[pre-commit.ci] pre-commit autoupdate

.pre-commit-config.yaml

@@ -18,15 +18,15 @@ repos:
 
 # Ruff linter, replacement for flake8, isort, pydocstyle
 - repo: https://github.com/astral-sh/ruff-pre-commit
-  rev: 'v0.15.12'
+  rev: 'v0.16.3'
   hooks:
     - id: ruff
       args: [--fix, --show-fixes, --exit-non-zero-on-fix]
     - id: ruff-format
 
 # Python type checking
 - repo: https://github.com/pre-commit/mirrors-mypy
-  rev: 'v2.0.0'
+  rev: 'v2.3.1'
   hooks:
   - id: mypy
     args: [--allow-redefinition, --ignore-missing-imports]

src/resample/__init__.py

@@ -19,9 +19,9 @@
 __version__ = version("resample")
 
 __all__ = [
-    "jackknife",
+    "__version__",
     "bootstrap",
-    "permutation",
     "empirical",
-    "__version__",
+    "jackknife",
+    "permutation",
 ]

src/resample/_util.py

@@ -1,13 +1,11 @@
-from typing import Optional, Tuple, Union
-
 import numpy as np
 from numpy.typing import ArrayLike
 
 __all__ = ["normalize_rng", "wilson_score_interval"]
 
 
 def normalize_rng(
-    random_state: Optional[Union[int, np.random.Generator]],
+    random_state: int | np.random.Generator | None,
 ) -> np.random.Generator:
     """Return normalized RNG object."""
     if random_state is None:
@@ -19,7 +17,7 @@ def normalize_rng(
 
 def wilson_score_interval(
     n1: "ArrayLike", n: "ArrayLike", z: float
-) -> Tuple[np.ndarray, Tuple[np.ndarray, np.ndarray]]:
+) -> tuple[np.ndarray, tuple[np.ndarray, np.ndarray]]:
     """Return binomial fraction and Wilson score interval."""
     p = n1 / n
     norm = 1 / (1 + z**2 / n)

src/resample/bootstrap.py

@@ -13,23 +13,17 @@
 """
 
 __all__ = [
-    "resample",
     "bootstrap",
-    "variance",
-    "covariance",
     "confidence_interval",
+    "covariance",
+    "resample",
+    "variance",
 ]
 
+from collections.abc import Callable, Collection, Generator
 from typing import (
     Any,
-    Callable,
-    Collection,
-    Dict,
-    Generator,
-    List,
     Optional,
-    Tuple,
-    Union,
 )
 
 import numpy as np
@@ -47,7 +41,7 @@ def resample(
     size: int = 100,
     method: str = "balanced",
     strata: Optional["ArrayLike"] = None,
-    random_state: Optional[Union[np.random.Generator, int]] = None,
+    random_state: np.random.Generator | int | None = None,
 ) -> Generator[np.ndarray, None, None]:
     """
     Return generator of bootstrap samples.
@@ -147,7 +141,7 @@ def resample(
     """
     sample_np = np.atleast_1d(sample)
     n_sample = len(sample_np)
-    args_np: List[np.ndarray] = []
+    args_np: list[np.ndarray] = []
 
     if args:
         if not isinstance(args[0], Collection):
@@ -158,7 +152,7 @@ def resample(
                 "deprecated",
                 FutureWarning,
             )
-            kwargs: Dict[str, Any] = {
+            kwargs: dict[str, Any] = {
                 "size": size,
                 "method": method,
                 "strata": strata,
@@ -381,7 +375,7 @@ def confidence_interval(
     cl: float = 0.95,
     ci_method: str = "bca",
     **kwargs: Any,
-) -> Tuple[float, float]:
+) -> tuple[float, float]:
     """
     Calculate bootstrap confidence intervals.
 
@@ -491,7 +485,7 @@ def _resample_ordinary_1(
 
 
 def _resample_ordinary_n(
-    samples: List[np.ndarray], size: int, rng: np.random.Generator
+    samples: list[np.ndarray], size: int, rng: np.random.Generator
 ) -> Generator[np.ndarray, None, None]:
     n = len(samples[0])
     indices = np.arange(n)
@@ -513,7 +507,7 @@ def _resample_balanced_1(
 
 
 def _resample_balanced_n(
-    samples: List[np.ndarray], size: int, rng: np.random.Generator
+    samples: list[np.ndarray], size: int, rng: np.random.Generator
 ) -> Generator[np.ndarray, None, None]:
     n = len(samples[0])
     indices = rng.permutation(n * size)
@@ -533,7 +527,7 @@ def _resample_extended_1(
 
 
 def _resample_extended_n(
-    samples: List[np.ndarray], size: int, rng: np.random.Generator
+    samples: list[np.ndarray], size: int, rng: np.random.Generator
 ) -> Generator[np.ndarray, None, None]:
     n = len(samples[0])
     for i in range(size):
@@ -543,7 +537,7 @@ def _resample_extended_n(
 
 def _fit_parametric_family(
     dist: stats.rv_continuous, sample: np.ndarray
-) -> Tuple[float, ...]:
+) -> tuple[float, ...]:
     if dist == stats.multivariate_normal:
         # has no fit method...
         return np.mean(sample, axis=0), np.cov(sample.T, ddof=1)
@@ -579,14 +573,14 @@ def _resample_parametric(
 
 def _confidence_interval_percentile(
     thetas: np.ndarray, alpha_half: float
-) -> Tuple[float, float]:
+) -> tuple[float, float]:
     quant = quantile_function_gen(thetas)
     return quant(alpha_half), quant(1 - alpha_half)
 
 
 def _confidence_interval_bca(
     theta: float, thetas: np.ndarray, j_thetas: np.ndarray, alpha_half: float
-) -> Tuple[float, float]:
+) -> tuple[float, float]:
     norm = stats.norm
 
     # bias correction; implementation notes:

src/resample/empirical.py

@@ -5,9 +5,10 @@
 like the empirical CDF. Implemented here are mostly tools used internally.
 """
 
-__all__ = ["cdf_gen", "quantile_function_gen", "influence"]
+__all__ = ["cdf_gen", "influence", "quantile_function_gen"]
 
-from typing import Callable, Union
+from collections.abc import Callable
+from typing import Union
 
 import numpy as np
 from numpy.typing import ArrayLike
@@ -37,7 +38,7 @@ def cdf_gen(sample: "ArrayLike") -> Callable[[np.ndarray], np.ndarray]:
 
 def quantile_function_gen(
     sample: "ArrayLike",
-) -> Callable[[Union[float, "ArrayLike"]], Union[float, np.ndarray]]:
+) -> Callable[[Union[float, "ArrayLike"]], float | np.ndarray]:
     """
     Return the empirical quantile function for the given sample.
 
@@ -57,7 +58,7 @@ class QuantileFn:
         def __init__(self, sample: "ArrayLike"):
             self._sorted = np.sort(sample, axis=0)
 
-        def __call__(self, p: Union[float, "ArrayLike"]) -> Union[float, np.ndarray]:
+        def __call__(self, p: Union[float, "ArrayLike"]) -> float | np.ndarray:
             ndim = np.ndim(p)  # must come before atleast_1d
             p = np.atleast_1d(p)
             result = np.empty(len(p))

src/resample/jackknife.py

@@ -17,15 +17,16 @@
 """
 
 __all__ = [
-    "resample",
-    "jackknife",
     "bias",
     "bias_corrected",
-    "variance",
     "cross_validation",
+    "jackknife",
+    "resample",
+    "variance",
 ]
 
-from typing import Any, Callable, Collection, Generator, List
+from collections.abc import Callable, Collection, Generator
+from typing import Any
 
 import numpy as np
 from numpy.typing import ArrayLike
@@ -136,7 +137,7 @@ def _resample_1(sample: np.ndarray, copy: bool) -> Generator[np.ndarray, None, N
         yield x.copy() if copy else x
 
 
-def _resample_n(samples: List[np.ndarray], copy: bool) -> Generator[Any, None, None]:
+def _resample_n(samples: list[np.ndarray], copy: bool) -> Generator[Any, None, None]:
     x = [a[1:].copy() for a in samples]
     yield (xi.copy() for xi in x)
     for i in range(len(samples[0]) - 1):
@@ -363,5 +364,5 @@ def cross_validation(
     deltas = []
     for i, (x_in, y_in) in enumerate(resample(x, y, copy=False)):
         yip = predict(x_in, y_in, x[i], *args)
-        deltas.append((y[i] - yip))
+        deltas.append(y[i] - yip)
     return np.var(deltas)  # type:ignore

src/resample/permutation.py

@@ -23,19 +23,20 @@
 
 __all__ = [
     "TestResult",
-    "usp",
-    "same_population",
     "anova",
     "kruskal",
     "pearsonr",
+    "same_population",
     "spearmanr",
     "ttest",
+    "usp",
 ]
 
 import sys
 import warnings
+from collections.abc import Callable
 from dataclasses import dataclass
-from typing import Any, Callable, Optional, Tuple, Union
+from typing import Any
 
 import numpy as np
 from numpy.typing import ArrayLike, NDArray
@@ -89,7 +90,7 @@ def __len__(self) -> int:
         """Return length of tuple."""
         return 3
 
-    def __getitem__(self, idx: int) -> Union[float, NDArray]:
+    def __getitem__(self, idx: int) -> float | NDArray:
         """Return fields by index."""
         if idx == 0:
             return self.statistic
@@ -105,7 +106,7 @@ def usp(
     *,
     size: int = 9999,
     method: str = "auto",
-    random_state: Optional[Union[np.random.Generator, int]] = None,
+    random_state: np.random.Generator | int | None = None,
 ) -> TestResult:
     """
     Test independence of two discrete data sets with the U-statistic.
@@ -198,9 +199,9 @@ def same_population(
     x: "ArrayLike",
     y: "ArrayLike",
     *args: "ArrayLike",
-    transform: Optional[Callable[[NDArray], NDArray]] = None,
+    transform: Callable[[NDArray], NDArray] | None = None,
     size: int = 9999,
-    random_state: Optional[Union[np.random.Generator, int]] = None,
+    random_state: np.random.Generator | int | None = None,
 ) -> TestResult:
     """
     Compute p-value for hypothesis that samples originate from same population.
@@ -511,7 +512,7 @@ def __call__(self, *args: NDArray) -> float:
         )
         return between_group_variability / within_group_variability
 
-    def _init(self, args: Tuple[NDArray, ...]) -> None:
+    def _init(self, args: tuple[NDArray, ...]) -> None:
         n = sum(len(a) for a in args)
         k = len(args)
         self.km1 = k - 1