test-integration.yml

name: Run integration tests for TRAPI
# Run test at each push to master or develop, if changes to package files
on:
  workflow_call:
  workflow_dispatch:
  push:
    branches: [ master, develop ]
    paths:
    - 'pyproject.toml'
    - 'src/**'
    - 'tests/**'
    - '.github/workflows/test-integration.yml'

jobs:

  CodeQL-Analysis:
    runs-on: ubuntu-latest
    permissions:
      security-events: write # required for all workflows
      # only required for workflows in private repositories:
      actions: read
      contents: read

    steps:
      - name: Checkout repository
        uses: actions/checkout@v3

      - name: Initialize CodeQL
        uses: github/codeql-action/init@v2
        with:
          languages: python

      # Autobuild attempts to build any compiled languages (C/C++, C#, Go, or Java).
      # If this step fails, then you should remove it and run the build manually
      - name: Autobuild
        uses: github/codeql-action/autobuild@v2

      - name: Perform CodeQL Analysis
        uses: github/codeql-action/analyze@v2


  tests-coverage:
    runs-on: ubuntu-latest
    strategy:
      matrix:
        python-version: [3.8]

    steps:
    - uses: actions/checkout@v3
      with:
        # Disabling shallow clone is recommended for improving relevancy of reporting
        fetch-depth: 0

    - name: Set up Python ${{ matrix.python-version }}
      uses: actions/setup-python@v4
      with:
        python-version: ${{ matrix.python-version }}

    - uses: actions/setup-java@v3
      with:
        distribution: 'zulu'
        java-version: '11' # The JDK version to make available on the path.

    - uses: vemonet/setup-spark@v1
      with:
        spark-version: '3.0.2'

    - uses: iterative/setup-dvc@v1

    - name: Setup SonarCloud
      uses: warchant/setup-sonar-scanner@v3

    - name: Pull data with dvc
      run: |
        dvc pull

    - name: Install dependencies
      run: |
        pip install -e ".[train,test,dev]"

    - name: Test with pytest with coverage
      run: |
        pytest -s --cov src/openpredict --cov-report xml:coverage.xml tests/integration/*


    - name: Upload coverage to SonarCloud
      env:
        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
      run: sonar-scanner -Dsonar.login=${{ secrets.SONAR_TOKEN }} -Dsonar.organization=maastrichtu-ids  -Dsonar.host.url=https://sonarcloud.io/ -Dsonar.projectKey=MaastrichtU-IDS_translator-openpredict -Dsonar.python.coverage.reportPaths=coverage.xml

    # - name: SonarCloud Scan
    #   uses: SonarSource/sonarcloud-github-action@master
    #   env:
    #     GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
    #     SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }}