v3.1.0

Full Changelog: v3.0.2...v3.1.0

v3.0.2

Full Changelog: v3.0.1...v3.0.2

v3.0.1

Full Changelog: v3.0.0...v3.0.1

LZGraphs v3.0.0 — Complete C Rewrite

LZGraphs v3.0.0

Major release: the entire library has been rewritten as a C core with CPython bindings.

Highlights

• Unified LZGraph class — replaces AAPLZGraph, NDPLZGraph, NaiveLZGraph with a single class using variant='aap'|'ndp'|'naive'
• C performance — graph construction, simulation, and analytics run at native speed (80ms for 5K sequences, ~5K simulations/sec)
• LZ76 dictionary constraints — per-walk dynamic dictionary ensures every simulated sequence is a valid LZ76 decomposition
• Sentinel model — @/$ sentinels eliminate stop probabilities and end-of-sequence ambiguity

New Capabilities

• lzpgen() — exact generation probabilities (single or batch)
• simulate() — LZ-constrained sequence generation with optional V/J gene constraints
• Hill diversity numbers — D(0), D(1), D(2), and arbitrary orders via exact-probability importance sampling
• Occupancy predictions — predicted richness, overlap, and sharing spectra
• Graph algebra — union (|), intersection (&), difference (-), weighted_merge
• Bayesian posteriors — posterior() for personalized repertoire models
• ML feature extraction — reference-aligned vectors, mass profiles, 15-element stats vectors
• CLI tool (lzg) — 10 subcommands for terminal-based analysis
• Binary .lzg format — fast serialization with CRC-32C checksums

Documentation

• 39-page documentation site with tutorials, concept guides, and API reference
• Empirical comparison with IGoR, OLGA, and SONIA
• Performance benchmarks with real data

Breaking Changes

• AAPLZGraph(data) → LZGraph(sequences, variant='aap')
• walk_probability(seq) → lzpgen(seq)
• random_walk() / genomic_random_walk() → simulate(n)
• get_posterior() → posterior()
• pandas is no longer a dependency
• Serialization uses .lzg binary format (not pickle)

See the migration guide for details.

Install

pip install LZGraphs==3.0.0

Full documentation: https://MuteJester.github.io/LZGraphs/

v2.3.1

Release v2.3.1

v2.3.0

Release v2.3.0

v2.2.0

Release v2.2.0

v2.1.2

Release v2.1.2

v2.1.1

Release v2.1.1

v2.1.0

Release v2.1.0