phylogenie 1.0.1__py3-none-any.whl → 1.0.3__py3-none-any.whl

phylogenie/skyline/vector.py

@@ -1,5 +1,5 @@
 from collections.abc import Callable, Iterator
-from typing import TypeGuard, Union, overload
+from typing import TypeGuard, Union
 
 import phylogenie.typeguards as tg
 import phylogenie.typings as pgt
@@ -11,38 +11,51 @@ from phylogenie.skyline.parameter import (
     skyline_parameter,
 )
 
-SkylineVectorParams = pgt.OneOrMany[SkylineParameterLike]
 SkylineVectorOperand = Union[SkylineParameterLike, "SkylineVector"]
-SkylineVectorLike = Union[SkylineVectorParams, "SkylineVector"]
+SkylineVectorLike = Union[pgt.Many[SkylineParameterLike], "SkylineVector"]
+SkylineVectorCoercible = Union[pgt.OneOrMany[SkylineParameterLike], "SkylineVector"]
+
+
+def is_skyline_vector_operand(x: object) -> TypeGuard[SkylineVectorOperand]:
+    return isinstance(x, SkylineVector) or is_skyline_parameter_like(x)
+
+
+def is_skyline_vector_like(x: object) -> TypeGuard[SkylineVectorLike]:
+    return isinstance(x, SkylineVector) or is_many_skyline_parameters_like(x)
+
+
+def is_many_skyline_vectors_like(x: object) -> TypeGuard[pgt.Many[SkylineVectorLike]]:
+    return tg.is_many(x) and all(is_skyline_vector_like(v) for v in x)
 
 
 class SkylineVector:
     def __init__(
         self,
-        params: SkylineVectorParams | None = None,
-        value: pgt.Many[pgt.OneOrManyScalars] | None = None,
-        change_times: pgt.OneOrManyScalars | None = None,
+        params: pgt.Many[SkylineParameterLike] | None = None,
+        value: pgt.Many2DScalars | None = None,
+        change_times: pgt.ManyScalars | None = None,
     ) -> None:
         if params is not None and value is None and change_times is None:
-            if is_skyline_parameter_like(params):
-                self.params = [skyline_parameter(params)]
-            elif is_many_skyline_parameters_like(params):
+            if is_many_skyline_parameters_like(params):
                 self.params = [skyline_parameter(param) for param in params]
             else:
                 raise TypeError(
-                    f"It is impossible to create a SkylineVector from `params` {params} of type {type(params)}. Please provide a SkylineParameterLike object (i.e., a SkylineParameter or a scalar) or a sequence of them."
+                    f"It is impossible to create a SkylineVector from `params` {params} of type {type(params)}. Please provide a sequence of SkylineParameterLike objects (a SkylineParameterLike object can either be a SkylineParameter or a scalar)."
                 )
         elif value is not None and change_times is not None:
-            Ns = {len(row) for row in value if tg.is_many(row)}
-            if len(Ns) > 1:
-                raise ValueError(
-                    f"All rows in the `value` must be scalars or have the same length to create a SkylineVector (got value={value} with row lengths={Ns})."
+            if tg.is_many_2D_scalars(value):
+                vector_lengths = {len(vector) for vector in value}
+                if any(vl != len(value[0]) for vl in vector_lengths):
+                    raise ValueError(
+                        f"All rows in the `value` of a SkylineVector must have the same length (got value={value} with vector lengths={vector_lengths})."
+                    )
+            else:
+                raise TypeError(
+                    f"It is impossible to create a SkylineVector from `value` {value} of type {type(value)}. Please provide a nested (2D) sequence of scalar values."
                 )
-            N = Ns.pop() if Ns else 1
-            value = [[x] * N if isinstance(x, pgt.Scalar) else x for x in value]
             self.params = [
-                SkylineParameter([row[i] for row in value], change_times)
-                for i in range(N)
+                SkylineParameter([vector[i] for vector in value], change_times)
+                for i in range(len(value[0]))
             ]
         else:
             raise ValueError(
@@ -51,20 +64,18 @@ class SkylineVector:
 
     @property
     def change_times(self) -> pgt.Vector1D:
-        return tuple(
-            sorted(set(t for param in self.params for t in param.change_times))
-        )
+        return sorted(set(t for param in self.params for t in param.change_times))
 
     @property
     def value(self) -> pgt.Vector2D:
-        return tuple(self.get_value_at_time(t) for t in (0, *self.change_times))
+        return [self.get_value_at_time(t) for t in (0, *self.change_times)]
 
     @property
     def N(self) -> int:
         return len(self.params)
 
     def get_value_at_time(self, t: pgt.Scalar) -> pgt.Vector1D:
-        return tuple(param.get_value_at_time(t) for param in self.params)
+        return [param.get_value_at_time(t) for param in self.params]
 
     def operate(
         self,
@@ -117,48 +128,28 @@ class SkylineVector:
     def __iter__(self) -> Iterator[SkylineParameter]:
         return iter(self.params)
 
-    @overload
-    def __getitem__(self, item: int) -> SkylineParameter: ...
-    @overload
-    def __getitem__(self, item: slice) -> "SkylineVector": ...
-    def __getitem__(self, item: int | slice) -> "SkylineParameter | SkylineVector":
-        if isinstance(item, slice):
-            return SkylineVector(self.params[item])
+    def __getitem__(self, item: int) -> "SkylineParameter":
         return self.params[item]
 
     def __setitem__(self, item: int, value: SkylineParameterLike) -> None:
         if not is_skyline_parameter_like(value):
             raise TypeError(
-                f"`value` must be a SkylineParameterLike (got {type(value)})."
+                f"It is impossible to set item {item} of SkylineVector with value {value} of type {type(value)}. Please provide a SkylineParameterLike object (i.e., a scalar or a SkylineParameter)."
             )
         self.params[item] = skyline_parameter(value)
 
 
-def skyline_vector(x: SkylineVectorLike, N: int) -> SkylineVector:
+def skyline_vector(x: SkylineVectorCoercible, N: int) -> SkylineVector:
     if is_skyline_parameter_like(x):
         return SkylineVector([skyline_parameter(x)] * N)
-    if not isinstance(x, SkylineVector):
+    elif is_many_skyline_parameters_like(x):
         x = SkylineVector(x)
+    elif not isinstance(x, SkylineVector):
+        raise TypeError(
+            f"It is impossible to coerce {x} of type {type(x)} into a SkylineVector. Please provide a SkylineParameterLike object (i.e., a scalar or a SkylineParameter), or a sequence of them."
+        )
     if x.N != N:
         raise ValueError(
             f"Expected a SkylineVector of size {N}, got {x} of size {x.N}."
         )
     return x
-
-
-def is_skyline_vector_operand(value: object) -> TypeGuard[SkylineVectorOperand]:
-    return isinstance(value, SkylineVector) or is_skyline_parameter_like(value)
-
-
-def is_skyline_vector_like(value: object) -> TypeGuard[SkylineVectorLike]:
-    return (
-        isinstance(value, SkylineVector)
-        or is_skyline_parameter_like(value)
-        or is_many_skyline_parameters_like(value)
-    )
-
-
-def is_many_skyline_vectors_like(
-    value: object,
-) -> TypeGuard[pgt.Many[SkylineVectorLike]]:
-    return tg.is_many(value) and all(is_skyline_vector_like(v) for v in value)

phylogenie/typeguards.py

@@ -24,17 +24,19 @@ def is_many_one_or_many_scalars(x: object) -> TypeGuard[pgt.Many[pgt.OneOrManySc
     return is_many(x) and all(is_one_or_many_scalars(i) for i in x)
 
 
-def is_one_or_many_ints(x: object) -> TypeGuard[pgt.OneOrMany[int]]:
-    return isinstance(x, int) or is_many_ints(x)
-
-
 def is_many_2D_scalars(x: object) -> TypeGuard[pgt.Many2DScalars]:
     return is_many(x) and all(is_many_scalars(i) for i in x)
 
 
-def is_many_one_or_many_2d_scalars(
+def is_one_or_many_2D_scalars(x: object) -> TypeGuard[pgt.OneOrMany2DScalars]:
+    return isinstance(x, pgt.Scalar) or is_many_2D_scalars(x)
+
+
+def is_many_one_or_many_2D_scalars(
     x: object,
 ) -> TypeGuard[pgt.Many[pgt.OneOrMany2DScalars]]:
-    return is_many(x) and all(
-        isinstance(i, pgt.Scalar) or is_many_2D_scalars(i) for i in x
-    )
+    return is_many(x) and all(is_one_or_many_2D_scalars(i) for i in x)
+
+
+def is_many_3D_scalars(x: object) -> TypeGuard[pgt.Many3DScalars]:
+    return is_many(x) and all(is_many_2D_scalars(i) for i in x)

phylogenie/typings.py

@@ -11,12 +11,13 @@ OneOrMany2D = _T | Many2D[_T]
 Scalar = int | float
 OneOrManyScalars = OneOrMany[Scalar]
 ManyScalars = Many[Scalar]
-Many2DScalars = Many2D[Scalar]
 OneOrMany2DScalars = OneOrMany2D[Scalar]
+Many2DScalars = Many2D[Scalar]
+Many3DScalars = Many3D[Scalar]
+
+Vector1D = list[Scalar]
+IntVector1D = list[int]
+Vector2D = list[Vector1D]
+Vector3D = list[Vector2D]
 
-Vector1D = tuple[Scalar, ...]
-IntVector1D = tuple[int, ...]
-Vector1DLike = Scalar | Vector1D
-IntVector1DLike = int | IntVector1D
-Vector2D = tuple[Vector1D, ...]
-Vector3D = tuple[Vector2D, ...]
+Data = dict[str, str | Scalar | Vector1D | Vector2D | Vector3D]

{phylogenie-1.0.1.dist-info → phylogenie-1.0.3.dist-info}/METADATA

@@ -1,8 +1,8 @@
 Metadata-Version: 2.1
 Name: phylogenie
-Version: 1.0.1
+Version: 1.0.3
 Summary: Generate phylogenetic datasets with minimal setup effort
-Author: gabriele-marino
+Author: Gabriele Marino
 Author-email: gabmarino.8601@gmail.com
 Requires-Python: >=3.10,<4.0
 Classifier: Programming Language :: Python :: 3

phylogenie-1.0.3.dist-info/RECORD

@@ -0,0 +1,39 @@
+phylogenie/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+phylogenie/backend/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+phylogenie/backend/remaster/__init__.py,sha256=g1oMKi6SX60Geq_e2AjBlf7-pDvLfrsT3gW6AORdbMo,509
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+phylogenie/backend/remaster/reactions.py,sha256=oc2ZY9WtTajbOWjARDmA0JnS255tbVeMt1DmyCUp95M,5904
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phylogenie/core/typings.py

@@ -1,10 +0,0 @@
-import phylogenie.typings as pgt
-
-Data = dict[
-    str,
-    str
-    | pgt.Scalar
-    | list[pgt.Scalar]
-    | list[list[pgt.Scalar]]
-    | list[list[list[pgt.Scalar]]],
-]

phylogenie/utils.py

@@ -1,20 +0,0 @@
-from typing import overload
-
-import phylogenie.typeguards as tg
-import phylogenie.typings as pgt
-
-
-@overload
-def vectorify1D(x: pgt.OneOrMany[int]) -> pgt.IntVector1D: ...
-@overload
-def vectorify1D(x: pgt.OneOrManyScalars | None) -> pgt.Vector1D: ...
-def vectorify1D(x: pgt.OneOrManyScalars | None) -> pgt.Vector1D:
-    if x is None:
-        return ()
-    if isinstance(x, pgt.Scalar):
-        return (x,)
-    if tg.is_many_scalars(x):
-        return tuple(x)
-    raise TypeError(
-        f"It is impossible to coerce {x} of type {type(x)} into a 1D vector. Please provide a scalar or a sequence of scalars."
-    )

phylogenie-1.0.1.dist-info/RECORD

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