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When importing a PEtab problem, I would expect that the resulting objective on has the estimated parameters as parameters.
However, currently it has all (instead of `petab_problem.x_free_ids`):
http…
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Hi! I'm Jakob, a chemistry collaborator of Torkel's, and I was trying to see if I could figure out a way to utilize the Bayesian Inference implemented in PEtab for Catalyst (I really like the combinat…
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Documentation is inconsistent in using "observables table" and "observable table" https://petab.readthedocs.io/en/latest/documentation_data_format.html#observables-table
Code seems to be pretty co…
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Currently it is not allowed to use observable IDs in `noiseFormula` in the observables table (#368). It would be great to allow that.
This would convenient for specifying relative errors. Although …
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In the PEtab standard Laplace priors are allowed. However, this is not yet supported in PEtab.jl.
Should be straightforward to add since Distributions.jl support Laplace: https://juliastats.org/Dis…
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**Bug description**
`NegLogParameterPriors` evaluates prior density also on fixed parameters. This should not be the case and might be important in the case of model selection. Currently, this object…
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Consistently fails. Checking out why in process
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Hello,
I am getting a bit lost on how to deal with an event in my PEtab problem. I have a parameter ```L_0``` in my SBML model, which is an initial concentration of hormone in an experiment. This par…
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Had to set `warnonly = true` due to the following link errors. These should be fixed and the `warnonly` restored to the more strict setting
```julia
┌ Warning: Cannot resolve @ref for md"[computed u…
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`Benchmark Collection` workflow [fails](https://github.com/AMICI-dev/AMICI/actions/runs/9073914733) with:
```
FAILED test_petab_benchmark.py::test_benchmark_gradient[Lang_PLOSComputBiol2024-True] -…