Use Catalyst's remove_conserved = true option.

[TorkelE]

Catalyst have a feature for removing conservation laws from reaction systems (https://docs.sciml.ai/Catalyst/dev/model_creation/network_analysis/#network_analysis_conservation_laws) which could be useful to have as an option in PEtab to use. Currently, there are some MTK-induced problems (SciML/Catalyst.jl#952) which should be considered so that they are avoided.

[sebapersson]

Thanks!

This would be a good option for PEtab to have, especially for models where we have to perform steady-state simulations as for these, it is easier to compute the steady-state if the ODE RHS has an invertible Jacobian. Moreover, we can also use more fun and efficient gradient methods with an invertible Jacobian.

I checked the attached issue, and as I understood it, in order to update everything correctly parameter updates must be applied via remake at the moment?

I also have some models we can test this one, once PEtab has updated to Catalyst v14.

[sebapersson]

I changed the milestone to PEtab v4. This is a feature I would like to have, but will take some time to implement, and therefore will not be ready for PEtab v3.

On another note, along with this new gradient options for handling stead-states should be added. Will open a separate issue on that topic.