Fix all reportAssertTypeFailure+reportGeneralTypeIssues (#339)

pyproject.toml

@@ -84,6 +84,7 @@ extra-standard-library = [
 
 [tool.pyright]
 exclude = ["build", ".git"]
+stubPath = "./stubs"
 # Target oldest supported Python version
 pythonversion = "3.9"
 typeCheckingMode = "standard"
@@ -108,10 +109,6 @@ reportSelfClsParameterName = false
 # Not an error by default in standard mode
 reportUnsupportedDunderAll = "error"
 
-# Error reports to fix in code
-reportAssertTypeFailure = "none" # TODO
-reportGeneralTypeIssues = "none" # TODO
-
 [tool.mypy]
 # Target oldest supported Python version
 python_version = "3.9"

stubs/matplotlib/figure.pyi

@@ -75,7 +75,8 @@ class FigureBase(Artist):
     def add_artist(self, artist: Artist, clip: bool = False) -> Artist: ...
     def add_axes(self, *args, **kwargs) -> Axes: ...
     @overload
-    def add_subplot(self, *args, projection: Literal["3d"], **kwargs) -> Axes3D: ...
+    # Decorators make this look like a callable. This is an upstream issue
+    def add_subplot(self, *args, projection: Literal["3d"], **kwargs) -> Axes3D: ...  # pyright: ignore[reportGeneralTypeIssues]
     @overload
     def add_subplot(self, *args, projection: Literal["aitoff"], **kwargs) -> AitoffAxes: ...
     @overload

stubs/sklearn/cluster/_kmeans.pyi

@@ -18,7 +18,6 @@ from ..utils._param_validation import (
 )
 from ..utils._readonly_array_wrapper import ReadonlyArrayWrapper as ReadonlyArrayWrapper
 from ..utils.extmath import row_norms as row_norms, stable_cumsum as stable_cumsum
-from ..utils.fixes import threadpool_info as threadpool_info, threadpool_limits as threadpool_limits
 from ..utils.sparsefuncs import mean_variance_axis as mean_variance_axis
 from ..utils.sparsefuncs_fast import assign_rows_csr as assign_rows_csr
 from ..utils.validation import check_is_fitted as check_is_fitted

stubs/sklearn/conftest.pyi

@@ -20,7 +20,6 @@ from .datasets import (
     fetch_rcv1 as fetch_rcv1,
 )
 from .tests import random_seed as random_seed
-from .utils.fixes import parse_version as parse_version
 
 dataset_fetchers: dict = ...
 

stubs/sklearn/cross_decomposition/_pls.pyi

@@ -10,7 +10,6 @@ from ..exceptions import ConvergenceWarning as ConvergenceWarning
 from ..utils import check_array as check_array, check_consistent_length as check_consistent_length
 from ..utils._param_validation import Interval as Interval, StrOptions as StrOptions
 from ..utils.extmath import svd_flip as svd_flip
-from ..utils.fixes import parse_version as parse_version, sp_version as sp_version
 from ..utils.validation import FLOAT_DTYPES as FLOAT_DTYPES, check_is_fitted as check_is_fitted
 
 PLSSVD_Self = TypeVar("PLSSVD_Self", bound="PLSSVD")

stubs/sklearn/linear_model/_quantile.pyi

@@ -9,7 +9,6 @@ from .._typing import ArrayLike, Float, MatrixLike
 from ..base import BaseEstimator, RegressorMixin
 from ..exceptions import ConvergenceWarning as ConvergenceWarning
 from ..utils._param_validation import Hidden as Hidden, Interval as Interval, StrOptions as StrOptions
-from ..utils.fixes import parse_version as parse_version, sp_version as sp_version
 from ._base import LinearModel
 
 QuantileRegressor_Self = TypeVar("QuantileRegressor_Self", bound="QuantileRegressor")

stubs/sklearn/manifold/_spectral_embedding.pyi

@@ -15,7 +15,6 @@ from ..metrics.pairwise import rbf_kernel as rbf_kernel
 from ..neighbors import NearestNeighbors as NearestNeighbors, kneighbors_graph as kneighbors_graph
 from ..utils import check_array as check_array, check_random_state as check_random_state, check_symmetric as check_symmetric
 from ..utils._param_validation import Interval as Interval, StrOptions as StrOptions
-from ..utils.fixes import lobpcg
 
 SpectralEmbedding_Self = TypeVar("SpectralEmbedding_Self", bound="SpectralEmbedding")
 

stubs/sklearn/metrics/pairwise.pyi

@@ -23,7 +23,6 @@ from ..utils import (
     is_scalar_nan as is_scalar_nan,
 )
 from ..utils.extmath import row_norms as row_norms, safe_sparse_dot as safe_sparse_dot
-from ..utils.fixes import parse_version as parse_version, sp_version as sp_version
 from ..utils.parallel import Parallel as Parallel, delayed as delayed
 from ..utils.validation import check_non_negative as check_non_negative
 from ._pairwise_distances_reduction import ArgKmin as ArgKmin

stubs/sklearn/neighbors/_base.pyi

@@ -26,7 +26,6 @@ from ..metrics._pairwise_distances_reduction import ArgKmin as ArgKmin, RadiusNe
 from ..metrics.pairwise import PAIRWISE_DISTANCE_FUNCTIONS as PAIRWISE_DISTANCE_FUNCTIONS
 from ..utils import check_array as check_array, gen_even_slices as gen_even_slices
 from ..utils._param_validation import Interval as Interval, StrOptions as StrOptions
-from ..utils.fixes import parse_version as parse_version, sp_version as sp_version
 from ..utils.multiclass import check_classification_targets as check_classification_targets
 from ..utils.parallel import Parallel as Parallel, delayed as delayed
 from ..utils.validation import check_is_fitted as check_is_fitted, check_non_negative as check_non_negative

stubs/sklearn/utils/__init__.pyi

@@ -17,12 +17,12 @@ from scipy.sparse import issparse as issparse
 from .. import get_config as get_config
 from .._typing import ArrayLike, Int, MatrixLike
 from ..exceptions import DataConversionWarning as DataConversionWarning
+from . import metadata_routing
 from ._bunch import Bunch as Bunch
 from ._estimator_html_repr import estimator_html_repr as estimator_html_repr
 from .class_weight import compute_class_weight as compute_class_weight, compute_sample_weight as compute_sample_weight
 from .deprecation import deprecated as deprecated
 from .discovery import all_estimators as all_estimators
-from .fixes import parse_version as parse_version, threadpool_info as threadpool_info
 from .murmurhash import murmurhash3_32 as murmurhash3_32
 from .validation import (
     as_float_array as as_float_array,
@@ -59,17 +59,20 @@ __all__ = [
     "check_scalar",
     "indexable",
     "check_symmetric",
-    "indices_to_mask",
     "deprecated",
     "parallel_backend",
     "register_parallel_backend",
     "resample",
     "shuffle",
-    "check_matplotlib_support",
     "all_estimators",
     "DataConversionWarning",
     "estimator_html_repr",
     "Bunch",
+    "metadata_routing",
+    "safe_sqr",
+    "safe_mask",
+    "gen_batches",
+    "gen_even_slices",
 ]
 
 IS_PYPY = ...

stubs/sklearn/utils/_show_versions.pyi

@@ -1,8 +1,6 @@
 import platform
 import sys
 
-from ..utils.fixes import threadpool_info as threadpool_info
-
 # License: BSD 3 clause
 
 def show_versions(): ...

stubs/sklearn/utils/_testing.pyi

@@ -51,7 +51,6 @@ from numpy.testing import (
 from .._typing import ArrayLike, Float, Int, MatrixLike
 from ..metrics import accuracy_score as accuracy_score, r2_score as r2_score
 from . import IS_PYPY as IS_PYPY
-from .fixes import threadpool_info as threadpool_info
 from .multiclass import check_classification_targets as check_classification_targets
 from .validation import check_array as check_array, check_is_fitted as check_is_fitted, check_X_y as check_X_y
 
@@ -64,7 +63,8 @@ __all__ = [
     "assert_array_less",
     "assert_approx_equal",
     "assert_allclose",
-    "assert_run_python_script",
+    "assert_run_python_script_without_output",
+    "assert_no_warnings",
     "SkipTest",
 ]
 
@@ -116,6 +116,7 @@ class TempMemmap:
     def __exit__(self, exc_type, exc_val, exc_tb): ...
 
 def create_memmap_backed_data(data, mmap_mode: str = "r", return_folder: bool = False, aligned: bool = False): ...
+def assert_run_python_script_without_output(source_code, pattern=".+", timeout=60) -> None: ...
 def check_docstring_parameters(func: Callable, doc: None | str = None, ignore: Sequence | None = None) -> ndarray: ...
 def assert_run_python_script(source_code: str, timeout: Int = 60): ...
 def raises(

stubs/sklearn/utils/estimator_checks.pyi

@@ -56,7 +56,6 @@ from ..utils._param_validation import (
     generate_invalid_param_val as generate_invalid_param_val,
     make_constraint as make_constraint,
 )
-from ..utils.fixes import parse_version as parse_version, sp_version as sp_version
 from ..utils.validation import check_is_fitted as check_is_fitted
 from . import IS_PYPY as IS_PYPY, is_scalar_nan as is_scalar_nan, shuffle as shuffle
 from ._param_validation import Interval as Interval

stubs/sklearn/utils/fixes.pyi

@@ -1,43 +1,23 @@
-import sys
-from importlib import resources as resources
-from typing import Literal, Mapping
-
-import numpy as np
-import scipy
-import scipy.stats
-import sklearn
-import threadpoolctl
-from numpy import percentile as percentile
-from scipy.linalg import eigh as _eigh
-from scipy.optimize._linesearch import (  # explicitly re-exported
-    line_search_wolfe1 as line_search_wolfe1,
-    line_search_wolfe2 as line_search_wolfe2,
-)
-from threadpoolctl import _ThreadpoolLimiter
-
-from ..externals._lobpcg import lobpcg as lobpcg
-from ..externals._packaging.version import parse as parse_version
-from .deprecation import deprecated
-from .parallel import delayed
+# Version-based re-exports
+from numpy.exceptions import ComplexWarning as ComplexWarning, VisibleDeprecationWarning as VisibleDeprecationWarning
+from scipy.integrate import trapezoid as trapezoid
+from scipy.optimize._linesearch import line_search_wolfe1 as line_search_wolfe1, line_search_wolfe2 as line_search_wolfe2
+from scipy.sparse.csgraph import laplacian as laplacian
 
 np_version = ...
+np_base_version = ...
 sp_version = ...
+sp_base_version = ...
+CSR_CONTAINERS = ...
+CSC_CONTAINERS = ...
+COO_CONTAINERS = ...
+LIL_CONTAINERS = ...
+DOK_CONTAINERS = ...
+BSR_CONTAINERS = ...
+DIA_CONTAINERS = ...
+SPARRAY_PRESENT: bool
+SPARSE_ARRAY_PRESENT: bool
+percentile = ...
 
-class loguniform(scipy.stats.reciprocal): ...
-
-def threadpool_limits(
-    limits: None | Mapping | str | int = None,
-    user_api: None | Literal["blas", "openmp"] = None,
-) -> _ThreadpoolLimiter: ...
-
-threadpool_limits.__doc__ = ...
-
-def threadpool_info() -> list[dict[str, int | str] | dict[str, str | None | int]]: ...
-
-threadpool_info.__doc__ = ...
-
-@deprecated(
-    "The function `delayed` has been moved from `sklearn.utils.fixes` to "
-    "`sklearn.utils.parallel`. This import path will be removed in 1.5."
-)
-def delayed(function): ...
+def pd_fillna(pd, frame): ...
+def tarfile_extractall(tarfile, path) -> None: ...

stubs/sympy-stubs/core/__init__.pyi

@@ -28,7 +28,7 @@ from sympy.core.function import (
     expand_trig,
     nfloat,
 )
-from sympy.core.intfunc import integer_log, integer_nthroot
+from sympy.core.intfunc import integer_log, integer_nthroot, num_digits, trailing
 from sympy.core.kind import BooleanKind, NumberKind, UndefinedKind
 from sympy.core.mod import Mod
 from sympy.core.mul import Mul, prod
@@ -120,6 +120,8 @@ __all__ = [
     "Pow",
     "integer_nthroot",
     "integer_log",
+    "num_digits",
+    "trailing",
     "Mul",
     "prod",
     "Add",

stubs/sympy-stubs/matrices/__init__.pyi

@@ -1,4 +1,3 @@
-from sympy.matrices.common import NonSquareMatrixError, ShapeError
 from sympy.matrices.dense import (
     GramSchmidt,
     MutableDenseMatrix,
@@ -23,6 +22,7 @@ from sympy.matrices.dense import (
     wronskian,
     zeros,
 )
+from sympy.matrices.exceptions import NonSquareMatrixError, ShapeError
 from sympy.matrices.expressions import (
     Adjoint,
     BlockDiagMatrix,

stubs/sympy-stubs/ntheory/factor_.pyi

@@ -14,7 +14,6 @@ def smoothness(n) -> tuple[Literal[1], Literal[1]] | tuple[Any, Any]: ...
 def smoothness_p(
     n, m=..., power=..., visual=...
 ) -> str | dict[Any, Any] | tuple[Any, ...] | tuple[int, list[tuple[Any, tuple[Any, ...]]]] | LiteralString: ...
-def trailing(n) -> int: ...
 def multiplicity(p, n) -> int: ...
 def multiplicity_in_factorial(p, n): ...
 def perfect_power(n, candidates=..., big=..., factor=...): ...
@@ -130,7 +129,6 @@ def mersenne_prime_exponent(
     82589933,
 ]: ...
 def is_perfect(n) -> bool | None: ...
-def is_mersenne_prime(n) -> bool: ...
 def abundance(n): ...
 def is_abundant(n) -> bool: ...
 def is_deficient(n) -> bool: ...

stubs/sympy-stubs/ntheory/primetest.pyi

@@ -4,5 +4,6 @@ def mr(n, bases) -> bool: ...
 def is_lucas_prp(n) -> bool: ...
 def is_strong_lucas_prp(n) -> bool: ...
 def is_extra_strong_lucas_prp(n) -> bool: ...
+def is_mersenne_prime(n) -> bool: ...
 def isprime(n) -> bool: ...
 def is_gaussian_prime(num) -> bool: ...

stubs/sympy-stubs/polys/domains/gmpyintegerring.pyi

@@ -9,7 +9,7 @@ class GMPYIntegerRing(IntegerRing):
     dtype = GMPYInteger
     zero = dtype(0)
     one = dtype(1)
-    tp = type(one)
+    tp: type[dtype]
     alias = ...
     def __init__(self) -> None: ...
     def to_sympy(self, a) -> Integer: ...

stubs/sympy-stubs/polys/domains/gmpyrationalfield.pyi

@@ -9,7 +9,7 @@ class GMPYRationalField(RationalField):
     dtype = GMPYRational
     zero = dtype(0)
     one = dtype(1)
-    tp = type(one)
+    tp: type[dtype]
     alias = ...
     def __init__(self) -> None: ...
     def get_ring(self) -> Any: ...

stubs/sympy-stubs/polys/domains/integerring.pyi

@@ -13,7 +13,7 @@ class IntegerRing(Ring, CharacteristicZero, SimpleDomain):  # type: ignore
     dtype = MPZ
     zero = dtype(0)
     one = dtype(1)
-    tp = type(one)
+    tp: type[dtype]
     is_ZZ = ...
     is_Numerical = ...
     is_PID = ...

stubs/sympy-stubs/polys/domains/rationalfield.pyi

@@ -19,7 +19,7 @@ class RationalField(Field, CharacteristicZero, SimpleDomain):
     dtype = MPQ
     zero = dtype(0)
     one = dtype(1)
-    tp = type(one)
+    tp: type[dtype]
     def __init__(self) -> None: ...
     def get_ring(self) -> Any: ...
     def to_sympy(self, a) -> Rational | Integer: ...

utils/validate_stubs.py

@@ -1,4 +1,5 @@
 #!/bin/python
+from __future__ import annotations
 
 __doc__ = """Validate Stubs.
 
@@ -14,7 +15,6 @@ Options:
   --function=<f>     Restrict to the named function (or method if used with --class).
   --class=<c>        Restrict to the named class.
 """
-from __future__ import annotations
 
 import importlib
 import importlib.machinery