Changelog

All notable changes to LZGraphs are documented here.

This project follows Semantic Versioning.

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[Unreleased]

Added

• Professional documentation with MkDocs Material theme
• Comprehensive tutorials and how-to guides
• API reference documentation
• FAQ and troubleshooting guide

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[1.1.1] - 2024

Fixed

• Fixed gene_variation() to correctly identify V/J genes (gene names like "TRBV30-1*01")
• Fixed visualization functions to use correct graph attribute access
• Added clean_node() method to NaiveLZGraph for consistency

Added

• use_log parameter to walk_probability() for all graph types
• save() and load() methods to NaiveLZGraph
• Enhanced Jupyter notebook examples

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[1.1.0] - 2024

Added

• Custom exceptions module with comprehensive error hierarchy
• Automated CI/CD pipeline with semantic-release
• Type hints throughout the codebase
• py.typed marker for type checker support

Changed

• Updated minimum Python version to 3.9
• Improved docstrings for all public APIs
• Enhanced test coverage

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[1.0.0] - 2024

Added

• Initial stable release
• AAPLZGraph for amino acid sequences
• NDPLZGraph for nucleotide sequences
• NaiveLZGraph for non-positional analysis
• K-diversity metrics (K100, K500, K1000, K5000)
• Entropy and perplexity functions
• Jensen-Shannon divergence
• Visualization functions
• LZBOW vectorizer
• NodeEdgeSaturationProbe

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Version History

For the complete version history, see the GitHub Releases page.

Migration Guides

Upgrading to 1.1.x

No breaking changes. New features are additive.

Upgrading from Pre-1.0

If upgrading from early development versions:

1. Update import statements to use new module structure
2. Use AAPLZGraph instead of deprecated class names
3. Update column names to cdr3_amino_acid / cdr3_rearrangement