`PetabSimulator.simulate` should produce simulation data frame

[fbergmann]

What did you expect to happen?
after running

    petab_problem = Problem.from_yaml(args.yaml_file_name)
    simulator = PetabSimulator(petab_problem)
    sim_df = simulator.simulate()
    sim_df.to_csv(args.output_file, sep='\t', index=False)

I expected to get a simulation data frame, that I could use with petab.visualize. Specifically there should be a simulation column in the file.

What has happened instead?
Instead there was a measurement column in the file, and petab.visualize complained with a KeyError when accessing the simulation column.

To Reproduce
Steps to reproduce the behavior
Ideally include minimal code examples here

see above

AMICI version and system environment

• OS and version: [e.g. Ubuntu, iOS, Windows]
• AMICI interface: [e.g. Python, Matlab, C++]
• AMICI version:
• Additional information: Compiler name and version used, Python/Matlab version, ...

How to fix
Do you know how to resolve the problem?
yes, rename the measurement column to 'simulation' before returning from PetabSimulator.simulate.

Can you submit a pull request?

[dweindl]

Fixed via PEtab-dev/libpetab-python#199 (petab>=0.2.0)