Re-ran formatting.

Author: ZviBaratz

nipype/interfaces/mrtrix/preprocess.py

@@ -24,9 +24,7 @@ class MRConvertInputSpec(CommandLineInputSpec):
         position=-2,
         desc="voxel-order data filename",
     )
-    out_filename = File(
-        genfile=True, argstr="%s", position=-1, desc="Output filename"
-    )
+    out_filename = File(genfile=True, argstr="%s", position=-1, desc="Output filename")
     extract_at_axis = traits.Enum(
         1,
         2,
@@ -229,15 +227,11 @@ class DWI2TensorInputSpec(CommandLineInputSpec):
         position=1,
         desc=("Do not display information messages or progress " "status."),
     )
-    debug = traits.Bool(
-        argstr="-debug", position=1, desc="Display debugging messages."
-    )
+    debug = traits.Bool(argstr="-debug", position=1, desc="Display debugging messages.")
 
 
 class DWI2TensorOutputSpec(TraitedSpec):
-    tensor = File(
-        exists=True, desc="path/name of output diffusion tensor image"
-    )
+    tensor = File(exists=True, desc="path/name of output diffusion tensor image")
 
 
 class DWI2Tensor(CommandLine):
@@ -277,9 +271,7 @@ class Tensor2VectorInputSpec(CommandLineInputSpec):
         position=1,
         desc="Do not display information messages or progress status.",
     )
-    debug = traits.Bool(
-        argstr="-debug", position=1, desc="Display debugging messages."
-    )
+    debug = traits.Bool(argstr="-debug", position=1, desc="Display debugging messages.")
 
 
 class Tensor2VectorOutputSpec(TraitedSpec):
@@ -345,9 +337,7 @@ class Tensor2FractionalAnisotropyInputSpec(CommandLineInputSpec):
         position=1,
         desc="Do not display information messages or progress status.",
     )
-    debug = traits.Bool(
-        argstr="-debug", position=1, desc="Display debugging messages."
-    )
+    debug = traits.Bool(argstr="-debug", position=1, desc="Display debugging messages.")
 
 
 class Tensor2FractionalAnisotropyOutputSpec(TraitedSpec):
@@ -413,9 +403,7 @@ class Tensor2ApparentDiffusionInputSpec(CommandLineInputSpec):
         position=1,
         desc="Do not display information messages or progress status.",
     )
-    debug = traits.Bool(
-        argstr="-debug", position=1, desc="Display debugging messages."
-    )
+    debug = traits.Bool(argstr="-debug", position=1, desc="Display debugging messages.")
 
 
 class Tensor2ApparentDiffusionOutputSpec(TraitedSpec):
@@ -478,9 +466,7 @@ class MRMultiplyInputSpec(CommandLineInputSpec):
         position=1,
         desc="Do not display information messages or progress status.",
     )
-    debug = traits.Bool(
-        argstr="-debug", position=1, desc="Display debugging messages."
-    )
+    debug = traits.Bool(argstr="-debug", position=1, desc="Display debugging messages.")
 
 
 class MRMultiplyOutputSpec(TraitedSpec):
@@ -537,9 +523,7 @@ class MRTrixViewerInputSpec(CommandLineInputSpec):
         position=1,
         desc="Do not display information messages or progress status.",
     )
-    debug = traits.Bool(
-        argstr="-debug", position=1, desc="Display debugging messages."
-    )
+    debug = traits.Bool(argstr="-debug", position=1, desc="Display debugging messages.")
 
 
 class MRTrixViewerOutputSpec(TraitedSpec):
@@ -698,9 +682,7 @@ class ErodeInputSpec(CommandLineInputSpec):
         position=1,
         desc="Do not display information messages or progress status.",
     )
-    debug = traits.Bool(
-        argstr="-debug", position=1, desc="Display debugging messages."
-    )
+    debug = traits.Bool(argstr="-debug", position=1, desc="Display debugging messages.")
 
 
 class ErodeOutputSpec(TraitedSpec):
@@ -765,9 +747,7 @@ class ThresholdInputSpec(CommandLineInputSpec):
         argstr="-percent %s",
         desc="Specify threshold value as a percentage of the peak intensity in the input image.",
     )
-    invert = traits.Bool(
-        argstr="-invert", position=1, desc="Invert output binary mask"
-    )
+    invert = traits.Bool(argstr="-invert", position=1, desc="Invert output binary mask")
     replace_zeros_with_NaN = traits.Bool(
         argstr="-nan", position=1, desc="Replace all zero values with NaN"
     )
@@ -776,9 +756,7 @@ class ThresholdInputSpec(CommandLineInputSpec):
         position=1,
         desc="Do not display information messages or progress status.",
     )
-    debug = traits.Bool(
-        argstr="-debug", position=1, desc="Display debugging messages."
-    )
+    debug = traits.Bool(argstr="-debug", position=1, desc="Display debugging messages.")
 
 
 class ThresholdOutputSpec(TraitedSpec):
@@ -843,9 +821,7 @@ class MedianFilter3DInputSpec(CommandLineInputSpec):
         position=1,
         desc="Do not display information messages or progress status.",
     )
-    debug = traits.Bool(
-        argstr="-debug", position=1, desc="Display debugging messages."
-    )
+    debug = traits.Bool(argstr="-debug", position=1, desc="Display debugging messages.")
 
 
 class MedianFilter3DOutputSpec(TraitedSpec):
@@ -897,9 +873,7 @@ class MRTransformInputSpec(CommandLineInputSpec):
         position=-2,
         desc="Input images to be transformed",
     )
-    out_filename = File(
-        genfile=True, argstr="%s", position=-1, desc="Output image"
-    )
+    out_filename = File(genfile=True, argstr="%s", position=-1, desc="Output image")
     invert = traits.Bool(
         argstr="-inverse",
         position=1,
@@ -949,9 +923,7 @@ class MRTransformInputSpec(CommandLineInputSpec):
         position=1,
         desc="Do not display information messages or progress status.",
     )
-    debug = traits.Bool(
-        argstr="-debug", position=1, desc="Display debugging messages."
-    )
+    debug = traits.Bool(argstr="-debug", position=1, desc="Display debugging messages.")
 
 
 class MRTransformOutputSpec(TraitedSpec):

nipype/interfaces/mrtrix3/base.py

@@ -46,8 +46,7 @@ def looseversion(cls):
 class MRTrix3BaseInputSpec(CommandLineInputSpec):
     nthreads = traits.Int(
         argstr="-nthreads %d",
-        desc="number of threads. if zero, the number"
-        " of available cpus will be used",
+        desc="number of threads. if zero, the number" " of available cpus will be used",
         nohash=True,
     )
     # DW gradient table import options
@@ -116,18 +115,15 @@ def _parse_inputs(self, skip=None):
             skip = []
 
         try:
-            if isdefined(self.inputs.grad_file) or isdefined(
-                self.inputs.grad_fsl
-            ):
+            if isdefined(self.inputs.grad_file) or isdefined(self.inputs.grad_fsl):
                 skip += ["in_bvec", "in_bval"]
 
             is_bvec = isdefined(self.inputs.in_bvec)
             is_bval = isdefined(self.inputs.in_bval)
             if is_bvec or is_bval:
                 if not is_bvec or not is_bval:
                     raise RuntimeError(
-                        "If using bvecs and bvals inputs, both"
-                        "should be defined"
+                        "If using bvecs and bvals inputs, both" "should be defined"
                     )
                 skip += ["in_bval"]
         except AttributeError: