Merge pull request #185 from jorenham/optype-0.7

optype 0.7

Author: jorenham

poetry.lock

@@ -13,10 +13,6 @@ packages = [{include = "scipy-stubs"}]
 classifiers = [
     "Development Status :: 4 - Beta",
     "Operating System :: OS Independent",
-    "Programming Language :: Python :: 3.10",
-    "Programming Language :: Python :: 3.11",
-    "Programming Language :: Python :: 3.12",
-    "Programming Language :: Python :: 3.13",
     "Typing :: Stubs Only",
     "Typing :: Typed",
 ]
@@ -32,8 +28,8 @@ Funding = "https://github.com/sponsors/jorenham"
 scipy = ["scipy"]
 
 [tool.poetry.dependencies]
-python = "^3.10.1"
-optype = "^0.6.1"
+python = "^3.10"
+optype = "^0.7.1"
 scipy = {version = ">=1.10", optional = true}
 
 [tool.poetry.group.dev.dependencies]

pyproject.toml

@@ -4,25 +4,25 @@ from typing_extensions import TypeVar
 
 import numpy as np
 import numpy.typing as npt
-from scipy._typing import AnyInt, AnyReal
+import optype.numpy as onp
 
 _T = TypeVar("_T", bound=np.floating[Any] | npt.NDArray[np.floating[Any]])
 
 @overload
 def _derivative(
-    func: Callable[Concatenate[float, ...], AnyReal],
+    func: Callable[Concatenate[float, ...], onp.ToFloat],
     x0: float,
-    dx: AnyReal = 1.0,
-    n: AnyInt = 1,
+    dx: onp.ToFloat = 1.0,
+    n: onp.ToInt = 1,
     args: tuple[object, ...] = (),
-    order: AnyInt = 3,
+    order: onp.ToInt = 3,
 ) -> np.float64: ...
 @overload
 def _derivative(
-    func: Callable[Concatenate[_T, ...], AnyReal],
+    func: Callable[Concatenate[_T, ...], onp.ToFloat],
     x0: _T,
-    dx: AnyReal = 1.0,
-    n: AnyInt = 1,
+    dx: onp.ToFloat = 1.0,
+    n: onp.ToInt = 1,
     args: tuple[object, ...] = (),
-    order: AnyInt = 3,
+    order: onp.ToInt = 3,
 ) -> _T: ...

scipy-stubs/_lib/_finite_differences.pyi

@@ -14,13 +14,7 @@ __all__ = [
     "RNG",
     "Alternative",
     "AnyBool",
-    "AnyChar",
-    "AnyComplex",
-    "AnyInt",
-    "AnyReal",
-    "AnyScalar",
     "AnyShape",
-    "Array0D",
     "ByteOrder",
     "Casting",
     "CorrelateMode",
@@ -68,16 +62,8 @@ FileLike: TypeAlias = IO[_ByteSOrStr] | FileName
 FileModeRW: TypeAlias = Literal["r", "w"]
 FileModeRWA: TypeAlias = Literal[FileModeRW, "a"]
 
-_SCT = TypeVar("_SCT", bound=np.generic, default=np.generic)
-Array0D: TypeAlias = np.ndarray[tuple[()], np.dtype[_SCT]]
-
 # keep in sync with `numpy._typing._scalars`
 AnyBool: TypeAlias = bool | np.bool_ | Literal[0, 1]
-AnyInt: TypeAlias = int | np.integer[Any] | np.bool_
-AnyReal: TypeAlias = int | float | np.floating[Any] | np.integer[Any] | np.bool_
-AnyComplex: TypeAlias = int | float | complex | np.number[Any] | np.bool_
-AnyChar: TypeAlias = str | bytes  # `np.str_ <: builtins.str` and `np.bytes_ <: builtins.bytes`
-AnyScalar: TypeAlias = int | float | complex | AnyChar | np.generic
 
 # equivalent to `numpy._typing._shape._ShapeLike`
 AnyShape: TypeAlias = op.CanIndex | Sequence[op.CanIndex]

scipy-stubs/_typing.pyi

@@ -1,10 +1,9 @@
-from collections.abc import Callable, Sequence
+from collections.abc import Callable
 from types import ModuleType
 from typing import Any, Literal, TypeAlias, TypedDict, overload
 from typing_extensions import TypeVar, override
 
 import numpy as np
-import numpy.typing as npt
 import optype.numpy as onp
 from scipy._lib._disjoint_set import DisjointSet
 from scipy.spatial.distance import _MetricCallback, _MetricKind
@@ -47,7 +46,7 @@ __all__ = [
 _T = TypeVar("_T")
 _SCT = TypeVar("_SCT", bound=np.number[Any], default=np.float64)
 _LinkageMethod: TypeAlias = Literal["single", "complete", "average", "weighted", "centroid", "median", "ward"]
-_LinkageArray: TypeAlias = onp.Array[tuple[int, int], _SCT]
+_LinkageArray: TypeAlias = onp.Array2D[_SCT]
 _ClusterCriterion: TypeAlias = Literal["inconsistent", "distance", "maxclust", "monocrit", "maxclust_monocrit"]
 _SortOrder: TypeAlias = Literal["ascending", "descending"]
 
@@ -64,16 +63,16 @@ class _DendrogramResult(TypedDict):
 
 class ClusterWarning(UserWarning): ...
 
-def int_floor(arr: onp.AnyArray, xp: ModuleType) -> int: ...
-def single(y: onp.AnyArray) -> _LinkageArray: ...
-def complete(y: onp.AnyArray) -> _LinkageArray: ...
-def average(y: onp.AnyArray) -> _LinkageArray: ...
-def weighted(y: onp.AnyArray) -> _LinkageArray: ...
-def centroid(y: onp.AnyArray) -> _LinkageArray: ...
-def median(y: onp.AnyArray) -> _LinkageArray: ...
-def ward(y: onp.AnyArray) -> _LinkageArray: ...
+def int_floor(arr: onp.ToArrayND, xp: ModuleType) -> int: ...
+def single(y: onp.ToArrayND) -> _LinkageArray: ...
+def complete(y: onp.ToArrayND) -> _LinkageArray: ...
+def average(y: onp.ToArrayND) -> _LinkageArray: ...
+def weighted(y: onp.ToArrayND) -> _LinkageArray: ...
+def centroid(y: onp.ToArrayND) -> _LinkageArray: ...
+def median(y: onp.ToArrayND) -> _LinkageArray: ...
+def ward(y: onp.ToArrayND) -> _LinkageArray: ...
 def linkage(
-    y: onp.AnyArray,
+    y: onp.ToArrayND,
     method: _LinkageMethod = "single",
     metric: _MetricKind | _MetricCallback = "euclidean",
     optimal_ordering: bool = False,
@@ -109,61 +108,58 @@ class ClusterNode:
     def pre_order(self, /, func: Callable[[ClusterNode], _T]) -> list[_T]: ...
 
 def cut_tree(
-    Z: onp.AnyArray,
-    n_clusters: Sequence[int] | npt.NDArray[np.integer[Any]] | None = None,
-    height: Sequence[float] | npt.NDArray[np.integer[Any] | np.floating[Any]] | None = None,
-) -> onp.Array[tuple[int, int], np.int64]: ...
+    Z: onp.ToArray2D,
+    n_clusters: onp.ToInt1D | None = None,
+    height: onp.ToFloat1D | None = None,
+) -> onp.Array2D[np.int64]: ...
 @overload
-def to_tree(Z: onp.AnyArray, rd: Literal[False] = False) -> ClusterNode: ...
+def to_tree(Z: onp.ToArray2D, rd: Literal[False] = False) -> ClusterNode: ...
 @overload
-def to_tree(Z: onp.AnyArray, rd: Literal[True]) -> tuple[ClusterNode, list[ClusterNode]]: ...
+def to_tree(Z: onp.ToArray2D, rd: Literal[True]) -> tuple[ClusterNode, list[ClusterNode]]: ...
 def optimal_leaf_ordering(
-    Z: onp.AnyArray,
-    y: onp.AnyArray,
+    Z: onp.ToArray2D,
+    y: onp.ToArrayND,
     metric: _MetricKind | _MetricCallback = "euclidean",
 ) -> _LinkageArray: ...
 @overload
-def cophenet(Z: onp.AnyArray, Y: None = None) -> onp.Array[tuple[int], np.float64]: ...
+def cophenet(Z: onp.ToArray2D, Y: None = None) -> onp.Array1D[np.float64]: ...
 @overload
-def cophenet(
-    Z: onp.AnyArray,
-    Y: onp.AnyArray,
-) -> tuple[onp.Array[tuple[int], np.float64], onp.Array[tuple[int], np.float64]]: ...
-def inconsistent(Z: onp.AnyArray, d: int = 2) -> _LinkageArray: ...
-def from_mlab_linkage(Z: onp.AnyArray) -> _LinkageArray: ...
-def to_mlab_linkage(Z: onp.AnyArray) -> _LinkageArray: ...
-def is_monotonic(Z: onp.AnyArray) -> bool: ...
-def is_valid_im(R: onp.AnyArray, warning: bool = False, throw: bool = False, name: str | None = None) -> bool: ...
-def is_valid_linkage(Z: onp.AnyArray, warning: bool = False, throw: bool = False, name: str | None = None) -> bool: ...
-def num_obs_linkage(Z: onp.AnyArray) -> int: ...
-def correspond(Z: onp.AnyArray, Y: onp.AnyArray) -> bool: ...
+def cophenet(Z: onp.ToArray2D, Y: onp.ToArrayND) -> tuple[onp.Array1D[np.float64], onp.Array1D[np.float64]]: ...
+def inconsistent(Z: onp.ToArray2D, d: int = 2) -> _LinkageArray: ...
+def from_mlab_linkage(Z: onp.ToArray2D) -> _LinkageArray: ...
+def to_mlab_linkage(Z: onp.ToArray2D) -> _LinkageArray: ...
+def is_monotonic(Z: onp.ToArray2D) -> bool: ...
+def is_valid_im(R: onp.ToArrayND, warning: bool = False, throw: bool = False, name: str | None = None) -> bool: ...
+def is_valid_linkage(Z: onp.ToArray2D, warning: bool = False, throw: bool = False, name: str | None = None) -> bool: ...
+def num_obs_linkage(Z: onp.ToArray2D) -> int: ...
+def correspond(Z: onp.ToArray2D, Y: onp.ToArrayND) -> bool: ...
 def fcluster(
-    Z: onp.AnyArray,
+    Z: onp.ToArray2D,
     t: float | np.floating[Any] | np.integer[Any],
     criterion: _ClusterCriterion = "inconsistent",
     depth: int = 2,
-    R: onp.AnyArray | None = None,
-    monocrit: onp.AnyArray | None = None,
-) -> onp.Array[tuple[int], np.int32]: ...
+    R: onp.ToArrayND | None = None,
+    monocrit: onp.ToArrayND | None = None,
+) -> onp.Array1D[np.int32]: ...
 def fclusterdata(
-    X: onp.AnyArray,
+    X: onp.ToArrayND,
     t: float | np.floating[Any] | np.integer[Any],
     criterion: _ClusterCriterion = "inconsistent",
     metric: _MetricKind | _MetricCallback = "euclidean",
     depth: int = 2,
     method: _LinkageMethod = "single",
-    R: onp.AnyArray | None = None,
-) -> onp.Array[tuple[int], np.int32]: ...
-def leaves_list(Z: onp.AnyArray) -> onp.Array[tuple[int], np.int32]: ...
+    R: onp.ToArrayND | None = None,
+) -> onp.Array1D[np.int32]: ...
+def leaves_list(Z: onp.ToArray2D) -> onp.Array1D[np.int32]: ...
 def set_link_color_palette(palette: list[str] | tuple[str, ...] | None) -> None: ...
 def dendrogram(
-    Z: onp.AnyArray,
+    Z: onp.ToArray2D,
     p: int = 30,
     truncate_mode: Literal["lastp", "level"] | None = None,
     color_threshold: float | np.floating[Any] | None = None,
     get_leaves: bool = True,
     orientation: Literal["top", "bottom", "left", "right"] = "top",
-    labels: onp.AnyArray | None = None,
+    labels: onp.ToArrayND | None = None,
     count_sort: _SortOrder | bool = False,
     distance_sort: _SortOrder | bool = False,
     show_leaf_counts: bool = True,
@@ -177,8 +173,8 @@ def dendrogram(
     ax: _MatplotlibAxes | None = None,
     above_threshold_color: str = "C0",
 ) -> _DendrogramResult: ...
-def is_isomorphic(T1: onp.AnyArray, T2: onp.AnyArray) -> bool: ...
-def maxdists(Z: onp.AnyArray) -> onp.Array[tuple[int], np.float64]: ...
-def maxinconsts(Z: onp.AnyArray, R: onp.AnyArray) -> onp.Array[tuple[int], np.float64]: ...
-def maxRstat(Z: onp.AnyArray, R: onp.AnyArray, i: int) -> onp.Array[tuple[int], np.float64]: ...
-def leaders(Z: onp.AnyArray, T: onp.AnyArray) -> tuple[onp.Array[tuple[int], np.int32], onp.Array[tuple[int], np.int32]]: ...
+def is_isomorphic(T1: onp.ToArrayND, T2: onp.ToArrayND) -> bool: ...
+def maxdists(Z: onp.ToArray2D) -> onp.Array1D[np.float64]: ...
+def maxinconsts(Z: onp.ToArray2D, R: onp.ToArrayND) -> onp.Array1D[np.float64]: ...
+def maxRstat(Z: onp.ToArray2D, R: onp.ToArrayND, i: int) -> onp.Array1D[np.float64]: ...
+def leaders(Z: onp.ToArray2D, T: onp.ToArrayND) -> tuple[onp.Array1D[np.int32], onp.Array1D[np.int32]]: ...

scipy-stubs/cluster/hierarchy.pyi

@@ -1,50 +1,54 @@
-from collections.abc import Sequence
-from typing import Any, Literal, TypeAlias, overload
+from typing import Any, Literal, overload
 from typing_extensions import TypeVar
 
 import numpy as np
 import numpy.typing as npt
 import optype.numpy as onp
+from scipy._typing import Seed
 
 __all__ = ["kmeans", "kmeans2", "vq", "whiten"]
 
 _SCT_fc = TypeVar("_SCT_fc", bound=np.inexact[Any])
-_ArrayLike_1d_fc: TypeAlias = onp.AnyNumberArray | Sequence[complex | np.number[Any]]
-_ArrayLike_2d_fc: TypeAlias = onp.AnyNumberArray | Sequence[Sequence[complex | np.number[Any]]]
+
+###
 
 class ClusterError(Exception): ...
 
 @overload
-def whiten(obs: npt.NDArray[_SCT_fc], check_finite: bool = True) -> onp.Array[tuple[int, int], _SCT_fc]: ...
+def whiten(obs: npt.NDArray[_SCT_fc], check_finite: bool = True) -> onp.Array2D[_SCT_fc]: ...
 @overload
-def whiten(obs: _ArrayLike_2d_fc, check_finite: bool = True) -> onp.Array[tuple[int, int], np.inexact[Any]]: ...
+def whiten(obs: onp.ToComplex2D, check_finite: bool = True) -> onp.Array2D[np.inexact[Any]]: ...
+
+#
 def vq(
-    obs: _ArrayLike_2d_fc,
-    code_book: _ArrayLike_2d_fc,
+    obs: onp.ToComplex2D,
+    code_book: onp.ToComplex2D,
     check_finite: bool = True,
-) -> tuple[onp.Array[tuple[int], np.int32 | np.intp], onp.Array[tuple[int], _SCT_fc]]: ...
+) -> tuple[onp.Array1D[np.int32 | np.intp], onp.Array1D[_SCT_fc]]: ...
 def py_vq(
-    obs: _ArrayLike_2d_fc,
-    code_book: _ArrayLike_2d_fc,
+    obs: onp.ToComplex2D,
+    code_book: onp.ToComplex2D,
     check_finite: bool = True,
-) -> tuple[onp.Array[tuple[int], np.intp], onp.Array[tuple[int], _SCT_fc]]: ...
+) -> tuple[onp.Array1D[np.intp], onp.Array1D[_SCT_fc]]: ...
+
+#
 def kmeans(
-    obs: _ArrayLike_2d_fc,
+    obs: onp.ToComplex2D,
     k_or_guess: npt.ArrayLike,
     iter: int = 20,
     thresh: float = 1e-05,
     check_finite: bool = True,
     *,
-    seed: int | np.random.Generator | np.random.RandomState | None = None,
-) -> tuple[onp.Array[tuple[int, int], np.inexact[Any]], float]: ...
+    seed: Seed | None = None,
+) -> tuple[onp.Array2D[np.inexact[Any]], float]: ...
 def kmeans2(
-    data: _ArrayLike_1d_fc | _ArrayLike_2d_fc,
+    data: onp.ToComplex1D | onp.ToComplex2D,
     k: npt.ArrayLike,
     iter: int = 10,
     thresh: float = 1e-05,
     minit: Literal["random", "points", "++", "matrix"] = "random",
     missing: Literal["warn", "raise"] = "warn",
     check_finite: bool = True,
     *,
-    seed: int | np.random.Generator | np.random.RandomState | None = None,
-) -> tuple[onp.Array[tuple[int, int], np.inexact[Any]], onp.Array[tuple[int], np.int32]]: ...
+    seed: Seed | None = None,
+) -> tuple[onp.Array2D[np.inexact[Any]], onp.Array1D[np.int32]]: ...