[pre-commit.ci] pre-commit autoupdate #650
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| name: workflows-ci | |
| on: | |
| push: | |
| branches: | |
| - "main" | |
| pull_request: | |
| branches: | |
| - "main" | |
| - "pydantic_2" | |
| - "add-split-model" | |
| schedule: | |
| # Nightly tests run on main by default: | |
| # Scheduled workflows run on the latest commit on the default or base branch. | |
| # (from https://help.github.com/en/actions/reference/events-that-trigger-workflows#scheduled-events-schedule) | |
| - cron: "0 0 * * *" | |
| workflow_dispatch: | |
| merge_group: | |
| concurrency: | |
| group: "${{ github.workflow }}-${{ github.ref }}" | |
| cancel-in-progress: true | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| jobs: | |
| test: | |
| name: Test on ${{ matrix.os }}, Python ${{ matrix.python-version }} | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: [ubuntu-latest] | |
| python-version: ["3.11"] | |
| env: | |
| OE_LICENSE: ${{ github.workspace }}/oe_license.txt | |
| steps: | |
| - name: Checkout Repository | |
| uses: actions/checkout@v3 | |
| - name: Get Info About Runner | |
| run: | | |
| uname -a | |
| df -h | |
| ulimit -a | |
| - name: Get current date | |
| id: date | |
| run: echo "date=$(date +%Y-%m-%d)" >> "${GITHUB_OUTPUT}" | |
| # More info on options: https://github.com/mamba-org/provision-with-micromamba | |
| - name: Setup Conda Environment | |
| uses: mamba-org/setup-micromamba@v1 | |
| with: | |
| micromamba-version: latest | |
| environment-file: devtools/conda-envs/${{ matrix.os }}/workflows.yaml | |
| environment-name: workflows | |
| 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==${{ matrix.python-version }} | |
| - name: Install packages | |
| run: | | |
| micromamba install -n workflows --file devtools/conda-envs/${{ matrix.os }}/data.yaml | |
| micromamba install -n workflows --file devtools/conda-envs/${{ matrix.os }}/simulation.yaml | |
| micromamba install -n workflows --file devtools/conda-envs/${{ matrix.os }}/spectrum.yaml | |
| micromamba install -n workflows --file devtools/conda-envs/${{ matrix.os }}/cli.yaml | |
| micromamba install -n workflows --file devtools/conda-envs/${{ matrix.os }}/docking.yaml | |
| micromamba install -n workflows --file devtools/conda-envs/${{ matrix.os }}/dataviz.yaml | |
| python -m pip install -e ./drugforge-data --no-deps | |
| python -m pip install -e ./drugforge-modeling --no-deps | |
| python -m pip install -e ./drugforge-cli --no-deps | |
| python -m pip install -e ./drugforge-dataviz --no-deps | |
| python -m pip install -e ./drugforge-docking --no-deps | |
| python -m pip install -e ./drugforge-ml --no-deps | |
| python -m pip install -e ./drugforge-simulation --no-deps | |
| python -m pip install -e ./drugforge-spectrum --no-deps | |
| python -m pip install -e ./drugforge-workflows --no-deps | |
| micromamba list | |
| - name: Test OE License & Write License to File | |
| env: | |
| OE_LICENSE_TEXT: ${{ secrets.OE_LICENSE }} | |
| run: | | |
| echo "${OE_LICENSE_TEXT}" > ${OE_LICENSE} | |
| python -c "import openeye; assert openeye.oechem.OEChemIsLicensed(), 'OpenEye license checks failed!'" | |
| - name: Run tests | |
| env: | |
| CDDTOKEN: ${{ secrets.ASAP_CDD_VAULT_TOKEN_READ_ONLY }} | |
| MOONSHOT_CDD_VAULT_NUMBER: ${{ secrets.MOONSHOT_CDD_VAULT_NUMBER }} | |
| run: | | |
| # run each package test suite; append to coverage file | |
| # Exit immediately if a command exits with a non-zero status. | |
| set -e | |
| pytest -n auto --durations=10 -v --cov-report=xml --cov-report=term --color=yes \ | |
| --cov=drugforge-workflows \ | |
| drugforge-workflows/drugforge/workflows/tests | |
| - name: Upload Code Coverage to Codecov | |
| uses: codecov/codecov-action@v3 | |
| # Don't upload coverage scheduled or on fork | |
| if: ${{ github.repository == 'choderalab/drugforge' | |
| && github.event != 'schedule' }} | |
| with: | |
| file: ./coverage.xml | |
| flags: unittests | |
| name: codecov-${{ matrix.os }}-py${{ matrix.python-version }} | |
| fail_ci_if_error: false |