phylogenie 2.1.15__py3-none-any.whl → 2.1.17__py3-none-any.whl

phylogenie/plot.py

@@ -6,7 +6,7 @@ import matplotlib.pyplot as plt
 from matplotlib.axes import Axes
 
 from phylogenie.tree import Tree
-from phylogenie.utils import get_node_depths
+from phylogenie.utils import get_node_depth_levels, get_node_depths
 
 
 class Coloring(str, Enum):
@@ -22,15 +22,14 @@ def plot_tree(
     coloring: str | Coloring | None = None,
     cmap: str | None = None,
     show_legend: bool = True,
-    x_feature: str | None = None,
 ) -> Axes:
     if ax is None:
         ax = plt.gca()
 
     xs = (
-        get_node_depths(tree)
-        if x_feature is None
-        else {node: node.get(x_feature) for node in tree}
+        get_node_depth_levels(tree)
+        if any(node.branch_length is None for node in tree)
+        else get_node_depths(tree)
     )
     ys = {node: i for i, node in enumerate(tree.inorder_traversal())}
 

phylogenie/tree.py

@@ -1,5 +1,5 @@
 from collections import deque
-from collections.abc import Iterator
+from collections.abc import Callable, Iterator
 from typing import Any
 
 
@@ -26,7 +26,7 @@ class Tree:
     @property
     def depth(self) -> float:
         if self.parent is None:
-            return 0.0
+            return 0 if self.branch_length is None else self.branch_length
         if self.branch_length is None:
             raise ValueError(f"Branch length of node {self.name} is not set.")
         return self.parent.depth + self.branch_length
@@ -56,6 +56,10 @@ class Tree:
             return 0
         return 1 + max(child.height_level for child in self.children)
 
+    @property
+    def n_leaves(self) -> int:
+        return len(self.get_leaves())
+
     def set(self, key: str, value: Any) -> None:
         self._features[key] = value
 
@@ -122,10 +126,10 @@ class Tree:
     def get_leaves(self) -> tuple["Tree", ...]:
         return tuple(node for node in self if node.is_leaf())
 
-    def ladderize(self, feature: str) -> None:
-        self._children.sort(key=lambda x: x.get(feature))
+    def ladderize(self, criterion: Callable[["Tree"], Any]) -> None:
+        self._children.sort(key=criterion)
         for child in self.children:
-            child.ladderize(feature)
+            child.ladderize(criterion)
 
     def copy(self):
         new_tree = Tree(self.name, self.branch_length)

phylogenie/utils.py

@@ -22,7 +22,7 @@ def get_node_depths(tree: Tree) -> dict[Tree, float]:
     depths: dict[Tree, float] = {}
     for node in tree:
         if node.parent is None:
-            depths[node] = 0
+            depths[node] = 0 if node.branch_length is None else node.branch_length
         else:
             if node.branch_length is None:
                 raise ValueError(f"Branch length of node {node.name} is not set.")

{phylogenie-2.1.15.dist-info → phylogenie-2.1.17.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: phylogenie
-Version: 2.1.15
+Version: 2.1.17
 Summary: Generate phylogenetic datasets with minimal setup effort
 Author: Gabriele Marino
 Author-email: gabmarino.8601@gmail.com

{phylogenie-2.1.15.dist-info → phylogenie-2.1.17.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=5InWceLwjZV2qVYv2jaTJPs_0gfAEaKYGQt_jnLpaz0,3615
+phylogenie/plot.py,sha256=I1QH7bZ09t7KtI4LleQlph9YZZeyCwu_Jr-YH2JKrW0,3618
 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=EL2bn40AafxQfpA3NP7ohAVA5EoQ87d2JhtulPOyZqg,4413
+phylogenie/tree.py,sha256=qaHMEcnqEtjd8Jlo2wF1vw0Gi6tcMlXngK_6IKEaQkw,4568
 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=Nyg6R8XmMwZMSw1-dII81sU9uU7tDe-NMs8v1qKE4_M,5746
 phylogenie/typeguards.py,sha256=JtqmbEWJZBRHbWgCvcl6nrWm3VcBfzRbklbTBYHItn0,1325
 phylogenie/typings.py,sha256=GknvAFXyiaWeeYJ8Lk5d6E2VHT-xW6ONEojYbtJYiB8,476
-phylogenie/utils.py,sha256=l7kJ0mkdhplz_hTUseBxaGpEKngsWUOSiCMyLMIWYZQ,1936
-phylogenie-2.1.15.dist-info/LICENSE.txt,sha256=NUrDqElK-eD3I0WqC004CJsy6cs0JgsAoebDv_42-pw,1071
-phylogenie-2.1.15.dist-info/METADATA,sha256=Yrjt2kSAxD3Wx87slr4iu59T7XCHbIhg5JORHsxTxZg,5477
-phylogenie-2.1.15.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
-phylogenie-2.1.15.dist-info/entry_points.txt,sha256=Rt6_usN0FkBX1ZfiqCirjMN9FKOgFLG8rydcQ8kugeE,51
-phylogenie-2.1.15.dist-info/RECORD,,
+phylogenie/utils.py,sha256=faDicpAtjxM-QDwPKOv8AOxPe7skPUOGKmVWBZRzUbU,1990
+phylogenie-2.1.17.dist-info/LICENSE.txt,sha256=NUrDqElK-eD3I0WqC004CJsy6cs0JgsAoebDv_42-pw,1071
+phylogenie-2.1.17.dist-info/METADATA,sha256=TUa2AtURiUDVcWfYzt_6BQYaH7N4Izgco0O5vKVOuH0,5477
+phylogenie-2.1.17.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
+phylogenie-2.1.17.dist-info/entry_points.txt,sha256=Rt6_usN0FkBX1ZfiqCirjMN9FKOgFLG8rydcQ8kugeE,51
+phylogenie-2.1.17.dist-info/RECORD,,