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Update PEtab code #164
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When using the PEtab importer, I get the error message: I think this is related to this issue right? If I see it correctly, this is already implemented in PEtab. Would it be enough to delete the check for parameter dependent conditions (lines 165-169 in |
Deleting lines 165-169 in petab_import.py is not enough: it leads to an error in line 205, which results in an error message from /amici/sbml_import.py: |
I think this is due to constant species which should be handled as parameters. Not sure, if this is already implemented in PEtab |
Yes, I think this check can safely be removed to fix that issue. |
Can you provide an example and/or a full stack trace? |
This is the code I'm running:: import pypesto And this is the error: KeyError Traceback (most recent call last) ~/anaconda3/envs/ENV_AMICI/lib/python3.7/site-packages/pypesto/objective/petab_import.py in create_model(self, force_compile) ~/anaconda3/envs/ENV_AMICI/lib/python3.7/site-packages/pypesto/objective/petab_import.py in compile_model(self) ~/anaconda3/envs/ENV_AMICI/lib/python3.7/site-packages/amici/sbml_import.py in sbml2amici(self, modelName, output_dir, observables, constantParameters, sigmas, noise_distributions, verbose, assume_pow_positivity, compiler, allow_reinit_fixpar_initcond, compile) ~/anaconda3/envs/ENV_AMICI/lib/python3.7/site-packages/amici/sbml_import.py in processSBML(self, constantParameters) ~/anaconda3/envs/ENV_AMICI/lib/python3.7/site-packages/amici/sbml_import.py in processParameters(self, constantParameters) KeyError: 'Cannot make SP_53872_2 a constant parameter: Parameter does not exist.' |
Working on this issue in general has recently started, with #186 , to be precise. |
I think this is outdated. Closing. |
To deal with PEtab-dev/PEtab#92
Consider moving some model-processing code to AMICI.
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