nipy · effigies · Sep 21, 2022 · Sep 21, 2022
diff --git a/doc/devel/interface_specs.rst b/doc/devel/interface_specs.rst
@@ -148,7 +148,7 @@ base class down to subclasses).:
 
 	        ``SlicerCommandLineInputSpec``: Defines inputs common to all Slicer classes (``module``)
 
-Most developers will only need to code at the the interface-level (i.e. implementing custom class inheriting from one of the above classes).
+Most developers will only need to code at the interface-level (i.e. implementing custom class inheriting from one of the above classes).
 
 Output Specs
 ^^^^^^^^^^^^
@@ -519,7 +519,7 @@ SPM
 
 For SPM-mediated interfaces:
 
-* ``_jobtype`` and ``_jobname``: special names used used by the SPM job manager. You can find them by saving your batch job as an .m file and looking up the code.
+* ``_jobtype`` and ``_jobname``: special names used by the SPM job manager. You can find them by saving your batch job as an .m file and looking up the code.
 
 And optionally:
 

diff --git a/doc/devel/provenance.rst b/doc/devel/provenance.rst
@@ -5,7 +5,7 @@ W3C PROV support
 Overview
 --------
 
-We're using the the `W3C PROV data model <http://www.w3.org/TR/prov-dm/>`_ to
+We're using the `W3C PROV data model <http://www.w3.org/TR/prov-dm/>`_ to
 capture and represent provenance in Nipype.
 
 For an overview see:

diff --git a/nipype/interfaces/afni/utils.py b/nipype/interfaces/afni/utils.py
@@ -2151,7 +2151,7 @@ class NwarpCatInputSpec(AFNICommandInputSpec):
         usedefault=True,
     )
     expad = traits.Int(
-        desc="Pad the nonlinear warps by the given number of voxels voxels in "
+        desc="Pad the nonlinear warps by the given number of voxels in "
         "all directions. The warp displacements are extended by linear "
         "extrapolation from the faces of the input grid..",
         argstr="-expad %d",

diff --git a/nipype/interfaces/diffusion_toolkit/dti.py b/nipype/interfaces/diffusion_toolkit/dti.py
@@ -208,7 +208,7 @@ class DTITrackerInputSpec(CommandLineInputSpec):
         desc="set angle threshold. default value is 35 degree", argstr="-at %f"
     )
     angle_threshold_weight = traits.Float(
-        desc="set angle threshold weighting factor. weighting will be be applied "
+        desc="set angle threshold weighting factor. weighting will be applied "
         "on top of the angle_threshold",
         argstr="-atw %f",
     )

diff --git a/nipype/interfaces/dtitk/utils.py b/nipype/interfaces/dtitk/utils.py
@@ -161,7 +161,7 @@ class TVResampleInputSpec(CommandLineInputSpec):
         desc="how to align output volume to input volume",
     )
     interpolation = traits.Enum(
-        "LEI", "EI", argstr="-interp %s", desc="Log Euclidean Euclidean Interpolation"
+        "LEI", "EI", argstr="-interp %s", desc="Log Euclidean Interpolation"
     )
     array_size = traits.Tuple(
         (traits.Int(), traits.Int(), traits.Int()),

diff --git a/nipype/interfaces/minc/minc.py b/nipype/interfaces/minc/minc.py
@@ -1285,7 +1285,7 @@ class BeastInputSpec(CommandLineInputSpec):
      -positive:         Specify mask of positive segmentation (inside mask) instead of the default mask.
      -output_selection: Specify file to output selected files.
      -count:            Specify file to output the patch count.
-     -mask:             Specify a segmentation mask instead of the the default mask.
+     -mask:             Specify a segmentation mask instead of the default mask.
      -no_mask:          Do not apply a segmentation mask. Perform the segmentation over the entire image.
      -no_positive:      Do not apply a positive mask.
     Generic options for all commands:

diff --git a/nipype/interfaces/mipav/developer.py b/nipype/interfaces/mipav/developer.py
@@ -1253,7 +1253,7 @@ class MedicAlgorithmSPECTRE2010InputSpec(CommandLineInputSpec):
         traits.Bool,
         File(),
         hash_files=False,
-        desc="Tissue classification of of the whole input volume.",
+        desc="Tissue classification of the whole input volume.",
         argstr="--outFANTASM %s",
     )
     outd0 = traits.Either(
@@ -1310,7 +1310,7 @@ class MedicAlgorithmSPECTRE2010OutputSpec(TraitedSpec):
     )
     outPrior = File(desc="Probability prior from the atlas registrations", exists=True)
     outFANTASM = File(
-        desc="Tissue classification of of the whole input volume.", exists=True
+        desc="Tissue classification of the whole input volume.", exists=True
     )
     outd0 = File(desc="Initial Brainmask", exists=True)
     outMidsagittal = File(desc="Plane dividing the brain hemispheres", exists=True)

diff --git a/nipype/interfaces/semtools/diffusion/gtract.py b/nipype/interfaces/semtools/diffusion/gtract.py
@@ -1119,7 +1119,7 @@ class gtractCoRegAnatomyInputSpec(CommandLineInputSpec):
         argstr="--inputVolume %s",
     )
     inputAnatomicalVolume = File(
-        desc="Required: input anatomical image file name. It is recommended that that the input anatomical image has been skull stripped and has the same orientation as the DWI scan.",
+        desc="Required: input anatomical image file name. It is recommended that the input anatomical image has been skull stripped and has the same orientation as the DWI scan.",
         exists=True,
         argstr="--inputAnatomicalVolume %s",
     )

diff --git a/nipype/interfaces/slicer/generate_classes.py b/nipype/interfaces/slicer/generate_classes.py
@@ -196,7 +196,7 @@ def generate_class(
             if longFlagNode:
                 # Prefer to use longFlag as name if it is given, rather than the parameter name
                 longFlagName = longFlagNode[0].firstChild.nodeValue
-                # SEM automatically strips prefixed "--" or "-" from from xml before processing
+                # SEM automatically strips prefixed "--" or "-" from xml before processing
                 # we need to replicate that behavior here The following
                 # two nodes in xml have the same behavior in the program
                 # <longflag>--test</longflag>

diff --git a/nipype/interfaces/slicer/registration/brainsfit.py b/nipype/interfaces/slicer/registration/brainsfit.py
@@ -279,7 +279,7 @@ class BRAINSFitInputSpec(CommandLineInputSpec):
         argstr="--numberOfThreads %d",
     )
     forceMINumberOfThreads = traits.Int(
-        desc="Force the the maximum number of threads to use for non thread safe MI metric.  CAUTION: Inconsistent results my arise!",
+        desc="Force the maximum number of threads to use for non thread safe MI metric.  CAUTION: Inconsistent results my arise!",
         argstr="--forceMINumberOfThreads %d",
     )
     debugLevel = traits.Int(

diff --git a/nipype/interfaces/slicer/registration/brainsresample.py b/nipype/interfaces/slicer/registration/brainsresample.py
@@ -94,7 +94,7 @@ class BRAINSResample(SEMLikeCommandLine):
     category: Registration
 
     description:
-       This program resamples an image image using a deformation field or a transform (BSpline, Affine, Rigid, etc.).
+       This program resamples an image using a deformation field or a transform (BSpline, Affine, Rigid, etc.).
 
 
     version: 3.0.0

diff --git a/nipype/interfaces/spm/model.py b/nipype/interfaces/spm/model.py
@@ -616,7 +616,7 @@ class ThresholdInputSpec(SPMCommandInputSpec):
         desc=(
             "In case no clusters survive the "
             "topological inference step this "
-            "will pick a culster with the highes "
+            "will pick a culster with the highest "
             "sum of t-values. Use with care."
         ),
     )

diff --git a/nipype/pipeline/engine/utils.py b/nipype/pipeline/engine/utils.py
@@ -1030,7 +1030,7 @@ def generate_expanded_graph(graph_in):
             iterables = {}
             # the source node iterables values
             src_values = [getattr(iter_src.inputs, field) for field in src_fields]
-            # if there is one source field, then the key is the the source value,
+            # if there is one source field, then the key is the source value,
             # otherwise the key is the tuple of source values
             if len(src_values) == 1:
                 key = src_values[0]

diff --git a/nipype/utils/spm_flat_config.m b/nipype/utils/spm_flat_config.m
@@ -1,7 +1,7 @@
 function cfgstruct = spm_flat_config(print_names)
 % Get a flat spm_config structure, with option to print out names
 %
-% This calls spm_config() to get the the nested configuration
+% This calls spm_config() to get the nested configuration
 % structure from spm.  We use this to fetch documentation, the
 % flattened structure is much easier to search through.  If
 % print_names is true (value of 1) it will print out the configuration

diff --git a/nipype/utils/tests/test_filemanip.py b/nipype/utils/tests/test_filemanip.py
@@ -631,7 +631,7 @@ def test_path_strict_resolve(tmpdir):
     """Check the monkeypatch to test strict resolution of Path."""
     tmpdir.chdir()
 
-    # Default strict=False should work out out of the box
+    # Default strict=False should work out of the box
     testfile = Path("somefile.txt")
     resolved = "%s/somefile.txt" % tmpdir
     assert str(path_resolve(testfile)) == resolved