Merge pull request #1 from pvelasco/black-formatting

LINT: Black edits

Author: pvelasco

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",