def test_test_t_threshold(self):
current_working_directory = os.getcwd()
filepath = current_working_directory + "/GENOMICS_parameter.py"
gnx.make_parameters_file(filepath)
params = exec(open(filepath, 'r').read())
pop = None
self.assertEquals(True, burnin._test_t_threshold(pop, 2))
def test_test_adf_threshold(self):
current_working_directory = os.getcwd()
filepath = current_working_directory + "/GENOMICS_parameter.py"
gnx.make_parameters_file(filepath)
params = exec(open(filepath, 'r').read())
pop = None #TODO: place holder for pop after testing model
self.assertEquals(True, burnin._test_adf_threshold(pop, 1))
def test_make_defined_scape(self):
current_working_directory = os.getcwd()
filepath = current_working_directory + "/GENOMICS_parameter.py"
gnx.make_parameters_file(filepath)
params = exec(open(filepath, 'r').read())
dim = params.land.main.dim
res = params.land.main.res
ulc = params.land.main.ulc
def test_write_stats(self):
current_working_directory = os.getcwd()
filepath = current_working_directory + "/GENOMICS_parameter.py"
gnx.make_parameters_file(filepath)
params = exec(open(filepath, 'r').read())
land = landscape._make_landscape(params)
pop = population._make_population(land, params)
stats._calc_ld(pop)
def testMakeCommunity(self):
current_working_directory = os.getcwd()
filepath = current_working_directory + "/GENOMICS_parameter.py"
gnx.make_parameters_file(filepath)
params = exec(open(filepath, 'r').read())
land = landscape._make_landscape(params)
com = community._make_community(land, params)
self.assertEqual(com.n_pops, len(params.comm.pops))
self.assertEqual(com.t, -1)
def make_model_test_with_params(self):
filenames = set(os.listdir('.'))
g.make_parameters_file()
new_filenames = set(os.listdir('.'))
filename = [*new_filenames - filenames][0]
try:
g.make_model(filename)
except:
print("System error, fail make community test.")
def make_landscape_test(self):
filenames = set(os.listdir('.'))
g.make_parameters_file()
new_filenames = set(os.listdir('.'))
filename = [*new_filenames - filenames][0]
try:
g.make_landscape(filename)
except:
print("System error, fail make landscape test.")
def test_make_land(self):
current_working_directory = os.getcwd()
filepath = current_working_directory + "/GENOMICS_parameter.py"
gnx.make_parameters_file(filepath)
params = exec(open(filepath, 'r').read())
dim = params.land.main.dim
res = params.land.main.res
ulc = params.land.main.ulc
land = landscape._make_landscape(params, 2)
self.assertIsInstance(land, landscape.Landscape)
def test_make_random_scape(self):
current_working_directory = os.getcwd()
filepath = current_working_directory + "/GENOMICS_parameter.py"
gnx.make_parameters_file(filepath)
params = exec(open(filepath, 'r').read())
dim = params.land.main.dim
try:
random_scape = landscape._make_random_lyr(dim, 10)
except:
print("Can not make the random scape")
def make_genomic_architecture_test(self):
filenames = set(os.listdir('.'))
g.make_parameters_file()
new_filenames = set(os.listdir('.'))
filename = [*new_filenames - filenames][0]
landscape = g.make_landscape(filename)
try:
g.make_genomic_architecture(filename, landscape)
except:
print("System error, fail make community test.")
def make_population_test(self):
filenames = set(os.listdir('.'))
g.make_parameters_file()
new_filenames = set(os.listdir('.'))
filename = [*new_filenames - filenames][0]
landscape = g.make_landscape(filename)
try:
g.make_population(landscape, filename)
except:
print("System error, fail make population test.")
def test_make_recomb_array(self):
current_working_directory = os.getcwd()
filepath = current_working_directory + "/GENOMICS_parameter.py"
gnx.make_parameters_file(filepath)
params = exec(open(filepath, 'r').read())
g_params = params.genome
try:
genome._make_recomb_array(g_params, 1)
except:
print("Can't make the recomb array")
def test_make_genomic_architecture(self):
current_working_directory = os.getcwd()
filepath = current_working_directory + "/GENOMICS_parameter.py"
gnx.make_parameters_file(filepath)
params = exec(open(filepath, 'r').read())
g_params = params.genome
land = gnx.make_landscape(params)
Genomic_Architecture = gnx.make_genomic_architecture(params, land)
genome_arch = genome._make_genomic_architecture(params, land)
self.assertIsInstance(genome_arch, Genomic_Architecture)
def test_make_population(self):
current_working_directory = os.getcwd()
filepath = current_working_directory + "/GENOMICS_parameter.py"
gnx.make_parameters_file(filepath)
params = exec(open(filepath, 'r').read())
land = gnx.make_landscape(params)
#TODO: Need to update here
#in order to make population we need to have land, params, pop_params
pop = population._make_population(land, "aribitrary name", params)
self.assertIsInstance(pop, population.Population)
def test_make_individual_simple_case(self):
current_working_directory = os.getcwd()
filepath = current_working_directory + "/GNX_test_params.py"
gnx.make_parameters_file(filepath)
params = exec(open(filepath, 'r').read())
land = gnx.make_landscape(params)
genome_arch = gnx.structs.genome._make_genomic_architecture(params,
land)
ind = gnx.structs.individual._make_individual(1, True, None,
genome_arch)
self.assertIsInstance(ind, gnx.structs.individual.Individual)
print("It's an individual!")
def make_params_file_test(self):
try:
g.make_parameters_file()
except:
print("System error, fail make parameter faile test.")