tallynn_python.yml

name: tallynn

on: [push, pull_request]

jobs:
  build:
    name: TallyNN (${{ matrix.python-version }}, ${{ matrix.os }})
    runs-on: ${{ matrix.os }}

    strategy:
      fail-fast: false
      matrix:
        os: ["ubuntu-latest"]
        python-version: ["3.7"]

    defaults:
      run:
        shell: bash -l {0}

    steps:
      - uses: actions/checkout@v2
      - name: Cache conda
        uses: actions/cache@v1
        env:
          # Increase this value to reset cache if conda/environments/cgat-core.yml has not changed
          CACHE_NUMBER: 0
        with:
          path: ~/conda_pkgs_dir
          key:
            ${{ runner.os }}-conda-${{ env.CACHE_NUMBER }}-${{
            hashFiles('conda/environments/cgat-core.yml') }}
      - uses: conda-incubator/setup-miniconda@v2
        with:
          mamba-version: "*"
          python-version: ${{ matrix.python-version }}
          channels: conda-forge, bioconda, defaults
          channel-priority: true
          activate-environment: tallynn
          environment-file: conda/environments/tallynn.yml
      - name: Install UMI-tools
        run: |
          git clone https://github.com/Acribbs/UMI-tools.git
          cd UMI-tools
          python setup.py install
      - name: Show conda
        run: |
          conda info
          conda list
      - name: Test
        run: |
          nosetests -v tests/test_pipeline_control.py
          nosetests -v tests/test_import.py
          nosetests -v tests/test_style.py