def test_simulate_function(self, input_map, ini_pop):
s = BioSim(input_map, ini_pop, seed=123)
prev_number_of_animals = s.num_animals_per_species
s.simulate()
assert s.num_animals_per_species['Herbivore'] !=\
prev_number_of_animals['Herbivore']
assert s.num_animals_per_species['Carnivore'] !=\
prev_number_of_animals['Carnivore']
def test_num_animals_and_add_population(self, input_map, ini_pop,
add_carns):
""""""
s = BioSim(input_map, ini_pop, seed=1)
assert s.num_animals_per_species['Herbivore'] > 0
assert s.num_animals_per_species['Carnivore'] > 0
prev_carns = s.num_animals_per_species['Carnivore']
s.add_population(add_carns)
assert s.num_animals_per_species['Carnivore'] > prev_carns
def test_set_animal_parameters(self, input_map, ini_pop):
"""set_animal_parameters should change parameters successfully"""
s = BioSim(island_map=input_map, ini_pop=ini_pop, seed=1)
s.set_animal_parameters("Herbivore", {"zeta": 3.2, "xi": 1.8})
s.set_animal_parameters("Carnivore", {"zeta": 5.0, "xi": 2.0})
assert Herbivore.animal_params["zeta"] == 3.2
assert Herbivore.animal_params["xi"] == 1.8
assert Carnivore.animal_params["zeta"] == 5.0
assert Carnivore.animal_params["xi"] == 2.0
def test_figure_saved(figfile_root):
"""Test that figures are saved during simulation"""
sim = BioSim(
island_map="OOOO\nOJSO\nOOOO",
ini_pop=[],
seed=1,
img_base=figfile_root,
img_fmt="png",
)
sim.simulate(2, vis_years=1, img_years=1)
assert os.path.isfile(figfile_root + "_00000.png")
assert os.path.isfile(figfile_root + "_00001.png")
def test_invalid_boundary(bad_boundary):
"""Non-ocean boundary must raise error"""
with pytest.raises(ValueError):
BioSim(
island_map="{}OO\nOJO\nOOO".format(bad_boundary),
ini_pop=[],
seed=1,
)
def test_set_plot_limits():
"""Test that y-axis and color limits for plots can be set."""
BioSim(
island_map="O",
ini_pop=[],
seed=1,
ymax_animals=20,
cmax_animals={
"Herbivore": 10,
"Carnivore": 20
},
)
def test_animals_reproduce(self, input_map, ini_pop):
"""Animals should reproduce properly"""
s = BioSim(input_map, ini_pop, seed=1)
herb_count_prev = s.object_matrix[1][1].n_herbs
carn_count_prev = s.object_matrix[1][1].n_carns
c = Cycle(s.object_matrix)
c.food_grows()
c.animals_reproduce()
herb_count_curr = s.object_matrix[1][1].n_herbs
carn_count_curr = s.object_matrix[1][1].n_carns
assert carn_count_curr > carn_count_prev, "Animals have not reproduced"
assert herb_count_curr > herb_count_prev, "Animals have not reproduced"
def create_sim(self):
"""Creates a Simulation object"""
map = """\
OOOOOOOOO
OSSJJSSOO
OOOOOOOOO
"""
ini_herbs = [
{
"loc": (2, 2),
"pop": [
{"species": "Herbivore", "age": 5, "weight": 20}
for _ in range(200)
],
}
]
return BioSim(map, ini_herbs, seed=1)
def test_initial_population():
"""Test that population can be placed on construction"""
BioSim(
island_map="OOOO\nOJSO\nOOOO",
ini_pop=[
{
"loc": (1, 1),
"pop": [
{
"species": "Herbivore",
"age": 1,
"weight": 10.0
},
{
"species": "Carnivore",
"age": 1,
"weight": 10.0
},
],
},
{
"loc": (1, 2),
"pop": [
{
"species": "Herbivore",
"age": 1,
"weight": 10.0
},
{
"species": "Carnivore",
"age": 1,
"weight": 10.0
},
],
},
],
seed=1,
)
def test_set_param_animals(species, extra):
"""Parameters can be set on animal classes"""
params = {
"w_birth": 8.0,
"sigma_birth": 1.5,
"beta": 0.9,
"eta": 0.05,
"a_half": 40.0,
"phi_age": 0.2,
"w_half": 10.0,
"phi_weight": 0.1,
"mu": 0.25,
"gamma": 0.2,
"zeta": 3.5,
"xi": 1.2,
"omega": 0.4,
"F": 10.0,
}
params.update(extra)
BioSim(island_map="O", ini_pop=[],
seed=1).set_animal_parameters(species, params)
def create_s(self, input_map, ini_pop):
"""Makes BioSim object"""
return BioSim(input_map, ini_pop, seed=1)
def create_s(self, input_map, ini_pop):
"""Creates a Simulation object"""
s = BioSim(input_map, ini_pop, seed=1)
return s
def test_inconsistent_length():
"""Inconsistent line length must raise error"""
with pytest.raises(ValueError):
BioSim(island_map="OOO\nOJJO\nOOO", ini_pop=[], seed=1)
def test_invalid_landscape():
"""Invalid landscape type must raise error"""
with pytest.raises(ValueError):
BioSim(island_map="OOO\nORO\nOOO", ini_pop=[], seed=1)
from src.biosim.simulation import BioSim
from src.biosim.animals import Carnivore, Herbivore, BaseAnimal
default_population = [
{
"loc": (3, 3),
"pop": [{
"species": "Herbivore",
"age": 5,
"weight": 20
} for _ in range(2000)],
},
]
sim = BioSim(island_map='OOOOOOO\n'
'ODDDDDO\n'
'ODDDDDO\n'
'ODDDDDO\n'
'ODDDDDO\n'
'ODDDDDO\n'
'OOOOOOO',
ini_pop=default_population,
img_base='migrate_checker',
ymax_animals=3000)
sim.set_animal_parameters('Herbivore', {
'mu': 1e10,
'omega': 1e-10,
'eta': 1e-10
})
print(Herbivore.mu, Herbivore.omega, Herbivore.eta, Herbivore.w_birth,
Herbivore.sigma_birth)
sim.make_movie()
OSSSSSJJJJJJJJJJJJOOO
OSSSSSJJJDDJJJSJJJOOO
OSSJJJJJDDDJJJSSSSOOO
OOSSSSJJJDDJJJSOOOOOO
OSSSJJJJJDDJJJJJJJOOO
OSSSSJJJJDDJJJJOOOOOO
OOSSSSJJJJJJJJOOOOOOO
OOOSSSSJJJJJJJOOOOOOO
OOOOOOOOOOOOOOOOOOOOO"""
import textwrap
geostring = textwrap.dedent(geogr)
Landscape = Bio(geostring, poplist,seed =0, ymax_animals=None,
cmax_animals=None,
img_base=None,
img_fmt="png")
landscape, geostring_list = Landscape.create_landscape()
print(landscape)
herb, carn = Landscape.populate_island()
print(herb)
print(carn)
age = []
weight = []
for animal in range(len(herb)):
num_herb = len(herb)
num_carn = len(carn)
age.append(herb[animal]['age'])
weight.append(herb[animal]['weight'])
def test_minimal_island():
"""Island of single jungle cell"""
BioSim(island_map="OOO\nOJO\nOOO", ini_pop=[], seed=1)
def test_empty_island():
"""Empty island can be created"""
BioSim(island_map="OO\nOO", ini_pop=[], seed=1)
def plain_sim():
"""Return a simple island for used in various tests below"""
return BioSim(island_map="OOOO\nOJSO\nOOOO", ini_pop=[], seed=1)
def test_set_param_landscape(lscape, params):
"""Parameters can be set on landscape classes"""
BioSim(island_map="O", ini_pop=[],
seed=1).set_landscape_parameters(lscape, params)
"pop": [{
"species": "Herbivore",
"age": 5,
"weight": 20
} for _ in range(150)],
}]
ini_carns = [{
"loc": (10, 10),
"pop": [{
"species": "Carnivore",
"age": 5,
"weight": 20
} for _ in range(40)],
}]
sim = BioSim(island_map=geogr, ini_pop=ini_herbs, seed=123456)
sim.set_animal_parameters("Herbivore", {"zeta": 3.2, "xi": 1.8})
sim.set_animal_parameters(
"Carnivore",
{
"a_half": 70,
"phi_age": 0.5,
"omega": 0.3,
"F": 65,
"DeltaPhiMax": 9.0,
},
)
sim.set_landscape_parameters("J", {"f_max": 700})
sim.simulate(num_years=100, vis_years=1, img_years=2000)
def test_all_types():
"""All types of landscape can be created"""
BioSim(island_map="OOOO\nOJSO\nOMDO\nOOOO", ini_pop=[], seed=1)
} for _ in range(100)],
}]
ini_carns = [{
"loc": (10, 10),
"pop": [{
"species": "Carnivore",
"age": 5,
"weight": 20
} for _ in range(100)],
}]
# Should specify the total_years
sim = BioSim(island_map=geogr,
ini_pop=ini_herbs,
seed=123456,
total_years=2000,
img_base='Raw_Images',
cmax_animals={
'Herbivore': 100,
'Carnivore': 100
})
sim.set_animal_parameters("Herbivore", {"zeta": 3.2, "xi": 1.8})
sim.set_animal_parameters(
"Carnivore",
{
"a_half": 70,
"phi_age": 0.5,
"omega": 0.3,
"F": 65,
"DeltaPhiMax": 9.0,
},
{"species": "Herbivore", "age": 5, "weight": 20}
for _ in range(150)
],
}
]
ini_carns = [
{
"loc": (10, 10),
"pop": [
{"species": "Carnivore", "age": 5, "weight": 20}
for _ in range(40)
],
}
]
sim = BioSim(ini_pop=ini_herbs, seed=123456)
"""
sim.set_animal_parameters("Herbivore", {"zeta": 3.2, "xi": 1.8})
sim.set_animal_parameters(
"Carnivore",
{
"a_half": 70,
"phi_age": 0.5,
"omega": 0.3,
"F": 65,
"DeltaPhiMax": 9.0,
},
)
sim.set_landscape_parameters("J", {"f_max": 700})
"""
