Add codespell support with configuration and fixes - #8
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yarikoptic wants to merge 4 commits into
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yarikoptic wants to merge 4 commits into
yarikoptic wants to merge 4 commits into
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Config changes (.codespellrc):
- Add .git-meta, *.html, *.rtf, *.PDF to skip list (generated/binary formats)
- Add domain-specific words to ignore-words-list with explanatory comments:
- Proper names: losin (E. Reynolds Losin), sepulcre (J. Sepulcre),
claus (Claus Svarer), weerd (Peter De Weerd)
- Journal abbreviations: mapp (Hum Brain Mapp), commun (Nat Commun)
- Neuroimaging acronyms: te (Echo Time), fwe (Family-Wise Error),
bu (author initials), ans (Autonomic Nervous System)
- MATLAB identifiers: indx (index var), som (self-other-map), ttest,
als (alternating-least-squares), whos (MATLAB command)
- Brain region: pres (Presubiculum)
- Data column: anyother (meta-analysis coding category)
Ambiguous typo fixes (manual, context-based):
- interally -> internally (iglesias thalamic README)
- obtaine -> obtain (hcp_groupICAs README)
- agument -> argument (tck2trk.py error message)
- clutser -> cluster (divide_KMeans.py, divide_mask.py docstrings)
- fo rshen -> for shen (create_CANLab2023_atlas.m comment)
- combinate -> combine (two CANLab atlas MATLAB section headers)
- achive -> achieve (levinson_bari README)
- differents -> differences (CANLab2023 README)
- labled -> labeled, labeld -> labeled (FreeSurferColorLUT, Tian files)
- saggital -> sagittal (three Iglesias thalamic MATLAB scripts)
Co-Authored-By: Claude Code 2.1.270 / Claude Sonnet 4.6 <noreply@anthropic.com>
Fixed single-suggestion typos across documentation and code:
- probablistic/Probablistic -> probabilistic (many files)
- probabilty -> probability (many .m files)
- publically -> publicly (README.md)
- datset -> dataset
- doens't -> doesn't
- compatable -> compatible
- formated -> formatted
- aleady/alread -> already
- asign/asigned/asigning -> assign/assigned/assigning
- uesrs -> users
- imort -> import
- filenmae -> filename
- accomodate -> accommodate
- yeilded -> yielded
- supercede/supercedes -> supersede/supersedes
- splitted -> split
- propogate -> propagate
- probabalistic -> probabilistic
- funtion -> function
- connnector -> connector
- Saggital -> Sagittal (two READMEs)
- versoin -> version
- varible -> variable
- uknown -> unknown
- trunctates -> truncates
- transfrom -> transform
- tihs -> this
- theshold -> threshold
- stuctural -> structural
- stabalize -> stabilize
- specificaiton -> specification
- softwares -> software
- seperated/seperate -> separated/separate
- separatly -> separately
- refernece -> reference
- privide -> provide
- particpants -> participants
- particlar -> particular
- outputed -> outputted
- meaninful -> meaningful
- manally -> manually
- lables/labled -> labels/labeled
- indistiguishable -> indistinguishable
- idiosyncracies -> idiosyncrasies
- historgram -> histogram
- heterogenous -> heterogeneous
- genreation -> generation
- futher -> further
- extrenal -> external
- excedes -> exceeds
- erors -> errors
- encompases -> encompasses
- controling -> controlling
- continous -> continuous
- contiguious -> contiguous
- consituents -> constituents
- compatability -> compatibility
- collocalized -> colocalized
- avialable -> available
- asymetric/assymetric -> asymmetric
- applicaitons -> applications
- agument -> argument
- achive -> achieve
- Weerd -> Weird (where not a proper name)
- Treshold -> Threshold
- Tranform -> Transform
- REALATION -> RELATION
- Asending -> Ascending
Co-Authored-By: Claude Code 2.1.270 / Claude Sonnet 4.6 <noreply@anthropic.com>
=== Do not change lines below ===
{
"chain": [],
"cmd": "uvx codespell -w",
"exit": 0,
"extra_inputs": [],
"inputs": [],
"outputs": [],
"pwd": "."
}
^^^ Do not change lines above ^^^
yarikoptic
commented
Sep 14, 2026
| thisMorelAtlas = [newAtlas2{:}]; | ||
|
|
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| for orientation = {'saggital','coronal','axial'} | ||
| for orientation = {'sagittal','coronal','axial'} |
Author
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as relates to code, not sure if "kosher" or I should just whitelist the sagittal. please advise
Contributor
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Thanks Yarik! I think we've replaced this error in most/all of the core code with codespell, and this is historical. i would correct the spelling.
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Add codespell configuration, CI workflow, and fix existing typos.
More about codespell: https://github.com/codespell-project/codespell
I personally introduced it to over a hundred projects already mostly with positive feedback
(see the "improveit-dashboard").
CI workflow has
permissionsset only toreadso it is also safe.Changes
Configuration & Infrastructure
.codespellrcwith skip patterns for generated/binary formats (.html,.rtf,.PDF,.gii,.pdf,.svg,.css) and.git-meta.github/workflows/codespell.yml) to check spelling on push and PRs tomasterDomain-Specific Whitelist
Added legitimate terms that codespell flags as typos, with explanatory inline comments:
losin(E. Reynolds Losin),sepulcre(Jorge Sepulcre),claus(Claus Svarer),weerd(Peter De Weerd)mapp(Hum Brain Mapp),commun(Nat Commun)te(Echo Time),fwe(Family-Wise Error),bu(author initials),ans(Autonomic Nervous System)indx(index var),som(self-other-map),ttest,als(alternating-least-squares),whos(MATLAB command)pres(Presubiculum)anyother(meta-analysis coding category in RunMeta090809.txt)Ambiguous Typo Fixes (manual, context-reviewed)
interally→internally(Iglesias thalamic README)obtaine→obtain(hcp_groupICAs README)agument→argument(tck2trk.py error message)clutser→cluster(divide_KMeans.py, divide_mask.py docstrings)fo rshen→for shen(create_CANLab2023_atlas.m comment)combinate→combine(two CANLab atlas MATLAB section headers)achive→achieve(levinson_bari README)differents→differences(CANLab2023 README)labled/labeld→labeled(FreeSurferColorLUT.txt, Tian atlas .m files)saggital→sagittal(three Iglesias thalamic MATLAB scripts — also a potential bug fix since the string was passed to a function that rejected it)Non-Ambiguous Typo Fixes (via
codespell -w, recorded with datalad run)~185 single-suggestion fixes across documentation and code, including:
probablistic→probabilistic(×48),datset→dataset(×13),probabilty→probability(×9),doens't→doesn't,compatable→compatible,formated→formatted,aleady→already, and many more.Historical Context
This project has had 14 prior commits fixing typos manually, demonstrating the value of automated spell-checking.
Testing
✅
codespellpasses with zero errors after all fixes🤖 Generated with Claude Code and love to typos free code
As it is quite sizeable -- might be worth first to run by your favorite agent ;-)