Merge pull request #151 from kayjan/v0.15.1

V0.15.1

Author: kayjan

CHANGELOG.md

@@ -4,6 +4,14 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [0.15.1] - 2024-01-05
+### Added
+- Tree Constructor: `newick_to_tree` to convert Newick notation to tree.
+### Changed
+- Tree Exporter: `tree_to_newick` to accept more parameters to parse length and attributes.
+### Fixed
+- Misc: Automated doctest setup to use os operations instead of string operations.
+
 ## [0.15.0] - 2024-01-02
 ### Added
 - Tree Exporter: Export to Newick notation with `tree_to_newick`.
@@ -419,6 +427,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Utility Iterator: Tree traversal methods.
 - Workflow To Do App: Tree use case with to-do list implementation.
 
+[0.15.1]: https://github.com/kayjan/bigtree/compare/0.15.1...0.15.0
 [0.15.0]: https://github.com/kayjan/bigtree/compare/0.15.0...0.14.8
 [0.14.8]: https://github.com/kayjan/bigtree/compare/0.14.7...0.14.8
 [0.14.7]: https://github.com/kayjan/bigtree/compare/0.14.6...0.14.7

README.md

@@ -34,7 +34,7 @@ For **Tree** implementation, there are 9 main components.
    2. ``Node``, BaseNode with node name attribute
 2. [**✨ Constructing Tree**](https://bigtree.readthedocs.io/en/latest/bigtree/tree/construct.html)
    1. From `Node`, using parent and children constructors
-   2. From *str*, using tree display
+   2. From *str*, using tree display or Newick string notation
    3. From *list*, using paths or parent-child tuples
    4. From *nested dictionary*, using path-attribute key-value pairs or recursive structure
    5. From *pandas DataFrame*, using paths or parent-child columns
@@ -228,11 +228,11 @@ root.show(style="ascii")
 
 #### 2. **From *str***
 
-Construct nodes only.
+Construct nodes only. Newick string notation supports parsing attributes.
 
-{emphasize-lines="13"}
+{emphasize-lines="13,25"}
 ```python
-from bigtree import str_to_tree
+from bigtree import str_to_tree, newick_to_tree
 
 tree_str = """
 a
@@ -254,6 +254,18 @@ root.show()
 # │       └── h
 # └── c
 #     └── f
+
+newick_str = "((d,(g,h)e)b,(f)c)a"
+root = newick_to_tree(newick_str)
+root.show()
+# a
+# ├── b
+# │   ├── d
+# │   └── e
+# │       ├── g
+# │       └── h
+# └── c
+#     └── f
 ```
 
 #### 3. **From *list***

bigtree/tree/construct.py

@@ -998,6 +998,7 @@ def newick_to_tree(
     Variations supported
       - Support special characters ([, ], (, ), :, ,) in node name, attribute name, and attribute values if
         they are enclosed in single quotes i.e., '(name:!)'
+      - If there are no node names, it will be auto-filled with convention `nodeN` with N representing a number
 
     >>> from bigtree import newick_to_tree
     >>> root = newick_to_tree("((d,e)b,c)a")