def test_advance(self): big_pop = Population( [MockOrganism(1), MockOrganism(2), MockOrganism(90)], 3) big_pop.advance_generation() self.assertLessEqual(len(big_pop), 3)
class TestPopulationBitstring(unittest.TestCase): def setUp(self): bit0 = Bitstring("0000") bit1 = Bitstring("1111") col0 = ColicinBit(bit0) col1 = ColicinBit(bit1) org = Organism([col0], [ImmunityBit(bit0, 2)]) self.pop = Population([org for _ in range(5)]) def test_replicate(self): self.assertEqual(len(self.pop), 5) self.pop.replicate() self.assertEqual(len(self.pop), 10) def test_remove_self_toxic(self): self.assertEqual(len(self.pop), 5) self.pop.remove_self_toxic() self.assertEqual(len(self.pop), 5) def test_cull_by_iterative_colicin(self): self.assertEqual(len(self.pop), 5) self.pop.cull_by_iterative_colicin() self.assertEqual(len(self.pop), 5) def test_advance_generation(self): self.pop.advance_generation() def test_sample_with_replacement(self): self.pop.sample_with_replacement()
def test_advance(self): big_pop = Population( [MockOrganism(1), MockOrganism(2), MockOrganism(90)], 3) big_pop.advance_generation() self.assertLessEqual(len(big_pop), 3)
def colicin_int_demo(): org = Organism([Colicin(0)], [Immunity(0, 5)]) pop = Population(org for _ in range(5)) for gen in range(1000): pop.advance_generation() average_id = average_colicin_int(pop) if gen % 100 == 0: print("{}\t{}".format(gen, average_id))
def colicin_bitstring_demo(): mutate.mutation_rate = 0.05 bit = Bitstring("0000000000000000000") bit2 = Bitstring("1000000000000000000") col = ColicinBit(bit) imm = ImmunityBit(bit2, 1) org = Organism([col], [imm, imm]) pop = Population(org for _ in range(100)) for gen in range(101): pop.advance_generation() if gen % 10 == 0: average_dist = average_colicin_bitstring_distance(pop, col) print("{}\t{}".format(gen, average_dist))
class Lifecycle(object): def __init__(self, id, params): self.id = id self.params = params self.population = Population(self.params["population_size"]) self.best_fit = list() self.average_fit = list() self.iterations = 0 def start(self): for epoch in range(0, self.params["epochs"]): self.iterations += 1 elite = self.params["elite"] crossover = self.params["crossover"] mutation = self.params["mutation"] self.population.advance_generation(elite, crossover_rate=crossover, n_arena=4, mutation=mutation) self.best_fit.append(self.population.best_fitness()) self.average_fit.append(self.population.avg_fitness()) if epoch > 50: recent_best = self.best_fit[-50:] if max(recent_best) - min(recent_best) < 0.02: break def best_fitness(self): return self.population.best_fitness() def generate_graph(self, show=False, location=None): plt.plot(self.best_fit) plt.xlabel("Epoch") plt.ylabel("Best fitness") plt.title(self.get_params()) if show: plt.show() if location is not None: plt.savefig(location) def get_params(self): return_string = ("mutation: %d " % self.params['mutation']) return_string += ("crossover: %d " % self.params['crossover']) return_string += ("elite: %d " % self.params['elite']) return_string += ("iter: %d" % self.iterations) return return_string def get_csv(self): id = {'id': self.id} best_fitness = {'best_fit': self.best_fitness()} iter = {'iter': self.iterations} return {**id, **best_fitness, **self.params, **iter}
class TestPopulation(unittest.TestCase): def setUp(self): self.col = Colicin(0) self.imm = Immunity(-5, 5) self.org = Organism([self.col], [self.imm]) self.pop = Population([self.org.duplicate() for _ in range(10)]) def test_len(self): self.assertEqual(len(self.pop), 10) def test_replicate(self): self.pop.replicate() self.assertEqual(self.pop.pop.count(self.org), 10) self.assertEqual(len(self.pop), 20) def test_iter(self): for org in self.pop: self.assertEqual(org, self.org) else: return self.fail() def test_remove_self_toxic(self): org_toxic = Organism([Colicin(0)], [Immunity(10, 5)]) org_not_toxic = Organism([Colicin(0)], [Immunity(0, 5)]) self.pop.pop = [org_not_toxic, org_toxic] self.assertEqual(len(self.pop), 2) self.pop.remove_self_toxic() self.assertEqual(len(self.pop), 1) self.assertSequenceEqual(self.pop.pop, [org_not_toxic]) def test_cull_by_all_colicins(self): org_winner = Organism([Colicin(5)], [Immunity(0, 5)]) self.pop.pop.append(org_winner) self.pop.cull_by_all_colicins() self.assertSequenceEqual(self.pop.pop, [org_winner]) def test_cull_by_all_colicins_extinction(self): org_other = Organism([Colicin(5)], [Immunity(10, 5)]) self.pop.pop.append(org_other) self.pop.cull_by_all_colicins() self.assertEqual(len(self.pop), 0) def test_cull_by_single_colicin(self): org_other = Organism([Colicin(100)], [Immunity(100, 5)]) self.pop.pop.extend(org_other for _ in range(10)) self.pop.cull_by_single_colicin() self.assertEqual(len(self.pop), 10) def test_cull_by_single_colicin_extinction(self): self.pop.cull_by_single_colicin(Colicin(5)) self.assertEqual(len(self.pop), 0) def test_cull_by_iterative_colicin(self): org_winner = Organism([Colicin(5)], [Immunity(0, 5)]) self.pop.pop.append(org_winner) self.pop.cull_by_iterative_colicin() self.assertSequenceEqual(self.pop.pop, [org_winner]) def test_cull_by_iterative_colicin_extinction(self): org_other = Organism([Colicin(5)], [Immunity(10, 5)]) self.pop.pop.extend(org_other for _ in range(10)) self.pop.cull_by_iterative_colicin() self.assertEqual(len(self.pop), 10) def test_colicins_produced(self): colicins = set(self.pop.colicins_produced()) self.assertSetEqual({self.col}, colicins) other_colicin = Colicin(5) self.pop.pop.append(Organism([other_colicin], [Immunity(0, 5)])) colicins = set(self.pop.colicins_produced()) self.assertSetEqual({self.col, other_colicin}, colicins) def test_sample_with_replacement(self): self.pop.pop.extend(self.org for _ in range(20)) self.assertEqual(len(self.pop), 30) self.pop.sample_with_replacement() self.assertEqual(len(self.pop), 10) self.pop.pop = self.pop.pop[::2] self.assertEqual(len(self.pop), 5) self.pop.sample_with_replacement() self.assertEqual(len(self.pop), 10) self.assertEqual(self.pop.carrying_capacity, 10) def test_advance_generation(self): self.pop.advance_generation() self.assertEqual(len(self.pop), 10)