gh-ci.yaml

name: GH Actions CI
on:
  push:
    branches:
      - main
  pull_request:
    branches:
      - main
  schedule:
    # weekly tests, Sundays at midnight
    - cron: "0 0 * * 0"

concurrency:
  # Specific group naming so CI is only cancelled
  # within same PR or on merge to main
  group: ${{ github.ref }}-${{ github.head_ref }}-${{ github.workflow }}
  cancel-in-progress: true

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

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

jobs:
  main_tests:
    name: CI (${{ matrix.os }}, py-${{ matrix.python-version }}, rdkit=${{ matrix.include-rdkit }}, openeye=${{ matrix.include-openeye }}, dgl=${{ matrix.include-dgl }}), pydantic=${{ matrix.pydantic-version }}
    runs-on: ${{ matrix.os }}
    strategy:
        fail-fast: false
        matrix:
          os: [macOS-latest, ubuntu-latest]
          python-version: ["3.10", "3.11", "3.12"]
          pydantic-version: ["1", "2"]
          include-rdkit: [true, false]
          include-openeye: [true, false]
          include-dgl: [true, false]
          exclude:
            - include-rdkit: false
              include-openeye: false
            # broken OpenMM build for Mac on 3.10
            - os: "macOS-latest"
              python-version: "3.10"
            # no dgl for 3.12 yet
            - include-dgl: true
              python-version: "3.12"
            # no openeye for 3.12 yet
            - include-openeye: true
              python-version: "3.12"


    steps:
    - uses: actions/checkout@v3

    - name: Build information
      run: |
        uname -a
        df -h
        ulimit -a

    - name: Install environment
      uses: mamba-org/setup-micromamba@v1
      with:
        environment-file: devtools/conda-envs/test_env_dgl_${{ matrix.include-dgl }}.yaml
        create-args: >-
          python=${{ matrix.python-version }}
          pydantic=${{ matrix.pydantic-version }}

    - name: Install package
      run: |
        python -m pip install . --no-deps

    - name: Python information
      run: |
        which python
        conda info
        conda list

    - uses: ./.github/actions/include-openeye
      if: matrix.include-openeye == true
      with:
        openeye-license-text: ${{ secrets.OE_LICENSE }}
        openeye-license-file: ${{ env.OE_LICENSE }}

      
    - name: Uninstall OpenEye
      if: matrix.include-openeye == false
      run: conda remove --force openeye --yes || echo "openeye not installed"

    - name: Uninstall RDKit
      if: matrix.include-rdkit == false
      run: conda remove --force rdkit --yes || echo "rdkit not installed"

    - name: Check toolkit installations
      shell: bash -l -c "python -u {0}"
      run: |
        from openff.toolkit.utils.toolkits import OPENEYE_AVAILABLE, RDKIT_AVAILABLE
        assert str(OPENEYE_AVAILABLE).lower() == '${{ matrix.include-openeye }}'
        assert str(RDKIT_AVAILABLE).lower() == '${{ matrix.include-rdkit }}'

    - name: Run tests
      run: |
        python -m pytest -n 4 -v --cov=openff/nagl --cov-config=setup.cfg --cov-append --cov-report=xml --color=yes openff/nagl/

    - name: codecov
      uses: codecov/codecov-action@v3
      with:
        token: ${{ secrets.CODECOV_TOKEN }}
        file: ./coverage.xml
        verbose: True
        # name: codecov-${{ matrix.os }}-py${{ matrix.python-version }}
  
  nightly_check:
    name: Nightly check
    runs-on: ${{ matrix.os }}
    strategy:
        fail-fast: false
        matrix:
          os: [macOS-latest, ubuntu-latest]
          python-version: ["3.10", "3.11", "3.12"]
        exclude:
          # mdtraj currently doesn't support MacOS py3.12
          - os: "macOS-latest"
            python-version: "3.12"


    steps:
    - uses: actions/checkout@v3

    - name: Build information
      run: |
        uname -a
        df -h
        ulimit -a

    - name: Install environment
      uses: mamba-org/setup-micromamba@v1
      with:
        environment-file: devtools/conda-envs/nightly.yaml
        create-args: >-
          python=${{ matrix.python-version }}
          pydantic=2
    
    - name: Install nightly pytorch-lightning and DGL
      run: |
        python -m pip install --pre dgl -f https://data.dgl.ai/wheels-test/repo.html
        python -m pip install --pre dglgo -f https://data.dgl.ai/wheels-test/repo.html
        python -m pip install https://github.com/Lightning-AI/lightning/archive/refs/heads/master.zip -U  

    - name: Install package
      run: |
        python -m pip install . --no-deps

    - name: Python information
      run: |
        which python
        conda info
        conda list

    - name: Run tests
      run: |
        python -m pytest -n 4 -v --cov=openff/nagl --cov-config=setup.cfg --cov-append --cov-report=xml --color=yes openff/nagl/


  pylint_check:
    runs-on: ubuntu-latest

    steps:
    - uses: actions/checkout@v3

    - name: Set up Python
      uses: actions/setup-python@v3
      with:
        python-version: 3.9

    - name: Install Pylint
      run: |
        which pip
        which python
        pip install pylint

    - name: Run Pylint
      env:
        PYLINTRC: .pylintrc
      run: |
        pylint openff-nagl


  pypi_check:
    runs-on: ubuntu-latest

    steps:
    - uses: actions/checkout@v3

    - name: Set up Python
      uses: actions/setup-python@v3
      with:
        python-version: 3.9

    - name: Install dependencies
      run: |
        pip install setuptools twine

    - name: Build package
      run: |
        python setup.py sdist

    - name: Check package build
      run: |
        DISTRIBUTION=$(ls -t1 dist/openff-nagl-*.tar.gz | head -n 1)
        test -n "${DISTRIBUTION}" || { echo "no distribution dist/openff-nagl-*.tar.gz found"; exit 1; }
        echo "twine check $DISTRIBUTION"
        twine check $DISTRIBUTION
  
  install_from_source_conda:
    runs-on: ubuntu-latest
    strategy:
        fail-fast: false
        matrix:
          python-version: ["3.10", "3.11", "3.12"]

    steps:
    - uses: actions/checkout@v3

    - name: Install conda
      uses: conda-incubator/setup-miniconda@v2
      with:
        python-version: ${{ matrix.python-version }}
        add-pip-as-python-dependency: true
        architecture: x64
        miniforge-variant: Mambaforge
        use-mamba: true
        auto-update-conda: true
        show-channel-urls: true
        channels: conda-forge, defaults

    - name: Build from source
      run: |
        conda create --name openff-nagl
        conda activate openff-nagl
        conda list
    
        mamba env update --name openff-nagl --file devtools/conda-envs/test_env_dgl_false.yaml
        mamba env update --name openff-nagl --file devtools/conda-envs/docs_env.yaml
        python --version
        python -m pip install . --no-deps
        conda list

    - name: Check success
      run: |
        conda activate openff-nagl
        python -c "import openff.nagl ; print(openff.nagl.__version__)"