MNT: run ruff --fix

Also fix remaining issues manually.

doc/source/conf.py

@@ -30,11 +30,11 @@
 
 # Check for external Sphinx extensions we depend on
 try:
-    import numpydoc
+    import numpydoc  # noqa: F401
 except ImportError:
     raise RuntimeError('Need to install "numpydoc" package for doc build')
 try:
-    import texext
+    import texext  # noqa: F401
 except ImportError:
     raise RuntimeError('Need to install "texext" package for doc build')
 

doc/tools/apigen.py

@@ -405,7 +405,6 @@ 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
         ]

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]

nibabel/__init__.py

@@ -7,6 +7,8 @@
 #
 ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##
 
+# ruff: noqa: F401
+
 import os
 
 from .info import long_description as __doc__
@@ -39,12 +41,10 @@
 
 # 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
 

nibabel/cifti2/__init__.py

@@ -6,6 +6,7 @@
 #   copyright and license terms.
 #
 ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##
+# ruff: noqa: F401
 """CIFTI-2 format IO
 
 .. currentmodule:: nibabel.cifti2

nibabel/cifti2/tests/test_cifti2.py

@@ -7,7 +7,7 @@
 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

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():

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()

nibabel/cmdline/tests/test_roi.py

@@ -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:

nibabel/cmdline/tests/test_stats.py

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

nibabel/cmdline/tests/test_utils.py

@@ -12,8 +12,16 @@
 import pytest
 
 import nibabel as nib
-from nibabel.cmdline.diff import *
-from nibabel.cmdline.utils import *
+from nibabel.cmdline.diff import (
+    ap,
+    display_diff,
+    get_data_diff,
+    get_data_hash_diff,
+    get_headers_diff,
+    main,
+    safe_get,
+    table2string,
+)
 from nibabel.testing import data_path
 
 

nibabel/conftest.py

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

nibabel/freesurfer/__init__.py

@@ -1,6 +1,8 @@
 """Reading functions for freesurfer files
 """
 
+# ruff: noqa: F401
+
 from .io import (
     read_annot,
     read_geometry,

nibabel/gifti/__init__.py

@@ -16,6 +16,8 @@
    gifti
 """
 
+# ruff: noqa: F401
+
 from .gifti import (
     GiftiCoordSystem,
     GiftiDataArray,

nibabel/gifti/tests/test_gifti.py

@@ -2,12 +2,11 @@
 """
 import itertools
 import sys
-import warnings
 from io import BytesIO
 
 import numpy as np
 import pytest
-from numpy.testing import assert_array_almost_equal, assert_array_equal
+from numpy.testing import assert_array_equal
 
 from nibabel.tmpdirs import InTemporaryDirectory
 
@@ -312,7 +311,7 @@ def test_metadata_list_interface():
     assert md['foo'] == 'bar'
 
     # Append new NVPair
-    with pytest.warns(DeprecationWarning) as w:
+    with pytest.warns(DeprecationWarning) as _:
         nvpair = GiftiNVPairs('key', 'value')
     mdlist.append(nvpair)
     assert len(mdlist) == 2
@@ -327,15 +326,15 @@ def test_metadata_list_interface():
     assert len(md) == 0
 
     # Extension adds multiple keys
-    with pytest.warns(DeprecationWarning) as w:
+    with pytest.warns(DeprecationWarning) as _:
         foobar = GiftiNVPairs('foo', 'bar')
     mdlist.extend([nvpair, foobar])
     assert len(mdlist) == 2
     assert len(md) == 2
     assert md == {'key': 'value', 'foo': 'bar'}
 
     # Insertion updates list order, though we don't attempt to preserve it in the dict
-    with pytest.warns(DeprecationWarning) as w:
+    with pytest.warns(DeprecationWarning) as _:
         lastone = GiftiNVPairs('last', 'one')
     mdlist.insert(1, lastone)
     assert len(mdlist) == 3
@@ -358,14 +357,14 @@ def test_metadata_list_interface():
     mypair.value = 'strings'
     assert 'completelynew' not in md
     assert md == {'foo': 'bar', 'last': 'one'}
-    # Check popping from the end (lastone inserted before foobar)
-    lastpair = mdlist.pop()
+    # Check popping from the end (last one inserted before foobar)
+    _ = mdlist.pop()
     assert len(mdlist) == 1
     assert len(md) == 1
     assert md == {'last': 'one'}
 
     # And let's remove an old pair with a new object
-    with pytest.warns(DeprecationWarning) as w:
+    with pytest.warns(DeprecationWarning) as _:
         lastoneagain = GiftiNVPairs('last', 'one')
     mdlist.remove(lastoneagain)
     assert len(mdlist) == 0

nibabel/gifti/tests/test_parse_gifti_fast.py

@@ -433,13 +433,13 @@ def test_external_file_failure_cases():
         shutil.copy(DATA_FILE7, '.')
         filename = pjoin(tmpdir, basename(DATA_FILE7))
         with pytest.raises(GiftiParseError):
-            img = load(filename)
+            _ = load(filename)
     # load from in-memory xml string (parser requires it as bytes)
     with open(DATA_FILE7, 'rb') as f:
         xmldata = f.read()
     parser = GiftiImageParser()
     with pytest.raises(GiftiParseError):
-        img = parser.parse(xmldata)
+        _ = parser.parse(xmldata)
 
 
 def test_load_compressed():

nibabel/nicom/tests/test_ascconv.py

@@ -5,7 +5,6 @@
 from os.path import dirname
 from os.path import join as pjoin
 
-import numpy as np
 from numpy.testing import assert_array_almost_equal, assert_array_equal
 
 from .. import ascconv

nibabel/nicom/tests/test_csareader.py

@@ -1,7 +1,6 @@
 """Testing Siemens CSA header reader
 """
 import gzip
-import sys
 from copy import deepcopy
 from os.path import join as pjoin
 

nibabel/nicom/tests/test_dicomwrappers.py

@@ -626,7 +626,7 @@ def test_image_position(self):
     def test_affine(self):
         # Make sure we find orientation/position/spacing info
         dw = didw.wrapper_from_file(DATA_FILE_4D)
-        aff = dw.affine
+        _ = dw.affine
 
     @dicom_test
     @pytest.mark.xfail(reason='Not packaged in install', raises=FileNotFoundError)

nibabel/streamlines/__init__.py

@@ -3,10 +3,8 @@
 import os
 import warnings
 
-from .array_sequence import ArraySequence
-from .header import Field
 from .tck import TckFile
-from .tractogram import LazyTractogram, Tractogram
+from .tractogram import Tractogram
 from .tractogram_file import ExtensionWarning
 from .trk import TrkFile
 

nibabel/streamlines/tests/test_array_sequence.py

@@ -1,6 +1,5 @@
 import itertools
 import os
-import sys
 import tempfile
 import unittest
 
@@ -220,7 +219,7 @@ def test_arraysequence_extend(self):
             seq.extend(data)
 
         # Extend after extracting some slice
-        working_slice = seq[:2]
+        _ = seq[:2]
         seq.extend(ArraySequence(new_data))
 
     def test_arraysequence_getitem(self):

nibabel/streamlines/tests/test_streamlines.py

@@ -1,5 +1,4 @@
 import os
-import tempfile
 import unittest
 import warnings
 from io import BytesIO

nibabel/streamlines/tests/test_tck.py

@@ -8,7 +8,6 @@
 from numpy.testing import assert_array_equal
 
 from ...testing import data_path, error_warnings
-from .. import tck as tck_module
 from ..array_sequence import ArraySequence
 from ..tck import TckFile
 from ..tractogram import Tractogram
@@ -138,7 +137,7 @@ def test_load_file_with_wrong_information(self):
 
         # Simulate a TCK file with no `file` field.
         new_tck_file = tck_file.replace(b'\nfile: . 67', b'')
-        with pytest.warns(HeaderWarning, match="Missing 'file'") as w:
+        with pytest.warns(HeaderWarning, match="Missing 'file'") as _:
             tck = TckFile.load(BytesIO(new_tck_file))
         assert_array_equal(tck.header['file'], '. 56')
 

nibabel/streamlines/tests/test_tractogram.py

@@ -1,6 +1,5 @@
 import copy
 import operator
-import sys
 import unittest
 import warnings
 from collections import defaultdict

nibabel/streamlines/tests/test_trk.py

@@ -149,7 +149,7 @@ def test_load_file_with_wrong_information(self):
         # Simulate a TRK where `vox_to_ras` is invalid.
         trk_struct, trk_bytes = self.trk_with_bytes()
         trk_struct[Field.VOXEL_TO_RASMM] = np.diag([0, 0, 0, 1])
-        with clear_and_catch_warnings(record=True, modules=[trk_module]) as w:
+        with clear_and_catch_warnings(record=True, modules=[trk_module]) as _:
             with pytest.raises(HeaderError):
                 TrkFile.load(BytesIO(trk_bytes))
 

nibabel/testing/__init__.py

@@ -7,6 +7,9 @@
 #
 ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##
 """Utilities for testing"""
+
+# ruff: noqa: F401
+
 from __future__ import annotations
 
 import os

nibabel/tests/nibabel_data.py

@@ -3,9 +3,8 @@
 
 import unittest
 from os import environ, listdir
-from os.path import dirname, exists, isdir
+from os.path import dirname, exists, isdir, realpath
 from os.path import join as pjoin
-from os.path import realpath
 
 
 def get_nibabel_data():

nibabel/tests/scriptrunner.py

@@ -14,9 +14,8 @@
 """
 import os
 import sys
-from os.path import dirname, isdir, isfile
+from os.path import dirname, isdir, isfile, pathsep, realpath
 from os.path import join as pjoin
-from os.path import pathsep, realpath
 from subprocess import PIPE, Popen
 
 MY_PACKAGE = __package__

nibabel/tests/test_affines.py

@@ -225,7 +225,7 @@ def test_rescale_affine():
     orig_shape = rng.randint(low=20, high=512, size=(3,))
     orig_aff = np.eye(4)
     orig_aff[:3, :] = rng.normal(size=(3, 4))
-    orig_zooms = voxel_sizes(orig_aff)
+    orig_zooms = voxel_sizes(orig_aff)  # noqa: F841
     orig_axcodes = aff2axcodes(orig_aff)
     orig_centroid = apply_affine(orig_aff, (orig_shape - 1) // 2)
 

nibabel/tests/test_arraywriters.py

@@ -276,7 +276,7 @@ def test_slope_inter_castable():
         for out_dtt in NUMERIC_TYPES:
             for klass in (ArrayWriter, SlopeArrayWriter, SlopeInterArrayWriter):
                 arr = np.zeros((5,), dtype=in_dtt)
-                aw = klass(arr, out_dtt)  # no error
+                _ = klass(arr, out_dtt)  # no error
     # Test special case of none finite
     # This raises error for ArrayWriter, but not for the others
     arr = np.array([np.inf, np.nan, -np.inf])
@@ -285,8 +285,8 @@ def test_slope_inter_castable():
             in_arr = arr.astype(in_dtt)
             with pytest.raises(WriterError):
                 ArrayWriter(in_arr, out_dtt)
-            aw = SlopeArrayWriter(arr.astype(in_dtt), out_dtt)  # no error
-            aw = SlopeInterArrayWriter(arr.astype(in_dtt), out_dtt)  # no error
+            _ = SlopeArrayWriter(arr.astype(in_dtt), out_dtt)  # no error
+            _ = SlopeInterArrayWriter(arr.astype(in_dtt), out_dtt)  # no error
     for in_dtt, out_dtt, arr, slope_only, slope_inter, neither in (
         (np.float32, np.float32, 1, True, True, True),
         (np.float64, np.float32, 1, True, True, True),