Merge branch 'develop' into singleframereader_pathlib

MDAnalysis · Dec 17, 2024 · f785eea · f785eea
2 parents 33d6b4e + a3672f2
commit f785eea
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diff --git a/.git-blame-ignore-revs b/.git-blame-ignore-revs
@@ -0,0 +1,2 @@
+# black
+83e5f99051d86ca354b537be8854c40f9b6ce172
diff --git a/.github/actions/build-src/action.yaml b/.github/actions/build-src/action.yaml
@@ -66,6 +66,15 @@ runs:
         micromamba info
         micromamba list
 
+    - name: mda_deps
+      shell: bash -l {0}
+      run: |
+        # Install mdakit deps that depend on MDA
+        python -m pip install --no-deps \
+            waterdynamics   \
+            pathsimanalysis \
+            mdahole2
+
     - name: build_mda_main
       shell: bash -l {0}
       run: |
@@ -84,6 +93,12 @@ runs:
         fi
         python -m pip install ${BUILD_FLAGS} -v -e ./testsuite
 
+    - name: post_build_env_check
+      shell: bash -l {0}
+      run: |
+        pip list
+        micromamba list
+
     - name: build_docs
       if: ${{ inputs.build-docs == 'true' }}
       shell: bash -l {0}

diff --git a/.github/actions/setup-deps/action.yaml b/.github/actions/setup-deps/action.yaml
@@ -31,8 +31,6 @@ inputs:
     default: 'hypothesis'
   matplotlib:
     default: 'matplotlib-base'
-  mdahole2:
-    default: 'mdahole2-base'
   mda_xdrlib:
     default: 'mda-xdrlib'
   mmtf-python:
@@ -41,8 +39,6 @@ inputs:
     default: 'numpy'
   packaging:
     default: 'packaging'
-  pathsimanalysis:
-    default: 'pathsimanalysis'
   pip:
     default: 'pip'
   pytest:
@@ -53,8 +49,6 @@ inputs:
     default: 'threadpoolctl'
   tqdm:
     default: 'tqdm>=4.43.0'
-  waterdynamics:
-    default: 'waterdynamics'
   # conda-installed optional dependencies
   biopython:
     default: 'biopython>=1.80'
@@ -65,7 +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:
@@ -120,18 +114,15 @@ runs:
           ${{ inputs.griddataformats }}
           ${{ inputs.hypothesis }}
           ${{ inputs.matplotlib }}
-          ${{ inputs.mdahole2 }}
           ${{ inputs.mda_xdrlib }}
           ${{ inputs.mmtf-python }}
           ${{ inputs.numpy }}
           ${{ inputs.packaging }}
-          ${{ inputs.pathsimanalysis }}
           ${{ inputs.pip }}
           ${{ inputs.pytest }}
           ${{ inputs.scipy }}
           ${{ inputs.threadpoolctl }}
           ${{ inputs.tqdm }}
-          ${{ inputs.waterdynamics }}
         CONDA_OPT_DEPS: |
           ${{ inputs.biopython }}
           ${{ inputs.chemfiles-python }}

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-11, macosx_*, x86_64]
+          - [macos-13, macosx_*, x86_64]
           - [windows-2019, win_amd64, AMD64]
           - [macos-14, macosx_*, arm64]
-        python: ["cp39", "cp310", "cp311", "cp312"]
+        python: ["cp310", "cp311", "cp312", "cp313"]
     defaults:
       run:
         working-directory: ./package
@@ -51,7 +51,7 @@ jobs:
           fetch-depth: 0
 
       - name: Build wheels
-        uses: pypa/cibuildwheel@v2.16.5
+        uses: pypa/cibuildwheel@v2.20.0
         with:
           package-dir: package
         env:
@@ -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@v1.9.0
+        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@v1.9.0
+        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@v1.9.0
+        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@v1.9.0
+        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: >-
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1,2 @@
		# black
		83e5f99051d86ca354b537be8854c40f9b6ce172