def test_add_components(self):
mixture = Mixture()
# test that new mixture has no components
self.assertTrue(len(mixture.components) == 0)
component = Component('test_comp')
mixture.add_component(component)
# test that the new components was added to the mixture
self.assertTrue(mixture.get_component(component = component) is not None)
#test that it was added by copying
self.assertTrue(component not in mixture._components)
#test that the same component cannot be added again
with self.assertRaisesRegex(ValueError,f'{component} of the same type and name already in Mixture!'):
mixture.add_component(component)
#use the constructor the other way
mixture = Mixture(components = [component])
# test that the new components was added to the mixture
self.assertTrue(mixture.get_component(component = component) is not None)
#test that it was added by copying
self.assertTrue(component not in mixture._components)
species = Species('test_species')
# species are invalid components
with self.assertRaisesRegex(ValueError,f'add_components expected a list of Components.'):
mixture.add_components(species)
def test_update_species(self):
species = Species(name='H2O')
mixture = Mixture(species=[species])
self.assertTrue(species in mixture.update_species())
dna = DNA(name='test_DNA')
mixture.add_components(dna)
crn_list = mixture.update_species()
for s_dna in dna.update_species():
self.assertTrue(s_dna in crn_list)
def test_add_species_to_crn(self):
species = Species(name='H2O')
mixture = Mixture(species=[species])
mixture.add_species_to_crn(species, None)
self.assertTrue(species in mixture.crn.species)
dna = DNA(name='test_DNA')
mixture.add_components(dna)
mixture.add_species_to_crn(dna.update_species(), dna)
for s_dna in dna.update_species():
self.assertTrue(s_dna in mixture.crn.species)
def test_add_components(self):
mixture = Mixture()
# test that new mixture has no components
self.assertTrue(len(mixture.components) == 0)
component = Component('test_comp')
mixture.add_components(component)
# test that the new components was added to the mixture
self.assertTrue(component in mixture.components)
species = Species('test_species')
# species are invalid components
with self.assertRaisesRegexp(AssertionError,f'the object: {species} passed into mixture as component must be of the class Component'):
mixture.add_components(species)
def test_add_components(self):
from biocrnpyler import Mixture
from biocrnpyler import Component
from biocrnpyler import Species
mixture = Mixture()
self.assertTrue(len(mixture.components) == 0)
component = Component('test_comp')
mixture.add_components(component)
self.assertTrue(component in mixture.components)
species = Species('test_species')
with self.assertRaises(AssertionError):
mixture.add_components(species)
def test_update_species(self):
from biocrnpyler import Mixture
from biocrnpyler import Species
from biocrnpyler import DNA
# from biocrnpyler import Dilution
species = Species(name='H2O')
mixture = Mixture(species=[species])
self.assertTrue(species in mixture.update_species())
dna = DNA(name='test_DNA')
mixture.add_components(dna)
crn_list = mixture.update_species()
for s_dna in dna.update_species():
self.assertTrue(s_dna in crn_list)
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_get_component(self):
c1 = Component('c1')
c2 = Component('c2')
c3 = DNA('c1')
c4 = DNA("c2")
mixture = Mixture()
mixture.add_components([c1, c2, c3])
#Test with name
#nothing named c3 is in the mixture
self.assertTrue(mixture.get_component(name = "c3") is None)
#two things named c2 are in the mixture
self.assertTrue(type(mixture.get_component(name = "c1")) is list)
#one thing named c1 is in the mixture
self.assertTrue(type(mixture.get_component(name = "c2")) is Component)
#test with component
self.assertTrue(type(mixture.get_component(component = c1)) is Component)
self.assertTrue(type(mixture.get_component(component = c2)) is Component)
self.assertTrue(type(mixture.get_component(component = c3)) is DNA)
self.assertTrue(mixture.get_component(component = c4) is None)
#Test with index
self.assertTrue(type(mixture.get_component(index = 1)) is Component)
self.assertTrue(type(mixture.get_component(index = 2)) is DNA)
with self.assertRaisesRegex(IndexError,""):
mixture.get_component(index = 3)
with self.assertRaisesRegex(ValueError,""):
mixture.get_component(index = 3, component = c1)
with self.assertRaisesRegex(ValueError,""):
mixture.get_component(component = "c1")
with self.assertRaisesRegex(ValueError,""):
mixture.get_component(name = c1)
with self.assertRaisesRegex(ValueError,""):
mixture.get_component(index = c1)
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)