ci.yml

# https://docs.github.com/en/actions
# https://github.com/codecov/example-python
# https://stackoverflow.com/a/3237883
# https://stackoverflow.com/a/5688592
# https://stackoverflow.com/a/6270803
# https://github.com/actions/virtual-environments/issues/1341

name: CI

on:
  schedule:
    - cron: '37 4 * * 0'
  push:
    branches:
      - '**'
  pull_request:
    branches:
      - '**'

jobs:
  enable-workflow:
    runs-on: ubuntu-latest
    if: ${{ github.event_name == 'push' || github.event_name == 'pull_request' || (github.event_name == 'schedule' && github.repository == 'apriha/snps') }}
    steps:
      - name: Enable workflow based on preconditions
        run: echo "Workflow enabled."

  lint:
    needs: [enable-workflow]
    runs-on: ubuntu-latest
    steps:
    - uses: actions/checkout@v4
    - uses: actions/setup-python@v5
      with:
        python-version: '3.12'
    - name: Install Black
      run: |
        pip install black
    - name: Lint with Black
      run: |
        black --check --diff .

  build-docs:
    needs: [enable-workflow]
    runs-on: ubuntu-latest
    steps:
    - uses: actions/checkout@v4
    - uses: actions/setup-python@v5
      with:
        python-version: '3.12'
    - name: Install Sphinx
      run: |
        pip install -r docs/requirements.txt
        pip install .
    - name: Build docs with Sphinx
      run: |
        sphinx-build -W --keep-going -T -E -D language=en docs docs/_build

  test:
    needs: [lint, build-docs]
    runs-on: ${{ matrix.os }}
    strategy:
      matrix:
        os: [ubuntu-latest]
        python-version: ['3.8', '3.9', '3.10', '3.11', '3.12']
        include:
          - os: macos-latest
            python-version: '3.12'
          - os: windows-latest
            python-version: '3.12'

    env:
      JOB_ID: ${{ strategy.job-index }}
      NUM_JOBS: ${{ strategy.job-total }}

    steps:
    - uses: actions/checkout@v4
      with:
        persist-credentials: false
    - name: Setup Python ${{ matrix.python-version }}
      uses: actions/setup-python@v5
      with:
        python-version: ${{ matrix.python-version }}
    - name: Ensure Python and source code are on same drive (Windows)
      if: ${{ matrix.os == 'windows-latest' }}
      shell: cmd
      run: |
        mkdir C:\a
        xcopy D:\a C:\a /s /e
    - name: Determine if downloads are enabled for this job
      # for testing, limit downloads from the resource servers to only the selected job for
      # PRs and the master branch; note that the master branch is tested weekly via `cron`,
      # so this ensures all Python versions will be periodically integration tested with the
      # resource servers
      if: ${{ github.event_name == 'pull_request' || github.ref == 'refs/heads/master' }}
      shell: bash
      run: |
        SELECTED_JOB=$((10#$(date +%V) % $NUM_JOBS))
        if [[ $SELECTED_JOB == $JOB_ID ]]; then
          # set environment variable to download resources for selected job
          echo "DOWNLOADS_ENABLED=true" >> $GITHUB_ENV
        fi
    - name: Install dependencies
      run: |
        pip install pytest-cov
        pip install .
    - name: Test with pytest (Ubuntu & macOS)
      if: ${{ matrix.os != 'windows-latest' }}
      run: |
        pytest --cov=snps tests
    - name: Test with pytest (Windows)
      if: ${{ matrix.os == 'windows-latest' }}
      working-directory: C:\a\snps\snps
      run: |
        pytest --cov=snps tests
    - name: Upload coverage to Codecov
      uses: codecov/codecov-action@v3

  test-extras:
    needs: [lint, build-docs]
    runs-on: ${{ matrix.os }}
    strategy:
      matrix:
        os: [ubuntu-latest]
        python-version: ['3.8', '3.9', '3.10', '3.11']

    steps:
    - uses: actions/checkout@v4
      with:
        fetch-depth: 0
        persist-credentials: false
    - name: Setup Python ${{ matrix.python-version }}
      uses: actions/setup-python@v5
      with:
        python-version: ${{ matrix.python-version }}
    - name: Install dependencies
      run: |
        pip install --upgrade pip setuptools wheel
        pip install pytest-cov
        pip install .[ezancestry]
    - name: Test with pytest
      run: |
        pytest --cov=snps tests