phylogenie 2.0.10__py3-none-any.whl → 2.0.12__py3-none-any.whl

phylogenie/generators/configs.py

@@ -1,9 +1,6 @@
 from pydantic import BaseModel, ConfigDict
 
 import phylogenie.typings as pgt
-from phylogenie.skyline import SkylineMatrix as _SkylineMatrix
-from phylogenie.skyline import SkylineParameter as _SkylineParameter
-from phylogenie.skyline import SkylineVector as _SkylineVector
 
 
 class Distribution(BaseModel):
@@ -13,9 +10,9 @@ class Distribution(BaseModel):
 
 Integer = str | int
 Scalar = str | pgt.Scalar
-ManyScalars = str | list[Scalar]
-OneOrManyScalars = Scalar | list[Scalar]
-OneOrMany2DScalars = Scalar | list[list[Scalar]]
+ManyScalars = str | pgt.Many[Scalar]
+OneOrManyScalars = Scalar | pgt.Many[Scalar]
+OneOrMany2DScalars = Scalar | pgt.Many2D[Scalar]
 
 
 class StrictBaseModel(BaseModel):
@@ -28,19 +25,15 @@ class SkylineParameterModel(StrictBaseModel):
 
 
 class SkylineVectorModel(StrictBaseModel):
-    value: str | list[OneOrManyScalars]
+    value: str | pgt.Many[OneOrManyScalars]
     change_times: ManyScalars
 
 
 class SkylineMatrixModel(StrictBaseModel):
-    value: str | list[OneOrMany2DScalars]
+    value: str | pgt.Many[OneOrMany2DScalars]
     change_times: ManyScalars
 
 
-SkylineParameter = Scalar | SkylineParameterModel | _SkylineParameter
-SkylineVector = (
-    str | pgt.Scalar | list[SkylineParameter] | SkylineVectorModel | _SkylineVector
-)
-SkylineMatrix = (
-    str | pgt.Scalar | list[SkylineVector] | SkylineMatrixModel | None | _SkylineMatrix
-)
+SkylineParameter = Scalar | SkylineParameterModel
+SkylineVector = str | pgt.Scalar | pgt.Many[SkylineParameter] | SkylineVectorModel
+SkylineMatrix = str | pgt.Scalar | pgt.Many[SkylineVector] | SkylineMatrixModel | None

phylogenie/generators/dataset.py

@@ -41,21 +41,24 @@ 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:
+        if os.path.exists(output_dir):
+            print(f"Output directory {output_dir} already exists. Skipping.")
+            return
+
+        data_dir = (
+            output_dir
+            if self.context is None
+            else os.path.join(output_dir, DATA_DIRNAME)
+        )
+        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/generators/factories.py

@@ -80,8 +80,6 @@ def one_or_many_scalars(
 def skyline_parameter(
     x: cfg.SkylineParameter, data: dict[str, Any]
 ) -> SkylineParameterLike:
-    if isinstance(x, SkylineParameter):
-        return x
     if isinstance(x, cfg.Scalar):
         return scalar(x, data)
     return SkylineParameter(
@@ -93,8 +91,6 @@ def skyline_parameter(
 def skyline_vector(
     x: cfg.SkylineVector, data: dict[str, Any]
 ) -> SkylineVectorCoercible:
-    if isinstance(x, SkylineVector):
-        return x
     if isinstance(x, str):
         e = _eval_expression(x, data)
         if tg.is_one_or_many_scalars(e):
@@ -104,7 +100,7 @@ def skyline_vector(
         )
     if isinstance(x, pgt.Scalar):
         return x
-    if ctg.is_list_of_skyline_parameter_configs(x):
+    if ctg.is_many_skyline_parameter_configs(x):
         return [skyline_parameter(p, data) for p in x]
 
     assert isinstance(x, cfg.SkylineVectorModel)
@@ -155,8 +151,7 @@ def skyline_matrix(
 ) -> SkylineMatrixCoercible | None:
     if x is None:
         return None
-    if isinstance(x, SkylineMatrix):
-        return x
+
     if isinstance(x, str):
         e = _eval_expression(x, data)
         if tg.is_one_or_many_2D_scalars(e):
@@ -166,7 +161,7 @@ def skyline_matrix(
         )
     if isinstance(x, pgt.Scalar):
         return x
-    if ctg.is_list_of_skyline_vector_configs(x):
+    if ctg.is_many_skyline_vector_configs(x):
         return [skyline_vector(v, data) for v in x]
 
     assert isinstance(x, cfg.SkylineMatrixModel)

phylogenie/generators/typeguards.py

@@ -1,28 +1,25 @@
 from typing import Any, TypeGuard
 
 import phylogenie.generators.configs as cfg
+import phylogenie.typeguards as tg
 import phylogenie.typings as pgt
 
 
-def is_list(x: Any) -> TypeGuard[list[Any]]:
-    return isinstance(x, list)
+def is_many_scalar_configs(x: Any) -> TypeGuard[pgt.Many[cfg.Scalar]]:
+    return tg.is_many(x) and all(isinstance(v, cfg.Scalar) for v in x)
 
 
-def is_list_of_scalar_configs(x: Any) -> TypeGuard[list[cfg.Scalar]]:
-    return is_list(x) and all(isinstance(v, cfg.Scalar) for v in x)
-
-
-def is_list_of_skyline_parameter_configs(
+def is_many_skyline_parameter_configs(
     x: Any,
-) -> TypeGuard[list[cfg.SkylineParameter]]:
-    return is_list(x) and all(isinstance(v, cfg.SkylineParameter) for v in x)
+) -> TypeGuard[pgt.Many[cfg.SkylineParameter]]:
+    return tg.is_many(x) and all(isinstance(v, cfg.SkylineParameter) for v in x)
 
 
 def is_skyline_vector_config(x: Any) -> TypeGuard[cfg.SkylineVector]:
     return isinstance(
         x, str | pgt.Scalar | cfg.SkylineVectorModel
-    ) or is_list_of_skyline_parameter_configs(x)
+    ) or is_many_skyline_parameter_configs(x)
 
 
-def is_list_of_skyline_vector_configs(x: Any) -> TypeGuard[list[cfg.SkylineVector]]:
-    return is_list(x) and all(is_skyline_vector_config(v) for v in x)
+def is_many_skyline_vector_configs(x: Any) -> TypeGuard[pgt.Many[cfg.SkylineVector]]:
+    return tg.is_many(x) and all(is_skyline_vector_config(v) for v in x)

{phylogenie-2.0.10.dist-info → phylogenie-2.0.12.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: phylogenie
-Version: 2.0.10
+Version: 2.0.12
 Summary: Generate phylogenetic datasets with minimal setup effort
 Author: Gabriele Marino
 Author-email: gabmarino.8601@gmail.com

{phylogenie-2.0.10.dist-info → phylogenie-2.0.12.dist-info}/RECORD

@@ -1,11 +1,11 @@
 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=DAwJbAJ-1ZUTEvhPE5zs58KsIOA88gcRtrqVx0zONi4,1234
-phylogenie/generators/dataset.py,sha256=OB51YI9ilo-lrw8ETCDQAFh9iXWtPLBRyLg4JOjMi7c,2577
-phylogenie/generators/factories.py,sha256=lXGlN8DXFZmFNN5WwTpE8J80jWj01Zx6MkAYHrAvlTs,7108
+phylogenie/generators/configs.py,sha256=4jSBUZiFo2GacXWed5dy7lUEkaOWZkZG-KY9vHfhqGU,993
+phylogenie/generators/dataset.py,sha256=hbkN5McM4BKY7D0hLNaxdoAGsLHac6O-D4sgnZ0wFX4,2618
+phylogenie/generators/factories.py,sha256=0ckeAsKnPy69Vbdoi1rIyf6zRcqamz9VfSi0mAiTzds,6938
 phylogenie/generators/trees.py,sha256=jukaVXGcPGzDBEYMGJ1MKqWt4XbAB5EEfuHXDpwKTqM,9173
-phylogenie/generators/typeguards.py,sha256=Qph6ZnQ7wDMUNvB0VWQKlq42f8wkKOnM42cfMqhNov4,862
+phylogenie/generators/typeguards.py,sha256=yj4VkhOaUXJ2OrY-6zhOeY9C4yKIQxjZtk2d-vIxttQ,828
 phylogenie/io.py,sha256=ZXlofnSh7FX5UJiP0svRHrTraMSNgKa1GiAv0bMz7jU,2854
 phylogenie/main.py,sha256=vtvSpQxBNlYABoFQ25czl-l3fIr4QRo3svWVd-jcArw,1170
 phylogenie/msa.py,sha256=JDGyZUsAq6-m-SQjoCDjAkAZIxfgyl_PDIhdYn5HOow,2064
@@ -21,8 +21,8 @@ phylogenie/treesimulator/gillespie.py,sha256=4uMt_-Rr3cRXWGKC8veBIB-uqtKtN-dLbAH
 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-2.0.10.dist-info/LICENSE.txt,sha256=NUrDqElK-eD3I0WqC004CJsy6cs0JgsAoebDv_42-pw,1071
-phylogenie-2.0.10.dist-info/METADATA,sha256=YQSy1_-Vkuan10JzF5IkKTxs4fWRbUzhMUDYfk143k8,5473
-phylogenie-2.0.10.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
-phylogenie-2.0.10.dist-info/entry_points.txt,sha256=Rt6_usN0FkBX1ZfiqCirjMN9FKOgFLG8rydcQ8kugeE,51
-phylogenie-2.0.10.dist-info/RECORD,,
+phylogenie-2.0.12.dist-info/LICENSE.txt,sha256=NUrDqElK-eD3I0WqC004CJsy6cs0JgsAoebDv_42-pw,1071
+phylogenie-2.0.12.dist-info/METADATA,sha256=sZ7bmfmNAYLAlx1_cUAGzIBEnAGhS6yhFcfzgknh_BQ,5473
+phylogenie-2.0.12.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
+phylogenie-2.0.12.dist-info/entry_points.txt,sha256=Rt6_usN0FkBX1ZfiqCirjMN9FKOgFLG8rydcQ8kugeE,51
+phylogenie-2.0.12.dist-info/RECORD,,