Replace isort and black with ruff

.github/workflows/code-style.yml

@@ -19,20 +19,12 @@ jobs:
  uses: actions/setup-python@v5
  with:
  python-version: '3.10'
- #architecture: 'x64'
  - name: Install dependencies
  run: |
  python -m pip install --progress-bar off --upgrade pip setuptools wheel
  python -m pip install --progress-bar off .[style]
  - name: Run Ruff
  run: ruff check .
- - name: Run isort
- uses: isort/isort-action@master
- - name: Run black
- uses: psf/black@stable
- with:
- options: "--check --verbose"
- version: "23.10.1"
  - name: Run codespell
  uses: codespell-project/actions-codespell@master
  with:

pyproject.toml

@@ -68,9 +68,7 @@ doc = [
 ]
 style = [
  'bibclean',
- 'black',
  'codespell',
- 'isort',
  'pydocstyle[toml]',
  'ruff',
 ]
@@ -109,32 +107,6 @@ exclude = ['whippersnappy*tests']
 [tool.setuptools.package-data]
 whippersnappy = ['*.ttf']
 
-[tool.black]
-line-length = 88
-target-version = ['py310']
-include = '\.pyi?$'
-extend-exclude = '''
-(
- __pycache__
- | .github
- | setup.py
- | doc/
- | whippersnappy/read_geometry.py
-)
-'''
-
-[tool.isort]
-profile = 'black'
-multi_line_output = 3
-line_length = 88
-py_version = 310
-extend_skip_glob = [
- 'setup.py',
- 'data/*',
- 'doc/*',
- 'examples/*',
-]
-
 [tool.pydocstyle]
 convention = 'numpy'
 ignore-decorators = '(copy_doc|property|.*setter|.*getter|pyqtSlot|Slot)'
@@ -150,7 +122,21 @@ extend-exclude = [
 ]
 
 [tool.ruff.lint]
-select = ["NPY201"]
+# https://docs.astral.sh/ruff/linter/#rule-selection
+select = [
+ # pycodestyle
+ "E",
+ # Pyflakes
+ "F",
+ # pyupgrade
+ "UP",
+ # flake8-bugbear
+ "B",
+ # flake8-simplify
+ # "SIM",
+ # isort
+ "I",
+]
 
 [tool.ruff.lint.per-file-ignores]
 "__init__.py" = ["F401"]

whippersnappy/cli/whippersnap.py

@@ -103,9 +103,7 @@ def show_window(
  found_surfname = get_surf_name(sdir, hemi)
  if found_surfname is None:
  print(
- "[ERROR] Could not find a valid surf file in {} for hemi: {}!".format(
- sdir, hemi
- )
+ f"[ERROR] Could not find a valid surf file in {sdir} for hemi: {hemi}!"
  )
  sys.exit(0)
  meshpath = os.path.join(sdir, "surf", hemi + "." + found_surfname)

whippersnappy/config_app.py

@@ -46,7 +46,7 @@ def __init__(
  initial_fthresh_value=2.0,
  initial_fmax_value=4.0,
  ):
- super(ConfigWindow, self).__init__(parent)
+ super().__init__(parent)
 
  self.current_fthresh_value = initial_fthresh_value
  self.current_fmax_value = initial_fmax_value

whippersnappy/core.py

@@ -650,7 +650,7 @@ def create_colorbar(fmin, fmax, invert, neg=True, font_file=None):
  cwidth = 200
  cheight = 30
  # img = Image.new("RGB", (cwidth, cheight), color=(90, 90, 90))
- values = np.nan * np.ones((cwidth))
+ values = np.nan * np.ones(cwidth)
  gapspace = 0
  if fmin > 0.01:
  # leave gray gap
@@ -682,13 +682,13 @@ def create_colorbar(fmin, fmax, invert, neg=True, font_file=None):
  font = ImageFont.truetype(font_file, 12)
  if neg:
  # Left
- caption = " <{:.2f}".format(-fmax)
+ caption = f" <{-fmax:.2f}"
  xpos = 0 # 10- 0.5*(font.getlength(caption))
  ImageDraw.Draw(image).text(
  (xpos, image.height - 17), caption, (220, 220, 220), font=font
  )
  # Right
- caption = ">{:.2f} ".format(fmax)
+ caption = f">{fmax:.2f} "
  xpos = image.width - (font.getlength(caption))
  ImageDraw.Draw(image).text(
  (xpos, image.height - 17), caption, (220, 220, 220), font=font
@@ -700,25 +700,25 @@ def create_colorbar(fmin, fmax, invert, neg=True, font_file=None):
  (xpos, image.height - 17), caption, (220, 220, 220), font=font
  )
  else:
- caption = "{:.2f}".format(-fmin)
+ caption = f"{-fmin:.2f}"
  xpos = 0.5 * image.width - 0.5 * font.getlength(caption) - gapspace - 5
  ImageDraw.Draw(image).text(
  (xpos, image.height - 17), caption, (220, 220, 220), font=font
  )
- caption = "{:.2f}".format(fmin)
+ caption = f"{fmin:.2f}"
  xpos = 0.5 * image.width - 0.5 * font.getlength(caption) + gapspace + 5
  ImageDraw.Draw(image).text(
  (xpos, image.height - 17), caption, (220, 220, 220), font=font
  )
  else:
  # Right
- caption = ">{:.2f} ".format(fmax)
+ caption = f">{fmax:.2f} "
  xpos = image.width - (font.getlength(caption))
  ImageDraw.Draw(image).text(
  (xpos, image.height - 17), caption, (220, 220, 220), font=font
  )
  # Left
- caption = " {:.2f}".format(fmin)
+ caption = f" {fmin:.2f}"
  xpos = gapspace
  if gapspace == 0:
  caption = " 0"
@@ -824,9 +824,7 @@ def snap4(
 
  if found_surfname is None:
  print(
- "[ERROR] Could not find valid surf file in {} for hemi: {}!".format(
- sdir, hemi
- )
+ f"[ERROR] Could not find valid surface in {sdir} for hemi: {hemi}!"
  )
  sys.exit(1)
  meshpath = os.path.join(sdir, "surf", hemi + "." + found_surfname)
@@ -902,7 +900,7 @@ def snap4(
  image.paste(bar, (xpos, ypos))
 
  if outpath:
- print("[INFO] Saving snapshot to {}".format(outpath))
+ print(f"[INFO] Saving snapshot to {outpath}")
  image.save(outpath)
 
 

whippersnappy/read_geometry.py

@@ -1,16 +1,7 @@
-# IMPORTS
-import warnings
-from collections import OrderedDict
-
-import nibabel as nib
-import numpy as np
-
-"""
-Read FreeSurfer geometry (fix for dev, ll 126-128);
+"""Read FreeSurfer geometry (fix for dev, ll 126-128);
 
 Code was taken from nibabel.freesurfer package
 (https://github.com/nipy/nibabel/blob/master/nibabel/freesurfer/io.py).
-
 This software is licensed under the following license:
 
 The MIT License
@@ -42,10 +33,15 @@
 THE SOFTWARE.
 """
 
+import warnings
+from collections import OrderedDict
+
+import nibabel as nib
+import numpy as np
+
 
 def _fread3(fobj):
- """
- Read a 3-byte int from an open binary file object
+ """Read a 3-byte int from an open binary file object.
 
  Parameters
  ----------
@@ -62,15 +58,26 @@ def _fread3(fobj):
 
 
 def _read_volume_info(fobj):
- """Helper for reading the footer from a surface file."""
+ """Read the footer from a surface file.
+
+ Parameters
+ ----------
+ fobj : file
+ File descriptor
+
+ Returns
+ -------
+ volume_info : array
+ Key-value pairs found in the file.
+ """
  volume_info = OrderedDict()
  head = np.fromfile(fobj, ">i4", 1)
  if not np.array_equal(head, [20]): # Read two bytes more
  head = np.concatenate([head, np.fromfile(fobj, ">i4", 2)])
  if not np.array_equal(head, [2, 0, 20]) and not np.array_equal(
  head, [2, 1, 20]
  ):
- warnings.warn("Unknown extension code.")
+ warnings.warn("Unknown extension code.", stacklevel=2)
  return volume_info
  head = [2, 0, 20]
 
@@ -87,7 +94,7 @@ def _read_volume_info(fobj):
  ]:
  pair = fobj.readline().decode("utf-8").split("=")
  if pair[0].strip() != key or len(pair) != 2:
- raise IOError("Error parsing volume info.")
+ raise OSError("Error parsing volume info.")
  if key in ("valid", "filename"):
  volume_info[key] = pair[1].strip()
  elif key == "volume":
@@ -99,34 +106,23 @@ def _read_volume_info(fobj):
 
 
 def read_geometry(filepath, read_metadata=False, read_stamp=False):
- """
- Read a triangular format Freesurfer surface mesh.
+ """Read a triangular format Freesurfer surface mesh.
 
  Parameters
  ----------
  filepath : str
  Path to surface file.
  read_metadata : bool, optional
  If True, read and return metadata as key-value pairs.
-
  Valid keys:
-
  * 'head' : array of int
-
  * 'valid' : str
-
  * 'filename' : str
-
  * 'volume' : array of int, shape (3,)
-
  * 'voxelsize' : array of float, shape (3,)
-
  * 'xras' : array of float, shape (3,)
-
  * 'yras' : array of float, shape (3,)
-
  * 'zras' : array of float, shape (3,)
-
  * 'cras' : array of float, shape (3,)
  read_stamp : bool, optional
  Return the comment from the file
@@ -173,7 +169,7 @@ def read_geometry(filepath, read_metadata=False, read_stamp=False):
  ret = (coords, faces)
  if read_metadata:
  if len(volume_info) == 0:
- warnings.warn("No volume information contained in the file")
+ warnings.warn("No volume information contained in the file", stacklevel=2)
  ret += (volume_info,)
  if read_stamp:
  ret += (create_stamp,)
@@ -182,8 +178,8 @@ def read_geometry(filepath, read_metadata=False, read_stamp=False):
 
 
 def read_morph_data(filepath):
- """
- Read a Freesurfer morphometry data file.
+ """Read a Freesurfer morphometry data file.
+
  This function reads in what Freesurfer internally calls "curv" file types,
  (e.g. ?h. curv, ?h.thickness), but as that has the potential to cause
  confusion where "curv" also refers to the surface curvature values,
@@ -212,8 +208,7 @@ def read_morph_data(filepath):
 
 
 def read_mgh_data(filepath):
- """
- Read an MGH image file and return its data array.
+ """Read an MGH image file and return its data array.
 
  Parameters
  ----------
@@ -231,8 +226,6 @@ def read_mgh_data(filepath):
  len(data_array.shape) == 3
  and data_array.shape[1] == 1
  and data_array.shape[2] == 1
- ), "Expected data array to have shape Nx1x1. Instead, got {}".format(
- data_array.shape
- )
+ ), f"Expected data array to have shape Nx1x1. Instead, got {data_array.shape}"
 
  return data_array.squeeze()

whippersnappy/utils/_config.py

@@ -3,7 +3,7 @@
 import sys
 from functools import partial
 from importlib.metadata import requires, version
-from typing import IO, Callable, List, Optional
+from typing import IO, Callable, Optional
 
 import psutil
 
@@ -67,7 +67,7 @@ def sys_info(fid: Optional[IO] = None, developer: bool = False):
  _list_dependencies_info(out, ljust, dependencies)
 
 
-def _list_dependencies_info(out: Callable, ljust: int, dependencies: List[str]):
+def _list_dependencies_info(out: Callable, ljust: int, dependencies: list[str]):
  """List dependencies names and versions.
 
  Parameters