phylogenie 3.1.10__py3-none-any.whl → 3.1.13__py3-none-any.whl

phylogenie/__init__.py

@@ -1,11 +1,3 @@
-from phylogenie.draw import (
-    draw_colored_dated_tree_categorical,
-    draw_colored_dated_tree_continuous,
-    draw_colored_tree_categorical,
-    draw_colored_tree_continuous,
-    draw_dated_tree,
-    draw_tree,
-)
 from phylogenie.generators import (
     AliSimDatasetGenerator,
     BDEITreeDatasetGenerator,
@@ -71,12 +63,6 @@ from phylogenie.treesimulator import (
 )
 
 __all__ = [
-    "draw_colored_dated_tree_categorical",
-    "draw_colored_dated_tree_continuous",
-    "draw_colored_tree_categorical",
-    "draw_colored_tree_continuous",
-    "draw_dated_tree",
-    "draw_tree",
     "AliSimDatasetGenerator",
     "BDEITreeDatasetGenerator",
     "BDSSTreeDatasetGenerator",

phylogenie/draw.py

@@ -1,5 +1,5 @@
+import datetime
 from dataclasses import dataclass
-from datetime import datetime
 from typing import Any, Literal, overload
 
 import matplotlib.colors as mcolors
@@ -21,7 +21,7 @@ from phylogenie.treesimulator import (
 @dataclass
 class CalibrationNode:
     node: Tree
-    date: datetime
+    date: datetime.date
 
 
 Color = str | tuple[float, float, float] | tuple[float, float, float, float]
@@ -115,7 +115,7 @@ def draw_tree(
 
 def _depth_to_date(
     depth: float, calibration_nodes: tuple[CalibrationNode, CalibrationNode]
-) -> datetime:
+) -> datetime.date:
     """
     Convert a depth value to a date using linear interpolation between two calibration nodes.
 
@@ -128,7 +128,7 @@ def _depth_to_date(
 
     Returns
     -------
-    datetime
+    datetime.date
         The interpolated date corresponding to the given depth.
     """
     node1, node2 = calibration_nodes
@@ -224,7 +224,7 @@ def _init_colored_tree_categorical(
     color_by: str,
     ax: Axes | None = None,
     default_color: Color = "black",
-    colormap: str | Colormap = "tab20",
+    colormap: str | dict[str, Color] | Colormap = "tab20",
     show_legend: bool = True,
     labels: dict[Any, str] | None = None,
     legend_kwargs: dict[str, Any] | None = None,
@@ -242,8 +242,11 @@ def _init_colored_tree_categorical(
         The matplotlib Axes to draw on. If None, uses the current Axes.
     default_color : Color, optional
         The color to use for nodes without the specified metadata.
-    colormap : str | Colormap, optional
-        The colormap to use for coloring categories. Defaults to 'tab20'.
+    colormap : str | dict[str, Color] | Colormap, optional
+        The colormap to use for coloring categories.
+        If a string, it is used to get a matplotlib colormap.
+        If a dict, it maps category values to colors directly.
+        Defaults to 'tab20'.
     show_legend : bool, optional
         Whether to display a legend for the categories.
     labels : dict[Any, str] | None, optional
@@ -259,13 +262,16 @@ def _init_colored_tree_categorical(
     if ax is None:
         ax = plt.gca()
 
+    features = {node: node[color_by] for node in tree if color_by in node.metadata}
     if isinstance(colormap, str):
         colormap = plt.get_cmap(colormap)
+    if isinstance(colormap, Colormap):
+        feature_colors = {
+            f: mcolors.to_hex(colormap(i)) for i, f in enumerate(set(features.values()))
+        }
+    else:
+        feature_colors = colormap
 
-    features = {node: node[color_by] for node in tree if color_by in node.metadata}
-    feature_colors = {
-        f: mcolors.to_hex(colormap(i)) for i, f in enumerate(set(features.values()))
-    }
     colors = {
         node: feature_colors[features[node]] if node in features else default_color
         for node in tree
@@ -294,7 +300,7 @@ def draw_colored_tree_categorical(
     ax: Axes | None = None,
     backward_time: bool = False,
     default_color: Color = "black",
-    colormap: str | Colormap = "tab20",
+    colormap: str | dict[str, Color] | Colormap = "tab20",
     show_legend: bool = True,
     labels: dict[Any, str] | None = None,
     legend_kwargs: dict[str, Any] | None = None,
@@ -316,8 +322,11 @@ def draw_colored_tree_categorical(
         If True, the x-axis is inverted to represent time going backward.
     default_color : Color, optional
         The color to use for nodes without the specified metadata.
-    colormap : str | Colormap, optional
-        The colormap to use for coloring categories. Defaults to 'tab20'.
+    colormap : str | dict[str, Color] | Colormap, optional
+        The colormap to use for coloring categories.
+        If a string, it is used to get a matplotlib colormap.
+        If a dict, it maps category values to colors directly.
+        Defaults to 'tab20'.
     show_legend : bool, optional
         Whether to display a legend for the categories.
     labels : dict[Any, str] | None, optional
@@ -360,7 +369,7 @@ def draw_colored_dated_tree_categorical(
     color_by: str,
     ax: Axes | None = None,
     default_color: Color = "black",
-    colormap: str | Colormap = "tab20",
+    colormap: str | dict[str, Color] | Colormap = "tab20",
     show_legend: bool = True,
     labels: dict[Any, str] | None = None,
     legend_kwargs: dict[str, Any] | None = None,
@@ -381,8 +390,11 @@ def draw_colored_dated_tree_categorical(
         The matplotlib Axes to draw on. If None, uses the current Axes.
     default_color : Color, optional
         The color to use for nodes without the specified metadata.
-    colormap : str | Colormap, optional
-        The colormap to use for coloring categories. Defaults to 'tab20'.
+    colormap : str | dict[str, Color] | Colormap, optional
+        The colormap to use for coloring categories.
+        If a string, it is used to get a matplotlib colormap.
+        If a dict, it maps category values to colors directly.
+        Defaults to 'tab20'.
     show_legend : bool, optional
         Whether to display a legend for the categories.
     labels : dict[Any, str] | None, optional

{phylogenie-3.1.10.dist-info → phylogenie-3.1.13.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: phylogenie
-Version: 3.1.10
+Version: 3.1.13
 Summary: Generate phylogenetic datasets with minimal setup effort
 Requires-Python: >=3.10
 Description-Content-Type: text/markdown
@@ -23,7 +23,6 @@ Dynamic: license-file
 [![PyPI version](https://img.shields.io/pypi/v/phylogenie)](https://pypi.org/project/phylogenie/)
 ![Downloads](https://img.shields.io/pypi/dm/phylogenie)
 
-
 Phylogenie is a [Python](https://www.python.org/) package designed to easily simulate phylogenetic datasets—such as trees and multiple sequence alignments (MSAs)—with minimal setup effort. Simply specify the distributions from which your parameters should be sampled, and Phylogenie will handle the rest!
 
 ## ✨ Features
@@ -73,21 +72,21 @@ Phylogenie relies on [AliSim](https://iqtree.github.io/doc/AliSim) for simulatin
 
 ## 🚀 Quick Start
 
-Once you have installed Phylogenie, check out the [examples](https://github.com/gabriele-marino/phylogenie/tree/main/examples) folder.  
+Once you have installed Phylogenie, check out the [tutorials](https://github.com/gabriele-marino/phylogenie/tree/main/tutorials) folder.  
 It includes a collection of thoroughly commented configuration files, organized as a step-by-step tutorial. These examples will help you understand how to use Phylogenie in practice and can be easily adapted to fit your own workflow.
 
 For quick start, pick your favorite config file and run Phylogenie with:
 ```bash
-phylogenie examples/config_file.yaml
+phylogenie tutorials/config_file.yaml
 ```
 This command will create the output dataset in the folder specified inside the configuration file, including data directories and metadata files for each dataset split defined in the config.
 
 >❗ *Tip*: Can’t choose just one config file?
-You can run them all at once by pointing Phylogenie to the folder! Just use: `phylogenie examples`. In this mode, Phylogenie will automatically find all `.yaml` files in the folder you specified and run for each of them!
+You can run them all at once by pointing Phylogenie to the folder! Just use: `phylogenie tutorials`. In this mode, Phylogenie will automatically find all `.yaml` files in the folder you specified and run for each of them!
 
 ## 📖 Documentation
 
-- The [examples](https://github.com/gabriele-marino/phylogenie/tree/main/examples) folder contains many ready-to-use, extensively commented configuration files that serve as a step-by-step tutorial to guide you through using Phylogenie. You can explore them to learn how it works or adapt them directly to your own workflows.
+- The [tutorials](https://github.com/gabriele-marino/phylogenie/tree/main/tutorials) folder contains many ready-to-use, extensively commented configuration files that serve as a step-by-step tutorial to guide you through using Phylogenie. You can explore them to learn how it works or adapt them directly to your own workflows.
 - A complete user guide and API reference are under development. In the meantime, feel free to [reach out](mailto:gabmarino.8601@email.com) if you have any questions about integrating Phylogenie into your workflows.
 
 ## 📄 License

{phylogenie-3.1.10.dist-info → phylogenie-3.1.13.dist-info}/RECORD

@@ -1,5 +1,5 @@
-phylogenie/__init__.py,sha256=redo-SdvWwQPlyqOfdSW0TkkZf-aP98kLRCUIg4pB8c,3304
-phylogenie/draw.py,sha256=ZZvOQrmW_X9wUiOl5h2nvNBVX7BFH014EJ7evEI2orA,26840
+phylogenie/__init__.py,sha256=RyH_mcEXcKtELTkl9HRzWcl2ANWN-G4K0BLigqR3_B4,2888
+phylogenie/draw.py,sha256=z0f5g8t54DST-AxvFyNYREqpj41IhSIAjHIdrtVRH08,27449
 phylogenie/main.py,sha256=ry3B3HiwibZG3_qB58T5UhWy5dp6neYUtSqzL9LrSkA,1698
 phylogenie/mixins.py,sha256=wMwqP6zkqME9eMyzx5FS6-p9X8yW09jIC8jge8pHlkk,907
 phylogenie/msa.py,sha256=RGXxmo1WX9wi5NpEQTxMuH4zk8vM0f8A7Knm0YUJ9AI,2111
@@ -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=zqT9dzj413z_s0hqp3Cdq5NMO6lv-zuuaJlaqzaqaB8,1847
-phylogenie-3.1.10.dist-info/licenses/LICENSE.txt,sha256=NUrDqElK-eD3I0WqC004CJsy6cs0JgsAoebDv_42-pw,1071
-phylogenie-3.1.10.dist-info/METADATA,sha256=sdHbD8Gx14dS0TkKkN9dpmZkTKgt0ib__qtTX2noIo0,5195
-phylogenie-3.1.10.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-phylogenie-3.1.10.dist-info/entry_points.txt,sha256=BBH8LoReHnNFnvq4sROEsVFegfkKJ6c_oHZ7bgK7Jl4,52
-phylogenie-3.1.10.dist-info/top_level.txt,sha256=1YGZJhKA9tN9qI0Hcj6Cn_sOoDpba0HQlNcgQTjMD-8,11
-phylogenie-3.1.10.dist-info/RECORD,,
+phylogenie-3.1.13.dist-info/licenses/LICENSE.txt,sha256=NUrDqElK-eD3I0WqC004CJsy6cs0JgsAoebDv_42-pw,1071
+phylogenie-3.1.13.dist-info/METADATA,sha256=k0zK6rE7YTrt5ulq4i8doSKb-TH5GqoGdKmFt-Zam8c,5200
+phylogenie-3.1.13.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+phylogenie-3.1.13.dist-info/entry_points.txt,sha256=BBH8LoReHnNFnvq4sROEsVFegfkKJ6c_oHZ7bgK7Jl4,52
+phylogenie-3.1.13.dist-info/top_level.txt,sha256=1YGZJhKA9tN9qI0Hcj6Cn_sOoDpba0HQlNcgQTjMD-8,11
+phylogenie-3.1.13.dist-info/RECORD,,