Merge branch 'develop' of https://github.com/easybuilders/easybuild-e…

…asyconfigs into 20241031160830_new_pr_MultiQC1251

.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+# Can't rely on merge_commit_sha for pull_request_target as it might be outdated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 += '<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 += gitrepo.git.diff(f'HEAD:{neighbour}', f'HEAD:{new_file}')
+            comment += '\n```\n</details>\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}")

.github/workflows/tagbot.yml

@@ -0,0 +1,54 @@
+name: Tagbot
+on: [pull_request_target]
+
+concurrency:
+  group: "${{ github.workflow }}-${{ github.ref }}"
+  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: "${{ github.event.pull_request.head.sha }}"
+        path: 'pr'
+        fetch-depth: 0
+
+    - name: Attempt test merge
+      id: merge
+      run: |
+        git config user.name "github-workflow"
+        git config user.email "github-workflow@github.com"
+        git merge --no-commit --no-ff origin/${{ 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
+

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'

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'