Use Ruff for formatting (#1204)

* Use Ruff for formatting

* Remove Black

.github/workflows/code_quality.yml

@@ -17,6 +17,7 @@ jobs:
       fail-fast: false
       matrix:
         tox_env:
+          - format
           - lint
           - types
 
@@ -39,27 +40,6 @@ jobs:
       - name: Run check for tox env "${{ matrix.tox_env }}"
         run: tox -e ${{ matrix.tox_env }}
 
-  black:
-    name: Code formatting
-    runs-on: ubuntu-latest
-
-    steps:
-      - name: Set up Python
-        uses: actions/setup-python@v5
-        with:
-          python-version: "3.12"
-
-      - name: Checkout repository
-        uses: actions/checkout@v4
-        with:
-          fetch-depth: 0
-
-      - name: Install black
-        run: pip install black
-
-      - name: Run black
-        run: black --check --diff .
-
   docs:
     name: Documentation
     runs-on: ubuntu-latest

.pre-commit-config.yaml

@@ -21,7 +21,7 @@ repos:
     rev: v0.6.7
     hooks:
       - id: ruff
-      # - id: ruff-format
+      - id: ruff-format
 
   - repo: https://github.com/pre-commit/pygrep-hooks
     rev: v1.10.0

README.md

@@ -52,8 +52,8 @@ at [OpenAI](https://openai.com/) ([link](https://jack-clark.net/2020/03/17/)).
             <b>Code</b>
         </td>
         <td align="center">
-            <a href="https://github.com/psf/black">
-                <img src="https://img.shields.io/badge/code%20style-black-000000.svg" alt="Code quality">
+            <a href="https://docs.astral.sh/ruff/">
+                <img src="https://camo.githubusercontent.com/bb88127790fb054cba2caf3f3be2569c1b97bb45a44b47b52d738f8781a8ede4/68747470733a2f2f696d672e736869656c64732e696f2f656e64706f696e743f75726c3d68747470733a2f2f7261772e67697468756275736572636f6e74656e742e636f6d2f636861726c6965726d617273682f727566662f6d61696e2f6173736574732f62616467652f76312e6a736f6e" alt="Code style">
             </a>
             <a href="https://scrutinizer-ci.com/g/fepegar/torchio/?branch=main">
                 <img src="https://img.shields.io/scrutinizer/g/fepegar/torchio.svg?label=Code%20quality&logo=scrutinizer" alt="Code quality">

docs/examples/plot_3d_to_2d.py

@@ -8,6 +8,7 @@
 
 import matplotlib.pyplot as plt
 import torch
+
 import torchio as tio
 
 torch.manual_seed(0)

docs/examples/plot_custom_z_spacing.py

@@ -10,6 +10,7 @@
 """
 
 import torch
+
 import torchio as tio
 
 

docs/examples/plot_history.py

@@ -12,6 +12,7 @@
 
 import matplotlib.pyplot as plt
 import torch
+
 import torchio as tio
 
 torch.manual_seed(0)
@@ -38,9 +39,7 @@
 pprint.pprint(transformed.history)  # noqa: T203
 print('\nComposed transform to reproduce history:')  # noqa: T201
 print(transformed.get_composed_history())  # noqa: T201
-print(
-    '\nComposed transform to invert applied transforms when possible:'
-)  # noqa: T201, B950
+print('\nComposed transform to invert applied transforms when possible:')
 print(transformed.get_inverse_transform(ignore_intensity=False))  # noqa: T201
 
 loader = tio.SubjectsLoader(

docs/examples/plot_include_exclude.py

@@ -7,8 +7,8 @@
 """
 
 import torch
-import torchio as tio
 
+import torchio as tio
 
 torch.manual_seed(0)
 

docs/examples/plot_video.py

@@ -12,9 +12,10 @@
 import matplotlib.pyplot as plt
 import numpy as np
 import torch
-import torchio as tio
 from PIL import Image
 
+import torchio as tio
+
 
 def read_clip(path, undersample=4):
     """Read a GIF a return an array of shape (C, W, H, T)."""
@@ -49,7 +50,7 @@ def get_frame(image, i):
     )
 
 
-# Source: https://thehigherlearning.wordpress.com/2014/06/25/watching-a-cell-divide-under-an-electron-microscope-is-mesmerizing-gif/  # noqa: B950
+# Source: https://thehigherlearning.wordpress.com/2014/06/25/watching-a-cell-divide-under-an-electron-microscope-is-mesmerizing-gif/
 array, delay = read_clip('nBTu3oi.gif')
 plt.imshow(array[..., 0].transpose(1, 2, 0))
 plt.plot()

docs/source/README.rst

@@ -3,7 +3,7 @@ TorchIO
 #######
 
 |PyPI-downloads| |PyPI-version| |Conda-version| |Google-Colab-notebook|
-|Docs-status| |Tests-status| |Black|
+|Docs-status| |Tests-status| |Ruff|
 |Coverage-codecov| |Code-Quality| |Code-Maintainability| |pre-commit|
 |Slack| |Twitter| |Twitter-commits| |YouTube|
 
@@ -89,9 +89,9 @@ If you found a bug or have a feature request, please open an issue:
    :target: https://github.com/fepegar/torchio/actions/workflows/tests.yml
    :alt: Tests status
 
-.. |Black| image:: https://img.shields.io/badge/code%20style-black-000000.svg
-   :target: https://github.com/psf/black
-   :alt: Code style: black
+.. |Ruff| image:: https://camo.githubusercontent.com/bb88127790fb054cba2caf3f3be2569c1b97bb45a44b47b52d738f8781a8ede4/68747470733a2f2f696d672e736869656c64732e696f2f656e64706f696e743f75726c3d68747470733a2f2f7261772e67697468756275736572636f6e74656e742e636f6d2f636861726c6965726d617273682f727566662f6d61696e2f6173736574732f62616467652f76312e6a736f6e
+   :target: https://docs.astral.sh/ruff/
+   :alt: Code style: Ruff
 
 .. |Coverage-codecov| image:: https://codecov.io/gh/fepegar/torchio/branch/main/graphs/badge.svg
    :target: https://codecov.io/github/fepegar/torchio

docs/source/conf.py

@@ -109,7 +109,7 @@
 # further. For a list of options available for each theme, see the
 # documentation.
 #
-url = 'https://www.journals.elsevier.com/computer-methods-and-programs-in-biomedicine/most-downloaded-articles'  # noqa: B950
+url = 'https://www.journals.elsevier.com/computer-methods-and-programs-in-biomedicine/most-downloaded-articles'
 text = 'CMPB'
 html_href = f'<a href="{url}">{text}</a>'
 message = f'TorchIO becomes one of the most downloaded articles from {html_href}!'
@@ -221,9 +221,7 @@
 epub_exclude_files = ['search.html']
 
 # CopyButton configuration
-copybutton_prompt_text = (
-    r'>>> |\.\.\. |\$ |In \[\d*\]: | {2,5}\.\.\.: | {5,8}: '  # noqa: B950,FS003
-)
+copybutton_prompt_text = (r'>>> |\.\.\. |\$ |In \[\d*\]: | {2,5}\.\.\.: | {5,8}: ',)
 copybutton_prompt_is_regexp = True
 
 # def setup(app):

pyproject.toml

@@ -53,7 +53,6 @@ csv = [
     "pandas",
 ]
 dev = [
-    "black",
     "bump2version",
     "coverage",
     "mypy",
@@ -98,11 +97,6 @@ Source = "https://github.com/fepegar/torchio"
 Documentation = "http://torchio.rtfd.io"
 "Release notes" = "https://github.com/fepegar/torchio/releases"
 
-[tool.black]
-preview = false
-skip-string-normalization = true
-target-version = ['py311']
-
 [tool.mypy]
 pretty = true
 
@@ -127,11 +121,17 @@ markers = [
   "slow: marks tests as slow (deselect with '-m \"not slow\"')",
   "serial",
 ]
-
 filterwarnings = [
     # Ignore SimpleITK Swig warnings
     "ignore:builtin type .* has no __module__ attribute",
     "ignore:Casting complex values to real discards the imaginary part",
     # Raised by SimpleITK on CI
     "ignore:invalid escape sequence",
 ]
+
+[tool.ruff]
+format.quote-style = 'single'
+lint.select = ["F", "I"]
+
+[tool.ruff.lint.isort]
+force-single-line = true

src/torchio/__init__.py

@@ -5,29 +5,26 @@
 __version__ = '0.20.0'
 
 
+from . import datasets
+from . import reference
 from . import utils
 from .constants import *  # noqa: F401, F403
+from .data import GridAggregator
+from .data import GridSampler
+from .data import Image
+from .data import LabelMap
+from .data import LabelSampler
+from .data import Queue
+from .data import ScalarImage
+from .data import Subject
+from .data import SubjectsDataset
+from .data import SubjectsLoader
+from .data import UniformSampler
+from .data import WeightedSampler
+from .data import inference
+from .data import io
+from .data import sampler
 from .transforms import *  # noqa: F401, F403
-from .data import (
-    io,
-    sampler,
-    inference,
-    SubjectsDataset,
-    SubjectsLoader,
-    Image,
-    ScalarImage,
-    LabelMap,
-    Queue,
-    Subject,
-    WeightedSampler,
-    UniformSampler,
-    LabelSampler,
-    GridSampler,
-    GridAggregator,
-)
-from . import datasets
-from . import reference
-
 
 __all__ = [
     'utils',

src/torchio/cli/apply_transform.py

@@ -3,8 +3,9 @@
 from pathlib import Path
 
 import typer
-from rich.progress import Progress, SpinnerColumn, TextColumn
-
+from rich.progress import Progress
+from rich.progress import SpinnerColumn
+from rich.progress import TextColumn
 
 app = typer.Typer()
 
@@ -61,9 +62,10 @@ def main(
 
     Example:
     $ tiotr input.nrrd RandomMotion output.nii "degrees=(-5,15) num_transforms=3" -v
-    """  # noqa: B950
+    """
     # Imports are placed here so that the tool loads faster if not being run
     import torch
+
     import torchio.transforms as transforms
     from torchio.utils import apply_transform_to_file
 
@@ -79,7 +81,7 @@ def main(
         torch.manual_seed(seed)
     with Progress(
         SpinnerColumn(),
-        TextColumn('[progress.description]{task.description}'),  # noqa: FS003
+        TextColumn('[progress.description]{task.description}'),
         transient=True,
         disable=not show_progress,
     ) as progress:

src/torchio/cli/print_info.py

@@ -3,7 +3,6 @@
 
 import typer
 
-
 app = typer.Typer()
 
 

src/torchio/data/__init__.py

@@ -12,7 +12,6 @@
 from .sampler import WeightedSampler
 from .subject import Subject
 
-
 __all__ = [
     'Queue',
     'Subject',

src/torchio/data/dataset.py

@@ -62,7 +62,7 @@ class SubjectsDataset(Dataset):
 
     .. tip:: To quickly iterate over the subjects without loading the images,
         use :meth:`dry_iter()`.
-    """  # noqa: B950
+    """
 
     def __init__(
         self,

src/torchio/data/image.py

@@ -34,9 +34,9 @@
 from ..typing import TypeTripletFloat
 from ..typing import TypeTripletInt
 from ..utils import get_stem
-from ..utils import to_tuple
 from ..utils import guess_external_viewer
 from ..utils import is_iterable
+from ..utils import to_tuple
 from .io import check_uint_to_int
 from .io import ensure_4d
 from .io import get_rotation_and_spacing_from_affine
@@ -48,7 +48,6 @@
 from .io import sitk_to_nib
 from .io import write_image
 
-
 PROTECTED_KEYS = DATA, AFFINE, TYPE, PATH, STEM
 TypeBound = Tuple[float, float]
 TypeBounds = Tuple[TypeBound, TypeBound, TypeBound]
@@ -128,7 +127,7 @@ class Image(dict):
     .. _FSL docs: https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Orientation%20Explained
     .. _SimpleITK docs: https://simpleitk.readthedocs.io/en/master/fundamentalConcepts.html
     .. _Graham Wideman's website: http://www.grahamwideman.com/gw/brain/orientation/orientterms.htm
-    """  # noqa: B950
+    """
 
     def __init__(
         self,
@@ -470,7 +469,7 @@ def _parse_path(
             # https://github.com/fepegar/torchio/pull/838
             raise TypeError('The path argument cannot be a dictionary')
         elif self._is_paths_sequence(path):
-            return [self._parse_single_path(p) for p in path]  # type: ignore[union-attr]  # noqa: B950
+            return [self._parse_single_path(p) for p in path]  # type: ignore[union-attr]
         else:
             return self._parse_single_path(path)  # type: ignore[arg-type]
 
@@ -655,7 +654,7 @@ def from_sitk(cls, sitk_image):
             >>> sitk_image = sitk.Image((224, 224), sitk.sitkVectorFloat32, 3)
             >>> tio.ScalarImage.from_sitk(sitk_image)
             ScalarImage(shape: (3, 224, 224, 1); spacing: (1.00, 1.00, 1.00); orientation: LPS+; memory: 588.0 KiB; dtype: torch.FloatTensor)
-        """  # noqa: B950
+        """
         tensor, affine = sitk_to_nib(sitk_image)
         return cls(tensor=tensor, affine=affine)
 
@@ -712,7 +711,7 @@ def to_gif(
                 eliminating unused colors. This is only useful if the palette
                 can be compressed to the next smaller power of 2 elements.
             reverse: Reverse the temporal order of frames.
-        """  # noqa: B950
+        """
         from ..visualization import make_gif  # avoid circular import
 
         make_gif(

src/torchio/data/inference/aggregator.py

@@ -30,7 +30,7 @@ class GridAggregator:
     .. note:: Adapted from NiftyNet. See `this NiftyNet tutorial
         <https://niftynet.readthedocs.io/en/dev/window_sizes.html>`_ for more
         information about patch-based sampling.
-    """  # noqa: B950
+    """
 
     def __init__(self, sampler: GridSampler, overlap_mode: str = 'crop'):
         subject = sampler.subject

src/torchio/data/io.py

@@ -20,7 +20,6 @@
 from ..typing import TypeTripletFloat
 from ..typing import TypeTripletInt
 
-
 # Matrices used to switch between LPS and RAS
 FLIPXY_33 = np.diag([-1, -1, 1])
 FLIPXY_44 = np.diag([-1, -1, 1, 1])

src/torchio/data/loader.py

@@ -7,12 +7,11 @@
 
 import numpy as np
 import torch
-from torch.utils.data import Dataset
 from torch.utils.data import DataLoader
+from torch.utils.data import Dataset
 
 from .subject import Subject
 
-
 T = TypeVar('T')