phylogenie 3.1.2__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
@@ -48,10 +49,10 @@ def _draw_colored_tree(tree: Tree, ax: Axes, colors: Color | dict[Tree, Color])
 def draw_tree(
     tree: Tree,
     ax: Axes | None = None,
-    color_by: str | dict[Tree, Any] | None = None,
+    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,
@@ -67,17 +68,22 @@ def draw_tree(
     if color_by is None:
         return _draw_colored_tree(tree, ax, colors=default_color)
 
-    if isinstance(color_by, dict):
-        features = {node: color_by[node] for node in tree if node in color_by}
-    else:
+    if isinstance(color_by, str):
         features = {node: node[color_by] for node in tree if color_by in node.metadata}
+    else:
+        features = {node: color_by[node.name] for node in tree if node.name in color_by}
+    values = list(features.values())
 
     if coloring is None:
         coloring = (
             Coloring.CONTINUOUS
-            if any(isinstance(f, float) for f in features.values())
+            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 {
@@ -86,14 +92,12 @@ def draw_tree(
         }
 
     if coloring == Coloring.DISCRETE:
-        if any(isinstance(f, float) for f in features.values()):
+        if any(isinstance(f, float) for f in values):
             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(features.values()))
+            f: mcolors.to_hex(colormap(i)) for i, f in enumerate(set(values))
         }
         colors = _get_colors(lambda f: feature_colors[f])
 
@@ -114,10 +118,9 @@ def draw_tree(
         return _draw_colored_tree(tree, ax, colors)
 
     if coloring == Coloring.CONTINUOUS:
-        vmin = min(features.values()) if vmin is None else vmin
-        vmax = max(features.values()) if vmax is None else vmax
+        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:
@@ -127,7 +130,7 @@ def draw_tree(
             hist_ax = inset_axes(ax, **default_hist_axes_kwargs)  # pyright: ignore
 
             hist_kwargs = {} if hist_kwargs is None else hist_kwargs
-            _, bins, patches = hist_ax.hist(features, **hist_kwargs)  # pyright: ignore
+            _, bins, patches = hist_ax.hist(values, **hist_kwargs)  # pyright: ignore
 
             for patch, b0, b1 in zip(  # pyright: ignore
                 patches, bins[:-1], bins[1:]  # pyright: ignore

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/treesimulator/io/nexus.py

@@ -15,9 +15,9 @@ def _parse_translate_block(lines: Iterator[str]) -> dict[str, str]:
             if ";" in line:
                 return translations
             else:
-                raise ValueError(f"Invalid translate line: {line}")
+                raise ValueError(f"Invalid translate line. Expected '<num> <name>'.")
         translations[match.group(1)] = match.group(2)
-    raise ValueError("Translate block not terminated with ';'")
+    raise ValueError("Translate block not terminated with ';'.")
 
 
 def _parse_trees_block(lines: Iterator[str]) -> dict[str, Tree]:
@@ -33,9 +33,12 @@ def _parse_trees_block(lines: Iterator[str]) -> dict[str, Tree]:
             match = re.match(r"^TREE\s*\*?\s+(\S+)\s*=\s*(.+)$", line, re.IGNORECASE)
             if match is None:
                 raise ValueError(
-                    f"Invalid tree line. Expected 'TREE <name> = <newick>'"
+                    f"Invalid tree line. Expected 'TREE <name> = <newick>'."
                 )
-            trees[match.group(1)] = parse_newick(match.group(2), translations)
+            name = match.group(1)
+            if name in trees:
+                raise ValueError(f"Duplicate tree name found: {name}.")
+            trees[name] = parse_newick(match.group(2), translations)
     raise ValueError("Unterminated TREES block.")
 
 

{phylogenie-3.1.2.dist-info → phylogenie-3.1.4.dist-info}/METADATA

@@ -1,21 +1,17 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.4
 Name: phylogenie
-Version: 3.1.2
-Summary: Generate phylogenetic datasets with minimal setup effort
-Author: Gabriele Marino
-Author-email: gabmarino.8601@gmail.com
-Requires-Python: >=3.10,<4.0
-Classifier: Programming Language :: Python :: 3
-Classifier: Programming Language :: Python :: 3.10
-Classifier: Programming Language :: Python :: 3.11
-Classifier: Programming Language :: Python :: 3.12
-Requires-Dist: joblib (>=1.4.2,<2.0.0)
-Requires-Dist: matplotlib (>=3.10.6,<4.0.0)
-Requires-Dist: pandas (>=2.2.2,<3.0.0)
-Requires-Dist: pydantic (>=2.11.5,<3.0.0)
-Requires-Dist: pyyaml (>=6.0.2,<7.0.0)
-Requires-Dist: tqdm (>=4.66.4,<5.0.0)
+Version: 3.1.4
+Summary: Add your description here
+Requires-Python: >=3.10
 Description-Content-Type: text/markdown
+License-File: LICENSE.txt
+Requires-Dist: joblib>=1.5.2
+Requires-Dist: matplotlib>=3.10.7
+Requires-Dist: pandas>=2.3.3
+Requires-Dist: pydantic>=2.12.3
+Requires-Dist: pyyaml>=6.0.3
+Requires-Dist: tqdm>=4.67.1
+Dynamic: license-file
 
 <p align="center">
 <img src="https://raw.githubusercontent.com/gabriele-marino/phylogenie/main/logo.png" style="width:100%; height:auto;"/>
@@ -103,4 +99,3 @@ This project is licensed under [MIT License](https://raw.githubusercontent.com/g
 For questions, bug reports, or feature requests, please, consider opening an [issue on GitHub](https://github.com/gabriele-marino/phylogenie/issues), or [contact me directly](mailto:gabmarino.8601@email.com).
 
 If you need help with the configuration files, feel free to reach out —  I am always very available and happy to assist!
-

{phylogenie-3.1.2.dist-info → phylogenie-3.1.4.dist-info}/RECORD

@@ -1,5 +1,11 @@
 phylogenie/__init__.py,sha256=-4GKO2EKgc2GiOhzVRI0SQk6wQZ4AlP7Ron_Lp-s_r0,2913
-phylogenie/draw.py,sha256=6WHLxXXyTKq6pxuPBfDgZfEZti3UkJVhDory2pJzdIc,5499
+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
+phylogenie/typeguards.py,sha256=JtqmbEWJZBRHbWgCvcl6nrWm3VcBfzRbklbTBYHItn0,1325
+phylogenie/typings.py,sha256=p694PBe_tk25A6N8vGGWxuqoDtt3nHFUsIYJrwR_76Y,494
 phylogenie/generators/__init__.py,sha256=zsOxy28-9j9alOQLIgrOAFfmM58NNHO_NEtW-KXQXAY,888
 phylogenie/generators/alisim.py,sha256=oizyUz2xNKUdO4HrmZFqtVUfzPBN4BRgxgYczofgeYs,2809
 phylogenie/generators/configs.py,sha256=xDIyDgGxuaqdET9wVkpdrXk02jIbibSp8mgxuIcM5qQ,1489
@@ -9,32 +15,27 @@ phylogenie/generators/trees.py,sha256=8dO1CkU34E6mmMAHrYqiLV_VA8r54cSEOo-UzoHiN2
 phylogenie/generators/typeguards.py,sha256=yj4VkhOaUXJ2OrY-6zhOeY9C4yKIQxjZtk2d-vIxttQ,828
 phylogenie/io/__init__.py,sha256=eWDU6YDqAdx6TZlUMmMbsfO8gP3i5HP_cfUe_-0x2FA,69
 phylogenie/io/fasta.py,sha256=CUFO06m7wClprarsMheZojM4Os2NQf3ALYUXSWzfNL0,869
-phylogenie/main.py,sha256=vtvSpQxBNlYABoFQ25czl-l3fIr4QRo3svWVd-jcArw,1170
-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
 phylogenie/skyline/__init__.py,sha256=7pF4CUb4ZCLzNYJNhOjpuTOLTRhlK7L6ugfccNqjIGo,620
 phylogenie/skyline/matrix.py,sha256=v4SitY7VbXprqlqQckjWTzW5hwRmCyIF595R6IJMxWw,9268
 phylogenie/skyline/parameter.py,sha256=TVqkqirGXNN-VP8hnIJACPkOxUan6LkGa5o_JcPfwbY,4834
 phylogenie/skyline/vector.py,sha256=60jtp7PieiEaEH0Tp6zNjNKjyzpN_nT5uwBUXbgeATk,7261
 phylogenie/treesimulator/__init__.py,sha256=Qz__cFookXuEjq8AUp1A6XRON0qQ_xX-q2Q5ixP4XUg,1791
+phylogenie/treesimulator/features.py,sha256=XbuwGw8xjGs2lNhJvvUUvXVtheSTBaSN6qj39tWYEro,1391
+phylogenie/treesimulator/gillespie.py,sha256=ey2hdpJOSpNW88duwK7wTAdYSTnSuTSZ_yhZv9MlNHo,5323
+phylogenie/treesimulator/model.py,sha256=L0RsL6H1ynFDPecULniSs4Cs8dvz87ovviQOXFy5Qt0,4580
+phylogenie/treesimulator/tree.py,sha256=-yMW14018x9dw45TonS6nRlzWcwXcaHv3Jn5HYriLQQ,6009
+phylogenie/treesimulator/utils.py,sha256=OxZwVHxN004Jf-kYZ_GfJgIY0beo-0tYq80CuFGQt-M,3416
 phylogenie/treesimulator/events/__init__.py,sha256=w2tJ0D2WB5AiCbr3CsKN6vdADueiAEMzd_ve0rpa4zg,939
 phylogenie/treesimulator/events/base.py,sha256=JQKYUZmhB2Q-WQOy2ULGKQiabsMz-JvwMVfDoa3ZKyo,1170
 phylogenie/treesimulator/events/contact_tracing.py,sha256=t64omKEO2d-DfN_dhDJlXp_Kg9egy2ZE346yWjV3ZrA,5148
 phylogenie/treesimulator/events/core.py,sha256=bhgQgi5L-oaHsoWJmUOsTTzWxi0POYxVLoF-KrC8AGQ,8179
 phylogenie/treesimulator/events/mutations.py,sha256=8Nqa2fg7fwaVNe5XSkGDSwp9pIKQ7XaBQCCj-LYlfzA,3666
-phylogenie/treesimulator/features.py,sha256=XbuwGw8xjGs2lNhJvvUUvXVtheSTBaSN6qj39tWYEro,1391
-phylogenie/treesimulator/gillespie.py,sha256=ey2hdpJOSpNW88duwK7wTAdYSTnSuTSZ_yhZv9MlNHo,5323
 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=wmOueclNRp85Zcs72dpaoKFiDY13TtmEL0mabKYni0w,1703
-phylogenie/treesimulator/model.py,sha256=L0RsL6H1ynFDPecULniSs4Cs8dvz87ovviQOXFy5Qt0,4580
-phylogenie/treesimulator/tree.py,sha256=-yMW14018x9dw45TonS6nRlzWcwXcaHv3Jn5HYriLQQ,6009
-phylogenie/treesimulator/utils.py,sha256=OxZwVHxN004Jf-kYZ_GfJgIY0beo-0tYq80CuFGQt-M,3416
-phylogenie/typeguards.py,sha256=JtqmbEWJZBRHbWgCvcl6nrWm3VcBfzRbklbTBYHItn0,1325
-phylogenie/typings.py,sha256=p694PBe_tk25A6N8vGGWxuqoDtt3nHFUsIYJrwR_76Y,494
-phylogenie-3.1.2.dist-info/LICENSE.txt,sha256=NUrDqElK-eD3I0WqC004CJsy6cs0JgsAoebDv_42-pw,1071
-phylogenie-3.1.2.dist-info/METADATA,sha256=8bNrxXaHWW1N1nWmjDwf8CV9306fDaxguE2xoWmPufU,5476
-phylogenie-3.1.2.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
-phylogenie-3.1.2.dist-info/entry_points.txt,sha256=Rt6_usN0FkBX1ZfiqCirjMN9FKOgFLG8rydcQ8kugeE,51
-phylogenie-3.1.2.dist-info/RECORD,,
+phylogenie/treesimulator/io/nexus.py,sha256=tPZRPejnG0OEE7YTorwvyZe2vnZHv4KiC9f-N7Kx6qg,1849
+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,,

{phylogenie-3.1.2.dist-info → phylogenie-3.1.4.dist-info}/WHEEL

@@ -1,4 +1,5 @@
 Wheel-Version: 1.0
-Generator: poetry-core 1.9.0
+Generator: setuptools (80.9.0)
 Root-Is-Purelib: true
 Tag: py3-none-any
+

phylogenie-3.1.4.dist-info/entry_points.txt

@@ -0,0 +1,2 @@
+[console_scripts]
+phylogenie = phylogenie.main:main

phylogenie-3.1.4.dist-info/top_level.txt

@@ -0,0 +1 @@
+phylogenie

phylogenie-3.1.2.dist-info/entry_points.txt

@@ -1,3 +0,0 @@
-[console_scripts]
-phylogenie=phylogenie.main:main
-