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 ]
  pull_request:
    branches: [ master ]

jobs:
  build:

    runs-on: ubuntu-latest
    strategy:
      matrix:
        python-version: [3.6, 3.8]
        java-version: [1.11]
        java-version: [1.11]
        nextflow-version: [21.10.5]

    steps:
    - uses: actions/checkout@v2
    - name: Setup Java JDK # Nextflow relies on JDK
      uses: actions/setup-java@v1.4.3
      # The Java version to make available on the path. Takes a whole or semver Java version, or 1.x syntax (e.g. 1.8 => Java 8.x). Early access versions can be specified in the form of e.g. 14-ea, 14.0.0-ea, or 14.0.0-ea.28
      with:
        java-version: ${{ matrix.java-version }}
    - name: Set up Nextflow
      run: |
        mkdir /tmp/nextflow && cd /tmp/nextflow
        wget -qO- https://github.com/nextflow-io/nextflow/releases/download/v${{ matrix.nextflow-version }}/nextflow-${{ matrix.nextflow-version }}-all | bash
        echo "/tmp/nextflow" >> $GITHUB_PATH
        cd -
    - name: Set up BCFtools
      run: |
        sudo apt update
        sudo apt -y install samtools bcftools tabix
    - 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
        pip install flake8 pytest
        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
        python setup.py install
    - 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: |
        PYTHONPATH=. pytest tests