Domagoj Doresic

Thanks for the issue! True, this is a nice addition to the module. A user should be able to access the spline mapping after it's optimized. It was previously in...

(We discussed this, but I'll add it here too to remain documented) Yes, that can happen. The optimization of an inner problem requires an initialization of inner parameters. The inner...

Will look into and update

Yes, mostly done. That's the `calculate_directly` call of the `RelativeCalculator`. Amici is still called twice through `call_amici_twice` in some special cases. One of those is also if 2 is in...

Hi aidinbii, In the current implementation, parameter-dependent constraints are not allowed. However, there is an easy way to go around this problem. In your model, you can define the p3...

Yes, it should work. The error you're getting now is because you're defining Ke_3 twice: once in the parameter table, and once in the assignment rule. Notice that if you...

Did you re-compile the model since changing the petab problem (removing the parameter from the parameter df)? You can do so by adding a `force_compile=True` into the model creation ```...

Hmm tested it myself now. It should work nicely. What is your current parameter.tsv file, and model SBML file?

My mistake. I found the error. The definition of Ke_3 in the model should not be with an assignment `Ke_3 := Ke_30 + diff_Ke1`, but with an initial assignment `Ke_3...

Not sure. I haven't used yaml2sbml much myself. If it's possible it should be somewhere in the documentation https://yaml2sbml.readthedocs.io/en/latest/ Alternatively, you can use Antimony from Tellurium. A simple and similar...