Add ASV benchmarks for Contacts Analysis

Amarendra22 · Amarendra22 · commit d493eee50df0 · 2026-03-13T10:23:17.000+05:30
diff --git a/.github/workflows/deploy.yaml b/.github/workflows/deploy.yaml
@@ -45,12 +45,12 @@ jobs:
       run:
         working-directory: ./package
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
         with:
           fetch-depth: 0
 
       - name: Build wheels
-        uses: pypa/cibuildwheel@v3.2.0
+        uses: pypa/cibuildwheel@v3.4.0
         with:
           package-dir: package
         env:
@@ -62,7 +62,7 @@ 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@v7
         with:
           name: wheel-${{ matrix.buildplat[0] }}-${{ matrix.python }}
           path: wheelhouse/*.whl
@@ -77,7 +77,7 @@ jobs:
       run:
         working-directory: ./package
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
         with:
           fetch-depth: 0
 
@@ -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@v7
         with:
           name: sdist
           path: package/dist/*.tar.gz
@@ -103,7 +103,7 @@ jobs:
       run:
         working-directory: ./testsuite
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
         with:
           fetch-depth: 0
 
@@ -114,7 +114,7 @@ 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@v7
         with:
           name: sdist_tests
           path: testsuite/dist/*.tar.gz
@@ -133,7 +133,7 @@ jobs:
     runs-on: ubuntu-latest
     needs: [build_wheels, build_sdist, build_sdist_tests]
     steps:
-      - uses: actions/download-artifact@v4
+      - uses: actions/download-artifact@v8
         with:
           path: dist
           merge-multiple: true
@@ -162,7 +162,7 @@ jobs:
     runs-on: ubuntu-latest
     needs: [build_wheels, build_sdist, build_sdist_tests]
     steps:
-      - uses: actions/download-artifact@v4
+      - uses: actions/download-artifact@v8
         with:
           path: dist
           merge-multiple: true
@@ -192,7 +192,7 @@ jobs:
     runs-on: ubuntu-latest
     needs: [build_wheels, build_sdist, build_sdist_tests]
     steps:
-      - uses: actions/download-artifact@v4
+      - uses: actions/download-artifact@v8
         with:
           path: dist
           merge-multiple: true
@@ -218,7 +218,7 @@ jobs:
     runs-on: ubuntu-latest
     needs: [build_wheels, build_sdist, build_sdist_tests]
     steps:
-      - uses: actions/download-artifact@v4
+      - uses: actions/download-artifact@v8
         with:
           path: dist
           merge-multiple: true
@@ -257,7 +257,7 @@ jobs:
       MPLBACKEND: agg
 
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
 
       - name: setup_micromamba
         uses: mamba-org/setup-micromamba@v2
@@ -267,11 +267,9 @@ jobs:
             python=${{ matrix.python-version }}
             packaging
             pip
-          # jaime's shim to avoid pulling down the cudatoolkit
           # bioconda for clustalw things
           condarc: |
             channels:
-              - jaimergp/label/unsupported-cudatoolkit-shim
               - conda-forge
               - bioconda
 
diff --git a/.github/workflows/gh-ci-cron.yaml b/.github/workflows/gh-ci-cron.yaml
@@ -33,14 +33,14 @@ jobs:
     timeout-minutes: 60
 
     steps:
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v6
 
     - name: setup_os
       uses: ./.github/actions/setup-os
       with:
         os-type: "ubuntu"
 
-    - uses: actions/setup-python@v5
+    - uses: actions/setup-python@v6
 
     # minimally install nightly wheels & core deps
     - name: nightly_wheels
@@ -91,7 +91,7 @@ jobs:
     timeout-minutes: 60
 
     steps:
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v6
 
     - name: setup_os
       uses: ./.github/actions/setup-os
@@ -143,7 +143,7 @@ jobs:
         os: [ubuntu-22.04, macos-14]
 
     steps:
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v6
 
     - name: setup_os
       uses: ./.github/actions/setup-os
@@ -190,14 +190,14 @@ jobs:
         matrix:
           python-version: ["3.11", "3.12", "3.13", "3.14"]
     steps:
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v6
 
     - name: setup_os
       uses: ./.github/actions/setup-os
       with:
         os-type: "ubuntu"
 
-    - uses: actions/setup-python@v5
+    - uses: actions/setup-python@v6
       with:
         python-version: ${{ matrix.python-version }}
 
@@ -234,7 +234,7 @@ jobs:
           os: [ubuntu-latest, macos-13]
           python-version: ["3.10", "3.11", "3.12", "3.13"]
     steps:
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v6
 
     - name: setup_os
       uses: ./.github/actions/setup-os
@@ -280,15 +280,15 @@ jobs:
           wheels: ['true', 'false']
     steps:
       # Checkout to have access to local actions (i.e. setup-os)
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v6
 
       # We need this here in order to make sure we assign the correct compiler (i.e. clang for macos)
     - name: setup_os
       uses: ./.github/actions/setup-os
       with:
         os-type: ${{ matrix.os }}
 
-    - uses: actions/setup-python@v5
+    - uses: actions/setup-python@v6
       with:
         python-version: ${{ matrix.python-version }}
 
diff --git a/.github/workflows/gh-ci.yaml b/.github/workflows/gh-ci.yaml
@@ -73,7 +73,7 @@ jobs:
       MPLBACKEND: agg
 
     steps:
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v6
 
     - name: setup_os
       uses: ./.github/actions/setup-os
@@ -87,10 +87,8 @@ jobs:
         create-args: >-
           python=${{ matrix.python-version }}
           pip
-        # using jaime's shim to avoid pulling down the cudatoolkit
         condarc: |
           channels:
-            - jaimergp/label/unsupported-cudatoolkit-shim
             - conda-forge
             - bioconda
 
@@ -158,7 +156,7 @@ jobs:
       MPLBACKEND: agg
 
     steps:
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v6
 
     - name: setup_micromamba
       uses: mamba-org/setup-micromamba@v2
@@ -167,7 +165,6 @@ jobs:
         create-args: >-
           python=3.11
           pip
-        # using jaime's shim to avoid pulling down the cudatoolkit
         condarc: |
           channels:
             - conda-forge
@@ -256,9 +253,9 @@ jobs:
     timeout-minutes: 30
 
     steps:
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v6
 
-    - uses: actions/setup-python@v5
+    - uses: actions/setup-python@v6
       with:
         python-version: 3.11
 
diff --git a/.github/workflows/greetings.yaml b/.github/workflows/greetings.yaml
@@ -14,7 +14,7 @@ jobs:
     permissions:
       pull-requests: write
     steps:
-    - uses: actions/first-interaction@v1
+    - uses: actions/first-interaction@v3
       with:
         repo-token: ${{ secrets.GITHUB_TOKEN }}
         pr-message: 'Hello there first time contributor! Welcome to the MDAnalysis community! We ask that all contributors abide by our [Code of Conduct](https://www.mdanalysis.org/pages/conduct/) and that first time contributors introduce themselves on [GitHub Discussions](https://github.com/MDAnalysis/mdanalysis/discussions) so we can get to know you. You can learn more about [participating here](https://www.mdanalysis.org/#participating). Please also add yourself to `package/AUTHORS` as part of this PR.'
diff --git a/.github/workflows/labels.yaml b/.github/workflows/labels.yaml
@@ -10,7 +10,7 @@ jobs:
     runs-on: ubuntu-latest
     timeout-minutes: 10
     steps:
-    - uses: actions/labeler@v5
+    - uses: actions/labeler@v6
       with:
         repo-token: "${{ secrets.GITHUB_TOKEN }}"
         configuration-path: ".github/pr_path_labeler.yml"
diff --git a/.github/workflows/linters.yaml b/.github/workflows/linters.yaml
@@ -1,5 +1,6 @@
 name: "linters"
 on:
+  workflow_dispatch:
   pull_request:
     branches:
       - develop
@@ -25,11 +26,11 @@ jobs:
         shell: bash
 
     steps:
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v6
       with:
         fetch-depth: 0
 
-    - uses: actions/setup-python@v5
+    - uses: actions/setup-python@v6
       with:
         python-version: "3.11"
 
@@ -51,9 +52,9 @@ jobs:
     runs-on: ubuntu-latest
     timeout-minutes: 10
     steps:
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v6
 
-    - uses: actions/setup-python@v5
+    - uses: actions/setup-python@v6
       with:
         python-version: "3.11"
 
@@ -73,7 +74,7 @@ jobs:
     runs-on: ubuntu-latest
     timeout-minutes: 10
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
 
       - name: setup_micromamba
         uses: mamba-org/setup-micromamba@v2
diff --git a/azure-pipelines.yml b/azure-pipelines.yml
@@ -131,7 +131,7 @@ jobs:
     displayName: 'Check installed packages'
   - powershell: |
       cd testsuite
-      pytest MDAnalysisTests --disable-pytest-warnings -n logical --timeout=200 -rsx --cov=MDAnalysis
+      pytest MDAnalysisTests --disable-pytest-warnings -n logical --timeout=200 -rsx --cov=MDAnalysis --durations=50
     displayName: 'Run MDAnalysis Test Suite'
   - script: |
       curl -s https://codecov.io/bash | bash
diff --git a/package/AUTHORS b/package/AUTHORS
@@ -276,6 +276,7 @@ Chronological list of authors
   - Kunj Sinha
   - Ayush Agarwal
   - Amarendra Mohan
+  - Parth Uppal
 
 External code
 -------------
diff --git a/package/CHANGELOG b/package/CHANGELOG
@@ -42,6 +42,7 @@ Fixes
    DSSP by porting upstream PyDSSP 0.9.1 fix (Issue #4913)
 
 Enhancements
+ * Reduces duplication of code in _apply() function (Issue #5247, PR #5294)
  * Added new top-level `MDAnalysis.fetch` module (PR #4943)
  * Added new function `MDAnalysis.fetch.from_PDB` to download structure files from wwPDB
    using `pooch` as optional dependency (Issue #4907, PR #4943) 
diff --git a/package/MDAnalysis/core/selection.py b/package/MDAnalysis/core/selection.py
diff --git a/testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py b/testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py
