run: ruff check --fix [ignore-rev]

Author: effigies

.maint/update_authors.py

@@ -9,9 +9,10 @@
 # ///
 """Update and sort the creators list of the zenodo record."""
 
+import json
 import sys
 from pathlib import Path
-import json
+
 import click
 from fuzzywuzzy import fuzz, process
 
@@ -123,7 +124,7 @@ def get_git_lines(fname='line-contributors.txt'):
     if not lines and cmd[0]:
         print(f'Running {" ".join(cmd)!r} on repo')
         lines = sp.check_output(cmd).decode().splitlines()
-        lines = [l for l in lines if 'Not Committed Yet' not in l]
+        lines = [line for line in lines if 'Not Committed Yet' not in line]
         contrib_file.write_text('\n'.join(lines))
 
     if not lines:

docs/conf.py

@@ -8,7 +8,8 @@
 """
 
 from packaging.version import Version
-from sdcflows import __version__, __copyright__, __packagename__
+
+from sdcflows import __copyright__, __packagename__, __version__
 
 # -- Path setup --------------------------------------------------------------
 # If extensions (or modules to document with autodoc) are in another directory,

docs/notebooks/SDC - Theory and physics.ipynb

@@ -54,9 +54,10 @@
    "outputs": [],
    "source": [
     "from itertools import product\n",
+    "\n",
+    "import nibabel as nb\n",
     "import numpy as np\n",
     "from scipy import ndimage as ndi\n",
-    "import nibabel as nb\n",
     "from templateflow.api import get"
    ]
   },

docs/tools/apigen.py

@@ -21,7 +21,6 @@
 import os
 import re
 from inspect import getmodule
-
 from types import BuiltinFunctionType, FunctionType
 
 # suppress print statements (warnings for empty files)
@@ -43,7 +42,7 @@ def __init__(
         module_skip_patterns=None,
         other_defines=True,
     ):
-        """Initialize package for parsing
+        r"""Initialize package for parsing
 
         Parameters
         ----------
@@ -362,7 +361,7 @@ def _survives_exclude(self, matchstr, match_type):
         return True
 
     def discover_modules(self):
-        """Return module sequence discovered from ``self.package_name``
+        r"""Return module sequence discovered from ``self.package_name``
 
 
         Parameters
@@ -410,7 +409,6 @@ def discover_modules(self):
 
     def write_modules_api(self, modules, outdir):
         # upper-level modules
-        main_module = modules[0].split('.')[0]
         ulms = [
             '.'.join(m.split('.')[:2]) if m.count('.') >= 1 else m.split('.')[0] for m in modules
         ]

docs/tools/buildmodref.py

@@ -1,17 +1,17 @@
 #!/usr/bin/env python
 """Script to auto-generate API docs."""
 
-from __future__ import print_function, division
+from __future__ import division, print_function
 
 # stdlib imports
 import sys
 
-# local imports
-from apigen import ApiDocWriter
-
 # version comparison
 from distutils.version import LooseVersion as V
 
+# local imports
+from apigen import ApiDocWriter
+
 # *****************************************************************************
 
 

sdcflows/__init__.py

@@ -5,7 +5,7 @@
 try:
     from ._version import __version__
 except ModuleNotFoundError:
-    from importlib.metadata import version, PackageNotFoundError
+    from importlib.metadata import PackageNotFoundError, version
 
     try:
         __version__ = version(__packagename__)

sdcflows/cli/main.py

@@ -25,11 +25,12 @@
 
 def main(argv=None):
     """Entry point for SDCFlows' CLI."""
+    import atexit
     import gc
     import os
     import sys
     from tempfile import mktemp
-    import atexit
+
     from sdcflows import config
     from sdcflows.cli.parser import parse_args
 
@@ -59,6 +60,7 @@ def main(argv=None):
 
     if config.execution.dry_run:  # --dry-run: pretty print results
         from niworkflows.utils.bids import collect_participants
+
         from sdcflows.utils.wrangler import find_estimators
 
         subjects = collect_participants(
@@ -91,9 +93,9 @@ def main(argv=None):
     # Initialize process pool if multiprocessing
     _pool = None
     if config.nipype.plugin in ('MultiProc', 'LegacyMultiProc'):
-        from contextlib import suppress
         import multiprocessing as mp
         from concurrent.futures import ProcessPoolExecutor
+        from contextlib import suppress
 
         os.environ['OMP_NUM_THREADS'] = '1'
 

sdcflows/cli/parser.py

@@ -270,8 +270,8 @@ def _bids_filter(value):
 
 def parse_args(args=None, namespace=None):
     """Parse args and run further checks on the command line."""
-    from logging import DEBUG
     from json import loads
+    from logging import DEBUG
 
     parser = _parser()
     opts = parser.parse_args(args, namespace)

sdcflows/cli/tests/test_find_estimators.py

@@ -23,6 +23,7 @@
 """Check the CLI."""
 
 from importlib import reload
+
 import pytest
 from niworkflows.utils.testing import generate_bids_skeleton
 

sdcflows/config.py

@@ -124,8 +124,8 @@
     from importlib_metadata import version as get_version
 
 # Ignore annoying warnings
-from sdcflows._warnings import logging
 from sdcflows import __version__
+from sdcflows._warnings import logging
 
 _pre_exec_env = dict(os.environ)
 
@@ -426,8 +426,9 @@ def init(cls):
 
         if cls._layout is None:
             import re
-            from bids.layout.index import BIDSLayoutIndexer
+
             from bids.layout import BIDSLayout
+            from bids.layout.index import BIDSLayoutIndexer
 
             ignore_paths = [
                 # Ignore folders at the top if they don't start with /sub-<label>/
@@ -532,8 +533,8 @@ def init(cls):
 
         """
         if not cls._init:
-            from nipype import logging as nlogging
             from nipype import config as ncfg
+            from nipype import logging as nlogging
 
             cls.workflow = nlogging.getLogger('nipype.workflow')
             cls.interface = nlogging.getLogger('nipype.interface')