phylogenie 3.1.3__py3-none-any.whl → 3.1.4__py3-none-any.whl

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/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.dist-info → phylogenie-3.1.4.dist-info}/METADATA

@@ -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.dist-info → phylogenie-3.1.4.dist-info}/RECORD

@@ -1,6 +1,6 @@
 phylogenie/__init__.py,sha256=-4GKO2EKgc2GiOhzVRI0SQk6wQZ4AlP7Ron_Lp-s_r0,2913
-phylogenie/draw.py,sha256=qAFFA9bZPoVMvaOAceC4S-XzF5CXk-qTU2yIwbrA0Ac,5487
-phylogenie/main.py,sha256=vtvSpQxBNlYABoFQ25czl-l3fIr4QRo3svWVd-jcArw,1170
+phylogenie/draw.py,sha256=nT3FOHSm85G23qz2xxYf2MesEDonWRSxfKGJkVboTKY,5580
+phylogenie/main.py,sha256=DstKWUySyDXdcPN_P8O3Mmoau4IjUxCQ4iLWDVuAcws,1054
 phylogenie/mixins.py,sha256=kwxcHGYSS-Frk-r0nwuyILYS1g6NjSOhbUKEYt2g1B0,1319
 phylogenie/msa.py,sha256=JDGyZUsAq6-m-SQjoCDjAkAZIxfgyl_PDIhdYn5HOow,2064
 phylogenie/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
@@ -33,9 +33,9 @@ phylogenie/treesimulator/events/mutations.py,sha256=8Nqa2fg7fwaVNe5XSkGDSwp9pIKQ
 phylogenie/treesimulator/io/__init__.py,sha256=rfP-zp8SP8baq5_4dPAr10WH0W6KfoMCxdTZDCSXtzE,185
 phylogenie/treesimulator/io/newick.py,sha256=8Pr_jixByPOaVch18w-rFt62HYy0U97YMu0H-QSwIy0,3449
 phylogenie/treesimulator/io/nexus.py,sha256=tPZRPejnG0OEE7YTorwvyZe2vnZHv4KiC9f-N7Kx6qg,1849
-phylogenie-3.1.3.dist-info/licenses/LICENSE.txt,sha256=NUrDqElK-eD3I0WqC004CJsy6cs0JgsAoebDv_42-pw,1071
-phylogenie-3.1.3.dist-info/METADATA,sha256=1n5ZhRstpxMfZsQLOamnd82GZGTVgL2_zIAEKtXkcY4,5163
-phylogenie-3.1.3.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-phylogenie-3.1.3.dist-info/entry_points.txt,sha256=BBH8LoReHnNFnvq4sROEsVFegfkKJ6c_oHZ7bgK7Jl4,52
-phylogenie-3.1.3.dist-info/top_level.txt,sha256=1YGZJhKA9tN9qI0Hcj6Cn_sOoDpba0HQlNcgQTjMD-8,11
-phylogenie-3.1.3.dist-info/RECORD,,
+phylogenie-3.1.4.dist-info/licenses/LICENSE.txt,sha256=NUrDqElK-eD3I0WqC004CJsy6cs0JgsAoebDv_42-pw,1071
+phylogenie-3.1.4.dist-info/METADATA,sha256=en3CvCPhiUbQPZTAUYWpx8nQze6oqS-KQJJa3xGdvbI,5163
+phylogenie-3.1.4.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+phylogenie-3.1.4.dist-info/entry_points.txt,sha256=BBH8LoReHnNFnvq4sROEsVFegfkKJ6c_oHZ7bgK7Jl4,52
+phylogenie-3.1.4.dist-info/top_level.txt,sha256=1YGZJhKA9tN9qI0Hcj6Cn_sOoDpba0HQlNcgQTjMD-8,11
+phylogenie-3.1.4.dist-info/RECORD,,