Protocol to run plain MD simulations #2615
Workflow file for this run
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| name: "CI" | |
| on: | |
| pull_request: | |
| branches: | |
| - main | |
| push: | |
| branches: | |
| - main | |
| schedule: | |
| # At 07:00 UTC on Monday and Thursday. | |
| - cron: "0 7 * * *" | |
| release: | |
| types: | |
| - published | |
| concurrency: | |
| group: "${{ github.workflow }}-${{ github.ref }}" | |
| cancel-in-progress: true | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| jobs: | |
| tests: | |
| runs-on: ${{ matrix.OS }}-latest | |
| name: "tests" | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: ['ubuntu'] | |
| python-version: | |
| - "3.9" | |
| - "3.10" | |
| - "3.11" | |
| include: | |
| - os: 'macos' | |
| python-version: "3.11" | |
| steps: | |
| - uses: actions/checkout@v3 | |
| with: | |
| fetch-depth: 0 | |
| # More info on options: https://github.com/conda-incubator/setup-miniconda | |
| - name: Setup Micromamba | |
| uses: mamba-org/provision-with-micromamba@main | |
| with: | |
| environment-file: environment.yml | |
| environment-name: openfe_env | |
| cache-env: true | |
| cache-downloads: true | |
| extra-specs: | | |
| python==${{ matrix.python-version }} | |
| - name: "Install GUFE from main@HEAD" | |
| run: python -m pip install --no-deps git+https://github.com/OpenFreeEnergy/gufe@main | |
| - name: "Install" | |
| run: python -m pip install --no-deps -e . | |
| - name: "Test imports" | |
| run: | | |
| # if we add more to this, consider changing to for + env vars | |
| python -Ic "import openfe; print(openfe.__version__)" | |
| - name: "Environment Information" | |
| run: | | |
| micromamba info | |
| micromamba list | |
| - name: "Run tests" | |
| env: | |
| # Set the OFE_SLOW_TESTS to True if running a Cron job | |
| OFE_SLOW_TESTS: ${{ fromJSON('{"false":"false","true":"true"}')[github.event_name != 'pull_request'] }} | |
| run: | | |
| pytest -n auto -v --cov=openfe --cov=openfecli --cov-report=xml | |
| - name: codecov | |
| if: ${{ github.repository == 'OpenFreeEnergy/openfe' | |
| && github.event_name == 'pull_request' }} | |
| uses: codecov/codecov-action@v3 | |
| with: | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| file: coverage.xml | |
| fail_ci_if_error: False | |
| verbose: True |