STY: Black

Author: effigies

nipype/interfaces/ants/registration.py

@@ -592,7 +592,8 @@ class RegistrationOutputSpec(TraitedSpec):
         File(exists=True), desc="List of output transforms for forward registration"
     )
     reverse_forward_transforms = traits.List(
-        File(exists=True), desc="List of output transforms for forward registration reversed for antsApplyTransform"
+        File(exists=True),
+        desc="List of output transforms for forward registration reversed for antsApplyTransform",
     )
     reverse_transforms = traits.List(
         File(exists=True), desc="List of output transforms for reverse registration"
@@ -601,7 +602,8 @@ class RegistrationOutputSpec(TraitedSpec):
         traits.Bool(), desc="List of flags corresponding to the forward transforms"
     )
     reverse_forward_invert_flags = traits.List(
-        traits.Bool(), desc="List of flags corresponding to the forward transforms reversed for antsApplyTransform"
+        traits.Bool(),
+        desc="List of flags corresponding to the forward transforms reversed for antsApplyTransform",
     )
     reverse_invert_flags = traits.List(
         traits.Bool(), desc="List of flags corresponding to the reverse transforms"

nipype/interfaces/ants/segmentation.py

@@ -543,6 +543,7 @@ def _list_outputs(self):
             outputs["bias_image"] = os.path.abspath(self._out_bias_file)
         return outputs
 
+
 class CorticalThicknessInputSpec(ANTSCommandInputSpec):
     dimension = traits.Enum(
         3, 2, argstr="-d %d", usedefault=True, desc="image dimension (2 or 3)"

nipype/interfaces/ants/utils.py

@@ -138,18 +138,18 @@ class ImageMath(ANTSCommand, CopyHeaderInterface):
 
     def __init__(self, **inputs):
         super(ImageMath, self).__init__(**inputs)
-        if self.inputs.operation in ("PadImage", ):
+        if self.inputs.operation in ("PadImage",):
             self.inputs.copy_header = False
 
         self.inputs.on_trait_change(self._operation_update, "operation")
         self.inputs.on_trait_change(self._copyheader_update, "copy_header")
 
     def _operation_update(self):
-        if self.inputs.operation in ("PadImage", ):
+        if self.inputs.operation in ("PadImage",):
             self.inputs.copy_header = False
 
     def _copyheader_update(self):
-        if self.inputs.copy_header and self.inputs.operation in ("PadImage", ):
+        if self.inputs.copy_header and self.inputs.operation in ("PadImage",):
             warn("copy_header cannot be updated to True with PadImage as operation.")
             self.inputs.copy_header = False
 

nipype/interfaces/freesurfer/base.py

@@ -76,7 +76,7 @@ def looseversion(cls):
                 vstr = "6.0.0-dev" + githash
             elif vinfo[5][0] == "v":
                 vstr = vinfo[5][1:]
-            elif len([1 for val in vinfo[3] if val == '.']) == 2:
+            elif len([1 for val in vinfo[3] if val == "."]) == 2:
                 "version string: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b"
                 vstr = vinfo[3]
             else:

nipype/interfaces/freesurfer/preprocess.py

@@ -727,7 +727,10 @@ def cmdline(self):
         outdir = self._get_outdir()
         cmd = []
         if not os.path.exists(outdir):
-            cmdstr = "%s -c \"import os; os.makedirs('%s')\"" % (op.basename(sys.executable), outdir)
+            cmdstr = "%s -c \"import os; os.makedirs('%s')\"" % (
+                op.basename(sys.executable),
+                outdir,
+            )
             cmd.extend([cmdstr])
         infofile = os.path.join(outdir, "shortinfo.txt")
         if not os.path.exists(infofile):

nipype/interfaces/fsl/preprocess.py

@@ -174,9 +174,9 @@ def _list_outputs(self):
         outputs = self.output_spec().get()
         outputs["out_file"] = self._gen_outfilename()
 
-        basename = os.path.basename(outputs['out_file'])
-        cwd = os.path.dirname(outputs['out_file'])
-        kwargs = {'basename': basename, 'cwd': cwd}
+        basename = os.path.basename(outputs["out_file"])
+        cwd = os.path.dirname(outputs["out_file"])
+        kwargs = {"basename": basename, "cwd": cwd}
 
         if (isdefined(self.inputs.mesh) and self.inputs.mesh) or (
             isdefined(self.inputs.surfaces) and self.inputs.surfaces
@@ -189,9 +189,7 @@ def _list_outputs(self):
         ):
             outputs["mask_file"] = self._gen_fname(suffix="_mask", **kwargs)
         if isdefined(self.inputs.outline) and self.inputs.outline:
-            outputs["outline_file"] = self._gen_fname(
-                suffix="_overlay", **kwargs
-            )
+            outputs["outline_file"] = self._gen_fname(suffix="_overlay", **kwargs)
         if isdefined(self.inputs.surfaces) and self.inputs.surfaces:
             outputs["inskull_mask_file"] = self._gen_fname(
                 suffix="_inskull_mask", **kwargs
@@ -211,13 +209,9 @@ def _list_outputs(self):
             outputs["outskin_mesh_file"] = self._gen_fname(
                 suffix="_outskin_mesh", **kwargs
             )
-            outputs["skull_mask_file"] = self._gen_fname(
-                suffix="_skull_mask", **kwargs
-            )
+            outputs["skull_mask_file"] = self._gen_fname(suffix="_skull_mask", **kwargs)
         if isdefined(self.inputs.skull) and self.inputs.skull:
-            outputs["skull_file"] = self._gen_fname(
-                suffix="_skull", **kwargs
-            )
+            outputs["skull_file"] = self._gen_fname(suffix="_skull", **kwargs)
         if isdefined(self.inputs.no_output) and self.inputs.no_output:
             outputs["out_file"] = Undefined
         return outputs

nipype/interfaces/niftyreg/base.py

@@ -19,8 +19,7 @@
 import os
 
 from ... import logging
-from ..base import (CommandLine, CommandLineInputSpec, traits, Undefined,
-                    PackageInfo)
+from ..base import CommandLine, CommandLineInputSpec, traits, Undefined, PackageInfo
 from ...utils.filemanip import split_filename
 
 iflogger = logging.getLogger("nipype.interface")
@@ -31,7 +30,7 @@ def get_custom_path(command, env_dir="NIFTYREGDIR"):
 
 
 class Info(PackageInfo):
-    version_cmd = get_custom_path('reg_aladin') + ' --version'
+    version_cmd = get_custom_path("reg_aladin") + " --version"
 
     @staticmethod
     def parse_version(raw_info):

nipype/interfaces/spm/preprocess.py

@@ -1884,7 +1884,7 @@ class MultiChannelNewSegmentInputSpec(SPMCommandInputSpec):
                     - FWHM of Gaussian smoothness of bias
                     - which maps to save (Field, Corrected) - a tuple of two boolean values""",
                 field="channel",
-            )
+            ),
         ),
         desc="""A list of tuples (one per each channel) with the following fields:
             - a list of channel files (only 1rst channel files will be segmented)

nipype/pipeline/plugins/tests/test_legacymultiproc_nondaemon.py

@@ -134,7 +134,9 @@ def run_multiproc_nondaemon_with_flag(nondaemon_flag):
     return result
 
 
-@pytest.mark.skipif(sys.version_info >= (3, 8), reason="multiprocessing issues in Python 3.8")
+@pytest.mark.skipif(
+    sys.version_info >= (3, 8), reason="multiprocessing issues in Python 3.8"
+)
 def test_run_multiproc_nondaemon_false():
     """
     This is the entry point for the test. Two times a pipe of several
@@ -153,7 +155,9 @@ def test_run_multiproc_nondaemon_false():
     assert shouldHaveFailed
 
 
-@pytest.mark.skipif(sys.version_info >= (3, 8), reason="multiprocessing issues in Python 3.8")
+@pytest.mark.skipif(
+    sys.version_info >= (3, 8), reason="multiprocessing issues in Python 3.8"
+)
 def test_run_multiproc_nondaemon_true():
     # with nondaemon_flag = True, the execution should succeed
     result = run_multiproc_nondaemon_with_flag(True)

nipype/pipeline/plugins/tests/test_multiproc.py

@@ -34,7 +34,9 @@ def _list_outputs(self):
         return outputs
 
 
-@pytest.mark.skipif(sys.version_info >= (3, 8), reason="multiprocessing issues in Python 3.8")
+@pytest.mark.skipif(
+    sys.version_info >= (3, 8), reason="multiprocessing issues in Python 3.8"
+)
 def test_run_multiproc(tmpdir):
     tmpdir.chdir()
 
@@ -116,7 +118,9 @@ def test_no_more_threads_than_specified(tmpdir):
         pipe.run(plugin="MultiProc", plugin_args={"n_procs": max_threads})
 
 
-@pytest.mark.skipif(sys.version_info >= (3, 8), reason="multiprocessing issues in Python 3.8")
+@pytest.mark.skipif(
+    sys.version_info >= (3, 8), reason="multiprocessing issues in Python 3.8"
+)
 def test_hold_job_until_procs_available(tmpdir):
     tmpdir.chdir()