Ignore examples/ path when searching for coverage report
#6267
Workflow file for this run
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| name: CI | |
| on: | |
| push: | |
| branches: | |
| - "main" | |
| - "maintenance/.*" | |
| pull_request: | |
| branches: | |
| - "main" | |
| - "maintenance/.*" | |
| 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 * * *" | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| jobs: | |
| test: | |
| if: (github.event_name == 'schedule' && github.repository == 'openforcefield/openff-toolkit') || (github.event_name != 'schedule') | |
| name: Test on ${{ matrix.os }}, Python ${{ matrix.python-version }}, RDKit=${{ matrix.rdkit }}, OpenEye=${{ matrix.openeye }} | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: [ubuntu-latest, macos-12] | |
| python-version: ["3.10", "3.11", "3.12"] | |
| rdkit: [true, false] | |
| openeye: [true, false] | |
| exclude: | |
| - rdkit: false | |
| openeye: false | |
| - openeye: true | |
| python-version: "3.11" | |
| - openeye: true | |
| python-version: "3.12" | |
| env: | |
| OE_LICENSE: ${{ github.workspace }}/oe_license.txt | |
| PACKAGE: openff | |
| PYTEST_ARGS: -r fE --tb=short -nauto | |
| COV: --cov=openff/toolkit --cov-config=setup.cfg --cov-append --cov-report=xml | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 2 | |
| - name: Set environment variables | |
| run: | | |
| if [[ ${{ matrix.openeye }} == true && ${{ matrix.rdkit }} == true ]]; then | |
| echo "ENVFILE=test_env" >> $GITHUB_ENV | |
| echo "JOBNAME=RDKit and OpenEye" >> $GITHUB_ENV | |
| echo "TOOLKIT_CHECKS=RDKIT OPENEYE" >> $GITHUB_ENV | |
| echo "PACKAGES_TO_REMOVE=" >> $GITHUB_ENV | |
| fi | |
| if [[ ${{ matrix.openeye }} == true && ${{ matrix.rdkit }} == false ]]; then | |
| echo "ENVFILE=openeye" >> $GITHUB_ENV | |
| echo "JOBNAME=OpenEye" >> $GITHUB_ENV | |
| echo "TOOLKIT_CHECKS=OPENEYE" >> $GITHUB_ENV | |
| echo "PACKAGES_TO_REMOVE=ambertools rdkit" >> $GITHUB_ENV | |
| fi | |
| if [[ ${{ matrix.openeye }} == false && ${{ matrix.rdkit }} == true ]]; then | |
| echo "ENVFILE=rdkit" >> $GITHUB_ENV | |
| echo "JOBNAME=RDKit" >> $GITHUB_ENV | |
| echo "TOOLKIT_CHECKS=RDKIT" >> $GITHUB_ENV | |
| echo "PACKAGES_TO_REMOVE=openeye-toolkits" >> $GITHUB_ENV | |
| fi | |
| - name: Install environment with ${{ env.JOBNAME }} | |
| uses: mamba-org/setup-micromamba@v1 | |
| with: | |
| environment-file: devtools/conda-envs/${{ env.ENVFILE }}.yaml | |
| create-args: >- | |
| python=${{ matrix.python-version }} | |
| - name: Make oe_license.txt file from GH org secret "OE_LICENSE" | |
| env: | |
| OE_LICENSE_TEXT: ${{ secrets.OE_LICENSE }} | |
| run: echo "${OE_LICENSE_TEXT}" > ${OE_LICENSE} | |
| - name: Install package | |
| run: | | |
| # While Interchange is being installed with pip, there is no need to | |
| # force uninstall openff-toolkit-base since it's only pulled in when | |
| # Interchange is installed with conda. Un-comment this when testing | |
| # against a conda build of Interchange. (It may also be pulled down | |
| # by `openmmforcefields` and should be removed in that case a well.) | |
| micromamba remove --force openff-toolkit openff-toolkit-base | |
| python -m pip install . | |
| - name: Install test plugins | |
| run: python -m pip install utilities/test_plugins | |
| - name: Remove undesired toolkits | |
| run: | | |
| if [ ! -z "${{ env.PACKAGES_TO_REMOVE }}" ]; then | |
| for cpkg in ${{ env.PACKAGES_TO_REMOVE }}; do | |
| if [[ $(micromamba list | grep $cpkg) ]]; then micromamba remove --force $cpkg --yes ; fi | |
| done | |
| fi | |
| - name: Remove NAGL if no RDKit | |
| if: ${{ matrix.rdkit == false }} | |
| run: micromamba remove --force openff-nagl-base --yes | |
| - name: Check installed toolkits | |
| run: | | |
| for tk in ${{ env.TOOLKIT_CHECKS }}; do | |
| python -c "from openff.toolkit.utils.toolkits import ${tk}_AVAILABLE; assert ${tk}_AVAILABLE, '${tk} unavailable'" | |
| done | |
| - name: Check uninstalled toolkits | |
| run: | | |
| if [ ! -z "${{ env.PACKAGES_TO_REMOVE }}" ]; then | |
| for tk in ${{ env.PACKAGES_TO_REMOVE }}; do | |
| TK=$(echo ${tk%-*} | tr 'a-z' 'A-Z') | |
| python -c "from openff.toolkit.utils.toolkits import ${TK}_AVAILABLE; assert not ${TK}_AVAILABLE, '${TK} available'" | |
| done | |
| fi | |
| - name: Environment Information | |
| run: | | |
| micromamba info | |
| micromamba list | |
| - name: Check links | |
| if: ${{ matrix.rdkit == true && matrix.openeye == true }} | |
| run: pytest -r fE --tb=short openff/toolkit/_tests/test_links.py | |
| - name: Run mypy | |
| # subtle differences in Python/mypy versions, just keep it passing on one | |
| if: ${{ matrix.rdkit == true && matrix.openeye && matrix.python-version == 3.10 }} | |
| run: mypy -p "openff.toolkit" | |
| - name: Run unit tests | |
| run: | | |
| PYTEST_ARGS+=" --ignore=openff/toolkit/_tests/test_examples.py" | |
| PYTEST_ARGS+=" --ignore=openff/toolkit/_tests/test_links.py" | |
| if [[ "$GITHUB_EVENT_NAME" == "schedule" ]]; then | |
| PYTEST_ARGS+=" --runslow" | |
| fi | |
| python -m pytest --durations=20 $PYTEST_ARGS $COV | |
| - name: Run code snippets in docs | |
| if: ${{ matrix.rdkit == true && matrix.openeye == true }} | |
| run: pytest -v --no-cov --doctest-glob="docs/*.rst" --doctest-glob="docs/*.md" docs/ | |
| - name: Run notebooks in docs | |
| if: ${{ matrix.rdkit == true && matrix.openeye == true }} | |
| run: pytest -v --no-cov --nbval --ignore docs/_build/ docs/ | |
| - name: Run examples in docstrings | |
| if: ${{ matrix.rdkit == true && matrix.openeye == true }} | |
| run: | | |
| pytest openff \ | |
| -v -x -n logical --no-cov --doctest-modules \ | |
| --ignore-glob='openff/toolkit/_tests*' \ | |
| --ignore=openff/toolkit/data/ \ | |
| --ignore=openff/toolkit/utils/utils.py | |
| - name: Codecov | |
| uses: codecov/codecov-action@v4 | |
| with: | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| file: ./coverage.xml | |
| disable_search: true | |
| fail_ci_if_error: true |