MNT: blue/isort/flake8 → ruff

Author: DimitriPapadopoulos

.pre-commit-config.yaml

@@ -12,18 +12,13 @@ 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: v0.1.9
     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
+      - id: ruff
+        args: [--fix, --show-fix, --exit-non-zero-on-fix]
+        exclude: "^(doc|nisext|tools)/"
+      - id: ruff-format
         exclude: "^(doc|nisext|tools)/"
   - repo: https://github.com/pre-commit/mirrors-mypy
     rev: v1.5.1

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/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/dft.py

@@ -161,7 +161,7 @@ def as_nifti(self):
         data = numpy.ndarray(
             (len(self.storage_instances), self.rows, self.columns), dtype=numpy.int16
         )
-        for (i, si) in enumerate(self.storage_instances):
+        for i, si in enumerate(self.storage_instances):
             if i + 1 != si.instance_number:
                 raise InstanceStackError(self, i, si)
             logger.info('reading %d/%d' % (i + 1, len(self.storage_instances)))
@@ -243,7 +243,7 @@ def dicom(self):
 
 def _get_subdirs(base_dir, files_dict=None, followlinks=False):
     dirs = []
-    for (dirpath, dirnames, filenames) in os.walk(base_dir, followlinks=followlinks):
+    for dirpath, dirnames, filenames in os.walk(base_dir, followlinks=followlinks):
         abs_dir = os.path.realpath(dirpath)
         if abs_dir in dirs:
             raise CachingError(f'link cycle detected under {base_dir}')

nibabel/ecat.py

@@ -513,7 +513,6 @@ def read_subheaders(fileobj, mlist, endianness):
 
 
 class EcatSubHeader:
-
     _subhdrdtype = subhdr_dtype
     _data_type_codes = data_type_codes
 

nibabel/freesurfer/tests/test_mghformat.py

@@ -460,6 +460,7 @@ def test_as_byteswapped(self):
         for endianness in (None,) + LITTLE_CODES:
             with pytest.raises(ValueError):
                 hdr.as_byteswapped(endianness)
+
         # Note that contents is not rechecked on swap / copy
         class DC(self.header_class):
             def check_fix(self, *args, **kwargs):

nibabel/info.py

@@ -108,4 +108,4 @@
 
 .. _Digital Object Identifier: https://en.wikipedia.org/wiki/Digital_object_identifier
 .. _zenodo: https://zenodo.org
-"""   # noqa: E501
+"""  # noqa: E501

nibabel/openers.py

@@ -86,7 +86,6 @@ def _gzip_open(
     mtime: int = 0,
     keep_open: bool = False,
 ) -> gzip.GzipFile:
-
     if not HAVE_INDEXED_GZIP or mode != 'rb':
         gzip_file = DeterministicGzipFile(filename, mode, compresslevel, mtime=mtime)
 
@@ -129,6 +128,7 @@ class Opener:
         passed to opening method when `fileish` is str.  Change of defaults as
         for \*args
     """
+
     gz_def = (_gzip_open, ('mode', 'compresslevel', 'mtime', 'keep_open'))
     bz2_def = (BZ2File, ('mode', 'buffering', 'compresslevel'))
     zstd_def = (_zstd_open, ('mode', 'level_or_option', 'zstd_dict'))

nibabel/streamlines/tck.py

@@ -309,7 +309,6 @@ def _read_header(cls, fileobj):
         offset_data = 0
 
         with Opener(fileobj) as f:
-
             # Record start position
             start_position = f.tell()
 

nibabel/streamlines/tests/test_tractogram.py

@@ -165,7 +165,6 @@ def setup_module():
 
 
 def check_tractogram_item(tractogram_item, streamline, data_for_streamline={}, data_for_points={}):
-
     assert_array_equal(tractogram_item.streamline, streamline)
 
     assert len(tractogram_item.data_for_streamline) == len(data_for_streamline)