run black over touched files

Author: tclose

nipype/interfaces/mrtrix3/__init__.py

@@ -14,7 +14,7 @@
     MRResize,
     DWIExtract,
     SHConv,
-    SH2Amp
+    SH2Amp,
 )
 from .preprocess import (
     ResponseSD,

nipype/interfaces/mrtrix3/reconst.py

@@ -4,8 +4,7 @@
 
 import os.path as op
 
-from ..base import (
-    traits, TraitedSpec, File, Undefined, InputMultiObject, isdefined)
+from ..base import traits, TraitedSpec, File, Undefined, InputMultiObject, isdefined
 from .base import MRTrix3BaseInputSpec, MRTrix3Base
 
 
@@ -52,10 +51,12 @@ class FitTensorInputSpec(MRTrix3BaseInputSpec):
         ),
     )
     predicted_signal = File(
-        argstr='-predicted_signal %s',
+        argstr="-predicted_signal %s",
         desc=(
             "specify a file to contain the predicted signal from the tensor "
-            "fits. This can be used to calculate the residual signal"))
+            "fits. This can be used to calculate the residual signal"
+        ),
+    )
 
 
 class FitTensorOutputSpec(TraitedSpec):
@@ -89,8 +90,7 @@ def _list_outputs(self):
         outputs = self.output_spec().get()
         outputs["out_file"] = op.abspath(self.inputs.out_file)
         if isdefined(self.inputs.predicted_signal):
-            outputs['predicted_signal'] = op.abspath(
-                self.inputs.predicted_signal)
+            outputs["predicted_signal"] = op.abspath(self.inputs.predicted_signal)
         return outputs
 
 
@@ -155,13 +155,15 @@ class EstimateFODInputSpec(MRTrix3BaseInputSpec):
         ),
     )
     predicted_signal = File(
-        argstr='-predicted_signal %s',
+        argstr="-predicted_signal %s",
         desc=(
             "specify a file to contain the predicted signal from the FOD "
             "estimates. This can be used to calculate the residual signal."
             "Note that this is only valid if algorithm == 'msmt_csd'. "
             "For single shell reconstructions use a combination of SHConv "
-            "and SH2Amp instead."))
+            "and SH2Amp instead."
+        ),
+    )
 
 
 class EstimateFODOutputSpec(TraitedSpec):
@@ -207,12 +209,12 @@ def _list_outputs(self):
         if isdefined(self.inputs.csf_odf):
             outputs["csf_odf"] = op.abspath(self.inputs.csf_odf)
         if isdefined(self.inputs.predicted_signal):
-            if self.inputs.algorithm != 'msmt_csd':
+            if self.inputs.algorithm != "msmt_csd":
                 raise Exception(
                     "'predicted_signal' option can only be used with "
-                    "the 'msmt_csd' algorithm")
-            outputs["predicted_signal"] = op.abspath(
-                self.inputs.predicted_signal)
+                    "the 'msmt_csd' algorithm"
+                )
+            outputs["predicted_signal"] = op.abspath(self.inputs.predicted_signal)
         return outputs
 
 

nipype/interfaces/mrtrix3/utils.py

@@ -797,8 +797,7 @@ class SHConvInputSpec(CommandLineInputSpec):
 
 
 class SHConvOutputSpec(TraitedSpec):
-    out_file = File(exists=True,
-                    desc="the output convoluted spherical harmonics file")
+    out_file = File(exists=True, desc="the output convoluted spherical harmonics file")
 
 
 class SHConv(CommandLine):
@@ -829,7 +828,6 @@ def _list_outputs(self):
         return outputs
 
 
-
 class SH2AmpInputSpec(CommandLineInputSpec):
     in_file = File(
         exists=True,
@@ -845,8 +843,10 @@ class SH2AmpInputSpec(CommandLineInputSpec):
         mandatory=True,
         argstr="%s",
         position=-2,
-        desc=("The gradient directions along which to sample the spherical "
-              "harmonics MRtrix format"),
+        desc=(
+            "The gradient directions along which to sample the spherical "
+            "harmonics MRtrix format"
+        ),
     )
 
     out_file = File(
@@ -859,13 +859,12 @@ class SH2AmpInputSpec(CommandLineInputSpec):
     )
 
     nonnegative = traits.Bool(
-        argstr='-nonnegative',
-        desc="cap all negative amplitudes to zero")
+        argstr="-nonnegative", desc="cap all negative amplitudes to zero"
+    )
 
 
 class SH2AmpOutputSpec(TraitedSpec):
-    out_file = File(exists=True,
-                    desc="the output convoluted spherical harmonics file")
+    out_file = File(exists=True, desc="the output convoluted spherical harmonics file")
 
 
 class SH2Amp(CommandLine):