Merge pull request #3681 from DimitriPapadopoulos/F

STY: Apply ruff/Pyflakes rules (F)

nipype/__init__.py

@@ -25,7 +25,7 @@
     import faulthandler
 
     faulthandler.enable()
-except (ImportError, OSError) as e:
+except (ImportError, OSError):
     pass
 
 config = NipypeConfig()

nipype/algorithms/misc.py

@@ -1345,7 +1345,7 @@ def split_rois(in_file, mask=None, roishape=None):
     """
     import nibabel as nb
     import numpy as np
-    from math import sqrt, ceil
+    from math import ceil
     import os.path as op
 
     if roishape is None:

nipype/algorithms/tests/test_ErrorMap.py

@@ -1,11 +1,8 @@
 #!/usr/bin/env python
 
-import pytest
-from nipype.testing import example_data
 from nipype.algorithms.metrics import ErrorMap
 import nibabel as nb
 import numpy as np
-import os
 
 
 def test_errormap(tmpdir):

nipype/algorithms/tests/test_Overlap.py

@@ -2,7 +2,6 @@
 # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
 # vi: set ft=python sts=4 ts=4 sw=4 et:
 
-import os
 
 from nipype.testing import example_data
 

nipype/algorithms/tests/test_confounds.py

@@ -1,5 +1,4 @@
 #!/usr/bin/env python
-import os
 
 import pytest
 from nipype.testing import example_data

nipype/algorithms/tests/test_mesh_ops.py

@@ -1,10 +1,8 @@
 # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
 # vi: set ft=python sts=4 ts=4 sw=4 et:
 
-import os
 
 import pytest
-import nipype.testing as npt
 from nipype.testing import example_data
 import numpy as np
 from nipype.algorithms import mesh as m

nipype/algorithms/tests/test_modelgen.py

@@ -2,7 +2,6 @@
 # vi: set ft=python sts=4 ts=4 sw=4 et:
 
 from copy import deepcopy
-import os
 
 from nibabel import Nifti1Image
 import numpy as np

nipype/algorithms/tests/test_normalize_tpms.py

@@ -1,14 +1,11 @@
 # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
 # vi: set ft=python sts=4 ts=4 sw=4 et:
 
-import os
 
-import pytest
 from nipype.testing import example_data
 
 import numpy as np
 import nibabel as nb
-import nipype.testing as nit
 
 from nipype.algorithms.misc import normalize_tpms
 

nipype/algorithms/tests/test_splitmerge.py

@@ -6,8 +6,6 @@
 def test_split_and_merge(tmpdir):
     import numpy as np
     import nibabel as nb
-    import os.path as op
-    import os
 
     from nipype.algorithms.misc import split_rois, merge_rois
 

nipype/interfaces/afni/model.py

@@ -12,26 +12,19 @@
 import os
 
 from ..base import (
-    CommandLineInputSpec,
-    CommandLine,
-    Directory,
     TraitedSpec,
     traits,
     isdefined,
     File,
     InputMultiPath,
-    Undefined,
     Str,
     Tuple,
 )
-from ...external.due import BibTeX
 
 from .base import (
-    AFNICommandBase,
     AFNICommand,
     AFNICommandInputSpec,
     AFNICommandOutputSpec,
-    Info,
 )
 
 

nipype/interfaces/ants/base.py

@@ -2,7 +2,7 @@
 # vi: set ft=python sts=4 ts=4 sw=4 et:
 """The ants module provides basic functions for interfacing with ANTS tools."""
 import os
-from packaging.version import Version, parse
+from packaging.version import parse
 
 # Local imports
 from ... import logging

nipype/interfaces/ants/resampling.py

@@ -122,7 +122,7 @@ def _format_arg(self, opt, spec, val):
             if isdefined(self.inputs.invert_affine):
                 diff_inv = set(self.inputs.invert_affine) - set(affine_invert)
                 if diff_inv:
-                    raise Exceptions(
+                    raise Exception(
                         "Review invert_affine, not all indexes from invert_affine were used, "
                         "check the description for the full definition"
                     )
@@ -275,7 +275,7 @@ def _format_arg(self, opt, spec, val):
             if isdefined(self.inputs.invert_affine):
                 diff_inv = set(self.inputs.invert_affine) - set(affine_invert)
                 if diff_inv:
-                    raise Exceptions(
+                    raise Exception(
                         "Review invert_affine, not all indexes from invert_affine were used, "
                         "check the description for the full definition"
                     )

nipype/interfaces/cat12/preprocess.py

@@ -576,7 +576,7 @@ def _list_outputs(self):
         ]
 
         outputs["report"] = fname_presuffix(
-            f, prefix=os.path.join("report", f"cat_"), suffix=".xml", use_ext=False
+            f, prefix=os.path.join("report", "cat_"), suffix=".xml", use_ext=False
         )
 
         outputs["label_files"] = [

nipype/interfaces/cmtk/convert.py

@@ -2,7 +2,6 @@
 import os.path as op
 import datetime
 import string
-import networkx as nx
 
 from ...utils.filemanip import split_filename
 from ..base import (
@@ -13,7 +12,7 @@
     InputMultiPath,
     isdefined,
 )
-from .base import CFFBaseInterface, have_cfflib
+from .base import CFFBaseInterface
 
 
 def _read_pickle(fname):

nipype/interfaces/cmtk/nbs.py

@@ -18,7 +18,6 @@
     OutputMultiPath,
     isdefined,
 )
-from .base import have_cv
 
 iflogger = logging.getLogger("nipype.interface")
 

nipype/interfaces/cmtk/nx.py

@@ -18,7 +18,6 @@
     OutputMultiPath,
     isdefined,
 )
-from .base import have_cmp
 
 iflogger = logging.getLogger("nipype.interface")
 

nipype/interfaces/cmtk/parcellation.py

@@ -10,7 +10,6 @@
 
 from ... import logging
 from ..base import (
-    BaseInterface,
     LibraryBaseInterface,
     BaseInterfaceInputSpec,
     traits,
@@ -19,21 +18,20 @@
     Directory,
     isdefined,
 )
-from .base import have_cmp
 
 iflogger = logging.getLogger("nipype.interface")
 
 
 def create_annot_label(subject_id, subjects_dir, fs_dir, parcellation_name):
-    import cmp
+    from cmp.configuration import PipelineConfiguration
     from cmp.util import runCmd
 
     iflogger.info("Create the cortical labels necessary for our ROIs")
     iflogger.info("=================================================")
     fs_label_dir = op.join(op.join(subjects_dir, subject_id), "label")
     output_dir = op.abspath(op.curdir)
     paths = []
-    cmp_config = cmp.configuration.PipelineConfiguration()
+    cmp_config = PipelineConfiguration()
     cmp_config.parcellation_scheme = "Lausanne2008"
     for hemi in ["lh", "rh"]:
         spath = (
@@ -334,13 +332,13 @@ def create_annot_label(subject_id, subjects_dir, fs_dir, parcellation_name):
 def create_roi(subject_id, subjects_dir, fs_dir, parcellation_name, dilation):
     """Creates the ROI_%s.nii.gz files using the given parcellation information
     from networks. Iteratively create volume."""
-    import cmp
+    from cmp.configuration import PipelineConfiguration
     from cmp.util import runCmd
 
     iflogger.info("Create the ROIs:")
     output_dir = op.abspath(op.curdir)
     fs_dir = op.join(subjects_dir, subject_id)
-    cmp_config = cmp.configuration.PipelineConfiguration()
+    cmp_config = PipelineConfiguration()
     cmp_config.parcellation_scheme = "Lausanne2008"
     log = cmp_config.get_logger()
     parval = cmp_config._get_lausanne_parcellation("Lausanne2008")[parcellation_name]
@@ -469,12 +467,12 @@ def create_roi(subject_id, subjects_dir, fs_dir, parcellation_name, dilation):
 
 
 def create_wm_mask(subject_id, subjects_dir, fs_dir, parcellation_name):
-    import cmp
+    from cmp.configuration import PipelineConfiguration
     import scipy.ndimage.morphology as nd
 
     iflogger.info("Create white matter mask")
     fs_dir = op.join(subjects_dir, subject_id)
-    cmp_config = cmp.configuration.PipelineConfiguration()
+    cmp_config = PipelineConfiguration()
     cmp_config.parcellation_scheme = "Lausanne2008"
     pgpath = cmp_config._get_lausanne_parcellation("Lausanne2008")[parcellation_name][
         "node_information_graphml"
@@ -620,10 +618,11 @@ def create_wm_mask(subject_id, subjects_dir, fs_dir, parcellation_name):
 def crop_and_move_datasets(
     subject_id, subjects_dir, fs_dir, parcellation_name, out_roi_file, dilation
 ):
+    from cmp.configuration import PipelineConfiguration
     from cmp.util import runCmd
 
     fs_dir = op.join(subjects_dir, subject_id)
-    cmp_config = cmp.configuration.PipelineConfiguration()
+    cmp_config = PipelineConfiguration()
     cmp_config.parcellation_scheme = "Lausanne2008"
     log = cmp_config.get_logger()
     output_dir = op.abspath(op.curdir)

nipype/interfaces/cmtk/tests/test_nbs.py

@@ -8,7 +8,7 @@
 have_cv = True
 try:
     package_check("cviewer")
-except Exception as e:
+except Exception:
     have_cv = False
 
 
@@ -39,7 +39,7 @@ def test_importerror(creating_graphs, tmpdir):
     nbs.inputs.in_group2 = group2
     nbs.inputs.edge_key = "weight"
 
-    with pytest.raises(ImportError) as e:
+    with pytest.raises(ImportError):
         nbs.run()
 
 

nipype/interfaces/dipy/base.py

@@ -3,7 +3,6 @@
 import os.path as op
 import inspect
 import numpy as np
-from ... import logging
 from ..base import (
     traits,
     File,

nipype/interfaces/dipy/reconstruction.py

@@ -85,7 +85,6 @@ class RESTORE(DipyDiffusionInterface):
     def _run_interface(self, runtime):
         from scipy.special import gamma
         from dipy.reconst.dti import TensorModel
-        import gc
 
         img = nb.load(self.inputs.in_file)
         hdr = img.header.copy()
@@ -222,7 +221,6 @@ class EstimateResponseSH(DipyDiffusionInterface):
     output_spec = EstimateResponseSHOutputSpec
 
     def _run_interface(self, runtime):
-        from dipy.core.gradients import GradientTable
         from dipy.reconst.dti import fractional_anisotropy, mean_diffusivity
         from dipy.reconst.csdeconv import recursive_response, auto_response
 

nipype/interfaces/dipy/simulate.py

@@ -324,7 +324,7 @@ def _generate_gradients(ndirs=64, values=[1000, 3000], nb0s=1):
 
     """
     import numpy as np
-    from dipy.core.sphere import disperse_charges, Sphere, HemiSphere
+    from dipy.core.sphere import disperse_charges, HemiSphere
     from dipy.core.gradients import gradient_table
 
     theta = np.pi * np.random.rand(ndirs)

nipype/interfaces/freesurfer/longitudinal.py

@@ -13,18 +13,13 @@
     InputMultiPath,
     OutputMultiPath,
     isdefined,
-    InputMultiObject,
-    Directory,
 )
 from .base import (
     FSCommand,
     FSTraitedSpec,
     FSCommandOpenMP,
     FSTraitedSpecOpenMP,
-    CommandLine,
 )
-from .preprocess import ReconAllInputSpec
-from ..io import FreeSurferSource
 
 __docformat__ = "restructuredtext"
 iflogger = logging.getLogger("nipype.interface")

nipype/interfaces/freesurfer/tests/test_model.py

@@ -1,7 +1,6 @@
 # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
 # vi: set ft=python sts=4 ts=4 sw=4 et:
 
-import os
 import numpy as np
 import nibabel as nb
 

nipype/interfaces/fsl/aroma.py

@@ -11,7 +11,6 @@
     File,
     Directory,
     traits,
-    isdefined,
 )
 import os
 

nipype/interfaces/fsl/tests/test_base.py

@@ -4,7 +4,7 @@
 
 import nipype.interfaces.fsl as fsl
 from nipype.interfaces.base import InterfaceResult
-from nipype.interfaces.fsl import check_fsl, no_fsl
+from nipype.interfaces.fsl import no_fsl
 
 import pytest
 

nipype/interfaces/fsl/tests/test_epi.py

@@ -1,6 +1,5 @@
 # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
 # vi: set ft=python sts=4 ts=4 sw=4 et:
-import os
 
 import pytest
 from nipype.testing.fixtures import create_files_in_directory

nipype/interfaces/fsl/tests/test_model.py

@@ -1,6 +1,5 @@
 # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
 # vi: set ft=python sts=4 ts=4 sw=4 et:
-import os
 
 import pytest
 import nipype.interfaces.fsl.model as fsl

nipype/interfaces/fsl/tests/test_preprocess.py

@@ -4,7 +4,6 @@
 from copy import deepcopy
 
 import pytest
-import pdb
 from nipype.utils.filemanip import split_filename, ensure_list
 from .. import preprocess as fsl
 from nipype.interfaces.fsl import Info
@@ -579,7 +578,6 @@ def test_applywarp(setup_flirt):
 def setup_fugue(tmpdir):
     import nibabel as nb
     import numpy as np
-    import os.path as op
 
     d = np.ones((80, 80, 80))
     infile = tmpdir.join("dumbfile.nii.gz").strpath

nipype/interfaces/fsl/tests/test_utils.py

@@ -5,10 +5,9 @@
 
 import numpy as np
 
-import nibabel as nb
 import pytest
 import nipype.interfaces.fsl.utils as fsl
-from nipype.interfaces.fsl import no_fsl, Info
+from nipype.interfaces.fsl import no_fsl
 
 from nipype.testing.fixtures import create_files_in_directory_plus_output_type