python-package.yml

name: Python package

on:
  push:

jobs:
  cqa:
    runs-on: ubuntu-latest

    steps:
    - uses: actions/checkout@v3

    - name: Set up Python
      uses: actions/setup-python@v4
      with:
        python-version: "3.10"
        cache: pip
        cache-dependency-path: '**/setup.cfg'

    - name: Install test dependencies
      run: |
        python -m pip install --upgrade pip
        pip install --use-deprecated=legacy-resolver -e .[dev]

    - name: Lint with flake8
      run: |
        # stop the build if there are Python syntax errors or undefined names
        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics

    - name: Format check with isort
      run: |
        isort --check src

    - name: Format check with ruff
      run: |
        ruff format --check src

    - name: Security check with bandit
      run: |
        bandit -ll -r src

  test:
    runs-on: ubuntu-latest

    strategy:
      fail-fast: false
      matrix:
        python-version: ["3.10", "3.11", "3.12"]

    steps:
    - name: Install packages
      run: |
        sudo apt install libhts-dev libhts3 libhtscodecs-dev libhtscodecs2 tabix

    - uses: actions/checkout@v3

    - name: Set up Python ${{ matrix.python-version }}
      uses: actions/setup-python@v4
      with:
        python-version: ${{ matrix.python-version }}
        cache: pip
        cache-dependency-path: '**/setup.cfg'

    - name: Install dependencies
      run: |
        python -m pip install --upgrade pip
        make develop

    - name: Test with pytest
      run: |
        make test

  deploy:
    needs:
    # - cqa
    - test
    runs-on: ubuntu-latest

    steps:
    - name: Environment
      run: |
        echo "::group::Environment info"
        echo github.event_name = ${{ github.event_name }}
        echo refs = ${{ github.ref }}
        echo tags = ${{ startsWith(github.ref, 'refs/tags') }}
        echo "::endgroup::"

    - uses: actions/checkout@v3

    - name: Set up Python
      uses: actions/setup-python@v4
      with:
        python-version: "3.10"
        cache: pip
        cache-dependency-path: '**/setup.cfg'

    - name: Install dependencies
      run: |
        python -m pip install --upgrade pip
        pip install build twine

    - name: Build package
      run: python -m build

    - name: Publish package
      if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags')
      uses: pypa/gh-action-pypi-publish@release/v1
      with:
        password: ${{ secrets.PYPI_API_TOKEN }}