kayjan · kayjan · Dec 25, 2023 · Dec 25, 2023 · Dec 25, 2023 · Dec 25, 2023
diff --git a/.gitignore b/.gitignore
@@ -3,8 +3,7 @@
 *pytest_cache/
 *__pycache__*
 
-tests/*png
-tests/*dot
 dist/
 */build/
 *.DS_Store
+assets/docstr
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -4,6 +4,15 @@ 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).
 
+## [0.14.8] - 2023-12-25
+### Changed
+- Tree Modifier: Enhance documentation examples.
+- Workflow To Do App: Change import and export logic.
+- Misc: Organize assets folder based on whether it originated from README, docstrings, or sphinx documentation.
+- Misc: Rename functions in `plot.py` utils file for coverage report.
+### Fixed
+- Misc: Fixed doctests and automate doctest checks.
+
 ## [0.14.7] - 2023-12-22
 ### Changed
 - Tree Helper: `get_tree_diff` enhanced to compare tree attributes by taking in `attr_list` parameter, and indicates difference with `(~)`.

diff --git a/README.md b/README.md
@@ -183,10 +183,10 @@ root.show()
 # └── c
 
 graph = tree_to_dot(root, node_colour="gold")
-graph.write_png("assets/demo_tree.png")
+graph.write_png("assets/docs/demo_tree.png")
 ```
 
-![Sample Tree Output](https://github.com/kayjan/bigtree/raw/master/assets/demo_tree.png)
+![Sample Tree Output](https://github.com/kayjan/bigtree/raw/master/assets/docs/demo_tree.png)
 
 {emphasize-lines="8-10"}
 ```python
@@ -897,22 +897,22 @@ tree_to_dataframe(
 # 4    /a/c    c      a          60
 
 graph = tree_to_dot(root, node_colour="gold")
-graph.write_png("assets/demo.png")
+graph.write_png("assets/docs/demo_dot.png")
 
 pillow_image = tree_to_pillow(root)
-pillow_image.save("assets/demo_pillow.png")
+pillow_image.save("assets/docs/demo_pillow.png")
 
 mermaid_md = tree_to_mermaid(root)
 print(mermaid_md)
 ```
 
-- demo.png
+- demo_dot.png
 
-![Sample Dot Image Output](https://github.com/kayjan/bigtree/raw/master/assets/demo.png)
+![Sample Dot Image Output](https://github.com/kayjan/bigtree/raw/master/assets/docs/demo_dot.png)
 
 - demo_pillow.png
 
-![Sample Pillow Image Output](https://github.com/kayjan/bigtree/raw/master/assets/demo_pillow.png)
+![Sample Pillow Image Output](https://github.com/kayjan/bigtree/raw/master/assets/docs/demo_pillow.png)
 
 - Mermaid flowchart
 ```mermaid
@@ -954,10 +954,10 @@ g = BinaryNode(7, parent=c)
 h = BinaryNode(8, parent=d)
 
 graph = tree_to_dot(a, node_colour="gold")
-graph.write_png("assets/demo_binarytree.png")
+graph.write_png("assets/docs/demo_binarytree.png")
 ```
 
-![Sample DAG Output](https://github.com/kayjan/bigtree/raw/master/assets/demo_binarytree.png)
+![Sample DAG Output](https://github.com/kayjan/bigtree/raw/master/assets/docs/demo_binarytree.png)
 
 2. **From *list***
 
@@ -1058,10 +1058,10 @@ h = DAGNode("h")
 g = DAGNode("g", parents=[c], children=[h])
 
 graph = dag_to_dot(a, node_colour="gold")
-graph.write_png("assets/demo_dag.png")
+graph.write_png("assets/docs/demo_dag.png")
 ```
 
-![Sample DAG Output](https://github.com/kayjan/bigtree/raw/master/assets/demo_dag.png)
+![Sample DAG Output](https://github.com/kayjan/bigtree/raw/master/assets/docs/demo_dag.png)
 
 2. **From *list***
 

diff --git a/assets/binarytree.png b/assets/binarytree.png
diff --git a/assets/construct_binarytree.png b/assets/construct_binarytree.png
diff --git a/assets/demo.png b/assets/demo.png
diff --git a/assets/demo_binarytree.png b/assets/demo_binarytree.png
diff --git a/assets/demo_dag.png b/assets/demo_dag.png
diff --git a/assets/demo_tree.png b/assets/demo_tree.png
diff --git a/assets/docs/demo_binarytree.png b/assets/docs/demo_binarytree.png
diff --git a/assets/docs/demo_dag.png b/assets/docs/demo_dag.png
diff --git a/assets/docs/demo_dot.png b/assets/docs/demo_dot.png
diff --git a/assets/demo_pillow.png → assets/docs/demo_pillow.png b/assets/demo_pillow.png → assets/docs/demo_pillow.png
diff --git a/assets/docs/demo_tree.png b/assets/docs/demo_tree.png
diff --git a/assets/custom_tree.png → assets/export_tree_dot.png b/assets/custom_tree.png → assets/export_tree_dot.png
diff --git a/assets/custom_tree_callable.png → assets/export_tree_dot_callable.png b/assets/custom_tree_callable.png → assets/export_tree_dot_callable.png
diff --git a/assets/dag_construct.png → assets/sphinx/dag_construct.png b/assets/dag_construct.png → assets/sphinx/dag_construct.png
diff --git a/assets/modify_advanced.png → assets/sphinx/modify_advanced.png b/assets/modify_advanced.png → assets/sphinx/modify_advanced.png
diff --git a/assets/modify_shift_and_copy.png → assets/sphinx/modify_shift_and_copy.png b/assets/modify_shift_and_copy.png → assets/sphinx/modify_shift_and_copy.png
diff --git a/assets/tree_construct.png → assets/sphinx/tree_construct.png b/assets/tree_construct.png → assets/sphinx/tree_construct.png
diff --git a/assets/weighted_tree.png → assets/sphinx/weighted_tree.png b/assets/weighted_tree.png → assets/sphinx/weighted_tree.png
diff --git a/bigtree/__init__.py b/bigtree/__init__.py
@@ -1,4 +1,4 @@
-__version__ = "0.14.7"
+__version__ = "0.14.8"
 
 from bigtree.binarytree.construct import list_to_binarytree
 from bigtree.dag.construct import dataframe_to_dag, dict_to_dag, list_to_dag

diff --git a/bigtree/binarytree/construct.py b/bigtree/binarytree/construct.py
@@ -25,9 +25,9 @@ def list_to_binarytree(
         ├── 6
         └── 7
     >>> graph = tree_to_dot(root, node_colour="gold")
-    >>> graph.write_png("assets/binarytree.png")
+    >>> graph.write_png("assets/construct_binarytree.png")
 
-    .. image:: https://github.com/kayjan/bigtree/raw/master/assets/binarytree.png
+    .. image:: https://github.com/kayjan/bigtree/raw/master/assets/construct_binarytree.png
 
     Args:
         heapq_list (List[int]): list containing integer node names, ordered in heapq fashion

diff --git a/bigtree/dag/export.py b/bigtree/dag/export.py
@@ -206,11 +206,12 @@ def dag_to_dot(
     >>> from IPython.display import Image, display
     >>> plt = Image(dag_graph.create_png())
     >>> display(plt)
+    <IPython.core.display.Image object>
 
     Export to image, dot file, etc.
 
-    >>> dag_graph.write_png("tree_dag.png")
-    >>> dag_graph.write_dot("tree_dag.dot")
+    >>> dag_graph.write_png("assets/docstr/tree_dag.png")
+    >>> dag_graph.write_dot("assets/docstr/tree_dag.dot")
 
     Export to string
 

diff --git a/bigtree/tree/construct.py b/bigtree/tree/construct.py
@@ -54,7 +54,7 @@ def add_path_to_tree(
     All paths should start from the same root node.
       - For example: Path strings should be "a/b", "a/c", "a/b/d" etc., and should not start with another root node.
 
-    >>> from bigtree import add_path_to_tree
+    >>> from bigtree import add_path_to_tree, Node
     >>> root = Node("a")
     >>> add_path_to_tree(root, "a/b/c")
     Node(/a/b/c, )
@@ -249,7 +249,7 @@ def add_dataframe_to_tree_by_path(
       - For example: Path strings should be "a/b", "a/c", "a/b/d" etc. and should not start with another root node.
 
     >>> import pandas as pd
-    >>> from bigtree import add_dataframe_to_tree_by_path
+    >>> from bigtree import add_dataframe_to_tree_by_path, Node
     >>> root = Node("a")
     >>> path_data = pd.DataFrame([
     ...     ["a", 90],
@@ -348,7 +348,7 @@ def add_dataframe_to_tree_by_name(
     Note that if multiple nodes have the same name, attributes will be added to all nodes sharing same name.
 
     >>> import pandas as pd
-    >>> from bigtree import add_dataframe_to_tree_by_name
+    >>> from bigtree import add_dataframe_to_tree_by_name, Node
     >>> root = Node("a")
     >>> b = Node("b", parent=root)
     >>> name_data = pd.DataFrame([

diff --git a/bigtree/tree/export.py b/bigtree/tree/export.py
@@ -221,7 +221,7 @@ def yield_tree(
 
     **Printing tree**
 
-    >>> from bigtree import Node, print_tree
+    >>> from bigtree import Node, yield_tree
     >>> root = Node("a", age=90)
     >>> b = Node("b", age=65, parent=root)
     >>> c = Node("c", age=60, parent=root)
@@ -638,11 +638,12 @@ def tree_to_dot(
     >>> from IPython.display import Image, display
     >>> plt = Image(graph.create_png())
     >>> display(plt)
+    <IPython.core.display.Image object>
 
     Export to image, dot file, etc.
 
-    >>> graph.write_png("tree.png")
-    >>> graph.write_dot("tree.dot")
+    >>> graph.write_png("assets/docstr/tree.png")
+    >>> graph.write_dot("assets/docstr/tree.dot")
 
     Export to string
 
@@ -676,9 +677,9 @@ def tree_to_dot(
     >>> d = CustomNode("d", node_shape="square", edge_label="child", parent=b)
     >>> e = CustomNode("e", node_shape="square", edge_label="child", parent=b)
     >>> graph = tree_to_dot(root, node_colour="gold", node_shape="diamond", node_attr="node_attr", edge_attr="edge_attr")
-    >>> graph.write_png("assets/custom_tree.png")
+    >>> graph.write_png("assets/export_tree_dot.png")
 
-    .. image:: https://github.com/kayjan/bigtree/raw/master/assets/custom_tree.png
+    .. image:: https://github.com/kayjan/bigtree/raw/master/assets/export_tree_dot.png
 
     Alternative way to define node and edge attributes (using callable function)
 
@@ -694,9 +695,9 @@ def tree_to_dot(
     >>> d = CustomNode("d", parent=b)
     >>> e = CustomNode("e", parent=b)
     >>> graph = tree_to_dot(root, node_colour="gold", node_attr=get_node_attribute)
-    >>> graph.write_png("assets/custom_tree_callable.png")
+    >>> graph.write_png("assets/export_tree_dot_callable.png")
 
-    .. image:: https://github.com/kayjan/bigtree/raw/master/assets/custom_tree_callable.png
+    .. image:: https://github.com/kayjan/bigtree/raw/master/assets/export_tree_dot_callable.png
 
     Args:
         tree (Node/List[Node]): tree or list of trees to be exported
@@ -803,8 +804,8 @@ def tree_to_pillow(
 
     Export to image (PNG, JPG) file, etc.
 
-    >>> pillow_image.save("tree_pillow.png")
-    >>> pillow_image.save("tree_pillow.jpg")
+    >>> pillow_image.save("assets/docstr/tree_pillow.png")
+    >>> pillow_image.save("assets/docstr/tree_pillow.jpg")
 
     Args:
         tree (Node): tree to be exported

diff --git a/bigtree/utils/plot.py b/bigtree/utils/plot.py
@@ -67,12 +67,12 @@ def reingold_tilford(
         x_offset (float): graph offset of x-coordinates
         y_offset (float): graph offset of y-coordinates
     """
-    first_pass(tree_node, sibling_separation, subtree_separation)
-    x_adjustment = second_pass(tree_node, level_separation, x_offset, y_offset)
-    third_pass(tree_node, x_adjustment)
+    _first_pass(tree_node, sibling_separation, subtree_separation)
+    x_adjustment = _second_pass(tree_node, level_separation, x_offset, y_offset)
+    _third_pass(tree_node, x_adjustment)
 
 
-def first_pass(
+def _first_pass(
     tree_node: T, sibling_separation: float, subtree_separation: float
 ) -> None:
     """
@@ -116,7 +116,7 @@ def first_pass(
     """
     # Post-order iteration (LRN)
     for child in tree_node.children:
-        first_pass(child, sibling_separation, subtree_separation)
+        _first_pass(child, sibling_separation, subtree_separation)
 
     _x = 0.0
     _mod = 0.0
@@ -274,7 +274,7 @@ def _get_subtree_shift(
     return cum_shift + new_shift
 
 
-def second_pass(
+def _second_pass(
     tree_node: T,
     level_separation: float,
     x_offset: float,
@@ -322,7 +322,7 @@ def second_pass(
     if tree_node.children:
         return max(
             [
-                second_pass(
+                _second_pass(
                     child,
                     level_separation,
                     x_offset,
@@ -337,7 +337,7 @@ def second_pass(
     return max(x_adjustment, -final_x)
 
 
-def third_pass(tree_node: BaseNode, x_adjustment: float) -> None:
+def _third_pass(tree_node: BaseNode, x_adjustment: float) -> None:
     """Adjust all x-coordinates by an adjustment value so that every x-coordinate is greater than or equal to 0.
     Modifies tree in-place.
 
@@ -350,4 +350,4 @@ def third_pass(tree_node: BaseNode, x_adjustment: float) -> None:
 
         # Pre-order iteration (NLR)
         for child in tree_node.children:
-            third_pass(child, x_adjustment)
+            _third_pass(child, x_adjustment)
diff --git a/bigtree/workflows/app_todo.py b/bigtree/workflows/app_todo.py
@@ -5,8 +5,8 @@
 from typing import Any, List, Union
 
 from bigtree.node.node import Node
-from bigtree.tree.construct import dict_to_tree
-from bigtree.tree.export import print_tree, tree_to_dict
+from bigtree.tree.construct import nested_dict_to_tree
+from bigtree.tree.export import print_tree, tree_to_nested_dict
 from bigtree.tree.search import find_child_by_name, find_name
 
 logging.getLogger(__name__).addHandler(logging.NullHandler())
@@ -72,8 +72,8 @@ class AppToDo:
 
     *Exporting and Importing List*
 
-    >>> app.save("list.json")
-    >>> app2 = AppToDo.load("list.json")
+    >>> app.save("assets/docstr/list.json")
+    >>> app2 = AppToDo.load("assets/docstr/list.json")
     >>> app2.show()
     To Do App
     ├── General
@@ -242,7 +242,7 @@ def load(json_path: str) -> AppToDo:
         with open(json_path, "r") as fp:
             app_dict = json.load(fp)
         _app = AppToDo("dummy")
-        AppToDo.__setattr__(_app, "_root", dict_to_tree(app_dict["root"]))
+        AppToDo.__setattr__(_app, "_root", nested_dict_to_tree(app_dict["root"]))
         return _app
 
     def save(self, json_path: str) -> None:
@@ -254,7 +254,7 @@ def save(self, json_path: str) -> None:
         if not json_path.endswith(".json"):
             raise ValueError("Path should end with .json")
 
-        node_dict = tree_to_dict(self._root, all_attrs=True)
+        node_dict = tree_to_nested_dict(self._root, all_attrs=True)
         app_dict = {"root": node_dict}
         with open(json_path, "w") as fp:
             json.dump(app_dict, fp)
diff --git a/docs/source/bigtree/dag/construct.rst b/docs/source/bigtree/dag/construct.rst
@@ -23,8 +23,8 @@ Construct Directed Acyclic Graph (DAG) from list, dictionary, and pandas DataFra
 These functions are not standalone functions.
 Under the hood, they have the following dependency,
 
-.. image:: https://github.com/kayjan/bigtree/raw/master/assets/dag_construct.png
-   :target: https://github.com/kayjan/bigtree/raw/master/assets/dag_construct.png
+.. image:: https://github.com/kayjan/bigtree/raw/master/assets/sphinx/dag_construct.png
+   :target: https://github.com/kayjan/bigtree/raw/master/assets/sphinx/dag_construct.png
    :alt: DAG Constructor Dependency Diagram
 
 .. automodule:: bigtree.dag.construct

diff --git a/docs/source/bigtree/tree/construct.rst b/docs/source/bigtree/tree/construct.rst
@@ -57,8 +57,8 @@ To add attributes to existing tree,
 These functions are not standalone functions.
 Under the hood, they have the following dependency,
 
-.. image:: https://github.com/kayjan/bigtree/raw/master/assets/tree_construct.png
-   :target: https://github.com/kayjan/bigtree/raw/master/assets/tree_construct.png
+.. image:: https://github.com/kayjan/bigtree/raw/master/assets/sphinx/tree_construct.png
+   :target: https://github.com/kayjan/bigtree/raw/master/assets/sphinx/tree_construct.png
    :alt: Tree Constructor Dependency Diagram
 
 .. automodule:: bigtree.tree.construct

diff --git a/docs/source/bigtree/tree/modify.rst b/docs/source/bigtree/tree/modify.rst
@@ -91,8 +91,8 @@ All other methods calls these 2 methods directly.
 Tree Modification Illustration
 ----------------------------------
 
-.. image:: https://github.com/kayjan/bigtree/raw/master/assets/modify_shift_and_copy.png
-   :target: https://github.com/kayjan/bigtree/raw/master/assets/modify_shift_and_copy.png
+.. image:: https://github.com/kayjan/bigtree/raw/master/assets/sphinx/modify_shift_and_copy.png
+   :target: https://github.com/kayjan/bigtree/raw/master/assets/sphinx/modify_shift_and_copy.png
    :width: 80%
    :align: center
    :alt: Shift and Copy Example
@@ -126,8 +126,8 @@ Tree Modification Illustration
      - "/a/b/c"
      - Shift/copy node `c`, skip if "/a/c" cannot be found
 
-.. image:: https://github.com/kayjan/bigtree/raw/master/assets/modify_advanced.png
-   :target: https://github.com/kayjan/bigtree/raw/master/assets/modify_advanced.png
+.. image:: https://github.com/kayjan/bigtree/raw/master/assets/sphinx/modify_advanced.png
+   :target: https://github.com/kayjan/bigtree/raw/master/assets/sphinx/modify_advanced.png
    :alt: Advanced Shift Example
 
 .. list-table:: Sample Tree Modification (Advanced)

diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -28,12 +28,20 @@
     "myst_parser",
     "sphinxemoji.sphinxemoji",
     "sphinx.ext.mathjax",
+    "sphinx.ext.doctest",
 ]
 autodoc_default_options = {"autosummary": True}
 sphinxemoji_style = "twemoji"
 myst_enable_extensions = [
     "attrs_block",
 ]
+base_dir = "/".join(os.getcwd().split("/")[:-2])
+doctest_global_setup = f"""
+import os
+os.chdir("{base_dir}")
+if not os.path.exists("assets/docstr"):
+    os.mkdir("assets/docstr")
+"""
 
 templates_path = ["_templates"]
 exclude_patterns = []