python-test.yml

# This workflow will install Python dependencies, run tests and lint with a single version of Python
# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions

name: CI-PyTest

on:
  push:
    branches: [master]
  pull_request: {}

jobs:
  # Matrix strategy for parallel test execution
  test-matrix:
    runs-on: ubuntu-latest
    outputs:
      other_modified_files_count: ${{ steps.dependencies.outputs.other_modified_files_count }}
    strategy:
      fail-fast: false
      matrix:
        test-group: [
          "generic",
          "classification-histology",
          "classification-standard",
          "segmentation-2d",
          "segmentation-3d",
          "regression",
          "transunet",
          "entrypoints",
          "update_version"
        ]

    steps:
      - name: Checkout code
        uses: actions/checkout@v4

      - name: Call reusable workflow to install dependencies
        id: dependencies
        uses: ./.github/workflows/dependencies

      - name: Run test group - ${{ matrix.test-group }}
        if: ${{steps.dependencies.outputs.other_modified_files_count > 0}}
        run: |
          case "${{ matrix.test-group }}" in
            "generic")
              pytest --cov=. --cov-report=xml:coverage-generic.xml -k "generic" --cov-context=test | tee pytest-generic.log
              ;;
            "classification-histology")
              pytest --cov=. --cov-report=xml:coverage-classification-histology.xml -k "classification and histology" --cov-context=test | tee pytest-classification-histology.log
              ;;
            "classification-standard")
              pytest --cov=. --cov-report=xml:coverage-classification-standard.xml -k "classification and not histology" --cov-context=test | tee pytest-classification-standard.log
              ;;
            "segmentation-2d")
              pytest --cov=. --cov-report=xml:coverage-segmentation-2d.xml -k "segmentation and 2d and not transunet" --cov-context=test | tee pytest-segmentation-2d.log
              ;;
            "segmentation-3d")
              pytest --cov=. --cov-report=xml:coverage-segmentation-3d.xml -k "segmentation and 3d and not transunet" --cov-context=test | tee pytest-segmentation-3d.log
              ;;
            "regression")
              pytest --cov=. --cov-report=xml:coverage-regression.xml -k "regression" --cov-context=test | tee pytest-regression.log
              ;;
            "transunet")
              pytest --cov=. --cov-report=xml:coverage-transunet.xml -k "transunet" --cov-context=test | tee pytest-transunet.log
              ;;
            "entrypoints")
              pytest --cov=. --cov-report=xml:coverage-entrypoints.xml -k "entrypoints" --cov-context=test | tee pytest-entrypoints.log
              ;;
            "update_version")
              pytest --cov=. --cov-report=xml:coverage-update_version.xml -k "update_version" --cov-context=test | tee pytest-update_version.log
              ;;
          esac
        shell: bash

      - name: Upload coverage artifact
        if: ${{steps.dependencies.outputs.other_modified_files_count > 0}}
        uses: actions/upload-artifact@v4
        with:
          name: coverage-${{ matrix.test-group }}
          path: coverage-${{ matrix.test-group }}.xml
          retention-days: 1

  # Job to combine all coverage reports
  combine-coverage:
    needs: test-matrix
    runs-on: ubuntu-latest
    if: ${{ needs.test-matrix.outputs.other_modified_files_count > 0 && (always() && (needs.test-matrix.result == 'success' || needs.test-matrix.result == 'failure')) }}
    
    steps:
      - name: Checkout code
        uses: actions/checkout@v4

      - name: Set up Python
        uses: actions/setup-python@v4
        with:
          python-version: '3.11'

      - name: Download all coverage artifacts
        uses: actions/download-artifact@v4
        with:
          pattern: coverage-*
          path: coverage-reports
          merge-multiple: true

      - name: List downloaded coverage files
        run: |
          find coverage-reports -name "*.xml" -type f

      - name: Combine coverage reports
        run: |
          # Install coverage tools if not already available
          pip install coverage

          # Create combined coverage directory
          mkdir -p combined-coverage
          
          # Combine all XML coverage reports
          python -c "
          import xml.etree.ElementTree as ET
          import glob
          import os
          
          coverage_files = glob.glob('coverage-reports/**/*.xml', recursive=True)
          print(f'Found {len(coverage_files)} coverage files')
          
          if not coverage_files:
              print('No coverage files found')
              exit(1)
          
          # Use the first file as base
          combined_tree = ET.parse(coverage_files[0])
          combined_root = combined_tree.getroot()
          
          # Merge coverage from other files
          for coverage_file in coverage_files[1:]:
              tree = ET.parse(coverage_file)
              root = tree.getroot()
              
              # Merge packages
              for package in root.findall('.//package'):
                  package_name = package.get('name')
                  existing_package = combined_root.find(f'.//package[@name=\"{package_name}\"]')
                  
                  if existing_package is None:
                      # Add new package
                      packages = combined_root.find('.//packages')
                      if packages is not None:
                          packages.append(package)
                  else:
                      # Merge classes within package
                      for class_elem in package.findall('classes/class'):
                          class_name = class_elem.get('name')
                          existing_class = existing_package.find(f'.//class[@name=\"{class_name}\"]')
                          
                          if existing_class is None:
                              classes = existing_package.find('classes')
                              if classes is not None:
                                  classes.append(class_elem)
          
          # Write combined coverage
          combined_tree.write('combined-coverage/coverage.xml', encoding='utf-8', xml_declaration=True)
          print('Combined coverage report created')
          "

      - name: Upload combined coverage to Codecov
        uses: codecov/codecov-action@v4
        with:
          token: ${{ secrets.CODECOV_TOKEN }}
          file: ./combined-coverage/coverage.xml
          flags: unittests
          name: combined-coverage

      - name: Upload coverage to Codacy
        if: github.ref == 'refs/heads/master'
        uses: codacy/codacy-coverage-reporter-action@v1.3.0
        with:
          project-token: ${{ secrets.CODACY_PROJECT_TOKEN }}
          coverage-reports: ./combined-coverage/coverage.xml

  # Legacy single-system job for backward compatibility (optional)
  full-test:
    runs-on: ubuntu-latest
    if: false  # Disable this job since we are using the matrix approach

    steps:
      - name: Checkout code
        uses: actions/checkout@v4

      - name: Call reusable workflow to install dependencies
        id: dependencies
        uses: ./.github/workflows/dependencies

      - name: Run generic unit tests
        if: ${{steps.dependencies.outputs.other_modified_files_count > 0}} # Run on any non-docs change
        run: |
          pytest --cov=. --cov-report=xml -k "generic"
      - name: Run classification unit tests with histology
        if: ${{steps.dependencies.outputs.other_modified_files_count > 0}} # Run on any non-docs change
        run: |
          pytest --cov=. --cov-report=xml --cov-append -k "classification and histology"
      - name: Run classification unit tests
        if: ${{steps.dependencies.outputs.other_modified_files_count > 0}} # Run on any non-docs change
        run: |
          pytest --cov=. --cov-report=xml --cov-append -k "classification and not histology"
      - name: Run segmentation unit tests
        if: ${{steps.dependencies.outputs.other_modified_files_count > 0}} # Run on any non-docs change
        run: |
          pytest --cov=. --cov-report=xml --cov-append -k "segmentation and not transunet"
      - name: Run regression unit tests
        if: ${{steps.dependencies.outputs.other_modified_files_count > 0}} # Run on any non-docs change
        run: |
          pytest --cov=. --cov-report=xml --cov-append -k "regression"
      - name: Run transunet unit tests
        if: ${{steps.dependencies.outputs.other_modified_files_count > 0}} # Run on any non-docs change
        run: |
          pytest --cov=. --cov-report=xml --cov-append -k "transunet"
      - name: Run entrypoints tests
        if: ${{steps.dependencies.outputs.other_modified_files_count > 0}} # Run on any non-docs change
        run: |
          pytest --cov=. --cov-report=xml --cov-append -k "entrypoints"
      - name: Run test for update_version
        if: ${{steps.dependencies.outputs.other_modified_files_count > 0}} # Run on any non-docs change
        run: |
          pytest --cov=. --cov-report=xml --cov-append -k "update_version"

      - name: Upload coverage
        if: ${{steps.dependencies.outputs.other_modified_files_count > 0}} # Run on any non-docs change
        uses: codecov/codecov-action@v1
        with:
          token: ${{ secrets.CODECOV_TOKEN }}
          file: ./coverage.xml
          flags: unittests

      - name: Upload coverage to Codacy
        if: github.ref == 'refs/heads/master' # only run when on master
        uses: codacy/codacy-coverage-reporter-action@v1.3.0
        with:
          project-token: ${{ secrets.CODACY_PROJECT_TOKEN }}
          coverage-reports: ./coverage.xml