Levis: Programming by the Seat of Your Genes

A toolkit for genetic algorithms in Python. Pronounce it like the denim pants, because levis lets you program by the seat of your genes!

Overview

The levis package contains a collection of genetic traits meant to be composed to achieve a desired algorithm behavior.

To implement your own GA, you will probably want to extend from one of the classes in selection and one of the classes in logger. The former will give you proportionate or tournament selection, and the latter will enable logging (including verbosity).

You'll also want to override the crossover() and mutate() methods with implementations from the packages by the same name.

The examples each have three components: a genetic solution, a method to generate data, and a main method to wire in command line arguments. The examples will respond to a -h flag to display help.

Getting Started

Prerequisites

One of levis' design goals is to be runnable on the default Mac OS Python installation. As a result, levis targets Python 2.7+ and 3.2+. There are no dependencies to work with levis, but image rendering in the examples, when implemented, relies on svgwrite, and some data generation needs Faker.

$ pip install svgwrite
$ pip install fake-factory

Installing

Installation is now available via PyPI.

$ pip install levis

Running Examples

If you're looking at this project, you're probably more interested in the example implementations than in the core genetic behaviors. Each *.py file in the examples/ folder should respond to a -h argument to list its options. All should run without any options, but you'll want to tweak the parameters to better understand each algorithm.

$ cd examples/
$ python knapsack01.py -h
$ python knapsack01.py --iterations=10 --population-size=5

Testing

Running the Unit Tests

The examples of running the unit tests below should be run from the project's root directory.

To run all tests:

$ python all_tests.py

Running an individual test method:

$ python -m tests.test_behavior FinishWhenSlowGATestCase.test_doesnt_finish_when_fast

Running a single test case:

$ python -m tests.test_behavior FinishWhenSlowGATestCase

Running a single test file:

$ python -m tests.test_behavior

Testing Code Style

The code is periodically checked with pylint, if that sort of thing interests you. Note that several pylint warnings are currently ignored, but it's good to know your faults.

Planned Changes

You can expect the following in future releases:

• Additional crossover operators, such as cycle and merge crossover.
• Additional traits for crossover and mutation operators.
• The examples will be moved to another repository and several more will be added.
• API documentation and a user's guide will be available (probably at readthedocs.org)

Please be aware that the API is in flux, and changes between versions may still introduce breaking changes.

Change Log

v0.5.1:	Fixing an off by one error when randomly selecting points in crossover.multiple_points.
v0.5.0:	This version changes some behaviors to match more canonical implementations. Specifically: All crossover operators return a list of children. Most operators create two children from two parents. Mutation rate is now expressed as the probability of a mutation to any allele, not the probability that a chromosome will undergo a mutation. Additionally, a cut and splice crossover operator and a point mutation that may add or shrink chromosomes has been added for better support for list encoding schemes of heterogeneous length.
v0.4.0:	A big step toward a stable API, this version includes decomposed logging traits, an implementation of elitism that works with tournament selection, a number of bug fixes and minor improvements, and installation via pip/PyPI.

Versioning

Version numbers follow the SemVer scheme. For the versions available, see the tags on this repository.

Authors

Only one soul can be blamed for this:

• Jeremy Fisher, @thisisroot.

License

This project is licensed under the MIT License - see the LICENSE.md file for details.