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Sep 21, 2022
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DOC: Fix typos found by codespell #3512

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4f315a9
DOC: Fix typos found by codespell
DimitriPapadopoulos Sep 21, 2022
b303733
MNT: spaces and empty lines
DimitriPapadopoulos Sep 21, 2022
326880d
STY: Fix black formatting
DimitriPapadopoulos Sep 21, 2022
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1 change: 0 additions & 1 deletion THANKS.rst
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Expand Up @@ -19,4 +19,3 @@ and `UL1 TR000442 University of Iowa Clinical and Translational Science Program


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

2 changes: 1 addition & 1 deletion doc/_templates/indexsidebar.html
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Expand Up @@ -11,4 +11,4 @@ <h3>{{ _('Links') }}</h3>
<a href='https://pypi.python.org/pypi/nipype/'><img src='https://img.shields.io/pypi/pyversions/nipype.svg' alt='Python Versions' /></a></li>
</ul>

{% endblock %}
{% endblock %}
1 change: 0 additions & 1 deletion doc/_templates/navbar.html
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Expand Up @@ -13,4 +13,3 @@
<a class="navbar" href="{{pathto('developers')}}">Developers</a> ·
<a class="navbar" href="{{pathto('about')}}">About</a> ·
<a class="navbar" href="http://nipy.org">Nipy</a>

1 change: 0 additions & 1 deletion doc/devel/filename_generation.rst
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Expand Up @@ -169,4 +169,3 @@ absolute path is generated and used for the ``cmdline`` when run, but

In [80]: res.interface.inputs.outfile
Out[80]: 'bar.nii'

1 change: 0 additions & 1 deletion doc/devel/gitwash/forking_hell.rst
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Expand Up @@ -30,4 +30,3 @@ Create your own forked copy of nipype_
should find yourself at the home page for your own forked copy of nipype_.

.. include:: links.inc

1 change: 0 additions & 1 deletion doc/devel/gitwash/git_development.rst
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Expand Up @@ -13,4 +13,3 @@ Contents:
set_up_fork
configure_git
development_workflow

2 changes: 0 additions & 2 deletions doc/devel/gitwash/index.rst
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Expand Up @@ -14,5 +14,3 @@ Contents:
patching
git_development
git_resources


1 change: 0 additions & 1 deletion doc/devel/gitwash/set_up_fork.rst
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Expand Up @@ -65,4 +65,3 @@ Just for your own satisfaction, show yourself that you now have a new
origin git@github.com:your-user-name/nipype.git (push)

.. include:: links.inc

2 changes: 1 addition & 1 deletion nipype/caching/memory.py
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Expand Up @@ -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)
Expand Down
4 changes: 2 additions & 2 deletions nipype/interfaces/afni/base.py
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Expand Up @@ -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
----------
Expand Down
6 changes: 3 additions & 3 deletions nipype/interfaces/afni/model.py
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Expand Up @@ -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)")
Expand Down Expand Up @@ -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",
Expand Down Expand Up @@ -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"
)
Expand Down
20 changes: 10 additions & 10 deletions nipype/interfaces/afni/preprocess.py
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Expand Up @@ -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>`_
Expand Down Expand Up @@ -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",
)
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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.
Expand Down Expand Up @@ -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)
Expand Down Expand Up @@ -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'.

""",
Expand Down Expand Up @@ -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"],
Expand Down
18 changes: 9 additions & 9 deletions nipype/interfaces/afni/utils.py
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Expand Up @@ -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"],
)

Expand Down Expand Up @@ -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,
Expand Down Expand Up @@ -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.
Expand Down Expand Up @@ -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>`_
Expand Down
2 changes: 1 addition & 1 deletion nipype/interfaces/c3.py
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Expand Up @@ -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(
Expand Down
6 changes: 3 additions & 3 deletions nipype/interfaces/dcmstack.py
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Expand Up @@ -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:
Expand Down Expand Up @@ -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 = {}
Expand Down Expand Up @@ -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."
)


Expand Down
8 changes: 4 additions & 4 deletions nipype/interfaces/freesurfer/preprocess.py
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Expand Up @@ -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),
Expand All @@ -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],
Expand Down
16 changes: 8 additions & 8 deletions nipype/interfaces/io.py
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Expand Up @@ -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)
Expand Down Expand Up @@ -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,
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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))
)
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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"],
Expand Down
2 changes: 1 addition & 1 deletion nipype/interfaces/matlab.py
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Expand Up @@ -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)
Expand Down
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