In [2]:

    

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


    

In [3]:

    

cobra.__path__


    

    
Out[3]:





['/Users/niso/anaconda/envs/cameo3.4/lib/python3.4/site-packages/cobra']

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cobra.__version__


    

    
Out[4]:





'0.4.1'

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benchmark_results = {}


    

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m = create_test_model('ecoli')


    

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


    

    




10 loops, best of 3: 67.9 ms per loop






    
Out[7]:





<TimeitResult : 10 loops, best of 3: 67.9 ms per loop>

In [8]:

    

benchmark_results['add_reaction'] = _


    

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


    

    




10 loops, best of 3: 28.2 ms per loop






    
Out[9]:





<TimeitResult : 10 loops, best of 3: 28.2 ms per loop>

In [10]:

    

benchmark_results['add_reactions'] = _


    

In [15]:

    

%%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: 913 ms per loop






    
Out[15]:





<TimeitResult : 1 loop, best of 3: 913 ms per loop>

In [12]:

    

benchmark_results['remove_reaction'] = _


    

In [8]:

    

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


    

    




1 loop, best of 3: 589 ms per loop






    
Out[8]:





<TimeitResult : 1 loop, best of 3: 589 ms per loop>

In [9]:

    

benchmark_results['read_sbml_model'] = _


    

In [20]:

    

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


    

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


    

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benchmark_results['iteratete_all_reactions_set_objective_solve'] = _


    

In [13]:

    

%%timeit -o
model.copy()


    

    




10 loops, best of 3: 60.3 ms per loop






    
Out[13]:





<TimeitResult : 10 loops, best of 3: 60.3 ms per loop>

In [14]:

    

benchmark_results['model_copy'] = _


    

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