Bump codecov/codecov-action from 4 to 5 #253
Workflow file for this run
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| name: ci | |
| on: | |
| push: | |
| branches: | |
| - "main" | |
| - "add-torsion-models" | |
| pull_request: | |
| branches: | |
| - "main" | |
| - "add-torsion-models" | |
| workflow_dispatch: | |
| schedule: | |
| - cron: "7 0 * * *" | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| jobs: | |
| test: | |
| name: Test | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: | |
| - macos-latest | |
| - ubuntu-latest | |
| python-version: | |
| - "3.10" | |
| - "3.11" | |
| - "3.12" | |
| env: | |
| OE_LICENSE: ${{ github.workspace }}/oe_license.txt | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up conda environment | |
| uses: mamba-org/setup-micromamba@v2 | |
| with: | |
| environment-file: devtools/conda-envs/dev.yaml | |
| create-args: >- | |
| python=${{ matrix.python-version }} | |
| - name: Install PASCAL Compiler (MacOS) | |
| if: startsWith(matrix.os, 'mac') | |
| run: brew install fpc | |
| - name: Install PASCAL Compiler (Ubuntu) | |
| if: startsWith(matrix.os, 'ubuntu') | |
| run: sudo apt-get install fp-compiler | |
| - name: Install checkmol | |
| run: | | |
| curl https://homepage.univie.ac.at/norbert.haider/download/chemistry/checkmol/checkmol.pas > checkmol.pas | |
| fpc checkmol.pas -S2 | |
| echo $(pwd) >> $GITHUB_PATH | |
| - name: Install package | |
| run: python -m pip install -e . | |
| - name: Install and license OpenEye Toolkits | |
| run: | | |
| echo "${SECRET_OE_LICENSE}" > ${OE_LICENSE} | |
| python -c "from openeye import oechem; assert oechem.OEChemIsLicensed()" | |
| env: | |
| SECRET_OE_LICENSE: ${{ secrets.OE_LICENSE }} | |
| - name: Run tests | |
| run: | | |
| pytest -r fEx -n logical --durations=10 \ | |
| --cov=yammbs/ --cov-report=xml --cov-config=setup.cfg \ | |
| yammbs/ | |
| - name: Run mypy | |
| # RDKit packages have bad stubs on Linux for some reason | |
| if: ${{ matrix.python-version == '3.12' && matrix.os == 'macos-latest' }} | |
| run: pip install -r typing-requirements.txt && python -m mypy -p "yammbs" --exclude "yammbs/_tests" | |
| - name: CodeCov | |
| uses: codecov/codecov-action@v5 | |
| with: | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| file: ./coverage.xml | |
| flags: unittests |