diff --git a/nipype/algorithms/metrics.py b/nipype/algorithms/metrics.py index 1cbcce9409..1f0ca3a9f2 100644 --- a/nipype/algorithms/metrics.py +++ b/nipype/algorithms/metrics.py @@ -478,13 +478,13 @@ def _run_interface(self, runtime): if np.any(refdata > 1.0): iflogger.warning( - 'Values greater than 1.0 found in "in_ref" input, ' "scaling values." + 'Values greater than 1.0 found in "in_ref" input, scaling values.' ) refdata /= refdata.max() if np.any(tstdata > 1.0): iflogger.warning( - 'Values greater than 1.0 found in "in_tst" input, ' "scaling values." + 'Values greater than 1.0 found in "in_tst" input, scaling values.' ) tstdata /= tstdata.max() diff --git a/nipype/algorithms/misc.py b/nipype/algorithms/misc.py index e4168f01d0..b429ac8caa 100644 --- a/nipype/algorithms/misc.py +++ b/nipype/algorithms/misc.py @@ -668,7 +668,7 @@ def _run_interface(self, runtime): if isdefined(self.inputs.row_headings): iflogger.info( - 'Row headings have been provided. Adding "labels"' "column header." + 'Row headings have been provided. Adding "labels" column header.' ) prefix = f'"{self.inputs.row_heading_title}","' csv_headings = prefix + '","'.join(itertools.chain(headings)) + '"\n' diff --git a/nipype/interfaces/camino/utils.py b/nipype/interfaces/camino/utils.py index cc1416575c..93bd4fe5d4 100644 --- a/nipype/interfaces/camino/utils.py +++ b/nipype/interfaces/camino/utils.py @@ -46,7 +46,7 @@ class ImageStatsInputSpec(CommandLineInputSpec): "double", argstr="-outputdatatype %s", usedefault=True, - desc=('A Camino data type string, default is "float". ' "Type must be signed."), + desc=('A Camino data type string, default is "float". Type must be signed.'), ) output_root = File( argstr="-outputroot %s", diff --git a/nipype/interfaces/freesurfer/model.py b/nipype/interfaces/freesurfer/model.py index a7e7e28868..8d9ff0853a 100644 --- a/nipype/interfaces/freesurfer/model.py +++ b/nipype/interfaces/freesurfer/model.py @@ -1468,9 +1468,8 @@ class Label2LabelInputSpec(FSTraitedSpec): desc="Registration method", ) copy_inputs = traits.Bool( - desc="If running as a node, set this to True." - + "This will copy the input files to the node " - + "directory." + desc="If running as a node, set this to True. " + "This will copy the input files to the node directory." ) diff --git a/nipype/interfaces/freesurfer/preprocess.py b/nipype/interfaces/freesurfer/preprocess.py index a3e44b66ba..4ef330cf2d 100644 --- a/nipype/interfaces/freesurfer/preprocess.py +++ b/nipype/interfaces/freesurfer/preprocess.py @@ -2644,20 +2644,20 @@ class MNIBiasCorrectionInputSpec(FSTraitedSpec): hash_files=False, keep_extension=True, desc="output volume. Output can be any format accepted by mri_convert. " - + "If the output format is COR, then the directory must exist.", + "If the output format is COR, then the directory must exist.", ) iterations = traits.Int( 4, usedefault=True, argstr="--n %d", desc="Number of iterations to run nu_correct. Default is 4. This is the number of times " - + "that nu_correct is repeated (ie, using the output from the previous run as the input for " - + "the next). This is different than the -iterations option to nu_correct.", + "that nu_correct is repeated (ie, using the output from the previous run as the input for " + "the next). This is different than the -iterations option to nu_correct.", ) protocol_iterations = traits.Int( argstr="--proto-iters %d", desc="Passes Np as argument of the -iterations flag of nu_correct. This is different " - + "than the --n flag above. Default is not to pass nu_correct the -iterations flag.", + "than the --n flag above. Default is not to pass nu_correct the -iterations flag.", ) distance = traits.Int(argstr="--distance %d", desc="N3 -distance option") no_rescale = traits.Bool( @@ -3166,8 +3166,8 @@ class MRIsCALabelInputSpec(FSTraitedSpecOpenMP): seed = traits.Int(argstr="-seed %d", desc="") copy_inputs = traits.Bool( desc="Copies implicit inputs to node directory " - + "and creates a temp subjects_directory. " - + "Use this when running as a node" + "and creates a temp subjects_directory. " + "Use this when running as a node" ) @@ -3285,9 +3285,8 @@ class SegmentCCInputSpec(FSTraitedSpec): desc="Subject name", ) copy_inputs = traits.Bool( - desc="If running as a node, set this to True." - + "This will copy the input files to the node " - + "directory." + desc="If running as a node, set this to True. " + "This will copy the input files to the node directory." ) diff --git a/nipype/interfaces/freesurfer/registration.py b/nipype/interfaces/freesurfer/registration.py index 948714fb05..c668a2100a 100644 --- a/nipype/interfaces/freesurfer/registration.py +++ b/nipype/interfaces/freesurfer/registration.py @@ -251,7 +251,7 @@ class RegisterInputSpec(FSTraitedSpec): mandatory=True, position=-2, desc="The data to register to. In normal recon-all usage, " - + "this is a template file for average surface.", + "this is a template file for average surface.", ) in_sulc = File( exists=True, @@ -331,7 +331,7 @@ class PaintInputSpec(FSTraitedSpec): mandatory=True, position=-2, desc="Surface file with grid (vertices) onto which the " - + "template data is to be sampled or 'painted'", + "template data is to be sampled or 'painted'", ) template = File( argstr="%s", exists=True, mandatory=True, position=-3, desc="Template file" @@ -348,7 +348,7 @@ class PaintInputSpec(FSTraitedSpec): name_source=["in_surf"], keep_extension=False, desc="File containing a surface-worth of per-vertex values, " - + "saved in 'curvature' format.", + "saved in 'curvature' format.", ) diff --git a/nipype/interfaces/freesurfer/utils.py b/nipype/interfaces/freesurfer/utils.py index fdb652804c..ebd93aee82 100644 --- a/nipype/interfaces/freesurfer/utils.py +++ b/nipype/interfaces/freesurfer/utils.py @@ -2093,7 +2093,7 @@ class CheckTalairachAlignmentInputSpec(FSTraitedSpec): usedefault=True, argstr="-T %.3f", desc="Talairach transforms for subjects with p-values <= T " - + "are considered as very unlikely default=0.010", + "are considered as very unlikely default=0.010", ) @@ -2482,8 +2482,7 @@ class FixTopologyInputSpec(FSTraitedSpec): copy_inputs = traits.Bool( mandatory=True, desc="If running as a node, set this to True " - + "otherwise, the topology fixing will be done " - + "in place.", + "otherwise, the topology fixing will be done in place.", ) # optional @@ -2736,9 +2735,8 @@ class MakeSurfacesInputSpec(FSTraitedSpec): ) white = traits.String(argstr="-white %s", desc="White surface name") copy_inputs = traits.Bool( - desc="If running as a node, set this to True." - + "This will copy the input files to the node " - + "directory." + desc="If running as a node, set this to True. " + "This will copy the input files to the node directory." ) @@ -3011,9 +3009,8 @@ class CurvatureStatsInputSpec(FSTraitedSpec): ) write = traits.Bool(argstr="--writeCurvatureFiles", desc="Write curvature files") copy_inputs = traits.Bool( - desc="If running as a node, set this to True." - + "This will copy the input files to the node " - + "directory." + desc="If running as a node, set this to True. " + "This will copy the input files to the node directory." ) @@ -3236,7 +3233,7 @@ class VolumeMaskInputSpec(FSTraitedSpec): exists=True, xor=["in_aseg"], desc="Implicit aseg.mgz segmentation. " - + "Specify a different aseg by using the 'in_aseg' input.", + "Specify a different aseg by using the 'in_aseg' input.", ) subject_id = traits.String( "subject_id", @@ -3256,12 +3253,11 @@ class VolumeMaskInputSpec(FSTraitedSpec): save_ribbon = traits.Bool( argstr="--save_ribbon", desc="option to save just the ribbon for the " - + "hemispheres in the format ?h.ribbon.mgz", + "hemispheres in the format ?h.ribbon.mgz", ) copy_inputs = traits.Bool( - desc="If running as a node, set this to True." - + "This will copy the implicit input files to the " - + "node directory." + desc="If running as a node, set this to True. " + "This will copy the implicit input files to the node directory." ) @@ -3430,9 +3426,8 @@ class ParcellationStatsInputSpec(FSTraitedSpec): desc="Output annotation files's colortable to text file", ) copy_inputs = traits.Bool( - desc="If running as a node, set this to True." - + "This will copy the input files to the node " - + "directory." + desc="If running as a node, set this to True. " + "This will copy the input files to the node directory." ) th3 = traits.Bool( argstr="-th3", @@ -3622,9 +3617,8 @@ class ContrastInputSpec(FSTraitedSpec): exists=True, mandatory=True, desc="Implicit input file mri/rawavg.mgz" ) copy_inputs = traits.Bool( - desc="If running as a node, set this to True." - + "This will copy the input files to the node " - + "directory." + desc="If running as a node, set this to True. " + "This will copy the input files to the node directory." ) diff --git a/nipype/interfaces/fsl/dti.py b/nipype/interfaces/fsl/dti.py index 703fda7078..cd46067daa 100644 --- a/nipype/interfaces/fsl/dti.py +++ b/nipype/interfaces/fsl/dti.py @@ -941,7 +941,7 @@ class ProbTrackX2InputSpec(ProbTrackXBaseInputSpec): "OR", "AND", argstr="--waycond=%s", - desc=('Waypoint condition. Either "AND" (default) ' 'or "OR"'), + desc=('Waypoint condition. Either "AND" (default) or "OR"'), ) wayorder = traits.Bool( desc=( diff --git a/nipype/interfaces/fsl/model.py b/nipype/interfaces/fsl/model.py index 809a5a0101..9c038cfb3d 100644 --- a/nipype/interfaces/fsl/model.py +++ b/nipype/interfaces/fsl/model.py @@ -2365,8 +2365,8 @@ class GLMInputSpec(FSLCommandInputSpec): position=2, desc=( "file name of the GLM design matrix (text time" - + " courses for temporal regression or an image" - + " file for spatial regression)" + " courses for temporal regression or an image" + " file for spatial regression)" ), ) contrasts = File( @@ -2380,7 +2380,7 @@ class GLMInputSpec(FSLCommandInputSpec): argstr="--des_norm", desc=( "switch on normalization of the design" - + " matrix columns to unit std deviation" + " matrix columns to unit std deviation" ), ) dat_norm = traits.Bool( diff --git a/nipype/pipeline/engine/base.py b/nipype/pipeline/engine/base.py index 633353943d..f2e1009884 100644 --- a/nipype/pipeline/engine/base.py +++ b/nipype/pipeline/engine/base.py @@ -87,7 +87,7 @@ def clone(self, name): """ if name == self.name: - raise ValueError('Cloning requires a new name, "%s" is ' "in use." % name) + raise ValueError('Cloning requires a new name, "%s" is in use.' % name) clone = deepcopy(self) clone.name = name if hasattr(clone, "_id"): diff --git a/nipype/pipeline/engine/workflows.py b/nipype/pipeline/engine/workflows.py index fd7c8b9cd0..6a0275f905 100644 --- a/nipype/pipeline/engine/workflows.py +++ b/nipype/pipeline/engine/workflows.py @@ -1049,7 +1049,7 @@ def _get_dot( else: if colored: dotlist.append( - ('%s[label="%s", style=filled,' ' fillcolor="%s"];') + ('%s[label="%s", style=filled, fillcolor="%s"];') % (nodename, node_class_name, colorset[level]) ) else: diff --git a/tools/gitwash_dumper.py b/tools/gitwash_dumper.py index f906d48f5f..a69421077b 100755 --- a/tools/gitwash_dumper.py +++ b/tools/gitwash_dumper.py @@ -129,7 +129,7 @@ def make_link_targets( have_gh_url = True if not have_url or not have_ml_url: raise RuntimeError( - "Need command line or known project " "and / or mailing list URLs" + "Need command line or known project and / or mailing list URLs" ) lines = [] if url is not None: