Update PEtab code

[dweindl]

To deal with PEtab-dev/PEtab#92

Consider moving some model-processing code to AMICI.

[LeonardSchmiester]

When using the PEtab importer, I get the error message:
Parameter dependent conditions in the condition file are not yet supported.

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 petab_import.py) or are there more changes required?

[afvillaverde]

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:
'Cannot make %s a constant parameter: Parameter does not exist'.

[LeonardSchmiester]

I think this is due to constant species which should be handled as parameters. Not sure, if this is already implemented in PEtab

[dweindl]

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 petab_import.py) or are there more changes required?

Yes, I think this check can safely be removed to fix that issue.

[dweindl]

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:
'Cannot make %s a constant parameter: Parameter does not exist'.

Can you provide an example and/or a full stack trace?

[afvillaverde]

This is the code I'm running::

import pypesto
import amici
import petab
import numpy as np
import matplotlib.pyplot as plt
folder_base = "/home/alex/Documents/"
model_name = "speedy"
petab_problem = petab.Problem.from_folder(folder_base + model_name)
importer = pypesto.PetabImporter(petab_problem)
model = importer.create_model()

And this is the error:

KeyError Traceback (most recent call last)
in
----> 1 model = importer.create_model()
2 print(model.getParameterScale())
3 print("Model parameters:", list(model.getParameterIds()), '\n')
4 print("Model const parameters:", list(model.getFixedParameterIds()), '\n')
5 print("Model outputs: ", list(model.getObservableIds()), '\n')

~/anaconda3/envs/ENV_AMICI/lib/python3.7/site-packages/pypesto/objective/petab_import.py in create_model(self, force_compile)
113 logger.info(f"Compiling amici model to folder "
114 f"{self.output_folder}.")
--> 115 self.compile_model()
116 else:
117 logger.info(f"Using existing amici model in folder "

~/anaconda3/envs/ENV_AMICI/lib/python3.7/site-packages/pypesto/objective/petab_import.py in compile_model(self)
203 constantParameters=constant_parameter_ids,
204 sigmas=sigmas,
--> 205 noise_distributions=noise_distrs
206 )
207

~/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)
243
244 self.reset_symbols()
--> 245 self.processSBML(constantParameters)
246 self.processObservables(observables, sigmas, noise_distributions)
247 ode_model = ODEModel()

~/anaconda3/envs/ENV_AMICI/lib/python3.7/site-packages/amici/sbml_import.py in processSBML(self, constantParameters)
282 self.checkSupport()
283 self._gather_locals()
--> 284 self.processParameters(constantParameters)
285 self.processSpecies()
286 self.processReactions()

~/anaconda3/envs/ENV_AMICI/lib/python3.7/site-packages/amici/sbml_import.py in processParameters(self, constantParameters)
479 if not self.sbml.getParameter(parameter):
480 raise KeyError('Cannot make %s a constant parameter: '
--> 481 'Parameter does not exist.' % parameter)
482
483 parameter_ids = [par.getId() for par

KeyError: 'Cannot make SP_53872_2 a constant parameter: Parameter does not exist.'

[paulstapor]

Working on this issue in general has recently started, with #186 , to be precise.
I would say it's a valid goal for 0.0.10, to have the import moved to AMICI as far as possible.
Once this is done, I would consider this issue resolved...

[dweindl]

I think this is outdated. Closing.