Merge pull request #17 from jorenham/fix/scipy.stats.distributions

fix `scipy.stats.distributions` stubtests

README.md

@@ -115,7 +115,7 @@ pyright), the "type completeness score" is **42.6%**.
 | `scipy.special.cython_special`    | 2: partial      |
 | `scipy.stats`                     | 2: partial      |
 | `scipy.stats.contingency`         | 1: skeleton     |
-| `scipy.stats.distributions`       | 3: ready        |
+| `scipy.stats.distributions`       | 4: done         |
 | `scipy.stats.mstats`              | 1: skeleton     |
 | `scipy.stats.qmc`                 | 2: partial      |
 | `scipy.stats.sampling`            | 1: skeleton     |

pyproject.toml

@@ -48,11 +48,10 @@ type = "poetry"
 
 [tool.poe.tasks]
 lint = "ruff check"
-# stubtest = "stubtest --ignore-positional-only --mypy-config-file=pyproject.toml --allowlist=tests/stubtest/allowlist.txt scipy"
 verifytypes = "basedpyright --level error --verifytypes scipy-stubs"
 
 [tool.poe.tasks.stubtest]
-cmd = "stubtest --ignore-positional-only --mypy-config-file=pyproject.toml --allowlist=tests/stubtest/allowlist.txt $modules"
+cmd = "stubtest --mypy-config-file=pyproject.toml --allowlist=tests/stubtest/allowlist.txt $modules"
 args = [
   {name = "modules", positional = true, multiple = true, default = "scipy"},
 ]

scipy-stubs/_typing.pyi

@@ -16,6 +16,7 @@ __all__ = [
     "AnyScalar",
     "Array0D",
     "CorrelateMode",
+    "NanPolicy",
     "Seed",
     "Untyped",
     "UntypedArray",
@@ -49,6 +50,9 @@ AnyScalar: TypeAlias = int | float | complex | AnyChar | np.generic
 Seed: TypeAlias = int | np.random.Generator | np.random.RandomState
 CorrelateMode: TypeAlias = Literal["valid", "same", "full"]
 
+# scipy literals
+NanPolicy: TypeAlias = Literal["raise", "propagate", "omit"]
+
 # used in `scipy.linalg.blas` and `scipy.linalg.lapack`
 @type_check_only
 class _FortranFunction(Protocol):

scipy-stubs/stats/_continuous_distns.pyi

@@ -1,6 +1,10 @@
-from typing import Final
-from typing_extensions import deprecated
+from collections.abc import Sequence
+from typing import Any, ClassVar, Final, TypeAlias
+from typing_extensions import LiteralString, deprecated, override
 
+import numpy as np
+import numpy.typing as npt
+import optype.numpy as onpt
 from ._distn_infrastructure import rv_continuous
 
 __all__ = [
@@ -118,7 +122,14 @@ __all__ = [
 class ksone_gen(rv_continuous): ...
 class kstwo_gen(rv_continuous): ...
 class kstwobign_gen(rv_continuous): ...
-class norm_gen(rv_continuous): ...
+
+_Scalar_f8_in: TypeAlias = np.float64 | np.float32 | np.float16 | np.integer[Any] | np.bool_
+_AnyArray_f8_in: TypeAlias = float | onpt.CanArray[tuple[int, ...], np.dtype[_Scalar_f8_in]] | Sequence[_AnyArray_f8_in]
+
+class norm_gen(rv_continuous):
+    @override
+    def fit(self, /, data: _AnyArray_f8_in, **kwds: _Scalar_f8_in) -> tuple[np.float64, np.float64]: ...  # type: ignore[override]
+
 class alpha_gen(rv_continuous): ...
 class anglit_gen(rv_continuous): ...
 class arcsine_gen(rv_continuous): ...
@@ -197,7 +208,8 @@ class powerlognorm_gen(rv_continuous): ...
 class powernorm_gen(rv_continuous): ...
 class rdist_gen(rv_continuous): ...
 class rayleigh_gen(rv_continuous): ...
-class reciprocal_gen(rv_continuous): ...
+class reciprocal_gen(rv_continuous):
+    fit_note: ClassVar[LiteralString] = ...
 class rice_gen(rv_continuous): ...
 class irwinhall_gen(rv_continuous): ...
 class recipinvgauss_gen(rv_continuous): ...
@@ -222,7 +234,18 @@ class gennorm_gen(rv_continuous): ...
 class halfgennorm_gen(rv_continuous): ...
 class crystalball_gen(rv_continuous): ...
 class argus_gen(rv_continuous): ...
-class rv_histogram(rv_continuous): ...
+
+_Seed: TypeAlias = np.random.Generator | np.random.RandomState | int
+
+class rv_histogram(rv_continuous):
+    def __init__(
+        self,
+        histogram: tuple[npt.NDArray[np.floating[Any]], npt.NDArray[np.inexact[Any]]],
+        *args: float | LiteralString | _Seed,
+        density: bool | None = None,
+        **kwargs: float | LiteralString | _Seed,
+    ) -> None: ...
+
 class studentized_range_gen(rv_continuous): ...
 class rel_breitwigner_gen(rv_continuous): ...
 

scipy-stubs/stats/_discrete_distns.pyi

@@ -1,4 +1,4 @@
-from typing import Final
+from typing import ClassVar, Final
 
 from ._distn_infrastructure import rv_discrete
 
@@ -43,9 +43,15 @@ class zipfian_gen(rv_discrete): ...
 class dlaplace_gen(rv_discrete): ...
 class skellam_gen(rv_discrete): ...
 class yulesimon_gen(rv_discrete): ...
-class _nchypergeom_gen(rv_discrete): ...
-class nchypergeom_fisher_gen(_nchypergeom_gen): ...
-class nchypergeom_wallenius_gen(_nchypergeom_gen): ...
+class _nchypergeom_gen(rv_discrete):
+    rvs_name: ClassVar = None
+    dist: ClassVar = None
+class nchypergeom_fisher_gen(_nchypergeom_gen):
+    rvs_name: ClassVar = "rvs_fisher"
+    dist: ClassVar[type] = ...  # scipy.stats._biasedurn._PyFishersNCHypergeometric
+class nchypergeom_wallenius_gen(_nchypergeom_gen):
+    rvs_name: ClassVar = "rvs_wallenius"
+    dist: ClassVar[type] = ...  # scipy.stats._biasedurn._PyWalleniusNCHypergeometric
 
 binom: Final[binom_gen]
 bernoulli: Final[bernoulli_gen]