phylogenie 2.1.9__py3-none-any.whl → 2.1.10__py3-none-any.whl

phylogenie/plot.py

@@ -3,6 +3,7 @@ from enum import Enum
 import matplotlib.colors as mcolors
 import matplotlib.patches as mpatches
 import matplotlib.pyplot as plt
+from matplotlib.axes import Axes
 
 from phylogenie import Tree
 from phylogenie.tree import Tree
@@ -16,13 +17,13 @@ class Coloring(str, Enum):
 
 def plot_tree(
     tree: Tree,
-    ax: plt.Axes | None = None,  # pyright: ignore
+    ax: Axes | None = None,
     color_by: str | None = None,
     default_color: str = "black",
     coloring: str | Coloring | None = None,
     cmap: str | None = None,
     show_legend: bool = True,
-) -> plt.Axes:  # pyright: ignore
+) -> Axes:
     if ax is None:
         ax = plt.gca()
 

phylogenie/tree.py

@@ -22,6 +22,14 @@ class Tree:
     def features(self) -> dict[str, Any]:
         return self._features.copy()
 
+    @property
+    def time_to_parent(self) -> float:
+        if self.parent is None and self.branch_length is None:
+            return 0.0
+        if self.branch_length is None:
+            raise ValueError(f"Branch length of node {self.name} is not set.")
+        return self.branch_length
+
     def add_child(self, child: "Tree") -> "Tree":
         child._parent = self
         self._children.append(child)
@@ -69,14 +77,9 @@ class Tree:
     def get_leaves(self) -> tuple["Tree", ...]:
         return tuple(node for node in self if not node.children)
 
-    def parse_branch_length(self) -> float:
-        if self.branch_length is None:
-            raise ValueError(f"Branch length of node {self.name} is not set.")
-        return self.branch_length
-
     def get_time(self) -> float:
         parent_time = 0 if self.parent is None else self.parent.get_time()
-        return self.parse_branch_length() + parent_time
+        return self.time_to_parent + parent_time
 
     def set(self, key: str, value: Any) -> None:
         self._features[key] = value

phylogenie/utils.py

@@ -14,7 +14,7 @@ def get_times(tree: Tree) -> dict[str, float]:
     times: dict[str, float] = {}
     for node in tree:
         parent_time = 0 if node.parent is None else times[node.parent.name]
-        times[node.name] = node.parse_branch_length() + parent_time
+        times[node.name] = node.time_to_parent + parent_time
     return times
 
 

{phylogenie-2.1.9.dist-info → phylogenie-2.1.10.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: phylogenie
-Version: 2.1.9
+Version: 2.1.10
 Summary: Generate phylogenetic datasets with minimal setup effort
 Author: Gabriele Marino
 Author-email: gabmarino.8601@gmail.com

{phylogenie-2.1.9.dist-info → phylogenie-2.1.10.dist-info}/RECORD

@@ -10,13 +10,13 @@ phylogenie/io.py,sha256=nwy8DOknt0HqF9qMeFZHrCmSXpM5AGrU5oajwTtD6vY,3973
 phylogenie/main.py,sha256=vtvSpQxBNlYABoFQ25czl-l3fIr4QRo3svWVd-jcArw,1170
 phylogenie/models.py,sha256=pCg9ob0RpLUHwM49x4knKxL4FNPr3-EU_6zMXsvxtAg,370
 phylogenie/msa.py,sha256=JDGyZUsAq6-m-SQjoCDjAkAZIxfgyl_PDIhdYn5HOow,2064
-phylogenie/plot.py,sha256=9lXZokOi7sJ1HLDPQArzjODnQLL_nv16Fr7AtP-5eFE,2869
+phylogenie/plot.py,sha256=oQYlyKnahGSnC6pyWm0wHpGDzGorLjOJMCIms-sUXd0,2856
 phylogenie/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 phylogenie/skyline/__init__.py,sha256=7pF4CUb4ZCLzNYJNhOjpuTOLTRhlK7L6ugfccNqjIGo,620
 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=63A--s8C8K685KzZ_3hslkKM-lpqSM39-VFIuwBlIjk,3257
+phylogenie/tree.py,sha256=bWQqbr8CbWZZHKQr-iav4gU2sLbnGRXuBk5_ZJZEZBU,3345
 phylogenie/treesimulator/__init__.py,sha256=yqS2vtYMhdWSXc9RAnX1dd4zAqSQweMLyVKTnJLfGTU,1106
 phylogenie/treesimulator/events/__init__.py,sha256=6zSgZ0MEUMvTK4yPlSolJnRWzCARLS-jYreTzh45mQo,1033
 phylogenie/treesimulator/events/contact_tracing.py,sha256=_nJ85yhgGkeruQgMHvGpDYoyhheBf8M4LgZWiWdi5dY,4801
@@ -27,9 +27,9 @@ phylogenie/treesimulator/gillespie.py,sha256=LZHB2Ko147E78LoUCtN_BN7NYO1xhMYRy5P
 phylogenie/treesimulator/model.py,sha256=Ct0lfn6maKtjuFxivWx1MbFHvH3Y-fiJ0XXMdkN3Cak,5775
 phylogenie/typeguards.py,sha256=JtqmbEWJZBRHbWgCvcl6nrWm3VcBfzRbklbTBYHItn0,1325
 phylogenie/typings.py,sha256=GknvAFXyiaWeeYJ8Lk5d6E2VHT-xW6ONEojYbtJYiB8,476
-phylogenie/utils.py,sha256=JDe6_8-9AFYf7SuTrqUXTZ7n3CA-goQGg9vTi5UcHB8,878
-phylogenie-2.1.9.dist-info/LICENSE.txt,sha256=NUrDqElK-eD3I0WqC004CJsy6cs0JgsAoebDv_42-pw,1071
-phylogenie-2.1.9.dist-info/METADATA,sha256=V-aDacuPL0dfohsDmU69cvzHakcf6RfdDvrgK3zSCgc,5476
-phylogenie-2.1.9.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
-phylogenie-2.1.9.dist-info/entry_points.txt,sha256=Rt6_usN0FkBX1ZfiqCirjMN9FKOgFLG8rydcQ8kugeE,51
-phylogenie-2.1.9.dist-info/RECORD,,
+phylogenie/utils.py,sha256=tVorfhMuRkxogeNu45aBv4SDBflHg4faiIpnHNJPKPY,871
+phylogenie-2.1.10.dist-info/LICENSE.txt,sha256=NUrDqElK-eD3I0WqC004CJsy6cs0JgsAoebDv_42-pw,1071
+phylogenie-2.1.10.dist-info/METADATA,sha256=NRjmmmqUcJKklEr5G7mGPe_qrWv0Z7CQxvV1Mkz8sOc,5477
+phylogenie-2.1.10.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
+phylogenie-2.1.10.dist-info/entry_points.txt,sha256=Rt6_usN0FkBX1ZfiqCirjMN9FKOgFLG8rydcQ8kugeE,51
+phylogenie-2.1.10.dist-info/RECORD,,