test.yml

name: Run pytest unit tests

on: [push, pull_request]

jobs:
  test:
    runs-on: ubuntu-latest
    steps:
      - name: Checkout
        uses: actions/checkout@v2
      - name: Setup python 3.9
        uses: actions/setup-python@v2
        with:
          python-version: 3.9
      - name: Setup dependencies
        run: |
          pip install pipenv
          pipenv requirements --dev > requirements.txt
          pip install -r requirements.txt
      - name: Lint with ruff
        # default set of ruff rules with GitHub Annotations
        run: |
          ruff --format=github --target-version=py39 .
      - name: Test with pytest
        run: |
          pytest --cov=clincnv2vcf --junitxml=junit/test-results.xml --cov-report=xml --cov-report=html
      - name: Upload pytest test results
        uses: actions/upload-artifact@v3
        with:
          name: pytest-results
          path: junit/test-results.xml
        # Use always() to always run this step to publish test results when there are test failures
        if: ${{ always() }}
      - name: Upload pytest coverage results xml
        uses: actions/upload-artifact@v3
        with:
          name: pytest-coverage
          path: coverage.xml
        # Use always() to always run this step to publish test results when there are test failures
        if: ${{ always() }}
      - name: Upload pytest coverage results html
        uses: actions/upload-artifact@v3
        with:
          name: pytest-coverage
          path: htmlcov
        # Use always() to always run this step to publish test results when there are test failures
        if: ${{ always() }}