error in prune

[zakandrewking]

Trying to run prototype 41.

ipython nbconvert --to script prototype_41.ipynb
# comment out TODOs that converted incorrectly
python prototype_41.py

I get the following error:

Traceback (most recent call last):
  File "prototype_41.py", line 461, in <module>
    me.prune()
  File "/Users/zaking/sharedrepos/minime/minime/core/MEModel.py", line 144, in prune
    raise e
TypeError: cannot determine truth value of
-0.0224722222222222*mu + 1 < 0

[coltonlloyd]

Sorry, I forgot to mention that you'll need to pull the latest cobrapy commits in order to run prototype 41.

[zakandrewking]

OK. Moving in the right direction.

I didn't have Gurobi installed. Is it necessary here? I can install it.

Traceback (most recent call last):
  File "prototype_41.py", line 552, in <module>
    compiled_expressions=expressions, debug=False, solver = 'gurobi')
  File "/Users/zaking/sharedrepos/minime/minime/solve/algorithms.py", line 54, in binary_search
    solver = get_ME_solver(solver)
  File "/Users/zaking/sharedrepos/minime/minime/solve/algorithms.py", line 34, in get_ME_solver
    return solver_dict[solver]
KeyError: 'gurobi'

[coltonlloyd]

No it's not necessary. You can delete that argument and it'll use soplex. Gurobi is just faster, though inaccurate. We use it for quickly determining growth/no growth for debugging.

[zakandrewking]

awesome. it worked!