Fix nightly and conda CI #4526
Workflow file for this run
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: Examples | |
| on: | |
| push: | |
| branches: | |
| - "main" | |
| - "maintenance/.+" | |
| pull_request: | |
| branches: | |
| - "main" | |
| - "maintenance/.+" | |
| 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: ${{ 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"] | |
| rdkit: [true, false] | |
| openeye: [true, false] | |
| exclude: | |
| - rdkit: false | |
| openeye: false | |
| - rdkit: true | |
| openeye: true | |
| env: | |
| OE_LICENSE: ${{ github.workspace }}/oe_license.txt | |
| PACKAGE: openff | |
| PYTEST_ARGS: -r fE -v -x --tb=short -nauto | |
| NB_ARGS: --nbval-lax --dist loadscope --ignore=examples/deprecated | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 2 | |
| - name: Set environment variables | |
| run: | | |
| if [[ ${{ matrix.openeye }} == true && ${{ matrix.rdkit }} == false ]]; then | |
| echo "ENVFILE=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 "TOOLKIT_CHECKS=RDKIT" >> $GITHUB_ENV | |
| echo "PACKAGES_TO_REMOVE=openeye-toolkits" >> $GITHUB_ENV | |
| fi | |
| - name: Install conda environment with ${{ env.ENVFILE }} | |
| uses: mamba-org/setup-micromamba@v1 | |
| with: | |
| environment-file: devtools/conda-envs/${{env.ENVFILE}}-examples.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: Additional info about the build | |
| run: | | |
| uname -a | |
| df -h | |
| ulimit -a | |
| - name: Make oe_license.txt file from GH org secret "OE_LICENSE" | |
| env: | |
| OE_LICENSE_TEXT: ${{ secrets.OE_LICENSE }} | |
| run: | | |
| echo "${OE_LICENSE_TEXT}" > ${OE_LICENSE} | |
| - name: Install package | |
| run: | | |
| # Maybe remove the packaged openff-toolkit, installed as a dependency of openmmforcefields | |
| # and/or Interchange | |
| micromamba remove --force openff-toolkit-base | |
| python -m pip install . | |
| - name: Remove undesired toolkits | |
| run: | | |
| # If openmmforcefields is included in either environment file, | |
| # remove RDKit and AmberTools brought in by it. Currently it's not included, | |
| # so don't remove it. | |
| if [ ! -z "${{ env.PACKAGES_TO_REMOVE }}" ]; then | |
| for cpkg in ${{ env.PACKAGES_TO_REMOVE }}; do | |
| if [[ $(conda list | grep $cpkg) ]]; then micromamba remove --force $cpkg --yes ; fi | |
| done | |
| fi | |
| - name: Reinstall ParmEd | |
| if: ${{ matrix.rdkit == false }} | |
| run: | | |
| micromamba remove --force parmed --yes | |
| # See #1531, #1532, eventually this should work with 4 or 3 and 4 | |
| micromamba install "parmed =3" -c conda-forge -yq | |
| # Needed for other examples to run, but were removed incidentally alongside AmberTools | |
| micromamba install h5py -c conda-forge -yq | |
| - 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: | | |
| conda info | |
| conda list | |
| - name: Run example scripts | |
| run: | | |
| if [[ ${{ matrix.rdkit }} == false ]]; then | |
| PYTEST_ARGS+=" --ignore=examples/check_dataset_parameter_coverage" | |
| PYTEST_ARGS+=" --ignore=examples/QCArchive_interface" | |
| fi | |
| pytest $PYTEST_ARGS openff/toolkit/_tests/test_examples.py | |
| - name: Run example notebooks | |
| run: | | |
| if [[ ${{ matrix.rdkit }} == false ]]; then | |
| NB_ARGS+=" --ignore=examples/QCArchive_interface" | |
| NB_ARGS+=" --ignore=examples/visualization" | |
| NB_ARGS+=" --ignore=examples/check_dataset_parameter_coverage" | |
| NB_ARGS+=" --ignore=examples/conformer_energies" | |
| NB_ARGS+=" --ignore=examples/using_smirnoff_in_amber_or_gromacs" | |
| NB_ARGS+=" --ignore=examples/using_smirnoff_with_amber_protein_forcefield" | |
| NB_ARGS+=" --ignore=examples/SMIRNOFF_simulation" | |
| NB_ARGS+=" --ignore=examples/toolkit_showcase" | |
| fi | |
| # GROMACS builds are not stable on macOS + GHA | |
| if [[ ${{ matrix.os }} == macos-latest ]]; then | |
| NB_ARGS+=" --ignore=examples/using_smirnoff_in_amber_or_gromacs/" | |
| fi | |
| python -m pytest $PYTEST_ARGS $NB_ARGS examples |