phylogenie 2.1.1__tar.gz → 2.1.2__tar.gz

{phylogenie-2.1.1 → phylogenie-2.1.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: phylogenie
-Version: 2.1.1
+Version: 2.1.2
 Summary: Generate phylogenetic datasets with minimal setup effort
 Author: Gabriele Marino
 Author-email: gabmarino.8601@gmail.com

{phylogenie-2.1.1 → phylogenie-2.1.2}/phylogenie/tree.py

@@ -73,6 +73,14 @@ class Tree:
     def delete(self, key: str) -> None:
         del self._features[key]
 
+    def copy(self):
+        new_tree = Tree(self.id, self.branch_length)
+        for key, value in self._features.items():
+            new_tree.set(key, value)
+        for child in self.children:
+            new_tree.add_child(child.copy())
+        return new_tree
+
     def __iter__(self) -> Iterator["Tree"]:
         return self.preorder_traversal()
 

{phylogenie-2.1.1 → phylogenie-2.1.2}/phylogenie/treesimulator/model.py

@@ -1,7 +1,6 @@
 from abc import ABC, abstractmethod
 from collections import defaultdict
 from collections.abc import Sequence
-from copy import deepcopy
 from dataclasses import dataclass
 from typing import Any
 
@@ -122,7 +121,7 @@ class Model:
         return self._population[id].state
 
     def get_sampled_tree(self) -> Tree:
-        tree = deepcopy(self._tree)
+        tree = self._tree.copy()
         for node in list(tree.postorder_traversal()):
             if node.id not in self._sampled and not node.children:
                 if node.parent is None:
@@ -142,7 +141,7 @@ class Model:
         return tree
 
     def get_full_tree(self) -> Tree:
-        return deepcopy(self._tree)
+        return self._tree.copy()
 
     def get_population(self, states: str | None = None) -> list[int]:
         if states is None:

{phylogenie-2.1.1 → phylogenie-2.1.2}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "phylogenie"
-version = "2.1.1"
+version = "2.1.2"
 description = "Generate phylogenetic datasets with minimal setup effort"
 authors = ["Gabriele Marino <gabmarino.8601@gmail.com>"]
 readme = "README.md"