v0.4.4 - Core Refactoring and Cocycles Fix

🚀 Major Updates

Core Architecture Refactoring

• Modular Structure: Split monolithic ripser.rs into organized modules:
  • algorithm.rs - Main Ripser algorithm coordination
  • reduction.rs - Matrix reduction operations
  • assembly.rs - Column assembly logic
• Improved Code Organization: Enhanced maintainability and readability
• Better Separation of Concerns: Each module has clear responsibilities

🐛 Cocycles Compatibility Fix

• Fixed Empty Cocycles Issue: Resolved bug where cocycles were returning empty results
• Format Compatibility: Cocycles now match original ripser.py format exactly
• Proper Vertex and Coefficient Handling: Cocycles now correctly include edge vertices and normalized coefficients
• 2D Array Format: Cocycles are returned as (n_simplices, 3) arrays matching original ripser

🧪 Comprehensive Testing

• New Test Suite: Added test_cocycles.py with 11 comprehensive test cases
• Multiple Scenarios: Tests cover single holes, multiple holes, empty cases, sparse matrices
• Compatibility Verification: Direct comparison with original ripser.py
• Edge Case Handling: Tests for various coefficient fields and higher dimensions

📊 Test Coverage

✅ test_square_cocycles - Basic cocycle functionality
✅ test_triangle_no_cocycles - No holes case  
✅ test_no_cocycles_flag - Flag disabled case
✅ test_cocycles_compatibility_with_original - Direct ripser.py comparison
✅ test_higher_dimensional_cocycles - H2 and beyond
✅ test_cocycles_with_different_coefficients - Various modulus values
✅ test_multiple_cocycles - Multiple independent holes
✅ test_cocycles_format_consistency - Format validation
✅ test_cocycles_empty_cases - Edge cases
✅ test_cocycles_sparse_matrix - Sparse matrix support
✅ test_cocycles_comprehensive_comparison - Multi-case validation

🔧 Technical Improvements

• Enhanced Python Interface: Better handling of cocycle format conversion
• Memory Efficiency: Optimized cocycle storage and processing
• Error Handling: Improved robustness in edge cases
• Code Quality: Better documentation and structure

📈 Performance

• Maintained Speed: Refactoring preserved high-performance characteristics
• Better Cache Locality: Improved data structure organization
• Optimized Memory Usage: More efficient cocycle representation

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Full Changelog: v0.4.3...v0.4.4