python-package.yml

# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions

name: Python package

on:
  push:
    branches: [ master ]
    tags:
      - "v*"  # Tag events matching v*, i.e. v1.0, v20.15.10
  pull_request:
    branches: [ master ]
jobs:
  build:

    runs-on: ubuntu-latest
    strategy:
      matrix:
        python-version: ["3.7", "3.8", "3.9", "3.10", "3.11"]

    steps:
    - uses: actions/checkout@v2
    - name: Set up Python ${{ matrix.python-version }}
      uses: actions/setup-python@v2
      with:
        python-version: ${{ matrix.python-version }}
    - name: Install dependencies
      run: |
        python -m pip install --upgrade pip wheel setuptools
        pip install numpy cython pysam
        pip install -r requirements-dev.txt
        pip install -e .
    - 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: Test with pytest
      run: |
        pip install pytest
        pytest