Bump codecov/codecov-action from 4 to 5 #6419
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| 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-latest] | |
| 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 }} | |
| # default - will pull down 2.0 which we don't want! | |
| # micromamba-version: latest | |
| # pin to latest 1.x release | |
| micromamba-version: "1.5.10-0" | |
| - 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. | |
| # When possible re-enable this with OE+RDK=True, but for now rdkit builds often have bugs | |
| # in stubs and there are other subtleties (in the source code and builds) that reduce the number | |
| # of available builds. | |
| # See ex https://github.com/rdkit/rdkit/issues/7221 | |
| if: ${{ matrix.rdkit == false && matrix.openeye && matrix.python-version == 3.10 }} | |
| run: mypy -p "openff.toolkit" | |
| - name: Run unit tests | |
| run: | | |
| PYTEST_ARGS+=" --ignore=openff/toolkit/_tests/test_examples.py" | |
| PYTEST_ARGS+=" --ignore=openff/toolkit/_tests/test_links.py" | |
| if [[ "$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@v5 | |
| with: | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| files: ./coverage.xml | |
| disable_search: true | |
| fail_ci_if_error: true |