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: [3.8, 3.9]
        nextflow-version: [21.10.5, 22.10.7]
        java-version: [11]

    steps:
    - uses: actions/checkout@v2
    - name: Set up Java ${{ matrix.java-version }}
      uses: actions/setup-java@v2
      with:
        distribution: 'temurin'
        java-version: '${{ matrix.java-version }}'
    - name: Set up Python ${{ matrix.python-version }}
      uses: actions/setup-python@v2
      with:
        python-version: ${{ matrix.python-version }}
    - name: Install dependencies ${{ matrix.nextflow-version }}
      run: |
        python -m pip install --upgrade pip
        pip install flake8 pytest
        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
        python setup.py install
        # Install Nextflow
        mkdir /tmp/nextflow && cd /tmp/nextflow
        wget -qO- https://github.com/nextflow-io/nextflow/releases/download/v${{ matrix.nextflow-version }}/nextflow-${{ matrix.nextflow-version }}-all | bash
        echo "/tmp/nextflow" >> $GITHUB_PATH
        cd -
        # Build java dependencies
        tests/nextflow-tests/build_tests.sh
    - 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: |
        # reduce the default SSL security level to get around a misconfiguration in the Ensembl server
        # https://github.com/Ensembl/ensembl-rest/issues/427
        # See https://askubuntu.com/a/1233456
        sed 's/DEFAULT@SECLEVEL=2/DEFAULT@SECLEVEL=1/' /usr/lib/ssl/openssl.cnf > openssl_sec1.cnf
        export OPENSSL_CONF=openssl_sec1.cnf
        PYTHONPATH=. pytest tests
    - name: Test nextflow workflows
      run: |
        # Run nextflow tests
        tests/nextflow-tests/run_tests_validation.sh
        tests/nextflow-tests/run_tests_prep_brokering.sh
        tests/nextflow-tests/run_tests_accession_and_variant_load.sh
        tests/nextflow-tests/run_tests_accession_and_variant_load_human.sh
        tests/nextflow-tests/run_tests_clustering.sh
        tests/nextflow-tests/run_tests_remapping_clustering.sh