nipy · effigies · Apr 14, 2024 · Dec 26, 2023 · Dec 26, 2023 · Mar 5, 2024
diff --git a/.flake8 b/.flake8
diff --git a/.pep8speaks.yml b/.pep8speaks.yml
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -12,19 +12,14 @@ repos:
       - id: check-case-conflict
       - id: check-merge-conflict
       - id: check-vcs-permalinks
-  - repo: https://github.com/grantjenks/blue
-    rev: v0.9.1
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.3.4
     hooks:
-      - id: blue
-  - repo: https://github.com/pycqa/isort
-    rev: 5.12.0
-    hooks:
-      - id: isort
-  - repo: https://github.com/pycqa/flake8
-    rev: 6.1.0
-    hooks:
-      - id: flake8
-        exclude: "^(doc|nisext|tools)/"
+      - id: ruff
+        args: [--fix, --show-fix, --exit-non-zero-on-fix]
+        exclude: = ["doc", "tools"]
+      - id: ruff-format
+        exclude: = ["doc", "tools"]
   - repo: https://github.com/pre-commit/mirrors-mypy
     rev: v1.5.1
     hooks:

diff --git a/doc/source/conf.py b/doc/source/conf.py
@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 # emacs: -*- mode: python-mode; py-indent-offset: 4; indent-tabs-mode: nil -*-
 # vi: set ft=python sts=4 ts=4 sw=4 et:
 ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##

diff --git a/doc/tools/apigen.py b/doc/tools/apigen.py
@@ -405,10 +405,7 @@ def discover_modules(self):
 
     def write_modules_api(self, modules, outdir):
         # upper-level modules
-        main_module = modules[0].split('.')[0]
-        ulms = [
-            '.'.join(m.split('.')[:2]) if m.count('.') >= 1 else m.split('.')[0] for m in modules
-        ]
+        ulms = ['.'.join(m.split('.')[:2]) for m in modules]
 
         from collections import OrderedDict
 

diff --git a/doc/tools/build_modref_templates.py b/doc/tools/build_modref_templates.py
@@ -38,7 +38,7 @@ def abort(error):
 
     try:
         __import__(package)
-    except ImportError as e:
+    except ImportError:
         abort('Can not import ' + package)
 
     module = sys.modules[package]

diff --git a/nibabel/__init__.py b/nibabel/__init__.py
@@ -39,12 +39,10 @@
 
 # module imports
 from . import analyze as ana
-from . import ecat, imagestats, mriutils
+from . import ecat, imagestats, mriutils, orientations, streamlines, viewers
 from . import nifti1 as ni1
-from . import orientations
 from . import spm2analyze as spm2
 from . import spm99analyze as spm99
-from . import streamlines, viewers
 
 # isort: split
 

diff --git a/nibabel/_compression.py b/nibabel/_compression.py
@@ -7,6 +7,7 @@
 #
 ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##
 """Constants and types for dealing transparently with compression"""
+
 from __future__ import annotations
 
 import bz2

diff --git a/nibabel/affines.py b/nibabel/affines.py
@@ -1,6 +1,7 @@
 # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
 # vi: set ft=python sts=4 ts=4 sw=4 et:
 """Utility routines for working with points and affine transforms"""
+
 from functools import reduce
 
 import numpy as np

diff --git a/nibabel/analyze.py b/nibabel/analyze.py
@@ -81,6 +81,7 @@
 can be loaded with and without a default flip, so the saved zoom will not
 constrain the affine.
 """
+
 from __future__ import annotations
 
 import numpy as np

diff --git a/nibabel/arrayproxy.py b/nibabel/arrayproxy.py
@@ -25,6 +25,7 @@
 
 See :mod:`nibabel.tests.test_proxy_api` for proxy API conformance checks.
 """
+
 from __future__ import annotations
 
 import typing as ty
@@ -74,21 +75,19 @@ class ArrayLike(ty.Protocol):
     shape: tuple[int, ...]
 
     @property
-    def ndim(self) -> int:
-        ...  # pragma: no cover
+    def ndim(self) -> int: ...  # pragma: no cover
 
     # If no dtype is passed, any dtype might be returned, depending on the array-like
     @ty.overload
-    def __array__(self, dtype: None = ..., /) -> np.ndarray[ty.Any, np.dtype[ty.Any]]:
-        ...  # pragma: no cover
+    def __array__(
+        self, dtype: None = ..., /
+    ) -> np.ndarray[ty.Any, np.dtype[ty.Any]]: ...  # pragma: no cover
 
     # Any dtype might be passed, and *that* dtype must be returned
     @ty.overload
-    def __array__(self, dtype: _DType, /) -> np.ndarray[ty.Any, _DType]:
-        ...  # pragma: no cover
+    def __array__(self, dtype: _DType, /) -> np.ndarray[ty.Any, _DType]: ...  # pragma: no cover
 
-    def __getitem__(self, key, /) -> npt.NDArray:
-        ...  # pragma: no cover
+    def __getitem__(self, key, /) -> npt.NDArray: ...  # pragma: no cover
 
 
 class ArrayProxy(ArrayLike):

diff --git a/nibabel/arraywriters.py b/nibabel/arraywriters.py
@@ -28,6 +28,7 @@ def __init__(self, array, out_dtype=None)
 something else to make sense of conversions between float and int, or between
 larger ints and smaller.
 """
+
 import numpy as np
 
 from .casting import best_float, floor_exact, int_abs, shared_range, type_info

diff --git a/nibabel/benchmarks/bench_arrayproxy_slicing.py b/nibabel/benchmarks/bench_arrayproxy_slicing.py
@@ -56,7 +56,6 @@
 
 
 def bench_arrayproxy_slicing():
-
     print_git_title('\nArrayProxy gzip slicing')
 
     # each test is a tuple containing
@@ -100,7 +99,6 @@ def fmt_sliceobj(sliceobj):
         return f"[{', '.join(slcstr)}]"
 
     with InTemporaryDirectory():
-
         print(f'Generating test data... ({int(round(np.prod(SHAPE) * 4 / 1048576.0))} MB)')
 
         data = np.array(np.random.random(SHAPE), dtype=np.float32)
@@ -128,7 +126,6 @@ def fmt_sliceobj(sliceobj):
         seeds = [np.random.randint(0, 2**32) for s in SLICEOBJS]
 
         for ti, test in enumerate(tests):
-
             label = get_test_label(test)
             have_igzip, keep_open, sliceobj = test
             seed = seeds[SLICEOBJS.index(sliceobj)]

diff --git a/nibabel/benchmarks/butils.py b/nibabel/benchmarks/butils.py
@@ -1,5 +1,4 @@
-"""Benchmarking utilities
-"""
+"""Benchmarking utilities"""
 
 from .. import get_info
 

diff --git a/nibabel/brikhead.py b/nibabel/brikhead.py
@@ -26,6 +26,7 @@
 am aware) always be >= 1. This permits sub-brick indexing common in AFNI
 programs (e.g., example4d+orig'[0]').
 """
+
 import os
 import re
 from copy import deepcopy

diff --git a/nibabel/casting.py b/nibabel/casting.py
@@ -3,6 +3,7 @@
 Most routines work round some numpy oddities in floating point precision and
 casting.  Others work round numpy casting to and from python ints
 """
+
 from __future__ import annotations
 
 import warnings

diff --git a/nibabel/cifti2/cifti2.py b/nibabel/cifti2/cifti2.py
@@ -16,6 +16,7 @@
 
     http://www.nitrc.org/projects/cifti
 """
+
 import re
 from collections import OrderedDict
 from collections.abc import Iterable, MutableMapping, MutableSequence

diff --git a/nibabel/cifti2/cifti2_axes.py b/nibabel/cifti2/cifti2_axes.py
@@ -118,6 +118,7 @@
 ...                                     bm_cortex)))
 <class 'nibabel.cifti2.cifti2.Cifti2Header'>
 """
+
 import abc
 from operator import xor
 

diff --git a/nibabel/cifti2/tests/test_cifti2.py b/nibabel/cifti2/tests/test_cifti2.py
@@ -1,13 +1,13 @@
-"""Testing CIFTI-2 objects
-"""
+"""Testing CIFTI-2 objects"""
+
 import collections
 from xml.etree import ElementTree
 
 import numpy as np
 import pytest
 
 from nibabel import cifti2 as ci
-from nibabel.cifti2.cifti2 import Cifti2HeaderError, _float_01, _value_if_klass
+from nibabel.cifti2.cifti2 import _float_01, _value_if_klass
 from nibabel.nifti2 import Nifti2Header
 from nibabel.tests.test_dataobj_images import TestDataobjAPI as _TDA
 from nibabel.tests.test_image_api import DtypeOverrideMixin, SerializeMixin

diff --git a/nibabel/cifti2/tests/test_cifti2io_header.py b/nibabel/cifti2/tests/test_cifti2io_header.py
@@ -7,7 +7,6 @@
 #
 ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##
 
-import io
 from os.path import dirname
 from os.path import join as pjoin
 
@@ -38,7 +37,7 @@
 
 
 def test_space_separated_affine():
-    img = ci.Cifti2Image.from_filename(pjoin(NIBABEL_TEST_DATA, 'row_major.dconn.nii'))
+    ci.Cifti2Image.from_filename(pjoin(NIBABEL_TEST_DATA, 'row_major.dconn.nii'))
 
 
 def test_read_nifti2():

diff --git a/nibabel/cifti2/tests/test_new_cifti2.py b/nibabel/cifti2/tests/test_new_cifti2.py
@@ -6,6 +6,7 @@
 These functions are used in the tests to generate most CIFTI file types from
 scratch.
 """
+
 import numpy as np
 import pytest
 

diff --git a/nibabel/cmdline/__init__.py b/nibabel/cmdline/__init__.py
@@ -6,5 +6,4 @@
 #   copyright and license terms.
 #
 ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##
-"""Functionality to be exposed in the command line
-"""
+"""Functionality to be exposed in the command line"""
diff --git a/nibabel/cmdline/diff.py b/nibabel/cmdline/diff.py
@@ -231,7 +231,6 @@ def get_data_diff(files, max_abs=0, max_rel=0, dtype=np.float64):
         diffs1 = [None] * (i + 1)
 
         for j, d2 in enumerate(data[i + 1 :], i + 1):
-
             if d1.shape == d2.shape:
                 abs_diff = np.abs(d1 - d2)
                 mean_abs = (np.abs(d1) + np.abs(d2)) * 0.5
@@ -247,15 +246,14 @@ def get_data_diff(files, max_abs=0, max_rel=0, dtype=np.float64):
                         sub_thr = rel_diff <= max_rel
                         # Since we operated on sub-selected values already, we need
                         # to plug them back in
-                        candidates[
-                            tuple(indexes[sub_thr] for indexes in np.where(candidates))
-                        ] = False
+                        candidates[tuple(indexes[sub_thr] for indexes in np.where(candidates))] = (
+                            False
+                        )
                     max_rel_diff = np.max(rel_diff)
                 else:
                     max_rel_diff = 0
 
                 if np.any(candidates):
-
                     diff_rec = OrderedDict()  # so that abs goes before relative
 
                     diff_rec['abs'] = max_abs_diff.astype(dtype)
@@ -268,7 +266,6 @@ def get_data_diff(files, max_abs=0, max_rel=0, dtype=np.float64):
                 diffs1.append({'CMP': 'incompat'})
 
         if any(diffs1):
-
             diffs['DATA(diff %d:)' % (i + 1)] = diffs1
 
     return diffs

diff --git a/nibabel/cmdline/parrec2nii.py b/nibabel/cmdline/parrec2nii.py
@@ -1,5 +1,4 @@
-"""Code for PAR/REC to NIfTI converter command
-"""
+"""Code for PAR/REC to NIfTI converter command"""
 
 import csv
 import os

diff --git a/nibabel/cmdline/tck2trk.py b/nibabel/cmdline/tck2trk.py
@@ -1,6 +1,7 @@
 """
 Convert tractograms (TCK -> TRK).
 """
+
 import argparse
 import os
 

diff --git a/nibabel/cmdline/tests/test_convert.py b/nibabel/cmdline/tests/test_convert.py
@@ -119,7 +119,7 @@ def test_convert_imgtype(tmp_path, ext, img_class):
 
 def test_convert_nifti_int_fail(tmp_path):
     infile = get_test_data(fname='anatomical.nii')
-    outfile = tmp_path / f'output.nii'
+    outfile = tmp_path / 'output.nii'
 
     orig = nib.load(infile)
     assert not outfile.exists()

@@ -1,5 +1,5 @@
-"""Tests for the parrec2nii exe code
-"""
+"""Tests for the parrec2nii exe code"""
+
 from os.path import basename, isfile, join
 from unittest.mock import MagicMock, Mock, patch
 

@@ -1,5 +1,4 @@
 import os
-import unittest
 from unittest import mock
 
 import numpy as np
@@ -140,7 +139,7 @@ def test_entrypoint(capsys):
     # Check that we handle missing args as expected
     with mock.patch('sys.argv', ['nib-roi', '--help']):
         try:
-            retval = main()
+            main()
         except SystemExit:
             pass
         else:

@@ -8,9 +8,6 @@
 #
 ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##
 
-import sys
-from io import StringIO
-
 import numpy as np
 
 from nibabel import Nifti1Image

@@ -12,8 +12,18 @@
 import pytest
 
 import nibabel as nib
-from nibabel.cmdline.diff import *
-from nibabel.cmdline.utils import *
+from nibabel.cmdline.diff import (
+    display_diff,
+    get_data_diff,
+    get_data_hash_diff,
+    get_headers_diff,
+    main,
+)
+from nibabel.cmdline.utils import (
+    ap,
+    safe_get,
+    table2string,
+)
 from nibabel.testing import data_path
 
 

@@ -10,7 +10,6 @@
 Helper utilities to be used in cmdline applications
 """
 
-
 # global verbosity switch
 import re
 from io import StringIO

@@ -5,7 +5,7 @@
 
 # Ignore warning requesting help with nicom
 with pytest.warns(UserWarning):
-    import nibabel.nicom
+    import nibabel.nicom  # noqa :401
 
 
 @pytest.fixture(scope='session', autouse=True)