Tree [e6f9d6] master V_0_2 /
History



File Date Author Commit
.gitignore 2005-08-29 Ralf Schlatterbeck Ralf Schlatterbeck [acad1e] PGApy wrapper for PGAPACK genetic algorithm lib
Changelog 2005-11-01 Ralf Schlatterbeck Ralf Schlatterbeck [e2be33] Added Changelog for future announcements...
MANIFEST.in 2014-04-17 Ralf Schlatterbeck Ralf Schlatterbeck [e6f9d6] Release preparation
Makefile 2014-04-17 Ralf Schlatterbeck Ralf Schlatterbeck [e6f9d6] Release preparation
README.rst 2014-04-17 Ralf Schlatterbeck Ralf Schlatterbeck [e6f9d6] Release preparation
pgamodule.c 2013-06-08 Ralf Schlatterbeck Ralf Schlatterbeck [a86cae] Bug-fix in retrieving context: use long
setup.py 2014-04-17 Ralf Schlatterbeck Ralf Schlatterbeck [e6f9d6] Release preparation
test.py 2005-09-12 Ralf Schlatterbeck Ralf Schlatterbeck [4f8dfb] Memleaks, print_string

Read Me

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PGAPy: Python wrapper for pgapack parallel genetic algorithm library

Author:Ralf Schlatterbeck <rsc@runtux.com>

PGAPy is a wrapper for pgapack, the parallel genetic algorithm library (see pgapack Readme), a powerfull genetic algorithm library by D. Levine, Mathematics and Computer Science Division Argonne National Laboratory. The library is written in C. PGAPy wraps this library for use with Python. The original pgapack library is already quite old and not very actively maintained -- still I've found it one of the most complete and accurate (and fast, although this is not my major concern when wrapping it to python) genetic algorithm implementations out there with a lot of bells and whistles for experimentation. That's why I wanted to use it in Python, too.

There currently is not much documentation for PGAPy. You really, absolutely need to read the documentation that comes with pgapack -- and of course you need the pgapack library. The pgapack library can be downloaded from the pgapack ftp site, it is written in ANSI C and therefore should run on most platforms. I have tested it on Linux only and I'll currently not provide Windows versions.

For the Debian Linux distribution, pgapack is already included, install with a simple:

apt-get install pgapack

For debian the pre-built documentation is in /usr/share/doc/pgapack/user_guide.ps.gz

To get you started, I've included a very simple example in test.py that implements the "Maxbit" example -- modified to use integer genes instead of bits -- from the pgapack documentation. This illustrates several points:

  • Your class implementing the genetic algorithm needs to inherit from pga.PGA (pga is the PGAPy wrapper module).
  • You need to define an evaluation function called evaluate that returns a number indicating the fitness of the gene given with the parameters p and pop that can be used to fetch allele values from the gene using the get_allele method, for more details refer to the pgapack documentation.
  • You can define additional functions overriding built-in functions of the pgapack library, illustrated by the example of print_string. Note that we do a call to the original print_string method of our PGA superclass.
  • The constructor of the class needs to define the Gene type, in the example we use an integer (type (2), a python expression for the built-in integer datatype).
  • The length of the gene (100 in the example) needs to be given.
  • We want to maximize the numbers returned by our evaluation function, set the parameter maximize to False if you want to minimize.
  • We can define an array of init values each entry containing a sequence with lower and upper bound. The array has to have the length of the gene. Note that the upper bound is included in the range of possible values (unlike the python range operator but compatible with the pgapack definition).
  • In the constructor of the class we can add parameters of the genetic algorithm. Not all parameters of pgapack are wrapped yet, currently you would need to consult the sourcecode of PGAPy to find out which parameters are wrapped. In the example we define several print options.
  • Finally the genetic algorithm is started with the run method.

Naming conventions in PGAPy

When you extend PGAPy -- remember not all functions of pgapack are wrapped yet and you may need additional functions -- you should stick to my naming conventions when making changes. The following naming conventions were used for the wrapper:

  • Constants of pgapack like PGA_REPORT_STRING are used as-is in uppercase. These constants can be directly imported from the wrapper module. Not all constants are wrapped so far, if you need more, add them to the constdef array in pgamodule.c and send me a patch.
  • For methods of the pga.PGA class I've removed the PGA prefix used throughout pgapack and converted the method to lowercase with underscores between uppercase words in the original function name, so PGARun becomes run, PGACheckStoppingConditions becomes check_stopping_conditions.
  • Where possible I've made a single class method where pgapack needs a separate function for each datatype, so PGAGetBinaryAllele, PGAGetCharacterAllele, PGAGetIntegerAllele, PGAGetRealAllele all become get_allele. Same holds true for set_allele.
  • Internal method names in the wrapper program have a leading PGA_ -- so the class method set_allele is implemented by the C-function PGA_set_allele in pgamodule.c.

Missing Features

As already mentioned, not all functions and constants of pgapack are wrapped yet -- still for many applications the given set should be enough. If you need additional functions, you may want to wrap these and send me a patch.

Another feature of pgapack is currently not implemented in the wrapper, the usage of custom datatypes. With pgapack you can define your own datatypes complete with their custom implementations of the genetic algorithm functionality like crossover, mutation, etc. I don't expect problems implementing these, though.

Reporting Bugs

Please use the Sourceforge Bug Tracker and

  • give a short description of what you think is the correct behaviour
  • give a description of the observed behaviour
  • tell me exactly what you did.

Resources

Project information and download from Sourceforge main page

Changes

Version 0.2: Feature enhancements, Bug fixes

64 bit support, more pgapack functions and attributes wrapped, Readme-update: Sourceforge logo, Changes chapter.

  • Bug-fixes for 64 bit architectures
  • More functions and attributes of pgapack wrapped
  • Add a build-rule to setup.py to allow building for standard-install of pgapack -- this currently needs editing of setup.py -- should use autodetect here but this would require that I set up a machine with standard install of pgapack for testing.
  • Add Sourceforge logo as required
  • Add Changes chapter for automagic releases

Version 0.1: Initial freshmeat announcement

PGAPy is a wrapper for pgapack, the parallel genetic algorithm library, a powerful genetic algorithm library. PGAPy wraps this library for use with Python. Pgapack is one of the most complete and accurate genetic algorithm implementations out there with a lot of features for experimentation.

  • Initial Release