Changelog¶

All notable changes to this project will be documented in this file.

The format is based on Keep a Changelog and this project adheres to Semantic Versioning.

Unreleased ¶

Callable proliferation_model support for true cell division. A dividing cell reuses the existing row for daughter 1, appends daughter 2, copies post-update U/S counts to both daughters and samples both daughter latent states from the configured fate distribution.
Division metadata in simulation outputs: birth_parent, birth_time, generation and last_division_time.
Marker-overlap mappings for explicit shared-marker configurations between state groups.
AnnData output now stores raw spliced counts in X and keeps paired raw unspliced and spliced layers.
Example notebooks for quickstart, dynamic transition rates, proliferation and QAD differentiation.

transition_rates is now the public transition-graph API for static matrices and dynamic callbacks.
Marker genes are assigned deterministically in gene-index order, with scalar marker_overlap applied to state pairs connected by static non-zero transition rates.

transition_matrix as a public SimulationParameters argument. Passing it now raises a targeted error pointing users to transition_rates.
default_transition_rate from the public API. Omitting transition_rates still uses an internal dense fallback rate for convenience, but users do not configure that rate directly.

Markov-modulated simulator with configurable state graphs and expression profiles.
Continuous integration for multi-version pytest and distribution builds.
Example notebooks illustrating dense and sparse transition topologies.
Documentation site with usage guide and API reference.