phylogenie 2.1.1__py3-none-any.whl → 2.1.2__py3-none-any.whl

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/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.dist-info → phylogenie-2.1.2.dist-info}/METADATA

@@ -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.dist-info → phylogenie-2.1.2.dist-info}/RECORD

@@ -14,19 +14,19 @@ phylogenie/skyline/__init__.py,sha256=7pF4CUb4ZCLzNYJNhOjpuTOLTRhlK7L6ugfccNqjIG
 phylogenie/skyline/matrix.py,sha256=Gl8OgKjtieG0NwPYiPimKI36gefV8fm_OeorjdXxPTs,9146
 phylogenie/skyline/parameter.py,sha256=EM9qlPt0JhMBy3TbztM0dj24BaGNEy8KWKdTObDKhbI,4644
 phylogenie/skyline/vector.py,sha256=bJP7_FNX_Klt6wXqsyfj0KX3VNj6-dIhzCKSJuQcOV0,7115
-phylogenie/tree.py,sha256=fmCLDNIls3VjY413b-khzj-2jlaQ9rJo7AFN1cz4zXk,2411
+phylogenie/tree.py,sha256=Cum74mTdmgfGXk25dnvUngr4zDYRyWFq5zThBh0QFog,2677
 phylogenie/treesimulator/__init__.py,sha256=XG_xwETKWgDmCihqNUFCcMHtFg4WvZu5qbqWn9Dndt8,879
 phylogenie/treesimulator/events/__init__.py,sha256=UGfvXOVJ_ZAkk_8sBPihjmxciiaEnXZEPFIY53sttWI,940
 phylogenie/treesimulator/events/contact_tracing.py,sha256=_nJ85yhgGkeruQgMHvGpDYoyhheBf8M4LgZWiWdi5dY,4801
 phylogenie/treesimulator/events/core.py,sha256=JokGmieAv2xEX7KsjBWZr05jHN1jB-XZbpxe9gwdbDA,7953
 phylogenie/treesimulator/events/mutations.py,sha256=xkXUIppbLIWZqKwVf-hi7d-_pS42TG2EPVfJA_grxBg,3443
 phylogenie/treesimulator/gillespie.py,sha256=TMDNKBkFwVyAEhBlbwxCTA61GuGwP-42HxpsAVXiU0s,4275
-phylogenie/treesimulator/model.py,sha256=bWoFiO-99tTjHtueKPvGV9RSHQKYJ625XP1dvYbP1_Q,5454
+phylogenie/treesimulator/model.py,sha256=0Im6cFTlpMlJrSP4pTTKtvLT9qrQWV8MSTesAsBxT8g,5422
 phylogenie/typeguards.py,sha256=JtqmbEWJZBRHbWgCvcl6nrWm3VcBfzRbklbTBYHItn0,1325
 phylogenie/typings.py,sha256=GknvAFXyiaWeeYJ8Lk5d6E2VHT-xW6ONEojYbtJYiB8,476
 phylogenie/utils.py,sha256=pCg9ob0RpLUHwM49x4knKxL4FNPr3-EU_6zMXsvxtAg,370
-phylogenie-2.1.1.dist-info/LICENSE.txt,sha256=NUrDqElK-eD3I0WqC004CJsy6cs0JgsAoebDv_42-pw,1071
-phylogenie-2.1.1.dist-info/METADATA,sha256=Ay--Y2G4F1KwK9GgJFhtiTwGyKJ815JUCLYbXMyek1o,5375
-phylogenie-2.1.1.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
-phylogenie-2.1.1.dist-info/entry_points.txt,sha256=Rt6_usN0FkBX1ZfiqCirjMN9FKOgFLG8rydcQ8kugeE,51
-phylogenie-2.1.1.dist-info/RECORD,,
+phylogenie-2.1.2.dist-info/LICENSE.txt,sha256=NUrDqElK-eD3I0WqC004CJsy6cs0JgsAoebDv_42-pw,1071
+phylogenie-2.1.2.dist-info/METADATA,sha256=RoxXfMaPI6auRdjONAE8HfcfhZjHX0hTmx_oJlrzaws,5375
+phylogenie-2.1.2.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
+phylogenie-2.1.2.dist-info/entry_points.txt,sha256=Rt6_usN0FkBX1ZfiqCirjMN9FKOgFLG8rydcQ8kugeE,51
+phylogenie-2.1.2.dist-info/RECORD,,