Fix stage checking #908
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| name: CI | |
| on: | |
| # run once every Sunday at 5:55 UTC | |
| schedule: | |
| - cron: "55 5 * * 1" | |
| push: | |
| branches: | |
| - "develop" | |
| - "master" | |
| pull_request: | |
| branches: | |
| - "develop" | |
| concurrency: | |
| group: "${{ github.ref }}-${{ github.head_ref }}" | |
| cancel-in-progress: true | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| jobs: | |
| test: | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| # only test all GROMACS version on the oldest and latest | |
| # Python to keep the testing matrix manageable and only use 2 | |
| # macos runners (latest GROMACS, oldest and latest Python) | |
| os: [ubuntu-latest] | |
| python-version: ["3.10"] | |
| gromacs-version: ["4.6.5", "2018.6", "2020.6", "2021.1", "2022.4", "2023.1"] | |
| include: | |
| - os: ubuntu-latest | |
| python-version: "3.9" | |
| gromacs-version: "2023.1" | |
| - os: macos-latest | |
| python-version: "3.10" | |
| gromacs-version: "2023.1" | |
| env: | |
| MPLBACKEND: agg | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: mamba environment and package installation | |
| uses: mamba-org/setup-micromamba@v2 | |
| with: | |
| environment-file: devtools/conda-envs/test_env.yaml | |
| condarc: | | |
| channels: | |
| - conda-forge | |
| - bioconda | |
| channel_priority: flexible | |
| cache-downloads: true | |
| cache-environment: true | |
| create-args: >- | |
| python=${{ matrix.python-version }} | |
| - name: Python version information | |
| run: | | |
| python -c "import sys; print(sys.version)" | |
| - name: micromamba environment information | |
| run: | | |
| micromamba info | |
| micromamba list | |
| - name: Install pybol (fixture staging tool) | |
| run: | | |
| python -m pip install pybol | |
| - name: Install GROMACS (${{ matrix.gromacs-version }}) | |
| # include mdanalysis here AGAIN to work around micromamba removing mdanalysis | |
| # while downgrading libxml2 (see issue #252) | |
| run: | | |
| micromamba install 'gromacs==${{ matrix.gromacs-version }}' pocl mdanalysis | |
| - name: Install package (with no dependencies) | |
| run: | | |
| python -m pip install . --no-deps | |
| - name: Run tests | |
| run: | | |
| pytest -v --durations=20 --cov=mdpow --cov-report=xml --color=yes ./mdpow/tests | |
| - name: Codecov | |
| uses: codecov/codecov-action@v4 | |
| with: | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| name: codecov-${{ matrix.os }}-py${{ matrix.python-version }} | |
| file: ./coverage.xml | |
| fail_ci_if_error: true |