From 45d6550c881f9ceed55c2e87ba0b05aec8a9b666 Mon Sep 17 00:00:00 2001
From: William Song <30965609+Freakwill@users.noreply.github.com>
Date: Tue, 15 Sep 2020 19:53:49 +0800
Subject: [PATCH 01/44] Update tree.py

---
 treelib/tree.py | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/treelib/tree.py b/treelib/tree.py
index 6ee18c9..e2cfa3c 100644
--- a/treelib/tree.py
+++ b/treelib/tree.py
@@ -889,9 +889,8 @@ def subtree(self, nid, identifier=None):
             # define nodes parent/children in this tree
             # all pointers are the same as copied tree, except the root
             st[node_n].clone_pointers(self._identifier, st.identifier)
-            if node_n == nid:
-                # reset root parent for the new tree
-                st[node_n].set_predecessor(None, st.identifier)
+        # reset root parent for the new tree
+        st[nid].set_predecessor(None, st.identifier)
         return st
 
     def update_node(self, nid, **attrs):

From 5024c90f38f4905f0fad75746fdb32066a9d5bb7 Mon Sep 17 00:00:00 2001
From: William Song <30965609+Freakwill@users.noreply.github.com>
Date: Mon, 21 Jun 2021 09:28:46 +0800
Subject: [PATCH 02/44] Create random_tree.py

---
 examples/random_tree.py | 25 +++++++++++++++++++++++++
 1 file changed, 25 insertions(+)
 create mode 100644 examples/random_tree.py

diff --git a/examples/random_tree.py b/examples/random_tree.py
new file mode 100644
index 0000000..d1521e5
--- /dev/null
+++ b/examples/random_tree.py
@@ -0,0 +1,25 @@
+"""
+Generate a tree randomly
+"""
+
+import random
+from treelib import Tree
+
+def _random(max_depth=5, min_width=1, max_width=2, offset=(0,)):
+    # just have fun
+    tree = Tree()
+    root = tree.create_node(identifier=offset)
+    if max_depth == 0:
+        return tree
+    elif max_depth ==1:
+        nb = random.randint(min_width, max_width)
+        for i in range(nb):
+            tree.create_node(identifier=offset+(i,), parent=offset)
+    else:
+        nb = random.randint(min_width, max_width)
+        for i in range(nb):
+            subtree = _random(max_depth=max_depth-1, max_width=max_width, offset=offset+(i,))
+            tree.paste(offset, subtree)
+    return tree
+
+print(_random())

From 545a66d311c712dae461671859c4d7a8bf1a7d3a Mon Sep 17 00:00:00 2001
From: William Song <30965609+Freakwill@users.noreply.github.com>
Date: Mon, 21 Jun 2021 10:02:15 +0800
Subject: [PATCH 03/44] Update tree.py

---
 treelib/tree.py | 28 ++++++++++++++++++++++++++++
 1 file changed, 28 insertions(+)

diff --git a/treelib/tree.py b/treelib/tree.py
index e2cfa3c..2b673a1 100644
--- a/treelib/tree.py
+++ b/treelib/tree.py
@@ -295,6 +295,12 @@ def all_nodes_itr(self):
         Added by William Rusnack
         """
         return self._nodes.values()
+    
+    def iternodes(self):
+        """
+        alias of `all_nodes_itr` but conform to the convention of Python.
+        """
+        return self._nodes.values()
 
     def ancestor(self, nid, level=None):
         """
@@ -993,3 +999,25 @@ def to_graphviz(self, filename=None, shape='circle', graph='digraph'):
             print(f.getvalue())
 
         f.close()
+        
+        
+    def map(self, key):
+        """Morphism of tree
+        
+        Work like the built-in `map`
+        
+        Arguments
+            key: function of a node
+        """
+        tree = self._clone(with_tree=tree)
+        for a in tree.iternodes():
+            key(a)
+        return tree
+    
+    def map_data(self, key):
+        """morphism of tree, but act on data of nodes.
+        """
+        tree = self._clone(with_tree=tree)
+        for a in tree.iternodes():
+            a.data = key(a.data)
+        return tree

From 82d0614a043d3203025d56347014b5b9f5c74e91 Mon Sep 17 00:00:00 2001
From: William Song <30965609+Freakwill@users.noreply.github.com>
Date: Mon, 21 Jun 2021 10:06:36 +0800
Subject: [PATCH 04/44] Update tree.py

---
 treelib/tree.py | 14 +++++++++-----
 1 file changed, 9 insertions(+), 5 deletions(-)

diff --git a/treelib/tree.py b/treelib/tree.py
index 2b673a1..9b55b05 100644
--- a/treelib/tree.py
+++ b/treelib/tree.py
@@ -1001,23 +1001,27 @@ def to_graphviz(self, filename=None, shape='circle', graph='digraph'):
         f.close()
         
         
-    def map(self, key):
+    def map(self, key, deep=True):
         """Morphism of tree
         
         Work like the built-in `map`
         
         Arguments
-            key: function of a node
+            key -- function of a node
+            deep -- please keep it true
         """
-        tree = self._clone(with_tree=tree)
+        tree = self._clone(with_tree=tree, deep=deep)
         for a in tree.iternodes():
             key(a)
         return tree
     
-    def map_data(self, key):
+    def map_data(self, key, deep=True):
         """morphism of tree, but act on data of nodes.
+        
+        Arguments
+            key -- pure function of node.data
         """
-        tree = self._clone(with_tree=tree)
+        tree = self._clone(with_tree=tree, deep=deep)
         for a in tree.iternodes():
             a.data = key(a.data)
         return tree

From c33380f73f1595f7fbdc0140c62b1834dd6c49ad Mon Sep 17 00:00:00 2001
From: William Song <30965609+Freakwill@users.noreply.github.com>
Date: Mon, 21 Jun 2021 14:20:07 +0800
Subject: [PATCH 05/44] Update random_tree.py

---
 examples/random_tree.py | 19 +++++++++++++------
 1 file changed, 13 insertions(+), 6 deletions(-)

diff --git a/examples/random_tree.py b/examples/random_tree.py
index d1521e5..38f9ccd 100644
--- a/examples/random_tree.py
+++ b/examples/random_tree.py
@@ -1,12 +1,7 @@
-"""
-Generate a tree randomly
-"""
-
 import random
 from treelib import Tree
 
 def _random(max_depth=5, min_width=1, max_width=2, offset=(0,)):
-    # just have fun
     tree = Tree()
     root = tree.create_node(identifier=offset)
     if max_depth == 0:
@@ -22,4 +17,16 @@ def _random(max_depth=5, min_width=1, max_width=2, offset=(0,)):
             tree.paste(offset, subtree)
     return tree
 
-print(_random())
+def key(node):
+    node.tag = ''.join(map(str, node.identifier))
+
+def _map(tree, key):
+
+    tree = tree._clone(with_tree=True)
+    print(tree)
+    for a in tree.all_nodes_itr():
+        key(a)
+    return tree
+
+
+print(_map(_random(), key))

From 6f816bf4bd3a22d56f668e648ce5c4416d38f59d Mon Sep 17 00:00:00 2001
From: William Song <30965609+Freakwill@users.noreply.github.com>
Date: Fri, 29 Apr 2022 09:15:02 +0800
Subject: [PATCH 06/44] Update tree.py

rewrite the `contains` method
---
 treelib/tree.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/treelib/tree.py b/treelib/tree.py
index 9b55b05..f1bcaf8 100644
--- a/treelib/tree.py
+++ b/treelib/tree.py
@@ -340,7 +340,7 @@ def children(self, nid):
 
     def contains(self, nid):
         """Check if the tree contains node of given id"""
-        return True if nid in self._nodes else False
+        return nid in self._nodes
 
     def create_node(self, tag=None, identifier=None, parent=None, data=None):
         """

From a91d105488f972c7bafdb59086dd920692f865d4 Mon Sep 17 00:00:00 2001
From: William Song <30965609+Freakwill@users.noreply.github.com>
Date: Fri, 29 Apr 2022 21:40:11 +0800
Subject: [PATCH 07/44] Update tree.py

define `apply` method for a tree
---
 treelib/tree.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/treelib/tree.py b/treelib/tree.py
index f1bcaf8..ba0d52e 100644
--- a/treelib/tree.py
+++ b/treelib/tree.py
@@ -1001,7 +1001,7 @@ def to_graphviz(self, filename=None, shape='circle', graph='digraph'):
         f.close()
         
         
-    def map(self, key, deep=True):
+    def apply(self, key, deep=True):
         """Morphism of tree
         
         Work like the built-in `map`
@@ -1015,7 +1015,7 @@ def map(self, key, deep=True):
             key(a)
         return tree
     
-    def map_data(self, key, deep=True):
+    def apply_data(self, key, deep=True):
         """morphism of tree, but act on data of nodes.
         
         Arguments

From 5c7bbbde9dac7379e309a9624997388710ed9151 Mon Sep 17 00:00:00 2001
From: William Song <30965609+Freakwill@users.noreply.github.com>
Date: Fri, 29 Apr 2022 21:42:45 +0800
Subject: [PATCH 08/44] Update random_tree.py

---
 examples/random_tree.py | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/examples/random_tree.py b/examples/random_tree.py
index 38f9ccd..3fe1580 100644
--- a/examples/random_tree.py
+++ b/examples/random_tree.py
@@ -17,10 +17,8 @@ def _random(max_depth=5, min_width=1, max_width=2, offset=(0,)):
             tree.paste(offset, subtree)
     return tree
 
-def key(node):
-    node.tag = ''.join(map(str, node.identifier))
 
-def _map(tree, key):
+def _map(func, tree):
 
     tree = tree._clone(with_tree=True)
     print(tree)
@@ -29,4 +27,6 @@ def _map(tree, key):
     return tree
 
 
-print(_map(_random(), key))
+def key(node):
+    node.tag = ''.join(map(str, node.identifier))
+print(_map(key, _random()))

From ce6f8bdb4430ca80b3fd9fa317f0df9e6db078db Mon Sep 17 00:00:00 2001
From: William Song <30965609+Freakwill@users.noreply.github.com>
Date: Fri, 29 Apr 2022 22:28:51 +0800
Subject: [PATCH 09/44] Update tree.py

---
 treelib/tree.py | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/treelib/tree.py b/treelib/tree.py
index 5fd5fde..c14a43e 100644
--- a/treelib/tree.py
+++ b/treelib/tree.py
@@ -1007,21 +1007,21 @@ def apply(self, key, deep=True):
         Work like the built-in `map`
         
         Arguments
-            key -- function of a node
+            key -- impure function of a node
             deep -- please keep it true
         """
         tree = self._clone(with_tree=tree, deep=deep)
-        for a in tree.iternodes():
+        for a in tree.all_nodes():
             key(a)
         return tree
     
     def apply_data(self, key, deep=True):
         """morphism of tree, but act on data of nodes.
+        It calls the method `apply`
         
         Arguments
             key -- pure function of node.data
         """
-        tree = self._clone(with_tree=tree, deep=deep)
-        for a in tree.iternodes():
+        def _key(a):
             a.data = key(a.data)
-        return tree
+        return self.apply(_key, deep=deep)

From f9b8f04f821c6e5b8fd2f3f54560685aab8ef235 Mon Sep 17 00:00:00 2001
From: William Song <30965609+Freakwill@users.noreply.github.com>
Date: Fri, 28 Oct 2022 09:19:21 +0800
Subject: [PATCH 10/44] update

---
 examples/random_tree.py | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/examples/random_tree.py b/examples/random_tree.py
index 3fe1580..c5d8fdc 100644
--- a/examples/random_tree.py
+++ b/examples/random_tree.py
@@ -2,6 +2,7 @@
 from treelib import Tree
 
 def _random(max_depth=5, min_width=1, max_width=2, offset=(0,)):
+    # generate a tree randomly
     tree = Tree()
     root = tree.create_node(identifier=offset)
     if max_depth == 0:
@@ -19,14 +20,15 @@ def _random(max_depth=5, min_width=1, max_width=2, offset=(0,)):
 
 
 def _map(func, tree):
-
+    # tree as a functor
     tree = tree._clone(with_tree=True)
     print(tree)
     for a in tree.all_nodes_itr():
         key(a)
     return tree
 
-
 def key(node):
     node.tag = ''.join(map(str, node.identifier))
 print(_map(key, _random()))
+
+print(_random().apply(key))

From 5fbe23b261071d8290a5951747cb06aec4bbabff Mon Sep 17 00:00:00 2001
From: William Song <30965609+Freakwill@users.noreply.github.com>
Date: Thu, 11 Apr 2024 14:03:12 +0800
Subject: [PATCH 11/44] Create cluster_tree

Clustering Model Based on Decision Tree
---
 examples/cluster_tree | 94 +++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 94 insertions(+)
 create mode 100644 examples/cluster_tree

diff --git a/examples/cluster_tree b/examples/cluster_tree
new file mode 100644
index 0000000..73cbfbb
--- /dev/null
+++ b/examples/cluster_tree
@@ -0,0 +1,94 @@
+#!/usr/bin/env python3
+
+"""Clustering Model Based on Decision Tree
+"""
+
+import numpy as np
+import numpy.linalg as LA
+from scipy.stats import entropy
+from scipy.spatial.distance import cdist
+
+import pandas as pd
+
+from treelib import Node, Tree
+
+from sklearn.base import ClusterMixin, BaseEstimator
+from sklearn.cluster import KMeans
+
+
+class TreeCluster(BaseEstimator, ClusterMixin, Tree):
+    """Decision Tree for classification/cluster
+
+    epsilon: the threshold of info gain or other select method
+    selection_method: the selection method
+    features_: the features of the input vars
+    classes_: the classes of output vars
+    """
+
+    def __init__(self, epsilon=0.6, features=None, classes=None, *args, **kwargs):
+        super().__init__(*args, **kwargs)
+        self.epsilon = epsilon
+        self.features_ = features
+        self.classes_ = classes
+
+    def fit(self, X, Y=None, mean=None, level=(0,)):
+        """
+        calc cond_proba, proba, priori_proba, features
+        then call fit_with_proba
+        
+        Arguments:
+            X {2D array|list|dataframe} -- input vars
+        
+        Returns:
+            TreeCluster
+        """
+
+        kmeans = KMeans(n_clusters=2)
+
+        if mean is None:
+            mean = X.mean(axis=0)
+        self.add_node(Node(tag='-'.join(map(str, level)), identifier=level, data={'mean':mean}))
+
+        if len(X)>2:
+            kmeans.fit(X)
+            y = kmeans.predict(X)
+            classes_ = np.unique(y)
+            means_ = kmeans.cluster_centers_
+
+            gain = 1 - kmeans.inertia_ / LA.norm(X - mean, 'fro')**2  
+
+            if gain > self.epsilon:
+                for k, m in zip(classes_, means_):
+                    t = TreeCluster(epsilon=self.epsilon)
+                    t.fit(X[y==k], mean=m, level=level+(k,))
+                    self.paste(level, t)
+
+        if level == (0,):
+            # get cluster centers from the data of the nodes
+            self.cluster_centers_ = [node.data['mean'] for node in self.all_nodes_itr() if node.is_leaf()]
+            self.classes_ = np.arange(len(self.cluster_centers_))
+
+        return self
+
+    def predict_proba(self, X):
+        distances = np.exp(-cdist(X, self.cluster_centers_))
+        return distances / distances.sum(axis=0)[None,:]
+
+    def predict(self, X):
+        p = self.predict_proba(X)
+        return self.classes_[np.argmax(p, axis=1)]
+
+
+if __name__ == '__main__':
+
+    from sklearn import datasets
+
+    iris = datasets.load_iris()
+    X_train, y_train = iris.data, iris.target
+
+    tc = TreeCluster(epsilon=0.5)
+    tc.fit(X_train)
+    y_ = tc.predict(X_train)
+
+    print(tc)
+    print(tc.cluster_centers_)

From de4b6ed9f6d9c124783d7e6933da861269b0edfb Mon Sep 17 00:00:00 2001
From: William Song <30965609+Freakwill@users.noreply.github.com>
Date: Thu, 11 Apr 2024 14:11:10 +0800
Subject: [PATCH 12/44] Update tree.py

---
 treelib/tree.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/treelib/tree.py b/treelib/tree.py
index f10b944..5c3da66 100644
--- a/treelib/tree.py
+++ b/treelib/tree.py
@@ -1143,7 +1143,7 @@ def apply(self, key, deep=True):
             key -- impure function of a node
             deep -- please keep it true
         """
-        tree = self._clone(with_tree=tree, deep=deep)
+        tree = self._clone(with_tree=True, deep=deep)
         for a in tree.all_nodes():
             key(a)
         return tree

From fe921444fe05e47d22d1a93f556230c6da97196a Mon Sep 17 00:00:00 2001
From: William Song <30965609+Freakwill@users.noreply.github.com>
Date: Thu, 11 Apr 2024 14:45:20 +0800
Subject: [PATCH 13/44] Update cluster_tree

---
 examples/cluster_tree | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/examples/cluster_tree b/examples/cluster_tree
index 73cbfbb..b9f2191 100644
--- a/examples/cluster_tree
+++ b/examples/cluster_tree
@@ -31,7 +31,7 @@ class TreeCluster(BaseEstimator, ClusterMixin, Tree):
         self.features_ = features
         self.classes_ = classes
 
-    def fit(self, X, Y=None, mean=None, level=(0,)):
+    def fit(self, X, Y=None, mean=None, level=()):
         """
         calc cond_proba, proba, priori_proba, features
         then call fit_with_proba
@@ -63,7 +63,7 @@ class TreeCluster(BaseEstimator, ClusterMixin, Tree):
                     t.fit(X[y==k], mean=m, level=level+(k,))
                     self.paste(level, t)
 
-        if level == (0,):
+        if level == ():
             # get cluster centers from the data of the nodes
             self.cluster_centers_ = [node.data['mean'] for node in self.all_nodes_itr() if node.is_leaf()]
             self.classes_ = np.arange(len(self.cluster_centers_))

From d5a5f9baef4e4ecc114d27b8017084dfb8b83ee8 Mon Sep 17 00:00:00 2001
From: William Song <30965609+Freakwill@users.noreply.github.com>
Date: Thu, 11 Apr 2024 14:49:52 +0800
Subject: [PATCH 14/44] Update random_tree.py

---
 examples/random_tree.py | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/examples/random_tree.py b/examples/random_tree.py
index c5d8fdc..5db7c08 100644
--- a/examples/random_tree.py
+++ b/examples/random_tree.py
@@ -1,13 +1,13 @@
 import random
 from treelib import Tree
 
-def _random(max_depth=5, min_width=1, max_width=2, offset=(0,)):
+def _random(max_depth=5, min_width=1, max_width=2, offset=()):
     # generate a tree randomly
     tree = Tree()
     root = tree.create_node(identifier=offset)
     if max_depth == 0:
         return tree
-    elif max_depth ==1:
+    elif max_depth == 1:
         nb = random.randint(min_width, max_width)
         for i in range(nb):
             tree.create_node(identifier=offset+(i,), parent=offset)
@@ -27,8 +27,11 @@ def _map(func, tree):
         key(a)
     return tree
 
+
 def key(node):
     node.tag = ''.join(map(str, node.identifier))
+
+
 print(_map(key, _random()))
 
 print(_random().apply(key))

From ee1b1f695428efd6da11461a9434091713e16c7c Mon Sep 17 00:00:00 2001
From: William Song <30965609+Freakwill@users.noreply.github.com>
Date: Thu, 11 Apr 2024 14:52:01 +0800
Subject: [PATCH 15/44] Update random_tree.py

---
 examples/random_tree.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/examples/random_tree.py b/examples/random_tree.py
index 5db7c08..85cc0c9 100644
--- a/examples/random_tree.py
+++ b/examples/random_tree.py
@@ -1,10 +1,11 @@
 import random
 from treelib import Tree
 
+
 def _random(max_depth=5, min_width=1, max_width=2, offset=()):
     # generate a tree randomly
     tree = Tree()
-    root = tree.create_node(identifier=offset)
+    tree.create_node(identifier=offset)
     if max_depth == 0:
         return tree
     elif max_depth == 1:

From 1716b61c5efec00c9e814888967e8afa3cc9c132 Mon Sep 17 00:00:00 2001
From: William Song <30965609+Freakwill@users.noreply.github.com>
Date: Thu, 11 Apr 2024 15:07:00 +0800
Subject: [PATCH 16/44] Update tree.py

---
 treelib/tree.py | 11 +++++------
 1 file changed, 5 insertions(+), 6 deletions(-)

diff --git a/treelib/tree.py b/treelib/tree.py
index 5c3da66..d0c5475 100644
--- a/treelib/tree.py
+++ b/treelib/tree.py
@@ -335,7 +335,7 @@ def all_nodes_itr(self):
         Added by William Rusnack
         """
         return self._nodes.values()
-    
+
     def iternodes(self):
         """
         alias of `all_nodes_itr` but conform to the convention of Python.
@@ -1136,9 +1136,8 @@ def to_graphviz(
 
     def apply(self, key, deep=True):
         """Morphism of tree
-        
         Work like the built-in `map`
-        
+ 
         Arguments
             key -- impure function of a node
             deep -- please keep it true
@@ -1147,11 +1146,11 @@ def apply(self, key, deep=True):
         for a in tree.all_nodes():
             key(a)
         return tree
-    
+
     def apply_data(self, key, deep=True):
-        """morphism of tree, but act on data of nodes.
+        """morphism of tree, but acts on data of nodes.
         It calls the method `apply`
-        
+
         Arguments
             key -- pure function of node.data
         """

From 4fa9690d75ca8de08eaca5767b7897898054a032 Mon Sep 17 00:00:00 2001
From: William Song <30965609+Freakwill@users.noreply.github.com>
Date: Thu, 11 Apr 2024 15:08:40 +0800
Subject: [PATCH 17/44] Update tree.py

---
 treelib/tree.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/treelib/tree.py b/treelib/tree.py
index d0c5475..8b55c61 100644
--- a/treelib/tree.py
+++ b/treelib/tree.py
@@ -1137,7 +1137,7 @@ def to_graphviz(
     def apply(self, key, deep=True):
         """Morphism of tree
         Work like the built-in `map`
- 
+
         Arguments
             key -- impure function of a node
             deep -- please keep it true

From ad255c33538ce6f214b0514c0a12b507f585d084 Mon Sep 17 00:00:00 2001
From: William Song <30965609+Freakwill@users.noreply.github.com>
Date: Thu, 11 Apr 2024 15:12:07 +0800
Subject: [PATCH 18/44] Update tree.py

---
 treelib/tree.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/treelib/tree.py b/treelib/tree.py
index 8b55c61..377fe7b 100644
--- a/treelib/tree.py
+++ b/treelib/tree.py
@@ -1154,8 +1154,10 @@ def apply_data(self, key, deep=True):
         Arguments
             key -- pure function of node.data
         """
+
         def _key(a):
             a.data = key(a.data)
+
         return self.apply(_key, deep=deep)
 
     @classmethod

From c8a9d5b2932f84227eca0f602c6aa023727105f1 Mon Sep 17 00:00:00 2001
From: William Song <30965609+Freakwill@users.noreply.github.com>
Date: Thu, 11 Apr 2024 15:22:08 +0800
Subject: [PATCH 19/44] Update random_tree.py

---
 examples/random_tree.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/examples/random_tree.py b/examples/random_tree.py
index 85cc0c9..7b66d8c 100644
--- a/examples/random_tree.py
+++ b/examples/random_tree.py
@@ -1,3 +1,4 @@
+
 import random
 from treelib import Tree
 
@@ -11,7 +12,8 @@ def _random(max_depth=5, min_width=1, max_width=2, offset=()):
     elif max_depth == 1:
         nb = random.randint(min_width, max_width)
         for i in range(nb):
-            tree.create_node(identifier=offset+(i,), parent=offset)
+            identifier = offset + (i,)
+            tree.create_node(identifier=identifier, parent=offset)
     else:
         nb = random.randint(min_width, max_width)
         for i in range(nb):

From dbbb10c8c60d5dec73f1faf1f8249a25bf794182 Mon Sep 17 00:00:00 2001
From: William Song <30965609+Freakwill@users.noreply.github.com>
Date: Thu, 11 Apr 2024 15:25:15 +0800
Subject: [PATCH 20/44] Update random_tree.py

---
 examples/random_tree.py | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/examples/random_tree.py b/examples/random_tree.py
index 7b66d8c..9115d35 100644
--- a/examples/random_tree.py
+++ b/examples/random_tree.py
@@ -1,3 +1,8 @@
+#!/usr/bin/env python3
+
+"""
+Generate a tree randomly; Test the `apply` method;
+"""
 
 import random
 from treelib import Tree

From 574fcee7b72121c392c0955f57add93db6124143 Mon Sep 17 00:00:00 2001
From: William Song <30965609+Freakwill@users.noreply.github.com>
Date: Thu, 11 Apr 2024 15:26:21 +0800
Subject: [PATCH 21/44] Update random_tree.py

---
 examples/random_tree.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/examples/random_tree.py b/examples/random_tree.py
index 9115d35..78c95ed 100644
--- a/examples/random_tree.py
+++ b/examples/random_tree.py
@@ -22,7 +22,7 @@ def _random(max_depth=5, min_width=1, max_width=2, offset=()):
     else:
         nb = random.randint(min_width, max_width)
         for i in range(nb):
-            subtree = _random(max_depth=max_depth-1, max_width=max_width, offset=offset+(i,))
+            subtree = _random(max_depth=max_depth-1, max_width=max_width, offset=offset + (i,))
             tree.paste(offset, subtree)
     return tree
 

From b53ac6f31df74275fbf0f34981459382d8c048c0 Mon Sep 17 00:00:00 2001
From: William Song <30965609+Freakwill@users.noreply.github.com>
Date: Thu, 11 Apr 2024 15:27:32 +0800
Subject: [PATCH 22/44] Update random_tree.py

---
 examples/random_tree.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/examples/random_tree.py b/examples/random_tree.py
index 78c95ed..f06b7b1 100644
--- a/examples/random_tree.py
+++ b/examples/random_tree.py
@@ -22,7 +22,8 @@ def _random(max_depth=5, min_width=1, max_width=2, offset=()):
     else:
         nb = random.randint(min_width, max_width)
         for i in range(nb):
-            subtree = _random(max_depth=max_depth-1, max_width=max_width, offset=offset + (i,))
+            _offset = offset + (i,)
+            subtree = _random(max_depth=max_depth-1, max_width=max_width, offset=_offset)
             tree.paste(offset, subtree)
     return tree
 

From 004cce6f1eb80943928333b7bef9283f56f43e9d Mon Sep 17 00:00:00 2001
From: William Song <30965609+Freakwill@users.noreply.github.com>
Date: Thu, 11 Apr 2024 15:45:45 +0800
Subject: [PATCH 23/44] Update random_tree.py

---
 examples/random_tree.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/examples/random_tree.py b/examples/random_tree.py
index f06b7b1..d702b45 100644
--- a/examples/random_tree.py
+++ b/examples/random_tree.py
@@ -23,7 +23,8 @@ def _random(max_depth=5, min_width=1, max_width=2, offset=()):
         nb = random.randint(min_width, max_width)
         for i in range(nb):
             _offset = offset + (i,)
-            subtree = _random(max_depth=max_depth-1, max_width=max_width, offset=_offset)
+            max_depth -= 1
+            subtree = _random(max_depth=max_depth, max_width=max_width, offset=_offset)
             tree.paste(offset, subtree)
     return tree
 

From 734f46805ca7999a861b24120e438728c4919cdc Mon Sep 17 00:00:00 2001
From: William Song <30965609+Freakwill@users.noreply.github.com>
Date: Thu, 11 Apr 2024 16:23:00 +0800
Subject: [PATCH 24/44] Update random_tree.py

---
 examples/random_tree.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/examples/random_tree.py b/examples/random_tree.py
index d702b45..96827e8 100644
--- a/examples/random_tree.py
+++ b/examples/random_tree.py
@@ -39,7 +39,7 @@ def _map(func, tree):
 
 
 def key(node):
-    node.tag = ''.join(map(str, node.identifier))
+    node.tag = "-".join(map(str, node.identifier))
 
 
 print(_map(key, _random()))

From 0b42017bcfef1f4794bf72f8774daa03e2a7d1c8 Mon Sep 17 00:00:00 2001
From: William Song <30965609+Freakwill@users.noreply.github.com>
Date: Thu, 11 Apr 2024 16:25:07 +0800
Subject: [PATCH 25/44] Update tree.py

---
 treelib/tree.py | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/treelib/tree.py b/treelib/tree.py
index 377fe7b..a701ffe 100644
--- a/treelib/tree.py
+++ b/treelib/tree.py
@@ -521,6 +521,9 @@ def get_node(self, nid):
             return None
         return self._nodes[nid]
 
+    def get_root(self):
+        return self.get_node(self.root)
+
     def is_branch(self, nid):
         """
         Return the children (ID) list of nid.

From 9665b3a596e3f3be73c848672beba769e7daff1e Mon Sep 17 00:00:00 2001
From: William Song <30965609+Freakwill@users.noreply.github.com>
Date: Thu, 11 Apr 2024 18:45:31 +0800
Subject: [PATCH 26/44] Update tree.py

---
 treelib/tree.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/treelib/tree.py b/treelib/tree.py
index a701ffe..e18dc92 100644
--- a/treelib/tree.py
+++ b/treelib/tree.py
@@ -700,7 +700,7 @@ def paste(self, nid, new_tree, deep=False):
 
         for cid, node in iteritems(new_tree.nodes):
             if deep:
-                node = deepcopy(new_tree[node])
+                node = deepcopy(node)
             self._nodes.update({cid: node})
             node.clone_pointers(new_tree.identifier, self._identifier)
 

From 4b27b7168e07d19f2380474df8a8d65100c89ca2 Mon Sep 17 00:00:00 2001
From: William Song <30965609+Freakwill@users.noreply.github.com>
Date: Thu, 11 Apr 2024 21:32:51 +0800
Subject: [PATCH 27/44] Create huffman_tree.py

---
 examples/huffman_tree.py | 102 +++++++++++++++++++++++++++++++++++++++
 1 file changed, 102 insertions(+)
 create mode 100644 examples/huffman_tree.py

diff --git a/examples/huffman_tree.py b/examples/huffman_tree.py
new file mode 100644
index 0000000..95df1c8
--- /dev/null
+++ b/examples/huffman_tree.py
@@ -0,0 +1,102 @@
+#!/usr/bin/env python
+
+
+"""Huffman coding
+"""
+
+from copy import deepcopy
+
+from toolz import *
+from treelib import *
+
+import numpy as np
+
+
+def _get_symbols(tree):
+    a = tree.data['symbols'] if isinstance(tree, Node) else tree.get_node(tree.root).data['symbols']
+    if isinstance(a, str):
+        return [a]
+    else:
+        return a
+
+
+def _get_frequency(tree):
+    a = tree.data['frequency'] if isinstance(tree, Node) else tree.get_node(tree.root).data['frequency']
+    if isinstance(a, str):
+        return [a]
+    else:
+        return a
+
+
+def merge(trees, level=''):
+    """merge the trees to one tree by add a root
+    
+    Args:
+        trees (list): list of trees or nodes
+        level (tuple, optional): the prefix for identifier
+    
+    Returns:
+        Tree
+    """
+
+    data = list(concat(map(_get_symbols, trees)))
+    freq = sum(map(_get_frequency, trees))
+    t = Tree()
+    root = Node(tag='', identifier=level, data={'symbols':data, 'frequency':freq, 'code':''})
+    t.add_node(root)
+    t.root = level
+    root.tag = f"{root.data['code']}:{{{','.join(root.data['symbols'])}}}/{root.data['frequency']}"
+    for k, tree in enumerate(trees):
+        if isinstance(tree, Node):
+            tree.identifier = f'{k}' + tree.identifier
+            tree.data['code'] = f'{k}' + tree.data['code']
+            tree.tag = f"{tree.data['code']}:{{{','.join(tree.data['symbols'])}}}/{tree.data['frequency']}"
+            t.add_node(tree, parent=level)
+        else:
+            for n in tree.all_nodes_itr():
+                n.identifier = f'{k}' + n.identifier
+                n.data['code'] = f'{k}' + n.data['code']
+                n.tag = f"{n.data['code']}:{{{','.join(n.data['symbols'])}}}/{n.data['frequency']}"
+
+            nodes = {n.identifier:n for k, n in tree._nodes.items()}
+            tree._nodes = nodes
+            tree.root = f'{k}' + tree.root
+            for n in tree.all_nodes_itr():
+                if n.is_root():
+                    n.set_successors([f'{k}' + l for l in n._successors[tree.identifier]], tree.identifier)
+                elif n.is_leaf():
+                    n.set_predecessor(f'{k}'+ n._predecessor[tree.identifier], tree.identifier)
+                else:
+                    n.set_predecessor(f'{k}'+ n._predecessor[tree.identifier], tree.identifier)
+                    n.set_successors([f'{k}' + l for l in n._successors[tree.identifier]], tree.identifier)
+
+            t.paste(level, tree, deep=True)
+    return t
+
+
+def huffman_tree(trees, level='', n_branches=2):
+    """Huffman coding
+
+    Args:
+        trees (list): list of trees or nodes
+        level (tuple, optional): the prefix for identifier
+        set n_branches=2 by default
+
+    Returns:
+        Tree: Huffman tree
+    """
+    if len(trees) == 2:
+        return merge(trees, level=level)
+    else:
+        ks = np.argsort([_get_frequency(tree) for tree in trees])[:n_branches]
+        t = merge([trees[k] for k in ks], level=level)
+        t = huffman_tree([t]+[tree for i, tree in enumerate(trees) if i not in ks], level=level)
+        t.tag = 'root'
+        return t
+
+
+d = {'a':1, 'b':2, 'c':3, 'd':4, 'e':5}
+nodes =[Node(identifier='', data={'symbols':s, 'frequency':f, 'code':''}) for s, f in d.items()]
+t = huffman_tree(nodes)
+
+print(t)

From 3532fd13cc2e7ef9d63b9681b048ad6f4908aa83 Mon Sep 17 00:00:00 2001
From: William Song <30965609+Freakwill@users.noreply.github.com>
Date: Thu, 11 Apr 2024 21:38:50 +0800
Subject: [PATCH 28/44] Update huffman_tree.py

---
 examples/huffman_tree.py | 31 ++++++++++++++++++-------------
 1 file changed, 18 insertions(+), 13 deletions(-)

diff --git a/examples/huffman_tree.py b/examples/huffman_tree.py
index 95df1c8..d867a08 100644
--- a/examples/huffman_tree.py
+++ b/examples/huffman_tree.py
@@ -4,16 +4,17 @@
 """Huffman coding
 """
 
-from copy import deepcopy
-
-from toolz import *
-from treelib import *
+from toolz import concat
+from treelib import Tree, Node
 
 import numpy as np
 
 
 def _get_symbols(tree):
-    a = tree.data['symbols'] if isinstance(tree, Node) else tree.get_node(tree.root).data['symbols']
+    if isinstance(tree, Node):
+        a = tree.data['symbols']
+    else:
+        a = tree.get_node(tree.root).data['symbols']
     if isinstance(a, str):
         return [a]
     else:
@@ -21,7 +22,11 @@ def _get_symbols(tree):
 
 
 def _get_frequency(tree):
-    a = tree.data['frequency'] if isinstance(tree, Node) else tree.get_node(tree.root).data['frequency']
+    a = tree.data['frequency']
+    if isinstance(tree, Node):
+        a = tree.data['frequency']
+    else:
+        a = tree.get_node(tree.root).data['frequency']
     if isinstance(a, str):
         return [a]
     else:
@@ -30,7 +35,7 @@ def _get_frequency(tree):
 
 def merge(trees, level=''):
     """merge the trees to one tree by add a root
-    
+
     Args:
         trees (list): list of trees or nodes
         level (tuple, optional): the prefix for identifier
@@ -58,17 +63,17 @@ def merge(trees, level=''):
                 n.data['code'] = f'{k}' + n.data['code']
                 n.tag = f"{n.data['code']}:{{{','.join(n.data['symbols'])}}}/{n.data['frequency']}"
 
-            nodes = {n.identifier:n for k, n in tree._nodes.items()}
+            nodes = {n.identifier: n for k, n in tree._nodes.items()}
             tree._nodes = nodes
             tree.root = f'{k}' + tree.root
             for n in tree.all_nodes_itr():
                 if n.is_root():
-                    n.set_successors([f'{k}' + l for l in n._successors[tree.identifier]], tree.identifier)
+                    n.set_successors([f'{k}' + nid for nid in n._successors[tree.identifier]], tree.identifier)
                 elif n.is_leaf():
                     n.set_predecessor(f'{k}'+ n._predecessor[tree.identifier], tree.identifier)
                 else:
                     n.set_predecessor(f'{k}'+ n._predecessor[tree.identifier], tree.identifier)
-                    n.set_successors([f'{k}' + l for l in n._successors[tree.identifier]], tree.identifier)
+                    n.set_successors([f'{k}' + nid for nid in n._successors[tree.identifier]], tree.identifier)
 
             t.paste(level, tree, deep=True)
     return t
@@ -90,13 +95,13 @@ def huffman_tree(trees, level='', n_branches=2):
     else:
         ks = np.argsort([_get_frequency(tree) for tree in trees])[:n_branches]
         t = merge([trees[k] for k in ks], level=level)
-        t = huffman_tree([t]+[tree for i, tree in enumerate(trees) if i not in ks], level=level)
+        t = huffman_tree([t] + [tree for i, tree in enumerate(trees) if i not in ks], level=level)
         t.tag = 'root'
         return t
 
 
-d = {'a':1, 'b':2, 'c':3, 'd':4, 'e':5}
-nodes =[Node(identifier='', data={'symbols':s, 'frequency':f, 'code':''}) for s, f in d.items()]
+d = {'a': 1, 'b': 2, 'c': 3, 'd': 4, 'e': 5}
+nodes =[Node(identifier='', data={'symbols': s, 'frequency': f, 'code': ''}) for s, f in d.items()]
 t = huffman_tree(nodes)
 
 print(t)

From 31e4940dc50c58da841306d31fab0c09f2deadc6 Mon Sep 17 00:00:00 2001
From: William Song <30965609+Freakwill@users.noreply.github.com>
Date: Thu, 11 Apr 2024 21:41:47 +0800
Subject: [PATCH 29/44] Update huffman_tree.py

---
 examples/huffman_tree.py | 15 +++++++++------
 1 file changed, 9 insertions(+), 6 deletions(-)

diff --git a/examples/huffman_tree.py b/examples/huffman_tree.py
index d867a08..1d237ee 100644
--- a/examples/huffman_tree.py
+++ b/examples/huffman_tree.py
@@ -11,6 +11,8 @@
 
 
 def _get_symbols(tree):
+    """Get the symbols from the root of a tree or a node
+    """
     if isinstance(tree, Node):
         a = tree.data['symbols']
     else:
@@ -22,7 +24,8 @@ def _get_symbols(tree):
 
 
 def _get_frequency(tree):
-    a = tree.data['frequency']
+    """Get the frequency from the root of a tree or a node
+    """
     if isinstance(tree, Node):
         a = tree.data['frequency']
     else:
@@ -39,7 +42,7 @@ def merge(trees, level=''):
     Args:
         trees (list): list of trees or nodes
         level (tuple, optional): the prefix for identifier
-    
+
     Returns:
         Tree
     """
@@ -47,7 +50,7 @@ def merge(trees, level=''):
     data = list(concat(map(_get_symbols, trees)))
     freq = sum(map(_get_frequency, trees))
     t = Tree()
-    root = Node(tag='', identifier=level, data={'symbols':data, 'frequency':freq, 'code':''})
+    root = Node(tag='', identifier=level, data={'symbols': data, 'frequency': freq, 'code': ''})
     t.add_node(root)
     t.root = level
     root.tag = f"{root.data['code']}:{{{','.join(root.data['symbols'])}}}/{root.data['frequency']}"
@@ -70,9 +73,9 @@ def merge(trees, level=''):
                 if n.is_root():
                     n.set_successors([f'{k}' + nid for nid in n._successors[tree.identifier]], tree.identifier)
                 elif n.is_leaf():
-                    n.set_predecessor(f'{k}'+ n._predecessor[tree.identifier], tree.identifier)
+                    n.set_predecessor(f'{k}' + n._predecessor[tree.identifier], tree.identifier)
                 else:
-                    n.set_predecessor(f'{k}'+ n._predecessor[tree.identifier], tree.identifier)
+                    n.set_predecessor(f'{k}' + n._predecessor[tree.identifier], tree.identifier)
                     n.set_successors([f'{k}' + nid for nid in n._successors[tree.identifier]], tree.identifier)
 
             t.paste(level, tree, deep=True)
@@ -101,7 +104,7 @@ def huffman_tree(trees, level='', n_branches=2):
 
 
 d = {'a': 1, 'b': 2, 'c': 3, 'd': 4, 'e': 5}
-nodes =[Node(identifier='', data={'symbols': s, 'frequency': f, 'code': ''}) for s, f in d.items()]
+nodes = [Node(identifier='', data={'symbols': s, 'frequency': f, 'code': ''}) for s, f in d.items()]
 t = huffman_tree(nodes)
 
 print(t)

From f4b60fe9bc7710a254e03bf800c49981dc183e9d Mon Sep 17 00:00:00 2001
From: William Song <30965609+Freakwill@users.noreply.github.com>
Date: Thu, 11 Apr 2024 21:44:01 +0800
Subject: [PATCH 30/44] Update huffman_tree.py

---
 examples/huffman_tree.py | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/examples/huffman_tree.py b/examples/huffman_tree.py
index 1d237ee..a2c7962 100644
--- a/examples/huffman_tree.py
+++ b/examples/huffman_tree.py
@@ -11,7 +11,9 @@
 
 
 def _get_symbols(tree):
-    """Get the symbols from the root of a tree or a node
+    """Get `symbols` from the root of a tree or a node
+
+    tree: Tree or Node
     """
     if isinstance(tree, Node):
         a = tree.data['symbols']
@@ -24,7 +26,9 @@ def _get_symbols(tree):
 
 
 def _get_frequency(tree):
-    """Get the frequency from the root of a tree or a node
+    """Get `frequency` from the root of a tree or a node
+
+    tree: Tree or Node
     """
     if isinstance(tree, Node):
         a = tree.data['frequency']

From 3f5c6832883acb01f513052b4f033d78dac4bb61 Mon Sep 17 00:00:00 2001
From: William Song <30965609+Freakwill@users.noreply.github.com>
Date: Thu, 11 Apr 2024 21:48:01 +0800
Subject: [PATCH 31/44] Update huffman_tree.py

---
 examples/huffman_tree.py | 40 ++++++++++++++++++++--------------------
 1 file changed, 20 insertions(+), 20 deletions(-)

diff --git a/examples/huffman_tree.py b/examples/huffman_tree.py
index a2c7962..d660477 100644
--- a/examples/huffman_tree.py
+++ b/examples/huffman_tree.py
@@ -16,9 +16,9 @@ def _get_symbols(tree):
     tree: Tree or Node
     """
     if isinstance(tree, Node):
-        a = tree.data['symbols']
+        a = tree.data["symbols"]
     else:
-        a = tree.get_node(tree.root).data['symbols']
+        a = tree.get_node(tree.root).data["symbols"]
     if isinstance(a, str):
         return [a]
     else:
@@ -31,9 +31,9 @@ def _get_frequency(tree):
     tree: Tree or Node
     """
     if isinstance(tree, Node):
-        a = tree.data['frequency']
+        a = tree.data["frequency"]
     else:
-        a = tree.get_node(tree.root).data['frequency']
+        a = tree.get_node(tree.root).data["frequency"]
     if isinstance(a, str):
         return [a]
     else:
@@ -54,33 +54,33 @@ def merge(trees, level=''):
     data = list(concat(map(_get_symbols, trees)))
     freq = sum(map(_get_frequency, trees))
     t = Tree()
-    root = Node(tag='', identifier=level, data={'symbols': data, 'frequency': freq, 'code': ''})
+    root = Node(tag="", identifier=level, data={"symbols": data, "frequency": freq, "code": ""})
     t.add_node(root)
     t.root = level
-    root.tag = f"{root.data['code']}:{{{','.join(root.data['symbols'])}}}/{root.data['frequency']}"
+    root.tag = f"{root.data['code']}:{{{",".join(root.data['symbols'])}}}/{root.data['frequency']}"
     for k, tree in enumerate(trees):
         if isinstance(tree, Node):
-            tree.identifier = f'{k}' + tree.identifier
-            tree.data['code'] = f'{k}' + tree.data['code']
-            tree.tag = f"{tree.data['code']}:{{{','.join(tree.data['symbols'])}}}/{tree.data['frequency']}"
+            tree.identifier = f"{k}" + tree.identifier
+            tree.data['code'] = f"{k}" + tree.data['code']
+            tree.tag = f"{tree.data['code']}:{{{",".join(tree.data['symbols'])}}}/{tree.data['frequency']}"
             t.add_node(tree, parent=level)
         else:
             for n in tree.all_nodes_itr():
-                n.identifier = f'{k}' + n.identifier
-                n.data['code'] = f'{k}' + n.data['code']
-                n.tag = f"{n.data['code']}:{{{','.join(n.data['symbols'])}}}/{n.data['frequency']}"
+                n.identifier = f"{k}" + n.identifier
+                n.data['code'] = f"{k}" + n.data['code']
+                n.tag = f"{n.data['code']}:{{{",".join(n.data['symbols'])}}}/{n.data['frequency']}"
 
             nodes = {n.identifier: n for k, n in tree._nodes.items()}
             tree._nodes = nodes
-            tree.root = f'{k}' + tree.root
+            tree.root = f"{k}" + tree.root
             for n in tree.all_nodes_itr():
                 if n.is_root():
-                    n.set_successors([f'{k}' + nid for nid in n._successors[tree.identifier]], tree.identifier)
+                    n.set_successors([f"{k}" + nid for nid in n._successors[tree.identifier]], tree.identifier)
                 elif n.is_leaf():
-                    n.set_predecessor(f'{k}' + n._predecessor[tree.identifier], tree.identifier)
+                    n.set_predecessor(f"{k}" + n._predecessor[tree.identifier], tree.identifier)
                 else:
-                    n.set_predecessor(f'{k}' + n._predecessor[tree.identifier], tree.identifier)
-                    n.set_successors([f'{k}' + nid for nid in n._successors[tree.identifier]], tree.identifier)
+                    n.set_predecessor(f"{k}" + n._predecessor[tree.identifier], tree.identifier)
+                    n.set_successors([f"{k}" + nid for nid in n._successors[tree.identifier]], tree.identifier)
 
             t.paste(level, tree, deep=True)
     return t
@@ -103,12 +103,12 @@ def huffman_tree(trees, level='', n_branches=2):
         ks = np.argsort([_get_frequency(tree) for tree in trees])[:n_branches]
         t = merge([trees[k] for k in ks], level=level)
         t = huffman_tree([t] + [tree for i, tree in enumerate(trees) if i not in ks], level=level)
-        t.tag = 'root'
+        t.tag = "root"
         return t
 
 
-d = {'a': 1, 'b': 2, 'c': 3, 'd': 4, 'e': 5}
-nodes = [Node(identifier='', data={'symbols': s, 'frequency': f, 'code': ''}) for s, f in d.items()]
+d = {"a": 1, "b": 2, "c": 3, "d": 4, "e": 5}
+nodes = [Node(identifier="", data={"symbols": s, "frequency": f, "code": ""}) for s, f in d.items()]
 t = huffman_tree(nodes)
 
 print(t)

From ed65d07d1dd71b504b3ec1189e11d3a0b9633b38 Mon Sep 17 00:00:00 2001
From: William Song <30965609+Freakwill@users.noreply.github.com>
Date: Thu, 11 Apr 2024 21:50:56 +0800
Subject: [PATCH 32/44] Update huffman_tree.py

---
 examples/huffman_tree.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/examples/huffman_tree.py b/examples/huffman_tree.py
index d660477..b111f5a 100644
--- a/examples/huffman_tree.py
+++ b/examples/huffman_tree.py
@@ -57,18 +57,18 @@ def merge(trees, level=''):
     root = Node(tag="", identifier=level, data={"symbols": data, "frequency": freq, "code": ""})
     t.add_node(root)
     t.root = level
-    root.tag = f"{root.data['code']}:{{{",".join(root.data['symbols'])}}}/{root.data['frequency']}"
+    root.tag = f"{root.data['code']}:{{{','.join(root.data['symbols'])}}}/{root.data['frequency']}"
     for k, tree in enumerate(trees):
         if isinstance(tree, Node):
             tree.identifier = f"{k}" + tree.identifier
             tree.data['code'] = f"{k}" + tree.data['code']
-            tree.tag = f"{tree.data['code']}:{{{",".join(tree.data['symbols'])}}}/{tree.data['frequency']}"
+            tree.tag = f"{tree.data['code']}:{{{','.join(tree.data['symbols'])}}}/{tree.data['frequency']}"
             t.add_node(tree, parent=level)
         else:
             for n in tree.all_nodes_itr():
                 n.identifier = f"{k}" + n.identifier
                 n.data['code'] = f"{k}" + n.data['code']
-                n.tag = f"{n.data['code']}:{{{",".join(n.data['symbols'])}}}/{n.data['frequency']}"
+                n.tag = f"{n.data['code']}:{{{','.join(n.data['symbols'])}}}/{n.data['frequency']}"
 
             nodes = {n.identifier: n for k, n in tree._nodes.items()}
             tree._nodes = nodes

From 89917f87ca823dd6084f14a6ec700892a2a4eb9c Mon Sep 17 00:00:00 2001
From: William Song <30965609+Freakwill@users.noreply.github.com>
Date: Thu, 11 Apr 2024 21:54:03 +0800
Subject: [PATCH 33/44] Update huffman_tree.py

---
 examples/huffman_tree.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/examples/huffman_tree.py b/examples/huffman_tree.py
index b111f5a..85d3ede 100644
--- a/examples/huffman_tree.py
+++ b/examples/huffman_tree.py
@@ -40,7 +40,7 @@ def _get_frequency(tree):
         return a
 
 
-def merge(trees, level=''):
+def merge(trees, level=""):
     """merge the trees to one tree by add a root
 
     Args:
@@ -86,7 +86,7 @@ def merge(trees, level=''):
     return t
 
 
-def huffman_tree(trees, level='', n_branches=2):
+def huffman_tree(trees, level="", n_branches=2):
     """Huffman coding
 
     Args:

From cb2829fc0cc72ccb42044f25cdc15be14e4636d9 Mon Sep 17 00:00:00 2001
From: William Song <30965609+Freakwill@users.noreply.github.com>
Date: Thu, 11 Apr 2024 22:00:22 +0800
Subject: [PATCH 34/44] Update huffman_tree.py

---
 examples/huffman_tree.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/examples/huffman_tree.py b/examples/huffman_tree.py
index 85d3ede..a987584 100644
--- a/examples/huffman_tree.py
+++ b/examples/huffman_tree.py
@@ -54,7 +54,7 @@ def merge(trees, level=""):
     data = list(concat(map(_get_symbols, trees)))
     freq = sum(map(_get_frequency, trees))
     t = Tree()
-    root = Node(tag="", identifier=level, data={"symbols": data, "frequency": freq, "code": ""})
+    root = Node(identifier=level, data={"symbols": data, "frequency": freq, "code": ""})
     t.add_node(root)
     t.root = level
     root.tag = f"{root.data['code']}:{{{','.join(root.data['symbols'])}}}/{root.data['frequency']}"

From 4a82ee62c0880dc677be20c92765dbcdc6251012 Mon Sep 17 00:00:00 2001
From: William Song <30965609+Freakwill@users.noreply.github.com>
Date: Thu, 11 Apr 2024 22:03:02 +0800
Subject: [PATCH 35/44] Update huffman_tree.py

---
 examples/huffman_tree.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/examples/huffman_tree.py b/examples/huffman_tree.py
index a987584..4cf63e7 100644
--- a/examples/huffman_tree.py
+++ b/examples/huffman_tree.py
@@ -61,13 +61,13 @@ def merge(trees, level=""):
     for k, tree in enumerate(trees):
         if isinstance(tree, Node):
             tree.identifier = f"{k}" + tree.identifier
-            tree.data['code'] = f"{k}" + tree.data['code']
+            tree.data["code"] = f"{k}" + tree.data["code"]
             tree.tag = f"{tree.data['code']}:{{{','.join(tree.data['symbols'])}}}/{tree.data['frequency']}"
             t.add_node(tree, parent=level)
         else:
             for n in tree.all_nodes_itr():
                 n.identifier = f"{k}" + n.identifier
-                n.data['code'] = f"{k}" + n.data['code']
+                n.data["code"] = f"{k}" + n.data["code"]
                 n.tag = f"{n.data['code']}:{{{','.join(n.data['symbols'])}}}/{n.data['frequency']}"
 
             nodes = {n.identifier: n for k, n in tree._nodes.items()}

From baa4bb3344566a700ce32601627079e1af7a50c3 Mon Sep 17 00:00:00 2001
From: William Song <30965609+Freakwill@users.noreply.github.com>
Date: Thu, 11 Apr 2024 22:06:34 +0800
Subject: [PATCH 36/44] Update huffman_tree.py

---
 examples/huffman_tree.py | 11 +++++------
 1 file changed, 5 insertions(+), 6 deletions(-)

diff --git a/examples/huffman_tree.py b/examples/huffman_tree.py
index 4cf63e7..a33d9b8 100644
--- a/examples/huffman_tree.py
+++ b/examples/huffman_tree.py
@@ -70,17 +70,16 @@ def merge(trees, level=""):
                 n.data["code"] = f"{k}" + n.data["code"]
                 n.tag = f"{n.data['code']}:{{{','.join(n.data['symbols'])}}}/{n.data['frequency']}"
 
-            nodes = {n.identifier: n for k, n in tree._nodes.items()}
-            tree._nodes = nodes
+            tree._nodes = {n.identifier: n for k, n in tree._nodes.items()}
             tree.root = f"{k}" + tree.root
             for n in tree.all_nodes_itr():
                 if n.is_root():
-                    n.set_successors([f"{k}" + nid for nid in n._successors[tree.identifier]], tree.identifier)
+                    n.set_successors([f"{k}{nid}" for nid in n._successors[tree.identifier]], tree.identifier)
                 elif n.is_leaf():
-                    n.set_predecessor(f"{k}" + n._predecessor[tree.identifier], tree.identifier)
+                    n.set_predecessor(f"{k}{n._predecessor[tree.identifier]}", tree.identifier)
                 else:
-                    n.set_predecessor(f"{k}" + n._predecessor[tree.identifier], tree.identifier)
-                    n.set_successors([f"{k}" + nid for nid in n._successors[tree.identifier]], tree.identifier)
+                    n.set_predecessor(f"{k}{n._predecessor[tree.identifier]}", tree.identifier)
+                    n.set_successors([f"{k}{nid}" for nid in n._successors[tree.identifier]], tree.identifier)
 
             t.paste(level, tree, deep=True)
     return t

From 7395ba6ae242be9ff7b795c7b500a8db6d1fd7ef Mon Sep 17 00:00:00 2001
From: William Song <30965609+Freakwill@users.noreply.github.com>
Date: Thu, 11 Apr 2024 22:09:06 +0800
Subject: [PATCH 37/44] Update huffman_tree.py

---
 examples/huffman_tree.py | 11 ++++++-----
 1 file changed, 6 insertions(+), 5 deletions(-)

diff --git a/examples/huffman_tree.py b/examples/huffman_tree.py
index a33d9b8..d32c8d1 100644
--- a/examples/huffman_tree.py
+++ b/examples/huffman_tree.py
@@ -71,15 +71,16 @@ def merge(trees, level=""):
                 n.tag = f"{n.data['code']}:{{{','.join(n.data['symbols'])}}}/{n.data['frequency']}"
 
             tree._nodes = {n.identifier: n for k, n in tree._nodes.items()}
-            tree.root = f"{k}" + tree.root
+            tree.root = f"{k}{tree.root}"
+            tid = tree.identifier
             for n in tree.all_nodes_itr():
                 if n.is_root():
-                    n.set_successors([f"{k}{nid}" for nid in n._successors[tree.identifier]], tree.identifier)
+                    n.set_successors([f"{k}{nid}" for nid in n._successors[tid]], tid)
                 elif n.is_leaf():
-                    n.set_predecessor(f"{k}{n._predecessor[tree.identifier]}", tree.identifier)
+                    n.set_predecessor(f"{k}{n._predecessor[tid]}", tid)
                 else:
-                    n.set_predecessor(f"{k}{n._predecessor[tree.identifier]}", tree.identifier)
-                    n.set_successors([f"{k}{nid}" for nid in n._successors[tree.identifier]], tree.identifier)
+                    n.set_predecessor(f"{k}{n._predecessor[tid]}", tid)
+                    n.set_successors([f"{k}{nid}" for nid in n._successors[tid]], tid)
 
             t.paste(level, tree, deep=True)
     return t

From dc6a0ee799b927db9f225ea93f9677fc0dbeadb1 Mon Sep 17 00:00:00 2001
From: William Song <30965609+Freakwill@users.noreply.github.com>
Date: Thu, 11 Apr 2024 22:14:09 +0800
Subject: [PATCH 38/44] Update huffman_tree.py

---
 examples/huffman_tree.py | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/examples/huffman_tree.py b/examples/huffman_tree.py
index d32c8d1..acf602b 100644
--- a/examples/huffman_tree.py
+++ b/examples/huffman_tree.py
@@ -57,7 +57,7 @@ def merge(trees, level=""):
     root = Node(identifier=level, data={"symbols": data, "frequency": freq, "code": ""})
     t.add_node(root)
     t.root = level
-    root.tag = f"{root.data['code']}:{{{','.join(root.data['symbols'])}}}/{root.data['frequency']}"
+    root.tag = f"root:{{{','.join(root.data['symbols'])}}}/{root.data['frequency']}"
     for k, tree in enumerate(trees):
         if isinstance(tree, Node):
             tree.identifier = f"{k}" + tree.identifier
@@ -102,8 +102,7 @@ def huffman_tree(trees, level="", n_branches=2):
     else:
         ks = np.argsort([_get_frequency(tree) for tree in trees])[:n_branches]
         t = merge([trees[k] for k in ks], level=level)
-        t = huffman_tree([t] + [tree for i, tree in enumerate(trees) if i not in ks], level=level)
-        t.tag = "root"
+        t = huffman_tree( [t] + [tree for k, tree in enumerate(trees) if k not in ks], level=level )
         return t
 
 

From 8e0743a590220c9e0c519a484e4ee49d3878fd1b Mon Sep 17 00:00:00 2001
From: William Song <30965609+Freakwill@users.noreply.github.com>
Date: Thu, 11 Apr 2024 22:16:59 +0800
Subject: [PATCH 39/44] Update huffman_tree.py

---
 examples/huffman_tree.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/examples/huffman_tree.py b/examples/huffman_tree.py
index acf602b..4f2ff56 100644
--- a/examples/huffman_tree.py
+++ b/examples/huffman_tree.py
@@ -102,8 +102,8 @@ def huffman_tree(trees, level="", n_branches=2):
     else:
         ks = np.argsort([_get_frequency(tree) for tree in trees])[:n_branches]
         t = merge([trees[k] for k in ks], level=level)
-        t = huffman_tree( [t] + [tree for k, tree in enumerate(trees) if k not in ks], level=level )
-        return t
+        trees = [t, *(tree for k, tree in enumerate(trees) if k not in ks)]
+        return huffman_tree(trees, level=level)
 
 
 d = {"a": 1, "b": 2, "c": 3, "d": 4, "e": 5}

From efa63b0788af325036bdbb9e441ec083ac20c529 Mon Sep 17 00:00:00 2001
From: William Song <30965609+Freakwill@users.noreply.github.com>
Date: Thu, 11 Apr 2024 22:51:28 +0800
Subject: [PATCH 40/44] Update huffman_tree.py

---
 examples/huffman_tree.py | 15 +++++++++++++--
 1 file changed, 13 insertions(+), 2 deletions(-)

diff --git a/examples/huffman_tree.py b/examples/huffman_tree.py
index 4f2ff56..85ff596 100644
--- a/examples/huffman_tree.py
+++ b/examples/huffman_tree.py
@@ -97,6 +97,8 @@ def huffman_tree(trees, level="", n_branches=2):
     Returns:
         Tree: Huffman tree
     """
+    assert len(trees)>=2
+
     if len(trees) == 2:
         return merge(trees, level=level)
     else:
@@ -106,8 +108,17 @@ def huffman_tree(trees, level="", n_branches=2):
         return huffman_tree(trees, level=level)
 
 
+def make_node(s, f):
+    """Make `Node` object
+
+    s: str
+    f: number
+    """
+    return Node(identifier="", data={"symbols": s, "frequency": f, "code": ""})
+
+
 d = {"a": 1, "b": 2, "c": 3, "d": 4, "e": 5}
-nodes = [Node(identifier="", data={"symbols": s, "frequency": f, "code": ""}) for s, f in d.items()]
+nodes = [make_node(s, f) for s, f in d.items()]
+nodes = list(nodes)
 t = huffman_tree(nodes)
-
 print(t)

From 5787d5b1410d3ef956cb1ec795e83483152bab86 Mon Sep 17 00:00:00 2001
From: William Song <30965609+Freakwill@users.noreply.github.com>
Date: Thu, 11 Apr 2024 22:55:51 +0800
Subject: [PATCH 41/44] Update huffman_tree.py

---
 examples/huffman_tree.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/examples/huffman_tree.py b/examples/huffman_tree.py
index 85ff596..687703c 100644
--- a/examples/huffman_tree.py
+++ b/examples/huffman_tree.py
@@ -97,7 +97,7 @@ def huffman_tree(trees, level="", n_branches=2):
     Returns:
         Tree: Huffman tree
     """
-    assert len(trees)>=2
+    assert len(trees) >= 2
 
     if len(trees) == 2:
         return merge(trees, level=level)

From 0580b0f2e8360ec3160a073adc0ff36eb098af2c Mon Sep 17 00:00:00 2001
From: William Song <30965609+Freakwill@users.noreply.github.com>
Date: Thu, 11 Apr 2024 22:59:31 +0800
Subject: [PATCH 42/44] Update huffman_tree.py

---
 examples/huffman_tree.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/examples/huffman_tree.py b/examples/huffman_tree.py
index 687703c..783e44c 100644
--- a/examples/huffman_tree.py
+++ b/examples/huffman_tree.py
@@ -57,18 +57,18 @@ def merge(trees, level=""):
     root = Node(identifier=level, data={"symbols": data, "frequency": freq, "code": ""})
     t.add_node(root)
     t.root = level
-    root.tag = f"root:{{{','.join(root.data['symbols'])}}}/{root.data['frequency']}"
+    root.tag = f"root: {{{','.join(root.data['symbols'])}}}/{root.data['frequency']}"
     for k, tree in enumerate(trees):
         if isinstance(tree, Node):
             tree.identifier = f"{k}" + tree.identifier
             tree.data["code"] = f"{k}" + tree.data["code"]
-            tree.tag = f"{tree.data['code']}:{{{','.join(tree.data['symbols'])}}}/{tree.data['frequency']}"
+            tree.tag = f"{tree.data['code']}: {{{','.join(tree.data['symbols'])}}}/{tree.data['frequency']}"
             t.add_node(tree, parent=level)
         else:
             for n in tree.all_nodes_itr():
                 n.identifier = f"{k}" + n.identifier
                 n.data["code"] = f"{k}" + n.data["code"]
-                n.tag = f"{n.data['code']}:{{{','.join(n.data['symbols'])}}}/{n.data['frequency']}"
+                n.tag = f"{n.data['code']}: {{{','.join(n.data['symbols'])}}}/{n.data['frequency']}"
 
             tree._nodes = {n.identifier: n for k, n in tree._nodes.items()}
             tree.root = f"{k}{tree.root}"

From d6733b6aef0ddd44ebacc084b9b4e57bd1553b64 Mon Sep 17 00:00:00 2001
From: William Song <30965609+Freakwill@users.noreply.github.com>
Date: Sat, 13 Apr 2024 09:58:59 +0800
Subject: [PATCH 43/44] Update tree.py

---
 treelib/tree.py | 10 ++++++----
 1 file changed, 6 insertions(+), 4 deletions(-)

diff --git a/treelib/tree.py b/treelib/tree.py
index e18dc92..aadb62c 100644
--- a/treelib/tree.py
+++ b/treelib/tree.py
@@ -698,10 +698,12 @@ def paste(self, nid, new_tree, deep=False):
         if set_joint:
             raise ValueError("Duplicated nodes %s exists." % list(map(text, set_joint)))
 
-        for cid, node in iteritems(new_tree.nodes):
-            if deep:
-                node = deepcopy(node)
-            self._nodes.update({cid: node})
+        if deep:
+            new_nodes = {cid: deepcopy(node) for cid, node in iteritems(new_tree.nodes)}
+        else:
+            new_nodes = new_tree.nodes
+        self._nodes.update(new_nodes)
+        for _, node in iteritems(new_nodes):
             node.clone_pointers(new_tree.identifier, self._identifier)
 
         self.__update_bpointer(new_tree.root, nid)

From 49f8b346788b2befb17a1e43a09f2a6e3e04576b Mon Sep 17 00:00:00 2001
From: William Song <30965609+Freakwill@users.noreply.github.com>
Date: Sat, 13 Apr 2024 10:19:41 +0800
Subject: [PATCH 44/44] Update node.py

---
 treelib/node.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/treelib/node.py b/treelib/node.py
index 958c734..067f30b 100644
--- a/treelib/node.py
+++ b/treelib/node.py
@@ -267,7 +267,7 @@ def tag(self):
     @tag.setter
     def tag(self, value):
         """Set the value of `_tag`."""
-        self._tag = value if value is not None else None
+        self._tag = value
 
     def __repr__(self):
         name = self.__class__.__name__