Fixed PEtab parameters are treated as estimated if they don't exist in the SBML model

[dilpath]

What did you expect to happen? A PEtab parameter with estimate=0 is treated as a fixed parameter during import.

The parameter is defined in the PEtab parameters table, then the initial condition species(t=0) = parameter is specified in the PEtab conditions table. The parameter does not exist in the SBML model.

What has happened instead? The parameter is treated as estimated. I also see the warning

- amici.petab_import - WARNING - Column 'initial_Susceptible' used in condition table but not entity with the corresponding ID exists. Ignoring.

To Reproduce Compile the attached PEtab problem twice, with initial_Susceptible set to estimate=0 the first time, and estimate=1 the second time. The generated C++ are identical (the parameter isn't fixed in the first case).

AMICI version and system environment

• OS and version: Ubuntu 22.04
• AMICI interface: Python 3.10.12
• AMICI version: after v0.19.0, c038ff5264bc384e737d5aeee7f2411493fe2c22
• Additional information: GNU 10.5.0

Bertozzi_PNAS2020.zip