Release v0.2.0 - Production Ready #7
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…nd unified test data structure - Add security module with path validation and input sanitization - Implement comprehensive testing framework (property-based, benchmarks, integration, mutation testing) - Create unified test data structure with cross-format consistency - Add enhanced configuration system with multi-format support - Reorganize test data into datasets/ with legacy/ preservation - Update all parsers and writers for improved performance and validation - Add extensive documentation including CLAUDE.md ultrathink guide - Implement 226 total tests with 225 passing for robust code coverage 🤖 Generated with [Claude Code](https://claude.ai/code) Co-Authored-By: Claude <[email protected]>
Comprehensive release preparation including documentation reorganization, CI optimization, validation framework, and critical bug fixes. ## Documentation Improvements ### Reorganized Structure - Created docs/technical/validation/ with comprehensive validation reports - Moved validation documentation from root to organized location - Simplified README.md (262→170 lines, user-focused) - Updated CLAUDE.md with v0.2.0 features and metrics - Enhanced docs/README.md with validation section ### Version Updates - Updated all version references to 0.2.0 - Finalized CHANGELOG.md with complete v0.2.0 feature list - Updated CITATION.cff metadata ## CI/CD Optimization - Added fast feedback job (quick-test) running ubuntu+3.11 first - Full test matrix (5 jobs) now runs only if quick-test passes - Removed duplicate testing (excluded ubuntu+3.11 from matrix) - Fixed security check that was hiding failures (removed || true) - Lint job runs in parallel for faster feedback ## Test Fixes (4 failing tests → all passing) ### Fixed STS Format Validation (3 tests) - Updated test_all_parsers.py to accept both 3-column and 4-column STS formats - v0.2.0 enhancement: auto-detection of SIZE column when available - Maintains backward compatibility with 3-column format ### Fixed Header Validation (1 test) - Enhanced STS parser to validate header column names - Now properly rejects invalid headers (e.g., "NAME\tSEQ1\tSEQ2") - Validates presence of NAME/ID field and FORWARD/REVERSE keywords ## File Cleanup - Removed 3 obsolete .old workflow files - Added logo.png to .gitignore - Deleted SESSION_SUMMARY.md (temporary session notes) ## New Features (from previous work, now committed) ### Alignment Functionality - Added align.py with high-level alignment API - Implemented 4 alignment providers: - BLAST (fast alignment) - Exonerate (sensitive alignment) - merPCR (modern Python, recommended) - me-PCR (legacy C tool) - 36 comprehensive alignment tests ### Validation Framework - Created tests/validation/ with 430-line validator - Added report_generator.py for multi-format reports - 23 real-data tests with 100% pass rate - Real tool integration testing (BLAST, Exonerate, merPCR) ### Enhanced STS Format Support - Auto-detection of 3 vs 4-column formats - Header/headerless file support - Compatible with me-PCR and merPCR output ## Test Results Before: 632 passed, 4 failed After: 636 passed, 0 failed ✅ All 611 core tests + 23 validation tests + 2 new tests passing. ## Breaking Changes None in this commit - all changes are backward compatible. Legacy config removal was in previous commits. 🤖 Generated with Claude Code https://claude.com/claude-code Co-Authored-By: Claude <[email protected]>
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Release v0.2.0 - Production Ready
This release includes comprehensive enhancements, validation, and documentation improvements for PrePrimer.
🎯 Highlights
📦 What's New
Alignment Functionality
align_primers()function for primer-to-reference alignmentpreprimer align --primers primers.bed --reference genome.fasta --aligner merpcrEnhanced STS Format Support
Validation Framework
docs/technical/validation/Documentation Improvements
docs/technical/validation/README.md- Validation hubdocs/technical/validation/real-data-testing.md- Comprehensive test reportdocs/technical/validation/v0.2.0-validation.md- Release validationCI/CD Optimization
quick-testjob (ubuntu+3.11) runs first (~2-3 min)|| truethat was hiding failureslintjob runs in parallel withquick-test🐛 Bug Fixes
Test Fixes (4 failing tests → all passing)
STS Format Validation (3 tests fixed)
test_all_parsers.pyto accept both 3-column and 4-column STS formatsHeader Validation (1 test fixed)
📊 Test Results
Before: 632 passed, 4 failed
After: 636 passed, 0 failed ✅
🧹 Cleanup
.oldworkflow fileslogo.pngto.gitignore(989KB unused file)SESSION_SUMMARY.md(temporary session notes)None - All changes are backward compatible.
The legacy configuration removal (
PrePrimerConfig→EnhancedConfig) was in previous commits. See CHANGELOG.md for migration guide.📝 Complete Details
See CHANGELOG.md for complete version history and upgrade guide.
✅ Validation Status
v0.2.0 is production-ready! 🚀
🤖 Generated with Claude Code