phylogenie 1.0.2__py3-none-any.whl → 1.0.3__py3-none-any.whl

phylogenie/core/factories.py

@@ -1,4 +1,4 @@
-from typing import Any, overload
+from typing import Any, Literal, overload
 
 import numpy as np
 
@@ -23,10 +23,9 @@ def _eval_expression(expression: str, data: pgt.Data) -> Any:
             expression,
             {
                 "__builtins__": __builtins__,
-                # "np": np,
-                # **{k: np.array(v) for k, v in data.items()},
+                "np": np,
+                **{k: np.array(v) for k, v in data.items()},
             },
-            {k: np.array(v) for k, v in data.items()},
         )
     ).tolist()
 
@@ -101,20 +100,17 @@ def skyline_parameter_like_factory(
     )
 
 
-from typing import Literal
-
-
 @overload
 def _parse_skyline_vector_value_model(
     x: cfg.SkylineVectorValueModel, data: pgt.Data, coercible: Literal[True]
-) -> SkylineVector | SkylineParameter: ...
+) -> SkylineVectorCoercible: ...
 @overload
 def _parse_skyline_vector_value_model(
     x: cfg.SkylineVectorValueModel, data: pgt.Data, coercible: Literal[False]
-) -> SkylineVector: ...
+) -> SkylineVectorLike: ...
 def _parse_skyline_vector_value_model(
     x: cfg.SkylineVectorValueModel, data: pgt.Data, coercible: bool
-) -> SkylineVector | SkylineParameter:
+) -> SkylineVectorCoercible:
     change_times = many_scalars_factory(x.change_times, data)
     if isinstance(x.value, str):
         e = _eval_expression(x.value, data)
@@ -132,13 +128,13 @@ def _parse_skyline_vector_value_model(
             return SkylineParameter(value=value, change_times=change_times)
         else:
             raise ValueError(
-                f"Parsing SkylineVector value {x.value} yielded a sequence of scalars ({value}) when a nested (2D) sequence of scalars was expected."
+                f"Parsing SkylineVector config {x.value} yielded a sequence of scalars {value} when a nested (2D) sequence of scalars was expected."
             )
 
     Ns = {len(elem) for elem in value if tg.is_many(elem)}
     if len(Ns) > 1:
         raise ValueError(
-            f"All elements in the value of a SkylineVector config must be scalars or have the same length (got value={value} with inconsistent lengths {Ns})."
+            f"All elements in the value of a SkylineVector config must be scalars or have the same length (config {x.value} yielded value={value} with inconsistent lengths {Ns})."
         )
     (N,) = Ns
     value = [[p] * N if isinstance(p, pgt.Scalar) else p for p in value]
@@ -238,13 +234,13 @@ def skyline_matrix_coercible_factory(
             n_rows = len(elem)
             if any(len(row) != n_rows for row in elem):
                 raise ValueError(
-                    f"All elements in the value of a SkylineMatrix config must be scalars or square matrices (got non-square matrix: {elem})."
+                    f"All elements in the value of a SkylineMatrix config must be scalars or square matrices (config {x.value} yeilded a non-square matrix: {elem})."
                 )
             Ns.add(n_rows)
 
     if len(Ns) > 1:
         raise ValueError(
-            f"All elements in the value of a SkylineMatrix config must be scalars or have the same square shape (got value={value} with inconsistent lengths {Ns})."
+            f"All elements in the value of a SkylineMatrix config must be scalars or have the same square shape (config {x.value} yielded value={value} with inconsistent lengths {Ns})."
         )
     (N,) = Ns
     value = [[[p] * N] * N if isinstance(p, pgt.Scalar) else p for p in value]

{phylogenie-1.0.2.dist-info → phylogenie-1.0.3.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: phylogenie
-Version: 1.0.2
+Version: 1.0.3
 Summary: Generate phylogenetic datasets with minimal setup effort
 Author: Gabriele Marino
 Author-email: gabmarino.8601@gmail.com

{phylogenie-1.0.2.dist-info → phylogenie-1.0.3.dist-info}/RECORD

@@ -12,7 +12,7 @@ phylogenie/core/context/configs.py,sha256=zd-ADFzJbb6KPkol-tXxSdS8LUBeQYQq8fDzXo
 phylogenie/core/context/distributions.py,sha256=QF14tM2ibjE7f6WK3s4hTaz_sLQBTNVr2ZBNe2refeE,3059
 phylogenie/core/context/factories.py,sha256=QO96wZwrQbgX2Rkd0wY3qQDahiZ8fDg8Mg8KKY0lr2c,1390
 phylogenie/core/dataset.py,sha256=mgPAexXTat6x7YB9-BI6d5HWwrAvt8xydmiWVzwVD3M,2431
-phylogenie/core/factories.py,sha256=1ZXGWV8kWn-LZjb5dFk4LrWNtyhLGyH7jQ0DuuVjWN0,8912
+phylogenie/core/factories.py,sha256=Ph9qlQ6AthVKbzQZvvzj6EQye5LS2nl6d_r2dFuBfEo,8881
 phylogenie/core/msas/__init__.py,sha256=-2XjTmiTA6zAwiLs2ksKecCrSbNLheo7KKjDyvuLipg,207
 phylogenie/core/msas/alisim.py,sha256=TG4LAHJaH3rGWa3cwXzX6MgaXuh2tLzhdoALyOkoiXY,1047
 phylogenie/core/msas/base.py,sha256=cKH0FGALmObmOLZ2dJ3vrpb3jTLg2oeWJsIE6HznJ0Q,1803
@@ -32,8 +32,8 @@ phylogenie/skyline/parameter.py,sha256=wrtvQDho3OC5tzrMnnFTy95GXaYN20KN8P5Gwyf-r
 phylogenie/skyline/vector.py,sha256=NgmVbWjWG_itZ9a57q9QqSybvG9-Cr9X264RGPVyp_Q,6399
 phylogenie/typeguards.py,sha256=WBOSJSaOC8VDtrYoA2w_AYEXTpyKdCfmsM29KaKXl3A,1350
 phylogenie/typings.py,sha256=93VRedBxrpzXkT4uaNu_1JiMzsOjp7fUy4kLv_eYxUE,565
-phylogenie-1.0.2.dist-info/LICENSE.txt,sha256=NUrDqElK-eD3I0WqC004CJsy6cs0JgsAoebDv_42-pw,1071
-phylogenie-1.0.2.dist-info/METADATA,sha256=5RcgFLDSlV90GTGBblQdur97pV2C0drYMg_EGKytHD8,6251
-phylogenie-1.0.2.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
-phylogenie-1.0.2.dist-info/entry_points.txt,sha256=Rt6_usN0FkBX1ZfiqCirjMN9FKOgFLG8rydcQ8kugeE,51
-phylogenie-1.0.2.dist-info/RECORD,,
+phylogenie-1.0.3.dist-info/LICENSE.txt,sha256=NUrDqElK-eD3I0WqC004CJsy6cs0JgsAoebDv_42-pw,1071
+phylogenie-1.0.3.dist-info/METADATA,sha256=JVGcZNn6O2Wuuek_ZTQp5CBdw5_xoSHzvSyTmENmxNw,6251
+phylogenie-1.0.3.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
+phylogenie-1.0.3.dist-info/entry_points.txt,sha256=Rt6_usN0FkBX1ZfiqCirjMN9FKOgFLG8rydcQ8kugeE,51
+phylogenie-1.0.3.dist-info/RECORD,,