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)

nibabel/streamlines/tests/test_tractogram_file.py

@@ -8,7 +8,6 @@
 
 
 def test_subclassing_tractogram_file():
-
     # Missing 'save' method
     class DummyTractogramFile(TractogramFile):
         @classmethod

nibabel/streamlines/trk.py

@@ -366,7 +366,6 @@ def _read():
             tractogram = LazyTractogram.from_data_func(_read)
 
         else:
-
             # Speed up loading by guessing a suitable buffer size.
             with Opener(fileobj) as f:
                 old_file_position = f.tell()
@@ -773,6 +772,4 @@ def __str__(self):
 swap_yz: {swap_yz}
 swap_zx: {swap_zx}
 n_count: {NB_STREAMLINES}
-hdr_size: {hdr_size}""".format(
-            **vars
-        )
+hdr_size: {hdr_size}""".format(**vars)

nibabel/tests/test_funcs.py

@@ -58,7 +58,6 @@ def test_concat():
 
                 # Loop over every possible axis, including None (explicit and implied)
                 for axis in list(range(-(dim - 2), (dim - 1))) + [None, '__default__']:
-
                     # Allow testing default vs. passing explicit param
                     if axis == '__default__':
                         np_concat_kwargs = dict(axis=-1)

nibabel/tests/test_image_types.py

@@ -88,7 +88,6 @@ def check_img(img_path, img_klass, sniff_mode, sniff, expect_success, msg):
             irrelevant=b'a' * (sizeof_hdr - 1),  # A too-small sniff, query
             bad_sniff=b'a' * sizeof_hdr,  # Bad sniff, should fail
         ).items():
-
             for klass in img_klasses:
                 if klass == expected_img_klass:
                     # Class will load unless you pass a bad sniff,

nibabel/tests/test_nifti1.py

@@ -731,7 +731,6 @@ def unshear_44(affine):
 
 
 class TestNifti1SingleHeader(TestNifti1PairHeader):
-
     header_class = Nifti1Header
 
     def test_empty(self):

nibabel/tests/test_parrec.py

@@ -884,7 +884,6 @@ def test_dualTR():
 def test_ADC_map():
     # test reading an apparent diffusion coefficient map
     with open(ADC_PAR) as fobj:
-
         # two truncation warnings expected because general_info indicates:
         # 1.) multiple directions
         # 2.) multiple b-values

nibabel/tests/test_spatialimages.py

@@ -400,7 +400,7 @@ def test_slicer(self):
         in_data_template = np.arange(240, dtype=np.int16)
         base_affine = np.eye(4)
         t_axis = None
-        for dshape in ((4, 5, 6, 2), (8, 5, 6)):    # Time series      # Volume
+        for dshape in ((4, 5, 6, 2), (8, 5, 6)):  # Time series      # Volume
             in_data = in_data_template.copy().reshape(dshape)
             img = img_klass(in_data, base_affine.copy())
 

nisext/py3builder.py

@@ -6,7 +6,7 @@
 except ImportError:
     # 2.x - no parsing of code
     from distutils.command.build_py import build_py
-else:   # Python 3
+else:  # Python 3
     # Command to also apply 2to3 to doctests
     from distutils import log
 

nisext/testers.py

@@ -135,9 +135,7 @@ def run_mod_cmd(mod_name, pkg_path, cmd, script_dir=None, print_location=True):
     os.environ['PYTHONPATH'] = r'"{pkg_path}"'
 else:
     os.environ['PYTHONPATH'] = r'"{pkg_path}"' + os.path.pathsep + PYTHONPATH
-""".format(
-            **locals()
-        )
+""".format(**locals())
     if print_location:
         p_loc = f'print({mod_name}.__file__);'
     else:
@@ -155,9 +153,7 @@ def run_mod_cmd(mod_name, pkg_path, cmd, script_dir=None, print_location=True):
 {paths_add}
 import {mod_name}
 {p_loc}
-{cmd}""".format(
-                    **locals()
-                )
+{cmd}""".format(**locals())
             )
         res = back_tick(f'{PYTHON} script.py', ret_err=True)
     finally:

pyproject.toml

@@ -109,21 +109,32 @@ __version__ = version = {version!r}
 __version_tuple__ = version_tuple = {version_tuple!r}
 '''
 
-[tool.blue]
-line_length = 99
-target-version = ["py38"]
-force-exclude = """
-(
-  _version.py
-  | nibabel/externals/
-  | versioneer.py
-)
-"""
+[tool.ruff]
+line-length = 99
+exclude = ["version.py", "nibabel/externals", "versioneer.py"]
 
-[tool.isort]
-profile = "black"
-line_length = 99
-extend_skip = ["_version.py", "externals"]
+[tool.ruff.lint]
+select = ["E4", "E7", "E9", "F", "I", "Q"]
+ignore = [
+    # https://docs.astral.sh/ruff/formatter/#conflicting-lint-rules
+    "W191",
+    "E111",
+    "E114",
+    "E117",
+    "D206",
+    "D300",
+    "Q000",
+    "Q001",
+    "Q002",
+    "Q003",
+    "COM812",
+    "COM819",
+    "ISC001",
+    "ISC002",
+]
+
+[tool.ruff.format]
+quote-style = "single"
 
 [tool.mypy]
 python_version = "3.11"

tools/markdown_release_notes.py

@@ -27,7 +27,7 @@ def main():
                 if in_release_notes:
                     break
                 in_release_notes = match.group(1) == version
-                next(f)   # Skip the underline
+                next(f)  # Skip the underline
                 continue
 
             if in_release_notes:

tox.ini

@@ -139,15 +139,11 @@ commands =
 description = Check our style guide
 labels = check
 deps =
-  flake8
-  blue
-  # Broken extras, remove when fix is released
-  isort[colors]!=5.13.1
+  ruff>=0.1.9
 skip_install = true
 commands =
-  blue --check --diff --color nibabel
-  isort --check --diff --color nibabel
-  flake8 nibabel
+  ruff --check --diff nibabel
+  ruff --format --check --diff nibabel
 
 [testenv:style-fix]
 description = Auto-apply style guide to the extent possible