def test_initialization(self, known_microbiome, random_microbiome):
known = Microbiota(known_microbiome, init_abund=[1.0, 1.0])
assert len(known) == len(known_microbiome)
rand = Microbiota(random_microbiome, init_abund=[10.0, 1.0, 0.5])
assert len(rand) == len(random_microbiome)
with pytest.raises(ValueError):
Microbiota(known_microbiome, init_abund=[-1.0, 1.0])
def test_eat_order(self, random_microbiome):
rand1 = Microbiota(random_microbiome, init_abund=[1.0, 3.0, 2.0])
order = rand1.eat_order
assert len(order) == 3
assert set(order.pop() for _ in range(3)) == set(random_microbiome)
rand2 = Microbiota(random_microbiome, init_abund=[0.0, 0.0, 0.0])
order = rand2.eat_order
assert len(order) == 3
assert set(order.pop() for _ in range(3)) == set(random_microbiome)
def test_select_action(self, core_regulator_inst):
microbe, regulator = core_regulator_inst
media = Media(Microbiota([microbe], [1.0]), {})
flux_dict = microbe.ex_fluxes
conc_dict = microbe.get_model_media(media.concentrations)
action = regulator.select_action(conc_dict, flux_dict)
[(action_value, _)] = action.phi.values()
assert np.isclose(action_value, 0.0)
def test__encode_state(self, core_regulator_inst):
microbe, regulator = core_regulator_inst
media = Media(Microbiota([microbe], [1.0]), {})
flux_dict = microbe.ex_fluxes
conc_dict = microbe.get_model_media(media.concentrations)
state = regulator._encode_state(conc_dict, flux_dict)
conc_state = state[:len(conc_dict)]
assert 0 <= conc_state.mean() <= 1
assert conc_state.std() <= 1
flux_state = state[len(conc_dict):]
assert -1 <= flux_state.mean() <= 1
assert flux_state.std() <= 1
def test_abundances(self, random_microbiome):
rand = Microbiota(random_microbiome, init_abund=[1.0, 3.0, 2.0])
expected_abund = dict(
zip([m.id for m in random_microbiome], [1.0, 3.0, 2.0]))
assert rand.abundances == expected_abund
def test_ex_metabolites(self, random_microbiome):
rand = Microbiota(random_microbiome, init_abund=[1.0, 1.0, 1.0])
all_exmets = 0
for microbe in rand:
all_exmets += len(microbe.ex_metabolites)
assert len(rand.ex_metabolites) == all_exmets
def test_ex_reactions(self, random_microbiome):
rand = Microbiota(random_microbiome, init_abund=[1.0, 1.0, 1.0])
all_exrxns = 0
for microbe in rand:
all_exrxns += len(microbe.ex_reactions)
assert len(rand.ex_reactions) == all_exrxns
def test_get_microbe_byid(self, known_microbiome):
known = Microbiota(known_microbiome, init_abund=[1.0, 1.0])
core_microbe = known.get_microbe_byid('e_coli_core')
assert core_microbe.id == 'e_coli_core'