phylogenie 2.1.3__tar.gz → 2.1.5__tar.gz

{phylogenie-2.1.3 → phylogenie-2.1.5}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: phylogenie
-Version: 2.1.3
+Version: 2.1.5
 Summary: Generate phylogenetic datasets with minimal setup effort
 Author: Gabriele Marino
 Author-email: gabmarino.8601@gmail.com

{phylogenie-2.1.3 → phylogenie-2.1.5}/phylogenie/generators/alisim.py

@@ -6,7 +6,7 @@ from typing import Any, Literal
 from numpy.random import Generator, default_rng
 
 from phylogenie.generators.dataset import DatasetGenerator, DataType
-from phylogenie.generators.factories import data
+from phylogenie.generators.factories import data, string
 from phylogenie.generators.trees import TreeDatasetGeneratorConfig
 from phylogenie.io import dump_newick
 
@@ -19,7 +19,7 @@ class AliSimDatasetGenerator(DatasetGenerator):
     trees: TreeDatasetGeneratorConfig
     keep_trees: bool = False
     iqtree_path: str = "iqtree2"
-    args: dict[str, str | int | float]
+    args: dict[str, Any]
 
     def _generate_one_from_tree(
         self, filename: str, tree_file: str, rng: Generator, data: dict[str, Any]
@@ -35,9 +35,7 @@ class AliSimDatasetGenerator(DatasetGenerator):
         ]
 
         for key, value in self.args.items():
-            command.extend(
-                [key, value.format(**data) if isinstance(value, str) else str(value)]
-            )
+            command.extend([key, string(value, data)])
 
         command.extend(["-af", "fasta"])
         subprocess.run(command, check=True, stdout=subprocess.DEVNULL)

{phylogenie-2.1.3 → phylogenie-2.1.5}/phylogenie/generators/factories.py

@@ -1,3 +1,4 @@
+import re
 from typing import Any
 
 import numpy as np
@@ -53,6 +54,14 @@ def scalar(x: cfg.Scalar, data: dict[str, Any]) -> pgt.Scalar:
     return x
 
 
+def string(s: Any, data: dict[str, Any]) -> str:
+    if not isinstance(s, str):
+        return str(s)
+    return re.sub(
+        r"\{([^{}]+)\}", lambda match: str(_eval_expression(match.group(1), data)), s
+    )  # Match content inside curly braces
+
+
 def many_scalars(x: cfg.ManyScalars, data: dict[str, Any]) -> pgt.ManyScalars:
     if isinstance(x, str):
         e = _eval_expression(x, data)

{phylogenie-2.1.3 → phylogenie-2.1.5}/phylogenie/tree.py

@@ -61,7 +61,11 @@ class Tree:
     def get_time(self) -> float:
         parent_time = 0 if self.parent is None else self.parent.get_time()
         if self.branch_length is None:
-            raise ValueError(f"Branch length of node {self.id} is not set.")
+            if self.parent is not None:
+                raise ValueError(
+                    f"Branch length of non-root node {self.id} is not set."
+                )
+            return 0.0
         return self.branch_length + parent_time
 
     def set(self, key: str, value: Any) -> None:

{phylogenie-2.1.3 → phylogenie-2.1.5}/phylogenie/treesimulator/gillespie.py

@@ -49,7 +49,9 @@ def simulate_tree(
         current_time = 0.0
         change_times = sorted(set(t for e in events for t in e.rate.change_times))
         next_change_time = change_times.pop(0) if change_times else np.inf
-        target_n_tips = rng.integers(min_tips, max_tips) if max_time == np.inf else None
+        target_n_tips = (
+            rng.integers(min_tips, max_tips + 1) if max_time == np.inf else None
+        )
 
         while current_time < max_time:
             if time.perf_counter() - start_clock > timeout:
@@ -125,7 +127,7 @@ def generate_trees(
 
     if os.path.exists(output_dir):
         raise FileExistsError(f"Output directory {output_dir} already exists")
-    os.mkdir(output_dir)
+    os.makedirs(output_dir, exist_ok=True)
 
     rng = default_rng(seed)
     jobs = joblib.Parallel(n_jobs=n_jobs, return_as="generator_unordered")(

{phylogenie-2.1.3 → phylogenie-2.1.5}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "phylogenie"
-version = "2.1.3"
+version = "2.1.5"
 description = "Generate phylogenetic datasets with minimal setup effort"
 authors = ["Gabriele Marino <gabmarino.8601@gmail.com>"]
 readme = "README.md"
@@ -24,9 +24,6 @@ pytest = "^8.3.5"
 phylogenie = "phylogenie.main:main"
 
 [tool.pyright]
-include = [
-    "phylogenie",
-]
 typeCheckingMode = "strict"
 
 [build-system]