python-package.yml

name: Python package

on: [pull_request]

defaults:
  run:
    # for conda env activation
    shell: bash -l {0}

jobs:
  build:

    runs-on: ubuntu-latest
    strategy:
      matrix:
        python-version: ["3.12"]

    steps:
    - uses: actions/checkout@v2
    
    - name: Setup mamba
      uses: mamba-org/setup-micromamba@v1
      with:
        environment-file: test-env.yaml
        cache-downloads: true
        condarc: |
          channels:
            - conda-forge
            - bioconda
            - defaults
          channel_priority: flexible
        extra-specs: |
          python=${{ matrix.python-version }}

    - name: Debug Micromamba
      run: |
        micromamba env list
        micromamba info
        micromamba env export -n test-env
        
    - name: Run black manually
      run: |
        black --check --verbose ./

    # - name: Install dependencies
    #   run: |
    #     sudo apt-get install libhdf5-dev
    #     pip install -U setuptools>=40.1 wheel 'cmake<3.20' pytest
    #     pip install $(pwd)/scanpy-scripts
    #     # python -m pip install $(pwd)/scanpy --no-deps --ignore-installed -vv
    
    - name: Run unit tests
      run: |
        # needed for __version__ to be available
        pip install . --no-deps --ignore-installed
        pytest --doctest-modules -v ./
    
    - name: Test with bats
      run: |
        ./scanpy-scripts-tests.bats