Merge branch 'MDAnalysis:develop' into twice_workers_error

MDAnalysis · Nov 26, 2024 · 7b2b944 · 7b2b944
2 parents cfcc528 + 7e521de
commit 7b2b944
Show file tree

Hide file tree

Showing 380 changed files with 3,166 additions and 1,852 deletions.
diff --git a/.github/workflows/deploy.yaml b/.github/workflows/deploy.yaml
@@ -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@v1.10.2
+        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@v1.10.2
+        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@v1.10.2
+        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@v1.10.2
+        uses: pypa/gh-action-pypi-publish@v1.11.0
         with:
           packages_dir: testsuite/dist
 
@@ -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
@@ -104,7 +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: >-
@@ -157,7 +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: >-
@@ -249,7 +249,7 @@ 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: >-

diff --git a/.github/workflows/gh-ci.yaml b/.github/workflows/gh-ci.yaml
@@ -72,7 +72,7 @@ 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: >-
@@ -150,7 +150,7 @@ 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/linters.yaml b/.github/workflows/linters.yaml
@@ -76,7 +76,7 @@ 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: >-