MONSDA/.github/workflows/python-app.yaml at main · jfallmann/MONSDA · GitHub

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name: MONSDA CI

on:
  pull_request:
    types: [opened, synchronize, reopened, labeled, unlabeled]
  workflow_dispatch:
    inputs:
      run_full_pipeline:
        description: "Run full pipeline integration test"
        required: false
        default: false
        type: boolean

jobs:
  tests:
    name: Unit tests (pytest)
    runs-on: ubuntu-latest
    defaults:
      run:
        shell: bash -el {0}
    steps:
      - uses: actions/checkout@v4
        with:
          submodules: recursive
      - uses: conda-incubator/setup-miniconda@v3
        with:
          miniconda-version: "latest"
          activate-environment: monsda-test
          environment-file: environment.yml
          python-version: 3.12.2
          channels: conda-forge,bioconda
          allow-softlinks: true
          channel-priority: flexible
          show-channel-urls: true
          use-only-tar-bz2: false
          auto-activate-base: false
      - name: build and install MONSDA
        run: |
          cd ${{ github.workspace }}
          python -m pip install --upgrade pip
          python -m pip install -e .
          python -m pip install pytest
      - name: run unit tests
        run: |
          cd ${{ github.workspace }}
          pytest -q tests/test_Utils.py

  full-pipeline:
    name: Full pipeline integration test
    runs-on: ubuntu-latest
    needs: tests
    if: >-
      (github.event_name == 'workflow_dispatch' && inputs.run_full_pipeline) ||
      (github.event_name == 'pull_request' && contains(github.event.pull_request.labels.*.name, 'full-pipeline'))
    defaults:
      run:
        shell: bash -el {0}
    steps:
      - uses: actions/checkout@v4
        with:
          submodules: recursive
      - uses: conda-incubator/setup-miniconda@v3
        with:
          miniconda-version: "latest"
          activate-environment: monsda-test
          environment-file: environment.yml
          python-version: 3.12.2
          channels: conda-forge,bioconda
          allow-softlinks: true
          channel-priority: flexible
          show-channel-urls: true
          use-only-tar-bz2: false
          auto-activate-base: false
      - name: build and install MONSDA
        run: |
          cd ${{ github.workspace }}
          python -m pip install --upgrade pip
          python -m pip install -e .
      - name: prepare integration test config
        run: |
          cd ${{ github.workspace }}
          VERSION=$(monsda --version 2>&1 | sed 's/MONSDA version //g')
          sed -i "s/\"VERSION\": \"FIXME\"/\"VERSION\": \"${VERSION}\"/g" tests/data/config_Test.json
      - name: run full pipeline test
        run: |
          cd ${{ github.workspace }}/tests
          ln -fs data/* .
          mkdir -p CONDALIB
          monsda -j 6 -c config_Test.json --directory ${PWD} --use-conda --conda-prefix CONDALIB --save
      - name: upload test logs on failure
        if: failure()
        uses: actions/upload-artifact@v4
        with:
          name: full-pipeline-debug-artifacts
          path: |
            ${{ github.workspace }}/tests/LOGS
            ${{ github.workspace }}/tests/SUBSNAKES
            ${{ github.workspace }}/tests/FASTQ
            ${{ github.workspace }}/tests/MAPPED
            ${{ github.workspace }}/tests/QC
            ${{ github.workspace }}/tests/COUNTING
            ${{ github.workspace }}/tests/PEAKS
            ${{ github.workspace }}/tests/TRACKS