pytest.yml

name: Pytest

on: [push]

jobs:
  build:
    runs-on: ${{ matrix.os }}
    strategy:
      matrix:
        os: [ubuntu-latest, macos-latest]
        python-version: [ '3.8', '3.9', '3.10']
    name: Python ${{ matrix.python-version }} on ${{ matrix.os }}
    steps:
      - uses: actions/checkout@v3
      - uses: actions/setup-python@v4
        with:
          python-version: ${{ matrix.python-version }}
      # - name: Install xz for macOS to install HTSlib
      #   run: |
      #       if [ "$RUNNER_OS" == "macOS" ]; then
      #           brew install xz htslib
      #       fi
      - name: Install dependencies via pip
        run: |
          python -m pip install --upgrade pip
          python -m pip install pytest
          python -m pip install -r requirements.txt
      # - name: Set up Conda
      #   uses: conda-incubator/setup-miniconda@v2
      #   with:
      #     auto-update-conda: true
      #     channels: conda-forge, bioconda, anaconda
      #     python-version: ${{ matrix.python-version }}
      # - name: Install dependencies via conda
      #   run: |
      #     conda install --file requirements.txt --yes
      - name: Test with pytest
        run: |
          export PYTHONPATH=./src
          python -m pytest tests/ -p no:warnings