BifurcationKit test

[vyudu]

Wrote a test for the dependent parameters for BK from #1095, that can be uncommented once that works

[isaacsas]

Let’s merge this once MTK releases with your update since then v.4 should work here.

You can use @test_broken for now as that would let us know when the test starts working.

[isaacsas]

@vyudu if you want to merge master into this the SciMLBase cap will hopefully allow it to run through to completion.

[isaacsas]

@vyudu the doc folder Project.toml needs updating too.

[isaacsas]

OK, seems there are now new intialization related errors. That never happened under the old extension so I guess this is something broken by recent updates to the MTK-BifurcationKit extension (or initialization related changes).

If someone wants to take a look at what is going on feel free. I think for now I will just plan to disable this extension like we've disabled SI as I don't have the time or capacity to handle these breakages.

[ChrisRackauckas]

That never happened under the old extension so I guess this is something broken by recent updates to the MTK-BifurcationKit extension (or initialization related changes).

BifurcationKit is broken due to Krylov.jl things, completely unrelated to anything MTK?

[isaacsas]

BifurcationKit has fixed everything I believe. The issue now is system-based indexing is broken in some way (maybe related to the recent complete changes?).

[isaacsas]

And this CI failure is something else symbolic related: https://github.com/SciML/Catalyst.jl/actions/runs/11859907434/job/33053954257?pr=1101#step:6:1289

[isaacsas]

@vyudu I dropped your new test. It had a parameter that was not used and no value specified which was causing it to fail CI, and the ODESystem test part seems unrelated to BifurcationKit (so while a good test should probably be placed in a different location).

If you want to followup if/when this gets merged and modify those tests feel free (I've left them commented out for now).

Hopefully adding a parent field to ReactionSystems will fix the symbolic indexing issues.

[vyudu]

Ahh, I see, leaving ratechange in was sloppy sorry. Will revisit this after merge