gh-ci.yaml

name: GH Actions CI
on:
  push:
    branches:
      - main
  pull_request:
    branches:
      - main
  schedule:
    - cron: "0 0 * * 0"

concurrency:
  group: ${{ github.ref }}-${{ github.head_ref }}-${{ github.workflow }}
  cancel-in-progress: true

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

jobs:
  main-tests:
    if: "github.repository == 'Becksteinlab/propkatraj'"
    runs-on: ${{ matrix.os }}
    strategy:
      fail-fast: false
      matrix:
        os: [macOS-latest, ubuntu-latest, windows-latest]
        python-version: ["3.10", "3.11", "3.12"]
        mdanalysis-version: ["latest", "develop"]
        # Manually exclude any combinations of the test matrix that can't be run 
        exclude:
          # The latest release of MDAnalysis only supports up to Python 3.11
          # so we exclude 3.12 from the test matrix (issue #69)
          - python-version: "3.12"
            mdanalysis-version: "latest"
    steps:
    - uses: actions/checkout@v4
      with:
        fetch-depth: 0

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

    - name: Install conda dependencies
      uses: conda-incubator/setup-miniconda@v3
      with:
        python-version: ${{ matrix.python-version }}
        environment-file: devtools/environment.yml
        add-pip-as-python-dependency: true
        architecture: x64
        
        miniforge-variant: Mambaforge
        use-mamba: true
        channels: conda-forge, defaults
        
        activate-environment: propkatraj-test
        auto-update-conda: true
        auto-activate-base: false
        show-channel-urls: true

    - name: Install MDAnalysis version
      uses: MDAnalysis/install-mdanalysis@main
      with:
        version: ${{ matrix.mdanalysis-version }}
        install-tests: true
        installer:  mamba
        shell: bash -l {0} 
      
    - name: Install package
      run: |
        python --version
        python -m pip install .  --no-deps 

    - name: Python information
      run: |
        which python
        which pip
        pip list
        mamba info
        mamba list

    - name: Test imports
      run: |
        python -Ic "import propkatraj; print(propkatraj.__version__)"

    - name: Run tests
      run: |
        pytest -n auto --cov=propkatraj --cov-report=xml -v --color=yes propkatraj/tests/

    - name: codecov
      if: ${{ github.repository == 'Becksteinlab/propkatraj'
              && github.event_name != 'schedule' }}
      uses: codecov/codecov-action@v4
      with:
        token: ${{ secrets.CODECOV_TOKEN }}
        file: coverage.xml
        fail_ci_if_error: True
        verbose: True

  pylint_check:
    if: "github.repository == 'Becksteinlab/propkatraj'"
    runs-on: ubuntu-latest

    steps:
    - uses: actions/checkout@v3

    - name: Set up Python
      uses: actions/setup-python@v4
      with:
        python-version: "3.11"

    - name: Install Pylint
      run: |
        which pip
        which python
        pip install pylint MDAnalysis>=2.0.0
    - name: Run Pylint
      env:
        PYLINTRC: .pylintrc
      run: |
        pylint propkatraj

  pypi_check:
    if: "github.repository == 'Becksteinlab/propkatraj'"
    runs-on: ubuntu-latest

    steps:
    - uses: actions/checkout@v4

    - name: Set up Python
      uses: actions/setup-python@v4
      with:
        python-version: "3.11"

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

    - name: Build package
      run: |
        python -m pipx run build --sdist

    - name: Check package build
      run: |
        DISTRIBUTION=$(ls -t1 dist/propkatraj-*.tar.gz | head -n 1)
        test -n "${DISTRIBUTION}" || { echo "no distribution dist/propkatraj-*.tar.gz found"; exit 1; }
        echo "twine check $DISTRIBUTION"
        twine check $DISTRIBUTION