merge to dev

MDAnalysis · Jan 14, 2025 · e2243ea · e2243ea
2 parents 555520a + 6842fd7
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diff --git a/.git-blame-ignore-revs b/.git-blame-ignore-revs
@@ -0,0 +1,43 @@
+##### git-blame shows what revision and author last modified each line of a file
+##### The ".git-blame-ignore-revs" file is used to ignore certain revisions from being
+##### shown in the output of git blame (also on GitHub blame view).
+#
+# ~~~ Commits that only change the formatting of the code should be ignored. ~~~
+#
+# --- Automated Formatting with `black` ---
+# MDAnalysis was automatically formatted with `black` (end of 2024, beginning of 2025).
+# Formatting PRs (should) contain "[fmt]" in the title (and so do the related commits).
+# See https://github.com/MDAnalysis/mdanalysis/issues/2450 for more details.
+# The following commits are squash commits that contain only^ formatting changes.
+#    ^ This is not strictly true. See PRs for the nitty gritty details.
+#.     PR numbers are listed just above the commit being ignored.
+#4725 
+571431a169e5881f7d09930c4d7e633df0f2cd40
+#4726
+46be788d84a6cb149d90e4493a726c3a30b3cca0
+#4802
+441e2c67abdb8a0a5ffac4a0bc5e88bc7c329aa8
+#4804
+25e755fd78e0a6fb71a91c9d3d989328f021f34b
+#4809
+557f27d658ff0d4011bbe0efa03495f18aa2c1ce
+#4848
+b710e57a64654bed5250eb771f0f27a2dddfeebf
+#4850
+9110a6efe2765802856d028e650ebb0117d336bf
+#4851
+a10e23e681023f383baac7582c39dce4180e2263
+#4856
+c08cb797fd1a2cb45bc0b9e4522cabb15d1f36bd
+#4857
+29deccc9b43a09d2ec3b456bb9c70aae4c34c2cd
+#4859
+9312fa67f163ec055a66f5756a182206fbea3130
+#4861
+55cce24003d4c0975b1bba387b9e6ac20638780e
+#4874
+5eef34165b03281515e08a69159f6504e3a2ff8b
+#4875
+b8fe34b73c9df9330c1608229b2f8cddc6e275b4
+#4885
+263bbe65047e535fbad981852ad9c7327826f93d
diff --git a/.github/actions/setup-deps/action.yaml b/.github/actions/setup-deps/action.yaml
@@ -21,8 +21,8 @@ inputs:
     default: 'codecov'
   cython:
     default: 'cython'
-  fasteners:
-    default: 'fasteners'
+  filelock:
+    default: 'filelock'
   griddataformats:
     default: 'griddataformats'
   gsd:
@@ -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:
@@ -110,7 +110,7 @@ runs:
         CONDA_MIN_DEPS: |
           ${{ inputs.codecov }}
           ${{ inputs.cython }}
-          ${{ inputs.fasteners }}
+          ${{ inputs.filelock }}
           ${{ inputs.griddataformats }}
           ${{ inputs.hypothesis }}
           ${{ inputs.matplotlib }}

diff --git a/.github/workflows/darkerbot.yaml b/.github/workflows/darkerbot.yaml
diff --git a/.github/workflows/deploy.yaml b/.github/workflows/deploy.yaml
@@ -38,10 +38,10 @@ jobs:
       matrix:
         buildplat:
           - [ubuntu-22.04, manylinux_x86_64, x86_64]
-          - [macos-12, macosx_*, x86_64]
+          - [macos-13, 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
@@ -63,7 +63,7 @@ jobs:
         if: |
           (github.event_name == 'push' && startsWith(github.ref, 'refs/tags/package')) ||
           (github.event_name == 'release' && github.event.action == 'published')
-        uses: actions/upload-artifact@v4
+        uses: actions/upload-artifact@v3
         with:
           path: wheelhouse/*.whl
           retention-days: 7
@@ -88,7 +88,7 @@ jobs:
         if: |
           (github.event_name == 'push' && startsWith(github.ref, 'refs/tags/package')) ||
           (github.event_name == 'release' && github.event.action == 'published')
-        uses: actions/upload-artifact@v4
+        uses: actions/upload-artifact@v3
         with:
           path: package/dist/*.tar.gz
           retention-days: 7
@@ -113,7 +113,7 @@ jobs:
         if: |
           (github.event_name == 'push' && startsWith(github.ref, 'refs/tags/package')) ||
           (github.event_name == 'release' && github.event.action == 'published')
-        uses: actions/upload-artifact@v4
+        uses: actions/upload-artifact@v3
         with:
           path: testsuite/dist/*.tar.gz
           retention-days: 7
@@ -131,18 +131,18 @@ jobs:
     runs-on: ubuntu-latest
     needs: [build_wheels, build_sdist, build_sdist_tests]
     steps:
-      - uses: actions/download-artifact@v4
+      - uses: actions/download-artifact@v3
         with:
           name: artifact
           path: dist
 
       - name: move_test_dist
         run: |
           mkdir -p testsuite/dist
-          mv dist/MDAnalysisTests-* testsuite/dist
+          mv dist/mdanalysistests-* testsuite/dist
 
       - name: upload_source_and_wheels
-        uses: pypa/gh-action-pypi-publish@v1.10.1
+        uses: pypa/gh-action-pypi-publish@v1.11.0
         with:
           skip_existing: true
           repository_url: https://test.pypi.org/legacy/
@@ -160,18 +160,18 @@ jobs:
     runs-on: ubuntu-latest
     needs: [build_wheels, build_sdist, build_sdist_tests]
     steps:
-      - uses: actions/download-artifact@v4
+      - uses: actions/download-artifact@v3
         with:
           name: artifact
           path: dist
 
       - name: move_test_dist
         run: |
           mkdir -p testsuite/dist
-          mv dist/MDAnalysisTests-* testsuite/dist
+          mv dist/mdanalysistests-* testsuite/dist
 
       - name: upload_tests
-        uses: pypa/gh-action-pypi-publish@v1.10.1
+        uses: pypa/gh-action-pypi-publish@v1.11.0
         with:
           packages_dir: testsuite/dist
           skip_existing: true
@@ -190,18 +190,18 @@ jobs:
     runs-on: ubuntu-latest
     needs: [build_wheels, build_sdist, build_sdist_tests]
     steps:
-      - uses: actions/download-artifact@v4
+      - uses: actions/download-artifact@v3
         with:
           name: artifact
           path: dist
 
       - name: move_test_dist
         run: |
           mkdir -p testsuite/dist
-          mv dist/MDAnalysisTests-* testsuite/dist
+          mv dist/mdanalysistests-* testsuite/dist
 
       - name: upload_source_and_wheels
-        uses: pypa/gh-action-pypi-publish@v1.10.0
+        uses: pypa/gh-action-pypi-publish@v1.11.0
 
   upload_pypi_mdanalysistests:
     if: |
@@ -216,18 +216,18 @@ jobs:
     runs-on: ubuntu-latest
     needs: [build_wheels, build_sdist, build_sdist_tests]
     steps:
-      - uses: actions/download-artifact@v4
+      - uses: actions/download-artifact@v3
         with:
           name: artifact
           path: dist
 
       - name: move_test_dist
         run: |
           mkdir -p testsuite/dist
-          mv dist/MDAnalysisTests-* testsuite/dist
+          mv dist/mdanalysistests-* testsuite/dist
 
       - name: upload_tests
-        uses: pypa/gh-action-pypi-publish@v1.10.0
+        uses: pypa/gh-action-pypi-publish@v1.11.0
         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
@@ -256,7 +256,7 @@ jobs:
       - uses: actions/checkout@v4
 
       - name: setup_micromamba
-        uses: mamba-org/setup-micromamba@v1
+        uses: mamba-org/setup-micromamba@v2
         with:
           environment-name: mda
           create-args: >-

diff --git a/.github/workflows/gh-ci-cron.yaml b/.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
@@ -106,7 +104,7 @@ jobs:
         os-type: "ubuntu"
 
     - name: setup_micromamba
-      uses: mamba-org/setup-micromamba@v1
+      uses: mamba-org/setup-micromamba@v2
       with:
         environment-name: mda
         create-args: >-
@@ -148,7 +146,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: [ubuntu-20.04, macos-12]
+        os: [ubuntu-20.04, macos-13]
 
     steps:
     - uses: actions/checkout@v4
@@ -159,7 +157,7 @@ jobs:
         os-type: ${{ matrix.os }}
 
     - name: setup_micromamba
-      uses: mamba-org/setup-micromamba@v1
+      uses: mamba-org/setup-micromamba@v2
       with:
         environment-name: mda
         create-args: >-
@@ -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
 
@@ -239,9 +237,11 @@ jobs:
         fail-fast: false
         matrix:
           # Stick to macos-13 because some of our
-          # optional depss don't support arm64 (i.e. macos-14)
+          # optional deps don't support arm64 (i.e. macos-14)
+          #
+          # add "3.13" once conda-forge packages are available (see #4805)
           os: [ubuntu-latest, macos-13]
-          python-version: ["3.9", "3.10", "3.11", "3.12"]
+          python-version: ["3.10", "3.11", "3.12"]
     steps:
     - uses: actions/checkout@v4
 
@@ -251,7 +251,7 @@ jobs:
         os-type: ${{ matrix.os }}
 
     - name: setup_micromamba
-      uses: mamba-org/setup-micromamba@v1
+      uses: mamba-org/setup-micromamba@v2
       with:
         environment-name: mda
         create-args: >-
@@ -287,11 +287,8 @@ jobs:
         fail-fast: false
         matrix:
           os: [ubuntu-latest, macos-latest, macos-14, windows-latest]
-          python-version: ["3.9", "3.10", "3.11", "3.12"]
+          python-version: ["3.10", "3.11", "3.12", "3.13"]
           wheels: ['true', 'false']
-          exclude:
-          - os: "macos-14"
-            python-version: "3.9"
     steps:
       # Checkout to have access to local actions (i.e. setup-os)
     - uses: actions/checkout@v4