Add codespell support with configuration and fixes#20
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Two ambiguous typos required context review:
- proceded -> proceed in logic_operator_objects.py:38
(auxiliary "should" + infinitive: "string analysis should proceed")
- thorugh -> through in hierarchical_plot.py:40
(preposition: "looping through all of them")
Also added 'inactivate' to ignore-words-list in .codespellrc -- it is
a valid English/biology term used in the NOR_gate.py example
("any of them can inactivate the Promoter"); codespell incorrectly
suggested "deactivate".
Co-Authored-By: Claude Code 2.1.177 / Claude Opus 4.7 <noreply@anthropic.com>
Fixed 26 typos across 21 files:
- Indepedent -> Independent (README.md)
- conterparts -> counterparts (Synchronized_Cycles_of_Bacterial_Lysis.py)
- charcteristic, characteritics -> character(istic,istics) (01_Basic_Intro.ipynb)
- bellow/Bellow -> below/Below (5 occurrences: tutorial nb 01/18/20,
compiler_operator_functions.py, meta_class.py:1031, order_operators.py)
- acess -> access (3 occurrences: 01_Basic_Intro.ipynb, 09_Result_Data.ipynb,
hierarchical_plot.py)
- Futhermore -> Furthermore (11_Looping_Through_Species.ipynb)
- reapeat -> repeat (simulation.py)
- Characteritics -> Characteristics (compiler.py)
- apear -> appear (function_rate_code.py, logic_operator_objects.py)
- debbuging -> debugging (meta_class.py)
- writting -> writing (mobspy_expressions.py)
- generetes -> generates (species_string_generator.py)
- paramters -> parameters (parameters/README.md)
- experimetns -> experiments (basico_task_parametrization.py)
- statics -> statistics (default_plots.py)
- PLOTING -> PLOTTING (hierarchical_plot.py)
- addding -> adding (sbml_simulator/run.py)
Co-Authored-By: Claude Code 2.1.177 / Claude Opus 4.7 <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 ^^^
fabriciocravo
approved these changes
Jun 21, 2026
fabriciocravo
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Nice. Only typo fixes, no code was changed
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Thank you for your contribution Yaroslav. I do tend to make a massive amount of typos. The workflow application appears to be an import error. I will fix it in the next commit. The typo checker is not an issue and should be added. |
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Add codespell configuration, a GitHub Actions workflow that runs it on every push and PR, and fix the existing typos it detected.
I've personally introduced codespell to over a hundred of projects already mostly with positive feedback (see the "improveit-dashboard" for an example summary). The CI workflow has
permissions: contents: readand uses a pinned action SHA, so it should be safe.Changes
Configuration & Infrastructure
.codespellrcwith skip patterns (.git,.git-meta,.gitignore,.gitattributes,*.svg,.codespellrc),check-hidden = true, and anignore-regexthat skips embedded base64 images in notebook JSON..github/workflows/codespell.yml— runs codespell on push and PRs tomain, pinned tocodespell-project/actions-codespell@8f01853...(v2.2).Domain whitelist
inactivate— added toignore-words-listbecause it is a valid English (and biology) term used indocs/example_models/application_models/NOR_gate.py("any of them can inactivate the Promoter"). Codespell incorrectly suggested replacing it with "deactivate".Typo fixes
Ambiguous (manually fixed with context review) — 2 fixes:
proceded→proceedinmobspy/modules/logic_operator_objects.py:38(auxiliary "should" + infinitive: "string analysis should proceed")thorugh→throughinmobspy/plot_scripts/hierarchical_plot.py:40(preposition: "looping through all of them")Non-ambiguous (applied automatically via
codespell -w) — 26 fixes across 21 files. Common ones:bellow→below(5×)acess→access(3×)apear→appear(2×)Indepedent→Independent,Futhermore→Furthermore,conterparts→counterpartscharcteristic,characteritics,Characteritics→character(istic[s])reapeat→repeat,debbuging→debugging,writting→writinggeneretes→generates,paramters→parameters,experimetns→experimentsstatics→statistics(in a comment only; the variableplots_for_spe_i_stais unchanged)PLOTING→PLOTTING,addding→addingAll fixes are in comments, docstrings, markdown cells, and section headers. No regex patterns, variable names, or code identifiers were modified.
Historical context
There have been a handful of prior commits in this repo manually fixing typos (
607b3f3,30527eb,ae895e6,0a18615), which is exactly the kind of churn an automated check eliminates going forward.Testing
uvx codespellpasses with exit code 0 after all fixes.codespell -wwrapped indatalad run, so the exact command is recorded in the commit metadata and can be re-run withdatalad rerun.🤖 Generated with Claude Code and love to typo-free code