ci.yaml

name: ci

on:
  push:
    branches:
      - main
      - develop
  pull_request:
    branches:
      - main
      - develop
  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:
          - "3.10"
          - "3.11"
        pydantic-version:
          - "2"
        openeye:
          - true
          - false
        openmm:
          - true
          - false

    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
      with:
        fetch-depth: 0

    - name: Install conda environment
      uses: mamba-org/setup-micromamba@v1
      with:
        micromamba-version: '1.5.10-0'
        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: ${{ matrix.openeye == true }}
      run: |
        micromamba install "openeye-toolkits =2024.1.0" -c openeye
        echo "${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 -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 "lammps >=2023.08.02"

    - 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" "lammps >=2023.08.02" "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 fExs -n logical --durations=10

    - name: Run small molecule regression tests
      if: ${{ matrix.openeye == true && matrix.openmm == true }}
      run: |
        micromamba install "deepdiff =5" rich click -c conda-forge
        python -m pip install git+https://github.com/openforcefield/interchange-regression-testing.git@fa07b62824c39af591142b402bd68103f4043f8b

        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
      if: ${{ matrix.python-version == '3.11' }}
      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
        python -m mypy -p "openff.interchange" --exclude "openff/interchange/_tests/"
        python -m mypy plugins/nonbonded_plugins/

    - name: Codecov
      uses: codecov/codecov-action@v5
      with:
        token: ${{ secrets.CODECOV_TOKEN }}
        files: ./coverage.xml