fix #216: angle parameters are not being read from topology file #279
Workflow file for this run
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| 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: ["3.8", "3.9", "3.10", "3.11"] | |
| 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" | |
| # explicitly include a few macOS runners | |
| # (conda-forge GROMACS >= 2021 is compiled to use rdtscp CPU instruction but these | |
| # are not available in the macOS GitHub runner so we need to use a different GROMACS | |
| # version. Try 2018.5 from bioconda. (2021.5 worked previously but not anymore.) | |
| # Locally 2023.1 was successfully tested on Intel macOS 13.5.) | |
| - os: macOS-latest | |
| python-version: "3.11" | |
| gromacs-version: "2018.6" | |
| env: | |
| MPLBACKEND: agg | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: micromamba environment and package installation (Python ${{ matrix.python-version }}) | |
| uses: mamba-org/setup-micromamba@v1 | |
| with: | |
| environment-file: ci/conda-envs/test_env.yaml | |
| condarc: | | |
| channels: | |
| - conda-forge | |
| - bioconda | |
| channel_priority: flexible | |
| cache-downloads: true | |
| cache-environment: true | |
| create-args: >- | |
| python=${{ matrix.python-version }}.*=*_cpython | |
| - name: Python version information ${{ matrix.python-version }} | |
| run: | | |
| python -c "import sys; print(sys.version)" | |
| - name: micromamba environment information | |
| run: | | |
| micromamba info | |
| micromamba list | |
| cat /proc/cpuinfo || (/usr/sbin/system_profiler SPHardwareDataType; /usr/sbin/sysctl -a | grep machdep.cpu) | |
| - name: Install pytest and plugins | |
| run: | | |
| micromamba install pytest pytest-pep8 pytest-cov codecov | |
| - name: Install GROMACS (${{ matrix.gromacs-version }}) | |
| # UGLY HACK/FIX (probably to issues with bioconda packages) | |
| # - For 3.9, micromamba insists on using pypy 3.9 (and --py-pin does not help). | |
| # We can't freeze because then it's not possible to install older GROMACS versions from bioconda. | |
| run: | | |
| micromamba install 'gromacs==${{ matrix.gromacs-version }}' pocl numkit python=${{ matrix.python-version }}.*=*_cpython | |
| - 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@v3 | |
| with: | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| name: codecov-${{ matrix.os }}-py${{ matrix.python-version }} | |
| file: ./coverage.xml | |
| fail_ci_if_error: false |