phylogenie 2.0.7__py3-none-any.whl → 2.0.9__py3-none-any.whl

phylogenie/generators/dataset.py

@@ -41,19 +41,21 @@ class DatasetGenerator(ABC, cfg.StrictBaseModel):
         self._generate_one(filename=filename, rng=default_rng(seed), data=data)
 
     def _generate(self, rng: Generator, n_samples: int, output_dir: str) -> None:
-        data_dir = os.path.join(output_dir, DATA_DIRNAME)
-        if os.path.exists(data_dir):
-            print(f"Output directory {data_dir} already exists. Skipping.")
-            return
-        os.makedirs(data_dir)
-
         data: list[dict[str, Any]] = [{} for _ in range(n_samples)]
         if self.context is not None:
+            data_dir = os.path.join(output_dir, DATA_DIRNAME)
             for d, (k, v) in product(data, self.context.items()):
                 args = v.model_extra if v.model_extra is not None else {}
                 d[k] = np.array(getattr(rng, v.type)(**args)).tolist()
             df = pd.DataFrame([{"file_id": str(i), **d} for i, d in enumerate(data)])
             df.to_csv(os.path.join(output_dir, METADATA_FILENAME), index=False)
+        else:
+            data_dir = output_dir
+
+        if os.path.exists(data_dir):
+            print(f"Output directory {data_dir} already exists. Skipping.")
+            return
+        os.makedirs(data_dir)
 
         joblib.Parallel(n_jobs=self.n_jobs)(
             joblib.delayed(self.generate_one)(

phylogenie/tree.py

@@ -1,5 +1,4 @@
 from collections.abc import Iterator
-from typing import Any
 
 
 class Tree:
@@ -8,7 +7,6 @@ class Tree:
         self.branch_length = branch_length
         self.parent: Tree | None = None
         self.children: list[Tree] = []
-        self._features: dict[str, Any] = {}
 
     def add_child(self, child: "Tree") -> "Tree":
         child.parent = self
@@ -49,12 +47,6 @@ class Tree:
             new_tree.add_child(child.copy())
         return new_tree
 
-    def get(self, key: str, default: Any = None) -> Any:
-        return self._features.get(key, default)
-
-    def set(self, key: str, value: Any) -> None:
-        self._features[key] = value
-
     def __iter__(self) -> Iterator["Tree"]:
         return self.preorder_traversal()
 

{phylogenie-2.0.7.dist-info → phylogenie-2.0.9.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: phylogenie
-Version: 2.0.7
+Version: 2.0.9
 Summary: Generate phylogenetic datasets with minimal setup effort
 Author: Gabriele Marino
 Author-email: gabmarino.8601@gmail.com

{phylogenie-2.0.7.dist-info → phylogenie-2.0.9.dist-info}/RECORD

@@ -2,7 +2,7 @@ phylogenie/__init__.py,sha256=1w_0H9lg7hI3b-NLjKuzc34GbJJGyjLq9LrlogecTzI,1759
 phylogenie/generators/__init__.py,sha256=zsOxy28-9j9alOQLIgrOAFfmM58NNHO_NEtW-KXQXAY,888
 phylogenie/generators/alisim.py,sha256=dDqlSwLDbRE2u5SZlsq1mArobTBtuk0aeXY3m1N-bWA,2374
 phylogenie/generators/configs.py,sha256=5ZWdKhRUjlNifw7QKXbooKV1fElqfCk_jBGxfcjh8do,969
-phylogenie/generators/dataset.py,sha256=k6RYJpgxOL8a_yMq98WUF-dcJv8TwxaWnde0k13M4J0,2525
+phylogenie/generators/dataset.py,sha256=OB51YI9ilo-lrw8ETCDQAFh9iXWtPLBRyLg4JOjMi7c,2577
 phylogenie/generators/factories.py,sha256=O8wqL-PvZps0Dq6mQa_PTi4vBvky5LkQIy1jjfOUm-4,6944
 phylogenie/generators/trees.py,sha256=jukaVXGcPGzDBEYMGJ1MKqWt4XbAB5EEfuHXDpwKTqM,9173
 phylogenie/generators/typeguards.py,sha256=Qph6ZnQ7wDMUNvB0VWQKlq42f8wkKOnM42cfMqhNov4,862
@@ -14,15 +14,15 @@ phylogenie/skyline/__init__.py,sha256=7pF4CUb4ZCLzNYJNhOjpuTOLTRhlK7L6ugfccNqjIG
 phylogenie/skyline/matrix.py,sha256=Gl8OgKjtieG0NwPYiPimKI36gefV8fm_OeorjdXxPTs,9146
 phylogenie/skyline/parameter.py,sha256=EM9qlPt0JhMBy3TbztM0dj24BaGNEy8KWKdTObDKhbI,4644
 phylogenie/skyline/vector.py,sha256=bJP7_FNX_Klt6wXqsyfj0KX3VNj6-dIhzCKSJuQcOV0,7115
-phylogenie/tree.py,sha256=34gcxUoTGfj72EbIlpnrhWGnNFppUVjms3XEn1ZS3-g,1997
+phylogenie/tree.py,sha256=dk8Sj1tqyGOunVO2crtIqb0LH-ws-PXqA8SuNcYfVHI,1738
 phylogenie/treesimulator/__init__.py,sha256=INPU9LrPdUmt3dYGzWDRoRKrPR9xENcHu44pJVUbyNA,525
 phylogenie/treesimulator/events.py,sha256=X3_0U9qqMpYgh6-7TwQEnlUipANkHz6QTCXlm-qXFQk,9524
 phylogenie/treesimulator/gillespie.py,sha256=Fn-PyVICx3pWtpHko7rf6omf_kqOkkpebSJy56oPKnQ,3216
 phylogenie/treesimulator/model.py,sha256=XpzAicmg2O6K0Trk5YolH-B_HJZxoSauF2wZOMqp-Iw,5559
 phylogenie/typeguards.py,sha256=JtqmbEWJZBRHbWgCvcl6nrWm3VcBfzRbklbTBYHItn0,1325
 phylogenie/typings.py,sha256=O1X6lGKTjJ2YJz3ApQ-rYb_tEJNUIcHdUIeYlSM4s5o,500
-phylogenie-2.0.7.dist-info/LICENSE.txt,sha256=NUrDqElK-eD3I0WqC004CJsy6cs0JgsAoebDv_42-pw,1071
-phylogenie-2.0.7.dist-info/METADATA,sha256=REo_HAAqLn0XQiHeCPyNPbGuSsbT5p1QupjSxg5Zs_U,5472
-phylogenie-2.0.7.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
-phylogenie-2.0.7.dist-info/entry_points.txt,sha256=Rt6_usN0FkBX1ZfiqCirjMN9FKOgFLG8rydcQ8kugeE,51
-phylogenie-2.0.7.dist-info/RECORD,,
+phylogenie-2.0.9.dist-info/LICENSE.txt,sha256=NUrDqElK-eD3I0WqC004CJsy6cs0JgsAoebDv_42-pw,1071
+phylogenie-2.0.9.dist-info/METADATA,sha256=EHn9nzfQMQCfWXzl1Ddb_dTrowodP7Y4dsDQqsna2xw,5472
+phylogenie-2.0.9.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
+phylogenie-2.0.9.dist-info/entry_points.txt,sha256=Rt6_usN0FkBX1ZfiqCirjMN9FKOgFLG8rydcQ8kugeE,51
+phylogenie-2.0.9.dist-info/RECORD,,