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Commit 450be34

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Merge pull request #3549 from yarikoptic/enh-codespell
codespell: config, workflow, typos fixed
2 parents 6693536 + 318f179 commit 450be34

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19 files changed

+81
-50
lines changed

19 files changed

+81
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‎.codespellrc‎

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[codespell]
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skip = .git,*.pdf,*.svg,external
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# nd,nam - import module short
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# fith - oddness coming from AFNI
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# whos - smth used in matlab things
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# SMAL - Stanford CNI MRS Library
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# Suh - name
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# noo,crasher - field/var name used
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# Reson - short journal name
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# ALS, FWE - neuroimaging specific abbrevs
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# Comision - foreign word used
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ignore-words-list = te,inport,objekt,jist,nd,hel,inout,fith,whos,fot,ue,shs,smal,nam,filetest,suh,noo,reson,als,fwe,crasher,comision

‎.github/workflows/codespell.yml‎

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---
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name: Codespell
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on:
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push:
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branches: [master]
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pull_request:
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branches: [master]
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jobs:
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codespell:
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name: Check for spelling errors
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runs-on: ubuntu-latest
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steps:
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- name: Checkout
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uses: actions/checkout@v3
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- name: Codespell
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uses: codespell-project/actions-codespell@v1

‎doc/changelog/0.X.X-changelog.rst‎

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@@ -15,7 +15,7 @@
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* ENH: Generate Dockerfiles with neurodocker (https://github.com/nipy/nipype/pull/2202)
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* ENH: FLAIR options for recon-all (https://github.com/nipy/nipype/pull/2279)
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* ENH: Config option for setting maxtasksperchild when multiprocessing (https://github.com/nipy/nipype/pull/2284)
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* FIX: Testing maintainance and improvements (https://github.com/nipy/nipype/pull/2252)
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* FIX: Testing maintenance and improvements (https://github.com/nipy/nipype/pull/2252)
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* ENH: Add elapsed_time and final metric_value to ants.Registration (https://github.com/nipy/nipype/pull/1985)
2020
* ENH: Improve terminal_output feature (https://github.com/nipy/nipype/pull/2209)
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* ENH: Simple interface to FSL std2imgcoords (https://github.com/nipy/nipype/pull/2209, prev #1398)
@@ -39,7 +39,7 @@
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* ENH: Add cosine-basis high-pass-filter to CompCor, allow skip of initial volumes (https://github.com/nipy/nipype/pull/2107, https://github.com/nipy/nipype/pull/#2122)
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* FIX: Catch more dcm2niix DTI conversions (https://github.com/nipy/nipype/pull/2110)
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* FIX: Retrieve aseg + wmparc stats properly (https://github.com/nipy/nipype/pull/2117)
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* ENH: ANTs MeasureImageSimilarity Inteface (https://github.com/nipy/nipype/pull/2128)
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* ENH: ANTs MeasureImageSimilarity Interface (https://github.com/nipy/nipype/pull/2128)
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* FIX: CompCor filter_basis of correct size, pre-filter column headers (https://github.com/nipy/nipype/pull/2136, https://github.com/nipy/nipype/pull/2138)
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* ENH: FreeSurfer lta_convert and mri_coreg interfaces (https://github.com/nipy/nipype/pull/2140, https://github.com/nipy/nipype/pull/2172)
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* ENH: Speed up S3DataGrabber (https://github.com/nipy/nipype/pull/2143)
@@ -311,16 +311,16 @@ Release 0.11.0 (September 15, 2015)
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Release 0.10.0 (October 10, 2014)
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=================================
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* ENH: New miscelaneous interfaces: SplitROIs (mapper), MergeROIs (reducer)
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* ENH: New miscellaneous interfaces: SplitROIs (mapper), MergeROIs (reducer)
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to enable parallel processing of very large images.
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* ENH: Updated FSL interfaces: BEDPOSTX and XFibres, former interfaces are still
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available with the version suffix: BEDPOSTX4 and XFibres4. Added gpu
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versions of BEDPOSTX: BEDPOSTXGPU, BEDPOSTX5GPU, and BEDPOSTX4GPU
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* ENH: Added experimental support for MIPAV algorithms thorugh JIST plugins
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* ENH: Added experimental support for MIPAV algorithms through JIST plugins
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* ENH: New dipy interfaces: Denoise, Resample
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* ENH: New Freesurfer interfaces: Tkregister2 (for conversion of fsl style matrices to freesurfer format), MRIPretess
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* ENH: New FSL interfaces: WarpPoints, WarpPointsToStd, EpiReg, ProbTrackX2, WarpUtils, ConvertWarp
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* ENH: New miscelaneous interfaces: AddCSVRow, NormalizeProbabilityMapSet, AddNoise
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* ENH: New miscellaneous interfaces: AddCSVRow, NormalizeProbabilityMapSet, AddNoise
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* ENH: New AFNI interfaces: Eval, Means, SVMTest, SVMTrain
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* ENH: FUGUE interface has been refactored to use the name_template system, 3 examples
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added to doctests, some bugs solved.
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* API: By default inputs are removed from Node working directory
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* API: InterfaceResult class is now versioned and stores class type not instance
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* API: Added FIRST interface
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* API: Added max_jobs paramter to plugin_args. limits the number of jobs
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* API: Added max_jobs parameter to plugin_args. limits the number of jobs
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executing at any given point in time
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* API: crashdump_dir is now a config execution option
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* API: new config execution options for controlling hash checking, execution and

‎doc/changelog/1.X.X-changelog.rst‎

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@@ -443,7 +443,7 @@ Python 1.2.3 will be the last version to support Python 3.4.
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* FIX: ANTS LaplacianThickness cmdline opts fixed up (https://github.com/nipy/nipype/pull/2846)
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* FIX: Resolve LinAlgError during SVD (https://github.com/nipy/nipype/pull/2838)
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* ENH: Add interfaces wrapping DIPY worflows (https://github.com/nipy/nipype/pull/2830)
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* ENH: Add interfaces wrapping DIPY workflows (https://github.com/nipy/nipype/pull/2830)
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* ENH: Update BIDSDataGrabber for pybids 0.7 (https://github.com/nipy/nipype/pull/2737)
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* ENH: Add FSL `eddy_quad` interface (https://github.com/nipy/nipype/pull/2825)
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* ENH: Support tckgen -select in MRtrix3 v3+ (https://github.com/nipy/nipype/pull/2823)

‎nipype/algorithms/icc.py‎

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@@ -150,8 +150,8 @@ def ICC_rep_anova(Y, projection_matrix=None):
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SSR = SST - SSC - SSE
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MSR = SSR / dfr
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# ICC(3,1) = (mean square subjeT - mean square error) /
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# (mean square subjeT + (k-1)*-mean square error)
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# ICC(3,1) = (mean square subject - mean square error) /
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# (mean square subject + (k-1)*-mean square error)
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ICC = (MSR - MSE) / (MSR + dfc * MSE)
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e_var = MSE # variance of error

‎nipype/interfaces/ants/registration.py‎

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--write-composite-transform 0'
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One can use multiple similarity metrics in a single registration stage.The Node below first
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performs a linear registation using only the Mutual Information ('Mattes')-metric.
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performs a linear registration using only the Mutual Information ('Mattes')-metric.
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In a second stage, it performs a non-linear registration ('Syn') using both a
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Mutual Information and a local cross-correlation ('CC')-metric. Both metrics are weighted
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equally ('metric_weight' is .5 for both). The Mutual Information- metric uses 32 bins.

‎nipype/interfaces/ants/segmentation.py‎

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runtime = super(BrainExtraction, self)._run_interface(runtime)
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# Still, double-check if it didn't found N4
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if "we cant find" in runtime.stdout:
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if "we can't find" in runtime.stdout:
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for line in runtime.stdout.split("\n"):
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if line.strip().startswith("we cant find"):
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tool = line.strip().replace("we cant find the", "").split(" ")[0]
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if line.strip().startswith("we can't find"):
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tool = line.strip().replace("we can't find the", "").split(" ")[0]
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break
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errmsg = (

‎nipype/interfaces/base/specs.py‎

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return out
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def _clean_container(self, objekt, undefinedval=None, skipundefined=False):
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"""Convert a traited obejct into a pure python representation."""
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"""Convert a traited object into a pure python representation."""
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if isinstance(objekt, TraitDictObject) or isinstance(objekt, dict):
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out = {}
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for key, val in list(objekt.items()):

‎nipype/interfaces/base/tests/test_core.py‎

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_version = "0.6"
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has = WithInput()
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hasnt = WithoutInput()
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hasnot = WithoutInput()
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trying_anyway = WithoutInput(foo=3)
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assert has.inputs.foo == 3
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assert not nib.isdefined(hasnt.inputs.foo)
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assert not nib.isdefined(hasnot.inputs.foo)
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assert trying_anyway.inputs.foo == 3
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has.run()
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hasnt.run()
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hasnot.run()
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with pytest.raises(Exception):
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trying_anyway.run()
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# Still settable
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has.inputs.foo = 4
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hasnt.inputs.foo = 4
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hasnot.inputs.foo = 4
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trying_anyway.inputs.foo = 4
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assert has.inputs.foo == 4
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assert hasnt.inputs.foo == 4
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assert hasnot.inputs.foo == 4
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assert trying_anyway.inputs.foo == 4
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has.run()
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with pytest.raises(Exception):
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hasnt.run()
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hasnot.run()
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with pytest.raises(Exception):
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trying_anyway.run()
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‎nipype/interfaces/cmtk/nx.py‎

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"Saving extra measure file to %s in Pickle format",
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op.abspath(out_pickled_extra_measures),
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)
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with open(out_pickled_extra_measures, "w") as fo:
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pickle.dump(dict_measures, fo)
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with open(out_pickled_extra_measures, "w") as f:
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pickle.dump(dict_measures, f)
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iflogger.info("Saving MATLAB measures as %s", matlab)
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