Do not cast residue ids/numbers in Topology.from_openmm
#4488
Workflow file for this run
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| 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 |