phylogenie 3.1.8__tar.gz → 3.1.9__tar.gz

{phylogenie-3.1.8/src/phylogenie.egg-info → phylogenie-3.1.9}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: phylogenie
-Version: 3.1.8
+Version: 3.1.9
 Summary: Generate phylogenetic datasets with minimal setup effort
 Requires-Python: >=3.10
 Description-Content-Type: text/markdown

{phylogenie-3.1.8 → phylogenie-3.1.9}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "phylogenie"
-version = "3.1.8"
+version = "3.1.9"
 description = "Generate phylogenetic datasets with minimal setup effort"
 readme = "README.md"
 requires-python = ">=3.10"

{phylogenie-3.1.8 → phylogenie-3.1.9}/src/phylogenie/draw.py

@@ -382,7 +382,7 @@ def _init_colored_tree_continuous(
     vmin: float | None = ...,
     vmax: float | None = ...,
     *,
-    show_hist: Literal[True],
+    show_hist: Literal[True] = True,
     hist_kwargs: dict[str, Any] | None = ...,
     hist_axes_kwargs: dict[str, Any] | None = ...,
 ) -> tuple[Axes, dict[Tree, Color], Axes]: ...
@@ -394,7 +394,6 @@ def _init_colored_tree_continuous(
     colormap: str | Colormap = "viridis",
     vmin: float | None = None,
     vmax: float | None = None,
-    *,
     show_hist: bool = True,
     hist_kwargs: dict[str, Any] | None = None,
     hist_axes_kwargs: dict[str, Any] | None = None,
@@ -493,8 +492,7 @@ def draw_colored_tree_continuous(
     colormap: str | Colormap = "viridis",
     vmin: float | None = None,
     vmax: float | None = None,
-    *,
-    show_hist: Literal[True],
+    show_hist: Literal[True] = True,
     hist_kwargs: dict[str, Any] | None = None,
     hist_axes_kwargs: dict[str, Any] | None = None,
 ) -> tuple[Axes, Axes]: ...
@@ -602,8 +600,7 @@ def draw_colored_dated_tree_continuous(
     colormap: str | Colormap = "viridis",
     vmin: float | None = None,
     vmax: float | None = None,
-    *,
-    show_hist: Literal[True],
+    show_hist: Literal[True] = True,
     hist_kwargs: dict[str, Any] | None = None,
     hist_axes_kwargs: dict[str, Any] | None = None,
 ) -> tuple[Axes, Axes]: ...

{phylogenie-3.1.8 → phylogenie-3.1.9}/src/phylogenie/io/fasta.py

@@ -1,3 +1,4 @@
+from datetime import date
 from pathlib import Path
 from typing import Callable
 
@@ -5,7 +6,8 @@ from phylogenie.msa import MSA, Sequence
 
 
 def load_fasta(
-    fasta_file: str | Path, extract_time_from_id: Callable[[str], float] | None = None
+    fasta_file: str | Path,
+    extract_time_from_id: Callable[[str], float | date] | None = None,
 ) -> MSA:
     sequences: list[Sequence] = []
     with open(fasta_file, "r") as f:
@@ -17,10 +19,14 @@ def load_fasta(
             if extract_time_from_id is not None:
                 time = extract_time_from_id(id)
             elif "|" in id:
+                last_metadata = id.split("|")[-1]
                 try:
-                    time = float(id.split("|")[-1])
+                    time = float(last_metadata)
                 except ValueError:
-                    pass
+                    try:
+                        time = date.fromisoformat(last_metadata)
+                    except ValueError:
+                        pass
             chars = next(f).strip()
             sequences.append(Sequence(id, chars, time))
     return MSA(sequences)

{phylogenie-3.1.8 → phylogenie-3.1.9}/src/phylogenie/msa.py

@@ -1,5 +1,6 @@
 from collections.abc import Iterator
 from dataclasses import dataclass
+from datetime import date
 
 import numpy as np
 
@@ -8,7 +9,7 @@ import numpy as np
 class Sequence:
     id: str
     chars: str
-    time: float | None = None
+    time: float | date | None = None
 
 
 class MSA:
@@ -25,8 +26,8 @@ class MSA:
         return [sequence.id for sequence in self.sequences]
 
     @property
-    def times(self) -> list[float]:
-        times: list[float] = []
+    def times(self) -> list[float | date]:
+        times: list[float | date] = []
         for sequence in self:
             if sequence.time is None:
                 raise ValueError(f"Time is not set for sequence {sequence.id}.")

{phylogenie-3.1.8 → phylogenie-3.1.9/src/phylogenie.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: phylogenie
-Version: 3.1.8
+Version: 3.1.9
 Summary: Generate phylogenetic datasets with minimal setup effort
 Requires-Python: >=3.10
 Description-Content-Type: text/markdown