Merge branch 'easybuilders:develop' into 20230904124033_new_pr_PyTom11

.github/workflows/unit_tests.yml

@@ -13,7 +13,7 @@ jobs:
     runs-on: ubuntu-20.04
     strategy:
       matrix:
-        python: [3.6]
+        python: [3.6, '3.11']
         modules_tool: [Lmod-7.8.22, Lmod-8.6.8]
         module_syntax: [Lua, Tcl]
         # exclude some configurations: only test Tcl module syntax with Lmod 8.x and Python 3.6
@@ -147,10 +147,6 @@ jobs:
           eb --search '^foss-2019b.eb' | tee eb_search_foss.out
           grep '/foss-2019b.eb$' eb_search_foss.out
 
-          # make sure CVS easyconfigs are included in installation (cfr. issue #10325)
-          echo "Searching for CVS easyconfigs..."
-          eb --search '^CVS-' | grep '/CVS-'
-
           # try installing M4 with system toolchain (requires ConfigureMake easyblock + easyconfig)
           # use /tmp/sources because that has cached downloads (see cache step above)
           eb --prefix /tmp/$USER/$GITHUB_SHA --sourcepath /tmp/sources M4-1.4.18.eb
@@ -159,7 +155,7 @@ jobs:
     runs-on: ubuntu-20.04
     strategy:
       matrix:
-        python: [3.6]
+        python: [3.6, '3.11']
     steps:
     - uses: actions/checkout@v2
 
@@ -184,12 +180,3 @@ jobs:
           else
             echo "No .git folders found in source tarball: OK"
           fi
-
-          # CVS easyconfigs must be included in source tarball,
-          # see https://github.com/easybuilders/easybuild-easyconfigs/issues/10325
-          cvs_easyconfigs=$(find . -name 'CVS-*.eb')
-          if [ -z "$cvs_easyconfigs" ]; then
-            echo "CVS easyconfigs not found" && false
-          else
-            echo "Found CVS easyconfigs: $cvs_easyconfigs"
-          fi

.gitignore

@@ -11,3 +11,4 @@ dist/
 *.ropeproject/
 eb-*.log
 /MANIFEST
+/easybuild/easyconfigs/.eb-path-index

easybuild/easyconfigs/TEMPLATE.eb

@@ -24,7 +24,7 @@ dependencies = []
 # The sanity test MUST be tuned before going production and submitting your contribution to upstream git repositories
 sanity_check_paths = {
     'files': [],
-    'dirs': ["."]
+    'dirs': [],
 }
 
 # You SHOULD change the following line; Kindly consult other easyconfigs for possible options

easybuild/easyconfigs/a/ALAMODE/ALAMODE-1.4.2-foss-2022b.eb

@@ -0,0 +1,57 @@
+# with thanks to ComputeCanada for the initial easyconfig for 1.0.2-iomkl-2017.5.211.eb
+# updated for 1.4.2 by BEAR Software team at University of Birmingham
+easyblock = "CMakeMakeCp"
+
+name = 'ALAMODE'
+version = '1.4.2'
+
+homepage = 'http://alamode.readthedocs.io/en/latest/index.html'
+description = """ALAMODE is an open source software designed for analyzing lattice anharmonicity
+ and lattice thermal conductivity of solids. By using an external DFT package such as VASP and
+ Quantum ESPRESSO, you can extract harmonic and anharmonic force constants straightforwardly with ALAMODE.
+ Using the calculated anharmonic force constants, you can also estimate lattice thermal conductivity,
+ phonon linewidth, and other anharmonic phonon properties from first principles.
+"""
+
+toolchain = {'name': 'foss', 'version': '2022b'}
+toolchainopts = {'usempi': True, 'pic': True}
+
+source_urls = ['https://github.com/ttadano/alamode/archive/']
+sources = ['v.%(version)s.tar.gz']
+checksums = ['18fb80a183c2a9b68488aeeccd6efa95e8c21d4cb21b08319a557389d55c067a']
+
+builddependencies = [
+    ('binutils', '2.39'),
+    ('CMake', '3.24.3'),
+]
+
+dependencies = [
+    ('Boost', '1.81.0'),
+    ('Eigen', '3.4.0'),
+    ('spglib', '2.0.2'),
+    ('FFTW', '3.3.10'),
+    ('HDF5', '1.14.0'),
+    ('Python', '3.10.8'),
+]
+
+configopts = ' '.join([
+    "-DWITH_HDF5_SUPPORT=yes",
+    "-DUSE_MKL_FFT=no",
+    "-DSPGLIB_ROOT=$EBROOTSPGLIB"
+])
+
+local_binary_files = [
+    "alm/alm", "anphon/anphon", "tools/analyze_phonons", "tools/dfc2", "tools/fc_virtual",
+    "tools/parse_fcsxml", "tools/qe2alm", "tools/analyze_phonons.py", "tools/displace.py", "tools/extract.py",
+    "tools/GenDisplacement.py", "tools/makedisp_qe.py", "tools/plotband.py", "tools/plotdos.py",
+    "tools/scph_to_qefc.py",
+]
+
+files_to_copy = [([x for x in local_binary_files], 'bin'), 'docs', 'example']
+
+sanity_check_paths = {
+    'files': ['bin/alm'],
+    'dirs': ["docs", "example"]
+}
+
+moduleclass = 'chem'

easybuild/easyconfigs/a/ALL/ALL-0.9.2-foss-2022b.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': '2022b'}
+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', '3.24.3'),
+    ('Boost', '1.81.0'),  # only needed for tests
+]
+
+dependencies = [
+    ('VTK', '9.2.6'),
+]
+
+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'

easybuild/easyconfigs/a/AOFlagger/AOFlagger-3.4.0-foss-2022a.eb

@@ -0,0 +1,47 @@
+easyblock = 'CMakeMake'
+
+name = 'AOFlagger'
+version = '3.4.0'
+
+homepage = 'https://aoflagger.readthedocs.io/'
+description = """The AOFlagger is a tool that can find and remove radio-frequency interference (RFI)
+in radio astronomical observations. It can make use of Lua scripts to make flagging strategies flexible,
+and the tools are applicable to a wide set of telescopes."""
+
+toolchain = {'name': 'foss', 'version': '2022a'}
+
+sources = [{
+    'source_urls': ['https://gitlab.com/aroffringa/aoflagger/-/package_files/96704214/'],
+    'filename': '%(namelower)s-v%(version)s.tar.bz2',
+    'download_filename': 'download'  # provided source tarball is not versioned...
+}]
+checksums = ['9560b7381b68f37d842599f222a8aa2a5d3d3d501d1277471e1a0ba3d7b2aeba']
+
+builddependencies = [
+    ('CMake', '3.24.3'),
+]
+dependencies = [
+    ('casacore', '3.5.0'),
+    ('Boost', '1.79.0'),
+    ('CFITSIO', '4.2.0'),
+    ('GSL', '2.7'),
+    ('HDF5', '1.12.2'),
+    ('Python', '3.10.4'),
+    ('Lua', '5.4.4'),
+    ('libpng', '1.6.37'),
+    ('libxml2', '2.9.13'),
+]
+
+# Without this, the wrong (system) python is picked up by cmake
+# in cases where the system python is newer than the one used in these EasyConfigs
+# See PR # 19119
+configopts = '-DPython3_EXECUTABLE=$EBROOTPYTHON/bin/python '
+
+sanity_check_paths = {
+    'files': ['include/aoflagger.h', 'bin/aoflagger'],
+    'dirs': ['bin'],
+}
+
+sanity_check_commands = [('aoflagger', '-v')]
+
+moduleclass = 'lib'

easybuild/easyconfigs/a/ASAP3/ASAP3-3.13.2-foss-2023a.eb

@@ -0,0 +1,36 @@
+easyblock = "PythonPackage"
+
+name = 'ASAP3'
+version = '3.13.2'
+
+homepage = 'https://wiki.fysik.dtu.dk/asap/'
+description = """ASAP is a calculator for doing large-scale classical molecular
+dynamics within the Campos Atomic Simulation Environment (ASE)."""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+toolchainopts = {'pic': True, 'usempi': True, 'openmp': False}
+
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['c2e6f0570de8037be45afd9bf35f6b4e76e1f518a0af0207c6bf5809ddb1abb8']
+
+builddependencies = [
+    ('pkgconf', '1.9.5'),
+]
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('SciPy-bundle', '2023.07'),
+    ('ASE', '3.22.1'),
+    ('kim-api', '2.3.0'),
+]
+
+use_pip = True
+download_dep_fail = True
+sanity_pip_check = True
+
+sanity_check_paths = {
+    'files': [],
+    'dirs': ['lib/python%(pyshortver)s/site-packages/%(namelower)s']
+}
+
+moduleclass = 'phys'

easybuild/easyconfigs/a/ASCAT/ASCAT-3.1.2-foss-2022b-R-4.2.2.eb

@@ -0,0 +1,30 @@
+easyblock = 'RPackage'
+
+name = 'ASCAT'
+version = '3.1.2'
+versionsuffix = '-R-%(rver)s'
+
+homepage = 'https://github.com/VanLoo-lab/ascat'
+description = """ASCAT is a method to derive copy number profiles of tumor cells,
+ accounting for normal cell admixture and tumor aneuploidy."""
+
+toolchain = {'name': 'foss', 'version': '2022b'}
+
+source_urls = ['https://github.com/VanLoo-lab/ascat/archive/refs/tags/']
+sources = ['v%(version)s.tar.gz']
+checksums = ['5d65aef417ad12ea0e638b4179def5a9b8f25e1ccd757e41a6509534fe20eb17']
+
+dependencies = [
+    ('R', '4.2.2'),
+    ('R-bundle-Bioconductor', '3.16', versionsuffix),
+    ('alleleCount', '4.3.0'),
+]
+
+start_dir = '%(name)s'
+
+sanity_check_paths = {
+    'files': [],
+    'dirs': ['%(name)s']
+}
+
+moduleclass = 'bio'

easybuild/easyconfigs/a/ASE/ASE-3.22.1-gfbf-2023a.eb

@@ -0,0 +1,64 @@
+easyblock = 'PythonBundle'
+
+name = 'ASE'
+version = '3.22.1'
+
+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, {
+        'patches': [
+            'ASE-3.22.1-Compatibility-with-pytest-from-Python-3-10.patch',
+            'ASE-3.22.1-Compatibility-with-pytest-part-2.patch',
+            'ASE-3.22.1-Compatibility-with-Scipy-2022-05.patch',
+            'ASE-3.22.1-Compatibility-with-Flask-2-2-2.patch',
+        ],
+        'checksums': [
+            {'ase-3.22.1.tar.gz': '004df6b0ea04b1114c790fadfe45d4125eb0e53125c66a93425af853d82ab432'},
+            {'ASE-3.22.1-Compatibility-with-pytest-from-Python-3-10.patch':
+             '8184765ecc9e14081b183fee5c4470da716d77caa67c25164018ac1fdd225eac'},
+            {'ASE-3.22.1-Compatibility-with-pytest-part-2.patch':
+             '3a3473912f5f96ffc625119d87227781ba4ea581de15d4af6a58ba960cdf4601'},
+            {'ASE-3.22.1-Compatibility-with-Scipy-2022-05.patch':
+             'c1cb07160b063d432f098efd40dd4b3c9f015b7966572c838a908613a482e0c8'},
+            {'ASE-3.22.1-Compatibility-with-Flask-2-2-2.patch':
+             '2a05f98291dc970cb759904988783d1ecc3512ba6a0da852af1d3205667b398d'},
+        ],
+    }),
+    ('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'