🐛 fix typing errors on numpy<1.24 (#292)

.mypyignore

@@ -30,6 +30,10 @@ scipy\.(_lib|integrate|stats)\.((_|\w)+\.)+__replace__  # `NamedTuple` on `pytho
 scipy\.fftpack\.helper\.fftfreq
 scipy\.sparse\.(\w+)\.warn
 
+# numpy re-export with wrong annotations on numpy<1.24
+scipy.fftpack.fftfreq
+scipy.fftpack._helper.fftfreq
+
 # mypy fails recognize type-check-only ufunc subtypes as ufuncs
 # https://github.com/KotlinIsland/basedmypy/issues/816
 scipy\.special\._basic\.digamma

.pre-commit-config.yaml

@@ -7,7 +7,6 @@ ci:
     - typos
     - ruff
     - ruff-format
-    - typetest
     - basedmypy
     - basedpyright
 
@@ -74,21 +73,14 @@ repos:
 
   - repo: local
     hooks:
-      - id: typetest
-        name: typetest
-        entry: uv run poe typetest
+      - id: basedpyright
+        name: basedpyright
+        entry: uv run --no-sync basedpyright
         language: system
-        always_run: true
-        pass_filenames: false
+        types_or: [python, pyi]
 
       - id: basedmypy
         name: basedmypy
         entry: uv run poe mypy
         language: system
         types_or: [python, pyi]
-
-      - id: basedpyright
-        name: basedpyright
-        entry: uv run poe pyright
-        language: system
-        types_or: [python, pyi]

.vscode/settings.json

@@ -23,5 +23,5 @@
     "--config-file=${workspaceFolder}/pyproject.toml"
   ],
   "mypy-type-checker.cwd": "${fileDirname}",
-  "mypy-type-checker.path": ["uv", "run", "--no-editable", "mypy"]
+  "mypy-type-checker.path": ["uv", "run", "--no-sync", "mypy"]
 }

scipy-stubs/_lib/_array_api.pyi

@@ -3,7 +3,6 @@ from typing import Any, Literal, Protocol, TypeAlias, overload, type_check_only
 from typing_extensions import TypeVar
 
 import numpy as np
-import numpy.typing as npt
 import optype.numpy as onp
 from scipy._typing import AnyBool, OrderKACF
 
@@ -55,7 +54,7 @@ class _HasArrayAttrs(_HasShape[_ShapeT_co], _HasDevice[_DeviceT_co], Protocol[_S
 ###
 
 Array: TypeAlias = _HasArrayAttrs[_ShapeT_co, _DTypeT_co, _DeviceT_co]
-ArrayLike: TypeAlias = Array | npt.ArrayLike
+ArrayLike: TypeAlias = Array | onp.ToFloatND
 
 def _asarray(
     array: ArrayLike,

scipy-stubs/cluster/vq.pyi

@@ -2,7 +2,6 @@ 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
 
@@ -27,25 +26,53 @@ def vq(
     code_book: onp.ToComplex2D,
     check_finite: bool = True,
 ) -> tuple[onp.Array1D[np.int32 | np.intp], onp.Array1D[_SCT_fc]]: ...
+
+#
 def py_vq(
     obs: onp.ToComplex2D,
     code_book: onp.ToComplex2D,
     check_finite: bool = True,
 ) -> tuple[onp.Array1D[np.intp], onp.Array1D[_SCT_fc]]: ...
 
 #
+@overload  # real
+def kmeans(
+    obs: onp.ToFloat2D,
+    k_or_guess: onp.ToJustInt | onp.ToFloatND,
+    iter: int = 20,
+    thresh: float = 1e-05,
+    check_finite: bool = True,
+    *,
+    seed: Seed | None = None,
+) -> tuple[onp.Array2D[np.floating[Any]], float]: ...
+@overload  # complex
 def kmeans(
     obs: onp.ToComplex2D,
-    k_or_guess: npt.ArrayLike,
+    k_or_guess: onp.ToJustInt | onp.ToFloatND,
     iter: int = 20,
     thresh: float = 1e-05,
     check_finite: bool = True,
     *,
     seed: Seed | None = None,
 ) -> tuple[onp.Array2D[np.inexact[Any]], float]: ...
+
+#
+@overload  # real
+def kmeans2(
+    data: onp.ToFloat1D | onp.ToFloat2D,
+    k: onp.ToJustInt | onp.ToFloatND,
+    iter: int = 10,
+    thresh: float = 1e-05,
+    minit: Literal["random", "points", "++", "matrix"] = "random",
+    missing: Literal["warn", "raise"] = "warn",
+    check_finite: bool = True,
+    *,
+    seed: Seed | None = None,
+) -> tuple[onp.Array2D[np.floating[Any]], onp.Array1D[np.int32]]: ...
+@overload  # complex
 def kmeans2(
     data: onp.ToComplex1D | onp.ToComplex2D,
-    k: npt.ArrayLike,
+    k: onp.ToJustInt | onp.ToFloatND,
     iter: int = 10,
     thresh: float = 1e-05,
     minit: Literal["random", "points", "++", "matrix"] = "random",

scipy-stubs/fftpack/_helper.pyi

@@ -1,3 +1,6 @@
+# NOTE: this ignore is required for `numpy==1.23.5` compat
+# pyright: reportUnknownVariableType=false
+
 import numpy as np
 import optype.numpy as onp
 from numpy.fft import fftfreq, fftshift, ifftshift

scipy-stubs/interpolate/_pade.pyi

@@ -1,6 +1,6 @@
 import numpy as np
-import numpy.typing as npt
+import optype.numpy as onp
 
 __all__ = ["pade"]
 
-def pade(an: npt.ArrayLike, m: int, n: int | None = None) -> tuple[np.poly1d, np.poly1d]: ...
+def pade(an: onp.ToComplex1D, m: onp.ToJustInt, n: onp.ToJustInt | None = None) -> tuple[np.poly1d, np.poly1d]: ...

scipy-stubs/io/_fortran.pyi

@@ -8,9 +8,9 @@ from scipy._typing import EnterSelfMixin, FileLike, FileModeRW
 
 __all__ = ["FortranEOFError", "FortranFile", "FortranFormattingError"]
 
-@type_check_only
 @final
-class _DTypeKwargs(TypedDict):
+@type_check_only
+class _DTypeKwargs(TypedDict, total=False):
     dtype: npt.DTypeLike
 
 class FortranEOFError(TypeError, OSError): ...
@@ -19,7 +19,7 @@ class FortranFormattingError(TypeError, OSError): ...
 class FortranFile(EnterSelfMixin):
     def __init__(self, /, filename: FileLike[bytes], mode: FileModeRW = "r", header_dtype: npt.DTypeLike = ...) -> None: ...
     def close(self, /) -> None: ...
-    def write_record(self, /, *items: npt.ArrayLike) -> None: ...
+    def write_record(self, /, *items: onp.ToArrayND) -> None: ...
     @overload
     def read_record(self, /, *dtypes: npt.DTypeLike) -> onp.Array1D[np.void]: ...
     @overload

scipy-stubs/io/_mmio.pyi

@@ -2,7 +2,6 @@ from typing import Any, ClassVar, Literal, TypeAlias, TypedDict, type_check_only
 from typing_extensions import Unpack
 
 import numpy as np
-import numpy.typing as npt
 import optype.numpy as onp
 from scipy._typing import FileLike
 from scipy.sparse import coo_matrix, sparray, spmatrix
@@ -28,7 +27,7 @@ def mminfo(source: FileLike[bytes]) -> _Info: ...
 def mmread(source: FileLike[bytes]) -> onp.ArrayND[np.number[Any]] | coo_matrix: ...
 def mmwrite(
     target: FileLike[bytes],
-    a: spmatrix | sparray | npt.ArrayLike,
+    a: spmatrix | sparray | onp.ToArrayND,
     comment: str = "",
     field: _Field | None = None,
     precision: int | None = None,
@@ -75,7 +74,7 @@ class MMFile:
         self,
         /,
         target: FileLike[bytes],
-        a: spmatrix | sparray | npt.ArrayLike,
+        a: spmatrix | sparray | onp.ToArrayND,
         comment: str = "",
         field: _Field | None = None,
         precision: int | None = None,

scipy-stubs/io/matlab/_mio4.pyi

@@ -3,7 +3,6 @@ from typing import IO, Any, Final, Generic, Literal, Protocol, TypeAlias, type_c
 from typing_extensions import LiteralString, TypeVar
 
 import numpy as np
-import numpy.typing as npt
 import optype.numpy as onp
 from scipy.sparse import coo_matrix, sparray, spmatrix
 from ._miobase import MatFileReader
@@ -119,7 +118,7 @@ class VarWriter4:
     def write_bytes(self, /, arr: onp.ArrayND) -> None: ...
     def write_string(self, /, s: str) -> None: ...
     def write_header(self, /, name: str, shape: Sequence[int], P: _MDType = 0, T: _MClass = 0, imagf: int = 0) -> None: ...
-    def write(self, /, arr: npt.ArrayLike, name: str) -> None: ...
+    def write(self, /, arr: onp.ToArrayND, name: str) -> None: ...
     def write_numeric(self, /, arr: onp.ArrayND[np.number[Any]], name: str) -> None: ...
     def write_char(self, /, arr: onp.ArrayND[np.character], name: str) -> None: ...
     def write_sparse(self, /, arr: spmatrix | sparray, name: str) -> None: ...

scipy-stubs/io/matlab/_mio5.pyi

@@ -3,7 +3,6 @@ from collections.abc import Iterable, Mapping
 from typing import IO, Any, Final, Literal, TypeAlias, TypedDict, final, type_check_only
 
 import numpy as np
-import numpy.typing as npt
 import optype.numpy as onp
 from scipy._typing import AnyShape, ByteOrder
 from scipy.sparse import sparray, spmatrix
@@ -75,8 +74,8 @@ class VarWriter5:
         nzmax: int = 0,
     ) -> None: ...
     def update_matrix_tag(self, /, start_pos: int) -> None: ...
-    def write_top(self, /, arr: npt.ArrayLike, name: str, is_global: bool) -> None: ...
-    def write(self, /, arr: npt.ArrayLike) -> None: ...
+    def write_top(self, /, arr: onp.ToArrayND, name: str, is_global: bool) -> None: ...
+    def write(self, /, arr: onp.ToArrayND) -> None: ...
     def write_numeric(self, /, arr: onp.ArrayND[np.bool_ | np.number[Any]]) -> None: ...
     def write_char(self, /, arr: onp.ArrayND[np.str_], codec: str = "ascii") -> None: ...
     def write_sparse(self, /, arr: spmatrix | sparray) -> None: ...

scipy-stubs/linalg/_misc.pyi

@@ -51,15 +51,15 @@ def norm(
 ) -> np.float64: ...
 @overload  # float64-coercible array, keepdims: True (positional)
 def norm(
-    a: onp.CanArrayND[_SubScalar, _ShapeT],
+    a: onp.ArrayND[_SubScalar, _ShapeT],
     ord: _Order | None,
     axis: _Axis | None,
     keepdims: _Truthy,
     check_finite: AnyBool = True,
 ) -> onp.ArrayND[np.float64, _ShapeT]: ...
 @overload  # float64-coercible array, keepdims: True (keyword)
 def norm(
-    a: onp.CanArrayND[_SubScalar, _ShapeT],
+    a: onp.ArrayND[_SubScalar, _ShapeT],
     ord: _Order | None = None,
     axis: _Axis | None = None,
     *,
@@ -85,15 +85,15 @@ def norm(
 ) -> onp.ArrayND[np.float64]: ...
 @overload  # shaped inexact array, keepdims: True (positional)
 def norm(
-    a: onp.CanArrayND[np.inexact[_NBitT], _ShapeT],
+    a: onp.ArrayND[np.inexact[_NBitT], _ShapeT],
     ord: _Order | None,
     axis: _Axis | None,
     keepdims: _Truthy,
     check_finite: AnyBool = True,
 ) -> onp.ArrayND[np.floating[_NBitT], _ShapeT]: ...
 @overload  # shaped inexact array, keepdims: True (keyword)
 def norm(
-    a: onp.CanArrayND[np.inexact[_NBitT], _ShapeT],
+    a: onp.ArrayND[np.inexact[_NBitT], _ShapeT],
     ord: _Order | None = None,
     axis: _Axis | None = None,
     *,
@@ -144,7 +144,7 @@ def norm(
 ) -> onp.ArrayND[np.floating[Any]]: ...
 @overload  # catch-all
 def norm(
-    a: npt.ArrayLike,
+    a: onp.ToArrayND,
     ord: _Order | None = None,
     axis: _Axis | None = None,
     keepdims: AnyBool = False,