test_pipelines.yml

name: Python package

on: [push]

jobs:
  Build_and_Test:

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

    steps:
    - uses: actions/checkout@v2
    - uses: eWaterCycle/setup-apptainer@v2
      with:
        apptainer-version: 1.1.2
    - name: Add singularity hub remote
      run: |
        apptainer remote add --no-login SylabsCloud cloud.sylabs.io
        apptainer remote use SylabsCloud
    - name: Set up Python ${{ matrix.python-version }}
      uses: actions/setup-python@v2
      with:
        python-version: ${{ matrix.python-version }}
    - name: Set up conda using miniforge
      uses: conda-incubator/setup-miniconda@v3
      with:
        environment-file: environment_minimal.yml
        miniforge-version: latest
        miniforge-variant: Mambaforge
        python-version: ${{ matrix.python-version }}
        use-mamba: true
    - name: Install package dependencies
      run: |
        mamba env update -n test -f environment_minimal.yml
      shell: bash -l {0}
    - name: Install testing dependencies
      run: |
        mamba env update -n test -f testing.yml
      shell: bash -l {0}
    - name: Install the package
      shell: bash -l {0}
      run: |
        pip install .
    - name: Conda list
      shell: pwsh
      run: mamba list
    - name: Test design works
      shell: pwsh
      run: |
        seqnado-design chip tests/data/fastq/CTCF*.fastq.gz
    - name: Test with pytest
      shell: pwsh
      run: |
        pytest -s --cores 4