Merge pull request #1 from pvelasco/black-formatting

LINT: Black edits

doc/devel/matlab_example1.py

@@ -1,6 +1,10 @@
 from nipype.interfaces.matlab import MatlabCommand
-from nipype.interfaces.base import TraitedSpec, \
-    BaseInterface, BaseInterfaceInputSpec, File
+from nipype.interfaces.base import (
+    TraitedSpec,
+    BaseInterface,
+    BaseInterfaceInputSpec,
+    File,
+)
 import os
 from string import Template
 
@@ -19,14 +23,15 @@ class ConmapTxt2Mat(BaseInterface):
     output_spec = ConmapTxt2MatOutputSpec
 
     def _run_interface(self, runtime):
-        d = dict(in_file=self.inputs.in_file,
-                 out_file=self.inputs.out_file)
+        d = dict(in_file=self.inputs.in_file, out_file=self.inputs.out_file)
         # This is your MATLAB code template
-        script = Template("""in_file = '$in_file';
+        script = Template(
+            """in_file = '$in_file';
                              out_file = '$out_file';
                              ConmapTxt2Mat(in_file, out_file);
                              exit;
-                          """).substitute(d)
+                          """
+        ).substitute(d)
 
         # mfile = True  will create an .m file with your script and executed.
         # Alternatively

doc/devel/matlab_example2.py

@@ -4,8 +4,7 @@
 
 
 class HelloWorldInputSpec(MatlabInputSpec):
-    name = traits.Str(mandatory=True,
-                      desc='Name of person to say hello to')
+    name = traits.Str(mandatory=True, desc='Name of person to say hello to')
 
 
 class HelloWorldOutputSpec(TraitedSpec):
@@ -29,6 +28,7 @@ class HelloWorld(MatlabCommand):
     >>> out = hello.run()
     >>> print out.outputs.matlab_output
     """
+
     input_spec = HelloWorldInputSpec
     output_spec = HelloWorldOutputSpec
 
@@ -37,7 +37,9 @@ def _my_script(self):
         script = """
         disp('Hello %s Python')
         two = 1 + 1
-        """ % (self.inputs.name)
+        """ % (
+            self.inputs.name
+        )
         return script
 
     def run(self, **inputs):

nipype/algorithms/misc.py

@@ -968,7 +968,6 @@ class CalculateNormalizedMoments(BaseInterface):
     output_spec = CalculateNormalizedMomentsOutputSpec
 
     def _run_interface(self, runtime):
-
         self._moments = calc_moments(self.inputs.timeseries_file, self.inputs.moment)
         return runtime
 

nipype/algorithms/tests/test_ErrorMap.py

@@ -10,7 +10,6 @@
 
 
 def test_errormap(tmpdir):
-
     # Single-Spectual
     # Make two fake 2*2*2 voxel volumes
     # John von Neumann's birthday

nipype/algorithms/tests/test_misc.py

@@ -13,7 +13,6 @@
 
 
 def test_CreateNifti(create_analyze_pair_file_in_directory):
-
     filelist, outdir = create_analyze_pair_file_in_directory
 
     create_nifti = misc.CreateNifti()
@@ -35,7 +34,6 @@ def test_CreateNifti(create_analyze_pair_file_in_directory):
 
 
 def test_CalculateMedian(create_analyze_pair_file_in_directory):
-
     mean = misc.CalculateMedian()
 
     with pytest.raises(TypeError):

nipype/algorithms/tests/test_normalize_tpms.py

@@ -16,7 +16,6 @@
 
 
 def test_normalize_tpms(tmpdir):
-
     in_mask = example_data("tpms_msk.nii.gz")
     mskdata = np.asanyarray(nb.load(in_mask).dataobj)
     mskdata[mskdata > 0.0] = 1.0

nipype/conftest.py

@@ -27,7 +27,6 @@ def _docdir(request):
     # Trigger ONLY for the doctests.
     doctest_plugin = request.config.pluginmanager.getplugin("doctest")
     if isinstance(request.node, doctest_plugin.DoctestItem):
-
         # Get the fixture dynamically by its name.
         tmpdir = pp.local(data_dir)
 

nipype/external/cloghandler.py

@@ -151,7 +151,9 @@ def __init__(
                 )
         try:
             BaseRotatingHandler.__init__(self, filename, mode, encoding)
-        except TypeError:  # Due to a different logging release without encoding support  (Python 2.4.1 and earlier?)
+        except (
+            TypeError
+        ):  # Due to a different logging release without encoding support  (Python 2.4.1 and earlier?)
             BaseRotatingHandler.__init__(self, filename, mode)
             self.encoding = encoding
 

nipype/interfaces/afni/preprocess.py

@@ -1133,7 +1133,6 @@ class ClipLevel(AFNICommandBase):
     output_spec = ClipLevelOutputSpec
 
     def aggregate_outputs(self, runtime=None, needed_outputs=None):
-
         outputs = self._outputs()
 
         outfile = os.path.join(os.getcwd(), "stat_result.json")
@@ -2295,7 +2294,6 @@ class Seg(AFNICommandBase):
     output_spec = AFNICommandOutputSpec
 
     def aggregate_outputs(self, runtime=None, needed_outputs=None):
-
         import glob
 
         outputs = self._outputs()

nipype/interfaces/afni/utils.py

@@ -302,7 +302,6 @@ class BrickStat(AFNICommandBase):
     output_spec = BrickStatOutputSpec
 
     def aggregate_outputs(self, runtime=None, needed_outputs=None):
-
         outputs = self._outputs()
 
         outfile = os.path.join(os.getcwd(), "stat_result.json")
@@ -2595,7 +2594,6 @@ def _format_arg(self, name, spec, value):
 
 
 class ResampleInputSpec(AFNICommandInputSpec):
-
     in_file = File(
         desc="input file to 3dresample",
         argstr="-inset %s",

nipype/interfaces/base/core.py

@@ -389,7 +389,6 @@ def run(self, cwd=None, ignore_exception=None, **inputs):
         self._check_version_requirements(self.inputs)
 
         with rtc(self, cwd=cwd, redirect_x=self._redirect_x) as runtime:
-
             # Grab inputs now, as they should not change during execution
             inputs = self.inputs.get_traitsfree()
             outputs = None

nipype/interfaces/base/traits_extension.py

@@ -405,7 +405,6 @@ class MultiObject(traits.List):
     """Abstract class - shared functionality of input and output MultiObject"""
 
     def validate(self, objekt, name, value):
-
         # want to treat range and other sequences (except str) as list
         if not isinstance(value, (str, bytes)) and isinstance(value, Sequence):
             value = list(value)

nipype/interfaces/brainsuite/brainsuite.py

@@ -19,7 +19,6 @@
 
 
 class BseInputSpec(CommandLineInputSpec):
-
     inputMRIFile = File(mandatory=True, argstr="-i %s", desc="input MRI volume")
     outputMRIVolume = File(
         desc="output brain-masked MRI volume. If unspecified, output file name will be auto generated.",

nipype/interfaces/cat12/preprocess.py

@@ -537,7 +537,6 @@ def _list_outputs(self):
         ]
 
         for tidx, tissue in enumerate(["gm", "wm", "csf"]):
-
             for image, prefix in [("modulated", "mw"), ("dartel", "r"), ("native", "")]:
                 outtype = f"{tissue}_output_{image}"
                 if isdefined(getattr(self.inputs, outtype)) and getattr(
@@ -594,7 +593,6 @@ def _list_outputs(self):
 
 
 class CAT12SANLMDenoisingInputSpec(SPMCommandInputSpec):
-
     in_files = InputMultiPath(
         ImageFileSPM(exists=True),
         field="data",
@@ -679,7 +677,6 @@ class CAT12SANLMDenoisingInputSpec(SPMCommandInputSpec):
 
 
 class CAT12SANLMDenoisingOutputSpec(TraitedSpec):
-
     out_file = File(desc="out file")
 
 

nipype/interfaces/cmtk/cmtk.py

@@ -272,7 +272,6 @@ def cmat(
 
     dis = 0
     for i in range(endpoints.shape[0]):
-
         # ROI start => ROI end
         try:
             startROI = int(

nipype/interfaces/freesurfer/model.py

@@ -449,7 +449,6 @@ class GLMFitInputSpec(FSTraitedSpec):
 
 
 class GLMFitOutputSpec(TraitedSpec):
-
     glm_dir = Directory(exists=True, desc="output directory")
     beta_file = File(exists=True, desc="map of regression coefficients")
     error_file = File(desc="map of residual error")

nipype/interfaces/freesurfer/petsurfer.py

@@ -24,7 +24,6 @@
 
 
 class GTMSegInputSpec(FSTraitedSpec):
-
     subject_id = traits.String(argstr="--s %s", desc="subject id", mandatory=True)
 
     xcerseg = traits.Bool(
@@ -136,7 +135,6 @@ def _list_outputs(self):
 
 
 class GTMPVCInputSpec(FSTraitedSpec):
-
     in_file = File(
         exists=True,
         argstr="--i %s",
@@ -422,7 +420,6 @@ class GTMPVCInputSpec(FSTraitedSpec):
 
 
 class GTMPVCOutputSpec(TraitedSpec):
-
     pvc_dir = Directory(desc="output directory")
     ref_file = File(desc="Reference TAC in .dat")
     hb_nifti = File(desc="High-binding TAC in nifti")

nipype/interfaces/freesurfer/preprocess.py

@@ -1833,7 +1833,6 @@ class BBRegister(FSCommand):
     output_spec = BBRegisterOutputSpec
 
     def _list_outputs(self):
-
         outputs = self.output_spec().get()
         _in = self.inputs
 
@@ -1893,7 +1892,6 @@ def _format_arg(self, name, spec, value):
         return super(BBRegister, self)._format_arg(name, spec, value)
 
     def _gen_filename(self, name):
-
         if name == "out_reg_file":
             return self._list_outputs()[name]
         return None
@@ -2180,7 +2178,6 @@ def _gen_filename(self, name):
 
 
 class RobustRegisterInputSpec(FSTraitedSpec):
-
     source_file = File(
         exists=True, mandatory=True, argstr="--mov %s", desc="volume to be registered"
     )
@@ -2302,7 +2299,6 @@ class RobustRegisterInputSpec(FSTraitedSpec):
 
 
 class RobustRegisterOutputSpec(TraitedSpec):
-
     out_reg_file = File(exists=True, desc="output registration file")
     registered_file = File(exists=True, desc="output image with registration applied")
     weights_file = File(exists=True, desc="image of weights used")
@@ -2388,7 +2384,6 @@ def _list_outputs(self):
 
 
 class FitMSParamsInputSpec(FSTraitedSpec):
-
     in_files = traits.List(
         File(exists=True),
         argstr="%s",
@@ -2408,7 +2403,6 @@ class FitMSParamsInputSpec(FSTraitedSpec):
 
 
 class FitMSParamsOutputSpec(TraitedSpec):
-
     t1_image = File(exists=True, desc="image of estimated T1 relaxation values")
     pd_image = File(exists=True, desc="image of estimated proton density values")
     t2star_image = File(exists=True, desc="image of estimated T2* values")
@@ -2466,7 +2460,6 @@ def _gen_filename(self, name):
 
 
 class SynthesizeFLASHInputSpec(FSTraitedSpec):
-
     fixed_weighting = traits.Bool(
         position=1,
         argstr="-w",
@@ -2495,7 +2488,6 @@ class SynthesizeFLASHInputSpec(FSTraitedSpec):
 
 
 class SynthesizeFLASHOutputSpec(TraitedSpec):
-
     out_file = File(exists=True, desc="synthesized FLASH acquisition")
 
 

nipype/interfaces/freesurfer/tests/test_FSSurfaceCommand.py

@@ -35,7 +35,6 @@ def test_associated_file(tmpdir):
         ("./lh.white", "./lh.pial"),
         (fsavginfo["white"], fsavginfo["pial"]),
     ]:
-
         # Unspecified paths, possibly with missing hemisphere information,
         # are equivalent to using the same directory and hemisphere
         for name in ("pial", "lh.pial", pial):

nipype/interfaces/freesurfer/tests/test_utils.py

@@ -17,7 +17,6 @@
 
 @pytest.mark.skipif(fs.no_freesurfer(), reason="freesurfer is not installed")
 def test_sample2surf(create_files_in_directory_plus_dummy_file):
-
     s2s = fs.SampleToSurface()
     # Test underlying command
     assert s2s.cmd == "mri_vol2surf"
@@ -65,7 +64,6 @@ def set_illegal_range():
 
 @pytest.mark.skipif(fs.no_freesurfer(), reason="freesurfer is not installed")
 def test_surfsmooth(create_surf_file_in_directory):
-
     smooth = fs.SurfaceSmooth()
 
     # Test underlying command
@@ -104,7 +102,6 @@ def test_surfsmooth(create_surf_file_in_directory):
 
 @pytest.mark.skipif(fs.no_freesurfer(), reason="freesurfer is not installed")
 def test_surfxfm(create_surf_file_in_directory):
-
     xfm = fs.SurfaceTransform()
 
     # Test underlying command
@@ -141,7 +138,6 @@ def test_surfxfm(create_surf_file_in_directory):
 
 @pytest.mark.skipif(fs.no_freesurfer(), reason="freesurfer is not installed")
 def test_surfshots(create_files_in_directory_plus_dummy_file):
-
     fotos = fs.SurfaceSnapshots()
 
     # Test underlying command