Refactor plotting functions, improve tests, and update README

.gitignore

@@ -11,3 +11,9 @@ evn*
 tmp
 .idea
 .coverage
+*.egg-info
+dist
+build
+test.ipynb
+.tox
+.python-version

CHANGELOG.md

@@ -10,7 +10,23 @@ Fixes:
 
 -  -->
 
-## 0.0.13 (2025-03-31)
+## 0.0.15 (2026-07-16)
+
+Features:
+
+- Replaced `ete3` runtime dependency with a custom `TreeNode`/`Tree` implementation in `src/pymutspec/annotation/phylo_tree.py`
+- Added BioPython-based Newick parsing and an ete3-compatible tree API (node iteration, branch traversal, distance computation, node search, and Newick serialisation)
+- Added `tests/test_tree_vs_ete3.py` to verify parity with ete3 `PhyloTree` for tree loading and node/edge iteration
+
+Fixes:
+
+- Kept `ete3` only in `dev` extras for comparison tests
+- Fixed `get_tree_len` name to `get_tree_height` to better reflect its purpose (computing tree height from root to leaves)
+- Removed requirement for trees have outgroup and be named "ROOT"; now any tree can be used, and the ingroup is defined as the sister node of the outgroup if present, or the root if not.
+
+**Full Changelog**: https://github.com/mitoclub/PyMutSpec/compare/0.0.14...0.0.15
+
+## 0.0.14 (2025-03-31)
 
 Features:
 

LICENSE

@@ -1,4 +1,4 @@
-Copyright (c) 2025 mitofungen.com
+Copyright (c) 2025 kpotoh
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal