[WIP] Add tests and coverage

2025-09-08 10:52:58 +02:00
parent be99b3e601
commit 657b273975
21 changed files with 7919 additions and 158 deletions
@@ -0,0 +1,287 @@
+# GitLab CI/CD Pipeline for Gallery Generator
+# Tests container building and runs unit tests inside Apptainer
+
+stages:
+  - build
+  - test
+  - deploy
+
+variables:
+  CONTAINER_IMAGE: "gallery-generator.sif"
+  APPTAINER_CACHE_DIR: "$CI_PROJECT_DIR/.apptainer-cache"
+  PIP_CACHE_DIR: "$CI_PROJECT_DIR/.pip-cache"
+
+# Cache to speed up builds
+cache:
+  key: "$CI_COMMIT_REF_SLUG"
+  paths:
+    - .apptainer-cache/
+    - .pip-cache/
+
+# Build the Apptainer container
+build:container:
+  stage: build
+  image: ubuntu:22.04
+  before_script:
+    # Install Apptainer
+    - apt-get update -qq
+    - apt-get install -y wget
+    - wget -O- http://neuro.debian.net/lists/jammy.us-ca.full | tee /etc/apt/sources.list.d/neurodebian.sources.list
+    - apt-key adv --recv-keys --keyserver hkps://keyserver.ubuntu.com 0xA5D32F012649A5A9
+    - apt-get update -qq
+    - apt-get install -y apptainer
+    # Create cache directory
+    - mkdir -p $APPTAINER_CACHE_DIR
+  script:
+    - echo "Building Apptainer container..."
+    - apptainer --version
+    - apptainer build $CONTAINER_IMAGE Singularity.def
+    - ls -lh $CONTAINER_IMAGE
+    - echo "Container built successfully"
+  artifacts:
+    paths:
+      - $CONTAINER_IMAGE
+    expire_in: 1 hour
+  only:
+    - main
+    - merge_requests
+    - develop
+
+# Test container build process
+test:container-build:
+  stage: test
+  image: ubuntu:22.04
+  dependencies:
+    - build:container
+  before_script:
+    # Install Apptainer
+    - apt-get update -qq
+    - apt-get install -y wget
+    - wget -O- http://neuro.debian.net/lists/jammy.us-ca.full | tee /etc/apt/sources.list.d/neurodebian.sources.list
+    - apt-key adv --recv-keys --keyserver hkps://keyserver.ubuntu.com 0xA5D32F012649A5A9
+    - apt-get update -qq
+    - apt-get install -y apptainer python3
+  script:
+    - echo "Testing container build process..."
+    - python3 tests/test_build_container.py
+  only:
+    - main
+    - merge_requests
+    - develop
+
+# Run tests inside the container with coverage
+test:unit-tests:
+  stage: test
+  image: ubuntu:22.04
+  dependencies:
+    - build:container
+  before_script:
+    # Install Apptainer
+    - apt-get update -qq
+    - apt-get install -y wget
+    - wget -O- http://neuro.debian.net/lists/jammy.us-ca.full | tee /etc/apt/sources.list.d/neurodebian.sources.list
+    - apt-key adv --recv-keys --keyserver hkps://keyserver.ubuntu.com 0xA5D32F012649A5A9
+    - apt-get update -qq
+    - apt-get install -y apptainer
+  script:
+    - echo "Running unit tests inside container..."
+    - apptainer --version
+    - ls -la $CONTAINER_IMAGE
+    # Test that container works
+    - apptainer exec $CONTAINER_IMAGE python3 --version
+    - apptainer exec $CONTAINER_IMAGE pip list
+    # Run the container test suite
+    - apptainer exec $CONTAINER_IMAGE python3 /src/tests/test_container.py
+  artifacts:
+    reports:
+      junit: test-results.xml
+    when: always
+  only:
+    - main
+    - merge_requests
+    - develop
+
+# Run automated coverage testing
+test:coverage:
+  stage: test
+  image: ubuntu:22.04
+  dependencies:
+    - build:container
+  before_script:
+    # Install Apptainer
+    - apt-get update -qq
+    - apt-get install -y wget
+    - wget -O- http://neuro.debian.net/lists/jammy.us-ca.full | tee /etc/apt/sources.list.d/neurodebian.sources.list
+    - apt-key adv --recv-keys --keyserver hkps://keyserver.ubuntu.com 0xA5D32F012649A5A9
+    - apt-get update -qq
+    - apt-get install -y apptainer
+  script:
+    - echo "Running automated coverage analysis..."
+    - apptainer --version
+    - ls -la $CONTAINER_IMAGE
+    # Run automated coverage testing
+    - apptainer exec $CONTAINER_IMAGE python3 /src/tests/run_coverage.py
+    # Extract coverage report from container
+    - apptainer exec $CONTAINER_IMAGE cat /src/coverage.xml > coverage.xml || true
+    - apptainer exec $CONTAINER_IMAGE ls -la /src/coverage_html_report/ || true
+  coverage: '/TOTAL.+?(\d+\.\d+)%/'
+  artifacts:
+    reports:
+      coverage_report:
+        coverage_format: cobertura
+        path: coverage.xml
+    paths:
+      - coverage.xml
+    expire_in: 30 days
+  only:
+    - main
+    - merge_requests
+    - develop
+
+# Test gallery generation functionality
+test:gallery-generation:
+  stage: test
+  image: ubuntu:22.04
+  dependencies:
+    - build:container
+  before_script:
+    # Install Apptainer
+    - apt-get update -qq
+    - apt-get install -y wget
+    - wget -O- http://neuro.debian.net/lists/jammy.us-ca.full | tee /etc/apt/sources.list.d/neurodebian.sources.list
+    - apt-key adv --recv-keys --keyserver hkps://keyserver.ubuntu.com 0xA5D32F012649A5A9
+    - apt-get update -qq
+    - apt-get install -y apptainer
+  script:
+    - echo "Testing gallery generation..."
+    # Create test data
+    - mkdir -p test_input
+    - echo "%PDF-1.4" > test_input/test.pdf
+    - echo "title: Test Gallery" > test_input/metadata.yaml
+    # Test the main script
+    - apptainer exec $CONTAINER_IMAGE python3 /src/generate_gallery.py --help || true
+    - echo "Gallery generation test completed"
+  only:
+    - main
+    - merge_requests
+    - develop
+
+# Performance and integration tests
+test:performance:
+  stage: test
+  image: ubuntu:22.04
+  dependencies:
+    - build:container
+  before_script:
+    - apt-get update -qq
+    - apt-get install -y wget time
+    - wget -O- http://neuro.debian.net/lists/jammy.us-ca.full | tee /etc/apt/sources.list.d/neurodebian.sources.list
+    - apt-key adv --recv-keys --keyserver hkps://keyserver.ubuntu.com 0xA5D32F012649A5A9
+    - apt-get update -qq
+    - apt-get install -y apptainer
+  script:
+    - echo "Running performance tests..."
+    # Test container startup time
+    - time apptainer exec $CONTAINER_IMAGE python3 -c "print('Container startup test')"
+    # Test memory usage
+    - apptainer exec $CONTAINER_IMAGE python3 -c "
+        import psutil;
+        print(f'Memory usage: {psutil.virtual_memory().percent}%')"
+    - echo "Performance tests completed"
+  only:
+    - main
+    - merge_requests
+  allow_failure: true
+
+# Security scan (optional)
+test:security:
+  stage: test
+  image: ubuntu:22.04
+  dependencies:
+    - build:container
+  before_script:
+    - apt-get update -qq
+    - apt-get install -y wget
+    - wget -O- http://neuro.debian.net/lists/jammy.us-ca.full | tee /etc/apt/sources.list.d/neurodebian.sources.list
+    - apt-key adv --recv-keys --keyserver hkps://keyserver.ubuntu.com 0xA5D32F012649A5A9
+    - apt-get update -qq
+    - apt-get install -y apptainer
+  script:
+    - echo "Running basic security checks..."
+    # Check for known vulnerabilities in base image
+    - apptainer exec $CONTAINER_IMAGE python3 -c "
+        import sys;
+        print(f'Python version: {sys.version}');
+        import subprocess;
+        result = subprocess.run(['pip', 'list'], capture_output=True, text=True);
+        print('Installed packages:');
+        print(result.stdout)"
+    - echo "Security scan completed"
+  only:
+    - main
+    - merge_requests
+  allow_failure: true
+
+# Documentation and examples
+test:documentation:
+  stage: test
+  image: python:3.11-slim
+  script:
+    - echo "Validating documentation..."
+    - python3 -c "
+        import pathlib;
+        docs = ['README.md', 'tests/README.md', 'Singularity.def'];
+        for doc in docs:
+            if pathlib.Path(doc).exists():
+                print(f'✅ {doc} exists');
+            else:
+                print(f'❌ {doc} missing')"
+    - echo "Documentation validation completed"
+  only:
+    - main
+    - merge_requests
+
+# Deploy (if needed)
+deploy:registry:
+  stage: deploy
+  image: ubuntu:22.04
+  dependencies:
+    - build:container
+  before_script:
+    - apt-get update -qq
+    - apt-get install -y wget
+    - wget -O- http://neuro.debian.net/lists/jammy.us-ca.full | tee /etc/apt/sources.list.d/neurodebian.sources.list
+    - apt-key adv --recv-keys --keyserver hkps://keyserver.ubuntu.com 0xA5D32F012649A5A9
+    - apt-get update -qq
+    - apt-get install -y apptainer
+  script:
+    - echo "Deploying container to registry (placeholder)..."
+    - echo "Container size:" 
+    - ls -lh $CONTAINER_IMAGE
+    - echo "Container would be pushed to registry here"
+    # Actual deployment would push to a container registry
+    # - apptainer push $CONTAINER_IMAGE oras://registry.example.com/gallery-generator:latest
+  only:
+    - main
+  when: manual
+
+# Job for creating releases
+create:release:
+  stage: deploy
+  image: ubuntu:22.04
+  dependencies:
+    - build:container
+  script:
+    - echo "Creating release artifacts..."
+    - mkdir -p release/
+    - cp $CONTAINER_IMAGE release/
+    - cp Singularity.def release/
+    - cp tests/test_container.py release/
+    - echo "Release artifacts created"
+  artifacts:
+    paths:
+      - release/
+    expire_in: 1 week
+  only:
+    - tags
+  when: manual