Test intramolecular interactions in polycyclic systems with Amber #3178
Workflow file for this run
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| name: ci | |
| on: | |
| push: | |
| branches: | |
| - main | |
| pull_request: | |
| branches: | |
| - main | |
| schedule: | |
| - cron: "0 0 * * *" | |
| workflow_dispatch: | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| jobs: | |
| test: | |
| name: Test on ${{ matrix.os }}, Python ${{ matrix.python-version }}, OpenMM ${{ matrix.openmm }}, Pydantic ${{ matrix.pydantic-version }}, OpenEye ${{ matrix.openeye }} | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: | |
| - macOS-latest | |
| - ubuntu-latest | |
| python-version: | |
| - "3.9" | |
| - "3.10" | |
| - "3.11" | |
| pydantic-version: | |
| - "1" | |
| - "2" | |
| openeye: | |
| - true | |
| - false | |
| openmm: | |
| - true | |
| - false | |
| exclude: | |
| - openeye: false | |
| python-version: "3.11" | |
| - pydantic-version: "1" | |
| python-version: "3.9" | |
| - pydantic-version: "1" | |
| python-version: "3.10" | |
| env: | |
| OE_LICENSE: ${{ github.workspace }}/oe_license.txt | |
| COV: --cov=openff/interchange --cov-report=xml --cov-config=setup.cfg --cov-append | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Install conda environment | |
| uses: mamba-org/setup-micromamba@v1 | |
| with: | |
| environment-file: devtools/conda-envs/test_env.yaml | |
| create-args: >- | |
| python=${{ matrix.python-version }} | |
| pydantic=${{ matrix.pydantic-version }} | |
| - name: Install package | |
| run: | | |
| # These packages are brought in by conda (via the toolkit) and must be removed manually | |
| # since pip doesn't know about the -base split and does not uninstall the -base package | |
| micromamba remove --force openff-interchange openff-interchange-base | |
| python -m pip install . plugins/ | |
| - name: Install and license OpenEye Toolkits | |
| if: ${{ matrix.openeye == true }} | |
| run: | | |
| micromamba install "openeye-toolkits >=2023.2" -c openeye | |
| echo "${SECRET_OE_LICENSE}" > ${OE_LICENSE} | |
| python -c "from openeye import oechem; assert oechem.OEChemIsLicensed()" | |
| env: | |
| SECRET_OE_LICENSE: ${{ secrets.OE_LICENSE }} | |
| - name: Install OpenMM | |
| if: ${{ matrix.openmm == true }} | |
| run: micromamba install openmm "smirnoff-plugins =2023" -c conda-forge | |
| - name: Uninstall OpenMM | |
| if: ${{ matrix.openmm == false && matrix.openeye == true }} | |
| run: | | |
| micromamba remove openmm mdtraj | |
| # Removing mBuild also removes some leaves, need to re-install them | |
| micromamba install rdkit packmol | |
| - name: Install AmberTools and RDKit | |
| if: ${{ matrix.openeye == false }} | |
| # Unclear why, but around October 2023 this downgrades JAX to broken 0.1.x builds | |
| # and also uninstalls RDKit | |
| run: micromamba install rdkit "ambertools =23" "jax >=0.3" "jaxlib >=0.3" -c conda-forge | |
| - name: Install Foyer | |
| run: micromamba install "foyer >=0.12.1" -c conda-forge -yq | |
| - name: Run tests | |
| if: always() | |
| run: | | |
| python -m pytest $COV openff/interchange/ \ | |
| -r fE -nauto --durations=10 \ | |
| -m "slow or not slow" \ | |
| --ignore=openff/interchange/_tests/energy_tests/test_energies.py | |
| - name: Run small molecule regression tests | |
| if: ${{ matrix.python-version == 3.9 && matrix.openeye == true && matrix.openmm == true }} | |
| run: | | |
| micromamba install deepdiff rich click -c conda-forge | |
| python -m pip install git+https://github.com/openforcefield/interchange-regression-testing.git | |
| create_openmm_systems \ | |
| --input "regression_tests/small-molecule/input-topologies.json" \ | |
| --output "regression_tests/small-molecule/" \ | |
| --using-interchange \ | |
| --force-field "openff-2.0.0.offxml" \ | |
| --n-procs 2 | |
| # Don't trust the interchange version here, for some reason, just put it in a new directory | |
| mkdir regression_tests/small-molecule/omm-systems-interchange-latest/ | |
| mv regression_tests/small-molecule/omm-systems-interchange-*/*xml regression_tests/small-molecule/omm-systems-interchange-latest/ | |
| compare_openmm_systems \ | |
| --input-dir-a "regression_tests/small-molecule/omm-systems-toolkit-0.10.6" \ | |
| --input-dir-b "regression_tests/small-molecule/omm-systems-interchange-latest" \ | |
| --output "regression_tests/differences.json" \ | |
| --settings "regression_tests/default-comparison-settings.json" \ | |
| --expected-changes "regression_tests/toolkit-to-interchange.json" \ | |
| --n-procs 2 | |
| python devtools/scripts/molecule-regressions.py | |
| - name: Run mypy | |
| continue-on-error: true | |
| run: | | |
| # As of 01/23, JAX with mypy is too slow to use without a pre-built cache | |
| # https://github.com/openforcefield/openff-interchange/pull/578#issuecomment-1369979875 | |
| micromamba remove jax | |
| mypy --show-error-codes --namespace-packages -p "openff.interchange" --exclude "openff/interchange/_tests/data/" | |
| mypy --show-error-codes plugins/nonbonded_plugins/ | |
| - name: Codecov | |
| uses: codecov/codecov-action@v4 | |
| with: | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| file: ./coverage.xml | |
| fail_ci_if_error: false |