Remove orphaned MDAnalysis directories after install

.github/workflows/gh-ci.yaml

@@ -26,9 +26,9 @@ defaults:
     shell: bash -l {0}
 
 env:
-  MDANALYSIS_DEVELOP_VERSION: "2.11.0-dev0"
-  MDANALYSIS_LATEST_RELEASE: "2.10.0"
-  MDANALYSIS_PREVIOUS_RELEASE: "2.9.0"
+  MDANALYSIS_DEVELOP_VERSION: "2.12.0-dev0"
+  MDANALYSIS_LATEST_RELEASE: "2.11.0"
+  MDANALYSIS_PREVIOUS_RELEASE: "2.10.0"
 
 jobs:
   gen-python-matrix:
@@ -39,7 +39,7 @@ jobs:
       oldest-python: ${{ steps.get-compatible-python.outputs.oldest-python }}
       stable-python: ${{ steps.get-compatible-python.outputs.stable-python }}
     steps:
-      - uses: actions/setup-python@v6
+      - uses: actions/setup-python@v7
         with:
           python-version: "3.13"
 
@@ -78,7 +78,7 @@ jobs:
             mdanalysis-version: "latest"
 
     steps:
-    - uses: actions/checkout@v6
+    - uses: actions/checkout@v7
 
     - id: environment-setup
       run: |
@@ -113,15 +113,13 @@ jobs:
       with:
         python-version: ${{ matrix.python-version }}
         add-pip-as-python-dependency: true
-        architecture: x64
-        mamba-version: "*"
-        channels: conda-forge, defaults
-        auto-update-conda: true
-        show-channel-urls: true
+        miniforge-version: "26.7.2-1"
+        channels: conda-forge
+        auto-update-conda: false
 
     - name: Setup Python ${{ matrix.python-version }}
       if: ${{ matrix.installer == 'pip' }}
-      uses: actions/setup-python@v6
+      uses: actions/setup-python@v7
       with:
         python-version: ${{ matrix.python-version }}
 
@@ -160,7 +158,7 @@ jobs:
     needs: gen-python-matrix
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v6
+      - uses: actions/checkout@v7
 
       - name: Install mamba Python ${{ needs.gen-python-matrix.outputs.stable-python }}
         uses: mamba-org/setup-micromamba@v3
@@ -190,10 +188,10 @@ jobs:
     needs: gen-python-matrix
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v6
+      - uses: actions/checkout@v7
 
       - name: Setup Python ${{ needs.gen-python-matrix.outputs.stable-python }}
-        uses: actions/setup-python@v6
+        uses: actions/setup-python@v7
         with:
           python-version: ${{ needs.gen-python-matrix.outputs.stable-python }}
 

action.yaml

@@ -70,6 +70,20 @@ runs:
           python -m pip uninstall -y MDAnalysis MDAnalysisTests
         done
 
+        # conda can leave behind partial dist-info directories when a pip
+        # install was overwritten by a conda install (e.g. pip-only files such
+        # as sboms/ in wheels from 2.11.0 on). These have no METADATA/RECORD,
+        # so pip can't uninstall them and fails on the next install.
+        python - <<'EOF'
+        import pathlib, shutil, sysconfig
+        for sp in {sysconfig.get_paths()[k] for k in ("purelib", "platlib")}:
+            for d in pathlib.Path(sp).glob("*.dist-info"):
+                name = d.name.split("-")[0].lower()
+                if name in ("mdanalysis", "mdanalysistests") and not (d / "METADATA").exists():
+                    print(f"Removing orphaned {d}")
+                    shutil.rmtree(d)
+        EOF
+
     - name: Setup install lines
       id: setup-install-line
       shell: ${{ inputs.shell }}