Change log

The changelog will be updated on each packaged release beginning with toytree v.3.0. Please see the GitHub repo for more detailed commit messages and the history prior to v.3.0.

2023/6/5 (v.3.0.0)

• new unittest framework for testing methods on GitHub CI.
• new subpackage structure to organize growing code base.
• new functools wrap to keep API and module-level methods synced.
• cli New CLI for fast tree drawings in browser toytree --ts p --width X --height Y
• color New ToyColor module for easier color type validation and conversion.
• io Improved inference of internal label type in toytree.tree
• io Support defaults to np.nan if not present in parsed tree.
• io Completely new newick parser function. More flexible parsing.
• io Nexus parser can handle more types of nexus formatting.
• io Show informative message on NHX parsing errors/formatting.
• io Write Node and Edge features separately to NHX format.
• distance separated tree and node distance methods in submodules.
• distance new faster node distance functions for path, up or down.
• distance much faster algorithm for computing node distances.
• distance bipartition based tree distance functions developed and tested.
• distance quartet based tree distance functions developed and tested.
• mod new rooting functions including minimal ancestor deviation (MAD).
• mod added unittests for root and mod methods across wide variety of cases.
• core set default Node.dist to 0, including for root on random trees.
• core implemented new generic Node query method. Replace regex arg w/ "~name".
• core simplified Node object, exposed iter functions, made edit funcs private.
• core ToyTree now has .edge_features set to store default and additional features that should be treated as edge data. Edge data in NHX is stored as such.
• enum created enum subpackage to group partition iterators and counters.
• data replaced get_node_values with get_node_data.
• data missing values in Node data default to np.nan on get_node_data()
• data new expand_node_mapping for faster expansion of Node queries w/ regex.
• drawing renamed ToytreeMark to ToyTreeMark
• drawing Use text extents when auto-building canvas size.
• drawing Store tip coords in layout/ToyTreeMark for extents, tip angles, etc.
• drawing used aspect='fit-range' on circular layouts.
• drawing bugfix for circular trees 'p' edge type SVG paths.
• drawing bugfix to allow ts='p' with new validators when no Ne feature.
• drawing unrooted layout EA or ED algorithms with improved tip angles.
• style New TreeStyle serialization and validation is faster and easier to debug.
• style general color_mapping approach developed as (feature, ...).
• style general value_mapping approach developed as (feature, ...). Replace normalize_values.
• style create a 'b' builtin style for showing support values easily.
• style use same validation method for tip and node data w/ size arg.
• annotate New annotation subpackage created for extensible add-on plots.
• annotate Basic Node/Edge annotation drawing methods developed.
• annotate Pie charts and general rectangle/bar methods developed.
• annotate Custom Marks to allow for shift in px units, not just data units.
• annotate moved add_scale_bar and axes_styling methods to annotate.
• pcm continuous and discrete brownian sim funcs w/ similar syntax.
• network network parsing module.

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