test_pipelines.yml

name: Python package

on: [push]

jobs:
  Test:
    runs-on: ubuntu-latest
    strategy:
      matrix:
        test: ["test_config", "test_design", "test_pipeline"]
        assay: ["atac", "chip-rx", "chip", "rna-rx", "rna", "snp"]

    steps:
      - uses: actions/checkout@v3
      - 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: Cache conda environment
        id: cache-conda
        uses: actions/cache@v3
        with:
          path: |
            ~/miniforge3/envs/test
            ~/.cache/pip
          key: ${{ runner.os }}-conda-${{ hashFiles('**/testing.yml') }}
          restore-keys: |
            ${{ runner.os }}-conda-

      - name: Set up conda using miniforge
        uses: conda-incubator/setup-miniconda@v3
        with:
          environment-file: testing.yml
          miniforge-variant: Mambaforge
          miniforge-version: latest
          use-mamba: true

      - name: Install the package
        shell: pwsh
        run: |
          pip install .

      # - name: Test ${{ matrix.test }} ${{ matrix.assay }}
      #   shell: pwsh
      #   run: |
      #     pytest tests/test_pipelines.py::${{ matrix.test }} -vv -s --cores 4 -k ${{ matrix.assay }}