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Merge pull request #3512 from DimitriPapadopoulos/codespell
DOC: Fix typos found by codespell
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‎THANKS.rst

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@@ -19,4 +19,3 @@ and `UL1 TR000442 University of Iowa Clinical and Translational Science Program
1919

2020

2121
We would also like to thank `JetBrains <http://www.jetbrains.com/>`__ for providing `Pycharm <http://www.jetbrains.com/pycharm/>`__ licenses.
22-

‎doc/_templates/indexsidebar.html

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@@ -11,4 +11,4 @@ <h3>{{ _('Links') }}</h3>
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<a href='https://pypi.python.org/pypi/nipype/'><img src='https://img.shields.io/pypi/pyversions/nipype.svg' alt='Python Versions' /></a></li>
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</ul>
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{% endblock %}
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{% endblock %}

‎doc/_templates/navbar.html

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@@ -13,4 +13,3 @@
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<a class="navbar" href="{{pathto('developers')}}">Developers</a> ·
1414
<a class="navbar" href="{{pathto('about')}}">About</a> ·
1515
<a class="navbar" href="http://nipy.org">Nipy</a>
16-

‎doc/devel/filename_generation.rst

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@@ -169,4 +169,3 @@ absolute path is generated and used for the ``cmdline`` when run, but
169169

170170
In [80]: res.interface.inputs.outfile
171171
Out[80]: 'bar.nii'
172-

‎doc/devel/gitwash/forking_hell.rst

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@@ -30,4 +30,3 @@ Create your own forked copy of nipype_
3030
should find yourself at the home page for your own forked copy of nipype_.
3131

3232
.. include:: links.inc
33-

‎doc/devel/gitwash/git_development.rst

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@@ -13,4 +13,3 @@ Contents:
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set_up_fork
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configure_git
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development_workflow
16-

‎doc/devel/gitwash/index.rst

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@@ -14,5 +14,3 @@ Contents:
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patching
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git_development
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git_resources
17-
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‎doc/devel/gitwash/set_up_fork.rst

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@@ -65,4 +65,3 @@ Just for your own satisfaction, show yourself that you now have a new
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origin git@github.com:your-user-name/nipype.git (push)
6666

6767
.. include:: links.inc
68-

‎nipype/caching/memory.py

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -287,7 +287,7 @@ def clear_runs_since(self, day=None, month=None, year=None, warn=True):
287287
os.remove(log_name)
288288

289289
def _clear_all_but(self, runs, warn=True):
290-
"""Remove all the runs appart from those given to the function
290+
"""Remove all the runs apart from those given to the function
291291
input.
292292
"""
293293
rm_all_but(self.base_dir, set(runs.keys()), warn=warn)

‎nipype/interfaces/afni/base.py

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -262,8 +262,8 @@ def _gen_fname(self, basename, cwd=None, suffix=None, change_ext=True, ext=None)
262262
Generate a filename based on the given parameters.
263263
264264
The filename will take the form: cwd/basename<suffix><ext>.
265-
If change_ext is True, it will use the extentions specified in
266-
<instance>intputs.output_type.
265+
If change_ext is True, it will use the extensions specified in
266+
<instance>inputs.output_type.
267267
268268
Parameters
269269
----------

‎nipype/interfaces/afni/model.py

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -265,7 +265,7 @@ class DeconvolveInputSpec(AFNICommandInputSpec):
265265
class DeconvolveOutputSpec(TraitedSpec):
266266
out_file = File(desc="output statistics file", exists=True)
267267
reml_script = File(
268-
desc="automatical generated script to run 3dREMLfit", exists=True
268+
desc="automatically generated script to run 3dREMLfit", exists=True
269269
)
270270
x1D = File(desc="save out X matrix", exists=True)
271271
cbucket = File(desc="output regression coefficients file (if generated)")
@@ -528,7 +528,7 @@ class RemlfitInputSpec(AFNICommandInputSpec):
528528
"be included.",
529529
argstr="-Rglt %s",
530530
)
531-
fitts_file = File(desc="ouput dataset for REML fitted model", argstr="-Rfitts %s")
531+
fitts_file = File(desc="output dataset for REML fitted model", argstr="-Rfitts %s")
532532
errts_file = File(
533533
desc="output dataset for REML residuals = data - fitted model",
534534
argstr="-Rerrts %s",
@@ -584,7 +584,7 @@ class RemlfitOutputSpec(AFNICommandOutputSpec):
584584
"but ONLY for the GLTs added on the REMLfit command "
585585
"line itself via 'gltsym' (if generated)"
586586
)
587-
fitts_file = File(desc="ouput dataset for REML fitted model (if generated)")
587+
fitts_file = File(desc="output dataset for REML fitted model (if generated)")
588588
errts_file = File(
589589
desc="output dataset for REML residuals = data - fitted model (if " "generated"
590590
)

‎nipype/interfaces/afni/preprocess.py

Lines changed: 10 additions & 10 deletions
Original file line numberDiff line numberDiff line change
@@ -821,7 +821,7 @@ class AutoTLRCInputSpec(CommandLineInputSpec):
821821

822822

823823
class AutoTLRC(AFNICommand):
824-
"""A minmal wrapper for the AutoTLRC script
824+
"""A minimal wrapper for the AutoTLRC script
825825
The only option currently supported is no_ss.
826826
For complete details, see the `3dQwarp Documentation.
827827
<https://afni.nimh.nih.gov/pub/dist/doc/program_help/@auto_tlrc.html>`_
@@ -1327,7 +1327,7 @@ class ECMInputSpec(CentralityInputSpec):
13271327
)
13281328
fecm = traits.Bool(
13291329
desc="Fast centrality method; substantial speed increase but cannot "
1330-
"accomodate thresholding; automatically selected if -thresh or "
1330+
"accommodate thresholding; automatically selected if -thresh or "
13311331
"-sparsity are not set",
13321332
argstr="-fecm",
13331333
)
@@ -2933,7 +2933,7 @@ class TProjectInputSpec(AFNICommandInputSpec):
29332933
the output dataset:
29342934
29352935
* mode = ZERO -- put zero values in their place;
2936-
output datset is same length as input
2936+
output dataset is same length as input
29372937
* mode = KILL -- remove those time points;
29382938
output dataset is shorter than input
29392939
* mode = NTRP -- censored values are replaced by interpolated
@@ -3073,7 +3073,7 @@ class TProject(AFNICommand):
30733073
as ``-passband``. In this way, you can bandpass time-censored data, and at
30743074
the same time, remove other time series of no interest
30753075
(e.g., physiological estimates, motion parameters).
3076-
Shifts voxel time series from input so that seperate slices are aligned to
3076+
Shifts voxel time series from input so that separate slices are aligned to
30773077
the same temporal origin.
30783078
30793079
Examples
@@ -3188,7 +3188,7 @@ class TShiftOutputSpec(AFNICommandOutputSpec):
31883188

31893189

31903190
class TShift(AFNICommand):
3191-
"""Shifts voxel time series from input so that seperate slices are aligned
3191+
"""Shifts voxel time series from input so that separate slices are aligned
31923192
to the same temporal origin.
31933193
31943194
For complete details, see the `3dTshift Documentation.
@@ -3658,7 +3658,7 @@ class QwarpInputSpec(AFNICommandInputSpec):
36583658
with 3dNwarpApply and 3dNwarpCat, for example.
36593659
* To be clear, this is the warp from source dataset
36603660
coordinates to base dataset coordinates, where the
3661-
values at each base grid point are the xyz displacments
3661+
values at each base grid point are the xyz displacements
36623662
needed to move that grid point's xyz values to the
36633663
corresponding xyz values in the source dataset:
36643664
base( (x,y,z) + WARP(x,y,z) ) matches source(x,y,z)
@@ -4034,7 +4034,7 @@ class QwarpInputSpec(AFNICommandInputSpec):
40344034
The goal is greater speed, and it seems to help this"
40354035
positively piggish program to be more expeditious."
40364036
* However, accuracy is somewhat lower with '-duplo',"
4037-
for reasons that currenly elude Zhark; for this reason,"
4037+
for reasons that currently elude Zhark; for this reason,"
40384038
the Emperor does not usually use '-duplo'.
40394039
40404040
""",
@@ -4225,21 +4225,21 @@ class QwarpInputSpec(AFNICommandInputSpec):
42254225
)
42264226
hel = traits.Bool(
42274227
desc="Hellinger distance: a matching function for the adventurous"
4228-
"This option has NOT be extensively tested for usefullness"
4228+
"This option has NOT be extensively tested for usefulness"
42294229
"and should be considered experimental at this infundibulum.",
42304230
argstr="-hel",
42314231
xor=["nmi", "mi", "lpc", "lpa", "pear"],
42324232
)
42334233
mi = traits.Bool(
42344234
desc="Mutual Information: a matching function for the adventurous"
4235-
"This option has NOT be extensively tested for usefullness"
4235+
"This option has NOT be extensively tested for usefulness"
42364236
"and should be considered experimental at this infundibulum.",
42374237
argstr="-mi",
42384238
xor=["mi", "hel", "lpc", "lpa", "pear"],
42394239
)
42404240
nmi = traits.Bool(
42414241
desc="Normalized Mutual Information: a matching function for the adventurous"
4242-
"This option has NOT been extensively tested for usefullness"
4242+
"This option has NOT been extensively tested for usefulness"
42434243
"and should be considered experimental at this infundibulum.",
42444244
argstr="-nmi",
42454245
xor=["nmi", "hel", "lpc", "lpa", "pear"],

‎nipype/interfaces/afni/utils.py

Lines changed: 9 additions & 9 deletions
Original file line numberDiff line numberDiff line change
@@ -539,27 +539,27 @@ class CatInputSpec(AFNICommandInputSpec):
539539
argstr="-sel %s",
540540
)
541541
out_int = traits.Bool(
542-
desc="specifiy int data type for output",
542+
desc="specify int data type for output",
543543
argstr="-i",
544544
xor=["out_format", "out_nice", "out_double", "out_fint", "out_cint"],
545545
)
546546
out_nice = traits.Bool(
547-
desc="specifiy nice data type for output",
547+
desc="specify nice data type for output",
548548
argstr="-n",
549549
xor=["out_format", "out_int", "out_double", "out_fint", "out_cint"],
550550
)
551551
out_double = traits.Bool(
552-
desc="specifiy double data type for output",
552+
desc="specify double data type for output",
553553
argstr="-d",
554554
xor=["out_format", "out_nice", "out_int", "out_fint", "out_cint"],
555555
)
556556
out_fint = traits.Bool(
557-
desc="specifiy int, rounded down, data type for output",
557+
desc="specify int, rounded down, data type for output",
558558
argstr="-f",
559559
xor=["out_format", "out_nice", "out_double", "out_int", "out_cint"],
560560
)
561561
out_cint = traits.Bool(
562-
desc="specifiy int, rounded up, data type for output",
562+
desc="specify int, rounded up, data type for output",
563563
xor=["out_format", "out_nice", "out_double", "out_fint", "out_int"],
564564
)
565565

@@ -693,7 +693,7 @@ class CenterMassInputSpec(CommandLineInputSpec):
693693
argstr="-set %f %f %f",
694694
)
695695
local_ijk = traits.Bool(
696-
desc="Output values as (i,j,k) in local orienation", argstr="-local_ijk"
696+
desc="Output values as (i,j,k) in local orientation", argstr="-local_ijk"
697697
)
698698
roi_vals = traits.List(
699699
traits.Int,
@@ -2554,11 +2554,11 @@ class ReHoInputSpec(CommandLineInputSpec):
25542554

25552555
class ReHoOutputSpec(TraitedSpec):
25562556
out_file = File(exists=True, desc="Voxelwise regional homogeneity map")
2557-
out_vals = File(desc="Table of labelwise regional homogenity values")
2557+
out_vals = File(desc="Table of labelwise regional homogeneity values")
25582558

25592559

25602560
class ReHo(AFNICommandBase):
2561-
"""Compute regional homogenity for a given neighbourhood.l,
2561+
"""Compute regional homogeneity for a given neighbourhood.l,
25622562
based on a local neighborhood of that voxel.
25632563
25642564
For complete details, see the `3dReHo Documentation.
@@ -2740,7 +2740,7 @@ class TCatSBInputSpec(AFNICommandInputSpec):
27402740

27412741
class TCatSubBrick(AFNICommand):
27422742
"""Hopefully a temporary function to allow sub-brick selection until
2743-
afni file managment is improved.
2743+
afni file management is improved.
27442744
27452745
For complete details, see the `3dTcat Documentation.
27462746
<https://afni.nimh.nih.gov/pub/dist/doc/program_help/3dTcat.html>`_

‎nipype/interfaces/c3.py

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -84,7 +84,7 @@ class C3dInputSpec(CommandLineInputSpec):
8484
desc=(
8585
"Write all images on the convert3d stack as multiple files."
8686
" Supports both list of output files or a pattern for the output"
87-
" filenames (using %d substituion)."
87+
" filenames (using %d substitution)."
8888
),
8989
)
9090
pix_type = traits.Enum(

‎nipype/interfaces/dcmstack.py

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -55,7 +55,7 @@ class NiftiGeneratorBase(BaseInterface):
5555
embedded meta data."""
5656

5757
def _get_out_path(self, meta, idx=None):
58-
"""Return the output path for the gernerated Nifti."""
58+
"""Return the output path for the generated Nifti."""
5959
if self.inputs.out_format:
6060
out_fmt = self.inputs.out_format
6161
else:
@@ -262,7 +262,7 @@ def _outputs(self):
262262
return outputs
263263

264264
def _run_interface(self, runtime):
265-
# If the 'meta_keys' input is a list, covert it to a dict
265+
# If the 'meta_keys' input is a list, convert it to a dict
266266
self._make_name_map()
267267
nw = NiftiWrapper.from_filename(self.inputs.in_file)
268268
self.result = {}
@@ -342,7 +342,7 @@ class MergeNiftiInputSpec(NiftiGeneratorBaseInputSpec):
342342
merge_dim = traits.Int(
343343
desc="Dimension to merge along. If not "
344344
"specified, the last singular or "
345-
"non-existant dimension is used."
345+
"non-existent dimension is used."
346346
)
347347

348348

‎nipype/interfaces/freesurfer/preprocess.py

Lines changed: 4 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -2361,8 +2361,8 @@ def _format_arg(self, name, spec, value):
23612361
def _list_outputs(self):
23622362
outputs = self.output_spec().get()
23632363
cwd = os.getcwd()
2364-
prefices = dict(src=self.inputs.source_file, trg=self.inputs.target_file)
2365-
suffices = dict(
2364+
prefixes = dict(src=self.inputs.source_file, trg=self.inputs.target_file)
2365+
suffixes = dict(
23662366
out_reg_file=("src", "_robustreg.lta", False),
23672367
registered_file=("src", "_robustreg", True),
23682368
weights_file=("src", "_robustweights", True),
@@ -2372,12 +2372,12 @@ def _list_outputs(self):
23722372
half_source_xfm=("src", "_robustxfm.lta", False),
23732373
half_targ_xfm=("trg", "_robustxfm.lta", False),
23742374
)
2375-
for name, sufftup in list(suffices.items()):
2375+
for name, sufftup in list(suffixes.items()):
23762376
value = getattr(self.inputs, name)
23772377
if value:
23782378
if value is True:
23792379
outputs[name] = fname_presuffix(
2380-
prefices[sufftup[0]],
2380+
prefixes[sufftup[0]],
23812381
suffix=sufftup[1],
23822382
newpath=cwd,
23832383
use_ext=sufftup[2],

‎nipype/interfaces/io.py

Lines changed: 8 additions & 8 deletions
Original file line numberDiff line numberDiff line change
@@ -764,7 +764,7 @@ def _list_outputs(self):
764764
out_files.append(s3dst)
765765
# Otherwise, copy locally src -> dst
766766
if not s3_flag or isdefined(self.inputs.local_copy):
767-
# Create output directory if it doesnt exist
767+
# Create output directory if it doesn't exist
768768
if not os.path.exists(path):
769769
try:
770770
os.makedirs(path)
@@ -1318,7 +1318,7 @@ class SelectFilesInputSpec(DynamicTraitedSpec, BaseInterfaceInputSpec):
13181318
sort_filelist = traits.Bool(
13191319
True,
13201320
usedefault=True,
1321-
desc="When matching mutliple files, return them" " in sorted order.",
1321+
desc="When matching multiple files, return them" " in sorted order.",
13221322
)
13231323
raise_on_empty = traits.Bool(
13241324
True,
@@ -1346,7 +1346,7 @@ class SelectFiles(IOBase):
13461346
13471347
This interface uses Python's {}-based string formatting syntax to plug
13481348
values (possibly known only at workflow execution time) into string
1349-
templates and collect files from persistant storage. These templates can
1349+
templates and collect files from persistent storage. These templates can
13501350
also be combined with glob wildcards (``*``, ``?``) and character ranges (``[...]``).
13511351
The field names in the formatting template (i.e. the terms in braces) will
13521352
become inputs fields on the interface, and the keys in the templates
@@ -1513,7 +1513,7 @@ class DataFinder(IOBase):
15131513
Will recursively search any subdirectories by default. This can be limited
15141514
with the min/max depth options.
15151515
Matched paths are available in the output 'out_paths'. Any named groups of
1516-
captured text from the regular expression are also available as ouputs of
1516+
captured text from the regular expression are also available as outputs of
15171517
the same name.
15181518
15191519
Examples
@@ -1583,7 +1583,7 @@ def _run_interface(self, runtime):
15831583
]
15841584
self.result = None
15851585
for root_path in self.inputs.root_paths:
1586-
# Handle tilda/env variables and remove extra seperators
1586+
# Handle tilda/env variables and remove extra separators
15871587
root_path = os.path.normpath(
15881588
os.path.expandvars(os.path.expanduser(root_path))
15891589
)
@@ -1612,7 +1612,7 @@ def _run_interface(self, runtime):
16121612
for key, vals in list(self.result.items()):
16131613
self.result[key] = vals[0]
16141614
else:
1615-
# sort all keys acording to out_paths
1615+
# sort all keys according to out_paths
16161616
for key in list(self.result.keys()):
16171617
if key == "out_paths":
16181618
continue
@@ -2083,15 +2083,15 @@ class XNATSinkInputSpec(DynamicTraitedSpec, BaseInterfaceInputSpec):
20832083

20842084
assessor_id = Str(
20852085
desc=(
2086-
"Option to customize ouputs representation in XNAT - "
2086+
"Option to customize outputs representation in XNAT - "
20872087
"assessor level will be used with specified id"
20882088
),
20892089
xor=["reconstruction_id"],
20902090
)
20912091

20922092
reconstruction_id = Str(
20932093
desc=(
2094-
"Option to customize ouputs representation in XNAT - "
2094+
"Option to customize outputs representation in XNAT - "
20952095
"reconstruction level will be used with specified id"
20962096
),
20972097
xor=["assessor_id"],

‎nipype/interfaces/matlab.py

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -191,7 +191,7 @@ def _gen_matlab_command(self, argstr, script_lines):
191191
else:
192192
prescript.insert(0, "fprintf(1,'Executing code at %s:\\n',datestr(now));")
193193
for path in paths:
194-
# addpath() is not available after compliation
194+
# addpath() is not available after compilation
195195
# https://www.mathworks.com/help/compiler/ismcc.html
196196
# https://www.mathworks.com/help/compiler/isdeployed.html
197197
prescript.append("if ~(ismcc || isdeployed), addpath('%s'); end;\n" % path)

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