CI.yml

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-12]
        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@v4
        with:
          token: ${{ secrets.CODECOV_TOKEN }}
          file: ./coverage.xml
          disable_search: true
          fail_ci_if_error: true