manual typing fixes on numpy 1.24 and python 3.10

pyproject.toml

@@ -85,6 +85,7 @@ cmd = """
 stubtest
     --mypy-config-file=pyproject.toml
     --allowlist=tests/stubtest/allowlist.txt
+    --ignore-unused-allowlist
     $modules
 """
 args = [{name = "modules", positional = true, multiple = true, default = "scipy"}]

scipy-stubs/_lib/_util.pyi

@@ -7,12 +7,6 @@ import numpy as np
 import numpy.typing as npt
 import optype.numpy as onpt
 from numpy._typing import _ArrayLikeInt
-from numpy.exceptions import (
-    AxisError as AxisError,
-    ComplexWarning as ComplexWarning,
-    DTypePromotionError as DTypePromotionError,
-    VisibleDeprecationWarning as VisibleDeprecationWarning,
-)
 from numpy.random import Generator as Generator  # noqa: ICN003
 from scipy._typing import RNG, EnterSelfMixin, Seed
 
@@ -23,13 +17,27 @@ _VT = TypeVar("_VT")
 _RT = TypeVar("_RT")
 _AxisT = TypeVar("_AxisT", bound=int | np.integer[Any])
 
+###
+
 np_long: Final[type[np.int32 | np.int64]] = ...
 np_ulong: Final[type[np.uint32 | np.uint64]] = ...
 copy_if_needed: Final[bool | None] = ...
 
 IntNumber: TypeAlias = int | np.integer[Any]
 DecimalNumber: TypeAlias = float | np.floating[Any] | np.integer[Any]
 
+class ComplexWarning(RuntimeWarning): ...
+class VisibleDeprecationWarning(UserWarning): ...
+class DTypePromotionError(TypeError): ...
+
+class AxisError(ValueError, IndexError):
+    axis: None | int
+    ndim: None | int
+    @overload
+    def __init__(self, /, axis: str, ndim: None = None, msg_prefix: None = None) -> None: ...
+    @overload
+    def __init__(self, /, axis: int, ndim: int, msg_prefix: str | None = None) -> None: ...
+
 class FullArgSpec(NamedTuple):
     args: Sequence[str]
     varargs: str | None

scipy-stubs/fftpack/helper.pyi

@@ -1,13 +1,20 @@
 # This module is not meant for public use and will be removed in SciPy v2.0.0.
+import sys
 from typing import Final
 from typing_extensions import deprecated
 
 __all__ = ["fftfreq", "fftshift", "ifftshift", "next_fast_len", "rfftfreq"]
 
 __MESSAGE: Final = "will be removed in SciPy v2.0.0"
 
-@deprecated(__MESSAGE)
-def fftfreq(n: object, d: object = ..., device: object = ...) -> object: ...
+if sys.version_info >= (3, 13):
+    # `device` was added in numpy 2
+    @deprecated(__MESSAGE)
+    def fftfreq(n: object, d: object = ..., device: object = ...) -> object: ...
+else:
+    @deprecated(__MESSAGE)
+    def fftfreq(n: object, d: object = ...) -> object: ...
+
 @deprecated(__MESSAGE)
 def fftshift(x: object, axes: object = ...) -> object: ...
 @deprecated(__MESSAGE)

scipy-stubs/integrate/_quad_vec.pyi

@@ -13,7 +13,7 @@ _S = TypeVar("_S")
 _T = TypeVar("_T")
 _VT = TypeVar("_VT", default=object)
 
-_FloatND: TypeAlias = np.ndarray[tuple[int, ...], np.dtype[np.floating[Any]]] | float | np.floating[Any]
+_FloatND: TypeAlias = np.ndarray[Any, np.dtype[np.floating[Any]]] | float | np.floating[Any]
 _NDT_f = TypeVar("_NDT_f", bound=_FloatND)
 _NDT_f_co = TypeVar("_NDT_f_co", bound=_FloatND, covariant=True, default=_FloatND)
 _SCT_f_co = TypeVar("_SCT_f_co", bound=np.floating[Any], covariant=True, default=np.float64)
@@ -147,7 +147,7 @@ def quad_vec(
 ) -> tuple[np.floating[_NBT], float, _Bunch[np.floating[_NBT]]]: ...
 @overload
 def quad_vec(
-    f: _QuadVecFunc[onpt.Array[_ShapeT, np.floating[_NBT]], Unpack[_Ts]],
+    f: _QuadVecFunc[np.ndarray[_ShapeT, np.dtype[np.floating[_NBT]]], Unpack[_Ts]],
     a: float,
     b: float,
     epsabs: float = 1e-200,

scipy-stubs/io/matlab/_mio5_params.pyi

@@ -53,7 +53,8 @@ __all__ = [
     "mxUINT64_CLASS",
 ]
 
-_ShapeT_co = TypeVar("_ShapeT_co", covariant=True, bound=tuple[int, ...], default=tuple[int, ...])
+# NOTE: explicit covariance can't be used, because shape types are invariant in `numpy<2.1`
+_ShapeT = TypeVar("_ShapeT", bound=tuple[int, ...], default=tuple[int, ...])
 
 @type_check_only
 class _CodecTemplateValue(TypedDict):
@@ -141,7 +142,7 @@ _MXName: TypeAlias = Literal[
 MDTYPES: Final[_MDTypes] = ...
 NP_TO_MTYPES: Final[_NP2M] = ...
 NP_TO_MXTYPES: Final[_NP2MX] = ...
-# TODO: use `np.dtypes.VoidDType[Literal[32]]` once we have `numpy >= 2.1.0`
+# TODO(jorenham): use `np.dtypes.VoidDType[Literal[32]]` once we have `numpy >= 2.1.0`
 OPAQUE_DTYPE: Final[np.dtype[np.void]] = ...
 
 codecs_template: Final[_CodecsTemplate] = ...
@@ -187,18 +188,18 @@ mxOBJECT_CLASS_FROM_MATRIX_H: Final[_MXType] = 18
 @final
 class mat_struct: ...
 
-class MatlabObject(np.ndarray[_ShapeT_co, np.dtype[np.void]], Generic[_ShapeT_co]):
+class MatlabObject(np.ndarray[_ShapeT, np.dtype[np.void]], Generic[_ShapeT]):
     classname: Final[str | None]
 
     def __new__(cls, input_array: onpt.AnyVoidArray, classname: str | None = None) -> Self: ...
     @override
     def __array_finalize__(self, /, obj: None | npt.NDArray[np.void]) -> None: ...
 
-class MatlabFunction(np.ndarray[_ShapeT_co, np.dtype[np.void]], Generic[_ShapeT_co]):
+class MatlabFunction(np.ndarray[_ShapeT, np.dtype[np.void]], Generic[_ShapeT]):
     @override
     def __new__(cls, input_array: onpt.AnyVoidArray) -> Self: ...
 
-class MatlabOpaque(np.ndarray[_ShapeT_co, np.dtype[np.void]], Generic[_ShapeT_co]):
+class MatlabOpaque(np.ndarray[_ShapeT, np.dtype[np.void]], Generic[_ShapeT]):
     @override
     def __new__(cls, input_array: onpt.AnyVoidArray) -> Self: ...
 

scipy-stubs/linalg/_special_matrices.pyi

@@ -1,7 +1,9 @@
 from typing import Literal, TypeAlias, overload
+from typing_extensions import TypeVar
 
 import numpy as np
 import numpy.typing as npt
+import optype.numpy as onpt
 import scipy._typing as spt
 
 __all__ = [
@@ -24,42 +26,43 @@ __all__ = [
     "toeplitz",
 ]
 
-_Array_2d: TypeAlias = np.ndarray[tuple[int, int], np.dtype[np.generic]]
-_Array_O_2d: TypeAlias = np.ndarray[tuple[int, int], np.dtypes.ObjectDType]
-_Array_u8_2d: TypeAlias = np.ndarray[tuple[int, int], np.dtypes.UInt64DType]
-_Array_i8_2d: TypeAlias = np.ndarray[tuple[int, int], np.dtypes.Int64DType]
-_Array_f8_2d: TypeAlias = np.ndarray[tuple[int, int], np.dtypes.Float64DType]
-_Array_c16_2d: TypeAlias = np.ndarray[tuple[int, int], np.dtypes.Complex128DType]
+_SCT = TypeVar("_SCT", bound=np.generic, default=np.generic)
 
-_SymmetryKind: TypeAlias = Literal["symmetric", "upper", "lower"]
+_Matrix: TypeAlias = onpt.Array[tuple[int, int], _SCT]
+_Kind: TypeAlias = Literal["symmetric", "upper", "lower"]
 
-def toeplitz(c: npt.ArrayLike, r: npt.ArrayLike | None = None) -> _Array_2d: ...
-def circulant(c: npt.ArrayLike) -> _Array_2d: ...
-def hankel(c: npt.ArrayLike, r: npt.ArrayLike | None = None) -> _Array_2d: ...
-def hadamard(n: spt.AnyInt, dtype: npt.DTypeLike = ...) -> _Array_2d: ...
-def leslie(f: npt.ArrayLike, s: npt.ArrayLike) -> _Array_2d: ...
-def kron(a: npt.ArrayLike, b: npt.ArrayLike) -> _Array_2d: ...
-def block_diag(*arrs: npt.ArrayLike) -> _Array_2d: ...
-def companion(a: npt.ArrayLike) -> _Array_2d: ...
-def helmert(n: spt.AnyInt, full: bool = False) -> _Array_f8_2d: ...
-def hilbert(n: spt.AnyInt) -> _Array_f8_2d: ...
+###
+
+# TODO(jorenham): transparent dtypes
+def toeplitz(c: npt.ArrayLike, r: npt.ArrayLike | None = None) -> _Matrix: ...
+def circulant(c: npt.ArrayLike) -> _Matrix: ...
+def hankel(c: npt.ArrayLike, r: npt.ArrayLike | None = None) -> _Matrix: ...
+def hadamard(n: spt.AnyInt, dtype: npt.DTypeLike = ...) -> _Matrix: ...
+def leslie(f: npt.ArrayLike, s: npt.ArrayLike) -> _Matrix: ...
+def kron(a: npt.ArrayLike, b: npt.ArrayLike) -> _Matrix: ...
+def block_diag(*arrs: npt.ArrayLike) -> _Matrix: ...
+def companion(a: npt.ArrayLike) -> _Matrix: ...
+def helmert(n: spt.AnyInt, full: bool = False) -> _Matrix[np.float64]: ...
+def hilbert(n: spt.AnyInt) -> _Matrix[np.float64]: ...
+def fiedler(a: npt.ArrayLike) -> _Matrix: ...
+def fiedler_companion(a: npt.ArrayLike) -> _Matrix: ...
+def convolution_matrix(a: npt.ArrayLike, n: spt.AnyInt, mode: spt.CorrelateMode = "full") -> _Matrix: ...
+
+#
 @overload
-def invhilbert(n: spt.AnyInt, exact: Literal[False] = False) -> _Array_f8_2d: ...
+def invhilbert(n: spt.AnyInt, exact: Literal[False] = False) -> _Matrix[np.float64]: ...
 @overload
-def invhilbert(n: spt.AnyInt, exact: Literal[True]) -> _Array_i8_2d | _Array_O_2d: ...
+def invhilbert(n: spt.AnyInt, exact: Literal[True]) -> _Matrix[np.int64] | _Matrix[np.object_]: ...
 @overload
-def pascal(n: spt.AnyInt, kind: _SymmetryKind = "symmetric", exact: Literal[True] = True) -> _Array_u8_2d | _Array_O_2d: ...
+def pascal(n: spt.AnyInt, kind: _Kind = "symmetric", exact: Literal[True] = True) -> _Matrix[np.uint64 | np.object_]: ...
 @overload
-def pascal(n: spt.AnyInt, kind: _SymmetryKind = "symmetric", *, exact: Literal[False]) -> _Array_f8_2d: ...
+def pascal(n: spt.AnyInt, kind: _Kind = "symmetric", *, exact: Literal[False]) -> _Matrix[np.float64]: ...
 @overload
-def pascal(n: spt.AnyInt, kind: _SymmetryKind, exact: Literal[False]) -> _Array_f8_2d: ...
+def pascal(n: spt.AnyInt, kind: _Kind, exact: Literal[False]) -> _Matrix[np.float64]: ...
 @overload
-def invpascal(n: spt.AnyInt, kind: _SymmetryKind = "symmetric", exact: Literal[True] = True) -> _Array_i8_2d | _Array_O_2d: ...
+def invpascal(n: spt.AnyInt, kind: _Kind = "symmetric", exact: Literal[True] = True) -> _Matrix[np.int64 | np.object_]: ...
 @overload
-def invpascal(n: spt.AnyInt, kind: _SymmetryKind = "symmetric", *, exact: Literal[False]) -> _Array_f8_2d: ...
+def invpascal(n: spt.AnyInt, kind: _Kind = "symmetric", *, exact: Literal[False]) -> _Matrix[np.float64]: ...
 @overload
-def invpascal(n: spt.AnyInt, kind: _SymmetryKind, exact: Literal[False]) -> _Array_f8_2d: ...
-def dft(n: spt.AnyInt, scale: Literal["sqrtn", "n"] | None = None) -> _Array_c16_2d: ...
-def fiedler(a: npt.ArrayLike) -> _Array_2d: ...
-def fiedler_companion(a: npt.ArrayLike) -> _Array_2d: ...
-def convolution_matrix(a: npt.ArrayLike, n: spt.AnyInt, mode: spt.CorrelateMode = "full") -> _Array_2d: ...
+def invpascal(n: spt.AnyInt, kind: _Kind, exact: Literal[False]) -> _Matrix[np.float64]: ...
+def dft(n: spt.AnyInt, scale: Literal["sqrtn", "n"] | None = None) -> _Matrix[np.complex128]: ...

scipy-stubs/linalg/blas.pyi

@@ -7,19 +7,19 @@ import scipy._typing as spt
 
 __all__ = ["find_best_blas_type", "get_blas_funcs"]
 
+# see `scipy.linalg.blas._type_conv`
 def find_best_blas_type(
     arrays: Sequence[npt.NDArray[np.generic]] = (),
     dtype: npt.DTypeLike | None = None,
 ) -> (
-    # see `scipy.linalg.blas._type_conv`
-    tuple[Literal["s"], np.dtypes.Float32DType, bool]
-    | tuple[Literal["f"], np.dtypes.Float64DType, bool]
-    | tuple[Literal["c"], np.dtypes.Complex64DType, bool]
-    | tuple[Literal["z"], np.dtypes.Complex128DType, bool]
+    tuple[Literal["s"], np.dtype[np.float32], bool]
+    | tuple[Literal["f"], np.dtype[np.float64], bool]
+    | tuple[Literal["c"], np.dtype[np.complex64], bool]
+    | tuple[Literal["z"], np.dtype[np.complex128], bool]
 ): ...
 def get_blas_funcs(
     names: Iterable[str] | str,
     arrays: Sequence[npt.NDArray[np.generic]] = (),
     dtype: npt.DTypeLike | None = None,
-    ilp64: Literal[True, False, "preferred"] = False,
+    ilp64: Literal[False, True, "preferred"] = False,
 ) -> list[spt._FortranFunction] | spt._FortranFunction: ...

scipy-stubs/signal/_bsplines.pyi

@@ -8,15 +8,15 @@ from scipy._typing import AnyInt, AnyReal
 
 __all__ = ["cspline1d", "cspline1d_eval", "gauss_spline", "qspline1d", "qspline1d_eval", "spline_filter"]
 
-_SCT_fc = TypeVar("_SCT_fc", np.float64, np.float32, np.complex128, np.complex64)
+_SCT_fc = TypeVar("_SCT_fc", bound=np.inexact[Any])
 
 @overload
 def gauss_spline(x: _ArrayLikeInt_co, n: AnyInt) -> npt.NDArray[np.float64]: ...
 @overload
-def gauss_spline(x: _ArrayLike[_SCT_fc], n: AnyInt) -> npt.NDArray[_SCT_fc]: ...
-@overload
 def gauss_spline(x: _ArrayLikeFloat_co, n: AnyInt) -> npt.NDArray[np.floating[Any]]: ...
 @overload
+def gauss_spline(x: _ArrayLike[_SCT_fc], n: AnyInt) -> npt.NDArray[_SCT_fc]: ...
+@overload
 def gauss_spline(x: _ArrayLikeComplex_co, n: AnyInt) -> npt.NDArray[np.inexact[Any]]: ...
 def spline_filter(Iin: _ArrayLike[_SCT_fc], lmbda: AnyReal = 5.0) -> npt.NDArray[_SCT_fc]: ...
 def cspline1d(signal: npt.NDArray[_SCT_fc], lamb: AnyReal = 0.0) -> npt.NDArray[_SCT_fc]: ...

scipy-stubs/sparse/bsr.pyi

@@ -1,4 +1,5 @@
 # This module is not meant for public use and will be removed in SciPy v2.0.0.
+import sys
 from typing_extensions import deprecated
 
 __all__ = [
@@ -57,15 +58,20 @@ def bsr_transpose(*args: object, **kwargs: object) -> object: ...
 def csr_matmat_maxnnz(*args: object, **kwargs: object) -> object: ...
 @deprecated("will be removed in SciPy v2.0.0")
 def isspmatrix_bsr(x: object) -> object: ...
-@deprecated("will be removed in SciPy v2.0.0")
-def warn(
-    message: object,
-    category: object = ...,
-    stacklevel: object = ...,
-    source: object = ...,
-    *,
-    skip_file_prefixes: object = ...,
-) -> None: ...
+
+if sys.version_info >= (3, 12):
+    @deprecated("will be removed in SciPy v2.0.0")
+    def warn(
+        message: object,
+        category: object = ...,
+        stacklevel: object = ...,
+        source: object = ...,
+        *,
+        skip_file_prefixes: object = ...,
+    ) -> None: ...
+else:
+    @deprecated("will be removed in SciPy v2.0.0")
+    def warn(message: object, category: object = ..., stacklevel: object = ..., source: object = ...) -> None: ...
 
 # sputils
 @deprecated("will be removed in SciPy v2.0.0")

scipy-stubs/sparse/compressed.pyi

@@ -1,5 +1,6 @@
 # This module is not meant for public use and will be removed in SciPy v2.0.0.
 import operator
+import sys
 from typing_extensions import deprecated
 
 __all__ = [
@@ -37,15 +38,20 @@ class IndexMixin:
     def __getitem__(self, key: object, /) -> object: ...
     def __setitem__(self, key: object, x: object, /) -> None: ...
 
-@deprecated("will be removed in SciPy v2.0.0")
-def warn(
-    message: object,
-    category: object = ...,
-    stacklevel: object = ...,
-    source: object = ...,
-    *,
-    skip_file_prefixes: object = ...,
-) -> None: ...
+if sys.version_info >= (3, 12):
+    @deprecated("will be removed in SciPy v2.0.0")
+    def warn(
+        message: object,
+        category: object = ...,
+        stacklevel: object = ...,
+        source: object = ...,
+        *,
+        skip_file_prefixes: object = ...,
+    ) -> None: ...
+else:
+    @deprecated("will be removed in SciPy v2.0.0")
+    def warn(message: object, category: object = ..., stacklevel: object = ..., source: object = ...) -> None: ...
+
 @deprecated("will be removed in SciPy v2.0.0")
 def csr_column_index1(*args: object, **kwargs: object) -> object: ...
 @deprecated("will be removed in SciPy v2.0.0")

scipy-stubs/sparse/coo.pyi

@@ -1,5 +1,6 @@
 # This module is not meant for public use and will be removed in SciPy v2.0.0.
 import operator
+import sys
 from typing import type_check_only
 from typing_extensions import deprecated
 
@@ -55,15 +56,20 @@ def coo_matvec(*args: object, **kwargs: object) -> object: ...
 def coo_tocsr(*args: object, **kwargs: object) -> object: ...
 @deprecated("will be removed in SciPy v2.0.0")
 def coo_todense(*args: object, **kwargs: object) -> object: ...
-@deprecated("will be removed in SciPy v2.0.0")
-def warn(
-    message: object,
-    category: object = ...,
-    stacklevel: object = ...,
-    source: object = ...,
-    *,
-    skip_file_prefixes: object = ...,
-) -> None: ...
+
+if sys.version_info >= (3, 12):
+    @deprecated("will be removed in SciPy v2.0.0")
+    def warn(
+        message: object,
+        category: object = ...,
+        stacklevel: object = ...,
+        source: object = ...,
+        *,
+        skip_file_prefixes: object = ...,
+    ) -> None: ...
+else:
+    @deprecated("will be removed in SciPy v2.0.0")
+    def warn(message: object, category: object = ..., stacklevel: object = ..., source: object = ...) -> None: ...
 
 # sputils
 @type_check_only