Changelog

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#

Added#

  • pycea.tl.ancestral_linkage now stores tdata.uns['{key_added}_symmetrized_linkage_stats'] when symmetrize is not False and test='permutation': a table with one row per unordered category pair giving the symmetrized value, permuted value, z-score, and a p-value for the symmetrized linkage.

Changed#

Fixed#

[0.3.0] - 2026-07-08#

Added#

  • pycea.tl.parsimony and pycea.tl.fitch_count for small-parsimony scoring and the FitchCount transition-count algorithm (migrated from Cassiopeia) (#59)

  • pycea.pl.ancestral_linkage for plotting the pairwise linkage matrix as a clustered heatmap (#58)

  • Added fast "sum" method to pycea.tl.ancestral_states (#54, #56)

  • Added additional node ploting customization - outline_width and option to directly specify color with hex code (#53)

  • pycea.tl.ancestral_linkage for computing relatedness of cells in different categories, with options for pairwise or target-category linkage permutation testing, and normalization. (#52, #55, #58)

  • Added angle_range parameter for plotting polar trees with pycea.pl.tree and pycea.pl.branches (#51)

Changed#

  • Added support for tdata.alignment != 'leaves' to relevant functions in pycea.pl and pycea.tl (#50)

  • Vectorized continuous color computation in pycea.pl.tree and pycea.pl.branches for improved node plotting performance (#48)

Fixed#

  • Fixed IndexError retrieving var_names/layer data under anndata>=0.13 by indexing the column directly instead of via the deprecated obs_vector (#58)

  • pycea.get.palette now correctly collects unique categories across all columns of array data, not just the first column (#57)

  • Fixed bug in LCA distance computation when for non-ultrametric tree (#49)

  • Legend placement now works with tight and constrained layouts (#45)

[0.2.0] - 2025-11-14#

Added#

  • Added pycea.tl.expansion_test for computing expansion p-values to detect clades under selection

  • pycea.tl.partition_test to test for statistically significant differences between leaf partitions. (#40)

  • pycea.tl.expansion_test for computing expansion p-values to detect expanding clades. (#38)

Changed#

  • Replaced tdata.obs_keys() with tdata.obs.keys() to conform with anndata API changes. (#41)

  • pycea.tl.fitness no longer returns a multi-indexed DataFrame when tdata contains a single tree. (#38)

Fixed#

  • Fixed node plotting when isinstance(nodes,str). (#39)

[0.1.0] - 2025-09-19#

Added#

  • pycea.get module for data retrieval (#32)

  • Added pycea.tl.n_extant and pycea.pl.n_extant for calculating and plotting the number of extant lineages over time (#33)

  • Added pycea.tl.fitness for estimating fitness of nodes in a tree (#35)

Changed#

  • Only require tree parameter to be specified when trees in tdata actually overlap (#37)

Fixed#

  • Sorting now preserves edge metadata (#31)

[0.0.1]#

Added#

  • Basic tool, preprocessing and plotting functions