ci.yaml

name: ci

on:
  push:
    branches:
      - "main"
  pull_request:
    branches:
      - "main"
  workflow_dispatch:
  schedule:
    - cron: "7 0 * * *"

defaults:
  run:
    shell: bash -l {0}

jobs:
  test:
    name: Test
    runs-on: ${{ matrix.os }}
    strategy:
      fail-fast: false
      matrix:
        os:
          - macos-latest
          - ubuntu-latest
        python-version:
          - "3.10"
          - "3.11"
          - "3.12"

    env:
      OE_LICENSE: ${{ github.workspace }}/oe_license.txt

    steps:
    - uses: actions/checkout@v4
      with:
        fetch-depth: 0

    - name: Set up conda environment
      uses: mamba-org/setup-micromamba@v2
      with:
        environment-file: devtools/conda-envs/dev.yaml
        create-args: >-
          python=${{ matrix.python-version }}

    - name: Install PASCAL Compiler (MacOS)
      if: startsWith(matrix.os, 'mac')
      run: brew install fpc

    - name: Install PASCAL Compiler (Ubuntu)
      if: startsWith(matrix.os, 'ubuntu')
      run: sudo apt-get install fp-compiler

    - name: Install checkmol
      run: |
        curl https://homepage.univie.ac.at/norbert.haider/download/chemistry/checkmol/checkmol.pas > checkmol.pas
        fpc checkmol.pas -S2

        echo $(pwd) >> $GITHUB_PATH

    - name: Install package
      run: python -m pip install -e .

    - name: Install and license OpenEye Toolkits
      run: |
        echo "${SECRET_OE_LICENSE}" > ${OE_LICENSE}
        python -c "from openeye import oechem; assert oechem.OEChemIsLicensed()"
      env:
        SECRET_OE_LICENSE: ${{ secrets.OE_LICENSE }}

    - name: Run tests
      run: |
        pytest -r fEx -n logical --durations=10 \
          --cov=yammbs/ --cov-report=xml --cov-config=setup.cfg \
          yammbs/

    - name: Run mypy
      # RDKit packages have bad stubs on Linux for some reason
      if: ${{ matrix.python-version == '3.12' && matrix.os == 'macos-latest' }}
      run: pip install -r typing-requirements.txt && python -m mypy -p "yammbs" --exclude "yammbs/_tests"

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