def test_script_reads_parameter_ranges_file_and_writes_files_correctly_in_different_folders(self, createParameterRangesFile):
createParameterRangesFile(multi=True)
self.l = Launcher('simulations', 'parameter_ranges.txt')
self.l.writeParameterFilesInFolders()
self.subfoldernames = ['pgg_first1.1secnd2.3third3.4','pgg_first1.1secnd2.3third3.5','pgg_first1.2secnd2.3third3.4','pgg_first1.2secnd2.3third3.5']
self.parvalues = [[1.1,2.3,3.4],[1.1,2.3,3.5],[1.2,2.3,3.4],[1.2,2.3,3.5]]
self.inputfiles = [INITIALISATION_FILE, INITIAL_PHENOTYPES_FILE, INITIAL_TECHNOLOGY_FILE, PARAMETER_FILE, FITNESS_PARAMETERS_FILE]
for comb in range(len(self.parvalues)):
folder = self.subfoldernames[comb]
assert os.path.exists('simulations/'+folder), "did not create specific simulation file: {0}".format(os.listdir('simulations'))
fileslist = os.listdir('simulations/'+folder)
try:
for file in self.inputfiles:
assert file in fileslist
pars = fman.extractColumnFromFile('simulations/'+folder+'/'+FITNESS_PARAMETERS_FILE, 0, str)
vals = fman.extractColumnFromFile('simulations/'+folder+'/'+FITNESS_PARAMETERS_FILE, 1, float)
assert pars == ['first','secnd','third'], "wrong parameter name"
assert pytest.approx(vals) == self.parvalues[comb], "wrong parameter value"
except AssertionError as e:
shutil.rmtree('simulations')
os.remove('parameter_ranges.txt')
assert False, "one or more parameter value(s) missing. File contents: {0},{1}".format(pars,vals)
shutil.rmtree('simulations')
os.remove('parameter_ranges.txt')
def test_demography_file_has_correct_output(self, pseudorandom, runSim,
clearOutputFiles):
pseudorandom(69)
self.pop = Pop(inst='test/test')
self.pop.mutationRate = 0.1
self.pop.numberOfDemes = 5
self.pop.initialDemeSize = 8
self.pop.fitnessParameters.clear()
self.pop.fitnessParameters.update({
"fb": 10,
"b": 0.5,
"c": 0.05,
"gamma": 0.01
})
self.pop.createAndPopulateDemes()
expDemog = []
for gen in range(5):
self.pop.lifecycle()
assert self.pop.numberOfDemes == 5
expDemog.append(self.pop.demography / self.pop.numberOfDemes)
pseudorandom(69)
runSim()
obsDemog = fman.extractColumnFromFile('test/test/out_demography.txt',
0, float)
assert obsDemog == expDemog, "unexpected value of group size has been printed"
clearOutputFiles('test/test/')
def test_initialisation_values_provided(self):
self.pathToFile = fman.getPathToFile(filename=INITIALISATION_FILE,
dirname='test/test')
self.pars = fman.extractColumnFromFile(self.pathToFile, 1, int)
for par in self.pars:
assert type(
par
) is int, "Did you insert a non integer value for deme number, deme size or generation number?"
assert par > 0, "Did you insert a negative value for deme number, deme size or generation number?"
def test_population_is_initialised_with_right_values(
self, objectAttributesExist, objectAttributesValues):
# First, the population is initialised according to the initialisation settings
self.pathToFile = fman.getPathToFile(filename=INITIALISATION_FILE,
dirname='test/test')
self.attributeNames = fman.extractColumnFromFile(
self.pathToFile, 0, str)
self.attributeValues = fman.extractColumnFromFile(
self.pathToFile, 1, int)
self.population = Pop(inst='test/test')
testAttr, whichAttr = objectAttributesExist(self.population,
self.attributeNames)
assert testAttr, "Population does not have attribute(s) {0}".format(
whichAttr)
testVal, attributes, expected, observed = objectAttributesValues(
self.population, self.attributeNames, self.attributeValues)
assert testVal, "Population has {1}={2} instead of {3}".format(
attributes, expected, observed)
def test_single_par_combination_gets_a_full_folder(self):
self.l = Launcher('simulations', 'parameter_ranges.txt')
self.l.createFolder(self.l.metafolder)
self.l.writeParameterFilesInFolder(fitfun='pgg', pname=('small','big'), pval=(0.3,0.5))
self.subfoldername = 'pgg_small0.3big0.5'
assert os.path.exists('simulations/'+self.subfoldername), "create subfolder"
self.fileslist = os.listdir('simulations/'+self.subfoldername)
self.inputfiles = [INITIALISATION_FILE, INITIAL_PHENOTYPES_FILE, INITIAL_TECHNOLOGY_FILE, PARAMETER_FILE, FITNESS_PARAMETERS_FILE]
try:
for file in self.inputfiles:
assert file in self.fileslist
pars = fman.extractColumnFromFile('simulations/'+self.subfoldername+'/'+FITNESS_PARAMETERS_FILE, 0, str)
vals = fman.extractColumnFromFile('simulations/'+self.subfoldername+'/'+FITNESS_PARAMETERS_FILE, 1, float)
assert pars == ['small','big'], "wrong parameter name"
assert vals == [0.3,0.5], "wrong parameter value"
shutil.rmtree('simulations')
except AssertionError as e:
shutil.rmtree('simulations')
assert False, "one or more parameter value(s) missing. File contents: {0},{1}".format(pars,vals)
def __init__(self, fit_fun='pgg', inst=None, mutationBoundaries=True):
logging.basicConfig(level=logging.INFO,
format='[%(asctime)s]::%(levelname)s %(message)s',
datefmt='%Y.%m.%d - %H:%M:%S')
logging.info('Creating population')
if inst is None:
self.pathToInputFiles = PARAMETER_FOLDER
self.pathToOutputFiles = OUTPUT_FOLDER
else:
self.pathToInputFiles = inst
self.pathToOutputFiles = inst
self.pathToInitFile = fman.getPathToFile(filename=INITIALISATION_FILE,
dirname=self.pathToInputFiles)
self.attrs = fman.extractColumnFromFile(self.pathToInitFile, 0, str)
self.vals = fman.extractColumnFromFile(self.pathToInitFile, 1, int)
for attr, val in zip(self.attrs, self.vals):
setattr(self, attr, val)
self.pathToPhenFile = fman.getPathToFile(
filename=INITIAL_PHENOTYPES_FILE, dirname=self.pathToInputFiles)
with open(self.pathToPhenFile) as f:
self.initialPhenotypes = [float(line) for line in f.readlines()]
self.pathToTechFile = fman.getPathToFile(
filename=INITIAL_TECHNOLOGY_FILE, dirname=self.pathToInputFiles)
self.initialTechnologyLevel = fman.extractColumnFromFile(
self.pathToTechFile, 0, float)[0]
self.pathToParFile = fman.getPathToFile(filename=PARAMETER_FILE,
dirname=self.pathToInputFiles)
self.parattrs = fman.extractColumnFromFile(self.pathToParFile, 0, str)
self.parvals = fman.extractColumnFromFile(self.pathToParFile, 1, float)
for parattr, parval in zip(self.parattrs, self.parvals):
setattr(self, parattr, parval)
self.pathToFitFile = fman.getPathToFile(
filename=FITNESS_PARAMETERS_FILE, dirname=self.pathToInputFiles)
self.fitattrs = fman.extractColumnFromFile(self.pathToFitFile, 0, str)
self.fitvals = fman.extractColumnFromFile(self.pathToFitFile, 1, float)
self.fitnessParameters = {}
for fitattr, fitval in zip(self.fitattrs, self.fitvals):
self.fitnessParameters[fitattr] = fitval
if hasattr(self, "individualBaseResources") == False:
setattr(self, "individualBaseResources", 1)
self.fit_fun = fit_fun
self.mutationBoundaries = mutationBoundaries
def test_resources_file_has_correct_output(self, pseudorandom, runSim,
clearOutputFiles):
parameters = {
"gamma": 0.01,
"p": 0.6,
"q": 0.9,
"d": 0.2,
"productionTime": 1,
"alphaResources": 0.6,
"rb": 10,
"atech": 2,
"btech": 0.2,
"betaTech": 0.6
}
pseudorandom(54)
self.pop = Pop(fit_fun='technology', inst='test/test')
self.pop.mutationRate = 0.1
self.pop.numberOfDemes = 5
self.pop.initialDemeSize = 8
self.pop.fitnessParameters.clear()
self.pop.fitnessParameters.update(parameters)
self.pop.createAndPopulateDemes()
expTotRes = []
for gen in range(5):
self.pop.lifecycle()
assert self.pop.numberOfDemes == 5
collectDemeTotRes = []
for deme in self.pop.demes:
collectDemeTotRes.append(deme.totalResources)
expTotRes.append(sum(collectDemeTotRes) / len(collectDemeTotRes))
pseudorandom(54)
runSim(fun='technology', pars=parameters)
obsTotRes = fman.extractColumnFromFile('test/test/out_resources.txt',
0, float)
assert obsTotRes == expTotRes, "unexpected value of total resources has been printed"
clearOutputFiles('test/test/')
def test_consensus_file_has_correct_output(self, pseudorandom, runSim,
clearOutputFiles):
parameters = {
"gamma": 0.01,
"aconsensus": 3,
"bconsensus": 2,
"epsilon": 0.01,
"aquality": 4,
"alphaquality": 0.9,
"alphaResources": 0.8,
"techcapital": 50,
"rb": 10
}
pseudorandom(22)
self.pop = Pop(fit_fun='debate', inst='test/test')
self.pop.mutationRate = 0.1
self.pop.numberOfDemes = 5
self.pop.initialDemeSize = 8
self.pop.fitnessParameters.clear()
self.pop.fitnessParameters.update(parameters)
self.pop.createAndPopulateDemes()
expCons = []
for gen in range(5):
self.pop.lifecycle()
assert self.pop.numberOfDemes == 5
collectDemeCons = []
for deme in self.pop.demes:
collectDemeCons.append(deme.politicsValues["consensusTime"])
expCons.append(sum(collectDemeCons) / len(collectDemeCons))
pseudorandom(22)
runSim(fun='debate', pars=parameters)
obsCons = fman.extractColumnFromFile('test/test/out_consensus.txt', 0,
float)
assert obsCons == expCons, "unexpected value of total resources has been printed"
clearOutputFiles('test/test/')