👽️ SciPy 1.16.1 support (#792)

Author: jorenham

.mypyignore

@@ -12,34 +12,6 @@ scipy\.((_|\w)+\.)+(__test__|test|tests(\..+)?)
 scipy\._lib\.(array_api_(compat|extra)|cobyqa|pyprima).*
 scipy\.fft\._pocketfft\..*
 
-# https://github.com/scipy/scipy/issues/23216
-scipy\.cluster\._?vq\.kmeans
-scipy\.cluster\._?vq\.kmeans2
-scipy\.interpolate(\._?polyint)?\.BarycentricInterpolator\.__init__
-scipy\.linalg(\._sketches)?\.clarkson_woodruff_transform
-scipy\.optimize(\._basinhopping)?\.basinhopping
-scipy\.optimize(\._differentialevolution)?\.differential_evolution
-scipy\.optimize(\._dual_annealing)?\.dual_annealing
-scipy\.optimize(\._optimize)?\.check_grad
-scipy\.sparse(\._construct)?\.random_array
-scipy\.sparse(\._construct)?\.random
-scipy\.sparse(\._construct)?\.rand
-scipy\.sparse\.linalg(\._eigen(\._svds)?)?\.svds
-scipy\.spatial\.distance\.directed_hausdorff
-scipy\.spatial\.transform(\._?rotation|\._rigid_transform)?\.Rotation\.random
-scipy\.stats(\._fit)?\.goodness_of_fit
-scipy\.stats(\._multicomp)?\.dunnett
-scipy\.stats(\._resampling)?\.bootstrap
-scipy\.stats(\._resampling)?\.permutation_test
-scipy\.stats(\._sensitivity_analysis)?\.sobol_indices
-scipy\.stats\._?qmc\.QMCEngine\.__init__
-scipy\.stats\._?qmc\.Halton\.__init__
-scipy\.stats\._?qmc\.LatinHypercube\.__init__
-scipy\.stats\._?qmc\.Sobol\.__init__
-scipy\.stats\._?qmc\.PoissonDisk\.__init__
-scipy\.stats\._?qmc\.MultivariateNormalQMC\.__init__
-scipy\.stats\._?qmc\.MultinomialQMC\.__init__
-
 # https://github.com/scipy/scipy/pull/23115
 # https://github.com/scipy/scipy/pull/23117
 scipy\.linalg\._decomp_interpolative\.__all__
@@ -54,7 +26,7 @@ scipy\.special\._precompute\..*
 # useless __new__
 scipy\.stats\.(_new_distributions\.)?Normal\.__new__
 
-# these require numpy/numtype to be released
+# these require numtype to be released
 scipy\.stats\._qmvnt\.phi(nv)?
 scipy\.special\._basic\.digamma
 scipy\.special\._support_alternative_backends\.betaincc?

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
 
 [project]
 name = "scipy-stubs"
-version = "1.16.0.3.dev0"
+version = "1.16.1.0.dev0"
 description = "Type annotations for SciPy"
 readme = "README.md"
 authors = [
@@ -33,7 +33,7 @@ requires-python = ">=3.11"
 dependencies = ["optype[numpy]>=0.13.1,<0.14"]
 
 [project.optional-dependencies]
-scipy = ["scipy>=1.16.0,<1.17"]
+scipy = ["scipy>=1.16.1,<1.17"]
 
 [project.urls]
 Homepage = "https://scipy.org/"
@@ -73,16 +73,12 @@ force-include = { ".mypyignore" = ".mypyignore" } # for scipy-stubs-feedstock
 [tool.poe.tasks.clean]
 cmd = """
 rm -rf
-    scipy-stubs/**/*.pyc
-    scipy-stubs/**/__pycache__
-    scripts/*.pyc
-    scripts/__pycache__
-    tests/**/*.pyc
-    tests/**/__pycache__
-    ./**/.cache
-    ./**/.mypy_cache
-    ./**/.ruff_cache
-    ./**/.tox
+    **/*.pyc
+    **/__pycache__
+    **/.cache
+    **/.mypy_cache
+    **/.ruff_cache
+    **/.tox
 """
 
 [tool.poe.tasks.stubtest]

scipy-stubs/interpolate/_polyint.pyi

@@ -177,8 +177,8 @@ class BarycentricInterpolator(_Interpolator1DWithDerivatives[_YT_co], Generic[_Y
         axis: int = 0,
         *,
         wi: onp.ArrayND[npc.floating] | None = None,
-        seed: onp.random.ToRNG | None = None,
         rng: onp.random.ToRNG | None = None,
+        random_state: onp.random.ToRNG | None = None,  # legacy
     ) -> None: ...
     @overload  # yi: c128
     def __init__(
@@ -189,8 +189,8 @@ class BarycentricInterpolator(_Interpolator1DWithDerivatives[_YT_co], Generic[_Y
         axis: int = 0,
         *,
         wi: onp.ArrayND[npc.floating] | None = None,
-        seed: onp.random.ToRNG | None = None,
         rng: onp.random.ToRNG | None = None,
+        random_state: onp.random.ToRNG | None = None,  # legacy
     ) -> None: ...
 
     #

scipy-stubs/optimize/_shgo_lib/_complex.pyi

@@ -1,5 +1,5 @@
 from collections.abc import Callable, Generator, Sequence
-from typing import Concatenate, Final, Generic, TypeAlias
+from typing import Concatenate, Final, Generic, Protocol, TypeAlias, type_check_only
 from typing_extensions import TypeVar
 
 import numpy as np
@@ -23,6 +23,10 @@ _Symmetry: TypeAlias = onp.ArrayND[npc.integer] | op.CanGetitem[int, op.CanIndex
 
 _HT = TypeVar("_HT", bound=VertexCacheBase, default=VertexCacheBase)
 
+@type_check_only
+class SplitEdgeFunction(Protocol):
+    def __call__(self, /, v1: VertexBase, v2: VertexBase) -> VertexBase: ...
+
 ###
 
 class Complex(Generic[_HT]):  # undocumented
@@ -49,6 +53,9 @@ class Complex(Generic[_HT]):  # undocumented
     cp: Generator[_Floats, None, _Floats]
     rls: Generator[VertexBase | _Floats]
 
+    # awkward annotation for `self.split_edge = functools.cache(self._split_edge)`
+    split_edge: Final[SplitEdgeFunction]
+
     def __init__(
         self,
         /,
@@ -78,7 +85,7 @@ class Complex(Generic[_HT]):  # undocumented
         self, /, origin: _Location, supremum: _Location, bounds: _Bounds, centroid: onp.ToBool = 1
     ) -> Generator[VertexBase | _Floats]: ...
     def refine_star(self, /, v: VertexBase) -> None: ...
-    def split_edge(self, /, v1: VertexBase, v2: VertexBase) -> VertexBase: ...
+    def _split_edge(self, /, v1: VertexBase, v2: VertexBase) -> VertexBase: ...
     def vpool(self, /, origin: _Location, supremum: _Location) -> set[VertexBase]: ...
     def vf_to_vv(self, /, vertices: Sequence[VertexBase], simplices: Sequence[tuple[onp.ToFloat1D, onp.ToFloat1D]]) -> None: ...
     def connect_vertex_non_symm(

scipy-stubs/optimize/optimize.pyi

@@ -59,7 +59,14 @@ def brute(
 ) -> object: ...
 @deprecated("will be removed in SciPy v2.0.0")
 def check_grad(
-    func: object, grad: object, x0: object, *args: object, epsilon: object = ..., direction: object = ..., rng: object = ...
+    func: object,
+    grad: object,
+    x0: object,
+    *args: object,
+    epsilon: object = ...,
+    direction: object = ...,
+    rng: object = None,
+    seed: object = None,
 ) -> object: ...
 @deprecated("will be removed in SciPy v2.0.0")
 def fmin(
@@ -95,6 +102,7 @@ def fmin_bfgs(
     c2: object = ...,
     hess_inv0: object = ...,
 ) -> object: ...
+@deprecated("will be removed in SciPy v2.0.0")
 def fmin_cg(
     f: object,
     x0: object,

scipy-stubs/sparse/construct.pyi

@@ -54,12 +54,23 @@ def random(
     n: object,
     density: object = ...,
     format: object = ...,
-    dtype: object = ...,
-    rng: object = ...,
-    data_rvs: object = ...,
+    dtype: object = None,
+    rng: object = None,
+    data_rvs: object = None,
+    *,
+    random_state: object = None,
 ) -> Any: ...
 @deprecated("will be removed in SciPy v2.0.0")
-def rand(m: object, n: object, density: object = ..., format: object = ..., dtype: object = ..., rng: object = ...) -> Any: ...
+def rand(
+    m: object,
+    n: object,
+    density: object = ...,
+    format: object = ...,
+    dtype: object = None,
+    rng: object = None,
+    *,
+    random_state: object = None,
+) -> Any: ...
 @deprecated("will be removed in SciPy v2.0.0")
 def kron(A: object, B: object, format: object = ...) -> Any: ...
 @deprecated("will be removed in SciPy v2.0.0")

scipy-stubs/sparse/linalg/eigen.pyi

@@ -75,4 +75,6 @@ def svds(
     solver: object = ...,
     rng: object = None,
     options: object = None,
+    *,
+    random_state: object = None,
 ) -> object: ...

scipy-stubs/version.pyi

@@ -1,7 +1,7 @@
 import typing as _t
 
-version: _t.Final = "1.16.0"
-full_version: _t.Final = "1.16.0"
-short_version: _t.Final = "1.16.0"
+version: _t.Final = "1.16.1"
+full_version: _t.Final = "1.16.1"
+short_version: _t.Final = "1.16.1"
 release: _t.Final = True
 git_revision: _t.Final[_t.LiteralString] = ...

tests/stats/test_make_distribution.pyi

@@ -1,5 +1,3 @@
-from typing import Literal
-
 import numpy as np
 
 from scipy.stats import distributions, make_distribution
@@ -9,7 +7,7 @@ LogUniform: type[ContinuousDistribution] = make_distribution(distributions.logun
 
 class _DuckRV:
     @property
-    def __make_distribution_version__(self) -> Literal["1.16.0"]: ...
+    def __make_distribution_version__(self) -> str: ...
     @property
     def parameters(self) -> dict[str, tuple[float, float]]: ...
     @property
@@ -18,7 +16,7 @@ class _DuckRV:
 
 class _MultiDuckRV:
     @property
-    def __make_distribution_version__(self) -> Literal["1.16.0"]: ...
+    def __make_distribution_version__(self) -> str: ...
     @property
     def parameters(self) -> tuple[dict[str, tuple[float, float]], dict[str, tuple[float, float]]]: ...
     def process_parameters(self, quack: float | None = None, swim: float | None = None) -> dict[str, float]: ...