phylogenie 2.1.9__tar.gz → 2.1.11__tar.gz

{phylogenie-2.1.9 → phylogenie-2.1.11}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: phylogenie
-Version: 2.1.9
+Version: 2.1.11
 Summary: Generate phylogenetic datasets with minimal setup effort
 Author: Gabriele Marino
 Author-email: gabmarino.8601@gmail.com

{phylogenie-2.1.9 → phylogenie-2.1.11}/phylogenie/__init__.py

@@ -12,6 +12,7 @@ from phylogenie.generators import (
 )
 from phylogenie.io import dump_newick, load_fasta, load_newick
 from phylogenie.msa import MSA
+from phylogenie.plot import Coloring, plot_tree
 from phylogenie.skyline import (
     SkylineMatrix,
     SkylineMatrixCoercible,
@@ -90,4 +91,6 @@ __all__ = [
     "load_fasta",
     "load_newick",
     "MSA",
+    "Coloring",
+    "plot_tree",
 ]

{phylogenie-2.1.9 → phylogenie-2.1.11}/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()
 
@@ -57,6 +58,10 @@ def plot_tree(
             norm = mcolors.Normalize(vmin=min(values), vmax=max(values))
             colormap = plt.get_cmap(cmap)
             colors = {node: colormap(norm(float(node.get(color_by)))) for node in tree}
+
+            sm = plt.cm.ScalarMappable(cmap=colormap, norm=norm)
+            fig = ax.get_figure()
+            fig.colorbar(sm, ax=ax, label=color_by)  # pyright: ignore
         else:
             raise ValueError(
                 f"Unknown coloring method: {coloring}. Choices are {list(Coloring)}."

{phylogenie-2.1.9 → phylogenie-2.1.11}/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-2.1.9 → phylogenie-2.1.11}/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 → phylogenie-2.1.11}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "phylogenie"
-version = "2.1.9"
+version = "2.1.11"
 description = "Generate phylogenetic datasets with minimal setup effort"
 authors = ["Gabriele Marino <gabmarino.8601@gmail.com>"]
 readme = "README.md"