phylogenie 2.1.4__py3-none-any.whl → 2.1.5__py3-none-any.whl

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/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/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-2.1.4.dist-info → phylogenie-2.1.5.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: phylogenie
-Version: 2.1.4
+Version: 2.1.5
 Summary: Generate phylogenetic datasets with minimal setup effort
 Author: Gabriele Marino
 Author-email: gabmarino.8601@gmail.com

{phylogenie-2.1.4.dist-info → phylogenie-2.1.5.dist-info}/RECORD

@@ -1,9 +1,9 @@
 phylogenie/__init__.py,sha256=T2mRLsYtoLlWt8GlxrrUnfXJ9XVioq7hTvVq3uJpwQI,2215
 phylogenie/generators/__init__.py,sha256=zsOxy28-9j9alOQLIgrOAFfmM58NNHO_NEtW-KXQXAY,888
-phylogenie/generators/alisim.py,sha256=3mANgyQrlozhslV3_ryt-m4ItkRcKKRLufWf6SNBTnQ,2781
+phylogenie/generators/alisim.py,sha256=6IQEn8zNoVSLdHLRT1HBnrv1wfZzYaT-38SQNXE_MU4,2702
 phylogenie/generators/configs.py,sha256=AiiFS6rpH9BPwDKCkT4SVrRzfLFFrwRCJM4CRj0Srdk,1072
 phylogenie/generators/dataset.py,sha256=loVKC_1G7gzkPDN9W3GF-Rj9od8AeOJgIC0aJJa-4KA,2110
-phylogenie/generators/factories.py,sha256=jLwDuq0mrmDz2U5rZM19KJ2hSpamG3r6zb83YCc6snA,7619
+phylogenie/generators/factories.py,sha256=OKCNg9jwF2KahZCJKTdJVxhLTeLNBDMOqJs7XSVXTqY,7881
 phylogenie/generators/trees.py,sha256=q03WPG82M4ucp-jyjoKEBy7TKMBzD3RkKn8hS0G0-i0,10463
 phylogenie/generators/typeguards.py,sha256=yj4VkhOaUXJ2OrY-6zhOeY9C4yKIQxjZtk2d-vIxttQ,828
 phylogenie/io.py,sha256=y7nQIvLgCvqELsXFKfm1GgKJO_saoQ-7zQpE3Kvajzc,3509
@@ -20,13 +20,13 @@ phylogenie/treesimulator/events/__init__.py,sha256=UGfvXOVJ_ZAkk_8sBPihjmxciiaEn
 phylogenie/treesimulator/events/contact_tracing.py,sha256=_nJ85yhgGkeruQgMHvGpDYoyhheBf8M4LgZWiWdi5dY,4801
 phylogenie/treesimulator/events/core.py,sha256=JokGmieAv2xEX7KsjBWZr05jHN1jB-XZbpxe9gwdbDA,7953
 phylogenie/treesimulator/events/mutations.py,sha256=xkXUIppbLIWZqKwVf-hi7d-_pS42TG2EPVfJA_grxBg,3443
-phylogenie/treesimulator/gillespie.py,sha256=naoxPyZixWVkd5f7B3KhEtOFiQI4NDIp_589NCLTHKM,4831
+phylogenie/treesimulator/gillespie.py,sha256=xdfiiMAsdC4ybLwmT6njC6ZrbgCeEptpuNX23Gnf-Vc,4877
 phylogenie/treesimulator/model.py,sha256=0Im6cFTlpMlJrSP4pTTKtvLT9qrQWV8MSTesAsBxT8g,5422
 phylogenie/typeguards.py,sha256=JtqmbEWJZBRHbWgCvcl6nrWm3VcBfzRbklbTBYHItn0,1325
 phylogenie/typings.py,sha256=GknvAFXyiaWeeYJ8Lk5d6E2VHT-xW6ONEojYbtJYiB8,476
 phylogenie/utils.py,sha256=pCg9ob0RpLUHwM49x4knKxL4FNPr3-EU_6zMXsvxtAg,370
-phylogenie-2.1.4.dist-info/LICENSE.txt,sha256=NUrDqElK-eD3I0WqC004CJsy6cs0JgsAoebDv_42-pw,1071
-phylogenie-2.1.4.dist-info/METADATA,sha256=xp3v_zG0Cua0UQN6TlF7yS9NuchhdlKnDf8-O3e-l_8,5375
-phylogenie-2.1.4.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
-phylogenie-2.1.4.dist-info/entry_points.txt,sha256=Rt6_usN0FkBX1ZfiqCirjMN9FKOgFLG8rydcQ8kugeE,51
-phylogenie-2.1.4.dist-info/RECORD,,
+phylogenie-2.1.5.dist-info/LICENSE.txt,sha256=NUrDqElK-eD3I0WqC004CJsy6cs0JgsAoebDv_42-pw,1071
+phylogenie-2.1.5.dist-info/METADATA,sha256=BIpsttapT2FwTo_rFg7AALZigoBVms5w9Q_pFTSGSus,5375
+phylogenie-2.1.5.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
+phylogenie-2.1.5.dist-info/entry_points.txt,sha256=Rt6_usN0FkBX1ZfiqCirjMN9FKOgFLG8rydcQ8kugeE,51
+phylogenie-2.1.5.dist-info/RECORD,,