def setUp(self):
self.ind_1 = Individual.Individual("01")
self.ind_2 = Individual.Individual("02")
self.ind_3 = Individual.Individual("03")
self.fam_1 = Family.Family("01")
self.fam_2 = Family.Family("02")
def tearDown(self):
self.ind_1 = Individual.Individual("01")
self.ind_2 = Individual.Individual("02")
self.ind_3 = Individual.Individual("03")
self.fam_1 = Family.Family("01")
self.fam_2 = Family.Family("02")
def run_algorithm(sched, n=NUM_GENERATIONS, m=POP_SIZE):
"""
Runs the genetic algorithm over n generations with a population of size m
using the provided schedule constraint and returns the found solution.
"""
# generate an initial population of individuals
population = []
for i in range(m):
soln = gen_rand_solution(sched.assignments)
population.append(Individual(soln, fitness(soln, sched)))
# evolve over n generations!
for i in range(n):
new_gen = []
for i in range(m):
# select 2 parents via tournament selection and breed them to
# create a child for the new generation
parents = tournament(population)
child_soln = crossover(parents[0].todos, parents[1].todos)
child = Individual(child_soln, fitness(child_soln, sched))
new_gen.append(child)
population = new_gen
# sort the final population by fitness and return the best one
population.sort(key=lambda indiv: indiv.fitness, reverse=True)
return population[0]
def create_model(cpr, tmm, poi, dmn, dmx):
model_map = collections.defaultdict(list)
infected = poi
#Creates young people
for element in range(round(int(cpr) * 0.9045)):
x = random.randint(0, tmm - 1)
y = random.randint(0, tmm - 1)
element = Individual((x, y), True)
if infected > poi - (poi * 0.9045):
element.infect(dmn, dmx)
infected -= 1
key = element.get_destination()
if key in model_map:
model_map[key].append(element)
else:
model_map[key] = [element]
#Creates old people
for element in range(round(int(cpr) * 0.0955)):
x = random.randint(0, tmm - 1)
y = random.randint(0, tmm - 1)
element = Individual((x, y), False)
if infected > 0:
element.infect(dmn, dmx)
infected -= 1
key = element.get_destination()
if key in model_map:
model_map[key].append(element)
else:
model_map[key] = [element]
return model_map
def test_were_parents_over_14(self):
""" test were_parents_over_14 method """
# husband is 20 and wife is 14 at the marriage date -> Both are over 14 -> True
husband: Individual = Individual(_id="I0",
birt={'date': "19 SEP 1995"})
wife: Individual = Individual(_id="I1", birt={'date': "3 JAN 2000"})
individuals: List[Individual] = [husband, wife]
family: Family = Family(_id="F0",
husb=husband.id,
wife=wife.id,
marr={'date': "11 FEB 2015"})
self.assertTrue(us.were_parents_over_14(family, individuals))
# husband 11, wife 20 -> Only wife is over 14 -> False
husband: Individual = Individual(_id="I2", birt={'date': "2 MAR 2007"})
wife: Individual = Individual(_id="I3", birt={'date': "11 FEB 2000"})
individuals: List[Individual] = [husband, wife]
family: Family = Family(_id="F1",
husb=husband.id,
wife=wife.id,
marr={'date': "11 FEB 2019"})
self.assertFalse(us.were_parents_over_14(family, individuals))
# husband 17, wife 10 -> Only husband is over 14 -> False
husband: Individual = Individual(_id="I4",
birt={'date': "22 AUG 2000"})
wife: Individual = Individual(_id="I5", birt={'date': "5 DEC 2007"})
individuals: List[Individual] = [husband, wife]
family: Family = Family(_id="F2",
husb=husband.id,
wife=wife.id,
marr={'date': "11 FEB 2018"})
self.assertFalse(us.were_parents_over_14(family, individuals))
# husband 12, wife 12 -> Both are under 14 -> False
husband: Individual = Individual(_id="I6",
birt={'date': "19 SEP 2007"})
wife: Individual = Individual(_id="I7", birt={'date': "3 JAN 2008"})
individuals: List[Individual] = [husband, wife]
family: Family = Family(_id="F3",
husb=husband.id,
wife=wife.id,
marr={'date': "11 FEB 2020"})
self.assertFalse(us.were_parents_over_14(family, individuals))
# husband 18, wife 16 -> Both are over 14 -> True
husband: Individual = Individual(_id="I8", birt={'date': "7 FEB 1980"})
wife: Individual = Individual(_id="I9", birt={'date': "8 FEB 1982"})
individuals: List[Individual] = [husband, wife]
family: Family = Family(_id="F4",
husb=husband.id,
wife=wife.id,
marr={'date': "11 FEB 1998"})
self.assertTrue(us.were_parents_over_14(family, individuals))
def parse_single_individual(gedlist, index, xref):
"""
Parses a single individual from a GEDCOM giving the starting index of an
'INDI' tag. Returns an Individual class
"""
indiv = Individual(xref)
date_type = None
for gedline in gedlist[index + 1:]:
if gedline.level == 0:
break
if gedline.tag == "NAME":
indiv.name = gedline.args
if gedline.tag == "SEX":
indiv.sex = gedline.args[0]
if gedline.tag == "BIRT":
date_type = "BIRT"
if gedline.tag == "DEAT":
date_type = "DEAT"
if gedline.tag == "FAMC":
indiv.famc.append(gedline.args[0])
if gedline.tag == "FAMS":
indiv.fams.append(gedline.args[0])
# This assumes the following date tag corresponds to prev tag
if gedline.tag == "DATE":
if date_type == "BIRT":
# Store birthdate as datetime object
indiv.birthdate = datetime(
int(gedline.args[2]),
datetime.strptime(gedline.args[1], '%b').month,
int(gedline.args[0]))
date_type = None
elif date_type == "DEAT":
# Store death as datetime object
indiv.death = datetime(
int(gedline.args[2]),
datetime.strptime(gedline.args[1], '%b').month,
int(gedline.args[0]))
date_type = None
else:
print "ERROR"
return indiv
def generate_classes(
lines: List[str]) -> Tuple[List[Individual], List[Family]]:
""" get lines read from a .ged file """
individuals: List[Individual] = []
families: List[Family] = []
current_record: Optional[Individual, Family] = None
current_tag: Optional[str] = None
for line in lines:
row_fields: List[str] = line.rstrip("\n").split(' ', 2)
pattern_type = pattern_finder(line)
if pattern_type == 'ZERO_1':
current_record = Individual(
) if row_fields[2] == 'INDI' else Family()
(individuals if isinstance(current_record, Individual) else families) \
.append(current_record)
current_record.id = row_fields[1]
elif pattern_type == 'ZERO_2':
pass # nothing to do with this
elif pattern_type == 'NO_ARGUMENT':
if row_fields[0] == '1':
setattr(current_record, row_fields[1].lower(), {})
current_tag = row_fields[1].lower()
elif pattern_type == 'ARGUMENT':
if row_fields[0] == '1':
if isinstance(getattr(current_record, row_fields[1].lower()),
list):
current_list = getattr(
current_record,
row_fields[1].lower()) + [row_fields[2]]
setattr(current_record, row_fields[1].lower(),
current_list)
else:
setattr(current_record, row_fields[1].lower(),
row_fields[2])
elif row_fields[0] == '2':
setattr(current_record, current_tag,
{row_fields[1].lower(): row_fields[2]})
return individuals, families
def mate(individual1: Individual, individual2: Individual) -> Individual:
mutation_probability = random.choice(
(individual1.mutation_probability, individual2.mutation_probability))
genome = set()
for genes in zip_longest(individual1.genome, individual2.genome):
if None in genes:
genes = [g for g in genes if g]
gene: Gene = random.choice(genes)
if random.random() <= mutation_probability:
gene = mutate(gene)
genome.add(gene)
if random.random() < mutation_probability:
genome.add(Gene())
return Individual(
mutate_float(mutation_probability, mutation_probability),
random.choice(
(individual1.consumption_rate, individual2.consumption_rate)),
genome,
)
def indi_stmt(self, *ts):
(args, ) = ts
individual = Individual.from_args(args)
self.individuals[individual.id_] = individual
return individual
i = 1
for key in err_list:
err_chart.add_row([i, err_list[key]])
i += 1
write_file.write("Individual\n")
write_file.write(indi_chart.get_string() + "\n")
write_file.write("Family\n")
write_file.write(fam_chart.get_string() + "\n")
write_file.write("Error\n")
if (i == 1): write_file.write("\nNo Errors found!")
else: write_file.write(err_chart.get_string())
write_file.close()
if __name__ == "__main__":
from models import Individual
from models import Family
indi_1 = Individual.Individual("01")
indi_2 = Individual.Individual("02")
fam_1 = Family.Family("10")
fam_2 = Family.Family("20")
indi_1.add_to_family(fam_1)
indi_2.add_to_family(fam_2)
fam_1.set_husband(indi_1)
fam_1.set_wife(indi_2)
fam_2.set_husband(indi_2)
fam_2.set_wife(indi_1)
print_pretty_table([indi_1, indi_2], [fam_1, fam_2], [])
return len(subject.genome.intersection(object_.genome)) * fitness
def choose_partner(individual: Individual, population: Population,
fitnesses: Dict[Individual, float]):
return max(population,
key=lambda i: evaluate_attractiveness(
individual, i, fitnesses.get(individual, 0)))
def consume_resources(cosmos: Cosmos) -> Tuple[Population, float]:
survivors = []
resources = cosmos.resources
for individual in sorted(cosmos.population,
key=lambda i: evaluate(cosmos.environment, i)):
if resources >= individual.consumption_rate:
resources -= individual.consumption_rate
survivors.append(individual)
else:
break
return survivors, resources
if __name__ == '__main__':
i1 = Individual()
i2 = Individual()
i3 = mate(i1, i2)
print(i1, i2, i3, sep='\n')
env = [Constraint() for _ in range(10)]
print(evaluate(env, i3))
def test_birth_before_death_of_parents(self):
""" test birth_before_death_of_parents method """
# mother and father are alive (no death date)
husband: Individual = Individual(_id="I0")
wife: Individual = Individual(_id="I1")
child: Individual = Individual(_id="I2", birt={'date': "4 OCT 2000"})
individuals: List[Individual] = [husband, wife, child]
family: Family = Family(_id="F0", husb=husband.id, wife=wife.id)
family.chil.append(child.id)
self.assertTrue(us.birth_before_death_of_parents(family, individuals))
# child born on: mother death, 270 day after father death
husband: Individual = Individual(_id="I0", deat={'date': "8 JAN 2000"})
wife: Individual = Individual(_id="I1", deat={'date': "4 OCT 2000"})
child: Individual = Individual(_id="I2", birt={'date': "4 OCT 2000"})
individuals: List[Individual] = [husband, wife, child]
family: Family = Family(_id="F1", husb=husband.id, wife=wife.id)
family.chil.append(child.id)
self.assertTrue(us.birth_before_death_of_parents(family, individuals))
# child born on: 1 day before mother death, 1 day after father death
husband: Individual = Individual(_id="I0", deat={'date': "3 OCT 2000"})
wife: Individual = Individual(_id="I1", deat={'date': "5 OCT 2000"})
child: Individual = Individual(_id="I2", birt={'date': "4 OCT 2000"})
individuals: List[Individual] = [husband, wife, child]
family: Family = Family(_id="F2", husb=husband.id, wife=wife.id)
family.chil.append(child.id)
self.assertTrue(us.birth_before_death_of_parents(family, individuals))
# child born on: after mother death, 10 day after father death
husband: Individual = Individual(_id="I0", deat={'date': "3 OCT 2000"})
wife: Individual = Individual(_id="I1", deat={'date': "12 OCT 2000"})
child: Individual = Individual(_id="I2", birt={'date': "13 OCT 2000"})
individuals: List[Individual] = [husband, wife, child]
family: Family = Family(_id="F3", husb=husband.id, wife=wife.id)
family.chil.append(child.id)
self.assertFalse(us.birth_before_death_of_parents(family, individuals))
# child born on: before mother death, 1 year after father death
husband: Individual = Individual(_id="I0",
deat={'date': "11 OCT 1999"})
wife: Individual = Individual(_id="I1", deat={'date': "12 OCT 2000"})
child: Individual = Individual(_id="I2", birt={'date': "11 OCT 2000"})
individuals: List[Individual] = [husband, wife, child]
family: Family = Family(_id="F4", husb=husband.id, wife=wife.id)
family.chil.append(child.id)
self.assertFalse(us.birth_before_death_of_parents(family, individuals))
def test_less_than_150(self):
individual = Individual(birt={'date': "20 Mar 1985"})
individual.deat = {'date': "15 Aug 2008"}
self.assertTrue(us.less_than_150(individual))
individual = Individual(birt={'date': "15 JAN 2000"})
self.assertTrue(us.less_than_150(individual))
individual = Individual(birt={'date': "15 Feb 2012"})
individual.deat = {'date': "21 JAN 2000"}
self.assertFalse(us.less_than_150(individual))
individual = Individual(birt={'date': "15 JAN 1500"})
self.assertFalse(us.less_than_150(individual))
individual = Individual(birt={'date': "15 JAN 2006"})
individual.deat = {'date': "15 JAN 1200"}
self.assertFalse(us.less_than_150(individual))
def test_divorce_before_death(self):
husband: Individual = Individual(_id="I0", deat={'date': "1 JAN 2020"})
wife: Individual = Individual(_id="I1", deat={'date': "2 JAN 2019"})
individuals: List[Individual] = [husband, wife]
family: Family = Family(husb=husband.id,
wife=wife.id,
div={'date': "11 FEB 1999"})
self.assertTrue(us.divorce_before_death(family, individuals))
"""Husband and wife they both die before their divorce so False (not possible)"""
husband: Individual = Individual(_id="I2", deat={'date': "1 JAN 2000"})
wife: Individual = Individual(_id="I3", deat={'date': "2 JAN 2000"})
individuals: List[Individual] = [husband, wife]
family: Family = Family(husb=husband.id,
wife=wife.id,
div={'date': "11 FEB 2001"})
self.assertFalse(us.divorce_before_death(family, individuals))
""" Husband dies before divorce wife is alive so False (not possible)"""
husband: Individual = Individual(_id="I4", deat={'date': "1 JAN 2000"})
wife: Individual = Individual(_id="I5")
individuals: List[Individual] = [husband, wife]
family: Family = Family(husb=husband.id,
wife=wife.id,
div={'date': "11 FEB 2001"})
self.assertFalse(us.divorce_before_death(family, individuals))
""" Husband dies after divorce and wife is alive so true"""
husband: Individual = Individual(_id="I4", deat={'date': "1 JAN 2002"})
wife: Individual = Individual(_id="I5")
individuals: List[Individual] = [husband, wife]
family: Family = Family(husb=husband.id,
wife=wife.id,
div={'date': "11 FEB 2001"})
self.assertTrue(us.divorce_before_death(family, individuals))
"""Wife dies before divorce and Husband is alive so False (not possible)"""
husband: Individual = Individual(_id="I6")
wife: Individual = Individual(_id="I7", deat={'date': "1 JAN 2000"})
individuals: List[Individual] = [husband, wife]
family: Family = Family(husb=husband.id,
wife=wife.id,
div={'date': "11 FEB 2001"})
self.assertFalse(us.divorce_before_death(family, individuals))
"""Wife dies after divorce and Husband is alive so true"""
husband: Individual = Individual(_id="I8")
wife: Individual = Individual(_id="I9", deat={'date': "1 JAN 2002"})
individuals: List[Individual] = [husband, wife]
family: Family = Family(husb=husband.id,
wife=wife.id,
div={'date': "11 FEB 2001"})
self.assertTrue(us.divorce_before_death(family, individuals))
""" Husband and wife they both are alive no divorce date is found so false"""
husband: Individual = Individual(_id="I10")
wife: Individual = Individual(_id="I11")
individuals: List[Individual] = [husband, wife]
family: Family = Family(husb=husband.id,
wife=wife.id,
div={'date': "11 FEB 2002"})
self.assertFalse(us.divorce_before_death(family, individuals))
def test_male_last_names(self):
husband: Individual = Individual(_id="I0",
name="Pablo /Escobar/",
sex='M')
wife: Individual = Individual(_id="I1",
name="Veronika /Esco/",
sex='F')
child1: Individual = Individual(_id="I2",
name="Terry /Escobart/",
sex='M')
child2: Individual = Individual(_id="I3",
name="Maria /Escobar/",
sex='F')
family = Family(husb=husband.id, wife=wife.id)
family.chil = [child1.id, child2.id]
individuals = [husband, wife, child1, child2]
self.assertFalse(us.male_last_names(family, individuals))
husband: Individual = Individual(_id="I112",
name="Naal /Wagas/",
sex='M')
wife: Individual = Individual(_id="I22",
name="Veron /Wagadi/",
sex='F')
child1: Individual = Individual(_id="I33",
name="Ter /Wagada/",
sex='M')
child2: Individual = Individual(_id="I44",
name="Mara /Wagadi/",
sex='F')
family = Family(husb=husband.id, wife=wife.id)
family.chil = [child1.id, child2.id]
individuals = [husband, wife, child1, child2]
self.assertFalse(us.male_last_names(family, individuals))
husband: Individual = Individual(_id="I9",
name="Eden /Hazard/",
sex='M')
wife: Individual = Individual(_id="I99", name="Veva /Hazard/", sex='F')
child1: Individual = Individual(_id="I999",
name="JR /Hazard/",
sex='M')
child2: Individual = Individual(_id="I9999",
name="SR /Hazard/",
sex='M')
family = Family(husb=husband.id, wife=wife.id)
family.chil = [child1.id, child2.id]
individuals = [husband, wife, child1, child2]
self.assertTrue(us.male_last_names(family, individuals))
husband: Individual = Individual(_id="I07",
name="Reese /Walter/",
sex='M')
wife: Individual = Individual(_id="I177",
name="Monica /Walter/",
sex='F')
child1: Individual = Individual(_id="I277",
name="Malcom /Walter/",
sex='M')
child2: Individual = Individual(_id="I377",
name="Hal /Walters/",
sex='M')
family = Family(husb=husband.id, wife=wife.id)
family.chil = [child1.id, child2.id]
individuals = [husband, wife, child1, child2]
self.assertFalse(us.male_last_names(family, individuals))
husband: Individual = Individual(_id="I007",
name="Elon /Drogba/",
sex='M')
wife: Individual = Individual(_id="I1008",
name="Emma /Drogba/",
sex='F')
child1: Individual = Individual(_id="I2009",
name="Agua /Drogba/",
sex='F')
child2: Individual = Individual(_id="I3000",
name="Win /Drogbaaa/",
sex='F')
family = Family(husb=husband.id, wife=wife.id)
family.chil = [child1.id, child2.id]
individuals = [husband, wife, child1, child2]
self.assertTrue(us.male_last_names(family, individuals))
def test_fewer_than_15_siblings(self):
husband: Individual = Individual(_id="I0")
wife: Individual = Individual(_id="I1")
child1: Individual = Individual(_id="I2")
child2: Individual = Individual(_id="I3")
child3: Individual = Individual(_id="I4")
child4: Individual = Individual(_id="I5")
child5: Individual = Individual(_id="I6")
child6: Individual = Individual(_id="I7")
child7: Individual = Individual(_id="I8")
child8: Individual = Individual(_id="I9")
child9: Individual = Individual(_id="I10")
child10: Individual = Individual(_id="I12")
child11: Individual = Individual(_id="I13")
child12: Individual = Individual(_id="I14")
child13: Individual = Individual(_id="I15")
child14: Individual = Individual(_id="I16")
child15: Individual = Individual(_id="I17")
family: Family = Family(husb=husband.id, wife=wife.id)
family.chil.extend([
child1.id, child2.id, child3.id, child4.id, child5.id, child6.id,
child7.id, child8.id, child9.id, child10.id, child11.id,
child12.id, child13.id, child14.id, child15.id
])
self.assertFalse(us.fewer_than_15_siblings(family))
family: Family = Family(husb=husband.id, wife=wife.id)
family.chil.extend(
[child1.id, child2.id, child3.id, child4.id, child5.id, child6.id])
self.assertTrue(us.fewer_than_15_siblings(family))