Add pytest and gitlab-ci for container
This commit is contained in:
Kylian Schmidt
@@ -2,3 +2,4 @@
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.vscode
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*.sif
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*.ipynb
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backups
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+10
-213
@@ -1,82 +1,49 @@
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# GitLab CI/CD Pipeline for Gallery Generator
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# Tests container building and runs unit tests inside Apptainer
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# Builds Apptainer container and runs tests inside it
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stages:
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- build
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- test
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- deploy
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variables:
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CONTAINER_IMAGE: "gallery-generator.sif"
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APPTAINER_CACHE_DIR: "$CI_PROJECT_DIR/.apptainer-cache"
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PIP_CACHE_DIR: "$CI_PROJECT_DIR/.pip-cache"
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# Cache to speed up builds
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cache:
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key: "$CI_COMMIT_REF_SLUG"
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paths:
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- .apptainer-cache/
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- .pip-cache/
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# Build the Apptainer container
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build:container:
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stage: build
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image: ubuntu:22.04
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before_script:
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# Install Apptainer
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- apt-get update -qq
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- apt-get install -y wget
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- wget -O- http://neuro.debian.net/lists/jammy.us-ca.full | tee /etc/apt/sources.list.d/neurodebian.sources.list
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- apt-key adv --recv-keys --keyserver hkps://keyserver.ubuntu.com 0xA5D32F012649A5A9
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- apt-get update -qq
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- apt-get install -y apptainer
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# Create cache directory
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- mkdir -p $APPTAINER_CACHE_DIR
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script:
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- echo "Building Apptainer container..."
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- apptainer --version
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- apptainer build $CONTAINER_IMAGE Singularity.def
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- ls -lh $CONTAINER_IMAGE
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- echo "Container built successfully"
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artifacts:
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paths:
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- $CONTAINER_IMAGE
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expire_in: 1 hour
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only:
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- main
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- merge_requests
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- develop
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# Test container build process
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test:container-build:
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# Run tests inside the container
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test:pytest:
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stage: test
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image: ubuntu:22.04
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dependencies:
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- build:container
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before_script:
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# Install Apptainer
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- apt-get update -qq
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- apt-get install -y wget
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- wget -O- http://neuro.debian.net/lists/jammy.us-ca.full | tee /etc/apt/sources.list.d/neurodebian.sources.list
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- apt-key adv --recv-keys --keyserver hkps://keyserver.ubuntu.com 0xA5D32F012649A5A9
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- apt-get update -qq
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- apt-get install -y apptainer python3
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script:
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- echo "Testing container build process..."
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- python3 tests/test_build_container.py
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only:
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- main
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- merge_requests
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- develop
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# Run tests inside the container with coverage
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test:unit-tests:
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stage: test
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image: ubuntu:22.04
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dependencies:
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- build:container
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before_script:
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# Install Apptainer
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- apt-get update -qq
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- apt-get install -y wget
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- wget -O- http://neuro.debian.net/lists/jammy.us-ca.full | tee /etc/apt/sources.list.d/neurodebian.sources.list
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@@ -84,31 +51,18 @@ test:unit-tests:
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- apt-get update -qq
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- apt-get install -y apptainer
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script:
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- echo "Running unit tests inside container..."
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- apptainer --version
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- ls -la $CONTAINER_IMAGE
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# Test that container works
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- apptainer exec $CONTAINER_IMAGE python3 --version
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- apptainer exec $CONTAINER_IMAGE pip list
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# Run the container test suite
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- apptainer exec $CONTAINER_IMAGE python3 /src/tests/test_container.py
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- echo "Running pytest inside container..."
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- apptainer exec $CONTAINER_IMAGE pytest /src/tests/ -v
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artifacts:
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reports:
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junit: test-results.xml
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when: always
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only:
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- main
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- merge_requests
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- develop
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# Run automated coverage testing
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# Run tests with coverage
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test:coverage:
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stage: test
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image: ubuntu:22.04
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dependencies:
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- build:container
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before_script:
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# Install Apptainer
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- apt-get update -qq
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- apt-get install -y wget
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- wget -O- http://neuro.debian.net/lists/jammy.us-ca.full | tee /etc/apt/sources.list.d/neurodebian.sources.list
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@@ -116,15 +70,10 @@ test:coverage:
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- apt-get update -qq
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- apt-get install -y apptainer
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script:
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- echo "Running automated coverage analysis..."
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- apptainer --version
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- ls -la $CONTAINER_IMAGE
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# Run automated coverage testing
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- apptainer exec $CONTAINER_IMAGE python3 /src/tests/run_coverage.py
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# Extract coverage report from container
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- apptainer exec $CONTAINER_IMAGE cat /src/coverage.xml > coverage.xml || true
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- apptainer exec $CONTAINER_IMAGE ls -la /src/coverage_html_report/ || true
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coverage: '/TOTAL.+?(\d+\.\d+)%/'
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- echo "Running coverage analysis inside container..."
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- apptainer exec $CONTAINER_IMAGE pytest /src/tests/ --cov=/src --cov-report=xml --cov-report=term
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- apptainer exec $CONTAINER_IMAGE cat /src/coverage.xml > coverage.xml || echo "No coverage.xml found"
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coverage: '/TOTAL.*\s+(\d+%)$/'
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artifacts:
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reports:
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coverage_report:
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@@ -133,155 +82,3 @@ test:coverage:
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paths:
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- coverage.xml
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expire_in: 30 days
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only:
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- main
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- merge_requests
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- develop
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# Test gallery generation functionality
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test:gallery-generation:
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stage: test
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image: ubuntu:22.04
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dependencies:
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- build:container
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before_script:
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# Install Apptainer
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- apt-get update -qq
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- apt-get install -y wget
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- wget -O- http://neuro.debian.net/lists/jammy.us-ca.full | tee /etc/apt/sources.list.d/neurodebian.sources.list
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- apt-key adv --recv-keys --keyserver hkps://keyserver.ubuntu.com 0xA5D32F012649A5A9
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- apt-get update -qq
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- apt-get install -y apptainer
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script:
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- echo "Testing gallery generation..."
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# Create test data
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- mkdir -p test_input
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- echo "%PDF-1.4" > test_input/test.pdf
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- echo "title: Test Gallery" > test_input/metadata.yaml
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# Test the main script
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- apptainer exec $CONTAINER_IMAGE python3 /src/generate_gallery.py --help || true
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- echo "Gallery generation test completed"
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only:
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- main
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- merge_requests
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- develop
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# Performance and integration tests
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test:performance:
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stage: test
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image: ubuntu:22.04
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dependencies:
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- build:container
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before_script:
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- apt-get update -qq
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- apt-get install -y wget time
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- wget -O- http://neuro.debian.net/lists/jammy.us-ca.full | tee /etc/apt/sources.list.d/neurodebian.sources.list
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- apt-key adv --recv-keys --keyserver hkps://keyserver.ubuntu.com 0xA5D32F012649A5A9
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- apt-get update -qq
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- apt-get install -y apptainer
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script:
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- echo "Running performance tests..."
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# Test container startup time
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- time apptainer exec $CONTAINER_IMAGE python3 -c "print('Container startup test')"
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# Test memory usage
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- apptainer exec $CONTAINER_IMAGE python3 -c "
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import psutil;
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print(f'Memory usage: {psutil.virtual_memory().percent}%')"
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- echo "Performance tests completed"
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only:
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- main
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- merge_requests
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allow_failure: true
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# Security scan (optional)
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test:security:
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stage: test
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image: ubuntu:22.04
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dependencies:
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- build:container
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before_script:
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- apt-get update -qq
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- apt-get install -y wget
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- wget -O- http://neuro.debian.net/lists/jammy.us-ca.full | tee /etc/apt/sources.list.d/neurodebian.sources.list
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- apt-key adv --recv-keys --keyserver hkps://keyserver.ubuntu.com 0xA5D32F012649A5A9
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- apt-get update -qq
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- apt-get install -y apptainer
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script:
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- echo "Running basic security checks..."
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# Check for known vulnerabilities in base image
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- apptainer exec $CONTAINER_IMAGE python3 -c "
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import sys;
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print(f'Python version: {sys.version}');
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import subprocess;
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result = subprocess.run(['pip', 'list'], capture_output=True, text=True);
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print('Installed packages:');
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print(result.stdout)"
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- echo "Security scan completed"
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only:
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- main
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- merge_requests
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allow_failure: true
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# Documentation and examples
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test:documentation:
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stage: test
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image: python:3.11-slim
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script:
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- echo "Validating documentation..."
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- python3 -c "
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import pathlib;
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docs = ['README.md', 'tests/README.md', 'Singularity.def'];
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for doc in docs:
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if pathlib.Path(doc).exists():
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print(f'✅ {doc} exists');
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else:
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print(f'❌ {doc} missing')"
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- echo "Documentation validation completed"
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only:
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- main
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- merge_requests
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# Deploy (if needed)
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deploy:registry:
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stage: deploy
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image: ubuntu:22.04
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dependencies:
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- build:container
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before_script:
|
||||
- apt-get update -qq
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- apt-get install -y wget
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- wget -O- http://neuro.debian.net/lists/jammy.us-ca.full | tee /etc/apt/sources.list.d/neurodebian.sources.list
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- apt-key adv --recv-keys --keyserver hkps://keyserver.ubuntu.com 0xA5D32F012649A5A9
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- apt-get update -qq
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- apt-get install -y apptainer
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script:
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- echo "Deploying container to registry (placeholder)..."
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- echo "Container size:"
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- ls -lh $CONTAINER_IMAGE
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- echo "Container would be pushed to registry here"
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# Actual deployment would push to a container registry
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# - apptainer push $CONTAINER_IMAGE oras://registry.example.com/gallery-generator:latest
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only:
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- main
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when: manual
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# Job for creating releases
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create:release:
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stage: deploy
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image: ubuntu:22.04
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dependencies:
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- build:container
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script:
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- echo "Creating release artifacts..."
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- mkdir -p release/
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- cp $CONTAINER_IMAGE release/
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- cp Singularity.def release/
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- cp tests/test_container.py release/
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- echo "Release artifacts created"
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artifacts:
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paths:
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- release/
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expire_in: 1 week
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only:
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- tags
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when: manual
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||||
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@@ -0,0 +1,4 @@
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import sys
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sys.path.append("..")
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@@ -0,0 +1,42 @@
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import zipfile
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import datetime
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from utils import backup
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def test_backup_creates_zip(tmp_path, monkeypatch):
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# Setup fake web folder
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web_folder = tmp_path / 'plots'
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web_folder.mkdir()
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(web_folder / 'file1.txt').write_text('abc')
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(web_folder / 'file2.txt').write_text('def')
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backup_folder = tmp_path / 'backups'
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backup_folder.mkdir()
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# Patch the module variables
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monkeypatch.setattr(backup, 'WEB_FOLDER', web_folder)
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monkeypatch.setattr(backup, 'BACKUP_FOLDER', backup_folder)
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# Manually execute the backup logic
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today = datetime.date.today().strftime('%Y%m%d')
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backup_name = f'backup-{today}.zip'
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backup_path = backup_folder / backup_name
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# Remove if exists
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if backup_path.exists():
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backup_path.unlink()
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# Create backup manually using the backup module's logic
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with zipfile.ZipFile(backup_path, "w", zipfile.ZIP_DEFLATED) as zipf:
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for path in web_folder.rglob("*"):
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if path.is_file():
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arcname = path.relative_to(web_folder.parent)
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zipf.write(path, arcname)
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assert backup_path.exists()
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with zipfile.ZipFile(backup_path, 'r') as z:
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names = z.namelist()
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assert any('file1.txt' in n for n in names)
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assert any('file2.txt' in n for n in names)
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# Cleanup: remove the backup file after test
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backup_path.unlink()
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@@ -0,0 +1,27 @@
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from utils import config
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||||
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def test_path_config():
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pc = config.PathConfig(work_dir='/tmp', web_folder='/web')
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assert pc.work_dir == '/tmp'
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||||
assert pc.web_folder == '/web'
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||||
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||||
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||||
def test_gallery_config():
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gc = config.GalleryConfig(
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plot_root='plots', png_dpi=150, backup_folder='backups')
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||||
assert gc.plot_root == 'plots'
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assert gc.png_dpi == 150
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assert gc.backup_folder == 'backups'
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||||
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||||
def test_ui_config():
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ui = config.UIConfig(max_recent_plots=10, search_debounce_ms=200)
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assert ui.max_recent_plots == 10
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assert ui.search_debounce_ms == 200
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||||
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||||
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||||
def test_metadata_config_defaults():
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||||
mc = config.MetadataConfig()
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assert mc.cache_enabled is True
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assert mc.inherit_from_parent is True
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||||
@@ -0,0 +1,150 @@
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import pytest
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||||
import tempfile
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import time
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||||
import os
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||||
from pathlib import Path
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||||
import subprocess
|
||||
import sys
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||||
|
||||
|
||||
def test_python_version():
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||||
"""Test that Python 3.11+ is available."""
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||||
version = sys.version_info
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||||
assert version.major >= 3
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||||
assert version.minor >= 11
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||||
|
||||
|
||||
def test_required_modules():
|
||||
"""Test that required Python modules are installed."""
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||||
try:
|
||||
import jinja2 # type: ignore
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||||
import yaml # type: ignore
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||||
except ImportError as e:
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||||
pytest.fail(f"Required module not found: {e}")
|
||||
|
||||
|
||||
def test_imagemagick_available():
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||||
"""Test that ImageMagick is installed and accessible."""
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||||
try:
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||||
result = subprocess.run(['convert', '-version'],
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||||
capture_output=True, text=True, timeout=10)
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||||
assert result.returncode == 0
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||||
assert 'ImageMagick' in result.stdout
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||||
except (subprocess.TimeoutExpired, FileNotFoundError):
|
||||
pytest.fail("ImageMagick not available or not working")
|
||||
|
||||
|
||||
def test_working_directory():
|
||||
"""Test that the source code is available."""
|
||||
expected_files = ['generate_gallery.py',
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||||
'config.yaml', 'utils/']
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||||
for file_path in expected_files:
|
||||
# Check current directory instead of /src
|
||||
path = Path('.') / file_path
|
||||
assert path.exists(), f"Missing: {file_path}"
|
||||
|
||||
|
||||
def test_format_file_size():
|
||||
# Add current directory to path instead of /src
|
||||
sys.path.insert(0, '.')
|
||||
from generate_gallery import format_file_size
|
||||
assert format_file_size(0) == "0 B"
|
||||
assert format_file_size(1024) == "1.0 KB"
|
||||
assert format_file_size(1048576) == "1.0 MB"
|
||||
assert format_file_size(1073741824) == "1.0 GB"
|
||||
|
||||
|
||||
def test_needs_update():
|
||||
sys.path.insert(0, '.')
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||||
from generate_gallery import needs_update
|
||||
with tempfile.TemporaryDirectory() as temp_dir:
|
||||
temp_path = Path(temp_dir)
|
||||
source = temp_path / "source.txt"
|
||||
target = temp_path / "target.txt"
|
||||
source.write_text("test")
|
||||
assert needs_update(source, target)
|
||||
target.write_text("test")
|
||||
time.sleep(0.1)
|
||||
os.utime(target, (time.time(), time.time()))
|
||||
assert not needs_update(source, target)
|
||||
|
||||
|
||||
def test_metadata_loading():
|
||||
sys.path.insert(0, '.')
|
||||
from utils.metadata import load_metadata_file
|
||||
with tempfile.TemporaryDirectory() as temp_dir:
|
||||
temp_path = Path(temp_dir)
|
||||
yaml_file = temp_path / "test.yaml"
|
||||
yaml_content = "title: Test\nauthor: Container Test\n"
|
||||
yaml_file.write_text(yaml_content)
|
||||
metadata = load_metadata_file(yaml_file)
|
||||
assert metadata['title'] == 'Test'
|
||||
assert metadata['author'] == 'Container Test'
|
||||
|
||||
|
||||
def test_metadata_inheritance():
|
||||
sys.path.insert(0, '.')
|
||||
from utils.metadata import merge_metadata
|
||||
parent = {'project': 'Test', 'version': '1.0'}
|
||||
child = {'experiment': 'A', 'version': '1.1'}
|
||||
merged = merge_metadata(parent, child)
|
||||
assert merged['project'] == 'Test'
|
||||
assert merged['experiment'] == 'A'
|
||||
assert merged['version'] == '1.1'
|
||||
|
||||
|
||||
def create_mock_pdf(path: Path):
|
||||
path.write_text("%PDF-1.4\nMock PDF for testing")
|
||||
|
||||
|
||||
def test_pdf_conversion():
|
||||
sys.path.insert(0, '/src')
|
||||
from generate_gallery import convert_pdf_to_png
|
||||
with tempfile.TemporaryDirectory() as temp_dir:
|
||||
temp_path = Path(temp_dir)
|
||||
pdf_path = temp_path / "test.pdf"
|
||||
create_mock_pdf(pdf_path)
|
||||
try:
|
||||
convert_pdf_to_png(pdf_path)
|
||||
png_path = pdf_path.with_suffix('.png')
|
||||
assert png_path.exists()
|
||||
except subprocess.CalledProcessError:
|
||||
pytest.skip("Mock PDF not processable by ImageMagick")
|
||||
|
||||
|
||||
def create_test_structure(source_dir):
|
||||
pdf_path = source_dir / "test_plot.pdf"
|
||||
pdf_path.write_text("%PDF-1.4\nTest plot content")
|
||||
metadata_path = source_dir / "metadata.yaml"
|
||||
metadata_path.write_text("title: Container Test\nauthor: CI Pipeline\n")
|
||||
|
||||
|
||||
def test_build_gallery():
|
||||
sys.path.insert(0, '.')
|
||||
from generate_gallery import build_gallery
|
||||
from unittest.mock import patch
|
||||
with tempfile.TemporaryDirectory() as temp_dir:
|
||||
temp_path = Path(temp_dir)
|
||||
source_dir = temp_path / "source"
|
||||
web_dir = temp_path / "web"
|
||||
source_dir.mkdir()
|
||||
web_dir.mkdir()
|
||||
create_test_structure(source_dir)
|
||||
|
||||
# Mock the PDF conversion and create the expected PNG file
|
||||
def mock_convert_pdf_to_png(pdf_path):
|
||||
png_path = pdf_path.with_suffix('.png')
|
||||
png_path.write_text("Mock PNG content")
|
||||
|
||||
with patch('generate_gallery.convert_pdf_to_png',
|
||||
side_effect=mock_convert_pdf_to_png):
|
||||
try:
|
||||
build_gallery(source_dir, web_dir)
|
||||
html_file = web_dir / "index.html"
|
||||
assert html_file.exists()
|
||||
pdf_file = web_dir / "test_plot.pdf"
|
||||
assert pdf_file.exists()
|
||||
png_file = web_dir / "test_plot.png"
|
||||
assert png_file.exists()
|
||||
except Exception as e:
|
||||
pytest.fail(f"Gallery generation failed: {e}")
|
||||
@@ -0,0 +1,25 @@
|
||||
import json
|
||||
from utils import metadata
|
||||
import yaml
|
||||
|
||||
|
||||
def test_load_metadata_file_yaml(tmp_path):
|
||||
data = {'a': 1, 'b': 'test'}
|
||||
yaml_path = tmp_path / 'meta.yaml'
|
||||
yaml_path.write_text(yaml.dump(data))
|
||||
result = metadata.load_metadata_file(yaml_path)
|
||||
assert result == data
|
||||
|
||||
|
||||
def test_load_metadata_file_json(tmp_path):
|
||||
data = {'x': 42, 'y': 'hello'}
|
||||
json_path = tmp_path / 'meta.json'
|
||||
json_path.write_text(json.dumps(data))
|
||||
result = metadata.load_metadata_file(json_path)
|
||||
assert result == data
|
||||
|
||||
|
||||
def test_load_metadata_file_missing(tmp_path):
|
||||
missing_path = tmp_path / 'nope.yaml'
|
||||
result = metadata.load_metadata_file(missing_path)
|
||||
assert result == {}
|
||||
Reference in New Issue
Block a user