[yarikoptic]

Submission Checklist

• Run unit tests: ./runTests.py src/test/unit — not run locally; the only code changes are comments and a same-length rename of a local test variable (sentinal → sentinel), so CI should cover it
• Run cpplint: make cpplint — not run locally; no line lengths changed
• Declare copyright holder and open-source license: see below

Summary

Add codespell config and a CI workflow, and fix the typos it currently finds.

I have added codespell to over a hundred projects already, mostly with positive feedback (see the "improveit-dashboard"). The workflow only has contents: read permission, so it should be safe. Git history has 200+ commits mentioning typo/spelling fixes, so automating this check seems worth it.

Details of changes

Configuration & CI

• .codespellrc skips lib/ (vendored rapidjson, stan_math submodule), licenses/stan-doc-license.txt (verbatim CC license text), plus generic caches / minified assets.
• ignore-words-list: alo (BFGS line search bracket variable, paired with ahi) and optin (clang-tidy check group in make/clang-tidy).
• .github/workflows/codespell.yml runs on push to and PRs against develop.

Ambiguous typos fixed manually

• enchanced → enhanced, tht → that (RELEASE-NOTES.txt)
• doesnt' → doesn't (RELEASE-NOTES.txt)

Intentional spelling kept

• src/test/unit/services/check_adaptation.hpp: "lements of inverse mass matrix:" is a deliberate substring match, so it is marked with // codespell:ignore-next-line.

Non-ambiguous typos fixed by codespell -w (recorded with datalad run)

• sentinal → sentinel — local variables in src/test/unit/io/*, optimization and pathfinder tests
• execption, implmentation — docstrings in src/stan/mcmc/chainset.hpp
• lincense (README.md), and many typos in historical RELEASE-NOTES.txt

None of these fixes change behavior (no functional bug fixes found).

I also ran an extended pass (--builtin clear,rare,usage,code,names). It only reported domain terms (warmup, ith, stdio, master), so I left those as they are.

Intended Effect

Catch new typos in CI, and fix the existing ones.

How to Verify

pip install codespell && codespell (or uvx codespell) should exit 0. The Codespell CI job should pass.

Side Effects

None expected. Contributors may sometimes need to add a word to ignore-words-list in .codespellrc or use an inline codespell:ignore comment.

Documentation

None needed.

AI disclosure

Per the Stan AI Contribution Policy: I prepared this with help from Claude Code. I reviewed every change and can explain and defend it.

Copyright and Licensing

Please list the copyright holder for the work you are submitting (this will be you or your assignee, such as a university or company):

Yaroslav Halchenko

By submitting this pull request, the copyright holder is agreeing to license the submitted work under the following licenses:

• Code: BSD 3-clause (https://opensource.org/licenses/BSD-3-Clause)
• Documentation: CC-BY 4.0 (https://creativecommons.org/licenses/by/4.0/)

---

🤖 Generated with Claude Code

[WardBrian]

If we’d like to add this sort of checking I think it might make sense to move it inside our Jenkins pipeline rather than a separate action, though I’m also unsure if it’s worth gating PRs on

[yarikoptic]

I don't have much (if any) experience with jenkins, but can easily strip github action off this PR, or ask claude to attempt to re-express it within present Jenkinsfile, just say.

[WardBrian]

Hi @yarikoptic, after some consideration I don't think spelling is something we'd like to gate CI on, but I'm planning on merging the spelling fixes you found as part of this effort. Thanks!

[stan-buildbot]

Name	Old Result	New Result	Ratio	Performance change( 1 - new / old )
stat_comp_benchmarks/benchmarks/gp_regr/gp_regr.stan	0.24	0.25	0.97	-3.02% slower
stat_comp_benchmarks/benchmarks/gp_regr/gen_gp_data.stan	0.06	0.06	1.0	-0.35% slower
stat_comp_benchmarks/benchmarks/low_dim_corr_gauss/low_dim_corr_gauss.stan	0.02	0.02	0.99	-1.11% slower
stat_comp_benchmarks/benchmarks/arma/arma.stan	0.7	0.69	1.02	1.67% faster
stat_comp_benchmarks/benchmarks/arK/arK.stan	3.4	3.39	1.0	0.35% faster
stat_comp_benchmarks/benchmarks/pkpd/one_comp_mm_elim_abs.stan	43.05	44.03	0.98	-2.28% slower
stat_comp_benchmarks/benchmarks/pkpd/sim_one_comp_mm_elim_abs.stan	0.59	0.59	1.0	-0.5% slower
stat_comp_benchmarks/benchmarks/gp_pois_regr/gp_pois_regr.stan	4.67	4.7	0.99	-0.52% slower
stat_comp_benchmarks/benchmarks/low_dim_gauss_mix_collapse/low_dim_gauss_mix_collapse.stan	22.24	22.1	1.01	0.64% faster
stat_comp_benchmarks/benchmarks/garch/garch.stan	1.01	1.01	1.0	-0.38% slower
stat_comp_benchmarks/benchmarks/eight_schools/eight_schools.stan	0.11	0.11	1.01	0.86% faster
stat_comp_benchmarks/benchmarks/irt_2pl/irt_2pl.stan	9.27	9.25	1.0	0.2% faster
stat_comp_benchmarks/benchmarks/low_dim_gauss_mix/low_dim_gauss_mix.stan	6.57	6.56	1.0	0.1% faster
stat_comp_benchmarks/benchmarks/sir/sir.stan	230.35	229.07	1.01	0.55% faster
performance.compilation	373.18	370.99	1.01	0.59% faster
Mean result: 0.9979964390027377

Jenkins Console Log
Jenkins Build Stages
Commit hash: e7cab1646d71f360d212c6aecb8537bca67ebe6f

Machine information

Distributor ID:	Ubuntu
Description:	Ubuntu 20.04.3 LTS
Release:	20.04
Codename:	focal

CPU:

Architecture:                            x86_64
CPU op-mode(s):                          32-bit, 64-bit
Byte Order:                              Little Endian
Address sizes:                           43 bits physical, 48 bits virtual
CPU(s):                                  256
On-line CPU(s) list:                     0-255
Thread(s) per core:                      2
Core(s) per socket:                      64
Socket(s):                               2
NUMA node(s):                            2
Vendor ID:                               AuthenticAMD
CPU family:                              23
Model:                                   49
Model name:                              AMD EPYC 7742 64-Core Processor
Stepping:                                0
Frequency boost:                         enabled
CPU MHz:                                 1494.369
CPU max MHz:                             3416.0681
CPU min MHz:                             1500.0000
BogoMIPS:                                4491.56
Virtualization:                          AMD-V
L1d cache:                               4 MiB
L1i cache:                               4 MiB
L2 cache:                                64 MiB
L3 cache:                                512 MiB
NUMA node0 CPU(s):                       0-63,128-191
NUMA node1 CPU(s):                       64-127,192-255
Vulnerability Gather data sampling:      Not affected
Vulnerability Indirect target selection: Not affected
Vulnerability Itlb multihit:             Not affected
Vulnerability L1tf:                      Not affected
Vulnerability Mds:                       Not affected
Vulnerability Meltdown:                  Not affected
Vulnerability Mmio stale data:           Not affected
Vulnerability Old microcode:             Not affected
Vulnerability Reg file data sampling:    Not affected
Vulnerability Retbleed:                  Mitigation; untrained return thunk; SMT enabled with STIBP protection
Vulnerability Spec rstack overflow:      Mitigation; Safe RET
Vulnerability Spec store bypass:         Mitigation; Speculative Store Bypass disabled via prctl
Vulnerability Spectre v1:                Mitigation; usercopy/swapgs barriers and __user pointer sanitization
Vulnerability Spectre v2:                Mitigation; Retpolines; IBPB conditional; STIBP always-on; RSB filling; PBRSB-eIBRS Not affected; BHI Not affected
Vulnerability Srbds:                     Not affected
Vulnerability Tsa:                       Not affected
Vulnerability Tsx async abort:           Not affected
Vulnerability Vmscape:                   Mitigation; IBPB before exit to userspace
Flags:                                   fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush mmx fxsr sse sse2 ht syscall nx mmxext fxsr_opt pdpe1gb rdtscp lm constant_tsc rep_good nopl xtopology nonstop_tsc cpuid extd_apicid aperfmperf rapl pni pclmulqdq monitor ssse3 fma cx16 sse4_1 sse4_2 x2apic movbe popcnt aes xsave avx f16c rdrand lahf_lm cmp_legacy svm extapic cr8_legacy abm sse4a misalignsse 3dnowprefetch osvw ibs skinit wdt tce topoext perfctr_core perfctr_nb bpext perfctr_llc mwaitx cpb cat_l3 cdp_l3 hw_pstate ssbd mba ibrs ibpb stibp vmmcall fsgsbase bmi1 avx2 smep bmi2 cqm rdt_a rdseed adx smap clflushopt clwb sha_ni xsaveopt xsavec xgetbv1 xsaves cqm_llc cqm_occup_llc cqm_mbm_total cqm_mbm_local clzero irperf xsaveerptr rdpru wbnoinvd amd_ppin arat npt lbrv svm_lock nrip_save tsc_scale vmcb_clean flushbyasid decodeassists pausefilter pfthreshold avic v_vmsave_vmload vgif v_spec_ctrl umip rdpid overflow_recov succor smca sev sev_es

G++:

g++ (Ubuntu 9.4.0-1ubuntu1~20.04) 9.4.0
Copyright (C) 2019 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

Clang:

clang version 10.0.0-4ubuntu1 
Target: x86_64-pc-linux-gnu
Thread model: posix
InstalledDir: /usr/bin