diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index 7ddb2c1253..302a32d626 100644 --- a/CONTRIBUTING.md +++ b/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 --git a/nipype/interfaces/afni/preprocess.py b/nipype/interfaces/afni/preprocess.py index 819ce663b4..a60a9f4617 100644 --- a/nipype/interfaces/afni/preprocess.py +++ b/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 --git a/nipype/interfaces/dcmstack.py b/nipype/interfaces/dcmstack.py index b3e898b0c4..b76255ab84 100644 --- a/nipype/interfaces/dcmstack.py +++ b/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 --git a/nipype/interfaces/dipy/base.py b/nipype/interfaces/dipy/base.py index fc8fe473e0..3f87d7d9bd 100644 --- a/nipype/interfaces/dipy/base.py +++ b/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 --git a/nipype/interfaces/freesurfer/preprocess.py b/nipype/interfaces/freesurfer/preprocess.py index b17249b046..a3e44b66ba 100644 --- a/nipype/interfaces/freesurfer/preprocess.py +++ b/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 --git a/nipype/interfaces/freesurfer/utils.py b/nipype/interfaces/freesurfer/utils.py index 7134b92f3b..a449bde9d7 100644 --- a/nipype/interfaces/freesurfer/utils.py +++ b/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 --git a/nipype/interfaces/io.py b/nipype/interfaces/io.py index d441a9cb72..975fe4537f 100644 --- a/nipype/interfaces/io.py +++ b/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 --git a/nipype/interfaces/semtools/brains/utilities.py b/nipype/interfaces/semtools/brains/utilities.py index a1241aca19..e3b035f96e 100644 --- a/nipype/interfaces/semtools/brains/utilities.py +++ b/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 --git a/nipype/interfaces/semtools/diffusion/gtract.py b/nipype/interfaces/semtools/diffusion/gtract.py index cb9bbaf638..d9bace5e59 100644 --- a/nipype/interfaces/semtools/diffusion/gtract.py +++ b/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 --git a/nipype/interfaces/semtools/diffusion/tractography/ukftractography.py b/nipype/interfaces/semtools/diffusion/tractography/ukftractography.py index 4be8a97811..cc3619f8ec 100644 --- a/nipype/interfaces/semtools/diffusion/tractography/ukftractography.py +++ b/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 --git a/nipype/interfaces/semtools/segmentation/specialized.py b/nipype/interfaces/semtools/segmentation/specialized.py index ba33e7a268..b00c2309eb 100644 --- a/nipype/interfaces/semtools/segmentation/specialized.py +++ b/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 --git a/nipype/interfaces/slicer/registration/brainsfit.py b/nipype/interfaces/slicer/registration/brainsfit.py index 3baf06648c..c9b61e8da0 100644 --- a/nipype/interfaces/slicer/registration/brainsfit.py +++ b/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 --git a/nipype/pipeline/plugins/sge.py b/nipype/pipeline/plugins/sge.py index 323a160133..ac89f2dfea 100644 --- a/nipype/pipeline/plugins/sge.py +++ b/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 --git a/tools/update_changes.sh b/tools/update_changes.sh index c3b20df5cd..5f7afc6057 100755 --- a/tools/update_changes.sh +++ b/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. #