ci.yml

name: continuous-integration

on:
  - push
  - pull_request

jobs:
  formatting:
    permissions:
      contents: read  # for actions/checkout to fetch code
      pull-requests: write  # for marocchino/sticky-pull-request-comment to create or update PR comment
    runs-on: ubuntu-latest
    strategy:
      matrix:
        java: ['16']

    steps:
      - uses: actions/checkout@v2
      - name: Set up JDK
        uses: actions/setup-java@v2
        with:
          java-version: ${{ matrix.java }}
          distribution: 'adopt'
      - name: Check formatting
        run: mvn com.coveo:fmt-maven-plugin:check -Dverbose=true
      - name: Comment PR
        if: github.event_name == 'pull_request' && failure()
        uses: marocchino/sticky-pull-request-comment@v2.2.0
        with:
          message: 'Please format your code with `mvn com.coveo:fmt-maven-plugin:format`.'
          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

  testing:
    runs-on: ubuntu-latest
    needs: formatting
    strategy:
      matrix:
        java: ['8', '16']
    
    steps:
      - uses: actions/checkout@v2
        with:
          lfs: true
      - name: Check out LFS objects
        run: git lfs fetch --all
      - name: Set up JDK
        uses: actions/setup-java@v2
        with:
          java-version: ${{ matrix.java }}
          distribution: 'adopt'

      - name: Build JAR with Maven without submitting coverage report
        run: >
          mvn
          --batch-mode
          --update-snapshots
          clean
          package

      - name: Run end-to-end tests
        run: |
          cd tests/hg19-chr22
          bash run-tests.sh

  testing-coverage:
    runs-on: ubuntu-latest
    needs: formatting
    strategy:
      matrix:
        java: ['16']

    steps:
      - uses: actions/checkout@v2
        with:
          lfs: true
      - name: Check out LFS objects
        run: git lfs fetch --all
      - name: Set up JDK
        uses: actions/setup-java@v2
        with:
          java-version: ${{ matrix.java }}
          distribution: 'adopt'

      - name: Run test with Maven and submit coverage report
        run: >
          mvn
          --define repoToken=${{ secrets.COVERALLS_REPO_TOKEN }}
          --batch-mode
          --update-snapshots
          clean
          test
          jacoco:report
          coveralls:report