Merge branch 'easybuild-easyconfigs-basemap' of github.com:julianmori…

…llo/easybuild-easyconfigs-ASE into easybuild-easyconfigs-basemap

.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+# Can't rely on merge_commit_sha for pull_request_target as it might be outdated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.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:
-    - 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: "${{ github.event.pull_request.head.sha }}"
+        path: 'pr'
         fetch-depth: 0
+
+    - name: Attempt test merge
+      id: merge
+      run: |
+        git config user.name "github-workflow"
+        git config user.email "[email protected]"
+        git merge --no-edit --no-ff origin/${{ 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/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'

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'

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'

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'