run_tests.yml

name: pytest

on:
  push:
    branches:
      - main
  pull_request:
    branches:
      - main

jobs:
  build:
    runs-on: ubuntu-latest
    strategy:
      max-parallel: 5
      fail-fast: false
      matrix:
        python-version: ["3.10", "3.11"]

    steps:
    - uses: actions/checkout@v4
    - name: Set up Python 
      uses: actions/setup-python@v5
      with:
        python-version: ${{ matrix.python-version }}
        cache: 'pip'
    - name: Add conda to system path
      run: |
        # $CONDA is an environment variable pointing to the root of the miniconda directory
        echo $CONDA/bin >> $GITHUB_PATH
    - name: Install dependencies
      run: |
        conda config --add channels conda-forge 
        conda config --add channels bioconda
        conda install -y python=${{ matrix.python-version }} meme=5.5.5
        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
    - name: Lint with flake8
      run: |
        pip 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: Test with pytest
      run: |
        pip install pytest
        # Ignore tests that should use GPU
        pytest --ignore=tests/black_box_test.py --ignore=tests/prune_archive_test.py