Support ODEs as equations in JumpSystem

[isaacsas]

• Needs JumpSystem cleanup #3180 merged and to then rebase on master.
• Needs tests.

Note this assumes a user has properly classified their jumps (i.e. they haven't made something a constant rate jump that has a condition that depends on a variable rate jump variable and/or an ODE modified variable).

[isaacsas]

This seemed like the best way to handle generating the underlying ODEProblem, but happy to consider alternative approaches if anyone has feedback.

[isaacsas]

@ChrisRackauckas where should callbacks be handled here, the ODEProblem or the JumpProblem? (And actually, I'm not even sure in the lower-level interface what is supposed to be done within JumpProcesses -- are passing some callbacks to both problems and/or just the wrapped ODEProblem allowed and supposed to work?)

[isaacsas]

For now I've made it that continuous events are passed to the generated ODEProblem but discrete events go via the JumpProblem. This will need some tests to check that works consistently.

[isaacsas]

@ChrisRackauckas assuming tests pass I think this is gtg.

[isaacsas]

@ChrisRackauckas I think the doc/extension/Catalyst failures here are all unrelated (they seem to be BifurcationKit related).

[ChrisRackauckas]

Yeah they are, I assume @rveltz knows?

[rveltz]

can you link me to the issue please?

[ChrisRackauckas]

  Failed to precompile BifurcationKit [0f109fa4-8a5d-4b75-95aa-f515264e7665] to "/home/runner/.julia/compiled/v1.11/BifurcationKit/jl_n8vjZY".
  ERROR: LoadError: ArgumentError: invalid type for argument A in method definition for rmul! at /home/runner/.julia/packages/BifurcationKit/KwA2l/src/BorderedArrays.jl:69
  Stacktrace:
   [1] top-level scope
     @ ~/.julia/packages/BifurcationKit/KwA2l/src/BorderedArrays.jl:69
   [2] include(mod::Module, _path::String)
     @ Base ./Base.jl:557
   [3] include(x::String)
     @ BifurcationKit ~/.julia/packages/BifurcationKit/KwA2l/src/BifurcationKit.jl:1
   [4] top-level scope
     @ ~/.julia/packages/BifurcationKit/KwA2l/src/BifurcationKit.jl:24
   [5] include
     @ ./Base.jl:557 [inlined]
   [6] include_package_for_output(pkg::Base.PkgId, input::String, depot_path::Vector{String}, dl_load_path::Vector{String}, load_path::Vector{String}, concrete_deps::Vector{Pair{Base.PkgId, UInt128}}, source::Nothing)
     @ Base ./loading.jl:2790
   [7] top-level scope
     @ stdin:5
  in expression starting at /home/runner/.julia/packages/BifurcationKit/KwA2l/src/BorderedArrays.jl:69
  in expression starting at /home/runner/.julia/packages/BifurcationKit/KwA2l/src/BifurcationKit.jl:1
  in expression starting at stdin:
  in expression starting at /home/runner/work/ModelingToolkit.jl/ModelingToolkit.jl/test/extensions/bifurcationkit.jl:1
Test Summary:                 | Error  Total  Time
BifurcationKit Extension Test |     1      1  4.4s

[ChrisRackauckas]

I assume that will show in your CI tests as of about 2 days ago?

[rveltz]

Yes that's a mistake from KrylovKit. I notified them