gh-ci.yaml

name: GH Actions CI
on:
  push:
    branches:
      - main
  pull_request:
    branches:
      - main
  schedule:
    # Weekly tests at midnight on Sundays 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 * * 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} 

jobs:
  main-tests:
    if: "github.repository == 'BecksteinLab/mdaadb-kit'"
    runs-on: ${{ matrix.os }}
    strategy:
        fail-fast: false
        matrix:
          os: [ubuntu-latest, macOS-latest, windows-latest]
          mdanalysis-version: ["latest", "develop"]
          python-version: ["3.10", "3.11", "3.12"]
          exclude:
            # Entries here exclude particular combinations of the matrix
            # Edit or remove as particular combinations come into or out of date
            # Below we exclude runs with the latest release and Python 3.12
            - mdanalysis-version: "latest"
              python-version: "3.12"

    steps:
    - uses: actions/checkout@v4

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


    # More info on options: https://github.com/conda-incubator/setup-miniconda
    - name: Install conda dependencies
      uses: conda-incubator/setup-miniconda@v3
      with:
        python-version: ${{ matrix.python-version }}
        environment-file: devtools/conda-envs/test_env.yaml
        add-pip-as-python-dependency: true
        architecture: x64

        miniforge-variant: Mambaforge
        use-mamba: true
        channels: conda-forge, defaults

        activate-environment: mdaadb-kit-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: false
        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

        conda info
        conda list


    - name: Run tests
      run: |
        pytest -n 2 -v --cov=mdaadb --cov-report=xml --color=yes mdaadb/tests/

    - name: codecov
      if: github.repository == 'BecksteinLab/mdaadb-kit' && github.event_name != 'schedule'
      uses: codecov/codecov-action@v4
      with:
        file: coverage.xml
        name: codecov-${{ matrix.os }}-py${{ matrix.python-version }}
        verbose: True
        # to upload coverage reports, set a secret called CODECOV_TOKEN
        # in the repository settings
        # (Obtain this from the Codecov website after setting up the repository there)
        token: ${{ secrets.CODECOV_TOKEN }}
        # To fail the CI if there's an error, keep this set to true
        # If repository forks need to run CI, you may need to set this to false
        # Forks can't access the CODECOV_TOKEN secret,
        # and a failed upload registers as an error
        fail_ci_if_error: true


  pylint_check:
    if: "github.repository == 'BecksteinLab/mdaadb-kit'"
    runs-on: ubuntu-latest

    steps:
    - uses: actions/checkout@v4

    - name: Set up Python
      uses: actions/setup-python@v5
      with:
        python-version: "3.11"

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

    - name: Run Pylint
      env:
        PYLINTRC: .pylintrc
      run: |
        pylint mdaadb-kit


  pypi_check:
    if: "github.repository == 'BecksteinLab/mdaadb-kit'"
    runs-on: ubuntu-latest

    steps:
    - uses: actions/checkout@v4

    - name: Set up Python
      uses: actions/setup-python@v5
      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=$(ls -t1 dist/mdaadb_kit-*.tar.gz | head -n 1)
        test -n "${DISTRIBUTION}" || { echo "no distribution dist/mdaadb-kit-*.tar.gz found"; exit 1; }
        echo "twine check $DISTRIBUTION"
        twine check $DISTRIBUTION