MNT: run ruff --fix and ruf format

Also fix remaining issues manually.

Author: DimitriPapadopoulos

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/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)]

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/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
@@ -255,7 +254,6 @@ def get_data_diff(files, max_abs=0, max_rel=0, dtype=np.float64):
                     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

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()