11 @@ toolchain = SYSTEM # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html sources = [ { - 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18478/'], + 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18478/'], 'filename': 'l_dpcpp-cpp-compiler_p_%(version)s.84_offline.sh', }, { - 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18481/'], + 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18481/'], 'filename': 'l_fortran-compiler_p_%(version)s.83_offline.sh', }, ] diff --git a/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2022.1.0.eb b/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2022.1.0.eb index f25617230ac..92ac06db492 100644 --- a/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2022.1.0.eb +++ b/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2022.1.0.eb @@ -9,11 +9,11 @@ toolchain = SYSTEM # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html sources = [ { - 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18717/'], + 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18717/'], 'filename': 'l_dpcpp-cpp-compiler_p_%(version)s.137_offline.sh', }, { - 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18703/'], + 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18703/'], 'filename': 'l_fortran-compiler_p_%(version)s.134_offline.sh', }, ] diff --git a/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2022.2.0.eb b/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2022.2.0.eb index 17262278b13..8c1390dae95 100644 --- a/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2022.2.0.eb +++ b/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2022.2.0.eb @@ -9,11 +9,11 @@ toolchain = SYSTEM # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html sources = [ { - 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18849/'], + 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18849/'], 'filename': 'l_dpcpp-cpp-compiler_p_%(version)s.8772_offline.sh', }, { - 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18909/'], + 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18909/'], 'filename': 'l_fortran-compiler_p_%(version)s.8773_offline.sh', }, ] diff --git a/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2022.2.1.eb b/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2022.2.1.eb index a6ae8170105..e67292301d5 100644 --- a/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2022.2.1.eb +++ b/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2022.2.1.eb @@ -9,11 +9,11 @@ toolchain = SYSTEM # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html sources = [ { - 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/irc_nas/19030/'], + 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/19030/'], 'filename': 'l_dpcpp-cpp-compiler_p_%(version)s.16991_offline.sh', }, { - 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18998/'], + 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18998/'], 'filename': 'l_fortran-compiler_p_%(version)s.16992_offline.sh', }, ] diff --git a/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2023.0.0.eb b/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2023.0.0.eb index 8d97d1ec3e5..f1e9b21f009 100644 --- a/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2023.0.0.eb +++ b/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2023.0.0.eb @@ -9,11 +9,11 @@ toolchain = SYSTEM # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html sources = [ { - 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/irc_nas/19123/'], + 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/19123/'], 'filename': 'l_dpcpp-cpp-compiler_p_%(version)s.25393_offline.sh', }, { - 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/irc_nas/19105/'], + 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/19105/'], 'filename': 'l_fortran-compiler_p_%(version)s.25394_offline.sh', }, ] diff --git a/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2024.2.0.eb b/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2024.2.0.eb new file mode 100644 index 00000000000..90e271fe60a --- /dev/null +++ b/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2024.2.0.eb @@ -0,0 +1,37 @@ +name = 'intel-compilers' +version = '2024.2.0' + +homepage = 'https://software.intel.com/content/www/us/en/develop/tools/oneapi/hpc-toolkit.html' +description = "Intel C, C++ & Fortran compilers (classic and oneAPI)" + +toolchain = SYSTEM + +# see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html +sources = [ + { + 'source_urls': [ + 'https://registrationcenter-download.intel.com/akdlm/IRC_NAS/6780ac84-6256-4b59-a647-330eb65f32b6/' + ], + 'filename': 'l_dpcpp-cpp-compiler_p_%(version)s.495_offline.sh', + }, + { + 'source_urls': [ + 'https://registrationcenter-download.intel.com/akdlm/IRC_NAS/801143de-6c01-4181-9911-57e00fe40181/' + ], + 'filename': 'l_fortran-compiler_p_%(version)s.426_offline.sh', + }, +] +checksums = [ + {'l_dpcpp-cpp-compiler_p_2024.2.0.495_offline.sh': + '9463aa979314d2acc51472d414ffcee032e9869ca85ac6ff4c71d39500e5173d'}, + {'l_fortran-compiler_p_2024.2.0.426_offline.sh': + 'fd19a302662b2f86f76fc115ef53a69f16488080278dba4c573cc705f3a52ffa'}, +] + +local_gccver = '13.3.0' +dependencies = [ + ('GCCcore', local_gccver), + ('binutils', '2.42', '', ('GCCcore', local_gccver)), +] + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2025.0.0.eb b/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2025.0.0.eb new file mode 100644 index 00000000000..34a1074639e --- /dev/null +++ b/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2025.0.0.eb @@ -0,0 +1,37 @@ +name = 'intel-compilers' +version = '2025.0.0' + +homepage = 'https://software.intel.com/content/www/us/en/develop/tools/oneapi/hpc-toolkit.html' +description = "Intel C, C++ & Fortran compilers" + +toolchain = SYSTEM + +# see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html +sources = [ + { + 'source_urls': [ + 'https://registrationcenter-download.intel.com/akdlm/IRC_NAS/ac92f2bb-4818-4e53-a432-f8b34d502f23/' + ], + 'filename': 'intel-dpcpp-cpp-compiler-%(version)s.740_offline.sh', + }, + { + 'source_urls': [ + 'https://registrationcenter-download.intel.com/akdlm/IRC_NAS/69f79888-2d6c-4b20-999e-e99d72af68d4/' + ], + 'filename': 'intel-fortran-compiler-%(version)s.723_offline.sh', + }, +] +checksums = [ + {'intel-dpcpp-cpp-compiler-2025.0.0.740_offline.sh': + '04fadf63789acee731895e631db63f65a98b8279db3d0f48bdf0d81e6103bdd8'}, + {'intel-fortran-compiler-2025.0.0.723_offline.sh': + '2be6d607ce84f35921228595b118fbc516d28587cbc4e6dcf6b7219e5cd1a9a9'}, +] + +local_gccver = '14.2.0' +dependencies = [ + ('GCCcore', local_gccver), + ('binutils', '2.42', '', ('GCCcore', local_gccver)), +] + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/intel/intel-2024a.eb b/easybuild/easyconfigs/i/intel/intel-2024a.eb new file mode 100644 index 00000000000..7b08707e0fc --- /dev/null +++ b/easybuild/easyconfigs/i/intel/intel-2024a.eb @@ -0,0 +1,22 @@ +easyblock = 'Toolchain' + +name = 'intel' +version = '2024a' + +homepage = 'https://easybuild.readthedocs.io/en/master/Common-toolchains.html#intel-toolchain' +description = "Compiler toolchain including Intel compilers, Intel MPI and Intel Math Kernel Library (MKL)." + +toolchain = SYSTEM + +local_comp_ver = '2024.2.0' +local_gccver = '13.3.0' +dependencies = [ + ('GCCcore', local_gccver), + ('binutils', '2.42', '', ('GCCcore', local_gccver)), + ('intel-compilers', local_comp_ver), + ('impi', '2021.13.0', '', ('intel-compilers', local_comp_ver)), + ('imkl', '2024.2.0', '', SYSTEM), + ('imkl-FFTW', '2024.2.0', '', ('iimpi', version)), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/i/intervaltree/intervaltree-0.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/i/intervaltree/intervaltree-0.1-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..06f61418ed7 --- /dev/null +++ b/easybuild/easyconfigs/i/intervaltree/intervaltree-0.1-GCCcore-12.2.0.eb @@ -0,0 +1,38 @@ +# Updated: Denis Kristak (INUITS) +# Updated: Petr Král (INUITS) + +easyblock = 'ConfigureMake' + +name = 'intervaltree' +version = '0.1' + +homepage = 'https://github.com/ekg/intervaltree' +description = """An interval tree can be used to efficiently find a set of numeric intervals + overlapping or containing another interval. This library provides a basic implementation of an + interval tree using C++ templates, allowing the insertion of arbitrary types into the tree. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +github_account = 'ekg' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +patches = ['%(name)s-%(version)s_fix-numeric_limits.patch'] +checksums = [ + '7ba41f164a98bdcd570f1416fde1634b23d3b0d885b11ccebeec76f58810c307', # v0.1.tar.gz + '1d69caf35af86c0a55000e1bde3f9a0f19dd63d1d2b6bd48e4e5fecbb1aaa6b0', # intervaltree-0.1_fix-numeric_limits.patch +] + +builddependencies = [('binutils', '2.39')] + +skipsteps = ['configure'] + +preinstallopts = 'DESTDIR="" PREFIX=%(installdir)s' + +sanity_check_paths = { + 'files': ['bin/interval_tree_test', 'include/intervaltree/IntervalTree.h'], + 'dirs': [], +} +sanity_check_commands = ["interval_tree_test"] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/i/intltool/intltool-0.51.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/i/intltool/intltool-0.51.0-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..e5797e51b02 --- /dev/null +++ b/easybuild/easyconfigs/i/intltool/intltool-0.51.0-GCCcore-13.3.0.eb @@ -0,0 +1,37 @@ +easyblock = 'ConfigureMake' + +name = 'intltool' +version = '0.51.0' + +homepage = 'https://freedesktop.org/wiki/Software/intltool/' +description = """intltool is a set of tools to centralize translation of + many different file formats using GNU gettext-compatible PO files.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://launchpad.net/intltool/trunk/%(version)s/+download/'] +sources = [SOURCE_TAR_GZ] +patches = ['intltool-%(version)s_fix-Perl-compat.patch'] +checksums = [ + '67c74d94196b153b774ab9f89b2fa6c6ba79352407037c8c14d5aeb334e959cd', # intltool-0.51.0.tar.gz + 'e839f7228b2b92301831bca88ed0bc7bce5dbf862568f1644642988204903db6', # intltool-0.51.0_fix-Perl-compat.patch +] + +builddependencies = [ + ('binutils', '2.42'), +] + +dependencies = [ + ('Perl-bundle-CPAN', '5.38.2'), +] + +fix_perl_shebang_for = ['bin/intltool-*'] + +sanity_check_paths = { + 'files': ['bin/intltool%s' % x for x in ['-extract', '-merge', '-prepare', '-update', 'ize']], + 'dirs': [] +} + +sanity_check_commands = ["intltool-merge --help"] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/i/ipympl/ipympl-0.9.3-foss-2023a.eb b/easybuild/easyconfigs/i/ipympl/ipympl-0.9.3-gfbf-2023a.eb similarity index 84% rename from easybuild/easyconfigs/i/ipympl/ipympl-0.9.3-foss-2023a.eb rename to easybuild/easyconfigs/i/ipympl/ipympl-0.9.3-gfbf-2023a.eb index e3b6c4b7437..47ab1aff28c 100644 --- a/easybuild/easyconfigs/i/ipympl/ipympl-0.9.3-foss-2023a.eb +++ b/easybuild/easyconfigs/i/ipympl/ipympl-0.9.3-gfbf-2023a.eb @@ -10,7 +10,7 @@ Besides, the figure canvas element is a proper Jupyter interactive widget which can be positioned in interactive widget layouts. """ -toolchain = {'name': 'foss', 'version': '2023a'} +toolchain = {'name': 'gfbf', 'version': '2023a'} dependencies = [ ('Python', '3.11.3'), @@ -29,9 +29,6 @@ exts_list = [ }), ] -modextrapaths = { - 'JUPYTER_PATH': 'share/jupyter', - 'JUPYTER_CONFIG_PATH': 'etc/jupyter', -} +modextrapaths = {'EB_ENV_JUPYTER_ROOT': ''} moduleclass = 'tools' diff --git a/easybuild/easyconfigs/i/ipympl/ipympl-0.9.4-gfbf-2023b.eb b/easybuild/easyconfigs/i/ipympl/ipympl-0.9.4-gfbf-2023b.eb new file mode 100644 index 00000000000..e780d34c757 --- /dev/null +++ b/easybuild/easyconfigs/i/ipympl/ipympl-0.9.4-gfbf-2023b.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonBundle' + +name = 'ipympl' +version = '0.9.4' + +homepage = 'https://matplotlib.org/ipympl' +description = """Leveraging the Jupyter interactive widgets framework, ipympl enables the +interactive features of matplotlib in the Jupyter notebook and in JupyterLab. +Besides, the figure canvas element is a proper Jupyter interactive widget which +can be positioned in interactive widget layouts. +""" + +toolchain = {'name': 'gfbf', 'version': '2023b'} + +dependencies = [ + ('Python', '3.11.5'), + ('JupyterLab', '4.2.0'), + ('matplotlib', '3.8.2'), + ('Pillow', '10.2.0'), +] + +sanity_pip_check = True +use_pip = True + +exts_list = [ + (name, version, { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['5b0c08c6f4f6ea655ba58239363457c10fb921557f5038c1a46db4457d6d6b0e'], + }), +] + +modextrapaths = {'EB_ENV_JUPYTER_ROOT': ''} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/i/itac/itac-2021.2.0.eb b/easybuild/easyconfigs/i/itac/itac-2021.2.0.eb index 3deaaa9e711..ea2cfcb2650 100644 --- a/easybuild/easyconfigs/i/itac/itac-2021.2.0.eb +++ b/easybuild/easyconfigs/i/itac/itac-2021.2.0.eb @@ -11,7 +11,7 @@ description = """The Intel Trace Collector is a low-overhead tracing library tha toolchain = SYSTEM -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/17686/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/17686/'] sources = ['l_itac_oneapi_p_%(version)s.152_offline.sh'] checksums = ['dca9d1cb2b77c43496009e191916e0d37c2e6606c228e37c11091778d038dd90'] diff --git a/easybuild/easyconfigs/i/itac/itac-2021.5.0.eb b/easybuild/easyconfigs/i/itac/itac-2021.5.0.eb index f9d10379c85..ea05e25db95 100644 --- a/easybuild/easyconfigs/i/itac/itac-2021.5.0.eb +++ b/easybuild/easyconfigs/i/itac/itac-2021.5.0.eb @@ -11,7 +11,7 @@ description = """The Intel Trace Collector is a low-overhead tracing library tha toolchain = SYSTEM -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18367/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18367/'] sources = ['l_itac_oneapi_p_%(version)s.370_offline.sh'] checksums = ['c2b31298d8b4069a62d9352873c7f6e17ce240ad7293f9bacdc6de3794675b58'] diff --git a/easybuild/easyconfigs/i/itac/itac-2021.6.0.eb b/easybuild/easyconfigs/i/itac/itac-2021.6.0.eb index 22e6230e15b..0f35b870046 100644 --- a/easybuild/easyconfigs/i/itac/itac-2021.6.0.eb +++ b/easybuild/easyconfigs/i/itac/itac-2021.6.0.eb @@ -11,7 +11,7 @@ description = """The Intel Trace Collector is a low-overhead tracing library tha toolchain = SYSTEM -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18694/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18694/'] sources = ['l_itac_oneapi_p_%(version)s.434_offline.sh'] checksums = ['1ecc2735da960041b051e377cadb9f6ab2f44e8aa44d0f642529a56a3cbba436'] diff --git a/easybuild/easyconfigs/j/JACUSA2helper/JACUSA2helper-1.9.9.9675-foss-2023a.eb b/easybuild/easyconfigs/j/JACUSA2helper/JACUSA2helper-1.9.9.9675-foss-2023a.eb new file mode 100644 index 00000000000..4b3003c89ec --- /dev/null +++ b/easybuild/easyconfigs/j/JACUSA2helper/JACUSA2helper-1.9.9.9675-foss-2023a.eb @@ -0,0 +1,36 @@ +easyblock = 'Bundle' + +name = 'JACUSA2helper' +version = '1.9.9.9675' + +homepage = 'https://dieterich-lab.github.io/JACUSA2helper/' +description = "Auxiliary R package for assessment of JACUSA2 results" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('R', '4.3.2'), + ('R-bundle-CRAN', '2023.12'), + ('R-bundle-Bioconductor', '3.18', '-R-%(rver)s'), +] + +exts_defaultclass = 'RPackage' + +exts_list = [ + (name, version, { + 'source_urls': ['https://github.com/dieterich-lab/JACUSA2helper/archive/refs/tags/'], + 'source_tmpl': 'v%(version)s.tar.gz', + 'checksums': ['5c8edb96a5691c7fb2895e50eb992ebe375f8d97234039da3f5540a7a9cb4816'], + }), +] + +sanity_check_paths = { + 'files': [], + 'dirs': [name], +} + +sanity_check_commands = ['Rscript -e "library(%(name)s)"'] + +modextrapaths = {'R_LIBS_SITE': ''} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/j/JAGS/JAGS-4.3.2-foss-2023a.eb b/easybuild/easyconfigs/j/JAGS/JAGS-4.3.2-foss-2023a.eb new file mode 100644 index 00000000000..8c83d04b731 --- /dev/null +++ b/easybuild/easyconfigs/j/JAGS/JAGS-4.3.2-foss-2023a.eb @@ -0,0 +1,38 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel + +easyblock = 'ConfigureMake' + +name = 'JAGS' +version = '4.3.2' + +homepage = 'http://mcmc-jags.sourceforge.net/' +description = """JAGS is Just Another Gibbs Sampler. It is a program for analysis + of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC) simulation """ + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = [ + ('https://sourceforge.net/projects/mcmc-%(namelower)s/files/%(name)s/%(version_major)s.x/Source/', 'download'), +] +sources = [SOURCE_TAR_GZ] +checksums = ['871f556af403a7c2ce6a0f02f15cf85a572763e093d26658ebac55c4ab472fc8'] + +configopts = ' --with-blas="$LIBBLAS" --with-lapack="$LIBLAPACK"' + + +sanity_check_paths = { + 'files': ['bin/%(namelower)s', 'libexec/%(namelower)s-terminal', 'lib/libjags.%s' % SHLIB_EXT], + 'dirs': [], +} + +sanity_check_commands = ["echo 'list modules' | %(namelower)s"] + +modextrapaths = { + 'JAGS_INCLUDE': 'include/%(name)s', + 'JAGS_LIB': 'lib', +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/j/JAGS/JAGS-4.3.2-foss-2024a.eb b/easybuild/easyconfigs/j/JAGS/JAGS-4.3.2-foss-2024a.eb new file mode 100644 index 00000000000..1077c8fc2a9 --- /dev/null +++ b/easybuild/easyconfigs/j/JAGS/JAGS-4.3.2-foss-2024a.eb @@ -0,0 +1,38 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel + +easyblock = 'ConfigureMake' + +name = 'JAGS' +version = '4.3.2' + +homepage = 'http://mcmc-jags.sourceforge.net/' +description = """JAGS is Just Another Gibbs Sampler. It is a program for analysis + of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC) simulation """ + +toolchain = {'name': 'foss', 'version': '2024a'} + +source_urls = [ + ('https://sourceforge.net/projects/mcmc-%(namelower)s/files/%(name)s/%(version_major)s.x/Source/', 'download'), +] +sources = [SOURCE_TAR_GZ] +checksums = ['871f556af403a7c2ce6a0f02f15cf85a572763e093d26658ebac55c4ab472fc8'] + +configopts = ' --with-blas="$LIBBLAS" --with-lapack="$LIBLAPACK"' + + +sanity_check_paths = { + 'files': ['bin/%(namelower)s', 'libexec/%(namelower)s-terminal', 'lib/libjags.%s' % SHLIB_EXT], + 'dirs': [], +} + +sanity_check_commands = ["echo 'list modules' | %(namelower)s"] + +modextrapaths = { + 'JAGS_INCLUDE': 'include/%(name)s', + 'JAGS_LIB': 'lib', +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/j/Jansson/Jansson-2.14-GCC-12.3.0.eb b/easybuild/easyconfigs/j/Jansson/Jansson-2.14-GCC-12.3.0.eb new file mode 100644 index 00000000000..a8aeb721b5f --- /dev/null +++ b/easybuild/easyconfigs/j/Jansson/Jansson-2.14-GCC-12.3.0.eb @@ -0,0 +1,41 @@ +# Contribution from Imperial College London +# uploaded by J. Sassmannshausen +# Update: P.Tománek (Inuits) + +easyblock = 'CMakeMake' + +name = 'Jansson' +version = "2.14" + +homepage = 'https://www.digip.org/jansson/' +description = """Jansson is a C library for encoding, decoding and manipulating JSON data. + Its main features and design principles are: + * Simple and intuitive API and data model + * Comprehensive documentation + * No dependencies on other libraries + * Full Unicode support (UTF-8) + * Extensive test suite""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +source_urls = ['https://github.com/akheron/jansson/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['c739578bf6b764aa0752db9a2fdadcfe921c78f1228c7ec0bb47fa804c55d17b'] + +# For configure, the ld.gold linker does not know anything about --default-symver and thus crashes +# So we simnply use the bfd linker +# preconfigopts = 'autoreconf -i && CC="$CC -fuse-ld=bfd" ' +# This is not required with CMake + +builddependencies = [('CMake', '3.26.3')] + +configopts = '-DJANSSON_BUILD_SHARED_LIBS=ON ' + +sanity_check_paths = { + 'files': ['lib/libjansson.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +runtest = 'check' + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/j/JasPer/JasPer-4.2.4-GCCcore-13.3.0.eb b/easybuild/easyconfigs/j/JasPer/JasPer-4.2.4-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..14ce45ca6ad --- /dev/null +++ b/easybuild/easyconfigs/j/JasPer/JasPer-4.2.4-GCCcore-13.3.0.eb @@ -0,0 +1,36 @@ +easyblock = 'CMakeMake' + +name = 'JasPer' +version = '4.2.4' + +homepage = 'https://www.ece.uvic.ca/~frodo/jasper/' + +description = """ + The JasPer Project is an open-source initiative to provide a free + software-based reference implementation of the codec specified in + the JPEG-2000 Part-1 standard. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +github_account = 'jasper-software' +source_urls = [GITHUB_SOURCE] +sources = ['version-%(version)s.tar.gz'] +checksums = ['23a3d58cdeacf3abdf9fa1d81dcefee58da6ab330940790c0f27019703bfd2cd'] + +builddependencies = [ + ('binutils', '2.42'), + ('CMake', '3.29.3'), +] + +configopts = '-DJAS_ENABLE_DOC=OFF ' + +sanity_check_paths = { + 'files': ['bin/jasper', ('lib/libjasper.%s' % SHLIB_EXT, 'lib64/libjasper.%s' % SHLIB_EXT)], + 'dirs': ['include'], +} + +sanity_check_commands = ['jasper --version'] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/j/Java/Java-21.0.5.eb b/easybuild/easyconfigs/j/Java/Java-21.0.5.eb new file mode 100644 index 00000000000..932318fd336 --- /dev/null +++ b/easybuild/easyconfigs/j/Java/Java-21.0.5.eb @@ -0,0 +1,32 @@ +name = 'Java' +version = '21.0.5' +local_build = '11' + +homepage = 'https://openjdk.org' +description = """Java Platform, Standard Edition (Java SE) lets you develop and deploy +Java applications on desktops and servers.""" + +toolchain = SYSTEM + +local_tarball_tmpl = 'OpenJDK%%(version_major)sU-jdk_%s_linux_hotspot_%%(version)s_%s.tar.gz' + +# Using the Adoptium Eclipse Temurin builds, recommended by https://whichjdk.com/#distributions + +source_urls = ['https://github.com/adoptium/temurin%%(version_major)s-binaries/releases/download/jdk-%%(version)s+%s/' + % local_build] +sources = [local_tarball_tmpl % ('%(jdkarch)s', local_build)] + +checksums = [ + { + local_tarball_tmpl % ('x64', local_build): + '3c654d98404c073b8a7e66bffb27f4ae3e7ede47d13284c132d40a83144bfd8c', + local_tarball_tmpl % ('aarch64', local_build): + '6482639ed9fd22aa2e704cc366848b1b3e1586d2bf1213869c43e80bca58fe5c', + local_tarball_tmpl % ('ppc64le', local_build): + '3c6f4c358facfb6c19d90faf02bfe0fc7512d6b0e80ac18146bbd7e0d01deeef', + local_tarball_tmpl % ('riscv64', local_build): + '2f1b3e401e36de803398dfb9818861f9f14ca8ae7db650ea0946ab048fefe3b9', + } +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/j/Java/Java-21.eb b/easybuild/easyconfigs/j/Java/Java-21.eb index 46e84105b35..c7aef391c20 100644 --- a/easybuild/easyconfigs/j/Java/Java-21.eb +++ b/easybuild/easyconfigs/j/Java/Java-21.eb @@ -9,6 +9,6 @@ Java applications on desktops and servers.""" toolchain = SYSTEM -dependencies = [('Java', '%(version)s.0.2')] +dependencies = [('Java', '%(version)s.0.5')] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.3.1-GCC-12.3.0.eb b/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.3.1-GCC-12.3.0.eb new file mode 100644 index 00000000000..82821a0cc38 --- /dev/null +++ b/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.3.1-GCC-12.3.0.eb @@ -0,0 +1,40 @@ +## +# This is a contribution from DeepThought HPC Service, Flinders University, Adelaide, Australia +# Homepage: https://staff.flinders.edu.au/research/deep-thought +# +# Authors:: Robert Qiao +# License:: GPLv3.0 +# +# Notes:: +## + +easyblock = 'ConfigureMake' + +name = 'Jellyfish' +version = '2.3.1' + +homepage = 'http://www.genome.umd.edu/jellyfish.html' +description = "Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA." + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +source_urls = ['https://github.com/gmarcais/Jellyfish/releases/download/v%(version)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['ee032b57257948ca0f0610883099267572c91a635eecbd88ae5d8974c2430fcd'] + +parallel = 1 + +# The tests for the Bloom filter are statistical tests and can randomly fail, +# they actually don't make a lot of sense +runtest = "check GTEST_FILTER=-'*Bloom*'" + +postinstallcmds = ["cp config.h %(installdir)s/include/%(namelower)s-%(version)s/%(namelower)s/"] + +sanity_check_paths = { + 'files': ['bin/jellyfish'], + 'dirs': [] +} + +modextrapaths = {'CPATH': 'include/%(namelower)s-%(version)s'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/j/JsonCpp/JsonCpp-1.9.5-GCCcore-13.2.0.eb b/easybuild/easyconfigs/j/JsonCpp/JsonCpp-1.9.5-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..dd5dda233d2 --- /dev/null +++ b/easybuild/easyconfigs/j/JsonCpp/JsonCpp-1.9.5-GCCcore-13.2.0.eb @@ -0,0 +1,29 @@ +easyblock = "CMakeNinja" + +name = 'JsonCpp' +version = '1.9.5' + +homepage = 'https://open-source-parsers.github.io/jsoncpp-docs/doxygen/index.html' +description = """ JsonCpp is a C++ library that allows manipulating JSON values, + including serialization and deserialization to and from strings. It can also preserve existing comment in + unserialization/serialization steps, making it a convenient format to store user input files. """ + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://github.com/open-source-parsers/jsoncpp/archive'] +sources = ['%(version)s.tar.gz'] +checksums = ['f409856e5920c18d0c2fb85276e24ee607d2a09b5e7d5f0a371368903c275da2'] + +builddependencies = [ + ('CMake', '3.27.6'), + ('Ninja', '1.11.1'), + ('pkgconf', '2.0.3'), + ('binutils', '2.40'), +] + +sanity_check_paths = { + 'files': ['include/json/json.h', 'lib/libjsoncpp.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/j/JsonCpp/JsonCpp-1.9.5-GCCcore-13.3.0.eb b/easybuild/easyconfigs/j/JsonCpp/JsonCpp-1.9.5-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..b1d3f620566 --- /dev/null +++ b/easybuild/easyconfigs/j/JsonCpp/JsonCpp-1.9.5-GCCcore-13.3.0.eb @@ -0,0 +1,29 @@ +easyblock = "CMakeNinja" + +name = 'JsonCpp' +version = '1.9.5' + +homepage = 'https://open-source-parsers.github.io/jsoncpp-docs/doxygen/index.html' +description = """ JsonCpp is a C++ library that allows manipulating JSON values, + including serialization and deserialization to and from strings. It can also preserve existing comment in + unserialization/serialization steps, making it a convenient format to store user input files. """ + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://github.com/open-source-parsers/jsoncpp/archive'] +sources = ['%(version)s.tar.gz'] +checksums = ['f409856e5920c18d0c2fb85276e24ee607d2a09b5e7d5f0a371368903c275da2'] + +builddependencies = [ + ('CMake', '3.29.3'), + ('Ninja', '1.12.1'), + ('pkgconf', '2.2.0'), + ('binutils', '2.42'), +] + +sanity_check_paths = { + 'files': ['include/json/json.h', 'lib/libjsoncpp.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/j/Judy/Judy-1.0.5-GCCcore-12.3.0.eb b/easybuild/easyconfigs/j/Judy/Judy-1.0.5-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..183e8e08ea4 --- /dev/null +++ b/easybuild/easyconfigs/j/Judy/Judy-1.0.5-GCCcore-12.3.0.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'Judy' +version = '1.0.5' + +homepage = 'http://judy.sourceforge.net/' +description = "A C library that implements a dynamic array." + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['http://downloads.sourceforge.net/judy'] +sources = ['%(name)s-%(version)s.tar.gz'] +patches = ['Judy-1.0.5_parallel-make.patch'] # fix Make dependencies, so parallel build also works + +builddependencies = [ + ('Autotools', '20220317'), + ('binutils', '2.40'), +] +checksums = [ + 'd2704089f85fdb6f2cd7e77be21170ced4b4375c03ef1ad4cf1075bd414a63eb', # Judy-1.0.5.tar.gz + '14c2eba71088f3db9625dc4605c6d7183d72412d75ef6c9fd9b95186165cf009', # Judy-1.0.5_parallel-make.patch +] + +preconfigopts = "sed -i 's/AM_CONFIG_HEADER/AC_CONFIG_HEADERS/g' configure.ac && " +preconfigopts += "autoreconf -i && " + +configopts = '--enable-shared --enable-static' + +sanity_check_paths = { + 'files': ["include/%(name)s.h", "lib/lib%(name)s.a", "lib/lib%(name)s.la", "lib/lib%%(name)s.%s" % SHLIB_EXT], + 'dirs': ["share/man"] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/j/Judy/Judy-1.0.5-GCCcore-13.3.0.eb b/easybuild/easyconfigs/j/Judy/Judy-1.0.5-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..ad7805e7167 --- /dev/null +++ b/easybuild/easyconfigs/j/Judy/Judy-1.0.5-GCCcore-13.3.0.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'Judy' +version = '1.0.5' + +homepage = 'http://judy.sourceforge.net/' +description = "A C library that implements a dynamic array." + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['http://downloads.sourceforge.net/judy'] +sources = ['%(name)s-%(version)s.tar.gz'] +patches = ['Judy-1.0.5_parallel-make.patch'] # fix Make dependencies, so parallel build also works + +builddependencies = [ + ('Autotools', '20231222'), + ('binutils', '2.42'), +] +checksums = [ + 'd2704089f85fdb6f2cd7e77be21170ced4b4375c03ef1ad4cf1075bd414a63eb', # Judy-1.0.5.tar.gz + '14c2eba71088f3db9625dc4605c6d7183d72412d75ef6c9fd9b95186165cf009', # Judy-1.0.5_parallel-make.patch +] + +preconfigopts = "sed -i 's/AM_CONFIG_HEADER/AC_CONFIG_HEADERS/g' configure.ac && " +preconfigopts += "autoreconf -i && " + +configopts = '--enable-shared --enable-static' + +sanity_check_paths = { + 'files': ["include/%(name)s.h", "lib/lib%(name)s.a", "lib/lib%(name)s.la", "lib/lib%%(name)s.%s" % SHLIB_EXT], + 'dirs': ["share/man"] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/j/Julia/Julia-1.10.0-linux-x86_64.eb b/easybuild/easyconfigs/j/Julia/Julia-1.10.0-linux-x86_64.eb index 6671e1cd4ff..6081619a331 100644 --- a/easybuild/easyconfigs/j/Julia/Julia-1.10.0-linux-x86_64.eb +++ b/easybuild/easyconfigs/j/Julia/Julia-1.10.0-linux-x86_64.eb @@ -11,21 +11,20 @@ toolchain = SYSTEM source_urls = ['https://julialang-s3.julialang.org/bin/linux/x64/%(version_major_minor)s/'] sources = ['%(namelower)s-%(version)s%(versionsuffix)s.tar.gz'] -checksums = ['a7298207f72f2b27b2ab1ce392a6ea37afbd1fbee0f1f8d190b054dcaba878fe'] +patches = [('julia.wrapper', 'bin/')] +checksums = [ + {'julia-1.10.0-linux-x86_64.tar.gz': 'a7298207f72f2b27b2ab1ce392a6ea37afbd1fbee0f1f8d190b054dcaba878fe'}, + {'julia.wrapper': 'd10aeaff53cca9875f7b0ce9218eae3bd21870b654e26c4c52aa8bfcc9da702d'}, +] + +# install wrapper with linking safeguards for Julia libraries +postinstallcmds = ["cd %(installdir)s/bin && mv julia julia.bin && mv julia.wrapper julia"] sanity_check_paths = { - 'files': ['bin/julia', 'include/julia/julia.h', 'lib/libjulia.%s' % SHLIB_EXT], - 'dirs': ['bin', 'etc', 'include', 'lib', 'share'] + 'files': ['bin/julia', 'bin/julia.bin', 'include/julia/julia.h', 'lib/libjulia.%s' % SHLIB_EXT], + 'dirs': ['bin', 'etc', 'include', 'lib', 'lib/julia', 'share'] } sanity_check_commands = ['julia --help'] -modextrapaths_append = { - # Use default DEPOT_PATH where first entry is user's depot. - # JULIA_DEPOT_PATH must be set to be able to load other JuliaPackage modules and have - # those installations appended to DEPOT_PATH without disabling any of the default paths. - # Appending ':' to make sure we don't override the user's custom JULIA_DEPOT_PATH if set. - 'JULIA_DEPOT_PATH': ':', -} - moduleclass = 'lang' diff --git a/easybuild/easyconfigs/j/Julia/Julia-1.10.3-linux-x86_64.eb b/easybuild/easyconfigs/j/Julia/Julia-1.10.3-linux-x86_64.eb new file mode 100644 index 00000000000..599edfd33ea --- /dev/null +++ b/easybuild/easyconfigs/j/Julia/Julia-1.10.3-linux-x86_64.eb @@ -0,0 +1,30 @@ +easyblock = 'Tarball' + +name = 'Julia' +version = '1.10.3' +versionsuffix = '-linux-x86_64' + +homepage = 'https://julialang.org' +description = "Julia is a high-level, high-performance dynamic programming language for numerical computing" + +toolchain = SYSTEM + +source_urls = ['https://julialang-s3.julialang.org/bin/linux/x64/%(version_major_minor)s/'] +sources = ['%(namelower)s-%(version)s%(versionsuffix)s.tar.gz'] +patches = [('julia.wrapper', 'bin/')] +checksums = [ + {'julia-1.10.3-linux-x86_64.tar.gz': '81b910c922fff0e27ae1f256f2cc803db81f3960215281eddd2d484721928c70'}, + {'julia.wrapper': 'd10aeaff53cca9875f7b0ce9218eae3bd21870b654e26c4c52aa8bfcc9da702d'}, +] + +# install wrapper with linking safeguards for Julia libraries +postinstallcmds = ["cd %(installdir)s/bin && mv julia julia.bin && mv julia.wrapper julia"] + +sanity_check_paths = { + 'files': ['bin/julia', 'bin/julia.bin', 'include/julia/julia.h', 'lib/libjulia.%s' % SHLIB_EXT], + 'dirs': ['bin', 'etc', 'include', 'lib', 'lib/julia', 'share'] +} + +sanity_check_commands = ['julia --help'] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/j/Julia/Julia-1.10.4-linux-x86_64.eb b/easybuild/easyconfigs/j/Julia/Julia-1.10.4-linux-x86_64.eb new file mode 100644 index 00000000000..767a23c33a4 --- /dev/null +++ b/easybuild/easyconfigs/j/Julia/Julia-1.10.4-linux-x86_64.eb @@ -0,0 +1,37 @@ +# This file is an EasyBuild reciPY as per https://easybuilders.github.io/easybuild/ +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics +# Updated by: Dugan Witherick, University of Warwick +# Robert Mijakovic +# Wahid Mainassara + +easyblock = 'Tarball' + +name = 'Julia' +version = '1.10.4' +versionsuffix = '-linux-x86_64' + +homepage = 'https://julialang.org' +description = "Julia is a high-level, high-performance dynamic programming language for numerical computing" + +toolchain = SYSTEM + +source_urls = ['https://julialang-s3.julialang.org/bin/linux/x64/%(version_major_minor)s/'] +sources = ['%(namelower)s-%(version)s%(versionsuffix)s.tar.gz'] +patches = [('julia.wrapper', 'bin/')] +checksums = [ + {'julia-1.10.4-linux-x86_64.tar.gz': '079f61757c3b5b40d2ade052b3cc4816f50f7ef6df668825772562b3746adff1'}, + {'julia.wrapper': 'd10aeaff53cca9875f7b0ce9218eae3bd21870b654e26c4c52aa8bfcc9da702d'}, +] + +# install wrapper with linking safeguards for Julia libraries +postinstallcmds = ["cd %(installdir)s/bin && mv julia julia.bin && mv julia.wrapper julia"] + +sanity_check_paths = { + 'files': ['bin/julia', 'bin/julia.bin', 'include/julia/julia.h', 'lib/libjulia.%s' % SHLIB_EXT], + 'dirs': ['bin', 'etc', 'include', 'lib', 'lib/julia', 'share'] +} +sanity_check_commands = ['julia --help'] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/j/Julia/Julia-1.10.5-linux-x86_64.eb b/easybuild/easyconfigs/j/Julia/Julia-1.10.5-linux-x86_64.eb new file mode 100644 index 00000000000..4c623699101 --- /dev/null +++ b/easybuild/easyconfigs/j/Julia/Julia-1.10.5-linux-x86_64.eb @@ -0,0 +1,38 @@ +# This file is an EasyBuild reciPY as per https://easybuilders.github.io/easybuild/ +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics +# Updated by: Dugan Witherick, University of Warwick +# Robert Mijakovic +# Wahid Mainassara +# Paul Melis + +easyblock = 'Tarball' + +name = 'Julia' +version = '1.10.5' +versionsuffix = '-linux-x86_64' + +homepage = 'https://julialang.org' +description = "Julia is a high-level, high-performance dynamic programming language for numerical computing" + +toolchain = SYSTEM + +source_urls = ['https://julialang-s3.julialang.org/bin/linux/x64/%(version_major_minor)s/'] +sources = ['%(namelower)s-%(version)s%(versionsuffix)s.tar.gz'] +patches = [('julia.wrapper', 'bin/')] +checksums = [ + {'julia-1.10.5-linux-x86_64.tar.gz': '33497b93cf9dd65e8431024fd1db19cbfbe30bd796775a59d53e2df9a8de6dc0'}, + {'julia.wrapper': 'd10aeaff53cca9875f7b0ce9218eae3bd21870b654e26c4c52aa8bfcc9da702d'}, +] + +# install wrapper with linking safeguards for Julia libraries +postinstallcmds = ["cd %(installdir)s/bin && mv julia julia.bin && mv julia.wrapper julia"] + +sanity_check_paths = { + 'files': ['bin/julia', 'bin/julia.bin', 'include/julia/julia.h', 'lib/libjulia.%s' % SHLIB_EXT], + 'dirs': ['bin', 'etc', 'include', 'lib', 'lib/julia', 'share'] +} +sanity_check_commands = ['julia --help'] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/j/Julia/Julia-1.6.0-linux-aarch64.eb b/easybuild/easyconfigs/j/Julia/Julia-1.6.0-linux-aarch64.eb index 225d86de75a..17abf7d929c 100644 --- a/easybuild/easyconfigs/j/Julia/Julia-1.6.0-linux-aarch64.eb +++ b/easybuild/easyconfigs/j/Julia/Julia-1.6.0-linux-aarch64.eb @@ -15,20 +15,20 @@ toolchain = SYSTEM source_urls = ['https://julialang-s3.julialang.org/bin/linux/aarch64/%(version_major_minor)s/'] sources = ['%(namelower)s-%(version)s%(versionsuffix)s.tar.gz'] -checksums = ['0f496972d26cea88151204d03e6bd87702aa1ff983de3b1e4f320c48ef67325f'] +patches = [('julia.wrapper', 'bin/')] +checksums = [ + {'julia-1.6.0-linux-aarch64.tar.gz': '0f496972d26cea88151204d03e6bd87702aa1ff983de3b1e4f320c48ef67325f'}, + {'julia.wrapper': 'd10aeaff53cca9875f7b0ce9218eae3bd21870b654e26c4c52aa8bfcc9da702d'}, +] + +# install wrapper with linking safeguards for Julia libraries +postinstallcmds = ["cd %(installdir)s/bin && mv julia julia.bin && mv julia.wrapper julia"] sanity_check_paths = { - 'files': ['bin/julia', 'include/julia/julia.h', 'lib/libjulia.%s' % SHLIB_EXT], - 'dirs': ['bin', 'etc', 'include', 'lib', 'share'] + 'files': ['bin/julia', 'bin/julia.bin', 'include/julia/julia.h', 'lib/libjulia.%s' % SHLIB_EXT], + 'dirs': ['bin', 'etc', 'include', 'lib', 'lib/julia', 'share'] } sanity_check_commands = ['julia --help'] -modextravars = { - # Use default DEPOT_PATH where first entry is user's depot - # JULIA_DEPOT_PATH must be set to be able to load other JuliaPackage modules and have - # those installations appended to DEPOT_PATH without disabling any of the default paths - 'JULIA_DEPOT_PATH': ':', -} - moduleclass = 'lang' diff --git a/easybuild/easyconfigs/j/Julia/Julia-1.6.5-linux-x86_64.eb b/easybuild/easyconfigs/j/Julia/Julia-1.6.5-linux-x86_64.eb index 45b365aa65d..dd9ad4890db 100644 --- a/easybuild/easyconfigs/j/Julia/Julia-1.6.5-linux-x86_64.eb +++ b/easybuild/easyconfigs/j/Julia/Julia-1.6.5-linux-x86_64.eb @@ -19,20 +19,20 @@ toolchain = SYSTEM source_urls = ['https://julialang-s3.julialang.org/bin/linux/x64/%(version_major_minor)s/'] sources = ['%(namelower)s-%(version)s%(versionsuffix)s.tar.gz'] -checksums = ['b8fe23ee547254a2fe14be587284ed77c78c06c2d8e9aad5febce0d21cab8e2c'] +patches = [('julia.wrapper', 'bin/')] +checksums = [ + {'julia-1.6.5-linux-x86_64.tar.gz': 'b8fe23ee547254a2fe14be587284ed77c78c06c2d8e9aad5febce0d21cab8e2c'}, + {'julia.wrapper': 'd10aeaff53cca9875f7b0ce9218eae3bd21870b654e26c4c52aa8bfcc9da702d'}, +] + +# install wrapper with linking safeguards for Julia libraries +postinstallcmds = ["cd %(installdir)s/bin && mv julia julia.bin && mv julia.wrapper julia"] sanity_check_paths = { - 'files': ['bin/julia', 'include/julia/julia.h', 'lib/libjulia.%s' % SHLIB_EXT], - 'dirs': ['bin', 'etc', 'include', 'lib', 'share'] + 'files': ['bin/julia', 'bin/julia.bin', 'include/julia/julia.h', 'lib/libjulia.%s' % SHLIB_EXT], + 'dirs': ['bin', 'etc', 'include', 'lib', 'lib/julia', 'share'] } sanity_check_commands = ['julia --help'] -modextravars = { - # Use default DEPOT_PATH where first entry is user's depot - # JULIA_DEPOT_PATH must be set to be able to load other JuliaPackage modules and have - # those installations appended to DEPOT_PATH without disabling any of the default paths - 'JULIA_DEPOT_PATH': ':', -} - moduleclass = 'lang' diff --git a/easybuild/easyconfigs/j/Julia/Julia-1.6.6-linux-x86_64.eb b/easybuild/easyconfigs/j/Julia/Julia-1.6.6-linux-x86_64.eb index 48c2259422e..03bdc16da5a 100644 --- a/easybuild/easyconfigs/j/Julia/Julia-1.6.6-linux-x86_64.eb +++ b/easybuild/easyconfigs/j/Julia/Julia-1.6.6-linux-x86_64.eb @@ -19,20 +19,19 @@ toolchain = SYSTEM source_urls = ['https://julialang-s3.julialang.org/bin/linux/x64/%(version_major_minor)s/'] sources = ['%(namelower)s-%(version)s%(versionsuffix)s.tar.gz'] -checksums = ['c25ff71a4242207ab2681a0fcc5df50014e9d99f814e77cacbc5027e20514945'] +patches = [('julia.wrapper', 'bin/')] +checksums = [ + {'julia-1.6.6-linux-x86_64.tar.gz': 'c25ff71a4242207ab2681a0fcc5df50014e9d99f814e77cacbc5027e20514945'}, + {'julia.wrapper': 'd10aeaff53cca9875f7b0ce9218eae3bd21870b654e26c4c52aa8bfcc9da702d'}, +] + +# install wrapper with linking safeguards for Julia libraries +postinstallcmds = ["cd %(installdir)s/bin && mv julia julia.bin && mv julia.wrapper julia"] sanity_check_paths = { - 'files': ['bin/julia', 'include/julia/julia.h', 'lib/libjulia.%s' % SHLIB_EXT], - 'dirs': ['bin', 'etc', 'include', 'lib', 'share'] + 'files': ['bin/julia', 'bin/julia.bin', 'include/julia/julia.h', 'lib/libjulia.%s' % SHLIB_EXT], + 'dirs': ['bin', 'etc', 'include', 'lib', 'lib/julia', 'share'] } - sanity_check_commands = ['julia --help'] -modextravars = { - # Use default DEPOT_PATH where first entry is user's depot - # JULIA_DEPOT_PATH must be set to be able to load other JuliaPackage modules and have - # those installations appended to DEPOT_PATH without disabling any of the default paths - 'JULIA_DEPOT_PATH': ':', -} - moduleclass = 'lang' diff --git a/easybuild/easyconfigs/j/Julia/Julia-1.6.7-linux-x86_64.eb b/easybuild/easyconfigs/j/Julia/Julia-1.6.7-linux-x86_64.eb index f5d1446913f..7046809d33d 100644 --- a/easybuild/easyconfigs/j/Julia/Julia-1.6.7-linux-x86_64.eb +++ b/easybuild/easyconfigs/j/Julia/Julia-1.6.7-linux-x86_64.eb @@ -19,20 +19,19 @@ toolchain = SYSTEM source_urls = ['https://julialang-s3.julialang.org/bin/linux/x64/%(version_major_minor)s/'] sources = ['%(namelower)s-%(version)s%(versionsuffix)s.tar.gz'] -checksums = ['6c4522d595e4cbcd00157ac458a72f8aec01757053d2073f99daa39e442b2a36'] +patches = [('julia.wrapper', 'bin/')] +checksums = [ + {'julia-1.6.7-linux-x86_64.tar.gz': '6c4522d595e4cbcd00157ac458a72f8aec01757053d2073f99daa39e442b2a36'}, + {'julia.wrapper': 'd10aeaff53cca9875f7b0ce9218eae3bd21870b654e26c4c52aa8bfcc9da702d'}, +] + +# install wrapper with linking safeguards for Julia libraries +postinstallcmds = ["cd %(installdir)s/bin && mv julia julia.bin && mv julia.wrapper julia"] sanity_check_paths = { - 'files': ['bin/julia', 'include/julia/julia.h', 'lib/libjulia.%s' % SHLIB_EXT], - 'dirs': ['bin', 'etc', 'include', 'lib', 'share'] + 'files': ['bin/julia', 'bin/julia.bin', 'include/julia/julia.h', 'lib/libjulia.%s' % SHLIB_EXT], + 'dirs': ['bin', 'etc', 'include', 'lib', 'lib/julia', 'share'] } - sanity_check_commands = ['julia --help'] -modextravars = { - # Use default DEPOT_PATH where first entry is user's depot - # JULIA_DEPOT_PATH must be set to be able to load other JuliaPackage modules and have - # those installations appended to DEPOT_PATH without disabling any of the default paths - 'JULIA_DEPOT_PATH': ':', -} - moduleclass = 'lang' diff --git a/easybuild/easyconfigs/j/Julia/Julia-1.7.0-linux-x86_64.eb b/easybuild/easyconfigs/j/Julia/Julia-1.7.0-linux-x86_64.eb index ecc3020f4c0..39df361aa99 100644 --- a/easybuild/easyconfigs/j/Julia/Julia-1.7.0-linux-x86_64.eb +++ b/easybuild/easyconfigs/j/Julia/Julia-1.7.0-linux-x86_64.eb @@ -19,20 +19,19 @@ toolchain = SYSTEM source_urls = ['https://julialang-s3.julialang.org/bin/linux/x64/%(version_major_minor)s/'] sources = ['%(namelower)s-%(version)s%(versionsuffix)s.tar.gz'] -checksums = ['7299f3a638aec5e0b9e14eaf0e6221c4fe27189aa0b38ac5a36f03f0dc4c0d40'] +patches = [('julia.wrapper', 'bin/')] +checksums = [ + {'julia-1.7.0-linux-x86_64.tar.gz': '7299f3a638aec5e0b9e14eaf0e6221c4fe27189aa0b38ac5a36f03f0dc4c0d40'}, + {'julia.wrapper': 'd10aeaff53cca9875f7b0ce9218eae3bd21870b654e26c4c52aa8bfcc9da702d'}, +] + +# install wrapper with linking safeguards for Julia libraries +postinstallcmds = ["cd %(installdir)s/bin && mv julia julia.bin && mv julia.wrapper julia"] sanity_check_paths = { - 'files': ['bin/julia', 'include/julia/julia.h', 'lib/libjulia.%s' % SHLIB_EXT], - 'dirs': ['bin', 'etc', 'include', 'lib', 'share'] + 'files': ['bin/julia', 'bin/julia.bin', 'include/julia/julia.h', 'lib/libjulia.%s' % SHLIB_EXT], + 'dirs': ['bin', 'etc', 'include', 'lib', 'lib/julia', 'share'] } - sanity_check_commands = ['julia --help'] -modextravars = { - # Use default DEPOT_PATH where first entry is user's depot - # JULIA_DEPOT_PATH must be set to be able to load other JuliaPackage modules and have - # those installations appended to DEPOT_PATH without disabling any of the default paths - 'JULIA_DEPOT_PATH': ':', -} - moduleclass = 'lang' diff --git a/easybuild/easyconfigs/j/Julia/Julia-1.7.1-linux-x86_64.eb b/easybuild/easyconfigs/j/Julia/Julia-1.7.1-linux-x86_64.eb index b8b0a744c04..87f911a7da0 100644 --- a/easybuild/easyconfigs/j/Julia/Julia-1.7.1-linux-x86_64.eb +++ b/easybuild/easyconfigs/j/Julia/Julia-1.7.1-linux-x86_64.eb @@ -19,20 +19,19 @@ toolchain = SYSTEM source_urls = ['https://julialang-s3.julialang.org/bin/linux/x64/%(version_major_minor)s/'] sources = ['%(namelower)s-%(version)s%(versionsuffix)s.tar.gz'] -checksums = ['44658e9c7b45e2b9b5b59239d190cca42de05c175ea86bc346c294a8fe8d9f11'] +patches = [('julia.wrapper', 'bin/')] +checksums = [ + {'julia-1.7.1-linux-x86_64.tar.gz': '44658e9c7b45e2b9b5b59239d190cca42de05c175ea86bc346c294a8fe8d9f11'}, + {'julia.wrapper': 'd10aeaff53cca9875f7b0ce9218eae3bd21870b654e26c4c52aa8bfcc9da702d'}, +] + +# install wrapper with linking safeguards for Julia libraries +postinstallcmds = ["cd %(installdir)s/bin && mv julia julia.bin && mv julia.wrapper julia"] sanity_check_paths = { - 'files': ['bin/julia', 'include/julia/julia.h', 'lib/libjulia.%s' % SHLIB_EXT], - 'dirs': ['bin', 'etc', 'include', 'lib', 'share'] + 'files': ['bin/julia', 'bin/julia.bin', 'include/julia/julia.h', 'lib/libjulia.%s' % SHLIB_EXT], + 'dirs': ['bin', 'etc', 'include', 'lib', 'lib/julia', 'share'] } - sanity_check_commands = ['julia --help'] -modextravars = { - # Use default DEPOT_PATH where first entry is user's depot - # JULIA_DEPOT_PATH must be set to be able to load other JuliaPackage modules and have - # those installations appended to DEPOT_PATH without disabling any of the default paths - 'JULIA_DEPOT_PATH': ':', -} - moduleclass = 'lang' diff --git a/easybuild/easyconfigs/j/Julia/Julia-1.7.2-linux-x86_64.eb b/easybuild/easyconfigs/j/Julia/Julia-1.7.2-linux-x86_64.eb index e88e509e098..5e48ff39fbe 100644 --- a/easybuild/easyconfigs/j/Julia/Julia-1.7.2-linux-x86_64.eb +++ b/easybuild/easyconfigs/j/Julia/Julia-1.7.2-linux-x86_64.eb @@ -19,20 +19,19 @@ toolchain = SYSTEM source_urls = ['https://julialang-s3.julialang.org/bin/linux/x64/%(version_major_minor)s/'] sources = ['%(namelower)s-%(version)s%(versionsuffix)s.tar.gz'] -checksums = ['a75244724f3b2de0e7249c861fbf64078257c16fb4203be78f1cf4dd5973ba95'] +patches = [('julia.wrapper', 'bin/')] +checksums = [ + {'julia-1.7.2-linux-x86_64.tar.gz': 'a75244724f3b2de0e7249c861fbf64078257c16fb4203be78f1cf4dd5973ba95'}, + {'julia.wrapper': 'd10aeaff53cca9875f7b0ce9218eae3bd21870b654e26c4c52aa8bfcc9da702d'}, +] + +# install wrapper with linking safeguards for Julia libraries +postinstallcmds = ["cd %(installdir)s/bin && mv julia julia.bin && mv julia.wrapper julia"] sanity_check_paths = { - 'files': ['bin/julia', 'include/julia/julia.h', 'lib/libjulia.%s' % SHLIB_EXT], - 'dirs': ['bin', 'etc', 'include', 'lib', 'share'] + 'files': ['bin/julia', 'bin/julia.bin', 'include/julia/julia.h', 'lib/libjulia.%s' % SHLIB_EXT], + 'dirs': ['bin', 'etc', 'include', 'lib', 'lib/julia', 'share'] } - sanity_check_commands = ['julia --help'] -modextravars = { - # Use default DEPOT_PATH where first entry is user's depot - # JULIA_DEPOT_PATH must be set to be able to load other JuliaPackage modules and have - # those installations appended to DEPOT_PATH without disabling any of the default paths - 'JULIA_DEPOT_PATH': ':', -} - moduleclass = 'lang' diff --git a/easybuild/easyconfigs/j/Julia/Julia-1.7.3-linux-x86_64.eb b/easybuild/easyconfigs/j/Julia/Julia-1.7.3-linux-x86_64.eb index dac9088825a..0f1649345d9 100644 --- a/easybuild/easyconfigs/j/Julia/Julia-1.7.3-linux-x86_64.eb +++ b/easybuild/easyconfigs/j/Julia/Julia-1.7.3-linux-x86_64.eb @@ -19,20 +19,19 @@ toolchain = SYSTEM source_urls = ['https://julialang-s3.julialang.org/bin/linux/x64/%(version_major_minor)s/'] sources = ['%(namelower)s-%(version)s%(versionsuffix)s.tar.gz'] -checksums = ['9b2f4fa12d92b4dcc5d11dc66fb118c47681a76d3df8da064cc97573f2f5c739'] +patches = [('julia.wrapper', 'bin/')] +checksums = [ + {'julia-1.7.3-linux-x86_64.tar.gz': '9b2f4fa12d92b4dcc5d11dc66fb118c47681a76d3df8da064cc97573f2f5c739'}, + {'julia.wrapper': 'd10aeaff53cca9875f7b0ce9218eae3bd21870b654e26c4c52aa8bfcc9da702d'}, +] + +# install wrapper with linking safeguards for Julia libraries +postinstallcmds = ["cd %(installdir)s/bin && mv julia julia.bin && mv julia.wrapper julia"] sanity_check_paths = { - 'files': ['bin/julia', 'include/julia/julia.h', 'lib/libjulia.%s' % SHLIB_EXT], - 'dirs': ['bin', 'etc', 'include', 'lib', 'share'] + 'files': ['bin/julia', 'bin/julia.bin', 'include/julia/julia.h', 'lib/libjulia.%s' % SHLIB_EXT], + 'dirs': ['bin', 'etc', 'include', 'lib', 'lib/julia', 'share'] } - sanity_check_commands = ['julia --help'] -modextravars = { - # Use default DEPOT_PATH where first entry is user's depot - # JULIA_DEPOT_PATH must be set to be able to load other JuliaPackage modules and have - # those installations appended to DEPOT_PATH without disabling any of the default paths - 'JULIA_DEPOT_PATH': ':', -} - moduleclass = 'lang' diff --git a/easybuild/easyconfigs/j/Julia/Julia-1.8.0-linux-x86_64.eb b/easybuild/easyconfigs/j/Julia/Julia-1.8.0-linux-x86_64.eb index c7f6214e4a8..701b6bcbde7 100644 --- a/easybuild/easyconfigs/j/Julia/Julia-1.8.0-linux-x86_64.eb +++ b/easybuild/easyconfigs/j/Julia/Julia-1.8.0-linux-x86_64.eb @@ -19,20 +19,19 @@ toolchain = SYSTEM source_urls = ['https://julialang-s3.julialang.org/bin/linux/x64/%(version_major_minor)s/'] sources = ['%(namelower)s-%(version)s%(versionsuffix)s.tar.gz'] -checksums = ['e80d732ccb7f79e000d798cb8b656dc3641ab59516d6e4e52e16765017892a00'] +patches = [('julia.wrapper', 'bin/')] +checksums = [ + {'julia-1.8.0-linux-x86_64.tar.gz': 'e80d732ccb7f79e000d798cb8b656dc3641ab59516d6e4e52e16765017892a00'}, + {'julia.wrapper': 'd10aeaff53cca9875f7b0ce9218eae3bd21870b654e26c4c52aa8bfcc9da702d'}, +] + +# install wrapper with linking safeguards for Julia libraries +postinstallcmds = ["cd %(installdir)s/bin && mv julia julia.bin && mv julia.wrapper julia"] sanity_check_paths = { - 'files': ['bin/julia', 'include/julia/julia.h', 'lib/libjulia.%s' % SHLIB_EXT], - 'dirs': ['bin', 'etc', 'include', 'lib', 'share'] + 'files': ['bin/julia', 'bin/julia.bin', 'include/julia/julia.h', 'lib/libjulia.%s' % SHLIB_EXT], + 'dirs': ['bin', 'etc', 'include', 'lib', 'lib/julia', 'share'] } - sanity_check_commands = ['julia --help'] -modextravars = { - # Use default DEPOT_PATH where first entry is user's depot - # JULIA_DEPOT_PATH must be set to be able to load other JuliaPackage modules and have - # those installations appended to DEPOT_PATH without disabling any of the default paths - 'JULIA_DEPOT_PATH': ':', -} - moduleclass = 'lang' diff --git a/easybuild/easyconfigs/j/Julia/Julia-1.8.2-linux-x86_64.eb b/easybuild/easyconfigs/j/Julia/Julia-1.8.2-linux-x86_64.eb index 37b817f557e..c85c5bdc291 100644 --- a/easybuild/easyconfigs/j/Julia/Julia-1.8.2-linux-x86_64.eb +++ b/easybuild/easyconfigs/j/Julia/Julia-1.8.2-linux-x86_64.eb @@ -19,20 +19,19 @@ toolchain = SYSTEM source_urls = ['https://julialang-s3.julialang.org/bin/linux/x64/%(version_major_minor)s/'] sources = ['%(namelower)s-%(version)s%(versionsuffix)s.tar.gz'] -checksums = ['671cf3a450b63a717e1eedd7f69087e3856f015b2e146cb54928f19a3c05e796'] +patches = [('julia.wrapper', 'bin/')] +checksums = [ + {'julia-1.8.2-linux-x86_64.tar.gz': '671cf3a450b63a717e1eedd7f69087e3856f015b2e146cb54928f19a3c05e796'}, + {'julia.wrapper': 'd10aeaff53cca9875f7b0ce9218eae3bd21870b654e26c4c52aa8bfcc9da702d'}, +] + +# install wrapper with linking safeguards for Julia libraries +postinstallcmds = ["cd %(installdir)s/bin && mv julia julia.bin && mv julia.wrapper julia"] sanity_check_paths = { - 'files': ['bin/julia', 'include/julia/julia.h', 'lib/libjulia.%s' % SHLIB_EXT], - 'dirs': ['bin', 'etc', 'include', 'lib', 'share'] + 'files': ['bin/julia', 'bin/julia.bin', 'include/julia/julia.h', 'lib/libjulia.%s' % SHLIB_EXT], + 'dirs': ['bin', 'etc', 'include', 'lib', 'lib/julia', 'share'] } - sanity_check_commands = ['julia --help'] -modextravars = { - # Use default DEPOT_PATH where first entry is user's depot - # JULIA_DEPOT_PATH must be set to be able to load other JuliaPackage modules and have - # those installations appended to DEPOT_PATH without disabling any of the default paths - 'JULIA_DEPOT_PATH': ':', -} - moduleclass = 'lang' diff --git a/easybuild/easyconfigs/j/Julia/Julia-1.8.5-linux-x86_64.eb b/easybuild/easyconfigs/j/Julia/Julia-1.8.5-linux-x86_64.eb index 1d5fa47c96c..6e60397495d 100644 --- a/easybuild/easyconfigs/j/Julia/Julia-1.8.5-linux-x86_64.eb +++ b/easybuild/easyconfigs/j/Julia/Julia-1.8.5-linux-x86_64.eb @@ -19,20 +19,19 @@ toolchain = SYSTEM source_urls = ['https://julialang-s3.julialang.org/bin/linux/x64/%(version_major_minor)s/'] sources = ['%(namelower)s-%(version)s%(versionsuffix)s.tar.gz'] -checksums = ['e71a24816e8fe9d5f4807664cbbb42738f5aa9fe05397d35c81d4c5d649b9d05'] +patches = [('julia.wrapper', 'bin/')] +checksums = [ + {'julia-1.8.5-linux-x86_64.tar.gz': 'e71a24816e8fe9d5f4807664cbbb42738f5aa9fe05397d35c81d4c5d649b9d05'}, + {'julia.wrapper': 'd10aeaff53cca9875f7b0ce9218eae3bd21870b654e26c4c52aa8bfcc9da702d'}, +] + +postinstallcmds = ["cd %(installdir)s/bin && mv julia julia.bin && mv julia.wrapper julia"] sanity_check_paths = { - 'files': ['bin/julia', 'include/julia/julia.h', 'lib/libjulia.%s' % SHLIB_EXT], - 'dirs': ['bin', 'etc', 'include', 'lib', 'share'] + 'files': ['bin/julia', 'bin/julia.bin', 'include/julia/julia.h', 'lib/libjulia.%s' % SHLIB_EXT], + 'dirs': ['bin', 'etc', 'include', 'lib', 'lib/julia', 'share'] } sanity_check_commands = ['julia --help'] -modextravars = { - # Use default DEPOT_PATH where first entry is user's depot - # JULIA_DEPOT_PATH must be set to be able to load other JuliaPackage modules and have - # those installations appended to DEPOT_PATH without disabling any of the default paths - 'JULIA_DEPOT_PATH': ':', -} - moduleclass = 'lang' diff --git a/easybuild/easyconfigs/j/Julia/Julia-1.9.0-linux-x86_64.eb b/easybuild/easyconfigs/j/Julia/Julia-1.9.0-linux-x86_64.eb index 2ee4230cbb9..2e89fb8640b 100644 --- a/easybuild/easyconfigs/j/Julia/Julia-1.9.0-linux-x86_64.eb +++ b/easybuild/easyconfigs/j/Julia/Julia-1.9.0-linux-x86_64.eb @@ -19,20 +19,19 @@ toolchain = SYSTEM source_urls = ['https://julialang-s3.julialang.org/bin/linux/x64/%(version_major_minor)s/'] sources = ['%(namelower)s-%(version)s%(versionsuffix)s.tar.gz'] -checksums = ['00c614466ef9809c2eb23480e38d196a2c577fff2730c4f83d135b913d473359'] +patches = [('julia.wrapper', 'bin/')] +checksums = [ + {'julia-1.9.0-linux-x86_64.tar.gz': '00c614466ef9809c2eb23480e38d196a2c577fff2730c4f83d135b913d473359'}, + {'julia.wrapper': 'd10aeaff53cca9875f7b0ce9218eae3bd21870b654e26c4c52aa8bfcc9da702d'}, +] + +# install wrapper with linking safeguards for Julia libraries +postinstallcmds = ["cd %(installdir)s/bin && mv julia julia.bin && mv julia.wrapper julia"] sanity_check_paths = { - 'files': ['bin/julia', 'include/julia/julia.h', 'lib/libjulia.%s' % SHLIB_EXT], - 'dirs': ['bin', 'etc', 'include', 'lib', 'share'] + 'files': ['bin/julia', 'bin/julia.bin', 'include/julia/julia.h', 'lib/libjulia.%s' % SHLIB_EXT], + 'dirs': ['bin', 'etc', 'include', 'lib', 'lib/julia', 'share'] } - sanity_check_commands = ['julia --help'] -modextravars = { - # Use default DEPOT_PATH where first entry is user's depot - # JULIA_DEPOT_PATH must be set to be able to load other JuliaPackage modules and have - # those installations appended to DEPOT_PATH without disabling any of the default paths - 'JULIA_DEPOT_PATH': ':', -} - moduleclass = 'lang' diff --git a/easybuild/easyconfigs/j/Julia/Julia-1.9.2-linux-x86_64.eb b/easybuild/easyconfigs/j/Julia/Julia-1.9.2-linux-x86_64.eb index a0d92b7aacb..fef2c5a347c 100644 --- a/easybuild/easyconfigs/j/Julia/Julia-1.9.2-linux-x86_64.eb +++ b/easybuild/easyconfigs/j/Julia/Julia-1.9.2-linux-x86_64.eb @@ -19,20 +19,19 @@ toolchain = SYSTEM source_urls = ['https://julialang-s3.julialang.org/bin/linux/x64/%(version_major_minor)s/'] sources = ['%(namelower)s-%(version)s%(versionsuffix)s.tar.gz'] -checksums = ['4c2d799f442d7fe718827b19da2bacb72ea041b9ce55f24eee7b1313f57c4383'] +patches = [('julia.wrapper', 'bin/')] +checksums = [ + {'julia-1.9.2-linux-x86_64.tar.gz': '4c2d799f442d7fe718827b19da2bacb72ea041b9ce55f24eee7b1313f57c4383'}, + {'julia.wrapper': 'd10aeaff53cca9875f7b0ce9218eae3bd21870b654e26c4c52aa8bfcc9da702d'}, +] + +postinstallcmds = ["cd %(installdir)s/bin && mv julia julia.bin && mv julia.wrapper julia"] sanity_check_paths = { - 'files': ['bin/julia', 'include/julia/julia.h', 'lib/libjulia.%s' % SHLIB_EXT], - 'dirs': ['bin', 'etc', 'include', 'lib', 'share'] + 'files': ['bin/julia', 'bin/julia.bin', 'include/julia/julia.h', 'lib/libjulia.%s' % SHLIB_EXT], + 'dirs': ['bin', 'etc', 'include', 'lib', 'lib/julia', 'share'] } sanity_check_commands = ['julia --help'] -modextravars = { - # Use default DEPOT_PATH where first entry is user's depot - # JULIA_DEPOT_PATH must be set to be able to load other JuliaPackage modules and have - # those installations appended to DEPOT_PATH without disabling any of the default paths - 'JULIA_DEPOT_PATH': ':', -} - moduleclass = 'lang' diff --git a/easybuild/easyconfigs/j/Julia/Julia-1.9.3-linux-x86_64.eb b/easybuild/easyconfigs/j/Julia/Julia-1.9.3-linux-x86_64.eb index 7b207dc635c..1d0f85d9874 100644 --- a/easybuild/easyconfigs/j/Julia/Julia-1.9.3-linux-x86_64.eb +++ b/easybuild/easyconfigs/j/Julia/Julia-1.9.3-linux-x86_64.eb @@ -19,20 +19,19 @@ toolchain = SYSTEM source_urls = ['https://julialang-s3.julialang.org/bin/linux/x64/%(version_major_minor)s/'] sources = ['%(namelower)s-%(version)s%(versionsuffix)s.tar.gz'] -checksums = ['d76670cc9ba3e0fd4c1545dd3d00269c0694976a1176312795ebce1692d323d1'] +patches = [('julia.wrapper', 'bin/')] +checksums = [ + {'julia-1.9.3-linux-x86_64.tar.gz': 'd76670cc9ba3e0fd4c1545dd3d00269c0694976a1176312795ebce1692d323d1'}, + {'julia.wrapper': 'd10aeaff53cca9875f7b0ce9218eae3bd21870b654e26c4c52aa8bfcc9da702d'}, +] + +# install wrapper with linking safeguards for Julia libraries +postinstallcmds = ["cd %(installdir)s/bin && mv julia julia.bin && mv julia.wrapper julia"] sanity_check_paths = { - 'files': ['bin/julia', 'include/julia/julia.h', 'lib/libjulia.%s' % SHLIB_EXT], - 'dirs': ['bin', 'etc', 'include', 'lib', 'share'] + 'files': ['bin/julia', 'bin/julia.bin', 'include/julia/julia.h', 'lib/libjulia.%s' % SHLIB_EXT], + 'dirs': ['bin', 'etc', 'include', 'lib', 'lib/julia', 'share'] } - sanity_check_commands = ['julia --help'] -modextravars = { - # Use default DEPOT_PATH where first entry is user's depot - # JULIA_DEPOT_PATH must be set to be able to load other JuliaPackage modules and have - # those installations appended to DEPOT_PATH without disabling any of the default paths - 'JULIA_DEPOT_PATH': ':', -} - moduleclass = 'lang' diff --git a/easybuild/easyconfigs/j/Julia/julia.wrapper b/easybuild/easyconfigs/j/Julia/julia.wrapper new file mode 100755 index 00000000000..613b8a831f1 --- /dev/null +++ b/easybuild/easyconfigs/j/Julia/julia.wrapper @@ -0,0 +1,2 @@ +#!/bin/sh +LD_LIBRARY_PATH="$EBROOTJULIA/lib:$EBROOTJULIA/lib/julia:$LD_LIBRARY_PATH" julia.bin "$@" diff --git a/easybuild/easyconfigs/j/Jupyter-bundle/Jupyter-bundle-20240522-GCCcore-13.2.0.eb b/easybuild/easyconfigs/j/Jupyter-bundle/Jupyter-bundle-20240522-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..e58d22ce229 --- /dev/null +++ b/easybuild/easyconfigs/j/Jupyter-bundle/Jupyter-bundle-20240522-GCCcore-13.2.0.eb @@ -0,0 +1,26 @@ +easyblock = 'Bundle' + +name = 'Jupyter-bundle' +version = '20240522' + +homepage = "https://jupyter.org/" + +description = """ + This bundle collects a range of Jupyter interfaces (Lab, Notebook and nbclassic), + extensions (Jupyter Server Proxy, Jupyter Resource Monitor, Jupyter Lmod) and + the JupyterHub. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +dependencies = [ + ('JupyterHub', '4.1.5'), + ('JupyterLab', '4.2.0'), + ('JupyterNotebook', '7.2.0'), + ('nbclassic', '1.0.0'), + ('jupyter-server-proxy', '4.1.2'), + ('jupyterlmod', '5.2.1'), + ('jupyter-resource-usage', '1.0.2'), +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/j/JupyterHub/JupyterHub-4.1.5-GCCcore-13.2.0.eb b/easybuild/easyconfigs/j/JupyterHub/JupyterHub-4.1.5-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..76751fb0f5f --- /dev/null +++ b/easybuild/easyconfigs/j/JupyterHub/JupyterHub-4.1.5-GCCcore-13.2.0.eb @@ -0,0 +1,109 @@ +easyblock = 'PythonBundle' + +name = 'JupyterHub' +version = '4.1.5' + +homepage = 'https://jupyter.org' +description = """JupyterHub is a multiuser version of the Jupyter (IPython) notebook designed + for centralized deployments in companies, university classrooms and research labs.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +builddependencies = [ + ('binutils', '2.40'), +] +dependencies = [ + ('Python', '3.11.5'), + ('IPython', '8.17.2'), + ('bcrypt', '4.1.3'), + ('configurable-http-proxy', '4.6.1'), + ('OpenSSL', '1.1', '', SYSTEM), + ('tornado', '6.4'), + ('PycURL', '7.45.3'), # optional, recommended with large number of users + ('SQLAlchemy', '2.0.29'), +] + +sanity_pip_check = True +use_pip = True + +exts_list = [ + ('certipy', '0.1.3', { + 'checksums': ['695704b7716b033375c9a1324d0d30f27110a28895c40151a90ec07ff1032859'], + }), + ('pamela', '1.1.0', { + 'checksums': ['d4b139fe600e192e176a2a368059207a6bffa0e7879879b13f4fcba0163481be'], + }), + ('async_generator', '1.10', { + 'checksums': ['6ebb3d106c12920aaae42ccb6f787ef5eefdcdd166ea3d628fa8476abe712144'], + }), + ('oauthlib', '3.2.2', { + 'checksums': ['9859c40929662bec5d64f34d01c99e093149682a3f38915dc0655d5a633dd918'], + }), + ('pyOpenSSL', '24.1.0', { + 'modulename': 'OpenSSL', + 'checksums': ['cabed4bfaa5df9f1a16c0ef64a0cb65318b5cd077a7eda7d6970131ca2f41a6f'], + }), + ('ruamel.yaml', '0.18.6', { + 'checksums': ['8b27e6a217e786c6fbe5634d8f3f11bc63e0f80f6a5890f28863d9c45aac311b'], + }), + ('ruamel.yaml.clib', '0.2.8', { + 'modulename': False, + 'checksums': ['beb2e0404003de9a4cab9753a8805a8fe9320ee6673136ed7f04255fe60bb512'], + }), + ('python-json-logger', '2.0.7', { + 'modulename': 'pythonjsonlogger', + 'checksums': ['23e7ec02d34237c5aa1e29a070193a4ea87583bb4e7f8fd06d3de8264c4b2e1c'], + }), + ('jupyter-telemetry', '0.1.0', { + 'source_tmpl': 'jupyter_telemetry-%(version)s.tar.gz', + 'checksums': ['445c613ae3df70d255fe3de202f936bba8b77b4055c43207edf22468ac875314'], + }), + ('prometheus_client', '0.20.0', { + 'checksums': ['287629d00b147a32dcb2be0b9df905da599b2d82f80377083ec8463309a4bb89'], + }), + ('jupyterhub', version, { + 'checksums': ['63ba1fc718436c151946a58a3b403ec4fe8b3f624fb195bc1d8e70c39b33e194'], + }), + ('batchspawner', '1.3.0', { + 'checksums': ['c0f422eb6a6288f7f711db8b780055b37c1a5c630283cdeb2ef9b5e94ba78caa'], + }), + ('jupyterhub-systemdspawner', '1.0.1', { + 'modulename': 'systemdspawner', + 'checksums': ['8d614f19d89564321fe55d80ecd134a0e2bf276274d45861495c9bb5a80add28'], + }), + ('jupyterhub-simplespawner', '0.1', { + 'modulename': 'simplespawner', + 'checksums': ['5fcc295b310dd7a99c0f00226be311121fd99b36a5d127e8685f3ffa29712d0d'], + }), + ('ldap3', '2.9.1', { + 'checksums': ['f3e7fc4718e3f09dda568b57100095e0ce58633bcabbed8667ce3f8fbaa4229f'], + }), + ('jupyterhub-ldapauthenticator', '1.3.2', { + 'modulename': 'ldapauthenticator', + 'checksums': ['758081bbdb28b26313bb18c9d8aa2b8fcdc9162e4d3ab196c626567e64f1ab8b'], + }), + ('PyJWT', '2.8.0', { + 'modulename': 'jwt', + 'checksums': ['57e28d156e3d5c10088e0c68abb90bfac3df82b40a71bd0daa20c65ccd5c23de'], + }), + ('jupyterhub-jwtauthenticator-v2', '2.0.3', { + 'modulename': 'jwtauthenticator', + 'checksums': ['b94b6dff8246250904c5ee511da3f062680eb657dabe766d75993cbe72747d41'], + }), + ('onetimepass', '1.0.1', { + 'checksums': ['a569dac076d6e3761cbc55e36952144a637ca1b075c6d509de1c1dbc5e7f6a27'], + }), + ('jupyterhub-nativeauthenticator', '1.2.0', { + 'modulename': 'nativeauthenticator', + 'checksums': ['826228e6e9ca37736361e2e60c5723e245ec72e34fdc42cc218fc54a67f968e1'], + }), +] + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(namelower)s'], +} + +sanity_check_commands = ['%(namelower)s --help'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/j/JupyterLab/JupyterLab-4.2.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/j/JupyterLab/JupyterLab-4.2.0-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..8410c3f15b8 --- /dev/null +++ b/easybuild/easyconfigs/j/JupyterLab/JupyterLab-4.2.0-GCCcore-13.2.0.eb @@ -0,0 +1,78 @@ +easyblock = 'PythonBundle' + +name = 'JupyterLab' +version = '4.2.0' + +homepage = 'https://jupyter.org/' +description = """JupyterLab is the next-generation user interface for Project Jupyter offering all the familiar + building blocks of the classic Jupyter Notebook (notebook, terminal, text editor, file browser, rich outputs, + etc.) in a flexible and powerful user interface. JupyterLab will eventually replace the classic Jupyter + Notebook.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +builddependencies = [ + ('binutils', '2.40'), + ('hatch-jupyter-builder', '0.9.1'), +] +dependencies = [ + ('Python', '3.11.5'), + ('IPython', '8.17.2'), + ('jupyter-server', '2.14.0'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('json5', '0.9.25', { + 'checksums': ['548e41b9be043f9426776f05df8635a00fe06104ea51ed24b67f908856e151ae'], + }), + ('jupyterlab_server', '2.27.1', { + 'checksums': ['097b5ac709b676c7284ac9c5e373f11930a561f52cd5a86e4fc7e5a9c8a8631d'], + }), + ('jupyter-lsp', '2.2.5', { + 'checksums': ['793147a05ad446f809fd53ef1cd19a9f5256fd0a2d6b7ce943a982cb4f545001'], + }), + ('async-lru', '2.0.4', { + 'checksums': ['b8a59a5df60805ff63220b2a0c5b5393da5521b113cd5465a44eb037d81a5627'], + }), + ('h11', '0.14.0', { + 'checksums': ['8f19fbbe99e72420ff35c00b27a34cb9937e902a8b810e2c88300c6f0a3b699d'], + }), + ('httpcore', '1.0.5', { + 'checksums': ['34a38e2f9291467ee3b44e89dd52615370e152954ba21721378a87b2960f7a61'], + }), + ('httpx', '0.27.0', { + 'checksums': ['a0cb88a46f32dc874e04ee956e4c2764aba2aa228f650b06788ba6bda2962ab5'], + }), + ('jupyterlab', version, { + 'checksums': ['356e9205a6a2ab689c47c8fe4919dba6c076e376d03f26baadc05748c2435dd5'], + }), +] + +sanity_check_paths = { + 'files': ['bin/jupyter-lab', 'bin/jupyter-labextension', 'bin/jupyter-labhub'], + 'dirs': ['etc/jupyter', 'share/jupyter'], +} + +sanity_check_commands = ['jupyter lab --help'] + +modextrapaths = {'EB_ENV_JUPYTER_ROOT': ''} +modextravars = { + # only one path allowed as JUPYTERLAB_DIR + 'JUPYTERLAB_DIR': '%(installdir)s/share/jupyter/lab', +} + +# keep user's configuration in their home directory +# note: '~' is not expanded by JupyterLab +modluafooter = """ +setenv("JUPYTERLAB_SETTINGS_DIR", pathJoin(os.getenv("HOME"), ".jupyter", "lab", "user-settings")) +setenv("JUPYTERLAB_WORKSPACES_DIR", pathJoin(os.getenv("HOME"), ".jupyter", "lab", "workspaces")) +""" +modtclfooter = """ +setenv JUPYTERLAB_SETTINGS_DIR "$::env(HOME)/.jupyter/lab/user-settings" +setenv JUPYTERLAB_WORKSPACES_DIR "$::env(HOME)/.jupyter/lab/workspaces" +""" + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/j/JupyterLab/JupyterLab-4.2.5-GCCcore-13.3.0.eb b/easybuild/easyconfigs/j/JupyterLab/JupyterLab-4.2.5-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..abe825dfa69 --- /dev/null +++ b/easybuild/easyconfigs/j/JupyterLab/JupyterLab-4.2.5-GCCcore-13.3.0.eb @@ -0,0 +1,78 @@ +easyblock = 'PythonBundle' + +name = 'JupyterLab' +version = '4.2.5' + +homepage = 'https://jupyter.org/' +description = """JupyterLab is the next-generation user interface for Project Jupyter offering all the familiar + building blocks of the classic Jupyter Notebook (notebook, terminal, text editor, file browser, rich outputs, + etc.) in a flexible and powerful user interface. JupyterLab will eventually replace the classic Jupyter + Notebook.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +builddependencies = [ + ('binutils', '2.42'), + ('hatch-jupyter-builder', '0.9.1'), +] +dependencies = [ + ('Python', '3.12.3'), + ('IPython', '8.28.0'), + ('jupyter-server', '2.14.2'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('json5', '0.9.25', { + 'checksums': ['548e41b9be043f9426776f05df8635a00fe06104ea51ed24b67f908856e151ae'], + }), + ('jupyterlab_server', '2.27.3', { + 'checksums': ['eb36caca59e74471988f0ae25c77945610b887f777255aa21f8065def9e51ed4'], + }), + ('jupyter-lsp', '2.2.5', { + 'checksums': ['793147a05ad446f809fd53ef1cd19a9f5256fd0a2d6b7ce943a982cb4f545001'], + }), + ('async-lru', '2.0.4', { + 'checksums': ['b8a59a5df60805ff63220b2a0c5b5393da5521b113cd5465a44eb037d81a5627'], + }), + ('h11', '0.14.0', { + 'checksums': ['8f19fbbe99e72420ff35c00b27a34cb9937e902a8b810e2c88300c6f0a3b699d'], + }), + ('httpcore', '1.0.6', { + 'checksums': ['73f6dbd6eb8c21bbf7ef8efad555481853f5f6acdeaff1edb0694289269ee17f'], + }), + ('httpx', '0.27.2', { + 'checksums': ['f7c2be1d2f3c3c3160d441802406b206c2b76f5947b11115e6df10c6c65e66c2'], + }), + ('jupyterlab', version, { + 'checksums': ['ae7f3a1b8cb88b4f55009ce79fa7c06f99d70cd63601ee4aa91815d054f46f75'], + }), +] + +sanity_check_paths = { + 'files': ['bin/jupyter-lab', 'bin/jupyter-labextension', 'bin/jupyter-labhub'], + 'dirs': ['etc/jupyter', 'share/jupyter'], +} + +sanity_check_commands = ['jupyter lab --help'] + +modextrapaths = {'EB_ENV_JUPYTER_ROOT': ''} +modextravars = { + # only one path allowed as JUPYTERLAB_DIR + 'JUPYTERLAB_DIR': '%(installdir)s/share/jupyter/lab', +} + +# keep user's configuration in their home directory +# note: '~' is not expanded by JupyterLab +modluafooter = """ +setenv("JUPYTERLAB_SETTINGS_DIR", pathJoin(os.getenv("HOME"), ".jupyter", "lab", "user-settings")) +setenv("JUPYTERLAB_WORKSPACES_DIR", pathJoin(os.getenv("HOME"), ".jupyter", "lab", "workspaces")) +""" +modtclfooter = """ +setenv JUPYTERLAB_SETTINGS_DIR "$::env(HOME)/.jupyter/lab/user-settings" +setenv JUPYTERLAB_WORKSPACES_DIR "$::env(HOME)/.jupyter/lab/workspaces" +""" + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/j/JupyterNotebook/JupyterNotebook-7.2.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/j/JupyterNotebook/JupyterNotebook-7.2.0-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..a391a9329e2 --- /dev/null +++ b/easybuild/easyconfigs/j/JupyterNotebook/JupyterNotebook-7.2.0-GCCcore-13.2.0.eb @@ -0,0 +1,42 @@ +easyblock = 'PythonPackage' + +name = 'JupyterNotebook' +version = '7.2.0' + +homepage = 'https://jupyter.org/' +description = """The Jupyter Notebook is the original web application for creating and + sharing computational documents. It offers a simple, streamlined, document-centric experience.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://pypi.python.org/packages/source/n/notebook'] +sources = ['notebook-%(version)s.tar.gz'] +checksums = ['34a2ba4b08ad5d19ec930db7484fb79746a1784be9e1a5f8218f9af8656a141f'] + +builddependencies = [ + ('binutils', '2.40'), + ('hatch-jupyter-builder', '0.9.1'), +] +dependencies = [ + ('Python', '3.11.5'), + ('IPython', '8.17.2'), + ('jupyter-server', '2.14.0'), + ('JupyterLab', '4.2.0'), +] + +download_dep_fail = True +sanity_pip_check = True +use_pip = True + +options = {'modulename': 'notebook'} + +sanity_check_paths = { + 'files': ['bin/jupyter-notebook'], + 'dirs': ['etc/jupyter', 'share/jupyter'], +} + +sanity_check_commands = ['jupyter notebook --help'] + +modextrapaths = {'EB_ENV_JUPYTER_ROOT': ''} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/j/jax/jax-0.4.25-gfbf-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/j/jax/jax-0.4.25-gfbf-2023a-CUDA-12.1.1.eb new file mode 100644 index 00000000000..75355c6c842 --- /dev/null +++ b/easybuild/easyconfigs/j/jax/jax-0.4.25-gfbf-2023a-CUDA-12.1.1.eb @@ -0,0 +1,135 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +# Updated by: Alex Domingo (Vrije Universiteit Brussel) +# Updated by: Pavel Tománek (INUITS) +# Updated by: Thomas Hoffmann (EMBL Heidelberg) +easyblock = 'PythonBundle' + +name = 'jax' +version = '0.4.25' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://jax.readthedocs.io/' +description = """Composable transformations of Python+NumPy programs: +differentiate, vectorize, JIT to GPU/TPU, and more""" + +toolchain = {'name': 'gfbf', 'version': '2023a'} +cuda_compute_capabilities = ["5.0", "6.0", "6.1", "7.0", "7.5", "8.0", "8.6", "9.0"] + +builddependencies = [ + ('Bazel', '6.3.1'), + ('pytest-xdist', '3.3.1'), + ('git', '2.41.0', '-nodocs'), # bazel uses git to fetch repositories + ('matplotlib', '3.7.2'), # required for tests/lobpcg_test.py + ('poetry', '1.5.1'), + ('pybind11', '2.11.1'), +] + +dependencies = [ + ('CUDA', '12.1.1', '', SYSTEM), + ('cuDNN', '8.9.2.26', versionsuffix, SYSTEM), + ('NCCL', '2.18.3', versionsuffix), + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('absl-py', '2.1.0'), + ('flatbuffers-python', '23.5.26'), + ('ml_dtypes', '0.3.2'), + ('zlib', '1.2.13'), +] + +# downloading xla and other tarballs to avoid that Bazel downloads it during the build +local_extract_cmd = 'mkdir -p %(builddir)s/archives && cp %s %(builddir)s/archives' +# note: following commits *must* be the exact same onces used upstream +# XLA_COMMIT from jax-jaxlib: third_party/xla/workspace.bzl +local_xla_commit = '4ccfe33c71665ddcbca5b127fefe8baa3ed632d4' +# TFRT_COMMIT from xla: third_party/tsl/third_party/tf_runtime/workspace.bzl +local_tfrt_commit = '0aeefb1660d7e37964b2bb71b1f518096bda9a25' + +# Use sources downloaded by EasyBuild +_jaxlib_buildopts = '--bazel_options="--distdir=%(builddir)s/archives" ' +# Use dependencies from EasyBuild +_jaxlib_buildopts += '--bazel_options="--action_env=TF_SYSTEM_LIBS=pybind11" ' +_jaxlib_buildopts += '--bazel_options="--action_env=CPATH=$EBROOTPYBIND11/include" ' +# Avoid warning (treated as error) in upb/table.c +_jaxlib_buildopts += '--bazel_options="--copt=-Wno-maybe-uninitialized" ' + +components = [ + ('jaxlib', version, { + 'sources': [ + { + 'source_urls': ['https://github.com/google/jax/archive/'], + 'filename': '%(name)s-v%(version)s.tar.gz', + }, + { + 'source_urls': ['https://github.com/openxla/xla/archive'], + 'download_filename': '%s.tar.gz' % local_xla_commit, + 'filename': 'xla-%s.tar.gz' % local_xla_commit[:8], + 'extract_cmd': local_extract_cmd, + }, + { + 'source_urls': ['https://github.com/tensorflow/runtime/archive'], + 'download_filename': '%s.tar.gz' % local_tfrt_commit, + 'filename': 'tf_runtime-%s.tar.gz' % local_tfrt_commit[:8], + 'extract_cmd': local_extract_cmd, + }, + ], + 'patches': ['jax-0.4.25_fix-pybind11-systemlib.patch'], + 'checksums': [ + {'jaxlib-v0.4.25.tar.gz': + 'fc1197c401924942eb14185a61688d0c476e3e81ff71f9dc95e620b57c06eec8'}, + {'xla-4ccfe33c.tar.gz': + '8a59b9af7d0850059d7043f7043c780066d61538f3af536e8a10d3d717f35089'}, + {'tf_runtime-0aeefb16.tar.gz': + 'a3df827d7896774cb1d80bf4e1c79ab05c268f29bd4d3db1fb5a4b9c2079d8e3'}, + {'jax-0.4.25_fix-pybind11-systemlib.patch': + 'daad5b726d1a138431b05eb60ecf4c89c7b5148eb939721800bdf43d804ca033'}, + ], + 'start_dir': 'jax-jaxlib-v%(version)s', + 'buildopts': _jaxlib_buildopts + }), +] + +# Some tests require an isolated run: +local_isolated_tests = [ + 'tests/host_callback_test.py::HostCallbackTapTest::test_tap_scan_custom_jvp', + 'tests/host_callback_test.py::HostCallbackTapTest::test_tap_transforms_doc', + 'tests/lax_scipy_special_functions_test.py::LaxScipySpcialFunctionsTest' + + '::testScipySpecialFun_gammainc_s_2x1x4_float32_float32', +] +# deliberately not testing in parallel, as that results in (additional) failing tests; +# use XLA_PYTHON_CLIENT_ALLOCATOR=platform to allocate and deallocate GPU memory during testing, +# see https://github.com/google/jax/issues/7323 and +# https://github.com/google/jax/blob/main/docs/gpu_memory_allocation.rst; +# use CUDA_VISIBLE_DEVICES=0 to avoid failing tests on systems with multiple GPUs; +# use NVIDIA_TF32_OVERRIDE=0 to avoid loosing numerical precision by disabling TF32 Tensor Cores; +local_test_exports = [ + "NVIDIA_TF32_OVERRIDE=0", + "CUDA_VISIBLE_DEVICES=0", + "XLA_PYTHON_CLIENT_ALLOCATOR=platform", + "JAX_ENABLE_X64=true", +] +local_test = ''.join(['export %s;' % x for x in local_test_exports]) +# run all tests at once except for local_isolated_tests: +local_test += "pytest -vv tests %s && " % ' '.join(['--deselect %s' % x for x in local_isolated_tests]) +# run remaining local_isolated_tests separately: +local_test += ' && '.join(['pytest -vv %s' % x for x in local_isolated_tests]) + +use_pip = True + +exts_list = [ + (name, version, { + 'source_tmpl': '%(name)s-v%(version)s.tar.gz', + 'source_urls': ['https://github.com/google/jax/archive/'], + 'patches': ['jax-0.4.25_fix_env_test_no_log_spam.patch'], + 'checksums': [ + {'jax-v0.4.25.tar.gz': '8b30af49688c0c13b82c6f5ce992727c00b5fc6d04a4c6962012f4246fa664eb'}, + {'jax-0.4.25_fix_env_test_no_log_spam.patch': + 'a18b5f147569d9ad41025124333a0f04fd0d0e0f9e4309658d7f6b9b838e2e2a'}, + ], + 'runtest': local_test, + }), +] + +sanity_pip_check = True + +moduleclass = 'ai' diff --git a/easybuild/easyconfigs/j/jax/jax-0.4.25-gfbf-2023a.eb b/easybuild/easyconfigs/j/jax/jax-0.4.25-gfbf-2023a.eb new file mode 100644 index 00000000000..a4a86382ad6 --- /dev/null +++ b/easybuild/easyconfigs/j/jax/jax-0.4.25-gfbf-2023a.eb @@ -0,0 +1,109 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +# Updated by: Alex Domingo (Vrije Universiteit Brussel) +# Updated by: Pavel Tománek (INUITS) +# Updated by: Thomas Hoffmann (EMBL Heidelberg) +easyblock = 'PythonBundle' + +name = 'jax' +version = '0.4.25' + +homepage = 'https://jax.readthedocs.io/' +description = """Composable transformations of Python+NumPy programs: +differentiate, vectorize, JIT to GPU/TPU, and more""" + +toolchain = {'name': 'gfbf', 'version': '2023a'} + +builddependencies = [ + ('Bazel', '6.3.1'), + ('pytest-xdist', '3.3.1'), + ('git', '2.41.0', '-nodocs'), # bazel uses git to fetch repositories + ('matplotlib', '3.7.2'), # required for tests/lobpcg_test.py + ('poetry', '1.5.1'), + ('pybind11', '2.11.1'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('absl-py', '2.1.0'), + ('flatbuffers-python', '23.5.26'), + ('ml_dtypes', '0.3.2'), + ('zlib', '1.2.13'), +] + +# downloading xla and other tarballs to avoid that Bazel downloads it during the build +local_extract_cmd = 'mkdir -p %(builddir)s/archives && cp %s %(builddir)s/archives' +# note: following commits *must* be the exact same onces used upstream +# XLA_COMMIT from jax-jaxlib: third_party/xla/workspace.bzl +local_xla_commit = '4ccfe33c71665ddcbca5b127fefe8baa3ed632d4' +# TFRT_COMMIT from xla: third_party/tsl/third_party/tf_runtime/workspace.bzl +local_tfrt_commit = '0aeefb1660d7e37964b2bb71b1f518096bda9a25' + +# Use sources downloaded by EasyBuild +_jaxlib_buildopts = '--bazel_options="--distdir=%(builddir)s/archives" ' +# Use dependencies from EasyBuild +_jaxlib_buildopts += '--bazel_options="--action_env=TF_SYSTEM_LIBS=pybind11" ' +_jaxlib_buildopts += '--bazel_options="--action_env=CPATH=$EBROOTPYBIND11/include" ' +# Avoid warning (treated as error) in upb/table.c +_jaxlib_buildopts += '--bazel_options="--copt=-Wno-maybe-uninitialized" ' + +components = [ + ('jaxlib', version, { + 'sources': [ + { + 'source_urls': ['https://github.com/google/jax/archive/'], + 'filename': '%(name)s-v%(version)s.tar.gz', + }, + { + 'source_urls': ['https://github.com/openxla/xla/archive'], + 'download_filename': '%s.tar.gz' % local_xla_commit, + 'filename': 'xla-%s.tar.gz' % local_xla_commit[:8], + 'extract_cmd': local_extract_cmd, + }, + { + 'source_urls': ['https://github.com/tensorflow/runtime/archive'], + 'download_filename': '%s.tar.gz' % local_tfrt_commit, + 'filename': 'tf_runtime-%s.tar.gz' % local_tfrt_commit[:8], + 'extract_cmd': local_extract_cmd, + }, + ], + 'patches': ['jax-0.4.25_fix-pybind11-systemlib.patch'], + 'checksums': [ + {'jaxlib-v0.4.25.tar.gz': + 'fc1197c401924942eb14185a61688d0c476e3e81ff71f9dc95e620b57c06eec8'}, + {'xla-4ccfe33c.tar.gz': + '8a59b9af7d0850059d7043f7043c780066d61538f3af536e8a10d3d717f35089'}, + {'tf_runtime-0aeefb16.tar.gz': + 'a3df827d7896774cb1d80bf4e1c79ab05c268f29bd4d3db1fb5a4b9c2079d8e3'}, + {'jax-0.4.25_fix-pybind11-systemlib.patch': + 'daad5b726d1a138431b05eb60ecf4c89c7b5148eb939721800bdf43d804ca033'}, + ], + 'start_dir': 'jax-jaxlib-v%(version)s', + 'buildopts': _jaxlib_buildopts + }), +] + +use_pip = True + +exts_list = [ + (name, version, { + 'sources': [ + { + 'source_urls': ['https://github.com/google/jax/archive/'], + 'filename': '%(name)s-v%(version)s.tar.gz', + }, + ], + 'patches': ['jax-0.4.25_fix_env_test_no_log_spam.patch'], + 'checksums': [ + {'jax-v0.4.25.tar.gz': '8b30af49688c0c13b82c6f5ce992727c00b5fc6d04a4c6962012f4246fa664eb'}, + {'jax-0.4.25_fix_env_test_no_log_spam.patch': + 'a18b5f147569d9ad41025124333a0f04fd0d0e0f9e4309658d7f6b9b838e2e2a'}, + ], + 'runtest': "pytest -n %(parallel)s tests", + }), +] + +sanity_pip_check = True + +moduleclass = 'ai' diff --git a/easybuild/easyconfigs/j/jax/jax-0.4.25_fix-pybind11-systemlib.patch b/easybuild/easyconfigs/j/jax/jax-0.4.25_fix-pybind11-systemlib.patch new file mode 100644 index 00000000000..c404ee6917f --- /dev/null +++ b/easybuild/easyconfigs/j/jax/jax-0.4.25_fix-pybind11-systemlib.patch @@ -0,0 +1,38 @@ +Add missing value for System Pybind11 Bazel config + +Author: Alexander Grund (TU Dresden) + +diff --git a/third_party/xla/fix-pybind11-systemlib.patch b/third_party/xla/fix-pybind11-systemlib.patch +new file mode 100644 +index 000000000..68bd2063d +--- /dev/null ++++ b/third_party/xla/fix-pybind11-systemlib.patch +@@ -0,0 +1,13 @@ ++--- xla-orig/third_party/tsl/third_party/systemlibs/pybind11.BUILD +++++ xla-4ccfe33c71665ddcbca5b127fefe8baa3ed632d4/third_party/tsl/third_party/systemlibs/pybind11.BUILD ++@@ -6,3 +6,10 @@ ++ "@tsl//third_party/python_runtime:headers", ++ ], ++ ) +++ +++# Needed by pybind11_bazel. +++config_setting( +++ name = "osx", +++ constraint_values = ["@platforms//os:osx"], +++) +++ +diff --git a/third_party/xla/workspace.bzl b/third_party/xla/workspace.bzl +index ebc8d9838..125e1c173 100644 +--- a/third_party/xla/workspace.bzl ++++ b/third_party/xla/workspace.bzl +@@ -29,6 +29,9 @@ def repo(): + sha256 = XLA_SHA256, + strip_prefix = "xla-{commit}".format(commit = XLA_COMMIT), + urls = tf_mirror_urls("https://github.com/openxla/xla/archive/{commit}.tar.gz".format(commit = XLA_COMMIT)), ++ patch_file = [ ++ "//third_party/xla:fix-pybind11-systemlib.patch", ++ ], + ) + + # For development, one often wants to make changes to the TF repository as well + diff --git a/easybuild/easyconfigs/j/jax/jax-0.4.25_fix_env_test_no_log_spam.patch b/easybuild/easyconfigs/j/jax/jax-0.4.25_fix_env_test_no_log_spam.patch new file mode 100644 index 00000000000..ad919608437 --- /dev/null +++ b/easybuild/easyconfigs/j/jax/jax-0.4.25_fix_env_test_no_log_spam.patch @@ -0,0 +1,18 @@ +# Thomas Hoffmann, EMBL Heidelberg, structures-it@embl.de, 2024/03 +# avoid overriding LD_LIBRARY_PATH, which would lead to test error: error while loading shared libraries: libpython3.11.so.1.0: cannot open shared object file: No such file or directory' +diff -ru jax-jax-v0.4.25/tests/logging_test.py jax-jax-v0.4.25_fix_env_test_no_log_spam/tests/logging_test.py +--- jax-jax-v0.4.25/tests/logging_test.py 2024-02-24 19:25:17.000000000 +0100 ++++ jax-jax-v0.4.25_fix_env_test_no_log_spam/tests/logging_test.py 2024-03-15 12:00:34.133022613 +0100 +@@ -72,8 +72,11 @@ + python = sys.executable + assert "python" in python + # Make sure C++ logging is at default level for the test process. ++ import os ++ tmp_env=os.environ.copy() ++ tmp_env['TF_CPP_MIN_LOG_LEVEL']='1' + proc = subprocess.run([python, "-c", program], capture_output=True, +- env={"TF_CPP_MIN_LOG_LEVEL": "1"}) ++ env=tmp_env) + + lines = proc.stdout.split(b"\n") + lines.extend(proc.stderr.split(b"\n")) diff --git a/easybuild/easyconfigs/j/jbigkit/jbigkit-2.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/j/jbigkit/jbigkit-2.1-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..ae9f9537e31 --- /dev/null +++ b/easybuild/easyconfigs/j/jbigkit/jbigkit-2.1-GCCcore-13.3.0.eb @@ -0,0 +1,45 @@ +easyblock = 'MakeCp' + +name = 'jbigkit' +version = '2.1' + +homepage = 'https://www.cl.cam.ac.uk/~mgk25/jbigkit/' +description = """JBIG-KIT is a software implementation of the JBIG1 data + compression standard (ITU-T T.82), which was designed for bi-level image + data, such as scanned documents.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.cl.cam.ac.uk/~mgk25/jbigkit/download'] +sources = [SOURCE_TAR_GZ] +patches = [ + '%(name)s-%(version)s_libpath.patch', + '%(name)s-%(version)s_shlib.patch', +] +checksums = [ + {'jbigkit-2.1.tar.gz': 'de7106b6bfaf495d6865c7dd7ac6ca1381bd12e0d81405ea81e7f2167263d932'}, + {'jbigkit-2.1_libpath.patch': '97c88956090097b484fcdb90e12eab82212e67ddc862f035d7c6446a696786ce'}, + {'jbigkit-2.1_shlib.patch': '54ae429e8ec949eceee0f902b676f572f1cdfbff46f77c7222acdeafb643a696'}, +] + +builddependencies = [ + ('binutils', '2.42'), + ('pkgconf', '2.2.0'), +] + +files_to_copy = [ + (['libjbig/libjbig%s.%s' % (x, y) for x in ['85', ''] for y in ['a', SHLIB_EXT, SHLIB_EXT + '.0']], 'lib'), + (['libjbig/jbig85.h', 'libjbig/jbig.h', 'libjbig/jbig_ar.h'], 'include'), + (['pbmtools/pbmtojbg', 'pbmtools/jbgtopbm'], 'bin'), +] + +sanity_check_paths = { + 'files': ['lib/libjbig85.a', 'lib/libjbig.a', + 'bin/pbmtojbg', 'bin/jbgtopbm', + 'include/jbig.h', 'include/jbig_ar.h', + ], + 'dirs': ['bin', 'include', 'lib'] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/j/jedi/jedi-0.18.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/j/jedi/jedi-0.18.1-GCCcore-11.3.0.eb index 5b2a8950603..daf043bb1a5 100644 --- a/easybuild/easyconfigs/j/jedi/jedi-0.18.1-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/j/jedi/jedi-0.18.1-GCCcore-11.3.0.eb @@ -3,9 +3,11 @@ easyblock = 'PythonBundle' name = 'jedi' version = "0.18.1" -homepage = 'https://jedi.readthedocs.io/en/latest/' +homepage = 'https://github.com/davidhalter/jedi' description = """ - Jedi is a static analysis tool for Python that is typically used in IDEs/editors plugins. + Jedi - an awesome autocompletion, static analysis and refactoring library for Python. + It is typically used in IDEs/editors plugins. Jedi has a focus on autocompletion and goto functionality. + Other features include refactoring, code search and finding references. """ toolchain = {'name': 'GCCcore', 'version': '11.3.0'} @@ -29,9 +31,4 @@ exts_list = [ }), ] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib'], -} - moduleclass = 'tools' diff --git a/easybuild/easyconfigs/j/jedi/jedi-0.19.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/j/jedi/jedi-0.19.0-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..fcdb1b6305b --- /dev/null +++ b/easybuild/easyconfigs/j/jedi/jedi-0.19.0-GCCcore-12.3.0.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonBundle' + +name = 'jedi' +version = "0.19.0" + +homepage = 'https://github.com/davidhalter/jedi' +description = """ + Jedi - an awesome autocompletion, static analysis and refactoring library for Python. + It is typically used in IDEs/editors plugins. Jedi has a focus on autocompletion and goto functionality. + Other features include refactoring, code search and finding references. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +builddependencies = [ + ('binutils', '2.40'), +] +dependencies = [ + ('Python', '3.11.3'), +] + +sanity_pip_check = True +use_pip = True + +exts_list = [ + ('parso', '0.8.3', { + 'checksums': ['8c07be290bb59f03588915921e29e8a50002acaf2cdc5fa0e0114f91709fafa0'], + }), + (name, version, { + 'checksums': ['bcf9894f1753969cbac8022a8c2eaee06bfa3724e4192470aaffe7eb6272b0c4'], + }), +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/j/jedi/jedi-0.19.1-GCCcore-13.2.0.eb b/easybuild/easyconfigs/j/jedi/jedi-0.19.1-GCCcore-13.2.0.eb index eca3a2e905d..a0891f77c33 100644 --- a/easybuild/easyconfigs/j/jedi/jedi-0.19.1-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/j/jedi/jedi-0.19.1-GCCcore-13.2.0.eb @@ -6,6 +6,8 @@ version = "0.19.1" homepage = 'https://github.com/davidhalter/jedi' description = """ Jedi - an awesome autocompletion, static analysis and refactoring library for Python. + It is typically used in IDEs/editors plugins. Jedi has a focus on autocompletion and goto functionality. + Other features include refactoring, code search and finding references. """ toolchain = {'name': 'GCCcore', 'version': '13.2.0'} @@ -29,9 +31,4 @@ exts_list = [ }), ] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python3.11/site-packages/jedi'], -} - moduleclass = 'tools' diff --git a/easybuild/easyconfigs/j/jedi/jedi-0.19.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/j/jedi/jedi-0.19.1-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..b477ad70774 --- /dev/null +++ b/easybuild/easyconfigs/j/jedi/jedi-0.19.1-GCCcore-13.3.0.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonBundle' + +name = 'jedi' +version = "0.19.1" + +homepage = 'https://github.com/davidhalter/jedi' +description = """ + Jedi - an awesome autocompletion, static analysis and refactoring library for Python. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +builddependencies = [ + ('binutils', '2.42'), +] +dependencies = [ + ('Python', '3.12.3'), +] + +sanity_pip_check = True +use_pip = True + +exts_list = [ + ('parso', '0.8.3', { + 'checksums': ['8c07be290bb59f03588915921e29e8a50002acaf2cdc5fa0e0114f91709fafa0'], + }), + (name, version, { + 'checksums': ['cf0496f3651bc65d7174ac1b7d043eff454892c708a87d1b683e57b569927ffd'], + }), +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/j/jemalloc/jemalloc-5.3.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/j/jemalloc/jemalloc-5.3.0-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..356d56465fa --- /dev/null +++ b/easybuild/easyconfigs/j/jemalloc/jemalloc-5.3.0-GCCcore-12.3.0.eb @@ -0,0 +1,37 @@ +easyblock = 'ConfigureMake' + +name = 'jemalloc' +version = '5.3.0' + +homepage = 'http://jemalloc.net' +description = """jemalloc is a general purpose malloc(3) implementation that emphasizes fragmentation avoidance and + scalable concurrency support.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://github.com/jemalloc/jemalloc/archive'] +sources = ['%(version)s.tar.gz'] +checksums = ['ef6f74fd45e95ee4ef7f9e19ebe5b075ca6b7fbe0140612b2a161abafb7ee179'] + +builddependencies = [ + ('Autotools', '20220317'), + ('binutils', '2.40'), +] + +# From version 5.2.1 (or maybe earlier) it does no longer build, +# nor try to install, documentation if xsltproc is missing. +# So we can use normal installation. +preconfigopts = "./autogen.sh && " +configopts = "--with-version=%(version)s-0-g0000 " # build with version info + +sanity_check_paths = { + 'files': ['bin/jeprof', 'lib/libjemalloc.a', 'lib/libjemalloc_pic.a', 'lib/libjemalloc.%s' % SHLIB_EXT, + 'include/jemalloc/jemalloc.h'], + 'dirs': [], +} + +# jemalloc can be used via $LD_PRELOAD, but we don't enable this by +# default, you need to opt-in to it +# modextrapaths = {'LD_PRELOAD': ['lib/libjemalloc.%s' % SHLIB_EXT]} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/j/jemalloc/jemalloc-5.3.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/j/jemalloc/jemalloc-5.3.0-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..023c3001dd3 --- /dev/null +++ b/easybuild/easyconfigs/j/jemalloc/jemalloc-5.3.0-GCCcore-13.3.0.eb @@ -0,0 +1,37 @@ +easyblock = 'ConfigureMake' + +name = 'jemalloc' +version = '5.3.0' + +homepage = 'http://jemalloc.net' +description = """jemalloc is a general purpose malloc(3) implementation that emphasizes fragmentation avoidance and + scalable concurrency support.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://github.com/jemalloc/jemalloc/archive'] +sources = ['%(version)s.tar.gz'] +checksums = ['ef6f74fd45e95ee4ef7f9e19ebe5b075ca6b7fbe0140612b2a161abafb7ee179'] + +builddependencies = [ + ('Autotools', '20231222'), + ('binutils', '2.42'), +] + +# From version 5.2.1 (or maybe earlier) it does no longer build, +# nor try to install, documentation if xsltproc is missing. +# So we can use normal installation. +preconfigopts = "./autogen.sh && " +configopts = "--with-version=%(version)s-0-g0000 " # build with version info + +sanity_check_paths = { + 'files': ['bin/jeprof', 'lib/libjemalloc.a', 'lib/libjemalloc_pic.a', 'lib/libjemalloc.%s' % SHLIB_EXT, + 'include/jemalloc/jemalloc.h'], + 'dirs': [], +} + +# jemalloc can be used via $LD_PRELOAD, but we don't enable this by +# default, you need to opt-in to it +# modextrapaths = {'LD_PRELOAD': ['lib/libjemalloc.%s' % SHLIB_EXT]} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/j/jiter/jiter-0.4.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/j/jiter/jiter-0.4.1-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..8ff0092960e --- /dev/null +++ b/easybuild/easyconfigs/j/jiter/jiter-0.4.1-GCCcore-12.3.0.eb @@ -0,0 +1,191 @@ +easyblock = 'CargoPythonBundle' + +name = 'jiter' +version = '0.4.1' + +homepage = 'https://github.com/pydantic/jiter/tree/main' +description = "Fast iterable JSON parser" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +crates = [ + ('ahash', '0.8.11'), + ('autocfg', '1.3.0'), + ('bencher', '0.1.5'), + ('bitflags', '2.5.0'), + ('bitvec', '1.0.1'), + ('cfg-if', '1.0.0'), + ('codspeed', '2.6.0'), + ('codspeed-bencher-compat', '2.6.0'), + ('colored', '2.1.0'), + ('equivalent', '1.0.1'), + ('funty', '2.0.0'), + ('getrandom', '0.2.15'), + ('hashbrown', '0.14.5'), + ('heck', '0.4.1'), + ('indexmap', '2.2.6'), + ('indoc', '2.0.5'), + ('itoa', '1.0.11'), + ('lazy_static', '1.4.0'), + ('lexical-parse-float', '0.8.5'), + ('lexical-parse-integer', '0.8.6'), + ('lexical-util', '0.8.5'), + ('libc', '0.2.155'), + ('lock_api', '0.4.12'), + ('memoffset', '0.9.1'), + ('num-bigint', '0.4.5'), + ('num-integer', '0.1.46'), + ('num-traits', '0.2.19'), + ('once_cell', '1.19.0'), + ('parking_lot', '0.12.3'), + ('parking_lot_core', '0.9.10'), + ('paste', '1.0.15'), + ('portable-atomic', '1.6.0'), + ('proc-macro2', '1.0.84'), + ('pyo3', '0.21.2'), + ('pyo3-build-config', '0.21.2'), + ('pyo3-ffi', '0.21.2'), + ('pyo3-macros', '0.21.2'), + ('pyo3-macros-backend', '0.21.2'), + ('quote', '1.0.36'), + ('radium', '0.7.0'), + ('redox_syscall', '0.5.1'), + ('ryu', '1.0.18'), + ('scopeguard', '1.2.0'), + ('serde', '1.0.203'), + ('serde_derive', '1.0.203'), + ('serde_json', '1.0.117'), + ('smallvec', '1.13.2'), + ('static_assertions', '1.1.0'), + ('syn', '2.0.66'), + ('tap', '1.0.1'), + ('target-lexicon', '0.12.14'), + ('unicode-ident', '1.0.12'), + ('unindent', '0.2.3'), + ('version_check', '0.9.4'), + ('wasi', '0.11.0+wasi-snapshot-preview1'), + ('windows-sys', '0.48.0'), + ('windows-targets', '0.48.5'), + ('windows-targets', '0.52.5'), + ('windows_aarch64_gnullvm', '0.48.5'), + ('windows_aarch64_gnullvm', '0.52.5'), + ('windows_aarch64_msvc', '0.48.5'), + ('windows_aarch64_msvc', '0.52.5'), + ('windows_i686_gnu', '0.48.5'), + ('windows_i686_gnu', '0.52.5'), + ('windows_i686_gnullvm', '0.52.5'), + ('windows_i686_msvc', '0.48.5'), + ('windows_i686_msvc', '0.52.5'), + ('windows_x86_64_gnu', '0.48.5'), + ('windows_x86_64_gnu', '0.52.5'), + ('windows_x86_64_gnullvm', '0.48.5'), + ('windows_x86_64_gnullvm', '0.52.5'), + ('windows_x86_64_msvc', '0.48.5'), + ('windows_x86_64_msvc', '0.52.5'), + ('wyz', '0.5.1'), + ('zerocopy', '0.7.34'), + ('zerocopy-derive', '0.7.34'), +] + +sources = [SOURCE_TAR_GZ] +checksums = [ + {'jiter-0.4.1.tar.gz': '741851cf5f37cf3583f2a56829d734c9fd17334770c9a326e6d25291603d4278'}, + {'ahash-0.8.11.tar.gz': 'e89da841a80418a9b391ebaea17f5c112ffaaa96f621d2c285b5174da76b9011'}, + {'autocfg-1.3.0.tar.gz': '0c4b4d0bd25bd0b74681c0ad21497610ce1b7c91b1022cd21c80c6fbdd9476b0'}, + {'bencher-0.1.5.tar.gz': '7dfdb4953a096c551ce9ace855a604d702e6e62d77fac690575ae347571717f5'}, + {'bitflags-2.5.0.tar.gz': 'cf4b9d6a944f767f8e5e0db018570623c85f3d925ac718db4e06d0187adb21c1'}, + {'bitvec-1.0.1.tar.gz': '1bc2832c24239b0141d5674bb9174f9d68a8b5b3f2753311927c172ca46f7e9c'}, + {'cfg-if-1.0.0.tar.gz': 'baf1de4339761588bc0619e3cbc0120ee582ebb74b53b4efbf79117bd2da40fd'}, + {'codspeed-2.6.0.tar.gz': '3a104ac948e0188b921eb3fcbdd55dcf62e542df4c7ab7e660623f6288302089'}, + {'codspeed-bencher-compat-2.6.0.tar.gz': 'ceaba84ea2634603a0f199c07fa39ff4dda61f89a3f9149fb89b035bc317b671'}, + {'colored-2.1.0.tar.gz': 'cbf2150cce219b664a8a70df7a1f933836724b503f8a413af9365b4dcc4d90b8'}, + {'equivalent-1.0.1.tar.gz': '5443807d6dff69373d433ab9ef5378ad8df50ca6298caf15de6e52e24aaf54d5'}, + {'funty-2.0.0.tar.gz': 'e6d5a32815ae3f33302d95fdcb2ce17862f8c65363dcfd29360480ba1001fc9c'}, + {'getrandom-0.2.15.tar.gz': 'c4567c8db10ae91089c99af84c68c38da3ec2f087c3f82960bcdbf3656b6f4d7'}, + {'hashbrown-0.14.5.tar.gz': 'e5274423e17b7c9fc20b6e7e208532f9b19825d82dfd615708b70edd83df41f1'}, + {'heck-0.4.1.tar.gz': '95505c38b4572b2d910cecb0281560f54b440a19336cbbcb27bf6ce6adc6f5a8'}, + {'indexmap-2.2.6.tar.gz': '168fb715dda47215e360912c096649d23d58bf392ac62f73919e831745e40f26'}, + {'indoc-2.0.5.tar.gz': 'b248f5224d1d606005e02c97f5aa4e88eeb230488bcc03bc9ca4d7991399f2b5'}, + {'itoa-1.0.11.tar.gz': '49f1f14873335454500d59611f1cf4a4b0f786f9ac11f4312a78e4cf2566695b'}, + {'lazy_static-1.4.0.tar.gz': 'e2abad23fbc42b3700f2f279844dc832adb2b2eb069b2df918f455c4e18cc646'}, + {'lexical-parse-float-0.8.5.tar.gz': '683b3a5ebd0130b8fb52ba0bdc718cc56815b6a097e28ae5a6997d0ad17dc05f'}, + {'lexical-parse-integer-0.8.6.tar.gz': '6d0994485ed0c312f6d965766754ea177d07f9c00c9b82a5ee62ed5b47945ee9'}, + {'lexical-util-0.8.5.tar.gz': '5255b9ff16ff898710eb9eb63cb39248ea8a5bb036bea8085b1a767ff6c4e3fc'}, + {'libc-0.2.155.tar.gz': '97b3888a4aecf77e811145cadf6eef5901f4782c53886191b2f693f24761847c'}, + {'lock_api-0.4.12.tar.gz': '07af8b9cdd281b7915f413fa73f29ebd5d55d0d3f0155584dade1ff18cea1b17'}, + {'memoffset-0.9.1.tar.gz': '488016bfae457b036d996092f6cb448677611ce4449e970ceaf42695203f218a'}, + {'num-bigint-0.4.5.tar.gz': 'c165a9ab64cf766f73521c0dd2cfdff64f488b8f0b3e621face3462d3db536d7'}, + {'num-integer-0.1.46.tar.gz': '7969661fd2958a5cb096e56c8e1ad0444ac2bbcd0061bd28660485a44879858f'}, + {'num-traits-0.2.19.tar.gz': '071dfc062690e90b734c0b2273ce72ad0ffa95f0c74596bc250dcfd960262841'}, + {'once_cell-1.19.0.tar.gz': '3fdb12b2476b595f9358c5161aa467c2438859caa136dec86c26fdd2efe17b92'}, + {'parking_lot-0.12.3.tar.gz': 'f1bf18183cf54e8d6059647fc3063646a1801cf30896933ec2311622cc4b9a27'}, + {'parking_lot_core-0.9.10.tar.gz': '1e401f977ab385c9e4e3ab30627d6f26d00e2c73eef317493c4ec6d468726cf8'}, + {'paste-1.0.15.tar.gz': '57c0d7b74b563b49d38dae00a0c37d4d6de9b432382b2892f0574ddcae73fd0a'}, + {'portable-atomic-1.6.0.tar.gz': '7170ef9988bc169ba16dd36a7fa041e5c4cbeb6a35b76d4c03daded371eae7c0'}, + {'proc-macro2-1.0.84.tar.gz': 'ec96c6a92621310b51366f1e28d05ef11489516e93be030060e5fc12024a49d6'}, + {'pyo3-0.21.2.tar.gz': 'a5e00b96a521718e08e03b1a622f01c8a8deb50719335de3f60b3b3950f069d8'}, + {'pyo3-build-config-0.21.2.tar.gz': '7883df5835fafdad87c0d888b266c8ec0f4c9ca48a5bed6bbb592e8dedee1b50'}, + {'pyo3-ffi-0.21.2.tar.gz': '01be5843dc60b916ab4dad1dca6d20b9b4e6ddc8e15f50c47fe6d85f1fb97403'}, + {'pyo3-macros-0.21.2.tar.gz': '77b34069fc0682e11b31dbd10321cbf94808394c56fd996796ce45217dfac53c'}, + {'pyo3-macros-backend-0.21.2.tar.gz': '08260721f32db5e1a5beae69a55553f56b99bd0e1c3e6e0a5e8851a9d0f5a85c'}, + {'quote-1.0.36.tar.gz': '0fa76aaf39101c457836aec0ce2316dbdc3ab723cdda1c6bd4e6ad4208acaca7'}, + {'radium-0.7.0.tar.gz': 'dc33ff2d4973d518d823d61aa239014831e521c75da58e3df4840d3f47749d09'}, + {'redox_syscall-0.5.1.tar.gz': '469052894dcb553421e483e4209ee581a45100d31b4018de03e5a7ad86374a7e'}, + {'ryu-1.0.18.tar.gz': 'f3cb5ba0dc43242ce17de99c180e96db90b235b8a9fdc9543c96d2209116bd9f'}, + {'scopeguard-1.2.0.tar.gz': '94143f37725109f92c262ed2cf5e59bce7498c01bcc1502d7b9afe439a4e9f49'}, + {'serde-1.0.203.tar.gz': '7253ab4de971e72fb7be983802300c30b5a7f0c2e56fab8abfc6a214307c0094'}, + {'serde_derive-1.0.203.tar.gz': '500cbc0ebeb6f46627f50f3f5811ccf6bf00643be300b4c3eabc0ef55dc5b5ba'}, + {'serde_json-1.0.117.tar.gz': '455182ea6142b14f93f4bc5320a2b31c1f266b66a4a5c858b013302a5d8cbfc3'}, + {'smallvec-1.13.2.tar.gz': '3c5e1a9a646d36c3599cd173a41282daf47c44583ad367b8e6837255952e5c67'}, + {'static_assertions-1.1.0.tar.gz': 'a2eb9349b6444b326872e140eb1cf5e7c522154d69e7a0ffb0fb81c06b37543f'}, + {'syn-2.0.66.tar.gz': 'c42f3f41a2de00b01c0aaad383c5a45241efc8b2d1eda5661812fda5f3cdcff5'}, + {'tap-1.0.1.tar.gz': '55937e1799185b12863d447f42597ed69d9928686b8d88a1df17376a097d8369'}, + {'target-lexicon-0.12.14.tar.gz': 'e1fc403891a21bcfb7c37834ba66a547a8f402146eba7265b5a6d88059c9ff2f'}, + {'unicode-ident-1.0.12.tar.gz': '3354b9ac3fae1ff6755cb6db53683adb661634f67557942dea4facebec0fee4b'}, + {'unindent-0.2.3.tar.gz': 'c7de7d73e1754487cb58364ee906a499937a0dfabd86bcb980fa99ec8c8fa2ce'}, + {'version_check-0.9.4.tar.gz': '49874b5167b65d7193b8aba1567f5c7d93d001cafc34600cee003eda787e483f'}, + {'wasi-0.11.0+wasi-snapshot-preview1.tar.gz': '9c8d87e72b64a3b4db28d11ce29237c246188f4f51057d65a7eab63b7987e423'}, + {'windows-sys-0.48.0.tar.gz': '677d2418bec65e3338edb076e806bc1ec15693c5d0104683f2efe857f61056a9'}, + {'windows-targets-0.48.5.tar.gz': '9a2fa6e2155d7247be68c096456083145c183cbbbc2764150dda45a87197940c'}, + {'windows-targets-0.52.5.tar.gz': '6f0713a46559409d202e70e28227288446bf7841d3211583a4b53e3f6d96e7eb'}, + {'windows_aarch64_gnullvm-0.48.5.tar.gz': '2b38e32f0abccf9987a4e3079dfb67dcd799fb61361e53e2882c3cbaf0d905d8'}, + {'windows_aarch64_gnullvm-0.52.5.tar.gz': '7088eed71e8b8dda258ecc8bac5fb1153c5cffaf2578fc8ff5d61e23578d3263'}, + {'windows_aarch64_msvc-0.48.5.tar.gz': 'dc35310971f3b2dbbf3f0690a219f40e2d9afcf64f9ab7cc1be722937c26b4bc'}, + {'windows_aarch64_msvc-0.52.5.tar.gz': '9985fd1504e250c615ca5f281c3f7a6da76213ebd5ccc9561496568a2752afb6'}, + {'windows_i686_gnu-0.48.5.tar.gz': 'a75915e7def60c94dcef72200b9a8e58e5091744960da64ec734a6c6e9b3743e'}, + {'windows_i686_gnu-0.52.5.tar.gz': '88ba073cf16d5372720ec942a8ccbf61626074c6d4dd2e745299726ce8b89670'}, + {'windows_i686_gnullvm-0.52.5.tar.gz': '87f4261229030a858f36b459e748ae97545d6f1ec60e5e0d6a3d32e0dc232ee9'}, + {'windows_i686_msvc-0.48.5.tar.gz': '8f55c233f70c4b27f66c523580f78f1004e8b5a8b659e05a4eb49d4166cca406'}, + {'windows_i686_msvc-0.52.5.tar.gz': 'db3c2bf3d13d5b658be73463284eaf12830ac9a26a90c717b7f771dfe97487bf'}, + {'windows_x86_64_gnu-0.48.5.tar.gz': '53d40abd2583d23e4718fddf1ebec84dbff8381c07cae67ff7768bbf19c6718e'}, + {'windows_x86_64_gnu-0.52.5.tar.gz': '4e4246f76bdeff09eb48875a0fd3e2af6aada79d409d33011886d3e1581517d9'}, + {'windows_x86_64_gnullvm-0.48.5.tar.gz': '0b7b52767868a23d5bab768e390dc5f5c55825b6d30b86c844ff2dc7414044cc'}, + {'windows_x86_64_gnullvm-0.52.5.tar.gz': '852298e482cd67c356ddd9570386e2862b5673c85bd5f88df9ab6802b334c596'}, + {'windows_x86_64_msvc-0.48.5.tar.gz': 'ed94fce61571a4006852b7389a063ab983c02eb1bb37b47f8272ce92d06d9538'}, + {'windows_x86_64_msvc-0.52.5.tar.gz': 'bec47e5bfd1bff0eeaf6d8b485cc1074891a197ab4225d504cb7a1ab88b02bf0'}, + {'wyz-0.5.1.tar.gz': '05f360fc0b24296329c78fda852a1e9ae82de9cf7b27dae4b7f62f118f77b9ed'}, + {'zerocopy-0.7.34.tar.gz': 'ae87e3fcd617500e5d106f0380cf7b77f3c6092aae37191433159dda23cfb087'}, + {'zerocopy-derive-0.7.34.tar.gz': '15e934569e47891f7d9411f1a451d947a60e000ab3bd24fbb970f000387d1b3b'}, +] + +_rust_ver = '1.75.0' +builddependencies = [ + ('binutils', '2.40'), + ('Rust', _rust_ver), + ('maturin', '1.4.0', '-Rust-%s' % _rust_ver), +] + +dependencies = [ + ('Python', '3.11.3'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + (name, version, { + 'checksums': ['741851cf5f37cf3583f2a56829d734c9fd17334770c9a326e6d25291603d4278'], + }), +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/j/joypy/joypy-0.2.6-foss-2023a.eb b/easybuild/easyconfigs/j/joypy/joypy-0.2.6-foss-2023a.eb new file mode 100644 index 00000000000..db6e77ea520 --- /dev/null +++ b/easybuild/easyconfigs/j/joypy/joypy-0.2.6-foss-2023a.eb @@ -0,0 +1,28 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 +# Update: Petr Král (INUITS) + +easyblock = 'PythonPackage' + +name = 'joypy' +version = '0.2.6' + +homepage = 'https://github.com/sbebo/joypy' +description = "Joyplots in Python with matplotlib & pandas" + +toolchain = {'name': 'foss', 'version': '2023a'} + +sources = [SOURCE_WHL] +checksums = ['fffe882e8281e56e08b374a3148436cb448562ba39e4d566204c7e8ee2caddab'] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('matplotlib', '3.7.2'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/j/json-c/json-c-0.17-GCCcore-13.3.0.eb b/easybuild/easyconfigs/j/json-c/json-c-0.17-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..87642888aa1 --- /dev/null +++ b/easybuild/easyconfigs/j/json-c/json-c-0.17-GCCcore-13.3.0.eb @@ -0,0 +1,32 @@ +easyblock = 'CMakeMake' + +name = 'json-c' +version = '0.17' +local_suff = '-20230812' + +homepage = 'https://github.com/json-c/json-c' +description = """JSON-C implements a reference counting object model that allows you to easily construct JSON objects + in C, output them as JSON formatted strings and parse JSON formatted strings back into the C representation of JSON +objects.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://github.com/json-c/json-c/archive/'] +sources = ['json-c-%%(version)s%s.tar.gz' % local_suff] +checksums = ['024d302a3aadcbf9f78735320a6d5aedf8b77876c8ac8bbb95081ca55054c7eb'] + +builddependencies = [ + ('binutils', '2.42'), + ('CMake', '3.29.3'), +] + +# disable using Valgrind during the tests to avoid failures caused by using an OS Valgrind +pretestopts = 'USE_VALGRIND=0 ' +runtest = 'test' + +sanity_check_paths = { + 'files': ['lib/libjson-c.a', 'lib/libjson-c.%s' % SHLIB_EXT, 'lib/pkgconfig/json-c.pc'], + 'dirs': ['include/json-c'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/j/json-fortran/json-fortran-8.5.2-GCC-13.2.0.eb b/easybuild/easyconfigs/j/json-fortran/json-fortran-8.5.2-GCC-13.2.0.eb new file mode 100644 index 00000000000..da205b23c09 --- /dev/null +++ b/easybuild/easyconfigs/j/json-fortran/json-fortran-8.5.2-GCC-13.2.0.eb @@ -0,0 +1,32 @@ +# J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'CMakeMake' + +name = 'json-fortran' +version = '8.5.2' + +homepage = 'https://github.com/jacobwilliams/json-fortran' +description = "JSON-Fortran: A Modern Fortran JSON API" + +toolchain = {'name': 'GCC', 'version': '13.2.0'} + +source_urls = ['https://github.com/jacobwilliams/json-fortran/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['ba7243ab28d4d06c5d0baef27dab0041cee0f050dea9ec3a854a03f4e3e9667a'] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.27.6'), +] + +configopts = '-DUSE_GNU_INSTALL_CONVENTION=TRUE' + +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libjsonfortran.a', 'lib/libjsonfortran.%s' % SHLIB_EXT, + 'include/json_module.mod', 'include/json_parameters.mod'], + 'dirs': ['include'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/j/json-fortran/json-fortran-8.5.2-intel-compilers-2023.2.1.eb b/easybuild/easyconfigs/j/json-fortran/json-fortran-8.5.2-intel-compilers-2023.2.1.eb new file mode 100644 index 00000000000..50d89ee34e2 --- /dev/null +++ b/easybuild/easyconfigs/j/json-fortran/json-fortran-8.5.2-intel-compilers-2023.2.1.eb @@ -0,0 +1,32 @@ +# J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'CMakeMake' + +name = 'json-fortran' +version = '8.5.2' + +homepage = 'https://github.com/jacobwilliams/json-fortran' +description = "JSON-Fortran: A Modern Fortran JSON API" + +toolchain = {'name': 'intel-compilers', 'version': '2023.2.1'} + +source_urls = ['https://github.com/jacobwilliams/json-fortran/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['ba7243ab28d4d06c5d0baef27dab0041cee0f050dea9ec3a854a03f4e3e9667a'] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.27.6'), +] + +configopts = '-DUSE_GNU_INSTALL_CONVENTION=TRUE' + +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libjsonfortran.a', 'lib/libjsonfortran.%s' % SHLIB_EXT, + 'include/json_module.mod', 'include/json_parameters.mod'], + 'dirs': ['include'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/j/json-fortran/json-fortran-9.0.2-GCC-12.3.0.eb b/easybuild/easyconfigs/j/json-fortran/json-fortran-9.0.2-GCC-12.3.0.eb new file mode 100644 index 00000000000..03dceec3b87 --- /dev/null +++ b/easybuild/easyconfigs/j/json-fortran/json-fortran-9.0.2-GCC-12.3.0.eb @@ -0,0 +1,32 @@ +# J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'CMakeMake' + +name = 'json-fortran' +version = '9.0.2' + +homepage = 'https://github.com/jacobwilliams/json-fortran' +description = "JSON-Fortran: A Modern Fortran JSON API" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +source_urls = ['https://github.com/jacobwilliams/json-fortran/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['a599a77e406e59cdb7672d780e69156b6ce57cb8ce515d21d1744c4065a85976'] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.26.3'), +] + +configopts = '-DUSE_GNU_INSTALL_CONVENTION=TRUE' + +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libjsonfortran.a', 'lib/libjsonfortran.%s' % SHLIB_EXT, + 'include/json_module.mod', 'include/json_parameters.mod'], + 'dirs': ['include'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/j/json-fortran/json-fortran-9.0.2-GCC-13.2.0.eb b/easybuild/easyconfigs/j/json-fortran/json-fortran-9.0.2-GCC-13.2.0.eb new file mode 100644 index 00000000000..3b32a332d54 --- /dev/null +++ b/easybuild/easyconfigs/j/json-fortran/json-fortran-9.0.2-GCC-13.2.0.eb @@ -0,0 +1,32 @@ +# J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'CMakeMake' + +name = 'json-fortran' +version = '9.0.2' + +homepage = 'https://github.com/jacobwilliams/json-fortran' +description = "JSON-Fortran: A Modern Fortran JSON API" + +toolchain = {'name': 'GCC', 'version': '13.2.0'} + +source_urls = ['https://github.com/jacobwilliams/json-fortran/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['a599a77e406e59cdb7672d780e69156b6ce57cb8ce515d21d1744c4065a85976'] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.27.6'), +] + +configopts = '-DUSE_GNU_INSTALL_CONVENTION=TRUE' + +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libjsonfortran.a', 'lib/libjsonfortran.%s' % SHLIB_EXT, + 'include/json_module.mod', 'include/json_parameters.mod'], + 'dirs': ['include'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/j/junos-eznc/junos-eznc-2.7.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/j/junos-eznc/junos-eznc-2.7.1-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..ceaec648de3 --- /dev/null +++ b/easybuild/easyconfigs/j/junos-eznc/junos-eznc-2.7.1-GCCcore-12.3.0.eb @@ -0,0 +1,54 @@ +easyblock = 'PythonBundle' + +name = 'junos-eznc' +version = '2.7.1' + +homepage = 'https://github.com/Juniper/py-junos-eznc' +description = "Python library for Junos automation." + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +builddependencies = [('binutils', '2.40')] +dependencies = [ + ('Python', '3.11.3'), + ('lxml', '4.9.2'), + ('PyYAML', '6.0'), + ('Python-bundle-PyPI', '2023.06'), + ('bcrypt', '4.0.1'), +] + +exts_list = [ + ('yamlordereddictloader', '0.4.2', { + 'checksums': ['36af2f6210fcff5da4fc4c12e1d815f973dceb41044e795e1f06115d634bca13'], + }), + ('transitions', '0.9.2', { + 'checksums': ['2f8490dbdbd419366cef1516032ab06d07ccb5839ef54905e842a472692d4204'], + }), + ('scp', '0.15.0', { + 'checksums': ['f1b22e9932123ccf17eebf19e0953c6e9148f589f93d91b872941a696305c83f'], + }), + ('pyserial', '3.5', { + 'modulename': 'serial', + 'checksums': ['3c77e014170dfffbd816e6ffc205e9842efb10be9f58ec16d3e8675b4925cddb'], + }), + ('ncclient', '0.6.15', { + 'checksums': ['6757cb41bc9160dfe47f22f5de8cf2f1adf22f27463fb50453cc415ab96773d8'], + }), + ('paramiko', '3.4.0', { + # Juniper fork of paramiko - compatible with junos-eznc + 'source_urls': ['https://github.com/Juniper/paramiko/archive/'], + 'sources': [{'download_filename': 'v%(version)s-JNPR.tar.gz', 'filename': '%(name)s-%(version)s-JNPR.tar.gz'}], + 'checksums': ['6b3b62e18a2b693169eaa50a7cdd2ab5637fc423205ce85e109cb37722f9eeda'], + }), + (name, version, { + 'modulename': 'jnpr.junos', + # delete 'os.system("pip install git+https://github.com/Juniper/paramiko.git@v3.4.0-JNPR")' from setup.py + 'preinstallopts': "sed -i '/pip install/d' setup.py && ", + 'checksums': ['371f0298bf03e0cb4c017c43f6f4122263584eda0d690d0112e93f13daae41ac'], + }), +] + +use_pip = True +sanity_pip_check = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/j/jupyter-collaboration/jupyter-collaboration-2.1.1-GCCcore-13.2.0.eb b/easybuild/easyconfigs/j/jupyter-collaboration/jupyter-collaboration-2.1.1-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..1755481085e --- /dev/null +++ b/easybuild/easyconfigs/j/jupyter-collaboration/jupyter-collaboration-2.1.1-GCCcore-13.2.0.eb @@ -0,0 +1,55 @@ +easyblock = 'PythonBundle' + +name = 'jupyter-collaboration' +version = "2.1.1" + +homepage = 'https://github.com/jupyterlab/jupyter-collaboration' +description = """JupyterLab Real-Time Collaboration is a Jupyter Server Extension and JupyterLab +extensions providing support for Y documents and adding collaboration UI +elements in JupyterLab.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +builddependencies = [ + ('binutils', '2.40'), + ('hatch-jupyter-builder', '0.9.1'), + ('maturin', '1.3.1'), +] +dependencies = [ + ('Python', '3.11.5'), + ('JupyterLab', '4.2.0'), +] + +sanity_pip_check = True +use_pip = True + +exts_list = [ + ('sqlite_anyio', '0.2.0', { + 'checksums': ['9ecbcddf105e5862f7975a9827b684a19a987aad46f10699eadb22ea33bbd060'], + }), + ('pycrdt', '0.8.27', { + 'checksums': ['a486a967ab82d92e51211757d888367b9d1882cfd4db6199485a8fd3d2271dce'], + }), + ('pycrdt_websocket', '0.13.4', { + 'checksums': ['dce8259345ac14e08e9cf124cd1d66ea1b9d17ab1af79e63f50a611fb676421c'], + }), + ('jupyter_ydoc', '2.0.1', { + 'checksums': ['716dda8cb8af881fec2fbc88aea3fb0d3bb24bbeb80a99a8aff2e01d089d5b0d'], + }), + ('jupyter_server_fileid', '0.9.2', { + 'checksums': ['ffb11460ca5f8567644f6120b25613fca8e3f3048b38d14c6e3fe1902f314a9b'], + }), + ('jupyter_collaboration', version, { + 'checksums': ['4f50c25c6d81126c16deaf92d2bd78a39b2fcb86690dce696b4006b740d71c1f'], + }), +] + +sanity_check_paths = { + 'files': ['bin/jupyter-fileid'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/', 'etc/jupyter', 'share/jupyter'], +} + +# Add the notebook extension to the search path for jupyter notebooks +modextrapaths = {'EB_ENV_JUPYTER_ROOT': ''} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/j/jupyter-contrib-nbextensions/jupyter-contrib-nbextensions-0.7.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/j/jupyter-contrib-nbextensions/jupyter-contrib-nbextensions-0.7.0-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..1e0ea2bdea5 --- /dev/null +++ b/easybuild/easyconfigs/j/jupyter-contrib-nbextensions/jupyter-contrib-nbextensions-0.7.0-GCCcore-12.3.0.eb @@ -0,0 +1,62 @@ +easyblock = "PythonBundle" + +name = 'jupyter-contrib-nbextensions' +version = '0.7.0' + +homepage = 'https://github.com/ipython-contrib/jupyter_contrib_nbextensions' +description = 'A collection of various notebook extensions for Jupyter' + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +builddependencies = [ + ('binutils', '2.40'), + ('nodejs', '18.17.1'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('IPython', '8.14.0'), + ('PyYAML', '6.0'), + ('jupyter-server', '2.7.2'), +] + +use_pip = True + +exts_list = [ + ('entrypoints', '0.4', { + 'checksums': ['b706eddaa9218a19ebcd67b56818f05bb27589b1ca9e8d797b74affad4ccacd4'], + }), + ('nbclassic', '1.0.0', { + 'checksums': ['0ae11eb2319455d805596bf320336cda9554b41d99ab9a3c31bf8180bffa30e3'], + }), + # need jupyter_client in v7 - notebook 6.5.7 has requirement jupyter-client<8,>=5.3.4 + ('jupyter_client', '7.4.9', { + 'checksums': ['52be28e04171f07aed8f20e1616a5a552ab9fee9cbbe6c1896ae170c3880d392'], + }), + # use notebook v6, in v7 the extension are moved to jupyter lab + ('notebook', '6.5.7', { + 'checksums': ['04eb9011dfac634fbd4442adaf0a8c27cd26beef831fe1d19faf930c327768e4'], + }), + ('jupyter_contrib_core', '0.4.2', { + 'checksums': ['1887212f3ca9d4487d624c0705c20dfdf03d5a0b9ea2557d3aaeeb4c38bdcabb'], + }), + ('jupyter_highlight_selected_word', '0.2.0', { + 'checksums': ['9fa740424859a807950ca08d2bfd28a35154cd32dd6d50ac4e0950022adc0e7b'], + }), + ('jupyter_nbextensions_configurator', '0.6.3', { + 'source_tmpl': '%(name)s-%(version)s-py2.py3-none-any.whl', + 'checksums': ['cece496f3f62cf80bb0b04867ea463c32ed5db19ff5814fe18a3a7f1bb9da95b'], + }), + ('jupyter_contrib_nbextensions', version, { + 'checksums': ['06e33f005885eb92f89cbe82711e921278201298d08ab0d886d1ba09e8c3e9ca'], + }), +] + +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/jupyter-contrib', 'bin/jupyter-contrib-nbextension', 'bin/jupyter-nbextensions_configurator'], + 'dirs': ['lib64/python%(pyshortver)s/site-packages'] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/j/jupyter-matlab-proxy/jupyter-matlab-proxy-0.12.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/j/jupyter-matlab-proxy/jupyter-matlab-proxy-0.12.2-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..095d491ef49 --- /dev/null +++ b/easybuild/easyconfigs/j/jupyter-matlab-proxy/jupyter-matlab-proxy-0.12.2-GCCcore-12.3.0.eb @@ -0,0 +1,48 @@ +easyblock = "PythonBundle" + +name = 'jupyter-matlab-proxy' +version = '0.12.2' + +homepage = 'https://github.com/mathworks/jupyter-matlab-proxy' +description = 'MATLAB Integration for Jupyter' + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +builddependencies = [ + ('binutils', '2.40'), + ('nodejs', '18.17.1'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('IPython', '8.14.0'), + ('jupyter-server-proxy', '4.0.0'), + ('matlab-proxy', '0.18.1'), +] + +use_pip = True + +exts_list = [ + ('jupyter_matlab_proxy', version, { + 'sources': ['%(name)s-%(version)s-py3-none-any.whl'], + 'checksums': ['2f1fcb8cba3b60ceccfbaa118ce1de0ca54d6c630c6d6ec61c052dca7f62cb6b'], + }), +] + +sanity_pip_check = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages', 'share/jupyter'], +} + +sanity_check_commands = [ + "python -c 'import jupyter_matlab_proxy'", + "python -c 'import jupyter_matlab_kernel'", +] + +modextrapaths = { + 'JUPYTER_PATH': 'share/jupyter', +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/j/jupyter-resource-usage/jupyter-resource-usage-1.0.2-GCCcore-13.2.0.eb b/easybuild/easyconfigs/j/jupyter-resource-usage/jupyter-resource-usage-1.0.2-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..3062f3f80b5 --- /dev/null +++ b/easybuild/easyconfigs/j/jupyter-resource-usage/jupyter-resource-usage-1.0.2-GCCcore-13.2.0.eb @@ -0,0 +1,41 @@ +easyblock = 'PythonBundle' + +name = 'jupyter-resource-usage' +version = "1.0.2" + +homepage = 'https://github.com/jupyter-server/jupyter-resource-usage' +description = "Jupyter Notebook Extension for monitoring your own Resource Usage (memory and/or CPU)" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +builddependencies = [ + ('binutils', '2.40'), + ('hatch-jupyter-builder', '0.9.1'), +] +dependencies = [ + ('Python', '3.11.5'), + ('IPython', '8.17.2'), + ('jupyter-server', '2.14.0'), +] + +sanity_pip_check = True +use_pip = True + +exts_list = [ + ('jupyter_resource_usage', version, { + 'checksums': ['20babc5a63fd53724b12e50b9046ca07784fb56004c39d0442990116fb925a4b'], + }), +] + +sanity_check_paths = { + 'files': [], + 'dirs': [ + 'lib/python%(pyshortver)s/site-packages/jupyter_resource_usage', + 'share/jupyter' + ], +} + +# Add the notebook extension to the search path for jupyter notebooks +modextrapaths = {'EB_ENV_JUPYTER_ROOT': ''} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/j/jupyter-rsession-proxy/jupyter-rsession-proxy-2.2.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/j/jupyter-rsession-proxy/jupyter-rsession-proxy-2.2.0-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..8a4e803d985 --- /dev/null +++ b/easybuild/easyconfigs/j/jupyter-rsession-proxy/jupyter-rsession-proxy-2.2.0-GCCcore-12.3.0.eb @@ -0,0 +1,29 @@ +easyblock = "PythonPackage" + +name = 'jupyter-rsession-proxy' +version = '2.2.0' + +homepage = 'https://github.com/jupyterhub/jupyter-rsession-proxy' +description = "Jupyter extensions for running an RStudio rsession proxy" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['4073f4b4241fe6e976de2c3d49a438b7d82589712e9ee06c19f325a8ec557018'] + +builddependencies = [ + ('binutils', '2.40'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('jupyter-server-proxy', '4.0.0'), +] + +download_dep_fail = True + +use_pip = True +sanity_pip_check = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/j/jupyter-server-proxy/jupyter-server-proxy-4.1.2-GCCcore-13.2.0.eb b/easybuild/easyconfigs/j/jupyter-server-proxy/jupyter-server-proxy-4.1.2-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..c71b66da33e --- /dev/null +++ b/easybuild/easyconfigs/j/jupyter-server-proxy/jupyter-server-proxy-4.1.2-GCCcore-13.2.0.eb @@ -0,0 +1,43 @@ +easyblock = 'PythonBundle' + +name = 'jupyter-server-proxy' +version = '4.1.2' + +homepage = 'https://github.com/jupyterhub/jupyter-server-proxy' +description = """Jupyter Server Proxy lets you run arbitrary external processes +(such as RStudio, Shiny Server, Syncthing, PostgreSQL, Code Server, etc) +alongside your notebook server and provide authenticated web access to them +using a path like /rstudio next to others like /lab. Alongside the python +package that provides the main functionality, the JupyterLab extension +(@jupyterlab/server-proxy) provides buttons in the JupyterLab launcher window +to get to RStudio for example.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +builddependencies = [ + ('binutils', '2.40'), + ('hatch-jupyter-builder', '0.9.1'), +] +dependencies = [ + ('Python', '3.11.5'), + ('IPython', '8.17.2'), + ('jupyter-server', '2.14.0'), + ('OpenSSL', '1.1', '', SYSTEM), + ('aiohttp', '3.9.5'), +] + +sanity_pip_check = True +use_pip = True + +exts_list = [ + ('simpervisor', '1.0.0', { + 'checksums': ['7eb87ca86d5e276976f5bb0290975a05d452c6a7b7f58062daea7d8369c823c1'], + }), + ('jupyter_server_proxy', version, { + 'checksums': ['6fd8ce88a0100e637b48f1d3aa32f09672bcb2813dc057d70567f0a40b1237f5'], + }), +] + +modextrapaths = {'EB_ENV_JUPYTER_ROOT': ''} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/j/jupyter-server/jupyter-core-5.7.2_fix_jupyter_path.patch b/easybuild/easyconfigs/j/jupyter-server/jupyter-core-5.7.2_fix_jupyter_path.patch new file mode 100644 index 00000000000..04788ab7eb6 --- /dev/null +++ b/easybuild/easyconfigs/j/jupyter-server/jupyter-core-5.7.2_fix_jupyter_path.patch @@ -0,0 +1,32 @@ +# Patch jupyter_core to help jupyter find the correct installation path. +# +# If jupyter is installed by EasyBuild, jupyter is not in the same place as python. +# `EB_ENV_JUPYTER_ROOT` is used to indicate where jupyter are and should be set to +# the instllation path in easyconfigs. +# Avoid using `ENV_JUPYTER_PATH` and `ENV_CONFIG_PATH`. Otherwise user configuration +# has lower priority and cannot save their own settings. +# Author: Chia-Jung Hsu, 2024-01-31 +--- a/jupyter_core/paths.py ++++ b/jupyter_core/paths.py +@@ -228,6 +228,10 @@ + + ENV_JUPYTER_PATH: list[str] = [str(Path(sys.prefix, "share", "jupyter"))] + ++if os.environ.get("EB_ENV_JUPYTER_ROOT"): ++ EB_ENV_JUPYTER_ROOT = [p.rstrip(os.sep) for p in os.environ["EB_ENV_JUPYTER_ROOT"].split(os.pathsep)] ++ ENV_JUPYTER_PATH = [str(Path(p, "share", "jupyter")) for p in EB_ENV_JUPYTER_ROOT] ++ + + def jupyter_path(*subdirs: str) -> list[str]: + """Return a list of directories to search for data files +@@ -306,6 +310,10 @@ + ] + ENV_CONFIG_PATH: list[str] = [str(Path(sys.prefix, "etc", "jupyter"))] + ++if os.environ.get("EB_ENV_JUPYTER_ROOT"): ++ EB_ENV_JUPYTER_ROOT = [p.rstrip(os.sep) for p in os.environ["EB_ENV_JUPYTER_ROOT"].split(os.pathsep)] ++ ENV_CONFIG_PATH = [str(Path(p, "etc", "jupyter")) for p in EB_ENV_JUPYTER_ROOT] ++ + + def jupyter_config_path() -> list[str]: + """Return the search path for Jupyter config files as a list. diff --git a/easybuild/easyconfigs/j/jupyter-server/jupyter-server-2.14.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/j/jupyter-server/jupyter-server-2.14.0-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..ee8dfa23154 --- /dev/null +++ b/easybuild/easyconfigs/j/jupyter-server/jupyter-server-2.14.0-GCCcore-13.2.0.eb @@ -0,0 +1,185 @@ +easyblock = 'PythonBundle' + +name = 'jupyter-server' +version = "2.14.0" + +homepage = 'https://jupyter.org/' +description = """The Jupyter Server provides the backend (i.e. the core services, APIs, and REST +endpoints) for Jupyter web applications like Jupyter notebook, JupyterLab, and +Voila.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +builddependencies = [ + ('binutils', '2.40'), + ('maturin', '1.3.1'), # needed by rpds_py + ('hatch-jupyter-builder', '0.9.1'), +] +dependencies = [ + ('Python', '3.11.5'), + ('IPython', '8.17.2'), + ('PyYAML', '6.0.1'), + ('PyZMQ', '25.1.2'), + ('tornado', '6.4'), + ('BeautifulSoup', '4.12.2'), # needed by nbconvert +] + +sanity_pip_check = True +use_pip = True + +# WARNING: the versions of ipywidgets, widgetsnbextension and jupyterlab_widgets are tied between them +# use the versions published in a single release commit instead of blindly pushing to last available version, +# see for instance https://github.com/jupyter-widgets/ipywidgets/commit/b728926f58ed3ffef08f716998ac6c226dafc1aa + +exts_list = [ + ('websocket_client', '1.8.0', { + 'modulename': 'websocket', + 'checksums': ['3239df9f44da632f96012472805d40a23281a991027ce11d2f45a6f24ac4c3da'], + }), + ('terminado', '0.18.1', { + 'checksums': ['de09f2c4b85de4765f7714688fff57d3e75bad1f909b589fde880460c753fd2e'], + }), + ('Send2Trash', '1.8.3', { + 'checksums': ['b18e7a3966d99871aefeb00cfbcfdced55ce4871194810fc71f4aa484b953abf'], + }), + ('prometheus_client', '0.20.0', { + 'checksums': ['287629d00b147a32dcb2be0b9df905da599b2d82f80377083ec8463309a4bb89'], + }), + ('overrides', '7.7.0', { + 'checksums': ['55158fa3d93b98cc75299b1e67078ad9003ca27945c76162c1c0766d6f91820a'], + }), + ('jupyter_core', '5.7.2', { + 'patches': ['jupyter-core-%(version)s_fix_jupyter_path.patch'], + 'checksums': [ + {'jupyter_core-5.7.2.tar.gz': 'aa5f8d32bbf6b431ac830496da7392035d6f61b4f54872f15c4bd2a9c3f536d9'}, + {'jupyter-core-5.7.2_fix_jupyter_path.patch': + '1ed5088728c1ad49687b66e31ed23965c36645ad285693785b2b96c4ff1b2f93'}, + ], + }), + ('fastjsonschema', '2.19.1', { + 'checksums': ['e3126a94bdc4623d3de4485f8d468a12f02a67921315ddc87836d6e456dc789d'], + }), + ('tinycss2', '1.3.0', { + 'checksums': ['152f9acabd296a8375fbca5b84c961ff95971fcfc32e79550c8df8e29118c54d'], + }), + ('pandocfilters', '1.5.1', { + 'checksums': ['002b4a555ee4ebc03f8b66307e287fa492e4a77b4ea14d3f934328297bb4939e'], + }), + ('mistune', '3.0.2', { + 'checksums': ['fc7f93ded930c92394ef2cb6f04a8aabab4117a91449e72dcc8dfa646a508be8'], + }), + ('deprecation', '2.1.0', { + 'checksums': ['72b3bde64e5d778694b0cf68178aed03d15e15477116add3fb773e581f9518ff'], + }), + ('jupyter_packaging', '0.12.3', { + 'checksums': ['9d9b2b63b97ffd67a8bc5391c32a421bc415b264a32c99e4d8d8dd31daae9cf4'], + }), + ('jupyterlab_pygments', '0.3.0', { + 'checksums': ['721aca4d9029252b11cfa9d185e5b5af4d54772bb8072f9b7036f4170054d35d'], + }), + ('defusedxml', '0.7.1', { + 'checksums': ['1bb3032db185915b62d7c6209c5a8792be6a32ab2fedacc84e01b52c51aa3e69'], + }), + ('bleach', '6.1.0', { + 'checksums': ['0a31f1837963c41d46bbf1331b8778e1308ea0791db03cc4e7357b97cf42a8fe'], + }), + ('nbformat', '5.10.4', { + 'checksums': ['322168b14f937a5d11362988ecac2a4952d3d8e3a2cbeb2319584631226d5b3a'], + }), + ('nbclient', '0.10.0', { + 'checksums': ['4b3f1b7dba531e498449c4db4f53da339c91d449dc11e9af3a43b4eb5c5abb09'], + }), + ('jupyter_client', '8.6.1', { + 'checksums': ['e842515e2bab8e19186d89fdfea7abd15e39dd581f94e399f00e2af5a1652d3f'], + }), + ('nbconvert', '7.16.4', { + 'checksums': ['86ca91ba266b0a448dc96fa6c5b9d98affabde2867b363258703536807f9f7f4'], + }), + ('jupyter_server_terminals', '0.5.3', { + 'checksums': ['5ae0295167220e9ace0edcfdb212afd2b01ee8d179fe6f23c899590e9b8a5269'], + }), + ('rfc3986_validator', '0.1.1', { + 'checksums': ['3d44bde7921b3b9ec3ae4e3adca370438eccebc676456449b145d533b240d055'], + }), + ('rfc3339_validator', '0.1.4', { + 'checksums': ['138a2abdf93304ad60530167e51d2dfb9549521a836871b88d7f4695d0022f6b'], + }), + ('rpds_py', '0.18.1', { + 'modulename': 'rpds', + 'checksums': ['dc48b479d540770c811fbd1eb9ba2bb66951863e448efec2e2c102625328e92f'], + }), + ('referencing', '0.35.1', { + 'checksums': ['25b42124a6c8b632a425174f24087783efb348a6f1e0008e63cd4466fedf703c'], + }), + ('python-json-logger', '2.0.7', { + 'modulename': 'pythonjsonlogger', + 'checksums': ['23e7ec02d34237c5aa1e29a070193a4ea87583bb4e7f8fd06d3de8264c4b2e1c'], + }), + ('jsonschema_specifications', '2023.12.1', { + 'checksums': ['48a76787b3e70f5ed53f1160d2b81f586e4ca6d1548c5de7085d1682674764cc'], + }), + ('jsonschema', '4.22.0', { + 'checksums': ['5b22d434a45935119af990552c862e5d6d564e8f6601206b305a61fdf661a2b7'], + }), + ('jupyter_events', '0.10.0', { + 'checksums': ['670b8229d3cc882ec782144ed22e0d29e1c2d639263f92ca8383e66682845e22'], + }), + ('argon2-cffi-bindings', '21.2.0', { + 'modulename': '_argon2_cffi_bindings', + 'checksums': ['bb89ceffa6c791807d1305ceb77dbfacc5aa499891d2c55661c6459651fc39e3'], + }), + ('argon2_cffi', '23.1.0', { + 'modulename': 'argon2', + 'checksums': ['879c3e79a2729ce768ebb7d36d4609e3a78a4ca2ec3a9f12286ca057e3d0db08'], + }), + ('sniffio', '1.3.1', { + 'checksums': ['f4324edc670a0f49750a81b895f35c3adb843cca46f0530f79fc1babb23789dc'], + }), + ('anyio', '4.3.0', { + 'checksums': ['f75253795a87df48568485fd18cdd2a3fa5c4f7c5be8e5e36637733fce06fed6'], + }), + ('jupyter_server', version, { + 'checksums': ['659154cea512083434fd7c93b7fe0897af7a2fd0b9dd4749282b42eaac4ae677'], + }), + ('jupyterlab_widgets', '3.0.10', { + 'checksums': ['04f2ac04976727e4f9d0fa91cdc2f1ab860f965e504c29dbd6a65c882c9d04c0'], + }), + ('widgetsnbextension', '4.0.10', { + 'checksums': ['64196c5ff3b9a9183a8e699a4227fb0b7002f252c814098e66c4d1cd0644688f'], + }), + ('comm', '0.2.2', { + 'checksums': ['3fd7a84065306e07bea1773df6eb8282de51ba82f77c72f9c85716ab11fe980e'], + }), + ('ipywidgets', '8.1.2', { + 'checksums': ['d0b9b41e49bae926a866e613a39b0f0097745d2b9f1f3dd406641b4a57ec42c9'], + }), + # The following few extensions are needed for e.g. JupyterLab but also nbclassic. + # Avoid duplication by making it part of this bundle + ('notebook_shim', '0.2.4', { + 'checksums': ['b4b2cfa1b65d98307ca24361f5b30fe785b53c3fd07b7a47e89acb5e6ac638cb'], + }), + ('nest_asyncio', '1.6.0', { + 'checksums': ['6f172d5449aca15afd6c646851f4e31e02c598d553a667e38cafa997cfec55fe'], + }), + ('ipykernel', '6.29.4', { + 'checksums': ['3d44070060f9475ac2092b760123fadf105d2e2493c24848b6691a7c4f42af5c'], + }), + ('ipython_genutils', '0.2.0', { + 'checksums': ['eb2e116e75ecef9d4d228fdc66af54269afa26ab4463042e33785b887c628ba8'], + }), + ('debugpy', '1.8.1', { + 'source_tmpl': '%(name)s-%(version)s-py2.py3-none-any.whl', + 'checksums': ['28acbe2241222b87e255260c76741e1fbf04fdc3b6d094fcf57b6c6f75ce1242'], + }), +] + +sanity_check_paths = { + 'files': ['bin/jupyter'], + 'dirs': ['share/jupyter', 'etc/jupyter'], +} + +sanity_check_commands = ['jupyter --help'] + +modextrapaths = {'EB_ENV_JUPYTER_ROOT': ''} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/j/jupyter-server/jupyter-server-2.14.2-GCCcore-13.3.0.eb b/easybuild/easyconfigs/j/jupyter-server/jupyter-server-2.14.2-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..e7bc1dceeb0 --- /dev/null +++ b/easybuild/easyconfigs/j/jupyter-server/jupyter-server-2.14.2-GCCcore-13.3.0.eb @@ -0,0 +1,185 @@ +easyblock = 'PythonBundle' + +name = 'jupyter-server' +version = "2.14.2" + +homepage = 'https://jupyter.org/' +description = """The Jupyter Server provides the backend (i.e. the core services, APIs, and REST +endpoints) for Jupyter web applications like Jupyter notebook, JupyterLab, and +Voila.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +builddependencies = [ + ('binutils', '2.42'), + ('maturin', '1.6.0'), # needed by rpds_py + ('hatch-jupyter-builder', '0.9.1'), +] +dependencies = [ + ('Python', '3.12.3'), + ('IPython', '8.28.0'), + ('PyYAML', '6.0.2'), + ('PyZMQ', '26.2.0'), + ('tornado', '6.4.1'), + ('BeautifulSoup', '4.12.3'), # needed by nbconvert +] + +sanity_pip_check = True +use_pip = True + +# WARNING: the versions of ipywidgets, widgetsnbextension and jupyterlab_widgets are tied between them +# use the versions published in a single release commit instead of blindly pushing to last available version, +# see for instance https://github.com/jupyter-widgets/ipywidgets/commit/b728926f58ed3ffef08f716998ac6c226dafc1aa + +exts_list = [ + ('websocket_client', '1.8.0', { + 'modulename': 'websocket', + 'checksums': ['3239df9f44da632f96012472805d40a23281a991027ce11d2f45a6f24ac4c3da'], + }), + ('terminado', '0.18.1', { + 'checksums': ['de09f2c4b85de4765f7714688fff57d3e75bad1f909b589fde880460c753fd2e'], + }), + ('Send2Trash', '1.8.3', { + 'checksums': ['b18e7a3966d99871aefeb00cfbcfdced55ce4871194810fc71f4aa484b953abf'], + }), + ('prometheus_client', '0.21.0', { + 'checksums': ['96c83c606b71ff2b0a433c98889d275f51ffec6c5e267de37c7a2b5c9aa9233e'], + }), + ('overrides', '7.7.0', { + 'checksums': ['55158fa3d93b98cc75299b1e67078ad9003ca27945c76162c1c0766d6f91820a'], + }), + ('jupyter_core', '5.7.2', { + 'patches': ['jupyter-core-%(version)s_fix_jupyter_path.patch'], + 'checksums': [ + {'jupyter_core-5.7.2.tar.gz': 'aa5f8d32bbf6b431ac830496da7392035d6f61b4f54872f15c4bd2a9c3f536d9'}, + {'jupyter-core-5.7.2_fix_jupyter_path.patch': + '1ed5088728c1ad49687b66e31ed23965c36645ad285693785b2b96c4ff1b2f93'}, + ], + }), + ('fastjsonschema', '2.20.0', { + 'checksums': ['3d48fc5300ee96f5d116f10fe6f28d938e6008f59a6a025c2649475b87f76a23'], + }), + ('tinycss2', '1.3.0', { + 'checksums': ['152f9acabd296a8375fbca5b84c961ff95971fcfc32e79550c8df8e29118c54d'], + }), + ('pandocfilters', '1.5.1', { + 'checksums': ['002b4a555ee4ebc03f8b66307e287fa492e4a77b4ea14d3f934328297bb4939e'], + }), + ('mistune', '3.0.2', { + 'checksums': ['fc7f93ded930c92394ef2cb6f04a8aabab4117a91449e72dcc8dfa646a508be8'], + }), + ('deprecation', '2.1.0', { + 'checksums': ['72b3bde64e5d778694b0cf68178aed03d15e15477116add3fb773e581f9518ff'], + }), + ('jupyter_packaging', '0.12.3', { + 'checksums': ['9d9b2b63b97ffd67a8bc5391c32a421bc415b264a32c99e4d8d8dd31daae9cf4'], + }), + ('jupyterlab_pygments', '0.3.0', { + 'checksums': ['721aca4d9029252b11cfa9d185e5b5af4d54772bb8072f9b7036f4170054d35d'], + }), + ('defusedxml', '0.7.1', { + 'checksums': ['1bb3032db185915b62d7c6209c5a8792be6a32ab2fedacc84e01b52c51aa3e69'], + }), + ('bleach', '6.1.0', { + 'checksums': ['0a31f1837963c41d46bbf1331b8778e1308ea0791db03cc4e7357b97cf42a8fe'], + }), + ('nbformat', '5.10.4', { + 'checksums': ['322168b14f937a5d11362988ecac2a4952d3d8e3a2cbeb2319584631226d5b3a'], + }), + ('nbclient', '0.10.0', { + 'checksums': ['4b3f1b7dba531e498449c4db4f53da339c91d449dc11e9af3a43b4eb5c5abb09'], + }), + ('jupyter_client', '8.6.3', { + 'checksums': ['35b3a0947c4a6e9d589eb97d7d4cd5e90f910ee73101611f01283732bd6d9419'], + }), + ('nbconvert', '7.16.4', { + 'checksums': ['86ca91ba266b0a448dc96fa6c5b9d98affabde2867b363258703536807f9f7f4'], + }), + ('jupyter_server_terminals', '0.5.3', { + 'checksums': ['5ae0295167220e9ace0edcfdb212afd2b01ee8d179fe6f23c899590e9b8a5269'], + }), + ('rfc3986_validator', '0.1.1', { + 'checksums': ['3d44bde7921b3b9ec3ae4e3adca370438eccebc676456449b145d533b240d055'], + }), + ('rfc3339_validator', '0.1.4', { + 'checksums': ['138a2abdf93304ad60530167e51d2dfb9549521a836871b88d7f4695d0022f6b'], + }), + ('rpds_py', '0.20.0', { + 'modulename': 'rpds', + 'checksums': ['d72a210824facfdaf8768cf2d7ca25a042c30320b3020de2fa04640920d4e121'], + }), + ('referencing', '0.35.1', { + 'checksums': ['25b42124a6c8b632a425174f24087783efb348a6f1e0008e63cd4466fedf703c'], + }), + ('python-json-logger', '2.0.7', { + 'modulename': 'pythonjsonlogger', + 'checksums': ['23e7ec02d34237c5aa1e29a070193a4ea87583bb4e7f8fd06d3de8264c4b2e1c'], + }), + ('jsonschema_specifications', '2024.10.1', { + 'checksums': ['0f38b83639958ce1152d02a7f062902c41c8fd20d558b0c34344292d417ae272'], + }), + ('jsonschema', '4.23.0', { + 'checksums': ['d71497fef26351a33265337fa77ffeb82423f3ea21283cd9467bb03999266bc4'], + }), + ('jupyter_events', '0.10.0', { + 'checksums': ['670b8229d3cc882ec782144ed22e0d29e1c2d639263f92ca8383e66682845e22'], + }), + ('argon2-cffi-bindings', '21.2.0', { + 'modulename': '_argon2_cffi_bindings', + 'checksums': ['bb89ceffa6c791807d1305ceb77dbfacc5aa499891d2c55661c6459651fc39e3'], + }), + ('argon2_cffi', '23.1.0', { + 'modulename': 'argon2', + 'checksums': ['879c3e79a2729ce768ebb7d36d4609e3a78a4ca2ec3a9f12286ca057e3d0db08'], + }), + ('sniffio', '1.3.1', { + 'checksums': ['f4324edc670a0f49750a81b895f35c3adb843cca46f0530f79fc1babb23789dc'], + }), + ('anyio', '4.3.0', { + 'checksums': ['f75253795a87df48568485fd18cdd2a3fa5c4f7c5be8e5e36637733fce06fed6'], + }), + ('jupyter_server', version, { + 'checksums': ['66095021aa9638ced276c248b1d81862e4c50f292d575920bbe960de1c56b12b'], + }), + ('jupyterlab_widgets', '3.0.13', { + 'checksums': ['a2966d385328c1942b683a8cd96b89b8dd82c8b8f81dda902bb2bc06d46f5bed'], + }), + ('widgetsnbextension', '4.0.13', { + 'checksums': ['ffcb67bc9febd10234a362795f643927f4e0c05d9342c727b65d2384f8feacb6'], + }), + ('comm', '0.2.2', { + 'checksums': ['3fd7a84065306e07bea1773df6eb8282de51ba82f77c72f9c85716ab11fe980e'], + }), + ('ipywidgets', '8.1.5', { + 'checksums': ['870e43b1a35656a80c18c9503bbf2d16802db1cb487eec6fab27d683381dde17'], + }), + # The following few extensions are needed for e.g. JupyterLab but also nbclassic. + # Avoid duplication by making it part of this bundle + ('notebook_shim', '0.2.4', { + 'checksums': ['b4b2cfa1b65d98307ca24361f5b30fe785b53c3fd07b7a47e89acb5e6ac638cb'], + }), + ('nest_asyncio', '1.6.0', { + 'checksums': ['6f172d5449aca15afd6c646851f4e31e02c598d553a667e38cafa997cfec55fe'], + }), + ('ipykernel', '6.29.5', { + 'checksums': ['f093a22c4a40f8828f8e330a9c297cb93dcab13bd9678ded6de8e5cf81c56215'], + }), + ('ipython_genutils', '0.2.0', { + 'checksums': ['eb2e116e75ecef9d4d228fdc66af54269afa26ab4463042e33785b887c628ba8'], + }), + ('debugpy', '1.8.7', { + 'source_tmpl': '%(name)s-%(version)s-py2.py3-none-any.whl', + 'checksums': ['57b00de1c8d2c84a61b90880f7e5b6deaf4c312ecbde3a0e8912f2a56c4ac9ae'], + }), +] + +sanity_check_paths = { + 'files': ['bin/jupyter'], + 'dirs': ['share/jupyter', 'etc/jupyter'], +} + +sanity_check_commands = ['jupyter --help'] + +modextrapaths = {'EB_ENV_JUPYTER_ROOT': ''} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/j/jupyter-server/jupyter-server-2.7.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/j/jupyter-server/jupyter-server-2.7.2-GCCcore-12.3.0.eb index 53722e2f4cb..9da7cc3f037 100644 --- a/easybuild/easyconfigs/j/jupyter-server/jupyter-server-2.7.2-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/j/jupyter-server/jupyter-server-2.7.2-GCCcore-12.3.0.eb @@ -16,7 +16,9 @@ builddependencies = [ ] dependencies = [ ('Python', '3.11.3'), + ('hatchling', '1.18.0'), # needed as dependency for hatch_jupyter_builder ('IPython', '8.14.0'), + ('BeautifulSoup', '4.12.2'), # needed by nbconvert ('PyYAML', '6.0'), ('PyZMQ', '25.1.1'), ('tornado', '6.3.2'), diff --git a/easybuild/easyconfigs/j/jupyter-vscode-proxy/jupyter-vscode-proxy-0.6-GCCcore-12.3.0.eb b/easybuild/easyconfigs/j/jupyter-vscode-proxy/jupyter-vscode-proxy-0.6-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..1f8a364ba25 --- /dev/null +++ b/easybuild/easyconfigs/j/jupyter-vscode-proxy/jupyter-vscode-proxy-0.6-GCCcore-12.3.0.eb @@ -0,0 +1,32 @@ +easyblock = "PythonBundle" + +name = 'jupyter-vscode-proxy' +version = '0.6' + +homepage = 'https://github.com/betatim/vscode-binder' +description = "VS Code extension for Jupyter" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +builddependencies = [ + ('binutils', '2.40'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('jupyter-server-proxy', '4.0.0'), + ('code-server', '4.90.2', '', SYSTEM), +] + +use_pip = True + +exts_list = [ + ('jupyter_vscode_proxy', version, { + 'sources': ['%(name)s-%(version)s-py3-none-any.whl'], + 'checksums': ['c72037d1234f0cd489ecb0ab40ec8b150fc9cd7006b4d9c7036200e76689da78'], + }), +] + +sanity_pip_check = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/j/jupyterlmod/jupyterlmod-5.2.1-GCCcore-13.2.0.eb b/easybuild/easyconfigs/j/jupyterlmod/jupyterlmod-5.2.1-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..2f0f8aabd7f --- /dev/null +++ b/easybuild/easyconfigs/j/jupyterlmod/jupyterlmod-5.2.1-GCCcore-13.2.0.eb @@ -0,0 +1,43 @@ +easyblock = 'PythonBundle' + +name = 'jupyterlmod' +version = '5.2.1' + +# This easyconfig installs the notebook and lab extension of Jupyter Lmod + +homepage = 'https://github.com/cmd-ntrf/jupyter-lmod' +description = """Jupyter interactive notebook server extension that allows users to interact with +environment modules before launching kernels. The extension uses Lmod's Python +interface to accomplish module-related tasks like loading, unloading, saving +collections, etc.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +builddependencies = [ + ('binutils', '2.40'), +] + +dependencies = [ + ('Python', '3.11.5'), + ('JupyterNotebook', '7.2.0'), +] + +use_pip = True + +exts_list = [ + (name, version, { + 'sources': ['%(name)s-%(version)s-py3-none-any.whl'], + 'checksums': ['6f9c94d80b813792a6b63aeff5f2672f7d485ce43a7fd5bb7f6fce1c0907cad5'], + }), +] + +sanity_pip_check = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages', 'share/jupyter'], +} + +modextrapaths = {'EB_ENV_JUPYTER_ROOT': ''} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/j/jxrlib/jxrlib-1.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/j/jxrlib/jxrlib-1.1-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..f8aeb2b413a --- /dev/null +++ b/easybuild/easyconfigs/j/jxrlib/jxrlib-1.1-GCCcore-12.3.0.eb @@ -0,0 +1,39 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author:: Denis Kristak (INUITS) +# Update: Thomas Hoffmann (EMBL) +## + +easyblock = 'CMakeMake' + +name = 'jxrlib' +version = '1.1' + +homepage = 'https://github.com/4creators/jxrlib' +description = """Open source implementation of jpegxr""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://deb.debian.org/debian/pool/main/j/jxrlib/'] +sources = ['%(name)s_%(version)s.orig.tar.gz'] +patches = [('jxrlib-%(version)s_cmake.patch', 1)] +checksums = [ + {'jxrlib_1.1.orig.tar.gz': 'c7287b86780befa0914f2eeb8be2ac83e672ebd4bd16dc5574a36a59d9708303'}, + {'jxrlib-1.1_cmake.patch': 'e96ea8b418fdab10e9cbc2f4cad95ca1f59a826ce7379c6a3192882050689a74'}, +] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.26.3'), +] + +sanity_check_paths = { + 'files': ['bin/JxrDecApp', 'bin/JxrEncApp', "lib/libjpegxr.%s" % SHLIB_EXT], + 'dirs': [], +} + +sanity_check_commands = ['JxrDecApp', 'JxrEncApp'] + +modextrapaths = {'CPATH': 'include/jxrlib'} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/k/KMCLib/KMCLib-2.0-a2-foss-2023a-Python-2.7.18.eb b/easybuild/easyconfigs/k/KMCLib/KMCLib-2.0-a2-foss-2023a-Python-2.7.18.eb new file mode 100644 index 00000000000..12cf687bb00 --- /dev/null +++ b/easybuild/easyconfigs/k/KMCLib/KMCLib-2.0-a2-foss-2023a-Python-2.7.18.eb @@ -0,0 +1,51 @@ +easyblock = 'CMakeMake' + +name = 'KMCLib' +version = '2.0-a2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/leetmaa/KMCLib' +description = """KMCLib - a general framework for lattice kinetic Monte Carlo (KMC) simulations""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['https://github.com/leetmaa/KMCLib/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['796620a67ad010df4b11734f703151c17441f82cef026f3d56386a34056d0213'] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.26.3'), + ('SWIG', '4.1.1'), +] + +dependencies = [ + ('Python', '2.7.18'), + ('numpy', '1.16.6', versionsuffix), +] + +start_dir = 'c++' + +preconfigopts = 'cd ../%(name)s-%(version)s/c++/externals && ' +preconfigopts += 'make CC="$CC" CXX="$CXX" CFLAGS="$CFLAGS" CXXFLAGS="$CXXFLAGS" && cd - && ' + +prebuildopts = 'export CPATH=$EBROOTPYTHON/include/python%(pyshortver)s:$CPATH && ' + +buildopts = ' && cp wrap/Backend.py wrap/_Backend.so wrap/Custom.py wrap/_Custom.so' +buildopts += ' "%(builddir)s/%(name)s-%(version)s/python/src/KMCLib/Backend/"' + +test_cmd = 'export PYTHONPATH="%(builddir)s/%(name)s-%(version)s/python/src:$PYTHONPATH" && ' +test_cmd += 'python "%(builddir)s/%(name)s-%(version)s/python/unittest/utest.py"' + +install_cmd = 'cp -r "%(builddir)s/%(name)s-%(version)s/python/src/KMCLib" "%(installdir)s/"' + +modextrapaths = {'PYTHONPATH': ''} + +sanity_check_paths = { + 'files': [], + 'dirs': ['KMCLib/Backend'], +} + +sanity_check_commands = ["python -c 'from KMCLib import *'"] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/k/Kaleido/Kaleido-0.2.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/k/Kaleido/Kaleido-0.2.1-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..231466bb169 --- /dev/null +++ b/easybuild/easyconfigs/k/Kaleido/Kaleido-0.2.1-GCCcore-12.3.0.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonBundle' + +name = 'Kaleido' +version = '0.2.1' + +homepage = 'https://github.com/plotly/Kaleido' +description = "Fast static image export for web-based visualization libraries with zero dependencies" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +builddependencies = [ + ('binutils', '2.40'), +] + +dependencies = [('Python', '3.11.3')] + +if ARCH == 'x86_64': + local_source_tmpl = '%(namelower)s-%(version)s-py2.py3-none-manylinux1_%(arch)s.whl' +elif ARCH == 'aarch64': + local_source_tmpl = '%(namelower)s-%(version)s-py2.py3-none-manylinux2014_%(arch)s.whl' + +exts_list = [ + (name, version, { + 'source_tmpl': local_source_tmpl, + 'checksums': ['aa21cf1bf1c78f8fa50a9f7d45e1003c387bd3d6fe0a767cfbbf344b95bdc3a8'], + }), +] + +use_pip = True +sanity_pip_check = True + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/k/Kaleido/Kaleido-0.2.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/k/Kaleido/Kaleido-0.2.1-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..7413eeebb71 --- /dev/null +++ b/easybuild/easyconfigs/k/Kaleido/Kaleido-0.2.1-GCCcore-13.3.0.eb @@ -0,0 +1,25 @@ +easyblock = 'PythonPackage' + +name = 'Kaleido' +version = '0.2.1' + +homepage = 'https://github.com/plotly/Kaleido' +description = "Fast static image export for web-based visualization libraries with zero dependencies" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +sources = ['%(namelower)s-%(version)s-py2.py3-none-manylinux1_%(arch)s.whl'] +checksums = ['aa21cf1bf1c78f8fa50a9f7d45e1003c387bd3d6fe0a767cfbbf344b95bdc3a8'] + +builddependencies = [ + ('binutils', '2.42'), +] +dependencies = [ + ('Python', '3.12.3'), +] + +download_dep_fail = True +sanity_pip_check = True +use_pip = True + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/k/Kent_tools/Kent_tools-461-GCC-12.2.0.eb b/easybuild/easyconfigs/k/Kent_tools/Kent_tools-461-GCC-12.2.0.eb new file mode 100644 index 00000000000..9679801e25f --- /dev/null +++ b/easybuild/easyconfigs/k/Kent_tools/Kent_tools-461-GCC-12.2.0.eb @@ -0,0 +1,44 @@ +easyblock = 'MakeCp' + +name = 'Kent_tools' +version = '461' + +homepage = 'https://genome.cse.ucsc.edu/' +description = """Kent utilities: collection of tools used by the UCSC genome browser.""" + +toolchain = {'name': 'GCC', 'version': '12.2.0'} +source_urls = [ + 'https://hgdownload.cse.ucsc.edu/admin/exe/', + 'https://hgdownload.cse.ucsc.edu/admin/exe/userApps.archive/', +] +sources = ['userApps.v%(version)s.src.tgz'] +checksums = [ + {'userApps.v461.src.tgz': 'ff350f030906bea2cdfa5c57d713568123e17c1a5c0ce578d2d9633ca1b742bc'}, +] + +dependencies = [ + ('MariaDB', '10.11.2'), + ('libpng', '1.6.38'), + ('zlib', '1.2.12'), + ('util-linux', '2.38.1'), + ('OpenSSL', '1.1', '', SYSTEM), + ('freetype', '2.12.1'), +] + +prebuildopts = 'sed -i "s/rsync -a /cp -a /" %(builddir)s/userApps/kent/src/parasol/makefile && ' + +buildopts = 'CC="$CC" COPT="$CFLAGS -fcommon" PNGLIB="-L$EBROOTLIBPNG/lib -lpng" ZLIB="-L$EBROOTZLIB/lib -lz" ' +buildopts += 'SSL_DIR="$EBROOTOPENSSL" SSLDIR="$EBROOTOPENSSL" MYSQLLIBS="-L$EBROOTMARIADB/lib -lmariadb -lstdc++" ' + +local_binaries = ['blat', 'bedPartition', 'getRna', 'liftOver', 'mafGene', 'splitFile', 'twoBitToFa'] + +files_to_copy = [(['bin/*'], 'bin'), 'licenseBlat.txt', 'licenseUcscGenomeBrowser.txt'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_binaries], + 'dirs': [], +} + +sanity_check_commands = ["%s 2>&1 | grep '^usage:'" % x for x in local_binaries] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/k/Kent_tools/Kent_tools-468-GCC-12.3.0.eb b/easybuild/easyconfigs/k/Kent_tools/Kent_tools-468-GCC-12.3.0.eb new file mode 100644 index 00000000000..e4fd527e908 --- /dev/null +++ b/easybuild/easyconfigs/k/Kent_tools/Kent_tools-468-GCC-12.3.0.eb @@ -0,0 +1,42 @@ +easyblock = 'MakeCp' + +name = 'Kent_tools' +version = '468' + +homepage = 'https://genome.cse.ucsc.edu/' +description = """Kent utilities: collection of tools used by the UCSC genome browser.""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} +source_urls = [ + 'https://hgdownload.cse.ucsc.edu/admin/exe/', + 'https://hgdownload.cse.ucsc.edu/admin/exe/userApps.archive/', +] +sources = ['userApps.v%(version)s.src.tgz'] +checksums = ['f57b49be7e4eeb0719ac9414ca8878f93916fc3eb8dd408c8f7e076a999d1ca8'] + +dependencies = [ + ('MariaDB', '11.6.0'), + ('libpng', '1.6.39'), + ('zlib', '1.2.13'), + ('util-linux', '2.39'), + ('OpenSSL', '1.1', '', SYSTEM), + ('freetype', '2.13.0'), +] + +prebuildopts = 'sed -i "s/rsync -a /cp -a /" %(builddir)s/userApps/kent/src/parasol/makefile && ' + +buildopts = 'CC="$CC" COPT="$CFLAGS -fcommon" PNGLIB="-L$EBROOTLIBPNG/lib -lpng" ZLIB="-L$EBROOTZLIB/lib -lz" ' +buildopts += 'SSL_DIR="$EBROOTOPENSSL" SSLDIR="$EBROOTOPENSSL" MYSQLLIBS="-L$EBROOTMARIADB/lib -lmariadb -lstdc++" ' + +local_binaries = ['blat', 'bedPartition', 'getRna', 'liftOver', 'mafGene', 'splitFile', 'twoBitToFa'] + +files_to_copy = [(['bin/*'], 'bin'), 'licenseBlat.txt', 'licenseUcscGenomeBrowser.txt'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_binaries], + 'dirs': [], +} + +sanity_check_commands = ["%s 2>&1 | grep '^usage:'" % x for x in local_binaries] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/k/kallisto/kallisto-0.51.1-gompi-2023a.eb b/easybuild/easyconfigs/k/kallisto/kallisto-0.51.1-gompi-2023a.eb new file mode 100644 index 00000000000..ae831c08a64 --- /dev/null +++ b/easybuild/easyconfigs/k/kallisto/kallisto-0.51.1-gompi-2023a.eb @@ -0,0 +1,46 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild + +easyblock = 'CMakeMake' + +name = 'kallisto' +version = '0.51.1' + +homepage = 'https://pachterlab.github.io/kallisto/' +description = """kallisto is a program for quantifying abundances of transcripts from RNA-Seq data, or more generally + of target sequences using high-throughput sequencing reads.""" + +toolchain = {'name': 'gompi', 'version': '2023a'} +toolchainopts = {'pic': True, 'usempi': True} + +github_account = 'pachterlab' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['a8bcc23bca6ac758f15e30bb77e9e169e628beff2da3be2e34a53e1d42253516'] + +builddependencies = [ + ('Autotools', '20220317'), + ('CMake', '3.26.3'), + ('zlib', '1.2.13'), +] + +dependencies = [ + ('HDF5', '1.14.0'), + ('HTSlib', '1.18'), +] + +parallel = 1 + +configopts = '-DUSE_HDF5=ON' + +sanity_check_paths = { + 'files': ['bin/%(name)s'], + 'dirs': [], +} + +sanity_check_commands = [ + "kallisto version", + "cd %(builddir)s/%(name)s-%(version)s/test && kallisto index -i ts.idx transcripts.fasta.gz", + "cd %(builddir)s/%(name)s-%(version)s/test && kallisto quant -i ts.idx -o out -b 100 reads_{1,2}.fastq.gz", +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/k/kallisto/kallisto-0.51.1-gompi-2023b.eb b/easybuild/easyconfigs/k/kallisto/kallisto-0.51.1-gompi-2023b.eb new file mode 100644 index 00000000000..68cf98992dd --- /dev/null +++ b/easybuild/easyconfigs/k/kallisto/kallisto-0.51.1-gompi-2023b.eb @@ -0,0 +1,46 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild + +easyblock = 'CMakeMake' + +name = 'kallisto' +version = '0.51.1' + +homepage = 'https://pachterlab.github.io/kallisto/' +description = """kallisto is a program for quantifying abundances of transcripts from RNA-Seq data, or more generally + of target sequences using high-throughput sequencing reads.""" + +toolchain = {'name': 'gompi', 'version': '2023b'} +toolchainopts = {'pic': True, 'usempi': True} + +github_account = 'pachterlab' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['a8bcc23bca6ac758f15e30bb77e9e169e628beff2da3be2e34a53e1d42253516'] + +builddependencies = [ + ('Autotools', '20220317'), + ('CMake', '3.27.6'), + ('zlib', '1.2.13'), +] + +dependencies = [ + ('HDF5', '1.14.3'), + ('HTSlib', '1.19.1'), +] + +parallel = 1 + +configopts = '-DUSE_HDF5=ON' + +sanity_check_paths = { + 'files': ['bin/%(name)s'], + 'dirs': [], +} + +sanity_check_commands = [ + "kallisto version", + "cd %(builddir)s/%(name)s-%(version)s/test && kallisto index -i ts.idx transcripts.fasta.gz", + "cd %(builddir)s/%(name)s-%(version)s/test && kallisto quant -i ts.idx -o out -b 100 reads_{1,2}.fastq.gz", +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/k/kim-api/kim-api-2.3.0-GCC-13.2.0.eb b/easybuild/easyconfigs/k/kim-api/kim-api-2.3.0-GCC-13.2.0.eb new file mode 100644 index 00000000000..5b1bf9a4cd6 --- /dev/null +++ b/easybuild/easyconfigs/k/kim-api/kim-api-2.3.0-GCC-13.2.0.eb @@ -0,0 +1,43 @@ +easyblock = 'CMakeMake' + +name = 'kim-api' +version = '2.3.0' + +homepage = 'https://openkim.org/' +description = """Open Knowledgebase of Interatomic Models. + +KIM is an API and OpenKIM is a collection of interatomic models (potentials) for +atomistic simulations. This is a library that can be used by simulation programs +to get access to the models in the OpenKIM database. + +This EasyBuild only installs the API, the models can be installed with the +package openkim-models, or the user can install them manually by running + kim-api-collections-management install user MODELNAME +or + kim-api-collections-management install user OpenKIM +to install them all. + """ + +toolchain = {'name': 'GCC', 'version': '13.2.0'} + +source_urls = ['https://s3.openkim.org/kim-api/'] +sources = ['%(name)s-%(version)s.txz'] +checksums = ['93673bb8fbc0625791f2ee67915d1672793366d10cabc63e373196862c14f991'] + +dependencies = [ + ('CMake', '3.27.6'), # Also needed to install models, thus not just a builddependency. +] + +parallel = 1 +separate_build_dir = True + +modextravars = { + 'KIM_API_CMAKE_PREFIX_DIR': '%(installdir)s/lib64' +} + +sanity_check_paths = { + 'files': ['bin/kim-api-collections-management', 'lib64/libkim-api.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/k/kineto/kineto-0.4.0-GCC-12.3.0.eb b/easybuild/easyconfigs/k/kineto/kineto-0.4.0-GCC-12.3.0.eb new file mode 100644 index 00000000000..4dd6b4afdf1 --- /dev/null +++ b/easybuild/easyconfigs/k/kineto/kineto-0.4.0-GCC-12.3.0.eb @@ -0,0 +1,35 @@ +easyblock = 'CMakeMake' + +name = 'kineto' +version = '0.4.0' + +homepage = 'https://github.com/pytorch/kineto' +description = "A CPU+GPU Profiling library that provides access to timeline traces and hardware performance counters" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +source_urls = ['https://github.com/pytorch/kineto/archive/'] +sources = [{ + 'git_config': { + 'url': 'https://github.com/pytorch', + 'repo_name': name, + 'tag': 'v%(version)s', + 'recursive': True, + }, + 'filename': SOURCE_TAR_GZ, +}] +checksums = [None] + +builddependencies = [ + ('CMake', '3.26.3'), + ('Python', '3.11.3'), +] + +start_dir = 'libkineto' + +sanity_check_paths = { + 'files': ['lib/libkineto.a'], + 'dirs': ['include/kineto'], +} + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/k/kyber/kyber-0.4.0-GCC-12.3.0.eb b/easybuild/easyconfigs/k/kyber/kyber-0.4.0-GCC-12.3.0.eb new file mode 100644 index 00000000000..14fa1faab67 --- /dev/null +++ b/easybuild/easyconfigs/k/kyber/kyber-0.4.0-GCC-12.3.0.eb @@ -0,0 +1,452 @@ +easyblock = 'Cargo' + +name = 'kyber' +version = '0.4.0' + +homepage = 'https://github.com/wdecoster/kyber' +description = """Tool to quickly make a minimalistic 600x600 pixels + heatmap image of read length (log-transformed) and read accuracy.""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +source_urls = ['https://github.com/wdecoster/kyber/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = ['kyber-0.4.0_requirements.patch'] +checksums = [ + {'v0.4.0.tar.gz': '1a89538d2795e5f589fd18280de4443d3311454ed70f595b3e6611bd8d8811e1'}, + {'ab_glyph_rasterizer-0.1.8.tar.gz': 'c71b1793ee61086797f5c80b6efa2b8ffa6d5dd703f118545808a7f2e27f7046'}, + {'adler-1.0.2.tar.gz': 'f26201604c87b1e01bd3d98f8d5d9a8fcbb815e8cedb41ffccbeb4bf593a35fe'}, + {'aho-corasick-0.7.20.tar.gz': 'cc936419f96fa211c1b9166887b38e5e40b19958e5b895be7c1f93adec7071ac'}, + {'approx-0.5.1.tar.gz': 'cab112f0a86d568ea0e627cc1d6be74a1e9cd55214684db5561995f6dad897c6'}, + {'autocfg-1.1.0.tar.gz': 'd468802bab17cbc0cc575e9b053f41e72aa36bfa6b7f55e3529ffa43161b97fa'}, + {'bio-types-0.13.0.tar.gz': 'dfa990f40a28735fa598dc3dd58d73e62e6b41458959d623903b927ba7b04c80'}, + {'bit_field-0.10.2.tar.gz': 'dc827186963e592360843fb5ba4b973e145841266c1357f7180c43526f2e5b61'}, + {'bitflags-1.3.2.tar.gz': 'bef38d45163c2f1dde094a7dfd33ccf595c92905c8f8f4fdc18d06fb1037718a'}, + {'bumpalo-3.12.0.tar.gz': '0d261e256854913907f67ed06efbc3338dfe6179796deefc1ff763fc1aee5535'}, + {'bytemuck-1.13.1.tar.gz': '17febce684fd15d89027105661fec94afb475cb995fbc59d2865198446ba2eea'}, + {'byteorder-1.4.3.tar.gz': 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('num-integer', '0.1.45'), + ('num-iter', '0.1.43'), + ('num-rational', '0.4.1'), + ('num-traits', '0.2.15'), + ('num_cpus', '1.15.0'), + ('once_cell', '1.17.1'), + ('openssl-src', '111.25.1+1.1.1t'), + ('openssl-sys', '0.9.81'), + ('os_str_bytes', '6.4.1'), + ('owned_ttf_parser', '0.15.2'), + ('paste', '1.0.12'), + ('percent-encoding', '2.2.0'), + ('pin-project', '1.0.12'), + ('pin-project-internal', '1.0.12'), + ('pkg-config', '0.3.26'), + ('png', '0.17.7'), + ('ppv-lite86', '0.2.17'), + ('proc-macro-error', '1.0.4'), + ('proc-macro-error-attr', '1.0.4'), + ('proc-macro2', '1.0.70'), + ('quick-error', '1.2.3'), + ('quote', '1.0.26'), + ('rand', '0.7.3'), + ('rand_chacha', '0.2.2'), + ('rand_core', '0.5.1'), + ('rand_distr', '0.2.2'), + ('rand_hc', '0.2.0'), + ('rawpointer', '0.2.1'), + ('rayon', '1.7.0'), + ('rayon-core', '1.11.0'), + ('regex', '1.7.1'), + ('regex-syntax', '0.6.28'), + ('rust-htslib', '0.43.1'), + ('rustc_version', '0.1.7'), + ('rustix', '0.36.9'), + ('rusttype', '0.9.3'), + ('rustversion', '1.0.12'), + ('safe_arch', '0.6.0'), + ('scoped_threadpool', '0.1.9'), + ('scopeguard', '1.1.0'), + ('semver', '0.1.20'), + ('simba', '0.7.3'), + ('simd-adler32', '0.3.5'), + ('smallvec', '1.10.0'), + ('spin', '0.9.6'), + ('strsim', '0.11.0'), + ('strum_macros', '0.24.3'), + ('syn', '1.0.109'), + ('syn', '2.0.12'), + ('termcolor', '1.2.0'), + ('thiserror', '1.0.39'), + ('thiserror-impl', '1.0.39'), + ('tiff', '0.8.1'), + ('tinyvec', '1.6.0'), + ('tinyvec_macros', '0.1.1'), + ('ttf-parser', '0.15.2'), + ('typenum', '1.16.0'), + ('unicode-bidi', '0.3.11'), + ('unicode-ident', '1.0.8'), + ('unicode-normalization', '0.1.22'), + ('url', '2.3.1'), + ('vcpkg', '0.2.15'), + ('version_check', '0.9.4'), + ('wasi', '0.9.0+wasi-snapshot-preview1'), + ('wasi', '0.11.0+wasi-snapshot-preview1'), + ('wasm-bindgen', '0.2.84'), + ('wasm-bindgen-backend', '0.2.84'), + ('wasm-bindgen-macro', '0.2.84'), + ('wasm-bindgen-macro-support', '0.2.84'), + ('wasm-bindgen-shared', '0.2.84'), + ('weezl', '0.1.7'), + ('wide', '0.7.8'), + ('winapi', '0.3.9'), + ('winapi-i686-pc-windows-gnu', '0.4.0'), + ('winapi-util', '0.1.5'), + ('winapi-x86_64-pc-windows-gnu', '0.4.0'), + ('windows-sys', '0.45.0'), + ('windows-sys', '0.48.0'), + ('windows-sys', '0.52.0'), + ('windows-targets', '0.42.2'), + ('windows-targets', '0.48.5'), + ('windows-targets', '0.52.0'), + ('windows_aarch64_gnullvm', '0.42.2'), + ('windows_aarch64_gnullvm', '0.48.5'), + ('windows_aarch64_gnullvm', '0.52.0'), + ('windows_aarch64_msvc', '0.42.2'), + ('windows_aarch64_msvc', '0.48.5'), + ('windows_aarch64_msvc', '0.52.0'), + ('windows_i686_gnu', '0.42.2'), + ('windows_i686_gnu', '0.48.5'), + ('windows_i686_gnu', '0.52.0'), + ('windows_i686_msvc', '0.42.2'), + ('windows_i686_msvc', '0.48.5'), + ('windows_i686_msvc', '0.52.0'), + ('windows_x86_64_gnu', '0.42.2'), + ('windows_x86_64_gnu', '0.48.5'), + ('windows_x86_64_gnu', '0.52.0'), + ('windows_x86_64_gnullvm', '0.42.2'), + ('windows_x86_64_gnullvm', '0.48.5'), + ('windows_x86_64_gnullvm', '0.52.0'), + ('windows_x86_64_msvc', '0.42.2'), + ('windows_x86_64_msvc', '0.48.5'), + ('windows_x86_64_msvc', '0.52.0'), + ('zune-inflate', '0.2.51'), +] + +builddependencies = [ + ('Rust', '1.75.0'), + ('CMake', '3.26.3'), +] + +dependencies = [ + ('bzip2', '1.0.8'), + ('OpenSSL', '1.1', '', SYSTEM), +] + +sanity_check_paths = { + 'files': ['bin/%(name)s'], + 'dirs': [], +} + +sanity_check_commands = ["%(name)s --version"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/k/kyber/kyber-0.4.0_requirements.patch b/easybuild/easyconfigs/k/kyber/kyber-0.4.0_requirements.patch new file mode 100644 index 00000000000..4f59f4a0e8e --- /dev/null +++ b/easybuild/easyconfigs/k/kyber/kyber-0.4.0_requirements.patch @@ -0,0 +1,521 @@ +Use newer `proc-macro2` to avoid the `proc_macro_span_shrink` error. +see https://github.com/dtolnay/proc-macro2/issues/356 + https://github.com/rust-lang/rust/issues/113152 +Author: Petr Král (INUITS) +diff -u 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b/easybuild/easyconfigs/l/LAME/LAME-3.100-GCCcore-11.2.0.eb @@ -25,9 +25,6 @@ dependencies = [('ncurses', '6.2')] preconfigopts = "autoconf && " -# configure is broken: add workaround to find libncurses... -configure_cmd_prefix = "FRONTEND_LDADD='-L${EBROOTNCURSES}/lib' " - sanity_check_paths = { 'files': ['bin/lame', 'include/lame/lame.h', 'lib/libmp3lame.%s' % SHLIB_EXT], 'dirs': [], diff --git a/easybuild/easyconfigs/l/LAME/LAME-3.100-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/LAME/LAME-3.100-GCCcore-11.3.0.eb index f067051ffe7..5efdefb761f 100644 --- a/easybuild/easyconfigs/l/LAME/LAME-3.100-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/l/LAME/LAME-3.100-GCCcore-11.3.0.eb @@ -25,9 +25,6 @@ dependencies = [('ncurses', '6.3')] preconfigopts = "autoconf && " -# configure is broken: add workaround to find libncurses... -configure_cmd_prefix = "FRONTEND_LDADD='-L${EBROOTNCURSES}/lib' " - sanity_check_paths = { 'files': ['bin/lame', 'include/lame/lame.h', 'lib/libmp3lame.%s' % SHLIB_EXT], 'dirs': [], diff --git a/easybuild/easyconfigs/l/LAME/LAME-3.100-GCCcore-12.2.0.eb b/easybuild/easyconfigs/l/LAME/LAME-3.100-GCCcore-12.2.0.eb index 4008e0b3455..7d4bae408d5 100644 --- a/easybuild/easyconfigs/l/LAME/LAME-3.100-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/l/LAME/LAME-3.100-GCCcore-12.2.0.eb @@ -25,9 +25,6 @@ dependencies = [('ncurses', '6.3')] preconfigopts = "autoconf && " -# configure is broken: add workaround to find libncurses... -configure_cmd_prefix = "FRONTEND_LDADD='-L${EBROOTNCURSES}/lib' " - sanity_check_paths = { 'files': ['bin/lame', 'include/lame/lame.h', 'lib/libmp3lame.%s' % SHLIB_EXT], 'dirs': [], diff --git a/easybuild/easyconfigs/l/LAME/LAME-3.100-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/LAME/LAME-3.100-GCCcore-12.3.0.eb index 4573d76f947..a4c7dbd4278 100644 --- a/easybuild/easyconfigs/l/LAME/LAME-3.100-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/l/LAME/LAME-3.100-GCCcore-12.3.0.eb @@ -25,9 +25,6 @@ dependencies = [('ncurses', '6.4')] preconfigopts = "autoconf && " -# configure is broken: add workaround to find libncurses... -configure_cmd_prefix = "FRONTEND_LDADD='-L${EBROOTNCURSES}/lib' " - sanity_check_paths = { 'files': ['bin/lame', 'include/lame/lame.h', 'lib/libmp3lame.%s' % SHLIB_EXT], 'dirs': [], diff --git a/easybuild/easyconfigs/l/LAME/LAME-3.100-GCCcore-13.2.0.eb b/easybuild/easyconfigs/l/LAME/LAME-3.100-GCCcore-13.2.0.eb index 7b163dff699..1bffb9a1939 100644 --- a/easybuild/easyconfigs/l/LAME/LAME-3.100-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/l/LAME/LAME-3.100-GCCcore-13.2.0.eb @@ -25,9 +25,6 @@ dependencies = [('ncurses', '6.4')] preconfigopts = "autoconf && " -# configure is broken: add workaround to find libncurses... -configure_cmd_prefix = "FRONTEND_LDADD='-L${EBROOTNCURSES}/lib' " - sanity_check_paths = { 'files': ['bin/lame', 'include/lame/lame.h', 'lib/libmp3lame.%s' % SHLIB_EXT], 'dirs': [], diff --git a/easybuild/easyconfigs/l/LAME/LAME-3.100-GCCcore-13.3.0.eb b/easybuild/easyconfigs/l/LAME/LAME-3.100-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..1fa3ca78fd9 --- /dev/null +++ b/easybuild/easyconfigs/l/LAME/LAME-3.100-GCCcore-13.3.0.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'LAME' +version = '3.100' + +homepage = 'http://lame.sourceforge.net/' +description = """LAME is a high quality MPEG Audio Layer III (MP3) encoder licensed under the LGPL.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://sourceforge.net/projects/lame/files/lame/%(version_major_minor)s/'] +sources = [SOURCELOWER_TAR_GZ] +patches = ['LAME-3.99.5_check-tgetent.patch'] +checksums = [ + 'ddfe36cab873794038ae2c1210557ad34857a4b6bdc515785d1da9e175b1da1e', # lame-3.100.tar.gz + '8bfb6a73f2db1511baf90fbd7174f11043ec4b592a4917edc30ccfb53bf37256', # LAME-3.99.5_check-tgetent.patch +] + +builddependencies = [ + ('binutils', '2.42'), + ('Autotools', '20231222'), +] + +dependencies = [('ncurses', '6.5')] + +preconfigopts = "autoconf && " + +# configure is broken: add workaround to find libncurses... +preconfigopts += "FRONTEND_LDADD='-L${EBROOTNCURSES}/lib' " + +sanity_check_paths = { + 'files': ['bin/lame', 'include/lame/lame.h', 'lib/libmp3lame.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-29Aug2024-foss-2023b-kokkos.eb b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-29Aug2024-foss-2023b-kokkos.eb new file mode 100644 index 00000000000..177e6b4d2ce --- /dev/null +++ b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-29Aug2024-foss-2023b-kokkos.eb @@ -0,0 +1,177 @@ +name = 'LAMMPS' +version = '29Aug2024' +versionsuffix = '-kokkos' + +homepage = 'https://www.lammps.org' +description = """LAMMPS is a classical molecular dynamics code, and an acronym +for Large-scale Atomic/Molecular Massively Parallel Simulator. LAMMPS has +potentials for solid-state materials (metals, semiconductors) and soft matter +(biomolecules, polymers) and coarse-grained or mesoscopic systems. It can be +used to model atoms or, more generically, as a parallel particle simulator at +the atomic, meso, or continuum scale. LAMMPS runs on single processors or in +parallel using message-passing techniques and a spatial-decomposition of the +simulation domain. The code is designed to be easy to modify or extend with new +functionality. +""" + +toolchain = {'name': 'foss', 'version': '2023b'} +toolchainopts = {'openmp': True, 'usempi': True} + +# 'https://github.com/lammps/lammps/archive/' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['stable_%(version)s.tar.gz'] +patches = [ + 'LAMMPS-2Aug2023_install_lammps_python_package_in_eb_software_module.patch', +] +checksums = [ + {'stable_29Aug2024.tar.gz': '6112e0cc352c3140a4874c7f74db3c0c8e30134024164509ecf3772b305fde2e'}, + {'LAMMPS-2Aug2023_install_lammps_python_package_in_eb_software_module.patch': + '723c944b62b9d28427d25e80a7a67049631702d344df49268a6846aa0cd0fe04'}, +] + +builddependencies = [ + ('CMake', '3.27.6'), + ('pkgconf', '2.0.3'), + ('archspec', '0.2.2'), +] +dependencies = [ + ('Python', '3.11.5'), + ('libpng', '1.6.40'), + ('libjpeg-turbo', '3.0.1'), + ('netCDF', '4.9.2'), + ('GSL', '2.7'), + ('zlib', '1.2.13'), + ('gzip', '1.13'), + ('cURL', '8.3.0'), + ('HDF5', '1.14.3'), + ('PCRE', '8.45'), + ('libxml2', '2.11.5'), + ('FFmpeg', '6.0'), + ('Voro++', '0.4.6'), + ('kim-api', '2.3.0'), + ('Eigen', '3.4.0'), + ('PLUMED', '2.9.2'), + ('SciPy-bundle', '2023.11'), + # VTK package is auto-disabled if this dep is not available + ('VTK', '9.3.0'), + # We use a custom build of MDI + ('MDI', '1.4.29'), +] +if ARCH == 'x86_64': + # TBB and ScaFaCos are an optional dependency when building on Intel arch + dependencies += [ + ('tbb', '2021.13.0'), + ('ScaFaCoS', '1.0.4'), + ] + +# To use additional custom configuration options, use the 'configopts' easyconfig parameter +# See docs and lammps easyblock for more information. +# https://github.com/lammps/lammps/blob/master/cmake/README.md#lammps-configuration-options + +# OpenMP-Kokkos build is default in the current easyblock. One can switch to serial backend of Kokkos, +# which is claimed to be faster in pure MPI calculations +# configopts = "-DKokkos_ENABLE_SERIAL=yes " + + +# packages auto-enabled by easyblock +# 'GPU' - if cuda package is present and kokkos is disabled +# 'KOKKOS' - if kokkos is enabled (by default) +# 'INTEL' - if builing on Intel CPU +# 'OPENMP' - if OpenMP swithed on in 'toolchainopts' + +# include the following extra packages into the build +general_packages = [ + 'AMOEBA', + 'ASPHERE', + 'ATC', + 'AWPMD', + 'BOCS', + 'BODY', + 'BPM', + 'BROWNIAN', + 'CG-DNA', + 'CG-SPICA', + 'CLASS2', + 'COLLOID', + 'COLVARS', + 'COMPRESS', + 'CORESHELL', + 'DIELECTRIC', + 'DIFFRACTION', + 'DIPOLE', + 'DPD-BASIC', + 'DPD-MESO', + 'DPD-REACT', + 'DPD-SMOOTH', + 'DRUDE', + 'EFF', + 'ELECTRODE', + 'EXTRA-COMPUTE', + 'EXTRA-DUMP', + 'EXTRA-FIX', + 'EXTRA-MOLECULE', + 'EXTRA-PAIR', + 'FEP', + 'GRANULAR', + 'H5MD', + 'INTERLAYER', + 'KIM', + 'KSPACE', + 'LATBOLTZ', + 'LEPTON', + 'MACHDYN', + 'MANIFOLD', + 'MANYBODY', + 'MC', + 'MDI', + 'MEAM', + 'MGPT', + 'MISC', + 'ML-IAP', + 'ML-PACE', + 'ML-POD', + 'ML-RANN', + 'ML-SNAP', + 'MOFFF', + 'MOLECULE', + 'MOLFILE', + 'MPIIO', + 'NETCDF', + 'OPT', + 'ORIENT', + 'PERI', + 'PHONON', + 'PLUGIN', + 'PLUMED', + 'POEMS', + 'PTM', + 'PYTHON', + 'QEQ', + 'QTB', + 'REACTION', + 'REAXFF', + 'REPLICA', + 'RIGID', + 'SCAFACOS', + 'SHOCK', + 'SMTBQ', + 'SPH', + 'SPIN', + 'SRD', + 'TALLY', + 'UEF', + 'VORONOI', + 'VTK', + 'YAFF', +] + +# Excluded packages due to requiring additional (non-trivial) deps +# - ADIOS +# - LATTE +# - MESONT (requires very large files downloaded during build) +# - ML-HDNNP (requires N2P2) +# - ML-QUIP +# - MSCG +# - QMMM (setup seems complex) + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/LAPACK/LAPACK-3.12.0-GCC-12.3.0.eb b/easybuild/easyconfigs/l/LAPACK/LAPACK-3.12.0-GCC-12.3.0.eb new file mode 100644 index 00000000000..d68bd9e25a5 --- /dev/null +++ b/easybuild/easyconfigs/l/LAPACK/LAPACK-3.12.0-GCC-12.3.0.eb @@ -0,0 +1,16 @@ +name = 'LAPACK' +version = '3.12.0' + +homepage = 'https://www.netlib.org/lapack/' +description = """LAPACK is written in Fortran90 and provides routines for solving systems of + simultaneous linear equations, least-squares solutions of linear systems of equations, eigenvalue + problems, and singular value problems.""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/Reference-LAPACK/lapack/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['eac9570f8e0ad6f30ce4b963f4f033f0f643e7c3912fc9ee6cd99120675ad48b'] + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/l/LDC/LDC-1.39.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/l/LDC/LDC-1.39.0-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..f0d3a361152 --- /dev/null +++ b/easybuild/easyconfigs/l/LDC/LDC-1.39.0-GCCcore-13.2.0.eb @@ -0,0 +1,39 @@ +easyblock = 'CMakeNinja' + +name = 'LDC' +version = '1.39.0' + +homepage = 'https://wiki.dlang.org/LDC' +description = "The LLVM-based D Compiler" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://github.com/ldc-developers/ldc/releases/download/v%(version)s'] +sources = ['ldc-%(version)s-src.tar.gz'] +checksums = ['839bac36f6073318e36f0b163767e03bdbd3f57d99256b97494ac439b59a4562'] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.27.6'), + ('Ninja', '1.11.1'), + # building LDC from source requires LDC + ('LDC', '1.24.0', '-%(arch)s', SYSTEM), +] + +dependencies = [ + ('LLVM', '16.0.6'), +] + +configopts = "-DLLVM_ROOT_DIR=$EBROOTLLVM" + +sanity_check_paths = { + 'files': ['bin/ldc2', 'bin/ldmd2'], + 'dirs': ['include/d', 'lib'], +} + +sanity_check_commands = [ + "ldc2 --help", + "ldmd2 --help", +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/l/LERC/LERC-4.0.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/l/LERC/LERC-4.0.0-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..f4d5e9a50be --- /dev/null +++ b/easybuild/easyconfigs/l/LERC/LERC-4.0.0-GCCcore-13.3.0.eb @@ -0,0 +1,45 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Updated: Denis Kristak +# Updated: Thomas Hoffmann (EMBL) +easyblock = 'CMakeMake' + +name = 'LERC' +version = '4.0.0' + +homepage = 'https://github.com/Esri/lerc' +description = """LERC is an open-source image or raster format which supports rapid encoding and decoding +for any pixel type (not just RGB or Byte). Users set the maximum compression error per pixel while encoding, +so the precision of the original input image is preserved (within user defined error bounds).""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://github.com/Esri/lerc/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['91431c2b16d0e3de6cbaea188603359f87caed08259a645fd5a3805784ee30a0'] + +builddependencies = [ + ('binutils', '2.42'), + ('CMake', '3.29.3'), +] + +configopts = '-DCMAKE_INSTALL_LIBDIR=lib' + +postinstallcmds = [ + # copy the LercTest source file to a LercTest subdir in the installation directory and compile it + # (needs to be done here instead of in the sanity check, else it won't work when RPATH linking is enabled) + "cd %(builddir)s/lerc-%(version)s/src/LercTest && sed -i -e 's@../LercLib/include/@@' main.cpp", + "mkdir %(installdir)s/LercTest", + "cp %(builddir)s/lerc-%(version)s/src/LercTest/main.cpp %(installdir)s/LercTest/main.cpp", + "cd %(installdir)s/LercTest && ${CXX} ${CXXFLAGS} main.cpp -o LercTest -I../include -L../lib -lLerc", +] + +sanity_check_commands = [ + "%(installdir)s/LercTest/LercTest", +] + +sanity_check_paths = { + 'files': ['include/Lerc_c_api.h', 'include/Lerc_types.h', 'lib/libLerc.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/LIBSVM-MATLAB/LIBSVM-MATLAB-3.30-GCCcore-11.3.0-MATLAB-2022b-r5.eb b/easybuild/easyconfigs/l/LIBSVM-MATLAB/LIBSVM-MATLAB-3.30-GCCcore-11.3.0-MATLAB-2022b-r5.eb new file mode 100644 index 00000000000..3da0742b89c --- /dev/null +++ b/easybuild/easyconfigs/l/LIBSVM-MATLAB/LIBSVM-MATLAB-3.30-GCCcore-11.3.0-MATLAB-2022b-r5.eb @@ -0,0 +1,42 @@ +easyblock = 'MakeCp' + +name = 'LIBSVM-MATLAB' +version = '3.30' +local_matlab_ver = '2022b-r5' +versionsuffix = '-MATLAB-%s' % local_matlab_ver + +homepage = 'https://www.csie.ntu.edu.tw/~cjlin/libsvm/' +description = """MATLAB interface of LIBSVM, an integrated software for support vector classification, + (C-SVC, nu-SVC), regression (epsilon-SVR, nu-SVR) and distribution estimation (one-class SVM). + It supports multi-class classification.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'openmp': True, 'pic': True} + +source_urls = ['https://github.com/cjlin1/libsvm/archive'] +sources = ['v%s.tar.gz' % version.replace('.', '')] +checksums = ['e4fe41308c87cc210aec73e4f5f0fb4da14234d90e7a131763fbad3788ca2d80'] + +builddependencies = [ + ('binutils', '2.38'), +] +dependencies = [ + ('MATLAB', local_matlab_ver, '', SYSTEM), +] + +start_dir = 'matlab' + +buildopts = "MATLABDIR=$EBROOTMATLAB" + +files_to_copy = [ + (['matlab/*.mexa64'], ''), +] + +sanity_check_paths = { + 'files': ['libsvmwrite.mexa64', 'libsvmread.mexa64', 'svmpredict.mexa64', 'svmtrain.mexa64'], + 'dirs': [], +} + +modextrapaths = {'MATLABPATH': ''} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/LIME/LIME-1.3.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/LIME/LIME-1.3.2-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..11dbbfa5025 --- /dev/null +++ b/easybuild/easyconfigs/l/LIME/LIME-1.3.2-GCCcore-12.3.0.eb @@ -0,0 +1,53 @@ +easyblock = 'ConfigureMake' + +name = "LIME" +version = "1.3.2" + +homepage = "http://usqcd-software.github.io/c-lime/" +description = """LIME (which can stand for Lattice QCD Interchange Message Encapsulation or more generally, +Large Internet Message Encapsulation) is a simple packaging scheme for combining records containing ASCII +and/or binary data. Its ancestors are the Unix cpio and tar formats and the Microsoft Corporation DIME +(Direct Internet Message Encapsulation) format. It is simpler and allows record sizes up to $2^{63}$ bytes, +making chunking unnecessary for the foreseeable future. Unlike tar and cpio, the records are not associated +with Unix files. They are identified only by a record-type (LIME type) character string, analogous to the +familiar MIME application type. The LIME software package consists of a C-language API for creating, reading, +writing, and manipulating LIME files and a small set of utilities for examining, packing and unpacking LIME files.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +builddependencies = [ + ('binutils', '2.40') +] + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://usqcd-software.github.io/downloads/c-lime/'] + +checksums = ['db5c07a72a152244f94a84c8bcc7395ec6fa084b8979ca1c8788b99a2870c881'] + +buildopts = "all" + +sanity_check_paths = { + 'files': [ + "bin/lime_pack", + "bin/lime_unpack", + "bin/lime_contents", + "bin/lime_extract_record", + "bin/lime_extract_type", + "lib/liblime.a", + "include/dcap-overload.h", + "include/lime_binary_header.h", + "include/lime_config.h", + "include/lime_config_internal.h", + "include/lime_defs.h", + "include/lime_fixed_types.h", + "include/lime_fseeko.h", + "include/lime.h", + "include/lime_header.h", + "include/lime_reader.h", + "include/lime_utils.h", + "include/lime_writer.h", + ], + 'dirs': [], +} + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/l/LIME/LIME-1.3.2-GCCcore-13.2.0.eb b/easybuild/easyconfigs/l/LIME/LIME-1.3.2-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..cd8ac72a902 --- /dev/null +++ b/easybuild/easyconfigs/l/LIME/LIME-1.3.2-GCCcore-13.2.0.eb @@ -0,0 +1,53 @@ +easyblock = 'ConfigureMake' + +name = "LIME" +version = "1.3.2" + +homepage = "http://usqcd-software.github.io/c-lime/" +description = """LIME (which can stand for Lattice QCD Interchange Message Encapsulation or more generally, +Large Internet Message Encapsulation) is a simple packaging scheme for combining records containing ASCII +and/or binary data. Its ancestors are the Unix cpio and tar formats and the Microsoft Corporation DIME +(Direct Internet Message Encapsulation) format. It is simpler and allows record sizes up to $2^{63}$ bytes, +making chunking unnecessary for the foreseeable future. Unlike tar and cpio, the records are not associated +with Unix files. They are identified only by a record-type (LIME type) character string, analogous to the +familiar MIME application type. The LIME software package consists of a C-language API for creating, reading, +writing, and manipulating LIME files and a small set of utilities for examining, packing and unpacking LIME files.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +builddependencies = [ + ('binutils', '2.40') +] + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://usqcd-software.github.io/downloads/c-lime/'] + +checksums = ['db5c07a72a152244f94a84c8bcc7395ec6fa084b8979ca1c8788b99a2870c881'] + +buildopts = "all" + +sanity_check_paths = { + 'files': [ + "bin/lime_pack", + "bin/lime_unpack", + "bin/lime_contents", + "bin/lime_extract_record", + "bin/lime_extract_type", + "lib/liblime.a", + "include/dcap-overload.h", + "include/lime_binary_header.h", + "include/lime_config.h", + "include/lime_config_internal.h", + "include/lime_defs.h", + "include/lime_fixed_types.h", + "include/lime_fseeko.h", + "include/lime.h", + "include/lime_header.h", + "include/lime_reader.h", + "include/lime_utils.h", + "include/lime_writer.h", + ], + 'dirs': [], +} + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/l/LIME/LIME-1.3.2-GCCcore-13.3.0.eb b/easybuild/easyconfigs/l/LIME/LIME-1.3.2-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..d36f23151c8 --- /dev/null +++ b/easybuild/easyconfigs/l/LIME/LIME-1.3.2-GCCcore-13.3.0.eb @@ -0,0 +1,53 @@ +easyblock = 'ConfigureMake' + +name = "LIME" +version = "1.3.2" + +homepage = "http://usqcd-software.github.io/c-lime/" +description = """LIME (which can stand for Lattice QCD Interchange Message Encapsulation or more generally, +Large Internet Message Encapsulation) is a simple packaging scheme for combining records containing ASCII +and/or binary data. Its ancestors are the Unix cpio and tar formats and the Microsoft Corporation DIME +(Direct Internet Message Encapsulation) format. It is simpler and allows record sizes up to $2^{63}$ bytes, +making chunking unnecessary for the foreseeable future. Unlike tar and cpio, the records are not associated +with Unix files. They are identified only by a record-type (LIME type) character string, analogous to the +familiar MIME application type. The LIME software package consists of a C-language API for creating, reading, +writing, and manipulating LIME files and a small set of utilities for examining, packing and unpacking LIME files.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +builddependencies = [ + ('binutils', '2.42') +] + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://usqcd-software.github.io/downloads/c-lime/'] + +checksums = ['db5c07a72a152244f94a84c8bcc7395ec6fa084b8979ca1c8788b99a2870c881'] + +buildopts = "all" + +sanity_check_paths = { + 'files': [ + "bin/lime_pack", + "bin/lime_unpack", + "bin/lime_contents", + "bin/lime_extract_record", + "bin/lime_extract_type", + "lib/liblime.a", + "include/dcap-overload.h", + "include/lime_binary_header.h", + "include/lime_config.h", + "include/lime_config_internal.h", + "include/lime_defs.h", + "include/lime_fixed_types.h", + "include/lime_fseeko.h", + "include/lime.h", + "include/lime_header.h", + "include/lime_reader.h", + "include/lime_utils.h", + "include/lime_writer.h", + ], + 'dirs': [], +} + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/l/LLVM/LLVM-18.1.8-GCCcore-13.3.0.eb b/easybuild/easyconfigs/l/LLVM/LLVM-18.1.8-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..a0c29eba130 --- /dev/null +++ b/easybuild/easyconfigs/l/LLVM/LLVM-18.1.8-GCCcore-13.3.0.eb @@ -0,0 +1,48 @@ +name = 'LLVM' +version = '18.1.8' + +homepage = "https://llvm.org/" +description = """The LLVM Core libraries provide a modern source- and target-independent + optimizer, along with code generation support for many popular CPUs + (as well as some less common ones!) These libraries are built around a well + specified code representation known as the LLVM intermediate representation + ("LLVM IR"). The LLVM Core libraries are well documented, and it is + particularly easy to invent your own language (or port an existing compiler) + to use LLVM as an optimizer and code generator.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'cstd': 'gnu++11', 'pic': True} + +source_urls = ['https://github.com/llvm/llvm-project/releases/download/llvmorg-%(version)s/'] +sources = [ + 'llvm-%(version)s.src.tar.xz', + 'cmake-%(version)s.src.tar.xz', + 'third-party-%(version)s.src.tar.xz', +] +checksums = [ + {'llvm-18.1.8.src.tar.xz': 'f68cf90f369bc7d0158ba70d860b0cb34dbc163d6ff0ebc6cfa5e515b9b2e28d'}, + {'cmake-18.1.8.src.tar.xz': '59badef592dd34893cd319d42b323aaa990b452d05c7180ff20f23ab1b41e837'}, + {'third-party-18.1.8.src.tar.xz': 'b76b810f3d3dc5d08e83c4236cb6e395aa9bd5e3ea861e8c319b216d093db074'}, +] + +builddependencies = [ + ('binutils', '2.42'), + ('CMake', '3.29.3'), + ('Python', '3.12.3'), +] + +dependencies = [ + ('ncurses', '6.5'), + ('zlib', '1.3.1'), +] + +build_shared_libs = True + +sanity_check_paths = { + 'files': ['bin/llvm-ar', 'bin/FileCheck'], + 'dirs': ['include/llvm', 'include/llvm-c'], +} + +sanity_check_commands = ["llvm-ar --help"] + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/l/LMDB/LMDB-0.9.31-GCCcore-13.2.0.eb b/easybuild/easyconfigs/l/LMDB/LMDB-0.9.31-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..946dd8e0961 --- /dev/null +++ b/easybuild/easyconfigs/l/LMDB/LMDB-0.9.31-GCCcore-13.2.0.eb @@ -0,0 +1,38 @@ +easyblock = 'MakeCp' + +name = 'LMDB' +version = '0.9.31' + +homepage = 'https://symas.com/lmdb' +description = """LMDB is a fast, memory-efficient database. With memory-mapped files, it has the read performance + of a pure in-memory database while retaining the persistence of standard disk-based databases.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://github.com/LMDB/lmdb/archive/'] +sources = ['%(name)s_%(version)s.tar.gz'] +checksums = ['dd70a8c67807b3b8532b3e987b0a4e998962ecc28643e1af5ec77696b081c9b0'] + +builddependencies = [('binutils', '2.40')] + +buildopts = 'CC="$CC" OPT="$CFLAGS"' + +runtest = 'test' + +local_binaries = ['mdb_copy', 'mdb_dump', 'mdb_load', 'mdb_stat'] + +files_to_copy = [ + (['lmdb.h', 'midl.h'], 'include'), + (local_binaries, 'bin'), + (['liblmdb.a', 'liblmdb.%s' % SHLIB_EXT], 'lib'), +] + +sanity_check_paths = { + 'files': ['bin/mdb_copy', 'bin/mdb_dump', 'bin/mdb_load', 'bin/mdb_stat', 'include/lmdb.h', + 'include/midl.h', 'lib/liblmdb.a', 'lib/liblmdb.%s' % SHLIB_EXT], + 'dirs': [], +} + +sanity_check_commands = ["%s -V" % x for x in local_binaries] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/LMDB/LMDB-0.9.31-GCCcore-13.3.0.eb b/easybuild/easyconfigs/l/LMDB/LMDB-0.9.31-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..a10be56a891 --- /dev/null +++ b/easybuild/easyconfigs/l/LMDB/LMDB-0.9.31-GCCcore-13.3.0.eb @@ -0,0 +1,38 @@ +easyblock = 'MakeCp' + +name = 'LMDB' +version = '0.9.31' + +homepage = 'https://symas.com/lmdb' +description = """LMDB is a fast, memory-efficient database. With memory-mapped files, it has the read performance + of a pure in-memory database while retaining the persistence of standard disk-based databases.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://github.com/LMDB/lmdb/archive/'] +sources = ['%(name)s_%(version)s.tar.gz'] +checksums = ['dd70a8c67807b3b8532b3e987b0a4e998962ecc28643e1af5ec77696b081c9b0'] + +builddependencies = [('binutils', '2.42')] + +buildopts = 'CC="$CC" OPT="$CFLAGS"' + +runtest = 'test' + +local_binaries = ['mdb_copy', 'mdb_dump', 'mdb_load', 'mdb_stat'] + +files_to_copy = [ + (['lmdb.h', 'midl.h'], 'include'), + (local_binaries, 'bin'), + (['liblmdb.a', 'liblmdb.%s' % SHLIB_EXT], 'lib'), +] + +sanity_check_paths = { + 'files': ['bin/mdb_copy', 'bin/mdb_dump', 'bin/mdb_load', 'bin/mdb_stat', 'include/lmdb.h', + 'include/midl.h', 'lib/liblmdb.a', 'lib/liblmdb.%s' % SHLIB_EXT], + 'dirs': [], +} + +sanity_check_commands = ["%s -V" % x for x in local_binaries] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/LRBinner/LRBinner-0.1-foss-2023a.eb b/easybuild/easyconfigs/l/LRBinner/LRBinner-0.1-foss-2023a.eb new file mode 100644 index 00000000000..143e59d35c5 --- /dev/null +++ b/easybuild/easyconfigs/l/LRBinner/LRBinner-0.1-foss-2023a.eb @@ -0,0 +1,44 @@ +easyblock = 'PythonBundle' + +name = 'LRBinner' +version = '0.1' + +homepage = 'https://github.com/anuradhawick/LRBinner' +description = "LRBinner is a long-read binning tool published in WABI 2021 proceedings and AMB. " + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('HMMER', '3.4'), + ('Seaborn', '0.13.2'), + ('h5py', '3.9.0'), + ('PyTorch', '2.1.2'), + ('tqdm', '4.66.1'), + ('Biopython', '1.83'), + ('scikit-learn', '1.3.1'), + ('FragGeneScan', '1.31'), + ('HDBSCAN', '0.8.38.post1'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('tabulate', '0.9.0', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['024ca478df22e9340661486f85298cff5f6dcdba14f3813e8830015b9ed1948f'], + }), + (name, version, { + 'modulename': 'mbcclr_utils', + 'preinstallopts': "sed -i 's/pytorch/torch/g' setup.py && ", + 'source_urls': ['https://github.com/anuradhawick/LRBinner/archive/'], + 'sources': ['v%(version)s.tar.gz'], + 'checksums': ['2d77dde8ab1272c432b20eb18a352326c622e929261562ef6d680c6638cc4bd1'], + }), +] + +sanity_check_commands = ['LRBinner --help'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/l/LZO/LZO-2.10-GCCcore-13.3.0.eb b/easybuild/easyconfigs/l/LZO/LZO-2.10-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..4d8ccd20b1f --- /dev/null +++ b/easybuild/easyconfigs/l/LZO/LZO-2.10-GCCcore-13.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'LZO' +version = '2.10' + +homepage = 'https://www.oberhumer.com/opensource/lzo/' +description = "Portable lossless data compression library" + +source_urls = [homepage + 'download/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['c0f892943208266f9b6543b3ae308fab6284c5c90e627931446fb49b4221a072'] + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +builddependencies = [('binutils', '2.42')] + +configopts = '--enable-shared' + +runtest = 'test' + +sanity_check_paths = { + 'files': ['lib/liblzo2.a', 'lib/liblzo2.%s' % SHLIB_EXT], + 'dirs': ['include'] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/l/LangChain/LangChain-0.2.1-foss-2023a.eb b/easybuild/easyconfigs/l/LangChain/LangChain-0.2.1-foss-2023a.eb new file mode 100644 index 00000000000..640990af4c3 --- /dev/null +++ b/easybuild/easyconfigs/l/LangChain/LangChain-0.2.1-foss-2023a.eb @@ -0,0 +1,67 @@ +easyblock = 'PythonBundle' + +name = 'LangChain' +version = '0.2.1' +_rust_ver = '1.75.0' + +homepage = 'https://github.com/langchain-ai/langchain' +description = """ +LangChain is a framework for developing applications powered by large language models (LLMs). +""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [ + ('hatchling', '1.18.0'), + ('Rust', _rust_ver), + ('maturin', '1.4.0', '-Rust-%s' % _rust_ver), + ('poetry', '1.5.1'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('aiohttp', '3.8.5'), + ('pydantic', '2.5.3'), + ('PyYAML', '6.0'), + ('SQLAlchemy', '2.0.25'), +] + +exts_list = [ + ('jsonpointer', '2.4', { + 'checksums': ['585cee82b70211fa9e6043b7bb89db6e1aa49524340dde8ad6b63206ea689d88'], + }), + ('jsonpatch', '1.33', { + 'checksums': ['9fcd4009c41e6d12348b4a0ff2563ba56a2923a7dfee731d004e212e1ee5030c'], + }), + ('packaging', '23.2', { + 'checksums': ['048fb0e9405036518eaaf48a55953c750c11e1a1b68e0dd1a9d62ed0c092cfc5'], + }), + ('langchain-core', '0.2.3', { + 'sources': ['langchain_core-%(version)s.tar.gz'], + 'checksums': ['fbc75a64b9c0b7655d96ca57a707df1e6c09efc1539c36adbd73260612549810'], + }), + ('langchain-text-splitters', '0.2.0', { + 'sources': ['langchain_text_splitters-%(version)s.tar.gz'], + 'checksums': ['b32ab4f7397f7d42c1fa3283fefc2547ba356bd63a68ee9092865e5ad83c82f9'], + }), + ('orjson', '3.9.14', { + 'checksums': ['06fb40f8e49088ecaa02f1162581d39e2cf3fd9dbbfe411eb2284147c99bad79'], + }), + ('langsmith', '0.1.65', { + 'checksums': ['d3c2eb2391478bd79989f02652cf66e29a7959d677614b6993a47cef43f7f43b'], + }), + ('tenacity', '8.3.0', { + 'checksums': ['953d4e6ad24357bceffbc9707bc74349aca9d245f68eb65419cf0c249a1949a2'], + }), + (name, version, { + 'modulename': 'langchain', + 'sources': ['langchain-%(version)s.tar.gz'], + 'checksums': ['5758a315e1ac92eb26dafec5ad0fafa03cafa686aba197d5bb0b1dd28cc03ebe'], + }), +] + +use_pip = True +sanity_pip_check = True + +moduleclass = 'ai' diff --git a/easybuild/easyconfigs/l/Leptonica/Leptonica-1.84.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/Leptonica/Leptonica-1.84.1-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..ee92fb98c62 --- /dev/null +++ b/easybuild/easyconfigs/l/Leptonica/Leptonica-1.84.1-GCCcore-12.3.0.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'Leptonica' +version = '1.84.1' + +homepage = 'http://www.leptonica.org' +description = """Leptonica is a collection of pedagogically-oriented open source software + that is broadly useful for image processing and image analysis applications.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://github.com/DanBloomberg/leptonica/releases/download/%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['2b3e1254b1cca381e77c819b59ca99774ff43530209b9aeb511e1d46588a64f6'] + +builddependencies = [('binutils', '2.40')] + +dependencies = [ + ('libpng', '1.6.39'), + ('LibTIFF', '4.5.0'), + ('libjpeg-turbo', '2.1.5.1'), + ('giflib', '5.2.1'), + ('libwebp', '1.3.1'), + ('zlib', '1.2.13'), +] + +sanity_check_paths = { + 'files': ['bin/convertformat'], + 'dirs': ['include/leptonica', 'lib/pkgconfig'] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/LevelDB/LevelDB-1.22-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/LevelDB/LevelDB-1.22-GCCcore-11.3.0.eb index 35889241c08..cf2d0aace66 100644 --- a/easybuild/easyconfigs/l/LevelDB/LevelDB-1.22-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/l/LevelDB/LevelDB-1.22-GCCcore-11.3.0.eb @@ -47,6 +47,6 @@ sanity_check_paths = { 'dirs': ['lib/python%(pyshortver)s/site-packages'], } -sanity_check_commands = ["pip check"] +sanity_check_commands = ["PIP_DISABLE_PIP_VERSION_CHECK=true python -s -m pip check"] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/l/LibLZF/LibLZF-3.6-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/LibLZF/LibLZF-3.6-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..500e9679115 --- /dev/null +++ b/easybuild/easyconfigs/l/LibLZF/LibLZF-3.6-GCCcore-12.3.0.eb @@ -0,0 +1,31 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +# Update: Thomas Hoffmann (EMBL), Denis Kristak +easyblock = 'ConfigureMake' + +name = 'LibLZF' +version = '3.6' + +homepage = 'http://oldhome.schmorp.de/marc/liblzf.html' +description = """LibLZF is a very small data compression library. It consists of only two .c and two .h files +and is very easy to incorporate into your own programs. The compression algorithm is very, very fast, yet still +written in portable C.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['http://dist.schmorp.de/liblzf/Attic/'] +sources = ['liblzf-%(version)s.tar.gz'] +checksums = ['9c5de01f7b9ccae40c3f619d26a7abec9986c06c36d260c179cedd04b89fb46a'] + +builddependencies = [ + ('binutils', '2.40'), +] + +sanity_check_commands = ['lzf -h'] + +sanity_check_paths = { + 'files': ['bin/lzf', 'lib/liblzf.a'], + 'dirs': ['bin', 'lib'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.6.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.6.0-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..01e24006610 --- /dev/null +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.6.0-GCCcore-13.3.0.eb @@ -0,0 +1,38 @@ +easyblock = 'ConfigureMake' + +name = 'LibTIFF' +version = '4.6.0' + +homepage = 'https://libtiff.gitlab.io/libtiff/' +description = "tiff: Library and tools for reading and writing TIFF data files" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://download.osgeo.org/libtiff/'] +sources = ['tiff-%(version)s.tar.gz'] +checksums = ['88b3979e6d5c7e32b50d7ec72fb15af724f6ab2cbf7e10880c360a77e4b5d99a'] + +builddependencies = [('binutils', '2.42')] + +dependencies = [ + ('zlib', '1.3.1'), + ('libjpeg-turbo', '3.0.1'), + ('XZ', '5.4.5'), + ('jbigkit', '2.1'), + ('zstd', '1.5.6'), + ('libdeflate', '1.20'), +] + +configopts = "--enable-ld-version-script " +configopts += "--disable-webp --disable-sphinx " + +sanity_check_paths = { + 'files': ['bin/tiffdump', 'bin/tiffinfo', 'include/tiff.h', 'lib/libtiff.a', 'lib/libtiff.%s' % SHLIB_EXT, + 'lib/libtiffxx.a', 'lib/libtiffxx.%s' % SHLIB_EXT, 'lib/pkgconfig/libtiff-4.pc'], + 'dirs': [], +} + +sanity_check_commands = ["tiffinfo -h"] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/LightGBM/LightGBM-4.5.0-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/l/LightGBM/LightGBM-4.5.0-foss-2023a-CUDA-12.1.1.eb new file mode 100644 index 00000000000..638330e8866 --- /dev/null +++ b/easybuild/easyconfigs/l/LightGBM/LightGBM-4.5.0-foss-2023a-CUDA-12.1.1.eb @@ -0,0 +1,56 @@ +easyblock = 'PythonBundle' + +name = "LightGBM" +version = "4.5.0" +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = "https://lightgbm.readthedocs.io" +description = """A fast, distributed, high performance gradient boosting (GBT, GBDT, GBRT, GBM +or MART) framework based on decision tree algorithms, used for ranking, +classification and many other machine learning tasks.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [ + ('scikit-build-core', '0.9.3'), + ('wget', '1.24.5'), +] + +dependencies = [ + ('CUDA', '12.1.1', '', SYSTEM), + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('Arrow', '14.0.1'), # optional + ('dask', '2023.9.2'), # optional + ('scikit-learn', '1.3.1'), # optional +] + +use_pip = True + +# example files are not distributed with the sources +_test_repo_url = "https://raw.githubusercontent.com/microsoft/LightGBM/refs/tags/v%(version)s/examples" +_test_cmds_pre = " && ".join([ + "mkdir regression", + "wget -P regression %s/regression/regression.test" % _test_repo_url, + "wget -P regression %s/regression/regression.train" % _test_repo_url, + "mkdir test", + "cd test", + "wget %s/python-guide/simple_example.py" % _test_repo_url, + "", +]) + +exts_list = [ + ('lightgbm', version, { + 'checksums': ['e1cd7baf0318d4e308a26575a63a4635f08df866ad3622a9d8e3d71d9637a1ba'], + 'installopts': "--config-settings=cmake.define.USE_CUDA=ON", + 'use_pip_extras': "arrow,dask,pandas,scikit-learn", + 'pretestopts': _test_cmds_pre, + 'runtest': 'python', + 'testopts': "simple_example.py", + 'testinstall': True, + }), +] + +sanity_pip_check = True + +moduleclass = 'ai' diff --git a/easybuild/easyconfigs/l/LightGBM/LightGBM-4.5.0-foss-2023a.eb b/easybuild/easyconfigs/l/LightGBM/LightGBM-4.5.0-foss-2023a.eb new file mode 100644 index 00000000000..b6a03faf9ca --- /dev/null +++ b/easybuild/easyconfigs/l/LightGBM/LightGBM-4.5.0-foss-2023a.eb @@ -0,0 +1,54 @@ +easyblock = 'PythonBundle' + +name = "LightGBM" +version = "4.5.0" + +homepage = "https://lightgbm.readthedocs.io" +description = """A fast, distributed, high performance gradient boosting (GBT, GBDT, GBRT, GBM +or MART) framework based on decision tree algorithms, used for ranking, +classification and many other machine learning tasks.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [ + ('scikit-build-core', '0.9.3'), + ('wget', '1.24.5'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('Arrow', '14.0.1'), # optional + ('dask', '2023.9.2'), # optional + ('scikit-learn', '1.3.1'), # optional +] + +use_pip = True + +# example files are not distributed with the sources +_test_repo_url = "https://raw.githubusercontent.com/microsoft/LightGBM/refs/tags/v%(version)s/examples" +_test_cmds_pre = " && ".join([ + "mkdir regression", + "wget -P regression %s/regression/regression.test" % _test_repo_url, + "wget -P regression %s/regression/regression.train" % _test_repo_url, + "mkdir test", + "cd test", + "wget %s/python-guide/simple_example.py" % _test_repo_url, + "", +]) + +exts_list = [ + ('lightgbm', version, { + 'checksums': ['e1cd7baf0318d4e308a26575a63a4635f08df866ad3622a9d8e3d71d9637a1ba'], + 'installopts': "--config-settings=cmake.define.USE_MPI=ON", + 'use_pip_extras': "arrow,dask,pandas,scikit-learn", + 'pretestopts': _test_cmds_pre, + 'runtest': 'python', + 'testopts': "simple_example.py", + 'testinstall': True, + }), +] + +sanity_pip_check = True + +moduleclass = 'ai' diff --git a/easybuild/easyconfigs/l/Lightning/Lightning-2.2.1-foss-2023a.eb b/easybuild/easyconfigs/l/Lightning/Lightning-2.2.1-foss-2023a.eb new file mode 100644 index 00000000000..5635e783f7c --- /dev/null +++ b/easybuild/easyconfigs/l/Lightning/Lightning-2.2.1-foss-2023a.eb @@ -0,0 +1,31 @@ +easyblock = 'PythonPackage' + +name = 'Lightning' +version = '2.2.1' + +homepage = 'https://github.com/Lightning-AI/pytorch-lightning' +description = """ +The deep learning framework to pretrain, finetune and deploy AI models. +Lightning has 4 core packages: + PyTorch Lightning: Train and deploy PyTorch at scale. + Lightning Fabric: Expert control. + Lightning Data: Blazing fast, distributed streaming of training data from cloud storage. + Lightning Apps: Build AI products and ML workflows. +""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['b3e46d596b32cafd1fb9b21fdba1b1767df97b1af5cc702693d1c51df60b19aa'] + +dependencies = [ + ('Python', '3.11.3'), + ('PyTorch', '2.1.2'), + ('PyTorch-Lightning', version), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/l/LittleCMS/LittleCMS-2.16-GCCcore-13.3.0.eb b/easybuild/easyconfigs/l/LittleCMS/LittleCMS-2.16-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..121d33200a2 --- /dev/null +++ b/easybuild/easyconfigs/l/LittleCMS/LittleCMS-2.16-GCCcore-13.3.0.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'LittleCMS' +version = '2.16' + +homepage = 'https://www.littlecms.com/' +description = """ Little CMS intends to be an OPEN SOURCE small-footprint color management engine, + with special focus on accuracy and performance. """ + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://sourceforge.net/projects/lcms/files/lcms/%s/' % '.'.join(version.split('.')[:2])] +sources = ['lcms2-%(version)s.tar.gz'] +checksums = ['d873d34ad8b9b4cea010631f1a6228d2087475e4dc5e763eb81acc23d9d45a51'] + +builddependencies = [('binutils', '2.42')] + +dependencies = [('libjpeg-turbo', '3.0.1')] + +sanity_check_paths = { + 'files': ['bin/jpgicc', 'bin/linkicc', 'bin/psicc', 'bin/transicc', 'include/lcms2.h', 'include/lcms2_plugin.h', + 'lib/liblcms2.a', 'lib/liblcms2.%s' % SHLIB_EXT, 'lib/pkgconfig/lcms2.pc'], + 'dirs': ['share/man'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/Longshot/Longshot-1.0.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/Longshot/Longshot-1.0.0-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..0a67a58490f --- /dev/null +++ b/easybuild/easyconfigs/l/Longshot/Longshot-1.0.0-GCCcore-12.3.0.eb @@ -0,0 +1,331 @@ +easyblock = 'Cargo' + +name = 'Longshot' +version = '1.0.0' + +homepage = 'https://github.com/pjedge/longshot' +description = """Longshot is a variant calling tool for diploid genomes using long error prone reads such as Pacific + Biosciences (PacBio) SMRT and Oxford Nanopore Technologies (ONT). It takes as input an aligned BAM file and outputs + a phased VCF file with variants and haplotype information. It can also output haplotype-separated BAM files that can + be used for downstream analysis. Currently, it only calls single nucleotide variants (SNVs).""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +crates = [ + ('addr2line', '0.24.2'), + ('adler2', '2.0.0'), + ('ahash', '0.7.8'), + ('aho-corasick', '1.1.3'), + ('android-tzdata', '0.1.1'), + ('android_system_properties', '0.1.5'), + ('ansi_term', '0.12.1'), + ('approx', '0.3.2'), + ('atty', '0.2.14'), + ('autocfg', '1.4.0'), + ('backtrace', '0.3.74'), + ('bio', '0.25.0'), + ('bio-types', '1.0.4'), + ('bit-set', '0.5.3'), + ('bit-vec', '0.6.3'), + ('bitflags', '1.3.2'), + ('bumpalo', '3.16.0'), + ('bv', '0.10.0'), + ('bytecount', '0.3.2'), + ('byteorder', '1.5.0'), + ('bzip2-sys', '0.1.11+1.0.8'), + ('cc', '1.1.30'), + ('cfg-if', '1.0.0'), + ('chrono', '0.4.38'), + ('clap', '2.34.0'), + ('cmake', '0.1.51'), + ('core-foundation-sys', '0.8.7'), + ('csv', '1.3.0'), + ('csv-core', '0.1.11'), + ('curl-sys', '0.4.77+curl-8.10.1'), + ('custom_derive', '0.1.7'), + ('derive-new', '0.5.9'), + ('derive-new', '0.6.0'), + ('either', '1.13.0'), + ('error-chain', '0.12.4'), + ('feature-probe', '0.1.1'), + ('fishers_exact', '1.0.1'), + ('fnv', '1.0.7'), + ('form_urlencoded', '1.2.1'), + ('fs-utils', '1.1.4'), + ('fuchsia-cprng', '0.1.1'), + ('fxhash', '0.2.1'), + ('getrandom', '0.2.15'), + ('gimli', '0.31.1'), + ('glob', '0.3.1'), + ('hashbrown', '0.11.2'), + ('heck', '0.5.0'), + ('hermit-abi', '0.1.19'), + ('hts-sys', '2.1.4'), + ('iana-time-zone', '0.1.61'), + ('iana-time-zone-haiku', '0.1.2'), + ('idna', '0.5.0'), + ('ieee754', '0.2.6'), + ('itertools', '0.7.11'), + ('itertools-num', '0.1.3'), + ('itoa', '1.0.11'), + ('jobserver', '0.1.32'), + ('js-sys', '0.3.72'), + ('lazy_static', '1.5.0'), + ('libc', '0.2.159'), + ('libz-sys', '1.1.20'), + ('linear-map', '1.2.0'), + ('log', '0.4.22'), + ('lzma-sys', '0.1.20'), + ('matrixmultiply', '0.1.15'), + ('memchr', '2.7.4'), + ('miniz_oxide', '0.8.0'), + ('multimap', '0.4.0'), + ('ndarray', '0.12.1'), + ('newtype_derive', '0.1.6'), + ('num-complex', '0.2.4'), + ('num-integer', '0.1.46'), + ('num-traits', '0.2.19'), + ('object', '0.36.5'), + ('once_cell', '1.20.2'), + ('openssl-src', '300.3.2+3.3.2'), + ('openssl-sys', '0.9.104'), + ('ordered-float', '1.1.1'), + ('percent-encoding', '2.3.1'), + ('pkg-config', '0.3.31'), + ('ppv-lite86', '0.2.20'), + ('proc-macro2', '1.0.88'), + ('quick-error', '1.2.3'), + ('quote', '1.0.37'), + ('rand', '0.3.23'), + ('rand', '0.4.6'), + ('rand', '0.8.5'), + ('rand_chacha', '0.3.1'), + ('rand_core', '0.3.1'), + ('rand_core', '0.4.2'), + ('rand_core', '0.6.4'), + ('rawpointer', '0.1.0'), + ('rdrand', '0.4.0'), + ('regex', '1.11.0'), + ('regex-automata', '0.4.8'), + ('regex-syntax', '0.8.5'), + ('rust-htslib', '0.38.2'), + ('rustc-demangle', '0.1.24'), + ('rustc_version', '0.1.7'), + ('rustversion', '1.0.18'), + ('ryu', '1.0.18'), + ('semver', '0.1.20'), + ('serde', '1.0.210'), + ('serde_derive', '1.0.210'), + ('shlex', '1.3.0'), + ('statrs', '0.9.0'), + ('strsim', '0.8.0'), + ('strum_macros', '0.26.4'), + ('syn', '1.0.109'), + ('syn', '2.0.79'), + ('textwrap', '0.11.0'), + ('thiserror', '1.0.64'), + ('thiserror-impl', '1.0.64'), + ('tinyvec', '1.8.0'), + ('tinyvec_macros', '0.1.1'), + ('unicode-bidi', '0.3.17'), + ('unicode-ident', '1.0.13'), + ('unicode-normalization', '0.1.24'), + ('unicode-width', '0.1.14'), + ('url', '2.5.2'), + ('vcpkg', '0.2.15'), + ('vec_map', '0.8.2'), + ('version_check', '0.9.5'), + ('wasi', '0.11.0+wasi-snapshot-preview1'), + ('wasm-bindgen', '0.2.95'), + ('wasm-bindgen-backend', '0.2.95'), + ('wasm-bindgen-macro', '0.2.95'), + ('wasm-bindgen-macro-support', '0.2.95'), + ('wasm-bindgen-shared', '0.2.95'), + ('winapi', '0.3.9'), + ('winapi-i686-pc-windows-gnu', '0.4.0'), + ('winapi-x86_64-pc-windows-gnu', '0.4.0'), + ('windows-core', '0.52.0'), + ('windows-sys', '0.52.0'), + ('windows-targets', '0.52.6'), + ('windows_aarch64_gnullvm', '0.52.6'), + ('windows_aarch64_msvc', '0.52.6'), + ('windows_i686_gnu', '0.52.6'), + ('windows_i686_gnullvm', '0.52.6'), + ('windows_i686_msvc', '0.52.6'), + ('windows_x86_64_gnu', '0.52.6'), + ('windows_x86_64_gnullvm', '0.52.6'), + ('windows_x86_64_msvc', '0.52.6'), + ('zerocopy', '0.7.35'), + ('zerocopy-derive', '0.7.35'), +] +source_urls = ['https://github.com/pjedge/longshot/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = [ + {'v1.0.0.tar.gz': 'f6981892beb966eef40986c46928301dec1fef38591cc291e00a546f9866c5e2'}, + {'addr2line-0.24.2.tar.gz': 'dfbe277e56a376000877090da837660b4427aad530e3028d44e0bffe4f89a1c1'}, + {'adler2-2.0.0.tar.gz': '512761e0bb2578dd7380c6baaa0f4ce03e84f95e960231d1dec8bf4d7d6e2627'}, + {'ahash-0.7.8.tar.gz': '891477e0c6a8957309ee5c45a6368af3ae14bb510732d2684ffa19af310920f9'}, + {'aho-corasick-1.1.3.tar.gz': '8e60d3430d3a69478ad0993f19238d2df97c507009a52b3c10addcd7f6bcb916'}, + {'android-tzdata-0.1.1.tar.gz': 'e999941b234f3131b00bc13c22d06e8c5ff726d1b6318ac7eb276997bbb4fef0'}, + {'android_system_properties-0.1.5.tar.gz': 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procedural syntax with powerful data description constructs based + on associative arrays and extensible semantics. Lua is dynamically typed, + runs by interpreting bytecode for a register-based virtual machine, + and has automatic memory management with incremental garbage collection, + making it ideal for configuration, scripting, and rapid prototyping.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.%(namelower)s.org/ftp/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['9fbf5e28ef86c69858f6d3d34eccc32e911c1a28b4120ff3e84aaa70cfbf1e30'] + +builddependencies = [ + ('binutils', '2.42'), +] +dependencies = [ + ('ncurses', '6.5'), + ('libreadline', '8.2'), +] + + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/l/langchain-anthropic/langchain-anthropic-0.1.15-foss-2023a.eb b/easybuild/easyconfigs/l/langchain-anthropic/langchain-anthropic-0.1.15-foss-2023a.eb new file mode 100644 index 00000000000..6031932aa6c --- /dev/null +++ b/easybuild/easyconfigs/l/langchain-anthropic/langchain-anthropic-0.1.15-foss-2023a.eb @@ -0,0 +1,60 @@ +easyblock = 'PythonBundle' + +name = 'langchain-anthropic' +version = '0.1.15' + +homepage = 'https://python.langchain.com' +description = """ +This package contains the LangChain integration for Anthropic's generative models. +""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [ + ('poetry', '1.5.1'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('LangChain', '0.2.1'), + ('tokenizers', '0.15.2'), + ('jiter', '0.4.1'), +] + +exts_list = [ + ('langchain-core', '0.2.3', { + 'sources': ['langchain_core-%(version)s.tar.gz'], + 'checksums': ['fbc75a64b9c0b7655d96ca57a707df1e6c09efc1539c36adbd73260612549810'], + }), + ('anyio', '4.4.0', { + 'checksums': ['5aadc6a1bbb7cdb0bede386cac5e2940f5e2ff3aa20277e991cf028e0585ce94'], + }), + ('h11', '0.14.0', { + 'checksums': ['8f19fbbe99e72420ff35c00b27a34cb9937e902a8b810e2c88300c6f0a3b699d'], + }), + ('httpcore', '1.0.5', { + 'checksums': ['34a38e2f9291467ee3b44e89dd52615370e152954ba21721378a87b2960f7a61'], + }), + ('httpx', '0.27.0', { + 'checksums': ['a0cb88a46f32dc874e04ee956e4c2764aba2aa228f650b06788ba6bda2962ab5'], + }), + ('sniffio', '1.3.1', { + 'checksums': ['f4324edc670a0f49750a81b895f35c3adb843cca46f0530f79fc1babb23789dc'], + }), + ('anthropic', '0.28.0', { + 'source_tmpl': 'anthropic-0.28.0-py3-none-any.whl', + 'checksums': ['2b620b21aee3d20c5d8005483c34df239d53ae895687113b26b8a36892a7e20f'], + }), + ('defusedxml', '0.7.1', { + 'checksums': ['1bb3032db185915b62d7c6209c5a8792be6a32ab2fedacc84e01b52c51aa3e69'], + }), + (name, version, { + 'sources': ['langchain_anthropic-%(version)s.tar.gz'], + 'checksums': ['c5c3c6eaccb11ed99a63886e50873ac21eaf8e9441e0f75c7ae7cd8cdef65155'], + }), +] + +use_pip = True +sanity_pip_check = True + +moduleclass = 'ai' diff --git a/easybuild/easyconfigs/l/langchain-mistralai/langchain-mistralai-0.1.8-foss-2023a.eb b/easybuild/easyconfigs/l/langchain-mistralai/langchain-mistralai-0.1.8-foss-2023a.eb new file mode 100644 index 00000000000..78fc26dda3f --- /dev/null +++ b/easybuild/easyconfigs/l/langchain-mistralai/langchain-mistralai-0.1.8-foss-2023a.eb @@ -0,0 +1,59 @@ +easyblock = 'PythonBundle' + +name = 'langchain-mistralai' +version = '0.1.8' + +homepage = 'https://github.com/langchain-ai/langchain' +description = """ +This package contains the LangChain integrations for MistralAI through their mistralai SDK. +""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [ + ('poetry', '1.5.1'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('LangChain', '0.2.1'), + ('tokenizers', '0.15.2'), + ('jiter', '0.4.1'), +] + +exts_list = [ + ('langchain-core', '0.2.3', { + 'sources': ['langchain_core-%(version)s.tar.gz'], + 'checksums': ['fbc75a64b9c0b7655d96ca57a707df1e6c09efc1539c36adbd73260612549810'], + }), + ('anyio', '4.4.0', { + 'checksums': ['5aadc6a1bbb7cdb0bede386cac5e2940f5e2ff3aa20277e991cf028e0585ce94'], + }), + ('h11', '0.14.0', { + 'checksums': ['8f19fbbe99e72420ff35c00b27a34cb9937e902a8b810e2c88300c6f0a3b699d'], + }), + ('httpcore', '1.0.5', { + 'checksums': ['34a38e2f9291467ee3b44e89dd52615370e152954ba21721378a87b2960f7a61'], + }), + ('httpx', '0.25.2', { + 'checksums': ['8b8fcaa0c8ea7b05edd69a094e63a2094c4efcb48129fb757361bc423c0ad9e8'], + }), + ('httpx-sse', '0.4.0', { + 'checksums': ['1e81a3a3070ce322add1d3529ed42eb5f70817f45ed6ec915ab753f961139721'], + }), + ('sniffio', '1.3.1', { + 'checksums': ['f4324edc670a0f49750a81b895f35c3adb843cca46f0530f79fc1babb23789dc'], + }), + ('mistralai', '0.4.0', { + 'checksums': ['1f21f02dec1fd6fefe12ca100d5937fd62542c11008c193d16df6f4a2d8554da'], + }), + (name, version, { + 'sources': ['langchain_mistralai-%(version)s.tar.gz'], + 'checksums': ['dc328f7aedfd9e88eeb79de5692dfc3907793b82ef59f0d6722d19c1c8bfcdc2'], + }), +] + +use_pip = True +sanity_pip_check = True + +moduleclass = 'ai' diff --git a/easybuild/easyconfigs/l/langchain-openai/langchain-openai-0.1.8-foss-2023a.eb b/easybuild/easyconfigs/l/langchain-openai/langchain-openai-0.1.8-foss-2023a.eb new file mode 100644 index 00000000000..e46f2e43b4c --- /dev/null +++ b/easybuild/easyconfigs/l/langchain-openai/langchain-openai-0.1.8-foss-2023a.eb @@ -0,0 +1,35 @@ +easyblock = 'PythonBundle' + +name = 'langchain-openai' +version = '0.1.8' + +homepage = 'https://github.com/langchain-ai/langchain' +description = """ +This package contains the LangChain integrations for OpenAI through their openai SDK. +""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [ + ('poetry', '1.5.1'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('LangChain', '0.2.1'), + ('tiktoken', '0.7.0'), # needs tiktoken >= 0.7.0 + ('openai-python', '1.30.5'), +] + +exts_list = [ + (name, version, { + 'sources': ['langchain_openai-%(version)s.tar.gz'], + 'checksums': ['a11fcce15def7917c44232abda6baaa63dfc79fe44be1531eea650d39a44cd95'], + }), +] + +use_pip = True +sanity_pip_check = True + +moduleclass = 'ai' diff --git a/easybuild/easyconfigs/l/libGLU/libGLU-9.0.3-GCCcore-13.3.0.eb b/easybuild/easyconfigs/l/libGLU/libGLU-9.0.3-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..8a01a3ac439 --- /dev/null +++ b/easybuild/easyconfigs/l/libGLU/libGLU-9.0.3-GCCcore-13.3.0.eb @@ -0,0 +1,30 @@ +easyblock = 'MesonNinja' + +name = 'libGLU' +version = '9.0.3' + +homepage = 'https://mesa.freedesktop.org/archive/glu/' +description = """The OpenGL Utility Library (GLU) is a computer graphics library for OpenGL. """ + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://mesa.freedesktop.org/archive/glu/'] +sources = ['glu-%(version)s.tar.xz'] +checksums = ['bd43fe12f374b1192eb15fe20e45ff456b9bc26ab57f0eee919f96ca0f8a330f'] + +builddependencies = [ + ('pkgconf', '2.2.0'), + ('binutils', '2.42'), + ('Ninja', '1.12.1'), + ('Meson', '1.4.0'), +] + +dependencies = [('Mesa', '24.1.3')] + +sanity_check_paths = { + 'files': ['lib/libGLU.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libabigail/libabigail-2.5-GCCcore-13.2.0.eb b/easybuild/easyconfigs/l/libabigail/libabigail-2.5-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..c414dda9011 --- /dev/null +++ b/easybuild/easyconfigs/l/libabigail/libabigail-2.5-GCCcore-13.2.0.eb @@ -0,0 +1,54 @@ +easyblock = 'ConfigureMake' + +name = 'libabigail' +version = '2.5' + +description = """ +ABIGAIL stands for the Application Binary Interface Generic Analysis and +Instrumentation Library. + +It’s a framework which aims at helping developers and software distributors +to spot some ABI-related issues like interface incompatibility in ELF shared +libraries by performing a static analysis of the ELF binaries at hand. + +The type of interface incompatibilities that Abigail focuses on is related to +changes on the exported ELF functions and variables symbols, as well as layout +and size changes of data types of the functions and variables exported by +shared libraries. + +In other words, if the return type of a function exported by a shared library +changes in an incompatible way from one version of a given shared library to +another, we want Abigail to help people catch that. +""" +homepage = 'https://sourceware.org/libabigail' +docurls = ['https://sourceware.org/libabigail/manual'] + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} +builddependencies = [('binutils', '2.40')] + +dependencies = [ + ('elfutils', '0.190'), + ('Python', '3.11.5'), + ('libxml2', '2.11.5'), +] + +source_urls = ['https://mirrors.kernel.org/sourceware/libabigail/'] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['7cfc4e9b00ae38d87fb0c63beabb32b9cbf9ce410e52ceeb5ad5b3c5beb111f3'] + +configopts = '--enable-manual=no --enable-apidoc=no --with-sysroot=%(sysroot)s' + +sanity_check_paths = { + 'files': [ + 'bin/abicompat', 'bin/abidiff', + 'lib/libabigail.a', 'lib/libabigail.%s' % SHLIB_EXT, + ], + 'dirs': ['include'], +} + +sanity_check_commands = [ + "abicompat --help | grep usage", + "abidiff --help | grep usage", +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/l/libaec/libaec-1.1.3-GCCcore-13.3.0.eb b/easybuild/easyconfigs/l/libaec/libaec-1.1.3-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..267acc5aa3d --- /dev/null +++ b/easybuild/easyconfigs/l/libaec/libaec-1.1.3-GCCcore-13.3.0.eb @@ -0,0 +1,36 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +easyblock = 'CMakeMake' + +name = 'libaec' +version = '1.1.3' + +homepage = 'https://gitlab.dkrz.de/k202009/libaec' +description = """Libaec provides fast lossless compression of 1 up to 32 bit wide signed or unsigned integers +(samples). The library achieves best results for low entropy data as often encountered in space imaging +instrument data or numerical model output from weather or climate simulations. While floating point representations +are not directly supported, they can also be efficiently coded by grouping exponents and mantissa.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://gitlab.dkrz.de/k202009/%(namelower)s/-/archive/v%(version)s'] +sources = [SOURCELOWER_TAR_GZ] +patches = ["libaec-1.1.3_install_binary.patch"] + +checksums = ['453de44eb6ea2500843a4cf4d2e97d1be251d2df7beae6c2ebe374edcb11e378', + '52fcdeacd9c27108dffafd8109012902fa63fb2e39803670a3ba16f313628f4c'] + +builddependencies = [ + ('CMake', '3.29.3'), + ('binutils', '2.42'), +] + +sanity_check_paths = { + 'files': ['bin/graec', 'include/%(name)s.h', 'include/szlib.h', + 'lib/libaec.a', 'lib/libaec.%s' % SHLIB_EXT], + 'dirs': [], +} + +sanity_check_commands = ['graec --help'] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libaec/libaec-1.1.3_install_binary.patch b/easybuild/easyconfigs/l/libaec/libaec-1.1.3_install_binary.patch new file mode 100644 index 00000000000..29d7f8e0c7b --- /dev/null +++ b/easybuild/easyconfigs/l/libaec/libaec-1.1.3_install_binary.patch @@ -0,0 +1,11 @@ +# The binary is not installed by default which caused the sanity check to fail +# @author Stefan Wolfsheimer, SURF + +diff -uNr libaec-v1.1.3.orig/src/CMakeLists.txt libaec-v1.1.3/src/CMakeLists.txt +--- libaec-v1.1.3.orig/src/CMakeLists.txt 2024-11-15 14:21:05.177185441 +0100 ++++ libaec-v1.1.3/src/CMakeLists.txt 2024-11-15 14:21:39.702841450 +0100 +@@ -76,3 +76,4 @@ + COMPILE_DEFINITIONS "${libaec_COMPILE_DEFINITIONS}") + + install(TARGETS aec_static aec_shared sz_static sz_shared) ++install(TARGETS graec RUNTIME DESTINATION bin) diff --git a/easybuild/easyconfigs/l/libaio/libaio-0.3.113-GCCcore-13.2.0.eb b/easybuild/easyconfigs/l/libaio/libaio-0.3.113-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..e5a7827cc4b --- /dev/null +++ b/easybuild/easyconfigs/l/libaio/libaio-0.3.113-GCCcore-13.2.0.eb @@ -0,0 +1,39 @@ +easyblock = 'MakeCp' + +name = 'libaio' +version = '0.3.113' +_libversion = '1.0.2' + +homepage = 'https://pagure.io/libaio' +description = "Asynchronous input/output library that uses the kernels native interface." + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://pagure.io/%(name)s/archive/%(name)s-%(version)s/'] +sources = ['%(name)s-%(version)s.tar.gz'] +checksums = ['1c561c20670c5c09cc8437a622008c0693c6a7816c1f30332da3796953b2f454'] + +builddependencies = [('binutils', '2.40')] + +_soname = "libaio.%s.%s" % (SHLIB_EXT, _libversion) + +files_to_copy = [ + (["src/libaio.a", "src/%s" % _soname], "lib"), + (["src/libaio.h"], "include"), +] + +# links to the shared library with generic names +_solinks = [ + "libaio.%s" % SHLIB_EXT, + "libaio.%s.1" % SHLIB_EXT, +] + +postinstallcmds = ["cd %%(installdir)s/lib && ln -s %s %s" % (_soname, l) for l in _solinks] + +sanity_check_paths = { + 'files': ['lib/%s' % l for l in ['libaio.a', _soname] + _solinks] + ['include/libaio.h'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libaio/libaio-0.3.113-GCCcore-13.3.0.eb b/easybuild/easyconfigs/l/libaio/libaio-0.3.113-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..b76bc3cecc4 --- /dev/null +++ b/easybuild/easyconfigs/l/libaio/libaio-0.3.113-GCCcore-13.3.0.eb @@ -0,0 +1,39 @@ +easyblock = 'MakeCp' + +name = 'libaio' +version = '0.3.113' +_libversion = '1.0.2' + +homepage = 'https://pagure.io/libaio' +description = "Asynchronous input/output library that uses the kernels native interface." + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://pagure.io/%(name)s/archive/%(name)s-%(version)s/'] +sources = ['%(name)s-%(version)s.tar.gz'] +checksums = ['1c561c20670c5c09cc8437a622008c0693c6a7816c1f30332da3796953b2f454'] + +builddependencies = [('binutils', '2.42')] + +_soname = "libaio.%s.%s" % (SHLIB_EXT, _libversion) + +files_to_copy = [ + (["src/libaio.a", "src/%s" % _soname], "lib"), + (["src/libaio.h"], "include"), +] + +# links to the shared library with generic names +_solinks = [ + "libaio.%s" % SHLIB_EXT, + "libaio.%s.1" % SHLIB_EXT, +] + +postinstallcmds = ["cd %%(installdir)s/lib && ln -s %s %s" % (_soname, l) for l in _solinks] + +sanity_check_paths = { + 'files': ['lib/%s' % l for l in ['libaio.a', _soname] + _solinks] + ['include/libaio.h'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libarchive/libarchive-3.7.4-GCCcore-13.3.0.eb b/easybuild/easyconfigs/l/libarchive/libarchive-3.7.4-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..d15d7381318 --- /dev/null +++ b/easybuild/easyconfigs/l/libarchive/libarchive-3.7.4-GCCcore-13.3.0.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'libarchive' +version = '3.7.4' + +homepage = 'https://www.libarchive.org/' + +description = """ + Multi-format archive and compression library +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://www.libarchive.org/downloads/'] +sources = [SOURCE_TAR_GZ] +checksums = [ + {'libarchive-3.7.4.tar.gz': '7875d49596286055b52439ed42f044bd8ad426aa4cc5aabd96bfe7abb971d5e8'}, +] + +builddependencies = [ + ('binutils', '2.42'), +] + +dependencies = [ + ('zlib', '1.3.1'), + ('XZ', '5.4.5'), + ('OpenSSL', '3', '', SYSTEM), +] + +sanity_check_paths = { + 'files': ['include/archive.h', 'lib/libarchive.%s' % SHLIB_EXT], + 'dirs': ['bin', 'share/man/man3'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/l/libavif/libavif-0.11.1-foss-2021a.eb b/easybuild/easyconfigs/l/libavif/libavif-0.11.1-GCCcore-10.3.0.eb similarity index 91% rename from easybuild/easyconfigs/l/libavif/libavif-0.11.1-foss-2021a.eb rename to easybuild/easyconfigs/l/libavif/libavif-0.11.1-GCCcore-10.3.0.eb index 2f4ed93c1c9..7ff457a5456 100644 --- a/easybuild/easyconfigs/l/libavif/libavif-0.11.1-foss-2021a.eb +++ b/easybuild/easyconfigs/l/libavif/libavif-0.11.1-GCCcore-10.3.0.eb @@ -11,7 +11,7 @@ description = """This library aims to be a friendly, portable C implementation o as described here: https://aomediacodec.github.io/av1-avif/ """ -toolchain = {'name': 'foss', 'version': '2021a'} +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} source_urls = ['https://github.com/AOMediaCodec/libavif/archive/'] sources = ['v%(version)s.tar.gz'] @@ -19,9 +19,7 @@ checksums = ['0eb49965562a0e5e5de58389650d434cff32af84c34185b6c9b7b2fccae06d4e'] builddependencies = [ ('CMake', '3.20.1'), -] - -dependencies = [ + ('binutils', '2.36.1'), ('NASM', '2.15.05'), ('Meson', '0.58.0'), ('Ninja', '1.10.2'), diff --git a/easybuild/easyconfigs/l/libavif/libavif-0.11.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/libavif/libavif-0.11.1-GCCcore-11.3.0.eb index 2d5b1cc7ab9..ac67210e4c9 100644 --- a/easybuild/easyconfigs/l/libavif/libavif-0.11.1-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/l/libavif/libavif-0.11.1-GCCcore-11.3.0.eb @@ -20,9 +20,6 @@ checksums = ['0eb49965562a0e5e5de58389650d434cff32af84c34185b6c9b7b2fccae06d4e'] builddependencies = [ ('CMake', '3.23.1'), ('binutils', '2.38'), -] - -dependencies = [ ('NASM', '2.15.05'), ('Meson', '0.62.1'), ('Ninja', '1.10.2'), diff --git a/easybuild/easyconfigs/l/libavif/libavif-0.11.1-foss-2022a.eb b/easybuild/easyconfigs/l/libavif/libavif-1.0.4-GCCcore-12.3.0.eb similarity index 70% rename from easybuild/easyconfigs/l/libavif/libavif-0.11.1-foss-2022a.eb rename to easybuild/easyconfigs/l/libavif/libavif-1.0.4-GCCcore-12.3.0.eb index b34d2a8449b..149561be6b0 100644 --- a/easybuild/easyconfigs/l/libavif/libavif-0.11.1-foss-2022a.eb +++ b/easybuild/easyconfigs/l/libavif/libavif-1.0.4-GCCcore-12.3.0.eb @@ -4,28 +4,26 @@ easyblock = 'CMakeMake' name = 'libavif' -version = '0.11.1' +version = '1.0.4' homepage = 'https://github.com/AOMediaCodec/libavif' description = """This library aims to be a friendly, portable C implementation of the AV1 Image File Format, as described here: https://aomediacodec.github.io/av1-avif/ """ -toolchain = {'name': 'foss', 'version': '2022a'} +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} source_urls = ['https://github.com/AOMediaCodec/libavif/archive/'] sources = ['v%(version)s.tar.gz'] -checksums = ['0eb49965562a0e5e5de58389650d434cff32af84c34185b6c9b7b2fccae06d4e'] +checksums = ['dc56708c83a4b934a8af2b78f67f866ba2fb568605c7cf94312acf51ee57d146'] builddependencies = [ - ('CMake', '3.23.1'), -] - -dependencies = [ - ('NASM', '2.15.05'), - ('Meson', '0.62.1'), - ('Ninja', '1.10.2'), - ('Rust', '1.60.0'), + ('CMake', '3.26.3'), + ('binutils', '2.40'), + ('NASM', '2.16.01'), + ('Meson', '1.1.1'), + ('Ninja', '1.11.1'), + ('Rust', '1.70.0'), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/l/libbraiding/libbraiding-1.2-GCCcore-13.2.0.eb b/easybuild/easyconfigs/l/libbraiding/libbraiding-1.2-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..172d0f449a2 --- /dev/null +++ b/easybuild/easyconfigs/l/libbraiding/libbraiding-1.2-GCCcore-13.2.0.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'libbraiding' +version = '1.2' + +homepage = 'https://github.com/miguelmarco/libbraiding' +description = """This is a project to expose the functionalitis of the Braiding program as a shared library. + The original goal is to include it as a component of SageMath, but it can be used in any other c++ program.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://github.com/miguelmarco/libbraiding/releases/download/%(version)s/'] +sources = [SOURCE_TAR_GZ] +checksums = ['73087d1145ace719eafeda1db1c28b5fe1c981b7e784dc59f2b1d6fc4ff75f80'] + +builddependencies = [ + ('binutils', '2.40'), +] + +sanity_check_paths = { + 'files': [ + 'include/braiding.h', + 'include/cbraid.h', + 'include/cbraid_implementation.h', + 'include/cbraid_interface.h', + 'lib/libbraiding.%s' % SHLIB_EXT, + ], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libcerf/libcerf-2.4-GCCcore-13.3.0.eb b/easybuild/easyconfigs/l/libcerf/libcerf-2.4-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..2714c4d2765 --- /dev/null +++ b/easybuild/easyconfigs/l/libcerf/libcerf-2.4-GCCcore-13.3.0.eb @@ -0,0 +1,32 @@ +easyblock = 'CMakeMake' + +name = 'libcerf' +version = '2.4' + +homepage = 'https://jugit.fz-juelich.de/mlz/libcerf' + +description = """ + libcerf is a self-contained numeric library that provides an efficient and + accurate implementation of complex error functions, along with Dawson, + Faddeeva, and Voigt functions. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://jugit.fz-juelich.de/mlz/libcerf/-/archive/v%(version)s/'] +sources = ['libcerf-v%(version)s.tar.gz'] +checksums = ['080b30ae564c3dabe3b89264522adaf5647ec754021572bee54929697b276cdc'] + +builddependencies = [ + ('binutils', '2.42'), + ('CMake', '3.29.3'), + ('Perl', '5.38.2'), # required for pod2html +] + +sanity_check_paths = { + 'files': ['lib/libcerf.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/l/libcint/libcint-5.4.0-gfbf-2023a-pypzpx.eb b/easybuild/easyconfigs/l/libcint/libcint-5.4.0-gfbf-2023a-pypzpx.eb new file mode 100644 index 00000000000..0bc083652f0 --- /dev/null +++ b/easybuild/easyconfigs/l/libcint/libcint-5.4.0-gfbf-2023a-pypzpx.eb @@ -0,0 +1,39 @@ +easyblock = 'CMakeMake' + +name = 'libcint' +version = '5.4.0' +versionsuffix = '-pypzpx' + +homepage = 'https://github.com/sunqm/libcint' +description = """libcint is an open source library for analytical Gaussian integrals. +This module of libcint uses the P orbitals convention (py, pz, px)""" + +toolchain = {'name': 'gfbf', 'version': '2023a'} + +source_urls = ['https://github.com/sunqm/%(name)s/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = ['%(name)s-4.4.0_remove_pyscftest.patch'] +checksums = [ + '42a8f2e9244e4575437e426e32cd1e60ef9559971c42a41f860c870efc745d99', # v5.4.0.tar.gz + '6449297a6aee30fef3d6a268aa892dea8dd5c3ca9669a50ae694ab9bcf17842d', # libcint-4.4.0_remove_pyscftest.patch +] + +builddependencies = [ + ('CMake', '3.26.3'), + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), +] + +configopts = "-DWITH_RANGE_COULOMB=on -DWITH_COULOMB_ERF=on -DWITH_F12=on -DENABLE_TEST=on -DPYPZPX=1" + +buildopts = 'VERBOSE=1' + +runtest = "test " +separate_build_dir = False # Must use the same directory for tests + +sanity_check_paths = { + 'files': ['include/cint.h', 'lib/%%(name)s.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/libcint/libcint-6.1.2-gfbf-2024a.eb b/easybuild/easyconfigs/l/libcint/libcint-6.1.2-gfbf-2024a.eb new file mode 100644 index 00000000000..ec3812fdaec --- /dev/null +++ b/easybuild/easyconfigs/l/libcint/libcint-6.1.2-gfbf-2024a.eb @@ -0,0 +1,42 @@ +easyblock = 'CMakeMake' + +name = 'libcint' +version = '6.1.2' + +homepage = 'https://github.com/sunqm/libcint' +description = "libcint is an open source library for analytical Gaussian integrals." + +toolchain = {'name': 'gfbf', 'version': '2024a'} + +source_urls = ['https://github.com/sunqm/%(name)s/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = [ + '%(name)s-4.4.0_remove_pyscftest.patch', + 'libcint-6.1.2_fix_tests.patch', +] + +checksums = [ + {'v6.1.2.tar.gz': '8287e1eaf2b8c8e19eb7a8ea92fd73898f0884023c503b84624610400adb25c4'}, + {'libcint-4.4.0_remove_pyscftest.patch': '6449297a6aee30fef3d6a268aa892dea8dd5c3ca9669a50ae694ab9bcf17842d'}, + {'libcint-6.1.2_fix_tests.patch': '2776dbe2320a44733f01e6d2baaf190d3af19fe9148ce656b449e09f65497be7'}, +] + +builddependencies = [ + ('CMake', '3.29.3'), + ('Python', '3.12.3'), + ('SciPy-bundle', '2024.05'), +] + +configopts = "-DWITH_RANGE_COULOMB=on -DWITH_COULOMB_ERF=on -DWITH_F12=on -DENABLE_TEST=on" + +buildopts = 'VERBOSE=1' + +runtest = "test " +separate_build_dir = False # Must use the same directory for tests + +sanity_check_paths = { + 'files': ['include/cint.h', 'lib/%(name)s.so'], + 'dirs': [], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/libcint/libcint-6.1.2_fix_tests.patch b/easybuild/easyconfigs/l/libcint/libcint-6.1.2_fix_tests.patch new file mode 100644 index 00000000000..f9f8927990b --- /dev/null +++ b/easybuild/easyconfigs/l/libcint/libcint-6.1.2_fix_tests.patch @@ -0,0 +1,147 @@ +What: Fix incorrect path to the shared library +Author: maxim-mnasterov (SURF) + +diff -Nru libcint-6.1.2.orig/testsuite/test_3c2e.py libcint-6.1.2/testsuite/test_3c2e.py +--- libcint-6.1.2.orig/testsuite/test_3c2e.py 2024-10-04 16:09:36.042124000 +0200 ++++ libcint-6.1.2/testsuite/test_3c2e.py 2024-10-04 16:12:57.158040824 +0200 +@@ -13,7 +13,7 @@ + import ctypes + import numpy + +-_cint = ctypes.CDLL(os.path.abspath(os.path.join(__file__, '../../build/libcint.so'))) ++_cint = ctypes.CDLL(os.path.abspath(os.path.join(__file__, '../../libcint.so'))) + + PTR_LIGHT_SPEED = 0 + PTR_COMMON_ORIG = 1 +diff -Nru libcint-6.1.2.orig/testsuite/test_c2s.py libcint-6.1.2/testsuite/test_c2s.py +--- libcint-6.1.2.orig/testsuite/test_c2s.py 2024-10-04 16:09:36.042595000 +0200 ++++ libcint-6.1.2/testsuite/test_c2s.py 2024-10-04 16:13:11.143154981 +0200 +@@ -3,7 +3,7 @@ + import ctypes + import numpy + +-_cint = numpy.ctypeslib.load_library('libcint', os.path.abspath(os.path.join(__file__, '../../build'))) ++_cint = numpy.ctypeslib.load_library('libcint', os.path.abspath(os.path.join(__file__, '../..'))) + + + PTR_EXPCUTOFF = 0 +diff -Nru libcint-6.1.2.orig/testsuite/test_cart2sph.py libcint-6.1.2/testsuite/test_cart2sph.py +--- libcint-6.1.2.orig/testsuite/test_cart2sph.py 2024-10-04 16:09:36.043003000 +0200 ++++ libcint-6.1.2/testsuite/test_cart2sph.py 2024-10-04 16:13:35.057998480 +0200 +@@ -10,7 +10,7 @@ + sys.path.insert(0, os.path.abspath(os.path.join(__file__, '../../scripts'))) + import cart2sph + +-_cint = ctypes.CDLL(os.path.abspath(os.path.join(__file__, '../../build/libcint.so'))) ++_cint = ctypes.CDLL(os.path.abspath(os.path.join(__file__, '../../libcint.so'))) + + pauli = np.array([[[0., 1.], + [1., 0.]], # x +diff -Nru libcint-6.1.2.orig/testsuite/test_cint4c1e.py libcint-6.1.2/testsuite/test_cint4c1e.py +--- libcint-6.1.2.orig/testsuite/test_cint4c1e.py 2024-10-04 16:09:36.043792000 +0200 ++++ libcint-6.1.2/testsuite/test_cint4c1e.py 2024-10-04 16:13:48.171695000 +0200 +@@ -13,7 +13,7 @@ + import ctypes + import numpy + +-_cint = numpy.ctypeslib.load_library('libcint', os.path.abspath(os.path.join(__file__, '../../build'))) ++_cint = numpy.ctypeslib.load_library('libcint', os.path.abspath(os.path.join(__file__, '../..'))) + + + PTR_LIGHT_SPEED = 0 +diff -Nru libcint-6.1.2.orig/testsuite/test_cint.py libcint-6.1.2/testsuite/test_cint.py +--- libcint-6.1.2.orig/testsuite/test_cint.py 2024-10-04 16:09:36.043395000 +0200 ++++ libcint-6.1.2/testsuite/test_cint.py 2024-10-04 16:12:23.988960299 +0200 +@@ -13,7 +13,7 @@ + import ctypes + import numpy + +-_cint = ctypes.CDLL(os.path.abspath(os.path.join(__file__, '../../build/libcint.so'))) ++_cint = ctypes.CDLL(os.path.abspath(os.path.join(__file__, '../../libcint.so'))) + + + PTR_EXPCUTOFF = 0 +diff -Nru libcint-6.1.2.orig/testsuite/test_int1e_grids.py libcint-6.1.2/testsuite/test_int1e_grids.py +--- libcint-6.1.2.orig/testsuite/test_int1e_grids.py 2024-10-04 16:09:36.045513000 +0200 ++++ libcint-6.1.2/testsuite/test_int1e_grids.py 2024-10-04 16:14:20.427552000 +0200 +@@ -13,7 +13,7 @@ + import ctypes + import numpy + +-_cint = ctypes.CDLL(os.path.abspath(os.path.join(__file__, '../../build/libcint.so'))) ++_cint = ctypes.CDLL(os.path.abspath(os.path.join(__file__, '../../libcint.so'))) + + PTR_EXPCUTOFF = 0 + PTR_COMMON_ORIG = 1 +diff -Nru libcint-6.1.2.orig/testsuite/test_int1e.py libcint-6.1.2/testsuite/test_int1e.py +--- libcint-6.1.2.orig/testsuite/test_int1e.py 2024-10-04 16:09:36.045015000 +0200 ++++ libcint-6.1.2/testsuite/test_int1e.py 2024-10-04 16:14:31.649911000 +0200 +@@ -5,7 +5,7 @@ + import ctypes + import numpy + +-_cint = numpy.ctypeslib.load_library('libcint', os.path.abspath(os.path.join(__file__, '../../build'))) ++_cint = numpy.ctypeslib.load_library('libcint', os.path.abspath(os.path.join(__file__, '../..'))) + #_cint4 = ctypes.cdll.LoadLibrary('libcint.so.4') + + from pyscf import gto, lib +diff -Nru libcint-6.1.2.orig/testsuite/test_int2c2e.py libcint-6.1.2/testsuite/test_int2c2e.py +--- libcint-6.1.2.orig/testsuite/test_int2c2e.py 2024-10-04 16:09:36.045952547 +0200 ++++ libcint-6.1.2/testsuite/test_int2c2e.py 2024-10-04 16:14:45.424744884 +0200 +@@ -3,7 +3,7 @@ + import ctypes + import numpy + +-_cint = ctypes.CDLL(os.path.abspath(os.path.join(__file__, '../../build/libcint.so'))) ++_cint = ctypes.CDLL(os.path.abspath(os.path.join(__file__, '../../libcint.so'))) + + from pyscf import gto, lib + +diff -Nru libcint-6.1.2.orig/testsuite/test_int2e_f12_etc.py libcint-6.1.2/testsuite/test_int2e_f12_etc.py +--- libcint-6.1.2.orig/testsuite/test_int2e_f12_etc.py 2024-10-04 16:09:36.046726088 +0200 ++++ libcint-6.1.2/testsuite/test_int2e_f12_etc.py 2024-10-04 16:14:57.223888132 +0200 +@@ -3,7 +3,7 @@ + import ctypes + import numpy + +-_cint = ctypes.CDLL(os.path.abspath(os.path.join(__file__, '../../build/libcint.so'))) ++_cint = ctypes.CDLL(os.path.abspath(os.path.join(__file__, '../../libcint.so'))) + + from pyscf import gto, lib + +diff -Nru libcint-6.1.2.orig/testsuite/test_int2e.py libcint-6.1.2/testsuite/test_int2e.py +--- libcint-6.1.2.orig/testsuite/test_int2e.py 2024-10-04 16:09:36.046362000 +0200 ++++ libcint-6.1.2/testsuite/test_int2e.py 2024-10-04 16:15:10.386953000 +0200 +@@ -5,7 +5,7 @@ + import ctypes + import numpy + +-_cint = numpy.ctypeslib.load_library('libcint', os.path.abspath(os.path.join(__file__, '../../build'))) ++_cint = numpy.ctypeslib.load_library('libcint', os.path.abspath(os.path.join(__file__, '../..'))) + #_cint4 = ctypes.cdll.LoadLibrary('libcint.so.4') + + from pyscf import gto, lib +diff -Nru libcint-6.1.2.orig/testsuite/test_int3c1e.py libcint-6.1.2/testsuite/test_int3c1e.py +--- libcint-6.1.2.orig/testsuite/test_int3c1e.py 2024-10-04 16:09:36.047153000 +0200 ++++ libcint-6.1.2/testsuite/test_int3c1e.py 2024-10-04 16:15:23.148032000 +0200 +@@ -3,7 +3,7 @@ + import ctypes + import numpy + +-_cint = numpy.ctypeslib.load_library('libcint', os.path.abspath(os.path.join(__file__, '../../build'))) ++_cint = numpy.ctypeslib.load_library('libcint', os.path.abspath(os.path.join(__file__, '../..'))) + #_cint4 = ctypes.cdll.LoadLibrary('libcint.so.4') + + from pyscf import gto, lib +diff -Nru libcint-6.1.2.orig/testsuite/test_int3c2e.py libcint-6.1.2/testsuite/test_int3c2e.py +--- libcint-6.1.2.orig/testsuite/test_int3c2e.py 2024-10-04 16:09:36.047561000 +0200 ++++ libcint-6.1.2/testsuite/test_int3c2e.py 2024-10-04 16:15:33.932008000 +0200 +@@ -3,7 +3,7 @@ + import ctypes + import numpy + +-_cint = ctypes.CDLL(os.path.abspath(os.path.join(__file__, '../../build/libcint.so'))) ++_cint = ctypes.CDLL(os.path.abspath(os.path.join(__file__, '../../libcint.so'))) + + from pyscf import gto, lib + diff --git a/easybuild/easyconfigs/l/libcircle/libcircle-0.3-gompi-2024a.eb b/easybuild/easyconfigs/l/libcircle/libcircle-0.3-gompi-2024a.eb new file mode 100644 index 00000000000..1ea2630b327 --- /dev/null +++ b/easybuild/easyconfigs/l/libcircle/libcircle-0.3-gompi-2024a.eb @@ -0,0 +1,38 @@ +## +# Authors: +# * Petar Forai +# * Robert Mijakovic +## +easyblock = 'ConfigureMake' + +name = 'libcircle' +version = '0.3' + +homepage = 'https://github.com/hpc/libcircle/' + +description = """ + An API to provide an efficient distributed queue on a cluster. libcircle is an + API for distributing embarrassingly parallel workloads using self-stabilization. +""" + +toolchain = {'name': 'gompi', 'version': '2024a'} +toolchainopts = {'usempi': True, 'pic': True} + +github_account = 'hpc' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['fd8bc6e4dcc6fdec9d2a3d1c78a4060948ae4f11f0b278792610d6c05d53e14c'] + +builddependencies = [ + ('Autotools', '20231222'), + ('pkgconf', '2.2.0'), +] + +preconfigopts = './autogen.sh && ' + +sanity_check_paths = { + 'files': ['include/%(name)s.h', 'lib/%(name)s.a', 'lib/%%(name)s.%s' % SHLIB_EXT], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libcroco/libcroco-0.6.13-GCCcore-13.3.0.eb b/easybuild/easyconfigs/l/libcroco/libcroco-0.6.13-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..21b015fd6ed --- /dev/null +++ b/easybuild/easyconfigs/l/libcroco/libcroco-0.6.13-GCCcore-13.3.0.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'libcroco' +version = '0.6.13' + +homepage = 'https://gitlab.gnome.org/Archive/libcroco' +description = """Libcroco is a standalone css2 parsing and manipulation library.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://download.gnome.org/sources/libcroco/%(version_major_minor)s/'] +sources = [SOURCE_TAR_XZ] +checksums = ['767ec234ae7aa684695b3a735548224888132e063f92db585759b422570621d4'] + +builddependencies = [ + ('binutils', '2.42'), + ('pkgconf', '2.2.0'), +] + +dependencies = [ + ('zlib', '1.3.1'), + ('libxml2', '2.12.7'), + ('GLib', '2.80.4'), +] + +sanity_check_paths = { + 'files': ['bin/csslint-%(version_major_minor)s', 'lib/libcroco-%%(version_major_minor)s.%s' % SHLIB_EXT, + 'lib/libcroco-%(version_major_minor)s.a'], + 'dirs': ['include/libcroco-%(version_major_minor)s', 'share'] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libdap/libdap-3.20.11-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/libdap/libdap-3.20.11-GCCcore-11.3.0.eb index 237260a43f7..063ce985f47 100644 --- a/easybuild/easyconfigs/l/libdap/libdap-3.20.11-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/l/libdap/libdap-3.20.11-GCCcore-11.3.0.eb @@ -9,14 +9,15 @@ description = """A C++ SDK which contains an implementation of DAP 2.0 and toolchain = {'name': 'GCCcore', 'version': '11.3.0'} -source_urls = ['https://www.opendap.org/pub/source/'] -sources = [SOURCE_TAR_GZ] -checksums = ['850debf6ee6991350bf31051308093bee35ddd2121e4002be7e130a319de1415'] +source_urls = ['https://github.com/OPENDAP/libdap4/archive/refs/tags/'] +sources = ['%(version)s.tar.gz'] +checksums = ['319e9771d037b6c796f04e6a96bb27db1706bc5931ca149c78347c623a747771'] builddependencies = [ ('binutils', '2.38'), ('Bison', '3.8.2'), ('flex', '2.6.4'), + ('Autotools', '20220317'), ] dependencies = [ @@ -27,6 +28,7 @@ dependencies = [ ('util-linux', '2.38'), ] +preconfigopts = "autoreconf -fi && " configopts = 'TIRPC_LIBS="-ltirpc"' sanity_check_paths = { diff --git a/easybuild/easyconfigs/l/libdap/libdap-3.20.11-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/libdap/libdap-3.20.11-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..a6dbd52797f --- /dev/null +++ b/easybuild/easyconfigs/l/libdap/libdap-3.20.11-GCCcore-12.3.0.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'libdap' +version = '3.20.11' + +homepage = 'https://www.opendap.org/software/libdap' +description = """A C++ SDK which contains an implementation of DAP 2.0 and + DAP4.0. This includes both Client- and Server-side support classes.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://github.com/OPENDAP/libdap4/archive/refs/tags/'] +sources = ['%(version)s.tar.gz'] +checksums = ['319e9771d037b6c796f04e6a96bb27db1706bc5931ca149c78347c623a747771'] + +builddependencies = [ + ('binutils', '2.40'), + ('Bison', '3.8.2'), + ('flex', '2.6.4'), + ('Autotools', '20220317'), +] + +dependencies = [ + ('cURL', '8.0.1'), + ('libxml2', '2.11.4'), + ('libtirpc', '1.3.3'), + ('PCRE', '8.45'), + ('util-linux', '2.39'), +] + +preconfigopts = "autoreconf -fi && " +configopts = 'TIRPC_LIBS="-ltirpc"' + + +sanity_check_paths = { + 'files': ['bin/getdap', 'bin/getdap4', 'bin/dap-config', 'lib/libdap.a', 'lib/libdap.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libdap/libdap-3.20.7-GCCcore-10.3.0.eb b/easybuild/easyconfigs/l/libdap/libdap-3.20.7-GCCcore-10.3.0.eb index e2bb8f718ab..c1cb33551f7 100644 --- a/easybuild/easyconfigs/l/libdap/libdap-3.20.7-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/l/libdap/libdap-3.20.7-GCCcore-10.3.0.eb @@ -9,14 +9,15 @@ description = """A C++ SDK which contains an implementation of DAP 2.0 and toolchain = {'name': 'GCCcore', 'version': '10.3.0'} -source_urls = ['https://www.opendap.org/pub/source/'] -sources = [SOURCE_TAR_GZ] -checksums = ['6856813d0b29e70a36e8a53e9cf20ad680d21d615952263e9c6586704539e78c'] +source_urls = ['https://github.com/OPENDAP/libdap4/archive/refs/tags/'] +sources = ['%(version)s.tar.gz'] +checksums = ['f6e907ea7a9f878965a3af2a858423450dde389d851fc67a33b0096b8b9b6085'] builddependencies = [ ('binutils', '2.36.1'), ('Bison', '3.7.6'), ('flex', '2.6.4'), + ('Autotools', '20210128'), ] dependencies = [ @@ -27,6 +28,7 @@ dependencies = [ ('util-linux', '2.36'), ] +preconfigopts = "autoreconf -fi && " configopts = 'TIRPC_LIBS="-ltirpc"' sanity_check_paths = { diff --git a/easybuild/easyconfigs/l/libdap/libdap-3.20.8-GCCcore-11.2.0.eb b/easybuild/easyconfigs/l/libdap/libdap-3.20.8-GCCcore-11.2.0.eb index b48c3f1b6bc..1172b66d8f2 100644 --- a/easybuild/easyconfigs/l/libdap/libdap-3.20.8-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/l/libdap/libdap-3.20.8-GCCcore-11.2.0.eb @@ -9,14 +9,15 @@ description = """A C++ SDK which contains an implementation of DAP 2.0 and toolchain = {'name': 'GCCcore', 'version': '11.2.0'} -source_urls = ['https://www.opendap.org/pub/source/'] -sources = [SOURCE_TAR_GZ] -checksums = ['65eb5c8f693cf74d58eece5eaa2e7c3c65f368926b1bffab0cf5b207757b94eb'] +source_urls = ['https://github.com/OPENDAP/libdap4/archive/refs/tags/'] +sources = ['%(version)s.tar.gz'] +checksums = ['e59b48f48bb37b36dcf9618043881e1d4150abd9b2ea3fa7474647c4ad622ccc'] builddependencies = [ ('binutils', '2.37'), ('Bison', '3.7.6'), ('flex', '2.6.4'), + ('Autotools', '20210726'), ] dependencies = [ @@ -27,6 +28,7 @@ dependencies = [ ('util-linux', '2.37'), ] +preconfigopts = "autoreconf -fi && " configopts = 'TIRPC_LIBS="-ltirpc"' sanity_check_paths = { diff --git a/easybuild/easyconfigs/l/libdap/libdap-3.21.0-131-GCCcore-13.3.0.eb b/easybuild/easyconfigs/l/libdap/libdap-3.21.0-131-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..ef7029f258f --- /dev/null +++ b/easybuild/easyconfigs/l/libdap/libdap-3.21.0-131-GCCcore-13.3.0.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'libdap' +version = '3.21.0-131' + +homepage = 'https://www.opendap.org/software/libdap' +description = """A C++ SDK which contains an implementation of DAP 2.0 and + DAP4.0. This includes both Client- and Server-side support classes.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://github.com/OPENDAP/libdap4/archive/refs/tags/'] +sources = ['%(version)s.tar.gz'] +checksums = ['c06b30e108608bc40dcb15df57302af4511023801dca004edb3f2df2cc0a72cc'] + +builddependencies = [ + ('binutils', '2.42'), + ('Bison', '3.8.2'), + ('flex', '2.6.4'), + ('Autotools', '20231222'), +] + +dependencies = [ + ('cURL', '8.7.1'), + ('libxml2', '2.12.7'), + ('libtirpc', '1.3.5'), + ('PCRE', '8.45'), + ('util-linux', '2.40'), +] + +preconfigopts = "autoreconf -fi && " +configopts = 'TIRPC_LIBS="-ltirpc"' + + +sanity_check_paths = { + 'files': ['bin/getdap', 'bin/getdap4', 'bin/dap-config', 'lib/libdap.a', 'lib/libdap.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libdap/libdap-3.21.0-27-GCCcore-13.3.0.eb b/easybuild/easyconfigs/l/libdap/libdap-3.21.0-27-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..707b32da095 --- /dev/null +++ b/easybuild/easyconfigs/l/libdap/libdap-3.21.0-27-GCCcore-13.3.0.eb @@ -0,0 +1,37 @@ +easyblock = 'ConfigureMake' + +name = 'libdap' +version = '3.21.0-27' + +homepage = 'https://www.opendap.org/software/libdap' +description = """A C++ SDK which contains an implementation of DAP 2.0 and + DAP4.0. This includes both Client- and Server-side support classes.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://www.opendap.org/pub/source/'] +sources = [SOURCE_TAR_GZ] +checksums = ['b5b8229d3aa97fea9bba4a0b11b1ee1c6446bd5f7ad2cff591f86064f465eacf'] + +builddependencies = [ + ('binutils', '2.42'), + ('Bison', '3.8.2'), + ('flex', '2.6.4'), +] + +dependencies = [ + ('cURL', '8.7.1'), + ('libxml2', '2.12.7'), + ('libtirpc', '1.3.5'), + ('PCRE', '8.45'), + ('util-linux', '2.40'), +] + +configopts = 'TIRPC_LIBS="-ltirpc"' + +sanity_check_paths = { + 'files': ['bin/getdap', 'bin/getdap4', 'bin/dap-config', 'lib/libdap.a', 'lib/libdap.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libde265/libde265-1.0.15-GCC-12.3.0.eb b/easybuild/easyconfigs/l/libde265/libde265-1.0.15-GCC-12.3.0.eb new file mode 100644 index 00000000000..9d6371e84ba --- /dev/null +++ b/easybuild/easyconfigs/l/libde265/libde265-1.0.15-GCC-12.3.0.eb @@ -0,0 +1,33 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +easyblock = 'CMakeMake' + +name = 'libde265' +version = '1.0.15' + +homepage = 'https://github.com/strukturag/libde265' +description = "libde265 is an open source implementation of the h.265 video codec" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +source_urls = ['https://github.com/strukturag/libde265/releases/download/v%(version)s/'] +sources = [SOURCE_TAR_GZ] +checksums = ['00251986c29d34d3af7117ed05874950c875dd9292d016be29d3b3762666511d'] + +builddependencies = [ + ('CMake', '3.26.3'), +] + +configopts = "-DENABLE_DECODER=ON -DENABLE_ENCODER=ON" + +sanity_check_paths = { + 'files': ['bin/dec265', 'bin/enc265', 'lib/libde265.%s' % SHLIB_EXT, 'lib/pkgconfig/libde265.pc'], + 'dirs': ['include/libde265', 'lib/cmake/libde265'], +} + +sanity_check_commands = [ + "dec265 --help", + "enc265 --help", +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/l/libdeflate/libdeflate-1.20-GCCcore-13.3.0.eb b/easybuild/easyconfigs/l/libdeflate/libdeflate-1.20-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..79e7db1b0d8 --- /dev/null +++ b/easybuild/easyconfigs/l/libdeflate/libdeflate-1.20-GCCcore-13.3.0.eb @@ -0,0 +1,37 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 + +easyblock = 'CMakeMake' + +name = 'libdeflate' +version = '1.20' + +homepage = 'https://github.com/ebiggers/libdeflate' +description = """Heavily optimized library for DEFLATE/zlib/gzip compression and decompression.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +github_account = 'ebiggers' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['ed1454166ced78913ff3809870a4005b7170a6fd30767dc478a09b96847b9c2a'] + +builddependencies = [ + ('binutils', '2.42'), + ('CMake', '3.29.3'), +] + +sanity_check_paths = { + 'files': [ + 'bin/%(name)s-gunzip', 'bin/%(name)s-gzip', + 'lib/%(name)s.a', 'lib/%%(name)s.%s' % SHLIB_EXT, + 'include/%(name)s.h', + ], + 'dirs': [], +} +sanity_check_commands = [ + '%(name)s-gzip -h', + '%(name)s-gunzip -h', +] + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/l/libdrm/libdrm-2.4.122-GCCcore-13.3.0.eb b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.122-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..beff58c433a --- /dev/null +++ b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.122-GCCcore-13.3.0.eb @@ -0,0 +1,32 @@ +easyblock = 'MesonNinja' + +name = 'libdrm' +version = '2.4.122' + +homepage = 'https://dri.freedesktop.org' +description = """Direct Rendering Manager runtime library.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://dri.freedesktop.org/libdrm/'] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['d9f5079b777dffca9300ccc56b10a93588cdfbc9dde2fae111940dfb6292f251'] + +builddependencies = [ + ('binutils', '2.42'), + ('pkgconf', '2.2.0'), + ('Meson', '1.4.0'), + ('Ninja', '1.12.1'), +] +dependencies = [('X11', '20240607')] + +# installing manpages requires an extra build dependency (docbook xsl) +configopts = '-Dman-pages=disabled' + +sanity_check_paths = { + 'files': ['lib/libdrm.%s' % SHLIB_EXT, 'include/libdrm/drm.h'], + 'dirs': ['include', 'lib'], +} + + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libdwarf/libdwarf-0.10.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/l/libdwarf/libdwarf-0.10.1-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..95a46c43114 --- /dev/null +++ b/easybuild/easyconfigs/l/libdwarf/libdwarf-0.10.1-GCCcore-13.3.0.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'libdwarf' +version = '0.10.1' + +homepage = 'https://www.prevanders.net/dwarf.html' +description = """The DWARF Debugging Information Format is of interest to programmers working on compilers +and debuggers (and anyone interested in reading or writing DWARF information))""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/davea42/libdwarf-code/releases/download/v%(version)s'] +sources = [SOURCE_TAR_XZ] +checksums = ['b511a2dc78b98786064889deaa2c1bc48a0c70115c187900dd838474ded1cc19'] + +builddependencies = [ + ('binutils', '2.42'), +] +dependencies = [ + ('elfutils', '0.191'), +] + +configopts = "--enable-shared " + +sanity_check_paths = { + 'files': ['bin/dwarfdump', 'lib/libdwarf.a', 'lib/libdwarf.%s' % SHLIB_EXT], + 'dirs': ['include'] +} + +sanity_check_commands = ['dwarfdump --help'] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/l/libdwarf/libdwarf-0.9.2-GCCcore-13.2.0.eb b/easybuild/easyconfigs/l/libdwarf/libdwarf-0.9.2-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..d8d25f32ed6 --- /dev/null +++ b/easybuild/easyconfigs/l/libdwarf/libdwarf-0.9.2-GCCcore-13.2.0.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'libdwarf' +version = '0.9.2' + +homepage = 'https://www.prevanders.net/dwarf.html' +description = """The DWARF Debugging Information Format is of interest to programmers working on compilers +and debuggers (and anyone interested in reading or writing DWARF information))""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/davea42/libdwarf-code/releases/download/v%(version)s'] +sources = [SOURCE_TAR_XZ] +checksums = ['c1cd51467f9cb8459cd27d4071857abc56191cc5d4182d8bdd7744030f88f830'] + +builddependencies = [ + ('binutils', '2.40'), +] +dependencies = [ + ('elfutils', '0.190'), +] + +configopts = "--enable-shared " + +sanity_check_paths = { + 'files': ['bin/dwarfdump', 'lib/libdwarf.a', 'lib/libdwarf.%s' % SHLIB_EXT], + 'dirs': ['include'] +} + +sanity_check_commands = ['dwarfdump --help'] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/l/libedit/libedit-20191231-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/libedit/libedit-20191231-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..9e85864f61d --- /dev/null +++ b/easybuild/easyconfigs/l/libedit/libedit-20191231-GCCcore-12.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'libedit' +version = '20191231' + +homepage = 'https://thrysoee.dk/editline/' +description = """ +This BSD-style licensed command line editor library provides generic line editing, +history, and tokenization functions, similar to those found in GNU Readline. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://thrysoee.dk/editline/'] +sources = ['%(namelower)s-%(version)s-3.1.tar.gz'] +checksums = ['dbb82cb7e116a5f8025d35ef5b4f7d4a3cdd0a3909a146a39112095a2d229071'] + +builddependencies = [('binutils', '2.40')] + +dependencies = [('ncurses', '6.4')] + +sanity_check_paths = { + 'files': ['include/editline/readline.h', 'lib/libedit.%s' % SHLIB_EXT, 'lib/libedit.a'], + 'dirs': [] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libedit/libedit-20240517-GCCcore-13.2.0.eb b/easybuild/easyconfigs/l/libedit/libedit-20240517-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..098fd8b7bde --- /dev/null +++ b/easybuild/easyconfigs/l/libedit/libedit-20240517-GCCcore-13.2.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'libedit' +version = '20240517' + +homepage = 'https://thrysoee.dk/editline/' +description = """ +This BSD-style licensed command line editor library provides generic line editing, +history, and tokenization functions, similar to those found in GNU Readline. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://thrysoee.dk/editline/'] +sources = ['%(namelower)s-%(version)s-3.1.tar.gz'] +checksums = ['3a489097bb4115495f3bd85ae782852b7097c556d9500088d74b6fa38dbd12ff'] + +builddependencies = [('binutils', '2.40')] + +dependencies = [('ncurses', '6.4')] + +sanity_check_paths = { + 'files': ['include/editline/readline.h', 'lib/libedit.%s' % SHLIB_EXT, 'lib/libedit.a'], + 'dirs': [] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libepoxy/libepoxy-1.5.10-GCCcore-13.3.0.eb b/easybuild/easyconfigs/l/libepoxy/libepoxy-1.5.10-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..bca992c268a --- /dev/null +++ b/easybuild/easyconfigs/l/libepoxy/libepoxy-1.5.10-GCCcore-13.3.0.eb @@ -0,0 +1,37 @@ +easyblock = 'MesonNinja' + +name = 'libepoxy' +version = '1.5.10' + +homepage = 'https://github.com/anholt/libepoxy' +description = "Epoxy is a library for handling OpenGL function pointer management for you" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +github_account = 'anholt' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['a7ced37f4102b745ac86d6a70a9da399cc139ff168ba6b8002b4d8d43c900c15'] + +builddependencies = [ + ('binutils', '2.42'), + ('Meson', '1.4.0'), + ('Ninja', '1.12.1'), + ('pkgconf', '2.2.0'), +] + +dependencies = [ + ('X11', '20240607'), + ('Mesa', '24.1.3'), +] + +configopts = '-Degl=yes --libdir %(installdir)s/lib ' + +sanity_check_paths = { + 'files': ['include/epoxy/%s.h' % x for x in ['common', 'egl_generated', 'egl', 'gl_generated', + 'gl', 'glx_generated', 'glx']] + + ['lib/libepoxy.%s' % SHLIB_EXT], + 'dirs': ['lib'] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libev/libev-4.33-GCC-12.3.0.eb b/easybuild/easyconfigs/l/libev/libev-4.33-GCC-12.3.0.eb new file mode 100644 index 00000000000..a2cd4ecd9b5 --- /dev/null +++ b/easybuild/easyconfigs/l/libev/libev-4.33-GCC-12.3.0.eb @@ -0,0 +1,31 @@ +# Author: J. Sassmannshausen (Imperial College London/UK) +# Update: Pavel Tománek (Inuits) +easyblock = 'ConfigureMake' + +name = 'libev' +version = '4.33' + +homepage = 'http://software.schmorp.de/pkg/libev.html' +description = """A full-featured and high-performance (see benchmark) +event loop that is loosely modelled after libevent, but without its +limitations and bugs. It is used in GNU Virtual Private Ethernet, +rxvt-unicode, auditd, the Deliantra MORPG Server and Client, and many +other programs.""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['http://dist.schmorp.de/libev/Attic'] +sources = ['%(name)s-%(version)s.tar.gz'] +checksums = ['507eb7b8d1015fbec5b935f34ebed15bf346bed04a11ab82b8eee848c4205aea'] + +builddependencies = [ + ('binutils', '2.40'), +] + +sanity_check_paths = { + 'files': ['lib/libev.%s' % SHLIB_EXT], + 'dirs': ['include/', 'share'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libevent/libevent-2.1.12-GCCcore-13.3.0.eb b/easybuild/easyconfigs/l/libevent/libevent-2.1.12-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..bd33821ffd7 --- /dev/null +++ b/easybuild/easyconfigs/l/libevent/libevent-2.1.12-GCCcore-13.3.0.eb @@ -0,0 +1,38 @@ +easyblock = 'ConfigureMake' + +name = 'libevent' +version = '2.1.12' + +homepage = 'https://libevent.org/' + +description = """ + The libevent API provides a mechanism to execute a callback function when + a specific event occurs on a file descriptor or after a timeout has been + reached. Furthermore, libevent also support callbacks due to signals or + regular timeouts. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/%(name)s/%(name)s/releases/download/release-%(version)s-stable/'] +sources = ['%(name)s-%(version)s-stable.tar.gz'] +checksums = ['92e6de1be9ec176428fd2367677e61ceffc2ee1cb119035037a27d346b0403bb'] + +builddependencies = [ + ('binutils', '2.42'), + ('pkgconf', '2.2.0'), +] + +dependencies = [ + ('zlib', '1.3.1'), + ('OpenSSL', '3', '', SYSTEM), +] + +sanity_check_paths = { + 'files': ['bin/event_rpcgen.py', 'include/event.h', 'include/event2/event.h', + 'lib/libevent_core.%s' % SHLIB_EXT, 'lib/pkgconfig/libevent.pc'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libfabric/libfabric-1.12.1-GCCcore-10.3.0.eb b/easybuild/easyconfigs/l/libfabric/libfabric-1.12.1-GCCcore-10.3.0.eb index 553ff1edf76..5a302fa1b83 100644 --- a/easybuild/easyconfigs/l/libfabric/libfabric-1.12.1-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/l/libfabric/libfabric-1.12.1-GCCcore-10.3.0.eb @@ -43,7 +43,10 @@ builddependencies = [ dependencies = [ ('numactl', '2.0.14'), - ('PSM2', '12.0.1'), + # PSM2 dependency for libfabric should be used on Omnipath systems, + # but that PSM2 has CUDA as dependency so it's commented out by default; + # PSM2 only compiles on x86_64 + # ('PSM2', {'arch=x86_64': '12.0.1', 'arch=*': False}), ] osdependencies = [OS_PKG_IBVERBS_DEV] diff --git a/easybuild/easyconfigs/l/libfabric/libfabric-1.13.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/l/libfabric/libfabric-1.13.0-GCCcore-11.2.0.eb index 9eed1d10b73..35245b93a33 100644 --- a/easybuild/easyconfigs/l/libfabric/libfabric-1.13.0-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/l/libfabric/libfabric-1.13.0-GCCcore-11.2.0.eb @@ -37,7 +37,10 @@ builddependencies = [ dependencies = [ ('numactl', '2.0.14'), - ('PSM2', '12.0.1'), + # PSM2 dependency for libfabric should be used on Omnipath systems, + # but that PSM2 has CUDA as dependency so it's commented out by default; + # PSM2 only compiles on x86_64 + # ('PSM2', {'arch=x86_64': '12.0.1', 'arch=*': False}), ] osdependencies = [OS_PKG_IBVERBS_DEV] diff --git a/easybuild/easyconfigs/l/libfabric/libfabric-1.13.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/l/libfabric/libfabric-1.13.1-GCCcore-11.2.0.eb index 103995357f0..c6011eea6ec 100644 --- a/easybuild/easyconfigs/l/libfabric/libfabric-1.13.1-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/l/libfabric/libfabric-1.13.1-GCCcore-11.2.0.eb @@ -37,7 +37,10 @@ builddependencies = [ dependencies = [ ('numactl', '2.0.14'), - ('PSM2', '12.0.1'), + # PSM2 dependency for libfabric should be used on Omnipath systems, + # but that PSM2 has CUDA as dependency so it's commented out by default; + # PSM2 only compiles on x86_64 + # ('PSM2', {'arch=x86_64': '12.0.1', 'arch=*': False}), ] osdependencies = [OS_PKG_IBVERBS_DEV] diff --git a/easybuild/easyconfigs/l/libfabric/libfabric-1.13.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/l/libfabric/libfabric-1.13.2-GCCcore-11.2.0.eb index 8ec4cbdf361..14531d3108d 100644 --- a/easybuild/easyconfigs/l/libfabric/libfabric-1.13.2-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/l/libfabric/libfabric-1.13.2-GCCcore-11.2.0.eb @@ -37,7 +37,10 @@ builddependencies = [ dependencies = [ ('numactl', '2.0.14'), - ('PSM2', '12.0.1'), + # PSM2 dependency for libfabric should be used on Omnipath systems, + # but that PSM2 has CUDA as dependency so it's commented out by default; + # PSM2 only compiles on x86_64 + # ('PSM2', {'arch=x86_64': '12.0.1', 'arch=*': False}), ] osdependencies = [OS_PKG_IBVERBS_DEV] diff --git a/easybuild/easyconfigs/l/libfabric/libfabric-1.15.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/libfabric/libfabric-1.15.1-GCCcore-11.3.0.eb index 20d2cd53407..6c50cdb4a4b 100644 --- a/easybuild/easyconfigs/l/libfabric/libfabric-1.15.1-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/l/libfabric/libfabric-1.15.1-GCCcore-11.3.0.eb @@ -37,7 +37,10 @@ builddependencies = [ dependencies = [ ('numactl', '2.0.14'), - ('PSM2', '12.0.1'), + # PSM2 dependency for libfabric should be used on Omnipath systems, + # but that PSM2 has CUDA as dependency so it's commented out by default; + # PSM2 only compiles on x86_64 + # ('PSM2', {'arch=x86_64': '12.0.1', 'arch=*': False}), ] osdependencies = [OS_PKG_IBVERBS_DEV] diff --git a/easybuild/easyconfigs/l/libfabric/libfabric-1.16.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/l/libfabric/libfabric-1.16.1-GCCcore-12.2.0.eb index d554608ff27..31c4ac02fac 100644 --- a/easybuild/easyconfigs/l/libfabric/libfabric-1.16.1-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/l/libfabric/libfabric-1.16.1-GCCcore-12.2.0.eb @@ -34,7 +34,10 @@ builddependencies = [ dependencies = [ ('numactl', '2.0.16'), - ('PSM2', '12.0.1'), + # PSM2 dependency for libfabric should be used on Omnipath systems, + # but that PSM2 has CUDA as dependency so it's commented out by default; + # PSM2 only compiles on x86_64 + # ('PSM2', {'arch=x86_64': '12.0.1', 'arch=*': False}), ] osdependencies = [OS_PKG_IBVERBS_DEV] diff --git a/easybuild/easyconfigs/l/libfabric/libfabric-1.18.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/libfabric/libfabric-1.18.0-GCCcore-12.3.0.eb index abb669e3494..c1fa6c1cebb 100644 --- a/easybuild/easyconfigs/l/libfabric/libfabric-1.18.0-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/l/libfabric/libfabric-1.18.0-GCCcore-12.3.0.eb @@ -34,7 +34,10 @@ builddependencies = [ dependencies = [ ('numactl', '2.0.16'), - ('PSM2', '12.0.1'), + # PSM2 dependency for libfabric should be used on Omnipath systems, + # but that PSM2 has CUDA as dependency so it's commented out by default; + # PSM2 only compiles on x86_64 + # ('PSM2', {'arch=x86_64': '12.0.1', 'arch=*': False}), ] osdependencies = [OS_PKG_IBVERBS_DEV] diff --git a/easybuild/easyconfigs/l/libfabric/libfabric-1.19.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/l/libfabric/libfabric-1.19.0-GCCcore-13.2.0.eb index ea4530cbc2b..5d80c15a258 100644 --- a/easybuild/easyconfigs/l/libfabric/libfabric-1.19.0-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/l/libfabric/libfabric-1.19.0-GCCcore-13.2.0.eb @@ -34,7 +34,10 @@ builddependencies = [ dependencies = [ ('numactl', '2.0.16'), - ('PSM2', '12.0.1'), + # PSM2 dependency for libfabric should be used on Omnipath systems, + # but that PSM2 has CUDA as dependency so it's commented out by default; + # PSM2 only compiles on x86_64 + # ('PSM2', {'arch=x86_64': '12.0.1', 'arch=*': False}), ] osdependencies = [OS_PKG_IBVERBS_DEV] diff --git a/easybuild/easyconfigs/l/libfabric/libfabric-1.21.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/l/libfabric/libfabric-1.21.0-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..04757a82748 --- /dev/null +++ b/easybuild/easyconfigs/l/libfabric/libfabric-1.21.0-GCCcore-13.3.0.eb @@ -0,0 +1,61 @@ +easyblock = 'ConfigureMake' + +name = 'libfabric' +version = '1.21.0' + +homepage = 'https://ofiwg.github.io/libfabric/' +description = """ +Libfabric is a core component of OFI. It is the library that defines and exports +the user-space API of OFI, and is typically the only software that applications +deal with directly. It works in conjunction with provider libraries, which are +often integrated directly into libfabric. +""" + +# The psm3 provider (enabled by default) requires an AVX capable system to run +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/ofiwg/libfabric/releases/download/v%(version)s'] +sources = [SOURCE_TAR_BZ2] +checksums = [ + {'libfabric-1.21.0.tar.bz2': '0c1b7b830d9147f661e5d7f359250b85b5a9885c330464cd3b5e5d35b86551c7'}, +] + +builddependencies = [ + ('binutils', '2.42'), + ('pkgconf', '2.2.0'), + ('Autotools', '20231222'), +] + +dependencies = [ + ('numactl', '2.0.18'), + # PSM2 dependency for libfabric should be used on Omnipath systems, + # but that PSM2 has CUDA as dependency so it's commented out by default; + # PSM2 only compiles on x86_64 + # ('PSM2', {'arch=x86_64': '12.0.1', 'arch=*': False}), +] + +osdependencies = [OS_PKG_IBVERBS_DEV] + +# Regenerate build files to pick up psm3-axv-config patch +preconfigopts = "./autogen.sh &&" + +# Disable deprecated "sockets" provider +configopts = "--disable-sockets " + +# Disable usNIC provider by default as this requires specific osdependencies +# If you want to enable this provider you need to uncomment the following line: +# osdependencies.append(('libnl3-devel', 'libnl3-dev')) +configopts += "--disable-usnic " + +buildopts = "V=1" + +sanity_check_paths = { + 'files': ['bin/fi_info', 'bin/fi_pingpong', 'bin/fi_strerror'] + + ['lib/libfabric.%s' % x for x in ['a', SHLIB_EXT]], + 'dirs': ['include/rdma', 'lib/pkgconfig', 'share'] +} + +sanity_check_commands = ['fi_info'] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libffi/libffi-3.4.5-GCCcore-13.3.0.eb b/easybuild/easyconfigs/l/libffi/libffi-3.4.5-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..34934544c93 --- /dev/null +++ b/easybuild/easyconfigs/l/libffi/libffi-3.4.5-GCCcore-13.3.0.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'libffi' +version = '3.4.5' + +homepage = 'https://sourceware.org/libffi/' +description = """The libffi library provides a portable, high level programming interface to + various calling conventions. This allows a programmer to call any function + specified by a call interface description at run-time.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/libffi/libffi/releases/download/v%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['96fff4e589e3b239d888d9aa44b3ff30693c2ba1617f953925a70ddebcc102b2'] + +builddependencies = [ + ('binutils', '2.42'), +] + +configopts = '--disable-exec-static-tramp ' + +sanity_check_paths = { + 'files': ['lib/libffi.a', 'lib/libffi.%s' % SHLIB_EXT], + 'dirs': ['include', 'share'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libffi/libffi-3.4.5.eb b/easybuild/easyconfigs/l/libffi/libffi-3.4.5.eb new file mode 100644 index 00000000000..df82da05952 --- /dev/null +++ b/easybuild/easyconfigs/l/libffi/libffi-3.4.5.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'libffi' +version = '3.4.5' + +homepage = 'https://sourceware.org/libffi/' +description = """The libffi library provides a portable, high level programming interface to + various calling conventions. This allows a programmer to call any function + specified by a call interface description at run-time.""" + +toolchain = SYSTEM +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/libffi/libffi/releases/download/v%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['96fff4e589e3b239d888d9aa44b3ff30693c2ba1617f953925a70ddebcc102b2'] + +configopts = '--disable-exec-static-tramp ' + +sanity_check_paths = { + 'files': ['lib/libffi.a', 'lib/libffi.%s' % SHLIB_EXT], + 'dirs': ['include', 'share'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libgcrypt/libgcrypt-1.10.3-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/libgcrypt/libgcrypt-1.10.3-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..113c8f30746 --- /dev/null +++ b/easybuild/easyconfigs/l/libgcrypt/libgcrypt-1.10.3-GCCcore-12.3.0.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'libgcrypt' +version = '1.10.3' + +homepage = 'https://gnupg.org/related_software/libgcrypt/index.html' +description = """Libgcrypt is a general purpose cryptographic library originally based on code from GnuPG""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://gnupg.org/ftp/gcrypt/%(name)s/'] +sources = [SOURCE_TAR_BZ2] +checksums = ['8b0870897ac5ac67ded568dcfadf45969cfa8a6beb0fd60af2a9eadc2a3272aa'] + +builddependencies = [('binutils', '2.40')] + +dependencies = [('libgpg-error', '1.48')] + +sanity_check_paths = { + 'files': ['bin/libgcrypt-config', 'include/gcrypt.h', 'lib/libgcrypt.%s' % SHLIB_EXT], + 'dirs': ['share'] +} + +sanity_check_commands = [ + 'dumpsexp --version', + 'hmac256 --version', + 'mpicalc --version', + 'libgcrypt-config --version | grep "%(version)s"', +] + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/l/libgd/libgd-2.3.3-GCCcore-13.2.0.eb b/easybuild/easyconfigs/l/libgd/libgd-2.3.3-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..8ebba5a4031 --- /dev/null +++ b/easybuild/easyconfigs/l/libgd/libgd-2.3.3-GCCcore-13.2.0.eb @@ -0,0 +1,37 @@ +easyblock = 'ConfigureMake' + +name = 'libgd' +version = '2.3.3' + +homepage = 'https://libgd.github.io' +description = "GD is an open source code library for the dynamic creation of images by programmers." + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/libgd/libgd/releases/download/gd-%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['dd3f1f0bb016edcc0b2d082e8229c822ad1d02223511997c80461481759b1ed2'] + +builddependencies = [ + ('binutils', '2.40'), +] + +dependencies = [ + ('fontconfig', '2.14.2'), + ('libjpeg-turbo', '3.0.1'), + ('libpng', '1.6.40'), + ('zlib', '1.2.13'), +] + +configopts = "--with-fontconfig=$EBROOTFONTCONFIG --with-jpeg=$EBROOTLIBJPEGMINTURBO " +configopts += "--with-png=$EBROOTLIBPNG --with-zlib=$EBROOTZLIB" + +sanity_check_paths = { + 'files': ['lib/libgd.a', 'lib/libgd.%s' % SHLIB_EXT], + 'dirs': ['bin', 'include'], +} + +sanity_check_commands = ['webpng --help'] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libgd/libgd-2.3.3-GCCcore-13.3.0.eb b/easybuild/easyconfigs/l/libgd/libgd-2.3.3-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..2c03aa92105 --- /dev/null +++ b/easybuild/easyconfigs/l/libgd/libgd-2.3.3-GCCcore-13.3.0.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'libgd' +version = '2.3.3' + +homepage = 'https://libgd.github.io' +description = "GD is an open source code library for the dynamic creation of images by programmers." + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/%(name)s/%(name)s/releases/download/gd-%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['dd3f1f0bb016edcc0b2d082e8229c822ad1d02223511997c80461481759b1ed2'] + +builddependencies = [ + ('binutils', '2.42'), +] +dependencies = [ + ('fontconfig', '2.15.0'), + ('libjpeg-turbo', '3.0.1'), + ('libpng', '1.6.43'), + ('zlib', '1.3.1'), +] + +configopts = "--with-fontconfig=$EBROOTFONTCONFIG --with-jpeg=$EBROOTLIBJPEGMINTURBO " +configopts += "--with-png=$EBROOTLIBPNG --with-zlib=$EBROOTZLIB" + +sanity_check_paths = { + 'files': ['lib/%(name)s.a', 'lib/%(name)s.so'], + 'dirs': ['bin', 'include'], +} + +sanity_check_commands = ['webpng --help'] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libgeotiff/libgeotiff-1.7.3-GCCcore-13.2.0.eb b/easybuild/easyconfigs/l/libgeotiff/libgeotiff-1.7.3-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..ce66887030e --- /dev/null +++ b/easybuild/easyconfigs/l/libgeotiff/libgeotiff-1.7.3-GCCcore-13.2.0.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'libgeotiff' +version = '1.7.3' + +homepage = 'https://directory.fsf.org/wiki/Libgeotiff' +description = """Library for reading and writing coordinate system information from/to GeoTIFF files""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://download.osgeo.org/geotiff/libgeotiff'] +sources = [SOURCE_TAR_GZ] +checksums = ['ba23a3a35980ed3de916e125c739251f8e3266be07540200125a307d7cf5a704'] + +builddependencies = [ + ('binutils', '2.40'), +] + +dependencies = [ + ('PROJ', '9.3.1'), + ('libjpeg-turbo', '3.0.1'), + ('zlib', '1.2.13'), + ('SQLite', '3.43.1'), + ('LibTIFF', '4.6.0'), + ('cURL', '8.3.0'), +] + +configopts = ' --with-libtiff=$EBROOTLIBTIFF --with-proj=$EBROOTPROJ --with-zlib=$EBROOTZLIB' +configopts += ' --with-jpeg=$EBROOTLIBJPEGMINTURBO' + +sanity_check_paths = { + 'files': ['bin/listgeo', 'lib/libgeotiff.a', 'lib/libgeotiff.%s' % SHLIB_EXT], + 'dirs': ['include', 'share'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libgeotiff/libgeotiff-1.7.3-GCCcore-13.3.0.eb b/easybuild/easyconfigs/l/libgeotiff/libgeotiff-1.7.3-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..41cba249999 --- /dev/null +++ b/easybuild/easyconfigs/l/libgeotiff/libgeotiff-1.7.3-GCCcore-13.3.0.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'libgeotiff' +version = '1.7.3' + +homepage = 'https://directory.fsf.org/wiki/Libgeotiff' +description = """Library for reading and writing coordinate system information from/to GeoTIFF files""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://download.osgeo.org/geotiff/libgeotiff'] +sources = [SOURCE_TAR_GZ] +checksums = ['ba23a3a35980ed3de916e125c739251f8e3266be07540200125a307d7cf5a704'] + +builddependencies = [ + ('binutils', '2.42'), +] + +dependencies = [ + ('PROJ', '9.4.1'), + ('libjpeg-turbo', '3.0.1'), + ('zlib', '1.3.1'), + ('SQLite', '3.45.3'), + ('LibTIFF', '4.6.0'), + ('cURL', '8.7.1'), +] + +configopts = ' --with-libtiff=$EBROOTLIBTIFF --with-proj=$EBROOTPROJ --with-zlib=$EBROOTZLIB' +configopts += ' --with-jpeg=$EBROOTLIBJPEGMINTURBO' + +sanity_check_paths = { + 'files': ['bin/listgeo', 'lib/libgeotiff.a', 'lib/libgeotiff.%s' % SHLIB_EXT], + 'dirs': ['include', 'share'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libgit2/libgit2-1.8.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/l/libgit2/libgit2-1.8.1-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..07da30e2a80 --- /dev/null +++ b/easybuild/easyconfigs/l/libgit2/libgit2-1.8.1-GCCcore-13.3.0.eb @@ -0,0 +1,34 @@ +easyblock = 'CMakeMake' + +name = 'libgit2' +version = '1.8.1' + +homepage = 'https://libgit2.org/' +description = """libgit2 is a portable, pure C implementation of the Git core methods provided as a re-entrant +linkable library with a solid API, allowing you to write native speed custom Git applications in any language +which supports C bindings.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = [GITHUB_SOURCE] +sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}] +checksums = ['8c1eaf0cf07cba0e9021920bfba9502140220786ed5d8a8ec6c7ad9174522f8e'] + +builddependencies = [ + ('binutils', '2.42'), + ('CMake', '3.29.3'), + ('pkgconf', '2.2.0'), +] +dependencies = [ + ('PCRE2', '10.43'), + ('OpenSSL', '3', '', SYSTEM), +] + +configopts = '-DREGEX_BACKEND=pcre2' + +sanity_check_paths = { + 'files': ['include/git2.h', 'lib64/%%(name)s.%s' % SHLIB_EXT, 'lib64/pkgconfig/%(name)s.pc'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/l/libglvnd/libglvnd-1.7.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/l/libglvnd/libglvnd-1.7.0-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..c6a03d1b419 --- /dev/null +++ b/easybuild/easyconfigs/l/libglvnd/libglvnd-1.7.0-GCCcore-13.3.0.eb @@ -0,0 +1,33 @@ +easyblock = 'MesonNinja' + +name = 'libglvnd' +version = '1.7.0' + +homepage = 'https://gitlab.freedesktop.org/glvnd/libglvnd' +description = "libglvnd is a vendor-neutral dispatch layer for arbitrating OpenGL API calls between multiple vendors." + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://gitlab.freedesktop.org/glvnd/libglvnd/-/archive/v%(version)s/'] +sources = ['libglvnd-v%(version)s.tar.gz'] +checksums = ['2b6e15b06aafb4c0b6e2348124808cbd9b291c647299eaaba2e3202f51ff2f3d'] + +builddependencies = [ + ('binutils', '2.42'), + ('pkgconf', '2.2.0'), + ('Meson', '1.4.0'), + ('Ninja', '1.12.1'), +] + +dependencies = [('X11', '20240607')] + +# Let EGL find system-installed vendor files in /etc/glvnd/egl_vendor.d etc. +allow_prepend_abs_path = True +modextrapaths = {"__EGL_VENDOR_LIBRARY_DIRS": "/etc/glvnd/egl_vendor.d:/usr/share/glvnd/egl_vendor.d"} + +sanity_check_paths = { + 'files': ['lib/lib%s.%s' % (x, SHLIB_EXT) for x in ['EGL', 'GL', 'GLX', 'OpenGL']], + 'dirs': ['include/%s' % x for x in ['EGL', 'GL', 'GLES', 'GLES2', 'GLES3', 'glvnd', 'KHR']] + ['lib/pkgconfig'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libgpg-error/libgpg-error-1.48-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/libgpg-error/libgpg-error-1.48-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..67edfd4a874 --- /dev/null +++ b/easybuild/easyconfigs/l/libgpg-error/libgpg-error-1.48-GCCcore-12.3.0.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'libgpg-error' +version = '1.48' + +homepage = 'https://gnupg.org/related_software/libgpg-error/index.html' +description = """Libgpg-error is a small library that defines common error values for all GnuPG components.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://gnupg.org/ftp/gcrypt/%(name)s/'] +sources = [SOURCE_TAR_BZ2] +checksums = ['89ce1ae893e122924b858de84dc4f67aae29ffa610ebf668d5aa539045663d6f'] + +builddependencies = [('binutils', '2.40')] + +sanity_check_paths = { + 'files': ['bin/gpg-error', 'include/gpg-error.h', 'lib/libgpg-error.%s' % SHLIB_EXT], + 'dirs': ['share'] +} + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/l/libheif/libheif-1.17.6-GCC-12.3.0.eb b/easybuild/easyconfigs/l/libheif/libheif-1.17.6-GCC-12.3.0.eb new file mode 100644 index 00000000000..ee355100089 --- /dev/null +++ b/easybuild/easyconfigs/l/libheif/libheif-1.17.6-GCC-12.3.0.eb @@ -0,0 +1,42 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +easyblock = 'CMakeMake' + +name = 'libheif' +version = '1.17.6' + +homepage = 'https://github.com/strukturag/libheif' +description = "libheif is an HEIF and AVIF file format decoder and encoder" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +source_urls = ['https://github.com/strukturag/libheif/releases/download/v%(version)s/'] +sources = [SOURCE_TAR_GZ] +checksums = ['8390baf4913eda0a183e132cec62b875fb2ef507ced5ddddc98dfd2f17780aee'] + +builddependencies = [ + ('CMake', '3.26.3'), +] + +dependencies = [ + ('libpng', '1.6.39'), + ('libjpeg-turbo', '2.1.5.1'), + ('libde265', '1.0.15'), + ('x265', '3.5'), + ('Gdk-Pixbuf', '2.42.10'), +] + +# build both static and shared libraries +configopts = [ + "-DBUILD_SHARED_LIBS=OFF", + "-DBUILD_SHARED_LIBS=ON", +] + +sanity_check_paths = { + 'files': ['bin/heif-info', 'lib/libheif.a', 'lib/libheif.%s' % SHLIB_EXT, 'lib/pkgconfig/libheif.pc'], + 'dirs': ['include/libheif'], +} + +sanity_check_commands = ["heif-info --help"] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/l/libiconv/libiconv-1.17-GCCcore-13.3.0.eb b/easybuild/easyconfigs/l/libiconv/libiconv-1.17-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..0532a96c234 --- /dev/null +++ b/easybuild/easyconfigs/l/libiconv/libiconv-1.17-GCCcore-13.3.0.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'libiconv' +version = '1.17' + +homepage = 'https://www.gnu.org/software/libiconv' +description = "Libiconv converts from one character encoding to another through Unicode conversion" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['8f74213b56238c85a50a5329f77e06198771e70dd9a739779f4c02f65d971313'] + +builddependencies = [('binutils', '2.42')] + +sanity_check_paths = { + 'files': ['bin/iconv', 'include/iconv.h', 'include/libcharset.h', 'include/localcharset.h', + 'lib/libcharset.a', 'lib/libcharset.%s' % SHLIB_EXT, 'lib/libiconv.%s' % SHLIB_EXT], + 'dirs': ['share'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libidn2/libidn2-2.3.4-GCCcore-12.2.0.eb b/easybuild/easyconfigs/l/libidn2/libidn2-2.3.4-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..b9ddb22009e --- /dev/null +++ b/easybuild/easyconfigs/l/libidn2/libidn2-2.3.4-GCCcore-12.2.0.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'libidn2' +version = '2.3.4' + +homepage = 'http://www.gnu.org/software/%(name)s' +description = """Libidn2 implements the revised algorithm for internationalized domain names called IDNA2008/TR46.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://ftp.gnu.org/gnu/libidn/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['93caba72b4e051d1f8d4f5a076ab63c99b77faee019b72b9783b267986dbb45f'] + +builddependencies = [('binutils', '2.39')] + +sanity_check_paths = { + 'files': ['bin/idn2', 'lib/libidn2.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +sanity_check_commands = ["idn2 --help"] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libidn2/libidn2-2.3.7-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/libidn2/libidn2-2.3.7-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..30a2e4a26f2 --- /dev/null +++ b/easybuild/easyconfigs/l/libidn2/libidn2-2.3.7-GCCcore-12.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'libidn2' +version = '2.3.7' + +homepage = 'http://www.gnu.org/software/%(name)s' +description = "Libidn2 implements the revised algorithm for internationalized domain names called IDNA2008/TR46." + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://ftp.gnu.org/gnu/libidn/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['4c21a791b610b9519b9d0e12b8097bf2f359b12f8dd92647611a929e6bfd7d64'] + +builddependencies = [ + ('binutils', '2.40'), +] + + +sanity_check_paths = { + 'files': ['bin/idn2', 'lib/%s.%s' % (name, SHLIB_EXT)], + 'dirs': ['include'], +} + +sanity_check_commands = ['idn2 --help'] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-3.0.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-3.0.1-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..f4a61f429a2 --- /dev/null +++ b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-3.0.1-GCCcore-13.3.0.eb @@ -0,0 +1,42 @@ +easyblock = 'CMakeMake' + +name = 'libjpeg-turbo' +version = '3.0.1' + +homepage = 'https://sourceforge.net/projects/libjpeg-turbo/' + +description = """ + libjpeg-turbo is a fork of the original IJG libjpeg which uses SIMD to + accelerate baseline JPEG compression and decompression. libjpeg is a library + that implements JPEG image encoding, decoding and transcoding. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['22429507714ae147b3acacd299e82099fce5d9f456882fc28e252e4579ba2a75'] + +builddependencies = [ + ('CMake', '3.29.3'), + ('binutils', '2.42'), +] + +dependencies = [ + ('NASM', '2.16.03'), +] + +configopts = ' -G"Unix Makefiles" -DWITH_JPEG8=1' + +runtest = "test" + +sanity_check_paths = { + 'files': ['bin/cjpeg', 'bin/djpeg', 'bin/jpegtran', 'bin/rdjpgcom', + 'bin/tjbench', 'bin/wrjpgcom', 'lib/libjpeg.a', + 'lib/libjpeg.%s' % SHLIB_EXT, 'lib/libturbojpeg.a', + 'lib/libturbojpeg.%s' % SHLIB_EXT], + 'dirs': ['include', 'share'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libjxl/libjxl-0.8.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/libjxl/libjxl-0.8.2-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..22bddfd467b --- /dev/null +++ b/easybuild/easyconfigs/l/libjxl/libjxl-0.8.2-GCCcore-12.3.0.eb @@ -0,0 +1,53 @@ +easyblock = 'CMakeMake' + +name = 'libjxl' +version = '0.8.2' +# Newer versions of libjxl require Highway >=1.0.7 + +homepage = 'https://github.com/libjxl/libjxl' +description = "JPEG XL image format reference implementation" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +github_account = 'libjxl' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['c70916fb3ed43784eb840f82f05d390053a558e2da106e40863919238fa7b420'] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.26.3'), + ('googletest', '1.13.0'), + ('pkgconf', '1.9.5'), + ('Highway', '1.0.4'), # Highway only has a static library +] + +dependencies = [ + ('LittleCMS', '2.15'), + ('Brotli', '1.0.9'), + ('libjpeg-turbo', '2.1.5.1'), + ('libpng', '1.6.39'), + ('zlib', '1.2.13'), + ('giflib', '5.2.1'), + ('libwebp', '1.3.1'), + ('OpenEXR', '3.1.7'), + ('gperftools', '2.12'), +] + +configopts = '-DJPEGXL_WARNINGS_AS_ERRORS=OFF -DJPEGXL_ENABLE_SJPEG=OFF -DJPEGXL_ENABLE_SKCMS=OFF ' +# building man pages requires/uses asciidoc (which may be installed in OS, and may fail) +configopts += '-DJPEGXL_ENABLE_MANPAGES=OFF ' +configopts += '-DJPEGXL_FORCE_SYSTEM_BROTLI=ON -DJPEGXL_FORCE_SYSTEM_HWY=ON ' +configopts += '-DJPEGXL_FORCE_SYSTEM_GTEST=ON -DJPEGXL_FORCE_SYSTEM_LCMS2=ON ' + +sanity_check_paths = { + 'files': ['bin/cjxl', 'bin/djxl', 'lib/libjxl.%s' % SHLIB_EXT], + 'dirs': ['include/jxl'], +} + +sanity_check_commands = [ + "cjxl --help", + "djxl --help", +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libmad/libmad-0.15.1b-GCCcore-13.3.0.eb b/easybuild/easyconfigs/l/libmad/libmad-0.15.1b-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..982f59275b1 --- /dev/null +++ b/easybuild/easyconfigs/l/libmad/libmad-0.15.1b-GCCcore-13.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'libmad' +version = '0.15.1b' + +homepage = 'https://www.underbit.com/products/mad/' +description = """MAD is a high-quality MPEG audio decoder.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://sourceforge.net/projects/mad/files/%(name)s/%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +patches = ['libmad-0.15.1b-remove-depreciated-gcc-option.patch'] +checksums = [ + 'bbfac3ed6bfbc2823d3775ebb931087371e142bb0e9bb1bee51a76a6e0078690', # libmad-0.15.1b.tar.gz + # libmad-0.15.1b-remove-depreciated-gcc-option.patch + '8f96a23a22ba66e62f32e20064d01f4c7f6a18ba0aab85d3be9ce63794b2c678', +] + +builddependencies = [('binutils', '2.42')] + +sanity_check_paths = { + 'files': ['include/mad.h', 'lib/libmad.a', 'lib/libmad.la', 'lib/libmad.%s' % SHLIB_EXT], + 'dirs': ['include', 'lib', 'lib64'] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libmatheval/003-guile2.0.patch b/easybuild/easyconfigs/l/libmatheval/003-guile2.0.patch new file mode 100644 index 00000000000..3f592cadb0d --- /dev/null +++ b/easybuild/easyconfigs/l/libmatheval/003-guile2.0.patch @@ -0,0 +1,402 @@ +Description: Increase precision of floating point tests + guile-2.0 has increased the precision of the floating point maths returns, + so the test suite needs to allow for the correct values to be returned + with higher precision. Thanks to Dave Pigott + Also adapt the configure script to build against guile-2.0 - patch from + Hilo Bengen . + . + libmatheval (1.1.11+dfsg-1.1) unstable; urgency=low + . + * Non-maintainer upload. + * Migrate to guile-2.0 - patch from Hilo Bengen, + extended to support higher precision of return values + by guile-2.0. (Closes: #746013) +Author: Neil Williams +Bug-Debian: https://bugs.debian.org/746013 + +--- + +--- libmatheval-1.1.11+dfsg.orig/configure.in ++++ libmatheval-1.1.11+dfsg/configure.in +@@ -60,10 +60,11 @@ dnl Checks for library functions. + AC_CHECK_FUNCS([bzero memset], [break]) + + dnl Additional Guile feature checks. ++CFLAGS="$CFLAGS $GUILE_CFLAGS" + AC_CHECK_TYPE([scm_t_bits], [AC_DEFINE([HAVE_SCM_T_BITS], [1], [Define to 1 if you have the `scm_t_bits' type.])], [], [#include ]) +-AC_CHECK_LIB([guile], [scm_c_define_gsubr], [AC_DEFINE([HAVE_SCM_C_DEFINE_GSUBR], [1], [Define to 1 if you have the `scm_c_define_gsubr' function.])], [], [$GUILE_LDFLAGS]) +-AC_CHECK_LIB([guile], [scm_make_gsubr], [AC_DEFINE([HAVE_SCM_MAKE_GSUBR], [1], [Define to 1 if you have the `scm_make_gsubr' function.])], [], [$GUILE_LDFLAGS]) +-AC_CHECK_LIB([guile], [scm_num2dbl], [AC_DEFINE([HAVE_SCM_NUM2DBL], [1], [Define to 1 if you have the `scm_num2dbl' function.])], [], [$GUILE_LDFLAGS]) ++AC_CHECK_LIB([guile-2.0], [scm_c_define_gsubr], [AC_DEFINE([HAVE_SCM_C_DEFINE_GSUBR], [1], [Define to 1 if you have the `scm_c_define_gsubr' function.])], [], [$GUILE_LDFLAGS]) ++AC_CHECK_LIB([guile-2.0], [scm_make_gsubr], [AC_DEFINE([HAVE_SCM_MAKE_GSUBR], [1], [Define to 1 if you have the `scm_make_gsubr' function.])], [], [$GUILE_LDFLAGS]) ++AC_CHECK_LIB([guile-2.0], [scm_num2dbl], [AC_DEFINE([HAVE_SCM_NUM2DBL], [1], [Define to 1 if you have the `scm_num2dbl' function.])], [], [$GUILE_LDFLAGS]) + + AC_CONFIG_FILES([Makefile doc/Makefile lib/Makefile]) + AC_OUTPUT(libmatheval.pc) +--- libmatheval-1.1.11+dfsg.orig/tests/basics.at ++++ libmatheval-1.1.11+dfsg/tests/basics.at +@@ -62,7 +62,7 @@ AT_DATA([basics.scm], + (display (evaluator-evaluate-x f 0)) + ]]) + +-AT_CHECK([matheval.sh basics.scm], [ignore], [10.0], [ignore]) ++AT_CHECK([matheval.sh basics.scm], [ignore], [10.000000000000002], [ignore]) + + AT_DATA([basics.scm], + [[ +@@ -70,7 +70,7 @@ AT_DATA([basics.scm], + (display (evaluator-evaluate-x f 0.7)) + ]]) + +-AT_CHECK([matheval.sh basics.scm], [ignore], [0.220966666722528], [ignore]) ++AT_CHECK([matheval.sh basics.scm], [ignore], [0.22096666672252796], [ignore]) + + AT_DATA([basics.scm], + [[ +@@ -78,7 +78,7 @@ AT_DATA([basics.scm], + (display (evaluator-evaluate-x-y f 0.4 -0.7)) + ]]) + +-AT_CHECK([matheval.sh basics.scm], [ignore], [-1.14962406520749], [ignore]) ++AT_CHECK([matheval.sh basics.scm], [ignore], [-1.1496240652074883], [ignore]) + + AT_DATA([basics.scm], + [[ +@@ -86,7 +86,7 @@ AT_DATA([basics.scm], + (display (evaluator-evaluate-x-y-z f 11.2 0.41 -0.66)) + ]]) + +-AT_CHECK([matheval.sh basics.scm], [ignore], [3.99876152571934], [ignore]) ++AT_CHECK([matheval.sh basics.scm], [ignore], [3.9987615257193383], [ignore]) + + AT_DATA([basics.scm], + [[ +--- libmatheval-1.1.11+dfsg.orig/tests/constants.at ++++ libmatheval-1.1.11+dfsg/tests/constants.at +@@ -29,7 +29,7 @@ AT_DATA([constant.scm], + (display (evaluator-evaluate-x f 0)) + ]]) + +-AT_CHECK([matheval.sh constant.scm], [ignore], [2.71828182845905], [ignore]) ++AT_CHECK([matheval.sh constant.scm], [ignore], [2.718281828459045], [ignore]) + + AT_DATA([constant.scm], + [[ +@@ -37,7 +37,7 @@ AT_DATA([constant.scm], + (display (evaluator-evaluate-x f 0)) + ]]) + +-AT_CHECK([matheval.sh constant.scm], [ignore], [1.44269504088896], [ignore]) ++AT_CHECK([matheval.sh constant.scm], [ignore], [1.4426950408889634], [ignore]) + + AT_DATA([constant.scm], + [[ +@@ -45,7 +45,7 @@ AT_DATA([constant.scm], + (display (evaluator-evaluate-x f 0)) + ]]) + +-AT_CHECK([matheval.sh constant.scm], [ignore], [0.434294481903252], [ignore]) ++AT_CHECK([matheval.sh constant.scm], [ignore], [0.4342944819032518], [ignore]) + + AT_DATA([constant.scm], + [[ +@@ -53,7 +53,7 @@ AT_DATA([constant.scm], + (display (evaluator-evaluate-x f 0)) + ]]) + +-AT_CHECK([matheval.sh constant.scm], [ignore], [0.693147180559945], [ignore]) ++AT_CHECK([matheval.sh constant.scm], [ignore], [0.6931471805599453], [ignore]) + + AT_DATA([constant.scm], + [[ +@@ -61,7 +61,7 @@ AT_DATA([constant.scm], + (display (evaluator-evaluate-x f 0)) + ]]) + +-AT_CHECK([matheval.sh constant.scm], [ignore], [2.30258509299405], [ignore]) ++AT_CHECK([matheval.sh constant.scm], [ignore], [2.302585092994046], [ignore]) + + AT_DATA([constant.scm], + [[ +@@ -69,7 +69,7 @@ AT_DATA([constant.scm], + (display (evaluator-evaluate-x f 0)) + ]]) + +-AT_CHECK([matheval.sh constant.scm], [ignore], [3.14159265358979], [ignore]) ++AT_CHECK([matheval.sh constant.scm], [ignore], [3.141592653589793], [ignore]) + + AT_DATA([constant.scm], + [[ +@@ -77,7 +77,7 @@ AT_DATA([constant.scm], + (display (evaluator-evaluate-x f 0)) + ]]) + +-AT_CHECK([matheval.sh constant.scm], [ignore], [1.5707963267949], [ignore]) ++AT_CHECK([matheval.sh constant.scm], [ignore], [1.5707963267948966], [ignore]) + + AT_DATA([constant.scm], + [[ +@@ -85,7 +85,7 @@ AT_DATA([constant.scm], + (display (evaluator-evaluate-x f 0)) + ]]) + +-AT_CHECK([matheval.sh constant.scm], [ignore], [0.785398163397448], [ignore]) ++AT_CHECK([matheval.sh constant.scm], [ignore], [0.7853981633974483], [ignore]) + + AT_DATA([constant.scm], + [[ +@@ -93,7 +93,7 @@ AT_DATA([constant.scm], + (display (evaluator-evaluate-x f 0)) + ]]) + +-AT_CHECK([matheval.sh constant.scm], [ignore], [0.318309886183791], [ignore]) ++AT_CHECK([matheval.sh constant.scm], [ignore], [0.3183098861837907], [ignore]) + + AT_DATA([constant.scm], + [[ +@@ -101,7 +101,7 @@ AT_DATA([constant.scm], + (display (evaluator-evaluate-x f 0)) + ]]) + +-AT_CHECK([matheval.sh constant.scm], [ignore], [0.636619772367581], [ignore]) ++AT_CHECK([matheval.sh constant.scm], [ignore], [0.6366197723675814], [ignore]) + + AT_DATA([constant.scm], + [[ +@@ -109,7 +109,7 @@ AT_DATA([constant.scm], + (display (evaluator-evaluate-x f 0)) + ]]) + +-AT_CHECK([matheval.sh constant.scm], [ignore], [1.12837916709551], [ignore]) ++AT_CHECK([matheval.sh constant.scm], [ignore], [1.1283791670955126], [ignore]) + + AT_DATA([constant.scm], + [[ +@@ -117,7 +117,7 @@ AT_DATA([constant.scm], + (display (evaluator-evaluate-x f 0)) + ]]) + +-AT_CHECK([matheval.sh constant.scm], [ignore], [1.4142135623731], [ignore]) ++AT_CHECK([matheval.sh constant.scm], [ignore], [1.4142135623730951], [ignore]) + + AT_DATA([constant.scm], + [[ +@@ -125,7 +125,7 @@ AT_DATA([constant.scm], + (display (evaluator-evaluate-x f 0)) + ]]) + +-AT_CHECK([matheval.sh constant.scm], [ignore], [0.707106781186548], [ignore]) ++AT_CHECK([matheval.sh constant.scm], [ignore], [0.7071067811865476], [ignore]) + + AT_DATA([constant.scm], + [[ +@@ -133,7 +133,7 @@ AT_DATA([constant.scm], + (display (evaluator-evaluate-x f 0)) + ]]) + +-AT_CHECK([matheval.sh constant.scm], [ignore], [10.0], [ignore]) ++AT_CHECK([matheval.sh constant.scm], [ignore], [10.000000000000002], [ignore]) + + AT_DATA([constant.scm], + [[ +--- libmatheval-1.1.11+dfsg.orig/tests/functions.at ++++ libmatheval-1.1.11+dfsg/tests/functions.at +@@ -29,7 +29,7 @@ AT_DATA([function.scm], + (display (evaluator-evaluate-x f 1)) + ]]) + +-AT_CHECK([matheval.sh function.scm], [ignore], [2.71828182845905], [ignore]) ++AT_CHECK([matheval.sh function.scm], [ignore], [2.718281828459045], [ignore]) + + AT_DATA([function.scm], + [[ +@@ -80,7 +80,7 @@ AT_DATA([function.scm], + (display (evaluator-evaluate-x f 1)) + ]]) + +-AT_CHECK([matheval.sh function.scm], [ignore], [0.841470984807897], [ignore]) ++AT_CHECK([matheval.sh function.scm], [ignore], [0.8414709848078965], [ignore]) + + AT_DATA([function.scm], + [[ +@@ -97,7 +97,7 @@ AT_DATA([function.scm], + (display (evaluator-evaluate-x f 1)) + ]]) + +-AT_CHECK([matheval.sh function.scm], [ignore], [0.54030230586814], [ignore]) ++AT_CHECK([matheval.sh function.scm], [ignore], [0.5403023058681398], [ignore]) + + AT_DATA([function.scm], + [[ +@@ -114,7 +114,7 @@ AT_DATA([function.scm], + (display (evaluator-evaluate-x f 1)) + ]]) + +-AT_CHECK([matheval.sh function.scm], [ignore], [1.5574077246549], [ignore]) ++AT_CHECK([matheval.sh function.scm], [ignore], [1.5574077246549023], [ignore]) + + AT_DATA([function.scm], + [[ +@@ -131,7 +131,7 @@ AT_DATA([function.scm], + (display (evaluator-evaluate-x f 1)) + ]]) + +-AT_CHECK([matheval.sh function.scm], [ignore], [0.642092615934331], [ignore]) ++AT_CHECK([matheval.sh function.scm], [ignore], [0.6420926159343306], [ignore]) + + AT_DATA([function.scm], + [[ +@@ -148,7 +148,7 @@ AT_DATA([function.scm], + (display (evaluator-evaluate-x f 1)) + ]]) + +-AT_CHECK([matheval.sh function.scm], [ignore], [1.85081571768093], [ignore]) ++AT_CHECK([matheval.sh function.scm], [ignore], [1.8508157176809255], [ignore]) + + AT_DATA([function.scm], + [[ +@@ -165,7 +165,7 @@ AT_DATA([function.scm], + (display (evaluator-evaluate-x f 1)) + ]]) + +-AT_CHECK([matheval.sh function.scm], [ignore], [1.18839510577812], [ignore]) ++AT_CHECK([matheval.sh function.scm], [ignore], [1.1883951057781212], [ignore]) + + AT_DATA([function.scm], + [[ +@@ -182,7 +182,7 @@ AT_DATA([function.scm], + (display (evaluator-evaluate-x f 1)) + ]]) + +-AT_CHECK([matheval.sh function.scm], [ignore], [1.5707963267949], [ignore]) ++AT_CHECK([matheval.sh function.scm], [ignore], [1.5707963267948966], [ignore]) + + AT_DATA([function.scm], + [[ +@@ -216,7 +216,7 @@ AT_DATA([function.scm], + (display (evaluator-evaluate-x f 1)) + ]]) + +-AT_CHECK([matheval.sh function.scm], [ignore], [0.785398163397448], [ignore]) ++AT_CHECK([matheval.sh function.scm], [ignore], [0.7853981633974483], [ignore]) + + AT_DATA([function.scm], + [[ +@@ -233,7 +233,7 @@ AT_DATA([function.scm], + (display (evaluator-evaluate-x f 1)) + ]]) + +-AT_CHECK([matheval.sh function.scm], [ignore], [0.785398163397448], [ignore]) ++AT_CHECK([matheval.sh function.scm], [ignore], [0.7853981633974483], [ignore]) + + AT_DATA([function.scm], + [[ +@@ -267,7 +267,7 @@ AT_DATA([function.scm], + (display (evaluator-evaluate-x f 1)) + ]]) + +-AT_CHECK([matheval.sh function.scm], [ignore], [1.5707963267949], [ignore]) ++AT_CHECK([matheval.sh function.scm], [ignore], [1.5707963267948966], [ignore]) + + AT_DATA([function.scm], + [[ +@@ -284,7 +284,7 @@ AT_DATA([function.scm], + (display (evaluator-evaluate-x f 1)) + ]]) + +-AT_CHECK([matheval.sh function.scm], [ignore], [1.1752011936438], [ignore]) ++AT_CHECK([matheval.sh function.scm], [ignore], [1.1752011936438014], [ignore]) + + AT_DATA([function.scm], + [[ +@@ -301,7 +301,7 @@ AT_DATA([function.scm], + (display (evaluator-evaluate-x f 1)) + ]]) + +-AT_CHECK([matheval.sh function.scm], [ignore], [1.54308063481524], [ignore]) ++AT_CHECK([matheval.sh function.scm], [ignore], [1.5430806348152437], [ignore]) + + AT_DATA([function.scm], + [[ +@@ -318,7 +318,7 @@ AT_DATA([function.scm], + (display (evaluator-evaluate-x f 1)) + ]]) + +-AT_CHECK([matheval.sh function.scm], [ignore], [0.761594155955765], [ignore]) ++AT_CHECK([matheval.sh function.scm], [ignore], [0.7615941559557649], [ignore]) + + AT_DATA([function.scm], + [[ +@@ -335,7 +335,7 @@ AT_DATA([function.scm], + (display (evaluator-evaluate-x f 1)) + ]]) + +-AT_CHECK([matheval.sh function.scm], [ignore], [1.31303528549933], [ignore]) ++AT_CHECK([matheval.sh function.scm], [ignore], [1.3130352854993315], [ignore]) + + AT_DATA([function.scm], + [[ +@@ -352,7 +352,7 @@ AT_DATA([function.scm], + (display (evaluator-evaluate-x f 1)) + ]]) + +-AT_CHECK([matheval.sh function.scm], [ignore], [0.648054273663885], [ignore]) ++AT_CHECK([matheval.sh function.scm], [ignore], [0.6480542736638855], [ignore]) + + AT_DATA([function.scm], + [[ +@@ -368,7 +368,7 @@ AT_DATA([function.scm], + (display (evaluator-evaluate-x f 1)) + ]]) + +-AT_CHECK([matheval.sh function.scm], [ignore], [0.850918128239322], [ignore]) ++AT_CHECK([matheval.sh function.scm], [ignore], [0.8509181282393216], [ignore]) + + AT_DATA([function.scm], + [[ +@@ -385,7 +385,7 @@ AT_DATA([function.scm], + (display (evaluator-evaluate-x f 1)) + ]]) + +-AT_CHECK([matheval.sh function.scm], [ignore], [0.881373587019543], [ignore]) ++AT_CHECK([matheval.sh function.scm], [ignore], [0.8813735870195429], [ignore]) + + AT_DATA([function.scm], + [[ +@@ -419,7 +419,7 @@ AT_DATA([function.scm], + (display (evaluator-evaluate-x f 0.5)) + ]]) + +-AT_CHECK([matheval.sh function.scm], [ignore], [0.549306144334055], [ignore]) ++AT_CHECK([matheval.sh function.scm], [ignore], [0.5493061443340549], [ignore]) + + AT_DATA([function.scm], + [[ +@@ -436,7 +436,7 @@ AT_DATA([function.scm], + (display (evaluator-evaluate-x f 2)) + ]]) + +-AT_CHECK([matheval.sh function.scm], [ignore], [0.549306144334055], [ignore]) ++AT_CHECK([matheval.sh function.scm], [ignore], [0.5493061443340549], [ignore]) + + AT_DATA([function.scm], + [[ +@@ -470,7 +470,7 @@ AT_DATA([function.scm], + (display (evaluator-evaluate-x f 1)) + ]]) + +-AT_CHECK([matheval.sh function.scm], [ignore], [0.881373587019543], [ignore]) ++AT_CHECK([matheval.sh function.scm], [ignore], [0.8813735870195429], [ignore]) + + AT_DATA([function.scm], + [[ +--- libmatheval-1.1.11+dfsg.orig/tests/numbers.at ++++ libmatheval-1.1.11+dfsg/tests/numbers.at +@@ -53,6 +53,6 @@ AT_DATA([number.scm], + (display (evaluator-evaluate-x f 0)) + ]]) + +-AT_CHECK([matheval.sh number.scm], [ignore], [0.644394014977254], [ignore]) ++AT_CHECK([matheval.sh number.scm], [ignore], [0.6443940149772542], [ignore]) + + AT_CLEANUP diff --git a/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.11-GCCcore-13.3.0.eb b/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.11-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..b8bf07966b1 --- /dev/null +++ b/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.11-GCCcore-13.3.0.eb @@ -0,0 +1,45 @@ +easyblock = 'ConfigureMake' + +name = 'libmatheval' +version = '1.1.11' # still the latest version available on the ftp mirror + +homepage = 'https://www.gnu.org/software/libmatheval/' +description = """GNU libmatheval is a library (callable from C and Fortran) to parse + and evaluate symbolic expressions input as text. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +patches = [ + '003-guile2.0.patch', + 'libmatheval-1.1.11_fix-matheval-test.patch' +] +checksums = [ + {'libmatheval-1.1.11.tar.gz': '474852d6715ddc3b6969e28de5e1a5fbaff9e8ece6aebb9dc1cc63e9e88e89ab'}, + {'003-guile2.0.patch': 'd0ad39d54800153cbaa26c01448f040d405f09e9fd57e1357eab170a274a9b5c'}, + {'libmatheval-1.1.11_fix-matheval-test.patch': '2888ee1ba32bb864b655e53e13b06eafc23b598faed80b90585d41c98e2ae073'}, +] + +builddependencies = [ + ('binutils', '2.42'), + ('flex', '2.6.4'), + ('Bison', '3.8.2'), + ('byacc', '2.0.20240109'), + # guile 2.2.X, 3.0.7 removed scm_num2dbl (among others), which are needed for libmatheval (at least for 1.1.11) + ('Guile', '2.0.14') +] + +configopts = '--with-pic ' + +# fix for guile-config being broken because shebang line contains full path to bin/guile +configopts += 'GUILE_CONFIG="$EBROOTGUILE/bin/guile -e main -s $EBROOTGUILE/bin/guile-config"' + +sanity_check_paths = { + 'files': ['lib/libmatheval.a', 'include/matheval.h'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libmbd/libmbd-0.12.6-foss-2022a.eb b/easybuild/easyconfigs/l/libmbd/libmbd-0.12.6-foss-2022a.eb new file mode 100644 index 00000000000..e0e689460f9 --- /dev/null +++ b/easybuild/easyconfigs/l/libmbd/libmbd-0.12.6-foss-2022a.eb @@ -0,0 +1,59 @@ +easyblock = 'CMakeMake' + +name = 'libmbd' +version = '0.12.6' + +homepage = 'https://libmbd.github.io/index.html' +description = """ +Libmbd implements the many-body dispersion (MBD) method in several programming languages and frameworks: + + - The Fortran implementation is the reference, most advanced implementation, with support for analytical + gradients and distributed parallelism, and additional functionality beyond the MBD method itself. + It provides a low-level and a high-level Fortran API, as well as a C API. Furthermore, Python bindings + to the C API are provided. + - The Python/Numpy implementation is intended for prototyping, and as a high-level language reference. + - The Python/Tensorflow implementation is an experiment that should enable rapid prototyping of machine + learning applications with MBD. + +The Python-based implementations as well as Python bindings to the Libmbd C API are accessible from the +Python package called Pymbd. +""" + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'usempi': True, 'pic': True} + +github_account = 'libmbd' +source_urls = [GITHUB_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['9f8154b6b2f57e78a8e33d3b315a244185e8e5ecb03661a469808af7512e761e'] + +builddependencies = [ + ('CMake', '3.23.1'), + ('pkgconf', '1.8.0'), +] + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('ELSI', '2.9.1', '-PEXSI'), +] + +# build scripts expect either a git repo or a defined version string in a file +_versiontag_file = '%(builddir)s/%(name)s-%(version)s/cmake/LibmbdVersionTag.cmake' +preconfigopts = "echo 'set(VERSION_TAG \"%%(version)s\")' > %s && " % _versiontag_file + +configopts = "-DENABLE_SCALAPACK_MPI=ON -DENABLE_ELSI=ON " +configopts += "-DMPIEXEC_MAX_NUMPROCS=1 " # number of procs in the tests + +# make sure that built libraries (libmbd.so) in build directory are picked when running tests +# this is required when RPATH linking is used +pretestopts = "export LD_LIBRARY_PATH=%(builddir)s/easybuild_obj:$LD_LIBRARY_PATH && " + +runtest = 'test' + +sanity_check_paths = { + 'files': ['lib/libmbd.%s' % SHLIB_EXT, 'include/mbd/mbd.h', 'include/mbd/mbd.mod'], + 'dirs': ['lib/cmake/mbd'], +} + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/l/libmbd/libmbd-0.12.6-foss-2023a.eb b/easybuild/easyconfigs/l/libmbd/libmbd-0.12.6-foss-2023a.eb new file mode 100644 index 00000000000..260ecb98ddb --- /dev/null +++ b/easybuild/easyconfigs/l/libmbd/libmbd-0.12.6-foss-2023a.eb @@ -0,0 +1,59 @@ +easyblock = 'CMakeMake' + +name = 'libmbd' +version = '0.12.6' + +homepage = 'https://libmbd.github.io/index.html' +description = """ +Libmbd implements the many-body dispersion (MBD) method in several programming languages and frameworks: + + - The Fortran implementation is the reference, most advanced implementation, with support for analytical + gradients and distributed parallelism, and additional functionality beyond the MBD method itself. + It provides a low-level and a high-level Fortran API, as well as a C API. Furthermore, Python bindings + to the C API are provided. + - The Python/Numpy implementation is intended for prototyping, and as a high-level language reference. + - The Python/Tensorflow implementation is an experiment that should enable rapid prototyping of machine + learning applications with MBD. + +The Python-based implementations as well as Python bindings to the Libmbd C API are accessible from the +Python package called Pymbd. +""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'usempi': True, 'pic': True} + +github_account = 'libmbd' +source_urls = [GITHUB_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['9f8154b6b2f57e78a8e33d3b315a244185e8e5ecb03661a469808af7512e761e'] + +builddependencies = [ + ('CMake', '3.26.3'), + ('pkgconf', '1.9.5'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('ELSI', '2.11.0', '-PEXSI'), +] + +# build scripts expect either a git repo or a defined version string in a file +_versiontag_file = '%(builddir)s/%(name)s-%(version)s/cmake/LibmbdVersionTag.cmake' +preconfigopts = "echo 'set(VERSION_TAG \"%%(version)s\")' > %s && " % _versiontag_file + +configopts = "-DENABLE_SCALAPACK_MPI=ON -DENABLE_ELSI=ON " +configopts += "-DMPIEXEC_MAX_NUMPROCS=1 " # number of procs in the tests + +# make sure that built libraries (libmbd.so) in build directory are picked when running tests +# this is required when RPATH linking is used +pretestopts = "export LD_LIBRARY_PATH=%(builddir)s/easybuild_obj:$LD_LIBRARY_PATH && " + +runtest = 'test' + +sanity_check_paths = { + 'files': ['lib/libmbd.%s' % SHLIB_EXT, 'include/mbd/mbd.h', 'include/mbd/mbd.mod'], + 'dirs': ['lib/cmake/mbd'], +} + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/l/libnsl/libnsl-2.0.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/libnsl/libnsl-2.0.1-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..a00b43e2177 --- /dev/null +++ b/easybuild/easyconfigs/l/libnsl/libnsl-2.0.1-GCCcore-12.3.0.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'libnsl' +version = '2.0.1' + +homepage = 'https://github.com/thkukuk/libnsl' +description = """The libnsl package contains the public client interface for NIS(YP).""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://github.com/thkukuk/%(name)s/releases/download/v%(version)s/'] +sources = [SOURCE_TAR_XZ] +checksums = ['5c9e470b232a7acd3433491ac5221b4832f0c71318618dc6aa04dd05ffcd8fd9'] + +builddependencies = [ + ('binutils', '2.40'), +] + +dependencies = [ + ('libtirpc', '1.3.3'), +] + +# Provide a symlink for libnsl.so.1, which used to be part of glibc. +# This new version of libnsl should be backwards compatible. +postinstallcmds = ['ln -s libnsl.so %(installdir)s/lib/libnsl.so.1'] + +sanity_check_paths = { + 'files': ['include/rpcsvc/yp.h', 'lib/libnsl.a', + 'lib/libnsl.%s' % SHLIB_EXT, 'lib/libnsl.%s.1' % SHLIB_EXT], + 'dirs': ['include'] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/l/libnsl/libnsl-2.0.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/l/libnsl/libnsl-2.0.1-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..818f1687a15 --- /dev/null +++ b/easybuild/easyconfigs/l/libnsl/libnsl-2.0.1-GCCcore-13.3.0.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'libnsl' +version = '2.0.1' + +homepage = 'https://github.com/thkukuk/libnsl' +description = """The libnsl package contains the public client interface for NIS(YP).""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://github.com/thkukuk/%(name)s/releases/download/v%(version)s/'] +sources = [SOURCE_TAR_XZ] +checksums = ['5c9e470b232a7acd3433491ac5221b4832f0c71318618dc6aa04dd05ffcd8fd9'] + +builddependencies = [ + ('binutils', '2.42'), +] + +dependencies = [ + ('libtirpc', '1.3.5'), +] + +# Provide a symlink for libnsl.so.1, which used to be part of glibc. +# This new version of libnsl should be backwards compatible. +postinstallcmds = ['ln -s libnsl.so %(installdir)s/lib/libnsl.so.1'] + +sanity_check_paths = { + 'files': ['include/rpcsvc/yp.h', 'lib/libnsl.a', + 'lib/libnsl.%s' % SHLIB_EXT, 'lib/libnsl.%s.1' % SHLIB_EXT], + 'dirs': ['include'] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/l/libogg/libogg-1.3.5-GCCcore-13.2.0.eb b/easybuild/easyconfigs/l/libogg/libogg-1.3.5-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..a2f34782696 --- /dev/null +++ b/easybuild/easyconfigs/l/libogg/libogg-1.3.5-GCCcore-13.2.0.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'libogg' +version = '1.3.5' + +homepage = 'https://xiph.org/ogg/' +description = """Ogg is a multimedia container format, and the native file and stream format for the Xiph.org +multimedia codecs.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://ftp.osuosl.org/pub/xiph/releases/ogg/'] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['c4d91be36fc8e54deae7575241e03f4211eb102afb3fc0775fbbc1b740016705'] + +builddependencies = [('binutils', '2.40')] + +configopts = '--enable-static --enable-shared' + +sanity_check_paths = { + 'files': ['lib/libogg.a', 'lib/libogg.%s' % SHLIB_EXT], + 'dirs': ['include/ogg'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libogg/libogg-1.3.5-GCCcore-13.3.0.eb b/easybuild/easyconfigs/l/libogg/libogg-1.3.5-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..810ddbe1169 --- /dev/null +++ b/easybuild/easyconfigs/l/libogg/libogg-1.3.5-GCCcore-13.3.0.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'libogg' +version = '1.3.5' + +homepage = 'https://xiph.org/ogg/' +description = """Ogg is a multimedia container format, and the native file and stream format for the Xiph.org +multimedia codecs.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://ftp.osuosl.org/pub/xiph/releases/ogg/'] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['c4d91be36fc8e54deae7575241e03f4211eb102afb3fc0775fbbc1b740016705'] + +builddependencies = [('binutils', '2.42')] + +configopts = '--enable-static --enable-shared' + +sanity_check_paths = { + 'files': ['lib/libogg.a', 'lib/libogg.%s' % SHLIB_EXT], + 'dirs': ['include/ogg'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libopus/libopus-1.5.2-GCCcore-13.2.0.eb b/easybuild/easyconfigs/l/libopus/libopus-1.5.2-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..7d0630bb477 --- /dev/null +++ b/easybuild/easyconfigs/l/libopus/libopus-1.5.2-GCCcore-13.2.0.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'libopus' +version = '1.5.2' + +homepage = 'https://www.opus-codec.org/' +description = """Opus is a totally open, royalty-free, highly versatile audio codec. Opus is unmatched for interactive + speech and music transmission over the Internet, but is also intended for storage and streaming applications. It is + standardized by the Internet Engineering Task Force (IETF) as RFC 6716 which incorporated technology from Skype’s + SILK codec and Xiph.Org’s CELT codec.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://downloads.xiph.org/releases/opus/'] +sources = ['opus-%(version)s.tar.gz'] +checksums = ['65c1d2f78b9f2fb20082c38cbe47c951ad5839345876e46941612ee87f9a7ce1'] + +builddependencies = [ + ('binutils', '2.40'), + ('pkgconf', '2.0.3'), +] + +configopts = '--enable-static --enable-shared' + +sanity_check_paths = { + 'files': ['lib/libopus.a', 'lib/libopus.%s' % SHLIB_EXT], + 'dirs': ['include/opus'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libopus/libopus-1.5.2-GCCcore-13.3.0.eb b/easybuild/easyconfigs/l/libopus/libopus-1.5.2-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..c09615c86f8 --- /dev/null +++ b/easybuild/easyconfigs/l/libopus/libopus-1.5.2-GCCcore-13.3.0.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'libopus' +version = '1.5.2' + +homepage = 'https://www.opus-codec.org/' +description = """Opus is a totally open, royalty-free, highly versatile audio codec. Opus is unmatched for interactive + speech and music transmission over the Internet, but is also intended for storage and streaming applications. It is + standardized by the Internet Engineering Task Force (IETF) as RFC 6716 which incorporated technology from Skype’s + SILK codec and Xiph.Org’s CELT codec.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://downloads.xiph.org/releases/opus/'] +sources = ['opus-%(version)s.tar.gz'] +checksums = ['65c1d2f78b9f2fb20082c38cbe47c951ad5839345876e46941612ee87f9a7ce1'] + +builddependencies = [ + ('binutils', '2.42'), + ('pkgconf', '2.2.0'), +] + +configopts = '--enable-static --enable-shared' + +sanity_check_paths = { + 'files': ['lib/libopus.a', 'lib/libopus.%s' % SHLIB_EXT], + 'dirs': ['include/opus'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.18.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.18.1-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..7b1be7bc436 --- /dev/null +++ b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.18.1-GCCcore-13.3.0.eb @@ -0,0 +1,29 @@ +easyblock = 'MesonNinja' + +name = 'libpciaccess' +version = '0.18.1' + +homepage = 'https://cgit.freedesktop.org/xorg/lib/libpciaccess/' +description = """Generic PCI access library.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://www.x.org/releases/individual/lib/'] +sources = [SOURCE_TAR_XZ] +checksums = ['4af43444b38adb5545d0ed1c2ce46d9608cc47b31c2387fc5181656765a6fa76'] + +builddependencies = [ + ('binutils', '2.42'), + ('Meson', '1.4.0'), + ('Ninja', '1.12.1'), + ('xorg-macros', '1.20.1'), +] + +configopts = "--default-library=both" # static and shared library + +sanity_check_paths = { + 'files': ['include/pciaccess.h', 'lib/libpciaccess.a'], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/l/libpng/libpng-1.6.43-GCCcore-13.3.0.eb b/easybuild/easyconfigs/l/libpng/libpng-1.6.43-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..04fc0f259cc --- /dev/null +++ b/easybuild/easyconfigs/l/libpng/libpng-1.6.43-GCCcore-13.3.0.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'libpng' +version = '1.6.43' + +homepage = 'http://www.libpng.org/pub/png/libpng.html' + +description = "libpng is the official PNG reference library" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['e804e465d4b109b5ad285a8fb71f0dd3f74f0068f91ce3cdfde618180c174925'] + +builddependencies = [('binutils', '2.42')] + +dependencies = [('zlib', '1.3.1')] + +local_majminver = '%(version_major)s%(version_minor)s' + +sanity_check_paths = { + 'files': ['include/pngconf.h', 'include/png.h', 'include/pnglibconf.h', + 'lib/libpng.a', 'lib/libpng.%s' % SHLIB_EXT, + 'lib/libpng%s.a' % local_majminver, + 'lib/libpng%s.%s' % (local_majminver, SHLIB_EXT)], + 'dirs': ['bin', 'include/libpng%s' % local_majminver, 'share/man'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-8.2-GCCcore-13.3.0.eb b/easybuild/easyconfigs/l/libreadline/libreadline-8.2-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..8cf47255fdc --- /dev/null +++ b/easybuild/easyconfigs/l/libreadline/libreadline-8.2-GCCcore-13.3.0.eb @@ -0,0 +1,41 @@ +easyblock = 'ConfigureMake' + +name = 'libreadline' +version = '8.2' + +homepage = 'https://tiswww.case.edu/php/chet/readline/rltop.html' +description = """ + The GNU Readline library provides a set of functions for use by applications + that allow users to edit command lines as they are typed in. Both Emacs and + vi editing modes are available. The Readline library includes additional + functions to maintain a list of previously-entered command lines, to recall + and perhaps reedit those lines, and perform csh-like history expansion on + previous commands. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://ftp.gnu.org/gnu/readline'] +sources = ['readline-%(version)s.tar.gz'] +checksums = ['3feb7171f16a84ee82ca18a36d7b9be109a52c04f492a053331d7d1095007c35'] + +builddependencies = [ + ('binutils', '2.42'), +] +dependencies = [ + ('ncurses', '6.5'), +] + +# for the termcap symbols, use EB ncurses +buildopts = "SHLIB_LIBS='-lncurses'" + +sanity_check_paths = { + 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + + ['include/readline/%s' % x + for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', + 'rlconf.h', 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/librosa/librosa-0.10.1-foss-2023a.eb b/easybuild/easyconfigs/l/librosa/librosa-0.10.1-foss-2023a.eb index 444e2ba800d..c26fed6c2e3 100644 --- a/easybuild/easyconfigs/l/librosa/librosa-0.10.1-foss-2023a.eb +++ b/easybuild/easyconfigs/l/librosa/librosa-0.10.1-foss-2023a.eb @@ -27,7 +27,6 @@ use_pip = True exts_list = [ ('soxr', '0.3.7', { - 'preinstallopts': 'python -m build && ', 'checksums': ['436ddff00c6eb2c75b79c19cfdca7527b1e31b5fad738652f044045ba6258593'], }), ('audioread', '3.0.1', { diff --git a/easybuild/easyconfigs/l/librsvg/librsvg-2.58.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/librsvg/librsvg-2.58.0-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..1391bcb955e --- /dev/null +++ b/easybuild/easyconfigs/l/librsvg/librsvg-2.58.0-GCCcore-12.3.0.eb @@ -0,0 +1,41 @@ +easyblock = 'ConfigureMake' + +name = 'librsvg' +version = '2.58.0' + +homepage = 'https://wiki.gnome.org/Projects/LibRsvg' +description = "Librsvg is a library to render SVG files using cairo." + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://download.gnome.org/sources/librsvg/%(version_major_minor)s/'] +sources = [SOURCE_TAR_XZ] +checksums = ['d7c444a926406b59790be0deae196e18ed26059da573fa1aa9ec9ca7658a559c'] + +builddependencies = [ + ('binutils', '2.40'), + ('pkgconf', '1.9.5'), + ('Rust', '1.75.0'), +] + +dependencies = [ + ('cairo', '1.17.8'), + ('freetype', '2.13.0'), + ('Gdk-Pixbuf', '2.42.10'), + ('HarfBuzz', '5.3.1'), + ('Pango', '1.50.14'), + ('GObject-Introspection', '1.76.1'), +] + +# don't GdkPixbuf loader (which gets added to the Gdk-Pixbuf installation directory) +configopts = "--disable-pixbuf-loader" + +sanity_check_paths = { + 'files': ['bin/rsvg-convert', 'lib/librsvg-%(version_major)s.a', 'lib/librsvg-%%(version_major)s.%s' % SHLIB_EXT, + 'lib/pkgconfig/librsvg-%(version_major)s.0.pc'], + 'dirs': ['include/librsvg-%(version_major)s.0/librsvg', 'share'], +} + +sanity_check_commands = ["rsvg-convert --help"] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libsigc++/libsigc++-3.6.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/l/libsigc++/libsigc++-3.6.0-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..8657a57fde1 --- /dev/null +++ b/easybuild/easyconfigs/l/libsigc++/libsigc++-3.6.0-GCCcore-12.2.0.eb @@ -0,0 +1,32 @@ +easyblock = 'CMakeMake' + +name = 'libsigc++' +version = '3.6.0' + +homepage = 'https://libsigcplusplus.github.io/libsigcplusplus/' +description = """The libsigc++ package implements a typesafe callback system +for standard C++.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['c3d23b37dfd6e39f2e09f091b77b1541fbfa17c4f0b6bf5c89baef7229080e17'] + +builddependencies = [ + ('binutils', '2.39'), + ('libxslt', '1.1.37'), + ('mm-common', '1.0.6'), + ('CMake', '3.24.3'), +] + +test_cmd = 'ctest' +runtest = '-j' + +sanity_check_paths = { + 'files': ['lib/libsigc-%%(version_major)s.0.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/l/libsigc++/libsigc++-3.6.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/libsigc++/libsigc++-3.6.0-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..4f452cbc432 --- /dev/null +++ b/easybuild/easyconfigs/l/libsigc++/libsigc++-3.6.0-GCCcore-12.3.0.eb @@ -0,0 +1,32 @@ +easyblock = 'CMakeMake' + +name = 'libsigc++' +version = '3.6.0' + +homepage = 'https://libsigcplusplus.github.io/libsigcplusplus/' +description = """The libsigc++ package implements a typesafe callback system +for standard C++.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['c3d23b37dfd6e39f2e09f091b77b1541fbfa17c4f0b6bf5c89baef7229080e17'] + +builddependencies = [ + ('binutils', '2.40'), + ('libxslt', '1.1.38'), + ('mm-common', '1.0.6'), + ('CMake', '3.26.3'), +] + +test_cmd = 'ctest' +runtest = '-j' + +sanity_check_paths = { + 'files': ['lib/libsigc-%%(version_major)s.0.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/l/libsigc++/libsigc++-3.6.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/l/libsigc++/libsigc++-3.6.0-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..e64e49e0f74 --- /dev/null +++ b/easybuild/easyconfigs/l/libsigc++/libsigc++-3.6.0-GCCcore-13.2.0.eb @@ -0,0 +1,32 @@ +easyblock = 'CMakeMake' + +name = 'libsigc++' +version = '3.6.0' + +homepage = 'https://libsigcplusplus.github.io/libsigcplusplus/' +description = """The libsigc++ package implements a typesafe callback system +for standard C++.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} +toolchainopts = {'pic': True} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['c3d23b37dfd6e39f2e09f091b77b1541fbfa17c4f0b6bf5c89baef7229080e17'] + +builddependencies = [ + ('binutils', '2.40'), + ('libxslt', '1.1.38'), + ('mm-common', '1.0.6'), + ('CMake', '3.27.6'), +] + +test_cmd = 'ctest' +runtest = '-j' + +sanity_check_paths = { + 'files': ['lib/libsigc-%%(version_major)s.0.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/l/libsndfile/libsndfile-1.2.2-GCCcore-13.2.0.eb b/easybuild/easyconfigs/l/libsndfile/libsndfile-1.2.2-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..66345e01105 --- /dev/null +++ b/easybuild/easyconfigs/l/libsndfile/libsndfile-1.2.2-GCCcore-13.2.0.eb @@ -0,0 +1,39 @@ +easyblock = 'CMakeMake' + +name = 'libsndfile' +version = '1.2.2' + +homepage = 'http://www.mega-nerd.com/libsndfile' +description = """Libsndfile is a C library for reading and writing files containing sampled sound + (such as MS Windows WAV and the Apple/SGI AIFF format) through one standard library interface.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://github.com/%(name)s/%(name)s/releases/download/%(version)s/'] +sources = [SOURCE_TAR_XZ] +checksums = ['3799ca9924d3125038880367bf1468e53a1b7e3686a934f098b7e1d286cdb80e'] + +builddependencies = [ + ('binutils', '2.40'), + ('pkgconf', '2.0.3'), + ('CMake', '3.27.6'), +] +dependencies = [ + ('FLAC', '1.4.3'), + ('libvorbis', '1.3.7'), + ('libopus', '1.5.2'), + ('LAME', '3.100'), +] + +configopts = [ + '', + '-DBUILD_SHARED_LIBS=ON', +] + + +sanity_check_paths = { + 'files': ['include/sndfile.h', 'include/sndfile.hh', 'lib/%(name)s.a', 'lib/%(name)s.so'], + 'dirs': ['bin'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libsndfile/libsndfile-1.2.2-GCCcore-13.3.0.eb b/easybuild/easyconfigs/l/libsndfile/libsndfile-1.2.2-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..e60ad09d1a1 --- /dev/null +++ b/easybuild/easyconfigs/l/libsndfile/libsndfile-1.2.2-GCCcore-13.3.0.eb @@ -0,0 +1,39 @@ +easyblock = 'CMakeMake' + +name = 'libsndfile' +version = '1.2.2' + +homepage = 'http://www.mega-nerd.com/libsndfile' +description = """Libsndfile is a C library for reading and writing files containing sampled sound + (such as MS Windows WAV and the Apple/SGI AIFF format) through one standard library interface.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://github.com/%(name)s/%(name)s/releases/download/%(version)s/'] +sources = [SOURCE_TAR_XZ] +checksums = ['3799ca9924d3125038880367bf1468e53a1b7e3686a934f098b7e1d286cdb80e'] + +builddependencies = [ + ('binutils', '2.42'), + ('pkgconf', '2.2.0'), + ('CMake', '3.29.3'), +] +dependencies = [ + ('FLAC', '1.4.3'), + ('libvorbis', '1.3.7'), + ('libopus', '1.5.2'), + ('LAME', '3.100'), +] + +configopts = [ + '', + '-DBUILD_SHARED_LIBS=ON', +] + + +sanity_check_paths = { + 'files': ['include/sndfile.h', 'include/sndfile.hh', 'lib/%(name)s.a', 'lib/%(name)s.so'], + 'dirs': ['bin'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libsodium/libsodium-1.0.20-GCCcore-13.3.0.eb b/easybuild/easyconfigs/l/libsodium/libsodium-1.0.20-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..e98d28304a8 --- /dev/null +++ b/easybuild/easyconfigs/l/libsodium/libsodium-1.0.20-GCCcore-13.3.0.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'libsodium' +version = '1.0.20' + +homepage = 'https://doc.libsodium.org/' +description = """ + Sodium is a modern, easy-to-use software library for encryption, decryption, + signatures, password hashing and more. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +source_urls = [ + 'https://download.%(name)s.org/%(name)s/releases/', + 'https://download.%(name)s.org/%(name)s/releases/old/', + 'https://download.%(name)s.org/%(name)s/releases/old/unsupported/', +] +sources = [SOURCE_TAR_GZ] +checksums = ['ebb65ef6ca439333c2bb41a0c1990587288da07f6c7fd07cb3a18cc18d30ce19'] + +builddependencies = [ + ('binutils', '2.42'), +] + + +sanity_check_paths = { + 'files': ['include/sodium.h', 'lib/%%(name)s.%s' % SHLIB_EXT, 'lib/%(name)s.a'], + 'dirs': ['include/sodium', 'lib/pkgconfig'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libspatialindex/libspatialindex-2.0.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/l/libspatialindex/libspatialindex-2.0.0-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..1752b337b05 --- /dev/null +++ b/easybuild/easyconfigs/l/libspatialindex/libspatialindex-2.0.0-GCCcore-13.3.0.eb @@ -0,0 +1,25 @@ +easyblock = 'CMakeMake' + +name = 'libspatialindex' +version = '2.0.0' + +homepage = 'https://libspatialindex.org' +description = "C++ implementation of R*-tree, an MVR-tree and a TPR-tree with C API" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://github.com/%(name)s/%(name)s/releases/download/%(version)s/'] +sources = ['spatialindex-src-%(version)s.tar.gz'] +checksums = ['f1d5a369681fa6ac3301a54db412ccf3180fc17163ebc3252f32c752f77345de'] + +builddependencies = [ + ('binutils', '2.42'), + ('CMake', '3.29.3'), +] + +sanity_check_paths = { + 'files': ['lib/%s.%s' % (name, SHLIB_EXT)], + 'dirs': ['include/spatialindex'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libtasn1/libtasn1-4.19.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/libtasn1/libtasn1-4.19.0-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..38372984a5f --- /dev/null +++ b/easybuild/easyconfigs/l/libtasn1/libtasn1-4.19.0-GCCcore-12.3.0.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'libtasn1' +version = '4.19.0' + +homepage = 'https://www.gnu.org/software/libtasn1/' +description = """Libtasn1 is the ASN.1 library used by GnuTLS, GNU Shishi and + some other packages. It was written by Fabio Fiorina, and has been shipped as + part of GnuTLS for some time but is now a proper GNU package.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['1613f0ac1cf484d6ec0ce3b8c06d56263cc7242f1c23b30d82d23de345a63f7a'] + +builddependencies = [('binutils', '2.40')] + +sanity_check_paths = { + 'files': ['bin/asn1%s' % x for x in ['Coding', 'Decoding', 'Parser']] + + ['lib/libtasn1.%s' % x for x in ['a', SHLIB_EXT]], + 'dirs': ['include'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libtirpc/libtirpc-1.3.5-GCCcore-13.3.0.eb b/easybuild/easyconfigs/l/libtirpc/libtirpc-1.3.5-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..a9fc2a5d749 --- /dev/null +++ b/easybuild/easyconfigs/l/libtirpc/libtirpc-1.3.5-GCCcore-13.3.0.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'libtirpc' +version = '1.3.5' + +homepage = 'https://sourceforge.net/projects/libtirpc/' +description = "Libtirpc is a port of Suns Transport-Independent RPC library to Linux." + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCE_TAR_BZ2] +checksums = ['9b31370e5a38d3391bf37edfa22498e28fe2142467ae6be7a17c9068ec0bf12f'] + +configopts = '--enable-static --enable-shared --disable-gssapi' + +builddependencies = [ + ('binutils', '2.42') +] + +sanity_check_paths = { + 'files': ['lib/libtirpc.%s' % (x,) for x in ['a', SHLIB_EXT]], + 'dirs': ['include/tirpc', 'lib'], +} + +modextrapaths = {'CPATH': 'include/tirpc'} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libtool/libtool-2.4.7-GCCcore-13.3.0.eb b/easybuild/easyconfigs/l/libtool/libtool-2.4.7-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..ae8cf1bd5b0 --- /dev/null +++ b/easybuild/easyconfigs/l/libtool/libtool-2.4.7-GCCcore-13.3.0.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'libtool' +version = '2.4.7' + +homepage = 'https://www.gnu.org/software/libtool' + +description = """ + GNU libtool is a generic library support script. Libtool hides the complexity + of using shared libraries behind a consistent, portable interface. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['04e96c2404ea70c590c546eba4202a4e12722c640016c12b9b2f1ce3d481e9a8'] + +builddependencies = [ + ('binutils', '2.42'), +] + +dependencies = [ + ('M4', '1.4.19'), +] + +sanity_check_paths = { + 'files': ['bin/libtool', 'bin/libtoolize', 'lib/libltdl.%s' % SHLIB_EXT], + 'dirs': ['include/libltdl', 'share/libtool/loaders', 'share/man/man1'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libunistring/libunistring-1.2-GCCcore-13.3.0.eb b/easybuild/easyconfigs/l/libunistring/libunistring-1.2-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..7fa2f46eb1f --- /dev/null +++ b/easybuild/easyconfigs/l/libunistring/libunistring-1.2-GCCcore-13.3.0.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'libunistring' +version = '1.2' + +homepage = 'https://www.gnu.org/software/libunistring/' + +description = """This library provides functions for manipulating Unicode strings and for + manipulating C strings according to the Unicode standard.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['632bd65ed74a881ca8a0309a1001c428bd1cbd5cd7ddbf8cedcd2e65f4dcdc44'] + +builddependencies = [ + ('binutils', '2.42'), +] + +dependencies = [ + ('libiconv', '1.17'), +] + +parallel = 1 + +sanity_check_paths = { + 'files': ['lib/libunistring.a', 'lib/libunistring.%s' % SHLIB_EXT] + + ['include/uni%s.h' % x for x in ['case', 'conv', 'ctype', 'lbrk', 'name', 'norm', + 'stdio', 'str', 'types', 'wbrk', 'width']], + 'dirs': ['include/unistring'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libunwind/libunwind-1.8.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/l/libunwind/libunwind-1.8.1-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..777376a73ae --- /dev/null +++ b/easybuild/easyconfigs/l/libunwind/libunwind-1.8.1-GCCcore-13.3.0.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'libunwind' +version = '1.8.1' + +homepage = 'https://www.nongnu.org/libunwind/' +description = """The primary goal of libunwind is to define a portable and efficient C programming interface + (API) to determine the call-chain of a program. The API additionally provides the means to manipulate the + preserved (callee-saved) state of each call-frame and to resume execution at any point in the call-chain + (non-local goto). The API supports both local (same-process) and remote (across-process) operation. + As such, the API is useful in a number of applications""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://github.com/libunwind/libunwind/releases/download/v%(version)s/'] +sources = [SOURCE_TAR_GZ] +checksums = ['ddf0e32dd5fafe5283198d37e4bf9decf7ba1770b6e7e006c33e6df79e6a6157'] + +builddependencies = [('binutils', '2.42')] + +dependencies = [ + ('XZ', '5.4.5'), +] + +preconfigopts = 'export LIBS="$LIBS -llzma" && export CFLAGS="$CFLAGS -fno-common" && ' + +sanity_check_paths = { + 'files': ['include/libunwind.h', 'lib/libunwind.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libuv/libuv-1.48.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/libuv/libuv-1.48.0-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..ee537f6dcb3 --- /dev/null +++ b/easybuild/easyconfigs/l/libuv/libuv-1.48.0-GCCcore-12.3.0.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'libuv' +version = '1.48.0' + +homepage = 'https://libuv.org' +description = "libuv is a multi-platform support library with a focus on asynchronous I/O." + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +github_account = 'libuv' +source_urls = [GITHUB_SOURCE] +sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCELOWER_TAR_GZ}] +checksums = ['8c253adb0f800926a6cbd1c6576abae0bc8eb86a4f891049b72f9e5b7dc58f33'] + +builddependencies = [ + ('binutils', '2.40'), + ('Autotools', '20220317'), +] + +preconfigopts = './autogen.sh; ' + +sanity_check_paths = { + 'files': ['include/uv.h', 'lib/libuv.a', 'lib/libuv.%s' % SHLIB_EXT, 'lib/pkgconfig/libuv.pc'], + 'dirs': [] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.3.2-foss-2018b.eb b/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.3.2-foss-2018b.eb index df2d4d407fe..411ee1867d8 100644 --- a/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.3.2-foss-2018b.eb +++ b/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.3.2-foss-2018b.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'libvdwxc' version = '0.3.2' -homepage = 'http://libvdwxc.org' +homepage = 'https://libvdwxc.materialsmodeling.org/' description = """libvdwxc is a general library for evaluating energy and potential for exchange-correlation (XC) functionals from the vdW-DF family that can be used with various of density functional theory (DFT) codes.""" diff --git a/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-foss-2019a.eb b/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-foss-2019a.eb index 99914532433..b750b9a414f 100644 --- a/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-foss-2019a.eb +++ b/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-foss-2019a.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'libvdwxc' version = '0.4.0' -homepage = 'http://libvdwxc.org' +homepage = 'https://libvdwxc.materialsmodeling.org/' description = """libvdwxc is a general library for evaluating energy and potential for exchange-correlation (XC) functionals from the vdW-DF family that can be used with various of density functional theory (DFT) codes.""" diff --git a/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-foss-2019b.eb b/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-foss-2019b.eb index c9f93a8ff91..a04a99002a9 100644 --- a/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-foss-2019b.eb +++ b/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-foss-2019b.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'libvdwxc' version = '0.4.0' -homepage = 'https://libvdwxc.org' +homepage = 'https://libvdwxc.materialsmodeling.org/' description = """libvdwxc is a general library for evaluating energy and potential for exchange-correlation (XC) functionals from the vdW-DF family that can be used with various of density functional theory (DFT) codes.""" diff --git a/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-foss-2020a.eb b/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-foss-2020a.eb index c6769e53157..dd9797af734 100644 --- a/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-foss-2020a.eb +++ b/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-foss-2020a.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'libvdwxc' version = '0.4.0' -homepage = 'https://libvdwxc.org' +homepage = 'https://libvdwxc.materialsmodeling.org/' description = """libvdwxc is a general library for evaluating energy and potential for exchange-correlation (XC) functionals from the vdW-DF family that can be used with various of density functional theory (DFT) codes.""" diff --git a/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-foss-2020b.eb b/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-foss-2020b.eb index 9dee6b6ef26..0e414c5d729 100644 --- a/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-foss-2020b.eb +++ b/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-foss-2020b.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'libvdwxc' version = '0.4.0' -homepage = 'https://libvdwxc.org' +homepage = 'https://libvdwxc.materialsmodeling.org/' description = """libvdwxc is a general library for evaluating energy and potential for exchange-correlation (XC) functionals from the vdW-DF family that can be used with various of density functional theory (DFT) codes.""" diff --git a/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-foss-2021a.eb b/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-foss-2021a.eb index eb7dd54a47d..843a00aaac2 100644 --- a/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-foss-2021a.eb +++ b/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-foss-2021a.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'libvdwxc' version = '0.4.0' -homepage = 'https://libvdwxc.org' +homepage = 'https://libvdwxc.materialsmodeling.org/' description = """libvdwxc is a general library for evaluating energy and potential for exchange-correlation (XC) functionals from the vdW-DF family that can be used with various of density functional theory (DFT) codes.""" diff --git a/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-foss-2021b.eb b/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-foss-2021b.eb index c5a0fad835b..1050fbf314f 100644 --- a/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-foss-2021b.eb +++ b/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-foss-2021b.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'libvdwxc' version = '0.4.0' -homepage = 'https://libvdwxc.org' +homepage = 'https://libvdwxc.materialsmodeling.org/' description = """libvdwxc is a general library for evaluating energy and potential for exchange-correlation (XC) functionals from the vdW-DF family that can be used with various of density functional theory (DFT) codes.""" diff --git a/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-foss-2022a.eb b/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-foss-2022a.eb index b1785ef119b..3b14a5ca707 100644 --- a/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-foss-2022a.eb +++ b/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-foss-2022a.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'libvdwxc' version = '0.4.0' -homepage = 'https://libvdwxc.org' +homepage = 'https://libvdwxc.materialsmodeling.org/' description = """libvdwxc is a general library for evaluating energy and potential for exchange-correlation (XC) functionals from the vdW-DF family that can be used with various of density functional theory (DFT) codes.""" diff --git a/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-foss-2023a.eb b/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-foss-2023a.eb index 9cf45cc3abe..7c8c009c9d0 100644 --- a/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-foss-2023a.eb +++ b/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-foss-2023a.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'libvdwxc' version = '0.4.0' -homepage = 'https://libvdwxc.org' +homepage = 'https://libvdwxc.materialsmodeling.org/' description = """libvdwxc is a general library for evaluating energy and potential for exchange-correlation (XC) functionals from the vdW-DF family that can be used with various of density functional theory (DFT) codes.""" diff --git a/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-foss-2024a.eb b/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-foss-2024a.eb new file mode 100644 index 00000000000..de1dca5e394 --- /dev/null +++ b/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-foss-2024a.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'libvdwxc' +version = '0.4.0' + +homepage = 'https://libvdwxc.materialsmodeling.org/' +description = """libvdwxc is a general library for evaluating energy and potential for +exchange-correlation (XC) functionals from the vdW-DF family that can be used with various +of density functional theory (DFT) codes.""" + +toolchain = {'name': 'foss', 'version': '2024a'} + +source_urls = ['https://launchpad.net/libvdwxc/stable/%(version)s/+download/'] +sources = [SOURCE_TAR_GZ] +checksums = ['3524feb5bb2be86b4688f71653502146b181e66f3f75b8bdaf23dd1ae4a56b33'] + +preconfigopts = 'unset CC && unset FC && ' + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['libvdwxc_fdtest', 'libvdwxc_maintest', + 'libvdwxc_q0test', 'libvdwxc_q0test2']] + + ['lib/lib%s.%s' % (x, y) for x in ['vdwxc', 'vdwxcfort'] + for y in ['a', SHLIB_EXT]], + 'dirs': ['include'], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-intel-2020b.eb b/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-intel-2020b.eb index 751488a0728..a610d3ec773 100644 --- a/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-intel-2020b.eb +++ b/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-intel-2020b.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'libvdwxc' version = '0.4.0' -homepage = 'https://libvdwxc.org' +homepage = 'https://libvdwxc.materialsmodeling.org/' description = """libvdwxc is a general library for evaluating energy and potential for exchange-correlation (XC) functionals from the vdW-DF family that can be used with various of density functional theory (DFT) codes.""" diff --git a/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-intel-2021a.eb b/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-intel-2021a.eb index cdc3abd5a19..e137148b85c 100644 --- a/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-intel-2021a.eb +++ b/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-intel-2021a.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'libvdwxc' version = '0.4.0' -homepage = 'https://libvdwxc.org' +homepage = 'https://libvdwxc.materialsmodeling.org/' description = """libvdwxc is a general library for evaluating energy and potential for exchange-correlation (XC) functionals from the vdW-DF family that can be used with various of density functional theory (DFT) codes.""" diff --git a/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-intel-2021b.eb b/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-intel-2021b.eb index c8c0d2a8644..5df0f660f1d 100644 --- a/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-intel-2021b.eb +++ b/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-intel-2021b.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'libvdwxc' version = '0.4.0' -homepage = 'https://libvdwxc.org' +homepage = 'https://libvdwxc.materialsmodeling.org/' description = """libvdwxc is a general library for evaluating energy and potential for exchange-correlation (XC) functionals from the vdW-DF family that can be used with various of density functional theory (DFT) codes.""" diff --git a/easybuild/easyconfigs/l/libvips/libvips-8.15.2-GCC-12.3.0.eb b/easybuild/easyconfigs/l/libvips/libvips-8.15.2-GCC-12.3.0.eb new file mode 100644 index 00000000000..088bc0e8299 --- /dev/null +++ b/easybuild/easyconfigs/l/libvips/libvips-8.15.2-GCC-12.3.0.eb @@ -0,0 +1,49 @@ +easyblock = 'MesonNinja' + +name = 'libvips' +version = '8.15.2' + +homepage = 'https://github.com/libvips/libvips' +description = 'libvips is a demand-driven, horizontally threaded image processing library.' + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +github_account = 'libvips' +source_urls = [GITHUB_LOWER_SOURCE] +sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}] +checksums = ['8c3ece7be367636fd676573a8ff22170c07e95e81fd94f2d1eb9966800522e1f'] + +builddependencies = [ + ('Meson', '1.1.1'), + ('Ninja', '1.11.1'), + ('pkgconf', '1.9.5'), +] + +dependencies = [ + ('GLib', '2.77.1'), + ('expat', '2.5.0'), + ('libjpeg-turbo', '2.1.5.1'), + ('FFTW', '3.3.10'), + ('libarchive', '3.6.2'), + ('libpng', '1.6.39'), + ('ImageMagick', '7.1.1-15'), + ('Highway', '1.0.4'), + ('MATIO', '1.5.26'), + ('libwebp', '1.3.1'), + ('CFITSIO', '4.3.0'), + ('OpenEXR', '3.1.7'), + ('OpenJPEG', '2.5.0'), + ('OpenSlide', '3.4.1', '-largefiles', ('GCCcore', '12.3.0')), +] + +runtest = 'meson test' +testopts = '' + +sanity_check_paths = { + 'files': ['bin/vips', 'include/vips/vips.h'], + 'dirs': ['share'], +} + +sanity_check_commands = ['vips --help'] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libvorbis/libvorbis-1.3.7-GCCcore-13.2.0.eb b/easybuild/easyconfigs/l/libvorbis/libvorbis-1.3.7-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..50a45ea05a1 --- /dev/null +++ b/easybuild/easyconfigs/l/libvorbis/libvorbis-1.3.7-GCCcore-13.2.0.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'libvorbis' +version = '1.3.7' + +homepage = 'https://xiph.org/vorbis/' +description = """Ogg Vorbis is a fully open, non-proprietary, patent-and-royalty-free, general-purpose compressed +audio format""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://ftp.osuosl.org/pub/xiph/releases/vorbis/'] +sources = [SOURCE_TAR_XZ] +checksums = ['b33cc4934322bcbf6efcbacf49e3ca01aadbea4114ec9589d1b1e9d20f72954b'] + +builddependencies = [ + ('binutils', '2.40'), + ('pkgconf', '2.0.3'), +] + +dependencies = [('libogg', '1.3.5')] + +configopts = '--enable-static --enable-shared' + +sanity_check_paths = { + 'files': ['lib/libvorbis.a', 'lib/libvorbis.%s' % SHLIB_EXT], + 'dirs': ['include/vorbis'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libvorbis/libvorbis-1.3.7-GCCcore-13.3.0.eb b/easybuild/easyconfigs/l/libvorbis/libvorbis-1.3.7-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..7e32c5c3a99 --- /dev/null +++ b/easybuild/easyconfigs/l/libvorbis/libvorbis-1.3.7-GCCcore-13.3.0.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'libvorbis' +version = '1.3.7' + +homepage = 'https://xiph.org/vorbis/' +description = """Ogg Vorbis is a fully open, non-proprietary, patent-and-royalty-free, general-purpose compressed +audio format""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://ftp.osuosl.org/pub/xiph/releases/vorbis/'] +sources = [SOURCE_TAR_XZ] +checksums = ['b33cc4934322bcbf6efcbacf49e3ca01aadbea4114ec9589d1b1e9d20f72954b'] + +builddependencies = [ + ('binutils', '2.42'), + ('pkgconf', '2.2.0'), +] + +dependencies = [('libogg', '1.3.5')] + +configopts = '--enable-static --enable-shared' + +sanity_check_paths = { + 'files': ['lib/libvorbis.a', 'lib/libvorbis.%s' % SHLIB_EXT], + 'dirs': ['include/vorbis'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libwebp/libwebp-1.3.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/libwebp/libwebp-1.3.1-GCCcore-12.3.0.eb index 4ac82164e4b..7a8453a029c 100644 --- a/easybuild/easyconfigs/l/libwebp/libwebp-1.3.1-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/l/libwebp/libwebp-1.3.1-GCCcore-12.3.0.eb @@ -10,6 +10,7 @@ webmasters and web developers can create smaller, richer images that make the web faster.""" toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +toolchainopts = {'pic': True} source_urls = ['https://storage.googleapis.com/downloads.webmproject.org/releases/webp'] sources = [SOURCELOWER_TAR_GZ] diff --git a/easybuild/easyconfigs/l/libwebp/libwebp-1.4.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/l/libwebp/libwebp-1.4.0-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..70084689c61 --- /dev/null +++ b/easybuild/easyconfigs/l/libwebp/libwebp-1.4.0-GCCcore-13.3.0.eb @@ -0,0 +1,45 @@ +easyblock = 'ConfigureMake' + +name = 'libwebp' +version = '1.4.0' + +homepage = 'https://developers.google.com/speed/webp/' +description = """WebP is a modern image format that provides superior +lossless and lossy compression for images on the web. Using WebP, +webmasters and web developers can create smaller, richer images that +make the web faster.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://storage.googleapis.com/downloads.webmproject.org/releases/webp'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['61f873ec69e3be1b99535634340d5bde750b2e4447caa1db9f61be3fd49ab1e5'] + +builddependencies = [ + ('binutils', '2.42'), +] +dependencies = [ + ('libjpeg-turbo', '3.0.1'), + ('libpng', '1.6.43'), + ('LibTIFF', '4.6.0'), + ('giflib', '5.2.1'), +] + +configopts = '--enable-libwebpmux' + +local_headers, local_libs = ( + ['decode.h', 'demux.h', 'encode.h', 'mux.h', 'mux_types.h', 'types.h'], + ['webp', 'webpdemux', 'webpmux'] +) + +sanity_check_paths = { + 'files': ( + ['include/webp/%s' % h for h in local_headers] + + ['lib/lib%s.a' % s for s in local_libs] + + ['lib/lib%s.%s' % (s, SHLIB_EXT) for s in local_libs] + ), + 'dirs': ['lib/'] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxc/libxc-6.2.2-GCC-13.2.0-nofhc.eb b/easybuild/easyconfigs/l/libxc/libxc-6.2.2-GCC-13.2.0-nofhc.eb new file mode 100644 index 00000000000..709703f2949 --- /dev/null +++ b/easybuild/easyconfigs/l/libxc/libxc-6.2.2-GCC-13.2.0-nofhc.eb @@ -0,0 +1,53 @@ +easyblock = 'CMakeMake' + +name = 'libxc' +version = '6.2.2' +versionsuffix = '-nofhc' + +homepage = 'https://libxc.gitlab.io' +description = """Libxc is a library of exchange-correlation functionals for density-functional theory. + The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" + +toolchain = {'name': 'GCC', 'version': '13.2.0'} + +source_urls = ['https://gitlab.com/libxc/libxc/-/archive/%(version)s/'] +sources = [SOURCE_TAR_GZ] +checksums = [('a0f6f1bba7ba5c0c85b2bfe65aca1591025f509a7f11471b4cd651a79491b045', + '3b0523924579cf494cafc6fea92945257f35692b004217d3dfd3ea7ca780e8dc')] + +builddependencies = [ + ('CMake', '3.27.6'), + ('Perl', '5.38.0'), +] + +local_common_configopts = "-DENABLE_FORTRAN=ON -DENABLE_XHOST=OFF " + +# don't disable building of third and fourth derivates, since it's required by some software that depends on libxc +# (like ABINIT, which requires "3rd derivatives of energy") +# see also https://github.com/pyscf/pyscf/issues/1103 +local_common_configopts += "-DDISABLE_KXC=OFF -DDISABLE_LXC=OFF" + +# Disable fhc, this needs to support codes (like VASP) relying on the projector augmented wave (PAW) approach +local_common_configopts += ' -DDISABLE_FHC=ON' + +# perform iterative build to get both static and shared libraries +configopts = [ + local_common_configopts + ' -DBUILD_SHARED_LIBS=OFF', + local_common_configopts + ' -DBUILD_SHARED_LIBS=ON', +] + +# make sure that built libraries (libxc*.so*) in build directory are picked when running tests +# this is required when RPATH linking is used +pretestopts = "export LD_LIBRARY_PATH=%(builddir)s/easybuild_obj:$LD_LIBRARY_PATH && " + +runtest = 'test' + +sanity_check_paths = { + 'files': ['bin/xc-info'] + + ['lib/libxc%s.%s' % (x, y) for x in ['', 'f03', 'f90'] for y in ['a', SHLIB_EXT]], + 'dirs': ['include', 'lib/pkgconfig', 'lib/cmake/Libxc'], +} + +sanity_check_commands = ['xc-info 1'] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/libxc/libxc-6.2.2-GCC-13.3.0.eb b/easybuild/easyconfigs/l/libxc/libxc-6.2.2-GCC-13.3.0.eb new file mode 100644 index 00000000000..9e4de5e8082 --- /dev/null +++ b/easybuild/easyconfigs/l/libxc/libxc-6.2.2-GCC-13.3.0.eb @@ -0,0 +1,52 @@ +easyblock = 'CMakeMake' + +name = 'libxc' +version = '6.2.2' + +homepage = 'https://libxc.gitlab.io' +description = """Libxc is a library of exchange-correlation functionals for density-functional theory. + The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" + +toolchain = {'name': 'GCC', 'version': '13.3.0'} + +source_urls = ['https://gitlab.com/%(name)s/%(name)s/-/archive/%(version)s/'] +sources = [SOURCE_TAR_GZ] +checksums = [ + ('a0f6f1bba7ba5c0c85b2bfe65aca1591025f509a7f11471b4cd651a79491b045', + '3b0523924579cf494cafc6fea92945257f35692b004217d3dfd3ea7ca780e8dc', + 'd1b65ef74615a1e539d87a0e6662f04baf3a2316706b4e2e686da3193b26b20f'), +] + +builddependencies = [ + ('CMake', '3.29.3'), + ('Perl', '5.38.2'), +] + +local_common_configopts = "-DENABLE_FORTRAN=ON -DENABLE_XHOST=OFF " + +# don't disable building of third and fourth derivates, since it's required by some software that depends on libxc +# (like ABINIT, which requires "3rd derivatives of energy") +# see also https://github.com/pyscf/pyscf/issues/1103 +local_common_configopts += "-DDISABLE_KXC=OFF -DDISABLE_LXC=OFF" + +# perform iterative build to get both static and shared libraries +configopts = [ + local_common_configopts + ' -DBUILD_SHARED_LIBS=OFF', + local_common_configopts + ' -DBUILD_SHARED_LIBS=ON', +] + +# make sure that built libraries (libxc*.so*) in build directory are picked when running tests +# this is required when RPATH linking is used +pretestopts = "export LD_LIBRARY_PATH=%(builddir)s/easybuild_obj:$LD_LIBRARY_PATH && " + +runtest = 'test' + +sanity_check_paths = { + 'files': ['bin/xc-info'] + + ['lib/libxc%s.%s' % (x, y) for x in ['', 'f03', 'f90'] for y in ['a', SHLIB_EXT]], + 'dirs': ['include', 'lib/pkgconfig', 'lib/cmake/Libxc'], +} + +sanity_check_commands = ['xc-info 1'] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.12.7-GCCcore-13.3.0.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.12.7-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..a8a21aceaa9 --- /dev/null +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.12.7-GCCcore-13.3.0.eb @@ -0,0 +1,27 @@ +name = 'libxml2' +version = '2.12.7' + +homepage = 'http://xmlsoft.org/' + +description = """ + Libxml2 is the XML C parser and toolchain developed for the Gnome project + (but usable outside of the Gnome platform). +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://download.gnome.org/sources/libxml2/%(version_major_minor)s/'] +sources = [SOURCE_TAR_XZ] +checksums = ['24ae78ff1363a973e6d8beba941a7945da2ac056e19b53956aeb6927fd6cfb56'] + +builddependencies = [ + ('binutils', '2.42'), +] + +dependencies = [ + ('XZ', '5.4.5'), + ('zlib', '1.3.1'), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.13.4-GCCcore-14.2.0.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.13.4-GCCcore-14.2.0.eb new file mode 100644 index 00000000000..5b194eb5a3b --- /dev/null +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.13.4-GCCcore-14.2.0.eb @@ -0,0 +1,27 @@ +name = 'libxml2' +version = '2.13.4' + +homepage = 'http://xmlsoft.org/' + +description = """ + Libxml2 is the XML C parser and toolchain developed for the Gnome project + (but usable outside of the Gnome platform). +""" + +toolchain = {'name': 'GCCcore', 'version': '14.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://download.gnome.org/sources/libxml2/%(version_major_minor)s/'] +sources = [SOURCE_TAR_XZ] +checksums = ['65d042e1c8010243e617efb02afda20b85c2160acdbfbcb5b26b80cec6515650'] + +builddependencies = [ + ('binutils', '2.42'), +] + +dependencies = [ + ('XZ', '5.6.3'), + ('zlib', '1.3.1'), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxslt/libxslt-1.1.42-GCCcore-13.3.0.eb b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.42-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..a38c53ef841 --- /dev/null +++ b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.42-GCCcore-13.3.0.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'libxslt' +version = '1.1.42' + +homepage = 'http://xmlsoft.org/' +description = """Libxslt is the XSLT C library developed for the GNOME project + (but usable outside of the Gnome platform).""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://download.gnome.org/sources/libxslt/%(version_major_minor)s/'] +sources = [SOURCE_TAR_XZ] +checksums = ['85ca62cac0d41fc77d3f6033da9df6fd73d20ea2fc18b0a3609ffb4110e1baeb'] + +builddependencies = [ + ('binutils', '2.42'), + ('pkgconf', '2.2.0'), +] + +dependencies = [ + ('zlib', '1.3.1'), + ('libxml2', '2.12.7'), +] + +# Make sure it doesn't pick up OS installed libgcrypt or Python +# enable building static libs +configopts = '--with-crypto=no --with-python=no --enable-static=yes ' + +sanity_check_paths = { + 'files': ['bin/xsltproc', 'include/libxslt/xslt.h', 'lib/%%(name)s.%s' % SHLIB_EXT, 'lib/%(name)s.a', + 'lib/libexslt.%s' % SHLIB_EXT, 'lib/libexslt.a'], + 'dirs': ['include/libxslt', 'include/libexslt'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libyaml/libyaml-0.2.5-GCCcore-13.3.0.eb b/easybuild/easyconfigs/l/libyaml/libyaml-0.2.5-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..4b2e8e66632 --- /dev/null +++ b/easybuild/easyconfigs/l/libyaml/libyaml-0.2.5-GCCcore-13.3.0.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'libyaml' +version = '0.2.5' + +homepage = 'https://pyyaml.org/wiki/LibYAML' +description = "LibYAML is a YAML parser and emitter written in C." + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://pyyaml.org/download/%(name)s/'] +sources = ['yaml-%(version)s.tar.gz'] +checksums = ['c642ae9b75fee120b2d96c712538bd2cf283228d2337df2cf2988e3c02678ef4'] + +builddependencies = [ + ('binutils', '2.42'), +] + + +sanity_check_paths = { + 'files': ['include/yaml.h', 'lib/libyaml.a', 'lib/libyaml.%s' % SHLIB_EXT], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libzip/libzip-1.10.1-GCCcore-13.2.0.eb b/easybuild/easyconfigs/l/libzip/libzip-1.10.1-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..99551efad57 --- /dev/null +++ b/easybuild/easyconfigs/l/libzip/libzip-1.10.1-GCCcore-13.2.0.eb @@ -0,0 +1,44 @@ +easyblock = 'CMakeMake' + +name = 'libzip' +version = '1.10.1' + +homepage = 'https://libzip.org/' +description = "libzip is a C library for reading, creating, and modifying zip archives." + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://github.com/nih-at/libzip/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['d56d857d1c3ad4a7f3a4c01a51c6a6e5530e35ab93503f62276e8ba2b306186a'] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.27.6'), +] + +dependencies = [ + ('OpenSSL', '1.1', '', SYSTEM), + ('zlib', '1.2.13'), + ('bzip2', '1.0.8'), + ('XZ', '5.4.4'), + ('zstd', '1.5.5'), +] + +sanity_check_paths = { + 'files': [ + 'bin/zipcmp', + 'bin/zipmerge', + 'bin/ziptool', + 'lib64/libzip.%s' % SHLIB_EXT, + ], + 'dirs': ['include', 'lib/pkgconfig'], +} + +sanity_check_commands = [ + "zipcmp -h", + "zipmerge -h", + "ziptool -h" +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/likwid/likwid-5.3.0-GCC-13.3.0.eb b/easybuild/easyconfigs/l/likwid/likwid-5.3.0-GCC-13.3.0.eb new file mode 100644 index 00000000000..b9d22fc36dc --- /dev/null +++ b/easybuild/easyconfigs/l/likwid/likwid-5.3.0-GCC-13.3.0.eb @@ -0,0 +1,54 @@ +easyblock = 'ConfigureMake' + +name = 'likwid' +version = '5.3.0' + +homepage = 'https://github.com/RRZE-HPC/likwid' + +description = """ +Likwid stands for Like I knew what I am doing. This project contributes easy +to use command line tools for Linux to support programmers in developing high +performance multi threaded programs. +""" + +toolchain = {'name': 'GCC', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/RRZE-HPC/%(name)s/archive/'] +sources = ['v%(version)s.tar.gz'] + +checksums = ['c290e554c4253124ac2ab8b056e14ee4d23966b8c9fbfa10ba81f75ae543ce4e'] + +builddependencies = [ + ('Perl', '5.38.2'), +] +dependencies = [ + ('hwloc', '2.10.0'), +] + +skipsteps = ['configure'] + +# include_GCC.mk is using ifort by default. +# Changing it to gfortran, to be consistent with GCC toolchain +prebuildopts = """sed -i 's@FC = ifort@FC = gfortran@g' make/include_GCC.mk && """ +prebuildopts += """sed -i 's@FCFLAGS = -module ./ # ifort@FCFLAGS = -J ./ -fsyntax-only #gfortran@g' """ +prebuildopts += """ make/include_GCC.mk && """ + +buildopts = 'CC="$CC" CFLAGS="$CFLAGS -std=c99" PREFIX=%(installdir)s BUILDFREQ="" ACCESSMODE=perf_event ' +buildopts += 'FORTRAN_INTERFACE=true ' +buildopts += 'CFG_FILE_PATH=%(installdir)s/etc/likwid.cfg TOPO_FILE_PATH=%(installdir)s/etc/likwid_topo.cfg ' +buildopts += 'HWLOC_INCLUDE_DIR=$EBROOTHWLOC/include HWLOC_LIB_DIR=$EBROOTHWLOC/lib HWLOC_LIB_NAME=hwloc ' + +maxparallel = 1 + +installopts = buildopts + 'INSTALL_CHOWN="" ' + +sanity_check_paths = { + 'files': ['bin/likwid-memsweeper', 'bin/likwid-mpirun', 'bin/likwid-perfctr', + 'bin/likwid-perfscope', 'bin/likwid-pin', 'bin/likwid-powermeter', + 'bin/likwid-topology', 'lib/liblikwidpin.%s' % SHLIB_EXT, + 'lib/liblikwid.%s' % SHLIB_EXT, 'include/likwid.mod'], + 'dirs': ['man/man1'] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/l/lil-aretomo/lil-aretomo-0.1.1-foss-2023a.eb b/easybuild/easyconfigs/l/lil-aretomo/lil-aretomo-0.1.1-foss-2023a.eb new file mode 100644 index 00000000000..121e49d9047 --- /dev/null +++ b/easybuild/easyconfigs/l/lil-aretomo/lil-aretomo-0.1.1-foss-2023a.eb @@ -0,0 +1,33 @@ +# Thomas Hoffmann, EMBL Heidelberg, structures-it@embl.de, 2024/05 +easyblock = 'PythonBundle' + +name = 'lil-aretomo' +version = '0.1.1' + +homepage = 'https://github.com/teamtomo/lil-aretomo' +description = """ +A lightweight Python API for AreTomo. +""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('mrcfile', '1.5.0'), + ('SciPy-bundle', '2023.07'), +] + +use_pip = True + +exts_list = [ + ('typer', '0.9.0', { + 'checksums': ['50922fd79aea2f4751a8e0408ff10d2662bd0c8bbfa84755a699f3bada2978b2'], + }), + ('lil_aretomo', version, { + 'checksums': ['02ccb0efbf2c06304570117f142e78331bfffdde46864e22de11c6cd7f30f178'], + }), +] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/l/line_profiler/line_profiler-4.1.2-GCCcore-13.2.0.eb b/easybuild/easyconfigs/l/line_profiler/line_profiler-4.1.2-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..b5f689a928f --- /dev/null +++ b/easybuild/easyconfigs/l/line_profiler/line_profiler-4.1.2-GCCcore-13.2.0.eb @@ -0,0 +1,41 @@ +easyblock = 'PythonPackage' + +name = 'line_profiler' +version = '4.1.2' + +homepage = 'https://github.com/pyutils/line_profiler' +description = """line_profiler is a module for doing line-by-line profiling +of functions. kernprof is a convenient script for running either +line_profiler or the Python standard library's cProfile or profile modules, +depending on what is available.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +github_account = 'pyutils' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['a1f3458c1dd1bf4b2d1d2657b78225f4e4e9046a1841f18cf528f01ebd3d5f43'] + +builddependencies = [ + ('binutils', '2.40'), + ('scikit-build', '0.17.6'), + ('CMake', '3.27.6'), + ('Ninja', '1.11.1'), +] +dependencies = [ + ('Python', '3.11.5'), + ('IPython', '8.17.2'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/kernprof'], + 'dirs': [], +} + +sanity_check_commands = ['kernprof --help'] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/l/longread_umi/longread_umi-0.3.2-foss-2023a.eb b/easybuild/easyconfigs/l/longread_umi/longread_umi-0.3.2-foss-2023a.eb new file mode 100644 index 00000000000..03393fb1618 --- /dev/null +++ b/easybuild/easyconfigs/l/longread_umi/longread_umi-0.3.2-foss-2023a.eb @@ -0,0 +1,84 @@ +easyblock = 'Bundle' + +name = 'longread_umi' +version = '0.3.2' + +homepage = 'https://github.com/SorenKarst/longread_umi' +description = "A collection of scripts for processing longread UMI data." +github_account = 'SorenKarst' + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('cutadapt', '4.9'), + ('BCFtools', '1.18'), + ('BWA', '0.7.17'), + ('Filtlong', '0.2.1'), + ('gawk', '5.3.0'), + ('medaka', '1.11.3'), + ('minimap2', '2.26'), + ('parallel', '20230722'), + ('Pysam', '0.22.0'), + ('Racon', '1.5.0'), + ('SAMtools', '1.18'), + ('seqtk', '1.4'), + ('VSEARCH', '2.25.0'), +] + +components = [ + (name, version, { + 'easyblock': 'Tarball', + 'source_urls': [GITHUB_LOWER_SOURCE], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}], + 'checksums': ['62b8e156c00c0ec10fa8eae1cde5430922462f167fc537417ce0b47cd50a20cb'], + 'start_dir': '%(name)s-%(version)s', + }), + # PythonPackage executes Bundle-level postinstallcmds for some reason, + # which rely on both components being installed, so Porechop is installed second + ('Porechop', '0.2.4', { + 'easyblock': 'PythonPackage', + 'source_urls': ['https://github.com/rrwick/Porechop/archive'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}], + 'checksums': ['44b499157d933be43f702cec198d1d693dcb9276e3c545669be63c2612493299'], + 'start_dir': '%(name)s-%(version)s', + 'use_pip': True, + 'download_dep_fail': True, + 'sanity_pip_check': True, + }), +] + +# Adapt the built-in tool check but make it fail on error, replace usearch with vsearch and use our version +local_deps_patch = ( + "sed -i " + "-e '2s;^;set -e ;' " + "-e 's/USEARCH=usearch/USEARCH=vsearch/' " + "-e 's;$(git --git-dir ${LONGREAD_UMI_PATH}/.git describe --tag);%(version)s;' " + "%(installdir)s/scripts/dependencies.sh" +) + +postinstallcmds = [ + 'find %(installdir)s -name "*.sh" -exec chmod +x {} \\;', + 'ln -s %(installdir)s/longread_umi.sh %(installdir)s/bin/longread_umi', + # Part of the installation process; longread uses porechop with custom adapters + 'cp %(installdir)s/scripts/adapters.py %(installdir)s/lib/python%(pyshortver)s/site-packages/porechop/', + local_deps_patch, + # -minsize option not supported by 'vsearch -cluster_fast', and probably not needed + "sed -i 's/-minsize 1//g' %(installdir)s/scripts/umi_binning.sh", +] + +sanity_check_paths = { + 'files': ['bin/longread_umi'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} +sanity_check_commands = [ + 'longread_umi -h | grep qc_pipeline', + 'longread_umi nanopore_pipeline -h | grep rrna_operon', + 'source %(installdir)s/scripts/dependencies.sh && longread_umi_version_dump', +] + +modextrapaths = { + 'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages'] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/l/lpsolve/lpsolve-5.5.2.11-GCC-12.3.0.eb b/easybuild/easyconfigs/l/lpsolve/lpsolve-5.5.2.11-GCC-12.3.0.eb new file mode 100644 index 00000000000..7681d5bf0a9 --- /dev/null +++ b/easybuild/easyconfigs/l/lpsolve/lpsolve-5.5.2.11-GCC-12.3.0.eb @@ -0,0 +1,33 @@ +easyblock = 'CmdCp' + +name = 'lpsolve' +version = '5.5.2.11' + +homepage = 'https://sourceforge.net/projects/lpsolve/' +description = "Mixed Integer Linear Programming (MILP) solver" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['lp_solve_%(version)s_source.tar.gz'] +checksums = ['6d4abff5cc6aaa933ae8e6c17a226df0fc0b671c438f69715d41d09fe81f902f'] + +local_lpsolve_ver = '%(version_major)s%(version_minor)s' +start_dir = 'lpsolve%s' % local_lpsolve_ver + +local_comp_cmd = 'sed -i "s/^c=.*/c=\'$CC\'/g" ccc && sed -i "s/^opts=.*/opts=\'$CFLAGS\'/g" ccc && ' +local_comp_cmd += "sh ccc" +cmds_map = [('.*', local_comp_cmd)] + +local_lpsolve_libname = 'liblpsolve%s' % local_lpsolve_ver +files_to_copy = [ + (['bin/ux64/%s.a' % local_lpsolve_libname, 'bin/ux64/%s.%s' % (local_lpsolve_libname, SHLIB_EXT)], 'lib'), + (['../lp*.h'], 'include'), +] + +sanity_check_paths = { + 'files': ['lib/%s.a' % local_lpsolve_libname, 'lib/%s.%s' % (local_lpsolve_libname, SHLIB_EXT)], + 'dirs': ['include'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/l/lpsolve/lpsolve-5.5.2.11-GCC-13.2.0.eb b/easybuild/easyconfigs/l/lpsolve/lpsolve-5.5.2.11-GCC-13.2.0.eb new file mode 100644 index 00000000000..03ed0716827 --- /dev/null +++ b/easybuild/easyconfigs/l/lpsolve/lpsolve-5.5.2.11-GCC-13.2.0.eb @@ -0,0 +1,33 @@ +easyblock = 'CmdCp' + +name = 'lpsolve' +version = '5.5.2.11' + +homepage = 'https://sourceforge.net/projects/lpsolve/' +description = "Mixed Integer Linear Programming (MILP) solver" + +toolchain = {'name': 'GCC', 'version': '13.2.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['lp_solve_%(version)s_source.tar.gz'] +checksums = ['6d4abff5cc6aaa933ae8e6c17a226df0fc0b671c438f69715d41d09fe81f902f'] + +local_lpsolve_ver = '%(version_major)s%(version_minor)s' +start_dir = 'lpsolve%s' % local_lpsolve_ver + +local_comp_cmd = 'sed -i "s/^c=.*/c=\'$CC\'/g" ccc && sed -i "s/^opts=.*/opts=\'$CFLAGS\'/g" ccc && ' +local_comp_cmd += "sh ccc" +cmds_map = [('.*', local_comp_cmd)] + +local_lpsolve_libname = 'liblpsolve%s' % local_lpsolve_ver +files_to_copy = [ + (['bin/ux64/%s.a' % local_lpsolve_libname, 'bin/ux64/%s.%s' % (local_lpsolve_libname, SHLIB_EXT)], 'lib'), + (['../lp*.h'], 'include'), +] + +sanity_check_paths = { + 'files': ['lib/%s.a' % local_lpsolve_libname, 'lib/%s.%s' % (local_lpsolve_libname, SHLIB_EXT)], + 'dirs': ['include'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/l/lrcalc/lrcalc-2.1-GCCcore-13.2.0.eb b/easybuild/easyconfigs/l/lrcalc/lrcalc-2.1-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..aa14572bef6 --- /dev/null +++ b/easybuild/easyconfigs/l/lrcalc/lrcalc-2.1-GCCcore-13.2.0.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'lrcalc' +version = '2.1' + +homepage = 'https://sites.math.rutgers.edu/~asbuch/lrcalc/' +description = """The Littlewood-Richardson Calculator is a program + designed to compute Littlewood-Richardson coefficients.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://math.rutgers.edu/~asbuch/lrcalc/'] +sources = [SOURCE_TAR_GZ] +checksums = ['996ac00e6ea8321ef09b34478f5379f613933c3254aeba624b6419b8afa5df57'] + +builddependencies = [ + ('binutils', '2.40'), +] + +sanity_check_paths = { + 'files': [ + 'bin/lrcalc', + 'lib/liblrcalc.%s' % SHLIB_EXT, + 'include/lrcalc/ivector.h', + ], + 'dirs': [] +} + +sanity_check_commands = ["lrcalc 2>&1 | grep '^Usage:'"] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/l/lrslib/lrslib-7.2-gompi-2023b.eb b/easybuild/easyconfigs/l/lrslib/lrslib-7.2-gompi-2023b.eb new file mode 100644 index 00000000000..ba6714df325 --- /dev/null +++ b/easybuild/easyconfigs/l/lrslib/lrslib-7.2-gompi-2023b.eb @@ -0,0 +1,41 @@ +easyblock = 'ConfigureMake' + +name = 'lrslib' +version = '7.2' + +homepage = 'http://cgm.cs.mcgill.ca/~avis/C/lrs.html' +description = """lrslib is a self-contained ANSI C implementation of the +reverse search algorithm for vertex enumeration/convex hull problems""" + +toolchain = {'name': 'gompi', 'version': '2023b'} +toolchainopts = {'usempi': True, 'pic': True} + +source_urls = ['http://cgm.cs.mcgill.ca/~avis/C/lrslib/archive/'] +sources = ['lrslib-0%(version_major)s%(version_minor)s.tar.gz'] +patches = ['lrslib-%(version)s-use-EB-values.patch'] +checksums = [ + {'lrslib-072.tar.gz': 'fc48754a1ded1d8445d40ecfbe3546e4f27d53aaee95dc2c8c0c79fb9cd532f0'}, + {'lrslib-7.2-use-EB-values.patch': '16b0b4d987a751a45c7961bb7e0cb12aac50410a562dab3299335186456ab2ad'}, +] + +dependencies = [ + ('GMP', '6.3.0'), +] + +skipsteps = ['configure'] + +# Default built plus mplrs +buildopts = 'lrs lrsgmp mplrs CFLAGS="$CFLAGS"' + +installopts = 'prefix=%(installdir)s' + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['lrs', 'lrsnash']] + + ['include/lrslib/lrs%s.h' % h for h in ['driver', 'gmp', 'lib', 'long', 'mp', 'restart']] + + ['lib/liblrs.%s' % SHLIB_EXT], + 'dirs': [] +} + +sanity_check_commands = ["lrsnash --help 2>&1 | grep 'usage.*lrsnash'"] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/l/lwgrp/lwgrp-1.0.6-gompi-2024a.eb b/easybuild/easyconfigs/l/lwgrp/lwgrp-1.0.6-gompi-2024a.eb new file mode 100644 index 00000000000..c36ee58b273 --- /dev/null +++ b/easybuild/easyconfigs/l/lwgrp/lwgrp-1.0.6-gompi-2024a.eb @@ -0,0 +1,36 @@ +# +# Author: Robert Mijakovic +# +easyblock = 'ConfigureMake' + +name = 'lwgrp' +version = '1.0.6' + +homepage = 'https://github.com/LLNL/lwgrp' +description = """The light-weight group library defines data structures and collective operations to +group MPI processes as an ordered set. Such groups are useful as substitutes for MPI communicators +when the overhead of communicator creation is too costly. For example, certain sorting algorithms +recursively divide processes into subgroups as the sort algorithm progresses. These groups may be +different with each invocation, so that it is inefficient to create and destroy communicators during +the sort routine.""" + +toolchain = {'name': 'gompi', 'version': '2024a'} + +github_account = 'LLNL' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['108e622441028b7f88223244c9117d5de18a91fd7c246bfa48802b5c585557d0'] + +builddependencies = [ + ('Autotools', '20231222'), + ('pkgconf', '2.2.0'), +] + +preconfigopts = './autogen.sh && ' + +sanity_check_paths = { + 'files': ['include/%(name)s.h', 'lib/lib%%(name)s.%s' % SHLIB_EXT], + 'dirs': ['share/%(name)s'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/lxml/lxml-5.3.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/l/lxml/lxml-5.3.0-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..0af2dcbed3f --- /dev/null +++ b/easybuild/easyconfigs/l/lxml/lxml-5.3.0-GCCcore-13.3.0.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonPackage' + +name = 'lxml' +version = '5.3.0' + +homepage = 'https://lxml.de/' +description = """The lxml XML toolkit is a Pythonic binding for the C libraries libxml2 and libxslt.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['4e109ca30d1edec1ac60cdbe341905dc3b8f55b16855e03a54aaf59e51ec8c6f'] + +builddependencies = [ + ('binutils', '2.42'), +] + +dependencies = [ + ('Python', '3.12.3'), + ('libxml2', '2.12.7'), + ('libxslt', '1.1.42'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/lz4/lz4-1.9.4-GCCcore-13.3.0.eb b/easybuild/easyconfigs/l/lz4/lz4-1.9.4-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..8f4914fbdde --- /dev/null +++ b/easybuild/easyconfigs/l/lz4/lz4-1.9.4-GCCcore-13.3.0.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'lz4' +version = '1.9.4' + +homepage = 'https://lz4.github.io/lz4/' +description = """LZ4 is lossless compression algorithm, providing compression speed at 400 MB/s per core. + It features an extremely fast decoder, with speed in multiple GB/s per core.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +github_account = '%(name)s' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['0b0e3aa07c8c063ddf40b082bdf7e37a1562bda40a0ff5272957f3e987e0e54b'] + +builddependencies = [('binutils', '2.42')] + +skipsteps = ['configure'] + +installopts = "PREFIX=%(installdir)s" + +runtest = 'check' + +sanity_check_paths = { + 'files': ["bin/lz4", "lib/liblz4.%s" % SHLIB_EXT, "include/lz4.h"], + 'dirs': ["lib/pkgconfig"] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.19-GCCcore-13.3.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.19-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..7ea1e75f83c --- /dev/null +++ b/easybuild/easyconfigs/m/M4/M4-1.4.19-GCCcore-13.3.0.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'M4' +version = '1.4.19' + +homepage = 'https://www.gnu.org/software/m4/m4.html' +description = """GNU M4 is an implementation of the traditional Unix macro processor. It is mostly SVR4 compatible + although it has some extensions (for example, handling more than 9 positional parameters to macros). + GNU M4 also has built-in functions for including files, running shell commands, doing arithmetic, etc.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['3be4a26d825ffdfda52a56fc43246456989a3630093cced3fbddf4771ee58a70'] + +# use same binutils version that was used when building GCC toolchain +builddependencies = [('binutils', '2.42', '', SYSTEM)] + +# '-fgnu89-inline' is required to avoid linking errors with older glibc's, +# see https://github.com/easybuilders/easybuild-easyconfigs/issues/529 +configopts = "--enable-c++ CPPFLAGS=-fgnu89-inline" + +sanity_check_paths = { + 'files': ['bin/m4'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.19-GCCcore-14.2.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.19-GCCcore-14.2.0.eb new file mode 100644 index 00000000000..c5c3ad83f3a --- /dev/null +++ b/easybuild/easyconfigs/m/M4/M4-1.4.19-GCCcore-14.2.0.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'M4' +version = '1.4.19' + +homepage = 'https://www.gnu.org/software/m4/m4.html' +description = """GNU M4 is an implementation of the traditional Unix macro processor. It is mostly SVR4 compatible + although it has some extensions (for example, handling more than 9 positional parameters to macros). + GNU M4 also has built-in functions for including files, running shell commands, doing arithmetic, etc.""" + +toolchain = {'name': 'GCCcore', 'version': '14.2.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['3be4a26d825ffdfda52a56fc43246456989a3630093cced3fbddf4771ee58a70'] + +# use same binutils version that was used when building GCC toolchain +builddependencies = [('binutils', '2.42', '', SYSTEM)] + +# '-fgnu89-inline' is required to avoid linking errors with older glibc's, +# see https://github.com/easybuilders/easybuild-easyconfigs/issues/529 +configopts = "--enable-c++ CPPFLAGS=-fgnu89-inline" + +sanity_check_paths = { + 'files': ['bin/m4'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/m/MAFFT/MAFFT-7.526-GCC-13.2.0-with-extensions.eb b/easybuild/easyconfigs/m/MAFFT/MAFFT-7.526-GCC-13.2.0-with-extensions.eb new file mode 100644 index 00000000000..175e1013f56 --- /dev/null +++ b/easybuild/easyconfigs/m/MAFFT/MAFFT-7.526-GCC-13.2.0-with-extensions.eb @@ -0,0 +1,51 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez (Swiss Institute of Bioinformatics, Biozentrum - University of Basel) +# 7.305 modified by: +# Adam Huffman (The Francis Crick Institute) +# 7.453 switch to Bundle by: +# Alex Domingo (Vrije Universiteit Brussel) +# Thomas Eylenbosch (Gluo NV) +# J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'Bundle' + +name = 'MAFFT' +version = '7.526' +versionsuffix = '-with-extensions' +local_commit = 'ee9799916df6a5d5103d46d54933f8eb6d28e244' + +homepage = 'https://mafft.cbrc.jp/alignment/software/source.html' +description = """MAFFT is a multiple sequence alignment program for unix-like operating systems. +It offers a range of multiple alignment methods, L-INS-i (accurate; for alignment +of <∼200 sequences), FFT-NS-2 (fast; for alignment of <∼30,000 sequences), etc.""" + +toolchain = {'name': 'GCC', 'version': '13.2.0'} + +default_easyblock = 'ConfigureMake' +default_component_specs = { + 'source_urls': ['https://gitlab.com/sysimm/mafft/-/archive/v%(version)s/'], + 'sources': ['mafft-%(version)s.tar.gz'], + 'checksums': ['6f536ec957b76f4e38e869d935d6626d318361ef8ee95e71c795b924f639ee10'], + 'skipsteps': ['configure'], + 'installopts': 'PREFIX=%(installdir)s', +} + +components = [ + (name, version, { + 'start_dir': 'mafft-v%%(version)s-%s/core' % local_commit, + }), + ('%s Extensions' % name, version, { + 'start_dir': 'mafft-v%%(version)s-%s/extensions' % local_commit, + }), +] + +sanity_check_paths = { + 'files': ['bin/mafft', 'libexec/mafft/mxscarnamod'], # mxscarnamod installed by MAFFT Extensions + 'dirs': ['libexec/mafft'], +} + +sanity_check_commands = ['mafft --version'] + +modextrapaths = {'MAFFT_BINARIES': 'libexec/mafft'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/MAGIC/MAGIC-3.0.0-foss-2023a.eb b/easybuild/easyconfigs/m/MAGIC/MAGIC-3.0.0-foss-2023a.eb new file mode 100644 index 00000000000..9e22b652a23 --- /dev/null +++ b/easybuild/easyconfigs/m/MAGIC/MAGIC-3.0.0-foss-2023a.eb @@ -0,0 +1,48 @@ +easyblock = 'PythonBundle' + +name = 'MAGIC' +version = '3.0.0' + +homepage = 'https://krishnaswamylab.org/projects/magic' +description = """Markov Affinity-based Graph Imputation of Cells (MAGIC) is an algorithm for denoising high-dimensional + data most commonly applied to single-cell RNA sequencing data.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('matplotlib', '3.7.2'), + ('scikit-learn', '1.3.1'), +] + +use_pip = True + +exts_list = [ + ('wrapt', '1.16.0', { + 'checksums': ['5f370f952971e7d17c7d1ead40e49f32345a7f7a5373571ef44d800d06b1899d'], + }), + ('Deprecated', '1.2.14', { + 'checksums': ['e5323eb936458dccc2582dc6f9c322c852a775a27065ff2b0c4970b9d53d01b3'], + }), + ('PyGSP', '0.5.1', { + 'checksums': ['4874ad88793d622d4f578b40c6617a99b1f02bc6c6c4077f0e48cd71c7275800'], + }), + ('graphtools', '1.5.3', { + 'checksums': ['b35ae2974d24c507fe01b110d10b1d8c949e20bc49ff9d7d04f94849f9795907'], + }), + ('scprep', '1.2.3', { + 'checksums': ['cc4ba4cedbba256935298f2ba6a973b4e74ea8cb9ad2632b693b6d4e6ab77c3f'], + }), + ('tasklogger', '1.2.0', { + 'checksums': ['b0a390dbe1d4c6f7465e58ee457b5bb381657b5ede3a85bcf45199cb56ac01a4'], + }), + ('magic-impute', version, { + 'modulename': 'magic', + 'checksums': ['0c3f6d17baf586c412c174709a19164f04e693fd1933a8c0399ae5c5bf1cfd7a'], + }), +] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/MATES/MATES-0.1.2-20240813-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/m/MATES/MATES-0.1.2-20240813-foss-2023a-CUDA-12.1.1.eb new file mode 100644 index 00000000000..dbba96ddf2f --- /dev/null +++ b/easybuild/easyconfigs/m/MATES/MATES-0.1.2-20240813-foss-2023a-CUDA-12.1.1.eb @@ -0,0 +1,58 @@ +easyblock = 'PythonBundle' + +name = 'MATES' +version = '0.1.2-20240813' +local_commit = 'd5ee15b' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/mcgilldinglab/MATES' +description = "A Deep Learning-Based Model for Quantifying Transposable Elements in Single-Cell Sequencing Data." + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('CUDA', '12.1.1', '', SYSTEM), + ('Python-bundle-PyPI', '2023.06'), + ('SciPy-bundle', '2023.07'), + ('matplotlib', '3.7.2'), + ('anndata', '0.10.5.post1'), + ('SAMtools', '1.18'), + ('pybedtools', '0.9.1'), + ('PyTorch-bundle', '2.1.2', versionsuffix), + ('Pysam', '0.22.0'), + ('tqdm', '4.66.1'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('sorted_nearest', '0.0.39', { + 'checksums': ['16a51d5db87ae226b47ace43c176bb672477a1b7ba8052ea9291a6356c9c69b1'], + }), + ('ncls', '0.0.68', { + 'checksums': ['81aaa5abb123bb21797ed2f8ef921e20222db14a3ecbc61ccf447532f2b7ba93'], + }), + ('natsort', '8.4.0', { + 'checksums': ['45312c4a0e5507593da193dedd04abb1469253b601ecaf63445ad80f0a1ea581'], + }), + ('pyranges', '0.0.129', { + 'checksums': ['bee83b4fad0062be9586668c6b0fc4270d5e761951975e018202993680071fb3'], + }), + (name, version, { + 'modulename': 'MATES', + # unpin exact versions of dependencies + 'preinstallopts': r"sed -i 's/==.*//g' requirements.txt && sed -i 's/==.*/\",/g' setup.py && ", + 'source_urls': ['https://github.com/mcgilldinglab/MATES/archive'], + 'sources': [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}], + 'checksums': ['aca36b2b99ebed975fdf61670a9b551c1ab7882ff2b9d4ed3f25f2e13805652c'], + }), +] + +sanity_check_commands = [ + "python -c 'from MATES import bam_processor, data_processor, MATES_model'", + "python -c 'from MATES import TE_quantifier, TE_quantifier_LongRead, TE_quantifier_Intronic'", +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/MATES/MATES-0.1.2-20240813-foss-2023a.eb b/easybuild/easyconfigs/m/MATES/MATES-0.1.2-20240813-foss-2023a.eb new file mode 100644 index 00000000000..e7e73a89e80 --- /dev/null +++ b/easybuild/easyconfigs/m/MATES/MATES-0.1.2-20240813-foss-2023a.eb @@ -0,0 +1,56 @@ +easyblock = 'PythonBundle' + +name = 'MATES' +version = '0.1.2-20240813' +local_commit = 'd5ee15b' + +homepage = 'https://github.com/mcgilldinglab/MATES' +description = "A Deep Learning-Based Model for Quantifying Transposable Elements in Single-Cell Sequencing Data." + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('SciPy-bundle', '2023.07'), + ('matplotlib', '3.7.2'), + ('anndata', '0.10.5.post1'), + ('SAMtools', '1.18'), + ('pybedtools', '0.9.1'), + ('PyTorch-bundle', '2.1.2'), + ('Pysam', '0.22.0'), + ('tqdm', '4.66.1'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('sorted_nearest', '0.0.39', { + 'checksums': ['16a51d5db87ae226b47ace43c176bb672477a1b7ba8052ea9291a6356c9c69b1'], + }), + ('ncls', '0.0.68', { + 'checksums': ['81aaa5abb123bb21797ed2f8ef921e20222db14a3ecbc61ccf447532f2b7ba93'], + }), + ('natsort', '8.4.0', { + 'checksums': ['45312c4a0e5507593da193dedd04abb1469253b601ecaf63445ad80f0a1ea581'], + }), + ('pyranges', '0.0.129', { + 'checksums': ['bee83b4fad0062be9586668c6b0fc4270d5e761951975e018202993680071fb3'], + }), + (name, version, { + 'modulename': 'MATES', + # unpin exact versions of dependencies + 'preinstallopts': r"sed -i 's/==.*//g' requirements.txt && sed -i 's/==.*/\",/g' setup.py && ", + 'source_urls': ['https://github.com/mcgilldinglab/MATES/archive'], + 'sources': [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}], + 'checksums': ['aca36b2b99ebed975fdf61670a9b551c1ab7882ff2b9d4ed3f25f2e13805652c'], + }), +] + +sanity_check_commands = [ + "python -c 'from MATES import bam_processor, data_processor, MATES_model'", + "python -c 'from MATES import TE_quantifier, TE_quantifier_LongRead, TE_quantifier_Intronic'", +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/MATES/MATES-0.1.5-20241121-foss-2023b.eb b/easybuild/easyconfigs/m/MATES/MATES-0.1.5-20241121-foss-2023b.eb new file mode 100644 index 00000000000..2c87d3d09bf --- /dev/null +++ b/easybuild/easyconfigs/m/MATES/MATES-0.1.5-20241121-foss-2023b.eb @@ -0,0 +1,53 @@ +easyblock = 'PythonBundle' + +name = 'MATES' +version = '0.1.5-20241121' +local_commit = '3846ad5' + +homepage = 'https://github.com/mcgilldinglab/MATES' +description = "A Deep Learning-Based Model for Quantifying Transposable Elements in Single-Cell Sequencing Data." + +toolchain = {'name': 'foss', 'version': '2023b'} + +dependencies = [ + ('Python', '3.11.5'), + ('Python-bundle-PyPI', '2023.10'), + ('SciPy-bundle', '2023.11'), + ('matplotlib', '3.8.2'), + ('anndata', '0.11.1'), + ('pybedtools', '0.10.0'), + ('PyTorch', '2.1.2'), + ('Pysam', '0.22.0'), + ('tqdm', '4.66.2'), + ('SAMtools', '1.19.2'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('sorted_nearest', '0.0.39', { + 'checksums': ['16a51d5db87ae226b47ace43c176bb672477a1b7ba8052ea9291a6356c9c69b1'], + }), + ('ncls', '0.0.68', { + 'checksums': ['81aaa5abb123bb21797ed2f8ef921e20222db14a3ecbc61ccf447532f2b7ba93'], + }), + ('pyranges', '0.0.129', { + 'checksums': ['bee83b4fad0062be9586668c6b0fc4270d5e761951975e018202993680071fb3'], + }), + (name, version, { + 'modulename': 'MATES', + # unpin exact versions of dependencies + 'preinstallopts': """sed -i 's/==.*//g' requirements.txt && sed -i 's/==.*/\",/g' setup.py && """, + 'source_urls': ['https://github.com/mcgilldinglab/MATES/archive'], + 'sources': [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}], + 'checksums': ['40fbb87dd72ca4c9e5347f2e984f9c0a0caa817d4eee692476be71e733e76f61'], + }), +] + +sanity_check_commands = [ + "python -c 'from MATES import bam_processor, data_processor, MATES_model'", + "python -c 'from MATES import TE_quantifier, TE_quantifier_LongRead, TE_quantifier_Intronic'", +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/MATLAB/MATLAB-2024b.eb b/easybuild/easyconfigs/m/MATLAB/MATLAB-2024b.eb new file mode 100644 index 00000000000..c53c320205f --- /dev/null +++ b/easybuild/easyconfigs/m/MATLAB/MATLAB-2024b.eb @@ -0,0 +1,28 @@ +name = 'MATLAB' +version = '2024b' + +homepage = 'https://www.mathworks.com/products/matlab' +description = """MATLAB is a high-level language and interactive environment + that enables you to perform computationally intensive tasks faster than with + traditional programming languages such as C, C++, and Fortran.""" + +toolchain = SYSTEM + +sources = ['R%s_Linux.iso' % (version)] +checksums = ['4e4499d93b4909b750ee2a6444af107cd5c1c62e75020c3e1625e946c6693573'] + +download_instructions = 'Download %s from mathworks.com' % sources[0] + +java_options = '-Xmx2048m' + +osdependencies = [('p7zip-plugins', 'p7zip-full')] # for extracting iso-files + +# Use EB_MATLAB_KEY environment variable or uncomment and modify license key +# key = '00000-00000-00000-00000-00000-00000-00000-00000-00000-00000-00000-00000' + +# Use EB_MATLAB_LICENSE_SERVER and EB_MATLAB_LICENSE_SERVER_PORT environment variables or +# uncomment and modify the following variables for installation with floating license server +# license_file = 'my-license-file' +# license_server_port = 'XXXXX' + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/m/MBX/MBX-1.1.0-foss-2023a.eb b/easybuild/easyconfigs/m/MBX/MBX-1.1.0-foss-2023a.eb new file mode 100644 index 00000000000..3f6da986d62 --- /dev/null +++ b/easybuild/easyconfigs/m/MBX/MBX-1.1.0-foss-2023a.eb @@ -0,0 +1,48 @@ +easyblock = 'ConfigureMake' + +name = 'MBX' +version = '1.1.0' + +homepage = 'https://github.com/paesanilab/MBX' +description = "MBX is an energy and force calculator for data-driven many-body simulations" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'pic': True, 'openmp': True} + +source_urls = ['https://github.com/paesanilab/MBX/archive/'] +sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}] +checksums = ['0f55f4950226defb46fd0814ad97f906ce4ffd6403af6817bd98cb3c68996692'] + +builddependencies = [('Autotools', '20220317')] +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('GSL', '2.7'), +] + +preconfigopts = 'export MBX_HOME=$PWD && autoreconf -fi && ' + +configopts = '--enable-shared --enable-verbose CXX="$CXX"' + +postinstallcmds = ["cp -a plugins %(installdir)s"] + +maxparallel = 2 + +runtest = 'check' + +modextrapaths = {'PYTHONPATH': 'plugins/python'} + +modextravars = {'MBX_HOME': '%(installdir)s'} + +sanity_check_paths = { + 'files': ['bin/mb_decomp', 'bin/optimize', 'bin/order_frames', 'bin/single_point', + 'lib/libmbx.a', 'lib/libmbx.%s' % SHLIB_EXT], + 'dirs': ['include', 'plugins/python/mbx', 'plugins/lammps/USER-MBX'], +} + +sanity_check_commands = [ + "optimize", + "python -c 'import mbx'", +] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/m/MCR/MCR-R2022b.10.eb b/easybuild/easyconfigs/m/MCR/MCR-R2022b.10.eb new file mode 100644 index 00000000000..43dcfb25294 --- /dev/null +++ b/easybuild/easyconfigs/m/MCR/MCR-R2022b.10.eb @@ -0,0 +1,18 @@ +name = 'MCR' +version = 'R2022b' # runtime version 9.13 +local_update = '10' +versionsuffix = '.%s' % local_update + +homepage = 'https://www.mathworks.com/products/compiler/mcr/' +description = """The MATLAB Runtime is a standalone set of shared libraries + that enables the execution of compiled MATLAB applications + or components on computers that do not have MATLAB installed.""" + +toolchain = SYSTEM + +source_urls = ['https://ssd.mathworks.com/supportfiles/downloads/%%(version)s/Release/%s/deployment_files/' + 'installer/complete/glnxa64/' % local_update] +sources = ['MATLAB_Runtime_%%(version)s_Update_%s_glnxa64.zip' % local_update] +checksums = ['5bcee3f2be7a4ccb6ed0b7d8938eca7b33e4a0d81ec5351d6eb06150a89245eb'] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/m/MCR/MCR-R2023b.9.eb b/easybuild/easyconfigs/m/MCR/MCR-R2023b.9.eb new file mode 100644 index 00000000000..b6832290ecb --- /dev/null +++ b/easybuild/easyconfigs/m/MCR/MCR-R2023b.9.eb @@ -0,0 +1,18 @@ +name = 'MCR' +version = 'R2023b' # runtime version 23.2 +local_update = '9' +versionsuffix = '.%s' % local_update + +homepage = 'https://www.mathworks.com/products/compiler/mcr/' +description = """The MATLAB Runtime is a standalone set of shared libraries + that enables the execution of compiled MATLAB applications + or components on computers that do not have MATLAB installed.""" + +toolchain = SYSTEM + +source_urls = ['https://ssd.mathworks.com/supportfiles/downloads/%%(version)s/Release/%s/deployment_files/' + 'installer/complete/glnxa64/' % local_update] +sources = ['MATLAB_Runtime_%%(version)s_Update_%s_glnxa64.zip' % local_update] +checksums = ['ef69a624806aa3864d692a88a67d969e3b641ae296b4a091969185ef056f13bd'] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/m/MCR/MCR-R2024a.4.eb b/easybuild/easyconfigs/m/MCR/MCR-R2024a.4.eb new file mode 100644 index 00000000000..bb746ac5151 --- /dev/null +++ b/easybuild/easyconfigs/m/MCR/MCR-R2024a.4.eb @@ -0,0 +1,18 @@ +name = 'MCR' +version = 'R2024a' # runtime version 24.1 +local_update = '4' +versionsuffix = '.%s' % local_update + +homepage = 'https://www.mathworks.com/products/compiler/mcr/' +description = """The MATLAB Runtime is a standalone set of shared libraries + that enables the execution of compiled MATLAB applications + or components on computers that do not have MATLAB installed.""" + +toolchain = SYSTEM + +source_urls = ['https://ssd.mathworks.com/supportfiles/downloads/%%(version)s/Release/%s/deployment_files/' + 'installer/complete/glnxa64/' % local_update] +sources = ['MATLAB_Runtime_%%(version)s_Update_%s_glnxa64.zip' % local_update] +checksums = ['ceed37dc342660c934b9f6297491f57b6d51a7f49cd1fb80b775b1f748b72d03'] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/m/MCR/MCR-R2024b.eb b/easybuild/easyconfigs/m/MCR/MCR-R2024b.eb new file mode 100644 index 00000000000..17ad8df12f6 --- /dev/null +++ b/easybuild/easyconfigs/m/MCR/MCR-R2024b.eb @@ -0,0 +1,17 @@ +name = 'MCR' +version = 'R2024b' # runtime version 24.2 +local_update = '0' + +homepage = 'https://www.mathworks.com/products/compiler/mcr/' +description = """The MATLAB Runtime is a standalone set of shared libraries + that enables the execution of compiled MATLAB applications + or components on computers that do not have MATLAB installed.""" + +toolchain = SYSTEM + +source_urls = ['https://ssd.mathworks.com/supportfiles/downloads/%%(version)s/Release/%s/deployment_files/' + 'installer/complete/glnxa64/' % local_update] +sources = ['MATLAB_Runtime_%(version)s_glnxa64.zip'] +checksums = ['c46f4b55747aa4a8c03c1ece5bd5360c4dbb2ca402608fbd44688ba55f9b7a54'] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/m/MDI/MDI-1.4.29-gompi-2023b.eb b/easybuild/easyconfigs/m/MDI/MDI-1.4.29-gompi-2023b.eb new file mode 100644 index 00000000000..0ff18b44f79 --- /dev/null +++ b/easybuild/easyconfigs/m/MDI/MDI-1.4.29-gompi-2023b.eb @@ -0,0 +1,54 @@ +# MDI package for LAMMPS +# Author: J. Saßmannshausen (Imperial College London) + +easyblock = 'CMakeMake' +name = 'MDI' +version = '1.4.29' + +homepage = 'https://github.com/MolSSI-MDI/MDI_Library' +description = """The MolSSI Driver Interface (MDI) project provides a +standardized API for fast, on-the-fly communication between computational +chemistry codes. This greatly simplifies the process of implementing +methods that require the cooperation of multiple software packages and +enables developers to write a single implementation that works across +many different codes. The API is sufficiently general to support a wide +variety of techniques, including QM/MM, ab initio MD, machine learning, +advanced sampling, and path integral MD, while also being straightforwardly +extensible. Communication between codes is handled by the MDI Library, which +enables tight coupling between codes using either the MPI or TCP/IP methods. +""" + +toolchain = {'name': 'gompi', 'version': '2023b'} + +source_urls = ['https://github.com/MolSSI-MDI/MDI_Library/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['6fb9ab2cf01c1a88a183bb481313f3131f0afd041ddea7aeacabe857fbdcb6ad'] + +builddependencies = [ + ('CMake', '3.27.6'), +] + +dependencies = [ + ('Python', '3.11.5'), +] + +# perform iterative build to get both static and shared libraries +local_common_configopts = '-DCMAKE_POSITION_INDEPENDENT_CODE=ON -DPython_EXECUTABLE=$EBROOTPYTHON/bin/python ' +configopts = [ + local_common_configopts + ' -Dlibtype=STATIC', + local_common_configopts + ' -DBUILD_SHARED_LIBS=ON', +] + +modextrapaths = { + 'LD_LIBRARY_PATH': 'lib/mdi', + 'LIBRARY_PATH': 'lib/mdi', +} + +sanity_check_paths = { + 'files': ['lib/mdi/libmdi.a', 'lib/mdi/libmdi.%s' % SHLIB_EXT], + 'dirs': ['include', 'share'], +} + +bin_lib_subdirs = ['lib/mdi'] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/m/MDStress/MDStress-20191228-gfbf-2023a.eb b/easybuild/easyconfigs/m/MDStress/MDStress-20191228-gfbf-2023a.eb new file mode 100644 index 00000000000..7be20fe7e5b --- /dev/null +++ b/easybuild/easyconfigs/m/MDStress/MDStress-20191228-gfbf-2023a.eb @@ -0,0 +1,41 @@ +easyblock = 'CMakeMake' + +name = 'MDStress' +version = '20191228' + +homepage = 'https://vanegaslab.org/software' +description = """MDStress library enable the calculation of local stress +fields from molecular dynamics simulations""" + +toolchain = {'name': 'gfbf', 'version': '2023a'} + +source_urls = ['https://vanegaslab.org/files'] +sources = ['mdstress-library-12282019.tar.gz'] +patches = [ + 'MDStress-20191228_use_external_voro++_and_EB_lapack.patch', +] +checksums = [ + {'mdstress-library-12282019.tar.gz': 'abea62dca77ca4645463415bec219a42554146cc0eefd480c760222e423c7db3'}, + {'MDStress-20191228_use_external_voro++_and_EB_lapack.patch': + '566c181f9a6784c81b04226d360ed71d96f99310a231a88919e7fac37e515e92'}, +] + +builddependencies = [ + ('CMake', '3.26.3'), +] + +dependencies = [ + ('Voro++', '0.4.6'), + ('Python', '3.11.3'), +] + +sanity_check_paths = { + 'files': ['bin/tensortools', 'include/mdstress/mds_basicops.h', 'lib/libmdstress.%s' % SHLIB_EXT], + 'dirs': [], +} + +modextrapaths = { + 'PYTHONPATH': 'bin', +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/MDStress/MDStress-20191228_use_external_voro++_and_EB_lapack.patch b/easybuild/easyconfigs/m/MDStress/MDStress-20191228_use_external_voro++_and_EB_lapack.patch new file mode 100644 index 00000000000..fd2458812bc --- /dev/null +++ b/easybuild/easyconfigs/m/MDStress/MDStress-20191228_use_external_voro++_and_EB_lapack.patch @@ -0,0 +1,80 @@ +use external EB Voro++ and flexi/openblas as needed + +Åke Sandgren, 2024-11-07 +diff -ru mdstress-library.orig/CMakeLists.txt mdstress-library/CMakeLists.txt +--- mdstress-library.orig/CMakeLists.txt 2019-12-28 15:48:10.000000000 +0100 ++++ mdstress-library/CMakeLists.txt 2024-11-07 11:19:48.125912695 +0100 +@@ -1,4 +1,5 @@ +-cmake_minimum_required(VERSION 2.8) ++cmake_minimum_required(VERSION 3.0) ++project('MDStress') + + enable_language(C) + enable_language(CXX) +@@ -27,42 +28,28 @@ + # COMMAND tar xaf voro++-0.4.6.tar.gz + # WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/contrib) + #endif() +-FILE(GLOB VORO_SOURCES_HH include/voro++/*.hh) +-FILE(GLOB VORO_SOURCES_CC contrib/voro++/src/*.cc) +-#FILE(MAKE_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/include/voro++) +-#FILE(COPY ${VORO_SOURCES_HH} DESTINATION ${CMAKE_CURRENT_SOURCE_DIR}/include/voro++) +-LIST(REMOVE_ITEM VORO_SOURCES_CC ${CMAKE_CURRENT_SOURCE_DIR}/contrib/voro++/src/voro++.cc) +-LIST(REMOVE_ITEM VORO_SOURCES_CC ${CMAKE_CURRENT_SOURCE_DIR}/contrib/voro++/src/v_base_wl.cc) ++#FILE(GLOB VORO_SOURCES_HH include/voro++/*.hh) ++#FILE(GLOB VORO_SOURCES_CC contrib/voro++/src/*.cc) ++##FILE(MAKE_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/include/voro++) ++##FILE(COPY ${VORO_SOURCES_HH} DESTINATION ${CMAKE_CURRENT_SOURCE_DIR}/include/voro++) ++#LIST(REMOVE_ITEM VORO_SOURCES_CC ${CMAKE_CURRENT_SOURCE_DIR}/contrib/voro++/src/voro++.cc) ++#LIST(REMOVE_ITEM VORO_SOURCES_CC ${CMAKE_CURRENT_SOURCE_DIR}/contrib/voro++/src/v_base_wl.cc) + +-SET(MDSTRESS_SOURCES ${MDSTRESS_SOURCES_CPP} ${MDSTRESS_SOURCES_H} ${VORO_SOURCES_CC} ${VORO_SOURCES_HH}) ++SET(MDSTRESS_SOURCES ${MDSTRESS_SOURCES_CPP} ${MDSTRESS_SOURCES_H}) + + INCLUDE_DIRECTORIES(include/mdstress) +-INCLUDE_DIRECTORIES(include/voro++) ++#INCLUDE_DIRECTORIES(include/voro++) + + # attempt to find LAPACK library +-FIND_LIBRARY(LAPACK_LIBRARY_SYS NAMES lapack liblapack HINTS /usr/lib REQUIRED) +-if (NOT LAPACK_LIBRARY_SYS) +- UNSET(LAPACK_LIBRARY_SYS-NOTFOUND) +- UNSET(LAPACK_LIBRARY_SYS) +- # check to see if we need to download LAPACK +- SET(LAPACK_URL http://www.netlib.org/lapack/lapack-3.8.0.tar.gz) +- SET(LAPACK_DOWNLOAD_PATH ${CMAKE_CURRENT_SOURCE_DIR}/contrib/lapack-3.8.0.tar.gz) +- FILE(DOWNLOAD ${LAPACK_URL} ${LAPACK_DOWNLOAD_PATH}) +- EXECUTE_PROCESS( +- COMMAND tar xaf lapack-3.8.0.tar.gz +- WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/contrib) +- ADD_SUBDIRECTORY(contrib/lapack-3.8.0) +-else() +- FIND_LIBRARY(LAPACK_LIBRARY NAMES lapack liblapack HINTS /usr/lib REQUIRED) +-endif() ++FIND_LIBRARY(LAPACK_LIBRARY NAMES flexiblas openblas lapack liblapack REQUIRED) + + ADD_LIBRARY(mdstress SHARED ${MDSTRESS_SOURCES}) +-TARGET_LINK_LIBRARIES(mdstress ${LAPACK_LIBRARY} ${PYTHON_LIBRARIES}) ++TARGET_LINK_LIBRARIES(mdstress ${LAPACK_LIBRARY} ${PYTHON_LIBRARIES} voro++) + +-INSTALL(TARGETS mdstress RUNTIME DESTINATION bin LIBRARY DESTINATION lib ARCHIVE DESTINATION lib/static) ++INSTALL(TARGETS mdstress RUNTIME DESTINATION bin LIBRARY DESTINATION lib ARCHIVE DESTINATION lib) + + INSTALL(FILES ${MDSTRESS_SOURCES_H} DESTINATION include/mdstress) +-INSTALL(FILES ${VORO_SOURCES_HH} DESTINATION include/voro++) ++#INSTALL(FILES ${VORO_SOURCES_HH} DESTINATION include/voro++) + + # only process python bindings if requested + if(MDS_BOOSTPYTHON) +diff -ru mdstress-library.orig/src/mds_stressgrid.cpp mdstress-library/src/mds_stressgrid.cpp +--- mdstress-library.orig/src/mds_stressgrid.cpp 2019-12-28 15:48:10.000000000 +0100 ++++ mdstress-library/src/mds_stressgrid.cpp 2024-11-07 09:08:35.761694010 +0100 +@@ -21,7 +21,7 @@ + =========================================================================*/ + + #include "mds_stressgrid.h" +-#include "voro++.hh" ++#include "voro++/voro++.hh" + + using namespace mds; + diff --git a/easybuild/easyconfigs/m/MDTraj/MDTraj-1.9.9-gfbf-2023a.eb b/easybuild/easyconfigs/m/MDTraj/MDTraj-1.9.9-gfbf-2023a.eb new file mode 100644 index 00000000000..8f172912989 --- /dev/null +++ b/easybuild/easyconfigs/m/MDTraj/MDTraj-1.9.9-gfbf-2023a.eb @@ -0,0 +1,39 @@ +# Updated: Pavel Grochal (INUITS) + +easyblock = 'PythonBundle' + +name = 'MDTraj' +version = '1.9.9' + +homepage = 'https://mdtraj.org' +description = "Read, write and analyze MD trajectories with only a few lines of Python code." + +toolchain = {'name': 'gfbf', 'version': '2023a'} +toolchainopts = {'openmp': True} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('zlib', '1.2.13'), +] + +use_pip = True +exts_list = [ + ('pyparsing', '3.1.0', { + 'checksums': ['edb662d6fe322d6e990b1594b5feaeadf806803359e3d4d42f11e295e588f0ea'], + }), + ('astunparse', '1.6.3', { + 'checksums': ['5ad93a8456f0d084c3456d059fd9a92cce667963232cbf763eac3bc5b7940872'], + }), + ('mdtraj', version, { + 'checksums': ['1b03f7ac753af5ca07cf874842689c8d49e791ee1242510875581df6100ca15e'], + }), +] + +# The unit tests of MDTraj are a pain to get to work: they require +# a massive number of extra dependencies. See +# https://github.com/mdtraj/mdtraj/blob/master/devtools/conda-recipe/meta.yaml + +sanity_pip_check = True + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/m/MEME/MEME-5.5.7-gompi-2023b.eb b/easybuild/easyconfigs/m/MEME/MEME-5.5.7-gompi-2023b.eb new file mode 100644 index 00000000000..08fdaab9f31 --- /dev/null +++ b/easybuild/easyconfigs/m/MEME/MEME-5.5.7-gompi-2023b.eb @@ -0,0 +1,63 @@ +# Contribution from the NIHR Biomedical Research Centre +# Guy's and St Thomas' NHS Foundation Trust and King's College London +# uploaded by J. Sassmannshausen + +easyblock = 'ConfigureMake' + +name = 'MEME' +version = '5.5.7' + +homepage = 'https://meme-suite.org/meme/index.html' +description = """The MEME Suite allows you to: * discover motifs using MEME, DREME (DNA only) or + GLAM2 on groups of related DNA or protein sequences, * search sequence databases with motifs using + MAST, FIMO, MCAST or GLAM2SCAN, * compare a motif to all motifs in a database of motifs, * associate + motifs with Gene Ontology terms via their putative target genes, and * analyse motif enrichment + using SpaMo or CentriMo.""" + +toolchain = {'name': 'gompi', 'version': '2023b'} + +source_urls = ['https://%(namelower)s-suite.org/%(namelower)s/%(namelower)s-software/%(version)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['1dca8d0e6d1d36570c1a88ab8dbe7e4b177733fbbeacaa2e8c4674febf57aaf4'] + +dependencies = [ + ('libxml2', '2.11.5'), + ('libxslt', '1.1.38'), + ('zlib', '1.2.13'), + ('Perl', '5.38.0'), + ('Python', '3.11.5'), + ('Ghostscript', '10.02.1'), + ('XML-Compile', '1.63'), +] + +configopts = '--with-perl=${EBROOTPERL}/bin/perl --with-python=${EBROOTPYTHON}/bin/python ' +configopts += '--with-gs=${EBROOTGHOSTSCRIPT}/bin/gs ' +# config.log should indicate that all required/optional dependencies were found (see scripts/dependencies.pl) +configopts += " && grep 'All required and optional Perl modules were found' config.log" + +pretestopts = "OMPI_MCA_rmaps_base_oversubscribe=1 " +# test xstreme4 fails on Ubuntu 20.04, see: https://groups.google.com/g/meme-suite/c/GlfpGwApz1Y +runtest = 'test' + +fix_perl_shebang_for = ['bin/*', 'libexec/meme-%(version)s/*'] +fix_python_shebang_for = ['bin/*', 'libexec/meme-%(version)s/*'] + +sanity_check_paths = { + 'files': ['bin/meme', 'bin/dreme', 'bin/meme-chip', 'libexec/meme-%(version)s/meme2meme'], + 'dirs': ['lib'], +} + +sanity_check_commands = [ + "mpirun meme -h 2>&1 | grep 'Usage:'", + "meme2meme --help", + "perl -e 'require MemeSAX'", + "python -c 'import sequence_py3'", +] + +modextrapaths = { + 'PATH': ['libexec/meme-%(version)s'], + 'PERL5LIB': ['lib/meme-%(version)s/perl'], + 'PYTHONPATH': ['lib/meme-%(version)s/python'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/METIS/METIS-5.1.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/m/METIS/METIS-5.1.0-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..417e4750ef9 --- /dev/null +++ b/easybuild/easyconfigs/m/METIS/METIS-5.1.0-GCCcore-13.3.0.eb @@ -0,0 +1,36 @@ +name = 'METIS' +version = '5.1.0' + +homepage = 'http://glaros.dtc.umn.edu/gkhome/metis/metis/overview' + +description = """ + METIS is a set of serial programs for partitioning graphs, partitioning + finite element meshes, and producing fill reducing orderings for sparse + matrices. The algorithms implemented in METIS are based on the multilevel + recursive-bisection, multilevel k-way, and multi-constraint partitioning + schemes. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +source_urls = [ + 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis', + 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis/OLD', +] +sources = [SOURCELOWER_TAR_GZ] +patches = ['%(name)s-%(version)s-use-doubles.patch'] +checksums = [ + {'metis-5.1.0.tar.gz': '76faebe03f6c963127dbb73c13eab58c9a3faeae48779f049066a21c087c5db2'}, + {'METIS-5.1.0-use-doubles.patch': '7e38a3ec8f2b8e3d189239bade5b28c0dd1c564485050109164fa71a6a767c67'}, +] + +# We use 32bit for indices and 64bit for content +builddependencies = [ + ('binutils', '2.42'), + ('CMake', '3.29.3'), +] + +configopts = ['', 'shared=1'] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/m/MOFA2/MOFA2-1.14.0-foss-2023a-R-4.3.2.eb b/easybuild/easyconfigs/m/MOFA2/MOFA2-1.14.0-foss-2023a-R-4.3.2.eb new file mode 100644 index 00000000000..99d3036b37a --- /dev/null +++ b/easybuild/easyconfigs/m/MOFA2/MOFA2-1.14.0-foss-2023a-R-4.3.2.eb @@ -0,0 +1,37 @@ +easyblock = 'RPackage' + +name = 'MOFA2' +version = '1.14.0' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://cran.r-project.org/web/packages/rhandsontable/index.html' +description = """MOFA is a factor analysis model that provides a general framework + for the integration of multi-omic data sets in an unsupervised fashion. Intuitively, + MOFA can be viewed as a versatile and statistically rigorous generalization of principal + component analysis to multi-omics data. Given several data matrices with measurements + of multiple -omics data types on the same or on overlapping sets of samples, + MOFA infers an interpretable low-dimensional representation in terms of a few latent factors. + These learnt factors represent the driving sources of variation across data modalities, + thus facilitating the identification of cellular states or disease subgroups.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = [ + 'https://bioconductor.org/packages/release/bioc/src/contrib/', + 'https://bioconductor.org/packages/3.19/bioc/src/contrib/', +] +sources = ['%(name)s_%(version)s.tar.gz'] +checksums = ['18975d2072c35160cc4f5218977e2c94ab82389478b65c5c6f3412c257dcc069'] + +dependencies = [ + ('R', '4.3.2'), + ('R-bundle-Bioconductor', '3.18', versionsuffix), + ('SeuratDisk', '20231104', versionsuffix), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['%(name)s'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/MOKIT/MOKIT-1.2.6_20240830-gfbf-2023a.eb b/easybuild/easyconfigs/m/MOKIT/MOKIT-1.2.6_20240830-gfbf-2023a.eb new file mode 100644 index 00000000000..5b4aedbdadb --- /dev/null +++ b/easybuild/easyconfigs/m/MOKIT/MOKIT-1.2.6_20240830-gfbf-2023a.eb @@ -0,0 +1,64 @@ +easyblock = 'Bundle' + +name = 'MOKIT' +version = '1.2.6_20240830' +_commit = 'd66560a6a7926e5e21b45cbcc9213aaa26bd997d' + +homepage = 'https://github.com/1234zou/MOKIT' +description = """ +MOKIT offers various utilities and modules to transfer MOs among various quantum chemistry software packages.""" + +toolchain = {'name': 'gfbf', 'version': '2023a'} +toolchainopts = {'openmp': True} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), +] + +_makefile = 'Makefile.gnu_openblas_conda' +maxparallel = 1 + +default_component_specs = { + 'source_urls': ['https://github.com/1234zou/MOKIT/archive'], + 'checksums': ['b4e7224ac5b56e6d0116f7759a3017c57d527b1d35c32e3b2733904f7f7c4de5'], + 'sources': [{ + 'download_filename': '%s.tar.gz' % _commit, + 'filename': SOURCE_TAR_GZ, + }], +} + +components = [ + (name, version, { + 'easyblock': 'MakeCp', + 'start_dir': 'MOKIT-%s/src' % _commit, + 'prebuildopts': 'sed -i -e "s/^MKL_FLAGS.*/MKL_FLAGS = $LIBBLAS/" %s && ' % _makefile, + 'buildopts': 'all -f %s' % _makefile, + 'files_to_copy': ['../bin'], + }), + ('mokit', version, { + 'easyblock': 'PythonPackage', + 'start_dir': 'MOKIT-%s' % _commit, + 'use_pip': True, + 'download_dep_fail': True, + 'sanity_pip_check': True, + 'options': {'modulename': 'mokit'}, + }), +] + +modextrapaths = { + 'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages'] +} + +sanity_check_commands = [ + 'fch2inp | grep Example', + 'geom_opt | grep Example', + "python -s -c 'from mokit.lib.gaussian import load_mol_from_fch'", +] + +sanity_check_paths = { + 'files': ['bin/geom_opt', 'bin/fch2inp'], + 'dirs': ['lib/python3.11/site-packages/mokit'], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/m/MOLGW/MOLGW-3.3-foss-2023a.eb b/easybuild/easyconfigs/m/MOLGW/MOLGW-3.3-foss-2023a.eb new file mode 100644 index 00000000000..9a4730345d8 --- /dev/null +++ b/easybuild/easyconfigs/m/MOLGW/MOLGW-3.3-foss-2023a.eb @@ -0,0 +1,73 @@ +easyblock = 'MakeCp' + +name = 'MOLGW' +version = '3.3' + +homepage = 'https://www.molgw.org' +description = """MOLGW is a code that implements the many-body perturbation theory (MBPT) to +describe the excited electronic states in finite systems (atoms, molecules, +clusters). It most importantly implements the approximation for the self-energy +and the Bethe-Salpeter equation for the optical excitations. + +MOLGW comes with a fully functional density-functional theory (DFT) code to +prepare the subsequent MBPT runs. Standard local and semi-local approximations +to DFT are available, as well as several hybrid functionals and range-separated +hybrid functionals. MOLGW uses a Gaussian-type orbitals basis set so to reuse +all the standard quantum-chemistry tools.""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'usempi': True} + +github_account = 'molgw' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['ff1c8eb736049e52608d4554a2d435ee9d15e47c4a9934d41712962748929e81'] + +dependencies = [ + ('libxc', '6.2.2'), + ('libcint', '5.4.0', '-pypzpx'), + # Python utilities + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('matplotlib', '3.7.2'), + ('PyYAML', '6.0'), +] + +_config_arch_params = { + 'FCFLAGS': '-cpp $FFLAGS', + 'CXXFLAGS': '-cpp $CXXFLAGS', + 'LAPACK': '$LIBLAPACK', + 'SCALAPACK': '$LIBSCALAPACK', + 'LIBXC_ROOT': '$EBROOTLIBXC', +} +_config_arch_sed = ';'.join(["s|^%s=.*|%s=%s|" % (k, k, v) for (k, v) in _config_arch_params.items()]) + +prebuildopts = 'cp config/my_machine_gfortran_mpi.arch src/my_machine.arch && ' +prebuildopts += 'sed "%s" -i src/my_machine.arch && ' % _config_arch_sed + +buildopts = 'molgw' + +runtest = 'test' + +files_to_copy = [ + (['molgw'], 'bin'), + (['basis', 'utils'], ''), +] + +fix_python_shebang_for = ['utils/*.py', 'utils/molgw/*.py'] + +postinstallcmds = ["cd %(installdir)s/bin && for pyfile in ../utils/*.py; do ln -s $pyfile; done"] + +sanity_check_paths = { + 'files': ['bin/molgw', 'bin/run_molgw.py'], + 'dirs': ['basis', 'utils'] +} + +sanity_check_commands = ["python -s -c 'import molgw'"] + +modextrapaths = { + 'PYTHONPATH': 'utils', + 'MOLGW_BASIS_PATH': 'basis', +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/m/MONAI/MONAI-1.3.0-foss-2022b.eb b/easybuild/easyconfigs/m/MONAI/MONAI-1.3.0-foss-2022b.eb new file mode 100644 index 00000000000..29dbbe424ba --- /dev/null +++ b/easybuild/easyconfigs/m/MONAI/MONAI-1.3.0-foss-2022b.eb @@ -0,0 +1,96 @@ +easyblock = 'PythonBundle' + +name = 'MONAI' +version = '1.3.0' + +homepage = 'https://monai.io/' +description = """ +MONAI is a PyTorch-based, open-source framework for deep learning in healthcare +imaging, part of PyTorch Ecosystem. +""" + +toolchain = {'name': 'foss', 'version': '2022b'} + +github_account = 'Project-MONAI' + +builddependencies = [ + ('Ninja', '1.11.1'), +] + +dependencies = [ + ('Python', '3.10.8'), + ('SciPy-bundle', '2023.02'), + ('PyTorch', '1.13.1'), + ('einops', '0.7.0'), + ('ITK', '5.3.0'), + ('NiBabel', '5.2.0'), + ('scikit-image', '0.21.0'), + ('tensorboard', '2.15.1'), + ('torchvision', '0.14.1'), + ('tqdm', '4.64.1'), + ('Pillow', '9.4.0'), + ('openslide-python', '1.3.1'), + ('BeautifulSoup', '4.11.1'), +] + +use_pip = True + +# install MONAI with list of 'extras', which require additional dependencies +local_pip_extras = "einops,fire,gdown,ignite,itk,jsonschema,lmdb,nibabel," +local_pip_extras += "openslide,pandas,pillow,psutil,pydicom,pyyaml,scipy," +local_pip_extras += "skimage,tensorboard,torchvision,tqdm" + +# PyTorch-Ignite v0.4.11 bundled as an extension because MONAI v1.3.0 has a strict requirement on it +exts_list = [ + ('gdown', '4.7.1', { + 'checksums': ['347f23769679aaf7efa73e5655270fcda8ca56be65eb84a4a21d143989541045'], + }), + ('lmdb', '1.4.1', { + 'checksums': ['1f4c76af24e907593487c904ef5eba1993beb38ed385af82adb25a858f2d658d'], + }), + ('termcolor', '2.3.0', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['3afb05607b89aed0ffe25202399ee0867ad4d3cb4180d98aaf8eefa6a5f7d475'], + }), + ('fire', '0.5.0', { + 'checksums': ['a6b0d49e98c8963910021f92bba66f65ab440da2982b78eb1bbf95a0a34aacc6'], + }), + ('pytorch-ignite', '0.4.11', { + 'modulename': 'ignite', + 'patches': ['PyTorch-Ignite-0.4.11_fix_error_on_importing_Events.patch'], + 'checksums': [ + {'pytorch-ignite-0.4.11.tar.gz': 'ee31096a58679417097ef7f3f27d88bec40b789ac5e13cd9ed08bc89ca8ce2e2'}, + {'PyTorch-Ignite-0.4.11_fix_error_on_importing_Events.patch': + 'd45c0da30c01f7ce47b7be49a6d5d6eb9529c94a0b9de89260d4b07d9d2359e0'}, + ], + }), + (name, version, { + 'preinstallopts': 'BUILD_MONAI=1', + 'source_urls': ['https://github.com/%(github_account)s/%(name)s/archive'], + 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}], + 'use_pip_extras': local_pip_extras, + # 2 valid checksums, as source tarball provided by GitHub for MONAI 1.3.0 slightly changed at some point + # see also https://github.com/easybuilders/easybuild-easyconfigs/issues/20617 + 'checksums': [('67e0f55678faad4bd38b1ea69d5de94586b20b551b8ad745415623a8b6c1c5e2', + '076d75458d490b4f2dafbf5974fcc8e07a86c03f39f5ef48c6689ab6e4347da9')], + }), +] + +sanity_pip_check = True + +# 'pip check' does not verify whether all optional dependencies required to support 'extras' +# are actually available, so we do it here via an import check; +local_extra_mod_check = {x: x for x in local_pip_extras.split(",")} +# Some special cases with different module name than extra name +local_extra_mod_check['pillow'] = 'PIL' +local_extra_mod_check['pyyaml'] = 'yaml' + +sanity_check_commands = ["python -c 'import monai; monai.config.print_config()'"] +sanity_check_commands += ["python -c 'import %s'" % local_extra_mod_check[x] for x in local_extra_mod_check] + +sanity_check_paths = { + 'files': ['lib/python%%(pyshortver)s/site-packages/%%(namelower)s/_C.%s' % SHLIB_EXT], + 'dirs': ['lib/python%(pyshortver)s/site-packages/ignite'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/m/MONAI/MONAI-1.3.0-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/m/MONAI/MONAI-1.3.0-foss-2023a-CUDA-12.1.1.eb index a72067a307e..5c196d917a9 100644 --- a/easybuild/easyconfigs/m/MONAI/MONAI-1.3.0-foss-2023a-CUDA-12.1.1.eb +++ b/easybuild/easyconfigs/m/MONAI/MONAI-1.3.0-foss-2023a-CUDA-12.1.1.eb @@ -73,7 +73,10 @@ exts_list = [ 'source_urls': ['https://github.com/%(github_account)s/%(name)s/archive'], 'sources': ['%(version)s.tar.gz'], 'use_pip_extras': local_pip_extras, - 'checksums': ['67e0f55678faad4bd38b1ea69d5de94586b20b551b8ad745415623a8b6c1c5e2'], + # 2 valid checksums, as source tarball provided by GitHub for MONAI 1.3.0 slightly changed at some point + # see also https://github.com/easybuilders/easybuild-easyconfigs/issues/20617 + 'checksums': [('67e0f55678faad4bd38b1ea69d5de94586b20b551b8ad745415623a8b6c1c5e2', + '076d75458d490b4f2dafbf5974fcc8e07a86c03f39f5ef48c6689ab6e4347da9')], }), ] diff --git a/easybuild/easyconfigs/m/MONAI/MONAI-1.3.0-foss-2023a.eb b/easybuild/easyconfigs/m/MONAI/MONAI-1.3.0-foss-2023a.eb index c00b11caf83..1132edecf91 100644 --- a/easybuild/easyconfigs/m/MONAI/MONAI-1.3.0-foss-2023a.eb +++ b/easybuild/easyconfigs/m/MONAI/MONAI-1.3.0-foss-2023a.eb @@ -71,7 +71,10 @@ exts_list = [ 'source_urls': ['https://github.com/%(github_account)s/%(name)s/archive'], 'sources': ['%(version)s.tar.gz'], 'use_pip_extras': local_pip_extras, - 'checksums': ['67e0f55678faad4bd38b1ea69d5de94586b20b551b8ad745415623a8b6c1c5e2'], + # 2 valid checksums, as source tarball provided by GitHub for MONAI 1.3.0 slightly changed at some point + # see also https://github.com/easybuilders/easybuild-easyconfigs/issues/20617 + 'checksums': [('67e0f55678faad4bd38b1ea69d5de94586b20b551b8ad745415623a8b6c1c5e2', + '076d75458d490b4f2dafbf5974fcc8e07a86c03f39f5ef48c6689ab6e4347da9')], }), ] diff --git a/easybuild/easyconfigs/m/MPC/MPC-1.3.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/m/MPC/MPC-1.3.1-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..dce3ae2d1d9 --- /dev/null +++ b/easybuild/easyconfigs/m/MPC/MPC-1.3.1-GCCcore-13.3.0.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'MPC' +version = '1.3.1' + +homepage = 'http://www.multiprecision.org/' +description = """Gnu Mpc is a C library for the arithmetic of + complex numbers with arbitrarily high precision and correct + rounding of the result. It extends the principles of the IEEE-754 + standard for fixed precision real floating point numbers to + complex numbers, providing well-defined semantics for every + operation. At the same time, speed of operation at high precision + is a major design goal.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://ftpmirror.gnu.org/gnu/mpc/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['ab642492f5cf882b74aa0cb730cd410a81edcdbec895183ce930e706c1c759b8'] + +builddependencies = [('binutils', '2.42')] + +dependencies = [ + ('GMP', '6.3.0'), + ('MPFR', '4.2.1'), +] + +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libmpc.%s' % SHLIB_EXT, 'include/mpc.h'], + 'dirs': [] +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/m/MPFI/MPFI-1.5.4-GCCcore-13.2.0.eb b/easybuild/easyconfigs/m/MPFI/MPFI-1.5.4-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..aa47b551aab --- /dev/null +++ b/easybuild/easyconfigs/m/MPFI/MPFI-1.5.4-GCCcore-13.2.0.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'MPFI' +version = '1.5.4' + +homepage = 'https://perso.ens-lyon.fr/nathalie.revol/software.html' +description = "MPFI stands for Multiple Precision Floating-point Interval library." + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://perso.ens-lyon.fr/nathalie.revol/softwares/'] +sources = ['mpfi-%(version)s.tar.bz2'] +checksums = ['d20ba56a8d57d0816f028be8b18a4aa909a068efcb9a260e69577939e4199752'] + +builddependencies = [('binutils', '2.40')] + +dependencies = [ + ('MPFR', '4.2.1'), +] + +sanity_check_paths = { + 'files': ['include/mpfi.h'] + ['lib/libmpfi.%s' % e for e in ['a', SHLIB_EXT]], + 'dirs': ['share'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/m/MPFR/MPFR-4.2.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/m/MPFR/MPFR-4.2.1-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..6b5fb75a0a3 --- /dev/null +++ b/easybuild/easyconfigs/m/MPFR/MPFR-4.2.1-GCCcore-13.3.0.eb @@ -0,0 +1,39 @@ +easyblock = 'ConfigureMake' + +name = 'MPFR' +version = '4.2.1' + +homepage = 'https://www.mpfr.org' + +description = """ + The MPFR library is a C library for multiple-precision floating-point + computations with correct rounding. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://www.mpfr.org/mpfr-%(version)s/'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['b9df93635b20e4089c29623b19420c4ac848a1b29df1cfd59f26cab0d2666aa0'] + +builddependencies = [ + ('binutils', '2.42'), +] + +dependencies = [ + ('GMP', '6.3.0'), +] + +runtest = 'check' + +# copy libmpfr.so* to /lib to make sure that it is picked up by tests +# when EasyBuild is configured with --rpath, and clean up afterwards (let 'make install' do its job) +pretestopts = "mkdir -p %%(installdir)s/lib && cp -a src/.libs/libmpfr.%s* %%(installdir)s/lib && " % SHLIB_EXT +testopts = " && rm -r %(installdir)s/lib" + +sanity_check_paths = { + 'files': ['lib/libmpfr.%s' % SHLIB_EXT, 'include/mpfr.h'], + 'dirs': [], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/m/MPICH/MPICH-4.2.1-GCC-12.3.0.eb b/easybuild/easyconfigs/m/MPICH/MPICH-4.2.1-GCC-12.3.0.eb new file mode 100644 index 00000000000..08f9b0e3d4d --- /dev/null +++ b/easybuild/easyconfigs/m/MPICH/MPICH-4.2.1-GCC-12.3.0.eb @@ -0,0 +1,20 @@ +name = 'MPICH' +version = '4.2.1' + +homepage = 'https://www.mpich.org/' +description = """MPICH is a high-performance and widely portable implementation +of the Message Passing Interface (MPI) standard (MPI-1, MPI-2 and MPI-3).""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +source_urls = ['https://www.mpich.org/static/downloads/%(version)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['23331b2299f287c3419727edc2df8922d7e7abbb9fd0ac74e03b9966f9ad42d7'] + +configopts = 'FFLAGS="-w -fallow-argument-mismatch -O2" --with-devices=ch4:ucx --with-ucx=$EBROOTUCX' + +dependencies = [ + ('UCX', '1.14.1'), +] + +moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/m/MPICH/MPICH-4.2.2-GCC-13.3.0.eb b/easybuild/easyconfigs/m/MPICH/MPICH-4.2.2-GCC-13.3.0.eb new file mode 100644 index 00000000000..2b2b2185ecc --- /dev/null +++ b/easybuild/easyconfigs/m/MPICH/MPICH-4.2.2-GCC-13.3.0.eb @@ -0,0 +1,21 @@ +name = 'MPICH' +version = '4.2.2' + +homepage = 'https://www.mpich.org/' +description = """MPICH is a high-performance and widely portable implementation +of the Message Passing Interface (MPI) standard (MPI-1, MPI-2 and MPI-3).""" + +toolchain = {'name': 'GCC', 'version': '13.3.0'} + +source_urls = ['https://www.mpich.org/static/downloads/%(version)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['883f5bb3aeabf627cb8492ca02a03b191d09836bbe0f599d8508351179781d41'] + +dependencies = [ + ('UCX', '1.16.0'), +] + +configopts = 'FFLAGS="-w -fallow-argument-mismatch -O2" --with-devices=ch4:ucx --with-ucx=$EBROOTUCX' + + +moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/m/MUMPS/MUMPS-5.6.1-foss-2023b-metis.eb b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.6.1-foss-2023b-metis.eb new file mode 100644 index 00000000000..b9fb9f3ce74 --- /dev/null +++ b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.6.1-foss-2023b-metis.eb @@ -0,0 +1,35 @@ +name = 'MUMPS' +version = '5.6.1' +versionsuffix = '-metis' + +homepage = 'https://graal.ens-lyon.fr/MUMPS/' +description = "A parallel sparse direct solver" + +toolchain = {'name': 'foss', 'version': '2023b'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://graal.ens-lyon.fr/MUMPS/'] +sources = ['%(name)s_%(version)s.tar.gz'] +patches = [ + '%(name)s-%(version)s_shared-pord.patch', # builds the shared libs of PORD + '%(name)s-%(version)s_shared-mumps.patch', # builds shared libs of MUMPS +] +checksums = [ + {'MUMPS_5.6.1.tar.gz': '1920426d543e34d377604070fde93b8d102aa38ebdf53300cbce9e15f92e2896'}, + {'MUMPS-5.6.1_shared-pord.patch': '51d3685208a42581b462592eea977f185d87e871fb65e8e90a54dd2ad18ac715'}, + {'MUMPS-5.6.1_shared-mumps.patch': '27f788a5f85e8c9a6a7ec1651097b87c1de0ede0be943df7a10fa7c1ff5f494f'}, +] + +dependencies = [ + ('SCOTCH', '7.0.4'), + ('METIS', '5.1.0'), +] + +parallel = 1 + +# fix 'Type mismatch between actual argument' errors with GCC 10.x +prebuildopts = 'export FFLAGS="$FFLAGS -fallow-argument-mismatch" && ' + +buildopts = 'all SONAME_VERSION="%(version)s"' + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/m/MUMPS/MUMPS-5.7.2-foss-2023b-parmetis.eb b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.7.2-foss-2023b-parmetis.eb new file mode 100644 index 00000000000..1b7b70075c2 --- /dev/null +++ b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.7.2-foss-2023b-parmetis.eb @@ -0,0 +1,27 @@ +name = 'MUMPS' +version = '5.7.2' +versionsuffix = '-parmetis' + +homepage = 'https://graal.ens-lyon.fr/MUMPS/' +description = "A parallel sparse direct solver" + +toolchain = {'name': 'foss', 'version': '2023b'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['http://mumps-solver.org/'] +sources = ['%(name)s_%(version)s.tar.gz'] +checksums = ['1362d377ce7422fc886c55212b4a4d2c381918b5ca4478f682a22d0627a8fbf8'] + +dependencies = [ + ('SCOTCH', '7.0.4'), + ('ParMETIS', '4.0.3'), +] + +parallel = 1 + +# fix 'Type mismatch between actual argument' errors with GCC 10.x +prebuildopts = 'export FFLAGS="$FFLAGS -fallow-argument-mismatch" && ' + +buildopts = 'all SONAME_VERSION="%(version)s"' + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/m/MUMPS/MUMPS-5.7.2-intel-2023b-parmetis.eb b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.7.2-intel-2023b-parmetis.eb new file mode 100644 index 00000000000..589710ed6ee --- /dev/null +++ b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.7.2-intel-2023b-parmetis.eb @@ -0,0 +1,27 @@ +name = 'MUMPS' +version = '5.7.2' +versionsuffix = '-parmetis' + +homepage = 'https://graal.ens-lyon.fr/MUMPS/' +description = "A parallel sparse direct solver" + +toolchain = {'name': 'intel', 'version': '2023b'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['http://mumps-solver.org/'] +sources = ['%(name)s_%(version)s.tar.gz'] +checksums = ['1362d377ce7422fc886c55212b4a4d2c381918b5ca4478f682a22d0627a8fbf8'] + +dependencies = [ + ('SCOTCH', '7.0.4'), + ('ParMETIS', '4.0.3'), +] + +parallel = 1 + +# fix 'Type mismatch between actual argument' errors with GCC 10.x +prebuildopts = 'export FFLAGS="$FFLAGS -fallow-argument-mismatch" && ' + +buildopts = 'all SONAME_VERSION="%(version)s"' + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/m/MUMmer/MUMmer-4.0.0rc1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/m/MUMmer/MUMmer-4.0.0rc1-GCCcore-11.2.0.eb index 609e244fec2..c261d2484b3 100644 --- a/easybuild/easyconfigs/m/MUMmer/MUMmer-4.0.0rc1-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/m/MUMmer/MUMmer-4.0.0rc1-GCCcore-11.2.0.eb @@ -8,7 +8,7 @@ easyblock = 'ConfigureMake' name = 'MUMmer' version = '4.0.0rc1' -homepage = 'http://mummer.sourceforge.net/' +homepage = 'https://mummer.sourceforge.net/' description = """ MUMmer is a system for rapidly aligning entire genomes, @@ -22,7 +22,15 @@ source_urls = ['https://github.com/gmarcais/mummer/releases/download/v%(version) sources = ['%(namelower)s-%(version)s.tar.gz'] checksums = ['85006adb2d6539c2f738c3e3bb14b58bb6f62cd6c6ca5ede884a87ae76e07d1d'] -builddependencies = [('binutils', '2.37')] +builddependencies = [ + ('binutils', '2.37'), +] + +dependencies = [ + ('gnuplot', '5.4.2'), +] + +configopts = 'GNUPLOT=gnuplot' sanity_check_paths = { 'files': ['bin/mummer', 'bin/annotate', 'bin/combineMUMs', 'bin/delta-filter', diff --git a/easybuild/easyconfigs/m/MUMmer/MUMmer-4.0.0rc1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/m/MUMmer/MUMmer-4.0.0rc1-GCCcore-11.3.0.eb index d078c854c66..f403869b209 100644 --- a/easybuild/easyconfigs/m/MUMmer/MUMmer-4.0.0rc1-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/m/MUMmer/MUMmer-4.0.0rc1-GCCcore-11.3.0.eb @@ -22,7 +22,15 @@ source_urls = ['https://github.com/gmarcais/mummer/releases/download/v%(version) sources = ['%(namelower)s-%(version)s.tar.gz'] checksums = ['85006adb2d6539c2f738c3e3bb14b58bb6f62cd6c6ca5ede884a87ae76e07d1d'] -builddependencies = [('binutils', '2.38')] +builddependencies = [ + ('binutils', '2.38'), +] + +dependencies = [ + ('gnuplot', '5.4.4'), +] + +configopts = 'GNUPLOT=gnuplot' sanity_check_paths = { 'files': ['bin/mummer', 'bin/annotate', 'bin/combineMUMs', 'bin/delta-filter', diff --git a/easybuild/easyconfigs/m/MUMmer/MUMmer-4.0.0rc1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/m/MUMmer/MUMmer-4.0.0rc1-GCCcore-12.2.0.eb index b2d716125cf..ce38884c04c 100644 --- a/easybuild/easyconfigs/m/MUMmer/MUMmer-4.0.0rc1-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/m/MUMmer/MUMmer-4.0.0rc1-GCCcore-12.2.0.eb @@ -24,7 +24,15 @@ source_urls = ['https://github.com/gmarcais/mummer/releases/download/v%(version) sources = ['%(namelower)s-%(version)s.tar.gz'] checksums = ['85006adb2d6539c2f738c3e3bb14b58bb6f62cd6c6ca5ede884a87ae76e07d1d'] -builddependencies = [('binutils', '2.39')] +builddependencies = [ + ('binutils', '2.39'), +] + +dependencies = [ + ('gnuplot', '5.4.6'), +] + +configopts = 'GNUPLOT=gnuplot' sanity_check_paths = { 'files': ['bin/mummer', 'bin/annotate', 'bin/combineMUMs', 'bin/delta-filter', diff --git a/easybuild/easyconfigs/m/MUMmer/MUMmer-4.0.0rc1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/m/MUMmer/MUMmer-4.0.0rc1-GCCcore-12.3.0.eb index 46bb7b4a03f..809143d9839 100644 --- a/easybuild/easyconfigs/m/MUMmer/MUMmer-4.0.0rc1-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/m/MUMmer/MUMmer-4.0.0rc1-GCCcore-12.3.0.eb @@ -25,7 +25,15 @@ source_urls = ['https://github.com/gmarcais/mummer/releases/download/v%(version) sources = ['%(namelower)s-%(version)s.tar.gz'] checksums = ['85006adb2d6539c2f738c3e3bb14b58bb6f62cd6c6ca5ede884a87ae76e07d1d'] -builddependencies = [('binutils', '2.40')] +builddependencies = [ + ('binutils', '2.40'), +] + +dependencies = [ + ('gnuplot', '5.4.8'), +] + +configopts = 'GNUPLOT=gnuplot' sanity_check_paths = { 'files': ['bin/mummer', 'bin/annotate', 'bin/combineMUMs', 'bin/delta-filter', diff --git a/easybuild/easyconfigs/m/MUSCLE/MUSCLE-5.1.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/m/MUSCLE/MUSCLE-5.1.0-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..8af91759937 --- /dev/null +++ b/easybuild/easyconfigs/m/MUSCLE/MUSCLE-5.1.0-GCCcore-12.2.0.eb @@ -0,0 +1,39 @@ +easyblock = 'MakeCp' + +name = 'MUSCLE' +version = '5.1.0' + +homepage = 'https://drive5.com/muscle/' +description = """MUSCLE is one of the best-performing multiple alignment programs + according to published benchmark tests, with accuracy and speed that are consistently + better than CLUSTALW. MUSCLE can align hundreds of sequences in seconds. Most users + learn everything they need to know about MUSCLE in a few minutes-only a handful of + command-line options are needed to perform common alignment tasks.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +github_account = 'rcedgar' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['2bba8b06e3ccabf6465fa26f459763b2029d7e7b9596881063e3aaba60d9e87d'] + +builddependencies = [ + ('binutils', '2.39'), +] + +start_dir = 'src' + +# Use build environment defined by EasyBuild +prebuildopts = "sed -i 's/$(CPPOPTS)/$(CPPOPTS) $(CXXFLAGS) $(CPPFLAGS)/g' Makefile &&" +buildopts = "CPP=${CXX} CC=${CC}" + +files_to_copy = [(['Linux/muscle'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/muscle'], + 'dirs': [], +} + +sanity_check_commands = ["muscle -h"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/Mako/Mako-1.3.5-GCCcore-13.3.0.eb b/easybuild/easyconfigs/m/Mako/Mako-1.3.5-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..6df66e4a2e0 --- /dev/null +++ b/easybuild/easyconfigs/m/Mako/Mako-1.3.5-GCCcore-13.3.0.eb @@ -0,0 +1,35 @@ +easyblock = 'PythonBundle' + +name = 'Mako' +version = '1.3.5' + +homepage = 'https://www.makotemplates.org' +description = """A super-fast templating language that borrows the best ideas from the existing templating languages""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +builddependencies = [('binutils', '2.42')] + +dependencies = [('Python', '3.12.3')] + +use_pip = True + +exts_list = [ + ('MarkupSafe', '2.1.5', { + 'checksums': ['d283d37a890ba4c1ae73ffadf8046435c76e7bc2247bbb63c00bd1a709c6544b'], + }), + (name, version, { + 'checksums': ['48dbc20568c1d276a2698b36d968fa76161bf127194907ea6fc594fa81f943bc'], + }), +] + +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/mako-render'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(namelower)s'], +} + +sanity_check_commands = ["mako-render --help"] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/m/MariaDB/MariaDB-11.6.0-GCC-12.3.0.eb b/easybuild/easyconfigs/m/MariaDB/MariaDB-11.6.0-GCC-12.3.0.eb new file mode 100644 index 00000000000..35743343440 --- /dev/null +++ b/easybuild/easyconfigs/m/MariaDB/MariaDB-11.6.0-GCC-12.3.0.eb @@ -0,0 +1,65 @@ +easyblock = 'CMakeMake' + +name = 'MariaDB' +version = '11.6.0' + +homepage = 'https://mariadb.org/' +description = """MariaDB is an enhanced, drop-in replacement for MySQL. +Included engines: myISAM, Aria, InnoDB, RocksDB, TokuDB, OQGraph, Mroonga.""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +source_urls = [ + 'https://archive.mariadb.org/mariadb-%(version)s/source/', + 'http://ftp.hosteurope.de/mirror/archive.mariadb.org/mariadb-%(version)s/source', +] +sources = [SOURCELOWER_TAR_GZ] +patches = ['MariaDB-10.1.13-link-rt-for-jemalloc.patch'] +checksums = [ + {'mariadb-11.6.0.tar.gz': '8fd5b593aee3920eb434c37ec44779d565fe96ef7dfd6b35a646fe7221103e11'}, + {'MariaDB-10.1.13-link-rt-for-jemalloc.patch': '8295837e623f6c782e1d64b00e0877ea98cce4bf8846755bb86c8a7732797c19'}, +] + +builddependencies = [ + ('CMake', '3.26.3'), + ('libaio', '0.3.113'), +] + +dependencies = [ + ('ncurses', '6.4'), + ('zlib', '1.2.13'), + ('LZO', '2.10'), # optional + ('lz4', '1.9.4'), # optional + ('XZ', '5.4.2'), # optional + ('jemalloc', '5.3.0'), # optional + ('snappy', '1.1.10'), # needed by RocksDB; optional for InnoDB + ('libxml2', '2.11.4'), # needed by Connect XML + ('Boost', '1.82.0'), # needed by OQGraph + ('Judy', '1.0.5'), # needed by OQGraph + ('PCRE2', '10.42'), + ('OpenSSL', '1.1', '', SYSTEM), # runtime dep for mysql and PCRE2 for mysqltest +] + +configopts = "-DCMAKE_SHARED_LINKER_FLAGS='-fuse-ld=bfd' " # Linking fails with default gold linker +configopts += "-DMYSQL_MAINTAINER_MODE=OFF " # disabled to not treat warnings as errors (-Werror) +configopts += "-DWITH_PCRE=auto " # External download sometimes fails so we build PCRE2 directly. +configopts += "-DWITH_ZLIB=system " +configopts += "-DWITH_EMBEDDED_SERVER=ON " # for libmysqld.so & co +configopts += "-DWITH_SAFEMALLOC=OFF " # Disable memory debugger with jemalloc + +sanity_check_commands = ["mysql --help", "mysqltest --help"] + +sanity_check_paths = { + 'files': ['bin/mysql', 'bin/mysqld_safe', 'lib/libmysqlclient.%s' % SHLIB_EXT, 'lib/libmysqld.%s' % SHLIB_EXT, + 'lib/plugin/ha_connect.%s' % SHLIB_EXT, 'lib/plugin/ha_rocksdb.%s' % SHLIB_EXT, + 'lib/plugin/ha_oqgraph.%s' % SHLIB_EXT, 'scripts/mysql_install_db'], + 'dirs': ['include', 'share'], +} + +modextrapaths = {'PATH': 'scripts'} + +# Ensure that jemalloc does not use transparent hugepages. +# Database workloads with THP can cause memory bloat, potentially hiting OOM errors. +modextravars = {'MALLOC_CONF': 'thp:never'} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/m/MariaDB/MariaDB-11.7.0-GCC-13.3.0.eb b/easybuild/easyconfigs/m/MariaDB/MariaDB-11.7.0-GCC-13.3.0.eb new file mode 100644 index 00000000000..437ed1edf42 --- /dev/null +++ b/easybuild/easyconfigs/m/MariaDB/MariaDB-11.7.0-GCC-13.3.0.eb @@ -0,0 +1,65 @@ +easyblock = 'CMakeMake' + +name = 'MariaDB' +version = '11.7.0' + +homepage = 'https://mariadb.org/' +description = """MariaDB is an enhanced, drop-in replacement for MySQL. +Included engines: myISAM, Aria, InnoDB, RocksDB, TokuDB, OQGraph, Mroonga.""" + +toolchain = {'name': 'GCC', 'version': '13.3.0'} + +source_urls = [ + 'https://archive.mariadb.org/mariadb-%(version)s/source/', + 'http://ftp.hosteurope.de/mirror/archive.mariadb.org/mariadb-%(version)s/source', +] +sources = [SOURCELOWER_TAR_GZ] +patches = ['MariaDB-10.1.13-link-rt-for-jemalloc.patch'] +checksums = [ + {'mariadb-11.7.0.tar.gz': 'b0059a9550bb277790f1ec51e0eb329a8fbb8acfd98b5adb259bc0560ff70553'}, + {'MariaDB-10.1.13-link-rt-for-jemalloc.patch': '8295837e623f6c782e1d64b00e0877ea98cce4bf8846755bb86c8a7732797c19'}, +] + +builddependencies = [ + ('CMake', '3.29.3'), + ('libaio', '0.3.113'), +] + +dependencies = [ + ('ncurses', '6.5'), + ('zlib', '1.3.1'), + ('LZO', '2.10'), # optional + ('lz4', '1.9.4'), # optional + ('XZ', '5.4.5'), # optional + ('jemalloc', '5.3.0'), # optional + ('snappy', '1.1.10'), # needed by RocksDB; optional for InnoDB + ('libxml2', '2.12.7'), # needed by Connect XML + ('Boost', '1.85.0'), # needed by OQGraph + ('Judy', '1.0.5'), # needed by OQGraph + ('PCRE2', '10.43'), + ('OpenSSL', '3', '', SYSTEM), # runtime dep for mysql and PCRE2 for mysqltest +] + +configopts = "-DCMAKE_SHARED_LINKER_FLAGS='-fuse-ld=bfd' " # Linking fails with default gold linker +configopts += "-DMYSQL_MAINTAINER_MODE=OFF " # disabled to not treat warnings as errors (-Werror) +configopts += "-DWITH_PCRE=auto " # External download sometimes fails so we build PCRE2 directly. +configopts += "-DWITH_ZLIB=system " +configopts += "-DWITH_EMBEDDED_SERVER=ON " # for libmysqld.so & co +configopts += "-DWITH_SAFEMALLOC=OFF " # Disable memory debugger with jemalloc + +sanity_check_commands = ["mysql --help", "mysqltest --help"] + +sanity_check_paths = { + 'files': ['bin/mysql', 'bin/mysqld_safe', 'lib/libmysqlclient.%s' % SHLIB_EXT, 'lib/libmysqld.%s' % SHLIB_EXT, + 'lib/plugin/ha_connect.%s' % SHLIB_EXT, 'lib/plugin/ha_rocksdb.%s' % SHLIB_EXT, + 'lib/plugin/ha_oqgraph.%s' % SHLIB_EXT, 'scripts/mysql_install_db'], + 'dirs': ['include', 'share'], +} + +modextrapaths = {'PATH': 'scripts'} + +# Ensure that jemalloc does not use transparent hugepages. +# Database workloads with THP can cause memory bloat, potentially hiting OOM errors. +modextravars = {'MALLOC_CONF': 'thp:never'} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/m/Markdown/Markdown-3.6-GCCcore-12.3.0.eb b/easybuild/easyconfigs/m/Markdown/Markdown-3.6-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..84b4c527498 --- /dev/null +++ b/easybuild/easyconfigs/m/Markdown/Markdown-3.6-GCCcore-12.3.0.eb @@ -0,0 +1,24 @@ +easyblock = 'PythonPackage' + +name = 'Markdown' +version = '3.6' + +homepage = 'https://python-markdown.github.io/' +description = """This is a Python implementation of John Gruber's Markdown. +It is almost completely compliant with the reference implementation, though there are a few known issues. +Additional features are supported by the Available Extensions. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['ed4f41f6daecbeeb96e576ce414c41d2d876daa9a16cb35fa8ed8c2ddfad0224'] + +builddependencies = [('binutils', '2.40')] +dependencies = [('Python', '3.11.3')] + +download_dep_fail = True +sanity_pip_check = True +use_pip = True + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/m/Markdown/Markdown-3.7-GCCcore-13.3.0.eb b/easybuild/easyconfigs/m/Markdown/Markdown-3.7-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..04b5629d6bf --- /dev/null +++ b/easybuild/easyconfigs/m/Markdown/Markdown-3.7-GCCcore-13.3.0.eb @@ -0,0 +1,24 @@ +easyblock = 'PythonPackage' + +name = 'Markdown' +version = '3.7' + +homepage = 'https://python-markdown.github.io/' +description = """This is a Python implementation of John Gruber's Markdown. +It is almost completely compliant with the reference implementation, though there are a few known issues. +Additional features are supported by the Available Extensions. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['2ae2471477cfd02dbbf038d5d9bc226d40def84b4fe2986e49b59b6b472bbed2'] + +builddependencies = [('binutils', '2.42')] +dependencies = [('Python', '3.12.3')] + +download_dep_fail = True +sanity_pip_check = True +use_pip = True + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/m/Maven/Maven-3.9.7.eb b/easybuild/easyconfigs/m/Maven/Maven-3.9.7.eb new file mode 100644 index 00000000000..63a55f376df --- /dev/null +++ b/easybuild/easyconfigs/m/Maven/Maven-3.9.7.eb @@ -0,0 +1,26 @@ +# Contribution from the Crick HPC team +# uploaded by J. Sassmannshausen + +easyblock = 'PackedBinary' + +name = 'Maven' +version = '3.9.7' + +homepage = 'https://maven.apache.org/index.html' +description = """Binary maven install, Apache Maven is a software project management and comprehension tool. Based on +the concept of a project object model (POM), Maven can manage a project's build, reporting and documentation from a +central piece of information. +""" + +toolchain = SYSTEM + +source_urls = ['https://archive.apache.org/dist/maven/maven-%(version_major)s/%(version)s/binaries/'] +sources = ['apache-maven-%(version)s-bin.tar.gz'] +checksums = ['c8fb9f620e5814588c2241142bbd9827a08e3cb415f7aa437f2ed44a3eeab62c'] + +sanity_check_paths = { + 'files': ['bin/mvn'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/m/Mercurial/Mercurial-6.8.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/m/Mercurial/Mercurial-6.8.1-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..a733004f29a --- /dev/null +++ b/easybuild/easyconfigs/m/Mercurial/Mercurial-6.8.1-GCCcore-13.3.0.eb @@ -0,0 +1,31 @@ +# # +# Author: Robert Mijakovic +# # +easyblock = 'PythonPackage' + +name = 'Mercurial' +version = '6.8.1' + +homepage = 'https://www.mercurial-scm.org' +description = """Mercurial is a free, distributed source control management tool. It efficiently handles projects +of any size and offers an easy and intuitive interface. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://www.%(namelower)s-scm.org/release/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['030e8a7a6d590e4eaeb403ee25675615cd80d236f3ab8a0b56dcc84181158b05'] + +dependencies = [ + ('binutils', '2.42'), + ('Python', '3.12.3'), +] + +download_dep_fail = True +sanity_pip_check = True +use_pip = True + +sanity_check_commands = ['hg --help'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-24.1.3-GCCcore-13.3.0.eb b/easybuild/easyconfigs/m/Mesa/Mesa-24.1.3-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..5eda042c494 --- /dev/null +++ b/easybuild/easyconfigs/m/Mesa/Mesa-24.1.3-GCCcore-13.3.0.eb @@ -0,0 +1,68 @@ +# This is a Mesa using software rendering via Gallium-DRI and libglvnd +# - libglvnd can dynamically choose between system-installed NVidia +# libGLX/libEGL or the software renderers provided by this Mesa +# - EGL is available +# +# Software renderers enabled (swr deprecated as of v22): +# - llvmpipe: uses LLVM for JIT code generation (multi-threaded) +# - softpipe: a reference Gallium driver +# Default renderer is llvmpipe. To use softpipe, set the environment +# variable GALLIUM_DRIVER=softpipe + +name = 'Mesa' +version = '24.1.3' + +homepage = 'https://www.mesa3d.org/' +description = """Mesa is an open-source implementation of the OpenGL specification - + a system for rendering interactive 3D graphics.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = [ + 'https://mesa.freedesktop.org/archive/', + 'https://mesa.freedesktop.org/archive/%(version)s', + 'ftp://ftp.freedesktop.org/pub/mesa/%(version)s', + 'ftp://ftp.freedesktop.org/pub/mesa/older-versions/%(version_major)s.x/%(version)s', + 'ftp://ftp.freedesktop.org/pub/mesa/older-versions/%(version_major)s.x', +] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['63236426b25a745ba6aa2d6daf8cd769d5ea01887b0745ab7124d2ef33a9020d'] + +builddependencies = [ + ('binutils', '2.42'), + ('Meson', '1.4.0'), + ('Ninja', '1.12.1'), + ('flex', '2.6.4'), + ('Bison', '3.8.2'), + ('pkgconf', '2.2.0'), + ('Mako', '1.3.5'), + ('libxml2', '2.12.7'), + ('expat', '2.6.2'), + ('gettext', '0.22.5'), +] + +dependencies = [ + ('zlib', '1.3.1'), + ('zstd', '1.5.6'), + ('libdrm', '2.4.122'), + ('libglvnd', '1.7.0'), + ('libunwind', '1.8.1'), + ('LLVM', '18.1.8'), + ('X11', '20240607'), + ('Wayland', '1.23.0'), +] + +configopts = "-Dplatforms=x11,wayland -Dosmesa=true -Dvulkan-drivers='swrast' -Dvulkan-layers='device-select' " +configopts += "-Dllvm=enabled -Dshared-llvm=enabled -Dlibunwind=enabled -Dglvnd=true " +configopts += "-Dvideo-codecs=vc1dec,h264dec,h264enc,h265dec,h265enc " + +# Easybuild will automatically add appropriate Gallium drivers for the processor architecture of the host +# If you need a different configuration, it possible to override those values by setting your own configopts +# configopts += " -Dgallium-drivers=swrast" + +# symlink indirect to mesa GLX, similar to Debian, see +# https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=881789 +# This helps in certain X forwarding situations (e.g. XQuartz) +postinstallcmds = ["ln -s libGLX_mesa.so.0 %(installdir)s/lib/libGLX_indirect.so.0"] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/m/MeshLab/MeshLab-2023.12-GCC-12.3.0.eb b/easybuild/easyconfigs/m/MeshLab/MeshLab-2023.12-GCC-12.3.0.eb new file mode 100644 index 00000000000..ca152c147be --- /dev/null +++ b/easybuild/easyconfigs/m/MeshLab/MeshLab-2023.12-GCC-12.3.0.eb @@ -0,0 +1,47 @@ +easyblock = 'CMakeNinja' + +name = 'MeshLab' +version = '2023.12' + +homepage = 'https://github.com/cnr-isti-vclab/meshlab' +description = 'The open source mesh processing system.' + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +sources = [{ + 'filename': '%(name)s-%(version)s.tar.gz', + 'git_config': { + 'url': 'https://github.com/cnr-isti-vclab', + 'repo_name': '%(namelower)s', + 'tag': '%(name)s-%(version)s', + 'recursive': True, + 'keep_git_dir': True, + }, +}] +checksums = [None] + +builddependencies = [ + ('CMake', '3.26.3'), + ('Ninja', '1.11.1'), + ('pkgconf', '1.9.5'), + ('patchelf', '0.18.0'), + ('Eigen', '3.4.0'), +] + +dependencies = [ + ('Qt5', '5.15.10'), + ('Mesa', '23.1.4'), + ('libGLU', '9.0.3'), + ('CGAL', '5.6'), + ('Boost', '1.82.0'), + ('MPFR', '4.2.0'), +] + +sanity_check_paths = { + 'files': ['bin/meshlab'], + 'dirs': ['share'], +} + +sanity_check_commands = ['meshlab --help'] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/m/Meson/Meson-1.4.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/m/Meson/Meson-1.4.0-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..7e8d5b0b7bb --- /dev/null +++ b/easybuild/easyconfigs/m/Meson/Meson-1.4.0-GCCcore-13.3.0.eb @@ -0,0 +1,36 @@ +easyblock = 'PythonPackage' + +name = 'Meson' +version = '1.4.0' + +homepage = 'https://mesonbuild.com' +description = "Meson is a cross-platform build system designed to be both as fast and as user friendly as possible." + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['8fd6630c25c27f1489a8a0392b311a60481a3c161aa699b330e25935b750138d'] + +builddependencies = [ + ('binutils', '2.42'), +] + +dependencies = [ + ('Python', '3.12.3'), # includes required 'wheel' package + ('Ninja', '1.12.1'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +options = {'modulename': 'mesonbuild'} + +sanity_check_paths = { + 'files': ['bin/meson'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["meson --help"] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/m/Miniconda3/Miniconda3-23.10.0-1.eb b/easybuild/easyconfigs/m/Miniconda3/Miniconda3-23.10.0-1.eb new file mode 100644 index 00000000000..3fd68df4e5c --- /dev/null +++ b/easybuild/easyconfigs/m/Miniconda3/Miniconda3-23.10.0-1.eb @@ -0,0 +1,27 @@ +easyblock = 'EB_Anaconda' + +name = 'Miniconda3' +version = '23.10.0-1' + +homepage = 'https://docs.conda.io/en/latest/miniconda.html' +description = """Miniconda is a free minimal installer for conda. It is a small, + bootstrap version of Anaconda that includes only conda, Python, the packages they + depend on, and a small number of other useful packages.""" + +toolchain = SYSTEM + +source_urls = ['https://repo.anaconda.com/miniconda/'] +local_arch = {'arm64': 'aarch64'}.get(ARCH, ARCH) +sources = ['%%(name)s-py311_%%(version)s-Linux-%s.sh' % local_arch] +checksums = [ + { + '%(name)s-py311_%(version)s-Linux-x86_64.sh': + 'd0643508fa49105552c94a523529f4474f91730d3e0d1f168f1700c43ae67595', + '%(name)s-py311_%(version)s-Linux-ppc64le.sh': + '1a2eda0a9a52a4bd058abbe9de5bb2bc751fcd7904c4755deffdf938d6f4436e', + '%(name)s-py311_%(version)s-Linux-aarch64.sh': + 'a60e70ad7e8ac5bb44ad876b5782d7cdc66e10e1f45291b29f4f8d37cc4aa2c8', + } +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/m/Miniconda3/Miniconda3-24.7.1-0.eb b/easybuild/easyconfigs/m/Miniconda3/Miniconda3-24.7.1-0.eb new file mode 100644 index 00000000000..c70f0086763 --- /dev/null +++ b/easybuild/easyconfigs/m/Miniconda3/Miniconda3-24.7.1-0.eb @@ -0,0 +1,17 @@ +easyblock = 'EB_Anaconda' + +name = 'Miniconda3' +version = '24.7.1-0' + +homepage = 'https://docs.conda.io/en/latest/miniconda.html' +description = """Miniconda is a free minimal installer for conda. It is a small, + bootstrap version of Anaconda that includes only conda, Python, the packages they + depend on, and a small number of other useful packages.""" + +toolchain = SYSTEM + +source_urls = ['https://repo.anaconda.com/miniconda/'] +sources = ['%(name)s-py312_%(version)s-Linux-x86_64.sh'] +checksums = ['33442cd3813df33dcbb4a932b938ee95398be98344dff4c30f7e757cd2110e4f'] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/m/ModelTest-NG/ModelTest-NG-0.2.0-dev_20220721-GCC-12.3.0.eb b/easybuild/easyconfigs/m/ModelTest-NG/ModelTest-NG-0.2.0-dev_20220721-GCC-12.3.0.eb new file mode 100644 index 00000000000..6973ef50246 --- /dev/null +++ b/easybuild/easyconfigs/m/ModelTest-NG/ModelTest-NG-0.2.0-dev_20220721-GCC-12.3.0.eb @@ -0,0 +1,60 @@ +easyblock = 'CMakeMakeCp' + +name = 'ModelTest-NG' +version = '0.2.0-dev_20220721' +_commit = '1066356' + +homepage = 'https://github.com/ddarriba/modeltest' +description = """ +ModelTest-NG is a tool for selecting the best-fit model of evolution for DNA and protein alignments. +ModelTest-NG supersedes jModelTest and ProtTest in one single tool, with graphical and command console interfaces. +""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +# use exact commits of pll-modules and libpll-2 as specified in CMakeLists.txt +sources = [ + { + 'source_urls': ['https://github.com/ddarriba/modeltest/archive'], + 'download_filename': '%s.tar.gz' % _commit, + 'filename': SOURCE_TAR_GZ, + }, + { + 'source_urls': ['https://github.com/ddarriba/pll-modules/archive'], + 'download_filename': '182ae28.tar.gz', + 'filename': 'pll-modules-182ae28.tar.gz', + 'extract_cmd': "tar -xzf %s -C %(builddir)s/modeltest*/libs/pll-modules/ --strip-components 1", + }, + { + 'source_urls': ['https://github.com/xflouris/libpll-2/archive'], + 'download_filename': 'a3146f3.tar.gz', + 'filename': 'libpll-a3146f3.tar.gz', + 'extract_cmd': "tar -xzf %s -C %(builddir)s/modeltest*/libs/pll-modules/libs/libpll/ --strip-components 1", + }, +] +checksums = [ + {'ModelTest-NG-0.2.0-dev_20220721.tar.gz': '1010630a9e0aff7ec125e2ab3dccd76625b935d535793b2d01b35a3a1e3021ae'}, + {'pll-modules-182ae28.tar.gz': 'd3bd1382e7bd5ef0a8f227bc1d47596bb806342113bb5fb2ad879e536e7873dd'}, + {'libpll-a3146f3.tar.gz': 'd4a36b30074e1f93530cab48744117f1b7e7c9c78ca7665f92624ca6a25f9b85'}, +] + +builddependencies = [('CMake', '3.26.3')] + +dependencies = [ + ('flex', '2.6.4'), + ('Bison', '3.8.2', '', SYSTEM), +] + +files_to_copy = ['bin'] + +sanity_check_paths = { + 'files': ["bin/modeltest-ng"], + 'dirs': [] +} + +sanity_check_commands = [ + "modeltest-ng --help", + "modeltest-ng -i %(builddir)s/*/example-data/dna/tiny.fas -t ml", +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/MoloVol/MoloVol-1.1.1-GCC-12.3.0.eb b/easybuild/easyconfigs/m/MoloVol/MoloVol-1.1.1-GCC-12.3.0.eb new file mode 100644 index 00000000000..45fc3443de9 --- /dev/null +++ b/easybuild/easyconfigs/m/MoloVol/MoloVol-1.1.1-GCC-12.3.0.eb @@ -0,0 +1,34 @@ +easyblock = 'CMakeMake' + +name = 'MoloVol' +version = '1.1.1' + +homepage = 'https://molovol.com/' +description = """ +MoloVol is a free, cross-plattform, scientific software for volume and surface computations of +single molecules and crystallographic unit cells. +""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +source_urls = ['https://github.com/molovol/MoloVol/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['b41ddd9d98156f602700504ec67bb2002c8621eb4a0b43b7d3d60b4a5d0e15bd'] + +builddependencies = [ + ('CMake', '3.26.3'), +] + +dependencies = [ + ('wxWidgets', '3.2.2.1'), + ('Xvfb', '21.1.8'), +] + +sanity_check_paths = { + 'files': ['bin/molovol'], + 'dirs': [], +} + +sanity_check_commands = ['xvfb-run molovol -h'] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/m/MrBayes/MrBayes-3.2.7-gompi-2023a.eb b/easybuild/easyconfigs/m/MrBayes/MrBayes-3.2.7-gompi-2023a.eb new file mode 100644 index 00000000000..a3537244720 --- /dev/null +++ b/easybuild/easyconfigs/m/MrBayes/MrBayes-3.2.7-gompi-2023a.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'MrBayes' +version = '3.2.7' + +homepage = "https://nbisweden.github.io/MrBayes/" +description = """MrBayes is a program for Bayesian inference and model choice across + a wide range of phylogenetic and evolutionary models.""" + +toolchain = {'name': 'gompi', 'version': '2023a'} + +source_urls = ['https://github.com/NBISweden/MrBayes/releases/download/v%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['39d9eb269969b501268d5c27f77687c6eaa2c71ccf15c724e6f330fc405f24b9'] + +dependencies = [ + ('libreadline', '8.2'), + ('beagle-lib', '4.0.1', '-CUDA-12.1.1'), +] + +configopts = "--with-mpi --with-readline --with-beagle=$EBROOTBEAGLEMINLIB " + +sanity_check_paths = { + 'files': ['bin/mb'], + 'dirs': ['share'], +} + +sanity_check_commands = ['mb -h'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/MultiQC/MultiQC-1.22.3-foss-2023b.eb b/easybuild/easyconfigs/m/MultiQC/MultiQC-1.22.3-foss-2023b.eb new file mode 100644 index 00000000000..ef34f8747cf --- /dev/null +++ b/easybuild/easyconfigs/m/MultiQC/MultiQC-1.22.3-foss-2023b.eb @@ -0,0 +1,80 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Adam Huffman +# The Francis Crick Institute +# Elements derived from work by Pablo Escobar +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +# Note that Click in Python 3 requires that you change your locale to unicode before invoking your Python script. +# See: https://click.palletsprojects.com/en/7.x/python3/ + +easyblock = 'PythonBundle' + +name = 'MultiQC' +version = '1.22.3' + +homepage = 'https://multiqc.info' +description = """Aggregate results from bioinformatics analyses across many samples into a single report. + + MultiQC searches a given directory for analysis logs and compiles an HTML report. It's a general + use tool, perfect for summarising the output from numerous bioinformatics tools.""" + +toolchain = {'name': 'foss', 'version': '2023b'} + +builddependencies = [('hatchling', '1.18.0')] + +dependencies = [ + ('Python', '3.11.5'), + ('Python-bundle-PyPI', '2023.10'), + ('Kaleido', '0.2.1'), + ('matplotlib', '3.8.2'), + ('plotly.py', '5.18.0'), + ('pydantic', '2.7.4'), + ('tqdm', '4.66.2'), + ('Pillow', '10.2.0'), + ('PyYAML', '6.0.1'), + ('networkx', '3.2.1'), +] + +use_pip = True + +exts_list = [ + ('colormath', '3.0.0', { + 'checksums': ['3d4605af344527da0e4f9f504fad7ddbebda35322c566a6c72e28edb1ff31217'], + }), + ('humanfriendly', '10.0', { + 'checksums': ['6b0b831ce8f15f7300721aa49829fc4e83921a9a301cc7f606be6686a2288ddc'], + }), + ('Markdown', '3.6', { + 'checksums': ['ed4f41f6daecbeeb96e576ce414c41d2d876daa9a16cb35fa8ed8c2ddfad0224'], + }), + ('coloredlogs', '15.0.1', { + 'checksums': ['7c991aa71a4577af2f82600d8f8f3a89f936baeaf9b50a9c197da014e5bf16b0'], + }), + ('humanize', '4.9.0', { + 'checksums': ['582a265c931c683a7e9b8ed9559089dea7edcf6cc95be39a3cbc2c5d5ac2bcfa'], + }), + ('pyaml_env', '1.2.1', { + 'checksums': ['6d5dc98c8c82df743a132c196e79963050c9feb05b0a6f25f3ad77771d3d95b0'], + }), + ('spectra', '0.0.11', { + 'checksums': ['8eb362a5187cb63cee13cd01186799c0c791a3ad3bec57b279132e12521762b8'], + }), + ('typeguard', '4.3.0', { + 'checksums': ['92ee6a0aec9135181eae6067ebd617fd9de8d75d714fb548728a4933b1dea651'], + }), + ('multiqc', version, { + 'checksums': ['5f2cc3c417b5ed4ad57bdff02d93bb7f4c6e6677768ddad1cde7b9b1e04b5854'], + }), +] + +sanity_check_paths = { + 'files': ['bin/multiqc'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["multiqc --help"] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/Mustache/Mustache-1.3.3-foss-2023b.eb b/easybuild/easyconfigs/m/Mustache/Mustache-1.3.3-foss-2023b.eb new file mode 100644 index 00000000000..214d5af84bf --- /dev/null +++ b/easybuild/easyconfigs/m/Mustache/Mustache-1.3.3-foss-2023b.eb @@ -0,0 +1,39 @@ +easyblock = 'PythonPackage' + +name = 'Mustache' +version = '1.3.3' + +homepage = 'https://github.com/ay-lab/mustache' +description = """Mustache (Multi-scale Detection of Chromatin Loops from Hi-C and Micro-C Maps using +Scale-Space Representation) is a tool for multi-scale detection of chromatin loops from Hi-C and Micro-C +contact maps in high resolutions (10kbp all the way to 500bp and even more). +Mustache uses recent technical advances in scale-space theory in +Computer Vision to detect chromatin loops caused by interaction of DNA segments with a variable size.""" + +toolchain = {'name': 'foss', 'version': '2023b'} + +source_urls = ['https://pypi.python.org/packages/source/m/mustache_hic'] +sources = [{'download_filename': 'mustache_hic-%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}] +checksums = ['fd7cca927e36145bf6e43903a79c3222ecfeeb497c8f57657d7647ec6eee5a6b'] + +dependencies = [ + ('Python', '3.11.5'), + ('Python-bundle-PyPI', '2023.10'), + ('SciPy-bundle', '2023.11'), + ('h5py', '3.11.0'), + ('HDF5', '1.14.3'), + ('cooler', '0.10.2'), + ('statsmodels', '0.14.1'), + ('hic-straw', '1.3.1'), +] + +# delete pathlib dependency from setup.py +preinstallopts = "sed -i 's/pathlib//' setup.py && " + +sanity_pip_check = True +use_pip = True +download_dep_fail = True + +options = {'modulename': 'mustache'} + +moduleclass = 'ai' diff --git a/easybuild/easyconfigs/m/maeparser/maeparser-1.3.1-gompi-2024a.eb b/easybuild/easyconfigs/m/maeparser/maeparser-1.3.1-gompi-2024a.eb new file mode 100644 index 00000000000..a757e81653a --- /dev/null +++ b/easybuild/easyconfigs/m/maeparser/maeparser-1.3.1-gompi-2024a.eb @@ -0,0 +1,26 @@ +easyblock = 'CMakeMake' + +name = 'maeparser' +version = '1.3.1' + +homepage = 'https://github.com/schrodinger/maeparser' +description = "maeparser is a parser for Schrodinger Maestro files." + +toolchain = {'name': 'gompi', 'version': '2024a'} + +source_urls = ['https://github.com/schrodinger/maeparser/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['a8d80f67d1b9be6e23b9651cb747f4a3200132e7d878a285119c86bf44568e36'] + +builddependencies = [ + ('CMake', '3.29.3'), +] + +dependencies = [('Boost', '1.85.0')] + +sanity_check_paths = { + 'files': ['lib/libmaeparser.%s' % SHLIB_EXT], + 'dirs': ['include/maeparser', 'lib/cmake'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/m/make/make-4.4.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/m/make/make-4.4.1-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..040ca1f7716 --- /dev/null +++ b/easybuild/easyconfigs/m/make/make-4.4.1-GCCcore-13.3.0.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'make' +version = '4.4.1' + +homepage = 'https://www.gnu.org/software/make/make.html' +description = "GNU version of make utility" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['dd16fb1d67bfab79a72f5e8390735c49e3e8e70b4945a15ab1f81ddb78658fb3'] + +builddependencies = [('binutils', '2.42')] + +postinstallcmds = ["cd %(installdir)s/bin && ln -s make gmake"] + +sanity_check_paths = { + 'files': ['bin/gmake', 'bin/make'], + 'dirs': [] +} + +sanity_check_commands = [ + "gmake --help", + "make --help", +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.9-GCCcore-13.2.0.eb b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.9-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..94178adcc23 --- /dev/null +++ b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.9-GCCcore-13.2.0.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'makedepend' +version = '1.0.9' + +homepage = 'https://linux.die.net/man/1/makedepend' +description = "The makedepend package contains a C-preprocessor like utility to determine build-time dependencies." + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = [XORG_UTIL_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['bc94ffda6cd4671603a69c39dbe8f96b317707b9185b2aaa3b54b5d134b41884'] + +builddependencies = [ + ('binutils', '2.40'), + ('xproto', '7.0.31'), + ('xorg-macros', '1.20.0'), +] + +sanity_check_paths = { + 'files': ['bin/makedepend'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.9-GCCcore-13.3.0.eb b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.9-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..20f151d30e1 --- /dev/null +++ b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.9-GCCcore-13.3.0.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'makedepend' +version = '1.0.9' + +homepage = 'https://linux.die.net/man/1/makedepend' +description = "The makedepend package contains a C-preprocessor like utility to determine build-time dependencies." + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = [XORG_UTIL_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['bc94ffda6cd4671603a69c39dbe8f96b317707b9185b2aaa3b54b5d134b41884'] + +builddependencies = [ + ('binutils', '2.42'), + ('xproto', '7.0.31'), + ('xorg-macros', '1.20.1'), +] + +sanity_check_paths = { + 'files': ['bin/makedepend'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/m/makefun/makefun-1.15.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/m/makefun/makefun-1.15.2-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..b4b0097cc53 --- /dev/null +++ b/easybuild/easyconfigs/m/makefun/makefun-1.15.2-GCCcore-12.3.0.eb @@ -0,0 +1,32 @@ +# Thomas Hoffmann, EMBL Heidelberg, structures-it@embl.de, 2024/02 +easyblock = 'PythonBundle' + +name = 'makefun' +version = '1.15.2' + +homepage = 'https://github.com/smarie/python-makefun' +description = """Small library to dynamically create python functions. +makefun helps you create functions dynamically, with the signature of your +choice. It was largely inspired by decorator and functools, and created mainly +to cover some of their limitations.""" +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +builddependencies = [ + ('binutils', '2.40'), + ('poetry', '1.5.1'), +] +dependencies = [ + ('Python', '3.11.3'), +] + +use_pip = True + +exts_list = [ + (name, version, { + 'checksums': ['16f2a2b34d9ee0c2b578c960a1808c974e2822cf79f6e9b9c455aace10882d45'], + }), +] + +sanity_pip_check = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/makeinfo/makeinfo-7.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/m/makeinfo/makeinfo-7.1-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..b2d35c079d4 --- /dev/null +++ b/easybuild/easyconfigs/m/makeinfo/makeinfo-7.1-GCCcore-13.3.0.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'makeinfo' +version = '7.1' + +homepage = 'https://www.gnu.org/software/texinfo/' +description = """makeinfo is part of the Texinfo project, the official documentation format of the GNU project.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://ftpmirror.gnu.org/gnu/texinfo'] +sources = ['texinfo-%(version)s.tar.xz'] +checksums = ['deeec9f19f159e046fdf8ad22231981806dac332cc372f1c763504ad82b30953'] + +builddependencies = [('binutils', '2.42')] +dependencies = [('Perl', '5.38.2')] + +sanity_check_paths = { + 'files': ['bin/makeinfo'], + 'dirs': ['share'], +} + +sanity_check_commands = ["makeinfo --help"] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/m/mallard-ducktype/mallard-ducktype-1.0.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/m/mallard-ducktype/mallard-ducktype-1.0.2-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..65102800699 --- /dev/null +++ b/easybuild/easyconfigs/m/mallard-ducktype/mallard-ducktype-1.0.2-GCCcore-12.3.0.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonPackage' + +name = 'mallard-ducktype' +version = '1.0.2' + +homepage = 'https://github.com/projectmallard/mallard-ducktype' +description = """Parser for the lightweight Ducktype syntax for Mallard""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +sources = ['mallard_ducktype-%(version)s-py3-none-any.whl'] +checksums = ['90c2d9e40934c634f3e83e0758285e2803f62c2c5db405702af2f5884e1a2918'] + +builddependencies = [ + ('binutils', '2.40'), +] + +dependencies = [ + ('Python', '3.11.3'), +] + +options = {'modulename': 'mallard.ducktype'} + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/m/manta/manta-1.6.0-GCC-10.2.0-Python-2.7.18.eb b/easybuild/easyconfigs/m/manta/manta-1.6.0-GCC-10.2.0-Python-2.7.18.eb index 4587e8e91df..ff224b45ba2 100644 --- a/easybuild/easyconfigs/m/manta/manta-1.6.0-GCC-10.2.0-Python-2.7.18.eb +++ b/easybuild/easyconfigs/m/manta/manta-1.6.0-GCC-10.2.0-Python-2.7.18.eb @@ -62,9 +62,7 @@ sanity_check_paths = { 'dirs': ['libexec'], } -sanity_check_commands = [ - 'python %(installdir)s/bin/runMantaWorkflowDemo.py' -] +sanity_check_commands = ['cd "$(mktemp -d)" && runMantaWorkflowDemo.py'] modextrapaths = { 'PATH': 'libexec', diff --git a/easybuild/easyconfigs/m/manta/manta-1.6.0-gompi-2019b-Python-2.7.16.eb b/easybuild/easyconfigs/m/manta/manta-1.6.0-gompi-2019b-Python-2.7.16.eb index 8e5943d0213..2d6c80a9b71 100644 --- a/easybuild/easyconfigs/m/manta/manta-1.6.0-gompi-2019b-Python-2.7.16.eb +++ b/easybuild/easyconfigs/m/manta/manta-1.6.0-gompi-2019b-Python-2.7.16.eb @@ -41,7 +41,7 @@ sanity_check_paths = { 'dirs': ['lib/python', 'share'], } -sanity_check_commands = ['runMantaWorkflowDemo.py'] +sanity_check_commands = ['cd "$(mktemp -d)" && runMantaWorkflowDemo.py'] modextrapaths = { 'PATH': 'libexec', diff --git a/easybuild/easyconfigs/m/manta/manta-1.6.0-gompi-2020a-Python-2.7.18.eb b/easybuild/easyconfigs/m/manta/manta-1.6.0-gompi-2020a-Python-2.7.18.eb index 0b2b3af8477..7633e9131e0 100644 --- a/easybuild/easyconfigs/m/manta/manta-1.6.0-gompi-2020a-Python-2.7.18.eb +++ b/easybuild/easyconfigs/m/manta/manta-1.6.0-gompi-2020a-Python-2.7.18.eb @@ -41,7 +41,7 @@ sanity_check_paths = { 'dirs': ['lib/python', 'share'], } -sanity_check_commands = ['runMantaWorkflowDemo.py'] +sanity_check_commands = ['cd "$(mktemp -d)" && runMantaWorkflowDemo.py'] modextrapaths = { 'PATH': 'libexec', diff --git a/easybuild/easyconfigs/m/matlab-proxy/matlab-proxy-0.18.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/m/matlab-proxy/matlab-proxy-0.18.1-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..bf1c9fec2ed --- /dev/null +++ b/easybuild/easyconfigs/m/matlab-proxy/matlab-proxy-0.18.1-GCCcore-12.3.0.eb @@ -0,0 +1,46 @@ +easyblock = "PythonBundle" + +name = 'matlab-proxy' +version = '0.18.1' + +homepage = 'https://github.com/mathworks/matlab-proxy' +description = "A Python package which enables you to launch MATLAB and access it from a web browser." + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +builddependencies = [ + ('binutils', '2.40'), + ('nodejs', '18.17.1'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('aiohttp', '3.8.5'), + ('Xvfb', '21.1.8'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('aiohttp-session', '2.12.0', { + 'checksums': ['0ccd11a7c77cb9e5a61f4daacdc9170d561112f9cfaf9e9a2d9867c0587d1950'], + }), + (name, version, { + 'patches': ['%(name)s-%(version)s_use_lic_from_eb_installed_matlab.patch'], + 'checksums': [ + {'matlab-proxy-0.18.1.tar.gz': 'c6ffe60de2e34b007f94b61c6c2f29b38115e4c9cb8b1e8f45d42a2713e0ac24'}, + {'matlab-proxy-0.18.1_use_lic_from_eb_installed_matlab.patch': + 'a6b994d8b511bd00f86f232c9d9cf230883090b575383a42c06857f26ea08210'}, + ], + }), +] + +sanity_check_paths = { + 'files': ['bin/matlab-proxy-app'], + 'dirs': ['lib64/python%(pyshortver)s/site-packages'] +} + +modloadmsg = 'matlab-proxy requires MATLAB to be loaded separately and BEFORE this module (2020b or later)' + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/m/matlab-proxy/matlab-proxy-0.18.1_use_lic_from_eb_installed_matlab.patch b/easybuild/easyconfigs/m/matlab-proxy/matlab-proxy-0.18.1_use_lic_from_eb_installed_matlab.patch new file mode 100644 index 00000000000..a37df91943d --- /dev/null +++ b/easybuild/easyconfigs/m/matlab-proxy/matlab-proxy-0.18.1_use_lic_from_eb_installed_matlab.patch @@ -0,0 +1,23 @@ +Use the license file from EB's MATLAB installation by default +Author: Mikael Öhman micketeer@gmail.com +--- matlab_proxy/settings.py.orig 2024-05-30 16:01:07.778707000 +0200 ++++ matlab_proxy/settings.py 2024-05-30 16:03:48.517654923 +0200 +@@ -357,9 +357,16 @@ + # folder may cause hinderance in this workflow. So specifying -licmode as 'file' + # overrides license_info.xml and enforces MLM_LICENSE_FILE to be the topmost priority + +- # NLM Connection String provided by MLM_LICENSE_FILE environment variable ++ license_file = None ++ if mwi_env.get_env_name_network_license_manager() in os.environ: ++ # NLM Connection String provided by MLM_LICENSE_FILE environment variable ++ license_file = os.environ.get(mwi_env.get_env_name_network_license_manager()) ++ elif 'EBROOTMATLAB' in os.environ: ++ # License file provided by MATLAB installation in EasyBuild ++ license_file = os.environ.get('EBROOTMATLAB') + '/licenses/network.lic' ++ + nlm_conn_str = mwi.validators.validate_mlm_license_file( +- os.environ.get(mwi_env.get_env_name_network_license_manager()) ++ license_file + ) + matlab_lic_mode = ["-licmode", "file"] if nlm_conn_str else "" + # flag to hide MATLAB Window diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.9.2-contourpy-fix-pybind-module.patch b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.9.2-contourpy-fix-pybind-module.patch new file mode 100644 index 00000000000..9a34eb1cdae --- /dev/null +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.9.2-contourpy-fix-pybind-module.patch @@ -0,0 +1,14 @@ +Fixes: error: macro "PYBIND11_MODULE" passed 3 arguments, but takes just 2 +Author: Anke Kreuzer (JSC) +diff -ruN src/wrap.cpp.orig src/wrap.cpp +--- src/wrap.cpp.orig 2024-09-02 21:07:13.893013182 +0200 ++++ src/wrap.cpp 2024-09-02 21:07:39.973005828 +0200 +@@ -18,7 +18,7 @@ + static contourpy::LineType mpl20xx_line_type = contourpy::LineType::SeparateCode; + static contourpy::FillType mpl20xx_fill_type = contourpy::FillType::OuterCode; + +-PYBIND11_MODULE(_contourpy, m, py::mod_gil_not_used()) { ++PYBIND11_MODULE(_contourpy, m) { + m.doc() = + "C++11 extension module wrapped using `pybind11`_.\n\n" + "It should not be necessary to access classes and functions in this extension module " diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.9.2-gfbf-2024a.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.9.2-gfbf-2024a.eb new file mode 100644 index 00000000000..33ddf00eb93 --- /dev/null +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.9.2-gfbf-2024a.eb @@ -0,0 +1,79 @@ +easyblock = 'PythonBundle' + +name = 'matplotlib' +version = '3.9.2' + +homepage = 'https://matplotlib.org' +description = """matplotlib is a python 2D plotting library which produces publication quality figures in a variety of + hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python + and ipython shell, web application servers, and six graphical user interface toolkits.""" + +toolchain = {'name': 'gfbf', 'version': '2024a'} + +builddependencies = [ + ('pkgconf', '2.2.0'), + ('cppy', '1.2.1'), + ('meson-python', '0.16.0'), +] + +dependencies = [ + ('Python', '3.12.3'), + ('SciPy-bundle', '2024.05'), + ('libpng', '1.6.43'), + ('freetype', '2.13.2'), + ('Tkinter', '%(pyver)s'), + ('Pillow-SIMD', '10.4.0'), + ('Qhull', '2020.2'), +] + +use_pip = True +sanity_pip_check = True + +_include_path = "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && " + +local_configopts = "--config-settings=setup-args='-Dsystem-qhull=true' && " +local_configopts += " --config-settings=setup-args='-Dsystem-freetype=true' && " +local_configopts += "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && " + +exts_list = [ + ('fonttools', '4.53.1', { + 'modulename': 'fontTools', + 'source_tmpl': '%(name)s-%(version)s.tar.gz', + 'checksums': ['e128778a8e9bc11159ce5447f76766cefbd876f44bd79aff030287254e4752c4'], + }), + ('Cycler', '0.12.1', { + 'modulename': 'cycler', + 'source_tmpl': 'cycler-%(version)s.tar.gz', + 'checksums': ['88bb128f02ba341da8ef447245a9e138fae777f6a23943da4540077d3601eb1c'], + }), + ('kiwisolver', '1.4.5', { + 'patches': ['kiwisolver-1.4.4-fix_version.patch'], + 'checksums': [ + {'kiwisolver-1.4.5.tar.gz': 'e57e563a57fb22a142da34f38acc2fc1a5c864bc29ca1517a88abc963e60d6ec'}, + {'kiwisolver-1.4.4-fix_version.patch': '6753afbb3a88856493fcfa0b33989f35742f57bfd41ff3b7f71a98797e1bfbd0'}, + ], + }), + ('contourpy', '1.3.0', { + 'patches': ['matplotlib-3.9.2-contourpy-fix-pybind-module.patch'], + 'checksums': [ + {'contourpy-1.3.0.tar.gz': '7ffa0db17717a8ffb127efd0c95a4362d996b892c2904db72428d5b52e1938a4'}, + {'matplotlib-3.9.2-contourpy-fix-pybind-module.patch': + 'a998438a1048524a550bf3bb607197658b13dce56e8e54169e24ce7c3c022a8f'}, + ], + }), + (name, version, { + 'configopts': "%(local_configopts)s", + 'checksums': ['96ab43906269ca64a6366934106fa01534454a69e471b7bf3d79083981aaab92'], + }), +] + +sanity_check_commands = [ + """python -c 'import matplotlib; matplotlib.use("Agg"); import matplotlib.pyplot' """, + "python -c 'from mpl_toolkits.mplot3d import Axes3D'", +] + +# use non-interactive plotting backend as default +# see https://matplotlib.org/tutorials/introductory/usage.html#what-is-a-backend +modextravars = {'MPLBACKEND': 'Agg'} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/m/maturin/maturin-1.6.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/m/maturin/maturin-1.6.0-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..b7a45d6c37a --- /dev/null +++ b/easybuild/easyconfigs/m/maturin/maturin-1.6.0-GCCcore-13.3.0.eb @@ -0,0 +1,659 @@ +easyblock = 'CargoPythonPackage' + +name = 'maturin' +version = '1.6.0' + +homepage = 'https://github.com/pyo3/maturin' +description = """This project is meant as a zero configuration +replacement for setuptools-rust and milksnake. It supports building +wheels for python 3.5+ on windows, linux, mac and freebsd, can upload +them to pypi and has basic pypy and graalpy support.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +crates = [ + ('adler', '1.0.2'), + ('ahash', '0.8.7'), + ('aho-corasick', '1.1.2'), + ('allocator-api2', '0.2.16'), + ('anstream', '0.6.11'), + ('anstyle', '1.0.4'), + ('anstyle-parse', '0.2.3'), + ('anstyle-query', '1.0.2'), + ('anstyle-wincon', '3.0.2'), + ('anyhow', '1.0.80'), + ('autocfg', '1.1.0'), + ('base64', '0.13.1'), + ('base64', '0.21.7'), + ('bitflags', '1.3.2'), + ('bitflags', '2.4.2'), + ('block-buffer', '0.10.4'), + ('bstr', '1.9.0'), + ('byteorder', '1.5.0'), + ('bytes', '1.5.0'), + ('bytesize', '1.3.0'), + ('bzip2', '0.4.4'), + ('bzip2-sys', '0.1.11+1.0.8'), + ('cab', '0.4.1'), + ('camino', '1.1.6'), + ('cargo-config2', '0.1.24'), + ('cargo-options', '0.7.4'), + ('cargo-platform', '0.1.6'), + ('cargo-xwin', '0.16.4'), + ('cargo-zigbuild', '0.18.4'), + ('cargo_metadata', '0.18.1'), + ('cbindgen', '0.26.0'), + ('cc', '1.0.88'), + ('cfb', '0.9.0'), + ('cfg-if', '1.0.0'), + ('charset', '0.1.3'), + ('chumsky', '0.9.3'), + ('clap', '4.4.18'), + ('clap_builder', '4.4.18'), + ('clap_complete', '4.4.9'), + ('clap_complete_command', '0.5.1'), + ('clap_complete_nushell', '0.1.11'), + ('clap_derive', '4.4.7'), + ('clap_lex', '0.6.0'), + ('cli-table', '0.4.7'), + ('colorchoice', '1.0.0'), + ('configparser', '3.0.4'), + ('console', '0.15.8'), + ('content_inspector', '0.2.4'), + ('core-foundation', '0.9.4'), + ('core-foundation-sys', '0.8.6'), + ('cpufeatures', '0.2.12'), + ('crc32fast', '1.3.2'), + ('crossbeam-channel', '0.5.11'), + ('crossbeam-deque', '0.8.5'), + ('crossbeam-epoch', '0.9.18'), + ('crossbeam-utils', '0.8.19'), + ('crypto-common', '0.1.6'), + ('data-encoding', '2.5.0'), + ('deranged', '0.3.11'), + ('derivative', '2.2.0'), + ('dialoguer', '0.11.0'), + ('diff', '0.1.13'), + ('digest', '0.10.7'), + ('dirs', '5.0.1'), + ('dirs-sys', '0.4.1'), + ('dissimilar', '1.0.7'), + ('dunce', '1.0.4'), + ('dyn-clone', '1.0.17'), + ('either', '1.9.0'), + ('encode_unicode', '0.3.6'), + ('encoding_rs', '0.8.33'), + ('equivalent', '1.0.1'), + ('errno', '0.3.8'), + ('expect-test', '1.4.1'), + ('fastrand', '2.0.1'), + ('fat-macho', '0.4.8'), + ('filetime', '0.2.23'), + ('flate2', '1.0.28'), + ('fnv', '1.0.7'), + ('foreign-types', '0.3.2'), + ('foreign-types-shared', '0.1.1'), + ('form_urlencoded', '1.2.1'), + ('fs-err', '2.11.0'), + ('futures', '0.3.30'), + ('futures-channel', '0.3.30'), + ('futures-core', '0.3.30'), + ('futures-executor', '0.3.30'), + ('futures-io', '0.3.30'), + ('futures-macro', '0.3.30'), + ('futures-sink', '0.3.30'), + ('futures-task', '0.3.30'), + ('futures-timer', '3.0.3'), + ('futures-util', '0.3.30'), + ('generic-array', '0.14.7'), + ('getrandom', '0.2.12'), + ('glob', '0.3.1'), + ('globset', '0.4.14'), + ('goblin', '0.8.0'), + ('hashbrown', '0.12.3'), + ('hashbrown', '0.14.3'), + ('heck', '0.4.1'), + 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'7a4191c47f15cc3ec71fcb4913cb83d58def65dd3787610213c649283b5ce178'}, + {'xattr-1.3.1.tar.gz': '8da84f1a25939b27f6820d92aed108f83ff920fdf11a7b19366c27c4cda81d4f'}, + {'xwin-0.5.0.tar.gz': 'c43e0202f5457b48558096cb7b36d0e473f267551a89c82ed72d73b01dfd4007'}, + {'yansi-0.5.1.tar.gz': '09041cd90cf85f7f8b2df60c646f853b7f535ce68f85244eb6731cf89fa498ec'}, + {'zerocopy-0.7.32.tar.gz': '74d4d3961e53fa4c9a25a8637fc2bfaf2595b3d3ae34875568a5cf64787716be'}, + {'zerocopy-derive-0.7.32.tar.gz': '9ce1b18ccd8e73a9321186f97e46f9f04b778851177567b1975109d26a08d2a6'}, + {'zeroize-1.7.0.tar.gz': '525b4ec142c6b68a2d10f01f7bbf6755599ca3f81ea53b8431b7dd348f5fdb2d'}, + {'zip-0.6.6.tar.gz': '760394e246e4c28189f19d488c058bf16f564016aefac5d32bb1f3b51d5e9261'}, +] + +builddependencies = [ + ('binutils', '2.42'), + ('setuptools-rust', '1.9.0'), +] +dependencies = [ + ('Python', '3.12.3'), + ('Rust', '1.78.0'), +] + +download_dep_fail = True +sanity_pip_check = True +use_pip = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/m/mcqd/mcqd-1.0.0-GCC-13.2.0.eb b/easybuild/easyconfigs/m/mcqd/mcqd-1.0.0-GCC-13.2.0.eb new file mode 100644 index 00000000000..87f92553548 --- /dev/null +++ b/easybuild/easyconfigs/m/mcqd/mcqd-1.0.0-GCC-13.2.0.eb @@ -0,0 +1,32 @@ +easyblock = 'CmdCp' + +name = 'mcqd' +version = '1.0.0' + +homepage = 'https://gitlab.com/janezkonc/mcqd' +description = """MaxCliqueDyn is a fast exact algorithm for finding a maximum clique in an undirected graph.""" + +toolchain = {'name': 'GCC', 'version': '13.2.0'} + +source_urls = ['https://gitlab.com/janezkonc/mcqd/-/archive/v%(version)s/'] +sources = ['mcqd-v%(version)s.tar.gz'] +checksums = ['37ff68ff88e047c929990d4c12ce474753f6f9c49324661a3aa1cfe77c26ad9d'] + +cmds_map = [('.*', '$CXX $CXXFLAGS $LDFLAGS mcqd.cpp -o mcqd')] + +files_to_copy = [ + (['mcqd'], 'bin'), + (['mcqd.h'], 'include'), +] + +sanity_check_paths = { + 'files': [ + 'bin/mcqd', + 'include/mcqd.h', + ], + 'dirs': [], +} + +sanity_check_commands = ["command -v mcqd"] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/m/mctc-lib/mctc-lib-0.3.1-GCC-12.3.0.eb b/easybuild/easyconfigs/m/mctc-lib/mctc-lib-0.3.1-GCC-12.3.0.eb new file mode 100644 index 00000000000..e8ec2b8435d --- /dev/null +++ b/easybuild/easyconfigs/m/mctc-lib/mctc-lib-0.3.1-GCC-12.3.0.eb @@ -0,0 +1,41 @@ +easyblock = 'CMakeMake' + +name = 'mctc-lib' +version = '0.3.1' + +homepage = 'https://grimme-lab.github.io/mctc-lib' +description = """Common tool chain for working with molecular structure data in various +applications. This library provides a unified way to perform operations on +molecular structure data, like reading and writing to common geometry file +formats.""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +github_account = 'grimme-lab' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['03dc8ccba37413da70e55a07cef8e8de53bce33f5bb52c1f8db5fec326abe083'] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.26.3'), +] + +dependencies = [ + ('json-fortran', '9.0.2'), +] + +configopts = ['-DBUILD_SHARED_LIBS=ON', '-DBUILD_SHARED_LIBS=OFF'] + +sanity_check_paths = { + 'files': ['bin/mctc-convert', 'lib/libmctc-lib.%s' % SHLIB_EXT], + 'dirs': ['include/%(name)s', 'lib/cmake', 'lib/pkgconfig'], +} + +sanity_check_commands = ["mctc-convert --help"] + +# run suite of tests with ctest +runtest = True + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/m/mctc-lib/mctc-lib-0.3.1-GCC-13.2.0.eb b/easybuild/easyconfigs/m/mctc-lib/mctc-lib-0.3.1-GCC-13.2.0.eb new file mode 100644 index 00000000000..781662c3dc2 --- /dev/null +++ b/easybuild/easyconfigs/m/mctc-lib/mctc-lib-0.3.1-GCC-13.2.0.eb @@ -0,0 +1,41 @@ +easyblock = 'CMakeMake' + +name = 'mctc-lib' +version = '0.3.1' + +homepage = 'https://grimme-lab.github.io/mctc-lib' +description = """Common tool chain for working with molecular structure data in various +applications. This library provides a unified way to perform operations on +molecular structure data, like reading and writing to common geometry file +formats.""" + +toolchain = {'name': 'GCC', 'version': '13.2.0'} +toolchainopts = {'pic': True} + +github_account = 'grimme-lab' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['03dc8ccba37413da70e55a07cef8e8de53bce33f5bb52c1f8db5fec326abe083'] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.27.6'), +] + +dependencies = [ + ('json-fortran', '9.0.2'), +] + +configopts = ['-DBUILD_SHARED_LIBS=ON', '-DBUILD_SHARED_LIBS=OFF'] + +sanity_check_paths = { + 'files': ['bin/mctc-convert', 'lib/libmctc-lib.%s' % SHLIB_EXT], + 'dirs': ['include/%(name)s', 'lib/cmake', 'lib/pkgconfig'], +} + +sanity_check_commands = ["mctc-convert --help"] + +# run suite of tests with ctest +runtest = True + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/m/medaka/medaka-1.12.0-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/m/medaka/medaka-1.12.0-foss-2023a-CUDA-12.1.1.eb new file mode 100644 index 00000000000..c9ac4870bf5 --- /dev/null +++ b/easybuild/easyconfigs/m/medaka/medaka-1.12.0-foss-2023a-CUDA-12.1.1.eb @@ -0,0 +1,85 @@ +# This is a contribution from HPCNow! (http://hpcnow.com) +# Copyright:: HPCNow! +# Authors:: Danilo Gonzalez +# License:: GPL-v3.0 +# Updated to foss-2020b to use with artic tool +# J. Sassmannshausen (GSTT/NHS UK) +# Updated to 1.5.0 +# Jasper Grimm (UoY) +# Updated: Petr Král (INUITS) + +easyblock = 'PythonBundle' + +name = 'medaka' +version = '1.12.0' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/nanoporetech/medaka' +description = "medaka is a tool to create a consensus sequence from nanopore sequencing data." + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'pic': True} + +builddependencies = [('Autotools', '20220317')] + +_minimap_ver = '2.26' +dependencies = [ + ('CUDA', '12.1.1', '', SYSTEM), + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), # includes cffi + ('TensorFlow', '2.15.1', versionsuffix), + ('Pysam', '0.22.0'), + ('SAMtools', '1.18'), + ('minimap2', _minimap_ver), + ('HTSlib', '1.18'), # for tabix, bgzip + ('Racon', '1.5.0'), + ('edlib', '1.3.9'), + ('pyspoa', '0.2.1'), + ('python-parasail', '1.3.4'), + ('ont-fast5-api', '4.1.2'), + ('WhatsHap', '2.2'), + ('intervaltree-python', '3.1.0'), + ('BCFtools', '1.18'), +] + +use_pip = True +sanity_pip_check = True + +local_sed_commands = [ + "sed -i 's/tensorflow.*/tensorflow/g;s/cffi==1.15.0/cffi/g' requirements.txt pyproject.toml", + # Python 3.11 support + "sed -i 's/8, 9, 10/8, 9, 10, 11/g;s/,<3.11//g' setup.py", +] + +exts_list = [ + ('mappy', _minimap_ver, { + 'checksums': ['e53fbe9a3ea8762a64b8103f4f779c9fb16d418eaa0a731f45cebc83867a9b71'], + }), + ('wurlitzer', '3.1.1', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['0b2749c2cde3ef640bf314a9f94b24d929fe1ca476974719a6909dfc568c3aac'], + }), + ('h5py', '3.10.0', { + 'checksums': ['d93adc48ceeb33347eb24a634fb787efc7ae4644e6ea4ba733d099605045c049'], + }), + ('pyabpoa', '1.5.1', { + 'checksums': ['878f981e890a421d92a0d7606705d0ad9813ae6086239460dfe4b0cfc7476174'], + }), + (name, version, { + 'checksums': ['039219204111a8114b1f72d87d0d3463e43473790cff4520c8afbd79cc8784d6'], + # Some requirements are too strict. + 'preinstallopts': " && ".join(local_sed_commands) + " && ", + }), +] + +sanity_check_paths = { + 'files': ['bin/medaka', 'bin/medaka_consensus', 'bin/medaka_version_report'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "medaka --help", + "medaka_version_report", +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/medaka/medaka-1.12.0-foss-2023a.eb b/easybuild/easyconfigs/m/medaka/medaka-1.12.0-foss-2023a.eb new file mode 100644 index 00000000000..af21d1b6a0d --- /dev/null +++ b/easybuild/easyconfigs/m/medaka/medaka-1.12.0-foss-2023a.eb @@ -0,0 +1,84 @@ +# This is a contribution from HPCNow! (http://hpcnow.com) +# Copyright:: HPCNow! +# Authors:: Danilo Gonzalez +# License:: GPL-v3.0 +# Updated to foss-2020b to use with artic tool +# J. Sassmannshausen (GSTT/NHS UK) +# Updated to 1.5.0 +# Jasper Grimm (UoY) +# Updated: Petr Král (INUITS) + +easyblock = 'PythonBundle' + +name = 'medaka' +version = '1.12.0' + +homepage = 'https://github.com/nanoporetech/medaka' +description = "medaka is a tool to create a consensus sequence from nanopore sequencing data." + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'pic': True} + +builddependencies = [('Autotools', '20220317')] + +_minimap_ver = '2.26' +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), # includes cffi + ('TensorFlow', '2.13.0'), + ('Pysam', '0.22.0'), + ('SAMtools', '1.18'), + ('minimap2', _minimap_ver), + ('HTSlib', '1.18'), # for tabix, bgzip + ('Racon', '1.5.0'), + ('edlib', '1.3.9'), + ('pyspoa', '0.2.1'), + ('python-parasail', '1.3.4'), + ('ont-fast5-api', '4.1.2'), + ('WhatsHap', '2.2'), + ('intervaltree-python', '3.1.0'), + ('BCFtools', '1.18'), +] + +use_pip = True +sanity_pip_check = True + +local_sed_commands = [ + "sed -i 's/tensorflow.*/tensorflow/g;s/cffi==1.15.0/cffi/g' requirements.txt pyproject.toml", + # Python 3.11 support + "sed -i 's/8, 9, 10/8, 9, 10, 11/g;s/,<3.11//g' setup.py", +] + +exts_list = [ + ('mappy', _minimap_ver, { + 'checksums': ['e53fbe9a3ea8762a64b8103f4f779c9fb16d418eaa0a731f45cebc83867a9b71'], + }), + ('wurlitzer', '3.1.1', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['0b2749c2cde3ef640bf314a9f94b24d929fe1ca476974719a6909dfc568c3aac'], + }), + # medaka 1.12.0 requires h5py ~=3.10.0 + ('h5py', '3.10.0', { + 'checksums': ['d93adc48ceeb33347eb24a634fb787efc7ae4644e6ea4ba733d099605045c049'], + }), + ('pyabpoa', '1.5.1', { + 'checksums': ['878f981e890a421d92a0d7606705d0ad9813ae6086239460dfe4b0cfc7476174'], + }), + (name, version, { + 'checksums': ['039219204111a8114b1f72d87d0d3463e43473790cff4520c8afbd79cc8784d6'], + # Some requirements are too strict. + 'preinstallopts': " && ".join(local_sed_commands) + " && ", + }), +] + +sanity_check_paths = { + 'files': ['bin/medaka', 'bin/medaka_consensus', 'bin/medaka_version_report'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "medaka --help", + "medaka_version_report", +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/medaka/medaka-1.12.1-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/m/medaka/medaka-1.12.1-foss-2023a-CUDA-12.1.1.eb new file mode 100644 index 00000000000..3e055e5d8dd --- /dev/null +++ b/easybuild/easyconfigs/m/medaka/medaka-1.12.1-foss-2023a-CUDA-12.1.1.eb @@ -0,0 +1,88 @@ +# This is a contribution from HPCNow! (http://hpcnow.com) +# Copyright:: HPCNow! +# Authors:: Danilo Gonzalez +# License:: GPL-v3.0 +# Updated to foss-2020b to use with artic tool +# J. Sassmannshausen (GSTT/NHS UK) +# Updated to 1.5.0 +# Jasper Grimm (UoY) +# Updated: Petr Král (INUITS) + +easyblock = 'PythonBundle' + +name = 'medaka' +version = '1.12.1' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/nanoporetech/medaka' +description = "medaka is a tool to create a consensus sequence from nanopore sequencing data." + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'pic': True} + +builddependencies = [('Autotools', '20220317')] + +_minimap_ver = '2.26' +dependencies = [ + ('CUDA', '12.1.1', '', SYSTEM), + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), # includes cffi + ('TensorFlow', '2.15.1', versionsuffix), + ('Pysam', '0.22.0'), + ('SAMtools', '1.18'), + ('minimap2', _minimap_ver), + ('HTSlib', '1.18'), # for tabix, bgzip + ('Racon', '1.5.0'), + ('edlib', '1.3.9'), + ('pyspoa', '0.2.1'), + ('python-parasail', '1.3.4'), + ('ont-fast5-api', '4.1.2'), + ('WhatsHap', '2.2'), + ('intervaltree-python', '3.1.0'), + ('BCFtools', '1.18'), +] + +use_pip = True +sanity_pip_check = True + +local_sed_commands = [ + "sed -i 's/tensorflow.*/tensorflow/g;s/cffi==1.15.0/cffi/g' requirements.txt pyproject.toml", + # Python 3.11 support + "sed -i 's/8, 9, 10/8, 9, 10, 11/g;s/,<3.11//g' setup.py", + # ont-parasail on PyPI is just pre-built wheels for (python-)parasail + "sed -i 's/ont-parasail/parasail/g' requirements.txt", +] + +exts_list = [ + ('mappy', _minimap_ver, { + 'checksums': ['e53fbe9a3ea8762a64b8103f4f779c9fb16d418eaa0a731f45cebc83867a9b71'], + }), + ('wurlitzer', '3.1.1', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['0b2749c2cde3ef640bf314a9f94b24d929fe1ca476974719a6909dfc568c3aac'], + }), + # medaka 1.12.0 requires h5py ~=3.10.0 + ('h5py', '3.10.0', { + 'checksums': ['d93adc48ceeb33347eb24a634fb787efc7ae4644e6ea4ba733d099605045c049'], + }), + ('pyabpoa', '1.5.2', { + 'checksums': ['be39c83b12e923c9e47073cb8f0abc4c42f609fa2c0ec13d6f6a4f5a0537ee06'], + }), + (name, version, { + 'checksums': ['df4baf7d1e9154de85229aef237919619ff6ae7f7d103abb0828e449ff977adf'], + # Some requirements are too strict. + 'preinstallopts': " && ".join(local_sed_commands) + " && ", + }), +] + +sanity_check_paths = { + 'files': ['bin/medaka', 'bin/medaka_consensus', 'bin/medaka_version_report'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "medaka --help", + "medaka_version_report", +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/medaka/medaka-1.12.1-foss-2023a.eb b/easybuild/easyconfigs/m/medaka/medaka-1.12.1-foss-2023a.eb new file mode 100644 index 00000000000..f95d01c89d9 --- /dev/null +++ b/easybuild/easyconfigs/m/medaka/medaka-1.12.1-foss-2023a.eb @@ -0,0 +1,86 @@ +# This is a contribution from HPCNow! (http://hpcnow.com) +# Copyright:: HPCNow! +# Authors:: Danilo Gonzalez +# License:: GPL-v3.0 +# Updated to foss-2020b to use with artic tool +# J. Sassmannshausen (GSTT/NHS UK) +# Updated to 1.5.0 +# Jasper Grimm (UoY) +# Updated: Petr Král (INUITS) + +easyblock = 'PythonBundle' + +name = 'medaka' +version = '1.12.1' + +homepage = 'https://github.com/nanoporetech/medaka' +description = "medaka is a tool to create a consensus sequence from nanopore sequencing data." + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'pic': True} + +builddependencies = [('Autotools', '20220317')] + +_minimap_ver = '2.26' +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), # includes cffi + ('TensorFlow', '2.13.0'), + ('Pysam', '0.22.0'), + ('SAMtools', '1.18'), + ('minimap2', _minimap_ver), + ('HTSlib', '1.18'), # for tabix, bgzip + ('Racon', '1.5.0'), + ('edlib', '1.3.9'), + ('pyspoa', '0.2.1'), + ('python-parasail', '1.3.4'), + ('ont-fast5-api', '4.1.2'), + ('WhatsHap', '2.2'), + ('intervaltree-python', '3.1.0'), + ('BCFtools', '1.18'), +] + +use_pip = True +sanity_pip_check = True + +local_sed_commands = [ + "sed -i 's/tensorflow.*/tensorflow/g;s/cffi==1.15.0/cffi/g' requirements.txt pyproject.toml", + # Python 3.11 support + "sed -i 's/8, 9, 10/8, 9, 10, 11/g;s/,<3.11//g' setup.py", + # ont-parasail on PyPI is just pre-built wheels for (python-)parasail + "sed -i 's/ont-parasail/parasail/g' requirements.txt", +] + +exts_list = [ + ('mappy', _minimap_ver, { + 'checksums': ['e53fbe9a3ea8762a64b8103f4f779c9fb16d418eaa0a731f45cebc83867a9b71'], + }), + ('wurlitzer', '3.1.1', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['0b2749c2cde3ef640bf314a9f94b24d929fe1ca476974719a6909dfc568c3aac'], + }), + # medaka 1.12.0 requires h5py ~=3.10.0 + ('h5py', '3.10.0', { + 'checksums': ['d93adc48ceeb33347eb24a634fb787efc7ae4644e6ea4ba733d099605045c049'], + }), + ('pyabpoa', '1.5.2', { + 'checksums': ['be39c83b12e923c9e47073cb8f0abc4c42f609fa2c0ec13d6f6a4f5a0537ee06'], + }), + (name, version, { + 'checksums': ['df4baf7d1e9154de85229aef237919619ff6ae7f7d103abb0828e449ff977adf'], + # Some requirements are too strict. + 'preinstallopts': " && ".join(local_sed_commands) + " && ", + }), +] + +sanity_check_paths = { + 'files': ['bin/medaka', 'bin/medaka_consensus', 'bin/medaka_version_report'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "medaka --help", + "medaka_version_report", +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/meshio/meshio-5.3.5-foss-2023b.eb b/easybuild/easyconfigs/m/meshio/meshio-5.3.5-foss-2023b.eb new file mode 100644 index 00000000000..d4b1a912aa3 --- /dev/null +++ b/easybuild/easyconfigs/m/meshio/meshio-5.3.5-foss-2023b.eb @@ -0,0 +1,39 @@ +easyblock = 'PythonBundle' + +name = 'meshio' +version = '5.3.5' + +homepage = 'https://github.com/nschloe/meshio' +description = "meshio is a tool for reading/writing various mesh formats representing unstructured meshes" + +toolchain = {'name': 'foss', 'version': '2023b'} + +dependencies = [ + ('Python', '3.11.5'), + ('Python-bundle-PyPI', '2023.10'), # includes rich + ('SciPy-bundle', '2023.11'), # includes numpy + ('h5py', '3.11.0'), + ('VTK', '9.3.0'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('appdirs', '1.4.4', { + 'checksums': ['7d5d0167b2b1ba821647616af46a749d1c653740dd0d2415100fe26e27afdf41'], + }), + ('pipdate', '0.5.6', { + 'checksums': ['1b6b7ec2c5468fb7036ec9d6b2ced7a8a538db55aaca03f30199216d3bbd264b'], + }), + (name, version, { + 'checksums': ['f21f01abd9f29ba06ea119304b3d39e610421cfe93b9dd23362834919f87586d'], + }), +] + +sanity_check_paths = { + 'files': ['bin/meshio', 'bin/pipdate'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'cae' diff --git a/easybuild/easyconfigs/m/meson-python/meson-python-0.16.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/m/meson-python/meson-python-0.16.0-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..1724208584f --- /dev/null +++ b/easybuild/easyconfigs/m/meson-python/meson-python-0.16.0-GCCcore-13.3.0.eb @@ -0,0 +1,37 @@ +easyblock = 'PythonBundle' + +name = 'meson-python' +version = '0.16.0' + +homepage = 'https://github.com/mesonbuild/meson-python' +description = "Python build backend (PEP 517) for Meson projects" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +builddependencies = [ + ('binutils', '2.42'), +] + +dependencies = [ + ('Python', '3.12.3'), + ('Python-bundle-PyPI', '2024.06'), # provides 'packaging' + ('Meson', '1.4.0'), +] + +use_pip = True + +exts_list = [ + ('pyproject-metadata', '0.8.0', { + 'sources': ['pyproject_metadata-%(version)s.tar.gz'], + 'checksums': ['376d5a00764ac29440a54579f88e66b7d9cb7e629d35c35a1c7248bfebc9b455'], + }), + (name, version, { + 'modulename': 'mesonpy', + 'sources': ['meson_python-%(version)s.tar.gz'], + 'checksums': ['9068c17e36c89d6c7ff709fffb2a8a9925e8cd0b02629728e5ceaf2ec505cb5f'], + }), +] + +sanity_pip_check = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/m/meteogrid/meteogrid-20240627-gfbf-2023a-R-4.3.2.eb b/easybuild/easyconfigs/m/meteogrid/meteogrid-20240627-gfbf-2023a-R-4.3.2.eb new file mode 100644 index 00000000000..8fca99e5298 --- /dev/null +++ b/easybuild/easyconfigs/m/meteogrid/meteogrid-20240627-gfbf-2023a-R-4.3.2.eb @@ -0,0 +1,34 @@ +easyblock = 'RPackage' + +name = 'meteogrid' +version = '20240627' +local_commit = '9da2345' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://github.com/harphub/meteogrid' +description = """ +R package for working with gridded meteorological data. +""" + +toolchain = {'name': 'gfbf', 'version': '2023a'} + +source_urls = ['https://github.com/harphub/%(name)s/archive/'] +sources = [{ + 'download_filename': '%s.tar.gz' % local_commit, + 'filename': '%%(name)s-%%(version)s-%s.tar.gz' % local_commit, +}] +checksums = ['ab89739e2e85d62bbdc8ee1a96d409654b19ebd2acf8251c2563a88f9d53d5c0'] + +dependencies = [ + ('R', '4.3.2'), + ('PROJ', '9.2.0'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': [name], +} + +sanity_check_commands = ['Rscript -e "library(meteogrid)"'] + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/m/micro-sam/micro-sam-1.0.1-foss-2023a.eb b/easybuild/easyconfigs/m/micro-sam/micro-sam-1.0.1-foss-2023a.eb new file mode 100644 index 00000000000..418740280e5 --- /dev/null +++ b/easybuild/easyconfigs/m/micro-sam/micro-sam-1.0.1-foss-2023a.eb @@ -0,0 +1,43 @@ +easyblock = 'PythonBundle' + +name = 'micro-sam' +version = '1.0.1' + +homepage = 'https://github.com/computational-cell-analytics/micro-sam/' +description = "Tools for segmentation and tracking in microscopy build on top of SegmentAnything." + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('torchvision', '0.16.0'), + ('napari', '0.4.18'), + ('zarr', '2.17.1'), + ('vigra', '1.11.2'), + ('python-elf', '0.5.1'), + ('z5py', '2.0.17'), + ('python-xxhash', '3.4.1'), + ('segment-anything', '1.0'), + ('torch-em', '0.7.1'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + (name, version, { + 'source_urls': ['https://github.com/computational-cell-analytics/micro-sam/archive/'], + 'sources': ['v%(version)s.tar.gz'], + 'checksums': ['5b7cc562a639d68de4f9462f3696f17b479ea0d669eaedb34687b65ceac715e9'], + }), +] + +sanity_check_commands = [ + "python -c 'import affogato'", + "python -c 'import napari.viewer'", + "micro_sam.annotator_2d -h", + "micro_sam.annotator_3d -h", +] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/m/miniasm/miniasm-0.3-20191007-GCCcore-12.3.0.eb b/easybuild/easyconfigs/m/miniasm/miniasm-0.3-20191007-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..a34b456c98c --- /dev/null +++ b/easybuild/easyconfigs/m/miniasm/miniasm-0.3-20191007-GCCcore-12.3.0.eb @@ -0,0 +1,46 @@ +easyblock = 'MakeCp' + +name = 'miniasm' +version = '0.3-20191007' +local_commit = 'ce615d1d6b8678d38f2f9d27c9dccd944436ae75' + +homepage = 'https://github.com/lh3/miniasm' +description = """Miniasm is a very fast OLC-based de novo assembler for noisy long reads. It +takes all-vs-all read self-mappings (typically by minimap) as input and outputs +an assembly graph in the GFA format. Different from mainstream assemblers, +miniasm does not have a consensus step. It simply concatenates pieces of read +sequences to generate the final unitig sequences. Thus the per-base error rate +is similar to the raw input reads.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +github_account = 'lh3' +source_urls = [GITHUB_SOURCE] +sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}] +checksums = ['31d62309e8b802d3aebd492c1fed8d2a9197a3243c128345745dccb762457e3d'] + +builddependencies = [ + ('binutils', '2.40'), +] + +dependencies = [ + ('zlib', '1.2.13'), +] + +buildopts = 'CC="${CC}" CFLAGS="${CFLAGS}" CPPFLAGS="${CPPFLAGS}"' + +files_to_copy = [ + (['%(name)s', 'minidot'], 'bin'), + (['*.h'], 'include'), + (['LICENSE.txt', 'PAF.md', 'README.md'], 'share'), + (['%(name)s.1'], 'share/man/man1'), +] + +sanity_check_paths = { + 'files': ['bin/%(name)s', 'bin/minidot'], + 'dirs': ['include', 'share'] +} + +sanity_check_commands = ["miniasm -V"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/minimap2/minimap2-2.28-GCCcore-13.2.0.eb b/easybuild/easyconfigs/m/minimap2/minimap2-2.28-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..94f332d290b --- /dev/null +++ b/easybuild/easyconfigs/m/minimap2/minimap2-2.28-GCCcore-13.2.0.eb @@ -0,0 +1,54 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Adam Huffman +# DeepThought, Flinders University +# Updated to 2.22 +# R.QIAO + +# Update Petr Král (INUITS) +easyblock = 'MakeCp' + +name = 'minimap2' +version = '2.28' + +homepage = 'https://github.com/lh3/minimap2' +description = """Minimap2 is a fast sequence mapping and alignment +program that can find overlaps between long noisy reads, or map long +reads or their assemblies to a reference genome optionally with detailed +alignment (i.e. CIGAR). At present, it works efficiently with query +sequences from a few kilobases to ~100 megabases in length at an error +rate ~15%. Minimap2 outputs in the PAF or the SAM format. On limited +test data sets, minimap2 is over 20 times faster than most other +long-read aligners. It will replace BWA-MEM for long reads and contig +alignment.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://github.com/lh3/%(name)s/releases/download/v%(version)s/'] +sources = ['%(name)s-%(version)s.tar.bz2'] +checksums = ['ffa5712735d229119f8c05722a0638ae0cc15aeb8938e29a3e52d5da5c92a0b4'] + +builddependencies = [('binutils', '2.40')] + +dependencies = [('zlib', '1.2.13')] + +buildopts = 'CC="${CC}" CFLAGS="${CFLAGS}" INCLUDES="${CPPFLAGS}"' + +files_to_copy = [ + (['%(name)s'], 'bin'), + (['lib%(name)s.a'], 'lib'), + (['*.h'], 'include'), + 'LICENSE.txt', 'NEWS.md', 'README.md', + (['%(name)s.1'], 'share/man/man1') +] + +sanity_check_paths = { + 'files': ['bin/%(name)s', 'lib/lib%(name)s.a'], + 'dirs': ['include'] +} + +sanity_check_commands = [ + "minimap2 --help", + "cd %(builddir)s/minimap2-%(version)s && minimap2 -a test/MT-human.fa test/MT-orang.fa > test.sam", +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/miniprot/miniprot-0.13-GCCcore-12.3.0.eb b/easybuild/easyconfigs/m/miniprot/miniprot-0.13-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..aa598c6869b --- /dev/null +++ b/easybuild/easyconfigs/m/miniprot/miniprot-0.13-GCCcore-12.3.0.eb @@ -0,0 +1,33 @@ +easyblock = "MakeCp" + +name = 'miniprot' +version = '0.13' + +homepage = 'https://github.com/lh3/miniprot' +description = """Miniprot aligns a protein sequence against a genome with affine gap penalty, splicing and frameshift. +It is primarily intended for annotating protein-coding genes in a new species using known genes from other species. +Miniprot is similar to GeneWise and Exonerate in functionality but it can map proteins to whole genomes and is much +faster at the residue alignment step.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://github.com/lh3/miniprot/archive'] +sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}] +checksums = ['be12d98d998beb78e4e06350c03d2f188bcdf3245d6bcaf43e2cc80785a617a4'] + +builddependencies = [('binutils', '2.40')] +dependencies = [('zlib', '1.2.13')] + +files_to_copy = [ + (['*.h', 'miniprot.1', 'test', 'tex'], 'lib'), + (['miniprot'], 'bin'), + 'README.md', + 'LICENSE.txt', +] + +sanity_check_paths = { + 'files': ['bin/miniprot'], + 'dirs': ['lib'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/ml-collections/ml-collections-0.1.1-foss-2023a.eb b/easybuild/easyconfigs/m/ml-collections/ml-collections-0.1.1-foss-2023a.eb new file mode 100644 index 00000000000..79034a7433d --- /dev/null +++ b/easybuild/easyconfigs/m/ml-collections/ml-collections-0.1.1-foss-2023a.eb @@ -0,0 +1,37 @@ +easyblock = 'PythonBundle' + +name = 'ml-collections' +version = '0.1.1' + +homepage = 'https://github.com/google/ml_collections' +description = """ +ML Collections is a library of Python Collections designed for ML use cases. +""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('PyYAML', '6.0'), +] + +use_pip = True + +exts_list = [ + ('absl-py', '2.1.0', { + 'modulename': 'absl', + 'checksums': ['7820790efbb316739cde8b4e19357243fc3608a152024288513dd968d7d959ff'], + }), + ('contextlib2', '21.6.0', { + 'checksums': ['ab1e2bfe1d01d968e1b7e8d9023bc51ef3509bba217bb730cee3827e1ee82869'], + }), + ('ml_collections', version, { + 'preinstallopts': "touch requirements.txt && touch requirements-test.txt && ", + 'checksums': ['3fefcc72ec433aa1e5d32307a3e474bbb67f405be814ea52a2166bfc9dbe68cc'], + }), +] + +sanity_pip_check = True + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/m/ml_dtypes/ml_dtypes-0.3.2-gfbf-2023a.eb b/easybuild/easyconfigs/m/ml_dtypes/ml_dtypes-0.3.2-gfbf-2023a.eb new file mode 100644 index 00000000000..9c3a18bfdb5 --- /dev/null +++ b/easybuild/easyconfigs/m/ml_dtypes/ml_dtypes-0.3.2-gfbf-2023a.eb @@ -0,0 +1,51 @@ +# Thomas Hoffmann, EMBL Heidelberg, structures-it@embl.de, 2024/02 +easyblock = 'PythonBundle' + +name = 'ml_dtypes' +version = '0.3.2' + +homepage = 'https://github.com/jax-ml/ml_dtypes' +description = """ +ml_dtypes is a stand-alone implementation of several NumPy dtype extensions used +in machine learning libraries, including: + +bfloat16: an alternative to the standard float16 format +float8_*: several experimental 8-bit floating point representations including: +float8_e4m3b11fnuz +float8_e4m3fn +float8_e4m3fnuz +float8_e5m2 +float8_e5m2fnuz +""" + +toolchain = {'name': 'gfbf', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), +] + + +use_pip = True + +default_easyblock = 'PythonPackage' + +exts_list = [ + ('opt_einsum', '3.3.0', { + 'checksums': ['59f6475f77bbc37dcf7cd748519c0ec60722e91e63ca114e68821c0c54a46549'], + }), + ('etils', '1.6.0', { + 'checksums': ['c635fbd02a79fed4ad76825d31306b581d22b40671721daa8bc279cf6333e48a'], + }), + (name, version, { + 'patches': [('ml_dtypes-0.3.2_EigenAvx512.patch', 1)], + 'checksums': [ + {'ml_dtypes-0.3.2.tar.gz': '533059bc5f1764fac071ef54598db358c167c51a718f68f5bb55e3dee79d2967'}, + {'ml_dtypes-0.3.2_EigenAvx512.patch': '197b05b0b7f611749824369f026099f6a172f9e8eab6ebb6504a16573746c892'}, + ], + }), +] + +sanity_pip_check = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/m/ml_dtypes/ml_dtypes-0.3.2_EigenAvx512.patch b/easybuild/easyconfigs/m/ml_dtypes/ml_dtypes-0.3.2_EigenAvx512.patch new file mode 100644 index 00000000000..42ea0606391 --- /dev/null +++ b/easybuild/easyconfigs/m/ml_dtypes/ml_dtypes-0.3.2_EigenAvx512.patch @@ -0,0 +1,1219 @@ +# Thomas Hoffmann, EMBL Heidelberg, structures-it@embl.de, 2024/01 +# ml_dtype 0.3.2 ships a copy of Eigen commit 7bf2968 (https://gitlab.com/libeigen/eigen/-/commit/7bf2968). +# This copy is missing the file src/Core/arch/AVX512/TrsmUnrolls.inc, which is added by the present patch. +diff -ru --new-file old/third_party_ori/eigen/Eigen/src/Core/arch/AVX512/TrsmUnrolls.inc new/third_party/eigen/Eigen/src/Core/arch/AVX512/TrsmUnrolls.inc +--- old/third_party/eigen/Eigen/src/Core/arch/AVX512/TrsmUnrolls.inc 1970-01-01 01:00:00.000000000 +0100 ++++ new/third_party/eigen/Eigen/src/Core/arch/AVX512/TrsmUnrolls.inc 2024-02-14 10:32:25.492978066 +0100 +@@ -0,0 +1,1212 @@ ++// This file is part of Eigen, a lightweight C++ template library ++// for linear algebra. ++// ++// Copyright (C) 2022 Intel Corporation ++// ++// This Source Code Form is subject to the terms of the Mozilla ++// Public License v. 2.0. If a copy of the MPL was not distributed ++// with this file, You can obtain one at http://mozilla.org/MPL/2.0/. ++ ++#ifndef EIGEN_CORE_ARCH_AVX512_TRSM_UNROLLS_H ++#define EIGEN_CORE_ARCH_AVX512_TRSM_UNROLLS_H ++ ++template ++EIGEN_ALWAYS_INLINE int64_t idA(int64_t i, int64_t j, int64_t LDA) { ++ EIGEN_IF_CONSTEXPR(isARowMajor) return i * LDA + j; ++ else return i + j * LDA; ++} ++ ++/** ++ * This namespace contains various classes used to generate compile-time unrolls which are ++ * used throughout the trsm/gemm kernels. The unrolls are characterized as for-loops (1-D), nested ++ * for-loops (2-D), or triple nested for-loops (3-D). Unrolls are generated using template recursion ++ * ++ * Example, the 2-D for-loop is unrolled recursively by first flattening to a 1-D loop. ++ * ++ * for(startI = 0; startI < endI; startI++) for(startC = 0; startC < endI*endJ; startC++) ++ * for(startJ = 0; startJ < endJ; startJ++) ----> startI = (startC)/(endJ) ++ * func(startI,startJ) startJ = (startC)%(endJ) ++ * func(...) ++ * ++ * The 1-D loop can be unrolled recursively by using enable_if and defining an auxillary function ++ * with a template parameter used as a counter. ++ * ++ * template ++ * std::enable_if_t<(counter <= 0)> <---- tail case. ++ * aux_func {} ++ * ++ * template ++ * std::enable_if_t<(counter > 0)> <---- actual for-loop ++ * aux_func { ++ * startC = endI*endJ - counter ++ * startI = (startC)/(endJ) ++ * startJ = (startC)%(endJ) ++ * func(startI, startJ) ++ * aux_func() ++ * } ++ * ++ * Note: Additional wrapper functions are provided for aux_func which hides the counter template ++ * parameter since counter usually depends on endI, endJ, etc... ++ * ++ * Conventions: ++ * 1) endX: specifies the terminal value for the for-loop, (ex: for(startX = 0; startX < endX; startX++)) ++ * ++ * 2) rem, remM, remK template parameters are used for deciding whether to use masked operations for ++ * handling remaining tails (when sizes are not multiples of PacketSize or EIGEN_AVX_MAX_NUM_ROW) ++ */ ++namespace unrolls { ++ ++template ++EIGEN_ALWAYS_INLINE auto remMask(int64_t m) { ++ EIGEN_IF_CONSTEXPR(N == 16) { return 0xFFFF >> (16 - m); } ++ else EIGEN_IF_CONSTEXPR(N == 8) { ++ return 0xFF >> (8 - m); ++ } ++ else EIGEN_IF_CONSTEXPR(N == 4) { ++ return 0x0F >> (4 - m); ++ } ++ return 0; ++} ++ ++template ++EIGEN_ALWAYS_INLINE void trans8x8blocks(PacketBlock &kernel); ++ ++template <> ++EIGEN_ALWAYS_INLINE void trans8x8blocks(PacketBlock &kernel) { ++ __m512 T0 = _mm512_unpacklo_ps(kernel.packet[0], kernel.packet[1]); ++ __m512 T1 = _mm512_unpackhi_ps(kernel.packet[0], kernel.packet[1]); ++ __m512 T2 = _mm512_unpacklo_ps(kernel.packet[2], kernel.packet[3]); ++ __m512 T3 = _mm512_unpackhi_ps(kernel.packet[2], kernel.packet[3]); ++ __m512 T4 = _mm512_unpacklo_ps(kernel.packet[4], kernel.packet[5]); ++ __m512 T5 = _mm512_unpackhi_ps(kernel.packet[4], kernel.packet[5]); ++ __m512 T6 = _mm512_unpacklo_ps(kernel.packet[6], kernel.packet[7]); ++ __m512 T7 = _mm512_unpackhi_ps(kernel.packet[6], kernel.packet[7]); ++ ++ kernel.packet[0] = _mm512_castpd_ps(_mm512_unpacklo_pd(_mm512_castps_pd(T0), _mm512_castps_pd(T2))); ++ kernel.packet[1] = _mm512_castpd_ps(_mm512_unpackhi_pd(_mm512_castps_pd(T0), _mm512_castps_pd(T2))); ++ kernel.packet[2] = _mm512_castpd_ps(_mm512_unpacklo_pd(_mm512_castps_pd(T1), _mm512_castps_pd(T3))); ++ kernel.packet[3] = _mm512_castpd_ps(_mm512_unpackhi_pd(_mm512_castps_pd(T1), _mm512_castps_pd(T3))); ++ kernel.packet[4] = _mm512_castpd_ps(_mm512_unpacklo_pd(_mm512_castps_pd(T4), _mm512_castps_pd(T6))); ++ kernel.packet[5] = _mm512_castpd_ps(_mm512_unpackhi_pd(_mm512_castps_pd(T4), _mm512_castps_pd(T6))); ++ kernel.packet[6] = _mm512_castpd_ps(_mm512_unpacklo_pd(_mm512_castps_pd(T5), _mm512_castps_pd(T7))); ++ kernel.packet[7] = _mm512_castpd_ps(_mm512_unpackhi_pd(_mm512_castps_pd(T5), _mm512_castps_pd(T7))); ++ ++ T0 = _mm512_castpd_ps(_mm512_permutex_pd(_mm512_castps_pd(kernel.packet[4]), 0x4E)); ++ T0 = _mm512_mask_blend_ps(0xF0F0, kernel.packet[0], T0); ++ T4 = _mm512_castpd_ps(_mm512_permutex_pd(_mm512_castps_pd(kernel.packet[0]), 0x4E)); ++ T4 = _mm512_mask_blend_ps(0xF0F0, T4, kernel.packet[4]); ++ T1 = _mm512_castpd_ps(_mm512_permutex_pd(_mm512_castps_pd(kernel.packet[5]), 0x4E)); ++ T1 = _mm512_mask_blend_ps(0xF0F0, kernel.packet[1], T1); ++ T5 = _mm512_castpd_ps(_mm512_permutex_pd(_mm512_castps_pd(kernel.packet[1]), 0x4E)); ++ T5 = _mm512_mask_blend_ps(0xF0F0, T5, kernel.packet[5]); ++ T2 = _mm512_castpd_ps(_mm512_permutex_pd(_mm512_castps_pd(kernel.packet[6]), 0x4E)); ++ T2 = _mm512_mask_blend_ps(0xF0F0, kernel.packet[2], T2); ++ T6 = _mm512_castpd_ps(_mm512_permutex_pd(_mm512_castps_pd(kernel.packet[2]), 0x4E)); ++ T6 = _mm512_mask_blend_ps(0xF0F0, T6, kernel.packet[6]); ++ T3 = _mm512_castpd_ps(_mm512_permutex_pd(_mm512_castps_pd(kernel.packet[7]), 0x4E)); ++ T3 = _mm512_mask_blend_ps(0xF0F0, kernel.packet[3], T3); ++ T7 = _mm512_castpd_ps(_mm512_permutex_pd(_mm512_castps_pd(kernel.packet[3]), 0x4E)); ++ T7 = _mm512_mask_blend_ps(0xF0F0, T7, kernel.packet[7]); ++ ++ kernel.packet[0] = T0; ++ kernel.packet[1] = T1; ++ kernel.packet[2] = T2; ++ kernel.packet[3] = T3; ++ kernel.packet[4] = T4; ++ kernel.packet[5] = T5; ++ kernel.packet[6] = T6; ++ kernel.packet[7] = T7; ++} ++ ++template <> ++EIGEN_ALWAYS_INLINE void trans8x8blocks(PacketBlock &kernel) { ++ ptranspose(kernel); ++} ++ ++/*** ++ * Unrolls for tranposed C stores ++ */ ++template ++class trans { ++ public: ++ using vec = typename std::conditional::value, vecFullFloat, vecFullDouble>::type; ++ using vecHalf = typename std::conditional::value, vecHalfFloat, vecFullDouble>::type; ++ static constexpr int64_t PacketSize = packet_traits::size; ++ ++ /*********************************** ++ * Auxillary Functions for: ++ * - storeC ++ *********************************** ++ */ ++ ++ /** ++ * aux_storeC ++ * ++ * 1-D unroll ++ * for(startN = 0; startN < endN; startN++) ++ * ++ * (endN <= PacketSize) is required to handle the fp32 case, see comments in transStoreC ++ * ++ **/ ++ template ++ static EIGEN_ALWAYS_INLINE std::enable_if_t<(counter > 0 && endN <= PacketSize)> aux_storeC( ++ Scalar *C_arr, int64_t LDC, PacketBlock &zmm, int64_t remM_ = 0) { ++ constexpr int64_t counterReverse = endN - counter; ++ constexpr int64_t startN = counterReverse; ++ ++ EIGEN_IF_CONSTEXPR(startN < EIGEN_AVX_MAX_NUM_ROW) { ++ EIGEN_IF_CONSTEXPR(remM) { ++ pstoreu( ++ C_arr + LDC * startN, ++ padd(ploadu((const Scalar *)C_arr + LDC * startN, remMask(remM_)), ++ preinterpret(zmm.packet[packetIndexOffset + (unrollN / PacketSize) * startN]), ++ remMask(remM_)), ++ remMask(remM_)); ++ } ++ else { ++ pstoreu(C_arr + LDC * startN, ++ padd(ploadu((const Scalar *)C_arr + LDC * startN), ++ preinterpret(zmm.packet[packetIndexOffset + (unrollN / PacketSize) * startN]))); ++ } ++ } ++ else { // This block is only needed for fp32 case ++ // Reinterpret as __m512 for _mm512_shuffle_f32x4 ++ vecFullFloat zmm2vecFullFloat = preinterpret( ++ zmm.packet[packetIndexOffset + (unrollN / PacketSize) * (startN - EIGEN_AVX_MAX_NUM_ROW)]); ++ // Swap lower and upper half of avx register. ++ zmm.packet[packetIndexOffset + (unrollN / PacketSize) * (startN - EIGEN_AVX_MAX_NUM_ROW)] = ++ preinterpret(_mm512_shuffle_f32x4(zmm2vecFullFloat, zmm2vecFullFloat, 0b01001110)); ++ ++ EIGEN_IF_CONSTEXPR(remM) { ++ pstoreu( ++ C_arr + LDC * startN, ++ padd(ploadu((const Scalar *)C_arr + LDC * startN, remMask(remM_)), ++ preinterpret( ++ zmm.packet[packetIndexOffset + (unrollN / PacketSize) * (startN - EIGEN_AVX_MAX_NUM_ROW)])), ++ remMask(remM_)); ++ } ++ else { ++ pstoreu( ++ C_arr + LDC * startN, ++ padd(ploadu((const Scalar *)C_arr + LDC * startN), ++ preinterpret( ++ zmm.packet[packetIndexOffset + (unrollN / PacketSize) * (startN - EIGEN_AVX_MAX_NUM_ROW)]))); ++ } ++ } ++ aux_storeC(C_arr, LDC, zmm, remM_); ++ } ++ ++ template ++ static EIGEN_ALWAYS_INLINE std::enable_if_t 0 && endN <= PacketSize)> aux_storeC( ++ Scalar *C_arr, int64_t LDC, PacketBlock &zmm, int64_t remM_ = 0) { ++ EIGEN_UNUSED_VARIABLE(C_arr); ++ EIGEN_UNUSED_VARIABLE(LDC); ++ EIGEN_UNUSED_VARIABLE(zmm); ++ EIGEN_UNUSED_VARIABLE(remM_); ++ } ++ ++ template ++ static EIGEN_ALWAYS_INLINE void storeC(Scalar *C_arr, int64_t LDC, ++ PacketBlock &zmm, ++ int64_t remM_ = 0) { ++ aux_storeC(C_arr, LDC, zmm, remM_); ++ } ++ ++ /** ++ * Transposes LxunrollN row major block of matrices stored EIGEN_AVX_MAX_NUM_ACC zmm registers to ++ * "unrollN"xL ymm registers to be stored col-major into C. ++ * ++ * For 8x48, the 8x48 block (row-major) is stored in zmm as follows: ++ * ++ * row0: zmm0 zmm1 zmm2 ++ * row1: zmm3 zmm4 zmm5 ++ * . ++ * . ++ * row7: zmm21 zmm22 zmm23 ++ * ++ * For 8x32, the 8x32 block (row-major) is stored in zmm as follows: ++ * ++ * row0: zmm0 zmm1 ++ * row1: zmm2 zmm3 ++ * . ++ * . ++ * row7: zmm14 zmm15 ++ * ++ * ++ * In general we will have {1,2,3} groups of avx registers each of size ++ * EIGEN_AVX_MAX_NUM_ROW. packetIndexOffset is used to select which "block" of ++ * avx registers are being transposed. ++ */ ++ template ++ static EIGEN_ALWAYS_INLINE void transpose(PacketBlock &zmm) { ++ // Note: this assumes EIGEN_AVX_MAX_NUM_ROW = 8. Unrolls should be adjusted ++ // accordingly if EIGEN_AVX_MAX_NUM_ROW is smaller. ++ constexpr int64_t zmmStride = unrollN / PacketSize; ++ PacketBlock r; ++ r.packet[0] = zmm.packet[packetIndexOffset + zmmStride * 0]; ++ r.packet[1] = zmm.packet[packetIndexOffset + zmmStride * 1]; ++ r.packet[2] = zmm.packet[packetIndexOffset + zmmStride * 2]; ++ r.packet[3] = zmm.packet[packetIndexOffset + zmmStride * 3]; ++ r.packet[4] = zmm.packet[packetIndexOffset + zmmStride * 4]; ++ r.packet[5] = zmm.packet[packetIndexOffset + zmmStride * 5]; ++ r.packet[6] = zmm.packet[packetIndexOffset + zmmStride * 6]; ++ r.packet[7] = zmm.packet[packetIndexOffset + zmmStride * 7]; ++ trans8x8blocks(r); ++ zmm.packet[packetIndexOffset + zmmStride * 0] = r.packet[0]; ++ zmm.packet[packetIndexOffset + zmmStride * 1] = r.packet[1]; ++ zmm.packet[packetIndexOffset + zmmStride * 2] = r.packet[2]; ++ zmm.packet[packetIndexOffset + zmmStride * 3] = r.packet[3]; ++ zmm.packet[packetIndexOffset + zmmStride * 4] = r.packet[4]; ++ zmm.packet[packetIndexOffset + zmmStride * 5] = r.packet[5]; ++ zmm.packet[packetIndexOffset + zmmStride * 6] = r.packet[6]; ++ zmm.packet[packetIndexOffset + zmmStride * 7] = r.packet[7]; ++ } ++}; ++ ++/** ++ * Unrolls for copyBToRowMajor ++ * ++ * Idea: ++ * 1) Load a block of right-hand sides to registers (using loadB). ++ * 2) Convert the block from column-major to row-major (transposeLxL) ++ * 3) Store the blocks from register either to a temp array (toTemp == true), or back to B (toTemp == false). ++ * ++ * We use at most EIGEN_AVX_MAX_NUM_ACC avx registers to store the blocks of B. The remaining registers are ++ * used as temps for transposing. ++ * ++ * Blocks will be of size Lx{U1,U2,U3}. packetIndexOffset is used to index between these subblocks ++ * For fp32, PacketSize = 2*EIGEN_AVX_MAX_NUM_ROW, so we reinterpret packets as packets half the size (zmm -> ymm). ++ */ ++template ++class transB { ++ public: ++ using vec = typename std::conditional::value, vecFullFloat, vecFullDouble>::type; ++ using vecHalf = typename std::conditional::value, vecHalfFloat, vecFullDouble>::type; ++ static constexpr int64_t PacketSize = packet_traits::size; ++ ++ /*********************************** ++ * Auxillary Functions for: ++ * - loadB ++ * - storeB ++ * - loadBBlock ++ * - storeBBlock ++ *********************************** ++ */ ++ ++ /** ++ * aux_loadB ++ * ++ * 1-D unroll ++ * for(startN = 0; startN < endN; startN++) ++ **/ ++ template ++ static EIGEN_ALWAYS_INLINE std::enable_if_t<(counter > 0)> aux_loadB( ++ Scalar *B_arr, int64_t LDB, PacketBlock &ymm, ++ int64_t remM_ = 0) { ++ constexpr int64_t counterReverse = endN - counter; ++ constexpr int64_t startN = counterReverse; ++ ++ EIGEN_IF_CONSTEXPR(remM) { ++ ymm.packet[packetIndexOffset + startN] = ++ ploadu((const Scalar *)&B_arr[startN * LDB], remMask(remM_)); ++ } ++ else ymm.packet[packetIndexOffset + startN] = ploadu((const Scalar *)&B_arr[startN * LDB]); ++ ++ aux_loadB(B_arr, LDB, ymm, remM_); ++ } ++ ++ template ++ static EIGEN_ALWAYS_INLINE std::enable_if_t<(counter <= 0)> aux_loadB( ++ Scalar *B_arr, int64_t LDB, PacketBlock &ymm, ++ int64_t remM_ = 0) { ++ EIGEN_UNUSED_VARIABLE(B_arr); ++ EIGEN_UNUSED_VARIABLE(LDB); ++ EIGEN_UNUSED_VARIABLE(ymm); ++ EIGEN_UNUSED_VARIABLE(remM_); ++ } ++ ++ /** ++ * aux_storeB ++ * ++ * 1-D unroll ++ * for(startN = 0; startN < endN; startN++) ++ **/ ++ template ++ static EIGEN_ALWAYS_INLINE std::enable_if_t<(counter > 0)> aux_storeB( ++ Scalar *B_arr, int64_t LDB, PacketBlock &ymm, int64_t rem_ = 0) { ++ constexpr int64_t counterReverse = endN - counter; ++ constexpr int64_t startN = counterReverse; ++ ++ EIGEN_IF_CONSTEXPR(remK || remM) { ++ pstoreu(&B_arr[startN * LDB], ymm.packet[packetIndexOffset + startN], ++ remMask(rem_)); ++ } ++ else { ++ pstoreu(&B_arr[startN * LDB], ymm.packet[packetIndexOffset + startN]); ++ } ++ ++ aux_storeB(B_arr, LDB, ymm, rem_); ++ } ++ ++ template ++ static EIGEN_ALWAYS_INLINE std::enable_if_t<(counter <= 0)> aux_storeB( ++ Scalar *B_arr, int64_t LDB, PacketBlock &ymm, int64_t rem_ = 0) { ++ EIGEN_UNUSED_VARIABLE(B_arr); ++ EIGEN_UNUSED_VARIABLE(LDB); ++ EIGEN_UNUSED_VARIABLE(ymm); ++ EIGEN_UNUSED_VARIABLE(rem_); ++ } ++ ++ /** ++ * aux_loadBBlock ++ * ++ * 1-D unroll ++ * for(startN = 0; startN < endN; startN += EIGEN_AVX_MAX_NUM_ROW) ++ **/ ++ template ++ static EIGEN_ALWAYS_INLINE std::enable_if_t<(counter > 0)> aux_loadBBlock( ++ Scalar *B_arr, int64_t LDB, Scalar *B_temp, int64_t LDB_, ++ PacketBlock &ymm, int64_t remM_ = 0) { ++ constexpr int64_t counterReverse = endN - counter; ++ constexpr int64_t startN = counterReverse; ++ transB::template loadB(&B_temp[startN], LDB_, ymm); ++ aux_loadBBlock(B_arr, LDB, B_temp, LDB_, ymm, remM_); ++ } ++ ++ template ++ static EIGEN_ALWAYS_INLINE std::enable_if_t<(counter <= 0)> aux_loadBBlock( ++ Scalar *B_arr, int64_t LDB, Scalar *B_temp, int64_t LDB_, ++ PacketBlock &ymm, int64_t remM_ = 0) { ++ EIGEN_UNUSED_VARIABLE(B_arr); ++ EIGEN_UNUSED_VARIABLE(LDB); ++ EIGEN_UNUSED_VARIABLE(B_temp); ++ EIGEN_UNUSED_VARIABLE(LDB_); ++ EIGEN_UNUSED_VARIABLE(ymm); ++ EIGEN_UNUSED_VARIABLE(remM_); ++ } ++ ++ /** ++ * aux_storeBBlock ++ * ++ * 1-D unroll ++ * for(startN = 0; startN < endN; startN += EIGEN_AVX_MAX_NUM_ROW) ++ **/ ++ template ++ static EIGEN_ALWAYS_INLINE std::enable_if_t<(counter > 0)> aux_storeBBlock( ++ Scalar *B_arr, int64_t LDB, Scalar *B_temp, int64_t LDB_, ++ PacketBlock &ymm, int64_t remM_ = 0) { ++ constexpr int64_t counterReverse = endN - counter; ++ constexpr int64_t startN = counterReverse; ++ ++ EIGEN_IF_CONSTEXPR(toTemp) { ++ transB::template storeB(&B_temp[startN], LDB_, ymm, remK_); ++ } ++ else { ++ transB::template storeB(&B_arr[0 + startN * LDB], LDB, ++ ymm, remM_); ++ } ++ aux_storeBBlock(B_arr, LDB, B_temp, LDB_, ymm, remM_); ++ } ++ ++ template ++ static EIGEN_ALWAYS_INLINE std::enable_if_t<(counter <= 0)> aux_storeBBlock( ++ Scalar *B_arr, int64_t LDB, Scalar *B_temp, int64_t LDB_, ++ PacketBlock &ymm, int64_t remM_ = 0) { ++ EIGEN_UNUSED_VARIABLE(B_arr); ++ EIGEN_UNUSED_VARIABLE(LDB); ++ EIGEN_UNUSED_VARIABLE(B_temp); ++ EIGEN_UNUSED_VARIABLE(LDB_); ++ EIGEN_UNUSED_VARIABLE(ymm); ++ EIGEN_UNUSED_VARIABLE(remM_); ++ } ++ ++ /******************************************************** ++ * Wrappers for aux_XXXX to hide counter parameter ++ ********************************************************/ ++ ++ template ++ static EIGEN_ALWAYS_INLINE void loadB(Scalar *B_arr, int64_t LDB, ++ PacketBlock &ymm, ++ int64_t remM_ = 0) { ++ aux_loadB(B_arr, LDB, ymm, remM_); ++ } ++ ++ template ++ static EIGEN_ALWAYS_INLINE void storeB(Scalar *B_arr, int64_t LDB, ++ PacketBlock &ymm, ++ int64_t rem_ = 0) { ++ aux_storeB(B_arr, LDB, ymm, rem_); ++ } ++ ++ template ++ static EIGEN_ALWAYS_INLINE void loadBBlock(Scalar *B_arr, int64_t LDB, Scalar *B_temp, int64_t LDB_, ++ PacketBlock &ymm, ++ int64_t remM_ = 0) { ++ EIGEN_IF_CONSTEXPR(toTemp) { transB::template loadB(&B_arr[0], LDB, ymm, remM_); } ++ else { ++ aux_loadBBlock(B_arr, LDB, B_temp, LDB_, ymm, remM_); ++ } ++ } ++ ++ template ++ static EIGEN_ALWAYS_INLINE void storeBBlock(Scalar *B_arr, int64_t LDB, Scalar *B_temp, int64_t LDB_, ++ PacketBlock &ymm, ++ int64_t remM_ = 0) { ++ aux_storeBBlock(B_arr, LDB, B_temp, LDB_, ymm, remM_); ++ } ++ ++ template ++ static EIGEN_ALWAYS_INLINE void transposeLxL(PacketBlock &ymm) { ++ // Note: this assumes EIGEN_AVX_MAX_NUM_ROW = 8. Unrolls should be adjusted ++ // accordingly if EIGEN_AVX_MAX_NUM_ROW is smaller. ++ PacketBlock r; ++ r.packet[0] = ymm.packet[packetIndexOffset + 0]; ++ r.packet[1] = ymm.packet[packetIndexOffset + 1]; ++ r.packet[2] = ymm.packet[packetIndexOffset + 2]; ++ r.packet[3] = ymm.packet[packetIndexOffset + 3]; ++ r.packet[4] = ymm.packet[packetIndexOffset + 4]; ++ r.packet[5] = ymm.packet[packetIndexOffset + 5]; ++ r.packet[6] = ymm.packet[packetIndexOffset + 6]; ++ r.packet[7] = ymm.packet[packetIndexOffset + 7]; ++ ptranspose(r); ++ ymm.packet[packetIndexOffset + 0] = r.packet[0]; ++ ymm.packet[packetIndexOffset + 1] = r.packet[1]; ++ ymm.packet[packetIndexOffset + 2] = r.packet[2]; ++ ymm.packet[packetIndexOffset + 3] = r.packet[3]; ++ ymm.packet[packetIndexOffset + 4] = r.packet[4]; ++ ymm.packet[packetIndexOffset + 5] = r.packet[5]; ++ ymm.packet[packetIndexOffset + 6] = r.packet[6]; ++ ymm.packet[packetIndexOffset + 7] = r.packet[7]; ++ } ++ ++ template ++ static EIGEN_ALWAYS_INLINE void transB_kernel(Scalar *B_arr, int64_t LDB, Scalar *B_temp, int64_t LDB_, ++ PacketBlock &ymm, ++ int64_t remM_ = 0) { ++ constexpr int64_t U3 = PacketSize * 3; ++ constexpr int64_t U2 = PacketSize * 2; ++ constexpr int64_t U1 = PacketSize * 1; ++ /** ++ * Unrolls needed for each case: ++ * - AVX512 fp32 48 32 16 8 4 2 1 ++ * - AVX512 fp64 24 16 8 4 2 1 ++ * ++ * For fp32 L and U1 are 1:2 so for U3/U2 cases the loads/stores need to be split up. ++ */ ++ EIGEN_IF_CONSTEXPR(unrollN == U3) { ++ // load LxU3 B col major, transpose LxU3 row major ++ constexpr int64_t maxUBlock = std::min(3 * EIGEN_AVX_MAX_NUM_ROW, U3); ++ transB::template loadBBlock(B_arr, LDB, B_temp, LDB_, ymm, remM_); ++ transB::template transposeLxL<0 * EIGEN_AVX_MAX_NUM_ROW>(ymm); ++ transB::template transposeLxL<1 * EIGEN_AVX_MAX_NUM_ROW>(ymm); ++ transB::template transposeLxL<2 * EIGEN_AVX_MAX_NUM_ROW>(ymm); ++ transB::template storeBBlock(B_arr, LDB, B_temp, LDB_, ymm, remM_); ++ ++ EIGEN_IF_CONSTEXPR(maxUBlock < U3) { ++ transB::template loadBBlock(&B_arr[maxUBlock * LDB], LDB, &B_temp[maxUBlock], LDB_, ++ ymm, remM_); ++ transB::template transposeLxL<0 * EIGEN_AVX_MAX_NUM_ROW>(ymm); ++ transB::template transposeLxL<1 * EIGEN_AVX_MAX_NUM_ROW>(ymm); ++ transB::template transposeLxL<2 * EIGEN_AVX_MAX_NUM_ROW>(ymm); ++ transB::template storeBBlock(&B_arr[maxUBlock * LDB], LDB, &B_temp[maxUBlock], LDB_, ++ ymm, remM_); ++ } ++ } ++ else EIGEN_IF_CONSTEXPR(unrollN == U2) { ++ // load LxU2 B col major, transpose LxU2 row major ++ constexpr int64_t maxUBlock = std::min(3 * EIGEN_AVX_MAX_NUM_ROW, U2); ++ transB::template loadBBlock(B_arr, LDB, B_temp, LDB_, ymm, remM_); ++ transB::template transposeLxL<0 * EIGEN_AVX_MAX_NUM_ROW>(ymm); ++ transB::template transposeLxL<1 * EIGEN_AVX_MAX_NUM_ROW>(ymm); ++ EIGEN_IF_CONSTEXPR(maxUBlock < U2) transB::template transposeLxL<2 * EIGEN_AVX_MAX_NUM_ROW>(ymm); ++ transB::template storeBBlock(B_arr, LDB, B_temp, LDB_, ymm, remM_); ++ ++ EIGEN_IF_CONSTEXPR(maxUBlock < U2) { ++ transB::template loadBBlock(&B_arr[maxUBlock * LDB], LDB, ++ &B_temp[maxUBlock], LDB_, ymm, remM_); ++ transB::template transposeLxL<0>(ymm); ++ transB::template storeBBlock(&B_arr[maxUBlock * LDB], LDB, ++ &B_temp[maxUBlock], LDB_, ymm, remM_); ++ } ++ } ++ else EIGEN_IF_CONSTEXPR(unrollN == U1) { ++ // load LxU1 B col major, transpose LxU1 row major ++ transB::template loadBBlock(B_arr, LDB, B_temp, LDB_, ymm, remM_); ++ transB::template transposeLxL<0>(ymm); ++ EIGEN_IF_CONSTEXPR(EIGEN_AVX_MAX_NUM_ROW < U1) { transB::template transposeLxL<1 * EIGEN_AVX_MAX_NUM_ROW>(ymm); } ++ transB::template storeBBlock(B_arr, LDB, B_temp, LDB_, ymm, remM_); ++ } ++ else EIGEN_IF_CONSTEXPR(unrollN == 8 && U1 > 8) { ++ // load Lx4 B col major, transpose Lx4 row major ++ transB::template loadBBlock<8, toTemp, remM>(B_arr, LDB, B_temp, LDB_, ymm, remM_); ++ transB::template transposeLxL<0>(ymm); ++ transB::template storeBBlock<8, toTemp, remM, 8>(B_arr, LDB, B_temp, LDB_, ymm, remM_); ++ } ++ else EIGEN_IF_CONSTEXPR(unrollN == 4 && U1 > 4) { ++ // load Lx4 B col major, transpose Lx4 row major ++ transB::template loadBBlock<4, toTemp, remM>(B_arr, LDB, B_temp, LDB_, ymm, remM_); ++ transB::template transposeLxL<0>(ymm); ++ transB::template storeBBlock<4, toTemp, remM, 4>(B_arr, LDB, B_temp, LDB_, ymm, remM_); ++ } ++ else EIGEN_IF_CONSTEXPR(unrollN == 2) { ++ // load Lx2 B col major, transpose Lx2 row major ++ transB::template loadBBlock<2, toTemp, remM>(B_arr, LDB, B_temp, LDB_, ymm, remM_); ++ transB::template transposeLxL<0>(ymm); ++ transB::template storeBBlock<2, toTemp, remM, 2>(B_arr, LDB, B_temp, LDB_, ymm, remM_); ++ } ++ else EIGEN_IF_CONSTEXPR(unrollN == 1) { ++ // load Lx1 B col major, transpose Lx1 row major ++ transB::template loadBBlock<1, toTemp, remM>(B_arr, LDB, B_temp, LDB_, ymm, remM_); ++ transB::template transposeLxL<0>(ymm); ++ transB::template storeBBlock<1, toTemp, remM, 1>(B_arr, LDB, B_temp, LDB_, ymm, remM_); ++ } ++ } ++}; ++ ++/** ++ * Unrolls for triSolveKernel ++ * ++ * Idea: ++ * 1) Load a block of right-hand sides to registers in RHSInPacket (using loadRHS). ++ * 2) Do triangular solve with RHSInPacket and a small block of A (triangular matrix) ++ * stored in AInPacket (using triSolveMicroKernel). ++ * 3) Store final results (in avx registers) back into memory (using storeRHS). ++ * ++ * RHSInPacket uses at most EIGEN_AVX_MAX_NUM_ACC avx registers and AInPacket uses at most ++ * EIGEN_AVX_MAX_NUM_ROW registers. ++ */ ++template ++class trsm { ++ public: ++ using vec = typename std::conditional::value, vecFullFloat, vecFullDouble>::type; ++ static constexpr int64_t PacketSize = packet_traits::size; ++ ++ /*********************************** ++ * Auxillary Functions for: ++ * - loadRHS ++ * - storeRHS ++ * - divRHSByDiag ++ * - updateRHS ++ * - triSolveMicroKernel ++ ************************************/ ++ /** ++ * aux_loadRHS ++ * ++ * 2-D unroll ++ * for(startM = 0; startM < endM; startM++) ++ * for(startK = 0; startK < endK; startK++) ++ **/ ++ template ++ static EIGEN_ALWAYS_INLINE std::enable_if_t<(counter > 0)> aux_loadRHS( ++ Scalar *B_arr, int64_t LDB, PacketBlock &RHSInPacket, int64_t rem = 0) { ++ constexpr int64_t counterReverse = endM * endK - counter; ++ constexpr int64_t startM = counterReverse / (endK); ++ constexpr int64_t startK = counterReverse % endK; ++ ++ constexpr int64_t packetIndex = startM * endK + startK; ++ constexpr int64_t startM_ = isFWDSolve ? startM : -startM; ++ const int64_t rhsIndex = (startK * PacketSize) + startM_ * LDB; ++ EIGEN_IF_CONSTEXPR(krem) { ++ RHSInPacket.packet[packetIndex] = ploadu(&B_arr[rhsIndex], remMask(rem)); ++ } ++ else { ++ RHSInPacket.packet[packetIndex] = ploadu(&B_arr[rhsIndex]); ++ } ++ aux_loadRHS(B_arr, LDB, RHSInPacket, rem); ++ } ++ ++ template ++ static EIGEN_ALWAYS_INLINE std::enable_if_t<(counter <= 0)> aux_loadRHS( ++ Scalar *B_arr, int64_t LDB, PacketBlock &RHSInPacket, int64_t rem = 0) { ++ EIGEN_UNUSED_VARIABLE(B_arr); ++ EIGEN_UNUSED_VARIABLE(LDB); ++ EIGEN_UNUSED_VARIABLE(RHSInPacket); ++ EIGEN_UNUSED_VARIABLE(rem); ++ } ++ ++ /** ++ * aux_storeRHS ++ * ++ * 2-D unroll ++ * for(startM = 0; startM < endM; startM++) ++ * for(startK = 0; startK < endK; startK++) ++ **/ ++ template ++ static EIGEN_ALWAYS_INLINE std::enable_if_t<(counter > 0)> aux_storeRHS( ++ Scalar *B_arr, int64_t LDB, PacketBlock &RHSInPacket, int64_t rem = 0) { ++ constexpr int64_t counterReverse = endM * endK - counter; ++ constexpr int64_t startM = counterReverse / (endK); ++ constexpr int64_t startK = counterReverse % endK; ++ ++ constexpr int64_t packetIndex = startM * endK + startK; ++ constexpr int64_t startM_ = isFWDSolve ? startM : -startM; ++ const int64_t rhsIndex = (startK * PacketSize) + startM_ * LDB; ++ EIGEN_IF_CONSTEXPR(krem) { ++ pstoreu(&B_arr[rhsIndex], RHSInPacket.packet[packetIndex], remMask(rem)); ++ } ++ else { ++ pstoreu(&B_arr[rhsIndex], RHSInPacket.packet[packetIndex]); ++ } ++ aux_storeRHS(B_arr, LDB, RHSInPacket, rem); ++ } ++ ++ template ++ static EIGEN_ALWAYS_INLINE std::enable_if_t<(counter <= 0)> aux_storeRHS( ++ Scalar *B_arr, int64_t LDB, PacketBlock &RHSInPacket, int64_t rem = 0) { ++ EIGEN_UNUSED_VARIABLE(B_arr); ++ EIGEN_UNUSED_VARIABLE(LDB); ++ EIGEN_UNUSED_VARIABLE(RHSInPacket); ++ EIGEN_UNUSED_VARIABLE(rem); ++ } ++ ++ /** ++ * aux_divRHSByDiag ++ * ++ * currM may be -1, (currM >=0) in enable_if checks for this ++ * ++ * 1-D unroll ++ * for(startK = 0; startK < endK; startK++) ++ **/ ++ template ++ static EIGEN_ALWAYS_INLINE std::enable_if_t<(counter > 0 && currM >= 0)> aux_divRHSByDiag( ++ PacketBlock &RHSInPacket, PacketBlock &AInPacket) { ++ constexpr int64_t counterReverse = endK - counter; ++ constexpr int64_t startK = counterReverse; ++ ++ constexpr int64_t packetIndex = currM * endK + startK; ++ RHSInPacket.packet[packetIndex] = pmul(AInPacket.packet[currM], RHSInPacket.packet[packetIndex]); ++ aux_divRHSByDiag(RHSInPacket, AInPacket); ++ } ++ ++ template ++ static EIGEN_ALWAYS_INLINE std::enable_if_t 0 && currM >= 0)> aux_divRHSByDiag( ++ PacketBlock &RHSInPacket, PacketBlock &AInPacket) { ++ EIGEN_UNUSED_VARIABLE(RHSInPacket); ++ EIGEN_UNUSED_VARIABLE(AInPacket); ++ } ++ ++ /** ++ * aux_updateRHS ++ * ++ * 2-D unroll ++ * for(startM = initM; startM < endM; startM++) ++ * for(startK = 0; startK < endK; startK++) ++ **/ ++ template ++ static EIGEN_ALWAYS_INLINE std::enable_if_t<(counter > 0)> aux_updateRHS( ++ Scalar *A_arr, int64_t LDA, PacketBlock &RHSInPacket, ++ PacketBlock &AInPacket) { ++ constexpr int64_t counterReverse = (endM - initM) * endK - counter; ++ constexpr int64_t startM = initM + counterReverse / (endK); ++ constexpr int64_t startK = counterReverse % endK; ++ ++ // For each row of A, first update all corresponding RHS ++ constexpr int64_t packetIndex = startM * endK + startK; ++ EIGEN_IF_CONSTEXPR(currentM > 0) { ++ RHSInPacket.packet[packetIndex] = ++ pnmadd(AInPacket.packet[startM], RHSInPacket.packet[(currentM - 1) * endK + startK], ++ RHSInPacket.packet[packetIndex]); ++ } ++ ++ EIGEN_IF_CONSTEXPR(startK == endK - 1) { ++ // Once all RHS for previous row of A is updated, we broadcast the next element in the column A_{i, currentM}. ++ EIGEN_IF_CONSTEXPR(startM == currentM && !isUnitDiag) { ++ // If diagonal is not unit, we broadcast reciprocals of diagonals AinPacket.packet[currentM]. ++ // This will be used in divRHSByDiag ++ EIGEN_IF_CONSTEXPR(isFWDSolve) ++ AInPacket.packet[currentM] = pset1(Scalar(1) / A_arr[idA(currentM, currentM, LDA)]); ++ else AInPacket.packet[currentM] = pset1(Scalar(1) / A_arr[idA(-currentM, -currentM, LDA)]); ++ } ++ else { ++ // Broadcast next off diagonal element of A ++ EIGEN_IF_CONSTEXPR(isFWDSolve) ++ AInPacket.packet[startM] = pset1(A_arr[idA(startM, currentM, LDA)]); ++ else AInPacket.packet[startM] = pset1(A_arr[idA(-startM, -currentM, LDA)]); ++ } ++ } ++ ++ aux_updateRHS( ++ A_arr, LDA, RHSInPacket, AInPacket); ++ } ++ ++ template ++ static EIGEN_ALWAYS_INLINE std::enable_if_t<(counter <= 0)> aux_updateRHS( ++ Scalar *A_arr, int64_t LDA, PacketBlock &RHSInPacket, ++ PacketBlock &AInPacket) { ++ EIGEN_UNUSED_VARIABLE(A_arr); ++ EIGEN_UNUSED_VARIABLE(LDA); ++ EIGEN_UNUSED_VARIABLE(RHSInPacket); ++ EIGEN_UNUSED_VARIABLE(AInPacket); ++ } ++ ++ /** ++ * aux_triSolverMicroKernel ++ * ++ * 1-D unroll ++ * for(startM = 0; startM < endM; startM++) ++ **/ ++ template ++ static EIGEN_ALWAYS_INLINE std::enable_if_t<(counter > 0)> aux_triSolveMicroKernel( ++ Scalar *A_arr, int64_t LDA, PacketBlock &RHSInPacket, ++ PacketBlock &AInPacket) { ++ constexpr int64_t counterReverse = endM - counter; ++ constexpr int64_t startM = counterReverse; ++ ++ constexpr int64_t currentM = startM; ++ // Divides the right-hand side in row startM, by digonal value of A ++ // broadcasted to AInPacket.packet[startM-1] in the previous iteration. ++ // ++ // Without "if constexpr" the compiler instantiates the case <-1, numK> ++ // this is handled with enable_if to prevent out-of-bound warnings ++ // from the compiler ++ EIGEN_IF_CONSTEXPR(!isUnitDiag && startM > 0) ++ trsm::template divRHSByDiag(RHSInPacket, AInPacket); ++ ++ // After division, the rhs corresponding to subsequent rows of A can be partially updated ++ // We also broadcast the reciprocal of the next diagonal to AInPacket.packet[currentM] (if needed) ++ // to be used in the next iteration. ++ trsm::template updateRHS(A_arr, LDA, RHSInPacket, ++ AInPacket); ++ ++ // Handle division for the RHS corresponding to the final row of A. ++ EIGEN_IF_CONSTEXPR(!isUnitDiag && startM == endM - 1) ++ trsm::template divRHSByDiag(RHSInPacket, AInPacket); ++ ++ aux_triSolveMicroKernel(A_arr, LDA, RHSInPacket, ++ AInPacket); ++ } ++ ++ template ++ static EIGEN_ALWAYS_INLINE std::enable_if_t<(counter <= 0)> aux_triSolveMicroKernel( ++ Scalar *A_arr, int64_t LDA, PacketBlock &RHSInPacket, ++ PacketBlock &AInPacket) { ++ EIGEN_UNUSED_VARIABLE(A_arr); ++ EIGEN_UNUSED_VARIABLE(LDA); ++ EIGEN_UNUSED_VARIABLE(RHSInPacket); ++ EIGEN_UNUSED_VARIABLE(AInPacket); ++ } ++ ++ /******************************************************** ++ * Wrappers for aux_XXXX to hide counter parameter ++ ********************************************************/ ++ ++ /** ++ * Load endMxendK block of B to RHSInPacket ++ * Masked loads are used for cases where endK is not a multiple of PacketSize ++ */ ++ template ++ static EIGEN_ALWAYS_INLINE void loadRHS(Scalar *B_arr, int64_t LDB, ++ PacketBlock &RHSInPacket, int64_t rem = 0) { ++ aux_loadRHS(B_arr, LDB, RHSInPacket, rem); ++ } ++ ++ /** ++ * Load endMxendK block of B to RHSInPacket ++ * Masked loads are used for cases where endK is not a multiple of PacketSize ++ */ ++ template ++ static EIGEN_ALWAYS_INLINE void storeRHS(Scalar *B_arr, int64_t LDB, ++ PacketBlock &RHSInPacket, int64_t rem = 0) { ++ aux_storeRHS(B_arr, LDB, RHSInPacket, rem); ++ } ++ ++ /** ++ * Only used if Triangular matrix has non-unit diagonal values ++ */ ++ template ++ static EIGEN_ALWAYS_INLINE void divRHSByDiag(PacketBlock &RHSInPacket, ++ PacketBlock &AInPacket) { ++ aux_divRHSByDiag(RHSInPacket, AInPacket); ++ } ++ ++ /** ++ * Update right-hand sides (stored in avx registers) ++ * Traversing along the column A_{i,currentM}, where currentM <= i <= endM, and broadcasting each value to AInPacket. ++ **/ ++ template ++ static EIGEN_ALWAYS_INLINE void updateRHS(Scalar *A_arr, int64_t LDA, ++ PacketBlock &RHSInPacket, ++ PacketBlock &AInPacket) { ++ aux_updateRHS( ++ A_arr, LDA, RHSInPacket, AInPacket); ++ } ++ ++ /** ++ * endM: dimension of A. 1 <= endM <= EIGEN_AVX_MAX_NUM_ROW ++ * numK: number of avx registers to use for each row of B (ex fp32: 48 rhs => 3 avx reg used). 1 <= endK <= 3. ++ * isFWDSolve: true => forward substitution, false => backwards substitution ++ * isUnitDiag: true => triangular matrix has unit diagonal. ++ */ ++ template ++ static EIGEN_ALWAYS_INLINE void triSolveMicroKernel(Scalar *A_arr, int64_t LDA, ++ PacketBlock &RHSInPacket, ++ PacketBlock &AInPacket) { ++ static_assert(numK >= 1 && numK <= 3, "numK out of range"); ++ aux_triSolveMicroKernel(A_arr, LDA, RHSInPacket, AInPacket); ++ } ++}; ++ ++/** ++ * Unrolls for gemm kernel ++ * ++ * isAdd: true => C += A*B, false => C -= A*B ++ */ ++template ++class gemm { ++ public: ++ using vec = typename std::conditional::value, vecFullFloat, vecFullDouble>::type; ++ static constexpr int64_t PacketSize = packet_traits::size; ++ ++ /*********************************** ++ * Auxillary Functions for: ++ * - setzero ++ * - updateC ++ * - storeC ++ * - startLoadB ++ * - triSolveMicroKernel ++ ************************************/ ++ ++ /** ++ * aux_setzero ++ * ++ * 2-D unroll ++ * for(startM = 0; startM < endM; startM++) ++ * for(startN = 0; startN < endN; startN++) ++ **/ ++ template ++ static EIGEN_ALWAYS_INLINE std::enable_if_t<(counter > 0)> aux_setzero( ++ PacketBlock &zmm) { ++ constexpr int64_t counterReverse = endM * endN - counter; ++ constexpr int64_t startM = counterReverse / (endN); ++ constexpr int64_t startN = counterReverse % endN; ++ ++ zmm.packet[startN * endM + startM] = pzero(zmm.packet[startN * endM + startM]); ++ aux_setzero(zmm); ++ } ++ ++ template ++ static EIGEN_ALWAYS_INLINE std::enable_if_t<(counter <= 0)> aux_setzero( ++ PacketBlock &zmm) { ++ EIGEN_UNUSED_VARIABLE(zmm); ++ } ++ ++ /** ++ * aux_updateC ++ * ++ * 2-D unroll ++ * for(startM = 0; startM < endM; startM++) ++ * for(startN = 0; startN < endN; startN++) ++ **/ ++ template ++ static EIGEN_ALWAYS_INLINE std::enable_if_t<(counter > 0)> aux_updateC( ++ Scalar *C_arr, int64_t LDC, PacketBlock &zmm, int64_t rem_ = 0) { ++ EIGEN_UNUSED_VARIABLE(rem_); ++ constexpr int64_t counterReverse = endM * endN - counter; ++ constexpr int64_t startM = counterReverse / (endN); ++ constexpr int64_t startN = counterReverse % endN; ++ ++ EIGEN_IF_CONSTEXPR(rem) ++ zmm.packet[startN * endM + startM] = ++ padd(ploadu(&C_arr[(startN)*LDC + startM * PacketSize], remMask(rem_)), ++ zmm.packet[startN * endM + startM], remMask(rem_)); ++ else zmm.packet[startN * endM + startM] = ++ padd(ploadu(&C_arr[(startN)*LDC + startM * PacketSize]), zmm.packet[startN * endM + startM]); ++ aux_updateC(C_arr, LDC, zmm, rem_); ++ } ++ ++ template ++ static EIGEN_ALWAYS_INLINE std::enable_if_t<(counter <= 0)> aux_updateC( ++ Scalar *C_arr, int64_t LDC, PacketBlock &zmm, int64_t rem_ = 0) { ++ EIGEN_UNUSED_VARIABLE(C_arr); ++ EIGEN_UNUSED_VARIABLE(LDC); ++ EIGEN_UNUSED_VARIABLE(zmm); ++ EIGEN_UNUSED_VARIABLE(rem_); ++ } ++ ++ /** ++ * aux_storeC ++ * ++ * 2-D unroll ++ * for(startM = 0; startM < endM; startM++) ++ * for(startN = 0; startN < endN; startN++) ++ **/ ++ template ++ static EIGEN_ALWAYS_INLINE std::enable_if_t<(counter > 0)> aux_storeC( ++ Scalar *C_arr, int64_t LDC, PacketBlock &zmm, int64_t rem_ = 0) { ++ EIGEN_UNUSED_VARIABLE(rem_); ++ constexpr int64_t counterReverse = endM * endN - counter; ++ constexpr int64_t startM = counterReverse / (endN); ++ constexpr int64_t startN = counterReverse % endN; ++ ++ EIGEN_IF_CONSTEXPR(rem) ++ pstoreu(&C_arr[(startN)*LDC + startM * PacketSize], zmm.packet[startN * endM + startM], ++ remMask(rem_)); ++ else pstoreu(&C_arr[(startN)*LDC + startM * PacketSize], zmm.packet[startN * endM + startM]); ++ aux_storeC(C_arr, LDC, zmm, rem_); ++ } ++ ++ template ++ static EIGEN_ALWAYS_INLINE std::enable_if_t<(counter <= 0)> aux_storeC( ++ Scalar *C_arr, int64_t LDC, PacketBlock &zmm, int64_t rem_ = 0) { ++ EIGEN_UNUSED_VARIABLE(C_arr); ++ EIGEN_UNUSED_VARIABLE(LDC); ++ EIGEN_UNUSED_VARIABLE(zmm); ++ EIGEN_UNUSED_VARIABLE(rem_); ++ } ++ ++ /** ++ * aux_startLoadB ++ * ++ * 1-D unroll ++ * for(startL = 0; startL < endL; startL++) ++ **/ ++ template ++ static EIGEN_ALWAYS_INLINE std::enable_if_t<(counter > 0)> aux_startLoadB( ++ Scalar *B_t, int64_t LDB, PacketBlock &zmm, int64_t rem_ = 0) { ++ EIGEN_UNUSED_VARIABLE(rem_); ++ constexpr int64_t counterReverse = endL - counter; ++ constexpr int64_t startL = counterReverse; ++ ++ EIGEN_IF_CONSTEXPR(rem) ++ zmm.packet[unrollM * unrollN + startL] = ++ ploadu(&B_t[(startL / unrollM) * LDB + (startL % unrollM) * PacketSize], remMask(rem_)); ++ else zmm.packet[unrollM * unrollN + startL] = ++ ploadu(&B_t[(startL / unrollM) * LDB + (startL % unrollM) * PacketSize]); ++ ++ aux_startLoadB(B_t, LDB, zmm, rem_); ++ } ++ ++ template ++ static EIGEN_ALWAYS_INLINE std::enable_if_t<(counter <= 0)> aux_startLoadB( ++ Scalar *B_t, int64_t LDB, PacketBlock &zmm, int64_t rem_ = 0) { ++ EIGEN_UNUSED_VARIABLE(B_t); ++ EIGEN_UNUSED_VARIABLE(LDB); ++ EIGEN_UNUSED_VARIABLE(zmm); ++ EIGEN_UNUSED_VARIABLE(rem_); ++ } ++ ++ /** ++ * aux_startBCastA ++ * ++ * 1-D unroll ++ * for(startB = 0; startB < endB; startB++) ++ **/ ++ template ++ static EIGEN_ALWAYS_INLINE std::enable_if_t<(counter > 0)> aux_startBCastA( ++ Scalar *A_t, int64_t LDA, PacketBlock &zmm) { ++ constexpr int64_t counterReverse = endB - counter; ++ constexpr int64_t startB = counterReverse; ++ ++ zmm.packet[unrollM * unrollN + numLoad + startB] = pload1(&A_t[idA(startB, 0, LDA)]); ++ ++ aux_startBCastA(A_t, LDA, zmm); ++ } ++ ++ template ++ static EIGEN_ALWAYS_INLINE std::enable_if_t<(counter <= 0)> aux_startBCastA( ++ Scalar *A_t, int64_t LDA, PacketBlock &zmm) { ++ EIGEN_UNUSED_VARIABLE(A_t); ++ EIGEN_UNUSED_VARIABLE(LDA); ++ EIGEN_UNUSED_VARIABLE(zmm); ++ } ++ ++ /** ++ * aux_loadB ++ * currK: current K ++ * ++ * 1-D unroll ++ * for(startM = 0; startM < endM; startM++) ++ **/ ++ template ++ static EIGEN_ALWAYS_INLINE std::enable_if_t<(counter > 0)> aux_loadB( ++ Scalar *B_t, int64_t LDB, PacketBlock &zmm, int64_t rem_ = 0) { ++ EIGEN_UNUSED_VARIABLE(rem_); ++ if ((numLoad / endM + currK < unrollK)) { ++ constexpr int64_t counterReverse = endM - counter; ++ constexpr int64_t startM = counterReverse; ++ ++ EIGEN_IF_CONSTEXPR(rem) { ++ zmm.packet[endM * unrollN + (startM + currK * endM) % numLoad] = ++ ploadu(&B_t[(numLoad / endM + currK) * LDB + startM * PacketSize], remMask(rem_)); ++ } ++ else { ++ zmm.packet[endM * unrollN + (startM + currK * endM) % numLoad] = ++ ploadu(&B_t[(numLoad / endM + currK) * LDB + startM * PacketSize]); ++ } ++ ++ aux_loadB(B_t, LDB, zmm, rem_); ++ } ++ } ++ ++ template ++ static EIGEN_ALWAYS_INLINE std::enable_if_t<(counter <= 0)> aux_loadB( ++ Scalar *B_t, int64_t LDB, PacketBlock &zmm, int64_t rem_ = 0) { ++ EIGEN_UNUSED_VARIABLE(B_t); ++ EIGEN_UNUSED_VARIABLE(LDB); ++ EIGEN_UNUSED_VARIABLE(zmm); ++ EIGEN_UNUSED_VARIABLE(rem_); ++ } ++ ++ /** ++ * aux_microKernel ++ * ++ * 3-D unroll ++ * for(startM = 0; startM < endM; startM++) ++ * for(startN = 0; startN < endN; startN++) ++ * for(startK = 0; startK < endK; startK++) ++ **/ ++ template ++ static EIGEN_ALWAYS_INLINE std::enable_if_t<(counter > 0)> aux_microKernel( ++ Scalar *B_t, Scalar *A_t, int64_t LDB, int64_t LDA, PacketBlock &zmm, ++ int64_t rem_ = 0) { ++ EIGEN_UNUSED_VARIABLE(rem_); ++ constexpr int64_t counterReverse = endM * endN * endK - counter; ++ constexpr int startK = counterReverse / (endM * endN); ++ constexpr int startN = (counterReverse / (endM)) % endN; ++ constexpr int startM = counterReverse % endM; ++ ++ EIGEN_IF_CONSTEXPR(startK == 0 && startM == 0 && startN == 0) { ++ gemm::template startLoadB(B_t, LDB, zmm, rem_); ++ gemm::template startBCastA(A_t, LDA, zmm); ++ } ++ ++ { ++ // Interleave FMA and Bcast ++ EIGEN_IF_CONSTEXPR(isAdd) { ++ zmm.packet[startN * endM + startM] = ++ pmadd(zmm.packet[endM * endN + numLoad + (startN + startK * endN) % numBCast], ++ zmm.packet[endM * endN + (startM + startK * endM) % numLoad], zmm.packet[startN * endM + startM]); ++ } ++ else { ++ zmm.packet[startN * endM + startM] = ++ pnmadd(zmm.packet[endM * endN + numLoad + (startN + startK * endN) % numBCast], ++ zmm.packet[endM * endN + (startM + startK * endM) % numLoad], zmm.packet[startN * endM + startM]); ++ } ++ // Bcast ++ EIGEN_IF_CONSTEXPR(startM == endM - 1 && (numBCast + startN + startK * endN < endK * endN)) { ++ zmm.packet[endM * endN + numLoad + (startN + startK * endN) % numBCast] = pload1(&A_t[idA( ++ (numBCast + startN + startK * endN) % endN, (numBCast + startN + startK * endN) / endN, LDA)]); ++ } ++ } ++ ++ // We have updated all accumlators, time to load next set of B's ++ EIGEN_IF_CONSTEXPR((startN == endN - 1) && (startM == endM - 1)) { ++ gemm::template loadB(B_t, LDB, zmm, rem_); ++ } ++ aux_microKernel(B_t, A_t, LDB, LDA, zmm, rem_); ++ } ++ ++ template ++ static EIGEN_ALWAYS_INLINE std::enable_if_t<(counter <= 0)> aux_microKernel( ++ Scalar *B_t, Scalar *A_t, int64_t LDB, int64_t LDA, PacketBlock &zmm, ++ int64_t rem_ = 0) { ++ EIGEN_UNUSED_VARIABLE(B_t); ++ EIGEN_UNUSED_VARIABLE(A_t); ++ EIGEN_UNUSED_VARIABLE(LDB); ++ EIGEN_UNUSED_VARIABLE(LDA); ++ EIGEN_UNUSED_VARIABLE(zmm); ++ EIGEN_UNUSED_VARIABLE(rem_); ++ } ++ ++ /******************************************************** ++ * Wrappers for aux_XXXX to hide counter parameter ++ ********************************************************/ ++ ++ template ++ static EIGEN_ALWAYS_INLINE void setzero(PacketBlock &zmm) { ++ aux_setzero(zmm); ++ } ++ ++ /** ++ * Ideally the compiler folds these into vaddp{s,d} with an embedded memory load. ++ */ ++ template ++ static EIGEN_ALWAYS_INLINE void updateC(Scalar *C_arr, int64_t LDC, ++ PacketBlock &zmm, ++ int64_t rem_ = 0) { ++ EIGEN_UNUSED_VARIABLE(rem_); ++ aux_updateC(C_arr, LDC, zmm, rem_); ++ } ++ ++ template ++ static EIGEN_ALWAYS_INLINE void storeC(Scalar *C_arr, int64_t LDC, ++ PacketBlock &zmm, ++ int64_t rem_ = 0) { ++ EIGEN_UNUSED_VARIABLE(rem_); ++ aux_storeC(C_arr, LDC, zmm, rem_); ++ } ++ ++ /** ++ * Use numLoad registers for loading B at start of microKernel ++ */ ++ template ++ static EIGEN_ALWAYS_INLINE void startLoadB(Scalar *B_t, int64_t LDB, ++ PacketBlock &zmm, ++ int64_t rem_ = 0) { ++ EIGEN_UNUSED_VARIABLE(rem_); ++ aux_startLoadB(B_t, LDB, zmm, rem_); ++ } ++ ++ /** ++ * Use numBCast registers for broadcasting A at start of microKernel ++ */ ++ template ++ static EIGEN_ALWAYS_INLINE void startBCastA(Scalar *A_t, int64_t LDA, ++ PacketBlock &zmm) { ++ aux_startBCastA(A_t, LDA, zmm); ++ } ++ ++ /** ++ * Loads next set of B into vector registers between each K unroll. ++ */ ++ template ++ static EIGEN_ALWAYS_INLINE void loadB(Scalar *B_t, int64_t LDB, ++ PacketBlock &zmm, ++ int64_t rem_ = 0) { ++ EIGEN_UNUSED_VARIABLE(rem_); ++ aux_loadB(B_t, LDB, zmm, rem_); ++ } ++ ++ /** ++ * Generates a microkernel for gemm (row-major) with unrolls {1,2,4,8}x{U1,U2,U3} to compute C -= A*B. ++ * A matrix can be row/col-major. B matrix is assumed row-major. ++ * ++ * isARowMajor: is A row major ++ * endM: Number registers per row ++ * endN: Number of rows ++ * endK: Loop unroll for K. ++ * numLoad: Number of registers for loading B. ++ * numBCast: Number of registers for broadcasting A. ++ * ++ * Ex: microkernel: 8x48 unroll (24 accumulators), k unrolled 4 times, ++ * 6 register for loading B, 2 for broadcasting A. ++ * ++ * Note: Ideally the microkernel should not have any register spilling. ++ * The avx instruction counts should be: ++ * - endK*endN vbroadcasts{s,d} ++ * - endK*endM vmovup{s,d} ++ * - endK*endN*endM FMAs ++ * ++ * From testing, there are no register spills with clang. There are register spills with GNU, which ++ * causes a performance hit. ++ */ ++ template ++ static EIGEN_ALWAYS_INLINE void microKernel(Scalar *B_t, Scalar *A_t, int64_t LDB, int64_t LDA, ++ PacketBlock &zmm, ++ int64_t rem_ = 0) { ++ EIGEN_UNUSED_VARIABLE(rem_); ++ aux_microKernel(B_t, A_t, LDB, LDA, zmm, ++ rem_); ++ } ++}; ++} // namespace unrolls ++ ++#endif // EIGEN_CORE_ARCH_AVX512_TRSM_UNROLLS_H diff --git a/easybuild/easyconfigs/m/mm-common/mm-common-1.0.6-GCCcore-11.3.0.eb b/easybuild/easyconfigs/m/mm-common/mm-common-1.0.6-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..9a06d985675 --- /dev/null +++ b/easybuild/easyconfigs/m/mm-common/mm-common-1.0.6-GCCcore-11.3.0.eb @@ -0,0 +1,33 @@ +easyblock = 'MesonNinja' + +name = 'mm-common' +version = '1.0.6' + +homepage = 'https://gitlab.gnome.org/GNOME/mm-common' +description = """The mm-common module provides the build infrastructure and +utilities shared among the GNOME C++ binding libraries.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['b55c46037dbcdabc5cee3b389ea11cc3910adb68ebe883e9477847aa660862e7'] + +builddependencies = [ + ('binutils', '2.38'), + ('Meson', '0.62.1'), + ('Ninja', '1.10.2'), +] + +dependencies = [ + ('Python', '3.10.4'), +] + +sanity_check_paths = { + 'files': ['bin/mm-common-get', 'bin/mm-common-prepare', 'share/pkgconfig/mm-common-util.pc'], + 'dirs': ['share/man/man1'], +} + +sanity_check_commands = ["mm-common-prepare --help"] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/m/mm-common/mm-common-1.0.6-GCCcore-12.2.0.eb b/easybuild/easyconfigs/m/mm-common/mm-common-1.0.6-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..48aae0caae0 --- /dev/null +++ b/easybuild/easyconfigs/m/mm-common/mm-common-1.0.6-GCCcore-12.2.0.eb @@ -0,0 +1,33 @@ +easyblock = 'MesonNinja' + +name = 'mm-common' +version = '1.0.6' + +homepage = 'https://gitlab.gnome.org/GNOME/mm-common' +description = """The mm-common module provides the build infrastructure and +utilities shared among the GNOME C++ binding libraries.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['b55c46037dbcdabc5cee3b389ea11cc3910adb68ebe883e9477847aa660862e7'] + +builddependencies = [ + ('binutils', '2.39'), + ('Meson', '0.64.0'), + ('Ninja', '1.11.1'), +] + +dependencies = [ + ('Python', '3.10.8'), +] + +sanity_check_paths = { + 'files': ['bin/mm-common-get', 'bin/mm-common-prepare', 'share/pkgconfig/mm-common-util.pc'], + 'dirs': ['share/man/man1'], +} + +sanity_check_commands = ["mm-common-prepare --help"] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/m/mm-common/mm-common-1.0.6-GCCcore-12.3.0.eb b/easybuild/easyconfigs/m/mm-common/mm-common-1.0.6-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..0078e0948e9 --- /dev/null +++ b/easybuild/easyconfigs/m/mm-common/mm-common-1.0.6-GCCcore-12.3.0.eb @@ -0,0 +1,33 @@ +easyblock = 'MesonNinja' + +name = 'mm-common' +version = '1.0.6' + +homepage = 'https://gitlab.gnome.org/GNOME/mm-common' +description = """The mm-common module provides the build infrastructure and +utilities shared among the GNOME C++ binding libraries.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['b55c46037dbcdabc5cee3b389ea11cc3910adb68ebe883e9477847aa660862e7'] + +builddependencies = [ + ('binutils', '2.40'), + ('Meson', '1.1.1'), + ('Ninja', '1.11.1'), +] + +dependencies = [ + ('Python', '3.11.3'), +] + +sanity_check_paths = { + 'files': ['bin/mm-common-get', 'bin/mm-common-prepare', 'share/pkgconfig/mm-common-util.pc'], + 'dirs': ['share/man/man1'], +} + +sanity_check_commands = ["mm-common-prepare --help"] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/m/mm-common/mm-common-1.0.6-GCCcore-13.2.0.eb b/easybuild/easyconfigs/m/mm-common/mm-common-1.0.6-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..f545595fd96 --- /dev/null +++ b/easybuild/easyconfigs/m/mm-common/mm-common-1.0.6-GCCcore-13.2.0.eb @@ -0,0 +1,33 @@ +easyblock = 'MesonNinja' + +name = 'mm-common' +version = '1.0.6' + +homepage = 'https://gitlab.gnome.org/GNOME/mm-common' +description = """The mm-common module provides the build infrastructure and +utilities shared among the GNOME C++ binding libraries.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['b55c46037dbcdabc5cee3b389ea11cc3910adb68ebe883e9477847aa660862e7'] + +builddependencies = [ + ('binutils', '2.40'), + ('Meson', '1.2.3'), + ('Ninja', '1.11.1'), +] + +dependencies = [ + ('Python', '3.11.5'), +] + +sanity_check_paths = { + 'files': ['bin/mm-common-get', 'bin/mm-common-prepare', 'share/pkgconfig/mm-common-util.pc'], + 'dirs': ['share/man/man1'], +} + +sanity_check_commands = ["mm-common-prepare --help"] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb b/easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb new file mode 100644 index 00000000000..3d6ce8d2958 --- /dev/null +++ b/easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb @@ -0,0 +1,57 @@ +easyblock = 'PythonBundle' + +name = 'modin' +version = '0.32.0' + +homepage = 'https://github.com/modin-project/modin' +description = """Modin uses Ray, Dask or Unidist to provide an effortless way to speed up your pandas notebooks, +scripts, and libraries. """ + +toolchain = {'name': 'foss', 'version': '2024a'} + +builddependencies = [ + ('Cython', '3.0.10'), + # Needed for tests + ('boto3', '1.35.36'), + ('s3fs', '2024.9.0'), +] + +dependencies = [ + ('Python', '3.12.3'), + ('Python-bundle-PyPI', '2024.06'), + ('SciPy-bundle', '2024.05'), + ('dask', '2024.9.1'), + ('OpenMPI', '5.0.3'), + ('Ray-project', '2.37.0'), + ('Arrow', '17.0.0'), +] + +use_pip = True + +exts_list = [ + ('unidist', '0.7.2', { + 'checksums': ['6386e1ad5143fe132b9f96e232fe85fc39830ed2886515440e4ba1473255e4a0'], + }), + # The oversubscription is done in their own CI as well. + # Ray has limitations on unix socket path length, so it is not tested here. + (name, version, { + 'patches': ['modin-0.32.0_fix-pytest-config.patch'], + 'runtest': ( + "MODIN_ENGINE=unidist UNIDIST_ENGINE=mpi " + "mpiexec -n=1 --map-by :OVERSUBSCRIBE pytest modin/tests/pandas/test_general.py &&" + "MODIN_ENGINE=dask pytest modin/tests/pandas/test_general.py" + ), + 'source_tmpl': '%(version)s.tar.gz', + 'source_urls': ['https://github.com/modin-project/%(name)s/archive/refs/tags'], + 'testinstall': True, + 'checksums': [ + {'0.32.0.tar.gz': 'f2ef11f384a7d47eb6680a2f6f4bbc3404fa6290163d36384032daff3837b063'}, + {'modin-0.32.0_fix-pytest-config.patch': + 'c49bd5c072a87321760c7c5eebc957f4f6962763a3526a500fe6330cf3f2b765'}, + ], + }), +] + +sanity_pip_check = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/m/modin/modin-0.32.0_fix-pytest-config.patch b/easybuild/easyconfigs/m/modin/modin-0.32.0_fix-pytest-config.patch new file mode 100644 index 00000000000..990e053d328 --- /dev/null +++ b/easybuild/easyconfigs/m/modin/modin-0.32.0_fix-pytest-config.patch @@ -0,0 +1,20 @@ +Removes unnecessary options for pytest that induce additional dependencies. + +--- 0.32.0/foss-2024a/modin/modin-0.32.0/setup.cfg.orig 2024-10-17 15:56:55.245266649 +0200 ++++ 0.32.0/foss-2024a/modin/modin-0.32.0/setup.cfg 2024-10-17 15:57:34.748841878 +0200 +@@ -11,15 +11,6 @@ + tag_prefix = + parentdir_prefix = modin- + +-[tool:pytest] +-addopts = --cov-config=setup.cfg --cov=modin --cov-append --cov-report= -m "not exclude_by_default" +-xfail_strict=true +-markers = +- exclude_in_sanity +- exclude_by_default +-filterwarnings = +- error:.*defaulting to pandas.*:UserWarning +- + [isort] + profile = black + diff --git a/easybuild/easyconfigs/m/modkit/modkit-0.3.3-GCCcore-12.3.0.eb b/easybuild/easyconfigs/m/modkit/modkit-0.3.3-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..63e5c0110bf --- /dev/null +++ b/easybuild/easyconfigs/m/modkit/modkit-0.3.3-GCCcore-12.3.0.eb @@ -0,0 +1,572 @@ +easyblock = 'Cargo' + +name = 'modkit' +version = '0.3.3' + +homepage = 'https://github.com/nanoporetech/modkit' +description = 'A bioinformatics tool for working with modified bases.' + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://github.com/nanoporetech/modkit/archive/'] +sources = ['v%(version)s.tar.gz'] + +builddependencies = [ + ('binutils', '2.40'), + ('Rust', '1.75.0'), + ('Perl-bundle-CPAN', '5.36.1'), +] + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': [], +} + +sanity_check_commands = ["%(namelower)s --help"] + +crates = [ + ('adler2', '2.0.0'), + ('ahash', '0.8.11'), + ('aho-corasick', '1.1.3'), + ('android-tzdata', '0.1.1'), + ('android_system_properties', '0.1.5'), + ('ansi_term', '0.12.1'), + ('anstream', '0.6.15'), + ('anstyle', '1.0.8'), + ('anstyle-parse', '0.2.5'), + ('anstyle-query', '1.1.1'), + ('anstyle-wincon', '3.0.4'), + ('anyhow', '1.0.91'), + ('approx', '0.5.1'), + ('arc-swap', '1.7.1'), + ('assert_approx_eq', '1.1.0'), + ('autocfg', '1.4.0'), + ('bio', '1.6.0'), + ('bio-types', '1.0.4'), + ('bit-set', '0.5.3'), + ('bit-vec', '0.6.3'), + ('bitflags', '2.6.0'), + ('bitvec', '1.0.1'), + ('block-buffer', '0.10.4'), + ('bstr', '1.10.0'), + ('bumpalo', '3.16.0'), + ('bv', '0.11.1'), + ('bytecount', '0.6.8'), + ('bytemuck', '1.19.0'), + ('byteorder', '1.5.0'), + ('bytes', 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'65fc09f10666a9f147042251e0dda9c18f166ff7de300607007e96bdebc1068d'}, + {'wide-0.7.28.tar.gz': 'b828f995bf1e9622031f8009f8481a85406ce1f4d4588ff746d872043e855690'}, + {'winapi-0.3.9.tar.gz': '5c839a674fcd7a98952e593242ea400abe93992746761e38641405d28b00f419'}, + {'winapi-i686-pc-windows-gnu-0.4.0.tar.gz': 'ac3b87c63620426dd9b991e5ce0329eff545bccbbb34f3be09ff6fb6ab51b7b6'}, + {'winapi-x86_64-pc-windows-gnu-0.4.0.tar.gz': '712e227841d057c1ee1cd2fb22fa7e5a5461ae8e48fa2ca79ec42cfc1931183f'}, + {'windows-core-0.52.0.tar.gz': '33ab640c8d7e35bf8ba19b884ba838ceb4fba93a4e8c65a9059d08afcfc683d9'}, + {'windows-sys-0.52.0.tar.gz': '282be5f36a8ce781fad8c8ae18fa3f9beff57ec1b52cb3de0789201425d9a33d'}, + {'windows-sys-0.59.0.tar.gz': '1e38bc4d79ed67fd075bcc251a1c39b32a1776bbe92e5bef1f0bf1f8c531853b'}, + {'windows-targets-0.52.6.tar.gz': '9b724f72796e036ab90c1021d4780d4d3d648aca59e491e6b98e725b84e99973'}, + {'windows_aarch64_gnullvm-0.52.6.tar.gz': '32a4622180e7a0ec044bb555404c800bc9fd9ec262ec147edd5989ccd0c02cd3'}, + {'windows_aarch64_msvc-0.52.6.tar.gz': '09ec2a7bb152e2252b53fa7803150007879548bc709c039df7627cabbd05d469'}, + {'windows_i686_gnu-0.52.6.tar.gz': '8e9b5ad5ab802e97eb8e295ac6720e509ee4c243f69d781394014ebfe8bbfa0b'}, + {'windows_i686_gnullvm-0.52.6.tar.gz': '0eee52d38c090b3caa76c563b86c3a4bd71ef1a819287c19d586d7334ae8ed66'}, + {'windows_i686_msvc-0.52.6.tar.gz': '240948bc05c5e7c6dabba28bf89d89ffce3e303022809e73deaefe4f6ec56c66'}, + {'windows_x86_64_gnu-0.52.6.tar.gz': '147a5c80aabfbf0c7d901cb5895d1de30ef2907eb21fbbab29ca94c5b08b1a78'}, + {'windows_x86_64_gnullvm-0.52.6.tar.gz': '24d5b23dc417412679681396f2b49f3de8c1473deb516bd34410872eff51ed0d'}, + {'windows_x86_64_msvc-0.52.6.tar.gz': '589f6da84c646204747d1270a2a5661ea66ed1cced2631d546fdfb155959f9ec'}, + {'wyz-0.5.1.tar.gz': '05f360fc0b24296329c78fda852a1e9ae82de9cf7b27dae4b7f62f118f77b9ed'}, + {'zerocopy-0.7.35.tar.gz': '1b9b4fd18abc82b8136838da5d50bae7bdea537c574d8dc1a34ed098d6c166f0'}, + {'zerocopy-derive-0.7.35.tar.gz': 'fa4f8080344d4671fb4e831a13ad1e68092748387dfc4f55e356242fae12ce3e'}, +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/mold/mold-2.31.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/m/mold/mold-2.31.0-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..e918d8ff41e --- /dev/null +++ b/easybuild/easyconfigs/m/mold/mold-2.31.0-GCCcore-13.3.0.eb @@ -0,0 +1,36 @@ +easyblock = 'CMakeMake' + +name = 'mold' +version = '2.31.0' + +homepage = 'https://github.com/rui314/mold' +description = "mold is a high-performance drop-in replacement for existing Unix linkers." + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://github.com/rui314/mold/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['3dc3af83a5d22a4b29971bfad17261851d426961c665480e2ca294e5c74aa1e5'] + +builddependencies = [ + ('binutils', '2.42'), + ('CMake', '3.29.3'), +] +dependencies = [ + ('zlib', '1.3.1'), + ('OpenSSL', '3', '', SYSTEM), +] + +runtest = 'test' + +sanity_check_paths = { + 'files': ['bin/mold', 'lib/mold/mold-wrapper.%s' % SHLIB_EXT], + 'dirs': ['share/man'], +} + +sanity_check_commands = [ + "mold --help", + "mold --run gcc -v", +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/m/molmod/molmod-1.4.8-foss-2022a.eb b/easybuild/easyconfigs/m/molmod/molmod-1.4.8-foss-2022a.eb new file mode 100644 index 00000000000..e2e6b2f69cd --- /dev/null +++ b/easybuild/easyconfigs/m/molmod/molmod-1.4.8-foss-2022a.eb @@ -0,0 +1,37 @@ +easyblock = 'PythonPackage' + +name = 'molmod' +version = '1.4.8' + +homepage = 'https://molmod.github.io/molmod/' +description = "MolMod is a Python library with many compoments that are useful to write molecular modeling programs." + +toolchain = {'name': 'foss', 'version': '2022a'} + +source_urls = ['https://github.com/molmod/molmod/releases/download/%(version)s'] +sources = [SOURCE_TAR_GZ] +patches = ['molmod-1.4.8_fix-git-version-check.patch'] +checksums = [ + {'molmod-1.4.8.tar.gz': '759f8894f8a206e8d83f3f88882f29fcf73a7f9be375026e03c58e19496f42e8'}, + {'molmod-1.4.8_fix-git-version-check.patch': '6d1455f9dc3af07b723b05d144f6d8c3c0e5184e094eced1a6f59822f97dcf47'}, +] + +dependencies = [ + ('Python', '3.10.4'), + ('matplotlib', '3.5.2'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +# disable tests that require X11 by specifying "backend: agg" in matplotlibrc +runtest = "export MATPLOTLIBRC=$PWD; echo 'backend: agg' > $MATPLOTLIBRC/matplotlibrc;" +runtest += "python setup.py build_ext -i && pytest -ra" + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/m/molmod/molmod-1.4.8-gfbf-2022b.eb b/easybuild/easyconfigs/m/molmod/molmod-1.4.8-gfbf-2022b.eb new file mode 100644 index 00000000000..3f20a89299f --- /dev/null +++ b/easybuild/easyconfigs/m/molmod/molmod-1.4.8-gfbf-2022b.eb @@ -0,0 +1,42 @@ +easyblock = 'PythonPackage' + +name = 'molmod' +version = '1.4.8' + +homepage = 'https://molmod.github.io/molmod/' +description = "MolMod is a Python library with many compoments that are useful to write molecular modeling programs." + +toolchain = {'name': 'gfbf', 'version': '2022b'} + +source_urls = ['https://github.com/molmod/molmod/releases/download/%(version)s'] +sources = [SOURCE_TAR_GZ] +patches = [ + 'molmod-1.4.8_fix-git-version-check.patch', + 'molmod-1.4.8_fix-np-unicode.patch', +] +checksums = [ + {'molmod-1.4.8.tar.gz': '759f8894f8a206e8d83f3f88882f29fcf73a7f9be375026e03c58e19496f42e8'}, + {'molmod-1.4.8_fix-git-version-check.patch': '6d1455f9dc3af07b723b05d144f6d8c3c0e5184e094eced1a6f59822f97dcf47'}, + {'molmod-1.4.8_fix-np-unicode.patch': + '85bd2e2981d2cdd8cfab5d1c2cf37432e2967ff82de603700383d7c31530327c'}, +] + +dependencies = [ + ('Python', '3.10.8'), + ('matplotlib', '3.7.0'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +# disable tests that require X11 by specifying "backend: agg" in matplotlibrc +runtest = "export MATPLOTLIBRC=$PWD; echo 'backend: agg' > $MATPLOTLIBRC/matplotlibrc;" +runtest += "python setup.py build_ext -i && pytest -ra" + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/m/mosdepth/mosdepth-0.3.9-GCC-12.3.0.eb b/easybuild/easyconfigs/m/mosdepth/mosdepth-0.3.9-GCC-12.3.0.eb new file mode 100644 index 00000000000..8fcad4de92b --- /dev/null +++ b/easybuild/easyconfigs/m/mosdepth/mosdepth-0.3.9-GCC-12.3.0.eb @@ -0,0 +1,48 @@ +easyblock = 'Binary' + +name = 'mosdepth' +version = '0.3.9' +local_hts_nim_ver = '0.3.25' + +homepage = 'https://github.com/brentp/mosdepth' +description = "Fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +sources = [ + { + 'source_urls': ['https://github.com/brentp/hts-nim/archive/'], + 'download_filename': 'v%s.tar.gz' % local_hts_nim_ver, + 'filename': 'hts-nim-%s.tar.gz' % local_hts_nim_ver, + }, + { + 'source_urls': ['https://github.com/brentp/mosdepth/archive/'], + 'download_filename': 'v%(version)s.tar.gz', + 'filename': SOURCE_TAR_GZ, + }, +] +checksums = [ + {'hts-nim-0.3.25.tar.gz': 'b13b9bb5aa567a69bf17547aadbbd39e37beb4f71a28f267b83dfea9ea4d05e8'}, + {'mosdepth-0.3.9.tar.gz': '9171ea9a6ddaccd0091db5b85fa9e6cb79516bbe005c47ffc8dcfe49c978eb69'}, +] + +dependencies = [ + ('Nim', '2.2.0'), + ('HTSlib', '1.18'), + ('PCRE', '8.45'), +] + +extract_sources = True + +install_cmd = "cd %(builddir)s/hts-nim-*/ && nimble install --nimbleDir:%(installdir)s --verbose -y && " +install_cmd += "cd ../mosdepth-*/ && " +install_cmd += "nimble install --nimbleDir:%(installdir)s --verbose -y" + +sanity_check_paths = { + 'files': ['bin/mosdepth'], + 'dirs': [], +} + +sanity_check_commands = ["mosdepth --help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/mpi4py/mpi4py-4.0.1-gompi-2024a.eb b/easybuild/easyconfigs/m/mpi4py/mpi4py-4.0.1-gompi-2024a.eb new file mode 100644 index 00000000000..c3fc1a06dae --- /dev/null +++ b/easybuild/easyconfigs/m/mpi4py/mpi4py-4.0.1-gompi-2024a.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonBundle' + +name = 'mpi4py' +version = '4.0.1' + +homepage = 'https://github.com/mpi4py/mpi4py' +description = """MPI for Python (mpi4py) provides bindings of the Message Passing Interface (MPI) standard for + the Python programming language, allowing any Python program to exploit multiple processors.""" + +toolchain = {'name': 'gompi', 'version': '2024a'} + +builddependencies = [ + ('Cython', '3.0.10'), +] + +dependencies = [ + ('Python', '3.12.3'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + (name, version, { + 'checksums': ['f3174b245775d556f4fddb32519a2066ef0592edc810c5b5a59238f9a0a40c89'], + }), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/mpifileutils/mpifileutils-0.11.1-gompi-2024a.eb b/easybuild/easyconfigs/m/mpifileutils/mpifileutils-0.11.1-gompi-2024a.eb new file mode 100644 index 00000000000..f486ed4effd --- /dev/null +++ b/easybuild/easyconfigs/m/mpifileutils/mpifileutils-0.11.1-gompi-2024a.eb @@ -0,0 +1,45 @@ +easyblock = 'CMakeMake' + +name = 'mpifileutils' +version = "0.11.1" + +homepage = 'https://hpc.github.io/mpifileutils/' + +description = """ + MPI-Based File Utilities For Distributed Systems +""" + +toolchain = {'name': 'gompi', 'version': '2024a'} + +github_account = 'hpc' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['e2cba53309b5b3ee581b6ff82e4e66f54628370cce694c34224ed947fece32d4'] + +builddependencies = [ + ('CMake', '3.29.3'), +] + +dependencies = [ + ('attr', '2.5.2'), + ('bzip2', '1.0.8'), + ('lwgrp', '1.0.6'), + ('dtcmp', '1.1.5'), + ('libarchive', '3.7.4'), + ('libcircle', '0.3'), +] + +_binaries = [ + 'dbcast', 'dbz2', 'dchmod', 'dcmp', 'dcp', 'ddup', 'dfind', + 'dreln', 'drm', 'dstripe', 'dsync', 'dtar', 'dwalk' +] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in _binaries] + + ['include/mfu.h', 'lib/libmfu.%s' % SHLIB_EXT], + 'dirs': [] +} + +sanity_check_commands = ['%s --help 2>&1 | grep Usage' % x for x in _binaries] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/m/mpl-ascii/mpl-ascii-0.10.0-gfbf-2023a.eb b/easybuild/easyconfigs/m/mpl-ascii/mpl-ascii-0.10.0-gfbf-2023a.eb new file mode 100644 index 00000000000..8381b52dd43 --- /dev/null +++ b/easybuild/easyconfigs/m/mpl-ascii/mpl-ascii-0.10.0-gfbf-2023a.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonBundle' + +name = 'mpl-ascii' +version = '0.10.0' + +homepage = 'https://github.com/chriscave/mpl_ascii' +description = "A matplotlib backend that produces plots using only ASCII characters" + +toolchain = {'name': 'gfbf', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('matplotlib', '3.7.2'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + (name, version, { + 'source_tmpl': 'mpl_ascii-%(version)s.tar.gz', + 'checksums': ['8e4ae770d5a612dab0e8055c7677c6c3d271da4f5127cce46a60ce3ce4a4e72c'], + # relax version constraint for rich + 'preinstallopts': """sed -i 's/"rich>=.*"/"rich"/g' pyproject.toml && """, + }), +] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/m/mpl-ascii/mpl-ascii-0.10.0-gfbf-2023b.eb b/easybuild/easyconfigs/m/mpl-ascii/mpl-ascii-0.10.0-gfbf-2023b.eb new file mode 100644 index 00000000000..f17a99eb068 --- /dev/null +++ b/easybuild/easyconfigs/m/mpl-ascii/mpl-ascii-0.10.0-gfbf-2023b.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonBundle' + +name = 'mpl-ascii' +version = '0.10.0' + +homepage = 'https://github.com/chriscave/mpl_ascii' +description = "A matplotlib backend that produces plots using only ASCII characters" + +toolchain = {'name': 'gfbf', 'version': '2023b'} + +dependencies = [ + ('Python', '3.11.5'), + ('Python-bundle-PyPI', '2023.10'), + ('matplotlib', '3.8.2'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + (name, version, { + 'source_tmpl': 'mpl_ascii-%(version)s.tar.gz', + 'checksums': ['8e4ae770d5a612dab0e8055c7677c6c3d271da4f5127cce46a60ce3ce4a4e72c'], + # relax version constraint for rich + 'preinstallopts': """sed -i 's/"rich>=.*"/"rich"/g' pyproject.toml && """, + }), +] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/m/mpmath/mpmath-1.3.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/m/mpmath/mpmath-1.3.0-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..4e88d210ec2 --- /dev/null +++ b/easybuild/easyconfigs/m/mpmath/mpmath-1.3.0-GCCcore-12.3.0.eb @@ -0,0 +1,45 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Author: Adam Huffman +# adam.huffman@crick.ac.uk +# The Francis Crick Institute +# Update: Pavel Tománek (Inuits) + +easyblock = 'PythonPackage' + +name = 'mpmath' +version = '1.3.0' + +homepage = 'https://mpmath.org/' +description = """mpmath can be used as an arbitrary-precision substitute for Python's float/complex + types and math/cmath modules, but also does much more advanced mathematics. Almost any calculation + can be performed just as well at 10-digit or 1000-digit precision, with either real or complex + numbers, and in many cases mpmath implements efficient algorithms that scale well for extremely + high precision work.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['7a28eb2a9774d00c7bc92411c19a89209d5da7c4c9a9e227be8330a23a25b91f'] + +builddependencies = [ + ('binutils', '2.40') +] + +dependencies = [ + ('Python', '3.11.3'), + ('pytest', '7.4.2'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +runtest = 'python -c "import mpmath; mpmath.runtests();"' + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/m/mrcfile/mrcfile-1.4.3-gfbf-2022b.eb b/easybuild/easyconfigs/m/mrcfile/mrcfile-1.4.3-gfbf-2022b.eb new file mode 100644 index 00000000000..42492460fd9 --- /dev/null +++ b/easybuild/easyconfigs/m/mrcfile/mrcfile-1.4.3-gfbf-2022b.eb @@ -0,0 +1,40 @@ +# Thomas Hoffmann, EMBL Heidelberg, structures-it@embl.de, 2022/11 +easyblock = 'PythonPackage' + +name = 'mrcfile' +version = '1.4.3' + +homepage = 'https://github.com/ccpem/mrcfile' +description = """mrcfile is a Python implementation of the MRC2014 file format, which is used in +structural biology to store image and volume data. + +It allows MRC files to be created and opened easily using a very simple API, +which exposes the file’s header and data as numpy arrays. The code runs in +Python 2 and 3 and is fully unit-tested. + +This library aims to allow users and developers to read and write standard- +compliant MRC files in Python as easily as possible, and with no dependencies on +any compiled libraries except numpy. You can use it interactively to inspect +files, correct headers and so on, or in scripts and larger software packages to +provide basic MRC file I/O functions. """ + +toolchain = {'name': 'gfbf', 'version': '2022b'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['43c358c59ff8f583fc4dc2079a0099028719109ebf92066e388772bab389c5f5'] + +dependencies = [ + ('Python', '3.10.8'), + ('SciPy-bundle', '2023.02'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(namelower)s'] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/mstore/mstore-0.3.0-GCC-12.3.0.eb b/easybuild/easyconfigs/m/mstore/mstore-0.3.0-GCC-12.3.0.eb new file mode 100644 index 00000000000..a609b4e373b --- /dev/null +++ b/easybuild/easyconfigs/m/mstore/mstore-0.3.0-GCC-12.3.0.eb @@ -0,0 +1,37 @@ +# J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'CMakeMake' + +name = 'mstore' +version = '0.3.0' + +homepage = 'https://github.com/grimme-lab/mstore' +description = """Molecular structure store for testing""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +github_account = 'grimme-lab' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['56b3d778629eb74b8a515cd53c727d04609f858a07f8d3555fd5fd392a206dcc'] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.26.3'), +] + +dependencies = [ + ('mctc-lib', '0.3.1'), +] + +configopts = '-DBUILD_SHARED_LIBS=ON' + +sanity_check_paths = { + 'files': ['bin/mstore-fortranize', 'bin/mstore-info', 'lib/libmstore.%s' % SHLIB_EXT], + 'dirs': ['include/%(name)s', 'lib/cmake', 'lib/pkgconfig'], +} + +sanity_check_commands = ["mstore-info --help"] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/m/mstore/mstore-0.3.0-GCC-13.2.0.eb b/easybuild/easyconfigs/m/mstore/mstore-0.3.0-GCC-13.2.0.eb new file mode 100644 index 00000000000..639fb84a91b --- /dev/null +++ b/easybuild/easyconfigs/m/mstore/mstore-0.3.0-GCC-13.2.0.eb @@ -0,0 +1,37 @@ +# J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'CMakeMake' + +name = 'mstore' +version = '0.3.0' + +homepage = 'https://github.com/grimme-lab/mstore' +description = """Molecular structure store for testing""" + +toolchain = {'name': 'GCC', 'version': '13.2.0'} +toolchainopts = {'pic': True} + +github_account = 'grimme-lab' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['56b3d778629eb74b8a515cd53c727d04609f858a07f8d3555fd5fd392a206dcc'] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.27.6'), +] + +dependencies = [ + ('mctc-lib', '0.3.1'), +] + +configopts = '-DBUILD_SHARED_LIBS=ON' + +sanity_check_paths = { + 'files': ['bin/mstore-fortranize', 'bin/mstore-info', 'lib/libmstore.%s' % SHLIB_EXT], + 'dirs': ['include/%(name)s', 'lib/cmake', 'lib/pkgconfig'], +} + +sanity_check_commands = ["mstore-info --help"] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/m/muParser/muParser-2.3.4-GCCcore-12.3.0.eb b/easybuild/easyconfigs/m/muParser/muParser-2.3.4-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..506baa51977 --- /dev/null +++ b/easybuild/easyconfigs/m/muParser/muParser-2.3.4-GCCcore-12.3.0.eb @@ -0,0 +1,32 @@ +easyblock = 'CMakeMake' + +name = 'muParser' +version = '2.3.4' + +homepage = 'https://beltoforion.de/article.php?a=muparser' +description = """ + muParser is an extensible high performance math expression parser library + written in C++. It works by transforming a mathematical expression into + bytecode and precalculating constant parts of the expression. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/beltoforion/muparser/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['0c3fa54a3ebf36dda0ed3e7cd5451c964afbb15102bdbcba08aafb359a290121'] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.26.3'), +] + +configopts = "-DENABLE_SAMPLES=OFF -DBUILD_SHARED_LIBS=ON" + +sanity_check_paths = { + 'files': ['include/%(name)s.h', 'lib/libmuparser.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/m/multicharge/multicharge-0.3.0-gfbf-2023a.eb b/easybuild/easyconfigs/m/multicharge/multicharge-0.3.0-gfbf-2023a.eb new file mode 100644 index 00000000000..b4ccfa2544f --- /dev/null +++ b/easybuild/easyconfigs/m/multicharge/multicharge-0.3.0-gfbf-2023a.eb @@ -0,0 +1,39 @@ +# Author: J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'CMakeNinja' + +name = 'multicharge' +version = '0.3.0' + +homepage = 'https://github.com/grimme-lab/multicharge' +description = """Electronegativity equilibration model for atomic partial charges.""" + +toolchain = {'name': 'gfbf', 'version': '2023a'} + +github_account = 'grimme-lab' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['2fcc1f80871f404f005e9db458ffaec95bb28a19516a0245278cd3175b63a6b2'] + +builddependencies = [ + ('CMake', '3.26.3'), + ('Ninja', '1.11.1'), + ('binutils', '2.40'), +] + +dependencies = [ + ('mctc-lib', '0.3.1'), + ('mstore', '0.3.0'), +] + +sanity_check_paths = { + 'files': ['bin/multicharge', 'lib/libmulticharge.a'], + 'dirs': ['include/%(name)s', 'lib/cmake', 'lib/pkgconfig'], +} + +sanity_check_commands = ["multicharge --help"] + +# run suite of tests with ctest +runtest = True + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/m/multicharge/multicharge-0.3.0-gfbf-2023b.eb b/easybuild/easyconfigs/m/multicharge/multicharge-0.3.0-gfbf-2023b.eb new file mode 100644 index 00000000000..b6f9aad8442 --- /dev/null +++ b/easybuild/easyconfigs/m/multicharge/multicharge-0.3.0-gfbf-2023b.eb @@ -0,0 +1,39 @@ +# Author: J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'CMakeNinja' + +name = 'multicharge' +version = '0.3.0' + +homepage = 'https://github.com/grimme-lab/multicharge' +description = """Electronegativity equilibration model for atomic partial charges.""" + +toolchain = {'name': 'gfbf', 'version': '2023b'} + +github_account = 'grimme-lab' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['2fcc1f80871f404f005e9db458ffaec95bb28a19516a0245278cd3175b63a6b2'] + +builddependencies = [ + ('CMake', '3.27.6'), + ('Ninja', '1.11.1'), + ('binutils', '2.40'), +] + +dependencies = [ + ('mctc-lib', '0.3.1'), + ('mstore', '0.3.0'), +] + +sanity_check_paths = { + 'files': ['bin/multicharge', 'lib/libmulticharge.a'], + 'dirs': ['include/%(name)s', 'lib/cmake', 'lib/pkgconfig'], +} + +sanity_check_commands = ["multicharge --help"] + +# run suite of tests with ctest +runtest = True + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/m/multicharge/multicharge-0.3.0-gomkl-2023b.eb b/easybuild/easyconfigs/m/multicharge/multicharge-0.3.0-gomkl-2023b.eb new file mode 100644 index 00000000000..298e08395e3 --- /dev/null +++ b/easybuild/easyconfigs/m/multicharge/multicharge-0.3.0-gomkl-2023b.eb @@ -0,0 +1,39 @@ +# Author: J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'CMakeNinja' + +name = 'multicharge' +version = '0.3.0' + +homepage = 'https://github.com/grimme-lab/multicharge' +description = """Electronegativity equilibration model for atomic partial charges.""" + +toolchain = {'name': 'gomkl', 'version': '2023b'} + +github_account = 'grimme-lab' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['2fcc1f80871f404f005e9db458ffaec95bb28a19516a0245278cd3175b63a6b2'] + +builddependencies = [ + ('CMake', '3.27.6'), + ('Ninja', '1.11.1'), + ('binutils', '2.40'), +] + +dependencies = [ + ('mctc-lib', '0.3.1'), + ('mstore', '0.3.0'), +] + +sanity_check_paths = { + 'files': ['bin/multicharge', 'lib/libmulticharge.a'], + 'dirs': ['include/%(name)s', 'lib/cmake', 'lib/pkgconfig'], +} + +sanity_check_commands = ["multicharge --help"] + +# run suite of tests with ctest +runtest = True + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/m/multichoose/multichoose-1.0.3-GCCcore-12.2.0.eb b/easybuild/easyconfigs/m/multichoose/multichoose-1.0.3-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..9c2a1b09cfc --- /dev/null +++ b/easybuild/easyconfigs/m/multichoose/multichoose-1.0.3-GCCcore-12.2.0.eb @@ -0,0 +1,32 @@ +easyblock = 'MakeCp' + +name = 'multichoose' +version = '1.0.3' + +homepage = 'https://github.com/ekg/multichoose' +description = """generate multiset combinations (n multichoose k).""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +github_account = 'ekg' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +patches = ['%(name)s-%(version)s_improve-build-system.patch'] +checksums = [ + '74f0a223c670f5aa81b14191c53ad8d84281838a47471c10253ae391f736c877', # v1.0.3.tar.gz + '96abf6ac1105ee596be078d6e8fb478f870a4ae33fffe70f93e627c0360cfc77', # multichoose-1.0.3_improve-build-system.patch +] + +builddependencies = [('binutils', '2.39')] + +local_bins = [name, 'multipermute'] +files_to_copy = [(local_bins, 'bin'), (['*.h'], 'include/%(name)s')] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_bins], + 'dirs': [], +} + +sanity_check_commands = ['%(name)s 1 a'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/multiprocess/multiprocess-0.70.15-gfbf-2022b.eb b/easybuild/easyconfigs/m/multiprocess/multiprocess-0.70.15-gfbf-2022b.eb new file mode 100644 index 00000000000..2bac0d9bfe6 --- /dev/null +++ b/easybuild/easyconfigs/m/multiprocess/multiprocess-0.70.15-gfbf-2022b.eb @@ -0,0 +1,24 @@ +easyblock = 'PythonPackage' + +name = 'multiprocess' +version = '0.70.15' + +homepage = 'https://github.com/uqfoundation/multiprocess' +description = "better multiprocessing and multithreading in python" + +toolchain = {'name': 'gfbf', 'version': '2022b'} + +sources = [SOURCE_TAR_GZ] +checksums = ['f20eed3036c0ef477b07a4177cf7c1ba520d9a2677870a4f47fe026f0cd6787e'] + +dependencies = [ + ('Python', '3.10.8'), + ('dill', '0.3.7'), + ('Arrow', '11.0.0'), # if needed rebuild --from-pr 19758 +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/multiprocess/multiprocess-0.70.16-gfbf-2023b.eb b/easybuild/easyconfigs/m/multiprocess/multiprocess-0.70.16-gfbf-2023b.eb new file mode 100644 index 00000000000..956b6c8610d --- /dev/null +++ b/easybuild/easyconfigs/m/multiprocess/multiprocess-0.70.16-gfbf-2023b.eb @@ -0,0 +1,24 @@ +easyblock = 'PythonPackage' + +name = 'multiprocess' +version = '0.70.16' + +homepage = 'https://github.com/uqfoundation/multiprocess' +description = "better multiprocessing and multithreading in python" + +toolchain = {'name': 'gfbf', 'version': '2023b'} + +sources = [SOURCE_TAR_GZ] +checksums = ['161af703d4652a0e1410be6abccecde4a7ddffd19341be0a7011b94aeb171ac1'] + +dependencies = [ + ('Python', '3.11.5'), + ('dill', '0.3.8'), + ('Arrow', '16.1.0'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/mumott/mumott-2.1-foss-2022b.eb b/easybuild/easyconfigs/m/mumott/mumott-2.1-foss-2022b.eb new file mode 100644 index 00000000000..4cb23e2deff --- /dev/null +++ b/easybuild/easyconfigs/m/mumott/mumott-2.1-foss-2022b.eb @@ -0,0 +1,43 @@ +easyblock = 'PythonBundle' + +name = 'mumott' +version = '2.1' + +homepage = 'https://mumott.org/' +description = "mumott is a Python library for the analysis of multi-modal tensor tomography data." + +toolchain = {'name': 'foss', 'version': '2022b'} + +dependencies = [ + ('Python', '3.10.8'), + ('SciPy-bundle', '2023.02'), + ('numba', '0.58.1'), + ('matplotlib', '3.7.0'), + ('scikit-image', '0.21.0'), + ('h5py', '3.8.0'), + ('tqdm', '4.64.1') +] + + +use_pip = True + +exts_list = [ + ('colorcet', '3.1.0', { + 'checksums': ['2921b3cd81a2288aaf2d63dbc0ce3c26dcd882e8c389cc505d6886bf7aa9a4eb'], + }), + ('colorspacious', '1.1.2', { + 'checksums': ['5e9072e8cdca889dac445c35c9362a22ccf758e97b00b79ff0d5a7ba3e11b618'], + }), + (name, version, { + 'runtest': "pytest tests/cpu_tests/unit_tests", + 'source_urls': ['https://gitlab.com/liebi-group/software/%(name)s/-/archive/%(version)s/'], + 'testinstall': True, + 'checksums': ['018c3be97c3bdfb1409218a15e8f0deed9e78caf9b2cd62c7f5424c8772128b8'], + }), +] + +sanity_pip_check = True + +sanity_check_commands = ["python -c 'import mumott'"] + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/m/mygene/mygene-3.2.2-foss-2023a.eb b/easybuild/easyconfigs/m/mygene/mygene-3.2.2-foss-2023a.eb new file mode 100644 index 00000000000..1c49c2ece32 --- /dev/null +++ b/easybuild/easyconfigs/m/mygene/mygene-3.2.2-foss-2023a.eb @@ -0,0 +1,34 @@ +# Author: Pavel Grochal (INUITS) +# Update: Pavel Tománek (INUITS) +# License: GPLv2 + +easyblock = 'PythonBundle' + +name = 'mygene' +version = '3.2.2' + +homepage = 'https://github.com/biothings/mygene.py' +description = "Python Client for MyGene.Info services." + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('SciPy-bundle', '2023.07'), +] + +use_pip = True + +exts_list = [ + ('biothings_client', '0.3.1', { + 'checksums': ['c972bf2e02b6f9cc78f7f2fbc5ef02cc56fe4f8a2adcb8801ec902f4ab7011e6'], + }), + (name, version, { + 'checksums': ['e729cabbc28cf5afb221bca1ab637883b375cb1a3e2f067587ec79f71affdaea'], + }), +] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/n/NAMD/NAMD-3.0-foss-2024a-mpi.eb b/easybuild/easyconfigs/n/NAMD/NAMD-3.0-foss-2024a-mpi.eb new file mode 100644 index 00000000000..081fb8af634 --- /dev/null +++ b/easybuild/easyconfigs/n/NAMD/NAMD-3.0-foss-2024a-mpi.eb @@ -0,0 +1,38 @@ +name = 'NAMD' +version = '3.0' +versionsuffix = '-mpi' + +homepage = 'https://www.ks.uiuc.edu/Research/namd/' +description = """NAMD is a parallel molecular dynamics code designed for high-performance simulation of + large biomolecular systems.""" + +toolchain = {'name': 'foss', 'version': '2024a'} +toolchainopts = {'usempi': True, 'openmp': False, 'pic': True} + +source_urls = [ + 'https://www.ks.uiuc.edu/Research/%(namelower)s/%(version)s/download/946183/', + 'https://www.ks.uiuc.edu/Research/%(namelower)s/%(version)s/download/342056/', +] +sources = ['NAMD_%(version)s_Source.tar.gz'] + +patches = ['NAMD-3.0_fix_hwloc_build.patch'] + +checksums = [ + '301c64f0f1db860f7336efdb26223ccf66b5ab42bfc9141df8d81ec1e20bf472', # NAMD_3.0_Source.tar.gz + '03f7caa4027604e0483a9b149ebb5de310653a2aad99403faf3359ccc0015f02', # NAMD-3.0_fix_hwloc_build.patch +] + +# /bin/csh is required by 'config' script +builddependencies = [ + ('tcsh', '6.24.13'), + ('Autotools', '20231222'), +] +dependencies = [ + ('Tcl', '8.6.14'), +] + +# Hard to make charm build the mpi version with gcc on POWER, so we don't currently try +charm_arch = 'mpi-linux-%(arch)s' +charm_extra_cxxflags = '-fpermissive' + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/n/NAMD/NAMD-3.0_fix_hwloc_build.patch b/easybuild/easyconfigs/n/NAMD/NAMD-3.0_fix_hwloc_build.patch new file mode 100644 index 00000000000..4b6683cf226 --- /dev/null +++ b/easybuild/easyconfigs/n/NAMD/NAMD-3.0_fix_hwloc_build.patch @@ -0,0 +1,54 @@ +# What: Fix hwloc cmake build issue in charm-8.0.0, see https://github.com/charmplusplus/charm/issues/3843 +# This patch is based on the following PR: https://github.com/charmplusplus/charm/pull/3847 +# Author: maxim-masterov (SURF) +diff -Nru NAMD_3.0_Source.orig/charm-8.0.0/contrib/hwloc/config/hwloc.m4 NAMD_3.0_Source/charm-8.0.0/contrib/hwloc/config/hwloc.m4 +--- NAMD_3.0_Source.orig/charm-8.0.0/contrib/hwloc/config/hwloc.m4 2024-10-02 14:22:40.779651616 +0200 ++++ NAMD_3.0_Source/charm-8.0.0/contrib/hwloc/config/hwloc.m4 2024-10-23 17:15:35.921883766 +0200 +@@ -140,28 +140,43 @@ + AC_CONFIG_HEADERS(hwloc_config_prefix[include/private/autogen/config.h]) + AC_CONFIG_HEADERS(hwloc_config_prefix[include/hwloc/autogen/config.h]) + ++ + # What prefix are we using? +- AC_MSG_CHECKING([for hwloc symbol prefix]) ++ AH_VERBATIM([prefix_details_ifndef], ++ [ /* hwloc details should only be set once */ ++ #ifndef HWLOC_SYM_DETAILS ++ #define HWLOC_SYM_DETAILS ++ ]) ++ AC_MSG_CHECKING([for hwloc symbol prefix]) + AS_IF([test "$hwloc_symbol_prefix_value" = ""], + [AS_IF([test "$with_hwloc_symbol_prefix" = ""], + [hwloc_symbol_prefix_value=hwloc_], + [hwloc_symbol_prefix_value=$with_hwloc_symbol_prefix])]) ++ ++ + AC_DEFINE_UNQUOTED(HWLOC_SYM_PREFIX, [$hwloc_symbol_prefix_value], + [The hwloc symbol prefix]) + # Ensure to [] escape the whole next line so that we can get the + # proper tr tokens + [hwloc_symbol_prefix_value_caps="`echo $hwloc_symbol_prefix_value | tr '[:lower:]' '[:upper:]'`"] +- AC_DEFINE_UNQUOTED(HWLOC_SYM_PREFIX_CAPS, [$hwloc_symbol_prefix_value_caps], +- [The hwloc symbol prefix in all caps]) ++ AC_CHECK_DEFINE([HWLOC_SYM_PREFIX_CAPS],[0],AC_DEFINE_UNQUOTED(HWLOC_SYM_PREFIX_CAPS, [$hwloc_symbol_prefix_value_caps], ++ [The hwloc symbol prefix in all caps])) + AC_MSG_RESULT([$hwloc_symbol_prefix_value]) + +- # Give an easy #define to know if we need to transform all the ++ ++ # Give an easy #define to know if we need to transform all the + # hwloc names + AH_TEMPLATE([HWLOC_SYM_TRANSFORM], [Whether we need to re-define all the hwloc public symbols or not]) + AS_IF([test "$hwloc_symbol_prefix_value" = "hwloc_"], + [AC_DEFINE([HWLOC_SYM_TRANSFORM], [0])], + [AC_DEFINE([HWLOC_SYM_TRANSFORM], [1])]) + ++ AH_VERBATIM([prefix_details_endif], ++ [ /* HWLOC_DETAILS_SET */ ++ #endif ++ ]) ++ ++ + # Disabled for Charm++ due to https://github.com/charmplusplus/charm/issues/2606 + # hwloc 2.0+ requires a C99 compliant compiler + # AC_PROG_CC_C99 obsolete, detected inside AC_PROG_CC, since autoconf 2.70 diff --git a/easybuild/easyconfigs/n/NASM/NASM-2.16.03-GCCcore-13.3.0.eb b/easybuild/easyconfigs/n/NASM/NASM-2.16.03-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..7ecd06f10c0 --- /dev/null +++ b/easybuild/easyconfigs/n/NASM/NASM-2.16.03-GCCcore-13.3.0.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'NASM' +version = '2.16.03' + +homepage = 'https://www.nasm.us/' + +description = """NASM: General-purpose x86 assembler""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://www.nasm.us/pub/nasm/releasebuilds/%(version)s'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['bef3de159bcd61adf98bb7cc87ee9046e944644ad76b7633f18ab063edb29e57'] + +builddependencies = [ + ('binutils', '2.42'), +] + +sanity_check_paths = { + 'files': ['bin/nasm'], + 'dirs': [], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/n/NCCL/NCCL-2.18.3-GCCcore-12.3.0-CUDA-12.1.1.eb b/easybuild/easyconfigs/n/NCCL/NCCL-2.18.3-GCCcore-12.3.0-CUDA-12.1.1.eb index c85b7a97e48..569d09f9859 100644 --- a/easybuild/easyconfigs/n/NCCL/NCCL-2.18.3-GCCcore-12.3.0-CUDA-12.1.1.eb +++ b/easybuild/easyconfigs/n/NCCL/NCCL-2.18.3-GCCcore-12.3.0-CUDA-12.1.1.eb @@ -11,11 +11,15 @@ toolchain = {'name': 'GCCcore', 'version': '12.3.0'} github_account = 'NVIDIA' source_urls = [GITHUB_SOURCE] sources = ['v%(version)s-1.tar.gz'] -patches = ['NCCL-2.16.2_fix-cpuid.patch'] +patches = [ + 'NCCL-2.16.2_fix-cpuid.patch', + 'NCCL-2.18.3_fix-cudaMemcpyAsync.patch', +] checksums = [ ('6477d83c9edbb34a0ebce6d751a1b32962bc6415d75d04972b676c6894ceaef9', 'b4f5d7d9eea2c12e32e7a06fe138b2cfc75969c6d5c473aa6f819a792db2fc96'), {'NCCL-2.16.2_fix-cpuid.patch': '0459ecadcd32b2a7a000a2ce4f675afba908b2c0afabafde585330ff4f83e277'}, + {'NCCL-2.18.3_fix-cudaMemcpyAsync.patch': '7dc8d0d1b78e4f8acefbc400860f47432ef67c225b50d73c732999c23483de90'}, ] builddependencies = [('binutils', '2.40')] diff --git a/easybuild/easyconfigs/n/NCCL/NCCL-2.18.3_fix-cudaMemcpyAsync.patch b/easybuild/easyconfigs/n/NCCL/NCCL-2.18.3_fix-cudaMemcpyAsync.patch new file mode 100644 index 00000000000..68542656733 --- /dev/null +++ b/easybuild/easyconfigs/n/NCCL/NCCL-2.18.3_fix-cudaMemcpyAsync.patch @@ -0,0 +1,174 @@ +Backported from (original message attached below): +https://github.com/NVIDIA/nccl/commit/4365458757e4107ecbf629b2fd6e0e19a5d237c2 + +From: Kaiming Ouyang +Date: Wed, 20 Sep 2023 05:51:14 -0700 +Subject: [PATCH] Fix cudaMemcpyAsync bug + +We are trying to use the copy result of first cudaMemcpyAsync in the +second cudaMemcpyAsync without sync in between. This patch fixes it +by allocating a CPU side array to cache device side addr so that we +can avoid this consecutive cuda mem copy. + +Fixes #957 +--- + src/channel.cc | 12 ++++++++++++ + src/include/comm.h | 2 ++ + src/init.cc | 2 +- + src/transport.cc | 8 ++------ + src/transport/nvls.cc | 10 ++++------ + 5 files changed, 21 insertions(+), 13 deletions(-) + +diff --git a/src/channel.cc b/src/channel.cc +index 3edcc2f..245dfd5 100644 +--- a/src/channel.cc ++++ b/src/channel.cc +@@ -42,9 +42,11 @@ ncclResult_t initChannel(struct ncclComm* comm, int channelId) { + /* channel->devPeers is not shared, so just free it when calling commFree() */ + NCCLCHECK(ncclCudaCallocAsync(&channel->devPeers, nPeers, sharedRes->deviceStream.cudaStream)); + ncclCommPushCudaFree(comm, channel->devPeers); ++ NCCLCHECK(ncclCalloc(&channel->devPeersHostPtr, nPeers)); + for (int r = 0; r < nRanks; r++) { + uintptr_t addr = (uintptr_t)(comm->sharedRes->devPeers[channelId] + comm->topParentRanks[r]); + NCCLCHECK(ncclCudaMemcpyAsync((uintptr_t*)(channel->devPeers + r), (uintptr_t*)&addr, 1, sharedRes->deviceStream.cudaStream)); ++ channel->devPeersHostPtr[r] = (struct ncclDevChannelPeer*)addr; + } + } + +@@ -52,6 +54,8 @@ ncclResult_t initChannel(struct ncclComm* comm, int channelId) { + NCCLCHECK(ncclCudaCallocAsync(&channel->devRingUserRanks, nRanks, sharedRes->deviceStream.cudaStream)); + ncclCommPushCudaFree(comm, channel->devRingUserRanks); + ++ /* guarantee addr has been copied into channel->devPeers */ ++ NCCLCHECK(ncclStrongStreamSynchronize(&sharedRes->deviceStream)); + NCCLCHECK(ncclStrongStreamRelease(ncclCudaGraphNone(), &sharedRes->deviceStream)); + + return ncclSuccess; +@@ -77,6 +81,7 @@ ncclResult_t initNvlsChannel(struct ncclComm* comm, int channelId, struct ncclCo + uintptr_t addr = (uintptr_t)(parent->channels[channelId].nvlsDevPeers + tr); + channel->peers[comm->nRanks + 1 + r] = parent->channels[channelId].nvlsPeers + tr; + NCCLCHECK(ncclCudaMemcpyAsync((uintptr_t*)(channel->devPeers + comm->nRanks + 1 + r), (uintptr_t*)&addr, 1, sharedRes->deviceStream.cudaStream)); ++ channel->devPeersHostPtr[comm->nRanks + 1 + r] = (struct ncclDevChannelPeer*)addr; + ncclAtomicRefCountIncrement(&parent->channels[channelId].nvlsPeers[tr].refCount); + } + } else { +@@ -86,10 +91,12 @@ ncclResult_t initNvlsChannel(struct ncclComm* comm, int channelId, struct ncclCo + uintptr_t addr = (uintptr_t)(channel->nvlsDevPeers + r); + channel->peers[comm->nRanks + 1 + r] = channel->nvlsPeers + r; + NCCLCHECK(ncclCudaMemcpyAsync((uintptr_t*)(channel->devPeers + comm->nRanks + 1 + r), (uintptr_t*)&addr, 1, sharedRes->deviceStream.cudaStream)); ++ channel->devPeersHostPtr[comm->nRanks + 1 + r] = (struct ncclDevChannelPeer*)addr; + ncclAtomicRefCountIncrement(&channel->nvlsPeers[r].refCount); + } + } + ++ NCCLCHECK(ncclStrongStreamSynchronize(&sharedRes->deviceStream)); + NCCLCHECK(ncclStrongStreamRelease(ncclCudaGraphNone(), &sharedRes->deviceStream)); + + return ncclSuccess; +@@ -114,6 +121,7 @@ ncclResult_t initCollnetChannel(struct ncclComm* comm, int channelId, struct ncc + addr = (uintptr_t)parent->channels[channelId].collnetDevPeers; + channel->peers[comm->nRanks] = parent->channels[channelId].collnetPeers; + NCCLCHECK(ncclCudaMemcpyAsync((uintptr_t*)(channel->devPeers + comm->nRanks), (uintptr_t*)&addr, 1, sharedRes->deviceStream.cudaStream)); ++ channel->devPeersHostPtr[comm->nRanks] = (struct ncclDevChannelPeer*)addr; + ncclAtomicRefCountIncrement(&parent->channels[channelId].collnetPeers->refCount); + } else { + NCCLCHECK(ncclCalloc(&channel->collnetPeers, 1)); +@@ -121,9 +129,11 @@ ncclResult_t initCollnetChannel(struct ncclComm* comm, int channelId, struct ncc + addr = (uintptr_t)channel->collnetDevPeers; + channel->peers[comm->nRanks] = channel->collnetPeers; + NCCLCHECK(ncclCudaMemcpyAsync((uintptr_t*)(channel->devPeers + comm->nRanks), (uintptr_t*)&addr, 1, sharedRes->deviceStream.cudaStream)); ++ channel->devPeersHostPtr[comm->nRanks] = (struct ncclDevChannelPeer*)addr; + ncclAtomicRefCountIncrement(&channel->collnetPeers->refCount); + } + ++ NCCLCHECK(ncclStrongStreamSynchronize(&sharedRes->deviceStream)); + NCCLCHECK(ncclStrongStreamRelease(ncclCudaGraphNone(), &sharedRes->deviceStream)); + + return ncclSuccess; +@@ -156,5 +166,7 @@ ncclResult_t freeChannel(struct ncclChannel* channel, int nRanks, int collnetNRa + } + } + } ++ ++ free(channel->devPeersHostPtr); + return ncclSuccess; + } +diff --git a/src/include/comm.h b/src/include/comm.h +index e79bf54..8986f93 100644 +--- a/src/include/comm.h ++++ b/src/include/comm.h +@@ -124,6 +124,8 @@ struct ncclSharedResources { + struct ncclChannel { + struct ncclChannelPeer** peers; + struct ncclDevChannelPeer** devPeers; ++ /* devPeer pointer array used for host side access */ ++ struct ncclDevChannelPeer** devPeersHostPtr; + struct ncclRing ring; + int* devRingUserRanks; + struct ncclTree tree; +diff --git a/src/init.cc b/src/init.cc +index 1ea1d7e..309ce10 100644 +--- a/src/init.cc ++++ b/src/init.cc +@@ -437,7 +437,7 @@ static ncclResult_t devCommSetup(ncclComm_t comm) { + + NCCLCHECKGOTO(ncclCudaMemcpyAsync(devCommAndChans, &tmpCommAndChans, 1, comm->sharedRes->deviceStream.cudaStream), ret, fail); + exit: +- CUDACHECK(cudaStreamSynchronize(comm->sharedRes->deviceStream.cudaStream)); ++ NCCLCHECK(ncclStrongStreamSynchronize(&comm->sharedRes->deviceStream)); + NCCLCHECK(ncclStrongStreamRelease(ncclCudaGraphNone(), &comm->sharedRes->deviceStream)); + return ret; + fail: +diff --git a/src/transport.cc b/src/transport.cc +index f4b8a2a..9817beb 100644 +--- a/src/transport.cc ++++ b/src/transport.cc +@@ -147,11 +147,9 @@ ncclResult_t ncclTransportP2pSetup(struct ncclComm* comm, struct ncclTopoGraph* + if (conn->connected == 0) { + NCCLCHECKGOTO(conn->transportComm->connect(comm, sendData[i] + sendDataOffset++, 1, comm->rank, conn), ret, fail); + if (ret == ncclSuccess) { +- struct ncclDevChannelPeer* addr; + conn->connected = 1; + /* comm->channels[c].devPeers[sendPeer]->send[connIndex] is a device memory access. */ +- CUDACHECKGOTO(cudaMemcpyAsync(&addr, &comm->channels[c].devPeers[sendPeer], sizeof(struct ncclDevChannelPeer*), cudaMemcpyDeviceToHost, comm->sharedRes->hostStream.cudaStream), ret, fail); +- CUDACHECKGOTO(cudaMemcpyAsync(&addr->send[connIndex], &conn->conn, sizeof(struct ncclConnInfo), cudaMemcpyHostToDevice, comm->sharedRes->hostStream.cudaStream), ret, fail); ++ CUDACHECKGOTO(cudaMemcpyAsync(&comm->channels[c].devPeersHostPtr[sendPeer]->send[connIndex], &conn->conn, sizeof(struct ncclConnInfo), cudaMemcpyHostToDevice, comm->sharedRes->hostStream.cudaStream), ret, fail); + } else if (ret == ncclInProgress) { + allChannelsConnected = false; + } +@@ -167,11 +165,9 @@ ncclResult_t ncclTransportP2pSetup(struct ncclComm* comm, struct ncclTopoGraph* + if (conn->connected == 0) { + NCCLCHECKGOTO(conn->transportComm->connect(comm, recvData[i] + recvDataOffset++, 1, comm->rank, conn), ret, fail); + if (ret == ncclSuccess) { +- struct ncclDevChannelPeer* addr; + conn->connected = 1; + /* comm->channels[c].devPeers[recvPeer]->recv[connIndex] is a device memory access. */ +- CUDACHECKGOTO(cudaMemcpyAsync(&addr, &comm->channels[c].devPeers[recvPeer], sizeof(struct ncclDevChannelPeer*), cudaMemcpyDeviceToHost, comm->sharedRes->hostStream.cudaStream), ret, fail); +- CUDACHECKGOTO(cudaMemcpyAsync(&addr->recv[connIndex], &conn->conn, sizeof(struct ncclConnInfo), cudaMemcpyHostToDevice, comm->sharedRes->hostStream.cudaStream), ret, fail); ++ CUDACHECKGOTO(cudaMemcpyAsync(&comm->channels[c].devPeersHostPtr[recvPeer]->recv[connIndex], &conn->conn, sizeof(struct ncclConnInfo), cudaMemcpyHostToDevice, comm->sharedRes->hostStream.cudaStream), ret, fail); + } else if (ret == ncclInProgress) { + allChannelsConnected = false; + } +diff --git a/src/transport/nvls.cc b/src/transport/nvls.cc +index 633cb04..07be99d 100644 +--- a/src/transport/nvls.cc ++++ b/src/transport/nvls.cc +@@ -359,12 +359,10 @@ ncclResult_t ncclNvlsSetup(struct ncclComm* comm, struct ncclComm* parent) { + peer->send[0].conn.tail = (uint64_t*)(mem + buffSize + memSize / 2); + peer->send[0].conn.flags |= NCCL_NVLS_MIN_POLL; + +- struct ncclDevChannelPeer* addr; +- CUDACHECKGOTO(cudaMemcpyAsync(&addr, comm->channels[c].devPeers + nvlsPeer, sizeof(struct ncclDevChannelPeer*), cudaMemcpyDeviceToHost, comm->sharedRes->hostStream.cudaStream), res, cleanup); +- CUDACHECKGOTO(cudaMemcpyAsync(&addr->send[0], &peer->send[0].conn, sizeof(struct ncclConnInfo), cudaMemcpyHostToDevice, comm->sharedRes->hostStream.cudaStream), res, cleanup); +- CUDACHECKGOTO(cudaMemcpyAsync(&addr->recv[0], &peer->recv[0].conn, sizeof(struct ncclConnInfo), cudaMemcpyHostToDevice, comm->sharedRes->hostStream.cudaStream), res, cleanup); +- CUDACHECKGOTO(cudaMemcpyAsync(&addr->send[1], &peer->send[1].conn, sizeof(struct ncclConnInfo), cudaMemcpyHostToDevice, comm->sharedRes->hostStream.cudaStream), res, cleanup); +- CUDACHECKGOTO(cudaMemcpyAsync(&addr->recv[1], &peer->recv[1].conn, sizeof(struct ncclConnInfo), cudaMemcpyHostToDevice, comm->sharedRes->hostStream.cudaStream), res, cleanup); ++ CUDACHECKGOTO(cudaMemcpyAsync(&comm->channels[c].devPeersHostPtr[nvlsPeer]->send[0], &peer->send[0].conn, sizeof(struct ncclConnInfo), cudaMemcpyHostToDevice, comm->sharedRes->hostStream.cudaStream), res, cleanup); ++ CUDACHECKGOTO(cudaMemcpyAsync(&comm->channels[c].devPeersHostPtr[nvlsPeer]->recv[0], &peer->recv[0].conn, sizeof(struct ncclConnInfo), cudaMemcpyHostToDevice, comm->sharedRes->hostStream.cudaStream), res, cleanup); ++ CUDACHECKGOTO(cudaMemcpyAsync(&comm->channels[c].devPeersHostPtr[nvlsPeer]->send[1], &peer->send[1].conn, sizeof(struct ncclConnInfo), cudaMemcpyHostToDevice, comm->sharedRes->hostStream.cudaStream), res, cleanup); ++ CUDACHECKGOTO(cudaMemcpyAsync(&comm->channels[c].devPeersHostPtr[nvlsPeer]->recv[1], &peer->recv[1].conn, sizeof(struct ncclConnInfo), cudaMemcpyHostToDevice, comm->sharedRes->hostStream.cudaStream), res, cleanup); + + /*INFO(NCCL_INIT|NCCL_NVLS, "Peer %d Channel %d MC buff %p/%p UC Buff %p/%p", + nvlsPeer, c, +-- +2.45.2 diff --git a/easybuild/easyconfigs/n/NCCL/NCCL-2.22.3-GCCcore-13.3.0-CUDA-12.6.0.eb b/easybuild/easyconfigs/n/NCCL/NCCL-2.22.3-GCCcore-13.3.0-CUDA-12.6.0.eb new file mode 100644 index 00000000000..0534e538faa --- /dev/null +++ b/easybuild/easyconfigs/n/NCCL/NCCL-2.22.3-GCCcore-13.3.0-CUDA-12.6.0.eb @@ -0,0 +1,26 @@ +name = 'NCCL' +version = '2.22.3' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://developer.nvidia.com/nccl' +description = """The NVIDIA Collective Communications Library (NCCL) implements multi-GPU and multi-node collective +communication primitives that are performance optimized for NVIDIA GPUs.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +github_account = 'NVIDIA' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s-1.tar.gz'] +checksums = ['45151629a9494460e73375281e8b0fe379141528879301899ece9b776faca024'] + +builddependencies = [('binutils', '2.42')] + +dependencies = [ + ('CUDA', '12.6.0', '', SYSTEM), + ('UCX-CUDA', '1.16.0', versionsuffix), +] + +# default CUDA compute capabilities to use (override via --cuda-compute-capabilities) +cuda_compute_capabilities = ['5.0', '6.0', '7.0', '7.5', '8.0', '8.6', '9.0'] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/NCIPLOT/NCIPLOT-4.2-20221021-intel-compilers-2022.1.0.eb b/easybuild/easyconfigs/n/NCIPLOT/NCIPLOT-4.2-20221021-intel-compilers-2022.1.0.eb new file mode 100644 index 00000000000..e5656e89aff --- /dev/null +++ b/easybuild/easyconfigs/n/NCIPLOT/NCIPLOT-4.2-20221021-intel-compilers-2022.1.0.eb @@ -0,0 +1,50 @@ +easyblock = 'MakeCp' + +name = 'NCIPLOT' +_formal_version = '4.2' +version = '%s-20221021' % _formal_version +_commit = '800f1647a2a46c82dbdb5e1ae58086cdbbd90dc3' + +homepage = 'https://www.lct.jussieu.fr/pagesperso/contrera/index-nci.html' +description = """ NCIPLOT is a program for revealing non covalent interactions + based on the reduced density gradient. """ + +toolchain = {'name': 'intel-compilers', 'version': '2022.1.0'} +toolchainopts = {'openmp': True} + +github_account = 'juliacontrerasgarcia' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['%s.tar.gz' % _commit] +checksums = ['087ec61988d53e472542b91a5237680b65f2c4f85633d7db12298fb770802082'] + +start_dir = 'src_%%(namelower)s_%s' % _formal_version + +prebuildopts = "sed -i 's/include Makefile.inc//;s/nciplot: $(OBJS) $(LIBS)/nciplot: $(OBJS)/g' Makefile && " +prebuildopts += "make clean && " +buildopts = 'LIBS="$LIBS"' + +# test scripts are still hardcoded for old version 4.0 +pretestopts = "cd %(builddir)s/%(namelower)s-*/tests && " +pretestopts += r"find . -name runtests.sh -exec sed -i 's/nciplot_4.0/nciplot_%s/g' {} \; && " % _formal_version +pretestopts += "export OMP_NUM_THREADS=%(parallel)s && " +test_cmd = "bash" +runtest = "alltests.sh" + +files_to_copy = [ + 'dat', + (['nciplot'], 'bin'), + (['LICENSE', 'README', 'NCIPLOT_MANUAL.pdf'], 'share'), +] + +sanity_check_paths = { + 'files': ['bin/nciplot'], + 'dirs': ['dat', 'share'], +} + +modextrapaths = {'NCIPLOT_HOME': ''} + +modloadmsg = """ +Set environment variable OMP_NUM_THREADS equal to the number of available cores before running this program. +""" + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/n/NCO/NCO-5.1.9-foss-2023a.eb b/easybuild/easyconfigs/n/NCO/NCO-5.1.9-foss-2023a.eb new file mode 100644 index 00000000000..0e7dd9be31a --- /dev/null +++ b/easybuild/easyconfigs/n/NCO/NCO-5.1.9-foss-2023a.eb @@ -0,0 +1,44 @@ +easyblock = 'ConfigureMake' + +name = 'NCO' +version = '5.1.9' + +homepage = "https://github.com/nco/nco" +description = """The NCO toolkit manipulates and analyzes data stored in netCDF-accessible formats, +including DAP, HDF4, and HDF5.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['https://github.com/nco/nco/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['9cd90345c1e3860a690b53fd6c08b721d631a646d169431927884c99841c34e9'] + +builddependencies = [ + ('Bison', '3.8.2'), + ('flex', '2.6.4'), +] + +dependencies = [ + ('UDUNITS', '2.2.28'), + ('expat', '2.5.0'), + ('ANTLR', '2.7.7', '-Java-11'), + ('libdap', '3.20.11'), + ('GSL', '2.7'), + ('netCDF', '4.9.2'), + ('ESMF', '8.6.0'), # ncremap needs ESMF_RegridWeightGen +] + +configopts = "--enable-nco_cplusplus" + +sanity_check_paths = { + 'files': ['bin/nc%s' % x for x in ('ap2', 'atted', 'bo', 'diff', 'ea', 'ecat', 'es', + 'flint', 'ks', 'pdq', 'ra', 'rcat', 'rename', 'wa')] + + ['lib/libnco.a', 'lib/libnco.%s' % SHLIB_EXT, 'lib/libnco_c++.a', 'lib/libnco_c++.%s' % SHLIB_EXT], + 'dirs': ['include'], +} +sanity_check_commands = [ + "ncks -O -7 --cnk_dmn time,10 " + "%(builddir)s/%(namelower)s-%(version)s/data/in.nc %(builddir)s/%(namelower)s-%(version)s/data/in4.cdl" +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/n/NCO/NCO-5.2.9-foss-2024a.eb b/easybuild/easyconfigs/n/NCO/NCO-5.2.9-foss-2024a.eb new file mode 100644 index 00000000000..cf83d365785 --- /dev/null +++ b/easybuild/easyconfigs/n/NCO/NCO-5.2.9-foss-2024a.eb @@ -0,0 +1,44 @@ +easyblock = 'ConfigureMake' + +name = 'NCO' +version = '5.2.9' + +homepage = "https://github.com/nco/nco" +description = """The NCO toolkit manipulates and analyzes data stored in netCDF-accessible formats, +including DAP, HDF4, and HDF5.""" + +toolchain = {'name': 'foss', 'version': '2024a'} + +source_urls = ['https://github.com/nco/nco/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['6245886e2a18a4821b0fb768cf9906de09aeb47c303462c8e85f0d1a4f34956d'] + +builddependencies = [ + ('Bison', '3.8.2'), + ('flex', '2.6.4'), +] + +dependencies = [ + ('UDUNITS', '2.2.28'), + ('expat', '2.6.2'), + ('ANTLR', '2.7.7', '-Java-21.0.2'), + ('libdap', '3.21.0-131'), + ('GSL', '2.8'), + ('netCDF', '4.9.2'), + ('ESMF', '8.7.0'), # ncremap needs ESMF_RegridWeightGen +] + +configopts = "--enable-nco_cplusplus" + +sanity_check_paths = { + 'files': ['bin/nc%s' % x for x in ('ap2', 'atted', 'bo', 'diff', 'ea', 'ecat', 'es', + 'flint', 'ks', 'pdq', 'ra', 'rcat', 'rename', 'wa')] + + ['lib/libnco.a', 'lib/libnco.%s' % SHLIB_EXT, 'lib/libnco_c++.a', 'lib/libnco_c++.%s' % SHLIB_EXT], + 'dirs': ['include'], +} +sanity_check_commands = [ + "ncks -O -7 --cnk_dmn time,10 " + "%(builddir)s/%(namelower)s-%(version)s/data/in.nc %(builddir)s/%(namelower)s-%(version)s/data/in4.cdl" +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/n/NECAT/NECAT-0.0.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/n/NECAT/NECAT-0.0.1-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..15c35f4e31a --- /dev/null +++ b/easybuild/easyconfigs/n/NECAT/NECAT-0.0.1-GCCcore-12.3.0.eb @@ -0,0 +1,36 @@ +easyblock = 'MakeCp' + +name = 'NECAT' +version = '0.0.1' +_update = '20200803' + +homepage = 'https://github.com/xiaochuanle/NECAT' +description = "NECAT is an error correction and de-novo assembly tool for Nanopore long noisy reads." + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://github.com/xiaochuanle/NECAT/archive/'] +sources = ['v%%(version)s_update%s.tar.gz' % _update] +checksums = ['5ddd147b5be6b1fac2f6c10b18c9b587838f2304d2584087c4ed6f628eced06c'] + +builddependencies = [('binutils', '2.40')] + +dependencies = [ + ('Perl', '5.36.1'), +] + +start_dir = 'src' + +files_to_copy = [ + (['Linux-amd64/bin'], ''), +] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['necat.sh', 'oc2cns', 'oc2elr', 'oc2etr', + 'oc2lcr', 'pigz', 'pm4']], + 'dirs': [], +} + +sanity_check_commands = ['%(namelower)s.pl --help'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/n/NECAT/NECAT-0.0.1-GCCcore-13.2.0.eb b/easybuild/easyconfigs/n/NECAT/NECAT-0.0.1-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..a245da7c6bc --- /dev/null +++ b/easybuild/easyconfigs/n/NECAT/NECAT-0.0.1-GCCcore-13.2.0.eb @@ -0,0 +1,40 @@ +easyblock = 'MakeCp' + +name = 'NECAT' +version = '0.0.1' +_update = '20200803' + +homepage = 'https://github.com/xiaochuanle/NECAT' +description = "NECAT is an error correction and de-novo assembly tool for Nanopore long noisy reads." + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://github.com/xiaochuanle/NECAT/archive/'] +sources = ['v%%(version)s_update%s.tar.gz' % _update] +patches = ['%(name)s-0.0.1_add-cstdint-include.patch'] +checksums = [ + {'v0.0.1_update20200803.tar.gz': '5ddd147b5be6b1fac2f6c10b18c9b587838f2304d2584087c4ed6f628eced06c'}, + {'NECAT-0.0.1_add-cstdint-include.patch': 'a50d4e39e6df580d0f5e67d81c9b1569315b564bfd0f74eda7d228c2f4890171'}, +] + +builddependencies = [('binutils', '2.40')] + +dependencies = [ + ('Perl', '5.38.0'), +] + +start_dir = 'src' + +files_to_copy = [ + (['Linux-amd64/bin'], ''), +] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['necat.sh', 'oc2cns', 'oc2elr', 'oc2etr', + 'oc2lcr', 'pigz', 'pm4']], + 'dirs': [], +} + +sanity_check_commands = ['%(namelower)s.pl --help'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/n/NECAT/NECAT-0.0.1-foss-2023a.eb b/easybuild/easyconfigs/n/NECAT/NECAT-0.0.1-foss-2023a.eb new file mode 100644 index 00000000000..dbc35f62054 --- /dev/null +++ b/easybuild/easyconfigs/n/NECAT/NECAT-0.0.1-foss-2023a.eb @@ -0,0 +1,32 @@ +easyblock = 'MakeCp' + +name = 'NECAT' +version = '0.0.1' + +homepage = 'https://github.com/xiaochuanle/NECAT' +description = """NECAT is an error correction and de-novo assembly tool for Nanopore long noisy reads.).""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['https://github.com/xiaochuanle/NECAT/archive/'] +sources = ['v%(version)s_update20200803.tar.gz'] +checksums = ['5ddd147b5be6b1fac2f6c10b18c9b587838f2304d2584087c4ed6f628eced06c'] + +builddependencies = [('binutils', '2.40')] + +dependencies = [('Perl', '5.36.1')] + +start_dir = 'src' + +files_to_copy = [ + (['../Linux-amd64/bin/*'], 'bin'), +] + +sanity_check_paths = { + 'files': ['bin/%(namelower)s.pl'], + 'dirs': [], +} + +sanity_check_commands = ['%(namelower)s.pl --help'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/n/NECAT/NECAT-0.0.1_add-cstdint-include.patch b/easybuild/easyconfigs/n/NECAT/NECAT-0.0.1_add-cstdint-include.patch new file mode 100644 index 00000000000..a845baae899 --- /dev/null +++ b/easybuild/easyconfigs/n/NECAT/NECAT-0.0.1_add-cstdint-include.patch @@ -0,0 +1,14 @@ +Author: Jasper Grimm +Add include for gcc >= 13 support + +diff -Nru NECAT-0.0.1_update20200803.orig/src/fsa/simple_align.hpp NECAT-0.0.1_update20200803/src/fsa/simple_align.hpp +--- NECAT-0.0.1_update20200803.orig/src/fsa/simple_align.hpp 2024-10-09 15:51:42.877779089 +0100 ++++ NECAT-0.0.1_update20200803/src/fsa/simple_align.hpp 2024-10-09 15:52:17.356716279 +0100 +@@ -2,6 +2,7 @@ + #define FSA_ALIGN_SIMPLE_ALIGN_HPP + + #include ++#include + #include + #include + #include diff --git a/easybuild/easyconfigs/n/NECI/NECI-20230620-foss-2023a.eb b/easybuild/easyconfigs/n/NECI/NECI-20230620-foss-2023a.eb new file mode 100644 index 00000000000..09dce5c1aab --- /dev/null +++ b/easybuild/easyconfigs/n/NECI/NECI-20230620-foss-2023a.eb @@ -0,0 +1,52 @@ +easyblock = 'CMakeMakeCp' +name = 'NECI' +version = '20230620' +_commit = '558e88c5ae6c30d0505a9badbc69111be0866ba1' + +homepage = 'https://github.com/ghb24/NECI_STABLE' +description = """Standalone NECI codebase designed for FCIQMC and other stochastic quantum +chemistry methods.""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'usempi': True} + +sources = [{ + 'git_config': { + 'url': 'https://github.com/ghb24', + 'repo_name': 'NECI_STABLE', + 'recursive': True, + 'commit': _commit, + }, + 'filename': SOURCE_TAR_GZ, +}] +patches = ['NECI-20230620_segfault.patch'] +checksums = [ + None, + 'f0b5f62e115a1e07d6b90bc66ee9957a5f5d686bef65beba9c2be4bd8f29f0e4', +] + +builddependencies = [ + ('CMake', '3.26.3'), + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), +] + +dependencies = [ + ('HDF5', '1.14.0'), +] + +# enable support for HDF5 +configopts = "-DENABLE_HDF5=ON" + +test_cmd = 'ctest' +runtest = '-j' + +files_to_copy = ['bin', 'lib', (['modules'], 'include')] + +_binaries = ['dneci', 'kdneci', 'kmneci', 'kneci', 'mneci', 'neci'] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in _binaries] + ['lib/lib%s.a' % x for x in _binaries], + 'dirs': ['include'], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/n/NECI/NECI-20230620_segfault.patch b/easybuild/easyconfigs/n/NECI/NECI-20230620_segfault.patch new file mode 100644 index 00000000000..0a63b605dd3 --- /dev/null +++ b/easybuild/easyconfigs/n/NECI/NECI-20230620_segfault.patch @@ -0,0 +1,21 @@ +Fixes SEGFAULT error in tests. +See https://github.com/ghb24/NECI_STABLE/issues/18 +Author: Petr Král (INUITS) +--- unit_tests/back_spawn_excit_gen/test_back_spawn_excit_gen.F90.orig 2023-06-20 10:15:17.000000000 +0200 ++++ unit_tests/back_spawn_excit_gen/test_back_spawn_excit_gen.F90 2024-11-21 14:58:46.602604509 +0100 +@@ -64,6 +64,7 @@ + nmaxy = 2 + nmaxz = 2 + allocate(KPointToBasisFn(-nmaxx:nmaxx, -nmaxy:nmaxy, -nmaxz:nmaxz, 2)) ++ KPointToBasisFn = -1 + tOrbECutoff = .false. + + allocate(projedet(nel,1)); projedet(:,1) = [1,2] +@@ -403,6 +404,7 @@ + tOrbECutoff = .false. + niftot = 1 + allocate(KPointToBasisFn(-nmaxx:nmaxx, -nmaxy:nmaxy, -nmaxz:nmaxz, 2)) ++ KPointToBasisFn = -1 + + t_back_spawn_flex = .true. + occ_virt_level = 0 diff --git a/easybuild/easyconfigs/n/NLopt/NLopt-2.7.1-GCCcore-13.2.0.eb b/easybuild/easyconfigs/n/NLopt/NLopt-2.7.1-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..17c0db0f161 --- /dev/null +++ b/easybuild/easyconfigs/n/NLopt/NLopt-2.7.1-GCCcore-13.2.0.eb @@ -0,0 +1,33 @@ +easyblock = 'CMakeMake' + +name = 'NLopt' +version = '2.7.1' + +homepage = 'http://ab-initio.mit.edu/wiki/index.php/NLopt' +description = """ NLopt is a free/open-source library for nonlinear optimization, + providing a common interface for a number of different free optimization routines + available online as well as original implementations of various other algorithms. """ + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/stevengj/nlopt/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['db88232fa5cef0ff6e39943fc63ab6074208831dc0031cf1545f6ecd31ae2a1a'] + +builddependencies = [ + ('CMake', '3.27.6'), + ('binutils', '2.40'), +] + +configopts = [ + '-DBUILD_SHARED_LIBS=ON', + '-DBUILD_SHARED_LIBS=OFF' +] + +sanity_check_paths = { + 'files': ['lib/libnlopt.a', 'lib/libnlopt.%s' % SHLIB_EXT, 'include/nlopt.h'], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/n/NLopt/NLopt-2.7.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/n/NLopt/NLopt-2.7.1-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..b9bb438dc94 --- /dev/null +++ b/easybuild/easyconfigs/n/NLopt/NLopt-2.7.1-GCCcore-13.3.0.eb @@ -0,0 +1,33 @@ +easyblock = 'CMakeMake' + +name = 'NLopt' +version = '2.7.1' + +homepage = 'http://ab-initio.mit.edu/wiki/index.php/NLopt' +description = """ NLopt is a free/open-source library for nonlinear optimization, + providing a common interface for a number of different free optimization routines + available online as well as original implementations of various other algorithms. """ + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/stevengj/nlopt/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['db88232fa5cef0ff6e39943fc63ab6074208831dc0031cf1545f6ecd31ae2a1a'] + +builddependencies = [ + ('CMake', '3.29.3'), + ('binutils', '2.42'), +] + +configopts = [ + '-DBUILD_SHARED_LIBS=ON', + '-DBUILD_SHARED_LIBS=OFF' +] + +sanity_check_paths = { + 'files': ['lib/libnlopt.a', 'lib/libnlopt.%s' % SHLIB_EXT, 'include/nlopt.h'], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/n/NSPR/NSPR-4.35-GCCcore-13.3.0.eb b/easybuild/easyconfigs/n/NSPR/NSPR-4.35-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..9157abca1c4 --- /dev/null +++ b/easybuild/easyconfigs/n/NSPR/NSPR-4.35-GCCcore-13.3.0.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'NSPR' +version = '4.35' + +homepage = 'https://developer.mozilla.org/en-US/docs/Mozilla/Projects/NSPR' +description = """Netscape Portable Runtime (NSPR) provides a platform-neutral API for system level + and libc-like functions.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://ftp.mozilla.org/pub/%(namelower)s/releases/v%(version)s/src/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['7ea3297ea5969b5d25a5dd8d47f2443cda88e9ee746301f6e1e1426f8a6abc8f'] + +builddependencies = [ + ('binutils', '2.42'), +] + +configopts = "--disable-debug --enable-optimize --enable-64bit" + + +sanity_check_paths = { + 'files': ['bin/nspr-config', 'lib/libnspr%(version_major)s.a', 'lib/libnspr%%(version_major)s.%s' % SHLIB_EXT, + 'lib/libplc%(version_major)s.a', 'lib/libplc%%(version_major)s.%s' % SHLIB_EXT, + 'lib/libplds%(version_major)s.a', 'lib/libplds%%(version_major)s.%s' % SHLIB_EXT, + 'lib/pkgconfig/%(namelower)s.pc'], + 'dirs': ['include/%(namelower)s'], +} + +sanity_check_commands = ['%(namelower)s-config --version'] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/NSS/NSS-3.104-GCCcore-13.3.0.eb b/easybuild/easyconfigs/n/NSS/NSS-3.104-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..fb301be49d5 --- /dev/null +++ b/easybuild/easyconfigs/n/NSS/NSS-3.104-GCCcore-13.3.0.eb @@ -0,0 +1,64 @@ +easyblock = 'MakeCp' + +name = 'NSS' +version = '3.104' + +homepage = 'https://developer.mozilla.org/en-US/docs/Mozilla/Projects/NSS' +description = """Network Security Services (NSS) is a set of libraries designed to support cross-platform development + of security-enabled client and server applications.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://ftp.mozilla.org/pub/security/nss/releases/NSS_%s_RTM/src/' % version.replace('.', '_')] +sources = [SOURCELOWER_TAR_GZ] +patches = [ + '%(name)s-3.39_pkgconfig.patch', + '%(name)s-3.55_fix-ftbfs-glibc-invalid-oob-error.patch', +] +checksums = [ + {'nss-3.104.tar.gz': 'e2763223622d1e76b98a43030873856f248af0a41b03b2fa2ca06a91bc50ac8e'}, + {'NSS-3.39_pkgconfig.patch': '5c4b55842e5afd1e8e67b90635f6474510b89242963c4ac2622d3e3da9062774'}, + {'NSS-3.55_fix-ftbfs-glibc-invalid-oob-error.patch': + '15768297c5dd6918132af281531afcfe3e358f45a00bc2655d20a6cbe4310a9b'}, +] + +builddependencies = [ + ('binutils', '2.42'), + ('Perl', '5.38.2'), +] +dependencies = [ + ('NSPR', '4.35'), + ('zlib', '1.3.1'), +] + +# disable use of -Werror to work around compilation errors with newer glibc versions, +# see also https://sourceware.org/bugzilla/show_bug.cgi?id=27476 +buildopts = 'NSS_ENABLE_WERROR=0 BUILD_OPT=1 USE_64=1 ' +buildopts += 'CPATH="$EBROOTNSPR/include/nspr:$CPATH" OS_REL_CFLAGS="-D_XOPEN_SOURCE "' +buildopts += ' && cd config && make PREFIX=%(installdir)s BUILD_OPT=1 USE_64=1 && cd -' + +# building in parallel fails +parallel = 1 + +# optional testsuite (takes a long time) +# buildopts += " && cd %(builddir)s/%(namelower)s-%(version)s/%(namelower)s/tests && " +# buildopts += " BUILD_OPT=1 USE_64=1 ./all.sh " + +files_to_copy = [ + '../dist/Linux*.OBJ/*', + (['../dist/public/*'], 'include'), +] + +sanity_check_paths = { + 'files': ['bin/%(namelower)s-config', 'bin/multinit', 'lib/libnss.a'], + 'dirs': ['include/dbm', 'include/%(namelower)s'], +} + +sanity_check_commands = [ + "multinit --help", + "%(namelower)s-config --version", +] + +modextrapaths = {'CPATH': 'include/%(namelower)s'} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/NTL/NTL-11.5.1-GCC-13.3.0.eb b/easybuild/easyconfigs/n/NTL/NTL-11.5.1-GCC-13.3.0.eb new file mode 100644 index 00000000000..29fdd6e848f --- /dev/null +++ b/easybuild/easyconfigs/n/NTL/NTL-11.5.1-GCC-13.3.0.eb @@ -0,0 +1,44 @@ +# contributed by Guilherme Peretti-Pezzi (CSCS) +# updated by Alex Domingo (Vrije Universiteit Brussel) +# updated by Åke Sandgren(Umeå University) +# Update: Petr Král (INUITS) +easyblock = 'ConfigureMake' + +name = 'NTL' +version = '11.5.1' + +homepage = 'https://shoup.net/ntl/' + +description = """NTL is a high-performance, portable C++ library providing data structures and +algorithms for manipulating signed, arbitrary length integers, and for vectors, +matrices, and polynomials over the integers and over finite fields.""" + +toolchain = {'name': 'GCC', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +github_account = 'libntl' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['ef578fa8b6c0c64edd1183c4c303b534468b58dd3eb8df8c9a5633f984888de5'] + +builddependencies = [ + ('Perl', '5.38.2'), +] + +dependencies = [ + ('GMP', '6.3.0'), +] + +start_dir = 'src' + +prefix_opt = 'PREFIX=' +configopts = 'CXX="$CXX" CXXFLAGS="$CXXFLAGS" GMP_PREFIX="$EBROOTGMP" SHARED=on' + +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libntl.%s' % e for e in ['a', SHLIB_EXT]], + 'dirs': ['include/NTL', 'share/doc'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/n/NTPoly/NTPoly-2.7.1-foss-2022a.eb b/easybuild/easyconfigs/n/NTPoly/NTPoly-2.7.1-foss-2022a.eb new file mode 100644 index 00000000000..e6ef7ccfb3e --- /dev/null +++ b/easybuild/easyconfigs/n/NTPoly/NTPoly-2.7.1-foss-2022a.eb @@ -0,0 +1,28 @@ +easyblock = 'CMakeMake' + +name = 'NTPoly' +version = '2.7.1' + +homepage = 'https://github.com/william-dawson/NTPoly' +description = """is a massively parallel library for computing the functions of sparse, symmetric matrices based on +polynomial expansions. For sufficiently sparse matrices, most of the matrix functions +in NTPoly can be computed in linear time.""" + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'openmp': False, 'usempi': True} + +source_urls = ['https://github.com/william-dawson/NTPoly/archive/ntpoly-v%(version)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['c15d9f51ac054b4ef0565ce5c4c8589c10bdbab4dc3442ebd109691e2bbfc7e2'] + +builddependencies = [('CMake', '3.23.1')] + +build_shared_libs = True + +sanity_check_paths = { + 'files': ['include/%s.mod' % x for x in ['datatypesmodule', 'densitymatrixsolversmodule']] + + ['lib64/libNTPoly.%s' % SHLIB_EXT, 'lib/libNTPoly.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/n/NTPoly/NTPoly-3.1.0-foss-2023a.eb b/easybuild/easyconfigs/n/NTPoly/NTPoly-3.1.0-foss-2023a.eb new file mode 100644 index 00000000000..8f7a531ce0e --- /dev/null +++ b/easybuild/easyconfigs/n/NTPoly/NTPoly-3.1.0-foss-2023a.eb @@ -0,0 +1,28 @@ +easyblock = 'CMakeMake' + +name = 'NTPoly' +version = '3.1.0' + +homepage = 'https://github.com/william-dawson/NTPoly' +description = """is a massively parallel library for computing the functions of sparse, symmetric matrices based on +polynomial expansions. For sufficiently sparse matrices, most of the matrix functions +in NTPoly can be computed in linear time.""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'openmp': False, 'usempi': True} + +source_urls = ['https://github.com/william-dawson/NTPoly/archive/ntpoly-v%(version)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['71cd6827f20c68e384555dbcfc85422d0690e21d21d7b5d4f7375544a2755271'] + +builddependencies = [('CMake', '3.26.3')] + +build_shared_libs = True + +sanity_check_paths = { + 'files': ['include/%s.mod' % x for x in ['datatypesmodule', 'densitymatrixsolversmodule']] + + ['lib64/libNTPoly.%s' % SHLIB_EXT, 'lib/libNTPoly.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/n/NVHPC/NVHPC-24.11-CUDA-12.6.0.eb b/easybuild/easyconfigs/n/NVHPC/NVHPC-24.11-CUDA-12.6.0.eb new file mode 100644 index 00000000000..546b28e7147 --- /dev/null +++ b/easybuild/easyconfigs/n/NVHPC/NVHPC-24.11-CUDA-12.6.0.eb @@ -0,0 +1,73 @@ +name = 'NVHPC' +version = '24.11' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://developer.nvidia.com/hpc-sdk/' +description = """C, C++ and Fortran compilers included with the NVIDIA HPC SDK (previously: PGI)""" + +toolchain = SYSTEM + +local_tarball_tmpl = 'nvhpc_2024_%%(version_major)s%%(version_minor)s_Linux_%s_cuda_multi.tar.gz' +# By downloading, you accept the HPC SDK Software License Agreement +# https://docs.nvidia.com/hpc-sdk/eula/index.html +# accept_eula = True +source_urls = ['https://developer.download.nvidia.com/hpc-sdk/%(version)s/'] +sources = [local_tarball_tmpl % '%(arch)s'] +checksums = [ + { + local_tarball_tmpl % 'aarch64': + 'f2f64e5dec5e90dad5e12a31a992172b0aa19abf872ef1c54a1a437c7008eefb', + local_tarball_tmpl % 'x86_64': + '0c27d66ed0e2d3007d30ac904922a9abf96475197dc0f4dcc6316d235a1dc0c3', + } +] + +local_gccver = '13.3.0' +dependencies = [ + ('GCCcore', local_gccver), + ('binutils', '2.42', '', ('GCCcore', local_gccver)), + # This is necessary to avoid cases where just libnuma.so.1 is present in the system and -lnuma fails + ('numactl', '2.0.18', '', ('GCCcore', local_gccver)), + ('CUDA', '12.6.0', '', SYSTEM), +] + +module_add_cuda = False + +# specify default CUDA version that should be used by NVHPC +# should match one of the CUDA versions that are included with this NVHPC version +# (see install_components/Linux_x86_64/$version/cuda/) where $version is the NVHPC version +# this version can be tweaked from the EasyBuild command line with +# --try-amend=default_cuda_version="11.0" (for example) +default_cuda_version = '%(cudaver)s' + +# NVHPC EasyBlock supports some features, which can be set via CLI or this easyconfig. +# The following list gives examples for the easyconfig +# +# NVHPC needs CUDA to work. Two options are available: 1) Use NVHPC-bundled CUDA, 2) use system CUDA +# 1) Bundled CUDA +# If no easybuild dependency to CUDA is present, the bundled CUDA is taken. A version needs to be specified with +# default_cuda_version = "11.0" +# in this easyconfig file; alternatively, it can be specified through the command line during installation with +# --try-amend=default_cuda_version="10.2" +# 2) CUDA provided via EasyBuild +# Use CUDA as a dependency, for example +# dependencies = [('CUDA', '11.5.0')] +# The parameter default_cuda_version still can be set as above. +# If not set, it will be deduced from the CUDA module (via $EBVERSIONCUDA) +# +# Define a NVHPC-default Compute Capability +# cuda_compute_capabilities = "8.0" +# Can also be specified on the EasyBuild command line via --cuda-compute-capabilities=8.0 +# Only single values supported, not lists of values! +# +# Options to add/remove things to/from environment module (defaults shown) +# module_byo_compilers = False # Remove compilers from PATH (Bring-your-own compilers) +# module_nvhpc_own_mpi = False # Add NVHPC's own pre-compiled OpenMPI +# module_add_math_libs = False # Add NVHPC's math libraries (which should be there from CUDA anyway) +# module_add_profilers = False # Add NVHPC's NVIDIA Profilers +# module_add_nccl = False # Add NVHPC's NCCL library +# module_add_nvshmem = False # Add NVHPC's NVSHMEM library +# module_add_cuda = False # Add NVHPC's bundled CUDA + +# this bundle serves as a compiler-only toolchain, so it should be marked as compiler (important for HMNS) +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/n/NVHPC/NVHPC-24.9-CUDA-12.6.0.eb b/easybuild/easyconfigs/n/NVHPC/NVHPC-24.9-CUDA-12.6.0.eb new file mode 100644 index 00000000000..d164eabc04d --- /dev/null +++ b/easybuild/easyconfigs/n/NVHPC/NVHPC-24.9-CUDA-12.6.0.eb @@ -0,0 +1,73 @@ +name = 'NVHPC' +version = '24.9' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://developer.nvidia.com/hpc-sdk/' +description = """C, C++ and Fortran compilers included with the NVIDIA HPC SDK (previously: PGI)""" + +toolchain = SYSTEM + +local_tarball_tmpl = 'nvhpc_2024_%%(version_major)s%%(version_minor)s_Linux_%s_cuda_multi.tar.gz' +# By downloading, you accept the HPC SDK Software License Agreement +# https://docs.nvidia.com/hpc-sdk/eula/index.html +# accept_eula = True +source_urls = ['https://developer.download.nvidia.com/hpc-sdk/%(version)s/'] +sources = [local_tarball_tmpl % '%(arch)s'] +checksums = [ + { + local_tarball_tmpl % 'aarch64': + '8d900f798ef806c64993fd4fedf2c2c812dd1ccdbac2a0d33fabcd0cd36f19cf', + local_tarball_tmpl % 'x86_64': + '30c493350cf67481e84cea60a3a869e01fa0bcb71df8e898266273fbdf0a7f26', + } +] + +local_gccver = '13.3.0' +dependencies = [ + ('GCCcore', local_gccver), + ('binutils', '2.42', '', ('GCCcore', local_gccver)), + # This is necessary to avoid cases where just libnuma.so.1 is present in the system and -lnuma fails + ('numactl', '2.0.18', '', ('GCCcore', local_gccver)), + ('CUDA', '12.6.0', '', SYSTEM), +] + +module_add_cuda = False + +# specify default CUDA version that should be used by NVHPC +# should match one of the CUDA versions that are included with this NVHPC version +# (see install_components/Linux_x86_64/$version/cuda/) where $version is the NVHPC version +# this version can be tweaked from the EasyBuild command line with +# --try-amend=default_cuda_version="11.0" (for example) +default_cuda_version = '%(cudaver)s' + +# NVHPC EasyBlock supports some features, which can be set via CLI or this easyconfig. +# The following list gives examples for the easyconfig +# +# NVHPC needs CUDA to work. Two options are available: 1) Use NVHPC-bundled CUDA, 2) use system CUDA +# 1) Bundled CUDA +# If no easybuild dependency to CUDA is present, the bundled CUDA is taken. A version needs to be specified with +# default_cuda_version = "11.0" +# in this easyconfig file; alternatively, it can be specified through the command line during installation with +# --try-amend=default_cuda_version="10.2" +# 2) CUDA provided via EasyBuild +# Use CUDA as a dependency, for example +# dependencies = [('CUDA', '11.5.0')] +# The parameter default_cuda_version still can be set as above. +# If not set, it will be deduced from the CUDA module (via $EBVERSIONCUDA) +# +# Define a NVHPC-default Compute Capability +# cuda_compute_capabilities = "8.0" +# Can also be specified on the EasyBuild command line via --cuda-compute-capabilities=8.0 +# Only single values supported, not lists of values! +# +# Options to add/remove things to/from environment module (defaults shown) +# module_byo_compilers = False # Remove compilers from PATH (Bring-your-own compilers) +# module_nvhpc_own_mpi = False # Add NVHPC's own pre-compiled OpenMPI +# module_add_math_libs = False # Add NVHPC's math libraries (which should be there from CUDA anyway) +# module_add_profilers = False # Add NVHPC's NVIDIA Profilers +# module_add_nccl = False # Add NVHPC's NCCL library +# module_add_nvshmem = False # Add NVHPC's NVSHMEM library +# module_add_cuda = False # Add NVHPC's bundled CUDA + +# this bundle serves as a compiler-only toolchain, so it should be marked as compiler (important for HMNS) +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/n/NWChem/NWChem-7.2.3-intel-2024a.eb b/easybuild/easyconfigs/n/NWChem/NWChem-7.2.3-intel-2024a.eb new file mode 100644 index 00000000000..7b3190a3cd4 --- /dev/null +++ b/easybuild/easyconfigs/n/NWChem/NWChem-7.2.3-intel-2024a.eb @@ -0,0 +1,34 @@ +name = 'NWChem' +version = '7.2.3' + +homepage = 'https://nwchemgit.github.io/' +description = """NWChem aims to provide its users with computational chemistry tools that are scalable both in + their ability to treat large scientific computational chemistry problems efficiently, and in their use of available + parallel computing resources from high-performance parallel supercomputers to conventional workstation clusters. + NWChem software can handle: biomolecules, nanostructures, and solid-state; from quantum to classical, and all + combinations; Gaussian basis functions or plane-waves; scaling from one to thousands of processors; properties + and relativity.""" + +toolchain = {'name': 'intel', 'version': '2024a'} +toolchainopts = {'i8': True} + +source_urls = ['https://github.com/nwchemgit/nwchem/archive/refs/tags/'] +sources = ['v%(version)s-release.tar.gz'] +patches = [ + 'NWChem-7.0.2_fix_gnumakefile.patch', +] +checksums = [ + {'v7.2.3-release.tar.gz': 'fec76fbe650cdab8b00c8c1d7a5671554313e04a8e9e2fb300a7aad486910e6f'}, + {'NWChem-7.0.2_fix_gnumakefile.patch': '89c634a652d4c8c358f8388ac01ee441659e3c0256c39b6494e2885c91f9aca4'}, +] + +dependencies = [ + ('GlobalArrays', '5.8.2'), + ('Python', '3.12.3'), +] + +preconfigopts = "export EXTRA_LIBS=-lutil && " + +modules = "all python" + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/n/NanoCaller/NanoCaller-3.6.0-foss-2022b.eb b/easybuild/easyconfigs/n/NanoCaller/NanoCaller-3.6.0-foss-2022b.eb new file mode 100644 index 00000000000..037b70ab15e --- /dev/null +++ b/easybuild/easyconfigs/n/NanoCaller/NanoCaller-3.6.0-foss-2022b.eb @@ -0,0 +1,44 @@ +easyblock = 'Tarball' + +name = 'NanoCaller' +version = '3.6.0' + +homepage = 'https://github.com/WGLab/NanoCaller' +description = """NanoCaller is a computational method that integrates long reads in deep + convolutional neural network for the detection of SNPs/indels from long-read sequencing data.""" + +toolchain = {'name': 'foss', 'version': '2022b'} + +source_urls = ['https://github.com/WGLab/%(name)s/archive/'] +sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}] +checksums = ['d3df57ca47617365ed891f7acc6976ec5dec3c224e5e213f8bba2d3b2d973303'] + +dependencies = [ + ('Python', '3.10.8'), + ('SciPy-bundle', '2023.02'), + ('BCFtools', '1.17'), + ('python-parasail', '1.3.4'), + ('MUSCLE', '5.1.0'), + ('Pysam', '0.21.0'), + ('SAMtools', '1.17'), + ('TensorFlow', '2.13.0'), + ('WhatsHap', '2.1'), + ('vcflib', '1.0.9', '-R-4.2.2'), + ('intervaltree-python', '3.1.0'), + ('tqdm', '4.64.1'), + ('RTG-Tools', '3.12.1', '-Java-11', SYSTEM), +] + +modextrapaths = { + 'PATH': '', + 'PYTHONPATH': '', +} + +sanity_check_paths = { + 'files': ['NanoCaller'], + 'dirs': [], +} + +sanity_check_commands = ["NanoCaller --help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/n/NanoComp/NanoComp-1.24.0-foss-2023a.eb b/easybuild/easyconfigs/n/NanoComp/NanoComp-1.24.0-foss-2023a.eb new file mode 100644 index 00000000000..94de23b83da --- /dev/null +++ b/easybuild/easyconfigs/n/NanoComp/NanoComp-1.24.0-foss-2023a.eb @@ -0,0 +1,42 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 +# Update: Petr Král (INUITS) + +easyblock = 'PythonPackage' + +name = 'NanoComp' +version = '1.24.0' + +homepage = 'https://github.com/wdecoster/NanoComp' +description = "Comparing runs of Oxford Nanopore sequencing data and alignments" + +toolchain = {'name': 'foss', 'version': '2023a'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['2ce02bb38c76137ee00ebcc68b6b2654a4a459993e901aebde436c4d54287b09'] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('Pysam', '0.22.0'), + ('nanomath', '1.4.0'), + ('nanoget', '1.19.3'), + ('NanoPlot', '1.43.0'), + ('plotly.py', '5.16.0'), + ('plotly-orca', '1.3.1'), + ('joypy', '0.2.6'), +] + +download_dep_fail = True +use_pip = True + +sanity_check_paths = { + 'files': ['bin/NanoComp'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["NanoComp --help"] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/n/NanoFilt/NanoFilt-2.8.0-foss-2023a.eb b/easybuild/easyconfigs/n/NanoFilt/NanoFilt-2.8.0-foss-2023a.eb new file mode 100644 index 00000000000..fed069c1e75 --- /dev/null +++ b/easybuild/easyconfigs/n/NanoFilt/NanoFilt-2.8.0-foss-2023a.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonPackage' + +name = 'NanoFilt' +version = '2.8.0' + +homepage = 'https://github.com/wdecoster/nanofilt' +description = """Filtering and trimming of long read sequencing data.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +sources = [SOURCE_TAR_GZ] +checksums = ['47f4f4f8be834f011570a8d76d07cc12abe0686c8917607316a8ccfb3e20758c'] + +dependencies = [ + ('Python', '3.11.3'), + ('Biopython', '1.83'), +] + +download_dep_fail = True +use_pip = True + +sanity_check_commands = ["NanoFilt --help"] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/n/NanoFilt/NanoFilt-2.8.0-foss-2023b.eb b/easybuild/easyconfigs/n/NanoFilt/NanoFilt-2.8.0-foss-2023b.eb new file mode 100644 index 00000000000..1aef705dc4e --- /dev/null +++ b/easybuild/easyconfigs/n/NanoFilt/NanoFilt-2.8.0-foss-2023b.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonPackage' + +name = 'NanoFilt' +version = '2.8.0' + +homepage = 'https://github.com/wdecoster/nanofilt' +description = """Filtering and trimming of long read sequencing data.""" + +toolchain = {'name': 'foss', 'version': '2023b'} + +sources = [SOURCE_TAR_GZ] +checksums = ['47f4f4f8be834f011570a8d76d07cc12abe0686c8917607316a8ccfb3e20758c'] + +dependencies = [ + ('Python', '3.11.5'), + ('Biopython', '1.84'), +] + +download_dep_fail = True +use_pip = True + +sanity_check_commands = ["NanoFilt --help"] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/n/NanoLyse/NanoLyse-1.2.1-foss-2023a.eb b/easybuild/easyconfigs/n/NanoLyse/NanoLyse-1.2.1-foss-2023a.eb new file mode 100644 index 00000000000..1b21ec42201 --- /dev/null +++ b/easybuild/easyconfigs/n/NanoLyse/NanoLyse-1.2.1-foss-2023a.eb @@ -0,0 +1,48 @@ +## +# This is a contribution from SIB Swiss Institute of Bioinformatics +# Homepage: https://www.sib.swiss/research-infrastructure/competence-centers/vital-it +# +# Authors:: Sebastien Moretti +# +# Update: Petr Král (INUITS) +## + +easyblock = 'PythonBundle' + +name = 'NanoLyse' +version = '1.2.1' + +homepage = 'https://github.com/wdecoster/nanolyse' +description = """Remove reads mapping to the lambda phage genome from a fastq file.""" +software_license = 'LicenseGPLv3' + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('Biopython', '1.83'), + ('minimap2', '2.26'), +] + +use_pip = True + +# Fetch the tar.gz, not the whl files! +exts_list = [ + ('mappy', '2.28', { + 'checksums': ['0ebf7a5d62bd668f5456028215e26176e180ca68161ac18d4f7b48045484cebb'], + }), + (name, version, { + 'checksums': ['933ee668da805fc9ec9fa86c9fca81a073438d45b5f64e23cf606c01e715b1d5'], + }), +] + +sanity_check_paths = { + 'files': ['bin/NanoLyse'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["NanoLyse --version"] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/n/NanoPack/NanoPack-20230602-foss-2023a.eb b/easybuild/easyconfigs/n/NanoPack/NanoPack-20230602-foss-2023a.eb new file mode 100644 index 00000000000..00ae2ecf8e2 --- /dev/null +++ b/easybuild/easyconfigs/n/NanoPack/NanoPack-20230602-foss-2023a.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonPackage' + +name = 'NanoPack' +version = '20230602' +local_commit = '4059a0a' + +homepage = 'https://daler.github.io/pybedtools' +description = "Collection of long read processing and analysis tools." + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['https://github.com/wdecoster/nanopack/archive/'] +sources = ['%s.tar.gz' % local_commit] +checksums = ['b533dd54bf9688a24faf9cb724050ace87bba18b2f469e1116ae47c9ae26cdc1'] + +dependencies = [ + ('Python', '3.11.3'), + ('nanomath', '1.4.0'), + ('nanoget', '1.19.3'), + ('NanoStat', '1.6.0'), + ('NanoFilt', '2.8.0'), + ('NanoLyse', '1.2.1'), + ('NanoPlot', '1.43.0'), + ('NanoComp', '1.24.0'), + ('nanoQC', '0.9.4'), + ('kyber', '0.4.0'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/n/NanoPlot/NanoPlot-1.43.0-foss-2023a.eb b/easybuild/easyconfigs/n/NanoPlot/NanoPlot-1.43.0-foss-2023a.eb new file mode 100644 index 00000000000..4e547b9963b --- /dev/null +++ b/easybuild/easyconfigs/n/NanoPlot/NanoPlot-1.43.0-foss-2023a.eb @@ -0,0 +1,43 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 +# Update: Petr Král (INUITS) + +easyblock = 'PythonPackage' + +name = 'NanoPlot' +version = '1.43.0' + +homepage = 'https://github.com/wdecoster/NanoPlot' +description = "Plotting suite for long read sequencing data and alignments" + +toolchain = {'name': 'foss', 'version': '2023a'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['0f94096d689b552c32fd7246ad87cb6d5e5e2499dad5acc551091e0ff67f48df'] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('Biopython', '1.83'), + ('Pysam', '0.22.0'), + ('nanomath', '1.4.0'), + ('nanoget', '1.19.3'), + ('plotly.py', '5.16.0'), + ('statsmodels', '0.14.1'), + ('Arrow', '14.0.1'), # for pyarrow + ('Kaleido', '0.2.1'), +] + +download_dep_fail = True +use_pip = True + +sanity_check_paths = { + 'files': ['bin/NanoPlot'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["NanoPlot --help"] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/n/NanoStat/NanoStat-1.6.0-foss-2023a.eb b/easybuild/easyconfigs/n/NanoStat/NanoStat-1.6.0-foss-2023a.eb new file mode 100644 index 00000000000..8f0fa5a053c --- /dev/null +++ b/easybuild/easyconfigs/n/NanoStat/NanoStat-1.6.0-foss-2023a.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonPackage' + +name = 'NanoStat' +version = '1.6.0' + +homepage = 'https://github.com/wdecoster/nanostat' +description = """Calculate various statistics from a long read sequencing dataset in fastq, + bam or albacore sequencing summary format.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +sources = [SOURCE_TAR_GZ] +checksums = ['e45fa8d1ab49bdaed17596c26c0af148b44e4af46238391a8bb7a1b4cc940079'] + +dependencies = [ + ('Python', '3.11.3'), + ('nanoget', '1.19.3'), + ('nanomath', '1.4.0'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/NanoStat'], + 'dirs': [], +} + +sanity_check_commands = ["NanoStat --help"] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/n/NextDenovo/NextDenovo-2.5.2-20240510-GCCcore-12.3.0.eb b/easybuild/easyconfigs/n/NextDenovo/NextDenovo-2.5.2-20240510-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..84f6960102e --- /dev/null +++ b/easybuild/easyconfigs/n/NextDenovo/NextDenovo-2.5.2-20240510-GCCcore-12.3.0.eb @@ -0,0 +1,54 @@ +easyblock = 'MakeCp' + +name = 'NextDenovo' +version = '2.5.2-20240510' +local_commit = '0e5fa5d' + +homepage = 'https://github.com/Nextomics/NextDenovo' +description = 'NextDenovo is a string graph-based de novo assembler for long reads.' + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://github.com/Nextomics/NextDenovo/archive/'] +sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}] +checksums = ['bbe43124e7d63cbe33179c2abf2de60797bb7361a7f7a2b5fc33bf62a4479726'] + +builddependencies = [('binutils', '2.40')] +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('cURL', '8.0.1'), +] + +exts_defaultclass = 'PythonPackage' +exts_default_options = { + 'source_urls': [PYPI_SOURCE], + 'download_dep_fail': True, + 'use_pip': True, + 'sanity_pip_check': True, + 'preinstallopts': '', + 'installopts': '', +} + +exts_list = [ + ('Paralleltask', '0.2.3', { + 'modulename': 'paralleltask', + 'checksums': ['8015a8311d5021bc44edbfbf45ff2557a529999e235d25190bac62993fdf7b66'], + }), +] + +files_to_copy = ['bin', 'lib', 'test_data', 'LICENSE', 'nextDenovo'] + +sanity_check_paths = { + 'files': ['nextDenovo', 'bin/minimap2-nd', 'bin/paralleltask', 'bin/nextgraph'], + 'dirs': ['bin', 'test_data', 'lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ['nextDenovo --help'] + +modextrapaths = { + 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', + 'PATH': '', +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/n/NextGenMap/NextGenMap-0.5.5-GCC-12.3.0.eb b/easybuild/easyconfigs/n/NextGenMap/NextGenMap-0.5.5-GCC-12.3.0.eb new file mode 100644 index 00000000000..1792c3ecdfa --- /dev/null +++ b/easybuild/easyconfigs/n/NextGenMap/NextGenMap-0.5.5-GCC-12.3.0.eb @@ -0,0 +1,55 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild + +easyblock = 'CMakeMake' + +name = 'NextGenMap' +version = '0.5.5' + +homepage = 'http://cibiv.github.io/%(name)s/' +description = """NextGenMap is a flexible highly sensitive short read mapping tool that + handles much higher mismatch rates than comparable algorithms while still outperforming + them in terms of runtime.""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/Cibiv/%(namelower)s/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['c205e6cb312d2f495106435f10fb446e6fb073dd1474f4f74ab5980ba9803661'] + +builddependencies = [ + ('CMake', '3.26.3'), +] + +dependencies = [ + ('BamTools', '2.5.2'), + ('zlib', '1.2.13'), +] + +skipsteps = ['install'] + +preconfigopts = r"sed -i '/add_subdirectory.*\(bamtools\|zlib\).*/d' ../NextGenMap-%(version)s/CMakeLists.txt && " +preconfigopts += "sed -i 's/BamTools-static/bamtools/g' ../NextGenMap-%(version)s/{src,utils}/CMakeLists.txt && " +preconfigopts += "sed -i 's/zlibstatic/z/g' ../NextGenMap-%(version)s/{src,utils}/CMakeLists.txt && " + +buildopts = ' && cp -r ../%(name)s-%(version)s/bin/ngm-%(version)s/. %(installdir)s/bin/' + +postinstallcmds = [ + # avoid hard overwriting of $LD_LIBRARY_PATH in ngm wrapper script + r"sed -i 's/\(LD_LIBRARY_PATH=[^ ]*\)\"/\1:$LD_LIBRARY_PATH\"/g' %(installdir)s/bin/ngm", + # fix execution permissions for ngm* binaries/scripts + "chmod a+x %(installdir)s/bin/ngm*", + # link `libOpenCL.so.1` to the `lib` directory (required when using RPATH linking) + 'cd %(installdir)s && mkdir -p lib && ln -rfs bin/opencl/lib/libOpenCL.so.1 lib/libOpenCL.so.1', +] + +sanity_check_paths = { + 'files': ['lib/libOpenCL.so.1'] + ['bin/%s' % x for x in ['ngm', 'ngm-core', 'ngm-log', 'ngm-utils', 'oclTool']], + 'dirs': ['bin/opencl'] +} + +sanity_check_commands = [ + "ngm --help 2>&1 | grep 'Usage:[ ]*ngm'", +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/n/NextPolish/NextPolish-1.4.1-GCC-12.3.0.eb b/easybuild/easyconfigs/n/NextPolish/NextPolish-1.4.1-GCC-12.3.0.eb new file mode 100644 index 00000000000..51a31669463 --- /dev/null +++ b/easybuild/easyconfigs/n/NextPolish/NextPolish-1.4.1-GCC-12.3.0.eb @@ -0,0 +1,94 @@ +easyblock = 'MakeCp' + +name = 'NextPolish' +version = '1.4.1' + +homepage = 'https://github.com/Nextomics/NextPolish' +description = 'NextDenovo is a string graph-based de novo assembler for long reads.' + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +source_urls = ['https://github.com/Nextomics/NextPolish/releases/download/'] +sources = [{ + 'download_filename': 'v%(version)s/%(name)s.tgz', + 'filename': SOURCE_TAR_GZ, +}] +checksums = ['2a5f66f3db7f76e583a6b6e28f9c1f3c392258b8d755050d7abe129a2fbb48c4'] + +builddependencies = [('patchelf', '0.18.0')] +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('BWA', '0.7.17'), + ('SAMtools', '1.18'), + ('minimap2', '2.26'), + ('bzip2', '1.0.8'), +] + +exts_defaultclass = 'PythonPackage' +exts_default_options = { + 'source_urls': [PYPI_SOURCE], + 'download_dep_fail': True, + 'use_pip': True, + 'sanity_pip_check': True, + 'preinstallopts': '', + 'installopts': '', +} + +exts_list = [ + ('Paralleltask', '0.2.3', { + 'modulename': 'paralleltask', + 'checksums': ['8015a8311d5021bc44edbfbf45ff2557a529999e235d25190bac62993fdf7b66'], + }), +] + +# fix make -C util - warning: jobserver unavailable +parallel = 1 + +# fix bwa bug - https://github.com/Nextomics/NextPolish/issues/83 +# + use SAMtools and minimap2 from EB +prebuildopts = "sed -i 's/seq_count bwa samtools minimap2/seq_count/' Makefile && " +prebuildopts += "rm -rf util/bwa && rm -fr util/minimap2 && rm -rf util/samtools && " +prebuildopts += ( + "sed -i" + " -e 's/seq_split seq_count bwa_ samtools_ minimap2_/seq_split seq_count/'" + " -e '/BWADIR/d'" + " -e '/bwa_:/d'" + " -e '/SAMTOOLSDIR/d'" + " -e '/MINIMAP2DIR/d'" + " -e '/samtools_:/d'" + " -e '/minimap2_:/d'" + " util/Makefile && " +) +postinstallcmds = [ + # links to binaries + "cd %(installdir)s/bin && ln -s $EBROOTBWA/bin/bwa && " + "ln -s $EBROOTSAMTOOLS/bin/samtools && ln -s $EBROOTMINIMAP2/bin/minimap2", + # set RPATH to calgs.so, nextpolish1.so and nextpolish2.so + "if %(rpath_enabled)s; then " + "patchelf --force-rpath --set-rpath '$ORIGIN:$ORIGIN/../lib'" + '":$EBROOTZLIB/lib" %(installdir)s/lib/calgs.so && ' + "patchelf --force-rpath --set-rpath '$ORIGIN:$ORIGIN/../lib'" + '"$EBROOTZLIB/lib:$EBROOTBZIP2/lib:$EBROOTXZ/lib" %(installdir)s/lib/nextpolish1.so && ' + "patchelf --force-rpath --set-rpath '$ORIGIN:$ORIGIN/../lib'" + '"$EBROOTZLIB/lib:$EBROOTBZIP2/lib:$EBROOTXZ/lib" %(installdir)s/lib/nextpolish2.so; fi', +] + +files_to_copy = ['bin', 'lib', 'test_data', 'LICENSE', 'nextPolish'] + +sanity_check_paths = { + 'files': ['nextPolish', 'bin/minimap2', 'bin/paralleltask', 'bin/bwa', 'bin/samtools'], + 'dirs': ['test_data', 'lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + 'nextPolish --help', + 'nextPolish %(installdir)s/test_data/run.cfg' +] + +modextrapaths = { + 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', + 'PATH': '', +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/n/Nextflow/Nextflow-24.04.2.eb b/easybuild/easyconfigs/n/Nextflow/Nextflow-24.04.2.eb new file mode 100644 index 00000000000..21a90e473cc --- /dev/null +++ b/easybuild/easyconfigs/n/Nextflow/Nextflow-24.04.2.eb @@ -0,0 +1,35 @@ +easyblock = 'Binary' + +name = 'Nextflow' +version = '24.04.2' + +homepage = 'https://www.nextflow.io/' +description = """Nextflow is a reactive workflow framework and a programming DSL + that eases writing computational pipelines with complex data""" + +toolchain = SYSTEM + +source_urls = ['https://github.com/nextflow-io/nextflow/releases/download/v%(version)s/'] +sources = ['nextflow-%(version)s-all'] +checksums = ['1491a4efc06f0df9eed1fa6aa5a8c657435397fa99c34bf954281460e9b1c5ee'] + +dependencies = [('Java', '11')] + +install_cmds = [ + "mkdir -p %(installdir)s/bin", + "cp %(builddir)s/nextflow-%(version)s-all %(installdir)s/bin", + "cd %(installdir)s/bin && ln -s nextflow-%(version)s-all nextflow", + "cd %(installdir)s/bin && chmod +x %(installdir)s/bin/nextflow-%(version)s-all", +] + +sanity_check_paths = { + 'files': ['bin/nextflow-%(version)s-all', 'bin/nextflow'], + 'dirs': [] +} + +sanity_check_commands = [ + "nextflow -v", + "nextflow help", +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/n/Nextflow/Nextflow-24.04.4.eb b/easybuild/easyconfigs/n/Nextflow/Nextflow-24.04.4.eb new file mode 100644 index 00000000000..c718972b663 --- /dev/null +++ b/easybuild/easyconfigs/n/Nextflow/Nextflow-24.04.4.eb @@ -0,0 +1,35 @@ +easyblock = 'Binary' + +name = 'Nextflow' +version = '24.04.4' + +homepage = 'https://www.nextflow.io/' +description = """Nextflow is a reactive workflow framework and a programming DSL + that eases writing computational pipelines with complex data""" + +toolchain = SYSTEM + +source_urls = ['https://github.com/nextflow-io/nextflow/releases/download/v%(version)s/'] +sources = ['nextflow-%(version)s-all'] +checksums = ['9077cfb151d4bc8682f09a65a77f45346bf34dac5931e371dba0d51bf13a5076'] + +dependencies = [('Java', '11')] + +install_cmds = [ + "mkdir -p %(installdir)s/bin", + "cp %(builddir)s/nextflow-%(version)s-all %(installdir)s/bin", + "cd %(installdir)s/bin && ln -s nextflow-%(version)s-all nextflow", + "cd %(installdir)s/bin && chmod +x %(installdir)s/bin/nextflow-%(version)s-all", +] + +sanity_check_paths = { + 'files': ['bin/nextflow-%(version)s-all', 'bin/nextflow'], + 'dirs': [] +} + +sanity_check_commands = [ + "nextflow -v", + "nextflow help", +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/n/Nextflow/Nextflow-24.10.2.eb b/easybuild/easyconfigs/n/Nextflow/Nextflow-24.10.2.eb new file mode 100644 index 00000000000..75b0cb4a2d6 --- /dev/null +++ b/easybuild/easyconfigs/n/Nextflow/Nextflow-24.10.2.eb @@ -0,0 +1,36 @@ +easyblock = 'Binary' + +name = 'Nextflow' +version = '24.10.2' + +homepage = 'https://www.nextflow.io/' +description = """Nextflow is a reactive workflow framework and a programming DSL + that eases writing computational pipelines with complex data""" + +toolchain = SYSTEM + +source_urls = ['https://github.com/nextflow-io/nextflow/releases/download/v%(version)s/'] +sources = ['nextflow-%(version)s-dist'] +checksums = ['972bb4f4bcd30bb474c29c247ccf79289bbcd444f799f0307f61123e6b0f7475'] + +dependencies = [('Java', '21')] + +install_cmds = [ + "mkdir -p %(installdir)s/bin", + "cp %(builddir)s/nextflow-%(version)s-dist %(installdir)s/bin", + "cd %(installdir)s/bin && ln -s nextflow-%(version)s-dist nextflow", + "cd %(installdir)s/bin && chmod +x %(installdir)s/bin/nextflow-%(version)s-dist", +] + +sanity_check_paths = { + 'files': ['bin/nextflow-%(version)s-dist', 'bin/nextflow'], + 'dirs': [] +} + +sanity_check_commands = [ + "nextflow -v", + "nextflow help", + "nextflow info", +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/n/NiBabel/NiBabel-5.2.0-gfbf-2022b.eb b/easybuild/easyconfigs/n/NiBabel/NiBabel-5.2.0-gfbf-2022b.eb new file mode 100644 index 00000000000..a930785f65b --- /dev/null +++ b/easybuild/easyconfigs/n/NiBabel/NiBabel-5.2.0-gfbf-2022b.eb @@ -0,0 +1,46 @@ +easyblock = 'PythonBundle' + +name = 'NiBabel' +version = '5.2.0' + +homepage = 'https://nipy.github.io/nibabel' +description = """NiBabel provides read/write access to some common medical and neuroimaging file formats, + including: ANALYZE (plain, SPM99, SPM2 and later), GIFTI, NIfTI1, NIfTI2, MINC1, MINC2, MGH and ECAT + as well as Philips PAR/REC. We can read and write Freesurfer geometry, and read Freesurfer morphometry and + annotation files. There is some very limited support for DICOM. NiBabel is the successor of PyNIfTI.""" + +toolchain = {'name': 'gfbf', 'version': '2022b'} + +dependencies = [ + ('Python', '3.10.8'), + ('SciPy-bundle', '2023.02'), + ('Pillow', '9.4.0'), + ('pydicom', '2.4.4'), +] + +use_pip = True + +exts_list = [ + ('bz2file', '0.98', { + 'checksums': ['64c1f811e31556ba9931953c8ec7b397488726c63e09a4c67004f43bdd28da88'], + }), + ('nibabel', version, { + 'checksums': ['3df8f1ab981d1bd92f4331d565528d126ab9717fdbd4cfe68f43fcd1c2bf3f52'], + }), +] + +fix_python_shebang_for = ['bin/*'] + +sanity_check_paths = { + 'files': ['bin/nib-dicomfs', 'bin/nib-diff', 'bin/nib-ls', 'bin/nib-nifti-dx', 'bin/parrec2nii'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "nib-diff --help", + "parrec2nii --help", +] + +sanity_pip_check = True + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/n/Nim/Nim-2.2.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/n/Nim/Nim-2.2.0-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..2214b1c9493 --- /dev/null +++ b/easybuild/easyconfigs/n/Nim/Nim-2.2.0-GCCcore-12.3.0.eb @@ -0,0 +1,17 @@ +name = 'Nim' +version = '2.2.0' + +homepage = 'https://nim-lang.org/' +description = "Nim is a systems and applications programming language." + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://nim-lang.org/download/'] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['ce9842849c9760e487ecdd1cdadf7c0f2844cafae605401c7c72ae257644893c'] + +builddependencies = [('binutils', '2.40')] + +dependencies = [('libreadline', '8.2')] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/n/Ninja/Ninja-1.12.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/n/Ninja/Ninja-1.12.1-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..9e6a998f707 --- /dev/null +++ b/easybuild/easyconfigs/n/Ninja/Ninja-1.12.1-GCCcore-13.3.0.eb @@ -0,0 +1,31 @@ +easyblock = 'CmdCp' + +name = 'Ninja' +version = '1.12.1' + +homepage = 'https://ninja-build.org/' +description = "Ninja is a small build system with a focus on speed." + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://github.com/ninja-build/ninja/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['821bdff48a3f683bc4bb3b6f0b5fe7b2d647cf65d52aeb63328c91a6c6df285a'] + +builddependencies = [ + ('binutils', '2.42'), + ('Python', '3.12.3'), +] + +cmds_map = [('.*', "./configure.py --bootstrap")] + +files_to_copy = [(['ninja'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/ninja'], + 'dirs': [], +} + +sanity_check_commands = ["ninja --version"] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/n/Normaliz/Normaliz-3.10.3-gfbf-2023b.eb b/easybuild/easyconfigs/n/Normaliz/Normaliz-3.10.3-gfbf-2023b.eb new file mode 100644 index 00000000000..6651c1a848d --- /dev/null +++ b/easybuild/easyconfigs/n/Normaliz/Normaliz-3.10.3-gfbf-2023b.eb @@ -0,0 +1,47 @@ +easyblock = 'ConfigureMake' + +name = 'Normaliz' +version = '3.10.3' + +homepage = 'https://www.normaliz.uni-osnabrueck.de/' +description = """Normaliz is a open source tool for computations in affine monoids, vector +configurations, rational polyhedra and rational cones. Normaliz now computes +rational and algebraic polyhedra, i.e., polyhedra defined over real algebraic +extensions of QQ.""" + +toolchain = {'name': 'gfbf', 'version': '2023b'} +toolchainopts = {'pic': True, 'openmp': True, 'cstd': 'c++14'} + +github_account = 'Normaliz' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['d9536ab3568053a8dd9aeabe09ef901c1c0ebbda37be50775a120eb9e7ff47cb'] + +builddependencies = [ + ('Autotools', '20220317'), +] + +dependencies = [ + ('Boost', '1.83.0'), + ('GMP', '6.3.0'), + ('CoCoALib', '0.99850'), + ('FLINT', '3.1.1'), + ('E-ANTIC', '2.0.2'), + ('nauty', '2.8.8'), +] + +preconfigopts = "autoreconf -f -i && " + +configopts = "--with-gmp=$EBROOTGMP --with-cocoalib=$EBROOTCOCOALIB --with-flint=$EBROOTFLINT " +configopts += "--with-e-antic=$EBROOTEMINANTIC --with-nauty=$EBROOTNAUTY" + +runtest = 'check' + +sanity_check_paths = { + 'files': ['bin/normaliz'] + ['lib/libnormaliz.%s' % e for e in ['a', SHLIB_EXT]], + 'dirs': ['include/libnormaliz'] +} + +sanity_check_commands = ["normaliz --help"] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/n/n2v/n2v-0.3.3-foss-2023a.eb b/easybuild/easyconfigs/n/n2v/n2v-0.3.3-foss-2023a.eb new file mode 100644 index 00000000000..dfc99c9d4d3 --- /dev/null +++ b/easybuild/easyconfigs/n/n2v/n2v-0.3.3-foss-2023a.eb @@ -0,0 +1,87 @@ +easyblock = 'PythonBundle' + +name = 'n2v' +version = '0.3.3' + +homepage = 'https://github.com/juglab/n2v' +description = "Learning Denoising from Single Noisy Images" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('Pillow', '10.0.0'), + ('imagecodecs', '2024.1.1'), + ('ruamel.yaml', '0.17.32'), + ('CSBDeep', '0.7.4'), + ('xarray', '2023.9.0'), + ('imageio', '2.33.1'), + ('pydantic', '2.5.3'), +] + +use_pip = True + +exts_list = [ + ('typer', '0.12.3', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['070d7ca53f785acbccba8e7d28b08dcd88f79f1fbda035ade0aecec71ca5c914'], + }), + ('marshmallow_union', '0.1.15.post1', { + 'source_tmpl': SOURCE_WHL, + 'checksums': ['1e21b759c76735305f99179c1a16759ebb9629733159628241b3f2117ff55e86'], + }), + ('marshmallow_jsonschema', '0.13.0', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['2814f2afb94a6e01b3c0a5795b3dfb142b628763655f20378400af5c0a2307fb'], + }), + ('marshmallow', '3.21.3', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['86ce7fb914aa865001a4b2092c4c2872d13bc347f3d42673272cabfdbad386f1'], + }), + ('fire', '0.6.0', { + 'checksums': ['54ec5b996ecdd3c0309c800324a0703d6da512241bc73b553db959d98de0aa66'], + }), + ('ruyaml', '0.91.0', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['50e0ee3389c77ad340e209472e0effd41ae0275246df00cdad0a067532171755'], + }), + ('python_dotenv', '1.0.1', { + 'source_tmpl': SOURCE_PY3_WHL, + 'modulename': 'dotenv', + 'checksums': ['f7b63ef50f1b690dddf550d03497b66d609393b40b564ed0d674909a68ebf16a'], + }), + ('pydantic_settings', '2.2.1', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['0235391d26db4d2190cb9b31051c4b46882d28a51533f97440867f012d4da091'], + }), + ('loguru', '0.7.2', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['003d71e3d3ed35f0f8984898359d65b79e5b21943f78af86aa5491210429b8eb'], + }), + ('dnspython', '2.6.1', { + 'source_tmpl': SOURCE_PY3_WHL, + 'modulename': 'dns', + 'checksums': ['5ef3b9680161f6fa89daf8ad451b5f1a33b18ae8a1c6778cdf4b43f08c0a6e50'], + }), + ('email_validator', '2.2.0', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['561977c2d73ce3611850a06fa56b414621e0c8faa9d66f2611407d87465da631'], + }), + ('bioimageio.spec', '0.4.9.post5', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['a24ef7c0d6506d080655fbd8f322bc153a147329bd2258a8e958982d31885865'], + }), + ('bioimageio.core', '0.5.11', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['af8138f0c75fcebf7abbb873d01af8055d6209b2fd611269990b72e51fb991b5'], + }), + (name, version, { + 'source_tmpl': SOURCE_WHL, + 'checksums': ['be5b24fe0bf3cdc15cd4771c50e577a81b7d83b27300a0b90035cc87bb95c33c'], + }), +] + +sanity_pip_check = True + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/n/nano/nano-8.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/n/nano/nano-8.1-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..64684d1ff42 --- /dev/null +++ b/easybuild/easyconfigs/n/nano/nano-8.1-GCCcore-13.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'nano' +version = '8.1' + +homepage = 'https://www.nano-editor.org/' +docurls = 'https://www.nano-editor.org/docs.php' +description = """a simple editor, inspired by Pico""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://www.nano-editor.org/dist/v%(version_major)s/'] +sources = [SOURCE_TAR_GZ] +checksums = ['6508bfbcfe38153ecbdc1b7d3479323564353f134acc8c501910220371390675'] + +builddependencies = [('binutils', '2.42')] + +dependencies = [('ncurses', '6.5')] + +sanity_check_paths = { + 'files': ['bin/nano'], + 'dirs': ['bin', 'share'], +} + +sanity_check_commands = ['nano --version'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/n/nanoQC/nanoQC-0.9.4-foss-2023a.eb b/easybuild/easyconfigs/n/nanoQC/nanoQC-0.9.4-foss-2023a.eb new file mode 100644 index 00000000000..264a822a3ca --- /dev/null +++ b/easybuild/easyconfigs/n/nanoQC/nanoQC-0.9.4-foss-2023a.eb @@ -0,0 +1,31 @@ +easyblock = 'PythonPackage' + +name = 'nanoQC' +version = '0.9.4' + +homepage = 'https://github.com/wdecoster/nanoQC' +description = """Quality control tools for long read sequencing + data aiming to replicate some of the plots made by fastQC.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +sources = [SOURCE_TAR_GZ] +checksums = ['05685656138cbaf099b18831d1ceeaca93faf3399881cc2efda44c04d3b316e3'] + +dependencies = [ + ('Python', '3.11.3'), + ('Biopython', '1.83'), + ('SciPy-bundle', '2023.07'), + ('bokeh', '3.2.2'), +] + +download_dep_fail = True +use_pip = True + +options = {'modulename': 'nanoQC'} + +sanity_check_commands = ["nanoQC --help"] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/n/nanoget/nanoget-1.19.3-foss-2023a.eb b/easybuild/easyconfigs/n/nanoget/nanoget-1.19.3-foss-2023a.eb new file mode 100644 index 00000000000..2aeb2ceaf26 --- /dev/null +++ b/easybuild/easyconfigs/n/nanoget/nanoget-1.19.3-foss-2023a.eb @@ -0,0 +1,30 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 +# Update: Petr Král (INUITS) + +easyblock = 'PythonPackage' + +name = 'nanoget' +version = '1.19.3' + +homepage = 'https://github.com/wdecoster/nanoget' +description = "Functions to extract information from Oxford Nanopore sequencing data and alignments" + +toolchain = {'name': 'foss', 'version': '2023a'} + +sources = [SOURCE_TAR_GZ] +checksums = ['da981810edb1cbe42cbbfbe5fcf753f29bf5555204cd51256b28a284a036a71b'] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('Biopython', '1.83'), + ('Pysam', '0.22.0'), + ('nanomath', '1.4.0'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/n/nanomath/nanomath-1.4.0-foss-2023a.eb b/easybuild/easyconfigs/n/nanomath/nanomath-1.4.0-foss-2023a.eb new file mode 100644 index 00000000000..2a2f56955cc --- /dev/null +++ b/easybuild/easyconfigs/n/nanomath/nanomath-1.4.0-foss-2023a.eb @@ -0,0 +1,33 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 +# Update: Petr Král (INUITS) + +easyblock = 'PythonBundle' + +name = 'nanomath' +version = '1.4.0' + +homepage = 'https://github.com/wdecoster/nanomath' +description = "A few simple math functions for other Oxford Nanopore processing scripts" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('Python-Deprecated', '1.1.0', { + 'modulename': 'deprecated', + 'checksums': ['a242b3c1721f97912330b12cd5529abfa5b3876084a6c60a2c683a87d4b0dd6f'], + }), + (name, version, { + 'checksums': ['ed7a38fbb156d9a68a95c2570fe3c2035321d0a3e234580496750afca4927ced'], + }), +] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/n/nanopolish/nanopolish-0.14.0-foss-2023a.eb b/easybuild/easyconfigs/n/nanopolish/nanopolish-0.14.0-foss-2023a.eb new file mode 100644 index 00000000000..d32ee79a46a --- /dev/null +++ b/easybuild/easyconfigs/n/nanopolish/nanopolish-0.14.0-foss-2023a.eb @@ -0,0 +1,61 @@ +easyblock = 'MakeCp' + +name = 'nanopolish' +version = '0.14.0' + +homepage = 'https://github.com/jts/nanopolish' +description = "Software package for signal-level analysis of Oxford Nanopore sequencing data." + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = [ + 'https://github.com/jts/nanopolish/archive/', + 'https://github.com/mateidavid/fast5/archive/', +] +sources = [ + { + 'source_urls': ['https://github.com/jts/nanopolish/archive/'], + 'download_filename': 'v%(version)s.tar.gz', + 'filename': SOURCE_TAR_GZ, + }, + { + 'source_urls': ['https://github.com/hasindu2008/slow5lib/archive/'], + 'download_filename': 'v1.1.0.tar.gz', + 'filename': 'slow5lib-v1.1.0.tar.gz', + }, +] +checksums = [ + {'nanopolish-0.14.0.tar.gz': 'bcc1a7e2d23941592d817da3af9165b3843ae52b11a3ca5983d6417f1614ef78'}, + {'slow5lib-v1.1.0.tar.gz': 'f13f08b85a9a11086b5d9378251093d1858d0dc29d8e727eabacfa57a73f4277'}, +] + +builddependencies = [('Eigen', '3.4.0')] + +dependencies = [ + ('zlib', '1.2.13'), + ('Python', '3.11.3'), + ('Biopython', '1.83'), + ('Pysam', '0.22.0'), + ('HDF5', '1.14.0'), + ('HTSlib', '1.18'), + ('minimap2', '2.26'), + ('VBZ-Compression', '1.0.3'), +] + +prebuildopts = "rmdir slow5lib && ln -s %(builddir)s/slow5lib-*/ slow5lib && " +buildopts = "HDF5=noinstall EIGEN=noinstall HTS=noinstall MINIMAP2=noinstall" + +runtest = 'test ' + buildopts + +files_to_copy = [(['nanopolish'], 'bin'), 'scripts'] + +postinstallcmds = ["chmod a+rx %(installdir)s/scripts/*"] + +sanity_check_paths = { + 'files': ['bin/nanopolish'], + 'dirs': ['scripts'], +} + +modextrapaths = {'PATH': 'scripts'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/n/napari-denoiseg/napari-denoiseg-0.0.1-foss-2023a.eb b/easybuild/easyconfigs/n/napari-denoiseg/napari-denoiseg-0.0.1-foss-2023a.eb new file mode 100644 index 00000000000..8335ad90cba --- /dev/null +++ b/easybuild/easyconfigs/n/napari-denoiseg/napari-denoiseg-0.0.1-foss-2023a.eb @@ -0,0 +1,57 @@ +easyblock = 'PythonBundle' + +name = 'napari-denoiseg' +version = '0.0.1' + +homepage = 'https://juglab.github.io/napari-denoiseg/index.html' +description = """A napari plugin performing joint denoising and segmentation of microscopy images using DenoiSeg.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('napari', '0.4.18'), + ('PyQtGraph', '0.13.7'), + ('QtPy', '2.4.1'), + ('TensorFlow', '2.13.0'), + ('CSBDeep', '0.7.4'), + ('n2v', '0.3.3'), + ('numba', '0.58.1'), + ('scikit-learn', '1.3.1'), + ('autopep8', '2.2.0'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('napari-workflows', '0.2.10', { + 'checksums': ['d48f2020693b4b8c1dd639668a3b1588115beac8f19f42394fc241fc1672be12'], + }), + ('napari-tools-menu', '0.1.19', { + 'checksums': ['6b58ac45d7fe84bc5975e7a53142340d5d62beff9ade0f2f58d7a3a4a0a8e8f8'], + }), + ('magicgui', '0.8.3', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['ee763f3908a344cc73e1ed0981885114937ce3077e60e4feb8148e64f0e762a3'], + }), + ('napari_time_slicer', '0.5.0', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['6c7f53f762cb3410da097be43ba47b4f4213e89930a3ade3ec1c7c1beb9d605f'], + }), + ('denoiseg', '0.3.1', { + 'preinstallopts': 'sed -i "s/wrapt<=1.12.1/wrapt/g" setup.py && ', + 'checksums': ['fd720b78910b84ea5d65deda8c193d64e583c78090d9867990b7a39f72ed7ea3'], + }), + ('napari-denoiseg', '%(version)src2', { + 'preinstallopts': 'sed -i "s/vispy<=0.9.6/vispy/g;s/napari<=0.4.15/napari<=0.4.18/g" setup.cfg && ', + 'checksums': ['e244dbb820ee7d35212ee198d28eabf987439a70ce6695cbf63cfa52baab1ea8'], + }), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/n/napari/napari-0.4.19.post1-foss-2023a.eb b/easybuild/easyconfigs/n/napari/napari-0.4.19.post1-foss-2023a.eb new file mode 100644 index 00000000000..dd8ff3a3059 --- /dev/null +++ b/easybuild/easyconfigs/n/napari/napari-0.4.19.post1-foss-2023a.eb @@ -0,0 +1,121 @@ +# Thomas Hoffmann, EMBL Heidelberg, structures-it@emblde, 2024/01 +easyblock = 'PythonBundle' + +name = 'napari' +version = '0.4.19.post1' + +homepage = 'https://napari.org/' +description = """napari is a fast, interactive, multi-dimensional image viewer for Python. It's +designed for browsing, annotating, and analyzing large multi-dimensional images. +It's built on top of Qt (for the GUI), vispy (for performant GPU-based +rendering), and the scientific Python stack (numpy, scipy).""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [ + ('poetry', '1.5.1'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('PyQt5', '5.15.10'), + ('SciPy-bundle', '2023.07'), + ('PyYAML', '6.0'), + ('pydantic', '2.5.3'), + ('dask', '2023.9.2'), + ('PyOpenGL', '3.1.7'), + ('imageio', '2.33.1'), + ('tqdm', '4.66.1'), + ('IPython', '8.14.0'), + ('VisPy', '0.14.1'), + ('scikit-image', '0.22.0'), + ('matplotlib', '3.7.2'), + ('Qtconsole', '5.5.1'), + ('Pint', '0.23'), + ('wrapt', '1.15.0'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('in_n_out', '0.1.9', { + 'checksums': ['89feb944e420faf42d3c2542145681b4d57144355932c2b859695fcdc4f9a2da'], + }), + ('pydantic_compat', '0.1.2', { + 'checksums': ['c5c5bca39ca2d22cad00c02898e400e1920e5127649a8e860637f15566739373'], + }), + ('app_model', '0.2.4', { + 'checksums': ['127cda637003a34b26371c9c68ae5b24d7012682f071a10657a94900c8cd439d'], + }), + ('cachey', '0.2.1', { + 'checksums': ['0310ba8afe52729fa7626325c8d8356a8421c434bf887ac851e58dcf7cf056a6'], + }), + ('docstring_parser', '0.15', { + 'checksums': ['48ddc093e8b1865899956fcc03b03e66bb7240c310fac5af81814580c55bf682'], + }), + ('magicgui', '0.8.1', { + 'checksums': ['43553d8f11002a79dd5fee57caff3ba9d3e37d7d50e8ed40efe79b360adc806a'], + }), + ('numpydoc', '1.6.0', { + 'checksums': ['ae7a5380f0a06373c3afe16ccd15bd79bc6b07f2704cbc6f1e7ecc94b4f5fc0d'], + }), + ('psygnal', '0.9.5', { + 'checksums': ['4956ea6c36a75f7fc457558935b67dd8be2594661b4d08eeb3357d69c509c55f'], + }), + ('superqt', '0.6.1', { + 'checksums': ['f1a9e0499c4bbcef34b6f895eb57cd41301b3799242cd030029238124184dade'], + }), + ('napari-console', '0.0.9', { + 'modulename': 'napari_console', + 'checksums': ['3bc86dd96cf94b1af96bba1043f90a39b1369bb978a8df9038a1ac422e66b532'], + }), + ('napari-plugin-engine', '0.2.0', { + 'checksums': ['fa926f869d70e0d652c005661948cd0c7fee5508ae17d437937f34f5287590b3'], + }), + ('napari-svg', '0.1.10', { + 'checksums': ['18e642c888a71e09c9d1097f25bced1e7ef5dde1771469647bcd77975800f77d'], + }), + ('typer', '0.9.0', { + 'checksums': ['50922fd79aea2f4751a8e0408ff10d2662bd0c8bbfa84755a699f3bada2978b2'], + }), + ('pyproject_hooks', '1.0.0', { + 'checksums': ['f271b298b97f5955d53fb12b72c1fb1948c22c1a6b70b315c54cedaca0264ef5'], + }), + ('build', '1.1.1', { + 'checksums': ['8eea65bb45b1aac2e734ba2cc8dad3a6d97d97901a395bd0ed3e7b46953d2a31'], + }), + ('mdurl', '0.1.2', { + 'checksums': ['bb413d29f5eea38f31dd4754dd7377d4465116fb207585f97bf925588687c1ba'], + }), + ('markdown-it-py', '3.0.0', { + 'modulename': 'markdown_it', + 'checksums': ['e3f60a94fa066dc52ec76661e37c851cb232d92f9886b15cb560aaada2df8feb'], + }), + ('rich', '13.7.1', { + 'checksums': ['9be308cb1fe2f1f57d67ce99e95af38a1e2bc71ad9813b0e247cf7ffbcc3a432'], + }), + ('npe2', '0.7.4', { + 'checksums': ['969d5394b24225cff1ab6625f29ea1603a6509714bd9496c49e697c3e49077b0'], + }), + ('mypy_extensions', '1.0.0', { + 'checksums': ['75dbf8955dc00442a438fc4d0666508a9a97b6bd41aa2f0ffe9d2f2725af0782'], + }), + (name, version, { + 'checksums': ['88e298697c38c9f842d7c26c8d51d2e0fbb90d0be05575fdd159d27eede11301'], + }), +] + +fix_python_shebang_for = ['bin/napari'] + +sanity_check_paths = { + 'files': ['bin/%(name)s'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(name)s'], +} + +sanity_check_commands = [ + '%(name)s --help', + 'pyrcc5 -version 2>&1 |grep pyrcc5' # make sure PyQt5 module was not built with --no-tools +] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/n/nauty/nauty-2.8.8-GCC-13.2.0.eb b/easybuild/easyconfigs/n/nauty/nauty-2.8.8-GCC-13.2.0.eb new file mode 100644 index 00000000000..66a269da4e9 --- /dev/null +++ b/easybuild/easyconfigs/n/nauty/nauty-2.8.8-GCC-13.2.0.eb @@ -0,0 +1,53 @@ +easyblock = 'MakeCp' + +name = 'nauty' +version = '2.8.8' + +homepage = 'https://pallini.di.uniroma1.it/' +description = """nauty and Traces are programs for computing automorphism groups of graphs and +digraphs. They can also produce a canonical label.""" + +toolchain = {'name': 'GCC', 'version': '13.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://pallini.di.uniroma1.it'] +sources = ['nauty%s.tar.gz' % version.replace('.', '_')] +checksums = ['159d2156810a6bb240410cd61eb641add85088d9f15c888cdaa37b8681f929ce'] + +local_executables = [ + 'addedgeg', 'amtog', 'assembleg', 'biplabg', 'catg', 'complg', 'converseg', 'copyg', 'countg', 'cubhamg', + 'deledgeg', 'delptg', 'directg', 'dreadnaut', 'dretodot', 'dretog', 'edgetransg', 'genbg', 'genbgL', 'geng', + 'gengL', 'genquarticg', 'genrang', 'genspecialg', 'gentourng', 'gentreeg', 'hamheuristic', 'labelg', 'linegraphg', + 'listg', 'multig', 'newedgeg', 'NRswitchg', 'pickg', 'planarg', 'ranlabg', 'shortg', 'showg', 'subdivideg', + 'twohamg', 'underlyingg', 'vcolg', 'watercluster2' +] +local_headers = [ + 'gtools.h', 'gutils.h', 'naugroup.h', 'naugstrings.h', 'naurng.h', 'nausparse.h', 'nautaux.h', 'nautinv.h', + 'naututil.h', 'nautycliquer.h', 'nauty.h', 'planarity.h', 'quarticirred28.h', 'schreier.h', 'traces.h' +] +local_libs = ['nauty%s.a' % l for l in ['', '1', 'L', 'L1', 'W', 'W1']] + +# Configure and enable thread-local variables +prebuildopts = "./configure --enable-tls && " + +runtest = "checks" + +files_to_copy = [ + (local_executables, "bin"), + (local_headers, "include/%(name)s"), + (local_libs, "lib"), +] + +# prepend "lib" to library files to standarize their name +postinstallcmds = ["cd %%(installdir)s/lib/ && mv %s lib%s" % (l, l) for l in local_libs] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_executables] + + ['include/%%(name)s/%s' % h for h in local_headers] + + ['lib/lib%s' % l for l in local_libs], + 'dirs': [''] +} + +sanity_check_commands = ["dreadnaut --help"] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/n/nbclassic/nbclassic-1.0.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/n/nbclassic/nbclassic-1.0.0-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..26033ffa7ec --- /dev/null +++ b/easybuild/easyconfigs/n/nbclassic/nbclassic-1.0.0-GCCcore-13.2.0.eb @@ -0,0 +1,51 @@ +easyblock = 'PythonPackage' + +name = 'nbclassic' +version = "1.0.0" + +homepage = 'https://jupyter.org/' +description = """NbClassic provides a backwards compatible Jupyter Notebook interface + that you can install side-by-side with the latest versions: That way, you can fearlessly + upgrade without worrying about your classic extensions and customizations breaking.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +builddependencies = [ + ('binutils', '2.40'), + ('maturin', '1.3.1'), +] +dependencies = [ + ('Python', '3.11.5'), + ('jupyter-server', '2.14.0'), +] + +sources = [SOURCE_TAR_GZ] +patches = ['nbclassic-1.0.0_fix_setup_version.patch'] +checksums = [ + {'nbclassic-1.0.0.tar.gz': '0ae11eb2319455d805596bf320336cda9554b41d99ab9a3c31bf8180bffa30e3'}, + {'nbclassic-1.0.0_fix_setup_version.patch': 'c26d91ac1d0cea2b361b2619076acdaf5fcd5ff2363d9e5f5e1bd737b4b50736'}, +] + +download_dep_fail = True +sanity_pip_check = True +use_pip = True + +local_binaries = [ + 'jupyter-nbclassic', + 'jupyter-nbclassic-bundlerextension', + 'jupyter-nbclassic-extension', + 'jupyter-nbclassic-serverextension', +] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_binaries], + 'dirs': [], +} + +sanity_check_commands = ['jupyter nbclassic --help'] + +modextrapaths = { + 'JUPYTER_CONFIG_PATH': 'etc/jupyter', + 'JUPYTER_PATH': 'share/jupyter', +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-3.1.1-gompi-2023b.eb b/easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-3.1.1-gompi-2023b.eb new file mode 100644 index 00000000000..a7b4d99b54d --- /dev/null +++ b/easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-3.1.1-gompi-2023b.eb @@ -0,0 +1,38 @@ +easyblock = 'CMakeMake' + +name = 'ncbi-vdb' +version = '3.1.1' + +homepage = 'https://github.com/ncbi/ncbi-vdb' +description = """The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for + using data in the INSDC Sequence Read Archives.""" + +toolchain = {'name': 'gompi', 'version': '2023b'} + +github_account = 'ncbi' +source_urls = [GITHUB_SOURCE] +sources = [{'download_filename': '%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}] +checksums = ['e9766f259853c696be48e289b08cb5ae6e198d82d7ffee79f09ce7f720487991'] + +builddependencies = [ + ('Perl', '5.38.0'), + ('Python', '3.11.5'), + ('CMake', '3.27.6'), +] + +dependencies = [ + ('HDF5', '1.14.3'), + ('libxml2', '2.11.5'), + ('bzip2', '1.0.8'), +] + +configopts = "-DHDF5_INCDIR=$EBROOTHDF5/include -DHDF5_LIBDIR=$EBROOTHDF5/lib " +configopts += "-DXML2_INCDIR=$EBROOTLIBXML2/include -DXML2_LIBDIR=$EBROOTLIBXML2/lib " + +sanity_check_paths = { + 'files': ['include/ncbi/ncbi.h', 'include/ncbi/vdb-blast.h'] + + [('lib/libncbi-%s.%s' % (k, e)) for k in ['vdb', 'wvdb'] for e in ['a', SHLIB_EXT]], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/n/ncdu/ncdu-1.20-GCC-13.3.0.eb b/easybuild/easyconfigs/n/ncdu/ncdu-1.20-GCC-13.3.0.eb new file mode 100644 index 00000000000..e8f91407acf --- /dev/null +++ b/easybuild/easyconfigs/n/ncdu/ncdu-1.20-GCC-13.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'ncdu' +version = '1.20' + +homepage = 'https://dev.yorhel.nl/ncdu' +description = """Ncdu is a disk usage analyzer with an ncurses interface. It is designed to find space hogs on a + remote server where you don't have an entire graphical setup available, but it is a useful tool even on regular + desktop systems. Ncdu aims to be fast, simple and easy to use, and should be able to run in any minimal POSIX-like + environment with ncurses installed.""" + +toolchain = {'name': 'GCC', 'version': '13.3.0'} + +source_urls = ['https://dev.yorhel.nl/download/'] +sources = [SOURCE_TAR_GZ] +checksums = ['5fe2bb841abe72374bb242dbb93293c4ae053078432d896a7481b2ff10be9572'] + +dependencies = [ + ('ncurses', '6.5'), +] + +sanity_check_paths = { + 'files': ['bin/%(name)s'], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-6.5-GCCcore-13.3.0.eb b/easybuild/easyconfigs/n/ncurses/ncurses-6.5-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..c34643c0b37 --- /dev/null +++ b/easybuild/easyconfigs/n/ncurses/ncurses-6.5-GCCcore-13.3.0.eb @@ -0,0 +1,53 @@ +easyblock = 'ConfigureMake' + +name = 'ncurses' +version = '6.5' + +homepage = 'https://www.gnu.org/software/ncurses/' +description = """ + The Ncurses (new curses) library is a free software emulation of curses in + System V Release 4.0, and more. It uses Terminfo format, supports pads and + color and multiple highlights and forms characters and function-key mapping, + and has all the other SYSV-curses enhancements over BSD Curses. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['136d91bc269a9a5785e5f9e980bc76ab57428f604ce3e5a5a90cebc767971cc6'] + +builddependencies = [ + ('binutils', '2.42'), + ('pkgconf', '2.2.0'), +] + +local_common_configopts = "--with-shared --enable-overwrite --without-ada --enable-symlinks --with-versioned-syms " +local_common_configopts += "--enable-pc-files --with-pkg-config-libdir=%(installdir)s/lib/pkgconfig " +configopts = [ + # build ncurses: serial build in default paths with shared libraries + local_common_configopts + "--disable-widec", + # build ncursesw: serial with UTF-8 + local_common_configopts + "--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/", +] + +# Symlink libtinfo to libncurses +# libncurses with this configopts has all the symbols from libtinfo, but some packages look for libtinfo specifically +postinstallcmds = ['cd %(installdir)s/lib && for l in libncurses{.,_,w}*; do ln -s "${l}" "${l/ncurses/tinfo}"; done'] + +_target_suffix = ['', 'w'] # '': ncurses, 'w': ncursesw +_lib_suffix = ['%s%s' % (x, y) for x in _target_suffix for y in ['.a', '_g.a', '.' + SHLIB_EXT]] +_lib_names = ['form', 'menu', 'ncurses', 'panel', 'tinfo'] +_pc_names = ['form', 'menu', 'ncurses++', 'ncurses', 'panel'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses%(version_major)s-config", + "reset", "tabs", "tic", "toe", "tput", "tset"]] + + ['lib/lib%s%s' % (x, y) for x in _lib_names for y in _lib_suffix] + + ['lib/libncurses++%s.a' % x for x in _target_suffix] + + ['lib/pkgconfig/%s%s.pc' % (x, y) for x in _pc_names for y in _target_suffix], + 'dirs': ['include', 'include/ncursesw'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-6.5-GCCcore-14.2.0.eb b/easybuild/easyconfigs/n/ncurses/ncurses-6.5-GCCcore-14.2.0.eb new file mode 100644 index 00000000000..a7ad6d943b2 --- /dev/null +++ b/easybuild/easyconfigs/n/ncurses/ncurses-6.5-GCCcore-14.2.0.eb @@ -0,0 +1,53 @@ +easyblock = 'ConfigureMake' + +name = 'ncurses' +version = '6.5' + +homepage = 'https://www.gnu.org/software/ncurses/' +description = """ + The Ncurses (new curses) library is a free software emulation of curses in + System V Release 4.0, and more. It uses Terminfo format, supports pads and + color and multiple highlights and forms characters and function-key mapping, + and has all the other SYSV-curses enhancements over BSD Curses. +""" + +toolchain = {'name': 'GCCcore', 'version': '14.2.0'} +toolchainopts = {'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['136d91bc269a9a5785e5f9e980bc76ab57428f604ce3e5a5a90cebc767971cc6'] + +builddependencies = [ + ('binutils', '2.42'), + ('pkgconf', '2.3.0'), +] + +local_common_configopts = "--with-shared --enable-overwrite --without-ada --enable-symlinks --with-versioned-syms " +local_common_configopts += "--enable-pc-files --with-pkg-config-libdir=%(installdir)s/lib/pkgconfig " +configopts = [ + # build ncurses: serial build in default paths with shared libraries + local_common_configopts + "--disable-widec", + # build ncursesw: serial with UTF-8 + local_common_configopts + "--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/", +] + +# Symlink libtinfo to libncurses +# libncurses with this configopts has all the symbols from libtinfo, but some packages look for libtinfo specifically +postinstallcmds = ['cd %(installdir)s/lib && for l in libncurses{.,_,w}*; do ln -s "${l}" "${l/ncurses/tinfo}"; done'] + +_target_suffix = ['', 'w'] # '': ncurses, 'w': ncursesw +_lib_suffix = ['%s%s' % (x, y) for x in _target_suffix for y in ['.a', '_g.a', '.' + SHLIB_EXT]] +_lib_names = ['form', 'menu', 'ncurses', 'panel', 'tinfo'] +_pc_names = ['form', 'menu', 'ncurses++', 'ncurses', 'panel'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses%(version_major)s-config", + "reset", "tabs", "tic", "toe", "tput", "tset"]] + + ['lib/lib%s%s' % (x, y) for x in _lib_names for y in _lib_suffix] + + ['lib/libncurses++%s.a' % x for x in _target_suffix] + + ['lib/pkgconfig/%s%s.pc' % (x, y) for x in _pc_names for y in _target_suffix], + 'dirs': ['include', 'include/ncursesw'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-6.5.eb b/easybuild/easyconfigs/n/ncurses/ncurses-6.5.eb new file mode 100644 index 00000000000..a3ff51a30fc --- /dev/null +++ b/easybuild/easyconfigs/n/ncurses/ncurses-6.5.eb @@ -0,0 +1,48 @@ +easyblock = 'ConfigureMake' + +name = 'ncurses' +version = '6.5' + +homepage = 'https://www.gnu.org/software/ncurses/' +description = """ + The Ncurses (new curses) library is a free software emulation of curses in + System V Release 4.0, and more. It uses Terminfo format, supports pads and + color and multiple highlights and forms characters and function-key mapping, + and has all the other SYSV-curses enhancements over BSD Curses. +""" + +toolchain = SYSTEM + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['136d91bc269a9a5785e5f9e980bc76ab57428f604ce3e5a5a90cebc767971cc6'] + +local_common_configopts = "--with-shared --enable-overwrite --without-ada --enable-symlinks --with-versioned-syms " +configopts = [ + # build ncurses: serial build in default paths with shared libraries + local_common_configopts + "--disable-widec", + # build ncursesw: serial with UTF-8 + local_common_configopts + "--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/", +] + +# need to take care of $CFLAGS ourselves with SYSTEM toolchain +# we need to add -fPIC, but should also include -O* option to avoid compiling with -O0 (default for GCC) +buildopts = 'CFLAGS="-O2 -fPIC"' + +# Symlink libtinfo to libncurses +# libncurses with this configopts has all the symbols from libtinfo, but some packages look for libtinfo specifically +postinstallcmds = ['cd %(installdir)s/lib && for l in libncurses{.,_,w}*; do ln -s "${l}" "${l/ncurses/tinfo}"; done'] + +_target_suffix = ['', 'w'] # '': ncurses, 'w': ncursesw +_lib_suffix = ['%s%s' % (x, y) for x in _target_suffix for y in ['.a', '_g.a', '.' + SHLIB_EXT]] +_lib_names = ['form', 'menu', 'ncurses', 'panel', 'tinfo'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses%(version_major)s-config", + "reset", "tabs", "tic", "toe", "tput", "tset"]] + + ['lib/lib%s%s' % (x, y) for x in _lib_names for y in _lib_suffix] + + ['lib/libncurses++%s.a' % x for x in _target_suffix], + 'dirs': ['include', 'include/ncursesw'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/nellie/nellie-0.3.1-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/n/nellie/nellie-0.3.1-foss-2023a-CUDA-12.1.1.eb new file mode 100644 index 00000000000..35d0c5778dd --- /dev/null +++ b/easybuild/easyconfigs/n/nellie/nellie-0.3.1-foss-2023a-CUDA-12.1.1.eb @@ -0,0 +1,55 @@ +easyblock = 'PythonBundle' + +name = 'nellie' +version = '0.3.1' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/aelefebv/nellie/' +description = """ +Napari plugin for automated organelle segmentation, +tracking, and hierarchical feature extraction in 2D/3D live-cell microscopy. +""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('CUDA', '12.1.1', '', SYSTEM), + ('SciPy-bundle', '2023.07'), + ('napari', '0.4.18'), + ('scikit-image', '0.22.0'), + ('imagecodecs', '2024.1.1'), + ('matplotlib', '3.7.2'), + ('ome-types', '0.5.1.post1'), + ('CuPy', '13.0.0', versionsuffix), +] + +use_pip = True +sanity_pip_check = True + +local_preinstallopts = ( + "sed -i" + " -e 's/numpy==1.26.4/numpy/'" + " -e 's/scipy==1.12.0/scipy/'" + " -e 's/nd2==0.9.0/nd2/'" + " -e 's/pandas==2.2.1/pandas/'" + " -e 's/matplotlib==3.8.3/matplotlib/'" + " -e 's/napari[all]/napari/'" + " setup.cfg && " +) + +exts_list = [ + ('resource_backed_dask_array', '0.1.0', { + 'checksums': ['8fabcccf5c7e29059b5badd6786dd7675a258a203c58babf10077d9c90ada54f'], + }), + ('nd2', '0.10.1', { + 'checksums': ['88ee60f6ba39392722a162da58fb81bf0cdb8ed6c772772e4db91e90f97e490a'], + }), + (name, version, { + 'preinstallopts': local_preinstallopts, + 'checksums': ['3fd85bd1c7df5a8f24bff2118805cd7c82140b08871d520b2131d4d9a8c00d94'], + }), +] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/n/nellie/nellie-0.3.1-foss-2023a.eb b/easybuild/easyconfigs/n/nellie/nellie-0.3.1-foss-2023a.eb new file mode 100644 index 00000000000..34b3ce6299a --- /dev/null +++ b/easybuild/easyconfigs/n/nellie/nellie-0.3.1-foss-2023a.eb @@ -0,0 +1,52 @@ +easyblock = 'PythonBundle' + +name = 'nellie' +version = '0.3.1' + +homepage = 'https://github.com/aelefebv/nellie/' +description = """ +Napari plugin for automated organelle segmentation, +tracking, and hierarchical feature extraction in 2D/3D live-cell microscopy. +""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('SciPy-bundle', '2023.07'), + ('napari', '0.4.18'), + ('scikit-image', '0.22.0'), + ('imagecodecs', '2024.1.1'), + ('matplotlib', '3.7.2'), + ('ome-types', '0.5.1.post1'), +] + +use_pip = True +sanity_pip_check = True + +local_preinstallopts = ( + "sed -i" + " -e 's/numpy==1.26.4/numpy/'" + " -e 's/scipy==1.12.0/scipy/'" + " -e 's/nd2==0.9.0/nd2/'" + " -e 's/pandas==2.2.1/pandas/'" + " -e 's/matplotlib==3.8.3/matplotlib/'" + " -e 's/napari[all]/napari/'" + " setup.cfg && " +) + +exts_list = [ + ('resource_backed_dask_array', '0.1.0', { + 'checksums': ['8fabcccf5c7e29059b5badd6786dd7675a258a203c58babf10077d9c90ada54f'], + }), + ('nd2', '0.10.1', { + 'checksums': ['88ee60f6ba39392722a162da58fb81bf0cdb8ed6c772772e4db91e90f97e490a'], + }), + (name, version, { + 'preinstallopts': local_preinstallopts, + 'checksums': ['3fd85bd1c7df5a8f24bff2118805cd7c82140b08871d520b2131d4d9a8c00d94'], + }), +] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/n/netCDF-C++4/netCDF-C++4-4.3.1-gompi-2024a.eb b/easybuild/easyconfigs/n/netCDF-C++4/netCDF-C++4-4.3.1-gompi-2024a.eb new file mode 100644 index 00000000000..909bd06a674 --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF-C++4/netCDF-C++4-4.3.1-gompi-2024a.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'netCDF-C++4' +version = '4.3.1' + +homepage = 'https://www.unidata.ucar.edu/software/netcdf/' +description = """NetCDF (network Common Data Form) is a set of software libraries + and machine-independent data formats that support the creation, access, and sharing of array-oriented + scientific data.""" + +toolchain = {'name': 'gompi', 'version': '2024a'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/Unidata/netcdf-cxx4/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['e3fe3d2ec06c1c2772555bf1208d220aab5fee186d04bd265219b0bc7a978edc'] + +dependencies = [ + ('netCDF', '4.9.2'), +] + + +sanity_check_paths = { + 'files': ['include/netcdf', 'lib/libnetcdf_c++4.a', 'lib/libnetcdf_c++4.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.6.1-gompi-2024a.eb b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.6.1-gompi-2024a.eb new file mode 100644 index 00000000000..2bc6e207794 --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.6.1-gompi-2024a.eb @@ -0,0 +1,28 @@ +name = 'netCDF-Fortran' +version = '4.6.1' + +homepage = 'https://www.unidata.ucar.edu/software/netcdf/' +description = """NetCDF (network Common Data Form) is a set of software libraries + and machine-independent data formats that support the creation, access, and sharing of array-oriented + scientific data.""" + +toolchain = {'name': 'gompi', 'version': '2024a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://github.com/Unidata/%(namelower)s/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['40b534e0c81b853081c67ccde095367bd8a5eead2ee883431331674e7aa9509f'] + +builddependencies = [ + ('M4', '1.4.19'), +] +dependencies = [ + ('netCDF', '4.9.2'), + ('bzip2', '1.0.8'), +] + +# (too) parallel build fails, but single-core build is fairly quick anyway (~1min) +parallel = 1 + + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.9.2-gompi-2024a.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.9.2-gompi-2024a.eb new file mode 100644 index 00000000000..95e48775eeb --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.9.2-gompi-2024a.eb @@ -0,0 +1,54 @@ +name = 'netCDF' +version = '4.9.2' + +homepage = 'https://www.unidata.ucar.edu/software/netcdf/' +description = """NetCDF (network Common Data Form) is a set of software libraries + and machine-independent data formats that support the creation, access, and sharing of array-oriented + scientific data.""" + +toolchain = {'name': 'gompi', 'version': '2024a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://github.com/Unidata/%(namelower)s-c/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = ['%(name)s-%(version_major_minor)s.0_skip-nasa-test.patch'] +checksums = [ + {'v4.9.2.tar.gz': 'bc104d101278c68b303359b3dc4192f81592ae8640f1aee486921138f7f88cb7'}, + {'%(name)s-%(version_major_minor)s.0_skip-nasa-test.patch': + '19d99e03c048b037dc01f03f5b8ddc910ebaceb076d0f050540d348f26dfcd2a'}, +] + +builddependencies = [ + ('Autotools', '20231222'), + ('CMake', '3.29.3'), + ('Doxygen', '1.11.0'), +] +dependencies = [ + ('HDF5', '1.14.5'), + ('cURL', '8.7.1'), + ('Szip', '2.1.1'), + ('zstd', '1.5.6'), + ('bzip2', '1.0.8'), + ('libxml2', '2.12.7'), +] + +# disable Szip, zlib parallel I/O tests, since these can hang on some systems, e.g. generoso +# see: https://github.com/easybuilders/easybuild-easyconfigs/pull/16834 +# and https://github.com/easybuilders/easybuild-easyconfigs/pull/17107#issuecomment-1432947172 +preconfigopts = ("sed -i -e 's|@MPIEXEC@ -n 4 ./tst_parallel5|echo \"skipped by EasyBuild\"|g'" + " -e 's|@MPIEXEC@ -n 4 ./tst_parallel_zlib|echo \"skipped by EasyBuild\"|g'" + " -e 's|@MPIEXEC@ -n 4 ./tst_parallel_compress|echo \"skipped by EasyBuild\"|g'" + " %(builddir)s/%(namelower)s-c-%(version)s/nc_test4/run_par_test.sh.in &&") + +# make sure both static and shared libs are built +# and disable "remote" tests that access a unreliable external test server over internet +configopts = [ + "-DENABLE_DAP_REMOTE_TESTS=OFF -DBUILD_SHARED_LIBS=OFF", + "-DENABLE_DAP_REMOTE_TESTS=OFF -DBUILD_SHARED_LIBS=ON", +] + +# some tests try to start 16 MPI ranks, so we need to allow oversubscription to avoid failing tests +pretestopts = "PRTE_MCA_rmaps_default_mapping_policy=:oversubscribe " +runtest = 'test' + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.7.1.post2-foss-2024a.eb b/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.7.1.post2-foss-2024a.eb new file mode 100644 index 00000000000..912e23a55b7 --- /dev/null +++ b/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.7.1.post2-foss-2024a.eb @@ -0,0 +1,58 @@ +easyblock = 'PythonBundle' + +name = 'netcdf4-python' +version = '1.7.1.post2' + + +homepage = 'https://unidata.github.io/netcdf4-python/' +description = "Python/numpy interface to netCDF." + +toolchain = {'name': 'foss', 'version': '2024a'} +toolchainopts = {'usempi': True} + +builddependencies = [ + ('Cython', '3.0.10'), +] + +dependencies = [ + ('Python', '3.12.3'), + ('SciPy-bundle', '2024.05'), + ('netCDF', '4.9.2'), + ('cURL', '8.7.1'), + ('mpi4py', '4.0.1'), +] + +fix_python_shebang_for = ['bin/*'] +sanity_pip_check = True +use_pip = True + +exts_list = [ + ('cftime', '1.6.4', { + 'checksums': ['e325406193758a7ed67308deb52e727782a19e384e183378e7ff62098be0aedc'], + }), + (name, version, { + 'patches': [ + 'netcdf4-python-1.7.1.post2_relax_tolerance_compression_test.patch', + ], + 'source_tmpl': 'netcdf4-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/n/netCDF4'], + 'checksums': [ + {'netcdf4-1.7.1.post2.tar.gz': '37d557e36654889d7020192bfb56f9d5f93894cb32997eb837ae586c538fd7b6'}, + {'netcdf4-python-1.7.1.post2_relax_tolerance_compression_test.patch': + '7faa7e839ad1e816ffd0153e4b76b43ebce3e14d35f0534f812168dfaa78316c'}, + ], + }), +] + +sanity_check_paths = { + 'files': ['bin/nc3tonc4', 'bin/nc4tonc3', 'bin/ncinfo'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "nc4tonc3 --help", + "nc3tonc4 --help", + "ncinfo --help", +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.7.1.post2_relax_tolerance_compression_test.patch b/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.7.1.post2_relax_tolerance_compression_test.patch new file mode 100644 index 00000000000..be4deb77f96 --- /dev/null +++ b/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.7.1.post2_relax_tolerance_compression_test.patch @@ -0,0 +1,15 @@ +# Relax tolerance in the compression_szip test to avoid fails on some systems. +# author: maxim-masterov (SURF) +# +diff -Nru netcdf4-1.7.1.post2.orig/test/test_compression_szip.py netcdf4-1.7.1.post2/test/test_compression_szip.py +--- netcdf4-1.7.1.post2.orig/test/test_compression_szip.py 2024-10-07 16:01:21.276893761 +0200 ++++ netcdf4-1.7.1.post2/test/test_compression_szip.py 2024-10-07 16:27:47.424436617 +0200 +@@ -35,7 +35,7 @@ + assert_almost_equal(datarr,f.variables['data'][:]) + assert f.variables['data'].filters() ==\ + {'zlib':False,'szip':False,'zstd':False,'bzip2':False,'blosc':False,'shuffle':False,'complevel':0,'fletcher32':False} +- assert_almost_equal(datarr,f.variables['data_szip'][:]) ++ assert_almost_equal(datarr,f.variables['data_szip'][:], 6) + dtest = {'zlib': False, 'szip': {'coding': 'ec', 'pixels_per_block': 32}, 'zstd': False, 'bzip2': False, 'blosc': False, 'shuffle': False, 'complevel': 0, 'fletcher32': False} + assert f.variables['data_szip'].filters() == dtest + f.close() diff --git a/easybuild/easyconfigs/n/nettle/nettle-3.10-GCCcore-13.3.0.eb b/easybuild/easyconfigs/n/nettle/nettle-3.10-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..ef91cf135fe --- /dev/null +++ b/easybuild/easyconfigs/n/nettle/nettle-3.10-GCCcore-13.3.0.eb @@ -0,0 +1,38 @@ +easyblock = 'ConfigureMake' + +name = 'nettle' +version = '3.10' + +homepage = 'https://www.lysator.liu.se/~nisse/nettle/' +description = """Nettle is a cryptographic library that is designed to fit easily + in more or less any context: In crypto toolkits for object-oriented + languages (C++, Python, Pike, ...), in applications like LSH or GNUPG, + or even in kernel space.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['b4c518adb174e484cb4acea54118f02380c7133771e7e9beb98a0787194ee47c'] + +builddependencies = [ + ('binutils', '2.42'), + ('Autotools', '20231222'), +] + +dependencies = [ + ('GMP', '6.3.0'), +] + +configopts = '--disable-openssl ' # openssl is just used for the nettle-openssl example and requires openssl 1.1 + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['nettle-hash', 'nettle-lfib-stream', 'pkcs1-conv', 'sexp-conv']] + + [('lib/libhogweed.a', 'lib64/libhogweed.a'), + ('lib/libhogweed.%s' % SHLIB_EXT, 'lib64/libhogweed.%s' % SHLIB_EXT), + ('lib/libnettle.a', 'lib64/libnettle.a'), + ('lib/libnettle.%s' % SHLIB_EXT, 'lib64/libnettle.%s' % SHLIB_EXT)], + 'dirs': ['include/nettle'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/networkx/networkx-3.1-gfbf-2023a.eb b/easybuild/easyconfigs/n/networkx/networkx-3.1-gfbf-2023a.eb index 2cef5135036..03fe29675fd 100644 --- a/easybuild/easyconfigs/n/networkx/networkx-3.1-gfbf-2023a.eb +++ b/easybuild/easyconfigs/n/networkx/networkx-3.1-gfbf-2023a.eb @@ -10,7 +10,11 @@ and study of the structure, dynamics, and functions of complex networks.""" toolchain = {'name': 'gfbf', 'version': '2023a'} sources = [SOURCE_TAR_GZ] -checksums = ['de346335408f84de0eada6ff9fafafff9bcda11f0a0dfaa931133debb146ab61'] +patches = ['networkx-3.1_zero_division.patch'] +checksums = [ + {'networkx-3.1.tar.gz': 'de346335408f84de0eada6ff9fafafff9bcda11f0a0dfaa931133debb146ab61'}, + {'networkx-3.1_zero_division.patch': 'fb225e9942f18c87c67b49093b86e9f949e043fdf2f3c1ed467b6d3ad857aa35'}, +] dependencies = [ ('Python', '3.11.3'), diff --git a/easybuild/easyconfigs/n/networkx/networkx-3.1_zero_division.patch b/easybuild/easyconfigs/n/networkx/networkx-3.1_zero_division.patch new file mode 100644 index 00000000000..3110ca55530 --- /dev/null +++ b/easybuild/easyconfigs/n/networkx/networkx-3.1_zero_division.patch @@ -0,0 +1,42 @@ +Fixes the zero division bug `ZeroDivisionError: division by zero` +patch source: https://github.com/networkx/networkx/pull/6791 + +From 6e47bef10ba7c17514b0cbd2ec27c1f58ca21200 Mon Sep 17 00:00:00 2001 +From: juanis2112 +Date: Sat, 15 Jul 2023 14:22:02 -0500 +Subject: [PATCH] Fix empty graph zero division error for louvain + +--- + networkx/algorithms/community/louvain.py | 3 +++ + networkx/algorithms/community/tests/test_louvain.py | 7 +++++++ + 2 files changed, 10 insertions(+) + +diff --git a/networkx/algorithms/community/louvain.py b/networkx/algorithms/community/louvain.py +index ca71c0c30cb..94a8f7c98b9 100644 +--- a/networkx/algorithms/community/louvain.py ++++ b/networkx/algorithms/community/louvain.py +@@ -163,6 +163,9 @@ def louvain_partitions( + """ + + partition = [{u} for u in G.nodes()] ++ if nx.is_empty(G): ++ yield partition ++ return + mod = modularity(G, partition, resolution=resolution, weight=weight) + is_directed = G.is_directed() + if G.is_multigraph(): +diff --git a/networkx/algorithms/community/tests/test_louvain.py b/networkx/algorithms/community/tests/test_louvain.py +index ed5c2a38db6..e4942dfeb58 100644 +--- a/networkx/algorithms/community/tests/test_louvain.py ++++ b/networkx/algorithms/community/tests/test_louvain.py +@@ -185,3 +185,10 @@ def test_threshold(): + mod2 = nx.community.modularity(G, partition2) + + assert mod1 < mod2 ++ ++ ++def test_empty_graph(): ++ G = nx.Graph() ++ G.add_nodes_from(range(5)) ++ expected = [{0}, {1}, {2}, {3}, {4}] ++ assert nx.community.louvain_communities(G) == expected diff --git a/easybuild/easyconfigs/n/networkx/networkx-3.4.2-gfbf-2024a.eb b/easybuild/easyconfigs/n/networkx/networkx-3.4.2-gfbf-2024a.eb new file mode 100644 index 00000000000..9adfd4d5246 --- /dev/null +++ b/easybuild/easyconfigs/n/networkx/networkx-3.4.2-gfbf-2024a.eb @@ -0,0 +1,24 @@ +easyblock = 'PythonPackage' + +name = 'networkx' +version = '3.4.2' + +homepage = 'https://pypi.python.org/pypi/networkx' +description = """NetworkX is a Python package for the creation, manipulation, +and study of the structure, dynamics, and functions of complex networks.""" + +toolchain = {'name': 'gfbf', 'version': '2024a'} + +sources = [SOURCE_TAR_GZ] +checksums = ['307c3669428c5362aab27c8a1260aa8f47c4e91d3891f48be0141738d8d053e1'] + +dependencies = [ + ('Python', '3.12.3'), + ('SciPy-bundle', '2024.05'), # required for numpy, scipy, ... +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/n/nf-core/nf-core-2.14.1-foss-2024a.eb b/easybuild/easyconfigs/n/nf-core/nf-core-2.14.1-foss-2024a.eb new file mode 100644 index 00000000000..5b64c454d51 --- /dev/null +++ b/easybuild/easyconfigs/n/nf-core/nf-core-2.14.1-foss-2024a.eb @@ -0,0 +1,76 @@ +easyblock = 'PythonBundle' + +name = 'nf-core' +version = '2.14.1' + +homepage = 'https://github.com/nf-core/tools' +description = "Python package with helper tools for the nf-core community." + +toolchain = {'name': 'foss', 'version': '2024a'} + +builddependencies = [ + ('poetry', '1.8.3'), + ('PDM', '2.18.2'), +] +dependencies = [ + ('Python', '3.12.3'), + ('Python-bundle-PyPI', '2024.06'), + ('SciPy-bundle', '2024.05'), + ('GitPython', '3.1.43'), + ('Markdown', '3.7'), + ('Pillow', '10.4.0'), + ('prompt-toolkit', '3.0.36'), + ('pydantic', '2.9.1'), + ('pyfaidx', '0.8.1.2'), + ('pytest-workflow', '2.1.0'), + ('PyYAML', '6.0.2'), + ('tqdm', '4.66.5'), +] + +sanity_pip_check = True +use_pip = True + +exts_list = [ + ('humanfriendly', '10.0', {'checksums': ['6b0b831ce8f15f7300721aa49829fc4e83921a9a301cc7f606be6686a2288ddc']}), + ('coloredlogs', '15.0.1', {'checksums': ['7c991aa71a4577af2f82600d8f8f3a89f936baeaf9b50a9c197da014e5bf16b0']}), + ('typer', '0.12.5', {'checksums': ['f592f089bedcc8ec1b974125d64851029c3b1af145f04aca64d69410f0c9b722']}), + ('pephubclient', '0.4.4', {'checksums': ['0723b84f165024a08885057b80daa314987474ac6be04cb34e4b0611e7b91561']}), + ('peppy', '0.40.6', {'checksums': ['a872bf22da2ac9d2e60ea01fdac5a092618957e937d5620f8ba8cd8e552509fb']}), + ('eido', '0.2.3', {'checksums': ['c4e5cb2c8c4d7ae1812afbeafde0737c24cfdee21b22d45af5967c7b6848b565']}), + ('attmap', '0.13.2', {'checksums': ['fdffa45f8671c13428eb8c3a1702bfdd1123badb99f7af14d72ad53cc7e770de']}), + ('oyaml', '1.0', {'checksums': ['ed8fc096811f4763e1907dce29c35895d6d5936c4d0400fe843a91133d4744ed']}), + ('cattrs', '24.1.1', {'checksums': ['16e94a13f9aaf6438bd5be5df521e072b1b00481b4cf807bcb1acbd49f814c08']}), + ('yacman', '0.9.3', {'checksums': ['91f29ecad7abf32425be034619bd5b00a50fe2be23447b1827c34e1fd68c055d']}), + ('pipestat', '0.10.2', {'checksums': ['274cd7ddf44b1750fce854953c4b8d5cde36a23cb73597136442d05bc5a9acaa']}), + ('ubiquerg', '0.8.0', {'checksums': ['3dd8e817c736e45c563bbf9e0d9b252e2a0456729c5644203376a447ffc7e04f']}), + ('cfgv', '3.4.0', {'checksums': ['e52591d4c5f5dead8e0f673fb16db7949d2cfb3f7da4582893288f0ded8fe560']}), + ('nodeenv', '1.9.1', {'checksums': ['6ec12890a2dab7946721edbfbcd91f3319c6ccc9aec47be7c7e6b7011ee6645f']}), + ('logmuse', '0.2.8', {'checksums': ['a639d795f33d6876766033dea3c4ceb51617029e5f6e0aa390e7c4bc3012624d']}), + ('textual', '0.79.1', {'checksums': ['2aaa9778beac5e56957794ee492bd8d281d39516ccb0e507e726484a1327d8b2']}), + ('refgenconf', '0.12.2', {'checksums': ['6c9f9ecd8b91b4f75a535cfbdbdfb136f2dc9e9864142d07aa0352c61cf0cf78']}), + ('piper', '0.14.2', { + 'modulename': 'pypiper', + 'checksums': ['fff74a6e7cbf188a3ce023913a9ce63098e7c3acfa73833fd9e4c4096a578035'], + }), + ('url-normalize', '1.4.3', {'checksums': ['d23d3a070ac52a67b83a1c59a0e68f8608d1cd538783b401bc9de2c0fac999b2']}), + ('identify', '2.6.0', {'checksums': ['cb171c685bdc31bcc4c1734698736a7d5b6c8bf2e0c15117f4d469c8640ae5cf']}), + ('questionary', '2.0.1', {'checksums': ['bcce898bf3dbb446ff62830c86c5c6fb9a22a54146f0f5597d3da43b10d8fc8b']}), + ('pdiff', '1.1.4', {'checksums': ['9d8f6f8e7ed2ee61aa2f2526106c0047a2bd80eab7d1237f7086139a6e921c45']}), + ('filetype', '1.2.0', {'checksums': ['66b56cd6474bf41d8c54660347d37afcc3f7d1970648de365c102ef77548aadb']}), + ('requests-cache', '1.2.1', { + 'source_tmpl': 'requests_cache-%(version)s.tar.gz', + 'checksums': ['68abc986fdc5b8d0911318fbb5f7c80eebcd4d01bfacc6685ecf8876052511d1'], + }), + ('trogon', '0.5.0', {'checksums': ['61a57f0f1a38227d90601cd020f46960be8e36947b5e56c6932c2e01ecc5042a']}), + ('pre-commit', '3.8.0', { + 'source_tmpl': 'pre_commit-%(version)s.tar.gz', + 'checksums': ['8bb6494d4a20423842e198980c9ecf9f96607a07ea29549e180eef9ae80fe7af'], + }), + ('refgenie', '0.12.1', {'checksums': ['cfd007ed0981e00d019deb49aaea896952341096494165cb8378488850eec451']}), + (name, version, { + 'source_tmpl': 'nf_core-%(version)s.tar.gz', + 'checksums': ['35bd8d73ecca4eb87443fada31bc7b2562429de3a4bfbf7261db348d14bf54bb'], + }), +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/n/nghttp2/nghttp2-1.58.0-GCC-12.3.0.eb b/easybuild/easyconfigs/n/nghttp2/nghttp2-1.58.0-GCC-12.3.0.eb new file mode 100644 index 00000000000..95087f63a51 --- /dev/null +++ b/easybuild/easyconfigs/n/nghttp2/nghttp2-1.58.0-GCC-12.3.0.eb @@ -0,0 +1,55 @@ +# Author: J. Sassmannshausen (Imperial College London/UK) +# Update: Pavel Tománek (Inuits) + +easyblock = 'CMakeMake' + +name = 'nghttp2' +version = '1.58.0' + +homepage = 'https://github.com/nghttp2/nghttp2' +description = """ +This is an implementation of the Hypertext Transfer Protocol version 2 in C. + +The framing layer of HTTP/2 is implemented as a reusable C library. +On top of that, we have implemented an HTTP/2 client, server and proxy. +We have also developed load test and benchmarking tools for HTTP/2. + +An HPACK encoder and decoder are available as a public API.""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +github_account = 'nghttp2' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['7da19947b33a07ddcf97b9791331bfee8a8545e6b394275a9971f43cae9d636b'] + +builddependencies = [ + ('binutils', '2.40'), + ('pkgconf', '1.9.5'), + ('CMake', '3.26.3'), + ('CUnit', '2.1-3'), + ('Boost', '1.82.0'), +] + +dependencies = [ + ('OpenSSL', '1.1', '', SYSTEM), + ('nghttp3', '1.3.0'), + ('Python', '3.11.3'), + ('libxml2', '2.11.4'), + ('Jansson', '2.14'), + ('jemalloc', '5.3.0'), + ('ngtcp2', '1.2.0'), + ('libevent', '2.1.12'), + ('libev', '4.33'), + ('c-ares', '1.19.1'), +] + +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libnghttp2.%s' % SHLIB_EXT], + 'dirs': ['include/nghttp2', 'share'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/nghttp3/nghttp3-1.3.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/n/nghttp3/nghttp3-1.3.0-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..5800863a567 --- /dev/null +++ b/easybuild/easyconfigs/n/nghttp3/nghttp3-1.3.0-GCCcore-12.3.0.eb @@ -0,0 +1,43 @@ +easyblock = 'CMakeMake' + +name = 'nghttp3' +version = '1.3.0' + +homepage = 'https://github.com/ngtcp2/nghttp3' +description = """ nghttp3 is an implementation of RFC 9114 HTTP/3 +mapping over QUIC and RFC 9204 QPACK in C. +It does not depend on any particular QUIC transport implementation.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +# github_account = 'ngtcp2' +# source_urls = [GITHUB_SOURCE] +# sources = ['v%(version)s.tar.gz'] +sources = [{ + 'filename': 'v%(version)s.tar.gz', + 'git_config': { + 'url': 'https://github.com/ngtcp2', + 'repo_name': 'nghttp3', + 'tag': 'v%(version)s', + 'recursive': True, + 'keep_git_dir': True, + } +}] +checksums = [None] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.26.3'), + ('pkgconf', '1.9.5'), + ('CUnit', '2.1-3'), +] + +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libnghttp3.a', 'lib/libnghttp3.%s' % SHLIB_EXT], + 'dirs': ['include/nghttp3'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/nglview/nglview-3.1.2-foss-2023a.eb b/easybuild/easyconfigs/n/nglview/nglview-3.1.2-foss-2023a.eb new file mode 100644 index 00000000000..55899477fd5 --- /dev/null +++ b/easybuild/easyconfigs/n/nglview/nglview-3.1.2-foss-2023a.eb @@ -0,0 +1,37 @@ +easyblock = 'PythonBundle' + +name = 'nglview' +version = '3.1.2' + +homepage = 'https://github.com/arose/nglview' +description = "IPython widget to interactively view molecular structures and trajectories." + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [ + ('nodejs', '18.17.1'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('JupyterNotebook', '7.0.2'), + ('ASE', '3.22.1'), # optional + ('MDAnalysis', '2.7.0'), # optional + ('MDTraj', '1.9.9'), # optional +] + +use_pip = True + +exts_list = [ + (name, version, { + 'use_pip_extras': 'ase,MDAnalysis,mdtraj', + 'checksums': ['7f672efa2b6ca0db34de968e5b5766b14b1b3dade212d2f8a083c600a11345ce'], + }), +] + +sanity_pip_check = True + +modextrapaths = {'EB_ENV_JUPYTER_ROOT': ''} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/n/ngmlr/ngmlr-0.2.7-foss-2023a.eb b/easybuild/easyconfigs/n/ngmlr/ngmlr-0.2.7-foss-2023a.eb new file mode 100644 index 00000000000..ca0401d69c7 --- /dev/null +++ b/easybuild/easyconfigs/n/ngmlr/ngmlr-0.2.7-foss-2023a.eb @@ -0,0 +1,31 @@ +easyblock = 'CMakeMake' + +name = 'ngmlr' +version = '0.2.7' + +homepage = 'https://github.com/philres/ngmlr' +description = """Ngmlr is a long-read mapper designed to align PacBilo or Oxford Nanopore to a + reference genome with a focus on reads that span structural variations.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['https://github.com/philres/ngmlr/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['5126a6b3e726cac0da0713883daac688f38587f118428247a9a3ace5a55b29aa'] + +builddependencies = [ + ('CMake', '3.26.3'), +] + +dependencies = [ + ('zlib', '1.2.13'), +] + +sanity_check_paths = { + 'files': ['bin/ngmlr'], + 'dirs': [''] +} + +sanity_check_commands = ['%(name)s --help'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/n/ngtcp2/ngtcp2-1.2.0-GCC-12.3.0.eb b/easybuild/easyconfigs/n/ngtcp2/ngtcp2-1.2.0-GCC-12.3.0.eb new file mode 100644 index 00000000000..67309cf83e2 --- /dev/null +++ b/easybuild/easyconfigs/n/ngtcp2/ngtcp2-1.2.0-GCC-12.3.0.eb @@ -0,0 +1,45 @@ +# Author: J. Sassmannshausen (Imperial College London/UK) +# Update: P.Tománek (Inuits) + +easyblock = 'CMakeMake' + +name = 'ngtcp2' +version = '1.2.0' + +homepage = 'https://github.com/ngtcp2/ngtcp2' +description = """ +'Call it TCP/2. One More Time.' + +ngtcp2 project is an effort to implement RFC9000 QUIC protocol.""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +github_account = 'ngtcp2' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['15f3dd4cc4db2435bcd0b5253ccce4cbab26d18cc6ef4f00b5cb4af21ed06a0b'] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.26.3'), + ('CUnit', '2.1-3'), +] + +dependencies = [ + ('OpenSSL', '1.1', '', SYSTEM), + ('GnuTLS', '3.7.8'), + ('nghttp3', '1.3.0'), + ('libev', '4.33'), +] + +configopts = '-DENABLE_GNUTLS=True' + +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libngtcp2.%s' % SHLIB_EXT], + 'dirs': ['share/doc/ngtcp2'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/nifty/nifty-1.2.1-foss-2023a.eb b/easybuild/easyconfigs/n/nifty/nifty-1.2.1-foss-2023a.eb new file mode 100644 index 00000000000..37d6c62dec7 --- /dev/null +++ b/easybuild/easyconfigs/n/nifty/nifty-1.2.1-foss-2023a.eb @@ -0,0 +1,54 @@ +easyblock = 'CMakeMakeCp' + +name = 'nifty' +version = '1.2.1' + +homepage = 'https://github.com/DerThorsten/nifty/' +description = """A nifty library for 2D and 3D image segmentation, graph based segmentation an opt. +This library provided building blocks for segmentation algorithms and complex segmentation pipelines.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['https://github.com/DerThorsten/nifty/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['a5fd611463336ba18be828da3154da8828b6486603e2a04f14a4520cb357661a'] + +builddependencies = [('CMake', '3.26.3')] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('Boost', '1.82.0'), + ('h5py', '3.9.0'), + ('nlohmann_json', '3.11.2'), + ('scikit-image', '0.22.0'), + ('vigra', '1.11.2'), + ('xtensor', '0.24.7'), + ('zlib', '1.2.13'), + ('HDF5', '1.14.0'), +] + +# Add flags (nifty/.github/workflows/build_unix.sh) +configopts = '-DWITH_QPBO=OFF -DWITH_HDF5=ON -DWITH_Z5=OFF -DWITH_ZLIB=ON -DWITH_CPLEX=OFF -DWITH_GUROBI=OFF ' +# Fix path to python executable - it finds v3.6.8 from /usr/bin/ without this fix +configopts += '-DPYTHON_EXECUTABLE="$EBROOTPYTHON/bin/python" -DBUILD_NIFTY_PYTHON=ON ' + +# export PYTHON_MODULE_INSTALL_DIR to fix make install +preinstallopts = 'export PYTHON_MODULE_INSTALL_DIR="%(builddir)s/easybuild_obj/python/" && ' + +files_to_copy = [(['python/nifty'], 'lib/python%(pyshortver)s/site-packages')] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/nifty'], +} + +sanity_check_commands = [ + "python -c 'import nifty'", + "python -c 'from nifty.graph import UndirectedGraph'", + "python -c 'import nifty.tools'", +] + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/n/nlohmann_json/nlohmann_json-3.11.3-GCCcore-13.3.0.eb b/easybuild/easyconfigs/n/nlohmann_json/nlohmann_json-3.11.3-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..8be75746afa --- /dev/null +++ b/easybuild/easyconfigs/n/nlohmann_json/nlohmann_json-3.11.3-GCCcore-13.3.0.eb @@ -0,0 +1,25 @@ +easyblock = 'CMakeMake' + +name = 'nlohmann_json' +version = '3.11.3' + +homepage = 'https://github.com/nlohmann/json' +description = """JSON for Modern C++""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://github.com/nlohmann/json/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['0d8ef5af7f9794e3263480193c491549b2ba6cc74bb018906202ada498a79406'] + +builddependencies = [ + ('binutils', '2.42'), + ('CMake', '3.29.3'), +] + +sanity_check_paths = { + 'files': ['include/nlohmann/json.hpp'], + 'dirs': ['share/cmake', 'share/pkgconfig'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/nodejs/nodejs-20.13.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/n/nodejs/nodejs-20.13.1-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..b49990e46e7 --- /dev/null +++ b/easybuild/easyconfigs/n/nodejs/nodejs-20.13.1-GCCcore-13.3.0.eb @@ -0,0 +1,54 @@ +easyblock = 'ConfigureMake' + +name = 'nodejs' +version = '20.13.1' # LTS on 2024-05-24 +local_libversion = '115' + +homepage = 'https://nodejs.org' +description = """Node.js is a platform built on Chrome's JavaScript runtime + for easily building fast, scalable network applications. Node.js uses an + event-driven, non-blocking I/O model that makes it lightweight and efficient, + perfect for data-intensive real-time applications that run across distributed devices.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://nodejs.org/dist/v%(version)s/'] +sources = ['node-v%(version)s.tar.gz'] +checksums = ['a85ee53aa0a5c2f5ca94fa414cdbceb91eb7d18a77fc498358512c14cc6c6991'] + +builddependencies = [ + ('binutils', '2.42'), + ('Python', '3.12.3'), + ('pkgconf', '2.2.0'), +] + +dependencies = [ + ('ICU', '75.1'), + ('OpenSSL', '3', '', SYSTEM), +] + +# Use ICU and OpenSSL from EasyBuild +local_common_configopts = "--with-intl=system-icu --shared-openssl " + +configopts = [ + local_common_configopts, # Static build + '--shared %s' % local_common_configopts, # Build libnode.so in a second run +] + +# Link libv8 libs to libnode +local_extra_sonames = ['libnode', 'libv8', 'libv8_libbase', 'libv8_libplatform'] +local_extra_libs = ['%s.%s' % (x, SHLIB_EXT) for x in local_extra_sonames] +local_libnode_real = "libnode.%s.%s" % (SHLIB_EXT, local_libversion) + +postinstallcmds = [ + "cd %%(installdir)s/lib && ln -s %s %s" % (local_libnode_real, x) for x in local_extra_libs +] + +sanity_check_paths = { + 'files': ['bin/node', 'bin/npm'] + ['lib/%s' % x for x in [local_libnode_real] + local_extra_libs], + 'dirs': ['lib/node_modules', 'include/node'] +} + +sanity_check_commands = ["node --help"] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/n/nose3/nose3-1.3.8-GCCcore-12.2.0.eb b/easybuild/easyconfigs/n/nose3/nose3-1.3.8-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..3fb61c98db7 --- /dev/null +++ b/easybuild/easyconfigs/n/nose3/nose3-1.3.8-GCCcore-12.2.0.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonPackage' + +name = 'nose3' +version = '1.3.8' + +homepage = 'https://nose.readthedocs.io/' +description = """Nose extends unittest to make testing easier.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['762aae22cadb898b00b9d4f4bbb9f8e87f8e0dde6c49a88cd0c554f4e5925b76'] + +builddependencies = [('binutils', '2.39')] + +dependencies = [ + ('Python', '3.10.8'), + ('coverage', '7.2.3'), +] + +use_pip = True +sanity_pip_check = True +download_dep_fail = True + +sanity_check_paths = { + 'files': ['bin/nosetests'], + 'dirs': [], +} + +options = {'modulename': 'nose'} + +sanity_check_commands = ["nosetests --help"] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/nsync/nsync-1.29.2-GCCcore-13.3.0.eb b/easybuild/easyconfigs/n/nsync/nsync-1.29.2-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..e7c2035444b --- /dev/null +++ b/easybuild/easyconfigs/n/nsync/nsync-1.29.2-GCCcore-13.3.0.eb @@ -0,0 +1,26 @@ +easyblock = 'CMakeNinja' + +name = 'nsync' +version = '1.29.2' + +homepage = 'https://github.com/google/nsync' +description = """nsync is a C library that exports various synchronization primitives, such as mutexes""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://github.com/google/nsync/archive/refs/tags/'] +sources = ['%(version)s.tar.gz'] +checksums = ['1d63e967973733d2c97e841e3c05fac4d3fa299f01d14c86f2695594c7a4a2ec'] + +builddependencies = [ + ('binutils', '2.42'), + ('CMake', '3.29.3'), + ('Ninja', '1.12.1'), +] + +sanity_check_paths = { + 'files': ['include/nsync.h', 'lib/libnsync.a', 'lib/libnsync_cpp.a'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/numactl/numactl-2.0.18-GCCcore-13.3.0.eb b/easybuild/easyconfigs/n/numactl/numactl-2.0.18-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..119e66afaa7 --- /dev/null +++ b/easybuild/easyconfigs/n/numactl/numactl-2.0.18-GCCcore-13.3.0.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'numactl' +version = '2.0.18' + +homepage = 'https://github.com/numactl/numactl' + +description = """ + The numactl program allows you to run your application program on specific + cpu's and memory nodes. It does this by supplying a NUMA memory policy to + the operating system before running your program. The libnuma library provides + convenient ways for you to add NUMA memory policies into your own program. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/numactl/numactl/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['8cd6c13f3096e9c2293c1d732f56e2aa37a7ada1a98deed3fac7bd6da1aaaaf6'] + +builddependencies = [ + ('binutils', '2.42'), + ('Autotools', '20231222'), +] + +preconfigopts = "./autogen.sh && " + +sanity_check_paths = { + 'files': ['bin/numactl', 'bin/numastat', 'lib/libnuma.%s' % SHLIB_EXT, 'lib/libnuma.a'], + 'dirs': ['share/man', 'include'] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/n/numexpr/numexpr-2.9.0-foss-2023a.eb b/easybuild/easyconfigs/n/numexpr/numexpr-2.9.0-foss-2023a.eb new file mode 100644 index 00000000000..74e99150d4b --- /dev/null +++ b/easybuild/easyconfigs/n/numexpr/numexpr-2.9.0-foss-2023a.eb @@ -0,0 +1,21 @@ +name = 'numexpr' +version = '2.9.0' + +homepage = 'https://numexpr.readthedocs.io/en/latest/' +description = """The numexpr package evaluates multiple-operator array expressions many times faster than NumPy can. + It accepts the expression as a string, analyzes it, rewrites it more efficiently, and compiles it on the fly into + code for its internal virtual machine (VM). Due to its integrated just-in-time (JIT) compiler, it does not require a + compiler at runtime.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['https://github.com/pydata/numexpr/archive/refs/tags'] +sources = ['v%(version)s.tar.gz'] +checksums = ['4df4163fcab20030137e8f2aa23e88e1e42e6fe702387cfd95d7675e1d84645e'] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), +] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/n/numpy/numpy-1.16.2_relax-long-complex-test.patch b/easybuild/easyconfigs/n/numpy/numpy-1.16.2_relax-long-complex-test.patch new file mode 100644 index 00000000000..5649a5c63d2 --- /dev/null +++ b/easybuild/easyconfigs/n/numpy/numpy-1.16.2_relax-long-complex-test.patch @@ -0,0 +1,17 @@ +Relax test condition for test failing on PPC +See https://github.com/numpy/numpy/issues/15763 + +Author: Alexander Grund (TU Dresden) + +diff -aur numpy-1.16.2/numpy/core/tests/test_umath.py numpy-1.16.2-new/numpy/core/tests/test_umath.py +--- numpy-1.16.2/numpy/core/tests/test_umath.py 2021-03-29 12:29:48.950135026 +0200 ++++ numpy-1.16.2-new/numpy/core/tests/test_umath.py 2021-03-29 12:28:09.000000000 +0200 +@@ -2593,7 +2593,7 @@ + # are accurate down to a few epsilons. (Eg. on Linux 64-bit) + # So, give more leeway for long complex tests here: + # Can use 2.1 for > Ubuntu LTS Trusty (2014), glibc = 2.19. +- check(x_series, 50.0*eps) ++ check(x_series, 5e-19) + else: + check(x_series, 2.1*eps) + check(x_basic, 2.0*eps/1e-3) diff --git a/easybuild/easyconfigs/n/numpy/numpy-1.16.6-foss-2023a-Python-2.7.18.eb b/easybuild/easyconfigs/n/numpy/numpy-1.16.6-foss-2023a-Python-2.7.18.eb new file mode 100644 index 00000000000..a3367b39bd9 --- /dev/null +++ b/easybuild/easyconfigs/n/numpy/numpy-1.16.6-foss-2023a-Python-2.7.18.eb @@ -0,0 +1,37 @@ +name = 'numpy' +version = '1.16.6' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.numpy.org' +description = """NumPy is the fundamental package for scientific computing with Python. It contains among other things: + a powerful N-dimensional array object, sophisticated (broadcasting) functions, tools for integrating C/C++ and Fortran + code, useful linear algebra, Fourier transform, and random number capabilities. Besides its obvious scientific uses, + NumPy can also be used as an efficient multi-dimensional container of generic data. Arbitrary data-types can be + defined. This allows NumPy to seamlessly and speedily integrate with a wide variety of databases.""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'pic': True} + +sources = [SOURCE_ZIP] +patches = [ # patches copied from SciPy-bundle-2021.10-foss-2021b-Python-2.7.18.eb + 'numpy-1.16.2_relax-long-complex-test.patch', + 'numpy-1.16.6_add_flexiblas_detection.patch', + 'numpy-1.16.6_handle_failing_linalg_test.patch', + 'numpy-1.20.3_fix-fortran-compiler-error.patch', +] +checksums = [ + {'numpy-1.16.6.zip': 'e5cf3fdf13401885e8eea8170624ec96225e2174eb0c611c6f26dd33b489e3ff'}, + {'numpy-1.16.2_relax-long-complex-test.patch': '647dd4099c2968489e5103b50bcd1b3d970b5b536af25ec75efe86127dda07bb'}, + {'numpy-1.16.6_add_flexiblas_detection.patch': '32ca32dd7ee8d6fcdce5875067acd50970c731cbb2603c6d1ad84ff81ff8c6d5'}, + {'numpy-1.16.6_handle_failing_linalg_test.patch': + 'be9dce98649626b7322ed8d1241b74a4e28c1d1de070a8072dc912cad3eb143d'}, + {'numpy-1.20.3_fix-fortran-compiler-error.patch': + '016e0d02ffabe013248c4fd203a4456edee76839f747c05daf92ac1fe9925189'}, +] + +dependencies = [ + ('Python', '2.7.18'), + ('pytest', '4.6.11', versionsuffix), +] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/n/numpy/numpy-1.16.6_add_flexiblas_detection.patch b/easybuild/easyconfigs/n/numpy/numpy-1.16.6_add_flexiblas_detection.patch new file mode 100644 index 00000000000..02528b44bc3 --- /dev/null +++ b/easybuild/easyconfigs/n/numpy/numpy-1.16.6_add_flexiblas_detection.patch @@ -0,0 +1,181 @@ +Add flexiblas detection to numpy. +This is just a copy of the openblas detection with name changed. + +Åke Sandgren, 2022-01-13 +diff -ru numpy-1.16.6.orig/numpy/distutils/system_info.py numpy-1.16.6/numpy/distutils/system_info.py +--- numpy-1.16.6.orig/numpy/distutils/system_info.py 2019-12-27 17:24:44.000000000 +0100 ++++ numpy-1.16.6/numpy/distutils/system_info.py 2022-01-13 16:48:14.754235308 +0100 +@@ -20,6 +20,7 @@ + blas_info + lapack_info + openblas_info ++ flexiblas_info + blis_info + blas_opt_info # usage recommended + lapack_opt_info # usage recommended +@@ -395,6 +396,9 @@ + # openblas with embedded lapack + 'openblas_lapack': openblas_lapack_info, # use blas_opt instead + 'openblas_clapack': openblas_clapack_info, # use blas_opt instead ++ 'flexiblas': flexiblas_info, # use blas_opt instead ++ 'flexiblas_lapack': flexiblas_lapack_info, # use blas_opt instead ++ 'flexiblas_clapack': flexiblas_clapack_info, # use blas_opt instead + 'blis': blis_info, # use blas_opt instead + 'lapack_mkl': lapack_mkl_info, # use lapack_opt instead + 'blas_mkl': blas_mkl_info, # use blas_opt instead +@@ -1549,6 +1553,16 @@ + self.set_info(**lapack_mkl_info) + return + ++ flexiblas_info = get_info('flexiblas_lapack') ++ if flexiblas_info: ++ self.set_info(**flexiblas_info) ++ return ++ ++ flexiblas_info = get_info('flexiblas_clapack') ++ if flexiblas_info: ++ self.set_info(**flexiblas_info) ++ return ++ + openblas_info = get_info('openblas_lapack') + if openblas_info: + self.set_info(**openblas_info) +@@ -1633,6 +1647,11 @@ + self.set_info(**blis_info) + return + ++ flexiblas_info = get_info('flexiblas') ++ if flexiblas_info: ++ self.set_info(**flexiblas_info) ++ return ++ + openblas_info = get_info('openblas') + if openblas_info: + self.set_info(**openblas_info) +@@ -1749,6 +1768,126 @@ + return res + + ++class flexiblas_info(blas_info): ++ section = 'flexiblas' ++ dir_env_var = 'FLEXIBLAS' ++ _lib_names = ['flexiblas'] ++ notfounderror = BlasNotFoundError ++ ++ def check_embedded_lapack(self, info): ++ return True ++ ++ def calc_info(self): ++ c = customized_ccompiler() ++ ++ lib_dirs = self.get_lib_dirs() ++ ++ flexiblas_libs = self.get_libs('libraries', self._lib_names) ++ if flexiblas_libs == self._lib_names: # backward compat with 1.8.0 ++ flexiblas_libs = self.get_libs('flexiblas_libs', self._lib_names) ++ ++ info = self.check_libs(lib_dirs, flexiblas_libs, []) ++ ++ if c.compiler_type == "msvc" and info is None: ++ from numpy.distutils.fcompiler import new_fcompiler ++ f = new_fcompiler(c_compiler=c) ++ if f and f.compiler_type == 'gnu95': ++ # Try gfortran-compatible library files ++ info = self.check_msvc_gfortran_libs(lib_dirs, flexiblas_libs) ++ # Skip lapack check, we'd need build_ext to do it ++ assume_lapack = True ++ elif info: ++ assume_lapack = False ++ info['language'] = 'c' ++ ++ if info is None: ++ return ++ ++ # Add extra info for OpenBLAS ++ extra_info = self.calc_extra_info() ++ dict_append(info, **extra_info) ++ ++ if not (assume_lapack or self.check_embedded_lapack(info)): ++ return ++ ++ info['define_macros'] = [('HAVE_CBLAS', None)] ++ self.set_info(**info) ++ ++ def check_msvc_gfortran_libs(self, library_dirs, libraries): ++ # First, find the full path to each library directory ++ library_paths = [] ++ for library in libraries: ++ for library_dir in library_dirs: ++ # MinGW static ext will be .a ++ fullpath = os.path.join(library_dir, library + '.a') ++ if os.path.isfile(fullpath): ++ library_paths.append(fullpath) ++ break ++ else: ++ return None ++ ++ # Generate numpy.distutils virtual static library file ++ tmpdir = os.path.join(os.getcwd(), 'build', 'flexiblas') ++ if not os.path.isdir(tmpdir): ++ os.makedirs(tmpdir) ++ ++ info = {'library_dirs': [tmpdir], ++ 'libraries': ['flexiblas'], ++ 'language': 'f77'} ++ ++ fake_lib_file = os.path.join(tmpdir, 'flexiblas.fobjects') ++ fake_clib_file = os.path.join(tmpdir, 'flexiblas.cobjects') ++ with open(fake_lib_file, 'w') as f: ++ f.write("\n".join(library_paths)) ++ with open(fake_clib_file, 'w') as f: ++ pass ++ ++ return info ++ ++class flexiblas_lapack_info(flexiblas_info): ++ section = 'flexiblas' ++ dir_env_var = 'FLEXIBLAS' ++ _lib_names = ['flexiblas'] ++ notfounderror = BlasNotFoundError ++ ++ def check_embedded_lapack(self, info): ++ res = False ++ c = customized_ccompiler() ++ ++ tmpdir = tempfile.mkdtemp() ++ s = """void zungqr_(); ++ int main(int argc, const char *argv[]) ++ { ++ zungqr_(); ++ return 0; ++ }""" ++ src = os.path.join(tmpdir, 'source.c') ++ out = os.path.join(tmpdir, 'a.out') ++ # Add the additional "extra" arguments ++ try: ++ extra_args = info['extra_link_args'] ++ except Exception: ++ extra_args = [] ++ if sys.version_info < (3, 5) and sys.version_info > (3, 0) and c.compiler_type == "msvc": ++ extra_args.append("/MANIFEST") ++ try: ++ with open(src, 'wt') as f: ++ f.write(s) ++ obj = c.compile([src], output_dir=tmpdir) ++ try: ++ c.link_executable(obj, out, libraries=info['libraries'], ++ library_dirs=info['library_dirs'], ++ extra_postargs=extra_args) ++ res = True ++ except distutils.ccompiler.LinkError: ++ res = False ++ finally: ++ shutil.rmtree(tmpdir) ++ return res ++ ++class flexiblas_clapack_info(flexiblas_lapack_info): ++ _lib_names = ['flexiblas', 'lapack'] ++ + class openblas_info(blas_info): + section = 'openblas' + dir_env_var = 'OPENBLAS' diff --git a/easybuild/easyconfigs/n/numpy/numpy-1.16.6_handle_failing_linalg_test.patch b/easybuild/easyconfigs/n/numpy/numpy-1.16.6_handle_failing_linalg_test.patch new file mode 100644 index 00000000000..d85fb475809 --- /dev/null +++ b/easybuild/easyconfigs/n/numpy/numpy-1.16.6_handle_failing_linalg_test.patch @@ -0,0 +1,17 @@ +linalg/test_nan is marked xfail in at least 1.21.3 +Do so here too since it fails with newer openblas/compiler versions. + +Åke sandgren, 2022-01-13 +diff -ru numpy-1.16.6.orig/numpy/linalg/tests/test_linalg.py numpy-1.16.6/numpy/linalg/tests/test_linalg.py +--- numpy-1.16.6.orig/numpy/linalg/tests/test_linalg.py 2019-12-27 17:24:44.000000000 +0100 ++++ numpy-1.16.6/numpy/linalg/tests/test_linalg.py 2022-01-13 17:21:36.658857878 +0100 +@@ -740,6 +740,9 @@ + for A, p in itertools.product(As, p_neg): + linalg.cond(A, p) + ++ @pytest.mark.xfail(True, run=False, ++ reason="Platform/LAPACK-dependent failure, " ++ "see gh-18914") + def test_nan(self): + # nans should be passed through, not converted to infs + ps = [None, 1, -1, 2, -2, 'fro'] diff --git a/easybuild/easyconfigs/n/numpy/numpy-1.20.3_fix-fortran-compiler-error.patch b/easybuild/easyconfigs/n/numpy/numpy-1.20.3_fix-fortran-compiler-error.patch new file mode 100644 index 00000000000..32b41061f06 --- /dev/null +++ b/easybuild/easyconfigs/n/numpy/numpy-1.20.3_fix-fortran-compiler-error.patch @@ -0,0 +1,43 @@ +Using Fortran compilers which differ "too much" from GCC fails building NumPy with something like +> A valid Fortran version was not found in this string: [...] + +See https://github.com/easybuilders/easybuild-easyblocks/issues/2518 and https://github.com/numpy/numpy/pull/26502 + +Fix by converting the hard error into a warning as the issue would be handled later if required. +E.g. for building NumPy we don't need a Fortran compiler at all. + +Author: Alexander Grund (TU Dresden) + +diff --git a/numpy/distutils/fcompiler/gnu.py b/numpy/distutils/fcompiler/gnu.py +index eac4cbb477..8a1043fe26 100644 +--- a/numpy/distutils/fcompiler/gnu.py ++++ b/numpy/distutils/fcompiler/gnu.py +@@ -8,6 +8,7 @@ import hashlib + import base64 + import subprocess + from subprocess import Popen, PIPE, STDOUT ++from distutils import log + from numpy.distutils.exec_command import filepath_from_subprocess_output + from numpy.distutils.fcompiler import FCompiler + from distutils.version import LooseVersion +@@ -69,9 +70,9 @@ class GnuFCompiler(FCompiler): + # from the version string + return ('gfortran', v) + +- # If still nothing, raise an error to make the problem easy to find. +- err = 'A valid Fortran version was not found in this string:\n' +- raise ValueError(err + version_string) ++ # If still nothing, warn to make the problem easy to find. ++ log.warn('A valid Fortran version was not found in this string:\n' ++ + version_string) + + def version_match(self, version_string): + v = self.gnu_version_match(version_string) +@@ -539,7 +540,6 @@ def _can_target(cmd, arch): + + + if __name__ == '__main__': +- from distutils import log + from numpy.distutils import customized_fcompiler + log.set_verbosity(2) + diff --git a/easybuild/easyconfigs/o/OCaml/OCaml-5.1.1-GCC-13.2.0.eb b/easybuild/easyconfigs/o/OCaml/OCaml-5.1.1-GCC-13.2.0.eb new file mode 100644 index 00000000000..bd3ad98eb7e --- /dev/null +++ b/easybuild/easyconfigs/o/OCaml/OCaml-5.1.1-GCC-13.2.0.eb @@ -0,0 +1,54 @@ +name = 'OCaml' +version = '5.1.1' + +homepage = 'http://ocaml.org/' +description = """OCaml is a general purpose industrial-strength programming language + with an emphasis on expressiveness and safety. Developed for more than 20 years at Inria + it benefits from one of the most advanced type systems and supports functional, + imperative and object-oriented styles of programming.""" + +toolchain = {'name': 'GCC', 'version': '13.2.0'} + +local_opam_ver = '2.1.5' +source_urls = [ + 'https://github.com/ocaml/ocaml/archive', + 'https://github.com/ocaml/opam/releases/download/%s' % local_opam_ver, +] +sources = [ + '%s.tar.gz' % version, + 'opam-full-%s.tar.gz' % local_opam_ver, +] +checksums = [ + {'5.1.1.tar.gz': '57f7b382b3d71198413ede405d95ef3506f1cdc480cda1dca1e26b37cb090e17'}, + {'opam-full-2.1.5.tar.gz': '09f8d9e410b2f5723c2bfedbf7970e3b305f5017895fcd91759f05e753ddcea5'}, +] + +builddependencies = [ + ('Autotools', '20220317'), + ('pkgconf', '2.0.3'), +] + +dependencies = [ + ('ncurses', '6.4'), + ('libreadline', '8.2'), +] + +preconfigopts = 'export CFLAGS="$CFLAGS -lm -lpthread" && ' +preconfigopts += 'export AS=as && ' + +# parallel build tends to break +parallel = 1 + +# handled by OPAM, order matters! +# see https://opam.ocaml.org/packages +exts_list = [ + ('ocamlfind', '1.9.6'), + ('batteries', '3.8.0'), + ('conf-pkg-config', '3'), + ('dune-configurator', '3.14.2'), + ('dune', '3.14.2'), + ('base', 'v0.16.3'), + ('stdio', 'v0.16.0'), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/o/ONNX-Runtime/ONNX-Runtime-1.19.2-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/o/ONNX-Runtime/ONNX-Runtime-1.19.2-foss-2023a-CUDA-12.1.1.eb new file mode 100644 index 00000000000..91b8598722a --- /dev/null +++ b/easybuild/easyconfigs/o/ONNX-Runtime/ONNX-Runtime-1.19.2-foss-2023a-CUDA-12.1.1.eb @@ -0,0 +1,67 @@ +easyblock = 'PythonBundle' + +name = 'ONNX-Runtime' +version = '1.19.2' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://onnxruntime.ai' +description = """ONNX Runtime inference can enable faster customer experiences and lower costs, +supporting models from deep learning frameworks such as PyTorch and +TensorFlow/Keras as well as classical machine learning libraries such as +scikit-learn, LightGBM, XGBoost, etc. ONNX Runtime is compatible with different +hardware, drivers, and operating systems, and provides optimal performance by +leveraging hardware accelerators where applicable alongside graph optimizations +and transforms.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('CUDA', '12.1.1', '', SYSTEM), + ('Python', '3.11.3'), + ('ONNX', '1.15.0'), + ('flatbuffers-python', '23.5.26'), + ('sympy', '1.12'), +] + +use_pip = True + +local_whl_tmpl = 'onnxruntime_gpu-%%(version)s-cp311-cp311-manylinux_2_27_%s.manylinux_2_28_%s.whl' + +exts_list = [ + ('humanfriendly', '10.0', { + 'checksums': ['6b0b831ce8f15f7300721aa49829fc4e83921a9a301cc7f606be6686a2288ddc'], + }), + ('coloredlogs', '15.0.1', { + 'checksums': ['7c991aa71a4577af2f82600d8f8f3a89f936baeaf9b50a9c197da014e5bf16b0'], + }), + (name, version, { + 'source_urls': ['http://pypi.python.org/packages/source/o/onnxruntime-gpu'], + 'sources': [local_whl_tmpl % ('%(arch)s', '%(arch)s')], + 'checksums': [{ + local_whl_tmpl % ('x86_64', 'x86_64'): + '562fc7c755393eaad9751e56149339dd201ffbfdb3ef5f43ff21d0619ba9045f', + }], + 'modulename': 'onnxruntime', + }), +] + +# Due to its name 'onnxruntime-gpu', this package does not fullfil requirements on 'onnxruntime' although it provides +# the 'onnxruntime' python module. Fix this dependency issue in pip by creating a stub 'onnxruntime' dist-info folder +_py_sitepkgs = '%(installdir)s/lib/python%(pyshortver)s/site-packages' +postinstallcmds = [ + "cp -r %s/onnxruntime{_gpu,}-%%(version)s.dist-info" % _py_sitepkgs, + "sed -i 's/onnxruntime.gpu/onnxruntime/g' %s/onnxruntime-%%(version)s.dist-info/{METADATA,RECORD}" % _py_sitepkgs, +] + +sanity_pip_check = True + +_py_sitepkgs_dirs = ['onnxruntime', 'onnxruntime-%(version)s.dist-info', 'onnxruntime_gpu-%(version)s.dist-info'] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%%(pyshortver)s/site-packages/%s' % x for x in _py_sitepkgs_dirs], +} + +options = {'modulename': 'onnxruntime'} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/o/ONNX-Runtime/ONNX-Runtime-1.19.2-foss-2023a.eb b/easybuild/easyconfigs/o/ONNX-Runtime/ONNX-Runtime-1.19.2-foss-2023a.eb new file mode 100644 index 00000000000..440ae5d93e7 --- /dev/null +++ b/easybuild/easyconfigs/o/ONNX-Runtime/ONNX-Runtime-1.19.2-foss-2023a.eb @@ -0,0 +1,50 @@ +easyblock = 'PythonBundle' + +name = 'ONNX-Runtime' +version = '1.19.2' + +homepage = 'https://onnxruntime.ai' +description = """ONNX Runtime inference can enable faster customer experiences and lower costs, +supporting models from deep learning frameworks such as PyTorch and +TensorFlow/Keras as well as classical machine learning libraries such as +scikit-learn, LightGBM, XGBoost, etc. ONNX Runtime is compatible with different +hardware, drivers, and operating systems, and provides optimal performance by +leveraging hardware accelerators where applicable alongside graph optimizations +and transforms.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('ONNX', '1.15.0'), + ('flatbuffers-python', '23.5.26'), + ('sympy', '1.12'), +] + +use_pip = True + +local_whl_tmpl = 'onnxruntime-%%(version)s-cp311-cp311-manylinux_2_27_%s.manylinux_2_28_%s.whl' + +exts_list = [ + ('humanfriendly', '10.0', { + 'checksums': ['6b0b831ce8f15f7300721aa49829fc4e83921a9a301cc7f606be6686a2288ddc'], + }), + ('coloredlogs', '15.0.1', { + 'checksums': ['7c991aa71a4577af2f82600d8f8f3a89f936baeaf9b50a9c197da014e5bf16b0'], + }), + (name, version, { + 'source_urls': ['http://pypi.python.org/packages/source/o/onnxruntime'], + 'sources': [local_whl_tmpl % ('%(arch)s', '%(arch)s')], + 'checksums': [{ + local_whl_tmpl % ('x86_64', 'x86_64'): + 'a36511dc07c5c964b916697e42e366fa43c48cdb3d3503578d78cef30417cb84', + local_whl_tmpl % ('aarch64', 'aarch64'): + 'c1dfe4f660a71b31caa81fc298a25f9612815215a47b286236e61d540350d7b6', + }], + 'modulename': 'onnxruntime', + }), +] + +sanity_pip_check = True + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/o/OPARI2/OPARI2-2.0.8-GCCcore-13.3.0.eb b/easybuild/easyconfigs/o/OPARI2/OPARI2-2.0.8-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..503a56951d0 --- /dev/null +++ b/easybuild/easyconfigs/o/OPARI2/OPARI2-2.0.8-GCCcore-13.3.0.eb @@ -0,0 +1,45 @@ +# # +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2013-2024 Juelich Supercomputing Centre, Germany +# Authors:: Bernd Mohr +# Markus Geimer +# Jan André Reuter +# License:: 3-clause BSD +# +# This work is based on experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +# # + +easyblock = 'ConfigureMake' + +name = 'OPARI2' +version = '2.0.8' + +homepage = 'https://www.score-p.org' +description = """ + OPARI2, the successor of Forschungszentrum Juelich's OPARI, is a + source-to-source instrumentation tool for OpenMP and hybrid codes. + It surrounds OpenMP directives and runtime library calls with calls + to the POMP2 measurement interface. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['http://perftools.pages.jsc.fz-juelich.de/cicd/%(namelower)s/tags/%(namelower)s-%(version)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['196e59a2a625e6c795a6124c61e784bad142f9f38df0b4fa4d435ba9b9c19721'] + +builddependencies = [ + ('binutils', '2.42'), +] + + +sanity_check_paths = { + 'files': ['bin/opari2', 'include/opari2/pomp2_lib.h'], + 'dirs': [], +} + +sanity_check_commands = ['opari2-config --help'] + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/o/OPERA-MS/OPERA-MS-0.9.0-20240703-foss-2023a.eb b/easybuild/easyconfigs/o/OPERA-MS/OPERA-MS-0.9.0-20240703-foss-2023a.eb new file mode 100644 index 00000000000..620366c965b --- /dev/null +++ b/easybuild/easyconfigs/o/OPERA-MS/OPERA-MS-0.9.0-20240703-foss-2023a.eb @@ -0,0 +1,67 @@ +easyblock = 'MakeCp' + +name = 'OPERA-MS' +local_commit = '026f9a5' +version = '0.9.0-20240703' + +homepage = 'https://github.com/CSB5/OPERA-MS' +description = """OPERA-MS is a hybrid metagenomic assembler which combines the + advantages of short and long-read technologies to provide high quality + assemblies, addressing issues of low contiguity for short-read only assemblies, + and low base-pair quality for long-read only assemblies.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['https://github.com/CSB5/OPERA-MS/archive/'] +sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}] +checksums = ['72a3e16287dd1f2098adac41930d6a54779a033f5bf78c2659580afae5a7280c'] + +dependencies = [ + ('Perl', '5.36.1'), + ('Perl-bundle-CPAN', '5.36.1'), + ('Statistics-R', '0.34'), + ('Python', '3.11.3'), + ('SAMtools', '0.1.20'), +] + +prebuildopts = 'rm %(start_dir)s/tools_opera_ms/samtools && ' +prebuildopts += 'cd %(start_dir)s/tools_opera_ms && ln -s $EBROOTSAMTOOLS/bin/samtools && ' +prebuildopts += 'cd %(start_dir)s &&' +buildopts = 'CFLAGS="$CFLAGS"' + +files_to_copy = [ + 'OPERA-MS.pl', + 'bin', + 'src_utils', + 'tools_opera_ms', + (['OPERA-LG/bin'], 'OPERA-LG'), +] + +postinstallcmds = [ + "echo '#!/bin/sh\n exec perl %(installdir)s/OPERA-MS.pl $@' > %(installdir)s/bin/OPERA-MS", + 'chmod +x %(installdir)s/bin/OPERA-MS', + 'ln -s $EBROOTPERL/bin/perl %(installdir)s/tools_opera_ms/perl', + '%(installdir)s/bin/OPERA-MS ' + ' '.join([ + '--contig-file test_files/contigs.fasta', + '--short-read1 test_files/R1.fastq.gz', + '--short-read2 test_files/R2.fastq.gz', + '--long-read test_files/long_read.fastq', + '--no-ref-clustering', + '--out-dir $TMPDIR', + ]), +] + +fix_perl_shebang_for = ['bin/*.pl', 'OPERA-MS.pl', 'OPERA-LG/bin/*.pl'] +fix_python_shebang_for = ['bin/*.py', 'OPERA-LG/bin/*.py'] + +sanity_check_paths = { + 'files': ['bin/OPERA-MS'], + 'dirs': [], +} + +sanity_check_commands = [ + 'OPERA-MS --help', + 'OPERA-MS check-dependency', +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/o/ORCA/ORCA-6.0.0-foss-2023b-avx2.eb b/easybuild/easyconfigs/o/ORCA/ORCA-6.0.0-foss-2023b-avx2.eb new file mode 100644 index 00000000000..ff3112bb084 --- /dev/null +++ b/easybuild/easyconfigs/o/ORCA/ORCA-6.0.0-foss-2023b-avx2.eb @@ -0,0 +1,37 @@ +name = 'ORCA' +version = '6.0.0' +versionsuffix = '-avx2' + +homepage = 'https://orcaforum.kofo.mpg.de' +description = """ +ORCA is a flexible, efficient and easy-to-use general purpose tool for quantum +chemistry with specific emphasis on spectroscopic properties of open-shell +molecules. It features a wide variety of standard quantum chemical methods +ranging from semiempirical methods to DFT to single- and multireference +correlated ab initio methods. It can also treat environmental and relativistic +effects.""" + +toolchain = {'name': 'foss', 'version': '2023b'} + +download_instructions = "Shared build of ORCA: download from https://orcaforum.kofo.mpg.de" +# mostly dynamically linked (SCALAPACK, OpenBLAS are still embedded) +sources = ['%%(namelower)s_%s_linux_%%(orcaarch)s_avx2_shared_openmpi416.tar.xz' % version.replace('.', '_')] +checksums = [ + # orca_6_0_0_linux_x86-64_avx2_shared_openmpi416.tar.xz + '02c21294efe7b1b721e26cb90f98ee15ad682d02807201b7d217dfe67905a2fd', +] + +# optional dependency for ORCA, +# see also https://xtb-docs.readthedocs.io/en/latest/setup.html#using-xtb-with-orca +dependencies = [('xtb', '6.7.1')] + +postinstallcmds = ["cd %(installdir)s/bin && ln -s $EBROOTXTB/bin/xtb otool_xtb"] + +enhance_sanity_check = True + +sanity_check_paths = { + 'files': ['bin/orca', 'bin/otool_xtb'], + 'dirs': [], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/o/ORCA/ORCA-6.0.0-foss-2023b.eb b/easybuild/easyconfigs/o/ORCA/ORCA-6.0.0-foss-2023b.eb new file mode 100644 index 00000000000..f28a5a3ff99 --- /dev/null +++ b/easybuild/easyconfigs/o/ORCA/ORCA-6.0.0-foss-2023b.eb @@ -0,0 +1,36 @@ +name = 'ORCA' +version = '6.0.0' + +homepage = 'https://orcaforum.kofo.mpg.de' +description = """ +ORCA is a flexible, efficient and easy-to-use general purpose tool for quantum +chemistry with specific emphasis on spectroscopic properties of open-shell +molecules. It features a wide variety of standard quantum chemical methods +ranging from semiempirical methods to DFT to single- and multireference +correlated ab initio methods. It can also treat environmental and relativistic +effects.""" + +toolchain = {'name': 'foss', 'version': '2023b'} + +download_instructions = "Shared build of ORCA: download from https://orcaforum.kofo.mpg.de" +# mostly dynamically linked (SCALAPACK, OpenBLAS are still embedded) +sources = ['%%(namelower)s_%s_linux_%%(orcaarch)s_shared_openmpi416.tar.xz' % version.replace('.', '_')] +checksums = [ + # orca_6_0_0_linux_x86-64_shared_openmpi416.tar.xz + '219bd1deb6d64a63cb72471926cb81665cbbcdec19f9c9549761be67d49a29c6', +] + +# optional dependency for ORCA, +# see also https://xtb-docs.readthedocs.io/en/latest/setup.html#using-xtb-with-orca +dependencies = [('xtb', '6.7.1')] + +postinstallcmds = ["cd %(installdir)s/bin && ln -s $EBROOTXTB/bin/xtb otool_xtb"] + +enhance_sanity_check = True + +sanity_check_paths = { + 'files': ['bin/orca', 'bin/otool_xtb'], + 'dirs': [], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/o/ORCA/ORCA-6.0.0-gompi-2023a-avx2.eb b/easybuild/easyconfigs/o/ORCA/ORCA-6.0.0-gompi-2023a-avx2.eb new file mode 100644 index 00000000000..cdc92c16f64 --- /dev/null +++ b/easybuild/easyconfigs/o/ORCA/ORCA-6.0.0-gompi-2023a-avx2.eb @@ -0,0 +1,24 @@ +name = 'ORCA' +version = '6.0.0' +versionsuffix = '-avx2' + +homepage = 'https://orcaforum.kofo.mpg.de' +description = """ +ORCA is a flexible, efficient and easy-to-use general purpose tool for quantum +chemistry with specific emphasis on spectroscopic properties of open-shell +molecules. It features a wide variety of standard quantum chemical methods +ranging from semiempirical methods to DFT to single- and multireference +correlated ab initio methods. It can also treat environmental and relativistic +effects.""" + +toolchain = {'name': 'gompi', 'version': '2023a'} + +download_instructions = "Shared build of ORCA: download from https://orcaforum.kofo.mpg.de" +# mostly dynamically linked (SCALAPACK, OpenBLAS are still embedded) +sources = ['%%(namelower)s_%s_linux_%%(orcaarch)s_avx2_shared_openmpi416.tar.xz' % version.replace('.', '_')] +checksums = [ + # orca_6_0_0_linux_x86-64_avx2_shared_openmpi416.tar.xz + '02c21294efe7b1b721e26cb90f98ee15ad682d02807201b7d217dfe67905a2fd', +] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/o/ORCA/ORCA-6.0.0-gompi-2023a.eb b/easybuild/easyconfigs/o/ORCA/ORCA-6.0.0-gompi-2023a.eb new file mode 100644 index 00000000000..8bf88fa8129 --- /dev/null +++ b/easybuild/easyconfigs/o/ORCA/ORCA-6.0.0-gompi-2023a.eb @@ -0,0 +1,23 @@ +name = 'ORCA' +version = '6.0.0' + +homepage = 'https://orcaforum.kofo.mpg.de' +description = """ +ORCA is a flexible, efficient and easy-to-use general purpose tool for quantum +chemistry with specific emphasis on spectroscopic properties of open-shell +molecules. It features a wide variety of standard quantum chemical methods +ranging from semiempirical methods to DFT to single- and multireference +correlated ab initio methods. It can also treat environmental and relativistic +effects.""" + +toolchain = {'name': 'gompi', 'version': '2023a'} + +download_instructions = "Shared build of ORCA: download from https://orcaforum.kofo.mpg.de" +# mostly dynamically linked (SCALAPACK, OpenBLAS are still embedded) +sources = ['%%(namelower)s_%s_linux_%%(orcaarch)s_shared_openmpi416.tar.xz' % version.replace('.', '_')] +checksums = [ + # orca_6_0_0_linux_x86-64_shared_openmpi416.tar.xz + '219bd1deb6d64a63cb72471926cb81665cbbcdec19f9c9549761be67d49a29c6', +] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/o/ORCA/ORCA-6.0.1-gompi-2023a-avx2.eb b/easybuild/easyconfigs/o/ORCA/ORCA-6.0.1-gompi-2023a-avx2.eb new file mode 100644 index 00000000000..bc34fff4fe8 --- /dev/null +++ b/easybuild/easyconfigs/o/ORCA/ORCA-6.0.1-gompi-2023a-avx2.eb @@ -0,0 +1,24 @@ +name = 'ORCA' +version = '6.0.1' +versionsuffix = '-avx2' + +homepage = 'https://orcaforum.kofo.mpg.de' +description = """ +ORCA is a flexible, efficient and easy-to-use general purpose tool for quantum +chemistry with specific emphasis on spectroscopic properties of open-shell +molecules. It features a wide variety of standard quantum chemical methods +ranging from semiempirical methods to DFT to single- and multireference +correlated ab initio methods. It can also treat environmental and relativistic +effects.""" + +toolchain = {'name': 'gompi', 'version': '2023a'} + +download_instructions = "Shared build of ORCA: download from https://orcaforum.kofo.mpg.de" +# mostly dynamically linked (SCALAPACK, OpenBLAS are still embedded) +sources = ['%%(namelower)s_%s_linux_%%(orcaarch)s_shared_openmpi416_avx2.tar.xz' % version.replace('.', '_')] +checksums = [ + # orca_6_0_1_linux_x86-64_shared_openmpi416_avx2.tar.xz + 'f31f98256a0c6727b6ddfe50aa3ac64c45549981138d670a57e90114b4b9c9d2', +] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/o/ORCA/ORCA-6.0.1-gompi-2023b-avx2.eb b/easybuild/easyconfigs/o/ORCA/ORCA-6.0.1-gompi-2023b-avx2.eb new file mode 100644 index 00000000000..6194413a4f1 --- /dev/null +++ b/easybuild/easyconfigs/o/ORCA/ORCA-6.0.1-gompi-2023b-avx2.eb @@ -0,0 +1,24 @@ +name = 'ORCA' +version = '6.0.1' +versionsuffix = '-avx2' + +homepage = 'https://orcaforum.kofo.mpg.de' +description = """ +ORCA is a flexible, efficient and easy-to-use general purpose tool for quantum +chemistry with specific emphasis on spectroscopic properties of open-shell +molecules. It features a wide variety of standard quantum chemical methods +ranging from semiempirical methods to DFT to single- and multireference +correlated ab initio methods. It can also treat environmental and relativistic +effects.""" + +toolchain = {'name': 'gompi', 'version': '2023b'} + +download_instructions = "Shared build of ORCA: download from https://orcaforum.kofo.mpg.de" +# mostly dynamically linked (SCALAPACK, OpenBLAS are still embedded) +sources = ['%%(namelower)s_%s_linux_%%(orcaarch)s_shared_openmpi416_avx2.tar.xz' % version.replace('.', '_')] +checksums = [ + # orca_6_0_1_linux_x86-64_shared_openmpi416_avx2.tar.xz + 'f31f98256a0c6727b6ddfe50aa3ac64c45549981138d670a57e90114b4b9c9d2', +] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-7.4-gompi-2024.05.eb b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-7.4-gompi-2024.05.eb new file mode 100644 index 00000000000..60bfb29130b --- /dev/null +++ b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-7.4-gompi-2024.05.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'OSU-Micro-Benchmarks' +version = '7.4' + +homepage = 'https://mvapich.cse.ohio-state.edu/benchmarks/' +description = """OSU Micro-Benchmarks""" + +toolchain = {'name': 'gompi', 'version': '2024.05'} +toolchainopts = {'usempi': True} + +source_urls = ['https://mvapich.cse.ohio-state.edu/download/mvapich/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['1edd0c2efa61999409bfb28740a7f39689a5b42b1a1b4c66d1656e5637f7cefc'] + +local_benchmark_dirs = [ + 'libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt', 'startup'] +] +modextrapaths = {'PATH': local_benchmark_dirs} + +sanity_check_paths = { + 'files': [], + 'dirs': local_benchmark_dirs, +} + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-7.4-gompi-2024a.eb b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-7.4-gompi-2024a.eb new file mode 100644 index 00000000000..0d9573028dd --- /dev/null +++ b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-7.4-gompi-2024a.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'OSU-Micro-Benchmarks' +version = '7.4' + +homepage = 'https://mvapich.cse.ohio-state.edu/benchmarks/' +description = """OSU Micro-Benchmarks""" + +toolchain = {'name': 'gompi', 'version': '2024a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://mvapich.cse.ohio-state.edu/download/mvapich/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['1edd0c2efa61999409bfb28740a7f39689a5b42b1a1b4c66d1656e5637f7cefc'] + +local_benchmark_dirs = [ + 'libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt', 'startup'] +] +modextrapaths = {'PATH': local_benchmark_dirs} + +sanity_check_paths = { + 'files': [], + 'dirs': local_benchmark_dirs, +} + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-7.4-iimpi-2024a.eb b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-7.4-iimpi-2024a.eb new file mode 100644 index 00000000000..3122923be15 --- /dev/null +++ b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-7.4-iimpi-2024a.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'OSU-Micro-Benchmarks' +version = '7.4' + +homepage = 'https://mvapich.cse.ohio-state.edu/benchmarks/' +description = """OSU Micro-Benchmarks""" + +toolchain = {'name': 'iimpi', 'version': '2024a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://mvapich.cse.ohio-state.edu/download/mvapich/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['1edd0c2efa61999409bfb28740a7f39689a5b42b1a1b4c66d1656e5637f7cefc'] + +local_benchmark_dirs = [ + 'libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt', 'startup'] +] +modextrapaths = {'PATH': local_benchmark_dirs} + +sanity_check_paths = { + 'files': [], + 'dirs': local_benchmark_dirs, +} + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-7.5-gompi-2023b-CUDA-12.4.0.eb b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-7.5-gompi-2023b-CUDA-12.4.0.eb new file mode 100644 index 00000000000..52593680dff --- /dev/null +++ b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-7.5-gompi-2023b-CUDA-12.4.0.eb @@ -0,0 +1,38 @@ +easyblock = 'ConfigureMake' + +name = 'OSU-Micro-Benchmarks' +version = '7.5' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://mvapich.cse.ohio-state.edu/benchmarks/' +description = """OSU Micro-Benchmarks""" + +toolchain = {'name': 'gompi', 'version': '2023b'} +toolchainopts = {'usempi': True} + +source_urls = ['https://mvapich.cse.ohio-state.edu/download/mvapich/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['1cf84ac5419456202757a757c5f9a4f5c6ecd05c65783c7976421cfd6020b3b3'] + +dependencies = [ + ('CUDA', '12.4.0', '', SYSTEM), + ('NCCL', '2.20.5', versionsuffix), + ('UCX-CUDA', '1.15.0', versionsuffix), + ('UCC-CUDA', '1.2.0', versionsuffix), +] + +configopts = ' --enable-cuda --with-cuda=$EBROOTCUDA --enable-ncclomb --with-nccl=$EBROOTNCCL' + +local_benchmark_dirs = [ + 'libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt', 'startup'] +] + [ + 'libexec/osu-micro-benchmarks/xccl/%s' % x for x in ['collective', 'pt2pt'] +] +modextrapaths = {'PATH': local_benchmark_dirs} + +sanity_check_paths = { + 'files': [], + 'dirs': local_benchmark_dirs, +} + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/o/OTF2/OTF2-3.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/o/OTF2/OTF2-3.0-GCCcore-11.3.0.eb index 6e982449e9e..fe8a5244c12 100644 --- a/easybuild/easyconfigs/o/OTF2/OTF2-3.0-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/o/OTF2/OTF2-3.0-GCCcore-11.3.0.eb @@ -3,6 +3,7 @@ # Copyright:: Copyright 2013-2019 Juelich Supercomputing Centre, Germany # Authors:: Bernd Mohr # Markus Geimer +# Jan Andre Reuter # License:: 3-clause BSD # # This work is based on experiences from the UNITE project @@ -34,17 +35,21 @@ builddependencies = [ dependencies = [ # SIONlib container support (optional): ('SIONlib', '1.7.7', '-tools'), + # OTF2 Python bindings + ('Python', '3.10.4'), ] +local_pyshortver = '3.10' configopts = '--enable-shared' +modextrapaths = {'PYTHONPATH': ['lib64/python%s/site-packages' % local_pyshortver]} sanity_check_paths = { 'files': ['bin/otf2-config', 'include/otf2/otf2.h', 'lib/libotf2.a', 'lib/libotf2.%s' % SHLIB_EXT], 'dirs': [], } - -sanity_check_commands = ['%(namelower)s-config --help'] +sanity_check_commands = ['%(namelower)s-config --help', + 'python -c "import %(namelower)s"'] moduleclass = 'perf' diff --git a/easybuild/easyconfigs/o/OTF2/OTF2-3.0.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/o/OTF2/OTF2-3.0.2-GCCcore-11.2.0.eb index 7c4d60f0514..488b8e0de0d 100644 --- a/easybuild/easyconfigs/o/OTF2/OTF2-3.0.2-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/o/OTF2/OTF2-3.0.2-GCCcore-11.2.0.eb @@ -3,6 +3,7 @@ # Copyright:: Copyright 2013-2019 Juelich Supercomputing Centre, Germany # Authors:: Bernd Mohr # Markus Geimer +# Jan Andre Reuter # License:: 3-clause BSD # # This work is based on experiences from the UNITE project @@ -34,17 +35,22 @@ builddependencies = [ dependencies = [ # SIONlib container support (optional): ('SIONlib', '1.7.7', '-tools'), + # OTF2 Python bindings + ('Python', '3.9.6'), ] +local_pyshortver = '3.9' configopts = '--enable-shared' +modextrapaths = {'PYTHONPATH': ['lib64/python%s/site-packages' % local_pyshortver]} sanity_check_paths = { 'files': ['bin/otf2-config', 'include/otf2/otf2.h', 'lib/libotf2.a', 'lib/libotf2.%s' % SHLIB_EXT], 'dirs': [], } +sanity_check_commands = ['%(namelower)s-config --help', + 'python -c "import %(namelower)s"'] -sanity_check_commands = ['%(namelower)s-config --help'] moduleclass = 'perf' diff --git a/easybuild/easyconfigs/o/OTF2/OTF2-3.0.2-GCCcore-11.3.0.eb b/easybuild/easyconfigs/o/OTF2/OTF2-3.0.2-GCCcore-11.3.0.eb index 61eba75f5f0..6756aa72eac 100644 --- a/easybuild/easyconfigs/o/OTF2/OTF2-3.0.2-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/o/OTF2/OTF2-3.0.2-GCCcore-11.3.0.eb @@ -3,6 +3,7 @@ # Copyright:: Copyright 2013-2019 Juelich Supercomputing Centre, Germany # Authors:: Bernd Mohr # Markus Geimer +# Jan Andre Reuter # License:: 3-clause BSD # # This work is based on experiences from the UNITE project @@ -34,17 +35,21 @@ builddependencies = [ dependencies = [ # SIONlib container support (optional): ('SIONlib', '1.7.7', '-tools'), + # OTF2 Python bindings + ('Python', '3.10.4'), ] +local_pyshortver = '3.10' configopts = '--enable-shared' +modextrapaths = {'PYTHONPATH': ['lib64/python%s/site-packages' % local_pyshortver]} sanity_check_paths = { 'files': ['bin/otf2-config', 'include/otf2/otf2.h', 'lib/libotf2.a', 'lib/libotf2.%s' % SHLIB_EXT], 'dirs': [], } - -sanity_check_commands = ['%(namelower)s-config --help'] +sanity_check_commands = ['%(namelower)s-config --help', + 'python -c "import %(namelower)s"'] moduleclass = 'perf' diff --git a/easybuild/easyconfigs/o/OTF2/OTF2-3.0.3-GCCcore-12.2.0.eb b/easybuild/easyconfigs/o/OTF2/OTF2-3.0.3-GCCcore-12.2.0.eb index 54478bf62fa..f4c842e0450 100644 --- a/easybuild/easyconfigs/o/OTF2/OTF2-3.0.3-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/o/OTF2/OTF2-3.0.3-GCCcore-12.2.0.eb @@ -3,6 +3,7 @@ # Copyright:: Copyright 2013-2019 Juelich Supercomputing Centre, Germany # Authors:: Bernd Mohr # Markus Geimer +# Jan Andre Reuter # License:: 3-clause BSD # # This work is based on experiences from the UNITE project @@ -34,17 +35,21 @@ builddependencies = [ dependencies = [ # SIONlib container support (optional): ('SIONlib', '1.7.7', '-tools'), + # OTF2 Python bindings + ('Python', '3.10.8'), ] +local_pyshortver = '3.10' configopts = '--enable-shared' +modextrapaths = {'PYTHONPATH': ['lib64/python%s/site-packages' % local_pyshortver]} sanity_check_paths = { 'files': ['bin/otf2-config', 'include/otf2/otf2.h', 'lib/libotf2.a', 'lib/libotf2.%s' % SHLIB_EXT], 'dirs': [], } - -sanity_check_commands = ['%(namelower)s-config --help'] +sanity_check_commands = ['%(namelower)s-config --help', + 'python -c "import %(namelower)s"'] moduleclass = 'perf' diff --git a/easybuild/easyconfigs/o/OTF2/OTF2-3.0.3-GCCcore-12.3.0.eb b/easybuild/easyconfigs/o/OTF2/OTF2-3.0.3-GCCcore-12.3.0.eb index 17595d97acb..db786b12a41 100644 --- a/easybuild/easyconfigs/o/OTF2/OTF2-3.0.3-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/o/OTF2/OTF2-3.0.3-GCCcore-12.3.0.eb @@ -3,6 +3,7 @@ # Copyright:: Copyright 2013-2019 Juelich Supercomputing Centre, Germany # Authors:: Bernd Mohr # Markus Geimer +# Jan Andre Reuter # License:: 3-clause BSD # # This work is based on experiences from the UNITE project @@ -34,17 +35,22 @@ builddependencies = [ dependencies = [ # SIONlib container support (optional): ('SIONlib', '1.7.7', '-tools'), + # OTF2 Python bindings + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), ] +local_pyshortver = '3.11' configopts = '--enable-shared' +modextrapaths = {'PYTHONPATH': ['lib64/python%s/site-packages' % local_pyshortver]} sanity_check_paths = { 'files': ['bin/otf2-config', 'include/otf2/otf2.h', 'lib/libotf2.a', 'lib/libotf2.%s' % SHLIB_EXT], 'dirs': [], } - -sanity_check_commands = ['%(namelower)s-config --help'] +sanity_check_commands = ['%(namelower)s-config --help', + 'python -c "import %(namelower)s"'] moduleclass = 'perf' diff --git a/easybuild/easyconfigs/o/OTF2/OTF2-3.0.3-GCCcore-13.2.0.eb b/easybuild/easyconfigs/o/OTF2/OTF2-3.0.3-GCCcore-13.2.0.eb index 48cbf931ec5..c5108c8daca 100644 --- a/easybuild/easyconfigs/o/OTF2/OTF2-3.0.3-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/o/OTF2/OTF2-3.0.3-GCCcore-13.2.0.eb @@ -3,6 +3,7 @@ # Copyright:: Copyright 2013-2019 Juelich Supercomputing Centre, Germany # Authors:: Bernd Mohr # Markus Geimer +# Jan Andre Reuter # License:: 3-clause BSD # # This work is based on experiences from the UNITE project @@ -34,17 +35,22 @@ builddependencies = [ dependencies = [ # SIONlib container support (optional): ('SIONlib', '1.7.7', '-tools'), + # OTF2 Python bindings + ('Python', '3.11.5'), + ('Python-bundle-PyPI', '2023.10'), ] +local_pyshortver = '3.11' configopts = '--enable-shared' +modextrapaths = {'PYTHONPATH': ['lib64/python%s/site-packages' % local_pyshortver]} sanity_check_paths = { 'files': ['bin/otf2-config', 'include/otf2/otf2.h', 'lib/libotf2.a', 'lib/libotf2.%s' % SHLIB_EXT], 'dirs': [], } - -sanity_check_commands = ['%(namelower)s-config --help'] +sanity_check_commands = ['%(namelower)s-config --help', + 'python -c "import %(namelower)s"'] moduleclass = 'perf' diff --git a/easybuild/easyconfigs/o/OTF2/OTF2-3.0.3-GCCcore-13.3.0.eb b/easybuild/easyconfigs/o/OTF2/OTF2-3.0.3-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..fdf78e0772d --- /dev/null +++ b/easybuild/easyconfigs/o/OTF2/OTF2-3.0.3-GCCcore-13.3.0.eb @@ -0,0 +1,60 @@ +# # +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild +# Copyright:: Copyright 2013-2024 Juelich Supercomputing Centre, Germany +# Authors:: Bernd Mohr +# Markus Geimer +# Jan André Reuter +# License:: 3-clause BSD +# +# This work is based on experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +# # + +easyblock = 'EB_Score_minus_P' + +name = 'OTF2' +version = '3.0.3' + +homepage = 'https://www.score-p.org' +description = """ + The Open Trace Format 2 is a highly scalable, memory efficient event trace + data format plus support library. It is the new standard trace format for + Scalasca, Vampir, and TAU and is open for other tools. + +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['http://perftools.pages.jsc.fz-juelich.de/cicd/%(namelower)s/tags/%(namelower)s-%(version)s'] +sources = [SOURCELOWER_TAR_GZ] +patches = ['otf2-3.0.3-update-py-compile.patch'] +checksums = [ + '18a3905f7917340387e3edc8e5766f31ab1af41f4ecc5665da6c769ca21c4ee8', # otf2-3.0.3.tar.gz + '5b1dad8788642eaa97bc03003c9329380340ba10649e556a30ce541165cf8da4', # otf2-3.0.3-update-py-compile.patch +] + +builddependencies = [ + ('binutils', '2.42'), +] +dependencies = [ + # SIONlib container support (optional): + ('SIONlib', '1.7.7', '-tools'), + # OTF2 Python bindings + ('Python', '3.12.3'), + ('Python-bundle-PyPI', '2024.06'), +] + +local_pyshortver = '3.12' +configopts = '--enable-shared' + +modextrapaths = {'PYTHONPATH': ['lib64/python%s/site-packages' % local_pyshortver]} + +sanity_check_paths = { + 'files': ['bin/otf2-config', 'include/otf2/otf2.h', + 'lib/libotf2.a', 'lib/libotf2.%s' % SHLIB_EXT], + 'dirs': [], +} +sanity_check_commands = ['%(namelower)s-config --help', + 'python -c "import %(namelower)s"'] + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/o/OTF2/otf2-3.0.3-update-py-compile.patch b/easybuild/easyconfigs/o/OTF2/otf2-3.0.3-update-py-compile.patch new file mode 100644 index 00000000000..539726fbf14 --- /dev/null +++ b/easybuild/easyconfigs/o/OTF2/otf2-3.0.3-update-py-compile.patch @@ -0,0 +1,252 @@ +This patch updates the py-compile file used by OTF2 during the install process +to fix the removal of the imp module in Python 3.12 which was long deprecated. +With this, OTF2 can be installed with Python 3.12, which would previously fail +with a module not found error. + +--- build-config/py-compile 2023-02-12 17:32:31.274132086 +0100 ++++ ../../otf2/build-config/py-compile 2024-08-22 17:44:59.939242651 +0200 +@@ -1,7 +1,7 @@ + #!/bin/sh + # py-compile - Compile a Python program + +-scriptversion=2011-06-08.12; # UTC ++scriptversion=2023-03-30.00; # UTC + + # Copyright (C) 2000-2013 Free Software Foundation, Inc. + +@@ -27,7 +27,7 @@ + # bugs to or send patches to + # . + +-if [ -z "$PYTHON" ]; then ++if test -z "$PYTHON"; then + PYTHON=python + fi + +@@ -79,13 +79,20 @@ + ;; + -h|--help) + cat <<\EOF +-Usage: py-compile [--help] [--version] [--basedir DIR] [--destdir DIR] [--silent] FILES..." ++Usage: py-compile [options] FILES... + + Byte compile some python scripts FILES. Use --destdir to specify any + leading directory path to the FILES that you don't want to include in the + byte compiled file. Specify --basedir for any additional path information you + do want to be shown in the byte compiled file. + ++Options: ++ --basedir DIR Prefix all FILES with DIR, and include in error messages. ++ --destdir DIR Prefix all FILES with DIR before compiling. ++ -v, --version Display version information. ++ -h, --help This help screen. ++ --silent Operate silently. ++ + Example: + py-compile --destdir /tmp/pkg-root --basedir /usr/share/test test.py test2.py + +@@ -114,87 +121,165 @@ + shift + done + +-files=$* +-if test -z "$files"; then +- usage_error "no files given" ++if test $# -eq 0; then ++ usage_error "no files given" + fi + + # if basedir was given, then it should be prepended to filenames before + # byte compilation. +-if [ -z "$basedir" ]; then +- pathtrans="path = file" ++if test -z "$basedir"; then ++ pathtrans="path = file" + else +- pathtrans="path = os.path.join('$basedir', file)" ++ pathtrans="path = os.path.join('$basedir', file)" + fi + + # if destdir was given, then it needs to be prepended to the filename to + # byte compile but not go into the compiled file. +-if [ -z "$destdir" ]; then +- filetrans="filepath = path" ++if test -z "$destdir"; then ++ filetrans="filepath = path" + else +- filetrans="filepath = os.path.normpath('$destdir' + os.sep + path)" ++ filetrans="filepath = os.path.normpath('$destdir' + os.sep + path)" ++fi ++ ++python_major=`$PYTHON -c 'import sys; print(sys.version_info[0])'` ++if test -z "$python_major"; then ++ usage_error "could not determine $PYTHON major version" + fi + ++case $python_major in ++[01]) ++ usage_error "python version 0.x and 1.x not supported" ++ ;; ++esac ++ ++python_minor=`$PYTHON -c 'import sys; print(sys.version_info[1])'` ++ ++# NB: When adding support for newer versions, prefer copying & adding new cases ++# rather than try to keep things merged with shell variables. ++ ++# First byte compile (no optimization) all the modules. ++# This works for all currently known Python versions. + $PYTHON -c " +-import sys, os, py_compile, imp ++import sys, os, py_compile ++ ++try: ++ import importlib ++except ImportError: ++ importlib = None ++ ++# importlib.util.cache_from_source was added in 3.4 ++if ( ++ hasattr(importlib, 'util') ++ and hasattr(importlib.util, 'cache_from_source') ++): ++ destpath = importlib.util.cache_from_source ++else: ++ destpath = lambda filepath: filepath + 'c' + +-files = '''$files''' + silent = $silent + blu = '''$blu''' + std = '''$std''' + + if not silent: +- sys.stdout.write('Byte-compiling python modules...') +-for file in files.split(): ++ sys.stdout.write('Byte-compiling python modules...\n') ++for file in sys.argv[1:]: + $pathtrans + $filetrans +- if not os.path.exists(filepath) or not (len(filepath) >= 3 +- and filepath[-3:] == '.py'): +- continue ++ if ( ++ not os.path.exists(filepath) ++ or not (len(filepath) >= 3 and filepath[-3:] == '.py') ++ ): ++ continue + if not silent: +- sys.stdout.write(' ' + file) ++ sys.stdout.write(file + ' ') + sys.stdout.flush() + else: +- sys.stdout.write(' PYTHON {}{}{}\n'.format(blu, filepath + 'c', std)) +- if hasattr(imp, 'get_tag'): +- py_compile.compile(filepath, imp.cache_from_source(filepath), path) +- else: +- py_compile.compile(filepath, filepath + 'c', path) ++ sys.stdout.write(' PYCACHE {}{}{}\n'.format(blu, destpath(filepath), std)) ++ py_compile.compile(filepath, destpath(filepath), path) + if not silent: +- sys.stdout.write('\n')" || exit $? ++ sys.stdout.write('\n')" "$@" || exit $? + +-# this will fail for python < 1.5, but that doesn't matter ... ++# Then byte compile w/optimization all the modules. + $PYTHON -O -c " +-import sys, os, py_compile, imp ++import sys, os, py_compile ++ ++try: ++ import importlib ++except ImportError: ++ importlib = None ++ ++# importlib.util.cache_from_source was added in 3.4 ++if ( ++ hasattr(importlib, 'util') ++ and hasattr(importlib.util, 'cache_from_source') ++): ++ destpath = importlib.util.cache_from_source ++else: ++ destpath = lambda filepath: filepath + 'o' + +-# pypy does not use .pyo optimization +-if hasattr(sys, 'pypy_translation_info'): ++# pypy2 does not use .pyo optimization ++if sys.version_info.major <= 2 and hasattr(sys, 'pypy_translation_info'): + sys.exit(0) + +-files = '''$files''' + silent = $silent + blu = '''$blu''' + std = '''$std''' + + if not silent: +- sys.stdout.write('Byte-compiling python modules (optimized versions)...') +-for file in files.split(): ++ sys.stdout.write('Byte-compiling python modules (optimized versions) ...\n') ++for file in sys.argv[1:]: + $pathtrans + $filetrans +- if not os.path.exists(filepath) or not (len(filepath) >= 3 +- and filepath[-3:] == '.py'): +- continue ++ if ( ++ not os.path.exists(filepath) ++ or not (len(filepath) >= 3 and filepath[-3:] == '.py') ++ ): ++ continue + if not silent: +- sys.stdout.write(' ' + file) ++ sys.stdout.write(file + ' ') + sys.stdout.flush() + else: +- sys.stdout.write(' PYTHON {}{}{}\n'.format(blu, filepath + 'o', std)) +- if hasattr(imp, 'get_tag'): +- py_compile.compile(filepath, imp.cache_from_source(filepath, False), path) ++ sys.stdout.write(' PYCACHE {}{}{}\n'.format(blu, destpath(filepath), std)) ++ py_compile.compile(filepath, destpath(filepath), path) ++if not silent: ++ sys.stdout.write('\n')" "$@" 2>/dev/null || exit $? ++ ++# Then byte compile w/more optimization. ++# Only do this for Python 3.5+, see https://bugs.gnu.org/38043 for background. ++case $python_major.$python_minor in ++2.*|3.[0-4]) ++ ;; ++*) ++ $PYTHON -OO -c " ++import sys, os, py_compile, importlib ++ ++destpath = importlib.util.cache_from_source ++ ++silent = $silent ++blu = '''$blu''' ++std = '''$std''' ++ ++if not silent: ++ sys.stdout.write('Byte-compiling python modules (more optimized versions)' ++ ' ...\n') ++for file in sys.argv[1:]: ++ $pathtrans ++ $filetrans ++ if ( ++ not os.path.exists(filepath) ++ or not (len(filepath) >= 3 and filepath[-3:] == '.py') ++ ): ++ continue ++ if not silent: ++ sys.stdout.write(file + ' ') ++ sys.stdout.flush() + else: +- py_compile.compile(filepath, filepath + 'o', path) ++ sys.stdout.write(' PYCACHE {}{}{}\n'.format(blu, destpath(filepath), std)) ++ py_compile.compile(filepath, destpath(filepath), path) + if not silent: +- sys.stdout.write('\n')" 2>/dev/null || : ++ sys.stdout.write('\n')" "$@" 2>/dev/null || exit $? ++ ;; ++esac + + # Local Variables: + # mode: shell-script diff --git a/easybuild/easyconfigs/o/OpenAI-Gym/OpenAI-Gym-0.26.2-foss-2023a.eb b/easybuild/easyconfigs/o/OpenAI-Gym/OpenAI-Gym-0.26.2-foss-2023a.eb new file mode 100644 index 00000000000..c7ad7c7c04f --- /dev/null +++ b/easybuild/easyconfigs/o/OpenAI-Gym/OpenAI-Gym-0.26.2-foss-2023a.eb @@ -0,0 +1,53 @@ +easyblock = 'PythonBundle' + +name = 'OpenAI-Gym' +version = '0.26.2' + +homepage = 'https://gym.openai.com' +description = "A toolkit for developing and comparing reinforcement learning algorithms." + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [ + ('CMake', '3.26.3'), + ('SWIG', '4.1.1'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('Arcade-Learning-Environment', '0.8.1'), + ('OpenCV', '4.8.1', '-contrib'), + ('lz4', '1.9.4'), + ('pygame', '2.5.2'), + ('MuJoCo', '3.1.4'), +] + +use_pip = True + +exts_list = [ + ('cloudpickle', '3.0.0', { + 'checksums': ['996d9a482c6fb4f33c1a35335cf8afd065d2a56e973270364840712d9131a882'], + }), + ('gym-notices', '0.0.8', { + 'checksums': ['ad25e200487cafa369728625fe064e88ada1346618526102659b4640f2b4b911'], + }), + ('box2d-py', '2.3.8', { + 'modulename': 'Box2D', + 'checksums': ['bdacfbbc56079bb317548efe49d3d5a86646885cc27f4a2ee97e4b2960921ab7'], + }), + ('lz4', '4.3.3', { + 'checksums': ['01fe674ef2889dbb9899d8a67361e0c4a2c833af5aeb37dd505727cf5d2a131e'], + }), + ('gym', version, { + 'use_pip_extras': 'all', + 'checksums': ['e0d882f4b54f0c65f203104c24ab8a38b039f1289986803c7d02cdbe214fbcc4'], + }), +] + +local_envs = ['box2d', 'classic_control', 'mujoco', 'toy_text'] +sanity_check_commands = ["python -c 'import gym.envs.%s'" % e for e in local_envs] + +sanity_pip_check = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.24-GCC-13.2.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.24-GCC-13.2.0.eb index 4835813e357..8d2315fbe6e 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.24-GCC-13.2.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.24-GCC-13.2.0.eb @@ -20,6 +20,7 @@ patches = [ 'OpenBLAS-0.3.21_fix-order-vectorization.patch', 'OpenBLAS-0.3.23_disable-xDRGES-LAPACK-test.patch', 'OpenBLAS-0.3.24_fix-czasum.patch', + 'OpenBLAS-0.3.24_fix-A64FX.patch', ] checksums = [ {'v0.3.24.tar.gz': 'ceadc5065da97bd92404cac7254da66cc6eb192679cf1002098688978d4d5132'}, @@ -33,8 +34,8 @@ checksums = [ '08af834e5d60441fd35c128758ed9c092ba6887c829e0471ecd489079539047d'}, {'OpenBLAS-0.3.23_disable-xDRGES-LAPACK-test.patch': 'ab7e0af05f9b2a2ced32f3875e1e3767d9c3531a455421a38f7324350178a0ff'}, - {'OpenBLAS-0.3.24_fix-czasum.patch': - '8132b87c519fb08caa3bd7291fe8a1d0e1afe6fcb667d16f3020b46122afe20c'}, + {'OpenBLAS-0.3.24_fix-czasum.patch': '8132b87c519fb08caa3bd7291fe8a1d0e1afe6fcb667d16f3020b46122afe20c'}, + {'OpenBLAS-0.3.24_fix-A64FX.patch': '3712e8c3f0024c7bb327958779c388ad0234ad6d58b7b118e605256ec089964c'}, ] builddependencies = [ diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.24_fix-A64FX.patch b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.24_fix-A64FX.patch new file mode 100644 index 00000000000..ff4a16dea8d --- /dev/null +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.24_fix-A64FX.patch @@ -0,0 +1,138 @@ +fix installation of OpenBLAS 0.3.24 on Arm A64FX, +see https://github.com/OpenMathLib/OpenBLAS/pull/4258 + https://github.com/OpenMathLib/OpenBLAS/issues/4257 +diff --git a/kernel/arm64/KERNEL.A64FX b/kernel/arm64/KERNEL.A64FX +index bd25f7cd8a..ccbce27e1b 100644 +--- a/kernel/arm64/KERNEL.A64FX ++++ b/kernel/arm64/KERNEL.A64FX +@@ -57,7 +57,7 @@ CAMAXKERNEL = zamax.S + ZAMAXKERNEL = zamax.S + + SAXPYKERNEL = axpy.S +-DAXPYKERNEL = axpy.S ++DAXPYKERNEL = daxpy_thunderx2t99.S + CAXPYKERNEL = zaxpy.S + ZAXPYKERNEL = zaxpy.S + +@@ -81,45 +81,35 @@ DGEMVTKERNEL = gemv_t.S + CGEMVTKERNEL = zgemv_t.S + ZGEMVTKERNEL = zgemv_t.S + +- +-SASUMKERNEL = asum.S +-DASUMKERNEL = asum.S +-CASUMKERNEL = casum.S +-ZASUMKERNEL = zasum.S +- +-SCOPYKERNEL = copy.S +-DCOPYKERNEL = copy.S +-CCOPYKERNEL = copy.S +-ZCOPYKERNEL = copy.S +- +-SSWAPKERNEL = swap.S +-DSWAPKERNEL = swap.S +-CSWAPKERNEL = swap.S +-ZSWAPKERNEL = swap.S +- +-ISAMAXKERNEL = iamax.S +-IDAMAXKERNEL = iamax.S +-ICAMAXKERNEL = izamax.S +-IZAMAXKERNEL = izamax.S +- +-SNRM2KERNEL = nrm2.S +-DNRM2KERNEL = nrm2.S +-CNRM2KERNEL = znrm2.S +-ZNRM2KERNEL = znrm2.S +- +-DDOTKERNEL = dot.S +-ifneq ($(C_COMPILER), PGI) +-SDOTKERNEL = ../generic/dot.c +-else +-SDOTKERNEL = dot.S +-endif +-ifneq ($(C_COMPILER), PGI) +-CDOTKERNEL = zdot.S +-ZDOTKERNEL = zdot.S +-else +-CDOTKERNEL = ../arm/zdot.c +-ZDOTKERNEL = ../arm/zdot.c +-endif ++SASUMKERNEL = sasum_thunderx2t99.c ++DASUMKERNEL = dasum_thunderx2t99.c ++CASUMKERNEL = casum_thunderx2t99.c ++ZASUMKERNEL = zasum_thunderx2t99.c ++ ++SCOPYKERNEL = copy_thunderx2t99.c ++DCOPYKERNEL = copy_thunderx2t99.c ++CCOPYKERNEL = copy_thunderx2t99.c ++ZCOPYKERNEL = copy_thunderx2t99.c ++ ++SSWAPKERNEL = swap_thunderx2t99.S ++DSWAPKERNEL = swap_thunderx2t99.S ++CSWAPKERNEL = swap_thunderx2t99.S ++ZSWAPKERNEL = swap_thunderx2t99.S ++ ++ISAMAXKERNEL = iamax_thunderx2t99.c ++IDAMAXKERNEL = iamax_thunderx2t99.c ++ICAMAXKERNEL = izamax_thunderx2t99.c ++IZAMAXKERNEL = izamax_thunderx2t99.c ++ ++SNRM2KERNEL = scnrm2_thunderx2t99.c ++DNRM2KERNEL = dznrm2_thunderx2t99.c ++CNRM2KERNEL = scnrm2_thunderx2t99.c ++ZNRM2KERNEL = dznrm2_thunderx2t99.c ++ ++DDOTKERNEL = dot.c ++SDOTKERNEL = dot.c ++CDOTKERNEL = zdot_thunderx2t99.c ++ZDOTKERNEL = zdot_thunderx2t99.c + DSDOTKERNEL = dot.S + + DGEMM_BETA = dgemm_beta.S +@@ -128,10 +118,10 @@ SGEMM_BETA = sgemm_beta.S + SGEMMKERNEL = sgemm_kernel_sve_v2x$(SGEMM_UNROLL_N).S + STRMMKERNEL = strmm_kernel_sve_v1x$(SGEMM_UNROLL_N).S + +-SGEMMINCOPY = sgemm_ncopy_sve_v1.c +-SGEMMITCOPY = sgemm_tcopy_sve_v1.c +-SGEMMONCOPY = sgemm_ncopy_$(DGEMM_UNROLL_N).S +-SGEMMOTCOPY = sgemm_tcopy_$(DGEMM_UNROLL_N).S ++SGEMMINCOPY = gemm_ncopy_sve_v1x$(SGEMM_UNROLL_N).c ++SGEMMITCOPY = gemm_tcopy_sve_v1x$(SGEMM_UNROLL_N).c ++SGEMMONCOPY = sgemm_ncopy_$(SGEMM_UNROLL_N).S ++SGEMMOTCOPY = sgemm_tcopy_$(SGEMM_UNROLL_N).S + + SGEMMINCOPYOBJ = sgemm_incopy$(TSUFFIX).$(SUFFIX) + SGEMMITCOPYOBJ = sgemm_itcopy$(TSUFFIX).$(SUFFIX) +@@ -149,8 +139,8 @@ SSYMMLCOPY_M = symm_lcopy_sve.c + DGEMMKERNEL = dgemm_kernel_sve_v2x$(DGEMM_UNROLL_N).S + DTRMMKERNEL = dtrmm_kernel_sve_v1x$(DGEMM_UNROLL_N).S + +-DGEMMINCOPY = dgemm_ncopy_sve_v1.c +-DGEMMITCOPY = dgemm_tcopy_sve_v1.c ++DGEMMINCOPY = gemm_ncopy_sve_v1x$(DGEMM_UNROLL_N).c ++DGEMMITCOPY = gemm_tcopy_sve_v1x$(DGEMM_UNROLL_N).c + DGEMMONCOPY = dgemm_ncopy_$(DGEMM_UNROLL_N).S + DGEMMOTCOPY = dgemm_tcopy_$(DGEMM_UNROLL_N).S + +@@ -170,8 +160,8 @@ DSYMMLCOPY_M = symm_lcopy_sve.c + CGEMMKERNEL = cgemm_kernel_sve_v1x$(ZGEMM_UNROLL_N).S + CTRMMKERNEL = ctrmm_kernel_sve_v1x$(ZGEMM_UNROLL_N).S + +-CGEMMINCOPY = cgemm_ncopy_sve_v1.c +-CGEMMITCOPY = cgemm_tcopy_sve_v1.c ++CGEMMINCOPY = gemm_ncopy_complex_sve_v1x$(ZGEMM_UNROLL_N).c ++CGEMMITCOPY = gemm_tcopy_complex_sve_v1x$(ZGEMM_UNROLL_N).c + CGEMMONCOPY = ../generic/zgemm_ncopy_$(ZGEMM_UNROLL_N).c + CGEMMOTCOPY = ../generic/zgemm_tcopy_$(ZGEMM_UNROLL_N).c + +@@ -194,8 +184,8 @@ CSYMMLCOPY_M = zsymm_lcopy_sve.c + ZGEMMKERNEL = zgemm_kernel_sve_v1x$(ZGEMM_UNROLL_N).S + ZTRMMKERNEL = ztrmm_kernel_sve_v1x$(ZGEMM_UNROLL_N).S + +-ZGEMMINCOPY = zgemm_ncopy_sve_v1.c +-ZGEMMITCOPY = zgemm_tcopy_sve_v1.c ++ZGEMMINCOPY = gemm_ncopy_complex_sve_v1x$(ZGEMM_UNROLL_N).c ++ZGEMMITCOPY = gemm_tcopy_complex_sve_v1x$(ZGEMM_UNROLL_N).c + ZGEMMONCOPY = ../generic/zgemm_ncopy_$(ZGEMM_UNROLL_N).c + ZGEMMOTCOPY = ../generic/zgemm_tcopy_$(ZGEMM_UNROLL_N).c + diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.26_lapack_qr_noninittest.patch b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.26_lapack_qr_noninittest.patch new file mode 100644 index 00000000000..f6940980d1f --- /dev/null +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.26_lapack_qr_noninittest.patch @@ -0,0 +1,640 @@ +See https://github.com/OpenMathLib/OpenBLAS/issues/4625 +Uninitialized test results in the GEQP3RK routines introduced with LAPACK 3.12 +and in OpenBLAS 0.3.26 are causing abnormal number of errors. +Fixed with https://github.com/OpenMathLib/OpenBLAS/pull/4647 +(should not be needed for OpenBLAS > 0.3.27) +index 79d6add72e..b794d4664c 100644 +--- lapack-netlib/TESTING/LIN/cchkqp3rk.f.orig ++++ lapack-netlib/TESTING/LIN/cchkqp3rk.f +@@ -608,6 +608,9 @@ SUBROUTINE CCHKQP3RK( DOTYPE, NM, MVAL, NN, NVAL, NNS, NSVAL, + CALL CLACPY( 'All', M, NRHS, COPYB, LDA, + $ B, LDA ) + CALL ICOPY( N, IWORK( 1 ), 1, IWORK( N+1 ), 1 ) ++ DO I = 1, NTESTS ++ RESULT( I ) = ZERO ++ END DO + * + ABSTOL = -1.0 + RELTOl = -1.0 +@@ -652,16 +655,6 @@ SUBROUTINE CCHKQP3RK( DOTYPE, NM, MVAL, NN, NVAL, NNS, NSVAL, + RESULT( 1 ) = CQRT12( M, N, A, LDA, S, WORK, + $ LWORK , RWORK ) + * +- DO T = 1, 1 +- IF( RESULT( T ).GE.THRESH ) THEN +- IF( NFAIL.EQ.0 .AND. NERRS.EQ.0 ) +- $ CALL ALAHD( NOUT, PATH ) +- WRITE( NOUT, FMT = 9999 ) 'CGEQP3RK', M, N, +- $ NRHS, KMAX, ABSTOL, RELTOL, NB, NX, +- $ IMAT, T, RESULT( T ) +- NFAIL = NFAIL + 1 +- END IF +- END DO + NRUN = NRUN + 1 + * + * End test 1 +@@ -675,7 +668,7 @@ SUBROUTINE CCHKQP3RK( DOTYPE, NM, MVAL, NN, NVAL, NNS, NSVAL, + * 1-norm( A*P - Q*R ) / ( max(M,N) * 1-norm(A) * EPS ) + * + RESULT( 2 ) = CQPT01( M, N, KFACT, COPYA, A, LDA, TAU, +- $ IWORK( N+1 ), WORK, LWORK ) ++ $ IWORK( N+1 ), WORK, LWORK ) + * + * Compute test 3: + * +@@ -684,21 +677,8 @@ SUBROUTINE CCHKQP3RK( DOTYPE, NM, MVAL, NN, NVAL, NNS, NSVAL, + * 1-norm( Q**T * Q - I ) / ( M * EPS ) + * + RESULT( 3 ) = CQRT11( M, KFACT, A, LDA, TAU, WORK, +- $ LWORK ) ++ $ LWORK ) + * +-* Print information about the tests that did not pass +-* the threshold. +-* +- DO T = 2, 3 +- IF( RESULT( T ).GE.THRESH ) THEN +- IF( NFAIL.EQ.0 .AND. NERRS.EQ.0 ) +- $ CALL ALAHD( NOUT, PATH ) +- WRITE( NOUT, FMT = 9999 ) 'CGEQP3RK', M, N, +- $ NRHS, KMAX, ABSTOL, RELTOL, +- $ NB, NX, IMAT, T, RESULT( T ) +- NFAIL = NFAIL + 1 +- END IF +- END DO + NRUN = NRUN + 2 + * + * Compute test 4: +@@ -717,8 +697,8 @@ SUBROUTINE CCHKQP3RK( DOTYPE, NM, MVAL, NN, NVAL, NNS, NSVAL, + * + DO J = 1, KFACT-1, 1 + * +- DTEMP = (( ABS( A( (J-1)*M+J ) ) - +- $ ABS( A( (J)*M+J+1 ) ) ) / ++ DTEMP = (( ABS( A( (J-1)*LDA+J ) ) - ++ $ ABS( A( (J)*LDA+J+1 ) ) ) / + $ ABS( A(1) ) ) + * + IF( DTEMP.LT.ZERO ) THEN +@@ -727,20 +707,6 @@ SUBROUTINE CCHKQP3RK( DOTYPE, NM, MVAL, NN, NVAL, NNS, NSVAL, + * + END DO + * +-* Print information about the tests that did not +-* pass the threshold. +-* +- DO T = 4, 4 +- IF( RESULT( T ).GE.THRESH ) THEN +- IF( NFAIL.EQ.0 .AND. NERRS.EQ.0 ) +- $ CALL ALAHD( NOUT, PATH ) +- WRITE( NOUT, FMT = 9999 ) 'CGEQP3RK', +- $ M, N, NRHS, KMAX, ABSTOL, RELTOL, +- $ NB, NX, IMAT, T, +- $ RESULT( T ) +- NFAIL = NFAIL + 1 +- END IF +- END DO + NRUN = NRUN + 1 + * + * End test 4. +@@ -762,42 +728,41 @@ SUBROUTINE CCHKQP3RK( DOTYPE, NM, MVAL, NN, NVAL, NNS, NSVAL, + * + LWORK_MQR = MAX(1, NRHS) + CALL CUNMQR( 'Left', 'Conjugate transpose', +- $ M, NRHS, KFACT, A, LDA, TAU, B, LDA, +- $ WORK, LWORK_MQR, INFO ) ++ $ M, NRHS, KFACT, A, LDA, TAU, B, LDA, ++ $ WORK, LWORK_MQR, INFO ) + * + DO I = 1, NRHS + * + * Compare N+J-th column of A and J-column of B. + * + CALL CAXPY( M, -CONE, A( ( N+I-1 )*LDA+1 ), 1, +- $ B( ( I-1 )*LDA+1 ), 1 ) ++ $ B( ( I-1 )*LDA+1 ), 1 ) + END DO + * +- RESULT( 5 ) = +- $ ABS( +- $ CLANGE( 'One-norm', M, NRHS, B, LDA, RDUMMY ) / +- $ ( REAL( M )*SLAMCH( 'Epsilon' ) ) +- $ ) +-* +-* Print information about the tests that did not pass +-* the threshold. +-* +- DO T = 5, 5 +- IF( RESULT( T ).GE.THRESH ) THEN +- IF( NFAIL.EQ.0 .AND. NERRS.EQ.0 ) +- $ CALL ALAHD( NOUT, PATH ) +- WRITE( NOUT, FMT = 9999 ) 'CGEQP3RK', M, N, +- $ NRHS, KMAX, ABSTOL, RELTOL, +- $ NB, NX, IMAT, T, RESULT( T ) +- NFAIL = NFAIL + 1 +- END IF +- END DO ++ RESULT( 5 ) = ABS( ++ $ CLANGE( 'One-norm', M, NRHS, B, LDA, RDUMMY ) / ++ $ ( REAL( M )*SLAMCH( 'Epsilon' ) ) ) ++* + NRUN = NRUN + 1 + * + * End compute test 5. + * + END IF + * ++* Print information about the tests that did not pass ++* the threshold. ++* ++ DO T = 1, NTESTS ++ IF( RESULT( T ).GE.THRESH ) THEN ++ IF( NFAIL.EQ.0 .AND. NERRS.EQ.0 ) ++ $ CALL ALAHD( NOUT, PATH ) ++ WRITE( NOUT, FMT = 9999 ) 'CGEQP3RK', M, N, ++ $ NRHS, KMAX, ABSTOL, RELTOL, ++ $ NB, NX, IMAT, T, RESULT( T ) ++ NFAIL = NFAIL + 1 ++ END IF ++ END DO ++* + * END DO KMAX = 1, MIN(M,N)+1 + * + END DO +diff --git a/TESTING/LIN/dchkqp3rk.f b/TESTING/LIN/dchkqp3rk.f +index 434d2067e2..1834e63282 100755 +--- lapack-netlib/TESTING/LIN/dchkqp3rk.f.orig ++++ lapack-netlib/TESTING/LIN/dchkqp3rk.f +@@ -605,6 +605,9 @@ SUBROUTINE DCHKQP3RK( DOTYPE, NM, MVAL, NN, NVAL, NNS, NSVAL, + CALL DLACPY( 'All', M, NRHS, COPYB, LDA, + $ B, LDA ) + CALL ICOPY( N, IWORK( 1 ), 1, IWORK( N+1 ), 1 ) ++ DO I = 1, NTESTS ++ RESULT( I ) = ZERO ++ END DO + * + ABSTOL = -1.0 + RELTOL = -1.0 +@@ -648,16 +651,6 @@ SUBROUTINE DCHKQP3RK( DOTYPE, NM, MVAL, NN, NVAL, NNS, NSVAL, + RESULT( 1 ) = DQRT12( M, N, A, LDA, S, WORK, + $ LWORK ) + * +- DO T = 1, 1 +- IF( RESULT( T ).GE.THRESH ) THEN +- IF( NFAIL.EQ.0 .AND. NERRS.EQ.0 ) +- $ CALL ALAHD( NOUT, PATH ) +- WRITE( NOUT, FMT = 9999 ) 'DGEQP3RK', M, N, +- $ NRHS, KMAX, ABSTOL, RELTOL, NB, NX, +- $ IMAT, T, RESULT( T ) +- NFAIL = NFAIL + 1 +- END IF +- END DO + NRUN = NRUN + 1 + * + * End test 1 +@@ -671,7 +664,7 @@ SUBROUTINE DCHKQP3RK( DOTYPE, NM, MVAL, NN, NVAL, NNS, NSVAL, + * 1-norm( A*P - Q*R ) / ( max(M,N) * 1-norm(A) * EPS ) + * + RESULT( 2 ) = DQPT01( M, N, KFACT, COPYA, A, LDA, TAU, +- $ IWORK( N+1 ), WORK, LWORK ) ++ $ IWORK( N+1 ), WORK, LWORK ) + * + * Compute test 3: + * +@@ -680,21 +673,8 @@ SUBROUTINE DCHKQP3RK( DOTYPE, NM, MVAL, NN, NVAL, NNS, NSVAL, + * 1-norm( Q**T * Q - I ) / ( M * EPS ) + * + RESULT( 3 ) = DQRT11( M, KFACT, A, LDA, TAU, WORK, +- $ LWORK ) +-* +-* Print information about the tests that did not pass +-* the threshold. ++ $ LWORK ) + * +- DO T = 2, 3 +- IF( RESULT( T ).GE.THRESH ) THEN +- IF( NFAIL.EQ.0 .AND. NERRS.EQ.0 ) +- $ CALL ALAHD( NOUT, PATH ) +- WRITE( NOUT, FMT = 9999 ) 'DGEQP3RK', M, N, +- $ NRHS, KMAX, ABSTOL, RELTOL, +- $ NB, NX, IMAT, T, RESULT( T ) +- NFAIL = NFAIL + 1 +- END IF +- END DO + NRUN = NRUN + 2 + * + * Compute test 4: +@@ -713,8 +693,8 @@ SUBROUTINE DCHKQP3RK( DOTYPE, NM, MVAL, NN, NVAL, NNS, NSVAL, + * + DO J = 1, KFACT-1, 1 + +- DTEMP = (( ABS( A( (J-1)*M+J ) ) - +- $ ABS( A( (J)*M+J+1 ) ) ) / ++ DTEMP = (( ABS( A( (J-1)*LDA+J ) ) - ++ $ ABS( A( (J)*LDA+J+1 ) ) ) / + $ ABS( A(1) ) ) + * + IF( DTEMP.LT.ZERO ) THEN +@@ -723,20 +703,6 @@ SUBROUTINE DCHKQP3RK( DOTYPE, NM, MVAL, NN, NVAL, NNS, NSVAL, + * + END DO + * +-* Print information about the tests that did not +-* pass the threshold. +-* +- DO T = 4, 4 +- IF( RESULT( T ).GE.THRESH ) THEN +- IF( NFAIL.EQ.0 .AND. NERRS.EQ.0 ) +- $ CALL ALAHD( NOUT, PATH ) +- WRITE( NOUT, FMT = 9999 ) 'DGEQP3RK', +- $ M, N, NRHS, KMAX, ABSTOL, RELTOL, +- $ NB, NX, IMAT, T, +- $ RESULT( T ) +- NFAIL = NFAIL + 1 +- END IF +- END DO + NRUN = NRUN + 1 + * + * End test 4. +@@ -758,42 +724,41 @@ SUBROUTINE DCHKQP3RK( DOTYPE, NM, MVAL, NN, NVAL, NNS, NSVAL, + * + LWORK_MQR = MAX(1, NRHS) + CALL DORMQR( 'Left', 'Transpose', +- $ M, NRHS, KFACT, A, LDA, TAU, B, LDA, +- $ WORK, LWORK_MQR, INFO ) ++ $ M, NRHS, KFACT, A, LDA, TAU, B, LDA, ++ $ WORK, LWORK_MQR, INFO ) + * + DO I = 1, NRHS + * + * Compare N+J-th column of A and J-column of B. + * + CALL DAXPY( M, -ONE, A( ( N+I-1 )*LDA+1 ), 1, +- $ B( ( I-1 )*LDA+1 ), 1 ) ++ $ B( ( I-1 )*LDA+1 ), 1 ) + END DO + * +- RESULT( 5 ) = +- $ ABS( +- $ DLANGE( 'One-norm', M, NRHS, B, LDA, RDUMMY ) / +- $ ( DBLE( M )*DLAMCH( 'Epsilon' ) ) +- $ ) +-* +-* Print information about the tests that did not pass +-* the threshold. +-* +- DO T = 5, 5 +- IF( RESULT( T ).GE.THRESH ) THEN +- IF( NFAIL.EQ.0 .AND. NERRS.EQ.0 ) +- $ CALL ALAHD( NOUT, PATH ) +- WRITE( NOUT, FMT = 9999 ) 'DGEQP3RK', M, N, +- $ NRHS, KMAX, ABSTOL, RELTOL, +- $ NB, NX, IMAT, T, RESULT( T ) +- NFAIL = NFAIL + 1 +- END IF +- END DO ++ RESULT( 5 ) = ABS( ++ $ DLANGE( 'One-norm', M, NRHS, B, LDA, RDUMMY ) / ++ $ ( DBLE( M )*DLAMCH( 'Epsilon' ) ) ) ++* + NRUN = NRUN + 1 + * + * End compute test 5. + * + END IF + * ++* Print information about the tests that did not ++* pass the threshold. ++* ++ DO T = 1, NTESTS ++ IF( RESULT( T ).GE.THRESH ) THEN ++ IF( NFAIL.EQ.0 .AND. NERRS.EQ.0 ) ++ $ CALL ALAHD( NOUT, PATH ) ++ WRITE( NOUT, FMT = 9999 ) 'DGEQP3RK', M, N, ++ $ NRHS, KMAX, ABSTOL, RELTOL, NB, NX, ++ $ IMAT, T, RESULT( T ) ++ NFAIL = NFAIL + 1 ++ END IF ++ END DO ++* + * END DO KMAX = 1, MIN(M,N)+1 + * + END DO +diff --git a/TESTING/LIN/schkqp3rk.f b/TESTING/LIN/schkqp3rk.f +index 36cf9370ea..c5ce7ff609 100755 +--- lapack-netlib/TESTING/LIN/schkqp3rk.f.orig ++++ lapack-netlib/TESTING/LIN/schkqp3rk.f +@@ -604,6 +604,9 @@ SUBROUTINE SCHKQP3RK( DOTYPE, NM, MVAL, NN, NVAL, NNS, NSVAL, + CALL SLACPY( 'All', M, NRHS, COPYB, LDA, + $ B, LDA ) + CALL ICOPY( N, IWORK( 1 ), 1, IWORK( N+1 ), 1 ) ++ DO I = 1, NTESTS ++ RESULT( I ) = ZERO ++ END DO + * + ABSTOL = -1.0 + RELTOL = -1.0 +@@ -647,16 +650,6 @@ SUBROUTINE SCHKQP3RK( DOTYPE, NM, MVAL, NN, NVAL, NNS, NSVAL, + RESULT( 1 ) = SQRT12( M, N, A, LDA, S, WORK, + $ LWORK ) + * +- DO T = 1, 1 +- IF( RESULT( T ).GE.THRESH ) THEN +- IF( NFAIL.EQ.0 .AND. NERRS.EQ.0 ) +- $ CALL ALAHD( NOUT, PATH ) +- WRITE( NOUT, FMT = 9999 ) 'SGEQP3RK', M, N, +- $ NRHS, KMAX, ABSTOL, RELTOL, NB, NX, +- $ IMAT, T, RESULT( T ) +- NFAIL = NFAIL + 1 +- END IF +- END DO + NRUN = NRUN + 1 + * + * End test 1 +@@ -670,7 +663,7 @@ SUBROUTINE SCHKQP3RK( DOTYPE, NM, MVAL, NN, NVAL, NNS, NSVAL, + * 1-norm( A*P - Q*R ) / ( max(M,N) * 1-norm(A) * EPS ) + * + RESULT( 2 ) = SQPT01( M, N, KFACT, COPYA, A, LDA, TAU, +- $ IWORK( N+1 ), WORK, LWORK ) ++ $ IWORK( N+1 ), WORK, LWORK ) + * + * Compute test 3: + * +@@ -679,21 +672,8 @@ SUBROUTINE SCHKQP3RK( DOTYPE, NM, MVAL, NN, NVAL, NNS, NSVAL, + * 1-norm( Q**T * Q - I ) / ( M * EPS ) + * + RESULT( 3 ) = SQRT11( M, KFACT, A, LDA, TAU, WORK, +- $ LWORK ) ++ $ LWORK ) + * +-* Print information about the tests that did not pass +-* the threshold. +-* +- DO T = 2, 3 +- IF( RESULT( T ).GE.THRESH ) THEN +- IF( NFAIL.EQ.0 .AND. NERRS.EQ.0 ) +- $ CALL ALAHD( NOUT, PATH ) +- WRITE( NOUT, FMT = 9999 ) 'SGEQP3RK', M, N, +- $ NRHS, KMAX, ABSTOL, RELTOL, +- $ NB, NX, IMAT, T, RESULT( T ) +- NFAIL = NFAIL + 1 +- END IF +- END DO + NRUN = NRUN + 2 + * + * Compute test 4: +@@ -712,8 +692,8 @@ SUBROUTINE SCHKQP3RK( DOTYPE, NM, MVAL, NN, NVAL, NNS, NSVAL, + * + DO J = 1, KFACT-1, 1 + +- DTEMP = (( ABS( A( (J-1)*M+J ) ) - +- $ ABS( A( (J)*M+J+1 ) ) ) / ++ DTEMP = (( ABS( A( (J-1)*LDA+J ) ) - ++ $ ABS( A( (J)*LDA+J+1 ) ) ) / + $ ABS( A(1) ) ) + * + IF( DTEMP.LT.ZERO ) THEN +@@ -722,20 +702,6 @@ SUBROUTINE SCHKQP3RK( DOTYPE, NM, MVAL, NN, NVAL, NNS, NSVAL, + * + END DO + * +-* Print information about the tests that did not +-* pass the threshold. +-* +- DO T = 4, 4 +- IF( RESULT( T ).GE.THRESH ) THEN +- IF( NFAIL.EQ.0 .AND. NERRS.EQ.0 ) +- $ CALL ALAHD( NOUT, PATH ) +- WRITE( NOUT, FMT = 9999 ) 'SGEQP3RK', +- $ M, N, NRHS, KMAX, ABSTOL, RELTOL, +- $ NB, NX, IMAT, T, +- $ RESULT( T ) +- NFAIL = NFAIL + 1 +- END IF +- END DO + NRUN = NRUN + 1 + * + * End test 4. +@@ -757,42 +723,41 @@ SUBROUTINE SCHKQP3RK( DOTYPE, NM, MVAL, NN, NVAL, NNS, NSVAL, + * + LWORK_MQR = MAX(1, NRHS) + CALL SORMQR( 'Left', 'Transpose', +- $ M, NRHS, KFACT, A, LDA, TAU, B, LDA, +- $ WORK, LWORK_MQR, INFO ) ++ $ M, NRHS, KFACT, A, LDA, TAU, B, LDA, ++ $ WORK, LWORK_MQR, INFO ) + * + DO I = 1, NRHS + * + * Compare N+J-th column of A and J-column of B. + * + CALL SAXPY( M, -ONE, A( ( N+I-1 )*LDA+1 ), 1, +- $ B( ( I-1 )*LDA+1 ), 1 ) ++ $ B( ( I-1 )*LDA+1 ), 1 ) + END DO + * +- RESULT( 5 ) = +- $ ABS( +- $ SLANGE( 'One-norm', M, NRHS, B, LDA, RDUMMY ) / +- $ ( REAL( M )*SLAMCH( 'Epsilon' ) ) +- $ ) +-* +-* Print information about the tests that did not pass +-* the threshold. +-* +- DO T = 5, 5 +- IF( RESULT( T ).GE.THRESH ) THEN +- IF( NFAIL.EQ.0 .AND. NERRS.EQ.0 ) +- $ CALL ALAHD( NOUT, PATH ) +- WRITE( NOUT, FMT = 9999 ) 'SGEQP3RK', M, N, +- $ NRHS, KMAX, ABSTOL, RELTOL, +- $ NB, NX, IMAT, T, RESULT( T ) +- NFAIL = NFAIL + 1 +- END IF +- END DO ++ RESULT( 5 ) = ABS( ++ $ SLANGE( 'One-norm', M, NRHS, B, LDA, RDUMMY ) / ++ $ ( REAL( M )*SLAMCH( 'Epsilon' ) ) ) ++* + NRUN = NRUN + 1 + * + * End compute test 5. + * + END IF + * ++* Print information about the tests that did not pass ++* the threshold. ++* ++ DO T = 1, NTESTS ++ IF( RESULT( T ).GE.THRESH ) THEN ++ IF( NFAIL.EQ.0 .AND. NERRS.EQ.0 ) ++ $ CALL ALAHD( NOUT, PATH ) ++ WRITE( NOUT, FMT = 9999 ) 'SGEQP3RK', M, N, ++ $ NRHS, KMAX, ABSTOL, RELTOL, ++ $ NB, NX, IMAT, T, RESULT( T ) ++ NFAIL = NFAIL + 1 ++ END IF ++ END DO ++* + * END DO KMAX = 1, MIN(M,N)+1 + * + END DO +diff --git a/TESTING/LIN/zchkqp3rk.f b/TESTING/LIN/zchkqp3rk.f +index 302c7b1a87..5092058837 100644 +--- lapack-netlib/TESTING/LIN/zchkqp3rk.f.orig ++++ lapack-netlib/TESTING/LIN/zchkqp3rk.f +@@ -608,6 +608,9 @@ SUBROUTINE ZCHKQP3RK( DOTYPE, NM, MVAL, NN, NVAL, NNS, NSVAL, + CALL ZLACPY( 'All', M, NRHS, COPYB, LDA, + $ B, LDA ) + CALL ICOPY( N, IWORK( 1 ), 1, IWORK( N+1 ), 1 ) ++ DO I = 1, NTESTS ++ RESULT( I ) = ZERO ++ END DO + * + ABSTOL = -1.0 + RELTOl = -1.0 +@@ -652,16 +655,6 @@ SUBROUTINE ZCHKQP3RK( DOTYPE, NM, MVAL, NN, NVAL, NNS, NSVAL, + RESULT( 1 ) = ZQRT12( M, N, A, LDA, S, WORK, + $ LWORK , RWORK ) + * +- DO T = 1, 1 +- IF( RESULT( T ).GE.THRESH ) THEN +- IF( NFAIL.EQ.0 .AND. NERRS.EQ.0 ) +- $ CALL ALAHD( NOUT, PATH ) +- WRITE( NOUT, FMT = 9999 ) 'ZGEQP3RK', M, N, +- $ NRHS, KMAX, ABSTOL, RELTOL, NB, NX, +- $ IMAT, T, RESULT( T ) +- NFAIL = NFAIL + 1 +- END IF +- END DO + NRUN = NRUN + 1 + * + * End test 1 +@@ -675,7 +668,7 @@ SUBROUTINE ZCHKQP3RK( DOTYPE, NM, MVAL, NN, NVAL, NNS, NSVAL, + * 1-norm( A*P - Q*R ) / ( max(M,N) * 1-norm(A) * EPS ) + * + RESULT( 2 ) = ZQPT01( M, N, KFACT, COPYA, A, LDA, TAU, +- $ IWORK( N+1 ), WORK, LWORK ) ++ $ IWORK( N+1 ), WORK, LWORK ) + * + * Compute test 3: + * +@@ -684,21 +677,8 @@ SUBROUTINE ZCHKQP3RK( DOTYPE, NM, MVAL, NN, NVAL, NNS, NSVAL, + * 1-norm( Q**T * Q - I ) / ( M * EPS ) + * + RESULT( 3 ) = ZQRT11( M, KFACT, A, LDA, TAU, WORK, +- $ LWORK ) ++ $ LWORK ) + * +-* Print information about the tests that did not pass +-* the threshold. +-* +- DO T = 2, 3 +- IF( RESULT( T ).GE.THRESH ) THEN +- IF( NFAIL.EQ.0 .AND. NERRS.EQ.0 ) +- $ CALL ALAHD( NOUT, PATH ) +- WRITE( NOUT, FMT = 9999 ) 'ZGEQP3RK', M, N, +- $ NRHS, KMAX, ABSTOL, RELTOL, +- $ NB, NX, IMAT, T, RESULT( T ) +- NFAIL = NFAIL + 1 +- END IF +- END DO + NRUN = NRUN + 2 + * + * Compute test 4: +@@ -717,8 +697,8 @@ SUBROUTINE ZCHKQP3RK( DOTYPE, NM, MVAL, NN, NVAL, NNS, NSVAL, + * + DO J = 1, KFACT-1, 1 + * +- DTEMP = (( ABS( A( (J-1)*M+J ) ) - +- $ ABS( A( (J)*M+J+1 ) ) ) / ++ DTEMP = (( ABS( A( (J-1)*LDA+J ) ) - ++ $ ABS( A( (J)*LDA+J+1 ) ) ) / + $ ABS( A(1) ) ) + * + IF( DTEMP.LT.ZERO ) THEN +@@ -727,20 +707,6 @@ SUBROUTINE ZCHKQP3RK( DOTYPE, NM, MVAL, NN, NVAL, NNS, NSVAL, + * + END DO + * +-* Print information about the tests that did not +-* pass the threshold. +-* +- DO T = 4, 4 +- IF( RESULT( T ).GE.THRESH ) THEN +- IF( NFAIL.EQ.0 .AND. NERRS.EQ.0 ) +- $ CALL ALAHD( NOUT, PATH ) +- WRITE( NOUT, FMT = 9999 ) 'ZGEQP3RK', +- $ M, N, NRHS, KMAX, ABSTOL, RELTOL, +- $ NB, NX, IMAT, T, +- $ RESULT( T ) +- NFAIL = NFAIL + 1 +- END IF +- END DO + NRUN = NRUN + 1 + * + * End test 4. +@@ -762,42 +728,41 @@ SUBROUTINE ZCHKQP3RK( DOTYPE, NM, MVAL, NN, NVAL, NNS, NSVAL, + * + LWORK_MQR = MAX(1, NRHS) + CALL ZUNMQR( 'Left', 'Conjugate transpose', +- $ M, NRHS, KFACT, A, LDA, TAU, B, LDA, +- $ WORK, LWORK_MQR, INFO ) ++ $ M, NRHS, KFACT, A, LDA, TAU, B, LDA, ++ $ WORK, LWORK_MQR, INFO ) + * + DO I = 1, NRHS + * + * Compare N+J-th column of A and J-column of B. + * + CALL ZAXPY( M, -CONE, A( ( N+I-1 )*LDA+1 ), 1, +- $ B( ( I-1 )*LDA+1 ), 1 ) ++ $ B( ( I-1 )*LDA+1 ), 1 ) + END DO + * +- RESULT( 5 ) = +- $ ABS( +- $ ZLANGE( 'One-norm', M, NRHS, B, LDA, RDUMMY ) / +- $ ( DBLE( M )*DLAMCH( 'Epsilon' ) ) +- $ ) +-* +-* Print information about the tests that did not pass +-* the threshold. +-* +- DO T = 5, 5 +- IF( RESULT( T ).GE.THRESH ) THEN +- IF( NFAIL.EQ.0 .AND. NERRS.EQ.0 ) +- $ CALL ALAHD( NOUT, PATH ) +- WRITE( NOUT, FMT = 9999 ) 'ZGEQP3RK', M, N, +- $ NRHS, KMAX, ABSTOL, RELTOL, +- $ NB, NX, IMAT, T, RESULT( T ) +- NFAIL = NFAIL + 1 +- END IF +- END DO ++ RESULT( 5 ) = ABS( ++ $ ZLANGE( 'One-norm', M, NRHS, B, LDA, RDUMMY ) / ++ $ ( DBLE( M )*DLAMCH( 'Epsilon' ) ) ) ++* + NRUN = NRUN + 1 + * + * End compute test 5. + * + END IF + * ++* Print information about the tests that did not pass ++* the threshold. ++* ++ DO T = 1, NTESTS ++ IF( RESULT( T ).GE.THRESH ) THEN ++ IF( NFAIL.EQ.0 .AND. NERRS.EQ.0 ) ++ $ CALL ALAHD( NOUT, PATH ) ++ WRITE( NOUT, FMT = 9999 ) 'ZGEQP3RK', M, N, ++ $ NRHS, KMAX, ABSTOL, RELTOL, ++ $ NB, NX, IMAT, T, RESULT( T ) ++ NFAIL = NFAIL + 1 ++ END IF ++ END DO ++* + * END DO KMAX = 1, MIN(M,N)+1 + * + END DO diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.27-GCC-13.2.0-seq-iface64.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.27-GCC-13.2.0-seq-iface64.eb new file mode 100644 index 00000000000..f205e063da9 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.27-GCC-13.2.0-seq-iface64.eb @@ -0,0 +1,60 @@ +name = 'OpenBLAS' +version = '0.3.27' +versionsuffix = '-seq-iface64' + +homepage = 'https://www.openblas.net/' +description = "OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version." + +toolchain = {'name': 'GCC', 'version': '13.2.0'} + +source_urls = [ + # order matters, trying to download the large.tgz/timing.tgz LAPACK tarballs from GitHub causes trouble + 'https://www.netlib.org/lapack/timing/', + 'https://github.com/xianyi/OpenBLAS/archive/', +] +sources = ['v%(version)s.tar.gz'] +patches = [ + ('large.tgz', '.'), + ('timing.tgz', '.'), + 'OpenBLAS-0.3.15_workaround-gcc-miscompilation.patch', + 'OpenBLAS-0.3.21_fix-order-vectorization.patch', + 'OpenBLAS-0.3.26_lapack_qr_noninittest.patch', + 'OpenBLAS-0.3.27_fix_zscal.patch', + 'OpenBLAS-0.3.27_riscv-drop-static-fortran-flag.patch', +] +checksums = [ + {'v0.3.27.tar.gz': 'aa2d68b1564fe2b13bc292672608e9cdeeeb6dc34995512e65c3b10f4599e897'}, + {'large.tgz': 'f328d88b7fa97722f271d7d0cfea1c220e0f8e5ed5ff01d8ef1eb51d6f4243a1'}, + {'timing.tgz': '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af'}, + {'OpenBLAS-0.3.15_workaround-gcc-miscompilation.patch': + 'e6b326fb8c4a8a6fd07741d9983c37a72c55c9ff9a4f74a80e1352ce5f975971'}, + {'OpenBLAS-0.3.21_fix-order-vectorization.patch': + '08af834e5d60441fd35c128758ed9c092ba6887c829e0471ecd489079539047d'}, + {'OpenBLAS-0.3.26_lapack_qr_noninittest.patch': '4781bf1d7b239374fd8069e15b4e2c0ef0e8efaa1a7d4c33557bd5b27e5de77c'}, + {'OpenBLAS-0.3.27_fix_zscal.patch': '9210d7b66538dabaddbe1bfceb16f8225708856f60876ca5561b19d3599f9fd1'}, + {'OpenBLAS-0.3.27_riscv-drop-static-fortran-flag.patch': + 'f374e41efffd592ab1c9034df9e7abf1045ed151f4fc0fd0da618ce9826f2d4b'}, +] + +builddependencies = [ + ('make', '4.4.1'), + # required by LAPACK test suite + ('Python', '3.11.5'), +] + +# INTERFACE64=1 needs if you link OpenBLAS for fortran code compied with 64 bit integers (-i8) +# This would be in intel library naming convention ilp64 +# The USE_OPENMP=0 and USE_THREAD=0 needs for the single threaded version +# The USE_LOCKING=1 needs for thread safe version (if threaded software calls OpenBLAS, without it +# OpenBLAS is not thread safe (so only single threaded software would be able to use it) +buildopts = "INTERFACE64=1 USE_OPENMP=0 USE_THREAD=0 USE_LOCKING=1 " +testopts = buildopts +installopts = buildopts + +run_lapack_tests = True +max_failing_lapack_tests_num_errors = 150 + +# extensive testing can be enabled by uncommenting the line below +# runtest = 'PATH=.:$PATH lapack-timing' + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.27-GCC-13.3.0-seq-iface64.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.27-GCC-13.3.0-seq-iface64.eb new file mode 100644 index 00000000000..5527c667f66 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.27-GCC-13.3.0-seq-iface64.eb @@ -0,0 +1,60 @@ +name = 'OpenBLAS' +version = '0.3.27' +versionsuffix = '-seq-iface64' + +homepage = 'https://www.openblas.net/' +description = "OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version." + +toolchain = {'name': 'GCC', 'version': '13.3.0'} + +source_urls = [ + # order matters, trying to download the large.tgz/timing.tgz LAPACK tarballs from GitHub causes trouble + 'https://www.netlib.org/lapack/timing/', + 'https://github.com/xianyi/OpenBLAS/archive/', +] +sources = ['v%(version)s.tar.gz'] +patches = [ + ('large.tgz', '.'), + ('timing.tgz', '.'), + 'OpenBLAS-0.3.15_workaround-gcc-miscompilation.patch', + 'OpenBLAS-0.3.21_fix-order-vectorization.patch', + 'OpenBLAS-0.3.26_lapack_qr_noninittest.patch', + 'OpenBLAS-0.3.27_fix_zscal.patch', + 'OpenBLAS-0.3.27_riscv-drop-static-fortran-flag.patch', +] +checksums = [ + {'v0.3.27.tar.gz': 'aa2d68b1564fe2b13bc292672608e9cdeeeb6dc34995512e65c3b10f4599e897'}, + {'large.tgz': 'f328d88b7fa97722f271d7d0cfea1c220e0f8e5ed5ff01d8ef1eb51d6f4243a1'}, + {'timing.tgz': '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af'}, + {'OpenBLAS-0.3.15_workaround-gcc-miscompilation.patch': + 'e6b326fb8c4a8a6fd07741d9983c37a72c55c9ff9a4f74a80e1352ce5f975971'}, + {'OpenBLAS-0.3.21_fix-order-vectorization.patch': + '08af834e5d60441fd35c128758ed9c092ba6887c829e0471ecd489079539047d'}, + {'OpenBLAS-0.3.26_lapack_qr_noninittest.patch': '4781bf1d7b239374fd8069e15b4e2c0ef0e8efaa1a7d4c33557bd5b27e5de77c'}, + {'OpenBLAS-0.3.27_fix_zscal.patch': '9210d7b66538dabaddbe1bfceb16f8225708856f60876ca5561b19d3599f9fd1'}, + {'OpenBLAS-0.3.27_riscv-drop-static-fortran-flag.patch': + 'f374e41efffd592ab1c9034df9e7abf1045ed151f4fc0fd0da618ce9826f2d4b'}, +] + +builddependencies = [ + ('make', '4.4.1'), + # required by LAPACK test suite + ('Python', '3.12.3'), +] + +# INTERFACE64=1 needs if you link OpenBLAS for fortran code compied with 64 bit integers (-i8) +# This would be in intel library naming convention ilp64 +# The USE_OPENMP=0 and USE_THREAD=0 needs for the single threaded version +# The USE_LOCKING=1 needs for thread safe version (if threaded software calls OpenBLAS, without it +# OpenBLAS is not thread safe (so only single threaded software would be able to use it) +buildopts = "INTERFACE64=1 USE_OPENMP=0 USE_THREAD=0 USE_LOCKING=1 " +testopts = buildopts +installopts = buildopts + +run_lapack_tests = True +max_failing_lapack_tests_num_errors = 150 + +# extensive testing can be enabled by uncommenting the line below +# runtest = 'PATH=.:$PATH lapack-timing' + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.27-GCC-13.3.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.27-GCC-13.3.0.eb new file mode 100644 index 00000000000..c65deccb6e9 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.27-GCC-13.3.0.eb @@ -0,0 +1,50 @@ +name = 'OpenBLAS' +version = '0.3.27' + +homepage = 'https://www.openblas.net/' +description = "OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version." + +toolchain = {'name': 'GCC', 'version': '13.3.0'} + +source_urls = [ + # order matters, trying to download the large.tgz/timing.tgz LAPACK tarballs from GitHub causes trouble + 'https://www.netlib.org/lapack/timing/', + 'https://github.com/xianyi/OpenBLAS/archive/', +] +sources = ['v%(version)s.tar.gz'] +patches = [ + ('large.tgz', '.'), + ('timing.tgz', '.'), + 'OpenBLAS-0.3.15_workaround-gcc-miscompilation.patch', + 'OpenBLAS-0.3.21_fix-order-vectorization.patch', + 'OpenBLAS-0.3.26_lapack_qr_noninittest.patch', + 'OpenBLAS-0.3.27_fix_zscal.patch', + 'OpenBLAS-0.3.27_riscv-drop-static-fortran-flag.patch', +] +checksums = [ + {'v0.3.27.tar.gz': 'aa2d68b1564fe2b13bc292672608e9cdeeeb6dc34995512e65c3b10f4599e897'}, + {'large.tgz': 'f328d88b7fa97722f271d7d0cfea1c220e0f8e5ed5ff01d8ef1eb51d6f4243a1'}, + {'timing.tgz': '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af'}, + {'OpenBLAS-0.3.15_workaround-gcc-miscompilation.patch': + 'e6b326fb8c4a8a6fd07741d9983c37a72c55c9ff9a4f74a80e1352ce5f975971'}, + {'OpenBLAS-0.3.21_fix-order-vectorization.patch': + '08af834e5d60441fd35c128758ed9c092ba6887c829e0471ecd489079539047d'}, + {'OpenBLAS-0.3.26_lapack_qr_noninittest.patch': '4781bf1d7b239374fd8069e15b4e2c0ef0e8efaa1a7d4c33557bd5b27e5de77c'}, + {'OpenBLAS-0.3.27_fix_zscal.patch': '9210d7b66538dabaddbe1bfceb16f8225708856f60876ca5561b19d3599f9fd1'}, + {'OpenBLAS-0.3.27_riscv-drop-static-fortran-flag.patch': + 'f374e41efffd592ab1c9034df9e7abf1045ed151f4fc0fd0da618ce9826f2d4b'}, +] + +builddependencies = [ + ('make', '4.4.1'), + # required by LAPACK test suite + ('Python', '3.12.3'), +] + +run_lapack_tests = True +max_failing_lapack_tests_num_errors = 150 + +# extensive testing can be enabled by uncommenting the line below +# runtest = 'PATH=.:$PATH lapack-timing' + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.27_fix_zscal.patch b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.27_fix_zscal.patch new file mode 100644 index 00000000000..81c1b32e77a --- /dev/null +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.27_fix_zscal.patch @@ -0,0 +1,38 @@ +From 62f7b244ff5c268f311e5f080d1f44c3b432f3d0 Mon Sep 17 00:00:00 2001 +From: Bart Oldeman +Date: Fri, 24 May 2024 17:20:27 +0000 +Subject: [PATCH] Replace use of FLT_MAX in x86_64 zscal.c by isinf() + +Commit def4996 fixed issues with inf and nan values in zscal, +but used FLT_MAX, where DBL_MAX or isinf() is more appropriate, +as FLT_MAX is for single precision only. +Using FLT_MAX caused test case failures in the LAPACK tests. + +isinf() is consistent with the later fix 969601a1 +--- + kernel/x86_64/zscal.c | 4 ++-- + 1 file changed, 2 insertions(+), 2 deletions(-) + +diff --git a/kernel/x86_64/zscal.c b/kernel/x86_64/zscal.c +index bc79c0cafd..075b6091fe 100644 +--- a/kernel/x86_64/zscal.c ++++ b/kernel/x86_64/zscal.c +@@ -394,7 +394,7 @@ int CNAME(BLASLONG n, BLASLONG dummy0, BLASLONG dummy1, FLOAT da_r, FLOAT da_i, + } + + } +- else if (da_r < -FLT_MAX || da_r > FLT_MAX) { ++ else if (isinf(da_r)) { + while(j < n) + { + x[i]= NAN; +@@ -410,7 +410,7 @@ int CNAME(BLASLONG n, BLASLONG dummy0, BLASLONG dummy1, FLOAT da_r, FLOAT da_i, + while(j < n) + { + temp0 = -da_i * x[i+1]; +- if (x[i] < -FLT_MAX || x[i] > FLT_MAX) ++ if (isinf(x[i])) + temp0 = NAN; + x[i+1] = da_i * x[i]; + if ( x[i] == x[i]) //preserve NaN + diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.27_riscv-drop-static-fortran-flag.patch b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.27_riscv-drop-static-fortran-flag.patch new file mode 100644 index 00000000000..262c6bc5bd0 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.27_riscv-drop-static-fortran-flag.patch @@ -0,0 +1,31 @@ +From df87aeb5a2a3785e15a3d94dbf92e2e03448500f Mon Sep 17 00:00:00 2001 +From: Martin Kroeker +Date: Tue, 4 Jun 2024 09:49:18 +0200 +Subject: [PATCH] Drop the -static Fortran flag from generic builds as it + breaks OpenMP + +--- + Makefile.riscv64 | 6 +++--- + 1 file changed, 3 insertions(+), 3 deletions(-) + +diff --git a/Makefile.riscv64 b/Makefile.riscv64 +index 113cc57c53..9f6e48b7ad 100644 +--- a/Makefile.riscv64 ++++ b/Makefile.riscv64 +@@ -8,13 +8,13 @@ FCOMMON_OPT += -march=rv64imafdcv_zba_zbb_zfh -mabi=lp64d -static + endif + ifeq ($(CORE), RISCV64_ZVL256B) + CCOMMON_OPT += -march=rv64imafdcv_zvl256b -mabi=lp64d +-FCOMMON_OPT += -march=rv64imafdcv -mabi=lp64d -static ++FCOMMON_OPT += -march=rv64imafdcv -mabi=lp64d + endif + ifeq ($(CORE), RISCV64_ZVL128B) + CCOMMON_OPT += -march=rv64imafdcv -mabi=lp64d +-FCOMMON_OPT += -march=rv64imafdcv -mabi=lp64d -static ++FCOMMON_OPT += -march=rv64imafdcv -mabi=lp64d + endif + ifeq ($(CORE), RISCV64_GENERIC) + CCOMMON_OPT += -march=rv64imafdc -mabi=lp64d +-FCOMMON_OPT += -march=rv64imafdc -mabi=lp64d -static ++FCOMMON_OPT += -march=rv64imafdc -mabi=lp64d + endif diff --git a/easybuild/easyconfigs/o/OpenEXR/OpenEXR-3.2.4-GCCcore-13.3.0.eb b/easybuild/easyconfigs/o/OpenEXR/OpenEXR-3.2.4-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..f6e66db69ae --- /dev/null +++ b/easybuild/easyconfigs/o/OpenEXR/OpenEXR-3.2.4-GCCcore-13.3.0.eb @@ -0,0 +1,38 @@ +easyblock = 'CMakeMake' + +name = 'OpenEXR' +version = '3.2.4' + +homepage = 'https://www.openexr.com/' +description = """OpenEXR is a high dynamic-range (HDR) image file format developed by Industrial Light & Magic + for use in computer imaging applications""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://github.com/%(namelower)s/%(namelower)s/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['81e6518f2c4656fdeaf18a018f135e96a96e7f66dbe1c1f05860dd94772176cc'] + +builddependencies = [ + ('binutils', '2.42'), + ('CMake', '3.29.3'), +] +dependencies = [ + ('Imath', '3.1.11'), + ('zlib', '1.3.1') +] + +local_libs, local_bins = [ + ['Iex', 'IlmThread', 'OpenEXR', 'OpenEXRUtil'], + ['envmap', 'header', 'makepreview', 'maketiled', 'multipart', 'multiview', 'stdattr'] +] + +sanity_check_paths = { + 'files': ( + ['lib/lib%s.%s' % (s, SHLIB_EXT) for s in local_libs] + + ['bin/exr%s' % b for b in local_bins] + ), + 'dirs': ['include/%(name)s', 'share'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/o/OpenFOAM-Extend/OpenFOAM-Extend-4.1-20210705-foss-2023a-Python-2.7.18.eb b/easybuild/easyconfigs/o/OpenFOAM-Extend/OpenFOAM-Extend-4.1-20210705-foss-2023a-Python-2.7.18.eb new file mode 100644 index 00000000000..b65ce71cf76 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenFOAM-Extend/OpenFOAM-Extend-4.1-20210705-foss-2023a-Python-2.7.18.eb @@ -0,0 +1,66 @@ +easyblock = 'EB_OpenFOAM' + +name = 'OpenFOAM-Extend' +local_commit = 'aa97a0' +version = '4.1-20210705' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.extend-project.de/' +description = """OpenFOAM is a free, open source CFD software package. +OpenFOAM has an extensive range of features to solve anything from complex fluid flows +involving chemical reactions, turbulence and heat transfer, +to solid dynamics and electromagnetics.""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'usempi': True} + +sources = [{ + 'filename': '%%(name)s-%%(version)s-%s.tar.gz' % local_commit, + 'git_config': { + 'url': 'https://git.code.sf.net/p/foam-extend/', + 'repo_name': 'foam-extend-4.1', + 'commit': local_commit, + }, +}] +patches = [ + 'OpenFOAM-Extend-3.2-ParMGridGen.patch', + 'OpenFOAM-Extend-3.1_build-qa.patch', + 'OpenFOAM-Extend-4.1_comp-mpi.patch', + 'OpenFOAM-Extend-3.1_skip-ThirdParty-OpenMPI.patch', + 'OpenFOAM-Extend-4.1-20210705_fix-private-PackedList.patch', +] +checksums = [ + # no checksum for OpenFOAM-Extend-4.1-20200408-f2c557.tar.gz since it's created from git repo, + # and hence resuluting tarball won't be exactly the same on all systems + None, + 'f7676a7a12ced7c74caea64c62826a28449fdb2beb8b5be2c4ae7528ffece16e', # OpenFOAM-Extend-3.2-ParMGridGen.patch + '14dcc12ea7191ba42a9c297fcb2f4fbc2c55bf57226029489aa116e2d060b4bf', # OpenFOAM-Extend-3.1_build-qa.patch + 'e71a77b6f39653f9a0d4b0ce6691433c742df74f23402782c69a8b736c98eb7a', # OpenFOAM-Extend-4.1_comp-mpi.patch + # OpenFOAM-Extend-3.1_skip-ThirdParty-OpenMPI.patch + 'c88b23cd2f5dcf3bd86e02d7ea5dc6719c2049cf4b20e39f1b3262381dee3c50', + # OpenFOAM-Extend-4.1-20210705_fix-private-PackedList.patch + '47868f35d9a899047be8da451df46e165fc813bc809b96b1c35a0cccddb1a9e6', +] + +builddependencies = [ + ('flex', '2.6.4'), + ('Bison', '3.8.2'), + ('M4', '1.4.19'), + ('CMake', '3.26.3'), +] + +dependencies = [ + ('hwloc', '2.9.1'), + ('ParMETIS', '4.0.3'), + ('METIS', '5.1.0'), # order matters, METIS need to be listed after ParMETIS to get $CPATH right + ('SCOTCH', '7.0.3'), + ('Mesquite', '2.3.0'), + ('ParMGridGen', '1.0'), + ('Python', '2.7.18'), + # Libccmio v2.6.1, zoltan v3.5 +] + +# too many builds in parallel actually slows down the build +maxparallel = 4 + +moduleclass = 'cae' diff --git a/easybuild/easyconfigs/o/OpenFOAM-Extend/OpenFOAM-Extend-4.1-20210705_fix-private-PackedList.patch b/easybuild/easyconfigs/o/OpenFOAM-Extend/OpenFOAM-Extend-4.1-20210705_fix-private-PackedList.patch new file mode 100644 index 00000000000..84229fdd90a --- /dev/null +++ b/easybuild/easyconfigs/o/OpenFOAM-Extend/OpenFOAM-Extend-4.1-20210705_fix-private-PackedList.patch @@ -0,0 +1,14 @@ +fix for: +error: class Foam::UList Foam::UList::UList is private within this context +see also https://sourceforge.net/p/foam-extend/tickets/68/ +--- foam-extend-4.1-20210705/src/foam/containers/Lists/PackedList/PackedList.H.orig 2024-09-12 21:13:26.103914000 +0200 ++++ foam-extend-4.1-20210705/src/foam/containers/Lists/PackedList/PackedList.H 2024-09-12 21:13:53.608924991 +0200 +@@ -147,7 +147,7 @@ + class PackedList + : + public PackedListCore, +- private List ++ public List + { + protected: + diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-10-foss-2022a-20230119-int64.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-10-foss-2022a-20230119-int64.eb new file mode 100644 index 00000000000..5c5f4d70f9f --- /dev/null +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-10-foss-2022a-20230119-int64.eb @@ -0,0 +1,42 @@ +name = 'OpenFOAM' + +version = '10' +_version_patch = '20230119' +versionsuffix = '-%s-int64' % _version_patch + +homepage = 'https://www.openfoam.org/' +description = """OpenFOAM is a free, open source CFD software package. + OpenFOAM has an extensive range of features to solve anything from complex fluid flows + involving chemical reactions, turbulence and heat transfer, + to solid dynamics and electromagnetics.""" + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'vectorize': False, 'i8': True} + +source_urls = ['https://github.com/OpenFOAM/OpenFOAM-%(version_major)s/archive'] +sources = [{ + 'download_filename': '%s.tar.gz' % _version_patch, + 'filename': 'OpenFOAM-%s-%s.tar.gz' % (version, _version_patch), +}] +patches = ['OpenFOAM-%(version_major)s-ThirdParty.patch'] +checksums = [ + {'OpenFOAM-10-20230119.tar.gz': '86f8cb18d4f59812b129ce7d669e8ff498da442fbdb46705492fbba3cbda82ab'}, + {'OpenFOAM-10-ThirdParty.patch': '307df0206cdb24533f4974378843332064f4a2d85cf0638c20fc4c87b1524b43'}, +] + +builddependencies = [ + ('Bison', '3.8.2'), + ('CMake', '3.23.1'), + ('flex', '2.6.4'), +] + +dependencies = [ + ('ncurses', '6.3'), + ('METIS', '5.1.0', '-int64'), + ('SCOTCH', '7.0.1', '-int64'), + ('CGAL', '4.14.3'), + ('ParaView', '5.10.1', '-mpi'), + ('gnuplot', '5.4.4'), +] + +moduleclass = 'cae' diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-10-foss-2022a-20230119.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-10-foss-2022a-20230119.eb index f9ebf346635..fd18ec3e287 100644 --- a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-10-foss-2022a-20230119.eb +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-10-foss-2022a-20230119.eb @@ -11,6 +11,7 @@ description = """OpenFOAM is a free, open source CFD software package. to solid dynamics and electromagnetics.""" toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'vectorize': False} source_urls = ['https://github.com/OpenFOAM/OpenFOAM-%(version_major)s/archive'] sources = [{ diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-10-foss-2022a.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-10-foss-2022a.eb index 7fafa63937c..3bdaaf4f06e 100644 --- a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-10-foss-2022a.eb +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-10-foss-2022a.eb @@ -8,6 +8,7 @@ description = """OpenFOAM is a free, open source CFD software package. to solid dynamics and electromagnetics.""" toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'vectorize': False} source_urls = ['https://github.com/OpenFOAM/OpenFOAM-%(version_major)s/archive'] sources = ['version-%(version)s.tar.gz'] diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-10-foss-2023a.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-10-foss-2023a.eb index c4358543285..4989e318c7c 100644 --- a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-10-foss-2023a.eb +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-10-foss-2023a.eb @@ -8,6 +8,7 @@ description = """OpenFOAM is a free, open source CFD software package. to solid dynamics and electromagnetics.""" toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'vectorize': False} source_urls = ['https://github.com/OpenFOAM/OpenFOAM-%(version_major)s/archive'] sources = ['version-%(version)s.tar.gz'] diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-11-foss-2022a.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-11-foss-2022a.eb index 9481f562349..e4abfa2f3e2 100644 --- a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-11-foss-2022a.eb +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-11-foss-2022a.eb @@ -8,6 +8,7 @@ description = """OpenFOAM is a free, open source CFD software package. to solid dynamics and electromagnetics.""" toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'vectorize': False} source_urls = ['https://github.com/OpenFOAM/OpenFOAM-%(version_major)s/archive'] sources = ['version-%(version)s.tar.gz'] diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-11-foss-2023a.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-11-foss-2023a.eb index 1ce1045701d..c2cabe755a3 100644 --- a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-11-foss-2023a.eb +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-11-foss-2023a.eb @@ -8,6 +8,7 @@ description = """OpenFOAM is a free, open source CFD software package. to solid dynamics and electromagnetics.""" toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'vectorize': False} source_urls = ['https://github.com/OpenFOAM/OpenFOAM-%(version_major)s/archive'] sources = ['version-%(version)s.tar.gz'] diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-12-ThirdParty.patch b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-12-ThirdParty.patch new file mode 100644 index 00000000000..e8a0b33adf7 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-12-ThirdParty.patch @@ -0,0 +1,397 @@ +# This patch removes all need for the ThirdParty files of OpenFOAM: +# we use EB dependencies for everything. It adjusts the paths, variables, etc +# We also let the install dir, compiler, etc be set by EB. +# Aligned hunks by Leon Kos and updated by Simon Branford (University of Birmingham). +# Based on patch for OpenFOAM 5.0 and 4.1 by Kenneth Hoste (HPC-UGent) and Ward Poelmans + +diff -ru OpenFOAM-12-version-12/applications/utilities/postProcessing/graphics/PVReaders/Allwmake OpenFOAM-12/applications/utilities/postProcessing/graphics/PVReaders/Allwmake +--- OpenFOAM-12-version-12/applications/utilities/postProcessing/graphics/PVReaders/Allwmake ++++ OpenFOAM-12/applications/utilities/postProcessing/graphics/PVReaders/Allwmake +@@ -11,8 +11,8 @@ + fi + + # Ensure CMake gets the correct C/C++ compilers +-[ -n "$WM_CC" ] && export CC="$WM_CC" +-[ -n "$WM_CXX" ] && export CXX="$WM_CXX" ++#[ -n "$WM_CC" ] && export CC="$WM_CC" ++#[ -n "$WM_CXX" ] && export CXX="$WM_CXX" + + wmake $targetType vtkPVblockMesh + wmake $targetType vtkPVFoam +diff -ru OpenFOAM-12-version-12/applications/utilities/postProcessing/graphics/PVReaders/CMakeLists.txt OpenFOAM-12/applications/utilities/postProcessing/graphics/PVReaders/CMakeLists.txt +--- OpenFOAM-12-version-12/applications/utilities/postProcessing/graphics/PVReaders/CMakeLists.txt ++++ OpenFOAM-12/applications/utilities/postProcessing/graphics/PVReaders/CMakeLists.txt +@@ -2,6 +2,8 @@ + + PROJECT(PVReaders) + ++FIND_PACKAGE(MPI REQUIRED) ++ + FIND_PACKAGE(ParaView REQUIRED) + + INCLUDE(GNUInstallDirs) +diff -ru OpenFOAM-12-version-12/etc/bashrc OpenFOAM-12/etc/bashrc +--- OpenFOAM-12-version-12/etc/bashrc ++++ OpenFOAM-12/etc/bashrc +@@ -43,12 +43,13 @@ + # + [ "$BASH" ] && bashrcFile=${BASH_SOURCE} + [ "$ZSH_NAME" ] && bashrcFile=$0 +-if [ -n "$bashrcFile" ] +-then +- export FOAM_INST_DIR=$(cd $(dirname $bashrcFile)/../.. && pwd -P) +-else +- export FOAM_INST_DIR=$HOME/$WM_PROJECT +-fi ++#if [ -n "$bashrcFile" ] ++#then ++# export FOAM_INST_DIR=$(cd $(dirname $bashrcFile)/../.. && pwd -P) ++#else ++# export FOAM_INST_DIR=$HOME/$WM_PROJECT ++#fi ++# For Easybuild: set by the module + unset bashrcFile + # + # Please set to the appropriate path if the above default is not correct. E.g., +diff -ru OpenFOAM-12-version-12/etc/config.sh/gperftools OpenFOAM-12/etc/config.sh/gperftools +--- OpenFOAM-12-version-12/etc/config.sh/gperftools ++++ OpenFOAM-12/etc/config.sh/gperftools +@@ -29,13 +29,7 @@ + # + #------------------------------------------------------------------------------ + +-version=svn +-gperftools_install=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER +- +-GPERFTOOLS_VERSION=gperftools-$version +-GPERFTOOLS_ARCH_PATH=$gperftools_install/$GPERFTOOLS_VERSION +- +-export PATH=$GPERFTOOLS_ARCH_PATH/bin:$PATH +-export LD_LIBRARY_PATH=$GPERFTOOLS_ARCH_PATH/lib:$LD_LIBRARY_PATH ++GPERFTOOLS_VERSION=gperftools-$EBVERSIONGPERFTOOLS ++GPERFTOOLS_ARCH_PATH=$EBROOTGPERFTOOLS + + #------------------------------------------------------------------------------ +diff -ru OpenFOAM-12-version-12/etc/config.sh/metis OpenFOAM-12/etc/config.sh/metis +--- OpenFOAM-12-version-12/etc/config.sh/metis ++++ OpenFOAM-12/etc/config.sh/metis +@@ -37,32 +37,8 @@ + # Load functions + . $WM_PROJECT_DIR/etc/config.sh/functions + +-# Find the path to the metis installation +-case "$METIS_TYPE" in +-none) +- ;; +-system) +- export METIS_VERSION=system +- export METIS_ARCH_PATH=/usr +- ;; +-OpenFOAM | ThirdParty) +- # Look for the source directory +- if [ -z "$METIS_VERSION" ] +- then +- metisSrcDir=$(_foamMostRecentDir "$WM_THIRD_PARTY_DIR"/metis-*) +- else +- metisSrcDir=$WM_THIRD_PARTY_DIR/metis-$METIS_VERSION +- fi +- # Set the version and the installation path +- if [ -d "$metisSrcDir" ] +- then +- export METIS_VERSION=${metisSrcDir##*metis-} +- export METIS_ARCH_PATH=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER$WM_PRECISION_OPTION$WM_LABEL_OPTION/metis-$METIS_VERSION +- fi +- # Clean up +- unset metisSrcDir +- ;; +-esac ++export METIS_VERSION=metis-$EBVERSIONMETIS ++export METIS_ARCH_PATH=$EBROOTMETIS + + # Unload functions + . $WM_PROJECT_DIR/etc/config.sh/functions +diff -ru OpenFOAM-12-version-12/etc/config.sh/mpi OpenFOAM-12/etc/config.sh/mpi +--- OpenFOAM-12-version-12/etc/config.sh/mpi ++++ OpenFOAM-12/etc/config.sh/mpi +@@ -254,6 +254,9 @@ + _foamAddPath $MPI_ARCH_PATH/bin64 + _foamAddLib $MPI_ARCH_PATH/lib/release + ;; ++EASYBUILDMPI) ++ export FOAM_MPI=mpi ++ ;; + *) + export FOAM_MPI=dummy + ;; +diff -ru OpenFOAM-12-version-12/etc/config.sh/paraview OpenFOAM-12/etc/config.sh/paraview +--- OpenFOAM-12-version-12/etc/config.sh/paraview ++++ OpenFOAM-12/etc/config.sh/paraview +@@ -38,117 +38,13 @@ + ) \ + && PATH="$cleaned" + +-# Detect the most recent version of cmake available and add to the PATH +-cmakeDir=$(_foamMostRecentDir "$WM_THIRD_PARTY_DIR"/platforms/$WM_ARCH$WM_COMPILER/cmake-*) +-if [ -n "$cmakeDir" ] +-then +- export PATH=$cmakeDir/bin:$PATH +-fi +-unset cmakeDir +- +-# Set up the paraview environment +-case "$ParaView_TYPE" in +-none) +- ;; +- +-system) +- +- # Look for a paraview installation +- if pvserverExe=$(which pvserver 2> /dev/null) +- then +- paraviewBinDir=$(dirname $pvserverExe) +- paraviewBinDir=$(cd $paraviewBinDir && pwd -P) +- fi +- +- # Set the environment +- if [ -d "$paraviewBinDir" ] +- then +- export ParaView_DIR=$(dirname $paraviewBinDir) +- export ParaView_LIB_DIR=$(unset LD_LIBRARY_PATH && \ +- ldd $paraviewBinDir/paraview | \ +- grep -o "/.*/libpqCore-pv.*.so" | \ +- xargs dirname) +- export ParaView_VERSION=$(unset LD_LIBRARY_PATH && \ +- pvserver --version 2> /dev/null | \ +- awk '{print $NF}') +- export ParaView_MAJOR=${ParaView_VERSION%.*} +- export ParaView_INCLUDE_DIR=$ParaView_DIR/include/paraview-$ParaView_MAJOR +- export PV_PLUGIN_PATH=$FOAM_LIBBIN/paraview-$ParaView_MAJOR +- +- # Add to the library path +- export LD_LIBRARY_PATH=$ParaView_LIB_DIR:$PV_PLUGIN_PATH:$LD_LIBRARY_PATH +- fi +- +- unset pvserverExe paraviewBinDir +- ;; +- +-paraviewopenfoam) +- +- # Look for a paraview installation. The version should be set externally. +- if [ -n "$ParaView_VERSION" ] +- then +- export ParaView_MAJOR=${ParaView_VERSION%.*} +- paraviewDir=/opt/paraviewopenfoam$(echo "$ParaView_MAJOR" | tr -d '.') +- fi +- +- # Set the environment +- if [ -d "$paraviewDir" ] +- then +- export ParaView_DIR=$paraviewDir +- export ParaView_LIB_DIR=$(echo "$ParaView_DIR"/lib* | tr ' ' ':') +- export ParaView_INCLUDE_DIR=$ParaView_DIR/include/paraview-$ParaView_MAJOR +- export PV_PLUGIN_PATH=$FOAM_LIBBIN/paraview-$ParaView_MAJOR +- +- # Add to the path and the library path +- export PATH=$ParaView_DIR/bin:$PATH +- export LD_LIBRARY_PATH=$ParaView_LIB_DIR:$PV_PLUGIN_PATH:$LD_LIBRARY_PATH +- fi +- +- unset paraviewDir +- ;; +- +-OpenFOAM | ThirdParty) +- +- # Look for a paraview installation +- if [ -z "$ParaView_VERSION" ] +- then +- paraviewDir=$(_foamMostRecentDir "$WM_THIRD_PARTY_DIR"/platforms/$WM_ARCH$WM_COMPILER/ParaView-*) +- else +- paraviewDir=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER/ParaView-$ParaView_VERSION +- fi +- +- # Set the environment +- if [ -d "$paraviewDir" ] +- then +- export ParaView_DIR=$paraviewDir +- export ParaView_LIB_DIR=$(echo "$ParaView_DIR"/lib* | tr ' ' ':') +- export ParaView_VERSION=${paraviewDir##*ParaView-} +- export ParaView_MAJOR=${ParaView_VERSION%.*} +- export ParaView_INCLUDE_DIR=$paraviewDir/include/paraview-$ParaView_MAJOR +- export PV_PLUGIN_PATH=$FOAM_LIBBIN/paraview-$ParaView_MAJOR +- +- # Add to the path and the library path +- export PATH=$ParaView_DIR/bin:$PATH +- export LD_LIBRARY_PATH=$ParaView_LIB_DIR:$PV_PLUGIN_PATH:$LD_LIBRARY_PATH +- +- # Add in python libraries if required +- paraviewPython=$ParaView_DIR/Utilities/VTKPythonWrapping +- if [ -r "$paraviewPython" ] +- then +- if [ "$PYTHONPATH" ] +- then +- export PYTHONPATH=$PYTHONPATH:$paraviewPython:$ParaView_LIB_DIR +- else +- export PYTHONPATH=$paraviewPython:$ParaView_LIB_DIR +- fi +- fi +- unset paraviewPython +- fi +- +- unset paraviewDir +- ;; +- +-esac ++export ParaView_VERSION=$EBVERSIONPARAVIEW ++export ParaView_MAJOR=${ParaView_VERSION%.*} ++export ParaView_DIR=$EBROOTPARAVIEW ++export ParaView_LIB_DIR=$ParaView_DIR/lib ++export ParaView_INCLUDE_DIR=$ParaView_DIR/include/paraview-$ParaView_MAJOR ++export PV_PLUGIN_PATH=$FOAM_LIBBIN/paraview-$ParaView_MAJOR ++export LD_LIBRARY_PATH=$ParaView_LIB_DIR:$PV_PLUGIN_PATH:$LD_LIBRARY_PATH + + # Report + if [ "$FOAM_VERBOSE" ] && [ "$PS1" ] && [ -d "$ParaView_DIR" ] +diff -ru OpenFOAM-12-version-12/etc/config.sh/scotch OpenFOAM-12/etc/config.sh/scotch +--- OpenFOAM-12-version-12/etc/config.sh/scotch ++++ OpenFOAM-12/etc/config.sh/scotch +@@ -37,32 +37,8 @@ + # Load functions + . $WM_PROJECT_DIR/etc/config.sh/functions + +-# Find the path to the scotch installation +-case "$SCOTCH_TYPE" in +-none) +- ;; +-system) +- export SCOTCH_VERSION=system +- export SCOTCH_ARCH_PATH=/usr +- ;; +-OpenFOAM | ThirdParty) +- # Look for the source directory +- if [ -z "$SCOTCH_VERSION" ] +- then +- scotchSrcDir=$(_foamMostRecentDir "$WM_THIRD_PARTY_DIR"/scotch_*) +- else +- scotchSrcDir=$WM_THIRD_PARTY_DIR/scotch_$SCOTCH_VERSION +- fi +- # Set the version and the installation path +- if [ -d "$scotchSrcDir" ] +- then +- export SCOTCH_VERSION=${scotchSrcDir##*scotch_} +- export SCOTCH_ARCH_PATH=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER$WM_PRECISION_OPTION$WM_LABEL_OPTION/scotch_$SCOTCH_VERSION +- fi +- # Clean up +- unset scotchSrcDir +- ;; +-esac ++export SCOTCH_VERSION=scotch_$EBVERSIONSCOTCH ++export SCOTCH_ARCH_PATH=$EBROOTSCOTCH + + # Unload functions + . $WM_PROJECT_DIR/etc/config.sh/functions +diff -ru OpenFOAM-12-version-12/etc/config.sh/zoltan OpenFOAM-12/etc/config.sh/zoltan +--- OpenFOAM-12-version-12/etc/config.sh/zoltan ++++ OpenFOAM-12/etc/config.sh/zoltan +@@ -37,32 +37,8 @@ + # Load functions + . $WM_PROJECT_DIR/etc/config.sh/functions + +-# Find the path to the zoltan installation +-case "$ZOLTAN_TYPE" in +-none) +- ;; +-system) +- export ZOLTAN_VERSION=system +- export ZOLTAN_ARCH_PATH=/usr +- ;; +-OpenFOAM | ThirdParty) +- # Look for the source directory +- if [ -z "$ZOLTAN_VERSION" ] +- then +- zoltanSrcDir=$(_foamMostRecentDir "$WM_THIRD_PARTY_DIR"/Zoltan-*) +- else +- zoltanSrcDir=$WM_THIRD_PARTY_DIR/Zoltan-$ZOLTAN_VERSION +- fi +- # Set the version and the installation path +- if [ -d "$zoltanSrcDir" ] +- then +- export ZOLTAN_VERSION=${zoltanSrcDir##*Zoltan-} +- export ZOLTAN_ARCH_PATH=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER$WM_PRECISION_OPTION$WM_LABEL_OPTION/Zoltan-$ZOLTAN_VERSION +- fi +- # Clean up +- unset zoltanSrcDir +- ;; +-esac ++export ZOLTAN_VERSION=Zoltan-$EBVERSIONZOLTAN ++export ZOLTAN_ARCH_PATH=$EBROOTZOLTAN + + # Unload functions + . $WM_PROJECT_DIR/etc/config.sh/functions +diff -ru OpenFOAM-12-version-12/etc/config.sh/settings OpenFOAM-12/etc/config.sh/settings +--- OpenFOAM-12-version-12/etc/config.sh/settings ++++ OpenFOAM-12/etc/config.sh/settings +@@ -63,11 +63,11 @@ + 64) + WM_ARCH=linux64 + export WM_COMPILER_LIB_ARCH=64 +- export WM_CC='gcc' +- export WM_CXX='g++' +- export WM_CFLAGS='-m64 -fPIC' +- export WM_CXXFLAGS='-m64 -fPIC -std=c++0x' +- export WM_LDFLAGS='-m64' ++ export WM_CC=$CC ++ export WM_CXX=$CXX ++ export WM_CFLAGS=$CFLAGS ++ export WM_CXXFLAGS=$CXXFLAGS ++ export WM_LDFLAGS=$LDFLAGS + ;; + *) + echo "Unknown WM_ARCH_OPTION '$WM_ARCH_OPTION', should be 32 or 64"\ +diff -ru OpenFOAM-12-version-12/src/parallel/decompose/ptscotch/Make/options OpenFOAM-12/src/parallel/decompose/ptscotch/Make/options +--- OpenFOAM-12-version-12/src/parallel/decompose/ptscotch/Make/options ++++ OpenFOAM-12/src/parallel/decompose/ptscotch/Make/options +@@ -6,15 +6,7 @@ + $(PFLAGS) $(PINC) \ + -I$(FOAM_SRC)/Pstream/mpi/lnInclude \ + -I$(SCOTCH_ARCH_PATH)/include/$(FOAM_MPI) \ +- -I$(SCOTCH_ARCH_PATH)/include \ +- -I$(or $(PTSCOTCH_INCLUDE_DIR),/usr/include/scotch) \ + -I../decompositionMethods/lnInclude + + LIB_LIBS = \ +- -L$(SCOTCH_ARCH_PATH)/lib \ +- $(if $(PTSCOTCH_LIB_DIR),-L$(PTSCOTCH_LIB_DIR)) \ +- -L$(FOAM_EXT_LIBBIN)/$(FOAM_MPI) \ +- -lptscotch \ +- -lptscotcherrexit \ +- -lscotch \ +- -lrt ++ -L$(SCOTCH_ARCH_PATH)/lib -L$(FOAM_EXT_LIBBIN)/$(FOAM_MPI) -lptscotch -lptscotcherrexit -lscotch ${LINK_FLAGS} -lrt +diff -ru OpenFOAM-12-version-12/src/parallel/decompose/ptscotch/ptscotch.C OpenFOAM-12/src/parallel/decompose/ptscotch/ptscotch.C +--- OpenFOAM-12-version-12/src/parallel/decompose/ptscotch/ptscotch.C ++++ OpenFOAM-12/src/parallel/decompose/ptscotch/ptscotch.C +@@ -31,10 +31,11 @@ + #include "SubField.H" + #include "PstreamGlobals.H" + ++#include ++#include ++ + extern "C" + { + #include +- #include +- #include "ptscotch.h" + } + +diff -ru OpenFOAM-12-version-12/src/parallel/decompose/scotch/Make/options OpenFOAM-12/src/parallel/decompose/scotch/Make/options +--- OpenFOAM-12-version-12/src/parallel/decompose/scotch/Make/options ++++ OpenFOAM-12/src/parallel/decompose/scotch/Make/options +@@ -6,7 +6,6 @@ + EXE_INC = \ + $(PFLAGS) $(PINC) \ + -I$(SCOTCH_ARCH_PATH)/include \ +- -I$(or $(SCOTCH_INCLUDE_DIR),/usr/include/scotch) \ + -I../decompositionMethods/lnInclude + + LIB_LIBS = \ diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-12-foss-2023a.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-12-foss-2023a.eb new file mode 100644 index 00000000000..ed565315859 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-12-foss-2023a.eb @@ -0,0 +1,38 @@ +name = 'OpenFOAM' +version = '12' + +homepage = 'https://www.openfoam.org/' +description = """OpenFOAM is a free, open source CFD software package. + OpenFOAM has an extensive range of features to solve anything from complex fluid flows + involving chemical reactions, turbulence and heat transfer, + to solid dynamics and electromagnetics.""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'vectorize': False} + +source_urls = ['https://github.com/OpenFOAM/OpenFOAM-%(version_major)s/archive'] +sources = ['version-%(version)s.tar.gz'] +patches = ['OpenFOAM-12-ThirdParty.patch'] +checksums = [ + {'version-12.tar.gz': 'e59fad54c62e64f1bb89dbaebe5f99a76dc0a6a91d9aad86042a7c4cef6d0744'}, + {'OpenFOAM-12-ThirdParty.patch': 'b8a9abf3b8479d32d87654d833501f54abe57ceb9f06f7d2412a3e52d20108ec'}, +] + +builddependencies = [ + ('Bison', '3.8.2'), + ('CMake', '3.26.3'), + ('flex', '2.6.4'), +] + +dependencies = [ + ('ncurses', '6.4'), + # OpenFOAM requires 64 bit METIS using 32 bit indexes (array indexes) + ('METIS', '5.1.0'), + ('SCOTCH', '7.0.3'), + ('CGAL', '5.6'), + ('ParaView', '5.11.2'), + ('gnuplot', '5.4.8'), + ('Zoltan', '3.901'), +] + +moduleclass = 'cae' diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2212-wmake-OpenMPI.patch b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2212-wmake-OpenMPI.patch index 0cd23ac34f7..4c442fa0060 100644 --- a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2212-wmake-OpenMPI.patch +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2212-wmake-OpenMPI.patch @@ -1,6 +1,36 @@ +# - Corrected output of "wmake -show-c" and "wmake -show-c++" with OpenMPI in +# order to allow compilation of paraFoam. This is required as we define the +# compiler as "OMPI_CC=gcc mpicc" when using OpenMPI +# (this patch should not be removed in future versions due to this definition) # - Add mplibEASYBUILDMPI configuration for wmake (OpenMPI version) # # author: Jiri Furst +--- OpenFOAM-v2112/wmake/makefiles/info.orig 2019-11-07 18:12:53.000000000 +0100 ++++ OpenFOAM-v2112/wmake/makefiles/info 2019-11-23 12:52:50.700688579 +0100 +@@ -73,19 +73,19 @@ + + .PHONY: c + c: +- @echo "$(firstword $(cc))" ++ @echo "$(lastword $(cc))" + + .PHONY: cxx + cxx: +- @echo "$(firstword $(CC))" ++ @echo "$(lastword $(CC))" + + .PHONY: cflags + cflags: +- @echo "$(wordlist 2,$(words $(COMPILE_C)), $(COMPILE_C))" ++ @echo "$(wordlist 3,$(words $(COMPILE_C)), $(COMPILE_C))" + + .PHONY: cxxflags + cxxflags: +- @echo "$(wordlist 2,$(words $(COMPILE_CXX)), $(COMPILE_CXX))" ++ @echo "$(wordlist 3,$(words $(COMPILE_CXX)), $(COMPILE_CXX))" + + .PHONY: cflags-arch + cflags-arch: --- /dev/null 2023-03-06 18:30:28.397302047 +0100 +++ OpenFOAM-v2212/wmake/rules/General/mplibEASYBUILDMPI 2023-03-10 14:52:38.100740228 +0100 @@ -0,0 +1,6 @@ diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2306-foss-2022b.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2306-foss-2022b.eb index 74d81fdd5a1..02ee224e98b 100644 --- a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2306-foss-2022b.eb +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2306-foss-2022b.eb @@ -22,7 +22,7 @@ patches = [ checksums = [ {'OpenFOAM-v2306.tgz': 'd7fba773658c0f06ad17f90199565f32e9bf502b7bb03077503642064e1f5344'}, {'OpenFOAM-v2206-cleanup.patch': '25333124581acae57c173587de4ebd6e143b894b1a26e4f0326db8b7e0cb1972'}, - {'OpenFOAM-v2212-wmake-OpenMPI.patch': '4f5110e98df1f057dc4b478a004e4ae2dc5cc763899f0d3ceb6773315c5c8ba9'}, + {'OpenFOAM-v2212-wmake-OpenMPI.patch': '241dc4898c22aab0cbd10c1ea931a07a786508ee03462d45dbc1c202fee3ebe8'}, ] builddependencies = [ @@ -30,6 +30,8 @@ builddependencies = [ ('CMake', '3.24.3'), ('flex', '2.6.4'), ('CGAL', '5.5.2'), # header only + ('GMP', '6.2.1'), + ('MPFR', '4.2.0'), ] dependencies = [ diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2312-foss-2023a.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2312-foss-2023a.eb index 661327ff9a6..b7f522ba479 100644 --- a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2312-foss-2023a.eb +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2312-foss-2023a.eb @@ -22,7 +22,7 @@ patches = [ checksums = [ {'OpenFOAM-v2312.tgz': 'f113183a4d027c93939212af8967053c5f8fe76fb62e5848cb11bbcf8e829552'}, {'OpenFOAM-v2312-cleanup.patch': 'f1389e5d89510209d99d35917a4a6bd727134121bbbaa12471235042e675dacf'}, - {'OpenFOAM-v2212-wmake-OpenMPI.patch': '4f5110e98df1f057dc4b478a004e4ae2dc5cc763899f0d3ceb6773315c5c8ba9'}, + {'OpenFOAM-v2212-wmake-OpenMPI.patch': '241dc4898c22aab0cbd10c1ea931a07a786508ee03462d45dbc1c202fee3ebe8'}, ] builddependencies = [ @@ -39,6 +39,8 @@ dependencies = [ ('SCOTCH', '7.0.3'), ('KaHIP', '3.16'), ('CGAL', '5.6'), + ('GMP', '6.2.1'), + ('MPFR', '4.2.0'), ('ParaView', '5.11.2'), ('gnuplot', '5.4.8'), ] diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2406-cleanup.patch b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2406-cleanup.patch new file mode 100644 index 00000000000..ac5229788c5 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2406-cleanup.patch @@ -0,0 +1,182 @@ +# Replaces OpenFOAM third-party libraries with EASYBUILD variants. +# Uses the OpenFOAM prefs mechanism and the FOAM_CONFIG_ETC variable +# to define the preferred settings without patching the original files +# +# Authors: Mark Olesen +# +# ChangeLog: +# - v2312 - activate METIS, KaHIP and readline support in etc/config.sh/setup +# author: Jiri Furst +# - v2406 - set MPFR_ARCH_PATH and GMP_ARCH_PATH to CGAL config +# author: Jiri Furst +# +# ------------------------------------------------------------------------- +--- /dev/null 2020-12-14 09:05:45.272769166 +0100 ++++ OpenFOAM-v2012/etc/prefs.sh 2020-12-14 10:02:26.488430802 +0100 +@@ -0,0 +1,7 @@ ++##Easybuild## settings -*- sh -*- ++ ++export FOAM_CONFIG_ETC="etc/easybuild" ++ ++export WM_MPLIB=EASYBUILDMPI ++ ++##Easybuild## +--- /dev/null 2020-12-14 09:05:45.272769166 +0100 ++++ OpenFOAM-v2012/etc/easybuild/config.sh/CGAL 2020-12-14 10:10:55.991841204 +0100 +@@ -0,0 +1,8 @@ ++##Easybuild## settings -*- sh -*- ++ ++export MPFR_ARCH_PATH="$EBROOTMPFR" ++export GMP_ARCH_PATH="$EBROOTGMP" ++export BOOST_ARCH_PATH="$EBROOTBOOST" ++export CGAL_ARCH_PATH="$EBROOTCGAL" ++ ++##Easybuild## +--- /dev/null 2020-12-14 09:05:45.272769166 +0100 ++++ OpenFOAM-v2012/etc/easybuild/config.sh/FFTW 2020-12-14 10:10:53.735843322 +0100 +@@ -0,0 +1,5 @@ ++##Easybuild## settings -*- sh -*- ++ ++export FFTW_ARCH_PATH="$EBROOTFFTW" ++ ++##EasyBuild## +--- /dev/null 2020-12-14 09:05:45.272769166 +0100 ++++ OpenFOAM-v2012/etc/easybuild/config.sh/metis 2020-12-11 21:23:28.774934024 +0100 +@@ -0,0 +1,6 @@ ++##Easybuild## settings -*- sh -*- ++ ++METIS_VERSION="metis-$EBVERSIONMETIS" ++[ -d "$METIS_ARCH_PATH" ] || METIS_ARCH_PATH="$EBROOTMETIS" ++ ++##Easybuild## +--- /dev/null 2022-12-01 18:21:35.103878336 +0100 ++++ OpenFOAM-v2206/etc/easybuild/config.sh/kahip 2022-12-12 20:24:07.538408981 +0100 +@@ -0,0 +1,6 @@ ++##Easybuild## settings -*- sh -*- ++ ++KAHIP_VERSION="kahip-$EBVERSIONKAHIP" ++export KAHIP_ARCH_PATH="$EBROOTKAHIP" ++ ++##Easybuild## +--- /dev/null 2020-12-14 09:05:45.272769166 +0100 ++++ OpenFOAM-v2012/etc/easybuild/config.sh/readline 2020-12-11 21:23:22.534951043 +0100 +@@ -0,0 +1,5 @@ ++##Easybuild## settings -*- sh -*- ++ ++export READLINE_ARCH_PATH="$EBROOTLIBREADLINE" ++ ++##Easybuild## +--- /dev/null 2020-12-14 09:05:45.272769166 +0100 ++++ OpenFOAM-v2012/etc/easybuild/config.sh/scotch 2020-12-11 21:23:17.586964539 +0100 +@@ -0,0 +1,7 @@ ++##Easybuild## settings -*- sh -*- ++ ++export SCOTCH_VERSION="scotch_$EBVERSIONSCOTCH" ++export SCOTCH_ARCH_PATH="$EBROOTSCOTCH" ++[ -d "$SCOTCH_ARCH_PATH" ] || SCOTCH_ARCH_PATH="$SCOTCH_ROOT" ++ ++##Easybuild## +--- /dev/null 2020-12-14 09:05:45.272769166 +0100 ++++ OpenFOAM-v2012/etc/easybuild/config.sh/vtk 2020-12-11 21:22:55.463024882 +0100 +@@ -0,0 +1,9 @@ ++##Easybuild## settings -*- sh -*- ++ ++export VTK_DIR="$EBROOTVTK" ++export MESA_ARCH_PATH="$EBROOTMESA" ++ ++# Define paraview-mesa directory as required ++unset ParaView_MESA_DIR ++ ++##Easybuild## +--- /dev/null 2020-12-14 09:05:45.272769166 +0100 ++++ OpenFOAM-v2012/etc/easybuild/config.sh/paraview 2020-12-14 10:13:53.583674383 +0100 +@@ -0,0 +1,75 @@ ++##Easybuild## settings -*- sh -*- ++# ++# Largely a knockoff of the OpenFOAM etc/config.sh/paraview-system ++# readjusted for easybuild ++# ++# Copyright (C) 2020 OpenCFD Ltd. ++# ++#------------------------------------------------------------------------------ ++# Compiler-specific location for ThirdParty installations ++archDir="$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER" ++ ++# Clean path and library path of previous settings ++eval \ ++ "$($WM_PROJECT_DIR/bin/foamCleanPath -sh-env=PATH \ ++ $ParaView_DIR $archDir/ParaView- $archDir/qt-)" ++ ++eval \ ++ "$($WM_PROJECT_DIR/bin/foamCleanPath -sh-env=LD_LIBRARY_PATH \ ++ $ParaView_DIR $archDir/ParaView- $archDir/qt-)" ++ ++ ++#------------------------------------------------------------------------------ ++ ++##Easybuild## settings ++ ++ParaView_VERSION="$EBVERSIONPARAVIEW" ++export ParaView_DIR="$EBROOTPARAVIEW" ++ ++#------------------------------------------------------------------------------ ++ ++unset PV_PLUGIN_PATH ++ ++# Set API to correspond to VERSION ++# pv_api is . from ParaView_VERSION ++#- ++# Extract API from VERSION ++pv_api=$(echo "$ParaView_VERSION" | \ ++ sed -ne 's/^[^0-9]*\([0-9][0-9]*\.[0-9][0-9]*\).*$/\1/p') ++ ++pv_plugin_dir="$FOAM_LIBBIN/paraview-$pv_api" ++ ++# Set paths if binaries are present ++if [ -r "$ParaView_DIR" ] ++then ++ export PATH="$ParaView_DIR/bin:$PATH" ++ ++ # ParaView libraries ++ # - 5.5 and later: lib/, but could also be lib64/ ++ for libDir in lib64 lib ++ do ++ pvLibDir="$libDir/paraview-$pv_api" ++ if [ -d "$ParaView_DIR/$pvLibDir" ] ++ then ++ export LD_LIBRARY_PATH="$ParaView_DIR/$libDir:$LD_LIBRARY_PATH" ++ break ++ fi ++ done ++ ++ # OpenFOAM plugin directory must be the first in PV_PLUGIN_PATH ++ # and have paraview-major.minor encoded in its name ++ if [ -d "$pv_plugin_dir" ] ++ then ++ export PV_PLUGIN_PATH="$pv_plugin_dir" ++ fi ++fi ++ ++ ++#------------------------------------------------------------------------------ ++ ++unset ParaView_VERSION ++ ++unset archDir libDir ++unset pv_api pv_plugin_dir pvLibDir ++ ++#------------------------------------------------------------------------------ +--- OpenFOAM-v2312/etc/config.sh/setup.orig 2024-01-11 09:49:24.823571481 +0100 ++++ OpenFOAM-v2312/etc/config.sh/setup 2024-01-11 09:51:40.545969774 +0100 +@@ -207,7 +207,9 @@ + _foamEtc -config CGAL + _foamEtc -config scotch + _foamEtc -config FFTW +- ++_foamEtc -config metis ++_foamEtc -config kahip ++_foamEtc -config readline + + # Finalize library paths + # ~~~~~~~~~~~~~~~~~~~~~~ + diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2406-foss-2023a.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2406-foss-2023a.eb new file mode 100644 index 00000000000..0e2885c064f --- /dev/null +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2406-foss-2023a.eb @@ -0,0 +1,55 @@ +name = 'OpenFOAM' +version = 'v2406' + +homepage = 'https://www.openfoam.com/' +description = """OpenFOAM is a free, open source CFD software package. + OpenFOAM has an extensive range of features to solve anything from complex fluid flows + involving chemical reactions, turbulence and heat transfer, + to solid dynamics and electromagnetics.""" + +toolchain = {'name': 'foss', 'version': '2023a'} +# Users have found that vectorizion caused OpenFOAM to produce some very incorrect results. +# Disabling vectorize was confirmed to fix the the known issues. +# With no test suite, sticking to known working toolchain options until proven otherwise. +toolchainopts = {'cstd': 'c++14', 'vectorize': False} + +source_urls = ['https://sourceforge.net/projects/openfoam/files/%(version)s/'] +sources = [ + SOURCE_TGZ, + { + 'filename': '%(name)s-plugins-%(version)s.tgz', + 'extract_cmd': 'tar --strip-components=1 -C %(installdir)s/%(name)s-%(version)s/ -xzf %s' + } +] +patches = [ + ('OpenFOAM-v2406-cleanup.patch', 1), + ('OpenFOAM-v2212-wmake-OpenMPI.patch', 1), +] +checksums = [ + {'OpenFOAM-v2406.tgz': '8d1450fb89eec1e7cecc55c3bb7bc486ccbf63d069379d1d5d7518fa16a4686a'}, + {'OpenFOAM-plugins-v2406.tgz': '1d008f86fad06a4a568d194c6e3d5ab52be2b20c83a3b9b1b0230e2de2d0558b'}, + {'OpenFOAM-v2406-cleanup.patch': '3abff48a517fb63719ad57fa32af746bc379a1e80c72d3e5852aa17cd13cf03e'}, + {'OpenFOAM-v2212-wmake-OpenMPI.patch': '241dc4898c22aab0cbd10c1ea931a07a786508ee03462d45dbc1c202fee3ebe8'}, +] + +builddependencies = [ + ('Bison', '3.8.2'), + ('CMake', '3.26.3'), + ('flex', '2.6.4'), +] + +dependencies = [ + ('libreadline', '8.2'), + ('ncurses', '6.4'), + # OpenFOAM requires 64 bit METIS using 32 bit indexes (array indexes) + ('METIS', '5.1.0'), + ('SCOTCH', '7.0.3'), + ('KaHIP', '3.16'), + ('CGAL', '5.6'), + ('GMP', '6.2.1'), + ('MPFR', '4.2.0'), + ('ParaView', '5.11.2'), + ('gnuplot', '5.4.8'), +] + +moduleclass = 'cae' diff --git a/easybuild/easyconfigs/o/OpenForceField-Toolkit/OpenForceField-Toolkit-0.16.0-foss-2023a.eb b/easybuild/easyconfigs/o/OpenForceField-Toolkit/OpenForceField-Toolkit-0.16.0-foss-2023a.eb new file mode 100644 index 00000000000..f323c61f065 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenForceField-Toolkit/OpenForceField-Toolkit-0.16.0-foss-2023a.eb @@ -0,0 +1,144 @@ +easyblock = 'PythonBundle' + +name = 'OpenForceField-Toolkit' +version = '0.16.0' + +homepage = 'https://github.com/openforcefield/openff-toolkit' +description = """The Open Force Field Toolkit provides implementations of the SMIRNOFF format, +parameterization engine, and other tools.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [('poetry', '1.5.1')] +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('SciPy-bundle', '2023.07'), + ('networkx', '3.1'), + ('typing-extensions', '4.9.0'), + ('pydantic', '2.5.3'), + ('tqdm', '4.66.1'), + ('OpenMM', '8.0.0'), + ('PyYAML', '6.0'), + ('RDKit', '2024.03.3'), + ('MDTraj', '1.9.9'), + ('JupyterNotebook', '7.0.2'), + ('AmberTools', '23.6'), + ('Pint', '0.23'), + ('nglview', '3.1.2'), +] + +use_pip = True + +exts_list = [ + ('qcelemental', '0.26.0', { + 'checksums': ['a14e8510cdbfda645ef1461c1afd02efb599311733dbba5f83fcd1d6168a6ddd'], + }), + ('PyJWT', '2.8.0', { + 'modulename': 'jwt', + 'checksums': ['57e28d156e3d5c10088e0c68abb90bfac3df82b40a71bd0daa20c65ccd5c23de'], + }), + ('apsw', '3.46.0.0', { + 'checksums': ['e128ccaab511f9a7fc48be6414f99a9197f83a69624d8ba40c1ca241bdef418e'], + }), + ('zstandard', '0.18.0', { + 'checksums': ['0ac0357a0d985b4ff31a854744040d7b5754385d1f98f7145c30e02c6865cb6f'], + }), + ('qcportal', '0.55', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['f6eb86d6ace4ae6a71bbd8e2ee054305aff2c1da0198a3741b0d589c572a31b3'], + }), + ('cached-property', '1.5.2', { + 'checksums': ['9fa5755838eecbb2d234c3aa390bd80fbd3ac6b6869109bfc1b499f7bd89a130'], + }), + ('cachetools', '5.3.3', { + 'checksums': ['ba29e2dfa0b8b556606f097407ed1aa62080ee108ab0dc5ec9d6a723a007d105'], + }), + ('python-constraint', '1.4.0', { + 'modulename': 'constraint', + 'source_tmpl': '%(name)s-%(version)s.tar.bz2', + 'checksums': ['501d6f17afe0032dfc6ea6c0f8acc12e44f992733f00e8538961031ef27ccb8e'], + }), + ('bson', '0.5.10', { + 'checksums': ['d6511b2ab051139a9123c184de1a04227262173ad593429d21e443d6462d6590'], + }), + ('xmltodict', '0.13.0', { + 'checksums': ['341595a488e3e01a85a9d8911d8912fd922ede5fecc4dce437eb4b6c8d037e56'], + }), + ('intermol', '0.1.2', { + 'source_urls': ['https://github.com/shirtsgroup/InterMol/archive/'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['a3065133ba16585a5db3807466a36242d191156525c33079cf46a97cedcfe835'], + }), + ('SMIRNOFF99Frosst', '1.1.0', { + 'source_urls': ['https://github.com/openforcefield/smirnoff99Frosst/archive/'], + 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['940c4ed3cd720e746549a3335f10b7b0d9047a67bc216ad45dd875be5c8ec467'], + }), + ('SMIRNOFF-Plugins', '2024.01.0', { + 'source_urls': ['https://github.com/openforcefield/smirnoff-plugins/archive/'], + 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['8ba4dbc6ed320f06f30bf42e8f70399bc3818becd668990693b51ddca183ff74'], + }), + ('OpenForceField-ForceFields', '2024.04.0', { + 'modulename': 'openforcefields', + 'source_urls': ['https://github.com/openforcefield/openff-forcefields/archive/'], + 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['fc7094cdb74bf9f0ed665dfc716cc62c5a37def3fc7e852adeae0ae4b60169c7'], + }), + ('OpenForceField-Amber-FF-Ports', '0.0.4', { + 'modulename': 'openff.amber_ff_ports', + 'source_urls': ['https://github.com/openforcefield/openff-amber-ff-ports/archive/'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['dbf2d1ccce06b0627b1eccae7e227ad800ff1cbac3e869344de265b178cc0207'], + }), + ('OpenForceField-Utilities', '0.1.12', { + 'modulename': 'openff.utilities', + 'source_urls': ['https://github.com/openforcefield/openff-utilities/archive/'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['92882c5b87b40bdb4ee1e8c84c0ecc0fc83f26eaf3e3befde41bfdcf93d75dea'], + }), + ('OpenForceField-Units', '0.2.2', { + 'modulename': 'openff.units', + 'source_urls': ['https://github.com/openforcefield/openff-units/archive/'], + 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['532746534c1937938580d5cfe98f414aff9bfbcc66970e115a88a38f6d5a2581'], + }), + ('OpenForceField-NAGL-Models', '0.2.0', { + 'modulename': 'openff.nagl_models', + 'source_urls': ['https://github.com/openforcefield/openff-nagl-models/archive/'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['5ccc55d7f0fcd24577796fd8b2bfd85b035ee8060e441c1f7dfc6f1949b9dee5'], + }), + ('OpenForceField-Models', '0.1.2', { + 'modulename': 'openff.models', + 'source_urls': ['https://github.com/openforcefield/openff-models/archive/'], + 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['cf2aa7ef467721f141149e4ce96134db390b27012f09996c4442a3fad2371653'], + }), + ('OpenForceField-Interchange', '0.3.27', { + 'modulename': 'openff.interchange', + 'source_urls': ['https://github.com/openforcefield/openff-interchange/archive/'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['6b44ba8a89921b3843a5f9fc41dc4f8a0c784ba12221e3ea0fb8c1b01a10cf2e'], + }), + (name, version, { + 'modulename': 'openff.toolkit', + 'source_urls': ['https://github.com/openforcefield/openff-toolkit/archive/'], + 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['70a81e914e86efd933819a5db05fc4400dcd23e12ad29398fdad46f2765b5634'], + }), +] + +sanity_check_commands = [ + "python -c 'from openff.toolkit import Molecule, Topology, ForceField'", + "python -c 'from openff.interchange import Interchange'", + "python -c 'from openff.units import unit'", + "python -c 'from openff.interchange.components.mdconfig import MDConfig'", + "python -c 'from openff.interchange.models import TopologyKey'", + "python -c 'from openff.toolkit.typing.engines.smirnoff import ForceField'", +] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/o/OpenImageIO/OpenImageIO-2.5.15.0-GCC-13.3.0.eb b/easybuild/easyconfigs/o/OpenImageIO/OpenImageIO-2.5.15.0-GCC-13.3.0.eb new file mode 100644 index 00000000000..2b2aff2aaab --- /dev/null +++ b/easybuild/easyconfigs/o/OpenImageIO/OpenImageIO-2.5.15.0-GCC-13.3.0.eb @@ -0,0 +1,39 @@ +easyblock = 'CMakeMake' + +name = 'OpenImageIO' +version = '2.5.15.0' + +homepage = 'https://openimageio.org/' +description = """OpenImageIO is a library for reading and writing images, and a bunch of related classes, utilities, + and applications.""" + +toolchain = {'name': 'GCC', 'version': '13.3.0'} + +source_urls = ['https://github.com/OpenImageIO/oiio/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] +checksums = [('7779ef2c3d03c5ed95e13ff292de85c3f8cee301cd46baad0d2dc83c93bfe85c')] + +builddependencies = [ + ('CMake', '3.29.3'), + ('git', '2.45.1'), +] +dependencies = [ + ('Boost', '1.85.0'), + ('libjpeg-turbo', '3.0.1'), + ('libpng', '1.6.43'), + ('LibTIFF', '4.6.0'), + ('OpenEXR', '3.2.4'), + ('freetype', '2.13.2'), + ('zlib', '1.3.1'), +] + +separate_build_dir = True + +configopts = '-DSTOP_ON_WARNING=OFF -DUSE_PYTHON=OFF' + +sanity_check_paths = { + 'files': ['bin/oiiotool', 'lib/libOpenImageIO.%s' % SHLIB_EXT, 'lib/libOpenImageIO_Util.%s' % SHLIB_EXT], + 'dirs': ['include/OpenImageIO', 'share'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/o/OpenJPEG/OpenJPEG-2.5.2-GCCcore-13.3.0.eb b/easybuild/easyconfigs/o/OpenJPEG/OpenJPEG-2.5.2-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..8ee5d1477f8 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenJPEG/OpenJPEG-2.5.2-GCCcore-13.3.0.eb @@ -0,0 +1,42 @@ +easyblock = 'CMakeMake' + +name = 'OpenJPEG' +version = '2.5.2' + +homepage = 'https://www.openjpeg.org/' +description = """OpenJPEG is an open-source JPEG 2000 codec written in + C language. It has been developed in order to promote the use of JPEG 2000, + a still-image compression standard from the Joint Photographic Experts Group + (JPEG). Since may 2015, it is officially recognized by ISO/IEC and ITU-T as + a JPEG 2000 Reference Software.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/uclouvain/%(namelower)s/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['90e3896fed910c376aaf79cdd98bdfdaf98c6472efd8e1debf0a854938cbda6a'] + +builddependencies = [ + ('binutils', '2.42'), + ('CMake', '3.29.3'), +] +# for running the binary of openjpeg like opj_compress you need the libraries like zlib etc. +dependencies = [ + ('zlib', '1.3.1'), + ('libpng', '1.6.43'), + ('LibTIFF', '4.6.0'), +] + +sanity_check_paths = { + 'files': [ + 'bin/opj_compress', + 'bin/opj_decompress', + 'bin/opj_dump', + 'include/openjpeg-%(version_major)s.%(version_minor)s/openjpeg.h', + 'lib/libopenjp2.%s' % SHLIB_EXT + ], + 'dirs': ['bin', 'include', 'lib'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/o/OpenMEEG/OpenMEEG-2.5.7-foss-2023a.eb b/easybuild/easyconfigs/o/OpenMEEG/OpenMEEG-2.5.7-foss-2023a.eb index 8926a0833fa..42b0118bbe8 100644 --- a/easybuild/easyconfigs/o/OpenMEEG/OpenMEEG-2.5.7-foss-2023a.eb +++ b/easybuild/easyconfigs/o/OpenMEEG/OpenMEEG-2.5.7-foss-2023a.eb @@ -47,8 +47,8 @@ sanity_check_paths = { sanity_check_commands = [ "om_mesh_info --help", - "pip check", - "python -c 'import openmeeg'", + "PIP_DISABLE_PIP_VERSION_CHECK=true python -s -m pip check", + "python -s -c 'import openmeeg'", ] modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} diff --git a/easybuild/easyconfigs/o/OpenMM-Torch/OpenMM-Torch-20240816-foss-2023a.eb b/easybuild/easyconfigs/o/OpenMM-Torch/OpenMM-Torch-20240816-foss-2023a.eb new file mode 100644 index 00000000000..8e40a8c95af --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMM-Torch/OpenMM-Torch-20240816-foss-2023a.eb @@ -0,0 +1,51 @@ +easyblock = 'CMakeMake' + +name = 'OpenMM-Torch' +version = '20240816' +local_commit = '8893c0f' + +homepage = 'https://openmm.org/' +description = """ +OpenMM-Torch is an OpenMM plugin to define forces with neural networks. +The OpenMM-Torch package provides an interface to the PyTorch machine learning framework. +It lets you define new types of forces through PyTorch code. +""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'cstd': 'c++17'} + +source_urls = ['https://github.com/openmm/%(namelower)s/archive'] +sources = ['%s.tar.gz' % local_commit] +checksums = ['c2abf0bfce61b6e2e1f42d27a89032b4b994f7d67eb238ddf1a7d299cae551bf'] + +builddependencies = [ + ('CMake', '3.26.3'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('PyTorch', '2.1.2'), + ('OpenMM', '8.0.0'), +] + +configopts = '-DOPENMM_DIR="${EBROOTOPENMM}" ' +configopts += '-DPYTORCH_DIR="${EBROOTPYTORCH}/lib/python%(pyshortver)s/site-packages/torch"' + +# install Python bindings +postinstallcmds = [ + "sed -i 's|pip install |pip install --prefix=%(installdir)s |' %(start_dir)s/python/CMakeLists.txt", + "make PythonInstall", +] + +sanity_check_paths = { + 'files': ['lib/python%(pyshortver)s/site-packages/openmmtorch.py'], + 'dirs': ['lib', 'include'], +} + +sanity_check_commands = [ + "python -c 'import openmmtorch'", +] + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/o/OpenMM/OpenMM-8.0.0-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/o/OpenMM/OpenMM-8.0.0-foss-2023a-CUDA-12.1.1.eb new file mode 100644 index 00000000000..8cf271071e7 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMM/OpenMM-8.0.0-foss-2023a-CUDA-12.1.1.eb @@ -0,0 +1,70 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics +# Update to 7.5.1 +# J. Sassmannshausen / GSTT + +easyblock = 'CMakeMake' + +name = 'OpenMM' +version = '8.0.0' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://openmm.org' +description = "OpenMM is a toolkit for molecular simulation." + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'opt': True} + +source_urls = ['https://github.com/openmm/openmm/archive/'] +sources = ['%(version)s.tar.gz'] +patches = ['OpenMM-8.0.0_add_no_tree_vectorize.patch'] +checksums = [ + 'dc63d7b47c8bb7b169c409cfd63d909ed0ce1ae114d37c627bf7a4231acf488e', # 8.0.0.tar.gz + '4bacf45443a2472e59798743f27d07481e065d784cbbea7be22aa6427af0d2bd', # OpenMM-8.0.0_add_no_tree_vectorize.patch +] + +builddependencies = [ + ('CMake', '3.26.3'), + ('Doxygen', '1.9.7'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('SWIG', '4.1.1'), + ('CUDA', '12.1.1', '', SYSTEM), +] + +# Set the OPENMM_CUDA_COMPILER variable to make sure that all tests use the right nvcc, +# Otherwise they will use the wrong path: `/usr/local/cuda/bin/nvcc` +pretestopts = ' export OPENMM_CUDA_COMPILER=${EBROOTCUDA}/bin/nvcc && ' +pretestopts += " CTEST_OUTPUT_ON_FAILURE=1" +# Skip CudaCompiler test as it doesn't work when the OPENMM_CUDA_COMPILER variable is set +local_ignore_pattern = "(Integrator)|(Thermostat)|(Barostat)|(Rpmd)|(Amoeba)|(CudaCompiler)" +runtest = """test -e ARGS="-E \'%s\'" """ % local_ignore_pattern + +preinstallopts = ' export OPENMM_INCLUDE_PATH=%(installdir)s/include && ' +preinstallopts += ' export OPENMM_LIB_PATH=%(installdir)s/lib && ' + +# required to install the python API +installopts = ' && cd python && python setup.py build && python setup.py install --prefix=%(installdir)s' + +sanity_check_paths = { + 'files': ['lib/libOpenMM.%s' % SHLIB_EXT], + 'dirs': ['lib/python%(pyshortver)s/site-packages'] +} + +sanity_check_commands = [ + "python -c 'import simtk.openmm'", + "python -m openmm.testInstallation", +] + +modextrapaths = { + 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages/OpenMM-%(version)s-py%(pyshortver)s-linux-%(arch)s.egg', + 'OPENMM_INCLUDE_PATH': 'include', + 'OPENMM_LIB_PATH': 'lib', +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/o/OpenMM/OpenMM-8.1.2-foss-2023b.eb b/easybuild/easyconfigs/o/OpenMM/OpenMM-8.1.2-foss-2023b.eb new file mode 100644 index 00000000000..7b4e30add53 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMM/OpenMM-8.1.2-foss-2023b.eb @@ -0,0 +1,60 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics +# Update to 7.5.1 +# J. Sassmannshausen / GSTT + +easyblock = 'CMakeMake' + +name = 'OpenMM' +version = '8.1.2' + +homepage = 'https://openmm.org' +description = "OpenMM is a toolkit for molecular simulation." + +toolchain = {'name': 'foss', 'version': '2023b'} +toolchainopts = {'opt': True} + +source_urls = ['https://github.com/openmm/openmm/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['afc888a4e46486d8d68dac4d403e2b0b28f51b95e52e821e34c38e8b428e040e'] + +builddependencies = [ + ('CMake', '3.27.6'), + ('Doxygen', '1.9.8'), +] + +dependencies = [ + ('Python', '3.11.5'), + ('SciPy-bundle', '2023.11'), + ('SWIG', '4.1.1'), +] + +pretestopts = " CTEST_OUTPUT_ON_FAILURE=1" +local_ignore_pattern = "(Integrator)|(Thermostat)|(Barostat)|(Rpmd)|(Amoeba)" +runtest = """test -e ARGS="-E \'%s\'" """ % local_ignore_pattern + +preinstallopts = ' export OPENMM_INCLUDE_PATH=%(installdir)s/include && ' +preinstallopts += ' export OPENMM_LIB_PATH=%(installdir)s/lib && ' + +# required to install the python API +installopts = ' && cd python && python setup.py build && python setup.py install --prefix=%(installdir)s' + +sanity_check_paths = { + 'files': ['lib/libOpenMM.%s' % SHLIB_EXT], + 'dirs': ['lib/python%(pyshortver)s/site-packages'] +} + +sanity_check_commands = [ + "python -c 'import simtk.openmm'", + "python -m openmm.testInstallation", +] + +modextrapaths = { + 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages/OpenMM-%(version)s-py%(pyshortver)s-linux-%(arch)s.egg', + 'OPENMM_INCLUDE_PATH': 'include', + 'OPENMM_LIB_PATH': 'lib', +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/o/OpenMMTools/OpenMMTools-0.23.1-foss-2023a.eb b/easybuild/easyconfigs/o/OpenMMTools/OpenMMTools-0.23.1-foss-2023a.eb new file mode 100644 index 00000000000..1bec0ef4891 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMMTools/OpenMMTools-0.23.1-foss-2023a.eb @@ -0,0 +1,61 @@ +easyblock = 'PythonBundle' + +name = 'OpenMMTools' +version = '0.23.1' + +homepage = 'https://github.com/choderalab/openmmtools' +description = """A batteries-included toolkit for the GPU-accelerated OpenMM molecular simulation engine. +openmmtools is a Python library layer that sits on top of OpenMM to provide access to a variety of useful tools +for building full-featured molecular simulation packages. +""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'usempi': True} + +builddependencies = [ + ('hatchling', '1.18.0'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('OpenMM', '8.0.0'), + ('netcdf4-python', '1.6.4'), + ('MDTraj', '1.9.9'), + ('PyYAML', '6.0'), + ('numba', '0.58.1'), + ('jupyter-server', '2.7.2'), +] + +use_pip = True +exts_list = [ + ('pymbar', '3.1', { + # pymbar 3.1 is not available via PyPI, see https://github.com/choderalab/pymbar/issues/475 + 'source_urls': ['https://github.com/choderalab/pymbar/archive/'], + 'sources': ['%(version)s.tar.gz'], + 'checksums': ['7a996e5d3fd8143378f9e18662483446a4a2fe7e57917511e96beb6b07fd6232'], + }), + ('mpiplus', '0.0.2', { + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/choderalab/mpiplus/archive/'], + 'checksums': ['5f051210b8cd321fdcbfa97a6e1606b63e6d6c7214c393bc04f93a8545b6d3a8'], + }), + (name, version, { + 'source_tmpl': '%(version)s.tar.gz', + 'source_urls': ['https://github.com/choderalab/openmmtools/archive/'], + 'checksums': ['9281f50896a91f3f9e1ea16f0636f2aff494287a51a4ec03ae8e26f1b8edaccc'], + # import check requires use of mpirun, handled via sanity_check_commands + 'modulename': False, + }), +] + +sanity_check_paths = { + 'files': ['bin/test-openmm-platforms'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["%(mpi_cmd_prefix)s python -c 'import %(namelower)s'"] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.4-GCC-11.3.0.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.4-GCC-11.3.0.eb index 6471a45d999..06b168671f7 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.4-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.4-GCC-11.3.0.eb @@ -11,6 +11,7 @@ sources = [SOURCELOWER_TAR_BZ2] patches = [ 'OpenMPI-4.1.1_build-with-internal-cuda-header.patch', 'OpenMPI-4.1.1_opal-datatype-cuda-performance.patch', + 'OpenMPI-4.1.4_fix-implicit-cuda-function-declaration.patch', 'OpenMPI-4.1.x_add_atomic_wmb.patch', ] checksums = [ @@ -19,6 +20,8 @@ checksums = [ '63eac52736bdf7644c480362440a7f1f0ae7c7cae47b7565f5635c41793f8c83'}, {'OpenMPI-4.1.1_opal-datatype-cuda-performance.patch': 'b767c7166cf0b32906132d58de5439c735193c9fd09ec3c5c11db8d5fa68750e'}, + {'OpenMPI-4.1.4_fix-implicit-cuda-function-declaration.patch': + 'ec1c2f07d03574b86fc5fb462eed96eb6f5658deb8a6412cf37007d687a28673'}, {'OpenMPI-4.1.x_add_atomic_wmb.patch': '9494bbc546d661ba5189e44b4c84a7f8df30a87cdb9d96ce2e73a7c8fecba172'}, ] diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.4-GCC-12.2.0.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.4-GCC-12.2.0.eb index fbb50478eec..f4fbe865280 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.4-GCC-12.2.0.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.4-GCC-12.2.0.eb @@ -11,6 +11,7 @@ sources = [SOURCELOWER_TAR_BZ2] patches = [ 'OpenMPI-4.1.1_build-with-internal-cuda-header.patch', 'OpenMPI-4.1.1_opal-datatype-cuda-performance.patch', + 'OpenMPI-4.1.4_fix-implicit-cuda-function-declaration.patch', 'OpenMPI-4.1.x_add_atomic_wmb.patch', ] checksums = [ @@ -19,6 +20,8 @@ checksums = [ '63eac52736bdf7644c480362440a7f1f0ae7c7cae47b7565f5635c41793f8c83'}, {'OpenMPI-4.1.1_opal-datatype-cuda-performance.patch': 'b767c7166cf0b32906132d58de5439c735193c9fd09ec3c5c11db8d5fa68750e'}, + {'OpenMPI-4.1.4_fix-implicit-cuda-function-declaration.patch': + 'ec1c2f07d03574b86fc5fb462eed96eb6f5658deb8a6412cf37007d687a28673'}, {'OpenMPI-4.1.x_add_atomic_wmb.patch': '9494bbc546d661ba5189e44b4c84a7f8df30a87cdb9d96ce2e73a7c8fecba172'}, ] diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.4-NVHPC-22.7-CUDA-11.7.0.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.4-NVHPC-22.7-CUDA-11.7.0.eb index 9ef5b5d1bb4..a69c1e2b8d4 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.4-NVHPC-22.7-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.4-NVHPC-22.7-CUDA-11.7.0.eb @@ -11,6 +11,7 @@ sources = [SOURCELOWER_TAR_BZ2] patches = [ 'OpenMPI-4.1.1_build-with-internal-cuda-header.patch', 'OpenMPI-4.1.1_opal-datatype-cuda-performance.patch', + 'OpenMPI-4.1.4_fix-implicit-cuda-function-declaration.patch', 'OpenMPI-4.1.x_add_atomic_wmb.patch', ] checksums = [ @@ -19,6 +20,8 @@ checksums = [ '63eac52736bdf7644c480362440a7f1f0ae7c7cae47b7565f5635c41793f8c83'}, {'OpenMPI-4.1.1_opal-datatype-cuda-performance.patch': 'b767c7166cf0b32906132d58de5439c735193c9fd09ec3c5c11db8d5fa68750e'}, + {'OpenMPI-4.1.4_fix-implicit-cuda-function-declaration.patch': + 'ec1c2f07d03574b86fc5fb462eed96eb6f5658deb8a6412cf37007d687a28673'}, {'OpenMPI-4.1.x_add_atomic_wmb.patch': '9494bbc546d661ba5189e44b4c84a7f8df30a87cdb9d96ce2e73a7c8fecba172'}, ] diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.4_fix-implicit-cuda-function-declaration.patch b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.4_fix-implicit-cuda-function-declaration.patch new file mode 100644 index 00000000000..3ccb7d43d82 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.4_fix-implicit-cuda-function-declaration.patch @@ -0,0 +1,31 @@ +Fix a left-over function causing compilation warnings or errors: +mtl_ofi_component.c:298:5: error: implicit declaration of function 'mca_common_cuda_fini'; did you mean 'ompi_comm_cid_init'? [-Werror=implicit-function-declaration] + mca_common_cuda_fini(); + ^~~~~~~~~~~~~~~~~~~~ + +See https://github.com/open-mpi/ompi/issues/11381 + +From 7676618c43d489b145e730d1d7603f0292a031c0 Mon Sep 17 00:00:00 2001 +From: Jingyin Tang +Date: Mon, 6 Feb 2023 13:48:51 -0500 +Subject: [PATCH] Fix compilation issue in OFI with CUDA + +Signed-off-by: Jingyin Tang +--- + ompi/mca/mtl/ofi/mtl_ofi_component.c | 3 --- + 1 file changed, 3 deletions(-) + +diff --git a/ompi/mca/mtl/ofi/mtl_ofi_component.c b/ompi/mca/mtl/ofi/mtl_ofi_component.c +index c1aac6934d0..e36f020b206 100644 +--- a/ompi/mca/mtl/ofi/mtl_ofi_component.c ++++ b/ompi/mca/mtl/ofi/mtl_ofi_component.c +@@ -294,9 +294,6 @@ ompi_mtl_ofi_component_query(mca_base_module_t **module, int *priority) + static int + ompi_mtl_ofi_component_close(void) + { +-#if OPAL_CUDA_SUPPORT +- mca_common_cuda_fini(); +-#endif + return opal_common_ofi_close(); + } + diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-5.0.2_build-with-internal-cuda-header.patch b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-5.0.2_build-with-internal-cuda-header.patch new file mode 100644 index 00000000000..2d935fda64a --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-5.0.2_build-with-internal-cuda-header.patch @@ -0,0 +1,139 @@ +Allow building Open MPI with an internal CUDA header and stub library via +--with-cuda=%(start_dir)s/opal/mca/cuda +by providing an internal minimal cuda.h header file, and function stubs. +This eliminates the CUDA (build)dependency; as long as the runtime CUDA version is 8.0+, +the system's libcuda.so will be used successfully by dynamically loaded plugins in +$EBROOTOPENMPI/lib/openmpi, not by the main libmpi.so. + +Author: Bart Oldeman +diff -urN openmpi-5.0.2.orig/opal/mca/cuda/cuda.c openmpi-5.0.2/opal/mca/cuda/cuda.c +--- openmpi-5.0.2.orig/opal/mca/cuda/lib/cuda.c 1970-01-01 00:00:00.000000000 +0000 ++++ openmpi-5.0.2/opal/mca/cuda/lib/cuda.c 2024-02-15 01:39:24.969142045 +0000 +@@ -0,0 +1,28 @@ ++#include "cuda.h" ++ ++CUresult cuPointerGetAttribute(void *, CUpointer_attribute, CUdeviceptr) { return CUDA_ERROR_UNKNOWN; } ++CUresult cuMemcpyAsync(CUdeviceptr, CUdeviceptr, size_t, CUstream) { return CUDA_ERROR_UNKNOWN; } ++CUresult cuMemAlloc(CUdeviceptr *, size_t) { return CUDA_ERROR_UNKNOWN; } ++CUresult cuMemFree(CUdeviceptr buf) { return CUDA_ERROR_UNKNOWN; } ++CUresult cuCtxGetCurrent(void *cuContext) { return CUDA_ERROR_UNKNOWN; } ++CUresult cuStreamCreate(CUstream *, int) { return CUDA_ERROR_UNKNOWN; } ++CUresult cuEventCreate(CUevent *, int) { return CUDA_ERROR_UNKNOWN; } ++CUresult cuEventRecord(CUevent, CUstream) { return CUDA_ERROR_UNKNOWN; } ++CUresult cuEventQuery(CUevent) { return CUDA_ERROR_UNKNOWN; } ++CUresult cuEventDestroy(CUevent) { return CUDA_ERROR_UNKNOWN; } ++CUresult cuMemHostRegister(void *, size_t, unsigned int) { return CUDA_ERROR_UNKNOWN; } ++CUresult cuMemHostUnregister(void *) { return CUDA_ERROR_UNKNOWN; } ++CUresult cuMemGetAddressRange(CUdeviceptr *, size_t *, CUdeviceptr) { return CUDA_ERROR_UNKNOWN; } ++CUresult cuIpcGetEventHandle(CUipcEventHandle *, CUevent) { return CUDA_ERROR_UNKNOWN; } ++CUresult cuIpcOpenEventHandle(CUevent *, CUipcEventHandle) { return CUDA_ERROR_UNKNOWN; } ++CUresult cuIpcOpenMemHandle(CUdeviceptr *, CUipcMemHandle, unsigned int) { return CUDA_ERROR_UNKNOWN; } ++CUresult cuIpcCloseMemHandle(CUdeviceptr) { return CUDA_ERROR_UNKNOWN; } ++CUresult cuIpcGetMemHandle(CUipcMemHandle *, CUdeviceptr) { return CUDA_ERROR_UNKNOWN; } ++CUresult cuCtxGetDevice(CUdevice *) { return CUDA_ERROR_UNKNOWN; } ++CUresult cuDeviceCanAccessPeer(int *, CUdevice, CUdevice) { return CUDA_ERROR_UNKNOWN; } ++CUresult cuCtxSetCurrent(CUcontext) { return CUDA_ERROR_UNKNOWN; } ++CUresult cuStreamSynchronize(CUstream) { return CUDA_ERROR_UNKNOWN; } ++CUresult cuStreamDestroy(CUstream) { return CUDA_ERROR_UNKNOWN; } ++CUresult cuPointerSetAttribute(const void *, CUpointer_attribute, CUdeviceptr) { return CUDA_ERROR_UNKNOWN; } ++CUresult cuDeviceGetPCIBusId(char*, int, CUdevice) { return CUDA_ERROR_UNKNOWN; } ++CUresult cuPointerGetAttributes(unsigned int, CUpointer_attribute *, void **, CUdeviceptr) { return CUDA_ERROR_UNKNOWN; } +diff -urN openmpi-5.0.2.orig/opal/mca/cuda/include/cuda.h openmpi-5.0.2/opal/mca/cuda/include/cuda.h +--- openmpi-5.0.2.orig/opal/mca/cuda/include/cuda.h 1970-01-01 00:00:00.000000000 +0000 ++++ openmpi-5.0.2/opal/mca/cuda/include/cuda.h 2024-02-15 03:07:26.480531383 +0000 +@@ -0,0 +1,95 @@ ++/* This header provides minimal parts of the CUDA Driver API, without having to ++ rely on the proprietary CUDA toolkit. ++ ++ References (to avoid copying from NVidia's proprietary cuda.h): ++ https://github.com/gcc-mirror/gcc/blob/master/include/cuda/cuda.h ++ https://github.com/Theano/libgpuarray/blob/master/src/loaders/libcuda.h ++ https://github.com/CPFL/gdev/blob/master/cuda/driver/cuda.h ++ https://github.com/CudaWrangler/cuew/blob/master/include/cuew.h ++*/ ++ ++#ifndef OMPI_CUDA_H ++#define OMPI_CUDA_H ++ ++#include ++ ++#define CUDA_VERSION 8000 ++ ++typedef void *CUcontext; ++typedef int CUdevice; ++#if defined(__LP64__) || defined(_WIN64) ++typedef unsigned long long CUdeviceptr; ++#else ++typedef unsigned CUdeviceptr; ++#endif ++typedef void *CUevent; ++typedef void *CUstream; ++ ++typedef enum { ++ CUDA_SUCCESS = 0, ++ CUDA_ERROR_INVALID_VALUE = 1, ++ CUDA_ERROR_NOT_INITIALIZED = 3, ++ CUDA_ERROR_DEINITIALIZED = 4, ++ CUDA_ERROR_ALREADY_MAPPED = 208, ++ CUDA_ERROR_NOT_READY = 600, ++ CUDA_ERROR_UNKNOWN = 999, ++} CUresult; ++ ++enum { ++ CU_EVENT_DISABLE_TIMING = 0x2, ++ CU_EVENT_INTERPROCESS = 0x4, ++}; ++ ++enum { ++ CU_IPC_MEM_LAZY_ENABLE_PEER_ACCESS = 0x1, ++}; ++ ++typedef enum { ++ CU_POINTER_ATTRIBUTE_CONTEXT = 1, ++ CU_POINTER_ATTRIBUTE_MEMORY_TYPE = 2, ++ CU_POINTER_ATTRIBUTE_SYNC_MEMOPS = 6, ++ CU_POINTER_ATTRIBUTE_BUFFER_ID = 7, ++ CU_POINTER_ATTRIBUTE_IS_MANAGED = 8, ++} CUpointer_attribute; ++ ++typedef enum { ++ CU_MEMORYTYPE_HOST = 0x01, ++} CUmemorytype; ++ ++#define CU_IPC_HANDLE_SIZE 64 ++typedef struct CUipcEventHandle_st { ++ char reserved[CU_IPC_HANDLE_SIZE]; ++} CUipcEventHandle; ++ ++typedef struct CUipcMemHandle_st { ++ char reserved[CU_IPC_HANDLE_SIZE]; ++} CUipcMemHandle; ++ ++CUresult cuPointerGetAttribute(void *, CUpointer_attribute, CUdeviceptr); ++CUresult cuMemcpyAsync(CUdeviceptr, CUdeviceptr, size_t, CUstream); ++CUresult cuMemAlloc(CUdeviceptr *, size_t); ++CUresult cuMemFree(CUdeviceptr buf); ++CUresult cuCtxGetCurrent(void *cuContext); ++CUresult cuStreamCreate(CUstream *, int); ++CUresult cuEventCreate(CUevent *, int); ++CUresult cuEventRecord(CUevent, CUstream); ++CUresult cuEventQuery(CUevent); ++CUresult cuEventDestroy(CUevent); ++CUresult cuMemHostRegister(void *, size_t, unsigned int); ++CUresult cuMemHostUnregister(void *); ++CUresult cuMemGetAddressRange(CUdeviceptr *, size_t *, CUdeviceptr); ++CUresult cuIpcGetEventHandle(CUipcEventHandle *, CUevent); ++CUresult cuIpcOpenEventHandle(CUevent *, CUipcEventHandle); ++CUresult cuIpcOpenMemHandle(CUdeviceptr *, CUipcMemHandle, unsigned int); ++CUresult cuIpcCloseMemHandle(CUdeviceptr); ++CUresult cuIpcGetMemHandle(CUipcMemHandle *, CUdeviceptr); ++CUresult cuCtxGetDevice(CUdevice *); ++CUresult cuDeviceCanAccessPeer(int *, CUdevice, CUdevice); ++CUresult cuCtxSetCurrent(CUcontext); ++CUresult cuStreamSynchronize(CUstream); ++CUresult cuStreamDestroy(CUstream); ++CUresult cuPointerSetAttribute(const void *, CUpointer_attribute, CUdeviceptr); ++CUresult cuDeviceGetPCIBusId(char*, int, CUdevice); ++CUresult cuPointerGetAttributes(unsigned int, CUpointer_attribute *, void **, CUdeviceptr); ++ ++#endif diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-5.0.3-GCC-13.3.0.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-5.0.3-GCC-13.3.0.eb new file mode 100644 index 00000000000..6864e213a9f --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-5.0.3-GCC-13.3.0.eb @@ -0,0 +1,38 @@ +name = 'OpenMPI' +version = '5.0.3' + +homepage = 'https://www.open-mpi.org/' +description = """The Open MPI Project is an open source MPI-3 implementation.""" + +toolchain = {'name': 'GCC', 'version': '13.3.0'} + +source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] +sources = [SOURCELOWER_TAR_BZ2] +patches = [('OpenMPI-5.0.2_build-with-internal-cuda-header.patch', 1)] +checksums = [ + {'openmpi-5.0.3.tar.bz2': '990582f206b3ab32e938aa31bbf07c639368e4405dca196fabe7f0f76eeda90b'}, + {'OpenMPI-5.0.2_build-with-internal-cuda-header.patch': + 'f52dc470543f35efef10d651dd159c771ae25f8f76a420d20d87abf4dc769ed7'}, +] + +builddependencies = [ + ('pkgconf', '2.2.0'), + ('Autotools', '20231222'), +] + +dependencies = [ + ('zlib', '1.3.1'), + ('hwloc', '2.10.0'), + ('libevent', '2.1.12'), + ('UCX', '1.16.0'), + ('libfabric', '1.21.0'), + ('PMIx', '5.0.2'), + ('PRRTE', '3.0.5'), + ('UCC', '1.3.0'), +] + +# CUDA related patches and custom configure option can be removed if CUDA support isn't wanted. +preconfigopts = 'gcc -Iopal/mca/cuda/include -shared opal/mca/cuda/lib/cuda.c -o opal/mca/cuda/lib/libcuda.so && ' +configopts = '--with-cuda=%(start_dir)s/opal/mca/cuda --with-show-load-errors=no ' + +moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-5.0.3-NVHPC-24.9-CUDA-12.6.0.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-5.0.3-NVHPC-24.9-CUDA-12.6.0.eb new file mode 100644 index 00000000000..e6c772bf64e --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-5.0.3-NVHPC-24.9-CUDA-12.6.0.eb @@ -0,0 +1,63 @@ +name = 'OpenMPI' +version = '5.0.3' + +homepage = 'https://www.open-mpi.org/' +description = """The Open MPI Project is an open source MPI-3 implementation.""" + +toolchain = {'name': 'NVHPC', 'version': '24.9-CUDA-12.6.0'} + +source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] +sources = [SOURCELOWER_TAR_BZ2] +patches = [ + 'OpenMPI-5.0.3_fix_hle_make_errors.patch', + 'OpenMPI-5.0.3_disable_opal_path_nfs_test.patch', + ('OpenMPI-5.0.2_build-with-internal-cuda-header.patch', 1) +] +checksums = [ + {'openmpi-5.0.3.tar.bz2': + '990582f206b3ab32e938aa31bbf07c639368e4405dca196fabe7f0f76eeda90b'}, + {'OpenMPI-5.0.3_fix_hle_make_errors.patch': + '881c907a9f5901d5d6af41cd33dffdcecba4a67a9e5123e602542aea57a80895'}, + {'OpenMPI-5.0.3_disable_opal_path_nfs_test.patch': + '75d4417e35252ea3a19b2792f1b06e9aeb408c253aa4921d77226d57b71dee45'}, + {'OpenMPI-5.0.2_build-with-internal-cuda-header.patch': + 'f52dc470543f35efef10d651dd159c771ae25f8f76a420d20d87abf4dc769ed7'}, +] + +builddependencies = [ + ('pkgconf', '2.2.0'), + ('Perl', '5.38.2'), + ('Autotools', '20231222'), +] + +dependencies = [ + ('zlib', '1.3.1'), + ('hwloc', '2.10.0'), + ('libevent', '2.1.12'), + ('UCX', '1.16.0'), + ('UCX-CUDA', '1.16.0', '-CUDA-%(cudaver)s'), + ('libfabric', '1.21.0'), + ('PMIx', '5.0.2'), + ('PRRTE', '3.0.5'), + ('UCC', '1.3.0'), + ('UCC-CUDA', '1.3.0', '-CUDA-%(cudaver)s'), +] + +# CUDA related patches and custom configure option can be removed if CUDA support isn't wanted. +preconfigopts = 'nvc -Iopal/mca/cuda/include -shared opal/mca/cuda/lib/cuda.c -o opal/mca/cuda/lib/libcuda.so && ' +# Update configure to include changes from the "disable_opal_path_nfs_test" patch +preconfigopts += './autogen.pl --force && ' + +configopts = '--with-cuda=%(start_dir)s/opal/mca/cuda ' +# Required to prevent internal compiler error in opal. +configopts += '--enable-alt-short-float=no ' +# Set PGI compilers manually, as NVHPC compilers are not correctly detected +configopts += 'CC=pgcc CXX=pgc++ FC=pgfortran ' + +# site specific options +# configopts += '--without-psm2 ' +# configopts += '--disable-oshmem ' +# configopts += '--with-gpfs ' +configopts += '--with-slurm ' + +moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-5.0.3_disable_opal_path_nfs_test.patch b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-5.0.3_disable_opal_path_nfs_test.patch new file mode 100644 index 00000000000..09d9f829f06 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-5.0.3_disable_opal_path_nfs_test.patch @@ -0,0 +1,33 @@ +Disable opal_path_nfs test in OpenMPI 5.0.3 as this test can easily fail on some systems, +when NFS mounts are used. Generally, this test is flaky, which may prevent users +from installing OpenMPI for no apparent reason. + +diff --git a/test/util/Makefile.am b/test/util/Makefile.am +index e5ad472..33d63c4 100644 +--- a/test/util/Makefile.am ++++ b/test/util/Makefile.am +@@ -38,7 +38,6 @@ AM_CPPFLAGS = -I$(top_srcdir)/test/support + + check_PROGRAMS = \ + opal_bit_ops \ +- opal_path_nfs \ + bipartite_graph \ + opal_sha256 + +@@ -80,11 +79,11 @@ opal_bit_ops_LDADD = \ + $(top_builddir)/test/support/libsupport.a + opal_bit_ops_DEPENDENCIES = $(opal_path_nfs_LDADD) + +-opal_path_nfs_SOURCES = opal_path_nfs.c +-opal_path_nfs_LDADD = \ +- $(top_builddir)/opal/lib@OPAL_LIB_NAME@.la \ +- $(top_builddir)/test/support/libsupport.a +-opal_path_nfs_DEPENDENCIES = $(opal_path_nfs_LDADD) ++# opal_path_nfs_SOURCES = opal_path_nfs.c ++# opal_path_nfs_LDADD = \ ++# $(top_builddir)/opal/lib@OPAL_LIB_NAME@.la \ ++# $(top_builddir)/test/support/libsupport.a ++# opal_path_nfs_DEPENDENCIES = $(opal_path_nfs_LDADD) + + #opal_os_path_SOURCES = opal_os_path.c + #opal_os_path_LDADD = \ diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-5.0.3_fix_hle_make_errors.patch b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-5.0.3_fix_hle_make_errors.patch new file mode 100644 index 00000000000..dc9b0671658 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-5.0.3_fix_hle_make_errors.patch @@ -0,0 +1,25 @@ +On JUWELS, building OpenMPI 5.0.5 with NVHPC 24.9 fails with errors +related to `__ATOMIC_HLE_ACQUIRE` and `__ATOMIC_HLE_RELEASE` not being +defined. Add an additional macro check to let the build succeed. + +--- a/opal/include/opal/sys/gcc_builtin/atomic.h 2024-07-23 01:23:20.567556032 +0200 ++++ a/opal/include/opal/sys/gcc_builtin/atomic.h 2024-10-02 12:19:53.130698758 +0200 +@@ -187,7 +187,7 @@ + * + *********************************************************************/ + +-#if defined(__HLE__) ++#if defined(__HLE__) && defined(__ATOMIC_HLE_ACQUIRE) && defined(__ATOMIC_HLE_RELEASE) + + # include + +@@ -225,7 +225,7 @@ + __ATOMIC_RELEASE | __ATOMIC_HLE_RELEASE); + } + +-#else /* #if defined(__HLE__) */ ++#else /* #if defined(__HLE__) && defined(__ATOMIC_HLE_ACQUIRE) && defined(__ATOMIC_HLE_RELEASE) */ + + #include "opal/sys/atomic_impl_spinlock.h" + + diff --git a/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-GCCcore-13.3.0.eb b/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..cbf6bca94d7 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-GCCcore-13.3.0.eb @@ -0,0 +1,44 @@ +easyblock = 'ConfigureMake' + +name = 'OpenPGM' +version = '5.2.122' + +homepage = 'https://code.google.com/p/openpgm/' +description = """ + OpenPGM is an open source implementation of the Pragmatic General Multicast + (PGM) specification in RFC 3208 available at www.ietf.org. PGM is a reliable + and scalable multicast protocol that enables receivers to detect loss, request + retransmission of lost data, or notify an application of unrecoverable loss. + PGM is a receiver-reliable protocol, which means the receiver is responsible + for ensuring all data is received, absolving the sender of reception + responsibility. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://storage.googleapis.com/google-code-archive-downloads/v2/code.google.com/%(namelower)s/'] +sources = ['libpgm-%(version)s.tar.gz'] +patches = [ + '%(name)s-%(version)s-pkgconfig_includes.patch', + '%(name)s-%(version)s-python3-compliant.patch', +] +checksums = [ + '6b895f550b95284dcde7189b01e04a9a1c1f94579af31b1eebd32c2207a1ba2c', # libpgm-%(version)s.tar.gz + '4a9fc7fbb6e73e325639a895cd19c1ac6918b575f715c057caa01f826de40114', # %(name)s-%(version)s-pkgconfig_includes.patch + 'a3bf6b4127473d287d72767b0335b8705940e56ffbccc8d4d3bdbf23a2fc8618', # %(name)s-%(version)s-python3-compliant.patch +] + +builddependencies = [ + ('binutils', '2.42'), + ('Python', '3.12.3'), +] + +start_dir = 'pgm' + +sanity_check_paths = { + 'files': ['lib/libpgm.%s' % SHLIB_EXT, 'lib/libpgm.a'], + 'dirs': ['include'], +} + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/o/OpenSlide/OpenSlide-3.4.1-GCCcore-12.2.0-largefiles.eb b/easybuild/easyconfigs/o/OpenSlide/OpenSlide-3.4.1-GCCcore-12.2.0-largefiles.eb new file mode 100644 index 00000000000..a8bdbafa429 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenSlide/OpenSlide-3.4.1-GCCcore-12.2.0-largefiles.eb @@ -0,0 +1,56 @@ +easyblock = 'ConfigureMake' + +name = 'OpenSlide' +version = '3.4.1' +versionsuffix = '-largefiles' + +homepage = 'https://openslide.org/' +description = """OpenSlide is a C library that provides a simple interface to +read whole-slide images (also known as virtual slides).""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = [GITHUB_SOURCE] +sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}] +patches = ['%(name)s-%(version)s_large_file_support.patch'] +checksums = [ + # v3.4.1.tar.gz + 'a5d869916e370125421535dcce778b2ba625dc50d920aa4ca93bbaaa6a7b470c', + # %(name)s-%(version_major_minor)s.1_large_file_support.patch + 'cb618053f4ae6c3ce37d1b8b0e4ef7c55fd17378776d13be4aa4efab91706b8c', +] + +builddependencies = [ + ('Autotools', '20220317'), + ('M4', '1.4.19'), + ('pkgconf', '1.9.3'), + ('binutils', '2.39'), +] + +dependencies = [ + ('zlib', '1.2.12'), + ('libpng', '1.6.38'), + ('libjpeg-turbo', '2.1.4'), + ('LibTIFF', '4.4.0'), + ('OpenJPEG', '2.5.0'), + ('libxml2', '2.10.3'), + ('SQLite', '3.39.4'), + ('cairo', '1.17.4'), + ('Gdk-Pixbuf', '2.42.10'), +] + +preconfigopts = "autoreconf -f -i && " + +sanity_check_paths = { + 'files': [ + 'bin/openslide-quickhash1sum', + 'bin/openslide-show-properties', + 'bin/openslide-write-png', + 'lib/libopenslide.la', + 'lib/libopenslide.%s' % SHLIB_EXT + ], + 'dirs': ['include/openslide'] +} + + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/o/OpenStackClient/OpenStackClient-5.5.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/o/OpenStackClient/OpenStackClient-5.5.0-GCCcore-10.2.0.eb index b013362d2e5..50dab938d40 100644 --- a/easybuild/easyconfigs/o/OpenStackClient/OpenStackClient-5.5.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/o/OpenStackClient/OpenStackClient-5.5.0-GCCcore-10.2.0.eb @@ -16,9 +16,9 @@ dependencies = [ ] builddependencies = [('binutils', '2.35')] -exts_default_options = { - 'use_pip': True, -} +sanity_pip_check = True +use_pip = True + exts_list = [ ('pbr', '5.6.0', { 'checksums': ['42df03e7797b796625b1029c0400279c7c34fd7df24a7d7818a1abb5b38710dd'], @@ -121,7 +121,6 @@ exts_list = [ }), ] -sanity_pip_check = True enhance_sanity_check = True sanity_check_commands = ['openstack -h'] diff --git a/easybuild/easyconfigs/o/OpenStackClient/OpenStackClient-5.8.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/o/OpenStackClient/OpenStackClient-5.8.0-GCCcore-11.2.0.eb index e590dd730ca..d92bda87180 100644 --- a/easybuild/easyconfigs/o/OpenStackClient/OpenStackClient-5.8.0-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/o/OpenStackClient/OpenStackClient-5.8.0-GCCcore-11.2.0.eb @@ -16,9 +16,9 @@ dependencies = [ ] builddependencies = [('binutils', '2.37')] -exts_default_options = { - 'use_pip': True, -} +sanity_pip_check = True +use_pip = True + exts_list = [ ('pyperclip', '1.8.2', { 'checksums': ['105254a8b04934f0bc84e9c24eb360a591aaf6535c9def5f29d92af107a9bf57'], @@ -121,7 +121,6 @@ exts_list = [ }), ] -sanity_pip_check = True enhance_sanity_check = True sanity_check_commands = ['openstack -h'] diff --git a/easybuild/easyconfigs/o/OpenStackClient/OpenStackClient-6.0.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/o/OpenStackClient/OpenStackClient-6.0.0-GCCcore-12.2.0.eb index 6b695f63279..bdf0b5c45a6 100644 --- a/easybuild/easyconfigs/o/OpenStackClient/OpenStackClient-6.0.0-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/o/OpenStackClient/OpenStackClient-6.0.0-GCCcore-12.2.0.eb @@ -15,9 +15,9 @@ dependencies = [ ] builddependencies = [('binutils', '2.39')] -exts_default_options = { - 'use_pip': True, -} +sanity_pip_check = True +use_pip = True + exts_list = [ ('pyperclip', '1.8.2', { 'checksums': ['105254a8b04934f0bc84e9c24eb360a591aaf6535c9def5f29d92af107a9bf57'], @@ -114,7 +114,6 @@ exts_list = [ }), ] -sanity_pip_check = True enhance_sanity_check = True sanity_check_commands = ['openstack -h'] diff --git a/easybuild/easyconfigs/o/Optax/Optax-0.2.2-gfbf-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/o/Optax/Optax-0.2.2-gfbf-2023a-CUDA-12.1.1.eb new file mode 100644 index 00000000000..61000b1388c --- /dev/null +++ b/easybuild/easyconfigs/o/Optax/Optax-0.2.2-gfbf-2023a-CUDA-12.1.1.eb @@ -0,0 +1,37 @@ +easyblock = 'PythonBundle' + +name = 'Optax' +version = '0.2.2' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/deepmind/optax' +description = """Optax is a gradient processing and optimization library for JAX.""" + +toolchain = {'name': 'gfbf', 'version': '2023a'} + +dependencies = [ + ('CUDA', '12.1.1', '', SYSTEM), + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('jax', '0.4.25', versionsuffix), +] + +use_pip = True + +exts_list = [ + ('toolz', '0.12.1', { + 'checksums': ['ecca342664893f177a13dac0e6b41cbd8ac25a358e5f215316d43e2100224f4d'], + }), + ('chex', '0.1.86', { + 'checksums': ['e8b0f96330eba4144659e1617c0f7a57b161e8cbb021e55c6d5056c7378091d1'], + }), + ('optax', version, { + 'checksums': ['f09bf790ef4b09fb9c35f79a07594c6196a719919985f542dc84b0bf97812e0e'], + }), +] + +sanity_pip_check = True + +sanity_check_commands = ["python -c 'from optax import GradientTransformation'"] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/o/Optax/Optax-0.2.2-gfbf-2023a.eb b/easybuild/easyconfigs/o/Optax/Optax-0.2.2-gfbf-2023a.eb new file mode 100644 index 00000000000..d447a77bbd2 --- /dev/null +++ b/easybuild/easyconfigs/o/Optax/Optax-0.2.2-gfbf-2023a.eb @@ -0,0 +1,35 @@ +easyblock = 'PythonBundle' + +name = 'Optax' +version = '0.2.2' + +homepage = 'https://github.com/deepmind/optax' +description = """Optax is a gradient processing and optimization library for JAX.""" + +toolchain = {'name': 'gfbf', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('jax', '0.4.25'), +] + +use_pip = True + +exts_list = [ + ('toolz', '0.12.1', { + 'checksums': ['ecca342664893f177a13dac0e6b41cbd8ac25a358e5f215316d43e2100224f4d'], + }), + ('chex', '0.1.86', { + 'checksums': ['e8b0f96330eba4144659e1617c0f7a57b161e8cbb021e55c6d5056c7378091d1'], + }), + ('optax', version, { + 'checksums': ['f09bf790ef4b09fb9c35f79a07594c6196a719919985f542dc84b0bf97812e0e'], + }), +] + +sanity_pip_check = True + +sanity_check_commands = ["python -c 'from optax import GradientTransformation'"] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/o/Optuna/Optuna-3.6.1-foss-2023b.eb b/easybuild/easyconfigs/o/Optuna/Optuna-3.6.1-foss-2023b.eb new file mode 100644 index 00000000000..35dec40e234 --- /dev/null +++ b/easybuild/easyconfigs/o/Optuna/Optuna-3.6.1-foss-2023b.eb @@ -0,0 +1,50 @@ +easyblock = 'PythonBundle' + +name = 'Optuna' +version = '3.6.1' + +homepage = "https://optuna.org/" +description = """Optuna is an automatic hyperparameter optimization software framework, +particularly designed for machine learning. It features an imperative, +define-by-run style user API. Thanks to our define-by-run API, the code written +with Optuna enjoys high modularity, and the user of Optuna can dynamically +construct the search spaces for the hyperparameters.""" + + +toolchain = {'name': 'foss', 'version': '2023b'} + +dependencies = [ + ('Python', '3.11.5'), + ('PyYAML', '6.0.1'), + ('SciPy-bundle', '2023.11'), + ('tqdm', '4.66.2'), + ('matplotlib', '3.8.2'), # optional + ('plotly.py', '5.18.0'), # optional + ('redis-py', '5.0.9'), # optional + ('scikit-learn', '1.4.0'), # optional + ('SQLAlchemy', '2.0.29'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('cmaes', '0.11.1', { + 'checksums': ['cf71fa3679814723be771f2c9edd85f465b1bc1e409e1ad6d8a9e481efcd5160'], + }), + ('colorlog', '6.8.2', { + 'checksums': ['3e3e079a41feb5a1b64f978b5ea4f46040a94f11f0e8bbb8261e3dbbeca64d44'], + }), + ('optuna', version, { + 'use_pip_extras': 'optional', + 'checksums': ['146e530b57b4b9afd7526b3e642fbe65491f7e292b405913355f8e438e361ecf'], + }), +] + +sanity_check_paths = { + 'files': ['bin/optuna'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} +sanity_check_commands = [('optuna', '--help')] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/o/ocamlbuild/ocamlbuild-0.14.3-GCC-13.2.0.eb b/easybuild/easyconfigs/o/ocamlbuild/ocamlbuild-0.14.3-GCC-13.2.0.eb new file mode 100644 index 00000000000..209be487770 --- /dev/null +++ b/easybuild/easyconfigs/o/ocamlbuild/ocamlbuild-0.14.3-GCC-13.2.0.eb @@ -0,0 +1,41 @@ +easyblock = 'ConfigureMake' + +name = 'ocamlbuild' +version = '0.14.3' + +homepage = 'https://github.com/ocaml/ocamlbuild' +description = """OCamlbuild is a generic build tool, + that has built-in rules for building OCaml library and programs.""" + +toolchain = {'name': 'GCC', 'version': '13.2.0'} + +source_urls = ['https://github.com/ocaml/ocamlbuild/archive'] +sources = ['%(version)s.tar.gz'] +checksums = ['ce151bfd2141abc6ee0b3f25ba609e989ff564a48bf795d6fa7138a4db0fc2e1'] + +builddependencies = [ + ('binutils', '2.40'), +] + +dependencies = [ + ('OCaml', '5.1.1'), + ('zstd', '1.5.5'), +] + +skipsteps = ['configure'] + +prebuildopts = 'make configure && ' + +buildopts = 'CXX="$CXX" CFLAGS="$CXXFLAGS"' + +installopts = 'DESTDIR="%(installdir)s" INSTALL_BINDIR="%(installdir)s/bin" ' +installopts += 'INSTALL_LIBDIR="%(installdir)s/lib" INSTALL_MANDIR="%(installdir)s/man" ' + +sanity_check_paths = { + 'files': ['bin/%(name)s', 'lib/ocamlbuild/%(name)slib.a'], + 'dirs': ['man'], +} + +sanity_check_commands = ['%(name)s --help'] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/o/ome-types/ome-types-0.5.1.post1-foss-2023a.eb b/easybuild/easyconfigs/o/ome-types/ome-types-0.5.1.post1-foss-2023a.eb new file mode 100644 index 00000000000..0de34e3542b --- /dev/null +++ b/easybuild/easyconfigs/o/ome-types/ome-types-0.5.1.post1-foss-2023a.eb @@ -0,0 +1,52 @@ +easyblock = 'PythonBundle' + +name = 'ome-types' +version = '0.5.1.post1' + +homepage = 'https://github.com/tlambert03/ome-types/' +description = """ +ome_types provides a set of python dataclasses and utility functions for parsing +the OME-XML format into fully-typed python objects for interactive or programmatic access in python. +""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [ + ('poetry', '1.5.1'), + ('hatchling', '1.18.0'), + ('maturin', '1.4.0', '-Rust-1.75.0'), +] +dependencies = [ + ('Python', '3.11.3'), + ('pydantic', '2.5.3'), + ('Python-bundle-PyPI', '2023.06'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('ruff', '0.3.0', { + 'checksums': ['0886184ba2618d815067cf43e005388967b67ab9c80df52b32ec1152ab49f53a'], + }), + ('pydantic_compat', '0.1.2', { + 'checksums': ['c5c5bca39ca2d22cad00c02898e400e1920e5127649a8e860637f15566739373'], + }), + ('untokenize', '0.1.1', { + 'checksums': ['3865dbbbb8efb4bb5eaa72f1be7f3e0be00ea8b7f125c69cbd1f5fda926f37a2'], + }), + ('docformatter', '1.7.5', { + 'checksums': ['ffed3da0daffa2e77f80ccba4f0e50bfa2755e1c10e130102571c890a61b246e'], + }), + ('toposort', '1.10', { + 'checksums': ['bfbb479c53d0a696ea7402601f4e693c97b0367837c8898bc6471adfca37a6bd'], + }), + ('xsdata', '23.8', { + 'checksums': ['55f03d4c88236f047266affe550ba0dd19476adfce6a01f3e0aefac7c8078e56'], + }), + ('ome_types', version, { + 'checksums': ['cadda5e36ad4d33dad2034fd43f32113a736fe47c67fd9e06bbb8d3858d1dc58'], + }), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/o/ont-remora/ont-remora-3.3.0-foss-2023a.eb b/easybuild/easyconfigs/o/ont-remora/ont-remora-3.3.0-foss-2023a.eb new file mode 100644 index 00000000000..7d065263f5b --- /dev/null +++ b/easybuild/easyconfigs/o/ont-remora/ont-remora-3.3.0-foss-2023a.eb @@ -0,0 +1,60 @@ +easyblock = 'PythonBundle' + +name = 'ont-remora' +version = '3.3.0' + +homepage = 'https://github.com/nanoporetech/remora' +description = """Methylation/modified base calling separated from basecalling. Remora primarily +provides an API to call modified bases for basecaller programs such as Bonito. +Remora also provides the tools to prepare datasets, train modified base models +and run simple inference.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('ONNX-Runtime', '1.19.2'), + ('PyTorch', '2.1.2'), + ('scikit-learn', '1.3.1'), + ('tqdm', '4.66.1'), + ('python-parasail', '1.3.4'), + ('polars', '0.20.2'), + ('Pysam', '0.22.0'), + ('pod5-file-format', '0.3.10'), + ('statsmodels', '0.14.1'), +] + +use_pip = True + +exts_list = [ + ('thop', '0.1.1.post2209072238', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['01473c225231927d2ad718351f78ebf7cffe6af3bed464c4f1ba1ef0f7cdda27'], + }), + ('mizani', '0.9.3', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['ac5d49b913de88dc2fb28d82141e9777b97407a6971a158f758093ad5bb820a1'], + }), + ('plotnine', '0.12.4', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['12748f346f107c33f3e0658ac46fbb052205ae7e97ffaf52be68310e5d29f799'], + }), + (name, version, { + 'modulename': 'remora', + 'checksums': ['3c899e7333ae33ebec31c8a59650ab4d553e8a62c0abf7b03899e2ee9a0bc88a'], + }), +] + +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/remora'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + ('remora', '--help'), +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/o/openai-python/openai-python-1.30.5-foss-2023a.eb b/easybuild/easyconfigs/o/openai-python/openai-python-1.30.5-foss-2023a.eb new file mode 100644 index 00000000000..e5fa3228a07 --- /dev/null +++ b/easybuild/easyconfigs/o/openai-python/openai-python-1.30.5-foss-2023a.eb @@ -0,0 +1,53 @@ +easyblock = 'PythonBundle' + +name = 'openai-python' +version = '1.30.5' + +homepage = 'https://github.com/openai/openai-python' +description = """ +The OpenAI Python library provides convenient access to the OpenAI REST API from any +Python 3.7+ application. The library includes type definitions for all request params and +response fields, and offers both synchronous and asynchronous clients powered by httpx. +""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [ + ('hatchling', '1.18.0'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('pydantic', '2.5.3'), + ('typing-extensions', '4.9.0'), + ('tqdm', '4.66.1'), +] + +exts_list = [ + ('h11', '0.14.0', { + 'checksums': ['8f19fbbe99e72420ff35c00b27a34cb9937e902a8b810e2c88300c6f0a3b699d'], + }), + ('httpcore', '1.0.5', { + 'checksums': ['34a38e2f9291467ee3b44e89dd52615370e152954ba21721378a87b2960f7a61'], + }), + ('httpx', '0.27.0', { + 'checksums': ['a0cb88a46f32dc874e04ee956e4c2764aba2aa228f650b06788ba6bda2962ab5'], + }), + ('anyio', '4.4.0', { + 'checksums': ['5aadc6a1bbb7cdb0bede386cac5e2940f5e2ff3aa20277e991cf028e0585ce94'], + }), + ('sniffio', '1.3.1', { + 'checksums': ['f4324edc670a0f49750a81b895f35c3adb843cca46f0530f79fc1babb23789dc'], + }), + ('openai', version, { + # needs a README or will get "Fragment file 'README.md' not found." error + 'preinstallopts': "touch README.md && ", + 'checksums': ['5366562eb2c5917e6116ae0391b7ae6e3acd62b0ae3f565ada32b35d8fcfa106'], + }), +] + +use_pip = True +sanity_pip_check = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/o/openslide-python/openslide-python-1.3.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/o/openslide-python/openslide-python-1.3.1-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..bbbaa753b40 --- /dev/null +++ b/easybuild/easyconfigs/o/openslide-python/openslide-python-1.3.1-GCCcore-12.2.0.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonPackage' + +name = 'openslide-python' +version = '1.3.1' + +homepage = 'https://github.com/openslide/openslide-python' +description = "OpenSlide Python is a Python interface to the OpenSlide library." + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://github.com/openslide/openslide-python/archive'] +sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}] +checksums = ['3f56bc9d02ae4a5b7257cf5e35214c5cc45f429ff3d5ef849c6c8e2460c1f9cd'] + +builddependencies = [('binutils', '2.39')] + +dependencies = [ + ('Python', '3.10.8'), + ('OpenSlide', '3.4.1', '-largefiles'), + ('Pillow-SIMD', '9.5.0'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +options = {'modulename': 'openslide'} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/o/orjson/orjson-3.9.15-GCCcore-12.3.0.eb b/easybuild/easyconfigs/o/orjson/orjson-3.9.15-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..410c8131df9 --- /dev/null +++ b/easybuild/easyconfigs/o/orjson/orjson-3.9.15-GCCcore-12.3.0.eb @@ -0,0 +1,38 @@ +easyblock = 'PythonBundle' + +name = 'orjson' +version = '3.9.15' + +homepage = 'https://github.com/ijl/orjson' +description = """Fast, correct Python JSON library supporting dataclasses, datetimes, and numpy.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +builddependencies = [ + ('binutils', '2.40'), + ('maturin', '1.4.0', '-Rust-1.75.0'), +] +dependencies = [ + ('Python', '3.11.3'), +] + +use_pip = True + +exts_list = [ + ('ruff', '0.4.8', { + 'checksums': ['16d717b1d57b2e2fd68bd0bf80fb43931b79d05a7131aa477d66fc40fbd86268'], + }), + ('mypy_extensions', '1.0.0', { + 'checksums': ['75dbf8955dc00442a438fc4d0666508a9a97b6bd41aa2f0ffe9d2f2725af0782'], + }), + ('mypy', '1.10.0', { + 'checksums': ['3d087fcbec056c4ee34974da493a826ce316947485cef3901f511848e687c131'], + }), + (name, version, { + 'checksums': ['95cae920959d772f30ab36d3b25f83bb0f3be671e986c72ce22f8fa700dae061'], + }), +] + +sanity_pip_check = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/PALM/PALM-23.10-foss-2023a.eb b/easybuild/easyconfigs/p/PALM/PALM-23.10-foss-2023a.eb new file mode 100644 index 00000000000..7517506de97 --- /dev/null +++ b/easybuild/easyconfigs/p/PALM/PALM-23.10-foss-2023a.eb @@ -0,0 +1,103 @@ +easyblock = 'Binary' + +name = 'PALM' +version = '23.10' + +homepage = 'https://palm.muk.uni-hannover.de' +description = """PALM is an advanced and state-of-the-art meteorological +modeling system for atmospheric and oceanic boundary layer flows.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['https://gitlab.palm-model.org/releases/palm_model_system/-/archive/v%(version)s/'] +sources = ['palm_model_system-v%(version)s.tar.gz'] +checksums = ['2b13bcff9cc95ba3c80e037f239a4a96525138143598a3f52ce04ff40bfadb80'] + +builddependencies = [ + ('CMake', '3.26.3'), + ('flex', '2.6.4'), + ('Bison', '3.8.2'), + ('hatchling', '1.18.0'), +] + +# required Python package: see various requirements.txt files in source directory +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), # for numpy, scipy + ('netCDF-Fortran', '4.6.1'), + ('netcdf4-python', '1.6.4'), # for netCDF4 + ('PyQt5', '5.15.10'), + ('PyYAML', '6.0'), +] + +buildininstalldir = True + +extract_sources = True + +install_cmd = "bash install -p %(installdir)s" + +exts_defaultclass = 'PythonPackage' + +exts_default_options = { + 'source_urls': [PYPI_SOURCE], + 'download_dep_fail': True, + 'use_pip': True, +} + +exts_list = [ + ('argcomplete', '3.2.3', { + 'checksums': ['bf7900329262e481be5a15f56f19736b376df6f82ed27576fa893652c5de6c23'], + }), + ('mike', '2.0.0', { + 'checksums': ['566f1cab1a58cc50b106fb79ea2f1f56e7bfc8b25a051e95e6eaee9fba0922de'], + }), + ('Markdown', '3.6', { + 'checksums': ['ed4f41f6daecbeeb96e576ce414c41d2d876daa9a16cb35fa8ed8c2ddfad0224'], + }), + ('ghp-import', '2.1.0', { + 'checksums': ['9c535c4c61193c2df8871222567d7fd7e5014d835f97dc7b7439069e2413d343'], + }), + ('mergedeep', '1.3.4', { + 'checksums': ['0096d52e9dad9939c3d975a774666af186eda617e6ca84df4c94dec30004f2a8'], + }), + ('pyyaml_env_tag', '0.1', { + 'checksums': ['70092675bda14fdec33b31ba77e7543de9ddc88f2e5b99160396572d11525bdb'], + 'modulename': 'yaml_env_tag', + }), + ('watchdog', '4.0.1', { + 'checksums': ['eebaacf674fa25511e8867028d281e602ee6500045b57f43b08778082f7f8b44'], + }), + ('mkdocs', '1.5.3', { + 'checksums': ['eb7c99214dcb945313ba30426c2451b735992c73c2e10838f76d09e39ff4d0e2'], + }), + ('mkdocs-macros-plugin', '1.0.5', { + 'checksums': ['fe348d75f01c911f362b6d998c57b3d85b505876dde69db924f2c512c395c328'], + 'modulename': 'mkdocs_macros', + }), + ('pymdown_extensions', '10.7.1', { + 'checksums': ['c70e146bdd83c744ffc766b4671999796aba18842b268510a329f7f64700d584'], + 'modulename': 'pymdownx.magiclink', + }), + ('termcolor', '2.4.0', { + 'checksums': ['aab9e56047c8ac41ed798fa36d892a37aca6b3e9159f3e0c24bc64a9b3ac7b7a'], + # fix for: "Unknown classifier in field project.classifiers: Programming Language :: Python :: 3.13" + 'preinstallopts': "sed -i '/Python.*3.13/d' pyproject.toml && ", + }), + ('verspec', '0.1.0', { + 'checksums': ['c4504ca697b2056cdb4bfa7121461f5a0e81809255b41c03dda4ba823637c01e'], + }), +] + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +sanity_check_paths = { + 'files': ['bin/palmrun'], + 'dirs': ['lib/python%(pyshortver)s/site-packages', 'rrtmg'], +} + +sanity_check_commands = [ + "export PYTHONNOUSERSITE=1 && python%(pyshortver)s -m pip check", + "palmrun ?", +] + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/p/PAPI/PAPI-7.1.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/p/PAPI/PAPI-7.1.0-GCCcore-13.2.0.eb index fafbe94664c..27c5255c39a 100644 --- a/easybuild/easyconfigs/p/PAPI/PAPI-7.1.0-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/p/PAPI/PAPI-7.1.0-GCCcore-13.2.0.eb @@ -23,7 +23,11 @@ toolchain = {'name': 'GCCcore', 'version': '13.2.0'} source_urls = ['https://icl.utk.edu/projects/papi/downloads'] sources = [SOURCELOWER_TAR_GZ] -checksums = ['5818afb6dba3ece57f51e65897db5062f8e3464e6ed294b654ebf34c3991bc4f'] +patches = ['%(name)s-%(version)s_add_initial_riscv_support.patch'] +checksums = [ + '5818afb6dba3ece57f51e65897db5062f8e3464e6ed294b654ebf34c3991bc4f', + {'PAPI-7.1.0_add_initial_riscv_support.patch': '6c7d0d63ccf2b8c46f2ed736fbd4c58303038fb2a45315aed94c026b773af35a'} +] builddependencies = [ ('binutils', '2.40'), diff --git a/easybuild/easyconfigs/p/PAPI/PAPI-7.1.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/p/PAPI/PAPI-7.1.0-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..5c653a9d515 --- /dev/null +++ b/easybuild/easyconfigs/p/PAPI/PAPI-7.1.0-GCCcore-13.3.0.eb @@ -0,0 +1,53 @@ +## +# Author: Robert Mijakovic +# Updated: Alexander Grund +## + +easyblock = 'ConfigureMake' + +name = 'PAPI' +version = '7.1.0' + +homepage = 'https://icl.cs.utk.edu/projects/papi/' +description = """ + PAPI provides the tool designer and application engineer with a consistent + interface and methodology for use of the performance counter hardware found + in most major microprocessors. PAPI enables software engineers to see, in near + real time, the relation between software performance and processor events. + In addition Component PAPI provides access to a collection of components + that expose performance measurement opportunites across the hardware and + software stack. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://icl.utk.edu/projects/papi/downloads'] +sources = [SOURCELOWER_TAR_GZ] +patches = ['%(name)s-%(version)s_add_initial_riscv_support.patch'] +checksums = [ + '5818afb6dba3ece57f51e65897db5062f8e3464e6ed294b654ebf34c3991bc4f', + {'PAPI-7.1.0_add_initial_riscv_support.patch': '6c7d0d63ccf2b8c46f2ed736fbd4c58303038fb2a45315aed94c026b773af35a'} +] + +builddependencies = [ + ('binutils', '2.42'), +] + +start_dir = 'src' + +configopts = "--with-components=rapl " # for energy measurements + +# There is also "fulltest" that is a superset of "test" but hangs on some processors +# indefinitely with a defunct `make` process. So use only "test". +runtest = 'test' + +sanity_check_paths = { + 'files': ["bin/papi_%s" % x + for x in ["avail", "clockres", "command_line", "component_avail", + "cost", "decode", "error_codes", "event_chooser", + "mem_info", "multiplex_cost", "native_avail", + "version", "xml_event_info"]], + 'dirs': [], +} + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/p/PAPI/PAPI-7.1.0_add_initial_riscv_support.patch b/easybuild/easyconfigs/p/PAPI/PAPI-7.1.0_add_initial_riscv_support.patch new file mode 100644 index 00000000000..ac57971d845 --- /dev/null +++ b/easybuild/easyconfigs/p/PAPI/PAPI-7.1.0_add_initial_riscv_support.patch @@ -0,0 +1,64 @@ +From b464420f3a2855b2c800413a4c5767b69e088087 Mon Sep 17 00:00:00 2001 +From: Vince Weaver +Date: Tue, 9 Jan 2024 21:50:26 +0000 +Subject: [PATCH] add initial riscv support + +This adds basic support for the RISC-V architecture + +After this PAPI will compile and the tools will run, however no events will +work because of missing libpfm4 support. + +Tested on a BeagleV-Ahead board +--- + src/linux-context.h | 2 ++ + src/linux-timer.c | 2 +- + src/mb.h | 10 ++++++++++ + 3 files changed, 13 insertions(+), 1 deletion(-) + +diff --git a/src/linux-context.h b/src/linux-context.h +index f46e5577b..394a4804d 100644 +--- a/src/linux-context.h ++++ b/src/linux-context.h +@@ -39,6 +39,8 @@ typedef ucontext_t hwd_ucontext_t; + #define OVERFLOW_ADDRESS(ctx) ctx.ucontext->uc_mcontext.pc + #elif defined(__hppa__) + #define OVERFLOW_ADDRESS(ctx) ctx.ucontext->uc_mcontext.sc_iaoq[0] ++#elif defined(__riscv) ++#define OVERFLOW_ADDRESS(ctx) ctx.ucontext->uc_mcontext.__gregs[REG_PC] + #else + #error "OVERFLOW_ADDRESS() undefined!" + #endif +diff --git a/src/linux-timer.c b/src/linux-timer.c +index 0eaa79c66..be489f325 100644 +--- a/src/linux-timer.c ++++ b/src/linux-timer.c +@@ -281,7 +281,7 @@ static inline long long get_cycles() + return retval; + } + +-#elif (defined(__arm__) || defined(__mips__) || defined(__hppa__)) ++#elif (defined(__arm__) || defined(__mips__) || defined(__hppa__)) || defined(__riscv) + static inline long long + get_cycles( void ) + { +diff --git a/src/mb.h b/src/mb.h +index 81797c553..56d980410 100644 +--- a/src/mb.h ++++ b/src/mb.h +@@ -63,6 +63,16 @@ + #define rmb() asm volatile("lfence":::"memory") + #endif + ++ ++#elif defined (__riscv) ++#define RISCV_FENCE(p, s) \ ++ __asm__ __volatile__ ("fence " #p "," #s : : : "memory") ++ ++/* These barriers need to enforce ordering on both devices or memory. */ ++#define mb() RISCV_FENCE(iorw,iorw) ++#define rmb() RISCV_FENCE(ir,ir) ++#define wmb() RISCV_FENCE(ow,ow) ++ + #else + #error Need to define rmb for this architecture! + #error See the kernel source directory: tools/perf/perf.h file diff --git a/easybuild/easyconfigs/p/PASA/PASA-2.5.3-foss-2023a.eb b/easybuild/easyconfigs/p/PASA/PASA-2.5.3-foss-2023a.eb new file mode 100644 index 00000000000..8d42086755c --- /dev/null +++ b/easybuild/easyconfigs/p/PASA/PASA-2.5.3-foss-2023a.eb @@ -0,0 +1,57 @@ +easyblock = 'ConfigureMake' + +name = 'PASA' +version = '2.5.3' + +homepage = 'https://github.com/PASApipeline/PASApipeline' +description = """PASA, acronym for Program to Assemble Spliced Alignments (and pronounced 'pass-uh'), + is a eukaryotic genome annotation tool that exploits spliced alignments of expressed transcript + sequences to automatically model gene structures, and to maintain gene structure annotation consistent + with the most recently available experimental sequence data. PASA also identifies and classifies all + splicing variations supported by the transcript alignments.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['https://github.com/PASApipeline/PASApipeline/archive/'] +sources = ['%(namelower)s-v%(version)s.tar.gz'] +checksums = ['9b2f6a301b73fd8c713af0977cf6e97f3d928988d6b79715ebe81e19b51152eb'] + +dependencies = [ + ('SQLite', '3.42.0'), + ('GMAP-GSNAP', '2023-04-20'), + ('pblat', '2.5.1'), + ('minimap2', '2.26'), + ('FASTA', '36.3.8i'), +] + +buildininstalldir = True + +skipsteps = ['configure', 'install'] + +unpack_options = '--strip-components=1' + +local_bins = [ + '%(namelower)s', + 'cdbfasta', + 'cdbyank', + 'cln2qual', + 'mdust', + 'psx', + 'seqclean', + 'seqclean.psx', + 'slclust', + 'trimpoly', +] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_bins], + 'dirs': [] +} + +modextrapaths = { + 'PASAHOME': '', +} + +sanity_check_commands = ['command -v %(namelower)s'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/PCAngsd/PCAngsd-1.2-gfbf-2023a.eb b/easybuild/easyconfigs/p/PCAngsd/PCAngsd-1.2-gfbf-2023a.eb new file mode 100644 index 00000000000..d534bfa0f78 --- /dev/null +++ b/easybuild/easyconfigs/p/PCAngsd/PCAngsd-1.2-gfbf-2023a.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonBundle' + +name = 'PCAngsd' +version = '1.2' + +homepage = "https://www.popgen.dk/software/index.php/PCAngsd" +description = "Framework for analyzing low depth NGS data in heterogeneous populations using PCA." + +toolchain = {'name': 'gfbf', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('Cython', '3.0.8'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + (name, version, { + 'modulename': False, + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/Rosemeis/pcangsd/archive/refs/tags/'], + 'checksums': ['286f09851c37e380c9abf5859595e7cd0ad8cb49f1d48b1b0ae409aab0eae62e'], + }), +] + +sanity_check_commands = [ + 'pcangsd --help', +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/PCL/PCL-1.14.1-foss-2023a.eb b/easybuild/easyconfigs/p/PCL/PCL-1.14.1-foss-2023a.eb new file mode 100644 index 00000000000..97f57817025 --- /dev/null +++ b/easybuild/easyconfigs/p/PCL/PCL-1.14.1-foss-2023a.eb @@ -0,0 +1,32 @@ +easyblock = 'CMakeMake' + +name = 'PCL' +version = '1.14.1' + +homepage = 'https://pointclouds.org/' +description = """The Point Cloud Library (PCL) is a standalone, large scale, open project for 2D/3D image and + point cloud processing.""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/PointCloudLibrary/pcl/archive/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['5dc5e09509644f703de9a3fb76d99ab2cc67ef53eaf5637db2c6c8b933b28af6'] + +builddependencies = [('CMake', '3.26.3')] + +dependencies = [ + ('Boost', '1.82.0'), + ('Eigen', '3.4.0'), + ('FLANN', '1.9.2'), + ('VTK', '9.3.0'), + ('Qhull', '2020.2'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['bin', 'include/pcl-%(version_major_minor)s/pcl', 'lib', 'share/pcl-%(version_major_minor)s'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/PCRE/PCRE-8.45-GCCcore-13.3.0.eb b/easybuild/easyconfigs/p/PCRE/PCRE-8.45-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..c378f2e1bab --- /dev/null +++ b/easybuild/easyconfigs/p/PCRE/PCRE-8.45-GCCcore-13.3.0.eb @@ -0,0 +1,43 @@ +easyblock = 'ConfigureMake' + +name = 'PCRE' +version = '8.45' + +homepage = 'https://www.pcre.org/' +description = """ + The PCRE library is a set of functions that implement regular expression + pattern matching using the same syntax and semantics as Perl 5. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +source_urls = [ + SOURCEFORGE_SOURCE, + 'https://ftp.%(namelower)s.org/pub/%(namelower)s/', +] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['4e6ce03e0336e8b4a3d6c2b70b1c5e18590a5673a98186da90d4f33c23defc09'] + +builddependencies = [ + ('binutils', '2.42'), +] +dependencies = [ + ('bzip2', '1.0.8'), + ('zlib', '1.3.1'), +] + +configopts = "--enable-utf --enable-unicode-properties --enable-pcre16 --enable-pcre32" + + +sanity_check_paths = { + 'files': [ + 'bin/%(namelower)s-config', + 'include/%(namelower)s.h', + 'share/man/man3/%(namelower)s.3', + 'lib/libpcre32.%s' % SHLIB_EXT + ], + 'dirs': ['lib/pkgconfig', 'share/doc/%(namelower)s/html', 'share/man/man1'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/PCRE2/PCRE2-10.43-GCCcore-13.3.0.eb b/easybuild/easyconfigs/p/PCRE2/PCRE2-10.43-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..fcbe54f5a34 --- /dev/null +++ b/easybuild/easyconfigs/p/PCRE2/PCRE2-10.43-GCCcore-13.3.0.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'PCRE2' +version = '10.43' + +homepage = 'https://www.pcre.org/' +description = """ + The PCRE library is a set of functions that implement regular expression pattern matching using the same syntax + and semantics as Perl 5. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/PCRE2Project/%(namelower)s/releases/download/%(namelower)s-%(version)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['889d16be5abb8d05400b33c25e151638b8d4bac0e2d9c76e9d6923118ae8a34e'] + +builddependencies = [('binutils', '2.42')] + +configopts = "--enable-shared --enable-jit --enable-pcre2-16 --enable-unicode" + +sanity_check_paths = { + 'files': ["bin/pcre2-config", "bin/pcre2grep", "bin/pcre2test", "lib/libpcre2-8.a", "lib/libpcre2-16.a"], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/PDM/PDM-2.18.2-GCCcore-13.3.0.eb b/easybuild/easyconfigs/p/PDM/PDM-2.18.2-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..b56e431ecba --- /dev/null +++ b/easybuild/easyconfigs/p/PDM/PDM-2.18.2-GCCcore-13.3.0.eb @@ -0,0 +1,57 @@ +easyblock = 'PythonBundle' + +name = 'PDM' +version = '2.18.2' + +homepage = 'https://pdm-project.org' +description = "A modern Python package and dependency manager supporting the latest PEP standards." + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +builddependencies = [ + ('binutils', '2.42'), + ('poetry', '1.8.3'), +] +dependencies = [ + ('Python', '3.12.3'), + ('Python-bundle-PyPI', '2024.06'), +] + +sanity_pip_check = True +use_pip = True + +exts_list = [ + ('pdm_backend', '2.3.3', { + 'modulename': 'pdm.backend', + 'checksums': ['a8616f628ec84353d7a0ba86b228dcf01bab5debc9e4d1a29e5311a52425d594'], + }), + ('installer', '0.7.0', {'checksums': ['a26d3e3116289bb08216e0d0f7d925fcef0b0194eedfa0c944bcaaa106c4b631']}), + ('sniffio', '1.3.1', {'checksums': ['f4324edc670a0f49750a81b895f35c3adb843cca46f0530f79fc1babb23789dc']}), + ('h11', '0.14.0', {'checksums': ['8f19fbbe99e72420ff35c00b27a34cb9937e902a8b810e2c88300c6f0a3b699d']}), + ('httpcore', '1.0.5', {'checksums': ['34a38e2f9291467ee3b44e89dd52615370e152954ba21721378a87b2960f7a61']}), + ('anyio', '4.4.0', {'checksums': ['5aadc6a1bbb7cdb0bede386cac5e2940f5e2ff3aa20277e991cf028e0585ce94']}), + ('httpx', '0.27.2', {'checksums': ['f7c2be1d2f3c3c3160d441802406b206c2b76f5947b11115e6df10c6c65e66c2']}), + ('unearth', '0.17.2', {'checksums': ['0b8a2afd3476f1ab6155fc579501ac47fffe43547d88a70e5a5b76a7fe6caa2c']}), + ('installer', '0.7.0', {'checksums': ['a26d3e3116289bb08216e0d0f7d925fcef0b0194eedfa0c944bcaaa106c4b631']}), + ('truststore', '0.9.2', {'checksums': ['a1dee0d0575ff22d2875476343783a5d64575419974e228f3248772613c3d993']}), + ('resolvelib', '1.0.1', {'checksums': ['04ce76cbd63fded2078ce224785da6ecd42b9564b1390793f64ddecbe997b309']}), + ('python-dotenv', '1.0.1', { + 'modulename': 'dotenv', + 'checksums': ['e324ee90a023d808f1959c46bcbc04446a10ced277783dc6ee09987c37ec10ca'], + }), + ('pyproject_hooks', '1.1.0', {'checksums': ['4b37730834edbd6bd37f26ece6b44802fb1c1ee2ece0e54ddff8bfc06db86965']}), + ('pbs-installer', '2024.9.9', { + 'source_tmpl': 'pbs_installer-%(version)s.tar.gz', + 'checksums': ['bed162d05ef71c53a0e5e5c6349bab1b07a3d0e5af1800d619a4414a1fda309a'], + }), + ('hishel', '0.0.30', {'checksums': ['656393ee77e9c39a0d6c527c74810e15d96e598dcb9b191f20a788608ceaca99']}), + ('findpython', '0.6.1', {'checksums': ['56e52b409a92bcbd495cf981c85acf137f3b3e51cc769b46eba219bb1ab7533c']}), + ('dep-logic', '0.4.6', { + 'source_tmpl': 'dep_logic-%(version)s.tar.gz', + 'checksums': ['673d45402e9f11c4e501b08ebaea1efaa5e9bc6f69410684a9e448f8f5b26d6a'], + }), + ('blinker', '1.8.2', {'checksums': ['8f77b09d3bf7c795e969e9486f39c2c5e9c39d4ee07424be2bc594ece9642d83']}), + ('pdm', version, {'checksums': ['6d93a18d52edca056fafed7b262fe48ddc61984dabf73eb9365ad61a90caebb6']}), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/PDT/PDT-3.25.2-GCCcore-13.3.0.eb b/easybuild/easyconfigs/p/PDT/PDT-3.25.2-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..74328c99ae7 --- /dev/null +++ b/easybuild/easyconfigs/p/PDT/PDT-3.25.2-GCCcore-13.3.0.eb @@ -0,0 +1,40 @@ +# # +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2013-2019 Juelich Supercomputing Centre, Germany +# Authors:: Bernd Mohr +# Markus Geimer +# License:: 3-clause BSD +# +# This work is based on experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +# # + +name = 'PDT' +version = '3.25.2' + +homepage = 'https://www.cs.uoregon.edu/research/pdt/' +description = """ + Program Database Toolkit (PDT) is a framework for analyzing source code + written in several programming languages and for making rich program + knowledge accessible to developers of static and dynamic analysis tools. + PDT implements a standard program representation, the program database + (PDB), that can be accessed in a uniform way through a class library + supporting common PDB operations. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['http://tau.uoregon.edu/pdt_releases/'] +sources = ['pdtoolkit-%(version)s.tar.gz'] +# Might now be available as direct download although e.g. http://tau.uoregon.edu/pdt.tgz may work +download_instructions = ("Download from https://www.cs.uoregon.edu/research/pdt/downloads.php " + + "and rename to " + sources[0]) +checksums = ['01c2d403bc6672b2b264a182c325806541066c5ed5713878eb598f5506428cbe'] + +builddependencies = [ + ('binutils', '2.42'), +] + + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/p/PEcAn/PEcAn-1.8.0.9000-foss-2023a-R-4.3.2.eb b/easybuild/easyconfigs/p/PEcAn/PEcAn-1.8.0.9000-foss-2023a-R-4.3.2.eb new file mode 100644 index 00000000000..b5747815246 --- /dev/null +++ b/easybuild/easyconfigs/p/PEcAn/PEcAn-1.8.0.9000-foss-2023a-R-4.3.2.eb @@ -0,0 +1,217 @@ +easyblock = 'Bundle' + +name = 'PEcAn' +version = '1.8.0.9000' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://github.com/PecanProject/pecan' +description = """Ecosystem science, policy, and management informed by the best available data and models.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('R', '4.3.2'), + ('R-bundle-Bioconductor', '3.18', versionsuffix), + ('PostgreSQL', '16.1'), + ('CDO', '2.2.2'), + ('HDF5', '1.14.0'), + ('netCDF', '4.9.2'), + ('UDUNITS', '2.2.28'), + ('texlive', '20230313'), + ('NCO', '5.1.9'), + ('ncview', '2.1.8'), + ('rjags', '4-15', versionsuffix), + ('Redland', '1.0.17'), +] + +exts_defaultclass = 'RPackage' +exts_default_options = { + 'sources': ['%(name)s_%(version)s.tar.gz'], + 'source_urls': [ + 'https://cran.r-project.org/src/contrib/', # current version of packages + 'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + 'https://pecanproject.r-universe.dev/src/contrib/', # PEcAn sources + ], +} + +exts_list = [ + ('PEcAn.logger', '1.8.2.9000', { + 'checksums': ['1092f72fa63d58d83ca939a06bfa51ad3b3b4cd94ca4e68202cdb08fd3ada099'], + }), + ('PEcAn.remote', version, { + 'checksums': ['b3c7208c85d37aa6c12ca99182262a9886e57e2591faefd909232b8c89111b20'], + }), + ('PEcAn.utils', version, { + 'checksums': ['524c3231a21a1e5fc48ebc53d17e49c82f018b87c274095cd0362103fe322ec5'], + }), + ('PEcAn.DB', version, { + 'checksums': ['9b7e9b40a07879c1265d9ab6087b7448dfd34c3601c64ddcb41511c97399fece'], + }), + ('PEcAn.settings', version, { + 'checksums': ['555a7d81eec7e97b8457cef51888087af6b5d7d07f527ca58cbab07ed847fabc'], + }), + ('PEcAn.MA', '1.7.3.9000', { + 'checksums': ['680290e0ee52526db1242d95c4ca06a1e0ad117337ff721d79387797bc7e40ed'], + }), + ('PEcAn.emulator', version, { + 'checksums': ['68944ebdf1f37ff84f9b09bf02c709de9eda823728bbdea073a36d7ef19cfb9c'], + }), + ('PEcAn.priors', '1.7.3.9000', { + 'checksums': ['e942a31ae02af61b1b8e36d1c5df58f39829b3d0c29421edc151f2f063ff4c1f'], + }), + ('PEcAn.uncertainty', version, { + 'checksums': ['65e392536e17e1de2bf8f66c2cd8f46fcb26dcb3294acf0132551b6736722196'], + }), + ('amerifluxr', '1.0.0', { + 'checksums': ['ec54dce4b8e4108832eaadb60f7ef8ad28b459d3381316537492dcd755d83b25'], + }), + ('geonames', '0.999', { + 'checksums': ['1dd7bbd82d9425d14eb36f8e5bf431feaccfe3b0c4e70bf38f44f13dfc59e17b'], + }), + ('solartime', '0.0.2', { + 'checksums': ['5dd7a28db2bd4881ab740cd7004b88cd05c61e0954e3a10c8e18ebbe07d3e7d1'], + }), + ('bigleaf', '0.8.2', { + 'checksums': ['e41d82fb6298150c46f57128e959a1f1c6cfa55e916c32544bab7be69b0b6df7'], + }), + ('REddyProc', '1.3.3', { + 'checksums': ['3f673bd24f41813f631bf25139c9595bd91483e898ec31b7207c4eb8b7ff486b'], + }), + ('suntools', '1.0.0', { + 'checksums': ['42b7b39bd23ad48ded002150a0e7798fab94ed9828e5b5fdd8e5e1c9040697e2'], + }), + ('fauxpas', '0.5.2', { + 'checksums': ['84d07361a146b419cb1dcb7751654e3d5f159cf2704faf498e5ea56c8de61ef6'], + }), + ('nneo', '0.1.0', { + 'checksums': ['ca503e78cf4f4c85de6e18ad3ffde0c08d6a507ff5dc5ff91a50b3e04bf84a49'], + }), + ('PEcAn.data.atmosphere', version, { + 'checksums': ['28fb884cdeeff6405252352a261c3a884ad33202e556e88cee262aba96e1aea4'], + }), + ('redland', '1.0.17-18', { + 'checksums': ['e999ba22321733df7ed056f528e38fc4be535d36bbac8106395c14f9f60a75a0'], + }), + ('datapack', '1.4.1', { + 'checksums': ['6149733ae90e6bbbb53d5f85ca29cec5f811825e794b56029b7f325de6637493'], + }), + ('dplR', '1.7.7', { + 'checksums': ['0e35a4d2a22773499f9e4592d1a198a08c9842388ce1e5a35394990ed4cdb2bd'], + }), + ('neonUtilities', '2.4.2', { + 'checksums': ['37b4efd0ed3b724de999d08d4d430954a6c717b1d943bc84c513c4fe8dbca057'], + }), + ('storr', '1.2.5', { + 'checksums': ['4224c3991d9c043a45ce530d0698d7f2cdca231b26fe31b45e0db865026e5f63'], + }), + ('thor', '1.1.5', { + 'checksums': ['99802d8c8471ce351403f8428c1efab48ccf20f359fbd368db84f25ef8f7ecae'], + }), + ('duckdb', '1.0.0-2', { + 'patches': ['PEcAn-1.8.0.9000_duckdb.patch'], + 'checksums': [ + {'duckdb_1.0.0-2.tar.gz': '3735d51f22d62a7411aa514142cd569ce28bdaec4eb58d5f0893a476b9ccbf01'}, + {'PEcAn-1.8.0.9000_duckdb.patch': 'fb47b668b23e6c9274ce5365725af71e56f2d99771efdd343dc4283f68ab0c21'}, + ], + }), + ('duckdbfs', '0.0.4', { + 'checksums': ['90b2aff2bdefff1db4f855e2a9c9b19a404f522027105424aebd3c7e45944334'], + }), + ('neonstore', '0.5.1', { + 'checksums': ['f911e957861d558adead8ca77e4d1575a47dceb9553f1aa9d818460126deab9b'], + }), + ('HDInterval', '0.2.4', { + 'checksums': ['bb07f0edd660a02ed18e578c2798eb8c2db0e181a5e0c3e23db182d13e9494f6'], + }), + ('kknn', '1.3.1', { + 'checksums': ['22840e70ec2afa40371e274b583634c8f6d27149a87253ee411747d5db78f3db'], + }), + ('timeSeries', '4032.109', { + 'checksums': ['5e0c47584e0b01ea4011ed5ced217d95f8bb872611f6b029b0797d95eebd731f'], + }), + ('gss', '2.2-7', { + 'checksums': ['3b13144702c570c83462b4ea2ad17f4bd630cff5bf2ab0347a33c7e86a4f3f6a'], + }), + ('fBasics', '4032.96', { + 'checksums': ['e1556909871c836668b10bf90e1676aac6a2892a04663d7ab00c22a64c0b8690'], + }), + ('rmutil', '1.1.10', { + 'checksums': ['819fd7ce695cc742b4594705986eb06764460fc88521ea32de793c49de7ca5f9'], + }), + ('stable', '1.1.6', { + 'checksums': ['2238788a35b5aa9e175ad7b92348640c3dcad68b6ab0a0bc04aeec9084d29da4'], + }), + ('statip', '0.2.3', { + 'checksums': ['56a81a1882856cd1c5711ba133417b64f09071dda356e74280a0dba0db60d54f'], + }), + ('modeest', '2.4.0', { + 'checksums': ['1a949409bf64679d32400d20aa3d53e65a9a20f5bd1a40993b95f81100e0ed20'], + }), + ('runjags', '2.2.2-4', { + 'checksums': ['6f656e4d0620c0806e596ddb4bfec3934534ec17c02da699fcbfd6720a6f424f'], + }), + ('swfscMisc', '1.6.5', { + 'checksums': ['a49cb390643c4079f02986862eb2dfd33db4e6b6498e849bb418f73ffd6882e1'], + }), + ('CDM', '8.2-6', { + 'checksums': ['144a85e36c120e9f8a5bd35c1db50cf089ea4807721ac14460137b9a4b1c98d1'], + }), + ('TAM', '4.2-21', { + 'checksums': ['0d1782e42e89c1863edab12c1861d0e2628ea9ee1a1e37d268f27a3deaf3d568'], + }), + ('pbv', '0.5-47', { + 'checksums': ['e17a04efa96a601ab72172b59f555f36d28bb824f02f363cc5806b05d7d7c792'], + }), + ('sirt', '4.1-15', { + 'checksums': ['c12ffcb83bea5b549c7a34c12561f3e57798b83d68a887c5da0d9a66efac3066'], + }), + ('hoardr', '0.5.4', { + 'checksums': ['4e031ac1317584451c09bc8288ed73fb2d6ceea3c10d29dbb4be08157e489a37'], + }), + ('traits', '0.5.1', { + 'checksums': ['3080887a454d69814cd6cb9683a6750db02cf4c77b40b022ef50d40171ba6aca'], + }), + ('SimilarityMeasures', '1.4', { + 'checksums': ['b26bbc3a402d21f030cc8e4ff6baca644eb4c63a4fb33423dbc9436229a393f0'], + }), + ('PEcAn.benchmark', '1.7.3.9000', { + 'checksums': ['2e8b285869b4df148228cdde5de44a67dfe0b584b2a7cd614280134259e33ed4'], + }), + ('PEcAn.visualization', version, { + 'checksums': ['f77dcb756871a419a85e46cde4a1fb0a1993c29cce8578255d5a46db722ece43'], + }), + ('PEcAn.data.land', version, { + 'checksums': ['19c572e95c11362f4714d9c3d9cc7b2d17c2e3a34513c7ed629e7bdb99bdd0ec'], + }), + ('MODISTools', '1.1.5', { + 'checksums': ['0a6b3762865424e299e1a5ec28de78b8dcca3f673e61f42a37dae19ed78db3e3'], + }), + ('PEcAn.data.remote', version, { + 'checksums': ['c097d9395d9dbb6c123f404525cae7fdb1a99b142b32c1a40b0143060444e184'], + }), + ('SparseGrid', '0.8.2', { + 'checksums': ['1d84ae83db2a390b111589a10570d55b378c2dd3310d3bc588a94ab8845cfd14'], + }), + ('lqmm', '1.5.8', { + 'checksums': ['11eddeeeed6b9d3190a80a3b3cc3d64519c6e9cb208746a3736139340df691fb'], + }), + ('PEcAn.workflow', version, { + 'checksums': ['91a1849c040089da1088c02469b973a5f301a419237db7c840fe4ca2922f4b9d'], + }), + ('PEcAn.assim.batch', version, { + 'checksums': ['a1403a5a4591791e37e7e48ca9e9d49f66f4270757711b68b72fd38aadd411cb'], + }), + ('PEcAn.all', version, { + 'checksums': ['6fe594fb890b5680977d1bf58232b941c6d522456e7803e3dc9c4418b92db737'], + }), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['%(name)s.all'], +} + +modextrapaths = {'R_LIBS_SITE': ''} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/p/PEcAn/PEcAn-1.8.0.9000_duckdb.patch b/easybuild/easyconfigs/p/PEcAn/PEcAn-1.8.0.9000_duckdb.patch new file mode 100644 index 00000000000..940992bf5ba --- /dev/null +++ b/easybuild/easyconfigs/p/PEcAn/PEcAn-1.8.0.9000_duckdb.patch @@ -0,0 +1,16 @@ +Fixes the `prefix_back_ was not declared` error, see https://github.com/duckdb/duckdb/pull/12344 +Source: https://patch-diff.githubusercontent.com/raw/duckdb/duckdb/pull/12344.diff +diff -u src/duckdb/third_party/re2/re2/prog.cc.orig src/duckdb/third_party/re2/re2/prog.cc +--- src/duckdb/third_party/re2/re2/prog.cc.orig 2024-07-19 14:46:13.000000000 +0200 ++++ src/duckdb/third_party/re2/re2/prog.cc 2024-08-21 15:51:17.394266979 +0200 +@@ -1143,8 +1143,8 @@ + const __m256i* bp = reinterpret_cast( + reinterpret_cast(data) + prefix_size_-1); + const __m256i* endfp = fp + size/sizeof(__m256i); +- const __m256i f_set1 = _mm256_set1_epi8(prefix_front_); +- const __m256i b_set1 = _mm256_set1_epi8(prefix_back_); ++ const __m256i f_set1 = _mm256_set1_epi8(prefix_front_back.prefix_front_); ++ const __m256i b_set1 = _mm256_set1_epi8(prefix_front_back.prefix_back_); + do { + const __m256i f_loadu = _mm256_loadu_si256(fp++); + const __m256i b_loadu = _mm256_loadu_si256(bp++); diff --git a/easybuild/easyconfigs/p/PLINK/PLINK-1.90-beta-7.4-x86_64.eb b/easybuild/easyconfigs/p/PLINK/PLINK-1.90-beta-7.4-x86_64.eb new file mode 100644 index 00000000000..51357650dbb --- /dev/null +++ b/easybuild/easyconfigs/p/PLINK/PLINK-1.90-beta-7.4-x86_64.eb @@ -0,0 +1,22 @@ +easyblock = 'PackedBinary' + +name = 'PLINK' +version = '1.90-beta-7.4-x86_64' + +homepage = 'https://www.cog-genomics.org/plink/1.9/' +description = 'plink-1.9-x86_64: Whole-genome association analysis toolset' + +toolchain = SYSTEM + +source_urls = ['https://s3.amazonaws.com/plink1-assets/'] +sources = ['plink_linux_x86_64_20240818.zip'] +checksums = ['0ac294ffcd5d82f5b0d2d7f579ac85a87017f6fc46485b21793f5aff9c719e3d'] + +sanity_check_paths = { + 'files': ['plink', 'prettify', 'toy.map', 'toy.ped'], + 'dirs': [], +} + +sanity_check_commands = ["plink --help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/PLINK/PLINK-2.00a3.7-foss-2022a.eb b/easybuild/easyconfigs/p/PLINK/PLINK-2.00a3.7-foss-2022a.eb index 60ba9b0260b..6141b6cb6fe 100644 --- a/easybuild/easyconfigs/p/PLINK/PLINK-2.00a3.7-foss-2022a.eb +++ b/easybuild/easyconfigs/p/PLINK/PLINK-2.00a3.7-foss-2022a.eb @@ -48,7 +48,7 @@ components = [ ] # run tests (<1h) -postinstallcmds = ["cd Tests && sh run_tests.sh %(installdir)s/bin"] +postinstallcmds = ["cd Tests && bash run_tests.sh %(installdir)s/bin"] sanity_check_paths = { 'files': ['bin/plink', 'bin/plink2', 'bin/pgen_compress'], diff --git a/easybuild/easyconfigs/p/PLINK/PLINK-2.00a3.7-gfbf-2023a.eb b/easybuild/easyconfigs/p/PLINK/PLINK-2.00a3.7-gfbf-2023a.eb index c6d897b040b..7c69a0665b6 100644 --- a/easybuild/easyconfigs/p/PLINK/PLINK-2.00a3.7-gfbf-2023a.eb +++ b/easybuild/easyconfigs/p/PLINK/PLINK-2.00a3.7-gfbf-2023a.eb @@ -48,7 +48,7 @@ components = [ ] # run tests (<1h) -postinstallcmds = ["cd Tests && sh run_tests.sh %(installdir)s/bin"] +postinstallcmds = ["cd Tests && bash run_tests.sh %(installdir)s/bin"] sanity_check_paths = { 'files': ['bin/plink', 'bin/plink2', 'bin/pgen_compress'], diff --git a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.7.2-foss-2021a.eb b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.7.2-foss-2021a.eb index 3a0b31731ee..502cbfbd652 100644 --- a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.7.2-foss-2021a.eb +++ b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.7.2-foss-2021a.eb @@ -38,11 +38,6 @@ if ARCH == 'x86_64': configopts += '--enable-asmjit ' prebuildopts = 'source sourceme.sh && ' -# make sure that ld.gold linker is used -# required to work around problems like "ld: BFD (GNU Binutils) 2.30 assertion fail elf.c:3564" -# (problem with intel build but maintain consistency between easyconfigs) -buildopts = 'LD_RO="ld.gold -r -o"' - # install path for PLUMED libraries must be included in $LD_LIBRARY_PATH when Python bindings get built/installed preinstallopts = 'LD_LIBRARY_PATH="%(installdir)s/lib:$LD_LIBRARY_PATH" ' diff --git a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.7.2-intel-2021a.eb b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.7.2-intel-2021a.eb index ba0747ac705..d84282472f8 100644 --- a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.7.2-intel-2021a.eb +++ b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.7.2-intel-2021a.eb @@ -36,11 +36,6 @@ configopts += '--enable-boost_graph --enable-boost_serialization ' configopts += '--enable-asmjit ' prebuildopts = 'source sourceme.sh && ' -# make sure that ld.gold linker is used -# required to work around problems like "ld: BFD (GNU Binutils) 2.30 assertion fail elf.c:3564" -# (problem with intel build but maintain consistency between easyconfigs) -buildopts = 'LD_RO="ld.gold -r -o"' - # install path for PLUMED libraries must be included in $LD_LIBRARY_PATH when Python bindings get built/installed preinstallopts = 'LD_LIBRARY_PATH="%(installdir)s/lib:$LD_LIBRARY_PATH" ' diff --git a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.7.3-foss-2021b.eb b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.7.3-foss-2021b.eb index c653aa77c5b..d39ecac24b5 100644 --- a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.7.3-foss-2021b.eb +++ b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.7.3-foss-2021b.eb @@ -38,11 +38,6 @@ if ARCH == 'x86_64': configopts += '--enable-asmjit ' prebuildopts = 'source sourceme.sh && ' -# make sure that ld.gold linker is used -# required to work around problems like "ld: BFD (GNU Binutils) 2.30 assertion fail elf.c:3564" -# (problem with intel build but maintain consistency between easyconfigs) -buildopts = 'LD_RO="ld.gold -r -o"' - # install path for PLUMED libraries must be included in $LD_LIBRARY_PATH when Python bindings get built/installed preinstallopts = 'LD_LIBRARY_PATH="%(installdir)s/lib:$LD_LIBRARY_PATH" ' diff --git a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.8.0-foss-2021b.eb b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.8.0-foss-2021b.eb index 8dcdc9293d7..378a40f25d3 100644 --- a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.8.0-foss-2021b.eb +++ b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.8.0-foss-2021b.eb @@ -35,11 +35,6 @@ configopts = '--exec-prefix=%(installdir)s --enable-gsl --enable-modules=all --e configopts += '--enable-boost_graph --enable-boost_serialization ' prebuildopts = 'source sourceme.sh && ' -# make sure that ld.gold linker is used -# required to work around problems like "ld: BFD (GNU Binutils) 2.30 assertion fail elf.c:3564" -# (problem with intel build but maintain consistency between easyconfigs) -buildopts = 'LD_RO="ld.gold -r -o"' - # install path for PLUMED libraries must be included in $LD_LIBRARY_PATH when Python bindings get built/installed preinstallopts = 'LD_LIBRARY_PATH="%(installdir)s/lib:$LD_LIBRARY_PATH" ' diff --git a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.8.1-foss-2022a.eb b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.8.1-foss-2022a.eb index 846670014d4..b0fe4443cc6 100644 --- a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.8.1-foss-2022a.eb +++ b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.8.1-foss-2022a.eb @@ -35,11 +35,6 @@ configopts = '--exec-prefix=%(installdir)s --enable-gsl --enable-modules=all --e configopts += '--enable-boost_graph --enable-boost_serialization ' prebuildopts = 'source sourceme.sh && ' -# make sure that ld.gold linker is used -# required to work around problems like "ld: BFD (GNU Binutils) 2.30 assertion fail elf.c:3564" -# (problem with intel build but maintain consistency between easyconfigs) -buildopts = 'LD_RO="ld.gold -r -o"' - # install path for PLUMED libraries must be included in $LD_LIBRARY_PATH when Python bindings get built/installed preinstallopts = 'LD_LIBRARY_PATH="%(installdir)s/lib:$LD_LIBRARY_PATH" ' diff --git a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.9.0-foss-2022b.eb b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.9.0-foss-2022b.eb index a2971db49f7..92cdbe73b2a 100644 --- a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.9.0-foss-2022b.eb +++ b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.9.0-foss-2022b.eb @@ -35,11 +35,6 @@ configopts = '--exec-prefix=%(installdir)s --enable-gsl --enable-modules=all --e configopts += '--enable-boost_graph --enable-boost_serialization ' prebuildopts = 'source sourceme.sh && ' -# make sure that ld.gold linker is used -# required to work around problems like "ld: BFD (GNU Binutils) 2.30 assertion fail elf.c:3564" -# (problem with intel build but maintain consistency between easyconfigs) -buildopts = 'LD_RO="ld.gold -r -o"' - # install path for PLUMED libraries must be included in $LD_LIBRARY_PATH when Python bindings get built/installed preinstallopts = 'LD_LIBRARY_PATH="%(installdir)s/lib:$LD_LIBRARY_PATH" ' diff --git a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.9.0-foss-2023a.eb b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.9.0-foss-2023a.eb index 8ca97130960..b08db49309a 100644 --- a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.9.0-foss-2023a.eb +++ b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.9.0-foss-2023a.eb @@ -35,11 +35,6 @@ configopts = '--exec-prefix=%(installdir)s --enable-gsl --enable-modules=all --e configopts += '--enable-boost_graph --enable-boost_serialization ' prebuildopts = 'source sourceme.sh && ' -# make sure that ld.gold linker is used -# required to work around problems like "ld: BFD (GNU Binutils) 2.30 assertion fail elf.c:3564" -# (problem with intel build but maintain consistency between easyconfigs) -buildopts = 'LD_RO="ld.gold -r -o"' - # install path for PLUMED libraries must be included in $LD_LIBRARY_PATH when Python bindings get built/installed preinstallopts = 'LD_LIBRARY_PATH="%(installdir)s/lib:$LD_LIBRARY_PATH" ' diff --git a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.9.2-foss-2023b.eb b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.9.2-foss-2023b.eb new file mode 100644 index 00000000000..3ed5ad9b823 --- /dev/null +++ b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.9.2-foss-2023b.eb @@ -0,0 +1,54 @@ +easyblock = 'ConfigureMake' + +name = 'PLUMED' +version = '2.9.2' + +homepage = 'https://www.plumed.org' +description = """PLUMED is an open source library for free energy calculations in molecular systems which + works together with some of the most popular molecular dynamics engines. Free energy calculations can be + performed as a function of many order parameters with a particular focus on biological problems, using + state of the art methods such as metadynamics, umbrella sampling and Jarzynski-equation based steered MD. + The software, written in C++, can be easily interfaced with both fortran and C/C++ codes. +""" + +toolchain = {'name': 'foss', 'version': '2023b'} +toolchainopts = {'usempi': 'True'} + +source_urls = ['https://github.com/plumed/plumed2/releases/download/v%(version)s/'] +sources = [SOURCE_TGZ] +checksums = ['6fc23fe31074ad6b7a0eb9e2441fce5b3d92514d0d87206594c59c75e4c83d6e'] + +builddependencies = [ + ('xxd', '9.1.0307'), +] + +dependencies = [ + ('zlib', '1.2.13'), + ('GSL', '2.7'), + ('Python', '3.11.5'), + ('SciPy-bundle', '2023.11'), + ('Boost', '1.83.0'), +] + +preconfigopts = 'env FC=$MPIF90 LIBS="$LIBLAPACK $LIBS" ' +configopts = '--exec-prefix=%(installdir)s --enable-gsl --enable-modules=all --enable-python ' +configopts += '--enable-boost_graph --enable-boost_serialization ' +prebuildopts = 'source sourceme.sh && ' + +# install path for PLUMED libraries must be included in $LD_LIBRARY_PATH when Python bindings get built/installed +preinstallopts = 'LD_LIBRARY_PATH="%(installdir)s/lib:$LD_LIBRARY_PATH" ' + +sanity_check_paths = { + 'files': ['bin/plumed', 'lib/libplumedKernel.%s' % SHLIB_EXT, 'lib/libplumed.%s' % SHLIB_EXT], + 'dirs': [], +} + +sanity_check_commands = ["python -c 'import plumed'"] + +modextrapaths = { + 'PLUMED_KERNEL': 'lib/libplumedKernel.%s' % SHLIB_EXT, + 'PLUMED_ROOT': 'lib/plumed', + 'PYTHONPATH': 'lib/plumed/python', +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/p/PLY/PLY-3.11-GCCcore-13.2.0.eb b/easybuild/easyconfigs/p/PLY/PLY-3.11-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..74ab008fb99 --- /dev/null +++ b/easybuild/easyconfigs/p/PLY/PLY-3.11-GCCcore-13.2.0.eb @@ -0,0 +1,22 @@ +easyblock = 'PythonPackage' + +name = 'PLY' +version = '3.11' + +homepage = "https://www.dabeaz.com/ply/" +description = """PLY is yet another implementation of lex and yacc for Python.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['00c7c1aaa88358b9c765b6d3000c6eec0ba42abca5351b095321aef446081da3'] + +builddependencies = [('binutils', '2.40')] + +dependencies = [('Python', '3.11.5')] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/PLY/PLY-3.11-GCCcore-13.3.0.eb b/easybuild/easyconfigs/p/PLY/PLY-3.11-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..a5620c426d6 --- /dev/null +++ b/easybuild/easyconfigs/p/PLY/PLY-3.11-GCCcore-13.3.0.eb @@ -0,0 +1,22 @@ +easyblock = 'PythonPackage' + +name = 'PLY' +version = '3.11' + +homepage = "https://www.dabeaz.com/ply/" +description = """PLY is yet another implementation of lex and yacc for Python.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['00c7c1aaa88358b9c765b6d3000c6eec0ba42abca5351b095321aef446081da3'] + +builddependencies = [('binutils', '2.42')] + +dependencies = [('Python', '3.12.3')] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/PMIx/PMIx-5.0.2-GCCcore-13.3.0.eb b/easybuild/easyconfigs/p/PMIx/PMIx-5.0.2-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..1d6208ff9f0 --- /dev/null +++ b/easybuild/easyconfigs/p/PMIx/PMIx-5.0.2-GCCcore-13.3.0.eb @@ -0,0 +1,45 @@ +easyblock = 'ConfigureMake' + +name = 'PMIx' +version = '5.0.2' + +homepage = 'https://pmix.org/' +description = """Process Management for Exascale Environments +PMI Exascale (PMIx) represents an attempt to +provide an extended version of the PMI standard specifically designed +to support clusters up to and including exascale sizes. The overall +objective of the project is not to branch the existing pseudo-standard +definitions - in fact, PMIx fully supports both of the existing PMI-1 +and PMI-2 APIs - but rather to (a) augment and extend those APIs to +eliminate some current restrictions that impact scalability, and (b) +provide a reference implementation of the PMI-server that demonstrates +the desired level of scalability. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/openpmix/openpmix/releases/download/v%(version)s'] +sources = ['%(namelower)s-%(version)s.tar.bz2'] +checksums = ['28227ff2ba925da2c3fece44502f23a91446017de0f5a58f5cea9370c514b83c'] + +builddependencies = [('binutils', '2.42')] + +dependencies = [ + ('libevent', '2.1.12'), + ('zlib', '1.3.1'), + ('hwloc', '2.10.0'), +] + +configopts = ' --with-libevent=$EBROOTLIBEVENT --with-zlib=$EBROOTZLIB' +configopts += ' --with-hwloc=$EBROOTHWLOC' +configopts += ' --enable-pmix-binaries' + +buildopts = 'V=1' + +sanity_check_paths = { + 'files': ['bin/pevent', 'bin/plookup', 'bin/pmix_info', 'bin/pps'], + 'dirs': ['etc', 'include', 'lib', 'share'] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/POT/POT-0.9.3-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/p/POT/POT-0.9.3-foss-2023a-CUDA-12.1.1.eb new file mode 100644 index 00000000000..1eddcba72f5 --- /dev/null +++ b/easybuild/easyconfigs/p/POT/POT-0.9.3-foss-2023a-CUDA-12.1.1.eb @@ -0,0 +1,47 @@ +easyblock = 'PythonBundle' + +name = 'POT' +version = '0.9.3' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/rflamary/POT' +description = """POT (Python Optimal Transport) is a Python library provide several solvers for optimization problems + related to Optimal Transport for signal, image processing and machine learning.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('matplotlib', '3.7.2'), + ('scikit-learn', '1.3.1'), + ('CUDA', '12.1.1', '', SYSTEM), + ('PyTorch', '2.1.2', versionsuffix), + ('jax', '0.4.25', versionsuffix), + ('CVXOPT', '1.3.2'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('autograd', '1.7.0', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['49680300f842f3a8722b060ac0d3ed7aca071d1ad4d3d38c9fdadafdcc73c30b'], + }), + ('versioneer', '0.29', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['0f1a137bb5d6811e96a79bb0486798aeae9b9c6efc24b389659cebb0ee396cb9'], + }), + ('pymanopt', '2.2.1', { + # Requirements forbid some versions of `scipy` which are known to have a bug but we have fixed it. + # see `scipy-1.11.1_vectorization_error.patch` + 'preinstallopts': """sed -i 's/"scipy>=1.0[^"]*"/"scipy>=1.0"/g' pyproject.toml && """, + 'checksums': ['c784929a436eb06d73371b53ae5db3cdc19c5e60280f8131553bc805cbf7a1da'], + }), + (name, version, { + 'modulename': 'ot', + 'checksums': ['eecf2394390a73472e727ef75f7c801fc47509039f00c40f8fc64fdeea617c86'], + }), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/PROJ/PROJ-9.4.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/p/PROJ/PROJ-9.4.1-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..1307155f8f7 --- /dev/null +++ b/easybuild/easyconfigs/p/PROJ/PROJ-9.4.1-GCCcore-13.3.0.eb @@ -0,0 +1,49 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2014-2015 The Cyprus Institute +# Authors:: Thekla Loizou +# License:: MIT/GPL +# +## +easyblock = 'CMakeMake' + +name = 'PROJ' +version = '9.4.1' + +homepage = 'https://proj.org' +description = """Program proj is a standard Unix filter function which converts +geographic longitude and latitude coordinates into cartesian coordinates""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://download.osgeo.org/proj/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['ffe20170ee2b952207adf8a195e2141eab12cda181e49fdeb54425d98c7171d7'] + +builddependencies = [ + ('pkgconf', '2.2.0'), + ('binutils', '2.42'), + ('CMake', '3.29.3'), + ('googletest', '1.15.2'), +] + +dependencies = [ + ('SQLite', '3.45.3'), + ('LibTIFF', '4.6.0'), + ('cURL', '8.7.1'), + ('XZ', '5.4.5'), + ('nlohmann_json', '3.11.3'), +] + +# build twice, once for static, once for shared libraries +configopts = ['', '-DBUILD_SHARED_LIBS=OFF'] + +sanity_check_paths = { + 'files': ['bin/cct', 'bin/cs2cs', 'bin/geod', 'bin/gie', 'bin/proj', 'bin/projinfo', + 'lib/libproj.a', 'lib/libproj.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/PRRTE/PRRTE-3.0.5-GCCcore-13.3.0.eb b/easybuild/easyconfigs/p/PRRTE/PRRTE-3.0.5-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..2a8688776d8 --- /dev/null +++ b/easybuild/easyconfigs/p/PRRTE/PRRTE-3.0.5-GCCcore-13.3.0.eb @@ -0,0 +1,38 @@ +easyblock = 'ConfigureMake' + +name = 'PRRTE' +version = '3.0.5' + +homepage = 'https://docs.prrte.org/' +description = """PRRTE is the PMIx Reference RunTime Environment""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/openpmix/prrte/releases/download/v%(version)s'] +sources = ['%(namelower)s-%(version)s.tar.bz2'] +checksums = ['75ce732b02f3bc7eff5e51b81469e4373f1effc6a42d8445e2935d3670e58c8e'] + +builddependencies = [('binutils', '2.42')] + +dependencies = [ + ('libevent', '2.1.12'), + ('hwloc', '2.10.0'), + ('PMIx', '5.0.2'), +] + +configopts = ' --with-libevent=$EBROOTLIBEVENT' +configopts += ' --with-hwloc=$EBROOTHWLOC --with-pmix=$EBROOTPMIX' + +buildopts = 'V=1' + +local_binaries = ['prte', 'prte_info', 'prterun', 'prun', 'pterm'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_binaries] + ['lib/libprrte.%s' % SHLIB_EXT], + 'dirs': ['etc', 'include', 'share'] +} + +sanity_check_commands = ['%s --version' % x for x in local_binaries] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/PRSice/PRSice-2.3.5-GCCcore-13.3.0.eb b/easybuild/easyconfigs/p/PRSice/PRSice-2.3.5-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..85f8b20972c --- /dev/null +++ b/easybuild/easyconfigs/p/PRSice/PRSice-2.3.5-GCCcore-13.3.0.eb @@ -0,0 +1,44 @@ +# Contribution from the NIHR Biomedical Research Centre +# Guy's and St Thomas' NHS Foundation Trust and King's College London +# uploaded by J. Sassmannshausen + +easyblock = 'CMakeMakeCp' + +name = 'PRSice' +version = '2.3.5' + +homepage = 'https://choishingwan.github.io/PRSice/' +description = """PRSice (pronounced 'precise') is a Polygenic Risk +Score software for calculating, applying, evaluating and +plotting the results of polygenic risk scores (PRS) analyses.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://github.com/choishingwan/%(name)s/archive/'] +sources = ['%(version)s.tar.gz'] +patches = ['PRSice-2.3.5_remove_sysctl.patch'] +checksums = [ + '0a7e649ddebe4e969cd8400c5ad977a7b900be4f5c920a84483cb8930367354d', # 2.3.5.tar.gz + 'ab8286e8a0700ea163f552de66458e409c396e06b57c9adfff3b7f63083f7798', # PRSice-2.3.5_remove_sysctl.patch +] + +builddependencies = [ + ('CMake', '3.29.3'), + ('binutils', '2.42'), + ('Eigen', '3.4.0'), +] + +files_to_copy = [ + (['bin/%(name)s'], 'bin'), + 'README.md', + 'LICENSE', +] + +sanity_check_paths = { + 'files': ['bin/%(name)s'], + 'dirs': [], +} + +sanity_check_commands = ['%(name)s --help'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/PRSice/PRSice-2.3.5_remove_sysctl.patch b/easybuild/easyconfigs/p/PRSice/PRSice-2.3.5_remove_sysctl.patch new file mode 100644 index 00000000000..04a71e26a8b --- /dev/null +++ b/easybuild/easyconfigs/p/PRSice/PRSice-2.3.5_remove_sysctl.patch @@ -0,0 +1,194 @@ +# What: sysctl.h is removed in glibc v2.32. This patch is based on the following commits +# from https://github.com/choishingwan/PRSice: +# f285b243856b857a461d9a2b27e1f2f0ac25216e +# 53641c11750a7e0bdd06a925fbf28c1e3978ee72 +# Also see issue https://github.com/choishingwan/PRSice/issues/338 and PR https://github.com/choishingwan/PRSice/pull/243 +# Author: maxim-masterov (SURF) + +diff -Nru PRSice-2.3.5.orig/inc/misc.hpp PRSice-2.3.5/inc/misc.hpp +--- PRSice-2.3.5.orig/inc/misc.hpp 2024-10-23 18:13:58.539539000 +0200 ++++ PRSice-2.3.5/inc/misc.hpp 2024-10-23 18:14:29.383991502 +0200 +@@ -38,7 +38,6 @@ + #include + #include + #include +-#include + #elif defined _WIN32 + #include + // psapi must go after windows, or will generate error +@@ -48,7 +47,6 @@ + #include "stdlib.h" + #include "string.h" + #include +-#include + #include + #include + #endif +@@ -86,9 +84,6 @@ + #include + #include + #include +-#if defined(BSD) +-#include +-#endif + + #else + #error "Unable to define getMemorySize( ) for an unknown OS." +@@ -170,73 +165,7 @@ + // TODO: Delete this, doesn't seems to give robust answer + inline size_t current_ram_usage() { return 0; } + // TODO: Delete this, doesn't seems to give robust answer +-inline size_t total_ram_available() +-{ +-#ifdef __APPLE__ +- int32_t mib[2]; +- size_t sztmp; +-#endif +- unsigned char* bigstack_ua = nullptr; // ua = unaligned +- int64_t llxx; +- intptr_t default_alloc_mb; +- intptr_t malloc_size_mb = 0; +-#ifdef __APPLE__ +- mib[0] = CTL_HW; +- mib[1] = HW_MEMSIZE; +- llxx = 0; +- +- sztmp = sizeof(int64_t); +- sysctl(mib, 2, &llxx, &sztmp, nullptr, 0); +- llxx /= 1048576; +-#else +-#ifdef _WIN32 +- MEMORYSTATUSEX memstatus; +- memstatus.dwLength = sizeof(memstatus); +- GlobalMemoryStatusEx(&memstatus); +- llxx = memstatus.ullTotalPhys / 1048576; +-#else +- llxx = ((uint64_t) sysconf(_SC_PHYS_PAGES)) +- * ((size_t) sysconf(_SC_PAGESIZE)) / 1048576; +-#endif +-#endif +- if (!llxx) { default_alloc_mb = BIGSTACK_DEFAULT_MB; } +- else if (llxx < (BIGSTACK_MIN_MB * 2)) +- { +- default_alloc_mb = BIGSTACK_MIN_MB; +- } +- else +- { +- default_alloc_mb = llxx / 2; +- } +- if (!malloc_size_mb) { malloc_size_mb = default_alloc_mb; } +- else if (malloc_size_mb < BIGSTACK_MIN_MB) +- { +- malloc_size_mb = BIGSTACK_MIN_MB; +- } +- std::string message = ""; +-#ifndef __LP64__ +- if (malloc_size_mb > 2047) { malloc_size_mb = 2047; } +-#endif +- bigstack_ua = +- (unsigned char*) malloc(malloc_size_mb * 1048576 * sizeof(char)); +- // if fail, return nullptr which will then get into the while loop +- while (!bigstack_ua) +- { +- malloc_size_mb = (malloc_size_mb * 3) / 4; +- if (malloc_size_mb < BIGSTACK_MIN_MB) +- { malloc_size_mb = BIGSTACK_MIN_MB; } +- bigstack_ua = +- (unsigned char*) malloc(malloc_size_mb * 1048576 * sizeof(char)); +- if (bigstack_ua) {} +- else if (malloc_size_mb == BIGSTACK_MIN_MB) +- { +- throw std::runtime_error("Failed to allocate required memory"); +- } +- } +- free(bigstack_ua); +- bigstack_ua = nullptr; +- return malloc_size_mb * 1024 * 1024; +-} ++ + // function from John D.Cook + // https://www.johndcook.com/blog/standard_deviation/ + class RunningStat +@@ -1398,82 +1327,5 @@ + return (size_t) 0L; /* Unsupported. */ + #endif + } +- +- +-/** +- * Returns the size of physical memory (RAM) in bytes. +- */ +-inline size_t getMemorySize() +-{ +-#if defined(_WIN32) && (defined(__CYGWIN__) || defined(__CYGWIN32__)) +- /* Cygwin under Windows. ------------------------------------ */ +- /* New 64-bit MEMORYSTATUSEX isn't available. Use old 32.bit */ +- MEMORYSTATUS status; +- status.dwLength = sizeof(status); +- GlobalMemoryStatus(&status); +- return (size_t) status.dwTotalPhys; +- +-#elif defined(_WIN32) +- /* Windows. ------------------------------------------------- */ +- /* Use new 64-bit MEMORYSTATUSEX, not old 32-bit MEMORYSTATUS */ +- MEMORYSTATUSEX status; +- status.dwLength = sizeof(status); +- GlobalMemoryStatusEx(&status); +- return (size_t) status.ullTotalPhys; +- +-#elif defined(__unix__) || defined(__unix) || defined(unix) \ +- || (defined(__APPLE__) && defined(__MACH__)) +- /* UNIX variants. ------------------------------------------- */ +- /* Prefer sysctl() over sysconf() except sysctl() HW_REALMEM and HW_PHYSMEM +- */ +- +-#if defined(CTL_HW) && (defined(HW_MEMSIZE) || defined(HW_PHYSMEM64)) +- int mib[2]; +- mib[0] = CTL_HW; +-#if defined(HW_MEMSIZE) +- mib[1] = HW_MEMSIZE; /* OSX. --------------------- */ +-#elif defined(HW_PHYSMEM64) +- mib[1] = HW_PHYSMEM64; /* NetBSD, OpenBSD. --------- */ +-#endif +- int64_t size = 0; /* 64-bit */ +- size_t len = sizeof(size); +- if (sysctl(mib, 2, &size, &len, NULL, 0) == 0) return (size_t) size; +- return 0L; /* Failed? */ +- +-#elif defined(_SC_AIX_REALMEM) +- /* AIX. ----------------------------------------------------- */ +- return (size_t) sysconf(_SC_AIX_REALMEM) * (size_t) 1024L; +- +-#elif defined(_SC_PHYS_PAGES) && defined(_SC_PAGESIZE) +- /* FreeBSD, Linux, OpenBSD, and Solaris. -------------------- */ +- return (size_t) sysconf(_SC_PHYS_PAGES) * (size_t) sysconf(_SC_PAGESIZE); +- +-#elif defined(_SC_PHYS_PAGES) && defined(_SC_PAGE_SIZE) +- /* Legacy. -------------------------------------------------- */ +- return (size_t) sysconf(_SC_PHYS_PAGES) * (size_t) sysconf(_SC_PAGE_SIZE); +- +-#elif defined(CTL_HW) && (defined(HW_PHYSMEM) || defined(HW_REALMEM)) +- /* DragonFly BSD, FreeBSD, NetBSD, OpenBSD, and OSX. -------- */ +- int mib[2]; +- mib[0] = CTL_HW; +-#if defined(HW_REALMEM) +- mib[1] = HW_REALMEM; /* FreeBSD. ----------------- */ +-#elif defined(HW_PYSMEM) +- mib[1] = HW_PHYSMEM; /* Others. ------------------ */ +-#endif +- unsigned int size = 0; /* 32-bit */ +- size_t len = sizeof(size); +- if (sysctl(mib, 2, &size, &len, NULL, 0) == 0) return (size_t) size; +- return 0L; /* Failed? */ +-#endif /* sysctl and sysconf variants */ +- +-#else +- return 0L; /* Unknown OS. */ +-#endif + } + +-inline unsigned long long remain_memory(const double& adjFactor = 0.8) +-{ +- return (misc::getMemorySize() * adjFactor - getCurrentRSS()); +-} +-} diff --git a/easybuild/easyconfigs/p/PSI4/PSI4-1.9.1-foss-2023a.eb b/easybuild/easyconfigs/p/PSI4/PSI4-1.9.1-foss-2023a.eb new file mode 100644 index 00000000000..771a55a0f20 --- /dev/null +++ b/easybuild/easyconfigs/p/PSI4/PSI4-1.9.1-foss-2023a.eb @@ -0,0 +1,87 @@ +easyblock = 'EB_PSI' + +name = 'PSI4' +version = '1.9.1' + +homepage = 'https://www.psicode.org/' +description = """PSI4 is an open-source suite of ab initio quantum chemistry programs designed for +efficient, high-accuracy simulations of a variety of molecular properties. We can routinely perform +computations with more than 2500 basis functions running serially or in parallel. +""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://github.com/psi4/psi4/archive'] +sources = ['v%(version)s.tar.gz'] +patches = [ + 'PSI4-%(version)s_fix_cmake_release.patch', + 'PSI4-1.7_fix_snsmp2_version.patch', +] +checksums = [ + {'v1.9.1.tar.gz': 'ccd69bdc1d8319470513b4d3c1e0d737fc7788a50d7e48f8db762a0fcf795dad'}, + {'PSI4-1.9.1_fix_cmake_release.patch': '8f2bb210508cbb78a258c8d85d10d456c61e0f828865f3efb8d3bac9184df24e'}, + {'PSI4-1.7_fix_snsmp2_version.patch': '064dcf60e74e0c449f77bb6e4dcf4b3338edad7d9a046089ecc2979aed1a00f9'}, +] + +dependencies = [ + ('Python', '3.11.3'), + ('libxc', '6.2.2'), + ('CheMPS2', '1.8.12'), + ('networkx', '3.1'), + ('pytest', '7.4.2'), + ('Boost', '1.82.0'), + ('PyYAML', '6.0'), + ('SciPy-bundle', '2023.07'), + ('Pint', '0.23'), + ('pydantic', '2.5.3'), + ('py-cpuinfo', '9.0.0'), +] + +builddependencies = [ + ('CMake', '3.26.3'), + ('Eigen', '3.4.0'), + ('poetry', '1.7.1'), # for qcelemental +] + +configopts = '-DENABLE_MPI=ON -DENABLE_PLUGINS=ON -DENABLE_XHOST=OFF ' +# Install python module to the standard location instead of lib +configopts += '-DPYMOD_INSTALL_LIBDIR=/python%(pyshortver)s/site-packages ' +# Add bundled (downloaded) packages +# -DENABLE_simint=ON does not work with intel/2018, so have to make with GCCcore +configopts += '-DENABLE_dkh=ON -DENABLE_gdma=ON -DENABLE_resp=ON -DENABLE_snsmp2=ON ' +# allow PSI4 to download and build a forked version of PCMSolver otherwise tests fail +configopts += '-DENABLE_PCMSolver=ON ' + +# runtest uses ctest, and some of the tests have to be manually compared +# to the reference output (those tests are marked failed) +# After installing PSI4, you can test the package using psi4 --test command. (This uses pytest framework) +# runtest = '-L smoke' +runtest = False + +exts_defaultclass = 'PythonPackage' +exts_filter = ("python -s -c 'import %(ext_name)s'", '') +exts_default_options = { + 'source_urls': [PYPI_SOURCE], + 'download_dep_fail': True, + 'use_pip': True, +} + +exts_list = [ + ('qcelemental', '0.28.0', { + 'checksums': ['da96fddb88c1701f812b25369a6a169d35f2d5446c37c62e86048cb0f1b168a2'], + }), + ('qcengine', '0.30.0', { + 'checksums': ['ba62d34dbcf487e8368f6c19762a19e1c5f06af7e705f6c583c0632b35bccf7d'], + }), + ('snsmp2', '1.0.0', { + 'source_tmpl': '%(name)s-%(version)s-py2.py3-none-any.whl', + 'checksums': ['acfc95f8eb40e18d9d0c737b42fc8dfa786c381a5510a3094772b82538d211ed'], + }), +] + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +sanity_check_commands = ["python -s -c 'import psi4'"] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/p/PSI4/PSI4-1.9.1_fix_cmake_release.patch b/easybuild/easyconfigs/p/PSI4/PSI4-1.9.1_fix_cmake_release.patch new file mode 100644 index 00000000000..7eea87a86e1 --- /dev/null +++ b/easybuild/easyconfigs/p/PSI4/PSI4-1.9.1_fix_cmake_release.patch @@ -0,0 +1,95 @@ +remove CMAKE_BUILD_TYPE check (because it is set to EasyBuildRelease to avoid -O3 optimization flag) +original patch by B. Hajgato - (Free University Brussels - VUB) +ported to PSI4 1.3.1 by Kenneth Hoste (HPC-UGent) +ported to PSI4 1.7 by Neil Douglas (neil.douglas@york.ac.uk) +ported to PSI4 1.9.1 by Samuel Moors (Vrije Universiteit Brussel) +diff -ur psi4-1.9.1.orig/cmake/autocmake_safeguards.cmake psi4-1.9.1/cmake/autocmake_safeguards.cmake +--- psi4-1.9.1.orig/cmake/autocmake_safeguards.cmake 2024-02-08 22:08:35.000000000 +0100 ++++ psi4-1.9.1/cmake/autocmake_safeguards.cmake 2024-09-19 18:06:50.961414596 +0200 +@@ -19,9 +19,3 @@ + string(TOLOWER "${CMAKE_BUILD_TYPE}" cmake_build_type_tolower) + string(TOUPPER "${CMAKE_BUILD_TYPE}" cmake_build_type_toupper) + +-if(NOT cmake_build_type_tolower STREQUAL "debug" AND +- NOT cmake_build_type_tolower STREQUAL "release" AND +- NOT cmake_build_type_tolower STREQUAL "minsizerel" AND +- NOT cmake_build_type_tolower STREQUAL "relwithdebinfo") +- message(FATAL_ERROR "Unknown build type \"${CMAKE_BUILD_TYPE}\". Allowed values are Debug, Release, RelWithDebInfo, MinSizeRel (case-insensitive).") +-endif() +diff -ur psi4-1.9.1.orig/external/upstream/dkh/CMakeLists.txt psi4-1.9.1/external/upstream/dkh/CMakeLists.txt +--- psi4-1.9.1.orig/external/upstream/dkh/CMakeLists.txt 2024-02-08 22:08:35.000000000 +0100 ++++ psi4-1.9.1/external/upstream/dkh/CMakeLists.txt 2024-09-19 18:09:27.904110642 +0200 +@@ -24,6 +24,7 @@ + DEPENDS lapack_external + URL https://github.com/psi4/dkh/archive/3ba0128.tar.gz # v1.2 + cmake + UPDATE_COMMAND "" ++ PATCH_COMMAND sed -e "s/debug/easybuildrelease/" -i cmake/autocmake_safeguards.cmake + CMAKE_ARGS -DCMAKE_INSTALL_PREFIX=${STAGED_INSTALL_PREFIX} + -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE} + -DCMAKE_C_COMPILER=${CMAKE_C_COMPILER} +diff -ur psi4-1.9.1.orig/external/upstream/gau2grid/CMakeLists.txt psi4-1.9.1/external/upstream/gau2grid/CMakeLists.txt +--- psi4-1.9.1.orig/external/upstream/gau2grid/CMakeLists.txt 2024-02-08 22:08:35.000000000 +0100 ++++ psi4-1.9.1/external/upstream/gau2grid/CMakeLists.txt 2024-09-19 19:00:53.785308308 +0200 +@@ -20,6 +20,7 @@ + DEPENDS pybind11_external + URL https://github.com/dgasmith/gau2grid/archive/v2.0.7.tar.gz + UPDATE_COMMAND "" ++ PATCH_COMMAND sed -e "s/debug/easybuildrelease/" -i cmake/autocmake_safeguards.cmake + CMAKE_ARGS -DCMAKE_INSTALL_PREFIX=${STAGED_INSTALL_PREFIX} + -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE} + -DCMAKE_C_COMPILER=${CMAKE_C_COMPILER} +diff -ur psi4-1.9.1.orig/external/upstream/gdma/CMakeLists.txt psi4-1.9.1/external/upstream/gdma/CMakeLists.txt +--- psi4-1.9.1.orig/external/upstream/gdma/CMakeLists.txt 2024-02-08 22:08:35.000000000 +0100 ++++ psi4-1.9.1/external/upstream/gdma/CMakeLists.txt 2024-09-19 18:09:47.177430325 +0200 +@@ -24,6 +24,7 @@ + DEPENDS pybind11_external + URL https://github.com/psi4/gdma/archive/v2.3.3.tar.gz # Stone's upstream c2e0b548 plus commits from Andy Simmonett for lib, Holger Kruse for I/O, Lori Burns for CMake & Python + UPDATE_COMMAND "" ++ PATCH_COMMAND sed -e "s/debug/easybuildrelease/" -i cmake/autocmake_safeguards.cmake + CMAKE_ARGS -DCMAKE_INSTALL_PREFIX=${STAGED_INSTALL_PREFIX} + -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE} + -DCMAKE_C_COMPILER=${CMAKE_C_COMPILER} +diff -ur psi4-1.9.1.orig/external/upstream/libefp/CMakeLists.txt psi4-1.9.1/external/upstream/libefp/CMakeLists.txt +--- psi4-1.9.1.orig/external/upstream/libefp/CMakeLists.txt 2024-02-08 22:08:35.000000000 +0100 ++++ psi4-1.9.1/external/upstream/libefp/CMakeLists.txt 2024-09-19 18:10:04.346993747 +0200 +@@ -21,6 +21,7 @@ + DEPENDS lapack_external + URL https://github.com/ilyak/libefp/archive/15cd7ce.tar.gz # v1.5.0 + 10 (docs and a cmake lapack patch) + UPDATE_COMMAND "" ++ PATCH_COMMAND sed -e "s/debug/easybuildrelease/" -i cmake/autocmake_safeguards.cmake + CMAKE_ARGS -DCMAKE_INSTALL_PREFIX=${STAGED_INSTALL_PREFIX} + -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE} + -DCMAKE_C_COMPILER=${CMAKE_C_COMPILER} +diff -ur psi4-1.9.1.orig/external/upstream/libint/CMakeLists.txt psi4-1.9.1/external/upstream/libint/CMakeLists.txt +--- psi4-1.9.1.orig/external/upstream/libint/CMakeLists.txt 2024-02-08 22:08:35.000000000 +0100 ++++ psi4-1.9.1/external/upstream/libint/CMakeLists.txt 2024-09-19 18:10:45.532297897 +0200 +@@ -15,6 +15,7 @@ + ExternalProject_Add(libint_external + # "git checkout" fails on Windows, because of "*" in filenames (e.g. basis set files) + URL https://github.com/loriab/libint/archive/libint_t.tar.gz ++ PATCH_COMMAND sed -e "s/debug/easybuildrelease/" -i cmake/autocmake_safeguards.cmake + CMAKE_ARGS -DCMAKE_INSTALL_PREFIX=${STAGED_INSTALL_PREFIX} + -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE} + -DCMAKE_C_COMPILER=${CMAKE_C_COMPILER} +diff -ur psi4-1.9.1.orig/external/upstream/libxc/CMakeLists.txt psi4-1.9.1/external/upstream/libxc/CMakeLists.txt +--- psi4-1.9.1.orig/external/upstream/libxc/CMakeLists.txt 2024-02-08 22:08:35.000000000 +0100 ++++ psi4-1.9.1/external/upstream/libxc/CMakeLists.txt 2024-09-19 18:11:17.460151143 +0200 +@@ -24,6 +24,7 @@ + #GIT_REPOSITORY https://gitlab.com/libxc/libxc.git + #GIT_TAG 5.1.5 + #UPDATE_COMMAND "" ++ PATCH_COMMAND sed -e "s/debug/easybuildrelease/" -i cmake/autocmake_safeguards.cmake + CMAKE_ARGS -DCMAKE_INSTALL_PREFIX=${STAGED_INSTALL_PREFIX} + -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE} + -DCMAKE_C_COMPILER=${CMAKE_C_COMPILER} +diff -ur psi4-1.9.1.orig/external/upstream/pcmsolver/CMakeLists.txt psi4-1.9.1/external/upstream/pcmsolver/CMakeLists.txt +--- psi4-1.9.1.orig/external/upstream/pcmsolver/CMakeLists.txt 2024-02-08 22:08:35.000000000 +0100 ++++ psi4-1.9.1/external/upstream/pcmsolver/CMakeLists.txt 2024-09-19 20:53:02.637798342 +0200 +@@ -33,6 +33,7 @@ + #URL https://github.com/loriab/pcmsolver/archive/v1211.tar.gz + URL https://github.com/loriab/pcmsolver/archive/v123_plus_ming.tar.gz + UPDATE_COMMAND "" ++ PATCH_COMMAND sed -e "s/debug/easybuildrelease/" -i cmake/downloaded/autocmake_safeguards.cmake + CMAKE_ARGS -DCMAKE_INSTALL_PREFIX=${STAGED_INSTALL_PREFIX} + -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE} + -DCMAKE_C_COMPILER=${CMAKE_C_COMPILER} diff --git a/easybuild/easyconfigs/p/PSIPRED/PSIPRED-4.02-GCC-12.3.0.eb b/easybuild/easyconfigs/p/PSIPRED/PSIPRED-4.02-GCC-12.3.0.eb new file mode 100644 index 00000000000..9f9d2f1539f --- /dev/null +++ b/easybuild/easyconfigs/p/PSIPRED/PSIPRED-4.02-GCC-12.3.0.eb @@ -0,0 +1,30 @@ +easyblock = 'MakeCp' + +name = 'PSIPRED' +version = '4.02' + +homepage = 'http://bioinf.cs.ucl.ac.uk' +description = 'Accurate protein secondary structure prediction' + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +source_urls = ['http://bioinfadmin.cs.ucl.ac.uk/downloads/psipred/'] +sources = ['%(namelower)s.%(version)s.tar.gz'] +patches = ['PSIPRED-4.02_fix_segfault.patch'] +checksums = [ + {'psipred.4.02.tar.gz': 'b4009b6a5f8b76c6d60ac91c4a743512d844864cf015c492fb6d1dc0d092c467'}, + {'PSIPRED-4.02_fix_segfault.patch': 'd9e52ecf43b04640ebd0693df37871659d598abaec7a2c66264e9a79ee1baa82'}, +] + +parallel = 1 +start_dir = 'src' +build_cmd_targets = 'all install' # install copies binaries to ../bin + +files_to_copy = ['bin', 'data', 'LICENSE'] + +sanity_check_paths = { + 'files': ['bin/chkparse', 'bin/psipass2', 'bin/psipred', 'bin/seq2mtx'], + 'dirs': ['bin', 'data'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/PSM2/PSM2-12.0.1-GCCcore-10.3.0.eb b/easybuild/easyconfigs/p/PSM2/PSM2-12.0.1-GCCcore-10.3.0.eb index a7f0ee5d469..1f6981d1dae 100644 --- a/easybuild/easyconfigs/p/PSM2/PSM2-12.0.1-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/p/PSM2/PSM2-12.0.1-GCCcore-10.3.0.eb @@ -15,15 +15,17 @@ source_urls = ['https://github.com/cornelisnetworks/opa-psm2/archive/refs/tags'] sources = ['%(name)s_%(version)s.tar.gz'] patches = [ ('PSM2-11.2.80_hfi-user.patch', 1), + ('PSM2-12.0.1_build-with-internal-cuda-header.patch', 1), ] checksums = [ {'PSM2_12.0.1.tar.gz': 'e41af2d7d36a6ab67639ecbd5c1012aa20b2b464bf5cfbdac60e7eb37bfe58de'}, {'PSM2-11.2.80_hfi-user.patch': 'e43138859387213506050af9b76e193c3cd0a162d148998c39e551f220392abb'}, + {'PSM2-12.0.1_build-with-internal-cuda-header.patch': + '0016327d7eade9e763ffbc468cf25c182d743074dca2885dea7ef0cf7e3b23cf'}, ] builddependencies = [ ('binutils', '2.36.1'), - ('CUDA', '11.3.1', '', SYSTEM), ] dependencies = [ diff --git a/easybuild/easyconfigs/p/PSM2/PSM2-12.0.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/PSM2/PSM2-12.0.1-GCCcore-11.2.0.eb index 779d6bcdd0a..325c404a055 100644 --- a/easybuild/easyconfigs/p/PSM2/PSM2-12.0.1-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/p/PSM2/PSM2-12.0.1-GCCcore-11.2.0.eb @@ -15,15 +15,17 @@ source_urls = ['https://github.com/cornelisnetworks/opa-psm2/archive/refs/tags'] sources = ['%(name)s_%(version)s.tar.gz'] patches = [ ('PSM2-11.2.80_hfi-user.patch', 1), + ('PSM2-12.0.1_build-with-internal-cuda-header.patch', 1), ] checksums = [ {'PSM2_12.0.1.tar.gz': 'e41af2d7d36a6ab67639ecbd5c1012aa20b2b464bf5cfbdac60e7eb37bfe58de'}, {'PSM2-11.2.80_hfi-user.patch': 'e43138859387213506050af9b76e193c3cd0a162d148998c39e551f220392abb'}, + {'PSM2-12.0.1_build-with-internal-cuda-header.patch': + '0016327d7eade9e763ffbc468cf25c182d743074dca2885dea7ef0cf7e3b23cf'}, ] builddependencies = [ ('binutils', '2.37'), - ('CUDA', '11.5.2', '', SYSTEM), ] dependencies = [ diff --git a/easybuild/easyconfigs/p/PSM2/PSM2-12.0.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/PSM2/PSM2-12.0.1-GCCcore-11.3.0.eb index 7fa4c192e3b..b93b34dc43e 100644 --- a/easybuild/easyconfigs/p/PSM2/PSM2-12.0.1-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/p/PSM2/PSM2-12.0.1-GCCcore-11.3.0.eb @@ -15,15 +15,17 @@ source_urls = ['https://github.com/cornelisnetworks/opa-psm2/archive/refs/tags'] sources = ['%(name)s_%(version)s.tar.gz'] patches = [ ('PSM2-11.2.80_hfi-user.patch', 1), + ('PSM2-12.0.1_build-with-internal-cuda-header.patch', 1), ] checksums = [ {'PSM2_12.0.1.tar.gz': 'e41af2d7d36a6ab67639ecbd5c1012aa20b2b464bf5cfbdac60e7eb37bfe58de'}, {'PSM2-11.2.80_hfi-user.patch': 'e43138859387213506050af9b76e193c3cd0a162d148998c39e551f220392abb'}, + {'PSM2-12.0.1_build-with-internal-cuda-header.patch': + '0016327d7eade9e763ffbc468cf25c182d743074dca2885dea7ef0cf7e3b23cf'}, ] builddependencies = [ ('binutils', '2.38'), - ('CUDA', '11.7.0', '', SYSTEM), ] dependencies = [ diff --git a/easybuild/easyconfigs/p/PSM2/PSM2-12.0.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/p/PSM2/PSM2-12.0.1-GCCcore-12.2.0.eb index fbf417d2bc8..fa91a78538e 100644 --- a/easybuild/easyconfigs/p/PSM2/PSM2-12.0.1-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/p/PSM2/PSM2-12.0.1-GCCcore-12.2.0.eb @@ -15,15 +15,17 @@ source_urls = ['https://github.com/cornelisnetworks/opa-psm2/archive/refs/tags'] sources = ['%(name)s_%(version)s.tar.gz'] patches = [ ('PSM2-11.2.80_hfi-user.patch', 1), + ('PSM2-12.0.1_build-with-internal-cuda-header.patch', 1), ] checksums = [ {'PSM2_12.0.1.tar.gz': 'e41af2d7d36a6ab67639ecbd5c1012aa20b2b464bf5cfbdac60e7eb37bfe58de'}, {'PSM2-11.2.80_hfi-user.patch': 'e43138859387213506050af9b76e193c3cd0a162d148998c39e551f220392abb'}, + {'PSM2-12.0.1_build-with-internal-cuda-header.patch': + '0016327d7eade9e763ffbc468cf25c182d743074dca2885dea7ef0cf7e3b23cf'}, ] builddependencies = [ ('binutils', '2.39'), - ('CUDA', '12.0.0', '', SYSTEM), ] dependencies = [ diff --git a/easybuild/easyconfigs/p/PSM2/PSM2-12.0.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/PSM2/PSM2-12.0.1-GCCcore-12.3.0.eb index 0470fe64363..169b08b1e36 100644 --- a/easybuild/easyconfigs/p/PSM2/PSM2-12.0.1-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/p/PSM2/PSM2-12.0.1-GCCcore-12.3.0.eb @@ -15,15 +15,17 @@ source_urls = ['https://github.com/cornelisnetworks/opa-psm2/archive/refs/tags'] sources = ['%(name)s_%(version)s.tar.gz'] patches = [ ('PSM2-11.2.80_hfi-user.patch', 1), + ('PSM2-12.0.1_build-with-internal-cuda-header.patch', 1), ] checksums = [ {'PSM2_12.0.1.tar.gz': 'e41af2d7d36a6ab67639ecbd5c1012aa20b2b464bf5cfbdac60e7eb37bfe58de'}, {'PSM2-11.2.80_hfi-user.patch': 'e43138859387213506050af9b76e193c3cd0a162d148998c39e551f220392abb'}, + {'PSM2-12.0.1_build-with-internal-cuda-header.patch': + '0016327d7eade9e763ffbc468cf25c182d743074dca2885dea7ef0cf7e3b23cf'}, ] builddependencies = [ ('binutils', '2.40'), - ('CUDA', '12.1.1', '', SYSTEM), ] dependencies = [ diff --git a/easybuild/easyconfigs/p/PSM2/PSM2-12.0.1-GCCcore-13.2.0.eb b/easybuild/easyconfigs/p/PSM2/PSM2-12.0.1-GCCcore-13.2.0.eb index cfe3fe9f1e4..ee265c55610 100644 --- a/easybuild/easyconfigs/p/PSM2/PSM2-12.0.1-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/p/PSM2/PSM2-12.0.1-GCCcore-13.2.0.eb @@ -15,15 +15,17 @@ source_urls = ['https://github.com/cornelisnetworks/opa-psm2/archive/refs/tags'] sources = ['%(name)s_%(version)s.tar.gz'] patches = [ ('PSM2-11.2.80_hfi-user.patch', 1), + ('PSM2-12.0.1_build-with-internal-cuda-header.patch', 1), ] checksums = [ {'PSM2_12.0.1.tar.gz': 'e41af2d7d36a6ab67639ecbd5c1012aa20b2b464bf5cfbdac60e7eb37bfe58de'}, {'PSM2-11.2.80_hfi-user.patch': 'e43138859387213506050af9b76e193c3cd0a162d148998c39e551f220392abb'}, + {'PSM2-12.0.1_build-with-internal-cuda-header.patch': + '0016327d7eade9e763ffbc468cf25c182d743074dca2885dea7ef0cf7e3b23cf'}, ] builddependencies = [ ('binutils', '2.40'), - ('CUDA', '12.4.0', '', SYSTEM), ] dependencies = [ diff --git a/easybuild/easyconfigs/p/PSM2/PSM2-12.0.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/p/PSM2/PSM2-12.0.1-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..aff3d686fc7 --- /dev/null +++ b/easybuild/easyconfigs/p/PSM2/PSM2-12.0.1-GCCcore-13.3.0.eb @@ -0,0 +1,46 @@ +easyblock = 'ConfigureMake' + +name = 'PSM2' +version = '12.0.1' + +homepage = 'https://github.com/cornelisnetworks/opa-psm2/' +description = """ +Low-level user-space communications interface for the Intel(R) OPA family of products. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/cornelisnetworks/opa-psm2/archive/refs/tags'] +sources = ['%(name)s_%(version)s.tar.gz'] +patches = [ + ('PSM2-11.2.80_hfi-user.patch', 1), + ('PSM2-12.0.1_build-with-internal-cuda-header.patch', 1), +] +checksums = [ + {'PSM2_12.0.1.tar.gz': 'e41af2d7d36a6ab67639ecbd5c1012aa20b2b464bf5cfbdac60e7eb37bfe58de'}, + {'PSM2-11.2.80_hfi-user.patch': 'e43138859387213506050af9b76e193c3cd0a162d148998c39e551f220392abb'}, + {'PSM2-12.0.1_build-with-internal-cuda-header.patch': + '0016327d7eade9e763ffbc468cf25c182d743074dca2885dea7ef0cf7e3b23cf'}, +] + +builddependencies = [ + ('binutils', '2.42'), +] + +dependencies = [ + ('numactl', '2.0.18'), +] + +skipsteps = ['configure'] + +prebuildopts = "sed -i 's|fprintf(stderr,|_HFI_DBG(|' psm_context.c && sed -i 's|/usr|/|' Makefile && " +buildopts = "arch=%s USE_PSM_UUID=1 PSM_CUDA=1 WERROR=" % ARCH +installopts = "arch=%s UDEVDIR=/lib/udev DESTDIR=%%(installdir)s" % ARCH + +sanity_check_paths = { + 'files': ['lib/lib%%(namelower)s.%s' % SHLIB_EXT, 'include/%(namelower)s.h'], + 'dirs': [] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/PSM2/PSM2-12.0.1_build-with-internal-cuda-header.patch b/easybuild/easyconfigs/p/PSM2/PSM2-12.0.1_build-with-internal-cuda-header.patch new file mode 100644 index 00000000000..3e3ffd8038e --- /dev/null +++ b/easybuild/easyconfigs/p/PSM2/PSM2-12.0.1_build-with-internal-cuda-header.patch @@ -0,0 +1,88 @@ +Allow building PSM2 without a CUDA builddependency, by providing an +internal minimal cuda.h header file. +As long as the runtime CUDA version is 8.0+, libcuda.so will be dlopen'ed and +used successfully. + +Author: Bart Oldeman +diff -urN opa-psm2-PSM2_12.0.1.orig/include/cuda.h opa-psm2-PSM2_12.0.1/include/cuda.h +--- opa-psm2-PSM2_12.0.1.orig/include/cuda.h 1970-01-01 00:00:00.000000000 +0000 ++++ opa-psm2-PSM2_12.0.1/include/cuda.h 2024-06-11 18:39:38.242975935 +0000 +@@ -0,0 +1,73 @@ ++/* This header provides minimal parts of the CUDA Driver API, without having to ++ rely on the proprietary CUDA toolkit. ++ ++ References (to avoid copying from NVidia's proprietary cuda.h): ++ https://github.com/gcc-mirror/gcc/blob/master/include/cuda/cuda.h ++ https://github.com/Theano/libgpuarray/blob/master/src/loaders/libcuda.h ++ https://github.com/CPFL/gdev/blob/master/cuda/driver/cuda.h ++ https://github.com/CudaWrangler/cuew/blob/master/include/cuew.h ++*/ ++ ++#ifndef PSM2_CUDA_H ++#define PSM2_CUDA_H ++ ++#include ++ ++#define CUDA_VERSION 8000 ++ ++typedef void *CUcontext; ++typedef int CUdevice; ++#if defined(__LP64__) || defined(_WIN64) ++typedef unsigned long long CUdeviceptr; ++#else ++typedef unsigned CUdeviceptr; ++#endif ++typedef void *CUevent; ++typedef void *CUstream; ++ ++typedef enum { ++ CUDA_SUCCESS = 0, ++ CUDA_ERROR_ALREADY_MAPPED = 208, ++ CUDA_ERROR_NOT_READY = 600, ++} CUresult; ++ ++enum { ++ CU_EVENT_DEFAULT = 0x0, ++}; ++ ++enum { ++ CU_IPC_MEM_LAZY_ENABLE_PEER_ACCESS = 0x1, ++}; ++ ++typedef enum { ++ CU_POINTER_ATTRIBUTE_MEMORY_TYPE = 2, ++ CU_POINTER_ATTRIBUTE_SYNC_MEMOPS = 6, ++ CU_POINTER_ATTRIBUTE_IS_MANAGED = 8, ++} CUpointer_attribute; ++ ++ ++typedef enum { ++ CU_MEMORYTYPE_HOST = 0x01, ++ CU_MEMORYTYPE_DEVICE = 0x02, ++} CUmemorytype; ++ ++#define CU_IPC_HANDLE_SIZE 64 ++ ++typedef struct CUipcMemHandle_st { ++ char reserved[CU_IPC_HANDLE_SIZE]; ++} CUipcMemHandle; ++ ++typedef enum { ++ CU_DEVICE_ATTRIBUTE_UNIFIED_ADDRESSING = 41, ++ CU_DEVICE_ATTRIBUTE_COMPUTE_CAPABILITY_MAJOR = 75, ++} CUdevice_attribute; ++ ++enum { ++ CU_STREAM_NON_BLOCKING = 1 ++}; ++ ++enum { ++ CU_MEMHOSTALLOC_PORTABLE = 0x01, ++}; ++ ++#endif +diff -urN opa-psm2-PSM2_12.0.1.orig/include/driver_types.h opa-psm2-PSM2_12.0.1/include/driver_types.h +--- opa-psm2-PSM2_12.0.1.orig/include/driver_types.h 1970-01-01 00:00:00.000000000 +0000 ++++ opa-psm2-PSM2_12.0.1/include/driver_types.h 2024-06-12 13:46:04.123858352 +0000 +@@ -0,0 +1 @@ ++/* this file is empty */ diff --git a/easybuild/easyconfigs/p/PaStiX/PaStiX-6.3.2-foss-2023b.eb b/easybuild/easyconfigs/p/PaStiX/PaStiX-6.3.2-foss-2023b.eb new file mode 100644 index 00000000000..64b3fd907c7 --- /dev/null +++ b/easybuild/easyconfigs/p/PaStiX/PaStiX-6.3.2-foss-2023b.eb @@ -0,0 +1,47 @@ +easyblock = 'CMakeMake' + +name = 'PaStiX' +version = '6.3.2' + +homepage = 'http://pastix.gforge.inria.fr/' +description = """PaStiX (Parallel Sparse matriX package) is a scientific library that provides a high performance + parallel solver for very large sparse linear systems based on direct methods.""" + +toolchain = {'name': 'foss', 'version': '2023b'} +toolchainopts = {'pic': True} + +source_urls = ['https://files.inria.fr/pastix/releases/v6/'] +sources = ['%(namelower)s-%(version)s.tar.gz'] +checksums = ['c4da8802d1933eecf8c09d7e63c014c81ccf353fe623142e9f5c5fc65ed82ee0'] + +builddependencies = [ + ('CMake', '3.27.6'), + ('pkgconf', '2.0.3'), +] + +dependencies = [ + ('hwloc', '2.9.2'), + ('SCOTCH', '7.0.4'), +] + +configopts = [ + '-DBUILD_SHARED_LIBS=OFF -DPASTIX_INT64=OFF -DPASTIX_WITH_MPI=ON', + '-DBUILD_SHARED_LIBS=ON -DPASTIX_INT64=OFF -DPASTIX_WITH_MPI=ON' +] + +sanity_check_paths = { + 'files': ['bin/pastix_env.sh', + 'bin/spm_env.sh', + 'lib/libpastix.a', + 'lib/libpastixf.a', + 'lib/libpastix.%s' % SHLIB_EXT, + 'lib/libpastixf.%s' % SHLIB_EXT, + 'lib/libspm.a', + 'lib/libspmf.a', + 'lib/libspm.%s' % SHLIB_EXT, + 'lib/libspmf.%s' % SHLIB_EXT, + ], + 'dirs': ['bin', 'include', 'lib/pkgconfig', 'share'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/p/PaStiX/PaStiX-6.3.2-intel-2023b.eb b/easybuild/easyconfigs/p/PaStiX/PaStiX-6.3.2-intel-2023b.eb new file mode 100644 index 00000000000..d53ebd66755 --- /dev/null +++ b/easybuild/easyconfigs/p/PaStiX/PaStiX-6.3.2-intel-2023b.eb @@ -0,0 +1,47 @@ +easyblock = 'CMakeMake' + +name = 'PaStiX' +version = '6.3.2' + +homepage = 'http://pastix.gforge.inria.fr/' +description = """PaStiX (Parallel Sparse matriX package) is a scientific library that provides a high performance + parallel solver for very large sparse linear systems based on direct methods.""" + +toolchain = {'name': 'intel', 'version': '2023b'} +toolchainopts = {'pic': True} + +source_urls = ['https://files.inria.fr/pastix/releases/v6/'] +sources = ['%(namelower)s-%(version)s.tar.gz'] +checksums = ['c4da8802d1933eecf8c09d7e63c014c81ccf353fe623142e9f5c5fc65ed82ee0'] + +builddependencies = [ + ('CMake', '3.27.6'), + ('pkgconf', '2.0.3'), +] + +dependencies = [ + ('hwloc', '2.9.2'), + ('SCOTCH', '7.0.4'), +] + +configopts = [ + '-DBUILD_SHARED_LIBS=OFF -DPASTIX_INT64=OFF -DPASTIX_WITH_MPI=ON', + '-DBUILD_SHARED_LIBS=ON -DPASTIX_INT64=OFF -DPASTIX_WITH_MPI=ON' +] + +sanity_check_paths = { + 'files': ['bin/pastix_env.sh', + 'bin/spm_env.sh', + 'lib/libpastix.a', + 'lib/libpastixf.a', + 'lib/libpastix.%s' % SHLIB_EXT, + 'lib/libpastixf.%s' % SHLIB_EXT, + 'lib/libspm.a', + 'lib/libspmf.a', + 'lib/libspm.%s' % SHLIB_EXT, + 'lib/libspmf.%s' % SHLIB_EXT, + ], + 'dirs': ['bin', 'include', 'lib/pkgconfig', 'share'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/p/Pango/Pango-1.54.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/p/Pango/Pango-1.54.0-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..cfbbc1eb16b --- /dev/null +++ b/easybuild/easyconfigs/p/Pango/Pango-1.54.0-GCCcore-13.3.0.eb @@ -0,0 +1,41 @@ +easyblock = 'MesonNinja' + +name = 'Pango' +version = '1.54.0' + +homepage = 'https://pango.gnome.org/' +description = """Pango is a library for laying out and rendering of text, with an emphasis on internationalization. +Pango can be used anywhere that text layout is needed, though most of the work on Pango so far has been done in the +context of the GTK+ widget toolkit. Pango forms the core of text and font handling for GTK+-2.x.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['8a9eed75021ee734d7fc0fdf3a65c3bba51dfefe4ae51a9b414a60c70b2d1ed8'] + +builddependencies = [ + ('binutils', '2.42'), + ('Meson', '1.4.0'), + ('Ninja', '1.12.1'), + ('GObject-Introspection', '1.80.1'), + ('pkgconf', '2.2.0'), +] + +dependencies = [ + ('X11', '20240607'), + ('GLib', '2.80.4'), + ('cairo', '1.18.0'), + ('HarfBuzz', '9.0.0'), + ('FriBidi', '1.0.15'), +] + +configopts = "--buildtype=release --default-library=both " + +sanity_check_paths = { + 'files': ['bin/pango-view', 'lib/libpango-1.0.%s' % SHLIB_EXT, 'lib/libpangocairo-1.0.%s' % SHLIB_EXT, + 'lib/libpangoft2-1.0.%s' % SHLIB_EXT, 'lib/libpangoxft-1.0.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/Panoply/Panoply-5.5.1.eb b/easybuild/easyconfigs/p/Panoply/Panoply-5.5.1.eb new file mode 100644 index 00000000000..f82b44f3ee5 --- /dev/null +++ b/easybuild/easyconfigs/p/Panoply/Panoply-5.5.1.eb @@ -0,0 +1,32 @@ +easyblock = 'PackedBinary' + +name = 'Panoply' +version = '5.5.1' + +homepage = 'https://www.giss.nasa.gov/tools/panoply' +description = "Panoply plots geo-referenced and other arrays from netCDF, HDF, GRIB, and other datasets." + + +toolchain = SYSTEM + +source_urls = ['https://www.giss.nasa.gov/tools/panoply/download/'] +sources = ['%(name)sJ-%(version)s.tgz'] +checksums = ['14196be2dd83721e475dfa0b230859b9e102bfdcc62119536ececbf8dcbbbb96'] + +dependencies = [ + ('Java', '11', '', SYSTEM), +] + +postinstallcmds = [ + 'mkdir %(installdir)s/bin', + 'mv %(installdir)s/panoply.sh %(installdir)s/bin', + 'sed -i "s,jars,../jars,g" %(installdir)s/bin/panoply.sh', + 'ln -s %(installdir)s/bin/panoply.sh %(installdir)s/bin/panoply', +] + +sanity_check_paths = { + 'files': ['bin/panoply'], + 'dirs': ['jars'] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-gompi-2023b.eb b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-gompi-2023b.eb new file mode 100644 index 00000000000..ae247e2b7c5 --- /dev/null +++ b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-gompi-2023b.eb @@ -0,0 +1,29 @@ +## +# Author: Robert Mijakovic +## +name = 'ParMETIS' +version = '4.0.3' + +homepage = 'http://glaros.dtc.umn.edu/gkhome/metis/parmetis/overview' +description = """ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning + unstructured graphs, meshes, and for computing fill-reducing orderings of sparse matrices. ParMETIS extends the + functionality provided by METIS and includes routines that are especially suited for parallel AMR computations and + large scale numerical simulations. The algorithms implemented in ParMETIS are based on the parallel multilevel k-way + graph-partitioning, adaptive repartitioning, and parallel multi-constrained partitioning schemes.""" + +toolchain = {'name': 'gompi', 'version': '2023b'} +toolchainopts = {'usempi': True, 'pic': True} + +source_urls = [ + 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis', + 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis/OLD', +] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['f2d9a231b7cf97f1fee6e8c9663113ebf6c240d407d3c118c55b3633d6be6e5f'] + +builddependencies = [('CMake', '3.27.6')] + +# Build static and shared libraries +configopts = ['', '-DSHARED=1'] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-iimpi-2023b.eb b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-iimpi-2023b.eb new file mode 100644 index 00000000000..a2804c40d1c --- /dev/null +++ b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-iimpi-2023b.eb @@ -0,0 +1,29 @@ +## +# Author: Robert Mijakovic +## +name = 'ParMETIS' +version = '4.0.3' + +homepage = 'http://glaros.dtc.umn.edu/gkhome/metis/parmetis/overview' +description = """ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning + unstructured graphs, meshes, and for computing fill-reducing orderings of sparse matrices. ParMETIS extends the + functionality provided by METIS and includes routines that are especially suited for parallel AMR computations and + large scale numerical simulations. The algorithms implemented in ParMETIS are based on the parallel multilevel k-way + graph-partitioning, adaptive repartitioning, and parallel multi-constrained partitioning schemes.""" + +toolchain = {'name': 'iimpi', 'version': '2023b'} +toolchainopts = {'usempi': True, 'pic': True} + +source_urls = [ + 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis', + 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis/OLD', +] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['f2d9a231b7cf97f1fee6e8c9663113ebf6c240d407d3c118c55b3633d6be6e5f'] + +builddependencies = [('CMake', '3.27.6')] + +# Build static and shared libraries +configopts = ['', '-DSHARED=1'] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/p/ParMGridGen/ParMGridGen-1.0-gompi-2023a.eb b/easybuild/easyconfigs/p/ParMGridGen/ParMGridGen-1.0-gompi-2023a.eb new file mode 100644 index 00000000000..bee93301eb9 --- /dev/null +++ b/easybuild/easyconfigs/p/ParMGridGen/ParMGridGen-1.0-gompi-2023a.eb @@ -0,0 +1,40 @@ +easyblock = 'MakeCp' + +name = 'ParMGridGen' +version = '1.0' + +homepage = 'http://www-users.cs.umn.edu/~moulitsa/software.html' +description = """ParMGridGen is an MPI-based parallel library that is based on the serial package MGridGen, + that implements (serial) algorithms for obtaining a sequence of successive coarse grids that are well-suited + for geometric multigrid methods.""" + +toolchain = {'name': 'gompi', 'version': '2023a'} +toolchainopts = {'usempi': True, 'pic': True} + +source_urls = ['https://download.sourceforge.net/foam-extend/ThirdParty'] +sources = [SOURCE_TAR_GZ] +patches = [ + 'ParMGridGen-%(version)s_malloc_include.patch', + 'ParMGridGen-%(version)s_gompiOpenFOAM-Extend.patch', +] +checksums = [ + '62cdb6e48cfc59124e5d5d360c2841e0fc2feecafe65bda110b74e942740b395', # ParMGridGen-1.0.tar.gz + '3e0d72f82b3b56cbfcb1e3c9afc6594eb25316a0faeb49237faa8d969b4daeaa', # ParMGridGen-1.0_malloc_include.patch + '60cc46d156e99101b21bde9d23cf6c2db3dcdef1704f1830a7baa0320003c02a', # ParMGridGen-1.0_gompiOpenFOAM-Extend.patch +] + +buildopts = 'parallel make=make CC="$CC" PARCC="$CC" PARLD="$CC" COPTIONS="$CFLAGS" LDOPTIONS="$CFLAGS" BINDIR="."' + +files_to_copy = [ + (['MGridGen/Programs/mgridgen', 'ParMGridGen/Programs/parmgridgen'], 'bin'), + (['mgridgen.h', 'parmgridgen.h', 'MGridGen/IMlib/IMlib.h'], 'include'), + (['libmgrid.a', 'libMGridGen.a', 'libparmgrid.a', 'MGridGen/IMlib/libIMlib.a'], 'lib'), +] + +sanity_check_paths = { + 'files': ['bin/mgridgen', 'bin/parmgridgen', 'include/mgridgen.h', 'include/parmgridgen.h', + 'include/IMlib.h', 'lib/libmgrid.a', 'lib/libMGridGen.a', 'lib/libparmgrid.a', 'lib/libIMlib.a'], + 'dirs': [], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/p/ParaView/ParaView-5.11.1-foss-2022b-CUDA-12.2.0.eb b/easybuild/easyconfigs/p/ParaView/ParaView-5.11.1-foss-2022b-CUDA-12.2.0.eb index 8f312f89318..340952c3338 100644 --- a/easybuild/easyconfigs/p/ParaView/ParaView-5.11.1-foss-2022b-CUDA-12.2.0.eb +++ b/easybuild/easyconfigs/p/ParaView/ParaView-5.11.1-foss-2022b-CUDA-12.2.0.eb @@ -44,7 +44,7 @@ dependencies = [ _copts = [ # Basic configuration - '-DPARAVIEW_INSTALL_DEVELOPMENT_FILES=ON' + '-DPARAVIEW_INSTALL_DEVELOPMENT_FILES=ON', '-DPARAVIEW_BUILD_SHARED_LIBS=ON', '-DPARAVIEW_USE_MPI=ON', '-DPARAVIEW_ENABLE_FFMPEG=ON', diff --git a/easybuild/easyconfigs/p/ParaView/ParaView-5.12.0-foss-2023b-Qt5.eb b/easybuild/easyconfigs/p/ParaView/ParaView-5.12.0-foss-2023b-Qt5.eb new file mode 100644 index 00000000000..abec428859f --- /dev/null +++ b/easybuild/easyconfigs/p/ParaView/ParaView-5.12.0-foss-2023b-Qt5.eb @@ -0,0 +1,72 @@ +easyblock = 'CMakeMake' + +name = 'ParaView' +version = '5.12.0' +versionsuffix = '-Qt5' + +homepage = 'https://www.paraview.org' +description = "ParaView is a scientific parallel visualizer." + +toolchain = {'name': 'foss', 'version': '2023b'} +toolchainopts = {'pic': True, 'usempi': True} + +local_download_suffix = 'download.php?submit=Download&version=v%(version_major_minor)s&type=source&os=all&downloadFile=' +source_urls = ['https://www.paraview.org/paraview-downloads/%s' % local_download_suffix] +sources = ["%(name)s-v%(version)s.tar.gz"] +patches = ['ParaView-5.11.1-remove_glew_init_warning.patch'] +checksums = [ + {'ParaView-v5.12.0.tar.gz': '2cc5733608fd508e2da8fc5d4ee693523d350dc1e1f89f9a89a78dc63107f70e'}, + {'ParaView-5.11.1-remove_glew_init_warning.patch': + 'dd86134f3a5b2c1b834224c69665dd31f99ef7d367688fe77dbaada212758710'}, +] + +builddependencies = [('CMake', '3.27.6')] + +dependencies = [ + ('Python', '3.11.5'), + ('SciPy-bundle', '2023.11'), + ('Boost', '1.83.0'), + ('XZ', '5.4.4'), + ('HDF5', '1.14.3'), + ('netCDF', '4.9.2'), + ('libdrm', '2.4.117'), + ('Mesa', '23.1.9'), + ('Qt5', '5.15.13'), + ('zlib', '1.2.13'), + ('FFmpeg', '6.0'), + ('Szip', '2.1.1'), +] + +_copts = [ + # Basic configuration + '-DPARAVIEW_INSTALL_DEVELOPMENT_FILES=ON', + '-DPARAVIEW_BUILD_SHARED_LIBS=ON', + '-DPARAVIEW_USE_MPI=ON', + '-DPARAVIEW_ENABLE_FFMPEG=ON', + '-DPARAVIEW_USE_PYTHON=ON', + '-DPython3_ROOT_DIR=$EBROOTPYTHON', + # Useful input formats + '-DPARAVIEW_ENABLE_XDMF2=ON', + '-DPARAVIEW_ENABLE_XDMF3=ON', + # EGL, X and Mesa + '-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s' % SHLIB_EXT, + '-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include', + '-DEGL_INCLUDE_DIR=$EBROOTLIBGLVND/include', + '-DEGL_LIBRARY=$EBROOTLIBGLVND/lib/libEGL.%s' % SHLIB_EXT, + '-DEGL_opengl_LIBRARY=$EBROOTLIBGLVND/libOpenGL.%s' % SHLIB_EXT, + '-DVTK_OPENGL_HAS_EGL=ON', + '-DVTK_USE_X=ON', + '-DVTK_OPENGL_HAS_OSMESA=OFF', + '-DVTK_PYTHON_OPTIONAL_LINK=OFF'] +configopts = ' '.join(_copts) + +sanity_check_paths = { + 'files': ['bin/paraview', 'bin/pvserver', 'bin/pvpython'], + 'dirs': ['include/paraview-%(version_major_minor)s', 'lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ['python -c "import paraview"'] + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/ParaView/ParaView-5.12.0-foss-2023b.eb b/easybuild/easyconfigs/p/ParaView/ParaView-5.12.0-foss-2023b.eb index 018edd70431..ed8408c9301 100644 --- a/easybuild/easyconfigs/p/ParaView/ParaView-5.12.0-foss-2023b.eb +++ b/easybuild/easyconfigs/p/ParaView/ParaView-5.12.0-foss-2023b.eb @@ -12,11 +12,15 @@ toolchainopts = {'pic': True, 'usempi': True} local_download_suffix = 'download.php?submit=Download&version=v%(version_major_minor)s&type=source&os=all&downloadFile=' source_urls = ['https://www.paraview.org/paraview-downloads/%s' % local_download_suffix] sources = ["%(name)s-v%(version)s.tar.gz"] -patches = ['ParaView-5.11.1-remove_glew_init_warning.patch'] +patches = [ + 'ParaView-5.11.1-remove_glew_init_warning.patch', + 'ParaView-5.12.0-qt6_fixes.patch', +] checksums = [ {'ParaView-v5.12.0.tar.gz': '2cc5733608fd508e2da8fc5d4ee693523d350dc1e1f89f9a89a78dc63107f70e'}, {'ParaView-5.11.1-remove_glew_init_warning.patch': 'dd86134f3a5b2c1b834224c69665dd31f99ef7d367688fe77dbaada212758710'}, + {'ParaView-5.12.0-qt6_fixes.patch': '015d07ac6b74c7355b56ed7f67166f0d5b765f9d6ac135b7246a675a317063df'}, ] builddependencies = [('CMake', '3.27.6')] @@ -58,7 +62,9 @@ _copts = [ '-DEGL_opengl_LIBRARY=$EBROOTLIBGLVND/libOpenGL.%s' % SHLIB_EXT, '-DVTK_OPENGL_HAS_EGL=ON', '-DVTK_USE_X=ON', - '-DVTK_OPENGL_HAS_OSMESA=OFF'] + '-DVTK_OPENGL_HAS_OSMESA=OFF', + '-DVTK_PYTHON_OPTIONAL_LINK=OFF'] + configopts = ' '.join(_copts) sanity_check_paths = { diff --git a/easybuild/easyconfigs/p/ParaView/ParaView-5.12.0-qt6_fixes.patch b/easybuild/easyconfigs/p/ParaView/ParaView-5.12.0-qt6_fixes.patch new file mode 100644 index 00000000000..838d6fe5d32 --- /dev/null +++ b/easybuild/easyconfigs/p/ParaView/ParaView-5.12.0-qt6_fixes.patch @@ -0,0 +1,126 @@ +This patch solves qt6 compatibility issues. For details see +https://gitlab.kitware.com/paraview/paraview/-/merge_requests/6836 + +diff --git a/Plugins/CAVEInteraction/pqVRDockPanel.cxx b/Plugins/CAVEInteraction/pqVRDockPanel.cxx +index 7a3d352b993f2930716b47dd98512ca88697374c..448ac4d3833ec1582d99139b3f3fea6bbdf7d3ce 100644 +--- a/Plugins/CAVEInteraction/pqVRDockPanel.cxx ++++ b/Plugins/CAVEInteraction/pqVRDockPanel.cxx +@@ -159,8 +159,8 @@ void pqVRDockPanel::initStyles() + this->Internals->stylesCombo->addItem(QString::fromStdString(styleDescs[i])); + } + +- connect(this->Internals->stylesCombo, SIGNAL(currentIndexChanged(QString)), this, +- SLOT(styleComboChanged(QString)), Qt::UniqueConnection); ++ QObject::connect(this->Internals->stylesCombo, &QComboBox::currentTextChanged, this, ++ &pqVRDockPanel::styleComboChanged, Qt::UniqueConnection); + } + + //----------------------------------------------------------------------------- +diff --git a/Qt/Components/pqCustomFilterDefinitionWizard.cxx b/Qt/Components/pqCustomFilterDefinitionWizard.cxx +index 9c140a37abca11b19f0c04bf7c41645b756457d6..acd7bd99e19017a5557a41c4585586b39e5ffc58 100644 +--- a/Qt/Components/pqCustomFilterDefinitionWizard.cxx ++++ b/Qt/Components/pqCustomFilterDefinitionWizard.cxx +@@ -134,8 +134,8 @@ pqCustomFilterDefinitionWizard::pqCustomFilterDefinitionWizard( + SLOT(clearNameOverwrite(const QString&))); + + // When combo selection changes, update new label to be same as old. +- QObject::connect(this->Form->PropertyCombo, SIGNAL(currentIndexChanged(const QString&)), +- this->Form->PropertyName, SLOT(setText(const QString&))); ++ QObject::connect(this->Form->PropertyCombo, &QComboBox::currentTextChanged, ++ this->Form->PropertyName, &QLineEdit::setText); + } + + //----------------------------------------------------------------------------- +diff --git a/Qt/Components/pqDataInformationWidget.cxx b/Qt/Components/pqDataInformationWidget.cxx +index f151d584fc8b683b5666c11c7dfad85219c1e94f..7079507a14bad98dd10bff7ddf65af896cf5e919 100644 +--- a/Qt/Components/pqDataInformationWidget.cxx ++++ b/Qt/Components/pqDataInformationWidget.cxx +@@ -103,8 +103,8 @@ pqDataInformationWidget::pqDataInformationWidget(QWidget* _parent /*=0*/) + this->Model->setActiveView(pqActiveObjects::instance().activeView()); + + // Clicking on the header should sort the column. +- QObject::connect(this->View->horizontalHeader(), SIGNAL(sectionClicked(int)), this->View, +- SLOT(sortByColumn(int))); ++ QObject::connect(this->View->horizontalHeader(), &QHeaderView::sectionClicked, this->View, ++ [=](int col) { this->View->sortByColumn(col, Qt::AscendingOrder); }); + + // Set the context menu policy for the header. + this->View->horizontalHeader()->setContextMenuPolicy(Qt::CustomContextMenu); +diff --git a/Qt/Components/pqDisplayRepresentationWidget.cxx b/Qt/Components/pqDisplayRepresentationWidget.cxx +index 3e08e05e560618457e628afc9bf1fdbf3167b9f0..4d9bc9958a0034e3e2b1e7920a333a5d7f794db6 100644 +--- a/Qt/Components/pqDisplayRepresentationWidget.cxx ++++ b/Qt/Components/pqDisplayRepresentationWidget.cxx +@@ -111,8 +111,8 @@ pqDisplayRepresentationWidget::pqDisplayRepresentationWidget(QWidget* _p) + { + this->Internal = new pqDisplayRepresentationWidget::pqInternals(); + this->Internal->setupUi(this); +- this->connect(this->Internal->comboBox, SIGNAL(currentIndexChanged(const QString&)), +- SLOT(comboBoxChanged(const QString&))); ++ QObject::connect(this->Internal->comboBox, &QComboBox::currentTextChanged, this, ++ &pqDisplayRepresentationWidget::comboBoxChanged); + } + + //----------------------------------------------------------------------------- +diff --git a/Qt/Components/pqLinksEditor.cxx b/Qt/Components/pqLinksEditor.cxx +index 6f02d16d44b82f616a236557f16174d3ffa96425..ae66b1c97c3d82425c2f8b849c6d656deecc64a8 100644 +--- a/Qt/Components/pqLinksEditor.cxx ++++ b/Qt/Components/pqLinksEditor.cxx +@@ -452,8 +452,8 @@ pqLinksEditor::pqLinksEditor(vtkSMLink* link, QWidget* p) + QObject::connect(this->Ui->lineEdit, SIGNAL(textChanged(const QString&)), this, + SLOT(updateEnabledState()), Qt::QueuedConnection); + +- QObject::connect(this->Ui->comboBox, SIGNAL(currentIndexChanged(const QString&)), this, +- SLOT(updateSelectedProxies()), Qt::QueuedConnection); ++ QObject::connect(this->Ui->comboBox, &QComboBox::currentTextChanged, this, ++ &pqLinksEditor::updateSelectedProxies, Qt::QueuedConnection); + + QObject::connect( + this->Ui->interactiveViewLinkCheckBox, &QCheckBox::stateChanged, this, +diff --git a/Qt/Core/pqFileDialog.cxx b/Qt/Core/pqFileDialog.cxx +index 2a87c723a5ef4af856c71e3589ce9a5efa95b65b..6f369d1163a32e5ae3c7e3bcc00a22081e81e2a2 100644 +--- a/Qt/Core/pqFileDialog.cxx ++++ b/Qt/Core/pqFileDialog.cxx +@@ -322,7 +322,7 @@ pqFileDialog::pqFileDialog(pqServer* server, QWidget* p, const QString& title, + QObject::connect( + impl.Ui.NavigateForward, SIGNAL(clicked(bool)), this, SLOT(onNavigateForward())); + impl.Ui.NavigateUp->setIcon(style()->standardPixmap(QStyle::SP_FileDialogToParent)); +- impl.Ui.NavigateUp->setShortcut(Qt::ALT + Qt::Key_Up); ++ impl.Ui.NavigateUp->setShortcut(Qt::ALT | Qt::Key_Up); + impl.Ui.NavigateUp->setToolTip( + tr("Navigate Up (%1)").arg(impl.Ui.NavigateUp->shortcut().toString())); + impl.Ui.CreateFolder->setIcon(style()->standardPixmap(QStyle::SP_FileDialogNewFolder)); +@@ -378,8 +378,8 @@ pqFileDialog::pqFileDialog(pqServer* server, QWidget* p, const QString& title, + QObject::connect( + impl.Ui.Parents, SIGNAL(activated(const QString&)), this, SLOT(onNavigate(const QString&))); + +- QObject::connect(impl.Ui.EntityType, SIGNAL(currentIndexChanged(const QString&)), this, +- SLOT(onFilterChange(const QString&))); ++ QObject::connect( ++ impl.Ui.EntityType, &QComboBox::currentTextChanged, this, &pqFileDialog::onFilterChange); + + QObject::connect(impl.Ui.Favorites, SIGNAL(clicked(const QModelIndex&)), this, + SLOT(onClickedFavorite(const QModelIndex&))); +diff --git a/Qt/Widgets/pqSignalAdaptors.cxx b/Qt/Widgets/pqSignalAdaptors.cxx +index 0015c9148b80eddd926ba37c17b7d777250c1a78..8e218b945c5f7a8962ffaced17d4a011c00db153 100644 +--- a/Qt/Widgets/pqSignalAdaptors.cxx ++++ b/Qt/Widgets/pqSignalAdaptors.cxx +@@ -16,10 +16,15 @@ + pqSignalAdaptorComboBox::pqSignalAdaptorComboBox(QComboBox* p) + : QObject(p) + { +- QObject::connect(p, SIGNAL(currentIndexChanged(const QString&)), this, +- SIGNAL(currentTextChanged(const QString&))); +- +- QObject::connect(p, SIGNAL(currentIndexChanged(int)), this, SIGNAL(currentIndexChanged(int))); ++ QObject::connect( ++ p, &QComboBox::currentTextChanged, this, &pqSignalAdaptorComboBox::currentTextChanged); ++ ++#if QT_VERSION > QT_VERSION_CHECK(6, 0, 0) ++ QObject::connect( ++ p, &QComboBox::currentIndexChanged, this, &pqSignalAdaptorComboBox::currentIndexChanged); ++#else ++ QObject::connect(p, SIGNAL(currentIndexChanged(int)), this, SLOT(currentIndexChanged(int))); ++#endif + } + + //---------------------------------------------------------------------------- diff --git a/easybuild/easyconfigs/p/Paraver/Paraver-4.11.4-GCC-12.3.0.eb b/easybuild/easyconfigs/p/Paraver/Paraver-4.11.4-GCC-12.3.0.eb new file mode 100644 index 00000000000..72f3e310448 --- /dev/null +++ b/easybuild/easyconfigs/p/Paraver/Paraver-4.11.4-GCC-12.3.0.eb @@ -0,0 +1,21 @@ +name = 'Paraver' +version = '4.11.4' + +homepage = 'https://tools.bsc.es/paraver' +description = """A very powerful performance visualization and analysis tool based on + traces that can be used to analyse any information that is expressed on its input trace format. + Traces for parallel MPI, OpenMP and other programs can be genereated with Extrae.""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +source_urls = ['https://ftp.tools.bsc.es/wxparaver/'] +sources = ['wxparaver-%(version)s-src.tar.bz2'] +checksums = ['8f65fbeacaef003b544ecc0244a4ed9a99e9521cdd027889106fbce0b052fd8d'] + +dependencies = [ + ('zlib', '1.2.13'), + ('Boost', '1.82.0'), + ('wxWidgets', '3.2.2.1'), +] + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/p/Parsl/Parsl-2024.4.22-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/Parsl/Parsl-2024.4.22-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..5a3161592c0 --- /dev/null +++ b/easybuild/easyconfigs/p/Parsl/Parsl-2024.4.22-GCCcore-12.3.0.eb @@ -0,0 +1,75 @@ +easyblock = 'PythonBundle' + +name = 'Parsl' +version = '2024.4.22' + +homepage = 'https://parsl-project.org/' +description = """ +Parsl extends parallelism in Python beyond a single computer. +You can use Parsl just like Python's parallel executors but across multiple +cores and nodes. However, the real power of Parsl is in expressing multi-step +workflows of functions. Parsl lets you chain functions together and will launch +each function as inputs and computing resources are available. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +builddependencies = [ + ('binutils', '2.40'), + ('hatchling', '1.18.0'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('PyZMQ', '25.1.1'), + ('dill', '0.3.7'), + ('typing-extensions', '4.9.0'), + ('paramiko', '3.2.0'), +] + +use_pip = True + +exts_list = [ + ('types-paramiko', '3.4.0.20240423', { + 'modulename': False, + 'checksums': ['aaa98dda232c47886563d66743d3a8b66c432790c596bc3bdd3f17f91be2a8c1'], + }), + ('types-urllib3', '1.26.25.14', { + 'modulename': False, + 'checksums': ['229b7f577c951b8c1b92c1bc2b2fdb0b49847bd2af6d1cc2a2e3dd340f3bda8f'], + }), + ('typeguard', '4.2.0', { + 'checksums': ['2aeae510750fca88d0a2ceca3e86de7f71aa43b6c3e6c267737ce1f5effc4b34'], + }), + ('PyJWT', '2.8.0', { + 'modulename': 'jwt', + 'checksums': ['57e28d156e3d5c10088e0c68abb90bfac3df82b40a71bd0daa20c65ccd5c23de'], + }), + ('globus-sdk', '3.40.0', { + 'source_tmpl': 'globus_sdk-%(version)s.tar.gz', + 'checksums': ['6394f01c35b2b3275622f4f7c194eaf6750cb6c1e82cb2448dac2eb4ec394d75'], + }), + ('tblib', '3.0.0', { + 'checksums': ['93622790a0a29e04f0346458face1e144dc4d32f493714c6c3dff82a4adb77e6'], + }), + ('setproctitle', '1.3.3', { + 'checksums': ['c913e151e7ea01567837ff037a23ca8740192880198b7fbb90b16d181607caae'], + }), + ('filelock', '3.13.4', { + 'checksums': ['d13f466618bfde72bd2c18255e269f72542c6e70e7bac83a0232d6b1cc5c8cf4'], + }), + ('parsl', version, { + 'checksums': ['99d2b48173bcd22214cb275e3b94be818de6297d5e7bbe606327c961750366f8'], + }), +] + +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/parsl-perf'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/'], +} + +sanity_check_commands = ['parsl-perf --help'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/PennyLane/PennyLane-0.37.0-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/p/PennyLane/PennyLane-0.37.0-foss-2023a-CUDA-12.1.1.eb new file mode 100644 index 00000000000..75368e7c82d --- /dev/null +++ b/easybuild/easyconfigs/p/PennyLane/PennyLane-0.37.0-foss-2023a-CUDA-12.1.1.eb @@ -0,0 +1,68 @@ +easyblock = 'PythonBundle' + +name = 'PennyLane' +version = '0.37.0' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = "https://pennylane.ai/" +description = """PennyLane is a cross-platform Python library for +quantum computing, quantum machine learning, and quantum +chemistry. Train a quantum computer the same way as a neural network.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +local_pennylane_test_backends = [ + # tests to enable when testing pennylane + ('jax', '0.4.25', versionsuffix), + ('PyTorch', '2.1.2', versionsuffix), + ('TensorFlow', '2.15.1', versionsuffix), +] + +local_pennylane_lightning_extras = ['qubit', 'gpu', 'kokkos'] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('networkx', '3.1'), + ('rustworkx', '0.15.1'), + ('CUDA', '12.1.1', '', SYSTEM), +] + +if 'gpu' in local_pennylane_lightning_extras: + dependencies += [ + ('cuQuantum', '24.08.0.5', versionsuffix, SYSTEM) + ] + +builddependencies = [ + ('CMake', '3.26.3'), + ('Ninja', '1.11.1'), + ('pybind11', '2.11.1'), +] + local_pennylane_test_backends + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('autograd', '1.6.2', { + 'checksums': ['8731e08a0c4e389d8695a40072ada4512641c113b6cace8f4cfbe8eb7e9aedeb'], + }), + ('autoray', '0.6.12', { + 'checksums': ['721328aa06fc3577155d988052614a7b4bd6e4d01b340695344031ee4abd2a1e'], + }), + ('cachetools', '5.2.1', { + 'checksums': ['5991bc0e08a1319bb618d3195ca5b6bc76646a49c21d55962977197b301cc1fe'], + }), + ('pennylane', version, { + 'source_urls': ['https://github.com/PennyLaneAI/pennylane/archive/refs/tags'], + 'sources': [{'filename': '%(name)s-v%(version)s.tar.gz', 'download_filename': 'v%(version)s.tar.gz'}], + 'checksums': ['3e5eaab9da28ac43099e5850fde0c5763bc4e37271804463fc35dab8b08e2f15'], + }), + ('pennylane_lightning', version, { + 'source_urls': ['https://github.com/PennyLaneAI/pennylane-lightning/archive/refs/tags'], + 'sources': [{'filename': '%(name)s-v%(version)s.tar.gz', 'download_filename': 'v%(version)s.tar.gz'}], + 'checksums': ['3f70e3e3b7e4d0f6a679919c0c83e451e129666b021bb529dd02eb915d0666a0'], + 'use_pip_extras': 'qubit,gpu,kokkos', + }), +] + +moduleclass = 'ai' diff --git a/easybuild/easyconfigs/p/Perl-bundle-CPAN/Cwd-3.7.5_fix-cwd_enoent-test.patch b/easybuild/easyconfigs/p/Perl-bundle-CPAN/PathTools-3.75_fix-cwd_enoent-test.patch similarity index 100% rename from easybuild/easyconfigs/p/Perl-bundle-CPAN/Cwd-3.7.5_fix-cwd_enoent-test.patch rename to easybuild/easyconfigs/p/Perl-bundle-CPAN/PathTools-3.75_fix-cwd_enoent-test.patch diff --git a/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.36.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.36.1-GCCcore-12.3.0.eb index 50d708b9a26..1c02282d891 100644 --- a/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.36.1-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.36.1-GCCcore-12.3.0.eb @@ -1767,17 +1767,13 @@ exts_list = [ 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JD/JDHEDDEN'], 'checksums': ['9dfd6ca2822724347e0eb6759d00709425814703ad5c66bdb6214579868bcac4'], }), - ('Time::HiRes', '1.9764', { - 'runtest': False, # https://github.com/easybuilders/easybuild-easyconfigs/issues/20145 unreliable atime tests - 'source_tmpl': 'Time-HiRes-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AT/ATOOMIC'], - 'checksums': ['9841be5587bfb7cd1f2fe267b5e5ac04ce25e79d5cc77e5ef9a9c5abd101d7b1'], - }), ('Term::ReadLine::Gnu', '1.45', { 'modulename': 'Term::ReadLine', 'source_tmpl': 'Term-ReadLine-Gnu-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAYASHI'], 'checksums': ['9f4f7abbc69ea58ab7f24992d47f7391bb4aed6fb701fedaeb1a9f1cdc7fab8a'], + # make sure that library provided by ncurses dependency is used instead of libtermcap + 'preinstallopts': "sed -s 's/-ltermcap/-lncurses/g' Makefile.PL && ", }), ('ExtUtils::MakeMaker', '7.70', { 'source_tmpl': 'ExtUtils-MakeMaker-%(version)s.tar.gz', @@ -1923,10 +1919,11 @@ exts_list = [ ('Cwd', '3.75', { 'source_tmpl': 'PathTools-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/X/XS/XSAWYERX'], - 'patches': ['Cwd-3.7.5_fix-cwd_enoent-test.patch'], + 'patches': ['PathTools-3.75_fix-cwd_enoent-test.patch'], 'checksums': [ 'a558503aa6b1f8c727c0073339081a77888606aa701ada1ad62dd9d8c3f945a2', - {'Cwd-3.7.5_fix-cwd_enoent-test.patch': '7a456a99d9b04a36359f3623f0deef8fe7f472c742f99cdcf0215c50afbbe7b1'}, + {'PathTools-3.75_fix-cwd_enoent-test.patch': + '7a456a99d9b04a36359f3623f0deef8fe7f472c742f99cdcf0215c50afbbe7b1'}, ], }), ('MIME::Base64', '3.16', { diff --git a/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.38.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.38.0-GCCcore-13.2.0.eb index 2ee75d5ffc3..35ab629e89e 100644 --- a/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.38.0-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.38.0-GCCcore-13.2.0.eb @@ -1770,16 +1770,13 @@ exts_list = [ 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JD/JDHEDDEN'], 'checksums': ['9dfd6ca2822724347e0eb6759d00709425814703ad5c66bdb6214579868bcac4'], }), - ('Time::HiRes', '1.9764', { - 'source_tmpl': 'Time-HiRes-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AT/ATOOMIC'], - 'checksums': ['9841be5587bfb7cd1f2fe267b5e5ac04ce25e79d5cc77e5ef9a9c5abd101d7b1'], - }), ('Term::ReadLine::Gnu', '1.46', { 'modulename': 'Term::ReadLine', 'source_tmpl': 'Term-ReadLine-Gnu-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAYASHI'], 'checksums': ['b13832132e50366c34feac12ce82837c0a9db34ca530ae5d27db97cf9c964c7b'], + # make sure that library provided by ncurses dependency is used instead of libtermcap + 'preinstallopts': "sed -s 's/-ltermcap/-lncurses/g' Makefile.PL && ", }), ('ExtUtils::MakeMaker', '7.70', { 'source_tmpl': 'ExtUtils-MakeMaker-%(version)s.tar.gz', @@ -1926,7 +1923,12 @@ exts_list = [ 'runtest': False, # Single failure about a tainted PATH 'source_tmpl': 'PathTools-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/X/XS/XSAWYERX'], - 'checksums': ['a558503aa6b1f8c727c0073339081a77888606aa701ada1ad62dd9d8c3f945a2'], + 'patches': ['PathTools-3.75_fix-cwd_enoent-test.patch'], + 'checksums': [ + 'a558503aa6b1f8c727c0073339081a77888606aa701ada1ad62dd9d8c3f945a2', + {'PathTools-3.75_fix-cwd_enoent-test.patch': + '7a456a99d9b04a36359f3623f0deef8fe7f472c742f99cdcf0215c50afbbe7b1'}, + ], }), ('MIME::Base64', '3.16', { 'source_tmpl': 'MIME-Base64-%(version)s.tar.gz', diff --git a/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.38.2-GCCcore-13.3.0.eb b/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.38.2-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..cee5ad02ae6 --- /dev/null +++ b/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.38.2-GCCcore-13.3.0.eb @@ -0,0 +1,2155 @@ +easyblock = 'PerlBundle' + +name = 'Perl-bundle-CPAN' +version = '5.38.2' + +homepage = 'https://www.perl.org/' +description = """A set of common packages from CPAN""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +builddependencies = [ + ('binutils', '2.42'), + ('groff', '1.23.0'), +] + +dependencies = [ + ('Perl', version), + ('zlib', '1.3.1'), # for Net::SSLeay + ('expat', '2.6.2'), # for XML::Parser + ('ncurses', '6.5'), # for Term::ReadLine::Gnu + ('libreadline', '8.2'), # for Term::ReadLine::Gnu + ('OpenSSL', '3', '', SYSTEM), # required for Net::SSLeay +] + +# !! order of extensions is important !! +# extensions updated on 2024-07-08 +exts_list = [ + ('Config::General', '2.65', { + 'source_tmpl': 'Config-General-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TL/TLINDEN'], + 'checksums': ['4d6d5754be3a9f30906836f0cc10e554c8832e14e7a1341efb15b05d706fc58f'], + }), + ('HTTP::Date', '6.06', { + 'source_tmpl': 'HTTP-Date-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/O/OA/OALDERS'], + 'checksums': ['7b685191c6acc3e773d1fc02c95ee1f9fae94f77783175f5e78c181cc92d2b52'], + }), + ('File::Listing', '6.16', { + 'source_tmpl': 'File-Listing-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PL/PLICEASE'], + 'checksums': ['189b3a13fc0a1ba412b9d9ec5901e9e5e444cc746b9f0156d4399370d33655c6'], + }), + ('ExtUtils::Config', '0.009', { + 'source_tmpl': 'ExtUtils-Config-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + 'checksums': ['4ef84e73aad50a3be332885d2a3b12f3cab1b1e0bad24e88297a123b4f39f3ce'], + }), + ('ExtUtils::InstallPaths', '0.013', { + 'source_tmpl': 'ExtUtils-InstallPaths-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + 'checksums': ['65969d3ad8a3a2ea8ef5b4213ed5c2c83961bb5bd12f7ad35128f6bd5b684aa0'], + }), + ('ExtUtils::Helpers', '0.027', { + 'source_tmpl': 'ExtUtils-Helpers-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + 'checksums': ['9d592131dc5845a86dc28be9143f764e73cb62db06fedf50a895be1324b6cec5'], + }), + ('Test::Harness', '3.48', { + 'source_tmpl': 'Test-Harness-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + 'checksums': ['e73ff89c81c1a53f6baeef6816841b89d3384403ad97422a7da9d1eeb20ef9c5'], + }), + ('CPAN::Meta::Requirements', '2.143', { + 'source_tmpl': 'CPAN-Meta-Requirements-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS/'], + 'checksums': ['6ec7e4697bb5a8cea0ee3c8bd5d4b20ce086168a8084778d6e7a4c37356fdf8b'], + }), + ('CPAN::Requirements::Dynamic', '0.001', { + 'source_tmpl': 'CPAN-Requirements-Dynamic-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + 'checksums': ['4b590e712b9aca680c3631855ee16a50b84fa0227c362e13b237a75a01489ef5'], + }), + ('Module::Build::Tiny', '0.048', { + 'source_tmpl': 'Module-Build-Tiny-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + 'checksums': ['79a73e506fb7badabdf79137a45c6c5027daaf6f9ac3dcfb9d4ffcce92eb36bd'], + }), + ('aliased', '0.34', { + 'source_tmpl': 'aliased-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['c350524507cd827fab864e5d4c2cc350b1babaa12fa95aec0ca00843fcc7deeb'], + }), + ('Text::Glob', '0.11', { + 'source_tmpl': 'Text-Glob-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RC/RCLAMP'], + 'checksums': ['069ccd49d3f0a2dedb115f4bdc9fbac07a83592840953d1fcdfc39eb9d305287'], + }), + ('Regexp::Common', '2017060201', { + 'source_tmpl': 'Regexp-Common-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AB/ABIGAIL'], + 'checksums': ['ee07853aee06f310e040b6bf1a0199a18d81896d3219b9b35c9630d0eb69089b'], + }), + ('IO::String', '1.08', { + 'source_tmpl': 'IO-String-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + 'checksums': ['2a3f4ad8442d9070780e58ef43722d19d1ee21a803bf7c8206877a10482de5a0'], + }), + ('Data::Stag', '0.14', { + 'source_tmpl': 'Data-Stag-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CM/CMUNGALL'], + 'checksums': ['4ab122508d2fb86d171a15f4006e5cf896d5facfa65219c0b243a89906258e59'], + }), + ('GO::Utils', '0.15', { + 'source_tmpl': 'go-perl-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CM/CMUNGALL'], + 'checksums': ['423d26155ee85ca51ab2270cee59f4e85b193e57ac3a29aff827298c0a396b12'], + }), + ('Module::Pluggable', '5.2', { + 'source_tmpl': 'Module-Pluggable-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SI/SIMONW'], + 'checksums': ['b3f2ad45e4fd10b3fb90d912d78d8b795ab295480db56dc64e86b9fa75c5a6df'], + }), + ('Try::Tiny', '0.31', { + 'source_tmpl': 'Try-Tiny-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['3300d31d8a4075b26d8f46ce864a1d913e0e8467ceeba6655d5d2b2e206c11be'], + }), + ('Test::Fatal', '0.017', { + 'source_tmpl': 'Test-Fatal-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['37dfffdafb84b762efe96b02fb2aa41f37026c73e6b83590db76229697f3c4a6'], + }), + ('Test::Warnings', '0.033', { + 'source_tmpl': 'Test-Warnings-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['b9c375719f2c61c5f97aa5ee6cf4c901a972347c415969379b0b51f67c48bbcb'], + }), + ('Class::Inspector', '1.36', { + 'source_tmpl': 'Class-Inspector-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PL/PLICEASE'], + 'checksums': ['cc295d23a472687c24489d58226ead23b9fdc2588e522f0b5f0747741700694e'], + }), + ('File::ShareDir::Install', '0.14', { + 'source_tmpl': 'File-ShareDir-Install-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['8f9533b198f2d4a9a5288cbc7d224f7679ad05a7a8573745599789428bc5aea0'], + }), + ('File::ShareDir', '1.118', { + 'source_tmpl': 'File-ShareDir-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RE/REHSACK'], + 'checksums': ['3bb2a20ba35df958dc0a4f2306fc05d903d8b8c4de3c8beefce17739d281c958'], + }), + ('IPC::System::Simple', '1.30', { + 'source_tmpl': 'IPC-System-Simple-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JK/JKEENAN'], + 'checksums': ['22e6f5222b505ee513058fdca35ab7a1eab80539b98e5ca4a923a70a8ae9ba9e'], + }), + ('Importer', '0.026', { + 'source_tmpl': 'Importer-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + 'checksums': ['e08fa84e13cb998b7a897fc8ec9c3459fcc1716aff25cc343e36ef875891b0ef'], + }), + ('Term::Table', '0.018', { + 'source_tmpl': 'Term-Table-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + 'checksums': ['9159b9131ee6b3f3956b74f45422985553574babbfaeba60be5c17bc114ac011'], + }), + ('Scope::Guard', '0.21', { + 'source_tmpl': 'Scope-Guard-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CH/CHOCOLATE'], + 'checksums': ['8c9b1bea5c56448e2c3fadc65d05be9e4690a3823a80f39d2f10fdd8f777d278'], + }), + ('Sub::Info', '0.002', { + 'source_tmpl': 'Sub-Info-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + 'checksums': ['ea3056d696bdeff21a99d340d5570887d39a8cc47bff23adfc82df6758cdd0ea'], + }), + ('Test2::Require::Module', '0.000163', { + 'source_tmpl': 'Test2-Suite-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + 'checksums': ['e336c2d92d43c4f0068aa0d67019d56723ab82471e1bd9028300bb6a1602c0a9'], + }), + ('Test2::Plugin::NoWarnings', '0.10', { + 'source_tmpl': 'Test2-Plugin-NoWarnings-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + 'checksums': ['c97cb1122cc6e3e4a079059da71e12f65760bfb0671d19d25a7ec7c5f1f240fb'], + }), + ('Class::Tiny', '1.008', { + 'source_tmpl': 'Class-Tiny-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], + 'checksums': ['ee058a63912fa1fcb9a72498f56ca421a2056dc7f9f4b67837446d6421815615'], + }), + ('Path::Tiny', '0.146', { + 'source_tmpl': 'Path-Tiny-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], + 'checksums': ['861ef09bca68254e9ab24337bb6ec9d58593a792e9d68a27ee6bec2150f06741'], + }), + ('Test::Deep', '1.204', { + 'source_tmpl': 'Test-Deep-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['b6591f6ccdd853c7efc9ff3c5756370403211cffe46047f082b1cd1611a84e5f'], + }), + ('Test::File', '1.993', { + 'source_tmpl': 'Test-File-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BD/BDFOY'], + 'checksums': ['ef2ffe1aaec7b42d874ad411ec647547b9b9bc2f5fb93e49e3399488456afc7a'], + }), + ('Test::Needs', '0.002010', { + 'source_tmpl': 'Test-Needs-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG'], + 'checksums': ['923ffdc78fcba96609753e4bae26b0ba0186893de4a63cd5236e012c7c90e208'], + }), + ('Test::Requires', '0.11', { + 'source_tmpl': 'Test-Requires-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TOKUHIROM'], + 'checksums': ['4b88de549597eecddf7c3c38a4d0204a16f59ad804577b671896ac04e24e040f'], + }), + ('File::Copy::Recursive', '0.45', { + 'source_tmpl': 'File-Copy-Recursive-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DM/DMUEY'], + 'checksums': ['d3971cf78a8345e38042b208bb7b39cb695080386af629f4a04ffd6549df1157'], + }), + ('Test::File::ShareDir::Dist', '1.001002', { + 'source_tmpl': 'Test-File-ShareDir-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/K/KE/KENTNL'], + 'checksums': ['b33647cbb4b2f2fcfbde4f8bb4383d0ac95c2f89c4c5770eb691f1643a337aad'], + }), + ('CPAN::Meta::Check', '0.018', { + 'source_tmpl': 'CPAN-Meta-Check-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + 'checksums': ['f619d2df5ea0fd91c8cf83eb54acccb5e43d9e6ec1a3f727b3d0ac15d0cf378a'], + }), + ('Sub::Exporter::Progressive', '0.001013', { + 'source_tmpl': 'Sub-Exporter-Progressive-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/F/FR/FREW'], + 'checksums': ['d535b7954d64da1ac1305b1fadf98202769e3599376854b2ced90c382beac056'], + }), + ('Module::Runtime', '0.016', { + 'source_tmpl': 'Module-Runtime-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/Z/ZE/ZEFRAM'], + 'checksums': ['68302ec646833547d410be28e09676db75006f4aa58a11f3bdb44ffe99f0f024'], + }), + ('Module::Implementation', '0.09', { + 'source_tmpl': 'Module-Implementation-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + 'checksums': ['c15f1a12f0c2130c9efff3c2e1afe5887b08ccd033bd132186d1e7d5087fd66d'], + }), + ('B::Hooks::EndOfScope', '0.28', { + 'source_tmpl': 'B-Hooks-EndOfScope-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['edac77a17fc36620c8324cc194ce1fad2f02e9fcbe72d08ad0b2c47f0c7fd8ef'], + }), + ('Package::Stash', '0.40', { + 'source_tmpl': 'Package-Stash-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['5a9722c6d9cb29ee133e5f7b08a5362762a0b5633ff5170642a5b0686e95e066'], + }), + ('namespace::clean', '0.27', { + 'source_tmpl': 'namespace-clean-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RI/RIBASUSHI'], + 'checksums': ['8a10a83c3e183dc78f9e7b7aa4d09b47c11fb4e7d3a33b9a12912fd22e31af9d'], + }), + ('Sub::Identify', '0.14', { + 'source_tmpl': 'Sub-Identify-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RG/RGARCIA'], + 'checksums': ['068d272086514dd1e842b6a40b1bedbafee63900e5b08890ef6700039defad6f'], + }), + ('namespace::autoclean', '0.29', { + 'source_tmpl': 'namespace-autoclean-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['45ebd8e64a54a86f88d8e01ae55212967c8aa8fed57e814085def7608ac65804'], + }), + ('Eval::Closure', '0.14', { + 'source_tmpl': 'Eval-Closure-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DO/DOY'], + 'checksums': ['ea0944f2f5ec98d895bef6d503e6e4a376fea6383a6bc64c7670d46ff2218cad'], + }), + ('Exporter::Tiny', '1.006002', { + 'source_tmpl': 'Exporter-Tiny-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TOBYINK'], + 'checksums': ['6f295e2cbffb1dbc15bdb9dadc341671c1e0cd2bdf2d312b17526273c322638d'], + }), + ('Type::Tiny', '2.004000', { + 'source_tmpl': 'Type-Tiny-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TOBYINK'], + 'checksums': ['697e7f775edfc85f4cf07792d04fd19b09c25285f98f5938e8efc4f74507a128'], + }), + ('Class::Data::Inheritable', '0.09', { + 'source_tmpl': 'Class-Data-Inheritable-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RS/RSHERER'], + 'checksums': ['44088d6e90712e187b8a5b050ca5b1c70efe2baa32ae123e9bd8f59f29f06e4d'], + }), + ('Devel::StackTrace', '2.05', { + 'source_tmpl': 'Devel-StackTrace-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + 'checksums': ['63cb6196e986a7e578c4d28b3c780e7194835bfc78b68eeb8f00599d4444888c'], + }), + ('Exception::Class', '1.45', { + 'source_tmpl': 'Exception-Class-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + 'checksums': ['5482a77ef027ca1f9f39e1f48c558356e954936fc8fbbdee6c811c512701b249'], + }), + ('Role::Tiny', '2.002004', { + 'source_tmpl': 'Role-Tiny-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG'], + 'checksums': ['d7bdee9e138a4f83aa52d0a981625644bda87ff16642dfa845dcb44d9a242b45'], + }), + ('MRO::Compat', '0.15', { + 'source_tmpl': 'MRO-Compat-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG'], + 'checksums': ['0d4535f88e43babd84ab604866215fc4d04398bd4db7b21852d4a31b1c15ef61'], + }), + ('Sub::Quote', '2.006008', { + 'source_tmpl': 'Sub-Quote-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG'], + 'checksums': ['94bebd500af55762e83ea2f2bc594d87af828072370c7110c60c238a800d15b2'], + }), + ('Specio', '0.48', { + 'source_tmpl': 'Specio-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + 'checksums': ['0c85793580f1274ef08173079131d101f77b22accea7afa8255202f0811682b2'], + }), + ('Test::Without::Module', '0.22', { + 'source_tmpl': 'Test-Without-Module-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CO/CORION'], + 'checksums': ['27cde4394891028c7d8ecef22a2806308a3389597b70f6a9a421b4247e69052f'], + }), + ('Params::ValidationCompiler', '0.31', { + 'source_tmpl': 'Params-ValidationCompiler-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + 'checksums': ['7b6497173f1b6adb29f5d51d8cf9ec36d2f1219412b4b2410e9d77a901e84a6d'], + }), + ('DateTime::Locale', '1.42', { + 'source_tmpl': 'DateTime-Locale-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + 'checksums': ['7d8a138fa32faf24af30a1dbdee4dd11988ddb6a129138004d220b6cc4053cb0'], + }), + ('Class::Singleton', '1.6', { + 'source_tmpl': 'Class-Singleton-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHAY'], + 'checksums': ['27ba13f0d9512929166bbd8c9ef95d90d630fc80f0c9a1b7458891055e9282a4'], + }), + ('DateTime::TimeZone', '2.62', { + 'source_tmpl': 'DateTime-TimeZone-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + 'checksums': ['6214f9c9c8dfa2000bae912ef2b8ebc5b163a83a0b5b2a82705162dad63466fa'], + }), + ('Module::Build', '0.4234', { + 'source_tmpl': 'Module-Build-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + 'checksums': ['66aeac6127418be5e471ead3744648c766bd01482825c5b66652675f2bc86a8f'], + }), + ('Params::Validate', '1.31', { + 'source_tmpl': 'Params-Validate-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + 'checksums': ['1bf2518ef2c4869f91590e219f545c8ef12ed53cf313e0eb5704adf7f1b2961e'], + }), + ('List::MoreUtils::XS', '0.430', { + 'source_tmpl': 'List-MoreUtils-XS-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RE/REHSACK'], + 'checksums': ['e8ce46d57c179eecd8758293e9400ff300aaf20fefe0a9d15b9fe2302b9cb242'], + }), + ('List::MoreUtils', '0.430', { + 'source_tmpl': 'List-MoreUtils-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RE/REHSACK'], + 'checksums': ['63b1f7842cd42d9b538d1e34e0330de5ff1559e4c2737342506418276f646527'], + }), + ('DateTime', '1.65', { + 'source_tmpl': 'DateTime-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + 'checksums': ['0bfda7ff0253fb3d88cf4bdb5a14afb8cea24d147975d5bdf3c88b40e7ab140e'], + }), + ('Number::Compare', '0.03', { + 'source_tmpl': 'Number-Compare-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RC/RCLAMP'], + 'checksums': ['83293737e803b43112830443fb5208ec5208a2e6ea512ed54ef8e4dd2b880827'], + }), + ('File::Find::Rule', '0.34', { + 'source_tmpl': 'File-Find-Rule-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RC/RCLAMP'], + 'checksums': ['7e6f16cc33eb1f29ff25bee51d513f4b8a84947bbfa18edb2d3cc40a2d64cafe'], + }), + ('Params::Util', '1.102', { + 'source_tmpl': 'Params-Util-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RE/REHSACK'], + 'checksums': ['499bb1b482db24fda277a51525596ad092c2bd51dd508fa8fec2e9f849097402'], + }), + ('File::Find::Rule::Perl', '1.16', { + 'source_tmpl': 'File-Find-Rule-Perl-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['ae1886050d9ca21223c073e2870abdc80dc30e3f55289a11c37da3820a8321ff'], + }), + ('Readonly', '2.05', { + 'source_tmpl': 'Readonly-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SA/SANKO'], + 'checksums': ['4b23542491af010d44a5c7c861244738acc74ababae6b8838d354dfb19462b5e'], + }), + ('Git', '0.42', { + 'source_tmpl': 'Git-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MS/MSOUTH'], + 'checksums': ['9469a9f398f3a2bf2b0500566ee41d3ff6fae460412a137185767a1cc4783a6d'], + }), + ('File::Slurp::Tiny', '0.004', { + 'source_tmpl': 'File-Slurp-Tiny-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + 'checksums': ['452995beeabf0e923e65fdc627a725dbb12c9e10c00d8018c16d10ba62757f1e'], + }), + ('Tree::DAG_Node', '1.32', { + 'source_tmpl': 'Tree-DAG_Node-%(version)s.tgz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RS/RSAVAGE'], + 'checksums': ['22d9de3d6e6f4afd89e6d825c664f9482878bd49e29cb81342a707af40542d3d'], + }), + ('Template', '3.102', { + 'source_tmpl': 'Template-Toolkit-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TODDR'], + 'checksums': ['d161c89dee9b213a7c55709ea782e2dd5923dbd1215b9576612889e6e74a2e06'], + }), + ('DBI', '1.643', { + 'source_tmpl': 'DBI-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TI/TIMB'], + 'checksums': ['8a2b993db560a2c373c174ee976a51027dd780ec766ae17620c20393d2e836fa'], + 'pretestopts': 'LC_ALL=C ', # Test fails if run in localized environments + }), + ('DBD::SQLite', '1.74', { + 'source_tmpl': 'DBD-SQLite-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IS/ISHIGAKI'], + 'checksums': ['8994997d84b9feb4547795f78746c661fb72e3cb6a25dbdd789b731f5688a4dd'], + }), + ('Math::Bezier', '0.01', { + 'source_tmpl': 'Math-Bezier-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AB/ABW'], + 'checksums': ['11a815fc45fdf0efabb1822ab77faad8b9eea162572c5f0940c8ed7d56e6b8b8'], + }), + ('Archive::Extract', '0.88', { + 'source_tmpl': 'Archive-Extract-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + 'checksums': ['cffcf135cd0622287d3b02154f7d6716495449fcaed03966621948e25ea5f742'], + }), + ('DBIx::Simple', '1.37', { + 'source_tmpl': 'DBIx-Simple-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JU/JUERD'], + 'checksums': ['46d311aa2ce08907401c56119658426dbb044c5a40de73d9a7b79bf50390cae3'], + }), + ('Shell', '0.73', { + 'source_tmpl': 'Shell-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/F/FE/FERREIRA'], + 'checksums': ['f7dbebf65261ed0e5abd0f57052b64d665a1a830bab4c8bbc220f235bd39caf5'], + }), + ('Test::Simple', '1.302199', { + 'source_tmpl': 'Test-Simple-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + 'checksums': ['7b4b03cee7f9e928fe10e8a3efef02b2a286f0877979694b2a9ef99250bd8c5c'], + }), + ('Set::Scalar', '1.29', { + 'source_tmpl': 'Set-Scalar-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAVIDO'], + 'checksums': ['a3dc1526f3dde72d3c64ea00007b86ce608cdcd93567cf6e6e42dc10fdc4511d'], + }), + ('IO::Stringy', '2.113', { + 'source_tmpl': 'IO-Stringy-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CA/CAPOEIRAB'], + 'checksums': ['51220fcaf9f66a639b69d251d7b0757bf4202f4f9debd45bdd341a6aca62fe4e'], + }), + ('Encode::Locale', '1.05', { + 'source_tmpl': 'Encode-Locale-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + 'checksums': ['176fa02771f542a4efb1dbc2a4c928e8f4391bf4078473bd6040d8f11adb0ec1'], + }), + ('XML::SAX::Base', '1.09', { + 'source_tmpl': 'XML-SAX-Base-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GR/GRANTM'], + 'checksums': ['66cb355ba4ef47c10ca738bd35999723644386ac853abbeb5132841f5e8a2ad0'], + }), + ('XML::NamespaceSupport', '1.12', { + 'source_tmpl': 'XML-NamespaceSupport-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PE/PERIGRIN'], + 'checksums': ['47e995859f8dd0413aa3f22d350c4a62da652e854267aa0586ae544ae2bae5ef'], + }), + ('XML::SAX', '1.02', { + 'source_tmpl': 'XML-SAX-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GR/GRANTM'], + 'checksums': ['4506c387043aa6a77b455f00f57409f3720aa7e553495ab2535263b4ed1ea12a'], + }), + ('Test::LeakTrace', '0.17', { + 'source_tmpl': 'Test-LeakTrace-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEEJO'], + 'checksums': ['777d64d2938f5ea586300eef97ef03eacb43d4c1853c9c3b1091eb3311467970'], + }), + ('Sub::Uplevel', '0.2800', { + 'source_tmpl': 'Sub-Uplevel-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], + 'checksums': ['b4f3f63b80f680a421332d8851ddbe5a8e72fcaa74d5d1d98f3c8cc4a3ece293'], + }), + ('Test::Exception', '0.43', { + 'source_tmpl': 'Test-Exception-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + 'checksums': ['156b13f07764f766d8b45a43728f2439af81a3512625438deab783b7883eb533'], + }), + ('Text::Aligner', '0.16', { + 'source_tmpl': 'Text-Aligner-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHLOMIF'], + 'checksums': ['5c857dbce586f57fa3d7c4ebd320023ab3b2963b2049428ae01bd3bc4f215725'], + }), + ('Text::Table', '1.135', { + 'source_tmpl': 'Text-Table-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHLOMIF'], + 'checksums': ['fca3c16e83127f7c44dde3d3f7e3c73ea50d109a1054445de8082fea794ca5d2'], + }), + ('MIME::Types', '2.26', { + 'source_tmpl': 'MIME-Types-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MARKOV'], + 'checksums': ['bc738483cb4cdb47d61e85fe9304fa929aa9ab927e3171ec2ba2ab1cd7cefdff'], + }), + ('Cwd::Guard', '0.05', { + 'source_tmpl': 'Cwd-Guard-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/K/KA/KAZEBURO'], + 'checksums': ['7afc7ca2b9502e440241938ad97a3e7ebd550180ebd6142e1db394186b268e77'], + }), + ('Capture::Tiny', '0.48', { + 'source_tmpl': 'Capture-Tiny-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], + 'checksums': ['6c23113e87bad393308c90a207013e505f659274736638d8c79bac9c67cc3e19'], + }), + ('File::Copy::Recursive::Reduced', '0.008', { + 'source_tmpl': 'File-Copy-Recursive-Reduced-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JK/JKEENAN'], + 'checksums': ['462bd66bf55e74b78f29ebdc9626af622d4f0115b5191b03167e82164db98f5a'], + }), + ('Module::Build::XSUtil', '0.19', { + 'source_tmpl': 'Module-Build-XSUtil-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HI/HIDEAKIO'], + 'checksums': ['9063b3c346edeb422807ffe49ffb23038c4f900d4a77b845ce4b53d97bf29400'], + }), + ('Tie::Function', '0.02', { + 'source_tmpl': 'Tie-Function-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAVIDNICO/handy_tied_functions'], + 'checksums': ['0b1617af218dfab911ba0fbd72210529a246efe140332da77fe3e03d11000117'], + }), + ('Number::Format', '1.76', { + 'source_tmpl': 'Number-Format-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['0e0060eb363635a885706c6a26f5fcaafeae759f7b2acae49dda70e195dd44d6'], + }), + ('Template::Plugin::Number::Format', '1.06', { + 'source_tmpl': 'Template-Plugin-Number-Format-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DARREN'], + 'checksums': ['0865836a1bcbc34d4a0ee34b5ccc14d7b511f1fd300bf390f002dac349539843'], + }), + ('HTML::Tagset', '3.24', { + 'source_tmpl': 'HTML-Tagset-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PE/PETDANCE'], + 'checksums': ['eb89e145a608ed1f8f141a57472ee5f69e67592a432dcd2e8b1dbb445f2b230b'], + }), + ('URI', '5.28', { + 'source_tmpl': 'URI-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/O/OA/OALDERS'], + 'checksums': ['e7985da359b15efd00917fa720292b711c396f2f9f9a7349e4e7dec74aa79765'], + }), + ('B::COW', '0.007', { + 'source_tmpl': 'B-COW-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AT/ATOOMIC'], + 'checksums': ['1290daf227e8b09889a31cf182e29106f1cf9f1a4e9bf7752f9de92ed1158b44'], + }), + ('Clone', '0.46', { + 'source_tmpl': 'Clone-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GARU'], + 'checksums': ['aadeed5e4c8bd6bbdf68c0dd0066cb513e16ab9e5b4382dc4a0aafd55890697b'], + }), + ('IO::HTML', '1.004', { + 'source_tmpl': 'IO-HTML-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CJ/CJM'], + 'checksums': ['c87b2df59463bbf2c39596773dfb5c03bde0f7e1051af339f963f58c1cbd8bf5'], + }), + ('LWP::MediaTypes', '6.04', { + 'source_tmpl': 'LWP-MediaTypes-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/O/OA/OALDERS'], + 'checksums': ['8f1bca12dab16a1c2a7c03a49c5e58cce41a6fec9519f0aadfba8dad997919d9'], + }), + ('HTTP::Message', '6.46', { + 'source_tmpl': 'HTTP-Message-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/O/OA/OALDERS'], + 'checksums': ['e27443434150d2d1259bb1e5c964429f61559b0ae34b5713090481994936e2a5'], + }), + ('HTML::Parser', '3.82', { + 'source_tmpl': 'HTML-Parser-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/O/OA/OALDERS'], + 'checksums': ['5b1f20dd0e471a049c13a53d0fcd0442f58518889180536c6f337112c9a430d8'], + }), + ('Date::Handler', '1.2', { + 'source_tmpl': 'Date-Handler-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BB/BBEAUSEJ'], + 'checksums': ['c36fd2b68d48c2e17417bf2873c78820f3ae02460fdf5976b8eeab887d59e16c'], + }), + ('XML::Parser', '2.47', { + 'source_tmpl': 'XML-Parser-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TODDR'], + 'checksums': ['ad4aae643ec784f489b956abe952432871a622d4e2b5c619e8855accbfc4d1d8'], + }), + ('Data::Grove', '0.08', { + 'source_tmpl': 'libxml-perl-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/K/KM/KMACLEOD'], + 'checksums': ['4571059b7b5d48b7ce52b01389e95d798bf5cf2020523c153ff27b498153c9cb'], + }), + ('Class::ISA', '0.36', { + 'source_tmpl': 'Class-ISA-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SM/SMUELLER'], + 'checksums': ['8816f34e9a38e849a10df756030dccf9fe061a196c11ac3faafd7113c929b964'], + }), + ('DBIx::ContextualFetch', '1.03', { + 'source_tmpl': 'DBIx-ContextualFetch-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TM/TMTM'], + 'checksums': ['85e2f805bfc81cd738c294316b27a515397036f397a0ff1c6c8d754c38530306'], + }), + ('Ima::DBI', '0.35', { + 'source_tmpl': 'Ima-DBI-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PE/PERRIN'], + 'checksums': ['8b481ceedbf0ae4a83effb80581550008bfdd3885ef01145e3733c7097c00a08'], + }), + ('Tie::IxHash', '1.23', { + 'source_tmpl': 'Tie-IxHash-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CH/CHORNY'], + 'checksums': ['fabb0b8c97e67c9b34b6cc18ed66f6c5e01c55b257dcf007555e0b027d4caf56'], + }), + ('Parse::RecDescent', '1.967015', { + 'source_tmpl': 'Parse-RecDescent-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JT/JTBRAUN'], + 'checksums': ['1943336a4cb54f1788a733f0827c0c55db4310d5eae15e542639c9dd85656e37'], + }), + ('GO', '0.04', { + 'runtest': False, # Problem with indirect dependency DBD::Pg + 'source_tmpl': 'go-db-perl-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SJ/SJCARBON'], + 'checksums': ['8eb73d591ad767e7cf26def40cffd84833875f1ad51e456960b9ed73dc23641b'], + }), + ('Class::Trigger', '0.15', { + 'source_tmpl': 'Class-Trigger-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MI/MIYAGAWA'], + 'checksums': ['b7a878d44dea67d64df2ca18020d9d868a95596debd16f1a264874209332b07f'], + }), + ('Class::Accessor', '0.51', { + 'source_tmpl': 'Class-Accessor-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/K/KA/KASEI'], + 'checksums': ['bf12a3e5de5a2c6e8a447b364f4f5a050bf74624c56e315022ae7992ff2f411c'], + }), + ('UNIVERSAL::moniker', '0.08', { + 'source_tmpl': 'UNIVERSAL-moniker-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/K/KA/KASEI'], + 'checksums': ['94ce27a546cd57cb52e080a8f2533a7cc2350028388582485bd1039a37871f9c'], + }), + ('Class::DBI', 'v3.0.17', { + 'source_tmpl': 'Class-DBI-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TM/TMTM'], + 'checksums': ['541354fe361c56850cb11261f6ca089a14573fa764792447444ff736ae626206'], + }), + ('Class::DBI::SQLite', '0.11', { + 'source_tmpl': 'Class-DBI-SQLite-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MI/MIYAGAWA'], + 'checksums': ['c4661b00afb7e53c97ac36e13f34dde43c1a93540a2f4ff97e6182b0c731e4e7'], + }), + ('File::Slurper', '0.014', { + 'source_tmpl': 'File-Slurper-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + 'checksums': ['d5a36487339888c3cd758e648160ee1d70eb4153cacbaff57846dbcefb344b0c'], + }), + ('Pod::POM', '2.01', { + 'source_tmpl': 'Pod-POM-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NE/NEILB'], + 'checksums': ['1b50fba9bbdde3ead192beeba0eaddd0c614e3afb1743fa6fff805f57c56f7f4'], + }), + ('Math::Round', '0.08', { + 'source_tmpl': 'Math-Round-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NE/NEILB'], + 'checksums': ['7b4d2775ad3b859a5fd61f7f3fc5cfba42b1a10df086d2ed15a0ae712c8fd402'], + }), + ('Algorithm::Diff', '1.201', { + 'source_tmpl': 'Algorithm-Diff-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['0022da5982645d9ef0207f3eb9ef63e70e9713ed2340ed7b3850779b0d842a7d'], + }), + ('Text::Diff', '1.45', { + 'source_tmpl': 'Text-Diff-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NE/NEILB'], + 'checksums': ['e8baa07b1b3f53e00af3636898bbf73aec9a0ff38f94536ede1dbe96ef086f04'], + }), + ('Log::Message', '0.08', { + 'source_tmpl': 'Log-Message-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + 'checksums': ['bd697dd62aaf26d118e9f0a0813429deb1c544e4501559879b61fcbdfe99fe46'], + }), + ('Log::Message::Simple', '0.10', { + 'source_tmpl': 'Log-Message-Simple-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + 'checksums': ['aa12d1a4c0ac260b94d448fa01feba242a8a85cb6cbfdc66432e3b5b468add96'], + }), + ('Net::SSLeay', '1.94', { + 'preconfigopts': "export OPENSSL_PREFIX=$EBROOTOPENSSL && ", + 'source_tmpl': 'Net-SSLeay-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CH/CHRISN'], + 'checksums': ['9d7be8a56d1bedda05c425306cc504ba134307e0c09bda4a788c98744ebcd95d'], + }), + ('IO::Socket::SSL', '2.087', { + 'source_tmpl': 'IO-Socket-SSL-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SU/SULLR'], + 'checksums': ['936a46c58312df272313fedb4bb39faea7481629c163d83a8cdd283a0e28c578'], + }), + ('Fennec::Lite', '0.004', { + 'source_tmpl': 'Fennec-Lite-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + 'checksums': ['dce28e3932762c2ff92aa52d90405c06e898e81cb7b164ccae8966ae77f1dcab'], + }), + ('Meta::Builder', '0.004', { + 'source_tmpl': 'Meta-Builder-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + 'checksums': ['acb499aa7206eb9db21eb85357a74521bfe3bdae4a6416d50a7c75b939cf56fe'], + }), + ('Exporter::Declare', '0.114', { + 'source_tmpl': 'Exporter-Declare-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + 'checksums': ['4bd70d6ca76f6f6ba7e4c618d4ac93b8593a58f1233ccbe18b10f5f204f1d4e4'], + }), + ('Mouse', 'v2.5.10', { + 'source_tmpl': 'Mouse-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SK/SKAJI'], + 'checksums': ['ce8dc23946153a467ff09765167ee2590f5c502120f48a2d9441733f39aa32ee'], + }), + ('Test::Version', '2.09', { + 'source_tmpl': 'Test-Version-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PL/PLICEASE'], + 'checksums': ['9ce1dd2897a5f30e1b7f8966ec66f57d8d8f280f605f28c7ca221fa79aca38e0'], + }), + ('Class::Method::Modifiers', '2.15', { + 'source_tmpl': 'Class-Method-Modifiers-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['65cd85bfe475d066e9186f7a8cc636070985b30b0ebb1cde8681cf062c2e15fc'], + }), + ('Moo', '2.005005', { + 'source_tmpl': 'Moo-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG'], + 'checksums': ['fb5a2952649faed07373f220b78004a9c6aba387739133740c1770e9b1f4b108'], + }), + ('Data::Dumper::Concise', '2.023', { + 'source_tmpl': 'Data-Dumper-Concise-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['a6c22f113caf31137590def1b7028a7e718eface3228272d0672c25e035d5853'], + }), + ('DBIx::Admin::CreateTable', '2.11', { + 'source_tmpl': 'DBIx-Admin-CreateTable-%(version)s.tgz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RS/RSAVAGE'], + 'checksums': ['07b1427fbc15455657ca57217749004162a50c04abb243022a5b479e4b2a5912'], + }), + ('Config::Tiny', '2.30', { + 'source_tmpl': 'Config-Tiny-%(version)s.tgz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RS/RSAVAGE'], + 'checksums': ['b2f7345619b3b8e636dd39ea010731c9dc2bfb8f022bcbd86ae6ad17866e110d'], + }), + ('File::Slurp', '9999.32', { + 'source_tmpl': 'File-Slurp-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CA/CAPOEIRAB'], + 'checksums': ['4c3c21992a9d42be3a79dd74a3c83d27d38057269d65509a2f555ea0fb2bc5b0'], + }), + ('DBIx::Admin::DSNManager', '2.02', { + 'source_tmpl': 'DBIx-Admin-DSNManager-%(version)s.tgz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RS/RSAVAGE'], + 'checksums': ['c25511f42328ccb606a0cd78413a74181c87fb37a382d38aa3fad106b540adcb'], + }), + ('Lingua::EN::PluralToSingular', '0.21', { + 'source_tmpl': 'Lingua-EN-PluralToSingular-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BK/BKB'], + 'checksums': ['f8a8b7de28c25c96190d7f48c90b5ad9b9bf517f3835c77641f0e8fa546c0d1d'], + }), + ('Test::Warn', '0.37', { + 'source_tmpl': 'Test-Warn-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BIGJ'], + 'checksums': ['98ca32e7f2f5ea89b8bfb9a0609977f3d153e242e2e51705126cb954f1a06b57'], + }), + ('Test::Differences', '0.71', { + 'runtest': False, # Cryptic test failing + 'source_tmpl': 'Test-Differences-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DC/DCANTRELL'], + 'checksums': ['cac16a56cd843b0809e5b49199d60d75a8dbad7ca9a08380dbf3f5cc3aaa38d9'], + }), + ('Test::Most', '0.38', { + 'source_tmpl': 'Test-Most-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/O/OV/OVID'], + 'checksums': ['089eb894f7bace4c37c6334e0e290eb20338ee10223af0c82cbe7281c78382df'], + }), + ('Const::Fast', '0.014', { + 'source_tmpl': 'Const-Fast-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + 'checksums': ['f805953a08c57846a16a4d85d7b766398afaf7c36c1465fcb1dea09e5fa394db'], + }), + ('Ref::Util', '0.204', { + 'source_tmpl': 'Ref-Util-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AR/ARC'], + 'checksums': ['415fa73dbacf44f3d5d79c14888cc994562720ab468e6f71f91cd1f769f105e1'], + }), + ('Class::XSAccessor', '1.19', { + 'source_tmpl': 'Class-XSAccessor-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SM/SMUELLER'], + 'checksums': ['99c56b395f1239af19901f2feeb125d9ecb4e351a0d80daa9529211a4700a6f2'], + }), + ('Hash::Objectify', '0.008', { + 'source_tmpl': 'Hash-Objectify-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], + 'checksums': ['236d5829cdebf3ba648d34e1295cd9099a20506d8d0284668e617e0058cebeed'], + }), + ('Const::Exporter', 'v1.2.3', { + 'source_tmpl': 'Const-Exporter-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RR/RRWO'], + 'checksums': ['53e59b4764aebcf79bbed533ab5a6107339fe516b7f2f607b1bae8dd9dcf7015'], + }), + ('HTML::Entities::Interpolate', '1.10', { + 'source_tmpl': 'HTML-Entities-Interpolate-%(version)s.tgz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RS/RSAVAGE'], + 'checksums': ['f15a9df92c282419f7010964aca1ada844ddfae7afc735cd2ba1bb20883e955c'], + }), + ('List::SomeUtils', '0.59', { + 'source_tmpl': 'List-SomeUtils-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + 'checksums': ['fab30372e4c67bf5a46062da38d1d0c8756279feada866eb439fa29571a2dc7b'], + }), + ('List::UtilsBy', '0.12', { + 'source_tmpl': 'List-UtilsBy-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PE/PEVANS'], + 'checksums': ['fff1281fd469fe982b1a58044becfd970f313bff3a26e1c7b2b3f4c0a5ed71e0'], + }), + ('List::AllUtils', '0.19', { + 'source_tmpl': 'List-AllUtils-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + 'checksums': ['30a8146ab21a7787b8c56d5829cf9a7f2b15276d3b3fca07336ac38d3002ffbc'], + }), + ('Unicode::EastAsianWidth', '12.0', { + 'source_tmpl': 'Unicode-EastAsianWidth-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AU/AUDREYT'], + 'checksums': ['2a5bfd926c4fe5f77e6137da2c31ac2545282ae5fec6e9af0fdd403555a90ff4'], + }), + ('String::TtyLength', '0.03', { + 'source_tmpl': 'String-TtyLength-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NE/NEILB'], + 'checksums': ['4fedaf72028511d80eb6afba523993e9aaa245d7af558345d5d4ed46e2e82ce1'], + }), + ('Text::Table::Manifold', '1.03', { + 'source_tmpl': 'Text-Table-Manifold-%(version)s.tgz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RS/RSAVAGE'], + 'checksums': ['e680713169557b0768952fa6932f25576a61dccfb96bd9036dcf6fcefb35e09e'], + }), + ('DBIx::Admin::TableInfo', '3.04', { + 'source_tmpl': 'DBIx-Admin-TableInfo-%(version)s.tgz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RS/RSAVAGE'], + 'checksums': ['b9625992683b97378bea0947773f50e3c9f81974048b84f4c3422cae7e6082f4'], + }), + ('Net::HTTP', '6.23', { + 'runtest': False, # Fragile tests + 'source_tmpl': 'Net-HTTP-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/O/OA/OALDERS'], + 'checksums': ['0d65c09dd6c8589b2ae1118174d3c1a61703b6ecfc14a3442a8c74af65e0c94e'], + }), + ('Clone::Choose', '0.010', { + 'source_tmpl': 'Clone-Choose-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HE/HERMES'], + 'checksums': ['5623481f58cee8edb96cd202aad0df5622d427e5f748b253851dfd62e5123632'], + }), + ('Hash::Merge', '0.302', { + 'source_tmpl': 'Hash-Merge-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HE/HERMES'], + 'checksums': ['ae0522f76539608b61dde14670e79677e0f391036832f70a21f31adde2538644'], + }), + ('SQL::Abstract', '2.000001', { + 'source_tmpl': 'SQL-Abstract-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MS/MSTROUT'], + 'checksums': ['35a642662c349420d44be6e0ef7d8765ea743eb12ad14399aa3a232bb94e6e9a'], + }), + ('HTML::Form', '6.11', { + 'source_tmpl': 'HTML-Form-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SI/SIMBABQUE'], + 'checksums': ['43bfaa7087393487d2d51261a1aa7f6f81a97b1d8fef7a48fcf6ef32b16d6454'], + }), + ('IPC::Run', '20231003.0', { + 'source_tmpl': 'IPC-Run-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TODDR'], + 'checksums': ['eb25bbdf5913d291797ef1bfe998f15130b455d3ed02aacde6856f0b25e4fe57'], + }), + ('File::Remove', '1.61', { + 'source_tmpl': 'File-Remove-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHLOMIF'], + 'checksums': ['fd857f585908fc503461b9e48b3c8594e6535766bc14beb17c90ba58d5dc4975'], + }), + ('YAML::Tiny', '1.74', { + 'source_tmpl': 'YAML-Tiny-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['7b38ca9f5d3ce24230a6b8bdc1f47f5b2db348e7f7f9666c26f5955636e33d6c'], + }), + ('Module::Install', '1.21', { + 'source_tmpl': 'Module-Install-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['fbf91007f30565f3920e106055fd0d4287981d5e7dad8b35323ce4b733f15a7b'], + }), + ('Test::ClassAPI', '1.07', { + 'source_tmpl': 'Test-ClassAPI-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['30e9dbfc5e0cc2ee14eae8f3465a908a710daecbd0a3ebdb2888fc4504fa18aa'], + }), + ('HTTP::Tiny', '0.088', { + 'source_tmpl': 'HTTP-Tiny-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], + 'checksums': ['7ce6367e861883b6868d6dd86168af33524717d8cc94100c2abf9bd86a82b4d8'], + }), + ('Sub::Install', '0.929', { + 'source_tmpl': 'Sub-Install-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['80b1e281d8cd3b2b31dac711f5c8a1657a87cd80bbe69af3924bcbeb4e5db077'], + }), + ('Package::DeprecationManager', '0.18', { + 'source_tmpl': 'Package-DeprecationManager-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + 'checksums': ['b68d3f0ced55b7615fddbb6029b89f92a34fe0dd8c6fd6bceffc157d56834fe8'], + }), + ('Digest::SHA1', '2.13', { + 'source_tmpl': 'Digest-SHA1-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + 'checksums': ['68c1dac2187421f0eb7abf71452a06f190181b8fc4b28ededf5b90296fb943cc'], + }), + ('Date::Language', '2.33', { + 'source_tmpl': 'TimeDate-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AT/ATOOMIC'], + 'checksums': ['c0b69c4b039de6f501b0d9f13ec58c86b040c1f7e9b27ef249651c143d605eb2'], + }), + ('version', '0.9932', { + 'source_tmpl': 'version-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + 'checksums': ['e7b5e8fcb8dfd1d6147b931a382e9dc377b3485ade18bea342dad11226be6f7f'], + }), + ('XML::Bare', '0.53', { + 'source_tmpl': 'XML-Bare-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CO/CODECHILD'], + 'checksums': ['865e198e98d904be1683ef5a53a4948f02dabdacde59fc554a082ffbcc5baefd'], + }), + ('Dist::CheckConflicts', '0.11', { + 'source_tmpl': 'Dist-CheckConflicts-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DO/DOY'], + 'checksums': ['ea844b9686c94d666d9d444321d764490b2cde2f985c4165b4c2c77665caedc4'], + }), + ('Sub::Name', '0.27', { + 'source_tmpl': 'Sub-Name-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['ecf36fba1c47ca93e1daa394968ed39c4186867459d9cd173c421e2b972043e8'], + }), + ('Time::Piece', '1.3401', { + 'source_tmpl': 'Time-Piece-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ES/ESAYM'], + 'checksums': ['4b55b7bb0eab45cf239a54dfead277dfa06121a43e63b3fce0853aecfdb04c27'], + }), + ('Digest::HMAC', '1.04', { + 'source_tmpl': 'Digest-HMAC-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AR/ARODLAND'], + 'checksums': ['d6bc8156aa275c44d794b7c18f44cdac4a58140245c959e6b19b2c3838b08ed4'], + }), + ('HTTP::Negotiate', '6.01', { + 'source_tmpl': 'HTTP-Negotiate-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + 'checksums': ['1c729c1ea63100e878405cda7d66f9adfd3ed4f1d6cacaca0ee9152df728e016'], + }), + ('Email::Date::Format', '1.008', { + 'source_tmpl': 'Email-Date-Format-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['432b7c83ff88749af128003f5257c573aec1a463418db90ed22843cbbc258b4f'], + }), + ('MIME::Lite', '3.033', { + 'source_tmpl': 'MIME-Lite-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['78a279f1d2e242551c347ef97a13fc675766602cb84c2a80c569400f4f368bab'], + }), + ('Crypt::Rijndael', '1.16', { + 'source_tmpl': 'Crypt-Rijndael-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + 'checksums': ['6540085e3804b82a6f0752c1122cf78cadd221990136dd6fd4c097d056c84d40'], + }), + ('B::Lint', '1.20', { + 'runtest': False, # One failing subtest + 'source_tmpl': 'B-Lint-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['dc49408964fd8b7963859c92e013f0b9f92f74be5a7c2a78e3996279827c10b3'], + }), + ('Canary::Stability', '2013', { + 'source_tmpl': 'Canary-Stability-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/ML/MLEHMANN'], + 'checksums': ['a5c91c62cf95fcb868f60eab5c832908f6905221013fea2bce3ff57046d7b6ea'], + }), + ('AnyEvent', '7.17', { + 'source_tmpl': 'AnyEvent-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/ML/MLEHMANN'], + 'checksums': ['50beea689c098fe4aaeb83806c40b9fe7f946d5769acf99f849f099091a4b985'], + }), + ('Object::Accessor', '0.48', { + 'source_tmpl': 'Object-Accessor-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + 'checksums': ['76cb824a27b6b4e560409fcf6fd5b3bfbbd38b72f1f3d37ed0b54bd9c0baeade'], + }), + ('Data::UUID', '1.227', { + 'source_tmpl': 'Data-UUID-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GT/GTERMARS'], + 'checksums': ['95bda7276265f57bc48ffdeddec5ef28cd6f765e3a183757fa5f09f0ce6b98ac'], + }), + ('Test::Pod', '1.52', { + 'source_tmpl': 'Test-Pod-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['60a8dbcc60168bf1daa5cc2350236df9343e9878f4ab9830970a5dde6fe8e5fc'], + }), + ('AppConfig', '1.71', { + 'source_tmpl': 'AppConfig-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NE/NEILB'], + 'checksums': ['1177027025ecb09ee64d9f9f255615c04db5e14f7536c344af632032eb887b0f'], + }), + ('Net::SMTP::SSL', '1.04', { + 'source_tmpl': 'Net-SMTP-SSL-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['7b29c45add19d3d5084b751f7ba89a8e40479a446ce21cfd9cc741e558332a00'], + }), + ('XML::Tiny', '2.07', { + 'source_tmpl': 'XML-Tiny-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DC/DCANTRELL'], + 'checksums': ['ce39fcb53e0fe9f1cbcd86ddf152e1db48566266b70ec0769ef364eeabdd8941'], + }), + ('HTML::Tree', '5.07', { + 'source_tmpl': 'HTML-Tree-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/K/KE/KENTNL'], + 'checksums': ['f0374db84731c204b86c1d5b90975fef0d30a86bd9def919343e554e31a9dbbf'], + }), + ('Devel::GlobalDestruction', '0.14', { + 'source_tmpl': 'Devel-GlobalDestruction-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG'], + 'checksums': ['34b8a5f29991311468fe6913cadaba75fd5d2b0b3ee3bb41fe5b53efab9154ab'], + }), + ('WWW::RobotRules', '6.02', { + 'source_tmpl': 'WWW-RobotRules-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + 'checksums': ['46b502e7a288d559429891eeb5d979461dd3ecc6a5c491ead85d165b6e03a51e'], + }), + ('IO::Tty', '1.20', { + 'source_tmpl': 'IO-Tty-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TODDR'], + 'checksums': ['b15309fc85623893289cb9b2b88dfa9ed1e69156b75f29938553a45be6d730af'], + }), + ('Expect', '1.38', { + 'source_tmpl': 'Expect-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JA/JACOBY'], + 'checksums': ['7b1048335f327958903867cea079dc072ea07f4eafae1b40c2e6f25db21686c0'], + }), + ('Term::UI', '0.50', { + 'source_tmpl': 'Term-UI-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + 'checksums': ['60bfdd6d4c158b88d370133fc65b20485a36a45b12d906000b81c78ca524163d'], + }), + ('Net::SNMP', 'v6.0.1', { + 'source_tmpl': 'Net-SNMP-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DT/DTOWN'], + 'checksums': ['14c37bc1cbb3f3cdc7d6c13e0f27a859f14cdcfd5ea54a0467a88bc259b0b741'], + }), + ('XML::Filter::BufferText', '1.01', { + 'source_tmpl': 'XML-Filter-BufferText-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RB/RBERJON'], + 'checksums': ['8fd2126d3beec554df852919f4739e689202cbba6a17506e9b66ea165841a75c'], + }), + ('XML::SAX::Writer', '0.57', { + 'source_tmpl': 'XML-SAX-Writer-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PE/PERIGRIN'], + 'checksums': ['3d61d07ef43b0126f5b4de4f415a256fa859fa88dc4fdabaad70b7be7c682cf0'], + }), + ('Statistics::Descriptive', '3.0801', { + 'source_tmpl': 'Statistics-Descriptive-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHLOMIF'], + 'checksums': ['047b70a63fdcaa916168e0ff2d58e155e0ebbc68ed4ccbd73a7213dca3028f65'], + }), + ('Data::OptList', '0.114', { + 'source_tmpl': 'Data-OptList-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['9fd1093b917a21fb79ae1607db53d113b4e0ad8fe0ae776cb077a7e50044fdf3'], + }), + ('Class::Load', '0.25', { + 'source_tmpl': 'Class-Load-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['2a48fa779b5297e56156380e8b32637c6c58decb4f4a7f3c7350523e11275f8f'], + }), + ('HTTP::Daemon', '6.16', { + 'source_tmpl': 'HTTP-Daemon-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/O/OA/OALDERS'], + 'checksums': ['b38d092725e6fa4e0c4dc2a47e157070491bafa0dbe16c78a358e806aa7e173d'], + }), + ('Test::RequiresInternet', '0.05', { + 'source_tmpl': 'Test-RequiresInternet-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MALLEN'], + 'checksums': ['bba7b32a1cc0d58ce2ec20b200a7347c69631641e8cae8ff4567ad24ef1e833e'], + }), + ('HTTP::Cookies', '6.11', { + 'source_tmpl': 'HTTP-Cookies-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/O/OA/OALDERS'], + 'checksums': ['8c9a541a4a39f6c0c7e3d0b700b05dfdb830bd490a1b1942a7dedd1b50d9a8c8'], + }), + ('HTTP::CookieJar', '0.014', { + 'source_tmpl': 'HTTP-CookieJar-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], + 'checksums': ['7094ea5c91f536d263b85e83ab4e9a963e11c4408ce08ecae553fa9c0cc47e73'], + }), + ('LWP::Simple', '6.77', { + 'source_tmpl': 'libwww-perl-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/O/OA/OALDERS'], + 'checksums': ['94a907d6b3ea8d966ef43deffd4fa31f5500142b4c00489bfd403860a5f060e4'], + }), + ('Time::Piece::MySQL', '0.06', { + 'source_tmpl': 'Time-Piece-MySQL-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/K/KA/KASEI'], + 'checksums': ['319601feec17fae344988a5ee91cfc6a0bcfe742af77dba254724c3268b2a60f'], + }), + ('Package::Stash::XS', '0.30', { + 'source_tmpl': 'Package-Stash-XS-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['26bad65c1959c57379b3e139dc776fbec5f702906617ef27cdc293ddf1239231'], + }), + ('Want', '0.29', { + 'source_tmpl': 'Want-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RO/ROBIN'], + 'checksums': ['b4e4740b8d4cb783591273c636bd68304892e28d89e88abf9273b1de17f552f7'], + }), + ('Set::Array', '0.30', { + 'source_tmpl': 'Set-Array-%(version)s.tgz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RS/RSAVAGE'], + 'checksums': ['d9f024c8e3637feccdebcf6479b6754b6c92f1209f567feaf0c23818af31ee3c'], + }), + ('boolean', '0.46', { + 'source_tmpl': 'boolean-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IN/INGY'], + 'checksums': ['95c088085c3e83bf680fe6ce16d8264ec26310490f7d1680e416ea7a118f156a'], + }), + ('Test::NoWarnings', '1.06', { + 'source_tmpl': 'Test-NoWarnings-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG'], + 'checksums': ['c2dc51143b7eb63231210e27df20d2c8393772e0a333547ec8b7a205ed62f737'], + }), + ('Crypt::DES', '2.07', { + 'source_tmpl': 'Crypt-DES-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DP/DPARIS'], + 'checksums': ['2db1ebb5837b4cb20051c0ee5b733b4453e3137df0a92306034c867621edd7e7'], + }), + ('XML::XPath', '1.48', { + 'source_tmpl': 'XML-XPath-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MANWAR'], + 'checksums': ['7bc75be36b239e5b2e700a9570d2b53b43093d467f2abe6a743f9ff9093790cd'], + }), + ('JSON', '4.10', { + 'source_tmpl': 'JSON-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IS/ISHIGAKI'], + 'checksums': ['df8b5143d9a7de99c47b55f1a170bd1f69f711935c186a6dc0ab56dd05758e35'], + }), + ('Sub::Exporter', '0.991', { + 'source_tmpl': 'Sub-Exporter-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['2a95695d35c5d0d5373a7e145c96b9b016113b74e94116835ac05450cae4d445'], + }), + ('Class::Load::XS', '0.10', { + 'source_tmpl': 'Class-Load-XS-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['5bc22cf536ebfd2564c5bdaf42f0d8a4cee3d1930fc8b44b7d4a42038622add1'], + }), + ('Data::Types', '0.17', { + 'source_tmpl': 'Data-Types-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MANWAR'], + 'checksums': ['860751feb79b7dfc1af71c4b7fe920220ec6d31c4ab9402b8f178f7f4b8293c1'], + }), + ('Set::IntSpan::Fast', '1.15', { + 'source_tmpl': 'Set-IntSpan-Fast-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AN/ANDYA'], + 'checksums': ['cfb1768c24f55208e87405b17f537f0f303fa141891d0b22d509a941aa57e24e'], + }), + ('Text::Iconv', '1.7', { + 'source_tmpl': 'Text-Iconv-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MP/MPIOTR'], + 'checksums': ['5b80b7d5e709d34393bcba88971864a17b44a5bf0f9e4bcee383d029e7d2d5c3'], + }), + ('Text::Balanced', '2.06', { + 'source_tmpl': 'Text-Balanced-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHAY'], + 'checksums': ['773e0f0f21c0cb2cf664cee6ba28ff70259babcc892f9b650f9cbda00be092ad'], + }), + ('strictures', '2.000006', { + 'source_tmpl': 'strictures-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG'], + 'checksums': ['09d57974a6d1b2380c802870fed471108f51170da81458e2751859f2714f8d57'], + }), + ('Switch', '2.17', { + 'source_tmpl': 'Switch-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CH/CHORNY'], + 'checksums': ['31354975140fe6235ac130a109496491ad33dd42f9c62189e23f49f75f936d75'], + }), + ('File::Which', '1.27', { + 'source_tmpl': 'File-Which-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PL/PLICEASE'], + 'checksums': ['3201f1a60e3f16484082e6045c896842261fc345de9fb2e620fd2a2c7af3a93a'], + }), + ('Error', '0.17029', { + 'source_tmpl': 'Error-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHLOMIF'], + 'checksums': ['1a23f7913032aed6d4b68321373a3899ca66590f4727391a091ec19c95bf7adc'], + }), + ('Mock::Quick', '1.111', { + 'source_tmpl': 'Mock-Quick-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + 'checksums': ['ff786008bf8c022064ececd3b7ed89c76b35e8d1eac6cf472a9f51771c1c9f2c'], + }), + ('Text::CSV', '2.04', { + 'source_tmpl': 'Text-CSV-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IS/ISHIGAKI'], + 'checksums': ['4f80122e4ea0b05079cad493e386564030f18c8d7b1f9af561df86985a653fe3'], + }), + ('Test::Output', '1.034', { + 'source_tmpl': 'Test-Output-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BD/BDFOY'], + 'checksums': ['cd42e2801c0d2b482d18c9fb4b06c757054818bcbb2824e5dfbf33ad7a3d69a0'], + }), + ('File::CheckTree', '4.42', { + 'source_tmpl': 'File-CheckTree-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['66fb417f8ff8a5e5b7ea25606156e70e204861c59fa8c3831925b4dd3f155f8a'], + }), + ('Math::VecStat', '0.08', { + 'source_tmpl': 'Math-VecStat-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AS/ASPINELLI'], + 'checksums': ['409a8e0e4b1025c8e80f628f65a9778aa77ab285161406ca4a6c097b13656d0d'], + }), + ('Pod::Parser', '1.67', { + 'configopts': 'INSTALLDIRS=site', + 'source_tmpl': 'Pod-Parser-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MAREKR'], + 'checksums': ['5deccbf55d750ce65588cd211c1a03fa1ef3aaa15d1ac2b8d85383a42c1427ea'], + }), + ('Pod::LaTeX', '0.61', { + 'source_tmpl': 'Pod-LaTeX-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TJ/TJENNESS'], + 'checksums': ['15a840ea1c8a76cd3c865fbbf2fec33b03615c0daa50f9c800c54e0cf0659d46'], + }), + ('XML::Twig', '3.52', { + 'source_tmpl': 'XML-Twig-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MI/MIROD'], + 'checksums': ['fef75826c24f2b877d0a0d2645212fc4fb9756ed4d2711614ac15c497e8680ad'], + }), + ('XML::Simple', '2.25', { + 'source_tmpl': 'XML-Simple-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GR/GRANTM'], + 'checksums': ['531fddaebea2416743eb5c4fdfab028f502123d9a220405a4100e68fc480dbf8'], + }), + ('Pod::Plainer', '1.04', { + 'source_tmpl': 'Pod-Plainer-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RM/RMBARKER'], + 'checksums': ['1bbfbf7d1d4871e5a83bab2137e22d089078206815190eb1d5c1260a3499456f'], + }), + ('Data::Section::Simple', '0.07', { + 'source_tmpl': 'Data-Section-Simple-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MI/MIYAGAWA'], + 'checksums': ['0b3035ffdb909aa1f7ded6b608fa9d894421c82c097d51e7171170d67579a9cb'], + }), + ('File::HomeDir', '1.006', { + 'source_tmpl': 'File-HomeDir-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RE/REHSACK'], + 'checksums': ['593737c62df0f6dab5d4122e0b4476417945bb6262c33eedc009665ef1548852'], + }), + ('Authen::SASL', '2.1700', { + 'source_tmpl': 'Authen-SASL-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EH/EHUELS'], + 'checksums': ['b86d5a576b8d387aee24f39f47a54afd14bb66b09003db5065001f1de03a8ece'], + }), + ('Import::Into', '1.002005', { + 'source_tmpl': 'Import-Into-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG'], + 'checksums': ['bd9e77a3fb662b40b43b18d3280cd352edf9fad8d94283e518181cc1ce9f0567'], + }), + ('DateTime::Tiny', '1.07', { + 'runtest': False, # One subset fails due to locale + 'source_tmpl': 'DateTime-Tiny-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], + 'checksums': ['83568a22838cb518fbeb9e060460ec7f59d5a0b0a1cc06562954c3674d7cf7e4'], + }), + ('Text::Format', '0.62', { + 'source_tmpl': 'Text-Format-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHLOMIF'], + 'checksums': ['7d429057319e123c590ba0765334f0ade4a5eb9ea8db7c0ec4d3902de5f90404'], + }), + ('Devel::CheckCompiler', '0.07', { + 'source_tmpl': 'Devel-CheckCompiler-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SY/SYOHEX'], + 'checksums': ['768b7697b4b8d4d372c7507b65e9dd26aa4223f7100183bbb4d3af46d43869b5'], + }), + ('Log::Handler', '0.90', { + 'source_tmpl': 'Log-Handler-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BL/BLOONIX'], + 'checksums': ['3a5c80e7128454770f83acab8cbd3e70e5ec3d59a61dc32792a178f0b31bf74d'], + }), + ('Term::ReadKey', '2.38', { + 'source_tmpl': 'TermReadKey-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JS/JSTOWE'], + 'checksums': ['5a645878dc570ac33661581fbb090ff24ebce17d43ea53fd22e105a856a47290'], + }), + ('Set::IntSpan', '1.19', { + 'source_tmpl': 'Set-IntSpan-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SW/SWMCD'], + 'checksums': ['11b7549b13ec5d87cc695dd4c777cd02983dd5fe9866012877fb530f48b3dfd0'], + }), + ('Module::Runtime::Conflicts', '0.003', { + 'source_tmpl': 'Module-Runtime-Conflicts-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['707cdc75038c70fe91779b888ac050f128565d3967ba96680e1b1c7cc9733875'], + }), + ('File::pushd', '1.016', { + 'source_tmpl': 'File-pushd-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], + 'checksums': ['d73a7f09442983b098260df3df7a832a5f660773a313ca273fa8b56665f97cdc'], + }), + ('Test::CleanNamespaces', '0.24', { + 'source_tmpl': 'Test-CleanNamespaces-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['338d5569e8e89a654935f843ec0bc84aaa486fe8dd1898fb9cab3eccecd5327a'], + }), + ('Devel::OverloadInfo', '0.007', { + 'source_tmpl': 'Devel-OverloadInfo-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IL/ILMARI'], + 'checksums': ['21a184163b90f91f06ffc7f5de0b968356546ae9b400a9d75c573c958c246222'], + }), + ('Moose', '2.2207', { + 'source_tmpl': 'Moose-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['7c2daddc49754ded93f65b8ce9e3ac9b6d11ab27d111ec77f95a8528cf4ac409'], + }), + ('Algorithm::Dependency', '1.112', { + 'source_tmpl': 'Algorithm-Dependency-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['7e0fb7c39f56a2dccf9d0295c82f3031ee116e807f6a12a438fa4dd41b0ec187'], + }), + ('Font::TTF', '1.06', { + 'source_tmpl': 'Font-TTF-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BH/BHALLISSY'], + 'checksums': ['4b697d444259759ea02d2c442c9bffe5ffe14c9214084a01f743693a944cc293'], + }), + ('IPC::Run3', '0.049', { + 'source_tmpl': 'IPC-Run3-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['9d048ae7b9ae63871bae976ba01e081d887392d904e5d48b04e22d35ed22011a'], + }), + ('SQL::Statement', '1.414', { + 'source_tmpl': 'SQL-Statement-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RE/REHSACK'], + 'checksums': ['dde8bdcfa6a136eedda06519ba0f3efaec085c39db0df9c472dc0ec6cd781a49'], + }), + ('Package::Constants', '0.06', { + 'source_tmpl': 'Package-Constants-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + 'checksums': ['0b58be78706ccc4e4bd9bbad41767470427fd7b2cfad749489de101f85bc5df5'], + }), + ('CPANPLUS', '0.9914', { + 'source_tmpl': 'CPANPLUS-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + 'checksums': ['76c3e5da623a4af60fe64adec448fb1f8e0cae9f6798a36b68865974044e9b67'], + }), + ('IO::Tty', '1.20', { + 'source_tmpl': 'IO-Tty-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TODDR'], + 'checksums': ['b15309fc85623893289cb9b2b88dfa9ed1e69156b75f29938553a45be6d730af'], + }), + ('Text::Soundex', '3.05', { + 'source_tmpl': 'Text-Soundex-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['f6dd55b4280b25dea978221839864382560074e1d6933395faee2510c2db60ed'], + }), + ('Mail::Util', '2.21', { + 'source_tmpl': 'MailTools-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MARKOV'], + 'checksums': ['4ad9bd6826b6f03a2727332466b1b7d29890c8d99a32b4b3b0a8d926ee1a44cb'], + }), + ('Test::More::UTF8', '0.05', { + 'source_tmpl': 'Test-More-UTF8-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MO/MONS'], + 'checksums': ['b9f1c4b36a97cdfefaa53ed1115dd38f4b483037775f6559ee1df14acfd1ce04'], + }), + ('Text::Template', '1.61', { + 'source_tmpl': 'Text-Template-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MS/MSCHOUT'], + 'checksums': ['a295ea7d1ef241ae2640c1f7864b628f8e6f99ec14fb1da781b2f5f2168dcf09'], + }), + ('PadWalker', '2.5', { + 'source_tmpl': 'PadWalker-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RO/ROBIN'], + 'checksums': ['07b26abb841146af32072a8d68cb90176ffb176fd9268e6f2f7d106f817a0cd0'], + }), + ('Devel::Cycle', '1.12', { + 'source_tmpl': 'Devel-Cycle-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LD/LDS'], + 'checksums': ['fd3365c4d898b2b2bddbb78a46d507a18cca8490a290199547dab7f1e7390bc2'], + }), + ('Test::Memory::Cycle', '1.06', { + 'source_tmpl': 'Test-Memory-Cycle-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PE/PETDANCE'], + 'checksums': ['9d53ddfdc964cd8454cb0da4c695b6a3ae47b45839291c34cb9d8d1cfaab3202'], + }), + ('PDF::API2', '2.047', { + 'source_tmpl': 'PDF-API2-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SS/SSIMMS'], + 'checksums': ['84d6318279d77844923e4de4275fe4345cd08b225edd7f9ed6a16f87a91aca39'], + }), + ('Devel::CheckLib', '1.16', { + 'source_tmpl': 'Devel-CheckLib-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MATTN'], + 'checksums': ['869d38c258e646dcef676609f0dd7ca90f085f56cf6fd7001b019a5d5b831fca'], + }), + ('SVG', '2.87', { + 'source_tmpl': 'SVG-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MANWAR'], + 'checksums': ['b3fa58c1c59942b4ebef003da97c3e01e531480ca29e8efbe327ff0589c0bd3c'], + }), + ('Statistics::Basic', '1.6611', { + 'source_tmpl': 'Statistics-Basic-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JE/JETTERO'], + 'checksums': ['6855ce5615fd3e1af4cfc451a9bf44ff29a3140b4e7130034f1f0af2511a94fb'], + }), + ('Log::Log4perl', '1.57', { + 'source_tmpl': 'Log-Log4perl-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETJ'], + 'checksums': ['0f8fcb7638a8f3db4c797df94fdbc56013749142f2f94cbc95b43c9fca096a13'], + }), + ('Math::CDF', '0.1', { + 'source_tmpl': 'Math-CDF-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CA/CALLAHAN'], + 'checksums': ['7896bf250835ce47dcc813cb8cf9dc576c5455de42e822dcd7d8d3fef2125565'], + }), + ('Array::Utils', '0.5', { + 'source_tmpl': 'Array-Utils-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/Z/ZM/ZMIJ/Array'], + 'checksums': ['89dd1b7fcd9b4379492a3a77496e39fe6cd379b773fd03a6b160dd26ede63770'], + }), + ('File::Grep', '0.02', { + 'source_tmpl': 'File-Grep-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MN/MNEYLON'], + 'checksums': ['462e15274eb6278521407ea302d9eea7252cd44cab2382871f7de833d5f85632'], + }), + ('File::Temp', '0.2311', { + 'source_tmpl': 'File-Temp-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['2290d61bf5c39882fc3311da9ce1c7f42dbdf825ae169e552c59fe4598b36f4a'], + }), + ('Set::Object', '1.42', { + 'source_tmpl': 'Set-Object-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RU/RURBAN'], + 'checksums': ['d18c5a8a233eabbd0206cf3da5b00fcdd7b37febf12a93dcc3d1c026e6fdec45'], + }), + ('Heap', '0.80', { + 'source_tmpl': 'Heap-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JM/JMM'], + 'checksums': ['ccda29f3c93176ad0fdfff4dd6f5e4ac90b370cba4b028386b7343bf64139bde'], + }), + ('Graph', '0.9729', { + 'source_tmpl': 'Graph-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETJ'], + 'checksums': ['3efbed46ca82f78f25253d034232b0cc9cfadfbd867437e63f9275850f85abb0'], + }), + ('XML::Writer', '0.900', { + 'source_tmpl': 'XML-Writer-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JO/JOSEPHW'], + 'checksums': ['73c8f5bd3ecf2b350f4adae6d6676d52e08ecc2d7df4a9f089fa68360d400d1f'], + }), + ('Parse::Yapp', '1.21', { + 'source_tmpl': 'Parse-Yapp-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/W/WB/WBRASWELL'], + 'checksums': ['3810e998308fba2e0f4f26043035032b027ce51ce5c8a52a8b8e340ca65f13e5'], + }), + ('Graph::ReadWrite', '2.10', { + 'source_tmpl': 'Graph-ReadWrite-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NE/NEILB'], + 'checksums': ['516c1ea9facb995dbc38d1735d58974b2399862567e731b729c8d0bc2ee5a14b'], + }), + ('PerlIO::utf8_strict', '0.010', { + 'source_tmpl': 'PerlIO-utf8_strict-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + 'checksums': ['bcd2848b72df290b5e984fae8b1a6ca96f6d072003cf222389a8c9e8e1c570cd'], + }), + ('Digest::MD5::File', '0.08', { + 'source_tmpl': 'Digest-MD5-File-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DM/DMUEY'], + 'checksums': ['adb43a54e32627b4f7e57c9640e6eb06d0bb79d8ea54cd0bd79ed35688fb1218'], + }), + ('String::RewritePrefix', '0.009', { + 'source_tmpl': 'String-RewritePrefix-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['44918bec96a54af8ca37ca897e436709ec284a07b28516ef3cce4666869646d5'], + }), + ('Getopt::Long::Descriptive', '0.114', { + 'source_tmpl': 'Getopt-Long-Descriptive-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['410e842114a9cbfd3fd3a5fd248a96703c07c5d879b2aa5f9db0333f23276016'], + }), + ('IO::TieCombine', '1.005', { + 'source_tmpl': 'IO-TieCombine-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['402d4db8300b3d271632f4995e0ade329d89280a7e47f2badf8b38af6e5569af'], + }), + ('App::Cmd', '0.336', { + 'source_tmpl': 'App-Cmd-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['df966b57d59abb196e00304885e5bf117ca958182ae3f4eedf17218ea2838e81'], + }), + ('Carp::Clan', '6.08', { + 'source_tmpl': 'Carp-Clan-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['c75f92e34422cc5a65ab05d155842b701452434e9aefb649d6e2289c47ef6708'], + }), + ('Sub::Exporter::ForMethods', '0.100055', { + 'source_tmpl': 'Sub-Exporter-ForMethods-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['791f4203ba7c0f7d8380bc01bec20215f7c8bc70d7ed03e552eee44541abe94e'], + }), + ('MooseX::Types', '0.50', { + 'source_tmpl': 'MooseX-Types-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['9cd87b3492cbf0be9d2df9317b2adf9fc30663770e69906654bea3f41b17cb08'], + }), + ('Variable::Magic', '0.64', { + 'source_tmpl': 'Variable-Magic-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/V/VP/VPIT'], + 'checksums': ['9f7853249c9ea3b4df92fb6b790c03a60680fc029f44c8bf9894dccf019516bd'], + 'pretestopts': 'LC_ALL=C ', # Test fails if run in localized environments + }), + ('MooseX::Types::Perl', '0.101344', { + 'source_tmpl': 'MooseX-Types-Perl-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['87644354f74fa65235cb2bfca44277930a7eabe51acc5f81fb631530a8355e24'], + }), + ('Log::Dispatch', '2.71', { + 'source_tmpl': 'Log-Dispatch-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + 'checksums': ['9d60d9648c35ce2754731eb4deb7f05809ece1bd633b74d74795aed9ec732570'], + }), + ('JSON::MaybeXS', '1.004005', { + 'source_tmpl': 'JSON-MaybeXS-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['f5b6bc19f579e66b7299f8748b8ac3e171936dc4e7fcb72a8a257a9bd482a331'], + }), + ('String::Flogger', '1.101246', { + 'source_tmpl': 'String-Flogger-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['15f8491e07818bb3cfa9f6bd3aabf6430ba9b4e309f18114358be3d81bff3a0f'], + }), + ('Log::Dispatch::Array', '1.005', { + 'source_tmpl': 'Log-Dispatch-Array-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['311640b7a967f8dd7c9bb41a227073565636d70df4fcc1d44fed8a8223b347ca'], + }), + ('Sub::Exporter::GlobExporter', '0.006', { + 'source_tmpl': 'Sub-Exporter-GlobExporter-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['de743f08026701c2a6a222a8b41c4cdc254b1a4afe7ef98987cd3aba4ce52696'], + }), + ('Log::Dispatchouli', '3.007', { + 'source_tmpl': 'Log-Dispatchouli-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['988118965952ba49a8fa791a6536880c89017f4eb9d72c1745ed67d15c0d272c'], + }), + ('Test::FailWarnings', '0.008', { + 'source_tmpl': 'Test-FailWarnings-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], + 'checksums': ['da34ef9029f6849d6026201d49127d054ee6ac4b979c82210315f5721964a96f'], + }), + ('Data::Section', '0.200008', { + 'source_tmpl': 'Data-Section-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['83acc7a55d3dd7ed36e9d78d350af3138c69cfa178a44765822712ff433b990e'], + }), + ('Test::CheckDeps', '0.010', { + 'source_tmpl': 'Test-CheckDeps-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + 'checksums': ['66fccca6c6f330e7ecc898bd6a51846e2145b3e02d78c4997ba6b7de23b551ee'], + }), + ('Software::License', '0.104006', { + 'runtest': False, # This test just suddenly started to fail + 'source_tmpl': 'Software-License-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + 'checksums': ['65c8ee1c2da2a4de10139863df668fa6b3b3e24a39d69a7cca39f284fb6b9c0f'], + }), + ('MooseX::SetOnce', '0.203', { + 'source_tmpl': 'MooseX-SetOnce-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['3cd2f3664e438382cf844b679350a2e428b760927e2cf18fccdc468a7bc3066f'], + }), + ('Term::Encoding', '0.03', { + 'source_tmpl': 'Term-Encoding-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MI/MIYAGAWA'], + 'checksums': ['95ba9687d735d25a3cbe64508d7894f009c7fa2a1726c3e786e9e21da2251d0b'], + }), + ('Throwable', '1.001', { + 'source_tmpl': 'Throwable-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['d0cb5e9d7d06d70f2cc56eecf857a83a45eaca43850dcdda91d3feb4ddde4c51'], + }), + ('Role::Identifiable::HasIdent', '0.009', { + 'source_tmpl': 'Role-Identifiable-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['5a735e9f7177f9ebae047eb7bae29b7ec29ec020ae37637aea5350d30c087b76'], + }), + ('MooseX::Role::Parameterized', '1.11', { + 'source_tmpl': 'MooseX-Role-Parameterized-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['1cfe766c5d7f0ecab57f733dcca430a2a2acd6b995757141b940ade3692bec9e'], + }), + ('MooseX::OneArgNew', '0.007', { + 'source_tmpl': 'MooseX-OneArgNew-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['84282435f1169cf09d7513fa9387e2091791635cf35a078b500b829aeea06138'], + }), + ('MooseX::LazyRequire', '0.11', { + 'source_tmpl': 'MooseX-LazyRequire-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['ef620c1e019daf9cf3f23a943d25a94c91e93ab312bcd63be2e9740ec0b94288'], + }), + ('String::Formatter', '1.235', { + 'source_tmpl': 'String-Formatter-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['08236a913b911ce652cf08598e7c07d2df3f369fc47bf401a485a504a1660783'], + }), + ('String::Errf', '0.009', { + 'source_tmpl': 'String-Errf-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['e1fedbf9b4fd64b64ea81038ddb76a4c6cd85f5db15bc21f10656a298349dc1f'], + }), + ('Role::HasMessage', '0.007', { + 'source_tmpl': 'Role-HasMessage-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['5e267a4d7620b368481204c88ea2044b8b2a58ff8b05577f2717b2754c0414ce'], + }), + ('Config::MVP', '2.200013', { + 'source_tmpl': 'Config-MVP-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['018d161623ee3a67f860d9e680e22e61b79eae6018f0e7c3b525fc934f5b7d45'], + }), + ('Mixin::Linewise::Readers', '0.111', { + 'source_tmpl': 'Mixin-Linewise-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['d28e88516ce9b5295c31631dcccdc0fc8f2ab7d8a5cc876bb1b20131087b01db'], + }), + ('Config::INI', '0.029', { + 'source_tmpl': 'Config-INI-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['0bbe797a730210644a907d90cd4aa2b23ad580cb27bd39393bfc6a7ef9fdfdea'], + }), + ('String::Truncate', '1.100603', { + 'source_tmpl': 'String-Truncate-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['ab45602cce2dd9515edfbb2e6e5cde19cdd5498d61a23afd8c46c1f11f8eec62'], + }), + ('Pod::Eventual', '0.094003', { + 'source_tmpl': 'Pod-Eventual-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['7f060cc34d11656ce069db061e3d60edc0cabc8f89a4a2dc7eaae95dac856d2d'], + }), + ('Pod::Elemental', '0.103006', { + 'source_tmpl': 'Pod-Elemental-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['750c3a79d8e1824758a6ef7d2dd077dcddca503542b8c34eccd5acbb779dc423'], + }), + ('Test::Object', '0.08', { + 'source_tmpl': 'Test-Object-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['65278964147837313f4108e55b59676e8a364d6edf01b3dc198aee894ab1d0bb'], + }), + ('Hook::LexWrap', '0.26', { + 'source_tmpl': 'Hook-LexWrap-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['b60bdc5f98f94f9294b06adef82b1d996da192d5f183f9f434b610fd1137ec2d'], + }), + ('Test::SubCalls', '1.10', { + 'source_tmpl': 'Test-SubCalls-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['cbc1e9b35a05e71febc13e5ef547a31c8249899bb6011dbdc9d9ff366ddab6c2'], + }), + ('PPI', '1.278', { + 'source_tmpl': 'PPI-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/O/OA/OALDERS'], + 'checksums': ['1c867b2e9b10056978db9ddaadab599af9a5c9a66805ed03ef4b201f1105d427'], + }), + ('Config::MVP::Reader::INI', '2.101465', { + 'source_tmpl': 'Config-MVP-Reader-INI-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['13c7aa27c1df98cd33ada399e59ff38fabfa9d65513e42af02f72c2d3f636247'], + }), + ('Pod::Weaver', '4.020', { + 'source_tmpl': 'Pod-Weaver-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['655fcf261206c1adbc3038981790b116c31508485135c648093b99b3b3de09d2'], + }), + ('CPAN::Uploader', '0.103018', { + 'source_tmpl': 'CPAN-Uploader-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['c4ffe4ede9db79b396e3bfc5e7cdf0e2e9821e1f1e087f523bcfa74c9fc9e248'], + }), + ('Devel::FindPerl', '0.016', { + 'source_tmpl': 'Devel-FindPerl-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + 'checksums': ['43a2bf2f787a3f1b881179063162b2aa3e7cb044f6e5e76ec6466ae90a861138'], + }), + ('Module::Path', '0.19', { + 'source_tmpl': 'Module-Path-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NE/NEILB'], + 'checksums': ['b33179ce4dd73dfcde7d46808804b9ffbb11db0245fe455a7d001747562feaca'], + }), + ('Perl::PrereqScanner', '1.100', { + 'source_tmpl': 'Perl-PrereqScanner-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['01181d38a2e7aff838d262122563c50636ba4b3652ee5d1d4f8ef5ba3f5b186b'], + }), + ('Dist::Zilla', '6.032', { + 'source_tmpl': 'Dist-Zilla-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['5c771a1dc2daab5afae0fd59e5046111970f73bf3eaec9df70d8e07346f8165e'], + }), + ('XML::RegExp', '0.04', { + 'source_tmpl': 'XML-RegExp-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TJ/TJMATHER'], + 'checksums': ['df1990096036085c8e2d45904fe180f82bfed40f1a7e05243f334ea10090fc54'], + }), + ('XML::DOM', '1.46', { + 'source_tmpl': 'XML-DOM-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TJ/TJMATHER'], + 'checksums': ['8ba24b0b459b01d6c5e5b0408829c7d5dfe47ff79b3548c813759048099b175e'], + }), + ('Data::Dump', '1.25', { + 'source_tmpl': 'Data-Dump-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GARU'], + 'checksums': ['a4aa6e0ddbf39d5ad49bddfe0f89d9da864e3bc00f627125d1bc580472f53fbd'], + }), + ('File::Next', '1.18', { + 'source_tmpl': 'File-Next-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PE/PETDANCE'], + 'checksums': ['f900cb39505eb6e168a9ca51a10b73f1bbde1914b923a09ecd72d9c02e6ec2ef'], + }), + ('App::cpanminus', '1.7047', { + 'source_tmpl': 'App-cpanminus-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MI/MIYAGAWA'], + 'checksums': ['963e63c6e1a8725ff2f624e9086396ae150db51dd0a337c3781d09a994af05a5'], + }), + ('Parallel::ForkManager', '2.02', { + 'source_tmpl': 'Parallel-ForkManager-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/Y/YA/YANICK'], + 'checksums': ['c1b2970a8bb666c3de7caac4a8f4dbcc043ab819bbc337692ec7bf27adae4404'], + }), + ('Object::InsideOut', '4.05', { + 'source_tmpl': 'Object-InsideOut-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JD/JDHEDDEN'], + 'checksums': ['9dfd6ca2822724347e0eb6759d00709425814703ad5c66bdb6214579868bcac4'], + }), + ('Logger::Simple', '2.0', { + 'source_tmpl': 'Logger-Simple-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TS/TSTANLEY'], + 'checksums': ['2e63fd3508775b5902132ba1bfb03b42bee468dfaf35dfe42e1909ff6d291b2d'], + }), + ('Scalar::Util::Numeric', '0.40', { + 'source_tmpl': 'Scalar-Util-Numeric-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CH/CHOCOLATE'], + 'checksums': ['d7501b6d410703db5b1c1942fbfc41af8964a35525d7f766058acf5ca2cc4440'], + }), + ('Spiffy', '0.46', { + 'source_tmpl': 'Spiffy-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IN/INGY'], + 'checksums': ['8f58620a8420255c49b6c43c5ff5802bd25e4f09240c51e5bf2b022833d41da3'], + }), + ('Test::Base', '0.89', { + 'source_tmpl': 'Test-Base-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IN/INGY'], + 'checksums': ['2794a1aaaeb1d3a287dd2c7286258663796562f7db9ccc6b424bc4f1de8ad014'], + }), + ('Test::YAML', '1.07', { + 'source_tmpl': 'Test-YAML-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TI/TINITA'], + 'checksums': ['1f300d034f46298cb92960912cc04bac33fb27f05b8852d8f051e110b9cd995f'], + }), + ('YAML', '1.31', { + 'source_tmpl': 'YAML-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IN/INGY'], + 'checksums': ['a0ce30381657dce8e694df9a09e95d818d13beb03698fd2cf79d0c8d564a9b8e'], + }), + ('Object::InsideOut', '4.05', { + 'source_tmpl': 'Object-InsideOut-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JD/JDHEDDEN'], + 'checksums': ['9dfd6ca2822724347e0eb6759d00709425814703ad5c66bdb6214579868bcac4'], + }), + ('Term::ReadLine::Gnu', '1.46', { + 'modulename': 'Term::ReadLine', + 'source_tmpl': 'Term-ReadLine-Gnu-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAYASHI'], + 'checksums': ['b13832132e50366c34feac12ce82837c0a9db34ca530ae5d27db97cf9c964c7b'], + # make sure that library provided by ncurses dependency is used instead of libtermcap + 'preinstallopts': "sed -s 's/-ltermcap/-lncurses/g' Makefile.PL && ", + }), + ('ExtUtils::MakeMaker', '7.70', { + 'source_tmpl': 'ExtUtils-MakeMaker-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + 'checksums': ['f108bd46420d2f00d242825f865b0f68851084924924f92261d684c49e3e7a74'], + }), + ('Scalar::Util', '1.63', { + 'source_tmpl': 'Scalar-List-Utils-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PE/PEVANS'], + 'checksums': ['cafbdf212f6827dc9a0dd3b57b6ee50e860586d7198228a33262d55c559eb2a9'], + }), + ('Module::CoreList', '5.20240702', { + 'source_tmpl': 'Module-CoreList-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + 'checksums': ['f2fa93960b1419ab3aaa186d4ce2a538de229d1af8a9eecd76265c78252c011b'], + }), + ('Module::Metadata', '1.000038', { + 'source_tmpl': 'Module-Metadata-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['b599d8770a9a9fa0a8ae3cd0ed395a9cf71b4eb53aed82989a6bece33485a9cd'], + }), + ('Params::Check', '0.38', { + 'configopts': 'INSTALLDIRS=site', # Force it to correctly use site_perl + 'source_tmpl': 'Params-Check-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + 'checksums': ['f0c9d33876c36b1bca1475276d26d2efaf449b256d7cc8118fae012e89a26290'], + }), + ('Locale::Maketext::Simple', '0.21', { + 'configopts': 'INSTALLDIRS=site', # Force it to correctly use site_perl + 'source_tmpl': 'Locale-Maketext-Simple-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JE/JESSE'], + 'checksums': ['b009ff51f4fb108d19961a523e99b4373ccf958d37ca35bf1583215908dca9a9'], + }), + ('Perl::OSType', '1.010', { + 'source_tmpl': 'Perl-OSType-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], + 'checksums': ['e7ed4994b5d547cb23aadb84dc6044c5eb085d5a67a6c5624f42542edd3403b2'], + }), + ('IPC::Cmd', '1.04', { + 'source_tmpl': 'IPC-Cmd-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + 'checksums': ['d110a0f60e35c65721454200f0d2f0f8965529a2add9649d1fa6f4f9eccb6430'], + }), + ('Pod::Escapes', '1.07', { + 'source_tmpl': 'Pod-Escapes-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NE/NEILB'], + 'checksums': ['dbf7c827984951fb248907f940fd8f19f2696bc5545c0a15287e0fbe56a52308'], + }), + ('if', '0.0608', { + 'configopts': 'INSTALLDIRS=site', # Force it to correctly use site_perl + 'modulename': False, + 'source_tmpl': 'if-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/X/XS/XSAWYERX'], + 'checksums': ['37206e10919c4d99273020008a3581bf0947d364e859b8966521c3145b4b3700'], + }), + ('Test', '1.26', { + 'configopts': 'INSTALLDIRS=site', # Force it to correctly use site_perl + 'source_tmpl': 'Test-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JE/JESSE'], + 'checksums': ['f7701bd28e05e7f82fe9a181bbab38f53fa6aeae48d2a810da74d1b981d4f392'], + }), + ('ExtUtils::Constant', '0.25', { + 'runtest': False, # Somehow has syntax errors in tests + 'source_tmpl': 'ExtUtils-Constant-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NW/NWCLARK'], + 'checksums': ['6933d0e963b62281ef7561068e6aecac8c4ac2b476b2bba09ab0b90fbac9d757'], + }), + ('ExtUtils::CBuilder', '0.280236', { + 'source_tmpl': 'ExtUtils-CBuilder-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AM/AMBS'], + 'checksums': ['abc21827eb8a513171bf7fdecefce9945132cb76db945036518291f607b1491f'], + }), + ('Carp::Heavy', '1.50', { + 'source_tmpl': 'Carp-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/X/XS/XSAWYERX'], + 'checksums': ['f5273b4e1a6d51b22996c48cb3a3cbc72fd456c4038f5c20b127e2d4bcbcebd9'], + }), + ('Pod::Simple', '3.45', { + 'source_tmpl': 'Pod-Simple-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/K/KH/KHW'], + 'checksums': ['8483bb95cd3e4307d66def092a3779f843af772482bfdc024e3e00d0c4db0cfa'], + }), + ('Socket', '2.038', { + 'source_tmpl': 'Socket-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PE/PEVANS'], + 'checksums': ['563d11731ff44307fa2779a6958fd2d2f6643fbd9a3174cbf350228b159681f8'], + }), + ('Time::Local', '1.35', { + 'source_tmpl': 'Time-Local-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + 'checksums': ['1d136b71bd041cbe6f66c43180ee79e675b72ad5a3596abd6a44d211072ada29'], + }), + ('Storable', '3.25', { + 'source_tmpl': 'Storable-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NW/NWCLARK'], + 'checksums': ['e1e96b24a076792fde52154789fe4b76034b9ad39c8a1a819ead77d50d5f1817'], + }), + ('ExtUtils::ParseXS', '3.51', { + 'source_tmpl': 'ExtUtils-ParseXS-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + 'checksums': ['82431a57425d78682acefb3a2cc9287683d091c8d034b825c584d9805bed6535'], + }), + ('Pod::Man', '5.01', { + 'source_tmpl': 'podlators-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RR/RRA'], + 'checksums': ['ccfd1df9f1a47f095bce6d718fad5af40f78ce2491f2c7239626e15b7020bc71'], + }), + ('Mozilla::CA', '20240313', { + 'source_tmpl': 'Mozilla-CA-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LW/LWP'], + 'checksums': ['624873939e309833894f881464a95dfe74ab77cab5d557308c010487161698e7'], + }), + ('LWP::Protocol::https', '6.14', { + 'source_tmpl': 'LWP-Protocol-https-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/O/OA/OALDERS'], + 'checksums': ['59cdeabf26950d4f1bef70f096b0d77c5b1c5a7b5ad1b66d71b681ba279cbb2a'], + }), + ('Module::Load', '0.36', { + 'source_tmpl': 'Module-Load-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + 'checksums': ['d825020ac00b220e89f9524e24d838f9438b072fcae8c91938e4026677bef6e0'], + }), + ('Module::Load::Conditional', '0.74', { + 'source_tmpl': 'Module-Load-Conditional-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + 'checksums': ['54c354a9393820f1ebc2a095da084ea0392dcbccb0cb38a187a71831cc60a730'], + }), + ('parent', '0.241', { + 'source_tmpl': 'parent-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CO/CORION'], + 'checksums': ['b10b3960ab3997dab7571ffe975ba462d979d086450740a1e08b3959e75128fe'], + }), + ('Net::Domain', '3.15', { + 'source_tmpl': 'libnet-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHAY'], + 'checksums': ['a71f4db580e1a767d6936faa5baf38f1fa617824342da078b561283e86f8f4a2'], + }), + ('Encode', '3.21', { + 'source_tmpl': 'Encode-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DANKOGAI'], + 'checksums': ['eacf71c5eb49e0e590de797f1982d7fb95d8481e4d13c3ce79eb32ef9373b3db'], + }), + ('Cwd', '3.75', { + 'runtest': False, # Single failure about a tainted PATH + 'source_tmpl': 'PathTools-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/X/XS/XSAWYERX'], + 'patches': ['PathTools-3.75_fix-cwd_enoent-test.patch'], + 'checksums': [ + {'PathTools-3.75.tar.gz': 'a558503aa6b1f8c727c0073339081a77888606aa701ada1ad62dd9d8c3f945a2'}, + {'PathTools-3.75_fix-cwd_enoent-test.patch': + '7a456a99d9b04a36359f3623f0deef8fe7f472c742f99cdcf0215c50afbbe7b1'}, + ], + }), + ('MIME::Base64', '3.16', { + 'source_tmpl': 'MIME-Base64-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CA/CAPOEIRAB'], + 'checksums': ['77f73d6f7aeb8d33be08b0d8c2617f9b6c77fb7fc45422d507ca8bafe4246017'], + }), + ('ExtUtils::CppGuess', '0.27', { + 'runtest': False, # Poorly written test + 'source_tmpl': 'ExtUtils-CppGuess-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETJ'], + 'checksums': ['b2c7b581901054a32dfcea12536fda8626457ed0bfbc02600bd354bde7e2a9b4'], + }), + ('XSLoader', '0.24', { + 'source_tmpl': 'XSLoader-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SA/SAPER'], + 'checksums': ['e819a35a6b8e55cb61b290159861f0dc00fe9d8c4f54578eb24f612d45c8d85f'], + }), + ('AutoLoader', '5.74', { + 'source_tmpl': 'AutoLoader-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SM/SMUELLER'], + 'checksums': ['2fac75b05309f71a6871804cd25e1a3ba0a28f43f294fb54528077558da3aff4'], + }), + ('Set::IntervalTree', '0.12', { + 'source_tmpl': 'Set-IntervalTree-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SL/SLOYD'], + 'checksums': ['6fd4000e4022968e2ce5b83c07b189219ef1925ecb72977b52a6f7d76adbc349'], + }), + ('MCE::Mutex', '1.897', { + 'runtest': False, # Single failing subtest + 'source_tmpl': 'MCE-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MARIOROY'], + 'checksums': ['673d337d14fc2d7a12576ca6615c729821dc616ee76e0ecc9c0f32de8a9f9c39'], + }), + ('Text::CSV_XS', '1.55', { + 'source_tmpl': 'Text-CSV_XS-%(version)s.tgz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HM/HMBRAND'], + 'checksums': ['e4b623b31b4ac35e99d7b797d5b7c2205a5b984bcd88dee1a9460a6a39d40b5e'], + }), + ('DBD::CSV', '0.60', { + 'source_tmpl': 'DBD-CSV-%(version)s.tgz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HM/HMBRAND'], + 'checksums': ['018b83a30f799979bc8c3c3044c8b1c8001cdf60bdc3e746848818195254b4e7'], + }), + ('Array::Transpose', '0.06', { + 'source_tmpl': 'Array-Transpose-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MR/MRDVT'], + 'checksums': ['d58667f64381a105f375226f592d0af71068e640a5a9f4d5ecf27c90feb32676'], + }), + ('Config::Simple', '4.58', { + 'source_tmpl': 'Config-Simple-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHERZODR'], + 'checksums': ['dd9995706f0f9384a15ccffe116c3b6e22f42ba2e58d8f24ed03c4a0e386edb4'], + }), + ('Business::ISBN::Data', '20240614.001', { + 'source_tmpl': 'Business-ISBN-Data-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BR/BRIANDFOY'], + 'checksums': ['38d7f0e24152e1aef07b1517a16104c1763b6669095dbad5083c3b91fc27232b'], + }), + ('Business::ISBN', '3.009', { + 'source_tmpl': 'Business-ISBN-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BR/BRIANDFOY'], + 'checksums': ['d2ec1970454af1b2c099dd34caa7a348ca6fd323bb7ddbfad55389bd7f96789b'], + }), + ('common::sense', '3.75', { + 'source_tmpl': 'common-sense-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/ML/MLEHMANN'], + 'checksums': ['a86a1c4ca4f3006d7479064425a09fa5b6689e57261fcb994fe67d061cba0e7e'], + }), + ('Compress::Raw::Zlib', '2.212', { + 'source_tmpl': 'Compress-Raw-Zlib-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PM/PMQS'], + 'checksums': ['6d9de0c11921fd520dfd99a3f6b0ca9f1fd9850274f8bec10bbaa4f6803cc049'], + }), + ('Compress::Raw::Bzip2', '2.212', { + 'source_tmpl': 'Compress-Raw-Bzip2-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PM/PMQS'], + 'checksums': ['6caeee843c428f45fa9646ea98dc675470db63dbac0ee3e2d8e9ee4eb58a856d'], + }), + ('IO::Compress::Zip', '2.212', { + 'source_tmpl': 'IO-Compress-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PM/PMQS'], + 'checksums': ['687490dbf9c4be42c22a945c4601812be5f4d38a9836018148915ba9e0ea65b1'], + }), + ('Types::Serialiser', '1.01', { + 'source_tmpl': 'Types-Serialiser-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/ML/MLEHMANN'], + 'checksums': ['f8c7173b0914d0e3d957282077b366f0c8c70256715eaef3298ff32b92388a80'], + }), + ('JSON::XS', '4.03', { + 'source_tmpl': 'JSON-XS-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/ML/MLEHMANN'], + 'checksums': ['515536f45f2fa1a7e88c8824533758d0121d267ab9cb453a1b5887c8a56b9068'], + }), + ('Authen::NTLM', '1.09', { + 'source_tmpl': 'NTLM-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NB/NBEBOUT'], + 'checksums': ['c823e30cda76bc15636e584302c960e2b5eeef9517c2448f7454498893151f85'], + }), + ('Types::Serialiser', '1.01', { + 'source_tmpl': 'Types-Serialiser-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/ML/MLEHMANN'], + 'checksums': ['f8c7173b0914d0e3d957282077b366f0c8c70256715eaef3298ff32b92388a80'], + }), + ('XML::SAX::Expat', '0.51', { + 'source_tmpl': 'XML-SAX-Expat-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BJ/BJOERN'], + 'checksums': ['4c016213d0ce7db2c494e30086b59917b302db8c292dcd21f39deebd9780c83f'], + }), + ('Inline', '0.86', { + 'source_tmpl': 'Inline-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IN/INGY'], + 'checksums': ['510a7de2d011b0db80b0874e8c0f7390010991000ae135cff7474df1e6d51e3a'], + }), + ('Test::Sys::Info', '0.23', { + # test fails on systems without /etc/fstab - so comment it out + 'preconfigopts': "sed -i 's/ok( my %fs/# ok( my %fs/' lib/Test/Sys/Info/Driver.pm && ", + 'source_tmpl': 'Test-Sys-Info-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BU/BURAK'], + 'checksums': ['30c5f2c4cfee8e1ae6d9fb6291f79addbff5739ba4efa5b1e034520f18fbc95a'], + }), + ('Sys::Info::Base', '0.7807', { + 'source_tmpl': 'Sys-Info-Base-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BU/BURAK'], + 'checksums': ['132362b0046e8dc4f12e1560903623a88a8871d09bf1c29d93d48d3f4a582acb'], + }), + ('Sys::Info::Driver::Unknown::Device::CPU', '0.79', { + 'source_tmpl': 'Sys-Info-Driver-Unknown-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BU/BURAK'], + 'checksums': ['02408843c8e36ea3d507e9f33fee48d6908543829ebe320f13d1bfe76af31e09'], + }), + ('Unix::Processors', '2.046', { + 'source_tmpl': 'Unix-Processors-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/W/WS/WSNYDER'], + 'checksums': ['3973ebdc44682c9c15c776f66e8be242cb4ff1dd52caf43ff446b74d4dccca06'], + }), + ('Sys::Info::Driver::Linux::Device::CPU', '0.7905', { + 'source_tmpl': 'Sys-Info-Driver-Linux-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BU/BURAK'], + 'checksums': ['899c329bd3508ec5849ad0e5dadfa7c3679bbacaea9dda12404a7893032e8b7b'], + }), + ('Sys::Info', '0.7811', { + 'source_tmpl': 'Sys-Info-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BU/BURAK'], + 'checksums': ['566482bff3427c198d7955468ed945a8e736c4a2925151fdef96801ef8a401e1'], + }), + ('CGI', '4.66', { + 'source_tmpl': 'CGI-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEEJO'], + 'checksums': ['4697437688a193e3f02556e1d223015590c1f2800b40becf83dc12d5cc5ed8e1'], + }), + ('HTML::Template', '2.97', { + 'source_tmpl': 'HTML-Template-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SA/SAMTREGAR'], + 'checksums': ['6547af61f3aa85793f8616190938d677d7995fb3b720c16258040bc935e2129f'], + }), + ('MIME::Charset', 'v1.013.1', { + 'source_tmpl': 'MIME-Charset-1.013.1.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NE/NEZUMI'], + 'checksums': ['1bb7a6e0c0d251f23d6e60bf84c9adefc5b74eec58475bfee4d39107e60870f0'], + }), + ('Unicode::LineBreak', '2019.001', { + 'source_tmpl': 'Unicode-LineBreak-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NE/NEZUMI'], + 'checksums': ['486762e4cacddcc77b13989f979a029f84630b8175e7fef17989e157d4b6318a'], + }), + ('String::Print', '0.94', { + 'source_tmpl': 'String-Print-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MARKOV'], + 'checksums': ['9b3cd677adb7a40cb183bd6c60db80d96adcabd5aae27e324e3ee37e3275229b'], + }), + ('Log::Report::Optional', '1.07', { + 'source_tmpl': 'Log-Report-Optional-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MARKOV'], + 'checksums': ['b2658b53176df5afa5d02789368715c86b98c8d04ecd930252bcd7f832cc6224'], + }), + ('Log::Report', '1.37', { + 'source_tmpl': 'Log-Report-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MARKOV'], + 'checksums': ['9135798e9cb391e949a3c829c101631d182baa4feaaf821efcee8deba7fdee67'], + }), + ('Sys::Info::Driver::Unknown', '0.79', { + 'source_tmpl': 'Sys-Info-Driver-Unknown-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BU/BURAK'], + 'checksums': ['02408843c8e36ea3d507e9f33fee48d6908543829ebe320f13d1bfe76af31e09'], + }), + ('Sys::Info::Driver::Linux', '0.7905', { + 'source_tmpl': 'Sys-Info-Driver-Linux-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BU/BURAK'], + 'checksums': ['899c329bd3508ec5849ad0e5dadfa7c3679bbacaea9dda12404a7893032e8b7b'], + }), + ('Unix::Processors', '2.046', { + 'source_tmpl': 'Unix-Processors-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/W/WS/WSNYDER'], + 'checksums': ['3973ebdc44682c9c15c776f66e8be242cb4ff1dd52caf43ff446b74d4dccca06'], + }), + ('local::lib', '2.000029', { + 'source_tmpl': 'local-lib-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG'], + 'checksums': ['8df87a10c14c8e909c5b47c5701e4b8187d519e5251e87c80709b02bb33efdd7'], + }), + ('Module::Path', '0.19', { + 'source_tmpl': 'Module-Path-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NE/NEILB'], + 'checksums': ['b33179ce4dd73dfcde7d46808804b9ffbb11db0245fe455a7d001747562feaca'], + }), + ('Devel::Size', '0.84', { + 'source_tmpl': 'Devel-Size-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NW/NWCLARK'], + 'checksums': ['db2e4d65f688dbf59273b5e82101ac3f1a66f665afb0594dce168b8650a4d0e4'], + }), + ('Math::Utils', '1.14', { + 'source_tmpl': 'Math-Utils-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JG/JGAMBLE'], + 'checksums': ['88a20ae0736a622671b92bb2a350969af424d7610284530b277c8020235f2695'], + }), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Perl/PathTools-3.75_fix-cwd_enoent-test.patch b/easybuild/easyconfigs/p/Perl/PathTools-3.75_fix-cwd_enoent-test.patch new file mode 100644 index 00000000000..0cba1221f98 --- /dev/null +++ b/easybuild/easyconfigs/p/Perl/PathTools-3.75_fix-cwd_enoent-test.patch @@ -0,0 +1,50 @@ +From 8508806268d1abe6c533393333ad151e12adfc2d Mon Sep 17 00:00:00 2001 +From: Slaven Rezic +Date: Wed, 3 Oct 2018 10:07:32 -0400 +Subject: [PATCH] Accept also ESTALE (fix for RT #133534) + +ESTALE may occur in some environments when accessing a +now non-existing directory, e.g. when using NFS or in docker +containers. +--- + dist/PathTools/t/cwd_enoent.t | 9 ++++++--- + 1 file changed, 6 insertions(+), 3 deletions(-) + +diff --git a/dist/PathTools/t/cwd_enoent.t b/dist/PathTools/t/cwd_enoent.t +index 8f3a1fb1fb3e..510c65ed0c9a 100644 +--- a/dist/PathTools/t/cwd_enoent.t ++++ b/dist/PathTools/t/cwd_enoent.t +@@ -2,7 +2,7 @@ use warnings; + use strict; + + use Config; +-use Errno qw(ENOENT); ++use Errno qw(); + use File::Temp qw(tempdir); + use Test::More; + +@@ -19,6 +19,7 @@ unless(mkdir("$tmp/testdir") && chdir("$tmp/testdir") && rmdir("$tmp/testdir")){ + plan tests => 8; + require Cwd; + ++my @acceptable_errnos = (&Errno::ENOENT, (defined &Errno::ESTALE ? &Errno::ESTALE : ())); + foreach my $type (qw(regular perl)) { + SKIP: { + skip "_perl_abs_path() not expected to work", 4 +@@ -36,12 +37,14 @@ foreach my $type (qw(regular perl)) { + $res = Cwd::getcwd(); + $eno = 0+$!; + is $res, undef, "$type getcwd result on non-existent directory"; +- is $eno, ENOENT, "$type getcwd errno on non-existent directory"; ++ ok((grep { $eno == $_ } @acceptable_errnos), "$type getcwd errno on non-existent directory") ++ or diag "Got errno code $eno, expected " . join(", ", @acceptable_errnos); + $! = 0; + $res = Cwd::abs_path("."); + $eno = 0+$!; + is $res, undef, "$type abs_path result on non-existent directory"; +- is $eno, ENOENT, "$type abs_path errno on non-existent directory"; ++ ok((grep { $eno == $_ } @acceptable_errnos), "$type abs_path errno on non-existent directory") ++ or diag "Got errno code $eno, expected " . join(", ", @acceptable_errnos); + } + } + diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.32.1-GCCcore-10.3.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.32.1-GCCcore-10.3.0.eb index b4cb6226cf0..486e71ce429 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.32.1-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.32.1-GCCcore-10.3.0.eb @@ -234,7 +234,12 @@ exts_list = [ ('File::Spec', '3.75', { 'source_tmpl': 'PathTools-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/X/XS/XSAWYERX'], - 'checksums': ['a558503aa6b1f8c727c0073339081a77888606aa701ada1ad62dd9d8c3f945a2'], + 'patches': ['PathTools-3.75_fix-cwd_enoent-test.patch'], + 'checksums': [ + 'a558503aa6b1f8c727c0073339081a77888606aa701ada1ad62dd9d8c3f945a2', + {'PathTools-3.75_fix-cwd_enoent-test.patch': + '7a456a99d9b04a36359f3623f0deef8fe7f472c742f99cdcf0215c50afbbe7b1'}, + ], }), ('Test::Simple', '1.302183', { 'source_tmpl': 'Test-Simple-%(version)s.tar.gz', @@ -1673,7 +1678,12 @@ exts_list = [ ('Cwd', '3.75', { 'source_tmpl': 'PathTools-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/X/XS/XSAWYERX'], - 'checksums': ['a558503aa6b1f8c727c0073339081a77888606aa701ada1ad62dd9d8c3f945a2'], + 'patches': ['PathTools-3.75_fix-cwd_enoent-test.patch'], + 'checksums': [ + 'a558503aa6b1f8c727c0073339081a77888606aa701ada1ad62dd9d8c3f945a2', + {'PathTools-3.75_fix-cwd_enoent-test.patch': + '7a456a99d9b04a36359f3623f0deef8fe7f472c742f99cdcf0215c50afbbe7b1'}, + ], }), ('MIME::Base64', '3.16', { 'source_tmpl': 'MIME-Base64-%(version)s.tar.gz', diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.34.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.34.0-GCCcore-11.2.0.eb index c0b5956c8b3..944e2124f79 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.34.0-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.34.0-GCCcore-11.2.0.eb @@ -231,7 +231,12 @@ exts_list = [ ('File::Spec', '3.75', { 'source_tmpl': 'PathTools-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/X/XS/XSAWYERX'], - 'checksums': ['a558503aa6b1f8c727c0073339081a77888606aa701ada1ad62dd9d8c3f945a2'], + 'patches': ['PathTools-3.75_fix-cwd_enoent-test.patch'], + 'checksums': [ + 'a558503aa6b1f8c727c0073339081a77888606aa701ada1ad62dd9d8c3f945a2', + {'PathTools-3.75_fix-cwd_enoent-test.patch': + '7a456a99d9b04a36359f3623f0deef8fe7f472c742f99cdcf0215c50afbbe7b1'}, + ], }), ('Test::Simple', '1.302186', { 'source_tmpl': 'Test-Simple-%(version)s.tar.gz', @@ -1500,6 +1505,8 @@ exts_list = [ 'source_tmpl': 'Term-ReadLine-Gnu-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAYASHI'], 'checksums': ['3c5f1281da2666777af0f34de0289564e6faa823aea54f3945c74c98e95a5e73'], + # make sure that library provided by ncurses dependency is used instead of libtermcap + 'preinstallopts': "sed -s 's/-ltermcap/-lncurses/g' Makefile.PL && ", }), ('ExtUtils::MakeMaker', '7.62', { 'source_tmpl': 'ExtUtils-MakeMaker-%(version)s.tar.gz', @@ -1670,7 +1677,12 @@ exts_list = [ ('Cwd', '3.75', { 'source_tmpl': 'PathTools-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/X/XS/XSAWYERX'], - 'checksums': ['a558503aa6b1f8c727c0073339081a77888606aa701ada1ad62dd9d8c3f945a2'], + 'patches': ['PathTools-3.75_fix-cwd_enoent-test.patch'], + 'checksums': [ + 'a558503aa6b1f8c727c0073339081a77888606aa701ada1ad62dd9d8c3f945a2', + {'PathTools-3.75_fix-cwd_enoent-test.patch': + '7a456a99d9b04a36359f3623f0deef8fe7f472c742f99cdcf0215c50afbbe7b1'}, + ], }), ('MIME::Base64', '3.16', { 'source_tmpl': 'MIME-Base64-%(version)s.tar.gz', diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.34.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.34.1-GCCcore-11.3.0.eb index f30c0c81715..497e05a273d 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.34.1-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.34.1-GCCcore-11.3.0.eb @@ -286,7 +286,12 @@ exts_list = [ ('File::Spec', '3.75', { 'source_tmpl': 'PathTools-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/X/XS/XSAWYERX'], - 'checksums': ['a558503aa6b1f8c727c0073339081a77888606aa701ada1ad62dd9d8c3f945a2'], + 'patches': ['PathTools-3.75_fix-cwd_enoent-test.patch'], + 'checksums': [ + 'a558503aa6b1f8c727c0073339081a77888606aa701ada1ad62dd9d8c3f945a2', + {'PathTools-3.75_fix-cwd_enoent-test.patch': + '7a456a99d9b04a36359f3623f0deef8fe7f472c742f99cdcf0215c50afbbe7b1'}, + ], }), ('Test::Simple', '1.302190', { 'source_tmpl': 'Test-Simple-%(version)s.tar.gz', @@ -1605,6 +1610,8 @@ exts_list = [ 'source_tmpl': 'Term-ReadLine-Gnu-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAYASHI'], 'checksums': ['3c5f1281da2666777af0f34de0289564e6faa823aea54f3945c74c98e95a5e73'], + # make sure that library provided by ncurses dependency is used instead of libtermcap + 'preinstallopts': "sed -s 's/-ltermcap/-lncurses/g' Makefile.PL && ", }), ('ExtUtils::MakeMaker', '7.64', { 'source_tmpl': 'ExtUtils-MakeMaker-%(version)s.tar.gz', @@ -1775,7 +1782,12 @@ exts_list = [ ('Cwd', '3.75', { 'source_tmpl': 'PathTools-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/X/XS/XSAWYERX'], - 'checksums': ['a558503aa6b1f8c727c0073339081a77888606aa701ada1ad62dd9d8c3f945a2'], + 'patches': ['PathTools-3.75_fix-cwd_enoent-test.patch'], + 'checksums': [ + 'a558503aa6b1f8c727c0073339081a77888606aa701ada1ad62dd9d8c3f945a2', + {'PathTools-3.75_fix-cwd_enoent-test.patch': + '7a456a99d9b04a36359f3623f0deef8fe7f472c742f99cdcf0215c50afbbe7b1'}, + ], }), ('MIME::Base64', '3.16', { 'source_tmpl': 'MIME-Base64-%(version)s.tar.gz', diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.1.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.1.0.eb index c865a27e6aa..54c05db3b92 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.1.0.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.1.0.eb @@ -286,7 +286,12 @@ exts_list = [ ('File::Spec', '3.75', { 'source_tmpl': 'PathTools-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/X/XS/XSAWYERX'], - 'checksums': ['a558503aa6b1f8c727c0073339081a77888606aa701ada1ad62dd9d8c3f945a2'], + 'patches': ['PathTools-3.75_fix-cwd_enoent-test.patch'], + 'checksums': [ + 'a558503aa6b1f8c727c0073339081a77888606aa701ada1ad62dd9d8c3f945a2', + {'PathTools-3.75_fix-cwd_enoent-test.patch': + '7a456a99d9b04a36359f3623f0deef8fe7f472c742f99cdcf0215c50afbbe7b1'}, + ], }), ('Test::Simple', '1.302191', { 'source_tmpl': 'Test-Simple-%(version)s.tar.gz', @@ -1598,6 +1603,8 @@ exts_list = [ 'source_tmpl': 'Term-ReadLine-Gnu-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAYASHI'], 'checksums': ['3c5f1281da2666777af0f34de0289564e6faa823aea54f3945c74c98e95a5e73'], + # make sure that library provided by ncurses dependency is used instead of libtermcap + 'preinstallopts': "sed -s 's/-ltermcap/-lncurses/g' Makefile.PL && ", }), ('ExtUtils::MakeMaker', '7.64', { 'source_tmpl': 'ExtUtils-MakeMaker-%(version)s.tar.gz', @@ -1767,7 +1774,12 @@ exts_list = [ ('Cwd', '3.75', { 'source_tmpl': 'PathTools-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/X/XS/XSAWYERX'], - 'checksums': ['a558503aa6b1f8c727c0073339081a77888606aa701ada1ad62dd9d8c3f945a2'], + 'patches': ['PathTools-3.75_fix-cwd_enoent-test.patch'], + 'checksums': [ + 'a558503aa6b1f8c727c0073339081a77888606aa701ada1ad62dd9d8c3f945a2', + {'PathTools-3.75_fix-cwd_enoent-test.patch': + '7a456a99d9b04a36359f3623f0deef8fe7f472c742f99cdcf0215c50afbbe7b1'}, + ], }), ('MIME::Base64', '3.16', { 'source_tmpl': 'MIME-Base64-%(version)s.tar.gz', diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.2.0.eb index cd326152ab6..3a6727d62a4 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.2.0.eb @@ -286,7 +286,12 @@ exts_list = [ ('File::Spec', '3.75', { 'source_tmpl': 'PathTools-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/X/XS/XSAWYERX'], - 'checksums': ['a558503aa6b1f8c727c0073339081a77888606aa701ada1ad62dd9d8c3f945a2'], + 'patches': ['PathTools-3.75_fix-cwd_enoent-test.patch'], + 'checksums': [ + 'a558503aa6b1f8c727c0073339081a77888606aa701ada1ad62dd9d8c3f945a2', + {'PathTools-3.75_fix-cwd_enoent-test.patch': + '7a456a99d9b04a36359f3623f0deef8fe7f472c742f99cdcf0215c50afbbe7b1'}, + ], }), ('Test::Simple', '1.302191', { 'source_tmpl': 'Test-Simple-%(version)s.tar.gz', @@ -1605,6 +1610,8 @@ exts_list = [ 'source_tmpl': 'Term-ReadLine-Gnu-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAYASHI'], 'checksums': ['3c5f1281da2666777af0f34de0289564e6faa823aea54f3945c74c98e95a5e73'], + # make sure that library provided by ncurses dependency is used instead of libtermcap + 'preinstallopts': "sed -s 's/-ltermcap/-lncurses/g' Makefile.PL && ", }), ('ExtUtils::MakeMaker', '7.64', { 'source_tmpl': 'ExtUtils-MakeMaker-%(version)s.tar.gz', @@ -1775,7 +1782,12 @@ exts_list = [ ('Cwd', '3.75', { 'source_tmpl': 'PathTools-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/X/XS/XSAWYERX'], - 'checksums': ['a558503aa6b1f8c727c0073339081a77888606aa701ada1ad62dd9d8c3f945a2'], + 'patches': ['PathTools-3.75_fix-cwd_enoent-test.patch'], + 'checksums': [ + 'a558503aa6b1f8c727c0073339081a77888606aa701ada1ad62dd9d8c3f945a2', + {'PathTools-3.75_fix-cwd_enoent-test.patch': + '7a456a99d9b04a36359f3623f0deef8fe7f472c742f99cdcf0215c50afbbe7b1'}, + ], }), ('MIME::Base64', '3.16', { 'source_tmpl': 'MIME-Base64-%(version)s.tar.gz', diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.36.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.36.1-GCCcore-12.3.0.eb index 6233aaee505..6c8805fbbb9 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.36.1-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.36.1-GCCcore-12.3.0.eb @@ -54,7 +54,12 @@ exts_list = [ ('File::Spec', '3.75', { 'source_tmpl': 'PathTools-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/X/XS/XSAWYERX'], - 'checksums': ['a558503aa6b1f8c727c0073339081a77888606aa701ada1ad62dd9d8c3f945a2'], + 'patches': ['PathTools-3.75_fix-cwd_enoent-test.patch'], + 'checksums': [ + 'a558503aa6b1f8c727c0073339081a77888606aa701ada1ad62dd9d8c3f945a2', + {'PathTools-3.75_fix-cwd_enoent-test.patch': + '7a456a99d9b04a36359f3623f0deef8fe7f472c742f99cdcf0215c50afbbe7b1'}, + ], }), ('IO::File', '1.51', { 'source_tmpl': 'IO-%(version)s.tar.gz', diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.36.1-GCCcore-13.1.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.36.1-GCCcore-13.1.0.eb index 9666a1b1a4d..3ecf2a9c4ee 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.36.1-GCCcore-13.1.0.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.36.1-GCCcore-13.1.0.eb @@ -54,7 +54,12 @@ exts_list = [ ('File::Spec', '3.75', { 'source_tmpl': 'PathTools-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/X/XS/XSAWYERX'], - 'checksums': ['a558503aa6b1f8c727c0073339081a77888606aa701ada1ad62dd9d8c3f945a2'], + 'patches': ['PathTools-3.75_fix-cwd_enoent-test.patch'], + 'checksums': [ + 'a558503aa6b1f8c727c0073339081a77888606aa701ada1ad62dd9d8c3f945a2', + {'PathTools-3.75_fix-cwd_enoent-test.patch': + '7a456a99d9b04a36359f3623f0deef8fe7f472c742f99cdcf0215c50afbbe7b1'}, + ], }), ('IO::File', '1.51', { 'source_tmpl': 'IO-%(version)s.tar.gz', diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.38.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.38.0-GCCcore-13.2.0.eb index 1620e4f9dfa..95b8a2f7556 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.38.0-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.38.0-GCCcore-13.2.0.eb @@ -49,7 +49,12 @@ exts_list = [ ('File::Spec', '3.75', { 'source_tmpl': 'PathTools-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/X/XS/XSAWYERX'], - 'checksums': ['a558503aa6b1f8c727c0073339081a77888606aa701ada1ad62dd9d8c3f945a2'], + 'patches': ['PathTools-3.75_fix-cwd_enoent-test.patch'], + 'checksums': [ + 'a558503aa6b1f8c727c0073339081a77888606aa701ada1ad62dd9d8c3f945a2', + {'PathTools-3.75_fix-cwd_enoent-test.patch': + '7a456a99d9b04a36359f3623f0deef8fe7f472c742f99cdcf0215c50afbbe7b1'}, + ], }), ('IO::File', '1.51', { 'source_tmpl': 'IO-%(version)s.tar.gz', diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.38.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.38.0.eb index 059a04bfd90..c70f7d59df9 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.38.0.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.38.0.eb @@ -54,7 +54,12 @@ exts_list = [ ('File::Spec', '3.75', { 'source_tmpl': 'PathTools-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/X/XS/XSAWYERX'], - 'checksums': ['a558503aa6b1f8c727c0073339081a77888606aa701ada1ad62dd9d8c3f945a2'], + 'patches': ['PathTools-3.75_fix-cwd_enoent-test.patch'], + 'checksums': [ + 'a558503aa6b1f8c727c0073339081a77888606aa701ada1ad62dd9d8c3f945a2', + {'PathTools-3.75_fix-cwd_enoent-test.patch': + '7a456a99d9b04a36359f3623f0deef8fe7f472c742f99cdcf0215c50afbbe7b1'}, + ], }), ('IO::File', '1.51', { 'source_tmpl': 'IO-%(version)s.tar.gz', diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.38.2-GCCcore-13.3.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.38.2-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..f704ad30bdd --- /dev/null +++ b/easybuild/easyconfigs/p/Perl/Perl-5.38.2-GCCcore-13.3.0.eb @@ -0,0 +1,86 @@ +name = 'Perl' +version = '5.38.2' + +homepage = 'https://www.perl.org/' +description = """Larry Wall's Practical Extraction and Report Language + +Includes a small selection of extra CPAN packages for core functionality. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.cpan.org/src/%(version_major)s.0'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['a0a31534451eb7b83c7d6594a497543a54d488bc90ca00f5e34762577f40655e'] + +builddependencies = [ + ('binutils', '2.42'), +] + +dependencies = [ + ('zlib', '1.3.1'), +] + +# !! order of extensions is important !! +# extensions updated on 2023-09-03 +# includes all dependencies for Autotools +exts_list = [ + ('threads', '2.21', { + 'source_tmpl': 'threads-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JD/JDHEDDEN'], + 'checksums': ['28394c98a2bcae6f20ffb8a3d965a1c194b764c650169e2050ee38dbaa10f110'], + }), + ('constant', '1.33', { + 'source_tmpl': 'constant-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['79965d4130eb576670e27ca0ae6899ef0060c76da48b02b97682166882f1b504'], + }), + ('Getopt::Long', '2.57', { + 'source_tmpl': 'Getopt-Long-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JV/JV'], + 'checksums': ['d3791e6bf167708364ea5ad3be578dc9173a0076167160a4341c05a1e979795e'], + }), + ('File::Path', '2.18', { + 'source_tmpl': 'File-Path-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JK/JKEENAN/'], + 'checksums': ['980f0a17edb353df46e9cd7b357f9f5929cde0f80c45fd7a06cf7e0e8bd6addd'], + }), + ('File::Spec', '3.75', { + 'source_tmpl': 'PathTools-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/X/XS/XSAWYERX'], + 'checksums': ['a558503aa6b1f8c727c0073339081a77888606aa701ada1ad62dd9d8c3f945a2'], + }), + ('IO::File', '1.55', { + 'source_tmpl': 'IO-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TODDR/'], + 'checksums': ['0443afebb9a48f29611e9b17a017f430b51167a498fa4646c07f8dce03b6b95f'], + }), + ('Thread::Queue', '3.13', { + 'source_tmpl': 'Thread-Queue-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JD/JDHEDDEN'], + 'checksums': ['6ba3dacddd2fbb66822b4aa1d11a0a5273cd04c825cb3ff31c20d7037cbfdce8'], + }), + ('Carp', '1.50', { + 'source_tmpl': 'Carp-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/X/XS/XSAWYERX'], + 'checksums': ['f5273b4e1a6d51b22996c48cb3a3cbc72fd456c4038f5c20b127e2d4bcbcebd9'], + }), + ('Exporter', '5.78', { + 'source_tmpl': 'Exporter-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TODDR'], + 'checksums': ['bd17e99219aa2fb6a8acb3d11deffcb588708c70fc29f346e20ea7f71d3a48f0'], + }), + ('Text::ParseWords', '3.31', { + 'source_tmpl': 'Text-ParseWords-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NE/NEILB/'], + 'checksums': ['2ae555ba084d75b2b8feeeb8d1a00911276815ada86bccb1452236964d5a2fc7'], + }), + ('Data::Dumper', '2.183', { + 'source_tmpl': 'Data-Dumper-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NW/NWCLARK/'], + 'checksums': ['e42736890b7dae1b37818d9c5efa1f1fdc52dec04f446a33a4819bf1d4ab5ad3'], + }), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Phonopy-Spectroscopy/Phonopy-Spectroscopy-20240308-foss-2023a.eb b/easybuild/easyconfigs/p/Phonopy-Spectroscopy/Phonopy-Spectroscopy-20240308-foss-2023a.eb new file mode 100644 index 00000000000..d2eb062ba0e --- /dev/null +++ b/easybuild/easyconfigs/p/Phonopy-Spectroscopy/Phonopy-Spectroscopy-20240308-foss-2023a.eb @@ -0,0 +1,43 @@ +easyblock = 'Tarball' + +name = 'Phonopy-Spectroscopy' +version = '20240308' +local_commit = '316fbf4' + +homepage = 'https://github.com/skelton-group/Phonopy-Spectroscopy' +description = """ +Phonopy-Spectroscopy is a project to add the capability to simulate vibrational spectra to +the Phonopy code. +""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['https://github.com/skelton-group/Phonopy-Spectroscopy/archive/'] +sources = ['%s.tar.gz' % local_commit] +checksums = ['4fbfed5253ddaebee70e8a3b650ca83184785b04024920060753cdb283c48b8b'] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), # for numpy + ('PyYAML', '6.0'), + ('phonopy', '2.20.0'), +] + +postinstallcmds = ['chmod +x %(installdir)s/scripts/*'] + +sanity_check_paths = { + 'files': ['scripts/phonopy-ir'], + 'dirs': ['lib/spectroscopy'], +} + +sanity_check_commands = [ + 'phonopy-ir --help', + 'xyz2poscar -h', +] + +modextrapaths = { + 'PYTHONPATH': 'lib', + 'PATH': 'scripts', +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/Pillow-SIMD/Pillow-SIMD-10.4.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/p/Pillow-SIMD/Pillow-SIMD-10.4.0-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..e752171a582 --- /dev/null +++ b/easybuild/easyconfigs/p/Pillow-SIMD/Pillow-SIMD-10.4.0-GCCcore-13.3.0.eb @@ -0,0 +1,48 @@ +easyblock = 'PythonPackage' + +name = 'Pillow-SIMD' +version = '10.4.0' + +homepage = 'https://github.com/uploadcare/pillow-simd' +description = """Pillow is the 'friendly PIL fork' by Alex Clark and Contributors. + PIL is the Python Imaging Library by Fredrik Lundh and Contributors.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://github.com/uploadcare/pillow-simd/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['8c7c3c0fc2952ff11b9a8c60365e098ee5334427dd5688c3584e77c25a7e1b3f'] + +builddependencies = [('binutils', '2.42')] + +dependencies = [ + ('Python', '3.12.3'), + ('libjpeg-turbo', '3.0.1'), + ('libpng', '1.6.43'), + ('zlib', '1.3.1'), + ('LibTIFF', '4.6.0'), + ('freetype', '2.13.2'), + ('libwebp', '1.4.0'), + ('OpenJPEG', '2.5.2'), + ('LittleCMS', '2.16'), +] + +use_pip = True +download_dep_fail = True + +# patch setup.py to prefix hardcoded /usr/* and /lib paths with value of %(sysroot) template +# (which will be empty if EasyBuild is not configured to use an alternate sysroot); +# see also https://gitlab.com/eessi/support/-/issues/9 +preinstallopts = """sed -i 's@"/usr/@"%(sysroot)s/usr/@g' setup.py && """ +preinstallopts += """sed -i 's@"/lib@"%(sysroot)s/lib@g' setup.py && """ + +options = {'modulename': 'PIL'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/PIL'], +} + +sanity_pip_check = True + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-10.4.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/p/Pillow/Pillow-10.4.0-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..34c086c859a --- /dev/null +++ b/easybuild/easyconfigs/p/Pillow/Pillow-10.4.0-GCCcore-13.3.0.eb @@ -0,0 +1,43 @@ +easyblock = 'PythonPackage' + +name = 'Pillow' +version = '10.4.0' + +homepage = 'https://pillow.readthedocs.org/' +description = """Pillow is the 'friendly PIL fork' by Alex Clark and Contributors. + PIL is the Python Imaging Library by Fredrik Lundh and Contributors.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['166c1cd4d24309b30d61f79f4a9114b7b2313d7450912277855ff5dfd7cd4a06'] + +builddependencies = [('binutils', '2.42')] +dependencies = [ + ('Python', '3.12.3'), + ('libjpeg-turbo', '3.0.1'), + ('libpng', '1.6.43'), + ('zlib', '1.3.1'), + ('LibTIFF', '4.6.0'), + ('freetype', '2.13.2'), + ('libwebp', '1.4.0'), + ('OpenJPEG', '2.5.2'), + ('LittleCMS', '2.16'), +] + +# patch setup.py to prefix hardcoded /usr/* and /lib paths with value of %(sysroot) template +# (which will be empty if EasyBuild is not configured to use an alternate sysroot); +# see also https://gitlab.com/eessi/support/-/issues/9 +preinstallopts = """sed -i 's@"/usr/@"%(sysroot)s/usr/@g' setup.py && """ +preinstallopts += """sed -i 's@"/lib@"%(sysroot)s/lib@g' setup.py && """ + +# avoid that hardcoded paths like /usr/include are used in build commands +installopts = "--global-option=build_ext --global-option='--disable-platform-guessing' " + +download_dep_fail = True +sanity_pip_check = True +use_pip = True + +options = {'modulename': 'PIL'} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/Pint/Pint-0.24-GCCcore-13.2.0.eb b/easybuild/easyconfigs/p/Pint/Pint-0.24-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..40b50dbb060 --- /dev/null +++ b/easybuild/easyconfigs/p/Pint/Pint-0.24-GCCcore-13.2.0.eb @@ -0,0 +1,43 @@ +easyblock = 'PythonBundle' + +name = 'Pint' +version = '0.24' + +homepage = 'https://github.com/hgrecco/pint' +description = """Pint is a Python package to define, operate and +manipulate physical quantities: the product of a numerical value and a +unit of measurement. It allows arithmetic operations between them and +conversions from and to different units.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +builddependencies = [ + ('binutils', '2.40'), + ('hatchling', '1.18.0'), +] + +dependencies = [ + ('Python', '3.11.5'), +] + +use_pip = True + +exts_list = [ + ('appdirs', '1.4.4', { + 'checksums': ['7d5d0167b2b1ba821647616af46a749d1c653740dd0d2415100fe26e27afdf41'], + }), + ('flexcache', '0.3', { + 'checksums': ['18743bd5a0621bfe2cf8d519e4c3bfdf57a269c15d1ced3fb4b64e0ff4600656'], + }), + ('flexparser', '0.3.1', { + 'checksums': ['36f795d82e50f5c9ae2fde1c33f21f88922fdd67b7629550a3cc4d0b40a66856'], + }), + (name, version, { + 'sources': [SOURCELOWER_TAR_GZ], + 'checksums': ['c6c7c027b821413db1ac46b3b7bd296592848b5aec29a88cfc6e378fd1371903'], + }), +] + +sanity_pip_check = True + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/p/Platypus-Opt/Platypus-Opt-1.2.0-foss-2022b.eb b/easybuild/easyconfigs/p/Platypus-Opt/Platypus-Opt-1.2.0-foss-2022b.eb new file mode 100644 index 00000000000..a0e995d4f45 --- /dev/null +++ b/easybuild/easyconfigs/p/Platypus-Opt/Platypus-Opt-1.2.0-foss-2022b.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'Platypus-Opt' +version = '1.2.0' + +homepage = 'https://github.com/Project-Platypus/Platypus' +description = """Platypus is a framework for evolutionary computing in Python with a focus on + multiobjective evolutionary algorithms (MOEAs).""" + +toolchain = {'name': 'foss', 'version': '2022b'} + +sources = [SOURCE_TAR_GZ] +checksums = ['f7150de2e24f8003c911259c575493c9351a7dcfb132445a3f3b096728634e6a'] + +dependencies = [ + ('Python', '3.10.8'), + ('SciPy-bundle', '2023.02'), + ('mpi4py', '3.1.4'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +options = {'modulename': 'platypus'} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/p/PnetCDF/PnetCDF-1.13.0-gompi-2024a.eb b/easybuild/easyconfigs/p/PnetCDF/PnetCDF-1.13.0-gompi-2024a.eb new file mode 100644 index 00000000000..b586cfd0da4 --- /dev/null +++ b/easybuild/easyconfigs/p/PnetCDF/PnetCDF-1.13.0-gompi-2024a.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'PnetCDF' +version = '1.13.0' + +homepage = 'https://parallel-netcdf.github.io/' +description = "Parallel netCDF: A Parallel I/O Library for NetCDF File Access" + +toolchain = {'name': 'gompi', 'version': '2024a'} + +source_urls = ['https://parallel-netcdf.github.io/Release'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['aba0f1c77a51990ba359d0f6388569ff77e530ee574e40592a1e206ed9b2c491'] + +builddependencies = [ + ('Autotools', '20231222'), + ('Perl', '5.38.2'), +] + +preconfigopts = "autoreconf -f -i && " +configopts = [ + '', + '--enable-shared', +] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['ncmpidiff', 'ncmpidump', 'ncmpigen', 'ncoffsets', + 'ncvalidator', 'pnetcdf-config', 'pnetcdf_version']] + + ['lib/lib%(namelower)s.a', 'lib/lib%%(namelower)s.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +modextrapaths = {'PNETCDF': ''} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/p/PoPoolation-TE2/PoPoolation-TE2-1.10.03-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/PoPoolation-TE2/PoPoolation-TE2-1.10.03-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..e93f4a079c6 --- /dev/null +++ b/easybuild/easyconfigs/p/PoPoolation-TE2/PoPoolation-TE2-1.10.03-GCCcore-12.3.0.eb @@ -0,0 +1,60 @@ +easyblock = 'JAR' + +name = 'PoPoolation-TE2' +version = '1.10.03' + +homepage = 'https://sourceforge.net/p/popoolation-te2/wiki/Home/' +description = """ +PoPoolationTE2: enables comparative population genomics of transposable elements (TE). As a +major innovation PoPoolation TE2 introduces the physical pileup file which allows to +homogenize the power to identify TEs and thus enables an unbiased comparison of TE abundance +between samples, where samples could be pooled populations, tissues or sequenced individuals. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +builddependencies = [('binutils', '2.40')] + +dependencies = [ + ('BWA', '0.7.17'), + ('Java', '11', '', SYSTEM), +] + +source_urls = ['https://sourceforge.net/projects/popoolation-te2/files/'] +sources = [ + { + 'filename': 'popte2.jar', + 'download_filename': 'popte2-v%(version)s.jar', + }, + 'walkthrough-refgenome.zip', + 'walkthrough-reads.zip', + +] +checksums = [ + {'popte2.jar': '95eca422a6d295277d20ec1cbbcb9000bad1f380ae7cba9005f20ff211907e32'}, + {'walkthrough-refgenome.zip': 'ce3cb0b952a99fcae6b348cd888ee6f4c3a45d7e0b208e211ecb290cacde618c'}, + {'walkthrough-reads.zip': '909a8f1d507bb20518f6ef1ac313a59b8e8b02b70fc911e2d6d6efdce2e258f3'}, +] + +postinstallcmds = [ + "cd %(installdir)s && unzip walkthrough-refgenome.zip", + "cd %(installdir)s && unzip walkthrough-reads.zip", + "cd %(installdir)s && rm walkthrough-refgenome.zip walkthrough-reads.zip", +] + +sanity_check_commands = [ + 'java -jar $EBROOTPOPOOLATIONMINTE2/popte2.jar --help 2>&1 | grep "Usage: java"', +] + +sanity_check_paths = { + 'files': ['popte2.jar'], + 'dirs': ['walkthrough-refgenome', 'walkthrough-reads'], +} + +modloadmsg = """ +To execute PoPoolation-TE2 run: java -jar $EBROOTPOPOOLATIONMINTE2/popte2.jar +The reference genome and the Te-hierachy can be found in $EBROOTPOPOOLATIONMINTE2/walkthrough-refgenome +Reads provided by the developer can be found under $EBROOTPOPOOLATIONMINTE2/walkthrough-reads +""" + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/Porechop/Porechop-0.2.4-20240119-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/Porechop/Porechop-0.2.4-20240119-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..e1dfa5d567c --- /dev/null +++ b/easybuild/easyconfigs/p/Porechop/Porechop-0.2.4-20240119-GCCcore-12.3.0.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonPackage' + +name = 'Porechop' +version = '0.2.4-20240119' +local_commit = 'd2e77c6' + +homepage = 'https://github.com/dehui333/Porechop' +description = """Porechop is a tool for finding and removing adapters from Oxford Nanopore reads. + Adapters on the ends of reads are trimmed off, and when a read has an adapter in its middle, + it is treated as chimeric and chopped into separate reads. Porechop performs thorough alignments + to effectively find adapters, even at low sequence identity.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://github.com/dehui333/Porechop/archive/'] +sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}] +checksums = ['6e5ff3a780fc2855b0101b4a6102437d9a0fc201e40ffabc44c0c67d7c9ad621'] + +builddependencies = [('binutils', '2.40')] +dependencies = [('Python', '3.11.3')] + +sanity_pip_check = True +use_pip = True +download_dep_fail = True + +sanity_check_commands = ['%(namelower)s -h'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-16.4-GCCcore-13.3.0.eb b/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-16.4-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..9b4c1f62855 --- /dev/null +++ b/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-16.4-GCCcore-13.3.0.eb @@ -0,0 +1,43 @@ +easyblock = 'ConfigureMake' + +name = 'PostgreSQL' +version = '16.4' + +homepage = 'https://www.postgresql.org/' +description = """PostgreSQL is a powerful, open source object-relational database system. + It is fully ACID compliant, has full support for foreign keys, + joins, views, triggers, and stored procedures (in multiple languages). + It includes most SQL:2008 data types, including INTEGER, + NUMERIC, BOOLEAN, CHAR, VARCHAR, DATE, INTERVAL, and TIMESTAMP. + It also supports storage of binary large objects, including pictures, + sounds, or video. It has native programming interfaces for C/C++, Java, + .Net, Perl, Python, Ruby, Tcl, ODBC, among others, and exceptional documentation.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['http://ftp.postgresql.org/pub/source/v%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['2e17a90062403e15d6540480fdec50c8b005eb48729a91cb4989ffeb04df193c'] + +builddependencies = [ + ('binutils', '2.42'), + ('Bison', '3.8.2'), + ('flex', '2.6.4'), + ('Perl', '5.38.2'), + ('Python', '3.12.3'), +] + +dependencies = [ + ('libreadline', '8.2'), + ('zlib', '1.3.1'), + ('OpenSSL', '3', '', SYSTEM), +] + +configopts = '--with-python --with-openssl --without-icu' + +sanity_check_paths = { + 'files': ['bin/psql', 'bin/pg_config', 'lib/libpq.a', 'lib/libpq.%s' % SHLIB_EXT], + 'dirs': ['share/postgresql'], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/p/PretextMap/PretextMap-0.1.9-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/PretextMap/PretextMap-0.1.9-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..69972971936 --- /dev/null +++ b/easybuild/easyconfigs/p/PretextMap/PretextMap-0.1.9-GCCcore-12.3.0.eb @@ -0,0 +1,41 @@ +easyblock = 'MesonNinja' + +name = 'PretextMap' +version = '0.1.9' + +homepage = 'https://github.com/sanger-tol/PretextMap/' +description = """Paired REad TEXTure Mapper. Converts SAM formatted read pairs into genome contact maps.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +sources = [{ + 'filename': '%(version)s.tar.gz', + 'git_config': { + 'url': 'https://github.com/sanger-tol', + 'repo_name': '%(name)s', + 'tag': '%(version)s', + 'recursive': True, + 'keep_git_dir': True, + }, +}] +checksums = [None] + +builddependencies = [ + ('binutils', '2.40'), + ('Meson', '1.1.1'), + ('Ninja', '1.11.1'), + ('Clang', '16.0.6'), +] + +preconfigopts = 'CXX=clang && ' +configure_cmd = 'meson setup --buildtype=release --unity on' +runtest = 'meson test' + +sanity_check_paths = { + 'files': [], + 'dirs': ['bin'] +} + +sanity_check_commands = ["command -v PretextMap"] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/ProteinMPNN/ProteinMPNN-1.0.1-20230627-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/p/ProteinMPNN/ProteinMPNN-1.0.1-20230627-foss-2022a-CUDA-11.7.0.eb new file mode 100644 index 00000000000..db7151ab47f --- /dev/null +++ b/easybuild/easyconfigs/p/ProteinMPNN/ProteinMPNN-1.0.1-20230627-foss-2022a-CUDA-11.7.0.eb @@ -0,0 +1,46 @@ +# Author: Lara Peeters (UGent) + +easyblock = 'Tarball' + +name = 'ProteinMPNN' +version = '1.0.1-20230627' +local_commit = '8907e6671bfbfc92303b5f79c4b5e6ce47cdef57' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/dauparas/ProteinMPNN' +description = """A deep learning based protein sequence design method is +described that is widely applicable to current design challenges and shows +outstanding performance in both in silico and experimental tests. +""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +github_account = 'dauparas' +source_urls = [GITHUB_SOURCE] +sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}] +checksums = ['2e11f385074facb06e12496acde80756b34504f0f70bf78714fb07fe9244f398'] + +dependencies = [ + ('CUDA', '11.7.0', '', SYSTEM), + ('PyTorch', '1.12.0', versionsuffix), + ('torchvision', '0.13.1', versionsuffix), + ('torchaudio', '0.12.0', '-PyTorch-1.12.0' + versionsuffix), +] + +postinstallcmds = [ + 'chmod a+x %(installdir)s/protein_mpnn_run.py', + 'chmod a+x %(installdir)s/helper_scripts/*.py' +] + +sanity_check_paths = { + 'files': ['protein_mpnn_run.py'], + 'dirs': ['examples'], +} + +fix_python_shebang_for = ['protein_mpnn_run.py', 'helper_scripts/*.py'] + +sanity_check_commands = ['protein_mpnn_run.py --help'] + +modextrapaths = {'PATH': ['', 'helper_scripts']} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/Proteinortho/Proteinortho-6.3.2-gompi-2023a.eb b/easybuild/easyconfigs/p/Proteinortho/Proteinortho-6.3.2-gompi-2023a.eb new file mode 100644 index 00000000000..4cd050e7d31 --- /dev/null +++ b/easybuild/easyconfigs/p/Proteinortho/Proteinortho-6.3.2-gompi-2023a.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'Proteinortho' +version = '6.3.2' + +homepage = 'https://www.bioinf.uni-leipzig.de/Software/proteinortho' +description = "Proteinortho is a tool to detect orthologous genes within different species." + +toolchain = {'name': 'gompi', 'version': '2023a'} + +source_urls = ['https://gitlab.com/paulklemm_PHD/proteinortho/-/archive/v%(version)s/'] +sources = ['proteinortho-v%(version)s.tar.gz'] +checksums = ['3b3c58e814ca10f77a25954b0bcddc479b9f61682f3dc5c93d85b07f109342a4'] + +dependencies = [ + ('Perl', '5.36.1'), + ('Python', '3.11.3'), + ('BLAST+', '2.14.1'), + ('DIAMOND', '2.1.8'), +] + +skipsteps = ['configure'] + +preinstallopts = "mkdir -p %(installdir)s/bin && " +installopts = "PREFIX=%(installdir)s/bin" + +sanity_check_paths = { + 'files': ['bin/proteinortho', 'bin/proteinortho%(version_major)s.pl', 'bin/proteinortho_clustering'], + 'dirs': [], +} + +sanity_check_commands = ["proteinortho --help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/PyAEDT/PyAEDT-0.8.7-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/PyAEDT/PyAEDT-0.8.7-GCCcore-12.3.0.eb index aee9ba9ea19..894b488cd3e 100644 --- a/easybuild/easyconfigs/p/PyAEDT/PyAEDT-0.8.7-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/p/PyAEDT/PyAEDT-0.8.7-GCCcore-12.3.0.eb @@ -43,6 +43,7 @@ exts_list = [ ('ansys-pythonnet', '3.1.0rc3', { 'checksums': ['369a0a5a838a0991f755b6d63c319ab6997f9dc464d016187227be5cd860a9cb'], 'modulename': 'pythonnet', + 'preinstallopts': 'export OPENSSL_ENABLE_SHA1_SIGNATURES=1 &&', }), ('pytomlpp', '1.0.13', { 'checksums': ['a0bd639a8f624d1bdf5b3ea94363ca23dbfef38ab7b5b9348881a84afab434ad'], diff --git a/easybuild/easyconfigs/p/PyAEDT/PyAEDT-0.9.9-gfbf-2023b.eb b/easybuild/easyconfigs/p/PyAEDT/PyAEDT-0.9.9-gfbf-2023b.eb new file mode 100644 index 00000000000..f2436367baa --- /dev/null +++ b/easybuild/easyconfigs/p/PyAEDT/PyAEDT-0.9.9-gfbf-2023b.eb @@ -0,0 +1,78 @@ +easyblock = 'PythonBundle' + +name = 'PyAEDT' +version = '0.9.9' + +homepage = 'https://aedt.docs.pyansys.com/version/stable' +description = """PyAEDT is a Python library that interacts directly with the +Ansys Electronics Desktop (AEDT) API, enabling straightforward and efficient +automation in your workflow.""" + +toolchain = {'name': 'gfbf', 'version': '2023b'} + +builddependencies = [ + ('binutils', '2.40'), + ('hatchling', '1.18.0'), +] + +dependencies = [ + ('dotNET-Core', '8.0', '', SYSTEM), + ('libspatialindex', '1.9.3'), + ('Python', '3.11.5'), + ('Python-bundle-PyPI', '2023.10'), + ('Pillow', '10.2.0'), + ('pydantic', '2.6.4'), + ('SciPy-bundle', '2023.11'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('dotnetcore2', '3.1.23', { + 'sources': ['dotnetcore2-3.1.23-py3-none-manylinux1_x86_64.whl'], + 'checksums': ['5f076ddc39da0c685e7de20ecb91ee81185928918ec86fbeb3bffc55dd867ab5'], + }), + ('clr_loader', '0.2.6', { + 'checksums': ['019348ae6b6a83c7a406d14537c277cecf7a3a53b263ec342c81ded5845a67ee'], + }), + ('defusedxml', '0.7.1', { + 'checksums': ['1bb3032db185915b62d7c6209c5a8792be6a32ab2fedacc84e01b52c51aa3e69'], + }), + ('fonttools', '4.53.1', { + 'modulename': 'fontTools', + 'checksums': ['e128778a8e9bc11159ce5447f76766cefbd876f44bd79aff030287254e4752c4'], + }), + ('ansys-pythonnet', '3.1.0rc3', { + 'modulename': 'pythonnet', + 'checksums': ['369a0a5a838a0991f755b6d63c319ab6997f9dc464d016187227be5cd860a9cb'], + 'preinstallopts': 'export OPENSSL_ENABLE_SHA1_SIGNATURES=1 &&', + }), + ('pytomlpp', '1.0.13', { + 'checksums': ['a0bd639a8f624d1bdf5b3ea94363ca23dbfef38ab7b5b9348881a84afab434ad'], + }), + ('fpdf2', '2.7.9', { + 'modulename': 'fpdf', + 'checksums': ['f364c0d816a5e364eeeda9761cf5c961bae8c946f080cf87fed7f38ab773b318'], + }), + ('plumbum', '1.8.3', { + 'checksums': ['6092c85ab970b7a7a9d5d85c75200bc93be82b33c9bdf640ffa87d2d7c8709f0'], + }), + ('rpyc', '6.0.0', { + 'checksums': ['a7e12b31f40978cbd6b74e0b713da389d4b2565cef612adcb0f4b41aeb188230'], + }), + ('rtree', '1.3.0', { + 'modulename': 'rtree', + 'checksums': ['b36e9dd2dc60ffe3d02e367242d2c26f7281b00e1aaf0c39590442edaaadd916'], + }), + ('pyedb', '0.21.0', { + 'checksums': ['3c91cb8a72a080864d3582ae7ec1de2f04d90aee477dadc096a7144f7823258d'], + }), + ('pyaedt', version, { + 'checksums': ['714728230ab3ede4744a30a7c0d45aaa104cdc1887bfbfe8feb928a8f10cc72f'], + }), +] + +modloadmsg = "NOTE: You also need load a AEDT module before you start using PyAEDT." + +moduleclass = "phys" diff --git a/easybuild/easyconfigs/p/PyBEL/PyBEL-0.15.5-gfbf-2023a.eb b/easybuild/easyconfigs/p/PyBEL/PyBEL-0.15.5-gfbf-2023a.eb new file mode 100644 index 00000000000..40c17e035ce --- /dev/null +++ b/easybuild/easyconfigs/p/PyBEL/PyBEL-0.15.5-gfbf-2023a.eb @@ -0,0 +1,76 @@ +easyblock = 'PythonBundle' + +name = 'PyBEL' +version = '0.15.5' + +homepage = 'https://github.com/pybel/pybel' +description = """ +PyBEL is a pure Python software package that parses BEL (Biological Expression Language) +documents, validates their semantics, and facilitates data interchange between common formats +and database systems like JSON, CSV, Excel, SQL, CX, and Neo4J. +""" + +toolchain = {'name': 'gfbf', 'version': '2023a'} + +builddependencies = [ + ('hatchling', '1.18.0'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('networkx', '3.1'), + ('SQLAlchemy', '2.0.25'), + ('tqdm', '4.66.1'), + ('pydantic', '2.5.3'), # for bioregistry +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('multisplitby', '0.0.1', { + 'checksums': ['e40489fa174fd7afd28a895477e6eefc64d6cfd863cca6900530e436a40e356f'], + }), + ('bel_resources', '0.0.3', { + 'checksums': ['ec2d6390f89c0a98d67868bf02f7538709df0ba5b5ba6ddeb105512da07e82b5'], + }), + ('PyTrie', '0.4.0', { + 'checksums': ['8f4488f402d3465993fb6b6efa09866849ed8cda7903b50647b7d0342b805379'], + }), + ('curies', '0.7.9', { + 'checksums': ['3b63c5fea7b0e967629a3a384b1a8c59b56c503487c1dcbacddeab59e25db4d8'], + }), + ('more_click', '0.1.2', { + 'checksums': ['085da66d5a9b823c5d912a888dca1fa0c8b3a14ed1b21ea9c8a1b814857a3981'], + }), + ('bioregistry', '0.11.10', { + 'checksums': ['d3e155ba38d88f5e4a84a2d337c33109f3434f6b2e64a285eba14817ed5c4492'], + }), + ('click-plugins', '1.1.1', { + 'checksums': ['46ab999744a9d831159c3411bb0c79346d94a444df9a3a3742e9ed63645f264b'], + }), + ('humanize', '4.8.0', { + 'checksums': ['9783373bf1eec713a770ecaa7c2d7a7902c98398009dfa3d8a2df91eec9311e8'], + }), + ('psycopg2-binary', '2.9.9', { + 'modulename': 'psycopg2', + 'checksums': ['7f01846810177d829c7692f1f5ada8096762d9172af1b1a28d4ab5b77c923c1c'], + }), + ('pystow', '0.5.4', { + 'checksums': ['2692180cb405bd77259bee6c7f4db545d10e81939980064730609f21750567ff'], + }), + ('ratelimit', '2.2.1', { + 'checksums': ['af8a9b64b821529aca09ebaf6d8d279100d766f19e90b5059ac6a718ca6dee42'], + }), + ('requests_file', '2.1.0', { + 'checksums': ['0f549a3f3b0699415ac04d167e9cb39bccfb730cb832b4d20be3d9867356e658'], + }), + ('pybel', version, { + 'checksums': ['c2aabd0ad65b9f205f9ed6eae126d19875c1312f8e35641f4f42bcc1fc573f9e'], + }), +] + +sanity_check_commands = ["pybel --help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/PyBerny/PyBerny-0.6.3-foss-2023a.eb b/easybuild/easyconfigs/p/PyBerny/PyBerny-0.6.3-foss-2023a.eb new file mode 100644 index 00000000000..71cb5554837 --- /dev/null +++ b/easybuild/easyconfigs/p/PyBerny/PyBerny-0.6.3-foss-2023a.eb @@ -0,0 +1,43 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 +# Update: Petr Král (INUITS) + +easyblock = 'PythonBundle' + +name = 'PyBerny' +version = '0.6.3' + +homepage = 'https://github.com/jhrmnn/pyberny' +description = """PyBerny is an optimizer of molecular geometries with respect to the total energy, +using nuclear gradient information.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [ + ('poetry', '1.7.1'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), +] + +use_pip = True + +exts_list = [ + ('pyberny', version, { + 'modulename': 'berny', + 'checksums': ['b4bd9d3d2d58261e8f1d91b8204cc563617044d4b9daf6aae8feee31893cb336'], + }), +] + +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/berny'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["berny -h"] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/p/PyBioLib/PyBioLib-1.1.2250-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/PyBioLib/PyBioLib-1.1.2250-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..02c4c54ce07 --- /dev/null +++ b/easybuild/easyconfigs/p/PyBioLib/PyBioLib-1.1.2250-GCCcore-12.3.0.eb @@ -0,0 +1,54 @@ +easyblock = "PythonBundle" + +name = 'PyBioLib' +version = '1.1.2250' + +homepage = 'https://biolib.com/' +description = """PyBioLib is a Python package for running BioLib applications from Python +scripts and the command line. +BioLib is a library of biological data science applications. Applications on +BioLib range from small bioinformatics utilities to state-of-the-art machine +learning algorithms for predicting characteristics of biological molecules.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +builddependencies = [ + ('binutils', '2.40'), + ('poetry', '1.5.1'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('Flask', '2.3.3'), + ('PyYAML', '6.0'), +] + +use_pip = True + +exts_list = [ + ('websocket_client', '1.8.0', { + 'modulename': 'websocket', + 'checksums': ['3239df9f44da632f96012472805d40a23281a991027ce11d2f45a6f24ac4c3da'], + }), + ('docker', '7.1.0', { + 'checksums': ['ad8c70e6e3f8926cb8a92619b832b4ea5299e2831c14284663184e200546fa6c'], + }), + ('PyJWT', '2.9.0', { + 'modulename': 'jwt', + 'source_tmpl': SOURCELOWER_TAR_GZ, + 'checksums': ['7e1e5b56cc735432a7369cbfa0efe50fa113ebecdc04ae6922deba8b84582d0c'], + }), + ('gunicorn', '23.0.0', { + 'checksums': ['f014447a0101dc57e294f6c18ca6b40227a4c90e9bdb586042628030cba004ec'], + }), + ('pybiolib', version, { + 'modulename': 'biolib', + 'preinstallopts': "sed -i 's/< 8.1.0/< 8.2.0/' pyproject.toml &", + 'checksums': ['1a0fb4a0256bfa8345b881ac9697cf94a50bcab2caa9ad063689dfc0035fe5a2'], + }), +] + +sanity_pip_check = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/PyBioLib/PyBioLib-1.2.205-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/PyBioLib/PyBioLib-1.2.205-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..fe4e8b0e393 --- /dev/null +++ b/easybuild/easyconfigs/p/PyBioLib/PyBioLib-1.2.205-GCCcore-12.3.0.eb @@ -0,0 +1,68 @@ +easyblock = "PythonBundle" + +name = 'PyBioLib' +version = '1.2.205' + +homepage = 'https://biolib.com/' +description = """PyBioLib is a Python package for running BioLib applications from Python +scripts and the command line. +BioLib is a library of biological data science applications. Applications on +BioLib range from small bioinformatics utilities to state-of-the-art machine +learning algorithms for predicting characteristics of biological molecules.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +builddependencies = [ + ('binutils', '2.40'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('Flask', '2.3.3'), + ('PyYAML', '6.0'), +] + +use_pip = True + +exts_list = [ + ('commonmark', '0.9.1', { + 'source_tmpl': SOURCE_WHL, + 'checksums': ['da2f38c92590f83de410ba1a3cbceafbc74fee9def35f9251ba9a971d6d66fd9'], + }), + ('rich', '13.9.2', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['8c82a3d3f8dcfe9e734771313e606b39d8247bb6b826e196f4914b333b743cf1'], + }), + ('pycryptodome', '3.21.0', { + 'modulename': 'Crypto.PublicKey.RSA', + 'checksums': ['f7787e0d469bdae763b876174cf2e6c0f7be79808af26b1da96f1a64bcf47297'], + }), + ('websocket_client', '1.8.0', { + 'modulename': 'websocket', + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['17b44cc997f5c498e809b22cdf2d9c7a9e71c02c8cc2b6c56e7c2d1239bfa526'], + }), + ('docker', '7.1.0', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['c96b93b7f0a746f9e77d325bcfb87422a3d8bd4f03136ae8a85b37f1898d5fc0'], + }), + ('PyJWT', '2.9.0', { + 'modulename': 'jwt', + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['3b02fb0f44517787776cf48f2ae25d8e14f300e6d7545a4315cee571a415e850'], + }), + ('gunicorn', '23.0.0', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['ec400d38950de4dfd418cff8328b2c8faed0edb0d517d3394e457c317908ca4d'], + }), + ('pybiolib', version, { + 'modulename': 'biolib', + # 'preinstallopts': "sed -i 's/< 8.1.0/< 8.2.0/' pyproject.toml &", + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['56030cdeec254ac751b47dab4f9418caa0c8af3d2604cc2daaa5cea2ab61312a'], + }), +] + +sanity_pip_check = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/PyBullet/PyBullet-3.2.6-gfbf-2023a.eb b/easybuild/easyconfigs/p/PyBullet/PyBullet-3.2.6-gfbf-2023a.eb new file mode 100644 index 00000000000..47fce7ec459 --- /dev/null +++ b/easybuild/easyconfigs/p/PyBullet/PyBullet-3.2.6-gfbf-2023a.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonBundle' + +name = 'PyBullet' +version = '3.2.6' + +homepage = 'https://github.com/bulletphysics/bullet3' +description = """Bullet Physics SDK: real-time collision detection and +multi-physics simulation for VR, games, visual effects, robotics, +machine learning etc.""" + +toolchain = {'name': 'gfbf', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('pybullet', version, { + 'checksums': ['da27525433c88698dc9fd8bc20fa4ae4d07738b4656633659ebd82c2d2884e08'], + }), +] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/PyCUDA/PyCUDA-2024.1-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/p/PyCUDA/PyCUDA-2024.1-foss-2022a-CUDA-11.7.0.eb new file mode 100644 index 00000000000..b184c749e34 --- /dev/null +++ b/easybuild/easyconfigs/p/PyCUDA/PyCUDA-2024.1-foss-2022a-CUDA-11.7.0.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonBundle' + +name = 'PyCUDA' +version = '2024.1' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://mathema.tician.de/software/pycuda' +description = 'PyCUDA lets you access Nvidia’s CUDA parallel computation API from Python.' + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('CUDA', '11.7.0', '', SYSTEM), + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('Mako', '1.2.0'), +] + +use_pip = True + +exts_list = [ + ('pytools', '2023.1.1', { + 'checksums': ['80637873d206f6bcedf7cdb46ad93e868acb4ea2256db052dfcca872bdd0321f'], + }), + (name, version, { + 'preinstallopts': './configure.py --cuda-root="$EBROOTCUDA" && ', + 'source_tmpl': '%(namelower)s-%(version)s.tar.gz', + 'checksums': ['d50d23ff6371482cff7d4b953ef40ab81c9df038ecb614484f9fd5347327327e'], + }), +] + +sanity_pip_check = True + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/PyCUDA/PyCUDA-2024.1-gfbf-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/p/PyCUDA/PyCUDA-2024.1-gfbf-2023a-CUDA-12.1.1.eb new file mode 100644 index 00000000000..1706b5b8372 --- /dev/null +++ b/easybuild/easyconfigs/p/PyCUDA/PyCUDA-2024.1-gfbf-2023a-CUDA-12.1.1.eb @@ -0,0 +1,38 @@ +easyblock = 'PythonBundle' + +name = 'PyCUDA' +version = '2024.1' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://mathema.tician.de/software/pycuda' +description = 'PyCUDA lets you access Nvidia’s CUDA parallel computation API from Python.' + +toolchain = {'name': 'gfbf', 'version': '2023a'} + +dependencies = [ + ('CUDA', '12.1.1', '', SYSTEM), + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('Mako', '1.2.4'), + ('PyOpenGL', '3.1.7'), +] + +use_pip = True + +exts_list = [ + ('pytools', '2023.1.1', { + 'checksums': ['80637873d206f6bcedf7cdb46ad93e868acb4ea2256db052dfcca872bdd0321f'], + }), + (name, version, { + 'preinstallopts': './configure.py --cuda-root="$EBROOTCUDA" --cuda-enable-gl && ', + 'source_tmpl': '%(namelower)s-%(version)s.tar.gz', + 'checksums': ['d50d23ff6371482cff7d4b953ef40ab81c9df038ecb614484f9fd5347327327e'], + }), +] + +sanity_pip_check = True +sanity_check_commands = [ + 'python -c "import pycuda.gl"' +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/PyCharm/PyCharm-2024.1.6.eb b/easybuild/easyconfigs/p/PyCharm/PyCharm-2024.1.6.eb new file mode 100644 index 00000000000..37d00512c27 --- /dev/null +++ b/easybuild/easyconfigs/p/PyCharm/PyCharm-2024.1.6.eb @@ -0,0 +1,20 @@ +easyblock = 'Tarball' + +name = 'PyCharm' +version = "2024.1.6" + +homepage = 'https://www.jetbrains.com/pycharm/' +description = """PyCharm Community Edition: Python IDE for Professional Developers""" + +toolchain = SYSTEM + +source_urls = ['https://download-cf.jetbrains.com/python'] +sources = ['pycharm-community-%(version)s.tar.gz'] +checksums = ['539961408de4217a68b84d666d5c10ddb8d7bcf919e3a569f2489438a3237f1a'] + +sanity_check_paths = { + 'files': ["bin/pycharm.sh"], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/PyCheMPS2/PyCheMPS2-1.8.12-foss-2023a.eb b/easybuild/easyconfigs/p/PyCheMPS2/PyCheMPS2-1.8.12-foss-2023a.eb new file mode 100644 index 00000000000..222a89010a0 --- /dev/null +++ b/easybuild/easyconfigs/p/PyCheMPS2/PyCheMPS2-1.8.12-foss-2023a.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonBundle' + +name = 'PyCheMPS2' +version = '1.8.12' + +homepage = 'https://sebwouters.github.io/CheMPS2' +description = """PyCheMPS2 is a python interface to CheMPS2, for compilation without +MPI. CheMPS2 is a scientific library which contains a spin-adapted +implementation of the density matrix renormalization group (DMRG) +for ab initio quantum chemistry.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('CheMPS2', version), +] + +use_pip = True + +exts_list = [ + (name, version, { + 'modulename': '%(name)s', + 'source_urls': ['https://github.com/SebWouters/CheMPS2/archive/'], + 'source_tmpl': 'v%(version)s.tar.gz', + 'checksums': ['eef1b92d74ac07fde58c043f64e8cac02b5400c209c44dcbb51641f86e0c7c83'], + 'install_src': './%(name)s', + }), +] + +sanity_pip_check = True + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/p/PyClone/PyClone-2020.9b2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/PyClone/PyClone-2020.9b2-GCCcore-10.2.0.eb index ee4425b49c5..96d813edcce 100644 --- a/easybuild/easyconfigs/p/PyClone/PyClone-2020.9b2-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/PyClone/PyClone-2020.9b2-GCCcore-10.2.0.eb @@ -21,9 +21,8 @@ dependencies = [ ('Python', '3.8.6'), ] -exts_default_options = { - 'use_pip': True -} +sanity_pip_check = True +use_pip = True exts_list = [ ('Logbook', '1.5.3', { @@ -37,6 +36,4 @@ exts_list = [ }), ] -sanity_pip_check = True - moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/PyHMMER/PyHMMER-0.10.15-gompi-2023b.eb b/easybuild/easyconfigs/p/PyHMMER/PyHMMER-0.10.15-gompi-2023b.eb new file mode 100644 index 00000000000..2d6165976d9 --- /dev/null +++ b/easybuild/easyconfigs/p/PyHMMER/PyHMMER-0.10.15-gompi-2023b.eb @@ -0,0 +1,47 @@ +# Thomas Hoffmann, EMBL Heidelberg, structures-it@embl.de, 2024/02 +# Update: Petr Král (INUITS) + +easyblock = 'PythonBundle' + +name = 'PyHMMER' +version = '0.10.15' + +homepage = 'https://github.com/althonos/pyhmmer' +description = """ +HMMER is a biological sequence analysis tool that uses profile hidden Markov +models to search for sequence homologs. HMMER3 is developed and maintained by +the Eddy/Rivas Laboratory at Harvard University. + +pyhmmer is a Python package, implemented using the Cython language, that +provides bindings to HMMER3. It directly interacts with the HMMER internals, +which has the following advantages over CLI wrappers (like hmmer-py)""" + +toolchain = {'name': 'gompi', 'version': '2023b'} + +builddependencies = [ + ('Cython', '3.0.10'), +] + +dependencies = [ + ('Python', '3.11.5'), + ('HMMER', '3.4'), + ('psutil', '6.1.0') +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('%(namelower)s', version, { + # Requirement for `psutil` is too strict. + 'preinstallopts': "sed -i 's/psutil ~=5.8/psutil >=5.8/g' setup.cfg && ", + 'checksums': ['bf8e97ce8da6fb5850298f3074640f3e998d5a655877f865c1592eb057dc7921'], + }), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(namelower)s'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/PyHMMER/PyHMMER-0.10.6-gompi-2023a.eb b/easybuild/easyconfigs/p/PyHMMER/PyHMMER-0.10.6-gompi-2023a.eb new file mode 100644 index 00000000000..a9a329832ba --- /dev/null +++ b/easybuild/easyconfigs/p/PyHMMER/PyHMMER-0.10.6-gompi-2023a.eb @@ -0,0 +1,43 @@ +# Thomas Hoffmann, EMBL Heidelberg, structures-it@embl.de, 2024/02 +easyblock = 'PythonBundle' + +name = 'PyHMMER' +version = '0.10.6' + +homepage = 'https://github.com/althonos/pyhmmer' +description = """ +HMMER is a biological sequence analysis tool that uses profile hidden Markov +models to search for sequence homologs. HMMER3 is developed and maintained by +the Eddy/Rivas Laboratory at Harvard University. + +pyhmmer is a Python package, implemented using the Cython language, that +provides bindings to HMMER3. It directly interacts with the HMMER internals, +which has the following advantages over CLI wrappers (like hmmer-py)""" + +toolchain = {'name': 'gompi', 'version': '2023a'} + +builddependencies = [ + ('Cython', '3.0.7'), +] +dependencies = [ + ('Python', '3.11.3'), + ('HMMER', '3.4'), + ('psutil', '5.9.8') +] + +use_pip = True + +exts_list = [ + ('pyhmmer', version, { + 'checksums': ['47e017ccc523046400312afc937d4d68306f6ca0ed82e313deb3697d4fd8ccff'], + }), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(namelower)s'], +} + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.5-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.5-GCCcore-11.3.0.eb index 11986d88534..c30243b0d0d 100644 --- a/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.5-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.5-GCCcore-11.3.0.eb @@ -92,12 +92,12 @@ sanity_check_paths = { } sanity_check_commands = [ - "python -c 'import PyQt5.QtCore'", + "python -s -c 'import PyQt5.QtCore'", "sip5 --help", "pyuic5 --help", "pylupdate5 -version 2>&1 | grep 'pylupdate5 v%(version)s'", "pyrcc5 -version 2>&1 | grep 'pyrcc5 v%(version)s'", - "pip check", + "PIP_DISABLE_PIP_VERSION_CHECK=true python -s -m pip check", ] modextrapaths = { diff --git a/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.7-GCCcore-12.2.0.eb b/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.7-GCCcore-12.2.0.eb index 0987fcacdf5..97be3ae2aa6 100644 --- a/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.7-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.7-GCCcore-12.2.0.eb @@ -103,12 +103,12 @@ sanity_check_paths = { } sanity_check_commands = [ - "python -c 'import PyQt5.QtCore'", + "python -s -c 'import PyQt5.QtCore'", "sip5 --help", "pyuic5 --help", "pylupdate5 -version 2>&1 | grep 'pylupdate5 v%(version)s'", "pyrcc5 -version 2>&1 | grep 'pyrcc5 v%(version)s'", - "pip check", + "PIP_DISABLE_PIP_VERSION_CHECK=true python -s -m pip check", ] modextrapaths = { diff --git a/easybuild/easyconfigs/p/PyQtGraph/PyQtGraph-0.13.7-foss-2023a.eb b/easybuild/easyconfigs/p/PyQtGraph/PyQtGraph-0.13.7-foss-2023a.eb new file mode 100644 index 00000000000..ff061fd9577 --- /dev/null +++ b/easybuild/easyconfigs/p/PyQtGraph/PyQtGraph-0.13.7-foss-2023a.eb @@ -0,0 +1,31 @@ +# updated: Denis Kristak +easyblock = 'PythonPackage' +# TH77EMBL adapted from PyQtGraph-0.11.0-foss-2019b-Python-3.7.4.eb +# update: Petr Král (INUITS) +name = 'PyQtGraph' +version = '0.13.7' + +homepage = 'http://www.pyqtgraph.org/' +description = """PyQtGraph is a pure-python graphics and GUI library built on PyQt5/PySide2 and numpy.""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'pic': True} + +github_account = 'pyqtgraph' +source_urls = [GITHUB_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['28c5fb6eaf60ff3ea7b7b6e0f8935cf85f34e7b5c554f154eeb10649c6b21573'] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('PyQt5', '5.15.10'), + ('PyOpenGL', '3.1.7'), +] + +use_pip = True +download_dep_fail = True + +sanity_pip_check = True + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/PyRosetta/PyRosetta-4.release-384-gompi-2022a.eb b/easybuild/easyconfigs/p/PyRosetta/PyRosetta-4.release-384-gompi-2022a.eb new file mode 100644 index 00000000000..5769add932d --- /dev/null +++ b/easybuild/easyconfigs/p/PyRosetta/PyRosetta-4.release-384-gompi-2022a.eb @@ -0,0 +1,38 @@ +easyblock = 'PythonBundle' + +name = 'PyRosetta' +version = '4.release-384' + +homepage = 'https://www.pyrosetta.org/' +description = """ +PyRosetta is an interactive Python-based interface to the powerful Rosetta molecular modeling +suite. It enables users to design their own custom molecular modeling algorithms using Rosetta +sampling methods and energy functions. +""" + +toolchain = {'name': 'gompi', 'version': '2022a'} +toolchainopts = {'usempi': True} + +builddependencies = [('binutils', '2.38')] + +dependencies = [ + ('Python', '3.10.4'), +] + +use_pip = True + +local_source_tmpl = '%(name)s%(version_major)s.Release.python%(pymajver)s%(pyminver)s.linux.%(version_minor)s.tar.bz2' +local_source_urls = 'https://graylab.jhu.edu/download/PyRosetta4/archive/release/PyRosetta4.Release.python310.linux/' + +exts_list = [ + (name, version, { + 'source_tmpl': local_source_tmpl, + 'source_urls': [local_source_urls], + 'start_dir': 'setup', + 'checksums': ['630108f2bac166563fd2a4046a1d82e51e14693bb0e20dd3174e71c02b0760c2'], + }), +] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/PyRosetta/PyRosetta-4.release-387-gompi-2023a.eb b/easybuild/easyconfigs/p/PyRosetta/PyRosetta-4.release-387-gompi-2023a.eb new file mode 100644 index 00000000000..c37102d5a81 --- /dev/null +++ b/easybuild/easyconfigs/p/PyRosetta/PyRosetta-4.release-387-gompi-2023a.eb @@ -0,0 +1,38 @@ +easyblock = 'PythonBundle' + +name = 'PyRosetta' +version = '4.release-387' + +homepage = 'https://www.pyrosetta.org/' +description = """ +PyRosetta is an interactive Python-based interface to the powerful Rosetta molecular modeling +suite. It enables users to design their own custom molecular modeling algorithms using Rosetta +sampling methods and energy functions. +""" + +toolchain = {'name': 'gompi', 'version': '2023a'} +toolchainopts = {'usempi': True} + +builddependencies = [('binutils', '2.40')] + +dependencies = [ + ('Python', '3.11.3'), +] + +use_pip = True + +local_source_tmpl = '%(name)s%(version_major)s.Release.python%(pymajver)s%(pyminver)s.linux.%(version_minor)s.tar.bz2' +local_source_urls = 'https://graylab.jhu.edu/download/PyRosetta4/archive/release/PyRosetta4.Release.python311.linux/' + +exts_list = [ + (name, version, { + 'source_tmpl': local_source_tmpl, + 'source_urls': [local_source_urls], + 'start_dir': 'setup', + 'checksums': ['42a10efd16cba7739d87a5c4035a2cd8792bc193804963fc26bb2f82f7ac2a1a'], + }), +] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/PySCF/PySCF-2.7.0-foss-2023a.eb b/easybuild/easyconfigs/p/PySCF/PySCF-2.7.0-foss-2023a.eb new file mode 100644 index 00000000000..d2efdfa6e27 --- /dev/null +++ b/easybuild/easyconfigs/p/PySCF/PySCF-2.7.0-foss-2023a.eb @@ -0,0 +1,138 @@ +easyblock = 'CMakeMakeCp' +name = 'PySCF' +version = '2.7.0' + +homepage = 'http://www.pyscf.org' +description = "PySCF is an open-source collection of electronic structure modules powered by Python." + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['https://github.com/pyscf/pyscf/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['f2f94e6dae8556085bb765eb5250f61589e977b4f12540c748241101d40da241'] + +builddependencies = [ + ('CMake', '3.26.3'), + ('pybind11', '2.11.1'), # needed by zquatev +] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), # for numpy, scipy + ('h5py', '3.9.0'), + ('libcint', '5.4.0'), + ('libxc', '6.2.2'), + ('XCFun', '2.1.1'), + ('CPPE', '0.3.1'), # extra + ('PyBerny', '0.6.3'), # extra + ('PyCheMPS2', '1.8.12'), # needed by dmrgscf + ('Block', '1.5.3-20200525'), # needed by dmrgscf + ('NECI', '20230620'), # needed by fciqmc + ('Dice', '20240702'), # needed by icmpspt + ('tblis', '20230422'), +] + +exts_defaultclass = 'PythonPackage' +exts_default_options = { + 'download_dep_fail': True, + 'use_pip': True, + 'modulename': 'pyscf.%(name)s', + 'source_urls': ['https://github.com/pyscf/%(name)s/archive/'], + 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], +} + +# The following list of extensions is equivalent to installing PySCF with extras: +# all + dmrgscf + fciqmcscf + hci + mbd + tblis + zquatev +exts_list = [ + ('dftd3', '94091d8', { + 'checksums': ['a69ae44b3d02d2c06fd531373f20ee1251ef27fc932d40a7cafea6c09d8784fc'], + }), + ('doci', '08079a9', { + 'checksums': ['f492ba45dfe50c9b459e53a946a677528af0dc2097ff77ea3767aa4f46c5d9ba'], + }), + ('icmpspt', '50c386e', { + 'patches': [('PySCF-2.1.1_icmpspt-exe-path.patch', 0)], + 'checksums': [ + {'icmpspt-50c386e.tar.gz': '08029863ae8740939a730fe5e104661c67d8dd0b8a8555b603fc8a0777096d48'}, + {'PySCF-2.1.1_icmpspt-exe-path.patch': 'e972e377b34b964c48a99909301bf21a9c73d8eb9ecb96a889621d71471c56c9'}, + ], + }), + ('properties', '8b94d8d', { + 'modulename': 'pyscf.prop', + 'checksums': ['b40e071472a6bdfcaec8cd358c7c58c58748c59d8b188fdca09d6eca63329914'], + }), + ('qsdopt', '3ad2c02', { + 'checksums': ['cc639150e5f9efad8ffe496b3dccd2952a1f60fdad51f611cffba701892b384e'], + }), + ('semiempirical', '470d716', { + 'checksums': ['0bbe304867fd053ed647445ac84c4c76787ad23def9f72415aec297740121eef'], + }), + ('shciscf', '7edb54d', { + 'checksums': ['ae54265f6600b73a350b00274c95bb0de940ddcd6e1b47b434594e18136b1bed'], + }), + ('MCfun', '0.2.3', { + 'modulename': 'mcfun', + 'source_urls': ['https://github.com/Multi-collinear/%(name)s/archive/'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['3741b49b839df0fde891d51292520ed9094fa1d3c9b5d9c042d4f26087cf6a13'], + }), + ('pyqmc', '0.6.0', { + 'modulename': 'pyqmc', + 'source_urls': ['https://github.com/WagnerGroup/%(name)s/archive/'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['6e9f612c2d0bf2198154520e01dce57cf3a6e474840c1892466de3171eaeb7db'], + }), + ('dmrgscf', 'a03f7b6', { + 'patches': [('PySCF-2.1.1_dmrgscf-settings.patch', 0)], + 'checksums': [ + {'dmrgscf-a03f7b6.tar.gz': 'dee40abe3d2aebab7a2d0eade4e464a6ae851b4c2b49a2cde4c3aa88f0651b04'}, + {'PySCF-2.1.1_dmrgscf-settings.patch': 'a0310a2a90e96bd64d1560b2cc73a805717e129d2921e91cc5e6038b9f153677'}, + ], + }), + ('fciqmc', 'ee98fb4', { + 'modulename': 'pyscf.fciqmcscf', + 'checksums': ['b2f081ac295df0e622c6d1b3bff6d7834f97131f1f0fc87ec8bcff2137ef4199'], + }), + ('mbd', '485c18c', { + 'patches': [('PySCF-2.1.1_mbd-fix-init.patch', 0)], + 'checksums': [ + {'mbd-485c18c.tar.gz': 'de1fb14650fcb87909cae33dc318d2e213653ac4393ced7e070dfa6308d95846'}, + {'PySCF-2.1.1_mbd-fix-init.patch': '4f8e4b2e39b77428187851c4b6ced39401561bc81f4f3a4605da5d5c7b798cbc'}, + ], + }), + ('naive-hci', '0c28d6e', { + 'modulename': 'pyscf.hci', + 'checksums': ['de247d17b80133655df5966341e5adb691b0df150cd9b0f1980cf62ec55229d5'], + }), + ('tblis', 'c67c8af', { + 'modulename': 'pyscf.tblis_einsum', + # Use our `tblis`. + 'preinstallopts': 'CMAKE_CONFIGURE_ARGS="-DVENDOR_TBLIS=off" ', + 'source_urls': ['https://github.com/pyscf/pyscf-tblis/archive/'], + 'checksums': ['9a40a760e3be1d0b7f49faab5897388dcdf75094f75e06b4c344b3642a0401d6'], + }), + ('zquatev', '4eb41b1', { + 'modulename': 'zquatev', + 'preinstallopts': "sed -i 's/add_subdirectory(pybind11)/find_package(pybind11 REQUIRED)/' CMakeLists.txt && ", + 'source_urls': ['https://github.com/sunqm/%(name)s/archive/'], + 'checksums': ['4caf08e3831a5d86e6bc22f3b4028cc159101cb9658d09de16e382e268a5a2e9'], + }), +] + +start_dir = 'pyscf/lib' +configopts = "-DBUILD_LIBCINT=OFF -DBUILD_LIBXC=OFF -DBUILD_XCFUN=OFF" +prebuildopts = "export PYSCF_INC_DIR=$EBROOTQCINT/include:$EBROOTLIBXC/lib && " + +_py_site_packages = 'lib/python%(pyshortver)s/site-packages' +files_to_copy = [(['pyscf'], _py_site_packages)] + +sanity_check_paths = { + 'files': [_py_site_packages + '/pyscf/__init__.py'], + 'dirs': [_py_site_packages + d for d in ['/pyscf/data', '/pyscf/lib']], +} + +sanity_check_commands = ["python -c 'import pyscf'"] + +modextrapaths = {'PYTHONPATH': _py_site_packages} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/p/PyTorch-Geometric/PyTorch-Geometric-2.5.0-foss-2023a-PyTorch-2.1.2.eb b/easybuild/easyconfigs/p/PyTorch-Geometric/PyTorch-Geometric-2.5.0-foss-2023a-PyTorch-2.1.2.eb new file mode 100644 index 00000000000..9c8f282ccee --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch-Geometric/PyTorch-Geometric-2.5.0-foss-2023a-PyTorch-2.1.2.eb @@ -0,0 +1,100 @@ +easyblock = 'PythonBundle' + +name = 'PyTorch-Geometric' +version = '2.5.0' +local_pytorchver = '2.1.2' +versionsuffix = '-PyTorch-%s' % local_pytorchver + +homepage = 'https://github.com/rusty1s/pytorch_geometric' +description = "PyTorch Geometric (PyG) is a geometric deep learning extension library for PyTorch." + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [ + ('PDM', '2.12.4'), + ('Parallel-Hashmap', '1.3.12'), # header only +] + +dependencies = [ + ('Python', '3.11.3'), + ('PyTorch', local_pytorchver), + ('scikit-learn', '1.3.1'), + ('scikit-image', '0.22.0'), + ('numba', '0.58.1'), + ('h5py', '3.9.0'), + ('tqdm', '4.66.1'), + ('RDFlib', '7.0.0'), + ('ASE', '3.22.1'), + ('YACS', '0.1.8'), + ('aiohttp', '3.8.5'), +] + +use_pip = True + +exts_list = [ + ('googledrivedownloader', '0.4', { + 'modulename': 'google_drive_downloader', + 'checksums': ['4b34c1337b2ff3bf2bd7581818efbdcaea7d50ffd484ccf80809688f5ca0e204'], + }), + ('plyfile', '1.0.3', { + 'patches': ['plyfile-1.0.3_use_pdm_backend.patch'], + 'checksums': [ + {'plyfile-1.0.3.tar.gz': '0ecbe8e7ce55a7bbc6c9dea24242fffa0ab7d9bed33fbd5ad567ca013bcc5222'}, + {'plyfile-1.0.3_use_pdm_backend.patch': '815611863f16e785ef03a7992a0b99e433150212ff03559c7f6fce4e86d9e0a7'}, + ], + }), + ('torch_scatter', '2.1.2', { + 'source_urls': ['https://github.com/rusty1s/pytorch_scatter/archive/refs/tags/'], + 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['6f375dbc9cfe03f330aa29ea553e9c7432e9b040d039b041f08bf05df1a8bf37'], + 'runtest': 'pytest', + 'testinstall': True, + }), + ('torch_sparse', '0.6.18', { + 'source_urls': ['https://github.com/rusty1s/pytorch_sparse/archive/refs/tags/'], + 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['a9e194cddc17481001ac4592a058450493ce13780e8ce3eb54d4f79706e69c91'], + 'runtest': 'pytest -k "not test_spmm[dtype10-device10-sum] and not test_spmm[dtype16-device16-add]"', # flaky + 'testinstall': True, + }), + ('torch_cluster', '1.6.3', { + 'source_urls': ['https://github.com/rusty1s/pytorch_cluster/archive/refs/tags/'], + 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['0e2b08095e03cf87ce9b23b7a7352236a25d3ed92d92351dc020fd927ea8dbfe'], + 'runtest': 'pytest', + 'testinstall': True, + }), + ('torch_spline_conv', '1.2.2', { + 'source_urls': ['https://github.com/rusty1s/pytorch_spline_conv/archive/refs/tags/'], + 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['258947394514ba487b2617268ae7102e9a06fd15d79f5d8239a96211a85adc3d'], + 'runtest': 'pytest', + 'testinstall': True, + }), + ('python-louvain', '0.16', { + 'modulename': 'community.community_louvain', + 'checksums': ['b7ba2df5002fd28d3ee789a49532baad11fe648e4f2117cf0798e7520a1da56b'], + }), + ('torch_geometric', version, { + 'source_urls': ['https://github.com/pyg-team/pytorch_geometric/archive/refs/tags/'], + 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['f9abf00dc7fd1039ef1d9734a0fbd8c52196e39ca9fc4816afd98a8f311265be'], + 'runtest': ( + 'pytest' + ' --ignore=test/test_edge_index.py' # many tests require PyTorch with MKL + ' --ignore=test/nn/models/test_graph_unet.py' # requires PyTorch with MKL + ' --ignore=test/nn/pool/test_asap.py' # requires PyTorch with MKL + ' --ignore=test/transforms/test_add_metapaths.py' # requires PyTorch with MKL + ' --ignore=test/transforms/test_two_hop.py' # requires PyTorch with MKL + ' --ignore=test/test_inspector.py' # test failing due to typing change + ' --ignore=test/nn/conv/test_hetero_conv.py' # unknown jit compilation issue + ' --ignore=test/nn/conv/test_sage_conv.py' # unknown jit compilation issue + ' -k "not test_multithreading_neighbor_loader" ' # picky about number of cores in the environment + ), + 'testinstall': True, + }), +] + +sanity_pip_check = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/PyTorch-bundle/PyTorch-bundle-2.1.2-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/p/PyTorch-bundle/PyTorch-bundle-2.1.2-foss-2023a-CUDA-12.1.1.eb index dcaf6c933d5..d7e1c6cc2e0 100644 --- a/easybuild/easyconfigs/p/PyTorch-bundle/PyTorch-bundle-2.1.2-foss-2023a-CUDA-12.1.1.eb +++ b/easybuild/easyconfigs/p/PyTorch-bundle/PyTorch-bundle-2.1.2-foss-2023a-CUDA-12.1.1.eb @@ -80,7 +80,6 @@ exts_list = [ 'checksums': ['7f6b125602ac6d743e523ae0bfa71e1a697a2f5534064528c6ff84c2f7c2fc7f'], }), ('torchvision', '0.16.2', { - 'preinstallopts': 'WITH_CUDA=1 TORCHVISION_INCLUDE="$EBROOTLIBJPEGMINTURBO/include:$TORCHVISION_INCLUDE"', 'installopts': '-v', 'patches': [ 'torchvision-0.16.2_ffmpeg-6.0-fix.patch', diff --git a/easybuild/easyconfigs/p/PyTorch-bundle/PyTorch-bundle-2.1.2-foss-2023a.eb b/easybuild/easyconfigs/p/PyTorch-bundle/PyTorch-bundle-2.1.2-foss-2023a.eb index 10b6b0d37d6..4c8d8ef847a 100644 --- a/easybuild/easyconfigs/p/PyTorch-bundle/PyTorch-bundle-2.1.2-foss-2023a.eb +++ b/easybuild/easyconfigs/p/PyTorch-bundle/PyTorch-bundle-2.1.2-foss-2023a.eb @@ -76,7 +76,6 @@ exts_list = [ 'checksums': ['7f6b125602ac6d743e523ae0bfa71e1a697a2f5534064528c6ff84c2f7c2fc7f'], }), ('torchvision', '0.16.2', { - 'preinstallopts': 'WITH_CUDA=0 TORCHVISION_INCLUDE="$EBROOTLIBJPEGMINTURBO/include:$TORCHVISION_INCLUDE"', 'installopts': '-v', 'patches': [ 'torchvision-0.16.2_ffmpeg-6.0-fix.patch', diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2-foss-2022a.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2-foss-2022a.eb index 0f6d51fd1bb..4c9324b7479 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2-foss-2022a.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2-foss-2022a.eb @@ -46,6 +46,7 @@ patches = [ 'PyTorch-2.1.2_fix-vsx-vector-abs.patch', 'PyTorch-2.1.2_fix-vsx-vector-div.patch', 'PyTorch-2.1.2_skip-cpu_repro-test-without-vectorization.patch', + 'PyTorch-2.1.2_skip-memory-leak-test.patch', 'PyTorch-2.1.2_workaround_dynamo_failure_without_nnpack.patch', ] checksums = [ @@ -111,6 +112,7 @@ checksums = [ {'PyTorch-2.1.2_fix-vsx-vector-div.patch': '11f497a6892eb49b249a15320e4218e0d7ac8ae4ce67de39e4a018a064ca1acc'}, {'PyTorch-2.1.2_skip-cpu_repro-test-without-vectorization.patch': '7ace835af60c58d9e0754a34c19d4b9a0c3a531f19e5d0eba8e2e49206eaa7eb'}, + {'PyTorch-2.1.2_skip-memory-leak-test.patch': '8d9841208e8a00a498295018aead380c360cf56e500ef23ca740adb5b36de142'}, {'PyTorch-2.1.2_workaround_dynamo_failure_without_nnpack.patch': 'fb96eefabf394617bbb3fbd3a7a7c1aa5991b3836edc2e5d2a30e708bfe49ba1'}, ] diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2-foss-2022b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2-foss-2022b.eb index 146e42cb2b8..ee2c8731bb8 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2-foss-2022b.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2-foss-2022b.eb @@ -47,6 +47,7 @@ patches = [ 'PyTorch-2.1.2_fix-vsx-vector-abs.patch', 'PyTorch-2.1.2_fix-vsx-vector-div.patch', 'PyTorch-2.1.2_skip-cpu_repro-test-without-vectorization.patch', + 'PyTorch-2.1.2_skip-memory-leak-test.patch', 'PyTorch-2.1.2_workaround_dynamo_failure_without_nnpack.patch', ] checksums = [ @@ -113,6 +114,7 @@ checksums = [ {'PyTorch-2.1.2_fix-vsx-vector-div.patch': '11f497a6892eb49b249a15320e4218e0d7ac8ae4ce67de39e4a018a064ca1acc'}, {'PyTorch-2.1.2_skip-cpu_repro-test-without-vectorization.patch': '7ace835af60c58d9e0754a34c19d4b9a0c3a531f19e5d0eba8e2e49206eaa7eb'}, + {'PyTorch-2.1.2_skip-memory-leak-test.patch': '8d9841208e8a00a498295018aead380c360cf56e500ef23ca740adb5b36de142'}, {'PyTorch-2.1.2_workaround_dynamo_failure_without_nnpack.patch': 'fb96eefabf394617bbb3fbd3a7a7c1aa5991b3836edc2e5d2a30e708bfe49ba1'}, ] diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2-foss-2023a-CUDA-12.1.1.eb index 7990dd1511b..65dfced1701 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2-foss-2023a-CUDA-12.1.1.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2-foss-2023a-CUDA-12.1.1.eb @@ -59,6 +59,7 @@ patches = [ 'PyTorch-2.1.2_remove-nccl-backend-default-without-gpus.patch', 'PyTorch-2.1.2_skip-cpu_repro-test-without-vectorization.patch', 'PyTorch-2.1.2_skip-failing-test_dtensor_ops-subtests.patch', + 'PyTorch-2.1.2_skip-memory-leak-test.patch', 'PyTorch-2.1.2_skip-test_fsdp_tp_checkpoint_integration.patch', 'PyTorch-2.1.2_workaround_dynamo_failure_without_nnpack.patch', ] @@ -145,6 +146,7 @@ checksums = [ '7ace835af60c58d9e0754a34c19d4b9a0c3a531f19e5d0eba8e2e49206eaa7eb'}, {'PyTorch-2.1.2_skip-failing-test_dtensor_ops-subtests.patch': '6cf711bf26518550903b09ed4431de9319791e79d61aab065785d6608fd5cc88'}, + {'PyTorch-2.1.2_skip-memory-leak-test.patch': '8d9841208e8a00a498295018aead380c360cf56e500ef23ca740adb5b36de142'}, {'PyTorch-2.1.2_skip-test_fsdp_tp_checkpoint_integration.patch': '943ee92f5fd518f608a59e43fe426b9bb45d7e7ad0ba04639e516db2d61fa57d'}, {'PyTorch-2.1.2_workaround_dynamo_failure_without_nnpack.patch': diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2-foss-2023a.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2-foss-2023a.eb index 413e3254f8a..a79f709480c 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2-foss-2023a.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2-foss-2023a.eb @@ -48,6 +48,7 @@ patches = [ 'PyTorch-2.1.2_fix-vsx-vector-abs.patch', 'PyTorch-2.1.2_fix-vsx-vector-div.patch', 'PyTorch-2.1.2_skip-cpu_repro-test-without-vectorization.patch', + 'PyTorch-2.1.2_skip-memory-leak-test.patch', 'PyTorch-2.1.2_workaround_dynamo_failure_without_nnpack.patch', ] checksums = [ @@ -116,6 +117,7 @@ checksums = [ {'PyTorch-2.1.2_fix-vsx-vector-div.patch': '11f497a6892eb49b249a15320e4218e0d7ac8ae4ce67de39e4a018a064ca1acc'}, {'PyTorch-2.1.2_skip-cpu_repro-test-without-vectorization.patch': '7ace835af60c58d9e0754a34c19d4b9a0c3a531f19e5d0eba8e2e49206eaa7eb'}, + {'PyTorch-2.1.2_skip-memory-leak-test.patch': '8d9841208e8a00a498295018aead380c360cf56e500ef23ca740adb5b36de142'}, {'PyTorch-2.1.2_workaround_dynamo_failure_without_nnpack.patch': 'fb96eefabf394617bbb3fbd3a7a7c1aa5991b3836edc2e5d2a30e708bfe49ba1'}, ] diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2-foss-2023b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2-foss-2023b.eb index 151e13356fe..bce1b68aa7b 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2-foss-2023b.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2-foss-2023b.eb @@ -48,6 +48,7 @@ patches = [ 'PyTorch-2.1.2_fix-vsx-vector-abs.patch', 'PyTorch-2.1.2_fix-vsx-vector-div.patch', 'PyTorch-2.1.2_skip-cpu_repro-test-without-vectorization.patch', + 'PyTorch-2.1.2_skip-memory-leak-test.patch', 'PyTorch-2.1.2_workaround_dynamo_failure_without_nnpack.patch', ] checksums = [ @@ -116,6 +117,7 @@ checksums = [ {'PyTorch-2.1.2_fix-vsx-vector-div.patch': '11f497a6892eb49b249a15320e4218e0d7ac8ae4ce67de39e4a018a064ca1acc'}, {'PyTorch-2.1.2_skip-cpu_repro-test-without-vectorization.patch': '7ace835af60c58d9e0754a34c19d4b9a0c3a531f19e5d0eba8e2e49206eaa7eb'}, + {'PyTorch-2.1.2_skip-memory-leak-test.patch': '8d9841208e8a00a498295018aead380c360cf56e500ef23ca740adb5b36de142'}, {'PyTorch-2.1.2_workaround_dynamo_failure_without_nnpack.patch': 'fb96eefabf394617bbb3fbd3a7a7c1aa5991b3836edc2e5d2a30e708bfe49ba1'}, ] diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2_skip-memory-leak-test.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2_skip-memory-leak-test.patch new file mode 100644 index 00000000000..cbebd761d98 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2_skip-memory-leak-test.patch @@ -0,0 +1,17 @@ +Reports from various sites show that this test is unreliable. +As it is not critical just skip it. + +@Author: Alexander Grund (TU Dresden) + +diff --git a/test/test_jit.py b/test/test_jit.py +index 2cdc5413dfe..5b145458630 100644 +--- a/test/test_jit.py ++++ b/test/test_jit.py +@@ -12838,6 +12838,7 @@ dedent """ + data = reader.get_record(str(offset)) + assert(data == buffers[i]) + ++ @unittest.skip("The memory allocation tracking is not reliable on all systems") + def test_file_reader_no_memory_leak(self): + num_iters = 10000 + filename, _, _ = self._make_filereader_test_file() diff --git a/easybuild/easyconfigs/p/PyVista/PyVista-0.43.8-foss-2022a.eb b/easybuild/easyconfigs/p/PyVista/PyVista-0.43.8-foss-2022a.eb new file mode 100644 index 00000000000..6a80df15a1b --- /dev/null +++ b/easybuild/easyconfigs/p/PyVista/PyVista-0.43.8-foss-2022a.eb @@ -0,0 +1,53 @@ +easyblock = 'PythonBundle' + +name = 'PyVista' +version = '0.43.8' + +homepage = 'https://docs.pyvista.org/' +description = """ +3D plotting and mesh analysis through a streamlined interface for the +Visualization Toolkit (VTK)""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('VTK', '9.2.2'), + ('imageio', '2.22.2'), + ('matplotlib', '3.5.2'), + ('Pillow', '9.1.1'), +] + +use_pip = True + +exts_list = [ + ('scooby', '0.10.0', { + 'checksums': ['7ea33c262c0cc6a33c6eeeb5648df787be4f22660e53c114e5fff1b811a8854f'], + }), + ('cmocean', '4.0.3', { + 'checksums': ['37868399fb5f41b4eac596e69803f9bfaea49946514dfb2e7f48886854250d7c'], + }), + ('colorcet', '3.1.0', { + 'checksums': ['2921b3cd81a2288aaf2d63dbc0ce3c26dcd882e8c389cc505d6886bf7aa9a4eb'], + }), + ('commonmark', '0.9.1', { + 'checksums': ['452f9dc859be7f06631ddcb328b6919c67984aca654e5fefb3914d54691aed60'], + }), + ('rich', '12.6.0', { + 'checksums': ['ba3a3775974105c221d31141f2c116f4fd65c5ceb0698657a11e9f295ec93fd0'], + }), + ('meshio', '5.3.5', { + 'checksums': ['f21f01abd9f29ba06ea119304b3d39e610421cfe93b9dd23362834919f87586d'], + }), + ('pooch', '1.6.0', { + 'checksums': ['57d20ec4b10dd694d2b05bb64bc6b109c6e85a6c1405794ce87ed8b341ab3f44'], + }), + ('pyvista', version, { + 'use_pip_extras': 'colormaps,io', + 'checksums': ['b9220753ae94fb8ca3047d291a706a4046b06659016c0000c184b5f24504f8d0'], + }), +] + +sanity_pip_check = True + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/PyVista/PyVista-0.43.8-foss-2023a.eb b/easybuild/easyconfigs/p/PyVista/PyVista-0.43.8-foss-2023a.eb new file mode 100644 index 00000000000..b89bae3b057 --- /dev/null +++ b/easybuild/easyconfigs/p/PyVista/PyVista-0.43.8-foss-2023a.eb @@ -0,0 +1,45 @@ +easyblock = 'PythonBundle' + +name = 'PyVista' +version = '0.43.8' + +homepage = 'https://docs.pyvista.org/' +description = """ +3D plotting and mesh analysis through a streamlined interface for the +Visualization Toolkit (VTK)""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('VTK', '9.3.0'), + ('imageio', '2.33.1'), + ('matplotlib', '3.7.2'), + ('Pillow', '10.0.0'), +] + +use_pip = True + +exts_list = [ + ('scooby', '0.10.0', { + 'checksums': ['7ea33c262c0cc6a33c6eeeb5648df787be4f22660e53c114e5fff1b811a8854f'], + }), + ('cmocean', '4.0.3', { + 'checksums': ['37868399fb5f41b4eac596e69803f9bfaea49946514dfb2e7f48886854250d7c'], + }), + ('colorcet', '3.1.0', { + 'checksums': ['2921b3cd81a2288aaf2d63dbc0ce3c26dcd882e8c389cc505d6886bf7aa9a4eb'], + }), + ('meshio', '5.3.5', { + 'checksums': ['f21f01abd9f29ba06ea119304b3d39e610421cfe93b9dd23362834919f87586d'], + }), + ('pyvista', version, { + 'use_pip_extras': 'colormaps,io', + 'checksums': ['b9220753ae94fb8ca3047d291a706a4046b06659016c0000c184b5f24504f8d0'], + }), +] + +sanity_pip_check = True + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/PyWavelets/PyWavelets-1.7.0-foss-2023a.eb b/easybuild/easyconfigs/p/PyWavelets/PyWavelets-1.7.0-foss-2023a.eb new file mode 100644 index 00000000000..f68a1a2ba06 --- /dev/null +++ b/easybuild/easyconfigs/p/PyWavelets/PyWavelets-1.7.0-foss-2023a.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'PyWavelets' +version = '1.7.0' + +homepage = 'https://pywavelets.readthedocs.io' +description = "PyWavelets is open source wavelet transform software for Python." + +toolchain = {'name': 'foss', 'version': '2023a'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['b47250e5bb853e37db5db423bafc82847f4cde0ffdf7aebb06336a993bc174f6'] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), # for numpy + ('meson-python', '0.13.2'), + ('Cython', '3.0.8'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +options = {'modulename': 'pywt'} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/PyYAML/PyYAML-6.0.2-GCCcore-13.3.0.eb b/easybuild/easyconfigs/p/PyYAML/PyYAML-6.0.2-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..50b9ad427e6 --- /dev/null +++ b/easybuild/easyconfigs/p/PyYAML/PyYAML-6.0.2-GCCcore-13.3.0.eb @@ -0,0 +1,31 @@ +easyblock = 'PythonPackage' + +name = 'PyYAML' +version = '6.0.2' + +homepage = 'https://github.com/yaml/pyyaml' +description = "PyYAML is a YAML parser and emitter for the Python programming language." + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +sources = ['https://github.com/yaml/pyyaml/archive/refs/tags/%(version)s.tar.gz'] +checksums = ['9377c381ac3fccad8df73d96b5139ef8b1a2c57a0d913e95ab0a2275d66b5caa'] + +builddependencies = [ + ('binutils', '2.42'), + ('Cython', '3.0.10'), +] +dependencies = [ + ('Python', '3.12.3'), + ('libyaml', '0.2.5'), + ('Python-bundle-PyPI', '2024.06'), +] + +download_dep_fail = True +sanity_pip_check = True +use_pip = True +options = {'modulename': 'yaml'} + +sanity_check_commands = ["python -c 'import yaml; yaml.CLoader'"] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/PyZMQ/PyZMQ-26.2.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-26.2.0-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..05949337114 --- /dev/null +++ b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-26.2.0-GCCcore-13.3.0.eb @@ -0,0 +1,31 @@ +easyblock = 'PythonPackage' + +name = 'PyZMQ' +version = '26.2.0' + +homepage = 'https://www.zeromq.org/bindings:python' +description = "Python bindings for ZeroMQ" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['070672c258581c8e4f640b5159297580a9974b026043bd4ab0470be9ed324f1f'] + +builddependencies = [ + ('binutils', '2.42'), + ('scikit-build-core', '0.10.6'), + ('Cython', '3.0.10'), +] +dependencies = [ + ('Python', '3.12.3'), + ('Python-bundle-PyPI', '2024.06'), + ('ZeroMQ', '4.3.5'), +] + +download_dep_fail = True +sanity_pip_check = True +use_pip = True +options = {'modulename': 'zmq'} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/PycURL/PycURL-7.45.3-GCCcore-13.2.0.eb b/easybuild/easyconfigs/p/PycURL/PycURL-7.45.3-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..8c337a0cb79 --- /dev/null +++ b/easybuild/easyconfigs/p/PycURL/PycURL-7.45.3-GCCcore-13.2.0.eb @@ -0,0 +1,29 @@ +# This easyconfig was created by Simon Branford of the BEAR Software team at the University of Birmingham. +easyblock = 'PythonPackage' + +name = 'PycURL' +version = '7.45.3' + +homepage = 'http://pycurl.io/' +description = """PycURL is a Python interface to libcurl. PycURL can be used to fetch objects identified by a URL + from a Python program, similar to the urllib Python module. PycURL is mature, very fast, and supports a lot of + features.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['8c2471af9079ad798e1645ec0b0d3d4223db687379d17dd36a70637449f81d6b'] + +builddependencies = [ + ('binutils', '2.40'), +] +dependencies = [ + ('Python', '3.11.5'), + ('cURL', '8.3.0'), +] + +download_dep_fail = True +sanity_pip_check = True +use_pip = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/Pygments/Pygments-2.18.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/Pygments/Pygments-2.18.0-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..54edd0b830e --- /dev/null +++ b/easybuild/easyconfigs/p/Pygments/Pygments-2.18.0-GCCcore-12.3.0.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonPackage' + +name = 'Pygments' +version = '2.18.0' + +homepage = 'https://pygments.org/' +description = """Generic syntax highlighter suitable for use in code hosting, forums, wikis or other applications + that need to prettify source code.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +sources = [SOURCELOWER_PY3_WHL] +checksums = ['b8e6aca0523f3ab76fee51799c488e38782ac06eafcf95e7ba832985c8e7b13a'] + +builddependencies = [ + ('binutils', '2.40'), +] + +dependencies = [ + ('Python', '3.11.3'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/pygmentize'], + 'dirs': [], +} + +sanity_check_commands = ['pygmentize --help'] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/Pylint/Pylint-3.2.5-GCCcore-13.2.0.eb b/easybuild/easyconfigs/p/Pylint/Pylint-3.2.5-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..c919c6c4dd4 --- /dev/null +++ b/easybuild/easyconfigs/p/Pylint/Pylint-3.2.5-GCCcore-13.2.0.eb @@ -0,0 +1,56 @@ +easyblock = 'PythonBundle' + +name = 'Pylint' +version = '3.2.5' + +homepage = 'https://www.pylint.org/' +description = """Pylint is a tool that checks for errors in Python code, tries to enforce + a coding standard and looks for code smells. It can also look for certain type errors, + it can recommend suggestions about how particular blocks can be refactored and + can offer you details about the code's complexity.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +builddependencies = [ + ('binutils', '2.40'), + ('poetry', '1.6.1'), +] + +dependencies = [ + ('Python', '3.11.5'), +] + +use_pip = True + +exts_list = [ + ('dill', '0.3.8', { + 'checksums': ['3ebe3c479ad625c4553aca177444d89b486b1d84982eeacded644afc0cf797ca'], + }), + ('platformdirs', '4.2.2', { + 'checksums': ['38b7b51f512eed9e84a22788b4bce1de17c0adb134d6becb09836e37d8654cd3'], + }), + ('tomlkit', '0.12.5', { + 'checksums': ['eef34fba39834d4d6b73c9ba7f3e4d1c417a4e56f89a7e96e090dd0d24b8fb3c'], + }), + ('astroid', '3.2.2', { + 'checksums': ['8ead48e31b92b2e217b6c9733a21afafe479d52d6e164dd25fb1a770c7c3cf94'], + }), + ('isort', '5.13.2', { + 'checksums': ['48fdfcb9face5d58a4f6dde2e72a1fb8dcaf8ab26f95ab49fab84c2ddefb0109'], + }), + ('mccabe', '0.7.0', { + 'checksums': ['348e0240c33b60bbdf4e523192ef919f28cb2c3d7d5c7794f74009290f236325'], + }), + ('pylint', version, { + 'checksums': ['e9b7171e242dcc6ebd0aaa7540481d1a72860748a0a7816b8fe6cf6c80a6fe7e'], + }), +] + +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/pylint'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/Pyomo/Pyomo-6.7.3-foss-2023a.eb b/easybuild/easyconfigs/p/Pyomo/Pyomo-6.7.3-foss-2023a.eb new file mode 100644 index 00000000000..64ee6de4f2b --- /dev/null +++ b/easybuild/easyconfigs/p/Pyomo/Pyomo-6.7.3-foss-2023a.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonBundle' + +name = 'Pyomo' +version = '6.7.3' + +homepage = 'https://www.pyomo.org/' +description = """ Pyomo is a Python-based open-source software package that supports a diverse set of optimization + capabilities for formulating and analyzing optimization models. """ + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('mpi4py', '3.1.4'), + ('PLY', '3.11'), +] + +exts_list = [ + ('PyUtilib', '6.0.0', { + 'preinstallopts': """sed -i "s/'nose',//g" setup.py && """, + 'checksums': ['d3c14f8ed9028a831b2bf51b8ab7776eba87e66cfc58a06b99c359aaa640f040'], + }), + (name, version, { + 'checksums': ['b7f0441c405af4f42f38527ae38826a5c0a4984dd7bea1fe07172789d8594770'], + }), +] + +use_pip = True +sanity_pip_check = True + +sanity_check_commands = ['pyomo -h'] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/p/Pysam/Pysam-0.22.1-GCC-13.3.0.eb b/easybuild/easyconfigs/p/Pysam/Pysam-0.22.1-GCC-13.3.0.eb new file mode 100644 index 00000000000..2920aeda78e --- /dev/null +++ b/easybuild/easyconfigs/p/Pysam/Pysam-0.22.1-GCC-13.3.0.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonPackage' + +name = 'Pysam' +version = '0.22.1' + +homepage = 'https://github.com/pysam-developers/pysam' +description = """Pysam is a python module for reading and manipulating Samfiles. + It's a lightweight wrapper of the samtools C-API. Pysam also includes an interface for tabix.""" + +toolchain = {'name': 'GCC', 'version': '13.3.0'} + +source_urls = ['https://github.com/pysam-developers/pysam/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['e4981524d7627c53fa0d3f8cbec2bd65c2ea7520092f25e1029af12cb7b82ff6'] + +builddependencies = [ + ('Cython', '3.0.10') +] + +dependencies = [ + ('Python', '3.12.3'), + ('Python-bundle-PyPI', '2024.06'), + ('ncurses', '6.5'), + ('cURL', '8.7.1'), + ('XZ', '5.4.5'), +] + +download_dep_fail = True +use_pip = True + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/Python-bundle-PyPI/Python-bundle-PyPI-2023.06-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/Python-bundle-PyPI/Python-bundle-PyPI-2023.06-GCCcore-12.3.0.eb index 6a91bcca5e4..808285d9f26 100644 --- a/easybuild/easyconfigs/p/Python-bundle-PyPI/Python-bundle-PyPI-2023.06-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/p/Python-bundle-PyPI/Python-bundle-PyPI-2023.06-GCCcore-12.3.0.eb @@ -26,11 +26,8 @@ dependencies = [ ('virtualenv', '20.23.1'), ] -exts_default_options = { - 'download_dep_fail': True, - 'sanity_pip_check': True, - 'use_pip': True, -} +sanity_pip_check = True +use_pip = True # order is important! # package versions updated 2023-06-26 diff --git a/easybuild/easyconfigs/p/Python-bundle-PyPI/Python-bundle-PyPI-2023.10-GCCcore-13.2.0.eb b/easybuild/easyconfigs/p/Python-bundle-PyPI/Python-bundle-PyPI-2023.10-GCCcore-13.2.0.eb index d551945f5e7..d97f7a93c0f 100644 --- a/easybuild/easyconfigs/p/Python-bundle-PyPI/Python-bundle-PyPI-2023.10-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/p/Python-bundle-PyPI/Python-bundle-PyPI-2023.10-GCCcore-13.2.0.eb @@ -26,11 +26,8 @@ dependencies = [ ('virtualenv', '20.24.6'), ] -exts_default_options = { - 'download_dep_fail': True, - 'sanity_pip_check': True, - 'use_pip': True, -} +sanity_pip_check = True +use_pip = True # order is important! # package versions updated 2023-10-29 diff --git a/easybuild/easyconfigs/p/Python-bundle-PyPI/Python-bundle-PyPI-2024.06-GCCcore-13.3.0.eb b/easybuild/easyconfigs/p/Python-bundle-PyPI/Python-bundle-PyPI-2024.06-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..42df4fd52a1 --- /dev/null +++ b/easybuild/easyconfigs/p/Python-bundle-PyPI/Python-bundle-PyPI-2024.06-GCCcore-13.3.0.eb @@ -0,0 +1,497 @@ +easyblock = 'PythonBundle' + +name = 'Python-bundle-PyPI' +version = '2024.06' + +homepage = 'https://python.org/' +description = "Bundle of Python packages from PyPI" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +builddependencies = [ + ('binutils', '2.42'), + ('UnZip', '6.0'), + ('pkgconf', '2.2.0'), + ('git', '2.45.1'), # required for pbr + ('hatchling', '1.24.2'), + ('poetry', '1.8.3'), + ('scikit-build', '0.17.6'), + ('flit', '3.9.0'), + ('setuptools-rust', '1.9.0'), # required for dulwich + ('maturin', '1.6.0'), # required for rpds-py +] + +dependencies = [ + ('Python', '3.12.3'), + ('cryptography', '42.0.8'), + ('virtualenv', '20.26.2'), +] + +sanity_pip_check = True +use_pip = True + +# order is important! +# package versions updated 2024-06-14 +exts_list = [ + ('blist', '1.3.6', { + 'patches': [ + 'Python-3_9-blist-1.3.6-fix-undefined_symbol_PyObject_GC_IS_TRACKED.patch', + 'Python-3.10-bist-1.3.6-compatibility.patch', + 'Python-3.11-bist-1.3.6-compatibility.patch', + ], + 'checksums': [ + {'blist-1.3.6.tar.gz': '3a12c450b001bdf895b30ae818d4d6d3f1552096b8c995f0fe0c74bef04d1fc3'}, + {'Python-3_9-blist-1.3.6-fix-undefined_symbol_PyObject_GC_IS_TRACKED.patch': + '18a643d1d1565b05df7dcc9a612a86dcf7b3b352435032f6425a61b597f911d0'}, + {'Python-3.10-bist-1.3.6-compatibility.patch': + '0fb2d92e06b2c39bfc79e229e6fde6053f9aa9538733029377c9a743650a4741'}, + {'Python-3.11-bist-1.3.6-compatibility.patch': + 'da283300bc5f0524b9982c9d9de4670908711634667849d3d81ccd87fc82c4ee'}, + ], + }), + ('pbr', '6.0.0', { + 'checksums': ['d1377122a5a00e2f940ee482999518efe16d745d423a670c27773dfbc3c9a7d9'], + }), + ('six', '1.16.0', { + 'checksums': ['1e61c37477a1626458e36f7b1d82aa5c9b094fa4802892072e49de9c60c4c926'], + }), + ('toml', '0.10.2', { + 'checksums': ['b3bda1d108d5dd99f4a20d24d9c348e91c4db7ab1b749200bded2f839ccbe68f'], + }), + ('tomli', '2.0.1', { + 'checksums': ['de526c12914f0c550d15924c62d72abc48d6fe7364aa87328337a31007fe8a4f'], + }), + ('packaging', '24.1', { + 'checksums': ['026ed72c8ed3fcce5bf8950572258698927fd1dbda10a5e981cdf0ac37f4f002'], + }), + ('python-dateutil', '2.9.0.post0', { + 'modulename': 'dateutil', + 'checksums': ['37dd54208da7e1cd875388217d5e00ebd4179249f90fb72437e91a35459a0ad3'], + }), + ('decorator', '5.1.1', { + 'checksums': ['637996211036b6385ef91435e4fae22989472f9d571faba8927ba8253acbc330'], + }), + ('liac-arff', '2.5.0', { + 'modulename': 'arff', + 'checksums': ['3220d0af6487c5aa71b47579be7ad1d94f3849ff1e224af3bf05ad49a0b5c4da'], + }), + ('pycryptodome', '3.20.0', { + 'modulename': 'Crypto.PublicKey.RSA', + 'checksums': ['09609209ed7de61c2b560cc5c8c4fbf892f8b15b1faf7e4cbffac97db1fffda7'], + }), + ('ecdsa', '0.19.0', { + 'checksums': ['60eaad1199659900dd0af521ed462b793bbdf867432b3948e87416ae4caf6bf8'], + }), + ('ipaddress', '1.0.23', { + 'checksums': ['b7f8e0369580bb4a24d5ba1d7cc29660a4a6987763faf1d8a8046830e020e7e2'], + }), + ('asn1crypto', '1.5.1', { + 'checksums': ['13ae38502be632115abf8a24cbe5f4da52e3b5231990aff31123c805306ccb9c'], + }), + ('idna', '3.7', { + 'checksums': ['028ff3aadf0609c1fd278d8ea3089299412a7a8b9bd005dd08b9f8285bcb5cfc'], + }), + ('pycparser', '2.22', { + 'checksums': ['491c8be9c040f5390f5bf44a5b07752bd07f56edf992381b05c701439eec10f6'], + }), + ('cffi', '1.16.0', { + 'checksums': ['bcb3ef43e58665bbda2fb198698fcae6776483e0c4a631aa5647806c25e02cc0'], + }), + ('semantic-version', '2.10.0', { + 'sources': ['semantic_version-%(version)s.tar.gz'], + 'checksums': ['bdabb6d336998cbb378d4b9db3a4b56a1e3235701dc05ea2690d9a997ed5041c'], + }), + ('pyasn1', '0.6.0', { + 'checksums': ['3a35ab2c4b5ef98e17dfdec8ab074046fbda76e281c5a706ccd82328cfc8f64c'], + }), + ('PyNaCl', '1.5.0', { + 'modulename': 'nacl', + 'checksums': ['8ac7448f09ab85811607bdd21ec2464495ac8b7c66d146bf545b0f08fb9220ba'], + }), + ('pyparsing', '3.1.2', { + 'checksums': ['a1bac0ce561155ecc3ed78ca94d3c9378656ad4c94c1270de543f621420f94ad'], + }), + ('netifaces', '0.11.0', { + 'checksums': ['043a79146eb2907edf439899f262b3dfe41717d34124298ed281139a8b93ca32'], + }), + ('netaddr', '1.3.0', { + 'checksums': ['5c3c3d9895b551b763779ba7db7a03487dc1f8e3b385af819af341ae9ef6e48a'], + }), + ('mock', '5.1.0', { + 'checksums': ['5e96aad5ccda4718e0a229ed94b2024df75cc2d55575ba5762d31f5767b8767d'], + }), + ('pytz', '2024.1', { + 'checksums': ['2a29735ea9c18baf14b448846bde5a48030ed267578472d8955cd0e7443a9812'], + }), + ('bitarray', '2.9.2', { + 'checksums': ['a8f286a51a32323715d77755ed959f94bef13972e9a2fe71b609e40e6d27957e'], + }), + ('bitstring', '4.2.3', { + 'checksums': ['e0c447af3fda0d114f77b88c2d199f02f97ee7e957e6d719f40f41cf15fbb897'], + }), + ('appdirs', '1.4.4', { + 'checksums': ['7d5d0167b2b1ba821647616af46a749d1c653740dd0d2415100fe26e27afdf41'], + }), + ('distlib', '0.3.8', { + 'checksums': ['1530ea13e350031b6312d8580ddb6b27a104275a31106523b8f123787f494f64'], + }), + ('zipp', '3.19.2', { + 'checksums': ['bf1dcf6450f873a13e952a29504887c89e6de7506209e5b1bcc3460135d4de19'], + }), + ('importlib-metadata', '7.1.0', { + 'sources': ['importlib_metadata-%(version)s.tar.gz'], + 'checksums': ['b78938b926ee8d5f020fc4772d487045805a55ddbad2ecf21c6d60938dc7fcd2'], + }), + ('backports.entry-points-selectable', '1.3.0', { + 'sources': ['backports.entry_points_selectable-%(version)s.tar.gz'], + 'checksums': ['17a8b44ae700fba548686dd274ddc91c060371565cd63806c20a1d33911746e6'], + }), + ('pathspec', '0.12.1', { + 'checksums': ['a482d51503a1ab33b1c67a6c3813a26953dbdc71c31dacaef9a838c4e29f5712'], + }), + ('pluggy', '1.5.0', { + 'checksums': ['2cffa88e94fdc978c4c574f15f9e59b7f4201d439195c3715ca9e2486f1d0cf1'], + }), + ('editables', '0.5', { + 'checksums': ['309627d9b5c4adc0e668d8c6fa7bac1ba7c8c5d415c2d27f60f081f8e80d1de2'], + }), + ('filelock', '3.15.1', { + 'checksums': ['58a2549afdf9e02e10720eaa4d4470f56386d7a6f72edd7d0596337af8ed7ad8'], + }), + ('platformdirs', '4.2.2', { + 'checksums': ['38b7b51f512eed9e84a22788b4bce1de17c0adb134d6becb09836e37d8654cd3'], + }), + ('scandir', '1.10.0', { + 'checksums': ['4d4631f6062e658e9007ab3149a9b914f3548cb38bfb021c64f39a025ce578ae'], + }), + ('pathlib2', '2.3.7.post1', { + 'checksums': ['9fe0edad898b83c0c3e199c842b27ed216645d2e177757b2dd67384d4113c641'], + }), + ('importlib-resources', '6.4.0', { + 'sources': ['importlib_resources-%(version)s.tar.gz'], + 'checksums': ['cdb2b453b8046ca4e3798eb1d84f3cce1446a0e8e7b5ef4efb600f19fc398145'], + }), + ('docopt', '0.6.2', { + 'checksums': ['49b3a825280bd66b3aa83585ef59c4a8c82f2c8a522dbe754a8bc8d08c85c491'], + }), + ('joblib', '1.4.2', { + 'checksums': ['2382c5816b2636fbd20a09e0f4e9dad4736765fdfb7dca582943b9c1366b3f0e'], + }), + ('chardet', '5.2.0', { + 'checksums': ['1b3b6ff479a8c414bc3fa2c0852995695c4a026dcd6d0633b2dd092ca39c1cf7'], + }), + ('certifi', '2024.6.2', { + 'checksums': ['3cd43f1c6fa7dedc5899d69d3ad0398fd018ad1a17fba83ddaf78aa46c747516'], + }), + ('urllib3', '2.2.1', { + 'checksums': ['d0570876c61ab9e520d776c38acbbb5b05a776d3f9ff98a5c8fd5162a444cf19'], + }), + ('charset-normalizer', '3.3.2', { + 'checksums': ['f30c3cb33b24454a82faecaf01b19c18562b1e89558fb6c56de4d9118a032fd5'], + }), + ('requests', '2.32.3', { + 'checksums': ['55365417734eb18255590a9ff9eb97e9e1da868d4ccd6402399eaf68af20a760'], + }), + ('xlrd', '2.0.1', { + 'checksums': ['f72f148f54442c6b056bf931dbc34f986fd0c3b0b6b5a58d013c9aef274d0c88'], + }), + ('py-expression-eval', '0.3.14', { + 'sources': ['py_expression_eval-%(version)s.tar.gz'], + 'checksums': ['ea60f9404a18346d5a63854db21c50666dfb4274ae111000165b31c6f8ab93f1'], + }), + ('tabulate', 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'checksums': ['cd372a1ec446a1bc5a90624a52c88e83b9330218e39047a6c9a48ae37d116745'], + }), + ('tomlkit', '0.12.5', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['af914f5a9c59ed9d0762c7b64d3b5d5df007448eb9cd2edc8a46b1eafead172f'], + }), + ('shellingham', '1.5.4', { + 'checksums': ['8dbca0739d487e5bd35ab3ca4b36e11c4078f3a234bfce294b0a0291363404de'], + }), + ('requests-toolbelt', '1.0.0', { + 'checksums': ['7681a0a3d047012b5bdc0ee37d7f8f07ebe76ab08caeccfc3921ce23c88d5bc6'], + }), + ('pyrsistent', '0.20.0', { + 'checksums': ['4c48f78f62ab596c679086084d0dd13254ae4f3d6c72a83ffdf5ebdef8f265a4'], + }), + ('pkginfo', '1.11.1', { + 'checksums': ['2e0dca1cf4c8e39644eed32408ea9966ee15e0d324c62ba899a393b3c6b467aa'], + }), + ('ptyprocess', '0.7.0', { + 'source_tmpl': '%(name)s-%(version)s-py2.py3-none-any.whl', + 'checksums': ['4b41f3967fce3af57cc7e94b888626c18bf37a083e3651ca8feeb66d492fef35'], + }), + ('pexpect', '4.9.0', { + 'checksums': 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('pydevtool', '0.3.0', { + 'checksums': ['25e3ba4f3d33ccac33ee2b9775995848d49e9b318b7a146477fb5d52f786fc8a'], + }), + ('mdurl', '0.1.2', { + 'checksums': ['bb413d29f5eea38f31dd4754dd7377d4465116fb207585f97bf925588687c1ba'], + }), + ('markdown-it-py', '3.0.0', { + 'modulename': 'markdown_it', + 'checksums': ['e3f60a94fa066dc52ec76661e37c851cb232d92f9886b15cb560aaada2df8feb'], + }), + ('rich', '13.7.1', { + 'checksums': ['9be308cb1fe2f1f57d67ce99e95af38a1e2bc71ad9813b0e247cf7ffbcc3a432'], + }), + ('rich-click', '1.8.3', { + 'sources': ['rich_click-%(version)s.tar.gz'], + 'checksums': ['6d75bdfa7aa9ed2c467789a0688bc6da23fbe3a143e19aa6ad3f8bac113d2ab3'], + }), + ('commonmark', '0.9.1', { + 'checksums': ['452f9dc859be7f06631ddcb328b6919c67984aca654e5fefb3914d54691aed60'], + }), + ('execnet', '2.1.1', { + 'checksums': ['5189b52c6121c24feae288166ab41b32549c7e2348652736540b9e6e7d4e72e3'], + }), + ('pytest-xdist', '3.6.1', { + 'modulename': 'xdist', + 'sources': ['pytest_xdist-%(version)s.tar.gz'], + 'checksums': ['ead156a4db231eec769737f57668ef58a2084a34b2e55c4a8fa20d861107300d'], + }), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-3.12.3-GCCcore-13.3.0.eb b/easybuild/easyconfigs/p/Python/Python-3.12.3-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..af5f4d13235 --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-3.12.3-GCCcore-13.3.0.eb @@ -0,0 +1,72 @@ +name = 'Python' +version = '3.12.3' + +homepage = 'https://python.org/' +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] +patches = ['Python-3.12.3_avoid-tkinter-build.patch'] +checksums = [ + {'Python-3.12.3.tgz': 'a6b9459f45a6ebbbc1af44f5762623fa355a0c87208ed417628b379d762dddb0'}, + {'Python-3.12.3_avoid-tkinter-build.patch': '34fa44ca67fc08d41c58db2e289317f12f32777a352a982dca2e63459fc089e3'}, +] + +builddependencies = [ + ('UnZip', '6.0'), + ('pkgconf', '2.2.0'), +] + +dependencies = [ + ('binutils', '2.42'), + ('bzip2', '1.0.8'), # required for bz2 package in Python stdlib + ('zlib', '1.3.1'), + ('libreadline', '8.2'), + ('ncurses', '6.5'), + ('SQLite', '3.45.3'), + ('XZ', '5.4.5'), + ('libffi', '3.4.5'), + ('OpenSSL', '3', '', SYSTEM), +] + +install_pip = True + +exts_default_options = { + 'source_urls': [PYPI_SOURCE], + 'use_pip': True, +} + +# order is important! +# package versions updated 2024-05-21 +exts_list = [ + ('flit_core', '3.9.0', { + 'checksums': ['72ad266176c4a3fcfab5f2930d76896059851240570ce9a98733b658cb786eba'], + }), + ('wheel', '0.43.0', { + 'checksums': ['465ef92c69fa5c5da2d1cf8ac40559a8c940886afcef87dcf14b9470862f1d85'], + }), + ('tomli', '2.0.1', { + 'checksums': ['de526c12914f0c550d15924c62d72abc48d6fe7364aa87328337a31007fe8a4f'], + }), + ('packaging', '24.0', { + 'checksums': ['eb82c5e3e56209074766e6885bb04b8c38a0c015d0a30036ebe7ece34c9989e9'], + }), + ('typing_extensions', '4.11.0', { + 'checksums': ['83f085bd5ca59c80295fc2a82ab5dac679cbe02b9f33f7d83af68e241bea51b0'], + }), + ('setuptools', '70.0.0', { + 'checksums': ['f211a66637b8fa059bb28183da127d4e86396c991a942b028c6650d4319c3fd0'], + }), + ('setuptools_scm', '8.1.0', { + 'checksums': ['42dea1b65771cba93b7a515d65a65d8246e560768a66b9106a592c8e7f26c8a7'], + }), + ('pip', '24.0', { + 'checksums': ['ea9bd1a847e8c5774a5777bb398c19e80bcd4e2aa16a4b301b718fe6f593aba2'], + }), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-3.12.3_avoid-tkinter-build.patch b/easybuild/easyconfigs/p/Python/Python-3.12.3_avoid-tkinter-build.patch new file mode 100644 index 00000000000..cd6261321c0 --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-3.12.3_avoid-tkinter-build.patch @@ -0,0 +1,17 @@ +Explicitly disable building of _tkinter module +Simon Branford (University of Birmingham) +--- configure.orig 2024-05-24 11:09:00.888859445 +0100 ++++ configure 2024-05-24 11:52:11.840124559 +0100 +@@ -30585,11 +30585,11 @@ + { printf "%s\n" "$as_me:${as_lineno-$LINENO}: checking for stdlib extension module _tkinter" >&5 + printf %s "checking for stdlib extension module _tkinter... " >&6; } + if test "$py_cv_module__tkinter" != "n/a" + then : + +- if true ++ if false + then : + if test "$have_tcltk" = "yes" + then : + py_cv_module__tkinter=yes + else $as_nop diff --git a/easybuild/easyconfigs/p/p11-kit/p11-kit-0.25.3-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/p11-kit/p11-kit-0.25.3-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..64d64977241 --- /dev/null +++ b/easybuild/easyconfigs/p/p11-kit/p11-kit-0.25.3-GCCcore-12.3.0.eb @@ -0,0 +1,41 @@ +easyblock = 'ConfigureMake' + +name = 'p11-kit' +version = '0.25.3' + +homepage = 'https://p11-glue.freedesktop.org/p11-kit.html' +description = """Provides a way to load and enumerate PKCS#11 modules. + Provides a standard configuration setup for installing + PKCS#11 modules in such a way that they're discoverable. + Also solves problems with coordinating the use of PKCS#11 + by different components or libraries living in the same process.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://github.com/p11-glue/p11-kit/releases/download/%(version)s/'] +sources = [SOURCE_TAR_XZ] +checksums = ['d8ddce1bb7e898986f9d250ccae7c09ce14d82f1009046d202a0eb1b428b2adc'] + +builddependencies = [ + ('binutils', '2.40'), + ('pkgconf', '1.9.5'), +] + +dependencies = [ + ('libtasn1', '4.19.0'), + ('libffi', '3.4.4'), +] + +preconfigopts = "bashcompdir=%(installdir)s/share/bash-completions " + +configopts = "--without-systemd" + +sanity_check_paths = { + 'files': ['bin/p11-kit', 'bin/trust'] + + ['lib/libp11-kit.%s' % SHLIB_EXT], + 'dirs': ['include/p11-kit-1/p11-kit'], +} + +sanity_check_commands = ["p11-kit --help"] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/p7zip/p7zip-17.05-GCCcore-13.3.0.eb b/easybuild/easyconfigs/p/p7zip/p7zip-17.05-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..f691f95e191 --- /dev/null +++ b/easybuild/easyconfigs/p/p7zip/p7zip-17.05-GCCcore-13.3.0.eb @@ -0,0 +1,47 @@ +easyblock = 'MakeCp' + +name = 'p7zip' +version = '17.05' + +homepage = 'https://github.com/p7zip-project/p7zip/' +description = """p7zip is a quick port of 7z.exe and 7za.exe (CLI version of +7zip) for Unix. 7-Zip is a file archiver with highest compression ratio.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['d2788f892571058c08d27095c22154579dfefb807ebe357d145ab2ddddefb1a6'] + +builddependencies = [ + ('binutils', '2.42'), +] + +prebuildopts = "cp makefile.linux_amd64 makefile.linux &&" +buildopts = 'all3 CC="$CC" CXX="$CXX" OPTFLAGS="$CFLAGS"' + +github_account = '%(name)s-project' +# put script in place for 7z, since it *must* be called full path, to ensure that 7z.so is found in the same directory +# see also http://sourceforge.net/p/p7zip/discussion/383044/thread/5e4085ab/ +postinstallcmds = [ + """echo '#!/bin/sh +%(installdir)s/libexec/7z $@' > %(installdir)s/bin/7z""", + "chmod +x %(installdir)s/bin/7z", # set execution bits according to current umask +] +files_to_copy = [ + (['bin/7za', 'bin/7zr', 'bin/7zCon.sfx'], 'bin'), # stand-alone binaries + (['bin/7z', 'bin/7z.so', 'bin/Codecs'], 'libexec'), +] # 7z requires 7z.so plugin in same directory + +sanity_check_paths = { + 'files': ['bin/7z', 'bin/7za', 'bin/7zCon.sfx', 'bin/7zr', 'libexec/7z', 'libexec/7z.%s' % SHLIB_EXT], + 'dirs': ['libexec/Codecs'], +} + +sanity_check_commands = [ + "7z --help", + "7z x || test $? -gt 0", + """! 7z i | grep -q "Can't load" """, +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/packmol/packmol-20.14.4-GCC-12.3.0.eb b/easybuild/easyconfigs/p/packmol/packmol-20.14.4-GCC-12.3.0.eb new file mode 100644 index 00000000000..4f5dd6ed6b8 --- /dev/null +++ b/easybuild/easyconfigs/p/packmol/packmol-20.14.4-GCC-12.3.0.eb @@ -0,0 +1,24 @@ +easyblock = 'MakeCp' + +name = 'packmol' +version = '20.14.4' + +homepage = 'http://m3g.iqm.unicamp.br/packmol' +description = "Packing Optimization for Molecular Dynamics Simulations" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +source_urls = ['https://github.com/m3g/packmol/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['45ec33798d5f10c0aac6046675531a0e98567890c1a76f753450c5fc6b1aaa2f'] + +buildopts = 'FORTRAN="$F90"' + +files_to_copy = [(['packmol'], 'bin'), 'AUTHORS', 'LICENSE'] + +sanity_check_paths = { + 'files': ['bin/packmol', 'AUTHORS', 'LICENSE'], + 'dirs': [], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/p/pagmo/pagmo-2.19.0-gfbf-2022b.eb b/easybuild/easyconfigs/p/pagmo/pagmo-2.19.0-gfbf-2022b.eb new file mode 100644 index 00000000000..6f64905045c --- /dev/null +++ b/easybuild/easyconfigs/p/pagmo/pagmo-2.19.0-gfbf-2022b.eb @@ -0,0 +1,35 @@ +easyblock = 'CMakeMake' + +name = 'pagmo' +version = '2.19.0' + +homepage = 'https://esa.github.io/pagmo2' +description = "pagmo is a C++ scientific library for massively parallel optimization." + +toolchain = {'name': 'gfbf', 'version': '2022b'} + +source_urls = ['https://github.com/esa/pagmo2/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['701ada528de7d454201e92a5d88903dd1c22ea64f43861d9694195ddfef82a70'] + +builddependencies = [ + ('CMake', '3.24.3'), +] + +dependencies = [ + ('Boost', '1.81.0'), + ('tbb', '2021.9.0'), + ('Eigen', '3.4.0'), + ('NLopt', '2.7.1'), +] + +configopts = "-DPAGMO_WITH_EIGEN3=ON -DPAGMO_WITH_NLOPT=ON -DPAGMO_BUILD_TESTS=ON" + +runtest = 'test' + +sanity_check_paths = { + 'files': ['lib/libpagmo.%s' % SHLIB_EXT], + 'dirs': ['include/pagmo', 'lib/cmake/pagmo'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/parallel/parallel-20230722-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/parallel/parallel-20230722-GCCcore-12.3.0.eb index 7725cf4990a..32a4662d685 100644 --- a/easybuild/easyconfigs/p/parallel/parallel-20230722-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/p/parallel/parallel-20230722-GCCcore-12.3.0.eb @@ -14,13 +14,19 @@ checksums = ['55f991ad195a72f0abfaf1ede8fc1d03dd255cac91bc5eb900f9aa2873d1ff87'] builddependencies = [('binutils', '2.40')] -dependencies = [('Perl', '5.36.1')] +dependencies = [ + ('Perl', '5.36.1'), + ('Perl-bundle-CPAN', '5.36.1'), +] sanity_check_paths = { 'files': ['bin/parallel'], 'dirs': [] } -sanity_check_commands = ["parallel --help"] +sanity_check_commands = [ + 'parallel --help', + 'time parallel --csv echo < <(echo -e "task1\ntask2\ntask3")', +] moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/parallel/parallel-20240322-GCCcore-13.2.0.eb b/easybuild/easyconfigs/p/parallel/parallel-20240322-GCCcore-13.2.0.eb index 53acb414c76..4673651a654 100644 --- a/easybuild/easyconfigs/p/parallel/parallel-20240322-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/p/parallel/parallel-20240322-GCCcore-13.2.0.eb @@ -14,13 +14,19 @@ checksums = ['0b17029a203dabf7ba6ca7e52c2d3910fff46b2979476e12a9110920b79e6a95'] builddependencies = [('binutils', '2.40')] -dependencies = [('Perl', '5.38.0')] +dependencies = [ + ('Perl', '5.38.0'), + ('Perl-bundle-CPAN', '5.38.0'), +] sanity_check_paths = { 'files': ['bin/parallel'], 'dirs': [] } -sanity_check_commands = ["parallel --help"] +sanity_check_commands = [ + 'parallel --help', + 'time parallel --csv echo < <(echo -e "task1\ntask2\ntask3")', +] moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/parallel/parallel-20240722-GCCcore-13.3.0.eb b/easybuild/easyconfigs/p/parallel/parallel-20240722-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..e3f60b06f2c --- /dev/null +++ b/easybuild/easyconfigs/p/parallel/parallel-20240722-GCCcore-13.3.0.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'parallel' +version = '20240722' + +homepage = 'https://savannah.gnu.org/projects/parallel/' +description = """parallel: Build and execute shell commands in parallel""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['c7335471f776af28bea9464ad85a50f2ed120f78fbf75ead6647aeea8e0e53f0'] + +builddependencies = [('binutils', '2.42')] + +dependencies = [ + ('Perl', '5.38.2'), + ('Perl-bundle-CPAN', '5.38.2'), +] + +sanity_check_paths = { + 'files': ['bin/parallel'], + 'dirs': [] +} + +sanity_check_commands = [ + 'parallel --help', + 'time parallel --csv echo < <(echo -e "task1\ntask2\ntask3")', +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/parasail/parasail-2.6.2-GCC-13.2.0.eb b/easybuild/easyconfigs/p/parasail/parasail-2.6.2-GCC-13.2.0.eb new file mode 100644 index 00000000000..ddb3e791f30 --- /dev/null +++ b/easybuild/easyconfigs/p/parasail/parasail-2.6.2-GCC-13.2.0.eb @@ -0,0 +1,26 @@ +easyblock = 'CMakeMake' + +name = 'parasail' +version = '2.6.2' + +homepage = 'https://github.com/jeffdaily/parasail' +description = """parasail is a SIMD C (C99) library containing implementations + of the Smith-Waterman (local), Needleman-Wunsch (global), and semi-global + pairwise sequence alignment algorithms. """ + +toolchain = {'name': 'GCC', 'version': '13.2.0'} + +github_account = 'jeffdaily' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['9057041db8e1cde76678f649420b85054650414e5de9ea84ee268756c7ea4b4b'] + +builddependencies = [('CMake', '3.27.6')] + +sanity_check_paths = { + 'files': ['bin/parasail_aligner', 'bin/parasail_stats', + 'lib/libparasail.%s' % SHLIB_EXT, 'include/parasail.h'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/patchelf/patchelf-0.18.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/patchelf/patchelf-0.18.0-GCCcore-12.3.0.eb index b87a53d6bda..d213a037191 100644 --- a/easybuild/easyconfigs/p/patchelf/patchelf-0.18.0-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/p/patchelf/patchelf-0.18.0-GCCcore-12.3.0.eb @@ -10,7 +10,11 @@ toolchain = {'name': 'GCCcore', 'version': '12.3.0'} source_urls = ['https://github.com/NixOS/patchelf/archive/'] sources = ['%(version)s.tar.gz'] -checksums = ['1451d01ee3a21100340aed867d0b799f46f0b1749680028d38c3f5d0128fb8a7'] +patches = ['patchelf-0.18.0_fix-alignment.patch'] +checksums = [ + {'0.18.0.tar.gz': '1451d01ee3a21100340aed867d0b799f46f0b1749680028d38c3f5d0128fb8a7'}, + {'patchelf-0.18.0_fix-alignment.patch': '87936627643b2212e8261b0f3d5905f12d0fc91f73503e12124f93ff972e0a03'}, +] builddependencies = [ ('binutils', '2.40'), diff --git a/easybuild/easyconfigs/p/patchelf/patchelf-0.18.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/p/patchelf/patchelf-0.18.0-GCCcore-13.2.0.eb index 62d26c800db..6dd3411d14b 100644 --- a/easybuild/easyconfigs/p/patchelf/patchelf-0.18.0-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/p/patchelf/patchelf-0.18.0-GCCcore-13.2.0.eb @@ -10,7 +10,11 @@ toolchain = {'name': 'GCCcore', 'version': '13.2.0'} source_urls = ['https://github.com/NixOS/patchelf/archive/'] sources = ['%(version)s.tar.gz'] -checksums = ['1451d01ee3a21100340aed867d0b799f46f0b1749680028d38c3f5d0128fb8a7'] +patches = ['patchelf-0.18.0_fix-alignment.patch'] +checksums = [ + {'0.18.0.tar.gz': '1451d01ee3a21100340aed867d0b799f46f0b1749680028d38c3f5d0128fb8a7'}, + {'patchelf-0.18.0_fix-alignment.patch': '87936627643b2212e8261b0f3d5905f12d0fc91f73503e12124f93ff972e0a03'}, +] builddependencies = [ ('binutils', '2.40'), diff --git a/easybuild/easyconfigs/p/patchelf/patchelf-0.18.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/p/patchelf/patchelf-0.18.0-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..10b4831c5f7 --- /dev/null +++ b/easybuild/easyconfigs/p/patchelf/patchelf-0.18.0-GCCcore-13.3.0.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'patchelf' +version = '0.18.0' + +homepage = 'https://github.com/NixOS/patchelf' +description = """PatchELF is a small utility to modify the dynamic linker and RPATH of ELF executables.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://github.com/NixOS/patchelf/archive/'] +sources = ['%(version)s.tar.gz'] +patches = ['patchelf-0.18.0_fix-alignment.patch'] +checksums = [ + {'0.18.0.tar.gz': '1451d01ee3a21100340aed867d0b799f46f0b1749680028d38c3f5d0128fb8a7'}, + {'patchelf-0.18.0_fix-alignment.patch': '87936627643b2212e8261b0f3d5905f12d0fc91f73503e12124f93ff972e0a03'}, +] + +builddependencies = [ + ('binutils', '2.42'), + ('Autotools', '20231222'), +] + +preconfigopts = "sh bootstrap.sh && " + +sanity_check_paths = { + 'files': ['bin/patchelf'], + 'dirs': ['share'], +} + +sanity_check_commands = ["patchelf --help"] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/patchelf/patchelf-0.18.0_fix-alignment.patch b/easybuild/easyconfigs/p/patchelf/patchelf-0.18.0_fix-alignment.patch new file mode 100644 index 00000000000..20a233ddc66 --- /dev/null +++ b/easybuild/easyconfigs/p/patchelf/patchelf-0.18.0_fix-alignment.patch @@ -0,0 +1,31 @@ +Author - Pavel Tománek +Fix alignment problem when rewriting sections +https://github.com/NixOS/patchelf/pull/566 +--- src/patchelf.cc.orig 2024-10-07 16:45:17.515584318 +0200 ++++ src/patchelf.cc 2024-10-07 16:47:14.622270000 +0200 +@@ -843,7 +843,7 @@ + neededSpace += headerTableSpace; + debug("needed space is %d\n", neededSpace); + +- Elf_Off startOffset = roundUp(fileContents->size(), getPageSize()); ++ Elf_Off startOffset = roundUp(fileContents->size(), alignStartPage); + + // In older version of binutils (2.30), readelf would check if the dynamic + // section segment is strictly smaller than the file (and not same size). +@@ -879,7 +879,7 @@ + rdi(lastSeg.p_type) == PT_LOAD && + rdi(lastSeg.p_flags) == (PF_R | PF_W) && + rdi(lastSeg.p_align) == alignStartPage) { +- auto segEnd = roundUp(rdi(lastSeg.p_offset) + rdi(lastSeg.p_memsz), getPageSize()); ++ auto segEnd = roundUp(rdi(lastSeg.p_offset) + rdi(lastSeg.p_memsz), alignStartPage); + if (segEnd == startOffset) { + auto newSz = startOffset + neededSpace - rdi(lastSeg.p_offset); + wri(lastSeg.p_filesz, wri(lastSeg.p_memsz, newSz)); +@@ -898,6 +898,7 @@ + wri(phdr.p_filesz, wri(phdr.p_memsz, neededSpace)); + wri(phdr.p_flags, PF_R | PF_W); + wri(phdr.p_align, alignStartPage); ++ assert(startPage % alignStartPage == startOffset % alignStartPage); + } + + normalizeNoteSegments(); diff --git a/easybuild/easyconfigs/p/pblat/pblat-2.5.1-foss-2023a.eb b/easybuild/easyconfigs/p/pblat/pblat-2.5.1-foss-2023a.eb new file mode 100644 index 00000000000..a49d5fb0a74 --- /dev/null +++ b/easybuild/easyconfigs/p/pblat/pblat-2.5.1-foss-2023a.eb @@ -0,0 +1,41 @@ +easyblock = 'MakeCp' + +name = 'pblat' +version = '2.5.1' + +homepage = 'https://github.com/icebert/pblat' +description = """When the query file format is fasta, you can specify many threads to process it. + It can reduce run time linearly, and use almost equal memory as the original blat program. + This is useful when you blat a big query file to a huge reference like human whole genome sequence.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +github_account = 'icebert' +source_urls = [GITHUB_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['e85a4d752b8e159502d529f0f9e47579851a6b466b6c2f1f4d49f598642bc615'] + +dependencies = [ + ('HTSlib', '1.18'), + ('zlib', '1.2.13'), + ('OpenSSL', '1.1', '', SYSTEM), +] + +# use HTSlib dependency provided through EasyBuild +prebuildopts = "sed -i '5s/.\\/htslib/$\\{EBROOTHTSLIB\\}\\/include\\/htslib/' Makefile && " +prebuildopts += "sed -i '40s/ htslib\\/libhts.a//' Makefile && " +prebuildopts += "sed -i '41s/htslib\\/libhts.a/-lhts -lcurl/' Makefile && " +prebuildopts += "sed -i -e '/htslib\\/libhts.a:/,+2d' Makefile && " + +files_to_copy = [ + (['%(name)s'], 'bin'), +] + +sanity_check_paths = { + 'files': ['bin/%(name)s'], + 'dirs': [] +} + +sanity_check_commands = ["command -v %(name)s"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/pdsh/pdsh-2.34-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/pdsh/pdsh-2.34-GCCcore-11.3.0.eb index 2ad121fa5b7..514caad6711 100644 --- a/easybuild/easyconfigs/p/pdsh/pdsh-2.34-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/p/pdsh/pdsh-2.34-GCCcore-11.3.0.eb @@ -10,7 +10,11 @@ toolchain = {'name': 'GCCcore', 'version': '11.3.0'} source_urls = ['https://github.com/chaos/pdsh/releases/download/pdsh-%(version)s/'] sources = [SOURCE_TAR_GZ] -checksums = ['b47b3e4662736ef44b6fe86e3d380f95e591863e69163aa0592e9f9f618521e9'] +patches = ['pdsh-2.34_fix-slurm-23.x.patch'] +checksums = [ + {'pdsh-2.34.tar.gz': 'b47b3e4662736ef44b6fe86e3d380f95e591863e69163aa0592e9f9f618521e9'}, + {'pdsh-2.34_fix-slurm-23.x.patch': 'cba3a60f5cbc2ca6dc32cda16998c43818f740c0998aba201dfbe334349e60b9'}, +] builddependencies = [ ('binutils', '2.38'), diff --git a/easybuild/easyconfigs/p/pdsh/pdsh-2.34-GCCcore-12.2.0.eb b/easybuild/easyconfigs/p/pdsh/pdsh-2.34-GCCcore-12.2.0.eb index 1b8e1f8ed55..eb35068da2a 100644 --- a/easybuild/easyconfigs/p/pdsh/pdsh-2.34-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/p/pdsh/pdsh-2.34-GCCcore-12.2.0.eb @@ -10,7 +10,11 @@ toolchain = {'name': 'GCCcore', 'version': '12.2.0'} source_urls = ['https://github.com/chaos/pdsh/releases/download/pdsh-%(version)s/'] sources = [SOURCE_TAR_GZ] -checksums = ['b47b3e4662736ef44b6fe86e3d380f95e591863e69163aa0592e9f9f618521e9'] +patches = ['pdsh-2.34_fix-slurm-23.x.patch'] +checksums = [ + {'pdsh-2.34.tar.gz': 'b47b3e4662736ef44b6fe86e3d380f95e591863e69163aa0592e9f9f618521e9'}, + {'pdsh-2.34_fix-slurm-23.x.patch': 'cba3a60f5cbc2ca6dc32cda16998c43818f740c0998aba201dfbe334349e60b9'}, +] builddependencies = [ ('binutils', '2.39'), diff --git a/easybuild/easyconfigs/p/pdsh/pdsh-2.34-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/pdsh/pdsh-2.34-GCCcore-12.3.0.eb index 75dde8cd89c..90ebe848ded 100644 --- a/easybuild/easyconfigs/p/pdsh/pdsh-2.34-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/p/pdsh/pdsh-2.34-GCCcore-12.3.0.eb @@ -10,7 +10,11 @@ toolchain = {'name': 'GCCcore', 'version': '12.3.0'} source_urls = ['https://github.com/chaos/pdsh/releases/download/pdsh-%(version)s/'] sources = [SOURCE_TAR_GZ] -checksums = ['b47b3e4662736ef44b6fe86e3d380f95e591863e69163aa0592e9f9f618521e9'] +patches = ['pdsh-2.34_fix-slurm-23.x.patch'] +checksums = [ + {'pdsh-2.34.tar.gz': 'b47b3e4662736ef44b6fe86e3d380f95e591863e69163aa0592e9f9f618521e9'}, + {'pdsh-2.34_fix-slurm-23.x.patch': 'cba3a60f5cbc2ca6dc32cda16998c43818f740c0998aba201dfbe334349e60b9'}, +] builddependencies = [ ('binutils', '2.40'), diff --git a/easybuild/easyconfigs/p/pdsh/pdsh-2.34_fix-slurm-23.x.patch b/easybuild/easyconfigs/p/pdsh/pdsh-2.34_fix-slurm-23.x.patch new file mode 100644 index 00000000000..1889f83a15b --- /dev/null +++ b/easybuild/easyconfigs/p/pdsh/pdsh-2.34_fix-slurm-23.x.patch @@ -0,0 +1,22 @@ +see https://github.com/chaos/pdsh/issues/152 + https://github.com/chaos/pdsh/pull/153 +diff --git a/src/modules/slurm.c b/src/modules/slurm.c +index 5594c4f..c227337 100644 +--- a/src/modules/slurm.c ++++ b/src/modules/slurm.c +@@ -50,6 +50,16 @@ + * with our internal List datatype. + */ + #define __list_datatypes_defined 1 ++/* ++ * Also, Slurm>=23.x requires that `struct xlist` be typedef'd to list_t: ++ */ ++typedef struct xlist list_t; ++typedef struct listIterator list_itr_t; ++/* ++ * Also, Slurm exports the hostlist_t interface as well: ++ */ ++#define __hostlist_t_defined 1 ++ + #include + #include + diff --git a/easybuild/easyconfigs/p/petsc4py/petsc4py-3.17.4-foss-2022a.eb b/easybuild/easyconfigs/p/petsc4py/petsc4py-3.17.4-foss-2022a.eb new file mode 100644 index 00000000000..a944c674694 --- /dev/null +++ b/easybuild/easyconfigs/p/petsc4py/petsc4py-3.17.4-foss-2022a.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonPackage' + +name = 'petsc4py' +version = '3.17.4' + +homepage = 'https://bitbucket.org/petsc/petsc4py' +description = "petsc4py are Python bindings for PETSc, the Portable, Extensible Toolchain for Scientific Computation." + +toolchain = {'name': 'foss', 'version': '2022a'} + +sources = [SOURCE_TAR_GZ] +checksums = ['216c3da074557946615d37d0826bc89f1f2e599323e2dacbdc45326d78bd50c6'] + +dependencies = [ + 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+ ('android_system_properties', '0.1.5'), + ('anstream', '0.6.15'), + ('anstyle', '1.0.8'), + ('anstyle-parse', '0.2.5'), + ('anstyle-query', '1.1.1'), + ('anstyle-wincon', '3.0.4'), + ('askama', '0.12.1'), + ('askama_derive', '0.12.5'), + ('askama_escape', '0.10.3'), + ('askama_parser', '0.2.1'), + ('atty', '0.2.14'), + ('autocfg', '1.3.0'), + ('base64', '0.13.1'), + ('basic-toml', '0.1.9'), + ('bindgen', '0.69.4'), + ('bio-types', '1.0.4'), + ('bitflags', '1.3.2'), + ('bitflags', '2.6.0'), + ('bumpalo', '3.16.0'), + ('byteorder', '1.5.0'), + ('bzip2-sys', '0.1.11+1.0.8'), + ('cc', '1.1.15'), + ('cexpr', '0.6.0'), + ('cfg-if', '1.0.0'), + ('chrono', '0.4.38'), + ('clang-sys', '1.8.1'), + ('clap', '3.2.25'), + ('clap_derive', '3.2.25'), + ('clap_lex', '0.2.4'), + ('cmake', '0.1.51'), + ('colorchoice', '1.0.2'), + ('core-foundation-sys', '0.8.7'), + ('crossbeam-deque', '0.8.5'), + ('crossbeam-epoch', '0.9.18'), + ('crossbeam-utils', '0.8.20'), + ('ctor', '0.2.8'), + ('curl-sys', '0.4.74+curl-8.9.0'), + ('custom_derive', '0.1.7'), + ('darling', '0.20.10'), + ('darling_core', '0.20.10'), + ('darling_macro', '0.20.10'), + ('deranged', '0.3.11'), + ('derive-new', '0.5.9'), + ('derive-new', '0.6.0'), + ('dyn-clone', '1.0.17'), + ('either', '1.13.0'), + ('env_filter', '0.1.2'), + ('env_logger', '0.11.5'), + ('erased-serde', '0.4.5'), + ('fnv', '1.0.7'), + ('form_urlencoded', '1.2.1'), + ('fs-utils', '1.1.4'), + ('getrandom', '0.2.15'), + ('glob', '0.3.1'), + ('hashbrown', '0.12.3'), + ('heck', '0.4.1'), + ('heck', '0.5.0'), + ('hermit-abi', '0.1.19'), + ('hex', '0.4.3'), + ('hts-sys', '2.1.4'), + ('humansize', '2.1.3'), + ('humantime', '2.1.0'), + ('iana-time-zone', '0.1.60'), + ('iana-time-zone-haiku', '0.1.2'), + ('ident_case', '1.0.1'), + ('idna', '0.5.0'), + ('ieee754', '0.2.6'), + ('indexmap', '1.9.3'), + ('is_terminal_polyfill', '1.70.1'), + ('itertools', '0.12.1'), + ('itoa', '1.0.11'), + ('jobserver', '0.1.32'), + ('js-sys', '0.3.70'), + ('lazy_static', '1.5.0'), + ('lazycell', '1.3.0'), + ('libc', '0.2.158'), + ('libloading', '0.8.5'), + ('libm', '0.2.8'), + ('libz-sys', '1.1.20'), + ('linear-map', '1.2.0'), + ('log', '0.4.22'), + ('lzma-sys', '0.1.20'), + ('memchr', '2.7.4'), + ('mime', '0.3.17'), + ('mime_guess', '2.0.5'), + ('minimal-lexical', '0.2.1'), + ('newtype_derive', '0.1.6'), + ('nom', '7.1.3'), + ('num-conv', '0.1.0'), + ('num-traits', '0.2.19'), + ('once_cell', '1.19.0'), + ('openssl-src', '300.3.1+3.3.1'), + ('openssl-sys', '0.9.103'), + ('os_str_bytes', '6.6.1'), + ('percent-encoding', '2.3.1'), + ('pkg-config', '0.3.30'), + ('plotly', '0.9.0'), + ('plotly_derive', '0.9.0'), + ('powerfmt', '0.2.0'), + ('ppv-lite86', '0.2.20'), + ('proc-macro-error', '1.0.4'), + ('proc-macro-error-attr', '1.0.4'), + ('proc-macro2', '1.0.86'), + ('quick-error', '1.2.3'), + ('quote', '1.0.37'), + ('rand', '0.8.5'), + ('rand_chacha', '0.3.1'), + ('rand_core', '0.6.4'), + ('rayon', '1.10.0'), + ('rayon-core', '1.12.1'), + ('regex', '1.10.6'), + ('regex-automata', '0.4.7'), + ('regex-syntax', '0.8.4'), + ('rust-htslib', '0.47.0'), + ('rustc-hash', '1.1.0'), + ('rustc_version', '0.1.7'), + ('rustversion', '1.0.17'), + ('ryu', '1.0.18'), + ('semver', '0.1.20'), + ('serde', '1.0.209'), + ('serde_derive', '1.0.209'), + ('serde_json', '1.0.127'), + ('serde_repr', '0.1.19'), + ('serde_with', '2.3.3'), + ('serde_with_macros', '2.3.3'), + ('shlex', '1.3.0'), + ('strsim', '0.10.0'), + ('strsim', '0.11.1'), + ('strum_macros', '0.26.4'), + ('syn', '1.0.109'), + ('syn', '2.0.76'), + ('termcolor', '1.4.1'), + ('textwrap', '0.16.1'), + ('thiserror', '1.0.63'), + ('thiserror-impl', '1.0.63'), + ('time', '0.3.36'), + ('time-core', '0.1.2'), + ('time-macros', '0.2.18'), + ('tinyvec', '1.8.0'), + ('tinyvec_macros', '0.1.1'), + ('typeid', '1.0.2'), + ('unicase', '2.7.0'), + ('unicode-bidi', '0.3.15'), + ('unicode-ident', '1.0.12'), + ('unicode-normalization', '0.1.23'), + ('unzip-n', '0.1.2'), + ('url', '2.5.2'), + ('utf8parse', '0.2.2'), + ('vcpkg', '0.2.15'), + ('version_check', '0.9.5'), + ('wasi', '0.11.0+wasi-snapshot-preview1'), + ('wasm-bindgen', '0.2.93'), + ('wasm-bindgen-backend', '0.2.93'), + ('wasm-bindgen-macro', '0.2.93'), + ('wasm-bindgen-macro-support', '0.2.93'), + ('wasm-bindgen-shared', '0.2.93'), + ('winapi', '0.3.9'), + ('winapi-i686-pc-windows-gnu', '0.4.0'), + ('winapi-util', '0.1.9'), + ('winapi-x86_64-pc-windows-gnu', '0.4.0'), + ('windows-core', '0.52.0'), + ('windows-sys', '0.52.0'), + ('windows-sys', '0.59.0'), + ('windows-targets', '0.52.6'), + ('windows_aarch64_gnullvm', '0.52.6'), + ('windows_aarch64_msvc', '0.52.6'), + ('windows_i686_gnu', '0.52.6'), + ('windows_i686_gnullvm', '0.52.6'), + ('windows_i686_msvc', '0.52.6'), + ('windows_x86_64_gnu', '0.52.6'), + ('windows_x86_64_gnullvm', '0.52.6'), + ('windows_x86_64_msvc', '0.52.6'), + ('zerocopy', '0.7.35'), + ('zerocopy-derive', '0.7.35'), +] + +builddependencies = [ + ('Rust', '1.75.0'), + ('CMake', '3.26.3'), + ('Clang', '16.0.6'), +] + +dependencies = [ + ('bzip2', '1.0.8'), + ('OpenSSL', '1.1', '', SYSTEM), + ('Perl', '5.36.1'), + ('Perl-bundle-CPAN', '5.36.1'), +] + +sanity_check_paths = { + 'files': ['bin/%(name)s'], + 'dirs': [], +} + +sanity_check_commands = ["%(name)s --version"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/phonemizer/phonemizer-3.2.1-gfbf-2023a.eb b/easybuild/easyconfigs/p/phonemizer/phonemizer-3.2.1-gfbf-2023a.eb index 907228d9281..2569dce3fb5 100644 --- a/easybuild/easyconfigs/p/phonemizer/phonemizer-3.2.1-gfbf-2023a.eb +++ b/easybuild/easyconfigs/p/phonemizer/phonemizer-3.2.1-gfbf-2023a.eb @@ -13,12 +13,15 @@ It is using four backends: espeak, espeak-mbrola, festival and segments. toolchain = {'name': 'gfbf', 'version': '2023a'} +builddependencies = [ + ('hatchling', '1.18.0'), +] + dependencies = [ ('Python', '3.11.3'), ('Python-bundle-PyPI', '2023.06'), ('eSpeak-NG', '1.51'), ('festival', '2.5.0'), - ('hatchling', '1.18.0'), ('RDFlib', '7.0.0'), ('lxml', '4.9.2'), ] diff --git a/easybuild/easyconfigs/p/phonopy/phonopy-2.12.0-foss-2020b.eb b/easybuild/easyconfigs/p/phonopy/phonopy-2.12.0-foss-2020b.eb index 3a1f3d0bc3b..2aa223e2c83 100644 --- a/easybuild/easyconfigs/p/phonopy/phonopy-2.12.0-foss-2020b.eb +++ b/easybuild/easyconfigs/p/phonopy/phonopy-2.12.0-foss-2020b.eb @@ -3,7 +3,7 @@ easyblock = 'PythonPackage' name = 'phonopy' version = '2.12.0' -homepage = 'https://atztogo.github.io/phonopy/' +homepage = 'https://phonopy.github.io/phonopy/' description = """Phonopy is an open source package of phonon calculations based on the supercell approach.""" toolchain = {'name': 'foss', 'version': '2020b'} diff --git a/easybuild/easyconfigs/p/phonopy/phonopy-2.16.3-foss-2022a.eb b/easybuild/easyconfigs/p/phonopy/phonopy-2.16.3-foss-2022a.eb index d06fecee5a2..bd922d7ded0 100644 --- a/easybuild/easyconfigs/p/phonopy/phonopy-2.16.3-foss-2022a.eb +++ b/easybuild/easyconfigs/p/phonopy/phonopy-2.16.3-foss-2022a.eb @@ -3,7 +3,7 @@ easyblock = 'PythonPackage' name = 'phonopy' version = '2.16.3' -homepage = 'https://atztogo.github.io/phonopy/' +homepage = 'https://phonopy.github.io/phonopy/' description = """Phonopy is an open source package of phonon calculations based on the supercell approach.""" toolchain = {'name': 'foss', 'version': '2022a'} diff --git a/easybuild/easyconfigs/p/phonopy/phonopy-2.20.0-foss-2023a.eb b/easybuild/easyconfigs/p/phonopy/phonopy-2.20.0-foss-2023a.eb index aa68af8a495..c243d21a148 100644 --- a/easybuild/easyconfigs/p/phonopy/phonopy-2.20.0-foss-2023a.eb +++ b/easybuild/easyconfigs/p/phonopy/phonopy-2.20.0-foss-2023a.eb @@ -3,7 +3,7 @@ easyblock = 'PythonPackage' name = 'phonopy' version = '2.20.0' -homepage = 'https://atztogo.github.io/phonopy/' +homepage = 'https://phonopy.github.io/phonopy/' description = """Phonopy is an open source package of phonon calculations based on the supercell approach.""" toolchain = {'name': 'foss', 'version': '2023a'} @@ -18,6 +18,7 @@ dependencies = [ ('PyYAML', '6.0'), ('h5py', '3.9.0'), ('spglib-python', '2.1.0'), + ('cp2k-input-tools', '0.9.1'), ] download_dep_fail = True diff --git a/easybuild/easyconfigs/p/phonopy/phonopy-2.7.1-intel-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/p/phonopy/phonopy-2.7.1-intel-2019b-Python-3.7.4.eb index 694e7938d28..310c8045b34 100644 --- a/easybuild/easyconfigs/p/phonopy/phonopy-2.7.1-intel-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/p/phonopy/phonopy-2.7.1-intel-2019b-Python-3.7.4.eb @@ -4,7 +4,7 @@ name = 'phonopy' version = '2.7.1' versionsuffix = '-Python-%(pyver)s' -homepage = 'https://atztogo.github.io/phonopy/' +homepage = 'https://phonopy.github.io/phonopy/' description = """Phonopy is an open source package of phonon calculations based on the supercell approach.""" toolchain = {'name': 'intel', 'version': '2019b'} diff --git a/easybuild/easyconfigs/p/phonopy/phonopy-2.7.1-intel-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/p/phonopy/phonopy-2.7.1-intel-2020a-Python-3.8.2.eb index 5744c456a63..2d2fef61b17 100644 --- a/easybuild/easyconfigs/p/phonopy/phonopy-2.7.1-intel-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/p/phonopy/phonopy-2.7.1-intel-2020a-Python-3.8.2.eb @@ -4,7 +4,7 @@ name = 'phonopy' version = '2.7.1' versionsuffix = '-Python-%(pyver)s' -homepage = 'https://atztogo.github.io/phonopy/' +homepage = 'https://phonopy.github.io/phonopy/' description = """Phonopy is an open source package of phonon calculations based on the supercell approach.""" toolchain = {'name': 'intel', 'version': '2020a'} diff --git a/easybuild/easyconfigs/p/phylo-treetime/phylo-treetime-0.11.4-foss-2023a.eb b/easybuild/easyconfigs/p/phylo-treetime/phylo-treetime-0.11.4-foss-2023a.eb new file mode 100644 index 00000000000..8eaaa826af5 --- /dev/null +++ b/easybuild/easyconfigs/p/phylo-treetime/phylo-treetime-0.11.4-foss-2023a.eb @@ -0,0 +1,41 @@ +easyblock = 'PythonBundle' + +name = 'phylo-treetime' +version = '0.11.4' + +homepage = 'https://treetime.readthedocs.io/en/latest/index.html' +description = """TreeTime provides routines for ancestral sequence reconstruction and inference of + molecular-clock phylogenies, i.e., a tree where all branches are scaled such that the positions + of terminal nodes correspond to their sampling times and internal nodes are placed at the most + likely time of divergence. +""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [ + ('hatchling', '1.18.0'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('matplotlib', '3.7.2'), + ('Biopython', '1.83'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + (name, version, { + 'checksums': ['f6b1506a58819204b010f5abe36627a127c0efa4cfd5008ea7f25dc0718c0f88'], + 'modulename': 'treetime', + }), +] + +sanity_check_paths = { + 'files': ['bin/treetime'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/picard/picard-3.3.0-Java-17.eb b/easybuild/easyconfigs/p/picard/picard-3.3.0-Java-17.eb new file mode 100644 index 00000000000..8aafd645195 --- /dev/null +++ b/easybuild/easyconfigs/p/picard/picard-3.3.0-Java-17.eb @@ -0,0 +1,62 @@ +## +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild +# +# This is a contribution from Phoenix HPC Service, The University of Adelaide, Australia +# Homepage: https://www.adelaide.edu.au/phoenix/ +# +# Copyright:: adelaide.edu.au/phoenix +# Authors:: Robert Qiao , Exe Escobedo +# License:: MIT +# +# 2.10.1: +# Adam Huffman +# The Francis Crick Institute +# 2.18.11: +# Jonas Demeulemeester +# The Francis Crick Institute +# 2.21.1 +# Pavel Grochal (INUITS) +# 2.25.1 +# J. Sassmannshausen (GSTT) +# 2.25.5 +# Erica Bianco (HPCNow!) +# 2.26.10 +# Christoph Siegert (Leipzig University) +# 3.0.0 +# Graham Derryberry (UTK) +# 3.3.0 +# Emik Lin (HKUMed CPOS) +## + +easyblock = 'JAR' + +name = 'picard' +version = '3.3.0' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'https://broadinstitute.github.io/picard/' +description = """A set of tools (in Java) for working with next generation sequencing data in the BAM format.""" + +toolchain = SYSTEM + +source_urls = ['https://github.com/broadinstitute/picard/releases/download/%(version)s'] +sources = [{ + 'filename': '%(name)s-%(version)s.jar', + 'download_filename': '%(name)s.jar', +}] +checksums = ['58819a7660646b74b34e282f5d4d21c8dbaea22ddeff96e3258755dafa0f86dc'] + +postinstallcmds = ["mv %(installdir)s/%(name)s-%(version)s.jar %(installdir)s/%(name)s.jar"] + +dependencies = [('Java', '17')] + +sanity_check_commands = ['java -jar $EBROOTPICARD/picard.jar 2>&1 | grep USAGE'] + +sanity_check_paths = { + 'files': ['picard.jar'], + 'dirs': [], +} + +modloadmsg = "To execute picard run: java -jar $EBROOTPICARD/%(name)s.jar" + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/pixman/pixman-0.43.4-GCCcore-13.3.0.eb b/easybuild/easyconfigs/p/pixman/pixman-0.43.4-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..b15cf9f2ef6 --- /dev/null +++ b/easybuild/easyconfigs/p/pixman/pixman-0.43.4-GCCcore-13.3.0.eb @@ -0,0 +1,30 @@ +easyblock = 'MesonNinja' + +name = 'pixman' +version = '0.43.4' + +homepage = 'http://www.pixman.org/' +description = """ + Pixman is a low-level software library for pixel manipulation, providing + features such as image compositing and trapezoid rasterization. Important + users of pixman are the cairo graphics library and the X server. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://cairographics.org/releases/'] +sources = [SOURCE_TAR_GZ] +checksums = ['a0624db90180c7ddb79fc7a9151093dc37c646d8c38d3f232f767cf64b85a226'] + +builddependencies = [ + ('binutils', '2.42'), + ('Meson', '1.4.0'), + ('Ninja', '1.12.1'), +] + +sanity_check_paths = { + 'files': ['lib/libpixman-1.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/pkgconf/pkgconf-2.2.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/p/pkgconf/pkgconf-2.2.0-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..aaaecf30a9a --- /dev/null +++ b/easybuild/easyconfigs/p/pkgconf/pkgconf-2.2.0-GCCcore-13.3.0.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'pkgconf' +version = '2.2.0' + +homepage = 'https://github.com/pkgconf/pkgconf' + +description = """pkgconf is a program which helps to configure compiler and linker flags for development libraries. + It is similar to pkg-config from freedesktop.org.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://distfiles.ariadne.space/pkgconf/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['28f8dfc279a10ef66148befa3f6eb266e5f3570316600208ed50e9781c7269d8'] + +builddependencies = [('binutils', '2.42')] + +postinstallcmds = ["cd %(installdir)s/bin && ln -s pkgconf pkg-config"] + +sanity_check_paths = { + 'files': ['bin/pkg-config', 'bin/pkgconf'], + 'dirs': [], +} + +sanity_check_commands = [ + "pkg-config --help", + "pkgconf --help", +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/pkgconf/pkgconf-2.2.0.eb b/easybuild/easyconfigs/p/pkgconf/pkgconf-2.2.0.eb new file mode 100644 index 00000000000..3440e388cc3 --- /dev/null +++ b/easybuild/easyconfigs/p/pkgconf/pkgconf-2.2.0.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'pkgconf' +version = '2.2.0' + +homepage = 'https://github.com/pkgconf/pkgconf' + +description = """pkgconf is a program which helps to configure compiler and linker flags for development libraries. + It is similar to pkg-config from freedesktop.org.""" + +toolchain = SYSTEM + +source_urls = ['https://distfiles.ariadne.space/pkgconf/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['28f8dfc279a10ef66148befa3f6eb266e5f3570316600208ed50e9781c7269d8'] + +# add pkgconfig directories in the system to list of default search paths +preconfigopts = 'EB_SYS_PC_PATH=":$(find /usr -xdev -type d -name "pkgconfig" -printf %p: 2>/dev/null)";' +configopts = '--with-pkg-config-dir="%(installdir)s/lib/pkgconfig:%(installdir)s/share/pkgconfig${EB_SYS_PC_PATH%:}"' + +postinstallcmds = ["cd %(installdir)s/bin && ln -s pkgconf pkg-config"] + +sanity_check_paths = { + 'files': ['bin/pkg-config', 'bin/pkgconf'], + 'dirs': [], +} + +sanity_check_commands = [ + "pkg-config --help", + "pkgconf --help", +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/pkgconf/pkgconf-2.3.0-GCCcore-14.2.0.eb b/easybuild/easyconfigs/p/pkgconf/pkgconf-2.3.0-GCCcore-14.2.0.eb new file mode 100644 index 00000000000..de13aa5fb33 --- /dev/null +++ b/easybuild/easyconfigs/p/pkgconf/pkgconf-2.3.0-GCCcore-14.2.0.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'pkgconf' +version = '2.3.0' + +homepage = 'https://github.com/pkgconf/pkgconf' + +description = """pkgconf is a program which helps to configure compiler and linker flags for development libraries. + It is similar to pkg-config from freedesktop.org.""" + +toolchain = {'name': 'GCCcore', 'version': '14.2.0'} + +source_urls = ['https://distfiles.ariadne.space/pkgconf/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['a2df680578e85f609f2fa67bd3d0fc0dc71b4bf084fc49119de84cd6ed28e723'] + +builddependencies = [('binutils', '2.42')] + +postinstallcmds = ["cd %(installdir)s/bin && ln -s pkgconf pkg-config"] + +sanity_check_paths = { + 'files': ['bin/pkg-config', 'bin/pkgconf'], + 'dirs': [], +} + +sanity_check_commands = [ + "pkg-config --help", + "pkgconf --help", +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/pkgconf/pkgconf-2.3.0.eb b/easybuild/easyconfigs/p/pkgconf/pkgconf-2.3.0.eb new file mode 100644 index 00000000000..c90cecda0a1 --- /dev/null +++ b/easybuild/easyconfigs/p/pkgconf/pkgconf-2.3.0.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'pkgconf' +version = '2.3.0' + +homepage = 'https://github.com/pkgconf/pkgconf' + +description = """pkgconf is a program which helps to configure compiler and linker flags for development libraries. + It is similar to pkg-config from freedesktop.org.""" + +toolchain = SYSTEM + +source_urls = ['https://distfiles.ariadne.space/pkgconf/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['a2df680578e85f609f2fa67bd3d0fc0dc71b4bf084fc49119de84cd6ed28e723'] + +# add pkgconfig directories in the system to list of default search paths +preconfigopts = 'EB_SYS_PC_PATH=":$(find /usr -xdev -type d -name "pkgconfig" -printf %p: 2>/dev/null)";' +configopts = '--with-pkg-config-dir="%(installdir)s/lib/pkgconfig:%(installdir)s/share/pkgconfig${EB_SYS_PC_PATH%:}"' + +postinstallcmds = ["cd %(installdir)s/bin && ln -s pkgconf pkg-config"] + +sanity_check_paths = { + 'files': ['bin/pkg-config', 'bin/pkgconf'], + 'dirs': [], +} + +sanity_check_commands = [ + "pkg-config --help", + "pkgconf --help", +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.5.5-GCCcore-13.3.0-python.eb b/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.5.5-GCCcore-13.3.0-python.eb new file mode 100644 index 00000000000..f66c2f13358 --- /dev/null +++ b/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.5.5-GCCcore-13.3.0-python.eb @@ -0,0 +1,31 @@ +easyblock = 'PythonPackage' + +name = 'pkgconfig' +version = '1.5.5' +# The -python versionsuffix is used to avoid confusion between +# pkg-config (the tool) and pkgconfig (the Python wrappers) +versionsuffix = '-python' + +homepage = 'https://github.com/matze/pkgconfig' +description = """pkgconfig is a Python module to interface with the pkg-config command line tool""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['deb4163ef11f75b520d822d9505c1f462761b4309b1bb713d08689759ea8b899'] + +builddependencies = [ + ('binutils', '2.42'), + ('poetry', '1.8.3'), +] + +dependencies = [ + ('Python', '3.12.3'), + ('pkgconf', '2.2.0'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/planarity/planarity-3.0.2.0-GCC-13.2.0.eb b/easybuild/easyconfigs/p/planarity/planarity-3.0.2.0-GCC-13.2.0.eb new file mode 100644 index 00000000000..5578e11ec0e --- /dev/null +++ b/easybuild/easyconfigs/p/planarity/planarity-3.0.2.0-GCC-13.2.0.eb @@ -0,0 +1,37 @@ +easyblock = 'ConfigureMake' + +name = 'planarity' +version = '3.0.2.0' + +homepage = "https://github.com/graph-algorithms/edge-addition-planarity-suite" +description = """A library for implementing graph algorithms""" + +source_urls = ['https://github.com/graph-algorithms/edge-addition-planarity-suite/archive'] +checksums = ['40f4ee7bbd5d8535460c60fc0fc1f806b10909a1419618fd9235746a420a04c6'] +sources = ['Version_%(version)s.tar.gz'] + +toolchain = {'name': 'GCC', 'version': '13.2.0'} + +builddependencies = [ + ('Autotools', '20220317'), +] + +start_dir = 'edge-addition-planarity-suite-Version_%(version)s' +preconfigopts = './autogen.sh && ' + +sanity_check_paths = { + 'files': [ + 'bin/planarity', + 'lib/libplanarity.a', + 'lib/libplanarity.%s' % SHLIB_EXT, + ], + 'dirs': [ + 'include/planarity', + 'share/doc', + 'share/man', + ] +} + +sanity_check_commands = ['%(name)s -h'] + +moduleclass = "lib" diff --git a/easybuild/easyconfigs/p/plmc/plmc-20230121-GCCcore-12.3.0-32bit.eb b/easybuild/easyconfigs/p/plmc/plmc-20230121-GCCcore-12.3.0-32bit.eb new file mode 100644 index 00000000000..d32ed87425b --- /dev/null +++ b/easybuild/easyconfigs/p/plmc/plmc-20230121-GCCcore-12.3.0-32bit.eb @@ -0,0 +1,37 @@ +easyblock = 'MakeCp' + +name = 'plmc' +version = '20230121' +versionsuffix = '-32bit' +local_commit = '18c9e55' + +homepage = 'https://github.com/debbiemarkslab/plmc' +description = """ +Inference of couplings in proteins and RNAs from sequence variation. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +github_account = 'debbiemarkslab' +source_urls = [GITHUB_SOURCE] +sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}] +checksums = ['780b657246749adeb8c5ec01746b7283d1b94598c547abd61b87f1efd996d619'] + +builddependencies = [ + ('binutils', '2.40'), +] + +buildopts = 'all-openmp32' + +files_to_copy = ['*'] + +sanity_check_paths = { + 'files': [], + 'dirs': ['bin'], +} + +sanity_check_commands = [ + "plmc -h 2>&1| grep Usage:", +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/plotly-orca/plotly-orca-1.3.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/plotly-orca/plotly-orca-1.3.1-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..fcf1a67d7ff --- /dev/null +++ b/easybuild/easyconfigs/p/plotly-orca/plotly-orca-1.3.1-GCCcore-12.3.0.eb @@ -0,0 +1,34 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 +# Update: Petr Král (INUITS) + +easyblock = 'Binary' + +name = 'plotly-orca' +version = '1.3.1' + +homepage = 'https://github.com/plotly/orca' +description = """Orca is an Electron app that generates images and reports of Plotly things like + plotly.js graphs, dash apps, dashboards from the command line.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://github.com/plotly/orca/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['25ebf207d75769c140dcea033a984e7a3a6d919bb8e110a14c890c8cf430f14d'] + +builddependencies = [('binutils', '2.40')] + +dependencies = [ + ('nodejs', '18.17.1'), +] + +install_cmd = 'npm install --no-package-lock -g --prefix %(installdir)s electron@6.1.4 v%(version)s.tar.gz' + +sanity_check_paths = { + 'files': ['bin/orca'], + 'dirs': ['lib/node_modules/orca'], +} +sanity_check_commands = ['orca --help'] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/plotly.py/plotly.py-5.24.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/p/plotly.py/plotly.py-5.24.1-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..97bb6e12c8d --- /dev/null +++ b/easybuild/easyconfigs/p/plotly.py/plotly.py-5.24.1-GCCcore-13.3.0.eb @@ -0,0 +1,39 @@ +easyblock = 'PythonBundle' + +name = 'plotly.py' +version = '5.24.1' + +homepage = 'https://plot.ly/python' +description = "An open-source, interactive graphing library for Python" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +builddependencies = [ + ('binutils', '2.42'), +] +dependencies = [ + ('Python', '3.12.3'), +] + +use_pip = True + +exts_list = [ + ('tenacity', '9.0.0', { + 'patches': ['tenacity-9.0.0_fix_version.patch'], + 'preinstallopts': "sed -i 's/EB_TENACITY_VERSION/%(version)s/' setup.cfg && ", + 'checksums': [ + {'tenacity-9.0.0.tar.gz': '807f37ca97d62aa361264d497b0e31e92b8027044942bfa756160d908320d73b'}, + {'tenacity-9.0.0_fix_version.patch': '71a533470f03aab802439bda078494ab98804439afdb16f8287337bd3e0c8a82'}, + ], + }), + ('packaging', '24.1', { + 'checksums': ['026ed72c8ed3fcce5bf8950572258698927fd1dbda10a5e981cdf0ac37f4f002'], + }), + ('plotly', version, { + 'checksums': ['dbc8ac8339d248a4bcc36e08a5659bacfe1b079390b8953533f4eb22169b4bae'], + }), +] + +sanity_pip_check = True + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/plotly.py/tenacity-9.0.0_fix_version.patch b/easybuild/easyconfigs/p/plotly.py/tenacity-9.0.0_fix_version.patch new file mode 100644 index 00000000000..9bd6e65af16 --- /dev/null +++ b/easybuild/easyconfigs/p/plotly.py/tenacity-9.0.0_fix_version.patch @@ -0,0 +1,15 @@ +# What: Putting a manually typed version in setup.cfg, as it wouldnt resolve automatically. +# Author: Denis Kristak (Inuits)diff -ruN tenacity-8.2.3_orig/setup.cfg tenacity-8.2.3/setup.cfg +# Updated for v9.0.0 by maxim-masterov (SURF) +# Updated with magic string to avoid having to update the patch for every version by Samuel Moors (Vrije Universiteit Brussel) +diff -Nru tenacity-9.0.0.orig/setup.cfg tenacity-9.0.0/setup.cfg +--- tenacity-9.0.0.orig/setup.cfg 2024-10-10 16:50:28.669538307 +0200 ++++ tenacity-9.0.0/setup.cfg 2024-10-10 16:50:54.881500726 +0200 +@@ -1,6 +1,7 @@ + [metadata] + name = tenacity + license = Apache 2.0 ++version = 'EB_TENACITY_VERSION' + url = https://github.com/jd/tenacity + summary = Retry code until it succeeds + long_description = Tenacity is a general-purpose retrying library to simplify the task of adding retry behavior to just about anything. diff --git a/easybuild/easyconfigs/p/pmt/pmt-1.3.1-GCCcore-13.3.0-CUDA-12.6.0.eb b/easybuild/easyconfigs/p/pmt/pmt-1.3.1-GCCcore-13.3.0-CUDA-12.6.0.eb new file mode 100644 index 00000000000..695a90190e0 --- /dev/null +++ b/easybuild/easyconfigs/p/pmt/pmt-1.3.1-GCCcore-13.3.0-CUDA-12.6.0.eb @@ -0,0 +1,33 @@ +easyblock = 'CMakeMake' + +name = 'pmt' +version = '1.3.1' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://git.astron.nl/RD/pmt' +description = """PMT is a high-level software library capable of + collecting power consumption measurements on various hardware.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://git.astron.nl/RD/pmt/-/archive/%(version)s'] +sources = ['pmt-%(version)s.tar.gz'] +checksums = ['cf8c669ffb0fda4cb594550fb233f9654252db50671b59147826eadc0a3d5565'] + +builddependencies = [ + ('CMake', '3.29.3'), + ('binutils', '2.42'), +] + +dependencies = [ + ('CUDA', '12.6.0', '', SYSTEM) +] + +configopts = '-DPMT_BUILD_RAPL=1 -DPMT_BUILD_NVML=1 -DPMT_BUILD_NVIDIA=1' + +sanity_check_paths = { + 'files': ["lib/libpmt.%s" % SHLIB_EXT, "include/pmt/NVIDIA.h", "include/pmt/Rapl.h", "include/pmt/NVML.h"], + 'dirs': ["lib", "include"], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/pocl/pocl-6.0-GCC-13.3.0.eb b/easybuild/easyconfigs/p/pocl/pocl-6.0-GCC-13.3.0.eb new file mode 100644 index 00000000000..4a188f7473b --- /dev/null +++ b/easybuild/easyconfigs/p/pocl/pocl-6.0-GCC-13.3.0.eb @@ -0,0 +1,48 @@ +# https://github.com/pocl/pocl/issues/1219 +# "PoCL 3.1 supports LLVM only up to 15", so need 4.0 for working with Clang 16 +easyblock = 'CMakeNinja' + +name = 'pocl' +version = '6.0' + +homepage = 'http://portablecl.org' +description = """PoCL is a portable open source (MIT-licensed) implementation +of the OpenCL standard (1.2 with some 2.0 features supported).""" + +toolchain = {'name': 'GCC', 'version': '13.3.0'} + +source_urls = ['https://github.com/pocl/pocl/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = [] +checksums = [ + 'de9710223fc1855f833dbbf42ea2681e06aa8ec0464f0201104dc80a74dfd1f2', # v6.0.tar.gz +] + +builddependencies = [ + ('CMake', '3.29.3'), + ('Ninja', '1.12.1'), + ('pkgconf', '2.2.0'), +] + +dependencies = [ + ('Clang', '18.1.8'), + ('hwloc', '2.10.0'), + ('libtool', '2.4.7'), + ('libxml2', '2.12.7'), +] + +separate_build_dir = True + +# disable attempt to find an ICD loader, always build libOpenCL.so +configopts = "-DENABLE_ICD=0 -DINSTALL_OPENCL_HEADERS=1 " +# make sure we use the easybuild Clang +configopts += "-DWITH_LLVM_CONFIG=$EBROOTCLANG/bin/llvm-config -DSTATIC_LLVM=ON " +# avoid host CPU auto-detection (which may fail on recent CPUs) +configopts += "-DLLC_HOST_CPU=native " + +sanity_check_paths = { + 'files': ['bin/poclcc', 'lib64/libOpenCL.%s' % SHLIB_EXT], + 'dirs': ['include/CL', 'lib64/pkgconfig'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/pod5-file-format/pod5-file-format-0.3.10-foss-2023a.eb b/easybuild/easyconfigs/p/pod5-file-format/pod5-file-format-0.3.10-foss-2023a.eb new file mode 100644 index 00000000000..9db2243c96e --- /dev/null +++ b/easybuild/easyconfigs/p/pod5-file-format/pod5-file-format-0.3.10-foss-2023a.eb @@ -0,0 +1,110 @@ +easyblock = 'CMakeMake' + +name = 'pod5-file-format' +version = '0.3.10' + +homepage = 'https://github.com/nanoporetech/pod5-file-format' +description = """POD5 is a file format for storing nanopore dna data in an easily accessible way. + The format is able to be written in a streaming manner which allows a sequencing + instrument to directly write the format.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['https://github.com/nanoporetech/%(name)s/archive/'] +sources = [{'download_filename': '%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}] +patches = ['pod5-file-format-0.3.10_dep_fix.patch'] +checksums = [ + {'pod5-file-format-0.3.10.tar.gz': 'eb177018b310e508f7ad6b5d486cc29166404dd5f82879d0c26aceaff51d3768'}, + {'pod5-file-format-0.3.10_dep_fix.patch': '20dc87ab82d4b52ff7fb769d17c2478daf95f787b2a184c9d985e33e03038e31'}, +] + +builddependencies = [ + ('poetry', '1.5.1'), + ('CMake', '3.26.3'), + ('pkgconfig', '1.5.5', '-python'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('Arrow', '14.0.1'), + ('SciPy-bundle', '2023.07'), + ('zstd', '1.5.5'), + ('flatbuffers', '23.5.26'), + ('pybind11', '2.11.1'), + ('Boost', '1.82.0'), + ('build', '1.0.3'), + ('HDF5', '1.14.0'), + ('h5py', '3.9.0'), + ('tqdm', '4.66.1'), + ('polars', '0.20.2'), +] + +exts_defaultclass = 'PythonPackage' +exts_default_options = { + 'source_urls': [PYPI_SOURCE], + 'download_dep_fail': True, + 'use_pip': True, + 'sanity_pip_check': True, + 'installopts': '', +} + +# unpin polars and h5py versions in pod5 +local_preinstallopts = ( + "sed -i" + " -e 's/polars~=0.19/polars/'" + " -e 's/h5py~=3.10.0/h5py/'" + " pyproject.toml && " +) + +exts_list = [ + ('vbz_h5py_plugin', '1.0.1', { + 'checksums': ['c784458bb0aad6303474cb2f10956179116b35555803fd1154eb4ef362519341'], + }), + ('iso8601', '2.1.0', { + 'checksums': ['6b1d3829ee8921c4301998c909f7829fa9ed3cbdac0d3b16af2d743aed1ba8df'], + }), + ('pod5', version, { + 'preinstallopts': local_preinstallopts, + 'checksums': ['f2dcb1938fcf51c725393345e480c1d12711089d542a27446fb92fbe2e18ae60'], + }), +] + +# create POD5Version.cmake +# python -m setuptools_scm && python -m pod5_make_version shows wrong version +local_ver_sub_minor = version.split('.')[2] +preconfigopts = ( + 'cd %%(builddir)s/%%(name)s-%%(version)s/cmake && ' + 'touch POD5Version.cmake && ' + 'echo "set(POD5_VERSION_MAJOR %%(version_major)s)">POD5Version.cmake && ' + 'echo "set(POD5_VERSION_MINOR %%(version_minor)s)">>POD5Version.cmake && ' + 'echo "set(POD5_VERSION_REV %s)">>POD5Version.cmake && ' + 'echo "set(POD5_NUMERIC_VERSION %%(version)s)">>POD5Version.cmake && ' + 'echo "set(POD5_FULL_VERSION %%(version)s)">>POD5Version.cmake && ' % local_ver_sub_minor +) + +# delete add_subdirectory(third_party/pybind11) from CMakeLists.txt +preconfigopts += "cd %(builddir)s/%(name)s-%(version)s && sed -i '/add_subdirectory(third_party/d' CMakeLists.txt && " +preconfigopts += 'cd %(builddir)s/easybuild_obj && ' + +configopts = ' -DBUILD_PYTHON_WHEEL=ON -DZSTD_LIB="$EBROOTZSTD/lib" -DZSTD_INCLUDE_DIR="$EBROOTZSTD/include"' + +# install lib_pod5 from wheel - dependency of pod5 +installopts = ' && export XDG_CACHE_HOME=%(builddir)s && cd %(installdir)s' +installopts += ' && pip install --no-deps --ignore-installed --prefix %(installdir)s lib_pod5-%(version)s-*.whl' + +postinstallcmds = ['rm %(installdir)s/lib_pod5-%(version)s-*.whl'] + +sanity_check_paths = { + 'files': ['bin/pod5', 'lib/libpod5_format.a'], + 'dirs': ['include/pod5_format', 'lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "pod5 subset --help", + "python -c 'import lib_pod5'", +] + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/pod5-file-format/pod5-file-format-0.3.10_dep_fix.patch b/easybuild/easyconfigs/p/pod5-file-format/pod5-file-format-0.3.10_dep_fix.patch new file mode 100644 index 00000000000..a053f870ebe --- /dev/null +++ b/easybuild/easyconfigs/p/pod5-file-format/pod5-file-format-0.3.10_dep_fix.patch @@ -0,0 +1,32 @@ +Flatbuffers 2.0.7 uses capital 'B' in 'FlatBuffersConfig.cmake' +We want to use our pybind11 instead of the one in git submodules +Author: Petr Král (INUITS) +diff -u c++/CMakeLists.txt.orig c++/CMakeLists.txt +--- c++/CMakeLists.txt.orig 2023-02-23 19:17:13.000000000 +0100 ++++ c++/CMakeLists.txt 2023-04-25 14:07:28.174884834 +0200 +@@ -3,7 +3,7 @@ + if (ENABLE_CONAN) + find_package(Arrow REQUIRED CONFIG) + find_package(Boost REQUIRED CONFIG) +- find_package(Flatbuffers REQUIRED CONFIG) ++ find_package(FlatBuffers REQUIRED CONFIG) + find_package(zstd REQUIRED CONFIG) + find_package(ZLIB REQUIRED CONFIG) + +@@ -17,7 +17,7 @@ + COMPONENTS + headers + ) +- find_package(Flatbuffers REQUIRED) ++ find_package(FlatBuffers REQUIRED) + find_package(zstd REQUIRED) + find_package(ZLIB REQUIRED) + +@@ -27,6 +27,7 @@ + endif() + + find_package(Threads REQUIRED) ++find_package(pybind11 REQUIRED) + + find_program( + FLATBUFFERS_FLATC_EXECUTABLE diff --git a/easybuild/easyconfigs/p/poetry/poetry-1.8.3-GCCcore-13.3.0.eb b/easybuild/easyconfigs/p/poetry/poetry-1.8.3-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..030ca7ce42e --- /dev/null +++ b/easybuild/easyconfigs/p/poetry/poetry-1.8.3-GCCcore-13.3.0.eb @@ -0,0 +1,181 @@ +easyblock = 'PythonBundle' + +name = 'poetry' +version = '1.8.3' + +homepage = 'https://python-poetry.org' +description = """Python packaging and dependency management made easy. Poetry helps you declare, manage and install + dependencies of Python projects, ensuring you have the right stack everywhere.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +builddependencies = [ + ('binutils', '2.42'), + ('pkgconf', '2.2.0'), + ('scikit-build', '0.17.6'), + ('Rust', '1.78.0'), + ('setuptools-rust', '1.9.0'), + ('maturin', '1.6.0'), +] + +dependencies = [ + ('Python', '3.12.3'), + ('hatchling', '1.24.2'), + ('cryptography', '42.0.8'), + ('virtualenv', '20.26.2'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('six', '1.16.0', { + 'checksums': ['1e61c37477a1626458e36f7b1d82aa5c9b094fa4802892072e49de9c60c4c926'], + }), + ('idna', '3.7', { + 'checksums': ['028ff3aadf0609c1fd278d8ea3089299412a7a8b9bd005dd08b9f8285bcb5cfc'], + }), + ('certifi', '2024.6.2', { + 'checksums': ['3cd43f1c6fa7dedc5899d69d3ad0398fd018ad1a17fba83ddaf78aa46c747516'], + }), + ('urllib3', '2.2.1', { + 'checksums': ['d0570876c61ab9e520d776c38acbbb5b05a776d3f9ff98a5c8fd5162a444cf19'], + }), + ('charset-normalizer', '3.3.2', { + 'checksums': ['f30c3cb33b24454a82faecaf01b19c18562b1e89558fb6c56de4d9118a032fd5'], + }), + ('dulwich', '0.21.7', { + 'checksums': ['a9e9c66833cea580c3ac12927e4b9711985d76afca98da971405d414de60e968'], + }), + ('crashtest', '0.4.1', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['8d23eac5fa660409f57472e3851dab7ac18aba459a8d19cbbba86d3d5aecd2a5'], + }), + ('zipp', '3.19.2', { + 'checksums': ['bf1dcf6450f873a13e952a29504887c89e6de7506209e5b1bcc3460135d4de19'], + }), + ('importlib-metadata', '7.1.0', { + 'sources': ['importlib_metadata-%(version)s.tar.gz'], + 'checksums': ['b78938b926ee8d5f020fc4772d487045805a55ddbad2ecf21c6d60938dc7fcd2'], + }), + ('jeepney', '0.8.0', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['c0a454ad016ca575060802ee4d590dd912e35c122fa04e70306de3d076cce755'], + }), + ('SecretStorage', '3.3.3', { + 'checksums': ['2403533ef369eca6d2ba81718576c5e0f564d5cca1b58f73a8b23e7d4eeebd77'], + }), + ('more-itertools', '10.3.0', { + 'checksums': ['e5d93ef411224fbcef366a6e8ddc4c5781bc6359d43412a65dd5964e46111463'], + }), + ('jaraco.classes', '3.4.0', { + 'checksums': ['47a024b51d0239c0dd8c8540c6c7f484be3b8fcf0b2d85c13825780d3b3f3acd'], + }), + ('keyring', '24.3.1', { + 'modulename': False, + 'checksums': ['c3327b6ffafc0e8befbdb597cacdb4928ffe5c1212f7645f186e6d9957a898db'], + }), + ('pyproject-hooks', '1.1.0', { + 'sources': ['pyproject_hooks-%(version)s.tar.gz'], + 'checksums': ['4b37730834edbd6bd37f26ece6b44802fb1c1ee2ece0e54ddff8bfc06db86965'], + }), + ('build', '1.2.1', { + 'checksums': ['526263f4870c26f26c433545579475377b2b7588b6f1eac76a001e873ae3e19d'], + }), + ('installer', '0.7.0', { + 'checksums': ['a26d3e3116289bb08216e0d0f7d925fcef0b0194eedfa0c944bcaaa106c4b631'], + }), + ('webencodings', '0.5.1', { + 'checksums': ['b36a1c245f2d304965eb4e0a82848379241dc04b865afcc4aab16748587e1923'], + }), + ('html5lib', '1.1', { + 'checksums': ['b2e5b40261e20f354d198eae92afc10d750afb487ed5e50f9c4eaf07c184146f'], + }), + ('rapidfuzz', '3.9.3', { + 'checksums': ['b398ea66e8ed50451bce5997c430197d5e4b06ac4aa74602717f792d8d8d06e2'], + }), + ('cleo', '2.1.0', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['4a31bd4dd45695a64ee3c4758f583f134267c2bc518d8ae9a29cf237d009b07e'], + }), + ('attrs', '23.2.0', { + 'modulename': 'attr', + 'checksums': ['935dc3b529c262f6cf76e50877d35a4bd3c1de194fd41f47a2b7ae8f19971f30'], + }), + ('pyrsistent', '0.20.0', { + 'checksums': ['4c48f78f62ab596c679086084d0dd13254ae4f3d6c72a83ffdf5ebdef8f265a4'], + }), + ('requests-toolbelt', '1.0.0', { + 'checksums': ['7681a0a3d047012b5bdc0ee37d7f8f07ebe76ab08caeccfc3921ce23c88d5bc6'], + }), + ('pkginfo', '1.11.1', { + 'checksums': ['2e0dca1cf4c8e39644eed32408ea9966ee15e0d324c62ba899a393b3c6b467aa'], + }), + ('ptyprocess', '0.7.0', { + 'source_tmpl': '%(name)s-%(version)s-py2.py3-none-any.whl', + 'checksums': ['4b41f3967fce3af57cc7e94b888626c18bf37a083e3651ca8feeb66d492fef35'], + }), + ('pexpect', '4.9.0', { + 'checksums': ['ee7d41123f3c9911050ea2c2dac107568dc43b2d3b0c7557a33212c398ead30f'], + }), + ('jsonschema-specifications', '2023.12.1', { + 'sources': ['jsonschema_specifications-%(version)s.tar.gz'], + 'checksums': ['48a76787b3e70f5ed53f1160d2b81f586e4ca6d1548c5de7085d1682674764cc'], + }), + ('referencing', '0.35.1', { + 'checksums': ['25b42124a6c8b632a425174f24087783efb348a6f1e0008e63cd4466fedf703c'], + }), + ('rpds-py', '0.18.1', { + 'sources': ['rpds_py-%(version)s.tar.gz'], + 'checksums': ['dc48b479d540770c811fbd1eb9ba2bb66951863e448efec2e2c102625328e92f'], + 'modulename': 'rpds', + }), + ('jsonschema', '4.22.0', { + 'checksums': ['5b22d434a45935119af990552c862e5d6d564e8f6601206b305a61fdf661a2b7'], + }), + ('platformdirs', '4.2.2', { + 'checksums': ['38b7b51f512eed9e84a22788b4bce1de17c0adb134d6becb09836e37d8654cd3'], + }), + ('shellingham', '1.5.4', { + 'checksums': ['8dbca0739d487e5bd35ab3ca4b36e11c4078f3a234bfce294b0a0291363404de'], + }), + ('tomlkit', '0.12.5', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['af914f5a9c59ed9d0762c7b64d3b5d5df007448eb9cd2edc8a46b1eafead172f'], + }), + ('requests', '2.32.3', { + 'checksums': ['55365417734eb18255590a9ff9eb97e9e1da868d4ccd6402399eaf68af20a760'], + }), + ('msgpack', '1.0.8', { + 'checksums': ['95c02b0e27e706e48d0e5426d1710ca78e0f0628d6e89d5b5a5b91a5f12274f3'], + }), + ('CacheControl', '0.14.0', { + 'sources': ['cachecontrol-%(version)s.tar.gz'], + 'checksums': ['7db1195b41c81f8274a7bbd97c956f44e8348265a1bc7641c37dfebc39f0c938'], + }), + ('lockfile', '0.12.2', { + 'checksums': ['6aed02de03cba24efabcd600b30540140634fc06cfa603822d508d5361e9f799'], + }), + ('poetry-core', '1.9.0', { + 'modulename': 'poetry.core', + 'sources': ['poetry_core-%(version)s.tar.gz'], + 'checksums': ['fa7a4001eae8aa572ee84f35feb510b321bd652e5cf9293249d62853e1f935a2'], + }), + ('poetry-plugin-export', '1.8.0', { + 'sources': ['poetry_plugin_export-%(version)s.tar.gz'], + 'checksums': ['1fa6168a85d59395d835ca564bc19862a7c76061e60c3e7dfaec70d50937fc61'], + }), + ('fastjsonschema', '2.19.1', { + 'checksums': ['e3126a94bdc4623d3de4485f8d468a12f02a67921315ddc87836d6e456dc789d'], + }), + (name, version, { + 'checksums': ['67f4eb68288eab41e841cc71a00d26cf6bdda9533022d0189a145a34d0a35f48'], + }), +] + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(namelower)s'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/poppler/poppler-24.04.0-GCC-13.2.0.eb b/easybuild/easyconfigs/p/poppler/poppler-24.04.0-GCC-13.2.0.eb new file mode 100644 index 00000000000..b87358a52ff --- /dev/null +++ b/easybuild/easyconfigs/p/poppler/poppler-24.04.0-GCC-13.2.0.eb @@ -0,0 +1,60 @@ +easyblock = 'Bundle' + +name = 'poppler' +version = '24.04.0' + +homepage = 'https://poppler.freedesktop.org' +description = "Poppler is a PDF rendering library" + +toolchain = {'name': 'GCC', 'version': '13.2.0'} + +builddependencies = [ + ('CMake', '3.27.6'), + ('pkgconf', '2.0.3'), + ('Python', '3.11.5'), +] + +dependencies = [ + ('freetype', '2.13.2'), + ('fontconfig', '2.14.2'), + ('libjpeg-turbo', '3.0.1'), + ('libpng', '1.6.40'), + ('NSS', '3.94'), + ('LibTIFF', '4.6.0'), + ('Qt6', '6.6.3'), + ('Boost', '1.83.0'), + ('cairo', '1.18.0'), + ('OpenJPEG', '2.5.0'), + ('zlib', '1.2.13'), + ('gnupg-bundle', '20240306'), +] + +default_easyblock = 'CMakeMake' + +default_component_specs = { + 'start_dir': '%(name)s-%(version)s', +} + +components = [ + (name, version, { + 'source_urls': ['https://poppler.freedesktop.org/'], + 'sources': [SOURCE_TAR_XZ], + 'checksums': ['1e804ec565acf7126eb2e9bb3b56422ab2039f7e05863a5dfabdd1ffd1bb77a7'], + 'configopts': "-DENABLE_BOOST=ON -DENABLE_QT5=OFF -DENABLE_LCMS=OFF", + }), + ('poppler-data', '0.4.12', { + 'source_urls': ['https://poppler.freedesktop.org/'], + 'sources': [SOURCE_TAR_GZ], + 'checksums': ['c835b640a40ce357e1b83666aabd95edffa24ddddd49b8daff63adb851cdab74'], + }), +] + +sanity_check_paths = { + 'files': ['bin/pdfinfo', 'lib/libpoppler.%s' % SHLIB_EXT, 'lib/libpoppler-cpp.%s' % SHLIB_EXT, + 'lib/libpoppler-glib.%s' % SHLIB_EXT, 'lib/libpoppler-qt6.%s' % SHLIB_EXT], + 'dirs': ['include/poppler', 'lib/pkgconfig', 'share'], +} + +sanity_check_commands = ["pdfinfo --help"] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/popt/popt-1.18.eb b/easybuild/easyconfigs/p/popt/popt-1.18.eb new file mode 100644 index 00000000000..6abfaaedede --- /dev/null +++ b/easybuild/easyconfigs/p/popt/popt-1.18.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'popt' +version = "1.18" + +homepage = "http://freecode.com/projects/popt" +description = """Popt is a C library for parsing command line parameters.""" +toolchain = SYSTEM + +source_urls = ['http://ftp.rpm.org/popt/releases/popt-1.x/'] +sources = [SOURCE_TAR_GZ] +checksums = ['5159bc03a20b28ce363aa96765f37df99ea4d8850b1ece17d1e6ad5c24fdc5d1'] + +toolchainopts = {'optarch': False} +sanity_check_paths = { + 'files': ['include/popt.h', + ('lib/libpopt.a', 'lib64/libpopt.a'), + ('lib/libpopt.%s' % SHLIB_EXT, 'lib64/libpopt.%s' % SHLIB_EXT)], + 'dirs': [], +} + +maxparallel = 1 + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/popt/popt-1.19-GCCcore-13.3.0.eb b/easybuild/easyconfigs/p/popt/popt-1.19-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..91b5c7c74ba --- /dev/null +++ b/easybuild/easyconfigs/p/popt/popt-1.19-GCCcore-13.3.0.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'popt' +version = '1.19' + +homepage = 'https://github.com/rpm-software-management/popt' +description = 'Popt is a C library for parsing command line parameters.' + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['http://ftp.rpm.org/popt/releases/popt-1.x'] +sources = [SOURCE_TAR_GZ] +checksums = ['c25a4838fc8e4c1c8aacb8bd620edb3084a3d63bf8987fdad3ca2758c63240f9'] + +builddependencies = [ + ('binutils', '2.42') +] + +sanity_check_paths = { + 'files': ['include/%(name)s.h', ('lib/libpopt.a', 'lib64/libpopt.a'), ('lib/libpopt.so', 'lib64/libpopt.so')], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/preseq/preseq-3.2.0-GCC-12.2.0.eb b/easybuild/easyconfigs/p/preseq/preseq-3.2.0-GCC-12.2.0.eb new file mode 100644 index 00000000000..e97deba5b85 --- /dev/null +++ b/easybuild/easyconfigs/p/preseq/preseq-3.2.0-GCC-12.2.0.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'preseq' +version = '3.2.0' + +homepage = 'https://smithlabresearch.org/software/preseq' +description = "Software for predicting library complexity and genome coverage in high-throughput sequencing." + +toolchain = {'name': 'GCC', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/smithlabcode/preseq/releases/download/v%(version)s'] +sources = [SOURCE_TAR_GZ] +checksums = ['95b81c9054e0d651de398585c7e96b807ad98f0bdc541b3e46665febbe2134d9'] + +dependencies = [ + ('GSL', '2.7'), + ('HTSlib', '1.17'), + ('zlib', '1.2.12'), +] + +configopts = '--enable-hts CPPFLAGS="-I$EBROOTHTSLIB/include" LDFLAGS="-L$EBROOTHTSLIB/lib"' + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['preseq', 'to-mr']], + 'dirs': [], +} + +sanity_check_commands = ['preseq'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/pretty-yaml/pretty-yaml-24.7.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/pretty-yaml/pretty-yaml-24.7.0-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..7a8779a9412 --- /dev/null +++ b/easybuild/easyconfigs/p/pretty-yaml/pretty-yaml-24.7.0-GCCcore-12.3.0.eb @@ -0,0 +1,31 @@ +easyblock = 'PythonPackage' + +name = 'pretty-yaml' +local_mod = 'pyaml' +version = '24.7.0' + +homepage = 'https://github.com/mk-fg/pretty-yaml' +description = """PyYAML-based python module to produce pretty and readable YAML-serialized data. +This module is for serialization only, see ruamel.yaml module for literate YAML +parsing (keeping track of comments, spacing, line/column numbers of values, etc).""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://pypi.python.org/packages/source/p/%s/' % local_mod] +sources = ['%s-%%(version)s.tar.gz' % local_mod] +checksums = ['5d0fdf9e681036fb263a783d0298fc3af580a6e2a6cf1a3314ffc48dc3d91ccb'] + +builddependencies = [('binutils', '2.40')] + +dependencies = [ + ('Python', '3.11.3'), + ('PyYAML', '6.0'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +options = {'modulename': local_mod} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/pretty-yaml/pretty-yaml-24.7.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/p/pretty-yaml/pretty-yaml-24.7.0-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..ef58228ef61 --- /dev/null +++ b/easybuild/easyconfigs/p/pretty-yaml/pretty-yaml-24.7.0-GCCcore-13.3.0.eb @@ -0,0 +1,31 @@ +easyblock = 'PythonPackage' + +name = 'pretty-yaml' +local_mod = 'pyaml' +version = '24.7.0' + +homepage = 'https://github.com/mk-fg/pretty-yaml' +description = """PyYAML-based python module to produce pretty and readable YAML-serialized data. +This module is for serialization only, see ruamel.yaml module for literate YAML +parsing (keeping track of comments, spacing, line/column numbers of values, etc).""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://pypi.python.org/packages/source/p/%s/' % local_mod] +sources = ['%s-%%(version)s.tar.gz' % local_mod] +checksums = ['5d0fdf9e681036fb263a783d0298fc3af580a6e2a6cf1a3314ffc48dc3d91ccb'] + +builddependencies = [('binutils', '2.42')] + +dependencies = [ + ('Python', '3.12.3'), + ('PyYAML', '6.0.2'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +options = {'modulename': local_mod} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/primecount/primecount-7.14-GCCcore-13.2.0.eb b/easybuild/easyconfigs/p/primecount/primecount-7.14-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..556cc0f1507 --- /dev/null +++ b/easybuild/easyconfigs/p/primecount/primecount-7.14-GCCcore-13.2.0.eb @@ -0,0 +1,31 @@ +easyblock = 'CMakeMake' + +name = 'primecount' +version = '7.14' + +homepage = 'https://github.com/kimwalisch/primecount' +description = """primecount is a command-line program and C/C++ library that counts the number of primes ≤ x + (maximum 1031) using highly optimized implementations of the combinatorial prime counting algorithms.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://github.com/kimwalisch/primecount/archive/refs/tags'] +sources = ['v%(version)s.tar.gz'] +checksums = ['d867ac18cc52c0f7014682169988a76f39e4cd56f8ce78fb56e064499b1d66bb'] + +builddependencies = [ + ('CMake', '3.27.6'), + ('binutils', '2.40'), +] + +configopts = '-DBUILD_SHARED_LIBS=ON ' + +sanity_check_paths = { + 'files': ['bin/primecount', 'include/primecount.h'] + + ['lib/libprimecount.%s' % e for e in ['a', SHLIB_EXT]], + 'dirs': ['share'], +} + +sanity_check_commands = ["primecount -h"] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/p/primecountpy/primecountpy-0.1.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/p/primecountpy/primecountpy-0.1.0-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..11244361d59 --- /dev/null +++ b/easybuild/easyconfigs/p/primecountpy/primecountpy-0.1.0-GCCcore-13.2.0.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'primecountpy' +version = '0.1.0' + +homepage = 'https://pypi.org/project/primecountpy' +description = "This is a Cython interface to the C++ library primecount." + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['78fe7cc32115f0669a45d7c90faaf39f7ce3939e39e2e7e5f14c17fe4bff0676'] + +builddependencies = [('binutils', '2.40')] + +dependencies = [ + ('Python', '3.11.5'), + ('Cython', '3.0.10'), + ('cysignals', '1.11.4'), + ('primecount', '7.14'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/p/prompt-toolkit/prompt-toolkit-3.0.36-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/prompt-toolkit/prompt-toolkit-3.0.36-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..dfcdad173d1 --- /dev/null +++ b/easybuild/easyconfigs/p/prompt-toolkit/prompt-toolkit-3.0.36-GCCcore-12.3.0.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonPackage' + +name = 'prompt-toolkit' +version = '3.0.36' + +homepage = 'https://github.com/jonathanslenders/python-prompt-toolkit' +description = """prompt_toolkit is a Python library for building powerful interactive command lines and + terminal applications.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +builddependencies = [('binutils', '2.40')] + +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), +] + +sources = ['prompt_toolkit-%(version)s-py3-none-any.whl'] +checksums = ['aa64ad242a462c5ff0363a7b9cfe696c20d55d9fc60c11fd8e632d064804d305'] + +use_pip = True +sanity_pip_check = True +download_dep_fail = True + +options = {'modulename': 'prompt_toolkit'} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/prompt-toolkit/prompt-toolkit-3.0.36-GCCcore-13.3.0.eb b/easybuild/easyconfigs/p/prompt-toolkit/prompt-toolkit-3.0.36-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..8cbde894708 --- /dev/null +++ b/easybuild/easyconfigs/p/prompt-toolkit/prompt-toolkit-3.0.36-GCCcore-13.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'prompt-toolkit' +version = '3.0.36' + +homepage = 'https://github.com/jonathanslenders/python-prompt-toolkit' +description = """prompt_toolkit is a Python library for building powerful interactive command lines and + terminal applications.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +builddependencies = [('binutils', '2.42')] +dependencies = [ + ('Python', '3.12.3'), + ('Python-bundle-PyPI', '2024.06'), +] + +sources = ['prompt_toolkit-%(version)s-py3-none-any.whl'] +checksums = ['aa64ad242a462c5ff0363a7b9cfe696c20d55d9fc60c11fd8e632d064804d305'] + +download_dep_fail = True +sanity_pip_check = True +use_pip = True + +options = {'modulename': 'prompt_toolkit'} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/protobuf-python/protobuf-python-5.28.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/p/protobuf-python/protobuf-python-5.28.0-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..ed4aac1448e --- /dev/null +++ b/easybuild/easyconfigs/p/protobuf-python/protobuf-python-5.28.0-GCCcore-13.3.0.eb @@ -0,0 +1,35 @@ +easyblock = 'PythonPackage' + +name = 'protobuf-python' +version = '5.28.0' + +homepage = 'https://github.com/google/protobuf/' +description = "Python Protocol Buffers runtime library." + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://pypi.python.org/packages/source/p/protobuf'] +sources = ['protobuf-%(version)s.tar.gz'] +checksums = ['dde74af0fa774fa98892209992295adbfb91da3fa98c8f67a88afe8f5a349add'] + +builddependencies = [('binutils', '2.42')] + +dependencies = [ + ('Python', '3.12.3'), + ('protobuf', version[2:]), # Major version is only used for the Python bindings +] + +download_dep_fail = True +sanity_pip_check = True +use_pip = True + +options = {'modulename': 'google.protobuf'} + +# Make sure protobuf is installed as a regular folder or it will not be found if +# other google packages are installed in other site-packages folders +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/google/protobuf'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/protobuf/protobuf-28.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/p/protobuf/protobuf-28.0-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..b5f959fc06b --- /dev/null +++ b/easybuild/easyconfigs/p/protobuf/protobuf-28.0-GCCcore-13.3.0.eb @@ -0,0 +1,35 @@ +easyblock = 'CMakeMake' + +name = 'protobuf' +version = '28.0' + +homepage = 'https://github.com/protocolbuffers/protobuf' +description = """Protocol Buffers (a.k.a., protobuf) are Google's +language-neutral, platform-neutral, extensible mechanism for +serializing structured data.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +github_account = 'protocolbuffers' +source_urls = [GITHUB_RELEASE] +sources = [SOURCE_TAR_GZ] +checksums = ['13e7749c30bc24af6ee93e092422f9dc08491c7097efa69461f88eb5f61805ce'] + +builddependencies = [ + ('binutils', '2.42'), + ('CMake', '3.29.3'), +] +dependencies = [ + ('Abseil', '20240722.0'), +] + +srcdir = '.' + +configopts = '-Dprotobuf_BUILD_TESTS=OFF -Dprotobuf_BUILD_SHARED_LIBS=ON -Dprotobuf_ABSL_PROVIDER="package" ' + +sanity_check_paths = { + 'files': ['bin/protoc', 'lib/libprotobuf.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/psutil/psutil-5.9.8-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/psutil/psutil-5.9.8-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..554ec684e83 --- /dev/null +++ b/easybuild/easyconfigs/p/psutil/psutil-5.9.8-GCCcore-12.3.0.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonBundle' + +name = 'psutil' +version = '5.9.8' + +homepage = 'https://github.com/giampaolo/psutil' +description = """A cross-platform process and system utilities module for Python""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +builddependencies = [('binutils', '2.40')] + +dependencies = [('Python', '3.11.3')] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + (name, version, { + 'source_urls': ['https://github.com/giampaolo/psutil/archive'], + 'sources': ['%(name)s-%(version)s.tar.gz'], + 'checksums': ['6be126e3225486dff286a8fb9a06246a5253f4c7c53b475ea5f5ac934e64194c'], + }), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/psutil/psutil-6.0.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/p/psutil/psutil-6.0.0-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..d6b6501e7da --- /dev/null +++ b/easybuild/easyconfigs/p/psutil/psutil-6.0.0-GCCcore-13.3.0.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonBundle' + +name = 'psutil' +version = '6.0.0' + +homepage = 'https://github.com/giampaolo/psutil' +description = """A cross-platform process and system utilities module for Python""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +builddependencies = [('binutils', '2.42')] + +dependencies = [('Python', '3.12.3')] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + (name, version, { + 'source_urls': ['https://github.com/giampaolo/psutil/archive'], + 'sources': ['%(name)s-%(version)s.tar.gz'], + 'checksums': ['8faae4f310b6d969fa26ca0545338b21f73c6b15db7c4a8d934a5482faa818f2'], + }), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/psutil/psutil-6.1.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/p/psutil/psutil-6.1.0-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..5ba7c5d9380 --- /dev/null +++ b/easybuild/easyconfigs/p/psutil/psutil-6.1.0-GCCcore-13.2.0.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonBundle' + +name = 'psutil' +version = '6.1.0' + +homepage = 'https://github.com/giampaolo/psutil' +description = """A cross-platform process and system utilities module for Python""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +builddependencies = [('binutils', '2.40')] + +dependencies = [('Python', '3.11.5')] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + (name, version, { + 'source_urls': ['https://github.com/giampaolo/psutil/archive'], + 'sources': ['release-%(version)s.tar.gz'], + 'checksums': ['0ffb8a92fac0e89c10b0beb152acae27975fd488d0b9938e441106f319e7599c'], + }), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/psycopg/psycopg-3.2.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/psycopg/psycopg-3.2.1-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..5c0aab8a54e --- /dev/null +++ b/easybuild/easyconfigs/p/psycopg/psycopg-3.2.1-GCCcore-12.3.0.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonBundle' + +name = 'psycopg' +version = '3.2.1' + +homepage = 'https://psycopg.org/' +description = "Psycopg is the most popular PostgreSQL adapter for the Python programming language." + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +builddependencies = [('binutils', '2.40')] +dependencies = [ + ('Python', '3.11.3'), + ('PostgreSQL', '16.1'), +] + +exts_list = [ + (name, version, { + 'checksums': ['dc8da6dc8729dacacda3cc2f17d2c9397a70a66cf0d2b69c91065d60d5f00cb7'], + }), +] + +use_pip = True +sanity_pip_check = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/psycopg/psycopg-3.2.3-GCCcore-13.3.0.eb b/easybuild/easyconfigs/p/psycopg/psycopg-3.2.3-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..28b9128ff66 --- /dev/null +++ b/easybuild/easyconfigs/p/psycopg/psycopg-3.2.3-GCCcore-13.3.0.eb @@ -0,0 +1,24 @@ +easyblock = 'PythonPackage' + +name = 'psycopg' +version = '3.2.3' + +homepage = 'https://psycopg.org/' +description = "Psycopg is the most popular PostgreSQL adapter for the Python programming language." + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['a5764f67c27bec8bfac85764d23c534af2c27b893550377e37ce59c12aac47a2'] + +builddependencies = [('binutils', '2.42')] +dependencies = [ + ('Python', '3.12.3'), + ('PostgreSQL', '16.4'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/py3Dmol/py3Dmol-2.1.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/py3Dmol/py3Dmol-2.1.0-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..0ff64a7f07a --- /dev/null +++ b/easybuild/easyconfigs/p/py3Dmol/py3Dmol-2.1.0-GCCcore-12.3.0.eb @@ -0,0 +1,31 @@ +easyblock = 'PythonBundle' + +name = 'py3Dmol' +version = '2.1.0' + +homepage = 'https://github.com/3dmol/3Dmol.js/tree/master/py3Dmol' +description = "A simple IPython/Jupyter widget to embed an interactive 3Dmol.js viewer in a notebook." + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +builddependencies = [ + ('binutils', '2.40'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('IPython', '8.14.0'), +] + +use_pip = True + +exts_list = [ + (name, version, { + 'modulename': "%(name)s", + 'checksums': ['83d2f25a9107b4cef125c0c1f5caa4dce9b7577f1346fc0a3f7d12972e11c0e8'], + }), +] + +sanity_pip_check = True + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/pyBigWig/pyBigWig-0.3.22-gfbf-2023a.eb b/easybuild/easyconfigs/p/pyBigWig/pyBigWig-0.3.22-gfbf-2023a.eb new file mode 100644 index 00000000000..8e9947f8e5b --- /dev/null +++ b/easybuild/easyconfigs/p/pyBigWig/pyBigWig-0.3.22-gfbf-2023a.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonPackage' + +name = 'pyBigWig' +version = '0.3.22' + +homepage = 'https://github.com/deeptools/pyBigWig' +description = """A python extension, written in C, for quick access to bigBed +files and access to and creation of bigWig files.""" + +toolchain = {'name': 'gfbf', 'version': '2023a'} + +sources = [SOURCE_TAR_GZ] +checksums = ['5d4426f754bd7b7f6dc21d6c3f93b58a96a65b6eb2e578ae03b31a71272d2243'] + +dependencies = [ + ('Python', '3.11.3'), + ('cURL', '8.0.1'), + ('NSS', '3.89.1'), # provides libfreebl3 + ('SciPy-bundle', '2023.07'), # optional, for numpy support +] + +use_pip = True +download_dep_fail = True + +options = {'modulename': name} + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/pyGenomeTracks/pyGenomeTracks-3.9-foss-2023a.eb b/easybuild/easyconfigs/p/pyGenomeTracks/pyGenomeTracks-3.9-foss-2023a.eb new file mode 100644 index 00000000000..aa1c8985476 --- /dev/null +++ b/easybuild/easyconfigs/p/pyGenomeTracks/pyGenomeTracks-3.9-foss-2023a.eb @@ -0,0 +1,58 @@ +easyblock = 'PythonBundle' + +name = 'pyGenomeTracks' +version = '3.9' + +homepage = 'https://pygenometracks.readthedocs.io' +description = "pyGenomeTracks aims to produce high-quality genome browser tracks that are highly customizable." + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('matplotlib', '3.7.2'), + ('bx-python', '0.10.0'), + ('pybedtools', '0.9.1'), + ('pyBigWig', '0.3.22'), + ('pyfaidx', '0.8.1.1'), + ('Pysam', '0.22.0'), + ('tqdm', '4.66.1'), + ('PyTables', '3.8.0'), + ('h5py', '3.9.0'), + ('PyYAML', '6.0'), + ('cooler', '0.10.2'), + ('HiCMatrix', '17.2'), +] + +use_pip = True +exts_list = [ + ('argcomplete', '3.4.0', { + 'checksums': ['c2abcdfe1be8ace47ba777d4fce319eb13bf8ad9dace8d085dcad6eded88057f'], + }), + ('argh', '0.31.2', { + 'checksums': ['db1c34885804f7d4646c385dc2fb19b45298561322f4c15eae1b133993f9e323'], + }), + ('gffutils', '0.13', { + 'checksums': ['b0d52f35c014cc0330fb5c4e3c6fea127c90ccf4c5384a825cdb5c8ff330d4eb'], + }), + ('pypairix', '0.3.7', { + 'checksums': ['c1b47c05f92b5be628923c60a27344503ddeba5d8f35a3752d646271d38e0525'], + }), + (name, version, { + 'source_tmpl': '%(version)s.tar.gz', + 'source_urls': ['https://github.com/deeptools/pyGenomeTracks/archive/refs/tags'], + 'checksums': ['4318cb642422ee16d83675d571f4cd49b14784d7ee135ab53d8946fc7ad663f6'], + }), +] + +sanity_check_paths = { + 'files': ['bin/pyGenomeTracks'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["pyGenomeTracks --help"] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/pyMBE/pyMBE-0.8.0-foss-2023b.eb b/easybuild/easyconfigs/p/pyMBE/pyMBE-0.8.0-foss-2023b.eb new file mode 100644 index 00000000000..6e676c32455 --- /dev/null +++ b/easybuild/easyconfigs/p/pyMBE/pyMBE-0.8.0-foss-2023b.eb @@ -0,0 +1,67 @@ +easyblock = 'PythonBundle' + +name = 'pyMBE' +version = '0.8.0' + +homepage = '' +description = """pyMBE: the Python-based Molecule Builder for ESPResSo + +pyMBE provides tools to facilitate building up molecules with complex architectures +in the Molecular Dynamics software ESPResSo.""" + +toolchain = {'name': 'foss', 'version': '2023b'} + +builddependencies = [('hatchling', '1.18.0')] + +dependencies = [ + ('Python', '3.11.5'), + ('SciPy-bundle', '2023.11'), + ('Pint', '0.24'), + ('tqdm', '4.66.2'), + ('matplotlib', '3.8.2'), + ('ESPResSo', '4.2.2'), +] + +use_pip = True +# pyMBE is not installable and should just be copied to the installation directory +exts_classmap = {'pyMBE': 'Tarball'} + +# pyMBE itself should be the first one in the list, +# otherwise the Tarball easyblock will copy the sources of all extensions to the installation directory +exts_list = [ + (name, version, { + 'source_urls': ['https://github.com/pyMBE-dev/pyMBE/archive/'], + 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['f143ae655b477d6d2ab6d97190a387fa9c7e854502a38c72c24eac48e37ea663'], + }), + ('looseversion', '1.1.2', { + 'checksums': ['94d80bdbd0b6d57c11b886147ba1601f7d1531571621b81933b34537cbe469ad'], + }), + ('mmtf-python', '1.1.3', { + 'modulename': 'mmtf', + 'checksums': ['12a02fe1b7131f0a2b8ce45b46f1e0cdd28b9818fe4499554c26884987ea0c32'], + }), + ('Pint-Pandas', '0.5', { + 'checksums': ['48ec96d457f802a347763dee1d3e1a273f11f90e4e595df17fd44613dd14a61c'], + }), + ('biopandas', '0.5.1.dev0', { + 'checksums': ['6dc9de631babf8221c1ac60230133717039e08911f15e8ac48498c787022de12'], + }), +] + +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['pyMBE.py'], + 'dirs': ['figs', 'lib', 'maintainer', 'parameters', 'refs', 'samples', 'testsuite', 'tutorials', 'visualization'], +} + +sanity_check_commands = [ + 'python -c "import pyMBE"', + # running the full test suite takes a long time, so just stick to the unit tests + 'cd %(installdir)s && make unit_tests' +] + +modextrapaths = {'PYTHONPATH': ['.']} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/p/pyWannier90/pyWannier90-2024-01-28-foss-2023a.eb b/easybuild/easyconfigs/p/pyWannier90/pyWannier90-2024-01-28-foss-2023a.eb new file mode 100644 index 00000000000..89191292693 --- /dev/null +++ b/easybuild/easyconfigs/p/pyWannier90/pyWannier90-2024-01-28-foss-2023a.eb @@ -0,0 +1,73 @@ +easyblock = 'MakeCp' + +name = 'pyWannier90' +local_commit = 'c3f65d7' +version = '2024-01-28' + +homepage = 'https://github.com/hungpham2017/pyWannier90' +description = "A Wannier90 Python interface for VASP and PySCF" + +toolchain = {'name': 'foss', 'version': '2023a'} + +local_wannier90_version = '3.1.0' + +sources = [ + { + 'source_urls': ['https://github.com/hungpham2017/pyWannier90/archive/'], + 'download_filename': '%s.tar.gz' % local_commit, + 'filename': SOURCE_TAR_GZ + }, + { + 'source_urls': ['https://github.com/wannier-developers/wannier90/archive/'], + 'download_filename': 'v%s.tar.gz' % local_wannier90_version, + 'filename': 'Wannier90-%s.tar.gz' % local_wannier90_version, + }, +] +checksums = [ + {'pyWannier90-2024-01-28.tar.gz': '9828dcdde92b9627cfe888b5be530040c1c51c97f5a3c930d82ef24d862610e3'}, + {'Wannier90-3.1.0.tar.gz': '40651a9832eb93dec20a8360dd535262c261c34e13c41b6755fa6915c936b254'}, +] + +builddependencies = [ + ('pybind11', '2.11.1'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('PySCF', '2.7.0'), +] + +local_wannier90_make = 'make -j %(parallel)s F90="$F90" FCOPTS="$FFLAGS -fPIC" LDOPTS="$FFLAGS" ' +local_wannier90_make += 'LIBDIR="$LAPACK_LIB_DIR" LIBS="$LIBLAPACK"' + +prebuildopts = "sed -i 's/ -undefined dynamic_lookup//g' src/Makefile && " +prebuildopts += "cd %%(builddir)s/wannier90-%s && touch make.inc && " % local_wannier90_version +prebuildopts += "cp %(builddir)s/pyWannier90-*/src/wannier_lib.F90 src/wannier_lib.F90 && " +prebuildopts += local_wannier90_make + " && " +prebuildopts += local_wannier90_make + " lib && " +prebuildopts += "cd %(builddir)s/pyWannier90-*/src && " + +buildopts = 'CPP="$CXX" LIBS="-L%%(builddir)s/wannier90-%s $LIBLAPACK -lwannier" ' % local_wannier90_version +# with Intel compilers, use libwannier90_intel as make target +# with GCC compilers, use libwannier90_gf as make target +buildopts += "libwannier90_gf && " +buildopts += """sed -i "s@W90LIB = .*@W90LIB = '%(installdir)s'@g" pywannier90.py""" + +files_to_copy = [ + (['src/pywannier90.py', 'src/libwannier90.*.%s' % SHLIB_EXT], 'lib/python%(pyshortver)s/site-packages'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "python -c 'import libwannier90'", + "python -c 'import pywannier90'", +] + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/p/pybedtools/pybedtools-0.10.0-foss-2023b.eb b/easybuild/easyconfigs/p/pybedtools/pybedtools-0.10.0-foss-2023b.eb new file mode 100644 index 00000000000..2f643966cdb --- /dev/null +++ b/easybuild/easyconfigs/p/pybedtools/pybedtools-0.10.0-foss-2023b.eb @@ -0,0 +1,25 @@ +easyblock = 'PythonPackage' + +name = 'pybedtools' +version = '0.10.0' + +homepage = 'https://daler.github.io/pybedtools' +description = "pybedtools wraps and extends BEDTools and offers feature-level manipulations from within Python." + +toolchain = {'name': 'foss', 'version': '2023b'} + +sources = [SOURCE_TAR_GZ] +checksums = ['1a6fbaad23b013becc741d7d5922a2df03e391bc44ff92772ffb7dd456711161'] + +dependencies = [ + ('Python', '3.11.5'), + ('SciPy-bundle', '2023.11'), + ('BEDTools', '2.31.1'), + ('Pysam', '0.22.0'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/pybind11/pybind11-2.12.0-GCC-13.3.0.eb b/easybuild/easyconfigs/p/pybind11/pybind11-2.12.0-GCC-13.3.0.eb new file mode 100644 index 00000000000..e4e0460d13e --- /dev/null +++ b/easybuild/easyconfigs/p/pybind11/pybind11-2.12.0-GCC-13.3.0.eb @@ -0,0 +1,33 @@ +name = 'pybind11' +version = '2.12.0' + +homepage = 'https://pybind11.readthedocs.io' +description = """pybind11 is a lightweight header-only library that exposes C++ types in Python and vice versa, + mainly to create Python bindings of existing C++ code.""" + +toolchain = {'name': 'GCC', 'version': '13.3.0'} + +source_urls = ['https://github.com/pybind/pybind11/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = [ + 'pybind11-2.10.3_require-catch.patch', +] +checksums = [ + {'v2.12.0.tar.gz': 'bf8f242abd1abcd375d516a7067490fb71abd79519a282d22b6e4d19282185a7'}, + {'pybind11-2.10.3_require-catch.patch': '4a27ba3ef1d5c535d120d6178a6e876ae678e4899a07500aab37908357b0b60b'}, +] + +builddependencies = [ + ('CMake', '3.29.3'), + # Test dependencies + ('Eigen', '3.4.0'), + ('Catch2', '2.13.10'), + ('Python-bundle-PyPI', '2024.06'), # to provide pytest +] + +dependencies = [ + ('Boost', '1.85.0'), + ('Python', '3.12.3'), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/pycocotools/pycocotools-2.0.7-foss-2023a.eb b/easybuild/easyconfigs/p/pycocotools/pycocotools-2.0.7-foss-2023a.eb new file mode 100644 index 00000000000..666074add24 --- /dev/null +++ b/easybuild/easyconfigs/p/pycocotools/pycocotools-2.0.7-foss-2023a.eb @@ -0,0 +1,25 @@ +easyblock = 'PythonPackage' + +name = 'pycocotools' +version = '2.0.7' + +homepage = 'https://pypi.org/project/pycocotools' +description = "Official APIs for the MS-COCO dataset" + +toolchain = {'name': 'foss', 'version': '2023a'} + +sources = [SOURCE_TAR_GZ] +checksums = ['da8b7815196eebf0adabf67fcc459126cbc6498bbc6ab1fd144c371465d86879'] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('matplotlib', '3.7.2'), +] + +download_dep_fail = True +use_pip = True + +sanity_pip_check = True + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/p/pycodestyle/pycodestyle-2.11.1-foss-2023a.eb b/easybuild/easyconfigs/p/pycodestyle/pycodestyle-2.11.1-foss-2023a.eb new file mode 100644 index 00000000000..66965820b1d --- /dev/null +++ b/easybuild/easyconfigs/p/pycodestyle/pycodestyle-2.11.1-foss-2023a.eb @@ -0,0 +1,22 @@ +easyblock = 'PythonPackage' + +name = 'pycodestyle' +version = '2.11.1' + +homepage = "https://pycodestyle.readthedocs.io" +description = """pycodestyle is a tool to check your Python code against some of the style conventions in PEP 8.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +sources = [SOURCE_TAR_GZ] +checksums = ['41ba0e7afc9752dfb53ced5489e89f8186be00e599e712660695b7a75ff2663f'] + +dependencies = [ + ('Python', '3.11.3'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/pydantic/pydantic-2.7.4-GCCcore-13.2.0.eb b/easybuild/easyconfigs/p/pydantic/pydantic-2.7.4-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..efc3388a073 --- /dev/null +++ b/easybuild/easyconfigs/p/pydantic/pydantic-2.7.4-GCCcore-13.2.0.eb @@ -0,0 +1,126 @@ +easyblock = 'CargoPythonBundle' + +name = 'pydantic' +version = '2.7.4' + +homepage = 'https://github.com/samuelcolvin/pydantic' +description = """Data validation and settings management using Python type hinting.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +builddependencies = [ + ('binutils', '2.40'), + ('Rust', '1.76.0'), + ('maturin', '1.5.0', '-Rust-1.76.0'), + ('hatchling', '1.18.0'), +] + +dependencies = [ + ('Python', '3.11.5'), + ('typing-extensions', '4.10.0'), +] + +use_pip = True +sanity_pip_check = True + +crates = [ + ('ahash', '0.8.10'), + ('aho-corasick', '1.0.2'), + ('autocfg', '1.1.0'), + ('base64', '0.21.7'), + ('bitflags', '1.3.2'), + ('bitvec', '1.0.1'), + ('cc', '1.0.79'), + ('cfg-if', '1.0.0'), + ('enum_dispatch', '0.3.13'), + ('equivalent', '1.0.1'), + ('form_urlencoded', '1.2.1'), + ('funty', '2.0.0'), + ('getrandom', '0.2.10'), + ('hashbrown', '0.14.3'), + ('heck', '0.4.1'), + ('idna', '0.5.0'), + ('indexmap', '2.2.2'), + ('indoc', '2.0.4'), + ('itoa', '1.0.8'), + ('jiter', '0.4.1'), + ('lexical-parse-float', '0.8.5'), + ('lexical-parse-integer', '0.8.6'), + ('lexical-util', '0.8.5'), + ('libc', '0.2.147'), + ('lock_api', '0.4.10'), + ('memchr', '2.6.3'), + ('memoffset', '0.9.0'), + ('num-bigint', '0.4.4'), + ('num-integer', '0.1.45'), + ('num-traits', '0.2.16'), + ('once_cell', '1.18.0'), + ('parking_lot', '0.12.1'), + ('parking_lot_core', '0.9.8'), + ('percent-encoding', '2.3.1'), + ('portable-atomic', '1.6.0'), + ('proc-macro2', '1.0.76'), + ('pyo3', '0.21.2'), + ('pyo3-build-config', '0.21.2'), + ('pyo3-ffi', '0.21.2'), + ('pyo3-macros', '0.21.2'), + 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'c55115c6fbe2d2bef26eb09ad74bde02d8255476fc0c7b515ef09fbb35742d82'}), + ({'tinyvec_macros-0.1.1.tar.gz': '1f3ccbac311fea05f86f61904b462b55fb3df8837a366dfc601a0161d0532f20'}), + ({'unicode-bidi-0.3.15.tar.gz': '08f95100a766bf4f8f28f90d77e0a5461bbdb219042e7679bebe79004fed8d75'}), + ({'unicode-ident-1.0.12.tar.gz': '3354b9ac3fae1ff6755cb6db53683adb661634f67557942dea4facebec0fee4b'}), + ({'unicode-normalization-0.1.23.tar.gz': 'a56d1686db2308d901306f92a263857ef59ea39678a5458e7cb17f01415101f5'}), + ({'unindent-0.2.3.tar.gz': 'c7de7d73e1754487cb58364ee906a499937a0dfabd86bcb980fa99ec8c8fa2ce'}), + ({'url-2.5.2.tar.gz': '22784dbdf76fdde8af1aeda5622b546b422b6fc585325248a2bf9f5e41e94d6c'}), + ({'utf16_iter-1.0.5.tar.gz': 'c8232dd3cdaed5356e0f716d285e4b40b932ac434100fe9b7e0e8e935b9e6246'}), + ({'utf8_iter-1.0.4.tar.gz': 'b6c140620e7ffbb22c2dee59cafe6084a59b5ffc27a8859a5f0d494b5d52b6be'}), + ({'uuid-1.10.0.tar.gz': '81dfa00651efa65069b0b6b651f4aaa31ba9e3c3ce0137aaad053604ee7e0314'}), + ({'version_check-0.9.5.tar.gz': '0b928f33d975fc6ad9f86c8f283853ad26bdd5b10b7f1542aa2fa15e2289105a'}), + ({'wasi-0.11.0+wasi-snapshot-preview1.tar.gz': '9c8d87e72b64a3b4db28d11ce29237c246188f4f51057d65a7eab63b7987e423'}), + ({'write16-1.0.0.tar.gz': 'd1890f4022759daae28ed4fe62859b1236caebfc61ede2f63ed4e695f3f6d936'}), + ({'writeable-0.5.5.tar.gz': '1e9df38ee2d2c3c5948ea468a8406ff0db0b29ae1ffde1bcf20ef305bcc95c51'}), + ({'wyz-0.5.1.tar.gz': '05f360fc0b24296329c78fda852a1e9ae82de9cf7b27dae4b7f62f118f77b9ed'}), + ({'yoke-0.7.4.tar.gz': '6c5b1314b079b0930c31e3af543d8ee1757b1951ae1e1565ec704403a7240ca5'}), + ({'yoke-derive-0.7.4.tar.gz': '28cc31741b18cb6f1d5ff12f5b7523e3d6eb0852bbbad19d73905511d9849b95'}), + ({'zerocopy-0.7.34.tar.gz': 'ae87e3fcd617500e5d106f0380cf7b77f3c6092aae37191433159dda23cfb087'}), + ({'zerocopy-derive-0.7.34.tar.gz': '15e934569e47891f7d9411f1a451d947a60e000ab3bd24fbb970f000387d1b3b'}), + ({'zerofrom-0.1.4.tar.gz': '91ec111ce797d0e0784a1116d0ddcdbea84322cd79e5d5ad173daeba4f93ab55'}), + ({'zerofrom-derive-0.1.4.tar.gz': '0ea7b4a3637ea8669cedf0f1fd5c286a17f3de97b8dd5a70a6c167a1730e63a5'}), + ({'zerovec-0.10.4.tar.gz': 'aa2b893d79df23bfb12d5461018d408ea19dfafe76c2c7ef6d4eba614f8ff079'}), + ({'zerovec-derive-0.10.3.tar.gz': '6eafa6dfb17584ea3e2bd6e76e0cc15ad7af12b09abdd1ca55961bed9b1063c6'}), +] + +exts_list = [ + ('annotated_types', '0.7.0', { + 'checksums': ['aff07c09a53a08bc8cfccb9c85b05f1aa9a2a6f23728d790723543408344ce89'], + }), + ('pydantic_core', '2.23.3', { + 'checksums': ['3cb0f65d8b4121c1b015c60104a685feb929a29d7cf204387c7f2688c7974690'], + }), + (name, version, { + 'preinstallopts': "sed -i '/Framework :: Pydantic/d' pyproject.toml && ", + 'checksums': ['1363c7d975c7036df0db2b4a61f2e062fbc0aa5ab5f2772e0ffc7191a4f4bce2'], + }), +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/pydicom/pydicom-2.4.4-GCCcore-12.2.0.eb b/easybuild/easyconfigs/p/pydicom/pydicom-2.4.4-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..a1071f66e07 --- /dev/null +++ b/easybuild/easyconfigs/p/pydicom/pydicom-2.4.4-GCCcore-12.2.0.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonPackage' + +name = 'pydicom' +version = '2.4.4' + +homepage = 'https://pydicom.github.io/' +description = "Pure python package for DICOM medical file reading and writing." + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = [GITHUB_SOURCE] +sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}] +checksums = ['42c06ed74331174111dd42c89db774a13fc472abe18015f22c5aba80cddb7843'] + +builddependencies = [ + ('binutils', '2.39'), +] +dependencies = [ + ('Python', '3.10.8'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/pydot/pydot-2.0.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/p/pydot/pydot-2.0.0-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..d39e368e0cd --- /dev/null +++ b/easybuild/easyconfigs/p/pydot/pydot-2.0.0-GCCcore-12.2.0.eb @@ -0,0 +1,25 @@ +# updated: Denis Kristak, Pavel Tománek (INUITS) +easyblock = 'PythonBundle' + +name = 'pydot' +version = '2.0.0' + +homepage = 'https://github.com/pydot/pydot' +description = "Python interface to Graphviz's Dot language." + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +builddependencies = [('binutils', '2.39')] + +dependencies = [('Python', '3.10.8')] + +exts_list = [ + (name, version, { + 'checksums': ['60246af215123fa062f21cd791be67dda23a6f280df09f68919e637a1e4f3235'], + }), +] + +use_pip = True +sanity_pip_check = True + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/pyfaidx/pyfaidx-0.8.1.2-GCCcore-13.3.0.eb b/easybuild/easyconfigs/p/pyfaidx/pyfaidx-0.8.1.2-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..f54906c30b3 --- /dev/null +++ b/easybuild/easyconfigs/p/pyfaidx/pyfaidx-0.8.1.2-GCCcore-13.3.0.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonPackage' + +name = 'pyfaidx' +version = '0.8.1.2' + +homepage = 'https://pypi.python.org/pypi/pyfaidx' +description = "pyfaidx: efficient pythonic random access to fasta subsequences" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['d8452470455b1e778f93969447db8ea24deb4624c7c40769516459cb6f87bc33'] + +builddependencies = [('binutils', '2.42')] + +dependencies = [ + ('Python', '3.12.3'), + ('Python-bundle-PyPI', '2024.06'), +] + +download_dep_fail = True +use_pip = True + +sanity_check_paths = { + 'files': ['bin/faidx'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["faidx --help"] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/pyfasta/pyfasta-0.5.2-foss-2023a.eb b/easybuild/easyconfigs/p/pyfasta/pyfasta-0.5.2-foss-2023a.eb new file mode 100644 index 00000000000..127a798d38a --- /dev/null +++ b/easybuild/easyconfigs/p/pyfasta/pyfasta-0.5.2-foss-2023a.eb @@ -0,0 +1,44 @@ +easyblock = 'PythonBundle' + +name = 'pyfasta' +version = '0.5.2' + +homepage = 'https://pypi.org/project/pyfasta/' +description = """fast, memory-efficient, pythonic (and command-line) access to fasta sequence files""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), +] + +use_pip = True + +local_preinstallopts = ( + "sed -i" + " -e 's/from fasta/from pyfasta.fasta/'" + " -e 's/from records/from pyfasta.records/'" + " -e 's/from split_fasta/from pyfasta.split_fasta/'" + " %(name)s/__init__.py && " +) +local_preinstallopts += "sed -i 's/from collections/from collections.abc/' pyfasta/fasta.py && " +local_preinstallopts += "sed -i 's/from records/from pyfasta.records/' pyfasta/fasta.py && " +local_preinstallopts += "sed -i 's/import cPickle/import _pickle as cPickle/' pyfasta/records.py && " +local_preinstallopts += "sed -i 's/from cStringIO import StringIO/from io import StringIO/' pyfasta/split_fasta.py && " + +exts_list = [ + (name, version, { + 'preinstallopts': local_preinstallopts, + 'checksums': ['ab08d75fa90253bc91933d10567d5d9cca2718f4796ef3bdc36b68df0e45b258'], + }), +] + +sanity_check_paths = { + 'files': ['bin/pyfasta'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} +sanity_check_commands = ['pyfasta extract --help'] +sanity_pip_check = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/pygmo/pygmo-2.19.5-gfbf-2022b.eb b/easybuild/easyconfigs/p/pygmo/pygmo-2.19.5-gfbf-2022b.eb new file mode 100644 index 00000000000..20109f00554 --- /dev/null +++ b/easybuild/easyconfigs/p/pygmo/pygmo-2.19.5-gfbf-2022b.eb @@ -0,0 +1,58 @@ +easyblock = 'CMakePythonPackage' + +name = 'pygmo' +version = '2.19.5' + +homepage = 'https://esa.github.io/pygmo2' +description = "pygmo is a scientific Python library for massively parallel optimization." + +toolchain = {'name': 'gfbf', 'version': '2022b'} + +source_urls = ['https://github.com/esa/pygmo2/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['742ff0c3d535cb2af94d5095968d8f29c23ed7bdbd4ddd8259ca787eef881aa2'] + +builddependencies = [ + ('CMake', '3.24.3'), + ('pybind11', '2.10.3'), +] + +dependencies = [ + ('Python', '3.10.8'), + ('SciPy-bundle', '2023.02'), + ('Boost', '1.81.0'), + ('pagmo', '2.19.0'), + ('matplotlib', '3.7.0'), + ('networkx', '3.0'), +] + +# make sure that all files are installed in the correct location (-DCMAKE_INSTALL_PREFIX is not enough)... +configopts = "-DPYGMO_INSTALL_PATH=%(installdir)s/lib/python%(pyshortver)s/site-packages" + +runtest = False + +exts_defaultclass = 'PythonPackage' + +exts_default_options = { + 'source_urls': [PYPI_SOURCE], + 'download_dep_fail': True, + 'use_pip': True, +} + +exts_list = [ + ('cloudpickle', '2.2.1', { + 'checksums': ['d89684b8de9e34a2a43b3460fbca07d09d6e25ce858df4d5a44240403b6178f5'], + }), + ('dill', '0.3.6', { + 'checksums': ['e5db55f3687856d8fbdab002ed78544e1c4559a130302693d839dfe8f93f2373'], + }), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/pygmo'], +} + +sanity_pip_check = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb new file mode 100644 index 00000000000..79469b4b140 --- /dev/null +++ b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb @@ -0,0 +1,114 @@ +easyblock = 'PythonBundle' + +name = 'pyiron' +version = '0.5.1' + +homepage = 'https://github.com/pyiron/pyiron' +description = "An integrated development environment (IDE) for computational materials science." + + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [('poetry', '1.5.1')] +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('Python-bundle-PyPI', '2023.06'), + ('matplotlib', '3.7.2'), + ('h5py', '3.9.0'), + ('PyYAML', '6.0'), + ('phonopy', '2.20.0'), + ('ASE', '3.22.1'), + ('PyTables', '3.8.0'), + ('nglview', '3.1.2'), + ('tqdm', '4.66.1'), + ('molmod', '1.4.8'), + ('scikit-learn', '1.3.1'), + ('yaff', '1.6.0'), + ('TAMkin', '1.2.6'), + ('QuickFF', '2.2.7'), + ('plotly.py', '5.16.0'), + ('GitPython', '3.1.40'), + ('dill', '0.3.7'), + ('sympy', '1.12'), + ('pymatgen', '2023.12.18'), + ('Pint', '0.23'), + ('SQLAlchemy', '2.0.25'), +] + +check_ldshared = True +use_pip = True + +exts_list = [ + ('h5io', '0.1.2', { + 'checksums': ['6400543224c489f1cf487be551f892310fa7060fcd4935b84e515efdc1e1fa43'], + }), + ('defusedxml', '0.6.0', { + 'checksums': ['f684034d135af4c6cbb949b8a4d2ed61634515257a67299e5f940fbaa34377f5'], + }), + ('pysqa', '0.1.7', { + 'checksums': ['fdc37e0178649750e7386b4e9b8287693ee2d47559723c11b9ad42afcfc55900'], + }), + ('pyfiglet', '0.8.post1', { + 'checksums': ['c6c2321755d09267b438ec7b936825a4910fec696292139e664ca8670e103639'], + }), + ('mendeleev', '0.14.0', { + 'checksums': ['1a89ccf05c708aebe627c5eb19ff5c6379585a2f9e588e1dcf9b03182fe61f3c'], + }), + ('pyfileindex', '0.0.18', { + 'checksums': ['6d5acf2500f568667aa5273ae57692c2b62facbcaae7c0bbbf21ba3bdd904961'], + }), + ('seekpath', '2.1.0', { + 'checksums': ['31cec579628262e6d4a4c3693fefa70d6ccae1ceeef7c9d10ea3cd48988452c4'], + }), + (name, version, { + 'modulename': False, + 'checksums': ['2e5e3f892b7e49a15443569870aa4ea049951b71fe2ad1ad7f4ac7551d475788'], + }), + ('pyiron_base', '0.6.12', { + 'patches': ['pyiron-0.5.1_fix-pyiron-base-version.patch'], + 'source_urls': ['https://github.com/pyiron/pyiron_base/archive/refs/tags/'], + 'checksums': [ + {'pyiron_base-0.6.12.tar.gz': '7ef8fa8b21724776c1ced3ee1efb8484984234150a7f3da296577f90c63751cb'}, + {'pyiron-0.5.1_fix-pyiron-base-version.patch': + 'a6390dcd366e17361fb71f26c6d3b75835526bdf773d9ef535c02836fe551b31'}, + ], + }), + ('atomistics', '0.1.15', { + 'patches': ['pyiron-0.5.1_fix-atomistics-requirements.patch'], + 'source_urls': ['https://github.com/pyiron/atomistics/archive/refs/tags/'], + 'checksums': [ + {'atomistics-0.1.15.tar.gz': 'e9c505cace0cbeb9ea5ed33799f332f5cc95230a05ba14b646475cff1bdecaee'}, + {'pyiron-0.5.1_fix-atomistics-requirements.patch': + 'deaa57c27be147efc7e4926f6795bfa421280a299fc96de8c0bae342e4770d6c'}, + ], + }), + ('pyiron_atomistics', '0.3.11', { + 'patches': ['pyiron-0.5.1_fix-pyiron-atomistics-version.patch'], + 'source_urls': ['https://github.com/pyiron/pyiron_atomistics/archive/refs/tags/'], + 'checksums': [ + {'pyiron_atomistics-0.3.11.tar.gz': '8c73c452fe60cb808961d22361f9b749488e3d50a8bda7f5c0132aea2f69e00f'}, + {'pyiron-0.5.1_fix-pyiron-atomistics-version.patch': + '5c9b987cb63508f482bff696e252987e10df9b8ee8e860491583c8e547d4568c'}, + ], + }), + ('pylammpsmpi', '0.2.10', { + 'patches': ['pyiron-0.5.1_fix-pylammpsmpi.patch'], + 'source_urls': ['https://github.com/pyiron/pylammpsmpi/archive/refs/tags/'], + 'checksums': [ + {'%(name)s-%(version)s.tar.gz': 'bd5af29a935dacbee743c3cc0bcc799e24e7c2483801f56cb9092a79f016f2ed'}, + {'pyiron-0.5.1_fix-pylammpsmpi.patch': + 'd7cacf8eb73cb43e47526bfa3f98157073c01cd88918f191f87d7e75ab4c7c30'}, + ], + }), + ('pympipool', '0.7.9', { + 'checksums': ['5698181bc5dc9a69595fd00ff6a8ba651b77734ccf00df79ae3aea8aaf32790a'], + }), + ('structuretoolkit', '0.0.15', { + 'checksums': ['1a258a072055d0c20e9d56156afd4481cfc94c2612c1b908de4b274b423cc6e6'], + }), +] + +sanity_pip_check = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1_fix-atomistics-requirements.patch b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1_fix-atomistics-requirements.patch new file mode 100644 index 00000000000..5b47f86d759 --- /dev/null +++ b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1_fix-atomistics-requirements.patch @@ -0,0 +1,17 @@ +Relax requirements of `atomistics`. + +--- 0.5.1/foss-2023a/atomistics/atomistics-atomistics-0.1.15/pyproject.toml.orig 2024-01-09 12:42:59.508409527 +0000 ++++ 0.5.1/foss-2023a/atomistics/atomistics-atomistics-0.1.15/pyproject.toml 2024-01-09 12:43:44.589293464 +0000 +@@ -26,9 +26,9 @@ + ] + dependencies = [ + "ase==3.22.1", +- "numpy==1.26.2", +- "scipy==1.11.4", +- "spglib==2.2.0", ++ "numpy>=1.25.1", ++ "scipy>=1.11.1", ++ "spglib>=2.1.0", + ] + dynamic = ["version"] + diff --git a/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1_fix-pyiron-atomistics-version.patch b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1_fix-pyiron-atomistics-version.patch new file mode 100644 index 00000000000..46ab8c36467 --- /dev/null +++ b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1_fix-pyiron-atomistics-version.patch @@ -0,0 +1,73 @@ +Fixes use of dynamic versioning in pyproject.toml and puts in a specific version instead. + +--- 0.5.1/foss-2023a/pyiron_atomistics/pyiron_atomistics-pyiron_atomistics-0.3.11/pyproject.toml.orig 2024-01-22 10:12:31.768251943 +0000 ++++ 0.5.1/foss-2023a/pyiron_atomistics/pyiron_atomistics-pyiron_atomistics-0.3.11/pyproject.toml 2024-01-22 10:26:21.997455595 +0000 +@@ -26,24 +26,24 @@ + dependencies = [ + "ase==3.22.1", +- "atomistics==0.1.12", +- "defusedxml==0.7.1", +- "h5py==3.10.0", +- "matplotlib==3.8.2", +- "mendeleev==0.14.0", +- "mp-api==0.39.1", +- "numpy==1.26.2", +- "pandas==2.1.3", +- "phonopy==2.21.0", ++ "atomistics>=0.1.12", ++ "defusedxml>=0.6.0", ++ "h5py>=3.9.0", ++ "matplotlib>=3.7.2", ++ "mendeleev>=0.14.0", ++ "mp-api>=0.39.1", ++ "numpy>=1.25.1", ++ "pandas>=2.0.3", ++ "phonopy>=2.20.0", +- "pint==0.22", ++ "pint>=0.22", + "pyiron_base==0.6.12", +- "pylammpsmpi==0.2.9", ++ "pylammpsmpi>=0.2.9", +- "scipy==1.11.4", +- "scikit-learn==1.3.2", +- "seekpath==2.1.0", +- "spglib==2.1.0", ++ "scipy>=1.11.1", ++ "scikit-learn>=1.3.1", ++ "seekpath>=2.1.0", ++ "spglib>=2.1.0", + "structuretoolkit==0.0.15", + ] +-dynamic = ["version"] ++version = '0.3.11' + + [project.urls] + Homepage = "https://pyiron.org" +@@ -55,13 +55,3 @@ + + [tool.setuptools.package-data] + "*" = ["data/*.csv"] +- +-[tool.setuptools.dynamic] +-version = {attr = "pyiron_atomistics.__version__"} +- +-[tool.versioneer] +-VCS = "git" +-style = "pep440-pre" +-versionfile_source = "pyiron_atomistics/_version.py" +-parentdir_prefix = "pyiron_atomistics" +-tag_prefix = "pyiron_atomistics-" + +--- 0.5.1/foss-2023a-Python-3.11.3/pyiron_atomistics/pyiron_atomistics-pyiron_atomistics-0.3.11/setup.py.orig 2023-12-13 17:16:26.902513343 +0000 ++++ 0.5.1/foss-2023a-Python-3.11.3/pyiron_atomistics/pyiron_atomistics-pyiron_atomistics-0.3.111/setup.py 2023-12-13 17:18:56.504736380 +0000 +@@ -3,6 +3,6 @@ + import versioneer + + setup( +- version=versioneer.get_version(), +- cmdclass=versioneer.get_cmdclass(), +-) +\ No newline at end ++ version="0.3.11", ++) ++ diff --git a/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1_fix-pyiron-base-version.patch b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1_fix-pyiron-base-version.patch new file mode 100644 index 00000000000..9efc42afbb9 --- /dev/null +++ b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1_fix-pyiron-base-version.patch @@ -0,0 +1,72 @@ +Fixes use of dynamic versioning in pyproject.toml and puts in a specific version instead. + +--- 0.5.1/foss-2023a-Python-3.11.3/pyiron_base/pyiron_base-pyiron_base-0.6.12/pyproject.toml.orig 2023-12-13 15:51:48.895090935 +0000 ++++ 0.5.1/foss-2023a-Python-3.11.3/pyiron_base/pyiron_base-pyiron_base-0.6.12/pyproject.toml 2023-12-13 15:53:26.626579151 +0000 +@@ -24,23 +24,23 @@ + "Programming Language :: Python :: 3.11", + ] + dependencies = [ +- "dill==0.3.7", +- "gitpython==3.1.40", +- "h5io==0.1.9", +- "h5py==3.10.0", +- "jinja2==3.1.2", +- "numpy==1.26.2", +- "pandas==2.1.3", +- "pint==0.22", +- "psutil==5.9.5", +- "pyfileindex==0.0.18", +- "pysqa==0.1.7", +- "sqlalchemy==2.0.23", +- "tables==3.9.2", +- "tqdm==4.66.1", +- "traitlets==5.14.0", ++ "dill>=0.3.2", ++ "gitpython>=3.1.8", ++ "h5io>=0.1.2", ++ "h5py>=3.9.0", ++ "jinja2>=3.1.2", ++ "numpy>=1.25.1", ++ "pandas>=2.0.3", ++ "pint>=0.22", ++ "psutil>=5.9.5", ++ "pyfileindex>=0.0.18", ++ "pysqa>=0.1.7", ++ "sqlalchemy>=2.0.23", ++ "tables>=3.8.0", ++ "tqdm>=4.66.1", ++ "traitlets>=5.9.0", + ] +-dynamic = ["version"] ++version = "0.6.12" + + [project.urls] + Homepage = "https://github.com/pyiron/pyiron_base" +@@ -53,12 +53,3 @@ + [tool.setuptools.packages.find] + include = ["pyiron_base*"] + +-[tool.setuptools.dynamic] +-version = {attr = "pyiron_base.__version__"} +- +-[tool.versioneer] +-VCS = "git" +-style = "pep440-pre" +-versionfile_source = "pyiron_base/_version.py" +-parentdir_prefix = "pyiron_base" +-tag_prefix = "pyiron_base-" + +--- 0.5.1/foss-2023a-Python-3.11.3/pyiron_base/pyiron_base-pyiron_base-0.6.12/setup.py.orig 2023-12-13 17:16:26.902513343 +0000 ++++ 0.5.1/foss-2023a-Python-3.11.3/pyiron_base/pyiron_base-pyiron_base-0.6.12/setup.py 2023-12-13 17:18:56.504736380 +0000 +@@ -3,6 +3,6 @@ + import versioneer + + setup( +- version=versioneer.get_version(), +- cmdclass=versioneer.get_cmdclass(), +-) +\ No newline at end ++ version="0.6.12", ++) ++ + diff --git a/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1_fix-pylammpsmpi.patch b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1_fix-pylammpsmpi.patch new file mode 100644 index 00000000000..c306bf08da9 --- /dev/null +++ b/easybuild/easyconfigs/p/pyiron/pyiron-0.5.1_fix-pylammpsmpi.patch @@ -0,0 +1,47 @@ +Fix versioning issue and relax requirements. + +--- 0.5.1/foss-2023a/pylammpsmpi/pylammpsmpi-pylammpsmpi-0.2.10/setup.py.orig 2023-12-21 17:27:54.405181324 +0000 ++++ 0.5.1/foss-2023a/pylammpsmpi/pylammpsmpi-pylammpsmpi-0.2.10/setup.py 2023-12-21 17:31:38.136048756 +0000 +@@ -1,8 +1,4 @@ + from setuptools import setup + +-import versioneer ++setup(version='0.2.10') + +-setup( +- version=versioneer.get_version(), +- cmdclass=versioneer.get_cmdclass(), +-) +\ Ingen nyrad vid filslut + +--- 0.5.1/foss-2023a/pylammpsmpi/pylammpsmpi-pylammpsmpi-0.2.10/pyproject.toml.orig 2023-12-21 17:57:36.066162000 +0000 ++++ 0.5.1/foss-2023a/pylammpsmpi/pylammpsmpi-pylammpsmpi-0.2.10/pyproject.toml 2023-12-21 17:58:37.373851635 +0000 +@@ -24,11 +24,11 @@ + "Programming Language :: Python :: 3.11", + ] + dependencies = [ +- "mpi4py==3.1.5", ++ "mpi4py>=3.1.4", + "pympipool==0.7.9", +- "numpy==1.26.2", ++ "numpy>=1.25.1", + ] +-dynamic = ["version"] ++version = '0.2.10' + + [project.urls] + Homepage = "https://github.com/pyiron/pylammpsmpi" +@@ -43,13 +43,3 @@ + + [tool.setuptools.packages.find] + include = ["pylammpsmpi*"] +- +-[tool.setuptools.dynamic] +-version = {attr = "pylammpsmpi.__version__"} +- +-[tool.versioneer] +-VCS = "git" +-style = "pep440-pre" +-versionfile_source = "pylammpsmpi/_version.py" +-parentdir_prefix = "pylammpsmpi" +-tag_prefix = "pylammpsmpi-" diff --git a/easybuild/easyconfigs/p/pyperf/pyperf-2.7.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/pyperf/pyperf-2.7.0-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..0c4a1504248 --- /dev/null +++ b/easybuild/easyconfigs/p/pyperf/pyperf-2.7.0-GCCcore-12.3.0.eb @@ -0,0 +1,35 @@ +easyblock = 'PythonPackage' + +name = 'pyperf' +version = '2.7.0' + +homepage = 'https://github.com/psf/pyperf' +description = "The Python pyperf module is a toolkit to write, run and analyze benchmarks" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['4201c6601032f374e9c900c6d2544a2f5891abedc1a96eec0e7b2338a6247589'] + +builddependencies = [ + ('binutils', '2.40'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('psutil', '5.9.8'), +] + +download_dep_fail = True +use_pip = True + +sanity_check_paths = { + 'files': ['bin/pyperf'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["pyperf --help"] + +sanity_pip_check = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/pyproj/pyproj-3.7.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/p/pyproj/pyproj-3.7.0-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..c76c4f5371b --- /dev/null +++ b/easybuild/easyconfigs/p/pyproj/pyproj-3.7.0-GCCcore-13.3.0.eb @@ -0,0 +1,39 @@ +easyblock = 'PythonPackage' + +name = 'pyproj' +version = '3.7.0' + +homepage = 'https://pyproj4.github.io/pyproj' +description = "Python interface to PROJ4 library for cartographic transformations" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['bf658f4aaf815d9d03c8121650b6f0b8067265c36e31bc6660b98ef144d81813'] + +builddependencies = [ + ('binutils', '2.42'), + ('Cython', '3.0.10'), +] + +dependencies = [ + ('Python', '3.12.3'), + ('Python-bundle-PyPI', '2024.06'), + ('PROJ', '9.4.1'), +] + +download_dep_fail = True +use_pip = True + +preinstallopts = "export PROJ_DIR=$EBROOTPROJ && " + +sanity_check_paths = { + 'files': ['bin/pyproj'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ['pyproj --help'] + +sanity_pip_check = True + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/p/pyro-ppl/pyro-ppl-1.9.0-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/p/pyro-ppl/pyro-ppl-1.9.0-foss-2023a-CUDA-12.1.1.eb new file mode 100644 index 00000000000..4add431b9a3 --- /dev/null +++ b/easybuild/easyconfigs/p/pyro-ppl/pyro-ppl-1.9.0-foss-2023a-CUDA-12.1.1.eb @@ -0,0 +1,47 @@ +# Author: Denis Krišťák (INUITS) + +easyblock = 'PythonBundle' + +name = 'pyro-ppl' +version = '1.9.0' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/pyro-ppl/pyro' +description = "Pyro is a flexible, scalable deep probabilistic programming library built on PyTorch." + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('CUDA', '12.1.1', '', SYSTEM), + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('PyTorch', '2.1.2', versionsuffix), + ('tqdm', '4.66.1'), +] + +use_pip = True + +exts_list = [ + ('opt-einsum', '3.3.0', { + 'source_tmpl': 'opt_einsum-%(version)s.tar.gz', + 'checksums': ['59f6475f77bbc37dcf7cd748519c0ec60722e91e63ca114e68821c0c54a46549'], + }), + ('pyro-api', '0.1.2', { + 'modulename': 'pyroapi', + 'checksums': ['a1b900d9580aa1c2fab3b123ab7ff33413744da7c5f440bd4aadc4d40d14d920'], + }), + (name, version, { + 'modulename': 'pyro', + 'checksums': ['41f4c005159568280fbc511648960a98a2b1a410027d8bd0a43220ac9b102cdf'], + }), +] + +sanity_pip_check = True + +sanity_check_commands = [ + "python -c 'from pyroapi import distributions as dist'", + "python -c 'from pyroapi import infer, ops, optim, pyro, pyro_backend'", + "python -c 'from pyro import infer, nn, distributions'", +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/pyro-ppl/pyro-ppl-1.9.0-foss-2023a.eb b/easybuild/easyconfigs/p/pyro-ppl/pyro-ppl-1.9.0-foss-2023a.eb new file mode 100644 index 00000000000..28ed959d3b2 --- /dev/null +++ b/easybuild/easyconfigs/p/pyro-ppl/pyro-ppl-1.9.0-foss-2023a.eb @@ -0,0 +1,45 @@ +# Author: Denis Krišťák (INUITS) + +easyblock = 'PythonBundle' + +name = 'pyro-ppl' +version = '1.9.0' + +homepage = 'https://github.com/pyro-ppl/pyro' +description = "Pyro is a flexible, scalable deep probabilistic programming library built on PyTorch." + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('PyTorch', '2.1.2'), + ('tqdm', '4.66.1'), +] + +use_pip = True + +exts_list = [ + ('opt-einsum', '3.3.0', { + 'source_tmpl': 'opt_einsum-%(version)s.tar.gz', + 'checksums': ['59f6475f77bbc37dcf7cd748519c0ec60722e91e63ca114e68821c0c54a46549'], + }), + ('pyro-api', '0.1.2', { + 'modulename': 'pyroapi', + 'checksums': ['a1b900d9580aa1c2fab3b123ab7ff33413744da7c5f440bd4aadc4d40d14d920'], + }), + (name, version, { + 'modulename': 'pyro', + 'checksums': ['41f4c005159568280fbc511648960a98a2b1a410027d8bd0a43220ac9b102cdf'], + }), +] + +sanity_pip_check = True + +sanity_check_commands = [ + "python -c 'from pyroapi import distributions as dist'", + "python -c 'from pyroapi import infer, ops, optim, pyro, pyro_backend'", + "python -c 'from pyro import infer, nn, distributions'", +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/pyseer/pyseer-1.3.12-foss-2023a.eb b/easybuild/easyconfigs/p/pyseer/pyseer-1.3.12-foss-2023a.eb new file mode 100644 index 00000000000..16cf7b1a00c --- /dev/null +++ b/easybuild/easyconfigs/p/pyseer/pyseer-1.3.12-foss-2023a.eb @@ -0,0 +1,56 @@ +# Borrowed from the BEAR RSG team, University of Birmingham +# Update: Petr Král (INUITS) +easyblock = 'PythonBundle' + +name = 'pyseer' +version = '1.3.12' + +homepage = 'https://github.com/mgalardini/pyseer' +description = """pyseer was first written a python reimplementation of seer, which was written in C++. pyseer uses + linear models with fixed or mixed effects to estimate the effect of genetic variation in a bacterial population + on a phenotype of interest, while accounting for potentially very strong confounding population structure. + This allows for genome-wide association studies (GWAS) to be performed in clonal organisms + such as bacteria and viruses.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('pybedtools', '0.9.1'), + ('statsmodels', '0.14.1'), + ('scikit-learn', '1.3.1'), + ('Pysam', '0.22.0'), + ('DendroPy', '4.6.1'), + ('matplotlib', '3.7.2'), + ('tqdm', '4.66.1'), +] + +use_pip = True + +exts_list = [ + ('glmnet-python', '1.0.2', { + 'source_urls': ['https://github.com/johnlees/glmnet_python/archive'], + 'sources': ['v%(version)s.tar.gz'], + 'checksums': ['7a5550514140dabbd27ad4eb1c04db64199d9bb89541e088d9bb162570205e76'], + }), + (name, version, { + 'source_urls': ['https://github.com/mgalardini/pyseer/archive'], + 'sources': ['%(version)s.tar.gz'], + 'checksums': ['aa07fc1bd5346d02123ff36ba64a1ff4dbbb85a21c37a12f35ad7d5be7e21e9c'], + }), +] + +sanity_check_paths = { + 'files': ['bin/pyseer', 'bin/square_mash'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + '%(namelower)s --help', + 'square_mash --help', +] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/pyspoa/pyspoa-0.2.1-GCC-13.2.0.eb b/easybuild/easyconfigs/p/pyspoa/pyspoa-0.2.1-GCC-13.2.0.eb new file mode 100644 index 00000000000..127ab6861d9 --- /dev/null +++ b/easybuild/easyconfigs/p/pyspoa/pyspoa-0.2.1-GCC-13.2.0.eb @@ -0,0 +1,62 @@ +easyblock = 'PythonPackage' + +name = 'pyspoa' +version = '0.2.1' + +local_cereal_version = '1.3.2' + +homepage = 'https://github.com/nanoporetech/pyspoa' +description = "Python bindings to spoa." + +toolchain = {'name': 'GCC', 'version': '13.2.0'} + +toolchainopts = {'extra_cflags': "-fpermissive"} + +sources = [ + { + 'filename': '%(name)s-%(version)s.tar.gz', + 'git_config': { + 'url': 'https://github.com/nanoporetech', + 'repo_name': 'pyspoa', + 'tag': 'v%(version)s', + 'recursive': True, + 'keep_git_dir': True, + } + }, + { + 'source_urls': ['https://github.com/USCiLab/cereal/archive/'], + 'download_filename': 'v%s.tar.gz' % local_cereal_version, + 'filename': 'cereal-%s.tar.gz' % local_cereal_version, + }, +] + +patches = ['pyspoa-%(version)s_use-spoa-dep.patch'] + +checksums = [ + None, + '16a7ad9b31ba5880dac55d62b5d6f243c3ebc8d46a3514149e56b5e7ea81f85f', + 'dffd946e3b36e4872846fe983d287f992b5bf177798e11141bf0d645cfc0664d', +] + +builddependencies = [('CMake', '3.27.6')] + +dependencies = [ + ('Python', '3.11.5'), + ('pybind11', '2.11.1'), + ('spoa', '4.1.0'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +preinstallopts = "mkdir -p src/vendor/cereal && ln -s %(builddir)s/cereal-*/include src/vendor/cereal/include && " +# strip out cmake requirements, since we provide that as proper dependency +preinstallopts += "sed -i 's/.cmake==[0-9.]*.//g' setup.py && " +preinstallopts += "export libspoa=$EBROOTSPOA/lib/libspoa.a && " + +options = {'modulename': 'spoa'} + +sanity_check_commands = ["cd %(builddir)s/*/tests && python test_pyspoa.py"] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/pystencils/pystencils-1.3.4-gfbf-2023b.eb b/easybuild/easyconfigs/p/pystencils/pystencils-1.3.4-gfbf-2023b.eb new file mode 100644 index 00000000000..2c08948afa0 --- /dev/null +++ b/easybuild/easyconfigs/p/pystencils/pystencils-1.3.4-gfbf-2023b.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonBundle' + +name = 'pystencils' +version = '1.3.4' + +homepage = 'https://pycodegen.pages.i10git.cs.fau.de/pystencils' +description = "pystencils uses sympy to define stencil operations, that can be executed on numpy arrays" + +toolchain = {'name': 'gfbf', 'version': '2023b'} + +dependencies = [ + ('Python', '3.11.5'), + ('SciPy-bundle', '2023.11'), + ('sympy', '1.12'), + ('PyYAML', '6.0.1'), +] + +use_pip = True + +exts_list = [ + (name, version, { + 'checksums': ['d8c502ad27d5e270c5048558a3c8b316beef8d7ac6a8a9f72b78632a6e0ca317'], + # remove strict version requirement for sympy + 'preinstallopts': """sed -i 's/"sympy[^"]*"/"sympy"/g' pyproject.toml && """, + }), +] + +sanity_pip_check = True + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/p/pysteps/pysteps-1.10.0-foss-2023a.eb b/easybuild/easyconfigs/p/pysteps/pysteps-1.10.0-foss-2023a.eb new file mode 100644 index 00000000000..f60f3a18e87 --- /dev/null +++ b/easybuild/easyconfigs/p/pysteps/pysteps-1.10.0-foss-2023a.eb @@ -0,0 +1,41 @@ +easyblock = 'PythonBundle' + +name = 'pysteps' +version = '1.10.0' + +homepage = 'https://pysteps.github.io/' +description = """Pysteps is an open-source and community-driven Python library for probabilistic +precipitation nowcasting, i.e. short-term ensemble prediction systems.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('OpenCV', '4.8.1', '-contrib'), + ('Pillow', '10.0.0'), + ('pyproj', '3.6.0'), + ('matplotlib', '3.7.2'), + ('netcdf4-python', '1.6.4'), + ('dask', '2023.9.2'), # needed by pysteps-nwp-importers + ('xarray', '2023.9.0'), # needed by pysteps-nwp-importers +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('jsmin', '3.0.1', { + 'checksums': ['c0959a121ef94542e807a674142606f7e90214a2b3d1eb17300244bbb5cc2bfc'], + }), + (name, version, { + 'checksums': ['28b51d61c3411fccf5c5f80792b9effe8f92a515e5984ffc5ad9ce810603a62d'], + }), + ('pysteps-nwp-importers', '20240624', { + 'source_urls': ['https://github.com/pySTEPS/pysteps-nwp-importers/archive/'], + 'sources': [{'download_filename': '73b3573.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['d5835023c739056aa04c6938e256e6ba24ed9585a252cdf3f10b6dc0b92f0730'], + }), +] + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/p/pytest-flakefinder/pytest-flakefinder-1.1.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/p/pytest-flakefinder/pytest-flakefinder-1.1.0-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..7a512df4e25 --- /dev/null +++ b/easybuild/easyconfigs/p/pytest-flakefinder/pytest-flakefinder-1.1.0-GCCcore-13.3.0.eb @@ -0,0 +1,24 @@ +easyblock = 'PythonPackage' + +name = 'pytest-flakefinder' +version = '1.1.0' + +homepage = 'https://github.com/dropbox/pytest-flakefinder' +description = "Runs tests multiple times to expose flakiness." + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +builddependencies = [('binutils', '2.42')] +dependencies = [ + ('Python', '3.12.3'), + ('Python-bundle-PyPI', '2024.06'), +] + +sources = [SOURCE_TAR_GZ] +checksums = ['e2412a1920bdb8e7908783b20b3d57e9dad590cc39a93e8596ffdd493b403e0e'] + +use_pip = True +sanity_pip_check = True +download_dep_fail = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/pytest-workflow/pytest-workflow-2.1.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/p/pytest-workflow/pytest-workflow-2.1.0-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..25aaab957da --- /dev/null +++ b/easybuild/easyconfigs/p/pytest-workflow/pytest-workflow-2.1.0-GCCcore-13.3.0.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonBundle' + +name = 'pytest-workflow' +version = '2.1.0' + +homepage = 'https://github.com/LUMC/pytest-workflow' +description = """Configure workflow/pipeline tests using yaml files. + +pytest-workflow is a workflow-system agnostic testing framework that aims to make pipeline/workflow testing easy by +using YAML files for the test configuration. +Whether you write your pipelines in WDL, snakemake, nextflow, bash or any other workflow framework, +pytest-workflow makes testing easy. +pytest-workflow is build on top of the pytest test framework.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +builddependencies = [('binutils', '2.42')] +dependencies = [ + ('Python', '3.12.3'), + ('PyYAML', '6.0.2'), + ('python-isal', '1.7.0'), + ('zlib-ng', '2.2.1'), +] + +sanity_pip_check = True +use_pip = True + +exts_list = [ + ('zstandard', '0.23.0', {'checksums': ['b2d8c62d08e7255f68f7a740bae85b3c9b8e5466baa9cbf7f57f1cde0ac6bc09']}), + ('xopen', '2.0.2', {'checksums': ['f19d83de470f5a81725df0140180ec71d198311a1d7dad48f5467b4ad5df6154']}), + (name, version, {'checksums': ['dc86ad9a5f94482aec14926788f6b78b428be68ee0428cbca22f89b6326f8b7a']}), +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/pytest-xdist/pytest-xdist-3.6.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/p/pytest-xdist/pytest-xdist-3.6.1-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..254e2c6a8b9 --- /dev/null +++ b/easybuild/easyconfigs/p/pytest-xdist/pytest-xdist-3.6.1-GCCcore-13.3.0.eb @@ -0,0 +1,64 @@ +easyblock = 'PythonBundle' + +name = 'pytest-xdist' +version = '3.6.1' + +homepage = 'https://github.com/pytest-dev/pytest-xdist' +description = """xdist: pytest distributed testing plugin + +The pytest-xdist plugin extends pytest with some unique test execution modes: + + * test run parallelization: if you have multiple CPUs or hosts you + can use those for a combined test run. This allows to speed up + development or to use special resources of remote machines. + + * --looponfail: run your tests repeatedly in a subprocess. After + each run pytest waits until a file in your project changes and + then re-runs the previously failing tests. This is repeated + until all tests pass after which again a full run is + performed. + + * Multi-Platform coverage: you can specify different Python + interpreters or different platforms and run tests in parallel on + all of them. + +Before running tests remotely, pytest efficiently “rsyncs” your +program source code to the remote place. All test results are reported +back and displayed to your local terminal. You may specify different +Python versions and interpreters.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +builddependencies = [ + ('binutils', '2.42'), + ('hatchling', '1.24.2'), +] + +dependencies = [ + ('Python', '3.12.3'), + ('pytest', '8.3.3'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('apipkg', '3.0.2', { + 'checksums': ['c7aa61a4f82697fdaa667e70af1505acf1f7428b1c27b891d204ba7a8a3c5e0d'], + }), + ('execnet', '2.1.1', { + 'checksums': ['5189b52c6121c24feae288166ab41b32549c7e2348652736540b9e6e7d4e72e3'], + }), + (name, version, { + 'modulename': 'xdist', + 'source_tmpl': 'pytest_xdist-%(version)s.tar.gz', + 'checksums': ['ead156a4db231eec769737f57668ef58a2084a34b2e55c4a8fa20d861107300d'], + }), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/pytest/pytest-4.6.11-GCC-12.3.0-Python-2.7.18.eb b/easybuild/easyconfigs/p/pytest/pytest-4.6.11-GCC-12.3.0-Python-2.7.18.eb new file mode 100644 index 00000000000..470efa5624e --- /dev/null +++ b/easybuild/easyconfigs/p/pytest/pytest-4.6.11-GCC-12.3.0-Python-2.7.18.eb @@ -0,0 +1,102 @@ +easyblock = 'PythonBundle' + +name = 'pytest' +version = '4.6.11' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://pytest.org' +description = """pytest: simple powerful testing with Python""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +dependencies = [('Python', '2.7.18')] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('contextlib2', '0.6.0.post1', { + 'source_tmpl': SOURCE_WHL, + 'checksums': ['3355078a159fbb44ee60ea80abd0d87b80b78c248643b49aa6d94673b413609b'], + }), + ('zipp', '1.2.0', { + 'source_tmpl': SOURCE_WHL, + 'checksums': ['e0d9e63797e483a30d27e09fffd308c59a700d365ec34e93cc100844168bf921'], + }), + ('importlib_metadata', '2.1.3', { + 'source_tmpl': SOURCE_WHL, + 'checksums': ['52e65a0856f9ba7ea8f2c4ced253fb6c88d1a8c352cb1e916cff4eb17d5a693d'], + }), + ('typing', '3.10.0.0', { + 'source_tmpl': SOURCE_PY2_WHL, + 'checksums': ['c7219ef20c5fbf413b4567092adfc46fa6203cb8454eda33c3fc1afe1398a308'], + }), + ('py', '1.11.0', { + 'source_tmpl': SOURCE_WHL, + 'checksums': ['607c53218732647dff4acdfcd50cb62615cedf612e72d1724fb1a0cc6405b378'], + }), + ('attrs', '21.4.0', { + 'modulename': 'attr', + 'source_tmpl': SOURCE_WHL, + 'checksums': ['2d27e3784d7a565d36ab851fe94887c5eccd6a463168875832a1be79c82828b4'], + }), + ('pluggy', '0.13.1', { + 'source_tmpl': SOURCE_WHL, + 'checksums': ['966c145cd83c96502c3c3868f50408687b38434af77734af1e9ca461a4081d2d'], + }), + ('atomicwrites', '1.4.1', { + 'checksums': ['81b2c9071a49367a7f770170e5eec8cb66567cfbbc8c73d20ce5ca4a8d71cf11'], + }), + ('more_itertools', '5.0.0', { + 'source_tmpl': SOURCE_PY2_WHL, + 'checksums': ['c0a5785b1109a6bd7fac76d6837fd1feca158e54e521ccd2ae8bfe393cc9d4fc'], + }), + ('scandir', '1.10.0', { + 'checksums': ['4d4631f6062e658e9007ab3149a9b914f3548cb38bfb021c64f39a025ce578ae'], + }), + ('pathlib2', '2.3.7.post1', { + 'source_tmpl': SOURCE_WHL, + 'checksums': ['5266a0fd000452f1b3467d782f079a4343c63aaa119221fbdc4e39577489ca5b'], + }), + ('six', '1.16.0', { + 'source_tmpl': SOURCE_WHL, + 'checksums': ['8abb2f1d86890a2dfb989f9a77cfcfd3e47c2a354b01111771326f8aa26e0254'], + }), + ('funcsigs', '1.0.2', { + 'source_tmpl': SOURCE_WHL, + 'checksums': ['330cc27ccbf7f1e992e69fef78261dc7c6569012cf397db8d3de0234e6c937ca'], + }), + ('configparser', '4.0.2', { + 'source_tmpl': SOURCE_WHL, + 'checksums': ['254c1d9c79f60c45dfde850850883d5aaa7f19a23f13561243a050d5a7c3fe4c'], + }), + ('pyparsing', '2.4.7', { + 'source_tmpl': SOURCE_WHL, + 'checksums': ['ef9d7589ef3c200abe66653d3f1ab1033c3c419ae9b9bdb1240a85b024efc88b'], + }), + ('packaging', '20.9', { + 'source_tmpl': SOURCE_WHL, + 'checksums': ['67714da7f7bc052e064859c05c595155bd1ee9f69f76557e21f051443c20947a'], + }), + ('backports.functools_lru_cache', '1.6.6', { + 'source_tmpl': SOURCE_WHL, + 'checksums': ['77e27d0ffbb463904bdd5ef8b44363f6cd5ef503e664b3f599a3bf5843ed37cf'], + }), + ('wcwidth', '0.2.13', { + 'source_tmpl': SOURCE_WHL, + 'checksums': ['3da69048e4540d84af32131829ff948f1e022c1c6bdb8d6102117aac784f6859'], + }), + (name, version, { + 'source_tmpl': SOURCE_WHL, + 'checksums': ['a00a7d79cbbdfa9d21e7d0298392a8dd4123316bfac545075e6f8f24c94d8c97'], + }), +] + +sanity_check_paths = { + 'files': ['bin/pytest'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ['pytest --help'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/pytest/pytest-7.4.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/pytest/pytest-7.4.2-GCCcore-12.3.0.eb index 9d0b6f0c25d..45ab5fae484 100644 --- a/easybuild/easyconfigs/p/pytest/pytest-7.4.2-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/p/pytest/pytest-7.4.2-GCCcore-12.3.0.eb @@ -13,11 +13,12 @@ toolchain = {'name': 'GCCcore', 'version': '12.3.0'} builddependencies = [ ('binutils', '2.40'), ('hatchling', '1.18.0'), + ('flit', '3.9.0'), ] dependencies = [ ('Python', '3.11.3'), - ('Python-bundle-PyPI', '2023.06'), + ('hypothesis', '6.82.0'), ] use_pip = True @@ -39,15 +40,14 @@ _skip_tests = [ _ignore_tests = ' --ignore='.join(_skip_tests) exts_list = [ - ('setuptools-scm', '8.0.4', { - 'checksums': ['b5f43ff6800669595193fd09891564ee9d1d7dcb196cab4b2506d53a2e1c95c7'], + ('iniconfig', '2.0.0', { + 'checksums': ['2d91e135bf72d31a410b17c16da610a82cb55f6b0477d1a902134b24a455b8b3'], }), - ('flit-core', '3.9.0', { - 'source_tmpl': 'flit_core-%(version)s.tar.gz', - 'checksums': ['72ad266176c4a3fcfab5f2930d76896059851240570ce9a98733b658cb786eba'], + ('exceptiongroup', '1.1.1', { + 'checksums': ['d484c3090ba2889ae2928419117447a14daf3c1231d5e30d0aae34f354f01785'], }), - ('hypothesis', '6.88.1', { - 'checksums': ['f4c2c004b9ec3e0e25332ad2cb6b91eba477a855557a7b5c6e79068809ff8b51'], + ('pluggy', '1.2.0', { + 'checksums': ['d12f0c4b579b15f5e054301bb226ee85eeeba08ffec228092f8defbaa3a4c4b3'], }), ('elementpath', '4.1.5', { 'checksums': ['c2d6dc524b29ef751ecfc416b0627668119d8812441c555d7471da41d4bacb8d'], diff --git a/easybuild/easyconfigs/p/pytest/pytest-8.3.3-GCCcore-13.3.0.eb b/easybuild/easyconfigs/p/pytest/pytest-8.3.3-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..0701b7af348 --- /dev/null +++ b/easybuild/easyconfigs/p/pytest/pytest-8.3.3-GCCcore-13.3.0.eb @@ -0,0 +1,72 @@ +easyblock = 'PythonBundle' + +name = 'pytest' +version = '8.3.3' + +homepage = 'https://docs.pytest.org/en/latest/' +description = """The pytest framework makes it easy to write small, +readable tests, and can scale to support complex functional testing for +applications and libraries.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +builddependencies = [ + ('binutils', '2.42'), + ('hatchling', '1.24.2'), +] + +dependencies = [ + ('Python', '3.12.3'), + ('Python-bundle-PyPI', '2024.06'), +] + +use_pip = True + +exts_default_options = {'source_urls': [PYPI_LOWER_SOURCE]} + +# Note! Some of the file system related tests may fail on shared file systems. +# Notably TestPOSIXLocalPath.test_copy_stat_file, TestPOSIXLocalPath.test_copy_stat_dir +# and test_source_mtime_long_long are known to fail on GPFS +# Build with buildpath and tmpdir set to a local file system to avoid this +# or use --ignore-test-failures +_skip_tests = [ + 'testing/io/test_terminalwriter.py', + 'testing/test_terminal.py', + 'testing/test_debugging.py', + 'testing/test_config.py', + 'testing/test_helpconfig.py', +] +_ignore_tests = ' --ignore='.join(_skip_tests) + +exts_list = [ + ('setuptools-scm', '8.1.0', { + 'source_tmpl': 'setuptools_scm-%(version)s.tar.gz', + 'checksums': ['42dea1b65771cba93b7a515d65a65d8246e560768a66b9106a592c8e7f26c8a7'], + }), + ('flit-core', '3.10.1', { + 'source_tmpl': 'flit_core-%(version)s.tar.gz', + 'checksums': ['66e5b87874a0d6e39691f0e22f09306736b633548670ad3c09ec9db03c5662f7'], + }), + ('hypothesis', '6.119.0', { + 'checksums': ['ca441c6ef55d17f27f642fa08657e80f9c13d9da7ae191c8ad58fbc2f16acd1b'], + }), + ('elementpath', '4.6.0', { + 'checksums': ['ba46bf07f66774927727ade55022b6c435fac06b2523cb3cd7689a1884d33468'], + }), + ('xmlschema', '3.4.3', { + 'checksums': ['0c638dac81c7d6c9da9a8d7544402c48cffe7ee0e13cc47fc0c18794d1395dfb'], + }), + (name, version, { + 'checksums': ['70b98107bd648308a7952b06e6ca9a50bc660be218d53c257cc1fc94fda10181'], + }), +] + +sanity_check_commands = [ + "python -c 'import pytest'", + 'cd %%(builddir)s/%%(name)s/%%(name)s-%%(version)s && %%(installdir)s/bin/pytest --ignore=%s testing' + % _ignore_tests, +] + +sanity_pip_check = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/python-blosc/python-blosc-1.11.0-foss-2023a.eb b/easybuild/easyconfigs/p/python-blosc/python-blosc-1.11.0-foss-2023a.eb new file mode 100644 index 00000000000..3a8083cc0d5 --- /dev/null +++ b/easybuild/easyconfigs/p/python-blosc/python-blosc-1.11.0-foss-2023a.eb @@ -0,0 +1,36 @@ +easyblock = 'PythonBundle' + +name = 'python-blosc' +version = '1.11.0' + +homepage = 'https://github.com/Blosc/python-blosc/' +description = "A Python wrapper for the extremely fast Blosc compression library." + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [ + ('scikit-build', '0.17.6'), + ('CMake', '3.26.3'), +] +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('Blosc', '1.21.5'), +] + +use_pip = True +sanity_pip_check = True + +local_preinstallopts = 'export USE_SYSTEM_BLOSC=1 && ' +local_preinstallopts += 'export Blosc_ROOT=$EBROOTBLOSC && ' + +exts_list = [ + ('blosc', version, { + 'preinstallopts': local_preinstallopts, + 'checksums': ['c985b8f435dbc49b190fe88947539ed710ad0e9aaaf83778acc506a71ada7bd2'], + }), +] + +sanity_check_commands = ["python -m blosc.test"] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/python-elf/python-elf-0.5.1-foss-2023a.eb b/easybuild/easyconfigs/p/python-elf/python-elf-0.5.1-foss-2023a.eb new file mode 100644 index 00000000000..c3fe23a272a --- /dev/null +++ b/easybuild/easyconfigs/p/python-elf/python-elf-0.5.1-foss-2023a.eb @@ -0,0 +1,72 @@ +easyblock = 'PythonBundle' + +name = 'python-elf' +version = '0.5.1' + +homepage = 'https://github.com/constantinpape/elf' +description = "Utils and convenience functions for large-scale bio-image analysis." + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [ + ('scikit-build', '0.17.6'), + ('CMake', '3.26.3'), +] +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('imageio', '2.33.1'), + ('scikit-image', '0.22.0'), + ('scikit-learn', '1.3.1'), + ('h5py', '3.9.0'), + ('zarr', '2.17.1'), + ('mrcfile', '1.5.0'), + ('numba', '0.58.1'), + ('tqdm', '4.66.1'), + ('vigra', '1.11.2'), + ('python-blosc', '1.11.0'), + ('openpyxl', '3.1.2'), + ('nifty', '1.2.1'), + ('z5py', '2.0.17'), + ('affogato', '0.3.3'), + ('napari', '0.4.18'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('nose2', '0.14.1', { + 'checksums': ['7f8f03a21c9de2c33015933afcef72bf8e4a2d5dfec3b40092287de6e41b093a'], + }), + ('intern', '1.4.1', { + 'checksums': ['7cdc6caa66716760f93dbbadaa67cc8a03866d6c5f33a6a3285cb9e5f4994315'], + }), + ('skan', '0.11.1', { + 'checksums': ['d5439c17fbf5f86386a7548acb6ab11482961164a6284047b9bdc6652a0d1faf'], + }), + (name, version, { + 'modulename': 'elf', + 'source_urls': ['https://github.com/constantinpape/elf/archive/'], + 'sources': ['%(version)s.tar.gz'], + 'checksums': ['29c542dfb953a1975e2d45f72c84b8f8a2f79fcb0cb2d855dae5493cadbbaa9d'], + }), +] + +sanity_check_commands = [ + "python -c 'import elf.segmentation.multicut'", + "python -c 'import elf.segmentation.features'", + "python -c 'import elf.segmentation.embeddings'", + "python -c 'from elf.segmentation.mutex_watershed import mutex_watershed_clustering'", + "python -c 'from elf.segmentation.utils import load_mutex_watershed_problem'", + "python -c 'import elf.htm'", + "python -c 'from elf.parallel.label import label'", + "python -c 'from elf.evaluation import rand_index'", + "python -c 'from elf.io import open_file'", + "python -c 'from elf.visualisation import visualise_edges'", + "python -c 'import elf.tracking.tracking_utils'", + "python -c 'import elf.transformation'", + "python -c 'import elf.util'", +] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/python-igraph/python-igraph-0.10.6-foss-2022b.eb b/easybuild/easyconfigs/p/python-igraph/python-igraph-0.10.6-foss-2022b.eb index 01e1aa2d9c6..3b61ec3f869 100644 --- a/easybuild/easyconfigs/p/python-igraph/python-igraph-0.10.6-foss-2022b.eb +++ b/easybuild/easyconfigs/p/python-igraph/python-igraph-0.10.6-foss-2022b.eb @@ -20,6 +20,7 @@ dependencies = [ ('Clang', '16.0.4'), ('libxml2', '2.10.3'), ('zlib', '1.2.12'), + ('cairo', '1.17.4'), ] use_pip = True diff --git a/easybuild/easyconfigs/p/python-isal/python-isal-1.7.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/p/python-isal/python-isal-1.7.0-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..96885969511 --- /dev/null +++ b/easybuild/easyconfigs/p/python-isal/python-isal-1.7.0-GCCcore-13.3.0.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonPackage' + +name = 'python-isal' +version = '1.7.0' + +homepage = 'https://github.com/pycompression/python-isal' +description = """Faster zlib and gzip compatible compression and decompression + by providing python bindings for the isa-l library. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +builddependencies = [ + ('binutils', '2.42'), + ('versioningit', '3.1.2'), +] +dependencies = [ + ('Python', '3.12.3'), + ('ISA-L', '2.31.0'), +] + +source_urls = [PYPI_SOURCE.replace('%(name)s', 'isal')] +sources = ['isal-%(version)s.tar.gz'] +checksums = ['9eb9457ed27fd0a8a7b403a5f4f9e6c8d1a44c2ca28ecd2f2bf3aed90b0a74bf'] + +download_dep_fail = True +sanity_pip_check = True +use_pip = True + +preinstallopts = 'PYTHON_ISAL_LINK_DYNAMIC=true' + +options = {'modulename': 'isal'} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/python-libsbml/python-libsbml-5.20.2-foss-2021b.eb b/easybuild/easyconfigs/p/python-libsbml/python-libsbml-5.20.2-foss-2021b.eb new file mode 100644 index 00000000000..f0bd3d688c2 --- /dev/null +++ b/easybuild/easyconfigs/p/python-libsbml/python-libsbml-5.20.2-foss-2021b.eb @@ -0,0 +1,44 @@ +# This is a contribution from SIB Swiss Institute of Bioinformatics +# Homepage: https://www.sib.swiss/research-infrastructure/competence-centers/vital-it +# Authors: Sebastien Moretti +# Update: Pavel Tománek (INUITS) + +easyblock = 'PythonBundle' + +name = 'python-libsbml' +version = '5.20.2' + +homepage = 'https://sbml.org/' +description = """LibSBML Python API.""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +builddependencies = [ + ('binutils', '2.37'), + ('CMake', '3.21.1'), + ('make', '4.3'), + ('Check', '0.15.2'), + ('SWIG', '4.0.2'), + ('expat', '2.4.1'), + ('bzip2', '1.0.8'), + ('zlib', '1.2.11'), +] + +dependencies = [ + ('Python', '3.9.6'), + ('libxml2', '2.9.10'), + ('libxslt', '1.1.34'), +] + +use_pip = True + +exts_list = [ + (name, version, { + 'modulename': 'libsbml', + 'checksums': ['0af5cbff68c9b52bac4bd7bb261f93a60832dc8cb31dafc90d3aff51467935b7'], + }), +] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/python-louvain/python-louvain-0.16-foss-2022b.eb b/easybuild/easyconfigs/p/python-louvain/python-louvain-0.16-foss-2022b.eb new file mode 100644 index 00000000000..5c6085a41e6 --- /dev/null +++ b/easybuild/easyconfigs/p/python-louvain/python-louvain-0.16-foss-2022b.eb @@ -0,0 +1,25 @@ +easyblock = 'PythonPackage' + +name = 'python-louvain' +version = '0.16' + +homepage = 'https://pypi.org/project/python-louvain' +description = "Louvain algorithm for community detection" + +toolchain = {'name': 'foss', 'version': '2022b'} + +sources = [SOURCE_TAR_GZ] +checksums = ['b7ba2df5002fd28d3ee789a49532baad11fe648e4f2117cf0798e7520a1da56b'] + +dependencies = [ + ('Python', '3.10.8'), + ('networkx', '3.0'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +options = {'modulename': 'community'} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/python-louvain/python-louvain-0.16-foss-2023a.eb b/easybuild/easyconfigs/p/python-louvain/python-louvain-0.16-foss-2023a.eb new file mode 100644 index 00000000000..6f730914bc2 --- /dev/null +++ b/easybuild/easyconfigs/p/python-louvain/python-louvain-0.16-foss-2023a.eb @@ -0,0 +1,25 @@ +easyblock = 'PythonPackage' + +name = 'python-louvain' +version = '0.16' + +homepage = 'https://pypi.org/project/python-louvain' +description = "Louvain algorithm for community detection" + +toolchain = {'name': 'foss', 'version': '2023a'} + +sources = [SOURCE_TAR_GZ] +checksums = ['b7ba2df5002fd28d3ee789a49532baad11fe648e4f2117cf0798e7520a1da56b'] + +dependencies = [ + ('Python', '3.11.3'), + ('networkx', '3.1'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +options = {'modulename': 'community'} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/python-parasail/python-parasail-1.3.4-foss-2023b.eb b/easybuild/easyconfigs/p/python-parasail/python-parasail-1.3.4-foss-2023b.eb new file mode 100644 index 00000000000..46bbb77dda9 --- /dev/null +++ b/easybuild/easyconfigs/p/python-parasail/python-parasail-1.3.4-foss-2023b.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonPackage' + +name = 'python-parasail' +version = '1.3.4' + +homepage = 'https://github.com/jeffdaily/parasail-python' +description = "Python Bindings for the Parasail C Library" + +toolchain = {'name': 'foss', 'version': '2023b'} + +sources = ['parasail-%(version)s.tar.gz'] +checksums = ['d6a7035dfae3ef5aafdd7e6915711214c22b572ea059fa69d9d7ecbfb9b61b0f'] + +builddependencies = [ + ('parasail', '2.6.2'), +] + +dependencies = [ + ('Python', '3.11.5'), + ('SciPy-bundle', '2023.11'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +# make sure setup.py finds the parasail library +preinstallopts = "ln -s $EBROOTPARASAIL/lib/libparasail.so parasail/libparasail.%s && " % SHLIB_EXT + +options = {'modulename': 'parasail'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/python-xxhash/python-xxhash-3.4.1-GCCcore-13.2.0.eb b/easybuild/easyconfigs/p/python-xxhash/python-xxhash-3.4.1-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..9f43a8f2759 --- /dev/null +++ b/easybuild/easyconfigs/p/python-xxhash/python-xxhash-3.4.1-GCCcore-13.2.0.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonBundle' + +name = 'python-xxhash' +version = '3.4.1' + +homepage = 'https://github.com/ifduyue/python-xxhash' +description = 'xxhash is a Python binding for the xxHash library by Yann Collet.' + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +builddependencies = [ + ('binutils', '2.40'), +] + +dependencies = [ + ('Python', '3.11.5'), + ('xxHash', '0.8.2'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('xxhash', version, { + 'preinstallopts': 'XXHASH_LINK_SO=1', + 'checksums': ['0379d6cf1ff987cd421609a264ce025e74f346e3e145dd106c0cc2e3ec3f99a9'], + }), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/pyvips/pyvips-2.2.3-GCC-12.3.0.eb b/easybuild/easyconfigs/p/pyvips/pyvips-2.2.3-GCC-12.3.0.eb new file mode 100644 index 00000000000..b690235bd4c --- /dev/null +++ b/easybuild/easyconfigs/p/pyvips/pyvips-2.2.3-GCC-12.3.0.eb @@ -0,0 +1,41 @@ +easyblock = 'PythonPackage' + +name = 'pyvips' +version = '2.2.3' + +homepage = 'https://github.com/libvips/pyvips' +description = """This module wraps the libvips image processing library. +libvips is a demand-driven, horizontally threaded image processing library.""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +github_account = 'libvips' +local_pyshortver = '3.11' # no pyshortver with Python-bundle-PyPI + +source_urls = ['https://github.com/%s/%s/archive/refs/tags/' % (github_account, name)] +sources = ['v%(version)s.tar.gz'] +checksums = ['d70f21a557523404884dd2a192505227e1e6a50ed74315d73c416489b43e9414'] + +dependencies = [ + ('libvips', '8.15.2'), + ('Python-bundle-PyPI', '2023.06'), + ('pyperf', '2.7.0'), + ('pkgconfig', '1.5.5', '-python'), +] + +download_dep_fail = True +use_pip = True + +testinstall = True +runtest = 'pytest' + +sanity_check_paths = { + 'files': ['lib/python%s/site-packages/pyvips/base.py' % local_pyshortver], + 'dirs': ['lib/python%s/site-packages' % local_pyshortver], +} + +sanity_check_commands = ['python -c "import pyvips"'] + +sanity_pip_check = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/q/QCG-PilotJob/QCG-PilotJob-0.14.1-gfbf-2024a.eb b/easybuild/easyconfigs/q/QCG-PilotJob/QCG-PilotJob-0.14.1-gfbf-2024a.eb new file mode 100644 index 00000000000..ae1b1f87ea1 --- /dev/null +++ b/easybuild/easyconfigs/q/QCG-PilotJob/QCG-PilotJob-0.14.1-gfbf-2024a.eb @@ -0,0 +1,70 @@ +easyblock = 'PythonBundle' + +name = 'QCG-PilotJob' +version = '0.14.1' + +homepage = 'https://qcg-pilotjob.readthedocs.org' +description = "A python service for easy execution of many tasks inside a single allocation." + +toolchain = {'name': 'gfbf', 'version': '2024a'} + +dependencies = [ + ('Python', '3.12.3'), + ('SciPy-bundle', '2024.05'), + ('PyZMQ', '26.2.0'), + ('Kaleido', '0.2.1'), + ('statsmodels', '0.14.4'), + ('plotly.py', '5.24.1'), + ('hatchling', '1.24.2'), +] + +use_pip = True + +exts_list = [ + ('patsy', '0.5.6', { + 'checksums': ['95c6d47a7222535f84bff7f63d7303f2e297747a598db89cf5c67f0c0c7d2cdb'], + }), + ('plotly_express', '0.4.1', { + 'checksums': ['ff73a41ce02fb43d1d8e8fa131ef3e6589857349ca216b941b8f3f862bce0278'], + }), + ('prompt_toolkit', '3.0.48', { + 'checksums': ['d6623ab0477a80df74e646bdbc93621143f5caf104206aa29294d53de1a03d90'], + }), + ('trove-classifiers', '2024.10.13', { + 'patches': ['trove-classifiers-2024.10.13_fix_setup.patch'], + 'source_tmpl': 'trove_classifiers-2024.10.13.tar.gz', + 'checksums': [ + {'trove_classifiers-2024.10.13.tar.gz': 'b820fc6f9544543afa15e5d9cfc426cde3b20fc2246dff6f019b835731508cef'}, + {'trove-classifiers-2024.10.13_fix_setup.patch': + 'c90cace5dd0b8a98c60c68681fe453aea97c99038df21c8ad10e11c6816d84af'}, + ], + }), + ('hatch_vcs', '0.4.0', { + 'checksums': ['093810748fe01db0d451fabcf2c1ac2688caefd232d4ede967090b1c1b07d9f7'], + }), + ('setuptools-scm', '8.1.0', { + 'source_tmpl': 'setuptools_scm-8.1.0.tar.gz', + 'checksums': ['42dea1b65771cba93b7a515d65a65d8246e560768a66b9106a592c8e7f26c8a7'], + }), + ('termcolor', '2.5.0', { + 'checksums': ['998d8d27da6d48442e8e1f016119076b690d962507531df4890fcd2db2ef8a6f'], + }), + ('qcg-pilotjob', version, { + 'modulename': 'qcg.pilotjob', + 'checksums': [ + {'qcg-pilotjob-0.14.1.tar.gz': 'f7e162851dce8d94ee424113bc528bfd0d8cc4668e33a3fd9f058ffce9ef409b'}, + ], + }), + ('qcg-pilotjob-cmds', version, { + 'modulename': 'qcg.pilotjob.cmds', + 'checksums': ['58b2b14a278fc255cad0cec308316242b82cb3a08d6e6a517206af1930b09fe3'], + }), + ('qcg-pilotjob-executor-api', version, { + 'modulename': 'qcg.pilotjob.api', + 'checksums': ['66277105b31d5a6ee3cf87d980ce63298d05f466dd102c2ec65ecdb30545e154'], + }), +] + +sanity_pip_check = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/q/QCG-PilotJob/trove-classifiers-2024.10.13_fix_setup.patch b/easybuild/easyconfigs/q/QCG-PilotJob/trove-classifiers-2024.10.13_fix_setup.patch new file mode 100644 index 00000000000..b1a4d34af27 --- /dev/null +++ b/easybuild/easyconfigs/q/QCG-PilotJob/trove-classifiers-2024.10.13_fix_setup.patch @@ -0,0 +1,13 @@ +# What: Put manually typed version in setup.py +# Author: maxim-masterov (SURF) +diff -Nru trove_classifiers-2024.10.13.orig/setup.py trove_classifiers-2024.10.13/setup.py +--- trove_classifiers-2024.10.13.orig/setup.py 2024-10-14 23:32:23.824712949 +0200 ++++ trove_classifiers-2024.10.13/setup.py 2024-10-14 23:33:35.655405794 +0200 +@@ -12,6 +12,7 @@ + setup( + name="trove-classifiers", + description="Canonical source for classifiers on PyPI (pypi.org).", ++ version="2024.10.13", + long_description=long_description, + long_description_content_type="text/markdown", + url="https://github.com/pypa/trove-classifiers", diff --git a/easybuild/easyconfigs/q/QUAST/QUAST-5.2.0-gfbf-2023a.eb b/easybuild/easyconfigs/q/QUAST/QUAST-5.2.0-gfbf-2023a.eb new file mode 100644 index 00000000000..2d46e6cf6b9 --- /dev/null +++ b/easybuild/easyconfigs/q/QUAST/QUAST-5.2.0-gfbf-2023a.eb @@ -0,0 +1,51 @@ +easyblock = 'PythonBundle' + +name = 'QUAST' +version = '5.2.0' + +homepage = 'https://github.com/ablab/quast' +description = """QUAST evaluates genome assemblies by computing various metrics. +It works both with and without reference genomes. The tool accepts multiple +assemblies, thus is suitable for comparison.""" + +toolchain = {'name': 'gfbf', 'version': '2023a'} +toolchainopts = {'pic': True} + +dependencies = [ + ('Python', '3.11.3'), + ('Perl', '5.36.1'), + ('matplotlib', '3.7.2'), + ('Java', '11', '', SYSTEM), + ('Boost', '1.82.0'), +] + +use_pip = True + +github_account = 'ablab' +exts_list = [ + (name, version, { + 'source_urls': [GITHUB_LOWER_SOURCE], + 'sources': ['%(namelower)s_%(version)s.tar.gz'], + 'checksums': ['db903a6e4dd81384687f1c38d47cbe0f51bdf7f6d5e5c0bd30c13796391f4f04'], + 'modulename': 'quast_libs', + }), +] + +postinstallcmds = [ + "cd %(installdir)s/bin && ln -s %(namelower)s.py %(namelower)s", + "cp -a %(builddir)s/QUAST/quast*%(version)s/test_data %(installdir)s/", +] + +sanity_check_paths = { + 'files': ['bin/%(namelower)s', 'bin/%(namelower)s.py', 'bin/meta%(namelower)s.py'], + 'dirs': ['lib/python%(pyshortver)s/site-packages', 'test_data'], +} + +sanity_check_commands = [ + "quast -h", + "mkdir -p %(builddir)s && cp -a %(installdir)s/test_data %(builddir)s && cd %(builddir)s && quast.py --test", +] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/q/QUAST/QUAST-5.2.0-gfbf-2023b.eb b/easybuild/easyconfigs/q/QUAST/QUAST-5.2.0-gfbf-2023b.eb new file mode 100644 index 00000000000..dd6df4bb5ed --- /dev/null +++ b/easybuild/easyconfigs/q/QUAST/QUAST-5.2.0-gfbf-2023b.eb @@ -0,0 +1,51 @@ +easyblock = 'PythonBundle' + +name = 'QUAST' +version = '5.2.0' + +homepage = 'https://github.com/ablab/quast' +description = """QUAST evaluates genome assemblies by computing various metrics. +It works both with and without reference genomes. The tool accepts multiple +assemblies, thus is suitable for comparison.""" + +toolchain = {'name': 'gfbf', 'version': '2023b'} +toolchainopts = {'pic': True} + +dependencies = [ + ('Python', '3.11.5'), + ('Perl', '5.38.0'), + ('matplotlib', '3.8.2'), + ('Java', '11', '', SYSTEM), + ('Boost', '1.83.0'), +] + +use_pip = True + +github_account = 'ablab' +exts_list = [ + (name, version, { + 'source_urls': [GITHUB_LOWER_SOURCE], + 'sources': ['%(namelower)s_%(version)s.tar.gz'], + 'checksums': ['db903a6e4dd81384687f1c38d47cbe0f51bdf7f6d5e5c0bd30c13796391f4f04'], + 'modulename': 'quast_libs', + }), +] + +postinstallcmds = [ + "cd %(installdir)s/bin && ln -s %(namelower)s.py %(namelower)s", + "cp -a %(builddir)s/QUAST/quast*%(version)s/test_data %(installdir)s/", +] + +sanity_check_paths = { + 'files': ['bin/%(namelower)s', 'bin/%(namelower)s.py', 'bin/meta%(namelower)s.py'], + 'dirs': ['lib/python%(pyshortver)s/site-packages', 'test_data'], +} + +sanity_check_commands = [ + "quast -h", + "mkdir -p %(builddir)s && cp -a %(installdir)s/test_data %(builddir)s && cd %(builddir)s && quast.py --test", +] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/q/Qhull/Qhull-2020.2-GCCcore-13.3.0.eb b/easybuild/easyconfigs/q/Qhull/Qhull-2020.2-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..400fecee609 --- /dev/null +++ b/easybuild/easyconfigs/q/Qhull/Qhull-2020.2-GCCcore-13.3.0.eb @@ -0,0 +1,40 @@ +easyblock = 'CMakeMake' + +name = 'Qhull' +version = '2020.2' + +homepage = 'http://www.qhull.org' + +description = """ + Qhull computes the convex hull, Delaunay triangulation, Voronoi diagram, + halfspace intersection about a point, furthest-site Delaunay triangulation, + and furthest-site Voronoi diagram. The source code runs in 2-d, 3-d, 4-d, and + higher dimensions. Qhull implements the Quickhull algorithm for computing the + convex hull. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['http://www.qhull.org/download/'] +sources = ['%(namelower)s-%(version_major)s-src-8.0.2.tgz'] +checksums = ['b5c2d7eb833278881b952c8a52d20179eab87766b00b865000469a45c1838b7e'] + +builddependencies = [ + ('binutils', '2.42'), + ('CMake', '3.29.3'), +] + +sanity_check_paths = { + 'files': ['bin/qhull', 'lib/libqhull_r.%s' % SHLIB_EXT, + 'lib/pkgconfig/qhull_r.pc'], + 'dirs': [], +} + +modextrapaths = { + 'CPATH': ['qhull/include'], +} + +parallel = 1 + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/q/Qt6/Qt6-6.7.2-GCCcore-13.3.0.eb b/easybuild/easyconfigs/q/Qt6/Qt6-6.7.2-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..deb2902a42a --- /dev/null +++ b/easybuild/easyconfigs/q/Qt6/Qt6-6.7.2-GCCcore-13.3.0.eb @@ -0,0 +1,90 @@ +easyblock = 'CMakeNinja' + +name = 'Qt6' +version = '6.7.2' + +homepage = 'https://qt.io/' +description = "Qt is a comprehensive cross-platform C++ application framework." + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +# disabling use of -ftree-vectorize is required to avoid compilation failures on some systems (e.g. Intel Skylake X) +toolchainopts = {'vectorize': False} + +source_urls = [ + 'https://download.qt.io/official_releases/qt/%(version_major_minor)s/%(version)s/single/', + 'https://download.qt.io/archive/qt/%(version_major_minor)s/%(version)s/single/', + 'https://download.qt.io/new_archive/qt/%(version_major_minor)s/%(version)s/single/', +] +sources = ['qt-everywhere-src-%(version)s.tar.xz'] +patches = [ + '%(name)s-6.6.3_fix_OF-Gentoo.patch', + 'Qt6-6.7.2_fix_cpu_features.patch', +] +checksums = [ + {'qt-everywhere-src-6.7.2.tar.xz': '0aaea247db870193c260e8453ae692ca12abc1bd841faa1a6e6c99459968ca8a'}, + {'Qt6-6.6.3_fix_OF-Gentoo.patch': 'd4d4878ac76cb985e45eb3b6e90ba2233f65807d6bd9bbe2b71365b181347b7b'}, + {'Qt6-6.7.2_fix_cpu_features.patch': '3f37e7a4e4ed38cc82037be9504bc644e48bf258555ffff848183142725c9dc8'}, +] + +builddependencies = [ + ('binutils', '2.42'), + ('pkgconf', '2.2.0'), + ('CMake', '3.29.3'), + ('Ninja', '1.12.1'), + # deps for QtWebEngine + ('Bison', '3.8.2'), + ('flex', '2.6.4'), + ('gperf', '3.1'), + ('re2c', '3.1'), +] +dependencies = [ + ('double-conversion', '3.3.0'), + ('GLib', '2.80.4'), + ('PCRE2', '10.43'), + ('libpng', '1.6.43'), + ('LibTIFF', '4.6.0'), + ('libwebp', '1.4.0'), + ('JasPer', '4.2.4'), + ('HarfBuzz', '9.0.0'), + ('SQLite', '3.45.3'), + ('graphite2', '1.3.14'), + ('assimp', '5.4.3'), # for Qt 3D + ('FFmpeg', '7.0.2'), + ('X11', '20240607'), + ('fontconfig', '2.15.0'), + ('zlib', '1.3.1'), + ('Python', '3.12.3'), + ('Python-bundle-PyPI', '2024.06'), + ('freetype', '2.13.2'), # WebEngine + ('DBus', '1.15.8'), + ('libevent', '2.1.12'), # WebEngine + ('libGLU', '9.0.3'), + ('libjpeg-turbo', '3.0.1'), # WebEngine + ('NSS', '3.104'), # WebEngine, required + ('snappy', '1.2.1'), # WebEngine + ('OpenSSL', '3', '', SYSTEM), + ('ICU', '75.1'), + ('nodejs', '20.13.1'), + # ('gRPC', '1.52.2'), # WebEngine needs older Abseil/gRPC/protobuf +] + +preconfigopts = 'sed -i "s/MultiMedia/Multimedia/g" ../qt-everywhere-src-%(version)s/qtcharts/CMakeLists.txt && ' + +preconfigopts += 'sed -i "23i set(Python3_ROOT_DIR \\$ENV{EBROOTPYTHON})" ' +preconfigopts += '../qt-everywhere-src-%(version)s/qtwebengine/src/gn/CMakeLists.txt && ' # Typo + +configopts = "-Wno-dev -DFEATURE_qtpdf_build=OFF -DQT_AVOID_CMAKE_ARCHIVING_API=ON " +configopts += "-DPython3_ROOT_DIR=$EBROOTPYTHON -DBUILD_qtwayland=OFF " + + +# Removed from Qt6.0.0 but may be added back in the future +# configopts += '-DBUILD_qtgamepad=OFF ' # Does not work on CentOS 7 + +sanity_check_paths = { + 'files': ['bin/qmake6', 'lib/libQt6Core.%s' % SHLIB_EXT, 'lib/libQt6WebEngineCore.%s' % SHLIB_EXT], + 'dirs': ['include/QtCore', 'include/QtWebEngineCore'], +} + +sanity_check_commands = ['qmake6 --help'] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/q/Qt6/Qt6-6.7.2_fix_cpu_features.patch b/easybuild/easyconfigs/q/Qt6/Qt6-6.7.2_fix_cpu_features.patch new file mode 100644 index 00000000000..0109ba0726b --- /dev/null +++ b/easybuild/easyconfigs/q/Qt6/Qt6-6.7.2_fix_cpu_features.patch @@ -0,0 +1,56 @@ +# What: Comment out incorrect detection of CPU features when only AVX2 flag is set. +# See relevant bug reports: +# https://bugs.gentoo.org/908420 +# https://bugs.gentoo.org/898644 +# Author: maxim-masterov (SURF) +diff -Nru qt-everywhere-src-6.7.2.orig/qtbase/src/corelib/global/qsimd_p.h qt-everywhere-src-6.7.2/qtbase/src/corelib/global/qsimd_p.h +--- qt-everywhere-src-6.7.2.orig/qtbase/src/corelib/global/qsimd_p.h 2024-09-20 12:05:26.732359000 +0200 ++++ qt-everywhere-src-6.7.2/qtbase/src/corelib/global/qsimd_p.h 2024-09-23 22:31:44.861936347 +0200 +@@ -227,14 +227,14 @@ + # if defined(__AVX2__) + // List of features present with -march=x86-64-v3 and not architecturally + // implied by __AVX2__ +-# define ARCH_HASWELL_MACROS \ +- (__AVX2__ + __BMI__ + __BMI2__ + __F16C__ + __FMA__ + __LZCNT__ + __POPCNT__) +-# if ARCH_HASWELL_MACROS != 7 +-# error "Please enable all x86-64-v3 extensions; you probably want to use -march=haswell or -march=x86-64-v3 instead of -mavx2" +-# endif +-static_assert(ARCH_HASWELL_MACROS, "Undeclared identifiers indicate which features are missing."); +-# define __haswell__ 1 +-# undef ARCH_HASWELL_MACROS ++//# define ARCH_HASWELL_MACROS \ ++// (__AVX2__ + __BMI__ + __BMI2__ + __F16C__ + __FMA__ + __LZCNT__ + __POPCNT__) ++//# if ARCH_HASWELL_MACROS != 7 ++//# error "Please enable all x86-64-v3 extensions; you probably want to use -march=haswell or -march=x86-64-v3 instead of -mavx2" ++//# endif ++//static_assert(ARCH_HASWELL_MACROS, "Undeclared identifiers indicate which features are missing."); ++//# define __haswell__ 1 ++//# undef ARCH_HASWELL_MACROS + # endif + + // x86-64 sub-architecture version 4 +@@ -244,15 +244,15 @@ + // with AVX512 support and it includes all of these too. The GNU libc subdir for + // this is "glibc-hwcaps/x86-64-v4". + // +-# define ARCH_SKX_MACROS (__AVX512F__ + __AVX512BW__ + __AVX512CD__ + __AVX512DQ__ + __AVX512VL__) +-# if ARCH_SKX_MACROS != 0 +-# if ARCH_SKX_MACROS != 5 +-# error "Please enable all x86-64-v4 extensions; you probably want to use -march=skylake-avx512 or -march=x86-64-v4 instead of -mavx512f" +-# endif +-static_assert(ARCH_SKX_MACROS, "Undeclared identifiers indicate which features are missing."); +-# define __skylake_avx512__ 1 +-# endif +-# undef ARCH_SKX_MACROS ++//# define ARCH_SKX_MACROS (__AVX512F__ + __AVX512BW__ + __AVX512CD__ + __AVX512DQ__ + __AVX512VL__) ++//# if ARCH_SKX_MACROS != 0 ++//# if ARCH_SKX_MACROS != 5 ++//# error "Please enable all x86-64-v4 extensions; you probably want to use -march=skylake-avx512 or -march=x86-64-v4 instead of -mavx512f" ++//# endif ++//static_assert(ARCH_SKX_MACROS, "Undeclared identifiers indicate which features are missing."); ++//# define __skylake_avx512__ 1 ++//# endif ++//# undef ARCH_SKX_MACROS + #endif /* Q_PROCESSOR_X86 */ + + // NEON intrinsics diff --git a/easybuild/easyconfigs/q/Qualimap/Qualimap-2.3-foss-2022b-R-4.2.2.eb b/easybuild/easyconfigs/q/Qualimap/Qualimap-2.3-foss-2022b-R-4.2.2.eb new file mode 100644 index 00000000000..c6a3e40d231 --- /dev/null +++ b/easybuild/easyconfigs/q/Qualimap/Qualimap-2.3-foss-2022b-R-4.2.2.eb @@ -0,0 +1,33 @@ +easyblock = 'Tarball' + +name = 'Qualimap' +version = '2.3' +versionsuffix = '-R-%(rver)s' + +homepage = 'http://qualimap.bioinfo.cipf.es/' +description = """Qualimap 2 is a platform-independent application written in Java and R that provides both + a Graphical User Inteface (GUI) and a command-line interface to facilitate the quality control of + alignment sequencing data and its derivatives like feature counts.""" + +toolchain = {'name': 'foss', 'version': '2022b'} + +source_urls = ['https://bitbucket.org/kokonech/qualimap/downloads/'] +sources = ['qualimap_v%(version)s.zip'] +checksums = ['2a04dd864b712da30923cce3bc8dfc6ea59612118e8b0ff1a246fe43b8d34c40'] + +dependencies = [ + ('Java', '11', '', SYSTEM), + ('R', '4.2.2'), + ('R-bundle-Bioconductor', '3.16', versionsuffix), +] + +sanity_check_paths = { + 'files': ['qualimap'], + 'dirs': [], +} + +sanity_check_commands = ["qualimap --help"] + +modextrapaths = {'PATH': ''} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.7-foss-2021a.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.7-foss-2021a.eb index 5438527c158..bdff659a888 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.7-foss-2021a.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.7-foss-2021a.eb @@ -29,7 +29,8 @@ checksums = [ dependencies = [ ('HDF5', '1.10.7'), - ('ELPA', '2021.05.001'), + # From the QE configure help, this version of ELPA is not compatible + # ('ELPA', '2021.05.001'), ('libxc', '5.1.5'), ] @@ -41,4 +42,7 @@ buildopts = 'all gwl xspectra couple epw gipaw w90' # parallel build tends to fail parallel = 1 +# allow some test failures (not investigated for old easyconfig) +test_suite_max_failed = 4 + moduleclass = 'chem' diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.7-intel-2021a.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.7-intel-2021a.eb index 90cb839d1f7..99d05042d92 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.7-intel-2021a.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.7-intel-2021a.eb @@ -29,7 +29,8 @@ checksums = [ dependencies = [ ('HDF5', '1.10.7'), - ('ELPA', '2021.05.001'), + # From the QE configure help, this version of ELPA is not compatible + # ('ELPA', '2021.05.001'), ('libxc', '5.1.5'), ] @@ -41,4 +42,7 @@ buildopts = 'all gwl xspectra couple epw gipaw w90' # parallel build tends to fail parallel = 1 +# allow some test failures (not investigated for old easyconfig) +test_suite_max_failed = 2 + moduleclass = 'chem' diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.8-foss-2021b.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.8-foss-2021b.eb index fc8ad317547..aedc3282d14 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.8-foss-2021b.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.8-foss-2021b.eb @@ -41,4 +41,7 @@ buildopts = 'all gwl xspectra couple epw gipaw w90' # parallel build tends to fail parallel = 1 +# don't run the tests (not investigated for old easyconfig) +skipsteps = ['test'] + moduleclass = 'chem' diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.8-intel-2021a.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.8-intel-2021a.eb index 4b187cd70ee..5982b4efde6 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.8-intel-2021a.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.8-intel-2021a.eb @@ -41,4 +41,7 @@ buildopts = 'all gwl xspectra couple epw gipaw w90' # parallel build tends to fail parallel = 1 +# allow some test failures (not investigated for old easyconfig) +test_suite_max_failed = 4 + moduleclass = 'chem' diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.0-foss-2021b.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.0-foss-2021b.eb index a0a1ebea9ea..9f62ca5ad84 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.0-foss-2021b.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.0-foss-2021b.eb @@ -41,4 +41,7 @@ buildopts = 'all gwl xspectra couple epw gipaw w90' # parallel build tends to fail parallel = 1 +# allow some test failures (not investigated for old easyconfig) +test_suite_max_failed = 3 + moduleclass = 'chem' diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.0-intel-2021b.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.0-intel-2021b.eb index febc60c8c61..3aef60958a6 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.0-intel-2021b.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.0-intel-2021b.eb @@ -41,4 +41,7 @@ buildopts = 'all gwl xspectra couple epw gipaw w90' # parallel build tends to fail parallel = 1 +# don't run the tests (not investigated for old easyconfig) +skipsteps = ['test'] + moduleclass = 'chem' diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.1-foss-2022a.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.1-foss-2022a.eb index 87066c6ae6d..3f34e98c970 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.1-foss-2022a.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.1-foss-2022a.eb @@ -48,4 +48,7 @@ buildopts = 'all gwl xspectra couple epw gipaw w90' # parallel build tends to fail parallel = 1 +# don't run the tests (not investigated for old easyconfig) +skipsteps = ['test'] + moduleclass = 'chem' diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.1-intel-2022a.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.1-intel-2022a.eb index a81be226c25..931d16c7f63 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.1-intel-2022a.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.1-intel-2022a.eb @@ -48,4 +48,7 @@ buildopts = 'all gwl xspectra couple epw gipaw w90' # parallel build tends to fail parallel = 1 +# don't run the tests (not investigated for old easyconfig) +skipsteps = ['test'] + moduleclass = 'chem' diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.2-foss-2022b.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.2-foss-2022b.eb index 376073c6808..9362d5a9fb8 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.2-foss-2022b.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.2-foss-2022b.eb @@ -45,6 +45,8 @@ dependencies = [ # which depends on qe source buildopts = 'all gwl xspectra couple epw gipaw w90' +with_fox = True + # parallel build tends to fail parallel = 1 diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.2-foss-2023a.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.2-foss-2023a.eb index 4a79d7df97a..8369f3fb31a 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.2-foss-2023a.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.2-foss-2023a.eb @@ -46,6 +46,8 @@ dependencies = [ # which depends on qe source buildopts = "all gwl xspectra couple epw gipaw w90" +with_fox = True + # parallel build tends to fail parallel = 1 diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.2-intel-2022b.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.2-intel-2022b.eb index 8b78a44b1f6..53852bd770b 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.2-intel-2022b.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.2-intel-2022b.eb @@ -9,7 +9,9 @@ It is based on density-functional theory, plane waves, and pseudopotentials """ toolchain = {'name': 'intel', 'version': '2022b'} -toolchainopts = {'usempi': True, 'openmp': True} +# OpenMP is not working with Intel ifort/ifx compilers (Fortran) starting from version 2021.2.0 +# toolchainopts = {'usempi': True, 'openmp': True} +toolchainopts = {'usempi': True} sources = [ { @@ -45,6 +47,8 @@ dependencies = [ # which depends on qe source buildopts = 'all gwl xspectra couple epw gipaw w90' +with_fox = True + # parallel build tends to fail parallel = 1 diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.3-foss-2023a.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.3-foss-2023a.eb index 208c3041689..dff22dff1e6 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.3-foss-2023a.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.3-foss-2023a.eb @@ -52,4 +52,7 @@ buildopts = "all gwl xspectra couple epw gipaw w90" # parallel build tends to fail parallel = 1 +# allow some test failures (see https://github.com/EESSI/software-layer/pull/504#issuecomment-2039605740) +test_suite_max_failed = 2 + moduleclass = 'chem' diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.3.1-foss-2023a.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.3.1-foss-2023a.eb new file mode 100644 index 00000000000..ff3277e87b3 --- /dev/null +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.3.1-foss-2023a.eb @@ -0,0 +1,158 @@ +name = "QuantumESPRESSO" +version = "7.3.1" + +homepage = "https://www.quantum-espresso.org" +description = """Quantum ESPRESSO is an integrated suite of computer codes +for electronic-structure calculations and materials modeling at the nanoscale. +It is based on density-functional theory, plane waves, and pseudopotentials +(both norm-conserving and ultrasoft). +""" + +toolchain = {"name": "foss", "version": "2023a"} +toolchainopts = { + "usempi": True, + "openmp": True, +} + +# Check hashes inside external/submodule_commit_hash_records when making file for new version +local_lapack_hash = "12d825396fcef1e0a1b27be9f119f9e554621e55" +local_mbd_hash = "82005cbb65bdf5d32ca021848eec8f19da956a77" +local_devxlib_hash = "a6b89ef77b1ceda48e967921f1f5488d2df9226d" +local_fox_hash = "3453648e6837658b747b895bb7bef4b1ed2eac40" +# Different from the one at tag qe-7.3.1 because of: +# https://gitlab.com/QEF/q-e/-/issues/666 +local_d3q_hash = "de4718351e7bbb9d1d12aad2b7ca232d06775b83" +# Different from the one at tag qe-7.3.1 because of: +# https://github.com/dceresoli/qe-gipaw/issues/19 +local_qe_gipaw_hash = "79d3a03b7bdc4325e66f3fad02a24c6e6e3e5806" +local_qmcpack_hash = "f72ab25fa4ea755c1b4b230ae8074b47d5509c70" +local_w90_hash = "1d6b187374a2d50b509e5e79e2cab01a79ff7ce1" + + +sources = [ + { + "filename": "q-e-qe-%(version)s.tar.gz", + "extract_cmd": "mkdir -p %(builddir)s/qe-%(version)s && tar xzvf %s --strip-components=1 -C $_", + "source_urls": ["https://gitlab.com/QEF/q-e/-/archive/qe-%(version)s"], + }, + { + "filename": "lapack-%s.tar.gz" % local_lapack_hash, + "git_config": { + "url": "https://github.com/Reference-LAPACK", + "repo_name": "lapack", + "commit": local_lapack_hash, + }, + }, + { + "filename": "mbd-%s.tar.gz" % local_mbd_hash, + "git_config": { + "url": "https://github.com/libmbd", + "repo_name": "libmbd", + "commit": local_mbd_hash, + 'clone_into': 'mbd', + }, + }, + { + "filename": "devxlib-%s.tar.gz" % local_devxlib_hash, + "git_config": { + "url": "https://gitlab.com/max-centre/components", + "repo_name": "devicexlib", + "commit": local_devxlib_hash, + 'clone_into': 'devxlib', + }, + }, + { + "filename": "d3q-%s.tar.gz" % local_d3q_hash, + "git_config": { + "url": "https://github.com/anharmonic", + "repo_name": "d3q", + "commit": local_d3q_hash, + }, + }, + { + "filename": "fox-%s.tar.gz" % local_fox_hash, + "git_config": { + "url": "https://github.com/pietrodelugas", + "repo_name": "fox", + "commit": local_fox_hash, + }, + }, + { + "filename": "qe-gipaw-%s.tar.gz" % local_qe_gipaw_hash, + "git_config": { + "url": "https://github.com/dceresoli", + "repo_name": "qe-gipaw", + "commit": local_qe_gipaw_hash, + }, + }, + { + "filename": "pw2qmcpack-%s.tar.gz" % local_qmcpack_hash, + "git_config": { + "url": "https://github.com/QMCPACK", + "repo_name": "pw2qmcpack", + "commit": local_qmcpack_hash, + }, + }, + { + "filename": "wannier90-%s.tar.gz" % local_w90_hash, + "git_config": { + "url": "https://github.com/wannier-developers", + "repo_name": "wannier90", + "commit": local_w90_hash, + }, + }, +] +# Holding off checksum checks untill 5.0.x +# https://github.com/easybuilders/easybuild-framework/pull/4248 +# checksums = [ +# {'q-e-qe-7.3.1.tar.gz': '2c58b8fadfe4177de5a8b69eba447db5e623420b070dea6fd26c1533b081d844'}, +# {'lapack-%s.tar.gz' % local_lapack_hash: 'c05532ae0e5fe35f473206dda12970da5f2e2214620487d71837ddcf0ea6b21d'}, +# {'mbd-%s.tar.gz' % local_mbd_hash: 'a180682c00bb890c9b1e26a98addbd68e32f970c06439acf7582415f4c589800'}, +# {'devxlib-%s.tar.gz' % local_devxlib_hash: '76da8fe5a2050f58efdc92fa8831efec25c19190df7f4e5e39c173a5fbae83b4'}, +# {'d3q-%s.tar.gz' % local_d3q_hash: '43e50753a56af05d181b859d3e29d842fb3fc4352f00cb7fe229a435a1f20c31'}, +# {'fox-%s.tar.gz' % local_fox_hash: '99b6a899a3f947d7763aa318e86f9f08db684568bfdcd293f3318bee9d7f1948'}, +# {'qe-gipaw-%s.tar.gz' % local_qe_gipaw_hash: '9ac8314363d29cc2f1ce85abd8f26c1a3ae311d54f6e6034d656442dd101c928'}, +# {'pw2qmcpack-%s.tar.gz' % local_qmcpack_hash: 'a8136da8429fc49ab560ef7356cd6f0a2714dfbb137baff7961f46dfe32061eb'}, +# {'wannier90-%s.tar.gz' % local_w90_hash: 'f989497790ec9777bdc159945bbf42156edb7268011f972874dec67dd4f58658'}, +# ] +checksums = [ + '2c58b8fadfe4177de5a8b69eba447db5e623420b070dea6fd26c1533b081d844', + None, None, None, None, None, None, None, None +] + +builddependencies = [ + ("M4", "1.4.19"), + ("CMake", "3.26.3"), + ("pkgconf", "1.9.5"), +] +dependencies = [ + ("HDF5", "1.14.0"), + ("ELPA", "2023.05.001"), + ("libxc", "6.2.2"), +] + +# Disabled because of +# https://gitlab.com/QEF/q-e/-/issues/667 +# https://github.com/anharmonic/d3q/issues/15 +build_shared_libs = False +with_scalapack = True +with_fox = True +with_gipaw = True +with_d3q = True +with_qmcpack = True + +moduleclass = "chem" + +test_suite_threshold = ( + 0.4 # Low threshold because of https://gitlab.com/QEF/q-e/-/issues/665 +) +test_suite_max_failed = ( + 5 # Allow for some flaky tests (failed due to strict thresholds) +) +test_suite_allow_failures = [ + "test_qe_xclib_", # 7.3.1: https://gitlab.com/QEF/q-e/-/issues/640 + "--hp_", # 7.3.1: Broken testsuite (https://gitlab.com/QEF/q-e/-/issues/665) + "--ph_", # 7.3.1: Broken testsuite (https://gitlab.com/QEF/q-e/-/issues/665) + "--epw_", # 7.3.1: Broken testsuite (https://gitlab.com/QEF/q-e/-/issues/665) + "--tddfpt_", # 7.3.1: Broken testsuite (https://gitlab.com/QEF/q-e/-/issues/665) +] diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.3.1-foss-2024a.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.3.1-foss-2024a.eb new file mode 100644 index 00000000000..8cbd539a51d --- /dev/null +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.3.1-foss-2024a.eb @@ -0,0 +1,159 @@ +name = 'QuantumESPRESSO' +version = '7.3.1' + +homepage = 'https://www.quantum-espresso.org' +description = """Quantum ESPRESSO is an integrated suite of computer codes +for electronic-structure calculations and materials modeling at the nanoscale. +It is based on density-functional theory, plane waves, and pseudopotentials +(both norm-conserving and ultrasoft). +""" + +toolchain = {'name': 'foss', 'version': '2024a'} + +toolchainopts = { + "usempi": True, + "openmp": True, +} + +# Check hashes inside external/submodule_commit_hash_records when making file for new version +local_lapack_hash = "12d825396fcef1e0a1b27be9f119f9e554621e55" +local_mbd_hash = "82005cbb65bdf5d32ca021848eec8f19da956a77" +local_devxlib_hash = "a6b89ef77b1ceda48e967921f1f5488d2df9226d" +local_fox_hash = "3453648e6837658b747b895bb7bef4b1ed2eac40" +# Different from the one at tag qe-7.3.1 because of: +# https://gitlab.com/QEF/q-e/-/issues/666 +local_d3q_hash = "de4718351e7bbb9d1d12aad2b7ca232d06775b83" +# Different from the one at tag qe-7.3.1 because of: +# https://github.com/dceresoli/qe-gipaw/issues/19 +local_qe_gipaw_hash = "79d3a03b7bdc4325e66f3fad02a24c6e6e3e5806" +local_qmcpack_hash = "f72ab25fa4ea755c1b4b230ae8074b47d5509c70" +local_w90_hash = "1d6b187374a2d50b509e5e79e2cab01a79ff7ce1" + + +sources = [ + { + "filename": "q-e-qe-%(version)s.tar.gz", + "extract_cmd": "mkdir -p %(builddir)s/qe-%(version)s && tar xzvf %s --strip-components=1 -C $_", + "source_urls": ["https://gitlab.com/QEF/q-e/-/archive/qe-%(version)s"], + }, + { + "filename": "lapack-%s.tar.gz" % local_lapack_hash, + "git_config": { + "url": "https://github.com/Reference-LAPACK", + "repo_name": "lapack", + "commit": local_lapack_hash, + }, + }, + { + "filename": "mbd-%s.tar.gz" % local_mbd_hash, + "git_config": { + "url": "https://github.com/libmbd", + "repo_name": "libmbd", + "commit": local_mbd_hash, + 'clone_into': 'mbd', + }, + }, + { + "filename": "devxlib-%s.tar.gz" % local_devxlib_hash, + "git_config": { + "url": "https://gitlab.com/max-centre/components", + "repo_name": "devicexlib", + "commit": local_devxlib_hash, + 'clone_into': 'devxlib', + }, + }, + { + "filename": "d3q-%s.tar.gz" % local_d3q_hash, + "git_config": { + "url": "https://github.com/anharmonic", + "repo_name": "d3q", + "commit": local_d3q_hash, + }, + }, + { + "filename": "fox-%s.tar.gz" % local_fox_hash, + "git_config": { + "url": "https://github.com/pietrodelugas", + "repo_name": "fox", + "commit": local_fox_hash, + }, + }, + { + "filename": "qe-gipaw-%s.tar.gz" % local_qe_gipaw_hash, + "git_config": { + "url": "https://github.com/dceresoli", + "repo_name": "qe-gipaw", + "commit": local_qe_gipaw_hash, + }, + }, + { + "filename": "pw2qmcpack-%s.tar.gz" % local_qmcpack_hash, + "git_config": { + "url": "https://github.com/QMCPACK", + "repo_name": "pw2qmcpack", + "commit": local_qmcpack_hash, + }, + }, + { + "filename": "wannier90-%s.tar.gz" % local_w90_hash, + "git_config": { + "url": "https://github.com/wannier-developers", + "repo_name": "wannier90", + "commit": local_w90_hash, + }, + }, +] +# Holding off checksum checks untill 5.0.x +# https://github.com/easybuilders/easybuild-framework/pull/4248 +# checksums = [ +# {'q-e-qe-7.3.1.tar.gz': '2c58b8fadfe4177de5a8b69eba447db5e623420b070dea6fd26c1533b081d844'}, +# {'lapack-%s.tar.gz' % local_lapack_hash: 'c05532ae0e5fe35f473206dda12970da5f2e2214620487d71837ddcf0ea6b21d'}, +# {'mbd-%s.tar.gz' % local_mbd_hash: 'a180682c00bb890c9b1e26a98addbd68e32f970c06439acf7582415f4c589800'}, +# {'devxlib-%s.tar.gz' % local_devxlib_hash: '76da8fe5a2050f58efdc92fa8831efec25c19190df7f4e5e39c173a5fbae83b4'}, +# {'d3q-%s.tar.gz' % local_d3q_hash: '43e50753a56af05d181b859d3e29d842fb3fc4352f00cb7fe229a435a1f20c31'}, +# {'fox-%s.tar.gz' % local_fox_hash: '99b6a899a3f947d7763aa318e86f9f08db684568bfdcd293f3318bee9d7f1948'}, +# {'qe-gipaw-%s.tar.gz' % local_qe_gipaw_hash: '9ac8314363d29cc2f1ce85abd8f26c1a3ae311d54f6e6034d656442dd101c928'}, +# {'pw2qmcpack-%s.tar.gz' % local_qmcpack_hash: 'a8136da8429fc49ab560ef7356cd6f0a2714dfbb137baff7961f46dfe32061eb'}, +# {'wannier90-%s.tar.gz' % local_w90_hash: 'f989497790ec9777bdc159945bbf42156edb7268011f972874dec67dd4f58658'}, +# ] +checksums = [ + '2c58b8fadfe4177de5a8b69eba447db5e623420b070dea6fd26c1533b081d844', + None, None, None, None, None, None, None, None +] + +builddependencies = [ + ('M4', '1.4.19'), + ('CMake', '3.29.3'), + ('pkgconf', '2.2.0'), +] +dependencies = [ + ('HDF5', '1.14.5'), + ('ELPA', '2024.05.001'), + ('libxc', '6.2.2'), +] + +# Disabled because of +# https://gitlab.com/QEF/q-e/-/issues/667 +# https://github.com/anharmonic/d3q/issues/15 +build_shared_libs = False +with_scalapack = True +with_fox = True +with_gipaw = True +with_d3q = True +with_qmcpack = True + +moduleclass = "chem" + +test_suite_threshold = ( + 0.4 # Low threshold because of https://gitlab.com/QEF/q-e/-/issues/665 +) +test_suite_max_failed = ( + 5 # Allow for some flaky tests (failed due to strict thresholds) +) +test_suite_allow_failures = [ + "test_qe_xclib_", # 7.3.1: https://gitlab.com/QEF/q-e/-/issues/640 + "--hp_", # 7.3.1: Broken testsuite (https://gitlab.com/QEF/q-e/-/issues/665) + "--ph_", # 7.3.1: Broken testsuite (https://gitlab.com/QEF/q-e/-/issues/665) + "--epw_", # 7.3.1: Broken testsuite (https://gitlab.com/QEF/q-e/-/issues/665) + "--tddfpt_", # 7.3.1: Broken testsuite (https://gitlab.com/QEF/q-e/-/issues/665) +] diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.3.1-intel-2023a.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.3.1-intel-2023a.eb new file mode 100644 index 00000000000..d6ffe3c80c1 --- /dev/null +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.3.1-intel-2023a.eb @@ -0,0 +1,150 @@ +name = 'QuantumESPRESSO' +version = '7.3.1' + +homepage = 'https://www.quantum-espresso.org' +description = """Quantum ESPRESSO is an integrated suite of computer codes +for electronic-structure calculations and materials modeling at the nanoscale. +It is based on density-functional theory, plane waves, and pseudopotentials +(both norm-conserving and ultrasoft). +""" + +toolchain = {'name': 'intel', 'version': '2023a'} +toolchainopts = { + 'usempi': True, + 'openmp': True, +} + +# Check hashes inside external/submodule_commit_hash_records when making file for new version +local_lapack_hash = "12d825396fcef1e0a1b27be9f119f9e554621e55" +local_mbd_hash = "82005cbb65bdf5d32ca021848eec8f19da956a77" +local_devxlib_hash = "a6b89ef77b1ceda48e967921f1f5488d2df9226d" +local_fox_hash = "3453648e6837658b747b895bb7bef4b1ed2eac40" +# Different from the one at tag qe-7.3.1 because of: +# https://gitlab.com/QEF/q-e/-/issues/666 +local_d3q_hash = "de4718351e7bbb9d1d12aad2b7ca232d06775b83" +local_qe_gipaw_hash = "75b01b694c9ba4df55d294cacc27cf28591b2161" +local_qmcpack_hash = "f72ab25fa4ea755c1b4b230ae8074b47d5509c70" +local_w90_hash = "1d6b187374a2d50b509e5e79e2cab01a79ff7ce1" + +sources = [ + { + 'filename': 'q-e-qe-%(version)s.tar.gz', + 'extract_cmd': 'mkdir -p %(builddir)s/qe-%(version)s && tar xzvf %s --strip-components=1 -C $_', + 'source_urls': ['https://gitlab.com/QEF/q-e/-/archive/qe-%(version)s'] + }, + { + "filename": "lapack-%s.tar.gz" % local_lapack_hash, + "git_config": { + "url": "https://github.com/Reference-LAPACK", + "repo_name": "lapack", + "commit": local_lapack_hash, + }, + }, + { + "filename": "mbd-%s.tar.gz" % local_mbd_hash, + "git_config": { + "url": "https://github.com/libmbd", + "repo_name": "libmbd", + "commit": local_mbd_hash, + 'clone_into': 'mbd', + }, + }, + { + "filename": "devxlib-%s.tar.gz" % local_devxlib_hash, + "git_config": { + "url": "https://gitlab.com/max-centre/components", + "repo_name": "devicexlib", + "commit": local_devxlib_hash, + 'clone_into': 'devxlib', + }, + }, + { + "filename": "d3q-%s.tar.gz" % local_d3q_hash, + "git_config": { + "url": "https://github.com/anharmonic", + "repo_name": "d3q", + "commit": local_d3q_hash, + }, + }, + { + "filename": "fox-%s.tar.gz" % local_fox_hash, + "git_config": { + "url": "https://github.com/pietrodelugas", + "repo_name": "fox", + "commit": local_fox_hash, + }, + }, + { + "filename": "qe-gipaw-%s.tar.gz" % local_qe_gipaw_hash, + "git_config": { + "url": "https://github.com/dceresoli", + "repo_name": "qe-gipaw", + "commit": local_qe_gipaw_hash, + }, + }, + { + "filename": "pw2qmcpack-%s.tar.gz" % local_qmcpack_hash, + "git_config": { + "url": "https://github.com/QMCPACK", + "repo_name": "pw2qmcpack", + "commit": local_qmcpack_hash, + }, + }, + { + "filename": "wannier90-%s.tar.gz" % local_w90_hash, + "git_config": { + "url": "https://github.com/wannier-developers", + "repo_name": "wannier90", + "commit": local_w90_hash, + }, + }, +] +# Holding off checksum checks untill 5.0.x +# https://github.com/easybuilders/easybuild-framework/pull/4248 +# checksums = [ +# {'q-e-qe-7.3.1.tar.gz': '2c58b8fadfe4177de5a8b69eba447db5e623420b070dea6fd26c1533b081d844'}, +# {'lapack-%s.tar.gz' % local_lapack_hash: 'c05532ae0e5fe35f473206dda12970da5f2e2214620487d71837ddcf0ea6b21d'}, +# {'mbd-%s.tar.gz' % local_mbd_hash: 'a180682c00bb890c9b1e26a98addbd68e32f970c06439acf7582415f4c589800'}, +# {'devxlib-%s.tar.gz' % local_devxlib_hash: '76da8fe5a2050f58efdc92fa8831efec25c19190df7f4e5e39c173a5fbae83b4'}, +# {'d3q-%s.tar.gz' % local_d3q_hash: '43e50753a56af05d181b859d3e29d842fb3fc4352f00cb7fe229a435a1f20c31'}, +# {'fox-%s.tar.gz' % local_fox_hash: '99b6a899a3f947d7763aa318e86f9f08db684568bfdcd293f3318bee9d7f1948'}, +# {'qe-gipaw-%s.tar.gz' % local_qe_gipaw_hash: '9ac8314363d29cc2f1ce85abd8f26c1a3ae311d54f6e6034d656442dd101c928'}, +# {'pw2qmcpack-%s.tar.gz' % local_qmcpack_hash: 'a8136da8429fc49ab560ef7356cd6f0a2714dfbb137baff7961f46dfe32061eb'}, +# {'wannier90-%s.tar.gz' % local_w90_hash: 'f989497790ec9777bdc159945bbf42156edb7268011f972874dec67dd4f58658'}, +# ] +checksums = [ + '2c58b8fadfe4177de5a8b69eba447db5e623420b070dea6fd26c1533b081d844', + None, None, None, None, None, None, None, None +] + +builddependencies = [ + ('M4', '1.4.19'), + ('CMake', '3.26.3'), + ("pkgconf", "1.9.5"), +] +dependencies = [ + ('HDF5', '1.14.0'), + ('ELPA', '2023.05.001'), + ('libxc', '6.2.2'), +] + +# Disabled because of +# https://gitlab.com/QEF/q-e/-/issues/667 +# https://github.com/anharmonic/d3q/issues/15 +build_shared_libs = False +with_scalapack = True +with_gipaw = False # https://github.com/dceresoli/qe-gipaw/issues/19 +with_d3q = True +with_qmcpack = True + +moduleclass = 'chem' + +test_suite_threshold = 0.4 # Low threshold because of https://gitlab.com/QEF/q-e/-/issues/665 +test_suite_max_failed = 5 # Allow for some flaky tests (failed due to strict thresholds) +test_suite_allow_failures = [ + 'test_qe_xclib_', # 7.3.1: https://gitlab.com/QEF/q-e/-/issues/640 + '--hp_', # 7.3.1: Broken testsuite (https://gitlab.com/QEF/q-e/-/issues/665) + '--ph_', # 7.3.1: Broken testsuite (https://gitlab.com/QEF/q-e/-/issues/665) + '--epw_', # 7.3.1: Broken testsuite (https://gitlab.com/QEF/q-e/-/issues/665) + '--tddfpt_', # 7.3.1: Broken testsuite (https://gitlab.com/QEF/q-e/-/issues/665) +] diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.4-d3q.patch b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.4-d3q.patch new file mode 100644 index 00000000000..d2a91a510b6 --- /dev/null +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.4-d3q.patch @@ -0,0 +1,30 @@ +Fix line length greather than 132 characters. +Also fix the use of ZGEMM3M, which is not available in the FlexiBLAS library. +See https://github.com/anharmonic/d3q/issues/22 +--- a/d3q/thermal2/PROGRAM_r2q.f90 ++++ b/d3q/thermal2/PROGRAM_r2q.f90 +@@ -744,7 +744,8 @@ PROGRAM r2q + + + WRITE(*,'(2x,a,f12.8)') "Note: q-point and path length in units of 2pi/alat, conversion to bohr^-1: ", S%tpiba +- WRITE(*,'(2x,2(a,f12.8))') "Note: phonons are in cm^-1, conversion to Rydberg: ", 1.d+5/RY_TO_CMM1,"E-5 to THz:", RY_TO_THZ/RY_TO_CMM1 ++ WRITE(*,'(2x,2(a,f12.8))') "Note: phonons are in cm^-1, conversion to Rydberg: ", & ++ 1.d+5/RY_TO_CMM1,"E-5 to THz:", RY_TO_THZ/RY_TO_CMM1 + + IF( input%calculation=="dos") THEN + CALL PH_DOS(input,S,fc2) +diff --git a/thermal2/functions.f90 b/thermal2/functions.f90 +index 90d8a90..9e9adb2 100644 +--- a/d3q/thermal2/functions.f90 ++++ b/d3q/thermal2/functions.f90 +@@ -465,8 +465,8 @@ end subroutine quicksort_idx + ! + !rotate_d2 = MATMUL(TRANSPOSE(CONJG(U)), MATMUL(D,U)) + ! +- CALL ZGEMM3M('N', 'N', nat3, nat3, nat3, alpha, D, nat3, U, nat3, beta, A, nat3) +- CALL ZGEMM3M('C', 'N', nat3, nat3, nat3, alpha, U, nat3, A, nat3, beta, rotate_d2, nat3) ++ CALL ZGEMM('N', 'N', nat3, nat3, nat3, alpha, D, nat3, U, nat3, beta, A, nat3) ++ CALL ZGEMM('C', 'N', nat3, nat3, nat3, alpha, U, nat3, A, nat3, beta, rotate_d2, nat3) + ! + END FUNCTION + ! diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.4-foss-2024a.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.4-foss-2024a.eb new file mode 100644 index 00000000000..f017367700b --- /dev/null +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.4-foss-2024a.eb @@ -0,0 +1,147 @@ +name = 'QuantumESPRESSO' +version = '7.4' + +homepage = 'https://www.quantum-espresso.org' +description = """Quantum ESPRESSO is an integrated suite of computer codes +for electronic-structure calculations and materials modeling at the nanoscale. +It is based on density-functional theory, plane waves, and pseudopotentials +(both norm-conserving and ultrasoft). +""" + +toolchain = {'name': 'foss', 'version': '2024a'} + +toolchainopts = { + "usempi": True, + "openmp": True, +} + +# Check hashes inside external/submodule_commit_hash_records when making file for new version +local_lapack_hash = "12d825396fcef1e0a1b27be9f119f9e554621e55" +local_mbd_hash = "89a3cc199c0a200c9f0f688c3229ef6b9a8d63bd" +local_devxlib_hash = "a6b89ef77b1ceda48e967921f1f5488d2df9226d" +local_fox_hash = "3453648e6837658b747b895bb7bef4b1ed2eac40" +# Different from the one at tag qe-7.4, see https://github.com/anharmonic/d3q/issues/22 +local_d3q_hash = "808acbaf012468f42147d8d6af452ec64b9e5ab0" +# Different from the one at tag qe-7.4 +local_qe_gipaw_hash = "9b2ae1a46cae045cc04ef02c1072f2e1e74873b2" +local_qmcpack_hash = "f72ab25fa4ea755c1b4b230ae8074b47d5509c70" +local_w90_hash = "1d6b187374a2d50b509e5e79e2cab01a79ff7ce1" + + +sources = [ + { + "filename": "q-e-qe-%(version)s.tar.gz", + "extract_cmd": "mkdir -p %(builddir)s/qe-%(version)s && tar xzvf %s --strip-components=1 -C $_", + "source_urls": ["https://gitlab.com/QEF/q-e/-/archive/qe-%(version)s"], + }, + { + "filename": "lapack-%s.tar.gz" % local_lapack_hash, + "git_config": { + "url": "https://github.com/Reference-LAPACK", + "repo_name": "lapack", + "commit": local_lapack_hash, + }, + }, + { + "filename": "mbd-%s.tar.gz" % local_mbd_hash, + "git_config": { + "url": "https://github.com/libmbd", + "repo_name": "libmbd", + "commit": local_mbd_hash, + 'clone_into': 'mbd', + }, + }, + { + "filename": "devxlib-%s.tar.gz" % local_devxlib_hash, + "git_config": { + "url": "https://gitlab.com/max-centre/components", + "repo_name": "devicexlib", + "commit": local_devxlib_hash, + 'clone_into': 'devxlib', + }, + }, + { + "filename": "d3q-%s.tar.gz" % local_d3q_hash, + "git_config": { + "url": "https://github.com/anharmonic", + "repo_name": "d3q", + "commit": local_d3q_hash, + }, + }, + { + "filename": "fox-%s.tar.gz" % local_fox_hash, + "git_config": { + "url": "https://github.com/pietrodelugas", + "repo_name": "fox", + "commit": local_fox_hash, + }, + }, + { + "filename": "qe-gipaw-%s.tar.gz" % local_qe_gipaw_hash, + "git_config": { + "url": "https://github.com/dceresoli", + "repo_name": "qe-gipaw", + "commit": local_qe_gipaw_hash, + }, + }, + { + "filename": "pw2qmcpack-%s.tar.gz" % local_qmcpack_hash, + "git_config": { + "url": "https://github.com/QMCPACK", + "repo_name": "pw2qmcpack", + "commit": local_qmcpack_hash, + }, + }, + { + "filename": "wannier90-%s.tar.gz" % local_w90_hash, + "git_config": { + "url": "https://github.com/wannier-developers", + "repo_name": "wannier90", + "commit": local_w90_hash, + }, + }, +] +patches = [ + { + 'name': 'QuantumESPRESSO-7.4-d3q.patch', + 'sourcepath': '../' # Needed as patches are normally applied to the first `finalpath` directory + }, +] +# Holding off git clone checksum checks untill 5.0.x +# See https://github.com/easybuilders/easybuild-framework/pull/4248 +checksums = [ + 'b15dcfe25f4fbf15ccd34c1194021e90996393478226e601d876f7dea481d104', + None, None, None, None, None, None, None, None, + '1f1686365fbf0cc56f634e072a92b3d336fe454348e514d0b4136d447f0d4923' +] + +builddependencies = [ + ('M4', '1.4.19'), + ('CMake', '3.29.3'), + ('pkgconf', '2.2.0'), +] +dependencies = [ + ('HDF5', '1.14.5'), + ('ELPA', '2024.05.001'), + ('libxc', '6.2.2'), +] + +# Disabled because of +# https://gitlab.com/QEF/q-e/-/issues/667 +# https://github.com/anharmonic/d3q/issues/15 +build_shared_libs = False +with_scalapack = True +with_fox = True +with_gipaw = True +with_d3q = True +with_qmcpack = True + +moduleclass = "chem" + +test_suite_threshold = ( + 0.98 +) +test_suite_max_failed = ( + 5 # Allow for some flaky tests (failed due to strict thresholds) +) +test_suite_allow_failures = [] diff --git a/easybuild/easyconfigs/q/QuickFF/QuickFF-2.2.7-foss-2023a.eb b/easybuild/easyconfigs/q/QuickFF/QuickFF-2.2.7-foss-2023a.eb new file mode 100644 index 00000000000..5bf05e90cf8 --- /dev/null +++ b/easybuild/easyconfigs/q/QuickFF/QuickFF-2.2.7-foss-2023a.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonPackage' + +name = 'QuickFF' +version = '2.2.7' + +homepage = 'https://molmod.github.io/QuickFF/' +description = """QuickFF is a Python package developed at the Center for +Molecular Modeling (CMM) to quickly derive accurate force fields from ab initio +calculations.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['https://github.com/molmod/QuickFF/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['a71922dd39869770b03809355f13bcabdbb8d50429f4d3574cf427ea762f4023'] + +dependencies = [ + ('Python', '3.11.3'), + ('matplotlib', '3.7.2'), + ('molmod', '1.4.8'), + ('yaff', '1.6.0'), +] + +download_dep_fail = True +use_pip = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(namelower)s'], +} + +sanity_pip_check = True + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/q/Qwt/Qwt-6.3.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/q/Qwt/Qwt-6.3.0-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..f208a034542 --- /dev/null +++ b/easybuild/easyconfigs/q/Qwt/Qwt-6.3.0-GCCcore-12.3.0.eb @@ -0,0 +1,39 @@ +easyblock = 'ConfigureMake' + +name = 'Qwt' +version = '6.3.0' + +homepage = 'https://qwt.sourceforge.io/' +description = """The Qwt library contains GUI Components and utility classes which are primarily useful for programs + with a technical background.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_BZ2] +patches = ['Qwt-6.2.0_fix-install-prefix.patch'] +checksums = [ + {'qwt-6.3.0.tar.bz2': 'dcb085896c28aaec5518cbc08c0ee2b4e60ada7ac929d82639f6189851a6129a'}, + {'Qwt-6.2.0_fix-install-prefix.patch': 'ac5c329c0693d565b461cdd3b36c1b96b4d09885e1e0c10929fc7a9021c03bad'}, +] + +builddependencies = [ + ('binutils', '2.40'), + ('pkgconf', '1.9.5'), +] + +dependencies = [ + ('Qt5', '5.15.10'), +] + +skipsteps = ['configure'] + +prebuildopts = 'export QWT_PREFIX=%(installdir)s && ' +prebuildopts += "qmake qwt.pro && " + +sanity_check_paths = { + 'files': ['lib/libqwt.%s' % SHLIB_EXT, 'lib/pkgconfig/Qt5Qwt6.pc'], + 'dirs': ['doc', 'features', 'include', 'plugins'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/q/qcat/qcat-1.1.0-foss-2023a.eb b/easybuild/easyconfigs/q/qcat/qcat-1.1.0-foss-2023a.eb new file mode 100644 index 00000000000..0c20434dec2 --- /dev/null +++ b/easybuild/easyconfigs/q/qcat/qcat-1.1.0-foss-2023a.eb @@ -0,0 +1,35 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 +# Update: Petr Král (INUITS) +easyblock = 'PythonPackage' + +name = 'qcat' +version = '1.1.0' + +homepage = 'https://github.com/nanoporetech/qcat' +description = "qcat is a Python command-line tool for demultiplexing Oxford Nanopore reads from FASTQ files" + +toolchain = {'name': 'foss', 'version': '2023a'} + +sources = [SOURCE_TAR_GZ] +checksums = ['56f225321a48eef43e2b83a33cbbb47bf1b1edcd569f3db4d088a1bc0199e20a'] + +dependencies = [ + ('Python', '3.11.3'), + ('Biopython', '1.83'), + ('python-parasail', '1.3.4'), + ('PyYAML', '6.0'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/qcat'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["qcat --help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/q/qcat/qcat-1.1.0-foss-2023b.eb b/easybuild/easyconfigs/q/qcat/qcat-1.1.0-foss-2023b.eb new file mode 100644 index 00000000000..347b09bccf3 --- /dev/null +++ b/easybuild/easyconfigs/q/qcat/qcat-1.1.0-foss-2023b.eb @@ -0,0 +1,35 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 +# Update: Petr Král (INUITS) +easyblock = 'PythonPackage' + +name = 'qcat' +version = '1.1.0' + +homepage = 'https://github.com/nanoporetech/qcat' +description = "qcat is a Python command-line tool for demultiplexing Oxford Nanopore reads from FASTQ files" + +toolchain = {'name': 'foss', 'version': '2023b'} + +sources = [SOURCE_TAR_GZ] +checksums = ['56f225321a48eef43e2b83a33cbbb47bf1b1edcd569f3db4d088a1bc0199e20a'] + +dependencies = [ + ('Python', '3.11.5'), + ('Biopython', '1.84'), + ('python-parasail', '1.3.4'), + ('PyYAML', '6.0.1'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/qcat'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["qcat --help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/q/qnorm/qnorm-0.8.1-foss-2022b.eb b/easybuild/easyconfigs/q/qnorm/qnorm-0.8.1-foss-2022b.eb new file mode 100644 index 00000000000..99c6ebe1e23 --- /dev/null +++ b/easybuild/easyconfigs/q/qnorm/qnorm-0.8.1-foss-2022b.eb @@ -0,0 +1,36 @@ +easyblock = 'PythonPackage' + +name = 'qnorm' +version = '0.8.1' + +homepage = 'https://github.com/Maarten-vd-Sande/qnorm' +description = "Fast-ish (and correct!) quantile normalization in Python" + +toolchain = {'name': 'foss', 'version': '2022b'} + +dependencies = [ + ('Python', '3.10.8'), + ('SciPy-bundle', '2023.02'), + ('numba', '0.58.1'), +] + +sources = [SOURCE_TAR_GZ] +checksums = ['61b2f3ef09a9c552a4f3b83dc438cb13f191fa190164361a3a508c4777eed3c7'] + +download_dep_fail = True +use_pip = True + +# pyproject.toml included in qnorm source tarball does not include standard fields, +# it's only there to be read by setup.py... +preinstallopts = "sed -i 's/pyproject.toml/pyproject.toml_/g' setup.py && mv pyproject.toml pyproject.toml_ && " + +sanity_check_paths = { + 'files': ['bin/qnorm'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["qnorm --help"] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/q/qnorm/qnorm-0.8.1-foss-2023a.eb b/easybuild/easyconfigs/q/qnorm/qnorm-0.8.1-foss-2023a.eb new file mode 100644 index 00000000000..fe306fc5314 --- /dev/null +++ b/easybuild/easyconfigs/q/qnorm/qnorm-0.8.1-foss-2023a.eb @@ -0,0 +1,36 @@ +easyblock = 'PythonPackage' + +name = 'qnorm' +version = '0.8.1' + +homepage = 'https://github.com/Maarten-vd-Sande/qnorm' +description = "Fast-ish (and correct!) quantile normalization in Python" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('numba', '0.58.1'), +] + +sources = [SOURCE_TAR_GZ] +checksums = ['61b2f3ef09a9c552a4f3b83dc438cb13f191fa190164361a3a508c4777eed3c7'] + +download_dep_fail = True +use_pip = True + +# pyproject.toml included in qnorm source tarball does not include standard fields, +# it's only there to be read for setup.py +preinstallopts = "sed -i 's/pyproject.toml/pyproject.toml_/g' setup.py && mv pyproject.toml pyproject.toml_ && " + +sanity_check_paths = { + 'files': ['bin/qnorm'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["qnorm --help"] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/r/R-INLA/R-INLA-24.01-18_fix-hardcoded-deps.patch b/easybuild/easyconfigs/r/R-INLA/R-INLA-24.01-18_fix-hardcoded-deps.patch new file mode 100644 index 00000000000..5fd0b954d98 --- /dev/null +++ b/easybuild/easyconfigs/r/R-INLA/R-INLA-24.01-18_fix-hardcoded-deps.patch @@ -0,0 +1,55 @@ +use dependencies provided by EasyBuild +authors: Denis Kristak (INUITS), Kenneth Hoste (HPC-UGent) +diff -ru r-inla-Version_24.01.18.orig/inlaprog/Makefile r-inla-Version_24.01.18/inlaprog/Makefile +--- r-inla-Version_24.01.18.orig/inlaprog/Makefile 2024-01-18 20:34:05.000000000 +0100 ++++ r-inla-Version_24.01.18/inlaprog/Makefile 2024-01-19 13:58:44.694060467 +0100 +@@ -9,13 +9,11 @@ + + ## *** chose either one of these; rgeneric requires the second version *** + ifeq ($(INLA_WITHOUT_LIBR),1) +- RLIB_INC = -DINLA_WITH_RMATH \ +- -I/usr/include/R -I/usr/share/R/include +- RLIB_LIB = -L/usr/lib -lRmath ++ RLIB_INC = -DINLA_WITH_RMATH ++ RLIB_LIB = -lRmath + else +- RLIB_INC = -DINLA_WITH_RMATH -DINLA_LIBR \ +- -I/usr/include/R -I/usr/share/R/include +- RLIB_LIB = -L/usr/lib -lRmath -L/usr/lib/R/lib -lR ++ RLIB_INC = -DINLA_WITH_RMATH -DINLA_LIBR ++ RLIB_LIB = -lRmath -lR + endif + + # select compilers and optimized compiler-options, add -fopenmp or similar to use OpenMP +@@ -32,7 +30,7 @@ + + # The external libraries to link with + EXTLIBS1 = -L$(PREFIX)/lib -lGMRFLib -L$(LEXTPREFIX)/lib +-EXTLIBS2 = -lgsl -ltaucs -lmetis -llapack -lblas -lgslcblas -lamd -lmuparser -lz -lgfortran -lcrypto ++EXTLIBS2 = -lgsl -ltaucs -lmetis -lscalapack -lflexiblas -lgslcblas -lamd -lmuparser -lz -lgfortran -lcrypto + EXTLIBS3 = -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -lm + + ################################################################################ +@@ -92,8 +90,8 @@ + done; \ + install -m755 $(INLA) $(PREFIX)/bin/$(INLA);\ + install -m755 $(INLA) $(PREFIX)/bin/$(INLA)-$(VERSION);\ +- rsync -auv --no-p --no-o --no-g --chmod=ugo=rwX --delete doc/* $(PREFIX)/doc/inla; \ +- rsync -auv --no-p --no-o --no-g --chmod=ugo=rwX --delete examples/* $(PREFIX)/doc/inla/examples; ++ # rsync -auv --no-p --no-o --no-g --chmod=ugo=rwX --delete doc/* $(PREFIX)/doc/inla; \ ++ # rsync -auv --no-p --no-o --no-g --chmod=ugo=rwX --delete examples/* $(PREFIX)/doc/inla/examples; + + clean:; -$(RM) $(OBJ) $(INLA) + +diff -ru r-inla-Version_24.01.18.orig/inlaprog/src/eval.c r-inla-Version_24.01.18/inlaprog/src/eval.c +--- r-inla-Version_24.01.18.orig/inlaprog/src/eval.c 2024-01-18 20:34:05.000000000 +0100 ++++ r-inla-Version_24.01.18/inlaprog/src/eval.c 2024-01-19 13:55:57.883885401 +0100 +@@ -34,7 +34,7 @@ + #include + #include + +-#include ++#include + + #include "GMRFLib/GMRFLib.h" + #include "inla.h" diff --git a/easybuild/easyconfigs/r/R-INLA/R-INLA-24.01-18_remove-hardcoding.patch b/easybuild/easyconfigs/r/R-INLA/R-INLA-24.01-18_remove-hardcoding.patch new file mode 100644 index 00000000000..747e9e81781 --- /dev/null +++ b/easybuild/easyconfigs/r/R-INLA/R-INLA-24.01-18_remove-hardcoding.patch @@ -0,0 +1,44 @@ +remove hardcoded paths from scripts +authors: Denis Kristak (INUTS) + Kenneth Hoste (HPC-UGent) +diff -ru r-inla-Version_24.01.18.orig/rinla/inst/bin/linux/64bit/fmesher.run r-inla-Version_24.01.18/rinla/inst/bin/linux/64bit/fmesher.run +--- r-inla-Version_24.01.18.orig/rinla/inst/bin/linux/64bit/fmesher.run 2024-01-18 20:34:05.000000000 +0100 ++++ r-inla-Version_24.01.18/rinla/inst/bin/linux/64bit/fmesher.run 2024-01-19 15:51:25.789786893 +0100 +@@ -4,17 +4,6 @@ + prog=${tmp%%.run} + DIR=$(dirname "$cmd") + +-D="" +-for d in {,/usr}/lib64 /usr/lib64/R/lib {,/usr}/lib/x86_64-linux-gnu {,/usr}/lib; do +- if [ -d "$d" ]; then +- if [ -z "$D" ]; then +- D="$d" +- else +- D="$D:$d" +- fi +- fi +-done +-export LD_LIBRARY_PATH="$DIR/first:$D:$DIR:$LD_LIBRARY_PATH" + + if [ "${INLA_DEBUG}XX" != "XX" ]; then + echo "LD_LIBRARY_PATH=$LD_LIBRARY_PATH" +diff -ru r-inla-Version_24.01.18.orig/rinla/inst/bin/linux/64bit/inla.run r-inla-Version_24.01.18/rinla/inst/bin/linux/64bit/inla.run +--- r-inla-Version_24.01.18.orig/rinla/inst/bin/linux/64bit/inla.run 2024-01-18 20:34:05.000000000 +0100 ++++ r-inla-Version_24.01.18/rinla/inst/bin/linux/64bit/inla.run 2024-01-19 15:56:17.584566196 +0100 +@@ -13,17 +13,6 @@ + fi + fi + +-D="" +-for d in {,/usr}/lib64 /usr/lib64/R/lib {,/usr}/lib/x86_64-linux-gnu {,/usr}/lib; do +- if [ -d "$d" ]; then +- if [ -z "$D" ]; then +- D="$d" +- else +- D="$D:$d" +- fi +- fi +-done +- + for f in $DIR/first/lib*.so*; do + case "$f" in + $DIR/first/libjemalloc.so*) diff --git a/easybuild/easyconfigs/r/R-INLA/R-INLA-24.01.18-foss-2023a.eb b/easybuild/easyconfigs/r/R-INLA/R-INLA-24.01.18-foss-2023a.eb new file mode 100644 index 00000000000..6691aea2a24 --- /dev/null +++ b/easybuild/easyconfigs/r/R-INLA/R-INLA-24.01.18-foss-2023a.eb @@ -0,0 +1,104 @@ +easyblock = 'Bundle' + +name = 'R-INLA' +version = '24.01.18' + +homepage = 'https://www.r-inla.org' +description = "R-INLA is a package in R that do approximate Bayesian inference for Latent Gaussian Models." + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'openmp': True} + +dependencies = [ + ('R', '4.3.2'), + ('R-bundle-CRAN', '2023.12'), + ('GSL', '2.7'), + ('zlib', '1.2.13'), + ('SuiteSparse', '7.1.0'), + ('METIS', '5.1.0'), + ('muParser', '2.3.4'), + ('Rmath', '%(rver)s'), + ('X11', '20230603'), + ('libtool', '2.4.7'), # provides libltdl +] + +default_easyblock = 'ConfigureMake' +# all components are installed from the same source tarball +default_component_specs = { + 'source_urls': ['https://github.com/hrue/r-inla/archive/refs/tags/'], + 'sources': [{'download_filename': 'Version_%s.tar.gz' % version, 'filename': 'R-INLA-%s.tar.gz' % version}], + 'skipsteps': ['configure'], + 'checksums': ['ad166a01b8d774d52e4e9a1dc94547439c263af6539605f47735d3a3cc294145'], +} + +local_gmrflib_buildopts = ' -C r-inla-*/gmrflib PREFIX=%(installdir)s CC="$CC" FC="$FC" ' +local_gmrflib_buildopts += ' FLAGS="$CXXFLAGS -DINLA_LINK_WITH_OPENBLAS " ' + +# enable linking with fake PARDISO library (since PARDISO is not freely available) +local_rinla_prebuildopts = "sed -i 's@src/tweedie.o@src/tweedie.o src/libpardiso.o@g' r-inla-*/inlaprog/Makefile && " +local_rinla_prebuildopts += "export CPATH=$EBROOTR/lib64/R/include/:$CPATH && " + +local_inla_buildopts = '-C r-inla-*/inlaprog PREFIX=%(installdir)s ' +local_inla_buildopts += ' CC="$CC" CXX="$CXX" FC="$FC" LD="$CXX -lltdl" ' +local_inla_buildopts += ' FLAGS="$CXXFLAGS -DINLA_LINK_WITH_OPENBLAS"' + +components = [ + ('taucs', version, { + 'easyblock': 'MakeCp', + 'prebuildopts': "cd r-inla-*/extlibs && tar xvfz taucs-2.2--my-fix.tgz && cd taucs-2.2--my-fix && ", + 'buildopts': 'CC="$CC" CFLAGS="$CFLAGS" FC="$FC" FFLAGS="$FFLAGS" LIBBLAS="$LIBBLAS" LIBLAPACK="$LIBLAPACK"', + 'files_to_copy': [(['r-inla-*/extlibs/taucs-2.2--my-fix/lib/linux/libtaucs.a'], 'lib')], + }), + ('fmesher-R-INLA', version, { + 'patches': ['R-INLA-24.01-18_fix-hardcoded-deps.patch'], + 'checksums': default_component_specs['checksums'] + [ + '6dadd25dff99862f6271513cb97330549b74e29580209c0b204cd93192f98507', + ], + 'buildopts': '-C r-inla-*/fmesher PREFIX=%(installdir)s CC="$CC" CXX="$CXX" LD="$CXX" FLAGS="$CXXFLAGS"', + 'installopts': '-C r-inla-*/fmesher PREFIX=%(installdir)s', + }), + ('GMRFLib', version, { + 'buildopts': local_gmrflib_buildopts, + 'installopts': '-C r-inla-*/gmrflib PREFIX=%(installdir)s', + }), + ('fmesher', '0.1.5', { + 'easyblock': 'RPackage', + 'source_urls': [ + 'https://cran.r-project.org/src/contrib/Archive/fmesher', # package archive + 'https://cran.r-project.org/src/contrib/', # current version of packages + ], + 'sources': ['fmesher_%(version)s.tar.gz'], + 'checksums': ['f6f7af8a88e87d1b0580afbea5284ca1140124686356da72c51fb3929791f85f'], + 'start_dir': 'fmesher', + }), + ('rinla', version, { + 'patches': ['R-INLA-24.01-18_remove-hardcoding.patch'], + 'checksums': default_component_specs['checksums'] + [ + 'fca2bab58ad0bfd08422c06af8991a85f537caccbfbfe1bd6cb5e6892503c7d4', + ], + 'easyblock': 'RPackage', + 'start_dir': 'r-inla-Version_%(version)s/rinla', + 'preinstallopts': "export R_LIBS_SITE=%(installdir)s:$R_LIBS_SITE && ", + }), + (name, version, { + 'prebuildopts': local_rinla_prebuildopts, + 'buildopts': local_inla_buildopts, + 'installopts': '-C r-inla-*/inlaprog PREFIX=%(installdir)s', + }), +] + +local_bins = ['inla', 'fmesher'] + +postinstallcmds = ['ln -s %%(installdir)s/bin/%s %%(installdir)s/INLA/bin/linux/64bit/%s' % (x, x) for x in local_bins] + +sanity_check_paths = { + 'files': ['%s/%s' % (p, x) for p in ['bin', 'INLA/bin/linux/64bit'] for x in local_bins] + + ['lib/libGMRFLib.a', 'lib/libtaucs.a'], + 'dirs': ['doc', 'include/GMRFLib'], +} + +sanity_check_commands = ["Rscript -e 'library(INLA)'"] + ["%s -h" % x for x in local_bins] + +modextrapaths = {'R_LIBS_SITE': ''} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.18-foss-2023a-R-4.3.2.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.18-foss-2023a-R-4.3.2.eb index 48c86d2ed02..7d2ebad2d77 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.18-foss-2023a-R-4.3.2.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.18-foss-2023a-R-4.3.2.eb @@ -1352,6 +1352,15 @@ exts_list = [ ('plyranges', '1.22.0', { 'checksums': ['fcdcad1082fadd1a365dd2d2cc7d955601b737ecd4a567d888d2b445756297fc'], }), + ('seqPattern', '1.34.0', { + 'checksums': ['6037d3685bab94e2d1f6046bdc19369a786a595ef421e6ce7d8a34408a6f4967'], + }), + ('genomation', '1.34.0', { + 'checksums': ['6c7e40caee1115a28617c2a0a0837c92701dbce7511277c078a5957a50e877ed'], + }), + ('ChIPseeker', '1.38.0', { + 'checksums': ['a0d4710fccda620b750f933916acac6d12999a077e1c17632d8823848a2fa82f'], + }), ] modextrapaths = {'R_LIBS_SITE': ''} diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.19-foss-2023b-R-4.4.1.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.19-foss-2023b-R-4.4.1.eb new file mode 100644 index 00000000000..f426b6ffbc5 --- /dev/null +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.19-foss-2023b-R-4.4.1.eb @@ -0,0 +1,1362 @@ +easyblock = 'Bundle' + +name = 'R-bundle-Bioconductor' +version = '3.19' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://bioconductor.org' +description = """Bioconductor provides tools for the analysis and coprehension + of high-throughput genomic data.""" + +toolchain = {'name': 'foss', 'version': '2023b'} + +builddependencies = [('pkgconf', '2.0.3')] + +dependencies = [ + ('R', '4.4.1'), + ('Boost', '1.83.0'), # for mzR + ('GSL', '2.7'), # for flowClust + ('arrow-R', '16.1.0', versionsuffix), # required by RcisTarget +] + +exts_default_options = { + 'source_urls': [ + 'https://bioconductor.org/packages/3.19/bioc/src/contrib/', + 'https://bioconductor.org/packages/3.19/bioc/src/contrib/Archive/%(name)s', + 'https://bioconductor.org/packages/3.19/data/annotation/src/contrib/', + 'https://bioconductor.org/packages/3.19/data/experiment/src/contrib/', + 'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'https://cran.r-project.org/src/contrib/', # current version of packages + 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + ], + 'sources': ['%(name)s_%(version)s.tar.gz'], +} + +exts_defaultclass = 'RPackage' + +# check whether correct version is installed in extension filter +# (some versions in this bundle may be newer than the ones provided by R) +local_ext_version_check = "pkgver = packageVersion('%(ext_name)s'); if (pkgver != '%(ext_version)s') " +local_stop_msg = "stop('%(ext_name)s %(ext_version)s not installed, found ', pkgver, ' instead')" +exts_filter = ("R -q --no-save", "%s { %s }" % (local_ext_version_check, local_stop_msg)) + +# CRAN packages on which these Bioconductor packages depend are available in R module on which this depends +# !! order of packages is important !! +# packages updated on 24 June 2024 +exts_list = [ + ('BiocGenerics', '0.50.0', { + 'checksums': ['11d72e20c087911a58d08db7898d47424930e00265d6e65ae87d14d786f20014'], + }), + ('Biobase', '2.64.0', { + 'checksums': ['a21e35cdf4eeb71fc144712bb619d4ea5124c4013ceb14034a4d638231a0b627'], + }), + ('S4Vectors', '0.42.0', { + 'checksums': ['a94ac904e9e86cccefcade949f27992956727ce3ad2f15d8134421aac191002b'], + }), + ('IRanges', '2.38.0', { + 'checksums': ['62e646697a1dc2f292b2ea374abb1026ccbe2deedc2f1e5a87e2f99e2142e610'], + }), + ('GenomeInfoDbData', '1.2.12', { + 'checksums': ['f7556dc1a0e7b8c33ae7b86519f3f4af15d77c3e2a7be2f6e4a291bf0a95a355'], + }), + ('UCSC.utils', '1.0.0', { + 'checksums': ['349de171d96d28875fdbac104e4a10f0d6c891fdec6676d755d1fa6c5a2f2e71'], + }), + ('GenomeInfoDb', '1.40.1', { + 'checksums': ['80432e8531dc1573a573f940ac3da294faf1b801bbc66a9eef71b5754f90bc94'], + }), + ('zlibbioc', '1.50.0', { + 'checksums': ['0298d59b3bb87179a6accd506a51c80fb9ff922defd24208beb2c93e5032b894'], + }), + ('XVector', '0.44.0', { + 'checksums': ['42a35e3056f4289369082b3f04f6fdd66ea8cccf2dddb7388117f074ea49bb3b'], + }), + ('Biostrings', '2.72.1', { + 'checksums': ['fac10383d8a70ccf0f9b30fb0bc44676160462bbcc81b8edd46d5d7db6f0fb18'], + }), + ('KEGGREST', '1.44.1', { + 'checksums': ['3a4ae05edf81e8667c0b56145e987e52aa768d056873a79c5843c1f257d30d27'], + }), + ('AnnotationDbi', '1.66.0', { + 'checksums': ['3aa793c6888ad50a63d88e2a2df59655c6384ada9db2c5d84473ca76fafa5ebc'], + }), + ('GenomicRanges', '1.56.1', { + 'checksums': ['aaceaadc4562c1bd363370df53c8533ecf2a90fc36c5ceafe0bd5d54626a143c'], + }), + ('BiocParallel', '1.38.0', { + 'checksums': ['7e96e07beb4e59ab08d8064aaf6b4e414c9ccd7657e9949d7d9b2325b2113cd6'], + }), + ('Rhtslib', '3.0.0', { + 'checksums': ['dbecc8c9c6763f636eef38e207be238bd2e80feec0813149f6d8b1ce07592711'], + }), + ('Rsamtools', '2.20.0', { + 'checksums': ['689d914c78a085d15cf6d8a2511cd9ae2c6f2c95755ded799228beca7f039f12'], + }), + ('MatrixGenerics', '1.16.0', { + 'checksums': ['ccff61558f067237b96ea71509e4ca95ad465000294067eb21101892d02df6e4'], + }), + ('S4Arrays', '1.4.1', { + 'checksums': ['94b7e95a5f18e4106d8de1f4d8b1c25a8273aca0fe04519d227a7a6870b8bf71'], + }), + ('SparseArray', '1.4.8', { + 'checksums': ['b5c56eec735d429bafae4b9628818b0dae92e1813c6dc67480009c00a3d91caa'], + }), + ('DelayedArray', '0.30.1', { + 'checksums': ['a66af4adea2ab37be5b7bbc1322bb5d9c7f1f18a9171f6f2e3e839f1b3bad758'], + }), + ('SummarizedExperiment', '1.34.0', { + 'checksums': ['e0c2b2c512dcf273b6c74115bac49093932753b69bb0d95ff80fbcb7057e9b09'], + }), + ('GenomicAlignments', '1.40.0', { + 'checksums': ['fa68d1745004157501460f38d79b6ebb00975ad8a270bf97373665a0ac6c5f96'], + }), + ('pwalign', '1.0.0', { + 'checksums': ['67f1cc7342b2bf887e46fdee8e7ce41be9c4c61fffdfe952bbbab8284b0d12d4'], + }), + ('ShortRead', '1.62.0', { + 'checksums': ['550ead16ef1aa2dca0f221a570ca8216b077d1627701c824cf45773145c7b174'], + }), + ('graph', '1.82.0', { + 'checksums': ['1ba6c6c24905dd081880b9faeb8c3fdf11e67b267cd150a354d45ca4920641f1'], + }), + ('affyio', '1.74.0', { + 'checksums': ['10ed36d8317a1998e7d833e1d2268831f015202adc9f8a06b801f89fa48cda94'], + }), + ('preprocessCore', '1.66.0', { + 'installopts': "--configure-args='--disable-threading'", + 'checksums': ['b59794e3a0dce5b80392c88eef087e6c18a832c69a10a6bd84c2dd35550ca9b1'], + }), + ('BiocManager', '1.30.23', { + 'checksums': ['f7b45dbc49c97b2e6ec4b96ec1d472c6f1a5ad9bc0f933eea4c3ebc90dd8f34c'], + }), + ('affy', '1.82.0', { + 'checksums': ['be770650fec7477b478b7f03f0a3481b036bc2ee08a3dbcee4338fe60313e2a7'], + }), + ('GO.db', '3.19.1', { + 'checksums': ['0f6e6045e5cce6c842ad2ca73a13573b6838ed38f71661dd99d127033c993ba5'], + }), + ('limma', '3.60.3', { + 'checksums': ['ef46a3a924730d359df02f0f439ab2c3923a98b1252b977600e3789865a5c33b'], + }), + ('RBGL', '1.80.0', { + 'checksums': ['63376ec40804f76035ef64dfe6f697ae179071b43a6d33feaf263eba5976d9d8'], + }), + ('org.Hs.eg.db', '3.19.1', { + 'checksums': ['1932eff4d5d46c1ab219565dfff6706c93cfddc6bcbc65223832cc583f702bf7'], + }), + ('AnnotationForge', '1.46.0', { + 'checksums': ['c1b234391b582f5d10b87a80a3bbe00d3d2800d5fc3acf03ff12e8b0608a79c6'], + }), + ('annaffy', '1.76.0', { + 'checksums': ['b22e1f1b513684ffa1f2b7328e96afad1857aa27eda21838c62092ef91ad2889'], + }), + ('gcrma', '2.76.0', { + 'checksums': ['e35a659cbd927fd21341888e9ca04f0eeed4bd0f8272254a1104fa1436596905'], + }), + ('oligoClasses', '1.66.0', { + 'checksums': ['962c4f90080dd104bdaeb91178baa1552f761d3261130695bfd2667e2b732c96'], + }), + ('edgeR', '4.2.0', { + 'checksums': ['0f4343a340dbb609b6688d9b1eecb99bc474572c720c8ae7a21e4b30e0b86df0'], + }), + ('PFAM.db', '3.19.1', { + 'checksums': 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['1f5aef1116f9767e3a76a820e19563e616bc33b62fd1371e7a352864495eae72'], + }), + ('reactome.db', '1.88.0', { + 'checksums': ['8762f24cab5c1056aacd714e0dc355576c8f3b5a325e638dc21bd2b947718bbb'], + }), + ('graphite', '1.50.0', { + 'checksums': ['fab5eb46d8d48d149a2ad4ca42d2970dd074d4560fff71629a2113f9e07bd5f7'], + }), + ('ReactomePA', '1.48.0', { + 'checksums': ['667e432e42ea75ce3d39d7f4d0360cb1d3634843d8670aba0c9a7df37ecbb244'], + }), + ('flowClean', '1.42.0', { + 'checksums': ['59cbcb27f4e291c8b71cd419939b7af9c6678108c00d7efaa520e0613a47a8a8'], + }), + ('flowAI', '1.34.0', { + 'checksums': ['0aa7cd379275346141554b9b0b634909d7dc2cb6df2d88c6a765aa2892fa38ea'], + }), + ('flowFP', '1.62.0', { + 'checksums': ['0c8e7ca9ea8f2c44bc16990a758dd16de8b7fafffe3eff80e56629c2c9c4f5e6'], + }), + ('simplifyEnrichment', '1.14.0', { + 'checksums': ['1166ba940119c40865320791896333f96007d1608bfcb8c224fdb127e8cc6180'], + }), + ('RPMG', '2.2-7', { + 'checksums': ['c413de3c126bc377fe31a948887d27f404a9637c57fe0e07b087d5509cb99f11'], + }), + ('Rwave', '2.6-5', { + 'checksums': ['6c9ef75bb376f2e3f5c5dcd3b3fdca7d86797ce809da34f444632657189be2e4'], + }), + ('RSEIS', '4.2-0', { + 'checksums': ['93ec391f69660fffdeee79a16b312522dada399a83a35758e69422145e682d14'], + }), + ('splancs', '2.01-45', { + 'checksums': ['8bccf1d61d7feaab52da07a9c95aa66bcd3986a6b214f13b232c1e2bea4b76d3'], + }), + ('MBA', '0.1-0', { + 'checksums': ['78039905c5b98be2bb79a5f292187a2aca21ef449daeefea58b0cac53a5283af'], + }), + ('GEOmap', '2.5-5', { + 'checksums': ['8a17a78926cda3f885584f797db6765d218f89b39eda512ff8af379651fb483f'], + }), + ('RFOC', '3.4-10', { + 'checksums': ['b1211db8960b482ebb516233c86b075d1a1f006a88191a72fa98babd5a8e2100'], + }), + ('flowDensity', '1.38.0', { + 'checksums': ['8cc17c977423544785dda174e8ffd44292ffb7cfbb09f500e709bc97b51c649f'], + }), + ('flowPeaks', '1.50.0', { + 'checksums': ['c5dd336f4819ed27f4bc32fd6ca1026398e41a2669e8b9cce00218151b9db618'], + }), + ('SamSPECTRAL', '1.58.0', { + 'checksums': ['8abe70ee30a05ce4a3da9a012e90b274c27bbe4337d02f287aa0a7a80c7d2317'], + }), + ('ddPCRclust', '1.24.0', { + 'checksums': ['b789c218722571e5bb1d6c643f235ba71eb6f98325ba119317ceafcfa787b65a'], + }), + ('feature', '1.2.15', { + 'checksums': ['de38292b7e800068a20824e2a9e7d5d4d0b465b7925db0d165346aa5030ff67b'], + }), + ('flowMerge', '2.52.0', { + 'checksums': ['ddbb80ed0ac59917d6be9e987ad397880500be087cd9017ab2206a39642dc7fc'], + }), + ('TrajectoryUtils', '1.12.0', { + 'checksums': ['30612e70306819f030dba4b462a8a82b67970e4ee66cc130158e328b08ae0197'], + }), + ('slingshot', '2.12.0', { + 'checksums': ['cc2622ffd37dcb60e54b807730e0bec12e0a7a87380904229c24d92515f5ad14'], + }), + ('TreeSummarizedExperiment', '2.12.0', { + 'checksums': ['b1b4b15858730b62cf07cbaa8506a8a8fe0f393e55a315577efd16b56ce2ff79'], + }), + ('decontam', '1.24.0', { + 'checksums': ['67bdfd2d95036f0d70c03a0c406fe9c5f38083a8ff79eb4c73cf48dabf4c4df6'], + }), + ('DECIPHER', '3.0.0', { + 'checksums': ['95da04138348bf370254893a41d96bc2cee7770b1ff199fb73bd50e2f5a0ffad'], + }), + ('mia', '1.12.0', { + 'checksums': ['512805cf6f77c62b25d95ebc3ed16988cf3297be5b712934c3f8130bcfa2c2f2'], + }), + ('ANCOMBC', '2.6.0', { + 'checksums': ['a8ac172f3308c60d17823c064aac2e9f2edf70ab42fee3c40f143e3836734d92'], + }), + ('decoupleR', '2.10.0', { + 'checksums': ['2c561626029234a3d9ed191c4e6b2db80b1d7eb6218aa20edc0dcc4f61e11c18'], + }), + ('UCell', '2.8.0', { + 'checksums': ['bb8617224382e61a190fc2c5a074a24440dd8edd7f1787f0defbf1e673262627'], + }), + ('intervals', '0.15.4', { + 'checksums': ['50c0e1e3aab3e7b72cc1f0a6559d96caa3a360e969c38538479907e6cbe39f8f'], + }), + ('oompaBase', '3.2.9', { + 'checksums': ['14ca2b8e713a6a7ce13758f7f5c183dbc4fdfedc4f1244ca31bbdadf8a16bcb2'], + }), + ('oompaData', '3.1.4', { + 'checksums': ['06252409a94f9eaf4ef723becd24d17e1ef7b495aada44853f4661d942292d3d'], + }), + ('TailRank', '3.2.2', { + 'checksums': ['21ed95ea47d21155f08ae2ad7bca9547f89f492000bc1defe1cc5ec172739d09'], + }), + ('RnBeads', '2.22.0', { + 'checksums': ['720b927f27713b7a16d703a1c77c1cb481f2c263b625a064dd004fed57fded6c'], + }), + ('RnBeads.hg19', '1.36.0', { + 'checksums': ['c991085a2420b01c075b1f3a27645ed4c7a3b8e11b5c9efa52e6c4b4ffb0c77a'], + }), + ('RnBeads.hg38', '1.36.0', { + 'checksums': ['1498b7131f3e30fc3860977829f8c457306bdd364e3a8807b5367d7314eace15'], + }), + ('RnBeads.mm9', '1.36.0', { + 'checksums': ['0b9456e3c19d7f9cd62a36290bc6d048d5eeae2fa09fbe701d2d4c59a292a5ad'], + }), + ('RnBeads.mm10', '2.12.0', { + 'checksums': ['d4b5f53c0b5da080f7c252965032e250a657e41a80c8181c28c8b9327cdd3194'], + }), + ('RnBeads.rn5', '1.36.0', { + 'checksums': ['8e384bffbe6de580c00779415fd7fefb7f01a7b9e0090a11200f284680f11b25'], + }), + ('log4r', '0.4.3', { + 'checksums': ['dfe3d49d35a8d8f3ad63f156d18e860540a01bd0af0e343cbab3e31a2cf5904c'], + }), + ('MSstatsConvert', '1.14.0', { + 'checksums': ['f55f9381d611b80027c489e52de539d8261d84671817b82afeaa617266e45de0'], + }), + ('MSstats', '4.12.0', { + 'checksums': ['773bfef999416c0c0f5f207984991e9cf209598cd6ae32411aae76bd2404305b'], + }), + ('MSstatsTMT', '2.12.1', { + 'checksums': ['f676d71dcd9abfe2eb88b909dc9945622ed19e50bd482f486a7ce4850be4d60e'], + }), + ('MSstatsPTM', '2.6.0', { + 'checksums': ['7063d7c540b188cbf20c083c94d28431e2ecd8fc47c7630d8c5c67ae44eb6c47'], + }), + ('factoextra', '1.0.7', { + 'checksums': ['624ff01c74933352aca55966f8a052b1ccc878f52c2c307e47f88e0665db94aa'], + }), + ('MSstatsLiP', '1.10.0', { + 'checksums': ['40a60aef2d736da2936f1a4b624a962ed69490e6e38a2587df8b6cf5eff2eece'], + }), + ('babelgene', '22.9', { + 'checksums': ['ce6601dcb78352516d3b0355042c52a20e154b39d3b27b93ff52150a59c885e2'], + }), + ('msigdbr', '7.5.1', { + 'checksums': ['dc30487bdf3594425ae9faec1ca0d7d0cd7278f4f177689133f92880e74acaca'], + }), + ('escape', '2.0.0', { + 'checksums': ['5dfcdaf7d1b1836c276a1284ebbc6bbcaeb35da11805a2491bd4cb795acf8b0f'], + }), + ('plyranges', '1.24.0', { + 'checksums': ['a8505d774d0cf9c1488205343abd1817dd5d016082597bb173d002d496a10566'], + }), +] + +modextrapaths = {'R_LIBS_SITE': ''} + +sanity_check_paths = { + 'files': [], + 'dirs': ['AnnotationDbi', 'BiocManager', 'GenomicFeatures'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2023.12-foss-2023a.eb b/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2023.12-foss-2023a.eb index 57ab900fc6c..972a8488f6a 100644 --- a/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2023.12-foss-2023a.eb +++ b/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2023.12-foss-2023a.eb @@ -43,10 +43,6 @@ configopts = "--with-pic --enable-threads --enable-R-shlib" # we're installing them anyway below configopts += " --with-recommended-packages=no" -# specify that at least EasyBuild v3.5.0 is required, -# since we rely on the updated easyblock for R to configure correctly w.r.t. BLAS/LAPACK -easybuild_version = '3.5.0' - exts_defaultclass = 'RPackage' exts_default_options = { @@ -871,7 +867,10 @@ exts_list = [ 'checksums': ['8e50415e415702402473caf622d86b89ddc881f6e5d888079a4818a8807ac9a2'], }), ('bold', '1.3.0', { - 'checksums': ['0ead11d4386c4c0cd578d3a956f809db2001e387e449a431b4ad503f3da38f5f'], + 'checksums': [ + ('0ead11d4386c4c0cd578d3a956f809db2001e387e449a431b4ad503f3da38f5f', + '4920fbebd22fb1d0f1a31ccc09c98aec446bb6cb5f65a2610437e405c0512c68'), + ], }), ('rredlist', '0.7.1', { 'checksums': ['92a10c37a211dc19b41b93f9ceb13d7ce1c3d3a7290cbba4c1688d944353ae85'], @@ -3425,6 +3424,12 @@ exts_list = [ ('XBRL', '0.99.19.1', { 'checksums': ['ad9ebb5431bdfecc38b8bf3b2552f1a048878a9ac02f5a9d71279b3b099a9757'], }), + ('rhandsontable', '0.3.8', { + 'checksums': ['901ed9c59936f7fa52ad8db3111c8904ab962f9c74f1b6cd40f81683af35d21d'], + }), + ('missMDA', '1.19', { + 'checksums': ['f9675884829b2fef75237c335b21991d163674320e766523c71c7a853f95e65c'], + }), ] modextrapaths = {'R_LIBS_SITE': ''} diff --git a/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2024.06-foss-2023b.eb b/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2024.06-foss-2023b.eb new file mode 100644 index 00000000000..09e8f65ae06 --- /dev/null +++ b/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2024.06-foss-2023b.eb @@ -0,0 +1,3481 @@ +easyblock = 'Bundle' + +name = 'R-bundle-CRAN' +version = '2024.06' + +homepage = 'https://www.r-project.org/' +description = "Bundle of R packages from CRAN" + +toolchain = {'name': 'foss', 'version': '2023b'} + +builddependencies = [ + ('pkgconf', '2.0.3'), + ('Xvfb', '21.1.9'), + ('Autotools', '20220317'), + ('CMake', '3.27.6'), +] + +dependencies = [ + ('R', '4.4.1'), + ('libxml2', '2.11.5'), # for XML + ('GMP', '6.3.0'), # for igraph + ('NLopt', '2.7.1'), # for nlopt + ('FFTW', '3.3.10'), # for fftw + ('libsndfile', '1.2.2'), # for seewave + ('ICU', '74.1'), # for rJava & gdsfmt + ('HDF5', '1.14.3'), # for hdf5r + ('UDUNITS', '2.2.28'), # for units + ('GSL', '2.7'), # for RcppGSL + ('ImageMagick', '7.1.1-34'), + ('GLPK', '5.0'), # for Rglpk + ('nodejs', '20.9.0'), # for V8 (required by rstan) + ('GDAL', '3.9.0'), # for sf + ('MPFR', '4.2.1'), # for Rmpfr + ('PostgreSQL', '16.1'), # for RPostgreSQL +] + +# Some R extensions (mclust, quantreg, waveslim for example) require the math library (-lm) to avoid undefined symbols. +# Adding it to FLIBS makes sure it is present when needed. +preconfigopts = 'export FLIBS="$FLIBS -lm" && ' + +configopts = "--with-pic --enable-threads --enable-R-shlib" +# some recommended packages may fail in a parallel build (e.g. Matrix), and +# we're installing them anyway below +configopts += " --with-recommended-packages=no" + +exts_defaultclass = 'RPackage' + +exts_default_options = { + 'source_urls': [ + 'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'https://cran.r-project.org/src/contrib/', # current version of packages + 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + ], + 'source_tmpl': '%(name)s_%(version)s.tar.gz', +} + +# check whether correct version is installed in extension filter +# (some versions in this bundle may be newer than the ones provided by R) +local_ext_version_check = "pkgver = packageVersion('%(ext_name)s'); if (pkgver != '%(ext_version)s') " +local_stop_msg = "stop('%(ext_name)s %(ext_version)s not installed, found ', pkgver, ' instead')" +exts_filter = ("R -q --no-save", "%s { %s }" % (local_ext_version_check, local_stop_msg)) + +# the dbarts extension needs an additional compiler flag on Arm systems to prevent "incompatible types" errors +# cfr. https://github.com/vdorie/dbarts/issues/66 +if ARCH == 'aarch64': + local_dbarts_preinstallopts = 'sed -i "s|-c partition_neon.c|-flax-vector-conversions -c partition_neon.c|"' + local_dbarts_preinstallopts += ' src/misc/Makefile && ' +else: + local_dbarts_preinstallopts = '' + +# !! order of packages is important !! +# packages updated on 24 June 2024 +exts_list = [ + ('abind', '1.4-5', { + 'checksums': ['3a3ace5afbcb86e56889efcebf3bf5c3bb042a282ba7cc4412d450bb246a3f2c'], + }), + ('magic', '1.6-1', { + 'checksums': ['ca79ec7ae92b736cb128556c081abf547f49956c326e053a76579889cbcb7976'], + }), + ('RcppProgress', '0.4.2', { + 'checksums': ['b1624b21b7aeb1dafb30f092b2a4bef4c3504efd2d6b00b2cdf55dc9df194b48'], + }), + ('lpSolve', '5.6.20', { + 'checksums': ['3ffe06a0685123c36cd306b874f89a59a70c864c8f78c5569f82a86abedc21db'], + }), + ('linprog', '0.9-4', { + 'checksums': ['81a6aa2fdc075f12dc912794d0554f87705a8b872b99c89a90a69ee9ada864b4'], + }), + ('geometry', '0.4.7', { + 'checksums': ['96204205f51b4d63c2e7a7b00365def27d131f3c9ec66db56b510046e5d2013b'], + }), + ('bit', '4.0.5', { + 'checksums': ['f0f2536a8874b6a30b80baefbc68cb21f0ffbf51f3877bda8038c3f9f354bfbc'], + }), + ('filehash', '2.4-5', { + 'checksums': ['3b1ee2794dd61e525ee44db16611c65957691d77bb26ae481eba988bb55da22c'], + }), + ('ff', '4.0.12', { + 'checksums': ['08af355a9a10fe29d48d085abc7cf1f975e1a4a670668a4f8d9632d087fb41bf'], + }), + ('bnlearn', '4.9.4', { + 'checksums': ['ce3d8d89451fed9277f879c03bb02bc17acab13f1f35587aab8175b80246eeea'], + }), + ('bootstrap', '2019.6', { + 'checksums': ['5252fdfeb944cf1fae35016d35f9333b1bd1fc8c6d4a14e33901160e21968694'], + }), + ('combinat', '0.0-8', { + 'checksums': ['1513cf6b6ed74865bfdd9f8ca58feae12b62f38965d1a32c6130bef810ca30c1'], + }), + ('deal', '1.2-42', { + 'checksums': ['a17f452a94fc3964c939c5b147ad6d4f326a0990493519d376d6700cf733a134'], + }), + ('fdrtool', '1.2.17', { + 'checksums': ['3452601adbead9be4820794e3af2666f710fdf9b801186df565b80b43629c5dd'], + }), + ('formatR', '1.14', { + 'checksums': ['4ebaab2c3f8527871655246b62abd060bc75dae1cec7f962ca4752b8080f474c'], + }), + ('gtools', '3.9.5', { + 'checksums': ['dee9b6c1152db1a5dc427d074b32bbbb738708683f17a95e0e95e4d79fdf174b'], + }), + ('gdata', '3.0.0', { + 'checksums': 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('TMB', '1.9.12', { + 'checksums': ['db5801f43e55fdeea520355628286c491c694f1165e8567eecd5f3d864cfc7f0'], + }), + ('glmmTMB', '1.1.9', { + 'checksums': ['93d5a6b907b0f71f97c13134e0c450c951b3636365a369f48edb804207e78963'], + }), + ('gmp', '0.7-4', { + 'checksums': ['a7d6b40f77d2619c11db5170b8f47336f7c5fa1db7eed0ac9d8a432e41053919'], + }), + ('ROI', '1.0-1', { + 'checksums': ['d4ff143304f1422ecc455eb1a00896530193c1a227ed7f3e9da2baa95d921616'], + }), + ('Rglpk', '0.6-5.1', { + 'checksums': ['e528b8c487e9dfef16ade3b834a17fc93cc898869978a5dd79bee2c5bf9cb6c9'], + }), + ('ROI.plugin.glpk', '1.0-0', { + 'checksums': ['b361b0d4222d74b21432cdc6990762affecdbcec8fd6bbdb13b78b59cb04b444'], + }), + ('spaMM', '4.5.0', { + 'checksums': ['bbf9a15620f707f49c81b465f9d87a6f151be8afffdc18f060cbbe719e2424db'], + }), + ('qgam', '1.3.4', { + 'checksums': ['7633120a48a85ab73f7e1bc8b02c98319285c2abd05f9d13d25339d7aaaacacb'], + }), + ('DHARMa', '0.4.6', { + 'checksums': ['32fd3d5cd354ff6b5457599d7fb870b94c7d86401a47c7c553bca26f782a4b73'], + }), + ('mvnfast', '0.2.8', { + 'checksums': ['8871e0ce54b87afc556fd94ca77c3db72dcbb8c245558287e0fe342e30eec9a0'], + }), + ('bridgesampling', '1.1-2', { + 'checksums': ['54ecd39aa2e36d4d521d3d36425f9fe56a3f8547df6048c814c5931d790f3e6b'], + }), + ('BayesianTools', '0.1.8', { + 'checksums': ['f543bdd6b61ec7fd31a7e4040bd7835341d9079243fa4eb0cd5e684e5e39bdd1'], + }), + ('gomms', '1.0', { + 'checksums': ['52828c6fe9b78d66bde5474e45ff153efdb153f2bd9f0e52a20a668e842f2dc5'], + }), + ('feather', '0.3.5', { + 'checksums': ['50ff06d5e24d38b5d5d62f84582861bd353b82363e37623f95529b520504adbf'], + }), + ('dummies', '1.5.6', { + 'checksums': ['7551bc2df0830b98c53582cac32145d5ce21f5a61d97e2bb69fd848e3323c805'], + }), + ('SimSeq', '1.4.0', { + 'checksums': ['5ab9d4fe2cb1b7634432ff125a9e04d2f574fed06246a93859f8004e10790f19'], + }), + ('uniqueAtomMat', '0.1-3-2', { + 'checksums': ['f7024e73274e1e76a870ce5e26bd58f76e8f6df0aa9775c631b861d83f4f53d7'], + }), + ('PoissonSeq', '1.1.2', { + 'checksums': ['6f3dc30ad22e33e4fcfa37b3427c093d591c02f1b89a014d85e63203f6031dc2'], + }), + ('aod', '1.3.3', { + 'checksums': ['b7245e8abf7d78cdfa7f74f6d90f79a418b883058aa3edd5977a60bdbed4087e'], + }), + ('cghFLasso', '0.2-1', { + 'checksums': ['6e697959b35a3ceb2baa1542ef81f0335006a5a9c937f0173c6483979cb4302c'], + }), + ('svd', '0.5.5', { + 'checksums': ['e20139794ad1a8c7d7fdffb8dac068c6fbdc8f0b65929341cb5c4d2ff1f98cc6'], + }), + ('Rssa', '1.0.5', { + 'checksums': ['475819636afb330a4467722b0a664fa54d6114d782b681f681ccb123f3be522d'], + }), + ('JBTools', '0.7.2.9', { + 'checksums': ['b33cfa17339df7113176ad1832cbb0533acf5d25c36b95e888f561d586c5d62f'], + }), + ('RUnit', '0.4.33', { + 'checksums': ['b2a4c5afc7ef9534dac5006f6ef1b2af68630bb73eb74ef70ec7ed53dae6cb5f'], + }), + ('DistributionUtils', '0.6-1', { + 'checksums': ['31e79eaa8871b0b9fb8ac63a3fbd852f9ed3047bc584c233ac030b50e1b963d7'], + }), + ('gapfill', '0.9.6-1', { + 'checksums': ['22f04755873e34a9077bb1b1de8d16f5bc56cb8c395c4f797f9ad0b209b1b996'], + }), + ('gee', '4.13-27', { + 'checksums': ['3fb4773fd58fe6aa8bd0ae031add8ee7c33d0e43dfec92e89db04b5dc709a49c'], + }), + ('Matching', '4.10-14', { + 'checksums': ['bfb4286a5da29dcfcc4ddee6299e2d91c0de177720b060b8946fd16f32f6a6b0'], + }), + ('chk', '0.9.1', { + 'checksums': ['f9b43dcf1002c6244dc87965f21dff6e65256eb634b826deb7b5cdfc26f505a7'], + }), + ('MatchIt', '4.5.5', { + 'checksums': ['ae39cafdd3a52487e3ebff1b49642f516cf64321fea90fa57ce3d545a259859e'], + }), + ('RItools', '0.3-4', { + 'checksums': ['047684b8d135d9a90156a7be6625c2961c8f6789bf80533b525a201a69ee52d7'], + }), + ('mitools', '2.4', { + 'checksums': ['f204f3774e29d79810f579f128de892539518f2cbe6ed237e08c8e7283155d30'], + }), + ('survey', '4.4-2', { + 'checksums': ['8a4a0f3122f0971f7c8756805add781192c655f507b235801dd78457a8d2f1bd'], + }), + ('rlemon', '0.2.1', { + 'checksums': ['4a18fa034f197c68daf48daf25c0e41f1b8acbe71d030c6bc1f55e3062a10375'], + }), + ('optmatch', '0.10.7', { + 'checksums': ['330fc251ebe6901a6fbf931457943ee113bc882f786b2b14d837cd59f4327d1d'], + }), + ('SPAtest', '3.1.2', { + 'checksums': ['b3d74ed2b0a6475a9966dd50eb5d363d0b2985636271dfbf82f0472b8d22b9f4'], + }), + ('RSpectra', '0.16-1', { + 'checksums': ['cba5d3403d6a7d0e27abf6279fbfea6e0d0fe36b28c688bbadb8eafb3841329a'], + }), + ('SKAT', '2.2.5', { + 'checksums': ['1441fa46b6a78a060007442fb8cb8c87753bdc2b1ea2dc24ff951ac3fef651f4'], + }), + ('GillespieSSA', '0.6.2', { + 'checksums': ['f4233b4a44c7d4b9e3459b1efa9a8087a602ef93806b4d70eadbb537b67567c2'], + }), + ('startupmsg', '0.9.6.1', { + 'checksums': ['431b4eea5fe9f1f421518b24cd4ae27c9228f3311ac11bfcaf22620f86a65881'], + }), + ('distr', '2.9.3', { + 'checksums': ['15ac7c835bca5b90121fe42fab35f8151a3bd876d3c88a41eb5339c4bdd7db58'], + }), + ('distrEx', '2.9.2', { + 'checksums': ['d06bcaa1ccb52ef775f7c8b2d6d4676408dbc2813dfc128da34ffa4c7740f3e4'], + }), + ('minerva', '1.5.10', { + 'checksums': ['2f26353d8fcc989ac698c4e45bb683801b1a7bb60b14903d05a4d73c629c590f'], + }), + ('RcppTOML', '0.2.2', { + 'checksums': ['371391f9ca82221e76a424082ea9ebc5ea2c50f14e8408469b09d7dc3e6f63aa'], + }), + ('here', '1.0.1', { + 'checksums': ['08ed908033420d3d665c87248b3a14d1b6e2b37844bf736be620578c20ca346b'], + }), + ('reticulate', '1.38.0', { + 'checksums': ['cb2f313e2351a3cde03be55561b592318ec5376fba3b10e371eeff1986deca8d'], + }), + ('umap', '0.2.10.0', { + 'checksums': ['8d4786929345e8980bb8be8bb4b6300a679bba03a5984eed59e5e00c626b6ea9'], + }), + ('KODAMA', '2.4', { + 'checksums': ['78f2ea3596f3697fc06a080947e82a54c5270ed90f86916b91902e5db6ec85e7'], + }), + ('locfdr', '1.1-8', { + 'checksums': ['42d6e12593ae6d541e6813a140b92591dabeb1df94432a515507fc2eee9a54b9'], + }), + ('ica', '1.0-3', { + 'checksums': ['474d3530b16b76a1bf1a1114d24092678ea7215fa57c6fdcee6333f1e768b865'], + }), + ('dtw', '1.23-1', { + 'checksums': ['6ed6a3b52be673ce2617b8d48723c7c488c95aab88fe2912d7e00507838e826d'], + }), + ('SDMTools', '1.1-221.2', { + 'checksums': ['f0dd8c5f98d2f2c012536fa56d8f7a58aaf0c11cbe3527e66d4ee3194f6a6cf7'], + }), + ('ggridges', '0.5.6', { + 'checksums': ['efccaa309a150d11c6b402b912e618ea041f25cca3101f32cd821a6f41684e35'], + }), + ('TFisher', '0.2.0', { + 'checksums': ['bd9b7484d6fba0165841596275b446f85ba446d40e92f3b9cb37381a3827e76f'], + }), + ('lsei', '1.3-0', { + 'checksums': ['6289058f652989ca8a5ad6fa324ce1762cc9e36c42559c00929b70f762066ab6'], + }), + ('npsurv', '0.5-0', { + 'checksums': ['bc87db76e7017e178c2832a684fcd49c42e20054644b21b586413d26c8821dc6'], + }), + ('fitdistrplus', '1.1-11', { + 'checksums': ['26274f2b710b2417a8bca314d400abf320d4ccf0387ad082743056699501b53d'], + }), + ('hdf5r', '1.3.10', { + 'installopts': '--configure-args="--with-hdf5=$EBROOTHDF5/bin/h5pcc"', + 'preinstallopts': "unset LIBS && ", + 'checksums': ['92496e0693a27c0a1c8caba671c51fcecc3a120f8ef7eb0cb3cd686a3e49124e'], + }), + ('DTRreg', '2.2', { + 'checksums': ['9c8954d5c342af85611d13dab5be64c4a7a5904644a6e04ff21d5494559e2fc7'], + }), + ('pulsar', '0.3.11', { + 'checksums': ['ee82ef25b2be4bbac713c34bca85d8ea1fa0e32eb8c800dad7256e145fc79393'], + }), + ('bayesm', '3.1-6', { + 'checksums': ['17d72b9cdc090845f98e7a04640380d0baef8bc23d1487c8f64dc192fdb93cb5'], + }), + ('gsl', '2.1-8', { + 'checksums': ['f33609bf485abd190e65ff5d0fdab438b759294c47b921d983d89d6f053a2d95'], + }), + ('energy', '1.7-11', { + 'checksums': ['c29f8fb000c979d2504f6f6d3a99c773004f77d58793e7e2a5766155272b6511'], + }), + ('compositions', '2.0-8', { + 'checksums': ['c5063488f456992b5821458b3237322addffd3451ae91f9474707886971ef290'], + }), + ('clustree', '0.5.1', { + 'checksums': ['b5f2496e596e3fd140ace69c4837085e13f3abb850f5eb57d496380691fdd117'], + }), + ('tweedie', '2.3.5', { + 'checksums': ['983c745fee5a780d46e8dd04c2eb1c10cb2e222d3679654f0d6934d3db7b1c3e'], + }), + ('RcppGSL', '0.3.13', { + 'checksums': ['fe5e73bc119c6424e1a40b6fea17417a7bba93e81dbe9b7cf86dde9b8e8d93e7'], + }), + ('mvabund', '4.2.1', { + 'checksums': ['ed6946c95609443584081100cd38624d2309f7f5d210fd4b8ec12ad25bd27a06'], + }), + ('fishMod', '0.29', { + 'checksums': ['5989e49ca6d6b2c5d514655e61f75b019528a8c975f0d6056143f17dc4277a5d'], + }), + ('alabama', '2023.1.0', { + 'checksums': ['925f67c72d9cdb677105377777bd09e9b56a61573bea7e3f69e0a49595c7bf1c'], + }), + ('gllvm', '1.4.3', { + 'checksums': ['63b77040e9cf2694882d1d80a3bc3030b3a348819ea38e6728417e4c5de07ecc'], + }), + ('grpreg', '3.4.0', { + 'checksums': ['fd57d20baf63d2cc5821998bca5c3fdcbe46c933c9553caa492911b12654d6ad'], + }), + ('trust', '0.1-8', { + 'checksums': ['952e348b62aec35988b103fd152329662cb6a451538f184549252fbf49d7dcac'], + }), + ('lpSolveAPI', '5.5.2.0-17.11', { + 'checksums': ['b08d6cae4fc17575adf5df0113ea5f4f819bb2c7f87987e0d66c8eabfc933fa4'], + }), + ('ergm', '4.6.0', { + 'checksums': ['b471a60c39eb5b478e06dd0caf1d085f4b0927f1c260de699f1c8d4fe831a7f7'], + }), + ('networkLite', '1.0.5', { + 'checksums': ['aaab55d4f8f0b330fe7c1ecbab3c44746c52c2fda99c53c6b46042bb8775718b'], + }), + ('networkDynamic', '0.11.4', { + 'checksums': ['6bf3e216a444f183ff925e29560fae4c2362cc2a9fed19b3e116a9d9f1184a46'], + }), + ('ergm.multi', '0.2.1', { + 'checksums': ['e09dd0d7207a8214746ea251a50c93f6f5de255175309dc8757206f419a01902'], + }), + ('tergm', '4.2.0', { + 'checksums': ['dcf5a26cc2c4d165766706af08f8ea4f36e328158f5b682490c2a351f7fbda69'], + }), + ('ergm.count', '4.1.2', { + 'checksums': ['9bce70b64a2f60b242603b771370b40d7f7aeed37ed426670131fd966c13b020'], + }), + ('tsna', '0.3.5', { + 'checksums': ['4ee2f773d573f0f4bd93131156fdccf01d7f1a3f725eff3e885021098c6bff65'], + }), + ('statnet', '2019.6', { + 'checksums': ['0903e1a81ed1b6289359cefd12da1424c92456d19e062c3f74197b69e536b29d'], + }), + ('aggregation', '1.0.1', { + 'checksums': ['86f88a02479ddc8506bafb154117ebc3b1a4a44fa308e0193c8c315109302f49'], + }), + ('ComICS', '1.0.4', { + 'checksums': ['0af7901215876f95f309d7da6e633c38e4d7faf04112dd6fd343bc15fc593a2f'], + }), + ('dtangle', '2.0.9', { + 'checksums': ['c375068c1877c2e8cdc5601cfd5a9c821645c3dff90ddef64817f788f372e179'], + }), + ('mcmc', '0.9-8', { + 'checksums': ['6a06440d4b58e8a7f122747d92046ff40da4bb58a20bf642228a648a0c826ea7'], + }), + ('MCMCpack', '1.7-0', { + 'checksums': ['846073d710017ec1dc9a2b4616cb6aeb60ce04e3500a37214522818d34045def'], + }), + ('shinythemes', '1.2.0', { + 'checksums': ['37d68569ce838c7da9f0ea7e2b162ecf38fba2ae448a4888b6dd29c4bb5b2963'], + }), + ('csSAM', '1.2.4', { + 'checksums': ['3d6442ad8c41fa84633cbbc275cd67e88490a160927a5c55d29da55a36e148d7'], + }), + ('bridgedist', '0.1.2', { + 'checksums': ['7210c97fc864e78ea8502067359d642bbd95bf2df30d33da193fc5c004e45baf'], + }), + ('asnipe', '1.1.17', { + 'checksums': ['e7b4010fa1adf27534420db2971dae3c63190920a4323c86fd586842e22d9b07'], + }), + ('liquidSVM', '1.2.4', { + 'patches': ['liquidSVM-1.2.4-fix_ppc_and_aarch64_build.patch'], + # Don't add optimization flags by liquidSVM which may not be known e.g. on PPC + 'preinstallopts': 'LIQUIDSVM_TARGET="empty"', + 'checksums': [ + {'liquidSVM_1.2.4.tar.gz': '15a9c7f2930e2ed3f4c5bcd9b042884ea580d2b2e52e1c68041600c196046aba'}, + {'liquidSVM-1.2.4-fix_ppc_and_aarch64_build.patch': + '46b09e441c3b59af535f20d8db0dee7f1d6a7ddd511175d252115b53cb8b86f8'}, + ], + }), + ('oddsratio', '2.0.1', { + 'checksums': ['2097e7a8bf623379d55652de5dce4946d05163e85d30df50dc19055962bf60b5'], + }), + ('mltools', '0.3.5', { + 'checksums': ['7093ffceccdf5d4c3f045d8c8143deaa8ab79935cc6d5463973ffc7d3812bb10'], + }), + ('h2o', '3.44.0.3', { + 'checksums': ['61a85f6c2f15e8e96839f8a4fd3a45eaa6bca90517bb20a4dd36e951d6fd0c82'], + }), + ('mlegp', '3.1.9', { + 'checksums': ['63296d17a162fdce0958b10f45cb7d5dab4b3ee29340528d33cedcae08a040b3'], + }), + ('itertools', '0.1-3', { + 'checksums': ['b69b0781318e175532ad2d4f2840553bade9637e04de215b581704b5635c45d3'], + }), + ('missForest', '1.5', { + 'checksums': ['417055a03b02ad8359cf1bdc8f89d49531a3a8ee2c98edf90c8a01432f44838d'], + }), + ('bartMachineJARs', '1.2.1', { + 'checksums': ['9f7a20acf4aec249e16f83d81f5ec796aa718deb1b8bc24393fc0421eb8ce1c0'], + }), + ('bartMachine', '1.3.4.1', { + 'checksums': ['3b0a5250f5425a8efe460adcb58ea1342f1d845ae3a8db29dbf4806653884b89'], + }), + ('lqa', '1.0-3', { + 'checksums': ['3889675dc4c8cbafeefe118f4f20c3bd3789d4875bb725933571f9991a133990'], + }), + ('PresenceAbsence', '1.1.11', { + 'checksums': ['c63a6453783865b7c69c580a09a769e99390dd8b2e0f63e48fbfc86da3bee4b7'], + }), + ('GUTS', '1.2.5', { + 'checksums': ['9d983a566daa07d3e0036fe7011efe94f29e31a611493ba16bd316b61730a7b7'], + }), + ('GenSA', '1.1.14', { + 'checksums': ['66e455bb0e66d3c04af84d9dddc9b89f40b4cf9fe9ad1cf0714bcf30aa1b6837'], + }), + ('parsedate', '1.3.1', { + 'checksums': ['1fc31ab9813b61680abf4f4c2705b8f484d56d1d3ef256df84b342b628b6d1b1'], + }), + ('circular', '0.5-0', { + 'checksums': ['4bf4da5de29e555d1a7ae7ea64f8a5dda037e5c423f1078944f0bbb6eb9a7b92'], + }), + ('cobs', '1.3-8', { + 'checksums': ['2c2049c7cb868a2e4e1a530fe7218fac56e6157ef64ad57b91c5bb457dbc9821'], + }), + ('resample', '0.6', { + 'checksums': ['1b958009b18c92a47971847c782af76952ea4e85d5f1e3e1e70fa35c67b95265'], + }), + ('MIIVsem', '0.5.8', { + 'checksums': ['a908f51e1598290d25864c358d57201bd50c1c40775d4d0405cbc8077bee61e1'], + }), + ('medflex', '0.6-10', { + 'checksums': ['bd89a8fe939f3becd71a9dab30fe27fa43c96572d8309d2c1a70633117d4cb33'], + }), + ('Rserve', '1.8-13', { + 'checksums': ['7e5d312fca8029d746f60e7d9e701129561942f97dfc33b036b123f159d69a4c'], + }), + ('spls', '2.2-3', { + 'checksums': ['bbd693da80487eef2939c37aba199f6d811ec289828c763d9416a05fa202ab2e'], + }), + ('Boruta', '8.0.0', { + 'checksums': ['38e75b1ebc8b2d1c54b3373a42529b819c7b4773fd4932f57bc9701d1e3e3dc7'], + }), + ('dr', '3.0.10', { + 'checksums': ['ce523c1bdb62a9dda30afc12b1dd96975cc34695c61913012236f3b80e24bf36'], + }), + ('CovSel', '1.2.1', { + 'checksums': ['b375d00cc567e125ff106b4357654f43bba3abcadeed2238b6dea4b7a68fda09'], + }), + ('tmle', '2.0.1.1', { + 'checksums': ['8c2448f176ed94201affb8a9c42a5d0f56f26e88131ff2c1f4a9d14c5a0d87f6'], + }), + ('ctmle', '0.1.2', { + 'checksums': ['e3fa0722cd87aa0e0b209c2dddf3fc44c6d09993f1e66a6c43285fe950948161'], + }), + ('BayesPen', '1.0', { + 'checksums': ['772df9ae12cd8a3da1d5b7d1f1629602c7693f0eb03945784df2809e2bb061b0'], + }), + ('inline', '0.3.19', { + 'checksums': ['0ee9309bb7dab0b97761ddd18381aa12bd7d54678ccd7bec00784e831f4c99d5'], + }), + ('BMA', '3.18.17', { + 'checksums': ['6d8c514fa179f8a48c2105b551a8a08e28ea4375d06150a4b8ab4ccda577daf5'], + }), + ('BCEE', '1.3.2', { + 'checksums': ['f0e0a6a4eb11213073aa2f0cd6c76d87e8b3965124d8ca509538eb3c128533a0'], + }), + ('bacr', '1.0.1', { + 'checksums': ['c847272e2c03fd08ed79b3b739f57fe881af77404b6fd087caa0c398c90ef993'], + }), + ('clue', '0.3-65', { + 'checksums': ['bdf8fdd35fb2b1c65d09766da79d930fa664a00aa497f03b636400eecb623ef8'], + }), + ('bdsmatrix', '1.3-7', { + 'checksums': ['c3505e5ac06d5e01b3a6bad94177f8375cd9867bb0146cc9c63d92424ecb7922'], + }), + ('fftwtools', '0.9-11', { + 'checksums': ['f1f0c9a9086c7b2f72c5fb0334717cc917213a004eaef8448eab4940c9852c7f'], + }), + ('imagerExtra', '1.3.2', { + 'checksums': ['0ebfa1eabb89459d774630ab73c7a97a93b9481ea5afc55482975475acebd5b8'], + }), + ('MALDIquant', '1.22.2', { + 'checksums': ['6051b07019003c698ae016d79f13945bfe2edec26f8a688126b978cb90adcfff'], + }), + ('threejs', '0.3.3', { + 'checksums': ['76c759c8b20fb34f4f7a01cbd1b961296e1f19f4df6dded69aae7f1bca80219c'], + }), + ('LaplacesDemon', '16.1.6', { + 'checksums': ['57b53882fd7a195b38bbdbbf0b17745405eb3159b1b42f7f11ce80c78ab94eb7'], + }), + ('rda', '1.2-1', { + 'checksums': ['37038a9131c9133519f5e64fa1a86dbe28b21f519cf6528503234648a139ae9a'], + }), + ('sampling', '2.10', { + 'checksums': ['fdec976ec0abfb5c690049d76f89ebcb8ab3650e2eb28a5b54c3984d17372775'], + }), + ('lda', '1.5.2', { + 'checksums': ['95d354786e002352a973052df993b9d3acfc9f9598a053afb95ac27c7e150fd4'], + }), + ('jiebaRD', '0.1', { + 'checksums': ['045ee670f5378fe325a45b40fd55136b355cbb225e088cb229f512c51abb4df1'], + }), + ('jiebaR', '0.11', { + 'checksums': ['adde8b0b21c01ec344735d49cd33929511086719c99f8e10dce4ca9479276623'], + }), + ('hdm', '0.3.2', { + 'checksums': ['3354b22752f0aa0c0d9c8c12b38810202b6380f2587e539be11d9a358412fe6a'], + }), + ('abe', '3.0.1', { + 'checksums': ['66d2e9ac78ba64b7d27b22b647fc00378ea832f868e51c18df50d6fffb8029b8'], + }), + ('SignifReg', '4.3', { + 'checksums': ['f755808fcb618582acb862729b20e267d9c2214f22e6e7a0c8d29073d8faa7b8'], + }), + ('bbmle', '1.0.25.1', { + 'checksums': ['d92a0cf819fe4c08b8eb17f5e03275c8accde7f3b54f990cbba5ab926575b60b'], + }), + ('emdbook', '1.3.13', { + 'checksums': ['26044b7ea1b42304b4dfde48afa94dd487acf979da4db2bf670ba41222083c19'], + }), + ('SOAR', '0.99-11', { + 'checksums': ['d5a0fba3664087308ce5295a1d57d10bad149eb9771b4fe67478deae4b7f68d8'], + }), + ('rasterVis', '0.51.6', { + 'checksums': ['61bd0d19d045b50c6764f3a7c95ce1e734af9e5f964449825d002afe02109489'], + }), + ('tictoc', '1.2.1', { + 'checksums': ['8fcdb7c9a1e4b4817bcab654effd64dea6ec749a7901d4060d5b5c625fc88833'], + }), + ('ISOcodes', '2024.02.12', { + 'checksums': ['02cb7b918034085dffcba0d329a2bc52514873f898a3a716560ebf17b57ae2e6'], + }), + ('stopwords', '2.3', { + 'checksums': ['c5ec1c6ab1bad1786d87d7823d4b63abc94d2fd84ed7d8e985906e96fb6321b2'], + }), + ('janeaustenr', '1.0.0', { + 'checksums': ['b4c32ee1395ee4a8efe714c535c0fe578b0dbf5f3bb85b41fa5cc87569b8e8aa'], + }), + ('SnowballC', '0.7.1', { + 'checksums': ['753cf13f3206751662c03b1cf39bce9e680024f6d9f8503b836a83797181c034'], + }), + ('tokenizers', '0.3.0', { + 'checksums': ['24571e4642a1a2d9f4f4c7a363b514eece74788d59c09012a5190ee718a91c29'], + }), + ('hunspell', '3.0.3', { + 'checksums': ['fdaa1473a62dff2a5923b9bd958d87e546069ca22ce113f44e88c761338442f3'], + }), + ('topicmodels', '0.2-16', { + 'checksums': ['0d5c9c65dd7ba031ba81adc0984d3e36b0309ada2204644bf816370ae656e905'], + }), + ('tidytext', '0.4.2', { + 'checksums': ['0cf4180c2ab9fdb158337a7bfb6ba32f15fb61aae28abce425deaa5933ed2d54'], + }), + ('splitstackshape', '1.4.8', { + 'checksums': ['656032c3f1e3dd5b8a3ee19ffcae617e07104c0e342fc3da4d863637a770fe56'], + }), + ('grImport2', '0.3-1', { + 'checksums': ['216a1a5bb18c7a7dfb13c6c162228c6c81c45408f04d7784b6e60ae6cd4745d2'], + }), + ('preseqR', '4.0.0', { + 'checksums': ['0143db473fb9a811f9cf582a348226a5763e62d9857ce3ef4ec41412abb559bc'], + }), + ('idr', '1.3', { + 'checksums': ['6b3910dc48495439cd01828f8999823864a6712f73560ee3e6c903065c67d1e4'], + }), + ('entropy', '1.3.1', { + 'checksums': ['6f5a89f5ce0e90cbed1695b81259326c976e7a8f538157e223ee5f63b54412b8'], + }), + ('kedd', '1.0.4', { + 'checksums': ['bb944389a61cff22bb3bdde938a0ff6c16700a1ca725ef36b391b97812c45b26'], + }), + ('HiddenMarkov', '1.8-13', { + 'checksums': ['7186d23e561818f3e1f01376a4fb2af9ccee775ce5afc1e3175f3b07a81db515'], + }), + ('lmerTest', '3.1-3', { + 'checksums': ['35aa75e9f5f2871398ff56a482b013e6828135ef04916ced7d1d7e35257ea8fd'], + }), + ('distributional', '0.4.0', { + 'checksums': ['09b5f3279bed4c79575f75d5f7f5e3e593c7838434a78c89f0b7184e8f20e602'], + }), + ('posterior', '1.5.0', { + 'checksums': ['4a10307fcae321f2cd4ca7871504a0c6c9152b8473dc9a033721e8dcda18e2de'], + }), + ('loo', '2.7.0', { + 'checksums': ['7664f331555e569d6037100048681e3a696fb9ca2e87907712eb54faa85bcb36'], + }), + ('RcppParallel', '5.1.7', { + 'checksums': ['f9c30eb9ce1abffc590825d513d6d28dcbe970e36032dd7521febf04e905b29c'], + }), + ('StanHeaders', '2.32.9', { + 'checksums': ['27b0feb34e1200193e3a31a951d28c5adc91c93dc0454732545b8078132e0b33'], + }), + ('V8', '4.4.2', { + 'installopts': '--configure-vars="INCLUDE_DIR=$CPATH LIB_DIR=$LIBRARY_PATH"', + 'preinstallopts': "export CPATH=$EBROOTNODEJS/include/node:$CPATH && ", + 'checksums': ['e7bc35f3420f5f537121d681a90c16a74b36dc17210c9425e7f03842493a9670'], + }), + ('QuickJSR', '1.2.2', { + 'checksums': ['51842f846585c8dfdab155eb5a26be0735cae280fa1c1bff1907d718525968ed'], + }), + ('rstan', '2.32.6', { + 'checksums': ['3390d00191bbd3b0739dd19fe437b99a041a6b04be208877b48419d1348a1a70'], + }), + ('Rborist', '0.3-7', { + 'checksums': ['011efef9e6f304f752bd5013627dc8482f0e9d4cf1ec49503e97d3718f542596'], + }), + ('VSURF', '1.2.0', { + 'checksums': ['c027b1e19762f1eaf4a559c2592f3530210fefd21ee3d7c787c73b776c683393'], + }), + ('mRMRe', '2.1.2.1', { + 'checksums': ['d53c392e82a437005b71d0e8b97350d0237608fffafe087700fe7f6770167fd9'], + }), + ('dHSIC', '2.1', { + 'checksums': ['94c86473790cf69f11c68ed8ba9d6ae98218c7c69b7a9a093f235d175cf83db0'], + }), + ('ggsci', '3.2.0', { + 'checksums': ['41d8ed4c01c3740028bdf2ba9c5550f1142061e4a40c93b1d2160719c59c3c4a'], + }), + ('ggsignif', '0.6.4', { + 'checksums': ['112051af425a0c0f2998ce187dacad066bc16f55af01e3e7b76d62ff6954b20a'], + }), + ('corrplot', '0.92', { + 'checksums': ['e8c09f963f9c4837036c439ebfe00fa3a6e462ccbb786d2cf90850ddcd9428bd'], + }), + ('rstatix', '0.7.2', { + 'checksums': ['e0c6f5ab1d9c5d84713defabc5d149aad3d55944cffdb903cc128b694e5221a1'], + }), + ('ggfan', '0.1.3', { + 'checksums': ['5c888b203ecf5e3dc7a317a790ca059c733002fbca4b4bc1a4f62b7ded5f70dc'], + }), + ('ggpubr', '0.6.0', { + 'checksums': ['2e6ec5d8151991d17ef8832259cf545fa0d1a50b326ba8c1c4657700171df774'], + }), + ('yaImpute', '1.0-34', { + 'checksums': ['b4c898c95fca784480bbbc239c78c85dc9f45a96c34c563ea7e81248ef8a8a73'], + }), + ('intrinsicDimension', '1.2.0', { + 'checksums': ['6cc9180a83aa0d123f1e420136bb959c0d5877867fa170b79536f5ee22106a32'], + }), + ('leiden', '0.4.3.1', { + 'checksums': ['a9ecbbcfa2724d8fdd0133af569278e036b25b6e2cbb23d453092cc6b3fc30e2'], + }), + ('sctransform', '0.4.1', { + 'checksums': ['5f6be7f8be543e4c32c8007207b603a750881459370b7bb5afd63e8c8fabf171'], + }), + ('packrat', '0.9.2', { + 'checksums': ['69df5943257e6c4d06f3d907241b668b53dedece72158ca935260b8b8e1672d7'], + }), + ('colourpicker', '1.3.0', { + 'checksums': ['c7f2618cd1ae1f7ac15aee072c648e6494dfff6714e13dc7cd1da993d1102510'], + }), + ('ggExtra', '0.10.1', { + 'checksums': ['6879edfe8e3905a2c299cbd18777422223ad30042bc6e20614ca5109a75de82c'], + }), + ('findpython', '1.0.8', { + 'checksums': ['0f8a90cbafd4949c0333a86808383a358fb7ec3268953d8a4887d5d22264cdb7'], + }), + ('argparse', '2.2.3', { + 'checksums': ['a50cc4e1221f063e472a8cfe7e881a1d4abed5ef93cf40d5f65a2528cdfd2674'], + }), + ('intergraph', '2.0-4', { + 'checksums': 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['e684f07f7dfec922380d4202922c11094f859721f77b31ff38b0d35d0f42c743'], + }), + ('stdReg', '3.4.1', { + 'checksums': ['285335dbe29b6898641e1151ab2f06acf76c6f4d6fbeadd66d151c25d7e38a74'], + }), + ('mcmcse', '1.5-0', { + 'checksums': ['4a820dc22c48efd32b7f9d1e1b897b4b3f165cd64b2ff85ba7029621cf9e7463'], + }), + ('copCAR', '2.0-4', { + 'checksums': ['8b4ed53c58a665f70e48bdca689a992a81d5ecb5a6051ca7361d3870e13c77f3'], + }), + ('batchmeans', '1.0-4', { + 'checksums': ['8694573009d9070a76007281407d3314da78902e122a9d8aec1f819d3bbe562c'], + }), + ('ngspatial', '1.2-2', { + 'checksums': ['3fa79e45d3a502a58c1454593ec83dfc73144e92b34c14f617a6126557dd0d26'], + }), + ('BIGL', '1.9.1', { + 'checksums': ['c2136a7a5b3a6b71c8ba3cdfc7e83c14b400c9197c1544f0967297659e3b8631'], + }), + ('drugCombo', '1.2.1', { + 'checksums': ['9a605c655c159604033558d757711e6d83d33dfc286c1280f722d4cb7d130f80'], + }), + ('betareg', '3.1-4', { + 'checksums': ['5106986096a68b2b516215968158589b71969ce7912879253d6e930355a18101'], + }), + ('unmarked', '1.4.1', { + 'checksums': ['1c277248ad00122f404aabd0f0bbdeaf1cd69c58b65faaf23e36ee39f1e750c7'], + }), + ('maxlike', '0.1-11', { + 'checksums': ['6dde7bb4a46d5509a1fee024c2fd1d13c82e14a80806969ec89359103ade01e9'], + }), + ('coxme', '2.2-20', { + 'checksums': ['a0eeeadaabe81458b4fe80d26ca9770ff17dc3a2a41a37b2d1b09fadb887cb62'], + }), + ('AICcmodavg', '2.3-3', { + 'checksums': ['4055b5f1fc12917b9f812c056e6a2dbf23bbd0169e468f567306ddf29d699f7a'], + }), + ('pacman', '0.5.1', { + 'checksums': ['9ec9a72a15eda5b8f727adc877a07c4b36f8372fe7ed80a1bc6c2068dab3ef7c'], + }), + ('spaa', '0.2.2', { + 'checksums': ['a5a54454d4a7af473ce797875f849bd893005cb04325bf3e0dbddb19fe8d7198'], + }), + ('maxnet', '0.1.4', { + 'checksums': ['fd21e5ecf3c1ac00ef1bbe79fab4cdd62789e0c4c45f126f1b64bda667238216'], + }), + ('oai', '0.4.0', { + 'checksums': ['f540de066de5538e303cd535cbd2e771b40474bc2c6e8d08a4894a868543ee33'], + }), + ('wellknown', '0.7.4', { + 'checksums': ['483e6fc43edf09ed583e74ce5ca7e2d7838ef8a32291e06d774c37546eed1a34'], + }), + ('rgbif', '3.8.0', { + 'checksums': ['8b5cd096404291d39778ec4fed36cd25719fa0ca4225866e67566c4d346d2ce8'], + }), + ('rgdal', '1.6-7', { + 'checksums': ['555cedfdadb05db90b061d4b056f96d8b7010c00ea54bc6c1bbcc7684fadae33'], + }), + ('rgeos', '0.6-4', { + 'checksums': ['9d03c4de96fd3fad55ff8d1ff8113dcaaa00f15d9d0588e54c9f91751bcede11'], + }), + ('mapproj', '1.2.11', { + 'checksums': ['db2d201cc939de26717566066bf44225a967ccde6fc34731af845f03c086347d'], + }), + ('rbison', '1.0.0', { + 'checksums': ['9957e5f85ce68f5dd0ddc3c4b2b3c9d2f52d6f37587e1022ab8a44863534a83c'], + }), + ('rebird', '1.3.0', { + 'checksums': ['b238d3f246aa0249145894e1f3a90f46902f6615fc2f23b24c99bb5feecc55d3'], + }), + ('rvertnet', '0.8.4', { + 'checksums': ['b1826899f33640541752f2b68ed4d23530fe62744ac4714adf79ff748fc6701a'], + }), + ('ridigbio', '0.3.8', { + 'checksums': ['e518dbaeaf7f0dd0b833d83a6a094e07c5bd84935279c9e35bb69fe35ee00288'], + }), + ('spocc', '1.2.3', { + 'checksums': ['ee14de78a9a91bf4220b3317d724f9e4953fda8b5478b2083690c984903db951'], + }), + ('spThin', '0.2.0', { + 'checksums': ['2e997afb79a2a990eded34c71afaac83986669cfa9ac51b15ae3f2b558902048'], + }), + ('RPostgreSQL', '0.7-6', { + 'checksums': ['385939708b6a3657663409f91e165ded0ff5268d1dc6225e0f9b34764baf2d2c'], + }), + ('fasterize', '1.0.5', { + 'checksums': ['d44f101aec29aee285c4c7b578e26d11b6add423336ace90a7c22e07cfc1c3b4'], + }), + ('BIEN', '1.2.6', { + 'checksums': ['fa7a25d89f26c10686fb4ab4d0aa704beb50dc44b173ff56abe4ab3e5991f99f'], + }), + ('rangeModelMetadata', '0.1.5', { + 'checksums': ['289620500522d489aafbb03c85f68182ef0a6701fed5f9d09b55fae337e2647b'], + }), + ('ENMeval', '2.0.4', { + 'checksums': ['6d9f3c460fa7ab3131cede904fcb9280cf69f4fdd43f67115a3abcb8ed5b64d1'], + }), + ('plotmo', '3.6.3', { + 'checksums': ['6917cd8185325f1f2998fb14def9e6a8d93f1b708cf70d7c443d3960c9189b7b'], + }), + ('earth', '5.3.3', { + 'checksums': ['786a0fcabb3db13e0e0a4ba61ecccb7e171030b39bc97926f8e7159485d2f572'], + }), + ('mda', '0.5-4', { + 'checksums': ['f25f7f28807d0fa478b1b55eb9d026ebc30577d9d5ff288f9abfe1f3fdb8a759'], + }), + ('xgboost', '1.7.7.1', { + 'checksums': ['f7912ccf3a583a27208f74ca15c3b272cc930bae6b10ae7e5958ff2951ee9723'], + }), + ('biomod2', '4.2-5-2', { + 'checksums': ['1c4ca427b8d6af54de548023dcbe25c7e9cbea7afb684c58b66f4210af9eb4e5'], + }), + ('poLCA', '1.6.0.1', { + 'checksums': ['ed8c60a42bff0402c9ba2f9ce1422dd171e711c1a64498c4d96010ddb29f6b16'], + }), + ('PermAlgo', '1.2', { + 'checksums': ['aa2c774d6c6dcfeec882c1936e8723ef49bd36030fb10c17ca60bb9d4a519443'], + }), + ('coxed', '0.3.3', { + 'checksums': ['d0d6cb8fea9516b3c63b34d0d81f3804c18a07f97a83e51555575c8ed4c75626'], + }), + ('testit', '0.13', { + 'checksums': ['90d47168ab6bdbd1274b600b457626ac07697ce09792c92b2043be5f5b678d80'], + }), + ('NISTunits', '1.0.1', { + 'checksums': ['eaccd68db5c73d6a089ce5b323cdd51bc6a6a58ce467987158ba8c9be6a0a94e'], + }), + ('celestial', '1.4.6', { + 'checksums': ['9f647f41465ac65b254717698f1978871c378ad8e6ccaa693abf579437069abe'], + }), + ('RPMM', '1.25', { + 'checksums': ['f04a524b13918062616beda50c4e759ce2719ce14150a0e677d07132086c88c8'], + }), + ('RefFreeEWAS', '2.2', { + 'checksums': ['de2812f166caabf6ea01c0533402e5cd9d8a525a2a7583e4757decf22319caab'], + }), + ('wordcloud', '2.6', { + 'checksums': ['53716954430acd4f164bfd8eacd7068a908ee3358293ded6cd992d53b7f72649'], + }), + ('JADE', '2.0-4', { + 'checksums': ['d4b3d65a33cae454d3ab13343bceabfb3f6b8004ac64ae7bd86dee92a1cd2055'], + }), + ('awsMethods', '1.1-1', { + 'checksums': ['50934dc20cf4e015f1304a89de6703fed27e7bd54c6b9fc9fb253cdf2ecb7541'], + }), + ('aws', '2.5-5', { + 'checksums': ['b27cb2795cb59592d474cfaf49a21657a8878404da4f01c556f7323e953b4c5b'], + }), + ('ruv', '0.9.7.1', { + 'checksums': ['a0c54e56ba3d8f6ae178ae4d0e417a79295abf5dcb68bbae26c4b874734d98d8'], + }), + ('mhsmm', '0.4.21', { + 'checksums': ['293544afb194934b1d58cf88c6f8c372f537745514b6e428cf83ae62e87d2bba'], + }), + ('dbarts', '0.9-28', { + 'checksums': ['d2e4b4ee1c191e7c506be3fec5a5e877c1b36754cba558bd75eaac9cc6ac0138'], + 'preinstallopts': local_dbarts_preinstallopts, + }), + ('proftools', '0.99-3', { + 'checksums': ['e034eb1531af54013143da3e15229e1d4c2260f8eb79c93846014db3bdefb724'], + }), + ('NCmisc', '1.2.0', { + 'checksums': ['26fcfbc79810f23a28389a5ce5519e6ddc2470c5e924ba8cf4dd19a1b0fd9f83'], + }), + ('reader', '1.0.6', { + 'checksums': ['905c7c5a1b035ac8213fc533fa26e511abfeea40bd22e3edfde42a49074e88f4'], + }), + ('gnumeric', '0.7-10', { + 'checksums': ['f6fcd9012f2fa777127c86ba520d8dc834f4ea746a6e29623edd072479191c75'], + }), + ('tcltk2', '1.2-11', { + 'checksums': ['ad183ae3b7190501504a0589e0b3be480f04267303e3384fef00987446a37dc5'], + }), + ('minty', '0.0.1', { + 'checksums': ['cfbdc6603c8fb54ea4d43091e2aee4c99212e6e20a335ed89576156d86237acd'], + }), + ('readODS', '2.3.0', { + 'checksums': ['1e120ff8fdb34c7e00f07726b4843cfaeee9c680bfdc2982e83422c24e4c0491'], + }), + ('nortest', '1.0-4', { + 'checksums': ['a3850a048181d5d059c1e74903437569873b430c915b709808237d71fee5209f'], + }), + ('EnvStats', '2.8.1', { + 'checksums': ['12952b9eaa64b7bdbaaa5c6b7acb3aa1028ddfa4e5de7ddfea54f900c452d6a6'], + }), + ('outliers', '0.15', { + 'checksums': ['cc31d7f2faefd2c3a27f8ce78c7e67d3b321dcd6690292fad2468125e5e635fb'], + }), + ('gWidgets2', '1.0-9', { + 'checksums': ['d4d9ef7b2788efeb8209aa8dd610af4cd86286392fbdf9ea70bcfeafda95d4c5'], + }), + ('gWidgets2tcltk', '1.0-8', { + # need to run installation via xvfb-run to avoid problems on headless systems: + # no DISPLAY variable so Tk is not available + # [tcl] invalid command name "font" + 'preinstallopts': "xvfb-run ", + 'checksums': ['10399cc636eeeb5484c3379970c37c56df10d979bf866a35b66d0c75b7222c0a'], + # skip 'import' check with library(gWidgets2tcltk), since it also fails on headless systems... + 'modulename': False, + }), + ('mgsub', '1.7.3', { + 'checksums': ['c9ae2560fe2690bedc5248af3fc89e7ef2bc6c147d46ced28f9824584c3791d5'], + }), + ('ie2misc', '0.9.1', { + 'checksums': ['f1db0c66c8fa05e99c4059c1799abc3eb7effd7113baf03f38d26853ac05c425'], + }), + ('assertive.base', '0.0-9', { + 'checksums': ['4bf0910b0eaa507e0e11c3c43c316b524500c548d307eb045d6f89047e6ba01e'], + }), + ('assertive.properties', '0.0-5', { + 'checksums': ['b68954f53082561f0242682611bf3373e0bf30d8ac2256d82474edc5f992f4dd'], + }), + ('assertive.types', '0.0-3', { + 'checksums': ['ab6db2eb926e7bc885f2043fab679330aa336d07755375282d89bf9f9d0cb87f'], + }), + ('assertive.numbers', '0.0-2', { + 'checksums': ['bae18c0b9e5b960a20636e127eb738ecd8a266e5fc29d8bc5ca712498cd68349'], + }), + ('assertive.strings', '0.0-3', { + 'checksums': ['d541d608a01640347d661cc9a67af8202904142031a20caa270f1c83d0ccd258'], + }), + ('assertive.datetimes', '0.0-3', { + 'checksums': ['014e2162f5a8d95138ed8330f7477e71c908a29341697c09a1b7198b7e012d94'], + }), + ('assertive.files', '0.0-2', { + 'checksums': ['be6adda6f18a0427449249e44c2deff4444a123244b16fe82c92f15d24faee0a'], + }), + ('assertive.sets', '0.0-3', { + 'checksums': ['876975a16ed911ea1ad12da284111c6eada6abfc0118585033abc0edb5801bb3'], + }), + ('assertive.matrices', '0.0-2', { + 'checksums': ['3462a7a7e11d7cc24180330d48cc3067cf92eab1699b3e4813deec66d99f5e9b'], + }), + ('assertive.models', '0.0-2', { + 'checksums': ['b9a6d8786f352d53371dbe8c5f2f2a62a7866e30313f268e69626d5c3691c42e'], + }), + ('assertive.data', '0.0-3', { + 'checksums': ['5a00fb48ad870d9b3c872ce3d6aa20a7948687a980f49fe945b455339e789b01'], + }), + ('assertive.data.uk', '0.0-2', { + 'checksums': ['ab48dab6977e8f43d6fffb33228d158865f68dde7026d123c693d77339dcf2bb'], + }), + ('assertive.data.us', '0.0-2', { + 'checksums': ['180e64dfe6339d25dd27d7fe9e77619ef697ef6e5bb6a3cf4fb732a681bdfaad'], + }), + ('assertive.reflection', '0.0-5', { + 'checksums': ['c2ca9b27cdddb9b9876351afd2ebfaf0fbe72c636cd12aa2af5d64e33fbf34bd'], + }), + ('assertive.code', '0.0-4', { + 'checksums': ['2f820474ed20e06f65b284962c87cd1e85220a11cc7fcde09716f0eee5821387'], + }), + ('assertive', '0.3-6', { + 'checksums': ['c403169e83c433b65e911f7fd640b378e2a4a4765a36063584b8458168a4ea0a'], + }), + ('rdrop2', '0.8.2.1', { + 'checksums': ['b9add765fe8e7c966f0d36eef939a9e38f253958bd2a3c656b890cbb0366300b'], + }), + ('Exact', '3.2', { + 'checksums': ['53b4e20cbb57615970c572fc4e7a780a510bde8b5deadec3880095f6e17a6328'], + }), + ('lmom', '3.0', { + 'checksums': ['4b0ae8638a63b45ddedfd65c15e3206d34e947a2b5d31e9aa8c55446d69a0291'], + }), + ('gld', '2.6.6', { + 'checksums': ['ea23e9781207b5d47ed04e4d5758d9652cab5d1eedcf9fbc9c2ee4d3babffdc4'], + }), + ('DescTools', '0.99.54', { + 'checksums': ['470a16405d52d7e8595ac025a0d2bf50b78edaebe83af358903e201168a80b9b'], + }), + ('orthopolynom', '1.0-6.1', { + 'checksums': ['ec4a6ed266532f2f6d37a4ca6bd1b74c1df28a8c2caeab60e5d6af15bdbfe2c5'], + }), + ('gaussquad', '1.0-3', { + 'checksums': ['a3337ce52bc53435cb4565a38bf48b72b384be397d2e86bb66f62973004dc810'], + }), + ('nlsem', '0.8-1', { + 'checksums': ['0674ec2a1ae7e50b08ee1b156674c2f2100258b14d6a9068f7dd6ad1ee128377'], + }), + ('tableone', '0.13.2', { + 'checksums': ['b1cf15579abd4240e24435d2d9aad255c839d2a0293e28cb2eef0c808c4727af'], + }), + ('jstable', '1.2.6', { + 'checksums': ['b759553446892a4b8697be0c696f5d2c5aafdb64cff1ca1b22557687ea7218bd'], + }), + ('RCAL', '2.0', { + 'checksums': ['10f5f938a8322d8737159e1e49ce9d12419a5130699b8a19c6ca53d6508da8cc'], + }), + ('stargazer', '5.2.3', { + 'checksums': ['208e9b48a11cf56ce142731c204f3d2bcb5b68719f84309a36362cd925414265'], + }), + ('sensemakr', '0.1.4', { + 'checksums': ['6a1354f05392fa9343b90f69a54022c995651fb3c3d05cb08fa088ef52258caf'], + }), + ('CompQuadForm', '1.4.3', { + 'checksums': ['042fc56c800dd8f5f47a017e2efa832caf74f0602824abf7099898d9708660c4'], + }), + ('nonnest2', '0.5-7', { + 'checksums': ['e440c2464b3bd3b452e02583bb280eecba6acecf0f2c04b6b9fe4dcdd128db3e'], + }), + ('blavaan', '0.5-5', { + 'checksums': ['a8d3bc5e9d15a2e8496950e87ed3c6bc6d769e761ec068e1f063f2d255330b6d'], + }), + ('mathjaxr', '1.6-0', { + 'checksums': ['ecc47607111b788d84789459af7f4f9102719f98640b7a23bd5a4eb1a6d3c179'], + }), + ('metadat', '1.2-0', { + 'checksums': ['f0cce5e30c3d256eaf5a41e4f52ffc7108e195016a4b99409e0ab4c2ef58f5b8'], + }), + ('metafor', '4.6-0', { + 'checksums': ['07344cc3bd87b8bd25ef998e9a6ce322ae8e448ef5af06ec3e79631724e18666'], + }), + ('RNifti', '1.7.0', { + 'checksums': ['e58cf73a0f5fbf5d6a2c845bfdeea193eb5262c73d0f329beae17d68f40e18e8'], + }), + ('oro.nifti', '0.11.4', { + 'checksums': ['efe4f5d2c2e37ff6c3e9250f54ef775e4d452c1334f781f22f219ed53148b606'], + }), + ('fmri', '1.9.12', { + 'checksums': ['d8b55f8867bb0487d1a8241b340099c41d990ae5aa49768b2dc0f9db58af65b3'], + }), + ('linkcomm', '1.0-14', { + 'checksums': ['36f1557c65d862fc87635eedfad77f18a5deb66da00895e50e2d5eac0f23b597'], 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['ad9ebb5431bdfecc38b8bf3b2552f1a048878a9ac02f5a9d71279b3b099a9757'], + }), + ('rhandsontable', '0.3.8', { + 'checksums': ['901ed9c59936f7fa52ad8db3111c8904ab962f9c74f1b6cd40f81683af35d21d'], + }), + ('missMDA', '1.19', { + 'checksums': ['f9675884829b2fef75237c335b21991d163674320e766523c71c7a853f95e65c'], + }), + ('insight', '0.20.3', { + 'checksums': ['b60e189849cd3c368e9c2b2174e89c2dfbba3b34e84feb8a20af1bb758116bb2'], + }), + ('datawizard', '0.12.2', { + 'checksums': ['fee36520440131596394878eb19f295609ef5d7997a3a5614c059f2a8d2be081'], + }), + ('bayestestR', '0.14.0', { + 'checksums': ['fa0f94204b414df05ecf7340b37fbb5fbe6dff2d057e2425a6990b6510054880'], + }), + ('performance', '0.12.2', { + 'checksums': ['b55e663eb45b8e88625c704506f20c4068a1c892c5a6a94d7bd0c0e3a7ed4028'], + }), + ('fastlogranktest', '0.2.1', { + 'checksums': ['457c411240b5ee73108042370ccea0f8fa1999e876b2306456d4723be27eb5c8'], + }), + ('pbmcapply', '1.5.1', { + 'checksums': ['7ffc2854a384962f0dd523aa9ef33ce8fc290997206b71b840a49049d87112dd'], + }), + ('PWEALL', '1.3.0.1', { + 'checksums': ['6fb7eaf557f9bd17bcb94945814dbd77a081d709976bc8046746ff0be7c1dcdc'], + }), + ('goldilocks', '0.3.0', { + 'checksums': ['94df7f9d3550dc3790ea3c8f3f364f7131c907a235f498473c8c4e4f959b26c0'], + }), + ('r2rtf', '1.1.1', { + 'checksums': ['d64b88187b5eb7bc69eae37f493fdae8417d5127d0a44f1586a00827bc321f52'], + }), + ('gsDesign', '3.6.4', { + 'checksums': ['b96075650a5bcbb9ebab78b7094d51f451d086b7c97a3a427635b52fece176d2'], + }), +] + +modextrapaths = {'R_LIBS_SITE': ''} + +sanity_check_paths = { + 'files': [], + 'dirs': ['abind', 'base64', 'calibrate'], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R-tesseract/R-tesseract-5.2.1-foss-2023a.eb b/easybuild/easyconfigs/r/R-tesseract/R-tesseract-5.2.1-foss-2023a.eb new file mode 100644 index 00000000000..4981b999b95 --- /dev/null +++ b/easybuild/easyconfigs/r/R-tesseract/R-tesseract-5.2.1-foss-2023a.eb @@ -0,0 +1,51 @@ +easyblock = 'Bundle' + +name = 'R-tesseract' +version = '5.2.1' + +homepage = 'https://cran.r-project.org/package=tesseract' +description = "The R extension for using tesseract" + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [('pkgconf', '1.9.5')] + +dependencies = [ + ('R', '4.3.2'), + ('poppler', '23.09.0'), + ('tesseract', '5.3.4'), +] + +exts_defaultclass = 'RPackage' + +exts_default_options = { + 'source_urls': [ + 'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'https://cran.r-project.org/src/contrib/', # current version of packages + 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + ], + 'source_tmpl': '%(name)s_%(version)s.tar.gz', +} + +exts_list = [ + ('qpdf', '1.3.3', { + 'checksums': ['415610be6fa73f60a31872b81fea089288b07f9cb6d078088009207c5e60fe53'], + }), + ('pdftools', '3.4.0', { + 'checksums': ['0b9d7b2100a6d7959c56e144285b9638ca6ff4a7f484a31ff814a99d71482c64'], + }), + ('tesseract', version, { + 'preinstallopts': 'INCLUDE_DIR="$EBROOTTESSERACT/include/tesseract -I$EBROOTLEPTONICA/include/leptonica"' + ' LIB_DIR=$EBROOTTESSERACT/lib', + 'checksums': ['ffaba641c5d531a2b6d4ded3608a669206b1e0690cb5e013e3fc9db8aea117fe'], + }), +] + +sanity_check_paths = { + 'files': ['tesseract/libs/tesseract.%s' % SHLIB_EXT, 'tesseract/R/tesseract'], + 'dirs': ['qpdf', 'pdftools'], +} + +modextrapaths = {'R_LIBS_SITE': ''} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb index d8b9d1c97fe..9d09c819514 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb @@ -57,6 +57,10 @@ dependencies = [ osdependencies = [OS_PKG_OPENSSL_DEV] +# Some R extensions (mclust, quantreg, waveslim for example) require the math library (-lm) to avoid undefined symbols. +# Adding it to FLIBS makes sure it is present when needed. +preconfigopts = 'export FLIBS="$FLIBS -lm" && ' + configopts = "--with-pic --enable-threads --enable-R-shlib" # some recommended packages may fail in a parallel build (e.g. Matrix), and # we're installing them anyway below diff --git a/easybuild/easyconfigs/r/R/R-4.4.1-gfbf-2023b.eb b/easybuild/easyconfigs/r/R/R-4.4.1-gfbf-2023b.eb new file mode 100644 index 00000000000..09a46feeaa1 --- /dev/null +++ b/easybuild/easyconfigs/r/R/R-4.4.1-gfbf-2023b.eb @@ -0,0 +1,371 @@ +name = 'R' +version = '4.4.1' + +homepage = 'https://www.r-project.org/' +description = """R is a free software environment for statistical computing + and graphics.""" + +toolchain = {'name': 'gfbf', 'version': '2023b'} + +source_urls = ['https://cloud.r-project.org/src/base/R-%(version_major)s'] +sources = [SOURCE_TAR_GZ] +checksums = ['b4cb675deaaeb7299d3b265d218cde43f192951ce5b89b7bb1a5148a36b2d94d'] + +builddependencies = [ + ('pkgconf', '2.0.3'), + ('Autotools', '20220317'), +] +dependencies = [ + ('X11', '20231019'), + ('Mesa', '23.1.9'), + ('libGLU', '9.0.3'), + ('cairo', '1.18.0'), + ('libreadline', '8.2'), + ('ncurses', '6.4'), + ('bzip2', '1.0.8'), + ('XZ', '5.4.4'), + ('zlib', '1.2.13'), + ('SQLite', '3.43.1'), + ('PCRE2', '10.42'), + ('libpng', '1.6.40'), # for plotting in R + ('libjpeg-turbo', '3.0.1'), # for plottting in R + ('LibTIFF', '4.6.0'), + ('Java', '11', '', SYSTEM), + ('libgit2', '1.7.2'), + ('OpenSSL', '1.1', '', SYSTEM), + ('cURL', '8.3.0'), + ('Tk', '8.6.13'), # for tcltk + ('HarfBuzz', '8.2.2'), # for textshaping + ('FriBidi', '1.0.13'), # for textshaping + +] + +# Some R extensions (mclust, quantreg, waveslim for example) require the math library (-lm) to avoid undefined symbols. +# Adding it to FLIBS makes sure it is present when needed. +preconfigopts = 'export FLIBS="$FLIBS -lm" && ' + +configopts = "--with-pic --enable-threads --enable-R-shlib" +# some recommended packages may fail in a parallel build (e.g. Matrix), and +# we're installing them anyway below +configopts += " --with-recommended-packages=no" + +exts_default_options = { + 'source_urls': [ + 'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'https://cran.r-project.org/src/contrib/', # current version of packages + 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + ], + 'source_tmpl': '%(name)s_%(version)s.tar.gz', +} + +# !! order of packages is important !! +# packages updated on 24 June 2024 +exts_list = [ + # include packages that are part of the base installation of R, + # both to make sure they are available (via sanity check), + # and to be able to pass the check for required dependencies when installing extensions in parallel + 'base', + 'compiler', + 'datasets', + 'graphics', + 'grDevices', + 'grid', + 'methods', + 'parallel', + 'splines', + 'stats', + 'stats4', + 'tcltk', + 'tools', + 'utils', + ('rlang', '1.1.4', { + 'checksums': 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['6e542216c03b5286cb9901175d1a7937a664db2572bc28bb51e9000269fcdda0'], + }), + ('htmlwidgets', '1.6.4', { + 'checksums': ['7cb08f0b30485dac26f72e4056ec4ed8825d1398e8b9f25ed63db228fe3a0ed0'], + }), + ('profvis', '0.3.8', { + 'checksums': ['ec02c75bc9907a73564e691adfa8e06651ca0bd73b7915412960231cd265b4b2'], + }), + ('urlchecker', '1.0.1', { + 'checksums': ['62165ddbe1b748b58c71a50c8f07fdde6f3d19a7b39787b9fa2b4f9216250318'], + }), + ('later', '1.3.2', { + 'checksums': ['52f5073d33cd0d3c12e56526c9c53c323ebafcc79b22cc6e51fb0c41ee2b561e'], + }), + ('promises', '1.3.0', { + 'checksums': ['f8209df3bab33340c1bc8c0d26caee2890fafb93129ff1423302abae5931fad3'], + }), + ('xtable', '1.8-4', { + 'checksums': ['5abec0e8c27865ef0880f1d19c9f9ca7cc0fd24eadaa72bcd270c3fb4075fd1c'], + }), + ('httpuv', '1.6.15', { + 'checksums': ['5e6ded3623a39df3e1db6cb7e7292b4c03c80b3c6c5faaac3b78b711cb205ed0'], + }), + ('sourcetools', '0.1.7-1', { + 'checksums': ['96812bdb7a0dd99690d84e4b0a3def91389e4290f53f01919ef28a50554e31d1'], + }), + ('shiny', '1.8.1.1', { + 'checksums': ['a38d5fb5d750e2c2091ce9101f138c1f9bc7009bbb195227a3519c5d97e36753'], + }), + ('miniUI', '0.1.1.1', { + 'checksums': ['452b41133289f630d8026507263744e385908ca025e9a7976925c1539816b0c0'], + }), + ('brew', '1.0-10', { + 'checksums': ['4181f7334e032ae0775c5dec49d6137eb25d5430ca3792d321793307b3dda38f'], + }), + ('roxygen2', '7.3.1', { + 'checksums': ['215e9fa9c0e73cb33f9870854c97b25c1a6386f519f69f397123f1a66656e2c8'], + }), + ('rversions', '2.1.2', { + 'checksums': ['de5818233e8271132fe8ea70145618950b35786e0d2f270e39bf3338f3b8b160'], + }), + ('sessioninfo', '1.2.2', { + 'checksums': ['f56283857c53ac8691e3747ed48fe03e893d8ff348235bff7364658bcfb0c7cb'], + }), + ('xopen', '1.0.1', { + 'checksums': ['e3b278b8c324a1aa2650141dd89d01253eea5c2555007422c797915689b29aec'], + }), + ('rcmdcheck', '1.4.0', { + 'checksums': ['bbd4ef7d514b8c2076196a7c4a6041d34623d55fbe73f2771758ce61fd32c9d0'], + }), + ('remotes', '2.5.0', { + 'checksums': ['4d663f1426cd88d42f4070f23d969305c575e0499ed1397be6607b0770d2850c'], + }), + ('clipr', '0.8.0', { + 'checksums': ['32c2931992fbec9c31b71de3e27059f1cbb45b4b1f45fd42e0e8dbcec6de3be9'], + }), + ('ini', '0.3.1', { + 'checksums': ['7b191a54019c8c52d6c2211c14878c95564154ec4865f57007953742868cd813'], + }), + ('gitcreds', '0.1.2', { + 'checksums': ['41c6abcca5635062b123ffb5af2794770eca5ebd97b05c5a64b24fa1c803c75d'], + }), + ('httr2', '1.0.1', { + 'checksums': ['33e92d830981b33cd5e55068b500c57dbfb72329c2fce54be3163c63b217f1b2'], + }), + ('gh', '1.4.1', { + 'checksums': ['76bd3f2a31eeaf76a633362899a20b0f7e8fb6159d4777baf3da2a47854292af'], + }), + ('credentials', '2.0.1', { + 'checksums': ['2c7cfc45bd4afa9a2c2b85d43e907b212da3468781e1b617737bd095253c358b'], + }), + ('zip', '2.3.1', { + 'checksums': ['83754408781c525917f36535865d28214893de0778b5f337e050cb543cacc28f'], + }), + ('gert', '2.0.1', { + 'checksums': ['0ed784837809ce89797ea77834d420e89351728f70d8d2f4b34487df813cd092'], + }), + ('usethis', '2.2.3', { + 'checksums': ['8d0c98995c23b5f4b5b95cd453557d2d15faa7399cc01bff304f5b15cb0cdeb3'], + }), + ('devtools', '2.4.5', { + 'checksums': ['38160ebd839acdec7ebf0699a085b4ab1ebd5500d3c57a9fa7ae484f1909904b'], + }), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R2jags/R2jags-0.8-9-foss-2023a-R-4.3.2.eb b/easybuild/easyconfigs/r/R2jags/R2jags-0.8-9-foss-2023a-R-4.3.2.eb new file mode 100644 index 00000000000..0784b3e87c1 --- /dev/null +++ b/easybuild/easyconfigs/r/R2jags/R2jags-0.8-9-foss-2023a-R-4.3.2.eb @@ -0,0 +1,29 @@ +easyblock = 'RPackage' + +name = 'R2jags' +version = '0.8-9' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://cran.r-project.org/web/packages/R2jags' +description = "Providing wrapper functions to implement Bayesian analysis in JAGS." + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = [ + 'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'https://cran.r-project.org/src/contrib/', # current version of packages +] +sources = ['%(name)s_%(version)s.tar.gz'] +checksums = ['df06b8f919eed8dd65bca29bbe7e337718142734d6a31818ce1e49db8faee14c'] + +dependencies = [ + ('R', '4.3.2'), + ('rjags', '4-15', versionsuffix), +] + +sanity_check_paths = { + 'files': [], + 'dirs': [name], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/r/RAPIDS/RAPIDS-24.4-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/r/RAPIDS/RAPIDS-24.4-foss-2023a-CUDA-12.1.1.eb new file mode 100644 index 00000000000..287feaf2e3f --- /dev/null +++ b/easybuild/easyconfigs/r/RAPIDS/RAPIDS-24.4-foss-2023a-CUDA-12.1.1.eb @@ -0,0 +1,215 @@ +easyblock = 'PythonBundle' + +name = 'RAPIDS' +version = '24.4' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://rapids.ai/' +description = """RAPIDS provides unmatched speed with familiar APIs that match the most popular +PyData libraries. Built on state-of-the-art foundations like NVIDIA CUDA and +Apache Arrow, it unlocks the speed of GPUs with code you already know.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [ + ('hatchling', '1.18.0'), # needed by treelite + ('CMake', '3.26.3'), # needed by treelite +] + +dependencies = [ + ('CUDA', '12.1.1', '', SYSTEM), + ('cuDNN', '8.9.2.26', versionsuffix, SYSTEM), + ('NCCL', '2.18.3', versionsuffix), + ('Python', '3.11.3'), + ('CUDA-Python', '12.1.0', versionsuffix), + ('Python-bundle-PyPI', '2023.06'), + ('SciPy-bundle', '2023.07'), + ('aiohttp', '3.8.5'), + ('Arrow', '14.0.1'), + ('dask', '2023.9.2'), + ('geopandas', '0.14.2'), + ('jupyter-server-proxy', '4.0.0'), + ('numba', '0.58.1'), + ('protobuf-python', '4.24.0'), + ('pyproj', '3.6.0'), + ('scikit-image', '0.22.0'), + ('Shapely', '2.0.1'), + ('tqdm', '4.66.1'), + ('xarray', '2023.9.0'), +] + +# Installation based on wheels provided by Nvidia on pypi.nvidia.com +# Some of the extensions have alternatives as regular dependencies, such as +# cupy or ucx-py. However, they are still installed as extensions because the +# other wheels from Nvidia require those packages but with special cuda +# suffixes (e.g. "cupy_cuda12x" instead of "cupy") + +use_pip = True + +_whl_name_cuda = '%(name)s_cu%(cudamajver)s-%(version)s' +_whl_py_noneany = '-py%(pymajver)s-none-any.whl' +_whl_cp_version = '-cp%(pymajver)s%(pyminver)s-cp%(pymajver)s%(pyminver)s' +_whl_cp_linux28 = '-manylinux_2_28_x86_64.whl' +_whl_cp_linux27 = '-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl' +_whl_cp_linux17 = '-manylinux_2_17_x86_64.manylinux2014_x86_64.whl' +_whl_cp_linux14 = '-manylinux2014_x86_64.whl' + +exts_default_options = { + 'source_urls': [PYPI_SOURCE, 'https://pypi.nvidia.com/%(name)s-cu%(cudamajver)s'], + 'source_tmpl': SOURCE_TAR_GZ, +} + +exts_list = [ + ('cudf', '24.4.1', { + 'source_tmpl': _whl_name_cuda + _whl_cp_version + _whl_cp_linux28, + 'checksums': ['545c8845402b49bfbd35cda3653c12a6c776cfc873cada181f866c61223cde34'], + }), + ('dask_cudf', '24.4.1', { + 'source_tmpl': _whl_name_cuda + _whl_py_noneany, + 'source_urls': ['https://pypi.nvidia.com/dask-cudf-cu%(cudamajver)s'], + 'checksums': ['b18846636c846722b915af1a6828f6f70f17f5f8aff0d61bb19c3e6067e03b3e'], + }), + ('cuml', '24.4.0', { + 'source_tmpl': _whl_name_cuda + _whl_cp_version + _whl_cp_linux17, + 'checksums': ['6c7e7209a01a872a9699bfb851678b30dde47cb003859bca059ca5395add46d3'], + }), + ('cugraph', '24.4.0', { + 'source_tmpl': _whl_name_cuda + _whl_cp_version + _whl_cp_linux17, + 'checksums': ['968d3733a8559812574ffa4dd226b6c6eac19ef8dc395088121f2e37e1f00f38'], + }), + ('cuspatial', '24.4.0', { + 'source_tmpl': _whl_name_cuda + _whl_cp_version + _whl_cp_linux17, + 'checksums': ['3ec862f6fd82e6e79f2ce90c416ef4323e489a02494b67424ea380143531d121'], + }), + ('cuproj', '24.4.0', { + 'source_tmpl': _whl_name_cuda + _whl_cp_version + _whl_cp_linux17, + 'checksums': ['46b6a0e5174039bdcf2352e12c9b2bf67f4f6a1da23b3302293779e291dc9b7b'], + }), + ('cuxfilter', '24.4.1', { + 'source_tmpl': _whl_name_cuda + _whl_py_noneany, + 'checksums': ['c8f2f11a5e908854e5368c489b045fc578794fcb28978aa56351831025f570e5'], + }), + ('cucim', '24.4.0', { + 'source_tmpl': _whl_name_cuda + _whl_cp_version + _whl_cp_linux17, + 'checksums': ['5cf9e5de6403d21679a79fa6d1fe9b18f6823687658a60292e4f092474363326'], + }), + ('pylibraft', '24.4.0', { + 'source_tmpl': _whl_name_cuda + _whl_cp_version + _whl_cp_linux17, + 'checksums': ['245733dd2f2f3cb4286619966b83695387d76df7b91fda8dd8d934936b8db987'], + }), + ('raft_dask', '24.4.0', { + 'source_tmpl': _whl_name_cuda + _whl_cp_version + _whl_cp_linux17, + 'source_urls': ['https://pypi.nvidia.com/raft-dask-cu%(cudamajver)s'], + 'checksums': ['97e39a93aee39876168fe61f9734f1a137ca9f3cb5801a22f08fe857e3ee269d'], + }), + ('cuvs', '24.4.0', { + 'source_tmpl': _whl_name_cuda + _whl_cp_version + _whl_cp_linux17, + 'checksums': ['e9e5def770bfe69f94563a8470d2d68730abf3ddfb0ab2ebf0392e73a9ba0fdc'], + }), + ('cupy-cuda12x', '13.2.0', { + 'modulename': 'cupy', + 'source_tmpl': 'cupy_cuda%(cudamajver)sx-%(version)s' + _whl_cp_version + _whl_cp_linux14, + 'checksums': ['6474fa977e7df03e92374698f2b757065c5b14733b2bbacc19301cc440acafdd'], + }), + ('nvtx', '0.2.10', { + 'source_tmpl': '%(name)s-%(version)s' + _whl_cp_version + _whl_cp_linux17, + 'checksums': ['71a1a641d4db137da8166d689d835a42f92b97cf2658ea069cbed162b8c5dd79'], + }), + ('pynvjitlink-cu12', '0.3.0', { + 'modulename': 'pynvjitlink', + 'source_tmpl': 'pynvjitlink_cu%(cudamajver)s-%(version)s' + _whl_cp_version + _whl_cp_linux27, + 'checksums': ['f56395025da610cb3aeaf4b04f4cbeb15676fb922738426028cc663324147ca4'], + }), + ('rmm', '24.4.0', { + 'source_tmpl': _whl_name_cuda + _whl_cp_version + _whl_cp_linux17, + 'checksums': ['bd0f4a0a63be30381aafb169912130dadb3c107dd489c95f6dec14638bc0cb48'], + }), + ('rapids_dask_dependency', '24.4.1', { + 'source_tmpl': SOURCE_PY3_WHL, + 'source_urls': ['https://pypi.nvidia.com/rapids-dask-dependency'], + 'checksums': ['0713b99711cc2beda5e9bc52e4436c9d9131e9ab63c67c6628511703a7fefe3f'], + }), + ('dask_cuda', '24.4.0', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['0f70bbbac8c7f19071ad9a78398ce7a3d17f10e5c70212810a9f1de8c50eae7f'], + }), + ('pynvml', '11.4.1', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['d27be542cd9d06558de18e2deffc8022ccd7355bc7382255d477038e7e424c6c'], + }), + ('ucx_py', '0.37.0', { + 'modulename': 'ucp', + 'source_tmpl': _whl_name_cuda + _whl_cp_version + _whl_cp_linux17, + 'source_urls': ['https://pypi.nvidia.com/ucx-py-cu%(cudamajver)s'], + 'checksums': ['32235eaf1191ea4fa0e795704ee51ec7bffc879ce075cbbbdd60ff994daed79c'], + }), + ('pylibcugraph', '24.4.0', { + 'source_tmpl': _whl_name_cuda + _whl_cp_version + _whl_cp_linux17, + 'checksums': ['1deb52562124343314cef504a92ac62afb5b6448cfffa19db8d208e6affe21b7'], + }), + ('multipledispatch', '1.0.0', { + 'checksums': ['5c839915465c68206c3e9c473357908216c28383b425361e5d144594bf85a7e0'], + }), + ('colorcet', '3.1.0', { + 'checksums': ['2921b3cd81a2288aaf2d63dbc0ce3c26dcd882e8c389cc505d6886bf7aa9a4eb'], + }), + ('pyct', '0.5.0', { + 'checksums': ['dd9f4ac5cbd8e37c352c04036062d3c5f67efec76d404761ef16b0cbf26aa6a0'], + }), + ('param', '2.1.1', { + 'checksums': ['3b1da14abafa75bfd908572378a58696826b3719a723bc31b40ffff2e9a5c852'], + }), + ('datashader', '0.16.3', { + 'checksums': ['9d0040c7887f7a5a5edd374c297402fd208a62bf6845e87631b54f03b9ae479d'], + }), + ('pyviz_comms', '3.0.2', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['31541b976a21b7738557c3ea23bd8e44e94e736b9ed269570dcc28db4449d7e3'], + }), + ('holoviews', '1.19.1', { + 'checksums': ['b9e85e8c07275a456c0ef8d06bc157d02b37eff66fb3602aa12f5c86f084865c'], + }), + ('uc-micro-py', '1.0.3', { + 'modulename': 'uc_micro', + 'checksums': ['d321b92cff673ec58027c04015fcaa8bb1e005478643ff4a500882eaab88c48a'], + }), + ('linkify-it-py', '2.0.3', { + 'modulename': 'linkify_it', + 'checksums': ['68cda27e162e9215c17d786649d1da0021a451bdc436ef9e0fa0ba5234b9b048'], + }), + ('Markdown', '3.6', { + 'checksums': ['ed4f41f6daecbeeb96e576ce414c41d2d876daa9a16cb35fa8ed8c2ddfad0224'], + }), + ('mdit_py_plugins', '0.4.1', { + 'checksums': ['834b8ac23d1cd60cec703646ffd22ae97b7955a6d596eb1d304be1e251ae499c'], + }), + ('panel', '1.2.3', { + 'source_tmpl': SOURCE_WHL, + 'checksums': ['0805bacf4a613e8869163bf80f50e59a89838afe76bdbe6a05ab5637f32683f7'], + }), + ('fastrlock', '0.8.2', { + 'checksums': ['644ec9215cf9c4df8028d8511379a15d9c1af3e16d80e47f1b6fdc6ba118356a'], + }), + ('dask', '2024.1.1', { + # overload dependency on dask due to strict requirement by rapids_dask_dependency + 'checksums': ['d0dc92e81ce68594a0a0ce23ba33f4d648f2c2f4217ab9b79068b7ecfb0416c7'], + }), + ('distributed', '2024.1.1', { + 'checksums': ['28cf5e9f4f07197b03ea8e5272e374ce2b9e9dc6742f6c9b525fd81645213c67'], + }), + ('dask-expr', '0.4.0', { + 'checksums': ['ee86ac5a5d3a892341af7ffab58e3a579c12aacbe332f2fe7477f668ac260279'], + }), + ('cachetools', '5.3.3', { + 'checksums': ['ba29e2dfa0b8b556606f097407ed1aa62080ee108ab0dc5ec9d6a723a007d105'], + }), + ('treelite', '4.1.2', { + 'checksums': ['d6e6338b601fb3304425966de8a0f1073cb9f7917bcd6e3cdaeaf3492f247425'], + }), +] + +# RAPIDS v24.4 only supports GPUs with NVIDIA Volta architecture or newer +# Sanity checks need a physical GPU device +sanity_pip_check = True + +moduleclass = 'ai' diff --git a/easybuild/easyconfigs/r/RAxML-NG/RAxML-NG-1.2.2-GCC-13.2.0.eb b/easybuild/easyconfigs/r/RAxML-NG/RAxML-NG-1.2.2-GCC-13.2.0.eb new file mode 100644 index 00000000000..a181d6523c8 --- /dev/null +++ b/easybuild/easyconfigs/r/RAxML-NG/RAxML-NG-1.2.2-GCC-13.2.0.eb @@ -0,0 +1,53 @@ +# EasyBuild easyconfig +# +# Contributed from Fred Hutchinson Cancer Research Center, Seattle WA, US +# John Dey jfdey@fredhutch.org +# +easyblock = 'CMakeMake' + +name = 'RAxML-NG' +version = '1.2.2' + +homepage = 'https://github.com/amkozlov/raxml-ng' +description = """RAxML-NG is a phylogenetic tree inference tool which uses maximum-likelihood (ML) + optimality criterion. Its search heuristic is based on iteratively performing a series of Subtree + Pruning and Regrafting (SPR) moves, which allows to quickly navigate to the best-known ML tree.""" + +toolchain = {'name': 'GCC', 'version': '13.2.0'} + +sources = [{ + 'filename': '%(version)s.tar.gz', + 'git_config': { + 'url': 'https://github.com/amkozlov', + 'repo_name': '%(namelower)s', + 'tag': '%(version)s', + 'recursive': True, + 'keep_git_dir': True, + } +}] +checksums = [None] + +builddependencies = [ + ('CMake', '3.27.6'), + ('Bison', '3.8.2'), + ('flex', '2.6.4'), + ('googletest', '1.14.0'), +] + +dependencies = [ + ('GMP', '6.3.0'), +] + +preconfigopts = "sed -i 's/c++11/c++14/g' %(builddir)s/raxml-ng/CMakeLists.txt && " +configopts = '-DUSE_GMP=ON ' + +runtest = 'test ' + +sanity_check_paths = { + 'files': ['bin/raxml-ng'], + 'dirs': [], +} + +sanity_check_commands = ["raxml-ng --help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/r/RCall/RCall-0.13.17-foss-2022a-R-4.2.1-Julia-1.9.2.eb b/easybuild/easyconfigs/r/RCall/RCall-0.13.17-foss-2022a-R-4.2.1-Julia-1.9.2.eb index a7789bd8358..bb9b6221bf8 100644 --- a/easybuild/easyconfigs/r/RCall/RCall-0.13.17-foss-2022a-R-4.2.1-Julia-1.9.2.eb +++ b/easybuild/easyconfigs/r/RCall/RCall-0.13.17-foss-2022a-R-4.2.1-Julia-1.9.2.eb @@ -16,8 +16,6 @@ dependencies = [ ('Julia', local_juliaver, '-linux-%s' % ARCH, SYSTEM), ] -preinstallopts = "export LD_LIBRARY_PATH=$EBROOTJULIA/lib/julia:$LD_LIBRARY_PATH && " - exts_default_options = { 'source_tmpl': 'v%(version)s.tar.gz', } @@ -224,17 +222,15 @@ exts_list = [ }), ] -sanity_check_commands = ["julia -e 'using Pkg;Pkg.test(\"%(name)s\")'"] +local_julia_env = "%(installdir)s/environments/v" + '.'.join(local_juliaver.split('.')[:2]) + +sanity_check_commands = [ + """julia -e 'using Pkg; Pkg.activate("%s"); Pkg.test("%%(name)s")'""" % local_julia_env, +] sanity_check_paths = { 'files': [], 'dirs': ['packages/%(name)s'], } -# When loading R and Julia, there seems to be a library collision and Julia (namely Pkg module) doesn't work properly -# This is a workaround to make Julia find the correct libraries -modluafooter = """ -prepend_path("LD_LIBRARY_PATH", os.getenv("EBROOTJULIA") .. "/lib/julia") -""" - moduleclass = 'tools' diff --git a/easybuild/easyconfigs/r/RDFlib/RDFlib-7.0.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/r/RDFlib/RDFlib-7.0.0-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..4be8dccf690 --- /dev/null +++ b/easybuild/easyconfigs/r/RDFlib/RDFlib-7.0.0-GCCcore-13.3.0.eb @@ -0,0 +1,35 @@ +easyblock = 'PythonBundle' + +name = 'RDFlib' +version = '7.0.0' + +homepage = 'https://github.com/RDFLib/rdflib' +description = """RDFLib is a Python library for working with RDF, a simple yet powerful language + for representing information.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +builddependencies = [ + ('binutils', '2.42'), + ('poetry', '1.8.3'), +] + +dependencies = [ + ('Python', '3.12.3'), + ('Python-bundle-PyPI', '2024.06'), +] + +use_pip = True + +exts_list = [ + ('isodate', '0.6.1', { + 'checksums': ['48c5881de7e8b0a0d648cb024c8062dc84e7b840ed81e864c7614fd3c127bde9'], + }), + ('rdflib', version, { + 'checksums': ['9995eb8569428059b8c1affd26b25eac510d64f5043d9ce8c84e0d0036e995ae'], + }), +] + +sanity_pip_check = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/r/RDKit/RDKit-2024.03.3-foss-2023a.eb b/easybuild/easyconfigs/r/RDKit/RDKit-2024.03.3-foss-2023a.eb new file mode 100644 index 00000000000..5af2865d609 --- /dev/null +++ b/easybuild/easyconfigs/r/RDKit/RDKit-2024.03.3-foss-2023a.eb @@ -0,0 +1,73 @@ +easyblock = 'CMakeMake' + +name = 'RDKit' +version = '2024.03.3' + +homepage = 'https://www.rdkit.org' +description = "RDKit is a collection of cheminformatics and machine-learning software written in C++ and Python." + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['https://github.com/rdkit/rdkit/archive/'] +sources = ['Release_%s.tar.gz' % version.replace('.', '_')] +checksums = ['52f79c6bf1d446cdb5c86a35de655d96bad0c52a5f4ecbe15f08eaf334e6f76a'] + +builddependencies = [ + ('CMake', '3.26.3'), + ('Eigen', '3.4.0'), + ('pkgconf', '1.9.5'), +] +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('SQLite', '3.42.0'), + ('matplotlib', '3.7.2'), + ('Pillow', '10.0.0'), + ('Boost.Python', '1.82.0'), + ('cairo', '1.17.8'), +] + +separate_build_dir = True + +configopts = "-DPy_ENABLE_SHARED=1 -DRDK_INSTALL_STATIC_LIBS=OFF -DRDK_INSTALL_INTREE=OFF " +configopts += "-DRDK_BUILD_INCHI_SUPPORT=ON " +configopts += "-DBOOST_ROOT=$EBROOTBOOST" + +# ingnore failing test pythonSourceTests - from . import rdBase failing +prebuildopts = "sed -i '22d' %(builddir)s/rdkit-Release_2024_03_3/rdkit/CMakeLists.txt && " +# ignore failing testUFFAngleConstraints +# https://github.com/rdkit/rdkit/discussions/7588 +prebuildopts += "sed -i 's/def testUFFAngleConstraints(self):/def ignore_testUFFAngleConstraints(self):/' " +prebuildopts += "%(builddir)s/rdkit-Release_2024_03_3/Code/ForceField/Wrap/testConstraints.py && " + +# merge source directory into build directory in order to run the tests +buildopts = '&& cp -RT %(builddir)s/%(namelower)s-*/ ./ && ' +buildopts += 'export RDBASE=$PWD && export PYTHONPATH=$PWD:$PYTHONPATH && ' + +# Specify path for libraries so that they are found during the tests when the module is built with --rpath flag. +buildopts += 'export LD_LIBRARY_PATH=%(builddir)s/easybuild_obj/lib:${LD_LIBRARY_PATH} && ' + +# 'ctest' allows to pass additional arguments opposed to 'make test' +buildopts += 'ctest --output-on-failure' + +local_libs = ['Alignment', 'Catalogs', 'ChemicalFeatures', 'ChemReactions', 'ChemTransforms', 'coordgen', 'DataStructs', + 'Depictor', 'Descriptors', 'DistGeometry', 'DistGeomHelpers', 'EigenSolvers', 'FileParsers', + 'FilterCatalog', 'Fingerprints', 'FMCS', 'ForceFieldHelpers', 'ForceField', 'FragCatalog', 'GraphMol', + 'hc', 'InfoTheory', 'maeparser', 'MMPA', 'MolAlign', 'MolCatalog', 'MolChemicalFeatures', 'MolDraw2D', + 'MolHash', 'MolInterchange', 'MolStandardize', 'MolTransforms', 'Optimizer', 'PartialCharges', 'RDBoost', + 'RDGeneral', 'RDGeometryLib', 'RDStreams', 'ReducedGraphs', 'RGroupDecomposition', 'RingDecomposerLib', + 'ScaffoldNetwork', 'ShapeHelpers', 'SimDivPickers', 'SLNParse', 'SmilesParse', 'Subgraphs', + 'SubstructLibrary', 'SubstructMatch', 'Trajectory'] + +sanity_check_paths = { + 'files': ['lib/libRDKit%s.%s' % (x, SHLIB_EXT) for x in local_libs], + 'dirs': ['include/rdkit', 'lib/python%(pyshortver)s/site-packages/rdkit'], +} + +sanity_check_commands = [ + "python -c 'import rdkit.rdBase'", +] + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/r/RE2/RE2-2024-07-02-GCCcore-13.3.0.eb b/easybuild/easyconfigs/r/RE2/RE2-2024-07-02-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..3719af682fd --- /dev/null +++ b/easybuild/easyconfigs/r/RE2/RE2-2024-07-02-GCCcore-13.3.0.eb @@ -0,0 +1,34 @@ +easyblock = "CMakeMake" + +name = 'RE2' +version = '2024-07-02' + +homepage = 'https://github.com/google/re2' +description = """ +RE2 is a fast, safe, thread-friendly alternative to backtracking regular +expression engines like those used in PCRE, Perl, and Python. It is a C++ +library. """ + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +github_account = 'google' +source_urls = [GITHUB_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['eb2df807c781601c14a260a507a5bb4509be1ee626024cb45acbd57cb9d4032b'] + +builddependencies = [ + ('binutils', '2.42'), + ('CMake', '3.29.3'), +] + +dependencies = [ + ('Abseil', '20240722.0'), +] + +sanity_check_paths = { + 'files': ['lib/libre2.a'], + 'dirs': ['include/re2'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/r/RHEIA/RHEIA-1.1.11-foss-2023a.eb b/easybuild/easyconfigs/r/RHEIA/RHEIA-1.1.11-foss-2023a.eb new file mode 100644 index 00000000000..d218a83dc02 --- /dev/null +++ b/easybuild/easyconfigs/r/RHEIA/RHEIA-1.1.11-foss-2023a.eb @@ -0,0 +1,41 @@ +easyblock = 'PythonBundle' + +name = 'RHEIA' +version = '1.1.11' + +homepage = 'https://github.com/rheia-framework/RHEIA' +description = "Robust design optimization of renewable Hydrogen and dErIved energy cArrier systems" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), # deap, numpy, pandas, scipy + ('h5py', '3.9.0'), + ('matplotlib', '3.7.2'), +] + +use_pip = True + +exts_list = [ + ('pvlib', '0.11.0', { + 'checksums': ['88b31c44dc07f0435af1e2d5ddcac067e6ce15917251a9f270366f61e9bd015b'], + }), + ('pyDOE', '0.3.8', { + 'modulename': '%(name)s', + 'source_tmpl': '%(name)s-%(version)s.zip', + 'checksums': ['cbd6f14ae26d3c9f736013205f53ea1191add4567033c3ee77b7dd356566c4b6'], + }), + ('SobolSequence', '0.2.1', { + 'modulename': 'sobol', + 'checksums': ['b2b4b57451b8d2e79ddb07efa23bc471dfdd436ea357d6368666bdc364df3eb1'], + }), + ('rheia', version, { + 'sources': ['%(namelower)s-%(version)s.tar.gz'], + 'checksums': ['d6b1ea991f6338cca136b59e8e413bae2167c5ebd631163ec68fafe0040aa143'], + }), +] + +sanity_pip_check = True + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/r/RMBlast/RMBlast-2.14.1-gompi-2023a.eb b/easybuild/easyconfigs/r/RMBlast/RMBlast-2.14.1-gompi-2023a.eb new file mode 100644 index 00000000000..22e6ed85f93 --- /dev/null +++ b/easybuild/easyconfigs/r/RMBlast/RMBlast-2.14.1-gompi-2023a.eb @@ -0,0 +1,65 @@ +## +# EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos , Kenneth Hoste (UGent) +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of +# the policy: https://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +# +# Update: Petr Král (INUITS) +## + +easyblock = 'ConfigureMake' + +name = 'RMBlast' +version = '2.14.1' + +homepage = 'https://www.repeatmasker.org/rmblast/' +description = """RMBlast is a RepeatMasker compatible version of the standard NCBI BLAST suite. The primary + difference between this distribution and the NCBI distribution is the addition of a new program 'rmblastn' + for use with RepeatMasker and RepeatModeler.""" + +toolchain = {'name': 'gompi', 'version': '2023a'} +toolchainopts = {'usempi': True} + +# RMBlast is distributed as a patch that applies on top of BLAST+ +source_urls = ['https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/%(version)s/'] +sources = ['ncbi-blast-%(version)s+-src.tar.gz'] +patches = [('https://www.repeatmasker.org/%(namelower)s/isb-%(version)s+-%(namelower)s.patch.gz', 2)] +checksums = [ + {'ncbi-blast-2.14.1+-src.tar.gz': '712c2dbdf0fb13cc1c2d4f4ef5dd1ce4b06c3b57e96dfea8f23e6e99f5b1650e'}, + {'isb-2.14.1+-rmblast.patch.gz': '9c8091eb2aec97ac83287859d2bfec83cb08c082d5a121cbefe3cc626f933763'}, +] + +dependencies = [ + ('zlib', '1.2.13'), + ('bzip2', '1.0.8'), + ('PCRE', '8.45'), + ('Boost.MPI', '1.82.0'), + ('GMP', '6.2.1'), + ('libpng', '1.6.39'), + ('libjpeg-turbo', '2.1.5.1'), + ('LMDB', '0.9.31'), +] + +# Disable auto-vectorization for the API on CPUs with AVX512 (Intel Skylake and onwards) +# Compilation fails on src/algo/blast/api/prelim_stage.cpp +local_apimake = 'src/algo/blast/api/Makefile.xblast.lib' +preconfigopts = "sed -i 's/FAST_CXXFLAGS)/FAST_CXXFLAGS) -fno-tree-vectorize/g' %s &&" % local_apimake + +configopts = "--with-64 --with-z=$EBROOTZLIB --with-bz2=$EBROOTBZIP2 " +configopts += "--with-pcre=$EBROOTPCRE --with-boost=$EBROOTBOOST " +configopts += "--with-gmp=$EBROOTGMP --with-png=$EBROOTLIBPNG " +configopts += "--with-jpeg=$EBROOTLIBJPEGMINTURBO --with-lmdb=$EBROOTLMDB" + +prebuildopts = "sed -i 's/LIBS =/LIBS = $(BLAST_THIRD_PARTY_LIBS)/' src/app/rmblastn/Makefile.rmblastn.app && " + +sanity_check_paths = { + 'files': ['bin/blastp', 'bin/blastn', 'bin/deltablast', 'bin/rmblastn'], + 'dirs': [] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/r/ROOT/ROOT-6.12.06_cling-runtime-sysroot.patch b/easybuild/easyconfigs/r/ROOT/ROOT-6.12.06_cling-runtime-sysroot.patch new file mode 100644 index 00000000000..7bf22bc1d8e --- /dev/null +++ b/easybuild/easyconfigs/r/ROOT/ROOT-6.12.06_cling-runtime-sysroot.patch @@ -0,0 +1,25 @@ +This patch disables the runtime sysroot feature for cling since we would not be cross-compiling in an EasyBuild context. + +Reusing existing patch found in Gentoo ebuild for ROOT, see url: +https://github.com/gentoo/gentoo/blob/master/sci-physics/root/files/root-6.12.06_cling-runtime-sysroot.patch + +Patch needed for at runtime for ROOT in EESSI: +https://github.com/EESSI/software-layer/pull/769 + +Index: root-6.12.06/interpreter/cling/lib/Utils/Paths.cpp +=================================================================== +--- root-6.12.06.orig/interpreter/cling/lib/Utils/Paths.cpp ++++ root-6.12.06/interpreter/cling/lib/Utils/Paths.cpp +@@ -57,11 +57,6 @@ using namespace clang; + void CopyIncludePaths(const clang::HeaderSearchOptions& Opts, + llvm::SmallVectorImpl& incpaths, + bool withSystem, bool withFlags) { +- if (withFlags && Opts.Sysroot != "/") { +- incpaths.push_back("-isysroot"); +- incpaths.push_back(Opts.Sysroot); +- } +- + /// User specified include entries. + for (unsigned i = 0, e = Opts.UserEntries.size(); i != e; ++i) { + const HeaderSearchOptions::Entry &E = Opts.UserEntries[i]; + diff --git a/easybuild/easyconfigs/r/ROOT/ROOT-6.24.06-foss-2021b.eb b/easybuild/easyconfigs/r/ROOT/ROOT-6.24.06-foss-2021b.eb index 91350423753..b7662891803 100644 --- a/easybuild/easyconfigs/r/ROOT/ROOT-6.24.06-foss-2021b.eb +++ b/easybuild/easyconfigs/r/ROOT/ROOT-6.24.06-foss-2021b.eb @@ -10,7 +10,13 @@ toolchainopts = {'pic': True} source_urls = ['https://root.cern.ch/download/'] sources = ['%(namelower)s_v%(version)s.source.tar.gz'] -checksums = ['907f69f4baca1e4f30eeb4979598ca7599b6aa803ca046e80e25b6bbaa0ef522'] +patches = [ + 'ROOT-6.12.06_cling-runtime-sysroot.patch', +] +checksums = [ + {'root_v6.24.06.source.tar.gz': '907f69f4baca1e4f30eeb4979598ca7599b6aa803ca046e80e25b6bbaa0ef522'}, + {'ROOT-6.12.06_cling-runtime-sysroot.patch': '63db7cb8371408dfa35dc58a500cd1de70d06db6b87674d5694b02e4092b6bd0'}, +] builddependencies = [ ('CMake', '3.22.1'), diff --git a/easybuild/easyconfigs/r/ROOT/ROOT-6.26.06-foss-2022a.eb b/easybuild/easyconfigs/r/ROOT/ROOT-6.26.06-foss-2022a.eb index e3109d99f7d..0514357e262 100644 --- a/easybuild/easyconfigs/r/ROOT/ROOT-6.26.06-foss-2022a.eb +++ b/easybuild/easyconfigs/r/ROOT/ROOT-6.26.06-foss-2022a.eb @@ -10,7 +10,13 @@ toolchainopts = {'pic': True} source_urls = ['https://root.cern.ch/download/'] sources = ['%(namelower)s_v%(version)s.source.tar.gz'] -checksums = ['b1f73c976a580a5c56c8c8a0152582a1dfc560b4dd80e1b7545237b65e6c89cb'] +patches = [ + 'ROOT-6.12.06_cling-runtime-sysroot.patch', +] +checksums = [ + {'root_v6.26.06.source.tar.gz': 'b1f73c976a580a5c56c8c8a0152582a1dfc560b4dd80e1b7545237b65e6c89cb'}, + {'ROOT-6.12.06_cling-runtime-sysroot.patch': '63db7cb8371408dfa35dc58a500cd1de70d06db6b87674d5694b02e4092b6bd0'}, +] builddependencies = [ ('CMake', '3.23.1'), diff --git a/easybuild/easyconfigs/r/ROOT/ROOT-6.26.10-foss-2022b.eb b/easybuild/easyconfigs/r/ROOT/ROOT-6.26.10-foss-2022b.eb index 6e41414b19b..845b0e4db80 100644 --- a/easybuild/easyconfigs/r/ROOT/ROOT-6.26.10-foss-2022b.eb +++ b/easybuild/easyconfigs/r/ROOT/ROOT-6.26.10-foss-2022b.eb @@ -10,7 +10,13 @@ toolchainopts = {'pic': True} source_urls = ['https://root.cern.ch/download/'] sources = ['%(namelower)s_v%(version)s.source.tar.gz'] -checksums = ['8e56bec397104017aa54f9eb554de7a1a134474fe0b3bb0f43a70fc4fabd625f'] +patches = [ + 'ROOT-6.12.06_cling-runtime-sysroot.patch', +] +checksums = [ + {'root_v6.26.10.source.tar.gz': '8e56bec397104017aa54f9eb554de7a1a134474fe0b3bb0f43a70fc4fabd625f'}, + {'ROOT-6.12.06_cling-runtime-sysroot.patch': '63db7cb8371408dfa35dc58a500cd1de70d06db6b87674d5694b02e4092b6bd0'}, +] builddependencies = [ ('CMake', '3.24.3'), diff --git a/easybuild/easyconfigs/r/ROOT/ROOT-6.30.06-foss-2023a.eb b/easybuild/easyconfigs/r/ROOT/ROOT-6.30.06-foss-2023a.eb new file mode 100644 index 00000000000..a95692ea233 --- /dev/null +++ b/easybuild/easyconfigs/r/ROOT/ROOT-6.30.06-foss-2023a.eb @@ -0,0 +1,59 @@ +name = 'ROOT' +version = '6.30.06' + +homepage = 'https://root.cern.ch' +description = """The ROOT system provides a set of OO frameworks with all the functionality + needed to handle and analyze large amounts of data in a very efficient way.""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'pic': True} + +source_urls = ['https://root.cern.ch/download/'] +sources = ['%(namelower)s_v%(version)s.source.tar.gz'] +patches = [ + 'ROOT-6.12.06_cling-runtime-sysroot.patch', +] +checksums = [ + {'root_v6.30.06.source.tar.gz': '300db7ed1b678ed2fb9635ca675921a1945c7c2103da840033b493091f55700c'}, + {'ROOT-6.12.06_cling-runtime-sysroot.patch': '63db7cb8371408dfa35dc58a500cd1de70d06db6b87674d5694b02e4092b6bd0'}, +] + +builddependencies = [ + ('CMake', '3.26.3'), + ('pkgconf', '1.9.5'), +] + +dependencies = [ + ('GSL', '2.7'), + ('libxml2', '2.11.4'), + ('PCRE', '8.45'), + ('CFITSIO', '4.3.0'), + ('freetype', '2.13.0'), + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('zlib', '1.2.13'), + ('X11', '20230603'), + ('Mesa', '23.1.4'), + ('libGLU', '9.0.3'), + ('GL2PS', '1.4.2'), + ('FFTW', '3.3.10'), + ('SQLite', '3.42.0'), + ('XZ', '5.4.2'), + ('libpng', '1.6.39'), +] + +# NOTE: Ensure that each configopts string begins with a blank +# disable some components +configopts = " -Dxrootd=OFF -Dmysql=OFF -Dkrb5=OFF -Dodbc=OFF -Doracle=OFF -Dpgsql=OFF -Dqt=OFF" + +# make sure some components are enabled +configopts += " -Dpcre=ON -Dzlib=ON -Dpyroot=ON" +configopts += " -Dunuran=ON -Dexplicitlink=ON -Dminuit2=ON -Droofit=ON " + +# Add component-specific settings based on dependencies +configopts += ' -Dfftw3=ON -Dgsl=ON -DOpenGL_GL_PREFERENCE=GLVND' + +# Set C++ standard to C++17 for better stability +configopts += ' -DCMAKE_CXX_STANDARD=17' + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/r/RSEM/RSEM-1.3.3-foss-2023a.eb b/easybuild/easyconfigs/r/RSEM/RSEM-1.3.3-foss-2023a.eb new file mode 100644 index 00000000000..559d54704d5 --- /dev/null +++ b/easybuild/easyconfigs/r/RSEM/RSEM-1.3.3-foss-2023a.eb @@ -0,0 +1,54 @@ +## +# This is a contribution from DeepThought HPC Service, Flinders University, Adelaide, Australia +# Homepage: https://staff.flinders.edu.au/research/deep-thought +# +# Authors:: Robert Qiao +# License:: GPLv3.0 +# +# Notes:: +## + +easyblock = 'ConfigureMake' + +name = 'RSEM' +version = '1.3.3' + +homepage = 'https://deweylab.github.io/RSEM/' +description = "RNA-Seq by Expectation-Maximization" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'openmp': True} + +source_urls = ['https://github.com/deweylab/RSEM/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = ['RSEM-1.3.0_makefiles.patch'] +checksums = [ + '90e784dd9df8346caa2a7e3ad2ad07649608a51df1c69bfb6e16f45e611a40dc', # v1.3.3.tar.gz + '2d244659206c78655b92f1bd519ee65f28a6b5f9418dfad04e887b64eca6641b', # RSEM-1.3.0_makefiles.patch +] + +skipsteps = ['configure'] + +installopts = "prefix=%(installdir)s" + +dependencies = [ + ('Java', '11', '', SYSTEM), + ('ncurses', '6.4'), + ('zlib', '1.2.13'), + ('Perl', '5.36.1'), + ('Perl-bundle-CPAN', '5.36.1'), + ('R', '4.3.2'), + ('R-bundle-CRAN', '2023.12'), + ('HISAT2', '2.2.1'), + ('STAR', '2.7.11a'), + ('Bowtie2', '2.5.1'), + ('Bowtie', '1.3.1'), +] + +sanity_check_paths = { + 'files': ['bin/rsem-calculate-expression', 'bin/rsem-plot-model', 'bin/rsem-plot-transcript-wiggles', + 'bin/rsem-bam2wig', 'bin/rsem-generate-data-matrix', 'bin/rsem-run-em', 'bin/convert-sam-for-rsem'], + 'dirs': ['bin/samtools-1.3'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/r/RStudio-Server/RStudio-Server-2023.09.1+494-foss-2023a-Java-11-R-4.3.2.eb b/easybuild/easyconfigs/r/RStudio-Server/RStudio-Server-2023.09.1+494-foss-2023a-Java-11-R-4.3.2.eb new file mode 100644 index 00000000000..56585dad1c0 --- /dev/null +++ b/easybuild/easyconfigs/r/RStudio-Server/RStudio-Server-2023.09.1+494-foss-2023a-Java-11-R-4.3.2.eb @@ -0,0 +1,108 @@ +easyblock = 'CMakeNinja' + +name = 'RStudio-Server' +version = "2023.09.1+494" +versionsuffix = '-Java-%(javaver)s-R-%(rver)s' +local_git_rev = 'cd7011dce393115d3a7c3db799dda4b1c7e88711' + +homepage = 'https://www.rstudio.com/' +description = """This is the RStudio Server version. +RStudio is a set of integrated tools designed to help you be more productive with R. + +The server can be started with: + rserver --server-daemonize=0 --www-port=8787 + +If you need a database config one can be created with: + MYTMP=`mktemp -d` && echo -e "provider=sqlite\\ndirectory=${MYTMP}/sqlite" > "${MYTMP}/db.conf" +and then used with: + rserver ... --database-config-file="${MYTMP}/db.conf" +""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['https://github.com/rstudio/rstudio/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['38526a5816e980b12aeaef7debd2151f08ef2e54fed83af2622eb7cdeeb479a2'] + +builddependencies = [ + ('ant', '1.10.14', '-Java-%(javaver)s', SYSTEM), + ('CMake', '3.26.3'), + ('Ninja', '1.11.1'), + ('pkgconf', '1.9.5'), + ('nodejs', '18.17.1'), +] + +dependencies = [ + ('Boost', '1.82.0'), + ('Java', '11', '', SYSTEM), + ('R', '4.3.2'), + ('R-bundle-CRAN', '2023.12'), + ('SOCI', '4.0.3'), + ('yaml-cpp', '0.7.0'), +] + +osdependencies = [ + ('pam-devel', 'libpam0g-dev') +] + +preconfigopts = " && ".join([ + # Install dependencies via scripts. Done in subshell to preserve PWD + "(export RSTUDIO_TOOLS_ROOT='%(builddir)s'", + "cd '%(start_dir)s/dependencies/common'", + "./install-cef", + "./install-dictionaries", + "./install-mathjax", + "./install-pandoc", + "./install-panmirror", + "./install-npm-dependencies)", + "" +]) + +configopts = " ".join([ + "-DRSTUDIO_TOOLS_ROOT='%(builddir)s'", + "-DRSTUDIO_TARGET=Server", + "-DRSTUDIO_USE_SYSTEM_BOOST=ON", + "-DRSTUDIO_USE_SYSTEM_SOCI=ON", + "-DRSTUDIO_USE_SYSTEM_YAML_CPP=ON", + "-DQUARTO_ENABLED=OFF", # Not available on all archs, use pandoc fallback + "-DRSTUDIO_GIT_REVISION_HASH=" + local_git_rev +]) + +sanity_check_commands = [ + # RSession requires environment variables R_HOME and R_DOC_DIR + 'R_HOME="$EBROOTR/lib64/R" R_DOC_DIR="$R_HOME/doc" rsession --verify-installation=1', + # RServer requires a db conf (this may also be needed for live use) + # Also create and set a soem dirs so it doesn't try to use $HOME + ' '.join([ + 'MYTMP=`mktemp -d`', + '&& export RSTUDIO_CONFIG_DIR="$MYTMP"', + '&& export XDG_DATA_HOME="$MYTMP/.data"', + '&& export XDG_CACHE_HOME="$MYTMP/.cache"', + '&& mkdir "$XDG_DATA_HOME" "$XDG_CACHE_HOME"', + '&& export RS_LOG_DIR="$MYTMP/log"', + '&& echo -e "provider=sqlite\\ndirectory=$MYTMP/db" >> "$MYTMP/db.conf"', + '&& rserver', + '--verify-installation=1', + '--server-user="$USER"', + '--database-config-file="$MYTMP/db.conf"', + '--server-data-dir="$MYTMP/sdd"', + '--secure-cookie-key-file="$MYTMP/secure-cookie-key"', + ]), +] + +sanity_check_paths = { + 'files': ['bin/rstudio-server'], + 'dirs': ['bin', 'extras', 'resources', 'www', 'www-symbolmaps', 'R'], +} + +modloadmsg = """ +The server can be started with: + rserver --server-daemonize=0 --www-port=8787 + +If you need a database config one can be created with: + MYTMP=`mktemp -d` && echo -e "provider=sqlite\\ndirectory=${MYTMP}/sqlite" > "${MYTMP}/db.conf" +and then used with: + rserver ... --database-config-file="${MYTMP}/db.conf" +""" + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/RStudio-Server/RStudio-Server-2023.12.1+402-gfbf-2023b-Java-11-R-4.3.3.eb b/easybuild/easyconfigs/r/RStudio-Server/RStudio-Server-2023.12.1+402-gfbf-2023b-Java-11-R-4.3.3.eb new file mode 100644 index 00000000000..7821f9f4b06 --- /dev/null +++ b/easybuild/easyconfigs/r/RStudio-Server/RStudio-Server-2023.12.1+402-gfbf-2023b-Java-11-R-4.3.3.eb @@ -0,0 +1,98 @@ +easyblock = 'CMakeNinja' + +name = 'RStudio-Server' +version = "2023.12.1+402" +versionsuffix = '-Java-%(javaver)s-R-%(rver)s' +local_git_rev = '4da58325ffcff29d157d9264087d4b1ab27f7204' + +homepage = 'https://www.rstudio.com/' +description = """This is the RStudio Server version. +RStudio is a set of integrated tools designed to help you be more productive with R. + +The server can be started with: + rserver --server-daemonize=0 --www-port=8787 + +If you need a database config one can be created with: + MYTMP=`mktemp -d` && echo -e "provider=sqlite\\ndirectory=${MYTMP}/sqlite" > "${MYTMP}/db.conf" +and then used with: + rserver ... --database-config-file="${MYTMP}/db.conf" +""" + +toolchain = {'name': 'gfbf', 'version': '2023b'} + +source_urls = ['https://github.com/rstudio/rstudio/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['196d31094d580a74737fbf689d2d0b302da5fec13694aa1d63f8875d3e45e4dd'] + +builddependencies = [ + ('ant', '1.10.14', '-Java-%(javaver)s', SYSTEM), + ('CMake', '3.27.6'), + ('Ninja', '1.11.1'), + ('pkgconf', '2.0.3'), + ('nodejs', '20.9.0'), +] + +dependencies = [ + ('Boost', '1.83.0'), + ('Java', '11', '', SYSTEM), + ('R', '4.3.3'), + ('SOCI', '4.0.3'), + ('yaml-cpp', '0.8.0'), +] + +osdependencies = [ + ('pam-devel', 'libpam0g-dev') +] + +preconfigopts = " && ".join([ + # Install dependencies via scripts. Done in subshell to preserve PWD + "(export RSTUDIO_TOOLS_ROOT='%(builddir)s'", + "cd '%(start_dir)s/dependencies/common'", + "./install-cef", + "./install-dictionaries", + "./install-mathjax", + "./install-pandoc", + "./install-packages", + "./install-panmirror", + "./install-npm-dependencies)", + "" +]) + +configopts = " ".join([ + "-DRSTUDIO_TOOLS_ROOT='%(builddir)s'", + "-DRSTUDIO_TARGET=Server", + "-DRSTUDIO_USE_SYSTEM_BOOST=ON", + "-DRSTUDIO_USE_SYSTEM_SOCI=ON", + "-DRSTUDIO_USE_SYSTEM_YAML_CPP=ON", + "-DQUARTO_ENABLED=OFF", # Not available on all archs, use pandoc fallback + "-DRSTUDIO_GIT_REVISION_HASH=" + local_git_rev +]) + +sanity_check_commands = [ + # RSession requires environment variables R_HOME and R_DOC_DIR + 'R_HOME="$EBROOTR/lib64/R" R_DOC_DIR="$R_HOME/doc" rsession --verify-installation=1', + # RServer requires a db conf (this may also be needed for live use) + # Also create and set a soem dirs so it doesn't try to use $HOME + ' '.join([ + 'MYTMP=`mktemp -d`', + '&& export RSTUDIO_CONFIG_DIR="$MYTMP"', + '&& export XDG_DATA_HOME="$MYTMP/.data"', + '&& export XDG_CACHE_HOME="$MYTMP/.cache"', + '&& mkdir "$XDG_DATA_HOME" "$XDG_CACHE_HOME"', + '&& export RS_LOG_DIR="$MYTMP/log"', + '&& echo -e "provider=sqlite\\ndirectory=$MYTMP/db" >> "$MYTMP/db.conf"', + '&& rserver', + '--verify-installation=1', + '--server-user="$USER"', + '--database-config-file="$MYTMP/db.conf"', + '--server-data-dir="$MYTMP/sdd"', + '--secure-cookie-key-file="$MYTMP/secure-cookie-key"', + ]), +] + +sanity_check_paths = { + 'files': ['bin/rstudio-server'], + 'dirs': ['bin', 'extras', 'resources', 'www', 'www-symbolmaps', 'R'], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/RStudio-Server/RStudio-Server-2024.09.0+375-foss-2023b-Java-11-R-4.4.1.eb b/easybuild/easyconfigs/r/RStudio-Server/RStudio-Server-2024.09.0+375-foss-2023b-Java-11-R-4.4.1.eb new file mode 100644 index 00000000000..2c81f46688a --- /dev/null +++ b/easybuild/easyconfigs/r/RStudio-Server/RStudio-Server-2024.09.0+375-foss-2023b-Java-11-R-4.4.1.eb @@ -0,0 +1,98 @@ +easyblock = 'CMakeNinja' + +name = 'RStudio-Server' +version = '2024.09.0+375' +versionsuffix = '-Java-%(javaver)s-R-%(rver)s' +local_git_rev = 'c8fc7aee6dc218d5687553f9041c6b1e5ea268ff' + +homepage = 'https://www.rstudio.com/' +description = """This is the RStudio Server version. +RStudio is a set of integrated tools designed to help you be more productive with R. + +The server can be started with: + rserver --server-daemonize=0 --www-port=8787 + +If you need a database config one can be created with: + MYTMP=`mktemp -d` && echo -e "provider=sqlite\\ndirectory=${MYTMP}/sqlite" > "${MYTMP}/db.conf" +and then used with: + rserver ... --database-config-file="${MYTMP}/db.conf" +""" + +toolchain = {'name': 'foss', 'version': '2023b'} + +source_urls = ['https://github.com/rstudio/rstudio/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['8a29b77c53a3db8379d824a9f4a491843036003d105ed71981cd40fe39d2c8c8'] + +builddependencies = [ + ('ant', '1.10.14', '-Java-%(javaver)s', SYSTEM), + ('CMake', '3.27.6'), + ('Ninja', '1.11.1'), + ('pkgconf', '2.0.3'), + ('nodejs', '20.9.0'), +] + +dependencies = [ + ('Boost', '1.83.0'), + ('Java', '11', '', SYSTEM), + ('R', '4.4.1'), + ('R-bundle-CRAN', '2024.06'), + ('SOCI', '4.0.3'), + ('yaml-cpp', '0.8.0'), +] + +osdependencies = [ + ('pam-devel', 'libpam0g-dev') +] + +preconfigopts = " && ".join([ + # Install dependencies via scripts. Done in subshell to preserve PWD + "(export RSTUDIO_TOOLS_ROOT='%(builddir)s'", + "cd '%(start_dir)s/dependencies/common'", + "./install-cef", + "./install-dictionaries", + "./install-mathjax", + "./install-pandoc", + "./install-panmirror", + "./install-npm-dependencies)", + "" +]) + +configopts = " ".join([ + "-DRSTUDIO_TOOLS_ROOT='%(builddir)s'", + "-DRSTUDIO_TARGET=Server", + "-DRSTUDIO_USE_SYSTEM_BOOST=ON", + "-DRSTUDIO_USE_SYSTEM_SOCI=ON", + "-DRSTUDIO_USE_SYSTEM_YAML_CPP=ON", + "-DQUARTO_ENABLED=OFF", # Not available on all archs, use pandoc fallback + "-DRSTUDIO_GIT_REVISION_HASH=" + local_git_rev +]) + +sanity_check_commands = [ + # RSession requires environment variables R_HOME and R_DOC_DIR + 'R_HOME="$EBROOTR/lib64/R" R_DOC_DIR="$R_HOME/doc" rsession --verify-installation=1', + # RServer requires a db conf (this may also be needed for live use) + # Also create and set a soem dirs so it doesn't try to use $HOME + ' '.join([ + 'MYTMP=`mktemp -d`', + '&& export RSTUDIO_CONFIG_DIR="$MYTMP"', + '&& export XDG_DATA_HOME="$MYTMP/.data"', + '&& export XDG_CACHE_HOME="$MYTMP/.cache"', + '&& mkdir "$XDG_DATA_HOME" "$XDG_CACHE_HOME"', + '&& export RS_LOG_DIR="$MYTMP/log"', + '&& echo -e "provider=sqlite\\ndirectory=$MYTMP/db" >> "$MYTMP/db.conf"', + '&& rserver', + '--verify-installation=1', + '--server-user="$USER"', + '--database-config-file="$MYTMP/db.conf"', + '--server-data-dir="$MYTMP/sdd"', + '--secure-cookie-key-file="$MYTMP/secure-cookie-key"', + ]), +] + +sanity_check_paths = { + 'files': ['bin/rstudio-server'], + 'dirs': ['bin', 'extras', 'resources', 'www', 'www-symbolmaps', 'R'], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/Racon/Racon-1.5.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/r/Racon/Racon-1.5.0-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..de4df21150d --- /dev/null +++ b/easybuild/easyconfigs/r/Racon/Racon-1.5.0-GCCcore-13.2.0.eb @@ -0,0 +1,29 @@ +easyblock = 'CMakeMake' + +name = 'Racon' +version = '1.5.0' + +homepage = 'https://github.com/lbcb-sci/racon' +description = """Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +github_account = 'lbcb-sci' +source_urls = [GITHUB_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['41e362f71cc03b934f17d6e2c0d626e1b2997258261b14551586de006666424a'] + +builddependencies = [ + ('CMake', '3.27.6'), + ('binutils', '2.40'), + ('git', '2.42.0'), +] + +sanity_check_paths = { + 'files': ['bin/racon'], + 'dirs': [], +} + +sanity_check_commands = ['racon --help'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/r/RapidJSON/RapidJSON-1.1.0-20240409-GCCcore-13.2.0.eb b/easybuild/easyconfigs/r/RapidJSON/RapidJSON-1.1.0-20240409-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..4f36c473ec4 --- /dev/null +++ b/easybuild/easyconfigs/r/RapidJSON/RapidJSON-1.1.0-20240409-GCCcore-13.2.0.eb @@ -0,0 +1,31 @@ +easyblock = 'CMakeMake' + +name = 'RapidJSON' +# no new release since Aug'16 so using latest commit; +# see also https://github.com/Tencent/rapidjson/issues/2202 +version = '1.1.0-20240409' +local_commit = 'ab1842a' + +homepage = 'https://rapidjson.org' +description = "A fast JSON parser/generator for C++ with both SAX/DOM style API" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://github.com/Tencent/%(namelower)s/archive/'] +sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': 'v%(version)s.tar.gz'}] +checksums = ['39f96f17b40f7201042c9b45d6444cb7eae1b7adfb7455412a86f6140450d32d'] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.27.6'), +] + +# strip out hardcoded use of -march=native, EasyBuild should be in control of this +preconfigopts = "sed -i 's/-march=native//g' ../rapidjson-*/CMakeLists.txt && " + +sanity_check_paths = { + 'files': ['lib/pkgconfig/%(name)s.pc'], + 'dirs': ['include/%(namelower)s', 'lib/cmake', 'share'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/r/RapidJSON/RapidJSON-1.1.0-20240815-GCCcore-13.3.0.eb b/easybuild/easyconfigs/r/RapidJSON/RapidJSON-1.1.0-20240815-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..b296d76e7b7 --- /dev/null +++ b/easybuild/easyconfigs/r/RapidJSON/RapidJSON-1.1.0-20240815-GCCcore-13.3.0.eb @@ -0,0 +1,31 @@ +easyblock = 'CMakeMake' + +name = 'RapidJSON' +# no new release since Aug'16 so using latest commit; +# see also https://github.com/Tencent/rapidjson/issues/2202 +version = '1.1.0-20240815' +local_commit = '7c73dd7' + +homepage = 'https://rapidjson.org' +description = "A fast JSON parser/generator for C++ with both SAX/DOM style API" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://github.com/Tencent/%(namelower)s/archive/'] +sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': 'v%(version)s.tar.gz'}] +checksums = ['91138ebc9c980e554e6bcf9d13537f9eebf42710e0b956fdca46181ad645f94d'] + +builddependencies = [ + ('binutils', '2.42'), + ('CMake', '3.29.3'), +] + +# strip out hardcoded use of -march=native, EasyBuild should be in control of this +preconfigopts = "sed -i 's/-march=native//g' ../rapidjson-*/CMakeLists.txt && " + +sanity_check_paths = { + 'files': ['lib/pkgconfig/%(name)s.pc'], + 'dirs': ['include/%(namelower)s', 'lib/cmake', 'share'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/r/Raptor/Raptor-2.0.16-GCCcore-12.3.0.eb b/easybuild/easyconfigs/r/Raptor/Raptor-2.0.16-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..61c358020c8 --- /dev/null +++ b/easybuild/easyconfigs/r/Raptor/Raptor-2.0.16-GCCcore-12.3.0.eb @@ -0,0 +1,55 @@ +## +# This is a contribution from SIB Swiss Institute of Bioinformatics +# Homepage: https://www.sib.swiss/research-infrastructure/competence-centers/vital-it +# +# Authors:: Sebastien Moretti +# +# Based on Raptor2 RPM spec file: +# https://git.rockylinux.org/staging/rpms/raptor2/-/blob/r8/SPECS/raptor2.spec +# The RPM patches have been integrated in the version 2.0.16 +# +# Update: Petr Král (INUITS) +## +easyblock = 'ConfigureMake' + +name = 'Raptor' +version = '2.0.16' +homepage = 'https://librdf.org/raptor/' +description = """Set of parsers and serializers that generate Resource Description Framework +(RDF) triples by parsing syntaxes or serialize the triples into a syntax.""" +# software_license = 'LicenseLGPLv2.1 + LicenseGPLv2 + LicenseApachev2' + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://download.librdf.org/source'] +sources = ['raptor2-%(version)s.tar.gz'] +checksums = ['089db78d7ac982354bdbf39d973baf09581e6904ac4c92a98c5caadb3de44680'] + +builddependencies = [ + ('Autotools', '20220317'), + ('binutils', '2.40'), + ('make', '4.4.1'), +] + +dependencies = [ + ('libxml2', '2.11.4'), + ('libxslt', '1.1.38'), + ('cURL', '8.0.1'), + ('ICU', '73.2'), +] + +configopts = "--disable-static --enable-release --disable-gtk-doc --with-yajl=no" + +# fix error: 'xmlEntity' {aka 'struct _xmlEntity'} has no member named 'checked' +# see https://github.com/dajobe/raptor/pull/58 +local_sed_replacement = r's/LIBXML_VERSION >= 20627/LIBXML_VERSION >= 2062 \&\& LIBXML_VERSION < 21100/g' +prebuildopts = "sed -i '%s' src/raptor_libxml.c && " % local_sed_replacement + +sanity_check_paths = { + 'files': ['bin/rapper', 'lib/libraptor2.%s' % SHLIB_EXT], + 'dirs': ['include/raptor2/'] +} + +sanity_check_commands = ["rapper --help"] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/r/Rasqal/Rasqal-0.9.33-GCCcore-12.3.0.eb b/easybuild/easyconfigs/r/Rasqal/Rasqal-0.9.33-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..3d5e0ad9d83 --- /dev/null +++ b/easybuild/easyconfigs/r/Rasqal/Rasqal-0.9.33-GCCcore-12.3.0.eb @@ -0,0 +1,38 @@ +easyblock = 'ConfigureMake' + +name = 'Rasqal' +version = '0.9.33' +homepage = 'hhttps://librdf.org/rasqal' +description = """A library handling RDF query syntaxes, construction and execution""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://download.librdf.org/source'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['6924c9ac6570bd241a9669f83b467c728a322470bf34f4b2da4f69492ccfd97c'] + +builddependencies = [ + ('Autotools', '20220317'), + ('binutils', '2.40'), + ('Raptor', '2.0.16'), +] + +dependencies = [ + ('libgcrypt', '1.10.3'), + ('MPFR', '4.2.0'), + ('PCRE', '8.45'), + ('gtk-doc', '1.34.0'), + ('ICU', '73.2'), +] + +preconfigopts = "autoreconf -f -i && " +configopts = "--disable-static --enable-release" + +sanity_check_paths = { + 'files': ['bin/roqet', 'lib/librasqal.%s' % SHLIB_EXT], + 'dirs': ['include/rasqal/'] +} + +sanity_check_commands = ["roqet --help"] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/r/Ray-project/Ray-project-2.37.0-foss-2024a.eb b/easybuild/easyconfigs/r/Ray-project/Ray-project-2.37.0-foss-2024a.eb new file mode 100644 index 00000000000..9b52d2bc91f --- /dev/null +++ b/easybuild/easyconfigs/r/Ray-project/Ray-project-2.37.0-foss-2024a.eb @@ -0,0 +1,67 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 + +easyblock = 'PythonBundle' + +name = 'Ray-project' +version = '2.37.0' + +homepage = "https://docs.ray.io/en/latest/" +description = "Ray is a fast and simple framework for building and running distributed applications." + +toolchain = {'name': 'foss', 'version': '2024a'} +toolchainopts = {'usempi': True} + +builddependencies = [ + ('redis-py', '5.1.1'), + ('hatchling', '1.24.2'), + ('Cython', '3.0.10') +] + +dependencies = [ + ('Python', '3.12.3'), + ('SciPy-bundle', '2024.05'), + ('protobuf-python', '5.28.0'), + ('PyYAML', '6.0.2'), + ('lz4', '1.9.4'), + ('mpi4py', '4.0.1'), +] + +use_pip = True + +exts_list = [ + ('grpcio', '1.62.1', { + 'modulename': 'grpc', + 'preinstallopts': "export GRPC_PYTHON_BUILD_EXT_COMPILER_JOBS=%(parallel)s && ", + 'checksums': ['6c455e008fa86d9e9a9d85bb76da4277c0d7d9668a3bfa70dbe86e9f3c759947'], + }), + ('aiosignal', '1.3.1', { + 'checksums': ['54cd96e15e1649b75d6c87526a6ff0b6c1b0dd3459f43d9ca11d48c339b68cfc'], + }), + ('expandvars', '0.12.0', { + 'checksums': ['7d1adfa55728cf4b5d812ece3d087703faea953e0c0a1a78415de9df5024d844'], + }), + ('frozenlist', '1.4.1', { + 'checksums': ['c037a86e8513059a2613aaba4d817bb90b9d9b6b69aace3ce9c877e8c8ed402b'], + }), + ('lz4', '4.3.3', { + 'checksums': ['01fe674ef2889dbb9899d8a67361e0c4a2c833af5aeb37dd505727cf5d2a131e'], + }), + ('Ray', version, { + 'source_tmpl': '%(namelower)s-%(version)s-cp312-cp312-manylinux2014_%(arch)s.whl', + 'checksums': ['0268c7bc2e8bb6ef9bb8969299deb5857bf672bfcb59da95db7495a8a502f8ba'], + }), +] + +sanity_check_paths = { + 'files': ['bin/ray'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + 'ray --help' +] + +sanity_pip_check = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/r/Ray-project/Ray-project-2.9.1-foss-2023a.eb b/easybuild/easyconfigs/r/Ray-project/Ray-project-2.9.1-foss-2023a.eb new file mode 100644 index 00000000000..67ab662077d --- /dev/null +++ b/easybuild/easyconfigs/r/Ray-project/Ray-project-2.9.1-foss-2023a.eb @@ -0,0 +1,73 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 + +easyblock = 'PythonBundle' + +name = 'Ray-project' +version = '2.9.1' + +homepage = "https://docs.ray.io/en/latest/" +description = "Ray is a fast and simple framework for building and running distributed applications." + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'usempi': True} + +builddependencies = [ + ('redis-py', '5.0.1'), + ('hatchling', '1.18.0'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('protobuf-python', '4.24.0'), + ('PyYAML', '6.0'), + ('lz4', '1.9.4'), + ('mpi4py', '3.1.4'), +] + +use_pip = True + +exts_list = [ + ('grpcio', '1.62.1', { + 'modulename': 'grpc', + 'preinstallopts': "export GRPC_PYTHON_BUILD_EXT_COMPILER_JOBS=%(parallel)s && ", + 'checksums': ['6c455e008fa86d9e9a9d85bb76da4277c0d7d9668a3bfa70dbe86e9f3c759947'], + }), + ('aiosignal', '1.3.1', { + 'checksums': ['54cd96e15e1649b75d6c87526a6ff0b6c1b0dd3459f43d9ca11d48c339b68cfc'], + }), + ('expandvars', '0.12.0', { + 'checksums': ['7d1adfa55728cf4b5d812ece3d087703faea953e0c0a1a78415de9df5024d844'], + }), + ('frozenlist', '1.4.1', { + 'checksums': ['c037a86e8513059a2613aaba4d817bb90b9d9b6b69aace3ce9c877e8c8ed402b'], + }), + ('lz4', '4.3.3', { + 'checksums': ['01fe674ef2889dbb9899d8a67361e0c4a2c833af5aeb37dd505727cf5d2a131e'], + }), + ('Ray', version, { + 'source_tmpl': '%(namelower)s-%(version)s-cp311-cp311-manylinux2014_%(arch)s.whl', + 'checksums': [{ + '%(namelower)s-%(version)s-cp311-cp311-manylinux2014_x86_64.whl': ( + 'fabc520990c1b98dde592813d62737e5e817460e0ac359f32ba029ace292cbe2' + ), + '%(namelower)s-%(version)s-cp311-cp311-manylinux2014_aarch64.whl': ( + '1907649d69efdc1b9ffbc03db086f6d768216cb73908ebd4038ac5030effef9e' + ), + }], + }), +] + +sanity_check_paths = { + 'files': ['bin/ray'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + 'ray --help' +] + +sanity_pip_check = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.3.2.eb b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.3.2.eb index b8237231c17..7e01526d78c 100644 --- a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.3.2.eb +++ b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.3.2.eb @@ -29,6 +29,8 @@ exts_list = [ }), ('reframe', version, { 'preinstallopts': "export PATH=%(installdir)s/bin:$PATH && " + # use PyYAML 6.0.1 to solve Cython 3 incompatibility issues + "sed -i 's@PyYAML==6.0@PyYAML==6.0.1@' requirements.txt && " "./bootstrap.sh +docs +pygelf && cp -r external %(installdir)s && " "PYTHONPATH=%(builddir)s/reframe/reframe-%(version)s/external:$PYTHONPATH ", 'source_tmpl': 'v%(version)s.tar.gz', diff --git a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.3.3.eb b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.3.3.eb index af6b22f4846..f4319b13ae5 100644 --- a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.3.3.eb +++ b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.3.3.eb @@ -30,6 +30,8 @@ exts_list = [ }), ('reframe', version, { 'preinstallopts': "export PATH=%(installdir)s/bin:$PATH && " + # use PyYAML 6.0.1 to solve Cython 3 incompatibility issues + "sed -i 's@PyYAML==6.0@PyYAML==6.0.1@' requirements.txt && " "./bootstrap.sh +docs +pygelf && cp -r external %(installdir)s && " "PYTHONPATH=%(builddir)s/reframe/reframe-%(version)s/external:$PYTHONPATH ", 'source_tmpl': 'v%(version)s.tar.gz', diff --git a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..9046d5c9362 --- /dev/null +++ b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-12.3.0.eb @@ -0,0 +1,76 @@ +easyblock = 'PythonBundle' + +name = 'ReFrame' +version = '4.6.2' + +homepage = 'https://github.com/reframe-hpc/reframe' +description = '''ReFrame is a framework for writing regression tests for HPC systems.''' + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +builddependencies = [ + ('binutils', '2.40'), + ('cURL', '8.0.1'), # Used by ReFrame to download pip in the bootstrap +] + +# Note that for ReFrame's CPU autodetect to work +# the system also needs to provide (new enough versions of) these dependencies +dependencies = [ + ('Python', '3.11.3'), + ('libxslt', '1.1.38'), # Required by lxml, which is installed by ReFrame's bootstrap installer + ('libxml2', '2.11.4'), # Required by lxml, which is installed by ReFrame's bootstrap installer +] + +use_pip = True + +exts_list = [ + # ReFrame's bootstrap script is intended to run with zero dependencies. It downloads all python deps for ReFrame + # into a %(installdir)/external directory. ReFrame's main executable (reframe) adds this dir to python's sys.path + # so that ReFrame (and only ReFrame) will find & use all of these dependencies. + # In EasyBuild, we should adhere to this installation method because a) it is how ReFrame is meant to be used and + # b) it isolates all of ReFrame dependencies from any other python code you run. Thus, there is no chance that + # a test will pick up on any python deps from ReFrame itself. + # For this to work, we need to disable download_dep_fail and sanity_pip_check, as both are _expected_ to fail + # for this setup. + ('reframe', version, { + # Deps are downloaded to %(installdir)/external, which won't polute the PYTHONPATH, so is ok + 'download_dep_fail': False, + # ReFrame uses its custom sys.path to find necessary packages, they are not on PYTYHONPATH + # Thus, the regular pip sanity check is expected to fail, even if ReFrame would run just fine + 'sanity_pip_check': False, + # Set modulename to False, as to skip the sanity_check-step from extension.py (python -c "import reframe") + # This step would fail, since the regular python interpreter wouldn't find the additional packages in + # %(installdir)/external. That's fine, as ReFrame should never be imported directly, only through the + # reframe command. + 'modulename': False, + 'preinstallopts': "export PATH=%(installdir)s/bin:$PATH && " + "./bootstrap.sh +docs +pygelf && cp -r external %(installdir)s && ", + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/reframe-hpc/reframe/archive/'], + 'checksums': ['d3343815ee3d2c330b91a1cdb924ba184119ed7d9fc88a4a754b939a4259df82'], + }), +] + +postinstallcmds = [ + "cp -a tools examples %(installdir)s", + "mkdir -p %(installdir)s/share && cp -a share/completions %(installdir)s/share/completions", + r"sed -i 's@/\(python[0-9.]*\)$@/\1 -S@g' %(installdir)s/bin/reframe", +] + +sanity_check_paths = { + 'files': ['bin/reframe', + 'share/completions/reframe.bash', + 'share/completions/reframe.fish', + 'share/completions/reframe.tcsh'], + 'dirs': ['external', 'lib', 'tools', 'examples'] +} + +sanity_check_commands = ['reframe -V'] + +# Since this is at the GCCcore toolchain level, make sure ReFrame is configured to purge modules before running +# any tests by default +modextravars = { + 'RFM_PURGE_ENVIRONMENT': '1', +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-13.2.0.eb b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..e2adb9db1d9 --- /dev/null +++ b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-13.2.0.eb @@ -0,0 +1,76 @@ +easyblock = 'PythonBundle' + +name = 'ReFrame' +version = '4.6.2' + +homepage = 'https://github.com/reframe-hpc/reframe' +description = '''ReFrame is a framework for writing regression tests for HPC systems.''' + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +builddependencies = [ + ('binutils', '2.40'), + ('cURL', '8.3.0'), # Used by ReFrame to download pip in the bootstrap +] + +# Note that for ReFrame's CPU autodetect to work +# the system also needs to provide (new enough versions of) these dependencies +dependencies = [ + ('Python', '3.11.5'), + ('libxslt', '1.1.38'), # Required by lxml, which is installed by ReFrame's bootstrap installer + ('libxml2', '2.11.5'), # Required by lxml, which is installed by ReFrame's bootstrap installer +] + +use_pip = True + +exts_list = [ + # ReFrame's bootstrap script is intended to run with zero dependencies. It downloads all python deps for ReFrame + # into a %(installdir)/external directory. ReFrame's main executable (reframe) adds this dir to python's sys.path + # so that ReFrame (and only ReFrame) will find & use all of these dependencies. + # In EasyBuild, we should adhere to this installation method because a) it is how ReFrame is meant to be used and + # b) it isolates all of ReFrame dependencies from any other python code you run. Thus, there is no chance that + # a test will pick up on any python deps from ReFrame itself. + # For this to work, we need to disable download_dep_fail and sanity_pip_check, as both are _expected_ to fail + # for this setup. + ('reframe', version, { + # Deps are downloaded to %(installdir)/external, which won't polute the PYTHONPATH, so is ok + 'download_dep_fail': False, + # ReFrame uses its custom sys.path to find necessary packages, they are not on PYTYHONPATH + # Thus, the regular pip sanity check is expected to fail, even if ReFrame would run just fine + 'sanity_pip_check': False, + # Set modulename to False, as to skip the sanity_check-step from extension.py (python -c "import reframe") + # This step would fail, since the regular python interpreter wouldn't find the additional packages in + # %(installdir)/external. That's fine, as ReFrame should never be imported directly, only through the + # reframe command. + 'modulename': False, + 'preinstallopts': "export PATH=%(installdir)s/bin:$PATH && " + "./bootstrap.sh +docs +pygelf && cp -r external %(installdir)s && ", + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/reframe-hpc/reframe/archive/'], + 'checksums': ['d3343815ee3d2c330b91a1cdb924ba184119ed7d9fc88a4a754b939a4259df82'], + }), +] + +postinstallcmds = [ + "cp -a tools examples %(installdir)s", + "mkdir -p %(installdir)s/share && cp -a share/completions %(installdir)s/share/completions", + r"sed -i 's@/\(python[0-9.]*\)$@/\1 -S@g' %(installdir)s/bin/reframe", +] + +sanity_check_paths = { + 'files': ['bin/reframe', + 'share/completions/reframe.bash', + 'share/completions/reframe.fish', + 'share/completions/reframe.tcsh'], + 'dirs': ['external', 'lib', 'tools', 'examples'] +} + +sanity_check_commands = ['reframe -V'] + +# Since this is at the GCCcore toolchain level, make sure ReFrame is configured to purge modules before running +# any tests by default +modextravars = { + 'RFM_PURGE_ENVIRONMENT': '1', +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-Python-3.6.eb b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-Python-3.6.eb new file mode 100644 index 00000000000..4e58793cd0a --- /dev/null +++ b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-Python-3.6.eb @@ -0,0 +1,95 @@ +# This EasyConfig is made with older setuptools and wheel versions, so that it still works with Python-3.6.X +# For newer python versions, we suggest to use ReFrame-4.6.2.eb (without suffix) +easyblock = 'PythonBundle' + +name = 'ReFrame' +version = '4.6.2' +versionsuffix = '-Python-3.6' + +homepage = 'https://github.com/reframe-hpc/reframe' +description = '''ReFrame is a framework for writing regression tests for HPC systems.''' + +toolchain = SYSTEM + +allow_system_deps = [('Python', SYS_PYTHON_VERSION)] + +# Required by lxml, which is installed by ReFrame's bootstrap installer +osdependencies = [ + ('libxml2'), + ('libxslt', 'libxslt1.1'), +] + +# Listed as python_requires in https://github.com/reframe-hpc/reframe/blob/v4.6.2/setup.cfg +req_py_majver = 3 +req_py_minver = 6 + +# The setuptools in this EasyConfig is the latest that works for Python 3.6, but is too old for Python 3.12 +# See https://github.com/easybuilders/easybuild-easyconfigs/pull/21269#discussion_r1741570244 +max_py_majver = 3 +max_py_minver = 11 + +use_pip = True + +exts_list = [ + # stick to pip 21.3.1, which is compatible with Python 3.6 + # we still need pip outside of ReFrame's external dependencies, since the install cmd uses pip + ('pip', '21.3.1', { + 'use_pip': False, + 'checksums': ['fd11ba3d0fdb4c07fbc5ecbba0b1b719809420f25038f8ee3cd913d3faa3033a'], + }), + # Require new enough setuptools to install with e.g. pyproject.toml + # 59.6.0 is the latest compatible with Python 3.6 + ('setuptools', '59.6.0', { + 'use_pip': False, + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], + 'checksums': ['22c7348c6d2976a52632c67f7ab0cdf40147db7789f9aed18734643fe9cf3373'], + }), + # stick to wheel 0.37.1, which is compatible with Python 3.6 + ('wheel', '0.37.1', { + 'source_tmpl': 'wheel-%(version)s-py2.py3-none-any.whl', + 'checksums': ['4bdcd7d840138086126cd09254dc6195fb4fc6f01c050a1d7236f2630db1d22a'], + }), + # ReFrame's bootstrap script is intended to run with zero dependencies. It downloads all python deps for ReFrame + # into a %(installdir)/external directory. ReFrame's main executable (reframe) adds this dir to python's sys.path + # so that ReFrame (and only ReFrame) will find & use all of these dependencies. + # In EasyBuild, we should adhere to this installation method because a) it is how ReFrame is meant to be used and + # b) it isolates all of ReFrame dependencies from any other python code you run. Thus, there is no chance that + # a test will pick up on any python deps from ReFrame itself. + # For this to work, we need to disable download_dep_fail and sanity_pip_check, as both are _expected_ to fail + # for this setup. + ('reframe', version, { + # Deps are downloaded to %(installdir)/external, which won't polute the PYTHONPATH, so is ok + 'download_dep_fail': False, + # ReFrame uses its custom sys.path to find necessary packages, they are not on PYTYHONPATH + # Thus, the regular pip sanity check is expected to fail, even if ReFrame would run just fine + 'sanity_pip_check': False, + # Set modulename to False, as to skip the sanity_check-step from extension.py (python -c "import reframe") + # This step would fail, since the regular python interpreter wouldn't find the additional packages in + # %(installdir)/external. That's fine, as ReFrame should never be imported directly, only through the + # reframe command. + 'modulename': False, + 'preinstallopts': "export PATH=%(installdir)s/bin:$PATH && " + "./bootstrap.sh +docs +pygelf && cp -r external %(installdir)s && ", + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/reframe-hpc/reframe/archive/'], + 'checksums': ['d3343815ee3d2c330b91a1cdb924ba184119ed7d9fc88a4a754b939a4259df82'], + }), +] + +postinstallcmds = [ + "cp -a tools examples %(installdir)s", + "mkdir -p %(installdir)s/share && cp -a share/completions %(installdir)s/share/completions", + r"sed -i 's@/\(python[0-9.]*\)$@/\1 -S@g' %(installdir)s/bin/reframe", +] + +sanity_check_paths = { + 'files': ['bin/reframe', + 'share/completions/reframe.bash', + 'share/completions/reframe.fish', + 'share/completions/reframe.tcsh'], + 'dirs': ['external', 'lib', 'tools', 'examples'] +} + +sanity_check_commands = ['reframe -V'] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2.eb b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2.eb new file mode 100644 index 00000000000..26e331c131e --- /dev/null +++ b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2.eb @@ -0,0 +1,91 @@ +easyblock = 'PythonBundle' + +name = 'ReFrame' +version = '4.6.2' + +homepage = 'https://github.com/reframe-hpc/reframe' +description = '''ReFrame is a framework for writing regression tests for HPC systems.''' + +toolchain = SYSTEM + +allow_system_deps = [('Python', SYS_PYTHON_VERSION)] + +# Required by lxml, which is installed by ReFrame's bootstrap installer +osdependencies = [ + ('libxml2'), + ('libxslt', 'libxslt1.1'), +] + +# We use pip, setuptools and wheel compatible with Python 3.7 and above +# Note that ReFrame itself is compatible also with Python 3.6 +# As listed in the python_requires in https://github.com/reframe-hpc/reframe/blob/v4.6.2/setup.cfg +# To use with Python 3.6, please install ReFrame-4.6.2-Python-3.6.eb instead +req_py_majver = 3 +req_py_minver = 7 + +use_pip = True + +exts_list = [ + # stick to pip 24.0, which is compatible with Python 3.7 + # we still need pip outside of ReFrame's external dependencies, since the install cmd uses pip + ('pip', '24.0', { + 'use_pip': False, + 'checksums': ['ea9bd1a847e8c5774a5777bb398c19e80bcd4e2aa16a4b301b718fe6f593aba2'], + }), + # Require new enough setuptools to work with Python 3.12, which doesn't have pkgutil.ImpImporter anymore + # See https://github.com/pypa/setuptools/commit/6653e747c3815b140156249205397ef3719581ee + # 68.0.0 is the latest compatible with Python 3.7 + ('setuptools', '68.0.0', { + 'use_pip': False, + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], + 'checksums': ['baf1fdb41c6da4cd2eae722e135500da913332ab3f2f5c7d33af9b492acb5235'], + }), + # stick to wheel 0.42.0, which is compatible with Python 3.7 + ('wheel', '0.42.0', { + 'source_tmpl': 'wheel-%(version)s-py3-none-any.whl', + 'checksums': ['177f9c9b0d45c47873b619f5b650346d632cdc35fb5e4d25058e09c9e581433d'], + }), + # ReFrame's bootstrap script is intended to run with zero dependencies. It downloads all python deps for ReFrame + # into a %(installdir)/external directory. ReFrame's main executable (reframe) adds this dir to python's sys.path + # so that ReFrame (and only ReFrame) will find & use all of these dependencies. + # In EasyBuild, we should adhere to this installation method because a) it is how ReFrame is meant to be used and + # b) it isolates all of ReFrame dependencies from any other python code you run. Thus, there is no chance that + # a test will pick up on any python deps from ReFrame itself. + # For this to work, we need to disable download_dep_fail and sanity_pip_check, as both are _expected_ to fail + # for this setup. + ('reframe', version, { + # Deps are downloaded to %(installdir)/external, which won't polute the PYTHONPATH, so is ok + 'download_dep_fail': False, + # ReFrame uses its custom sys.path to find necessary packages, they are not on PYTYHONPATH + # Thus, the regular pip sanity check is expected to fail, even if ReFrame would run just fine + 'sanity_pip_check': False, + # Set modulename to False, as to skip the sanity_check-step from extension.py (python -c "import reframe") + # This step would fail, since the regular python interpreter wouldn't find the additional packages in + # %(installdir)/external. That's fine, as ReFrame should never be imported directly, only through the + # reframe command. + 'modulename': False, + 'preinstallopts': "export PATH=%(installdir)s/bin:$PATH && " + "./bootstrap.sh +docs +pygelf && cp -r external %(installdir)s && ", + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/reframe-hpc/reframe/archive/'], + 'checksums': ['d3343815ee3d2c330b91a1cdb924ba184119ed7d9fc88a4a754b939a4259df82'], + }), +] + +postinstallcmds = [ + "cp -a tools examples %(installdir)s", + "mkdir -p %(installdir)s/share && cp -a share/completions %(installdir)s/share/completions", + r"sed -i 's@/\(python[0-9.]*\)$@/\1 -S@g' %(installdir)s/bin/reframe", +] + +sanity_check_paths = { + 'files': ['bin/reframe', + 'share/completions/reframe.bash', + 'share/completions/reframe.fish', + 'share/completions/reframe.tcsh'], + 'dirs': ['external', 'lib', 'tools', 'examples'] +} + +sanity_check_commands = ['reframe -V'] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.3-GCCcore-13.3.0.eb b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.3-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..6541b14b799 --- /dev/null +++ b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.3-GCCcore-13.3.0.eb @@ -0,0 +1,76 @@ +easyblock = 'PythonBundle' + +name = 'ReFrame' +version = '4.6.3' + +homepage = 'https://github.com/reframe-hpc/reframe' +description = '''ReFrame is a framework for writing regression tests for HPC systems.''' + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +builddependencies = [ + ('binutils', '2.42'), + ('cURL', '8.7.1'), # Used by ReFrame to download pip in the bootstrap +] + +# Note that for ReFrame's CPU autodetect to work +# the system also needs to provide (new enough versions of) these dependencies +dependencies = [ + ('Python', '3.12.3'), + ('libxslt', '1.1.42'), # Required by lxml, which is installed by ReFrame's bootstrap installer + ('libxml2', '2.12.7'), # Required by lxml, which is installed by ReFrame's bootstrap installer +] + +use_pip = True + +exts_list = [ + # ReFrame's bootstrap script is intended to run with zero dependencies. It downloads all python deps for ReFrame + # into a %(installdir)/external directory. ReFrame's main executable (reframe) adds this dir to python's sys.path + # so that ReFrame (and only ReFrame) will find & use all of these dependencies. + # In EasyBuild, we should adhere to this installation method because a) it is how ReFrame is meant to be used and + # b) it isolates all of ReFrame dependencies from any other python code you run. Thus, there is no chance that + # a test will pick up on any python deps from ReFrame itself. + # For this to work, we need to disable download_dep_fail and sanity_pip_check, as both are _expected_ to fail + # for this setup. + ('reframe', version, { + # Deps are downloaded to %(installdir)/external, which won't polute the PYTHONPATH, so is ok + 'download_dep_fail': False, + # ReFrame uses its custom sys.path to find necessary packages, they are not on PYTYHONPATH + # Thus, the regular pip sanity check is expected to fail, even if ReFrame would run just fine + 'sanity_pip_check': False, + # Set modulename to False, as to skip the sanity_check-step from extension.py (python -c "import reframe") + # This step would fail, since the regular python interpreter wouldn't find the additional packages in + # %(installdir)/external. That's fine, as ReFrame should never be imported directly, only through the + # reframe command. + 'modulename': False, + 'preinstallopts': "export PATH=%(installdir)s/bin:$PATH && " + "./bootstrap.sh +docs +pygelf && cp -r external %(installdir)s && ", + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/reframe-hpc/reframe/archive/'], + 'checksums': ['0f335e588d21a26d76beb011bc86baf80ba633d875512ecd564d0aeb320fcf2c'], + }), +] + +postinstallcmds = [ + "cp -a tools examples %(installdir)s", + "mkdir -p %(installdir)s/share && cp -a share/completions %(installdir)s/share/completions", + r"sed -i 's@/\(python[0-9.]*\)$@/\1 -S@g' %(installdir)s/bin/reframe", +] + +sanity_check_paths = { + 'files': ['bin/reframe', + 'share/completions/reframe.bash', + 'share/completions/reframe.fish', + 'share/completions/reframe.tcsh'], + 'dirs': ['external', 'lib', 'tools', 'examples'] +} + +sanity_check_commands = ['reframe -V'] + +# Since this is at the GCCcore toolchain level, make sure ReFrame is configured to purge modules before running +# any tests by default +modextravars = { + 'RFM_PURGE_ENVIRONMENT': '1', +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/r/Redis/Redis-7.4.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/r/Redis/Redis-7.4.1-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..299d66ea0b3 --- /dev/null +++ b/easybuild/easyconfigs/r/Redis/Redis-7.4.1-GCCcore-13.3.0.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'Redis' +version = '7.4.1' + +homepage = 'https://redis.io' +description = """Redis is an open source (BSD licensed), in-memory data structure store, used as +a database, cache, and message broker. Redis provides data structures such as +strings, hashes, lists, sets, sorted sets with range queries, bitmaps, +hyperloglogs, geospatial indexes, and streams. Redis has built-in replication, +Lua scripting, LRU eviction, transactions, and different levels of on-disk +persistence, and provides high availability via Redis Sentinel and automatic +partitioning with Redis Cluster.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://download.redis.io/releases'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['bc34b878eb89421bbfca6fa78752343bf37af312a09eb0fae47c9575977dfaa2'] + +builddependencies = [ + ('binutils', '2.42'), + ('pkgconf', '2.2.0'), +] + +skipsteps = ['configure'] + +# tests must be run from a local filesystem +# runtest = 'test' + +installopts = 'PREFIX="%(installdir)s"' + +sanity_check_paths = { + 'files': ['bin/redis-cli', 'bin/redis-server'], + 'dirs': [], +} + +sanity_check_commands = [('redis-server', '--version')] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/r/Redland/Redland-1.0.17-GCC-12.3.0.eb b/easybuild/easyconfigs/r/Redland/Redland-1.0.17-GCC-12.3.0.eb new file mode 100644 index 00000000000..7217999a898 --- /dev/null +++ b/easybuild/easyconfigs/r/Redland/Redland-1.0.17-GCC-12.3.0.eb @@ -0,0 +1,38 @@ +easyblock = 'ConfigureMake' + +name = 'Redland' +version = '1.0.17' + +homepage = 'https://librdf.org/raptor' +description = """Redland is a set of free software C libraries that + provide support for the Resource Description Framework (RDF).""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +source_urls = ['https://download.librdf.org/source'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['de1847f7b59021c16bdc72abb4d8e2d9187cd6124d69156f3326dd34ee043681'] + +dependencies = [ + ('Rasqal', '0.9.33'), + ('Raptor', '2.0.16'), + ('PostgreSQL', '16.1'), + ('MariaDB', '11.6.0'), + ('unixODBC', '2.3.12'), + ('SQLite', '3.42.0'), + ('libtool', '2.4.7'), +] + +sanity_check_paths = { + 'files': [ + 'include/%(namelower)s.h', + 'bin/%(namelower)s-config', + 'bin/%(namelower)s-db-upgrade', + 'lib/librdf.%s' % SHLIB_EXT, + ], + 'dirs': ['share/%(namelower)s'], +} + +sanity_check_commands = ['%(namelower)s-config --help'] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/r/Regenie/Regenie-3.1.2-GCC-11.2.0.eb b/easybuild/easyconfigs/r/Regenie/Regenie-3.1.2-GCC-11.2.0.eb new file mode 100644 index 00000000000..09b2ac462d6 --- /dev/null +++ b/easybuild/easyconfigs/r/Regenie/Regenie-3.1.2-GCC-11.2.0.eb @@ -0,0 +1,47 @@ +# Contribution from the NIHR Biomedical Research Centre +# Guy's and St Thomas' NHS Foundation Trust and King's College London +# uploaded by J. Sassmannshausen +# we recommend to use --download-timeout=1000 when fetching the files + +easyblock = 'MakeCp' + +name = 'Regenie' +version = '3.1.2' + +homepage = 'https://rgcgithub.github.io/regenie' +description = """Regenie is a C++ program for whole genome regression modelling of large genome-wide +association studies. It is developed and supported by a team of scientists at the Regeneron Genetics Center.""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +source_urls = ['https://github.com/rgcgithub/regenie/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = ['%(namelower)s-%(version)s_Makefile.patch'] +checksums = [ + 'b2e5e98bb310d9b9071ae5c63c5207be853bb1ec7918574e1acfdd0c83e744ff', # v3.1.2.tar.gz + '8be5d4b3b237d7a1820727061227857770554970aa136da614b71c14767e655e', # regenie-3.1.2_Makefile.patch +] + +dependencies = [ + ('Boost', '1.55.0'), + ('BGEN-enkre', '1.1.7'), + ('OpenBLAS', '0.3.18'), +] + +build_cmd = "make BGEN_PATH=$EBROOTBGENMINENKRE HAS_BOOST_IOSTREAM=1 " +build_cmd += "OPENBLAS_ROOT=$EBROOTOPENBLAS BOOST=$EBROOTBOOST STATIC=0" + +files_to_copy = [ + (['regenie'], 'bin'), + (['example/*'], 'example'), + (['docs/*'], 'docs'), +] + +sanity_check_commands = ['regenie --help'] + +sanity_check_paths = { + 'files': ['bin/regenie'], + 'dirs': ['bin', 'example', 'docs'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/r/Regenie/regenie-3.1.2_Makefile.patch b/easybuild/easyconfigs/r/Regenie/regenie-3.1.2_Makefile.patch new file mode 100644 index 00000000000..3fc4820cc4d --- /dev/null +++ b/easybuild/easyconfigs/r/Regenie/regenie-3.1.2_Makefile.patch @@ -0,0 +1,41 @@ +Patch to remove 3rd party software and replace lapack(e) with openblas and boost 1.55 +base on the work of Author: J. Sassmannshausen NHS/GSTT +diff -ruN regenie-3.1.1.orig/Makefile regenie-3.1.1/Makefile +--- regenie-3.1.1.orig/Makefile 2022-05-05 10:59:29.000000000 -0700 ++++ regenie-3.1.1/Makefile 2022-06-21 13:34:54.464076000 -0700 +@@ -44,7 +44,7 @@ + # detect OS architecture and add flags + UNAME_S := $(shell uname -s) + ifeq ($(UNAME_S),Linux) +- INC = -I${BGEN_PATH}/3rd_party/boost_1_55_0 ++ INC = -I${BOOST} + CFLAGS += -fopenmp + ifeq ($(strip $(STATIC)),1) + LPATHS = -static-libgcc -static-libstdc++ +@@ -103,10 +103,10 @@ + INC += -I${OPENBLAS_ROOT}/include/ + # static linking + ifeq ($(strip $(STATIC)),1) +- SLIBS += -Wl,-rpath=${OPENBLAS_ROOT}/lib/ -llapack -llapacke -lopenblas ++ SLIBS += -Wl,-rpath=${OPENBLAS_ROOT}/lib/ -lopenblas + # dynamic linking + else +- DLIBS += -Wl,-rpath=${OPENBLAS_ROOT}/lib/ -llapack -llapacke -lopenblas ++ DLIBS += -Wl,-rpath=${OPENBLAS_ROOT}/lib/ -lopenblas -lgfortran + endif + endif + endif +@@ -119,11 +119,10 @@ + OBJECTS = $(patsubst %.cpp,%.o,$(wildcard ./src/*.cpp)) + + PGEN_PATH = ./external_libs/pgenlib/ +-INC += -I${PGEN_PATH} -I${PGEN_PATH}/simde/ -I${PGEN_PATH}/include/ -I./external_libs/cxxopts/include/ -I./external_libs/LBFGSpp/include/ -I${BGEN_PATH} -I./external_libs/eigen-3.4.0/ -I${BGEN_PATH}/genfile/include/ -I${BGEN_PATH}/3rd_party/boost_1_55_0/ -I${BGEN_PATH}/3rd_party/zstd-1.1.0/lib -I${BGEN_PATH}/db/include/ -I${BGEN_PATH}/3rd_party/sqlite3 -I./external_libs/ ++INC += -I${PGEN_PATH} -I${PGEN_PATH}/simde/ -I${PGEN_PATH}/include/ -I./external_libs/cxxopts/include/ -I./external_libs/LBFGSpp/include/ -I./external_libs/eigen-3.4.0/ -I${BGEN_PATH}/include/ -I${BOOST}/include -I./external_libs/ + +-LPATHS += ${LIBMKL} -L${BGEN_PATH}/build/ -L${BGEN_PATH}/build/3rd_party/zstd-1.1.0/ -L${BGEN_PATH}/build/db/ -L${BGEN_PATH}/build/3rd_party/sqlite3/ -L${BGEN_PATH}/build/3rd_party/boost_1_55_0 -L/usr/lib/ + +-LIBS += ${SLIBS} -lbgen -lzstd -ldb -lsqlite3 -lboost ++LIBS += ${SLIBS} -lbgen -lzstd -ldb -lsqlite3 -lboost_system -lboost_filesystem -lboost_thread -lboost_timer + LIBS += -lz ${DLIBS} -lm -ldl -lgfortran + + diff --git a/easybuild/easyconfigs/r/RepeatMasker/RepeatMasker-4.1.7-p1-foss-2023a.eb b/easybuild/easyconfigs/r/RepeatMasker/RepeatMasker-4.1.7-p1-foss-2023a.eb new file mode 100644 index 00000000000..90b43c163a0 --- /dev/null +++ b/easybuild/easyconfigs/r/RepeatMasker/RepeatMasker-4.1.7-p1-foss-2023a.eb @@ -0,0 +1,57 @@ +easyblock = 'Tarball' + +name = 'RepeatMasker' +version = '4.1.7-p1' + +homepage = 'https://www.repeatmasker.org/' +description = """RepeatMasker is a program that screens DNA sequences for interspersed repeats + and low complexity DNA sequences.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['https://www.repeatmasker.org/%(name)s'] +sources = [ + SOURCE_TAR_GZ, + # optional but recommended: RepBase RepeatMasker Edition + # requires subscription and academic license, download from here: https://www.girinst.org/server/RepBase/index.php + # { + # 'filename': 'RepBaseRepeatMaskerEdition-20181026.tar.gz', + # 'extract_cmd': "tar -xzf %s -C %(builddir)s/%(name)s/Libraries --strip-components 1", + # }, +] +checksums = ['15222b39178f19c116282437190b64c5ba68f62b0f2044b3bbcbda5e02748993'] + +dependencies = [ + ('Python', '3.11.3'), + ('Perl', '5.36.1'), + ('TRF', '4.09.1'), + ('h5py', '3.9.0'), + # At least one search engine of: RMBlast, HMMER, ABBlast/WUBlast, Cross_Match + ('HMMER', '3.4'), + ('RMBlast', '2.14.1'), +] + +local_default_search_engine = 'RMBlast' + +local_config_command = 'cd %(installdir)s &&' +local_config_command += './configure -perlbin "$EBROOTPERL/bin/perl" -trf_prgm "$EBROOTTRF/bin/trf" ' +local_config_command += '-hmmer_dir "$EBROOTHMMER/bin" -rmblast_dir "$EBROOTRMBLAST/bin" ' +local_config_command += '-default_search_engine %s' % local_default_search_engine.lower() + +postinstallcmds = [local_config_command] + +fix_perl_shebang_for = ['RepeatMasker'] + +sanity_check_paths = { + 'files': ['RepeatMasker', 'RepeatMaskerConfig.pm'], + 'dirs': ['Libraries', 'util'], +} + +sanity_check_commands = ['RepeatMasker -help'] + +modextrapaths = { + 'PATH': '', + 'PERL5LIB': '', +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/r/ResistanceGA/ResistanceGA-4.2-5-foss-2022a-R-4.2.1-Julia-1.9.2.eb b/easybuild/easyconfigs/r/ResistanceGA/ResistanceGA-4.2-5-foss-2022a-R-4.2.1-Julia-1.9.2.eb index 83987de1e5a..03e40a493f2 100644 --- a/easybuild/easyconfigs/r/ResistanceGA/ResistanceGA-4.2-5-foss-2022a-R-4.2.1-Julia-1.9.2.eb +++ b/easybuild/easyconfigs/r/ResistanceGA/ResistanceGA-4.2-5-foss-2022a-R-4.2.1-Julia-1.9.2.eb @@ -14,8 +14,9 @@ toolchain = {'name': 'foss', 'version': '2022a'} dependencies = [ ('R', '4.2.1'), ('Julia', local_juliaver, '-linux-%s' % ARCH, SYSTEM), + ('RCall', '0.13.17', versionsuffix), # order matters! RCall must be loaded before Circuitscape (#19281) ('Circuitscape', '5.12.3', '-Julia-%s' % local_juliaver, SYSTEM), - ('RCall', '0.13.17', versionsuffix), + ('Suppressor', '0.2.4', '-Julia-%s' % local_juliaver, SYSTEM), ] exts_defaultclass = 'RPackage' @@ -31,14 +32,6 @@ exts_default_options = { } exts_list = [ - ('Suppressor', '0.2.4', { - 'easyblock': 'JuliaPackage', - 'exts_filter': ("julia -e 'using %(ext_name)s'", ''), - 'preinstallopts': "export LD_LIBRARY_PATH=$EBROOTJULIA/lib/julia:$LD_LIBRARY_PATH && ", - 'source_tmpl': 'v%(version)s.tar.gz', - 'source_urls': ['https://github.com/JuliaIO/Suppressor.jl/archive/'], - 'checksums': ['5075b06ed6aa0956c786e5b5fe3d77571a4dd34e6d63b45e113c312729384cf4'], - }), ('GA', '3.2.2', { 'checksums': ['6245c634a11b8414bde7ed326b8c615512645489b19969619484c865e900bf8c'], }), @@ -73,12 +66,6 @@ modextrapaths = { 'R_LIBS_SITE': '', } -# When loading R and Julia, there seems to be a library collision and Julia (namely Pkg module) doesn't work properly -# This is a workaround to make Julia find the correct libraries -modluafooter = """ -prepend_path("LD_LIBRARY_PATH", os.getenv("EBROOTJULIA") .. "/lib/julia") -""" - sanity_check_paths = { 'files': [], 'dirs': ['%(name)s'], diff --git a/easybuild/easyconfigs/r/Rmath/Rmath-4.3.2-foss-2023a.eb b/easybuild/easyconfigs/r/Rmath/Rmath-4.3.2-foss-2023a.eb new file mode 100644 index 00000000000..8378d7f8a8e --- /dev/null +++ b/easybuild/easyconfigs/r/Rmath/Rmath-4.3.2-foss-2023a.eb @@ -0,0 +1,46 @@ +# Easyconfig for Rmath +# Author: Caspar van Leeuwen +# SURFsara, Amsterdam, The Netherlands + +easyblock = 'ConfigureMake' + +name = 'Rmath' +version = '4.3.2' + +homepage = "https://www.r-project.org/" +description = """Rmath is the standalone version of the R math library. + Rmath can be used in your own C/C++ routines.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['http://cran.us.r-project.org/src/base/R-%(version_major)s/'] +sources = ['R-%(version)s.tar.gz'] +checksums = ['b3f5760ac2eee8026a3f0eefcb25b47723d978038eee8e844762094c860c452a'] + +dependencies = [ + ('bzip2', '1.0.8'), + ('cURL', '8.0.1'), + ('libreadline', '8.2'), + ('PCRE2', '10.42'), + ('XZ', '5.4.2'), + ('zlib', '1.2.13') +] + +# Copied from R-3.3.1-intel-2016b.eb. +# Again, unsure if these affect R-math: R documentation doesn't specify. +configopts = "--with-pic --enable-threads --with-x=no --with-pcre2" + +# Since we're only installing Rmath anyway, we don't care about R packages. +configopts += " --with-recommended-packages=no" + +# To build Rmath, docs say you need to execute 'make' in src/nmath/standalone +# https://cran.r-project.org/doc/manuals/r-devel/R-admin.html#Configuration-options +prebuildopts = 'cd src/nmath/standalone;' +preinstallopts = prebuildopts + +sanity_check_paths = { + 'files': ['lib/libRmath.a', 'lib/libRmath.%s' % SHLIB_EXT, 'include/Rmath.h'], + 'dirs': [] +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/r/Rust/Rust-1.78.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/r/Rust/Rust-1.78.0-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..ed5d13cb4a4 --- /dev/null +++ b/easybuild/easyconfigs/r/Rust/Rust-1.78.0-GCCcore-13.3.0.eb @@ -0,0 +1,31 @@ +name = 'Rust' +version = '1.78.0' + +homepage = 'https://www.rust-lang.org' +description = """Rust is a systems programming language that runs blazingly fast, prevents segfaults, + and guarantees thread safety.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://static.rust-lang.org/dist/'] +sources = ['rustc-%(version)s-src.tar.gz'] +patches = ['Rust-1.70_sysroot-fix-interpreter.patch'] +checksums = [ + {'rustc-1.78.0-src.tar.gz': 'ff544823a5cb27f2738128577f1e7e00ee8f4c83f2a348781ae4fc355e91d5a9'}, + {'Rust-1.70_sysroot-fix-interpreter.patch': '220129db55e022a98d25028da5dcc9f26b252dd995c3ac92f6312dbb1e362cb1'}, +] + +builddependencies = [ + ('binutils', '2.42'), + ('CMake', '3.29.3'), + ('Python', '3.12.3'), + ('Ninja', '1.12.1'), + ('pkgconf', '2.2.0'), + ('patchelf', '0.18.0'), # only required when RPATH linking is enabled +] + +dependencies = [ + ('OpenSSL', '3', '', SYSTEM), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/Rust/Rust-1.79.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/r/Rust/Rust-1.79.0-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..88962930f30 --- /dev/null +++ b/easybuild/easyconfigs/r/Rust/Rust-1.79.0-GCCcore-13.3.0.eb @@ -0,0 +1,31 @@ +name = 'Rust' +version = '1.79.0' + +homepage = 'https://www.rust-lang.org' +description = """Rust is a systems programming language that runs blazingly fast, prevents segfaults, + and guarantees thread safety.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://static.rust-lang.org/dist/'] +sources = ['rustc-%(version)s-src.tar.gz'] +patches = ['Rust-1.70_sysroot-fix-interpreter.patch'] +checksums = [ + {'rustc-1.79.0-src.tar.gz': '172ecf3c7d1f9d9fb16cd2a628869782670416ded0129e524a86751f961448c0'}, + {'Rust-1.70_sysroot-fix-interpreter.patch': '220129db55e022a98d25028da5dcc9f26b252dd995c3ac92f6312dbb1e362cb1'}, +] + +builddependencies = [ + ('binutils', '2.42'), + ('CMake', '3.29.3'), + ('Python', '3.12.3'), + ('Ninja', '1.12.1'), + ('pkgconf', '2.2.0'), + ('patchelf', '0.18.0'), # only required when RPATH linking is enabled +] + +dependencies = [ + ('OpenSSL', '3', '', SYSTEM), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/Rust/Rust-1.81.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/r/Rust/Rust-1.81.0-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..ca97c690c02 --- /dev/null +++ b/easybuild/easyconfigs/r/Rust/Rust-1.81.0-GCCcore-13.3.0.eb @@ -0,0 +1,31 @@ +name = 'Rust' +version = '1.81.0' + +homepage = 'https://www.rust-lang.org' +description = """Rust is a systems programming language that runs blazingly fast, prevents segfaults, + and guarantees thread safety.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://static.rust-lang.org/dist/'] +sources = ['rustc-%(version)s-src.tar.gz'] +patches = ['Rust-1.70_sysroot-fix-interpreter.patch'] +checksums = [ + {'rustc-1.81.0-src.tar.gz': '872448febdff32e50c3c90a7e15f9bb2db131d13c588fe9071b0ed88837ccfa7'}, + {'Rust-1.70_sysroot-fix-interpreter.patch': '220129db55e022a98d25028da5dcc9f26b252dd995c3ac92f6312dbb1e362cb1'}, +] + +builddependencies = [ + ('binutils', '2.42'), + ('CMake', '3.29.3'), + ('Python', '3.12.3'), + ('Ninja', '1.12.1'), + ('pkgconf', '2.2.0'), + ('patchelf', '0.18.0'), # only required when RPATH linking is enabled +] + +dependencies = [ + ('OpenSSL', '3', '', SYSTEM), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/rMATS-long/rMATS-long-1.0.0-20240502-foss-2023a-R-4.3.2.eb b/easybuild/easyconfigs/r/rMATS-long/rMATS-long-1.0.0-20240502-foss-2023a-R-4.3.2.eb new file mode 100644 index 00000000000..6074c273fac --- /dev/null +++ b/easybuild/easyconfigs/r/rMATS-long/rMATS-long-1.0.0-20240502-foss-2023a-R-4.3.2.eb @@ -0,0 +1,44 @@ +easyblock = 'Tarball' + +name = 'rMATS-long' +local_commit = "592cb32" +version = '1.0.0-20240502' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://github.com/Xinglab/rMATS-long' +description = """rMATS-long is a collection of tools for analyzing long-read data.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['https://github.com/Xinglab/%(name)s/archive/'] +sources = [{ + 'download_filename': '%s.tar.gz' % local_commit, + 'filename': '%(name)s-%(version)s.tar.gz', +}] +checksums = ['9f4f859c05be5a274b8c0aaf79a18f8c02839f8e6d71330d07f77d027ddba003'] + +dependencies = [ + ('Python', '3.11.3'), + ('matplotlib', '3.7.2'), + ('networkx', '3.1'), + ('SciPy-bundle', '2023.07'), + ('R', '4.3.2'), + ('R-bundle-CRAN', '2023.12'), + ('R-bundle-Bioconductor', '3.18', '-R-%(rver)s'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['scripts'], +} + +sanity_check_commands = [ + 'cd %(installdir)s/scripts && python rmats_long.py -h', +] + +modloadmsg = """ +To run rMATS-long scripts first go to scripts directory: +$ cd $EBROOTRMATSMINLONG/scripts +""" + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/r/rankwidth/rankwidth-0.9-foss-2023b.eb b/easybuild/easyconfigs/r/rankwidth/rankwidth-0.9-foss-2023b.eb new file mode 100644 index 00000000000..090a4aaf87a --- /dev/null +++ b/easybuild/easyconfigs/r/rankwidth/rankwidth-0.9-foss-2023b.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'rankwidth' +version = '0.9' + +homepage = 'https://sourceforge.net/projects/rankwidth/' +description = """rw calculates rank-width and rank-decompositions. +It is based on ideas from "Computing rank-width exactly" by Sang-il Oum, +"Sopra una formula numerica" by Ernesto Pascal, "Generation of a Vector +from the Lexicographical Index" by B.P. Buckles and M. Lybanon and "Fast +additions on masked integers" by Michael D. Adams and David S. Wise.""" + +toolchain = {'name': 'foss', 'version': '2023b'} + +source_urls = ['https://master.dl.sourceforge.net/project/rankwidth'] +sources = ['rw-%(version)s.tar.gz'] +checksums = ['c1e03506fe25cdfcb428c051fc56b2d2affb5b06fba3f2ce756631466befb441'] + +dependencies = [('igraph', '0.10.12')] + +# fix `too few arguments to function igraph_get_adjacency` error +prebuildopts = 'sed -i "s/IGRAPH_GET_ADJACENCY_BOTH/IGRAPH_GET_ADJACENCY_BOTH, 0/g" simplerw.c && ' + +sanity_check_paths = { + 'files': [ + 'bin/rw', + 'include/rw.h', + 'lib/librw.%s' % SHLIB_EXT, + ], + 'dirs': ['share'], +} + +sanity_check_commands = ['rw --help | grep Usage:'] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/r/rapidNJ/rapidNJ-2.3.3-GCCcore-12.2.0.eb b/easybuild/easyconfigs/r/rapidNJ/rapidNJ-2.3.3-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..b6fc9da5925 --- /dev/null +++ b/easybuild/easyconfigs/r/rapidNJ/rapidNJ-2.3.3-GCCcore-12.2.0.eb @@ -0,0 +1,41 @@ +# This seems to be actively maintained version of the code by the looks of it. +# See issue #5 +# https://github.com/somme89/rapidNJ/issues/5 +# why -march=native will not be used +# Author: J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'MakeCp' + +name = 'rapidNJ' +version = '2.3.3' + +homepage = 'https://github.com/somme89/rapidNJ' +description = """RapidNJ is an algorithmic engineered implementation of canonical +neighbour-joining. It uses an efficient search heuristic to speed-up the core +computations of the neighbour-joining method that enables RapidNJ to +outperform other state-of-the-art neighbour-joining implementations.""" + +citing = """Rapid Neighbour Joining. Martin Simonsen, Thomas Mailund and Christian N. S. Pedersen. +In: Proceedings of the 8th Workshop in Algorithms in Bioinformatics (WABI), LNBI 5251, 113-122, +Springer Verlag, October 2008. +doi: 10.1007/978-3-540-87361-7_10""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://github.com/somme89/rapidNJ/archive/'] +sources = [{'filename': 'v%(version)s.tar.gz', 'download_filename': 'latest.tar.gz'}] +checksums = ['662f864cc3e5bc68aea23129f02e0062cac9ebd37e414b54c5c5e616ff4f245d'] + +builddependencies = [('binutils', '2.39')] + +files_to_copy = [(['bin/rapidnj'], 'bin')] + +# That is returning 1 instead of 0, so disabled for now +# sanity_check_commands = ['rapidnj --help'] + +sanity_check_paths = { + 'files': ['bin/rapidnj'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/r/rapidNJ/rapidNJ-2.3.3-GCCcore-12.3.0.eb b/easybuild/easyconfigs/r/rapidNJ/rapidNJ-2.3.3-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..5a6e44436d9 --- /dev/null +++ b/easybuild/easyconfigs/r/rapidNJ/rapidNJ-2.3.3-GCCcore-12.3.0.eb @@ -0,0 +1,41 @@ +# This seems to be actively maintained version of the code by the looks of it. +# See issue #5 +# https://github.com/somme89/rapidNJ/issues/5 +# why -march=native will not be used +# Author: J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'MakeCp' + +name = 'rapidNJ' +version = '2.3.3' + +homepage = 'https://github.com/somme89/rapidNJ' +description = """RapidNJ is an algorithmic engineered implementation of canonical +neighbour-joining. It uses an efficient search heuristic to speed-up the core +computations of the neighbour-joining method that enables RapidNJ to +outperform other state-of-the-art neighbour-joining implementations.""" + +citing = """Rapid Neighbour Joining. Martin Simonsen, Thomas Mailund and Christian N. S. Pedersen. +In: Proceedings of the 8th Workshop in Algorithms in Bioinformatics (WABI), LNBI 5251, 113-122, +Springer Verlag, October 2008. +doi: 10.1007/978-3-540-87361-7_10""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://github.com/somme89/rapidNJ/archive/'] +sources = [{'filename': 'v%(version)s.tar.gz', 'download_filename': 'latest.tar.gz'}] +checksums = ['662f864cc3e5bc68aea23129f02e0062cac9ebd37e414b54c5c5e616ff4f245d'] + +builddependencies = [('binutils', '2.40')] + +files_to_copy = [(['bin/rapidnj'], 'bin')] + +# That is returning 1 instead of 0, so disabled for now +# sanity_check_commands = ['rapidnj --help'] + +sanity_check_paths = { + 'files': ['bin/rapidnj'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/r/rclone/rclone-1.68.1.eb b/easybuild/easyconfigs/r/rclone/rclone-1.68.1.eb new file mode 100644 index 00000000000..12c72ff4ab8 --- /dev/null +++ b/easybuild/easyconfigs/r/rclone/rclone-1.68.1.eb @@ -0,0 +1,34 @@ +easyblock = 'GoPackage' + +name = 'rclone' +version = '1.68.1' + +homepage = 'https://rclone.org' + +description = """ + Rclone is a command line program to sync files and directories to and from + a variety of online storage services +""" + +toolchain = SYSTEM + +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['26259526855a12499d00e3a3135ee95e7aeb3ecf2f85886d8c837a2e7b236226'] + +builddependencies = [('Go', '1.22.1', '', SYSTEM)] + +postinstallcmds = [ + "mkdir -p %(installdir)s/share/{doc,man/man1}", + "cp README.* MANUAL.* %(installdir)s/share/doc/", + "cp rclone.1 %(installdir)s/share/man/man1/", +] + +sanity_check_paths = { + 'files': ['bin/rclone', 'share/doc/README.md', 'share/man/man1/rclone.1'], + 'dirs': [] +} + +sanity_check_commands = ['rclone --version'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/r/re2c/re2c-3.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/r/re2c/re2c-3.1-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..d40fa786722 --- /dev/null +++ b/easybuild/easyconfigs/r/re2c/re2c-3.1-GCCcore-13.3.0.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 're2c' +version = '3.1' + +homepage = 'https://re2c.org' +description = """re2c is a free and open-source lexer generator for C and C++. Its main goal is generating +fast lexers: at least as fast as their reasonably optimized hand-coded counterparts. Instead of using +traditional table-driven approach, re2c encodes the generated finite state automata directly in the form +of conditional jumps and comparisons.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://github.com/skvadrik/%(name)s/releases/download/%(version)s'] +sources = [SOURCE_TAR_XZ] +checksums = ['0ac299ad359e3f512b06a99397d025cfff81d3be34464ded0656f8a96676c029'] + +builddependencies = [ + ('binutils', '2.42'), + ('Python', '3.12.3'), +] + +configopts = '--disable-rust' + + +sanity_check_paths = { + 'files': ['bin/%(name)s'], + 'dirs': [], +} + +sanity_check_commands = ['%(name)s --help'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/r/read2tree/read2tree-0.1.5-foss-2023a.eb b/easybuild/easyconfigs/r/read2tree/read2tree-0.1.5-foss-2023a.eb new file mode 100644 index 00000000000..64d84b4a1ec --- /dev/null +++ b/easybuild/easyconfigs/r/read2tree/read2tree-0.1.5-foss-2023a.eb @@ -0,0 +1,58 @@ +easyblock = 'PythonBundle' + +name = 'read2tree' +version = '0.1.5' + +homepage = 'https://github.com/DessimozLab/read2tree' +description = """read2tree is a software tool that allows to obtain alignment matrices for tree inference. + For this purpose it makes use of the OMA database and a set of reads. Its strength lies in the fact that + it bipasses the several standard steps when obtaining such a matrix in regular analysis. These steps are + read filtereing, assembly, gene prediction, gene annotation, all vs all comparison, orthology prediction, + alignment and concatination.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('Biopython', '1.83'), + ('ETE', '3.1.3'), + ('lxml', '4.9.2'), + ('tqdm', '4.66.1'), + ('pyparsing', '3.1.1'), + ('PyYAML', '6.0'), + ('DendroPy', '4.6.1'), + ('MAFFT', '7.520', '-with-extensions'), + ('IQ-TREE', '2.3.5'), + ('ngmlr', '0.2.7'), + ('NextGenMap', '0.5.5'), + ('SAMtools', '1.18'), + ('Pysam', '0.22.0'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('natsort', '8.4.0', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['4732914fb471f56b5cce04d7bae6f164a592c7712e1c85f9ef585e197299521c'], + }), + ('filelock', '3.16.1', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['2082e5703d51fbf98ea75855d9d5527e33d8ff23099bec374a134febee6946b0'], + }), + ('pyham', '1.2.0', { + 'source_tmpl': SOURCE_WHL, + 'checksums': ['57c91020ceb4d55dc5e8bfff40ad83d2410e15dad35f2d5c4bcbf4451031ad88'], + }), + (name, version, { + 'source_urls': ['https://github.com/DessimozLab/read2tree/archive/'], + 'sources': ['v%(version)s.tar.gz'], + 'checksums': ['c1a7f4801c0abc4742ff03c9af4e8817e4e8c9aa9ced0735e2275df2c7dd8e3d'], + }), +] + +sanity_check_commands = ['%(name)s --help'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/r/redis-py/redis-py-5.0.9-GCCcore-13.2.0.eb b/easybuild/easyconfigs/r/redis-py/redis-py-5.0.9-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..b877029e19a --- /dev/null +++ b/easybuild/easyconfigs/r/redis-py/redis-py-5.0.9-GCCcore-13.2.0.eb @@ -0,0 +1,37 @@ +easyblock = 'PythonBundle' + +name = 'redis-py' +version = '5.0.9' + +homepage = 'https://github.com/redis/redis-py' +description = "The Python interface to the Redis key-value store." + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +builddependencies = [ + ('binutils', '2.40'), +] + +dependencies = [ + ('Python', '3.11.5'), + ('typing-extensions', '4.10.0'), + ('Redis', '7.2.4'), +] + +use_pip = True + +exts_list = [ + ('async-timeout', '4.0.3', { + 'checksums': ['4640d96be84d82d02ed59ea2b7105a0f7b33abe8703703cd0ab0bf87c427522f'], + }), + (name, version, { + 'modulename': 'redis', + 'source_urls': ['https://github.com/redis/redis-py/archive/refs/tags/'], + 'sources': ['v%(version)s.tar.gz'], + 'checksums': ['c107fddbaa40414559ddd21f0a78bc7d466cd6b20a800839ac18b9bb54e5c150'], + }), +] + +sanity_pip_check = True + +moduleclass = "data" diff --git a/easybuild/easyconfigs/r/redis-py/redis-py-5.1.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/r/redis-py/redis-py-5.1.1-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..257c413dbaa --- /dev/null +++ b/easybuild/easyconfigs/r/redis-py/redis-py-5.1.1-GCCcore-13.3.0.eb @@ -0,0 +1,37 @@ +easyblock = 'PythonBundle' + +name = 'redis-py' +version = '5.1.1' + +homepage = 'https://github.com/redis/redis-py' +description = "The Python interface to the Redis key-value store." + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +builddependencies = [ + ('binutils', '2.42'), +] + +dependencies = [ + ('Python', '3.12.3'), + ('typing-extensions', '4.11.0'), + ('Redis', '7.4.1'), +] + +use_pip = True + +exts_list = [ + ('async-timeout', '4.0.3', { + 'checksums': ['4640d96be84d82d02ed59ea2b7105a0f7b33abe8703703cd0ab0bf87c427522f'], + }), + (name, version, { + 'modulename': 'redis', + 'source_urls': ['https://github.com/redis/redis-py/archive/refs/tags/'], + 'sources': ['v%(version)s.tar.gz'], + 'checksums': ['e1df6dd98eb2bdbc68dabb4b19a5167468ae36dbb53a1c777d5cf7ba8345450e'], + }), +] + +sanity_pip_check = True + +moduleclass = "data" diff --git a/easybuild/easyconfigs/r/regionmask/regionmask-0.12.1-foss-2023a.eb b/easybuild/easyconfigs/r/regionmask/regionmask-0.12.1-foss-2023a.eb new file mode 100644 index 00000000000..4172bf592e3 --- /dev/null +++ b/easybuild/easyconfigs/r/regionmask/regionmask-0.12.1-foss-2023a.eb @@ -0,0 +1,31 @@ +easyblock = 'PythonBundle' + +name = 'regionmask' +version = '0.12.1' + +homepage = 'https://regionmask.readthedocs.io' +description = """regionmask creates masks of geographical regions. It determines to which +geographic region each grid point belongs.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('geopandas', '0.14.2'), + ('rasterio', '1.3.9'), + ('Shapely', '2.0.1'), + ('xarray', '2023.9.0'), +] + +use_pip = True + +exts_list = [ + (name, version, { + 'checksums': ['7ef1e70c6ebab7bfc6a80e13f6fe771945b8b6a31b7f8980fc88c8b8505bb854'], + }), +] + +sanity_pip_check = True + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/r/rjags/rjags-4-15-foss-2023a-R-4.3.2.eb b/easybuild/easyconfigs/r/rjags/rjags-4-15-foss-2023a-R-4.3.2.eb new file mode 100644 index 00000000000..f793f925da6 --- /dev/null +++ b/easybuild/easyconfigs/r/rjags/rjags-4-15-foss-2023a-R-4.3.2.eb @@ -0,0 +1,30 @@ +easyblock = 'RPackage' + +name = 'rjags' +version = '4-15' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://cran.r-project.org/web/packages/rjags' +description = """The rjags package is an interface to the JAGS library.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = [ + 'https://cran.r-project.org/src/contrib/', + 'https://cran.r-project.org/src/contrib/Archive/rjags/', +] +sources = ['%(name)s_%(version)s.tar.gz'] +checksums = ['35cd4c1faaaa8523b87ac053b881dccf29798f073f438459589e786b95ef18a1'] + +dependencies = [ + ('R', '4.3.2'), + ('R-bundle-CRAN', '2023.12'), + ('JAGS', '4.3.2'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['rjags'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/r/rnamotif/rnamotif-20240904-GCCcore-12.3.0.eb b/easybuild/easyconfigs/r/rnamotif/rnamotif-20240904-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..742dabcaa85 --- /dev/null +++ b/easybuild/easyconfigs/r/rnamotif/rnamotif-20240904-GCCcore-12.3.0.eb @@ -0,0 +1,44 @@ +# This easyconfig was created by the BEAR Software team at the University of Birmingham. +easyblock = 'MakeCp' + +name = 'rnamotif' +version = '20240904' +_commit = '697ee7fda4ff2f5181a33c0c3eac54d7b97409fa' + +homepage = "https://github.com/dacase/rnamotif" +description = """The rnamotif program searchs input sequences for portions that match a given descriptor or "motif". + Matching sequences can also be ranked by various scoring functions.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +github_account = 'dacase' +source_urls = [GITHUB_SOURCE] +sources = ['%s.tar.gz' % _commit] +checksums = ['e9432e128ce7f1bfcf4898a36d56435272ad9b4e2d37f1866a95aa159c81fdfe'] + +builddependencies = [ + ('binutils', '2.40'), + ('Bison', '3.8.2'), + ('flex', '2.6.4'), + +] + +prebuildopts = 'sed -i "s/CFLAGS= -O2 -Wall/CFLAGS=$CFLAGS/" config.h &&' +pretestopts = 'EFNDATA=%%(builddir)s/%%(name)s-%s/efndata' % _commit +runtest = 'test' + +files_to_copy = [ + (['src/rnamotif', 'src/rmprune', 'src/rmfmt', 'src/rm2ct'], 'bin'), + 'LICENSE', 'efndata', 'Ecoli.trna.example', +] + +sanity_check_paths = { + 'files': ['bin/%(name)s'], + 'dirs': ['efndata'], +} + +sanity_check_commands = ['rnamotif -h 2>&1 | grep usage'] + +modextravars = {'EFNDATA': 'efndata'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/r/rpmrebuild/rpmrebuild-2.18.eb b/easybuild/easyconfigs/r/rpmrebuild/rpmrebuild-2.18.eb new file mode 100644 index 00000000000..64cae582362 --- /dev/null +++ b/easybuild/easyconfigs/r/rpmrebuild/rpmrebuild-2.18.eb @@ -0,0 +1,26 @@ +easyblock = "Tarball" + +name = "rpmrebuild" +version = "2.18" + +homepage = 'http://rpmrebuild.sourceforge.net/' +description = """rpmrebuild is a tool to build an RPM file from a package that has already been +installed in a basic use""" + +toolchain = SYSTEM + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['919ca6252eafbfb58dd54b0efa3ca4e6da293364937dcfe32c32a35b238a5837'] + +modextrapaths = {'PATH': ['']} +modextravars = {'RPMREBUILD_ROOT_DIR': '%(installdir)s'} + +sanity_check_paths = { + 'files': ["rpmrebuild"], + 'dirs': [] +} + +sanity_check_commands = ['rpmrebuild -h'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/r/ruamel.yaml/ruamel.yaml-0.18.6-GCCcore-13.3.0.eb b/easybuild/easyconfigs/r/ruamel.yaml/ruamel.yaml-0.18.6-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..48d0b0d8bb5 --- /dev/null +++ b/easybuild/easyconfigs/r/ruamel.yaml/ruamel.yaml-0.18.6-GCCcore-13.3.0.eb @@ -0,0 +1,60 @@ +easyblock = 'PythonBundle' + +name = 'ruamel.yaml' +version = '0.18.6' + +homepage = 'https://sourceforge.net/projects/ruamel-yaml' +description = "ruamel.yaml is a YAML 1.2 loader/dumper package for Python." + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +builddependencies = [ + ('binutils', '2.42'), + ('poetry', '1.8.3'), +] + +dependencies = [ + ('Python', '3.12.3'), + ('Python-bundle-PyPI', '2024.06'), +] + +use_pip = True + +exts_list = [ + ('ruamel.yaml.jinja2', '0.2.7', { + 'checksums': ['8449be29d9a157fa92d1648adc161d718e469f0d38a6b21e0eabb76fd5b3e663'], + }), + ('ruamel.yaml.clib', '0.2.8', { + 'modulename': False, + 'checksums': ['beb2e0404003de9a4cab9753a8805a8fe9320ee6673136ed7f04255fe60bb512'], + }), + (name, version, { + 'checksums': ['8b27e6a217e786c6fbe5634d8f3f11bc63e0f80f6a5890f28863d9c45aac311b'], + }), + ('configobj', '5.0.8', { + 'checksums': ['6f704434a07dc4f4dc7c9a745172c1cad449feb548febd9f7fe362629c627a97'], + }), + ('lz4', '4.3.3', { + 'checksums': ['01fe674ef2889dbb9899d8a67361e0c4a2c833af5aeb37dd505727cf5d2a131e'], + }), + ('ruamel.yaml.base', '0.3.2', { + 'checksums': ['88b6edc8ace60c12d98f05fda22e5d9d69ba9a4b531cf54783142151145b0372'], + }), + ('ruamel.yaml.convert', '0.3.2', { + 'checksums': ['065ed9492a3189291d5bc0256709afc0231b52e4a01376fc91cf1757560ac9c4'], + }), + ('ruamel.yaml.cmd', '0.6.5', { + 'checksums': ['49af59514cb87d7637d1186e31c9345c9947120a9ce49cf6975435aa7abd5aa8'], + }), +] + +sanity_check_paths = { + 'files': ['bin/yaml'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["yaml --help"] + +sanity_pip_check = True + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/rustworkx/rustworkx-0.12.1-foss-2023a.eb b/easybuild/easyconfigs/r/rustworkx/rustworkx-0.12.1-foss-2023a.eb new file mode 100644 index 00000000000..2a86b64c9ae --- /dev/null +++ b/easybuild/easyconfigs/r/rustworkx/rustworkx-0.12.1-foss-2023a.eb @@ -0,0 +1,170 @@ +easyblock = "CargoPythonPackage" + +name = 'rustworkx' +version = '0.12.1' + +homepage = 'https://github.com/Qiskit/rustworkx' +description = """rustworkx (previously retworkx) is a general purpose graph library for Python written in Rust to take +advantage of the performance and safety that Rust provides. It is designed to provide a high performance general +purpose graph library for any Python application.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [ + ('Rust', '1.75.0'), + ('setuptools-rust', '1.6.0'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), +] + +crates = [ + ('ahash', '0.7.6'), + ('autocfg', '1.1.0'), + ('bitflags', '1.3.2'), + ('cfg-if', '1.0.0'), + ('crossbeam-channel', '0.5.4'), + ('crossbeam-deque', '0.8.1'), + ('crossbeam-epoch', '0.9.8'), + ('crossbeam-utils', '0.8.8'), + ('either', '1.6.1'), + ('fixedbitset', '0.4.2'), + ('getrandom', '0.2.6'), + ('hashbrown', '0.11.2'), + ('hermit-abi', '0.1.19'), + ('indexmap', '1.7.0'), + ('indoc', '1.0.6'), + ('instant', '0.1.12'), + ('itoa', '1.0.2'), + ('lazy_static', '1.4.0'), + ('libc', '0.2.126'), + ('lock_api', '0.4.7'), + ('matrixmultiply', '0.2.4'), + ('memchr', '2.5.0'), + ('memoffset', '0.6.5'), + ('ndarray', '0.13.1'), + ('num-bigint', '0.4.3'), + ('num-complex', '0.2.4'), + ('num-complex', '0.4.1'), + ('num-integer', '0.1.45'), + ('num-traits', '0.2.15'), + ('num_cpus', '1.13.1'), + ('numpy', '0.17.2'), + ('once_cell', '1.12.0'), + ('parking_lot', '0.11.2'), + ('parking_lot_core', '0.8.5'), + ('petgraph', '0.6.2'), + ('ppv-lite86', '0.2.16'), + ('priority-queue', '1.2.0'), + ('proc-macro2', '1.0.39'), + ('pyo3', '0.17.3'), + ('pyo3-build-config', '0.17.3'), + ('pyo3-ffi', '0.17.3'), + ('pyo3-macros', '0.17.3'), + ('pyo3-macros-backend', '0.17.3'), + ('quick-xml', '0.22.0'), + ('quote', '1.0.18'), + ('rand', '0.8.5'), + ('rand_chacha', '0.3.1'), + ('rand_core', '0.6.3'), + ('rand_pcg', '0.3.1'), + ('rawpointer', '0.2.1'), + ('rayon', '1.5.3'), + ('rayon-core', '1.9.3'), + ('redox_syscall', '0.2.13'), + ('ryu', '1.0.10'), + ('scopeguard', '1.1.0'), + ('serde', '1.0.145'), + ('serde_derive', '1.0.145'), + ('serde_json', '1.0.89'), + ('smallvec', '1.8.0'), + ('syn', '1.0.96'), + ('target-lexicon', '0.12.4'), + ('unicode-ident', 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for Python written in Rust to take +advantage of the performance and safety that Rust provides. It is designed to provide a high performance general +purpose graph library for any Python application.""" + +toolchain = {'name': 'gfbf', 'version': '2023a'} + +builddependencies = [ + ('Rust', _rust_ver), + ('setuptools-rust', '1.6.0'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), +] + +crates = [ + ('ahash', '0.8.11'), + ('alga', '0.9.3'), + ('allocator-api2', '0.2.18'), + ('approx', '0.3.2'), + ('autocfg', '1.3.0'), + ('bitflags', '2.6.0'), + ('cfg-if', '1.0.0'), + ('crossbeam-deque', '0.8.5'), + ('crossbeam-epoch', '0.9.18'), + ('crossbeam-utils', '0.8.20'), + ('either', '1.13.0'), + ('equivalent', '1.0.1'), + ('fixedbitset', '0.4.2'), + ('getrandom', '0.2.15'), + ('hashbrown', '0.12.3'), + ('hashbrown', '0.14.5'), + ('heck', '0.4.1'), + ('hermit-abi', '0.3.9'), + ('indexmap', '1.9.3'), + ('indexmap', '2.2.6'), + ('indoc', '2.0.5'), + ('itertools', '0.10.5'), + ('itertools', '0.11.0'), + ('itoa', '1.0.11'), + ('libc', '0.2.155'), + ('libm', 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'15e934569e47891f7d9411f1a451d947a60e000ab3bd24fbb970f000387d1b3b'}, +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.21-GCC-13.3.0.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.21-GCC-13.3.0.eb new file mode 100644 index 00000000000..775ce37b311 --- /dev/null +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.21-GCC-13.3.0.eb @@ -0,0 +1,38 @@ +# This is a contribution from DeepThought HPC Service, Flinders University, Adelaide, Australia +# Homepage: https://staff.flinders.edu.au/research/deep-thought +# +# Authors:: Robert Qiao +# License:: MIT +# +# Notes:: +# +# Updated to 1.14 and gcc-11.2.0 +# J. Sassmannshausen / GSTT +# Updated to 1.21 jpecar / EMBL + +name = 'SAMtools' +version = '1.21' + +homepage = 'https://www.htslib.org/' +description = """SAM Tools provide various utilities for manipulating alignments in the SAM format, + including sorting, merging, indexing and generating alignments in a per-position format.""" + +toolchain = {'name': 'GCC', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/%(namelower)s/%(namelower)s/releases/download/%(version)s'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['05724b083a6b6f0305fcae5243a056cc36cf826309c3cb9347a6b89ee3fc5ada'] + +# The htslib component of SAMtools >= 1.4 uses zlib, bzip2 and lzma compression. +# The latter is currently provided by XZ. +dependencies = [ + ('ncurses', '6.5'), + ('zlib', '1.3.1'), + ('bzip2', '1.0.8'), + ('XZ', '5.4.5'), + ('cURL', '8.7.1'), +] + + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SCENICplus/SCENICplus-1.0a1-20240513-foss-2023a.eb b/easybuild/easyconfigs/s/SCENICplus/SCENICplus-1.0a1-20240513-foss-2023a.eb new file mode 100644 index 00000000000..796eb9a63b6 --- /dev/null +++ b/easybuild/easyconfigs/s/SCENICplus/SCENICplus-1.0a1-20240513-foss-2023a.eb @@ -0,0 +1,279 @@ +easyblock = 'PythonBundle' + +name = 'SCENICplus' +version = '1.0a1-20240513' +local_commit = "fa55dae" + +homepage = 'https://github.com/aertslab/scenicplus' +description = """SCENIC+ is a python package to build gene regulatory networks (GRNs) +using combined or separate single-cell gene expression (scRNA-seq) and single-cell +chromatin accessibility (scATAC-seq) data.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [ + ('poetry', '1.5.1'), + ('maturin', '1.4.0', '-Rust-1.75.0'), + ('CMake', '3.26.3'), +] +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('SciPy-bundle', '2023.07'), + ('Single-cell-python-bundle', '2024.02'), + ('anndata', '0.10.5.post1'), + ('BeautifulSoup', '4.12.2'), + ('h5py', '3.9.0'), + ('python-igraph', '0.11.4'), + ('imageio', '2.33.1'), + ('leidenalg', '0.10.2'), + ('lxml', '4.9.2'), + ('MACS2', '2.2.9.1'), + ('numba', '0.58.1'), + ('polars', '0.20.2'), + ('Arrow', '14.0.1'), + ('plotly.py', '5.16.0'), + ('pybedtools', '0.9.1'), + ('pyBigWig', '0.3.22'), + ('pyGAM', '0.9.1'), + ('Pysam', '0.22.0'), + ('Ray-project', '2.9.1'), + ('scikit-image', '0.22.0'), + ('snakemake', '8.4.2'), + ('statsmodels', '0.14.1'), + ('IPython', '8.14.0'), + ('Pandoc', '3.1.2', '', SYSTEM), + ('ipympl', '0.9.3'), + ('PyTables', '3.8.0'), + ('Sphinx-RTD-Theme', '2.0.0'), + ('scrublet', '0.2.3'), + ('numexpr', '2.9.0'), + ('Kaleido', '0.2.1'), + ('pyfasta', '0.5.2'), + ('gensim', '4.3.2'), +] + +# fix requirements.txt of scenicplus +local_preinstallopts = ( + "sed -i" + " -e '/typing==3.7.4.3/d'" + " -e 's/==.*//g'" + " -e '/pyarrow-hotfix/d'" + " -e '/line-profiler/d'" + " -e '/ndindex/d'" + " -e '/sinfo/d'" + " requirements.txt && " +) +# unpin version restriction and delete typing requirement +local_pycistopic_preinstallopts = ( + "sed -i" + " -e 's/pyscenic>=0.12.0/pyscenic/'" + " -e 's/pandas==1.5/pandas/'" + " -e 's/python-Levenshtein/Levenshtein/'" + " -e 's/python-igraph/igraph/'" + " -e '/typing/d'" + # delete pyscenic and loomxpy req from commit - have versions now + " -e '/pyscenic@git/d'" + " -e '/loomxpy@git/d'" + " requirements.txt && " + "sed -i" + " -e 's/pandas == 1.5/pandas/'" + " -e 's/matplotlib < 3.7/matplotlib/'" + " pyproject.toml && " +) +# delete typing from requirements +local_pycistarget_preinstallopts = "sed -i '/typing/d' requirements.txt && " +# unpin version restriction and delete poetry.lock +local_loomxpy_preinstallopts = "sed -i 's/pyscenic>=0.12.0/pyscenic/' requirements.txt && " +local_loomxpy_preinstallopts += "sed -i 's/pyscenic = \">=0.12.0\"/pyscenic = \"*\"/' pyproject.toml && " +local_loomxpy_preinstallopts += "rm poetry.lock && " + +use_pip = True +sanity_pip_check = True + +exts_list = [ + 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['0f21bc8b4f2dce67c6e5287af895f5f28a8c6eb123d809e3ab5679e2131dbf58'], + }), + ('pybiomart', '0.2.0', { + 'checksums': ['e9eac20db921820670c646d99725b0ee279e407379e5e8c3ec7245a07425d8fe'], + }), + ('sorted_nearest', '0.0.39', { + 'checksums': ['16a51d5db87ae226b47ace43c176bb672477a1b7ba8052ea9291a6356c9c69b1'], + }), + ('pyranges', '0.0.111', { + 'checksums': ['d2cf3c31c1b9c6e1bf6e1e89254d8bd993bfb4401f2c4ede0ebc9c8e0678147d'], + }), + ('pyrle', '0.0.39', { + 'checksums': ['1be4be7814d3941db907aaf19f311bd46a407244316cadbf4b73109685c055c5'], + }), + ('pyvis', '0.3.2', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['5720c4ca8161dc5d9ab352015723abb7a8bb8fb443edeb07f7a322db34a97555'], + }), + ('url-normalize', '1.4.3', { + 'checksums': ['d23d3a070ac52a67b83a1c59a0e68f8608d1cd538783b401bc9de2c0fac999b2'], + }), + ('cattrs', '23.2.3', { + 'checksums': ['a934090d95abaa9e911dac357e3a8699e0b4b14f8529bcc7d2b1ad9d51672b9f'], + }), + ('requests_cache', '1.2.0', { + 'checksums': ['db1c709ca343cc1cd5b6c8b1a5387298eceed02306a6040760db538c885e3838'], + }), + ('scanorama', '1.7.4', { + 'checksums': ['67de100e63abc3028c7780d3a217e43e920a5781230bc6b6a51349d4605e005c'], + }), + ('rich_argparse', '1.4.0', { + 'checksums': ['c275f34ea3afe36aec6342c2a2298893104b5650528941fb53c21067276dba19'], + }), + ('scatac_fragment_tools', '0.1.0', { + 'checksums': ['e77a03ad1b7170c212f1ac672dad2c5d7e7f091b94e47b36a2ec2adc42051857'], + }), + ('snakemake_interface_common', '1.17.1', { + 'checksums': ['555c8218d9b68ddc1046f94a517e7d0f22e15bdc839d6ce149608d8ec137b9ae'], + }), + ('snakemake_interface_report_plugins', '1.0.0', { + 'checksums': ['02311cdc4bebab2a1c28469b5e6d5c6ac6e9c66998ad4e4b3229f1472127490f'], + }), + ('statistics', '1.0.3.5', { + 'checksums': ['2dc379b80b07bf2ddd5488cad06b2b9531da4dd31edb04dc9ec0dc226486c138'], + }), + ('globre', '0.1.5', { + 'checksums': ['ee214204f237e9114b8f61eeb61c2abd1e665ca3b59e5a6a0b070971c0bb12e2'], + }), + ('bidict', '0.23.1', { + 'checksums': ['03069d763bc387bbd20e7d49914e75fc4132a41937fa3405417e1a5a2d006d71'], + }), + ('tmtoolkit', '0.12.0', { + 'checksums': ['6df5429cd675989f21d9f075ddb11fe5ae273d6544fc337a2589bab2bc331909'], + }), + ('tspex', '0.6.3', { + 'checksums': ['315bfa1f60ea582777c549313cad9e9da0a4d11c5f69a6fc767bd0823dc46316'], + }), + ('plumbum', '1.8.3', { + 'checksums': ['6092c85ab970b7a7a9d5d85c75200bc93be82b33c9bdf640ffa87d2d7c8709f0'], + }), + ('pandoc', '2.3', { + 'checksums': ['e772c2c6d871146894579828dbaf1efd538eb64fc7e71d4a6b3a11a18baef90d'], + }), + ('nbsphinx', '0.9.4', { + 'checksums': ['042a60806fc23d519bc5bef59d95570713913fe442fda759d53e3aaf62104794'], + }), + ('nbsphinx-link', '1.3.0', { + 'checksums': ['fa3079a74c0dff1b2079e79a34babe770706ba8aa9cc0609c6dbfd593461a077'], + }), + ('numpydoc', '1.7.0', { + 'checksums': ['866e5ae5b6509dcf873fc6381120f5c31acf13b135636c1a81d68c166a95f921'], + }), + ('pyOpenSSL', '23.2.0', { + 'modulename': 'OpenSSL', + 'checksums': ['276f931f55a452e7dea69c7173e984eb2a4407ce413c918aa34b55f82f9b8bac'], + }), + ('entrypoints', '0.4', { + 'checksums': ['b706eddaa9218a19ebcd67b56818f05bb27589b1ca9e8d797b74affad4ccacd4'], + }), + ('ansicolors', '1.1.8', { + 'modulename': 'colors', + 'source_tmpl': '%(name)s-%(version)s-py2.py3-none-any.whl', + 'checksums': ['00d2dde5a675579325902536738dd27e4fac1fd68f773fe36c21044eb559e187'], + }), + ('papermill', '2.6.0', { + 'checksums': ['9fe2a91912fd578f391b4cc8d6d105e73124dcd0cde2a43c3c4a1c77ac88ea24'], + }), + ('mypy_extensions', '1.0.0', { + 'checksums': ['75dbf8955dc00442a438fc4d0666508a9a97b6bd41aa2f0ffe9d2f2725af0782'], + }), + ('typing_inspect', '0.9.0', { + 'checksums': ['b23fc42ff6f6ef6954e4852c1fb512cdd18dbea03134f91f856a95ccc9461f78'], + }), + ('marshmallow', '3.21.1', { + 'checksums': ['4e65e9e0d80fc9e609574b9983cf32579f305c718afb30d7233ab818571768c3'], + }), + ('dataclasses_json', '0.6.4', { + 'checksums': ['73696ebf24936560cca79a2430cbc4f3dd23ac7bf46ed17f38e5e5e7657a6377'], + }), + ('loomxpy', '0.4.2', { + 'preinstallopts': local_loomxpy_preinstallopts, + 'checksums': ['188411b77e04fa8458c0a7f02cfb3f15b58410a020f81f522957e922e79cdd82'], + }), + ('pycisTopic', '2.0a-dca4bb6', { + 'modulename': 'pycisTopic', + 'preinstallopts': local_pycistopic_preinstallopts, + # download commit dca4bb6 to be compatible with pycistarget + 'source_urls': ['https://github.com/aertslab/pycisTopic/archive/'], + 'sources': [{'download_filename': 'dca4bb6.tar.gz', 'filename': '%(name)s-%(version)s-dca4bb6.tar.gz'}], + 'checksums': ['82edc9313bbb587aeb1540fd5b095b6eafb422fa12a5fc97ba090b99b684b240'], + }), + ('pycistarget', '1.0a1-16d14b9', { + 'preinstallopts': local_pycistarget_preinstallopts, + # download commit 16d14b9 to make '$ scenicplus' work + 'source_urls': ['https://github.com/aertslab/pycistarget/archive/'], + 'sources': [{'download_filename': '16d14b9.tar.gz', 'filename': '%(name)s-%(version)s-16d14b9.tar.gz'}], + 'checksums': ['7285ac03be9d148437442a726366d7c6f9f5f86bc6636369149a2bc2cd8e0e29'], + }), + ('scenicplus', version, { + 'preinstallopts': local_preinstallopts, + 'source_urls': ['https://github.com/aertslab/scenicplus/archive/'], + 'sources': [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}], + 'checksums': ['88cddec1ab2618861e5c93e8a0b17b8e9e2aa3a76410d882c35d472f98724e29'], + }), +] + +# copy files to let 'scenicplus init_snakemake' works +postinstallcmds = [ + "cp -r %%(builddir)s/scenicplus/scenicplus-%s*/src/scenicplus/snakemake " + "%%(installdir)s/lib/python%%(pyshortver)s/site-packages/scenicplus" % local_commit +] + +sanity_check_commands = ['scenicplus init_snakemake --help'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-7.0.4-iimpi-2023b.eb b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-7.0.4-iimpi-2023b.eb new file mode 100644 index 00000000000..03292d90476 --- /dev/null +++ b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-7.0.4-iimpi-2023b.eb @@ -0,0 +1,26 @@ +name = 'SCOTCH' +version = '7.0.4' + +homepage = 'https://www.labri.fr/perso/pelegrin/scotch/' +description = """Software package and libraries for sequential and parallel graph partitioning, +static mapping, and sparse matrix block ordering, and sequential mesh and hypergraph partitioning.""" + +toolchain = {'name': 'iimpi', 'version': '2023b'} +toolchainopts = {'pic': True} + +source_urls = ['https://gitlab.inria.fr/scotch/scotch/-/archive/v%(version)s/'] +sources = ['%(namelower)s-v%(version)s.tar.gz'] +checksums = ['8ef4719d6a3356e9c4ca7fefd7e2ac40deb69779a5c116f44da75d13b3d2c2c3'] + +threadedmpi = False + +builddependencies = [ + ('Bison', '3.8.2'), + ('flex', '2.6.4'), +] + +dependencies = [ + ('zlib', '1.2.13'), +] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/SCRIPro/SCRIPro-1.0.18-foss-2023a.eb b/easybuild/easyconfigs/s/SCRIPro/SCRIPro-1.0.18-foss-2023a.eb new file mode 100644 index 00000000000..e7d07a0b329 --- /dev/null +++ b/easybuild/easyconfigs/s/SCRIPro/SCRIPro-1.0.18-foss-2023a.eb @@ -0,0 +1,69 @@ +easyblock = 'PythonBundle' + +name = 'SCRIPro' +version = '1.0.18' +local_commit = 'e9087fd' + +homepage = 'https://github.com/xuyunfan9991/SCRIPro' +description = "SCRIPro, an extended framework of SCRIP that suits both single-cell and spatial multi-ome data" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('SciPy-bundle', '2023.07'), + ('matplotlib', '3.7.2'), + ('h5py', '3.9.0'), + ('scanpy', '1.9.8'), + ('Seaborn', '0.13.2'), + ('PyTables', '3.8.0'), + ('tqdm', '4.66.1'), + ('dill', '0.3.7'), + ('leidenalg', '0.10.2'), + ('PyTorch', '2.1.2'), + ('PyTorch-bundle', '2.1.2'), # provides PyTorch-Ignite + ('tensorboardX', '2.6.2.2'), + ('pybedtools', '0.9.1'), + ('jupyter-server', '2.7.2'), # ipywidgets +] + +use_pip = True + +exts_list = [ + ('lisa2', '2.3.2', { + 'checksums': ['dc9df3495322c94f93c12372fb8d88d355447f7b8b69ea639394fc6274e9affb'], + 'modulename': 'lisa', + }), + ('parse', '1.20.1', { + 'checksums': ['09002ca350ad42e76629995f71f7b518670bcf93548bdde3684fd55d2be51975'], + }), + ('pynvml', '11.5.0', { + 'checksums': ['d027b21b95b1088b9fc278117f9f61b7c67f8e33a787e9f83f735f0f71ac32d0'], + }), + ('sparse', '0.15.1', { + 'checksums': ['973adcb88a8db8e3d8047953331e26d3f64a5657f9b46a6b859c47663c3eef99'], + # replace use of 'version_file' (which requires setuptools-scm >= 8.0) with 'write_to' + 'preinstallopts': "sed -i 's/^version_file/write_to/' pyproject.toml && ", + }), + ('scglue', '0.3.2', { + 'checksums': ['fd57ebfa400233cbb1ab4fab4ad6a9dbf4db2c5ca715ba31c71c7a36cc931241'], + }), + ('scripro', version, { + 'preinstallopts': "sed -i 's/==/>=/g' requirements.txt && ", + 'source_urls': ['https://github.com/xuyunfan9991/SCRIPro/archive'], + 'sources': [{'download_filename': 'e9087fd.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['6636c31f3f5797d33d57a5d0266c89f80cc37389dd9c139806b4d17ecad74252'], + }), +] + +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/scripro'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["scripro --help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SDL2/SDL2-2.30.6-GCCcore-13.3.0.eb b/easybuild/easyconfigs/s/SDL2/SDL2-2.30.6-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..1c8130b397c --- /dev/null +++ b/easybuild/easyconfigs/s/SDL2/SDL2-2.30.6-GCCcore-13.3.0.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'SDL2' +version = '2.30.6' + +homepage = 'https://www.libsdl.org/' +description = "SDL: Simple DirectMedia Layer, a cross-platform multimedia library" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://www.libsdl.org/release/'] +sources = [SOURCE_TAR_GZ] +checksums = ['c6ef64ca18a19d13df6eb22df9aff19fb0db65610a74cc81dae33a82235cacd4'] + +builddependencies = [('binutils', '2.42')] + +dependencies = [ + ('X11', '20240607'), +] + +sanity_check_paths = { + 'files': ['bin/sdl2-config', 'lib/libSDL2.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/SHAP/SHAP-0.43.0-foss-2023a.eb b/easybuild/easyconfigs/s/SHAP/SHAP-0.43.0-foss-2023a.eb new file mode 100644 index 00000000000..6be374eb213 --- /dev/null +++ b/easybuild/easyconfigs/s/SHAP/SHAP-0.43.0-foss-2023a.eb @@ -0,0 +1,37 @@ +easyblock = 'PythonBundle' + +name = 'SHAP' +version = '0.43.0' + +homepage = "https://github.com/shap/shap" +description = """SHAP (SHapley Additive exPlanations) is a game theoretic approach to explain the output of any + machine learning model. It connects optimal credit allocation with local explanations using the classic Shapley + values from game theory and their related extensions.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('scikit-learn', '1.3.1'), + ('tqdm', '4.66.1'), + ('numba', '0.58.1'), +] + +sanity_pip_check = True +use_pip = True + +exts_list = [ + ('cloudpickle', '3.0.0', { + 'checksums': ['996d9a482c6fb4f33c1a35335cf8afd065d2a56e973270364840712d9131a882'], + }), + ('slicer', '0.0.7', { + 'checksums': ['f5d5f7b45f98d155b9c0ba6554fa9770c6b26d5793a3e77a1030fb56910ebeec'], + }), + (name, version, { + 'sources': ['%(namelower)s-%(version)s.tar.gz'], + 'checksums': ['1eabe01444a24e181ef6a7c9593b4d7c7143eefaeb1fa4d97bd5d9fdc96c4c1e'], + }), +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.7-GCCcore-11.2.0-tools.eb b/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.7-GCCcore-11.2.0-tools.eb index 7cb1689c5c2..30b9729414a 100644 --- a/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.7-GCCcore-11.2.0-tools.eb +++ b/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.7-GCCcore-11.2.0-tools.eb @@ -31,12 +31,18 @@ toolchain = {'name': 'GCCcore', 'version': '11.2.0'} source_urls = ['https://apps.fz-juelich.de/jsc/%(namelower)s/download.php?version=%(version)sl'] sources = ['%(namelower)s-%(version)sl.tar.gz'] -checksums = ['3b5072d8a32a9e9858d85dfe4dc01e7cfdbf54cdaa60660e760b634ee08d8a4c'] +# 1.7.7 was rereleased with code changes. Old checksum was: +# 3b5072d8a32a9e9858d85dfe4dc01e7cfdbf54cdaa60660e760b634ee08d8a4c +checksums = ['e37c42975b47dead4649d34fbcaf5a95d2257240039756a0d7f3c1ff312aebcc'] builddependencies = [ ('binutils', '2.37'), ] +# remove -m64 flag from PFLAG variable in Makefiles for CPU architectures that don't support it +if ARCH != 'x86_64': + preconfigopts = 'sed -i "s|PFLAG = -m\\$(PREC)|PFLAG = |" mf/Makefile.defs.linux-gomp* && ' + configopts = '--disable-cxx --disable-fortran --disable-ompi ' # Comment it out if you have Xeon Phi: diff --git a/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.7-GCCcore-11.3.0-tools.eb b/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.7-GCCcore-11.3.0-tools.eb index 9d094c2cb89..f948c852c2d 100644 --- a/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.7-GCCcore-11.3.0-tools.eb +++ b/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.7-GCCcore-11.3.0-tools.eb @@ -31,12 +31,18 @@ toolchain = {'name': 'GCCcore', 'version': '11.3.0'} source_urls = ['https://apps.fz-juelich.de/jsc/%(namelower)s/download.php?version=%(version)sl'] sources = ['%(namelower)s-%(version)sl.tar.gz'] -checksums = ['3b5072d8a32a9e9858d85dfe4dc01e7cfdbf54cdaa60660e760b634ee08d8a4c'] +# 1.7.7 was rereleased with code changes. Old checksum was: +# 3b5072d8a32a9e9858d85dfe4dc01e7cfdbf54cdaa60660e760b634ee08d8a4c +checksums = ['e37c42975b47dead4649d34fbcaf5a95d2257240039756a0d7f3c1ff312aebcc'] builddependencies = [ ('binutils', '2.38'), ] +# remove -m64 flag from PFLAG variable in Makefiles for CPU architectures that don't support it +if ARCH != 'x86_64': + preconfigopts = 'sed -i "s|PFLAG = -m\\$(PREC)|PFLAG = |" mf/Makefile.defs.linux-gomp* && ' + configopts = '--disable-cxx --disable-fortran --disable-ompi ' # Comment it out if you have Xeon Phi: diff --git a/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.7-GCCcore-12.2.0-tools.eb b/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.7-GCCcore-12.2.0-tools.eb index 5bf659a141a..3921083e94f 100644 --- a/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.7-GCCcore-12.2.0-tools.eb +++ b/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.7-GCCcore-12.2.0-tools.eb @@ -31,12 +31,18 @@ toolchain = {'name': 'GCCcore', 'version': '12.2.0'} source_urls = ['https://apps.fz-juelich.de/jsc/%(namelower)s/download.php?version=%(version)sl'] sources = ['%(namelower)s-%(version)sl.tar.gz'] -checksums = ['3b5072d8a32a9e9858d85dfe4dc01e7cfdbf54cdaa60660e760b634ee08d8a4c'] +# 1.7.7 was rereleased with code changes. Old checksum was: +# 3b5072d8a32a9e9858d85dfe4dc01e7cfdbf54cdaa60660e760b634ee08d8a4c +checksums = ['e37c42975b47dead4649d34fbcaf5a95d2257240039756a0d7f3c1ff312aebcc'] builddependencies = [ ('binutils', '2.39'), ] +# remove -m64 flag from PFLAG variable in Makefiles for CPU architectures that don't support it +if ARCH != 'x86_64': + preconfigopts = 'sed -i "s|PFLAG = -m\\$(PREC)|PFLAG = |" mf/Makefile.defs.linux-gomp* && ' + configopts = '--disable-cxx --disable-fortran --disable-ompi ' # Comment it out if you have Xeon Phi: diff --git a/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.7-GCCcore-12.3.0-tools.eb b/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.7-GCCcore-12.3.0-tools.eb index 7cae952e521..2a1c723de5a 100644 --- a/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.7-GCCcore-12.3.0-tools.eb +++ b/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.7-GCCcore-12.3.0-tools.eb @@ -31,12 +31,18 @@ toolchain = {'name': 'GCCcore', 'version': '12.3.0'} source_urls = ['https://apps.fz-juelich.de/jsc/%(namelower)s/download.php?version=%(version)sl'] sources = ['%(namelower)s-%(version)sl.tar.gz'] -checksums = ['3b5072d8a32a9e9858d85dfe4dc01e7cfdbf54cdaa60660e760b634ee08d8a4c'] +# 1.7.7 was rereleased with code changes. Old checksum was: +# 3b5072d8a32a9e9858d85dfe4dc01e7cfdbf54cdaa60660e760b634ee08d8a4c +checksums = ['e37c42975b47dead4649d34fbcaf5a95d2257240039756a0d7f3c1ff312aebcc'] builddependencies = [ ('binutils', '2.40'), ] +# remove -m64 flag from PFLAG variable in Makefiles for CPU architectures that don't support it +if ARCH != 'x86_64': + preconfigopts = 'sed -i "s|PFLAG = -m\\$(PREC)|PFLAG = |" mf/Makefile.defs.linux-gomp* && ' + configopts = '--disable-cxx --disable-fortran --disable-ompi ' # Comment it out if you have Xeon Phi: diff --git a/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.7-GCCcore-13.2.0-tools.eb b/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.7-GCCcore-13.2.0-tools.eb index 4ac7b2ae50d..90f04ab5dff 100644 --- a/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.7-GCCcore-13.2.0-tools.eb +++ b/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.7-GCCcore-13.2.0-tools.eb @@ -31,12 +31,18 @@ toolchain = {'name': 'GCCcore', 'version': '13.2.0'} source_urls = ['https://apps.fz-juelich.de/jsc/%(namelower)s/download.php?version=%(version)sl'] sources = ['%(namelower)s-%(version)sl.tar.gz'] -checksums = ['3b5072d8a32a9e9858d85dfe4dc01e7cfdbf54cdaa60660e760b634ee08d8a4c'] +# 1.7.7 was rereleased with code changes. Old checksum was: +# 3b5072d8a32a9e9858d85dfe4dc01e7cfdbf54cdaa60660e760b634ee08d8a4c +checksums = ['e37c42975b47dead4649d34fbcaf5a95d2257240039756a0d7f3c1ff312aebcc'] builddependencies = [ ('binutils', '2.40'), ] +# remove -m64 flag from PFLAG variable in Makefiles for CPU architectures that don't support it +if ARCH != 'x86_64': + preconfigopts = 'sed -i "s|PFLAG = -m\\$(PREC)|PFLAG = |" mf/Makefile.defs.linux-gomp* && ' + configopts = '--disable-cxx --disable-fortran --disable-ompi ' # Comment it out if you have Xeon Phi: diff --git a/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.7-GCCcore-13.3.0-tools.eb b/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.7-GCCcore-13.3.0-tools.eb new file mode 100644 index 00000000000..ff0762c0c4e --- /dev/null +++ b/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.7-GCCcore-13.3.0-tools.eb @@ -0,0 +1,57 @@ +# # +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2016-2019 Juelich Supercomputing Centre, Germany +# Authors:: Markus Geimer +# Modified 2017 by Andreas Henkel +# License:: 3-clause BSD +# # + +easyblock = 'ConfigureMake' + +name = 'SIONlib' +version = '1.7.7' +# Provide a stripped-down version with renamed symbols for tools, +# see description for further details +versionsuffix = '-tools' + +homepage = 'https://www.fz-juelich.de/ias/jsc/EN/Expertise/Support/Software/SIONlib/_node.html' +description = """ + SIONlib is a scalable I/O library for parallel access to task-local files. + The library not only supports writing and reading binary data to or from + several thousands of processors into a single or a small number of physical + files, but also provides global open and close functions to access SIONlib + files in parallel. This package provides a stripped-down installation of + SIONlib for use with performance tools (e.g., Score-P), with renamed symbols + to avoid conflicts when an application using SIONlib itself is linked against + a tool requiring a different SIONlib version. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://apps.fz-juelich.de/jsc/%(namelower)s/download.php?version=%(version)sl'] +sources = ['%(namelower)s-%(version)sl.tar.gz'] +# 1.7.7 was rereleased with code changes. Old checksum was: +# 3b5072d8a32a9e9858d85dfe4dc01e7cfdbf54cdaa60660e760b634ee08d8a4c +checksums = ['e37c42975b47dead4649d34fbcaf5a95d2257240039756a0d7f3c1ff312aebcc'] + +builddependencies = [ + ('binutils', '2.42'), +] + +# remove -m64 flag from PFLAG variable in Makefiles for CPU architectures that don't support it +if ARCH != 'x86_64': + preconfigopts = 'sed -i "s|PFLAG = -m\\$(PREC)|PFLAG = |" mf/Makefile.defs.linux-gomp* && ' + +configopts = '--disable-cxx --disable-fortran --disable-ompi ' + +# Comment it out if you have Xeon Phi: +configopts += '--disable-mic ' + +sanity_check_paths = { + 'files': ['bin/sionconfig'] + + ['lib/lib%s_64.a' % x for x in ['lsioncom', 'lsiongen', 'lsionser']], + 'dirs': [] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/SIP/SIP-6.8.3-GCCcore-13.2.0.eb b/easybuild/easyconfigs/s/SIP/SIP-6.8.3-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..7e615a60c0a --- /dev/null +++ b/easybuild/easyconfigs/s/SIP/SIP-6.8.3-GCCcore-13.2.0.eb @@ -0,0 +1,42 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Bart Verleye +# Center for eResearch, Auckland +# update 6.8.1: THEMBL +easyblock = 'PythonPackage' + +name = 'SIP' +version = '6.8.3' + +homepage = 'http://www.riverbankcomputing.com/software/sip/' +description = """SIP is a tool that makes it very easy to create Python bindings for C and C++ libraries.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['888547b018bb24c36aded519e93d3e513d4c6aa0ba55b7cc1affbd45cf10762c'] + +builddependencies = [ + ('binutils', '2.40'), +] +dependencies = [ + ('Python', '3.11.5'), + ('Python-bundle-PyPI', '2023.10'), + ('PLY', '3.11'), +] + +download_dep_fail = True +use_pip = True + +local_tools = ['build', 'distinfo', 'install', 'module', 'sdist', 'wheel'] +sanity_check_paths = { + 'files': ['bin/sip-%s' % x for x in local_tools], + 'dirs': ['lib/python%(pyshortver)s/site-packages/sipbuild'], +} + +sanity_pip_check = True + +sanity_check_commands = ['sip-%s --help' % x for x in local_tools] + +options = {'modulename': 'sipbuild'} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/s/SIRIUS/SIRIUS-7.5.2-foss-2023a.eb b/easybuild/easyconfigs/s/SIRIUS/SIRIUS-7.5.2-foss-2023a.eb new file mode 100644 index 00000000000..5c7da32ecff --- /dev/null +++ b/easybuild/easyconfigs/s/SIRIUS/SIRIUS-7.5.2-foss-2023a.eb @@ -0,0 +1,40 @@ +easyblock = 'CMakeMake' + +name = 'SIRIUS' +version = '7.5.2' + +homepage = 'https://github.com/electronic-structure/SIRIUS' +description = """SIRIUS is a domain specific library for electronic structure calculations. +It implements pseudopotential plane wave (PP-PW) and +full potential linearized augmented plane wave (FP-LAPW) methods.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['https://github.com/electronic-structure/SIRIUS/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['9ae01935578532c84f1d0d673dbbcdd490e26be22efa6c4acf7129f9dc1a0c60'] + +builddependencies = [ + ('CMake', '3.26.3'), + ('pkgconf', '1.9.5'), +] +dependencies = [ + ('GSL', '2.7'), + ('libxc', '6.2.2'), + ('HDF5', '1.14.0'), + ('spglib', '2.5.0'), + ('SpFFT', '1.1.0'), + ('spla', '1.6.1'), + ('COSTA', '2.2.2'), + ('Umpire', '2024.02.1'), +] + +sanity_check_paths = { + 'files': [ + 'bin/sirius.scf', + 'lib/libsirius.%s' % SHLIB_EXT, + ], + 'dirs': ['bin', 'include/sirius'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/SKA2/SKA2-0.3.7-GCCcore-12.2.0.eb b/easybuild/easyconfigs/s/SKA2/SKA2-0.3.7-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..ec330ffc75d --- /dev/null +++ b/easybuild/easyconfigs/s/SKA2/SKA2-0.3.7-GCCcore-12.2.0.eb @@ -0,0 +1,395 @@ +easyblock = 'Cargo' + +name = 'SKA2' +version = '0.3.7' + +homepage = 'https://docs.rs/ska/latest/ska/' +description = """Split k-mer analysis (version 2) uses exact matching of split k-mer sequences to align closely + related sequences, typically small haploid genomes such as bacteria and viruses.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +sources = [] +checksums = [ + {'ska-0.3.7.tar.gz': '42febc3b657772569c9f6de9e19c3a02ec306ce1bc72d3032044ebaf6f9b23f6'}, + {'adler-1.0.2.tar.gz': 'f26201604c87b1e01bd3d98f8d5d9a8fcbb815e8cedb41ffccbeb4bf593a35fe'}, + {'ahash-0.8.11.tar.gz': 'e89da841a80418a9b391ebaea17f5c112ffaaa96f621d2c285b5174da76b9011'}, + {'aho-corasick-1.1.2.tar.gz': 'b2969dcb958b36655471fc61f7e416fa76033bdd4bfed0678d8fee1e2d07a1f0'}, + {'allocator-api2-0.2.16.tar.gz': '0942ffc6dcaadf03badf6e6a2d0228460359d5e34b57ccdc720b7382dfbd5ec5'}, + {'anstream-0.6.13.tar.gz': 'd96bd03f33fe50a863e394ee9718a706f988b9079b20c3784fb726e7678b62fb'}, + {'anstyle-1.0.6.tar.gz': '8901269c6307e8d93993578286ac0edf7f195079ffff5ebdeea6a59ffb7e36bc'}, + {'anstyle-parse-0.2.3.tar.gz': 'c75ac65da39e5fe5ab759307499ddad880d724eed2f6ce5b5e8a26f4f387928c'}, + 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{'windows_x86_64_gnullvm-0.52.4.tar.gz': '77ca79f2451b49fa9e2af39f0747fe999fcda4f5e241b2898624dca97a1f2177'}, + {'windows_x86_64_msvc-0.48.5.tar.gz': 'ed94fce61571a4006852b7389a063ab983c02eb1bb37b47f8272ce92d06d9538'}, + {'windows_x86_64_msvc-0.52.4.tar.gz': '32b752e52a2da0ddfbdbcc6fceadfeede4c939ed16d13e648833a61dfb611ed8'}, + {'xz2-0.1.7.tar.gz': '388c44dc09d76f1536602ead6d325eb532f5c122f17782bd57fb47baeeb767e2'}, + {'yansi-0.5.1.tar.gz': '09041cd90cf85f7f8b2df60c646f853b7f535ce68f85244eb6731cf89fa498ec'}, + {'zerocopy-0.7.32.tar.gz': '74d4d3961e53fa4c9a25a8637fc2bfaf2595b3d3ae34875568a5cf64787716be'}, + {'zerocopy-derive-0.7.32.tar.gz': '9ce1b18ccd8e73a9321186f97e46f9f04b778851177567b1975109d26a08d2a6'}, +] + +crates = [ + ('ska', version), + ('adler', '1.0.2'), + ('ahash', '0.8.11'), + ('aho-corasick', '1.1.2'), + ('allocator-api2', '0.2.16'), + ('anstream', '0.6.13'), + ('anstyle', '1.0.6'), + ('anstyle-parse', '0.2.3'), + ('anstyle-query', '1.0.2'), + ('anstyle-wincon', '3.0.2'), + ('anyhow', '1.0.81'), + ('argmin', '0.9.0'), + ('argmin-math', '0.3.0'), + ('assert_fs', '1.1.1'), + ('autocfg', '1.1.0'), + ('bincode', '1.3.3'), + ('bit-vec', '0.6.3'), + ('bitflags', '1.3.2'), + ('bitflags', '2.4.2'), + ('bstr', '1.9.1'), + ('buffer-redux', '1.0.1'), + ('bytecount', '0.6.7'), + ('byteorder', '1.5.0'), + ('bytes', '1.5.0'), + ('bzip2', '0.4.4'), + ('bzip2-sys', '0.1.11+1.0.8'), + ('cc', '1.0.90'), + ('cfg-if', '1.0.0'), + ('ciborium', '0.2.2'), + ('ciborium-io', '0.2.2'), + ('ciborium-ll', '0.2.2'), + ('clap', '4.5.2'), + ('clap_builder', '4.5.2'), + ('clap_derive', '4.5.0'), + ('clap_lex', '0.7.0'), + ('colorchoice', '1.0.0'), + ('colored', '2.1.0'), + ('console', '0.15.8'), + ('crc32fast', '1.4.0'), + ('crossbeam-channel', '0.5.12'), + ('crossbeam-deque', '0.8.5'), + ('crossbeam-epoch', '0.9.18'), + ('crossbeam-utils', '0.8.19'), + ('crunchy', '0.2.2'), + ('deranged', '0.3.11'), + ('diff', '0.1.13'), + ('difflib', '0.4.0'), + ('dirs-next', '2.0.0'), + ('dirs-sys-next', '0.1.2'), + ('doc-comment', '0.3.3'), + ('either', '1.10.0'), + ('encode_unicode', '0.3.6'), + ('equivalent', '1.0.1'), + ('errno', '0.3.8'), + ('fastrand', '2.0.1'), + ('flate2', '1.0.28'), + ('float-cmp', '0.9.0'), + ('getrandom', '0.2.12'), + ('globset', '0.4.14'), + ('globwalk', '0.9.1'), + ('half', '2.4.0'), + ('hashbrown', '0.14.3'), + ('heck', '0.4.1'), + ('hermit-abi', '0.3.9'), + ('ignore', '0.4.22'), + ('indexmap', '2.2.5'), + ('indicatif', '0.17.8'), + ('instant', '0.1.12'), + ('is-terminal', '0.4.12'), + ('itertools', '0.10.5'), + ('itoa', '1.0.10'), + ('lazy_static', '1.4.0'), + ('libc', '0.2.153'), + ('libm', '0.2.8'), + ('libredox', '0.0.1'), + ('linux-raw-sys', '0.4.13'), + ('log', '0.4.21'), + ('lzma-sys', '0.1.20'), + ('matrixmultiply', '0.3.8'), + ('memchr', '2.7.1'), + ('miniz_oxide', '0.7.2'), + ('ndarray', '0.15.6'), + ('needletail', '0.5.1'), + ('noodles-bgzf', '0.26.0'), + ('noodles-core', '0.14.0'), + ('noodles-csi', '0.30.0'), + ('noodles-tabix', '0.36.0'), + ('noodles-vcf', '0.49.0'), + ('normalize-line-endings', '0.3.0'), + ('num-complex', '0.4.5'), + ('num-conv', '0.1.0'), + ('num-integer', '0.1.46'), + ('num-traits', '0.2.18'), + ('num_cpus', '1.16.0'), + ('num_threads', '0.1.7'), + ('number_prefix', '0.4.0'), + ('once_cell', '1.19.0'), + ('paste', '1.0.14'), + ('percent-encoding', '2.3.1'), + ('pkg-config', '0.3.30'), + ('portable-atomic', '1.6.0'), + ('powerfmt', '0.2.0'), + ('ppv-lite86', '0.2.17'), + ('predicates', '2.1.5'), + ('predicates', '3.1.0'), + ('predicates-core', '1.0.6'), + ('predicates-tree', '1.0.9'), + ('pretty_assertions', '1.4.0'), + ('proc-macro2', '1.0.79'), + ('quote', '1.0.35'), + ('rand', '0.8.5'), + ('rand_chacha', '0.3.1'), + ('rand_core', '0.6.4'), + ('rand_xoshiro', '0.6.0'), + ('rawpointer', '0.2.1'), + ('rayon', '1.9.0'), + ('rayon-core', '1.12.1'), + ('redox_syscall', '0.4.1'), + ('redox_users', '0.4.4'), + ('regex', '1.10.3'), + ('regex-automata', '0.4.6'), + ('regex-syntax', '0.8.2'), + ('rustix', '0.38.31'), + ('rustversion', '1.0.14'), + ('ryu', '1.0.17'), + ('same-file', '1.0.6'), + ('serde', '1.0.197'), + ('serde_derive', '1.0.197'), + ('serde_json', '1.0.114'), + ('similar', '2.4.0'), + ('simple_logger', '4.3.3'), + ('slog', '2.7.0'), + ('slog-async', '2.8.0'), + ('slog-json', '2.6.1'), + ('slog-term', '2.9.1'), + ('snap', '1.1.1'), + ('snapbox', '0.4.17'), + ('snapbox-macros', '0.3.8'), + ('strsim', '0.11.0'), + ('syn', '2.0.52'), + ('take_mut', '0.2.2'), + ('tempfile', '3.10.1'), + ('term', '0.7.0'), + ('termtree', '0.4.1'), + ('thiserror', '1.0.58'), + ('thiserror-impl', '1.0.58'), + ('thread_local', '1.1.8'), + ('time', '0.3.34'), + ('time-core', '0.1.2'), + ('time-macros', '0.2.17'), + ('unicode-ident', '1.0.12'), + ('unicode-width', '0.1.11'), + ('utf8parse', '0.2.1'), + ('version_check', '0.9.4'), + ('walkdir', '2.5.0'), + ('wasi', '0.11.0+wasi-snapshot-preview1'), + ('winapi', '0.3.9'), + ('winapi-i686-pc-windows-gnu', '0.4.0'), + ('winapi-util', '0.1.6'), + ('winapi-x86_64-pc-windows-gnu', '0.4.0'), + ('windows-sys', '0.48.0'), + ('windows-sys', '0.52.0'), + ('windows-targets', '0.48.5'), + ('windows-targets', '0.52.4'), + ('windows_aarch64_gnullvm', '0.48.5'), + ('windows_aarch64_gnullvm', '0.52.4'), + ('windows_aarch64_msvc', '0.48.5'), + ('windows_aarch64_msvc', '0.52.4'), + ('windows_i686_gnu', '0.48.5'), + ('windows_i686_gnu', '0.52.4'), + ('windows_i686_msvc', '0.48.5'), + ('windows_i686_msvc', '0.52.4'), + ('windows_x86_64_gnu', '0.48.5'), + ('windows_x86_64_gnu', '0.52.4'), + ('windows_x86_64_gnullvm', '0.48.5'), + ('windows_x86_64_gnullvm', '0.52.4'), + ('windows_x86_64_msvc', '0.48.5'), + ('windows_x86_64_msvc', '0.52.4'), + ('xz2', '0.1.7'), + ('yansi', '0.5.1'), + ('zerocopy', '0.7.32'), + ('zerocopy-derive', '0.7.32'), +] + +builddependencies = [ + ('binutils', '2.39'), + ('Rust', '1.75.0'), +] + +sanity_check_paths = { + 'files': ['bin/ska'], + 'dirs': [], +} + +sanity_check_commands = ["ska --help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SNAP-ESA/SNAP-ESA-10.0.0-Java-11.eb b/easybuild/easyconfigs/s/SNAP-ESA/SNAP-ESA-10.0.0-Java-11.eb new file mode 100644 index 00000000000..06a2de7582c --- /dev/null +++ b/easybuild/easyconfigs/s/SNAP-ESA/SNAP-ESA-10.0.0-Java-11.eb @@ -0,0 +1,71 @@ +easyblock = 'Binary' + +name = 'SNAP-ESA' +version = '10.0.0' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'https://step.esa.int/main/toolboxes/snap/' +description = """ +The Sentinel Application Platform (SNAP) is a common architecture for all +Sentinel Toolboxes being jointly developed by Brockmann Consult, SkyWatch and +C-S. +The SNAP architecture is ideal for Earth Observation processing and analysis +due to the following technological innovations: Extensibility, Portability, +Modular Rich Client Platform, Generic EO Data Abstraction, Tiled Memory +Management, and a Graph Processing Framework.""" + +toolchain = SYSTEM + +local_installer = 'esa-snap_all_linux-%(version)s.sh' +local_varfile = 'SNAP-ESA-8.0-response.varfile' + +source_urls = [ + 'https://download.esa.int/step/snap/%(version_major)s_%(version_minor)s/installers', + 'https://step.esa.int/downloads/%(version_major_minor)s/installers', +] +sources = [local_installer] +patches = [(local_varfile, '.')] +checksums = [ + {'esa-snap_all_linux-10.0.0.sh': 'c928fd886c983fa7c09c09a3c48593542e71b0636d493ae1401b4c964348698a'}, + {'SNAP-ESA-8.0-response.varfile': '5ea98e3376bb3df52b9c4c99ab4986015296b815021e16486b58e4aad58e21a4'}, +] + +# The installation is executed with the bundled JRE 1.8.0_242 (Zulu) +# At runtime we switch to an external JDK (SNAP developers recommend any OpenJDK distribution) +dependencies = [ + ('Java', '11'), +] + +install_cmd = "INSTALL4J_TEMP='%(builddir)s' " +install_cmd += "bash %s -dir '%%(installdir)s'" % local_installer +install_cmd += " -q -varfile '%s'" % local_varfile + +postinstallcmds = [ + # set paths + 'sed -i "s|jdkhome.*|jdkhome=$JAVA_HOME|" %(installdir)s/etc/snap.conf', + 'sed -i "s|#snap.home.*|snap.home=%(installdir)s|" %(installdir)s/etc/snap.properties', + # remove default maximum memory allocation pool + 'sed -i "s|-J-Xmx[0-9G]* ||" %(installdir)s/etc/snap.conf', + # disable update checks + "echo 'snap.versionCheck.interval=NEVER' >> %(installdir)s/etc/snap.properties", + "sed -i 's|dpiaware=false|& -J-Dplugin.manager.check.interval=NEVER|' %(installdir)s/etc/snap.conf", + # (optional) update all modules to latest version + # the update command is buggy and it hangs after doing the update, kill it whenever it prints "updates=0" + # see issue https://senbox.atlassian.net/browse/SNAP-927 + # ('LOG="$(mktemp -d)/snap-update.log"; mkfifo $LOG; trap "rm -f $LOG" EXIT;' + # 'SNAPCMD="%(installdir)s/bin/snap --nosplash --nogui --userdir "%(builddir)s/snap" --modules --update-all";' + # '$SNAPCMD 2>&1 > $LOG & SNAPPID=$!;' + # 'while read line; do echo "$line"; [ "$line" = "updates=0" ] && kill $SNAPPID; done < $LOG;'), +] + +sanity_check_paths = { + 'files': ['bin/snap', 'bin/gpt'], + 'dirs': ['rstb', 'smos', 'snap'], +} + +sanity_check_commands = [ + "snap --nosplash --nogui --modules --help | grep 'Additional module options'", + "gpt -h", +] + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/s/SNAP-HMM/SNAP-HMM-20221022-GCC-12.3.0.eb b/easybuild/easyconfigs/s/SNAP-HMM/SNAP-HMM-20221022-GCC-12.3.0.eb new file mode 100644 index 00000000000..06b3173938e --- /dev/null +++ b/easybuild/easyconfigs/s/SNAP-HMM/SNAP-HMM-20221022-GCC-12.3.0.eb @@ -0,0 +1,45 @@ +easyblock = 'MakeCp' + +name = 'SNAP-HMM' +version = '20221022' +_commit = '4ad1e95' + +homepage = 'https://korflab.github.io/' +description = """ +SNAP is a general purpose gene finding program suitable for both eukaryotic and +prokaryotic genomes. SNAP is an acroynm for Semi-HMM-based Nucleic Acid +Parser. +""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +source_urls = ['https://github.com/KorfLab/SNAP/archive'] +sources = [{'download_filename': '%s.tar.gz' % _commit, 'filename': '%(version)s.tar.gz'}] +patches = ['%(name)s-20190603_makefile_correction.patch'] +checksums = [ + {'20221022.tar.gz': 'a85726b7d4199da1b213b613057600012a392ef1aa20198f1d571fac55bf643f'}, + {'SNAP-HMM-20190603_makefile_correction.patch': 'd518750d4cf01278ba5403ab5717cfcd65b75b5a7c6573ae140f1cdb56b9e655'}, +] + +prebuildopts = 'export CFLAGS="$CFLAGS -fcommon" && ' + +files_to_copy = [ + (['hmm-assembler.pl', 'zff2gff3.pl', 'fathom', 'forge', 'snap', 'Zoe/zoe-loop'], 'bin'), + 'DNA', + 'HMM', + 'Zoe', +] + +sanity_check_paths = { + 'files': ['bin/snap', 'bin/forge', 'bin/zoe-loop'], + 'dirs': ['Zoe'], +} + +sanity_check_commands = [ + 'snap 2>&1 | grep "^usage:"', + 'zoe-loop | grep "^usage:"', +] + +modextrapaths = {'ZOE': 'Zoe'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SNPTEST/SNPTEST-2.5.6.eb b/easybuild/easyconfigs/s/SNPTEST/SNPTEST-2.5.6.eb new file mode 100644 index 00000000000..a404d99e468 --- /dev/null +++ b/easybuild/easyconfigs/s/SNPTEST/SNPTEST-2.5.6.eb @@ -0,0 +1,33 @@ +easyblock = 'Tarball' + +name = 'SNPTEST' +version = '2.5.6' + +homepage = 'https://www.chg.ox.ac.uk/~gav/snptest/' +description = """SNPTEST is a program for the analysis of single SNP association in genome-wide studies. + The tests implemented include + + Binary (case-control) phenotypes, single and multiple quantitative phenotypes + Bayesian and Frequentist tests + Ability to condition upon an arbitrary set of covariates and/or SNPs. + Various different methods for the dealing with imputed SNPs. +""" + +toolchain = SYSTEM + +source_urls = ['https://www.well.ox.ac.uk/~gav/resources/'] +sources = ['snptest_v2.5.6_CentOS_Linux7.8-x86_64_dynamic.tgz'] +checksums = ['c2c829def961dd2f6377c388d8aa22cab17945961c47e39c4a94493466c0a52e'] + +postinstallcmds = ["cd %(installdir)s && ln -s snptest_v2.5.6 snptest"] + +sanity_check_paths = { + 'files': ['LICENCE'], + 'dirs': ['doc', 'example'], +} + +modextrapaths = {'PATH': ''} + +sanity_check_commands = ["snptest -help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SOCI/SOCI-4.0.3-GCC-12.3.0.eb b/easybuild/easyconfigs/s/SOCI/SOCI-4.0.3-GCC-12.3.0.eb new file mode 100644 index 00000000000..e100da22edb --- /dev/null +++ b/easybuild/easyconfigs/s/SOCI/SOCI-4.0.3-GCC-12.3.0.eb @@ -0,0 +1,52 @@ +easyblock = 'CMakeMake' + +name = 'SOCI' +version = '4.0.3' + +homepage = 'http://soci.sourceforge.net/' +description = """SOCI is a database access library for C++ that makes the illusion of embedding SQL queries in the + regular C++ code, staying entirely within the Standard C++.""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +source_urls = ['https://github.com/SOCI/soci/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['4b1ff9c8545c5d802fbe06ee6cd2886630e5c03bf740e269bb625b45cf934928'] + +builddependencies = [ + ('CMake', '3.26.3'), +] + +dependencies = [ + ('Boost', '1.82.0'), + ('SQLite', '3.42.0'), + ('PostgreSQL', '16.1'), +] + +# Matches RStudio (1.4.1717) install options +# https://github.com/rstudio/rstudio/blob/ddcd7191ec89c4da00e77afae7e9f27e61e87c36/dependencies/common/install-soci +configopts = "-DCMAKE_POSITION_INDEPENDENT_CODE:BOOL=true " +configopts += "-DSOCI_TESTS=OFF " +configopts += "-DSOCI_CXX11=ON " +configopts += "-DSOCI_EMPTY=OFF " +configopts += '-DCMAKE_INCLUDE_PATH="$EBROOTBOOST/include" ' +configopts += "-DBoost_USE_STATIC_LIBS=ON " +configopts += '-DCMAKE_LIBRARY_PATH="$EBROOTBOOST/lib" ' +configopts += "-DWITH_BOOST=ON " +configopts += "-DWITH_POSTGRESQL=ON " +configopts += "-DWITH_SQLITE3=ON " +configopts += "-DWITH_DB2=OFF " +configopts += "-DWITH_MYSQL=OFF " +configopts += "-DWITH_ORACLE=OFF " +configopts += "-DWITH_FIREBIRD=OFF " +configopts += "-DWITH_ODBC=OFF " +configopts += "-DBoost_DEBUG=1 " + +local_dbs = ['postgresql', 'sqlite3'] + +sanity_check_paths = { + 'files': ['lib/libsoci_%s.%s' % (x, SHLIB_EXT) for x in local_dbs + ['core']], + 'dirs': ['include/soci/%s' % x for x in local_dbs], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/s/SOCI/SOCI-4.0.3-GCC-13.2.0.eb b/easybuild/easyconfigs/s/SOCI/SOCI-4.0.3-GCC-13.2.0.eb new file mode 100644 index 00000000000..9f4329a7316 --- /dev/null +++ b/easybuild/easyconfigs/s/SOCI/SOCI-4.0.3-GCC-13.2.0.eb @@ -0,0 +1,52 @@ +easyblock = 'CMakeMake' + +name = 'SOCI' +version = '4.0.3' + +homepage = 'http://soci.sourceforge.net/' +description = """SOCI is a database access library for C++ that makes the illusion of embedding SQL queries in the + regular C++ code, staying entirely within the Standard C++.""" + +toolchain = {'name': 'GCC', 'version': '13.2.0'} + +source_urls = ['https://github.com/SOCI/soci/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['4b1ff9c8545c5d802fbe06ee6cd2886630e5c03bf740e269bb625b45cf934928'] + +builddependencies = [ + ('CMake', '3.27.6'), +] + +dependencies = [ + ('Boost', '1.83.0'), + ('SQLite', '3.43.1'), + ('PostgreSQL', '16.1'), +] + +# Matches RStudio (1.4.1717) install options +# https://github.com/rstudio/rstudio/blob/ddcd7191ec89c4da00e77afae7e9f27e61e87c36/dependencies/common/install-soci +configopts = "-DCMAKE_POSITION_INDEPENDENT_CODE:BOOL=true " +configopts += "-DSOCI_TESTS=OFF " +configopts += "-DSOCI_CXX11=ON " +configopts += "-DSOCI_EMPTY=OFF " +configopts += '-DCMAKE_INCLUDE_PATH="$EBROOTBOOST/include" ' +configopts += "-DBoost_USE_STATIC_LIBS=ON " +configopts += '-DCMAKE_LIBRARY_PATH="$EBROOTBOOST/lib" ' +configopts += "-DWITH_BOOST=ON " +configopts += "-DWITH_POSTGRESQL=ON " +configopts += "-DWITH_SQLITE3=ON " +configopts += "-DWITH_DB2=OFF " +configopts += "-DWITH_MYSQL=OFF " +configopts += "-DWITH_ORACLE=OFF " +configopts += "-DWITH_FIREBIRD=OFF " +configopts += "-DWITH_ODBC=OFF " +configopts += "-DBoost_DEBUG=1 " + +local_dbs = ['postgresql', 'sqlite3'] + +sanity_check_paths = { + 'files': ['lib/libsoci_%s.%s' % (x, SHLIB_EXT) for x in local_dbs + ['core']], + 'dirs': ['include/soci/%s' % x for x in local_dbs], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/s/SPRNG/SPRNG-5.0-gompi-2023b.eb b/easybuild/easyconfigs/s/SPRNG/SPRNG-5.0-gompi-2023b.eb new file mode 100644 index 00000000000..bf9aa5e5827 --- /dev/null +++ b/easybuild/easyconfigs/s/SPRNG/SPRNG-5.0-gompi-2023b.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'SPRNG' +version = '5.0' + +homepage = 'http://www.sprng.org/' +description = "Scalable Parallel Pseudo Random Number Generators Library" + +toolchain = {'name': 'gompi', 'version': '2023b'} +toolchainopts = {'pic': True, 'opt': True, 'usempi': True, 'cstd': 'c++14'} + +source_urls = ['http://www.sprng.org/Version%(version)s/'] +sources = ['%(namelower)s%(version_major)s.tar.bz2'] +patches = ['%(name)s-%(version)s_MPI-lmpi.patch'] +checksums = [ + {'sprng5.tar.bz2': '696ef452bdd998d2e66586e73d81dac875082e35d08de419cede1a1bb2555b59'}, + {'SPRNG-5.0_MPI-lmpi.patch': 'a6bb936b2e7cf9efd74e0bf06702bf444c98ecb11877492308a3551c5b9dff5c'}, +] + +builddependencies = [ + ('Autotools', '20220317'), + ('TestU01', '1.2.3'), +] + +preconfigopts = 'autoreconf -f -i && ' +configopts = '--with-fortran=yes --with-mpi=yes --with-testu01=$EBROOTTESTU01' + +sanity_check_paths = { + 'files': ['bin/checksprng', 'include/sprng.h', 'include/sprng_f.h', 'lib/libsprng.a'], + 'dirs': ['bin', 'include', 'lib', 'share'], +} + +sanity_check_commands = ['cd %(builddir)s/sprng5/check && checksprng'] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/SPRNG/SPRNG-5.0-iimpi-2023b.eb b/easybuild/easyconfigs/s/SPRNG/SPRNG-5.0-iimpi-2023b.eb new file mode 100644 index 00000000000..ea7f852cd44 --- /dev/null +++ b/easybuild/easyconfigs/s/SPRNG/SPRNG-5.0-iimpi-2023b.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'SPRNG' +version = '5.0' + +homepage = 'http://www.sprng.org/' +description = "Scalable Parallel Pseudo Random Number Generators Library" + +toolchain = {'name': 'iimpi', 'version': '2023b'} +toolchainopts = {'pic': True, 'opt': True, 'usempi': True, 'cstd': 'c++14'} + +source_urls = ['http://www.sprng.org/Version%(version)s/'] +sources = ['%(namelower)s%(version_major)s.tar.bz2'] +patches = ['%(name)s-%(version)s_MPI-lmpicxx.patch'] +checksums = [ + {'sprng5.tar.bz2': '696ef452bdd998d2e66586e73d81dac875082e35d08de419cede1a1bb2555b59'}, + {'SPRNG-5.0_MPI-lmpicxx.patch': 'fc0903d81886a76a8cf2af73930b0347e3bcc047ad32215fdafd5a936f519545'}, +] + +builddependencies = [ + ('Autotools', '20220317'), + ('TestU01', '1.2.3'), +] + +preconfigopts = 'autoreconf -f -i && ' +configopts = '--with-fortran=yes --with-mpi=yes --with-testu01=$EBROOTTESTU01' + +sanity_check_paths = { + 'files': ['bin/checksprng', 'include/sprng.h', 'include/sprng_f.h', 'lib/libsprng.a'], + 'dirs': ['bin', 'include', 'lib', 'share'], +} + +sanity_check_commands = ['cd %(builddir)s/sprng5/check && checksprng'] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/SPRNG/SPRNG-5.0_MPI-lmpi.patch b/easybuild/easyconfigs/s/SPRNG/SPRNG-5.0_MPI-lmpi.patch new file mode 100644 index 00000000000..c09f74fa073 --- /dev/null +++ b/easybuild/easyconfigs/s/SPRNG/SPRNG-5.0_MPI-lmpi.patch @@ -0,0 +1,12 @@ +diff -Nru sprng5-orig/configure.ac sprng5/configure.ac +--- sprng5-orig/configure.ac 2021-06-08 18:37:02.000000000 +0200 ++++ sprng5/configure.ac 2024-08-29 19:21:40.393998554 +0200 +@@ -89,7 +89,7 @@ + + if test $use_mpi = y; then + MPI_DEF="-DSPRNG_MPI" +- MPI_CXXLIB="-lmpi_cxx" ++ MPI_CXXLIB="-lmpi" + else + MPI_DEF="" + MPI_CXXLIB="" diff --git a/easybuild/easyconfigs/s/SPRNG/SPRNG-5.0_MPI-lmpicxx.patch b/easybuild/easyconfigs/s/SPRNG/SPRNG-5.0_MPI-lmpicxx.patch new file mode 100644 index 00000000000..a45691c9b04 --- /dev/null +++ b/easybuild/easyconfigs/s/SPRNG/SPRNG-5.0_MPI-lmpicxx.patch @@ -0,0 +1,12 @@ +diff -Nru sprng5-orig/configure.ac sprng5/configure.ac +--- sprng5-orig/configure.ac 2021-06-08 18:37:02.000000000 +0200 ++++ sprng5/configure.ac 2024-08-29 19:18:56.124716693 +0200 +@@ -89,7 +89,7 @@ + + if test $use_mpi = y; then + MPI_DEF="-DSPRNG_MPI" +- MPI_CXXLIB="-lmpi_cxx" ++ MPI_CXXLIB="-lmpicxx" + else + MPI_DEF="" + MPI_CXXLIB="" diff --git a/easybuild/easyconfigs/s/SQLAlchemy/SQLAlchemy-2.0.36-GCCcore-13.3.0.eb b/easybuild/easyconfigs/s/SQLAlchemy/SQLAlchemy-2.0.36-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..293b3bf2452 --- /dev/null +++ b/easybuild/easyconfigs/s/SQLAlchemy/SQLAlchemy-2.0.36-GCCcore-13.3.0.eb @@ -0,0 +1,45 @@ +easyblock = 'PythonBundle' + +name = 'SQLAlchemy' +version = '2.0.36' + +homepage = 'https://www.sqlalchemy.org/' +description = """SQLAlchemy is the Python SQL toolkit and Object Relational Mapper that gives +application developers the full power and flexibility of SQL. SQLAlchemy +provides a full suite of well known enterprise-level persistence patterns, +designed for efficient and high-performing database access, adapted into a +simple and Pythonic domain language.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +builddependencies = [('binutils', '2.42')] + +dependencies = [ + ('Python', '3.12.3'), + ('Greenlet', '3.1.1'), + ('psycopg', '3.2.3'), # optional, postgresql extra + ('Mako', '1.3.5'), # needed by alembic +] + +use_pip = True + +exts_list = [ + ('async-timeout', '5.0.1', { + 'sources': ['async_timeout-%(version)s.tar.gz'], + 'checksums': ['d9321a7a3d5a6a5e187e824d2fa0793ce379a202935782d555d6e9d2735677d3'], + }), + ('asyncpg', '0.30.0', { + 'checksums': ['c551e9928ab6707602f44811817f82ba3c446e018bfe1d3abecc8ba5f3eac851'], + }), + ('sqlalchemy', version, { + 'use_pip_extras': 'asyncio,postgresql,postgresql_asyncpg', + 'checksums': ['7f2767680b6d2398aea7082e45a774b2b0767b5c8d8ffb9c8b683088ea9b29c5'], + }), + ('alembic', '1.14.0', { + 'checksums': ['b00892b53b3642d0b8dbedba234dbf1924b69be83a9a769d5a624b01094e304b'], + }), +] + +sanity_pip_check = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.45.3-GCCcore-13.3.0.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.45.3-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..2a1d41ffc3c --- /dev/null +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.45.3-GCCcore-13.3.0.eb @@ -0,0 +1,39 @@ +easyblock = 'ConfigureMake' + +name = 'SQLite' +version = '3.45.3' +local_filename_version = '3450300' + +homepage = 'https://www.sqlite.org/' +description = "SQLite: SQL Database Engine in a C Library" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.sqlite.org/2024/'] +sources = ['%%(namelower)s-autoconf-%s.tar.gz' % (local_filename_version)] +checksums = ['b2809ca53124c19c60f42bf627736eae011afdcc205bb48270a5ee9a38191531'] + +builddependencies = [ + ('binutils', '2.42'), +] +dependencies = [ + ('libreadline', '8.2'), + ('Tcl', '8.6.14'), +] + +# enable additional APIs that provide access to meta-data about tables and queries +# needed for GDAL when it used as a dep for QGIS +buildopts = 'CC="$CC" CFLAGS="$CFLAGS -DSQLITE_ENABLE_COLUMN_METADATA"' + +sanity_check_paths = { + 'files': ['bin/sqlite3', 'include/sqlite3ext.h', 'include/sqlite3.h', + 'lib/libsqlite3.a', 'lib/libsqlite3.%s' % SHLIB_EXT], + 'dirs': ['lib/pkgconfig'], +} + +sanity_check_commands = [ + 'sqlite3 --version | grep ^%(version)s', +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/s/SRA-Toolkit/SRA-Toolkit-3.1.1-gompi-2023b.eb b/easybuild/easyconfigs/s/SRA-Toolkit/SRA-Toolkit-3.1.1-gompi-2023b.eb new file mode 100644 index 00000000000..624658d8e2b --- /dev/null +++ b/easybuild/easyconfigs/s/SRA-Toolkit/SRA-Toolkit-3.1.1-gompi-2023b.eb @@ -0,0 +1,76 @@ +# updated: Denis Kristak (INUITS) +# updated: Sebastien Moretti (SIB - Vital-IT) +# updated: Pavel Tománek (INUITS) +easyblock = 'CMakeMake' + +name = 'SRA-Toolkit' +version = '3.1.1' + +homepage = 'https://github.com/ncbi/sra-tools' +description = """The SRA Toolkit, and the source-code SRA System Development + Kit (SDK), will allow you to programmatically access data housed within SRA + and convert it from the SRA format""" +github_account = 'ncbi' + +toolchain = {'name': 'gompi', 'version': '2023b'} +toolchainopts = {'extra_cflags': '-DH5_USE_110_API'} + +source_urls = ['https://github.com/ncbi/sra-tools/archive/refs/tags/'] +sources = [{'download_filename': '%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}] +checksums = ['96b110bd5a30ad312e2f02552062b48a77d40c763e6aba5bb84e83662a505cf1'] + +builddependencies = [ + ('CMake', '3.27.6'), + ('flex', '2.6.4'), + ('Bison', '3.8.2'), + ('Perl', '5.38.0'), +] + +dependencies = [ + ('Python', '3.11.5'), + ('Java', '11', '', SYSTEM), + ('OpenSSL', '1.1', '', SYSTEM), + ('ncbi-vdb', version), + ('bzip2', '1.0.8'), + ('file', '5.43'), + ('HDF5', '1.14.3'), + ('libxml2', '2.11.5'), + ('zlib', '1.2.13'), +] + +configopts = '-DVDB_INCDIR="$EBROOTNCBIMINVDB/include" -DVDB_LIBDIR="$EBROOTNCBIMINVDB/lib" ' +configopts += '-DBUILD_TOOLS_LOADERS=ON -DBUILD_TOOLS_INTERNAL=ON' + +postinstallcmds = [ + "cp -r %(start_dir)s/ngs/ngs-python/ %(installdir)s/", +] + +_sra_bin = [ + 'abi-dump', 'abi-load', 'align-info', 'bam-load', 'cache-mgr', 'cg-load', 'copycat', 'fasterq-dump', 'fastq-dump', + 'fastq-load', 'helicos-load', 'illumina-dump', 'illumina-load', 'kar', 'kdbmeta', 'latf-load', 'pacbio-load', + 'prefetch', 'rcexplain', 'sam-dump', 'sff-dump', 'sff-load', 'srapath', 'sra-pileup', 'sra-sort', 'sra-stat', + 'sratools', 'srf-load', 'test-sra', 'vdb-config', 'vdb-copy', 'vdb-decrypt', 'vdb-dump', 'vdb-encrypt', 'vdb-lock', + 'vdb-unlock', 'vdb-validate', +] + +_ngs_libs = ['libncbi-ngs.a', 'libncbi-ngs-c++.a', 'libncbi-ngs.%s' % SHLIB_EXT, + 'libngs-c++.a', 'libngs-c++.%s' % SHLIB_EXT] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in _sra_bin] + ['lib/%s' % y for y in _ngs_libs], + 'dirs': ['jar', 'include/ncbi-vdb', 'include/ngs'] +} + +sanity_check_commands = [ + "abi-dump --help", + "kar --help", + "sra-sort --help", + "python -c 'import ngs'", +] + +modextrapaths = { + 'CLASSPATH': 'jar/ngs-java.jar', + 'PYTHONPATH': 'ngs-python', +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/STAR/STAR-2.7.11a-GCC-12.2.0.eb b/easybuild/easyconfigs/s/STAR/STAR-2.7.11a-GCC-12.2.0.eb index 42f094bb67b..a61fe5e85bb 100644 --- a/easybuild/easyconfigs/s/STAR/STAR-2.7.11a-GCC-12.2.0.eb +++ b/easybuild/easyconfigs/s/STAR/STAR-2.7.11a-GCC-12.2.0.eb @@ -24,6 +24,10 @@ checksums = [ {'STAR-%(version)s_use-external-htslib.patch': '2fdc3ed9372d983f77d861d6f16a60a553598358dce9ff8216f96eb20e63ce4e'}, ] +builddependencies = [ + ('xxd', '9.0.1696'), +] + dependencies = [ ('HTSlib', '1.17'), ('zlib', '1.2.12'), @@ -31,6 +35,9 @@ dependencies = [ start_dir = 'source' +# by default this is set to -mavx2 which makes it fail on non x86 systems +prebuildopts = 'CXXFLAGS_SIMD= ' + buildopts = ' STAR && make STARlong' files_to_copy = [ diff --git a/easybuild/easyconfigs/s/STAR/STAR-2.7.11a-GCC-12.3.0.eb b/easybuild/easyconfigs/s/STAR/STAR-2.7.11a-GCC-12.3.0.eb index 1943af96d5e..a017a2ba109 100644 --- a/easybuild/easyconfigs/s/STAR/STAR-2.7.11a-GCC-12.3.0.eb +++ b/easybuild/easyconfigs/s/STAR/STAR-2.7.11a-GCC-12.3.0.eb @@ -24,6 +24,10 @@ checksums = [ {'STAR-%(version)s_use-external-htslib.patch': '2fdc3ed9372d983f77d861d6f16a60a553598358dce9ff8216f96eb20e63ce4e'}, ] +builddependencies = [ + ('xxd', '9.0.2112'), +] + dependencies = [ ('HTSlib', '1.18'), ('zlib', '1.2.13'), @@ -31,6 +35,9 @@ dependencies = [ start_dir = 'source' +# by default this is set to -mavx2 which makes it fail on non x86 systems +prebuildopts = 'CXXFLAGS_SIMD= ' + buildopts = ' STAR && make STARlong' files_to_copy = [ diff --git a/easybuild/easyconfigs/s/STAR/STAR-2.7.11b-GCC-12.3.0.eb b/easybuild/easyconfigs/s/STAR/STAR-2.7.11b-GCC-12.3.0.eb index cf16b5c2979..67cac5d0f47 100644 --- a/easybuild/easyconfigs/s/STAR/STAR-2.7.11b-GCC-12.3.0.eb +++ b/easybuild/easyconfigs/s/STAR/STAR-2.7.11b-GCC-12.3.0.eb @@ -24,6 +24,10 @@ checksums = [ {'STAR-2.7.11a_use-external-htslib.patch': '2fdc3ed9372d983f77d861d6f16a60a553598358dce9ff8216f96eb20e63ce4e'}, ] +builddependencies = [ + ('xxd', '9.0.2112'), +] + dependencies = [ ('HTSlib', '1.18'), ('zlib', '1.2.13'), @@ -31,6 +35,9 @@ dependencies = [ start_dir = 'source' +# by default this is set to -mavx2 which makes it fail on non x86 systems +prebuildopts = 'CXXFLAGS_SIMD= ' + buildopts = ' STAR && make STARlong' files_to_copy = [ diff --git a/easybuild/easyconfigs/s/STAR/STAR-2.7.11b-GCC-13.2.0.eb b/easybuild/easyconfigs/s/STAR/STAR-2.7.11b-GCC-13.2.0.eb index a86f215d8dd..886aa0a24c5 100644 --- a/easybuild/easyconfigs/s/STAR/STAR-2.7.11b-GCC-13.2.0.eb +++ b/easybuild/easyconfigs/s/STAR/STAR-2.7.11b-GCC-13.2.0.eb @@ -35,6 +35,9 @@ dependencies = [ start_dir = 'source' +# by default this is set to -mavx2 which makes it fail on non x86 systems +prebuildopts = 'CXXFLAGS_SIMD= ' + buildopts = ' STAR && make STARlong' files_to_copy = [ diff --git a/easybuild/easyconfigs/s/STAR/STAR-2.7.11b_alpha_2024-02-09-GCC-12.3.0.eb b/easybuild/easyconfigs/s/STAR/STAR-2.7.11b_alpha_2024-02-09-GCC-12.3.0.eb new file mode 100644 index 00000000000..a0a119a428c --- /dev/null +++ b/easybuild/easyconfigs/s/STAR/STAR-2.7.11b_alpha_2024-02-09-GCC-12.3.0.eb @@ -0,0 +1,57 @@ +# Contribution from the NIHR Biomedical Research Centre +# Guy's and St Thomas' NHS Foundation Trust and King's College London +# Based on STAR-2.7.7a-GCC-10.2.0.eb +# uploaded by J. Sassmannshausen +# modified by Thomas Eylenbosch + +easyblock = 'MakeCp' + +name = 'STAR' +version = '2.7.11b_alpha_2024-02-09' + +homepage = 'https://github.com/dobinlab/STAR_pre_releases' +description = "STAR aligns RNA-seq reads to a reference genome using uncompressed suffix arrays." + +toolchain = {'name': 'GCC', 'version': '12.3.0'} +toolchainopts = {'openmp': True} + +source_urls = ['https://github.com/dobinlab/STAR_pre_releases/archive/'] +sources = ['%(version)s.tar.gz'] +patches = ['STAR-2.7.11a_use-external-htslib.patch'] +checksums = [ + {'2.7.11b_alpha_2024-02-09.tar.gz': '7a7bae1f802fc5bc5b270da89e66a824480fb33e21f7ebfbf7ed56e1d4907c1c'}, + {'STAR-2.7.11a_use-external-htslib.patch': '2fdc3ed9372d983f77d861d6f16a60a553598358dce9ff8216f96eb20e63ce4e'}, +] + +builddependencies = [ + ('xxd', '9.0.2112'), +] + +dependencies = [ + ('HTSlib', '1.18'), + ('zlib', '1.2.13'), +] + +start_dir = 'source' + +# by default this is set to -mavx2 which makes it fail on non x86 systems +prebuildopts = 'CXXFLAGS_SIMD= ' + +buildopts = ' STAR && make STARlong' + +files_to_copy = [ + (['source/%(name)s', 'source/%(name)slong'], 'bin'), + 'CHANGES.md', 'doc', 'extras', 'LICENSE', 'README.md', 'RELEASEnotes.md', +] + +sanity_check_paths = { + 'files': ['bin/%(name)s', 'bin/%(name)slong'], + 'dirs': [], +} + +sanity_check_commands = [ + "STAR --help", + "STARlong --help", +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/STREAM/STREAM-5.10-intel-compilers-2024.2.0.eb b/easybuild/easyconfigs/s/STREAM/STREAM-5.10-intel-compilers-2024.2.0.eb new file mode 100644 index 00000000000..17fdbcab3a4 --- /dev/null +++ b/easybuild/easyconfigs/s/STREAM/STREAM-5.10-intel-compilers-2024.2.0.eb @@ -0,0 +1,39 @@ +easyblock = 'CmdCp' + +name = 'STREAM' +version = '5.10' + +homepage = 'https://www.cs.virginia.edu/stream/' +description = """The STREAM benchmark is a simple synthetic benchmark program that measures sustainable + memory bandwidth (in MB/s) and the corresponding computation rate for simple vector kernels.""" + +toolchain = {'name': 'intel-compilers', 'version': '2024.2.0'} +toolchainopts = {'openmp': True} + +source_urls = ['https://www.cs.virginia.edu/stream/FTP/Code/'] +sources = [{'download_filename': '%(namelower)s.c', 'filename': 'stream-%(version)s.c', 'extract_cmd': "cp %s ."}] +checksums = ['a52bae5e175bea3f7832112af9c085adab47117f7d2ce219165379849231692b'] + +# 10 million array elements (1000 runs): requires ~224MB of memory +local_cmds = "$CC $CFLAGS %(source)s -mcmodel=large -DSTREAM_ARRAY_SIZE=10000000 -DNTIMES=1000 -o stream_1Kx10M; " +# 100 million array elements (1000 runs): requires ~2.2GiB of memory +local_cmds += "$CC $CFLAGS %(source)s -mcmodel=large -DSTREAM_ARRAY_SIZE=100000000 -DNTIMES=1000 -o stream_1Kx100M; " +# 1 billion array elements (1000 runs): requires ~22.4 GiB of memory +local_cmds += "$CC $CFLAGS %(source)s -mcmodel=large -DSTREAM_ARRAY_SIZE=1000000000 -DNTIMES=1000 -o stream_1Kx1B; " +# 2.5 billion array elements (1000 runs): requires ~56 GiB of memory +local_cmds += "$CC $CFLAGS %(source)s -mcmodel=large -DSTREAM_ARRAY_SIZE=2500000000 -DNTIMES=1000 -o stream_1Kx2.5B; " +# 5 billion array elements (1000 runs): requires ~111 GiB of memory +local_cmds += "$CC $CFLAGS %(source)s -mcmodel=large -DSTREAM_ARRAY_SIZE=5000000000 -DNTIMES=1000 -o stream_1Kx5B; " + +cmds_map = [('stream-%(version)s.c', local_cmds)] + +files_to_copy = [(['stream_1Kx10M', 'stream_1Kx100M', 'stream_1Kx1B', 'stream_1Kx2.5B', 'stream_1Kx5B'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/stream_1Kx10M', 'bin/stream_1Kx100M', 'bin/stream_1Kx1B', 'bin/stream_1Kx2.5B', 'bin/stream_1Kx5B'], + 'dirs': [], +} + +tests = ['%(installdir)s/bin/stream_1Kx10M'] + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/s/STRUMPACK/STRUMPACK-7.1.0-foss-2023b.eb b/easybuild/easyconfigs/s/STRUMPACK/STRUMPACK-7.1.0-foss-2023b.eb new file mode 100644 index 00000000000..dd1f8cff948 --- /dev/null +++ b/easybuild/easyconfigs/s/STRUMPACK/STRUMPACK-7.1.0-foss-2023b.eb @@ -0,0 +1,46 @@ +easyblock = 'CMakeMake' + +name = 'STRUMPACK' +version = '7.1.0' + +homepage = 'https://fastmath-scidac.llnl.gov/software/strumpack.html' +description = """STRUMPACK - STRUctured Matrix PACKage - Fast linear solvers and preconditioner + for both dense and sparse systems using low-rank structured factorization with randomized sampling.""" + +toolchain = {'name': 'foss', 'version': '2023b'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://github.com/pghysels/%(name)s/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['a3e80e0530ea1cc6b62c22699cfe5f02f81794321f225440f0e08bceed69c241'] + +builddependencies = [ + ('CMake', '3.27.6'), +] + +dependencies = [ + ('zlib', '1.2.13'), + ('ParMETIS', '4.0.3'), + ('SCOTCH', '7.0.4'), +] + +configopts = '-DSTRUMPACK_USE_OPENMP=ON ' +configopts += '-DTPL_METIS_INCLUDE_DIRS=${EBROOTPARMETIS}/include ' +configopts += '-DTPL_METIS_LIBRARY_DIR=${EBROOTPARMETIS}/lib ' +configopts += '-DTPL_ENABLE_PARMETIS=ON ' +configopts += '-DTPL_PARMETIS_INCLUDE_DIRS=${EBROOTPARMETIS}/include ' +configopts += '-DTPL_PARMETIS_LIBRARY_DIR=${EBROOTPARMETIS}/lib ' +configopts += '-DTPL_ENABLE_SCOTCH=ON ' +configopts += '-DTPL_SCOTCH_INCLUDE_DIRS=${EBROOTSCOTCH}/include ' +configopts += '-DTPL_SCOTCH_LIBRARY_DIR=${EBROOTSCOTCH}/lib ' +configopts += '-DTPL_ENABLE_BPACK=OFF ' +configopts += '-DTPL_ENABLE_ZFP=OFF ' +configopts += '-DTPL_ENABLE_SLATE=OFF ' + +sanity_check_paths = { + 'files': ['lib/libstrumpack.a'], + 'dirs': ['include/%s' % x for x in ['BLR', 'clustering', 'dense', 'HSS', 'kernel', 'misc', 'python', 'sparse']] + + ['lib'], +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/s/STRUMPACK/STRUMPACK-7.1.0-intel-2023b.eb b/easybuild/easyconfigs/s/STRUMPACK/STRUMPACK-7.1.0-intel-2023b.eb new file mode 100644 index 00000000000..b6ff89201c8 --- /dev/null +++ b/easybuild/easyconfigs/s/STRUMPACK/STRUMPACK-7.1.0-intel-2023b.eb @@ -0,0 +1,47 @@ +easyblock = 'CMakeMake' + +name = 'STRUMPACK' +version = '7.1.0' + +homepage = 'https://fastmath-scidac.llnl.gov/software/strumpack.html' +description = """STRUMPACK - STRUctured Matrix PACKage - Fast linear solvers and preconditioner + for both dense and sparse systems using low-rank structured factorization with randomized sampling.""" + +toolchain = {'name': 'intel', 'version': '2023b'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://github.com/pghysels/%(name)s/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['a3e80e0530ea1cc6b62c22699cfe5f02f81794321f225440f0e08bceed69c241'] + +builddependencies = [ + ('CMake', '3.27.6'), +] + +dependencies = [ + ('zlib', '1.2.13'), + ('ParMETIS', '4.0.3'), + ('SCOTCH', '7.0.4'), +] + +configopts = '-DSTRUMPACK_USE_OPENMP=ON ' +configopts += '-DTPL_SCALAPACK_LIBRARIES="${LIBSCALAPACK_MT}" ' +configopts += '-DTPL_METIS_INCLUDE_DIRS=${EBROOTPARMETIS}/include ' +configopts += '-DTPL_METIS_LIBRARY_DIR=${EBROOTPARMETIS}/lib ' +configopts += '-DTPL_ENABLE_PARMETIS=ON ' +configopts += '-DTPL_PARMETIS_INCLUDE_DIRS=${EBROOTPARMETIS}/include ' +configopts += '-DTPL_PARMETIS_LIBRARY_DIR=${EBROOTPARMETIS}/lib ' +configopts += '-DTPL_ENABLE_SCOTCH=ON ' +configopts += '-DTPL_SCOTCH_INCLUDE_DIRS=${EBROOTSCOTCH}/include ' +configopts += '-DTPL_SCOTCH_LIBRARY_DIR=${EBROOTSCOTCH}/lib ' +configopts += '-DTPL_ENABLE_BPACK=OFF ' +configopts += '-DTPL_ENABLE_ZFP=OFF ' +configopts += '-DTPL_ENABLE_SLATE=OFF ' + +sanity_check_paths = { + 'files': ['lib/libstrumpack.a'], + 'dirs': ['include/%s' % x for x in ['BLR', 'clustering', 'dense', 'HSS', 'kernel', 'misc', 'python', 'sparse']] + + ['lib'], +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/s/SURVIVOR/SURVIVOR-1.0.7-20231201-GCC-13.3.0.eb b/easybuild/easyconfigs/s/SURVIVOR/SURVIVOR-1.0.7-20231201-GCC-13.3.0.eb new file mode 100644 index 00000000000..072cc459dd8 --- /dev/null +++ b/easybuild/easyconfigs/s/SURVIVOR/SURVIVOR-1.0.7-20231201-GCC-13.3.0.eb @@ -0,0 +1,29 @@ +easyblock = 'MakeCp' + +name = 'SURVIVOR' +local_commit = 'd613ec5' +version = '1.0.7-20231201' + +homepage = 'https://github.com/fritzsedlazeck/SURVIVOR' +description = "Toolset for SV simulation, comparison and filtering" + +toolchain = {'name': 'GCC', 'version': '13.3.0'} + +github_account = 'fritzsedlazeck' +source_urls = [GITHUB_SOURCE] +sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}] +checksums = ['848733bcccb3b485eea95d649a8cbaa2ac1b82d180020340121f71125b543861'] + +start_dir = 'Debug' +files_to_copy = ['Debug/%(name)s'] + +sanity_check_paths = { + 'files': ['%(name)s'], + 'dirs': [], +} + +sanity_check_commands = ['%(name)s'] + +modextrapaths = {'PATH': ''} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SVDSS2/SVDSS2-2.0.0-alpha.3-GCC-12.3.0.eb b/easybuild/easyconfigs/s/SVDSS2/SVDSS2-2.0.0-alpha.3-GCC-12.3.0.eb new file mode 100644 index 00000000000..404f2ce58f3 --- /dev/null +++ b/easybuild/easyconfigs/s/SVDSS2/SVDSS2-2.0.0-alpha.3-GCC-12.3.0.eb @@ -0,0 +1,56 @@ +easyblock = 'CMakeMakeCp' + +name = 'SVDSS2' +version = '2.0.0-alpha.3' + +homepage = 'https://github.com/Parsoa/SVDSS' +description = "Improved structural variant discovery in accurate long reads using sample-specific strings (SFS)." + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +sources = [{ + 'filename': 'v%(version)s.tar.gz', + 'git_config': { + 'url': 'https://github.com/Parsoa', + 'repo_name': 'SVDSS', + 'tag': 'v%(version)s', + 'recursive': True, + 'keep_git_dir': True, + } +}] +checksums = [None] + +builddependencies = [ + ('CMake', '3.26.3'), + ('make', '4.4.1'), + ('Autotools', '20220317'), + ('zlib', '1.2.13'), + ('bzip2', '1.0.8'), + ('XZ', '5.4.2'), + ('SAMtools', '1.18'), + ('BCFtools', '1.18'), +] +dependencies = [ + ('HTSlib', '1.18'), + ('libdeflate', '1.18'), + ('parasail', '2.6.2'), + ('spdlog', '1.11.0'), +] + +files_to_copy = [ + (['SVDSS'], 'bin'), + (['*'], 'lib'), +] + +separate_build_dir = False + +postinstallcmds = ["cd %(installdir)s/lib && rm SVDSS"] + +sanity_check_paths = { + 'files': ['bin/SVDSS'], + 'dirs': ['lib'], +} + +sanity_check_commands = ['SVDSS --version'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SWIG/SWIG-4.2.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/s/SWIG/SWIG-4.2.1-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..4e73a2c53c9 --- /dev/null +++ b/easybuild/easyconfigs/s/SWIG/SWIG-4.2.1-GCCcore-13.3.0.eb @@ -0,0 +1,27 @@ +name = 'SWIG' +version = '4.2.1' + +homepage = 'http://www.swig.org/' +description = """SWIG is a software development tool that connects programs written in C and C++ with + a variety of high-level programming languages.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['fa045354e2d048b2cddc69579e4256245d4676894858fcf0bab2290ecf59b7d8'] + +builddependencies = [ + ('binutils', '2.42'), + ('Bison', '3.8.2'), +] + +dependencies = [ + ('zlib', '1.3.1'), + ('PCRE2', '10.43'), +] + +configopts = '--without-alllang --with-boost=no' + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/s/SYMMETRICA/SYMMETRICA-2.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/s/SYMMETRICA/SYMMETRICA-2.0-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..9381f0a71c8 --- /dev/null +++ b/easybuild/easyconfigs/s/SYMMETRICA/SYMMETRICA-2.0-GCCcore-13.2.0.eb @@ -0,0 +1,43 @@ +easyblock = 'MakeCp' + +name = 'SYMMETRICA' +version = '2.0' + +homepage = 'https://www.algorithm.uni-bayreuth.de/en/research/SYMMETRICA' +description = "Symmetrica is a Collection of C routines for representation theory." + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} +toolchainopts = {'pic': True} + +source_urls = [homepage] +sources = [{'download_filename': 'SYM2_0_tar.gz', 'filename': SOURCE_TAR_GZ}] +patches = ['SYMMETRICA-2.0_makefile.patch'] +checksums = [ + {'SYMMETRICA-2.0.tar.gz': 'bf52788dedc14c482e89f5e7efe8c60864a633314ddd446dd4602d5fdaca0ee2'}, + {'SYMMETRICA-2.0_makefile.patch': 'd38a8935a3c1e7d9fbafd941e43f933b241fbe8bc012ef8b3a32610ab3be25df'}, +] + +builddependencies = [('binutils', '2.40')] + +local_sharedlib = 'libsymmetrica.%s' % SHLIB_EXT + +buildopts = 'test && $CC -shared $CFLAGS $LDFLAGS -o %s *.o' % local_sharedlib + +files_to_copy = [ + (['factorial'], 'bin'), + (['*.doc'], 'share/doc'), + ([local_sharedlib], 'lib'), + (['def.h', 'macro.h'], 'include/symmetrica'), +] + +sanity_check_paths = { + 'files': ['bin/factorial', + 'share/doc/intro.doc', + 'lib/%s' % local_sharedlib, + 'include/symmetrica/def.h', 'include/symmetrica/macro.h'], + 'dirs': [], +} + +sanity_check_commands = ["echo 5 | %(installdir)s/bin/factorial | grep 120"] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/Safetensors/Safetensors-0.4.3-gfbf-2023a.eb b/easybuild/easyconfigs/s/Safetensors/Safetensors-0.4.3-gfbf-2023a.eb new file mode 100644 index 00000000000..3c686b7380e --- /dev/null +++ b/easybuild/easyconfigs/s/Safetensors/Safetensors-0.4.3-gfbf-2023a.eb @@ -0,0 +1,295 @@ +easyblock = "CargoPythonBundle" + +name = 'Safetensors' +version = '0.4.3' +_rustver = '1.75.0' + +homepage = 'https://huggingface.co/docs/safetensors' +description = """Safetensors is a new simple format for storing tensors safely (as opposed to +pickle) and that is still fast (zero-copy). Safetensors is really fast. + +This variant of Safetensors is installed with support for numpy and PyTorch +""" + +toolchain = {'name': 'gfbf', 'version': '2023a'} + +builddependencies = [ + ('Rust', _rustver), + ('maturin', '1.4.0', '-Rust-' + _rustver), +] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), +] + +# crates generated on 2024-05-24 from directories savetensors/ and bindings/python/ +crates = [ + ('aho-corasick', '1.1.3'), + ('anes', '0.1.6'), + ('anstyle', '1.0.7'), + ('autocfg', '1.2.0'), + ('autocfg', '1.3.0'), + ('bitflags', '1.3.2'), + ('bitflags', '2.5.0'), + ('bit-set', '0.5.3'), + ('bit-vec', '0.6.3'), + ('bumpalo', '3.16.0'), + ('cast', '0.3.0'), + ('cfg-if', '1.0.0'), + ('ciborium', '0.2.2'), + ('ciborium-io', '0.2.2'), + ('ciborium-ll', '0.2.2'), + ('clap', '4.5.4'), + ('clap_builder', '4.5.2'), + ('clap_lex', '0.7.0'), + ('criterion', '0.5.1'), + ('criterion-plot', '0.5.0'), + ('crossbeam-deque', '0.8.5'), + ('crossbeam-epoch', '0.9.18'), + ('crossbeam-utils', '0.8.20'), + ('crunchy', '0.2.2'), + ('either', '1.12.0'), + ('errno', '0.3.9'), + ('fastrand', '2.1.0'), + ('fnv', '1.0.7'), + ('getrandom', '0.2.15'), + ('half', '2.4.1'), + ('heck', '0.4.1'), + ('hermit-abi', '0.3.9'), + ('indoc', '2.0.5'), + ('is-terminal', '0.4.12'), + ('itertools', '0.10.5'), + ('itoa', '1.0.11'), + ('js-sys', '0.3.69'), + ('lazy_static', '1.4.0'), + ('libc', '0.2.153'), + ('libc', '0.2.155'), + ('libm', '0.2.8'), + ('linux-raw-sys', '0.4.14'), + ('lock_api', '0.4.11'), + ('log', '0.4.21'), + ('memchr', '2.7.2'), + ('memmap2', '0.9.4'), + ('memoffset', '0.9.1'), + ('num-traits', '0.2.19'), + ('once_cell', '1.19.0'), + ('oorandom', '11.1.3'), + ('parking_lot', '0.12.1'), + ('parking_lot_core', '0.9.9'), + ('plotters', '0.3.6'), + ('plotters-backend', '0.3.6'), + ('plotters-svg', '0.3.6'), + ('portable-atomic', '1.6.0'), + ('ppv-lite86', '0.2.17'), + ('proc-macro2', '1.0.80'), + ('proc-macro2', '1.0.83'), + ('proptest', '1.4.0'), + ('pyo3', '0.21.1'), + ('pyo3-build-config', '0.21.1'), + ('pyo3-ffi', '0.21.1'), + ('pyo3-macros', '0.21.1'), + ('pyo3-macros-backend', '0.21.1'), + ('quick-error', '1.2.3'), + ('quote', '1.0.36'), + ('rand', '0.8.5'), + ('rand_chacha', '0.3.1'), + ('rand_core', '0.6.4'), + ('rand_xorshift', '0.3.0'), + ('rayon', '1.10.0'), + ('rayon-core', '1.12.1'), + ('redox_syscall', '0.4.1'), + ('regex', '1.10.4'), + ('regex-automata', '0.4.6'), + ('regex-syntax', '0.8.3'), + ('rustix', '0.38.34'), + ('rusty-fork', '0.3.0'), + ('ryu', '1.0.17'), + ('ryu', '1.0.18'), + ('same-file', '1.0.6'), + ('scopeguard', '1.2.0'), + ('serde', '1.0.197'), + ('serde', '1.0.202'), + ('serde_derive', '1.0.197'), + ('serde_derive', '1.0.202'), + ('serde_json', '1.0.115'), + ('serde_json', '1.0.117'), + ('smallvec', '1.13.2'), + ('syn', '2.0.59'), + ('syn', '2.0.66'), + ('target-lexicon', '0.12.14'), + ('tempfile', '3.10.1'), + ('tinytemplate', '1.2.1'), + ('unarray', '0.1.4'), + ('unicode-ident', '1.0.12'), + ('unindent', '0.2.3'), + ('wait-timeout', '0.2.0'), + ('walkdir', '2.5.0'), + ('wasi', '0.11.0+wasi-snapshot-preview1'), + ('wasm-bindgen', '0.2.92'), + ('wasm-bindgen-backend', '0.2.92'), + ('wasm-bindgen-macro', '0.2.92'), + ('wasm-bindgen-macro-support', '0.2.92'), + ('wasm-bindgen-shared', '0.2.92'), + ('web-sys', '0.3.69'), + ('winapi-util', '0.1.8'), + ('windows_aarch64_gnullvm', '0.48.5'), + ('windows_aarch64_gnullvm', '0.52.5'), + ('windows_aarch64_msvc', '0.48.5'), + ('windows_aarch64_msvc', '0.52.5'), + ('windows_i686_gnu', '0.48.5'), + ('windows_i686_gnu', '0.52.5'), + ('windows_i686_gnullvm', '0.52.5'), + ('windows_i686_msvc', '0.48.5'), + ('windows_i686_msvc', '0.52.5'), + ('windows-sys', '0.52.0'), + ('windows-targets', '0.48.5'), + ('windows-targets', '0.52.5'), + ('windows_x86_64_gnu', '0.48.5'), + ('windows_x86_64_gnu', '0.52.5'), + ('windows_x86_64_gnullvm', '0.48.5'), + ('windows_x86_64_gnullvm', '0.52.5'), + ('windows_x86_64_msvc', '0.48.5'), + ('windows_x86_64_msvc', '0.52.5'), +] + +checksums = [ + {'aho-corasick-1.1.3.tar.gz': '8e60d3430d3a69478ad0993f19238d2df97c507009a52b3c10addcd7f6bcb916'}, + {'anes-0.1.6.tar.gz': '4b46cbb362ab8752921c97e041f5e366ee6297bd428a31275b9fcf1e380f7299'}, + {'anstyle-1.0.7.tar.gz': '038dfcf04a5feb68e9c60b21c9625a54c2c0616e79b72b0fd87075a056ae1d1b'}, + {'autocfg-1.2.0.tar.gz': 'f1fdabc7756949593fe60f30ec81974b613357de856987752631dea1e3394c80'}, + {'autocfg-1.3.0.tar.gz': '0c4b4d0bd25bd0b74681c0ad21497610ce1b7c91b1022cd21c80c6fbdd9476b0'}, + {'bitflags-1.3.2.tar.gz': 'bef38d45163c2f1dde094a7dfd33ccf595c92905c8f8f4fdc18d06fb1037718a'}, + {'bitflags-2.5.0.tar.gz': 'cf4b9d6a944f767f8e5e0db018570623c85f3d925ac718db4e06d0187adb21c1'}, + {'bit-set-0.5.3.tar.gz': '0700ddab506f33b20a03b13996eccd309a48e5ff77d0d95926aa0210fb4e95f1'}, + {'bit-vec-0.6.3.tar.gz': '349f9b6a179ed607305526ca489b34ad0a41aed5f7980fa90eb03160b69598fb'}, + {'bumpalo-3.16.0.tar.gz': 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'282be5f36a8ce781fad8c8ae18fa3f9beff57ec1b52cb3de0789201425d9a33d'}, + {'windows-targets-0.48.5.tar.gz': '9a2fa6e2155d7247be68c096456083145c183cbbbc2764150dda45a87197940c'}, + {'windows-targets-0.52.5.tar.gz': '6f0713a46559409d202e70e28227288446bf7841d3211583a4b53e3f6d96e7eb'}, + {'windows_x86_64_gnu-0.48.5.tar.gz': '53d40abd2583d23e4718fddf1ebec84dbff8381c07cae67ff7768bbf19c6718e'}, + {'windows_x86_64_gnu-0.52.5.tar.gz': '4e4246f76bdeff09eb48875a0fd3e2af6aada79d409d33011886d3e1581517d9'}, + {'windows_x86_64_gnullvm-0.48.5.tar.gz': '0b7b52767868a23d5bab768e390dc5f5c55825b6d30b86c844ff2dc7414044cc'}, + {'windows_x86_64_gnullvm-0.52.5.tar.gz': '852298e482cd67c356ddd9570386e2862b5673c85bd5f88df9ab6802b334c596'}, + {'windows_x86_64_msvc-0.48.5.tar.gz': 'ed94fce61571a4006852b7389a063ab983c02eb1bb37b47f8272ce92d06d9538'}, + {'windows_x86_64_msvc-0.52.5.tar.gz': 'bec47e5bfd1bff0eeaf6d8b485cc1074891a197ab4225d504cb7a1ab88b02bf0'}, +] + +use_pip = True + +exts_list = [ + ('safetensors', version, { + 'checksums': ['2f85fc50c4e07a21e95c24e07460fe6f7e2859d0ce88092838352b798ce711c2'], + }), +] + +sanity_pip_check = True + +moduleclass = 'ai' diff --git a/easybuild/easyconfigs/s/Safetensors/Safetensors-0.4.4-gfbf-2023b.eb b/easybuild/easyconfigs/s/Safetensors/Safetensors-0.4.4-gfbf-2023b.eb new file mode 100644 index 00000000000..50ead1b54c1 --- /dev/null +++ b/easybuild/easyconfigs/s/Safetensors/Safetensors-0.4.4-gfbf-2023b.eb @@ -0,0 +1,153 @@ +easyblock = "CargoPythonBundle" + +name = 'Safetensors' +version = '0.4.4' +_rustver = '1.76.0' + +homepage = 'https://huggingface.co/docs/safetensors' +description = """Safetensors is a new simple format for storing tensors safely (as opposed to +pickle) and that is still fast (zero-copy). Safetensors is really fast. + +This variant of Safetensors is installed with support for numpy and PyTorch +""" + +toolchain = {'name': 'gfbf', 'version': '2023b'} + +builddependencies = [ + ('Rust', _rustver), + ('maturin', '1.5.0', '-Rust-' + _rustver), +] + +dependencies = [ + ('Python', '3.11.5'), + ('SciPy-bundle', '2023.11'), +] + +# crates generated on 2024-08-21 from directories savetensors/ and bindings/python/ +crates = [ + ('aho-corasick', '1.1.3'), + ('anes', '0.1.6'), + ('anstyle', '1.0.8'), + ('autocfg', '1.3.0'), + ('bit-set', '0.5.3'), + ('bit-vec', '0.6.3'), + ('bitflags', '2.6.0'), + ('bumpalo', '3.16.0'), + ('byteorder', '1.5.0'), + ('cast', '0.3.0'), + ('cfg-if', '1.0.0'), + ('ciborium', '0.2.2'), + ('ciborium-io', '0.2.2'), + ('ciborium-ll', '0.2.2'), + ('clap', '4.5.16'), + ('clap_builder', '4.5.15'), + ('clap_lex', '0.7.2'), + ('criterion', '0.5.1'), + ('criterion-plot', '0.5.0'), + ('crossbeam-deque', '0.8.5'), + ('crossbeam-epoch', '0.9.18'), + ('crossbeam-utils', '0.8.20'), + ('crunchy', '0.2.2'), + ('either', '1.13.0'), + ('errno', '0.3.9'), + ('fastrand', '2.1.0'), + ('fnv', '1.0.7'), + ('getrandom', '0.2.15'), + ('half', '2.4.1'), + ('heck', '0.5.0'), + ('hermit-abi', '0.4.0'), + ('indoc', '2.0.5'), + ('is-terminal', '0.4.13'), + ('itertools', '0.10.5'), + ('itoa', '1.0.11'), + ('js-sys', '0.3.70'), + ('lazy_static', '1.5.0'), + ('libc', '0.2.155'), + ('libc', '0.2.158'), + ('libm', '0.2.8'), + ('linux-raw-sys', '0.4.14'), + ('log', '0.4.22'), + ('memchr', '2.7.4'), + ('memmap2', '0.9.4'), + ('memoffset', '0.9.1'), + ('num-traits', '0.2.19'), + ('once_cell', '1.19.0'), + ('oorandom', '11.1.4'), + ('plotters', '0.3.6'), + ('plotters-backend', '0.3.6'), + ('plotters-svg', '0.3.6'), + ('portable-atomic', '1.7.0'), + ('ppv-lite86', '0.2.20'), + ('proc-macro2', '1.0.86'), + ('proptest', '1.5.0'), + ('pyo3', '0.22.2'), + ('pyo3-build-config', '0.22.2'), + ('pyo3-ffi', '0.22.2'), + ('pyo3-macros', '0.22.2'), + ('pyo3-macros-backend', '0.22.2'), + ('quick-error', '1.2.3'), + ('quote', '1.0.36'), + ('rand', '0.8.5'), + ('rand_chacha', '0.3.1'), + ('rand_core', '0.6.4'), + ('rand_xorshift', '0.3.0'), + ('rayon', '1.10.0'), + ('rayon-core', '1.12.1'), + ('regex', '1.10.6'), + ('regex-automata', '0.4.7'), + ('regex-syntax', '0.8.4'), + ('rustix', '0.38.34'), + ('rusty-fork', '0.3.0'), + ('ryu', '1.0.18'), + ('same-file', '1.0.6'), + ('serde', '1.0.204'), + ('serde', '1.0.208'), + ('serde_derive', '1.0.204'), + ('serde_derive', '1.0.208'), + ('serde_json', '1.0.122'), + ('serde_json', '1.0.125'), + ('syn', '2.0.72'), + ('syn', '2.0.75'), + ('target-lexicon', '0.12.16'), + ('tempfile', '3.12.0'), + ('tinytemplate', '1.2.1'), + ('unarray', '0.1.4'), + ('unicode-ident', '1.0.12'), + ('unindent', '0.2.3'), + ('wait-timeout', '0.2.0'), + ('walkdir', '2.5.0'), + ('wasi', '0.11.0+wasi-snapshot-preview1'), + ('wasm-bindgen', '0.2.93'), + ('wasm-bindgen-backend', '0.2.93'), + ('wasm-bindgen-macro', '0.2.93'), + ('wasm-bindgen-macro-support', '0.2.93'), + ('wasm-bindgen-shared', '0.2.93'), + ('web-sys', '0.3.70'), + ('winapi-util', '0.1.9'), + ('windows-sys', '0.52.0'), + ('windows-sys', '0.59.0'), + ('windows-targets', '0.52.6'), + ('windows_aarch64_gnullvm', '0.52.6'), + ('windows_aarch64_msvc', '0.52.6'), + ('windows_i686_gnu', '0.52.6'), + ('windows_i686_gnullvm', '0.52.6'), + ('windows_i686_msvc', '0.52.6'), + ('windows_x86_64_gnu', '0.52.6'), + ('windows_x86_64_gnullvm', '0.52.6'), + ('windows_x86_64_msvc', '0.52.6'), + ('zerocopy', '0.7.35'), + ('zerocopy-derive', '0.7.35'), +] + + +use_pip = True + +exts_list = [ + ('safetensors', version, { + 'checksums': ['5fe3e9b705250d0172ed4e100a811543108653fb2b66b9e702a088ad03772a07'], + }), +] + +sanity_pip_check = True + +moduleclass = 'ai' diff --git a/easybuild/easyconfigs/s/Sagemath/Sagemath-10.4-foss-2023b.eb b/easybuild/easyconfigs/s/Sagemath/Sagemath-10.4-foss-2023b.eb new file mode 100644 index 00000000000..dcc9d919c13 --- /dev/null +++ b/easybuild/easyconfigs/s/Sagemath/Sagemath-10.4-foss-2023b.eb @@ -0,0 +1,158 @@ +easyblock = 'PythonBundle' + +name = 'Sagemath' +version = '10.4' + +homepage = 'https://doc.sagemath.org/html/en/index.html' +description = """Sage is open source mathematical software released under the GNU General Public Licence GPLv2+, + and includes packages that have compatible software licenses. + People all around the globe have contributed to the development of Sage. Full documentation is available online.""" + +toolchain = {'name': 'foss', 'version': '2023b'} + +builddependencies = [ + ('Cython', '3.0.10'), + ('Python-bundle-PyPI', '2023.10'), + ('Boost', '1.83.0'), +] + +dependencies = [ + ('Python', '3.11.5'), + ('SciPy-bundle', '2023.11'), + ('ECL', '24.5.10'), + ('FFLAS-FFPACK', '2.5.0'), + ('eclib', '20240408'), + ('GSL', '2.7'), + ('LinBox', '1.7.0'), + ('Singular', '4.4.0'), + ('libpng', '1.6.40'), + ('libgd', '2.3.3'), + ('m4ri', '20200125'), + ('cysignals', '1.11.4'), + ('gmpy2', '2.1.5'), + ('GMP-ECM', '7.0.5'), + ('MPFI', '1.5.4'), + ('cliquer', '1.21'), + ('nauty', '2.8.8'), + ('SYMMETRICA', '2.0'), + ('lcalc', '2.0.5'), + ('gap', '4.13.0'), + ('giac', '1.9.0-99'), + ('m4rie', '20200125'), + ('libhomfly', '1.02r6'), + ('libbraiding', '1.2'), + ('planarity', '3.0.2.0'), + ('rankwidth', '0.9'), + ('BRiAl', '1.2.12'), + ('bliss', '0.77'), + ('coxeter', '20180226'), + ('mcqd', '1.0.0'), + ('SharedMeatAxe', '1.0.1'), + ('sirocco', '2.1.0'), + ('tdlib', '0.9.3'), + ('pkgconfig', '1.5.5', '-python'), + ('matplotlib', '3.8.2'), + ('networkx', '3.2.1'), + ('sympy', '1.12'), + ('IPython', '8.17.2'), + ('Pillow', '10.2.0'), + ('fpylll', '0.6.1'), + ('primecountpy', '0.1.0'), + ('lrcalc', '2.1'), + ('PyZMQ', '25.1.2'), + ('tornado', '6.4'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('cypari2', '2.2.0', { + 'checksums': ['817606bf661b71d33e1d012421907a4f8fb09dd81b7d3e3ae179b3978020bbf1'], + }), + ('memory_allocator', '0.1.4', { + 'checksums': ['d609216b03031967e2b45a804b12ff9029578f4ec019fde42cf6aed6ca09efe4'], + }), + ('sage_setup', version, { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['4797ceae2f5f636a756f4121011246445611f7a56bced2df431328fe013c52c7'], + }), + ('conway_polynomials', '0.10', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['a354b4ac0a9985da75e2ac6ec6d7de2902396eff48913eeed86a962486171c28'], + }), + ('comm', '0.2.2', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['e6fb86cb70ff661ee8c9c14e7d36d6de3b4066f1441be4063df9c5009f0a64d3'], + }), + ('debugpy', '1.8.5', { + 'source_tmpl': SOURCE_WHL, + 'checksums': ['55919dce65b471eff25901acf82d328bbd5b833526b6c1364bd5133754777a44'], + }), + ('nest_asyncio', '1.6.0', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['87af6efd6b5e897c81050477ef65c62e2b2f35d51703cae01aff2905b1852e1c'], + }), + ('ipykernel', '6.29.5', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['afdb66ba5aa354b09b91379bac28ae4afebbb30e8b39510c9690afb7a10421b5'], + }), + ('jupyterlab_widgets', '3.0.13', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['e3cda2c233ce144192f1e29914ad522b2f4c40e77214b0cc97377ca3d323db54'], + }), + ('widgetsnbextension', '4.0.13', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['74b2692e8500525cc38c2b877236ba51d34541e6385eeed5aec15a70f88a6c71'], + }), + ('ipywidgets', '8.1.5', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['3290f526f87ae6e77655555baba4f36681c555b8bdbbff430b70e52c34c86245'], + }), + ('jupyter_core', '5.7.2', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['4f7315d2f6b4bcf2e3e7cb6e46772eba760ae459cd1f59d29eb57b0a01bd7409'], + }), + ('jupyter_client', '8.6.2', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['50cbc5c66fd1b8f65ecb66bc490ab73217993632809b6e505687de18e9dea39f'], + }), + ('lrcalc', '2.1', { + 'checksums': ['e3a0509aeda487b412b391a52e817ca36b5c063a8305e09fd54d53259dd6aaa9'], + }), + ('%(namelower)s_standard', version, { + 'modulename': 'sage', + 'checksums': ['f6579e85f33bd9bb6e9b991bfc4c49dab1e649858ed9ee41c7cec75cb92d4c62'], + }), + ('%(namelower)s_bliss', version, { + 'modulename': False, + 'checksums': ['70cccef849908436c2f9f1aabb3992a21c90d3ce99d1a965743f0fdec3735d32'], + }), + ('%(namelower)s_coxeter3', version, { + 'modulename': False, + 'checksums': ['c4f20204b91a696caeb7ad7cf33d2b0398d26d287085b2cb9434e8b067716fca'], + }), + ('%(namelower)s_mcqd', version, { + 'modulename': False, + 'checksums': ['6a140d8b3866ea27aa5966f3aab86a882785862fb00ae37087beb09105b94175'], + }), + ('%(namelower)s_meataxe', version, { + 'modulename': False, + 'checksums': ['5b625333c3168fc2ab55d32ad7e8c41912858bde8010b5aadc70c6450fa967e8'], + }), + ('%(namelower)s_sirocco', version, { + 'modulename': False, + 'checksums': ['499304b3331751d7b0f62de8379afb073d55f144c5f73775da0c5b92160e3a7c'], + }), + ('%(namelower)s_tdlib', version, { + 'modulename': False, + 'checksums': ['018497a1e220d3320a37d1acb3eee59ec820d167c7916e95f0508709a2e31703'], + }), +] + +sanity_check_commands = [ + "sage --help", + "python -c 'from sage.all import *'", +] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/Salmon/Salmon-1.10.3-GCC-12.3.0.eb b/easybuild/easyconfigs/s/Salmon/Salmon-1.10.3-GCC-12.3.0.eb new file mode 100644 index 00000000000..9b52051eed3 --- /dev/null +++ b/easybuild/easyconfigs/s/Salmon/Salmon-1.10.3-GCC-12.3.0.eb @@ -0,0 +1,59 @@ +# # +# This is a contribution from DeepThought HPC Service, Flinders University, Adelaide, Australia +# Homepage: https://staff.flinders.edu.au/research/deep-thought +# +# Authors:: Robert Qiao +# License:: GLPv2 +# +# Notes:: +# # +# Contribution from the NIHR Biomedical Research Centre +# Guy's and St Thomas' NHS Foundation Trust and King's College London +# uploaded by J. Sassmannshausen +# Thanks to people like Simon Brandord, Mikael Oehmann and Kenneth Hoste +# for their help with the ICE + +easyblock = 'CMakeMake' + +name = 'Salmon' +version = '1.10.3' + +homepage = 'https://github.com/COMBINE-lab/salmon' +description = """Salmon is a wicked-fast program to produce a highly-accurate, + transcript-level quantification estimate from RNA-seq data.""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/COMBINE-lab/salmon/archive'] +sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}] +checksums = ['a053fba63598efc4ade3684aa2c8e8e2294186927d4fcdf1041c36edc2aa0871'] + +builddependencies = [ + ('CMake', '3.26.3'), + ('pkgconf', '1.9.5'), + ('jemalloc', '5.3.0'), + ('Cereal', '1.3.2', '', SYSTEM), +] +dependencies = [ + ('Boost', '1.82.0'), + ('tbb', '2021.11.0'), + ('cURL', '8.0.1'), + ('libiconv', '1.17'), + ('bzip2', '1.0.8'), + ('XZ', '5.4.2'), + ('zlib', '1.2.13'), +] + +configopts = "-DJEMALLOC_ROOT=$EBROOTJEMALLOC" + +runtest = 'test' + +sanity_check_paths = { + 'files': ['bin/%(namelower)s', 'lib/libgraphdump.a', 'lib/libntcard.a', 'lib/libsalmon_core.a', 'lib/libtwopaco.a'], + 'dirs': [], +} + +sanity_check_commands = ['%(namelower)s --help'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/Satsuma2/Satsuma2-20220304-GCC-11.3.0.eb b/easybuild/easyconfigs/s/Satsuma2/Satsuma2-20220304-GCC-11.3.0.eb index e709378f6ea..304dbf50669 100644 --- a/easybuild/easyconfigs/s/Satsuma2/Satsuma2-20220304-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/s/Satsuma2/Satsuma2-20220304-GCC-11.3.0.eb @@ -21,6 +21,12 @@ checksums = [ builddependencies = [('CMake', '3.23.1')] +# Define SATSUMA2_PATH as per: +# https://github.com/bioinfologics/satsuma2/blob/37c5f386819614cd3ce96016b423ddc4df1d86ec/README.md#running-satsuma2 +modextravars = { + 'SATSUMA2_PATH': '%(installdir)s/bin', +} + sanity_check_paths = { 'files': ['bin/ChromosomePaint', 'bin/MatchDump', 'bin/SatsumaSynteny2'], 'dirs': [], diff --git a/easybuild/easyconfigs/s/ScaFaCoS/ScaFaCoS-1.0.4-foss-2023b.eb b/easybuild/easyconfigs/s/ScaFaCoS/ScaFaCoS-1.0.4-foss-2023b.eb new file mode 100644 index 00000000000..d724f5b9015 --- /dev/null +++ b/easybuild/easyconfigs/s/ScaFaCoS/ScaFaCoS-1.0.4-foss-2023b.eb @@ -0,0 +1,43 @@ +easyblock = 'ConfigureMake' + +name = 'ScaFaCoS' +version = '1.0.4' + +homepage = 'http://www.scafacos.de/' +description = """ScaFaCoS is a library of scalable fast coulomb solvers.""" + +toolchain = {'name': 'foss', 'version': '2023b'} +toolchainopts = {'usempi': True} + +source_urls = ['https://github.com/%(namelower)s/%(namelower)s/releases/download/v%(version)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = [ + '6634c4202e825e771d1dd75bbe9cac5cee41136c87653fde98fbd634681c1be6', # scafacos-1.0.1.tar.gz +] + +builddependencies = [ + ('Autotools', '20220317'), + ('pkgconf', '2.0.3'), +] + +dependencies = [ + ('GMP', '6.3.0'), + ('GSL', '2.7'), +] + +preconfigopts = 'unset F77 && ' + +configopts = 'FCFLAGS="-fallow-argument-mismatch $FCFLAGS" ' +configopts += '--enable-shared --enable-static --disable-doc ' +# tell it where to find provided FFTW +configopts += '--without-internal-fftw --with-fftw3-includedir=$EBROOTFFTW/include --with-fftw3-libdir=$EBROOTFFTW/lib ' +# only include the solvers supported for LAMMPS +# (for p2nfft we need an additonal dependency) +configopts += '--enable-fcs-solvers=direct,ewald,fmm,p3m ' + +sanity_check_paths = { + 'files': ['lib/libfcs.a', 'include/fcs.h', 'include/fcs_module.mod'], + 'dirs': [], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.2.0-gmpich-2024.06-fb.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.2.0-gmpich-2024.06-fb.eb new file mode 100644 index 00000000000..28d4f766d52 --- /dev/null +++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.2.0-gmpich-2024.06-fb.eb @@ -0,0 +1,40 @@ +name = 'ScaLAPACK' +version = '2.2.0' +versionsuffix = '-fb' + +homepage = 'https://www.netlib.org/scalapack/' +description = """The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines + redesigned for distributed memory MIMD parallel computers.""" + +toolchain = {'name': 'gmpich', 'version': '2024.06'} +toolchainopts = {'extra_fflags': '-lpthread', 'openmp': True, 'pic': True, 'usempi': True} + +source_urls = [homepage] +sources = [SOURCELOWER_TGZ] +patches = ['ScaLAPACK-%(version)s_fix-GCC-10.patch'] +checksums = [ + '40b9406c20735a9a3009d863318cb8d3e496fb073d201c5463df810e01ab2a57', # scalapack-2.2.0.tgz + 'f6bc3c6dee012ba4a696548a2e12b6aae932ce4fd5a142153b338839f52b5906', # ScaLAPACK-2.2.0_fix-GCC-10.patch +] + +builddependencies = [ + ('CMake', '3.26.3'), +] + +dependencies = [ + ('FlexiBLAS', '3.3.1'), +] + +# Config Opts based on AOCL User Guide: +# https://developer.amd.com/wp-content/resources/AOCL_User%20Guide_2.2.pdf + +configopts = '-DBUILD_SHARED_LIBS=ON ' +configopts += '-DBLAS_LIBRARIES="$EBROOTFLEXIBLAS/lib/libflexiblas.%s" ' % SHLIB_EXT +configopts += '-DLAPACK_LIBRARIES="$EBROOTFLEXIBLAS/lib/libflexiblas.%s" ' % SHLIB_EXT + +sanity_check_paths = { + 'files': ['lib/libscalapack.%s' % SHLIB_EXT, 'lib64/libscalapack.%s' % SHLIB_EXT], + 'dirs': ["lib", "lib64"], +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.2.0-gompi-2024.05-fb.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.2.0-gompi-2024.05-fb.eb new file mode 100644 index 00000000000..4bdfa045feb --- /dev/null +++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.2.0-gompi-2024.05-fb.eb @@ -0,0 +1,40 @@ +name = 'ScaLAPACK' +version = '2.2.0' +versionsuffix = '-fb' + +homepage = 'https://www.netlib.org/scalapack/' +description = """The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines + redesigned for distributed memory MIMD parallel computers.""" + +toolchain = {'name': 'gompi', 'version': '2024.05'} +toolchainopts = {'extra_fflags': '-lpthread', 'openmp': True, 'pic': True, 'usempi': True} + +source_urls = [homepage] +sources = [SOURCELOWER_TGZ] +patches = ['ScaLAPACK-%(version)s_fix-GCC-10.patch'] +checksums = [ + '40b9406c20735a9a3009d863318cb8d3e496fb073d201c5463df810e01ab2a57', # scalapack-2.2.0.tgz + 'f6bc3c6dee012ba4a696548a2e12b6aae932ce4fd5a142153b338839f52b5906', # ScaLAPACK-2.2.0_fix-GCC-10.patch +] + +builddependencies = [ + ('CMake', '3.29.3'), +] + +dependencies = [ + ('FlexiBLAS', '3.4.4'), +] + +# Config Opts based on AOCL User Guide: +# https://developer.amd.com/wp-content/resources/AOCL_User%20Guide_2.2.pdf + +configopts = '-DBUILD_SHARED_LIBS=ON ' +configopts += '-DBLAS_LIBRARIES="$EBROOTFLEXIBLAS/lib/libflexiblas.%s" ' % SHLIB_EXT +configopts += '-DLAPACK_LIBRARIES="$EBROOTFLEXIBLAS/lib/libflexiblas.%s" ' % SHLIB_EXT + +sanity_check_paths = { + 'files': ['lib/libscalapack.%s' % SHLIB_EXT, 'lib64/libscalapack.%s' % SHLIB_EXT], + 'dirs': ["lib", "lib64"], +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.2.0-gompi-2024a-fb.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.2.0-gompi-2024a-fb.eb new file mode 100644 index 00000000000..1bccc16f38b --- /dev/null +++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.2.0-gompi-2024a-fb.eb @@ -0,0 +1,40 @@ +name = 'ScaLAPACK' +version = '2.2.0' +versionsuffix = '-fb' + +homepage = 'https://www.netlib.org/scalapack/' +description = """The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines + redesigned for distributed memory MIMD parallel computers.""" + +toolchain = {'name': 'gompi', 'version': '2024a'} +toolchainopts = {'extra_fflags': '-lpthread', 'openmp': True, 'pic': True, 'usempi': True} + +source_urls = [homepage] +sources = [SOURCELOWER_TGZ] +patches = ['ScaLAPACK-%(version)s_fix-GCC-10.patch'] +checksums = [ + '40b9406c20735a9a3009d863318cb8d3e496fb073d201c5463df810e01ab2a57', # scalapack-2.2.0.tgz + 'f6bc3c6dee012ba4a696548a2e12b6aae932ce4fd5a142153b338839f52b5906', # ScaLAPACK-2.2.0_fix-GCC-10.patch +] + +builddependencies = [ + ('CMake', '3.29.3'), +] + +dependencies = [ + ('FlexiBLAS', '3.4.4'), +] + +# Config Opts based on AOCL User Guide: +# https://developer.amd.com/wp-content/resources/AOCL_User%20Guide_2.2.pdf + +configopts = '-DBUILD_SHARED_LIBS=ON ' +configopts += '-DBLAS_LIBRARIES="$EBROOTFLEXIBLAS/lib/libflexiblas.%s" ' % SHLIB_EXT +configopts += '-DLAPACK_LIBRARIES="$EBROOTFLEXIBLAS/lib/libflexiblas.%s" ' % SHLIB_EXT + +sanity_check_paths = { + 'files': ['lib/libscalapack.%s' % SHLIB_EXT, 'lib64/libscalapack.%s' % SHLIB_EXT], + 'dirs': ["lib", "lib64"], +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/s/SciANN/SciANN-0.7.0.1-foss-2022a.eb b/easybuild/easyconfigs/s/SciANN/SciANN-0.7.0.1-foss-2022a.eb new file mode 100644 index 00000000000..9b14f9ce1be --- /dev/null +++ b/easybuild/easyconfigs/s/SciANN/SciANN-0.7.0.1-foss-2022a.eb @@ -0,0 +1,37 @@ +easyblock = 'PythonBundle' + +name = 'SciANN' +version = '0.7.0.1' + +homepage = 'https://github.com/ehsanhaghighat/sciann' +description = """ +A Keras/Tensorflow wrapper for scientific computations and physics-informed deep learning +using artificial neural networks. +""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('PyYAML', '6.0'), + ('h5py', '3.7.0'), + ('scikit-learn', '1.1.2'), + ('TensorFlow', '2.11.0'), + ('pymatgen', '2023.3.10'), # for pybtex and latexcodec + ('matplotlib', '3.5.2'), + ('pygraphviz', '1.10'), + ('pydot', '1.4.2'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + (name, version, { + 'modulename': 'sciann', + 'checksums': ['7d7acf61346b4201628c5656e2c904e9a9c7cda78086e76d075b5c7bb90adf3c'], + }), +] + +moduleclass = 'ai' diff --git a/easybuild/easyconfigs/s/SciKeras/SciKeras-0.12.0-foss-2022a.eb b/easybuild/easyconfigs/s/SciKeras/SciKeras-0.12.0-foss-2022a.eb new file mode 100644 index 00000000000..7ef8def71d7 --- /dev/null +++ b/easybuild/easyconfigs/s/SciKeras/SciKeras-0.12.0-foss-2022a.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonBundle' + +name = 'SciKeras' +version = '0.12.0' + +homepage = 'https://adriangb.com/scikeras' +description = """ +Scikit-Learn API wrapper for Keras. The goal of scikeras is to make it possible to use +Keras/TensorFlow with sklearn. This is achieved by providing a wrapper around Keras that has +an Scikit-Learn interface. +""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('scikit-learn', '1.1.2'), + ('TensorFlow', '2.11.0'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('scikeras', version, { + 'checksums': ['f60d81255a8904671bd33cbff060926cfa5ddd52fa234b12290afe3cb69dcc6c'], + }), +] + +moduleclass = 'ai' diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2021.05-foss-2021a.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2021.05-foss-2021a.eb index 2c0770da7e9..8d80f74fa66 100644 --- a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2021.05-foss-2021a.eb +++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2021.05-foss-2021a.eb @@ -23,12 +23,15 @@ exts_list = [ ('numpy', '1.20.3', { 'sources': [SOURCE_ZIP], 'patches': [ + 'numpy-1.20.3_fix-fortran-compiler-error.patch', 'numpy-1.20.3_skip-ppc-long-complex-test.patch', 'numpy-1.20.3_xfail-test-nan.patch', 'numpy-1.20.3_fix-target-test-ccompiler-opt.patch', ], 'checksums': [ 'e55185e51b18d788e49fe8305fd73ef4470596b33fc2c1ceb304566b99c71a69', # numpy-1.20.3.zip + {'numpy-1.20.3_fix-fortran-compiler-error.patch': + '016e0d02ffabe013248c4fd203a4456edee76839f747c05daf92ac1fe9925189'}, # numpy-1.20.3_skip-ppc-long-complex-test.patch '2f9a12e3a352b39076db84a7622fc8f4796abd3cb7f97f71958a495e864659a4', 'f0ce961f7d79551598e23050d92f46e827e300f6a7e5a6112e58efcc10385d4d', # numpy-1.20.3_xfail-test-nan.patch diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2021.05-gomkl-2021a.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2021.05-gomkl-2021a.eb index 3f0596710cc..21890734ddf 100644 --- a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2021.05-gomkl-2021a.eb +++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2021.05-gomkl-2021a.eb @@ -25,6 +25,7 @@ exts_list = [ 'numpy-1.18.2-mkl.patch', 'numpy-1.20.3_disable-broken-override-test.patch', 'numpy-1.20.3_fix-cpu-feature-detection-intel-compilers.patch', + 'numpy-1.20.3_fix-fortran-compiler-error.patch', 'numpy-1.20.3_fix-target-test-ccompiler-opt.patch', 'numpy-1.20.3_disable_fortran_callback_test.patch', ], @@ -36,6 +37,8 @@ exts_list = [ '43cc2e675c52db1776efcc6c84ebd5fc008b48e6355c81087420d5e790e4af9b', # numpy-1.20.3_fix-cpu-feature-detection-intel-compilers.patch '4c0b194c9d2e2c6b9798ebc271d4517f4c3cdbf2b3cbd68de16c7d4b068bb046', + {'numpy-1.20.3_fix-fortran-compiler-error.patch': + '016e0d02ffabe013248c4fd203a4456edee76839f747c05daf92ac1fe9925189'}, # numpy-1.20.3_fix-target-test-ccompiler-opt.patch '3d84e8b7d48387778974a5f6ae342a690ab5989547206b6add9d9667f8d7572a', # numpy-1.20.3_disable_fortran_callback_test.patch diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2021.05-intel-2021a.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2021.05-intel-2021a.eb index 3deadeac9d6..730ac590d33 100644 --- a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2021.05-intel-2021a.eb +++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2021.05-intel-2021a.eb @@ -25,6 +25,7 @@ exts_list = [ 'numpy-1.18.2-mkl.patch', 'numpy-1.20.3_disable-broken-override-test.patch', 'numpy-1.20.3_fix-cpu-feature-detection-intel-compilers.patch', + 'numpy-1.20.3_fix-fortran-compiler-error.patch', 'numpy-1.20.3_fix-target-test-ccompiler-opt.patch', 'numpy-1.20.3_disable_fortran_callback_test.patch', ], @@ -36,6 +37,8 @@ exts_list = [ '43cc2e675c52db1776efcc6c84ebd5fc008b48e6355c81087420d5e790e4af9b', # numpy-1.20.3_fix-cpu-feature-detection-intel-compilers.patch '4c0b194c9d2e2c6b9798ebc271d4517f4c3cdbf2b3cbd68de16c7d4b068bb046', + {'numpy-1.20.3_fix-fortran-compiler-error.patch': + '016e0d02ffabe013248c4fd203a4456edee76839f747c05daf92ac1fe9925189'}, # numpy-1.20.3_fix-target-test-ccompiler-opt.patch '3d84e8b7d48387778974a5f6ae342a690ab5989547206b6add9d9667f8d7572a', # numpy-1.20.3_disable_fortran_callback_test.patch diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2021.10-foss-2021b-Python-2.7.18.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2021.10-foss-2021b-Python-2.7.18.eb index f806bd48d7a..1bd36b39378 100644 --- a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2021.10-foss-2021b-Python-2.7.18.eb +++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2021.10-foss-2021b-Python-2.7.18.eb @@ -29,6 +29,7 @@ exts_list = [ 'numpy-1.16.2_relax-long-complex-test.patch', 'numpy-1.16.6_add_flexiblas_detection.patch', 'numpy-1.16.6_handle_failing_linalg_test.patch', + 'numpy-1.20.3_fix-fortran-compiler-error.patch', ], 'sources': ['%(name)s-%(version)s.zip'], 'checksums': [ @@ -39,6 +40,8 @@ exts_list = [ '32ca32dd7ee8d6fcdce5875067acd50970c731cbb2603c6d1ad84ff81ff8c6d5', # numpy-1.16.6_handle_failing_linalg_test.patch 'be9dce98649626b7322ed8d1241b74a4e28c1d1de070a8072dc912cad3eb143d', + {'numpy-1.20.3_fix-fortran-compiler-error.patch': + '016e0d02ffabe013248c4fd203a4456edee76839f747c05daf92ac1fe9925189'}, ], }), ('ply', '3.11', { diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2021.10-foss-2021b.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2021.10-foss-2021b.eb index 46f9647ad26..3e1d85982cc 100644 --- a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2021.10-foss-2021b.eb +++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2021.10-foss-2021b.eb @@ -25,9 +25,14 @@ use_pip = True exts_list = [ ('numpy', '1.21.3', { 'sources': ['%(name)s-%(version)s.zip'], - 'patches': ['numpy-1.20.3_skip-ppc-long-complex-test.patch'], + 'patches': [ + 'numpy-1.20.3_fix-fortran-compiler-error.patch', + 'numpy-1.20.3_skip-ppc-long-complex-test.patch', + ], 'checksums': [ '63571bb7897a584ca3249c86dd01c10bcb5fe4296e3568b2e9c1a55356b6410e', # numpy-1.21.3.zip + {'numpy-1.20.3_fix-fortran-compiler-error.patch': + '016e0d02ffabe013248c4fd203a4456edee76839f747c05daf92ac1fe9925189'}, # numpy-1.20.3_skip-ppc-long-complex-test.patch '2f9a12e3a352b39076db84a7622fc8f4796abd3cb7f97f71958a495e864659a4', ], diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2021.10-intel-2021b.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2021.10-intel-2021b.eb index 87a1dfe3175..68420c45219 100644 --- a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2021.10-intel-2021b.eb +++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2021.10-intel-2021b.eb @@ -29,6 +29,7 @@ exts_list = [ 'numpy-1.18.2-mkl.patch', 'numpy-1.20.3_disable-broken-override-test.patch', 'numpy-1.20.3_disable_fortran_callback_test.patch', + 'numpy-1.20.3_fix-fortran-compiler-error.patch', ], 'checksums': [ '63571bb7897a584ca3249c86dd01c10bcb5fe4296e3568b2e9c1a55356b6410e', # numpy-1.21.3.zip @@ -37,6 +38,8 @@ exts_list = [ '43cc2e675c52db1776efcc6c84ebd5fc008b48e6355c81087420d5e790e4af9b', # numpy-1.20.3_disable_fortran_callback_test.patch '44975a944544fd0e771b7e63c32590d257a3713070f8f7fdf60105dc516f1d75', + {'numpy-1.20.3_fix-fortran-compiler-error.patch': + '016e0d02ffabe013248c4fd203a4456edee76839f747c05daf92ac1fe9925189'}, ], }), ('ply', '3.11', { diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2022.05-foss-2022.05.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2022.05-foss-2022.05.eb index e07fdee1c03..613b1853e88 100644 --- a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2022.05-foss-2022.05.eb +++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2022.05-foss-2022.05.eb @@ -26,6 +26,7 @@ exts_list = [ ('numpy', '1.22.3', { 'patches': [ 'numpy-1.20.3_disable_fortran_callback_test.patch', + 'numpy-1.20.3_fix-fortran-compiler-error.patch', 'numpy-1.22.3_disable-broken-override-test.patch', ], 'sources': ['%(name)s-%(version)s.zip'], @@ -33,6 +34,8 @@ exts_list = [ 'dbc7601a3b7472d559dc7b933b18b4b66f9aa7452c120e87dfb33d02008c8a18', # numpy-1.22.3.zip # numpy-1.20.3_disable_fortran_callback_test.patch '44975a944544fd0e771b7e63c32590d257a3713070f8f7fdf60105dc516f1d75', + {'numpy-1.20.3_fix-fortran-compiler-error.patch': + '016e0d02ffabe013248c4fd203a4456edee76839f747c05daf92ac1fe9925189'}, # numpy-1.22.3_disable-broken-override-test.patch '9c589bb073b28b25ff45eb3c63c57966aa508dd8b318d0b885b6295271e4983c', ], diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2022.05-foss-2022a.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2022.05-foss-2022a.eb index ce504e9607a..21a801b8fb9 100644 --- a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2022.05-foss-2022a.eb +++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2022.05-foss-2022a.eb @@ -26,6 +26,7 @@ exts_list = [ ('numpy', '1.22.3', { 'patches': [ 'numpy-1.20.3_disable_fortran_callback_test.patch', + 'numpy-1.20.3_fix-fortran-compiler-error.patch', 'numpy-1.22.3_disable-broken-override-test.patch', '%(name)s-%(version)s_skip-ppc-long-complex-test.patch', ], @@ -34,6 +35,8 @@ exts_list = [ 'dbc7601a3b7472d559dc7b933b18b4b66f9aa7452c120e87dfb33d02008c8a18', # numpy-1.22.3.zip # numpy-1.20.3_disable_fortran_callback_test.patch '44975a944544fd0e771b7e63c32590d257a3713070f8f7fdf60105dc516f1d75', + {'numpy-1.20.3_fix-fortran-compiler-error.patch': + '016e0d02ffabe013248c4fd203a4456edee76839f747c05daf92ac1fe9925189'}, # numpy-1.22.3_disable-broken-override-test.patch '9c589bb073b28b25ff45eb3c63c57966aa508dd8b318d0b885b6295271e4983c', # numpy-1.22.3_skip-ppc-long-complex-test.patch diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2022.05-intel-2022.05.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2022.05-intel-2022.05.eb index 06ad5e918f6..97966712185 100644 --- a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2022.05-intel-2022.05.eb +++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2022.05-intel-2022.05.eb @@ -27,6 +27,7 @@ exts_list = [ 'patches': [ 'numpy-1.18.2-mkl.patch', 'numpy-1.20.3_disable_fortran_callback_test.patch', + 'numpy-1.20.3_fix-fortran-compiler-error.patch', 'numpy-1.22.3_disable-broken-override-test.patch', ], 'sources': ['%(name)s-%(version)s.zip'], @@ -35,6 +36,8 @@ exts_list = [ 'ea25ad5c0148c1398d282f0424e642fb9815a1a80f4512659b018e2adc378bcf', # numpy-1.18.2-mkl.patch # numpy-1.20.3_disable_fortran_callback_test.patch '44975a944544fd0e771b7e63c32590d257a3713070f8f7fdf60105dc516f1d75', + {'numpy-1.20.3_fix-fortran-compiler-error.patch': + '016e0d02ffabe013248c4fd203a4456edee76839f747c05daf92ac1fe9925189'}, # numpy-1.22.3_disable-broken-override-test.patch '9c589bb073b28b25ff45eb3c63c57966aa508dd8b318d0b885b6295271e4983c', ], diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2022.05-intel-2022a.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2022.05-intel-2022a.eb index a07d23a7f56..4e06a815c50 100644 --- a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2022.05-intel-2022a.eb +++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2022.05-intel-2022a.eb @@ -27,6 +27,7 @@ exts_list = [ 'patches': [ 'numpy-1.18.2-mkl.patch', 'numpy-1.20.3_disable_fortran_callback_test.patch', + 'numpy-1.20.3_fix-fortran-compiler-error.patch', 'numpy-1.22.3_disable-broken-override-test.patch', ], 'sources': ['%(name)s-%(version)s.zip'], @@ -35,6 +36,8 @@ exts_list = [ 'ea25ad5c0148c1398d282f0424e642fb9815a1a80f4512659b018e2adc378bcf', # numpy-1.18.2-mkl.patch # numpy-1.20.3_disable_fortran_callback_test.patch '44975a944544fd0e771b7e63c32590d257a3713070f8f7fdf60105dc516f1d75', + {'numpy-1.20.3_fix-fortran-compiler-error.patch': + '016e0d02ffabe013248c4fd203a4456edee76839f747c05daf92ac1fe9925189'}, # numpy-1.22.3_disable-broken-override-test.patch '9c589bb073b28b25ff45eb3c63c57966aa508dd8b318d0b885b6295271e4983c', ], diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.02-gfbf-2022b.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.02-gfbf-2022b.eb index e19bb6789f3..e9e059afe3a 100644 --- a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.02-gfbf-2022b.eb +++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.02-gfbf-2022b.eb @@ -28,9 +28,14 @@ use_pip = True # order is important! exts_list = [ ('numpy', '1.24.2', { - 'patches': ['numpy-1.22.3_disable-broken-override-test.patch'], + 'patches': [ + 'numpy-1.20.3_fix-fortran-compiler-error.patch', + 'numpy-1.22.3_disable-broken-override-test.patch', + ], 'checksums': [ {'numpy-1.24.2.tar.gz': '003a9f530e880cb2cd177cba1af7220b9aa42def9c4afc2a2fc3ee6be7eb2b22'}, + {'numpy-1.20.3_fix-fortran-compiler-error.patch': + '016e0d02ffabe013248c4fd203a4456edee76839f747c05daf92ac1fe9925189'}, {'numpy-1.22.3_disable-broken-override-test.patch': '9c589bb073b28b25ff45eb3c63c57966aa508dd8b318d0b885b6295271e4983c'}, ], diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.07-gfbf-2023a.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.07-gfbf-2023a.eb index 44b5725fe7d..424296cf1fe 100644 --- a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.07-gfbf-2023a.eb +++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.07-gfbf-2023a.eb @@ -16,6 +16,7 @@ builddependencies = [ ('Meson', '1.1.1'), ('Ninja', '1.11.1'), ('pkgconf', '1.9.5'), # required by scipy + ('Cython', '3.0.8'), ] dependencies = [ @@ -30,6 +31,7 @@ use_pip = True exts_list = [ ('numpy', '1.25.1', { 'patches': [ + 'numpy-1.20.3_fix-fortran-compiler-error.patch', 'numpy-1.22.3_disable-broken-override-test.patch', ('numpy-1.25.1_fix-duplicate-avx512-symbols.patch', 'numpy/core/src/npysort/x86-simd-sort'), 'numpy-1.25.1_fix-undefined-avx512-reference.patch', @@ -38,6 +40,8 @@ exts_list = [ ], 'checksums': [ {'numpy-1.25.1.tar.gz': '9a3a9f3a61480cc086117b426a8bd86869c213fc4072e606f01c4e4b66eb92bf'}, + {'numpy-1.20.3_fix-fortran-compiler-error.patch': + '016e0d02ffabe013248c4fd203a4456edee76839f747c05daf92ac1fe9925189'}, {'numpy-1.22.3_disable-broken-override-test.patch': '9c589bb073b28b25ff45eb3c63c57966aa508dd8b318d0b885b6295271e4983c'}, {'numpy-1.25.1_fix-duplicate-avx512-symbols.patch': @@ -70,12 +74,15 @@ exts_list = [ 'patches': [ 'scipy-1.11.1_disable-tests.patch', 'scipy-1.11.1_xfail-aarch64_test_maxiter_worsening.patch', + 'scipy-1.11.1_vectorization_error.patch', ], 'checksums': [ {'scipy-1.11.1.tar.gz': 'fb5b492fa035334fd249f0973cc79ecad8b09c604b42a127a677b45a9a3d4289'}, {'scipy-1.11.1_disable-tests.patch': '906bfb03397d94882ccdc1b93bc2c8e854e0e060c2d107c83042992394e6a4af'}, {'scipy-1.11.1_xfail-aarch64_test_maxiter_worsening.patch': '918c8e6fa8215d459126f267764c961bde729ea4a116c7f6287cddfdc58ffcea'}, + {'scipy-1.11.1_vectorization_error.patch': + 'bfba00ab84d7d6d73b87e4e94ea2487058d155f845c12212552c095fea9e5cae'}, ], }), ('numexpr', '2.8.4', { diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.07-iimkl-2023a.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.07-iimkl-2023a.eb index 95d1e9f41c4..a41da775912 100644 --- a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.07-iimkl-2023a.eb +++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.07-iimkl-2023a.eb @@ -16,6 +16,7 @@ builddependencies = [ ('Meson', '1.1.1'), ('Ninja', '1.11.1'), ('pkgconf', '1.9.5'), # required by scipy + ('Cython', '3.0.8'), ] dependencies = [ @@ -31,6 +32,7 @@ exts_list = [ ('numpy', '1.25.1', { 'patches': [ 'numpy-1.18.2-mkl.patch', + 'numpy-1.20.3_fix-fortran-compiler-error.patch', 'numpy-1.25.1_disable_fortran_callback_test.patch', 'numpy-1.22.3_disable-broken-override-test.patch', 'numpy-1.25.1_disable-broken-test_long_long_map.patch', @@ -41,6 +43,8 @@ exts_list = [ 'checksums': [ {'numpy-1.25.1.tar.gz': '9a3a9f3a61480cc086117b426a8bd86869c213fc4072e606f01c4e4b66eb92bf'}, {'numpy-1.18.2-mkl.patch': 'ea25ad5c0148c1398d282f0424e642fb9815a1a80f4512659b018e2adc378bcf'}, + {'numpy-1.20.3_fix-fortran-compiler-error.patch': + '016e0d02ffabe013248c4fd203a4456edee76839f747c05daf92ac1fe9925189'}, {'numpy-1.25.1_disable_fortran_callback_test.patch': '3c02bd9973b7082fde9f9d18edfeb05798226ccb5731a56f5677269200c345cf'}, {'numpy-1.22.3_disable-broken-override-test.patch': diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.11-gfbf-2023b.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.11-gfbf-2023b.eb index ae7ab11bbc4..38fb986242d 100644 --- a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.11-gfbf-2023b.eb +++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.11-gfbf-2023b.eb @@ -17,6 +17,7 @@ builddependencies = [ ('meson-python', '0.15.0'), ('Ninja', '1.11.1'), ('pkgconf', '2.0.3'), # required by scipy + ('Cython', '3.0.10'), ] dependencies = [ @@ -68,6 +69,7 @@ exts_list = [ 'scipy-1.11.1_disable-tests.patch', 'scipy-1.11.1_xfail-aarch64_test_maxiter_worsening.patch', 'scipy-1.11.4_fix-deps-ellip_harm_2.patch', + 'scipy-1.11.1_vectorization_error.patch', ], 'checksums': [ {'scipy-1.11.4.tar.gz': '90a2b78e7f5733b9de748f589f09225013685f9b218275257f8a8168ededaeaa'}, @@ -76,6 +78,8 @@ exts_list = [ '918c8e6fa8215d459126f267764c961bde729ea4a116c7f6287cddfdc58ffcea'}, {'scipy-1.11.4_fix-deps-ellip_harm_2.patch': '5c3b4d4dab76cd4c9398c87e6a67b39e3806994ef955fa35781b49f9f99328a8'}, + {'scipy-1.11.1_vectorization_error.patch': + 'bfba00ab84d7d6d73b87e4e94ea2487058d155f845c12212552c095fea9e5cae'}, ], 'enable_slow_tests': True, 'ignore_test_result': False, diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2024.05-gfbf-2024.05.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2024.05-gfbf-2024.05.eb new file mode 100644 index 00000000000..99d61098d6b --- /dev/null +++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2024.05-gfbf-2024.05.eb @@ -0,0 +1,103 @@ +easyblock = 'PythonBundle' + +name = 'SciPy-bundle' +version = '2024.05' + +homepage = 'https://python.org/' +description = "Bundle of Python packages for scientific software" + +toolchain = {'name': 'gfbf', 'version': '2024.05'} +toolchainopts = {'pic': True, 'lowopt': True} + +builddependencies = [ + ('hypothesis', '6.103.1'), + ('UnZip', '6.0'), + # scipy >= 1.9.0 uses Meson/Ninja + ('Meson', '1.4.0'), + ('meson-python', '0.16.0'), + ('Ninja', '1.12.1'), + ('pkgconf', '2.2.0'), # required by scipy + ('Cython', '3.0.10'), # required by numpy and scipy +] + +dependencies = [ + ('Python', '3.12.3'), + ('Python-bundle-PyPI', '2024.06'), + ('pybind11', '2.12.0'), # required by scipy +] + +use_pip = True + +# order is important! +exts_list = [ + ('numpy', '1.26.4', { + 'patches': [ + 'numpy-1.22.3_disable-broken-override-test.patch', + 'numpy-1.26.4_fix-riscv64-test-failures.patch', + ], + 'checksums': [ + {'numpy-1.26.4.tar.gz': '2a02aba9ed12e4ac4eb3ea9421c420301a0c6460d9830d74a9df87efa4912010'}, + {'numpy-1.22.3_disable-broken-override-test.patch': + '9c589bb073b28b25ff45eb3c63c57966aa508dd8b318d0b885b6295271e4983c'}, + {'numpy-1.26.4_fix-riscv64-test-failures.patch': + '81bd487dbca6da8285971a16a2c7b488718a051d3cd66450277bed6ff21741de'}, + ], + }), + ('ply', '3.11', { + 'checksums': ['00c7c1aaa88358b9c765b6d3000c6eec0ba42abca5351b095321aef446081da3'], + }), + ('gast', '0.5.4', { + 'checksums': ['9c270fe5f4b130969b54174de7db4e764b09b4f7f67ccfc32480e29f78348d97'], + }), + ('beniget', '0.4.1', { + 'checksums': ['75554b3b8ad0553ce2f607627dad3d95c60c441189875b98e097528f8e23ac0c'], + }), + ('pythran', '0.16.1', { + 'checksums': ['861748c0f9c7d422b32724b114b3817d818ed4eab86c09781aa0a3f7ceabb7f9'], + }), + ('versioneer', '0.29', { + 'checksums': ['5ab283b9857211d61b53318b7c792cf68e798e765ee17c27ade9f6c924235731'], + }), + ('scipy', '1.13.1', { + 'enable_slow_tests': True, + 'ignore_test_result': False, + 'patches': [ + 'scipy-1.11.1_disable-tests.patch', + 'scipy-1.11.1_xfail-aarch64_test_maxiter_worsening.patch', + ], + 'checksums': [ + {'scipy-1.13.1.tar.gz': '095a87a0312b08dfd6a6155cbbd310a8c51800fc931b8c0b84003014b874ed3c'}, + {'scipy-1.11.1_disable-tests.patch': '906bfb03397d94882ccdc1b93bc2c8e854e0e060c2d107c83042992394e6a4af'}, + {'scipy-1.11.1_xfail-aarch64_test_maxiter_worsening.patch': + '918c8e6fa8215d459126f267764c961bde729ea4a116c7f6287cddfdc58ffcea'}, + ], + }), + ('numexpr', '2.10.0', { + 'patches': ['numexpr-2.10.0_fix-numpy-1.x.patch'], + 'checksums': [ + {'numexpr-2.10.0.tar.gz': 'c89e930752639df040539160326d8f99a84159bbea41943ab8e960591edaaef0'}, + {'numexpr-2.10.0_fix-numpy-1.x.patch': '8d70b2e95579e6f0adc07bc615144f7657b3b607f9210ec328b6622458ca726d'}, + ], + }), + ('Bottleneck', '1.3.8', { + 'checksums': ['6780d896969ba7f53c8995ba90c87c548beb3db435dc90c60b9a10ed1ab4d868'], + }), + ('tzdata', '2024.1', { + 'checksums': ['2674120f8d891909751c38abcdfd386ac0a5a1127954fbc332af6b5ceae07efd'], + }), + ('pandas', '2.2.2', { + 'preinstallopts': "export PANDAS_CI=0 && ", + 'checksums': ['9e79019aba43cb4fda9e4d983f8e88ca0373adbb697ae9c6c43093218de28b54'], + }), + ('mpmath', '1.3.0', { + 'checksums': ['7a28eb2a9774d00c7bc92411c19a89209d5da7c4c9a9e227be8330a23a25b91f'], + }), + ('deap', '1.4.1', { + 'modulename': 'deap.base', + 'checksums': ['cc01de9892dfa7d1bc9803dab28892fead177f0182c81db47360a240ead778ff'], + }), +] + +sanity_pip_check = True + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2024.05-gfbf-2024a.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2024.05-gfbf-2024a.eb new file mode 100644 index 00000000000..5584d888f30 --- /dev/null +++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2024.05-gfbf-2024a.eb @@ -0,0 +1,106 @@ +easyblock = 'PythonBundle' + +name = 'SciPy-bundle' +version = '2024.05' + +homepage = 'https://python.org/' +description = "Bundle of Python packages for scientific software" + +toolchain = {'name': 'gfbf', 'version': '2024a'} +toolchainopts = {'pic': True, 'lowopt': True} + +builddependencies = [ + ('hypothesis', '6.103.1'), + ('UnZip', '6.0'), + # scipy >= 1.9.0 uses Meson/Ninja + ('Meson', '1.4.0'), + ('meson-python', '0.16.0'), + ('Ninja', '1.12.1'), + ('pkgconf', '2.2.0'), # required by scipy + ('Cython', '3.0.10'), # required by numpy and scipy +] + +dependencies = [ + ('Python', '3.12.3'), + ('Python-bundle-PyPI', '2024.06'), + ('pybind11', '2.12.0'), # required by scipy +] + +use_pip = True + +# order is important! +exts_list = [ + ('numpy', '1.26.4', { + 'patches': [ + 'numpy-1.22.3_disable-broken-override-test.patch', + 'numpy-1.26.4_fix-riscv64-test-failures.patch', + ], + 'checksums': [ + {'numpy-1.26.4.tar.gz': '2a02aba9ed12e4ac4eb3ea9421c420301a0c6460d9830d74a9df87efa4912010'}, + {'numpy-1.22.3_disable-broken-override-test.patch': + '9c589bb073b28b25ff45eb3c63c57966aa508dd8b318d0b885b6295271e4983c'}, + {'numpy-1.26.4_fix-riscv64-test-failures.patch': + '81bd487dbca6da8285971a16a2c7b488718a051d3cd66450277bed6ff21741de'}, + ], + }), + ('ply', '3.11', { + 'checksums': ['00c7c1aaa88358b9c765b6d3000c6eec0ba42abca5351b095321aef446081da3'], + }), + ('gast', '0.5.4', { + 'checksums': ['9c270fe5f4b130969b54174de7db4e764b09b4f7f67ccfc32480e29f78348d97'], + }), + ('beniget', '0.4.1', { + 'checksums': ['75554b3b8ad0553ce2f607627dad3d95c60c441189875b98e097528f8e23ac0c'], + }), + ('pythran', '0.16.1', { + 'checksums': ['861748c0f9c7d422b32724b114b3817d818ed4eab86c09781aa0a3f7ceabb7f9'], + }), + ('versioneer', '0.29', { + 'checksums': ['5ab283b9857211d61b53318b7c792cf68e798e765ee17c27ade9f6c924235731'], + }), + ('scipy', '1.13.1', { + 'enable_slow_tests': True, + 'ignore_test_result': False, + 'patches': [ + 'scipy-1.11.1_disable-tests.patch', + 'scipy-1.11.1_xfail-aarch64_test_maxiter_worsening.patch', + 'scipy-1.13.1_TestLinprogIPSparse.patch', + ], + 'checksums': [ + {'scipy-1.13.1.tar.gz': '095a87a0312b08dfd6a6155cbbd310a8c51800fc931b8c0b84003014b874ed3c'}, + {'scipy-1.11.1_disable-tests.patch': '906bfb03397d94882ccdc1b93bc2c8e854e0e060c2d107c83042992394e6a4af'}, + {'scipy-1.11.1_xfail-aarch64_test_maxiter_worsening.patch': + '918c8e6fa8215d459126f267764c961bde729ea4a116c7f6287cddfdc58ffcea'}, + {'scipy-1.13.1_TestLinprogIPSparse.patch': + '7213c2690b76c69f7e7103529cea3fa2098c05fbea556f04325fab9ca8c065f5'}, + ], + }), + ('numexpr', '2.10.0', { + 'patches': ['numexpr-2.10.0_fix-numpy-1.x.patch'], + 'checksums': [ + {'numexpr-2.10.0.tar.gz': 'c89e930752639df040539160326d8f99a84159bbea41943ab8e960591edaaef0'}, + {'numexpr-2.10.0_fix-numpy-1.x.patch': '8d70b2e95579e6f0adc07bc615144f7657b3b607f9210ec328b6622458ca726d'}, + ], + }), + ('Bottleneck', '1.3.8', { + 'checksums': ['6780d896969ba7f53c8995ba90c87c548beb3db435dc90c60b9a10ed1ab4d868'], + }), + ('tzdata', '2024.1', { + 'checksums': ['2674120f8d891909751c38abcdfd386ac0a5a1127954fbc332af6b5ceae07efd'], + }), + ('pandas', '2.2.2', { + 'preinstallopts': "export PANDAS_CI=0 && ", + 'checksums': ['9e79019aba43cb4fda9e4d983f8e88ca0373adbb697ae9c6c43093218de28b54'], + }), + ('mpmath', '1.3.0', { + 'checksums': ['7a28eb2a9774d00c7bc92411c19a89209d5da7c4c9a9e227be8330a23a25b91f'], + }), + ('deap', '1.4.1', { + 'modulename': 'deap.base', + 'checksums': ['cc01de9892dfa7d1bc9803dab28892fead177f0182c81db47360a240ead778ff'], + }), +] + +sanity_pip_check = True + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/s/SciPy-bundle/numexpr-2.10.0_fix-numpy-1.x.patch b/easybuild/easyconfigs/s/SciPy-bundle/numexpr-2.10.0_fix-numpy-1.x.patch new file mode 100644 index 00000000000..dff9bd069c9 --- /dev/null +++ b/easybuild/easyconfigs/s/SciPy-bundle/numexpr-2.10.0_fix-numpy-1.x.patch @@ -0,0 +1,18 @@ +fix for: error: PyDataType_SET_ELSIZE was not declared in this scope +see https://github.com/pydata/numexpr/pull/485 + +--- numexpr-2.10.0/numexpr/interpreter.cpp.orig 2024-06-14 21:47:27.999098607 +0200 ++++ numexpr-2.10.0/numexpr/interpreter.cpp 2024-06-14 21:49:53.403776961 +0200 +@@ -47,6 +47,12 @@ + #define AVAILABLE(Haystack, Haystack_Len, J, Needle_Len) \ + ((Haystack_Len) >= (J) + (Needle_Len)) + ++// To allow building with NumPy<2 locally define the new NumPy macros: ++#if NPY_ABI_VERSION < 0x02000000 ++ #define PyDataType_ELSIZE(descr) ((descr)->elsize) ++ #define PyDataType_SET_ELSIZE(descr, size) (descr)->elsize = size ++#endif ++ + #include "str-two-way.hpp" + + #ifdef DEBUG diff --git a/easybuild/easyconfigs/s/SciPy-bundle/numpy-1.20.3_fix-fortran-compiler-error.patch b/easybuild/easyconfigs/s/SciPy-bundle/numpy-1.20.3_fix-fortran-compiler-error.patch new file mode 100644 index 00000000000..32b41061f06 --- /dev/null +++ b/easybuild/easyconfigs/s/SciPy-bundle/numpy-1.20.3_fix-fortran-compiler-error.patch @@ -0,0 +1,43 @@ +Using Fortran compilers which differ "too much" from GCC fails building NumPy with something like +> A valid Fortran version was not found in this string: [...] + +See https://github.com/easybuilders/easybuild-easyblocks/issues/2518 and https://github.com/numpy/numpy/pull/26502 + +Fix by converting the hard error into a warning as the issue would be handled later if required. +E.g. for building NumPy we don't need a Fortran compiler at all. + +Author: Alexander Grund (TU Dresden) + +diff --git a/numpy/distutils/fcompiler/gnu.py b/numpy/distutils/fcompiler/gnu.py +index eac4cbb477..8a1043fe26 100644 +--- a/numpy/distutils/fcompiler/gnu.py ++++ b/numpy/distutils/fcompiler/gnu.py +@@ -8,6 +8,7 @@ import hashlib + import base64 + import subprocess + from subprocess import Popen, PIPE, STDOUT ++from distutils import log + from numpy.distutils.exec_command import filepath_from_subprocess_output + from numpy.distutils.fcompiler import FCompiler + from distutils.version import LooseVersion +@@ -69,9 +70,9 @@ class GnuFCompiler(FCompiler): + # from the version string + return ('gfortran', v) + +- # If still nothing, raise an error to make the problem easy to find. +- err = 'A valid Fortran version was not found in this string:\n' +- raise ValueError(err + version_string) ++ # If still nothing, warn to make the problem easy to find. ++ log.warn('A valid Fortran version was not found in this string:\n' ++ + version_string) + + def version_match(self, version_string): + v = self.gnu_version_match(version_string) +@@ -539,7 +540,6 @@ def _can_target(cmd, arch): + + + if __name__ == '__main__': +- from distutils import log + from numpy.distutils import customized_fcompiler + log.set_verbosity(2) + diff --git a/easybuild/easyconfigs/s/SciPy-bundle/numpy-1.26.4_fix-riscv64-test-failures.patch b/easybuild/easyconfigs/s/SciPy-bundle/numpy-1.26.4_fix-riscv64-test-failures.patch new file mode 100644 index 00000000000..ccc444e1f4d --- /dev/null +++ b/easybuild/easyconfigs/s/SciPy-bundle/numpy-1.26.4_fix-riscv64-test-failures.patch @@ -0,0 +1,156 @@ +From d9e88e32302b3842785a33d90cf22f8c1405cd05 Mon Sep 17 00:00:00 2001 +From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= +Date: Tue, 18 Jun 2024 13:28:35 +0200 +Subject: [PATCH 1/2] TST: Fix fp_noncontiguous and fpclass on riscv64 + +Modify fp_noncontiguous and fpclass so that they pass on riscv64. +The subtests that verify that the signs of negative NaNs are preserved +do not pass on riscv64 builds and are disabled. Many RISC-V +instructions that produce NaNs return a canonical NaN, as defined by +the RISC-V specification. The canonical NaNs are always positive. See +section 11.3 NaN Generation and Propagation of the RISC-V Unprivileged +ISA for more details. +--- + numpy/core/tests/test_umath.py | 44 +++++++++++++++++++++++++++++----- + 1 file changed, 38 insertions(+), 6 deletions(-) + +diff --git a/numpy/core/tests/test_umath.py b/numpy/core/tests/test_umath.py +index 963e740d8dcb..8444893c80c3 100644 +--- a/numpy/core/tests/test_umath.py ++++ b/numpy/core/tests/test_umath.py +@@ -1852,8 +1852,22 @@ def test_fpclass(self, stride): + assert_equal(np.isnan(arr_f64[::stride]), nan[::stride]) + assert_equal(np.isinf(arr_f32[::stride]), inf[::stride]) + assert_equal(np.isinf(arr_f64[::stride]), inf[::stride]) +- assert_equal(np.signbit(arr_f32[::stride]), sign[::stride]) +- assert_equal(np.signbit(arr_f64[::stride]), sign[::stride]) ++ if platform.processor() == 'riscv64': ++ # On RISC-V, many operations that produce NaNs, such as converting ++ # a -NaN from f64 to f32, return a canonical NaN. The canonical ++ # NaNs are always positive. See section 11.3 NaN Generation and ++ # Propagation of the RISC-V Unprivileged ISA for more details. ++ # We disable the sign test on riscv64 for -np.nan as we ++ # cannot assume that its sign will be honoured in these tests. ++ arr_f64_rv = np.copy(arr_f64) ++ arr_f32_rv = np.copy(arr_f32) ++ arr_f64_rv[1] = -1.0 ++ arr_f32_rv[1] = -1.0 ++ assert_equal(np.signbit(arr_f32_rv[::stride]), sign[::stride]) ++ assert_equal(np.signbit(arr_f64_rv[::stride]), sign[::stride]) ++ else: ++ assert_equal(np.signbit(arr_f32[::stride]), sign[::stride]) ++ assert_equal(np.signbit(arr_f64[::stride]), sign[::stride]) + assert_equal(np.isfinite(arr_f32[::stride]), finite[::stride]) + assert_equal(np.isfinite(arr_f64[::stride]), finite[::stride]) + +@@ -1874,23 +1888,37 @@ def test_fp_noncontiguous(self, dtype): + ncontig_in = data[1::3] + ncontig_out = out[1::3] + contig_in = np.array(ncontig_in) ++ ++ if platform.processor() == 'riscv64': ++ # Disable the -np.nan signbit tests on riscv64. See comments in ++ # test_fpclass for more details. ++ data_rv = np.copy(data) ++ data_rv[1] = -1.0 ++ ncontig_sign_in = data_rv[1::3] ++ contig_sign_in = np.array(ncontig_sign_in) ++ else: ++ ncontig_sign_in = ncontig_in ++ contig_sign_in = contig_in ++ + assert_equal(ncontig_in.flags.c_contiguous, False) + assert_equal(ncontig_out.flags.c_contiguous, False) + assert_equal(contig_in.flags.c_contiguous, True) ++ assert_equal(ncontig_sign_in.flags.c_contiguous, False) ++ assert_equal(contig_sign_in.flags.c_contiguous, True) + # ncontig in, ncontig out + assert_equal(np.isnan(ncontig_in, out=ncontig_out), nan[1::3]) + assert_equal(np.isinf(ncontig_in, out=ncontig_out), inf[1::3]) +- assert_equal(np.signbit(ncontig_in, out=ncontig_out), sign[1::3]) ++ assert_equal(np.signbit(ncontig_sign_in, out=ncontig_out), sign[1::3]) + assert_equal(np.isfinite(ncontig_in, out=ncontig_out), finite[1::3]) + # contig in, ncontig out + assert_equal(np.isnan(contig_in, out=ncontig_out), nan[1::3]) + assert_equal(np.isinf(contig_in, out=ncontig_out), inf[1::3]) +- assert_equal(np.signbit(contig_in, out=ncontig_out), sign[1::3]) ++ assert_equal(np.signbit(contig_sign_in, out=ncontig_out), sign[1::3]) + assert_equal(np.isfinite(contig_in, out=ncontig_out), finite[1::3]) + # ncontig in, contig out + assert_equal(np.isnan(ncontig_in), nan[1::3]) + assert_equal(np.isinf(ncontig_in), inf[1::3]) +- assert_equal(np.signbit(ncontig_in), sign[1::3]) ++ assert_equal(np.signbit(ncontig_sign_in), sign[1::3]) + assert_equal(np.isfinite(ncontig_in), finite[1::3]) + # contig in, contig out, nd stride + data_split = np.array(np.array_split(data, 2)) +@@ -1900,7 +1928,11 @@ def test_fp_noncontiguous(self, dtype): + finite_split = np.array(np.array_split(finite, 2)) + assert_equal(np.isnan(data_split), nan_split) + assert_equal(np.isinf(data_split), inf_split) +- assert_equal(np.signbit(data_split), sign_split) ++ if platform.processor() == 'riscv64': ++ data_split_rv = np.array(np.array_split(data_rv, 2)) ++ assert_equal(np.signbit(data_split_rv), sign_split) ++ else: ++ assert_equal(np.signbit(data_split), sign_split) + assert_equal(np.isfinite(data_split), finite_split) + + class TestLDExp: + +From ccb1d4adc01b49c7e900e5f532dc6361eac1362a Mon Sep 17 00:00:00 2001 +From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= +Date: Tue, 18 Jun 2024 13:30:00 +0200 +Subject: [PATCH 2/2] TST: Use platform.machine() for improved portability on + riscv64 + +Replace `platform.processor()` with `platform.machine()` considering the latter is more portable. More specifically, `platform.processor()` returns empty string on Arch Linux, and this PR fixes the corresponding test failure. +--- + numpy/core/tests/test_numeric.py | 2 +- + numpy/core/tests/test_umath.py | 6 +++--- + 2 files changed, 4 insertions(+), 4 deletions(-) + +diff --git a/numpy/core/tests/test_numeric.py b/numpy/core/tests/test_numeric.py +index e5edd3efce5a..ce5917a9b09f 100644 +--- a/numpy/core/tests/test_numeric.py ++++ b/numpy/core/tests/test_numeric.py +@@ -483,7 +483,7 @@ def setup_method(self): + # Propagation of the RISC-V Unprivileged ISA for more details. + # We disable the float32 sign test on riscv64 for -np.nan as the sign + # of the NaN will be lost when it's converted to a float32. +- if platform.processor() != 'riscv64': ++ if platform.machine() != 'riscv64': + self.signf[3::6][self.ef[3::6]] = -np.nan + self.signd[3::6][self.ed[3::6]] = -np.nan + self.signf[4::6][self.ef[4::6]] = -0. +diff --git a/numpy/core/tests/test_umath.py b/numpy/core/tests/test_umath.py +index 8444893c80c3..c5a3e2c81f83 100644 +--- a/numpy/core/tests/test_umath.py ++++ b/numpy/core/tests/test_umath.py +@@ -1852,7 +1852,7 @@ def test_fpclass(self, stride): + assert_equal(np.isnan(arr_f64[::stride]), nan[::stride]) + assert_equal(np.isinf(arr_f32[::stride]), inf[::stride]) + assert_equal(np.isinf(arr_f64[::stride]), inf[::stride]) +- if platform.processor() == 'riscv64': ++ if platform.machine() == 'riscv64': + # On RISC-V, many operations that produce NaNs, such as converting + # a -NaN from f64 to f32, return a canonical NaN. The canonical + # NaNs are always positive. See section 11.3 NaN Generation and +@@ -1889,7 +1889,7 @@ def test_fp_noncontiguous(self, dtype): + ncontig_out = out[1::3] + contig_in = np.array(ncontig_in) + +- if platform.processor() == 'riscv64': ++ if platform.machine() == 'riscv64': + # Disable the -np.nan signbit tests on riscv64. See comments in + # test_fpclass for more details. + data_rv = np.copy(data) +@@ -1928,7 +1928,7 @@ def test_fp_noncontiguous(self, dtype): + finite_split = np.array(np.array_split(finite, 2)) + assert_equal(np.isnan(data_split), nan_split) + assert_equal(np.isinf(data_split), inf_split) +- if platform.processor() == 'riscv64': ++ if platform.machine() == 'riscv64': + data_split_rv = np.array(np.array_split(data_rv, 2)) + assert_equal(np.signbit(data_split_rv), sign_split) + else: diff --git a/easybuild/easyconfigs/s/SciPy-bundle/scipy-1.11.1_vectorization_error.patch b/easybuild/easyconfigs/s/SciPy-bundle/scipy-1.11.1_vectorization_error.patch new file mode 100644 index 00000000000..6cf77dee6f5 --- /dev/null +++ b/easybuild/easyconfigs/s/SciPy-bundle/scipy-1.11.1_vectorization_error.patch @@ -0,0 +1,105 @@ +Fixes the vectorization bug. `ValueError: buffer source array is read-only` +see https://github.com/scipy/scipy/issues/16792 +patch source: https://github.com/scipy/scipy/pull/20195 +--- scipy/linalg/_cythonized_array_utils.pyx.orig ++++ scipy/linalg/_cythonized_array_utils.pyx +@@ -158,7 +158,7 @@ + + + @cython.initializedcheck(False) +-def bandwidth_c(np_numeric_t[:, ::1]A): ++def bandwidth_c(const np_numeric_t[:, ::1]A): + cdef int l, u + with nogil: + l, u = band_check_internal_c(A) +@@ -166,7 +166,7 @@ + + + @cython.initializedcheck(False) +-def bandwidth_noncontig(np_numeric_t[:, :]A): ++def bandwidth_noncontig(const np_numeric_t[:, :]A): + cdef int l, u + with nogil: + l, u = band_check_internal_noncontig(A) +@@ -176,7 +176,7 @@ + @cython.initializedcheck(False) + @cython.boundscheck(False) + @cython.wraparound(False) +-cdef inline (int, int) band_check_internal_c(np_numeric_t[:, ::1]A) noexcept nogil: ++cdef inline (int, int) band_check_internal_c(const np_numeric_t[:, ::1]A) noexcept nogil: + cdef Py_ssize_t n = A.shape[0], m = A.shape[1] + cdef Py_ssize_t lower_band = 0, upper_band = 0, r, c + cdef np_numeric_t zero = 0 +@@ -207,7 +207,7 @@ + @cython.initializedcheck(False) + @cython.boundscheck(False) + @cython.wraparound(False) +-cdef inline (int, int) band_check_internal_noncontig(np_numeric_t[:, :]A) noexcept nogil: ++cdef inline (int, int) band_check_internal_noncontig(const np_numeric_t[:, :]A) noexcept nogil: + cdef Py_ssize_t n = A.shape[0], m = A.shape[1] + cdef Py_ssize_t lower_band = 0, upper_band = 0, r, c + cdef np_numeric_t zero = 0 +@@ -324,7 +324,7 @@ + + + @cython.initializedcheck(False) +-def is_sym_her_real_c(np_numeric_t[:, ::1]A): ++def is_sym_her_real_c(const np_numeric_t[:, ::1]A): + cdef bint s + with nogil: + s = is_sym_her_real_c_internal(A) +@@ -332,7 +332,7 @@ + + + @cython.initializedcheck(False) +-def is_sym_her_real_noncontig(np_numeric_t[:, :]A): ++def is_sym_her_real_noncontig(const np_numeric_t[:, :]A): + cdef bint s + with nogil: + s = is_sym_her_real_noncontig_internal(A) +@@ -342,7 +342,7 @@ + @cython.initializedcheck(False) + @cython.boundscheck(False) + @cython.wraparound(False) +-cdef inline bint is_sym_her_real_c_internal(np_numeric_t[:, ::1]A) noexcept nogil: ++cdef inline bint is_sym_her_real_c_internal(const np_numeric_t[:, ::1]A) noexcept nogil: + cdef Py_ssize_t n = A.shape[0], r, c + + for r in xrange(n): +@@ -355,7 +355,7 @@ + @cython.initializedcheck(False) + @cython.boundscheck(False) + @cython.wraparound(False) +-cdef inline bint is_sym_her_real_noncontig_internal(np_numeric_t[:, :]A) noexcept nogil: ++cdef inline bint is_sym_her_real_noncontig_internal(const np_numeric_t[:, :]A) noexcept nogil: + cdef Py_ssize_t n = A.shape[0], r, c + + for r in xrange(n): +@@ -469,7 +469,7 @@ + + + @cython.initializedcheck(False) +-def is_sym_her_complex_c(np_complex_numeric_t[:, ::1]A): ++def is_sym_her_complex_c(const np_complex_numeric_t[:, ::1]A): + cdef bint s + with nogil: + s = is_sym_her_complex_c_internal(A) +@@ -485,7 +485,7 @@ + @cython.initializedcheck(False) + @cython.boundscheck(False) + @cython.wraparound(False) +-cdef inline bint is_sym_her_complex_c_internal(np_complex_numeric_t[:, ::1]A) noexcept nogil: ++cdef inline bint is_sym_her_complex_c_internal(const np_complex_numeric_t[:, ::1]A) noexcept nogil: + cdef Py_ssize_t n = A.shape[0], r, c + + for r in xrange(n): +@@ -497,7 +497,7 @@ + @cython.initializedcheck(False) + @cython.boundscheck(False) + @cython.wraparound(False) +-cdef inline bint is_sym_her_complex_noncontig_internal(np_complex_numeric_t[:, :]A) noexcept nogil: ++cdef inline bint is_sym_her_complex_noncontig_internal(const np_complex_numeric_t[:, :]A) noexcept nogil: + cdef Py_ssize_t n = A.shape[0], r, c + + for r in xrange(n): + diff --git a/easybuild/easyconfigs/s/SciPy-bundle/scipy-1.13.1_TestLinprogIPSparse.patch b/easybuild/easyconfigs/s/SciPy-bundle/scipy-1.13.1_TestLinprogIPSparse.patch new file mode 100644 index 00000000000..1b057319086 --- /dev/null +++ b/easybuild/easyconfigs/s/SciPy-bundle/scipy-1.13.1_TestLinprogIPSparse.patch @@ -0,0 +1,30 @@ +disable problematic tests +TestLinprogIPSparse::test_bug_6139 + TestLinprogIPSparsePresolve::test_bug_6139 fail on Grace Hopper aarch64 +author: Sebastian Achilles (Juelich Supercomputing Centre) + +diff --git a/scipy/optimize/tests/test_linprog.py b/scipy/optimize/tests/test_linprog.py +index 49a0f8de5..8ffbb0b47 100644 +--- a/scipy/optimize/tests/test_linprog.py ++++ b/scipy/optimize/tests/test_linprog.py +@@ -1977,6 +1977,10 @@ if has_umfpack: + class TestLinprogIPSparse(LinprogIPTests): + options = {"sparse": True, "cholesky": False, "sym_pos": False} + ++ @pytest.mark.skipif( ++ platform.machine() == 'aarch64', ++ reason="Fails on aarch64" ++ ) + @pytest.mark.xfail_on_32bit("This test is sensitive to machine epsilon level " + "perturbations in linear system solution in " + "_linprog_ip._sym_solve.") +@@ -2027,6 +2031,10 @@ class TestLinprogIPSparse(LinprogIPTests): + class TestLinprogIPSparsePresolve(LinprogIPTests): + options = {"sparse": True, "_sparse_presolve": True} + ++ @pytest.mark.skipif( ++ platform.machine() == 'aarch64', ++ reason="Fails on aarch64" ++ ) + @pytest.mark.xfail_on_32bit("This test is sensitive to machine epsilon level " + "perturbations in linear system solution in " + "_linprog_ip._sym_solve.") diff --git a/easybuild/easyconfigs/s/SciTools-Iris/SciTools-Iris-3.2.1-foss-2022a.eb b/easybuild/easyconfigs/s/SciTools-Iris/SciTools-Iris-3.2.1-foss-2022a.eb new file mode 100644 index 00000000000..2e1bf32ea15 --- /dev/null +++ b/easybuild/easyconfigs/s/SciTools-Iris/SciTools-Iris-3.2.1-foss-2022a.eb @@ -0,0 +1,42 @@ +easyblock = 'PythonBundle' + +name = 'SciTools-Iris' +version = '3.2.1' + +homepage = 'https://scitools-iris.readthedocs.io' +description = """A powerful, format-agnostic, community-driven Python package for analysing and +visualising Earth science data.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('Cartopy', '0.20.3'), + ('dask', '2022.10.0'), + ('matplotlib', '3.5.2'), + ('netcdf4-python', '1.6.1'), + ('python-xxhash', '3.1.0'), + ('UDUNITS', '2.2.28'), +] + +use_pip = True + +exts_list = [ + ('antlr4-python3-runtime', '4.7.2', { + 'modulename': 'antlr4', + 'checksums': ['168cdcec8fb9152e84a87ca6fd261b3d54c8f6358f42ab3b813b14a7193bb50b'], + }), + ('cf-units', '3.1.1', { + 'preinstallopts': 'UDUNITS2_XML_PATH="$EBROOTUDUNITS/share/udunits/udunits2.xml"', + 'checksums': ['d402b5a54c46b8ad2fb4fd815a054520c36ee7b483e4c9555e4b45b62af7558b'], + }), + ('scitools-iris', version, { + 'modulename': 'iris', + 'checksums': ['f09ea7e79664d633f35f11b9d5c3afd3ac5f97698864bd6f2293007fb06c5e72'], + }), +] + +sanity_pip_check = True + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/s/SciTools-Iris/SciTools-Iris-3.9.0-foss-2023a.eb b/easybuild/easyconfigs/s/SciTools-Iris/SciTools-Iris-3.9.0-foss-2023a.eb new file mode 100644 index 00000000000..e372ed94d82 --- /dev/null +++ b/easybuild/easyconfigs/s/SciTools-Iris/SciTools-Iris-3.9.0-foss-2023a.eb @@ -0,0 +1,42 @@ +easyblock = 'PythonBundle' + +name = 'SciTools-Iris' +version = '3.9.0' + +homepage = 'https://scitools-iris.readthedocs.io' +description = """A powerful, format-agnostic, community-driven Python package for analysing and +visualising Earth science data.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('Cartopy', '0.22.0'), + ('dask', '2023.9.2'), + ('matplotlib', '3.7.2'), + ('netcdf4-python', '1.6.4'), + ('python-xxhash', '3.4.1'), + ('UDUNITS', '2.2.28'), +] + +use_pip = True + +exts_list = [ + ('antlr4-python3-runtime', '4.7.2', { + 'modulename': 'antlr4', + 'checksums': ['168cdcec8fb9152e84a87ca6fd261b3d54c8f6358f42ab3b813b14a7193bb50b'], + }), + ('cf-units', '3.2.0', { + 'preinstallopts': 'UDUNITS2_XML_PATH="$EBROOTUDUNITS/share/udunits/udunits2.xml"', + 'checksums': ['88a9f140e4157fe4c2d322b5e079046c4c0a7d76cb4950c700a8363bc235074f'], + }), + ('scitools_iris', version, { + 'modulename': 'iris', + 'checksums': ['53c701899aa08014beeb9dd0040bd5584511229fff98e74ff30b6eab5d4d02aa'], + }), +] + +sanity_pip_check = True + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/s/Score-P/Score-P-8.4-gompi-2024a-CUDA-12.6.0.eb b/easybuild/easyconfigs/s/Score-P/Score-P-8.4-gompi-2024a-CUDA-12.6.0.eb new file mode 100644 index 00000000000..9d7b53221e9 --- /dev/null +++ b/easybuild/easyconfigs/s/Score-P/Score-P-8.4-gompi-2024a-CUDA-12.6.0.eb @@ -0,0 +1,57 @@ +# Copyright 2013-2020 Juelich Supercomputing Centre, Germany +# Copyright 2020-2024 TU Dresden, Germany +# Authors:: +# * Bernd Mohr +# * Markus Geimer +# * Alexander Grund +# * Robert Mijakovic +# License:: 3-clause BSD + +name = 'Score-P' +version = '8.4' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://www.score-p.org' +description = """ + The Score-P measurement infrastructure is a highly scalable and easy-to-use + tool suite for profiling, event tracing, and online analysis of HPC + applications. +""" + +toolchain = {'name': 'gompi', 'version': '2024a'} + +source_urls = ['https://perftools.pages.jsc.fz-juelich.de/cicd/scorep/tags/scorep-%(version)s'] +sources = ['scorep-%(version)s.tar.gz'] +checksums = ['7bbde9a0721d27cc6205baf13c1626833bcfbabb1f33b325a2d67976290f7f8a'] + +dependencies = [ + ('CUDA', '12.6.0', '', SYSTEM), + ('UCX-CUDA', '1.16.0', versionsuffix), + ('CubeLib', '4.8.2'), + ('CubeWriter', '4.8.2'), + ('libunwind', '1.8.1'), + ('OPARI2', '2.0.8'), + ('OTF2', '3.0.3'), + # Hardware counter support (optional): + ('PAPI', '7.1.0'), + # PDT source-to-source instrumentation support (optional): + ('PDT', '3.25.2'), +] + +configopts = '--enable-shared' + +local_adapters = [ + 'compiler_event', 'cuda_mgmt', 'compiler_mgmt', 'mpi_event', 'mpi_mgmt', 'opari2_mgmt', 'user_event', 'user_mgmt' +] +sanity_check_paths = { + 'files': + ['bin/scorep', 'include/scorep/SCOREP_User.h'] + + ['lib/libscorep_adapter_%s.%s' % (a, e) for a in local_adapters for e in ('a', SHLIB_EXT)], + 'dirs': [], +} +sanity_check_commands = ['scorep-config --help'] + +# Ensure that local metric documentation is found by CubeGUI +modextrapaths = {'CUBE_DOCPATH': 'share/doc/scorep/profile'} + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/s/Score-P/Score-P-8.4-gompi-2024a.eb b/easybuild/easyconfigs/s/Score-P/Score-P-8.4-gompi-2024a.eb new file mode 100644 index 00000000000..eda406cbe2a --- /dev/null +++ b/easybuild/easyconfigs/s/Score-P/Score-P-8.4-gompi-2024a.eb @@ -0,0 +1,55 @@ +# Copyright 2013-2024 Juelich Supercomputing Centre, Germany +# Copyright 2020-2024 TU Dresden, Germany +# Authors:: +# * Bernd Mohr +# * Markus Geimer +# * Alexander Grund +# * Robert Mijakovic +# * Jan André Reuter +# License:: 3-clause BSD + +name = 'Score-P' +version = '8.4' + +homepage = 'https://www.score-p.org' +description = """ + The Score-P measurement infrastructure is a highly scalable and easy-to-use + tool suite for profiling, event tracing, and online analysis of HPC + applications. +""" + +toolchain = {'name': 'gompi', 'version': '2024a'} + +source_urls = ['https://perftools.pages.jsc.fz-juelich.de/cicd/scorep/tags/scorep-%(version)s'] +sources = ['scorep-%(version)s.tar.gz'] +checksums = ['7bbde9a0721d27cc6205baf13c1626833bcfbabb1f33b325a2d67976290f7f8a'] + +dependencies = [ + ('CubeLib', '4.8.2'), + ('CubeWriter', '4.8.2'), + ('libunwind', '1.8.1'), + ('OPARI2', '2.0.8'), + ('OTF2', '3.0.3'), + # Hardware counter support (optional): + ('PAPI', '7.1.0'), + # PDT source-to-source instrumentation support (optional): + ('PDT', '3.25.2'), +] + +configopts = '--enable-shared' + +local_adapters = [ + 'compiler_event', 'compiler_mgmt', 'mpi_event', 'mpi_mgmt', 'opari2_mgmt', 'user_event', 'user_mgmt' +] +sanity_check_paths = { + 'files': + ['bin/scorep', 'include/scorep/SCOREP_User.h'] + + ['lib/libscorep_adapter_%s.%s' % (a, e) for a in local_adapters for e in ('a', SHLIB_EXT)], + 'dirs': [], +} +sanity_check_commands = ['scorep-config --help'] + +# Ensure that local metric documentation is found by CubeGUI +modextrapaths = {'CUBE_DOCPATH': 'share/doc/scorep/profile'} + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/s/Seaborn/Seaborn-0.13.2-gfbf-2023b.eb b/easybuild/easyconfigs/s/Seaborn/Seaborn-0.13.2-gfbf-2023b.eb new file mode 100644 index 00000000000..23ec87f56ed --- /dev/null +++ b/easybuild/easyconfigs/s/Seaborn/Seaborn-0.13.2-gfbf-2023b.eb @@ -0,0 +1,24 @@ +easyblock = 'PythonPackage' + +name = 'Seaborn' +version = '0.13.2' + +homepage = 'https://seaborn.pydata.org/' +description = """ Seaborn is a Python visualization library based on matplotlib. + It provides a high-level interface for drawing attractive statistical graphics. """ + +toolchain = {'name': 'gfbf', 'version': '2023b'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['93e60a40988f4d65e9f4885df477e2fdaff6b73a9ded434c1ab356dd57eefff7'] + +dependencies = [ + ('Python', '3.11.5'), + ('matplotlib', '3.8.2'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/Seaborn/Seaborn-0.13.2-gfbf-2024a.eb b/easybuild/easyconfigs/s/Seaborn/Seaborn-0.13.2-gfbf-2024a.eb new file mode 100644 index 00000000000..de14ff81ce9 --- /dev/null +++ b/easybuild/easyconfigs/s/Seaborn/Seaborn-0.13.2-gfbf-2024a.eb @@ -0,0 +1,24 @@ +easyblock = 'PythonPackage' + +name = 'Seaborn' +version = '0.13.2' + +homepage = 'https://seaborn.pydata.org/' +description = """ Seaborn is a Python visualization library based on matplotlib. + It provides a high-level interface for drawing attractive statistical graphics. """ + +toolchain = {'name': 'gfbf', 'version': '2024a'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['93e60a40988f4d65e9f4885df477e2fdaff6b73a9ded434c1ab356dd57eefff7'] + +dependencies = [ + ('Python', '3.12.3'), + ('matplotlib', '3.9.2'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SentencePiece/SentencePiece-0.2.0-GCC-13.2.0.eb b/easybuild/easyconfigs/s/SentencePiece/SentencePiece-0.2.0-GCC-13.2.0.eb new file mode 100644 index 00000000000..246989eefdc --- /dev/null +++ b/easybuild/easyconfigs/s/SentencePiece/SentencePiece-0.2.0-GCC-13.2.0.eb @@ -0,0 +1,70 @@ +easyblock = 'Bundle' + +name = 'SentencePiece' +version = '0.2.0' + +homepage = 'https://github.com/google/sentencepiece' +description = "Unsupervised text tokenizer for Neural Network-based text generation." +github_account = 'google' + +toolchain = {'name': 'GCC', 'version': '13.2.0'} + +builddependencies = [ + ('CMake', '3.27.6'), + ('pkgconf', '2.0.3'), +] + +dependencies = [ + ('Python', '3.11.5'), + ('gperftools', '2.13'), +] + +default_component_specs = { + 'source_urls': [GITHUB_LOWER_SOURCE], + 'sources': ['v%(version)s.tar.gz'], + 'checksums': ['9970f0a0afee1648890293321665e5b2efa04eaec9f1671fcf8048f456f5bb86'], +} + +local_external_absl = 'sed -i %(builddir)s/' + +components = [ + (name, version, { + 'easyblock': 'CMakeMake', + 'separate_build_dir': True, + 'start_dir': '%(namelower)s-%(version)s', + # using internal protobuf there is no matching pc file so requirement is removed: + 'preconfigopts': 'sed -i s/Requires.private.*// ../sentencepiece-%(version)s/sentencepiece.pc.in &&', + }), + ('sentencepiece', version, { + 'easyblock': 'PythonPackage', + 'start_dir': '%(namelower)s-%(version)s/python', + # Unpredicable where pc files end up; including both lib and lib64 + 'prebuildopts': 'export PKG_CONFIG_PATH=%(installdir)s/lib64/pkgconfig:%(installdir)s/lib/pkgconfig/:' + '$PKG_CONFIG_PATH && ', + 'preinstallopts': 'export PKG_CONFIG_PATH=%(installdir)s/lib64/pkgconfig:%(installdir)s/lib/pkgconfig/:' + '$PKG_CONFIG_PATH && ', + 'use_pip': True, + 'download_dep_fail': True, + 'sanity_pip_check': True, + }), +] + +postinstallcmds = ['cp -a %(builddir)s/%(namelower)s-%(version)s/{data,doc} %(installdir)s/'] + +sanity_check_paths = { + 'files': ['bin/spm_%s' % x for x in ['decode', 'encode', 'export_vocab', 'normalize', 'train']] + + ['lib/libsentencepiece.%s' % SHLIB_EXT, 'lib/libsentencepiece_train.%s' % SHLIB_EXT] + + ['include/sentencepiece_processor.h', 'include/sentencepiece_trainer.h'], + 'dirs': ['lib/python%(pyshortver)s/site-packages', 'data', 'doc'], +} + +sanity_check_commands = [ + 'spm_train --help | grep accept_language', # --help has exit code 1, so we check for output text + "python -c 'import sentencepiece'", +] + +modextrapaths = { + 'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages'] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/SeqKit/SeqKit-2.8.2.eb b/easybuild/easyconfigs/s/SeqKit/SeqKit-2.8.2.eb new file mode 100644 index 00000000000..820f9abf719 --- /dev/null +++ b/easybuild/easyconfigs/s/SeqKit/SeqKit-2.8.2.eb @@ -0,0 +1,26 @@ +easyblock = 'GoPackage' + +name = 'SeqKit' +version = '2.8.2' + +homepage = 'https://bioinf.shenwei.me/seqkit/' +description = """SeqKit - a cross-platform and ultrafast toolkit for FASTA/Q file manipulation""" + +toolchain = SYSTEM + +source_urls = ['https://github.com/shenwei356/seqkit/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['9cf1e744b785fa673af5a7a1ce2f96d52dc03e14b6537097df86aa6266204556'] + +builddependencies = [ + ('Go', '1.22.1'), +] + +installopts = './%(namelower)s' + +sanity_check_commands = [ + "seqkit version", + "seqkit genautocomplete" +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/Seurat/Seurat-5.1.0-foss-2023a-R-4.3.2.eb b/easybuild/easyconfigs/s/Seurat/Seurat-5.1.0-foss-2023a-R-4.3.2.eb new file mode 100644 index 00000000000..11f439e4017 --- /dev/null +++ b/easybuild/easyconfigs/s/Seurat/Seurat-5.1.0-foss-2023a-R-4.3.2.eb @@ -0,0 +1,76 @@ +easyblock = 'Bundle' + +name = 'Seurat' +version = '5.1.0' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://satijalab.org/seurat' +description = "Seurat is an R package designed for QC, analysis, and exploration of single cell RNA-seq data." + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('R', '4.3.2'), + ('R-bundle-Bioconductor', '3.18', versionsuffix), +] + +exts_defaultclass = 'RPackage' +exts_default_options = { + 'sources': ['%(name)s_%(version)s.tar.gz'], + 'source_urls': [ + 'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'https://cran.r-project.org/src/contrib/', # current version of packages + 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + ], +} + +exts_list = [ + ('Matrix', '1.6-4', { + 'checksums': ['70ca7bdaece68d4837da0523d067e1553947c3c81b0b55206223bb647617bb01'], + }), + ('sp', '2.1-4', { + 'checksums': ['e185e7fb61d2d7dbc50fd765a93e170fa778083a653588db1f5e99d019479f0a'], + }), + ('SeuratObject', '5.0.2', { + 'checksums': ['ded30d21f445b7e353fe4a0c4954d45ad19fbe162615d9addf6732f9318ba0cf'], + }), + ('sctransform', '0.4.1', { + 'checksums': ['5f6be7f8be543e4c32c8007207b603a750881459370b7bb5afd63e8c8fabf171'], + }), + ('uwot', '0.2.2', { + 'checksums': ['d9938c43d29530d4b36d1b2649cc679b09945a740db2cd3a266242b1aa9a6cd1'], + }), + ('spatstat.utils', '3.0-1', { + 'checksums': ['cba1c7806564fd9145ca15edf77233d6ba5609f0989f7812221f5fc1ece0b91a'], + }), + ('spatstat.data', '3.0-0', { + 'checksums': ['cff9058a88489020a4a05b9576cd452f37fa9b42084873c474d06931f5187057'], + }), + ('spatstat.geom', '3.0-3', { + 'checksums': ['6e5b56c60e774a0cdcaa5a8ffde071225f233832446a341588bd8a7840913c84'], + }), + ('spatstat.random', '3.0-1', { + 'checksums': ['938c845c063b8781bf894c0a67537e7b2a7c425a4beba4a95ec9d2c37b43e5b6'], + }), + ('spatstat.sparse', '3.0-0', { + 'checksums': ['99be0a3c7592760fdf1668dc0811f75ed91c400390d1ecc3d5e643255f501ad2'], + }), + ('spatstat.explore', '3.0-5', { + 'checksums': ['9f438a12fac3f3e1d0bd550b1393c1e5732be694517b0878db09da557d6dc862'], + }), + ('scattermore', '1.2', { + 'checksums': ['5534a87b0bdd1375f0fbffc1a5c980ad64e33a108435a67469b8324b580602d1'], + }), + (name, version, { + 'checksums': ['adcfb43d7a8cc55eaa7a0954a082ac95e14059a82901913379bfec115e224d59'], + }), +] + +sanity_check_paths = { + 'files': [], + 'dirs': [name], +} + +modextrapaths = {'R_LIBS_SITE': ''} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/Shapely/Shapely-2.0.6-gfbf-2024a.eb b/easybuild/easyconfigs/s/Shapely/Shapely-2.0.6-gfbf-2024a.eb new file mode 100644 index 00000000000..4488ff1f7e4 --- /dev/null +++ b/easybuild/easyconfigs/s/Shapely/Shapely-2.0.6-gfbf-2024a.eb @@ -0,0 +1,31 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Updated: Denis Kristak +easyblock = 'PythonPackage' + +name = 'Shapely' +version = '2.0.6' + +homepage = 'https://github.com/Toblerity/Shapely' +description = """Shapely is a BSD-licensed Python package for manipulation and analysis of planar geometric objects. +It is based on the widely deployed GEOS (the engine of PostGIS) and JTS (from which GEOS is ported) libraries.""" + +toolchain = {'name': 'gfbf', 'version': '2024a'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['997f6159b1484059ec239cacaa53467fd8b5564dabe186cd84ac2944663b0bf6'] + +builddependencies = [ + ('Cython', '3.0.10'), +] + +dependencies = [ + ('Python', '3.12.3'), + ('SciPy-bundle', '2024.05'), + ('GEOS', '3.12.2'), +] + +download_dep_fail = True +sanity_pip_check = True +use_pip = True + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/SharedMeatAxe/SharedMeatAxe-1.0.1-GCC-13.2.0.eb b/easybuild/easyconfigs/s/SharedMeatAxe/SharedMeatAxe-1.0.1-GCC-13.2.0.eb new file mode 100644 index 00000000000..36923c839cc --- /dev/null +++ b/easybuild/easyconfigs/s/SharedMeatAxe/SharedMeatAxe-1.0.1-GCC-13.2.0.eb @@ -0,0 +1,38 @@ +easyblock = 'ConfigureMake' + +name = 'SharedMeatAxe' +version = '1.0.1' + +homepage = 'https://github.com/simon-king-jena/SharedMeatAxe' +description = """This is an autotoolized shared library version of C MeatAxe 2.4.24, + a set of programs for computing with modular representations.""" + +toolchain = {'name': 'GCC', 'version': '13.2.0'} + +source_urls = ['https://github.com/simon-king-jena/SharedMeatAxe/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['e1e802ef60f3280cdacb3de6d693ebd71b43af93e33c739de2697605c59b1a3b'] + +builddependencies = [ + ('Autotools', '20220317'), +] + +preconfigopts = 'autoreconf --install && ' + +runtest = 'check' + +local_bins = [ + 'cfcomp', 'genmod', 'mkgraph', 'mkinc', 'orbrep', 'pwkond', 'symnew', 'zad', 'zcl', 'zcv', 'zfr', 'zmo', 'znu', + 'zpr', 'zro', 'zsp', 'zte', 'zuk', 'chop', 'mkcycl', 'mkhom', 'mksub', 'precond', 'rad', 'tcond', 'zbl', 'zcp', + 'zef', 'ziv', 'zmu', 'zor', 'zpt', 'zsc', 'zsy', 'ztr', 'zvp', 'decomp', 'mkdotl', 'mkhom_old', 'mktree', + 'pseudochop', 'soc', 'tuc', 'zcf', 'zct', 'zev', 'zkd', 'zmw', 'zpo', 'zqt', 'zsi', 'ztc', 'zts', +] + +sanity_check_paths = { + 'files': ['bin/%s' % bin for bin in local_bins] + ['include/meataxe.h', 'lib/libmtx.%s' % SHLIB_EXT], + 'dirs': [] +} + +sanity_check_commands = ['mktree --help'] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/SignalP/SignalP-6.0h-foss-2023a-CUDA-12.1.1-fast.eb b/easybuild/easyconfigs/s/SignalP/SignalP-6.0h-foss-2023a-CUDA-12.1.1-fast.eb new file mode 100644 index 00000000000..db9e6fe2fb3 --- /dev/null +++ b/easybuild/easyconfigs/s/SignalP/SignalP-6.0h-foss-2023a-CUDA-12.1.1-fast.eb @@ -0,0 +1,55 @@ +# This file is an EasyBuild reciPY as per https://easybuilders.github.io/easybuild/ +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'PythonPackage' + +name = 'SignalP' +version = '6.0h' +_suffix = 'fast' +versionsuffix = '-CUDA-%(cudaver)s-' + _suffix + +homepage = 'https://services.healthtech.dtu.dk/software.php' +description = """SignalP predicts the presence and location of signal peptide cleavage sites +in amino acid sequences from different organisms""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +download_instructions = """ +SignalP requires registration and acceptance of licence terms (academic use only). + [1] go to: https://services.healthtech.dtu.dk/service.php?SignalP-6.0 + [2] navigate to the "Downloads" tab + [3] select "%s" type under version "%%(version)s" + [4] complete the form; you should receive a download link via email +""" % _suffix + +sources = ['%%(namelower)s-%%(version)s.%s.tar.gz' % _suffix] +checksums = ['4afe3c004e23a1d6518cefb23448b4d5ede5f1c5b276db541f839f0615822125'] + +unpack_options = '--strip-components=1' + +dependencies = [ + ('CUDA', '12.1.1', '', SYSTEM), + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('tqdm', '4.66.1'), + ('PyTorch', '2.1.2', '-CUDA-%(cudaver)s'), + ('matplotlib', '3.7.2'), +] + +preinstallopts = "sed -i 's/torch.*/torch/g' requirements.txt && " + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +_bin = '%%(namelower)s%s' % version[0] +sanity_check_paths = { + 'files': ['bin/%s' % _bin], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(namelower)s'], +} + +sanity_check_commands = ['%s --help' % _bin] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SignalP/SignalP-6.0h-foss-2023a-fast.eb b/easybuild/easyconfigs/s/SignalP/SignalP-6.0h-foss-2023a-fast.eb new file mode 100644 index 00000000000..8e65da2a7d7 --- /dev/null +++ b/easybuild/easyconfigs/s/SignalP/SignalP-6.0h-foss-2023a-fast.eb @@ -0,0 +1,54 @@ +# This file is an EasyBuild reciPY as per https://easybuilders.github.io/easybuild/ +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'PythonPackage' + +name = 'SignalP' +version = '6.0h' +_suffix = 'fast' +versionsuffix = '-' + _suffix + +homepage = 'https://services.healthtech.dtu.dk/software.php' +description = """SignalP predicts the presence and location of signal peptide cleavage sites +in amino acid sequences from different organisms""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +download_instructions = """ +SignalP requires registration and acceptance of licence terms (academic use only). + [1] go to: https://services.healthtech.dtu.dk/service.php?SignalP-6.0 + [2] navigate to the "Downloads" tab + [3] select "%s" type under version "%%(version)s" + [4] complete the form; you should receive a download link via email +""" % _suffix + +sources = ['%%(namelower)s-%%(version)s.%s.tar.gz' % _suffix] +checksums = ['4afe3c004e23a1d6518cefb23448b4d5ede5f1c5b276db541f839f0615822125'] + +unpack_options = '--strip-components=1' + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('tqdm', '4.66.1'), + ('PyTorch', '2.1.2'), + ('matplotlib', '3.7.2'), +] + +preinstallopts = "sed -i 's/torch.*/torch/g' requirements.txt && " + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +_bin = '%%(namelower)s%s' % version[0] +sanity_check_paths = { + 'files': ['bin/%s' % _bin], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(namelower)s'], +} + +sanity_check_commands = ['%s --help' % _bin] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/Single-cell-python-bundle/Single-cell-python-bundle-2024.02-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/s/Single-cell-python-bundle/Single-cell-python-bundle-2024.02-foss-2023a-CUDA-12.1.1.eb new file mode 100644 index 00000000000..22eca6d4ed4 --- /dev/null +++ b/easybuild/easyconfigs/s/Single-cell-python-bundle/Single-cell-python-bundle-2024.02-foss-2023a-CUDA-12.1.1.eb @@ -0,0 +1,247 @@ +easyblock = 'PythonBundle' + +name = 'Single-cell-python-bundle' +version = '2024.02' +versionsuffix = '-CUDA-12.1.1' + +homepage = (None) +description = """Bundle of tools for single-cell sequence analysis.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [ + ('poetry', '1.5.1'), + ('CMake', '3.26.3'), + ('hatchling', '1.18.0'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('SciPy-bundle', '2023.07'), + ('matplotlib', '3.7.2'), + ('Seaborn', '0.13.2'), + ('PyTorch', '2.1.2', versionsuffix), + ('scanpy', '1.9.8'), + ('scib', '1.1.4'), + ('scVelo', '0.3.1'), + ('CellTypist', '1.6.2'), + ('epiScanpy', '0.4.0'), + ('scCODA', '0.1.9'), + ('infercnvpy', '0.4.3'), + ('pySCENIC', '0.12.1-20240311'), + ('CellRank', '2.0.2', versionsuffix), + ('Squidpy', '1.4.1'), + ('Cassiopeia', '2.0.0'), + ('scvi-tools', '1.1.2', versionsuffix), + ('scArches', '0.6.1', versionsuffix), + ('scib-metrics', '0.5.1', versionsuffix), + # deps of exts: + ('umap-learn', '0.5.5'), # bbknn + ('scikit-learn', '1.3.1'), # bbknn, sc_toolbox + ('PyYAML', '6.0'), # sc_toolbox + ('typing-extensions', '4.9.0'), # sc_toolbox + ('adjustText', '0.7.3'), # sc_toolbox + ('python-parasail', '1.3.4'), # scirpy + ('graph-tool', '2.59'), # schist + ('Pyomo', '6.7.3'), # pertpy + ('mpmath', '1.3.0'), # blitzgsea +] + +exts_list = [ + ('flit_core', '3.9.0', { + 'checksums': ['72ad266176c4a3fcfab5f2930d76896059851240570ce9a98733b658cb786eba'], + }), + ('annoy', '1.17.3', { + 'checksums': ['9cbfebefe0a5f843eba29c6be4c84d601f4f41ad4ded0486f1b88c3b07739c15'], + }), + ('pynndescent', '0.5.11', { + 'checksums': ['6f44ced9d5a9da2c87d9b2fff30bb5308540c0657605e4d5cde7ed3275bbad50'], + }), + ('bbknn', '1.6.0', { + 'checksums': ['1c01a9d6df2fc52a527de8a403617897a4b672724863299a7026f2132f1b041b'], + }), + ('tzlocal', '5.2', { + 'checksums': ['8d399205578f1a9342816409cc1e46a93ebd5755e39ea2d85334bea911bf0e6e'], + }), + ('anndata2ri', '1.3.1', { + 'checksums': ['0e3fa2f81789f682d19ef452fabdb401ec27899db9abe5a78e45e21dcc7caa42'], + }), + ('pypi-latest', '0.1.2', { + 'checksums': ['b195654567e6abaac6acfec37638d8e000838f419bc6b129962a896eedc4ed4e'], + }), + ('text-unidecode', '1.3', { + 'checksums': ['bad6603bb14d279193107714b288be206cac565dfa49aa5b105294dd5c4aab93'], + }), + ('python-slugify', '8.0.4', { + 'modulename': 'slugify', + 'checksums': ['59202371d1d05b54a9e7720c5e038f928f45daaffe41dd10822f3907b937c856'], + }), + ('prompt_toolkit', '3.0.36', { + 'checksums': ['3e163f254bef5a03b146397d7c1963bd3e2812f0964bb9a24e6ec761fd28db63'], + }), + ('binaryornot', '0.4.4', { + 'checksums': ['359501dfc9d40632edc9fac890e19542db1a287bbcfa58175b66658392018061'], + }), + ('types-python-dateutil', '2.9.0.20240316', { + 'modulename': False, + 'checksums': ['5d2f2e240b86905e40944dd787db6da9263f0deabef1076ddaed797351ec0202'], + }), + ('arrow', '1.3.0', { + 'checksums': ['d4540617648cb5f895730f1ad8c82a65f2dad0166f57b75f3ca54759c4d67a85'], + }), + ('cookiecutter', '2.6.0', { + 'checksums': ['db21f8169ea4f4fdc2408d48ca44859349de2647fbe494a9d6c3edfc0542c21c'], + }), + ('questionary', '2.0.1', { + 'checksums': ['bcce898bf3dbb446ff62830c86c5c6fb9a22a54146f0f5597d3da43b10d8fc8b'], + }), + ('rich', '13.7.1', { + 'checksums': ['9be308cb1fe2f1f57d67ce99e95af38a1e2bc71ad9813b0e247cf7ffbcc3a432'], + }), + ('sc_toolbox', '0.12.3', { + 'checksums': ['6ca22a364c269a095114e620eb3c6da8aac1950d8f43f58ceea08005a09cc2cb'], + }), + ('toolz', '0.12.1', { + 'checksums': ['ecca342664893f177a13dac0e6b41cbd8ac25a358e5f215316d43e2100224f4d'], + }), + ('altair', '5.2.0', { + 'checksums': ['2ad7f0c8010ebbc46319cc30febfb8e59ccf84969a201541c207bc3a4fa6cf81'], + }), + ('custom_inherit', '2.4.1', { + 'checksums': ['7052eb337bcce83551815264391cc4efc2bf70b295a3c52aba64f1ab57c3a8a2'], + }), + ('multipledispatch', '1.0.0', { + 'checksums': ['5c839915465c68206c3e9c473357908216c28383b425361e5d144594bf85a7e0'], + }), + ('pypng', '0.20220715.0', { + 'modulename': 'png', + 'checksums': ['739c433ba96f078315de54c0db975aee537cbc3e1d0ae4ed9aab0ca1e427e2c1'], + }), + ('reportlab', '4.1.0', { + 'checksums': ['3a99faf412691159c068b3ff01c15307ce2fd2cf6b860199434874e002040a84'], + }), + ('toyplot', '1.0.3', { + 'checksums': ['7b7b2bc5784fd75e5c695300bffc80d568c83bebef543bb54e6e6c2229912edd'], + }), + ('toytree', '2.0.5', { + 'checksums': ['7be04ca310067e0e9737449700d6ab1b68b4379b64e2d22f2f7697a70030ceb0'], + }), + ('tascCODA', '0.1.3', { + # strip out tensorflow-probability as required dependency, to ensure that 'pip check' passes + 'preinstallopts': "sed -i '/tensorflow-probability>=0.16/d' setup.py && ", + 'checksums': ['8c12ddccb72c41c96c6a5abceb52e7a76f439a9ab94fb092aa86ee3c1292383a'], + }), + ('harmonypy', '0.0.9', { + 'checksums': ['85bfdd4e6ec6e0fa8816a276639358d3598a40d60ba9f7a5d9dada8706be8c4d'], + }), + ('fbpca', '1.0', { + 'checksums': ['150677642479663f317fdbb5e06dab3f98721cf7031bb4a84113d7a631c472d1'], + }), + ('geosketch', '1.2', { + 'checksums': ['bbfe97366b91c5927b6076d5a6738d9cfbe094efb5ac1117aab7a30b6081cc4e'], + }), + ('python_circos', '0.3.0', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'modulename': 'pycircos', + 'checksums': ['410eaffc4eb2933cd688897356813da23310f5e2f14a8bceb003e9b96faa715b'], + }), + ('mizani', '0.9.3', { + 'checksums': ['fb61339e9e4711850e902ca286b1ae75255f483823d891aa0515b426d56c606d'], + }), + ('plotnine', '0.12.4', { + 'checksums': ['adc41a672503594445a8fa19872799253bd0784cdbd5a1cc16657a1dd20ba905'], + }), + ('ktplotspy', '0.2.3', { + 'checksums': ['9a1e3646217e6e99f59ab2258dfd76120cf1f50880c9cb2f9005de397c00f0a9'], + }), + ('cellphonedb', '5.0.0', { + 'checksums': ['1c96173d8527f1655216d265fc50a28ea3360d70486afa5050e3f5565fa3a8cd'], + }), + ('decoupler', '1.6.0', { + 'checksums': ['dde501f4d3e55a260f716e51b871bee403bc8aaa6b66799df0e42dee0787b98d'], + }), + ('mudata', '0.2.3', { + 'checksums': ['45288ac150bfc598d68acb7c2c1c43c38c5c39522107e04f7efbf3360c7f2035'], + }), + ('nodeenv', '1.9.0', { + 'checksums': ['07f144e90dae547bf0d4ee8da0ee42664a42a04e02ed68e06324348dafe4bdb1'], + }), + ('identify', '2.5.36', { + 'checksums': ['e5e00f54165f9047fbebeb4a560f9acfb8af4c88232be60a488e9b68d122745d'], + }), + ('cfgv', '3.4.0', { + 'checksums': ['e52591d4c5f5dead8e0f673fb16db7949d2cfb3f7da4582893288f0ded8fe560'], + }), + ('pre_commit', '3.7.1', { + 'checksums': ['8ca3ad567bc78a4972a3f1a477e94a79d4597e8140a6e0b651c5e33899c3654a'], + }), + ('muon', '0.1.6', { + 'checksums': ['762feeb6f52f865cf79d0d0332cc742fe91c1885f668ce15794b62b3952b02f9'], + }), + ('liana', '1.2.0', { + 'checksums': ['be899c69bfcbf3d0f8b61c04c35f225ac6b11fe1ea80e6ed4bdc0e6212cb2379'], + }), + ('squarify', '0.4.3', { + 'checksums': ['54091f6ad175f7f201f8934574e647ce1b50dedc478c5fd968688eb7d7469f95'], + }), + ('scikit_build_core', '0.9.3', { + 'checksums': ['341d113e473a5409dc62522e8b1b1b8b1647a0b95557ad15f6be2a36071fd390'], + }), + ('awkward-cpp', '33', { + 'checksums': ['550adebccd329d18d02e95226d0b89698188fd33e44f07450942c692881927d8'], + }), + ('awkward', '2.6.4', { + 'checksums': ['ee0cb27c64150f368749983dda499c108848c64dc830912480eb37b78c04300f'], + }), + ('yamlordereddictloader', '0.4.2', { + 'checksums': ['36af2f6210fcff5da4fc4c12e1d815f973dceb41044e795e1f06115d634bca13'], + }), + ('airr', '1.5.0', { + 'checksums': ['febc0a881bf46b1a9c29ac6a7089dd733ff9120d114585e75dede26403f68d42'], + }), + ('scirpy', '0.17.0', { + 'checksums': ['f61653a4f7387562ec89b00fbfd7cab762c0bf3320f21ccfc47df80a13cc5d41'], + }), + ('schist', '0.8.3', { + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/dawe/schist/archive/'], + 'checksums': ['9b98ec9d85554573288c24f18c4791ba7c4d315397cbc422ea25d4a7cdd42e6d'], + }), + ('typeguard', '2.13.3', { + 'checksums': ['00edaa8da3a133674796cf5ea87d9f4b4c367d77476e185e80251cc13dfbb8c4'], + }), + ('jaxtyping', '0.2.29', { + 'checksums': ['e1cd916ed0196e40402b0638449e7d051571562b2cd68d8b94961a383faeb409'], + }), + ('equinox', '0.11.4', { + 'checksums': ['0033d9731083f402a855b12a0777a80aa8507651f7aa86d9f0f9503bcddfd320'], + }), + ('lineax', '0.0.4', { + 'checksums': ['e68f1eba2f352122fdce9adc0556684f31eb8364b1a00acee484dd6e44a34e5e'], + }), + ('jaxopt', '0.8.3', { + 'checksums': ['4b06dfa6f915a4f3291699606245af6069371a48dc5c92d4c507840d62990646'], + }), + ('ott_jax', '0.4.6', { + 'modulename': 'ott', + 'checksums': ['bc91f8d512cdb344439f5584712d76cd0650b6716b6686d53b828cc67abdbcba'], + }), + ('sparsecca', '0.3.1', { + 'checksums': ['be1526baebac5ce6efbc7190fd62a1cec13288c493f5d427024f66ca6afaec13'], + }), + ('PubChemPy', '1.0.4', { + 'checksums': ['24e9dc2fc90ab153b2764bf805e510b1410700884faf0510a9e7cf0d61d8ed0e'], + }), + ('blitzgsea', '1.3.42', { + 'checksums': ['dcc997b5d29d190d8632474f3bb57b5ead7fb1370b478c7f824b42782325a1ca'], + }), + ('pertpy', '0.7.0', { + 'checksums': ['273723b5b70f3cb714bb36d3234462014b72e133111eeaf08aa47153c9df14aa'], + }), +] + +use_pip = True +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/Single-cell-python-bundle/Single-cell-python-bundle-2024.02-foss-2023a.eb b/easybuild/easyconfigs/s/Single-cell-python-bundle/Single-cell-python-bundle-2024.02-foss-2023a.eb new file mode 100644 index 00000000000..c0f6cb45631 --- /dev/null +++ b/easybuild/easyconfigs/s/Single-cell-python-bundle/Single-cell-python-bundle-2024.02-foss-2023a.eb @@ -0,0 +1,246 @@ +easyblock = 'PythonBundle' + +name = 'Single-cell-python-bundle' +version = '2024.02' + +homepage = (None) +description = """Bundle of tools for single-cell sequence analysis.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [ + ('poetry', '1.5.1'), + ('CMake', '3.26.3'), + ('hatchling', '1.18.0'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('SciPy-bundle', '2023.07'), + ('matplotlib', '3.7.2'), + ('Seaborn', '0.13.2'), + ('PyTorch', '2.1.2'), + ('scanpy', '1.9.8'), + ('scib', '1.1.4'), + ('scVelo', '0.3.1'), + ('CellTypist', '1.6.2'), + ('epiScanpy', '0.4.0'), + ('scCODA', '0.1.9'), + ('infercnvpy', '0.4.3'), + ('pySCENIC', '0.12.1-20240311'), + ('CellRank', '2.0.2'), + ('Squidpy', '1.4.1'), + ('Cassiopeia', '2.0.0'), + ('scvi-tools', '1.1.2'), + ('scArches', '0.6.1'), + ('scib-metrics', '0.5.1'), + # deps of exts: + ('umap-learn', '0.5.5'), # bbknn + ('scikit-learn', '1.3.1'), # bbknn, sc_toolbox + ('PyYAML', '6.0'), # sc_toolbox + ('typing-extensions', '4.9.0'), # sc_toolbox + ('adjustText', '0.7.3'), # sc_toolbox + ('python-parasail', '1.3.4'), # scirpy + ('graph-tool', '2.59'), # schist + ('Pyomo', '6.7.3'), # pertpy + ('mpmath', '1.3.0'), # blitzgsea +] + +exts_list = [ + ('flit_core', '3.9.0', { + 'checksums': ['72ad266176c4a3fcfab5f2930d76896059851240570ce9a98733b658cb786eba'], + }), + ('annoy', '1.17.3', { + 'checksums': ['9cbfebefe0a5f843eba29c6be4c84d601f4f41ad4ded0486f1b88c3b07739c15'], + }), + ('pynndescent', '0.5.11', { + 'checksums': ['6f44ced9d5a9da2c87d9b2fff30bb5308540c0657605e4d5cde7ed3275bbad50'], + }), + ('bbknn', '1.6.0', { + 'checksums': ['1c01a9d6df2fc52a527de8a403617897a4b672724863299a7026f2132f1b041b'], + }), + ('tzlocal', '5.2', { + 'checksums': ['8d399205578f1a9342816409cc1e46a93ebd5755e39ea2d85334bea911bf0e6e'], + }), + ('anndata2ri', '1.3.1', { + 'checksums': ['0e3fa2f81789f682d19ef452fabdb401ec27899db9abe5a78e45e21dcc7caa42'], + }), + ('pypi-latest', '0.1.2', { + 'checksums': ['b195654567e6abaac6acfec37638d8e000838f419bc6b129962a896eedc4ed4e'], + }), + ('text-unidecode', '1.3', { + 'checksums': ['bad6603bb14d279193107714b288be206cac565dfa49aa5b105294dd5c4aab93'], + }), + ('python-slugify', '8.0.4', { + 'modulename': 'slugify', + 'checksums': ['59202371d1d05b54a9e7720c5e038f928f45daaffe41dd10822f3907b937c856'], + }), + ('prompt_toolkit', '3.0.36', { + 'checksums': ['3e163f254bef5a03b146397d7c1963bd3e2812f0964bb9a24e6ec761fd28db63'], + }), + ('binaryornot', '0.4.4', { + 'checksums': ['359501dfc9d40632edc9fac890e19542db1a287bbcfa58175b66658392018061'], + }), + ('types-python-dateutil', '2.9.0.20240316', { + 'modulename': False, + 'checksums': ['5d2f2e240b86905e40944dd787db6da9263f0deabef1076ddaed797351ec0202'], + }), + ('arrow', '1.3.0', { + 'checksums': ['d4540617648cb5f895730f1ad8c82a65f2dad0166f57b75f3ca54759c4d67a85'], + }), + ('cookiecutter', '2.6.0', { + 'checksums': ['db21f8169ea4f4fdc2408d48ca44859349de2647fbe494a9d6c3edfc0542c21c'], + }), + ('questionary', '2.0.1', { + 'checksums': ['bcce898bf3dbb446ff62830c86c5c6fb9a22a54146f0f5597d3da43b10d8fc8b'], + }), + ('rich', '13.7.1', { + 'checksums': ['9be308cb1fe2f1f57d67ce99e95af38a1e2bc71ad9813b0e247cf7ffbcc3a432'], + }), + ('sc_toolbox', '0.12.3', { + 'checksums': ['6ca22a364c269a095114e620eb3c6da8aac1950d8f43f58ceea08005a09cc2cb'], + }), + ('toolz', '0.12.1', { + 'checksums': ['ecca342664893f177a13dac0e6b41cbd8ac25a358e5f215316d43e2100224f4d'], + }), + ('altair', '5.2.0', { + 'checksums': ['2ad7f0c8010ebbc46319cc30febfb8e59ccf84969a201541c207bc3a4fa6cf81'], + }), + ('custom_inherit', '2.4.1', { + 'checksums': ['7052eb337bcce83551815264391cc4efc2bf70b295a3c52aba64f1ab57c3a8a2'], + }), + ('multipledispatch', '1.0.0', { + 'checksums': ['5c839915465c68206c3e9c473357908216c28383b425361e5d144594bf85a7e0'], + }), + ('pypng', '0.20220715.0', { + 'modulename': 'png', + 'checksums': ['739c433ba96f078315de54c0db975aee537cbc3e1d0ae4ed9aab0ca1e427e2c1'], + }), + ('reportlab', '4.1.0', { + 'checksums': ['3a99faf412691159c068b3ff01c15307ce2fd2cf6b860199434874e002040a84'], + }), + ('toyplot', '1.0.3', { + 'checksums': ['7b7b2bc5784fd75e5c695300bffc80d568c83bebef543bb54e6e6c2229912edd'], + }), + ('toytree', '2.0.5', { + 'checksums': ['7be04ca310067e0e9737449700d6ab1b68b4379b64e2d22f2f7697a70030ceb0'], + }), + ('tascCODA', '0.1.3', { + # strip out tensorflow-probability as required dependency, to ensure that 'pip check' passes + 'preinstallopts': "sed -i '/tensorflow-probability>=0.16/d' setup.py && ", + 'checksums': ['8c12ddccb72c41c96c6a5abceb52e7a76f439a9ab94fb092aa86ee3c1292383a'], + }), + ('harmonypy', '0.0.9', { + 'checksums': ['85bfdd4e6ec6e0fa8816a276639358d3598a40d60ba9f7a5d9dada8706be8c4d'], + }), + ('fbpca', '1.0', { + 'checksums': ['150677642479663f317fdbb5e06dab3f98721cf7031bb4a84113d7a631c472d1'], + }), + ('geosketch', '1.2', { + 'checksums': ['bbfe97366b91c5927b6076d5a6738d9cfbe094efb5ac1117aab7a30b6081cc4e'], + }), + ('python_circos', '0.3.0', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'modulename': 'pycircos', + 'checksums': ['410eaffc4eb2933cd688897356813da23310f5e2f14a8bceb003e9b96faa715b'], + }), + ('mizani', '0.9.3', { + 'checksums': ['fb61339e9e4711850e902ca286b1ae75255f483823d891aa0515b426d56c606d'], + }), + ('plotnine', '0.12.4', { + 'checksums': ['adc41a672503594445a8fa19872799253bd0784cdbd5a1cc16657a1dd20ba905'], + }), + ('ktplotspy', '0.2.3', { + 'checksums': ['9a1e3646217e6e99f59ab2258dfd76120cf1f50880c9cb2f9005de397c00f0a9'], + }), + ('cellphonedb', '5.0.0', { + 'checksums': ['1c96173d8527f1655216d265fc50a28ea3360d70486afa5050e3f5565fa3a8cd'], + }), + ('decoupler', '1.6.0', { + 'checksums': ['dde501f4d3e55a260f716e51b871bee403bc8aaa6b66799df0e42dee0787b98d'], + }), + ('mudata', '0.2.3', { + 'checksums': ['45288ac150bfc598d68acb7c2c1c43c38c5c39522107e04f7efbf3360c7f2035'], + }), + ('nodeenv', '1.9.0', { + 'checksums': ['07f144e90dae547bf0d4ee8da0ee42664a42a04e02ed68e06324348dafe4bdb1'], + }), + ('identify', '2.5.36', { + 'checksums': ['e5e00f54165f9047fbebeb4a560f9acfb8af4c88232be60a488e9b68d122745d'], + }), + ('cfgv', '3.4.0', { + 'checksums': ['e52591d4c5f5dead8e0f673fb16db7949d2cfb3f7da4582893288f0ded8fe560'], + }), + ('pre_commit', '3.7.1', { + 'checksums': ['8ca3ad567bc78a4972a3f1a477e94a79d4597e8140a6e0b651c5e33899c3654a'], + }), + ('muon', '0.1.6', { + 'checksums': ['762feeb6f52f865cf79d0d0332cc742fe91c1885f668ce15794b62b3952b02f9'], + }), + ('liana', '1.2.0', { + 'checksums': ['be899c69bfcbf3d0f8b61c04c35f225ac6b11fe1ea80e6ed4bdc0e6212cb2379'], + }), + ('squarify', '0.4.3', { + 'checksums': ['54091f6ad175f7f201f8934574e647ce1b50dedc478c5fd968688eb7d7469f95'], + }), + ('scikit_build_core', '0.9.3', { + 'checksums': ['341d113e473a5409dc62522e8b1b1b8b1647a0b95557ad15f6be2a36071fd390'], + }), + ('awkward-cpp', '33', { + 'checksums': ['550adebccd329d18d02e95226d0b89698188fd33e44f07450942c692881927d8'], + }), + ('awkward', '2.6.4', { + 'checksums': ['ee0cb27c64150f368749983dda499c108848c64dc830912480eb37b78c04300f'], + }), + ('yamlordereddictloader', '0.4.2', { + 'checksums': ['36af2f6210fcff5da4fc4c12e1d815f973dceb41044e795e1f06115d634bca13'], + }), + ('airr', '1.5.0', { + 'checksums': ['febc0a881bf46b1a9c29ac6a7089dd733ff9120d114585e75dede26403f68d42'], + }), + ('scirpy', '0.17.0', { + 'checksums': ['f61653a4f7387562ec89b00fbfd7cab762c0bf3320f21ccfc47df80a13cc5d41'], + }), + ('schist', '0.8.3', { + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/dawe/schist/archive/'], + 'checksums': ['9b98ec9d85554573288c24f18c4791ba7c4d315397cbc422ea25d4a7cdd42e6d'], + }), + ('typeguard', '2.13.3', { + 'checksums': ['00edaa8da3a133674796cf5ea87d9f4b4c367d77476e185e80251cc13dfbb8c4'], + }), + ('jaxtyping', '0.2.29', { + 'checksums': ['e1cd916ed0196e40402b0638449e7d051571562b2cd68d8b94961a383faeb409'], + }), + ('equinox', '0.11.4', { + 'checksums': ['0033d9731083f402a855b12a0777a80aa8507651f7aa86d9f0f9503bcddfd320'], + }), + ('lineax', '0.0.4', { + 'checksums': ['e68f1eba2f352122fdce9adc0556684f31eb8364b1a00acee484dd6e44a34e5e'], + }), + ('jaxopt', '0.8.3', { + 'checksums': ['4b06dfa6f915a4f3291699606245af6069371a48dc5c92d4c507840d62990646'], + }), + ('ott_jax', '0.4.6', { + 'modulename': 'ott', + 'checksums': ['bc91f8d512cdb344439f5584712d76cd0650b6716b6686d53b828cc67abdbcba'], + }), + ('sparsecca', '0.3.1', { + 'checksums': ['be1526baebac5ce6efbc7190fd62a1cec13288c493f5d427024f66ca6afaec13'], + }), + ('PubChemPy', '1.0.4', { + 'checksums': ['24e9dc2fc90ab153b2764bf805e510b1410700884faf0510a9e7cf0d61d8ed0e'], + }), + ('blitzgsea', '1.3.42', { + 'checksums': ['dcc997b5d29d190d8632474f3bb57b5ead7fb1370b478c7f824b42782325a1ca'], + }), + ('pertpy', '0.7.0', { + 'checksums': ['273723b5b70f3cb714bb36d3234462014b72e133111eeaf08aa47153c9df14aa'], + }), +] + +use_pip = True +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SingleM/SingleM-0.16.0-foss-2023a.eb b/easybuild/easyconfigs/s/SingleM/SingleM-0.16.0-foss-2023a.eb new file mode 100644 index 00000000000..25fc18b7c63 --- /dev/null +++ b/easybuild/easyconfigs/s/SingleM/SingleM-0.16.0-foss-2023a.eb @@ -0,0 +1,107 @@ +easyblock = 'PythonBundle' + +name = 'SingleM' +version = '0.16.0' + +homepage = 'https://github.com/wwood/singlem' +description = """SingleM is a tool for profiling shotgun metagenomes. +It has a particular strength in detecting microbial lineages which are not in reference databases. +The method it uses also makes it suitable for some related tasks, such as assessing eukaryotic contamination, +finding bias in genome recovery, computing ecological diversity metrics, and lineage-targeted MAG recovery.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [('hatchling', '1.18.0')] +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('SciPy-bundle', '2023.07'), + ('Biopython', '1.83'), + ('polars', '0.20.2'), + ('tqdm', '4.66.1'), + ('Arrow', '14.0.1'), + ('DIAMOND', '2.1.8'), + ('HMMER', '3.4'), + ('MAFFT', '7.520', '-with-extensions'), + ('OrfM', '0.7.1'), + ('mfqe', '0.5.0'), + ('KronaTools', '2.8.1'), + ('pplacer', '1.1.alpha19', '', SYSTEM), + ('SRA-Toolkit', '3.0.10'), + ('Seqmagick', '0.8.6'), + ('ExpressBetaDiversity', '1.0.10'), + ('FastTree', '2.1.11'), + ('SQLAlchemy', '2.0.25'), + ('CD-HIT', '4.8.1'), + ('smafa', '0.8.0'), + ('prodigal', '2.6.3'), + ('biom-format', '2.1.15'), + ('DendroPy', '4.6.1'), + ('PyYAML', '6.0'), + ('psycopg', '3.2.1'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('psycopg2-binary', '2.9.9', { + 'modulename': 'psycopg2', + 'checksums': ['7f01846810177d829c7692f1f5ada8096762d9172af1b1a28d4ab5b77c923c1c'], + }), + ('sqlparse', '0.5.1', { + 'checksums': ['bb6b4df465655ef332548e24f08e205afc81b9ab86cb1c45657a7ff173a3a00e'], + }), + ('sorted_nearest', '0.0.39', { + 'checksums': ['16a51d5db87ae226b47ace43c176bb672477a1b7ba8052ea9291a6356c9c69b1'], + }), + ('ncls', '0.0.68', { + 'checksums': ['81aaa5abb123bb21797ed2f8ef921e20222db14a3ecbc61ccf447532f2b7ba93'], + }), + ('natsort', '8.4.0', { + 'checksums': ['45312c4a0e5507593da193dedd04abb1469253b601ecaf63445ad80f0a1ea581'], + }), + ('argparse-manpage-birdtools', '1.7.0', { + 'modulename': 'build_manpages', + 'checksums': ['20eae3079a4a2dbe1a7557ef7276a4d8e5a44c7c4223afb50f4f1d0ae0e7d103'], + }), + ('taxtastic', '0.10.0', { + 'checksums': ['32db30aa2e499fbae913b991cd087fa69684ac4ff934b957c30b6085866f1748'], + }), + ('zenodo_backpack', '0.3.1', { + 'checksums': ['dc91f3c427f976465789746e94736abfa536cf42dc2e49b6d6067382a9a39b26'], + }), + ('bird_tool_utils', '0.4.1', { + 'checksums': ['6fe80f9608626427e8d382c5341c24088d61f17336fb6ce834d40aa4577499b5'], + }), + ('fastalite', '0.4.1', { + 'checksums': ['e85413ee22bdb3fe0f73f5226771cf71eb33074ccdf8bbefff3a1bc6242de37c'], + }), + ('squarify', '0.4.3', { + 'checksums': ['54091f6ad175f7f201f8934574e647ce1b50dedc478c5fd968688eb7d7469f95'], + }), + ('pyranges', '0.0.129', { + 'checksums': ['bee83b4fad0062be9586668c6b0fc4270d5e761951975e018202993680071fb3'], + }), + ('extern', '0.4.1', { + 'checksums': ['0ff01adc2ad423f3d1e31641024b3974569fb0127b4d925bc6bed1cb86b6b1e4'], + }), + ('graftm', '0.15.1', { + 'checksums': ['80d828c311d2d6067977cfad5b6bac7cbc5d223ef8ab770d676b39bf2bc75163'], + }), + ('singlem', version, { + 'checksums': ['64e43a6a40795d68ff5aed7dfff9a94532b862f25a28c27de7d588d64a8c7f79'], + }), +] + +sanity_check_paths = { + 'files': ['bin/graftM', 'bin/singlem'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "graftM --help", + "singlem --help", +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/Singular/Singular-4.4.0-gfbf-2023b.eb b/easybuild/easyconfigs/s/Singular/Singular-4.4.0-gfbf-2023b.eb new file mode 100644 index 00000000000..b68c9946147 --- /dev/null +++ b/easybuild/easyconfigs/s/Singular/Singular-4.4.0-gfbf-2023b.eb @@ -0,0 +1,47 @@ +easyblock = 'ConfigureMake' + +name = 'Singular' +version = '4.4.0' + +homepage = 'https://www.singular.uni-kl.de/' +description = """Singular is a computer algebra system for polynomial computations, +with special emphasis on commutative and non-commutative algebra, algebraic geometry, +and singularity theory.""" + +toolchain = {'name': 'gfbf', 'version': '2023b'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/Singular/Singular/archive/refs/tags/'] +sources = ['Release-%s.tar.gz' % version.replace('.', '-')] +checksums = ['b60063628a223b2519e1d44310e05bc664b671735466da3ec192969681d2772c'] + +builddependencies = [ + ('Autotools', '20220317'), + ('Doxygen', '1.9.8'), + ('pkgconf', '2.0.3'), +] + +dependencies = [ + ('libreadline', '8.2'), + ('GMP', '6.3.0'), + ('MPFR', '4.2.1'), + ('FLINT', '3.1.1'), + ('NTL', '11.5.1'), + ('cddlib', '0.94m'), + ('4ti2', '1.6.10'), +] + +preconfigopts = "./autogen.sh && " +configopts = "--with-gmp=$EBROOTGMP --with-flint=$EBROOTFLINT --with-ntl=$EBROOTNTL" + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['ESingular', 'Singular', 'TSingular', 'libpolys-config', 'libsingular-config']] + + ['lib/lib%s.%s' % (l, e) for l in ['Singular', 'factory', 'omalloc', 'polys', 'singular_resources'] + for e in ['a', SHLIB_EXT]], + 'dirs': ['include/%s' % h for h in ['factory', 'omalloc', 'resources', 'singular']] + + ['libexec/singular', 'share'], +} + +sanity_check_commands = ["Singular --help"] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/Slideflow/Slideflow-3.0.1-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/s/Slideflow/Slideflow-3.0.1-foss-2023a-CUDA-12.1.1.eb new file mode 100644 index 00000000000..891faddbf05 --- /dev/null +++ b/easybuild/easyconfigs/s/Slideflow/Slideflow-3.0.1-foss-2023a-CUDA-12.1.1.eb @@ -0,0 +1,163 @@ +easyblock = 'PythonBundle' + +name = 'Slideflow' +version = '3.0.1' +versionsuffix = '-CUDA-12.1.1' + +homepage = 'https://slideflow.dev/' +description = """Slideflow is a Python package that provides a unified API for +building and testing deep learning models for histopathology, supporting both +Tensorflow/Keras and PyTorch.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [ + ('CMake', '3.26.3'), + ('Ninja', '1.11.1'), + ('scikit-build', '0.17.6'), + ('poetry', '1.7.1'), +] + +dependencies = [ + ('aiohttp', '3.8.5'), + ('numba', '0.58.1'), + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('pyvips', '2.2.3'), + ('Pillow', '10.0.0'), + ('PyTorch', '2.1.2', '-CUDA-12.1.1'), + ('scikit-learn', '1.3.1'), + ('scikit-image', '0.22.0'), + ('torchvision', '0.16.0', '-CUDA-12.1.1'), + ('tqdm', '4.66.1'), + ('SWIG', '4.1.1'), + ('SciPy-bundle', '2023.07'), + ('PyOpenGL', '3.1.7'), + ('spaCy', '3.7.4'), + ('h5py', '3.9.0'), + ('OpenCV', '4.8.1', '-CUDA-12.1.1-contrib'), + ('rasterio', '1.3.9'), + ('dask', '2023.9.2'), + ('psutil', '5.9.8'), + ('tensorboard', '2.15.1'), + ('umap-learn', '0.5.5'), + ('zarr', '2.17.1'), + ('Arrow', '14.0.1'), + ('BeautifulSoup', '4.12.2'), + ('wrapt', '1.15.0'), + ('GLFW', '3.4'), + ('Seaborn', '0.13.2'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('triangle', '20230923', { + 'sources': [{ + 'filename': '%(name)s-v%(version)s.tar.gz', + 'git_config': { + 'url': 'https://github.com/drufat', + 'repo_name': 'triangle', + 'tag': 'v20230923', 'recursive': True + } + }], + 'checksums': [None], + }), + (name, version, { + 'patches': ['%(name)s-%(version)s_fix-opencv-dep.patch'], + 'source_urls': ['https://github.com/jamesdolezal/%(namelower)s/archive/refs/tags/'], + 'sources': ['%(version)s.tar.gz'], + 'checksums': [ + {'3.0.1.tar.gz': '7fd6ca92805943e3d9d0208471205049ba48e46a9d8b910528d12788a01d5c2b'}, + {'Slideflow-3.0.1_fix-opencv-dep.patch': + '802438a42402a11de90fb09e1847336fa3664f0bca4d54512e15a1651171a8b9'}, + ], + }), + ('crc32c', '2.4', { + 'checksums': ['d985c4d9b1a1fd16c593d83f8735a8e4e156790a95338a1e0b199aac51ca1e5e'], + }), + ('ConfigSpace', '0.7.1', { + 'modulename': 'ConfigSpace', + 'checksums': ['57b5b8e28ed6ee14ecf6206fdca43ca698ef63bc1531f081d482b26acf4edf1a'], + }), + ('defusedxml', '0.7.1', { + 'checksums': ['1bb3032db185915b62d7c6209c5a8792be6a32ab2fedacc84e01b52c51aa3e69'], + }), + ('more-itertools', '9.1.0', { + 'checksums': ['cabaa341ad0389ea83c17a94566a53ae4c9d07349861ecb14dc6d0345cf9ac5d'], + }), + ('pyparsing', '3.1.0', { + 'checksums': ['edb662d6fe322d6e990b1594b5feaeadf806803359e3d4d42f11e295e588f0ea'], + }), + ('typing_extensions', '4.9.0', { + 'checksums': ['23478f88c37f27d76ac8aee6c905017a143b0b1b886c3c9f66bc2fd94f9f5783'], + }), + ('fpdf2', '2.7.9', { + 'modulename': 'fpdf', + 'checksums': ['f364c0d816a5e364eeeda9761cf5c961bae8c946f080cf87fed7f38ab773b318'], + }), + ('gdown', '5.2.0', { + 'checksums': ['2145165062d85520a3cd98b356c9ed522c5e7984d408535409fd46f94defc787'], + }), + ('glfw', '2.7.0', { + 'checksums': ['0e209ad38fa8c5be67ca590d7b17533d95ad1eb57d0a3f07b98131db69b79000'], + }), + ('imgui', '2.0.0', { + 'checksums': ['2fbdb8eed3b8dbd7ea98af9e4c1c6582b0bc4da942a258de16333d8c653d67e1'], + }), + ('lifelines', '0.28.0', { + 'checksums': ['eecf726453fd409c94fef8a521f8e593bcd09337f920fe885131f01cfe58b25e'], + }), + ('autograd', '1.6.2', { + 'checksums': ['8731e08a0c4e389d8695a40072ada4512641c113b6cace8f4cfbe8eb7e9aedeb'], + }), + ('autograd-gamma', '0.5.0', { + 'checksums': ['f27abb7b8bb9cffc8badcbf59f3fe44a9db39e124ecacf1992b6d952934ac9c4'], + }), + ('formulaic', '1.0.1', { + 'checksums': ['64dd7992a7aa5bbceb1e40679d0f01fc6f0ba12b7d23d78094a88c2edc68fba1'], + }), + ('interface_meta', '1.3.0', { + 'checksums': ['8a4493f8bdb73fb9655dcd5115bc897e207319e36c8835f39c516a2d7e9d79a1'], + }), + ('parameterized', '0.9.0', { + 'checksums': ['7fc905272cefa4f364c1a3429cbbe9c0f98b793988efb5bf90aac80f08db09b1'], + }), + ('pyperclip', '1.8.2', { + 'checksums': ['105254a8b04934f0bc84e9c24eb360a591aaf6535c9def5f29d92af107a9bf57'], + }), + ('cffi', '1.15.1', { + 'checksums': ['d400bfb9a37b1351253cb402671cea7e89bdecc294e8016a707f6d1d8ac934f9'], + }), + ('saliency', '0.2.1', { + 'checksums': ['79a3f64393a3ce89620bf46629af120c36a061019eff51b32b173378c8b18c63'], + }), + ('shapely', '2.0.4', { + 'checksums': ['5dc736127fac70009b8d309a0eeb74f3e08979e530cf7017f2f507ef62e6cfb8'], + }), + ('smac', '1.4.0', { + 'checksums': ['c58260af5ac2b2cd50b74f879202d5b5890c25d81e4c528abb51045ef4c679f9'], + }), + ('emcee', '3.1.6', { + 'checksums': ['11af4daf6ab8f9ca69681e3c29054665db7bbd87fd4eb8e437d2c3a1248c637d'], + }), + ('joblib', '1.2.0', { + 'checksums': ['e1cee4a79e4af22881164f218d4311f60074197fb707e082e803b61f6d137018'], + }), + ('pynisher', '0.6.4', { + 'checksums': ['111d91aad471375c0509a912415ff90053ef909100facf412511383af107c124'], + }), + ('pyrfr', '0.9.0', { + 'checksums': ['bc6e758317cf79579fe6b7ce5f01dd42f77c991bf707e33646e8c6a9112c186b'], + }), + ('regex', '2023.6.3', { + 'checksums': ['72d1a25bf36d2050ceb35b517afe13864865268dfb45910e2e17a84be6cbfeb0'], + }), + ('protobuf', '3.20.3', { + 'modulename': 'google.protobuf', + 'checksums': ['2e3427429c9cffebf259491be0af70189607f365c2f41c7c3764af6f337105f2'], + }), +] + +moduleclass = "ai" diff --git a/easybuild/easyconfigs/s/Slideflow/Slideflow-3.0.1_fix-opencv-dep.patch b/easybuild/easyconfigs/s/Slideflow/Slideflow-3.0.1_fix-opencv-dep.patch new file mode 100644 index 00000000000..cbd98f64f00 --- /dev/null +++ b/easybuild/easyconfigs/s/Slideflow/Slideflow-3.0.1_fix-opencv-dep.patch @@ -0,0 +1,12 @@ +Removes dependency on opencv-python-headless which causes conflicts. + +--- 3.0.1/foss-2023a-CUDA-12.1.1/Slideflow/slideflow-3.0.1/setup.py.orig 2024-10-02 14:50:03.699316470 +0200 ++++ 3.0.1/foss-2023a-CUDA-12.1.1/Slideflow/slideflow-3.0.1/setup.py 2024-10-02 14:50:31.615652542 +0200 +@@ -128,7 +128,6 @@ + 'scikit-learn', + 'matplotlib>=3.2', + 'imageio', +- opencv_pkg, + 'shapely', + 'umap-learn', + 'seaborn<0.14', diff --git a/easybuild/easyconfigs/s/SlurmViewer/SlurmViewer-1.0.1-GCCcore-13.2.0.eb b/easybuild/easyconfigs/s/SlurmViewer/SlurmViewer-1.0.1-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..371a8d85eea --- /dev/null +++ b/easybuild/easyconfigs/s/SlurmViewer/SlurmViewer-1.0.1-GCCcore-13.2.0.eb @@ -0,0 +1,56 @@ +easyblock = 'PythonBundle' + +name = 'SlurmViewer' +version = '1.0.1' + +homepage = 'https://gitlab.com/lkeb/slurm_viewer' +description = """View the status of a Slurm cluster, including nodes and queue.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +builddependencies = [ + ('binutils', '2.40'), + ('hatchling', '1.18.0'), + ('poetry', '1.6.1'), +] + +dependencies = [ + ('Python', '3.11.5'), + ('Python-bundle-PyPI', '2023.10'), + ('pydantic', '2.7.4'), +] + +use_pip = True + +exts_list = [ + ('plotext', '5.2.8', { + 'checksums': ['319a287baabeb8576a711995f973a2eba631c887aa6b0f33ab016f12c50ffebe'], + }), + ('textual', '0.85.2', { + 'checksums': ['2a416995c49d5381a81d0a6fd23925cb0e3f14b4f239ed05f35fa3c981bb1df2'], + }), + ('textual-plotext', '0.2.1', { + 'source_tmpl': 'textual_plotext-%(version)s.tar.gz', + 'checksums': ['bc6f2d75d8e20dda6321f8254dc3decda8f41f60e6e70a3ddd83b652b890c081'], + }), + ('asyncssh', '2.18.0', { + 'checksums': ['1a322161c01f60b9719dc8f39f80db71e61f3f5e04abbc3420ce503126d87123'], + }), + ('slurm-viewer', version, { + 'source_tmpl': 'slurm_viewer-%(version)s-py3-none-any.whl', + 'checksums': ['2e42662881458701a09770a52062cb065527e30a39aac35165056f4ccf288f52'], + }), +] + +sanity_check_paths = { + 'files': ['bin/slurm-viewer', 'bin/slurm-viewer-init'], + 'dirs': ['lib'] +} + +sanity_pip_check = True + +modloadmsg = """Slurm Viewer requires a configuration file. +You can make a default settings file in your home directory by running slurm-viewer-init, +or you can point to a settings file by setting the environment variable $SLURM_VIEW_CONFIG.""" + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/s/Sniffles/Sniffles-2.4-GCC-13.3.0.eb b/easybuild/easyconfigs/s/Sniffles/Sniffles-2.4-GCC-13.3.0.eb new file mode 100644 index 00000000000..ad8e962950a --- /dev/null +++ b/easybuild/easyconfigs/s/Sniffles/Sniffles-2.4-GCC-13.3.0.eb @@ -0,0 +1,38 @@ +easyblock = 'PythonBundle' + +name = 'Sniffles' +version = '2.4' + +homepage = 'https://github.com/fritzsedlazeck/Sniffles' +description = """A fast structural variant caller for long-read sequencing, + Sniffles2 accurately detect SVs on germline, somatic and population-level for PacBio and Oxford Nanopore read data.""" + +toolchain = {'name': 'GCC', 'version': '13.3.0'} + +dependencies = [ + ('Python', '3.12.3'), + ('Pysam', '0.22.1'), + ('edlib', '1.3.9.post1'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + (name, version, { + 'sources': [SOURCELOWER_TAR_GZ], + 'checksums': ['e3c2f552105cd5f5941d6291b9ee9dbfe634ad19b5e7a64fa26b9e2daa6547d4'], + }), +] + +sanity_check_paths = { + 'files': ['bin/sniffles'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "python -c 'from sniffles import sv'", + "sniffles --help", +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SoX/SoX-14.4.2-GCCcore-13.3.0.eb b/easybuild/easyconfigs/s/SoX/SoX-14.4.2-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..747709683fb --- /dev/null +++ b/easybuild/easyconfigs/s/SoX/SoX-14.4.2-GCCcore-13.3.0.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'SoX' +version = '14.4.2' + +homepage = 'http://sox.sourceforge.net/' +docurls = 'http://sox.sourceforge.net/Docs/Documentation' +description = """Sound eXchange, the Swiss Army knife of audio manipulation""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['b45f598643ffbd8e363ff24d61166ccec4836fea6d3888881b8df53e3bb55f6c'] + +builddependencies = [('binutils', '2.42')] + +dependencies = [ + ('FLAC', '1.4.3'), + ('LAME', '3.100'), + ('libmad', '0.15.1b'), + ('libvorbis', '1.3.7'), + ('FFmpeg', '7.0.2'), +] + +sanity_check_paths = { + 'files': ['bin/play', 'bin/rec', 'bin/sox', 'bin/soxi', 'include/sox.h', + 'lib/libsox.la', 'lib/libsox.a', 'lib/pkgconfig/sox.pc', 'lib/libsox.%s' % SHLIB_EXT], + 'dirs': ['bin', 'include', 'lib', 'lib/pkgconfig', 'share/man'], +} + +sanity_check_commands = ['sox --help'] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/s/Solids4foam/Solids4foam-2.1-foss-2023a.eb b/easybuild/easyconfigs/s/Solids4foam/Solids4foam-2.1-foss-2023a.eb new file mode 100644 index 00000000000..9c203d21c27 --- /dev/null +++ b/easybuild/easyconfigs/s/Solids4foam/Solids4foam-2.1-foss-2023a.eb @@ -0,0 +1,45 @@ +easyblock = 'Binary' + +name = 'Solids4foam' +version = '2.1' + +homepage = 'https://www.solids4foam.com/' +description = 'A toolbox for performing solid mechanics and fluid-solid interactions in OpenFOAM.' + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['https://github.com/solids4foam/solids4foam/archive/'] +sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}] +checksums = ['354dad483f8b086d64bf294829cf6fdf1e5784fd615578acff753791f2f391ca'] + +builddependencies = [('Eigen', '3.4.0')] +dependencies = [ + ('OpenFOAM', 'v2312'), + ('gnuplot', '5.4.8'), + ('M4', '1.4.19'), +] + +extract_sources = True + +# build + install cmds: +install_cmd = 'source $FOAM_BASH && ' +install_cmd += 'export WM_PROJECT_USER_DIR=%(installdir)s && ' +install_cmd += 'export FOAM_USER_APPBIN=%(installdir)s/bin && ' +install_cmd += 'export FOAM_USER_LIBBIN=%(installdir)s/lib && ' +install_cmd += 'export LD_LIBRARY_PATH=%(installdir)s/lib:$LD_LIBRARY_PATH && ' +install_cmd += 'export EIGEN_DIR=$EBROOTEIGEN && ' +install_cmd += 'export S4F_NO_FILE_FIXES=1 && ./Allwmake -j %(parallel)s' +# copy tests +install_cmd += ' && cp -av tutorials %(installdir)s' + +sanity_check_paths = { + 'files': ['bin/solids4Foam'], + 'dirs': ['lib'], +} +sanity_check_commands = [ + 'source $FOAM_BASH && cd %(installdir)s/tutorials && ./Alltest' +] + +modloadmsg = "Please run 'source $FOAM_BASH' before using Solids4foam." + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/s/SpFFT/SpFFT-1.1.0-foss-2023a.eb b/easybuild/easyconfigs/s/SpFFT/SpFFT-1.1.0-foss-2023a.eb new file mode 100644 index 00000000000..608918e373c --- /dev/null +++ b/easybuild/easyconfigs/s/SpFFT/SpFFT-1.1.0-foss-2023a.eb @@ -0,0 +1,30 @@ +easyblock = 'CMakeMake' + +name = 'SpFFT' +version = '1.1.0' + +homepage = 'https://github.com/eth-cscs/SpFFT/' +description = """Sparse 3D FFT library with MPI, OpenMP, CUDA and ROCm support.""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'openmp': True} + +source_urls = ['https://github.com/eth-cscs/SpFFT/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['d4673b3135aebfa1c440723226fe976d518ff881285b3d4787f1aa8210eac81e'] + +builddependencies = [ + ('CMake', '3.26.3'), +] + +configopts = "-DSPFFT_OMP=ON -DSPFFT_MPI=ON " + +sanity_check_paths = { + 'files': [ + 'include/spfft/spfft.h', + 'lib/libspfft.%s' % SHLIB_EXT, + ], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/Spectre/Spectre-0.2.1-foss-2023a.eb b/easybuild/easyconfigs/s/Spectre/Spectre-0.2.1-foss-2023a.eb new file mode 100644 index 00000000000..a2a82a58532 --- /dev/null +++ b/easybuild/easyconfigs/s/Spectre/Spectre-0.2.1-foss-2023a.eb @@ -0,0 +1,31 @@ +easyblock = 'PythonPackage' + +name = 'Spectre' +version = '0.2.1' + +homepage = 'https://github.com/fritzsedlazeck/Spectre' +description = """Spectre is a long read copy number variation (CNV) caller. Spectre is designed to detect large CNVs +(>100kb) in a couple of minutes depending on your hardware.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['https://pypi.org/packages/source/s/spectre-cnv/'] +sources = [{'download_filename': 'spectre_cnv-%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}] +checksums = ['a5ab6487bdf239f4df0158632020d57be3cc78831e0fb1f41f27c5a79060cf5a'] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('Pysam', '0.22.0'), + ('matplotlib', '3.7.2'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +sanity_check_commands = [ + "spectre --help", +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/Sphinx-RTD-Theme/Sphinx-RTD-Theme-2.0.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/s/Sphinx-RTD-Theme/Sphinx-RTD-Theme-2.0.0-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..c41639bc3ad --- /dev/null +++ b/easybuild/easyconfigs/s/Sphinx-RTD-Theme/Sphinx-RTD-Theme-2.0.0-GCCcore-12.3.0.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonBundle' + +name = 'Sphinx-RTD-Theme' +version = '2.0.0' + +homepage = 'https://sphinx-rtd-theme.readthedocs.io' +description = """Sphinx theme designed to provide a great reader experience + for documentation users on both desktop and mobile devices.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +builddependencies = [('binutils', '2.40')] + +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), +] + +use_pip = True + +exts_list = [ + ('sphinxcontrib-jquery', '4.1', { + 'modulename': 'sphinxcontrib.jquery', + 'checksums': ['1620739f04e36a2c779f1a131a2dfd49b2fd07351bf1968ced074365933abc7a'], + }), + ('sphinx_rtd_theme', version, { + 'checksums': ['bd5d7b80622406762073a04ef8fadc5f9151261563d47027de09910ce03afe6b'], + }), +] + +sanity_pip_check = True + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/s/Sphinx-RTD-Theme/Sphinx-RTD-Theme-2.0.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/s/Sphinx-RTD-Theme/Sphinx-RTD-Theme-2.0.0-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..6642b38d820 --- /dev/null +++ b/easybuild/easyconfigs/s/Sphinx-RTD-Theme/Sphinx-RTD-Theme-2.0.0-GCCcore-13.2.0.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonBundle' + +name = 'Sphinx-RTD-Theme' +version = '2.0.0' + +homepage = 'https://sphinx-rtd-theme.readthedocs.io' +description = """Sphinx theme designed to provide a great reader experience + for documentation users on both desktop and mobile devices.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +builddependencies = [('binutils', '2.40')] + +dependencies = [ + ('Python', '3.11.5'), + ('Python-bundle-PyPI', '2023.10'), +] + +use_pip = True + +exts_list = [ + ('sphinxcontrib-jquery', '4.1', { + 'modulename': 'sphinxcontrib.jquery', + 'checksums': ['1620739f04e36a2c779f1a131a2dfd49b2fd07351bf1968ced074365933abc7a'], + }), + ('sphinx_rtd_theme', version, { + 'checksums': ['bd5d7b80622406762073a04ef8fadc5f9151261563d47027de09910ce03afe6b'], + }), +] + +sanity_pip_check = True + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/s/Stable-Baselines3/Stable-Baselines3-2.3.2-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/s/Stable-Baselines3/Stable-Baselines3-2.3.2-foss-2023a-CUDA-12.1.1.eb new file mode 100644 index 00000000000..61d42c21a8a --- /dev/null +++ b/easybuild/easyconfigs/s/Stable-Baselines3/Stable-Baselines3-2.3.2-foss-2023a-CUDA-12.1.1.eb @@ -0,0 +1,36 @@ +easyblock = 'PythonBundle' + +name = 'Stable-Baselines3' +version = '2.3.2' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/DLR-RM/stable-baselines3' +description = """Stable Baselines3 (SB3) is a set of reliable implementations of +reinforcement learning algorithms in PyTorch.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('CUDA', '12.1.1', '', SYSTEM), + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('Gymnasium', '0.29.1', versionsuffix), + ('PyTorch', '2.1.2', versionsuffix), + ('matplotlib', '3.7.2'), +] + +use_pip = True + +exts_list = [ + ('cloudpickle', '3.0.0', { + 'checksums': ['996d9a482c6fb4f33c1a35335cf8afd065d2a56e973270364840712d9131a882'], + }), + ('stable_baselines3', version, { + 'use_pip_extras': 'extra', + 'checksums': ['2f8188916e607571c4c24f88a9ff6f84edafb2cf22d5d24f9c199563c12ff168'], + }), +] + +sanity_pip_check = True + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/Stable-Baselines3/Stable-Baselines3-2.3.2-foss-2023a.eb b/easybuild/easyconfigs/s/Stable-Baselines3/Stable-Baselines3-2.3.2-foss-2023a.eb new file mode 100644 index 00000000000..24aee360a6e --- /dev/null +++ b/easybuild/easyconfigs/s/Stable-Baselines3/Stable-Baselines3-2.3.2-foss-2023a.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonBundle' + +name = 'Stable-Baselines3' +version = '2.3.2' + +homepage = 'https://github.com/DLR-RM/stable-baselines3' +description = """Stable Baselines3 (SB3) is a set of reliable implementations of +reinforcement learning algorithms in PyTorch.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('Gymnasium', '0.29.1'), + ('SciPy-bundle', '2023.07'), + ('PyTorch', '2.1.2'), + ('matplotlib', '3.7.2'), +] + +use_pip = True + +exts_list = [ + ('cloudpickle', '3.0.0', { + 'checksums': ['996d9a482c6fb4f33c1a35335cf8afd065d2a56e973270364840712d9131a882'], + }), + ('stable_baselines3', version, { + 'use_pip_extras': 'extra', + 'checksums': ['2f8188916e607571c4c24f88a9ff6f84edafb2cf22d5d24f9c199563c12ff168'], + }), +] + +sanity_pip_check = True + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/Stack/Stack-3.1.1-x86_64.eb b/easybuild/easyconfigs/s/Stack/Stack-3.1.1-x86_64.eb new file mode 100644 index 00000000000..0a822a69cbd --- /dev/null +++ b/easybuild/easyconfigs/s/Stack/Stack-3.1.1-x86_64.eb @@ -0,0 +1,26 @@ +easyblock = 'Tarball' + +name = 'Stack' +version = '3.1.1' +versionsuffix = '-x86_64' + +homepage = 'https://docs.haskellstack.org' +description = """Stack is a cross-platform program for developing Haskell projects. +It is intended for Haskellers both new and experienced.""" + +toolchain = SYSTEM + +source_urls = ['https://github.com/commercialhaskell/stack/releases/download/v%(version)s/'] +sources = ['%(namelower)s-%(version)s-linux-x86_64.tar.gz'] +checksums = ['d096125ea3d987a55d17f7d4f8599ee2fd96bd2d0f033566e28ddfe248f730f9'] + +modextrapaths = {'PATH': ''} + +sanity_check_paths = { + 'files': ['stack'], + 'dirs': ['doc'], +} + +sanity_check_commands = ['stack --help'] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/s/Stacks/Stacks-2.68-foss-2023a.eb b/easybuild/easyconfigs/s/Stacks/Stacks-2.68-foss-2023a.eb new file mode 100644 index 00000000000..f5c8c3b976d --- /dev/null +++ b/easybuild/easyconfigs/s/Stacks/Stacks-2.68-foss-2023a.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'Stacks' +version = '2.68' + +homepage = 'https://catchenlab.life.illinois.edu/stacks/' +description = """Stacks is a software pipeline for building loci from short-read sequences, such as those generated on + the Illumina platform. Stacks was developed to work with restriction enzyme-based data, such as RAD-seq, + for the purpose of building genetic maps and conducting population genomics and phylogeography. +""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['https://catchenlab.life.illinois.edu/stacks/source/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['9dc51ea356d60eb4557b0b2d1a8854aafae492aed87f974e0249cc09aa5e7650'] + +dependencies = [ + ('zlib', '1.2.13'), +] + +sanity_check_paths = { + 'files': ['bin/clone_filter', 'bin/cstacks', 'bin/gstacks', 'bin/kmer_filter', 'bin/phasedstacks', + 'bin/populations', 'bin/process_radtags', 'bin/process_shortreads', 'bin/sstacks', + 'bin/tsv2bam', 'bin/ustacks'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/Statistics-R/Statistics-R-0.34-foss-2023a.eb b/easybuild/easyconfigs/s/Statistics-R/Statistics-R-0.34-foss-2023a.eb new file mode 100644 index 00000000000..7a351d75a26 --- /dev/null +++ b/easybuild/easyconfigs/s/Statistics-R/Statistics-R-0.34-foss-2023a.eb @@ -0,0 +1,28 @@ +easyblock = 'PerlModule' + +name = 'Statistics-R' +version = '0.34' + +homepage = 'https://metacpan.org/pod/Statistics::R' +description = "Perl interface with the R statistical program" + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['https://cpan.metacpan.org/authors/id/F/FA/FANGLY'] +sources = [SOURCE_TAR_GZ] +checksums = ['782dd064876ac94680d97899f24fb0e727df42c05ba474ec096a9116438fbed4'] + +dependencies = [ + ('Perl', '5.36.1'), + ('Perl-bundle-CPAN', '5.36.1'), + ('R', '4.3.2'), +] + +options = {'modulename': 'Statistics::R'} + +sanity_check_paths = { + 'files': ['lib/perl5/site_perl/%(perlver)s/Statistics/R.pm'], + 'dirs': ['lib/perl5/site_perl/%(perlver)s/Statistics/R'], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/s/Stellarscope/Stellarscope-1.4.1-foss-2023a.eb b/easybuild/easyconfigs/s/Stellarscope/Stellarscope-1.4.1-foss-2023a.eb new file mode 100644 index 00000000000..27dd6fd92b4 --- /dev/null +++ b/easybuild/easyconfigs/s/Stellarscope/Stellarscope-1.4.1-foss-2023a.eb @@ -0,0 +1,40 @@ +easyblock = 'PythonBundle' + +name = 'Stellarscope' +version = '1.4.1' + +homepage = 'https://github.com/nixonlab/stellarscope' +description = """Single-cell Transposable Element Locus Level Analysis of scRNA Sequencing.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('SciPy-bundle', '2023.07'), + ('PyYAML', '6.0'), + ('Pysam', '0.22.0'), + ('HTSlib', '1.18'), + ('intervaltree-python', '3.1.0'), + ('SAMtools', '1.18'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + (name, version, { + 'source_urls': ['https://github.com/nixonlab/stellarscope/archive/'], + 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['64aa3fa30e9ee1d4857572a0f491fd4983c15a5b5906edf9a3b7cacda780b99c'], + }), +] + +sanity_check_paths = { + 'files': ['bin/stellarscope'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["stellarscope -h"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/StringTie/StringTie-2.2.3-GCC-12.3.0.eb b/easybuild/easyconfigs/s/StringTie/StringTie-2.2.3-GCC-12.3.0.eb new file mode 100644 index 00000000000..b8bf61dd6cf --- /dev/null +++ b/easybuild/easyconfigs/s/StringTie/StringTie-2.2.3-GCC-12.3.0.eb @@ -0,0 +1,49 @@ +# This file is an EasyBuild reciPY as per https://easybuilders.github.io/easybuild/ +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'MakeCp' + +name = 'StringTie' +version = '2.2.3' + +homepage = 'https://ccb.jhu.edu/software/stringtie/' +description = 'StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts' + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +source_urls = ['https://github.com/gpertea/%(namelower)s/releases/download/v%(version)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['f372640b70a8fde763712d2f0565aff71f5facdc2300c8af829fea94a05ff208'] + +dependencies = [ + ('bzip2', '1.0.8'), + ('libdeflate', '1.18'), + ('XZ', '5.4.2'), + ('zlib', '1.2.13'), + ('HTSlib', '1.18'), + ('Python', '3.11.3'), +] + +local_libs = 'HTSLIB="$EBROOTHTSLIB/lib" LIBS="-lhts -lbz2 -llzma -ldeflate -lz $LIBS"' +buildopts = 'release ' + local_libs + +# the test script downloads some test data from the internet +runtest = 'test' +testopts = local_libs + +files_to_copy = [ + (['%(namelower)s', 'prepDE.py3'], 'bin'), + 'README.md', + 'LICENSE' +] + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': [], +} + +sanity_check_commands = ['%(namelower)s --help', 'prepDE.py3 --help'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/Subread/Subread-2.0.6-GCC-12.3.0.eb b/easybuild/easyconfigs/s/Subread/Subread-2.0.6-GCC-12.3.0.eb new file mode 100644 index 00000000000..b7c21d845bf --- /dev/null +++ b/easybuild/easyconfigs/s/Subread/Subread-2.0.6-GCC-12.3.0.eb @@ -0,0 +1,39 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 + +easyblock = 'MakeCp' + +name = 'Subread' +version = '2.0.6' + +homepage = 'https://subread.sourceforge.net/' +description = """High performance read alignment, quantification and mutation discovery""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%(namelower)s-%(version)s-source.tar.gz'] +checksums = ['f0fdda6b98634d2946028948c220253e10a0f27c7fa5f24913b65b3ac6cbb045'] + +start_dir = 'src' + +prebuildopts = "sed -i 's/-mtune=core2//g' Makefile.Linux && " +prebuildopts += "sed -i 's/-mtune=core2//g' longread-one/Makefile && " + +buildopts = " -f Makefile.Linux" + +files_to_copy = ['bin'] + +local_binaries_list = [ + 'exactSNP', 'featureCounts', 'subindel', 'subjunc', 'sublong', '%(namelower)s-align', '%(namelower)s-buildindex', +] +sanity_check_paths = { + 'files': ['bin/%s' % f for f in local_binaries_list], + 'dirs': ['bin/utilities'], +} + +sanity_check_commands = [ + 'cd %(builddir)s/%(namelower)s-%(version)s-source/test && bash test_all.sh' +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-7.7.0-foss-2023b-METIS-5.1.0.eb b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-7.7.0-foss-2023b-METIS-5.1.0.eb new file mode 100644 index 00000000000..260ca279304 --- /dev/null +++ b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-7.7.0-foss-2023b-METIS-5.1.0.eb @@ -0,0 +1,29 @@ +name = 'SuiteSparse' +version = '7.7.0' +local_metis_ver = '5.1.0' +versionsuffix = '-METIS-%s' % local_metis_ver + +homepage = 'https://faculty.cse.tamu.edu/davis/suitesparse.html' +description = """SuiteSparse is a collection of libraries to manipulate sparse matrices.""" + +toolchain = {'name': 'foss', 'version': '2023b'} +toolchainopts = {'unroll': True, 'pic': True} + +source_urls = ['https://github.com/DrTimothyAldenDavis/SuiteSparse/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['529b067f5d80981f45ddf6766627b8fc5af619822f068f342aab776e683df4f3'] + +builddependencies = [ + ('CMake', '3.27.6'), + ('M4', '1.4.19'), +] + +dependencies = [ + ('METIS', local_metis_ver), + ('MPFR', '4.2.1'), +] + +# make sure that bin/demo can find libsuitesparseconfig.so.5 during build +prebuildopts = "export LD_LIBRARY_PATH=%(builddir)s/SuiteSparse-%(version)s/lib:$LD_LIBRARY_PATH && " + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-7.8.2-foss-2024a-METIS-5.1.0.eb b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-7.8.2-foss-2024a-METIS-5.1.0.eb new file mode 100644 index 00000000000..7bcd3143b6f --- /dev/null +++ b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-7.8.2-foss-2024a-METIS-5.1.0.eb @@ -0,0 +1,29 @@ +name = 'SuiteSparse' +version = '7.8.2' +local_metis_ver = '5.1.0' +versionsuffix = '-METIS-%s' % local_metis_ver + +homepage = 'https://faculty.cse.tamu.edu/davis/suitesparse.html' +description = """SuiteSparse is a collection of libraries to manipulate sparse matrices.""" + +toolchain = {'name': 'foss', 'version': '2024a'} +toolchainopts = {'unroll': True, 'pic': True} + +source_urls = ['https://github.com/DrTimothyAldenDavis/SuiteSparse/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['996c48c87baaeb5fc04bd85c7e66d3651a56fe749c531c60926d75b4db5d2181'] + +builddependencies = [ + ('CMake', '3.29.3'), + ('M4', '1.4.19'), +] + +dependencies = [ + ('METIS', local_metis_ver), + ('MPFR', '4.2.1'), +] + +# make sure that bin/demo can find libsuitesparseconfig.so.5 during build +prebuildopts = "export LD_LIBRARY_PATH=%(builddir)s/SuiteSparse-%(version)s/lib:$LD_LIBRARY_PATH && " + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/s/SuperLU/SuperLU-6.0.1-foss-2023b.eb b/easybuild/easyconfigs/s/SuperLU/SuperLU-6.0.1-foss-2023b.eb new file mode 100644 index 00000000000..fb80e7ab219 --- /dev/null +++ b/easybuild/easyconfigs/s/SuperLU/SuperLU-6.0.1-foss-2023b.eb @@ -0,0 +1,21 @@ +name = 'SuperLU' +version = '6.0.1' + +homepage = 'https://crd-legacy.lbl.gov/~xiaoye/SuperLU/' +description = """SuperLU is a general purpose library for the +direct solution of large, sparse, nonsymmetric systems + of linear equations on high performance machines.""" + +toolchain = {'name': 'foss', 'version': '2023b'} +toolchainopts = {'pic': True, 'openmp': True} + +github_account = 'xiaoyeli' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ["v%(version)s.tar.gz"] +checksums = ['6c5a3a9a224cb2658e9da15a6034eed44e45f6963f5a771a6b4562f7afb8f549'] + +builddependencies = [('CMake', '3.27.6')] + +runtest = " test" + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/s/SuperLU_DIST/SuperLU_DIST-8.2.1-foss-2023b.eb b/easybuild/easyconfigs/s/SuperLU_DIST/SuperLU_DIST-8.2.1-foss-2023b.eb new file mode 100644 index 00000000000..a113fb7ef50 --- /dev/null +++ b/easybuild/easyconfigs/s/SuperLU_DIST/SuperLU_DIST-8.2.1-foss-2023b.eb @@ -0,0 +1,44 @@ +easyblock = "EB_SuperLU" + +name = 'SuperLU_DIST' +version = '8.2.1' + +homepage = 'https://crd-legacy.lbl.gov/~xiaoye/SuperLU/' +description = """SuperLU is a general purpose library for the direct solution of large, sparse, nonsymmetric systems + of linear equations on high performance machines.""" + +toolchain = {'name': 'foss', 'version': '2023b'} +toolchainopts = {'pic': True, 'openmp': True} + +github_account = 'xiaoyeli' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ["v%(version)s.tar.gz"] +checksums = ['b77d065cafa6bc1a1dcc15bf23fd854f54b05762b165badcffc195835ad2bddf'] + +builddependencies = [('CMake', '3.27.6')] + +dependencies = [ + ('ParMETIS', '4.0.3'), +] + +configopts = '-DTPL_PARMETIS_INCLUDE_DIRS="${EBROOTPARMETIS}/include" ' +configopts += '-DTPL_PARMETIS_LIBRARIES="${EBROOTPARMETIS}/lib/libparmetis.a;${EBROOTPARMETIS}/lib/libmetis.a" ' + +# Some tests run longer than default 1500s timeout on fairly big machine (36 cores). +# Include only first four tests, which should be fairly small to run +pretestopts = 'export ARGS="$ARGS --tests-regex pdtest_[21]x1_[13]_2_8_20_SP" && ' + +# remove broken symlink to libsuperlu.a +postinstallcmds = [ + "if [ -f %(installdir)s/lib64/libsuperlu.a ]; then rm %(installdir)s/lib64/libsuperlu.a; fi", + # This second one can be removed when https://github.com/easybuilders/easybuild-framework/pull/4435 is merged + # (i.e. in EasyBuild 5.0) + "if [ -f %(installdir)s/lib/libsuperlu.a ]; then rm %(installdir)s/lib/libsuperlu.a; fi" +] + +sanity_check_paths = { + 'files': ['lib64/libsuperlu_dist.a'], + 'dirs': ['include'] +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/s/Suppressor/Suppressor-0.2.4-Julia-1.9.2.eb b/easybuild/easyconfigs/s/Suppressor/Suppressor-0.2.4-Julia-1.9.2.eb new file mode 100644 index 00000000000..5b443b3fac5 --- /dev/null +++ b/easybuild/easyconfigs/s/Suppressor/Suppressor-0.2.4-Julia-1.9.2.eb @@ -0,0 +1,22 @@ +easyblock = 'JuliaPackage' + +name = 'Suppressor' +version = '0.2.4' +_julia_ver = '1.9.2' +versionsuffix = "-Julia-%s" % _julia_ver + +homepage = 'https://github.com/JuliaIO/Suppressor.jl' +description = """Julia macros for suppressing and/or capturing output (STDOUT), +warnings (STDERR) or both streams at the same time.""" + +toolchain = SYSTEM + +source_urls = ['https://github.com/JuliaIO/Suppressor.jl/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['5075b06ed6aa0956c786e5b5fe3d77571a4dd34e6d63b45e113c312729384cf4'] + +dependencies = [ + ('Julia', _julia_ver, '-linux-%s' % ARCH, SYSTEM), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-10.2.0.eb index 88e067c36e8..576e48c80b4 100644 --- a/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-10.2.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'Szip' version = '2.1.1' -homepage = 'https://www.hdfgroup.org/doc_resource/SZIP/' +homepage = 'https://support.hdfgroup.org/doc_resource/SZIP/' description = """ Szip compression software, providing lossless compression of scientific data @@ -12,7 +12,7 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '10.2.0'} toolchainopts = {'pic': True} -source_urls = ['https://www.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] +source_urls = ['https://support.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] sources = [SOURCELOWER_TAR_GZ] checksums = ['21ee958b4f2d4be2c9cabfa5e1a94877043609ce86fde5f286f105f7ff84d412'] diff --git a/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-10.3.0.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-10.3.0.eb index 10b926a9b61..5cc6a339682 100644 --- a/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-10.3.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'Szip' version = '2.1.1' -homepage = 'https://www.hdfgroup.org/doc_resource/SZIP/' +homepage = 'https://support.hdfgroup.org/doc_resource/SZIP/' description = """ Szip compression software, providing lossless compression of scientific data @@ -12,7 +12,7 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '10.3.0'} toolchainopts = {'pic': True} -source_urls = ['https://www.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] +source_urls = ['https://support.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] sources = [SOURCELOWER_TAR_GZ] checksums = ['21ee958b4f2d4be2c9cabfa5e1a94877043609ce86fde5f286f105f7ff84d412'] diff --git a/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-11.2.0.eb index b2d223898c7..70a9918dc8e 100644 --- a/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-11.2.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'Szip' version = '2.1.1' -homepage = 'https://www.hdfgroup.org/doc_resource/SZIP/' +homepage = 'https://support.hdfgroup.org/doc_resource/SZIP/' description = """ Szip compression software, providing lossless compression of scientific data @@ -12,7 +12,7 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '11.2.0'} toolchainopts = {'pic': True} -source_urls = ['https://www.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] +source_urls = ['https://support.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] sources = [SOURCELOWER_TAR_GZ] checksums = ['21ee958b4f2d4be2c9cabfa5e1a94877043609ce86fde5f286f105f7ff84d412'] diff --git a/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-11.3.0.eb index 3dc0b200849..6d34fd7a476 100644 --- a/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-11.3.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'Szip' version = '2.1.1' -homepage = 'https://www.hdfgroup.org/doc_resource/SZIP/' +homepage = 'https://support.hdfgroup.org/doc_resource/SZIP/' description = """ Szip compression software, providing lossless compression of scientific data @@ -12,7 +12,7 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '11.3.0'} toolchainopts = {'pic': True} -source_urls = ['https://www.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] +source_urls = ['https://support.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] sources = [SOURCELOWER_TAR_GZ] checksums = ['21ee958b4f2d4be2c9cabfa5e1a94877043609ce86fde5f286f105f7ff84d412'] diff --git a/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-12.2.0.eb index 6f536c566dd..e58b9c3ffef 100644 --- a/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-12.2.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'Szip' version = '2.1.1' -homepage = 'https://www.hdfgroup.org/doc_resource/SZIP/' +homepage = 'https://support.hdfgroup.org/doc_resource/SZIP/' description = """ Szip compression software, providing lossless compression of scientific data @@ -12,7 +12,7 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '12.2.0'} toolchainopts = {'pic': True} -source_urls = ['https://www.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] +source_urls = ['https://support.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] sources = [SOURCELOWER_TAR_GZ] checksums = ['21ee958b4f2d4be2c9cabfa5e1a94877043609ce86fde5f286f105f7ff84d412'] diff --git a/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-12.3.0.eb index e0a01221b9d..ee9fd884627 100644 --- a/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-12.3.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'Szip' version = '2.1.1' -homepage = 'https://www.hdfgroup.org/doc_resource/SZIP/' +homepage = 'https://support.hdfgroup.org/doc_resource/SZIP/' description = """ Szip compression software, providing lossless compression of scientific data @@ -12,7 +12,7 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '12.3.0'} toolchainopts = {'pic': True} -source_urls = ['https://www.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] +source_urls = ['https://support.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] sources = [SOURCELOWER_TAR_GZ] checksums = ['21ee958b4f2d4be2c9cabfa5e1a94877043609ce86fde5f286f105f7ff84d412'] diff --git a/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-13.2.0.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-13.2.0.eb index 8eb12670652..5fcc21050e5 100644 --- a/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-13.2.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'Szip' version = '2.1.1' -homepage = 'https://www.hdfgroup.org/doc_resource/SZIP/' +homepage = 'https://support.hdfgroup.org/doc_resource/SZIP/' description = """ Szip compression software, providing lossless compression of scientific data @@ -12,7 +12,7 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '13.2.0'} toolchainopts = {'pic': True} -source_urls = ['https://www.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] +source_urls = ['https://support.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] sources = [SOURCELOWER_TAR_GZ] checksums = ['21ee958b4f2d4be2c9cabfa5e1a94877043609ce86fde5f286f105f7ff84d412'] diff --git a/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..6ac6fb2e784 --- /dev/null +++ b/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-13.3.0.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'Szip' +version = '2.1.1' + +homepage = 'https://docs.hdfgroup.org/archive/support/doc_resource/SZIP/index.html' + +description = """ + Szip compression software, providing lossless compression of scientific data +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://support.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['21ee958b4f2d4be2c9cabfa5e1a94877043609ce86fde5f286f105f7ff84d412'] + +builddependencies = [ + ('binutils', '2.42'), +] + +sanity_check_paths = { + 'files': ["lib/libsz.a", "lib/libsz.%s" % SHLIB_EXT] + + ["include/%s" % x for x in ["ricehdf.h", "szip_adpt.h", "szlib.h"]], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-6.3.0.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-6.3.0.eb index f614a665648..5cebe3f7c68 100644 --- a/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-6.3.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'Szip' version = '2.1.1' -homepage = 'http://www.hdfgroup.org/doc_resource/SZIP/' +homepage = 'http://support.hdfgroup.org/doc_resource/SZIP/' description = """ Szip compression software, providing lossless compression of scientific data @@ -12,7 +12,7 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '6.3.0'} toolchainopts = {'pic': True} -source_urls = ['http://www.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] +source_urls = ['http://support.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] sources = [SOURCELOWER_TAR_GZ] checksums = ['21ee958b4f2d4be2c9cabfa5e1a94877043609ce86fde5f286f105f7ff84d412'] diff --git a/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-6.4.0.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-6.4.0.eb index 924f439ed4e..8edba3b1aa2 100644 --- a/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-6.4.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'Szip' version = '2.1.1' -homepage = 'http://www.hdfgroup.org/doc_resource/SZIP/' +homepage = 'http://support.hdfgroup.org/doc_resource/SZIP/' description = """ Szip compression software, providing lossless compression of scientific data @@ -12,7 +12,7 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '6.4.0'} toolchainopts = {'pic': True} -source_urls = ['http://www.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] +source_urls = ['http://support.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] sources = [SOURCELOWER_TAR_GZ] checksums = ['21ee958b4f2d4be2c9cabfa5e1a94877043609ce86fde5f286f105f7ff84d412'] diff --git a/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-7.3.0.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-7.3.0.eb index 4b9a4923df9..a9926ab81d1 100644 --- a/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-7.3.0.eb +++ b/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-7.3.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'Szip' version = '2.1.1' -homepage = 'http://www.hdfgroup.org/doc_resource/SZIP/' +homepage = 'http://support.hdfgroup.org/doc_resource/SZIP/' description = """ Szip compression software, providing lossless compression of scientific data @@ -12,7 +12,7 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '7.3.0'} toolchainopts = {'pic': True} -source_urls = ['http://www.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] +source_urls = ['http://support.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] sources = [SOURCELOWER_TAR_GZ] checksums = ['21ee958b4f2d4be2c9cabfa5e1a94877043609ce86fde5f286f105f7ff84d412'] diff --git a/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-8.2.0.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-8.2.0.eb index 7f564c5a0fa..0d07710e238 100644 --- a/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-8.2.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'Szip' version = '2.1.1' -homepage = 'http://www.hdfgroup.org/doc_resource/SZIP/' +homepage = 'http://support.hdfgroup.org/doc_resource/SZIP/' description = """ Szip compression software, providing lossless compression of scientific data @@ -12,7 +12,7 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '8.2.0'} toolchainopts = {'pic': True} -source_urls = ['http://www.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] +source_urls = ['http://support.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] sources = [SOURCELOWER_TAR_GZ] checksums = ['21ee958b4f2d4be2c9cabfa5e1a94877043609ce86fde5f286f105f7ff84d412'] diff --git a/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-8.3.0.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-8.3.0.eb index 69db79f2d43..e522a3ac747 100644 --- a/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-8.3.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'Szip' version = '2.1.1' -homepage = 'https://www.hdfgroup.org/doc_resource/SZIP/' +homepage = 'https://support.hdfgroup.org/doc_resource/SZIP/' description = """ Szip compression software, providing lossless compression of scientific data @@ -12,7 +12,7 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '8.3.0'} toolchainopts = {'pic': True} -source_urls = ['https://www.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] +source_urls = ['https://support.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] sources = [SOURCELOWER_TAR_GZ] checksums = ['21ee958b4f2d4be2c9cabfa5e1a94877043609ce86fde5f286f105f7ff84d412'] diff --git a/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-9.3.0.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-9.3.0.eb index 242c281b919..822080c60fe 100644 --- a/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-9.3.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'Szip' version = '2.1.1' -homepage = 'https://www.hdfgroup.org/doc_resource/SZIP/' +homepage = 'https://support.hdfgroup.org/doc_resource/SZIP/' description = """ Szip compression software, providing lossless compression of scientific data @@ -12,7 +12,7 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '9.3.0'} toolchainopts = {'pic': True} -source_urls = ['https://www.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] +source_urls = ['https://support.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] sources = [SOURCELOWER_TAR_GZ] checksums = ['21ee958b4f2d4be2c9cabfa5e1a94877043609ce86fde5f286f105f7ff84d412'] diff --git a/easybuild/easyconfigs/s/s3fs/s3fs-2024.9.0-foss-2024a.eb b/easybuild/easyconfigs/s/s3fs/s3fs-2024.9.0-foss-2024a.eb new file mode 100644 index 00000000000..9177b8c01b8 --- /dev/null +++ b/easybuild/easyconfigs/s/s3fs/s3fs-2024.9.0-foss-2024a.eb @@ -0,0 +1,32 @@ +easyblock = "PythonBundle" + +name = 's3fs' +version = '2024.9.0' + +homepage = 'https://github.com/fsspec/s3fs/' +description = """S3FS builds on aiobotocore to provide a convenient Python filesystem interface for S3..""" + +toolchain = {'name': 'foss', 'version': '2024a'} + +dependencies = [ + ('Python', '3.12.3'), + ('Python-bundle-PyPI', '2024.06'), + ('hatchling', '1.24.2'), + ('aiohttp', '3.10.10'), + ('wrapt', '1.16.0'), + ('boto3', '1.35.36'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('fsspec', version, { + 'checksums': ['4b0afb90c2f21832df142f292649035d80b421f60a9e1c027802e5a0da2b04e8'], + }), + (name, version, { + 'checksums': ['6493705abb50374d6b7994f9616d27adbdd8a219c8635100bdc286382efd91f5'], + }), +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/s/sPyRMSD/sPyRMSD-0.8.0-foss-2023a.eb b/easybuild/easyconfigs/s/sPyRMSD/sPyRMSD-0.8.0-foss-2023a.eb new file mode 100644 index 00000000000..3cff346fddb --- /dev/null +++ b/easybuild/easyconfigs/s/sPyRMSD/sPyRMSD-0.8.0-foss-2023a.eb @@ -0,0 +1,31 @@ +easyblock = 'PythonBundle' + +name = 'sPyRMSD' +version = '0.8.0' + +homepage = 'https://spyrmsd.readthedocs.io' +description = """ +sPyRMSD is a Python tool for symmetry-corrected RMSD calculations. +""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +# graph-tool is the default option, netwrokx and rustworkx are optional alternatives +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('graph-tool', '2.59'), + ('networkx', '3.1'), + ('rustworkx', '0.15.1'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('spyrmsd', version, { + 'checksums': ['401681c5338c06215321c7c3960ca28f22b575118478b7dec6f28b8823b58924'], + }), +] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/s/scArches/scArches-0.6.1-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/s/scArches/scArches-0.6.1-foss-2023a-CUDA-12.1.1.eb new file mode 100644 index 00000000000..bcabab4cc73 --- /dev/null +++ b/easybuild/easyconfigs/s/scArches/scArches-0.6.1-foss-2023a-CUDA-12.1.1.eb @@ -0,0 +1,57 @@ +easyblock = 'PythonBundle' + +name = 'scArches' +version = '0.6.1' +versionsuffix = '-CUDA-12.1.1' + +homepage = 'https://github.com/theislab/scarches' +description = """Single-cell architecture surgery (scArches) is a package for reference-based analysis of single-cell + data.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [ + ('hatchling', '1.18.0'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('Python-bundle-PyPI', '2023.06'), + ('matplotlib', '3.7.2'), + ('anndata', '0.10.5.post1'), + ('h5py', '3.9.0'), + ('leidenalg', '0.10.2'), + ('scanpy', '1.9.8'), + ('scikit-learn', '1.3.1'), + ('scvi-tools', '1.1.2', versionsuffix), + ('PyTorch', '2.1.2', versionsuffix), + ('tqdm', '4.66.1'), +] + +use_pip = True + +exts_list = [ + ('gdown', '5.1.0', { + 'checksums': ['550a72dc5ca2819fe4bcc15d80d05d7c98c0b90e57256254b77d0256b9df4683'], + }), + ('muon', '0.1.6', { + 'checksums': ['762feeb6f52f865cf79d0d0332cc742fe91c1885f668ce15794b62b3952b02f9'], + }), + ('newick', '1.9.0', { + 'checksums': ['9f81be96ec86aefca74d920fc0d6962d89a3156547003ca6915c2e6e31ad3ddf'], + }), + ('scHPL', '1.0.5', { + 'modulename': 'scHPL', + # unpin pandas and newick versions to be compatible with foss/2023a versions + 'preinstallopts': "sed -i 's/~=/>=/g' setup.py && sed -i 's/pandas>=1.1.2,<2/pandas/g' setup.py && ", + 'checksums': ['3eb62b2e65b1faba04b7bcb86f7bf6967a6301866a605551211b8f14fd27eced'], + }), + (name, version, { + 'checksums': ['187463c25781d5c5586c129ad137d96327a9f8604d530a696d5f568a9225d77c'], + }), +] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/scArches/scArches-0.6.1-foss-2023a.eb b/easybuild/easyconfigs/s/scArches/scArches-0.6.1-foss-2023a.eb new file mode 100644 index 00000000000..e6b6f8d4e59 --- /dev/null +++ b/easybuild/easyconfigs/s/scArches/scArches-0.6.1-foss-2023a.eb @@ -0,0 +1,56 @@ +easyblock = 'PythonBundle' + +name = 'scArches' +version = '0.6.1' + +homepage = 'https://github.com/theislab/scarches' +description = """Single-cell architecture surgery (scArches) is a package for reference-based analysis of single-cell + data.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [ + ('hatchling', '1.18.0'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('Python-bundle-PyPI', '2023.06'), + ('matplotlib', '3.7.2'), + ('anndata', '0.10.5.post1'), + ('h5py', '3.9.0'), + ('leidenalg', '0.10.2'), + ('scanpy', '1.9.8'), + ('scikit-learn', '1.3.1'), + ('scvi-tools', '1.1.2'), + ('PyTorch', '2.1.2'), + ('tqdm', '4.66.1'), +] + +use_pip = True + +exts_list = [ + ('gdown', '5.1.0', { + 'checksums': ['550a72dc5ca2819fe4bcc15d80d05d7c98c0b90e57256254b77d0256b9df4683'], + }), + ('muon', '0.1.6', { + 'checksums': ['762feeb6f52f865cf79d0d0332cc742fe91c1885f668ce15794b62b3952b02f9'], + }), + ('newick', '1.9.0', { + 'checksums': ['9f81be96ec86aefca74d920fc0d6962d89a3156547003ca6915c2e6e31ad3ddf'], + }), + ('scHPL', '1.0.5', { + 'modulename': 'scHPL', + # unpin pandas and newick versions to be compatible with foss/2023a versions + 'preinstallopts': "sed -i 's/~=/>=/g' setup.py && sed -i 's/pandas>=1.1.2,<2/pandas/g' setup.py && ", + 'checksums': ['3eb62b2e65b1faba04b7bcb86f7bf6967a6301866a605551211b8f14fd27eced'], + }), + (name, version, { + 'checksums': ['187463c25781d5c5586c129ad137d96327a9f8604d530a696d5f568a9225d77c'], + }), +] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/scCustomize/scCustomize-2.1.2-foss-2023a-R-4.3.2.eb b/easybuild/easyconfigs/s/scCustomize/scCustomize-2.1.2-foss-2023a-R-4.3.2.eb new file mode 100644 index 00000000000..2f94ec91206 --- /dev/null +++ b/easybuild/easyconfigs/s/scCustomize/scCustomize-2.1.2-foss-2023a-R-4.3.2.eb @@ -0,0 +1,65 @@ +easyblock = 'Bundle' + +name = 'scCustomize' +version = '2.1.2' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://cran.r-project.org/web/packages/scCustomize/index.html' +description = """ +Collection of functions created and/or curated to aid in the visualization and analysis of single-cell data using 'R'. +""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + # Seurat has its own module, but is either in R-bundle-Bioconductor + ('R', '4.3.2'), + ('R-bundle-CRAN', '2023.12'), + ('R-bundle-Bioconductor', '3.18', '-R-%(rver)s'), +] + +exts_default_options = { + 'source_urls': [ + 'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'https://cran.r-project.org/src/contrib/', # current version of packages + 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + ], + 'sources': ['%(name)s_%(version)s.tar.gz'], +} + +exts_defaultclass = 'RPackage' + +exts_list = [ + ('rlang', '1.1.3', { + 'checksums': ['24a3424b5dc2c4bd3e5f7c0b54fbe1355028e329181b2d41f4464c8ade28bf0a'], + }), + ('prismatic', '1.1.2', { + 'checksums': ['babf5b7ad4c9b52921c619de66f93936755dc385b2b69c6504d87c7d5a71e261'], + }), + ('paletteer', '1.6.0', { + 'checksums': ['b5de20300c93df203ddc4f3bfeb0a825ef2745c22d66590b33cef9e7448d92d8'], + }), + ('snakecase', '0.11.1', { + 'checksums': ['2a5f9791337ca42e392f23fb873eb44f74810583e9aa7c62fda2f28f9e750821'], + }), + ('janitor', '2.2.0', { + 'checksums': ['29d5d0185e4e824bb38f905b158162a12f52dc01c2e8a487fc730ce46bf6baae'], + }), + ('ggprism', '1.0.5', { + 'checksums': ['7f35eeb010ef3cb47f23cb23b0b084156c56af02cff534c217652ea38cdb5171'], + }), + (name, version, { + 'checksums': ['2b569a145fe6dd888ac72ced424352b100b7acc913d6027ddae7799ca4421094'], + }), +] + +sanity_check_paths = { + 'files': [], + 'dirs': [name], +} + +sanity_check_commands = ['Rscript -e "library(%(name)s)"'] + +modextrapaths = {'R_LIBS_SITE': ''} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/s/scFEA/scFEA-1.1-20221109-foss-2023a.eb b/easybuild/easyconfigs/s/scFEA/scFEA-1.1-20221109-foss-2023a.eb new file mode 100644 index 00000000000..3e1d6133015 --- /dev/null +++ b/easybuild/easyconfigs/s/scFEA/scFEA-1.1-20221109-foss-2023a.eb @@ -0,0 +1,32 @@ +easyblock = 'Tarball' + +name = 'scFEA' +local_commit = '4c1fb76' +version = '1.1-20221109' + +homepage = 'https://github.com/changwn/scFEA' +description = """scFEA: A graph neural network model to estimate cell-wise metabolic using single cell RNA-seq data""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['https://github.com/changwn/scFEA/archive'] +sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}] +checksums = ['79774974964fed427dd67ba1d51c202a5ff90418fd84f74ebd9b478113ff50f6'] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('matplotlib', '3.7.2'), + ('tqdm', '4.66.1'), + ('PyTorch', '2.1.2'), + ('MAGIC', '3.0.0'), +] + +sanity_check_paths = { + 'files': ['src/scFEA.py'], + 'dirs': [], +} + +sanity_check_commands = ["python %(installdir)s/src/scFEA.py --help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/scTIE/scTIE-20231205-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/s/scTIE/scTIE-20231205-foss-2023a-CUDA-12.1.1.eb new file mode 100644 index 00000000000..375e693aeba --- /dev/null +++ b/easybuild/easyconfigs/s/scTIE/scTIE-20231205-foss-2023a-CUDA-12.1.1.eb @@ -0,0 +1,46 @@ +easyblock = 'Tarball' + +name = 'scTIE' +version = '20231205' +local_commit = '044d91a' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/SydneyBioX/scTIE' +description = """scTIE (single-cell Temporal Integration and inference of multimodal Experiments) + is an autoencoder-based method for integrating multimodal profiling of scRNA-seq and scATAC-seq + data over a time course and inferring cell-type specific GRNs. scTIE projects cells from all time + points into a common embedding space, followed by extracting interpretable information from this + space to predict cell trajectories.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +github_account = 'SydneyBioX' +source_urls = [GITHUB_SOURCE] +sources = ['%s.tar.gz' % local_commit] +checksums = ['bcbf7c846539d0f04e7bbf3cc6ae2fe075a4ba11e3a4388c29def943d39af53e'] + +dependencies = [ + ('Python', '3.11.3'), + ('PyTorch', '2.1.2', versionsuffix), + ('SciPy-bundle', '2023.07'), + ('CUDA', '12.1.1', '', SYSTEM), + ('POT', '0.9.3', versionsuffix), +] + +postinstallcmds = ['cd %(installdir)s && mkdir bin && ln -r -s main.py bin/sctie && chmod a+x main.py'] + +fix_python_shebang_for = ['main.py'] + +modextrapaths = { + 'PATH': '', + 'PYTHONPATH': '', +} + +sanity_check_paths = { + 'files': ['bin/sctie'], + 'dirs': [], +} + +sanity_check_commands = ['sctie --help'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/scVelo/scVelo-0.2.5-foss-2022a.eb b/easybuild/easyconfigs/s/scVelo/scVelo-0.2.5-foss-2022a.eb new file mode 100644 index 00000000000..5e7f3b40ba6 --- /dev/null +++ b/easybuild/easyconfigs/s/scVelo/scVelo-0.2.5-foss-2022a.eb @@ -0,0 +1,47 @@ +easyblock = 'PythonBundle' + +name = 'scVelo' +version = '0.2.5' + +homepage = "https://scvelo.org" +description = """scVelo is a scalable toolkit for estimating and analyzing RNA velocities in single cells using + dynamical modeling.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +builddependencies = [ + ('pkgconf', '1.8.0'), +] + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('scikit-learn', '1.1.2'), + ('h5py', '3.7.0'), + ('matplotlib', '3.5.2'), + ('networkx', '2.8.4'), + ('numba', '0.56.4'), + ('PyTables', '3.8.0'), + ('statsmodels', '0.13.1'), + ('libpng', '1.6.37'), + ('freetype', '2.12.1'), + ('Tkinter', '%(pyver)s'), + ('tqdm', '4.64.0'), + ('scanpy', '1.9.1'), # also provides anndata + ('Seaborn', '0.12.1'), + ('loompy', '3.0.7'), # also provides numpy-groupies + ('umap-learn', '0.5.3'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + (name, version, { + 'modulename': 'scvelo', + 'source_tmpl': '%(namelower)s-%(version)s.tar.gz', + 'checksums': ['7e32d9e34245971330d69c12f4339cebe0acebb61e59a8b1aca9b369078b5207'], + }), +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/scanpy/scanpy-1.9.8-foss-2023a.eb b/easybuild/easyconfigs/s/scanpy/scanpy-1.9.8-foss-2023a.eb index dc34504eeee..49724e4ae26 100644 --- a/easybuild/easyconfigs/s/scanpy/scanpy-1.9.8-foss-2023a.eb +++ b/easybuild/easyconfigs/s/scanpy/scanpy-1.9.8-foss-2023a.eb @@ -13,6 +13,10 @@ description = """Scanpy is a scalable toolkit for analyzing single-cell gene exp toolchain = {'name': 'foss', 'version': '2023a'} toolchainopts = {'openmp': True} +builddependencies = [ + ('hatchling', '1.18.0'), +] + dependencies = [ ('Python', '3.11.3'), ('SciPy-bundle', '2023.07'), @@ -25,7 +29,6 @@ dependencies = [ ('networkx', '3.1'), ('numba', '0.58.1'), ('umap-learn', '0.5.5'), - ('hatchling', '1.18.0'), ('anndata', '0.10.5.post1'), ] diff --git a/easybuild/easyconfigs/s/scib-metrics/scib-metrics-0.5.1-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/s/scib-metrics/scib-metrics-0.5.1-foss-2023a-CUDA-12.1.1.eb new file mode 100644 index 00000000000..b021ceb3c20 --- /dev/null +++ b/easybuild/easyconfigs/s/scib-metrics/scib-metrics-0.5.1-foss-2023a-CUDA-12.1.1.eb @@ -0,0 +1,55 @@ +easyblock = 'PythonBundle' + +name = 'scib-metrics' +version = '0.5.1' +versionsuffix = '-CUDA-12.1.1' + +homepage = 'https://scib-metrics.readthedocs.io' +description = "Accelerated and Python-only metrics for benchmarking single-cell integration outputs" + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [ + ('hatchling', '1.18.0'), + ('poetry', '1.5.1'), +] +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('anndata', '0.10.5.post1'), + ('jax', '0.4.25', versionsuffix), + ('scikit-learn', '1.3.1'), + ('scanpy', '1.9.8'), + ('python-igraph', '0.11.4'), + ('matplotlib', '3.7.2'), + ('tqdm', '4.66.1'), + ('umap-learn', '0.5.5'), +] + +use_pip = True + +exts_list = [ + ('toolz', '0.12.1', { + 'checksums': ['ecca342664893f177a13dac0e6b41cbd8ac25a358e5f215316d43e2100224f4d'], + }), + ('plottable', '0.1.5', { + 'checksums': ['235d762a31c82129dc5bf74205c103a14b1e4393d0f921cc0231be5de884041d'], + }), + ('pynndescent', '0.5.11', { + 'checksums': ['6f44ced9d5a9da2c87d9b2fff30bb5308540c0657605e4d5cde7ed3275bbad50'], + }), + ('rich', '13.7.1', { + 'checksums': ['9be308cb1fe2f1f57d67ce99e95af38a1e2bc71ad9813b0e247cf7ffbcc3a432'], + }), + ('chex', '0.1.86', { + 'checksums': ['e8b0f96330eba4144659e1617c0f7a57b161e8cbb021e55c6d5056c7378091d1'], + }), + (name, version, { + 'sources': ['scib_metrics-%(version)s.tar.gz'], + 'checksums': ['74d10251acf1c11402b994faf063e55317881d7950fb78f6cef011d232a1e266'], + }), +] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/scib-metrics/scib-metrics-0.5.1-foss-2023a.eb b/easybuild/easyconfigs/s/scib-metrics/scib-metrics-0.5.1-foss-2023a.eb new file mode 100644 index 00000000000..68ef32b71ad --- /dev/null +++ b/easybuild/easyconfigs/s/scib-metrics/scib-metrics-0.5.1-foss-2023a.eb @@ -0,0 +1,54 @@ +easyblock = 'PythonBundle' + +name = 'scib-metrics' +version = '0.5.1' + +homepage = 'https://scib-metrics.readthedocs.io' +description = "Accelerated and Python-only metrics for benchmarking single-cell integration outputs" + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [ + ('hatchling', '1.18.0'), + ('poetry', '1.5.1'), +] +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('anndata', '0.10.5.post1'), + ('jax', '0.4.25'), + ('scikit-learn', '1.3.1'), + ('scanpy', '1.9.8'), + ('python-igraph', '0.11.4'), + ('matplotlib', '3.7.2'), + ('tqdm', '4.66.1'), + ('umap-learn', '0.5.5'), +] + +use_pip = True + +exts_list = [ + ('toolz', '0.12.1', { + 'checksums': ['ecca342664893f177a13dac0e6b41cbd8ac25a358e5f215316d43e2100224f4d'], + }), + ('plottable', '0.1.5', { + 'checksums': ['235d762a31c82129dc5bf74205c103a14b1e4393d0f921cc0231be5de884041d'], + }), + ('pynndescent', '0.5.11', { + 'checksums': ['6f44ced9d5a9da2c87d9b2fff30bb5308540c0657605e4d5cde7ed3275bbad50'], + }), + ('rich', '13.7.1', { + 'checksums': ['9be308cb1fe2f1f57d67ce99e95af38a1e2bc71ad9813b0e247cf7ffbcc3a432'], + }), + ('chex', '0.1.86', { + 'checksums': ['e8b0f96330eba4144659e1617c0f7a57b161e8cbb021e55c6d5056c7378091d1'], + }), + (name, version, { + 'sources': ['scib_metrics-%(version)s.tar.gz'], + 'checksums': ['74d10251acf1c11402b994faf063e55317881d7950fb78f6cef011d232a1e266'], + }), +] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/scikit-build-core/scikit-build-core-0.10.6-GCCcore-13.3.0.eb b/easybuild/easyconfigs/s/scikit-build-core/scikit-build-core-0.10.6-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..57e6f53d4c0 --- /dev/null +++ b/easybuild/easyconfigs/s/scikit-build-core/scikit-build-core-0.10.6-GCCcore-13.3.0.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonBundle' + +name = 'scikit-build-core' +version = '0.10.6' + +homepage = 'https://scikit-build.readthedocs.io/en/latest/' +description = """Scikit-build-core is a complete ground-up rewrite of scikit-build on top of +modern packaging APIs. It provides a bridge between CMake and the Python build +system, allowing you to make Python modules with CMake.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +builddependencies = [ + ('binutils', '2.42'), + ('hatchling', '1.24.2'), +] + +dependencies = [ + ('Python', '3.12.3'), + ('Python-bundle-PyPI', '2024.06'), + ('CMake', '3.29.3'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('scikit_build_core', version, { + 'checksums': ['5397db8f09ee050d145406c11deed06538bb0b261df95f8d2d6aaf8699f0126d'], + }), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/scikit-build-core/scikit-build-core-0.9.3-GCCcore-12.3.0.eb b/easybuild/easyconfigs/s/scikit-build-core/scikit-build-core-0.9.3-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..a17cdb279fe --- /dev/null +++ b/easybuild/easyconfigs/s/scikit-build-core/scikit-build-core-0.9.3-GCCcore-12.3.0.eb @@ -0,0 +1,37 @@ +easyblock = 'PythonBundle' + +name = 'scikit-build-core' +version = '0.9.3' + +homepage = 'https://scikit-build.readthedocs.io/en/latest/' +description = """Scikit-build-core is a complete ground-up rewrite of scikit-build on top of +modern packaging APIs. It provides a bridge between CMake and the Python build +system, allowing you to make Python modules with CMake.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +builddependencies = [ + ('binutils', '2.40'), + ('hatchling', '1.18.0'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('CMake', '3.26.3'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('pyproject-metadata', '0.8.0', { + 'sources': ['pyproject_metadata-%(version)s.tar.gz'], + 'checksums': ['376d5a00764ac29440a54579f88e66b7d9cb7e629d35c35a1c7248bfebc9b455'], + }), + ('scikit_build_core', version, { + 'checksums': ['341d113e473a5409dc62522e8b1b1b8b1647a0b95557ad15f6be2a36071fd390'], + }), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/scikit-build-core/scikit-build-core-0.9.3-GCCcore-13.2.0.eb b/easybuild/easyconfigs/s/scikit-build-core/scikit-build-core-0.9.3-GCCcore-13.2.0.eb index 691bd671f50..f95d5d59160 100644 --- a/easybuild/easyconfigs/s/scikit-build-core/scikit-build-core-0.9.3-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/s/scikit-build-core/scikit-build-core-0.9.3-GCCcore-13.2.0.eb @@ -25,6 +25,10 @@ use_pip = True sanity_pip_check = True exts_list = [ + ('pyproject-metadata', '0.8.0', { + 'sources': ['pyproject_metadata-%(version)s.tar.gz'], + 'checksums': ['376d5a00764ac29440a54579f88e66b7d9cb7e629d35c35a1c7248bfebc9b455'], + }), ('scikit_build_core', version, { 'checksums': ['341d113e473a5409dc62522e8b1b1b8b1647a0b95557ad15f6be2a36071fd390'], }), diff --git a/easybuild/easyconfigs/s/scikit-build/scikit-build-0.17.6-GCCcore-13.3.0.eb b/easybuild/easyconfigs/s/scikit-build/scikit-build-0.17.6-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..2d799810ee1 --- /dev/null +++ b/easybuild/easyconfigs/s/scikit-build/scikit-build-0.17.6-GCCcore-13.3.0.eb @@ -0,0 +1,38 @@ +easyblock = 'PythonBundle' + +name = 'scikit-build' +version = '0.17.6' + +homepage = 'https://scikit-build.readthedocs.io/en/latest' +description = """Scikit-Build, or skbuild, is an improved build system generator +for CPython C/C++/Fortran/Cython extensions.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +builddependencies = [ + ('binutils', '2.42'), + ('hatchling', '1.24.2'), +] + +dependencies = [ + ('Python', '3.12.3'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('packaging', '23.1', { + 'checksums': ['a392980d2b6cffa644431898be54b0045151319d1e7ec34f0cfed48767dd334f'], + }), + ('distro', '1.8.0', { + 'checksums': ['02e111d1dc6a50abb8eed6bf31c3e48ed8b0830d1ea2a1b78c61765c2513fdd8'], + }), + (name, version, { + 'modulename': 'skbuild', + 'sources': ['scikit_build-%(version)s.tar.gz'], + 'checksums': ['b51a51a36b37c42650994b5047912f59b22e3210b23e321f287611f9ef6e5c9d'], + }), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-1.5.2-gfbf-2024a.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-1.5.2-gfbf-2024a.eb new file mode 100644 index 00000000000..be9c3fd844c --- /dev/null +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-1.5.2-gfbf-2024a.eb @@ -0,0 +1,39 @@ +easyblock = 'PythonBundle' + +name = 'scikit-learn' +version = '1.5.2' + +homepage = 'https://scikit-learn.org/stable/index.html' +description = """Scikit-learn integrates machine learning algorithms in the tightly-knit scientific Python world, +building upon numpy, scipy, and matplotlib. As a machine-learning module, +it provides versatile tools for data mining and analysis in any field of science and engineering. +It strives to be simple and efficient, accessible to everybody, and reusable in various contexts.""" + +toolchain = {'name': 'gfbf', 'version': '2024a'} + +builddependencies = [ + ('Cython', '3.0.10'), + ('meson-python', '0.16.0'), +] + +dependencies = [ + ('Python', '3.12.3'), + ('Python-bundle-PyPI', '2024.06'), + ('SciPy-bundle', '2024.05'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + (name, version, { + 'modulename': 'sklearn', + 'sources': ['scikit_learn-%(version)s.tar.gz'], + 'checksums': ['b4237ed7b3fdd0a4882792e68ef2545d5baa50aca3bb45aa7df468138ad8f94d'], + }), + ('sklearn', '0.0', { + 'checksums': ['e23001573aa194b834122d2b9562459bf5ae494a2d59ca6b8aa22c85a44c0e31'], + }), +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/s/scikit-misc/scikit-misc-0.3.1-foss-2023a.eb b/easybuild/easyconfigs/s/scikit-misc/scikit-misc-0.3.1-foss-2023a.eb index e355180eb49..dda0a838bf3 100644 --- a/easybuild/easyconfigs/s/scikit-misc/scikit-misc-0.3.1-foss-2023a.eb +++ b/easybuild/easyconfigs/s/scikit-misc/scikit-misc-0.3.1-foss-2023a.eb @@ -9,6 +9,10 @@ description = "Miscellaneous tools for data analysis and scientific computing" toolchain = {'name': 'foss', 'version': '2023a'} +builddependencies = [ + ('pkgconf', '1.9.5'), +] + dependencies = [ ('Python', '3.11.3'), ('SciPy-bundle', '2023.07'), diff --git a/easybuild/easyconfigs/s/scrublet/scrublet-0.2.3-foss-2023a.eb b/easybuild/easyconfigs/s/scrublet/scrublet-0.2.3-foss-2023a.eb new file mode 100644 index 00000000000..5b6d65b6bb4 --- /dev/null +++ b/easybuild/easyconfigs/s/scrublet/scrublet-0.2.3-foss-2023a.eb @@ -0,0 +1,35 @@ +easyblock = 'PythonBundle' + +name = 'scrublet' +version = '0.2.3' + +homepage = 'https://github.com/swolock/scrublet' +description = "Single-Cell Remover of Doublets - Python code for identifying doublets in single-cell RNA-seq data" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('scikit-learn', '1.3.1'), + ('scikit-image', '0.22.0'), + ('matplotlib', '3.7.2'), + ('numba', '0.58.1'), + ('tqdm', '4.66.1'), + ('umap-learn', '0.5.5'), +] + +use_pip = True + +exts_list = [ + ('annoy', '1.17.3', { + 'checksums': ['9cbfebefe0a5f843eba29c6be4c84d601f4f41ad4ded0486f1b88c3b07739c15'], + }), + (name, version, { + 'checksums': ['2185f63070290267f82a36e5b4cae8c321f10415d2d0c9f7e5e97b1126bf653a'], + }), +] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/scvi-tools/scvi-tools-1.1.2-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/s/scvi-tools/scvi-tools-1.1.2-foss-2023a-CUDA-12.1.1.eb new file mode 100644 index 00000000000..c434f381cfd --- /dev/null +++ b/easybuild/easyconfigs/s/scvi-tools/scvi-tools-1.1.2-foss-2023a-CUDA-12.1.1.eb @@ -0,0 +1,57 @@ +easyblock = 'PythonBundle' + +name = 'scvi-tools' +version = '1.1.2' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/scverse/scvi-tools' +description = """scvi-tools (single-cell variational inference tools) is a package for probabilistic modeling and +analysis of single-cell omics data, built on top of PyTorch and AnnData.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [('hatchling', '1.18.0')] +dependencies = [ + ('CUDA', '12.1.1', '', SYSTEM), + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('anndata', '0.10.5.post1'), + ('matplotlib', '3.7.2'), + ('scikit-learn', '1.3.1'), + ('tqdm', '4.66.1'), + ('h5py', '3.9.0'), + ('jax', '0.4.25', versionsuffix), + ('Flax', '0.8.4', versionsuffix), + ('PyTorch-Lightning', '2.2.1', versionsuffix), + ('pyro-ppl', '1.9.0', versionsuffix), + ('ml-collections', '0.1.1'), +] + +use_pip = True + +exts_list = [ + ('mudata', '0.2.3', { + 'checksums': ['45288ac150bfc598d68acb7c2c1c43c38c5c39522107e04f7efbf3360c7f2035'], + }), + ('multipledispatch', '1.0.0', { + 'checksums': ['5c839915465c68206c3e9c473357908216c28383b425361e5d144594bf85a7e0'], + }), + ('numpyro', '0.15.0', { + 'checksums': ['e16c9f47cc31e2aa259584a0b6c944312081d33ca92406022632ad584b0e600d'], + }), + ('docrep', '0.3.2', { + 'checksums': ['ed8a17e201abd829ef8da78a0b6f4d51fb99a4cbd0554adbed3309297f964314'], + }), + ('lightning', '2.1.4', { + 'checksums': ['0e45098c700fa28c604a11ae233ce181b44aeffce2404debebc2616118431d9f'], + }), + (name, version, { + 'modulename': 'scvi', + 'sources': ['scvi_tools-%(version)s.tar.gz'], + 'checksums': ['104a11a30e8996f5ceaa907b8c81b48b1f4b380d492ef2dd9b9a5577ed81b0f9'], + }), +] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/scvi-tools/scvi-tools-1.1.2-foss-2023a.eb b/easybuild/easyconfigs/s/scvi-tools/scvi-tools-1.1.2-foss-2023a.eb new file mode 100644 index 00000000000..be427d2af9e --- /dev/null +++ b/easybuild/easyconfigs/s/scvi-tools/scvi-tools-1.1.2-foss-2023a.eb @@ -0,0 +1,55 @@ +easyblock = 'PythonBundle' + +name = 'scvi-tools' +version = '1.1.2' + +homepage = 'https://github.com/scverse/scvi-tools' +description = """scvi-tools (single-cell variational inference tools) is a package for probabilistic modeling and +analysis of single-cell omics data, built on top of PyTorch and AnnData.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [('hatchling', '1.18.0')] +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('anndata', '0.10.5.post1'), + ('matplotlib', '3.7.2'), + ('scikit-learn', '1.3.1'), + ('tqdm', '4.66.1'), + ('jax', '0.4.25'), + ('h5py', '3.9.0'), + ('PyTorch-Lightning', '2.2.1'), + ('pyro-ppl', '1.9.0'), + ('ml-collections', '0.1.1'), + ('Flax', '0.8.4'), +] + +use_pip = True + +exts_list = [ + ('mudata', '0.2.3', { + 'checksums': ['45288ac150bfc598d68acb7c2c1c43c38c5c39522107e04f7efbf3360c7f2035'], + }), + ('multipledispatch', '1.0.0', { + 'checksums': ['5c839915465c68206c3e9c473357908216c28383b425361e5d144594bf85a7e0'], + }), + ('numpyro', '0.15.0', { + 'checksums': ['e16c9f47cc31e2aa259584a0b6c944312081d33ca92406022632ad584b0e600d'], + }), + ('docrep', '0.3.2', { + 'checksums': ['ed8a17e201abd829ef8da78a0b6f4d51fb99a4cbd0554adbed3309297f964314'], + }), + ('lightning', '2.1.4', { + 'checksums': ['0e45098c700fa28c604a11ae233ce181b44aeffce2404debebc2616118431d9f'], + }), + (name, version, { + 'modulename': 'scvi', + 'sources': ['scvi_tools-%(version)s.tar.gz'], + 'checksums': ['104a11a30e8996f5ceaa907b8c81b48b1f4b380d492ef2dd9b9a5577ed81b0f9'], + }), +] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/sdsl-lite/sdsl-lite-2.0.3-GCCcore-12.2.0.eb b/easybuild/easyconfigs/s/sdsl-lite/sdsl-lite-2.0.3-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..d4bda3a4a9e --- /dev/null +++ b/easybuild/easyconfigs/s/sdsl-lite/sdsl-lite-2.0.3-GCCcore-12.2.0.eb @@ -0,0 +1,31 @@ +# This easyconfig was created by the BEAR Software team at the University of Birmingham. +easyblock = "CMakeMake" + +name = 'sdsl-lite' +version = '2.0.3' + +homepage = "https://github.com/simongog/sdsl-lite" +description = """The Succinct Data Structure Library (SDSL) is a powerful and flexible C++11 library implementing + succinct data structures. In total, the library contains the highlights of 40 research publications. Succinct + data structures can represent an object (such as a bitvector or a tree) in space close to the information-theoretic + lower bound of the object while supporting operations of the original object efficiently. The theoretical time + complexity of an operation performed on the classical data structure and the equivalent succinct data structure + are (most of the time) identical.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://github.com/simongog/%(name)s/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['08ece40ce44041906bfa425af81a20a8071d187285f674debd8816c2e3113c2f'] + +builddependencies = [ + ('CMake', '3.24.3'), + ('binutils', '2.39'), +] + +sanity_check_paths = { + 'files': ['lib/libdivsufsort64.a', 'lib/libdivsufsort.a', 'lib/libsdsl.a', 'include/divsufsort64.h'], + 'dirs': ['include/sdsl'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/s/segment-anything/segment-anything-1.0-foss-2023a.eb b/easybuild/easyconfigs/s/segment-anything/segment-anything-1.0-foss-2023a.eb new file mode 100644 index 00000000000..23c6de38a67 --- /dev/null +++ b/easybuild/easyconfigs/s/segment-anything/segment-anything-1.0-foss-2023a.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonPackage' + +name = 'segment-anything' +version = '1.0' + +homepage = 'https://github.com/facebookresearch/segment-anything' +description = """The Segment Anything Model (SAM) produces high quality object masks from input prompts + such as points or boxes, and it can be used to generate masks for all objects in an image. + It has been trained on a dataset of 11 million images and 1.1 billion masks, and has strong zero-shot + performance on a variety of segmentation tasks.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +sources = ['segment_anything-%(version)s.tar.gz'] +checksums = ['ed0c9f6fb07bbef9c6238a7028a13c8272f1ba6b6305ca73e3e064266503736b'] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('torchvision', '0.16.0'), + ('OpenCV', '4.8.1', '-contrib'), + ('pycocotools', '2.0.7'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'ai' diff --git a/easybuild/easyconfigs/s/setuptools-rust/setuptools-rust-1.6.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/s/setuptools-rust/setuptools-rust-1.6.0-GCCcore-12.3.0.eb index 8cbf2db9fe7..b2517ef684c 100644 --- a/easybuild/easyconfigs/s/setuptools-rust/setuptools-rust-1.6.0-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/s/setuptools-rust/setuptools-rust-1.6.0-GCCcore-12.3.0.eb @@ -18,11 +18,8 @@ dependencies = [ ('Python', '3.11.3'), ] -exts_default_options = { - 'download_dep_fail': True, - 'sanity_pip_check': True, - 'use_pip': True, -} +sanity_pip_check = True +use_pip = True exts_list = [ ('typing_extensions', '4.6.3', { diff --git a/easybuild/easyconfigs/s/setuptools-rust/setuptools-rust-1.8.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/s/setuptools-rust/setuptools-rust-1.8.0-GCCcore-13.2.0.eb index 669229c8f11..044d56266ae 100644 --- a/easybuild/easyconfigs/s/setuptools-rust/setuptools-rust-1.8.0-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/s/setuptools-rust/setuptools-rust-1.8.0-GCCcore-13.2.0.eb @@ -18,11 +18,8 @@ dependencies = [ ('Python', '3.11.5'), ] -exts_default_options = { - 'download_dep_fail': True, - 'sanity_pip_check': True, - 'use_pip': True, -} +sanity_pip_check = True +use_pip = True exts_list = [ ('typing_extensions', '4.8.0', { diff --git a/easybuild/easyconfigs/s/setuptools-rust/setuptools-rust-1.9.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/s/setuptools-rust/setuptools-rust-1.9.0-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..b763364ba26 --- /dev/null +++ b/easybuild/easyconfigs/s/setuptools-rust/setuptools-rust-1.9.0-GCCcore-13.3.0.eb @@ -0,0 +1,38 @@ +easyblock = 'PythonBundle' + +name = 'setuptools-rust' +version = '1.9.0' + +homepage = 'https://github.com/PyO3/setuptools-rust' +description = """setuptools-rust is a plugin for setuptools to build Rust Python extensions +implemented with PyO3 or rust-cpython.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +builddependencies = [ + ('binutils', '2.42'), +] + +dependencies = [ + ('Python', '3.12.3'), +] + +sanity_pip_check = True +use_pip = True + +exts_list = [ + ('typing-extensions', '4.12.2', { + 'sources': ['typing_extensions-%(version)s.tar.gz'], + 'checksums': ['1a7ead55c7e559dd4dee8856e3a88b41225abfe1ce8df57b7c13915fe121ffb8'], + }), + ('semantic-version', '2.10.0', { + 'sources': ['semantic_version-%(version)s.tar.gz'], + 'checksums': ['bdabb6d336998cbb378d4b9db3a4b56a1e3235701dc05ea2690d9a997ed5041c'], + }), + (name, version, { + 'checksums': ['704df0948f2e4cc60c2596ad6e840ea679f4f43e58ed4ad0c1857807240eab96'], + }), +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/s/sirocco/sirocco-2.1.0-GCC-13.2.0.eb b/easybuild/easyconfigs/s/sirocco/sirocco-2.1.0-GCC-13.2.0.eb new file mode 100644 index 00000000000..3819e493fe2 --- /dev/null +++ b/easybuild/easyconfigs/s/sirocco/sirocco-2.1.0-GCC-13.2.0.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'sirocco' +version = '2.1.0' + +homepage = 'https://github.com/miguelmarco/SIROCCO2/' +description = """C++ library that allows to compute piecewise linear + approximations of the path followed by the root of a complex polynomial""" + +toolchain = {'name': 'GCC', 'version': '13.2.0'} + +source_urls = ['https://github.com/miguelmarco/SIROCCO2/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['1fd66ae94d73095f1355389c1d3d94222437bed87579d77667f50548bdd9fa9a'] + +builddependencies = [ + ('Autotools', '20220317'), +] + +dependencies = [ + ('MPFR', '4.2.1'), +] + +preconfigopts = 'autoreconf --install && ' + +sanity_check_paths = { + 'files': [ + 'include/sirocco.h', + 'lib/libsirocco.%s' % SHLIB_EXT, + ], + 'dirs': [] +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/skani/skani-0.2.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/s/skani/skani-0.2.2-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..889947f5c2c --- /dev/null +++ b/easybuild/easyconfigs/s/skani/skani-0.2.2-GCCcore-12.3.0.eb @@ -0,0 +1,481 @@ +easyblock = 'Cargo' + +name = 'skani' +version = '0.2.2' + +homepage = 'https://github.com/bluenote-1577/skani' +description = "skani - accurate, fast nucleotide identity calculation for MAGs, genomes, and databases" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +github_account = 'bluenote-1577' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = [ + {'v0.2.2.tar.gz': 'e047d52b9f753625eff480fe90f1abb68f82cc6892d9d1910b18bfcedbfc0b9d'}, + {'adler-1.0.2.tar.gz': 'f26201604c87b1e01bd3d98f8d5d9a8fcbb815e8cedb41ffccbeb4bf593a35fe'}, + {'aho-corasick-1.1.2.tar.gz': 'b2969dcb958b36655471fc61f7e416fa76033bdd4bfed0678d8fee1e2d07a1f0'}, + {'anyhow-1.0.75.tar.gz': 'a4668cab20f66d8d020e1fbc0ebe47217433c1b6c8f2040faf858554e394ace6'}, + {'approx-0.5.1.tar.gz': 'cab112f0a86d568ea0e627cc1d6be74a1e9cd55214684db5561995f6dad897c6'}, + {'assert_cmd-1.0.8.tar.gz': 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{'trilean-1.1.0.tar.gz': '683ba5022fe6dbd7133cad150478ccf51bdb6d861515181e5fc6b4323d4fa424'}, + {'triple_accel-0.4.0.tar.gz': '22048bc95dfb2ffd05b1ff9a756290a009224b60b2f0e7525faeee7603851e63'}, + {'tsv-0.1.1.tar.gz': '418001090d0ccdf2284690ff051c0c10d18ddd320ea9dd8ff6d205cb8436a0aa'}, + {'typenum-1.17.0.tar.gz': '42ff0bf0c66b8238c6f3b578df37d0b7848e55df8577b3f74f92a69acceeb825'}, + {'unicode-ident-1.0.12.tar.gz': '3354b9ac3fae1ff6755cb6db53683adb661634f67557942dea4facebec0fee4b'}, + {'unicode-xid-0.1.0.tar.gz': 'fc72304796d0818e357ead4e000d19c9c174ab23dc11093ac919054d20a6a7fc'}, + {'vec_map-0.8.2.tar.gz': 'f1bddf1187be692e79c5ffeab891132dfb0f236ed36a43c7ed39f1165ee20191'}, + {'version_check-0.9.4.tar.gz': '49874b5167b65d7193b8aba1567f5c7d93d001cafc34600cee003eda787e483f'}, + {'wait-timeout-0.2.0.tar.gz': '9f200f5b12eb75f8c1ed65abd4b2db8a6e1b138a20de009dacee265a2498f3f6'}, + {'wasi-0.11.0+wasi-snapshot-preview1.tar.gz': '9c8d87e72b64a3b4db28d11ce29237c246188f4f51057d65a7eab63b7987e423'}, + {'wide-0.7.12.tar.gz': 'ebecebefc38ff1860b4bc47550bbfa63af5746061cf0d29fcd7fa63171602598'}, + {'winapi-0.3.9.tar.gz': '5c839a674fcd7a98952e593242ea400abe93992746761e38641405d28b00f419'}, + {'winapi-i686-pc-windows-gnu-0.4.0.tar.gz': 'ac3b87c63620426dd9b991e5ce0329eff545bccbbb34f3be09ff6fb6ab51b7b6'}, + {'winapi-util-0.1.6.tar.gz': 'f29e6f9198ba0d26b4c9f07dbe6f9ed633e1f3d5b8b414090084349e46a52596'}, + {'winapi-x86_64-pc-windows-gnu-0.4.0.tar.gz': '712e227841d057c1ee1cd2fb22fa7e5a5461ae8e48fa2ca79ec42cfc1931183f'}, + {'windows-sys-0.48.0.tar.gz': '677d2418bec65e3338edb076e806bc1ec15693c5d0104683f2efe857f61056a9'}, + {'windows-targets-0.48.5.tar.gz': '9a2fa6e2155d7247be68c096456083145c183cbbbc2764150dda45a87197940c'}, + {'windows_aarch64_gnullvm-0.48.5.tar.gz': '2b38e32f0abccf9987a4e3079dfb67dcd799fb61361e53e2882c3cbaf0d905d8'}, + {'windows_aarch64_msvc-0.48.5.tar.gz': 'dc35310971f3b2dbbf3f0690a219f40e2d9afcf64f9ab7cc1be722937c26b4bc'}, + {'windows_i686_gnu-0.48.5.tar.gz': 'a75915e7def60c94dcef72200b9a8e58e5091744960da64ec734a6c6e9b3743e'}, + {'windows_i686_msvc-0.48.5.tar.gz': '8f55c233f70c4b27f66c523580f78f1004e8b5a8b659e05a4eb49d4166cca406'}, + {'windows_x86_64_gnu-0.48.5.tar.gz': '53d40abd2583d23e4718fddf1ebec84dbff8381c07cae67ff7768bbf19c6718e'}, + {'windows_x86_64_gnullvm-0.48.5.tar.gz': '0b7b52767868a23d5bab768e390dc5f5c55825b6d30b86c844ff2dc7414044cc'}, + {'windows_x86_64_msvc-0.48.5.tar.gz': 'ed94fce61571a4006852b7389a063ab983c02eb1bb37b47f8272ce92d06d9538'}, + {'xz2-0.1.7.tar.gz': '388c44dc09d76f1536602ead6d325eb532f5c122f17782bd57fb47baeeb767e2'}, +] + +builddependencies = [ + ('binutils', '2.40'), + ('Rust', '1.75.0'), +] + +dependencies = [ + ('bzip2', '1.0.8'), + ('XZ', '5.4.2'), +] + +# Since we do the download of partitions, remove the download part from skani +prebuildopts = """sed -i -e 's/^partitions = {/#&/' -e 's/^#partitions = ".*/partitions = "0.2.4"/' Cargo.toml && """ + +crates = [ + ('adler', '1.0.2'), + ('aho-corasick', '1.1.2'), + ('anyhow', '1.0.75'), + ('approx', '0.5.1'), + ('assert_cmd', '1.0.8'), + ('atty', '0.2.14'), + ('autocfg', '0.1.8'), + ('autocfg', '1.1.0'), + ('bincode', '1.3.3'), + ('bio', '1.4.0'), + ('bio-types', '1.0.1'), + ('bit-set', '0.5.3'), + ('bit-vec', '0.5.1'), + ('bit-vec', '0.6.3'), + ('bitflags', '1.3.2'), + ('bitflags', '2.4.0'), + ('bstr', '0.2.17'), + ('buffer-redux', '1.0.0'), + ('bv', '0.11.1'), + ('bytecount', '0.6.4'), + ('bytemuck', '1.14.0'), + ('byteorder', '1.5.0'), + ('bzip2', '0.4.4'), + ('bzip2-sys', '0.1.11+1.0.8'), + ('cc', '1.0.83'), + ('cfg-if', '0.1.10'), + ('cfg-if', '1.0.0'), + ('clap', '3.2.25'), + ('clap_lex', '0.2.4'), + ('cloudabi', '0.0.3'), + ('crc32fast', '1.3.2'), + ('crossbeam-deque', '0.8.3'), + ('crossbeam-epoch', '0.9.15'), + ('crossbeam-utils', '0.8.16'), + ('csv', '1.3.0'), + ('csv-core', '0.1.11'), + ('custom_derive', '0.1.7'), + ('dashmap', '5.5.3'), + ('derive-new', '0.5.9'), + ('difference', '2.0.0'), + ('difflib', '0.4.0'), + ('doc-comment', '0.3.3'), + ('editdistancek', '1.0.2'), + ('either', '1.9.0'), + ('enum-map', '1.1.1'), + ('enum-map-derive', '0.6.0'), + ('equivalent', '1.0.1'), + ('errno', '0.3.5'), + ('fastrand', '1.9.0'), + ('fastrand', '2.0.1'), + ('feature-probe', '0.1.1'), + ('fixedbitset', '0.4.2'), + ('flate2', '1.0.27'), + ('float-cmp', '0.8.0'), + ('fnv', '1.0.7'), + ('fuchsia-cprng', '0.1.1'), + ('futures', '0.3.28'), + ('futures-channel', '0.3.28'), + ('futures-core', '0.3.28'), + ('futures-executor', '0.3.28'), + ('futures-io', '0.3.28'), + ('futures-sink', '0.3.28'), + ('futures-task', '0.3.28'), + ('futures-util', '0.3.28'), + ('fxhash', '0.2.1'), + ('gbdt', '0.1.1'), + ('gcollections', '1.5.0'), + ('getrandom', '0.2.10'), + ('getset', '0.1.2'), + ('hashbrown', '0.12.3'), + ('hashbrown', '0.14.1'), + ('heck', '0.4.1'), + ('hermit-abi', '0.1.19'), + ('indexed', '0.1.1'), + ('indexmap', '1.9.3'), + ('indexmap', '2.0.2'), + ('instant', '0.1.12'), + ('intervallum', '1.4.0'), + ('itertools', '0.10.5'), + ('itertools', '0.11.0'), + ('itertools-num', '0.1.3'), + ('itoa', '1.0.9'), + ('lazy_static', '1.4.0'), + ('libc', '0.2.149'), + ('libm', '0.2.8'), + ('linux-raw-sys', '0.4.10'), + ('lock_api', '0.4.10'), + ('log', '0.4.20'), + ('lzma-sys', '0.1.20'), + ('matrixmultiply', '0.3.8'), + ('memchr', '2.6.4'), + ('memoffset', '0.9.0'), + ('miniz_oxide', '0.7.1'), + ('multimap', '0.8.3'), + ('nalgebra', '0.29.0'), + ('nalgebra-macros', '0.1.0'), + ('ndarray', '0.15.6'), + ('needletail', '0.5.1'), + ('newtype_derive', '0.1.6'), + ('normalize-line-endings', '0.3.0'), + ('num-complex', '0.4.4'), + ('num-integer', '0.1.45'), + ('num-rational', '0.4.1'), + ('num-traits', '0.2.17'), + ('once_cell', '1.18.0'), + ('ordered-float', '3.9.1'), + ('os_str_bytes', '6.5.1'), + ('parking_lot', '0.12.1'), + ('parking_lot_core', '0.9.8'), + ('partitions', '0.2.4'), + ('paste', '1.0.14'), + ('petgraph', '0.6.4'), + ('pin-project-lite', '0.2.13'), + ('pin-utils', '0.1.0'), + ('pkg-config', '0.3.27'), + ('ppv-lite86', '0.2.17'), + ('predicates', '1.0.8'), + ('predicates', '2.1.5'), + ('predicates-core', '1.0.6'), + ('predicates-tree', '1.0.9'), + ('proc-macro-error', '1.0.4'), + ('proc-macro-error-attr', '1.0.4'), + ('proc-macro2', '0.2.3'), + ('proc-macro2', '1.0.69'), + ('proptest', '0.8.7'), + ('quick-error', '1.2.3'), + ('quote', '0.4.2'), + ('quote', '1.0.33'), + ('rand', '0.5.6'), + ('rand', '0.6.5'), + ('rand', '0.8.5'), + ('rand_chacha', '0.1.1'), + ('rand_chacha', '0.3.1'), + ('rand_core', '0.3.1'), + ('rand_core', '0.4.2'), + ('rand_core', '0.6.4'), + ('rand_distr', '0.4.3'), + ('rand_hc', '0.1.0'), + ('rand_isaac', '0.1.1'), + ('rand_jitter', '0.1.4'), + ('rand_os', '0.1.3'), + ('rand_pcg', '0.1.2'), + ('rand_xorshift', '0.1.1'), + ('rawpointer', '0.2.1'), + ('rayon', '1.8.0'), + ('rayon-core', '1.12.0'), + ('rdrand', '0.4.0'), + ('redox_syscall', '0.1.57'), + ('redox_syscall', '0.3.5'), + ('reflection', '0.1.3'), + ('reflection_derive', '0.1.1'), + ('regex', '1.10.0'), + ('regex-automata', '0.1.10'), + ('regex-automata', '0.4.1'), + ('regex-syntax', '0.6.29'), + ('regex-syntax', '0.8.0'), + ('rust-lapper', '1.1.0'), + ('rustc_version', '0.1.7'), + ('rustix', '0.38.18'), + ('rustversion', '1.0.14'), + ('rusty-fork', '0.2.2'), + ('ryu', '1.0.15'), + ('safe_arch', '0.7.1'), + ('safemem', '0.3.3'), + ('scopeguard', '1.2.0'), + ('semver', '0.1.20'), + ('serde', '1.0.188'), + ('serde_derive', '1.0.188'), + ('serde_derive_internals', '0.21.0'), + ('serde_json', '1.0.107'), + ('serial_test', '0.10.0'), + ('serial_test_derive', '0.10.0'), + ('simba', '0.6.0'), + ('simple-logging', '2.0.2'), + ('slab', '0.4.9'), + ('smallvec', '1.11.1'), + ('statrs', '0.16.0'), + ('strsim', '0.10.0'), + ('strum', '0.25.0'), + ('strum_macros', '0.25.2'), + ('syn', '0.12.15'), + ('syn', '1.0.109'), + ('syn', '2.0.38'), + ('tempfile', '3.8.0'), + ('termcolor', '1.3.0'), + ('termtree', '0.4.1'), + ('textwrap', '0.16.0'), + ('thiserror', '1.0.49'), + ('thiserror-impl', '1.0.49'), + ('thread-id', '3.3.0'), + ('tikv-jemalloc-sys', '0.5.4+5.3.0-patched'), + ('tikv-jemallocator', '0.5.4'), + ('trees', '0.2.1'), + ('trilean', '1.1.0'), + ('triple_accel', '0.4.0'), + ('tsv', '0.1.1'), + ('typenum', '1.17.0'), + ('unicode-ident', '1.0.12'), + ('unicode-xid', '0.1.0'), + ('vec_map', '0.8.2'), + ('version_check', '0.9.4'), + ('wait-timeout', '0.2.0'), + ('wasi', '0.11.0+wasi-snapshot-preview1'), + ('wide', '0.7.12'), + ('winapi', '0.3.9'), + ('winapi-i686-pc-windows-gnu', '0.4.0'), + ('winapi-util', '0.1.6'), + ('winapi-x86_64-pc-windows-gnu', '0.4.0'), + ('windows-sys', '0.48.0'), + ('windows-targets', '0.48.5'), + ('windows_aarch64_gnullvm', '0.48.5'), + ('windows_aarch64_msvc', '0.48.5'), + ('windows_i686_gnu', '0.48.5'), + ('windows_i686_msvc', '0.48.5'), + ('windows_x86_64_gnu', '0.48.5'), + ('windows_x86_64_gnullvm', '0.48.5'), + ('windows_x86_64_msvc', '0.48.5'), + ('xz2', '0.1.7'), +] + +sanity_check_paths = { + 'files': ['bin/skani'], + 'dirs': [], +} + +sanity_check_commands = [ + 'skani --help', +] + + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/skorch/skorch-0.15.0-foss-2023a-PyTorch-2.1.2-CUDA-12.1.1.eb b/easybuild/easyconfigs/s/skorch/skorch-0.15.0-foss-2023a-PyTorch-2.1.2-CUDA-12.1.1.eb new file mode 100644 index 00000000000..7db54f41b95 --- /dev/null +++ b/easybuild/easyconfigs/s/skorch/skorch-0.15.0-foss-2023a-PyTorch-2.1.2-CUDA-12.1.1.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonBundle' + +name = 'skorch' +version = '0.15.0' +local_torch_version = '2.1.2' +versionsuffix = '-PyTorch-' + local_torch_version + '-CUDA-%(cudaver)s' + +homepage = 'https://skorch.readthedocs.io/' +description = "A scikit-learn compatible neural network library that wraps PyTorch." + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('CUDA', '12.1.1', '', SYSTEM), + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('scikit-learn', '1.3.1'), + ('tqdm', '4.66.1'), + ('PyTorch', local_torch_version, '-CUDA-%(cudaver)s'), +] + +use_pip = True + +exts_list = [ + (name, version, { + 'checksums': ['dfd5d50650a66e0d7adb3f6e2fce0666b53ebfe33cc1a5db19d555ef66587fce'], + }), +] + +sanity_pip_check = True + +moduleclass = 'ai' diff --git a/easybuild/easyconfigs/s/slepc4py/slepc4py-3.17.2-foss-2022a.eb b/easybuild/easyconfigs/s/slepc4py/slepc4py-3.17.2-foss-2022a.eb new file mode 100644 index 00000000000..c34f17533e0 --- /dev/null +++ b/easybuild/easyconfigs/s/slepc4py/slepc4py-3.17.2-foss-2022a.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonPackage' + +name = 'slepc4py' +version = '3.17.2' + +homepage = 'https://bitbucket.org/slepc/slepc4py' +description = "Python bindings for SLEPc, the Scalable Library for Eigenvalue Problem Computations." + +toolchain = {'name': 'foss', 'version': '2022a'} + +sources = [SOURCE_TAR_GZ] +checksums = ['e5b235486b6901cd4ff0d94083f0e5eeacaef3a2893e1714769717ad488a3885'] + +dependencies = [ + ('Python', '3.10.4'), + ('SLEPc', version), + ('petsc4py', '3.17.4'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +sanity_check_commands = ["python -c 'from slepc4py import SLEPc'"] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/s/slepc4py/slepc4py-3.20.2-foss-2023a.eb b/easybuild/easyconfigs/s/slepc4py/slepc4py-3.20.2-foss-2023a.eb new file mode 100644 index 00000000000..c161116802d --- /dev/null +++ b/easybuild/easyconfigs/s/slepc4py/slepc4py-3.20.2-foss-2023a.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonPackage' + +name = 'slepc4py' +version = '3.20.2' + +homepage = 'https://bitbucket.org/slepc/slepc4py' +description = "Python bindings for SLEPc, the Scalable Library for Eigenvalue Problem Computations." + +toolchain = {'name': 'foss', 'version': '2023a'} + +sources = [SOURCE_TAR_GZ] +checksums = 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'1.5.0'), + ('bzip2', '0.4.4'), + ('bzip2-sys', '0.1.11+1.0.8'), + ('cargo-husky', '1.5.0'), + ('cc', '1.1.5'), + ('cfg-if', '1.0.0'), + ('clap', '4.5.9'), + ('clap_builder', '4.5.9'), + ('clap_lex', '0.7.1'), + ('cobs', '0.2.3'), + ('colorchoice', '1.0.1'), + ('colored', '1.9.4'), + ('crc32fast', '1.4.2'), + ('critical-section', '1.1.2'), + ('difference', '2.0.0'), + ('embedded-io', '0.4.0'), + ('env_logger', '0.10.2'), + ('environment', '0.1.1'), + ('errno', '0.3.9'), + ('failure', '0.1.8'), + ('failure_derive', '0.1.8'), + ('fastrand', '2.1.0'), + ('flate2', '1.0.30'), + ('gimli', '0.29.0'), + ('hash32', '0.2.1'), + ('heapless', '0.7.17'), + ('hermit-abi', '0.3.9'), + ('humantime', '2.1.0'), + ('is-terminal', '0.4.12'), + ('is_terminal_polyfill', '1.70.0'), + ('itoa', '1.0.11'), + ('lazy_static', '1.5.0'), + ('libc', '0.2.155'), + ('linux-raw-sys', '0.4.14'), + ('lock_api', '0.4.12'), + ('log', '0.4.22'), + ('lzma-sys', '0.1.20'), + ('memchr', '2.7.4'), + ('miniz_oxide', '0.7.4'), + ('needletail', '0.5.1'), + ('object', '0.36.1'), + ('pkg-config', '0.3.30'), + ('postcard', '1.0.8'), + ('proc-macro2', '1.0.86'), + ('quote', '1.0.36'), + ('regex', '1.10.5'), + ('regex-automata', '0.4.7'), + ('regex-syntax', '0.8.4'), + ('roff', '0.1.0'), + ('rustc-demangle', '0.1.24'), + ('rustc_version', '0.4.0'), + ('rustix', '0.38.34'), + ('ryu', '1.0.18'), + ('scopeguard', '1.2.0'), + ('semver', '1.0.23'), + ('serde', '1.0.204'), + ('serde_derive', '1.0.204'), + ('serde_json', '1.0.120'), + ('spin', '0.9.8'), + ('stable_deref_trait', '1.2.0'), + ('strsim', '0.11.1'), + ('syn', '1.0.109'), + ('syn', '2.0.71'), + ('synstructure', '0.12.6'), + ('tempfile', '3.10.1'), + ('termcolor', '1.4.1'), + ('unicode-ident', '1.0.12'), + ('unicode-xid', '0.2.4'), + ('utf8parse', '0.2.2'), + ('version-compare', '0.1.1'), + ('winapi', '0.3.9'), + ('winapi-i686-pc-windows-gnu', '0.4.0'), + ('winapi-util', '0.1.8'), + ('winapi-x86_64-pc-windows-gnu', '0.4.0'), + ('windows-sys', '0.52.0'), + ('windows-targets', '0.52.6'), + ('windows_aarch64_gnullvm', '0.52.6'), + ('windows_aarch64_msvc', '0.52.6'), + ('windows_i686_gnu', '0.52.6'), + ('windows_i686_gnullvm', '0.52.6'), + ('windows_i686_msvc', '0.52.6'), + ('windows_x86_64_gnu', '0.52.6'), + ('windows_x86_64_gnullvm', '0.52.6'), + ('windows_x86_64_msvc', '0.52.6'), + ('xz2', '0.1.7'), +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/smithwaterman/smithwaterman-20160702-GCCcore-12.2.0.eb b/easybuild/easyconfigs/s/smithwaterman/smithwaterman-20160702-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..d546525a5c9 --- /dev/null +++ b/easybuild/easyconfigs/s/smithwaterman/smithwaterman-20160702-GCCcore-12.2.0.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'smithwaterman' +version = '20160702' +local_commit = '2610e25' + +homepage = 'https://github.com/ekg/smithwaterman' +description = """smith-waterman-gotoh alignment algorithm.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +github_account = 'ekg' +source_urls = [GITHUB_SOURCE] +sources = ['%s.tar.gz' % local_commit] +patches = ['%(name)s-%(version)s_build-shared-lib.patch'] +checksums = [ + '8e1b37ab0e8cd9d3d5cbfdba80258c0ebd0862749b531e213f44cdfe2fc541d8', # 2610e25.tar.gz + '2aa63ec5cd0260efcab002eaf4bbf62497b91afc0e3f82d8290496803c35e582', # smithwaterman-20160702_build-shared-lib.patch +] + +builddependencies = [('binutils', '2.39')] + +skipsteps = ['configure'] + +installopts = 'PREFIX=%(installdir)s ' + +sanity_check_paths = { + 'files': ['bin/%(name)s', 'lib/libsw.%s' % SHLIB_EXT], + 'dirs': [], +} + +sanity_check_commands = ["%(name)s --help"] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/snappy/snappy-1.1.10-GCCcore-13.3.0.eb b/easybuild/easyconfigs/s/snappy/snappy-1.1.10-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..f72e577513b --- /dev/null +++ b/easybuild/easyconfigs/s/snappy/snappy-1.1.10-GCCcore-13.3.0.eb @@ -0,0 +1,38 @@ + +easyblock = 'CMakeMake' + +name = 'snappy' +version = '1.1.10' + +homepage = 'https://github.com/google/snappy' +description = """Snappy is a compression/decompression library. It does not aim +for maximum compression, or compatibility with any other compression library; +instead, it aims for very high speeds and reasonable compression.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://github.com/google/snappy/archive/'] +sources = ['%(version)s.tar.gz'] +patches = [ + '%(name)s-1.1.9_use-default-rtti.patch', +] +checksums = [ + {'1.1.10.tar.gz': '49d831bffcc5f3d01482340fe5af59852ca2fe76c3e05df0e67203ebbe0f1d90'}, + {'snappy-1.1.9_use-default-rtti.patch': 'af56538330b2d781677c7d94576c15fc36e004ae0b4f1ac7d86bbec22b65e73d'}, +] + +builddependencies = [ + ('binutils', '2.42'), + ('CMake', '3.29.3'), +] + +# Disable building tests and benchmarks - we're not using them and they require googletest and benchmark source code +_configopts = '-DSNAPPY_BUILD_TESTS=OFF -DSNAPPY_BUILD_BENCHMARKS=OFF' +configopts = ['%s' % _configopts, '-DBUILD_SHARED_LIBS=ON %s' % _configopts] + +sanity_check_paths = { + 'files': ['lib64/libsnappy.a', 'lib64/libsnappy.%s' % SHLIB_EXT, 'include/snappy.h'], + 'dirs': [] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/snappy/snappy-1.2.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/s/snappy/snappy-1.2.1-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..2310edf5555 --- /dev/null +++ b/easybuild/easyconfigs/s/snappy/snappy-1.2.1-GCCcore-13.3.0.eb @@ -0,0 +1,38 @@ + +easyblock = 'CMakeMake' + +name = 'snappy' +version = '1.2.1' + +homepage = 'https://github.com/google/snappy' +description = """Snappy is a compression/decompression library. It does not aim +for maximum compression, or compatibility with any other compression library; +instead, it aims for very high speeds and reasonable compression.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://github.com/google/%(name)s/archive/'] +sources = ['%(version)s.tar.gz'] +patches = ['%(name)s-1.1.9_use-default-rtti.patch'] +checksums = [ + {'1.2.1.tar.gz': '736aeb64d86566d2236ddffa2865ee5d7a82d26c9016b36218fcc27ea4f09f86'}, + {'snappy-1.1.9_use-default-rtti.patch': 'af56538330b2d781677c7d94576c15fc36e004ae0b4f1ac7d86bbec22b65e73d'}, +] + +builddependencies = [ + ('binutils', '2.42'), + ('CMake', '3.29.3'), +] + +configopts = [ + "-DSNAPPY_BUILD_TESTS=OFF -DSNAPPY_BUILD_BENCHMARKS=OFF", + "-DBUILD_SHARED_LIBS=ON -DSNAPPY_BUILD_TESTS=OFF -DSNAPPY_BUILD_BENCHMARKS=OFF", +] + + +sanity_check_paths = { + 'files': ['lib64/libsnappy.a', 'lib64/libsnappy.%s' % SHLIB_EXT, 'include/snappy.h'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/snpEff/snpEff-5.2c-GCCcore-12.2.0-Java-11.eb b/easybuild/easyconfigs/s/snpEff/snpEff-5.2c-GCCcore-12.2.0-Java-11.eb new file mode 100644 index 00000000000..3b25c1e949f --- /dev/null +++ b/easybuild/easyconfigs/s/snpEff/snpEff-5.2c-GCCcore-12.2.0-Java-11.eb @@ -0,0 +1,37 @@ +easyblock = 'Tarball' + +name = 'snpEff' +version = '5.2c' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'https://pcingola.github.io/SnpEff/' +description = """SnpEff is a variant annotation and effect prediction tool. + It annotates and predicts the effects of genetic variants (such as amino acid changes).""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://snpeff.blob.core.windows.net/versions/'] +sources = ['%%(name)s_v%s_core.zip' % version.replace('.', '_')] +checksums = ['9926f600662707e85478940abc283ef120a909f1d41c32a036f01d958cd51232'] + +dependencies = [ + # ignore website claim that Java 12+ is required, nothing is compiled for + # anything newer than Java 11 + ('Java', '11', '', SYSTEM), + ('Python', '3.10.8'), + ('Perl', '5.36.0'), +] + +fix_perl_shebang_for = ['scripts/*.pl'] +fix_python_shebang_for = ['scripts/*.py'] + +sanity_check_paths = { + 'files': ['%(name)s.jar', 'SnpSift.jar', 'scripts/%(name)s'], + 'dirs': [], +} + +sanity_check_commands = ["%(name)s -version"] + +modextrapaths = {'PATH': 'scripts'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/snpEff/snpEff-5.2c-GCCcore-12.3.0-Java-11.eb b/easybuild/easyconfigs/s/snpEff/snpEff-5.2c-GCCcore-12.3.0-Java-11.eb new file mode 100644 index 00000000000..c9f29979a1d --- /dev/null +++ b/easybuild/easyconfigs/s/snpEff/snpEff-5.2c-GCCcore-12.3.0-Java-11.eb @@ -0,0 +1,37 @@ +easyblock = 'Tarball' + +name = 'snpEff' +version = '5.2c' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'https://pcingola.github.io/SnpEff/' +description = """SnpEff is a variant annotation and effect prediction tool. + It annotates and predicts the effects of genetic variants (such as amino acid changes).""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://snpeff.blob.core.windows.net/versions/'] +sources = ['%%(name)s_v%s_core.zip' % version.replace('.', '_')] +checksums = ['9926f600662707e85478940abc283ef120a909f1d41c32a036f01d958cd51232'] + +dependencies = [ + # ignore website claim that Java 12+ is required, nothing is compiled for + # anything newer than Java 11 + ('Java', '11', '', SYSTEM), + ('Python', '3.11.3'), + ('Perl', '5.36.1'), +] + +fix_perl_shebang_for = ['scripts/*.pl'] +fix_python_shebang_for = ['scripts/*.py'] + +sanity_check_paths = { + 'files': ['%(name)s.jar', 'SnpSift.jar', 'scripts/%(name)s'], + 'dirs': [], +} + +sanity_check_commands = ["%(name)s -version"] + +modextrapaths = {'PATH': 'scripts'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/spaCy/spaCy-3.7.4-foss-2023a.eb b/easybuild/easyconfigs/s/spaCy/spaCy-3.7.4-foss-2023a.eb new file mode 100644 index 00000000000..e8c79ceb6bf --- /dev/null +++ b/easybuild/easyconfigs/s/spaCy/spaCy-3.7.4-foss-2023a.eb @@ -0,0 +1,86 @@ +easyblock = 'PythonBundle' + +name = 'spaCy' +version = '3.7.4' + +homepage = 'https://spacy.io/' +description = "Industrial-strength Natural Language Processing (NLP) in Python." + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [ + ('poetry', '1.7.1'), + ('hatchling', '1.18.0'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('tqdm', '4.66.1'), + ('pydantic', '2.5.3'), +] + +use_pip = True + +exts_list = [ + ('spacy-legacy', '3.0.12', { + 'checksums': ['b37d6e0c9b6e1d7ca1cf5bc7152ab64a4c4671f59c85adaf7a3fcb870357a774'], + }), + ('spacy-loggers', '1.0.5', { + 'checksums': ['d60b0bdbf915a60e516cc2e653baeff946f0cfc461b452d11a4d5458c6fe5f24'], + }), + ('cymem', '2.0.8', { + 'checksums': ['8fb09d222e21dcf1c7e907dc85cf74501d4cea6c4ed4ac6c9e016f98fb59cbbf'], + }), + ('murmurhash', '1.0.10', { + 'checksums': ['5282aab1317804c6ebd6dd7f69f15ba9075aee671c44a34be2bde0f1b11ef88a'], + }), + ('preshed', '3.0.9', { + 'checksums': ['721863c5244ffcd2651ad0928951a2c7c77b102f4e11a251ad85d37ee7621660'], + }), + ('blis', '0.7.11', { + 'checksums': ['cec6d48f75f7ac328ae1b6fbb372dde8c8a57c89559172277f66e01ff08d4d42'], + }), + ('confection', '0.1.4', { + 'checksums': ['e80f22fd008b5231a2e8852fac6de9e28f2276a04031d0536cff74fe4a990c8f'], + }), + ('thinc', '8.2.3', { + 'checksums': ['f5afc5222912a80bda8bdcec958362a2ba538d7027dc8db6154845d2859dca76'], + }), + ('ml_datasets', '0.2.0', { + 'checksums': ['3f9c8901f8d6be3dab5b23ec3a6c01e619a60d0184696b1030cde2e3086943f1'], + }), + ('wasabi', '1.1.2', { + 'checksums': ['1aaef3aceaa32edb9c91330d29d3936c0c39fdb965743549c173cb54b16c30b5'], + }), + ('srsly', '2.4.8', { + 'checksums': ['b24d95a65009c2447e0b49cda043ac53fecf4f09e358d87a57446458f91b8a91'], + }), + ('catalogue', '2.0.10', { + 'checksums': ['4f56daa940913d3f09d589c191c74e5a6d51762b3a9e37dd53b7437afd6cda15'], + }), + ('typer', '0.9.0', { + 'checksums': ['50922fd79aea2f4751a8e0408ff10d2662bd0c8bbfa84755a699f3bada2978b2'], + }), + ('smart-open', '6.4.0', { + 'source_tmpl': 'smart_open-%(version)s.tar.gz', + 'checksums': ['be3c92c246fbe80ebce8fbacb180494a481a77fcdcb7c1aadb2ea5b9c2bee8b9'], + }), + ('langcodes', '3.3.0', { + 'checksums': ['794d07d5a28781231ac335a1561b8442f8648ca07cd518310aeb45d6f0807ef6'], + }), + ('weasel', '0.3.4', { + 'checksums': ['eb16f92dc9f1a3ffa89c165e3a9acd28018ebb656e0da4da02c0d7d8ae3f6178'], + }), + ('cloudpathlib', '0.16.0', { + 'checksums': ['cdfcd35d46d529587d744154a0bdf962aca953b725c8784cd2ec478354ea63a3'], + }), + (name, version, { + 'sources': ['%(namelower)s-%(version)s.tar.gz'], + 'checksums': ['525f2ced2e40761562c8cace93ef6a1e6e8c483f27bd564bc1b15f608efbe85b'], + }), +] + +sanity_pip_check = True + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/s/spaln/spaln-3.0.6b-GCC-12.3.0.eb b/easybuild/easyconfigs/s/spaln/spaln-3.0.6b-GCC-12.3.0.eb new file mode 100644 index 00000000000..18fe5408f73 --- /dev/null +++ b/easybuild/easyconfigs/s/spaln/spaln-3.0.6b-GCC-12.3.0.eb @@ -0,0 +1,49 @@ +# updated: Denis Kristak (INUITS) +# Update: Petr Král (INUITS) +easyblock = 'ConfigureMake' + +name = 'spaln' +version = '3.0.6b' + +homepage = 'https://github.com/ogotoh/spaln' +description = """Spaln (space-efficient spliced alignment) is a stand-alone program that maps + and aligns a set of cDNA or protein sequences onto a whole genomic sequence in a single job.""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} +# disable use of -march=native, which makes compilation fail due to missing header files like fwd2s1_simd.h; +# see also https://github.com/ogotoh/spaln/issues/56 +toolchainopts = {'optarch': False} + +source_urls = ['https://github.com/ogotoh/spaln/archive/'] +sources = ['ver.%(version)s.tar.gz'] +checksums = ['8e496ef6d02696543f4a5e31922f464555eff9b8405da366587ba7bea27b4e76'] + +dependencies = [ + ('zlib', '1.2.13'), + ('Perl', '5.36.1'), +] + +start_dir = 'src' + +# not a standard `configure` - does not accept standard `--prefix` option +# see https://github.com/ogotoh/spaln/issues/74 +prefix_opt = '--exec_prefix=' + +configopts = "--exec_prefix=bin --table_dir=table --alndbs_dir=seqdb" + +installopts = 'DESTDIR=%(installdir)s/' + +fix_perl_shebang_for = ['seqdb/*.pl'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['makdbs', 'makmdm', 'sortgrcd', 'spaln']], + 'dirs': ['seqdb', 'table'], +} + +sanity_check_commands = ["spaln -h 2>&1 | grep 'SPALN version %(version)s'"] +modextrapaths = { + 'PATH': 'seqdb', + 'PERL5LIB': 'seqdb', +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/sparsehash/sparsehash-2.0.4-GCCcore-13.3.0.eb b/easybuild/easyconfigs/s/sparsehash/sparsehash-2.0.4-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..66056138103 --- /dev/null +++ b/easybuild/easyconfigs/s/sparsehash/sparsehash-2.0.4-GCCcore-13.3.0.eb @@ -0,0 +1,36 @@ +# Updated from previous easyconfig +# Author: Pavel Grochal (INUITS) +# Update: Pavel Tománek (INUITS) +# License: GPLv2 +# Updated to GCCcore-12.3.0 +# Author: J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'ConfigureMake' + +name = 'sparsehash' +version = '2.0.4' + +homepage = 'https://github.com/sparsehash/sparsehash' +description = """ + An extremely memory-efficient hash_map implementation. 2 bits/entry overhead! + The SparseHash library contains several hash-map implementations, including + implementations that optimize for space or speed. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +source_urls = [GITHUB_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['8cd1a95827dfd8270927894eb77f62b4087735cbede953884647f16c521c7e58'] + +builddependencies = [ + ('binutils', '2.42'), +] + +sanity_check_paths = { + 'files': ['include/google/type_traits.h'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/s/spektral/spektral-1.2.0-fosscuda-2020b-TensorFlow-2.5.0.eb b/easybuild/easyconfigs/s/spektral/spektral-1.2.0-fosscuda-2020b-TensorFlow-2.5.0.eb new file mode 100644 index 00000000000..75446a8cbff --- /dev/null +++ b/easybuild/easyconfigs/s/spektral/spektral-1.2.0-fosscuda-2020b-TensorFlow-2.5.0.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonBundle' + +name = 'spektral' +version = '1.2.0' +local_tf_version = '2.5.0' +versionsuffix = '-TensorFlow-%s' % local_tf_version + +homepage = 'https://graphneural.network' +description = "Spektral is a Python library for graph deep learning, based on the Keras API and TensorFlow 2" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('lxml', '4.6.2'), + ('networkx', '2.5'), + ('scikit-learn', '0.23.2'), + ('tqdm', '4.56.2'), + ('TensorFlow', local_tf_version), +] + +use_pip = True + +exts_list = [ + (name, version, { + 'checksums': ['215f148e5d5067081bc28abe282bfd0942ed8be6d68f128fd7786006a884abf7'], + }), +] + +sanity_pip_check = True + +moduleclass = 'ai' diff --git a/easybuild/easyconfigs/s/spektral/spektral-1.3.1-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/s/spektral/spektral-1.3.1-foss-2023a-CUDA-12.1.1.eb new file mode 100644 index 00000000000..d4b6fd82447 --- /dev/null +++ b/easybuild/easyconfigs/s/spektral/spektral-1.3.1-foss-2023a-CUDA-12.1.1.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonBundle' + +name = 'spektral' +version = '1.3.1' +versionsuffix = '-CUDA-12.1.1' + +homepage = 'https://graphneural.network' +description = "Spektral is a Python library for graph deep learning, based on the Keras API and TensorFlow 2" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('lxml', '4.9.2'), + ('networkx', '3.1'), + ('scikit-learn', '1.3.1'), + ('tqdm', '4.66.1'), + ('TensorFlow', '2.15.1', versionsuffix), +] + +use_pip = True + +exts_list = [ + (name, version, { + 'checksums': ['953d9954995b8b434dd0f464e25407ad83446d39fe7a23543a8e2fec8c01eb8b'], + }), +] + +sanity_pip_check = True + +moduleclass = 'ai' diff --git a/easybuild/easyconfigs/s/spektral/spektral-1.3.1-foss-2023a.eb b/easybuild/easyconfigs/s/spektral/spektral-1.3.1-foss-2023a.eb new file mode 100644 index 00000000000..244640d01f4 --- /dev/null +++ b/easybuild/easyconfigs/s/spektral/spektral-1.3.1-foss-2023a.eb @@ -0,0 +1,31 @@ +easyblock = 'PythonBundle' + +name = 'spektral' +version = '1.3.1' + +homepage = 'https://graphneural.network' +description = "Spektral is a Python library for graph deep learning, based on the Keras API and TensorFlow 2" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('lxml', '4.9.2'), + ('networkx', '3.1'), + ('scikit-learn', '1.3.1'), + ('tqdm', '4.66.1'), + ('TensorFlow', '2.13.0'), +] + +use_pip = True + +exts_list = [ + (name, version, { + 'checksums': ['953d9954995b8b434dd0f464e25407ad83446d39fe7a23543a8e2fec8c01eb8b'], + }), +] + +sanity_pip_check = True + +moduleclass = 'ai' diff --git a/easybuild/easyconfigs/s/spglib-python/spglib-python-2.5.0-gfbf-2023b.eb b/easybuild/easyconfigs/s/spglib-python/spglib-python-2.5.0-gfbf-2023b.eb new file mode 100644 index 00000000000..9f26cade5d3 --- /dev/null +++ b/easybuild/easyconfigs/s/spglib-python/spglib-python-2.5.0-gfbf-2023b.eb @@ -0,0 +1,37 @@ +easyblock = 'PythonBundle' + +name = 'spglib-python' +version = '2.5.0' + +homepage = 'https://pypi.python.org/pypi/spglib' +description = """Spglib for Python. + +Spglib is a library for finding and handling crystal symmetries written in C. +""" + +toolchain = {'name': 'gfbf', 'version': '2023b'} + +builddependencies = [ + ('scikit-build-core', '0.9.3') +] + +dependencies = [ + ('Python', '3.11.5'), + ('Python-bundle-PyPI', '2023.10'), + ('SciPy-bundle', '2023.11'), +] + +use_pip = True + +sanity_pip_check = True + +exts_list = [ + ('pyproject_metadata', '0.8.0', { + 'checksums': ['376d5a00764ac29440a54579f88e66b7d9cb7e629d35c35a1c7248bfebc9b455'], + }), + ('spglib', version, { + 'checksums': ['f8bb638897be91b9dbd4c085d9fde1f69048f5949e20f3832cb9438e57418d4b'], + }), +] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/s/spglib-python/spglib-python-2.5.0-gfbf-2024a.eb b/easybuild/easyconfigs/s/spglib-python/spglib-python-2.5.0-gfbf-2024a.eb new file mode 100644 index 00000000000..a6954207aa7 --- /dev/null +++ b/easybuild/easyconfigs/s/spglib-python/spglib-python-2.5.0-gfbf-2024a.eb @@ -0,0 +1,37 @@ +easyblock = 'PythonBundle' + +name = 'spglib-python' +version = '2.5.0' + +homepage = 'https://pypi.python.org/pypi/spglib' +description = """Spglib for Python. + +Spglib is a library for finding and handling crystal symmetries written in C. +""" + +toolchain = {'name': 'gfbf', 'version': '2024a'} + +builddependencies = [ + ('scikit-build-core', '0.10.6') +] + +dependencies = [ + ('Python', '3.12.3'), + ('Python-bundle-PyPI', '2024.06'), + ('SciPy-bundle', '2024.05'), +] + +use_pip = True + +sanity_pip_check = True + +exts_list = [ + ('pyproject_metadata', '0.8.0', { + 'checksums': ['376d5a00764ac29440a54579f88e66b7d9cb7e629d35c35a1c7248bfebc9b455'], + }), + ('spglib', version, { + 'checksums': ['f8bb638897be91b9dbd4c085d9fde1f69048f5949e20f3832cb9438e57418d4b'], + }), +] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/s/spglib/spglib-2.5.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/s/spglib/spglib-2.5.0-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..a7e62a33f21 --- /dev/null +++ b/easybuild/easyconfigs/s/spglib/spglib-2.5.0-GCCcore-12.3.0.eb @@ -0,0 +1,34 @@ +# with thanks to akesandgren for the easyconfig for 2022a +# updated for 2022b by BEAR Software team at University of Birmingham +# update to v2.5.0 for GCC/12.3.0 by Pavel Tománek (Inuits) + +easyblock = 'CMakeMake' + +name = 'spglib' +version = '2.5.0' + +homepage = 'https://spglib.github.io/spglib/' +description = """Spglib is a C library for finding and handling crystal symmetries.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://github.com/spglib/spglib/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['b6026f5e85106c0c9ee57e54b9399890d0f29982e20e96ede0428b3efbe6b914'] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.26.3'), +] + +postinstallcmds = ["cd %(installdir)s/include && mkdir spglib && ln -s ../spglib.h spglib/"] + +sanity_check_paths = { + 'files': [ + 'include/spglib.h', + 'lib/libsymspg.%s' % SHLIB_EXT + ], + 'dirs': [], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/s/spla/spla-1.6.1-foss-2023a.eb b/easybuild/easyconfigs/s/spla/spla-1.6.1-foss-2023a.eb new file mode 100644 index 00000000000..98308699678 --- /dev/null +++ b/easybuild/easyconfigs/s/spla/spla-1.6.1-foss-2023a.eb @@ -0,0 +1,31 @@ +easyblock = 'CMakeMake' + +name = 'spla' +version = '1.6.1' + +homepage = 'https://github.com/eth-cscs/spla/' +description = """SPLA provides specialized functions for linear algebra computations with a C++ and C interface, +which are inspired by requirements in computational material science codes.""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'openmp': True} + +source_urls = ['https://github.com/eth-cscs/spla/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['62b51e6ce05c41cfc1c6f6600410f9549a209c50f0331e1db41047f94493e02f'] + +builddependencies = [ + ('CMake', '3.26.3'), +] + +configopts = '-DBLA_VENDOR=FlexiBLAS' + +sanity_check_paths = { + 'files': [ + 'include/spla/spla.h', + 'lib/libspla.%s' % SHLIB_EXT, + ], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/spoa/spoa-4.1.0-GCC-13.2.0.eb b/easybuild/easyconfigs/s/spoa/spoa-4.1.0-GCC-13.2.0.eb new file mode 100644 index 00000000000..16062a7636e --- /dev/null +++ b/easybuild/easyconfigs/s/spoa/spoa-4.1.0-GCC-13.2.0.eb @@ -0,0 +1,29 @@ +easyblock = 'CMakeMake' + +name = 'spoa' +version = '4.1.0' + +homepage = 'https://github.com/rvaser/spoa' +description = """Spoa (SIMD POA) is a c++ implementation of the partial order alignment (POA) algorithm + which is used to generate consensus sequences""" + +toolchain = {'name': 'GCC', 'version': '13.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/rvaser/spoa/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['43238356f00bce2ad9698fc18b3e320024172a82182dcff24d57c5cf19e342c8'] + +builddependencies = [('CMake', '3.27.6')] + +configopts = "-Dspoa_build_executable=ON" + +sanity_check_paths = { + 'files': ['bin/spoa'] + ['include/spoa/%s' % x for x in ['alignment_engine.hpp', 'graph.hpp', 'spoa.hpp']] + + ['lib/libspoa.a'], + 'dirs': [], +} + +sanity_check_commands = ["spoa --help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/starcode/starcode-1.4-GCC-13.2.0.eb b/easybuild/easyconfigs/s/starcode/starcode-1.4-GCC-13.2.0.eb new file mode 100644 index 00000000000..dfc8917e067 --- /dev/null +++ b/easybuild/easyconfigs/s/starcode/starcode-1.4-GCC-13.2.0.eb @@ -0,0 +1,40 @@ +# easybuild easyconfig +# +# John Dey +# +# Fred Hutchinson Cancer Center - Seattle Washington US +# +easyblock = 'MakeCp' + +name = 'starcode' +version = '1.4' +local_commit = '8987b2e' + +homepage = 'https://github.com/gui11aume/starcode' +description = """Starcode is a DNA sequence clustering software. Starcode clustering is based on all pairs +search within a specified Levenshtein distance (allowing insertions and deletions), followed by a clustering +algorithm: Message Passing, Spheres or Connected Components.""" + +toolchain = {'name': 'GCC', 'version': '13.2.0'} + +github_account = 'gui11aume' +source_urls = [GITHUB_SOURCE] +sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}] +checksums = ['4343c070d9149760516e3a47a46edb2f2280325728a28b83796f6d344faf4e06'] + +dependencies = [ +] + +files_to_copy = [ + 'doc', 'misc', 'test', + (['starcode', 'starcode-umi'], 'bin'), +] + +sanity_check_paths = { + 'files': ['bin/%(name)s'], + 'dirs': [], +} + +sanity_check_commands = [('%(name)s', '--help')] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/statsmodels/statsmodels-0.14.4-gfbf-2024a.eb b/easybuild/easyconfigs/s/statsmodels/statsmodels-0.14.4-gfbf-2024a.eb new file mode 100644 index 00000000000..ee5cb197a7d --- /dev/null +++ b/easybuild/easyconfigs/s/statsmodels/statsmodels-0.14.4-gfbf-2024a.eb @@ -0,0 +1,35 @@ +easyblock = 'PythonBundle' + +name = 'statsmodels' +version = '0.14.4' + +homepage = 'https://www.statsmodels.org/' +description = """Statsmodels is a Python module that allows users to explore data, estimate statistical models, +and perform statistical tests.""" + +toolchain = {'name': 'gfbf', 'version': '2024a'} + +builddependencies = [('Cython', '3.0.10')] + +dependencies = [ + ('Python', '3.12.3'), + ('SciPy-bundle', '2024.05'), +] + +sanity_pip_check = True +use_pip = True + +exts_list = [ + ('patsy', '0.5.6', { + 'checksums': ['95c6d47a7222535f84bff7f63d7303f2e297747a598db89cf5c67f0c0c7d2cdb'], + }), + (name, version, { + 'patches': ['statsmodels-0.14.4_fix_setup.patch'], + 'checksums': [ + {'statsmodels-0.14.4.tar.gz': '5d69e0f39060dc72c067f9bb6e8033b6dccdb0bae101d76a7ef0bcc94e898b67'}, + {'statsmodels-0.14.4_fix_setup.patch': 'd24bedb6382945ac415927faa9279d75d0a71dad56fce7032a58485981b44fe5'}, + ], + }), +] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/statsmodels/statsmodels-0.14.4_fix_setup.patch b/easybuild/easyconfigs/s/statsmodels/statsmodels-0.14.4_fix_setup.patch new file mode 100644 index 00000000000..56e9c5f3e2c --- /dev/null +++ b/easybuild/easyconfigs/s/statsmodels/statsmodels-0.14.4_fix_setup.patch @@ -0,0 +1,13 @@ +# What: Put manually typed version in setup.py +# Author: maxim-masterov (SURF) +diff -Nru statsmodels-0.14.4.orig/setup.py statsmodels-0.14.4/setup.py +--- statsmodels-0.14.4.orig/setup.py 2024-10-10 16:20:53.020145000 +0200 ++++ statsmodels-0.14.4/setup.py 2024-10-10 16:21:08.330504032 +0200 +@@ -353,6 +353,7 @@ + ext_modules=extensions, + maintainer_email=MAINTAINER_EMAIL, + description=DESCRIPTION, ++ version="0.14.1", + license=LICENSE, + url=URL, + download_url=DOWNLOAD_URL, diff --git a/easybuild/easyconfigs/s/submitit/submitit-1.2.0-foss-2023a.eb b/easybuild/easyconfigs/s/submitit/submitit-1.2.0-foss-2023a.eb new file mode 100644 index 00000000000..0ce1edf2766 --- /dev/null +++ b/easybuild/easyconfigs/s/submitit/submitit-1.2.0-foss-2023a.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonBundle' + +name = 'submitit' +version = '1.2.0' + +homepage = 'https://github.com/facebookincubator/submitit' +description = """ +Submitit is a lightweight tool for submitting Python functions +for computation within a Slurm cluster. +""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), +] + +use_pip = True + +exts_list = [ + ('cloudpickle', '3.0.0', { + 'checksums': ['996d9a482c6fb4f33c1a35335cf8afd065d2a56e973270364840712d9131a882'], + }), + ('typing_extensions', '4.12.2', { + 'checksums': ['1a7ead55c7e559dd4dee8856e3a88b41225abfe1ce8df57b7c13915fe121ffb8'], + }), + (name, version, { + 'checksums': ['16c099ed80943fbf942a7a37c6356a598b1f2b9d7ce40dd5fe058a6c7827e600'], + }), +] + +sanity_pip_check = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/subset-bam/subset-bam-1.1.0.eb b/easybuild/easyconfigs/s/subset-bam/subset-bam-1.1.0.eb new file mode 100644 index 00000000000..f9e6778cec2 --- /dev/null +++ b/easybuild/easyconfigs/s/subset-bam/subset-bam-1.1.0.eb @@ -0,0 +1,24 @@ +easyblock = 'Binary' + +name = 'subset-bam' +version = '1.1.0' + +homepage = 'https://github.com/10XGenomics/subset-bam' +description = """subset-bam is a tool to subset a 10x Genomics BAM file based on a tag, +most commonly the cell barcode tag.""" + +toolchain = SYSTEM + +source_urls = ['https://github.com/10XGenomics/subset-bam/releases/download/v%(version)s/'] + +sources = [{'download_filename': 'subset-bam_linux', 'filename': name}] +checksums = ['05496ea56d52becdb7972528af0a486be1d52c1749e35bea9ae4c41215ed0a1b'] + +sanity_check_paths = { + 'dirs': [], + 'files': [name], +} + +sanity_check_commands = ["%(name)s --help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/svist4get/svist4get-1.3.1-foss-2022b.eb b/easybuild/easyconfigs/s/svist4get/svist4get-1.3.1-foss-2022b.eb new file mode 100644 index 00000000000..72d977763e9 --- /dev/null +++ b/easybuild/easyconfigs/s/svist4get/svist4get-1.3.1-foss-2022b.eb @@ -0,0 +1,61 @@ +# Author: J. Sassmannshausen (Imperial College London/UK) +# Update: Pavel Tománek (Inuits) + +easyblock = 'PythonBundle' + +name = 'svist4get' +version = '1.3.1' + +homepage = 'https://github.com/art-egorov/svist4get' +description = """Svist4get is a simple bioinformatics tool for visualization of +genomic signal tracks in user-defined genomic windows, either arbitrary selected +by genomic coordinates or anchored to particular transcripts or genes.""" + +toolchain = {'name': 'foss', 'version': '2022b'} + +dependencies = [ + ('Python', '3.10.8'), + ('pybedtools', '0.9.0'), + ('Biopython', '1.81'), + ('Pillow', '9.4.0'), + ('ImageMagick', '7.1.0-53'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('reportlab', '3.6.9', { + 'patches': ['reportlab-3.6.12-fontconfig.patch'], + 'checksums': ['5d0cc3682456ad213150f6dbffe7d47eab737d809e517c316103376be548fb84', + # reportlab-3.6.12-fontconfig.patch: + '2cc9b40e09650b7404ee9c4d72b134739acc89bacac3da58131cef2308726297'], + }), + ('configs', '3.0.3', { + 'sources': ['%(name)s-%(version)s.zip'], + 'checksums': ['a5ab09e04e441dac6aa856a71fbf5ffc62954352630f79d311b8f8a31d9ce19c'], + }), + ('argparse', '1.4.0', { + 'checksums': ['62b089a55be1d8949cd2bc7e0df0bddb9e028faefc8c32038cc84862aefdd6e4'], + }), + ('Wand', '0.6.10', { + 'checksums': ['373f4a7f2866c868c31ce910e1f9b36a92d132640a20068ec17cea3284fedc57'], + }), + (name, version, { + # unpin statistics dependency - it is old package and interfering with python lib statistics + 'preinstallopts': "sed -i 's/statistics//' setup.py && ", + 'checksums': ['22311fdc956cca531dac7ba924744e8f870a57bc6f27cbe4e8ba9854117e720c'], + }), +] + +sanity_check_paths = { + 'files': ['bin/svist4get', 'bin/svist4get_copier'], + 'dirs': ['lib'], +} + +sanity_check_commands = [ + "svist4get --help", + "svist4get -v", +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/svist4get/svist4get-1.3.1-foss-2023a.eb b/easybuild/easyconfigs/s/svist4get/svist4get-1.3.1-foss-2023a.eb new file mode 100644 index 00000000000..f44d27dd1f5 --- /dev/null +++ b/easybuild/easyconfigs/s/svist4get/svist4get-1.3.1-foss-2023a.eb @@ -0,0 +1,61 @@ +# Author: J. Sassmannshausen (Imperial College London/UK) +# Update: Pavel Tománek (Inuits) + +easyblock = 'PythonBundle' + +name = 'svist4get' +version = '1.3.1' + +homepage = 'https://github.com/art-egorov/svist4get' +description = """Svist4get is a simple bioinformatics tool for visualization of +genomic signal tracks in user-defined genomic windows, either arbitrary selected +by genomic coordinates or anchored to particular transcripts or genes.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('pybedtools', '0.9.1'), + ('Biopython', '1.83'), + ('Pillow', '10.0.0'), + ('ImageMagick', '7.1.1-15'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('reportlab', '3.6.9', { + 'patches': ['reportlab-3.6.12-fontconfig.patch'], + 'checksums': ['5d0cc3682456ad213150f6dbffe7d47eab737d809e517c316103376be548fb84', + # reportlab-3.6.12-fontconfig.patch: + '2cc9b40e09650b7404ee9c4d72b134739acc89bacac3da58131cef2308726297'], + }), + ('configs', '3.0.3', { + 'sources': ['%(name)s-%(version)s.zip'], + 'checksums': ['a5ab09e04e441dac6aa856a71fbf5ffc62954352630f79d311b8f8a31d9ce19c'], + }), + ('argparse', '1.4.0', { + 'checksums': ['62b089a55be1d8949cd2bc7e0df0bddb9e028faefc8c32038cc84862aefdd6e4'], + }), + ('Wand', '0.6.10', { + 'checksums': ['373f4a7f2866c868c31ce910e1f9b36a92d132640a20068ec17cea3284fedc57'], + }), + (name, version, { + # unpin statistics dependency - it is old package and interfering with python lib statistics + 'preinstallopts': "sed -i 's/statistics//' setup.py && ", + 'checksums': ['22311fdc956cca531dac7ba924744e8f870a57bc6f27cbe4e8ba9854117e720c'], + }), +] + +sanity_check_paths = { + 'files': ['bin/svist4get', 'bin/svist4get_copier'], + 'dirs': ['lib'], +} + +sanity_check_commands = [ + "svist4get --help", + "svist4get -v", +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/sympy/sympy-1.13.3-gfbf-2024a.eb b/easybuild/easyconfigs/s/sympy/sympy-1.13.3-gfbf-2024a.eb new file mode 100644 index 00000000000..98256c920da --- /dev/null +++ b/easybuild/easyconfigs/s/sympy/sympy-1.13.3-gfbf-2024a.eb @@ -0,0 +1,22 @@ +name = 'sympy' +version = '1.13.3' + +homepage = 'https://sympy.org/' +description = """SymPy is a Python library for symbolic mathematics. It aims to + become a full-featured computer algebra system (CAS) while keeping the code as + simple as possible in order to be comprehensible and easily extensible. SymPy + is written entirely in Python and does not require any external libraries.""" + +toolchain = {'name': 'gfbf', 'version': '2024a'} + +sources = [SOURCE_TAR_GZ] +checksums = ['b27fd2c6530e0ab39e275fc9b683895367e51d5da91baa8d3d64db2565fec4d9'] + +dependencies = [ + ('Python', '3.12.3'), + ('SciPy-bundle', '2024.05'), + ('gmpy2', '2.2.0'), +] + + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/t/TAMkin/TAMkin-1.2.6-foss-2022a.eb b/easybuild/easyconfigs/t/TAMkin/TAMkin-1.2.6-foss-2022a.eb new file mode 100644 index 00000000000..c672ef52e80 --- /dev/null +++ b/easybuild/easyconfigs/t/TAMkin/TAMkin-1.2.6-foss-2022a.eb @@ -0,0 +1,46 @@ +easyblock = 'PythonPackage' + +name = 'TAMkin' +version = '1.2.6' + +homepage = 'https://molmod.github.io/tamkin/' +description = """TAMkin is a post-processing toolkit for normal mode analysis, + thermochemistry and reaction kinetics. It uses a Hessian computation from a + standard computational chemistry program as its input.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +source_urls = ['https://github.com/molmod/tamkin/releases/download/%(version)s'] +sources = [SOURCE_TAR_GZ] +patches = [ + 'TAMkin-1.2.6_fix-python38.patch', + 'TAMkin-1.2.6_fix-test_vsa_no_mass.patch', +] +checksums = [ + {'TAMkin-1.2.6.tar.gz': '1bde275a09be91e5241616aaa9fedc60cb359a263f5c5909bb14431c3a4ed5fd'}, + {'TAMkin-1.2.6_fix-python38.patch': '1633d5b24b012f8c4b6731491e4072c819ebbba65574966b7185ecca52eeac9b'}, + {'TAMkin-1.2.6_fix-test_vsa_no_mass.patch': '67d8b8671d7c71123e8ee9a7b9ebea6562e9711edb41555d1926b1b51d549066'}, +] + +builddependencies = [('nose3', '1.3.8')] +dependencies = [ + ('Python', '3.10.4'), + ('matplotlib', '3.5.2'), + ('molmod', '1.4.8'), +] + +download_dep_fail = True +use_pip = True + +# disable tests that require X11 by specifying "backend: agg" in matplotlibrc +runtest = 'export MATPLOTLIBRC=$PWD; echo "backend: agg" > $MATPLOTLIBRC/matplotlibrc; ' +runtest += 'export OMP_NUM_THREADS=1; nosetests -v tamkin' + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_pip_check = True + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/t/TAMkin/TAMkin-1.2.6-foss-2022b.eb b/easybuild/easyconfigs/t/TAMkin/TAMkin-1.2.6-foss-2022b.eb new file mode 100644 index 00000000000..f0ac1c8820c --- /dev/null +++ b/easybuild/easyconfigs/t/TAMkin/TAMkin-1.2.6-foss-2022b.eb @@ -0,0 +1,46 @@ +easyblock = 'PythonPackage' + +name = 'TAMkin' +version = '1.2.6' + +homepage = 'https://molmod.github.io/tamkin/' +description = """TAMkin is a post-processing toolkit for normal mode analysis, + thermochemistry and reaction kinetics. It uses a Hessian computation from a + standard computational chemistry program as its input.""" + +toolchain = {'name': 'foss', 'version': '2022b'} + +source_urls = ['https://github.com/molmod/tamkin/releases/download/%(version)s'] +sources = [SOURCE_TAR_GZ] +patches = [ + 'TAMkin-1.2.6_fix-python38.patch', + 'TAMkin-1.2.6_fix-test_vsa_no_mass.patch', +] +checksums = [ + {'TAMkin-1.2.6.tar.gz': '1bde275a09be91e5241616aaa9fedc60cb359a263f5c5909bb14431c3a4ed5fd'}, + {'TAMkin-1.2.6_fix-python38.patch': '1633d5b24b012f8c4b6731491e4072c819ebbba65574966b7185ecca52eeac9b'}, + {'TAMkin-1.2.6_fix-test_vsa_no_mass.patch': '67d8b8671d7c71123e8ee9a7b9ebea6562e9711edb41555d1926b1b51d549066'}, +] + +builddependencies = [('nose3', '1.3.8')] +dependencies = [ + ('Python', '3.10.8'), + ('matplotlib', '3.7.0'), + ('molmod', '1.4.8'), +] + +download_dep_fail = True +use_pip = True + +# disable tests that require X11 by specifying "backend: agg" in matplotlibrc +runtest = 'export MATPLOTLIBRC=$PWD; echo "backend: agg" > $MATPLOTLIBRC/matplotlibrc; ' +runtest += 'export OMP_NUM_THREADS=1; nosetests -v tamkin' + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_pip_check = True + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/t/TAMkin/TAMkin-1.2.6-foss-2023a.eb b/easybuild/easyconfigs/t/TAMkin/TAMkin-1.2.6-foss-2023a.eb new file mode 100644 index 00000000000..b3b40928643 --- /dev/null +++ b/easybuild/easyconfigs/t/TAMkin/TAMkin-1.2.6-foss-2023a.eb @@ -0,0 +1,46 @@ +easyblock = 'PythonPackage' + +name = 'TAMkin' +version = '1.2.6' + +homepage = 'https://molmod.github.io/tamkin/' +description = """TAMkin is a post-processing toolkit for normal mode analysis, + thermochemistry and reaction kinetics. It uses a Hessian computation from a + standard computational chemistry program as its input.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['https://github.com/molmod/tamkin/releases/download/%(version)s'] +sources = [SOURCE_TAR_GZ] +patches = [ + 'TAMkin-1.2.6_fix-python38.patch', + 'TAMkin-1.2.6_fix-test_vsa_no_mass.patch', +] +checksums = [ + {'TAMkin-1.2.6.tar.gz': '1bde275a09be91e5241616aaa9fedc60cb359a263f5c5909bb14431c3a4ed5fd'}, + {'TAMkin-1.2.6_fix-python38.patch': '1633d5b24b012f8c4b6731491e4072c819ebbba65574966b7185ecca52eeac9b'}, + {'TAMkin-1.2.6_fix-test_vsa_no_mass.patch': '67d8b8671d7c71123e8ee9a7b9ebea6562e9711edb41555d1926b1b51d549066'}, +] + +dependencies = [ + ('Python', '3.11.3'), + ('matplotlib', '3.7.2'), + ('molmod', '1.4.8'), + ('nose3', '1.3.8'), +] + +download_dep_fail = True +use_pip = True + +# disable tests that require X11 by specifying "backend: agg" in matplotlibrc +runtest = 'export MATPLOTLIBRC=$PWD; echo "backend: agg" > $MATPLOTLIBRC/matplotlibrc; ' +runtest += 'export OMP_NUM_THREADS=1; nosetests -v tamkin' + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_pip_check = True + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/t/TELEMAC-MASCARET/TELEMAC-MASCARET-8p5r0-foss-2023a.eb b/easybuild/easyconfigs/t/TELEMAC-MASCARET/TELEMAC-MASCARET-8p5r0-foss-2023a.eb new file mode 100644 index 00000000000..ab96be49230 --- /dev/null +++ b/easybuild/easyconfigs/t/TELEMAC-MASCARET/TELEMAC-MASCARET-8p5r0-foss-2023a.eb @@ -0,0 +1,90 @@ +easyblock = 'Binary' + +name = 'TELEMAC-MASCARET' +version = '8p5r0' + +homepage = 'http://www.opentelemac.org' +description = """TELEMAC-MASCARET is an integrated suite of solvers for use in the field of free-surface flow. Having +been used in the context of many studies throughout the world, it has become one of the major standards in its field.""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'extra_fcflags': "-fallow-invalid-boz"} + +source_urls = ['https://gitlab.pam-retd.fr/otm/telemac-mascaret/-/archive/v%(version)s/'] +sources = ['telemac-mascaret-v%(version)s.tar.gz'] +checksums = ['2beb9793fb83d17de31b17f001f985fc30702c151e2ced614f5e0117e8e34aa0'] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), # provides numpy, scipy + ('matplotlib', '3.7.2'), + ('HDF5', '1.14.0'), + ('METIS', '5.1.0'), + ('SCOTCH', '7.0.3'), + ('MUMPS', '5.6.1', '-metis'), +] + +extract_sources = True +unpack_options = '--strip-components=1' + +buildininstalldir = True + +local_tweak_cfg_cmd = ' '.join([ + "sed -i -e 's/S10.gfortran/easybuild/g'", + # strip out use of AED, GOTM, MED (optional dependencies) + r"-e 's/\(^[a-z]*_aed:\).*/\1/g' -e 's/\(^[a-z]*_gotm:\).*/\1/g' -e 's/\(^[a-z]*_med:\).*/\1/g'", + # replace -O2 with desired compiler options + '-e "s/-O2/$F90FLAGS/g"', + # fix linker option for BLAS + '-e "s/ -lblas/ $LIBBLAS/g"', + # downgrade Fortran compiler error to warning + "-e 's/^fflags_gfo:/fflags_gfo: -fallow-invalid-boz/g'", + # Disable hyperthreading option + "-e 's/--use-hwthread-cpus//'", + "$HOMETEL/configs/systel.easybuild.cfg", +]) + +install_cmd = ' && '.join([ + "export HOMETEL=$PWD", + # add Python scripts to $PATH and $PYTHONPATH + "export PATH=$HOMETEL/scripts/python3/:$PATH", + "export PYTHONPATH=$HOMETEL/scripts/python3:$PYTHONPATH", + # force python to flush its output + "export PYTHONUNBUFFERED=1", + "cp $HOMETEL/configs/systel.edf.cfg $HOMETEL/configs/systel.easybuild.cfg", + local_tweak_cfg_cmd, + "export SYSTELCFG=$HOMETEL/configs/systel.easybuild.cfg", + "export USETELCFG=easybuild.dyn", + "export SCALAPACKHOME=$EBROOTSCALAPACK", + "export METISHOME=$EBROOTMETIS", + "export SCOTCHHOME=$EBROOTSCOTCH", + "export MUMPSHOME=$EBROOTMUMPS", + "export HDF5HOME=$EBROOTHDF5", + "config.py", + "compile_telemac.py -j %(parallel)s", +]) + +sanity_check_paths = { + 'files': ['builds/easybuild.dyn/bin/telemac2d', 'builds/easybuild.dyn/bin/telemac3d', + 'builds/easybuild.dyn/lib/libtelemac2d.%s' % SHLIB_EXT, + 'builds/easybuild.dyn/lib/libtelemac3d.%s' % SHLIB_EXT], + 'dirs': ['scripts/python3'], +} + +sanity_check_commands = [ + "tmpdir=$(mktemp -d) && cp -a %(installdir)s/examples/telemac2d/gouttedo $tmpdir/ && chmod -R u+w $tmpdir && " + "cd $tmpdir/gouttedo && telemac2d.py t2d_gouttedo.cas", +] + +modextrapaths = { + 'LD_LIBRARY_PATH': 'builds/easybuild.dyn/lib', + 'PATH': 'scripts/python3', + 'PYTHONPATH': 'scripts/python3', +} + +modextravars = { + 'SYSTELCFG': '%(installdir)s/configs/systel.easybuild.cfg', + 'USETELCFG': 'easybuild.dyn', +} + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/t/TEtranscripts/TEtranscripts-2.2.3-foss-2023a.eb b/easybuild/easyconfigs/t/TEtranscripts/TEtranscripts-2.2.3-foss-2023a.eb new file mode 100644 index 00000000000..ab7aa3071a8 --- /dev/null +++ b/easybuild/easyconfigs/t/TEtranscripts/TEtranscripts-2.2.3-foss-2023a.eb @@ -0,0 +1,42 @@ +easyblock = 'PythonPackage' + +name = 'TEtranscripts' +version = '2.2.3' + +homepage = 'https://github.com/mhammell-laboratory/TEtranscripts' +description = """TEtranscripts and TEcount takes RNA-seq (and similar data) and annotates reads +to both genes & transposable elements. +TEtranscripts then performs differential analysis using DESeq2.""" + +sources = [SOURCE_TAR_GZ] +checksums = ['e53577e8e73e41c6495fb819977e3e537bbeac7b2fa1635029201a37ee0bf7b8'] + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('Pysam', '0.22.0'), + ('R', '4.3.2'), + ('R-bundle-Bioconductor', '3.18', '-R-%(rver)s'), +] + +use_pip = True +download_dep_fail = True + +options = {'modulename': 'TEToolkit'} + +fix_python_shebang_for = ['bin/*'] + +sanity_check_paths = { + 'files': ['bin/TEtranscripts', 'bin/TEcount'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + 'TEtranscripts --version', + 'TEcount --version', +] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/t/TF-COMB/TF-COMB-1.1-foss-2022b.eb b/easybuild/easyconfigs/t/TF-COMB/TF-COMB-1.1-foss-2022b.eb new file mode 100644 index 00000000000..2c06e8c9c8f --- /dev/null +++ b/easybuild/easyconfigs/t/TF-COMB/TF-COMB-1.1-foss-2022b.eb @@ -0,0 +1,48 @@ +easyblock = 'PythonBundle' + +name = 'TF-COMB' +version = '1.1' + +homepage = 'https://github.com/loosolab/TF-COMB' +description = """Transcription Factor Co-Occurrence using Market Basket analysis.""" + +toolchain = {'name': 'foss', 'version': '2022b'} + +dependencies = [ + ('Python', '3.10.8'), + ('SciPy-bundle', '2023.02'), + ('tqdm', '4.64.1'), + ('Pysam', '0.21.0'), + ('matplotlib', '3.7.0'), + ('networkx', '3.0'), + ('Graphviz', '8.1.0'), + ('statsmodels', '0.14.0'), + ('dill', '0.3.7'), + ('Seaborn', '0.12.2'), + ('IPython', '8.14.0'), + ('TOBIAS', '0.16.1'), + ('python-louvain', '0.16'), + ('GOATOOLS', '1.4.5'), + ('qnorm', '0.8.1'), +] + +use_pip = True +sanity_pip_check = True + +# remove graphviz from deps - the pip check failing, should be "import gv" +local_tfcomb_preinstallopts = "sed -i '70d' setup.py && " +# fix "import graphviz" to "import gv" +local_tfcomb_preinstallopts += "sed -i 's/import graphviz/import gv as graphviz/' tfcomb/plotting.py && " + +exts_list = [ + ('uropa', '4.0.3', { + 'checksums': ['e0b648881b95f301e3f3ecc924314995312f10b0cbabf96d5a5ce2fb18c53a59'], + }), + (name, version, { + 'preinstallopts': local_tfcomb_preinstallopts, + 'modulename': 'tfcomb', + 'checksums': ['5b718061660e0f9f94d86459eb742ca81de5851b0defd8b08c8a7a7e3370c253'], + }), +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/t/TF-COMB/TF-COMB-1.1-foss-2023a.eb b/easybuild/easyconfigs/t/TF-COMB/TF-COMB-1.1-foss-2023a.eb new file mode 100644 index 00000000000..d95bedfc764 --- /dev/null +++ b/easybuild/easyconfigs/t/TF-COMB/TF-COMB-1.1-foss-2023a.eb @@ -0,0 +1,54 @@ +easyblock = 'PythonBundle' + +name = 'TF-COMB' +version = '1.1' + +homepage = 'https://github.com/loosolab/TF-COMB' +description = """Transcription Factor Co-Occurrence using Market Basket analysis.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('SciPy-bundle', '2023.07'), + ('tqdm', '4.66.1'), + ('Pysam', '0.22.0'), + ('matplotlib', '3.7.2'), + ('networkx', '3.1'), + ('Graphviz', '8.1.0'), + ('statsmodels', '0.14.1'), + ('dill', '0.3.7'), + ('Seaborn', '0.13.2'), + ('IPython', '8.14.0'), + ('TOBIAS', '0.16.1'), + ('python-louvain', '0.16'), + ('GOATOOLS', '1.4.5'), + ('qnorm', '0.8.1'), +] + +use_pip = True +sanity_pip_check = True + +# remove graphviz from deps - the pip check failing, should be "import gv" +local_tfcomb_preinstallopts = "sed -i '70d' setup.py && " +# fix "import graphviz" to "import gv" +local_tfcomb_preinstallopts += "sed -i 's/import graphviz/import gv as graphviz/' tfcomb/plotting.py && " +# unpin python version to works with python 3.11.3 +local_tfcomb_preinstallopts += "sed -i '59d' setup.py && " +# regenerate counting.c to works with python 3.11 +local_tfcomb_preinstallopts += "cd tfcomb && rm counting.c && cythonize -i counting.pyx && cd .. && " + + +exts_list = [ + ('uropa', '4.0.3', { + 'checksums': ['e0b648881b95f301e3f3ecc924314995312f10b0cbabf96d5a5ce2fb18c53a59'], + }), + (name, version, { + 'preinstallopts': local_tfcomb_preinstallopts, + 'modulename': 'tfcomb', + 'checksums': ['5b718061660e0f9f94d86459eb742ca81de5851b0defd8b08c8a7a7e3370c253'], + }), +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/t/TINKER/TINKER-8.11.3-foss-2023a.eb b/easybuild/easyconfigs/t/TINKER/TINKER-8.11.3-foss-2023a.eb new file mode 100644 index 00000000000..ac13f1e800f --- /dev/null +++ b/easybuild/easyconfigs/t/TINKER/TINKER-8.11.3-foss-2023a.eb @@ -0,0 +1,39 @@ +easyblock = 'CMakeMake' + +name = 'TINKER' +version = '8.11.3' + +homepage = 'https://dasher.wustl.edu/tinker' +description = """The Tinker molecular modeling software is a complete and general package for molecular mechanics + and dynamics, with some special features for biopolymers.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['https://dasher.wustl.edu/tinker/downloads/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['8dfbc9fb8f26742d91139187657e2c905744b0243538f81b75bc04cdc2606ff7'] + +builddependencies = [ + ('CMake', '3.26.3'), +] + +srcdir = 'cmake' + +test_cmd = 'cd ../tinker/test/ && ' +# fix path to executables in .run test scripts +test_cmd += r"sed -i 's|\.\./bin|../../easybuild_obj|g' *.run && " +# run all .run scripts +# manually compare test results with .log files in test dir +# (ifabp succeeds but exits with a memory error) +test_cmd += 'for x in *.run; do echo "START TEST: $x" && ./$x; done' + +postinstallcmds = ['cd %(start_dir)s && cp -a params perl python %(installdir)s'] + +sanity_check_paths = { + 'files': ['lib/libtinker.a'], + 'dirs': ['bin', 'params', 'perl', 'python'], +} + +# (no sanity_check_commands since all programs require multiple other inputs) + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/t/TOBIAS/TOBIAS-0.16.1-foss-2022b.eb b/easybuild/easyconfigs/t/TOBIAS/TOBIAS-0.16.1-foss-2022b.eb new file mode 100644 index 00000000000..9150965319e --- /dev/null +++ b/easybuild/easyconfigs/t/TOBIAS/TOBIAS-0.16.1-foss-2022b.eb @@ -0,0 +1,55 @@ +easyblock = 'PythonBundle' + +name = 'TOBIAS' +version = '0.16.1' + +homepage = 'https://github.com/loosolab/TOBIAS' +description = """TOBIAS is a collection of command-line bioinformatics tools +for performing footprinting analysis on ATAC-seq data.""" + +toolchain = {'name': 'foss', 'version': '2022b'} + +dependencies = [ + ('Python', '3.10.8'), + ('SciPy-bundle', '2023.02'), + ('matplotlib', '3.7.0'), + ('Seaborn', '0.12.2'), + ('Pysam', '0.21.0'), + ('pybedtools', '0.9.0'), + ('boto3', '1.26.163'), + ('pyBigWig', '0.3.22'), + ('scikit-learn', '1.2.1'), + ('PyYAML', '6.0'), + ('XlsxWriter', '3.1.2'), + ('svist4get', '1.3.1'), + ('adjustText', '0.7.3'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('kneed', '0.8.5', { + 'checksums': ['a4847ac4f1d04852fea278d5de7aa8bfdc3beb7fbca4a182fec0f0efee43f4b1'], + }), + ('logomaker', '0.8', { + 'checksums': ['d8c7501a7d6d7961cd68e5a44e939000ebf1b0c4197a0c9198351e1d681d3f6d'], + }), + ('MOODS-python', '1.9.4.1', { + 'modulename': 'MOODS', + 'checksums': ['b3b5e080cb0cd13c0fd175d0ee0d453fde3e42794fa7ac39a4f6db1ac5ddb4cc'], + }), + ('PyPDF2', '3.0.1', { + 'modulename': 'PyPDF2', + 'checksums': ['a74408f69ba6271f71b9352ef4ed03dc53a31aa404d29b5d31f53bfecfee1440'], + }), + ('tobias', version, { + # remove pyBigWig dependency - pip_check fails with "import pybigwig" + 'preinstallopts': "sed -i '81d' setup.py && ", + 'checksums': ['c46267c01287be06201b3e6f7a36daad1ad86d6c578f96e878501be7da7fd109'], + }), +] + +sanity_check_commands = ["python -c 'import pyBigWig'"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/t/TOBIAS/TOBIAS-0.16.1-foss-2023a.eb b/easybuild/easyconfigs/t/TOBIAS/TOBIAS-0.16.1-foss-2023a.eb new file mode 100644 index 00000000000..0404ad39d85 --- /dev/null +++ b/easybuild/easyconfigs/t/TOBIAS/TOBIAS-0.16.1-foss-2023a.eb @@ -0,0 +1,55 @@ +easyblock = 'PythonBundle' + +name = 'TOBIAS' +version = '0.16.1' + +homepage = 'https://github.com/loosolab/TOBIAS' +description = """TOBIAS is a collection of command-line bioinformatics tools +for performing footprinting analysis on ATAC-seq data.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [('hatchling', '1.18.0')] +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('SciPy-bundle', '2023.07'), + ('matplotlib', '3.7.2'), + ('Seaborn', '0.13.2'), + ('Pysam', '0.22.0'), + ('pybedtools', '0.9.1'), + ('boto3', '1.28.70'), + ('pyBigWig', '0.3.22'), + ('scikit-learn', '1.3.1'), + ('PyYAML', '6.0'), + ('XlsxWriter', '3.1.3'), + ('svist4get', '1.3.1'), + ('adjustText', '0.7.3'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('kneed', '0.8.5', { + 'checksums': ['a4847ac4f1d04852fea278d5de7aa8bfdc3beb7fbca4a182fec0f0efee43f4b1'], + }), + ('logomaker', '0.8', { + 'checksums': ['d8c7501a7d6d7961cd68e5a44e939000ebf1b0c4197a0c9198351e1d681d3f6d'], + }), + ('MOODS-python', '1.9.4.1', { + 'modulename': 'MOODS', + 'checksums': ['b3b5e080cb0cd13c0fd175d0ee0d453fde3e42794fa7ac39a4f6db1ac5ddb4cc'], + }), + ('PyPDF2', '3.0.1', { + 'modulename': 'PyPDF2', + 'checksums': ['a74408f69ba6271f71b9352ef4ed03dc53a31aa404d29b5d31f53bfecfee1440'], + }), + ('tobias', version, { + 'checksums': ['c46267c01287be06201b3e6f7a36daad1ad86d6c578f96e878501be7da7fd109'], + }), +] + +sanity_check_commands = ["python -c 'import pyBigWig'"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/t/TRF/TRF-4.09.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/t/TRF/TRF-4.09.1-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..cbf3e47917e --- /dev/null +++ b/easybuild/easyconfigs/t/TRF/TRF-4.09.1-GCCcore-12.3.0.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'TRF' +version = '4.09.1' + +homepage = 'https://tandem.bu.edu/trf/trf.html' +description = """Tandem Repeats Finder: a program to analyze DNA sequences.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +github_account = 'Benson-Genomics-Lab' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['516015b625473350c3d1c9b83cac86baea620c8418498ab64c0a67029c3fb28a'] + +builddependencies = [ + ('binutils', '2.40'), + ('Autotools', '20220317'), +] + +preconfigopts = "autoreconf -i -f && " + +sanity_check_paths = { + 'files': ['bin/trf'], + 'dirs': [], +} + +sanity_check_commands = ["trf -v"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.14-GCCcore-13.3.0.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.14-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..e81b854198b --- /dev/null +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.14-GCCcore-13.3.0.eb @@ -0,0 +1,41 @@ +easyblock = 'ConfigureMake' + +name = 'Tcl' +version = '8.6.14' + +homepage = 'https://www.tcl.tk/' +description = """ + Tcl (Tool Command Language) is a very powerful but easy to learn dynamic + programming language, suitable for a very wide range of uses, including web + and desktop applications, networking, administration, testing and many more. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] +sources = ['%(namelower)s%(version)s-src.tar.gz'] +checksums = ['5880225babf7954c58d4fb0f5cf6279104ce1cd6aa9b71e9a6322540e1c4de66'] + +builddependencies = [ + ('binutils', '2.42'), +] +dependencies = [ + ('zlib', '1.3.1'), +] + +configopts = '--enable-threads EXTRA_INSTALL="install-private-headers"' + +runtest = 'test' + +start_dir = 'unix' + +postinstallcmds = ['ln -s %(installdir)s/bin/tclsh%(version_major)s.%(version_minor)s %(installdir)s/bin/tclsh'] + +sanity_check_paths = { + 'files': ['bin/tclsh%(version_major)s.%(version_minor)s', 'bin/tclsh', + 'include/tcl.h', 'lib/libtcl%%(version_major)s.%%(version_minor)s.%s' % SHLIB_EXT, + 'lib/tclConfig.sh', 'man/man1/tclsh.1'], + 'dirs': ['share'], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1-foss-2023a-CUDA-12.1.1.eb new file mode 100644 index 00000000000..7b2f4888b23 --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1-foss-2023a-CUDA-12.1.1.eb @@ -0,0 +1,178 @@ +easyblock = 'PythonBundle' + +name = 'TensorFlow' +version = '2.15.1' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://www.tensorflow.org/' +description = "An open-source software library for Machine Intelligence" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'pic': True} + +use_pip = True +sanity_pip_check = True + +builddependencies = [ + ('Bazel', '6.1.0'), + # git 2.x required, see also https://github.com/tensorflow/tensorflow/issues/29053 + ('git', '2.41.0', '-nodocs'), + ('pybind11', '2.11.1'), + ('UnZip', '6.0'), + # Required to build some of the extensions + ('poetry', '1.5.1'), + # Protobuf disabled since 2.13.0 easyconfigs: + # Compiling with system protobuf don't seem to work, see: + # https://github.com/tensorflow/tensorflow/issues/61593 + # ('protobuf', '24.0'), +] + +dependencies = [ + ('CUDA', '12.1.1', '', SYSTEM), + ('cuDNN', '8.9.2.26', versionsuffix, SYSTEM), + ('NCCL', '2.18.3', versionsuffix), + ('Python', '3.11.3'), + ('h5py', '3.9.0'), + ('cURL', '8.0.1'), + ('dill', '0.3.7'), + ('double-conversion', '3.3.0'), + ('flatbuffers', '23.5.26'), + ('flatbuffers-python', '23.5.26'), + ('giflib', '5.2.1'), + ('hwloc', '2.9.1'), + ('ICU', '73.2'), + ('JsonCpp', '1.9.5'), + ('libjpeg-turbo', '2.1.5.1'), + ('ml_dtypes', '0.3.2'), + ('NASM', '2.16.01'), + ('nsync', '1.26.0'), + ('SQLite', '3.42.0'), + ('patchelf', '0.18.0'), + ('libpng', '1.6.39'), + ('snappy', '1.1.10'), + ('zlib', '1.2.13'), + ('tensorboard', '2.15.1'), +] + +# Dependencies created and updated using findPythonDeps, see: +# https://docs.easybuild.io/api/easybuild/scripts/findPythonDeps +# Notable changes since 2.13.0-foss-2023a +# - tensoboard-wit deprecated as of tensorboard 2.13.0 (tensorboard@33abcb54d7) +# - portpicker for tests no longer needed (TF@e85860e838) +# - opt_einsum now comes from ml_dtypes +exts_list = [ + ('wrapt', '1.14.1', { + 'checksums': ['380a85cf89e0e69b7cfbe2ea9f765f004ff419f34194018a6827ac0e3edfed4d'], + }), + ('termcolor', '2.3.0', { + 'checksums': ['b5b08f68937f138fe92f6c089b99f1e2da0ae56c52b78bf7075fd95420fd9a5a'], + }), + ('tensorflow-estimator', '2.15.0', { + 'source_tmpl': 'tensorflow_estimator-%(version)s-py2.py3-none-any.whl', + 'checksums': ['aedf21eec7fb2dc91150fc91a1ce12bc44dbb72278a08b58e79ff87c9e28f153'], + }), + ('keras', '2.15.0', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['2dcc6d2e30cf9c951064b63c1f4c404b966c59caf09e01f3549138ec8ee0dd1f'], + }), + ('google-pasta', '0.2.0', { + 'modulename': 'pasta', + 'checksums': ['c9f2c8dfc8f96d0d5808299920721be30c9eec37f2389f28904f454565c8a16e'], + }), + ('astunparse', '1.6.3', { + 'checksums': ['5ad93a8456f0d084c3456d059fd9a92cce667963232cbf763eac3bc5b7940872'], + }), + # Required by tests + ('tblib', '3.0.0', { + 'checksums': ['93622790a0a29e04f0346458face1e144dc4d32f493714c6c3dff82a4adb77e6'], + }), + ('astor', '0.8.1', { + 'checksums': ['6a6effda93f4e1ce9f618779b2dd1d9d84f1e32812c23a29b3fff6fd7f63fa5e'], + }), + (name, version, { + 'patches': [ + 'TensorFlow-2.1.0_fix-cuda-build.patch', + 'TensorFlow-2.4.0_dont-use-var-lock.patch', + 'TensorFlow-2.13.0_add-missing-system-protobuf-targets.patch', + 'TensorFlow-2.13.0_exclude-xnnpack-on-ppc.patch', + 'TensorFlow-2.15.1_remove-duplicate-gpu-tests.patch', + 'TensorFlow-2.15.1_remove-libclang-dep.patch', + 'TensorFlow-2.15.1_remove-io-gcs-filesystem-dep.patch', + 'TensorFlow-2.15.1_add-default-shell-env.patch', + 'TensorFlow-2.15.1_fix-AVX512-eigen-compilation.patch', + 'TensorFlow-2.15.1_fix-flatbuffer-license.patch', + 'TensorFlow-2.15.1_fix-pybind11-build.patch', + 'TensorFlow-2.15.1_fix-cuda_build_defs.patch', + 'TensorFlow-2.15.1_disable-avx512-extensions.patch', + 'TensorFlow-2.15.1_disable-tf32-in-fused-matmul-tests.patch' + ], + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/tensorflow/tensorflow/archive/'], + 'test_script': 'TensorFlow-2.x_mnist-test.py', + 'test_tag_filters_cpu': ( + '-gpu,-tpu,-no_cuda_on_cpu_tap,' + '-no_pip,-no_oss,-oss_serial,-benchmark-test,-v1only' + ), + 'test_tag_filters_gpu': ( + 'gpu,-no_gpu,-nogpu,-gpu_cupti,-no_cuda11,' + '-no_pip,-no_oss,-oss_serial,-benchmark-test,-v1only' + ), + 'test_targets': [ + '//tensorflow/core/...', + '-//tensorflow/core:example_java_proto', + '-//tensorflow/core/example:example_protos_closure', + '//tensorflow/cc/...', + '//tensorflow/c/...', + '//tensorflow/python/...', + '-//tensorflow/c/eager:c_api_test_gpu', + '-//tensorflow/c/eager:c_api_distributed_test', + '-//tensorflow/c/eager:c_api_distributed_test_gpu', + '-//tensorflow/c/eager:c_api_cluster_test_gpu', + '-//tensorflow/c/eager:c_api_remote_function_test_gpu', + '-//tensorflow/c/eager:c_api_remote_test_gpu', + '-//tensorflow/core/common_runtime:collective_param_resolver_local_test', + '-//tensorflow/core/kernels/mkl:mkl_fused_ops_test', + '-//tensorflow/core/kernels/mkl:mkl_fused_batch_norm_op_test', + '-//tensorflow/core/ir/importexport/tests/roundtrip/...', + ], + 'testopts': '--test_env=HOME=/tmp --test_timeout=3600 --test_size_filters=small ', + 'testopts_gpu': ( + '--test_env=HOME=/tmp --test_timeout=3600 --test_size_filters=small ' + '--run_under=//tensorflow/tools/ci_build/gpu_build:parallel_gpu_execute ' + ), + 'with_xla': True, + 'checksums': [ + {'v2.15.1.tar.gz': 'f36416d831f06fe866e149c7cd752da410a11178b01ff5620e9f265511ed57cf'}, + {'TensorFlow-2.1.0_fix-cuda-build.patch': + '78c20aeaa7784b8ceb46238a81e8c2461137d28e0b576deeba8357d23fbe1f5a'}, + {'TensorFlow-2.4.0_dont-use-var-lock.patch': + 'b14f2493fd2edf79abd1c4f2dde6c98a3e7d5cb9c25ab9386df874d5f072d6b5'}, + {'TensorFlow-2.13.0_add-missing-system-protobuf-targets.patch': + '77d8c8a5627493fc7c38b4de79d49e60ff6628b05ff969f4cd3ff9857176c459'}, + {'TensorFlow-2.13.0_exclude-xnnpack-on-ppc.patch': + 'd0818206846911d946666ded7d3216c0546e37cee1890a2f48dc1a9d71047cad'}, + {'TensorFlow-2.15.1_remove-duplicate-gpu-tests.patch': + 'd8810d5b875de5be8603afd743774ce9dd8c0d4a82314c7fe2f284a080be7498'}, + {'TensorFlow-2.15.1_remove-libclang-dep.patch': + '871b2f0221b7a150ac9f563ffad7187e052a7eedd95c20fb4524987d7edb6f21'}, + {'TensorFlow-2.15.1_remove-io-gcs-filesystem-dep.patch': + 'eba7351a4b0696c589b9c507bacb0257ebce8c39fde39ab72d5d6a69deaaec02'}, + {'TensorFlow-2.15.1_add-default-shell-env.patch': + '3d5196b4bf2e91048dc8a18f9e8f487a223fcd973d6302e80b0d4000ea3d652b'}, + {'TensorFlow-2.15.1_fix-AVX512-eigen-compilation.patch': + '761059e5f5f5eeeef8aed5517a7685a0eb0a9193d4afe8d45237527681c9c0a3'}, + {'TensorFlow-2.15.1_fix-flatbuffer-license.patch': + '2c04d5095977a628a238dbf93c5fada7159c86752a7183e64e0cf7c7ab00caf4'}, + {'TensorFlow-2.15.1_fix-pybind11-build.patch': + '3bb350ac92ab99c63c951c96b3b0160699f5f16822b64f72111ebfd2275cafce'}, + {'TensorFlow-2.15.1_fix-cuda_build_defs.patch': + '091581a7c4fc2fc7af282cab6661632c29029d2f36eccb6695ffa5783e065f88'}, + {'TensorFlow-2.15.1_disable-avx512-extensions.patch': + '506ceecff67237eed9cd9e9e114bc1461f35a343f77f83cb3dab710aa701dc0f'}, + {'TensorFlow-2.15.1_disable-tf32-in-fused-matmul-tests.patch': + 'f78aa0e8f814a57e8d2e6b24ff095df49e8654aadb797393fa95a9378d0aa662'}, + ], + }), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1-foss-2023a.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1-foss-2023a.eb new file mode 100644 index 00000000000..ebca59072d6 --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1-foss-2023a.eb @@ -0,0 +1,159 @@ +easyblock = 'PythonBundle' + +name = 'TensorFlow' +version = '2.15.1' + +homepage = 'https://www.tensorflow.org/' +description = "An open-source software library for Machine Intelligence" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'pic': True} + +use_pip = True +sanity_pip_check = True + +builddependencies = [ + ('Bazel', '6.1.0'), + # git 2.x required, see also https://github.com/tensorflow/tensorflow/issues/29053 + ('git', '2.41.0', '-nodocs'), + ('pybind11', '2.11.1'), + ('UnZip', '6.0'), + # Required to build some of the extensions + ('poetry', '1.5.1'), + # Protobuf disabled since 2.13.0 easyconfigs: + # Compiling with system protobuf don't seem to work, see: + # https://github.com/tensorflow/tensorflow/issues/61593 + # ('protobuf', '24.0'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('h5py', '3.9.0'), + ('cURL', '8.0.1'), + ('dill', '0.3.7'), + ('double-conversion', '3.3.0'), + ('flatbuffers', '23.5.26'), + ('flatbuffers-python', '23.5.26'), + ('giflib', '5.2.1'), + ('hwloc', '2.9.1'), + ('ICU', '73.2'), + ('JsonCpp', '1.9.5'), + ('libjpeg-turbo', '2.1.5.1'), + ('ml_dtypes', '0.3.2'), + ('NASM', '2.16.01'), + ('nsync', '1.26.0'), + ('SQLite', '3.42.0'), + ('patchelf', '0.18.0'), + ('libpng', '1.6.39'), + ('snappy', '1.1.10'), + ('zlib', '1.2.13'), + ('tensorboard', '2.15.1'), +] + +# Dependencies created and updated using findPythonDeps, see: +# https://docs.easybuild.io/api/easybuild/scripts/findPythonDeps +# Notable changes since 2.13.0-foss-2023a +# - tensoboard-wit deprecated as of tensorboard 2.13.0 (tensorboard@33abcb54d7) +# - portpicker for tests no longer needed (TF@e85860e838) +# - opt_einsum now comes from ml_dtypes +exts_list = [ + ('wrapt', '1.14.1', { + 'checksums': ['380a85cf89e0e69b7cfbe2ea9f765f004ff419f34194018a6827ac0e3edfed4d'], + }), + ('termcolor', '2.3.0', { + 'checksums': ['b5b08f68937f138fe92f6c089b99f1e2da0ae56c52b78bf7075fd95420fd9a5a'], + }), + ('tensorflow-estimator', '2.15.0', { + 'source_tmpl': 'tensorflow_estimator-%(version)s-py2.py3-none-any.whl', + 'checksums': ['aedf21eec7fb2dc91150fc91a1ce12bc44dbb72278a08b58e79ff87c9e28f153'], + }), + ('keras', '2.15.0', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['2dcc6d2e30cf9c951064b63c1f4c404b966c59caf09e01f3549138ec8ee0dd1f'], + }), + ('google-pasta', '0.2.0', { + 'modulename': 'pasta', + 'checksums': ['c9f2c8dfc8f96d0d5808299920721be30c9eec37f2389f28904f454565c8a16e'], + }), + ('astunparse', '1.6.3', { + 'checksums': ['5ad93a8456f0d084c3456d059fd9a92cce667963232cbf763eac3bc5b7940872'], + }), + # Required by tests + ('tblib', '3.0.0', { + 'checksums': ['93622790a0a29e04f0346458face1e144dc4d32f493714c6c3dff82a4adb77e6'], + }), + ('astor', '0.8.1', { + 'checksums': ['6a6effda93f4e1ce9f618779b2dd1d9d84f1e32812c23a29b3fff6fd7f63fa5e'], + }), + (name, version, { + 'patches': [ + 'TensorFlow-2.13.0_add-missing-system-protobuf-targets.patch', + 'TensorFlow-2.13.0_exclude-xnnpack-on-ppc.patch', + 'TensorFlow-2.15.1_remove-libclang-dep.patch', + 'TensorFlow-2.15.1_remove-io-gcs-filesystem-dep.patch', + 'TensorFlow-2.15.1_add-default-shell-env.patch', + 'TensorFlow-2.15.1_fix-AVX512-eigen-compilation.patch', + 'TensorFlow-2.15.1_fix-flatbuffer-license.patch', + 'TensorFlow-2.15.1_fix-pybind11-build.patch', + 'TensorFlow-2.15.1_disable-avx512-extensions.patch', + ], + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/tensorflow/tensorflow/archive/'], + 'test_script': 'TensorFlow-2.x_mnist-test.py', + 'test_tag_filters_cpu': ( + '-gpu,-tpu,-no_cuda_on_cpu_tap,' + '-no_pip,-no_oss,-oss_serial,-benchmark-test,-v1only' + ), + 'test_tag_filters_gpu': ( + 'gpu,-no_gpu,-nogpu,-gpu_cupti,-no_cuda11,' + '-no_pip,-no_oss,-oss_serial,-benchmark-test,-v1only' + ), + 'test_targets': [ + '//tensorflow/core/...', + '-//tensorflow/core:example_java_proto', + '-//tensorflow/core/example:example_protos_closure', + '//tensorflow/cc/...', + '//tensorflow/c/...', + '//tensorflow/python/...', + '-//tensorflow/c/eager:c_api_test_gpu', + '-//tensorflow/c/eager:c_api_distributed_test', + '-//tensorflow/c/eager:c_api_distributed_test_gpu', + '-//tensorflow/c/eager:c_api_cluster_test_gpu', + '-//tensorflow/c/eager:c_api_remote_function_test_gpu', + '-//tensorflow/c/eager:c_api_remote_test_gpu', + '-//tensorflow/core/common_runtime:collective_param_resolver_local_test', + '-//tensorflow/core/kernels/mkl:mkl_fused_ops_test', + '-//tensorflow/core/kernels/mkl:mkl_fused_batch_norm_op_test', + '-//tensorflow/core/ir/importexport/tests/roundtrip/...', + ], + 'testopts': '--test_env=HOME=/tmp --test_timeout=3600 --test_size_filters=small ', + 'testopts_gpu': ( + '--test_env=HOME=/tmp --test_timeout=3600 --test_size_filters=small ' + '--run_under=//tensorflow/tools/ci_build/gpu_build:parallel_gpu_execute ' + ), + 'with_xla': True, + 'checksums': [ + {'v2.15.1.tar.gz': 'f36416d831f06fe866e149c7cd752da410a11178b01ff5620e9f265511ed57cf'}, + {'TensorFlow-2.13.0_add-missing-system-protobuf-targets.patch': + '77d8c8a5627493fc7c38b4de79d49e60ff6628b05ff969f4cd3ff9857176c459'}, + {'TensorFlow-2.13.0_exclude-xnnpack-on-ppc.patch': + 'd0818206846911d946666ded7d3216c0546e37cee1890a2f48dc1a9d71047cad'}, + {'TensorFlow-2.15.1_remove-libclang-dep.patch': + '871b2f0221b7a150ac9f563ffad7187e052a7eedd95c20fb4524987d7edb6f21'}, + {'TensorFlow-2.15.1_remove-io-gcs-filesystem-dep.patch': + 'eba7351a4b0696c589b9c507bacb0257ebce8c39fde39ab72d5d6a69deaaec02'}, + {'TensorFlow-2.15.1_add-default-shell-env.patch': + '3d5196b4bf2e91048dc8a18f9e8f487a223fcd973d6302e80b0d4000ea3d652b'}, + {'TensorFlow-2.15.1_fix-AVX512-eigen-compilation.patch': + '761059e5f5f5eeeef8aed5517a7685a0eb0a9193d4afe8d45237527681c9c0a3'}, + {'TensorFlow-2.15.1_fix-flatbuffer-license.patch': + '2c04d5095977a628a238dbf93c5fada7159c86752a7183e64e0cf7c7ab00caf4'}, + {'TensorFlow-2.15.1_fix-pybind11-build.patch': + '3bb350ac92ab99c63c951c96b3b0160699f5f16822b64f72111ebfd2275cafce'}, + {'TensorFlow-2.15.1_disable-avx512-extensions.patch': + '506ceecff67237eed9cd9e9e114bc1461f35a343f77f83cb3dab710aa701dc0f'}, + ], + }), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1_add-default-shell-env.patch b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1_add-default-shell-env.patch new file mode 100644 index 00000000000..f1510205a04 --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1_add-default-shell-env.patch @@ -0,0 +1,51 @@ +Make TensorFlow use the environment as set by EasyBuild + +See https://github.com/tensorflow/tensorflow/pull/61591 + +Author: Alexander Grund (TU Dresden) + +Edit in 2.15.1: include also python api generator / Yunqi Shao (C3SE) + +diff --git a/tensorflow/python/tools/api/generator2/generate_api.bzl b/tensorflow/python/tools/api/generator2/generate_api.bzl index 64e9b96276e..afadd07bc3d 100644 +--- a/tensorflow/python/tools/api/generator2/generate_api.bzl ++++ b/tensorflow/python/tools/api/generator2/generate_api.bzl +@@ -95,6 +95,7 @@ def _api_extractor_impl(target, ctx): + outputs = [output], + arguments = [args], + progress_message = "Extracting " + api + " APIs for %{label} to %{output}.", ++ use_default_shell_env = True, + ) + + direct_api.append(output) +@@ -218,6 +219,7 @@ def _generate_api_impl(ctx): + outputs = ctx.outputs.output_files, + arguments = [args], + progress_message = "Generating APIs for %{label} to %{output}.", ++ use_default_shell_env = True, + ) + + # Convert output_paths to the list of corresponding modules for the further testing +diff --git a/tensorflow/lite/build_def.bzl b/tensorflow/lite/build_def.bzl +index cdc02ac2b26..6b4c8b9045f 100644 +--- a/tensorflow/lite/build_def.bzl ++++ b/tensorflow/lite/build_def.bzl +@@ -368,6 +368,7 @@ def _gen_selected_ops_impl(ctx): + executable = ctx.executable._generate_op_registrations, + mnemonic = "OpRegistration", + progress_message = "gen_selected_ops", ++ use_default_shell_env = True, + ) + + gen_selected_ops_rule = rule( +diff --git a/tensorflow/tensorflow.bzl b/tensorflow/tensorflow.bzl +index 6762ccd8f9b..de7c27a1275 100644 +--- a/tensorflow/tensorflow.bzl ++++ b/tensorflow/tensorflow.bzl +@@ -1325,6 +1325,7 @@ def _generate_op_reg_offsets_impl(ctx): + tools = [ctx.executable._offset_counter], + executable = ctx.executable._offset_counter, + arguments = [args], ++ use_default_shell_env = True, + ) + + generate_op_reg_offsets = rule( diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1_disable-avx512-extensions.patch b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1_disable-avx512-extensions.patch new file mode 100644 index 00000000000..7778d2b4a91 --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1_disable-avx512-extensions.patch @@ -0,0 +1,19 @@ +(Some of the) AVX512 extensions to Eigen introduced by TensorFlow are broken and return wrong values. +So disable them for now to keep AVX512 in the other code parts working. +See https://github.com/tensorflow/tensorflow/issues/49944 + +Author: Alexander Grund (TU Dresden) + +diff --git a/third_party/xla/third_party/tsl/tsl/framework/fixedpoint/FixedPoint.h b/third_party/xla/third_party/tsl/tsl/framework/fixedpoint/FixedPoint.h +index 5301914ad37..8923bfed7bf 100644 +--- a/third_party/xla/third_party/tsl/tsl/framework/fixedpoint/FixedPoint.h ++++ b/third_party/xla/third_party/tsl/tsl/framework/fixedpoint/FixedPoint.h +@@ -20,7 +20,7 @@ limitations under the License. + #include "tsl/framework/fixedpoint_types.h" + + // Use optimized implementations whenever available +-#if defined(EIGEN_VECTORIZE_AVX512DQ) || defined(EIGEN_VECTORIZE_AVX512BW) ++#if 0 + #include "tsl/framework/fixedpoint/PacketMathAVX512.h" + #include "tsl/framework/fixedpoint/TypeCastingAVX512.h" + diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1_disable-tf32-in-fused-matmul-tests.patch b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1_disable-tf32-in-fused-matmul-tests.patch new file mode 100644 index 00000000000..9cc742e53d0 --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1_disable-tf32-in-fused-matmul-tests.patch @@ -0,0 +1,46 @@ +Fixes failing FusedMatMul test on certain GPU models + +diff --git a/tensorflow/core/kernels/matmul_op_test.cc b/tensorflow/core/kernels/matmul_op_test.cc +index 8d81d4c796e..2de0365f067 100644 +--- a/tensorflow/core/kernels/matmul_op_test.cc ++++ b/tensorflow/core/kernels/matmul_op_test.cc +@@ -21,6 +21,7 @@ limitations under the License. + #include "tensorflow/core/framework/tensor.h" + #include "tensorflow/core/kernels/ops_testutil.h" + #include "tensorflow/core/lib/core/status_test_util.h" ++#include "tensorflow/core/platform/tensor_float_32_utils.h" + #include "tensorflow/core/platform/test.h" + #include "tensorflow/core/platform/test_benchmark.h" + #include "tensorflow/core/protobuf/rewriter_config.pb.h" +@@ -287,6 +288,7 @@ TYPED_TEST_SUITE_P(FusedMatMulWithBiasOpTest); + // -------------------------------------------------------------------------- // + + TYPED_TEST_P(FusedMatMulWithBiasOpTest, MatMul256x128x64) { ++ tensorflow::enable_tensor_float_32_execution(false); + this->VerifyMatMulWithBias(256, 128, 64, false, false); + this->VerifyMatMulWithBias(256, 128, 64, true, false); + this->VerifyMatMulWithBias(256, 128, 64, false, true); +@@ -294,6 +296,7 @@ TYPED_TEST_P(FusedMatMulWithBiasOpTest, MatMul256x128x64) { + } + + TYPED_TEST_P(FusedMatMulWithBiasOpTest, MatMul1x256x256) { ++ tensorflow::enable_tensor_float_32_execution(false); + this->VerifyMatMulWithBias(1, 256, 256, false, false); + this->VerifyMatMulWithBias(4, 128, 256, false, false); + this->VerifyMatMulWithBias(1, 256, 256, true, false); +@@ -302,6 +305,7 @@ TYPED_TEST_P(FusedMatMulWithBiasOpTest, MatMul1x256x256) { + } + + TYPED_TEST_P(FusedMatMulWithBiasOpTest, MatMul256x256x1) { ++ tensorflow::enable_tensor_float_32_execution(false); + this->VerifyMatMulWithBias(256, 256, 1, false, false); + this->VerifyMatMulWithBias(256, 128, 4, false, false); + this->VerifyMatMulWithBias(256, 256, 1, true, false); +@@ -314,6 +318,7 @@ TYPED_TEST_P(FusedMatMulWithBiasOpTest, MatMul1x256x1) { + } + + TYPED_TEST_P(FusedMatMulWithBiasOpTest, MatMul256x128x64WithActivation) { ++ tensorflow::enable_tensor_float_32_execution(false); + for (const string& activation : {"Relu", "Relu6", "Elu", "LeakyRelu"}) { + this->VerifyConv2DWithBiasAndActivation(256, 128, 64, false, false, + activation); diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1_fix-AVX512-eigen-compilation.patch b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1_fix-AVX512-eigen-compilation.patch new file mode 100644 index 00000000000..514f215cde9 --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1_fix-AVX512-eigen-compilation.patch @@ -0,0 +1,47 @@ +Fix a compilation error for CPUs with AVX512 features where an issue in Eigen leads to +> invalid 'static_cast' from type 'const Eigen::internal::eigen_packet_wrapper<__vector(4) long long int, 1>' to type '__vector(16) float' + +See https://gitlab.com/libeigen/eigen/-/issues/2829 + +Author: Alexander Grund (TU Dresden) + +diff --git a/third_party/eigen3/fix-avx512.patch b/third_party/eigen3/fix-avx512.patch +new file mode 100644 +index 00000000000..0650d52a0c9 +--- /dev/null ++++ b/third_party/eigen3/fix-avx512.patch +@@ -0,0 +1,22 @@ ++diff --git a/Eigen/src/Core/arch/AVX512/TypeCasting.h b/Eigen/src/Core/arch/AVX512/TypeCasting.h ++index 02c56282f..e253e6b49 100644 ++--- a/Eigen/src/Core/arch/AVX512/TypeCasting.h +++++ b/Eigen/src/Core/arch/AVX512/TypeCasting.h ++@@ -145,8 +145,6 @@ template<> EIGEN_STRONG_INLINE Packet8bf preinterpret(con ++ return _mm256_castsi256_si128(a); ++ } ++ ++-#ifndef EIGEN_VECTORIZE_AVX512FP16 ++- ++ template<> EIGEN_STRONG_INLINE Packet16f pcast(const Packet16h& a) { ++ return half2float(a); ++ } ++@@ -155,8 +153,6 @@ template<> EIGEN_STRONG_INLINE Packet16h pcast(const Packe ++ return float2half(a); ++ } ++ ++-#endif ++- ++ template<> EIGEN_STRONG_INLINE Packet16f pcast(const Packet16bf& a) { ++ return Bf16ToF32(a); ++ } +diff --git a/third_party/eigen3/workspace.bzl b/third_party/eigen3/workspace.bzl +index d1d8d4ac486..da549e37432 100644 +--- a/third_party/eigen3/workspace.bzl ++++ b/third_party/eigen3/workspace.bzl +@@ -14,6 +14,7 @@ def repo(): + tf_http_archive( + name = "eigen_archive", + build_file = "//third_party/eigen3:eigen_archive.BUILD", ++ patch_file = ["//third_party/eigen3:fix-avx512.patch"], + sha256 = EIGEN_SHA256, + strip_prefix = "eigen-{commit}".format(commit = EIGEN_COMMIT), + urls = tf_mirror_urls("https://gitlab.com/libeigen/eigen/-/archive/{commit}/eigen-{commit}.tar.gz".format(commit = EIGEN_COMMIT)), diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1_fix-cuda_build_defs.patch b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1_fix-cuda_build_defs.patch new file mode 100644 index 00000000000..0982df21bb9 --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1_fix-cuda_build_defs.patch @@ -0,0 +1,40 @@ +Backport cuda_build_defs path fix for TF 2.15, see: + +https://github.com/tensorflow/tensorflow/commit/1536f2ca228099f0cf7793d3031d9b9bebbf03ed + +diff --git a/third_party/nccl/system.BUILD.tpl b/third_party/nccl/system.BUILD.tpl +index 405d1e7298b..6e2a22a950b 100644 +--- a/third_party/nccl/system.BUILD.tpl ++++ b/third_party/nccl/system.BUILD.tpl +@@ -1,6 +1,6 @@ + load("@bazel_skylib//rules:write_file.bzl", "write_file") + load( +- "@org_tensorflow//tensorflow/platform/default:cuda_build_defs.bzl", ++ "@local_tsl//tsl/platform/default:cuda_build_defs.bzl", + "cuda_rpath_flags" + ) + +diff --git a/third_party/xla/third_party/nccl/system.BUILD.tpl b/third_party/xla/third_party/nccl/system.BUILD.tpl +index 13328fdeeac..6e2a22a950b 100644 +--- a/third_party/xla/third_party/nccl/system.BUILD.tpl ++++ b/third_party/xla/third_party/nccl/system.BUILD.tpl +@@ -1,6 +1,6 @@ + load("@bazel_skylib//rules:write_file.bzl", "write_file") + load( +- "@local_xla//tensorflow/platform/default:cuda_build_defs.bzl", ++ "@local_tsl//tsl/platform/default:cuda_build_defs.bzl", + "cuda_rpath_flags" + ) + +diff --git a/third_party/xla/third_party/tsl/third_party/nccl/system.BUILD.tpl b/third_party/xla/third_party/tsl/third_party/nccl/system.BUILD.tpl +index b45138eaa79..6e2a22a950b 100644 +--- a/third_party/xla/third_party/tsl/third_party/nccl/system.BUILD.tpl ++++ b/third_party/xla/third_party/tsl/third_party/nccl/system.BUILD.tpl +@@ -1,6 +1,6 @@ + load("@bazel_skylib//rules:write_file.bzl", "write_file") + load( +- "@local_tsl//tensorflow/platform/default:cuda_build_defs.bzl", ++ "@local_tsl//tsl/platform/default:cuda_build_defs.bzl", + "cuda_rpath_flags" + ) + diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1_fix-flatbuffer-license.patch b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1_fix-flatbuffer-license.patch new file mode 100644 index 00000000000..4970cd0b758 --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1_fix-flatbuffer-license.patch @@ -0,0 +1,13 @@ +diff --git a/third_party/flatbuffers/BUILD.system b/third_party/flatbuffers/BUILD.system +index 8fe4d7a5907..b1d63b4ca0f 100644 +--- a/third_party/flatbuffers/BUILD.system ++++ b/third_party/flatbuffers/BUILD.system +@@ -1,7 +1,7 @@ + licenses(["notice"]) # Apache 2.0 + + filegroup( +- name = "LICENSE.txt", ++ name = "LICENSE", + visibility = ["//visibility:public"], + ) + diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1_fix-pybind11-build.patch b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1_fix-pybind11-build.patch new file mode 100644 index 00000000000..c12c8726172 --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1_fix-pybind11-build.patch @@ -0,0 +1,14 @@ +diff --git a/third_party/systemlibs/pybind11.BUILD b/third_party/systemlibs/pybind11.BUILD +index 79a483d7b5d..463dd1a8ec7 100644 +--- a/third_party/systemlibs/pybind11.BUILD ++++ b/third_party/systemlibs/pybind11.BUILD +@@ -6,3 +6,9 @@ cc_library( + "@org_tensorflow//third_party/python_runtime:headers", + ], + ) ++ ++# Needed by pybind11_bazel. ++config_setting( ++ name = "osx", ++ constraint_values = ["@platforms//os:osx"], ++) diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1_remove-duplicate-gpu-tests.patch b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1_remove-duplicate-gpu-tests.patch new file mode 100644 index 00000000000..7c6d72c89c9 --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1_remove-duplicate-gpu-tests.patch @@ -0,0 +1,55 @@ +TensorFlow adds some GPU tests twice increasing the runtime of the test suite. +This filters out the test part meant for CPU. + +See https://github.com/tensorflow/tensorflow/issues/47081 +From https://github.com/tensorflow/tensorflow/pull/59129 + +Author: Alexander Grund (TU Dresden) +--- + tensorflow/tensorflow.bzl | 33 +++++++++++++++++---------------- + 1 file changed, 17 insertions(+), 16 deletions(-) + +diff --git a/tensorflow/tensorflow.bzl b/tensorflow/tensorflow.bzl +index a1531f55cca..3b9c977dcc4 100644 +--- a/tensorflow/tensorflow.bzl ++++ b/tensorflow/tensorflow.bzl +@@ -1626,22 +1626,23 @@ def tf_gpu_cc_test( + linkopts = [], + **kwargs): + targets = [] +- tf_cc_test( +- name = name, +- size = size, +- srcs = srcs, +- args = args, +- data = data, +- extra_copts = extra_copts + if_cuda(["-DNV_CUDNN_DISABLE_EXCEPTION"]), +- kernels = kernels, +- linkopts = linkopts, +- linkstatic = linkstatic, +- suffix = "_cpu", +- tags = tags, +- deps = deps, +- **kwargs +- ) +- targets.append(name + "_cpu") ++ if 'gpu' not in tags: ++ tf_cc_test( ++ name = name, ++ size = size, ++ srcs = srcs, ++ args = args, ++ data = data, ++ extra_copts = extra_copts + if_cuda(["-DNV_CUDNN_DISABLE_EXCEPTION"]), ++ kernels = kernels, ++ linkopts = linkopts, ++ linkstatic = linkstatic, ++ suffix = "_cpu", ++ tags = tags, ++ deps = deps, ++ **kwargs ++ ) ++ targets.append(name + "_cpu") + tf_cc_test( + name = name, + size = size, diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1_remove-io-gcs-filesystem-dep.patch b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1_remove-io-gcs-filesystem-dep.patch new file mode 100644 index 00000000000..911d4b651ed --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1_remove-io-gcs-filesystem-dep.patch @@ -0,0 +1,12 @@ +diff --git a/tensorflow/tools/pip_package/setup.py b/tensorflow/tools/pip_package/setup.py +index 17ba9dc3323..c62900882ad 100644 +--- a/tensorflow/tools/pip_package/setup.py ++++ b/tensorflow/tools/pip_package/setup.py +@@ -101,7 +101,6 @@ REQUIRED_PACKAGES = [ + 'termcolor >= 1.1.0', + 'typing_extensions >= 3.6.6', + 'wrapt >= 1.11.0, < 1.15', +- 'tensorflow-io-gcs-filesystem >= 0.23.1', + # grpcio does not build correctly on big-endian machines due to lack of + # BoringSSL support. + # See https://github.com/tensorflow/tensorflow/issues/17882. diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1_remove-libclang-dep.patch b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1_remove-libclang-dep.patch new file mode 100644 index 00000000000..377c6e5a377 --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1_remove-libclang-dep.patch @@ -0,0 +1,12 @@ +diff --git a/tensorflow/tools/pip_package/setup.py b/tensorflow/tools/pip_package/setup.py +index fc5fd364c47..17ba9dc3323 100644 +--- a/tensorflow/tools/pip_package/setup.py ++++ b/tensorflow/tools/pip_package/setup.py +@@ -88,7 +88,6 @@ REQUIRED_PACKAGES = [ + 'gast >=0.2.1,!=0.5.0,!=0.5.1,!=0.5.2', + 'google_pasta >= 0.1.1', + 'h5py >= 2.9.0', +- 'libclang >= 13.0.0', + 'ml_dtypes ~= 0.3.1', + 'numpy >= 1.23.5, < 2.0.0', + 'opt_einsum >= 2.3.2', diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.3.1-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.3.1-foss-2020a-Python-3.8.2.eb index 2cfb8444ca4..daa5022fb1f 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.3.1-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.3.1-foss-2020a-Python-3.8.2.eb @@ -40,9 +40,7 @@ dependencies = [ ('zlib', '1.2.11'), ] -exts_default_options = { - 'sanity_pip_check': True, -} +sanity_pip_check = True use_pip = True # Dependencies created and updated using findPythonDeps.sh: diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.3.1-fosscuda-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.3.1-fosscuda-2020a-Python-3.8.2.eb index 54fdbc44964..7a4a7766ca6 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.3.1-fosscuda-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.3.1-fosscuda-2020a-Python-3.8.2.eb @@ -42,9 +42,7 @@ dependencies = [ ('zlib', '1.2.11'), ] -exts_default_options = { - 'sanity_pip_check': True, -} +sanity_pip_check = True use_pip = True # Dependencies created and updated using findPythonDeps.sh: diff --git a/easybuild/easyconfigs/t/TestU01/TestU01-1.2.3-GCCcore-13.2.0.eb b/easybuild/easyconfigs/t/TestU01/TestU01-1.2.3-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..08b769c2f8d --- /dev/null +++ b/easybuild/easyconfigs/t/TestU01/TestU01-1.2.3-GCCcore-13.2.0.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'TestU01' +version = '1.2.3' + +homepage = 'https://simul.iro.umontreal.ca/testu01/tu01.html' +description = "Utilities for the empirical statistical testing of uniform random number generators" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://simul.iro.umontreal.ca/testu01/'] +sources = ['%(name)s.zip'] +checksums = ['bc1d1dd2aea7ed3b3d28eaad2c8ee55913f11ce67aec8fe4f643c1c0d2ed1cac'] + +builddependencies = [('binutils', '2.40')] + +sanity_check_paths = { + 'files': ['bin/tcode', 'lib/libmylib.%s' % SHLIB_EXT, + 'lib/libprobdist.%s' % SHLIB_EXT, 'lib/libtestu01.%s' % SHLIB_EXT], + 'dirs': ['bin', 'include', 'lib', 'share/TestU01/doc'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.14-GCCcore-13.3.0.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.14-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..4069dc5a048 --- /dev/null +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.14-GCCcore-13.3.0.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'Tk' +version = '8.6.14' + +homepage = 'https://www.tcl.tk/' +description = """Tk is an open source, cross-platform widget toolchain that provides a library of basic elements for + building a graphical user interface (GUI) in many different programming languages.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ["https://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] +checksums = ['8ffdb720f47a6ca6107eac2dd877e30b0ef7fac14f3a84ebbd0b3612cee41a94'] + +builddependencies = [('binutils', '2.42')] +dependencies = [ + ('Tcl', version), + ('X11', '20240607'), + ('zlib', '1.3.1'), +] + +configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib CFLAGS="-I$EBROOTTCL/include"' + +installopts = "&& make install-private-headers" + +postinstallcmds = ["ln -s wish%(version_major_minor)s %(installdir)s/bin/wish"] + +sanity_check_paths = { + 'files': ["bin/wish", "lib/tkConfig.sh", "include/tkInt.h"], + 'dirs': [], +} + +start_dir = 'unix' + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/t/Tkinter/Tkinter-3.12.3-GCCcore-13.3.0.eb b/easybuild/easyconfigs/t/Tkinter/Tkinter-3.12.3-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..00f02ee6424 --- /dev/null +++ b/easybuild/easyconfigs/t/Tkinter/Tkinter-3.12.3-GCCcore-13.3.0.eb @@ -0,0 +1,25 @@ +name = 'Tkinter' +version = '3.12.3' + +homepage = 'https://python.org/' +description = "Tkinter module, built with the Python buildsystem" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.python.org/ftp/python/%(version)s/'] +sources = ['Python-%(version)s.tgz'] +checksums = ['a6b9459f45a6ebbbc1af44f5762623fa355a0c87208ed417628b379d762dddb0'] + +builddependencies = [ + ('binutils', '2.42'), + ('libffi', '3.4.5'), +] + +dependencies = [ + ('Python', '3.12.3'), + ('Tk', '8.6.14'), + ('zlib', '1.3.1'), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/t/TorchIO/TorchIO-0.19.6-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/t/TorchIO/TorchIO-0.19.6-foss-2023a-CUDA-12.1.1.eb new file mode 100644 index 00000000000..ed04f4a9f40 --- /dev/null +++ b/easybuild/easyconfigs/t/TorchIO/TorchIO-0.19.6-foss-2023a-CUDA-12.1.1.eb @@ -0,0 +1,60 @@ +easyblock = 'PythonBundle' + +name = 'TorchIO' +version = '0.19.6' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://torchio.readthedocs.io/' +description = """ +TorchIO is an open-source Python library for efficient loading, preprocessing, +augmentation and patch-based sampling of 3D medical images in deep learning, +following the design of PyTorch. + +It includes multiple intensity and spatial transforms for data augmentation and +preprocessing. These transforms include typical computer vision operations such +as random affine transformations and also domain-specific ones such as +simulation of intensity artifacts due to MRI magnetic field inhomogeneity +(bias) or k-space motion artifacts.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [ + ('hatchling', '1.18.0'), +] + +dependencies = [ + ('CUDA', '12.1.1', '', SYSTEM), + ('Python', '3.11.3'), + ('PyTorch', '2.1.2', versionsuffix), + ('tqdm', '4.66.1'), + ('Deprecated', '1.2.14'), + ('SimpleITK', '2.3.1'), + ('NiBabel', '5.2.0'), +] + +use_pip = True + +exts_list = [ + ('humanize', '4.8.0', { + 'checksums': ['9783373bf1eec713a770ecaa7c2d7a7902c98398009dfa3d8a2df91eec9311e8'], + }), + ('typer', '0.9.0', { + 'checksums': ['50922fd79aea2f4751a8e0408ff10d2662bd0c8bbfa84755a699f3bada2978b2'], + }), + ('torchio', version, { + 'checksums': ['c3afe16c3d822b6cb4aa103ffd6ec28816c95faa03cbeb22f33ff4cf81ec05df'], + }), +] + +_bins = ['tiohd', 'tiotr', 'torchio-transform'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in _bins], + 'dirs': ['lib/python%(pyshortver)s/site-packages/'], +} + +sanity_check_commands = ['%s --help' % x for x in _bins] + +sanity_pip_check = True + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/t/TransDecoder/TransDecoder-5.7.1-GCC-12.3.0.eb b/easybuild/easyconfigs/t/TransDecoder/TransDecoder-5.7.1-GCC-12.3.0.eb new file mode 100644 index 00000000000..3f1bbc6fe83 --- /dev/null +++ b/easybuild/easyconfigs/t/TransDecoder/TransDecoder-5.7.1-GCC-12.3.0.eb @@ -0,0 +1,35 @@ +easyblock = 'Tarball' + +name = 'TransDecoder' +version = '5.7.1' + +homepage = 'https://github.com/TransDecoder/TransDecoder/wiki' +description = """TransDecoder identifies candidate coding regions within transcript sequences, + such as those generated by de novo RNA-Seq transcript assembly using Trinity, + or constructed based on RNA-Seq alignments to the genome using + Tophat and Cufflinks.""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +source_urls = ['https://github.com/TransDecoder/TransDecoder/archive/'] +sources = ['TransDecoder-v%(version)s.tar.gz'] +checksums = ['41dd5e95f6ba946ff21340417d867e5e99f123b4035779b25d3cffd20b828a30'] + +dependencies = [ + ('Perl', '5.36.1'), + ('CD-HIT', '4.8.1'), +] + +sanity_check_paths = { + 'files': ['TransDecoder.LongOrfs', 'TransDecoder.Predict'], + 'dirs': ['PerlLib', 'sample_data', 'util'], +} + +sanity_check_commands = [] + +modextrapaths = { + 'PATH': '', + 'PERL5LIB': 'PerlLib', +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/t/Transformers/Transformers-4.39.3-gfbf-2023a.eb b/easybuild/easyconfigs/t/Transformers/Transformers-4.39.3-gfbf-2023a.eb index cef130c9947..421741f8832 100644 --- a/easybuild/easyconfigs/t/Transformers/Transformers-4.39.3-gfbf-2023a.eb +++ b/easybuild/easyconfigs/t/Transformers/Transformers-4.39.3-gfbf-2023a.eb @@ -8,27 +8,19 @@ description = """State-of-the-art Natural Language Processing for PyTorch and Te toolchain = {'name': 'gfbf', 'version': '2023a'} -_rust_ver = '1.75.0' -builddependencies = [ - ('Rust', _rust_ver), - ('maturin', '1.4.0', '-Rust-%s' % _rust_ver), -] - dependencies = [ ('Python', '3.11.3'), ('SciPy-bundle', '2023.07'), ('PyYAML', '6.0'), ('tqdm', '4.66.1'), ('tokenizers', '0.15.2'), + ('Safetensors', '0.4.3'), ] use_pip = True sanity_pip_check = True exts_list = [ - ('safetensors', '0.4.2', { - 'checksums': ['acc85dcb09ec5e8aa787f588d7ad4d55c103f31e4ff060e17d92cc0e8b8cac73'], - }), ('regex', '2023.12.25', { 'checksums': ['29171aa128da69afdf4bde412d5bedc335f2ca8fcfe4489038577d05f16181e5'], }), diff --git a/easybuild/easyconfigs/t/Transformers/Transformers-4.44.0-gfbf-2023b.eb b/easybuild/easyconfigs/t/Transformers/Transformers-4.44.0-gfbf-2023b.eb new file mode 100644 index 00000000000..94a257d4b18 --- /dev/null +++ b/easybuild/easyconfigs/t/Transformers/Transformers-4.44.0-gfbf-2023b.eb @@ -0,0 +1,36 @@ +easyblock = 'PythonBundle' + +name = 'Transformers' +version = '4.44.0' + +homepage = 'https://github.com/huggingface/transformers' +description = """State-of-the-art Natural Language Processing for PyTorch and TensorFlow 2.0""" + +toolchain = {'name': 'gfbf', 'version': '2023b'} + +dependencies = [ + ('Python', '3.11.5'), + ('SciPy-bundle', '2023.11'), + ('PyYAML', '6.0.1'), + ('tqdm', '4.66.2'), + ('tokenizers', '0.19.1'), # tokenizers>=0.19,<0.20 + ('Safetensors', '0.4.4'), # safetensors>=0.4.1 +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('regex', '2024.7.24', { + 'checksums': ['9cfd009eed1a46b27c14039ad5bbc5e71b6367c5b2e6d5f5da0ea91600817506'], + }), + ('transformers', version, { + 'checksums': ['75699495e30b7635ca444d8d372e138c687ab51a875b387e33f1fb759c37f196'], + }), +] + +sanity_check_commands = [ + "python -c 'from transformers import AutoTokenizer'", +] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/t/Transrate/Transrate-1.0.3-GCC-12.3.0.eb b/easybuild/easyconfigs/t/Transrate/Transrate-1.0.3-GCC-12.3.0.eb new file mode 100644 index 00000000000..a70ecf2a901 --- /dev/null +++ b/easybuild/easyconfigs/t/Transrate/Transrate-1.0.3-GCC-12.3.0.eb @@ -0,0 +1,39 @@ +easyblock = 'RubyGem' + +name = 'Transrate' +version = '1.0.3' + +homepage = 'https://hibberdlab.com/transrate' +description = """Transrate is software for de-novo transcriptome assembly quality analysis. + It examines your assembly in detail and compares it to experimental evidence such as the sequencing reads, + reporting quality scores for contigs and assemblies. This allows you to choose between assemblers and parameters, + filter out the bad contigs from an assembly, and help decide when to stop trying to improve the assembly.""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +source_urls = ['https://github.com/blahah/transrate/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = ['Transrate-1.0.3_undefined_method_fix.patch'] +checksums = [ + {'v1.0.3.tar.gz': '2ccb101cfab5a33586ea9e62af2b2f14caf6bc016724d1fef796b427e39fe100'}, + {'Transrate-1.0.3_undefined_method_fix.patch': 'ead5e51318d6d810fb11b783d517ea38648f62ae2bdd5f3f4dac7baa9ae94d95'}, +] + +dependencies = [ + ('Ruby', '3.3.0'), + ('crb-blast', '0.6.9'), + ('colorize', '0.7.7'), + ('yell', '2.2.2'), +] + +# requirement is too strict +preinstallopts = """sed -i "s/'yell', '~> 2.0',/'yell',/g" transrate.gemspec && """ + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': ['gems/%(namelower)s-%(version)s'], +} + +sanity_check_commands = ["%(namelower)s --help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/t/Transrate/Transrate-1.0.3_undefined_method_fix.patch b/easybuild/easyconfigs/t/Transrate/Transrate-1.0.3_undefined_method_fix.patch new file mode 100644 index 00000000000..47526bd2242 --- /dev/null +++ b/easybuild/easyconfigs/t/Transrate/Transrate-1.0.3_undefined_method_fix.patch @@ -0,0 +1,42 @@ +to avoid the `terminal_columns': undefined method `winsize' for nil (NoMethodError)` error +Author: Petr Král (INUITS) +--- lib/transrate/cmdline.rb.orig 2016-06-06 15:10:26.000000000 +0200 ++++ lib/transrate/cmdline.rb 2024-07-25 11:23:20.250369056 +0200 +@@ -87,11 +87,6 @@ + end + end + +- def terminal_columns +- require 'io/console' +- IO.console.winsize.last +- end +- + def help_message + <<-EOS + +@@ -117,19 +112,17 @@ + end + + def transrate_banner +- if terminal_columns > 70 +- txp = '░▓▓▓^▓▓▓░' +- toptxp = txp.green +- midtxp = txp.yellow +- bottxp = txp.red +- puts <<-EOS ++ txp = '░▓▓▓^▓▓▓░' ++ toptxp = txp.green ++ midtxp = txp.yellow ++ bottxp = txp.red ++ puts <<-EOS + _ _ + | |_ _ __ __ _ _ __ ___ _ __ __ _ | |_ ___ + #{toptxp} | __|| '__|/ _` || '_ \\ / __|| '__|/ _` || __|/ _ \\ #{toptxp} + #{midtxp} | |_ | | | (_| || | | |\\__ \\| | | (_| || |_| __/ #{midtxp} + #{bottxp} \\__||_| \\__,_||_| |_||___/|_| \\__,_| \\__|\\___| #{bottxp} +- EOS +- end ++ EOS + "" + end + diff --git a/easybuild/easyconfigs/t/Triangle/Triangle-1.6-GCCcore-13.2.0.eb b/easybuild/easyconfigs/t/Triangle/Triangle-1.6-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..12d41a6857e --- /dev/null +++ b/easybuild/easyconfigs/t/Triangle/Triangle-1.6-GCCcore-13.2.0.eb @@ -0,0 +1,44 @@ +easyblock = 'MakeCp' + +name = 'Triangle' +version = '1.6' + +homepage = 'https://www.cs.cmu.edu/~quake/triangle.html' +description = """Triangle generates exact Delaunay triangulations, constrained Delaunay triangulations, + conforming Delaunay triangulations, Voronoi diagrams, and high-quality triangular meshes. + The latter can be generated with no small or large angles, + and are thus suitable for finite element analysis.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.netlib.org/voronoi/'] +sources = ['%(namelower)s.zip'] +checksums = [ + '1766327add038495fa3499e9b7cc642179229750f7201b94f8e1b7bee76f8480', # triangle.zip + '38fc1395c2392f627068b669275c30da0c25b1a6db8ed8b80d6bf05a98971568', # Triangle-1.6_makefile.patch +] + +patches = ['%(name)s-%(version)s_makefile.patch'] + +builddependencies = [('binutils', '2.40')] + +buildopts = 'triangle trilibrary' + +files_to_copy = [ + (['triangle', 'tricall'], 'bin'), + (['triangle.h'], 'include'), + (['libtriangle.a'], 'lib'), +] + +sanity_check_paths = { + 'files': ['bin/triangle', 'bin/tricall', 'include/triangle.h', 'lib/libtriangle.a'], + 'dirs': [] +} + +sanity_check_commands = [ + 'triangle -h', + 'tricall', +] + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.6.10-GCCcore-12.3.0.eb b/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.6.10-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..bf5c351c4fd --- /dev/null +++ b/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.6.10-GCCcore-12.3.0.eb @@ -0,0 +1,46 @@ +# Contribution from the Crick HPC team +# uploaded by J. Sassmannshausen +# Updated to version 0.6.2: Pavel Grochal (INUITS) +# Updated to version 0.6.5: Alex Domingo (VUB) +# Updated to version 0.6.7 by J. Sassmannshausen NHS/GSTT + +easyblock = 'Tarball' + +name = 'Trim_Galore' +version = '0.6.10' + +homepage = 'https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/' +description = """Trim Galore! is a wrapper script to automate quality and adapter +trimming as well as quality control, with some added functionality to remove biased +methylation positions for RRBS sequence files (for directional, non-directional +(or paired-end) sequencing).""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://github.com/FelixKrueger/TrimGalore/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['3a4e414fc658d6eb4356f1572351204e8475a9d7dc79f6798270b57d35bda017'] + +dependencies = [ + ('Python', '3.11.3'), + ('Java', '11', '', SYSTEM), + ('pigz', '2.8'), + ('Perl', '5.36.1'), + ('cutadapt', '4.9'), + ('FastQC', '0.11.9', '-Java-%(javaver)s', SYSTEM), +] + +postinstallcmds = [ + "mkdir %(installdir)s/bin && mv %(installdir)s/%(namelower)s %(installdir)s/bin/%(namelower)s", +] + +fix_perl_shebang_for = ['bin/%(namelower)s'] + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': [], +} + +sanity_check_commands = [('%(namelower)s', '-v')] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/t/Trimmomatic/Trimmomatic-0.39-Java-11.eb b/easybuild/easyconfigs/t/Trimmomatic/Trimmomatic-0.39-Java-11.eb index b5a28e53771..4108cd9de19 100644 --- a/easybuild/easyconfigs/t/Trimmomatic/Trimmomatic-0.39-Java-11.eb +++ b/easybuild/easyconfigs/t/Trimmomatic/Trimmomatic-0.39-Java-11.eb @@ -22,11 +22,18 @@ checksums = ['2f97e3a237378d55c221abfc38e4b11ea232c8a41d511b8b4871f00c0476abca'] dependencies = [('Java', '11')] -modloadmsg = """To execute Trimmomatic run: java -jar $EBROOTTRIMMOMATIC/trimmomatic-%(version)s.jar\n""" +postinstallcmds = [ + "mkdir %(installdir)s/bin", + """echo -e '#!/bin/bash\nexec java -jar "$EBROOTTRIMMOMATIC"/trimmomatic-*.jar "$@"' """ + """> %(installdir)s/bin/trimmomatic""", + "chmod a+rx %(installdir)s/bin/trimmomatic", +] sanity_check_paths = { - 'files': ["trimmomatic-%(version)s.jar"], + 'files': ["trimmomatic-%(version)s.jar", 'bin/trimmomatic'], 'dirs': [""], } +sanity_check_commands = ['trimmomatic -version'] + moduleclass = 'bio' diff --git a/easybuild/easyconfigs/t/Trimmomatic/Trimmomatic-0.39-Java-17.eb b/easybuild/easyconfigs/t/Trimmomatic/Trimmomatic-0.39-Java-17.eb index 5f9d39b5c69..bd49df5d0a8 100644 --- a/easybuild/easyconfigs/t/Trimmomatic/Trimmomatic-0.39-Java-17.eb +++ b/easybuild/easyconfigs/t/Trimmomatic/Trimmomatic-0.39-Java-17.eb @@ -22,11 +22,18 @@ checksums = ['2f97e3a237378d55c221abfc38e4b11ea232c8a41d511b8b4871f00c0476abca'] dependencies = [('Java', '17')] -modloadmsg = """To execute Trimmomatic run: java -jar $EBROOTTRIMMOMATIC/trimmomatic-%(version)s.jar\n""" +postinstallcmds = [ + "mkdir %(installdir)s/bin", + """echo -e '#!/bin/bash\nexec java -jar "$EBROOTTRIMMOMATIC"/trimmomatic-*.jar "$@"' """ + """> %(installdir)s/bin/trimmomatic""", + "chmod a+rx %(installdir)s/bin/trimmomatic", +] sanity_check_paths = { - 'files': ["trimmomatic-%(version)s.jar"], + 'files': ["trimmomatic-%(version)s.jar", 'bin/trimmomatic'], 'dirs': [""], } +sanity_check_commands = ['trimmomatic -version'] + moduleclass = 'bio' diff --git a/easybuild/easyconfigs/t/Trinity/Trinity-2.15.2-foss-2023a.eb b/easybuild/easyconfigs/t/Trinity/Trinity-2.15.2-foss-2023a.eb new file mode 100644 index 00000000000..7c85236b0a4 --- /dev/null +++ b/easybuild/easyconfigs/t/Trinity/Trinity-2.15.2-foss-2023a.eb @@ -0,0 +1,65 @@ +## +# This is a contribution from DeepThought HPC Service, Flinders University, Adelaide, Australia +# Homepage: https://staff.flinders.edu.au/research/deep-thought +# +# Authors:: Robert Qiao +# License:: Custom +# +# Notes:: +## + +name = 'Trinity' +version = '2.15.2' + +homepage = 'https://trinityrnaseq.github.io' +description = """Trinity represents a novel method for the efficient and robust de novo reconstruction + of transcriptomes from RNA-Seq data. Trinity combines three independent software modules: Inchworm, + Chrysalis, and Butterfly, applied sequentially to process large volumes of RNA-Seq reads.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['https://github.com/trinityrnaseq/trinityrnaseq/releases/download/%(name)s-v%(version)s'] +sources = ['trinityrnaseq-v%(version)s.FULL.tar.gz'] +patches = ['Trinity-%(version)s_fix-bamsifter.patch'] +checksums = [ + {'trinityrnaseq-v2.15.2.FULL.tar.gz': 'baab87e4878ad097e265c46de121414629bf88fa9342022baae5cac12432a15c'}, + {'Trinity-2.15.2_fix-bamsifter.patch': 'f557a3d462218e27f3601ac07edd2bbafe5fdb088ab81f642e7025edfe3e48ef'}, +] + +builddependencies = [ + ('Autotools', '20220317'), + ('CMake', '3.26.3'), +] + +# for reference, list of dependencies in the container image used upstream: +# https://github.com/trinityrnaseq/trinityrnaseq/blob/master/Docker/Dockerfile +dependencies = [ + ('Java', '11', '', SYSTEM), + ('ant', '1.10.14', '-Java-%(javaver)s', SYSTEM), + ('picard', '2.25.1', '-Java-%(javaver)s', SYSTEM), + ('GATK', '4.3.0.0', '-Java-%(javaver)s'), + ('Perl', '5.36.1'), + ('Perl-bundle-CPAN', '5.36.1'), + ('DB', '18.1.40'), # for DB_File + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('BLAST+', '2.14.1'), + ('BLAT', '3.7'), + ('Bowtie', '1.3.1'), + ('Bowtie2', '2.5.1'), + ('GMAP-GSNAP', '2023-04-20'), + ('HISAT2', '2.2.1'), + ('HTSlib', '1.18'), + ('Jellyfish', '2.3.1'), + ('kallisto', '0.51.1'), + ('ncurses', '6.4'), + ('RSEM', '1.3.3'), + ('Salmon', '1.10.3'), + ('SAMtools', '1.18'), + ('STAR', '2.7.11a'), + ('zlib', '1.2.13'), +] + +withsampledata = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/t/Trinity/Trinity-2.15.2_fix-bamsifter.patch b/easybuild/easyconfigs/t/Trinity/Trinity-2.15.2_fix-bamsifter.patch new file mode 100644 index 00000000000..9e414a414f1 --- /dev/null +++ b/easybuild/easyconfigs/t/Trinity/Trinity-2.15.2_fix-bamsifter.patch @@ -0,0 +1,18 @@ +Fix build of Trinity plugin bamsifter: +* use external HTSlib from EasyBuild environment +* use compilation flags from environment +author: Alex Domingo (Vrije Universiteit Brussel) +diff -ru trinityrnaseq-v2.15.2.orig/trinity-plugins/bamsifter/Makefile trinityrnaseq-v2.15.2/trinity-plugins/bamsifter/Makefile +--- trinityrnaseq-v2.15.2.orig/trinity-plugins/bamsifter/Makefile 2024-08-01 14:53:23.000000000 +0200 ++++ trinityrnaseq-v2.15.2/trinity-plugins/bamsifter/Makefile 2024-10-21 07:50:10.911559350 +0200 +@@ -2,8 +2,8 @@ + + cwd = $(shell pwd) + +-sift_bam_max_cov: sift_bam_max_cov.cpp htslib/version.h +- g++ -std=c++11 -o _sift_bam_max_cov sift_bam_max_cov.cpp -Wall -O2 -L./htslib/build/lib/ -I./htslib/build/include -lhts ++sift_bam_max_cov: sift_bam_max_cov.cpp ++ g++ -std=c++11 $(CXXFLAGS) -Wall -I$(EBROOTHTSLIB)/include -L$(EBROOTHTSLIB)/lib -lhts -o _sift_bam_max_cov sift_bam_max_cov.cpp + + + htslib/version.h : diff --git a/easybuild/easyconfigs/t/Trinotate/Trinotate-4.0.2-foss-2023a.eb b/easybuild/easyconfigs/t/Trinotate/Trinotate-4.0.2-foss-2023a.eb new file mode 100644 index 00000000000..b5c3d27e371 --- /dev/null +++ b/easybuild/easyconfigs/t/Trinotate/Trinotate-4.0.2-foss-2023a.eb @@ -0,0 +1,55 @@ +easyblock = 'Tarball' +name = 'Trinotate' +version = '4.0.2' + +homepage = 'https://github.com/Trinotate/Trinotate/wiki' +description = """Trinotate is a comprehensive annotation suite designed for automatic functional +annotation of transcriptomes, particularly de novo assembled transcriptomes, +from model or non-model organisms. Trinotate makes use of a number of different +well referenced methods for functional annotation including homology search to +known sequence data (BLAST+/SwissProt), protein domain identification +(HMMER/PFAM), protein signal peptide and transmembrane domain prediction +(signalP/tmHMM), and leveraging various annotation databases (eggNOG/GO/Kegg +databases). All functional annotation data derived from the analysis of +transcripts is integrated into a SQLite database which allows fast efficient +searching for terms with specific qualities related to a desired scientific +hypothesis or a means to create a whole annotation report for a transcriptome.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +github_account = '%(name)s' +source_urls = [GITHUB_SOURCE] +sources = ['%(name)s-v%(version)s.tar.gz'] +checksums = ['2f633df2e05e5d22e19159aa147060be7884a057314cad3e6db91dba8910fad1'] + +# # for reference, list of dependencies in the container image used upstream: +# # https://github.com/Trinotate/Trinotate/blob/master/Docker/Dockerfile +dependencies = [ + ('Perl', '5.36.1'), + ('Python', '3.11.3'), + ('Trinity', '2.15.2'), + ('BLAST+', '2.14.1'), + ('DIAMOND', '2.1.8'), + ('eggnog-mapper', '2.1.12'), + ('HMMER', '3.4'), + ('Infernal', '1.1.5'), + ('PyBioLib', '1.1.2250'), + ('SAMtools', '1.18'), + ('TransDecoder', '5.7.1'), +] + +sanity_check_paths = { + 'files': ['Trinotate', 'run_TrinotateWebserver.pl'], + 'dirs': ['PerlLib', 'resources', 'testing', 'util'], +} + +sanity_check_commands = [ + 'Trinotate --help 2>&1 | grep -q "Trinotate --db "', +] + +modextrapaths = { + 'PATH': '', + 'PERL5LIB': 'PerlLib', +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/t/Triton/Triton-2.1.0-disable_rocm_support.patch b/easybuild/easyconfigs/t/Triton/Triton-2.1.0-disable_rocm_support.patch new file mode 100644 index 00000000000..13d736b4bfc --- /dev/null +++ b/easybuild/easyconfigs/t/Triton/Triton-2.1.0-disable_rocm_support.patch @@ -0,0 +1,88 @@ +Disable experimental support for AMD GPUs +author: Alex Domingo (Vrije Universiteit Brussel) +author: Samuel Moors (Vrije Universiteit Brussel) +diff -ur triton-2.1.0.orig/CMakeLists.txt triton-2.1.0/CMakeLists.txt +--- triton-2.1.0.orig/CMakeLists.txt 2023-09-01 08:28:27.000000000 +0200 ++++ triton-2.1.0/CMakeLists.txt 2024-09-01 10:40:17.863374000 +0200 +@@ -70,7 +70,7 @@ + AMDGPUInfo AMDGPUcodegen + ) + else() +- find_package(LLVM 11 REQUIRED COMPONENTS "nvptx;amdgpu") ++ find_package(LLVM 11 REQUIRED COMPONENTS "nvptx") + endif() + + message(STATUS "Found LLVM ${LLVM_PACKAGE_VERSION}") +@@ -89,9 +89,7 @@ + LLVMNVPTXCodeGen + LLVMNVPTXDesc + LLVMNVPTXInfo +- LLVMAMDGPUDisassembler + LLVMMCDisassembler +- LLVMAMDGPUCodeGen + LLVMMIRParser + LLVMGlobalISel + LLVMSelectionDAG +@@ -116,10 +114,7 @@ + LLVMObject + LLVMTextAPI + LLVMBitReader +- LLVMAMDGPUAsmParser + LLVMMCParser +- LLVMAMDGPUDesc +- LLVMAMDGPUUtils + LLVMMC + LLVMDebugInfoCodeView + LLVMDebugInfoMSF +@@ -127,7 +122,6 @@ + LLVMRemarks + LLVMBitstreamReader + LLVMBinaryFormat +- LLVMAMDGPUInfo + LLVMSupport + LLVMDemangle + LLVMPasses +diff -ur triton-2.1.0.orig/lib/Target/HSACO/HSACOTranslation.cpp triton-2.1.0/lib/Target/HSACO/HSACOTranslation.cpp +--- triton-2.1.0.orig/lib/Target/HSACO/HSACOTranslation.cpp 2023-09-01 08:28:27.000000000 +0200 ++++ triton-2.1.0/lib/Target/HSACO/HSACOTranslation.cpp 2024-09-02 21:27:09.233712000 +0200 +@@ -37,13 +37,6 @@ + + namespace { + +-void init_llvm() { +- LLVMInitializeAMDGPUTarget(); +- LLVMInitializeAMDGPUTargetInfo(); +- LLVMInitializeAMDGPUTargetMC(); +- LLVMInitializeAMDGPUAsmParser(); +- LLVMInitializeAMDGPUAsmPrinter(); +-} + + std::unique_ptr + initialize_module(llvm::Module *module, const std::string &triple, +@@ -155,7 +148,6 @@ + llir_to_amdgcn_and_hsaco(llvm::Module *module, std::string gfx_arch, + std::string gfx_triple, std::string gfx_features) { + +- init_llvm(); + + // verify and store llvm + auto module_obj = llvm::CloneModule(*module); +diff -ur triton-2.1.0.orig/python/src/triton.cc triton-2.1.0/python/src/triton.cc +--- triton-2.1.0.orig/python/src/triton.cc 2023-09-01 08:28:27.000000000 +0200 ++++ triton-2.1.0/python/src/triton.cc 2024-09-01 10:41:29.146862440 +0200 +@@ -60,7 +60,6 @@ + enum backend_t { + HOST, + CUDA, +- ROCM, + }; + + void init_triton_runtime(py::module &&m) { +@@ -68,7 +67,6 @@ + py::enum_(m, "backend", py::module_local()) + .value("HOST", HOST) + .value("CUDA", CUDA) +- .value("ROCM", ROCM) + .export_values(); + } + diff --git a/easybuild/easyconfigs/t/Triton/Triton-2.1.0-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/t/Triton/Triton-2.1.0-foss-2023a-CUDA-12.1.1.eb new file mode 100644 index 00000000000..a1cdbe87df3 --- /dev/null +++ b/easybuild/easyconfigs/t/Triton/Triton-2.1.0-foss-2023a-CUDA-12.1.1.eb @@ -0,0 +1,56 @@ +easyblock = 'PythonPackage' + +name = 'Triton' +version = '2.1.0' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://triton-lang.org/' + +description = """Triton is a language and compiler for parallel programming. It aims to provide a +Python-based programming environment for productively writing custom DNN compute +kernels capable of running at maximal throughput on modern GPU hardware.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +github_account = 'openai' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] +patches = [ + '%(name)s-%(version)s-disable_rocm_support.patch', + '%(name)s-%(version)s-use_eb_env_python_build.patch', +] +checksums = [ + {'v2.1.0.tar.gz': '4338ca0e80a059aec2671f02bfc9320119b051f378449cf5f56a1273597a3d99'}, + {'Triton-2.1.0-disable_rocm_support.patch': 'e4d7c0947c3287b3f0871a004e8b483963f637c9fa3ef6212ac3a34660de2a7c'}, + {'Triton-2.1.0-use_eb_env_python_build.patch': 'd68bf766c699ad6a778d9449d3bccdadc2f20f1f86ba13e1359ad297b12fbf7c'}, +] + +builddependencies = [ + ('Clang', '17.0.0_20230515', versionsuffix), # this is the exact commit that would be downloaded by Triton + ('CMake', '3.26.3'), +] + +dependencies = [ + ('CUDA', '12.1.1', '', SYSTEM), + ('Python', '3.11.3'), + ('PyTorch', '2.1.2', versionsuffix), +] + +use_pip = True +download_dep_fail = True + +start_dir = 'python' + +preinstallopts = 'export LLVM_INCLUDE_DIRS=$EBROOTCLANG/include && ' +preinstallopts += 'export LLVM_LIBRARY_DIR=$EBROOTCLANG/lib && ' +preinstallopts += 'export LLVM_SYSPATH=$EBROOTCLANG && ' +preinstallopts += 'export TRITON_BUILD_WITH_CLANG_LLD=1 && ' + +# make pip print output of cmake +installopts = "-v " + +sanity_pip_check = True + +modluafooter = 'setenv("TRITON_PTXAS_PATH", pathJoin(os.getenv("CUDA_HOME"), "bin", "ptxas"))' + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/t/Triton/Triton-2.1.0-use_eb_env_python_build.patch b/easybuild/easyconfigs/t/Triton/Triton-2.1.0-use_eb_env_python_build.patch new file mode 100644 index 00000000000..650134e73be --- /dev/null +++ b/easybuild/easyconfigs/t/Triton/Triton-2.1.0-use_eb_env_python_build.patch @@ -0,0 +1,93 @@ +Fix Triton cmake build to use dependencies from EasyBuild +author: Alex Domingo (Vrije Universiteit Brussel) +author: Samuel Moors (Vrije Universiteit Brussel) +diff -ur triton-2.1.0.orig/lib/Target/LLVMIR/LLVMIRTranslation.cpp triton-2.1.0/lib/Target/LLVMIR/LLVMIRTranslation.cpp +--- triton-2.1.0.orig/lib/Target/LLVMIR/LLVMIRTranslation.cpp 2023-09-01 08:28:27.000000000 +0200 ++++ triton-2.1.0/lib/Target/LLVMIR/LLVMIRTranslation.cpp 2024-09-02 19:46:06.574421829 +0200 +@@ -35,6 +35,7 @@ + #endif + #include + #include ++#include // for getenv + + namespace fs = std::filesystem; + +@@ -177,6 +178,7 @@ + } + + if (!funcs.empty()) { ++ std::filesystem::path cuda_home = std::getenv("CUDA_HOME"); + static const std::string libdevice = "libdevice"; + // first search for environmental path + std::string env_path = ::triton::tools::getenv("TRITON_LIBDEVICE_PATH"); +@@ -189,8 +191,7 @@ + // `triton/third_party/cuda/lib/libdevice.10.bc` + static const auto this_library_path = getThisLibraryPath(); + static const auto runtime_path = +- this_library_path.parent_path().parent_path() / "third_party" / "cuda" / +- "lib" / "libdevice.10.bc"; ++ cuda_home / "nvvm" / "libdevice" / "libdevice.10.bc"; + if (fs::exists(runtime_path)) { + externLibs.try_emplace(libdevice, runtime_path.string()); + } else { +diff -ur triton-2.1.0.orig/python/setup.py triton-2.1.0/python/setup.py +--- triton-2.1.0.orig/python/setup.py 2023-09-01 08:28:27.000000000 +0200 ++++ triton-2.1.0/python/setup.py 2024-09-02 18:16:58.044760300 +0200 +@@ -202,13 +202,13 @@ + + def build_extension(self, ext): + lit_dir = shutil.which('lit') +- user_home = os.getenv("HOME") or os.getenv("USERPROFILE") or \ +- os.getenv("HOMEPATH") or None +- if not user_home: +- raise RuntimeError("Could not find user home directory") +- triton_cache_path = os.path.join(user_home, ".triton") ++ # user_home = os.getenv("HOME") or os.getenv("USERPROFILE") or \ ++ # os.getenv("HOMEPATH") or None ++ # if not user_home: ++ # raise RuntimeError("Could not find user home directory") ++ # triton_cache_path = os.path.join(user_home, ".triton") + # lit is used by the test suite +- thirdparty_cmake_args = get_thirdparty_packages(triton_cache_path) ++ # thirdparty_cmake_args = get_thirdparty_packages(triton_cache_path) + extdir = os.path.abspath(os.path.dirname(self.get_ext_fullpath(ext.path))) + # create build directories + if not os.path.exists(self.build_temp): +@@ -216,8 +216,9 @@ + # python directories + python_include_dir = sysconfig.get_path("platinclude") + cmake_args = [ ++ "-DCMAKE_VERBOSE_MAKEFILE:BOOL=ON", + "-DCMAKE_EXPORT_COMPILE_COMMANDS=ON", +- "-DLLVM_ENABLE_WERROR=ON", ++ # "-DLLVM_ENABLE_WERROR=ON", + "-DCMAKE_LIBRARY_OUTPUT_DIRECTORY=" + extdir, + "-DTRITON_BUILD_TUTORIALS=OFF", + "-DTRITON_BUILD_PYTHON_MODULE=ON", +@@ -227,7 +228,7 @@ + ] + if lit_dir is not None: + cmake_args.append("-DLLVM_EXTERNAL_LIT=" + lit_dir) +- cmake_args.extend(thirdparty_cmake_args) ++ # cmake_args.extend(thirdparty_cmake_args) + + # configuration + cfg = get_build_type() +@@ -245,7 +246,7 @@ + build_args += ["--", "/m"] + else: + cmake_args += ["-DCMAKE_BUILD_TYPE=" + cfg] +- max_jobs = os.getenv("MAX_JOBS", str(2 * os.cpu_count())) ++ max_jobs = os.getenv("MAX_JOBS", str(len(os.sched_getaffinity(0)))) + build_args += ['-j' + max_jobs] + + if check_env_flag("TRITON_BUILD_WITH_CLANG_LLD"): +@@ -262,7 +263,7 @@ + subprocess.check_call(["cmake", "--build", "."] + build_args, cwd=cmake_dir) + + +-download_and_copy_ptxas() ++# download_and_copy_ptxas() + + + setup( diff --git a/easybuild/easyconfigs/t/Trycycler/Trycycler-0.5.5-foss-2023a-R-4.3.2.eb b/easybuild/easyconfigs/t/Trycycler/Trycycler-0.5.5-foss-2023a-R-4.3.2.eb new file mode 100644 index 00000000000..00aa967bdc2 --- /dev/null +++ b/easybuild/easyconfigs/t/Trycycler/Trycycler-0.5.5-foss-2023a-R-4.3.2.eb @@ -0,0 +1,46 @@ +easyblock = 'PythonBundle' + +name = 'Trycycler' +version = '0.5.5' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://github.com/rrwick/Trycycler' +description = """A tool for generating consensus long-read assemblies for bacterial genomes.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('R', '4.3.2'), + ('R-bundle-CRAN', '2023.12'), + ('edlib', '1.3.9'), + ('Pillow', '10.0.0'), + ('pytest', '7.4.2'), + ('minimap2', '2.26'), + ('miniasm', '0.3-20191007'), + ('Mash', '2.3'), + ('MUSCLE', '5.1.0'), +] + +use_pip = True + +exts_list = [ + (name, version, { + 'source_urls': ['https://github.com/rrwick/Trycycler/archive/'], + 'sources': ['v%(version)s.tar.gz'], + 'checksums': ['5794a4520c3b8673adc69c975cee06d7658cd74ac6d9378d1fc7af860bec1a89'], + 'runtest': 'pytest', + }), +] + +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/trycycler'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["trycycler --help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/t/TurboVNC/TurboVNC-3.1.2-GCCcore-13.3.0.eb b/easybuild/easyconfigs/t/TurboVNC/TurboVNC-3.1.2-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..5b532a99e9f --- /dev/null +++ b/easybuild/easyconfigs/t/TurboVNC/TurboVNC-3.1.2-GCCcore-13.3.0.eb @@ -0,0 +1,63 @@ +easyblock = 'CMakeMake' + +name = 'TurboVNC' +version = '3.1.2' + +homepage = 'https://www.turbovnc.org' +description = """TurboVNC is a derivative of VNC (Virtual Network Computing) that is tuned to provide + peak performance for 3D and video workloads.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://github.com/%(name)s/%(namelower)s/archive'] +sources = ['%(version)s.tar.gz'] + +checksums = [ + '98629cd2b676df5d30df51c69edd97cf99b395c3080cc55e2f997ac33a7d40de', # 3.0.1.tar.gz +] + +builddependencies = [ + ('binutils', '2.42'), + ('CMake', '3.29.3'), +] + +dependencies = [ + ('Java', '21.0.2', '', SYSTEM), + ('X11', '20240607'), + ('pixman', '0.43.4'), + ('libjpeg-turbo', '3.0.1'), + ('Mesa', '24.1.3'), + ('libGLU', '9.0.3'), + ('libglvnd', '1.7.0'), + ('OpenSSL', '3', '', SYSTEM), +] + +osdependencies = [('pam-devel', 'libpam0g-dev')] + +configopts = "-DTVNC_BUILDJAVA=0 -DTVNC_SYSTEMX11=1 " +configopts += "-DX11_X11_LIB=$EBROOTX11/lib/libX11.%s " % SHLIB_EXT +configopts += "-DX11_Xau_LIB=$EBROOTX11/lib/libXau.%s " % SHLIB_EXT +configopts += "-DX11_SM_LIB=$EBROOTX11/lib/libSM.%s " % SHLIB_EXT +configopts += "-DX11_ICE_LIB=$EBROOTX11/lib/libICE.%s " % SHLIB_EXT +configopts += "-DX11_Pixman_LIB=$EBROOTPIXMAN/lib/libpixman-1.%s.0 " % SHLIB_EXT +configopts += "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT +configopts += "-DOPENGL_egl_LIBRARY=$EBROOTLIBGLVND/lib/libEGL.%s " % SHLIB_EXT +configopts += "-DOPENGL_opengl_LIBRARY=$EBROOTLIBGLVND/lib/libOpenGL.%s " % SHLIB_EXT +configopts += "-DOPENGL_glx_LIBRARY=$EBROOTLIBGLVND/lib/libGLX.%s " % SHLIB_EXT + +# if installdir starts with /opt, i.e. /opt/xxx, CMake will set SYSCONFDIR to /etc/opt/xxx instead of /opt/xxx/etc +# https://cmake.org/cmake/help/latest/module/GNUInstallDirs.html +# the solution is to define CMAKE_INSTALL_SYSCONFDIR explicitly +configopts += "-DCMAKE_INSTALL_SYSCONFDIR=%(installdir)s/etc " + +# remove etc/turbovncserver-security.conf, to avoid errors like: +# (EE) Fatal server error: +# (EE) ERROR: .../TurboVNC/2.2.3-GCCcore-8.2.0/etc/turbovncserver-security.conf must be owned by you or by root +postinstallcmds = ['rm -rf %(installdir)s/etc/turbovncserver-security.conf'] + +sanity_check_paths = { + 'files': ['bin/vncserver', 'bin/vncpasswd', 'bin/Xvnc'], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/t/t-SNE-CUDA/t-SNE-CUDA-3.0.1-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/t/t-SNE-CUDA/t-SNE-CUDA-3.0.1-foss-2023a-CUDA-12.1.1.eb new file mode 100644 index 00000000000..880e2f47538 --- /dev/null +++ b/easybuild/easyconfigs/t/t-SNE-CUDA/t-SNE-CUDA-3.0.1-foss-2023a-CUDA-12.1.1.eb @@ -0,0 +1,58 @@ +# Author: Jasper Grimm (UoY) +easyblock = 'CMakePythonPackage' + +name = 't-SNE-CUDA' +version = '3.0.1' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/CannyLab/tsne-cuda' +description = "GPU Accelerated t-SNE for CUDA with Python bindings" + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['https://github.com/CannyLab/tsne-cuda/archive'] +sources = ['%(version)s.tar.gz'] +patches = [ + '%(name)s-3.0.1_use-external-cxxopts.patch', + '%(name)s-3.0.1_avoid-overriding-cuda-compute-capabilities.patch', +] +checksums = [ + {'3.0.1.tar.gz': '0f778247191f483df22dc4dbed792c9a6a9152ee7404329c4d9da3fd9a8774d6'}, + {'t-SNE-CUDA-3.0.1_use-external-cxxopts.patch': 'be278f6a122ac12b02e05faffd53f3bce3e58b1d6b40af5e6af6b4182c6a25f1'}, + {'t-SNE-CUDA-3.0.1_avoid-overriding-cuda-compute-capabilities.patch': + '09a1ac23c8ca485478fdfccacfe7b04a5608530f3da33892f64c76064a834722'}, +] + +builddependencies = [ + ('CMake', '3.26.3'), + ('googletest', '1.13.0'), + ('cxxopts', '3.0.0', '', SYSTEM), +] + +dependencies = [ + ('Python', '3.11.3'), + ('CUDA', '12.1.1', '', SYSTEM), + ('Faiss', '1.7.4', versionsuffix), + ('gflags', '2.2.2'), +] + +_copts = [ + '-DBUILD_PYTHON=ON', + '-DWITH_ZMQ=FALSE', + '-DWITH_MKL=OFF', + '-DCMAKE_CUDA_ARCHITECTURES="%(cuda_cc_cmake)s"', +] + +configopts = ' '.join(_copts) + +install_cmd = ('cd %(builddir)s/easybuild_obj/python &&' + ' python -m pip install --prefix=%(installdir)s --no-build-isolation .') + +options = {'modulename': 'tsnecuda'} + +sanity_check_paths = { + 'files': ['lib/python%%(pyshortver)s/site-packages/tsnecuda/libtsnecuda.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/t/t-SNE-CUDA/t-SNE-CUDA-3.0.1_avoid-overriding-cuda-compute-capabilities.patch b/easybuild/easyconfigs/t/t-SNE-CUDA/t-SNE-CUDA-3.0.1_avoid-overriding-cuda-compute-capabilities.patch new file mode 100644 index 00000000000..b8586bf9c6e --- /dev/null +++ b/easybuild/easyconfigs/t/t-SNE-CUDA/t-SNE-CUDA-3.0.1_avoid-overriding-cuda-compute-capabilities.patch @@ -0,0 +1,109 @@ +Avoid overriding CUDA_ARCH if CMAKE_CUDA_ARCHITECTURES is non-empty +diff -Nru tsne-cuda-3.0.1.orig/CMakeLists.txt tsne-cuda-3.0.1/CMakeLists.txt +--- tsne-cuda-3.0.1.orig/CMakeLists.txt 2024-01-18 17:31:58.841767793 +0000 ++++ tsne-cuda-3.0.1/CMakeLists.txt 2024-01-18 18:17:35.153863840 +0000 +@@ -58,55 +58,56 @@ + set(CMAKE_CUDA_STANDARD_REQUIRED ON) + endif() + +-if(CUDAToolkit_VERSION_MAJOR EQUAL "10") +- set(CUDA_ARCH +- -gencode=arch=compute_30,code=sm_30 +- -gencode=arch=compute_35,code=sm_35 +- -gencode=arch=compute_37,code=sm_37 +- -gencode=arch=compute_50,code=sm_50 +- -gencode=arch=compute_52,code=sm_52 +- -gencode=arch=compute_60,code=sm_60 +- -gencode=arch=compute_61,code=sm_61 +- -gencode=arch=compute_70,code=sm_70 +- -gencode=arch=compute_75,code=sm_75 +- ) +-elseif(CUDAToolkit_VERSION_MAJOR EQUAL "11" AND CUDAToolkit_VERSION_MINOR LESS "1") +- set(CUDA_ARCH +- -gencode=arch=compute_35,code=sm_35 +- -gencode=arch=compute_37,code=sm_37 +- -gencode=arch=compute_50,code=sm_50 +- -gencode=arch=compute_52,code=sm_52 +- -gencode=arch=compute_60,code=sm_60 +- -gencode=arch=compute_61,code=sm_61 +- -gencode=arch=compute_70,code=sm_70 +- -gencode=arch=compute_75,code=sm_75 +- -gencode=arch=compute_80,code=sm_80 +- ) +-elseif(CUDAToolkit_VERSION_MAJOR EQUAL "11") +- set(CUDA_ARCH +- -gencode=arch=compute_35,code=sm_35 +- -gencode=arch=compute_37,code=sm_37 +- -gencode=arch=compute_50,code=sm_50 +- -gencode=arch=compute_52,code=sm_52 +- -gencode=arch=compute_60,code=sm_60 +- -gencode=arch=compute_61,code=sm_61 +- -gencode=arch=compute_70,code=sm_70 +- -gencode=arch=compute_75,code=sm_75 +- -gencode=arch=compute_80,code=sm_80 +- -gencode=arch=compute_86,code=sm_86 +- ) +-else() +- set(CUDA_ARCH +- -gencode=arch=compute_30,code=sm_30 +- -gencode=arch=compute_35,code=sm_35 +- -gencode=arch=compute_37,code=sm_37 +- -gencode=arch=compute_50,code=sm_50 +- -gencode=arch=compute_52,code=sm_52 +- -gencode=arch=compute_60,code=sm_60 +- -gencode=arch=compute_61,code=sm_61 ++if("${CMAKE_CUDA_ARCHITECTURES}" STREQUAL "") ++ if(CUDAToolkit_VERSION_MAJOR EQUAL "10") ++ set(CUDA_ARCH ++ -gencode=arch=compute_30,code=sm_30 ++ -gencode=arch=compute_35,code=sm_35 ++ -gencode=arch=compute_37,code=sm_37 ++ -gencode=arch=compute_50,code=sm_50 ++ -gencode=arch=compute_52,code=sm_52 ++ -gencode=arch=compute_60,code=sm_60 ++ -gencode=arch=compute_61,code=sm_61 ++ -gencode=arch=compute_70,code=sm_70 ++ -gencode=arch=compute_75,code=sm_75 + ) +-endif() +- ++ elseif(CUDAToolkit_VERSION_MAJOR EQUAL "11" AND CUDAToolkit_VERSION_MINOR LESS "1") ++ set(CUDA_ARCH ++ -gencode=arch=compute_35,code=sm_35 ++ -gencode=arch=compute_37,code=sm_37 ++ -gencode=arch=compute_50,code=sm_50 ++ -gencode=arch=compute_52,code=sm_52 ++ -gencode=arch=compute_60,code=sm_60 ++ -gencode=arch=compute_61,code=sm_61 ++ -gencode=arch=compute_70,code=sm_70 ++ -gencode=arch=compute_75,code=sm_75 ++ -gencode=arch=compute_80,code=sm_80 ++ ) ++ elseif(CUDAToolkit_VERSION_MAJOR EQUAL "11") ++ set(CUDA_ARCH ++ -gencode=arch=compute_35,code=sm_35 ++ -gencode=arch=compute_37,code=sm_37 ++ -gencode=arch=compute_50,code=sm_50 ++ -gencode=arch=compute_52,code=sm_52 ++ -gencode=arch=compute_60,code=sm_60 ++ -gencode=arch=compute_61,code=sm_61 ++ -gencode=arch=compute_70,code=sm_70 ++ -gencode=arch=compute_75,code=sm_75 ++ -gencode=arch=compute_80,code=sm_80 ++ -gencode=arch=compute_86,code=sm_86 ++ ) ++ else() ++ set(CUDA_ARCH ++ -gencode=arch=compute_30,code=sm_30 ++ -gencode=arch=compute_35,code=sm_35 ++ -gencode=arch=compute_37,code=sm_37 ++ -gencode=arch=compute_50,code=sm_50 ++ -gencode=arch=compute_52,code=sm_52 ++ -gencode=arch=compute_60,code=sm_60 ++ -gencode=arch=compute_61,code=sm_61 ++ ) ++ endif() ++endif() + + set(CUDA_OPTS + -O3 diff --git a/easybuild/easyconfigs/t/t-SNE-CUDA/t-SNE-CUDA-3.0.1_use-external-cxxopts.patch b/easybuild/easyconfigs/t/t-SNE-CUDA/t-SNE-CUDA-3.0.1_use-external-cxxopts.patch new file mode 100644 index 00000000000..d5d2e37012a --- /dev/null +++ b/easybuild/easyconfigs/t/t-SNE-CUDA/t-SNE-CUDA-3.0.1_use-external-cxxopts.patch @@ -0,0 +1,27 @@ +Update CMakeLists.txt to use an external cxxopts +diff -Nru tsne-cuda-3.0.1.orig/CMakeLists.txt tsne-cuda-3.0.1/CMakeLists.txt +--- tsne-cuda-3.0.1.orig/CMakeLists.txt 2024-01-18 17:31:58.841767793 +0000 ++++ tsne-cuda-3.0.1/CMakeLists.txt 2024-01-18 17:34:46.095207526 +0000 +@@ -157,6 +157,14 @@ + endif() + include_directories(${FAISS_INCLUDE_DIR}) + ++# CXXOPTS Configuration ++#------------------------------------------------------------------------------- ++find_package(CXXOPTS REQUIRED) ++if(NOT ${CXXOPTS_FOUND}) ++ message("-- CXXOPTS not installed. PLease install CXXOPTS.") ++endif() ++include_directories(${CXXOPTS_INCLUDE_DIR}) ++ + # Project Setup + #------------------------------------------------------------------------------- + include_directories( +@@ -164,7 +172,6 @@ + src/include + ${CUDA_INCLUDE_DIRS} + third_party/ +- third_party/cxxopts/include/ + ${ZMQ_INCLUDE_DIR} + ) + link_directories( diff --git a/easybuild/easyconfigs/t/tRNAscan-SE/tRNAscan-SE-2.0.12-foss-2023a.eb b/easybuild/easyconfigs/t/tRNAscan-SE/tRNAscan-SE-2.0.12-foss-2023a.eb new file mode 100644 index 00000000000..107e7dbb9c9 --- /dev/null +++ b/easybuild/easyconfigs/t/tRNAscan-SE/tRNAscan-SE-2.0.12-foss-2023a.eb @@ -0,0 +1,42 @@ +easyblock = 'ConfigureMake' + +name = 'tRNAscan-SE' +version = '2.0.12' + +homepage = 'http://trna.ucsc.edu/tRNAscan-SE/' +description = """tRNAscan-SE is the most widely employed tool for identifying + and annotating tRNA genes in genomes.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['https://github.com/UCSC-LoweLab/tRNAscan-SE/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['4b255c2c5e0255381194166f857ab2ea21c55aa7de409e201333ba615aa3dc61'] + +builddependencies = [ + # tRNAscan-SE's configure script really wants Autoconf 2.69 + ('Autoconf', '2.71', '', SYSTEM), +] + +dependencies = [ + ('Perl', '5.36.1'), + ('Infernal', '1.1.5'), +] + +parallel = 1 + +# tRNAscan-SE.conf sets the Infernal bin directory to be ours. +postinstallcmds = [ + "for b in $(ls $EBROOTINFERNAL/bin); do ln -s $EBROOTINFERNAL/bin/$b %(installdir)s/bin; done", +] + +fix_perl_shebang_for = ['bin/*'] + +sanity_check_paths = { + 'files': ['bin/tRNAscan-SE', 'lib/tRNAscan-SE/tRNAscanSE/tRNA.pm'], + 'dirs': ['include'], +} + +sanity_check_commands = ["tRNAscan-SE --help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/t/tabixpp/tabixpp-1.1.2-GCC-12.2.0.eb b/easybuild/easyconfigs/t/tabixpp/tabixpp-1.1.2-GCC-12.2.0.eb new file mode 100644 index 00000000000..452f3caa3fa --- /dev/null +++ b/easybuild/easyconfigs/t/tabixpp/tabixpp-1.1.2-GCC-12.2.0.eb @@ -0,0 +1,41 @@ +# Author: Jasper Grimm (UoY) +# Updated: Petr Král (INUITS) + +easyblock = 'ConfigureMake' + +name = 'tabixpp' +version = '1.1.2' + +homepage = 'https://github.com/ekg/tabixpp' +description = """C++ wrapper to tabix indexer""" + +toolchain = {'name': 'GCC', 'version': '12.2.0'} + +github_account = 'ekg' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +patches = ['%(name)s-%(version)s_use-external-HTSlib.patch'] + +checksums = [ + 'c850299c3c495221818a85c9205c60185c8ed9468d5ec2ed034470bb852229dc', # v1.1.2.tar.gz + 'a4684b6c3a69258d0686f601564b635ae3dc098e712783b46d9ca5b7ff996906', # tabixpp-1.1.2_use-external-HTSlib.patch +] + +dependencies = [ + ('zlib', '1.2.12'), + ('bzip2', '1.0.8'), + ('XZ', '5.2.7'), + ('HTSlib', '1.17'), + ('PCRE', '8.45'), +] + +skipsteps = ['configure'] + +preinstallopts = 'PREFIX=%(installdir)s' + +sanity_check_paths = { + 'files': ['bin/tabix++', 'lib/libtabixpp.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/t/tantan/tantan-50-GCC-12.3.0.eb b/easybuild/easyconfigs/t/tantan/tantan-50-GCC-12.3.0.eb new file mode 100644 index 00000000000..c4a4ce67c25 --- /dev/null +++ b/easybuild/easyconfigs/t/tantan/tantan-50-GCC-12.3.0.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'tantan' +version = '50' + +homepage = 'https://gitlab.com/mcfrith/tantan' +description = "tantan identifies simple regions / low complexity / tandem repeats in DNA or protein sequences" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +source_urls = ['https://gitlab.com/mcfrith/tantan/-/archive/%(version)s/'] +sources = ['tantan-%(version)s.tar.gz'] +checksums = ['a239e9fb3c059ed9eb4c25a29b3c44a2ef1c1b492a9780874f429de7ae8b5407'] + +skipsteps = ['configure'] + +installopts = "prefix=%(installdir)s" + +sanity_check_paths = { + 'files': ['bin/tantan'], + 'dirs': [], +} + +sanity_check_commands = ["tantan --help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/t/tbb/tbb-2021.13.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/t/tbb/tbb-2021.13.0-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..15af40d5548 --- /dev/null +++ b/easybuild/easyconfigs/t/tbb/tbb-2021.13.0-GCCcore-13.2.0.eb @@ -0,0 +1,32 @@ +easyblock = 'CMakeMake' + +name = 'tbb' +version = '2021.13.0' + +homepage = 'https://github.com/oneapi-src/oneTBB' +description = """Intel(R) Threading Building Blocks (Intel(R) TBB) lets you easily write parallel C++ programs that + take full advantage of multicore performance, that are portable, composable and have future-proof scalability.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +# The following option is needed to supress the "stringop-overflow error". +# See https://github.com/oneapi-src/oneTBB/issues/1180#issuecomment-1690958371 for details. +toolchainopts = {'extra_cxxflags': '-Wno-error=stringop-overflow'} + +source_urls = ['https://github.com/oneapi-src/oneTBB/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['3ad5dd08954b39d113dc5b3f8a8dc6dc1fd5250032b7c491eb07aed5c94133e1'] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.27.6'), +] + +dependencies = [('hwloc', '2.9.2')] + +sanity_check_paths = { + 'files': ['lib/libtbb.%s' % SHLIB_EXT, 'lib/libtbbmalloc.%s' % SHLIB_EXT], + 'dirs': ['lib', 'include', 'share'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/t/tbb/tbb-2021.13.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/t/tbb/tbb-2021.13.0-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..d75527cdfb0 --- /dev/null +++ b/easybuild/easyconfigs/t/tbb/tbb-2021.13.0-GCCcore-13.3.0.eb @@ -0,0 +1,33 @@ +easyblock = 'CMakeMake' + +name = 'tbb' +version = '2021.13.0' + +homepage = 'https://github.com/oneapi-src/oneTBB' +description = """Intel(R) Threading Building Blocks (Intel(R) TBB) lets you easily write parallel C++ programs that + take full advantage of multicore performance, that are portable, composable and have future-proof scalability.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +# The following option is needed to supress the "stringop-overflow error". +# See https://github.com/oneapi-src/oneTBB/issues/1180#issuecomment-1690958371 for details. +toolchainopts = {'extra_cxxflags': '-Wno-error=stringop-overflow'} + +source_urls = ['https://github.com/oneapi-src/oneTBB/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['3ad5dd08954b39d113dc5b3f8a8dc6dc1fd5250032b7c491eb07aed5c94133e1'] + +builddependencies = [ + ('binutils', '2.42'), + ('CMake', '3.29.3'), +] +dependencies = [ + ('hwloc', '2.10.0'), +] + + +sanity_check_paths = { + 'files': ['lib/libtbb.%s' % SHLIB_EXT, 'lib/libtbbmalloc.%s' % SHLIB_EXT], + 'dirs': ['lib', 'include', 'share'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/t/tbb/tbb-2021.9.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/t/tbb/tbb-2021.9.0-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..d0173aab4ea --- /dev/null +++ b/easybuild/easyconfigs/t/tbb/tbb-2021.9.0-GCCcore-12.2.0.eb @@ -0,0 +1,31 @@ +easyblock = 'CMakeMake' + +name = 'tbb' +version = '2021.9.0' + +homepage = 'https://github.com/oneapi-src/oneTBB' +description = """Intel(R) Threading Building Blocks (Intel(R) TBB) lets you easily write parallel C++ programs that + take full advantage of multicore performance, that are portable, composable and have future-proof scalability.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://github.com/oneapi-src/oneTBB/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['1ce48f34dada7837f510735ff1172f6e2c261b09460e3bf773b49791d247d24e'] + +builddependencies = [ + ('binutils', '2.39'), + ('CMake', '3.24.3'), +] + +dependencies = [('hwloc', '2.8.0')] + +# use -Wno-error as workaround for compiler error when building the tests +preconfigopts = 'export CXXFLAGS="$CXXFLAGS -Wno-stringop-overflow" && ' + +sanity_check_paths = { + 'files': ['lib/libtbb.%s' % SHLIB_EXT, 'lib/libtbbmalloc.%s' % SHLIB_EXT], + 'dirs': ['lib', 'include', 'share'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/t/tbl2asn/tbl2asn-20230713-GCCcore-12.3.0.eb b/easybuild/easyconfigs/t/tbl2asn/tbl2asn-20230713-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..dcf4c39e8d0 --- /dev/null +++ b/easybuild/easyconfigs/t/tbl2asn/tbl2asn-20230713-GCCcore-12.3.0.eb @@ -0,0 +1,64 @@ +# This file is an EasyBuild reciPY as per https://easybuilders.github.io/easybuild/ +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics +# revised by Ariel Lozano + +easyblock = 'Bundle' + +name = 'tbl2asn' +version = '20230713' + +homepage = 'https://www.ncbi.nlm.nih.gov/genbank/tbl2asn2/' +description = """Tbl2asn is a command-line program that automates the creation of + sequence records for submission to GenBank""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +builddependencies = [ + ('binutils', '2.40'), + ('patchelf', '0.18.0'), +] + +# libraries that are copied to installdir need to be patched to have an RPATH section +# when EasyBuild is configured to use RPATH linking (required to pass RPATH sanity check); + +default_easyblock = 'CmdCp' + +# It is not entirely clean how long NCBI keeps "older" versions. At April 29, 2022, we had six timestamps/versions, +# reporiting the same verion (tbl2asn --help -> 25.8) but 5 out of 6 (gunzipped) executables have different sha256 +# checksums. + +components = [ + ('libidn', '1.34', { + 'easyblock': 'ConfigureMake', + 'source_urls': [GNU_SOURCE], + 'sources': [SOURCELOWER_TAR_GZ], + 'start_dir': '%(namelower)s-%(version)s', + 'checksums': ['3719e2975f2fb28605df3479c380af2cf4ab4e919e1506527e4c7670afff6e3c'], + }), + (name, version, { + 'source_urls': ['https://ftp.ncbi.nih.gov/toolbox/ncbi_tools/converters/versions/%s/all/' % + (version[:4] + '-' + version[4:6] + '-' + version[6:])], + 'sources': [{'download_filename': 'tbl2asn.linux64.gz', + 'filename': '%(name)s-%(version)s%(versionsuffix)s.gz'}], + 'checksums': ['544c4a2a53f2121fd21c44778fc61980a701ce852ea0142979241c0465c38a0c'], + 'cmds_map': [('.*', "cp %(name)s-%(version)s%(versionsuffix)s tbl2asn")], + 'files_to_copy': [(['tbl2asn'], 'bin')], + }), +] + +postinstallcmds = [ + "if %(rpath_enabled)s; then " + " patchelf --force-rpath --set-rpath %(installdir)s/lib %(installdir)s/bin/tbl2asn;" + "fi", + "chmod +x %(installdir)s/bin/tbl2asn", +] + +sanity_check_paths = { + 'files': ['bin/tbl2asn', 'bin/idn', 'lib/libidn.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +sanity_check_commands = ['tbl2asn --help'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/t/tbl2asn/tbl2asn-20230713-GCCcore-13.3.0.eb b/easybuild/easyconfigs/t/tbl2asn/tbl2asn-20230713-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..12b79ddde0f --- /dev/null +++ b/easybuild/easyconfigs/t/tbl2asn/tbl2asn-20230713-GCCcore-13.3.0.eb @@ -0,0 +1,64 @@ +# This file is an EasyBuild reciPY as per https://easybuilders.github.io/easybuild/ +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics +# revised by Ariel Lozano + +easyblock = 'Bundle' + +name = 'tbl2asn' +version = '20230713' + +homepage = 'https://www.ncbi.nlm.nih.gov/genbank/tbl2asn2/' +description = """Tbl2asn is a command-line program that automates the creation of + sequence records for submission to GenBank""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +builddependencies = [ + ('binutils', '2.42'), + ('patchelf', '0.18.0'), +] + +# libraries that are copied to installdir need to be patched to have an RPATH section +# when EasyBuild is configured to use RPATH linking (required to pass RPATH sanity check); + +default_easyblock = 'CmdCp' + +# It is not entirely clean how long NCBI keeps "older" versions. At April 29, 2022, we had six timestamps/versions, +# reporiting the same verion (tbl2asn --help -> 25.8) but 5 out of 6 (gunzipped) executables have different sha256 +# checksums. + +components = [ + ('libidn', '1.34', { + 'easyblock': 'ConfigureMake', + 'source_urls': [GNU_SOURCE], + 'sources': [SOURCELOWER_TAR_GZ], + 'start_dir': '%(namelower)s-%(version)s', + 'checksums': ['3719e2975f2fb28605df3479c380af2cf4ab4e919e1506527e4c7670afff6e3c'], + }), + (name, version, { + 'source_urls': ['https://ftp.ncbi.nih.gov/toolbox/ncbi_tools/converters/versions/%s/all/' % + (version[:4] + '-' + version[4:6] + '-' + version[6:])], + 'sources': [{'download_filename': 'tbl2asn.linux64.gz', + 'filename': '%(name)s-%(version)s%(versionsuffix)s.gz'}], + 'checksums': ['544c4a2a53f2121fd21c44778fc61980a701ce852ea0142979241c0465c38a0c'], + 'cmds_map': [('.*', "cp %(name)s-%(version)s%(versionsuffix)s tbl2asn")], + 'files_to_copy': [(['tbl2asn'], 'bin')], + }), +] + +postinstallcmds = [ + "if %(rpath_enabled)s; then " + " patchelf --force-rpath --set-rpath %(installdir)s/lib %(installdir)s/bin/tbl2asn;" + "fi", + "chmod +x %(installdir)s/bin/tbl2asn", +] + +sanity_check_paths = { + 'files': ['bin/tbl2asn', 'bin/idn', 'lib/libidn.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +sanity_check_commands = ['tbl2asn --help'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/t/tblis/tblis-20230422-foss-2023a.eb b/easybuild/easyconfigs/t/tblis/tblis-20230422-foss-2023a.eb new file mode 100644 index 00000000000..77e022aa0cf --- /dev/null +++ b/easybuild/easyconfigs/t/tblis/tblis-20230422-foss-2023a.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'tblis' +version = '20230422' +local_commit = '4de1919' + +homepage = "https://github.com/devinamatthews/tblis" +description = """TBLIS is a library and framework for performing tensor + operations, especially tensor contraction, using native algorithms.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['https://github.com/devinamatthews/tblis/archive/'] +sources = ['%s.tar.gz' % local_commit] +checksums = ['85b72884022edd2612e3a0b3ed12aa6237d3989b581091d21f58124a7450aaeb'] + +sanity_check_paths = { + 'files': [ + 'include/tblis/tblis.h', + 'lib/libtblis.%s' % SHLIB_EXT, + ], + 'dirs': [] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/t/tcsh/tcsh-6.24.13-GCCcore-13.3.0.eb b/easybuild/easyconfigs/t/tcsh/tcsh-6.24.13-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..a7712f10368 --- /dev/null +++ b/easybuild/easyconfigs/t/tcsh/tcsh-6.24.13-GCCcore-13.3.0.eb @@ -0,0 +1,48 @@ +# # +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg/Computer Science and Communications Research Unit +# Authors:: Valentin Plugaru +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_05-06.html +# # +easyblock = 'ConfigureMake' + +name = 'tcsh' +version = '6.24.13' + +homepage = 'https://www.tcsh.org' +description = """Tcsh is an enhanced, but completely compatible version of the Berkeley UNIX C shell (csh). + It is a command language interpreter usable both as an interactive login shell and a shell script command + processor. It includes a command-line editor, programmable word completion, spelling correction, a history + mechanism, job control and a C-like syntax.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = [ + 'https://astron.com/pub/%(namelower)s', + 'https://astron.com/pub/%(namelower)s/old', + 'ftp://ftp.astron.com/pub/%(namelower)s', + 'ftp://ftp.astron.com/pub/%(namelower)s/old', +] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['1e927d52e9c85d162bf985f24d13c6ccede9beb880d86fec492ed15480a5c71a'] + +builddependencies = [ + ('binutils', '2.42'), +] +dependencies = [ + ('ncurses', '6.5'), +] + +postinstallcmds = ['ln -s %(name)s %(installdir)s/bin/csh'] + +sanity_check_paths = { + 'files': ['bin/%(name)s', 'bin/csh'], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/t/tdlib/tdlib-0.9.3-GCC-13.2.0.eb b/easybuild/easyconfigs/t/tdlib/tdlib-0.9.3-GCC-13.2.0.eb new file mode 100644 index 00000000000..63408d65ee7 --- /dev/null +++ b/easybuild/easyconfigs/t/tdlib/tdlib-0.9.3-GCC-13.2.0.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'tdlib' +version = '0.9.3' + +homepage = 'https://github.com/freetdi/tdlib/' +description = """treedec provides tree decomposition algorithms.""" + +toolchain = {'name': 'GCC', 'version': '13.2.0'} + +source_urls = ['https://github.com/freetdi/tdlib/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['d1730c98f41dcb23bbd0bd8de9dbec51df015304f28a38935848925901594ae8'] + +builddependencies = [ + ('Autotools', '20220317'), + ('Boost', '1.83.0'), + ('Python', '3.11.5'), +] + +preconfigopts = 'autoreconf --install && ' + +sanity_check_paths = { + 'files': [ + 'include/treedec/combinations.hpp', + ], + 'dirs': [] +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/t/tensorboard/tensorboard-2.10.0-foss-2022a.eb b/easybuild/easyconfigs/t/tensorboard/tensorboard-2.10.0-foss-2022a.eb index 4cf2f36f1d5..83fc611834b 100644 --- a/easybuild/easyconfigs/t/tensorboard/tensorboard-2.10.0-foss-2022a.eb +++ b/easybuild/easyconfigs/t/tensorboard/tensorboard-2.10.0-foss-2022a.eb @@ -9,6 +9,14 @@ and graphs.""" toolchain = {'name': 'foss', 'version': '2022a'} +postinstallpatches = [ + ('tensorboard-2.10_jupyterhub-support.patch', 'lib/python%(pyshortver)s/site-packages'), +] +checksums = [ + {'tensorboard-2.10_jupyterhub-support.patch': + '50a292e6ee518aecb5644595e0f3db4867be4f82e328e008e5a3f6a1f19baf87'}, +] + dependencies = [ ('Python', '3.10.4'), ('SciPy-bundle', '2022.05'), diff --git a/easybuild/easyconfigs/t/tensorboard/tensorboard-2.10_jupyterhub-support.patch b/easybuild/easyconfigs/t/tensorboard/tensorboard-2.10_jupyterhub-support.patch new file mode 100644 index 00000000000..211bf686256 --- /dev/null +++ b/easybuild/easyconfigs/t/tensorboard/tensorboard-2.10_jupyterhub-support.patch @@ -0,0 +1,103 @@ +From: qzchenwl +Date: Tue, 14 Jan 2020 15:22:27 +0800 +Subject: support jupyterhub with jupyter-server-proxy +Issue: https://github.com/tensorflow/tensorboard/pull/3142 + +--- a/tensorboard/notebook.py 2024-06-13 16:04:51.656772000 +0200 ++++ b/tensorboard/notebook.py 2024-06-13 16:06:38.749780722 +0200 +@@ -34,6 +34,7 @@ + # details). + _CONTEXT_COLAB = "_CONTEXT_COLAB" + _CONTEXT_IPYTHON = "_CONTEXT_IPYTHON" ++_CONTEXT_JUPYTERHUB = "_CONTEXT_JUPYTERHUB" + _CONTEXT_NONE = "_CONTEXT_NONE" + + +@@ -70,12 +71,31 @@ + else: + ipython = IPython.get_ipython() + if ipython is not None and ipython.has_trait("kernel"): ++ if os.environ.get("JUPYTERHUB_SERVICE_PREFIX") is not None: ++ return _CONTEXT_JUPYTERHUB + return _CONTEXT_IPYTHON + + # Otherwise, we're not in a known notebook context. + return _CONTEXT_NONE + + ++def _prefix_jupyterhub(port): ++ prefix = os.path.join( ++ os.environ["JUPYTERHUB_SERVICE_PREFIX"], "proxy/absolute" ++ ) ++ return "%s/%d/" % (prefix, port) ++ ++ ++def _patch_args_jupyterhub(parsed_args): ++ if "--port" in parsed_args: ++ arg_idx = parsed_args.index("--port") ++ port = int(parsed_args[arg_idx + 1]) ++ else: ++ port = 6006 ++ parsed_args += ["--port", str(port)] ++ return parsed_args + ["--path_prefix", _prefix_jupyterhub(port)] ++ ++ + def load_ipython_extension(ipython): + """Deprecated: use `%load_ext tensorboard` instead. + +@@ -149,6 +169,9 @@ + handle.update(IPython.display.Pretty(message)) + + parsed_args = shlex.split(args_string, comments=True, posix=True) ++ if context == _CONTEXT_JUPYTERHUB: ++ parsed_args = _patch_args_jupyterhub(parsed_args) ++ + start_result = manager.start(parsed_args) + + if isinstance(start_result, manager.StartLaunched): +@@ -305,6 +328,7 @@ + fn = { + _CONTEXT_COLAB: _display_colab, + _CONTEXT_IPYTHON: _display_ipython, ++ _CONTEXT_JUPYTERHUB: _display_jupyterhub, + _CONTEXT_NONE: _display_cli, + }[_get_context()] + return fn(port=port, height=height, display_handle=display_handle) +@@ -401,6 +425,36 @@ + for (k, v) in replacements: + shell = shell.replace(k, v) + iframe = IPython.display.HTML(shell) ++ if display_handle: ++ display_handle.update(iframe) ++ else: ++ IPython.display.display(iframe) ++ ++ ++def _display_jupyterhub(port, height, display_handle): ++ import IPython.display ++ ++ frame_id = "tensorboard-frame-{:08x}".format(random.getrandbits(64)) ++ shell = """ ++ ++ ++ """ ++ replacements = [ ++ ("%HTML_ID%", html.escape(frame_id, quote=True)), ++ ("%JSON_ID%", json.dumps(frame_id)), ++ ("%PREFIX%", _prefix_jupyterhub(port)), ++ ("%HEIGHT%", "%d" % height), ++ ] ++ for (k, v) in replacements: ++ shell = shell.replace(k, v) ++ iframe = IPython.display.HTML(shell) + if display_handle: + display_handle.update(iframe) + else: +From 5615204ba44a6b8718e58c9b4b875fef5027baaf Mon Sep 17 00:00:00 2001 diff --git a/easybuild/easyconfigs/t/tensorboard/tensorboard-2.15.1-gfbf-2022b.eb b/easybuild/easyconfigs/t/tensorboard/tensorboard-2.15.1-gfbf-2022b.eb new file mode 100644 index 00000000000..304e56b390f --- /dev/null +++ b/easybuild/easyconfigs/t/tensorboard/tensorboard-2.15.1-gfbf-2022b.eb @@ -0,0 +1,90 @@ +easyblock = 'PythonBundle' + +name = 'tensorboard' +version = '2.15.1' + +homepage = 'https://github.com/tensorflow/tensorboard' +description = """TensorBoard is a suite of web applications for inspecting and +understanding your TensorFlow runs and graphs.""" + +toolchain = {'name': 'gfbf', 'version': '2022b'} + +postinstallpatches = [ + ('tensorboard-2.10_jupyterhub-support.patch', 'lib/python%(pyshortver)s/site-packages'), +] +checksums = [ + {'tensorboard-2.10_jupyterhub-support.patch': + '50a292e6ee518aecb5644595e0f3db4867be4f82e328e008e5a3f6a1f19baf87'}, +] + +dependencies = [ + ('Python', '3.10.8'), + ('SciPy-bundle', '2023.02'), + ('protobuf-python', '4.23.0'), + ('grpcio', '1.57.0'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('absl-py', '2.1.0', { + 'modulename': 'absl', + 'checksums': ['7820790efbb316739cde8b4e19357243fc3608a152024288513dd968d7d959ff'], + }), + ('cachetools', '5.3.2', { + 'checksums': ['086ee420196f7b2ab9ca2db2520aca326318b68fe5ba8bc4d49cca91add450f2'], + }), + ('pyasn1_modules', '0.3.0', { + 'checksums': ['5bd01446b736eb9d31512a30d46c1ac3395d676c6f3cafa4c03eb54b9925631c'], + }), + ('rsa', '4.9', { + 'checksums': ['e38464a49c6c85d7f1351b0126661487a7e0a14a50f1675ec50eb34d4f20ef21'], + }), + ('google-auth', '2.26.2', { + 'modulename': 'google.auth', + 'checksums': ['97327dbbf58cccb58fc5a1712bba403ae76668e64814eb30f7316f7e27126b81'], + }), + ('oauthlib', '3.2.2', { + 'checksums': ['9859c40929662bec5d64f34d01c99e093149682a3f38915dc0655d5a633dd918'], + }), + ('requests-oauthlib', '1.3.1', { + 'checksums': ['75beac4a47881eeb94d5ea5d6ad31ef88856affe2332b9aafb52c6452ccf0d7a'], + }), + ('google-auth-oauthlib', '1.2.0', { + 'checksums': ['292d2d3783349f2b0734a0a0207b1e1e322ac193c2c09d8f7c613fb7cc501ea8'], + }), + ('Markdown', '3.5.2', { + 'checksums': ['e1ac7b3dc550ee80e602e71c1d168002f062e49f1b11e26a36264dafd4df2ef8'], + }), + ('tensorboard_data_server', '0.7.2', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['7e0610d205889588983836ec05dc098e80f97b7e7bbff7e994ebb78f578d0ddb'], + }), + ('gviz-api', '1.10.0', { + 'source_tmpl': 'gviz_api-%(version)s.tar.gz', + 'checksums': ['846692dd8cc73224fc31b18e41589bd934e1cc05090c6576af4b4b26c2e71b90'], + }), + ('tensorboard-plugin-profile', '2.15.1', { + 'source_tmpl': 'tensorboard_plugin_profile-%(version)s.tar.gz', + 'checksums': ['84bb33e446eb4a9c0616f669fc6a42cdd40eadd9ae1d74bf756f4f0479993273'], + }), + ('Werkzeug', '3.0.1', { + 'source_tmpl': '%(namelower)s-%(version)s.tar.gz', + 'checksums': ['507e811ecea72b18a404947aded4b3390e1db8f826b494d76550ef45bb3b1dcc'], + }), + (name, version, { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['c46c1d1cf13a458c429868a78b2531d8ff5f682058d69ec0840b0bc7a38f1c0f'], + }), +] + +# Relax restriction on protobuf dependency as issue was fixed +# in https://github.com/protocolbuffers/upb/pull/1514 +# see also: https://github.com/easybuilders/easybuild-easyconfigs/pull/19671 +postinstallcmds = [ + 'sed -i "s/Requires-Dist: protobuf.*/Requires-Dist: protobuf >=3.19.6/g" ' + + '%(installdir)s/lib/python%(pyshortver)s/site-packages/%(name)s-%(version)s.dist-info/METADATA', +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/t/tensorboard/tensorboard-2.15.1-gfbf-2023a.eb b/easybuild/easyconfigs/t/tensorboard/tensorboard-2.15.1-gfbf-2023a.eb index 9c74e1a8f87..ab499908831 100644 --- a/easybuild/easyconfigs/t/tensorboard/tensorboard-2.15.1-gfbf-2023a.eb +++ b/easybuild/easyconfigs/t/tensorboard/tensorboard-2.15.1-gfbf-2023a.eb @@ -9,6 +9,14 @@ understanding your TensorFlow runs and graphs.""" toolchain = {'name': 'gfbf', 'version': '2023a'} +postinstallpatches = [ + ('tensorboard-2.10_jupyterhub-support.patch', 'lib/python%(pyshortver)s/site-packages'), +] +checksums = [ + {'tensorboard-2.10_jupyterhub-support.patch': + '50a292e6ee518aecb5644595e0f3db4867be4f82e328e008e5a3f6a1f19baf87'}, +] + builddependencies = [ ('poetry', '1.5.1'), ] @@ -17,8 +25,12 @@ dependencies = [ ('Python', '3.11.3'), ('SciPy-bundle', '2023.07'), ('protobuf-python', '4.24.0'), + ('grpcio', '1.57.0'), ] +use_pip = True +sanity_pip_check = True + exts_list = [ ('absl-py', '2.1.0', { 'modulename': 'absl', @@ -46,11 +58,6 @@ exts_list = [ ('google-auth-oauthlib', '1.2.0', { 'checksums': ['292d2d3783349f2b0734a0a0207b1e1e322ac193c2c09d8f7c613fb7cc501ea8'], }), - ('grpcio', '1.60.0', { - 'modulename': 'grpc', - 'preinstallopts': "export GRPC_PYTHON_BUILD_EXT_COMPILER_JOBS=%(parallel)s && ", - 'checksums': ['2199165a1affb666aa24adf0c97436686d0a61bc5fc113c037701fb7c7fceb96'], - }), ('Markdown', '3.5.2', { 'checksums': ['e1ac7b3dc550ee80e602e71c1d168002f062e49f1b11e26a36264dafd4df2ef8'], }), @@ -58,9 +65,13 @@ exts_list = [ 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', 'checksums': ['7e0610d205889588983836ec05dc098e80f97b7e7bbff7e994ebb78f578d0ddb'], }), - ('tensorboard_plugin_wit', '1.8.1', { - 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', - 'checksums': ['ff26bdd583d155aa951ee3b152b3d0cffae8005dc697f72b44a8e8c2a77a8cbe'], + ('gviz-api', '1.10.0', { + 'source_tmpl': 'gviz_api-%(version)s.tar.gz', + 'checksums': ['846692dd8cc73224fc31b18e41589bd934e1cc05090c6576af4b4b26c2e71b90'], + }), + ('tensorboard-plugin-profile', '2.15.1', { + 'source_tmpl': 'tensorboard_plugin_profile-%(version)s.tar.gz', + 'checksums': ['84bb33e446eb4a9c0616f669fc6a42cdd40eadd9ae1d74bf756f4f0479993273'], }), ('Werkzeug', '3.0.1', { 'source_tmpl': '%(namelower)s-%(version)s.tar.gz', @@ -80,7 +91,4 @@ postinstallcmds = [ '%(installdir)s/lib/python%(pyshortver)s/site-packages/%(name)s-%(version)s.dist-info/METADATA', ] -use_pip = True -sanity_pip_check = True - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/t/tensorflow-probability/tensorflow-probability-0.20.0-foss-2023a.eb b/easybuild/easyconfigs/t/tensorflow-probability/tensorflow-probability-0.20.0-foss-2023a.eb index c86b16b035f..efede874267 100644 --- a/easybuild/easyconfigs/t/tensorflow-probability/tensorflow-probability-0.20.0-foss-2023a.eb +++ b/easybuild/easyconfigs/t/tensorflow-probability/tensorflow-probability-0.20.0-foss-2023a.eb @@ -28,6 +28,12 @@ dependencies = [ use_pip = True +# avoid pip check fail when tensorflow-probability is a dependency +local_postinstallcmds = "cd %(installdir)s/lib/python%(pyshortver)s/site-packages && " +local_postinstallcmds += "mv tfp_nightly-%(version)s.dist-info tensorflow_probability-%(version)s.dist-info && " +local_postinstallcmds += "sed -i 's/Name: tfp-nightly/Name: %(name)s/' " +local_postinstallcmds += "tensorflow_probability-%(version)s.dist-info/METADATA" + exts_list = [ ('cloudpickle', '3.0.0', { 'checksums': ['996d9a482c6fb4f33c1a35335cf8afd065d2a56e973270364840712d9131a882'], @@ -37,6 +43,7 @@ exts_list = [ 'source_tmpl': 'v%(version)s.tar.gz', 'source_urls': ['https://github.com/tensorflow/probability/archive/'], 'checksums': ['f0fb9a1f88a36a8f57d4d9cce4f9bf8dfacb6fc7778751729fe3c3067e5a1363'], + 'postinstallcmds': [local_postinstallcmds], }), ] diff --git a/easybuild/easyconfigs/t/tensorstore/tensorstore-0.1.65-foss-2023a.eb b/easybuild/easyconfigs/t/tensorstore/tensorstore-0.1.65-foss-2023a.eb new file mode 100644 index 00000000000..5dd271c0d88 --- /dev/null +++ b/easybuild/easyconfigs/t/tensorstore/tensorstore-0.1.65-foss-2023a.eb @@ -0,0 +1,62 @@ +# Thomas Hoffmann, EMBL Heidlelberg, structures-it@embl.de, 2024/10 +easyblock = 'PythonBundle' + +name = 'tensorstore' +version = '0.1.65' + +homepage = 'https://github.com/google/tensorstore' +description = """TensorStore is an open-source C++ and Python software library designed for +storage and manipulation of large multi-dimensional arrays.""" + +toolchain = {'name': 'foss', 'version': '2023a'} +builddependencies = [ + ('NASM', '2.16.01'), + ('pybind11', '2.11.1'), + ('Bazel', '6.3.1'), + + + + ('PyYAML', '6.0'), + ('zlib', '1.2.13'), + ('LibTIFF', '4.5.0'), + ('snappy', '1.1.10'), + ('Brotli', '1.0.9'), + ('protobuf', '24.0'), + ('bzip2', '1.0.8'), + ('zstd', '1.5.5'), + ('libwebp', '1.3.1'), + ('nlohmann_json', '3.11.2'), + ('Blosc', '1.21.5'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('ml_dtypes', '0.3.2'), +] + +use_pip = True + + +local_ts_useebbazel = """sed -i 's/bazel_path =.*/""" +local_ts_useebbazel += """bazel_path = os.path.join(os.getenv("EBROOTBAZEL"),"bin", "bazel")/g'""" +local_ts_useebbazel += " bazelisk.py&& " # TODO: patch? +local_ts_version = """sed -i "s/use_scm_version=/version='%(version)s',&/g" setup.py&&""" +local_ts_bzl_exp = """export TENSORSTORE_BAZEL_STARTUP_OPTIONS='--output_user_root %(builddir)s/cache' &&""" +# inject CFLAGS: +local_ts_bzl_exp += """export TENSORSTORE_BAZEL_BUILD_OPTIONS="$(for i in $CFLAGS;do echo --copt=$i; done)" &&""" + + +local_ts_preinstall = local_ts_version + local_ts_useebbazel + local_ts_bzl_exp + +exts_list = [ + (name, version, { + 'installopts': '-v', + 'preinstallopts': local_ts_preinstall, + 'checksums': ['65cbe5a600c32569bb0b9f597ea318cc298a13b42d5fc98168c97bb11f320eae'], + }), +] + +sanity_pip_check = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/t/tesseract/tesseract-5.3.4-GCCcore-12.3.0.eb b/easybuild/easyconfigs/t/tesseract/tesseract-5.3.4-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..94cf0915ff9 --- /dev/null +++ b/easybuild/easyconfigs/t/tesseract/tesseract-5.3.4-GCCcore-12.3.0.eb @@ -0,0 +1,66 @@ +easyblock = 'CMakeMake' + +name = 'tesseract' +version = '5.3.4' +_tessdata_ver = '4.1.0' + +homepage = 'https://github.com/tesseract-ocr/tesseract' +description = """Tesseract is an optical character recognition engine""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +github_account = 'tesseract-ocr' +source_urls = [GITHUB_SOURCE] +sources = [ + '%(version)s.tar.gz', + { + 'source_urls': ['https://github.com/tesseract-ocr/tessdata_best/archive/'], + 'download_filename': '%s.tar.gz' % _tessdata_ver, + 'filename': 'tessdata_best-%s.tar.gz' % _tessdata_ver, + }, +] +checksums = [ + {'5.3.4.tar.gz': '141afc12b34a14bb691a939b4b122db0d51bd38feda7f41696822bacea7710c7'}, + {'tessdata_best-4.1.0.tar.gz': 'bb05b738298ae73e7130e2913ed002b49d94cd1cea508e63be1928fe47770b32'}, +] + +builddependencies = [ + ('CMake', '3.26.3'), + ('binutils', '2.40'), + ('pkgconf', '1.9.5') +] + +dependencies = [ + ('zlib', '1.2.13'), + ('libpng', '1.6.39'), + ('libjpeg-turbo', '2.1.5.1'), + ('LibTIFF', '4.5.0'), + ('Leptonica', '1.84.1'), + ('libarchive', '3.6.2'), + ('ICU', '73.2'), + ('fontconfig', '2.14.2'), + ('GLib', '2.77.1'), + ('cairo', '1.17.8'), + ('Pango', '1.50.14'), +] + +configopts = ['-DBUILD_SHARED_LIBS=ON', '-DBUILD_SHARED_LIBS=OFF'] + +postinstallcmds = [ + 'rm %(builddir)s/tessdata_best-*/configs', + 'rm -rf %(builddir)s/tessdata_best-*/tessconfigs', + 'mv %(builddir)s/tessdata_best-*/* %(installdir)s/share/tessdata' +] + +modextrapaths = { + 'TESSDATA_PREFIX': 'share/tessdata', +} + +sanity_check_paths = { + 'files': ['bin/tesseract', 'lib/libtesseract.a', 'lib/libtesseract.%s' % SHLIB_EXT], + 'dirs': ['share/tessdata', 'include/tesseract'] +} + +sanity_check_commands = ['tesseract --version', 'tesseract --list-langs'] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/t/texlive/texlive-20230313-GCC-13.2.0.eb b/easybuild/easyconfigs/t/texlive/texlive-20230313-GCC-13.2.0.eb new file mode 100644 index 00000000000..5d21ba5f6d1 --- /dev/null +++ b/easybuild/easyconfigs/t/texlive/texlive-20230313-GCC-13.2.0.eb @@ -0,0 +1,78 @@ +# Based off the 2017 version by John Dey jfdey@fredhutch.org +# https://github.com/easybuilders/easybuild-easyconfigs/pull/5085 +easyblock = 'Tarball' + +name = 'texlive' +version = '20230313' +local_ver_year = version[:4] + +homepage = 'https://tug.org' +description = """TeX is a typesetting language. Instead of visually formatting your text, you enter your manuscript + text intertwined with TeX commands in a plain text file. You then run TeX to produce formatted output, such as a + PDF file. Thus, in contrast to standard word processors, your document is a separate file that does not pretend to + be a representation of the final typeset output, and so can be easily edited and manipulated.""" + +toolchain = {'name': 'GCC', 'version': '13.2.0'} + +source_urls = [ + 'ftp://tug.org/texlive/historic/%s/' % local_ver_year, + 'https://ftp.math.utah.edu/pub/tex/historic/systems/texlive/%s/' % local_ver_year, +] +sources = [ + { + 'download_filename': 'install-tl-unx.tar.gz', + 'filename': 'install-tl-unx-%(version)s.tar.gz' + } +] +checksums = ['d97bdb3b1903428e56373e70861b24db448243d74d950cdff96f4e888f008605'] + +dependencies = [ + ('X11', '20231019'), + ('libpng', '1.6.40'), + ('libGLU', '9.0.3'), + ('Perl', '5.38.0'), + ('HarfBuzz', '8.2.2'), + ('poppler', '24.04.0'), + ('cairo', '1.18.0'), + ('fontconfig', '2.14.2'), + ('zlib', '1.2.13'), + ('graphite2', '1.3.14'), +] + +# For the latest release, the tlnet-final repository isn't available yet, so we use the default +# But, the default can _not_ be used for the historic releases. The only way to write an EasyConfig +# that will work today and in the future, is to try one by one. +# Similarly, ftp is not available on all HPC systems, hence providing fallback to https +# See https://github.com/easybuilders/easybuild-easyconfigs/issues/17871 +local_install_tl = "%%(builddir)s/install-tl-%%(version)s/install-tl -profile %%(installdir)s/texlive.profile %s" +local_ftp = '-repository ftp://ftp.math.utah.edu/pub/tex/historic/systems/textlive/%s/tlnet-final' % local_ver_year +local_https = '-repository https://ftp.math.utah.edu/pub/tex/historic/systems/texlive/%s/tlnet-final' % local_ver_year +local_install_tl_or = ( + ' || '.join([ + local_install_tl % '', + local_install_tl % local_ftp, + local_install_tl % local_https, + ]) +) +postinstallcmds = [ + 'echo "TEXDIR %%(installdir)s/" > %%(installdir)s/texlive.profile && ' + 'echo "TEXMFLOCAL %%(installdir)s/texmf-local" >> %%(installdir)s/texlive.profile && ' + 'echo "TEXMFSYSCONFIG %%(installdir)s/texmf-config" >> %%(installdir)s/texlive.profile && ' + 'echo "TEXMFSYSVAR %%(installdir)s/texmf-var" >> %%(installdir)s/texlive.profile && ' + '%s' % local_install_tl_or +] + +sanity_check_paths = { + 'files': ['bin/%(arch)s-linux/tex', 'bin/%(arch)s-linux/latex'], + 'dirs': ['bin/%(arch)s-linux', 'texmf-dist'], +} + +modextrapaths = { + 'INFOPATH': 'texmf-dist/doc/info', + 'MANPATH': 'texmf-dist/doc/man', + 'PATH': 'bin/%(arch)s-linux', +} + +modextravars = {'TEXMFHOME': '%(installdir)s/texmf-dist'} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/t/tiktoken/tiktoken-0.7.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/t/tiktoken/tiktoken-0.7.0-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..3dc06c7edcb --- /dev/null +++ b/easybuild/easyconfigs/t/tiktoken/tiktoken-0.7.0-GCCcore-12.3.0.eb @@ -0,0 +1,135 @@ +easyblock = 'CargoPythonPackage' + +name = 'tiktoken' +version = '0.7.0' +_rust_ver = '1.75.0' + +homepage = 'https://github.com/openai/tiktoken' +description = "tiktoken is a fast BPE tokeniser for use with OpenAI's models" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +builddependencies = [ + ('binutils', '2.40'), + ('Rust', _rust_ver), + ('maturin', '1.4.0', '-Rust-%s' % _rust_ver), + ('hypothesis', '6.82.0') +] + +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), # regex (and pytest for tests) +] + +crates = [ + ('aho-corasick', '1.1.3'), + ('autocfg', '1.2.0'), + ('bit-set', '0.5.3'), + ('bit-vec', '0.6.3'), + ('bitflags', '1.3.2'), + ('bstr', '1.9.1'), + ('cfg-if', '1.0.0'), + ('fancy-regex', '0.11.0'), + ('heck', '0.4.1'), + ('indoc', '2.0.5'), + ('libc', '0.2.153'), + ('lock_api', '0.4.11'), + ('memchr', '2.7.2'), + ('memoffset', '0.9.1'), + ('once_cell', '1.19.0'), + ('parking_lot', '0.12.1'), + ('parking_lot_core', '0.9.9'), + ('portable-atomic', '1.6.0'), + ('proc-macro2', '1.0.79'), + ('pyo3', '0.20.3'), + ('pyo3-build-config', '0.20.3'), + ('pyo3-ffi', '0.20.3'), + ('pyo3-macros', '0.20.3'), + ('pyo3-macros-backend', '0.20.3'), + ('quote', '1.0.36'), + ('redox_syscall', '0.4.1'), + ('regex', '1.10.4'), + ('regex-automata', '0.4.6'), + ('regex-syntax', '0.8.3'), + ('rustc-hash', '1.1.0'), + ('scopeguard', '1.2.0'), + ('serde', '1.0.197'), + ('serde_derive', '1.0.197'), + ('smallvec', '1.13.2'), + ('syn', '2.0.58'), + ('target-lexicon', '0.12.14'), + ('unicode-ident', '1.0.12'), + ('unindent', '0.2.3'), + ('windows-targets', '0.48.5'), + ('windows_aarch64_gnullvm', '0.48.5'), + ('windows_aarch64_msvc', '0.48.5'), + ('windows_i686_gnu', '0.48.5'), + ('windows_i686_msvc', '0.48.5'), + ('windows_x86_64_gnu', '0.48.5'), + ('windows_x86_64_gnullvm', '0.48.5'), + ('windows_x86_64_msvc', '0.48.5'), +] +sources = [SOURCE_TAR_GZ] +checksums = [ + {'tiktoken-0.7.0.tar.gz': '1077266e949c24e0291f6c350433c6f0971365ece2b173a23bc3b9f9defef6b6'}, + {'aho-corasick-1.1.3.tar.gz': '8e60d3430d3a69478ad0993f19238d2df97c507009a52b3c10addcd7f6bcb916'}, + {'autocfg-1.2.0.tar.gz': 'f1fdabc7756949593fe60f30ec81974b613357de856987752631dea1e3394c80'}, + {'bit-set-0.5.3.tar.gz': '0700ddab506f33b20a03b13996eccd309a48e5ff77d0d95926aa0210fb4e95f1'}, + {'bit-vec-0.6.3.tar.gz': '349f9b6a179ed607305526ca489b34ad0a41aed5f7980fa90eb03160b69598fb'}, + {'bitflags-1.3.2.tar.gz': 'bef38d45163c2f1dde094a7dfd33ccf595c92905c8f8f4fdc18d06fb1037718a'}, + {'bstr-1.9.1.tar.gz': '05efc5cfd9110c8416e471df0e96702d58690178e206e61b7173706673c93706'}, + {'cfg-if-1.0.0.tar.gz': 'baf1de4339761588bc0619e3cbc0120ee582ebb74b53b4efbf79117bd2da40fd'}, + {'fancy-regex-0.11.0.tar.gz': 'b95f7c0680e4142284cf8b22c14a476e87d61b004a3a0861872b32ef7ead40a2'}, + {'heck-0.4.1.tar.gz': '95505c38b4572b2d910cecb0281560f54b440a19336cbbcb27bf6ce6adc6f5a8'}, + {'indoc-2.0.5.tar.gz': 'b248f5224d1d606005e02c97f5aa4e88eeb230488bcc03bc9ca4d7991399f2b5'}, + {'libc-0.2.153.tar.gz': '9c198f91728a82281a64e1f4f9eeb25d82cb32a5de251c6bd1b5154d63a8e7bd'}, + {'lock_api-0.4.11.tar.gz': '3c168f8615b12bc01f9c17e2eb0cc07dcae1940121185446edc3744920e8ef45'}, + {'memchr-2.7.2.tar.gz': '6c8640c5d730cb13ebd907d8d04b52f55ac9a2eec55b440c8892f40d56c76c1d'}, + {'memoffset-0.9.1.tar.gz': '488016bfae457b036d996092f6cb448677611ce4449e970ceaf42695203f218a'}, + {'once_cell-1.19.0.tar.gz': '3fdb12b2476b595f9358c5161aa467c2438859caa136dec86c26fdd2efe17b92'}, + {'parking_lot-0.12.1.tar.gz': '3742b2c103b9f06bc9fff0a37ff4912935851bee6d36f3c02bcc755bcfec228f'}, + {'parking_lot_core-0.9.9.tar.gz': '4c42a9226546d68acdd9c0a280d17ce19bfe27a46bf68784e4066115788d008e'}, + {'portable-atomic-1.6.0.tar.gz': '7170ef9988bc169ba16dd36a7fa041e5c4cbeb6a35b76d4c03daded371eae7c0'}, + {'proc-macro2-1.0.79.tar.gz': 'e835ff2298f5721608eb1a980ecaee1aef2c132bf95ecc026a11b7bf3c01c02e'}, + {'pyo3-0.20.3.tar.gz': '53bdbb96d49157e65d45cc287af5f32ffadd5f4761438b527b055fb0d4bb8233'}, + {'pyo3-build-config-0.20.3.tar.gz': 'deaa5745de3f5231ce10517a1f5dd97d53e5a2fd77aa6b5842292085831d48d7'}, + {'pyo3-ffi-0.20.3.tar.gz': '62b42531d03e08d4ef1f6e85a2ed422eb678b8cd62b762e53891c05faf0d4afa'}, + {'pyo3-macros-0.20.3.tar.gz': '7305c720fa01b8055ec95e484a6eca7a83c841267f0dd5280f0c8b8551d2c158'}, + {'pyo3-macros-backend-0.20.3.tar.gz': '7c7e9b68bb9c3149c5b0cade5d07f953d6d125eb4337723c4ccdb665f1f96185'}, + {'quote-1.0.36.tar.gz': '0fa76aaf39101c457836aec0ce2316dbdc3ab723cdda1c6bd4e6ad4208acaca7'}, + {'redox_syscall-0.4.1.tar.gz': '4722d768eff46b75989dd134e5c353f0d6296e5aaa3132e776cbdb56be7731aa'}, + {'regex-1.10.4.tar.gz': 'c117dbdfde9c8308975b6a18d71f3f385c89461f7b3fb054288ecf2a2058ba4c'}, + {'regex-automata-0.4.6.tar.gz': '86b83b8b9847f9bf95ef68afb0b8e6cdb80f498442f5179a29fad448fcc1eaea'}, + {'regex-syntax-0.8.3.tar.gz': 'adad44e29e4c806119491a7f06f03de4d1af22c3a680dd47f1e6e179439d1f56'}, + {'rustc-hash-1.1.0.tar.gz': '08d43f7aa6b08d49f382cde6a7982047c3426db949b1424bc4b7ec9ae12c6ce2'}, + {'scopeguard-1.2.0.tar.gz': '94143f37725109f92c262ed2cf5e59bce7498c01bcc1502d7b9afe439a4e9f49'}, + {'serde-1.0.197.tar.gz': '3fb1c873e1b9b056a4dc4c0c198b24c3ffa059243875552b2bd0933b1aee4ce2'}, + {'serde_derive-1.0.197.tar.gz': '7eb0b34b42edc17f6b7cac84a52a1c5f0e1bb2227e997ca9011ea3dd34e8610b'}, + {'smallvec-1.13.2.tar.gz': '3c5e1a9a646d36c3599cd173a41282daf47c44583ad367b8e6837255952e5c67'}, + {'syn-2.0.58.tar.gz': '44cfb93f38070beee36b3fef7d4f5a16f27751d94b187b666a5cc5e9b0d30687'}, + {'target-lexicon-0.12.14.tar.gz': 'e1fc403891a21bcfb7c37834ba66a547a8f402146eba7265b5a6d88059c9ff2f'}, + {'unicode-ident-1.0.12.tar.gz': '3354b9ac3fae1ff6755cb6db53683adb661634f67557942dea4facebec0fee4b'}, + {'unindent-0.2.3.tar.gz': 'c7de7d73e1754487cb58364ee906a499937a0dfabd86bcb980fa99ec8c8fa2ce'}, + {'windows-targets-0.48.5.tar.gz': '9a2fa6e2155d7247be68c096456083145c183cbbbc2764150dda45a87197940c'}, + {'windows_aarch64_gnullvm-0.48.5.tar.gz': '2b38e32f0abccf9987a4e3079dfb67dcd799fb61361e53e2882c3cbaf0d905d8'}, + {'windows_aarch64_msvc-0.48.5.tar.gz': 'dc35310971f3b2dbbf3f0690a219f40e2d9afcf64f9ab7cc1be722937c26b4bc'}, + {'windows_i686_gnu-0.48.5.tar.gz': 'a75915e7def60c94dcef72200b9a8e58e5091744960da64ec734a6c6e9b3743e'}, + {'windows_i686_msvc-0.48.5.tar.gz': '8f55c233f70c4b27f66c523580f78f1004e8b5a8b659e05a4eb49d4166cca406'}, + {'windows_x86_64_gnu-0.48.5.tar.gz': '53d40abd2583d23e4718fddf1ebec84dbff8381c07cae67ff7768bbf19c6718e'}, + {'windows_x86_64_gnullvm-0.48.5.tar.gz': '0b7b52767868a23d5bab768e390dc5f5c55825b6d30b86c844ff2dc7414044cc'}, + {'windows_x86_64_msvc-0.48.5.tar.gz': 'ed94fce61571a4006852b7389a063ab983c02eb1bb37b47f8272ce92d06d9538'}, +] + +use_pip = True +sanity_pip_check = True +download_dep_fail = True + +# https://github.com/openai/tiktoken/issues/194 +runtest = ( + 'ln -s $PWD/tests ../tests_%(name)s' + ' && cd ..' + ' && pytest tests_%(name)s/' +) +testinstall = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/t/time/time-1.9-GCCcore-13.3.0.eb b/easybuild/easyconfigs/t/time/time-1.9-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..acc1705405e --- /dev/null +++ b/easybuild/easyconfigs/t/time/time-1.9-GCCcore-13.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'time' +version = '1.9' + +homepage = 'https://www.gnu.org/software/time/' +description = """The `time' command runs another program, then displays information about the resources used by that + program, collected by the system while the program was running.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['fbacf0c81e62429df3e33bda4cee38756604f18e01d977338e23306a3e3b521e'] + +builddependencies = [('binutils', '2.42')] + +postinstallcmds = ["ln -s %(installdir)s/bin/%(name)s %(installdir)s/bin/gtime"] + +sanity_check_paths = { + 'files': ['bin/gtime', 'bin/%(name)s'], + 'dirs': [], +} + +sanity_check_commands = ["time echo test"] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/t/timm/timm-0.9.7-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/t/timm/timm-0.9.7-foss-2022a-CUDA-11.7.0.eb index f97e02d9b16..07cedb70489 100644 --- a/easybuild/easyconfigs/t/timm/timm-0.9.7-foss-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/t/timm/timm-0.9.7-foss-2022a-CUDA-11.7.0.eb @@ -139,14 +139,9 @@ crates = [ ('aho-corasick', '1.1.2'), ('anes', '0.1.6'), ('atty', '0.2.14'), - ('autocfg', '1.1.0'), ('bit-set', '0.5.3'), ('bit-vec', '0.6.3'), - ('bitflags', '1.3.2'), - ('bitflags', '2.4.2'), - ('bumpalo', '3.14.0'), ('cast', '0.3.0'), - ('cfg-if', '1.0.0'), ('ciborium', '0.2.2'), ('ciborium-io', '0.2.2'), ('ciborium-ll', '0.2.2'), @@ -154,91 +149,41 @@ crates = [ ('clap_lex', '0.2.4'), ('criterion', '0.4.0'), ('criterion-plot', '0.5.0'), - ('crossbeam-deque', '0.8.5'), - ('crossbeam-epoch', '0.9.18'), - ('crossbeam-utils', '0.8.19'), ('crunchy', '0.2.2'), - ('either', '1.9.0'), ('errno', '0.3.8'), ('fastrand', '2.0.1'), ('fnv', '1.0.7'), - ('getrandom', '0.2.12'), ('half', '2.3.1'), ('hashbrown', '0.12.3'), ('hermit-abi', '0.1.19'), ('indexmap', '1.9.3'), ('itertools', '0.10.5'), - ('itoa', '1.0.10'), - ('js-sys', '0.3.67'), - ('lazy_static', '1.4.0'), - ('libc', '0.2.152'), - ('libm', '0.2.8'), ('linux-raw-sys', '0.4.13'), - ('log', '0.4.20'), ('memchr', '2.7.1'), ('memmap2', '0.5.10'), - ('num-traits', '0.2.17'), - ('once_cell', '1.19.0'), ('oorandom', '11.1.3'), ('os_str_bytes', '6.6.1'), ('plotters', '0.3.5'), ('plotters-backend', '0.3.5'), ('plotters-svg', '0.3.5'), - ('ppv-lite86', '0.2.17'), - ('proc-macro2', '1.0.78'), - ('proptest', '1.4.0'), ('pyo3', '0.20.2'), ('pyo3-build-config', '0.20.2'), ('pyo3-ffi', '0.20.2'), ('pyo3-macros', '0.20.2'), ('pyo3-macros-backend', '0.20.2'), ('quick-error', '1.2.3'), - ('quote', '1.0.35'), - ('rand', '0.8.5'), - ('rand_chacha', '0.3.1'), - ('rand_core', '0.6.4'), - ('rand_xorshift', '0.3.0'), - ('rayon', '1.8.1'), - ('rayon-core', '1.12.1'), - ('redox_syscall', '0.4.1'), ('regex', '1.10.3'), ('regex-automata', '0.4.4'), - ('regex-syntax', '0.8.2'), ('rustix', '0.38.30'), ('rusty-fork', '0.3.0'), - ('ryu', '1.0.16'), ('same-file', '1.0.6'), - ('serde', '1.0.195'), - ('serde_derive', '1.0.195'), - ('serde_json', '1.0.111'), - ('syn', '2.0.48'), ('tempfile', '3.9.0'), ('textwrap', '0.16.0'), ('tinytemplate', '1.2.1'), - ('unarray', '0.1.4'), - ('unicode-ident', '1.0.12'), ('wait-timeout', '0.2.0'), ('walkdir', '2.4.0'), - ('wasi', '0.11.0+wasi-snapshot-preview1'), - ('wasm-bindgen', '0.2.90'), - ('wasm-bindgen-backend', '0.2.90'), - ('wasm-bindgen-macro', '0.2.90'), - ('wasm-bindgen-macro-support', '0.2.90'), - ('wasm-bindgen-shared', '0.2.90'), ('web-sys', '0.3.67'), - ('winapi', '0.3.9'), - ('winapi-i686-pc-windows-gnu', '0.4.0'), - ('winapi-util', '0.1.6'), - ('winapi-x86_64-pc-windows-gnu', '0.4.0'), ('windows-sys', '0.52.0'), - ('windows-targets', '0.52.0'), - ('windows_aarch64_gnullvm', '0.52.0'), - ('windows_aarch64_msvc', '0.52.0'), - ('windows_i686_gnu', '0.52.0'), - ('windows_i686_msvc', '0.52.0'), - ('windows_x86_64_gnu', '0.52.0'), - ('windows_x86_64_gnullvm', '0.52.0'), - ('windows_x86_64_msvc', '0.52.0'), ] sources = [SOURCE_TAR_GZ] checksums = [ @@ -352,14 +297,9 @@ checksums = [ {'aho-corasick-1.1.2.tar.gz': 'b2969dcb958b36655471fc61f7e416fa76033bdd4bfed0678d8fee1e2d07a1f0'}, {'anes-0.1.6.tar.gz': '4b46cbb362ab8752921c97e041f5e366ee6297bd428a31275b9fcf1e380f7299'}, {'atty-0.2.14.tar.gz': 'd9b39be18770d11421cdb1b9947a45dd3f37e93092cbf377614828a319d5fee8'}, - {'autocfg-1.1.0.tar.gz': 'd468802bab17cbc0cc575e9b053f41e72aa36bfa6b7f55e3529ffa43161b97fa'}, {'bit-set-0.5.3.tar.gz': '0700ddab506f33b20a03b13996eccd309a48e5ff77d0d95926aa0210fb4e95f1'}, {'bit-vec-0.6.3.tar.gz': '349f9b6a179ed607305526ca489b34ad0a41aed5f7980fa90eb03160b69598fb'}, - {'bitflags-1.3.2.tar.gz': 'bef38d45163c2f1dde094a7dfd33ccf595c92905c8f8f4fdc18d06fb1037718a'}, - {'bitflags-2.4.2.tar.gz': 'ed570934406eb16438a4e976b1b4500774099c13b8cb96eec99f620f05090ddf'}, - {'bumpalo-3.14.0.tar.gz': '7f30e7476521f6f8af1a1c4c0b8cc94f0bee37d91763d0ca2665f299b6cd8aec'}, {'cast-0.3.0.tar.gz': '37b2a672a2cb129a2e41c10b1224bb368f9f37a2b16b612598138befd7b37eb5'}, - {'cfg-if-1.0.0.tar.gz': 'baf1de4339761588bc0619e3cbc0120ee582ebb74b53b4efbf79117bd2da40fd'}, {'ciborium-0.2.2.tar.gz': '42e69ffd6f0917f5c029256a24d0161db17cea3997d185db0d35926308770f0e'}, {'ciborium-io-0.2.2.tar.gz': '05afea1e0a06c9be33d539b876f1ce3692f4afea2cb41f740e7743225ed1c757'}, {'ciborium-ll-0.2.2.tar.gz': '57663b653d948a338bfb3eeba9bb2fd5fcfaecb9e199e87e1eda4d9e8b240fd9'}, @@ -367,91 +307,40 @@ checksums = [ {'clap_lex-0.2.4.tar.gz': '2850f2f5a82cbf437dd5af4d49848fbdfc27c157c3d010345776f952765261c5'}, {'criterion-0.4.0.tar.gz': 'e7c76e09c1aae2bc52b3d2f29e13c6572553b30c4aa1b8a49fd70de6412654cb'}, {'criterion-plot-0.5.0.tar.gz': '6b50826342786a51a89e2da3a28f1c32b06e387201bc2d19791f622c673706b1'}, - 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b/easybuild/easyconfigs/t/timm/timm-1.0.8-foss-2023a-CUDA-12.1.1.eb @@ -0,0 +1,44 @@ +easyblock = 'PythonBundle' + +name = 'timm' +version = '1.0.8' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://huggingface.co/docs/timm' +description = """ +timm is a library containing SOTA computer vision models, layers, utilities, +optimizers, schedulers, data-loaders, augmentations, and training/evaluation +scripts. It comes packaged with >700 pretrained models, and is designed to be +flexible and easy to use. +""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('CUDA', '12.1.1', '', SYSTEM), + ('PyTorch', '2.1.2', versionsuffix), + ('PyYAML', '6.0'), + ('tqdm', '4.66.1'), + ('torchvision', '0.16.0', versionsuffix), + ('Safetensors', '0.4.3'), +] + +builddependencies = [ + ('PDM', '2.12.4'), +] + +use_pip = True + +exts_list = [ + ('huggingface_hub', '0.24.5', { + 'checksums': ['7b45d6744dd53ce9cbf9880957de00e9d10a9ae837f1c9b7255fc8fa4e8264f3'], + }), + (name, version, { + 'checksums': ['f54a579f1cc39c43d99a4b03603e39c4cee87d4f0a08aba9c22e19064b30bf95'], + }), +] + +sanity_pip_check = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/t/timm/timm-1.0.8-foss-2023a.eb b/easybuild/easyconfigs/t/timm/timm-1.0.8-foss-2023a.eb new file mode 100644 index 00000000000..a954aa9e443 --- /dev/null +++ b/easybuild/easyconfigs/t/timm/timm-1.0.8-foss-2023a.eb @@ -0,0 +1,42 @@ +easyblock = 'PythonBundle' + +name = 'timm' +version = '1.0.8' + +homepage = 'https://huggingface.co/docs/timm' +description = """ +timm is a library containing SOTA computer vision models, layers, utilities, +optimizers, schedulers, data-loaders, augmentations, and training/evaluation +scripts. It comes packaged with >700 pretrained models, and is designed to be +flexible and easy to use. +""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('PyTorch', '2.1.2'), + ('PyYAML', '6.0'), + ('tqdm', '4.66.1'), + ('torchvision', '0.16.0'), + ('Safetensors', '0.4.3'), +] + +builddependencies = [ + ('PDM', '2.12.4'), +] + +use_pip = True + +exts_list = [ + ('huggingface_hub', '0.24.5', { + 'checksums': ['7b45d6744dd53ce9cbf9880957de00e9d10a9ae837f1c9b7255fc8fa4e8264f3'], + }), + (name, version, { + 'checksums': ['f54a579f1cc39c43d99a4b03603e39c4cee87d4f0a08aba9c22e19064b30bf95'], + }), +] + +sanity_pip_check = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/t/tmux/tmux-3.4-GCCcore-13.2.0.eb b/easybuild/easyconfigs/t/tmux/tmux-3.4-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..8a3a24c2d12 --- /dev/null +++ b/easybuild/easyconfigs/t/tmux/tmux-3.4-GCCcore-13.2.0.eb @@ -0,0 +1,38 @@ +easyblock = 'ConfigureMake' + +name = 'tmux' +version = '3.4' + +homepage = 'https://github.com/tmux/tmux/' +description = """tmux is a terminal multiplexer: it enables a number of +terminals to be created, accessed, and controlled from a single screen. tmux +may be detached from a screen and continue running in the background, then +later reattached.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} +toolchainopts = {'optarch': True} + +source_urls = ['https://github.com/%(name)s/%(name)s/releases/download/%(version)s/'] +sources = [SOURCE_TAR_GZ] +checksums = ['551ab8dea0bf505c0ad6b7bb35ef567cdde0ccb84357df142c254f35a23e19aa'] + +builddependencies = [ + ('binutils', '2.40'), + ('Bison', '3.8.2'), + ('make', '4.4.1'), + ('pkgconf', '2.0.3'), +] + +dependencies = [ + ('libevent', '2.1.12'), + ('ncurses', '6.4'), +] + +sanity_check_paths = { + 'files': ['bin/tmux'], + 'dirs': [] +} + +sanity_check_commands = ["tmux --help 2>&1 | grep 'usage: tmux'"] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/t/tmux/tmux-3.4-GCCcore-13.3.0.eb b/easybuild/easyconfigs/t/tmux/tmux-3.4-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..43a1310c52d --- /dev/null +++ b/easybuild/easyconfigs/t/tmux/tmux-3.4-GCCcore-13.3.0.eb @@ -0,0 +1,38 @@ +easyblock = 'ConfigureMake' + +name = 'tmux' +version = '3.4' + +homepage = 'https://github.com/tmux/tmux/' +description = """tmux is a terminal multiplexer: it enables a number of +terminals to be created, accessed, and controlled from a single screen. tmux +may be detached from a screen and continue running in the background, then +later reattached.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'optarch': True} + +source_urls = ['https://github.com/%(name)s/%(name)s/releases/download/%(version)s/'] +sources = [SOURCE_TAR_GZ] +checksums = ['551ab8dea0bf505c0ad6b7bb35ef567cdde0ccb84357df142c254f35a23e19aa'] + +builddependencies = [ + ('binutils', '2.42'), + ('Bison', '3.8.2'), + ('make', '4.4.1'), + ('pkgconf', '2.2.0'), +] + +dependencies = [ + ('libevent', '2.1.12'), + ('ncurses', '6.5'), +] + +sanity_check_paths = { + 'files': ['bin/tmux'], + 'dirs': [] +} + +sanity_check_commands = ["tmux --help 2>&1 | grep 'usage: tmux'"] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/t/tmux/tmux-3.4.eb b/easybuild/easyconfigs/t/tmux/tmux-3.4.eb new file mode 100644 index 00000000000..d15f35e58ed --- /dev/null +++ b/easybuild/easyconfigs/t/tmux/tmux-3.4.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'tmux' +version = '3.4' + +homepage = 'https://github.com/tmux/tmux/' +description = """tmux is a terminal multiplexer: it enables a number of +terminals to be created, accessed, and controlled from a single screen. tmux +may be detached from a screen and continue running in the background, then +later reattached.""" + +toolchain = SYSTEM + +source_urls = ['https://github.com/%(name)s/%(name)s/releases/download/%(version)s/'] +sources = [SOURCE_TAR_GZ] +checksums = ['551ab8dea0bf505c0ad6b7bb35ef567cdde0ccb84357df142c254f35a23e19aa'] + +builddependencies = [ + ('Bison', '3.8.2'), +] + +dependencies = [ + ('libevent', '2.1.12'), + ('ncurses', '6.5'), +] + +sanity_check_paths = { + 'files': ['bin/tmux'], + 'dirs': [] +} + +sanity_check_commands = ["tmux --help 2>&1 | grep 'usage: tmux'"] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/t/tokenizers/tokenizers-0.19.1-GCCcore-13.2.0.eb b/easybuild/easyconfigs/t/tokenizers/tokenizers-0.19.1-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..3b5675b24df --- /dev/null +++ b/easybuild/easyconfigs/t/tokenizers/tokenizers-0.19.1-GCCcore-13.2.0.eb @@ -0,0 +1,567 @@ +easyblock = 'CargoPythonBundle' + +name = 'tokenizers' +version = '0.19.1' + +homepage = 'https://github.com/huggingface/tokenizers' +description = "Fast State-of-the-Art Tokenizers optimized for Research and Production" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +crates = [ + ('adler2', '2.0.0'), + ('aho-corasick', '1.1.3'), + ('anes', '0.1.6'), + ('anstream', '0.6.13'), + ('anstyle', '1.0.6'), + ('anstyle', '1.0.8'), + ('anstyle-parse', '0.2.3'), + ('anstyle-query', '1.0.2'), + ('anstyle-wincon', '3.0.2'), + ('assert_approx_eq', '1.1.0'), + ('autocfg', '1.2.0'), + ('autocfg', '1.3.0'), + ('base64', '0.13.1'), + ('base64', '0.22.1'), + ('bit-set', '0.5.3'), + ('bit-vec', '0.6.3'), + ('bitflags', '1.3.2'), + ('bitflags', '2.5.0'), + ('bitflags', '2.6.0'), + ('bumpalo', '3.16.0'), + ('byteorder', '1.5.0'), + ('cast', '0.3.0'), + ('cc', '1.0.94'), + ('cc', '1.1.13'), + ('cfg-if', '1.0.0'), + ('ciborium', '0.2.2'), + ('ciborium-io', '0.2.2'), + ('ciborium-ll', '0.2.2'), + ('clap', '4.5.16'), + ('clap_builder', '4.5.15'), + ('clap_lex', '0.7.2'), + ('colorchoice', '1.0.0'), + ('console', '0.15.8'), + ('core-foundation', '0.9.4'), + ('core-foundation-sys', '0.8.7'), + ('crc32fast', '1.4.2'), + ('criterion', '0.5.1'), + ('criterion-plot', '0.5.0'), + ('crossbeam-deque', '0.8.5'), + 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'1b9b4fd18abc82b8136838da5d50bae7bdea537c574d8dc1a34ed098d6c166f0'}, + {'zerocopy-derive-0.7.35.tar.gz': 'fa4f8080344d4671fb4e831a13ad1e68092748387dfc4f55e356242fae12ce3e'}, + {'zeroize-1.8.1.tar.gz': 'ced3678a2879b30306d323f4542626697a464a97c0a07c9aebf7ebca65cd4dde'}, +] + +_rust_ver = '1.76.0' +builddependencies = [ + ('binutils', '2.40'), + ('Rust', _rust_ver), + ('maturin', '1.5.0', '-Rust-%s' % _rust_ver), +] + +dependencies = [ + ('Python', '3.11.5'), + ('Python-bundle-PyPI', '2023.10'), # fsspec, filelock used by hf-hub + ('PyYAML', '6.0.1'), # used by hf-hub + ('tqdm', '4.66.2'), # used by hf-hub +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('huggingface-hub', '0.24.6', { + 'source_tmpl': 'huggingface_hub-%(version)s.tar.gz', + 'checksums': ['cc2579e761d070713eaa9c323e3debe39d5b464ae3a7261c39a9195b27bb8000'], + }), + (name, version, { + 'checksums': ['ee59e6680ed0fdbe6b724cf38bd70400a0c1dd623b07ac729087270caeac88e3'], + }), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/t/topaz/topaz-0.2.5.20231120-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/t/topaz/topaz-0.2.5.20231120-foss-2023a-CUDA-12.1.1.eb new file mode 100644 index 00000000000..8156c8d8dbc --- /dev/null +++ b/easybuild/easyconfigs/t/topaz/topaz-0.2.5.20231120-foss-2023a-CUDA-12.1.1.eb @@ -0,0 +1,61 @@ +# Thomas Hoffman, EMBL Heidelberg, structures-it@embl.de, 2023/11 +easyblock = 'PythonPackage' + +name = 'topaz' +_mainversion = '0.2.5' +_commitdate = '20231120' +_commit = '25cb2cb' +version = '%s.%s' % (_mainversion, _commitdate) +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'http://cb.csail.mit.edu/cb/topaz/' + +description = """Particle picking software for single particle cryo-electron microscopy using +convolutional neural networks and positive-unlabeled learning. Includes methods +for micrograph denoising.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('CUDA', '12.1.1', '', SYSTEM), + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('PyTorch-bundle', '2.1.2', versionsuffix), + ('scikit-learn', '1.3.1'), + ('scikit-image', '0.22.0'), +] + +source_urls = ['https://github.com/tbepler/topaz/archive'] +sources = [{ + 'download_filename': '%s.tar.gz' % _commit, + 'filename': '%(name)s-%(version)s.tar.gz' +}] +patches = [ + 'topaz-0.2.5_install_relion3_wrappers.patch', + 'topaz-0.2.5.20231120_helical-filament-picking.patch', + 'topaz-0.2.5.20231120_update-description.patch', +] +checksums = [ + {'topaz-0.2.5.20231120.tar.gz': 'ca0630f9a69622eb3e10c9de310f58ac846e60a5504c4533398a9a75b3091df9'}, + {'topaz-0.2.5_install_relion3_wrappers.patch': '0fe23a0ecaf887aaa89641a7e7cf37fafd3134384b0a8f46acb4e17537d1a151'}, + {'topaz-0.2.5.20231120_helical-filament-picking.patch': + '320466e4ac1d1f06ba392a419aefa369905baa6877717868cd8ea7135b6bc28f'}, + {'topaz-0.2.5.20231120_update-description.patch': + '073241dba2de63e543136a387ff7ef698a5e0139ab3356de021e370338fa57c1'}, +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +options = {'modulename': 'topaz'} + +_relion3_wrappers = ['denoise', 'pick', 'train', 'train_denoise'] + +sanity_check_paths = { + 'files': ["bin/run_topaz_%s.py" % x for x in _relion3_wrappers], + 'dirs': [], +} +sanity_check_commands = ['run_topaz_%s.py --help' % x for x in _relion3_wrappers] + ['topaz --help'] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/t/topaz/topaz-0.2.5.20231120_helical-filament-picking.patch b/easybuild/easyconfigs/t/topaz/topaz-0.2.5.20231120_helical-filament-picking.patch new file mode 100644 index 00000000000..2e8413fd5e3 --- /dev/null +++ b/easybuild/easyconfigs/t/topaz/topaz-0.2.5.20231120_helical-filament-picking.patch @@ -0,0 +1,289 @@ +From 4ea1710c88648ff4c5f7232e20ad5d9aa9535241 Mon Sep 17 00:00:00 2001 +From: scheres +Date: Wed, 5 Jan 2022 12:13:10 +0000 +Subject: [PATCH] implemented helical filament picking in extract.py + +--- + topaz/commands/extract.py | 225 ++++++++++++++++++++++++++++++++++++-- + 1 file changed, 215 insertions(+), 10 deletions(-) + +diff --git a/topaz/commands/extract.py b/topaz/commands/extract.py +index 3c3f032..6676618 100644 +--- a/topaz/commands/extract.py ++++ b/topaz/commands/extract.py +@@ -52,6 +52,11 @@ def add_arguments(parser): + parser.add_argument('--targets', help='path to file specifying particle coordinates. used to find extraction radius that maximizes the AUPRC') + parser.add_argument('--only-validate', action='store_true', help='flag indicating to only calculate validation metrics. does not report full prediction list') + ++ # Filament picking SHWS 30032021 ++ parser.add_argument('-f', '--filaments', action='store_true', help='flag for filament start-end picking.') ++ parser.add_argument('-fp', '--filaments_plot', action='store_true', help='flag for filament start-end picking plus plotting of its intermediate stages (useful for tuning parameters).') ++ parser.add_argument('-fl', '--filaments_length', default=-1, type=int, help='minimum length of straight filament segments to be picked (in Angstrom) (default: twice --radius)') ++ + parser.add_argument('-d', '--device', default=0, type=int, help='which device to use, <0 corresponds to CPU') + + parser.add_argument('-o', '--output', help='file path to write') +@@ -63,24 +68,219 @@ def add_arguments(parser): + + return parser + ++ ++def is_in_between(point, line): ++ dx = line[1][0] - line[0][0] ++ dy = line[1][1] - line[0][1] ++ dotp = (point[0] - line[0][0])*dx + (point[1] - line[0][1])*dy ++ return 0 <= dotp and dotp <= dx*dx + dy*dy ++ ++def distance_point_line(point, line): ++ x1=line[0][0] ++ x2=line[1][0] ++ y1=line[0][1] ++ y2=line[1][1] ++ x0=point[0] ++ y0=point[1] ++ dd = abs( (x2-x1)*(y1-y0) - (x1-x0)*(y2-y1) ) / np.sqrt( (x2-x1)*(x2-x1) + (y2-y1)*(y2-y1) ) ++ if not is_in_between(point,line): ++ closest = min(distance_point_point(point,line[0]), distance_point_point(point,line[1])) ++ return max(closest, dd) ++ else: ++ return dd ++ ++def distance_point_point(point1, point2): ++ x1=point1[0] ++ y1=point1[1] ++ x2=point2[0] ++ y2=point2[1] ++ return np.sqrt((x1-x2)*(x1-x2) + (y1-y2)*(y1-y2)) ++ ++def angle_line_line(line1, line2): ++ a1 = np.arctan2(line1[1][1]-line1[0][1], line1[1][0]-line1[0][0]) ++ a2 = np.arctan2(line2[1][1]-line2[0][1], line2[1][0]-line2[0][0]) ++ return abs(a2-a1) ++ ++def prune_lines(inlines, mind, min_ang, max_merge): ++ import math ++ lengths = [] ++ merged = [] ++ lines = np.asarray(inlines) ++ for line in lines: ++ lengths = np.append(lengths, np.linalg.norm(line[0]-line[1])) ++ merged = np.append(merged, 1) ++ sortidx = np.argsort(lengths); ++ ++ min_ang_rad = math.radians(min_ang) ++ NN = len(sortidx) ++ idx = NN - 1 ++ while idx >= 0: ++ i1 = sortidx[idx] ++ ++ for i2 in range(NN): ++ if (i1 != i2 and lengths[i2] > 0. and lengths[i1] > 0.): ++ ++ d11 = distance_point_line(lines[i1][0],lines[i2]) ++ d12 = distance_point_line(lines[i1][1],lines[i2]) ++ d21 = distance_point_line(lines[i2][0],lines[i1]) ++ d22 = distance_point_line(lines[i2][1],lines[i1]) ++ ang = angle_line_line(lines[i1], lines[i2]) ++ sum = 0 ++ if (d11 < mind): ++ sum = sum + 1 ++ if (d12 < mind): ++ sum = sum + 1 ++ if (d21 < mind): ++ sum = sum + 1 ++ if (d22 < mind): ++ sum = sum + 1 ++ ++ # merge lines if they haven't been merged too often already, they overlap two or more points and are parallel ++ if ( (merged[i1] + merged[i2] < max_merge) and (sum >= 2) and (ang < min_ang_rad or abs(ang-math.pi) < min_ang_rad) ): ++ ++ # select the two points with the furthest distance ++ maxd=0 ++ for i in range(2): ++ for j in range(2): ++ d = distance_point_point(lines[i1][i], lines[i2][j]) ++ if (d > maxd): ++ maxd = d ++ mymax0 = lines[i1][i] ++ mymax1 = lines[i2][j] ++ # perhaps original one was longer? ++ if maxd > lengths[i1]: ++ lines[i1][0] = mymax0 ++ lines[i1][1] = mymax1 ++ lengths[i1] = np.linalg.norm(lines[i1][0]-lines[i1][1]) ++ merged[i1] = merged[i1] + merged[i2] ++ ++ lines[i2][0][0] = -9999 ++ lines[i2][0][1] = -9999 ++ lines[i2][1][0] = -9999 ++ lines[i2][1][1] = -9999 ++ lengths[i2] = 0 ++ merged[i2] = 0 ++ idx = idx + 1 ++ break ++ ++ # remove smaller lines with both points close to longer one ++ elif (d21 < mind and d22 < mind): ++ lines[i2][0][0] = -9999 ++ lines[i2][0][1] = -9999 ++ lines[i2][1][0] = -9999 ++ lines[i2][1][1] = -9999 ++ lengths[i2] = 0 ++ ++ idx = idx - 1 ++ ++ return lines ++ ++ ++def pick_filaments(score, radius, threshold, filaments_length, filaments_plot): ++ from topaz import mrc ++ from skimage.filters import gaussian ++ from skimage.transform import probabilistic_hough_line ++ from skimage.morphology import skeletonize ++ import math ++ ++ #Parameters ++ thr = round(0.1*filaments_length) ++ line_length = filaments_length ++ gap = radius ++ mind= radius ++ min_angle = 10 ++ max_merge = 5 ++ ++ bin_score = (gaussian(score, 3) > threshold) ++ edges = skeletonize(bin_score) ++ houghs = probabilistic_hough_line(edges, threshold=thr, line_length=line_length, line_gap=gap) ++ lines = prune_lines(houghs, mind=mind, min_ang=min_angle, max_merge=max_merge) ++ ++ if filaments_plot: ++ import matplotlib.pyplot as plt ++ from matplotlib import cm ++ fig, axes = plt.subplots(1, 4, figsize=(15, 5), sharex=True, sharey=True) ++ ax = axes.ravel() ++ ++ ax[0].imshow(score, cmap=cm.binary, vmin=-20, vmax=5) ++ ax[0].imshow(bin_score, alpha=0.5, cmap=cm.Reds) ++ ax[0].set_title('FOM [-20,5] thr= ' + str(threshold)) ++ ++ ax[1].imshow(edges, cmap=cm.gray) ++ ax[1].set_title('Skeletonize') ++ ++ ax[2].imshow(edges * 0) ++ for hough in houghs: ++ p0, p1 = hough ++ ax[2].plot((p0[0], p1[0]), (p0[1], p1[1])) ++ ax[2].set_xlim((0, score.shape[1])) ++ ax[2].set_ylim((score.shape[0], 0)) ++ ax[2].set_title('Hough transform; len= ' + str(line_length) + ' gap= ' + str(gap)) ++ ++ ax[3].imshow(edges * 0) ++ for line in lines: ++ p0, p1 = line ++ ax[3].plot((p0[0], p1[0]), (p0[1], p1[1])) ++ ax[3].set_xlim((0, score.shape[1])) ++ ax[3].set_ylim((score.shape[0], 0)) ++ ax[3].set_title('Prune: mind= ' + str(mind)) ++ ++ for a in ax: ++ a.set_axis_off() ++ ++ plt.tight_layout() ++ plt.show() ++ ++ oldlines=lines ++ # Flatten lines into 2D array, as rest of topaz ++ NN=len(lines) ++ if NN>0: ++ lines = lines.reshape(2*NN, 2) ++ # Remove -9999 coordinates ++ newlines = [] ++ for i in range(2*NN): ++ if (lines[i,0] != -9999 and lines[i,1] != -9999): ++ newlines = np.append(newlines, lines[i]) ++ ++ NN=round(len(newlines)/2) ++ if (NN>0): ++ lines = newlines.reshape(NN, 2) ++ else: ++ lines = [] ++ ++ # Just set scores to zero, a they are meaningless now ++ scores = np.zeros(NN, dtype=np.float32) ++ ++ return scores, lines ++ ++ + class NonMaximumSuppression: +- def __init__(self, radius, threshold): ++ def __init__(self, radius, threshold, do_filaments=False, filaments_length=150, filaments_plot=False): + self.radius = radius + self.threshold = threshold ++ self.do_filaments = do_filaments ++ self.filaments_length = filaments_length ++ self.filaments_plot = filaments_plot + + def __call__(self, args): + name,score = args +- score,coords = non_maximum_suppression(score, self.radius, threshold=self.threshold) +- return name, score, coords ++ if self.do_filaments: ++ score,coords = pick_filaments(score, self.radius, threshold=self.threshold, length=self.filaments_length, filaments_plot = self.filaments_plot ) ++ else: ++ score,coords = non_maximum_suppression(score, self.radius, threshold=self.threshold, length=self.filaments_length) ++ return name, core, coords + +-def nms_iterator(scores, radius, threshold, pool=None): +- process = NonMaximumSuppression(radius, threshold) ++def nms_iterator(scores, radius, threshold, pool=None, do_filaments=False, filaments_length=150, filaments_plot=False): ++ process = NonMaximumSuppression(radius, threshold, do_filaments, filaments_length, filaments_plot) + if pool is not None: + for name,score,coords in pool.imap_unordered(process, scores): + yield name,score,coords + else: + for name,score in scores: +- score,coords = non_maximum_suppression(score, radius, threshold=threshold) ++ if do_filaments: ++ score,coords = pick_filaments(score, radius, threshold=threshold, filaments_length=filaments_length, filaments_plot=filaments_plot) ++ else: ++ score,coords = non_maximum_suppression(score, radius, threshold=threshold) + yield name,score,coords + + def iterate_score_target_pairs(scores, targets): +@@ -231,6 +431,12 @@ def main(args): + if radius is None: + radius = -1 + ++ do_filaments = args.filaments or args.filaments_plot ++ filaments_length = args.filaments_length ++ if (filaments_length < 0): ++ filaments_length = 2 * radius ++ filaments_plot = args.filaments_plot ++ + num_workers = args.num_workers + pool = None + if num_workers < 0: +@@ -284,12 +490,13 @@ def main(args): + + if not per_micrograph: + print('image_name\tx_coord\ty_coord\tscore', file=f) ++ + ## extract coordinates using radius +- for path,score,coords in nms_iterator(stream, radius, threshold, pool=pool): ++ for path,score,coords in nms_iterator(stream, radius, threshold, pool=pool, do_filaments=do_filaments, filaments_length=filaments_length, filaments_plot=filaments_plot): + basename = os.path.basename(path) + name = os.path.splitext(basename)[0] + ## scale the coordinates +- if scale != 1: ++ if scale != 1 and len(coords)>0: + coords = np.round(coords*scale).astype(int) + + if per_micrograph: +@@ -303,8 +510,6 @@ def main(args): + print(name + '\t' + str(coords[i,0]) + '\t' + str(coords[i,1]) + '\t' + str(score[i]), file=f) + + +- +- + if __name__ == '__main__': + import argparse + parser = argparse.ArgumentParser('Script for extracting particles from segmented images or images processed with a trained model. Uses a non maximum suppression algorithm.') diff --git a/easybuild/easyconfigs/t/topaz/topaz-0.2.5.20231120_update-description.patch b/easybuild/easyconfigs/t/topaz/topaz-0.2.5.20231120_update-description.patch new file mode 100644 index 00000000000..f52fac9497d --- /dev/null +++ b/easybuild/easyconfigs/t/topaz/topaz-0.2.5.20231120_update-description.patch @@ -0,0 +1,24 @@ +From 14b2bc331768b67b3267397523de57c707fa1253 Mon Sep 17 00:00:00 2001 +From: scheres +Date: Fri, 25 Mar 2022 09:27:07 +0000 +Subject: [PATCH] added description of new options and dependency on skimage + +--- + README.md | 4 ++++ + 1 file changed, 4 insertions(+) + +diff --git a/README.md b/README.md +index bed6f4f..a98993c 100644 +--- a/README.md ++++ b/README.md +@@ -3,6 +3,10 @@ A pipeline for particle detection in cryo-electron microscopy images using convo + + **Check out our [Discussion](https://github.com/tbepler/topaz/discussions) section for general help, suggestions, and tips on using Topaz.** + ++## New in modification for filament picking: ++- Added support for filament start-end coordinate picking (new options -f, -fp and -fl in the extract command), for subsequent helical reconstruction in RELION ++- This adds a new dependency to skimage (make sure you install this in your conda environment) ++ + ## New in v0.2.5 + - Added Relion integration scripts + - Topaz extract can now write particle coordinates to one file per input micrograph diff --git a/easybuild/easyconfigs/t/torch-em/torch-em-0.7.1-foss-2023a.eb b/easybuild/easyconfigs/t/torch-em/torch-em-0.7.1-foss-2023a.eb new file mode 100644 index 00000000000..425ec7e35af --- /dev/null +++ b/easybuild/easyconfigs/t/torch-em/torch-em-0.7.1-foss-2023a.eb @@ -0,0 +1,104 @@ +easyblock = 'PythonBundle' + +name = 'torch-em' +version = '0.7.1' + +homepage = 'https://github.com/constantinpape/torch-em/' +description = """Deep-learning based semantic and instance segmentation for 3D Electron Microscopy and +other bioimage analysis problems based on pytorch.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [ + ('maturin', '1.1.0'), + ('CMake', '3.26.3'), + ('hatchling', '1.18.0'), +] +dependencies = [ + ('Python', '3.11.3'), + ('torchvision', '0.16.0'), + ('h5py', '3.9.0'), + ('imagecodecs', '2024.1.1'), + ('tensorboard', '2.15.1'), + ('tqdm', '4.66.1'), + ('napari', '0.4.18'), + ('vigra', '1.11.2'), + ('python-elf', '0.5.1'), + ('z5py', '2.0.17'), + ('pydantic', '2.5.3'), + ('xarray', '2023.9.0'), + ('affogato', '0.3.3'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('termcolor', '2.3.0', { + 'checksums': ['b5b08f68937f138fe92f6c089b99f1e2da0ae56c52b78bf7075fd95420fd9a5a'], + }), + ('dnspython', '2.6.1', { + 'modulename': False, + 'checksums': ['e8f0f9c23a7b7cb99ded64e6c3a6f3e701d78f50c55e002b839dea7225cff7cc'], + }), + ('kornia_rs', '0.1.3', { + 'checksums': ['e299d110774fc10f82c547fb04b1b8bf450a0514010324e7be06206d2179ceaf'], + }), + ('email_validator', '2.1.1', { + 'checksums': ['200a70680ba08904be6d1eef729205cc0d687634399a5924d842533efb824b84'], + }), + ('annotated_types', '0.7.0', { + 'checksums': ['aff07c09a53a08bc8cfccb9c85b05f1aa9a2a6f23728d790723543408344ce89'], + }), + ('ruyaml', '0.91.0', { + 'checksums': ['6ce9de9f4d082d696d3bde264664d1bcdca8f5a9dff9d1a1f1a127969ab871ab'], + }), + ('python-dotenv', '1.0.1', { + 'modulename': 'dotenv', + 'checksums': ['e324ee90a023d808f1959c46bcbc04446a10ced277783dc6ee09987c37ec10ca'], + }), + ('pydantic_settings', '2.2.1', { + 'checksums': ['00b9f6a5e95553590434c0fa01ead0b216c3e10bc54ae02e37f359948643c5ed'], + }), + ('loguru', '0.7.2', { + 'checksums': ['e671a53522515f34fd406340ee968cb9ecafbc4b36c679da03c18fd8d0bd51ac'], + }), + ('fire', '0.6.0', { + 'checksums': ['54ec5b996ecdd3c0309c800324a0703d6da512241bc73b553db959d98de0aa66'], + }), + ('kornia', '0.7.2', { + 'checksums': ['f834ccd51188d071ed286a6727471c94344ea2a718903cc6f0e56a92f9c66ac5'], + }), + ('tifffile', '2024.5.10', { + 'checksums': ['aa1e1b12be952ab20717d6848bd6d4a5ee88d2aa319f1152bff4354ad728ec86'], + }), + ('bioimageio.core', '0.6.5', { + 'checksums': ['3b2851e44a2b074536c36fe3bb05b28dc1413ed358d3edd0eb272b75e6c9ca2b'], + }), + ('bioimageio.spec', '0.5.2.post5', { + # delete pin of pydantic version + 'preinstallopts': "sed -i 's/pydantic>=2.6.3,<3/pydantic/' setup.py && ", + 'checksums': ['3007aedc4da9f77f4fb46f72c134c8367bd469f05f6dd275db1a93f0fff48e97'], + }), + (name, version, { + 'source_urls': ['https://github.com/constantinpape/torch-em/archive/'], + 'sources': ['%(version)s.tar.gz'], + 'checksums': ['201aae9af1e698b5a0d8e878def4538b00b0cd8ab9165b71194a6c978ae50931'], + }), +] + +sanity_check_commands = [ + "python -c 'import torch_em.data.datasets.util'", + "python -c 'import torch_em.transform.label'", + "python -c 'import torch_em.data.sampler'", + "python -c 'import torch_em.segmentation'", + "python -c 'import torch_em.data.datasets.neurips_cell_seg'", + "python -c 'import torch_em.model'", + "python -c 'import torch_em.loss'", + "python -c 'import torch_em.trainer'", + # check if unpined pydantic version is woking + "python -c 'import bioimageio.spec.model.v0_5'", + "python -c 'from bioimageio.spec import save_bioimageio_package'", +] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/t/tornado/tornado-timeouts.patch b/easybuild/easyconfigs/t/tornado/tornado-6.1_increase-default-timeouts.patch similarity index 65% rename from easybuild/easyconfigs/t/tornado/tornado-timeouts.patch rename to easybuild/easyconfigs/t/tornado/tornado-6.1_increase-default-timeouts.patch index 635fa6d7143..1fc291ae62e 100644 --- a/easybuild/easyconfigs/t/tornado/tornado-timeouts.patch +++ b/easybuild/easyconfigs/t/tornado/tornado-6.1_increase-default-timeouts.patch @@ -1,7 +1,8 @@ -# Increase timeouts to prevent tornado from killing jupyter on compute nodes +Increase timeouts to prevent tornado from killing jupyter server on compute nodes +author: Alexandre Strube diff -Naur tornado.orig/tornado-6.1/tornado/httpclient.py tornado/tornado-6.1/tornado/httpclient.py ---- tornado.orig/tornado-6.1/tornado/httpclient.py 2020-10-30 21:17:45.000000000 +0100 -+++ tornado/tornado-6.1/tornado/httpclient.py 2022-05-01 22:01:50.923741948 +0200 +--- a/tornado/httpclient.py 2020-10-30 21:17:45.000000000 +0100 ++++ b/tornado/httpclient.py 2022-05-01 22:01:50.923741948 +0200 @@ -345,8 +345,8 @@ # Merged with the values on the request object by AsyncHTTPClient # implementations. diff --git a/easybuild/easyconfigs/t/tornado/tornado-6.3.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/t/tornado/tornado-6.3.2-GCCcore-12.3.0.eb index 9fd6757d976..eab25faf448 100644 --- a/easybuild/easyconfigs/t/tornado/tornado-6.3.2-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/t/tornado/tornado-6.3.2-GCCcore-12.3.0.eb @@ -9,10 +9,10 @@ description = "Tornado is a Python web framework and asynchronous networking lib toolchain = {"name": "GCCcore", "version": "12.3.0"} sources = [SOURCE_TAR_GZ] -patches = ['tornado-timeouts.patch'] +patches = ['tornado-6.1_increase-default-timeouts.patch'] checksums = [ {'tornado-6.3.2.tar.gz': '4b927c4f19b71e627b13f3db2324e4ae660527143f9e1f2e2fb404f3a187e2ba'}, - {'tornado-timeouts.patch': 'dd97748cb80506b36570f1274b19c8fc53d81e15f0eb2c5b6d0ba9d80141af34'}, + {'tornado-6.1_increase-default-timeouts.patch': '32e09dd8243acb8c55162f361880dc294d76770a7ff083c05aef6b8660e3bfb9'}, ] builddependencies = [ diff --git a/easybuild/easyconfigs/t/tornado/tornado-6.4-GCCcore-13.2.0.eb b/easybuild/easyconfigs/t/tornado/tornado-6.4-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..38b085529bf --- /dev/null +++ b/easybuild/easyconfigs/t/tornado/tornado-6.4-GCCcore-13.2.0.eb @@ -0,0 +1,29 @@ +easyblock = "PythonPackage" + +name = "tornado" +version = "6.4" + +homepage = "https://github.com/tornadoweb/tornado" +description = "Tornado is a Python web framework and asynchronous networking library." + +toolchain = {"name": "GCCcore", "version": "13.2.0"} + +sources = [SOURCE_TAR_GZ] +patches = ['tornado-6.1_increase-default-timeouts.patch'] +checksums = [ + {'tornado-6.4.tar.gz': '72291fa6e6bc84e626589f1c29d90a5a6d593ef5ae68052ee2ef000dfd273dee'}, + {'tornado-6.1_increase-default-timeouts.patch': '32e09dd8243acb8c55162f361880dc294d76770a7ff083c05aef6b8660e3bfb9'}, +] + +builddependencies = [ + ("binutils", "2.40"), +] +dependencies = [ + ("Python", "3.11.5"), +] + +download_dep_fail = True +sanity_pip_check = True +use_pip = True + +moduleclass = "lib" diff --git a/easybuild/easyconfigs/t/tornado/tornado-6.4.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/t/tornado/tornado-6.4.1-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..d4266c8c1c9 --- /dev/null +++ b/easybuild/easyconfigs/t/tornado/tornado-6.4.1-GCCcore-13.3.0.eb @@ -0,0 +1,29 @@ +easyblock = "PythonPackage" + +name = "tornado" +version = "6.4.1" + +homepage = "https://github.com/tornadoweb/tornado" +description = "Tornado is a Python web framework and asynchronous networking library." + +toolchain = {"name": "GCCcore", "version": "13.3.0"} + +sources = [SOURCE_TAR_GZ] +patches = ['tornado-6.1_increase-default-timeouts.patch'] +checksums = [ + {'tornado-6.4.1.tar.gz': '92d3ab53183d8c50f8204a51e6f91d18a15d5ef261e84d452800d4ff6fc504e9'}, + {'tornado-6.1_increase-default-timeouts.patch': '32e09dd8243acb8c55162f361880dc294d76770a7ff083c05aef6b8660e3bfb9'}, +] + +builddependencies = [ + ("binutils", "2.42"), +] +dependencies = [ + ("Python", "3.12.3"), +] + +download_dep_fail = True +sanity_pip_check = True +use_pip = True + +moduleclass = "lib" diff --git a/easybuild/easyconfigs/t/tqdm/tqdm-4.66.5-GCCcore-13.3.0.eb b/easybuild/easyconfigs/t/tqdm/tqdm-4.66.5-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..b9d92f49462 --- /dev/null +++ b/easybuild/easyconfigs/t/tqdm/tqdm-4.66.5-GCCcore-13.3.0.eb @@ -0,0 +1,24 @@ +# # +# Author: Robert Mijakovic +# # +easyblock = 'PythonPackage' + +name = 'tqdm' +version = '4.66.5' + +homepage = 'https://github.com/tqdm/tqdm' +description = "A fast, extensible progress bar for Python and CLI" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['e1020aef2e5096702d8a025ac7d16b1577279c9d63f8375b63083e9a5f0fcbad'] + +builddependencies = [('binutils', '2.42')] +dependencies = [('Python', '3.12.3')] + +download_dep_fail = True +sanity_pip_check = True +use_pip = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/t/treeseg/treeseg-0.2.2-foss-2023a.eb b/easybuild/easyconfigs/t/treeseg/treeseg-0.2.2-foss-2023a.eb new file mode 100644 index 00000000000..27d7480c372 --- /dev/null +++ b/easybuild/easyconfigs/t/treeseg/treeseg-0.2.2-foss-2023a.eb @@ -0,0 +1,48 @@ +easyblock = 'CMakeMake' + +name = 'treeseg' +version = '0.2.2' + +homepage = 'https://github.com/apburt/treeseg' +description = """ +treeseg has been developed to near-automatically segment individual tree point +clouds from high-density larger-area lidar point clouds acquired in forests. A +formal, albeit somewhat outdated description of the methods can be found in our +paper (https://doi.org/10.1111/2041-210X.13121).""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['https://github.com/apburt/treeseg/archive'] +sources = ['v%(version)s.tar.gz'] +patches = ['%(name)s-%(version)s_fix_boost_include.patch'] +checksums = [ + {'v0.2.2.tar.gz': '69d674ff5eafb24af5a5166fa3ed3b00ebafe9540e747f24a209bb5be3c5227c'}, + {'treeseg-0.2.2_fix_boost_include.patch': '5bc6704c07f61dc24255397327906ed7c2ccc95b2518b51d8b2c2089b746759f'}, +] + +builddependencies = [ + ('CMake', '3.26.3'), +] + +dependencies = [ + ('PCL', '1.14.1'), + ('Armadillo', '12.6.2'), +] + +_libs = ['libleafsep.%s' % SHLIB_EXT, 'libtreeseg.%s' % SHLIB_EXT] + +_bins = ['downsample', 'getcrownvolume', 'nearestneighbour', 'pcdPointXYZRGB2txt', 'segmentcrown', 'sepwoodleaf', + 'txtPointTreeseg2pcd', 'findstems', 'getdtmslice', 'pcdPointTreeseg2txt', 'plotcoords', 'segmentstem', 'thin'] + +install_cmd = ' && '.join([ + 'mkdir -p %(installdir)s/{lib,bin}', + 'cp %s %%(installdir)s/lib/' % ' '.join(_libs), + 'cp %s %%(installdir)s/bin/' % ' '.join(_bins), +]) + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in _bins] + ['lib/%s' % x for x in _libs], + 'dirs': [], +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/t/treeseg/treeseg-0.2.2_fix_boost_include.patch b/easybuild/easyconfigs/t/treeseg/treeseg-0.2.2_fix_boost_include.patch new file mode 100644 index 00000000000..baedd0de22f --- /dev/null +++ b/easybuild/easyconfigs/t/treeseg/treeseg-0.2.2_fix_boost_include.patch @@ -0,0 +1,58 @@ +From cc6ff5b3b53a227c34171ea91164f4eaa035c890 Mon Sep 17 00:00:00 2001 +From: david +Date: Mon, 20 Mar 2023 21:22:20 +0100 +Subject: [PATCH] fix make error: split is not a member of boost + +--- + src/pcdPointTreeseg2txt.cpp | 1 + + src/pcdPointXYZRGB2txt.cpp | 1 + + src/treeseg.cpp | 1 + + src/txtPointTreeseg2pcd.cpp | 1 + + 4 files changed, 4 insertions(+) + +diff --git a/src/pcdPointTreeseg2txt.cpp b/src/pcdPointTreeseg2txt.cpp +index b189e55..af4d865 100644 +--- a/src/pcdPointTreeseg2txt.cpp ++++ b/src/pcdPointTreeseg2txt.cpp +@@ -1,6 +1,7 @@ + #include "treeseg.h" + + #include ++#include + + int main (int argc, char **argv) + { +diff --git a/src/pcdPointXYZRGB2txt.cpp b/src/pcdPointXYZRGB2txt.cpp +index 9fd1520..f99458f 100644 +--- a/src/pcdPointXYZRGB2txt.cpp ++++ b/src/pcdPointXYZRGB2txt.cpp +@@ -1,4 +1,5 @@ + #include ++#include + + int main (int argc, char **argv) + { +diff --git a/src/treeseg.cpp b/src/treeseg.cpp +index a7a0fd3..590759e 100644 +--- a/src/treeseg.cpp ++++ b/src/treeseg.cpp +@@ -39,6 +39,7 @@ + #include + #include + #include ++#include + + //File IO + +diff --git a/src/txtPointTreeseg2pcd.cpp b/src/txtPointTreeseg2pcd.cpp +index cf8b2a0..04abfbe 100644 +--- a/src/txtPointTreeseg2pcd.cpp ++++ b/src/txtPointTreeseg2pcd.cpp +@@ -1,6 +1,7 @@ + #include "treeseg.h" + + #include ++#include + + int main (int argc, char **argv) + { diff --git a/easybuild/easyconfigs/t/trimesh/trimesh-4.4.9-gfbf-2024a.eb b/easybuild/easyconfigs/t/trimesh/trimesh-4.4.9-gfbf-2024a.eb new file mode 100644 index 00000000000..a25c1a4ac0f --- /dev/null +++ b/easybuild/easyconfigs/t/trimesh/trimesh-4.4.9-gfbf-2024a.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonPackage' + +name = 'trimesh' +version = '4.4.9' + +homepage = 'https://trimsh.org/' +description = """Trimesh is a Python (2.7- 3.3+) library for loading and using triangular meshes with an emphasis on +watertight meshes. The goal of the library is to provide a fully featured Trimesh object which allows for easy +manipulation and analysis, in the style of the excellent Polygon object in the Shapely library.""" + + +toolchain = {'name': 'gfbf', 'version': '2024a'} + +sources = [SOURCE_TAR_GZ] +checksums = ['e9f54cb4ef70f9db49446cad3845b7a8043fc7d62d9192b241741f3fb0d813ac'] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + + +dependencies = [ + ('Python', '3.12.3'), + ('SciPy-bundle', '2024.05'), # numpy required +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/t/trusTEr/trusTEr-0.1.1-20241025-foss-2023a.eb b/easybuild/easyconfigs/t/trusTEr/trusTEr-0.1.1-20241025-foss-2023a.eb new file mode 100644 index 00000000000..3bea1107bfc --- /dev/null +++ b/easybuild/easyconfigs/t/trusTEr/trusTEr-0.1.1-20241025-foss-2023a.eb @@ -0,0 +1,36 @@ +easyblock = 'PythonPackage' + +name = 'trusTEr' +version = '0.1.1-20241025' +local_commit = '6358eef' + +homepage = 'https://github.com/raquelgarza/truster' +description = """Takes fastq files from 10x single cell RNA sequencing, clusters cells using Seurat, +and can be used to produce read count matrices in a cluster level. +You can also quantify reads per cluster having predefined clusters.""" + +source_urls = ['https://github.com/raquelgarza/truster/archive/'] +sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}] +checksums = ['ef6f454a73f545e5f90a28a80d388afb763a43ac1256f3c182bf947728b4e39a'] + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('CellRanger', '8.0.1', '', SYSTEM), + ('R', '4.3.2'), + ('R-bundle-CRAN', '2023.12'), + ('Seurat', '5.1.0', '-R-%(rver)s'), + ('STAR', '2.7.11a'), + ('velocyto', '0.17.17'), + ('TEtranscripts', '2.2.3'), + ('bamtofastq', '1.4.1'), + ('subset-bam', '1.1.0', '', SYSTEM), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/t/typing-extensions/typing-extensions-4.11.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/t/typing-extensions/typing-extensions-4.11.0-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..552279e3ffe --- /dev/null +++ b/easybuild/easyconfigs/t/typing-extensions/typing-extensions-4.11.0-GCCcore-13.3.0.eb @@ -0,0 +1,21 @@ +easyblock = 'PythonPackage' + +name = 'typing-extensions' +version = '4.11.0' + +homepage = 'https://github.com/python/typing_extensions' +description = "Typing Extensions - Backported and Experimental Type Hints for Python" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +sources = ['typing_extensions-%(version)s.tar.gz'] +checksums = ['83f085bd5ca59c80295fc2a82ab5dac679cbe02b9f33f7d83af68e241bea51b0'] + +builddependencies = [('binutils', '2.42')] +dependencies = [('Python', '3.12.3')] + +download_dep_fail = True +sanity_pip_check = True +use_pip = True + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/u/UCC-CUDA/UCC-CUDA-1.2.0-GCCcore-13.2.0-CUDA-12.4.0.eb b/easybuild/easyconfigs/u/UCC-CUDA/UCC-CUDA-1.2.0-GCCcore-13.2.0-CUDA-12.4.0.eb new file mode 100644 index 00000000000..f8bba051951 --- /dev/null +++ b/easybuild/easyconfigs/u/UCC-CUDA/UCC-CUDA-1.2.0-GCCcore-13.2.0-CUDA-12.4.0.eb @@ -0,0 +1,55 @@ +easyblock = 'ConfigureMake' + +name = 'UCC-CUDA' +version = '1.2.0' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://www.openucx.org/' +description = """UCC (Unified Collective Communication) is a collective +communication operations API and library that is flexible, complete, and +feature-rich for current and emerging programming models and runtimes. + +This module adds the UCC CUDA support. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/openucx/ucc/archive/refs/tags'] +sources = ['v%(version)s.tar.gz'] +patches = [ + '%(name)s-%(version)s_link_against_existing_UCC_libs.patch', +] +checksums = [ + {'v1.2.0.tar.gz': 'c1552797600835c0cf401b82dc89c4d27d5717f4fb805d41daca8e19f65e509d'}, + {'UCC-CUDA-1.2.0_link_against_existing_UCC_libs.patch': + '84157be5eae96d2501df076bcf0598b104adf80abeca028a144c4fb098638207'}, +] + +builddependencies = [ + ('binutils', '2.40'), + ('Autotools', '20220317'), +] + +dependencies = [ + ('UCC', version), + ('CUDA', '12.4.0', '', SYSTEM), + ('UCX-CUDA', '1.15.0', '-CUDA-%(cudaver)s'), + ('NCCL', '2.20.5', '-CUDA-%(cudaver)s'), +] + +preconfigopts = "./autogen.sh && " + +buildopts = '-C src/components/mc/cuda V=1 && make -C src/components/tl/nccl V=1' +installopts = '-C src/components/mc/cuda && make -C src/components/tl/nccl install' + +sanity_check_paths = { + 'files': ['lib/ucc/libucc_mc_cuda.%s' % SHLIB_EXT, 'lib/ucc/libucc_tl_nccl.%s' % SHLIB_EXT], + 'dirs': ['lib'] +} + +sanity_check_commands = ["ucc_info -c"] + +modextrapaths = {'EB_UCC_EXTRA_COMPONENT_PATH': 'lib/ucc'} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/u/UCC-CUDA/UCC-CUDA-1.3.0-GCCcore-13.3.0-CUDA-12.6.0.eb b/easybuild/easyconfigs/u/UCC-CUDA/UCC-CUDA-1.3.0-GCCcore-13.3.0-CUDA-12.6.0.eb new file mode 100644 index 00000000000..a0b4865a721 --- /dev/null +++ b/easybuild/easyconfigs/u/UCC-CUDA/UCC-CUDA-1.3.0-GCCcore-13.3.0-CUDA-12.6.0.eb @@ -0,0 +1,55 @@ +easyblock = 'ConfigureMake' + +name = 'UCC-CUDA' +version = '1.3.0' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://www.openucx.org/' +description = """UCC (Unified Collective Communication) is a collective +communication operations API and library that is flexible, complete, and +feature-rich for current and emerging programming models and runtimes. + +This module adds the UCC CUDA support. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/openucx/ucc/archive/refs/tags'] +sources = ['v%(version)s.tar.gz'] +patches = [ + '%(name)s-%(version)s_link_against_existing_UCC_libs.patch', +] +checksums = [ + {'v1.3.0.tar.gz': 'b56379abe5f1c125bfa83be305d78d81a64aa271b7b5fff0ac17b86725ff3acf'}, + {'UCC-CUDA-1.3.0_link_against_existing_UCC_libs.patch': + '758228357ce2a6ae50fb26a0b43e9176feaf379e266365f38205ce679267fc0d'}, +] + +builddependencies = [ + ('binutils', '2.42'), + ('Autotools', '20231222'), +] + +dependencies = [ + ('UCC', version), + ('CUDA', '12.6.0', '', SYSTEM), + ('UCX-CUDA', '1.16.0', '-CUDA-%(cudaver)s'), + ('NCCL', '2.22.3', '-CUDA-%(cudaver)s'), +] + +preconfigopts = "./autogen.sh && " + +buildopts = '-C src/components/mc/cuda V=1 && make -C src/components/tl/nccl V=1' +installopts = '-C src/components/mc/cuda && make -C src/components/tl/nccl install' + +sanity_check_paths = { + 'files': ['lib/ucc/libucc_mc_cuda.%s' % SHLIB_EXT, 'lib/ucc/libucc_tl_nccl.%s' % SHLIB_EXT], + 'dirs': ['lib'] +} + +sanity_check_commands = ["ucc_info -c"] + +modextrapaths = {'EB_UCC_EXTRA_COMPONENT_PATH': 'lib/ucc'} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/u/UCC-CUDA/UCC-CUDA-1.3.0_link_against_existing_UCC_libs.patch b/easybuild/easyconfigs/u/UCC-CUDA/UCC-CUDA-1.3.0_link_against_existing_UCC_libs.patch new file mode 100644 index 00000000000..5d005e067f7 --- /dev/null +++ b/easybuild/easyconfigs/u/UCC-CUDA/UCC-CUDA-1.3.0_link_against_existing_UCC_libs.patch @@ -0,0 +1,27 @@ +Make CUDA/NCCL plugins link against the existing ucc libraries. + +Bart Oldeman, 2022-08-02 +Mikael OEhman, 2023-06-16 +diff -ur ucc-1.3.0.orig/src/components/mc/cuda/Makefile.am ucc-1.3.0/src/components/ec/cuda/Makefile.am +--- ucc-1.3.0.orig/src/components/mc/cuda/Makefile.am.orig 2023-06-16 12:56:53.205939925 +0200 ++++ ucc-1.3.0/src/components/mc/cuda/Makefile.am 2023-06-16 13:02:21.716110609 +0200 +@@ -14,7 +14,7 @@ + libucc_mc_cuda_la_CFLAGS = $(BASE_CFLAGS) + libucc_mc_cuda_la_LDFLAGS = -version-info $(SOVERSION) --as-needed $(CUDA_LDFLAGS) + libucc_mc_cuda_la_LIBADD = $(CUDA_LIBS) \ +- $(UCC_TOP_BUILDDIR)/src/libucc.la ++ -lucc + + include $(top_srcdir)/config/module.am + endif +diff -ur ucc-1.0.0.orig/src/components/tl/nccl/Makefile.am ucc-1.0.0/src/components/tl/nccl/Makefile.am +--- ucc-1.0.0.orig/src/components/tl/nccl/Makefile.am 2022-04-15 12:43:33.000000000 +0000 ++++ ucc-1.0.0/src/components/tl/nccl/Makefile.am 2022-08-02 12:13:59.334795989 +0000 +@@ -21,6 +21,6 @@ + libucc_tl_nccl_la_CPPFLAGS = $(AM_CPPFLAGS) $(BASE_CPPFLAGS) $(CUDA_CPPFLAGS) $(NCCL_CPPFLAGS) + libucc_tl_nccl_la_CFLAGS = $(BASE_CFLAGS) + libucc_tl_nccl_la_LDFLAGS = -version-info $(SOVERSION) --as-needed $(CUDA_LDFLAGS) $(NCCL_LDFLAGS) +-libucc_tl_nccl_la_LIBADD = $(CUDA_LIBS) $(NCCL_LIBADD) $(UCC_TOP_BUILDDIR)/src/libucc.la ++libucc_tl_nccl_la_LIBADD = $(CUDA_LIBS) $(NCCL_LIBADD) -lucc + + include $(top_srcdir)/config/module.am diff --git a/easybuild/easyconfigs/u/UCC/UCC-1.3.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/u/UCC/UCC-1.3.0-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..57314f2667e --- /dev/null +++ b/easybuild/easyconfigs/u/UCC/UCC-1.3.0-GCCcore-13.3.0.eb @@ -0,0 +1,41 @@ +easyblock = 'ConfigureMake' + +name = 'UCC' +version = '1.3.0' + +homepage = 'https://www.openucx.org/' +description = """UCC (Unified Collective Communication) is a collective +communication operations API and library that is flexible, complete, and +feature-rich for current and emerging programming models and runtimes. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/openucx/ucc/archive/refs/tags'] +sources = ['v%(version)s.tar.gz'] +patches = ['UCC-1.1.0-multiple_component_paths.patch'] +checksums = [ + {'v1.3.0.tar.gz': 'b56379abe5f1c125bfa83be305d78d81a64aa271b7b5fff0ac17b86725ff3acf'}, + {'UCC-1.1.0-multiple_component_paths.patch': '3081d0f694331daa4a88a0fa3fb54b9a918015248ae5eb7b3157b924abd31bee'}, +] + +builddependencies = [ + ('binutils', '2.42'), + ('Autotools', '20231222'), +] + +dependencies = [ + ('UCX', '1.16.0'), +] + +preconfigopts = "./autogen.sh && " + +sanity_check_paths = { + 'files': ['bin/ucc_info'], + 'dirs': ['include', 'lib'] +} + +sanity_check_commands = ["ucc_info -c"] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.15.0-GCCcore-13.2.0-CUDA-12.5.0.eb b/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.15.0-GCCcore-13.2.0-CUDA-12.5.0.eb new file mode 100644 index 00000000000..5c88f6a5c5d --- /dev/null +++ b/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.15.0-GCCcore-13.2.0-CUDA-12.5.0.eb @@ -0,0 +1,41 @@ +easyblock = 'EB_UCX_Plugins' + +name = 'UCX-CUDA' +version = '1.15.0' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'http://www.openucx.org/' +description = """Unified Communication X +An open-source production grade communication framework for data centric +and high-performance applications + +This module adds the UCX CUDA support. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/openucx/ucx/releases/download/v%(version)s'] +sources = [{'filename': 'ucx-%(version)s.tar.gz', 'alt_location': 'UCX'}] +patches = ['%(name)s-1.11.0_link_against_existing_UCX_libs.patch'] +checksums = [ + {'ucx-1.15.0.tar.gz': '4b202087076bc1c98f9249144f0c277a8ea88ad4ca6f404f94baa9cb3aebda6d'}, + {'UCX-CUDA-1.11.0_link_against_existing_UCX_libs.patch': + '457187fa020e526609ba91e7750c9941d57bd57d60d6eed317b40ad8824aca93'}, +] + +builddependencies = [ + ('binutils', '2.40'), + ('Autotools', '20220317'), + ('pkgconf', '2.0.3'), +] + +dependencies = [ + ('zlib', '1.2.13'), + ('UCX', version), + ('CUDA', '12.5.0', '', SYSTEM), + ('GDRCopy', '2.4'), +] + + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.16.0-GCCcore-13.3.0-CUDA-12.6.0.eb b/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.16.0-GCCcore-13.3.0-CUDA-12.6.0.eb new file mode 100644 index 00000000000..34271e18021 --- /dev/null +++ b/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.16.0-GCCcore-13.3.0-CUDA-12.6.0.eb @@ -0,0 +1,41 @@ +easyblock = 'EB_UCX_Plugins' + +name = 'UCX-CUDA' +version = '1.16.0' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'http://www.openucx.org/' +description = """Unified Communication X +An open-source production grade communication framework for data centric +and high-performance applications + +This module adds the UCX CUDA support. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/openucx/ucx/releases/download/v%(version)s'] +sources = [{'filename': 'ucx-%(version)s.tar.gz', 'alt_location': 'UCX'}] +patches = ['%(name)s-1.16.0_link_against_existing_UCX_libs.patch'] +checksums = [ + {'ucx-1.16.0.tar.gz': 'f73770d3b583c91aba5fb07557e655ead0786e057018bfe42f0ebe8716e9d28c'}, + {'UCX-CUDA-1.16.0_link_against_existing_UCX_libs.patch': + 'aa5bab38c188276958dd6829da4929ed9ff0b67cd55665b4459521cf3fbbe46d'}, +] + +builddependencies = [ + ('binutils', '2.42'), + ('Autotools', '20231222'), + ('pkgconf', '2.2.0'), +] + +dependencies = [ + ('zlib', '1.3.1'), + ('UCX', version), + ('CUDA', '12.6.0', '', SYSTEM), + ('GDRCopy', '2.4.1'), +] + + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.16.0_link_against_existing_UCX_libs.patch b/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.16.0_link_against_existing_UCX_libs.patch new file mode 100644 index 00000000000..92973cd7f80 --- /dev/null +++ b/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.16.0_link_against_existing_UCX_libs.patch @@ -0,0 +1,93 @@ +diff --git a/configure.ac b/configure.ac +index 8d8da54..2765fe0 100644 +--- a/configure.ac ++++ b/configure.ac +@@ -30,13 +30,13 @@ valgrind_libpath="" + AC_USE_SYSTEM_EXTENSIONS + AC_CONFIG_HEADERS([config.h]) + +-AC_CHECK_PROG(GITBIN, git, yes) +-AS_IF([test x"${GITBIN}" = x"yes"], +- [# remove preceding "refs/heads/" (11 characters) for symbolic ref +- AC_SUBST(SCM_BRANCH, esyscmd([sh -c 'git symbolic-ref --quiet HEAD | sed "s/^.\{11\}//"'])) +- AC_SUBST(SCM_VERSION, esyscmd([sh -c 'git rev-parse --short=7 HEAD']))], +- [AC_SUBST(SCM_BRANCH, "") +- AC_SUBST(SCM_VERSION, "0000000")]) ++#AC_CHECK_PROG(GITBIN, git, yes) ++#AS_IF([test x"${GITBIN}" = x"yes"], ++# [# remove preceding "refs/heads/" (11 characters) for symbolic ref ++# AC_SUBST(SCM_BRANCH, esyscmd([sh -c 'git symbolic-ref --quiet HEAD | sed "s/^.\{11\}//"'])) ++# AC_SUBST(SCM_VERSION, esyscmd([sh -c 'git rev-parse --short=7 HEAD']))], ++# [AC_SUBST(SCM_BRANCH, "") ++# AC_SUBST(SCM_VERSION, "0000000")]) + + AH_TOP([ + #ifndef UCX_CONFIG_H +diff --git a/src/ucm/cuda/Makefile.am b/src/ucm/cuda/Makefile.am +index 00bd224..22e719f 100644 +--- a/src/ucm/cuda/Makefile.am ++++ b/src/ucm/cuda/Makefile.am +@@ -9,7 +9,7 @@ if HAVE_CUDA + module_LTLIBRARIES = libucm_cuda.la + libucm_cuda_la_CPPFLAGS = $(BASE_CPPFLAGS) $(CUDA_CPPFLAGS) + libucm_cuda_la_CFLAGS = $(BASE_CFLAGS) $(CUDA_CFLAGS) +-libucm_cuda_la_LIBADD = ../libucm.la $(CUDA_LIBS) $(CUDART_LIBS) ++libucm_cuda_la_LIBADD = -lucm $(CUDA_LIBS) $(CUDART_LIBS) + libucm_cuda_la_LDFLAGS = $(UCM_MODULE_LDFLAGS) \ + $(patsubst %, -Xlinker %, $(CUDA_LDFLAGS)) \ + -version-info $(SOVERSION) +diff --git a/src/ucm/rocm/Makefile.am b/src/ucm/rocm/Makefile.am +index f9e183f..dcd1587 100644 +--- a/src/ucm/rocm/Makefile.am ++++ b/src/ucm/rocm/Makefile.am +@@ -10,7 +10,7 @@ if HAVE_ROCM + module_LTLIBRARIES = libucm_rocm.la + libucm_rocm_la_CPPFLAGS = $(BASE_CPPFLAGS) $(ROCM_CPPFLAGS) + libucm_rocm_la_CFLAGS = $(BASE_CFLAGS) $(ROCM_CFLAGS) +-libucm_rocm_la_LIBADD = ../libucm.la ++libucm_rocm_la_LIBADD = -lucm + libucm_rocm_la_LDFLAGS = $(UCM_MODULE_LDFLAGS) \ + $(ROCM_LDFLAGS) $(ROCM_LIBS) -version-info $(SOVERSION) \ + $(patsubst %, -Xlinker %, -L$(ROCM_ROOT)/lib -rpath $(ROCM_ROOT)/hip/lib -rpath $(ROCM_ROOT)/lib) \ +diff --git a/src/uct/cuda/Makefile.am b/src/uct/cuda/Makefile.am +index 00899ab..dcee6b0 100644 +--- a/src/uct/cuda/Makefile.am ++++ b/src/uct/cuda/Makefile.am +@@ -11,8 +11,8 @@ module_LTLIBRARIES = libuct_cuda.la + libuct_cuda_la_CPPFLAGS = $(BASE_CPPFLAGS) $(CUDA_CPPFLAGS) + libuct_cuda_la_CFLAGS = $(BASE_CFLAGS) $(CUDA_CFLAGS) + libuct_cuda_la_LDFLAGS = $(CUDA_LDFLAGS) -version-info $(SOVERSION) +-libuct_cuda_la_LIBADD = $(top_builddir)/src/ucs/libucs.la \ +- $(top_builddir)/src/uct/libuct.la \ ++libuct_cuda_la_LIBADD = -lucs \ ++ -luct \ + $(CUDA_LIBS) $(CUDART_LIBS) $(NVML_LIBS) + + noinst_HEADERS = \ +diff --git a/src/uct/cuda/gdr_copy/Makefile.am b/src/uct/cuda/gdr_copy/Makefile.am +index 47602c7..601cb9f 100644 +--- a/src/uct/cuda/gdr_copy/Makefile.am ++++ b/src/uct/cuda/gdr_copy/Makefile.am +@@ -9,7 +9,7 @@ module_LTLIBRARIES = libuct_cuda_gdrcopy.la + libuct_cuda_gdrcopy_la_CPPFLAGS = $(BASE_CPPFLAGS) $(GDR_COPY_CPPFLAGS) + libuct_cuda_gdrcopy_la_CFLAGS = $(BASE_CFLAGS) + libuct_cuda_gdrcopy_la_LDFLAGS = $(GDR_COPY_LDFLAGS) -version-info $(SOVERSION) +-libuct_cuda_gdrcopy_la_LIBADD = $(top_builddir)/src/ucs/libucs.la \ ++libuct_cuda_gdrcopy_la_LIBADD = -lucs \ + $(top_builddir)/src/uct/cuda/libuct_cuda.la \ + $(GDR_COPY_LIBS) + +diff --git a/src/uct/rocm/Makefile.am b/src/uct/rocm/Makefile.am +index c7abce1..257e33f 100644 +--- a/src/uct/rocm/Makefile.am ++++ b/src/uct/rocm/Makefile.am +@@ -8,8 +8,7 @@ if HAVE_ROCM + module_LTLIBRARIES = libuct_rocm.la + libuct_rocm_la_CPPFLAGS = $(BASE_CPPFLAGS) $(ROCM_CPPFLAGS) + libuct_rocm_la_CFLAGS = $(BASE_CFLAGS) +-libuct_rocm_la_LIBADD = $(top_builddir)/src/ucs/libucs.la \ +- $(top_builddir)/src/uct/libuct.la ++libuct_rocm_la_LIBADD = -lucs -luct + libuct_rocm_la_LDFLAGS = $(ROCM_LDFLAGS) $(ROCM_LIBS) -version-info $(SOVERSION) \ + $(patsubst %, -Xlinker %, -L$(ROCM_ROOT)/lib -rpath $(ROCM_ROOT)/hip/lib -rpath $(ROCM_ROOT)/lib) \ + $(patsubst %, -Xlinker %, --enable-new-dtags) \ diff --git a/easybuild/easyconfigs/u/UCX/UCX-1.16.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/u/UCX/UCX-1.16.0-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..e5a9d8a4954 --- /dev/null +++ b/easybuild/easyconfigs/u/UCX/UCX-1.16.0-GCCcore-13.3.0.eb @@ -0,0 +1,52 @@ +easyblock = 'ConfigureMake' + +name = 'UCX' +version = '1.16.0' + +homepage = 'https://www.openucx.org/' +description = """Unified Communication X +An open-source production grade communication framework for data centric +and high-performance applications +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/openucx/ucx/releases/download/v%(version)s'] +sources = ['%(namelower)s-%(version)s.tar.gz'] +patches = [ + 'UCX-1.13.1-dynamic_modules.patch', +] +checksums = [ + {'ucx-1.16.0.tar.gz': 'f73770d3b583c91aba5fb07557e655ead0786e057018bfe42f0ebe8716e9d28c'}, + {'UCX-1.13.1-dynamic_modules.patch': '00874687bd90b795fff61aaa183f6c6bea2210aa1003b28f23d9ebf7066f8782'}, +] + +builddependencies = [ + ('binutils', '2.42'), + ('Autotools', '20231222'), + ('pkgconf', '2.2.0'), +] + +osdependencies = [OS_PKG_IBVERBS_DEV] + +dependencies = [ + ('zlib', '1.3.1'), + ('numactl', '2.0.18'), +] + +configopts = '--enable-optimizations --enable-cma --enable-mt --with-verbs ' +configopts += '--without-java --without-go --disable-doxygen-doc ' +# include the configure options from contrib/configure-release +configopts += '--disable-logging --disable-debug --disable-assertions --disable-params-check ' + +buildopts = 'V=1' + +sanity_check_paths = { + 'files': ['bin/ucx_info', 'bin/ucx_perftest', 'bin/ucx_read_profile'], + 'dirs': ['include', 'lib', 'share'] +} + +sanity_check_commands = ["ucx_info -d"] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.2.28-GCCcore-13.3.0.eb b/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.2.28-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..12a51d8afd4 --- /dev/null +++ b/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.2.28-GCCcore-13.3.0.eb @@ -0,0 +1,44 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg, Ghent University +# Authors:: Fotis Georgatos , Kenneth Hoste (Ghent University) +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-97.html +## + +easyblock = 'ConfigureMake' + +name = 'UDUNITS' +version = '2.2.28' + +homepage = 'https://www.unidata.ucar.edu/software/udunits/' +description = """UDUNITS supports conversion of unit specifications between formatted and binary forms, + arithmetic manipulation of units, and conversion of values between compatible scales of measurement.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +source_urls = [ + 'https://artifacts.unidata.ucar.edu/repository/downloads-udunits/%(version)s/', + 'https://sources.easybuild.io/u/UDUNITS/', +] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['590baec83161a3fd62c00efa66f6113cec8a7c461e3f61a5182167e0cc5d579e'] + +builddependencies = [('binutils', '2.42')] + +dependencies = [('expat', '2.6.2')] + +sanity_check_paths = { + 'files': ['bin/udunits2', 'include/converter.h', 'include/udunits2.h', 'include/udunits.h', + 'lib/libudunits2.a', 'lib/libudunits2.%s' % SHLIB_EXT], + 'dirs': ['share'], +} + +parallel = 1 + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/u/Umpire/Umpire-2024.02.1-foss-2023a.eb b/easybuild/easyconfigs/u/Umpire/Umpire-2024.02.1-foss-2023a.eb new file mode 100644 index 00000000000..fddfdf851cf --- /dev/null +++ b/easybuild/easyconfigs/u/Umpire/Umpire-2024.02.1-foss-2023a.eb @@ -0,0 +1,33 @@ +easyblock = 'CMakeMake' + +name = 'Umpire' +version = '2024.02.1' + +homepage = 'https://github.com/LLNL/Umpire' +description = """Umpire is a resource management library that allows the discovery, provision, +and management of memory on machines with multiple memory devices like NUMA and GPUs.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +sources = [{ + 'filename': 'v%(version)s.tar.gz', + 'git_config': { + 'url': 'https://github.com/LLNL', + 'repo_name': 'Umpire', + 'tag': 'v%(version)s', + 'recursive': True, + 'keep_git_dir': True, + } +}] +checksums = [None] + +builddependencies = [ + ('CMake', '3.26.3'), +] + +sanity_check_paths = { + 'files': ['lib/libcamp.a', 'include/umpire/Umpire.hpp'], + 'dirs': ['bin', 'include'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/u/UnZip/UnZip-6.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/u/UnZip/UnZip-6.0-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..08f61c7f44c --- /dev/null +++ b/easybuild/easyconfigs/u/UnZip/UnZip-6.0-GCCcore-13.3.0.eb @@ -0,0 +1,59 @@ +easyblock = 'ConfigureMake' + +name = 'UnZip' +version = '6.0' + +homepage = 'http://www.info-zip.org/UnZip.html' +description = """UnZip is an extraction utility for archives compressed +in .zip format (also called "zipfiles"). Although highly compatible both +with PKWARE's PKZIP and PKUNZIP utilities for MS-DOS and with Info-ZIP's +own Zip program, our primary objectives have been portability and +non-MSDOS functionality.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://download.sourceforge.net/infozip'] +sources = ['%(namelower)s%(version_major)s%(version_minor)s.tar.gz'] +patches = [ + 'UnZip-%(version)s_various-security-and-other-fixes-from-Ubuntu.patch', +] +checksums = [ + '036d96991646d0449ed0aa952e4fbe21b476ce994abc276e49d30e686708bd37', # unzip60.tar.gz + # UnZip-6.0_various-security-and-other-fixes-from-Ubuntu.patch + '06b9307fd5aa018896bd4126818c00c1fd284a06cc3681cf0492f951ebb57ffe', +] + +builddependencies = [ + ('binutils', '2.42'), +] + +dependencies = [ + ('bzip2', '1.0.8'), +] + +skipsteps = ['configure'] + +local_cf = ['$CFLAGS', '$CPPFLAGS', '-I.', '-DACORN_FTYPE_NFS', '-DWILD_STOP_AT_DIR', '-DLARGE_FILE_SUPPORT' + '-DUNICODE_SUPPORT', '-DUNICODE_WCHAR', '-DUTF8_MAYBE_NATIVE', '-DNO_LCHMOD', '-DDATE_FORMAT=DF_YMD', + '-DUSE_BZIP2', '-DIZ_HAVE_UXUIDGID', '-DNOMEMCPY', '-DNO_WORKING_ISPRINT'] + +buildopts = ' '.join([ + "-f unix/Makefile", + 'CC="$CC"', + 'D_USE_BZ2=-DUSE_BZIP2', + 'L_BZ2=-lbz2', + 'LF2="$LDFLAGS"', + 'CF="%s"' % ' '.join(local_cf), + 'unzips', +]) + +installopts = '-f unix/Makefile prefix=%(installdir)s ' + +sanity_check_paths = { + 'files': ['bin/unzip', 'bin/zipinfo'], + 'dirs': ['man/man1'] +} + +sanity_check_commands = ["unzip -v"] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/u/Uni-Core/Uni-Core-0.0.3-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/u/Uni-Core/Uni-Core-0.0.3-foss-2022a-CUDA-11.7.0.eb new file mode 100644 index 00000000000..2ca769764aa --- /dev/null +++ b/easybuild/easyconfigs/u/Uni-Core/Uni-Core-0.0.3-foss-2022a-CUDA-11.7.0.eb @@ -0,0 +1,55 @@ +easyblock = 'PythonBundle' + +name = 'Uni-Core' +version = '0.0.3' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/dptech-corp/Uni-Core' +description = "An efficient distributed PyTorch framework" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('CUDA', '11.7.0', '', SYSTEM), + ('Python', '3.10.4'), + ('PyTorch', '1.12.0', versionsuffix), + ('jax', '0.3.25', versionsuffix), # provides absl-py + ('tensorboardX', '2.5.1'), + ('tqdm', '4.64.0'), + ('wandb', '0.13.4'), +] + +use_pip = True + +exts_list = [ + ('lmdb', '1.4.1', { + 'checksums': ['1f4c76af24e907593487c904ef5eba1993beb38ed385af82adb25a858f2d658d'], + }), + ('contextlib2', '21.6.0', { + 'checksums': ['ab1e2bfe1d01d968e1b7e8d9023bc51ef3509bba217bb730cee3827e1ee82869'], + }), + ('ml-collections', '0.1.1', { + 'sources': ['ml_collections-%(version)s.tar.gz'], + 'checksums': ['3fefcc72ec433aa1e5d32307a3e474bbb67f405be814ea52a2166bfc9dbe68cc'], + 'preinstallopts': "touch requirements.txt && touch requirements-test.txt && ", + }), + ('huggingface-hub', '0.17.3', { + 'source_tmpl': 'huggingface_hub-%(version)s.tar.gz', + 'checksums': ['40439632b211311f788964602bf8b0d9d6b7a2314fba4e8d67b2ce3ecea0e3fd'], + }), + ('tokenizers', '0.19.1', { + 'sources': ['tokenizers-%(version)s-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl'], + 'checksums': ['8b01afb7193d47439f091cd8f070a1ced347ad0f9144952a30a41836902fe09e'], + }), + (name, version, { + 'source_urls': ['https://github.com/dptech-corp/Uni-Core/archive/'], + 'sources': ['%(version)s.tar.gz'], + 'checksums': ['e7a1e938d7d340d7aa483a05ed5ecf715bfa22f5f32a92e46d096da5b9a08043'], + 'preinstallopts': "sed -i 's/torch>=[0-9.]*/torch/g' setup.py && ", + 'modulename': 'unicore', + }), +] + +sanity_pip_check = True + +moduleclass = 'ai' diff --git a/easybuild/easyconfigs/u/Uni-Core/Uni-Core-0.0.3-foss-2022a.eb b/easybuild/easyconfigs/u/Uni-Core/Uni-Core-0.0.3-foss-2022a.eb new file mode 100644 index 00000000000..d82f94349bc --- /dev/null +++ b/easybuild/easyconfigs/u/Uni-Core/Uni-Core-0.0.3-foss-2022a.eb @@ -0,0 +1,56 @@ +easyblock = 'PythonBundle' + +name = 'Uni-Core' +version = '0.0.3' + +homepage = 'https://github.com/dptech-corp/Uni-Core' +description = "An efficient distributed PyTorch framework" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('PyTorch', '1.12.0'), + ('jax', '0.3.25'), # provides absl-py + ('tensorboardX', '2.5.1'), + ('tqdm', '4.64.0'), + ('wandb', '0.13.4'), +] + +use_pip = True + +local_preinstallopts = "sed -i -e 's/DISABLE_CUDA_EXTENSION = False/DISABLE_CUDA_EXTENSION = True/g' " +local_preinstallopts += "-e 's/torch>=[0-9.]*/torch/g' setup.py && " + +exts_list = [ + ('lmdb', '1.4.1', { + 'checksums': ['1f4c76af24e907593487c904ef5eba1993beb38ed385af82adb25a858f2d658d'], + }), + ('contextlib2', '21.6.0', { + 'checksums': ['ab1e2bfe1d01d968e1b7e8d9023bc51ef3509bba217bb730cee3827e1ee82869'], + }), + ('ml-collections', '0.1.1', { + 'sources': ['ml_collections-%(version)s.tar.gz'], + 'checksums': ['3fefcc72ec433aa1e5d32307a3e474bbb67f405be814ea52a2166bfc9dbe68cc'], + 'preinstallopts': "touch requirements.txt && touch requirements-test.txt && ", + }), + ('huggingface-hub', '0.17.3', { + 'source_tmpl': 'huggingface_hub-%(version)s.tar.gz', + 'checksums': ['40439632b211311f788964602bf8b0d9d6b7a2314fba4e8d67b2ce3ecea0e3fd'], + }), + ('tokenizers', '0.19.1', { + 'sources': ['tokenizers-%(version)s-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl'], + 'checksums': ['8b01afb7193d47439f091cd8f070a1ced347ad0f9144952a30a41836902fe09e'], + }), + (name, version, { + 'source_urls': ['https://github.com/dptech-corp/Uni-Core/archive/'], + 'sources': ['%(version)s.tar.gz'], + 'checksums': ['e7a1e938d7d340d7aa483a05ed5ecf715bfa22f5f32a92e46d096da5b9a08043'], + 'preinstallopts': local_preinstallopts, + 'modulename': 'unicore', + }), +] + +sanity_pip_check = True + +moduleclass = 'ai' diff --git a/easybuild/easyconfigs/u/unixODBC/unixODBC-2.3.12-GCCcore-12.3.0.eb b/easybuild/easyconfigs/u/unixODBC/unixODBC-2.3.12-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..7e5cec281f2 --- /dev/null +++ b/easybuild/easyconfigs/u/unixODBC/unixODBC-2.3.12-GCCcore-12.3.0.eb @@ -0,0 +1,32 @@ +# Easyconfig for unixODBC +# Author: Lykle Voort +# SURFsara, Amsterdam, The Netherlands +# Updated: Petr Král (INUITS) + +easyblock = 'ConfigureMake' + +name = 'unixODBC' +version = '2.3.12' + +homepage = "https://www.unixodbc.org" +description = """unixODBC provides a uniform interface between +application and database driver""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['https://www.unixodbc.org/'] +checksums = ['f210501445ce21bf607ba51ef8c125e10e22dffdffec377646462df5f01915ec'] + +builddependencies = [('binutils', '2.40')] + +sanity_check_paths = { + 'files': [ + 'lib/libodbc.%s' % SHLIB_EXT, + 'lib/libodbccr.%s' % SHLIB_EXT, + 'lib/libodbcinst.%s' % SHLIB_EXT, + ], + 'dirs': [] +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/u/utf8proc/utf8proc-2.9.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/u/utf8proc/utf8proc-2.9.0-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..3ae6a55c205 --- /dev/null +++ b/easybuild/easyconfigs/u/utf8proc/utf8proc-2.9.0-GCCcore-13.2.0.eb @@ -0,0 +1,30 @@ +easyblock = 'CMakeMake' + +name = 'utf8proc' +version = '2.9.0' + +homepage = 'https://github.com/JuliaStrings/utf8proc' +description = """utf8proc is a small, clean C library that provides Unicode normalization, case-folding, +and other operations for data in the UTF-8 encoding.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://github.com/JuliaStrings/utf8proc/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['18c1626e9fc5a2e192311e36b3010bfc698078f692888940f1fa150547abb0c1'] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.27.6'), +] + +separate_build_dir = True + +configopts = ['-DBUILD_SHARED_LIBS=OFF', '-DBUILD_SHARED_LIBS=ON'] + +sanity_check_paths = { + 'files': ['include/utf8proc.h', 'lib/libutf8proc.a', 'lib/libutf8proc.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/u/utf8proc/utf8proc-2.9.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/u/utf8proc/utf8proc-2.9.0-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..c0a4954721b --- /dev/null +++ b/easybuild/easyconfigs/u/utf8proc/utf8proc-2.9.0-GCCcore-13.3.0.eb @@ -0,0 +1,30 @@ +easyblock = 'CMakeMake' + +name = 'utf8proc' +version = '2.9.0' + +homepage = 'https://github.com/JuliaStrings/utf8proc' +description = """utf8proc is a small, clean C library that provides Unicode normalization, case-folding, +and other operations for data in the UTF-8 encoding.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://github.com/JuliaStrings/utf8proc/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['18c1626e9fc5a2e192311e36b3010bfc698078f692888940f1fa150547abb0c1'] + +builddependencies = [ + ('binutils', '2.42'), + ('CMake', '3.29.3'), +] + +separate_build_dir = True + +configopts = ['-DBUILD_SHARED_LIBS=OFF', '-DBUILD_SHARED_LIBS=ON'] + +sanity_check_paths = { + 'files': ['include/utf8proc.h', 'lib/libutf8proc.a', 'lib/libutf8proc.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/u/util-linux/util-linux-2.40-GCCcore-13.3.0.eb b/easybuild/easyconfigs/u/util-linux/util-linux-2.40-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..7ca00a929ad --- /dev/null +++ b/easybuild/easyconfigs/u/util-linux/util-linux-2.40-GCCcore-13.3.0.eb @@ -0,0 +1,46 @@ +easyblock = 'ConfigureMake' + +name = 'util-linux' +version = '2.40' + +homepage = 'https://www.kernel.org/pub/linux/utils/util-linux' + +description = "Set of Linux utilities" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['%s/v%%(version_major_minor)s' % homepage] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['2a51d08cb71fd8e491e0cf633032c928f9a2848417f8441cb8cf7ef9971de916'] + +builddependencies = [ + ('binutils', '2.42'), + ('Autotools', '20231222'), # for fix_waitpid patch + ('pkgconf', '2.2.0'), # for fix_waitpid patch +] + +dependencies = [ + ('ncurses', '6.5'), + ('zlib', '1.3.1'), + ('SQLite', '3.45.3'), +] + +# disable account related utilities (they need OS dependent pam-devel files) +# disable wall and friends (requires group changing permissions for install user) +# install systemd service files in install dir +# install bash completion files in install dir +configopts = "--disable-chfn-chsh --disable-login --disable-su --disable-rfkill " +configopts += "--disable-wall --disable-use-tty-group " +configopts += "--disable-makeinstall-chown --disable-makeinstall-setuid " +configopts += "--with-systemdsystemunitdir='${prefix}/systemd' " +configopts += "--with-bashcompletiondir='${prefix}/share/bash-completion/completions' " +# disable building Python bindings (since we don't include Python as a dep) +configopts += "--without-python " + +sanity_check_paths = { + 'files': ['lib/lib%s.a' % x for x in ['blkid', 'mount', 'uuid']], + 'dirs': ['include', 'bin', 'share', 'sbin'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/v/VASPKIT/VASPKIT-1.5.1-foss-2023a.eb b/easybuild/easyconfigs/v/VASPKIT/VASPKIT-1.5.1-foss-2023a.eb new file mode 100644 index 00000000000..5222a9aba25 --- /dev/null +++ b/easybuild/easyconfigs/v/VASPKIT/VASPKIT-1.5.1-foss-2023a.eb @@ -0,0 +1,42 @@ +easyblock = 'Tarball' + +name = 'VASPKIT' +version = '1.5.1' + +homepage = 'https://vaspkit.com/' +description = """ +VASPKIT aims at providing a powerful and user-friendly interface to perform high throughput +analysis of various material properties from the raw calculated data using the widely-used +VASP code. +""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('matplotlib', '3.7.2'), +] + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%(namelower)s.%(version)s.linux.x64.tar.gz'] +patches = ['%(name)s-1.5.1_fix-envvars.patch'] +checksums = [ + {'vaspkit.1.5.1.linux.x64.tar.gz': '41bbdc0759f72cd43ef7e2f541d228a639bd95dba2a549398b28f47d760d72b1'}, + {'VASPKIT-1.5.1_fix-envvars.patch': '952e2530b53e4632c3f8ab2ec24f88c61d76e263d9a377772c44c3ad071c1970'}, +] + +sanity_check_paths = { + 'files': ["bin/vaspkit", "how_to_set_environment_variables"], + 'dirs': ["bin"], +} + +# remove setup.sh to avoid users to run it +postinstallcmds = ['rm %(installdir)s/setup.sh'] + +modloadmsg = """ +When using this module for the first time run: +cp $EBROOTVASPKIT/how_to_set_environment_variables ~/.vaspkit +and modify paths set in ~/.vaspkit as needed. +""" + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/v/VASPKIT/VASPKIT-1.5.1_fix-envvars.patch b/easybuild/easyconfigs/v/VASPKIT/VASPKIT-1.5.1_fix-envvars.patch new file mode 100644 index 00000000000..d5af158a61f --- /dev/null +++ b/easybuild/easyconfigs/v/VASPKIT/VASPKIT-1.5.1_fix-envvars.patch @@ -0,0 +1,66 @@ +Set correct environment variables, add instructions to set POTCAR paths, translate example job script to slurm +Author: Cintia Willemyns (Vrije Universiteit Brussel) +diff -Naur vaspkit.1.5.1.orig/how_to_set_auto_plot vaspkit.1.5.1/how_to_set_auto_plot +--- vaspkit.1.5.1.orig/how_to_set_auto_plot 2024-06-18 10:57:18.521696013 +0200 ++++ vaspkit.1.5.1/how_to_set_auto_plot 2024-06-18 11:55:12.298424299 +0200 +@@ -1,7 +1,7 @@ + (1) Make sure you have installed python3, numpy, scipy, matplotlib, etc. + (2) Add the following parameters in the ~/.vaspkit file; + ####################################################################### +- PYTHON_BIN ~/anaconda3/bin/python3 ++ PYTHON_BIN $EBROOTPYTHON/bin/python3 + AUTO_PLOT .TRUE. + ####################################################################### + (3) Copy the plot presets from the vaspkit/how_to_set_environment_variable file to the ~/.vaspkit file. Must copy the block from #BEGIN_CUSTOMIZE_PLOT to #END_CUSTOMIZE_PLOT. +diff -Naur vaspkit.1.5.1.orig/how_to_set_environment_variables vaspkit.1.5.1/how_to_set_environment_variables +--- vaspkit.1.5.1.orig/how_to_set_environment_variables 2024-06-18 10:57:17.784058000 +0200 ++++ vaspkit.1.5.1/how_to_set_environment_variables 2024-06-18 13:59:20.120174533 +0200 +@@ -1,11 +1,13 @@ + # cp how_to_set_environment_variables ~/.vaspkit and modify the ~/.vaspkit file based on the settings in your supercomputer! ++# Modify paths as needed, e.g if you want to make PBE-POTCAR file, use POTCAR_TYPE = PBE and set the PBE_PATH to where you unzipped the VASP PAW_PBE pseudo potentials. ++# Do not modify VASPKIT_UTILITIES_PATH or PYTHON_BIN paths! + # All environment variables are case sensitive. + VASP5 = .TRUE. # .TRUE. or .FALSE.; Set .FALSE. if you are using vasp.4.x +-LDA_PATH = ~/POTCAR/LDA # Path of LDA potential +-PBE_PATH = ~/POTCAR/PBE # Path of PBE potential +-GGA_PATH = ~/POTCAR/GGA # Path of PW91 potential +-VASPKIT_UTILITIES_PATH = ~/vaspkit/utilities # Path of VASPKIT +-PYTHON_BIN = ~/anaconda3/bin/python3 # Python executable program with its installation path. Recommend Anaconda package ++LDA_PATH = # Path of LDA potential ++PBE_PATH = # Path of PBE potential ++GGA_PATH = # Path of PW91 potential ++VASPKIT_UTILITIES_PATH = $EBROOTVASPKIT/utilities # Path of VASPKIT ++PYTHON_BIN = $EBROOTPYTHON/bin/python3 # Python executable program with its installation path. Recommend Anaconda package + POTCAR_TYPE = PBE # PBE, PW91 or LDA; Set PBE if you want to make PBE-POTCAR file + GW_POTCAR = .FALSE. # .TRUE. or .FALSE.; For example, H_GW, O_GW will be chose when POTCAR_GW set to .TRUE. + RECOMMENDED_POTCAR = .TRUE. # .TRUE. or .FALSE.; The recommended PAW potential will be chose when RECOMMENDED_POTCAR set to .TRUE. +@@ -42,7 +44,7 @@ + INTERPOLATION_SPACING = 0.04 # Determines the number of interpolation grids, in unit of A in real-space or 1/A in reciprocal space (default: 0.04) + INTERPOLATION_METHOD = 'cubic' # 'linear', 'cubic' (3rd order-spline interpolation), quartic (4th order-spline interpolation), or FFT available only for 2D and 3D grids (default method: 'cubic') + AUTO_SUBMIT_JOB = .FALSE. # .TRUE. or .FALSE. (default: .FASLE.). Whether to auto-submit vaspkit or vasp job or not. +-SUBMIT_JOB_COMMAND = 'qsub job.sh' # The command line to submit job ++SUBMIT_JOB_COMMAND = 'sbatch job.sh' # The command line to submit job + AUTO_PLOT = .FALSE. # TRUE. or .FALSE. (default: .FASLE.). Whether to auto-plot data graphs in the post-processing. + + # New added in Version 1.4.1 +@@ -69,12 +71,14 @@ + #| Must copy the block from #BEGIN_CUSTOMIZE_JOB_SCRIPT to #END_CUSTOMIZE_JOB_SCRIPT | + #+------------------------------------------------------------------------------------------------------------------+ + #BEGIN_CUSTOMIZE_JOB_SCRIPT +-#PBS -N name +-#PBS -o out +-#PBS -e err +-#PBS -l nodes=2:ppn=4 +-#PBS -r y +-cd $PBS_O_WORKDIR ++#!/bin/bash ++#SBATCH --job-name=name # Job name ++#SBATCH --output=out # Standard output ++#SBATCH --error=err # Standard error ++#SBATCH --nodes=2 # Number of nodes ++#SBATCH --ntasks-per-node=4 # Number of tasks per node ++#SBATCH --requeue # Requeue the job if it fails ++cd $SLURM_SUBMIT_DIR + mpirun -np 8 vasp_std > vasp-out + #END_CUSTOMIZE_JOB_SCRIPT + #+------------------------------------------------------------------------------------------------------------------+ diff --git a/easybuild/easyconfigs/v/VBZ-Compression/VBZ-Compression-1.0.3-gompi-2023a.eb b/easybuild/easyconfigs/v/VBZ-Compression/VBZ-Compression-1.0.3-gompi-2023a.eb new file mode 100644 index 00000000000..3a3c79f3875 --- /dev/null +++ b/easybuild/easyconfigs/v/VBZ-Compression/VBZ-Compression-1.0.3-gompi-2023a.eb @@ -0,0 +1,43 @@ +easyblock = 'CMakeMake' + +name = 'VBZ-Compression' +version = '1.0.3' + +homepage = 'https://github.com/nanoporetech/vbz_compression' +description = "VBZ compression HDF5 plugin for nanopolish" + +toolchain = {'name': 'gompi', 'version': '2023a'} + +source_urls = [ + 'https://github.com/nanoporetech/vbz_compression/archive', + 'https://github.com/lemire/streamvbyte/archive', +] +sources = [ + {'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}, + {'download_filename': 'v0.4.1.tar.gz', 'filename': 'streamvbyte-v0.4.1.tar.gz'}, +] +checksums = [ + {'VBZ-Compression-1.0.3.tar.gz': 'a7450e076db628681bbc0e2b3f941c6c21cc2981a7e1c78628807ffdf1b34f31'}, + {'streamvbyte-v0.4.1.tar.gz': '4c4e53134a60b0b06816d3faa7dcde28c3e5e8a656dd415d16d80ae6e3d39fcc'}, +] + +builddependencies = [('CMake', '3.26.3')] + +dependencies = [ + ('HDF5', '1.14.0'), + ('zstd', '1.5.5'), +] + +preconfigopts = "rmdir %(builddir)s/vbz_compression*/third_party/streamvbyte && " +preconfigopts += "mv %(builddir)s/streamvbyte-* %(builddir)s/streamvbyte && " +preconfigopts += "mv %(builddir)s/streamvbyte %(builddir)s/vbz_compression*/third_party/. && " +configopts = "-DENABLE_CONAN=OFF -DENABLE_PERF_TESTING=OFF -DENABLE_PYTHON=OFF " + +sanity_check_paths = { + 'files': ['hdf5/lib/plugin/libvbz_hdf_plugin.%s' % SHLIB_EXT], + 'dirs': [], +} + +modextrapaths = {'HDF5_PLUGIN_PATH': 'hdf5/lib/plugin/'} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/v/VEP/VEP-113.3-GCC-13.3.0.eb b/easybuild/easyconfigs/v/VEP/VEP-113.3-GCC-13.3.0.eb new file mode 100644 index 00000000000..1996303d91d --- /dev/null +++ b/easybuild/easyconfigs/v/VEP/VEP-113.3-GCC-13.3.0.eb @@ -0,0 +1,44 @@ +name = 'VEP' +version = '113.3' + +homepage = 'https://www.ensembl.org/info/docs/tools/vep' +description = """Variant Effect Predictor (VEP) determines the effect of your + variants (SNPs, insertions, deletions, CNVs or structural variants) on genes, + transcripts, and protein sequence, as well as regulatory regions. + Includes EnsEMBL-XS, which provides pre-compiled replacements for frequently + used routines in VEP.""" + +toolchain = {'name': 'GCC', 'version': '13.3.0'} + +source_urls = ['https://github.com/Ensembl/ensembl-vep/archive/release/'] +sources = ['%(version)s.tar.gz'] +checksums = ['ee68013eb035e17129e8f69977f525ebdd8321e73b3164a7bda6e103e2d10beb'] + +dependencies = [ + ('Perl', '5.38.2'), + ('Archive-Zip', '1.68'), + ('DBD-mysql', '4.051'), + ('BioPerl', '1.7.8'), + ('Bio-DB-HTS', '3.01'), + # VEP requires Compress::Raw::Zlib >= 2.103 + ('Compress-Raw-Zlib', '2.213'), +] + +# To select all species use 'all' (but this was broken as of 2024.02.01 and species need to explicitly listed +# with comma separation, see https://github.com/Ensembl/ensembl-vep/issues/1364#issuecomment-1753080504) +species = 'cyprinus_carpio_carpio' + +exts_defaultclass = 'PerlModule' +exts_filter = ("perl -e 'require %(ext_name)s'", "") + +exts_list = [ + ('Bio::EnsEMBL::XS', '2.3.2', { + 'source_urls': ['https://github.com/Ensembl/ensembl-xs/archive'], + 'sources': ['%(version)s.tar.gz'], + 'checksums': ['aafc59568cd1042259196575e99cdfeef9c0fb7966e5f915cfaf38c70885ffa5'], + }), +] + +sanity_check_commands = ['vep --help'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/v/VSEARCH/VSEARCH-2.28.1-GCC-10.2.0.eb b/easybuild/easyconfigs/v/VSEARCH/VSEARCH-2.28.1-GCC-10.2.0.eb new file mode 100644 index 00000000000..14ed6e6d975 --- /dev/null +++ b/easybuild/easyconfigs/v/VSEARCH/VSEARCH-2.28.1-GCC-10.2.0.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'VSEARCH' +version = '2.28.1' + +homepage = 'https://github.com/torognes/vsearch' +description = """VSEARCH supports de novo and reference based chimera detection, + clustering, full-length and prefix dereplication, rereplication, + reverse complementation, masking, all-vs-all pairwise global alignment, + exact and global alignment searching, shuffling, subsampling and sorting. + It also supports FASTQ file analysis, filtering, + conversion and merging of paired-end reads.""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +source_urls = ['https://github.com/torognes/vsearch/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['4f8bf0ad43fef77e573d152b59f55a1f81eb84c22d6545911757e6108f8de21c'] + +builddependencies = [ + ('Autotools', '20200321'), +] + +dependencies = [ + ('zlib', '1.2.11'), + ('bzip2', '1.0.8'), +] + +preconfigopts = './autogen.sh &&' + +configopts = '--disable-pdfman ' + +sanity_check_paths = { + 'files': ['bin/vsearch'], + 'dirs': [], +} + +sanity_check_commands = ['vsearch --help'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/v/VTK/VTK-9.2.6-foss-2023a.eb b/easybuild/easyconfigs/v/VTK/VTK-9.2.6-foss-2023a.eb new file mode 100644 index 00000000000..5c6c6f7a122 --- /dev/null +++ b/easybuild/easyconfigs/v/VTK/VTK-9.2.6-foss-2023a.eb @@ -0,0 +1,98 @@ +## +# Authors:: +# * Fotis Georgatos +# * Robert Mijakovic +# Update: Pavel Tománek (Inuits) +## + +easyblock = 'CMakeNinja' + +name = 'VTK' +version = '9.2.6' + +homepage = 'https://www.vtk.org' +description = """The Visualization Toolkit (VTK) is an open-source, freely available software system for + 3D computer graphics, image processing and visualization. VTK consists of a C++ class library and several + interpreted interface layers including Tcl/Tk, Java, and Python. VTK supports a wide variety of visualization + algorithms including: scalar, vector, tensor, texture, and volumetric methods; and advanced modeling techniques + such as: implicit modeling, polygon reduction, mesh smoothing, cutting, contouring, and Delaunay triangulation.""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://www.vtk.org/files/release/%(version_major_minor)s'] +sources = [ + SOURCE_TAR_GZ, + '%(name)sData-%(version)s.tar.gz', +] +patches = [('vtk-version.egg-info', '.')] +checksums = [ + {'VTK-9.2.6.tar.gz': '06fc8d49c4e56f498c40fcb38a563ed8d4ec31358d0101e8988f0bb4d539dd12'}, + {'VTKData-9.2.6.tar.gz': '032c4b827173f859c898403d25360dc99409a4674559ad58f48828f23a6258b8'}, + {'vtk-version.egg-info': '787b82415ae7a4a1f815b4db0e25f7abc809a05fc85d7d219627f3a7e5d3867b'}, +] + +builddependencies = [ + ('CMake', '3.26.3'), + ('Ninja', '1.11.1'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('XZ', '5.4.2'), + ('libGLU', '9.0.3'), + ('X11', '20230603'), + ('Qt5', '5.15.10'), +] + +separate_build_dir = True + +# OpenGL +configopts = "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT +configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT +configopts += "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include " +# Python +configopts += "-DVTK_WRAP_PYTHON=ON -DVTK_PYTHON_VERSION=3 -DVTK_PYTHON_OPTIONAL_LINK=OFF " +configopts += "-DPython3_EXECUTABLE=$EBROOTPYTHON/bin/python3 " +configopts += "-DPython3_INCLUDE_DIR=$EBROOTPYTHON/include/python%(pyshortver)s " +configopts += "-DPython3_LIBRARY=$EBROOTPYTHON/lib/libpython%(pyshortver)s.so " +# Other +configopts += "-DVTK_USE_MPI=ON " +configopts += "-DCMAKE_INSTALL_LIBDIR=lib " +configopts += "-DVTK_QT_VERSION=5 " +configopts += "-DQt5_DIR=$EBROOTQT5 " +configopts += "-DVTK_MODULE_ENABLE_VTK_GuiSupportQt=YES " +configopts += "-DVTK_MODULE_ENABLE_VTK_ViewsQt=YES" + +preinstallopts = "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " + +# Install a egg-info file so VTK is more python friendly, required for mayavi +local_egg_info_src = '%(builddir)s/VTK-%(version)s/vtk-version.egg-info' +local_egg_info_dest = '%(installdir)s/lib/python%(pyshortver)s/site-packages/vtk-%(version)s.egg-info' +postinstallcmds = [ + 'sed "s/#VTK_VERSION#/%%(version)s/" %s > %s' % (local_egg_info_src, local_egg_info_dest), +] + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +local_vtk_exec = ['vtk%s-%%(version_major_minor)s' % x + for x in ['WrapJava', 'ParseJava', 'WrapPythonInit', 'WrapPython', 'WrapHierarchy']] +local_vtk_exec += ['vtkpython'] +local_vtk_libs = ['CommonCore', 'IONetCDF', 'ParallelCore', 'RenderingOpenGL2'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_vtk_exec] + ['include/vtk-%(version_major_minor)s/vtkMPI.h'] + + ['lib/libvtk%s-%%(version_major_minor)s.%s' % (l, SHLIB_EXT) for l in local_vtk_libs], + 'dirs': ['lib/python%(pyshortver)s/site-packages/', 'include/vtk-%(version_major_minor)s'], +} + +sanity_check_commands = [ + "python -c 'import %(namelower)s'", + "python -c 'import pkg_resources; pkg_resources.get_distribution(\"vtk\")'", + # make sure that VTK Python libraries link to libpython (controlled via DVTK_PYTHON_OPTIONAL_LINK=OFF), + # see https://gitlab.kitware.com/vtk/vtk/-/issues/17881 + "ldd $EBROOTVTK/lib/libvtkPythonContext2D-%%(version_major_minor)s.%s | grep /libpython" % SHLIB_EXT, +] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/v/VTK/VTK-9.3.0-foss-2023a.eb b/easybuild/easyconfigs/v/VTK/VTK-9.3.0-foss-2023a.eb index 9278837da13..740fd888dfb 100644 --- a/easybuild/easyconfigs/v/VTK/VTK-9.3.0-foss-2023a.eb +++ b/easybuild/easyconfigs/v/VTK/VTK-9.3.0-foss-2023a.eb @@ -2,6 +2,7 @@ # Authors:: # * Fotis Georgatos # * Robert Mijakovic +# Update: Pavel Tománek (Inuits) ## easyblock = 'CMakeNinja' @@ -42,6 +43,7 @@ dependencies = [ ('XZ', '5.4.2'), ('libGLU', '9.0.3'), ('X11', '20230603'), + ('Qt5', '5.15.10'), ] separate_build_dir = True @@ -57,7 +59,11 @@ configopts += "-DPython3_INCLUDE_DIR=$EBROOTPYTHON/include/python%(pyshortver)s configopts += "-DPython3_LIBRARY=$EBROOTPYTHON/lib/libpython%(pyshortver)s.so " # Other configopts += "-DVTK_USE_MPI=ON " -configopts += "-DCMAKE_INSTALL_LIBDIR=lib" +configopts += "-DCMAKE_INSTALL_LIBDIR=lib " +configopts += "-DVTK_QT_VERSION=5 " +configopts += "-DQt5_DIR=$EBROOTQT5 " +configopts += "-DVTK_MODULE_ENABLE_VTK_GuiSupportQt=YES " +configopts += "-DVTK_MODULE_ENABLE_VTK_ViewsQt=YES" preinstallopts = "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " diff --git a/easybuild/easyconfigs/v/VTK/VTK-9.3.0-foss-2023b.eb b/easybuild/easyconfigs/v/VTK/VTK-9.3.0-foss-2023b.eb index 8a0452f863f..3be42a90bac 100644 --- a/easybuild/easyconfigs/v/VTK/VTK-9.3.0-foss-2023b.eb +++ b/easybuild/easyconfigs/v/VTK/VTK-9.3.0-foss-2023b.eb @@ -42,6 +42,7 @@ dependencies = [ ('XZ', '5.4.4'), ('libGLU', '9.0.3'), ('X11', '20231019'), + ('Qt5', '5.15.13'), ] separate_build_dir = True @@ -57,7 +58,11 @@ configopts += "-DPython3_INCLUDE_DIR=$EBROOTPYTHON/include/python%(pyshortver)s configopts += "-DPython3_LIBRARY=$EBROOTPYTHON/lib/libpython%(pyshortver)s.so " # Other configopts += "-DVTK_USE_MPI=ON " -configopts += "-DCMAKE_INSTALL_LIBDIR=lib" +configopts += "-DCMAKE_INSTALL_LIBDIR=lib " +configopts += "-DVTK_QT_VERSION=5 " +configopts += "-DQt5_DIR=$EBROOTQT5 " +configopts += "-DVTK_MODULE_ENABLE_VTK_GuiSupportQt=YES " +configopts += "-DVTK_MODULE_ENABLE_VTK_ViewsQt=YES" preinstallopts = "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " diff --git a/easybuild/easyconfigs/v/VTune/VTune-2018_update3.eb b/easybuild/easyconfigs/v/VTune/VTune-2018_update3.eb index 0938ca5f98f..8f1db4ac725 100644 --- a/easybuild/easyconfigs/v/VTune/VTune-2018_update3.eb +++ b/easybuild/easyconfigs/v/VTune/VTune-2018_update3.eb @@ -7,7 +7,7 @@ description = """Intel VTune Amplifier XE is the premier performance profiler fo toolchain = SYSTEM -source_urls = ['http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13079/'] +source_urls = ['http://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/13079/'] sources = ['vtune_amplifier_%(version)s.tar.gz'] checksums = ['a47e3b304b993bc28190d7efaac29dcb4a9b533837f2fe4cd9d5617c537f568a'] diff --git a/easybuild/easyconfigs/v/VTune/VTune-2019_update3.eb b/easybuild/easyconfigs/v/VTune/VTune-2019_update3.eb index bd9fed83da9..50053de3925 100644 --- a/easybuild/easyconfigs/v/VTune/VTune-2019_update3.eb +++ b/easybuild/easyconfigs/v/VTune/VTune-2019_update3.eb @@ -7,7 +7,7 @@ description = """Intel VTune Amplifier XE is the premier performance profiler fo toolchain = SYSTEM -source_urls = ['http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15214/'] +source_urls = ['http://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/15214/'] sources = ['vtune_amplifier_%(version)s.tar.gz'] checksums = ['d873abd0e98b477056030f3520fc8dfb1521dbb4dfaa6d20d830af02ec12a12d'] diff --git a/easybuild/easyconfigs/v/VTune/VTune-2019_update5.eb b/easybuild/easyconfigs/v/VTune/VTune-2019_update5.eb index 09f9e6b6120..1390fece377 100644 --- a/easybuild/easyconfigs/v/VTune/VTune-2019_update5.eb +++ b/easybuild/easyconfigs/v/VTune/VTune-2019_update5.eb @@ -7,7 +7,7 @@ description = """Intel VTune Amplifier XE is the premier performance profiler fo toolchain = SYSTEM -source_urls = ['http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15703/'] +source_urls = ['http://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/15703/'] sources = ['vtune_amplifier_%(version)s.tar.gz'] checksums = ['7b2124123347bbb593d1b8f8cf858d88829a05605769cba5c39444b0aa545473'] diff --git a/easybuild/easyconfigs/v/VTune/VTune-2020_update3.eb b/easybuild/easyconfigs/v/VTune/VTune-2020_update3.eb index b4c024b03be..ab1cb7c1ebc 100644 --- a/easybuild/easyconfigs/v/VTune/VTune-2020_update3.eb +++ b/easybuild/easyconfigs/v/VTune/VTune-2020_update3.eb @@ -7,7 +7,7 @@ description = """Intel VTune Amplifier XE is the premier performance profiler fo toolchain = SYSTEM -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/17095/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/17095/'] sources = [{'download_filename': 'vtune_profiler_2020.tar.gz', 'filename': 'vtune_profiler_%(version)s.tar.gz'}] checksums = ['b22dd61d3931ca6ab7d96df2cf8648e5e1061ab2db13b8d42e3c87586b07c974'] diff --git a/easybuild/easyconfigs/v/VTune/VTune-2021.6.0.eb b/easybuild/easyconfigs/v/VTune/VTune-2021.6.0.eb index 9b6582a6610..d33e54a7818 100644 --- a/easybuild/easyconfigs/v/VTune/VTune-2021.6.0.eb +++ b/easybuild/easyconfigs/v/VTune/VTune-2021.6.0.eb @@ -13,7 +13,7 @@ toolchain = SYSTEM # By downloading, you accept the Intel End User License Agreement # (https://software.intel.com/content/www/us/en/develop/articles/end-user-license-agreement.html) # accept_eula = True -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18012/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18012/'] sources = ['l_oneapi_vtune_p_%(version)s.411_offline.sh'] checksums = ['6b1df7da713337aa665bcc6ff23e4a006695b5bfaf71dffd305cbadca2e5560c'] diff --git a/easybuild/easyconfigs/v/VTune/VTune-2021.9.0.eb b/easybuild/easyconfigs/v/VTune/VTune-2021.9.0.eb index cd2356a18bb..b0f65557f62 100644 --- a/easybuild/easyconfigs/v/VTune/VTune-2021.9.0.eb +++ b/easybuild/easyconfigs/v/VTune/VTune-2021.9.0.eb @@ -13,7 +13,7 @@ toolchain = SYSTEM # By downloading, you accept the Intel End User License Agreement # (https://software.intel.com/content/www/us/en/develop/articles/end-user-license-agreement.html) # accept_eula = True -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18302/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18302/'] sources = ['l_oneapi_vtune_p_%(version)s.545_offline.sh'] checksums = ['55c8ac25e685f03c849bb5383da249c7caaf2138a2b57a10c8975a38fa3828bc'] diff --git a/easybuild/easyconfigs/v/VTune/VTune-2022.0.0.eb b/easybuild/easyconfigs/v/VTune/VTune-2022.0.0.eb index e205471e1e5..16f445c0f64 100644 --- a/easybuild/easyconfigs/v/VTune/VTune-2022.0.0.eb +++ b/easybuild/easyconfigs/v/VTune/VTune-2022.0.0.eb @@ -13,7 +13,7 @@ toolchain = SYSTEM # By downloading, you accept the Intel End User License Agreement # (https://software.intel.com/content/www/us/en/develop/articles/end-user-license-agreement.html) # accept_eula = True -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18406/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18406/'] sources = ['l_oneapi_vtune_p_%(version)s.94_offline.sh'] checksums = ['aa4d575c22e7be0c950b87d67d9e371f470f682906864c4f9b68e530ecd22bd7'] diff --git a/easybuild/easyconfigs/v/VTune/VTune-2022.2.0.eb b/easybuild/easyconfigs/v/VTune/VTune-2022.2.0.eb index 773718fc442..458b8143c02 100644 --- a/easybuild/easyconfigs/v/VTune/VTune-2022.2.0.eb +++ b/easybuild/easyconfigs/v/VTune/VTune-2022.2.0.eb @@ -13,7 +13,7 @@ toolchain = SYSTEM # By downloading, you accept the Intel End User License Agreement # (https://software.intel.com/content/www/us/en/develop/articles/end-user-license-agreement.html) # accept_eula = True -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18602/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18602/'] sources = ['l_oneapi_vtune_p_%(version)s.172_offline.sh'] checksums = ['d9f92ab6486a02c8ba226c98893492a54eda706d9edd3206a6b6143bfbc97195'] diff --git a/easybuild/easyconfigs/v/VTune/VTune-2022.3.0.eb b/easybuild/easyconfigs/v/VTune/VTune-2022.3.0.eb index b8a718b77b0..e2fea76fc3a 100644 --- a/easybuild/easyconfigs/v/VTune/VTune-2022.3.0.eb +++ b/easybuild/easyconfigs/v/VTune/VTune-2022.3.0.eb @@ -13,7 +13,7 @@ toolchain = SYSTEM # By downloading, you accept the Intel End User License Agreement # (https://software.intel.com/content/www/us/en/develop/articles/end-user-license-agreement.html) # accept_eula = True -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18656/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18656/'] sources = ['l_oneapi_vtune_p_%(version)s.195_offline.sh'] checksums = ['7921fce7fcc3b82575be22d9c36beec961ba2a9fb5262ba16a04090bcbd2e1a6'] diff --git a/easybuild/easyconfigs/v/VTune/VTune-2024.3.0.eb b/easybuild/easyconfigs/v/VTune/VTune-2024.3.0.eb new file mode 100644 index 00000000000..a7340fe52b8 --- /dev/null +++ b/easybuild/easyconfigs/v/VTune/VTune-2024.3.0.eb @@ -0,0 +1,25 @@ + +name = 'VTune' +version = '2024.3.0' + +homepage = 'https://www.intel.com/content/www/us/en/developer/tools/oneapi/vtune-profiler.html' +description = """Intel® VTune™ Profiler optimizes application performance, system performance, + and system configuration for HPC, cloud, IoT, media, storage, and more.""" + +toolchain = SYSTEM + +# By downloading, you accept the Intel End User License Agreement +# (https://software.intel.com/content/www/us/en/develop/articles/end-user-license-agreement.html) +# accept_eula = True +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/d7e1fdb1-cfc7-40fb-bf46-3719e9372d67/'] +sources = ['l_oneapi_vtune_p_%(version)s.31_offline.sh'] +checksums = ['da9f45ee4a5ea337756e85e58e40b235417cffbca6813cf224db49061947253d'] + +sanity_check_paths = { + 'files': ['%(namelower)s/%(version_major_minor)s/bin64/amplxe-perf'], + 'dirs': ['%(namelower)s/%(version_major_minor)s/bin64', + '%(namelower)s/%(version_major_minor)s/lib64', + '%(namelower)s/%(version_major_minor)s/include/intel64'] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/v/VTune/VTune-2025.0.0.eb b/easybuild/easyconfigs/v/VTune/VTune-2025.0.0.eb new file mode 100644 index 00000000000..1be37c7d69e --- /dev/null +++ b/easybuild/easyconfigs/v/VTune/VTune-2025.0.0.eb @@ -0,0 +1,24 @@ +name = 'VTune' +version = '2025.0.0' + +homepage = 'https://software.intel.com/en-us/vtune' +description = """Intel VTune Amplifier XE is the premier performance profiler for C, C++, C#, Fortran, + Assembly and Java.""" + +toolchain = SYSTEM + +# By downloading, you accept the Intel End User License Agreement +# (https://software.intel.com/content/www/us/en/develop/articles/end-user-license-agreement.html) +# accept_eula = True +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/e7797b12-ce87-4df0-aa09-df4a272fc5d9/'] +sources = ['intel-vtune-%(version)s.1130_offline.sh'] +checksums = ['6742e5c6b1cd6e4efb794bde5d995ba738be1a991ac84678e0efca04fc080074'] + +sanity_check_paths = { + 'files': ['%(namelower)s/%(version_major_minor)s/bin64/amplxe-perf'], + 'dirs': ['%(namelower)s/%(version_major_minor)s/bin64', + '%(namelower)s/%(version_major_minor)s/lib64', + '%(namelower)s/%(version_major_minor)s/include/intel64'] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/v/Valgrind/Valgrind-3.23.0-gompi-2023b.eb b/easybuild/easyconfigs/v/Valgrind/Valgrind-3.23.0-gompi-2023b.eb new file mode 100644 index 00000000000..c0874657c57 --- /dev/null +++ b/easybuild/easyconfigs/v/Valgrind/Valgrind-3.23.0-gompi-2023b.eb @@ -0,0 +1,46 @@ +easyblock = 'ConfigureMake' + +name = 'Valgrind' +version = '3.23.0' + +homepage = 'https://valgrind.org' +description = "Valgrind: Debugging and profiling tools" + +toolchain = {'name': 'gompi', 'version': '2023b'} +toolchainopts = {'optarch': True} + +source_urls = [ + 'https://sourceware.org/pub/valgrind/', + 'https://www.mirrorservice.org/sites/sourceware.org/pub/valgrind/', +] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['c5c34a3380457b9b75606df890102e7df2c702b9420c2ebef9540f8b5d56264d'] + +dependencies = [ + ('Perl', '5.38.0'), + ('Python', '3.11.5'), +] + +configopts = ' --with-mpicc="$MPICC"' + +local_binaries = [ + 'callgrind_annotate', 'callgrind_control', 'cg_annotate', 'cg_diff', + 'cg_merge', 'ms_print', 'valgrind', 'valgrind-listener', 'vgdb' +] +local_archs = ('amd64', 'arm64', 'ppc64le') + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_binaries] + + [['lib/valgrind/libmpiwrap-%s-linux.%s' % (a, SHLIB_EXT) for a in local_archs]], + 'dirs': [] +} + +sanity_check_commands = [ + 'callgrind_annotate --version 2>&1 | grep "%(version)s"', + 'cg_annotate --help', + 'ms_print --version 2>&1 | grep "%(version)s"', + 'valgrind --help', + 'vgdb --help', +] + +moduleclass = 'debugger' diff --git a/easybuild/easyconfigs/v/Valgrind/Valgrind-3.24.0-gompi-2024a.eb b/easybuild/easyconfigs/v/Valgrind/Valgrind-3.24.0-gompi-2024a.eb new file mode 100644 index 00000000000..2c2922383b6 --- /dev/null +++ b/easybuild/easyconfigs/v/Valgrind/Valgrind-3.24.0-gompi-2024a.eb @@ -0,0 +1,46 @@ +easyblock = 'ConfigureMake' + +name = 'Valgrind' +version = '3.24.0' + +homepage = 'https://valgrind.org' +description = "Valgrind: Debugging and profiling tools" + +toolchain = {'name': 'gompi', 'version': '2024a'} +toolchainopts = {'optarch': True} + +source_urls = [ + 'https://sourceware.org/pub/valgrind/', + 'https://www.mirrorservice.org/sites/sourceware.org/pub/valgrind/', +] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['71aee202bdef1ae73898ccf7e9c315134fa7db6c246063afc503aef702ec03bd'] + +dependencies = [ + ('Perl', '5.38.2'), + ('Python', '3.12.3'), +] + +configopts = ' --with-mpicc="$MPICC"' + +local_binaries = [ + 'callgrind_annotate', 'callgrind_control', 'cg_annotate', 'cg_diff', + 'cg_merge', 'ms_print', 'valgrind', 'valgrind-listener', 'vgdb' +] +local_archs = ('amd64', 'arm64', 'ppc64le') + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_binaries] + + [['lib/valgrind/libmpiwrap-%s-linux.%s' % (a, SHLIB_EXT) for a in local_archs]], + 'dirs': [] +} + +sanity_check_commands = [ + 'callgrind_annotate --version 2>&1 | grep "%(version)s"', + 'cg_annotate --help', + 'ms_print --version 2>&1 | grep "%(version)s"', + 'valgrind --help', + 'vgdb --help', +] + +moduleclass = 'debugger' diff --git a/easybuild/easyconfigs/v/VirtualGL/VirtualGL-3.1.1-GCC-13.3.0.eb b/easybuild/easyconfigs/v/VirtualGL/VirtualGL-3.1.1-GCC-13.3.0.eb new file mode 100644 index 00000000000..72cd90736a4 --- /dev/null +++ b/easybuild/easyconfigs/v/VirtualGL/VirtualGL-3.1.1-GCC-13.3.0.eb @@ -0,0 +1,47 @@ +# Contribution from the Crick HPC team +# uploaded by J. Sassmannshausen +# updated by Valentin Plugaru 2019-09-26 +# updated by Paul Melis 2022-10-07, 2023-08-18 + +easyblock = 'CMakeMake' + +name = 'VirtualGL' +version = '3.1.1' + +homepage = 'https://virtualgl.org/' +description = """VirtualGL is an open source toolkit that gives any Linux or +Unix remote display software the ability to run OpenGL applications with full +hardware acceleration.""" + +toolchain = {'name': 'GCC', 'version': '13.3.0'} + +source_urls = ['https://github.com/VirtualGL/virtualgl/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['79c0d76993814d9ed9fdc29908de1cc6da08f41931bc8363084fdfae03f53ce8'] +patches = [] + +builddependencies = [ + ('CMake', '3.29.3'), + ('binutils', '2.42'), +] + +dependencies = [ + ('libjpeg-turbo', '3.0.1'), + ('Mesa', '24.1.3'), + ('libGLU', '9.0.3'), + ('pocl', '6.0'), + ('X11', '20240607'), +] + +local_binaries = [ + 'cpustat', 'glreadtest', 'glxinfo', 'glxspheres64', 'nettest', 'tcbench', + 'vglclient', 'vglconfig', 'vglconnect', 'vglgenkey', 'vgllogin', 'vglrun', + 'vglserver_config' +] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_binaries], + 'dirs': ['lib64', 'share', 'include'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/v/VisPy/VisPy-0.14.1-foss-2023a.eb b/easybuild/easyconfigs/v/VisPy/VisPy-0.14.1-foss-2023a.eb new file mode 100644 index 00000000000..cc273eb0895 --- /dev/null +++ b/easybuild/easyconfigs/v/VisPy/VisPy-0.14.1-foss-2023a.eb @@ -0,0 +1,40 @@ +easyblock = 'PythonBundle' + +name = 'VisPy' +version = '0.14.1' + +homepage = 'https://vispy.org' +description = """VisPy is a high-performance interactive 2D/3D data visualization library + leveraging the computational power of modern Graphics Processing Units (GPUs) through the + OpenGL library to display very large datasets.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('PyQt5', '5.15.10'), + ('matplotlib', '3.7.2'), # for kiwisolver + ('freetype', '2.13.0') +] + +use_pip = True + +exts_list = [ + ('freetype_py', '2.4.0', { + 'modulename': 'freetype', + 'sources': ['freetype-py-2.4.0.zip'], + 'checksums': ['8ad81195d2f8f339aba61700cebfbd77defad149c51f59b75a2a5e37833ae12e'], + }), + ('hsluv', '5.0.3', { + 'checksums': ['2586bcb61d29d76e89e563a6836df24d86939961c9657f129a59f7617de45377'], + }), + ('vispy', version, { + 'checksums': ['249a50979fc00a8b65109283354dcf12cf415c1a5dcf9821e113f6e590b9b93c'], + 'use_pip': True + }), +] + +sanity_pip_check = True + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/v/Visit/Visit-3.4.1-foss-2023a.eb b/easybuild/easyconfigs/v/Visit/Visit-3.4.1-foss-2023a.eb new file mode 100644 index 00000000000..406d78fa312 --- /dev/null +++ b/easybuild/easyconfigs/v/Visit/Visit-3.4.1-foss-2023a.eb @@ -0,0 +1,64 @@ +easyblock = 'CMakeMake' + +name = 'Visit' +version = '3.4.1' + +homepage = 'https://github.com/visit-dav/visit' +description = """ +VisIt is an Open Source, interactive, scalable, visualization, animation +and analysis tool. From Unix, Windows or Mac workstations, users can +interactively visualize and analyze data ranging in scale from small +(<101 core) desktop-sized projects to large (>105 core) leadership-class +computing facility simulation campaigns. Users can quickly generate +visualizations, animate them through time, manipulate them with a +variety of operators and mathematical expressions, and save the +resulting images and animations for presentations. VisIt contains a rich +set of visualization features to enable users to view a wide variety of +data including scalar and vector fields defined on two- and +three-dimensional (2D and 3D) structured, adaptive and unstructured +meshes. Owing to its customizeable plugin design, VisIt is capabable of +visualizing data from over 120 different scientific data formats. +""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['https://github.com/visit-dav/visit/releases/download/v%(version)s/'] +sources = ['%(namelower)s%(version)s.tar.gz'] +checksums = ['942108cb294f4c9584a1628225b0be39c114c7e9e01805fb335d9c0b507689f5'] + +builddependencies = [('CMake', '3.26.3')] +dependencies = [ + ('zlib', '1.2.13'), + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('SciPy-bundle', '2023.07'), + ('X11', '20230603'), + ('Mesa', '23.1.4'), + ('libglvnd', '1.6.0'), + ('Qt5', '5.15.10'), + ('Qwt', '6.3.0'), + # Visit-3.4.1 needs VTK-9.2.x (not 9.3.x) - https://github.com/visit-dav/visit/issues/19547 + ('VTK', '9.2.6'), + ('FFmpeg', '6.0'), +] + +configopts = "-DVISIT_ZLIB_DIR=$EBROOTZLIB " +configopts += "-DVISIT_VTK_DIR=$EBROOTVTK -DVISIT_VTK_VERSION=$EBVERSIONVTK " +configopts += "-DVISIT_QWT_DIR=$EBROOTQWT " +configopts += "-DVISIT_QT_VERSION=$EBVERSIONQT5 -DVISIT_QT_DIR=$EBROOTQT5 " +configopts += "-DVISIT_OSMESA_DIR=$EBROOTMESA " +configopts += "-DVISIT_MESAGL_DIR=$EBROOTLIBGLVND " +configopts += "-DPYTHON_DIR=$EBROOTPYTHON " +configopts += "-DVISIT_PYTHON_SKIP_INSTALL=ON " +configopts += "-DVISIT_PARALLEL=ON -DVISIT_MPI_COMPILER=$MPICC -DVISIT_MPI_COMPILER_CXX=$MPICXX " +configopts += "-DOpenGL_GL_PREFERENCE=GLVND " + +# add missing include to fix make step +prebuildopts = "sed -i '23 a #include ' %(builddir)s/%(namelower)s%(version)s/src/gui/QvisStripChart.C && " + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['frontendlauncher', 'frontendlauncher.py', 'visit']], + 'dirs': ['%(version)s/bin'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/v/Voro++/Voro++-0.4.6-GCCcore-13.2.0.eb b/easybuild/easyconfigs/v/Voro++/Voro++-0.4.6-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..5c2cb573ca2 --- /dev/null +++ b/easybuild/easyconfigs/v/Voro++/Voro++-0.4.6-GCCcore-13.2.0.eb @@ -0,0 +1,43 @@ +## +# Author: Robert Mijakovic +## +easyblock = 'ConfigureMake' + +name = 'Voro++' +version = '0.4.6' + +homepage = 'http://math.lbl.gov/voro++/' +description = """Voro++ is a software library for carrying out three-dimensional computations of the Voronoi +tessellation. A distinguishing feature of the Voro++ library is that it carries out cell-based calculations, +computing the Voronoi cell for each particle individually. It is particularly well-suited for applications that +rely on cell-based statistics, where features of Voronoi cells (eg. volume, centroid, number of faces) can be used +to analyze a system of particles.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} +toolchainopts = {'pic': True} + +source_urls = [ + 'http://math.lbl.gov/voro++/download/dir/', + 'https://download.lammps.org/thirdparty', +] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['ef7970071ee2ce3800daa8723649ca069dc4c71cc25f0f7d22552387f3ea437e'] + +builddependencies = [('binutils', '2.40')] + + +# No configure +skipsteps = ['configure'] + +# Override CXX and CFLAGS variables from Makefile +buildopts = 'CXX="$CXX" CFLAGS="$CXXFLAGS"' + +# Override PREFIX variable from Makefile +installopts = "PREFIX=%(installdir)s" + +sanity_check_paths = { + 'files': ['bin/voro++', 'lib/libvoro++.a', 'include/voro++/voro++.hh'], + 'dirs': [], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/v/Voro++/Voro++-0.4.6-GCCcore-13.3.0.eb b/easybuild/easyconfigs/v/Voro++/Voro++-0.4.6-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..9f6458281b3 --- /dev/null +++ b/easybuild/easyconfigs/v/Voro++/Voro++-0.4.6-GCCcore-13.3.0.eb @@ -0,0 +1,43 @@ +## +# Author: Robert Mijakovic +## +easyblock = 'ConfigureMake' + +name = 'Voro++' +version = '0.4.6' + +homepage = 'http://math.lbl.gov/voro++/' +description = """Voro++ is a software library for carrying out three-dimensional computations of the Voronoi +tessellation. A distinguishing feature of the Voro++ library is that it carries out cell-based calculations, +computing the Voronoi cell for each particle individually. It is particularly well-suited for applications that +rely on cell-based statistics, where features of Voronoi cells (eg. volume, centroid, number of faces) can be used +to analyze a system of particles.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +source_urls = [ + 'http://math.lbl.gov/voro++/download/dir/', + 'https://download.lammps.org/thirdparty', +] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['ef7970071ee2ce3800daa8723649ca069dc4c71cc25f0f7d22552387f3ea437e'] + +builddependencies = [('binutils', '2.42')] + + +# No configure +skipsteps = ['configure'] + +# Override CXX and CFLAGS variables from Makefile +buildopts = 'CXX="$CXX" CFLAGS="$CXXFLAGS"' + +# Override PREFIX variable from Makefile +installopts = "PREFIX=%(installdir)s" + +sanity_check_paths = { + 'files': ['bin/voro++', 'lib/libvoro++.a', 'include/voro++/voro++.hh'], + 'dirs': [], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/v/vcflib/vcflib-1.0.9-foss-2022b-R-4.2.2.eb b/easybuild/easyconfigs/v/vcflib/vcflib-1.0.9-foss-2022b-R-4.2.2.eb new file mode 100644 index 00000000000..d22ff1aee07 --- /dev/null +++ b/easybuild/easyconfigs/v/vcflib/vcflib-1.0.9-foss-2022b-R-4.2.2.eb @@ -0,0 +1,81 @@ +# Author: Jasper Grimm (UoY) +# Updated: Denis Kristak (INUITS) +# Updated: Petr Král (INUITS) +easyblock = 'CMakeMake' + +name = 'vcflib' +version = '1.0.9' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://github.com/vcflib/vcflib' +description = """vcflib provides methods to manipulate and interpret sequence variation as it can be + described by VCF. The Variant Call Format (VCF) is a flat-file, tab-delimited textual format intended + to concisely describe reference-indexed genetic variations between individuals.""" + +toolchain = {'name': 'foss', 'version': '2022b'} +toolchainopts = {'openmp': True} + +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +patches = [ + 'vcflib-1.0.9_use-external-deps_and_fix_shared_lib.patch', +] +checksums = [ + {'v1.0.9.tar.gz': 'd17fcf8a34d65f1dfecf4b4290d058be744422b6baf34ecdef8ea912d59a4569'}, + {'vcflib-1.0.9_use-external-deps_and_fix_shared_lib.patch': + '82f622a6b4bac1501b10bbc82c4e6567e095869c17b7d34d92b8c4836816b5a1'}, +] + +builddependencies = [ + ('CMake', '3.24.3'), + ('pkgconf', '1.9.3'), + ('pybind11', '2.10.3'), +] + +dependencies = [ + ('Python', '3.10.8'), + ('Perl', '5.36.0'), + ('R', '4.2.2'), + ('XZ', '5.2.7'), + ('zlib', '1.2.12'), + ('bzip2', '1.0.8'), + ('HTSlib', '1.17'), + ('tabixpp', '1.1.2'), + ('intervaltree', '0.1'), + ('fastahack', '1.0.0'), + ('filevercmp', '20191210'), + ('fsom', '20151117'), + ('multichoose', '1.0.3'), + ('smithwaterman', '20160702'), + ('WFA2', '2.3.4'), +] + +preconfigopts = "find %(builddir)s/%(name)s-%(version)s/src -type f " +preconfigopts += r"-regextype egrep -regex '.*\.(h|cpp)' -exec sed -i" +preconfigopts += " -e 's|SmithWatermanGotoh.h|smithwaterman/SmithWatermanGotoh.h|g'" +preconfigopts += " -e 's|IntervalTree.h|intervaltree/IntervalTree.h|g'" +preconfigopts += " -e 's|multichoose.h|multichoose/multichoose.h|g' -e 's|filevercmp.h|filevercmp/filevercmp.h|g'" +preconfigopts += " -e 's|tabix.hpp|tabixpp/tabix.hpp|g' -e 's|Fasta.h|fastahack/Fasta.h|g'" +preconfigopts += r" -e 's|disorder.h|smithwaterman/disorder.h|g' {} \; && " + +configopts = "-DZIG=OFF -DWFA_GITMODULE=OFF -DWFA_INCLUDE_DIRS=$EBROOTWFA2/include/wfa2lib " +configopts += "-DPYTHON_EXECUTABLE=$EBROOTPYTHON/bin/python" + +postinstallcmds = ["cp -r %(builddir)s/%(name)s-%(version)s/scripts %(installdir)s"] + +modextrapaths = { + 'PATH': 'scripts', + 'PYTHONPATH': 'lib', +} + +sanity_check_paths = { + 'files': ['bin/vcffilter', 'bin/vcfcombine', 'lib/libvcflib.a', 'lib/libvcflib.%s' % SHLIB_EXT], + 'dirs': ['scripts', 'include'], +} + +sanity_check_commands = [ + "python -c 'import pyvcflib'", + "vcfwave --help", +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/v/velocyto/velocyto-0.17.17-foss-2023a.eb b/easybuild/easyconfigs/v/velocyto/velocyto-0.17.17-foss-2023a.eb new file mode 100644 index 00000000000..344d3ab3895 --- /dev/null +++ b/easybuild/easyconfigs/v/velocyto/velocyto-0.17.17-foss-2023a.eb @@ -0,0 +1,40 @@ +easyblock = 'PythonBundle' + +name = 'velocyto' +version = '0.17.17' + +homepage = 'https://velocyto.org/velocyto.py/' +description = "Velocyto is a library for the analysis of RNA velocity." + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('SciPy-bundle', '2023.07'), + ('matplotlib', '3.7.2'), + ('numba', '0.58.1'), + ('scikit-learn', '1.3.1'), + ('h5py', '3.9.0'), + ('Pysam', '0.22.0'), + ('loompy', '3.0.7'), +] + +use_pip = True + +exts_list = [ + (name, version, { + 'checksums': ['1ad65fc53292ce1970a70bc742d73491b370038e0b0065761303e787bf7ffe39'], + }), +] + +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/velocyto'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ['velocyto'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/v/versioningit/versioningit-3.1.2-GCCcore-13.2.0.eb b/easybuild/easyconfigs/v/versioningit/versioningit-3.1.2-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..3ea3731df79 --- /dev/null +++ b/easybuild/easyconfigs/v/versioningit/versioningit-3.1.2-GCCcore-13.2.0.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'versioningit' +version = '3.1.2' + +homepage = 'https://github.com/jwodder/versioningit' +description = """versioningit is yet another Python packaging plugin for automatically determining your +package’s version based on your version control repository’s tags. +Unlike others, it allows easy customization of the version format and even lets you easily override +the separate functions used for version extraction & calculation.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +builddependencies = [ + ('binutils', '2.40'), + ('hatchling', '1.18.0'), +] +dependencies = [('Python', '3.11.5')] + +sources = [SOURCE_TAR_GZ] +checksums = ['4db83ed99f56b07d83940bee3445ca46ca120d13b6b304cdb5fb44e5aa4edec0'] + +download_dep_fail = True +sanity_pip_check = True +use_pip = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/v/versioningit/versioningit-3.1.2-GCCcore-13.3.0.eb b/easybuild/easyconfigs/v/versioningit/versioningit-3.1.2-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..ab4e77dea46 --- /dev/null +++ b/easybuild/easyconfigs/v/versioningit/versioningit-3.1.2-GCCcore-13.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'versioningit' +version = '3.1.2' + +homepage = 'https://github.com/jwodder/versioningit' +description = """versioningit is yet another Python packaging plugin for automatically determining your +package’s version based on your version control repository’s tags. +Unlike others, it allows easy customization of the version format and even lets you easily override +the separate functions used for version extraction & calculation.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +builddependencies = [ + ('binutils', '2.42'), + ('hatchling', '1.24.2'), +] +dependencies = [('Python', '3.12.3')] + +sources = [SOURCE_TAR_GZ] +checksums = ['4db83ed99f56b07d83940bee3445ca46ca120d13b6b304cdb5fb44e5aa4edec0'] + +download_dep_fail = True +sanity_pip_check = True +use_pip = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/v/vigra/vigra-1.11.2-foss-2023a.eb b/easybuild/easyconfigs/v/vigra/vigra-1.11.2-foss-2023a.eb new file mode 100644 index 00000000000..6df5b9c0895 --- /dev/null +++ b/easybuild/easyconfigs/v/vigra/vigra-1.11.2-foss-2023a.eb @@ -0,0 +1,48 @@ +easyblock = 'CMakePythonPackage' + +name = 'vigra' +version = '1.11.2' + +homepage = 'https://ukoethe.github.io/vigra/' +description = """Vision with Generic Algorithms is an image processing and analysis library +that puts its main emphasis on customizable algorithms and data structures.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['https://github.com/ukoethe/vigra/archive/'] +sources = ['Version-1-11-2.tar.gz'] +checksums = ['4841936f5c3c137611ec782e293d961df29d3b5b70ade8cb711374de0f4cb5d3'] + +builddependencies = [ + ('CMake', '3.26.3'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('Boost.Python', '1.82.0'), + ('libjpeg-turbo', '2.1.5.1'), + ('OpenJPEG', '2.5.0'), + ('LibTIFF', '4.5.0'), + ('libpng', '1.6.39'), + ('OpenEXR', '3.1.7'), + ('HDF5', '1.14.0'), + ('FFTW', '3.3.10'), + ('nose3', '1.3.8'), +] + +# Fix python files path in make install step +_py_path = "%(builddir)s/%(name)s-Version-1-11-2/config/FindVIGRANUMPY_DEPENDENCIES.cmake" +_py_add = "SET(VIGRANUMPY_INSTALL_DIR ${CMAKE_INSTALL_PREFIX}/lib/python%(pyshortver)s/site-packages)" +preinstallopts = "sed -i '90,91d' %s && " % _py_path +preinstallopts += "sed -i '94d' %s && " % _py_path +preinstallopts += r"sed -i '89 a\%s' %s && " % (_py_add, _py_path) + +sanity_check_paths = { + 'files': ['bin/vigra-config'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/vigra'], +} + +sanity_check_commands = ["vigra-config --version", "python -c 'import vigra'"] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/v/virtualenv/virtualenv-20.23.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/v/virtualenv/virtualenv-20.23.1-GCCcore-12.3.0.eb index 122f3d8d6c8..c36c435d1da 100644 --- a/easybuild/easyconfigs/v/virtualenv/virtualenv-20.23.1-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/v/virtualenv/virtualenv-20.23.1-GCCcore-12.3.0.eb @@ -18,11 +18,8 @@ dependencies = [ ('Python', '3.11.3'), ] -exts_default_options = { - 'download_dep_fail': True, - 'sanity_pip_check': True, - 'use_pip': True, -} +sanity_pip_check = True +use_pip = True exts_list = [ ('distlib', '0.3.6', { diff --git a/easybuild/easyconfigs/v/virtualenv/virtualenv-20.24.6-GCCcore-13.2.0.eb b/easybuild/easyconfigs/v/virtualenv/virtualenv-20.24.6-GCCcore-13.2.0.eb index a0b9921fb5c..2820042ba9d 100644 --- a/easybuild/easyconfigs/v/virtualenv/virtualenv-20.24.6-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/v/virtualenv/virtualenv-20.24.6-GCCcore-13.2.0.eb @@ -18,11 +18,8 @@ dependencies = [ ('Python', '3.11.5'), ] -exts_default_options = { - 'download_dep_fail': True, - 'sanity_pip_check': True, - 'use_pip': True, -} +sanity_pip_check = True +use_pip = True exts_list = [ ('distlib', '0.3.7', { diff --git a/easybuild/easyconfigs/v/virtualenv/virtualenv-20.26.2-GCCcore-13.3.0.eb b/easybuild/easyconfigs/v/virtualenv/virtualenv-20.26.2-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..65f1ced6cae --- /dev/null +++ b/easybuild/easyconfigs/v/virtualenv/virtualenv-20.26.2-GCCcore-13.3.0.eb @@ -0,0 +1,46 @@ +easyblock = 'PythonBundle' + +name = 'virtualenv' +version = '20.26.2' + +homepage = 'https://github.com/pypa/virtualenv' +description = "A tool for creating isolated virtual python environments." + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +builddependencies = [ + ('binutils', '2.42'), + ('hatchling', '1.24.2'), +] + +dependencies = [ + ('Python', '3.12.3'), +] + +sanity_pip_check = True +use_pip = True + +exts_list = [ + ('distlib', '0.3.8', { + 'checksums': ['1530ea13e350031b6312d8580ddb6b27a104275a31106523b8f123787f494f64'], + }), + ('filelock', '3.15.1', { + 'checksums': ['58a2549afdf9e02e10720eaa4d4470f56386d7a6f72edd7d0596337af8ed7ad8'], + }), + ('platformdirs', '4.2.2', { + 'checksums': ['38b7b51f512eed9e84a22788b4bce1de17c0adb134d6becb09836e37d8654cd3'], + }), + (name, version, { + 'checksums': ['82bf0f4eebbb78d36ddaee0283d43fe5736b53880b8a8cdcd37390a07ac3741c'], + }), +] + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(namelower)s'], +} + +sanity_check_commands = ["virtualenv --help"] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/w/WEKA/WEKA-3.8.5-Java-11.eb b/easybuild/easyconfigs/w/WEKA/WEKA-3.8.5-Java-11.eb new file mode 100644 index 00000000000..a3db7b20d7e --- /dev/null +++ b/easybuild/easyconfigs/w/WEKA/WEKA-3.8.5-Java-11.eb @@ -0,0 +1,42 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel + +easyblock = "Tarball" + +name = 'WEKA' +version = '3.8.5' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'http://www.cs.waikato.ac.nz/ml/weka/index.html' +description = """ Weka is a collection of machine learning algorithms for data mining tasks. + The algorithms can either be applied directly to a dataset or called from your own Java code. + Weka contains tools for data pre-processing, classification, regression, clustering, + association rules, and visualization. It is also well-suited for developing new machine + learning schemes.""" + +toolchain = SYSTEM + +source_urls = ['http://prdownloads.sourceforge.net/weka/'] +sources = ['%s-%s.zip' % (name.lower(), version.replace('.', '-'))] +checksums = ['8eec27669cb6d23bcd844041189067281295d1616f45dabf09f816b093f9fb49'] + +dependencies = [('Java', '11')] + +sanity_check_paths = { + 'files': ['weka.jar'], + 'dirs': [] +} + +sanity_check_commands = [ + "java weka.Run -h", + "java weka.classifiers.trees.J48 -h", +] + +modextravars = {'WEKAINSTALL': '%(installdir)s'} + +modloadmsg = """Start WEKA GUI with `java -jar $EBROOTWEKA/weka.jar` +""" + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/w/WFA2/WFA2-2.3.4-GCCcore-12.2.0.eb b/easybuild/easyconfigs/w/WFA2/WFA2-2.3.4-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..cef70fe1233 --- /dev/null +++ b/easybuild/easyconfigs/w/WFA2/WFA2-2.3.4-GCCcore-12.2.0.eb @@ -0,0 +1,30 @@ +easyblock = 'CMakeMake' + +name = 'WFA2' +version = '2.3.4' + +homepage = 'https://github.com/smarco/WFA2-lib' +description = """The wavefront alignment (WFA) algorithm is an exact + gap-affine algorithm that takes advantage of homologous regions + between the sequences to accelerate the alignment process.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://github.com/smarco/WFA2-lib/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['3a02d19b45c7efcdcabdd956421b1e449e771fca0b0f072e02d7aa65ebb29f23'] + +builddependencies = [ + ('binutils', '2.39'), + ('CMake', '3.24.3'), + ('pkgconf', '1.9.3'), +] + +configopts = "-DOPENMP=ON" + +sanity_check_paths = { + 'files': ['lib/libwfa2.a'], + 'dirs': ['include/wfa2lib'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/w/WIEN2k/WIEN2k-23.2-intel-2021b.eb b/easybuild/easyconfigs/w/WIEN2k/WIEN2k-23.2-intel-2021b.eb index a8881dbe118..0dd0b641ceb 100644 --- a/easybuild/easyconfigs/w/WIEN2k/WIEN2k-23.2-intel-2021b.eb +++ b/easybuild/easyconfigs/w/WIEN2k/WIEN2k-23.2-intel-2021b.eb @@ -61,6 +61,10 @@ fix_perl_shebang_for = [ 'bashtime2csh.pl_lapw', ] +# skip running of serial/parallel benchmark, because links to download test_case.tar.gz and mpi-benchmark.tar.gz +# from http://www.wien2k.at/reg_user/benchmark/ that are used by WIEN2k easyblock are broken... +runtest = False + tests = [ # test case 1: NaCl ('NaCl', '-b', '-i 100', [r'^:DIS.*0.1', r'^:ENE.*-1248.1']), diff --git a/easybuild/easyconfigs/w/WRF/WRF-4.5.1-foss-2023a-dmpar.eb b/easybuild/easyconfigs/w/WRF/WRF-4.5.1-foss-2023a-dmpar.eb new file mode 100644 index 00000000000..5b7d53ec837 --- /dev/null +++ b/easybuild/easyconfigs/w/WRF/WRF-4.5.1-foss-2023a-dmpar.eb @@ -0,0 +1,45 @@ +name = 'WRF' +version = '4.5.1' +buildtype = 'dmpar' +versionsuffix = '-%s' % buildtype + +homepage = 'https://www.wrf-model.org' +description = """The Weather Research and Forecasting (WRF) Model is a next-generation mesoscale + numerical weather prediction system designed to serve both operational forecasting and atmospheric + research needs.""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'opt': False} # don't use agressive optimization, stick to -O2 + +github_account = 'wrf-model' +source_urls = [GITHUB_RELEASE] +sources = ['v%(version)s.tar.gz'] +patches = [ + 'WRF-4.5.1_netCDF-Fortran_separate_path.patch', # note: no longer required for version 4.5.2 +] +checksums = [ + {'v4.5.1.tar.gz': '9d557c34c105db4d41e727843ecb19199233c7cf82c5369b34a2ce8efe65e2d1'}, + {'WRF-4.5.1_netCDF-Fortran_separate_path.patch': + '951bff9a3fc651482b287cc03a9f3197979b7800d515fe61cc9c932d9e0dc62e'}, +] + +# csh is used by WRF install scripts +builddependencies = [ + ('Autotools', '20220317'), + ('tcsh', '6.24.10'), + ('time', '1.9'), + ('Perl', '5.36.1'), +] + +dependencies = [ + ('JasPer', '4.0.0'), + ('netCDF', '4.9.2'), + ('netCDF-Fortran', '4.6.1'), +] + +runtest = True + +# limit parallel build to 20 +maxparallel = 20 + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/w/WRF/WRF-4.5.1_netCDF-Fortran_separate_path.patch b/easybuild/easyconfigs/w/WRF/WRF-4.5.1_netCDF-Fortran_separate_path.patch new file mode 100644 index 00000000000..2e35f0dbb86 --- /dev/null +++ b/easybuild/easyconfigs/w/WRF/WRF-4.5.1_netCDF-Fortran_separate_path.patch @@ -0,0 +1,300 @@ +# Allow netCDF library with separate directories for C and Fortran +# ============================================================================ +# This patch has been around in EasyBuild since WRF3.5; it was committed by +# @boegel then. Adapted by @andreas-h to accomodate WRFv4 and foss toolchain +# +# updated for WPS v4.4 by Maxim Masterov (SURF) +# updated for WRF v4.5.1 by Stefan Wolfsheimer (SURF) + + +diff -Nru WRFV4.5.1.orig/arch/Config.pl WRFV4.5.1/arch/Config.pl +--- WRFV4.5.1.orig/arch/Config.pl 2023-07-25 23:14:55.214200451 +0200 ++++ WRFV4.5.1/arch/Config.pl 2023-09-07 18:29:05.423831752 +0200 +@@ -11,6 +11,7 @@ + select((select(STDOUT), $|=1)[0]); + $sw_perl_path = perl ; + $sw_netcdf_path = "" ; ++$sw_netcdff_path = "" ; + $sw_pnetcdf_path = "" ; + $sw_netcdfpar_path = "" ; + $sw_adios2_path = "" ; +@@ -96,6 +97,10 @@ + } + } + } ++ if ( substr( $ARGV[0], 1, 8 ) eq "netcdff=" ) ++ { ++ $sw_netcdff_path = substr( $ARGV[0], 9 ) ; ++ } + if ( substr( $ARGV[0], 1, 8 ) eq "pnetcdf=" ) + { + $sw_pnetcdf_path = substr( $ARGV[0], 9 ) ; +@@ -130,7 +135,8 @@ + } + if ( substr( $ARGV[0], 1, 11 ) eq "USENETCDFF=" ) + { +- $sw_usenetcdff = substr( $ARGV[0], 12 ) ; ++ $sw_usenetcdff = substr( $ARGV[0], 12 ) ; ++ $sw_usenetcdff =~ s/!/ /g ; + } + if ( substr( $ARGV[0], 1, 10 ) eq "USENETCDF=" ) + { +@@ -615,6 +621,7 @@ + { + $_ =~ s/CONFIGURE_PERL_PATH/$sw_perl_path/g ; + $_ =~ s/CONFIGURE_NETCDF_PATH/$sw_netcdf_path/g ; ++ $_ =~ s/CONFIGURE_NETCDFF_PATH/$sw_netcdff_path/g ; + $_ =~ s/CONFIGURE_PNETCDF_PATH/$sw_pnetcdf_path/g ; + $_ =~ s/CONFIGURE_NETCDFPAR_PATH/$sw_netcdfpar_path/g ; + $_ =~ s/CONFIGURE_ADIOS2_PATH/$sw_adios2_path/g ; +@@ -666,7 +673,7 @@ + } elsif ( $sw_os eq "Interix" ) { + $_ =~ s:CONFIGURE_NETCDFPAR_LIB_PATH:\$\(WRF_SRC_ROOT_DIR\)/external/io_netcdfpar/libwrfio_nfpar.a -L$sw_netcdfpar_path/lib $sw_usenetcdff $sw_usenetcdf : ; + } else { +- $_ =~ s:CONFIGURE_NETCDFPAR_LIB_PATH:-L\$\(WRF_SRC_ROOT_DIR\)/external/io_netcdfpar -lwrfio_nfpar -L$sw_netcdfpar_path/lib $sw_usenetcdff $sw_usenetcdf : ; ++ $_ =~ s:CONFIGURE_NETCDFPAR_LIB_PATH:-L\$\(WRF_SRC_ROOT_DIR\)/external/io_netcdfpar -lwrfio_nfpar -L$sw_netcdfpar_path/lib $sw_usenetcdff $sw_usenetcdf : ; + } + } + else +@@ -684,7 +691,7 @@ + } elsif ( $sw_os eq "Interix" ) { + $_ =~ s:CONFIGURE_NETCDF_LIB_PATH:\$\(WRF_SRC_ROOT_DIR\)/external/io_netcdf/libwrfio_nf.a -L$sw_netcdf_path/lib $sw_usenetcdff $sw_usenetcdf : ; + } else { +- $_ =~ s:CONFIGURE_NETCDF_LIB_PATH:-L\$\(WRF_SRC_ROOT_DIR\)/external/io_netcdf -lwrfio_nf -L$sw_netcdf_path/lib $sw_usenetcdff $sw_usenetcdf : ; ++ $_ =~ s:CONFIGURE_NETCDF_LIB_PATH:-L\$\(WRF_SRC_ROOT_DIR\)/external/io_netcdf -lwrfio_nf -L$sw_netcdff_path/lib -L$sw_netcdf_path/lib64 $sw_usenetcdff $sw_usenetcdf : ; + } + } + else +@@ -1072,7 +1079,7 @@ + } elsif ( $sw_os eq "Interix" ) { + $_ =~ s:CONFIGURE_NETCDF_LIB_PATH:\$\(WRF_SRC_ROOT_DIR\)/external/io_netcdf/libwrfio_nf.a -L$sw_netcdf_path/lib $sw_usenetcdff $sw_usenetcdf : ; + } else { +- $_ =~ s:CONFIGURE_NETCDF_LIB_PATH:-L\$\(WRF_SRC_ROOT_DIR\)/external/io_netcdf -lwrfio_nf -L$sw_netcdf_path/lib $sw_usenetcdff $sw_usenetcdf : ; ++ $_ =~ s:CONFIGURE_NETCDF_LIB_PATH:-L\$\(WRF_SRC_ROOT_DIR\)/external/io_netcdf -lwrfio_nf -L$sw_netcdff_path/lib -L$sw_netcdf_path/lib $sw_usenetcdff $sw_usenetcdf : ; + } + } + else +diff -Nru WRFV4.5.1.orig/arch/configure.defaults WRFV4.5.1/arch/configure.defaults +--- WRFV4.5.1.orig/arch/configure.defaults 2023-07-25 23:14:55.215890637 +0200 ++++ WRFV4.5.1/arch/configure.defaults 2023-09-07 14:20:06.651406753 +0200 +@@ -1638,6 +1638,7 @@ + + LIB_EXTERNAL = \ + ../external/io_netcdf/libwrfio_nf.a CONFIGURE_NETCDF_PATH/lib/libnetcdf.lib \ ++ CONFIGURE_NETCDFF_PATH/lib/libnetcdff.lib \ + ../external/wavelet/libWavelet.a ../external/wavelet/lib_wavelet.a + ESMF_IO_LIB = ../external/esmf_time_f90/libesmf_time.a + LIB_BUNDLED = \ +diff -Nru WRFV4.5.1.orig/arch/conf_tokens WRFV4.5.1/arch/conf_tokens +--- WRFV4.5.1.orig/arch/conf_tokens 2023-07-25 23:14:55.215165000 +0200 ++++ WRFV4.5.1/arch/conf_tokens 2023-09-07 14:20:50.194754577 +0200 +@@ -5,6 +5,7 @@ + CONFIGURE_DMPARALLEL + CONFIGURE_RWORDSIZE + CONFIGURE_NETCDF_FLAG ++CONFIGURE_NETCDFF_FLAG + CONFIGURE_GRIB2_FLAG + CONFIGURE_NETCDF_LIB_PATH + CONFIGURE_GRIB2_LIB +@@ -13,4 +14,5 @@ + CONFIGURE_WRFIO_NF + CONFIGURE_WRFIO_GRIB2 + CONFIGURE_NETCDF_PATH ++CONFIGURE_NETCDFF_PATH + CONFIGURE_GRIB2_INC +diff -Nru WRFV4.5.1.orig/arch/postamble WRFV4.5.1/arch/postamble +--- WRFV4.5.1.orig/arch/postamble 2023-07-25 23:14:55.219090000 +0200 ++++ WRFV4.5.1/arch/postamble 2023-09-07 16:01:17.500706228 +0200 +@@ -54,6 +54,7 @@ + -I$(WRF_SRC_ROOT_DIR)/phys \ + -I$(WRF_SRC_ROOT_DIR)/wrftladj \ + -I$(WRF_SRC_ROOT_DIR)/chem -I$(WRF_SRC_ROOT_DIR)/inc \ ++ -I$(NETCDFPATH)/include -I$(NETCDFFPATH)/include \ + -I$(NETCDFPATH)/include \ + CONFIGURE_RTTOV_INC CONFIGURE_CTSM_INC + REGISTRY = Registry +@@ -64,6 +65,7 @@ + ENVCOMPDEFS = CONFIGURE_COMPILEFLAGS + CPPFLAGS = $(ARCHFLAGS) $(ENVCOMPDEFS) -I$(LIBINCLUDE) $(TRADFLAG) CONFIGURE_COMMS_INCLUDE + NETCDFPATH = CONFIGURE_NETCDF_PATH ++NETCDFFPATH = CONFIGURE_NETCDFF_PATH + HDF5PATH = CONFIGURE_HDF5_PATH + WRFPLUSPATH = CONFIGURE_WRFPLUS_PATH + RTTOVPATH = CONFIGURE_RTTOV_PATH +@@ -96,18 +98,18 @@ + + wrfio_nf : + ( cd $(WRF_SRC_ROOT_DIR)/external/io_netcdf ; \ +- make $(J) NETCDFPATH="$(NETCDFPATH)" RANLIB="$(RANLIB)" CPP="$(CPP)" \ ++ make $(J) NETCDFPATH="$(NETCDFPATH)" NETCDFFPATH="$(NETCDFFPATH)" RANLIB="$(RANLIB)" CPP="$(CPP)" \ + CC="$(SCC)" CFLAGS="$(CFLAGS)" \ + FC="$(SFC) $(PROMOTION) $(OMP) $(FCFLAGS)" TRADFLAG="$(TRADFLAG)" AR="$(AR)" ARFLAGS="$(ARFLAGS)" ) + + wrfio_nfpar : + ( cd $(WRF_SRC_ROOT_DIR)/external/io_netcdfpar ; \ +- make $(J) NETCDFPARPATH="$(NETCDFPATH)" RANLIB="$(RANLIB)" CPP="$(CPP) $(ARCHFLAGS)" \ ++ make $(J) NETCDFPARPATH="$(NETCDFPATH)" NETCDFFPATH="$(NETCDFFPATH)" RANLIB="$(RANLIB)" CPP="$(CPP) $(ARCHFLAGS)" \ + FC="$(FC) $(PROMOTION) $(OMP) $(FCFLAGS)" TRADFLAG="$(TRADFLAG)" AR="$(AR)" ARFLAGS="$(ARFLAGS)" ) + + wrfio_pnf : + ( cd $(WRF_SRC_ROOT_DIR)/external/io_pnetcdf ; \ +- make $(J) NETCDFPATH="$(PNETCDFPATH)" RANLIB="$(RANLIB)" CPP="$(CPP) $(ARCHFLAGS)" \ ++ make $(J) NETCDFPATH="$(PNETCDFPATH)" NETCDFFPATH="$(PNETCDFPATH)" RANLIB="$(RANLIB)" CPP="$(CPP) $(ARCHFLAGS)" \ + FC="$(FC) $(PROMOTION) $(OMP) $(FCFLAGS)" TRADFLAG="$(TRADFLAG)" AR="$(AR)" ARFLAGS="$(ARFLAGS)" ) + + wrfio_adios2 : +diff -Nru WRFV4.5.1.orig/configure WRFV4.5.1/configure +--- WRFV4.5.1.orig/configure 2023-07-25 23:14:55.692864209 +0200 ++++ WRFV4.5.1/configure 2023-09-08 11:40:15.875789587 +0200 +@@ -214,17 +214,19 @@ + unset NETCDF4 + fi + +-USENETCDFF="" ++if [ -f "$NETCDFF/lib/libnetcdff.a" -o -f "$NETCDFF/lib/libnetcdff.so" -o -f "$NETCDFF/lib64/libnetcdff.so" -o -f "$NETCDFF/lib64/libnetcdff.so" ] ; then ++ USENETCDFF="-L$NETCDFF/lib!-L$NETCDFF/lib64!-lnetcdff" # ! will be replaced with space ++else ++ USENETCDFF=" " ++fi + USENETCDF="" + if [ -n "$NETCDF" ] ; then + echo "Will use NETCDF in dir: $NETCDF" + # Oh UNIDATA, why make it so hard ... + if [ -f "$NETCDF/lib/libnetcdff.a" -o -f "$NETCDF/lib/libnetcdff.so" -o -f "$NETCDF/lib/libnetcdff.dll.a" ] ; then + USENETCDFF="-lnetcdff" +- else +- USENETCDFF=" " + fi +- if [ -f "$NETCDF/lib/libnetcdf.a" -o -f "$NETCDF/lib/libnetcdf.so" -o -f "$NETCDF/lib/libnetcdf.dll.a" ] ; then ++ if [ -f "$NETCDF/lib/libnetcdf.a" -o -f "$NETCDF/lib/libnetcdf.so" -o -f "$NETCDF/lib64/libnetcdf.a" -o -f "$NETCDF/lib64/libnetcdf.so" ] ; then + USENETCDF="-lnetcdf" + else + USENETCDF=" " +@@ -572,7 +574,7 @@ + srch=`grep -i "^#ARCH.*$os" arch/configure.defaults | grep -i "$mach"` + if [ -n "$srch" ] ; then + $PERL arch/Config.pl -dmparallel=$COMMLIB -ompparallel=$OMP -perl=$PERL \ +- -netcdf=$NETCDF -pnetcdf=$PNETCDF -netcdfpar=$NETCDFPAR -adios2=$ADIOS2 -hdf5=$HDF5 -phdf5=$PHDF5 -os=$os -mach=$mach -ldflags=$ldflags \ ++ -netcdf=$NETCDF -netcdff=$NETCDFF -pnetcdf=$PNETCDF -netcdfpar=$NETCDFPAR -hdf5=$HDF5 -phdf5=$PHDF5 -os=$os -mach=$mach -ldflags=$ldflags \ + -compileflags=$compileflags -opt_level=$opt_level -USENETCDFF=$USENETCDFF -USENETCDF=$USENETCDF \ + -time=$FORTRAN_COMPILER_TIMER -tfl="$TFL" -cfl="$CFL" -config_line="$config_line" \ + -wrf_core=$wrf_core -gpfs=$GPFS_PATH -curl=$CURL_PATH -dep_lib_path="$DEP_LIB_PATH" +@@ -654,14 +656,14 @@ + echo "If you wish to change the default options, edit the file:" + echo " arch/configure.defaults" + +-if test -n "$NETCDF" ; then +- if [ ! -f $NETCDF/include/netcdf.inc ] ; then ++if test -n "$NETCDFF" ; then ++ if [ ! -f $NETCDFF/include/netcdf.inc ] ; then + echo +- echo "Error : Not found $NETCDF/include/netcdf.inc" ++ echo "Error : Not found $NETCDFF/include/netcdf.inc" + echo " Please check this installation of NetCDF and re-run this configure script" + exit -1 + fi +- grep nf_format_64bit $NETCDF/include/netcdf.inc > /dev/null ++ grep nf_format_64bit $NETCDFF/include/netcdf.inc > /dev/null + configure_aaaa=$? ; export configure_aaaa + if [ $configure_aaaa -a -z "$WRFIO_NCD_NO_LARGE_FILE_SUPPORT" ] ; then + echo "NetCDF users note:" +diff -Nru WRFV4.5.1.orig/external/io_netcdf/makefile WRFV4.5.1/external/io_netcdf/makefile +--- WRFV4.5.1.orig/external/io_netcdf/makefile 2023-07-25 23:14:55.935985000 +0200 ++++ WRFV4.5.1/external/io_netcdf/makefile 2023-09-07 14:33:23.630405047 +0200 +@@ -3,9 +3,9 @@ + OBJSL = wrf_io.o field_routines.o module_wrfsi_static.o + OBJS = $(OBJSL) + CODE = ext_ncd_get_dom_ti.code ext_ncd_get_var_td.code ext_ncd_get_var_ti.code ext_ncd_put_dom_ti.code ext_ncd_put_var_td.code ext_ncd_put_var_ti.code transpose.code +-FFLAGS = $(FCFLAGS) -I$(NETCDFPATH)/include -I../ioapi_share +-LIBS = $(LIB_LOCAL) -L$(NETCDFPATH)/lib -lnetcdf +-LIBFFS = $(LIB_LOCAL) -L$(NETCDFPATH)/lib -lnetcdff -lnetcdf $(NETCDF4_DEP_LIB) ++FFLAGS = $(FCFLAGS) -I$(NETCDFFPATH)/include -I../ioapi_share ++LIBS = $(LIB_LOCAL) -L$(NETCDFPATH)/lib -L$(NETCDFPATH)/lib64 -lnetcdf ++LIBFFS = $(LIB_LOCAL) -L$(NETCDFPATH)/lib -L$(NETCDFPATH)/lib64 -L$(NETCDFFPATH)/lib -L$(NETCDFFPATH)/lib64 -lnetcdff -lnetcdf $(NETCDF4_DEP_LIB) + CPP1 = $(CPP) -P $(TRADFLAG) + M4 = m4 -Uinclude -Uindex -Ulen + AR = ar +@@ -24,7 +24,7 @@ + $(RANLIB) $@ + + wrf_io.o: wrf_io.F90 $(CODE) +- grep nf_format_64bit $(NETCDFPATH)/include/netcdf.inc ;\ ++ grep nf_format_64bit $(NETCDFFPATH)/include/netcdf.inc ;\ + a=$$? ; export a ; \ + if [ $$a -a "$$WRFIO_NCD_LARGE_FILE_SUPPORT" = "1" ] ; then \ + $(CPP1) -DWRFIO_NCD_LARGE_FILE_SUPPORT -I../ioapi_share wrf_io.F90 | $(M4) - > wrf_io.f ; \ +@@ -43,14 +43,14 @@ + x=`echo "$(FC)" | awk '{print $$1}'` ; export x ; \ + if [ $$x = "gfortran" ] ; then \ + echo removing external declaration of iargc for gfortran ; \ +- $(CPP1) -I$(NETCDFPATH)/include -I../ioapi_share diffwrf.F90 | sed '/integer *, *external.*iargc/d' > diffwrf.f ;\ ++ $(CPP1) -I$(NETCDFFPATH)/include -I../ioapi_share diffwrf.F90 | sed '/integer *, *external.*iargc/d' > diffwrf.f ;\ + else \ +- $(CPP1) -I$(NETCDFPATH)/include -I../ioapi_share diffwrf.F90 > diffwrf.f ; \ ++ $(CPP1) -I$(NETCDFFPATH)/include -I../ioapi_share diffwrf.F90 > diffwrf.f ; \ + fi + $(FC) -c $(FFLAGS) diffwrf.f + @if [ \( -f ../../frame/wrf_debug.o \) -a \( -f ../../frame/module_wrf_error.o \) -a \( -f $(ESMF_MOD_DEPENDENCE) \) -a \( -f ../../frame/clog.o \) ] ; then \ + echo "diffwrf io_netcdf is being built now. " ; \ +- if [ \( -f $(NETCDFPATH)/lib/libnetcdff.a -o -f $(NETCDFPATH)/lib/libnetcdff.so -o -f $(NETCDFPATH)/lib/libnetcdff.dll.a \) ] ; then \ ++ if [ \( -f $(NETCDFFPATH)/lib/libnetcdff.a -o -f $(NETCDFFPATH)/lib/libnetcdff.so -o -f $(NETCDFFPATH)/lib/libnetcdff.dll.a \) ] ; then \ + $(FC) $(FFLAGS) $(LDFLAGS) -o diffwrf diffwrf.o $(OBJSL) ../../frame/wrf_debug.o ../../frame/module_wrf_error.o ../../frame/clog.o $(ESMF_IO_LIB_EXT) $(LIBFFS) ;\ + else \ + $(FC) $(FFLAGS) $(LDFLAGS) -o diffwrf diffwrf.o $(OBJSL) ../../frame/wrf_debug.o ../../frame/module_wrf_error.o ../../frame/clog.o $(ESMF_IO_LIB_EXT) $(LIBS) ;\ +diff -Nru WRFV4.5.1.orig/external/io_pnetcdf/Makefile WRFV4.5.1/external/io_pnetcdf/Makefile +--- WRFV4.5.1.orig/external/io_pnetcdf/Makefile 2023-07-25 23:14:55.952757000 +0200 ++++ WRFV4.5.1/external/io_pnetcdf/Makefile 2023-09-07 14:34:31.077960575 +0200 +@@ -9,8 +9,8 @@ + ext_pnc_put_var_td.code \ + ext_pnc_put_var_ti.code \ + transpose.code +-FFLAGS = $(FCFLAGS) -I$(NETCDFPATH)/include -I../ioapi_share +-LIBS = -L$(NETCDFPATH)/lib -lpnetcdf ++FFLAGS = $(FCFLAGS) -I$(NETCDFFPATH)/include -I../ioapi_share ++LIBS = -L$(NETCDFFPATH)/lib -lpnetcdf + CPP1 = $(CPP) -P $(TRADFLAG) + M4 = m4 -Uinclude -Uindex -Ulen + AR = ar +@@ -25,15 +25,15 @@ + $(RANLIB) libwrfio_pnf.a + + wrf_io.o: wrf_io.F90 $(CODE) +- $(CPP1) -I$(NETCDFPATH)/include -I../ioapi_share wrf_io.F90 | $(M4) - > wrf_io.f ++ $(CPP1) -I$(NETCDFFPATH)/include -I../ioapi_share wrf_io.F90 | $(M4) - > wrf_io.f + $(FC) $(FFLAGS) -c wrf_io.f + + module_wrfsi_static.o: module_wrfsi_static.F90 +- $(CPP1) -I$(NETCDFPATH)/include -I../ioapi_share module_wrfsi_static.F90 > module_wrfsi_static.f ++ $(CPP1) -I$(NETCDFFPATH)/include -I../ioapi_share module_wrfsi_static.F90 > module_wrfsi_static.f + $(FC) $(FFLAGS) -c module_wrfsi_static.f + + field_routines.o: field_routines.F90 wrf_io.o +- $(CPP1) -I$(NETCDFPATH)/include -I../ioapi_share field_routines.F90 > field_routines.f ++ $(CPP1) -I$(NETCDFFPATH)/include -I../ioapi_share field_routines.F90 > field_routines.f + $(FC) $(FFLAGS) -c field_routines.f + + superclean: +diff -Nru WRFV4.5.1.orig/Makefile WRFV4.5.1/Makefile +--- WRFV4.5.1.orig/Makefile 2023-07-25 23:14:55.185289891 +0200 ++++ WRFV4.5.1/Makefile 2023-09-07 14:36:58.707252929 +0200 +@@ -923,7 +923,7 @@ + @ echo '--------------------------------------' + ( cd frame ; $(MAKE) $(J) LLIST="$(LINKLIST)" framework ; \ + cd ../external/io_netcdf ; \ +- $(MAKE) NETCDFPATH="$(NETCDFPATH)" \ ++ $(MAKE) NETCDFPATH="$(NETCDFPATH)" NETCDFFPATH="$(NETCDFFPATH)" \ + FC="$(FC) $(FCBASEOPTS) $(PROMOTION) $(FCDEBUG) $(OMP)" RANLIB="$(RANLIB)" \ + CPP="$(CPP)" LDFLAGS="$(LDFLAGS)" TRADFLAG="$(TRADFLAG)" ESMF_IO_LIB_EXT="$(ESMF_IO_LIB_EXT)" \ + LIB_LOCAL="$(LIB_LOCAL)" \ +@@ -1070,9 +1070,9 @@ + # rule used by configure to test if this will compile with netcdf4 + nc4_test: + if [ $(USENETCDFPAR) -eq 0 ] ; then \ +- ( cd tools ; /bin/rm -f nc4_test.{exe,nc,o} ; $(SCC) -o nc4_test.exe nc4_test.c -I$(NETCDF)/include -L$(NETCDF)/lib -lnetcdf $(NETCDF4_DEP_LIB) ; cd .. ) ; \ ++ ( cd tools ; /bin/rm -f nc4_test.{exe,nc,o} ; $(SCC) -o nc4_test.exe nc4_test.c -I$(NETCDF)/include -L$(NETCDF)/lib64 -lnetcdf $(NETCDF4_DEP_LIB) ; cd .. ) ; \ + else \ +- ( cd tools ; /bin/rm -f nc4_test.{exe,nc,o} ; $(DM_CC) -o nc4_test.exe nc4_test.c -I$(NETCDF)/include -L$(NETCDF)/lib -lnetcdf $(NETCDF4_DEP_LIB) ; cd .. ) ; \ ++ ( cd tools ; /bin/rm -f nc4_test.{exe,nc,o} ; $(DM_CC) -o nc4_test.exe nc4_test.c -I$(NETCDF)/include -L$(NETCDF)/lib64 -lnetcdf $(NETCDF4_DEP_LIB) ; cd .. ) ; \ + fi + + # rule used by configure to test if Fortran 2003 IEEE signaling is available diff --git a/easybuild/easyconfigs/w/Wannier90/Wannier90-3.1.0-foss-2023a.eb b/easybuild/easyconfigs/w/Wannier90/Wannier90-3.1.0-foss-2023a.eb index 9807690b35c..57105d3bdb6 100644 --- a/easybuild/easyconfigs/w/Wannier90/Wannier90-3.1.0-foss-2023a.eb +++ b/easybuild/easyconfigs/w/Wannier90/Wannier90-3.1.0-foss-2023a.eb @@ -12,10 +12,12 @@ toolchainopts = {'usempi': True} github_account = 'wannier-developers' source_urls = [GITHUB_LOWER_SOURCE] sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCELOWER_TAR_GZ}] -patches = ['Wannier90_3x_ignore_makeinc.patch'] +patches = ['Wannier90_3x_ignore_makeinc.patch', + 'Wannier90_3.1.0_fix_mpi_include.patch'] checksums = [ '40651a9832eb93dec20a8360dd535262c261c34e13c41b6755fa6915c936b254', # wannier90-3.1.0.tar.gz '561c0d296e0e30b8bb303702cd6e41ded54c153d9b9e6cd9cab73858e5e2945e', # Wannier90_3x_ignore_makeinc.patch + 'dd7217d8bf12ac4161fd0b6504f7c085ebcc69b23ab2ac4abcf9251f34b8bc30', # Wannier90_3.1.0_fix_mpi_include.patch ] # The -fallow-argument-mismatch allows MPI communication calls to be @@ -25,10 +27,11 @@ buildopts = 'all F90=$F90 MPIF90=$MPIF90 FCOPTS="$FFLAGS -fallow-argument-mismat buildopts += 'LIBDIR="$LAPACK_LIB_DIR" LIBS="$LIBLAPACK" ' buildopts += 'COMMS=mpi' -files_to_copy = [(['wannier90.x', 'postw90.x'], 'bin'), (['libwannier.a'], 'lib')] +local_executables = ['wannier90.x', 'postw90.x', 'w90chk2chk.x', 'w90spn2spn.x'] +files_to_copy = [(local_executables, 'bin'), (['libwannier.a'], 'lib')] sanity_check_paths = { - 'files': ['bin/wannier90.x', 'bin/postw90.x', 'lib/libwannier.a'], + 'files': ['bin/%s' % x for x in local_executables] + ['lib/libwannier.a'], 'dirs': [] } diff --git a/easybuild/easyconfigs/w/Wannier90/Wannier90-3.1.0-foss-2024a.eb b/easybuild/easyconfigs/w/Wannier90/Wannier90-3.1.0-foss-2024a.eb new file mode 100644 index 00000000000..26e4b587a1f --- /dev/null +++ b/easybuild/easyconfigs/w/Wannier90/Wannier90-3.1.0-foss-2024a.eb @@ -0,0 +1,35 @@ +easyblock = 'MakeCp' + +name = 'Wannier90' +version = '3.1.0' + +homepage = 'http://www.wannier.org' +description = """A tool for obtaining maximally-localised Wannier functions""" + +toolchain = {'name': 'foss', 'version': '2024a'} +toolchainopts = {'usempi': True} + +github_account = 'wannier-developers' +source_urls = [GITHUB_LOWER_SOURCE] +sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCELOWER_TAR_GZ}] +patches = ['Wannier90_3x_ignore_makeinc.patch', + 'Wannier90_3.1.0_fix_mpi_include.patch'] +checksums = [ + '40651a9832eb93dec20a8360dd535262c261c34e13c41b6755fa6915c936b254', # wannier90-3.1.0.tar.gz + '561c0d296e0e30b8bb303702cd6e41ded54c153d9b9e6cd9cab73858e5e2945e', # Wannier90_3x_ignore_makeinc.patch + 'dd7217d8bf12ac4161fd0b6504f7c085ebcc69b23ab2ac4abcf9251f34b8bc30', # Wannier90_3.1.0_fix_mpi_include.patch +] + +buildopts = 'all F90=$F90 MPIF90=$MPIF90 FCOPTS="$FFLAGS -fallow-argument-mismatch" LDOPTS="$FFLAGS" ' +buildopts += 'LIBDIR="$LAPACK_LIB_DIR" LIBS="$LIBLAPACK" ' +buildopts += 'COMMS=mpi' + +local_executables = ['wannier90.x', 'postw90.x', 'w90chk2chk.x', 'w90spn2spn.x'] +files_to_copy = [(local_executables, 'bin'), (['libwannier.a'], 'lib')] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_executables] + ['lib/libwannier.a'], + 'dirs': [] +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/w/Wannier90/Wannier90-3.1.0-gomkl-2023a.eb b/easybuild/easyconfigs/w/Wannier90/Wannier90-3.1.0-gomkl-2023a.eb index 336ac8a3895..a3e59ef46a9 100644 --- a/easybuild/easyconfigs/w/Wannier90/Wannier90-3.1.0-gomkl-2023a.eb +++ b/easybuild/easyconfigs/w/Wannier90/Wannier90-3.1.0-gomkl-2023a.eb @@ -12,10 +12,12 @@ toolchainopts = {'usempi': True} github_account = 'wannier-developers' source_urls = [GITHUB_LOWER_SOURCE] sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCELOWER_TAR_GZ}] -patches = ['Wannier90_3x_ignore_makeinc.patch'] +patches = ['Wannier90_3x_ignore_makeinc.patch', + 'Wannier90_3.1.0_fix_mpi_include.patch'] checksums = [ '40651a9832eb93dec20a8360dd535262c261c34e13c41b6755fa6915c936b254', # wannier90-3.1.0.tar.gz '561c0d296e0e30b8bb303702cd6e41ded54c153d9b9e6cd9cab73858e5e2945e', # Wannier90_3x_ignore_makeinc.patch + 'dd7217d8bf12ac4161fd0b6504f7c085ebcc69b23ab2ac4abcf9251f34b8bc30', # Wannier90_3.1.0_fix_mpi_include.patch ] # The -fallow-argument-mismatch allows MPI communication calls to be @@ -25,10 +27,11 @@ buildopts = 'all F90=$F90 MPIF90=$MPIF90 FCOPTS="$FFLAGS -fallow-argument-mismat buildopts += 'LIBDIR="$LAPACK_LIB_DIR" LIBS="$LIBLAPACK" ' buildopts += 'COMMS=mpi' -files_to_copy = [(['wannier90.x', 'postw90.x'], 'bin'), (['libwannier.a'], 'lib')] +local_executables = ['wannier90.x', 'postw90.x', 'w90chk2chk.x', 'w90spn2spn.x'] +files_to_copy = [(local_executables, 'bin'), (['libwannier.a'], 'lib')] sanity_check_paths = { - 'files': ['bin/wannier90.x', 'bin/postw90.x', 'lib/libwannier.a'], + 'files': ['bin/%s' % x for x in local_executables] + ['lib/libwannier.a'], 'dirs': [] } diff --git a/easybuild/easyconfigs/w/Wannier90/Wannier90-3.1.0-gomkl-2023b.eb b/easybuild/easyconfigs/w/Wannier90/Wannier90-3.1.0-gomkl-2023b.eb new file mode 100644 index 00000000000..e1bedb6ba07 --- /dev/null +++ b/easybuild/easyconfigs/w/Wannier90/Wannier90-3.1.0-gomkl-2023b.eb @@ -0,0 +1,35 @@ +easyblock = 'MakeCp' + +name = 'Wannier90' +version = '3.1.0' + +homepage = 'http://www.wannier.org' +description = """A tool for obtaining maximally-localised Wannier functions""" + +toolchain = {'name': 'gomkl', 'version': '2023b'} +toolchainopts = {'usempi': True} + +github_account = 'wannier-developers' +source_urls = [GITHUB_LOWER_SOURCE] +sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCELOWER_TAR_GZ}] +patches = ['Wannier90_3x_ignore_makeinc.patch'] +checksums = [ + '40651a9832eb93dec20a8360dd535262c261c34e13c41b6755fa6915c936b254', # wannier90-3.1.0.tar.gz + '561c0d296e0e30b8bb303702cd6e41ded54c153d9b9e6cd9cab73858e5e2945e', # Wannier90_3x_ignore_makeinc.patch +] + +# The -fallow-argument-mismatch allows MPI communication calls to be +# called with arrays of different types at different places in the +# code. This otherwise cause an error in GCC 10.X +buildopts = 'all F90=$F90 MPIF90=$MPIF90 FCOPTS="$FFLAGS -fallow-argument-mismatch" LDOPTS="$FFLAGS" ' +buildopts += 'LIBDIR="$LAPACK_LIB_DIR" LIBS="$LIBLAPACK" ' +buildopts += 'COMMS=mpi' + +files_to_copy = [(['wannier90.x', 'postw90.x'], 'bin'), (['libwannier.a'], 'lib')] + +sanity_check_paths = { + 'files': ['bin/wannier90.x', 'bin/postw90.x', 'lib/libwannier.a'], + 'dirs': [] +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/w/Wannier90/Wannier90-3.1.0-intel-2023a.eb b/easybuild/easyconfigs/w/Wannier90/Wannier90-3.1.0-intel-2023a.eb index cf258368771..eb71d75290d 100644 --- a/easybuild/easyconfigs/w/Wannier90/Wannier90-3.1.0-intel-2023a.eb +++ b/easybuild/easyconfigs/w/Wannier90/Wannier90-3.1.0-intel-2023a.eb @@ -12,20 +12,23 @@ toolchainopts = {'usempi': True} github_account = 'wannier-developers' source_urls = [GITHUB_LOWER_SOURCE] sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCELOWER_TAR_GZ}] -patches = ['Wannier90_3x_ignore_makeinc.patch'] +patches = ['Wannier90_3x_ignore_makeinc.patch', + 'Wannier90_3.1.0_fix_mpi_include.patch'] checksums = [ '40651a9832eb93dec20a8360dd535262c261c34e13c41b6755fa6915c936b254', # wannier90-3.1.0.tar.gz '561c0d296e0e30b8bb303702cd6e41ded54c153d9b9e6cd9cab73858e5e2945e', # Wannier90_3x_ignore_makeinc.patch + 'dd7217d8bf12ac4161fd0b6504f7c085ebcc69b23ab2ac4abcf9251f34b8bc30', # Wannier90_3.1.0_fix_mpi_include.patch ] buildopts = 'all F90=$F90 MPIF90=$MPIF90 FCOPTS="$FFLAGS" LDOPTS="$FFLAGS" ' buildopts += 'LIBDIR="$LAPACK_LIB_DIR" LIBS="$LIBLAPACK" ' buildopts += 'COMMS=mpi' -files_to_copy = [(['wannier90.x', 'postw90.x'], 'bin'), (['libwannier.a'], 'lib')] +local_executables = ['wannier90.x', 'postw90.x', 'w90chk2chk.x', 'w90spn2spn.x'] +files_to_copy = [(local_executables, 'bin'), (['libwannier.a'], 'lib')] sanity_check_paths = { - 'files': ['bin/wannier90.x', 'bin/postw90.x', 'lib/libwannier.a'], + 'files': ['bin/%s' % x for x in local_executables] + ['lib/libwannier.a'], 'dirs': [] } diff --git a/easybuild/easyconfigs/w/Wannier90/Wannier90-3.1.0-intel-2024a.eb b/easybuild/easyconfigs/w/Wannier90/Wannier90-3.1.0-intel-2024a.eb new file mode 100644 index 00000000000..34d3457ccc4 --- /dev/null +++ b/easybuild/easyconfigs/w/Wannier90/Wannier90-3.1.0-intel-2024a.eb @@ -0,0 +1,35 @@ +easyblock = 'MakeCp' + +name = 'Wannier90' +version = '3.1.0' + +homepage = 'http://www.wannier.org' +description = """A tool for obtaining maximally-localised Wannier functions""" + +toolchain = {'name': 'intel', 'version': '2024a'} +toolchainopts = {'usempi': True} + +github_account = 'wannier-developers' +source_urls = [GITHUB_LOWER_SOURCE] +sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCELOWER_TAR_GZ}] +patches = ['Wannier90_3x_ignore_makeinc.patch', + 'Wannier90_3.1.0_fix_mpi_include.patch'] +checksums = [ + '40651a9832eb93dec20a8360dd535262c261c34e13c41b6755fa6915c936b254', # wannier90-3.1.0.tar.gz + '561c0d296e0e30b8bb303702cd6e41ded54c153d9b9e6cd9cab73858e5e2945e', # Wannier90_3x_ignore_makeinc.patch + 'dd7217d8bf12ac4161fd0b6504f7c085ebcc69b23ab2ac4abcf9251f34b8bc30', # Wannier90_3.1.0_fix_mpi_include.patch +] + +buildopts = 'all F90=$F90 MPIF90=$MPIF90 FCOPTS="$FFLAGS" LDOPTS="$FFLAGS" ' +buildopts += 'LIBDIR="$LAPACK_LIB_DIR" LIBS="$LIBLAPACK" ' +buildopts += 'COMMS=mpi' + +local_executables = ['wannier90.x', 'postw90.x', 'w90chk2chk.x', 'w90spn2spn.x'] +files_to_copy = [(local_executables, 'bin'), (['libwannier.a'], 'lib')] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_executables] + ['lib/libwannier.a'], + 'dirs': [] +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/w/Wannier90/Wannier90_3.1.0_fix_mpi_include.patch b/easybuild/easyconfigs/w/Wannier90/Wannier90_3.1.0_fix_mpi_include.patch new file mode 100644 index 00000000000..fdc859c8a7f --- /dev/null +++ b/easybuild/easyconfigs/w/Wannier90/Wannier90_3.1.0_fix_mpi_include.patch @@ -0,0 +1,27 @@ +Use "use mpi" to load all required interfaces. +See https://github.com/wannier-developers/wannier90/issues/521 +Author: Stefan Wolfsheimer (SURF) + + +diff -ruN wannier90-3.1.0.orig/src/comms.F90 wannier90-3.1.0/src/comms.F90 +--- wannier90-3.1.0.orig/src/comms.F90 2020-03-05 19:41:10.000000000 +0100 ++++ wannier90-3.1.0/src/comms.F90 2024-10-21 17:01:00.542755184 +0200 +@@ -23,15 +23,13 @@ + + use w90_constants, only: dp + use w90_io, only: io_error +- ++#ifdef MPI ++ use mpi ++#endif + implicit none + + private + +-#ifdef MPI +- include 'mpif.h' +-#endif +- + logical, public, save :: on_root + !! Are we the root node + integer, public, save :: num_nodes diff --git a/easybuild/easyconfigs/w/Wayland/Wayland-1.23.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/w/Wayland/Wayland-1.23.0-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..b774886e5cb --- /dev/null +++ b/easybuild/easyconfigs/w/Wayland/Wayland-1.23.0-GCCcore-13.3.0.eb @@ -0,0 +1,63 @@ +# Author: Jasper Grimm (UoY) +# URL of Wayland download changed to GitLab due to changes upstream +# Author: J. Sassmannshausen (Imperial College London/UK) +easyblock = 'Bundle' + +name = 'Wayland' +version = '1.23.0' + +homepage = 'https://wayland.freedesktop.org/' +description = """ +Wayland is a project to define a protocol for a compositor to talk to + its clients as well as a library implementation of the protocol. The + compositor can be a standalone display server running on Linux kernel + modesetting and evdev input devices, an X application, or a wayland + client itself. The clients can be traditional applications, X servers + (rootless or fullscreen) or other display servers. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +builddependencies = [ + ('CMake', '3.29.3'), + ('Meson', '1.4.0'), + ('Ninja', '1.12.1'), + ('pkgconf', '2.2.0'), + ('binutils', '2.42'), +] + +dependencies = [ + ('libffi', '3.4.5'), + ('expat', '2.6.2'), + ('libxml2', '2.12.7'), +] + +default_easyblock = 'MesonNinja' +default_component_specs = { + 'start_dir': '%(namelower)s-%(version)s', +} + +components = [ + ('wayland', version, { + 'source_urls': ['https://gitlab.freedesktop.org/wayland/%(namelower)s/-/releases/%(version)s/downloads'], + 'checksums': ['05b3e1574d3e67626b5974f862f36b5b427c7ceeb965cb36a4e6c2d342e45ab2'], + 'sources': [SOURCE_TAR_XZ], + 'configopts': "-Ddocumentation=false", + }), + ('wayland-protocols', '1.36', { + 'source_urls': ['https://gitlab.freedesktop.org/wayland/%(namelower)s/-/releases/%(version)s/downloads'], + 'checksums': ['71fd4de05e79f9a1ca559fac30c1f8365fa10346422f9fe795f74d77b9ef7e92'], + 'sources': [SOURCE_TAR_XZ], + 'preconfigopts': "PKG_CONFIG_PATH=%(installdir)s/lib/pkgconfig:$PKG_CONFIG_PATH " + }), +] + +_libs = ['lib/libwayland-%s.%s' % (x, SHLIB_EXT) for x in ['client', 'cursor', 'egl', 'server']] +sanity_check_paths = { + 'files': ['bin/wayland-scanner'] + _libs, + 'dirs': ['lib'], +} + +sanity_check_commands = ["wayland-scanner --help", "wayland-scanner --version"] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/w/Whisper/Whisper-20231117-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/w/Whisper/Whisper-20231117-foss-2023a-CUDA-12.1.1.eb new file mode 100644 index 00000000000..53a2aa183b1 --- /dev/null +++ b/easybuild/easyconfigs/w/Whisper/Whisper-20231117-foss-2023a-CUDA-12.1.1.eb @@ -0,0 +1,40 @@ +easyblock = 'PythonBundle' + +name = 'Whisper' +version = '20231117' +versionsuffix = '-CUDA-12.1.1' + +homepage = 'https://github.com/openai/whisper' +description = "Whisper is a general-purpose speech recognition model" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('tqdm', '4.66.1'), + ('numba', '0.58.1'), + ('PyTorch', '2.1.2', versionsuffix), + ('tiktoken', '0.7.0'), + ('Triton', '2.1.0', versionsuffix), +] + +use_pip = True + +exts_list = [ + ('openai-whisper', version, { + 'checksums': ['7af424181436f1800cc0b7d75cf40ede34e9ddf1ba4983a910832fcf4aade4a4'], + 'modulename': 'whisper', + }), +] + +sanity_check_paths = { + 'files': ['bin/whisper'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["whisper --help"] + +sanity_pip_check = True + +moduleclass = 'ai' diff --git a/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2023a-CUDA-12.1.1.eb new file mode 100644 index 00000000000..b77e1abbaca --- /dev/null +++ b/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2023a-CUDA-12.1.1.eb @@ -0,0 +1,63 @@ +# easyconfig file for waLBerla v6.1 +easyblock = 'CMakeMakeCp' + +name = 'waLBerla' +version = '6.1' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = "https://walberla.net/index.html" +description = """Widely applicable Lattics-Boltzmann from Erlangen is a +block-structured high-performance framework for multiphysics simulations""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'usempi': True, 'pic': True} + +source_urls = ['https://i10git.cs.fau.de/walberla/walberla/-/archive/v6.1'] +sources = ['%(name)s-v%(version)s.tar.gz'] +patches = ['waLBerla-6.1_fix_cmakelist_for_easybuild_without_python.patch'] +checksums = [ + {'waLBerla-v6.1.tar.gz': 'f0acdd9ad6543bc9306c8aae953dd5065986271d4398916ae0469db8b21c007a'}, + {'waLBerla-6.1_fix_cmakelist_for_easybuild_without_python.patch': + 'e64927d85ed6ac4c52921c33c504d4f6e7038fd618c89cf7efdadbcf638a1048'}, +] + +builddependencies = [('CMake', '3.26.3')] + +dependencies = [ + ('Boost.MPI', '1.82.0'), + ('CUDA', '12.1.1', '', SYSTEM), +] + +parallel = 1 + +# default CUDA compute capabilities to use (override via --cuda-compute-capabilities) +cuda_compute_capabilities = ['5.2', '6.0', '7.0', '7.5', '8.0', '8.6', '9.0'] + +configopts = "-DWALBERLA_BUILD_WITH_PYTHON=OFF " +configopts += "-DCMAKE_CUDA_ARCHITECTURES='%(cuda_cc_cmake)s' " +configopts += "-DWALBERLA_BUILD_WITH_CUDA=ON " +configopts += "-DWALBERLA_BUILD_SHOWCASES=OFF " +configopts += "-DWALBERLA_BUILD_DOC=OFF " +configopts += "-DWALBERLA_BUILD_BENCHMARKS=OFF" + + +files_to_copy = [ + (['%(builddir)s/easybuild_obj/*'], 'build'), + (['%(start_dir)s/src/*'], 'src'), +] + +sanity_check_paths = { + 'files': [ + 'build/src/waLBerlaDefinitions.h', + 'build/apps/tutorials/basics/01_Tutorial_BlocksAndFields1', + 'build/utilities/filterCompileCommands.py' + ], + 'dirs': ['src', 'build/apps', 'build/tests', 'build/utilities'] +} + +sanity_check_commands = [ + "mkdir -p %(builddir)s && cp -a %(installdir)s/build/apps/tutorials/lbm %(builddir)s/", + "cd %(builddir)s/lbm && chmod -R u+w . && ./01_BasicLBM 01_BasicLBM.prm", +] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2023a.eb b/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2023a.eb new file mode 100644 index 00000000000..85f6371e807 --- /dev/null +++ b/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2023a.eb @@ -0,0 +1,56 @@ +# easyconfig file for waLBerla v6.1 +easyblock = 'CMakeMakeCp' + +name = 'waLBerla' +version = '6.1' + +homepage = "https://walberla.net/index.html" +description = """Widely applicable Lattics-Boltzmann from Erlangen is a +block-structured high-performance framework for multiphysics simulations""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'usempi': True, 'pic': True} + +source_urls = ['https://i10git.cs.fau.de/walberla/walberla/-/archive/v6.1'] +sources = ['%(name)s-v%(version)s.tar.gz'] +patches = ['waLBerla-6.1_fix_cmakelist_for_easybuild_without_python.patch'] +checksums = [ + {'waLBerla-v6.1.tar.gz': 'f0acdd9ad6543bc9306c8aae953dd5065986271d4398916ae0469db8b21c007a'}, + {'waLBerla-6.1_fix_cmakelist_for_easybuild_without_python.patch': + 'e64927d85ed6ac4c52921c33c504d4f6e7038fd618c89cf7efdadbcf638a1048'}, +] + +builddependencies = [('CMake', '3.26.3')] + +dependencies = [ + ('Boost.MPI', '1.82.0'), +] + +parallel = 1 + +configopts = "-DWALBERLA_BUILD_WITH_PYTHON=OFF " +configopts += "-DWALBERLA_BUILD_SHOWCASES=OFF " +configopts += "-DWALBERLA_BUILD_DOC=OFF " +configopts += "-DWALBERLA_BUILD_BENCHMARKS=OFF" + + +files_to_copy = [ + (['%(builddir)s/easybuild_obj/*'], 'build'), + (['%(start_dir)s/src/*'], 'src'), +] + +sanity_check_paths = { + 'files': [ + 'build/src/waLBerlaDefinitions.h', + 'build/apps/tutorials/basics/01_Tutorial_BlocksAndFields1', + 'build/utilities/filterCompileCommands.py' + ], + 'dirs': ['src', 'build/apps', 'build/tests', 'build/utilities'] +} + +sanity_check_commands = [ + "mkdir -p %(builddir)s && cp -a %(installdir)s/build/apps/tutorials/lbm %(builddir)s/", + "cd %(builddir)s/lbm && chmod -R u+w . && ./01_BasicLBM 01_BasicLBM.prm", +] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/w/wandb/wandb-0.16.1-GCC-12.3.0.eb b/easybuild/easyconfigs/w/wandb/wandb-0.16.1-GCC-12.3.0.eb index 878f6cc3f72..b8bf8eefb30 100644 --- a/easybuild/easyconfigs/w/wandb/wandb-0.16.1-GCC-12.3.0.eb +++ b/easybuild/easyconfigs/w/wandb/wandb-0.16.1-GCC-12.3.0.eb @@ -9,13 +9,16 @@ tracking your machine learning experiments.""" toolchain = {'name': 'GCC', 'version': '12.3.0'} +builddependencies = [ + ('hatchling', '1.18.0'), +] + dependencies = [ ('Python', '3.11.3'), ('Python-bundle-PyPI', '2023.06'), ('GitPython', '3.1.40'), ('PyYAML', '6.0'), ('protobuf-python', '4.24.0'), - ('hatchling', '1.18.0'), ] use_pip = True diff --git a/easybuild/easyconfigs/w/weblogo/weblogo-2.8.2-foss-2022b.eb b/easybuild/easyconfigs/w/weblogo/weblogo-2.8.2-foss-2022b.eb new file mode 100644 index 00000000000..80923183514 --- /dev/null +++ b/easybuild/easyconfigs/w/weblogo/weblogo-2.8.2-foss-2022b.eb @@ -0,0 +1,45 @@ +easyblock = 'Tarball' + +name = 'weblogo' +version = '2.8.2' + +homepage = "https://weblogo.berkeley.edu" +description = """WebLogo is a web based application designed to make the generation of sequence logos as easy +and painless as possible.""" + +toolchain = {'name': 'foss', 'version': '2022b'} + +source_urls = ['https://weblogo.berkeley.edu/release'] +sources = ['weblogo.%(version)s.tar.gz'] +checksums = ['2d3e0040c0c1e363c1dfd57f8b585387eb682ed08b2cc2fe2e4cc2a33ac52266'] + +dependencies = [ + ('Perl', '5.36.0'), + ('Ghostscript', '10.0.0'), + ('ImageMagick', '7.1.0-53'), +] + +postinstallcmds = [ + 'mkdir %(installdir)s/bin', + 'mkdir -p %(installdir)s/lib', + 'mv %(installdir)s/seqlogo %(installdir)s/bin/', + 'cp %(installdir)s/template.eps %(installdir)s/bin/', + 'mv %(installdir)s/*.pm %(installdir)s/lib/', # Move all Perl modules to the lib directory + 'mv %(installdir)s/logo.cgi %(installdir)s/lib/', + 'chmod +x %(installdir)s/bin/seqlogo', +] + +modextrapaths = { + 'PERL5LIB': 'lib', # Use relative path +} + +sanity_check_paths = { + 'files': ['bin/seqlogo', 'lib/logo.pm', 'lib/template.pm'], + 'dirs': [], +} + +sanity_check_commands = [ + "seqlogo -f %(installdir)s/globin.fasta" +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/w/wget/wget-1.21.4-GCCcore-12.2.0.eb b/easybuild/easyconfigs/w/wget/wget-1.21.4-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..7dae35b8d9f --- /dev/null +++ b/easybuild/easyconfigs/w/wget/wget-1.21.4-GCCcore-12.2.0.eb @@ -0,0 +1,50 @@ +easyblock = 'ConfigureMake' + +name = 'wget' +version = '1.21.4' + +homepage = 'https://www.gnu.org/software/wget' +description = """GNU Wget is a free software package for retrieving files using HTTP, HTTPS and FTP, + the most widely-used Internet protocols. It is a non-interactive commandline tool, + so it may easily be called from scripts, cron jobs, terminals without X-Windows support, etc.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = [ + {SOURCE_TAR_GZ: '81542f5cefb8faacc39bbbc6c82ded80e3e4a88505ae72ea51df27525bcde04c'}, +] + +builddependencies = [ + ('binutils', '2.39'), + ('pkgconf', '1.9.3'), + ('Perl', '5.36.0'), +] +dependencies = [ + ('PCRE', '8.45'), + ('libidn2', '2.3.4'), + ('zlib', '1.2.12'), + ('OpenSSL', '1.1', '', SYSTEM), + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date gnutls for security reasons + # ('GnuTLS', '3.7.1'), +] + +# make sure pkgconfig picks up system packages (OpenSSL & co) +local_pc = "%(sysroot)s/usr/lib64/pkgconfig:" +local_pc += "%(sysroot)s/usr/lib/pkgconfig:" +local_pc += "%(sysroot)s/usr/lib/x86_64-linux-gnu/pkgconfig" +preconfigopts = "export PKG_CONFIG_PATH=%s && " % local_pc +configopts = '--with-ssl=openssl ' + +# Optionally, you can use gnutls (default) instead of OpenSSL. +# Do not forget to comment out configopts in that case. +# osdependencies = [('gnutls-devel', 'gnutls-dev', 'libgnutls-devel')] + +sanity_check_paths = { + 'files': ['bin/%(name)s'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/w/wget/wget-1.24.5-GCCcore-12.3.0.eb b/easybuild/easyconfigs/w/wget/wget-1.24.5-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..ea4438bce14 --- /dev/null +++ b/easybuild/easyconfigs/w/wget/wget-1.24.5-GCCcore-12.3.0.eb @@ -0,0 +1,50 @@ +easyblock = 'ConfigureMake' + +name = 'wget' +version = '1.24.5' + +homepage = 'https://www.gnu.org/software/wget' +description = """GNU Wget is a free software package for retrieving files using HTTP, HTTPS and FTP, + the most widely-used Internet protocols. It is a non-interactive commandline tool, + so it may easily be called from scripts, cron jobs, terminals without X-Windows support, etc.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = [ + {SOURCE_TAR_GZ: 'fa2dc35bab5184ecbc46a9ef83def2aaaa3f4c9f3c97d4bd19dcb07d4da637de'}, +] + +builddependencies = [ + ('binutils', '2.40'), + ('pkgconf', '1.9.5'), + ('Perl', '5.36.1'), +] +dependencies = [ + ('PCRE', '8.45'), + ('libidn2', '2.3.7'), + ('zlib', '1.2.13'), + ('OpenSSL', '1.1', '', SYSTEM), + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date gnutls for security reasons + # ('GnuTLS', '3.7.1'), +] + +# make sure pkgconfig picks up system packages (OpenSSL & co) +local_pc = "%(sysroot)s/usr/lib64/pkgconfig:" +local_pc += "%(sysroot)s/usr/lib/pkgconfig:" +local_pc += "%(sysroot)s/usr/lib/x86_64-linux-gnu/pkgconfig" +preconfigopts = "export PKG_CONFIG_PATH=%s && " % local_pc +configopts = '--with-ssl=openssl ' + +# Optionally, you can use gnutls (default) instead of OpenSSL. +# Do not forget to comment out configopts in that case. +# osdependencies = [('gnutls-devel', 'gnutls-dev', 'libgnutls-devel')] + +sanity_check_paths = { + 'files': ['bin/%(name)s'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/w/worker/worker-1.6.13-iimpi-2023a.eb b/easybuild/easyconfigs/w/worker/worker-1.6.13-iimpi-2023a.eb new file mode 100644 index 00000000000..f3b254591f5 --- /dev/null +++ b/easybuild/easyconfigs/w/worker/worker-1.6.13-iimpi-2023a.eb @@ -0,0 +1,49 @@ +easyblock = 'ConfigureMake' + +name = 'worker' +version = '1.6.13' + +homepage = 'https://github.com/gjbex/worker' +description = """The Worker framework has been developed to help deal with parameter exploration experiments + that would otherwise result in many jobs, forcing the user resort to scripting to retain her sanity; + see also https://vscentrum.be/neutral/documentation/cluster-doc/running-jobs/worker-framework.""" + +local_tcname = 'iimpi' +local_tcver = '2023a' +toolchain = {'name': local_tcname, 'version': local_tcver} +toolchainopts = {'usempi': True} + +source_urls = ['https://github.com/gjbex/worker/archive/'] +sources = ['%(version)s.tar.gz'] +patches = ['%(name)s-%(version)s_fixintel.patch'] +checksums = [ + 'b42b8566d82048c706427913c8f7edcd9f5892d61f190ce1f49e428113b7e1bc', # 1.6.13.tar.gz + 'c28bbc837ec5d6fb3390df668b06e0b5169ca31dede907336a2b0637c4a81504', # worker-1.6.13_fixintel.patch +] + +dependencies = [ + ('Perl', '5.36.1'), + ('Perl-bundle-CPAN', '5.36.1'), +] + +# adjust worker configuration file +# note: tweak this to your local setup +postinstallcmds = [ + 'sed -i "s/ cores_per_node = .*/ cores_per_node = 16/g" %(installdir)s/conf/worker.conf', + 'sed -i "s@ qsub = .*@ qsub = `which qsub`@g" %(installdir)s/conf/worker.conf', + 'sed -i "s/ email = .*/ email = hpc-support@example.com/g" %(installdir)s/conf/worker.conf', + 'sed -i "s/ unload_modules = .*/ unload_modules = %s/g" %%(installdir)s/conf/worker.conf' % (local_tcname), + 'sed -i "s@ mpi_module = .*@ mpi_module = %s/%s@g" %%(installdir)s/conf/worker.conf' % (local_tcname, local_tcver), + 'sed -i "s@ module_path = .*@ module_path = %(installdir)s/../../../modules/all@g" %(installdir)s/conf/worker.conf', + "echo PERL=\\'`which perl`\\' > %(installdir)s/conf/worker_perl.sh", +] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['wcat', 'wconvert', 'wload', 'worker', 'wreduce', 'wresume', 'wsub', + 'wsummarize']], + 'dirs': ['lib/perl', 'lib/tt'], +} + +sanity_check_commands = ["wsub -help"] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/w/wradlib/wradlib-2.0.3-foss-2022a.eb b/easybuild/easyconfigs/w/wradlib/wradlib-2.0.3-foss-2022a.eb new file mode 100644 index 00000000000..010b73f371b --- /dev/null +++ b/easybuild/easyconfigs/w/wradlib/wradlib-2.0.3-foss-2022a.eb @@ -0,0 +1,57 @@ +easyblock = 'PythonBundle' + +name = 'wradlib' +version = '2.0.3' + +homepage = 'https://docs.wradlib.org/' +description = """ +The wradlib project has been initiated in order to facilitate the use of weather +radar data as well as to provide a common platform for research on new +algorithms.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('xarray', '2022.6.0'), + ('Cartopy', '0.20.3'), + ('dask', '2022.10.0'), + ('matplotlib', '3.5.2'), + ('netcdf4-python', '1.6.1'), + ('h5netcdf', '1.2.0'), + ('geopandas', '0.12.2'), +] + +use_pip = True + +exts_list = [ + ('deprecation', '2.1.0', { + 'checksums': ['72b3bde64e5d778694b0cf68178aed03d15e15477116add3fb773e581f9518ff'], + }), + ('cmweather', '0.3.2', { + 'checksums': ['d374b068fcbfeed87bc511f1f77a6047ae752f4a175a852587414b615b4baa5a'], + }), + ('lat_lon_parser', '1.3.0', { + 'checksums': ['e3a65dacd5b25a18c56e3ae31b11cd724480be7fe8db2df1c46ed0dd322a1fca'], + }), + ('xarray-datatree', '0.0.13', { + 'modulename': 'datatree', + 'checksums': ['f42bd519cab8754eb8a98749464846893b59560318520c45212e85c46af692c9'], + }), + ('xmltodict', '0.13.0', { + 'checksums': ['341595a488e3e01a85a9d8911d8912fd922ede5fecc4dce437eb4b6c8d037e56'], + }), + ('xradar', '0.5.1', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['0337b4a0798ded019b26e0746b7b7baeb6f21344a2a2e3704965049972ccbf51'], + }), + (name, version, { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['e2b625d10bc9b3ea2f33356fe467683b474c0a5410ff10ea6a708238d9172a10'], + }), +] + +sanity_pip_check = True + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/w/wradlib/wradlib-2.0.3-foss-2023a.eb b/easybuild/easyconfigs/w/wradlib/wradlib-2.0.3-foss-2023a.eb new file mode 100644 index 00000000000..d53e56422bc --- /dev/null +++ b/easybuild/easyconfigs/w/wradlib/wradlib-2.0.3-foss-2023a.eb @@ -0,0 +1,59 @@ +easyblock = 'PythonBundle' + +name = 'wradlib' +version = '2.0.3' + +homepage = 'https://docs.wradlib.org/' +description = """ +The wradlib project has been initiated in order to facilitate the use of weather +radar data as well as to provide a common platform for research on new +algorithms.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [ + ('hatchling', '1.18.0'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('xarray', '2023.9.0'), + ('Cartopy', '0.22.0'), + ('dask', '2023.9.2'), + ('matplotlib', '3.7.2'), + ('netcdf4-python', '1.6.4'), + ('h5netcdf', '1.2.0'), + ('geopandas', '0.14.2'), +] + +use_pip = True + +exts_list = [ + ('deprecation', '2.1.0', { + 'checksums': ['72b3bde64e5d778694b0cf68178aed03d15e15477116add3fb773e581f9518ff'], + }), + ('cmweather', '0.3.2', { + 'checksums': ['d374b068fcbfeed87bc511f1f77a6047ae752f4a175a852587414b615b4baa5a'], + }), + ('lat_lon_parser', '1.3.0', { + 'checksums': ['e3a65dacd5b25a18c56e3ae31b11cd724480be7fe8db2df1c46ed0dd322a1fca'], + }), + ('xarray-datatree', '0.0.13', { + 'modulename': 'datatree', + 'checksums': ['f42bd519cab8754eb8a98749464846893b59560318520c45212e85c46af692c9'], + }), + ('xmltodict', '0.13.0', { + 'checksums': ['341595a488e3e01a85a9d8911d8912fd922ede5fecc4dce437eb4b6c8d037e56'], + }), + ('xradar', '0.5.1', { + 'checksums': ['b71021164b005f3270afd2079b8ed831a01ed43accbb7fc42c79e31a342546c5'], + }), + (name, version, { + 'checksums': ['0d5448a1dd0e030bdd36f7bbc69fa50aee7fb74dbc7b6407d2dc52d18ea40c49'], + }), +] + +sanity_pip_check = True + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/w/wrapt/wrapt-1.16.0-gfbf-2024a.eb b/easybuild/easyconfigs/w/wrapt/wrapt-1.16.0-gfbf-2024a.eb new file mode 100644 index 00000000000..10f6d8cf5cf --- /dev/null +++ b/easybuild/easyconfigs/w/wrapt/wrapt-1.16.0-gfbf-2024a.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonBundle' + +name = 'wrapt' +version = '1.16.0' + +homepage = 'https://pypi.org/project/wrapt/' +description = """The aim of the wrapt module is to provide a transparent object +proxy for Python, which can be used as the basis for the construction of +function wrappers and decorator functions.""" + +toolchain = {'name': 'gfbf', 'version': '2024a'} + +dependencies = [ + ('Python', '3.12.3'), + ('SciPy-bundle', '2024.05'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + (name, version, { + 'checksums': ['5f370f952971e7d17c7d1ead40e49f32345a7f7a5373571ef44d800d06b1899d'], + }), +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/w/wxWidgets/wxWidgets-3.2.6-GCC-13.3.0.eb b/easybuild/easyconfigs/w/wxWidgets/wxWidgets-3.2.6-GCC-13.3.0.eb new file mode 100644 index 00000000000..0c9c8976770 --- /dev/null +++ b/easybuild/easyconfigs/w/wxWidgets/wxWidgets-3.2.6-GCC-13.3.0.eb @@ -0,0 +1,71 @@ +easyblock = 'ConfigureMake' + +name = 'wxWidgets' +version = '3.2.6' + +homepage = 'https://www.wxwidgets.org' +description = """wxWidgets is a C++ library that lets developers create +applications for Windows, Mac OS X, Linux and other platforms with a +single code base. It has popular language bindings for Python, Perl, +Ruby and many other languages, and unlike other cross-platform toolkits, +wxWidgets gives applications a truly native look and feel because it +uses the platform's native API rather than emulating the GUI.""" + +toolchain = {'name': 'GCC', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +github_account = 'wxWidgets' +source_urls = [GITHUB_RELEASE] +sources = [SOURCE_TAR_BZ2] +checksums = ['939e5b77ddc5b6092d1d7d29491fe67010a2433cf9b9c0d841ee4d04acb9dce7'] + +builddependencies = [ + ('gettext', '0.22.5'), + ('pkgconf', '2.2.0'), + ('Python', '3.12.3'), +] + +dependencies = [ + ('libpng', '1.6.43'), + ('zlib', '1.3.1'), + ('libjpeg-turbo', '3.0.1'), + ('XZ', '5.4.5'), + ('jbigkit', '2.1'), + ('LibTIFF', '4.6.0'), + ('expat', '2.6.2'), + ('GTK3', '3.24.42'), + ('X11', '20240607'), + ('Mesa', '24.1.3'), + ('libGLU', '9.0.3'), + ('SDL2', '2.30.6'), + ('cairo', '1.18.0'), + ('GST-plugins-base', '1.24.8'), + ('GLib', '2.80.4'), +] + +local_cpath_ext = '$EBROOTGTKPLUS/include/gtk-3.0:$EBROOTGLIB/include/glib-2.0:$EBROOTGLIB/lib/glib-2.0/include' + +preconfigopts = 'CPATH=$CPATH:%s ' % local_cpath_ext + +configopts = '--enable-intl --enable-ipv6 ' +# Options required by wxPython +configopts += '--with-gtk=3 --with-gtk-prefix=$EBROOTGTKPLUS ' +# Note: the configure step might claim to find OpenGL headers in +# /usr/include, but it will still use the ones from the Mesa dependency above +configopts += '--with-opengl ' +configopts += '--enable-unicode --enable-sound --enable-graphics_ctx ' +configopts += '--enable-mediactrl --enable-display --enable-geometry ' +configopts += '--enable-debug_flag --enable-optimise --disable-debugreport ' +configopts += '--enable-autoidman --with-sdl ' +configopts += '--disable-webview --disable-webviewwebkit ' +configopts += '--disable-tests ' + + +prebuildopts = 'CPATH=$CPATH:%s ' % local_cpath_ext + +sanity_check_paths = { + 'files': ['bin/wx-config', 'bin/wxrc'], + 'dirs': ['include/wx-%(version_major_minor)s/wx', 'lib', 'share'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/x/X11/X11-20240607-GCCcore-13.3.0.eb b/easybuild/easyconfigs/x/X11/X11-20240607-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..64a4416b30e --- /dev/null +++ b/easybuild/easyconfigs/x/X11/X11-20240607-GCCcore-13.3.0.eb @@ -0,0 +1,214 @@ +easyblock = 'Bundle' + +name = 'X11' +version = '20240607' + +homepage = 'https://www.x.org' +description = "The X Window System (X11) is a windowing system for bitmap displays" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +builddependencies = [ + ('binutils', '2.42'), + ('Autotools', '20231222'), + ('Bison', '3.8.2'), + ('gettext', '0.22.5'), + ('pkgconf', '2.2.0'), + ('intltool', '0.51.0'), + ('Meson', '1.4.0'), + ('Ninja', '1.12.1'), + ('Doxygen', '1.11.0'), +] + +dependencies = [ + ('bzip2', '1.0.8'), + ('fontconfig', '2.15.0'), + ('freetype', '2.13.2'), + ('zlib', '1.3.1'), + ('xorg-macros', '1.20.1'), + ('libpciaccess', '0.18.1'), +] + +source_urls = [ + XORG_LIB_SOURCE, + XORG_PROTO_SOURCE, + 'https://xcb.freedesktop.org/dist/', + 'https://xkbcommon.org/download/', + XORG_DATA_SOURCE + '/xkeyboard-config', + XORG_DATA_SOURCE, +] + +default_easyblock = 'ConfigureMake' + +default_component_specs = { + 'sources': [SOURCE_TAR_GZ], + 'start_dir': '%(name)s-%(version)s', +} + +components = [ + ('libpthread-stubs', '0.5', { # 2023-07-18 + 'checksums': ['593196cc746173d1e25cb54a93a87fd749952df68699aab7e02c085530e87747'], + }), + ('xorgproto', '2024.1', { # 2024-03-26 + 'checksums': ['4f6b9b4faf91e5df8265b71843a91fc73dc895be6210c84117a996545df296ce'], + }), + ('libXau', '1.0.11', { # 2022-12-08 + 'checksums': ['3a321aaceb803577a4776a5efe78836eb095a9e44bbc7a465d29463e1a14f189'], + }), + ('libXdmcp', '1.1.5', { # 2024-03-02 + 'checksums': ['31a7abc4f129dcf6f27ae912c3eedcb94d25ad2e8f317f69df6eda0bc4e4f2f3'], + }), + ('xcb-proto', '1.17.0', { # 2024-04-15 + 'checksums': ['392d3c9690f8c8202a68fdb89c16fd55159ab8d65000a6da213f4a1576e97a16'], + }), + ('libxcb', '1.17.0', { # 2024-04-15 + 'checksums': ['2c69287424c9e2128cb47ffe92171e10417041ec2963bceafb65cb3fcf8f0b85'], + }), + ('xtrans', '1.5.0', { # 2023-06-03 + 'checksums': ['a806f8a92f879dcd0146f3f1153fdffe845f2fc0df9b1a26c19312b7b0a29c86'], + }), + ('libxkbcommon', '1.7.0', { # 2024-03-23 + 'easyblock': 'MesonNinja', + 'sources': [SOURCE_TAR_XZ], + 'checksums': ['65782f0a10a4b455af9c6baab7040e2f537520caa2ec2092805cdfd36863b247'], + 'preconfigopts': '', + 'configopts': '-Denable-wayland=false -Denable-docs=false ', + }), + ('libX11', '1.8.9', { # 2024-04-05 + 'checksums': ['57ca5f07d263788ad661a86f4139412e8b699662e6b60c20f1f028c25a935e48'], + }), + ('libXext', '1.3.6', { # 2024-02-04 + 'checksums': ['1a0ac5cd792a55d5d465ced8dbf403ed016c8e6d14380c0ea3646c4415496e3d'], + }), + ('libFS', '1.0.9', { # 2022-08-26 + 'checksums': ['8bc2762f63178905228a28670539badcfa2c8793f7b6ce3f597b7741b932054a'], + }), + ('libICE', '1.1.1', { # 2022-12-08 + 'checksums': ['04fbd34a11ba08b9df2e3cdb2055c2e3c1c51b3257f683d7fcf42dabcf8e1210'], + }), + ('libSM', '1.2.4', { # 2022-12-20 + 'checksums': ['51464ce1abce323d5b6707ceecf8468617106e1a8a98522f8342db06fd024c15'], + }), + ('libXScrnSaver', '1.2.4', { # 2022-12-05 + 'checksums': ['0656b2630475104d6df75d91ebb8e0153e61d14e9871ef1f403bcda4a62a838a'], + }), + ('libXt', '1.3.0', { # 2023-05-09 + 'checksums': ['de4a80c4cc7785b9620e572de71026805f68e85a2bf16c386009ef0e50be3f77'], + }), + ('libXmu', '1.2.1', { # 2024-04-16 + 'checksums': ['bf0902583dd1123856c11e0a5085bd3c6e9886fbbd44954464975fd7d52eb599'], + }), + ('libXpm', '3.5.17', { # 2023-10-03 + 'checksums': ['959466c7dfcfcaa8a65055bfc311f74d4c43d9257900f85ab042604d286df0c6'], + }), + ('libXaw', '1.0.16', { # 2024-03-10 + 'checksums': ['012f90adf8739f2f023d63a5fee1528949cf2aba92ef7ac1abcfc2ae9cf28798'], + }), + ('libXfixes', '6.0.1', { # 2023-04-09 + 'checksums': ['e69eaa321173c748ba6e2f15c7cf8da87f911d3ea1b6af4b547974aef6366bec'], + }), + ('libXcomposite', '0.4.6', { # 2022-12-04 + 'checksums': ['3599dfcd96cd48d45e6aeb08578aa27636fa903f480f880c863622c2b352d076'], + }), + ('libXrender', '0.9.11', { # 2022-10-22 + 'checksums': ['6aec3ca02e4273a8cbabf811ff22106f641438eb194a12c0ae93c7e08474b667'], + }), + ('libXcursor', '1.2.2', { # 2024-03-02 + 'checksums': ['98c3a30a3f85274c167d1ac5419d681ce41f14e27bfa5fe3003c8172cd8af104'], + }), + ('libXdamage', '1.1.6', { # 2022-12-04 + 'checksums': ['2afcc139eb6eb926ffe344494b1fc023da25def42874496e6e6d3aa8acef8595'], + }), + ('libfontenc', '1.1.8', { # 2024-03-02 + 'checksums': ['b55039f70959a1b2f02f4ec8db071e5170528d2c9180b30575dccf7510d7fb9f'], + }), + ('libXfont', '1.5.4', { # 2017-11-28 + 'checksums': ['59be6eab53f7b0feb6b7933c11d67d076ae2c0fd8921229c703fc7a4e9a80d6e'], + }), + ('libXfont2', '2.0.6', { # 2022-08-26 + 'checksums': ['a944df7b6837c8fa2067f6a5fc25d89b0acc4011cd0bc085106a03557fb502fc'], + }), + ('libXft', '2.3.8', { # 2023-04-17 + 'checksums': ['32e48fe2d844422e64809e4e99b9d8aed26c1b541a5acf837c5037b8d9f278a8'], + }), + ('libXi', '1.8.1', { # 2023-05-04 + 'checksums': ['3b5f47c223e4b63d7f7fe758886b8bf665b20a7edb6962c423892fd150e326ea'], + }), + ('libXinerama', '1.1.5', { # 2022-10-29 + 'checksums': ['2efa855cb42dc620eff3b77700d8655695e09aaa318f791f201fa60afa72b95c'], + }), + ('libXrandr', '1.5.4', { # 2023-10-04 + 'checksums': ['c72c94dc3373512ceb67f578952c5d10915b38cc9ebb0fd176a49857b8048e22'], + }), + ('libXres', '1.2.2', { # 2022-12-05 + 'checksums': ['8abce597ced4a7ab89032aee91f6f784d9960adc772b2b59f17e515cd4127950'], + }), + ('libXtst', '1.2.4', { # 2022-09-27 + 'checksums': ['01366506aeb033f6dffca5326af85f670746b0cabbfd092aabefb046cf48c445'], + }), + ('libXv', '1.0.12', { # 2022-12-05 + 'checksums': ['ce706619a970a580a0e35e9b5c98bdd2af243ac6494c65f44608a89a86100126'], + }), + ('libXvMC', '1.0.14', { # 2024-02-04 + 'checksums': ['3ad5d2b991219e2bf9b2f85d40b12c16f1afec038715e462f6058af73a9b5ef8'], + }), + ('libXxf86dga', '1.1.6', { # 2022-12-05 + 'checksums': ['87c7482b1e29b4eeb415815641c4f69c00545a8138e1b73ff1f361f7d9c22ac4'], + }), + ('libXxf86vm', '1.1.5', { # 2022-09-27 + 'checksums': ['f3f1c29fef8accb0adbd854900c03c6c42f1804f2bc1e4f3ad7b2e1f3b878128'], + }), + ('libdmx', '1.1.5', { # 2023-06-03 + 'checksums': ['070e82cc1daa1b21ee1339aef56a909eab04cbe7d430fabfbb01ecd21b2dd9f3'], + }), + ('libxkbfile', '1.1.3', { # 2024-02-04 + 'checksums': ['c4c2687729d1f920f165ebb96557a1ead2ef655809ab5eaa66a1ad36dc31050d'], + }), + ('libxshmfence', '1.3.2', { # 2022-12-08 + 'checksums': ['e93a85099604beb244ee756dcaf70e18b08701c1ca84c4de0126cd71bd6c8181'], + }), + ('xcb-util', '0.4.1', { # 2022-12-20 + 'checksums': ['21c6e720162858f15fe686cef833cf96a3e2a79875f84007d76f6d00417f593a'], + }), + ('xcb-util-image', '0.4.1', { # 2022-10-18 + 'checksums': ['0ebd4cf809043fdeb4f980d58cdcf2b527035018924f8c14da76d1c81001293b'], + }), + ('xcb-util-keysyms', '0.4.1', { # 2022-10-19 + 'checksums': ['1fa21c0cea3060caee7612b6577c1730da470b88cbdf846fa4e3e0ff78948e54'], + }), + ('xcb-util-renderutil', '0.3.10', { # 2022-10-19 + 'checksums': ['e04143c48e1644c5e074243fa293d88f99005b3c50d1d54358954404e635128a'], + }), + ('xcb-util-wm', '0.4.2', { # 2022-10-19 + 'checksums': ['dcecaaa535802fd57c84cceeff50c64efe7f2326bf752e16d2b77945649c8cd7'], + }), + ('xcb-util-cursor', '0.1.5', { # 2023-10-19 + 'checksums': ['0e9c5446dc6f3beb8af6ebfcc9e27bcc6da6fe2860f7fc07b99144dfa568e93b'], + }), + ('xkeyboard-config', '2.42', { # 2024-06-07 + 'easyblock': 'MesonNinja', + 'sources': [SOURCE_TAR_XZ], + 'checksums': ['a6b06ebfc1f01fc505f2f05f265f95f67cc8873a54dd247e3c2d754b8f7e0807'], + # required to overrule parent preconfigopts that runs autogen.sh if configure script is missing + 'preconfigopts': '', + }), + ('printproto', '1.0.5', { # 2011-01-06 + 'checksums': ['e8b6f405fd865f0ea7a3a2908dfbf06622f57f2f91359ec65d13b955e49843fc'], + }), + ('libXp', '1.0.4', { # 2022-09-12 + 'checksums': ['05e46af1ccb68f1752cca5879774a4fb9bf3b19fe088eb745034956e0c6fadba'], + }), + ('xbitmaps', '1.1.3', { # 2023-02-23 + 'checksums': ['93b433b7ff223c4685fdba583b4bd30f2706be2413a670021084422d85b0269d'], + }), +] + +preconfigopts = "if [ ! -f configure ]; then ./autogen.sh; fi && " + +sanity_check_paths = { + 'files': ['include/X11/Xlib.h', 'include/X11/Xutil.h'], + 'dirs': ['include/GL', 'include/X11', 'include/X11/extensions', 'lib/pkgconfig', + 'share/pkgconfig', 'share/X11/xkb'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/x/XCFun/XCFun-2.1.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/x/XCFun/XCFun-2.1.1-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..11a4eb62c8e --- /dev/null +++ b/easybuild/easyconfigs/x/XCFun/XCFun-2.1.1-GCCcore-12.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'CMakeMake' + +name = 'XCFun' +version = '2.1.1' + +homepage = 'https://xcfun.readthedocs.io' +description = """Arbitrary order exchange-correlation functional library""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://github.com/dftlibs/xcfun/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['8b602df74c7be83d501532565deafd1b7881946d94789122f24c309a669298ab'] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.26.3') +] + +modextravars = {'XCFun_DIR': '%(installdir)s/share/cmake/XCFun/'} + +sanity_check_paths = { + 'files': ['lib/libxcfun.%s' % SHLIB_EXT], + 'dirs': ['include/XCFun'] +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/x/XGBoost/XGBoost-2.1.1-gfbf-2023b.eb b/easybuild/easyconfigs/x/XGBoost/XGBoost-2.1.1-gfbf-2023b.eb new file mode 100644 index 00000000000..91e9be0529c --- /dev/null +++ b/easybuild/easyconfigs/x/XGBoost/XGBoost-2.1.1-gfbf-2023b.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonPackage' + +name = 'XGBoost' +version = '2.1.1' + +homepage = 'https://github.com/dmlc/xgboost' +description = """XGBoost is an optimized distributed gradient boosting library designed to be highly efficient, + flexible and portable.""" + +toolchain = {'name': 'gfbf', 'version': '2023b'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['4b1729837f9f1ba88a32ef1be3f8efb860fee6454a68719b196dc88032c23d97'] + +builddependencies = [ + ('CMake', '3.27.6'), + ('hatchling', '1.18.0'), +] + +dependencies = [ + ('Python', '3.11.5'), + ('SciPy-bundle', '2023.11'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'ai' diff --git a/easybuild/easyconfigs/x/XML-Compile/XML-Compile-1.63-GCCcore-13.2.0.eb b/easybuild/easyconfigs/x/XML-Compile/XML-Compile-1.63-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..7c564210edb --- /dev/null +++ b/easybuild/easyconfigs/x/XML-Compile/XML-Compile-1.63-GCCcore-13.2.0.eb @@ -0,0 +1,61 @@ +easyblock = 'Bundle' + +name = 'XML-Compile' +version = '1.63' + +homepage = 'https://metacpan.org/pod/XML::Compile' +description = "Perl module for compilation based XML processing" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +builddependencies = [ + ('pkgconf', '2.0.3'), + ('binutils', '2.40'), +] + +dependencies = [ + ('Perl', '5.38.0'), + ('XML-LibXML', '2.0210'), +] + +exts_defaultclass = 'PerlModule' +exts_filter = ("perl -e 'require %(ext_name)s'", '') + +exts_list = [ + ('XML::LibXML::Simple', '1.01', { + 'source_tmpl': 'XML-LibXML-Simple-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MARKOV/'], + 'checksums': ['cd98c8104b70d7672bfa26b4513b78adf2b4b9220e586aa8beb1a508500365a6'], + }), + ('XML::Compile', version, { + 'source_tmpl': 'XML-Compile-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MARKOV/'], + 'checksums': ['4b0871ef4a70bff37266d531bebcd1d065b109e8f5c5e996f87189a9f92d595f'], + }), + ('XML::Compile::Cache', '1.06', { + 'source_tmpl': 'XML-Compile-Cache-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MARKOV/'], + 'checksums': ['591b136bd92842c81a5176082503f47df6d5cc4d8e0d78953ef1557f747038a0'], + }), + ('XML::Compile::SOAP', '3.28', { + 'source_tmpl': 'XML-Compile-SOAP-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MARKOV/'], + 'checksums': ['0921699c4522537f7930e14fac056492de7801a9b9140d0e1faf33414ae6998f'], + }), + ('XML::Compile::WSDL11', '3.08', { + 'source_tmpl': 'XML-Compile-WSDL11-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MARKOV/'], + 'checksums': ['dd687ccf5083fe98fce1dd18540e1d0175042437a986e33eec105eca248f8d42'], + }), +] + +modextrapaths = { + 'PERL5LIB': 'lib/perl5/site_perl/%(perlver)s/', +} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/perl5/site_perl/%(perlver)s/XML/Compile'], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/x/XML-LibXML/XML-LibXML-2.0210-GCCcore-13.2.0.eb b/easybuild/easyconfigs/x/XML-LibXML/XML-LibXML-2.0210-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..9e8ac11247f --- /dev/null +++ b/easybuild/easyconfigs/x/XML-LibXML/XML-LibXML-2.0210-GCCcore-13.2.0.eb @@ -0,0 +1,65 @@ +# updated toolchain, version, and dependency versions +# Thomas Eylenbosch 5-Jun-23 + +easyblock = 'Bundle' + +name = 'XML-LibXML' +version = '2.0210' + +homepage = 'https://metacpan.org/pod/distribution/XML-LibXML/LibXML.pod' +description = "Perl binding for libxml2" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +builddependencies = [ + ('binutils', '2.40'), + ('pkgconf', '2.0.3'), +] + +dependencies = [ + ('Perl', '5.38.0'), + ('Perl-bundle-CPAN', '5.38.0'), + ('libxml2', '2.11.5'), +] + +exts_defaultclass = 'PerlModule' +exts_filter = ("perldoc -lm %(ext_name)s ", "") + +exts_list = [ + ('File::chdir', '0.1011', { + 'source_tmpl': 'File-chdir-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], + 'checksums': ['31ebf912df48d5d681def74b9880d78b1f3aca4351a0ed1fe3570b8e03af6c79'], + }), + ('Alien::Base', '2.83', { + 'source_tmpl': 'Alien-Build-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PL/PLICEASE/'], + 'checksums': ['4817270314431350ff397125547f55641dcff98bdde213b9e5efc613f7c8b85a'], + }), + ('Alien::Build::Plugin::Download::GitLab', '0.01', { + 'source_tmpl': 'Alien-Build-Plugin-Download-GitLab-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PL/PLICEASE'], + 'checksums': ['c1f089c8ea152a789909d48a83dbfcf2626f773daf30431c8622582b26aba902'], + }), + ('Alien::Libxml2', '0.19', { + 'source_tmpl': 'Alien-Libxml2-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PL/PLICEASE'], + 'checksums': ['f4a674099bbd5747c0c3b75ead841f3b244935d9ef42ba35368024bd611174c9'], + }), + ('XML::LibXML', version, { + 'source_tmpl': 'XML-LibXML-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHLOMIF/'], + 'checksums': ['a29bf3f00ab9c9ee04218154e0afc8f799bf23674eb99c1a9ed4de1f4059a48d'], + }), +] + +modextrapaths = { + 'PERL5LIB': 'lib/perl5/site_perl/%(perlver)s/', +} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/perl5/site_perl/%(perlver)s/%(arch)s-linux-thread-multi/XML/LibXML'], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/x/XML-LibXML/XML-LibXML-2.0210-GCCcore-13.3.0.eb b/easybuild/easyconfigs/x/XML-LibXML/XML-LibXML-2.0210-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..1d4cbe24543 --- /dev/null +++ b/easybuild/easyconfigs/x/XML-LibXML/XML-LibXML-2.0210-GCCcore-13.3.0.eb @@ -0,0 +1,65 @@ +# updated toolchain, version, and dependency versions +# Thomas Eylenbosch 5-Jun-23 + +easyblock = 'Bundle' + +name = 'XML-LibXML' +version = '2.0210' + +homepage = 'https://metacpan.org/pod/distribution/XML-LibXML/LibXML.pod' +description = "Perl binding for libxml2" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +builddependencies = [ + ('binutils', '2.42'), + ('pkgconf', '2.2.0'), +] + +dependencies = [ + ('Perl', '5.38.2'), + ('Perl-bundle-CPAN', '5.38.2'), + ('libxml2', '2.12.7'), +] + +exts_defaultclass = 'PerlModule' +exts_filter = ("perldoc -lm %(ext_name)s ", "") + +exts_list = [ + ('File::chdir', '0.1011', { + 'source_tmpl': 'File-chdir-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], + 'checksums': ['31ebf912df48d5d681def74b9880d78b1f3aca4351a0ed1fe3570b8e03af6c79'], + }), + ('Alien::Base', '2.83', { + 'source_tmpl': 'Alien-Build-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PL/PLICEASE/'], + 'checksums': ['4817270314431350ff397125547f55641dcff98bdde213b9e5efc613f7c8b85a'], + }), + ('Alien::Build::Plugin::Download::GitLab', '0.01', { + 'source_tmpl': 'Alien-Build-Plugin-Download-GitLab-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PL/PLICEASE'], + 'checksums': ['c1f089c8ea152a789909d48a83dbfcf2626f773daf30431c8622582b26aba902'], + }), + ('Alien::Libxml2', '0.19', { + 'source_tmpl': 'Alien-Libxml2-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PL/PLICEASE'], + 'checksums': ['f4a674099bbd5747c0c3b75ead841f3b244935d9ef42ba35368024bd611174c9'], + }), + ('XML::LibXML', version, { + 'source_tmpl': 'XML-LibXML-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHLOMIF/'], + 'checksums': ['a29bf3f00ab9c9ee04218154e0afc8f799bf23674eb99c1a9ed4de1f4059a48d'], + }), +] + +modextrapaths = { + 'PERL5LIB': 'lib/perl5/site_perl/%(perlver)s/', +} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/perl5/site_perl/%(perlver)s/%(arch)s-linux-thread-multi/XML/LibXML'], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/x/XML-Parser/XML-Parser-2.47-GCCcore-13.3.0-Perl-5.38.2.eb b/easybuild/easyconfigs/x/XML-Parser/XML-Parser-2.47-GCCcore-13.3.0-Perl-5.38.2.eb new file mode 100644 index 00000000000..2afd8c1daf8 --- /dev/null +++ b/easybuild/easyconfigs/x/XML-Parser/XML-Parser-2.47-GCCcore-13.3.0-Perl-5.38.2.eb @@ -0,0 +1,31 @@ +easyblock = 'PerlModule' + +name = 'XML-Parser' +version = '2.47' +versionsuffix = '-Perl-%(perlver)s' + +homepage = 'https://search.cpan.org/~toddr/XML-Parser-2.46/' +description = "This is a Perl extension interface to James Clark's XML parser, expat." + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://cpan.metacpan.org/authors/id/T/TO/TODDR/'] +sources = [SOURCE_TAR_GZ] +checksums = ['ad4aae643ec784f489b956abe952432871a622d4e2b5c619e8855accbfc4d1d8'] + +builddependencies = [ + ('binutils', '2.42'), +] +dependencies = [ + ('Perl', '5.38.2'), + ('expat', '2.6.2'), +] + +options = {'modulename': 'XML::Parser'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/perl5/site_perl/%(perlver)s/%(arch)s-linux-thread-multi/XML'], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.4.5-GCCcore-13.3.0.eb b/easybuild/easyconfigs/x/XZ/XZ-5.4.5-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..4e11c10a179 --- /dev/null +++ b/easybuild/easyconfigs/x/XZ/XZ-5.4.5-GCCcore-13.3.0.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'XZ' +version = '5.4.5' + +homepage = 'https://tukaani.org/xz/' +description = "xz: XZ utilities" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://tukaani.org/xz/'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['8ccf5fff868c006f29522e386fb4c6a1b66463fbca65a4cfc3c4bd596e895e79'] + +builddependencies = [ + # use gettext built with system toolchain as build dep to avoid cyclic dependency (XZ -> gettext -> libxml2 -> XZ) + ('gettext', '0.22.5', '', SYSTEM), + ('binutils', '2.42'), +] + +# may become useful in non-x86 archs +# configopts = ' --disable-assembler ' + +sanity_check_paths = { + 'files': ['bin/lzmainfo', 'bin/unxz', 'bin/xz'], + 'dirs': [] +} + +sanity_check_commands = [ + "xz --help", + "unxz --help", +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.6.3-GCCcore-14.2.0.eb b/easybuild/easyconfigs/x/XZ/XZ-5.6.3-GCCcore-14.2.0.eb new file mode 100644 index 00000000000..388a4bb239c --- /dev/null +++ b/easybuild/easyconfigs/x/XZ/XZ-5.6.3-GCCcore-14.2.0.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'XZ' +version = '5.6.3' + +homepage = 'https://tukaani.org/xz/' +description = "xz: XZ utilities" + +toolchain = {'name': 'GCCcore', 'version': '14.2.0'} + +source_urls = ['https://tukaani.org/xz/'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['a95a49147b2dbb5487517acc0adcd77f9c2032cf00664eeae352405357d14a6c'] + +builddependencies = [ + # use gettext built with system toolchain as build dep to avoid cyclic dependency (XZ -> gettext -> libxml2 -> XZ) + ('gettext', '0.22.5', '', SYSTEM), + ('binutils', '2.42'), +] + +# may become useful in non-x86 archs +# configopts = ' --disable-assembler ' + +sanity_check_paths = { + 'files': ['bin/lzmainfo', 'bin/unxz', 'bin/xz'], + 'dirs': [] +} + +sanity_check_commands = [ + "xz --help", + "unxz --help", +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.2.5-GCCcore-13.3.0.eb b/easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.2.5-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..d9cb7a779c7 --- /dev/null +++ b/easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.2.5-GCCcore-13.3.0.eb @@ -0,0 +1,39 @@ +easyblock = 'CMakeMake' + +name = 'Xerces-C++' +version = '3.2.5' + +homepage = 'https://xerces.apache.org/xerces-c/' + +description = """Xerces-C++ is a validating XML parser written in a portable +subset of C++. Xerces-C++ makes it easy to give your application the ability to +read and write XML data. A shared library is provided for parsing, generating, +manipulating, and validating XML documents using the DOM, SAX, and SAX2 +APIs.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://archive.apache.org/dist/xerces/c/%(version_major)s/sources/'] +sources = ['xerces-c-%(version)s.tar.gz'] +checksums = ['545cfcce6c4e755207bd1f27e319241e50e37c0c27250f11cda116018f1ef0f5'] + +builddependencies = [ + ('pkgconf', '2.2.0'), + ('binutils', '2.42'), + ('CMake', '3.29.3'), +] + +dependencies = [ + ('cURL', '8.7.1'), +] + +runtest = 'test' + +sanity_check_paths = { + 'files': ['bin/XInclude', + 'include/xercesc/xinclude/XIncludeUtils.hpp', + 'lib/libxerces-c-3.2.%s' % SHLIB_EXT], + 'dirs': ['bin', 'include', 'lib'] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/x/Xvfb/Xvfb-21.1.14-GCCcore-13.3.0.eb b/easybuild/easyconfigs/x/Xvfb/Xvfb-21.1.14-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..1ee18273171 --- /dev/null +++ b/easybuild/easyconfigs/x/Xvfb/Xvfb-21.1.14-GCCcore-13.3.0.eb @@ -0,0 +1,126 @@ +easyblock = 'Bundle' + +name = 'Xvfb' +version = '21.1.14' + +homepage = 'https://www.x.org/releases/X11R7.6/doc/man/man1/Xvfb.1.xhtml' +description = """Xvfb is an X server that can run on machines with no display hardware and no physical input devices. + It emulates a dumb framebuffer using virtual memory.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +builddependencies = [ + ('binutils', '2.42'), + ('pkgconf', '2.2.0'), + ('Python', '3.12.3'), + ('Meson', '1.4.0'), + ('Ninja', '1.12.1'), + ('libxslt', '1.1.42'), + ('gettext', '0.22.5'), + ('Bison', '3.8.2'), +] + +dependencies = [ + ('X11', '20240607'), + ('pixman', '0.43.4'), + ('libdrm', '2.4.122'), + ('Mesa', '24.1.3'), + ('nettle', '3.10'), + ('libunwind', '1.8.1'), + ('XZ', '5.4.5'), +] + +default_easyblock = 'ConfigureMake' + +local_xvfb_configopts = "--enable-xvfb --disable-xorg --disable-xnest --disable-xwin " +local_xvfb_configopts += "--disable-dri --disable-dri2 --disable-dri3 --disable-libunwind " +local_xvfb_configopts += "--with-fontrootdir=%(installdir)s/share/fonts/X11" + +# use 'make V=1' to see compiler commands +local_xvfb_buildopts = "V=1 " + +# use static libraries for nettle & libunwind, so avoid errors like "No rule to make target '-lnettle'" +local_xvfb_buildopts += 'SHA1_LIBS="$EBROOTNETTLE/lib*/libnettle.a" ' +local_xvfb_buildopts += 'LIBUNWIND_LIBS="$EBROOTLIBUNWIND/lib*/libunwind.a $EBROOTXZ/lib*/liblzma.a"' + +default_component_specs = { + 'sources': [SOURCE_TAR_GZ], + 'start_dir': '%(name)s-%(version)s', +} + +local_font_misc_preconfigopts = "export PKG_CONFIG_PATH=%(installdir)s/lib/pkgconfig:$PKG_CONFIG_PATH && " +local_font_misc_preconfigopts += "export PATH=%(installdir)s/bin:$PATH && " + +components = [ + ('mkfontscale', '1.2.3', { + 'source_urls': ['https://www.x.org/archive/individual/app/'], + 'checksums': ['3a026b468874eb672a1d0a57dbd3ddeda4f0df09886caf97d30097b70c2df3f8'], + }), + ('mkfontdir', '1.0.7', { + 'source_urls': ['https://www.x.org/archive/individual/app/'], + 'checksums': ['bccc5fb7af1b614eabe4a22766758c87bfc36d66191d08c19d2fa97674b7b5b7'], + }), + ('bdftopcf', '1.1', { + 'source_urls': ['https://www.x.org/archive/individual/app/'], + 'checksums': ['699d1a62012035b1461c7f8e3f05a51c8bd6f28f348983249fb89bbff7309b47'], + }), + ('font-util', '1.4.1', { + 'source_urls': ['https://www.x.org/archive/individual/font/'], + 'checksums': ['f029ae80cdd75d89bee7f7af61c21e07982adfb9f72344a158b99f91f77ef5ed'], + }), + ('font-misc-misc', '1.1.3', { + 'source_urls': ['https://www.x.org/archive/individual/font/'], + 'checksums': ['bece4a9482b3cb6f7fad2164fd3b394d22dfe1ad2f96f60030a703bcff30f5a5'], + 'preconfigopts': local_font_misc_preconfigopts, + }), + ('xkbcomp', '1.4.7', { + 'source_urls': ['https://www.x.org/archive/individual/app/'], + 'checksums': ['00cecc490fcbe2f789cf13c408c459673c2c33ab758d802677321cffcda35373'], + }), + ('xkeyboard-config', '2.43', { + 'easyblock': 'MesonNinja', + 'source_urls': ['https://www.x.org/archive/individual/data/xkeyboard-config/'], + 'sources': [SOURCE_TAR_XZ], + 'checksums': ['c810f362c82a834ee89da81e34cd1452c99789339f46f6037f4b9e227dd06c01'], + 'configopts': '-Dxorg-rules-symlinks=true', + }), + ('xauth', '1.1.3', { + 'source_urls': ['https://www.x.org/releases/individual/app/'], + 'checksums': ['88c288e0a30bf071631118644f5232cae3a79713a7c82dd31a236e8e2c6fca15'], + }), + ('libxcvt', '0.1.2', { + 'easyblock': 'MesonNinja', + 'source_urls': ['https://www.x.org/archive/individual/lib/'], + 'sources': [SOURCE_TAR_XZ], + 'checksums': ['0561690544796e25cfbd71806ba1b0d797ffe464e9796411123e79450f71db38'], + }), + (name, version, { + 'source_urls': ['https://www.x.org/releases/individual/xserver/'], + 'sources': ['xorg-server-%(version)s.tar.gz'], + 'patches': [('xvfb-run', '.')], + 'checksums': [ + 'b79dbaf668c67da25c4eb5b395eec60f2593240519aefdd3e8645023ef46226f', # xorg-server-21.1.14.tar.gz + 'fd6d13182b77871d4f65fccdaebb8a72387a726426066d3f8e6aa26b010ea0e8', # xvfb-run + ], + 'start_dir': 'xorg-server-%(version)s', + 'configopts': local_xvfb_configopts, + 'buildopts': local_xvfb_buildopts, + 'installopts': local_xvfb_buildopts, + }), +] + +# enable exec permissions for xvfb-run after copying; +# need to also enable user write permissions on xvfb-run to ensure that copying with preserved permissions works +postinstallcmds = ["chmod u+w xvfb-run && cp -a xvfb-run %(installdir)s/bin/ && chmod a+x %(installdir)s/bin/xvfb-run"] + +sanity_check_paths = { + 'files': ['bin/Xvfb', 'bin/xvfb-run'], + 'dirs': ['lib/xorg', 'share/fonts/X11/misc', 'share/fonts/X11/util'], +} + +sanity_check_commands = [ + "xvfb-run --help", + "xvfb-run --error-file %(builddir)s/xvfb-run-test.err echo hello", +] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/x/x264/x264-20231019-GCCcore-13.2.0.eb b/easybuild/easyconfigs/x/x264/x264-20231019-GCCcore-13.2.0.eb index a1d60486ce0..3a5bb6947d8 100644 --- a/easybuild/easyconfigs/x/x264/x264-20231019-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/x/x264/x264-20231019-GCCcore-13.2.0.eb @@ -14,7 +14,11 @@ toolchain = {'name': 'GCCcore', 'version': '13.2.0'} source_urls = ['https://code.videolan.org/videolan/%(name)s/-/archive/baee400f/'] sources = [{'download_filename': '%(name)s-9c3c7168.tar.gz', 'filename': SOURCE_TAR_GZ}] -checksums = ['bf6a61dcc7e1f4e623a44f09de02e843f06e7ec14f807557b43130fc84287f29'] +patches = ['x264-20231019_add-riscv-support.patch'] +checksums = [ + {'x264-20231019.tar.gz': 'bf6a61dcc7e1f4e623a44f09de02e843f06e7ec14f807557b43130fc84287f29'}, + {'x264-20231019_add-riscv-support.patch': 'd4455f3f643f255d4e907cf8a7bd803a3184ab2b6cc3445298bd2986fbb976f6'}, +] builddependencies = [ ('binutils', '2.40'), diff --git a/easybuild/easyconfigs/x/x264/x264-20231019_add-riscv-support.patch b/easybuild/easyconfigs/x/x264/x264-20231019_add-riscv-support.patch new file mode 100644 index 00000000000..b522010af86 --- /dev/null +++ b/easybuild/easyconfigs/x/x264/x264-20231019_add-riscv-support.patch @@ -0,0 +1,29 @@ +Add Risc-V 64 bit to config.guess +https://code.videolan.org/videolan/x264/-/merge_requests/121 + +From 941cae6d1d6d6344c9a1d27440eaf2872b18ca9a Mon Sep 17 00:00:00 2001 +From: Roger Hardiman +Date: Fri, 18 Nov 2022 20:15:40 +0000 +Subject: [PATCH] Add Risc-V 64 bit + +--- + config.guess | 3 +++ + 1 file changed, 3 insertions(+) + +diff --git a/config.guess b/config.guess +index d437be00..14c12963 100755 +--- a/config.guess ++++ b/config.guess +@@ -985,6 +985,9 @@ EOF + ppc:Linux:*:*) + echo powerpc-unknown-linux-gnu + exit ;; ++ riscv64:Linux:*:*) ++ echo ${UNAME_MACHINE}-unknown-linux-gnu ++ exit ;; + s390:Linux:*:* | s390x:Linux:*:*) + echo ${UNAME_MACHINE}-ibm-linux + exit ;; +-- +GitLab + diff --git a/easybuild/easyconfigs/x/x264/x264-20240513-GCCcore-13.3.0.eb b/easybuild/easyconfigs/x/x264/x264-20240513-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..a2a4cccf421 --- /dev/null +++ b/easybuild/easyconfigs/x/x264/x264-20240513-GCCcore-13.3.0.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'x264' +version = '20240513' + +homepage = 'https://www.videolan.org/developers/x264.html' +description = """ + x264 is a free software library and application for encoding video streams + into the H.264/MPEG-4 AVC compression format, and is released under the + terms of the GNU GPL. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://code.videolan.org/videolan/%(name)s/-/archive/31e19f92/'] +sources = [{'download_filename': '%(name)s-4613ac3c.tar.gz', 'filename': SOURCE_TAR_GZ}] +checksums = ['cf7e66bd0a75f3baba3502b58c80ee388b3d80a9a01be806337dd2214b8a290e'] + +builddependencies = [ + ('binutils', '2.42'), + ('pkgconf', '2.2.0'), + ('NASM', '2.16.03'), +] + +configopts = " --enable-shared --enable-static --disable-bashcompletion" + + +sanity_check_paths = { + 'files': ['bin/%(name)s', 'include/x264_config.h', 'include/%(name)s.h', 'lib/libx264.a', 'lib/libx264.so'], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/x/x265/x265-3.5-GCCcore-11.2.0.eb b/easybuild/easyconfigs/x/x265/x265-3.5-GCCcore-11.2.0.eb index 0732a992f17..e053931ce57 100644 --- a/easybuild/easyconfigs/x/x265/x265-3.5-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/x/x265/x265-3.5-GCCcore-11.2.0.eb @@ -25,7 +25,7 @@ builddependencies = [ start_dir = 'source' -configopts = '-DGIT_ARCHETYPE=1' +configopts = '-DGIT_ARCHETYPE=1 -DENABLE_PIC=ON' sanity_check_paths = { 'files': ['bin/x265', 'include/x265_config.h', 'include/x265.h', 'lib/libx265.a', 'lib/libx265.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/x/x265/x265-3.5-GCCcore-11.3.0.eb b/easybuild/easyconfigs/x/x265/x265-3.5-GCCcore-11.3.0.eb index 281db53772b..1544a97d4b6 100644 --- a/easybuild/easyconfigs/x/x265/x265-3.5-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/x/x265/x265-3.5-GCCcore-11.3.0.eb @@ -22,7 +22,7 @@ builddependencies = [ ('Yasm', '1.3.0'), ] -configopts = '-DGIT_ARCHETYPE=1' +configopts = '-DGIT_ARCHETYPE=1 -DENABLE_PIC=ON' start_dir = 'source' diff --git a/easybuild/easyconfigs/x/x265/x265-3.5-GCCcore-12.2.0.eb b/easybuild/easyconfigs/x/x265/x265-3.5-GCCcore-12.2.0.eb index 27b2b066296..d31e45da477 100644 --- a/easybuild/easyconfigs/x/x265/x265-3.5-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/x/x265/x265-3.5-GCCcore-12.2.0.eb @@ -22,7 +22,7 @@ builddependencies = [ ('Yasm', '1.3.0'), ] -configopts = '-DGIT_ARCHETYPE=1' +configopts = '-DGIT_ARCHETYPE=1 -DENABLE_PIC=ON' start_dir = 'source' diff --git a/easybuild/easyconfigs/x/x265/x265-3.5-GCCcore-12.3.0.eb b/easybuild/easyconfigs/x/x265/x265-3.5-GCCcore-12.3.0.eb index 4c754f3021d..4bd77d7f07e 100644 --- a/easybuild/easyconfigs/x/x265/x265-3.5-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/x/x265/x265-3.5-GCCcore-12.3.0.eb @@ -22,7 +22,7 @@ builddependencies = [ ('Yasm', '1.3.0'), ] -configopts = '-DGIT_ARCHETYPE=1' +configopts = '-DGIT_ARCHETYPE=1 -DENABLE_PIC=ON' start_dir = 'source' diff --git a/easybuild/easyconfigs/x/x265/x265-3.5-GCCcore-13.2.0.eb b/easybuild/easyconfigs/x/x265/x265-3.5-GCCcore-13.2.0.eb index d1bca35c8d7..1466e0c5f3c 100644 --- a/easybuild/easyconfigs/x/x265/x265-3.5-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/x/x265/x265-3.5-GCCcore-13.2.0.eb @@ -22,7 +22,7 @@ builddependencies = [ ('Yasm', '1.3.0'), ] -configopts = '-DGIT_ARCHETYPE=1' +configopts = '-DGIT_ARCHETYPE=1 -DENABLE_PIC=ON' start_dir = 'source' diff --git a/easybuild/easyconfigs/x/x265/x265-3.6-GCCcore-13.3.0.eb b/easybuild/easyconfigs/x/x265/x265-3.6-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..fc9ad81c0cb --- /dev/null +++ b/easybuild/easyconfigs/x/x265/x265-3.6-GCCcore-13.3.0.eb @@ -0,0 +1,34 @@ +easyblock = 'CMakeMake' + +name = 'x265' +version = '3.6' + +homepage = 'https://x265.org/' +description = """ + x265 is a free software library and application for encoding video streams + into the H.265 AVC compression format, and is released under the terms of + the GNU GPL. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://bitbucket.org/multicoreware/x265_git/downloads/'] +sources = ['%(name)s_%(version)s.tar.gz'] +checksums = ['663531f341c5389f460d730e62e10a4fcca3428ca2ca109693867bc5fe2e2807'] + +builddependencies = [ + ('binutils', '2.42'), + ('CMake', '3.29.3'), + ('Yasm', '1.3.0'), +] + +configopts = '-DGIT_ARCHETYPE=1 -DENABLE_PIC=ON' + +start_dir = 'source' + +sanity_check_paths = { + 'files': ['bin/%(name)s', 'include/x265_config.h', 'include/%(name)s.h', 'lib/libx265.a', 'lib/libx265.so'], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/x/xESMF/xESMF-0.8.6-foss-2023a.eb b/easybuild/easyconfigs/x/xESMF/xESMF-0.8.6-foss-2023a.eb new file mode 100644 index 00000000000..c77c2e324ed --- /dev/null +++ b/easybuild/easyconfigs/x/xESMF/xESMF-0.8.6-foss-2023a.eb @@ -0,0 +1,47 @@ +easyblock = 'PythonBundle' + +name = 'xESMF' +version = '0.8.6' + +homepage = 'https://xesmf.readthedocs.io' +description = "xESMF: Universal Regridder for Geospatial Data" + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [ + ('pytest', '7.4.2'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('ESMPy', '8.6.0'), + ('numba', '0.58.1'), + ('Shapely', '2.0.1'), + ('xarray', '2023.9.0'), + ('dask', '2023.9.2'), +] + +use_pip = True + +exts_list = [ + ('cftime', '1.6.2', { + 'checksums': ['8614c00fb8a5046de304fdd86dbd224f99408185d7b245ac6628d0276596e6d2'], + }), + ('cf_xarray', '0.9.3', { + 'checksums': ['5012444078964ef931cdc71d559f58488edd5fa9a175fbec326f9356e481b2cf'], + }), + ('sparse', '0.14.0', { + 'checksums': ['5f5827a37f6cd6f6730a541f994c95c60a3ae2329e01f4ba21ced5339aea0098'], + }), + ('xesmf', version, { + 'checksums': ['61c54f0db19fe4871623791db50b1ae589ea1a834d0df461cb58ffbd10d875de'], + 'runtest': 'pytest', + 'testopts': "-v --pyargs xesmf", + 'testinstall': True, + }), +] + +sanity_pip_check = True + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/x/xarray/xarray-2024.11.0-gfbf-2024a.eb b/easybuild/easyconfigs/x/xarray/xarray-2024.11.0-gfbf-2024a.eb new file mode 100644 index 00000000000..66965fa2a54 --- /dev/null +++ b/easybuild/easyconfigs/x/xarray/xarray-2024.11.0-gfbf-2024a.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonBundle' + +name = 'xarray' +version = '2024.11.0' + +homepage = 'https://github.com/pydata/xarray' +description = """xarray (formerly xray) is an open source project and Python package that aims to bring + the labeled data power of pandas to the physical sciences, by providing N-dimensional variants of the + core pandas data structures.""" + +toolchain = {'name': 'gfbf', 'version': '2024a'} + +dependencies = [ + ('Python', '3.12.3'), + ('SciPy-bundle', '2024.05'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + (name, version, { + 'preinstallopts': """sed -i 's/^dynamic = .*version.*/version = "%(version)s"/g' pyproject.toml && """, + 'checksums': ['1ccace44573ddb862e210ad3ec204210654d2c750bec11bbe7d842dfc298591f'], + }), +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/x/xarray/xarray-2024.5.0-gfbf-2023b.eb b/easybuild/easyconfigs/x/xarray/xarray-2024.5.0-gfbf-2023b.eb new file mode 100644 index 00000000000..09e90322293 --- /dev/null +++ b/easybuild/easyconfigs/x/xarray/xarray-2024.5.0-gfbf-2023b.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonBundle' + +name = 'xarray' +version = '2024.5.0' + +homepage = 'https://github.com/pydata/xarray' +description = """xarray (formerly xray) is an open source project and Python package that aims to bring + the labeled data power of pandas to the physical sciences, by providing N-dimensional variants of the + core pandas data structures.""" + +toolchain = {'name': 'gfbf', 'version': '2023b'} + +dependencies = [ + ('Python', '3.11.5'), + ('SciPy-bundle', '2023.11'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + (name, version, { + 'preinstallopts': """sed -i 's/^dynamic = .*version.*/version = "%(version)s"/g' pyproject.toml && """, + 'checksums': ['e0eb1cb265f265126795f388ed9591f3c752f2aca491f6c0576711fd15b708f2'], + }), +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.20.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.20.1-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..9d1905e4d33 --- /dev/null +++ b/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.20.1-GCCcore-13.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'xorg-macros' +version = '1.20.1' + +homepage = 'https://gitlab.freedesktop.org/xorg/util/macros' +description = """X.org macros utilities.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://gitlab.freedesktop.org/xorg/util/macros/-/archive/util-macros-%(version)s'] +sources = ['macros-util-macros-%(version)s.tar.gz'] +checksums = ['95c4331a2a7f4882374b9bbc845e522a4f1c77d95f495176300bf91d905c9b60'] + +builddependencies = [ + ('binutils', '2.42'), + ('Autotools', '20231222'), +] + +preconfigopts = './autogen.sh && ' + +sanity_check_paths = { + 'files': ['share/pkgconfig/xorg-macros.pc'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/x/xproto/xproto-7.0.31-GCCcore-13.3.0.eb b/easybuild/easyconfigs/x/xproto/xproto-7.0.31-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..b611b7c7304 --- /dev/null +++ b/easybuild/easyconfigs/x/xproto/xproto-7.0.31-GCCcore-13.3.0.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'xproto' +version = '7.0.31' + +homepage = 'https://www.freedesktop.org/wiki/Software/xlibs' +description = "X protocol and ancillary headers" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = [XORG_PROTO_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['6d755eaae27b45c5cc75529a12855fed5de5969b367ed05003944cf901ed43c7'] + +builddependencies = [ + ('binutils', '2.42'), + ('xorg-macros', '1.20.1'), +] + +sanity_check_paths = { + 'files': ['include/X11/%s' % x for x in ['ap_keysym.h', 'HPkeysym.h', 'keysym.h', 'Xalloca.h', 'Xatom.h', + 'XF86keysym.h', 'Xfuncs.h', 'Xmd.h', 'Xos.h', 'Xpoll.h', 'Xprotostr.h', + 'Xw32defs.h', 'Xwindows.h', 'DECkeysym.h', 'keysymdef.h', 'Sunkeysym.h', + 'Xarch.h', 'Xdefs.h', 'Xfuncproto.h', 'X.h', 'Xosdefs.h', 'Xos_r.h', + 'Xproto.h', 'Xthreads.h', 'XWDFile.h', 'Xwinsock.h']], + 'dirs': [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/x/xskillscore/xskillscore-0.0.26-foss-2023a.eb b/easybuild/easyconfigs/x/xskillscore/xskillscore-0.0.26-foss-2023a.eb new file mode 100644 index 00000000000..c8454e53dbb --- /dev/null +++ b/easybuild/easyconfigs/x/xskillscore/xskillscore-0.0.26-foss-2023a.eb @@ -0,0 +1,37 @@ +easyblock = "PythonBundle" + +name = 'xskillscore' +version = '0.0.26' + +homepage = 'https://xskillscore.readthedocs.io' +description = """ +xskillscore is an open source project and Python package that provides verification metrics of +deterministic (and probabilistic from properscoring) forecasts with xarray. +""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('dask', '2023.9.2'), + ('SciPy-bundle', '2023.07'), + ('statsmodels', '0.14.1'), + ('xarray', '2023.9.0'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('properscoring', '0.1', { + 'checksums': ['b0cc4963cc218b728d6c5f77b3259c8f835ae00e32e82678cdf6936049b93961'], + }), + ('xhistogram', '0.3.2', { + 'checksums': ['56b0751e1469eaed81710f644c8ba5c574b51883baa2feee26a95f2f708f91a1'], + }), + (name, version, { + 'checksums': ['780a424c1ab3eedf526a45ba8e6cf6dca61b17339252115a4e25ea8c5833ada5'], + }), +] + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/x/xtb-IFF/xtb-IFF-1.1.eb b/easybuild/easyconfigs/x/xtb-IFF/xtb-IFF-1.1.eb new file mode 100644 index 00000000000..ca25542f582 --- /dev/null +++ b/easybuild/easyconfigs/x/xtb-IFF/xtb-IFF-1.1.eb @@ -0,0 +1,26 @@ +easyblock = 'Tarball' + +name = 'xtb-IFF' +version = '1.1' + +homepage = 'https://github.com/grimme-lab/xtbiff' +description = """ +General Intermolecular Force Field based on Tight-Binding Quantum Chemical Calculations. +""" + +toolchain = SYSTEM + +source_urls = ['https://github.com/grimme-lab/xtbiff/releases/download/v1.1'] +sources = ['xtbiff.tar.xz'] +checksums = ['6d5dee10ba39ecb1e26374b7bf82e2364d8ebed5b6f35cdce4ced73245c296f5'] + +sanity_check_paths = { + 'files': ['xtbiff'], + 'dirs': [], +} + +sanity_check_commands = ["xtbiff --help"] + +modextrapaths = {'PATH': ''} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/x/xtb/xtb-6.7.0-gfbf-2023a.eb b/easybuild/easyconfigs/x/xtb/xtb-6.7.0-gfbf-2023a.eb index 97ce290bfe0..81ee768fed0 100644 --- a/easybuild/easyconfigs/x/xtb/xtb-6.7.0-gfbf-2023a.eb +++ b/easybuild/easyconfigs/x/xtb/xtb-6.7.0-gfbf-2023a.eb @@ -11,7 +11,13 @@ toolchain = {'name': 'gfbf', 'version': '2023a'} github_account = 'grimme-lab' source_urls = [GITHUB_LOWER_SOURCE] sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}] -checksums = ['9cf1997064d2d5bde7fae4cec6f873469602e6554872ad79de4079f022855ae2'] +patches = [ + 'xtb-6.7.0_fix-tblite-pr1072.patch' +] +checksums = [ + {'xtb-6.7.0.tar.gz': '9cf1997064d2d5bde7fae4cec6f873469602e6554872ad79de4079f022855ae2'}, + {'xtb-6.7.0_fix-tblite-pr1072.patch': 'cb8de869fc4a7c6bde44c61a479fc9edb3ccdc47c2a71f15ef124326f8a117e6'}, +] builddependencies = [ ('Meson', '1.1.1'), diff --git a/easybuild/easyconfigs/x/xtb/xtb-6.7.0_fix-tblite-pr1072.patch b/easybuild/easyconfigs/x/xtb/xtb-6.7.0_fix-tblite-pr1072.patch new file mode 100644 index 00000000000..74e2ea4950e --- /dev/null +++ b/easybuild/easyconfigs/x/xtb/xtb-6.7.0_fix-tblite-pr1072.patch @@ -0,0 +1,487 @@ +see https://github.com/grimme-lab/xtb/pull/1072 + https://github.com/grimme-lab/xtb/issues/1091 +diff -Naur xtb-6.7.0.orig/src/dipro/xtb.F90 xtb-6.7.0/src/dipro/xtb.F90 +--- xtb-6.7.0.orig/src/dipro/xtb.F90 2024-08-23 13:50:09.000345982 +0200 ++++ xtb-6.7.0/src/dipro/xtb.F90 2024-08-23 14:14:49.499145489 +0200 +@@ -50,11 +50,11 @@ + call fatal_error(error, "Unknown method '"//method//"' requested") + ! error stop + case("gfn2") +- call new_gfn2_calculator(xcalc, mol) ++ call new_gfn2_calculator(xcalc, mol, error) + case("gfn1") +- call new_gfn1_calculator(xcalc, mol) ++ call new_gfn1_calculator(xcalc, mol, error) + case("ipea1") +- call new_ipea1_calculator(xcalc, mol) ++ call new_ipea1_calculator(xcalc, mol, error) + end select + end subroutine get_calculator + #endif +diff -Naur xtb-6.7.0.orig/src/dipro.F90 xtb-6.7.0/src/dipro.F90 +--- xtb-6.7.0.orig/src/dipro.F90 2024-08-23 13:50:08.996896000 +0200 ++++ xtb-6.7.0/src/dipro.F90 2024-08-23 13:55:44.571958738 +0200 +@@ -130,6 +130,10 @@ + !=========================set up calculator=========================================== + + call get_calculator(xcalc, struc, tblite%method, error) ++ if (allocated(error)) then ++ call env%error(error%message, source) ++ return ++ end if + call new_wavefunction(wfn, struc%nat, xcalc%bas%nsh, xcalc%bas%nao, & + & 1, set%etemp * ktoau) + wfn%nspin=1 +@@ -258,6 +262,10 @@ + write(*,'(A,I2)') "unpaired e- of fragment : ", mfrag(ifr)%uhf + + call get_calculator(fcalc(ifr), mfrag(ifr), tblite%method, error) ++ if (allocated(error)) then ++ call env%error(error%message, source) ++ return ++ end if + !> mol%charge is updated automatically from wfn by tblite library + call new_wavefunction(wfx(ifr), mfrag(ifr)%nat, fcalc(ifr)%bas%nsh, fcalc(ifr)%bas%nao, & + & 1, set%etemp * ktoau) +diff -Naur xtb-6.7.0.orig/src/tblite/calculator.F90 xtb-6.7.0/src/tblite/calculator.F90 +--- xtb-6.7.0.orig/src/tblite/calculator.F90 2024-08-23 13:50:09.192101000 +0200 ++++ xtb-6.7.0/src/tblite/calculator.F90 2024-08-23 14:18:13.034251635 +0200 +@@ -144,11 +144,11 @@ + case default + call fatal_error(error, "Unknown method '"//method//"' requested") + case("gfn2") +- call new_gfn2_calculator(calc%tblite, struc) ++ call new_gfn2_calculator(calc%tblite, struc, error) + case("gfn1") +- call new_gfn1_calculator(calc%tblite, struc) ++ call new_gfn1_calculator(calc%tblite, struc, error) + case("ipea1") +- call new_ipea1_calculator(calc%tblite, struc) ++ call new_ipea1_calculator(calc%tblite, struc, error) + end select + end if + if (allocated(error)) then +diff -Naur xtb-6.7.0.orig/subprojects/mstore.wrap xtb-6.7.0/subprojects/mstore.wrap +--- xtb-6.7.0.orig/subprojects/mstore.wrap 2024-08-23 13:50:09.235197230 +0200 ++++ xtb-6.7.0/subprojects/mstore.wrap 2024-08-23 14:18:50.314014066 +0200 +@@ -1,4 +1,4 @@ + [wrap-git] + directory = mstore + url = https://github.com/grimme-lab/mstore +-revision = v0.2.0 ++revision = v0.3.0 +diff -Naur xtb-6.7.0.orig/test/unit/test_ptb.F90 xtb-6.7.0/test/unit/test_ptb.F90 +--- xtb-6.7.0.orig/test/unit/test_ptb.F90 2024-08-23 13:50:09.260760000 +0200 ++++ xtb-6.7.0/test/unit/test_ptb.F90 2024-08-23 14:34:18.302090669 +0200 +@@ -186,12 +186,37 @@ + !> (Scaled) overlap matrix + character(len=:), allocatable :: message + real(wp), parameter :: overlap_exp(6) = [ & +- & 0.93209460_wp, & ! 1,2 +- & 0.35489609_wp, & ! 1,3 +- & 0.65682608_wp, & ! 2,3 +- & 0.05627743_wp, & ! 1,15 +- & -0.14217162_wp, & ! 1,24; diffferent because of tblite ordering +- & 0.41844087_wp] ! 14,23; diffferent because of tblite ordering ++ & 0.93209460_wp, & ! s(Mg)-s(Mg) ++ & 0.35489609_wp, & ! s(Mg)-s(Mg) ++ & 0.65682608_wp, & ! s(Mg)-s(Mg) ++ & 0.05627743_wp, & ! s(Mg)-s(H) ++ & -0.14217162_wp, & ! s(Mg)-pz(H) ++ & 0.41844087_wp] ! dyz(Mg)-py(H) ++ ! 1: s(Mg) ++ ! 2: s(Mg) ++ ! 3: s(Mg) ++ ! 4: py(Mg) ++ ! 5: pz(Mg) ++ ! 6: px(Mg) ++ ! 7: py(Mg) ++ ! 8: pz(Mg) ++ ! 9: px(Mg) ++ ! 10: dxy(Mg) ++ ! 11: dyz(Mg) ++ ! 12: dz2(Mg) ++ ! 13: dxz(Mg) ++ ! 14: dx2-y2(Mg) ++ ! 15: s(H) ++ ! 16: s(H) ++ ! 17: py(H) ++ ! 18: pz(H) ++ ! 19: px(H) ++ ! 20: s(H) ++ ! 21: s(H) ++ ! 22: py(H) ++ ! 23: pz(H) ++ ! 24: px(H) ++ + real(wp), allocatable :: lattr(:, :) + real(wp) :: cutoff + +@@ -215,7 +240,7 @@ + call check_(error, ints%overlap(2, 3), overlap_exp(3), thr=thr) + call check_(error, ints%overlap(1, 15), overlap_exp(4), thr=thr) + call check_(error, ints%overlap(1, 23), overlap_exp(5), thr=thr) +- call check_(error, ints%overlap(12, 22), overlap_exp(6), thr=thr) ++ call check_(error, ints%overlap(11, 22), overlap_exp(6), thr=thr) + + end subroutine test_ptb_overlap + +@@ -249,12 +274,37 @@ + type(error_type), allocatable, intent(out) :: error + character(len=:), allocatable :: message + real(wp), parameter :: overlap_exp(6) = [ & +- & 0.95689468_wp, & ! 1,2 +- & 0.39195790_wp, & ! 1,3 +- & 0.62961212_wp, & ! 2,3 +- & 0.03782850_wp, & ! 1,15 +- &-0.13826216_wp, & ! 1,24; diffferent because of tblite ordering +- & 0.43334922_wp] ! 14,23; diffferent because of tblite ordering ++ & 0.95689468_wp, & ! s(Mg)-s(Mg) ++ & 0.39195790_wp, & ! s(Mg)-s(Mg) ++ & 0.62961212_wp, & ! s(Mg)-s(Mg) ++ & 0.03782850_wp, & ! s(Mg)-s(H) ++ &-0.13826216_wp, & ! s(Mg)-pz(H) ++ & 0.43334922_wp] ! dyz(Mg)-py(H) ++ ! 1: s(Mg) ++ ! 2: s(Mg) ++ ! 3: s(Mg) ++ ! 4: py(Mg) ++ ! 5: pz(Mg) ++ ! 6: px(Mg) ++ ! 7: py(Mg) ++ ! 8: pz(Mg) ++ ! 9: px(Mg) ++ ! 10: dxy(Mg) ++ ! 11: dyz(Mg) ++ ! 12: dz2(Mg) ++ ! 13: dxz(Mg) ++ ! 14: dx2-y2(Mg) ++ ! 15: s(H) ++ ! 16: s(H) ++ ! 17: py(H) ++ ! 18: pz(H) ++ ! 19: px(H) ++ ! 20: s(H) ++ ! 21: s(H) ++ ! 22: py(H) ++ ! 23: pz(H) ++ ! 24: px(H) ++ + real(wp), allocatable :: lattr(:, :) + real(wp) :: cutoff + +@@ -286,7 +336,7 @@ + & message=message) + call check_(error, auxints%overlap_h0_1(1, 23), overlap_exp(5), thr=thr, & + & message=message) +- call check_(error, auxints%overlap_h0_1(12, 22), overlap_exp(6), thr=thr, & ++ call check_(error, auxints%overlap_h0_1(11, 22), overlap_exp(6), thr=thr, & + & message=message) + + end subroutine test_ptb_overlap_h0 +@@ -319,12 +369,37 @@ + real(wp), allocatable :: overlap_sx(:, :), overlap_oneminusx(:, :) + character(len=:), allocatable :: message + real(wp), parameter :: overlap_oneminusx_exp(6) = [ & +- & 0.70788_wp, & ! 1,2 +- & 0.16203_wp, & ! 1,3 +- & 0.41532_wp, & ! 2,3 +- & 0.01449_wp, & ! 1,15 +- &-0.07203_wp, & ! 1,24; diffferent because of tblite ordering +- & 0.28751_wp] ! 14,23; diffferent because of tblite ordering ++ & 0.70788_wp, & ! s(Mg)-s(Mg) ++ & 0.16203_wp, & ! s(Mg)-s(Mg) ++ & 0.41532_wp, & ! s(Mg)-s(Mg) ++ & 0.01449_wp, & ! s(Mg)-s(H) ++ &-0.07203_wp, & ! s(Mg)-pz(H) ++ & 0.28751_wp] ! dyz(Mg)-py(H) ++ ! 1: s(Mg) ++ ! 2: s(Mg) ++ ! 3: s(Mg) ++ ! 4: py(Mg) ++ ! 5: pz(Mg) ++ ! 6: px(Mg) ++ ! 7: py(Mg) ++ ! 8: pz(Mg) ++ ! 9: px(Mg) ++ ! 10: dxy(Mg) ++ ! 11: dyz(Mg) ++ ! 12: dz2(Mg) ++ ! 13: dxz(Mg) ++ ! 14: dx2-y2(Mg) ++ ! 15: s(H) ++ ! 16: s(H) ++ ! 17: py(H) ++ ! 18: pz(H) ++ ! 19: px(H) ++ ! 20: s(H) ++ ! 21: s(H) ++ ! 22: py(H) ++ ! 23: pz(H) ++ ! 24: px(H) ++ + real(wp), allocatable :: lattr(:, :) + real(wp) :: cutoff + +@@ -356,7 +431,7 @@ + & message=message) + call check_(error, overlap_oneminusx(1, 23), overlap_oneminusx_exp(5), thr=thr2, & + & message=message) +- call check_(error, overlap_oneminusx(12, 22), overlap_oneminusx_exp(6), thr=thr2, & ++ call check_(error, overlap_oneminusx(11, 22), overlap_oneminusx_exp(6), thr=thr2, & + & message=message) + + end subroutine test_ptb_overlap_SX +@@ -392,10 +467,37 @@ + type(error_type), allocatable, intent(out) :: error + character(len=:), allocatable :: message + real(wp), parameter :: vecp_ref(4) = [ & +- & 0.077719_wp, & ! 1,1 ; diffferent because of tblite ordering +- & -0.059122_wp, & ! 1,3 ; diffferent because of tblite ordering +- & 0.052775_wp, & ! 3,5 ; diffferent because of tblite ordering +- & 0.117176_wp] ! 9,9 ; diffferent because of tblite ordering ++ & 0.077719_wp, & ! s(B)-s(B) ++ & -0.059122_wp, & ! s(B)-px(B) ++ & 0.052775_wp, & ! px(B)-px(B) ++ & 0.117176_wp] ! dx2-y2(B)-dx2-y2(B) ++ ! 1: s(B) ++ ! 2: s(B) ++ ! 3: py(B) ++ ! 4: pz(B) ++ ! 5: px(B) ++ ! 6: py(B) ++ ! 7: pz(B) ++ ! 8: px(B) ++ ! 9: dxy(B) ++ ! 10: dyz(B) ++ ! 11: dz2(B) ++ ! 12: dxz(B) ++ ! 13: dx2-y2(B) ++ ! 14: s(Cl) ++ ! 15: s(Cl) ++ ! 16: py(Cl) ++ ! 17: pz(Cl) ++ ! 18: px(Cl) ++ ! 19: py(Cl) ++ ! 20: pz(Cl) ++ ! 21: px(Cl) ++ ! 22: dxy(Cl) ++ ! 23: dyz(Cl) ++ ! 24: dz2(Cl) ++ ! 25: dxz(Cl) ++ ! 26: dx2-y2(Cl) ++ + real(wp), parameter :: xyz(3, 2) = reshape([ & + & 2.0_wp, 0.0_wp, 0.0_wp, & + & 0.0_wp, 0.0_wp, 0.0_wp], [3, 2]) +@@ -434,7 +536,7 @@ + & message=message) + call check_(error, vecp(5, 8), vecp_ref(3), thr=thr2, & + & message=message) +- call check_(error, vecp(12, 12), vecp_ref(4), thr=thr2, & ++ call check_(error, vecp(13, 13), vecp_ref(4), thr=thr2, & + & message=message) + end subroutine test_ptb_V_ECP + +@@ -629,12 +731,39 @@ + real(wp), allocatable :: vecp(:, :) + + real(wp), parameter :: h0_ref(6) = [ & +- & -1.59330281_wp, & ! 1,1 +- & -2.24996207_wp, & ! 1,2 +- & 0.34974782_wp, & ! 1,23 ; diffferent because of tblite ordering +- & 0.0_wp, & ! 7,11 ; different because of tblite ordering +- & -1.17757007_wp, & ! 3,6 ; different because of tblite ordering +- & 0.48301561_wp] ! 11,24 ; diffferent because of tblite ordering ++ & -1.59330281_wp, & ! s(B)-s(B) ++ & -2.24996207_wp, & ! s(B)-s(B) ++ & 0.34974782_wp, & ! s(B)-py(Cl) ++ & 0.0_wp, & ! dx2-y2(B)-py(B) ++ & -1.17757007_wp, & ! px(B)-px(B) ++ & 0.48301561_wp] ! dxy(B)-dxy(Cl) ++ ! 1: s(B) ++ ! 2: s(B) ++ ! 3: py(B) ++ ! 4: pz(B) ++ ! 5: px(B) ++ ! 6: py(B) ++ ! 7: pz(B) ++ ! 8: px(B) ++ ! 9: dxy(B) ++ ! 10: dyz(B) ++ ! 11: dz2(B) ++ ! 12: dxz(B) ++ ! 13: dx2-y2(B) ++ ! 14: s(Cl) ++ ! 15: s(Cl) ++ ! 16: py(Cl) ++ ! 17: pz(Cl) ++ ! 18: px(Cl) ++ ! 19: py(Cl) ++ ! 20: pz(Cl) ++ ! 21: px(Cl) ++ ! 22: dxy(Cl) ++ ! 23: dyz(Cl) ++ ! 24: dz2(Cl) ++ ! 25: dxz(Cl) ++ ! 26: dx2-y2(Cl) ++ + real(wp), parameter :: levels(10) = [ & + & -0.796651404_wp, & + & -0.269771638_wp, & +@@ -670,10 +799,10 @@ + message = "H0 matrix element not matching to expected value." + call check_(error, ints%hamiltonian(1, 1), h0_ref(1), thr=thr) + call check_(error, ints%hamiltonian(1, 2), h0_ref(2), thr=thr) +- call check_(error, ints%hamiltonian(1, 22), h0_ref(3), thr=thr) ++ call check_(error, ints%hamiltonian(1, 24), h0_ref(3), thr=thr) + call check_(error, ints%hamiltonian(13, 6), h0_ref(4), thr=thr) + call check_(error, ints%hamiltonian(8, 5), h0_ref(5), thr=thr) +- call check_(error, ints%hamiltonian(13, 26), h0_ref(6), thr=thr) ++ call check_(error, ints%hamiltonian(9, 22), h0_ref(6), thr=thr) + end subroutine test_ptb_hamiltonian_h0 + + subroutine test_ptb_V_XC(error) +@@ -708,10 +837,37 @@ + type(error_type), allocatable, intent(out) :: error + character(len=:), allocatable :: message + real(wp), parameter :: Vxc_ref(4) = [ & +- & -0.92793357_wp, & ! 1,1 +- & -0.85981333_wp, & ! 1,2 +- & 0.06632750_wp, & ! 1,23 ; diffferent because of tblite ordering +- & 0.00151880_wp] ! 11,24 ; diffferent because of tblite ordering ++ & -0.92793357_wp, & ! s(B)-s(B) ++ & -0.85981333_wp, & ! s(B)-s(B) ++ & 0.06632750_wp, & ! s(B)-dz2(Cl) ++ & 0.00151880_wp] ! dxy(B)-dxy(Cl) ++ ! 1: s(B) ++ ! 2: s(B) ++ ! 3: py(B) ++ ! 4: pz(B) ++ ! 5: px(B) ++ ! 6: py(B) ++ ! 7: pz(B) ++ ! 8: px(B) ++ ! 9: dxy(B) ++ ! 10: dyz(B) ++ ! 11: dz2(B) ++ ! 12: dxz(B) ++ ! 13: dx2-y2(B) ++ ! 14: s(Cl) ++ ! 15: s(Cl) ++ ! 16: py(Cl) ++ ! 17: pz(Cl) ++ ! 18: px(Cl) ++ ! 19: py(Cl) ++ ! 20: pz(Cl) ++ ! 21: px(Cl) ++ ! 22: dxy(Cl) ++ ! 23: dyz(Cl) ++ ! 24: dz2(Cl) ++ ! 25: dxz(Cl) ++ ! 26: dx2-y2(Cl) ++ + real(wp), parameter :: xyz(3, 2) = reshape([ & + & 2.0_wp, 0.0_wp, 0.0_wp, & + & 0.0_wp, 0.0_wp, 0.0_wp], [3, 2]) +@@ -769,9 +925,9 @@ + & message=message) + call check_(error, Vxc(1, 2), Vxc_ref(2), thr=thr, & + & message=message) +- call check_(error, Vxc(1, 22), Vxc_ref(3), thr=thr, & ++ call check_(error, Vxc(1, 24), Vxc_ref(3), thr=thr, & + & message=message) +- call check_(error, Vxc(13, 26), Vxc_ref(4), thr=thr, & ++ call check_(error, Vxc(9, 22), Vxc_ref(4), thr=thr, & + & message=message) + + end subroutine test_ptb_V_XC +@@ -957,10 +1113,35 @@ + !> Conversion factor from temperature to energy + real(wp), parameter :: kt = 3.166808578545117e-06_wp + real(wp), parameter :: coulomb_pot_ref(4) = [ & +- & -0.05693153_wp, & ! 1,1 +- & -0.33917531_wp, & ! 1,2 +- & -0.00539212_wp, & ! 1,21 ; diffferent because of tblite ordering +- & 0.01305793_wp] ! 6,24 ; diffferent because of tblite ordering ++ & -0.05693153_wp, & ! s(Mg)-s(Mg) ++ & -0.33917531_wp, & ! s(Mg)-s(Mg) ++ & -0.00539212_wp, & ! s(Mg)-s(H) ++ & 0.01305793_wp] ! pz(Mg)-pz(H) ++ ! 1: s(Mg) ++ ! 2: s(Mg) ++ ! 3: s(Mg) ++ ! 4: py(Mg) ++ ! 5: pz(Mg) ++ ! 6: px(Mg) ++ ! 7: py(Mg) ++ ! 8: pz(Mg) ++ ! 9: px(Mg) ++ ! 10: dxy(Mg) ++ ! 11: dyz(Mg) ++ ! 12: dz2(Mg) ++ ! 13: dxz(Mg) ++ ! 14: dx2-y2(Mg) ++ ! 15: s(H) ++ ! 16: s(H) ++ ! 17: py(H) ++ ! 18: pz(H) ++ ! 19: px(H) ++ ! 20: s(H) ++ ! 21: s(H) ++ ! 22: py(H) ++ ! 23: pz(H) ++ ! 24: px(H) ++ + real(wp), allocatable :: lattr(:, :) + real(wp) :: cutoff + +@@ -1044,10 +1225,36 @@ + integer, parameter :: nat = 2 + integer, parameter :: at(nat) = [5, 17] + real(wp), parameter :: plusU_pot_ref(4) = [ & +- & -0.0023185_wp, & ! 1,1 +- & -0.0018289_wp, & ! 1,2 +- & -0.5266562_wp, & ! 1,21 ; diffferent because of tblite ordering +- & -1.6745659_wp] ! 6,24 ; diffferent because of tblite ordering ++ & -0.0023185_wp, & ! s(B)-s(B) ++ & -0.0018289_wp, & ! s(B)-s(B) ++ & -0.5266562_wp, & ! s(B)-pz(Cl) ++ & -1.6745659_wp] ! px(B)-dxy(Cl) ++ ! 1: s(B) ++ ! 2: s(B) ++ ! 3: py(B) ++ ! 4: pz(B) ++ ! 5: px(B) ++ ! 6: py(B) ++ ! 7: pz(B) ++ ! 8: px(B) ++ ! 9: dxy(B) ++ ! 10: dyz(B) ++ ! 11: dz2(B) ++ ! 12: dxz(B) ++ ! 13: dx2-y2(B) ++ ! 14: s(Cl) ++ ! 15: s(Cl) ++ ! 16: py(Cl) ++ ! 17: pz(Cl) ++ ! 18: px(Cl) ++ ! 19: py(Cl) ++ ! 20: pz(Cl) ++ ! 21: px(Cl) ++ ! 22: dxy(Cl) ++ ! 23: dyz(Cl) ++ ! 24: dz2(Cl) ++ ! 25: dxz(Cl) ++ ! 26: dx2-y2(Cl) + + call new(mol, at, xyz) + allocate (ptbData) +@@ -1067,7 +1274,7 @@ + call check_(error, wfn%coeff(1, 1, 1), plusU_pot_ref(1), thr=thr) + call check_(error, wfn%coeff(1, 2, 1), plusU_pot_ref(2), thr=thr) + call check_(error, wfn%coeff(1, 20, 1), plusU_pot_ref(3), thr=thr) +- call check_(error, wfn%coeff(8, 26, 1), plusU_pot_ref(4), thr=thr) ++ call check_(error, wfn%coeff(8, 22, 1), plusU_pot_ref(4), thr=thr) + + end subroutine test_ptb_plus_U_potential + diff --git a/easybuild/easyconfigs/x/xtb/xtb-6.7.1-gfbf-2023b.eb b/easybuild/easyconfigs/x/xtb/xtb-6.7.1-gfbf-2023b.eb new file mode 100644 index 00000000000..09d459d356b --- /dev/null +++ b/easybuild/easyconfigs/x/xtb/xtb-6.7.1-gfbf-2023b.eb @@ -0,0 +1,50 @@ +easyblock = 'MesonNinja' + +name = 'xtb' +version = '6.7.1' + +homepage = 'https://xtb-docs.readthedocs.io' +description = """ xtb - An extended tight-binding semi-empirical program package. """ + +toolchain = {'name': 'gfbf', 'version': '2023b'} + +github_account = 'grimme-lab' +source_urls = [GITHUB_LOWER_SOURCE] +sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}] +patches = [ + 'xtb-6.7.1_fix-tblite-pr1072.patch', + 'xtb-6.7.1_fix-dftd4-test.patch', +] +checksums = [ + {'xtb-6.7.1.tar.gz': '52506a689147cdb4695bf1c666158b6d6d6b31726fecaa5bf53af7f4e3f3d20d'}, + {'xtb-6.7.1_fix-tblite-pr1072.patch': '1f10fef3e94c29926b1f632acc94c3ec92be861ee5c5139104194172726ffe68'}, + {'xtb-6.7.1_fix-dftd4-test.patch': '340e7d5cbc6bbaf0c53d4d292f3624cd67455b7a817818fe2cc8d26f5c34864b'}, +] + +builddependencies = [ + ('Meson', '1.2.3'), + ('Ninja', '1.11.1'), + ('pkgconf', '2.0.3'), +] + +configopts = "-Dlapack='custom' " +configopts += "-Dcustom_libraries='flexiblas' " +configopts += "--buildtype release " + +runtest = 'meson' +pretestopts = 'export OMP_NUM_THREADS=2 && ' +testopts = 'test -C %(builddir)s/easybuild_obj -t 60' # Ensure test don't timeout + +sanity_check_paths = { + 'files': ['bin/xtb', 'include/xtb.h'] + ['lib/libxtb.%s' % e for e in ('a', SHLIB_EXT)], + 'dirs': ['share'], +} + +sanity_check_commands = ["xtb --help"] + +modextravars = { + 'XTBHOME': '%(installdir)s', + 'XTBPATH': '%(installdir)s', +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/x/xtb/xtb-6.7.1_fix-dftd4-test.patch b/easybuild/easyconfigs/x/xtb/xtb-6.7.1_fix-dftd4-test.patch new file mode 100644 index 00000000000..0405b372a8a --- /dev/null +++ b/easybuild/easyconfigs/x/xtb/xtb-6.7.1_fix-dftd4-test.patch @@ -0,0 +1,20 @@ +fix for failing xtb test: + 72/148 dftd4 / param FAIL 1.85s exit status 1 + +from meson-logs/testlog.txt: +# Testing: param + Starting rational-damping ... (1/1) + ... rational-damping [FAILED] + Message: Condition not fullfilled + +see https://github.com/grimme-lab/xtb/pull/1085 +diff --git a/subprojects/dftd4.wrap b/subprojects/dftd4.wrap +index 46dc07ad9..e3e93f459 100644 +--- a/subprojects/dftd4.wrap ++++ b/subprojects/dftd4.wrap +@@ -1,4 +1,4 @@ + [wrap-git] + directory = dftd4 + url = https://github.com/dftd4/dftd4 +-revision = v3.5.0 ++revision = v3.6.0 diff --git a/easybuild/easyconfigs/x/xtb/xtb-6.7.1_fix-tblite-pr1072.patch b/easybuild/easyconfigs/x/xtb/xtb-6.7.1_fix-tblite-pr1072.patch new file mode 100644 index 00000000000..0684569d3e4 --- /dev/null +++ b/easybuild/easyconfigs/x/xtb/xtb-6.7.1_fix-tblite-pr1072.patch @@ -0,0 +1,528 @@ +see https://github.com/grimme-lab/xtb/pull/1072 + https://github.com/grimme-lab/xtb/issues/1091 +diff --git a/src/dipro.F90 b/src/dipro.F90 +index 42a136364..ab64e0710 100644 +--- a/src/dipro.F90 ++++ b/src/dipro.F90 +@@ -130,6 +130,10 @@ subroutine get_jab(env, tblite, mol, fragment, dipro) + !=========================set up calculator=========================================== + + call get_calculator(xcalc, struc, tblite%method, error) ++ if (allocated(error)) then ++ call env%error(error%message, source) ++ return ++ end if + call new_wavefunction(wfn, struc%nat, xcalc%bas%nsh, xcalc%bas%nao, & + & 1, set%etemp * ktoau) + wfn%nspin=1 +@@ -258,6 +262,10 @@ subroutine get_jab(env, tblite, mol, fragment, dipro) + write(*,'(A,I2)') "unpaired e- of fragment : ", mfrag(ifr)%uhf + + call get_calculator(fcalc(ifr), mfrag(ifr), tblite%method, error) ++ if (allocated(error)) then ++ call env%error(error%message, source) ++ return ++ end if + !> mol%charge is updated automatically from wfn by tblite library + call new_wavefunction(wfx(ifr), mfrag(ifr)%nat, fcalc(ifr)%bas%nsh, fcalc(ifr)%bas%nao, & + & 1, set%etemp * ktoau) +diff --git a/src/dipro/xtb.F90 b/src/dipro/xtb.F90 +index 95aff7848..4db948a3e 100644 +--- a/src/dipro/xtb.F90 ++++ b/src/dipro/xtb.F90 +@@ -50,11 +50,11 @@ subroutine get_calculator(xcalc, mol, method, error) + call fatal_error(error, "Unknown method '"//method//"' requested") + ! error stop + case("gfn2") +- call new_gfn2_calculator(xcalc, mol) ++ call new_gfn2_calculator(xcalc, mol, error) + case("gfn1") +- call new_gfn1_calculator(xcalc, mol) ++ call new_gfn1_calculator(xcalc, mol, error) + case("ipea1") +- call new_ipea1_calculator(xcalc, mol) ++ call new_ipea1_calculator(xcalc, mol, error) + end select + end subroutine get_calculator + #endif +diff --git a/src/tblite/calculator.F90 b/src/tblite/calculator.F90 +index 653e6b285..f05087414 100644 +--- a/src/tblite/calculator.F90 ++++ b/src/tblite/calculator.F90 +@@ -150,16 +150,16 @@ subroutine newTBLiteCalculator(env, mol, calc, input) + case default + call fatal_error(error, "Unknown method '"//method//"' requested") + case("gfn2") +- call new_gfn2_calculator(calc%tblite, struc) ++ call new_gfn2_calculator(calc%tblite, struc, error) + case("gfn1") +- call new_gfn1_calculator(calc%tblite, struc) ++ call new_gfn1_calculator(calc%tblite, struc, error) + case("ipea1") +- call new_ipea1_calculator(calc%tblite, struc) ++ call new_ipea1_calculator(calc%tblite, struc, error) + case("ceh") + calc%guess = method + calc%nspin = 1 +- calc%etemp = 5000.0_wp * kt +- call new_ceh_calculator(calc%tblite, struc) ++ calc%etemp = 4000.0_wp * kt ++ call new_ceh_calculator(calc%tblite, struc, error) + end select + end if + if (allocated(error)) then +@@ -244,18 +244,18 @@ subroutine newTBLiteWavefunction(env, mol, calc, chk) + block + use tblite_context, only : context_type, context_terminal + use tblite_context_terminal, only : escape +- use tblite_ceh_singlepoint, only : ceh_guess ++ use tblite_ceh_singlepoint, only : ceh_singlepoint + use tblite_lapack_solver, only : lapack_solver + use tblite_lapack_solver, only : lapack_algorithm + type(context_type) :: ctx +- ++ + ctx%solver = lapack_solver(lapack_algorithm%gvd) + ctx%terminal = context_terminal(calc%color) + + write (env%unit, '(1x,a)') escape(ctx%terminal%cyan) // "Calculation of CEH charges" // & + & escape(ctx%terminal%reset) +- +- call ceh_guess(ctx, calc%tblite, struc, error, wfn, calc%accuracy, 1) ++ ++ call ceh_singlepoint(ctx, calc%tblite, struc, wfn, calc%accuracy, 1) + end block + end select + end associate +diff --git a/subprojects/mstore.wrap b/subprojects/mstore.wrap +index acf5df9de..0dfe716c0 100644 +--- a/subprojects/mstore.wrap ++++ b/subprojects/mstore.wrap +@@ -1,4 +1,4 @@ + [wrap-git] + directory = mstore + url = https://github.com/grimme-lab/mstore +-revision = v0.2.0 ++revision = v0.3.0 +diff --git a/test/unit/test_ptb.F90 b/test/unit/test_ptb.F90 +index 16c14cbe4..5e585f90d 100644 +--- a/test/unit/test_ptb.F90 ++++ b/test/unit/test_ptb.F90 +@@ -186,12 +186,37 @@ subroutine test_ptb_overlap(error) + !> (Scaled) overlap matrix + character(len=:), allocatable :: message + real(wp), parameter :: overlap_exp(6) = [ & +- & 0.93209460_wp, & ! 1,2 +- & 0.35489609_wp, & ! 1,3 +- & 0.65682608_wp, & ! 2,3 +- & 0.05627743_wp, & ! 1,15 +- & -0.14217162_wp, & ! 1,24; diffferent because of tblite ordering +- & 0.41844087_wp] ! 14,23; diffferent because of tblite ordering ++ & 0.93209460_wp, & ! s(Mg)-s(Mg) ++ & 0.35489609_wp, & ! s(Mg)-s(Mg) ++ & 0.65682608_wp, & ! s(Mg)-s(Mg) ++ & 0.05627743_wp, & ! s(Mg)-s(H) ++ & -0.14217162_wp, & ! s(Mg)-pz(H) ++ & 0.41844087_wp] ! dyz(Mg)-py(H) ++ ! 1: s(Mg) ++ ! 2: s(Mg) ++ ! 3: s(Mg) ++ ! 4: py(Mg) ++ ! 5: pz(Mg) ++ ! 6: px(Mg) ++ ! 7: py(Mg) ++ ! 8: pz(Mg) ++ ! 9: px(Mg) ++ ! 10: dxy(Mg) ++ ! 11: dyz(Mg) ++ ! 12: dz2(Mg) ++ ! 13: dxz(Mg) ++ ! 14: dx2-y2(Mg) ++ ! 15: s(H) ++ ! 16: s(H) ++ ! 17: py(H) ++ ! 18: pz(H) ++ ! 19: px(H) ++ ! 20: s(H) ++ ! 21: s(H) ++ ! 22: py(H) ++ ! 23: pz(H) ++ ! 24: px(H) ++ + real(wp), allocatable :: lattr(:, :) + real(wp) :: cutoff + +@@ -215,7 +240,7 @@ subroutine test_ptb_overlap(error) + call check_(error, ints%overlap(2, 3), overlap_exp(3), thr=thr) + call check_(error, ints%overlap(1, 15), overlap_exp(4), thr=thr) + call check_(error, ints%overlap(1, 23), overlap_exp(5), thr=thr) +- call check_(error, ints%overlap(12, 22), overlap_exp(6), thr=thr) ++ call check_(error, ints%overlap(11, 22), overlap_exp(6), thr=thr) + + end subroutine test_ptb_overlap + +@@ -249,12 +274,37 @@ subroutine test_ptb_overlap_h0(error) + type(error_type), allocatable, intent(out) :: error + character(len=:), allocatable :: message + real(wp), parameter :: overlap_exp(6) = [ & +- & 0.95689468_wp, & ! 1,2 +- & 0.39195790_wp, & ! 1,3 +- & 0.62961212_wp, & ! 2,3 +- & 0.03782850_wp, & ! 1,15 +- &-0.13826216_wp, & ! 1,24; diffferent because of tblite ordering +- & 0.43334922_wp] ! 14,23; diffferent because of tblite ordering ++ & 0.95689468_wp, & ! s(Mg)-s(Mg) ++ & 0.39195790_wp, & ! s(Mg)-s(Mg) ++ & 0.62961212_wp, & ! s(Mg)-s(Mg) ++ & 0.03782850_wp, & ! s(Mg)-s(H) ++ &-0.13826216_wp, & ! s(Mg)-pz(H) ++ & 0.43334922_wp] ! dyz(Mg)-py(H) ++ ! 1: s(Mg) ++ ! 2: s(Mg) ++ ! 3: s(Mg) ++ ! 4: py(Mg) ++ ! 5: pz(Mg) ++ ! 6: px(Mg) ++ ! 7: py(Mg) ++ ! 8: pz(Mg) ++ ! 9: px(Mg) ++ ! 10: dxy(Mg) ++ ! 11: dyz(Mg) ++ ! 12: dz2(Mg) ++ ! 13: dxz(Mg) ++ ! 14: dx2-y2(Mg) ++ ! 15: s(H) ++ ! 16: s(H) ++ ! 17: py(H) ++ ! 18: pz(H) ++ ! 19: px(H) ++ ! 20: s(H) ++ ! 21: s(H) ++ ! 22: py(H) ++ ! 23: pz(H) ++ ! 24: px(H) ++ + real(wp), allocatable :: lattr(:, :) + real(wp) :: cutoff + +@@ -286,7 +336,7 @@ subroutine test_ptb_overlap_h0(error) + & message=message) + call check_(error, auxints%overlap_h0_1(1, 23), overlap_exp(5), thr=thr, & + & message=message) +- call check_(error, auxints%overlap_h0_1(12, 22), overlap_exp(6), thr=thr, & ++ call check_(error, auxints%overlap_h0_1(11, 22), overlap_exp(6), thr=thr, & + & message=message) + + end subroutine test_ptb_overlap_h0 +@@ -319,12 +369,37 @@ subroutine test_ptb_overlap_SX(error) + real(wp), allocatable :: overlap_sx(:, :), overlap_oneminusx(:, :) + character(len=:), allocatable :: message + real(wp), parameter :: overlap_oneminusx_exp(6) = [ & +- & 0.70788_wp, & ! 1,2 +- & 0.16203_wp, & ! 1,3 +- & 0.41532_wp, & ! 2,3 +- & 0.01449_wp, & ! 1,15 +- &-0.07203_wp, & ! 1,24; diffferent because of tblite ordering +- & 0.28751_wp] ! 14,23; diffferent because of tblite ordering ++ & 0.70788_wp, & ! s(Mg)-s(Mg) ++ & 0.16203_wp, & ! s(Mg)-s(Mg) ++ & 0.41532_wp, & ! s(Mg)-s(Mg) ++ & 0.01449_wp, & ! s(Mg)-s(H) ++ &-0.07203_wp, & ! s(Mg)-pz(H) ++ & 0.28751_wp] ! dyz(Mg)-py(H) ++ ! 1: s(Mg) ++ ! 2: s(Mg) ++ ! 3: s(Mg) ++ ! 4: py(Mg) ++ ! 5: pz(Mg) ++ ! 6: px(Mg) ++ ! 7: py(Mg) ++ ! 8: pz(Mg) ++ ! 9: px(Mg) ++ ! 10: dxy(Mg) ++ ! 11: dyz(Mg) ++ ! 12: dz2(Mg) ++ ! 13: dxz(Mg) ++ ! 14: dx2-y2(Mg) ++ ! 15: s(H) ++ ! 16: s(H) ++ ! 17: py(H) ++ ! 18: pz(H) ++ ! 19: px(H) ++ ! 20: s(H) ++ ! 21: s(H) ++ ! 22: py(H) ++ ! 23: pz(H) ++ ! 24: px(H) ++ + real(wp), allocatable :: lattr(:, :) + real(wp) :: cutoff + +@@ -356,7 +431,7 @@ subroutine test_ptb_overlap_SX(error) + & message=message) + call check_(error, overlap_oneminusx(1, 23), overlap_oneminusx_exp(5), thr=thr2, & + & message=message) +- call check_(error, overlap_oneminusx(12, 22), overlap_oneminusx_exp(6), thr=thr2, & ++ call check_(error, overlap_oneminusx(11, 22), overlap_oneminusx_exp(6), thr=thr2, & + & message=message) + + end subroutine test_ptb_overlap_SX +@@ -392,10 +467,37 @@ subroutine test_ptb_V_ECP(error) + type(error_type), allocatable, intent(out) :: error + character(len=:), allocatable :: message + real(wp), parameter :: vecp_ref(4) = [ & +- & 0.077719_wp, & ! 1,1 ; diffferent because of tblite ordering +- & -0.059122_wp, & ! 1,3 ; diffferent because of tblite ordering +- & 0.052775_wp, & ! 3,5 ; diffferent because of tblite ordering +- & 0.117176_wp] ! 9,9 ; diffferent because of tblite ordering ++ & 0.077719_wp, & ! s(B)-s(B) ++ & -0.059122_wp, & ! s(B)-px(B) ++ & 0.052775_wp, & ! px(B)-px(B) ++ & 0.117176_wp] ! dx2-y2(B)-dx2-y2(B) ++ ! 1: s(B) ++ ! 2: s(B) ++ ! 3: py(B) ++ ! 4: pz(B) ++ ! 5: px(B) ++ ! 6: py(B) ++ ! 7: pz(B) ++ ! 8: px(B) ++ ! 9: dxy(B) ++ ! 10: dyz(B) ++ ! 11: dz2(B) ++ ! 12: dxz(B) ++ ! 13: dx2-y2(B) ++ ! 14: s(Cl) ++ ! 15: s(Cl) ++ ! 16: py(Cl) ++ ! 17: pz(Cl) ++ ! 18: px(Cl) ++ ! 19: py(Cl) ++ ! 20: pz(Cl) ++ ! 21: px(Cl) ++ ! 22: dxy(Cl) ++ ! 23: dyz(Cl) ++ ! 24: dz2(Cl) ++ ! 25: dxz(Cl) ++ ! 26: dx2-y2(Cl) ++ + real(wp), parameter :: xyz(3, 2) = reshape([ & + & 2.0_wp, 0.0_wp, 0.0_wp, & + & 0.0_wp, 0.0_wp, 0.0_wp], [3, 2]) +@@ -434,7 +536,7 @@ subroutine test_ptb_V_ECP(error) + & message=message) + call check_(error, vecp(5, 8), vecp_ref(3), thr=thr2, & + & message=message) +- call check_(error, vecp(12, 12), vecp_ref(4), thr=thr2, & ++ call check_(error, vecp(13, 13), vecp_ref(4), thr=thr2, & + & message=message) + end subroutine test_ptb_V_ECP + +@@ -629,12 +731,39 @@ subroutine test_ptb_hamiltonian_h0(error) + real(wp), allocatable :: vecp(:, :) + + real(wp), parameter :: h0_ref(6) = [ & +- & -1.59330281_wp, & ! 1,1 +- & -2.24996207_wp, & ! 1,2 +- & 0.34974782_wp, & ! 1,23 ; diffferent because of tblite ordering +- & 0.0_wp, & ! 7,11 ; different because of tblite ordering +- & -1.17757007_wp, & ! 3,6 ; different because of tblite ordering +- & 0.48301561_wp] ! 11,24 ; diffferent because of tblite ordering ++ & -1.59330281_wp, & ! s(B)-s(B) ++ & -2.24996207_wp, & ! s(B)-s(B) ++ & 0.34974782_wp, & ! s(B)-py(Cl) ++ & 0.0_wp, & ! dx2-y2(B)-py(B) ++ & -1.17757007_wp, & ! px(B)-px(B) ++ & 0.48301561_wp] ! dxy(B)-dxy(Cl) ++ ! 1: s(B) ++ ! 2: s(B) ++ ! 3: py(B) ++ ! 4: pz(B) ++ ! 5: px(B) ++ ! 6: py(B) ++ ! 7: pz(B) ++ ! 8: px(B) ++ ! 9: dxy(B) ++ ! 10: dyz(B) ++ ! 11: dz2(B) ++ ! 12: dxz(B) ++ ! 13: dx2-y2(B) ++ ! 14: s(Cl) ++ ! 15: s(Cl) ++ ! 16: py(Cl) ++ ! 17: pz(Cl) ++ ! 18: px(Cl) ++ ! 19: py(Cl) ++ ! 20: pz(Cl) ++ ! 21: px(Cl) ++ ! 22: dxy(Cl) ++ ! 23: dyz(Cl) ++ ! 24: dz2(Cl) ++ ! 25: dxz(Cl) ++ ! 26: dx2-y2(Cl) ++ + real(wp), parameter :: levels(10) = [ & + & -0.796651404_wp, & + & -0.269771638_wp, & +@@ -665,15 +794,16 @@ subroutine test_ptb_hamiltonian_h0(error) + & alpha_scal=id_to_atom(mol, ptbData%hamiltonian%kalphah0l)) + allocate (vecp(bas%nao, bas%nao), source=0.0_wp) + ++ ints%hamiltonian = 0.0_wp + call get_hamiltonian(mol, list, bas, ptbData%hamiltonian, ptbData%hamiltonian%kla, auxints%overlap_h0_1, & + & levels, ints%hamiltonian, ptbGlobals%kpol, ptbGlobals%kitr, ptbGlobals%kitocod) + message = "H0 matrix element not matching to expected value." + call check_(error, ints%hamiltonian(1, 1), h0_ref(1), thr=thr) + call check_(error, ints%hamiltonian(1, 2), h0_ref(2), thr=thr) +- call check_(error, ints%hamiltonian(1, 22), h0_ref(3), thr=thr) ++ call check_(error, ints%hamiltonian(1, 24), h0_ref(3), thr=thr) + call check_(error, ints%hamiltonian(13, 6), h0_ref(4), thr=thr) + call check_(error, ints%hamiltonian(8, 5), h0_ref(5), thr=thr) +- call check_(error, ints%hamiltonian(13, 26), h0_ref(6), thr=thr) ++ call check_(error, ints%hamiltonian(9, 22), h0_ref(6), thr=thr) + end subroutine test_ptb_hamiltonian_h0 + + subroutine test_ptb_V_XC(error) +@@ -708,10 +838,37 @@ subroutine test_ptb_V_XC(error) + type(error_type), allocatable, intent(out) :: error + character(len=:), allocatable :: message + real(wp), parameter :: Vxc_ref(4) = [ & +- & -0.92793357_wp, & ! 1,1 +- & -0.85981333_wp, & ! 1,2 +- & 0.06632750_wp, & ! 1,23 ; diffferent because of tblite ordering +- & 0.00151880_wp] ! 11,24 ; diffferent because of tblite ordering ++ & -0.92793357_wp, & ! s(B)-s(B) ++ & -0.85981333_wp, & ! s(B)-s(B) ++ & 0.06632750_wp, & ! s(B)-dz2(Cl) ++ & 0.00151880_wp] ! dxy(B)-dxy(Cl) ++ ! 1: s(B) ++ ! 2: s(B) ++ ! 3: py(B) ++ ! 4: pz(B) ++ ! 5: px(B) ++ ! 6: py(B) ++ ! 7: pz(B) ++ ! 8: px(B) ++ ! 9: dxy(B) ++ ! 10: dyz(B) ++ ! 11: dz2(B) ++ ! 12: dxz(B) ++ ! 13: dx2-y2(B) ++ ! 14: s(Cl) ++ ! 15: s(Cl) ++ ! 16: py(Cl) ++ ! 17: pz(Cl) ++ ! 18: px(Cl) ++ ! 19: py(Cl) ++ ! 20: pz(Cl) ++ ! 21: px(Cl) ++ ! 22: dxy(Cl) ++ ! 23: dyz(Cl) ++ ! 24: dz2(Cl) ++ ! 25: dxz(Cl) ++ ! 26: dx2-y2(Cl) ++ + real(wp), parameter :: xyz(3, 2) = reshape([ & + & 2.0_wp, 0.0_wp, 0.0_wp, & + & 0.0_wp, 0.0_wp, 0.0_wp], [3, 2]) +@@ -769,9 +926,9 @@ subroutine test_ptb_V_XC(error) + & message=message) + call check_(error, Vxc(1, 2), Vxc_ref(2), thr=thr, & + & message=message) +- call check_(error, Vxc(1, 22), Vxc_ref(3), thr=thr, & ++ call check_(error, Vxc(1, 24), Vxc_ref(3), thr=thr, & + & message=message) +- call check_(error, Vxc(13, 26), Vxc_ref(4), thr=thr, & ++ call check_(error, Vxc(9, 22), Vxc_ref(4), thr=thr, & + & message=message) + + end subroutine test_ptb_V_XC +@@ -957,10 +1114,35 @@ subroutine test_ptb_coulomb_potential(error) + !> Conversion factor from temperature to energy + real(wp), parameter :: kt = 3.166808578545117e-06_wp + real(wp), parameter :: coulomb_pot_ref(4) = [ & +- & -0.05693153_wp, & ! 1,1 +- & -0.33917531_wp, & ! 1,2 +- & -0.00539212_wp, & ! 1,21 ; diffferent because of tblite ordering +- & 0.01305793_wp] ! 6,24 ; diffferent because of tblite ordering ++ & -0.05693153_wp, & ! s(Mg)-s(Mg) ++ & -0.33917531_wp, & ! s(Mg)-s(Mg) ++ & -0.00539212_wp, & ! s(Mg)-s(H) ++ & 0.01305793_wp] ! pz(Mg)-pz(H) ++ ! 1: s(Mg) ++ ! 2: s(Mg) ++ ! 3: s(Mg) ++ ! 4: py(Mg) ++ ! 5: pz(Mg) ++ ! 6: px(Mg) ++ ! 7: py(Mg) ++ ! 8: pz(Mg) ++ ! 9: px(Mg) ++ ! 10: dxy(Mg) ++ ! 11: dyz(Mg) ++ ! 12: dz2(Mg) ++ ! 13: dxz(Mg) ++ ! 14: dx2-y2(Mg) ++ ! 15: s(H) ++ ! 16: s(H) ++ ! 17: py(H) ++ ! 18: pz(H) ++ ! 19: px(H) ++ ! 20: s(H) ++ ! 21: s(H) ++ ! 22: py(H) ++ ! 23: pz(H) ++ ! 24: px(H) ++ + real(wp), allocatable :: lattr(:, :) + real(wp) :: cutoff + +@@ -1044,10 +1226,36 @@ subroutine test_ptb_plus_U_potential(error) + integer, parameter :: nat = 2 + integer, parameter :: at(nat) = [5, 17] + real(wp), parameter :: plusU_pot_ref(4) = [ & +- & -0.0023185_wp, & ! 1,1 +- & -0.0018289_wp, & ! 1,2 +- & -0.5266562_wp, & ! 1,21 ; diffferent because of tblite ordering +- & -1.6745659_wp] ! 6,24 ; diffferent because of tblite ordering ++ & -0.0023185_wp, & ! s(B)-s(B) ++ & -0.0018289_wp, & ! s(B)-s(B) ++ & -0.5266562_wp, & ! s(B)-pz(Cl) ++ & -1.6745659_wp] ! px(B)-dxy(Cl) ++ ! 1: s(B) ++ ! 2: s(B) ++ ! 3: py(B) ++ ! 4: pz(B) ++ ! 5: px(B) ++ ! 6: py(B) ++ ! 7: pz(B) ++ ! 8: px(B) ++ ! 9: dxy(B) ++ ! 10: dyz(B) ++ ! 11: dz2(B) ++ ! 12: dxz(B) ++ ! 13: dx2-y2(B) ++ ! 14: s(Cl) ++ ! 15: s(Cl) ++ ! 16: py(Cl) ++ ! 17: pz(Cl) ++ ! 18: px(Cl) ++ ! 19: py(Cl) ++ ! 20: pz(Cl) ++ ! 21: px(Cl) ++ ! 22: dxy(Cl) ++ ! 23: dyz(Cl) ++ ! 24: dz2(Cl) ++ ! 25: dxz(Cl) ++ ! 26: dx2-y2(Cl) + + call new(mol, at, xyz) + allocate (ptbData) +@@ -1067,7 +1275,7 @@ subroutine test_ptb_plus_U_potential(error) + call check_(error, wfn%coeff(1, 1, 1), plusU_pot_ref(1), thr=thr) + call check_(error, wfn%coeff(1, 2, 1), plusU_pot_ref(2), thr=thr) + call check_(error, wfn%coeff(1, 20, 1), plusU_pot_ref(3), thr=thr) +- call check_(error, wfn%coeff(8, 26, 1), plusU_pot_ref(4), thr=thr) ++ call check_(error, wfn%coeff(8, 22, 1), plusU_pot_ref(4), thr=thr) + + end subroutine test_ptb_plus_U_potential + diff --git a/easybuild/easyconfigs/x/xtensor/xtensor-0.24.7-foss-2023a.eb b/easybuild/easyconfigs/x/xtensor/xtensor-0.24.7-foss-2023a.eb new file mode 100644 index 00000000000..8b30ddf8a2f --- /dev/null +++ b/easybuild/easyconfigs/x/xtensor/xtensor-0.24.7-foss-2023a.eb @@ -0,0 +1,49 @@ +easyblock = 'Bundle' + +name = 'xtensor' +version = '0.24.7' + +homepage = 'https://github.com/xtensor-stack/xtensor' +description = "xtensor is a C++ library meant for numerical analysis with multi-dimensional array expressions." + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [ + ('CMake', '3.26.3'), + ('pybind11', '2.11.1'), +] +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), +] + +default_easyblock = 'CMakeMake' + +default_component_specs = { + 'source_urls': ['https://github.com/xtensor-stack/%(name)s/archive/'], + 'sources': ['%(version)s.tar.gz'], + 'start_dir': '%(name)s-%(version)s', +} + +components = [ + ('xtl', '0.7.5', { + 'checksums': ['3286fef5fee5d58f82f7b91375cd449c819848584bae9367893501114d923cbe'], + }), + ('xsimd', '8.0.5', { + 'checksums': ['0e1b5d973b63009f06a3885931a37452580dbc8d7ca8ad40d4b8c80d2a0f84d7'], + }), + ('xtensor', version, { + 'checksums': ['0fbbd524dde2199b731b6af99b16063780de6cf1d0d6cb1f3f4d4ceb318f3106'], + }), + ('xtensor-python', '0.26.1', { + 'checksums': ['eb64155c6824be471decf93927beedae3645714c8ce92f38e037434db2c2454a'], + 'configopts': '-DPYTHON_EXECUTABLE=$EBROOTPYTHON/bin/python', + }), +] + +sanity_check_paths = { + 'files': ['include/xtensor.hpp', 'lib/pkgconfig/xsimd.pc'], + 'dirs': ['include/xsimd', 'include/xtensor', 'include/xtensor-python', 'include/xtl', 'lib/cmake'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/x/xxHash/xxHash-0.8.2-GCCcore-13.2.0.eb b/easybuild/easyconfigs/x/xxHash/xxHash-0.8.2-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..75ee3c66d79 --- /dev/null +++ b/easybuild/easyconfigs/x/xxHash/xxHash-0.8.2-GCCcore-13.2.0.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'xxHash' +version = '0.8.2' + +homepage = 'https://cyan4973.github.io/xxHash' +description = "xxHash is an extremely fast non-cryptographic hash algorithm, working at RAM speed limit." + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://github.com/Cyan4973/xxHash/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['baee0c6afd4f03165de7a4e67988d16f0f2b257b51d0e3cb91909302a26a79c4'] + +builddependencies = [ + ('binutils', '2.40'), +] + +skipsteps = ['configure'] + +installopts = "PREFIX=%(installdir)s" + +sanity_check_paths = { + 'files': ['bin/xxhsum', 'include/xxh3.h', 'include/xxhash.h', + 'lib/libxxhash.a', 'lib/libxxhash.%s' % SHLIB_EXT, 'lib/pkgconfig/libxxhash.pc'], + 'dirs': ['share/man'], +} + +sanity_check_commands = ["xxhsum --help"] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/y/YACS/YACS-0.1.8-GCCcore-13.3.0.eb b/easybuild/easyconfigs/y/YACS/YACS-0.1.8-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..2ab12a60fca --- /dev/null +++ b/easybuild/easyconfigs/y/YACS/YACS-0.1.8-GCCcore-13.3.0.eb @@ -0,0 +1,31 @@ +easyblock = 'PythonPackage' + +name = 'YACS' +version = '0.1.8' + +homepage = "https://github.com/rbgirshick/yacs" +description = """YACS was created as a lightweight library to define and +manage system configurations, such as those commonly found in software +designed for scientific experimentation. These "configurations" +typically cover concepts like hyperparameters used in training a machine +learning model or configurable model hyperparameters, such as the depth +of a convolutional neural network.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['efc4c732942b3103bea904ee89af98bcd27d01f0ac12d8d4d369f1e7a2914384'] + +builddependencies = [('binutils', '2.42')] + +dependencies = [ + ('Python', '3.12.3'), + ('PyYAML', '6.0.2'), +] + +use_pip = True +download_dep_fail = True + +sanity_pip_check = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..5ac8fd8176f --- /dev/null +++ b/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-GCCcore-13.3.0.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'Yasm' +version = '1.3.0' + +homepage = 'https://www.tortall.net/projects/yasm/' +description = "Yasm: Complete rewrite of the NASM assembler with BSD license" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://github.com/%(namelower)s/%(namelower)s/releases/download/v%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['3dce6601b495f5b3d45b59f7d2492a340ee7e84b5beca17e48f862502bd5603f'] + +builddependencies = [ + ('binutils', '2.42'), +] + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': [], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/y/yaml-cpp/yaml-cpp-0.8.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/y/yaml-cpp/yaml-cpp-0.8.0-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..dc041455a41 --- /dev/null +++ b/easybuild/easyconfigs/y/yaml-cpp/yaml-cpp-0.8.0-GCCcore-13.2.0.eb @@ -0,0 +1,29 @@ +# This easyconfig was created by the BEAR Software team at the University of Birmingham. +easyblock = 'CMakeMake' +name = 'yaml-cpp' +version = "0.8.0" + +homepage = "https://github.com/jbeder/yaml-cpp" +description = """yaml-cpp is a YAML parser and emitter in C++ matching the YAML 1.2 spec""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/jbeder/%(name)s/archive/'] +sources = ['%(version)s.tar.gz'] + +checksums = [ + {'0.8.0.tar.gz': 'fbe74bbdcee21d656715688706da3c8becfd946d92cd44705cc6098bb23b3a16'}, +] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.27.6') +] + +sanity_check_paths = { + 'files': ['lib/libyaml-cpp.a', 'include/yaml-cpp/yaml.h'], + 'dirs': ['lib', 'include'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/y/yell/yell-2.2.2-GCC-12.3.0.eb b/easybuild/easyconfigs/y/yell/yell-2.2.2-GCC-12.3.0.eb new file mode 100644 index 00000000000..48cc38e0d7c --- /dev/null +++ b/easybuild/easyconfigs/y/yell/yell-2.2.2-GCC-12.3.0.eb @@ -0,0 +1,26 @@ +easyblock = 'RubyGem' + +name = 'yell' +version = '2.2.2' + +homepage = 'https://github.com/rudionrails/yell' +description = """Yell - Your Extensible Logging Library is a comprehensive logging replacement for Ruby.""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +source_urls = ['https://rubygems.org/downloads/'] +sources = ['%(name)s-%(version)s.gem'] +checksums = ['1d166f3cc3b6dc49a59778ea7156ed6d8de794c15106d48ffd6cbb061b9b26bc'] + +gem_file = '%(name)s-%(version)s.gem' + +dependencies = [ + ('Ruby', '3.3.0'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['gems/%(namelower)s-%(version)s'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/y/yelp-tools/yelp-tools-42.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/y/yelp-tools/yelp-tools-42.1-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..bbf260ff417 --- /dev/null +++ b/easybuild/easyconfigs/y/yelp-tools/yelp-tools-42.1-GCCcore-12.3.0.eb @@ -0,0 +1,50 @@ +easyblock = 'MesonNinja' + +name = 'yelp-tools' +version = '42.1' + +homepage = 'https://gitlab.gnome.org/GNOME/yelp-tools' +description = """yelp-tools is a collection of scripts and build utilities to help create, +manage, and publish documentation for Yelp and the web. Most of the heavy +lifting is done by packages like yelp-xsl and itstool. This package just +wraps things up in a developer-friendly way.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://gitlab.gnome.org/GNOME/yelp-tools/-/archive/%(version)s/'] +sources = [SOURCE_TAR_GZ] +checksums = ['4776766816aaa4fff5a9be7229d03e2444fca2f60a11f645c6171abe8bb73925'] + +builddependencies = [ + ('binutils', '2.40'), + ('Meson', '1.1.1'), + ('Ninja', '1.11.1'), + ('CMake', '3.26.3'), + ('Autotools', '20220317'), +] + +dependencies = [ + ('yelp-xsl', '42.1'), + ('ITSTool', '2.0.7'), + ('libxml2', '2.11.4'), + ('mallard-ducktype', '1.0.2'), + ('lxml', '4.9.2'), +] + +fix_python_shebang_for = ['bin/*'] + +sanity_check_paths = { + 'files': [ + 'bin/yelp-build', + 'bin/yelp-check', + 'bin/yelp-new', + ], + 'dirs': ['share/%(name)s'], +} + +sanity_check_commands = [ + 'yelp-build cache -h', + 'yelp-check hrefs -h', +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/y/yelp-xsl/yelp-xsl-42.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/y/yelp-xsl/yelp-xsl-42.1-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..ad7d8eddb4e --- /dev/null +++ b/easybuild/easyconfigs/y/yelp-xsl/yelp-xsl-42.1-GCCcore-12.3.0.eb @@ -0,0 +1,37 @@ +easyblock = 'ConfigureMake' + +name = 'yelp-xsl' +version = '42.1' + +homepage = "https://gitlab.gnome.org/GNOME/yelp-xslg" +description = """yelp-xsl is a collection of programs and data files to help you build, maintain, + and distribute documentation. It provides XSLT stylesheets that can be built upon for help + viewers and publishing systems. These stylesheets output JavaScript and CSS content, + and reference images provided by yelp-xsl. This package also redistributes copies + of the jQuery and jQuery.Syntax JavaScript libraries. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://gitlab.gnome.org/GNOME/yelp-xsl/-/archive/%(version)s/'] +sources = [SOURCE_TAR_GZ] +checksums = ['00f3ee8d9fa048d80063cc09477d24a09349e35c58ffdf9ecea253a4ca882068'] + +builddependencies = [ + ('binutils', '2.40'), + ('ITSTool', '2.0.7'), + ('gettext', '0.21.1'), + ('Autotools', '20220317'), +] + +preconfigopts = 'NOCONFIGURE=1 ./autogen.sh && ' + +sanity_check_paths = { + 'files': [], + 'dirs': [ + 'share/pkgconfig', + 'share/%(name)s', + ] +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/z/Z3/Z3-4.13.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/z/Z3/Z3-4.13.0-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..a925168f147 --- /dev/null +++ b/easybuild/easyconfigs/z/Z3/Z3-4.13.0-GCCcore-13.3.0.eb @@ -0,0 +1,50 @@ +easyblock = 'PythonBundle' + +name = 'Z3' +version = '4.13.0' + +homepage = 'https://github.com/Z3Prover/z3' +description = """Z3 is a theorem prover from Microsoft Research with support for bitvectors, +booleans, arrays, floating point numbers, strings, and other data types. This +module includes z3-solver, the Python interface of Z3. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +builddependencies = [ + ('CMake', '3.29.3'), + ('binutils', '2.42'), +] +dependencies = [ + ('Python', '3.12.3'), + ('GMP', '6.3.0'), +] + +use_pip = True + +_fix_parallelism = """sed -i 's/str(multiprocessing.cpu_count())/"%(parallel)s"/' setup.py && """ +_enable_gmp = """sed -i "s/Z3_USE_LIB_GMP.*/Z3_USE_LIB_GMP' : True,/" setup.py && """ + +exts_list = [ + ('z3-solver', version + '.0', { + 'modulename': 'z3', + 'checksums': ['52588e92aec7cb338fd6288ce93758ae01770f62ca0c80e8f4f2b2333feaf51b'], + 'preinstallopts': _fix_parallelism + _enable_gmp, + }), +] + +# make Z3 headers and libraries accessible in their usual location +local_z3_site_path = "lib/python%(pyshortver)s/site-packages/%(namelower)s" +postinstallcmds = [ + 'ln -s %s/include "%%(installdir)s/include"' % local_z3_site_path, + 'cd "%%(installdir)s"; for lib in %s/lib/*; do ln -s ../$lib lib/$(basename $lib); done' % local_z3_site_path +] + +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/z3', 'include/z3_api.h', 'lib/libz3.' + SHLIB_EXT], + 'dirs': ['include', 'lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.3.5-GCCcore-13.3.0.eb b/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.3.5-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..98db227b9aa --- /dev/null +++ b/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.3.5-GCCcore-13.3.0.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'ZeroMQ' +version = '4.3.5' + +homepage = 'https://www.zeromq.org/' +description = """ZeroMQ looks like an embeddable networking library but acts like a concurrency framework. + It gives you sockets that carry atomic messages across various transports like in-process, + inter-process, TCP, and multicast. You can connect sockets N-to-N with patterns like fanout, + pub-sub, task distribution, and request-reply. It's fast enough to be the fabric for clustered + products. Its asynchronous I/O model gives you scalable multicore applications, built as asynchronous + message-processing tasks. It has a score of language APIs and runs on most operating systems.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://github.com/%(namelower)s/libzmq/releases/download/v%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['6653ef5910f17954861fe72332e68b03ca6e4d9c7160eb3a8de5a5a913bfab43'] + +builddependencies = [ + ('binutils', '2.42'), + ('pkgconf', '2.2.0'), +] +dependencies = [ + ('OpenPGM', '5.2.122'), + ('libsodium', '1.0.20'), + ('util-linux', '2.40'), +] + +# Compialtion warnings in GCC 11, cf. https://github.com/zeromq/libzmq/issues/4178 +# Needto disable warnings as errors. +configopts = "--with-pic --with-pgm --with-libsodium --disable-Werror" + + +sanity_check_paths = { + 'files': ['lib/libzmq.%s' % SHLIB_EXT, 'lib/libzmq.a'], + 'dirs': ['include', 'lib'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/z/Zip/Zip-3.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/z/Zip/Zip-3.0-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..e85d9157eaf --- /dev/null +++ b/easybuild/easyconfigs/z/Zip/Zip-3.0-GCCcore-13.3.0.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'Zip' +version = '3.0' + +homepage = 'http://www.info-zip.org/Zip.html' +description = """Zip is a compression and file packaging/archive utility. +Although highly compatible both with PKWARE's PKZIP and PKUNZIP +utilities for MS-DOS and with Info-ZIP's own UnZip, our primary objectives +have been portability and other-than-MSDOS functionality""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://download.sourceforge.net/infozip'] +sources = ['%(namelower)s%(version_major)s%(version_minor)s.tar.gz'] +checksums = ['f0e8bb1f9b7eb0b01285495a2699df3a4b766784c1765a8f1aeedf63c0806369'] + +builddependencies = [ + ('binutils', '2.42'), +] +dependencies = [ + ('bzip2', '1.0.8'), +] + +skipsteps = ['configure'] + +buildopts = '-f unix/Makefile CC="$CC" IZ_OUR_BZIP2_DIR=$EBROOTBZIP2 ' +buildopts += 'CFLAGS="$CFLAGS -I. -DUNIX -DBZIP2_SUPPORT -DUNICODE_SUPPORT -DLARGE_FILE_SUPPORT" ' +buildopts += 'generic_gcc' + +installopts = '-f unix/Makefile prefix=%(installdir)s ' + +sanity_check_paths = { + 'files': ['bin/zip', 'bin/zipcloak', 'bin/zipnote', 'bin/zipsplit'], + 'dirs': ['man/man1'] +} + +sanity_check_commands = ["zip --version"] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/z/Zoltan/Zoltan-3.901-foss-2023a.eb b/easybuild/easyconfigs/z/Zoltan/Zoltan-3.901-foss-2023a.eb new file mode 100644 index 00000000000..57432d0e0ce --- /dev/null +++ b/easybuild/easyconfigs/z/Zoltan/Zoltan-3.901-foss-2023a.eb @@ -0,0 +1,46 @@ +# This easyconfig was created by the BEAR Software team at the University of Birmingham. +easyblock = 'ConfigureMake' + +name = 'Zoltan' +version = '3.901' + +homepage = "https://sandialabs.github.io/Zoltan/" +description = """Zoltan Dynamic Load Balancing and Graph Algorithm Toolkit""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'pic': True} + +github_account = 'sandialabs' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['030c22d9f7532d3076e40cba1f03a63b2ee961d8cc9a35149af4a3684922a910'] + +dependencies = [ + ('gzip', '1.12'), + ('SCOTCH', '7.0.3'), + ('ParMETIS', '4.0.3'), +] + +preconfigopts = 'mkdir build && cd build &&' +configure_cmd = '../configure' +configopts = ' '.join([ + '--enable-gzip', + '--with-scotch', + '--with-scotch-incdir=$EBROOTSCOTCH/include', + '--with-scotch-libdir=$EBROOTSCOTCH/lib', + '--with-parmetis', + '--with-parmetis-incdir=$EBROOTPARMETIS/include', + '--with-parmetis-libdir=$EBROOTPARMETIS/lib', + '--disable-examples', + '--disable-tests', +]) +prebuildopts = 'cd build &&' +buildopts = 'everything' +preinstallopts = 'cd build &&' + +sanity_check_paths = { + 'files': ['lib/libzoltan.a', 'include/zoltan.h'], + 'dirs': [], +} + +moduleclass = 'cae' diff --git a/easybuild/easyconfigs/z/Zopfli/Zopfli-1.0.3-GCCcore-12.3.0.eb b/easybuild/easyconfigs/z/Zopfli/Zopfli-1.0.3-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..8b4417a9e34 --- /dev/null +++ b/easybuild/easyconfigs/z/Zopfli/Zopfli-1.0.3-GCCcore-12.3.0.eb @@ -0,0 +1,37 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Updated: Denis Kristak +# Updated: Thomas Hoffmann (EMBL), Denis Kristak (Inuits) +easyblock = 'CMakeMake' + +name = 'Zopfli' +version = '1.0.3' + +homepage = 'https://github.com/google/zopfli' +description = """Zopfli Compression Algorithm is a compression library programmed in C to perform +very good, but slow, deflate or zlib compression.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/google/zopfli/archive/refs/tags/'] +sources = ['%(namelower)s-%(version)s.tar.gz'] +checksums = ['e955a7739f71af37ef3349c4fa141c648e8775bceb2195be07e86f8e638814bd'] + +builddependencies = [ + ('CMake', '3.26.3'), + ('binutils', '2.40'), +] + +configopts = [ + '-DBUILD_SHARED_LIBS=ON', + '-DBUILD_SHARED_LIBS=OFF', +] + +sanity_check_paths = { + 'files': ['bin/zopfli', 'include/zopfli.h', 'lib/libzopfli.a', 'lib/libzopfli.%s' % SHLIB_EXT], + 'dirs': [], +} + +sanity_check_commands = ["zopfli --help"] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/z/z5py/z5py-2.0.17-foss-2023a.eb b/easybuild/easyconfigs/z/z5py/z5py-2.0.17-foss-2023a.eb new file mode 100644 index 00000000000..3f3c8714771 --- /dev/null +++ b/easybuild/easyconfigs/z/z5py/z5py-2.0.17-foss-2023a.eb @@ -0,0 +1,50 @@ +easyblock = 'CMakeMakeCp' + +name = 'z5py' +version = '2.0.17' + +homepage = 'https://github.com/constantinpape/z5/' +description = """Lightweight C++ and Python interface for datasets in zarr and N5 format.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['https://github.com/constantinpape/z5/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['76acaeec7203b8d3baec45ccce82cd260dc1893f1516640acec5de6d74c078ef'] + +builddependencies = [('CMake', '3.26.3')] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('bzip2', '1.0.8'), + ('lz4', '1.9.4'), + ('XZ', '5.4.2'), + ('zlib', '1.2.13'), + ('xtensor', '0.24.7'), + ('python-blosc', '1.11.0'), + ('imageio', '2.33.1'), + ('h5py', '3.9.0'), + ('nlohmann_json', '3.11.2'), + ('zarr', '2.17.1'), + ('pybind11', '2.11.1'), +] + +configopts = '-DWITH_ZLIB=ON -DWITH_BZIP2=ON ' +# Fix path to python executable - it finds v3.6.8 from /usr/bin/ without this fix +configopts += '-DPYTHON_EXECUTABLE="$EBROOTPYTHON/bin/python" ' + +# export PYTHON_MODULE_INSTALL_DIR to fix make install +preinstallopts = 'export PYTHON_MODULE_INSTALL_DIR="%(builddir)s/easybuild_obj/python/" && ' + +files_to_copy = [(['python/z5py'], 'lib/python%(pyshortver)s/site-packages'), 'z5-config.cmake'] + +sanity_check_paths = { + 'files': ['z5-config.cmake'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/z5py'], +} +sanity_check_commands = ["python -c 'import z5py'"] + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/z/zfp/zfp-1.0.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/z/zfp/zfp-1.0.1-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..94719046584 --- /dev/null +++ b/easybuild/easyconfigs/z/zfp/zfp-1.0.1-GCCcore-12.3.0.eb @@ -0,0 +1,40 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +# Update: Thomas Hoffmann (EMBL) +easyblock = 'MakeCp' + +name = 'zfp' +version = '1.0.1' + +homepage = 'https://github.com/LLNL/zfp' +description = """zfp is a compressed format for representing multidimensional floating-point and integer arrays. +zfp provides compressed-array classes that support high throughput read and write random access to individual array +elements. zfp also supports serial and parallel (OpenMP and CUDA) compression of whole arrays, e.g., for applications +that read and write large data sets to and from disk.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/LLNL/zfp/archive'] +sources = ['%(version)s.tar.gz'] +checksums = ['4984db6a55bc919831966dd17ba5e47ca7ac58668f4fd278ebd98cd2200da66f'] + +builddependencies = [ + ('binutils', '2.40'), +] + +prebuildopts = "sed -i 's/FLAGS = -O3/FLAGS = $CFLAGS/g' Makefile && " +buildopts = 'ZFP_WITH_OPENMP=1' + +runtest = 'test' + +files_to_copy = ['bin', 'include', 'lib'] + +sanity_check_paths = { + 'files': ['bin/zfp', 'bin/testzfp', 'include/zfp.h', 'lib/libzfp.a'], + 'dirs': ['include/zfp'], +} + +sanity_check_commands = ["zfp --help 2>&1 | grep 'Usage: zfp'"] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/z/zlib-ng/zlib-ng-2.1.6-GCCcore-12.3.0.eb b/easybuild/easyconfigs/z/zlib-ng/zlib-ng-2.1.6-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..c29b31ffb34 --- /dev/null +++ b/easybuild/easyconfigs/z/zlib-ng/zlib-ng-2.1.6-GCCcore-12.3.0.eb @@ -0,0 +1,30 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Updated: Denis Kristak (Inuits) +# Updated: Thomas Hoffmann (EMBL), Denis Kristak (Inuits) +easyblock = 'CMakeMake' + +name = 'zlib-ng' +version = '2.1.6' + +homepage = 'https://github.com/zlib-ng/zlib-ng' +description = """zlib data compression library for the next generation systems""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://github.com/zlib-ng/zlib-ng/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['a5d504c0d52e2e2721e7e7d86988dec2e290d723ced2307145dedd06aeb6fef2'] + +builddependencies = [ + ('CMake', '3.26.3'), + ('binutils', '2.40'), +] + +configopts = ' -DZLIB_ENABLE_TESTS=True ' + +sanity_check_paths = { + 'files': ['include/zconf-ng.h', 'include/zlib-ng.h', 'lib/libz-ng.a', 'lib/libz-ng.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/z/zlib-ng/zlib-ng-2.2.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/z/zlib-ng/zlib-ng-2.2.1-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..266b927072a --- /dev/null +++ b/easybuild/easyconfigs/z/zlib-ng/zlib-ng-2.2.1-GCCcore-13.3.0.eb @@ -0,0 +1,50 @@ +easyblock = 'PythonBundle' + +name = 'zlib-ng' +version = '2.2.1' + +homepage = 'https://github.com/zlib-ng/zlib-ng' +description = """zlib data compression library for the next generation systems""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +builddependencies = [ + ('CMake', '3.29.3'), + ('binutils', '2.42'), + ('versioningit', '3.1.2'), +] + +dependencies = [ + ('Python', '3.12.3'), +] + +components = [ + (name, version, { + 'easyblock': 'CMakeMake', + 'source_urls': ['https://github.com/zlib-ng/zlib-ng/archive/'], + 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}], + 'checksums': ['ec6a76169d4214e2e8b737e0850ba4acb806c69eeace6240ed4481b9f5c57cdf'], + 'start_dir': '%(name)s-%(version)s', + 'configopts': '-DZLIB_ENABLE_TESTS=ON', + }), + +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + (name, '0.5.0', { + 'source_tmpl': 'zlib_ng-%(version)s.tar.gz', + 'checksums': ['3322c4300253a054af3d3aafa2f3858dceee3a577810122ba55eff756bf35ef2'], + 'preinstallopts': 'PYTHON_ZLIB_NG_LINK_DYNAMIC=true', + 'modulename': 'zlib_ng', + }), +] + +sanity_check_paths = { + 'files': ['include/zconf-ng.h', 'include/zlib-ng.h', 'lib/libz-ng.a', 'lib/libz-ng.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/z/zlib-ng/zlib-ng-2.2.2-GCCcore-13.2.0.eb b/easybuild/easyconfigs/z/zlib-ng/zlib-ng-2.2.2-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..8e1cf20a94d --- /dev/null +++ b/easybuild/easyconfigs/z/zlib-ng/zlib-ng-2.2.2-GCCcore-13.2.0.eb @@ -0,0 +1,50 @@ +easyblock = 'PythonBundle' + +name = 'zlib-ng' +version = '2.2.2' + +homepage = 'https://github.com/zlib-ng/zlib-ng' +description = """zlib data compression library for the next generation systems""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +builddependencies = [ + ('CMake', '3.27.6'), + ('binutils', '2.40'), + ('versioningit', '3.1.2'), +] + +dependencies = [ + ('Python', '3.11.5'), +] + +components = [ + (name, version, { + 'easyblock': 'CMakeMake', + 'source_urls': ['https://github.com/zlib-ng/zlib-ng/archive/'], + 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}], + 'checksums': ['fcb41dd59a3f17002aeb1bb21f04696c9b721404890bb945c5ab39d2cb69654c'], + 'start_dir': '%(name)s-%(version)s', + 'configopts': '-DZLIB_ENABLE_TESTS=ON', + }), + +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + (name, '0.5.1', { + 'source_tmpl': 'zlib_ng-%(version)s.tar.gz', + 'checksums': ['32a46649e8efc21ddd74776a55366a8d8be4e3a95b93dc1f0ffe3880718990d9'], + 'preinstallopts': 'PYTHON_ZLIB_NG_LINK_DYNAMIC=true', + 'modulename': 'zlib_ng', + }), +] + +sanity_check_paths = { + 'files': ['include/zconf-ng.h', 'include/zlib-ng.h', 'lib/libz-ng.a', 'lib/libz-ng.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.3.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/z/zlib/zlib-1.3.1-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..3f9304a080e --- /dev/null +++ b/easybuild/easyconfigs/z/zlib/zlib-1.3.1-GCCcore-13.3.0.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'zlib' +version = '1.3.1' + +homepage = 'https://www.zlib.net/' +description = """zlib is designed to be a free, general-purpose, legally unencumbered -- that is, + not covered by any patents -- lossless data-compression library for use on virtually any + computer hardware and operating system.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://zlib.net/fossils'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['9a93b2b7dfdac77ceba5a558a580e74667dd6fede4585b91eefb60f03b72df23'] + +# use same binutils version that was used when building GCC toolchain +builddependencies = [('binutils', '2.42', '', SYSTEM)] + +sanity_check_paths = { + 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.3.1-GCCcore-14.2.0.eb b/easybuild/easyconfigs/z/zlib/zlib-1.3.1-GCCcore-14.2.0.eb new file mode 100644 index 00000000000..187f8da34f7 --- /dev/null +++ b/easybuild/easyconfigs/z/zlib/zlib-1.3.1-GCCcore-14.2.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'zlib' +version = '1.3.1' + +homepage = 'https://www.zlib.net/' +description = """zlib is designed to be a free, general-purpose, legally unencumbered -- that is, + not covered by any patents -- lossless data-compression library for use on virtually any + computer hardware and operating system.""" + +toolchain = {'name': 'GCCcore', 'version': '14.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://zlib.net/fossils'] +sources = [SOURCELOWER_TAR_GZ] +# patches = ['zlib-%(version)s_fix-CC-logic-in-configure.patch'] +checksums = ['9a93b2b7dfdac77ceba5a558a580e74667dd6fede4585b91eefb60f03b72df23'] + +# use same binutils version that was used when building GCC toolchain +builddependencies = [('binutils', '2.42', '', SYSTEM)] + +sanity_check_paths = { + 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/z/zsh/zsh-5.9-GCCcore-13.3.0.eb b/easybuild/easyconfigs/z/zsh/zsh-5.9-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..2f5aa6a9ca5 --- /dev/null +++ b/easybuild/easyconfigs/z/zsh/zsh-5.9-GCCcore-13.3.0.eb @@ -0,0 +1,39 @@ +easyblock = 'ConfigureMake' + +name = 'zsh' + +version = '5.9' + +homepage = 'http://www.zsh.org/' +description = """ +Zsh is a shell designed for interactive use, although it is also a powerful scripting language. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['9b8d1ecedd5b5e81fbf1918e876752a7dd948e05c1a0dba10ab863842d45acd5'] + +configopts = '--without-tcsetpgrp' + +builddependencies = [ + ('binutils', '2.42'), +] + +dependencies = [ + ('ncurses', '6.5'), +] + +modextrapaths = { + 'FPATH': 'share/zsh/%(version)s/functions' +} + +sanity_check_paths = { + 'files': ['bin/zsh'], + 'dirs': ['lib/zsh/%(version)s', 'share'], +} + +sanity_check_commands = ['zsh --version'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/z/zstd/zstd-1.5.6-GCCcore-13.3.0.eb b/easybuild/easyconfigs/z/zstd/zstd-1.5.6-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..259e352beef --- /dev/null +++ b/easybuild/easyconfigs/z/zstd/zstd-1.5.6-GCCcore-13.3.0.eb @@ -0,0 +1,41 @@ +easyblock = 'ConfigureMake' + +name = 'zstd' +version = '1.5.6' + +homepage = 'https://facebook.github.io/zstd' +description = """Zstandard is a real-time compression algorithm, providing high compression ratios. + It offers a very wide range of compression/speed trade-off, while being backed by a very fast decoder. + It also offers a special mode for small data, called dictionary compression, and can create dictionaries + from any sample set.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +github_account = 'facebook' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['30f35f71c1203369dc979ecde0400ffea93c27391bfd2ac5a9715d2173d92ff7'] + +builddependencies = [ + ('binutils', '2.42'), +] + +dependencies = [ + ('zlib', '1.3.1'), + ('gzip', '1.13'), + ('XZ', '5.4.5'), + ('lz4', '1.9.4'), +] + +skipsteps = ['configure'] + +runtest = 'check' + +installopts = "PREFIX=%(installdir)s" + +sanity_check_paths = { + 'files': ["bin/zstd", "lib/libzstd.%s" % SHLIB_EXT, "include/zstd.h"], + 'dirs': ["lib/pkgconfig"] +} + +moduleclass = 'lib' diff --git a/setup.py b/setup.py index 58cbb040c4c..15cbcf7470d 100644 --- a/setup.py +++ b/setup.py @@ -44,7 +44,7 @@ # recent setuptools versions will *TRANSFORM* something like 'X.Y.Zdev' into 'X.Y.Z.dev0', with a warning like # UserWarning: Normalizing '2.4.0dev' to '2.4.0.dev0' # This causes problems further up the dependency chain... -VERSION = '4.9.2.dev0' +VERSION = '4.9.5.dev0' MAJ_VER = VERSION.split('.')[0] MAJMIN_VER = '.'.join(VERSION.split('.')[0:2]) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 0bc7f263274..4b1c4dd770e 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -439,6 +439,8 @@ def check_dep_vars(self, gen, dep, dep_vars): # filter out BLIS and libFLAME with -amd versionsuffix # (AMD forks, used in gobff/*-amd toolchains) (['BLIS', 'libFLAME'], '-amd'), + # filter out libcint with -pypzpx versionsuffix, used by MOLGW + ('libcint', '-pypzpx'), # filter out OpenBLAS with -int8 versionsuffix, used by GAMESS-US ('OpenBLAS', '-int8'), # filter out ScaLAPACK with -BLIS-* versionsuffix, used in goblf toolchain @@ -613,7 +615,8 @@ def check_dep_vars(self, gen, dep, dep_vars): ], 'pydantic': [ # GTDB-Tk v2.3.2 requires pydantic 1.x (see https://github.com/Ecogenomics/GTDBTk/pull/530) - ('1.10.13;', ['GTDB-Tk-2.3.2-']), + ('1.10.13;', ['GTDB-Tk-2.3.2-', 'GTDB-Tk-2.4.0-']), + ('2.7.4;', ['MultiQC-1.22.3-']), ], # medaka 1.1.*, 1.2.*, 1.4.* requires Pysam 0.16.0.1, # which is newer than what others use as dependency w.r.t. Pysam version in 2019b generation; @@ -626,7 +629,7 @@ def check_dep_vars(self, gen, dep, dep_vars): ], # OPERA requires SAMtools 0.x 'SAMtools': [(r'0\.', [r'ChimPipe-0\.9\.5', r'Cufflinks-2\.2\.1', r'OPERA-2\.0\.6', - r'CGmapTools-0\.1\.2', r'BatMeth2-2\.1'])], + r'CGmapTools-0\.1\.2', r'BatMeth2-2\.1', r'OPERA-MS-0\.9\.0-20240703'])], # NanoPlot, NanoComp use an older version of Seaborn 'Seaborn': [(r'0\.10\.1', [r'NanoComp-1\.13\.1-', r'NanoPlot-1\.33\.0-'])], # Shasta requires spoa 3.x @@ -660,6 +663,10 @@ def check_dep_vars(self, gen, dep, dep_vars): # for the sake of backwards compatibility, keep UCX-CUDA v1.11.0 which depends on UCX v1.11.0 # (for 2021b, UCX was updated to v1.11.2) 'UCX': [('1.11.0;', ['UCX-CUDA-1.11.0-'])], + # Napari 0.4.19post1 requires VisPy >=0.14.1 <0.15 + 'VisPy': [('0.14.1;', ['napari-0.4.19.post1-'])], + # Visit-3.4.1 requires VTK 9.2.x + 'VTK': [('9.2.6;', ['Visit-3.4.1-'])], # WPS 3.9.1 requires WRF 3.9.1.1 'WRF': [(r'3\.9\.1\.1', [r'WPS-3\.9\.1'])], # wxPython 4.2.0 depends on wxWidgets 3.2.0 @@ -996,14 +1003,13 @@ def test_easyconfig_locations(self): # ignore git/svn dirs & archived easyconfigs if '/.git/' in dirpath or '/.svn/' in dirpath or '__archive__' in dirpath: continue - # check whether list of .eb files is non-empty - easyconfig_files = [fn for fn in filenames if fn.endswith('eb')] + # check whether list of .eb files is non-empty, only exception: TEMPLATE.eb + easyconfig_files = [fn for fn in filenames if fn.endswith('eb') and fn != 'TEMPLATE.eb'] if easyconfig_files: # check whether path matches required pattern if not easyconfig_dirs_regex.search(dirpath): - # only exception: TEMPLATE.eb - if not (dirpath.endswith('/easybuild/easyconfigs') and filenames == ['TEMPLATE.eb']): - self.assertTrue(False, "List of easyconfig files in %s is empty: %s" % (dirpath, filenames)) + if not dirpath.endswith('/easybuild/easyconfigs'): + self.fail("There should be no easyconfig files in %s, found %s" % (dirpath, easyconfig_files)) def test_easyconfig_name_clashes(self): """Make sure there is not a name clash when all names are lowercase""" @@ -1024,7 +1030,7 @@ def test_easyconfig_name_clashes(self): duplicates[name] = names[name] if duplicates: - self.assertTrue(False, "EasyConfigs with case-insensitive name clash: %s" % duplicates) + self.fail("EasyConfigs with case-insensitive name clash: %s" % duplicates) @skip_if_not_pr_to_non_main_branch() def test_pr_sha256_checksums(self): @@ -1042,25 +1048,19 @@ def test_pr_sha256_checksums(self): 'R-bundle-Bioconductor-3.[2-5]', ] - # the check_sha256_checksums function (again) creates an EasyBlock instance - # for easyconfigs using the Bundle easyblock, this is a problem because the 'sources' easyconfig parameter - # is updated in place (sources for components are added to the 'parent' sources) in Bundle's __init__; - # therefore, we need to reset 'sources' to an empty list here if Bundle is used... - # likewise for 'patches' and 'checksums' - bundle_easyblocks = ['Bundle', 'CargoPythonBundle', 'PythonBundle', 'EB_OpenSSL_wrapper'] - for ec in self.changed_ecs: - if ec['easyblock'] in bundle_easyblocks or ec['name'] in ['Clang-AOMP']: - ec['sources'] = [] - ec['patches'] = [] - ec['checksums'] = [] - # filter out deprecated easyconfigs - retained_changed_ecs = [] - for ec in self.changed_ecs: - if not ec['deprecated']: - retained_changed_ecs.append(ec) - - checksum_issues = check_sha256_checksums(retained_changed_ecs, whitelist=whitelist) + retained_changed_ecs = [ec for ec in self.changed_ecs if not ec['deprecated']] + + # The check_sha256_checksums function creates an EasyBlock instance. + # For easyconfigs using the Bundle easyblock, this is a problem because the 'sources' easyconfig parameter + # is updated in place (sources for components are added to the 'parent' sources) in Bundle's __init__. + # Therefore, we need to a operate on a copy of those easyconfigs. + bundle_easyblocks = {'Bundle', 'CargoPythonBundle', 'PythonBundle', 'EB_OpenSSL_wrapper'} + + def is_bundle(ec): + return ec['easyblock'] in bundle_easyblocks or ec['name'] == 'Clang-AOMP' + ecs = [ec.copy() if is_bundle(ec) else ec for ec in retained_changed_ecs] + checksum_issues = check_sha256_checksums(ecs, whitelist=whitelist) self.assertTrue(len(checksum_issues) == 0, "No checksum issues:\n%s" % '\n'.join(checksum_issues)) @skip_if_not_pr_to_non_main_branch() @@ -1077,10 +1077,15 @@ def test_pr_python_packages(self): whitelist_pip_check = [ r'Mako-1.0.4.*Python-2.7.12.*', - # no pip 9.x or newer for configparser easyconfigs using a 2016a or 2016b toolchain - r'configparser-3.5.0.*-2016[ab].*', + # no pip 9.x or newer for easyconfigs using a 2016a or 2016b toolchain + r'.*-2016[ab]-Python-.*', # mympirun is installed with system Python, pip may not be installed for system Python r'vsc-mympirun.*', + # ReFrame intentionally installs its deps in a %(installdir)s/external subdir, which is added + # to sys.path by the ReFrame command, and is intentionally NOT on the PYTHONPATH. + # Thus, a pip check fails, but this is expected and ok, it is still a working ReFrame installation + # See https://github.com/easybuilders/easybuild-easyconfigs/pull/21269 for more info + r'ReFrame.*', ] failing_checks = [] @@ -1207,11 +1212,12 @@ def test_pr_sanity_check_paths(self): """Make sure a custom sanity_check_paths value is specified for easyconfigs that use a generic easyblock.""" # some generic easyblocks already have a decent customised sanity_check_paths, - # including CargoPythonPackage, CMakePythonPackage, GoPackage, JuliaBundle, PerlBundle, + # including CargoPythonPackage, CMakePythonPackage, GoPackage, JuliaBundle & JuliaPackage, PerlBundle, # PythonBundle & PythonPackage; # BuildEnv, ModuleRC and Toolchain easyblocks doesn't install anything so there is nothing to check. - whitelist = ['BuildEnv', 'CargoPythonBundle', 'CargoPythonPackage', 'CMakePythonPackage', 'CrayToolchain', - 'GoPackage', 'JuliaBundle', 'ModuleRC', 'PerlBundle', 'PythonBundle', 'PythonPackage', 'Toolchain'] + whitelist = ['BuildEnv', 'CargoPythonBundle', 'CargoPythonPackage', 'CMakePythonPackage', + 'ConfigureMakePythonPackage', 'CrayToolchain', 'GoPackage', 'JuliaBundle', 'JuliaPackage', + 'ModuleRC', 'PerlBundle', 'PythonBundle', 'PythonPackage', 'Toolchain'] # Bundles of dependencies without files of their own # Autotools: Autoconf + Automake + libtool, (recent) GCC: GCCcore + binutils, CUDA: GCC + CUDAcore, # CESM-deps: Python + Perl + netCDF + ESMF + git, FEniCS: DOLFIN and co, @@ -1359,6 +1365,51 @@ def test_pr_patch_descr(self): self.assertFalse(no_descr_patches, "No description found in patches: %s" % ', '.join(no_descr_patches)) +def verify_patch(specdir, patch_spec, checksum_idx, patch_checksums, extension_name=None): + """Verify existance and checksum of the given patch. + + specdir - Directory of the easyconfig + patch_spec - Patch entry + checksum_idx - Expected index in the checksum list + patch_checksums - List of checksums for patches + extension_name - Name of the extensions this patch is for if any + + Return a (possibly empty) list of failure messages + """ + patch_dir = specdir + if isinstance(patch_spec, str): + patch_name = patch_spec + elif isinstance(patch_spec, (tuple, list)): + patch_name = patch_spec[0] + elif isinstance(patch_spec, dict): + patch_name = patch_spec['name'] + alt_location = patch_spec.get('alt_location') + if alt_location: + basedir = os.path.dirname(os.path.dirname(specdir)) + patch_dir = os.path.join(basedir, letter_dir_for(alt_location), alt_location) + else: + # Should have already been verified + raise RuntimeError('Patch spec is not a string, tuple, list or dict: %s\nType: %s' % (patch_spec, + type(patch_spec))) + + patch_path = os.path.join(patch_dir, patch_name) + patch_descr = "patch file " + patch_name + if extension_name: + patch_descr += "of extension " + extension_name + + # only check actual patch files, not other files being copied via the patch functionality + if patch_path.endswith('.patch'): + if not os.path.isfile(patch_path): + return [patch_descr + "is missing"] + + if checksum_idx < len(patch_checksums): + checksum = patch_checksums[checksum_idx] + if not verify_checksum(patch_path, checksum): + return ["Invalid checksum for %s: %s" % (patch_descr, checksum)] + + return [] # No error + + def template_easyconfig_test(self, spec): """Tests for an individual easyconfig: parsing, instantiating easyblock, check patches, ...""" @@ -1455,6 +1506,9 @@ def template_easyconfig_test(self, spec): ] failing_checks.extend("Old URL '%s' found" % old_url for old_url in old_urls if old_url in ec.rawtxt) + # Note the use of app.cfg which might contain sources populated by e.g. the Cargo easyblock + sources, patches, checksums = app.cfg['sources'], app.cfg['patches'], app.cfg['checksums'] + # make sure binutils is included as a (build) dep if toolchain is GCCcore if ec['toolchain']['name'] == 'GCCcore': # easyblocks without a build step @@ -1471,7 +1525,7 @@ def template_easyconfig_test(self, spec): requires_binutils &= bool(ec['name'] not in binutils_complete_dependencies) # if no sources/extensions/components are specified, it's just a bundle (nothing is being compiled) - requires_binutils &= bool(ec['sources'] or ec['exts_list'] or ec.get('components')) + requires_binutils &= bool(sources or ec['exts_list'] or ec.get('components')) if requires_binutils: # dependencies() returns both build and runtime dependencies @@ -1502,36 +1556,18 @@ def template_easyconfig_test(self, spec): if openssl_osdep: failing_checks.append("OpenSSL should not be listed as OS dependency") - src_cnt = len(ec['sources']) - patch_checksums = ec['checksums'][src_cnt:] + src_cnt = len(sources) + patch_checksums = checksums[src_cnt:] # make sure all patch files are available specdir = os.path.dirname(spec) - basedir = os.path.dirname(os.path.dirname(specdir)) - for idx, patch in enumerate(ec['patches']): - patch_dir = specdir - if isinstance(patch, str): - patch_name = patch - elif isinstance(patch, (tuple, list)): - patch_name = patch[0] - elif isinstance(patch, dict): - patch_name = patch['name'] - if patch['alt_location']: - patch_dir = os.path.join(basedir, letter_dir_for(patch['alt_location']), patch['alt_location']) - - # only check actual patch files, not other files being copied via the patch functionality - patch_full = os.path.join(patch_dir, patch_name) - if patch_name.endswith('.patch') and not os.path.isfile(patch_full): - failing_checks.append("Patch file %s is missing" % patch_full) - # verify checksum for each patch file - elif idx < len(patch_checksums) and (os.path.exists(patch_full) or patch_name.endswith('.patch')): - checksum = patch_checksums[idx] - if not verify_checksum(patch_full, checksum): - failing_checks.append("Invalid checksum for patch file %s: %s" % (patch_name, checksum)) + + for idx, patch in enumerate(patches): + failing_checks.extend(verify_patch(specdir, patch, idx, patch_checksums)) # make sure 'source' step is not being skipped, # since that implies not verifying the checksum - if ec['checksums'] and ('source' in ec['skipsteps']): + if checksums and ('source' in ec['skipsteps']): failing_checks.append("'source' step should not be skipped, since that implies not verifying checksums") for ext in ec.get_ref('exts_list'): @@ -1557,21 +1593,7 @@ def template_easyconfig_test(self, spec): patch_checksums = checksums[src_cnt:] for idx, ext_patch in enumerate(ext.get('patches', [])): - if isinstance(ext_patch, (tuple, list)): - ext_patch = ext_patch[0] - - # only check actual patch files, not other files being copied via the patch functionality - ext_patch_full = os.path.join(specdir, ext_patch['name']) - if ext_patch_full.endswith('.patch') and not os.path.isfile(ext_patch_full): - failing_checks.append("Patch file %s for extension %s is missing." % (ext_patch['name'], ext_name)) - continue - - # verify checksum for each patch file - if idx < len(patch_checksums) and os.path.exists(ext_patch_full): - checksum = patch_checksums[idx] - if not verify_checksum(ext_patch_full, checksum): - failing_checks.append("Invalid checksum for patch %s for extension %s: %s." - % (ext_patch['name'], ext_name, checksum)) + failing_checks.extend(verify_patch(specdir, ext_patch, idx, patch_checksums, extension_name=ext_name)) # check whether all extra_options defined for used easyblock are defined extra_opts = app.extra_options()