Bump codecov/codecov-action from 3.1.1 to 3.1.4 #1350
Workflow file for this run
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| name: CI | |
| on: | |
| push: | |
| branches: | |
| - "main" | |
| pull_request: | |
| branches: | |
| - "main" | |
| schedule: | |
| - cron: "0 0 * * *" | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| concurrency: | |
| group: "${{ github.workflow }}-${{ github.ref }}" | |
| cancel-in-progress: true | |
| jobs: | |
| test: | |
| name: Test on ${{ matrix.os }}, Python ${{ matrix.python-version }} | |
| runs-on: ${{ matrix.os }} | |
| env: | |
| OE_LICENSE: ${{ github.workspace }}/oe_license.txt | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: [ubuntu-latest, macos-latest] | |
| python-version: ["3.9", "3.10"] # Add 3.11 in with AmberTools 23 | |
| exclude: | |
| - python-version: "3.10" | |
| os: macos-latest | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Setup Conda Environment | |
| uses: mamba-org/setup-micromamba@v1 | |
| with: | |
| environment-file: devtools/conda-envs/test_env.yaml | |
| create-args: >- | |
| python=${{ matrix.python-version }} | |
| - name: License OpenEye | |
| shell: bash -l {0} | |
| run: | | |
| echo "${SECRET_OE_LICENSE}" > ${OE_LICENSE} | |
| python -c "from openeye import oechem; assert oechem.OEChemIsLicensed()" | |
| env: | |
| SECRET_OE_LICENSE: ${{ secrets.OE_LICENSE }} | |
| - name: Install Package | |
| run: | | |
| pip list | |
| micromamba list | |
| micromamba remove --force openmmforcefields | |
| python -m pip install . | |
| - name: Conda Environment Information | |
| run: | | |
| micromamba info | |
| micromamba list | |
| python -c "from openmmforcefields import __version__, __file__; print(__version__, __file__)" | |
| - name: Test Installed Package | |
| run: | | |
| pytest -v --log-cli-level $LOGLEVEL $COV_ARGS --durations=20 \ | |
| openmmforcefields/tests/test_amber_import.py \ | |
| openmmforcefields/tests/test_template_generators.py \ | |
| openmmforcefields/tests/test_system_generator.py \ | |
| -k "not TestEspalomaTemplateGenerator" | |
| env: | |
| COV_ARGS: --cov=openmmforcefields --cov-config=setup.cfg --cov-append --cov-report=xml | |
| LOGLEVEL: "INFO" | |
| KMP_DUPLICATE_LIB_OK: "True" | |
| - name: Test AMBER conversion | |
| run: | | |
| python convert_amber.py --input gaff.yaml --log gaff-tests.csv --verbose | |
| working-directory: ./amber | |
| - name: Test CHARMM conversion | |
| run: | | |
| # TODO: Uncomment these tests when new ParmEd is released | |
| # TODO: Find a way to avoid timing out when running full charmm36.yaml conversion below | |
| # python convert_charmm.py --verbose --in files/waters.yaml && python convert_charmm.py --verbose --in files/charmm36.yaml | |
| # python convert_charmm.py --verbose --in files/waters.yaml | |
| # python convert_charmm.py --verbose | |
| # TODO: Uncomment this when tests are expected to work | |
| # python test_charmm.py --verbose | |
| working-directory: ./charmm | |
| - name: Run docstrings | |
| continue-on-error: True | |
| run: | | |
| pytest --doctest-modules openmmforcefields --ignore=openmmforcefields/tests | |
| - name: Upload coverage report to CodeCov | |
| uses: codecov/codecov-action@v3 | |
| if: ${{ github.repository == 'openmm/openmmforcefields' | |
| && github.event != 'schedule' }} | |
| with: | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| file: ./coverage.xml | |
| fail_ci_if_error: true |