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ensemble.ensure_steady_state() is broken #169

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raven44099 opened this issue Aug 19, 2022 · 0 comments
Open

ensemble.ensure_steady_state() is broken #169

raven44099 opened this issue Aug 19, 2022 · 0 comments

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@raven44099
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raven44099 commented Aug 19, 2022

I really really really admire the person who wrote the tutorial, it is beyond good. Unfortunately I learned fast and so I discovered that somthing is broken.
https://github.com/SBRG/masspy/blob/b29701ece7d81b4c5ca073e55e6485f867b7d55d/docs/tutorials/ensemble_modeling.ipynb

In the EM-tutorial, the following cell doesen't work anymore:

feasible, infeasible = ensemble.ensure_steady_state(
    models=positive, strategy="simulate",
    update_values=True, decimal_precision=True)

print("Reached steady state: {0}".format(len(feasible)))
print("No steady state reached: {0}".format(len(infeasible)))

It seems that it works on the official tutorial:
https://masspy.readthedocs.io/en/stable/tutorials/ensemble_modeling.html#Simulating-an-Ensemble-of-Models

I used the installation as follows:

%%capture
!pip install masspy==0.1.5
!pip install cobra==0.18.1 #0.18.1

The whole error looks as follows:


RuntimeError                              Traceback (most recent call last)
[<ipython-input-23-4bfbde04303c>](https://localhost:8080/#) in <module>
      1 feasible, infeasible = ensemble.ensure_steady_state(
      2     models=positive, strategy="simulate",
----> 3     update_values=True) 
      4     # , decimal_precision=True)
      5 

5 frames
[/usr/local/lib/python3.7/dist-packages/mass/simulation/ensemble.py](https://localhost:8080/#) in ensure_steady_state(models, strategy, perturbations, solver_options, update_values, **kwargs)
    415 
    416     simulation = _initialize_simulation(
--> 417         models[0], strategy, solver_options, kwargs.get("verbose")
    418     )
    419 

[/usr/local/lib/python3.7/dist-packages/mass/simulation/ensemble.py](https://localhost:8080/#) in _initialize_simulation(reference_model, strategy, solver_options, verbose)
    951 
    952     """
--> 953     simulation = Simulation(reference_model=reference_model, verbose=verbose)
    954 
    955     if solver_options:

[/usr/local/lib/python3.7/dist-packages/mass/simulation/simulation.py](https://localhost:8080/#) in __init__(self, reference_model, id, name, verbose, **kwargs)
    192             # Load model into RoadRunner
    193             rr = _load_model_into_roadrunner(
--> 194                 reference_model, rr=None, verbose=verbose, **_SBML_KWARGS
    195             )
    196         except MassSimulationError as e:

[/usr/local/lib/python3.7/dist-packages/mass/simulation/simulation.py](https://localhost:8080/#) in _load_model_into_roadrunner(mass_model, rr, verbose, **kwargs)
   1562     if rr is None:
   1563         # Create new roadrunner instance with model
-> 1564         rr = roadrunner.RoadRunner(sbml_str)
   1565     else:
   1566         try:

[/usr/local/lib/python3.7/dist-packages/roadrunner/roadrunner.py](https://localhost:8080/#) in _new_init(self, *args)
   4424 
   4425     # Otherwise, use regular init
-> 4426         RoadRunner._swig_init(self, *args)
   4427         RoadRunner._makeProperties(self)
   4428 

[/usr/local/lib/python3.7/dist-packages/roadrunner/roadrunner.py](https://localhost:8080/#) in __init__(self, *args)
   2709         RoadRunner copy constructor
   2710         """
-> 2711         _roadrunner.RoadRunner_swiginit(self, _roadrunner.new_RoadRunner(*args))
   2712     __swig_destroy__ = _roadrunner.delete_RoadRunner
   2713 

RuntimeError: std::get: wrong index for variant

@raven44099 raven44099 changed the title ensemble.ensure_steady_state is broken ensemble.ensure_steady_state() is broken Aug 19, 2022
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