Add sonarqube to test workflow

.github/workflows/test.yaml

@@ -0,0 +1,78 @@
+name: Test
+on: [push]
+
+jobs:
+  test:
+    name: Test
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        shell: bash -l {0}
+
+    steps:
+    - uses: actions/checkout@v4
+
+    - uses: actions/setup-python@v5
+      with:
+        python-version: '3.11'
+        cache: 'pip'
+
+    - name: Install packages
+      run: |
+        pip install .
+        pip install -r requirements-dev.txt
+
+    - name: pre-commit
+      run: pre-commit run --all-files
+
+    - name: 'Run unit tests'
+      id: runtests
+      run: |
+        coverage run -m pytest test/ --junitxml=test-execution.xml
+        rc=$?
+        coverage xml
+
+        echo "rc=$rc" >> $GITHUB_OUTPUT
+
+    - name: 'Save coverage report as an Artifact'
+      uses: actions/upload-artifact@v4
+      with:
+        name: coverage-report
+        path: ./coverage.xml
+
+    - name: 'Save execution report as an Artifact'
+      uses: actions/upload-artifact@v4
+      with:
+        name: execution-report
+        path: ./test-execution.xml
+
+  sonarqube:
+    name: SonarQube scan
+    runs-on: ubuntu-latest
+    needs: test
+    environment: production
+    if: github.ref == 'refs/heads/main' || github.ref == 'refs/heads/dev'
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0 # Shallow clones should be disabled for a better relevancy of analysis
+
+      # Download the coverage report artifact
+      - name: 'Download coverage and execution report'
+        uses: actions/download-artifact@v4
+        with:
+          pattern: '*-report'
+
+      # Perform the SonarQube scan
+      - uses: sonarsource/sonarqube-scan-action@master
+        env:
+          SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }}
+          SONAR_HOST_URL: ${{ secrets.SONAR_HOST_URL }}
+
+      # Optional: Fail the job if Quality Gate is red
+      # If you wish to fail your job when the Quality Gate is red, uncomment the
+      # following lines. This would typically be used to fail a deployment.
+      # - uses: sonarsource/sonarqube-quality-gate-action@master
+      #   timeout-minutes: 5
+      #   env:
+      #     SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }}

requirements-dev.txt

@@ -1,7 +1,9 @@
 black
 bump2version
 cloudpathlib[all]
+coverage
 cpg-utils>=4.12.1
 pre-commit
 pylint
+pytest
 toml

sonar-project.properties

@@ -0,0 +1,4 @@
+sonar.projectKey=populationgenomics_analysis-runner
+sonar.python.version=3.11
+sonar.python.coverage.reportPaths=coverage.xml
+sonar.python.xunit.reportPath=test-execution.xml