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Check the migration and comparison pages against the code and rewrite the parameter-tuning studies - #111
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A note, warning or tip directive takes no title argument in Sphinx, so the title written after the directive name rendered as the first line of the box text under the generic header. The 38 titled boxes use the admonition directive with a class, which renders the title in the header.
Each page states the question, the set-up, the results with their meaning, the choice of settings and the limits. Numbers, tables and commands are unchanged except where the script or the pinned code shows another value, and statements that no measurement supports are marked as inferences or removed. tuned-parameters.md, the guide and the comparison page agree with the studies, and every link into a study uses its title.
Each statement of cause is marked as measured or inferred, derived numbers state their arithmetic and the runs they come from, and tuned-parameters.md, the guide pages and the index agree with the studies.
…ripts The numbers of the init, benchmark, sampling, KEGG and homology studies are replaced by the values measured on 2026-11-01 with the scripts added to raven-toolbox under scripts/parameter_tuning/. Each study states its inputs, software and what is not reproducible. tuned-parameters.md and the guide pages follow the studies.
…RAVEN 3 and raven-toolbox sources
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The nine pages under "Migration guides" and "RAVEN 3 and raven-toolbox" state what changed between RAVEN 2.11.3 and RAVEN 3 and what each toolbox provides. Each statement that can be checked in the code has been checked against RAVEN 2.11.3, RAVEN 3 and raven-toolbox; a statement that only a run can settle says that it was not checked.
Corrections include the 65 removed functions and the folder moves, the argument positions that change meaning (counted among all arguments), the format differences of YAML, SBML and Excel, the download sources of data and binaries, the mapping counts between RAVEN and raven-toolbox, and the differences in results of the elemental balance, gap filling and ftINIT.
The installation pages state the same minimum MATLAB version and binary folder. The four guide pages that label a link as the full function mapping now point to the generated mapping page.
removeBadRxnsis listed as paired withremove_bad_reactionsinscripts/curated_pairs.yml.The seven parameter-tuning pages (benchmarks, Human-GEM validation, homology, ftINIT calibration, ftINIT reproducibility, KEGG HMM and sampling) are written anew with the same numbers, caveats and links. Each page states its result before the set-up.