main.yml

name: Tests

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

jobs:
  tests:
    runs-on: ubuntu-latest
    strategy:
      max-parallel: 5

    steps:
    - uses: actions/checkout@v2
    - name: Set up Python 3.11
      uses: actions/setup-python@v2
      with:
        python-version: 3.11
    - name: Add conda to system path
      run: |
        # $CONDA is an environment variable pointing to the root of the miniconda directory
        echo $CONDA/bin >> $GITHUB_PATH
    - name: Install dependencies
      run: |
        conda install -c conda-forge mamba
    - name: Lint with flake8
      run: |
        mamba install flake8
        # 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: Setup snakemake
      run: |
        mamba install -c conda-forge -c bioconda pytest snakemake singularity snakefmt
    - name: Lint with snakemake and snakefmt
      run: |
        snakemake --lint
        snakefmt workflow
    - name: Unit tests
      run: |
        pytest .tests/unit
    - name: Integration test
      run: |
        pytest .tests/integration