From 05e51a9ddaedcee8decd70597072b11807aa7af2 Mon Sep 17 00:00:00 2001 From: Irfan Alibay Date: Sun, 25 Oct 2026 08:54:01 +0000 Subject: [PATCH 1/7] Remove orphaned MDAnalysis directories after install Add script to remove orphaned MDAnalysis dist-info directories --- action.yaml | 14 ++++++++++++++ 1 file changed, 14 insertions(+) diff --git a/action.yaml b/action.yaml index 3f71ea3..605c787 100644 --- a/action.yaml +++ b/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 }} From c76a321a38b849784050de07b715c14809b50684 Mon Sep 17 00:00:00 2001 From: Irfan Alibay Date: Sun, 25 Oct 2026 09:02:54 +0000 Subject: [PATCH 2/7] Update MDAnalysis version variables in CI workflow --- .github/workflows/gh-ci.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/workflows/gh-ci.yaml b/.github/workflows/gh-ci.yaml index 29f3d07..ff2adc1 100644 --- a/.github/workflows/gh-ci.yaml +++ b/.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: From a8cdffb653056c7b449f2d238e366b17f9935087 Mon Sep 17 00:00:00 2001 From: Irfan Alibay Date: Sun, 25 Oct 2026 09:34:05 +0000 Subject: [PATCH 3/7] Update CI things --- .github/workflows/gh-ci.yaml | 15 +++++++-------- 1 file changed, 7 insertions(+), 8 deletions(-) diff --git a/.github/workflows/gh-ci.yaml b/.github/workflows/gh-ci.yaml index ff2adc1..5219bb9 100644 --- a/.github/workflows/gh-ci.yaml +++ b/.github/workflows/gh-ci.yaml @@ -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 +113,14 @@ jobs: with: python-version: ${{ matrix.python-version }} add-pip-as-python-dependency: true - architecture: x64 - mamba-version: "*" - channels: conda-forge, defaults + miniforge-version: latest + channels: conda-forge auto-update-conda: true show-channel-urls: true - 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 +159,7 @@ 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 @@ -190,7 +189,7 @@ 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 From dfd5d21f1ff7f57c73b4c2723ea621d9157d456b Mon Sep 17 00:00:00 2001 From: Irfan Alibay Date: Sun, 25 Oct 2026 09:39:29 +0000 Subject: [PATCH 4/7] Update Conda setup options in gh-ci.yaml Remove auto-update and show-channel-urls options from Conda setup. --- .github/workflows/gh-ci.yaml | 2 -- 1 file changed, 2 deletions(-) diff --git a/.github/workflows/gh-ci.yaml b/.github/workflows/gh-ci.yaml index 5219bb9..ab6c4ef 100644 --- a/.github/workflows/gh-ci.yaml +++ b/.github/workflows/gh-ci.yaml @@ -115,8 +115,6 @@ jobs: add-pip-as-python-dependency: true miniforge-version: latest channels: conda-forge - auto-update-conda: true - show-channel-urls: true - name: Setup Python ${{ matrix.python-version }} if: ${{ matrix.installer == 'pip' }} From 9c72e13b3bf6f268a524aaf89a8f3938d19a0b50 Mon Sep 17 00:00:00 2001 From: Irfan Alibay Date: Sun, 25 Oct 2026 09:47:55 +0000 Subject: [PATCH 5/7] Disable auto-update for conda in CI workflow --- .github/workflows/gh-ci.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/gh-ci.yaml b/.github/workflows/gh-ci.yaml index ab6c4ef..1157732 100644 --- a/.github/workflows/gh-ci.yaml +++ b/.github/workflows/gh-ci.yaml @@ -115,6 +115,7 @@ jobs: add-pip-as-python-dependency: true miniforge-version: latest channels: conda-forge + auto-update-conda: false - name: Setup Python ${{ matrix.python-version }} if: ${{ matrix.installer == 'pip' }} From 783bf506a080d6f2c3e64023c93bd521ecd304e8 Mon Sep 17 00:00:00 2001 From: Irfan Alibay Date: Sun, 25 Oct 2026 09:54:17 +0000 Subject: [PATCH 6/7] Specify miniforge version in CI workflow --- .github/workflows/gh-ci.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/gh-ci.yaml b/.github/workflows/gh-ci.yaml index 1157732..ca1191c 100644 --- a/.github/workflows/gh-ci.yaml +++ b/.github/workflows/gh-ci.yaml @@ -113,7 +113,7 @@ jobs: with: python-version: ${{ matrix.python-version }} add-pip-as-python-dependency: true - miniforge-version: latest + miniforge-version: "26.7.2-1" channels: conda-forge auto-update-conda: false From fb35f89e532e7ba8f486715b6531dbaf99c1ac5b Mon Sep 17 00:00:00 2001 From: Irfan Alibay Date: Sun, 25 Oct 2026 15:02:11 +0000 Subject: [PATCH 7/7] Update gh-ci.yaml --- .github/workflows/gh-ci.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/gh-ci.yaml b/.github/workflows/gh-ci.yaml index ca1191c..692cffe 100644 --- a/.github/workflows/gh-ci.yaml +++ b/.github/workflows/gh-ci.yaml @@ -191,7 +191,7 @@ jobs: - 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 }}