Build and lint updates

- Use ruff, move configuration for some things to pyproject.toml.
- Update namespace configuration.
- Deprecate py36 support, add tests for py310, py311.
- Add numba tests for py310, py311.
- Update pre-commit, add ruff.

.coveragerc

@@ -13,8 +13,7 @@ source =
 [report]
 show_missing = true
 precision = 2
-exclude_lines = 
+exclude_lines =
     pragma: no cover
     @overload
     @njit
-

.github/workflows/python-package.yml

@@ -13,14 +13,14 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest, windows-latest, macos-latest]
-        python-version: [3.6, 3.7, 3.8, 3.9, "3.10", pypy3]
+        python-version: [3.7, 3.8, 3.9, "3.10", "3.11", pypy3]
         optionals: [none, pandas, numba]
         exclude:
           - python-version: pypy3
             optionals: pandas
           - python-version: pypy3
             optionals: numba
-          - python-version: "3.10"
+          - python-version: "3.11"
             optionals: numba
           - os: macos-latest
             python-version: pypy3

.gitignore

@@ -16,6 +16,10 @@ develop-eggs
 # Installer logs
 pip-log.txt
 
+
+*~
+\#*\#
+
 # Unit test / coverage reports
 .coverage
 .tox

.pre-commit-config.yaml

@@ -2,7 +2,7 @@
 # See https://pre-commit.com/hooks.html for more hooks
 repos:
 -   repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v3.2.0
+    rev: v4.4.0
     hooks:
     -   id: trailing-whitespace
     -   id: end-of-file-fixer
@@ -15,6 +15,6 @@ repos:
     - id: ruff
       args: [ --fix, --exit-non-zero-on-fix ]
 -   repo: https://github.com/psf/black
-    rev: 21.5b2
+    rev: 23.7.0
     hooks:
     -   id: black

pyproject.toml

@@ -0,0 +1,15 @@
+[build-system]
+requires = ["setuptools>=56", "setuptools_scm[toml]>=3.4.1"]
+build-backend = "setuptools.build_meta"
+
+[tool.ruff]
+line-length = 120
+ignore = ["F405", "F403"]
+
+[tool.mypy]
+ignore_missing_imports = true
+warn_unused_configs = true
+warn_return_any = true
+
+[tool.black]
+line-length = 88

requirements.txt

@@ -1,4 +1,3 @@
 numpy
 pyerf
 typing_extensions>=4.1
-

src/scikits/bootstrap/bootstrap.py

@@ -2,7 +2,7 @@
 
 It also provides an algorithm which estimates the probability that the statistics
 lies satisfies some criteria, e.g. lies in some interval."""
-from __future__ import absolute_import, division, print_function
+from __future__ import absolute_import, division, print_function, annotations
 
 from math import ceil, sqrt
 from typing import Sequence, cast, overload
@@ -454,9 +454,7 @@ def ci(
         if nvals.ndim == 1:
             out = np.abs(statfunction(*tdata) - stat[nvals])[np.newaxis].T  # type: ignore
         else:
-            out = np.abs(
-                statfunction(*tdata) - stat[(nvals, np.indices(nvals.shape)[1:])]  # type: ignore
-            ).T.squeeze()
+            out = np.abs(statfunction(*tdata) - stat[(nvals, np.indices(nvals.shape)[1:])]).T.squeeze()  # type: ignore
     else:
         raise ValueError("Output option {0} is not supported.".format(output))
 
@@ -498,17 +496,17 @@ def _ci_abc(
         (statfunction(*tdata, weights=p0 - ep * di) for di in di_full), dtype=float
     )
     t1 = (tp - tm) / (2 * ep)
-    t2 = (tp - 2 * t0 + tm) / ep ** 2
+    t2 = (tp - 2 * t0 + tm) / ep**2
 
-    sighat = np.sqrt(np.sum(t1 ** 2)) / n
-    a = (np.sum(t1 ** 3)) / (6 * n ** 3 * sighat ** 3)
-    delta = t1 / (n ** 2 * sighat)
+    sighat = np.sqrt(np.sum(t1**2)) / n
+    a = (np.sum(t1**3)) / (6 * n**3 * sighat**3)
+    delta = t1 / (n**2 * sighat)
     cq = (
         statfunction(*tdata, weights=p0 + ep * delta)
         - 2 * t0
         + statfunction(*tdata, weights=p0 - ep * delta)
-    ) / (2 * sighat * ep ** 2)
-    bhat = np.sum(t2) / (2 * n ** 2)
+    ) / (2 * sighat * ep**2)
+    bhat = np.sum(t2) / (2 * n**2)
     curv = bhat / sighat - cq
     z0 = nppf(2 * ncdf(a) * ncdf(-curv))
     Z = z0 + nppf(alphas)

tests/bootstrap_test.py

@@ -16,7 +16,7 @@
 
 
 class TestCI:
-    def setup(self) -> None:
+    def setup_method(self) -> None:
         self.data = np.array(
             [
                 1.34016346,
@@ -124,7 +124,7 @@ def test_subsample_indices_fixed(self) -> None:
 
     def test_subsample_size_too_large(self) -> None:
         with pytest.raises(ValueError):
-            indices = boot.subsample_indices(self.data, 1000, 30)
+            boot.subsample_indices(self.data, 1000, 30)
 
     def test_subsample_indices_notsame(self) -> None:
         indices = boot.subsample_indices(np.arange(0, 50), 1000, -1)

tox.ini

@@ -1,12 +1,12 @@
 [tox]
-envlist = {py36,py37,py38,py39}-{pandas,none,numba,pandas-numba},pypy3,black,mypy,report
+envlist = {py37,py38,py39,py310,py311}-{pandas,none,numba,pandas-numba},pypy3,black,mypy,report
 
 [tool:pytest]
 testpath = tests
 
 [testenv]
 setenv =
-    py{,36,37,38,39}-{pandas,none,numba},pypy3: COVERAGE_FILE = .coverage.{envname}
+    py{37,38,39,310,311}-{pandas,none,numba},pypy3: COVERAGE_FILE = .coverage.{envname}
 commands =
     pytest --cov --cov-report=xml --cov-report=term-missing {posargs:-vv}
 deps =
@@ -17,9 +17,9 @@ deps =
     !pypy3-pandas: pandas
     !pypy3-numba: numba
 depends =
-    {,py36,py37,py38,py39}-{pandas,none,numba,pandas-numba},pypy3: clean
-    codecov: {,py36,py37,py38,py39}-{pandas,none,numba,pandas-numba},pypy3
-    report: {,py36,py37,py38,py39}-{pandas,none,numba,pandas-numba},pypy3
+    {py37,py38,py39,py311}-{pandas,none,numba,pandas-numba},pypy3: clean
+    codecov: {py37,py38,py39,py311}-{pandas,none,numba,pandas-numba},pypy3
+    report: {py37,py38,py39,py311}-{pandas,none,numba,pandas-numba},pypy3
 
 [testenv:black]
 description = run black with check-only under {basepython}