Merge pull request #3606 from DimitriPapadopoulos/codespell

DOC: Fix typos newly found by codespell

Author: effigies

Diff for: CONTRIBUTING.md

@@ -41,7 +41,7 @@ The current list of issue labels are [here][link_labels] and include:
 * [![Orphaned](https://img.shields.io/badge/-orphaned-9baddd.svg)][link_orphaned] *These pull requests have been closed for inactivity.*
 
     Before proposing a new pull request, browse through the "orphaned" pull requests.
-    You may find that someone has already made significant progress toward your goal, and you can re-use their
+    You may find that someone has already made significant progress toward your goal, and you can reuse their
     unfinished work.
     An adopted PR should be updated to merge or rebase the current master, and a new PR should be created (see
     below) that references the original PR.

Diff for: nipype/interfaces/afni/preprocess.py

@@ -621,7 +621,7 @@ class AutoTcorrelateInputSpec(AFNICommandInputSpec):
         copyfile=False,
     )
     polort = traits.Int(
-        desc="Remove polynomical trend of order m or -1 for no detrending",
+        desc="Remove polynomial trend of order m or -1 for no detrending",
         argstr="-polort %d",
     )
     eta2 = traits.Bool(desc="eta^2 similarity", argstr="-eta2")
@@ -2774,7 +2774,7 @@ class TCorrelateInputSpec(AFNICommandInputSpec):
         desc="Correlation is the normal Pearson correlation coefficient",
         argstr="-pearson",
     )
-    polort = traits.Int(desc="Remove polynomical trend of order m", argstr="-polort %d")
+    polort = traits.Int(desc="Remove polynomial trend of order m", argstr="-polort %d")
 
 
 class TCorrelate(AFNICommand):

Diff for: nipype/interfaces/dcmstack.py

@@ -100,7 +100,7 @@ class DcmStackInputSpec(NiftiGeneratorBaseInputSpec):
     )
     embed_meta = traits.Bool(desc="Embed DICOM meta data into result")
     exclude_regexes = traits.List(
-        desc="Meta data to exclude, suplementing any default exclude filters"
+        desc="Meta data to exclude, supplementing any default exclude filters"
     )
     include_regexes = traits.List(
         desc="Meta data to include, overriding any exclude filters"

Diff for: nipype/interfaces/dipy/base.py

@@ -188,7 +188,7 @@ def dipy_to_nipype_interface(cls_name, dipy_flow, BaseClass=DipyBaseInterface):
     cls_name: string
         new class name
     dipy_flow: Workflow class type.
-        It should be any children class of `dipy.workflows.workflow.Worflow`
+        It should be any children class of `dipy.workflows.workflow.Workflow`
     BaseClass: object
         nipype instance object
 

Diff for: nipype/interfaces/freesurfer/preprocess.py

@@ -2688,7 +2688,7 @@ class MNIBiasCorrectionOutputSpec(TraitedSpec):
 
 
 class MNIBiasCorrection(FSCommand):
-    """Wrapper for nu_correct, a program from the Montreal Neurological Insitute (MNI)
+    """Wrapper for nu_correct, a program from the Montreal Neurological Institute (MNI)
     used for correcting intensity non-uniformity (ie, bias fields). You must have the
     MNI software installed on your system to run this. See [www.bic.mni.mcgill.ca/software/N3]
     for more info.
@@ -3292,7 +3292,7 @@ class SegmentCCInputSpec(FSTraitedSpec):
 
 
 class SegmentCCOutputSpec(TraitedSpec):
-    out_file = File(exists=False, desc="Output segmentation uncluding corpus collosum")
+    out_file = File(exists=False, desc="Output segmentation including corpus collosum")
     out_rotation = File(exists=False, desc="Output lta rotation file")
 
 

Diff for: nipype/interfaces/freesurfer/utils.py

@@ -1906,7 +1906,7 @@ class Tkregister2InputSpec(FSTraitedSpec):
         desc="freesurfer-style registration file",
     )
     reg_header = traits.Bool(
-        False, argstr="--regheader", desc="compute regstration from headers"
+        False, argstr="--regheader", desc="compute registration from headers"
     )
     fstal = traits.Bool(
         False,

Diff for: nipype/interfaces/io.py

@@ -163,7 +163,7 @@ def _add_output_traits(self, base):
 # Class to track percentage of S3 file upload
 class ProgressPercentage:
     """
-    Callable class instsance (via __call__ method) that displays
+    Callable class instance (via __call__ method) that displays
     upload percentage of a file to S3
     """
 

Diff for: nipype/interfaces/semtools/brains/utilities.py

@@ -57,7 +57,7 @@ class HistogramMatchingFilterInputSpec(CommandLineInputSpec):
         argstr="--histogramAlgorithm %s",
     )
     verbose = traits.Bool(
-        desc=" verbose mode running for debbuging", argstr="--verbose "
+        desc=" verbose mode running for debugging", argstr="--verbose "
     )
 
 

Diff for: nipype/interfaces/semtools/diffusion/gtract.py

@@ -1194,15 +1194,15 @@ class gtractCoRegAnatomyInputSpec(CommandLineInputSpec):
         argstr="--samplingPercentage %f",
     )
     useMomentsAlign = traits.Bool(
-        desc="MomentsAlign assumes that the center of mass of the images represent similar structures.  Perform a MomentsAlign registration as part of the sequential registration steps.   This option MUST come first, and CAN NOT be used with either CenterOfHeadLAlign, GeometryAlign, or initialTransform file.  This family of options superceeds the use of transformType if any of them are set.",
+        desc="MomentsAlign assumes that the center of mass of the images represent similar structures.  Perform a MomentsAlign registration as part of the sequential registration steps.   This option MUST come first, and CAN NOT be used with either CenterOfHeadLAlign, GeometryAlign, or initialTransform file.  This family of options supersedes the use of transformType if any of them are set.",
         argstr="--useMomentsAlign ",
     )
     useGeometryAlign = traits.Bool(
-        desc="GeometryAlign on assumes that the center of the voxel lattice of the images represent similar structures. Perform a GeometryCenterAlign registration as part of the sequential registration steps.   This option MUST come first, and CAN NOT be used with either MomentsAlign, CenterOfHeadAlign, or initialTransform file.  This family of options superceeds the use of transformType if any of them are set.",
+        desc="GeometryAlign on assumes that the center of the voxel lattice of the images represent similar structures. Perform a GeometryCenterAlign registration as part of the sequential registration steps.   This option MUST come first, and CAN NOT be used with either MomentsAlign, CenterOfHeadAlign, or initialTransform file.  This family of options supersedes the use of transformType if any of them are set.",
         argstr="--useGeometryAlign ",
     )
     useCenterOfHeadAlign = traits.Bool(
-        desc="CenterOfHeadAlign attempts to find a hemisphere full of foreground voxels from the superior direction as an estimate of where the center of a head shape would be to drive a center of mass estimate.  Perform a CenterOfHeadAlign registration as part of the sequential registration steps.   This option MUST come first, and CAN NOT be used with either MomentsAlign, GeometryAlign, or initialTransform file.  This family of options superceeds the use of transformType if any of them are set.",
+        desc="CenterOfHeadAlign attempts to find a hemisphere full of foreground voxels from the superior direction as an estimate of where the center of a head shape would be to drive a center of mass estimate.  Perform a CenterOfHeadAlign registration as part of the sequential registration steps.   This option MUST come first, and CAN NOT be used with either MomentsAlign, GeometryAlign, or initialTransform file.  This family of options supersedes the use of transformType if any of them are set.",
         argstr="--useCenterOfHeadAlign ",
     )
     numberOfThreads = traits.Int(
@@ -1370,7 +1370,7 @@ class gtractCostFastMarchingInputSpec(CommandLineInputSpec):
         argstr="--anisotropyWeight %f",
     )
     stoppingValue = traits.Float(
-        desc="Terminiating value for vcl_cost function estimation",
+        desc="Terminating value for vcl_cost function estimation",
         argstr="--stoppingValue %f",
     )
     seedThreshold = traits.Float(

Diff for: nipype/interfaces/semtools/diffusion/tractography/ukftractography.py

@@ -55,7 +55,7 @@ class UKFTractographyInputSpec(CommandLineInputSpec):
         "1", "2", desc="Number of tensors used", argstr="--numTensor %s"
     )
     freeWater = traits.Bool(
-        desc="Adds a term for free water difusion to the model. (Note for experts: if checked, the 1T simple model is forced) ",
+        desc="Adds a term for free water diffusion to the model. (Note for experts: if checked, the 1T simple model is forced) ",
         argstr="--freeWater ",
     )
     recordFA = traits.Bool(

Diff for: nipype/interfaces/semtools/segmentation/specialized.py

@@ -587,7 +587,7 @@ class BinaryMaskEditorBasedOnLandmarksInputSpec(CommandLineInputSpec):
     )
     setCutDirectionForObliquePlane = InputMultiPath(
         traits.Str,
-        desc="If this is true, the mask will be thresholded out to the direction of inferior, posterior,  and/or left. Default behavrior is that cutting out to the direction of superior, anterior and/or right. ",
+        desc="If this is true, the mask will be thresholded out to the direction of inferior, posterior,  and/or left. Default behavior is that cutting out to the direction of superior, anterior and/or right. ",
         sep=",",
         argstr="--setCutDirectionForObliquePlane %s",
     )

Diff for: nipype/interfaces/slicer/registration/brainsfit.py

@@ -63,23 +63,23 @@ class BRAINSFitInputSpec(CommandLineInputSpec):
         argstr="--initializeTransformMode %s",
     )
     useRigid = traits.Bool(
-        desc="Perform a rigid registration as part of the sequential registration steps.  This family of options superceeds the use of transformType if any of them are set.",
+        desc="Perform a rigid registration as part of the sequential registration steps.  This family of options supersedes the use of transformType if any of them are set.",
         argstr="--useRigid ",
     )
     useScaleVersor3D = traits.Bool(
-        desc="Perform a ScaleVersor3D registration as part of the sequential registration steps.  This family of options superceeds the use of transformType if any of them are set.",
+        desc="Perform a ScaleVersor3D registration as part of the sequential registration steps.  This family of options supersedes the use of transformType if any of them are set.",
         argstr="--useScaleVersor3D ",
     )
     useScaleSkewVersor3D = traits.Bool(
-        desc="Perform a ScaleSkewVersor3D registration as part of the sequential registration steps.  This family of options superceeds the use of transformType if any of them are set.",
+        desc="Perform a ScaleSkewVersor3D registration as part of the sequential registration steps.  This family of options supersedes the use of transformType if any of them are set.",
         argstr="--useScaleSkewVersor3D ",
     )
     useAffine = traits.Bool(
-        desc="Perform an Affine registration as part of the sequential registration steps.  This family of options superceeds the use of transformType if any of them are set.",
+        desc="Perform an Affine registration as part of the sequential registration steps.  This family of options supersedes the use of transformType if any of them are set.",
         argstr="--useAffine ",
     )
     useBSpline = traits.Bool(
-        desc="Perform a BSpline registration as part of the sequential registration steps.  This family of options superceeds the use of transformType if any of them are set.",
+        desc="Perform a BSpline registration as part of the sequential registration steps.  This family of options supersedes the use of transformType if any of them are set.",
         argstr="--useBSpline ",
     )
     numberOfSamples = traits.Int(

Diff for: nipype/pipeline/plugins/sge.py

@@ -141,7 +141,7 @@ def _remove_old_jobs(self):
     def add_startup_job(self, taskid, qsub_command_line):
         """
         :param taskid: The job id
-        :param qsub_command_line: When initializing, re-use the job_queue_name
+        :param qsub_command_line: When initializing, reuse the job_queue_name
         :return: NONE
         """
         taskid = int(taskid)  # Ensure that it is an integer

Diff for: tools/update_changes.sh

@@ -1,7 +1,7 @@
 #!/bin/bash
 #
 # Collects the pull-requests since the latest release and
-# aranges them in the CHANGES.txt file.
+# arranges them in the CHANGES.txt file.
 #
 # This is a script to be run before releasing a new version.
 #