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Api doc proposed changes #862

Merged
merged 4 commits into from
Jun 4, 2024
Merged

Api doc proposed changes #862

merged 4 commits into from
Jun 4, 2024

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TorkelE
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@TorkelE TorkelE commented May 22, 2024

The minimum required changes to make the API build on the new version.

@TorkelE TorkelE force-pushed the api_doc_proposed_changes branch 2 times, most recently from 725af63 to ffbe3cc Compare May 23, 2024 18:48
@@ -35,37 +35,41 @@ corresponding chemical reaction ODE models, chemical Langevin equation SDE
models, and stochastic chemical kinetics jump process models.

```@example ex1
using Catalyst, DifferentialEquations, Plots
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I have tried to remove all cases of DifferentialEquations

t = default_t()
@parameters β γ
@species S(t) I(t) R(t)

rxs = [Reaction(β, [S,I], [I], [1,1], [2])
Reaction(γ, [I], [R])]
@named rs = ReactionSystem(rxs, t)
rs = complete(rs)
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completeness is now required for all systems.

jprob = JumpProblem(jumpsys, dprob, Direct())
sol = solve(jprob, SSAStepper())
jprob = JumpProblem(jumpsys, dprob, Direct(); save_positions = (false,false))
sol = solve(jprob, SSAStepper(), saveat = 2.0)
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When going through the doc build times, the rendering of large figures was the biggest problem. When building the docs (containing only the API) locally, reducing the saveat for these stochastic simulations reduced the build time from over 250 seconds to 15 seconds.

@TorkelE TorkelE closed this Jun 1, 2024
@TorkelE TorkelE reopened this Jun 1, 2024
@isaacsas isaacsas merged commit 04c0a13 into master Jun 4, 2024
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@isaacsas isaacsas deleted the api_doc_proposed_changes branch June 4, 2024 19:46
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2 participants