Conversation
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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. |
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 |
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@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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I have created a PR to get the docs building again: #1442 |
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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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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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. |
Checklist
contributor guidelines, in particular the SciML Style Guide and
COLPRAC.
Additional context
With Catalyst v16, I updated the import syntax for SBMLImporter. This PR updates the Catalyst doc to reflect this.