JumpSystem cleanup

[isaacsas]

As a first step before working on making JumpSystems support coupled ODEs/SDEs, I wanted to clean up the code a bit. This

1. Adds support for collect_vars! for JumpSystems.
2. Cleans up the constructor to be more in line with how the code works for other system types. If at some point refactoring of common code in constructors is done it should now be easier to see what is different in JumpSystems.

Note that JumpSystems would still need some more work to support hierarchical modeling (i.e. sub-systems and scoping).

[isaacsas]

My plan is to next make the ArrayPartition that stores the jumps also have a component for equations, which will be used to generate an ODESystem during ODEProblem(::JumpSystem, ...) (allowing a coupled ODE-jump system).

[AayushSabharwal]

Looks good. Could you check if removing the if !(sys isa JumpSystem) here now works? It was added because collect_vars! didn't work

[isaacsas]

Will update later for that. I think we need a dispatch on the trait I added in collect_scoped_vars!.

[isaacsas]

Should be updated now.

[isaacsas]

Lots of failures here, but as far as I can tell none are related to this PR. I formatted with JuliaFormatter v1.0.62 so not sure why that is failing either. Locally it reports there is nothing to format when run on the repo.

[isaacsas]

@ChrisRackauckas I think this is good to merge now -- the test failures all seem unrelated.

[ChrisRackauckas]

This looks good for now. Though I think the path forward really is that a symbolic JumpSystem should have its variables as discretes and use the hybrid system stuff when possible. The reason is the purely discrete variables would then not be in the ODE when the two are mixed, that could be a big performance win. We probably need to sync about this.

[isaacsas]

Happy to chat about that at some point. Maybe we can talk at the next office hours.

That would require changes in JumpProcesses too presumably? I thought what we are setting up here — really in the other WIP PR — would be pretty similar to what one would normally write by hand.

[ChrisRackauckas]

I don't think JumpProcesses.jl would need to change in order to accomodate it. It should just be a codegen change.