def test_animal_death():
island_map = "OOO\nOJO\nOOO"
ini_herbs = [{
"loc": (1, 1),
"pop": [{
"species": "Herbivore",
"age": 5,
"weight": rd.randint(1, 5)
} for _ in range(150)],
}]
ini_carns = [{
"loc": (1, 1),
"pop": [{
"species": "Carnivore",
"age": 5,
"weight": rd.randint(1, 5)
} for _ in range(40)],
}]
t = BioSim(island_map, ini_herbs, None)
t.add_population(ini_carns)
loc = (1, 1)
cell_object = t.island.cells[loc]
cell_object.die()
assert len(cell_object.population["Carnivore"]) < 40
assert len(cell_object.population["Herbivore"]) < 150
def test_population_to_cell():
""" Tests that you can add and store animals in a cell of the map. """
sim = BioSim(island_map="OOO\nOJO\nOOO",
ini_pop=[{
"loc": (1, 1),
"pop": [{
"species": "Herbivore",
"age": 1,
"weight": 15.0
}]
}],
seed=0)
assert len(sim.map.array_map[1, 1].present_herbivores) == 1
sim.add_population([
{
"loc": (1, 1),
"pop": [
{
"species": "Herbivore",
"age": 1,
"weight": 10.0
},
{
"species": "Carnivore",
"age": 1,
"weight": 10.0
},
],
},
])
assert len(sim.map.array_map[1, 1].present_herbivores) + len(
sim.map.array_map[1, 1].present_carnivores) == 3
def test_carnivore_feed():
"""Many testes for the method 'carnivore_feed()':
1. Test carnivore weight increases after feeding herbivore
"""
island_map = "OOO\nOJO\nOOO"
ini_herbs = [{
"loc": (1, 1),
"pop": [{
"species": "Herbivore",
"age": 5,
"weight": 40
} for _ in range(150)],
}]
ini_carns = [{
"loc": (1, 1),
"pop": [{
"species": "Carnivore",
"age": 5,
"weight": 40
} for _ in range(40)],
}]
t = BioSim(island_map, ini_herbs, None)
t.add_population(ini_carns)
loc = (1, 1)
cell_object = t.island.cells[loc]
carn_start_weight = np.sum(carn.weight
for carn in cell_object.population['Carnivore'])
cell_object.carnivore_feed()
carn_new_weight = np.sum(carn.weight
for carn in cell_object.population['Carnivore'])
assert carn_start_weight < carn_new_weight
def biosim_with_animals(self):
"""
Create Biosim instance with population for further testing
"""
biosim = BioSim(island_map='WWWWW\nWLDHW\nWWWWW', plot_graph=False)
biosim.add_population([{
"loc": (2, 2),
"pop": [{
"species": "Carnivore",
"age": 5,
"weight": 20
} for _ in range(20)]
}, {
"loc": (2, 2),
"pop": [{
"species": "Herbivore",
"age": 5,
"weight": None
} for _ in range(50)]
}, {
"loc": (2, 3),
"pop": [{
"species": "Herbivore",
"age": 5,
"weight": 0
} for _ in range(20)]
}])
return biosim
def test_consistensy_simulation_one_cell_two_species():
ini_herb = [{
"species": "Herbivore",
"age": 5,
"weight": 20
} for _ in range(100)]
ini_carn = [{
"species": "Carnivore",
"age": 5,
"weight": 20
} for _ in range(20)]
ini_pop = [{"loc": (2, 2), "pop": ini_herb}]
n_herb = 0
n_carn = 0
for _ in range(1, 51):
sim = BioSim(island_map="WWW\nWLW\nWWW", ini_pop=ini_pop, tmean=True)
sim.simulate(num_years=50, vis_years=1)
sim.add_population([{"loc": (2, 2), "pop": ini_carn}])
sim.simulate(num_years=150, vis_years=1)
n_herb += sim.mean["Herbivore"]
n_carn += sim.mean["Carnivore"]
n_herb /= 50
n_carn /= 50
assert n_herb == pt.approx(85, abs=17)
assert n_carn == pt.approx(41, abs=10)
def test_set_param_on_single_animal():
island_setup = BioSim(island_map="WWW\nWLW\nWWW", seed=1234, ini_pop=[])
island_setup.set_animal_parameters("Herbivore", {"beta": 20, "gamma": 100})
island_setup.add_population([{
"loc": (2, 2),
"pop": [{
'species': 'Herbivore',
'age': 5,
'weight': 100
} for _ in range(1)]
}])
animal = island_setup.island[(2, 2)].default["Herbivore"][0]
assert animal.var["beta"] == 20 and animal.var["gamma"] == 100
def test_add_population(self):
"""
Tests the population is added to cell on island.
Returns
-------
"""
s1 = BioSim(island_map=ISLE_MAP, ini_pop=INI_HERB, seed=123)
assert len(s1.island.cells[1, 1].herbivores) == 20
s1.add_population(INI_HERB)
assert len(s1.island.cells[1, 1].herbivores) == 40
assert len(s1.island.cells[1, 1].carnivores) == 0
s1.add_population(INI_CARN)
assert len(s1.island.cells[1, 1].carnivores) == 10
def test_add_population(self):
sim = BioSim()
assert sim.island.map[(1, 2)].num_animals == 0
sim.add_population([{
'loc': (1, 2),
'pop': [{
"species": "Herbivore",
"age": 5,
"weight": 40
}, {
"species": "Carnivore",
"age": 10,
"weight": 14.5
}]
}])
assert sim.island.map[(1, 2)].num_animals == 2
def test_set_param_more_animals():
island_setup = BioSim(island_map="WWW\nWLW\nWWW", seed=1234, ini_pop=[])
island_setup.set_animal_parameters("Herbivore", {"beta": 20, "gamma": 100})
island_setup.set_animal_parameters("Carnivore", {"eta": 20, "a_half": 100})
island_setup.add_population([{
"loc": (2, 2),
"pop": [{
'species': 'Herbivore',
'age': 5,
'weight': 100
}, {
'species': 'Carnivore',
'age': 5,
'weight': 100
}]
}])
herb = island_setup.island[(2, 2)].default["Herbivore"][0]
carn = island_setup.island[(2, 2)].default["Carnivore"][0]
assert herb.var["beta"] == 20 and herb.var["gamma"] == 100
assert carn.var["eta"] == 20 and carn.var["a_half"] == 100
ini_herbs = [
{'loc': (5, 5), 'pop': [{'species': 'Herbivore', 'age': 5, 'weight': 50} for _ in range(50)]}]
ini_carn = [
{'loc': (5, 5), 'pop': [{'species': 'Carnivore', 'age': 5, 'weight': 50} for _ in range(50)]}]
kart = """\
WWWWWWWWWWWWWWWWWWWWW
WWWWWWWWHWWWWLLLLLLLW
WHHHHHLLLLWWLLLLLLLWW
WHHHHHHHHHWWLLLLLLWWW
WHHHHHLLLLLLLLLLLLWWW
WHHHHHLLLDDLLLHLLLWWW
WHHLLLLLDDDLLLHHHHWWW
WWHHHHLLLDDLLLHWWWWWW
WHHHLLLLLDDLLLLLLLWWW
WHHHHLLLLDDLLLLWWWWWW
WWHHHHLLLLLLLLWWWWWWW
WWWHHHHLLLLLLLWWWWWWW
WWWWWWWWWWWWWWWWWWWWW"""
sim = BioSim(seed=123,
ini_pop=ini_herbs,
island_map=kart)
sim.simulate(num_years=5)
sim.add_population(ini_carn)
sim.set_animal_parameters('Carnivore', {'infected': True})
sim.simulate(num_years=100)
}]
sim = BioSim(
island_map=geogr, ini_pop=ini_herbs,
seed=123456) #cmax_animals={"Herbivore":100, "Carnivore": 50})
sim.set_animal_parameters('Herbivore', {
'mu': 1,
'omega': 0,
'gamma': 0,
'a_half': 1000
})
sim.set_animal_parameters('Carnivore', {
'mu': 1,
'omega': 0,
'gamma': 0,
'F': 0,
'a_half': 1000
})
sim.set_landscape_parameters("J", {"f_max": 700})
sim._img_pause_time = 1
sim.simulate(num_years=100, vis_years=1, img_years=2000)
sim.add_population(population=ini_carns)
sim.simulate(num_years=100, vis_years=1, img_years=2000)
plt.savefig("check_sim.pdf")
input("Press ENTER")
kart = """\
WWWWWWWWWW
WDDDDDDDDW
WDDDDDDDDW
WDDDDDDDDW
WDDDDDDDDW
WDDDDDDDDW
WDDDDDDDDW
WDDDDDDDDW
WDDDDDDDDW
WWWWWWWWWW"""
b = BioSim(seed=123, ini_pop=ini_herbs, island_map=kart)
b.set_animal_parameters('Herbivore', {
'mu': 1,
'omega': 0,
'gamma': 0,
'a_half': 10000
})
b.set_animal_parameters('Carnivore', {
'mu': 1,
'omega': 0,
'gamma': 0,
'F': 0,
'a_half': 10000
})
b.add_population(ini_carn)
b.simulate(num_years=10)
img_base=None,
ymax_animals=200,
cmax_animals=c_max)
print(
k.add_population([
{
"loc": (2, 2),
"pop": [{
"species": "Herbivore",
"age": 9,
"weight": 45.0
}, {
"species": "Herbivore",
"age": 5,
"weight": 17.0
}, {
"species": "Herbivore",
"age": 9,
"weight": 45.0
}, {
"species": "Herbivore",
"age": 5,
"weight": 17.0
}],
},
]))
k.simulate(50)
print(k.num_animals, 'live animals at year', k.year)
print('Added carnivores to simulation')
k.add_population([
{
class TestSimulation(object):
geo = """OOOOOOO
OJJJJJO
OJSMSJO
OSDJDSO
OJSMSJO
OJJJJJO
OOOOOOO"""
def __init__(self):
self.original_herb = Herbivore.params
self.original_carn = Carnivore.params
self.original_Jungle = Jungle.params
self.original_Savannah = Savannah.params
self.sim = None
def setup(self):
ini_carns = [{
'loc': (5, 3),
'pop': [{
'species': 'Carnivore',
'age': 5,
'weight': 20
} for _ in xrange(20)]
}]
ini_herbs = [{
'loc': (3, 3),
'pop': [{
'species': 'Herbivore',
'age': 5,
'weight': 20
} for _ in xrange(80)]
}]
ini_pop = ini_carns + ini_herbs
self.sim = BioSim(self.geo, ini_pop, 123456)
def teardown(self):
Herbivore.params = self.original_herb
Carnivore.params = self.original_carn
Jungle.params = self.original_Jungle
Savannah.params = self.original_Savannah
def test_add_population(self):
"""
Test that add_population function adds population in right cell with
given weight and age.
"""
num_carnivores = 5
num_herbivores = 10
herbs = [{
'loc': (2, 2),
'pop': [{
'species': 'Herbivore',
'age': 8,
'weight': 40
} for _ in xrange(num_herbivores)]
}]
carns = [{
'loc': (2, 2),
'pop': [{
'species': 'Carnivore',
'age': 7,
'weight': 30
} for _ in xrange(num_carnivores)]
}]
self.sim.add_population(herbs + carns)
nt.assert_equal(num_carnivores,
len(self.sim.island.island[1][1].carnivores))
nt.assert_equal(num_herbivores,
len(self.sim.island.island[1][1].herbivores))
for carn in self.sim.island.island[1][1].carnivores:
nt.assert_equal(carn.age, 7)
nt.assert_equal(carn.weight, 30)
for herb in self.sim.island.island[1][1].herbivores:
nt.assert_equal(herb.age, 8)
nt.assert_equal(herb.weight, 40)
herbs_ = [{
'loc': (2, 2),
'pop': [{
'species': 'Herbivore',
'age': 8,
'weight': 40
}]
}]
self.sim.add_population(herbs_)
def test_heatmap(self):
"""
Tests that heatmap makes array with correct number of herbivores.
:return:
"""
Carnivore.set_parameters({"gamma": 0, "omega": 0, "mu": 0})
Herbivore.set_parameters({"gamma": 0, "omega": 0, "mu": 0})
initial_herbivores = 80
initial_carnivores = 20
herbivores, carnivores = self.sim.heatmap(self.sim.island.one_year())
nt.assert_equal(initial_carnivores, np.sum(carnivores))
nt.assert_equal(initial_herbivores, np.sum(herbivores))
nt.assert_equal(initial_herbivores, herbivores[2][2])
nt.assert_equal(initial_carnivores, carnivores[4][2])
@staticmethod
def test_standard_arguments():
"""
Tests that simulation works without any given arguments.
"""
initial_herbivores = 150
initial_carnivores = 40
sim_ = BioSim()
Carnivore.set_parameters({"gamma": 0, "omega": 0, "mu": 0})
Herbivore.set_parameters({"gamma": 0, "omega": 0, "mu": 1})
for row in sim_.island.island:
for cell in row:
for herb in cell.herbivores:
herb.fitness = 1
sim_.island.migration()
herbivores, carnivores = sim_.heatmap(sim_.island.one_year())
nt.assert_equal(initial_carnivores, np.sum(carnivores))
nt.assert_equal(initial_herbivores, np.sum(herbivores))
nt.assert_equal(initial_carnivores, carnivores[2][2])
def test_number_animals(self):
"""
Tests that the animal function works
"""
total = 100
herbs = 80
carns = 20
animals = self.sim.animal()
nt.assert_equal(herbs, animals["Herbivores"])
nt.assert_equal(carns, animals["Carnivores"])
nt.assert_equal(total, animals["Herbivores"] + animals["Carnivores"])
