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genetics's Introduction

genetics

A python 3 library for genetic algorithms

Example

Finding Hello World

import string
import random

import genetics

letters = string.ascii_uppercase + string.ascii_lowercase + string.punctuation + ' '
solution = 'Hello World!'

class LetterComponent(genetics.DNAComponent):
    def mutate_value(self):
        return random.choice(letters)

class WordDNA(genetics.arrayed_segment(len(solution), LetterComponent)):
    def score(self):
        return sum(comp.value == letter for comp, letter in zip(self, solution))

    def __str__(self):
        return ''.join(comp.value for comp in self)

sim = genetics.DiscreteSimulation(
    population_size=100,
    mutation_mask=genetics.mutation_rate(0.05),  # Mutate at a 5% rate
    crossover_mask=genetics.two_point_crossover,
    selection_function=genetics.tournament(2),
    elite_size=2,
    initial_generator=WordDNA,
    fitness_function=WordDNA.score)


def dna_stats(population):
    '''Best DNA, best score, average score'''
    best_dna = max(population)
    best_score = best_dna.score
    average_score = sum(member.score for member in population) / len(population)

    return best_dna, best_score, average_score


population = sim.initial_population()

while True:
    best, best_score, average_score = dna_stats(population)

    print('{} | Average score: {}'.format(str(best), average_score))

    if str(best) == solution:
        break

    population = sim.step(population)

Sample Output:

&~$lo,{j'"wi | Average score: 0.148
&~$lo,{j'"wi | Average score: 0.292
H)Xl] ?lDf{@ | Average score: 0.506
H)Xlo {lZ!&@ | Average score: 0.816
H)Xlo {lZ!&@ | Average score: 1.154
HSlldpWjr`z> | Average score: 1.574
HeXyoKWqrl&K | Average score: 2.136
uello*c,rl"! | Average score: 2.722
uello*c,rl"! | Average score: 3.338
Heslo LKrlk! | Average score: 3.814
Heslo LKrlk! | Average score: 4.492
H(llooWIrld! | Average score: 5.258
Hello W,rl]! | Average score: 5.934
HeDlo World! | Average score: 6.628
HeDlo World! | Average score: 7.362
Hello World! | Average score: 8.004

TODO / Working on

Short term

  • Real documentation, not just examples
  • PyPI deployment

Medium term

  • Rebuilding to be better, faster, stronger, easier.
    • Taking advantage of the opportunities provided by the functional design

Long term

  • Comprehensive test coverage
  • New simulation types.
    • Fluid simulation removes discrete generations, allowing agents to combine and die randomly

genetics's People

Contributors

lucretiel avatar

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genetics's Issues

Hello World example

$ python3 test_1.py
Traceback (most recent call last):
File "test_1.py", line 45, in
best, best_score, average_score = dna_stats(population)
File "test_1.py", line 37, in dna_stats
average_score = sum(member.score for member in population) / len(population)
TypeError: unsupported operand type(s) for +: 'int' and 'method'

AttributeError: module 'genetics' has no attribute 'DNAComponent'

punched in a snippet of the example code to create my own GA and it returned this:

AttributeError: module 'genetics' has no attribute 'DNAComponent'

SYNTAX:

import string
import random
import genetics
import numpy
class genetic(genetics.DNAComponent):
def ed(e):
solution = e == 'win'

pypi package

Mage genetics an installable package via pip.

hello world! example

I have these error messages for the hello world example.

Traceback (most recent call last):
  File "/genetics-master/hello_world.py", line 42, in <module>
    best, best_score, average_score = dna_stats(population)
  File "/genetics-master/hello_world.py", line 32, in dna_stats
    best_dna = max(population)
TypeError: unorderable types: WordDNA() > WordDNA()

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