In [1]:

    

import cobra
from cobra.io import read_sbml_model
from cobra.test import create_test_model
from cobra import Model


    

In [2]:

    

cobra.__path__


    

    
Out[2]:





['/Users/niso/Dev/cobrapy-fork/cobra']

In [3]:

    

cobra.__version__


    

    
Out[3]:





'0.4.2b2.post32+gitf12ab3a'

In [4]:

    

benchmark_results = {}


    

In [5]:

    

m = create_test_model('ecoli')


    

In [17]:

    

m.solver = 'glpk'


    

In [18]:

    

%%timeit -o
m2 = Model()
for r in m.reactions:
    m2.add_reaction(r)


    

    




1 loop, best of 3: 2.58 s per loop






    
Out[18]:





<TimeitResult : 1 loop, best of 3: 2.58 s per loop>

In [19]:

    

benchmark_results['add_reaction'] = _


    

In [20]:

    

%%timeit -o
m2 = Model()
m2.add_reactions(m.reactions)


    

    




1 loop, best of 3: 1.79 s per loop






    
Out[20]:





<TimeitResult : 1 loop, best of 3: 1.79 s per loop>

In [19]:

    

benchmark_results['add_reactions'] = _


    

In [27]:

    

%%timeit -o
model = read_sbml_model("/Users/niso/Dev/cobrapy-fork/cobra/test/data/iJO1366.xml")
for reaction in model.reactions:
    model.remove_reactions([reaction])


    

    




1 loop, best of 3: 7.67 s per loop






    
Out[27]:





<TimeitResult : 1 loop, best of 3: 7.67 s per loop>

In [28]:

    

benchmark_results['remove_reaction'] = _


    

In [29]:

    

%%timeit -o
model = read_sbml_model("/Users/niso/Dev/cobrapy-fork/cobra/test/data/iJO1366.xml")
model.remove_reactions(model.reactions)


    

    




1 loop, best of 3: 7.05 s per loop






    
Out[29]:





<TimeitResult : 1 loop, best of 3: 7.05 s per loop>

In [28]:

    

benchmark_results['remove_reactions'] = _


    

In [ ]:

    

%%timeit -o
model = read_sbml_model("/Users/niso/Dev/cobrapy-fork/cobra/test/data/iJO1366.xml")


    

In [23]:

    

model = read_sbml_model("/Users/niso/Dev/cobrapy-fork/cobra/test/data/iJO1366.xml")


    

In [24]:

    

%%timeit -o
for reaction in model.reactions:
    model.objective = reaction
    solution = model.solve()
    solution.f


    

    




1 loop, best of 3: 13.7 s per loop






    
Out[24]:





<TimeitResult : 1 loop, best of 3: 13.7 s per loop>

In [25]:

    

benchmark_results['iteratete_all_reactions_set_objective_solve'] = _


    

In [13]:

    

%%timeit -o
model.copy()


    

    




1 loop, best of 3: 794 ms per loop






    
Out[13]:





<TimeitResult : 1 loop, best of 3: 794 ms per loop>

In [14]:

    

benchmark_results['model_copy'] = _


    

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