Merge pull request #3679 from DimitriPapadopoulos/ISC

 STY: Apply ruff/flake8-implicit-str-concat rules (ISC)

Author: effigies

Diff for: 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 for: nipype/algorithms/misc.py

@@ -669,7 +669,7 @@ 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 for: 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 for: nipype/interfaces/freesurfer/model.py

@@ -1469,9 +1469,8 @@ 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 for: nipype/interfaces/freesurfer/preprocess.py

@@ -2645,20 +2645,20 @@ 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(
@@ -3167,8 +3167,8 @@ 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"
     )
 
 
@@ -3286,9 +3286,8 @@ 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 for: 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 for: nipype/interfaces/freesurfer/utils.py

@@ -2094,7 +2094,7 @@ 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",
     )
 
 
@@ -2483,8 +2483,7 @@ 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
@@ -2737,9 +2736,8 @@ 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."
     )
 
 
@@ -3012,9 +3010,8 @@ 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."
     )
 
 
@@ -3237,7 +3234,7 @@ 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",
@@ -3257,12 +3254,11 @@ 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."
     )
 
 
@@ -3431,9 +3427,8 @@ 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",
@@ -3623,9 +3618,8 @@ 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 for: 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 for: nipype/interfaces/fsl/model.py

@@ -2366,8 +2366,8 @@ 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(
@@ -2381,7 +2381,7 @@ 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 for: 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 for: nipype/pipeline/engine/workflows.py

@@ -1046,7 +1046,7 @@ 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 for: 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: