Merge remote-tracking branch 'upstream/develop' into feature/mmcif

.git-blame-ignore-revs

@@ -0,0 +1,2 @@
+# black
+83e5f99051d86ca354b537be8854c40f9b6ce172

.github/actions/setup-deps/action.yaml

@@ -59,7 +59,7 @@ inputs:
   dask:
     default: 'dask'
   distopia:
-    default: 'distopia>=0.2.0'
+    default: 'distopia>=0.2.0,<0.3.0'
   h5py:
     default: 'h5py>=2.10'
   hole2:

.github/workflows/deploy.yaml

@@ -41,7 +41,7 @@ jobs:
           - [macos-12, macosx_*, x86_64]
           - [windows-2019, win_amd64, AMD64]
           - [macos-14, macosx_*, arm64]
-        python: ["cp310", "cp311", "cp312"]
+        python: ["cp310", "cp311", "cp312", "cp313"]
     defaults:
       run:
         working-directory: ./package
@@ -142,7 +142,7 @@ jobs:
           mv dist/MDAnalysisTests-* testsuite/dist
 
       - name: upload_source_and_wheels
-        uses: pypa/[email protected].1
+        uses: pypa/[email protected].2
         with:
           skip_existing: true
           repository_url: https://test.pypi.org/legacy/
@@ -171,7 +171,7 @@ jobs:
           mv dist/MDAnalysisTests-* testsuite/dist
 
       - name: upload_tests
-        uses: pypa/[email protected].1
+        uses: pypa/[email protected].2
         with:
           packages_dir: testsuite/dist
           skip_existing: true
@@ -201,7 +201,7 @@ jobs:
           mv dist/MDAnalysisTests-* testsuite/dist
 
       - name: upload_source_and_wheels
-        uses: pypa/[email protected].0
+        uses: pypa/[email protected].2
 
   upload_pypi_mdanalysistests:
     if: |
@@ -227,7 +227,7 @@ jobs:
           mv dist/MDAnalysisTests-* testsuite/dist
 
       - name: upload_tests
-        uses: pypa/[email protected].0
+        uses: pypa/[email protected].2
         with:
           packages_dir: testsuite/dist
 
@@ -243,7 +243,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest, macos-latest, windows-latest]
-        python-version: ["3.10", "3.11", "3.12"]
+        python-version: ["3.10", "3.11", "3.12", "3.13"]
         type: ["FULL", "MIN"]
         exclude:
           # Multiple deps don't like windows

.github/workflows/gh-ci-cron.yaml

@@ -40,9 +40,7 @@ jobs:
       with:
         os-type: "ubuntu"
 
-    - uses: actions/setup-python@v4
-      with:
-        python-version: ${{ matrix.python-version }}
+    - uses: actions/setup-python@v5
 
     # minimally install nightly wheels & core deps
     - name: nightly_wheels
@@ -197,7 +195,7 @@ jobs:
     strategy:
         fail-fast: false
         matrix:
-          python-version: ["3.10", "3.11", "3.12"]
+          python-version: ["3.10", "3.11", "3.12", "3.13"]
     steps:
     - uses: actions/checkout@v4
 

.github/workflows/gh-ci.yaml

@@ -32,6 +32,11 @@ jobs:
           full-deps: [true, ]
           codecov: [true, ]
           include:
+            - name: python_313
+              os: ubuntu-latest
+              python-version: "3.13"
+              full-deps: false
+              codecov: true
             - name: macOS_monterey_py311
               os: macOS-12
               python-version: "3.12"

.github/workflows/linters.yaml

@@ -16,12 +16,10 @@ defaults:
     shell: bash -l {0}
 
 jobs:
-  darker_lint:
+  black:
     if: "github.repository == 'MDAnalysis/mdanalysis'"
     runs-on: ubuntu-latest
     timeout-minutes: 10
-    permissions:
-      pull-requests: write
     defaults:
       run:
         shell: bash
@@ -35,66 +33,17 @@ jobs:
       with:
         python-version: "3.10"
 
-    - name: darker-main-code
-      id: darker-main-code
-      uses: akaihola/[email protected]
-      continue-on-error: true
+    - uses: psf/black@stable
       with:
-        version: "~=1.6.1"
-        options: "--check --diff --color"
-        src: "./package/MDAnalysis"
-        revision: "HEAD^"
-        lint: "flake8"
-
-    - name: darker-test-code
-      id: darker-test-code
-      uses: akaihola/[email protected]
-      continue-on-error: true
+        options: "--check --verbose"
+        src: "./package"
+        version: "~= 24.0"
+
+    - uses: psf/black@stable
       with:
-        version: "~=1.6.1"
-        options: "--check --diff --color"
-        src: "./testsuite/MDAnalysisTests"
-        revision: "HEAD^"
-        lint: "flake8"
-
-    - name: get-pr-info
-      uses: actions/github-script@v7
-      with:
-        script:
-            const prNumber = context.payload.number;
-            core.exportVariable('PULL_NUMBER', prNumber);
-
-    - name: save-status
-      env:
-        MAIN: ${{ steps.darker-main-code.outcome }}
-        TEST: ${{ steps.darker-test-code.outcome }}
-      shell: python
-      run: |
-        import os
-        import json
-        from pathlib import Path
-
-        Path('./darker_results/').mkdir(exist_ok=True)
-
-        d = {
-            'main_stat': os.environ['MAIN'],
-            'test_stat': os.environ['TEST'],
-            'PR_NUM': os.environ['PULL_NUMBER'],
-            'RUN_ID': os.environ['GITHUB_RUN_ID'],
-        }
-
-        with open('darker_results/status.json', 'w') as f:
-            json.dump(d, f)
-
-    - name: check-json
-      run: cat darker_results/status.json
-
-    - name: upload-status
-      uses: actions/upload-artifact@v4
-      with:
-        name: darkerlint
-        path: darker_results/
-        retention-days: 1
+        options: "--check --verbose"
+        src: "./testsuite"
+        version: "~= 24.0"
 
 
   pylint_check:

azure-pipelines.yml

@@ -47,7 +47,7 @@ jobs:
           PYTHON_VERSION: '3.12'
           PYTHON_ARCH: 'x64'
           BUILD_TYPE: 'wheel'
-          NUMPY_MIN: '1.26.0'
+          NUMPY_MIN: '2.1.0'
           imageName: 'ubuntu-latest'
         Linux-Python310-64bit-full-wheel:
           PYTHON_VERSION: '3.10'

benchmarks/benchmarks/topology.py

@@ -1,6 +1,6 @@
 import MDAnalysis
 import numpy as np
-from MDAnalysis.topology import guessers
+from MDAnalysis.guesser import DefaultGuesser
 
 try:
     from MDAnalysisTests.datafiles import GRO
@@ -26,7 +26,7 @@ def setup(self, num_atoms):
 
     def time_guessbonds(self, num_atoms):
         """Benchmark for guessing bonds"""
-        guessers.guess_bonds(self.ag, self.ag.positions,
+        DefaultGuesser(None).guess_bonds(self.ag, self.ag.positions,
                              box=self.ag.dimensions,
                              vdwradii=self.vdwradii)