phylogenie 3.1.3__tar.gz → 3.1.4__tar.gz

{phylogenie-3.1.3 → phylogenie-3.1.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: phylogenie
-Version: 3.1.3
+Version: 3.1.4
 Summary: Add your description here
 Requires-Python: >=3.10
 Description-Content-Type: text/markdown

{phylogenie-3.1.3 → phylogenie-3.1.4}/phylogenie/draw.py

@@ -5,6 +5,7 @@ import matplotlib.colors as mcolors
 import matplotlib.patches as mpatches
 import matplotlib.pyplot as plt
 from matplotlib.axes import Axes
+from matplotlib.colors import Colormap
 from mpl_toolkits.axes_grid1.inset_locator import inset_axes  # pyright: ignore
 
 from phylogenie.treesimulator import Tree, get_node_depth_levels, get_node_depths
@@ -51,7 +52,7 @@ def draw_tree(
     color_by: str | dict[str, Any] | None = None,
     coloring: str | Coloring | None = None,
     default_color: Color = "black",
-    cmap: str | None = None,
+    colormap: str | Colormap | None = None,
     vmin: float | None = None,
     vmax: float | None = None,
     show_legend: bool = True,
@@ -79,6 +80,10 @@ def draw_tree(
             if any(isinstance(f, float) for f in values)
             else Coloring.DISCRETE
         )
+    if colormap is None:
+        colormap = "tab20" if coloring == Coloring.DISCRETE else "viridis"
+    if isinstance(colormap, str):
+        colormap = plt.get_cmap(colormap)
 
     def _get_colors(feature_map: Callable[[Any], Color]) -> dict[Tree, Color]:
         return {
@@ -91,8 +96,6 @@ def draw_tree(
             raise ValueError(
                 "Discrete coloring selected but feature values are not all categorical."
             )
-
-        colormap = plt.get_cmap("tab20" if cmap is None else cmap)
         feature_colors = {
             f: mcolors.to_hex(colormap(i)) for i, f in enumerate(set(values))
         }
@@ -118,7 +121,6 @@ def draw_tree(
         vmin = min(values) if vmin is None else vmin
         vmax = max(values) if vmax is None else vmax
         norm = mcolors.Normalize(vmin=vmin, vmax=vmax)
-        colormap = plt.get_cmap("viridis" if cmap is None else cmap)
         colors = _get_colors(lambda f: colormap(norm(float(f))))
 
         if show_hist:

{phylogenie-3.1.3 → phylogenie-3.1.4}/phylogenie/main.py

@@ -15,14 +15,10 @@ def run(config_path: str) -> None:
     if os.path.isdir(config_path):
         for config_file in glob(os.path.join(config_path, "**/*.yaml"), recursive=True):
             with open(config_file, "r") as f:
-                config = safe_load(f)
-            generator = adapter.validate_python(config)
-            generator.generate()
+                adapter.validate_python(safe_load(f)).generate()
     else:
         with open(config_path, "r") as f:
-            config = safe_load(f)
-        generator = adapter.validate_python(config)
-        generator.generate()
+            adapter.validate_python(safe_load(f)).generate()
 
 
 def main() -> None:

{phylogenie-3.1.3 → phylogenie-3.1.4}/phylogenie.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: phylogenie
-Version: 3.1.3
+Version: 3.1.4
 Summary: Add your description here
 Requires-Python: >=3.10
 Description-Content-Type: text/markdown

{phylogenie-3.1.3 → phylogenie-3.1.4}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "phylogenie"
-version = "3.1.3"
+version = "3.1.4"
 description = "Add your description here"
 readme = "README.md"
 requires-python = ">=3.10"
@@ -13,6 +13,14 @@ dependencies = [
     "tqdm>=4.67.1",
 ]
 
+[dependency-groups]
+dev = [
+    "joblib-stubs>=1.5.2.0.20250831",
+    "pandas-stubs>=2.3.2.250926",
+    "pyright>=1.1.407",
+    "pytest>=8.4.2",
+]
+
 [tool.pyright]
 typeCheckingMode = "strict"
 
@@ -22,11 +30,3 @@ phylogenie = "phylogenie.main:main"
 [build-system]
 requires = ["setuptools>=42"]
 build-backend = "setuptools.build_meta"
-
-[dependency-groups]
-dev = [
-    "joblib-stubs>=1.5.2.0.20250831",
-    "pandas-stubs>=2.3.2.250926",
-    "pyright>=1.1.407",
-    "pytest>=8.4.2",
-]