CI #743
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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 * * *" | |
| workflow_dispatch: | |
| concurrency: | |
| group: "${{ github.workflow }}-${{ github.ref }}" | |
| cancel-in-progress: true | |
| defaults: | |
| run: | |
| shell: bash -leo pipefail {0} | |
| jobs: | |
| tests: | |
| runs-on: ${{ matrix.os }} | |
| name: "💻-${{matrix.os }} 🐍-${{ matrix.python-version }} 🔧-${{ matrix.bespokefit }}" | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: ["ubuntu-22.04", "macos-latest"] | |
| bespokefit: ["true", "false"] | |
| python-version: | |
| - "3.11" | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Get current date | |
| id: date | |
| run: echo "date=$(date +%Y-%m-%d)" >> "${GITHUB_OUTPUT}" | |
| - name: "Setup Micromamba" | |
| uses: mamba-org/setup-micromamba@v2 | |
| with: | |
| environment-file: conda-envs/${{ matrix.os }}-bespokefit-${{ matrix.bespokefit}}.yaml | |
| environment-name: openpharmflow | |
| cache-environment: true | |
| cache-downloads: true | |
| cache-environment-key: environment-${{ steps.date.outputs.date }} | |
| cache-downloads-key: downloads-${{ steps.date.outputs.date }} | |
| create-args: >- | |
| nbval | |
| pytest | |
| pytest-cov | |
| pytest-xdist | |
| python=${{ matrix.python-version }} | |
| packmol==21.0.4 | |
| init-shell: bash | |
| - name: "Install" | |
| run: python -m pip install --no-deps -e . | |
| - name: "Environment Information" | |
| run: | | |
| micromamba info | |
| micromamba list | |
| - name: "Run tests" | |
| run: pytest -n logical --nbval-lax --nbval-cell-timeout=3000 --dist loadscope -v --cov=openpharmmdflow --cov-report=xml --junitxml=junit.xml -o junit_family=legacy --durations=10 | |
| - name: codecov | |
| if: ${{ github.repository == 'omsf/OpenPharmMDFlow' }} | |
| uses: codecov/codecov-action@v4 | |
| with: | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| file: coverage.xml | |
| fail_ci_if_error: False | |
| verbose: True | |
| - name: Upload test results to Codecov | |
| if: ${{ !cancelled() }} | |
| uses: codecov/test-results-action@v1 | |
| with: | |
| token: ${{ secrets.CODECOV_TOKEN }} |