test_pipelines.yml

name: Python package

on: [push]

jobs:
  Test:
    if: github.event_name == 'pull_request' || github.event_name == 'push'
    runs-on: ubuntu-latest
    strategy:
      matrix:
        test: ["config", "design", "pipeline"]
        assay: ["atac", "chip-rx", "chip", "rna-rx", "rna", "snp"]

    steps:
      - uses: actions/checkout@v3

      - name: Cache dependencies
        id: cache-env
        uses: actions/cache@v3
        with:
          path: |
            ~/.conda
            ~/.cache/pip
          key: ${{ runner.os }}-env-${{ hashFiles('**/testing.yml') }}
          restore-keys: |
            ${{ runner.os }}-env-
      - name: Setup conda
        uses: conda-incubator/setup-miniconda@v3
        with:
          environment-file: testing.yml
          miniforge-variant: Mambaforge
          miniforge-version: latest
          use-mamba: true

      - name: Install package
        shell: pwsh
        run: |
          pip install .
      - name: Cache singularity
        if: matrix.test == 'pipeline'
        id: cache-singularity
        uses: actions/cache@v3
        with:
          path: ~/.apptainer
          key: ${{ runner.os }}-singularity-${{ hashFiles('tmp/*') }}
          restore-keys: |
            ${{ runner.os }}-singularity-
      - uses: eWaterCycle/setup-apptainer@v2
        if: matrix.test == 'pipeline'
        with:
          apptainer-version: 1.1.2

      - name: Add singularity hub remote
        if: matrix.test == 'pipeline'
        shell: pwsh
        run: |
          apptainer remote add --no-login SylabsCloud cloud.sylabs.io
          apptainer remote use SylabsCloud
      - name: Pull singularity images
        if: matrix.test == 'pipeline' && steps.cache-singularity.outputs.cache-hit != 'true'
        shell: bash
        run: |
          echo "Pulling singularity images from the remote repository..."
          mkdir -p tmp
          if [[ "${{ matrix.test }}" == "pipeline" ]]; then
            apptainer pull --force library://asmith151/seqnado/seqnado_pipeline:latest
          elif [[ "${{ matrix.assay }}" == "atac" || "${{ matrix.assay }}" == "chip" ]]; then
            apptainer pull --force library://asmith151/seqnado/seqnado_extra:latest
          elif [[ "${{ matrix.assay }}" == "rna-rx" ]]; then
            apptainer pull --force library://asmith151/seqnado/seqnado_report:latest
          fi
      - name: Test ${{ matrix.test }} ${{ matrix.assay }}
        shell: pwsh
        env:
          TMPDIR: /tmp
        run: |
          pytest tests/test_pipelines.py::test_${{ matrix.test }}[${{ matrix.assay }}] -vv -s --cores 4