ci.yaml

name: CI
on:
  push:
  pull_request:
  schedule:
    - cron: "0 0 1 * *"  # run monthly
jobs:
  build:
    runs-on: ubuntu-latest
    strategy:
      fail-fast: false
      matrix:
        modes: ["s", "p"]
        schedulers: ["gridengine", "slurm"]
    env:
      REGISTRY: ghcr.io
      NAME: ${{ matrix.schedulers }}-${{ matrix.modes }}
      IMAGE: ${{ github.repository_owner }}/sv-callers-${{ matrix.schedulers }}
      TAG: "1.2.2"
      ARGS: 0 ${{ matrix.modes }} ${{ matrix.schedulers }}
    steps:
      - name: Checkout repo
        uses: actions/checkout@v2
      - name: Set up Python
        uses: actions/setup-python@v1
        with:
          python-version: "3.7"
      - name: Python info
        run: |
          which python
          python --version
      - name: Install dependencies
        run: |
          python -m pip install --upgrade pip
          pip install -r test-requirements.txt
      - name: Show pip list
        run: pip list
      - name: Run unit tests
        run: |
          pytest --cov=helper_functions --cov-report=xml
          mv coverage.xml ${{ github.workspace }}
        working-directory: workflow
      - name: Log into registry
        uses: docker/login-action@v1
        with:
          registry: ${{ env.REGISTRY }}
          username: ${{ github.actor }}
          password: ${{ secrets.GITHUB_TOKEN }}
      - name: Run workflow
        run: |
          docker run -d -p 10000:22 --name $NAME ${REGISTRY}/${IMAGE,,}:${TAG}
          sleep 10
          docker ps -a
          docker exec -u xenon -t $NAME bash -c "cd sv-callers && ./run.sh $ARGS"
      - name: Upload coverage report to Codacy
        uses: codacy/codacy-coverage-reporter-action@master
        with:
          project-token: ${{ secrets.CODACY_PROJECT_TOKEN }}
          coverage-reports: coverage.xml