Add comprehensive local testing framework with golden master verifica… #106
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…tion This commit introduces a 4-layer testing architecture for LAAVA: 1. **Unit Tests** (test_unit_laava_modules.py) - Direct testing of LAAVA Python modules (prepare_annotation, summarize_alignment) - 11 tests covering core functions, error handling, and data integrity - Comprehensive documentation explaining test purpose and value 2. **Integration Tests** (test_integration_duplicate_removal.py) - End-to-end pipeline validation focusing on duplicate removal behavior - 6 tests validating data integrity and business logic - Clear documentation distinguishing from unit tests 3. **Golden Master Verification** (test_output_gold_verification.py) - Naive catch-all content verification using SHA256 hashes - 14 tests detecting ANY changes in pipeline outputs - Handles gzip timestamp issues by hashing decompressed content - Forces conscious decisions about output changes 4. **Enhanced Test Infrastructure** - Updated Makefile with test-local target running all 47 tests - Updated test/Makefile with comprehensive local testing - Updated README.md with comprehensive testing documentation - Updated src/make_report.sh for better local testing support - Clear separation of test types and their purposes Key Features: - 47 total tests (100% passing) - Deterministic golden master verification (fixed gzip timestamp issues) - Comprehensive documentation for maintainability - Easy local testing workflow: 'make test-local'
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Pull Request Overview
This PR introduces a comprehensive local testing framework for LAAVA by adding unit tests, integration tests, and golden master verification, along with updating Makefiles, the report generation script, and documentation for local conda‐based testing.
- Added 47 tests across unit, integration, and golden master categories
- Enhanced test infrastructure in Makefiles and supporting scripts for local testing workflows
- Updated documentation in README.md to guide conda-based local testing
Reviewed Changes
Copilot reviewed 7 out of 7 changed files in this pull request and generated no comments.
Show a summary per file
| File | Description |
|---|---|
| test/test_unit_laava_modules.py | New unit tests for core module functionality |
| test/test_output_gold_verification.py | Golden master tests ensuring output content consistency |
| test/test_integration_duplicate_removal.py | Integration tests validating duplicate removal and pipeline flow |
| test/Makefile | Added new targets (test-local, sc-local, ss-local) for local testing |
| src/make_report.sh | Updated to explicitly call Python scripts with dynamic path resolution |
| README.md | Added section documenting local conda-based testing |
| Makefile | Added test-local target to support local testing without Docker |
Comments suppressed due to low confidence (2)
test/Makefile:21
- The target references the variable '$(in_dir)' (e.g., $(in_dir)/sc.subsample005.bam) without a clear definition in this Makefile. Consider defining or documenting 'in_dir' to ensure maintainability and clarity.
sc-local: $(out_dir)/sc.reference_names.tsv
dougnukem
reviewed
Jun 25, 2025
| @@ -14,6 +14,52 @@ clean: | |||
| test: sc ss | |||
| pytest test_outputs.py | |||
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| # Local testing without Docker (using conda) | |||
| test-local: sc-local ss-local | |||
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@mcrocker-bioborg can you make sure these tests all get run in the github action CI/CD?
laava/.github/workflows/tests.yaml
Line 67 in f2c4cab
dougnukem
approved these changes
Jun 25, 2025
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…tion
This commit introduces a 4-layer testing architecture for LAAVA:
Unit Tests (test_unit_laava_modules.py)
Integration Tests (test_integration_duplicate_removal.py)
Golden Master Verification (test_output_gold_verification.py)
Enhanced Test Infrastructure
Key Features: