fixed all (!) stubtest errors (the non-stubtest ones)

README.md

@@ -83,33 +83,33 @@ pip install scipy-stubs
 | Module                            | Stubs status    |
 |---------------------------------- |---------------- |
 | `scipy`                           | 1: skeleton     |
-| `scipy._lib`                      | 1: skeleton     |
-| `scipy._lib.uarray`               | 1: skeleton     |
-| `scipy._lib.array_api_compat`     | 1: partial      |
+| `scipy._lib`                      | 2: partial      |
+| `scipy._lib.uarray`               | 2: ready        |
+| `scipy._lib.array_api_compat`     | 2: partial      |
 | `scipy.cluster`                   | 1: skeleton     |
 | `scipy.constants`                 | 3: ready        |
 | `scipy.datasets`                  | 1: skeleton     |
 | `scipy.fft`                       | 1: skeleton     |
-| `scipy.fft._pocketfft`            | 1: skeleton     |
+| `scipy.fft._pocketfft`            | 1: partial      |
 | `scipy.fftpack`                   | 1: skeleton     |
-| `scipy.integrate`                 | 1: skeleton     |
-| `scipy.integrate._ivp`            | 1: skeleton     |
-| `scipy.interpolate`               | 1: skeleton     |
+| `scipy.integrate`                 | 2: partial      |
+| `scipy.integrate._ivp`            | 1: partial      |
+| `scipy.interpolate`               | 2: partial      |
 | `scipy.io`                        | 1: skeleton     |
 | `scipy.io.arff`                   | 1: skeleton     |
-| `scipy.io.matlab`                 | 1: skeleton     |
+| `scipy.io.matlab`                 | 2: partial      |
 | `scipy.linalg`                    | 3: ready        |
 | `scipy.misc`                      | 0: missing      |
 | `scipy.ndimage`                   | 1: skeleton     |
 | `scipy.odr`                       | 1: skeleton     |
-| `scipy.optimize`                  | 1: skeleton     |
+| `scipy.optimize`                  | 2: partial      |
 | `scipy.optimize.cython_optimize`  | 0: missing      |
 | `scipy.optimize.zeros`            | 0: missing      |
-| `scipy.signal`                    | 1: skeleton     |
+| `scipy.signal`                    | 1: partial      |
 | `scipy.signal.windows`            | 1: skeleton     |
-| `scipy.sparse`                    | 1: skeleton     |
-| `scipy.sparse.csgraph`            | 1: skeleton     |
-| `scipy.sparse.linalg`             | 1: skeleton     |
+| `scipy.sparse`                    | 2: partial      |
+| `scipy.sparse.csgraph`            | 2: partial      |
+| `scipy.sparse.linalg`             | 2: partial      |
 | `scipy.spatial`                   | 2: partial      |
 | `scipy.spatial.distance`          | 3: ready        |
 | `scipy.special`                   | 3: ready        |

pyproject.toml

@@ -149,20 +149,18 @@ banned-from = [
 [tool.ruff.lint.isort]
 combine-as-imports = true
 known-first-party = ["scipy"]
-no-lines-before = ["local-folder"]
+no-lines-before = ["typing", "first-party", "local-folder"]
 section-order = [
   "standard-library",
   "typing",
   "third-party",
-  "typing-extra",
   "first-party",
   "local-folder",
 ]
 split-on-trailing-comma = true
 
 [tool.ruff.lint.isort.sections]
 typing = ["collections.abc", "types", "typing", "typing_extensions"]
-typing-extra = ["optype", "optype.numpy", "numpy.typing", "scipy._typing"]
 
 [tool.ruff.lint.flake8-annotations]
 allow-star-arg-any = true

scipy-stubs/__init__.pyi

@@ -1,7 +1,6 @@
-from scipy._typing import Untyped
-
 from scipy._lib._ccallback import LowLevelCallable as LowLevelCallable
 from scipy._lib._testutils import PytestTester as PytestTester
+from scipy._typing import Untyped
 
 msg: str
 np_minversion: str

scipy-stubs/_lib/_array_api.pyi

@@ -1,9 +1,8 @@
 from types import ModuleType
 from typing import Any, Literal
 
-from scipy._typing import Untyped
-
 from scipy._lib.array_api_compat import device, size
+from scipy._typing import Untyped
 
 __all__ = ["_asarray", "array_namespace", "device", "size"]
 

scipy-stubs/_lib/_ccallback.pyi

@@ -1,6 +1,5 @@
 import ctypes as ct
 from _ctypes import CFuncPtr as PyCFuncPtr
-
 from types import ModuleType
 from typing import ClassVar, Generic, Literal, TypeAlias
 from typing_extensions import CapsuleType, Self, TypeVar

scipy-stubs/_lib/_pep440.pyi

@@ -1,26 +1,29 @@
-from typing import NamedTuple
+from typing import Literal, NamedTuple
+from typing_extensions import override
 
 from scipy._typing import Untyped
 
 class Infinity:
-    def __hash__(self) -> Untyped: ...
-    def __lt__(self, other) -> Untyped: ...
-    def __le__(self, other) -> Untyped: ...
-    def __eq__(self, other) -> Untyped: ...
-    def __ne__(self, other) -> Untyped: ...
-    def __gt__(self, other) -> Untyped: ...
-    def __ge__(self, other) -> Untyped: ...
-    def __neg__(self) -> Untyped: ...
+    @override
+    def __eq__(self, other: object, /) -> bool: ...
+    @override
+    def __ne__(self, other: object, /) -> bool: ...
+    def __lt__(self, other: object, /) -> Literal[False]: ...
+    def __le__(self, other: object, /) -> Literal[False]: ...
+    def __gt__(self, other: object, /) -> Literal[True]: ...
+    def __ge__(self, other: object, /) -> Literal[True]: ...
+    def __neg__(self) -> NegativeInfinity: ...
 
 class NegativeInfinity:
-    def __hash__(self) -> Untyped: ...
-    def __lt__(self, other) -> Untyped: ...
-    def __le__(self, other) -> Untyped: ...
-    def __eq__(self, other) -> Untyped: ...
-    def __ne__(self, other) -> Untyped: ...
-    def __gt__(self, other) -> Untyped: ...
-    def __ge__(self, other) -> Untyped: ...
-    def __neg__(self) -> Untyped: ...
+    @override
+    def __eq__(self, other: object, /) -> bool: ...
+    @override
+    def __ne__(self, other: object, /) -> bool: ...
+    def __lt__(self, other: object, /) -> Literal[True]: ...
+    def __le__(self, other: object, /) -> Literal[True]: ...
+    def __gt__(self, other: object, /) -> Literal[False]: ...
+    def __ge__(self, other: object, /) -> Literal[False]: ...
+    def __neg__(self) -> Infinity: ...
 
 class _Version(NamedTuple):
     epoch: Untyped
@@ -35,13 +38,14 @@ def parse(version) -> Untyped: ...
 class InvalidVersion(ValueError): ...
 
 class _BaseVersion:
-    def __hash__(self) -> Untyped: ...
-    def __lt__(self, other) -> Untyped: ...
-    def __le__(self, other) -> Untyped: ...
-    def __eq__(self, other) -> Untyped: ...
-    def __ge__(self, other) -> Untyped: ...
-    def __gt__(self, other) -> Untyped: ...
-    def __ne__(self, other) -> Untyped: ...
+    @override
+    def __eq__(self, other: _BaseVersion, /) -> bool: ...  # type: ignore[override]
+    @override
+    def __ne__(self, other: _BaseVersion, /) -> bool: ...  # type: ignore[override]
+    def __lt__(self, other: _BaseVersion, /) -> bool: ...
+    def __le__(self, other: _BaseVersion, /) -> bool: ...
+    def __ge__(self, other: _BaseVersion, /) -> bool: ...
+    def __gt__(self, other: _BaseVersion, /) -> bool: ...
 
 class LegacyVersion(_BaseVersion):
     def __init__(self, version) -> None: ...
@@ -50,7 +54,7 @@ class LegacyVersion(_BaseVersion):
     @property
     def base_version(self) -> Untyped: ...
     @property
-    def local(self): ...
+    def local(self) -> Untyped: ...
     @property
     def is_prerelease(self) -> Untyped: ...
     @property

scipy-stubs/_lib/_uarray/_backend.pyi

@@ -1,7 +1,7 @@
 from collections.abc import Callable, Generator
 from typing import TypeAlias
 
-from scipy._typing import Untyped
+from scipy._typing import Untyped, UntypedCallable
 
 __all__ = [
     "BackendNotImplementedError",
@@ -49,7 +49,7 @@ def generate_multimethod(
     argument_extractor: ArgumentExtractorType,
     argument_replacer: ArgumentReplacerType,
     domain: str,
-    default: typing.Callable | None = None,
+    default: UntypedCallable | None = None,
 ): ...
 def set_backend(backend, coerce: bool = False, only: bool = False) -> Untyped: ...
 def skip_backend(backend) -> Untyped: ...

scipy-stubs/_lib/_util.pyi

@@ -3,7 +3,6 @@ from typing import Any, NamedTuple, TypeAlias
 from typing_extensions import TypeVar, override
 
 import numpy as np
-
 from scipy._typing import Untyped
 
 AxisError: type[Exception]

scipy-stubs/_lib/array_api_compat/common/_helpers.pyi

@@ -2,7 +2,6 @@ from types import ModuleType
 from typing_extensions import TypeIs
 
 import numpy as np
-
 from ._typing import Array, Device
 
 __all__ = [

scipy-stubs/_lib/array_api_compat/common/_typing.pyi

@@ -1,11 +1,9 @@
 import array as _array
 import mmap
-
 from typing import Any, Literal, Protocol, TypeAlias, TypeVar
 from typing_extensions import Buffer
 
 import numpy as np
-
 import optype as op
 
 __all__ = ["NestedSequence", "SupportsBufferProtocol"]

scipy-stubs/_lib/decorator.pyi

@@ -1,8 +1,7 @@
-from contextlib import GeneratorContextManager as _GeneratorContextManager
-
+from contextlib import _GeneratorContextManager
 from typing import NamedTuple
 
-from scipy._typing import Untyped
+from scipy._typing import Untyped, UntypedCallable
 
 __version__: str
 
@@ -52,18 +51,17 @@ class FunctionMaker:
         **attrs,
     ) -> Untyped: ...
 
-def decorate(func, caller) -> Untyped: ...
-def decorator(caller, _func: Untyped | None = None) -> Untyped: ...
+def decorate(func: UntypedCallable, caller) -> Untyped: ...
+def decorator(caller, _func: UntypedCallable | None = None) -> UntypedCallable: ...
 
-class ContextManager(_GeneratorContextManager):
-    def __call__(self, func) -> Untyped: ...
+class ContextManager(_GeneratorContextManager[Untyped]): ...
 
 init: Untyped
 n_args: Untyped
 
 def __init__(self, g, *a, **k): ...
 
-contextmanager: Untyped
+contextmanager: UntypedCallable
 
 def append(a, vancestors): ...
 def dispatch_on(*dispatch_args) -> Untyped: ...

scipy-stubs/_lib/deprecation.pyi

@@ -1,8 +1,20 @@
+from collections.abc import Callable
+from types import ModuleType
+from typing import Any, TypeVar
+
 from scipy._typing import Untyped
 
+__all__ = ["_deprecated"]
+
+_F = TypeVar("_F", bound=Callable[..., Any])
+
 class _DeprecationHelperStr:
-    def __init__(self, content, message) -> None: ...
-    def __hash__(self) -> Untyped: ...
-    def __eq__(self, other) -> Untyped: ...
+    def __init__(self, content: Untyped, message: str) -> None: ...
 
-def deprecate_cython_api(module, routine_name, new_name: Untyped | None = None, message: Untyped | None = None): ...
+def _deprecated(msg: str, stacklevel: int = 2) -> Callable[[_F], _F]: ...
+def deprecate_cython_api(
+    module: ModuleType,
+    routine_name: str,
+    new_name: str | None = None,
+    message: str | None = None,
+) -> None: ...

scipy-stubs/_typing.pyi

@@ -1,10 +1,11 @@
 # Helper types for internal use (type-check only).
+from collections.abc import Callable
 from typing import Literal, Protocol, TypeAlias, type_check_only
 from typing_extensions import LiteralString, TypeVar
 
 import numpy as np
-
 import numpy.typing as npt
+import optype.numpy as onpt
 
 __all__ = [
     "AnyBool",
@@ -17,11 +18,21 @@ __all__ = [
     "CorrelateMode",
     "Seed",
     "Untyped",
+    "UntypedArray",
+    "UntypedCallable",
+    "UntypedDict",
+    "UntypedList",
+    "UntypedTuple",
     "_FortranFunction",
 ]
 
-# placeholder for missing annotations
+# placeholders for missing annotations
 Untyped: TypeAlias = object
+UntypedTuple: TypeAlias = tuple[Untyped, ...]
+UntypedList: TypeAlias = list[Untyped]
+UntypedDict: TypeAlias = dict[Untyped, Untyped]
+UntypedCallable: TypeAlias = Callable[..., Untyped]
+UntypedArray: TypeAlias = onpt.Array[tuple[int, ...], np.generic]
 
 _SCT = TypeVar("_SCT", bound=np.generic, default=np.generic)
 Array0D: TypeAlias = np.ndarray[tuple[()], np.dtype[_SCT]]

scipy-stubs/cluster/__init__.pyi

@@ -1,4 +1,3 @@
-from scipy._typing import Untyped
-
 from scipy._lib._testutils import PytestTester as PytestTester
+from scipy._typing import Untyped
 from . import hierarchy as hierarchy, vq as vq

scipy-stubs/cluster/hierarchy.pyi

@@ -1,7 +1,40 @@
+from scipy._lib._disjoint_set import DisjointSet
 from scipy._typing import Untyped
 
-from scipy._lib._array_api import array_namespace as array_namespace, is_jax as is_jax, xp_copy as xp_copy
-from scipy._lib._disjoint_set import DisjointSet as DisjointSet
+__all__ = [
+    "ClusterNode",
+    "DisjointSet",
+    "average",
+    "centroid",
+    "complete",
+    "cophenet",
+    "correspond",
+    "cut_tree",
+    "dendrogram",
+    "fcluster",
+    "fclusterdata",
+    "from_mlab_linkage",
+    "inconsistent",
+    "is_isomorphic",
+    "is_monotonic",
+    "is_valid_im",
+    "is_valid_linkage",
+    "leaders",
+    "leaves_list",
+    "linkage",
+    "maxRstat",
+    "maxdists",
+    "maxinconsts",
+    "median",
+    "num_obs_linkage",
+    "optimal_leaf_ordering",
+    "set_link_color_palette",
+    "single",
+    "to_mlab_linkage",
+    "to_tree",
+    "ward",
+    "weighted",
+]
 
 class ClusterWarning(UserWarning): ...
 
@@ -24,7 +57,7 @@ class ClusterNode:
     def __init__(self, id, left: Untyped | None = None, right: Untyped | None = None, dist: int = 0, count: int = 1): ...
     def __lt__(self, node) -> Untyped: ...
     def __gt__(self, node) -> Untyped: ...
-    def __eq__(self, node) -> Untyped: ...
+    def __eq__(self, node) -> Untyped: ...  # type: ignore[override]
     def get_id(self) -> Untyped: ...
     def get_count(self) -> Untyped: ...
     def get_left(self) -> Untyped: ...