MNT: Bump ruff version

.pre-commit-config.yaml

@@ -13,7 +13,7 @@ repos:
       - id: check-merge-conflict
       - id: check-vcs-permalinks
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.1.9
+    rev: v0.3.0
     hooks:
       - id: ruff
         args: [--fix, --show-fix, --exit-non-zero-on-fix]

nibabel/_compression.py

@@ -7,6 +7,7 @@
 #
 ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##
 """Constants and types for dealing transparently with compression"""
+
 from __future__ import annotations
 
 import bz2

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

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

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):

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

nibabel/benchmarks/butils.py

@@ -1,5 +1,4 @@
-"""Benchmarking utilities
-"""
+"""Benchmarking utilities"""
 
 from .. import get_info
 

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

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

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

nibabel/cifti2/cifti2_axes.py

@@ -118,6 +118,7 @@
 ...                                     bm_cortex)))
 <class 'nibabel.cifti2.cifti2.Cifti2Header'>
 """
+
 import abc
 from operator import xor
 

nibabel/cifti2/tests/test_cifti2.py

@@ -1,5 +1,5 @@
-"""Testing CIFTI-2 objects
-"""
+"""Testing CIFTI-2 objects"""
+
 import collections
 from xml.etree import ElementTree
 

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
 

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"""

nibabel/cmdline/diff.py

@@ -246,9 +246,9 @@ 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

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

nibabel/cmdline/tck2trk.py

@@ -1,6 +1,7 @@
 """
 Convert tractograms (TCK -> TRK).
 """
+
 import argparse
 import os
 

nibabel/cmdline/tests/test_parrec2nii.py

@@ -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
 

nibabel/cmdline/utils.py

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

nibabel/data.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:
 """Utilities to find files from NIPY data packages"""
+
 import configparser
 import glob
 import os

nibabel/dataobj_images.py

@@ -7,6 +7,7 @@
 * returns an array from ``numpy.asanyarray(obj)``;
 * has an attribute or property ``shape``.
 """
+
 from __future__ import annotations
 
 import typing as ty

nibabel/deprecated.py

@@ -1,4 +1,5 @@
 """Module to help with deprecating objects and classes"""
+
 from __future__ import annotations
 
 import typing as ty

nibabel/deprecator.py

@@ -1,4 +1,5 @@
 """Class for recording and reporting deprecations"""
+
 from __future__ import annotations
 
 import functools

nibabel/dft.py

@@ -9,7 +9,6 @@
 # Copyright (C) 2011 Christian Haselgrove
 """DICOM filesystem tools"""
 
-
 import contextlib
 import getpass
 import logging
@@ -44,7 +43,6 @@ class VolumeError(DFTError):
 
 
 class InstanceStackError(DFTError):
-
     """bad series of instance numbers"""
 
     def __init__(self, series, i, si):

nibabel/ecat.py

@@ -42,6 +42,7 @@
 GPL and some of the header files are adapted from CTI files (called CTI code
 below).  It's not clear what the licenses are for these files.
 """
+
 import warnings
 from numbers import Integral
 

nibabel/environment.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:
 """Settings from the system environment relevant to NIPY"""
+
 import os
 from os.path import join as pjoin
 

nibabel/eulerangles.py

@@ -82,6 +82,7 @@
 ``y``, followed by rotation around ``x``, is known (confusingly) as
 "xyz", pitch-roll-yaw, Cardan angles, or Tait-Bryan angles.
 """
+
 import math
 from functools import reduce
 

nibabel/filebasedimages.py

@@ -7,6 +7,7 @@
 #
 ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##
 """Common interface for any image format--volume or surface, binary or xml"""
+
 from __future__ import annotations
 
 import io

nibabel/fileholders.py

@@ -7,6 +7,7 @@
 #
 ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##
 """Fileholder class"""
+
 from __future__ import annotations
 
 import io

nibabel/filename_parser.py

@@ -7,6 +7,7 @@
 #
 ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##
 """Create filename pairs, triplets etc, with expected extensions"""
+
 from __future__ import annotations
 
 import os

nibabel/fileslice.py

@@ -1,4 +1,5 @@
 """Utilities for getting array slices out of file-like objects"""
+
 import operator
 from functools import reduce
 from mmap import mmap

nibabel/freesurfer/__init__.py

@@ -1,5 +1,4 @@
-"""Reading functions for freesurfer files
-"""
+"""Reading functions for freesurfer files"""
 
 # ruff: noqa: F401
 

nibabel/freesurfer/io.py

@@ -1,5 +1,4 @@
-"""Read / write FreeSurfer geometry, morphometry, label, annotation formats
-"""
+"""Read / write FreeSurfer geometry, morphometry, label, annotation formats"""
 
 import getpass
 import time

nibabel/freesurfer/mghformat.py

@@ -10,6 +10,7 @@
 
 Author: Krish Subramaniam
 """
+
 from os.path import splitext
 
 import numpy as np

nibabel/funcs.py

@@ -7,6 +7,7 @@
 #
 ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##
 """Processor functions for images"""
+
 import numpy as np
 
 from .loadsave import load

nibabel/gifti/gifti.py

@@ -11,6 +11,7 @@
 The Gifti specification was (at time of writing) available as a PDF download
 from http://www.nitrc.org/projects/gifti/
 """
+
 from __future__ import annotations
 
 import base64

nibabel/gifti/tests/test_gifti.py

@@ -1,5 +1,5 @@
-"""Testing gifti objects
-"""
+"""Testing gifti objects"""
+
 import itertools
 import sys
 from io import BytesIO

nibabel/imageclasses.py

@@ -7,6 +7,7 @@
 #
 ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##
 """Define supported image classes and names"""
+
 from __future__ import annotations
 
 from .analyze import AnalyzeImage

nibabel/imageglobals.py

@@ -23,6 +23,7 @@
 
 Use ``logger.level = 1`` to see all messages.
 """
+
 import logging
 
 error_level = 40

nibabel/imagestats.py

@@ -7,6 +7,7 @@
 #
 ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##
 """Functions for computing image statistics"""
+
 import numpy as np
 
 from nibabel.imageclasses import spatial_axes_first

nibabel/loadsave.py

@@ -8,6 +8,7 @@
 ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##
 # module imports
 """Utilities to load and save image objects"""
+
 from __future__ import annotations
 
 import os

nibabel/minc1.py

@@ -7,6 +7,7 @@
 #
 ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##
 """Read MINC1 format images"""
+
 from __future__ import annotations
 
 from numbers import Integral

nibabel/minc2.py

@@ -25,6 +25,7 @@
 
     mincstats my_funny.mnc
 """
+
 import warnings
 
 import numpy as np

nibabel/nicom/__init__.py

@@ -19,6 +19,7 @@
    dwiparams
    structreader
 """
+
 import warnings
 
 warnings.warn(

nibabel/nicom/ascconv.py

@@ -3,6 +3,7 @@
 """
 Parse the "ASCCONV" meta data format found in a variety of Siemens MR files.
 """
+
 import ast
 import re
 from collections import OrderedDict

nibabel/nicom/csareader.py

@@ -1,5 +1,5 @@
-"""CSA header reader from SPM spec
-"""
+"""CSA header reader from SPM spec"""
+
 import numpy as np
 
 from .structreader import Unpacker