phylogenie 2.1.15__tar.gz → 2.1.17__tar.gz

{phylogenie-2.1.15 → phylogenie-2.1.17}/PKG-INFO

@@ -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 → phylogenie-2.1.17}/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-2.1.15 → phylogenie-2.1.17}/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-2.1.15 → phylogenie-2.1.17}/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 → phylogenie-2.1.17}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "phylogenie"
-version = "2.1.15"
+version = "2.1.17"
 description = "Generate phylogenetic datasets with minimal setup effort"
 authors = ["Gabriele Marino <gabmarino.8601@gmail.com>"]
 readme = "README.md"