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Update SBMLImporter tutorial#1441

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sebapersson wants to merge 1 commit intoSciML:masterfrom
sebapersson:sbmlimporter
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Update SBMLImporter tutorial#1441
sebapersson wants to merge 1 commit intoSciML:masterfrom
sebapersson:sbmlimporter

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@sebapersson
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With Catalyst v16, I updated the import syntax for SBMLImporter. This PR updates the Catalyst doc to reflect this.

@isaacsas
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@sebapersson thanks!

The failure is unrelated so I'll merge this. @TorkelE we probably now need to go around and update a bunch of packages for V16 if we want the docs to build again.

@sebapersson are there still issues using callbacks defined / stored via Catalyst? You can now store symbolic tstops in Catalyst too, so I think that should let us handle most callback types cleanly with the various MTK callback options now.

@sebapersson
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@sebapersson are there still issues using callbacks defined / stored via Catalyst? You can now store symbolic tstops in Catalyst too, so I think that should let us handle most callback types cleanly with the various MTK callback options now.

I have not looked to closely at this yet, but with tstops being supported I think I should be able to handle most SBML events in Catalyst. That said, SBML can be very intricate, so I will take a closer look once PEtab.jl is updated, and see if any additional Catalyst functionality would be needed

@TorkelE
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TorkelE commented Mar 10, 2026

@isaacsas I think FiniteStateProjection is the main one. We pulled its doc page but it is still a dependency. PEtab is another one we have docs for, but that one is not in doc dependeny. I think we might also need a new version of ReactionNetworkImporters, but that might be it.

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TorkelE commented Mar 10, 2026

I have created a PR to get the docs building again: #1442

@sebapersson
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PEtab is another one we have docs for, but that one is not in doc dependeny.

I will very soon (hopefully tomorrow) have a new release of PEtab.jl as well. With that I can also update the Catalyst docs to reflect the latest API

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TorkelE commented Mar 10, 2026

That would be a great help!

#1442 should solve the doc builds, but we will need a new version of ReactioNetworkImporters as well, but that might require some test updates before we actually can get it working on the latest Catalyst

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TorkelE commented Mar 10, 2026

Ok, #1442 is merged now so docs are building fine. However, we won't be able to get this tutorial running until we also have udpated ReactionnetworkImporters for Catalyst v16. But when that is done we can merge this one as well.

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