From 75136b2bb86426c22609449b3f48579ee9c2e4f5 Mon Sep 17 00:00:00 2001
From: Mathias Goncalves <goncalves.mathias@gmail.com>
Date: Thu, 9 Jan 2025 15:09:16 -0500
Subject: [PATCH 1/2] STY: Ruff format [git-blame-ignore-rev]
---
niworkflows/interfaces/bids.py | 8 ++++----
niworkflows/interfaces/confounds.py | 3 +--
niworkflows/interfaces/images.py | 3 +--
niworkflows/interfaces/itk.py | 3 +--
niworkflows/interfaces/nibabel.py | 2 +-
niworkflows/interfaces/surf.py | 2 +-
niworkflows/interfaces/workbench.py | 3 +--
niworkflows/tests/test_utils.py | 3 +--
niworkflows/tests/test_viz.py | 12 ++++++------
niworkflows/utils/testing.py | 2 +-
niworkflows/utils/tests/test_spaces.py | 6 +++---
11 files changed, 21 insertions(+), 26 deletions(-)
diff --git a/niworkflows/interfaces/bids.py b/niworkflows/interfaces/bids.py
index ec7131dff3a..53cefc3aead 100644
--- a/niworkflows/interfaces/bids.py
+++ b/niworkflows/interfaces/bids.py
@@ -773,7 +773,7 @@ def _run_interface(self, runtime):
_copy_any(in_file, out_file)
if self.inputs.metadata:
- sidecar = out_file.parent / f"{out_file.name.split('.', 1)[0]}.json"
+ sidecar = out_file.parent / f'{out_file.name.split(".", 1)[0]}.json'
sidecar.unlink(missing_ok=True)
sidecar.write_text(dumps(self.inputs.metadata, indent=2))
self._results['out_meta'].append(str(sidecar))
@@ -1236,7 +1236,7 @@ def _run_interface(self, runtime):
{k: getattr(self.inputs, k) for k in meta_fields if k not in self._static_traits}
)
if self._metadata:
- sidecar = out_file.parent / f"{out_file.name.split('.', 1)[0]}.json"
+ sidecar = out_file.parent / f'{out_file.name.split(".", 1)[0]}.json'
unlink(sidecar, missing_ok=True)
sidecar.write_text(dumps(self._metadata, sort_keys=True, indent=2))
self._results['out_meta'] = str(sidecar)
@@ -1482,6 +1482,6 @@ def _fmt_xyz(coords: list) -> str:
return f'{xyz} mm^3'
return (
- f"Template {space} ({_fmt_xyz(res_meta['zooms'])}),"
- f" curated by TemplateFlow {tf.__version__}"
+ f'Template {space} ({_fmt_xyz(res_meta["zooms"])}),'
+ f' curated by TemplateFlow {tf.__version__}'
)
diff --git a/niworkflows/interfaces/confounds.py b/niworkflows/interfaces/confounds.py
index 08ed16c63e7..6c14d68f483 100644
--- a/niworkflows/interfaces/confounds.py
+++ b/niworkflows/interfaces/confounds.py
@@ -176,8 +176,7 @@ class _SpikeRegressorsInputSpec(BaseInterfaceInputSpec):
concatenate = traits.Bool(
True,
usedefault=True,
- desc='Indicates whether to concatenate spikes to existing confounds '
- 'or return spikes only',
+ desc='Indicates whether to concatenate spikes to existing confounds or return spikes only',
)
output_format = traits.Enum(
'spikes', 'mask', usedefault=True, desc='Format of output (spikes or mask)'
diff --git a/niworkflows/interfaces/images.py b/niworkflows/interfaces/images.py
index bb04c82ec21..388dbea9bbb 100644
--- a/niworkflows/interfaces/images.py
+++ b/niworkflows/interfaces/images.py
@@ -702,8 +702,7 @@ def _run_interface(self, runtime):
# This check assumes all input masks have same dimensions
if img.shape[:3] != mask_imgs[0].shape[:3]:
raise NotImplementedError(
- 'Input image and mask should be of '
- 'same dimensions before running SignalExtraction'
+ 'Input image and mask should be of same dimensions before running SignalExtraction'
)
# Load the mask.
# If mask is a list, each mask is treated as its own ROI/parcel
diff --git a/niworkflows/interfaces/itk.py b/niworkflows/interfaces/itk.py
index ae9b0274f52..1c8e2c7c156 100644
--- a/niworkflows/interfaces/itk.py
+++ b/niworkflows/interfaces/itk.py
@@ -91,8 +91,7 @@ class _MultiApplyTransformsInputSpec(_FixTraitApplyTransformsInputSpec):
input_image = InputMultiObject(
File(exists=True),
mandatory=True,
- desc='input time-series as a list of volumes after splitting'
- ' through the fourth dimension',
+ desc='input time-series as a list of volumes after splitting through the fourth dimension',
)
num_threads = traits.Int(1, usedefault=True, nohash=True, desc='number of parallel processes')
save_cmd = traits.Bool(
diff --git a/niworkflows/interfaces/nibabel.py b/niworkflows/interfaces/nibabel.py
index d041164a692..172adfdb508 100644
--- a/niworkflows/interfaces/nibabel.py
+++ b/niworkflows/interfaces/nibabel.py
@@ -182,7 +182,7 @@ def _run_interface(self, runtime):
img = nb.load(in_file)
extra_dims = tuple(dim for dim in img.shape[3:] if dim > 1) or (1,)
if len(extra_dims) != 1:
- raise ValueError(f"Invalid shape {'x'.join(str(s) for s in img.shape)}")
+ raise ValueError(f'Invalid shape {"x".join(str(s) for s in img.shape)}')
img = img.__class__(
img.dataobj.reshape(img.shape[:3] + extra_dims), img.affine, img.header
)
diff --git a/niworkflows/interfaces/surf.py b/niworkflows/interfaces/surf.py
index 2a1fd76da21..0e75a501516 100644
--- a/niworkflows/interfaces/surf.py
+++ b/niworkflows/interfaces/surf.py
@@ -192,7 +192,7 @@ def _run_interface(self, runtime):
in_file = Path(self.inputs.in_file)
extension = ''.join(in_file.suffixes[-((in_file.suffixes[-1] == '.gz') + 1) :])
info = self._pattern.match(in_file.name[: -len(extension)]).groupdict()
- self._results['extension'] = f"{info.pop('extprefix', None) or ''}{extension}"
+ self._results['extension'] = f'{info.pop("extprefix", None) or ""}{extension}'
self._results.update(info)
if 'hemi' in self._results:
self._results['hemi'] = self._results['hemi'].upper()
diff --git a/niworkflows/interfaces/workbench.py b/niworkflows/interfaces/workbench.py
index 9ad60cf5a30..975f24f19f0 100644
--- a/niworkflows/interfaces/workbench.py
+++ b/niworkflows/interfaces/workbench.py
@@ -114,8 +114,7 @@ class MetricDilateInputSpec(OpenMPTraitedSpec):
argstr='-exponent %f ',
position=9,
default=6.0,
- desc='exponent n to use in (area / (distance ^ n)) as the '
- 'weighting function (default 6)',
+ desc='exponent n to use in (area / (distance ^ n)) as the weighting function (default 6)',
)
corrected_areas = File(
diff --git a/niworkflows/tests/test_utils.py b/niworkflows/tests/test_utils.py
index 278ddaee892..dbfff2d59ef 100644
--- a/niworkflows/tests/test_utils.py
+++ b/niworkflows/tests/test_utils.py
@@ -89,6 +89,5 @@ def test_compression(tmp_path):
size = int(os.stat(uncompressed).st_size)
size_compress = int(os.stat(compressed).st_size)
assert size >= size_compress, (
- f'The uncompressed report is smaller ({size})'
- f'than the compressed report ({size_compress})'
+ f'The uncompressed report is smaller ({size})than the compressed report ({size_compress})'
)
diff --git a/niworkflows/tests/test_viz.py b/niworkflows/tests/test_viz.py
index fe9d6a796c3..82b65d3a99d 100644
--- a/niworkflows/tests/test_viz.py
+++ b/niworkflows/tests/test_viz.py
@@ -54,8 +54,8 @@ def test_carpetplot(tr, sorting):
output_file=(
os.path.join(
save_artifacts,
- f"carpet_nosegs_{'index' if tr is None else 'time'}_"
- f"{'nosort' if sorting is None else sorting}.svg",
+ f'carpet_nosegs_{"index" if tr is None else "time"}_'
+ f'{"nosort" if sorting is None else sorting}.svg',
)
if save_artifacts
else None
@@ -87,8 +87,8 @@ def test_carpetplot(tr, sorting):
output_file=(
os.path.join(
save_artifacts,
- f"carpet_random_{'index' if tr is None else 'seg'}_"
- f"{'nosort' if sorting is None else sorting}.svg",
+ f'carpet_random_{"index" if tr is None else "seg"}_'
+ f'{"nosort" if sorting is None else sorting}.svg',
)
if save_artifacts
else None
@@ -114,8 +114,8 @@ def test_carpetplot(tr, sorting):
output_file=(
os.path.join(
save_artifacts,
- f"carpet_const_{'index' if tr is None else 'time'}_"
- f"{'nosort' if sorting is None else sorting}.svg",
+ f'carpet_const_{"index" if tr is None else "time"}_'
+ f'{"nosort" if sorting is None else sorting}.svg',
)
if save_artifacts
else None
diff --git a/niworkflows/utils/testing.py b/niworkflows/utils/testing.py
index cf0a271c800..ba6f7ed004a 100644
--- a/niworkflows/utils/testing.py
+++ b/niworkflows/utils/testing.py
@@ -96,4 +96,4 @@ def to_json(filename, data):
def combine_entities(**entities):
- return f"_{'_'.join([f'{lab}-{val}' for lab, val in entities.items()])}" if entities else ''
+ return f'_{"_".join([f"{lab}-{val}" for lab, val in entities.items()])}' if entities else ''
diff --git a/niworkflows/utils/tests/test_spaces.py b/niworkflows/utils/tests/test_spaces.py
index bf5cfca5b35..8b6e35f6d93 100644
--- a/niworkflows/utils/tests/test_spaces.py
+++ b/niworkflows/utils/tests/test_spaces.py
@@ -91,9 +91,9 @@ def test_space_action(parser, spaces, expected):
pargs = parser.parse_known_args(args=('--spaces',) + spaces)[0]
parsed_spaces = pargs.spaces
assert isinstance(parsed_spaces, SpatialReferences)
- assert all(
- isinstance(sp, Reference) for sp in parsed_spaces.references
- ), 'Every element must be a `Reference`'
+ assert all(isinstance(sp, Reference) for sp in parsed_spaces.references), (
+ 'Every element must be a `Reference`'
+ )
assert len(parsed_spaces.references) == len(expected)
for ref, expected_ref in zip(parsed_spaces.references, expected):
assert str(ref) == expected_ref
From 5536e4f6bd05eda10b794f3a9dce9742b18e770a Mon Sep 17 00:00:00 2001
From: Mathias Goncalves <goncalves.mathias@gmail.com>
Date: Thu, 9 Jan 2025 15:10:56 -0500
Subject: [PATCH 2/2] MAINT: Add git blame ignore file
---
.git-blame-ignore-revs | 2 ++
1 file changed, 2 insertions(+)
create mode 100644 .git-blame-ignore-revs
diff --git a/.git-blame-ignore-revs b/.git-blame-ignore-revs
new file mode 100644
index 00000000000..e1c9cff3819
--- /dev/null
+++ b/.git-blame-ignore-revs
@@ -0,0 +1,2 @@
+# 2025-01-09 - goncalves.mathias@gmail.com - STY: Ruff format [git-blame-ignore-rev]
+75136b2bb86426c22609449b3f48579ee9c2e4f5