unpin micromamba #413
Workflow file for this run
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| name: CI | |
| on: | |
| # run every month on day 14 and 28 at 4:44 UTC | |
| schedule: | |
| - cron: "44 4 14,28 * *" | |
| push: | |
| branches: | |
| - "main" | |
| pull_request: | |
| branches: | |
| - "main" | |
| 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: | |
| os: [ubuntu-latest] | |
| python-version: ["3.9", "3.10", "3.11", "3.12"] | |
| gromacs-version: ["2023.1"] | |
| # Test other GROMACS versions selectively on a recent Python. | |
| # On macOS only test one GROMACS version and two Python versions | |
| # to keep the testing matrix manageable. | |
| include: | |
| - os: ubuntu-latest | |
| python-version: "3.11" | |
| gromacs-version: "4.6.5" | |
| - os: ubuntu-latest | |
| python-version: "3.11" | |
| gromacs-version: "2018.6" | |
| - os: ubuntu-latest | |
| python-version: "3.11" | |
| gromacs-version: "2019.1" | |
| - os: ubuntu-latest | |
| python-version: "3.11" | |
| gromacs-version: "2020.6" | |
| - os: ubuntu-latest | |
| python-version: "3.11" | |
| gromacs-version: "2021.1" | |
| - os: ubuntu-latest | |
| python-version: "3.11" | |
| gromacs-version: "2022.4" | |
| - os: ubuntu-latest | |
| python-version: "3.11" | |
| gromacs-version: "2023.4" | |
| - os: ubuntu-latest | |
| python-version: "3.11" | |
| gromacs-version: "2024.2" | |
| # explicitly include a few macOS runners; finding a version that works | |
| # on the GH runners is tricky (eg some are compiled for rdtscp CPU instructions | |
| # that are not available); 2018.6 (bioconda) worked for a while, but then stopped | |
| # being resolved. 2024.2 (conda-forge) runs at the moment | |
| - os: macOS-latest | |
| python-version: "3.11" | |
| gromacs-version: "2024.2" | |
| - os: macOS-latest | |
| python-version: "3.12" | |
| gromacs-version: "2024.2" | |
| env: | |
| MPLBACKEND: agg | |
| steps: | |
| - name: git checkout | |
| uses: actions/checkout@v4 | |
| with: | |
| fetch-tags: true | |
| - name: micromamba package and testing environment installation (Python ${{ matrix.python-version }}, GROMACS ${{ matrix.gromacs-version }}) | |
| uses: mamba-org/setup-micromamba@v1 | |
| with: | |
| environment-file: ci/conda-envs/test_env.yaml | |
| condarc: | | |
| channels: | |
| - conda-forge | |
| - bioconda | |
| channel_priority: flexible | |
| cache-downloads: true | |
| cache-environment: true | |
| create-args: >- | |
| python=${{ matrix.python-version }}.*=*_cpython | |
| gromacs==${{ matrix.gromacs-version }} | |
| - name: Python version information ${{ matrix.python-version }} | |
| run: | | |
| python -c "import sys; print(sys.version)" | |
| - name: micromamba environment information | |
| run: | | |
| micromamba info | |
| micromamba list | |
| cat /proc/cpuinfo || (/usr/sbin/system_profiler SPHardwareDataType; /usr/sbin/sysctl -a | grep machdep.cpu) | |
| micromamba list | grep gromacs | grep ${{ matrix.gromacs-version }} | |
| micromamba list | grep python | grep ${{ matrix.python-version }} | |
| - name: Install package (with no dependencies) | |
| run: | | |
| python -m pip install --no-deps . | |
| - name: Run tests | |
| run: | | |
| pytest -v --disable-pytest-warnings --durations=20 --low-performance --cov=gromacs --cov-report=xml --color=yes ./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: false |