def test_minimal_island():
"""Island of single jungle cell"""
BioSim(island_geography="OOO\nOJO\nOOO", initial_population=[], seed=1)
def test_invalid_boundary(bad_boundary):
"""Non-ocean boundary must raise error"""
with pytest.raises(ValueError):
BioSim(island_map="{}WW\nWLW\nWWW".format(bad_boundary),
ini_pop=[],
seed=1)
def test_inconsistent_length():
"""Inconsistent line length must raise error"""
with pytest.raises(ValueError):
BioSim(island_map="WWW\nWLLW\nWWW", ini_pop=[], seed=1)
def plain_sim():
"""Return a simple island for used in various tests below"""
return BioSim(island_map="WWWW\nWLHW\nWWWW", ini_pop=[], seed=1)
def test_minimal_island():
"""Island of single jungle cell"""
BioSim(island_map="WWW\nWLW\nWWW", ini_pop=[], seed=1)
def test_all_types():
"""All types of landscape can be created"""
BioSim(island_map="OOOO\nOJSO\nOMDO\nOOOO", ini_pop=[], seed=1)
"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})
OJOJOJOJOO
OOJOJOJOJO
OJOJOJOJOO
OOOOOOOOOO
"""
checker_map = textwrap.dedent(checker_map)
checker_map2 = """
OOOOOOOOOO
ODJDJDJDJO
OJDJDJDJDO
ODJDJDJDJO
OJDJDJDJDO
ODJDJDJDJO
OJDJDJDJDO
ODJDJDJDJO
OJDJDJDJDO
OOOOOOOOOO
"""
checker_map2 = textwrap.dedent(checker_map2)
sim = BioSim(island_map=checker_map,
ini_pop=default_population,
img_base='checker_map_ocean',
ymax_animals=500,
cmax_animals={
'Herbivore': 100,
'Carnivore': 80
})
sim.simulate(100)
sim.make_movie()
desert_landscape = """
OOOOOOOOOOOOO
ODSSSDDDSDSDO
ODSDSDDSDSSDO
ODDDDDDDDSSDO
ODDDMMDSDDDDO
ODDMMSMMDSSDO
ODDDMDSDSSDDO
ODDDMMDMDSDDO
ODDSDSSMSDSDO
ODSDDMMMDDSDO
ODDDDSMDDDSDO
ODDSDSSDSDDDO
OOOOOOOOOOOOO
"""
desert_landscape = textwrap.dedent(desert_landscape)
sim = BioSim(island_map=desert_landscape, ini_pop=default_population,
ymax_animals=800,
cmax_animals={'Herbivore':40,
'Carnivore':30})
sim.set_animal_parameters('Herbivore', {'mu': 0.5,
'eta': 0.1})
sim.set_animal_parameters('Carnivore', {'eta': 0.075,
'F': 20,
'mu': 0.5,
'DeltaPhiMax': 0.75})
sim.simulate(1000)
sim.make_movie()
def test_simulation_set_animal_parameters():
"""Test to see that incorrect species string gives ValueError"""
sim = BioSim(island_map="OO\nOO", ini_pop=[], seed=1)
with pytest.raises(ValueError):
sim.set_animal_parameters("Omnivore", {"w_birth": 8.0})
def test_simulation_set_landscape_parameters():
"""Test to see that incorrect landscape string gives ValueError"""
sim = BioSim(island_map="OO\nOO", ini_pop=[], seed=1)
with pytest.raises(ValueError):
sim.set_landscape_parameters("D", {"fodder": 8.0})
def test_inconsistent_length():
"""Inconsistent line length must raise error"""
with pytest.raises(ValueError):
BioSim(island_geography="OOO\nOJJO\nOOO",
initial_population=[],
seed=1)
def test_invalid_landscape():
"""Invalid landscape type must raise error"""
with pytest.raises(ValueError):
BioSim(island_geography="OOO\nORO\nOOO", initial_population=[], seed=1)
def test_all_types():
"""All types of landscape can be created"""
BioSim(island_geography="OOOO\nOJSO\nOMDO\nOOOO",
initial_population=[],
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)
from biosim.simulation import BioSim
from biosim.logic import season_migration
if __name__ == '__main__':
this_fucking_thing = BioSim(island_map = "WWWW\nWLLW\nWWWW", ini_pop = [{'loc':(2,2) , 'pop':[ {"species":"herbivore","age":5,"weight":20} for _ in range(10)] } ] , seed = 1234)
the_map = this_fucking_thing.island
illigal_moves = this_fucking_thing.illigal_coord
for _ in range(30):
season_migration(the_map,illigal_moves)
for cell in the_map:
print("coord:",the_map[cell].coord,"animals:",the_map[cell].herb_default)
for C in the_map[cell].herb_default:
print(C.var["coord"], C.var["a"])
def test_minimal_island():
"""Island of single jungle cell"""
BioSim(island_map="OOO\nOJO\nOOO", ini_pop=[], seed=1)
} for _ in range(1000)]
}]
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)
OSSSSSJJJJJJJJJJJJOOO
OSSSSSJJJDDJJJSJJJOOO
OSSJJJJJDDDJJJSSSSOOO
OOSSSSJJJDDJJJSOOOOOO
OSSSJJJJJDDJJJJJJJOOO
OSSSSJJJJDDJJJJOOOOOO
OOSSSSJJJJJJJJOOOOOOO
OOOSSSSJJJJJJJOOOOOOO
OOOOOOOOOOOOOOOOOOOOO"""
geogr = textwrap.dedent(geogr)
ini_herbs = [{'loc': (10, 10),
'pop': [{'species': 'Herbivore',
'age': 5,
'weight': 20}
for _ in xrange(150)]}]
ini_carns = [{'loc': (10, 10),
'pop': [{'species': 'Carnivore',
'age': 5,
'weight': 20}
for _ in xrange(40)]}]
sim = BioSim(island_map=geogr, ini_pop=ini_herbs + ini_carns,
seed=656412)
sim.simulate(num_steps=100, vis_steps=1, img_steps=2000)
sim.add_population(population=ini_carns)
sim.simulate(num_steps=100, vis_steps=1, img_steps=2000)
raw_input('Press ENTER')
def test_set_plot_limits():
"""Test that y-axis and color limits for plots can be set."""
BioSim(island_map='W', ini_pop=[], seed=1, ymax_animals=20,
cmax_animals={'Herbivore': 10, 'Carnivore': 20})
# -*- coding: utf-8 -*-
"""
Island with single jungle cell, first herbivores only, later carnivores.
"""
__author__ = 'Hans Ekkehard Plesser, NMBU'
import textwrap
from biosim.simulation import BioSim
geogr = """\
WWW
WLW
WWW"""
geogr = textwrap.dedent(geogr)
ini_herbs = [{'loc': (2, 2),
'pop': [{'species': 'Herbivore',
'age': 5,
'weight': 20}
for _ in range(50)]}]
for seed in range(100, 103):
sim = BioSim(geogr, ini_herbs, seed=seed,
img_dir='results', img_base=f'mono_ho_{seed:05d}', img_years=300)
sim.simulate(301)
def test_configure_histograms(prop, config):
"""Test that y-axis and color limits for plots can be set."""
BioSim(island_map='W', ini_pop=[], seed=1, ymax_animals=20,
cmax_animals={'Herbivore': 10, 'Carnivore': 20},
hist_specs={prop: config})
def test_empty_island():
"""Empty island can be created"""
BioSim(island_map="WW\nWW", ini_pop=[], seed=1)
# -*- coding: utf-8 -*- """ """ __author__ = "Jon-Mikkel Korsvik & Petter Bøe Hørtvedt" __email__ = "[email protected] & [email protected]" from biosim.simulation import BioSim default_population = [{ "loc": (1, 1), "pop": [{ "species": "Herbivore", "age": 5, "weight": 20 } for _ in range(150)], }, { "loc": (1, 1), "pop": [{ "species": "Carnivore", "age": 5, "weight": 20 } for _ in range(40)], }] sim = BioSim(island_map='OOOOOO\nOJJJJO\nOJJJJO\nOJJJJO\nOJJJJO\nOOOOOO', ini_pop=default_population, img_base='even_island', ymax_animals=3000) sim.simulate(100) sim.make_movie()
def test_all_types():
"""All types of landscape can be created"""
BioSim(island_map="WWWW\nWLHW\nWWDW\nWWWW", ini_pop=[], seed=1)
for _ in range(150)]}]
ini_carns = [{'loc': (10, 10),
'pop': [{'species': 'Carnivore',
'age': 5,
'weight': 20}
for _ in range(40)]}]
ini_snake = [{'loc': (4, 15),
'pop': [{'species': 'Snake',
'age': 5,
'weight': 20}
for _ in range(40)]}]
sim = BioSim(island_map=geogr, ini_pop=ini_herbs, seed=123456,
hist_specs={'fitness': {'max': 1.0, 'delta': 0.05},
'age': {'max': 60.0, 'delta': 2},
'weight': {'max': 60, 'delta': 2}},
)
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.})
sim.set_landscape_parameters('L', {'f_max': 700})
sim.simulate(num_years=100, vis_years=1, img_years=2000)
new_map = """\
WWWWWWWWWWWWWWWWWWWWW
WWWWWWWWHWWWWLLLLLLLW
WWHHHHLLLLWWLLLLLLLWW
def test_invalid_landscape():
"""Invalid landscape type must raise error"""
with pytest.raises(ValueError):
BioSim(island_map="WWW\nWRW\nWWW", ini_pop=[], seed=1)
"loc": (10, 10),
"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,
hist_specs={
"fitness": {"max": 1.0, "delta": 0.05},
"age": {"max": 60.0, "delta": 2},
"weight": {"max": 60, "delta": 2},
},
)
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("L", {"f_max": 700})
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)
def test_set_param_landscape(lscape, params):
"""Parameters can be set on landscape classes"""
BioSim(island_map="W", ini_pop=[],
seed=1).set_landscape_parameters(lscape, params)
def test_empty_island():
"""Empty island can be created"""
BioSim(island_geography="OO\nOO", initial_population=[], seed=1)