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We are planning for a PEtab v2 release, ideally within the next 6 months. An open question is how to handle that in libpetab, as there will be quite some incompatible changes. This issue is to discuss…
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With PEtab v2 we will introduce [extensions](https://github.com/PEtab-dev/PEtab/pull/537) to PEtab that will add new functionality. (In exceptional cases, extensions might also change some existing ru…
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I have created an example network in this repository to experiment with, where I created a simple feed-forward network and exported it to ONNX. After experimenting with ONNX, I believe we should not u…
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Hi all,
it seems there are some issues with the amici prefixes on parameters. Example attached.
I am trying to import a petab problem, but the importer fails with a KeyError.
[amici_k.zip](https://…
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Some model entity IDs are replaced by `amici_{actual_id}` during model import, but the current PEtab parameter mapping generated by `amici.petab.parameter_mapping.create_parameter_mapping` will contai…
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When performing large-scale scans I noticed something odd:
In the `EndPoint` structure, the `supreme` field sometimes seems to be a complicated AD structure (an example is provided at the end). Is th…
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What is the proper way to utilize PEtab with other packages that use array variables?
at a [Discourse Discussion](https://discourse.julialang.org/t/petab-with-methodoflines/112647?u=kkakosim) @Chri…
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Using the composite problem method returns the following error:
AttributeError: 'CompositeProblem' object has no attribute 'extensions_config'
Suggestions?
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@matthiaskoenig and others have suggested we make our tables more [normalized](https://en.wikipedia.org/wiki/Database_normalization).
Instead of a timecourses table (#581), I would suggest an exper…
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Just writing stuff here as I get ideas, feel free to close/consolidate to single issues if easier to handle that way.
It could be neat to permit accessing a parameters (optimal) value from a PEtab …