def test_neighbour_cells():
"""Test if the method 'neighbour_cell(loc)' returns the correctly
habitable neighbours of a given localization"""
island_maps = ("OOOOO\nOJDJO\nOMJMO\nOJMJO\nOOOOO",
"OOOOO\nOJMJO\nOMJMO\nOJDJO\nOOOOO",
"OOOOO\nOJMJO\nODJMO\nOJMJO\nOOOOO",
"OOOOO\nOJMJO\nOMJDO\nOJMJO\nOOOOO")
ini_pop = [
{
"loc": (2, 2),
"pop": [
{"species": "Herbivore", "age": 5, "weight": 20}],
}]
for island_map in island_maps:
t = BioSim(island_map, ini_pop, None)
neighbours = [type(neighbour).__name__ for neighbour
in t.island.neighbour_cells(loc=(2, 2))]
assert 'Desert' in neighbours
assert len(neighbours) is 1
island_map = ("OOOOO\nOJDJO\nOOJJO\nOJSJO\nOOOOO")
t = BioSim(island_map, ini_pop, None)
neighbours = [type(neighbour).__name__ for neighbour
in t.island.neighbour_cells(loc=(2, 2))]
assert 'Jungle' in neighbours
assert 'Savannah' in neighbours
assert 'Desert' in neighbours
assert len(neighbours) is 3
def reset_landscape_defaults():
# no setup
yield
BioSim(island_map="W", ini_pop=[],
seed=1).set_landscape_parameters('L', {'f_max': 800.0})
BioSim(island_map="W", ini_pop=[],
seed=1).set_landscape_parameters('H', {'f_max': 300.0})
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_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 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_cannot_move_of_of_map():
""" Test that you don't raise any errors when trying to leave the map """
test_map = 'O'
sim = BioSim(island_map=test_map, ini_pop=[], seed=3)
sim.map.array_map[0, 0].present_herbivores.append(Herbivore(3, 20))
sim.migration_cycle()
assert len(sim.map.array_map[0, 0].present_herbivores) == 1
def test_set_animal_parameters():
"""Test if the method set_animal_parameters() raises a TypeError
if it is given a non-string type parameter_key argument.
* Test if the method set_animal_parameters() raises a TypeError
if it is given a non-dict type parameter_values argument.
* Test if the method set_animal_parameters() raises a ValueError
if it is given a unknown parameter.
* Test if the method set_animal_parameters() correctly sets the
parameters of all species and animal_objects"""
island_map = ("OOO\nOJO\nOOO")
ini_pop = [{
"loc": (1, 1),
"pop": [{
"species": "Herbivore",
"age": 5,
"weight": 20
}, {
"species": "Herbivore",
"age": 5,
"weight": 20
}, {
"species": "Carnivore",
"age": 5,
"weight": 20
}, {
"species": "Carnivore",
"age": 5,
"weight": 20
}]
}]
t = BioSim(island_map, ini_pop, None)
with pytest.raises(TypeError):
t.set_landscape_parameters(1, {'zeta': 3.2, 'xi': 1.8})
t.set_landscape_parameters('Herbivore', ['zeta', 3.2])
t.set_landscape_parameters('Carnivore', ['zeta', 3.2])
with pytest.raises(ValueError):
t.set_animal_parameters('Herbivore', {'eeta': 3.2})
t.set_animal_parameters('Carnivore', {'eeta': 3.2})
loc = (1, 1)
t.set_animal_parameters('Herbivore', {'zeta': 3.2, 'xi': 1.8})
t.set_animal_parameters('Carnivore', {'zeta': 3.2, 'xi': 1.8})
herb1_parameters = t.island.habitable_cells[loc].population['Herbivore'][
0].parameters
carn1_parameters = t.island.habitable_cells[loc].population['Carnivore'][
0].parameters
herb2_parameters = t.island.habitable_cells[loc].population['Herbivore'][
0].parameters
carn2_parameters = t.island.habitable_cells[loc].population['Carnivore'][
0].parameters
assert herb1_parameters['zeta'] and herb2_parameters['zeta'] is 3.2
assert herb1_parameters['xi'] and herb2_parameters['xi'] is 1.8
assert carn1_parameters['zeta'] and carn2_parameters['zeta'] is 3.2
assert carn1_parameters['xi'] and carn2_parameters['xi'] is 1.8
def test_figure_saved(figfile_root):
"""Test that figures are saved during simulation"""
sim = BioSim(
island_map="WWWW\nWLHW\nWWWW", 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_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_set_landscape_parameters(self):
BioSim.set_landscape_parameters('S', {'alpha': 3.9})
assert Savanna.alpha == 3.9
with pytest.raises(KeyError):
BioSim.set_landscape_parameters('B', {'alpha': 42, 'f_max': 42})
with pytest.raises(ValueError):
BioSim.set_landscape_parameters('S', {'alpha': 42, 'f_max': -5})
with pytest.raises(TypeError):
BioSim.set_landscape_parameters('S', {'alpha': 42, 'maximus': 42})
assert Savanna.alpha == 3.9
BioSim.set_landscape_parameters('S', {'alpha': 0.3, 'f_max': 300})
assert Savanna.alpha == 0.3
def test_figure_saved(figfile_root):
"""Test that figures are saved during simulation"""
sim = BioSim(
island_geography="OOOO\nOJSO\nOOOO",
initial_population=[],
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_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_consistensy_simulation_one_cell_one_species():
n_animals = 0
for _ in range(50):
sim = BioSim(island_map="WWW\nWLW\nWWW",
ini_pop=[{
"loc": (2, 2),
"pop": [{
"species": "Herbivore",
"age": 5,
"weight": 20
} for _ in range(100)]
}],
tmean=True)
sim.simulate(num_years=200, vis_years=None)
n_animals += sim.mean["Herbivore"]
assert n_animals / 50 == pt.approx(200, abs=25)
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_herbivore_feed():
"""Many testes for the method 'herbivore_feed()':
1. if the fodder reduces when a animal eats it.
2. if the weight of the animal increases after eat.
3. if the fitness of the animal updates after eat.
"""
island_map = "OOO\nOJO\nOOO"
ini_pop = [{
"loc": (1, 1),
"pop": [{
"species": "Herbivore",
"age": 10,
"weight": 10
}]
}]
t = BioSim(island_map, ini_pop, None)
loc = (1, 1)
previous_fodder = t.island.cells[loc].fodder
previous_herbivore_weight = t.island.cells[loc].population['Herbivore'][
0].weight
previous_herbivore_fitness = t.island.cells[loc].population['Herbivore'][
0].fitness
t.island.cells[loc].herbivore_feed()
afterwards_fodder = t.island.cells[loc].fodder
afterwards_herbivore_weight = t.island.cells[loc].population['Herbivore'][
0].weight
afterwards_herbivore_fitness = t.island.cells[loc].population['Herbivore'][
0].fitness
assert previous_fodder > afterwards_fodder
assert previous_herbivore_weight < afterwards_herbivore_weight
assert previous_herbivore_fitness is not afterwards_herbivore_fitness
def test_migration():
"""This tests the migration method checking if the animals have
moved to the all 4th neighbour cells."""
island_map = "OOOOO\nOMJMO\nOJDJO\nOMJMO\nOOOOO"
ini_pop = [{
"loc": (2, 2),
"pop": [{
"species": "Herbivore",
"age": np.random.randint(1, 5),
"weight": np.random.randint(20, 40)
} for _ in range(1000)],
}]
t, loc = BioSim(island_map, ini_pop, 1), (2, 2)
for k, v in t.island.habitable_cells.items():
v.migrate(t.island.neighbour_cells(k))
for k, v in t.island.habitable_cells.items():
v.add_new_migrated()
north_neighbour = t.island.cells[(1, 2)].population['Herbivore']
south_neighbour = t.island.cells[(3, 2)].population['Herbivore']
west_neighbour = t.island.cells[(2, 1)].population['Herbivore']
east_neighbour = t.island.cells[(2, 3)].population['Herbivore']
assert north_neighbour is not 0
assert south_neighbour is not 0
assert west_neighbour is not 0
assert east_neighbour is not 0
def test_animal_got_old():
"""Test if the method 'get_old()' correctly increases in 1 year all
the animal_objects stored in a specific geo_object"""
island_map = "OOOOO\nOJJJO\nOOOOO"
ini_pop = [{
"loc": (1, 2),
"pop": [{
"species": "Herbivore",
"age": 5,
"weight": 20
}, {
"species": "Herbivore",
"age": 2,
"weight": 20
}],
}]
t, loc = BioSim(island_map, ini_pop, None), (1, 2)
geo_object = t.island.habitable_cells[loc]
herb_object_1 = geo_object.population['Herbivore'][0]
herb_object_2 = geo_object.population['Herbivore'][1]
herb_young_1 = herb_object_1.age
herb_young_2 = herb_object_2.age
geo_object.get_old()
herb_older_1 = herb_object_1.age
herb_older_2 = herb_object_2.age
assert herb_older_1 is (herb_young_1 + 1)
assert herb_older_2 is (herb_young_2 + 1)
def test_initial_population():
"""Test that population can be placed on construction"""
BioSim(island_map="WWWW\nWLHW\nWWWW",
ini_pop=[{
'loc': (2, 2),
'pop': [{
'species': 'Herbivore',
'age': 1,
'weight': 10.
}, {
'species': 'Carnivore',
'age': 1,
'weight': 10.
}]
}, {
'loc': (2, 3),
'pop': [{
'species': 'Herbivore',
'age': 1,
'weight': 10.
}, {
'species': 'Carnivore',
'age': 1,
'weight': 10.
}]
}],
seed=1)
def test_animal_loose_weight():
"""Test if the method 'lose_weight()' correctly looses the weight
of the animal"""
island_map = "OOOOO\nOJJJO\nOOOOO"
ini_pop = [{
"loc": (1, 2),
"pop": [{
"species": "Herbivore",
"age": 5,
"weight": 20
}, {
"species": "Herbivore",
"age": 2,
"weight": 20
}],
}]
t, loc = BioSim(island_map, ini_pop, None), (1, 2)
geo_object = t.island.habitable_cells[loc]
herb_object_1 = geo_object.population['Herbivore'][0]
herb_object_2 = geo_object.population['Herbivore'][1]
before_weight_herb1 = herb_object_1.weight
before_weight_herb2 = herb_object_2.weight
geo_object.lose_weight()
after_weight_herb1 = herb_object_1.weight
after_weight_herb2 = herb_object_2.weight
assert before_weight_herb1 > after_weight_herb1
assert before_weight_herb2 > after_weight_herb2
def test_get_population_numbers():
"""Test if the method 'get_population_numbers()' correctly gets the
entire population of each geo_object and returns a dictionary, such
that: {'Row': [], 'Col': [], 'Herbivore': [], 'Carnivore': []}"""
island_map = "OOOOO\nOJJJO\nOOOOO"
ini_pop = [
{"loc": (1, 1),
"pop": [{"species": "Herbivore", "age": 5, "weight": 20},
{"species": "Herbivore", "age": 5, "weight": 20},
{"species": "Carnivore", "age": 5, "weight": 20}]},
{"loc": (1, 2),
"pop": [{"species": "Herbivore", "age": 5, "weight": 20},
{"species": "Carnivore", "age": 5, "weight": 20}]}]
t = BioSim(island_map, ini_pop, None)
pop = t.island.get_population_numbers()
row_loc, col_loc = pop['Row'][0], pop['Col'][0]
pop_herb, pop_carn = pop['Herbivore'][0], pop['Carnivore'][0]
assert (row_loc and col_loc and pop_herb and pop_carn) is 0
row_loc, col_loc = pop['Row'][6], pop['Col'][6]
pop_herb, pop_carn = pop['Herbivore'][6], pop['Carnivore'][6]
assert row_loc and col_loc is 1 and pop_herb is 2 and pop_carn is 1
row_loc, col_loc = pop['Row'][7], pop['Col'][7]
pop_herb, pop_carn = pop['Herbivore'][7], pop['Carnivore'][7]
assert row_loc is 1 and col_loc is 2 and pop_herb and pop_carn is 1
def test_animal_got_old():
"""Test if the method 'get_old()' correctly increases in 1 year a
specie_object age"""
island_map = "OOOOO\nOJJJO\nOOOOO"
ini_pop = [{
"loc": (1, 2),
"pop": [{
"species": "Herbivore",
"age": 5,
"weight": 20
}, {
"species": "Carnivore",
"age": 4,
"weight": 20
}],
}]
t, loc = BioSim(island_map, ini_pop, None), (1, 2)
herb_object = t.island.habitable_cells[loc].population['Herbivore'][0]
carn_object = t.island.habitable_cells[loc].population['Carnivore'][0]
herb_age_1 = herb_object.age
carn_age_1 = carn_object.age
herb_object.get_old()
carn_object.get_old()
herb_age_2 = herb_object.age
carn_age_2 = carn_object.age
assert herb_age_2 is (herb_age_1 + 1)
assert carn_age_2 is (carn_age_1 + 1)
def test_simulation_large_island():
"""Test to see that a island with column or row length bigger than 23
initialize self._large_island.
"""
map = """\
OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO
ODDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDO
ODDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDO
ODDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDO
ODDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDO
ODDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDO
ODDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDO
ODDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDO
OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO"""
sim = BioSim(island_map=map, ini_pop=[], seed=1)
sim.simulate(1, 1)
assert sim._large_island
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_change_weight_simulation():
""" Tests that a herbivore living in a jungle cell will gain weight. """
sim = BioSim(island_map="OOO\nOJO\nOOO",
ini_pop=[{
"loc": (1, 1),
"pop": [{
"species": "Herbivore",
"age": 1,
"weight": 35.0
}]
}],
seed=0)
assert sim.map.array_map[1, 1].present_herbivores[0].weight == 35.0
sim.simulate(5)
assert sim.map.array_map[1, 1].present_herbivores[0].weight != 35.0
def test_invalid_boundary(bad_boundary):
"""Non-ocean boundary must raise error"""
with pytest.raises(ValueError):
BioSim(
island_geography="{}OO\nOJO\nOOO".format(bad_boundary),
initial_population=[],
seed=1,
)
def test_sim_with_seed(self):
sim1 = BioSim(seed=1)
sim1.clean_simulation(10)
num_sim1 = sim1.num_animals_per_species
sim2 = BioSim(seed=1)
sim2.clean_simulation(10)
num_sim2 = sim2.num_animals_per_species
assert num_sim1 == num_sim2
def test_simulate(self):
sim = BioSim(img_base=r'test_sim_every_second_img')
sim.simulate(10, img_years=2)
assert os.path.isfile(r'test_sim_every_second_img' + '_00005' + '.png')
assert not os.path.isfile(r'test_sim_every_second_img' + '_00006' +
'.png')
with pytest.raises(ValueError):
sim = BioSim(img_base=r'test_sim')
sim.simulate(10, 5, 4)
def test_map_from_str(self):
"""
Test that the map string is properly saved
"""
island_map = """WWW
WDW
WWW"""
sim = BioSim(island_map=island_map)
assert sim._island.map_str == island_map
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},
)