Bifurcation kit extension

[TorkelE]

Enables BifurcationKit BifurcationProblems to be created from ReactionSystems.

Example workflow:

using Catalyst
wilhelm_2009_model = @reaction_network begin
    k1, Y --> 2X
    k2, 2X --> X + Y
    k3, X + Y --> Y
    k4, X --> 0
    k5, 0 --> X
end

using BifurcationKit
bif_par = :k1
u_guess = [:X => 5.0, :Y => 2.0]
p_start = [:k1 => 4.0, :k2 => 1.0, :k3 => 1.0, :k4 => 1.5, :k5 => 1.25]
plot_var = :X
bprob = BifurcationProblem(wilhelm_2009_model, u_guess, p_start, bif_par; plot_var=plot_var)

p_span = (2.0, 20.0)
opts_br = ContinuationPar(p_min = p_span[1], p_max = p_span[2], max_steps=1000)

bif_dia = bifurcationdiagram(bprob, PALC(), 2, (args...) -> opts_br; bothside=true)

using Plots
plot(bif_dia; xguide="k1", yguide="X")

[TorkelE]

Functionality is there (just need to add an error check), needs tests and docs. Requires SciML/ModelingToolkit.jl#2337 to merge to handle cases with conservation laws

[TorkelE]

The required MTK PR have now been merged. However, I think we still would need to wait for a new release to take advantage of it.

[isaacsas]

Does merging after flattening give the correct namespacing of parameters and variables? This seems like it is going to cause problems. Merging probably needs to happen before flattening.

[TorkelE]

Not, that is a good point. I just used the current order of things, but if you suggest changing than that is be better.

[isaacsas]

Can you add a test to check this?

[TorkelE]

You mean providing defaults to a convert for a system with sub-systems, which got defaults?

[isaacsas]

Yes

[isaacsas]

Can you check this works with coupled ODEs and add a corresponding test? (Do we want to allow coupled algebraic equations here too? If not, we probably need a check that any coupled equations are just ODEs.)

[TorkelE]

We cannot actually couple to ODEs: #727

I will couple to another ReactionSystem, should be enough.

fixed

[TorkelE]

This should be ready now. Unfortnatley the CI seems bugged out, keep giving stuff like:

[2048] signal (2): Interrupt
in expression starting at /home/runner/work/_temp/6799a5b3-ac8d-4e0e-a488-c620d88596be:24
epoll_wait at /lib/x86_64-linux-gnu/libc.so.6 (unknown line)
uv__io_poll at /workspace/srcdir/libuv/src/unix/epoll.c:236
uv_run at /workspace/srcdir/libuv/src/unix/core.c:400
ijl_task_get_next at /cache/build/builder-amdci4-4/julialang/julia-release-1-dot-9/src/partr.c:390
poptask at ./task.jl:974
wait at ./task.jl:983
task_done_hook at ./task.jl:672
jfptr_task_done_hook_27081.clone_1 at /opt/hostedtoolcache/julia/1.9.4/x64/lib/julia/sys.so (unknown line)
_jl_invoke at /cache/build/builder-amdci4-4/julialang/julia-release-1-dot-9/src/gf.c:2758 [inlined]
ijl_apply_generic at /cache/build/builder-amdci4-4/julialang/julia-release-1-dot-9/src/gf.c:2940
jl_apply at /cache/build/builder-amdci4-4/julialang/julia-release-1-dot-9/src/julia.h:1880 [inlined]
jl_finish_task at /cache/build/builder-amdci4-4/julialang/julia-release-1-dot-9/src/task.c:320
start_task at /cache/build/builder-amdci4-4/julialang/julia-release-1-dot-9/src/task.c:1103
unknown function (ip: (nil))
Allocations: 10537356 (Pool: 10521420; Big: 15936); GC: 22
Error: The operation was canceled.

in various places, and I have no idea why.

[TorkelE]

CI works on my computer, but keeps failing for reasons here. I the PR is done. I think if I rebase on the right stuff it should be good, just tell me when we can merge this one and I will rebase and it should hopefully work.
(I just want to avoid having to rebase this one 8 times over the next week or 2, each time potentially doing some git wrong)

[isaacsas]

Let's get this working with composed systems too. I think it should just require manually flattening in the BifurcationProblem before you start making checks and calculating conservation laws.

[isaacsas]

@TorkelE what is the status on this? I see doc build failures currently?

[TorkelE]

this is ready, think the doc failure has appeared recently though. I will rebase on master and if docs still fail fixing it should be relatively straightforward.

fixed