test.yml

# Runs test related tasks.

name: test

on:
  push:
    branches: [ main, dev ]
  pull_request:
    branches: [ main, dev ]

jobs:
  test:

    runs-on: ubuntu-22.04

    steps:
    - uses: actions/checkout@v2
    - uses: actions/setup-python@v4
      with:
        python-version: 3.9
    - name: Install dependencies
      run: |
        python -m pip install --upgrade pip
        pip install flake8 pytest pytest-cov
        pip install biopython pandas
    - 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: |
        python3 -m pytest --cov=./ --cov-report=xml
    - uses: codecov/codecov-action@v3
      with:
        token: ${{ secrets.CODECOV_TOKEN }}
        file: ./coverage.xml
        env_vars: OS,PYTHON
        name: codecov-upload
        fail_ci_if_error: true
        verbose: true
    - uses: actions/setup-java@v3
      with:
        distribution: 'zulu'
        java-version: '17'
    - name: Install Nextflow
      run: |
        # Install latest version of Nextflow
        curl -s https://get.nextflow.io | bash
        sudo mv nextflow /usr/bin
    - name: Regression tests
      run: ./tests/regression_tests.sh