import cobra
from cobra.io import read_sbml_model
from cobra.test import create_test_model
from cobra import Model
cobra.__path__
['/Users/niso/Dev/cobrapy-fork/cobra']
cobra.__version__
'0.4.2b2.post32+gitf12ab3a'
benchmark_results = {}
m = create_test_model('ecoli')
m.solver = 'glpk'
%%timeit -o
m2 = Model()
for r in m.reactions:
m2.add_reaction(r)
1 loop, best of 3: 2.58 s per loop
<TimeitResult : 1 loop, best of 3: 2.58 s per loop>
benchmark_results['add_reaction'] = _
%%timeit -o
m2 = Model()
m2.add_reactions(m.reactions)
1 loop, best of 3: 1.79 s per loop
<TimeitResult : 1 loop, best of 3: 1.79 s per loop>
benchmark_results['add_reactions'] = _
%%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
<TimeitResult : 1 loop, best of 3: 7.67 s per loop>
benchmark_results['remove_reaction'] = _
%%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
<TimeitResult : 1 loop, best of 3: 7.05 s per loop>
benchmark_results['remove_reactions'] = _
%%timeit -o
model = read_sbml_model("/Users/niso/Dev/cobrapy-fork/cobra/test/data/iJO1366.xml")
model = read_sbml_model("/Users/niso/Dev/cobrapy-fork/cobra/test/data/iJO1366.xml")
%%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
<TimeitResult : 1 loop, best of 3: 13.7 s per loop>
benchmark_results['iteratete_all_reactions_set_objective_solve'] = _
%%timeit -o
model.copy()
1 loop, best of 3: 794 ms per loop
<TimeitResult : 1 loop, best of 3: 794 ms per loop>
benchmark_results['model_copy'] = _