python_ci.yml

name: CI

on:
    push:
      branches: [ develop ]
    pull_request:
      branches: [ main, develop ]

jobs:
    run-ci:
      runs-on: ubuntu-latest
      strategy:
        matrix:
          python-version: ['3.10', '3.11', '3.12']

      steps:
        - uses: actions/checkout@v4
        - name: Initialize Python
          uses: actions/setup-python@v4.3.1
          with:
            python-version: ${{ matrix.python-version }}
        - name: Install package
          run: |
            python3 -m pip install --editable .[test,docs]
        - name: Run pytest tests with coverage
          run: |
            pytest --cov=phenopacket_mapper --cov-report=term --cov-report=xml:coverage.xml
        - name: Extract coverage percentage
          id: coverage
          run: |
            # Extract the percentage from the XML report
            coverage=$(grep -oP '(?<=line-rate=")[0-9.]+(?=")' coverage.xml)
            # Multiply by 100 to get the percentage
            COVERAGE=$(awk -v cov="$coverage" 'BEGIN {printf "%.2f\n", cov * 100}')
            echo "COVERAGE=${COVERAGE}" >> $GITHUB_ENV
            echo "Coverage percentage: $COVERAGE"
        - name: Display coverage
          run: |
            echo "Coverage: ${{ env.COVERAGE }}%"

        - name: Create Badge
          uses: schneegans/dynamic-badges-action@v1.7.0
          with:
            auth: ${{ secrets.GIST_SECRET }}
            gistID: 67304fe3700ce3d41079e75f4fe9609f
            filename: phenopacket_mapper_test_cov.JSON # Use test.svg if you want to use the SVG mode.
            label: Test Coverage
            message: ${{ env.COVERAGE }}%
            color: green