Generate model code for all test models in Python

[dweindl]

Currently AMICI C++ code is pre-generated from Matlab. For proper testing, models should be imported on the fly.

Requires:

• Allow for import of raw ODEs (YAML) Directly input ODE systems #654 sbml_flattener #857 Python SBML import: add support for SBML RateRules #732
• Python support for events Python SBML import: add support for events #757
• Python support for second order sensitivities move second order code from matlab to c++ code #264

Then

• Specify models as YAML
• Setup import and use in tests (tests/testModels.py)
• Remove pre-generated C++ files

[paulstapor]

Wanted to ask:
For events, we basically have test cases already in the python tests, the same for Heaviside functions.
What's now still missing is:

• Getting splines merged (would allow for the Swameye JAK/STAT model, which was a typical test case before)
• Getting second order code implemented

On the second order code, I wanted to ask how we want to proceed at all: The old trick of augmenting a model, or rather really implementig the additional total derivatives in C++-base of AMICI and performing some additional (very sparse) partial second order derivatives in python?

Pro first: Faster to be implemented
Pro second: More scalability to larger models, as more structure can be exploited and expressions are way more sparse...

[dweindl]

Pro second: More scalability to larger models, as more structure can be exploited and expressions are way more sparse...

Sounds more attractive. Although I can't really judge the extra effort.

[paulstapor]

Pro second: More scalability to larger models, as more structure can be exploited and expressions are way more sparse...

Sounds more attractive. Although I can't really judge the extra effort.

Always depends on the amount of free coffee... :D

[dweindl]

#2898