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move paradiseo/eo to deprecated/ before merge with eodev

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##########################################################################################
### EO Doc generation using Doxygen
##########################################################################################
IF (DOXYGEN_FOUND)
SET(DOC_DIR ${CMAKE_CURRENT_BINARY_DIR} CACHE PATH "EO documentation directory")
SET(EO_DOC_CONFIG_FILE "eo.cfg" CACHE PATH "EO documentation configuration file")
# Copy necessary doc files
CONFIGURE_FILE(${CMAKE_CURRENT_SOURCE_DIR}/index.h ${DOC_DIR}/index.h COPYONLY)
FILE(GLOB header_files RELATIVE ${CMAKE_CURRENT_SOURCE_DIR} ${CMAKE_CURRENT_SOURCE_DIR}/*.htm*)
FILE(GLOB pdf_files RELATIVE ${CMAKE_CURRENT_SOURCE_DIR} ${CMAKE_CURRENT_SOURCE_DIR}/*.pdf)
FILE(GLOB jpg_files RELATIVE ${CMAKE_CURRENT_SOURCE_DIR} ${CMAKE_CURRENT_SOURCE_DIR}/*.jpg)
FOREACH (file ${header_files} ${pdf_files} ${jpg_files})
CONFIGURE_FILE(${CMAKE_CURRENT_SOURCE_DIR}/${file} ${DOC_DIR}/${file} COPYONLY)
ENDFOREACH (file)
# define the doc target
IF (DOXYGEN_EXECUTABLE)
# Creating the custom target
if(UNIX AND NOT ${CMAKE_VERBOSE_MAKEFILE})
add_custom_target(doc-eo
COMMAND ${DOXYGEN_EXECUTABLE} ${EO_DOC_CONFIG_FILE} 2> /dev/null > /dev/null
WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
)
else(UNIX AND NOT ${CMAKE_VERBOSE_MAKEFILE})
ADD_CUSTOM_TARGET(doc-eo
COMMAND ${DOXYGEN_EXECUTABLE} ${EO_DOC_CONFIG_FILE}
WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
)
endif()
ENDIF (DOXYGEN_EXECUTABLE)
# configure cfg file
CONFIGURE_FILE(
"${CMAKE_CURRENT_SOURCE_DIR}/${EO_DOC_CONFIG_FILE}.cmake"
"${CMAKE_CURRENT_BINARY_DIR}/${EO_DOC_CONFIG_FILE}"
)
INSTALL(
DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
DESTINATION local/share${INSTALL_SUB_DIR}/eo COMPONENT doc
PATTERN "CMakeFiles" EXCLUDE
PATTERN "cmake_install.cmake" EXCLUDE
PATTERN "Makefile" EXCLUDE
PATTERN "eo.cfg" EXCLUDE
PATTERN "eo.doxytag" EXCLUDE
)
ELSE (DOXYGEN_FOUND)
MESSAGE(STATUS "Unable to generate the documentation, Doxygen package not found")
ENDIF (DOXYGEN_FOUND)

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2007-01-23 Jochen Küpper <jochen@fhi-berlin.mpg.de>
* eo.cfg (PROJECT_NUMBER): Bump to 1.0.1
2006-12-18 Jochen Küpper <jochen@fhi-berlin.mpg.de>
* mainpage.html, publications.html: Update for release.
* index.h: Add old ToDos
* eo.cfg (PROJECT_NUMBER): Bump version to 1.0
2006-12-03 Jochen Küpper <jochen@fhi-berlin.mpg.de>
* mainpage.html: update, add link to Niko Hansen's comparison
2006-12-01 Jochen Küpper <jochen@fhi-berlin.mpg.de>
* Makefile.am: Update for release-distribution.
* Local Variables:
* coding: iso-8859-1
* mode: flyspell
* fill-column: 80
* End:

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/** @mainpage Welcome to Evolving Objects
@section shortcuts In one word
The best place to learn about the features and approaches of %EO with the help of examples is to look at
the <a href="../../tutorial/html/eoTutorial.html">tutorial</a>.
Once you have understand the @ref design of %EO, you could search for advanced features by browsing the <a
href="modules.html">modules</a> page.
@section intro Introduction
%EO is a template-based, ANSI-C++ evolutionary computation library which helps you to write your own stochastic optimization algorithms insanely fast.
It contains classes for almost any kind of evolutionary computation you might come
up to - at least for the ones we could think of. It is component-based, so that
if you don't find the class you need in it, it is very easy to subclass existing
abstract or concrete classes.
Designing an algorithm with %EO consists in choosing what components you want to use for your specific needs, just as building a structure with Lego blocks.
If you have a classical problem for which available code exists (for example if you have a black-box problem with real-valued variables), you will just choose components to form an algorithm and connect it to your fitness function (which computes the quality of a given solution).
If your problem is a bit more exotic, you will have to code a class that represents how your individuals (a solution to your problem) are represented, and perhaps some variations operators, but most of the other operators (selection, replacement, stopping criteria, command-line interface, etc.) are already available in %EO.
@section design Overall Design
%EO is a framework. It is oriented toward facilitating the design of adhoc evolutionary algorithms.
It is not (at the moment) a complete library of algorithms ready to use on canonical problems.
If you have a well-known problem and want to solve it as soon as possible, try another software.
If you have a real problem and want to build the best evolutionary algorithm to solve it, you've made
the good choice.
Bascially, %EO manipulate "individuals" with a "fitness", that is objects
encoding a solution to a given optimization problem, associated with
the quality of this solution. The fitness is defined in the %EO class,
but the representation of a solution cannot be as generic. Thus, %EO
massively use templates, so that you will not be limited by interfaces
when using your own representation.
Once you have a representation, you will build your own evolutionary algorithm
by assembling @ref Operators in @ref Algorithms.
In %EO, most of the objects are functors, that is classes with an operator(), that you
can call just as if they were classical functions. For example, an algorithm is a
functor, that manipulate a population of individuals, it will be implemented as a functor,
with a member like: operator()(eoPop<EOT>). Once called on a given population, it will
search for the optimum of a given problem.
Generally, operators are instanciated once and then binded in an algorithm by reference.
Thus, you can easily build your own algorithm by trying several combination of operators.
For a more detailled introduction to the design of %EO you can look at the
slides from a talk at EA 2001 or at the corresponding
article in Lecture Notes In Computer Science, 2310, Selected Papers from the 5th European Conference on Artificial Evolution:
- http://portal.acm.org/citation.cfm?id=727742
- http://eodev.sourceforge.net/eo/doc/LeCreusot.pdf
- http://eodev.sourceforge.net/eo/doc/EO_EA2001.pdf
*/

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<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN"
"http://www.w3.org/TR/1999/REC-html401-19991224/loose.dtd">
<html>
<head>
<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
<meta name="author" content="EO development team">
<meta name="keywords" content="Class libraries, evolutionary computation, evolution strategies, genetic algorithms, genetic programming, simulated annealing, C++">
<meta name="resource-type" content="document">
<meta name="distribution" content="Global">
<title>EO Evolutionary Computation Framework</title>
<style type="text/css">
H2 {
font-family: Helvetica,Arial;
color: #ffffcc;
background: #00309c;
}
</style>
</head>
<body alink="#ff0000" bgcolor="#ffffcc" link="#0000ee" text="#00309c" vlink="#551a8b">
<center>
<h1>EO Evolutionary Computation Framework</h1>
</center>
<table bgcolor="#ffffcc" border="0" cellpadding="5" width="100%">
<tbody>
<tr>
<td class="TITLE" align="right" valign="top" width="100">
<h2>What is EO?</h2>
</td>
<td bgcolor="#ffcc99">
<p> EO is a templates-based, ANSI-C++ compliant evolutionary computation
library. It contains classes for almost any kind of evolutionary
computation you might come up to - at least for the ones we could think
of. It is component-based, so that if you don't find the class you need
in it, it is very easy to subclass existing abstract or concrete
classes. </p>
<p> EO was started by the <a href="http://geneura.ugr.es/">Geneura
Team</a> at the University of Granada, headed by <a
href="http://geneura.ugr.es/%7Ejmerelo/">Juan Julián Merelo</a>. The <a
href="http://geneura.ugr.es/~jmerelo/EO.orig.html"
target="_blank">original Web site</a> is also the only place where you
will find old releases of EO (up to 0.8.7), but beware that it is not
compatible at all with the current version. </p>
<p> The developement team has then been reinforced by <a
href="http://www.cs.vu.nl/~mkeijzer">Maarten Keijzer</a>, the C++
wizzard, and <a href="http://www.lri.fr/%7Emarc">Marc Schoenauer</a>.
Later came <a href="http://www.liacs.nl/%7Ejeggermo/">Jeroen
Eggermont</a>, who, among other things, did a lot of work on GP,
INRIA Dolphin Team, <a
href="mailto:okoenig@users.sourceforge.net">Olivier König</a>, who did a
lot of useful additions and cleaning of the code and <a
href="http://www.jochen-kuepper.de">Jochen Küpper</a>, working on
infrastructure maintenance. </p>
</td>
</tr>
<tr>
<td class="TITLE" align="right" valign="top" width="100">
<h2>Platforms</h2>
</td>
<td bgcolor="#ffcc99">
<p> EO should work on Windows and any Un*x-like operating system with a
standard-conforming C++ development system. </p>
<p> Recent versions of EO have been tested on the following platforms:
</p>
<ul>
<li>Linux x86 with GCC 3.x and 4.x</li>
<li>Linux x86_64 with GCC 3.x and GCC 4.x</li>
<li>MacOS X/Darwin PowerPC with GCC 3.x</li>
<li>MacOS X/Darwin x86 with GCC 4.x</li>
<li>Microsoft Windows using Cygwin's GCC 3.x (cygming special).
<li>Microsoft Windows using Visual Studio 2003/2005; projects files
are provided.</li>
<li>Solaris SPARC with GCC 3.x</li>
<li>Solaris x86 with GCC 3.x</li>
</ul>
<p> If you have tested EO on a system not listed here, please <a
href="mailto:eodev-main@lists.sourceforge.net?subject=test-report">let
us know</a>. </p>
<p> If you are working on a system with an older C++ compiler there
is a good chance that eo-0.9.3z.1 works. It is tested on Linux
with gcc-2.9x and several systems (IRIX, Solaris) with egcs. </p>
</td>
</tr>
<tr>
<td class="TITLE" align="right" valign="top" width="100">
<h2>Documentation</h2>
</td>
<td bgcolor="#ffcc99">
<p>The tutorial demonstrates that writing an evolutionary algorithm
evolving your own structures is now <em>easy</em>, using ready-to-use
template files. Although the tutorial has not been upgraded for some
time now and refers to version 0.9.2 of EO, it nevertheless remains the
best way to dive into EO. You can start by trying it on-line at <a
href="http://www.lri.fr/%7Emarc/EO/eo/tutorial/html/eoTutorial.html">LRI</a>
or <a
href="http://eodev.sourceforge.net/eo/tutorial/html/eoTutorial.html">SourceForge</a>,
before <a href="http://www.lri.fr/%7Emarc/EO/">downloading it</a>. The
tutorial is also included in the <a
href="http://sourceforge.net/project/showfiles.php?group_id=9775">released
sources</a>. </p>
<p>The latest <a
href="http://eodev.sourceforge.net/eo/tutorial/html/eoTutorial.html">tutorial
release</a>
</p>
<p>The complete code is also well documented and you can look at the
generated <a
href="http://eodev.sourceforge.net/eo/doc/html/index.html">interface
documentation</a>. </p>
<p>The easiest way to create a complete new EO-project, even for new
genomes, is to use the script provided in tutorial/Templates/; see
the README in that directory and lesson 5 of the tutorial for
detail.</p>
</td>
</tr>
<tr>
<td class="TITLE" align="right" valign="top" width="100">
<h2>Presentations</h2>
</td>
<td bgcolor="#ffcc99">
<p> A functional and "philosophical" overview of EO was presented at <a
href="http://www.cmap.polytechnique.fr/%7Eea01/">EA'01 conference</a>.
You can download <a
href="http://eodev.sourceforge.net/eo/doc/EO_EA2001.pdf">the paper</a>
or <a href="http://eodev.sourceforge.net/eo/doc/LeCreusot.pdf">the
slides</a>. </p>
<p> A <a href="http://geneura.ugr.es/~jmerelo/GAPPT/index.html"
target="_blank">PowerPoint presentation</a> shows the EO philosophy, and
it includes a Visual Basic macro for evolving objects in Visual Basic
for Applications. </p>
<p>You can also look a the <a href="publications.html">list of
publications</a> that used EO to solve real problems. </p>
</td>
</tr>
<tr>
<td class="TITLE" align="right" valign="top" width="100">
<h2>Download</h2>
</td>
<td bgcolor="#ffcc99">
<p> The current release is <a
href="http://sourceforge.net/project/showfiles.php?group_id=9775">EO 1.0</a>.
It supports any Standard-compliant C++ compiler. </p>
<p> You can obtain the latest version directly via <a
href="http://sourceforge.net/cvs/?group_id=9775">cvs</a> or download a
daily snapshot from <a
href="http://www.lri.fr/%7Emarc/EO/snapshot">LRI</a>. </p>
<p> All releases can be obtained from the SourceForge <a
href="http://sourceforge.net/project/showfiles.php?group_id=9775">download
area</a>. </p>
</td>
</tr>
<tr>
<td class="TITLE" align="right" valign="top" width="100">
<h2>Mailing Lists</h2>
</td>
<td bgcolor="#ffcc99">
We would like EO to be an open development effort; that is why we have
created mailing lists to discuss future developments, solve technical
problems, announce releases, publish patches, and discuss evolutionary
computation in general. Browse the archives or join the <a
href="http://sourceforge.net/mail/?group_id=9775">EO mailing lists</a>.
</td>
</tr>
<tr>
<td class="TITLE" align="right" valign="top" width="100">
<h2>EO@sourceforge</h2>
</td>
<td bgcolor="#ffcc99">
<p>The following resources are available, thanks to sourceforge</p>
<ul>
<li> <a href="http://sourceforge.net/project/?group_id=9775">EO
SourceForge Project Page</a></li>
<li><a href="http://eodev.sourceforge.net/eo/doc/html/index.html">EO
automatic documentation page at SF</a><br>
</li>
<li><a href="http://eodev.sourceforge.net/eo/tutorial/html/eoTutorial.html">EO
tutorial page at SF</a><br>
</li>
<li> <a href="https://sourceforge.net/project/showfiles.php?group_id=9775">Releases</a></li>
<li> <a href="http://sourceforge.net/mail/?group_id=9775">Mailing Lists</a></li>
<li> <a href="http://sourceforge.net/forum/?group_id=9775">Message Forums</a></li>
<li> <a href="http://sourceforge.net/bugs/?group_id=9775">Bug Submission and Tracking</a></li>
<li> <a href="http://sourceforge.net/support/?group_id=9775">Technical Support</a></li>
<li> <a href="http://sourceforge.net/patch/?group_id=9775">Patch Submission</a></li>
<li> <a href="http://sourceforge.net/cvs/?group_id=9775">CVS repository</a></li>
</ul>
</td>
</tr>
<tr>
<td class="TITLE" align="right" valign="top" width="100">
<h2>License</h2>
</td>
<td bgcolor="#ffcc99">EO is distributed under the
<a href="http://www.gnu.org/copyleft/lesser.html">GNU Lesser General
Public License</a>
</td>
</tr>
<tr>
<td class="TITLE" align="right" valign="top" width="100">
<h2>Related Apps</h2>
</td>
<td bgcolor="#ffcc99">
<p> <a href="http://paradiseo.gforge.inria.fr"
target="_blank">ParadisEO</a> provides EO extensions for
the flexible design of <b>single solution-based metaheuristics</b>,
metaheuristics for <b>multi objective optimization</b> as well as <b>hybrid, parallel and distributed
metaheuristics</b>.</p>
<p> <a href="http://geneura.ugr.es/~jmerelo/DegaX/"
target="_blank">DegaX</a> is an ActiveX control which embeds EO 0.8.4.
</p>
</td>
</tr>
<tr>
<td class="TITLE" align="right" valign="top" width="100">
<h2>Links</h2>
</td>
<td bgcolor="#ffcc99">
<ul>
<li><a href="http://www.aip.de/~ast/EvolCompFAQ" target="_blank">The
Hitch-Hiker's Guide to Evolutionary Computation</a>, FAQ for
<a href="news:comp.ai.genetic">comp.ai.genetic</a>.</li>
<li><a href="http://en.wikipedia.org/wiki/Evolutionary_algorithm" target="_blank">Wikipedia</a>
on Evolutionary algorithms.</li>
<li>Charles Darwin: <a href="http://en.wikipedia.org/wiki/The_Origin_of_Species" target="_blank">The
Origin of Species</a>.</li>
<li>Nikolaus Hansen: <a
href="http://www.bionik.tu-berlin.de/user/niko/cec2005.html" target="_blank">Comparison
of Evolutionary Algorithms on a Benchmark Function Set</a>.</li>
</ul>
</td>
</tr>
</tbody>
</table>
<center> <p> Hosted by:<br/><a href="http://sourceforge.net/"><img alt="SF logo"
src="http://eodev.sourceforge.net/eo/doc/sflogo-hammer1.jpg"></a> </p> </center>
<p> <a href="http://validator.w3.org/check?uri=referer"> <img
src="http://www.w3.org/Icons/valid-html401" alt="Valid HTML 4.01 Transitional"
height="31" width="88"></a> <br/> Please send comments on this webpage to the <a
href="mailto:eodev-main@lists.sourceforge.net?subject=webpage">EO mailing
list</a>. </p>
</body>
</html>
<!-- Local Variables: -->
<!-- coding: iso-8859-1 -->
<!-- fill-column: 80 -->
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<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN"
"http://www.w3.org/TR/1999/REC-html401-19991224/loose.dtd">
<html>
<head>
<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
<meta name="author" content="EO development team">
<meta name="keywords" content="Class libraries, evolutionary computation, evolution strategies, genetic algorithms, genetic programming, simulated annealing, C++">
<meta name="resource-type" content="document">
<meta name="distribution" content="Global">
<title>EO Evolutionary Computation Framework</title>
<style type="text/css">
H2 {
font-family: Helvetica,Arial;
color: #ffffcc;
background: #00309c;
}
</style>
</head>
<body alink="#ff0000" bgcolor="#ffffcc" link="#0000ee" text="#00309c" vlink="#551a8b">
<center>
<h1>List of publications using EO</h1>
</center>
<table bgcolor="#ffffcc" border="0" cellpadding="5" width="100%">
<tbody>
<tr>
<td bgcolor="#ffcc99">
<p>
<a href= "http://citeseer.ist.psu.edu/keijzer01evolving.html">M.
Keijzer, J.J. Merelo, G. Romero, G., M. Schoenauer: "Evolving
objects: A general purpose evolutionary computation
library", <i>Art. Evol.</i> <b>2310</b>, 231-242 (2002).</a>
</p>
</td>
</tr>
<tr>
<td bgcolor="#ffcc99">
<p>
<a href= "http://dx.doi.org/10.1103/PhysRevA.73.063410">J.J. Gilijamse, J. Küpper,
S. Hoekstra, S.Y.T. van de Meerakker, G. Meijer:
"Optimizing the Stark-decelerator beamline for the trapping of
cold molecules using evolutionary strategies"</a>,
<i> Phys. Rev.</i> A <bf>73</bf>, 063410 (2006). <br/>
Also available at <a href= "http://arxiv.org/abs/physics/0603108"><i>arXiv</i>
physics/0603108 (2006)</a>.
</p>
</td>
</tr>
</tbody>
</table>
<center>
<p>
Hosted by:<br/><a href="http://sourceforge.net/"><img alt="SF logo"
src="http://eodev.sourceforge.net/eo/doc/sflogo-hammer1.jpg"></a>
</p>
</center>
<p>
<a href="http://validator.w3.org/check?uri=referer">
<img src="http://www.w3.org/Icons/valid-html401"
alt="Valid HTML 4.01 Transitional"
height="31"
width="88"></a>
<br/>
Please send publications that belong on this page and general comments on
this webpage to
the <a href="mailto:eodev-main@lists.sourceforge.net?subject=publications">EO
mailing list</a>.
</p>
</body>
</html>
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