STY: black

Author: effigies

nipype/algorithms/confounds.py

@@ -577,7 +577,7 @@ class CompCor(SimpleInterface):
     ]
 
     def __init__(self, *args, **kwargs):
-        """ exactly the same as compcor except the header """
+        """exactly the same as compcor except the header"""
         super(CompCor, self).__init__(*args, **kwargs)
         self._header = "CompCor"
 
@@ -774,7 +774,7 @@ class ACompCor(CompCor):
     """
 
     def __init__(self, *args, **kwargs):
-        """ exactly the same as compcor except the header """
+        """exactly the same as compcor except the header"""
         super(ACompCor, self).__init__(*args, **kwargs)
         self._header = "aCompCor"
 
@@ -825,7 +825,7 @@ class TCompCor(CompCor):
     output_spec = TCompCorOutputSpec
 
     def __init__(self, *args, **kwargs):
-        """ exactly the same as compcor except the header """
+        """exactly the same as compcor except the header"""
         super(TCompCor, self).__init__(*args, **kwargs)
         self._header = "tCompCor"
         self._mask_files = []

nipype/algorithms/mesh.py

@@ -23,7 +23,7 @@
 
 
 class TVTKBaseInterface(BaseInterface):
-    """ A base class for interfaces using VTK """
+    """A base class for interfaces using VTK"""
 
     _redirect_x = True
 

nipype/algorithms/modelgen.py

@@ -516,7 +516,7 @@ def _generate_design(self, infolist=None):
         )
 
     def _run_interface(self, runtime):
-        """"""
+        """ """
         self._sessioninfo = None
         self._generate_design()
         return runtime

nipype/algorithms/tests/test_CompCor.py

@@ -11,7 +11,7 @@
 
 
 class TestCompCor:
-    """ Note: Tests currently do a poor job of testing functionality """
+    """Note: Tests currently do a poor job of testing functionality"""
 
     filenames = {
         "functionalnii": "compcorfunc.nii",

nipype/algorithms/tests/test_TSNR.py

@@ -14,7 +14,7 @@
 
 
 class TestTSNR:
-    """ Note: Tests currently do a poor job of testing functionality """
+    """Note: Tests currently do a poor job of testing functionality"""
 
     in_filenames = {"in_file": "tsnrinfile.nii"}
 

nipype/external/cloghandler.py

@@ -222,7 +222,7 @@ def flush(self):
         pass
 
     def _degrade(self, degrade, msg, *args):
-        """ Set degrade mode or not.  Ignore msg. """
+        """Set degrade mode or not.  Ignore msg."""
         self._rotateFailed = degrade
         del msg, args  # avoid pychecker warnings
 

nipype/interfaces/base/core.py

@@ -87,12 +87,12 @@ def version(self):
 
     @classmethod
     def _outputs(cls):
-        """ Initializes outputs"""
+        """Initializes outputs"""
         raise NotImplementedError
 
     @classmethod
     def help(cls, returnhelp=False):
-        """ Prints class help """
+        """Prints class help"""
         allhelp = format_help(cls)
         if returnhelp:
             return allhelp
@@ -112,7 +112,7 @@ def aggregate_outputs(self, runtime=None, needed_outputs=None):
         raise NotImplementedError
 
     def _list_outputs(self):
-        """ List expected outputs"""
+        """List expected outputs"""
         raise NotImplementedError
 
     @classmethod

nipype/interfaces/base/specs.py

@@ -58,7 +58,7 @@ class BaseTraitedSpec(traits.HasTraits):
     package_version = nipype_version
 
     def __init__(self, **kwargs):
-        """ Initialize handlers and inputs"""
+        """Initialize handlers and inputs"""
         # NOTE: In python 2.6, object.__init__ no longer accepts input
         # arguments.  HasTraits does not define an __init__ and
         # therefore these args were being ignored.
@@ -79,7 +79,7 @@ def items(self):
             yield name, self.traits()[name]
 
     def __repr__(self):
-        """ Return a well-formatted representation of the traits """
+        """Return a well-formatted representation of the traits"""
         outstr = []
         for name, value in sorted(self.trait_get().items()):
             outstr.append("%s = %s" % (name, value))

nipype/interfaces/cmtk/cmtk.py

@@ -190,7 +190,7 @@ def cmat(
     endpoint_name,
     intersections=False,
 ):
-    """ Create the connection matrix for each resolution using fibers and ROIs. """
+    """Create the connection matrix for each resolution using fibers and ROIs."""
     import scipy.io as sio
 
     stats = {}
@@ -460,7 +460,7 @@ def cmat(
 
 
 def save_fibers(oldhdr, oldfib, fname, indices):
-    """ Stores a new trackvis file fname using only given indices """
+    """Stores a new trackvis file fname using only given indices"""
     hdrnew = oldhdr.copy()
     outstreams = []
     for i in indices:

nipype/interfaces/dipy/base.py

@@ -27,13 +27,13 @@
 
 
 def no_dipy():
-    """ Check if dipy is available """
+    """Check if dipy is available"""
     global HAVE_DIPY
     return not HAVE_DIPY
 
 
 def dipy_version():
-    """ Check dipy version """
+    """Check dipy version"""
     if no_dipy():
         return None
 

nipype/interfaces/fsl/fix.py

@@ -375,7 +375,7 @@ class Cleaner(CommandLine):
     cmd = "fix -a"
 
     def _get_cleaned_functional_filename(self, artifacts_list_filename):
-        """ extract the proper filename from the first line of the artifacts file """
+        """extract the proper filename from the first line of the artifacts file"""
         artifacts_list_file = open(artifacts_list_filename, "r")
         functional_filename, extension = artifacts_list_file.readline().split(".")
         artifacts_list_file_path, artifacts_list_filename = os.path.split(

nipype/interfaces/fsl/preprocess.py

@@ -236,7 +236,7 @@ def _gen_filename(self, name):
 
 
 class FASTInputSpec(FSLCommandInputSpec):
-    """ Defines inputs (trait classes) for FAST """
+    """Defines inputs (trait classes) for FAST"""
 
     in_files = InputMultiPath(
         File(exists=True),

nipype/interfaces/io.py

@@ -169,7 +169,7 @@ class ProgressPercentage(object):
     """
 
     def __init__(self, filename):
-        """"""
+        """ """
 
         # Import packages
         import threading
@@ -181,7 +181,7 @@ def __init__(self, filename):
         self._lock = threading.Lock()
 
     def __call__(self, bytes_amount):
-        """"""
+        """ """
 
         # Import packages
         import sys
@@ -206,7 +206,7 @@ def __call__(self, bytes_amount):
 
 # DataSink inputs
 class DataSinkInputSpec(DynamicTraitedSpec, BaseInterfaceInputSpec):
-    """"""
+    """ """
 
     # Init inputspec data attributes
     base_directory = Str(desc="Path to the base directory for storing data.")

nipype/interfaces/matlab.py

@@ -42,7 +42,7 @@ def get_matlab_command():
 
 
 class MatlabInputSpec(CommandLineInputSpec):
-    """ Basic expected inputs to Matlab interface """
+    """Basic expected inputs to Matlab interface"""
 
     script = traits.Str(
         argstr='-r "%s;exit"', desc="m-code to run", mandatory=True, position=-1
@@ -187,7 +187,7 @@ def _format_arg(self, name, trait_spec, value):
         return super(MatlabCommand, self)._format_arg(name, trait_spec, value)
 
     def _gen_matlab_command(self, argstr, script_lines):
-        """ Generates commands and, if mfile specified, writes it to disk."""
+        """Generates commands and, if mfile specified, writes it to disk."""
         cwd = os.getcwd()
         mfile = self.inputs.mfile or self.inputs.uses_mcr
         paths = []

nipype/interfaces/niftyfit/asl.py

@@ -10,7 +10,7 @@
 
 
 class FitAslInputSpec(CommandLineInputSpec):
-    """ Input Spec for FitAsl. """
+    """Input Spec for FitAsl."""
 
     desc = "Filename of the 4D ASL (control/label) source image (mandatory)."
     source_file = File(
@@ -129,7 +129,7 @@ class FitAslInputSpec(CommandLineInputSpec):
 
 
 class FitAslOutputSpec(TraitedSpec):
-    """ Output Spec for FitAsl. """
+    """Output Spec for FitAsl."""
 
     desc = "Filename of the Cerebral Blood Flow map (in ml/100g/min)."
     cbf_file = File(exists=True, desc=desc)

nipype/interfaces/niftyfit/base.py

@@ -31,7 +31,7 @@ class NiftyFitCommand(CommandLine):
     _suffix = "_nf"
 
     def __init__(self, **inputs):
-        """ Init method calling super. No version to be checked."""
+        """Init method calling super. No version to be checked."""
         super(NiftyFitCommand, self).__init__(**inputs)
 
     def _gen_fname(self, basename, out_dir=None, suffix=None, ext=None):

nipype/interfaces/niftyfit/dwi.py

@@ -10,7 +10,7 @@
 
 
 class FitDwiInputSpec(CommandLineInputSpec):
-    """ Input Spec for FitDwi. """
+    """Input Spec for FitDwi."""
 
     # Inputs options
     source_file = File(
@@ -281,7 +281,7 @@ class FitDwiInputSpec(CommandLineInputSpec):
 
 
 class FitDwiOutputSpec(TraitedSpec):
-    """ Output Spec for FitDwi. """
+    """Output Spec for FitDwi."""
 
     error_file = File(desc="Filename of parameter error maps")
     res_file = File(desc="Filename of model residual map")
@@ -342,7 +342,7 @@ def _format_arg(self, name, trait_spec, value):
 
 
 class DwiToolInputSpec(CommandLineInputSpec):
-    """ Input Spec for DwiTool. """
+    """Input Spec for DwiTool."""
 
     desc = "The source image containing the fitted model."
     source_file = File(
@@ -540,7 +540,7 @@ class DwiToolInputSpec(CommandLineInputSpec):
 
 
 class DwiToolOutputSpec(TraitedSpec):
-    """ Output Spec for DwiTool. """
+    """Output Spec for DwiTool."""
 
     desc = "Filename of multi-compartment model parameter map \
 (-ivim,-ball,-nod)"

nipype/interfaces/niftyfit/qt1.py

@@ -11,7 +11,7 @@
 
 
 class FitQt1InputSpec(CommandLineInputSpec):
-    """ Input Spec for FitQt1. """
+    """Input Spec for FitQt1."""
 
     desc = "Filename of the 4D Multi-Echo T1 source image."
     source_file = File(
@@ -144,7 +144,7 @@ class FitQt1InputSpec(CommandLineInputSpec):
 
 
 class FitQt1OutputSpec(TraitedSpec):
-    """ Output Spec for FitQt1. """
+    """Output Spec for FitQt1."""
 
     t1map_file = File(desc="Filename of the estimated output T1 map (in ms)")
     m0map_file = File(desc="Filename of the m0 map")

nipype/interfaces/niftyfit/tests/test_asl.py

@@ -13,7 +13,7 @@
 
 @pytest.mark.skipif(no_nifty_tool(cmd="fit_asl"), reason="niftyfit is not installed")
 def test_fit_asl():
-    """ Testing FitAsl interface."""
+    """Testing FitAsl interface."""
     # Create the test node
     fit_asl = FitAsl()
 

nipype/interfaces/niftyfit/tests/test_dwi.py

@@ -12,7 +12,7 @@
 
 @pytest.mark.skipif(no_nifty_tool(cmd="fit_dwi"), reason="niftyfit is not installed")
 def test_fit_dwi():
-    """ Testing FitDwi interface."""
+    """Testing FitDwi interface."""
     # Create a node object
     fit_dwi = FitDwi()
 
@@ -60,7 +60,7 @@ def test_fit_dwi():
 
 @pytest.mark.skipif(no_nifty_tool(cmd="dwi_tool"), reason="niftyfit is not installed")
 def test_dwi_tool():
-    """ Testing DwiTool interface."""
+    """Testing DwiTool interface."""
     # Create a node object
     dwi_tool = DwiTool()
 

nipype/interfaces/niftyfit/tests/test_qt1.py

@@ -12,7 +12,7 @@
 
 @pytest.mark.skipif(no_nifty_tool(cmd="fit_qt1"), reason="niftyfit is not installed")
 def test_fit_qt1():
-    """ Testing FitQt1 interface."""
+    """Testing FitQt1 interface."""
     # Create a node object
     fit_qt1 = FitQt1()
 

nipype/interfaces/niftyreg/reg.py

@@ -15,7 +15,7 @@
 
 
 class RegAladinInputSpec(NiftyRegCommandInputSpec):
-    """ Input Spec for RegAladin. """
+    """Input Spec for RegAladin."""
 
     # Input reference file
     ref_file = File(
@@ -116,7 +116,7 @@ class RegAladinInputSpec(NiftyRegCommandInputSpec):
 
 
 class RegAladinOutputSpec(TraitedSpec):
-    """ Output Spec for RegAladin. """
+    """Output Spec for RegAladin."""
 
     aff_file = File(desc="The output affine file")
     res_file = File(desc="The output transformed image")
@@ -163,7 +163,7 @@ def _list_outputs(self):
 
 
 class RegF3DInputSpec(NiftyRegCommandInputSpec):
-    """ Input Spec for RegF3D. """
+    """Input Spec for RegF3D."""
 
     # Input reference file
     ref_file = File(
@@ -343,7 +343,7 @@ class RegF3DInputSpec(NiftyRegCommandInputSpec):
 
 
 class RegF3DOutputSpec(TraitedSpec):
-    """ Output Spec for RegF3D. """
+    """Output Spec for RegF3D."""
 
     cpp_file = File(desc="The output CPP file")
     res_file = File(desc="The output resampled image")