Merge pull request #217 from kayjan/fix-nan

Fix nan

Author: kayjan

.pre-commit-config.yaml

@@ -10,6 +10,10 @@ repos:
         args: ["--pytest-test-first"]
       - id: requirements-txt-fixer
       - id: trailing-whitespace
+  - repo: https://github.com/commitizen-tools/commitizen
+    rev: v3.18.3
+    hooks:
+      - id: commitizen
   - repo: https://github.com/pycqa/isort
     rev: 5.13.2
     hooks:

CHANGELOG.md

@@ -5,13 +5,18 @@ 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).
 
 ## [Unreleased]
+
+## [0.16.3] - 2024-03-14
 ### Added
 - BaseNode: Add diameter property.
 - Misc: Testing to include benchmark timings for tree creation, compare benchmark tests across commits, reject pull request if benchmark tests fails.
 - Misc: Documentation to include benchmark results.
 ### Changed
 - Misc: Documentation to enable zooming in of images, add navigation section headers, remove some meta tags.
 - Misc: Split up testing into multiple conftest files.
+### Fixed
+- Tree Constructor: Tree creation from dictionary adds None for empty attributes instead of np.nan.
+- [#216] Tree Exporter: `attr_omit_null` to handle nan/null values in addition to checking for None.
 
 ## [0.16.2] - 2024-02-06
 ### Added
@@ -502,7 +507,8 @@ 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.
 
-[Unreleased]: https://github.com/kayjan/bigtree/compare/0.16.2...HEAD
+[Unreleased]: https://github.com/kayjan/bigtree/compare/0.16.3...HEAD
+[0.16.3]: https://github.com/kayjan/bigtree/compare/0.16.2...0.16.3
 [0.16.2]: https://github.com/kayjan/bigtree/compare/0.16.1...0.16.2
 [0.16.1]: https://github.com/kayjan/bigtree/compare/0.16.0...0.16.1
 [0.16.0]: https://github.com/kayjan/bigtree/compare/0.15.7...0.16.0

bigtree/__init__.py

@@ -1,4 +1,4 @@
-__version__ = "0.16.2"
+__version__ = "0.16.3"
 
 from bigtree.binarytree.construct import list_to_binarytree
 from bigtree.dag.construct import dataframe_to_dag, dict_to_dag, list_to_dag

bigtree/tree/construct.py

@@ -233,6 +233,7 @@ def add_dict_to_tree_by_name(
 
     # Convert dictionary to dataframe
     data = pd.DataFrame(name_attrs).T.rename_axis("NAME").reset_index()
+    data = data.replace({float("nan"): None})
     return add_dataframe_to_tree_by_name(tree, data=data, join_type=join_type)
 
 
@@ -681,6 +682,7 @@ def dict_to_tree(
 
     # Convert dictionary to dataframe
     data = pd.DataFrame(path_attrs).T.rename_axis("PATH").reset_index()
+    data = data.replace({float("nan"): None})
     return dataframe_to_tree(
         data,
         sep=sep,

bigtree/tree/export.py

@@ -1,6 +1,7 @@
 from __future__ import annotations
 
 import collections
+import math
 from typing import Any, Callable, Dict, Iterable, List, Optional, Tuple, TypeVar, Union
 from urllib.request import urlopen
 
@@ -50,6 +51,20 @@
 T = TypeVar("T", bound=Node)
 
 
+def _isnull(value: Any) -> bool:
+    """Check if value is null
+
+    Args:
+        value (Any): value to check
+
+    Returns:
+        (bool)
+    """
+    if not value or math.isnan(value):
+        return True
+    return False
+
+
 def print_tree(
     tree: T,
     node_name_or_path: str = "",
@@ -195,7 +210,7 @@ def print_tree(
                     attr_str_list = [
                         f"{attr_name}={_node.get_attr(attr_name)}"
                         for attr_name in attr_list
-                        if _node.get_attr(attr_name)
+                        if not _isnull(_node.get_attr(attr_name))
                     ]
                 else:
                     attr_str_list = [

tests/tree/conftest.py

@@ -93,7 +93,7 @@ def tree_node_negative_null_attr():
     c = Node("c", age=0)
     d = Node("d", age=1)
     e = Node("e", age=None)
-    f = Node("f")
+    f = Node("f", age=float("nan"))
     g = Node("g")
     h = Node("h")
 

tests/tree/test_construct.py

@@ -582,6 +582,18 @@ def test_add_dict_to_tree_by_name_custom_node_type(self):
         assert_tree_structure_customnode_root_attr(root)
         assert_tree_structure_node_root(root)
 
+    def test_add_dict_to_tree_by_name_inconsistent_attributes(self):
+        name_dict = {
+            "a": {"age": 90},
+            "b": {},
+            "c": {"age": 60},
+        }
+        root = add_dict_to_tree_by_name(self.root, name_dict)
+        expected_root_str = "a [age=90.0]\n" "├── b\n" "└── c [age=60.0]\n"
+        assert_print_statement(
+            print_tree, expected_root_str, root, all_attrs=True, max_depth=2
+        )
+
 
 class TestAddDataFrameToTreeByPath(unittest.TestCase):
     def setUp(self):
@@ -1683,6 +1695,17 @@ def test_dict_to_tree_different_root_error():
             root1=root1, root2=root2
         )
 
+    @staticmethod
+    def test_dict_to_tree_inconsistent_attributes():
+        path_dict = {
+            "a": {"age": 90},
+            "a/b": {},
+            "a/c": {"age": 60},
+        }
+        root = dict_to_tree(path_dict)
+        expected_root_str = "a [age=90.0]\n" "├── b\n" "└── c [age=60.0]\n"
+        assert_print_statement(print_tree, expected_root_str, root, all_attrs=True)
+
 
 class TestNestedDictToTree(unittest.TestCase):
     def setUp(self):

tests/tree/test_export.py

@@ -100,7 +100,7 @@ def test_print_tree_attr_omit_null_false(tree_node_negative_null_attr):
             "│       ├── g\n"
             "│       └── h\n"
             "└── c [age=0]\n"
-            "    └── f\n"
+            "    └── f [age=nan]\n"
         )
         assert_print_statement(
             print_tree,