fixes for MTK changes

[TorkelE]

Updates conservation laws to work with new remake version.

[isaacsas]

This is probably never going to pass tests with the change in semantics for complete. We can no longer rely on the parameters of a completed system being the same as what was defined when creating the system, which I think a lot of tests rely on.

[isaacsas]

We can also no longer rely on issetequal(parmeters(sys), get_ps(sys)) for a flattened system.

[TorkelE]

Let's see how this turns out. If something like what you suggest is really changing it would be one of the largest changes to Catalyst ever, probably after moving to maps as inputs to problems. Would probably take ages to figure out all the implications.

[isaacsas]

@TorkelE let's just work in this PR to try to get tests working again.

I've handled the conservation law constants getting scalarized issue, and locally gotten tests in reactionsystem.jl working again.

[isaacsas]

TODO:

• isequivalent needs more comprehensive testing (perhaps a followup PR)?

[TorkelE]

I had some updates locally to sort out the new parameters, but there are quite a few recent MTK issues that are hard-blocking us so I stopped a bit:
SciML/ModelingToolkit.jl#3411
SciML/ModelingToolkit.jl#3410
SciML/ModelingToolkit.jl#3409
SciML/ModelingToolkit.jl#3408
SciML/ModelingToolkit.jl#3396

[isaacsas]

OK, I'll get as much fixed here as I can modulo those issues and then plan to merge.

FYI, take a look at the changes to isequivalent. The nice feature is I added a debug kwarg that will printout specifically which fields are not the same. (I seem to always want this functionality when writing tests).

[isaacsas]

@TorkelE everything before conservation laws should now work. I tried various combinations of guesses and missing but couldn’t get them to work. Are you ok if I merge this and we can resume if/when someone figures out how to handle that stuff?

[TorkelE]

If we want to merge this I am happy with it. Still quite a way to go to update to the latest everything, but not sure if it is possible yet.

[isaacsas]

No, we can keep this open. But it has a lot of fixes for the MTK changes, so we should just push to this PR as we work on tests going forward...

[isaacsas]

With the update to MTK in SciML/ModelingToolkit.jl#3496 tests now pass locally for me, so I think this is good once that is merged and a new MTK release is made.

[isaacsas]

@AayushSabharwal thanks for all your help with the various issues @TorkelE opened. We've finally got tests passing again! If as of now you find our tests start failing during MTK/SciMLBase downstream testing we would very much appreciate a heads up about what changes might be causing such issues and what we need to update.

[AayushSabharwal]

Not a problem! Glad to get everything green again. And yeah, I'll make sure to avoid breaking Catalyst CI or at least inform you if I find outdated code.