Make MD output settings optional #4220
Workflow file for this run
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| name: "CI" | |
| on: | |
| pull_request: | |
| branches: | |
| - main | |
| # Skip CI if changed files only affect the following folders | |
| # - docs: documentation changes don't need code validation | |
| # See here for more details: https://docs.github.com/en/actions/using-workflows/workflow-syntax-for-github-actions#example-excluding-paths | |
| paths-ignore: | |
| - "docs/*" | |
| push: | |
| branches: | |
| - main | |
| schedule: | |
| # At 07:00 UTC on Monday and Thursday. | |
| - cron: "0 7 * * *" | |
| workflow_dispatch: | |
| release: | |
| types: | |
| - published | |
| concurrency: | |
| group: "${{ github.workflow }}-${{ github.ref }}" | |
| cancel-in-progress: true | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| jobs: | |
| tests: | |
| runs-on: ${{ matrix.os }} | |
| name: "💻-${{matrix.os }} 🐍-${{ matrix.python-version }} 🗃️${{ matrix.pydantic-version }} oechem: ${{ matrix.openeye }}" | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: ["ubuntu-latest"] | |
| pydantic-version: [">1"] | |
| python-version: | |
| - "3.10" | |
| - "3.11" | |
| - "3.12" | |
| openeye: ["no"] | |
| include: | |
| - os: "macos-latest" | |
| python-version: "3.12" | |
| pydantic-version: ">1" | |
| - os: "ubuntu-latest" | |
| python-version: "3.11" | |
| pydantic-version: "<2" | |
| - os: "ubuntu-latest" | |
| python-version: "3.11" | |
| pydantic-version: ">1" | |
| openeye: "yes" | |
| - os: "macos-latest" | |
| python-version: "3.12" | |
| pydantic-version: ">1" | |
| omff-version: ">0.13" | |
| openeye: ["no"] | |
| env: | |
| OE_LICENSE: ${{ github.workspace }}/oe_license.txt | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| - name: Get current date | |
| id: date | |
| run: echo "date=$(date +%Y-%m-%d)" >> "${GITHUB_OUTPUT}" | |
| - name: "Setup Micromamba" | |
| uses: mamba-org/setup-micromamba@v1 | |
| with: | |
| micromamba-version: '1.5.6-0' | |
| micromamba-binary-path: ~/.local/bin/micromamba | |
| environment-file: environment.yml | |
| environment-name: openfe_env | |
| cache-environment: true | |
| cache-downloads: true | |
| cache-environment-key: environment-${{ steps.date.outputs.date }} | |
| cache-downloads-key: downloads-${{ steps.date.outputs.date }} | |
| create-args: >- | |
| python=${{ matrix.python-version }} | |
| pydantic=${{ matrix.pydantic-version }} | |
| init-shell: bash | |
| - name: "Install OpenEye" | |
| if: ${{ !github.event.pull_request.head.repo.fork | |
| && matrix.openeye == 'yes' }} | |
| env: | |
| OE_LICENSE_TEXT: ${{ secrets.OE_LICENSE }} | |
| run: | | |
| echo "${OE_LICENSE_TEXT}" > ${OE_LICENSE} | |
| micromamba install -c openeye openeye-toolkits | |
| python -c "import openeye; assert openeye.oechem.OEChemIsLicensed(), 'oechem license check failed!'" | |
| - 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 | |
| pip 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'] }} | |
| DUECREDIT_ENABLE: 'yes' | |
| run: | | |
| pytest -n auto -v --cov=openfe --cov=openfecli --cov-report=xml --durations=10 | |
| - name: codecov-pr | |
| if: ${{ github.repository == 'OpenFreeEnergy/openfe' | |
| && github.event_name == 'pull_request' }} | |
| uses: codecov/codecov-action@v4 | |
| with: | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| file: coverage.xml | |
| fail_ci_if_error: False | |
| verbose: True | |
| flags: fast-tests | |
| - name: codecov-merge | |
| # we only want to upload a slow report if | |
| # 1) it isn't a schedule run | |
| # 2) it wasn't from a PR (we don't run slow tests on PRs) | |
| if: ${{ github.repository == 'OpenFreeEnergy/openfe' | |
| && github.event_name != 'schedule' | |
| && github.event_name != 'pull_request' }} | |
| uses: codecov/codecov-action@v4 | |
| with: | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| file: coverage.xml | |
| fail_ci_if_error: False | |
| verbose: True | |
| flags: slow-tests |