Refactor ODE analyses to build models in the theory of signed polynomial ODE systems - #1363
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tim-at-topos wants to merge 70 commits into
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Refactor ODE analyses to build models in the theory of signed polynomial ODE systems#1363tim-at-topos wants to merge 70 commits into
tim-at-topos wants to merge 70 commits into
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WIP: Rethinking traits WIP: Some tests only half failing WIP: Tests passing; time to tidy ENH: Build derived model of th_signed_polynomial_ode_system in mass_action ENH: Mass-action for stock-flow; DEL: Mass-action for signed stock-flow ENH: struct for transition / flow interfaces WIP: Starting on Lotka-Volterra WIP: Failing tests FIX: Lotka-Volterra tests passing FIX: Working analysis (frontend) ENH: Lotka-Volterra equations ENH: Linear ODE refactor ENH: Linear ODE equations WIP: Starting on ODESemantics WIP: lotka_volterra_semantics() WIP: build_system_from_ode_semantics WIP: DblModelForODESemantics WIP: ODESemanticsAnalysis and ODESemanticsProblemData WIP: ODESemantics trait WIP: Documentation WIP: ODESemantics for mass-action WIP: Cleaning up types, but mass-action still frustrating WIP: Big reshuffle (moving functions out from a struct) WIP: Fixing mass-action again WIP: terrible code WIP: Changed from ObGen to Ob WIP: Stock-flow mass-action FIX: Passing catlog tests Rename LinearODE -> LCC FIX: Documentation TODO: Redesign
…n_config_form.tsx
WIP: Rethinking traits WIP: Some tests only half failing WIP: Tests passing; time to tidy ENH: Build derived model of th_signed_polynomial_ode_system in mass_action ENH: Mass-action for stock-flow; DEL: Mass-action for signed stock-flow ENH: struct for transition / flow interfaces WIP: Starting on Lotka-Volterra WIP: Failing tests FIX: Lotka-Volterra tests passing FIX: Working analysis (frontend) ENH: Lotka-Volterra equations ENH: Linear ODE refactor ENH: Linear ODE equations WIP: Starting on ODESemantics WIP: lotka_volterra_semantics() WIP: build_system_from_ode_semantics WIP: DblModelForODESemantics WIP: ODESemanticsAnalysis and ODESemanticsProblemData WIP: ODESemantics trait WIP: Documentation WIP: ODESemantics for mass-action WIP: Cleaning up types, but mass-action still frustrating WIP: Big reshuffle (moving functions out from a struct) WIP: Fixing mass-action again WIP: terrible code WIP: Changed from ObGen to Ob WIP: Stock-flow mass-action FIX: Passing catlog tests Rename LinearODE -> LCC FIX: Documentation TODO: Redesign
Refactor LaTeX methods in catlog-wasm and catlog
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Jul 31, 2026
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For some arcane GitHub reason, #1251 was automatically closed and I cannot reopen it. This is a clone with #1319 merged in. I'll repeat both of the original PR descriptions below for the sake of the reader.
This PR includes a massive redesign of the way that we handle ODE semantics, which has the bonus of introducing some new capabilities (#1177) as well as (hopefully) making adding new ODE semantics in the future considerably simpler.
For those reading (or reviewing) this code, my suggested reading order would be:
ode::polynomial_ode::build_system_custom_parametersto see how we interpret models ofth_signed_polynomial_ode_systemas systems of polynomial ODEsode::lotka_volterrato see an example of the main chunk of defining an ODE semantics: giving an implementation forODESemanticsAnalysisode::ode_semanticsto see where all the actual new code isode::mass_actionto see where things are still messy and need some extra finessingFEEDBACK, where I have some specific questions / highlight specific problems with this design.p.s. I know this PR adds quite a lot of code for something called a "refactor", but (a) I added a lot of documentation and some new tests, and (b) subsequent PRs focussing on the front-end parts should now be possible, allowing for much more code removal.
Now that more ODE analyses have LaTeX equations, we should be stricter about the use of
fmt::Displayonly for debugging.This PR introduces some new types and traits (
Latex,ToLatex,ToLatexWithMap) for dealing with LaTeX expressions and rendering object/morphism names nicely in the frontend. It also includes a bunch of tests for ODE semantics in the wasm layer. Finally, as a bonus, it removes a lot of repetitive code fromcatlog-wasm::src::analysesby definingode_semantics_simulationandode_semantics_equations, enabled by #1251, as well as removing some unnecessary types introduced there (such asLotkaVolterraEquationsData, which is justnull).Again, this refactor adds a lot of lines, but that's almost entirely due to how many nice new tests it adds 👼
As a bonus, this PR fixes the following issues:
fmt::Displayfor LaTeX output #1171Although further refactoring is possible (e.g.
lotka_volterra.tsxandlinear_ode.tsxshare a lot of code), I think that the "correct" solution to this would be to start looking at generating that code from the definitions of the analyses rather than manually refactoring it. But this is now a much larger, rather separate project, so I think it's a bit out of scope.With that in mind, I would suggest that this PR finally completes the last item in #1177 , and thus closes the RFC-0001 parent issue #1098.