DOC: Fix typos found by codespell

Author: DimitriPapadopoulos

nipype/caching/memory.py

@@ -287,7 +287,7 @@ def clear_runs_since(self, day=None, month=None, year=None, warn=True):
             os.remove(log_name)
 
     def _clear_all_but(self, runs, warn=True):
-        """Remove all the runs appart from those given to the function
+        """Remove all the runs apart from those given to the function
         input.
         """
         rm_all_but(self.base_dir, set(runs.keys()), warn=warn)

nipype/interfaces/afni/base.py

@@ -262,8 +262,8 @@ def _gen_fname(self, basename, cwd=None, suffix=None, change_ext=True, ext=None)
         Generate a filename based on the given parameters.
 
         The filename will take the form: cwd/basename<suffix><ext>.
-        If change_ext is True, it will use the extentions specified in
-        <instance>intputs.output_type.
+        If change_ext is True, it will use the extensions specified in
+        <instance>inputs.output_type.
 
         Parameters
         ----------

nipype/interfaces/afni/model.py

@@ -265,7 +265,7 @@ class DeconvolveInputSpec(AFNICommandInputSpec):
 class DeconvolveOutputSpec(TraitedSpec):
     out_file = File(desc="output statistics file", exists=True)
     reml_script = File(
-        desc="automatical generated script to run 3dREMLfit", exists=True
+        desc="automatically generated script to run 3dREMLfit", exists=True
     )
     x1D = File(desc="save out X matrix", exists=True)
     cbucket = File(desc="output regression coefficients file (if generated)")
@@ -528,7 +528,7 @@ class RemlfitInputSpec(AFNICommandInputSpec):
         "be included.",
         argstr="-Rglt %s",
     )
-    fitts_file = File(desc="ouput dataset for REML fitted model", argstr="-Rfitts %s")
+    fitts_file = File(desc="output dataset for REML fitted model", argstr="-Rfitts %s")
     errts_file = File(
         desc="output dataset for REML residuals = data - fitted model",
         argstr="-Rerrts %s",
@@ -584,7 +584,7 @@ class RemlfitOutputSpec(AFNICommandOutputSpec):
         "but ONLY for the GLTs added on the REMLfit command "
         "line itself via 'gltsym' (if generated)"
     )
-    fitts_file = File(desc="ouput dataset for REML fitted model (if generated)")
+    fitts_file = File(desc="output dataset for REML fitted model (if generated)")
     errts_file = File(
         desc="output dataset for REML residuals = data - fitted model (if " "generated"
     )

nipype/interfaces/afni/preprocess.py

@@ -821,7 +821,7 @@ class AutoTLRCInputSpec(CommandLineInputSpec):
 
 
 class AutoTLRC(AFNICommand):
-    """A minmal wrapper for the AutoTLRC script
+    """A minimal wrapper for the AutoTLRC script
     The only option currently supported is no_ss.
     For complete details, see the `3dQwarp Documentation.
     <https://afni.nimh.nih.gov/pub/dist/doc/program_help/@auto_tlrc.html>`_
@@ -1327,7 +1327,7 @@ class ECMInputSpec(CentralityInputSpec):
     )
     fecm = traits.Bool(
         desc="Fast centrality method; substantial speed increase but cannot "
-        "accomodate thresholding; automatically selected if -thresh or "
+        "accommodate thresholding; automatically selected if -thresh or "
         "-sparsity are not set",
         argstr="-fecm",
     )
@@ -2933,7 +2933,7 @@ class TProjectInputSpec(AFNICommandInputSpec):
 the output dataset:
 
 * mode = ZERO -- put zero values in their place;
-  output datset is same length as input
+  output dataset is same length as input
 * mode = KILL -- remove those time points;
   output dataset is shorter than input
 * mode = NTRP -- censored values are replaced by interpolated
@@ -3073,7 +3073,7 @@ class TProject(AFNICommand):
     as ``-passband``.  In this way, you can bandpass time-censored data, and at
     the same time, remove other time series of no interest
     (e.g., physiological estimates, motion parameters).
-    Shifts voxel time series from input so that seperate slices are aligned to
+    Shifts voxel time series from input so that separate slices are aligned to
     the same temporal origin.
 
     Examples
@@ -3188,7 +3188,7 @@ class TShiftOutputSpec(AFNICommandOutputSpec):
 
 
 class TShift(AFNICommand):
-    """Shifts voxel time series from input so that seperate slices are aligned
+    """Shifts voxel time series from input so that separate slices are aligned
     to the same temporal origin.
 
     For complete details, see the `3dTshift Documentation.
@@ -3658,7 +3658,7 @@ class QwarpInputSpec(AFNICommandInputSpec):
   with 3dNwarpApply and 3dNwarpCat, for example.
 * To be clear, this is the warp from source dataset
   coordinates to base dataset coordinates, where the
-  values at each base grid point are the xyz displacments
+  values at each base grid point are the xyz displacements
   needed to move that grid point's xyz values to the
   corresponding xyz values in the source dataset:
   base( (x,y,z) + WARP(x,y,z) ) matches source(x,y,z)
@@ -4034,7 +4034,7 @@ class QwarpInputSpec(AFNICommandInputSpec):
   The goal is greater speed, and it seems to help this"
   positively piggish program to be more expeditious."
 * However, accuracy is somewhat lower with '-duplo',"
-  for reasons that currenly elude Zhark; for this reason,"
+  for reasons that currently elude Zhark; for this reason,"
   the Emperor does not usually use '-duplo'.
 
 """,
@@ -4225,21 +4225,21 @@ class QwarpInputSpec(AFNICommandInputSpec):
     )
     hel = traits.Bool(
         desc="Hellinger distance: a matching function for the adventurous"
-        "This option has NOT be extensively tested for usefullness"
+        "This option has NOT be extensively tested for usefulness"
         "and should be considered experimental at this infundibulum.",
         argstr="-hel",
         xor=["nmi", "mi", "lpc", "lpa", "pear"],
     )
     mi = traits.Bool(
         desc="Mutual Information: a matching function for the adventurous"
-        "This option has NOT be extensively tested for usefullness"
+        "This option has NOT be extensively tested for usefulness"
         "and should be considered experimental at this infundibulum.",
         argstr="-mi",
         xor=["mi", "hel", "lpc", "lpa", "pear"],
     )
     nmi = traits.Bool(
         desc="Normalized Mutual Information: a matching function for the adventurous"
-        "This option has NOT been extensively tested for usefullness"
+        "This option has NOT been extensively tested for usefulness"
         "and should be considered experimental at this infundibulum.",
         argstr="-nmi",
         xor=["nmi", "hel", "lpc", "lpa", "pear"],

nipype/interfaces/afni/utils.py

@@ -539,27 +539,27 @@ class CatInputSpec(AFNICommandInputSpec):
         argstr="-sel %s",
     )
     out_int = traits.Bool(
-        desc="specifiy int data type for output",
+        desc="specify int data type for output",
         argstr="-i",
         xor=["out_format", "out_nice", "out_double", "out_fint", "out_cint"],
     )
     out_nice = traits.Bool(
-        desc="specifiy nice data type for output",
+        desc="specify nice data type for output",
         argstr="-n",
         xor=["out_format", "out_int", "out_double", "out_fint", "out_cint"],
     )
     out_double = traits.Bool(
-        desc="specifiy double data type for output",
+        desc="specify double data type for output",
         argstr="-d",
         xor=["out_format", "out_nice", "out_int", "out_fint", "out_cint"],
     )
     out_fint = traits.Bool(
-        desc="specifiy int, rounded down, data type for output",
+        desc="specify int, rounded down, data type for output",
         argstr="-f",
         xor=["out_format", "out_nice", "out_double", "out_int", "out_cint"],
     )
     out_cint = traits.Bool(
-        desc="specifiy int, rounded up, data type for output",
+        desc="specify int, rounded up, data type for output",
         xor=["out_format", "out_nice", "out_double", "out_fint", "out_int"],
     )
 
@@ -693,7 +693,7 @@ class CenterMassInputSpec(CommandLineInputSpec):
         argstr="-set %f %f %f",
     )
     local_ijk = traits.Bool(
-        desc="Output values as (i,j,k) in local orienation", argstr="-local_ijk"
+        desc="Output values as (i,j,k) in local orientation", argstr="-local_ijk"
     )
     roi_vals = traits.List(
         traits.Int,
@@ -2554,11 +2554,11 @@ class ReHoInputSpec(CommandLineInputSpec):
 
 class ReHoOutputSpec(TraitedSpec):
     out_file = File(exists=True, desc="Voxelwise regional homogeneity map")
-    out_vals = File(desc="Table of labelwise regional homogenity values")
+    out_vals = File(desc="Table of labelwise regional homogeneity values")
 
 
 class ReHo(AFNICommandBase):
-    """Compute regional homogenity for a given neighbourhood.l,
+    """Compute regional homogeneity for a given neighbourhood.l,
     based on a local neighborhood of that voxel.
 
     For complete details, see the `3dReHo Documentation.
@@ -2740,7 +2740,7 @@ class TCatSBInputSpec(AFNICommandInputSpec):
 
 class TCatSubBrick(AFNICommand):
     """Hopefully a temporary function to allow sub-brick selection until
-    afni file managment is improved.
+    afni file management is improved.
 
     For complete details, see the `3dTcat Documentation.
     <https://afni.nimh.nih.gov/pub/dist/doc/program_help/3dTcat.html>`_

nipype/interfaces/c3.py

@@ -84,7 +84,7 @@ class C3dInputSpec(CommandLineInputSpec):
         desc=(
             "Write all images on the convert3d stack as multiple files."
             " Supports both list of output files or a pattern for the output"
-            " filenames (using %d substituion)."
+            " filenames (using %d substitution)."
         ),
     )
     pix_type = traits.Enum(

nipype/interfaces/dcmstack.py

@@ -55,7 +55,7 @@ class NiftiGeneratorBase(BaseInterface):
     embedded meta data."""
 
     def _get_out_path(self, meta, idx=None):
-        """Return the output path for the gernerated Nifti."""
+        """Return the output path for the generated Nifti."""
         if self.inputs.out_format:
             out_fmt = self.inputs.out_format
         else:
@@ -262,7 +262,7 @@ def _outputs(self):
         return outputs
 
     def _run_interface(self, runtime):
-        # If the 'meta_keys' input is a list, covert it to a dict
+        # If the 'meta_keys' input is a list, convert it to a dict
         self._make_name_map()
         nw = NiftiWrapper.from_filename(self.inputs.in_file)
         self.result = {}
@@ -342,7 +342,7 @@ class MergeNiftiInputSpec(NiftiGeneratorBaseInputSpec):
     merge_dim = traits.Int(
         desc="Dimension to merge along. If not "
         "specified, the last singular or "
-        "non-existant dimension is used."
+        "non-existent dimension is used."
     )
 
 

nipype/interfaces/freesurfer/preprocess.py

@@ -2361,8 +2361,8 @@ def _format_arg(self, name, spec, value):
     def _list_outputs(self):
         outputs = self.output_spec().get()
         cwd = os.getcwd()
-        prefices = dict(src=self.inputs.source_file, trg=self.inputs.target_file)
-        suffices = dict(
+        prefixes = dict(src=self.inputs.source_file, trg=self.inputs.target_file)
+        suffixes = dict(
             out_reg_file=("src", "_robustreg.lta", False),
             registered_file=("src", "_robustreg", True),
             weights_file=("src", "_robustweights", True),
@@ -2372,12 +2372,12 @@ def _list_outputs(self):
             half_source_xfm=("src", "_robustxfm.lta", False),
             half_targ_xfm=("trg", "_robustxfm.lta", False),
         )
-        for name, sufftup in list(suffices.items()):
+        for name, sufftup in list(suffixes.items()):
             value = getattr(self.inputs, name)
             if value:
                 if value is True:
                     outputs[name] = fname_presuffix(
-                        prefices[sufftup[0]],
+                        prefixes[sufftup[0]],
                         suffix=sufftup[1],
                         newpath=cwd,
                         use_ext=sufftup[2],

nipype/interfaces/io.py

@@ -764,7 +764,7 @@ def _list_outputs(self):
                     out_files.append(s3dst)
                 # Otherwise, copy locally src -> dst
                 if not s3_flag or isdefined(self.inputs.local_copy):
-                    # Create output directory if it doesnt exist
+                    # Create output directory if it doesn't exist
                     if not os.path.exists(path):
                         try:
                             os.makedirs(path)
@@ -1318,7 +1318,7 @@ class SelectFilesInputSpec(DynamicTraitedSpec, BaseInterfaceInputSpec):
     sort_filelist = traits.Bool(
         True,
         usedefault=True,
-        desc="When matching mutliple files, return them" " in sorted order.",
+        desc="When matching multiple files, return them" " in sorted order.",
     )
     raise_on_empty = traits.Bool(
         True,
@@ -1346,7 +1346,7 @@ class SelectFiles(IOBase):
 
     This interface uses Python's {}-based string formatting syntax to plug
     values (possibly known only at workflow execution time) into string
-    templates and collect files from persistant storage. These templates can
+    templates and collect files from persistent storage. These templates can
     also be combined with glob wildcards (``*``, ``?``) and character ranges (``[...]``).
     The field names in the formatting template (i.e. the terms in braces) will
     become inputs fields on the interface, and the keys in the templates
@@ -1513,7 +1513,7 @@ class DataFinder(IOBase):
     Will recursively search any subdirectories by default. This can be limited
     with the min/max depth options.
     Matched paths are available in the output 'out_paths'. Any named groups of
-    captured text from the regular expression are also available as ouputs of
+    captured text from the regular expression are also available as outputs of
     the same name.
 
     Examples
@@ -1583,7 +1583,7 @@ def _run_interface(self, runtime):
             ]
         self.result = None
         for root_path in self.inputs.root_paths:
-            # Handle tilda/env variables and remove extra seperators
+            # Handle tilda/env variables and remove extra separators
             root_path = os.path.normpath(
                 os.path.expandvars(os.path.expanduser(root_path))
             )
@@ -1612,7 +1612,7 @@ def _run_interface(self, runtime):
             for key, vals in list(self.result.items()):
                 self.result[key] = vals[0]
         else:
-            # sort all keys acording to out_paths
+            # sort all keys according to out_paths
             for key in list(self.result.keys()):
                 if key == "out_paths":
                     continue
@@ -2083,15 +2083,15 @@ class XNATSinkInputSpec(DynamicTraitedSpec, BaseInterfaceInputSpec):
 
     assessor_id = Str(
         desc=(
-            "Option to customize ouputs representation in XNAT - "
+            "Option to customize outputs representation in XNAT - "
             "assessor level will be used with specified id"
         ),
         xor=["reconstruction_id"],
     )
 
     reconstruction_id = Str(
         desc=(
-            "Option to customize ouputs representation in XNAT - "
+            "Option to customize outputs representation in XNAT - "
             "reconstruction level will be used with specified id"
         ),
         xor=["assessor_id"],

nipype/interfaces/matlab.py

@@ -191,7 +191,7 @@ def _gen_matlab_command(self, argstr, script_lines):
         else:
             prescript.insert(0, "fprintf(1,'Executing code at %s:\\n',datestr(now));")
         for path in paths:
-            # addpath() is not available after compliation
+            # addpath() is not available after compilation
             # https://www.mathworks.com/help/compiler/ismcc.html
             # https://www.mathworks.com/help/compiler/isdeployed.html
             prescript.append("if ~(ismcc || isdeployed), addpath('%s'); end;\n" % path)