Merge branch 'easybuilders:develop' into wxWidgets-3.2.6

.github/workflows/tagbot.py

@@ -0,0 +1,182 @@
+import os
+import git
+import requests
+import json
+import difflib
+from datetime import datetime
+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:
+        print(f"{file_path} has no commit info, putting it last")
+        return datetime.datetime.min
+
+
+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 diff(old, new):
+    with open(old, 'r') as old_file, open(new, 'r') as new_file:
+        old_lines = list(old_file)
+        new_lines = list(new_file)
+        return ''.join(difflib.unified_diff(
+            old_lines,
+            new_lines,
+            fromfile=str(old),
+            tofile=str(new)))
+
+
+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")
+pr_ref_name = os.getenv("GITHUB_REF_NAME")
+
+with open(event_path) as f:
+    data = json.load(f)
+
+pr_number = data['pull_request']['number']
+
+print("PR number:", pr_number)
+print("Repo:", repo)
+print("Base branch name:", base_branch_name)
+print("PR ref:", pr_ref_name)
+
+gitrepo = git.Repo(".")
+
+
+target_commit = gitrepo.commit('origin/' + base_branch_name)
+pr_commit = gitrepo.commit('pull/' + pr_ref_name)
+pr_diff = target_commit.diff(pr_commit)
+
+new_ecs, changed_ecs = pr_ecs(pr_diff)
+
+print("Changed ECs:", changed_ecs)
+print("Newly added ECs:", new_ecs)
+
+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 += '<details>\n'
+            comment += f'<summary>Diff against <code>{neighbour.name}</code></summary>\n\n'
+            comment += f'[{neighbour}](https://github.com/{repo}/blob/{base_branch_name}/{neighbour})\n\n'
+            comment += '```diff\n'
+            comment += diff(neighbour, new_file)
+            comment += '```\n</details>\n\n'
+
+print("Adjusting labels")
+current_labels = [label['name'] for label in data['pull_request']['labels']]
+
+labels_add = []
+labels_del = []
+for condition, label in [(changed_ecs, 'change'), (new_software, 'new'), (updated_software, 'update')]:
+    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}")

.github/workflows/tagbot.yml

@@ -0,0 +1,30 @@
+name: Tagbot
+on: [pull_request]
+
+jobs:
+  tagbot:
+    runs-on: ubuntu-24.04
+    permissions:
+      pull-requests: write
+    steps:
+    - uses: actions/checkout@v4
+      with:
+        fetch-depth: 0
+
+    - run: |
+        # Make sure the script is unmodified
+        echo "8be2d295e8436ce557acc8a4d3b82a639913ae65de0d1a76871f21359b4e8d9f .github/workflows/tagbot.py"|sha256sum --check --status
+
+    - 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
+

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'

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'

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'

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'