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

…asyconfigs into 20241105144555_new_pr_Porechop02420240119

.github/workflows/tagbot.py

@@ -1,9 +1,11 @@
+# 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
-import difflib
-from datetime import datetime
 from pathlib import Path
 
 
@@ -12,8 +14,7 @@ def get_first_commit_date(repo, 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
+        raise ValueError(f'{file_path} has no commit info, this should not happen')
 
 
 def sort_by_added_date(repo, file_paths):
@@ -27,17 +28,6 @@ def similar_easyconfigs(repo, 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 = []
@@ -51,33 +41,38 @@ def pr_ecs(pr_diff):
 
 
 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")
+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+# Can't rely on merge_commit_sha for pull_request_target as it might be outdated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("Repo:", repo)
 print("Base branch name:", base_branch_name)
-print("PR ref:", pr_ref_name)
-
-gitrepo = git.Repo(".")
 
+# 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)
-pr_commit = gitrepo.commit('pull/' + pr_ref_name)
-pr_diff = target_commit.diff(pr_commit)
+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:", changed_ecs)
-print("Newly added ECs:", new_ecs)
+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
@@ -116,15 +111,20 @@ def pr_ecs(pr_diff):
             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'
+            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 [(changed_ecs, 'change'), (new_software, 'new'), (updated_software, 'update')]:
+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:

.github/workflows/tagbot.yml

@@ -1,19 +1,43 @@
 name: Tagbot
-on: [pull_request]
+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:
-    - uses: actions/checkout@v4
+    - 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: "${{ github.event.pull_request.head.sha }}"
+        path: 'pr'
         fetch-depth: 0
+
+    - name: Attempt test merge
+      id: merge
+      run: |
+        git config user.name "github-workflow"
+        git config user.email "[email protected]"
+        git merge --no-commit --no-ff origin/${{ github.event.pull_request.base.ref }}
+      continue-on-error: true
+      working-directory: pr
 
-    - run: |
-        # Make sure the script is unmodified
-        echo "8be2d295e8436ce557acc8a4d3b82a639913ae65de0d1a76871f21359b4e8d9f .github/workflows/tagbot.py"|sha256sum --check --status
+    - 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

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/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'

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'

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'

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'