STY: Fix flake8 warnings (#3044)

Except E501 (lines too long).

.maint/update_authors.py

@@ -121,7 +121,7 @@ def get_git_lines(fname="line-contributors.txt"):
     if not lines and git_line_summary_path:
         print("Running git-line-summary on repo")
         lines = sp.check_output([git_line_summary_path]).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:

.maint/update_zenodo.py

@@ -75,7 +75,7 @@ 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

@@ -22,7 +22,7 @@
 sys.path.append(os.path.abspath("sphinxext"))
 sys.path.insert(0, os.path.abspath("../wrapper"))
 
-from github_link import make_linkcode_resolve
+from github_link import make_linkcode_resolve  # noqa: E402
 
 # -- General configuration ------------------------------------------------
 

fmriprep/interfaces/confounds.py

@@ -31,15 +31,13 @@
 """
 import os
 import re
-import shutil
 
 import nibabel as nb
 import numpy as np
 import pandas as pd
 from nipype import logging
 from nipype.interfaces.base import (
     BaseInterfaceInputSpec,
-    Directory,
     File,
     InputMultiObject,
     OutputMultiObject,

fmriprep/interfaces/gifti.py

@@ -6,7 +6,6 @@
 import nibabel as nb
 import numpy as np
 from nipype.interfaces.base import File, SimpleInterface, TraitedSpec, isdefined, traits
-from nipype.utils.filemanip import fname_presuffix
 
 
 class CreateROIInputSpec(TraitedSpec):

fmriprep/workflows/bold/base.py

@@ -192,7 +192,7 @@ def init_func_preproc_wf(bold_file, has_fieldmap=False):
     from niworkflows.interfaces.reportlets.registration import (
         SimpleBeforeAfterRPT as SimpleBeforeAfter,
     )
-    from niworkflows.interfaces.utility import DictMerge, KeySelect
+    from niworkflows.interfaces.utility import KeySelect
 
     img = nb.load(bold_file[0] if isinstance(bold_file, (list, tuple)) else bold_file)
     nvols = 1 if img.ndim < 4 else img.shape[3]

fmriprep/workflows/bold/confounds.py

@@ -27,16 +27,11 @@
 .. autofunction:: init_bold_confs_wf
 
 """
-from os import getenv
-
 from nipype.algorithms import confounds as nac
-from nipype.interfaces import fsl
 from nipype.interfaces import utility as niu
 from nipype.pipeline import engine as pe
 from templateflow.api import get as get_template
 
-from fmriprep import config
-
 from ...config import DEFAULT_MEMORY_MIN_GB
 from ...interfaces import DerivativesDataSink
 from ...interfaces.confounds import (

fmriprep/workflows/bold/tests/test_base.py

@@ -1,7 +1,6 @@
 from copy import deepcopy
 
 import bids
-import pytest
 from niworkflows.utils.testing import generate_bids_skeleton
 from sdcflows.fieldmaps import clear_registry
 from sdcflows.utils.wrangler import find_estimators
@@ -64,7 +63,7 @@ def test_get_estimator_b0field_and_intendedfor(tmp_path):
 
     generate_bids_skeleton(bids_dir, spec)
     layout = bids.BIDSLayout(bids_dir)
-    estimators = find_estimators(layout=layout, subject='01')
+    _ = find_estimators(layout=layout, subject='01')
 
     bold_files = sorted(layout.get(suffix='bold', extension='.nii.gz', return_type='file'))
 
@@ -91,7 +90,7 @@ def test_get_estimator_overlapping_specs(tmp_path):
 
     generate_bids_skeleton(bids_dir, spec)
     layout = bids.BIDSLayout(bids_dir)
-    estimators = find_estimators(layout=layout, subject='01')
+    _ = find_estimators(layout=layout, subject='01')
 
     bold_files = sorted(layout.get(suffix='bold', extension='.nii.gz', return_type='file'))
 
@@ -115,7 +114,7 @@ def test_get_estimator_multiple_b0fields(tmp_path):
 
     generate_bids_skeleton(bids_dir, spec)
     layout = bids.BIDSLayout(bids_dir)
-    estimators = find_estimators(layout=layout, subject='01')
+    _ = find_estimators(layout=layout, subject='01')
 
     bold_files = sorted(layout.get(suffix='bold', extension='.nii.gz', return_type='file'))