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#

Changed#

  • pycea.tl.clades now resets tdata.uns["clade_colors"] when number of clades differs from number of colors (#45)

  • pycea.pl.branches and pycea.pl.tree now default depth_key to None, resolving to tdata.uns["default_depth"] if present, otherwise "depth"

Fixed#

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

  • 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