def test_compile_crn(self):
from biocrnpyler import ChemicalReactionNetwork
from biocrnpyler import Species
from biocrnpyler import Reaction
from biocrnpyler import Mixture
a = Species(name='a')
b = Species(name='b')
species_list = [a, b]
def mock_update_reactions():
rxn = Reaction(inputs=[a], outputs=[b], k=0.1)
return [rxn]
rxn = Reaction(inputs=[a], outputs=[b], k=0.1)
CRN = ChemicalReactionNetwork(species_list, [rxn])
mixture = Mixture(species=species_list)
mixture.update_reactions = mock_update_reactions
crn_from_mixture = mixture.compile_crn()
self.assertEqual(CRN.species, crn_from_mixture.species)
self.assertEqual(CRN.reactions, crn_from_mixture.reactions)
def test_update_reactions(self):
mixture = Mixture()
with self.assertRaisesRegexp(AttributeError, 'Mixture.crn_species not defined.'):
mixture.update_reactions()
component = Component(name='test_component')
# creating a mock update function to decouple the update process from the rest of the code
def mock_update_reactions():
rxn = Reaction(inputs=[], outputs=[], k=0.1)
return [rxn]
component.update_reactions = mock_update_reactions
mixture.add_components(component)
mixture.update_species()
crn_rxn = mixture.update_reactions()
crn_rxn_mock = mock_update_reactions()
self.assertEqual(crn_rxn, crn_rxn_mock)
def test_update_reactions(self):
from biocrnpyler import Mixture
from biocrnpyler import Reaction
from biocrnpyler import Component
mixture = Mixture()
with self.assertRaises(AttributeError):
mixture.update_reactions()
component = Component(name='test_component')
def mock_update_reactions():
rxn = Reaction(inputs=[], outputs=[], k=0.1)
return [rxn]
component.update_reactions = mock_update_reactions
mixture.add_components(component)
mixture.update_species()
crn_rxn = mixture.update_reactions()
crn_rxn_mock = mock_update_reactions()
self.assertEqual(crn_rxn, crn_rxn_mock)
def test_compile_crn(self):
a = Species(name='a')
b = Species(name='b')
species_list = [a, b]
# creating a mock update function to decouple the update process from the rest of the code
def mock_update_reactions():
rxn = Reaction(inputs=[a], outputs=[b], k=0.1)
return [rxn]
rxn = Reaction(inputs=[a], outputs=[b], k=0.1)
CRN = ChemicalReactionNetwork(species_list, [rxn])
mixture = Mixture(species=species_list)
mixture.update_reactions = mock_update_reactions
crn_from_mixture = mixture.compile_crn()
# test that the mixture has the same species as the manually build CRN object
self.assertEqual(CRN.species, crn_from_mixture.species)
# test that the mixture has the same reactions as the manually build CRN object
self.assertEqual(CRN.reactions, crn_from_mixture.reactions)