phylogenie 2.0.11__py3-none-any.whl → 2.0.13__py3-none-any.whl

phylogenie/__init__.py

@@ -8,6 +8,9 @@ from phylogenie.generators import (
     DatasetGeneratorConfig,
     EpidemiologicalTreeDatasetGenerator,
     FBDTreeDatasetGenerator,
+    SkylineMatrixModel,
+    SkylineParameterModel,
+    SkylineVectorModel,
     TreeDatasetGeneratorConfig,
 )
 from phylogenie.io import load_fasta, load_newick
@@ -48,13 +51,16 @@ __all__ = [
     "FBDTreeDatasetGenerator",
     "SkylineMatrix",
     "SkylineMatrixCoercible",
+    "SkylineMatrixModel",
     "skyline_matrix",
     "SkylineParameter",
     "SkylineParameterLike",
+    "SkylineParameterModel",
     "skyline_parameter",
     "SkylineVector",
     "SkylineVectorCoercible",
     "SkylineVectorLike",
+    "SkylineVectorModel",
     "skyline_vector",
     "Tree",
     "TreeDatasetGeneratorConfig",

phylogenie/generators/__init__.py

@@ -3,6 +3,11 @@ from typing import Annotated
 from pydantic import Field
 
 from phylogenie.generators.alisim import AliSimDatasetGenerator
+from phylogenie.generators.configs import (
+    SkylineMatrixModel,
+    SkylineParameterModel,
+    SkylineVectorModel,
+)
 from phylogenie.generators.dataset import DatasetGenerator
 from phylogenie.generators.trees import (
     BDEITreeDatasetGenerator,
@@ -29,4 +34,7 @@ __all__ = [
     "BDTreeDatasetGenerator",
     "BDEITreeDatasetGenerator",
     "BDSSTreeDatasetGenerator",
+    "SkylineMatrixModel",
+    "SkylineParameterModel",
+    "SkylineVectorModel",
 ]

phylogenie/generators/configs.py

@@ -10,9 +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):
@@ -25,15 +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
-SkylineVector = str | pgt.Scalar | list[SkylineParameter] | SkylineVectorModel
-SkylineMatrix = str | pgt.Scalar | list[SkylineVector] | SkylineMatrixModel | None
+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

@@ -100,7 +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)
@@ -161,7 +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-2.0.11.dist-info → phylogenie-2.0.13.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: phylogenie
-Version: 2.0.11
+Version: 2.0.13
 Summary: Generate phylogenetic datasets with minimal setup effort
 Author: Gabriele Marino
 Author-email: gabmarino.8601@gmail.com

{phylogenie-2.0.11.dist-info → phylogenie-2.0.13.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/__init__.py,sha256=4BytT42_M1K6T3W9eqHQCrKc6g0Lh5LTQxP8dGIJTsk,1915
+phylogenie/generators/__init__.py,sha256=VCpuvmOoY_N6p1h_Q0peYgGIIUIFLsvZT3T7vbHG6w0,1090
 phylogenie/generators/alisim.py,sha256=dDqlSwLDbRE2u5SZlsq1mArobTBtuk0aeXY3m1N-bWA,2374
-phylogenie/generators/configs.py,sha256=5ZWdKhRUjlNifw7QKXbooKV1fElqfCk_jBGxfcjh8do,969
-phylogenie/generators/dataset.py,sha256=OB51YI9ilo-lrw8ETCDQAFh9iXWtPLBRyLg4JOjMi7c,2577
-phylogenie/generators/factories.py,sha256=O8wqL-PvZps0Dq6mQa_PTi4vBvky5LkQIy1jjfOUm-4,6944
+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-2.0.11.dist-info/LICENSE.txt,sha256=NUrDqElK-eD3I0WqC004CJsy6cs0JgsAoebDv_42-pw,1071
-phylogenie-2.0.11.dist-info/METADATA,sha256=H9fTgI9BaoI2j7-Od2an5dPivAxl1jk2DACT3m9DCoE,5473
-phylogenie-2.0.11.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
-phylogenie-2.0.11.dist-info/entry_points.txt,sha256=Rt6_usN0FkBX1ZfiqCirjMN9FKOgFLG8rydcQ8kugeE,51
-phylogenie-2.0.11.dist-info/RECORD,,
+phylogenie-2.0.13.dist-info/LICENSE.txt,sha256=NUrDqElK-eD3I0WqC004CJsy6cs0JgsAoebDv_42-pw,1071
+phylogenie-2.0.13.dist-info/METADATA,sha256=XkYNiu3IYt516JJ8dw-iIo9zonC8LFiB_ZVGhNyw-eY,5473
+phylogenie-2.0.13.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
+phylogenie-2.0.13.dist-info/entry_points.txt,sha256=Rt6_usN0FkBX1ZfiqCirjMN9FKOgFLG8rydcQ8kugeE,51
+phylogenie-2.0.13.dist-info/RECORD,,