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Merge branch 'master' of ssh://eodev.git.sourceforge.net/gitroot/eodev/eodev

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This commit is contained in:
Caner Candan 2011-05-14 23:45:20 +02:00
commit 73028ac095
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221
eo/.cproject
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@ -1,221 +0,0 @@
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eo/.cvsignore
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*.la
*.lo
.deps
.libs
Makefile
Makefile.in
aclocal.m4
autom4te.cache
build*
confdefs.h
config.cache
config.guess
config.h
config.h.in
config.log
config.status
config.sub
configure
depcomp
install-sh
libtool
missing
mkinstalldirs
stamp-h
stamp-h.in

82
eo/.project
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@ -1,82 +0,0 @@
<?xml version="1.0" encoding="UTF-8"?>
<projectDescription>
<name>eo</name>
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1474
eo/CHANGELOG
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File diff suppressed because it is too large Load diff

13
eo/CMakeLists.txt
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@ -14,12 +14,11 @@ INCLUDE(eo-conf.cmake OPTIONAL)
# set the project name and other variables # set the project name and other variables
PROJECT(EO) PROJECT(EO)
SET(PROJECT_VERSION_MAJOR 1) #SET(PROJECT_VERSION_MAJOR 1)
SET(PROJECT_VERSION_MINOR 1) #SET(PROJECT_VERSION_MINOR 1)
SET(PROJECT_VERSION_PATCH 1) #SET(PROJECT_VERSION_PATCH 1)
SET(PROJECT_VERSION "${PROJECT_VERSION_MAJOR}.${PROJECT_VERSION_MINOR}.${PROJECT_VERSION_PATCH}" CACHE STRING "Package version" FORCE) SET(PROJECT_VERSION "${PROJECT_VERSION_MAJOR}.${PROJECT_VERSION_MINOR}.${PROJECT_VERSION_PATCH}" CACHE STRING "Package version" FORCE)
#SET(VERSION "${PROJECT_VERSION_MAJOR}.${PROJECT_VERSION_MINOR}" CACHE STRING "Global version" FORCE) SET(VERSION "${PROJECT_VERSION_MAJOR}.${PROJECT_VERSION_MINOR}${PROJECT_VERSION_MISC}" CACHE STRING "Global version" FORCE)
SET(VERSION "1.1.1-edge" CACHE STRING "Global version" FORCE)
SET(GLOBAL_VERSION "${VERSION}") SET(GLOBAL_VERSION "${VERSION}")
SET(PACKAGE_BUGREPORT "eodev-help@sourceforge.net" CACHE STRING "Package bug report" FORCE) SET(PACKAGE_BUGREPORT "eodev-help@sourceforge.net" CACHE STRING "Package bug report" FORCE)
@ -58,7 +57,9 @@ INCLUDE(FindGnuplot)
INCLUDE(CheckLibraryExists) INCLUDE(CheckLibraryExists)
INCLUDE(ConfigureChecks.cmake) IF(UNIX)
INCLUDE(ConfigureChecks.cmake)
ENDIF(UNIX)
INCLUDE(Dart OPTIONNAL) INCLUDE(Dart OPTIONNAL)

32
eo/ConfigureChecks.cmake
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@ -1,22 +1,22 @@
# NOTE: only add something here if it is really needed by EO # NOTE: only add something here if it is really needed by EO
include(CheckIncludeFile) INCLUDE(CheckIncludeFile)
include(CheckIncludeFiles) INCLUDE(CheckIncludeFiles)
include(CheckSymbolExists) INCLUDE(CheckSymbolExists)
include(CheckFunctionExists) INCLUDE(CheckFunctionExists)
include(CheckLibraryExists) INCLUDE(CheckLibraryExists)
check_library_exists(m cos "cos in libm" HAVE_LIBM) CHECK_LIBRARY_EXISTS(m cos "/usr/lib" HAVE_LIBM)
check_include_files(cmath.h "cmath.h" HAVE_CMATH_H) CHECK_INCLUDE_FILES(math.h "math.h" HAVE_MATH_H)
check_include_files(stdio.h "stdio.h" HAVE_STDIO_H) CHECK_INCLUDE_FILES(stdio.h "stdio.h" HAVE_STDIO_H)
check_include_files(stdlib.h "stdlib.h" HAVE_STDLIB_H) CHECK_INCLUDE_FILES(stdlib.h "stdlib.h" HAVE_STDLIB_H)
check_include_files(string.h "string.h" HAVE_STRING_H) CHECK_INCLUDE_FILES(string.h "string.h" HAVE_STRING_H)
check_include_files(strings.h "strings.h" HAVE_STRINGS_H) CHECK_INCLUDE_FILES(strings.h "strings.h" HAVE_STRINGS_H)
check_include_files(malloc.h "malloc.h" HAVE_MALLOC_H) CHECK_INCLUDE_FILES(malloc.h "malloc.h" HAVE_MALLOC_H)
check_include_files(limits.h "limits.h" HAVE_LIMITS_H) CHECK_INCLUDE_FILES(limits.h "limits.h" HAVE_LIMITS_H)
check_include_files(unistd.h "unistd.h" HAVE_UNISTD_H) CHECK_INCLUDE_FILES(unistd.h "unistd.h" HAVE_UNISTD_H)
check_include_files(stdint.h "stdint.h" HAVE_STDINT_H) CHECK_INCLUDE_FILES(stdint.h "stdint.h" HAVE_STDINT_H)
# Use check_symbol_exists to check for symbols in a reliable # Use check_symbol_exists to check for symbols in a reliable
@ -26,4 +26,4 @@ check_include_files(stdint.h "stdint.h" HAVE_STDINT_H)
# specific order. Refer to the man page for each symbol for which a # specific order. Refer to the man page for each symbol for which a
# check is to be added to get the proper set of headers. Example : # check is to be added to get the proper set of headers. Example :
#check_symbol_exists(asymbol "symbole.h" HAVE_SYMBOLE) #check_symbol_exists(asymbol "symbole.h" HAVE_SYMBOLE)

20
eo/ForRelease
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@ -1,19 +1,13 @@
In order to create a new release from the current cvs sources perform the In order to create a new release from the current repository, perform the
following steps: following steps:
- Set version number in configure.in and doc/eo.cfg - Create a branch named "eo_x.y.z"
- Set version number in eo-conf.cmake
- Check/update NEWS file, set release date and version in NEWS. - Check/update NEWS file, set release date and version in NEWS.
- Run `make check && make dist` - use the "archive_current.sh" script to create the source archive
- Test distribution (unpack, configure, make check) - Build the packages
- Tag released code in cvs, in order to allow a branch to be created at that - Put source archive and packages files at SourceForge
version if the necessity will arise later
- Put distribution files at SourceForge
- Post news on SourceForge project-page - Post news on SourceForge project-page
- Send announcement to mailing lists - Send announcement to mailing lists
- Bump version number to next x.y.z-cvs in configure.in and doc/eo.cfg - Bump version number to next "x.y.z-edge" in eo-conf.cmake
# Local Variables:
# coding: iso-8859-1
# mode: text
# fill-column: 80
# End:

275
eo/INSTALL
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@ -1,235 +1,86 @@
-----------------------------------------
| WARNING THOSE INSTRUCTIONA ARE OUTDATED |
-----------------------------------------
Copyright 1994, 1995, 1996, 1999, 2000, 2001, 2002 Free Software
Foundation, Inc.
This file is free documentation; the Free Software Foundation gives
unlimited permission to copy, distribute and modify it.
Basic Installation Basic Installation
================== ==================
These are generic installation instructions. The simplest way to compile the libraries or the provided softwares is to run
one of the script beginnig with "build_". Each script permits to build different
parts of the framework, with different options.
First, you need to generate a configure script using autoconf. To compile EO you will need CMake and a compiler for your system.
To do this, run the shell script sh ./autogen.sh.
The `configure' shell script attempts to guess correct values for So far the available scripts for posix systems using g++ are the following:
various system-dependent variables used during compilation. It uses * build_gcc_linux_release : the most usefull script, build the core libraries in release mode
those values to create a `Makefile' in each directory of the package. * build_gcc_linux_debug : build the core libraries with debugging informations in the binaries
It may also create one or more `.h' files containing system-dependent * build_gcc_linux_tutorial : build the core libraries and the tutorials
definitions. Finally, it creates a shell script `config.status' that * build_gcc_linux_unittest : build the core libraries and the tests executables
you can run in the future to recreate the current configuration, and a * build_gcc_linux_stl_parallel : build the core libraries enabling STL parallel algorithms (like sorting)
file `config.log' containing compiler output (useful mainly for * build_gcc_linux_pyeo : build the core libraries and the python module
debugging `configure'). * distclean : remove the "release/" and "debug/" directories where the build scripts put the binaries
It can also use an optional file (typically called `config.cache' For Windows systems using Visual Studio:
and enabled with `--cache-file=config.cache' or simply `-C') that saves * build_vs2008_release.bat
the results of its tests to speed up reconfiguring. (Caching is You may need to adapt the ID to your version of Visual Studio, edit
disabled by default to prevent problems with accidental use of stale the "Visual Studio 9 2008" string accordingly.
cache files.)
If you need to do unusual things to compile the package, please try The libraries are in the "release/lib/" or "debug/lib/" directories.
to figure out how `configure' could check whether to do them, and mail
diffs or instructions to the address given in the `README' so they can
be considered for the next release. If you are using the cache, and at
some point `config.cache' contains results you don't want to keep, you
may remove or edit it.
The file `configure.ac' (or `configure.in') is used to create
`configure' by a program called `autoconf'. You only need
`configure.ac' if you want to change it or regenerate `configure' using
a newer version of `autoconf'.
The simplest way to compile this package is:
1. `cd' to the directory containing the package's source code and type
`./configure' to configure the package for your system. If you're
using `csh' on an old version of System V, you might need to type
`sh ./configure' instead to prevent `csh' from trying to execute
`configure' itself.
Running `configure' takes awhile. While running, it prints some
messages telling which features it is checking for.
2. Type `make' to compile the package.
3. Optionally, type `make check' to run any self-tests that come with
the package.
4. Type `make install' to install the programs and any data files and
documentation.
5. You can remove the program binaries and object files from the
source code directory by typing `make clean'. To also remove the
files that `configure' created (so you can compile the package for
a different kind of computer), type `make distclean'. There is
also a `make maintainer-clean' target, but that is intended mainly
for the package's developers. If you use it, you may have to get
all sorts of other programs in order to regenerate files that came
with the distribution.
Compilers and Options Compilers and Options
===================== =====================
Some systems require unusual options for compilation or linking that The build scripts are really simple, take a look at them to see how to use the
the `configure' script does not know about. Run `./configure --help' build system.
for details on some of the pertinent environment variables.
You can give `configure' initial values for configuration parameters Basically, the steps are:
by setting variables in the command line or in the environment. Here 0. remove any old build directory that's on the way:
is an example: rm -rf build/
1. create a directory in which to put build files:
mkdir build/
2. go in this directory:
cd build/
3. call cmake with the options you want, using the "-D" option and passing the
EO directory as an argument, for example:
cmake -DCMAKE_BUILD_TYPE=Debug -DENABLE_CMAKE_TESTING =1 ..
4. now type your favorite "make" command, like:
make -j # use several processors at once when possible
5. enjoy:
./debug/test/t-eofitness
./configure CC=c89 CFLAGS=-O2 LIBS=-lposix Some of the available options are:
* CMAKE_BUILD_TYPE :
* "Debug" : embed debugging informations in the binaries) or
* "Release" : no debugging info and some optimizations (the default)
* ENABLE_EO_TUTORIAL : build the tutorial ("no" by default)
* ENABLE_CMAKE_TESTING : build the tests executables ("no" by default)
* ENABLE_PYEO : build the python module ("no" by default)
*Note Defining Variables::, for more details. You can pass generic options to the compiler, like:
* _GLIBCXX_PARALLEL : use the parallel version of the STL
Compiling For Multiple Architectures
====================================
You can compile the package for more than one kind of computer at the Installation using packages
same time, by placing the object files for each architecture in their ===========================
own directory. To do this, you must use a version of `make' that
supports the `VPATH' variable, such as GNU `make'. `cd' to the
directory where you want the object files and executables to go and run
the `configure' script. `configure' automatically checks for the
source code in the directory that `configure' is in and in `..'.
If you have to use a `make' that does not support the `VPATH' To construct a dummy template of the EO package you will need CPack. Be warned
variable, you have to compile the package for one architecture at a that those do not guarantee correct dependencies and version management.
time in the source code directory. After you have installed the
package for one architecture, use `make distclean' before reconfiguring
for another architecture.
Installation Names Use the "package_*" scripts:
* package_deb : for debian-like systems
* package_rpm : for red-hat-like systems
Or go through the following steps:
1. go in the build directory where your binaries are:
cd build/
2. call CPack specifying the desired package system:
cpack -G DEB
3. install the package:
sudo apt-get install EO-1.1.1-Linux.deb
Basic installation
================== ==================
By default, `make install' will install the package's files in To install the framework system-wide, copy the "eo/" directory somewhere in your
`/usr/local/bin', `/usr/local/man', etc. You can specify an path. The "lib/" directory should be reachable for the linker and the "src/"
installation prefix other than `/usr/local' by giving `configure' the directory must be in the compiler include path.
option `--prefix=PATH'.
You can specify separate installation prefixes for
architecture-specific files and architecture-independent files. If you
give `configure' the option `--exec-prefix=PATH', the package will use
PATH as the prefix for installing programs and libraries.
Documentation and other data files will still use the regular prefix.
In addition, if you use an unusual directory layout you can give
options like `--bindir=PATH' to specify different values for particular
kinds of files. Run `configure --help' for a list of the directories
you can set and what kinds of files go in them.
If the package supports it, you can cause programs to be installed
with an extra prefix or suffix on their names by giving `configure' the
option `--program-prefix=PREFIX' or `--program-suffix=SUFFIX'.
Optional Features
=================
Some packages pay attention to `--enable-FEATURE' options to
`configure', where FEATURE indicates an optional part of the package.
They may also pay attention to `--with-PACKAGE' options, where PACKAGE
is something like `gnu-as' or `x' (for the X Window System). The
`README' should mention any `--enable-' and `--with-' options that the
package recognizes.
For packages that use the X Window System, `configure' can usually
find the X include and library files automatically, but if it doesn't,
you can use the `configure' options `--x-includes=DIR' and
`--x-libraries=DIR' to specify their locations.
Specifying the System Type
==========================
There may be some features `configure' cannot figure out
automatically, but needs to determine by the type of machine the package
will run on. Usually, assuming the package is built to be run on the
_same_ architectures, `configure' can figure that out, but if it prints
a message saying it cannot guess the machine type, give it the
`--build=TYPE' option. TYPE can either be a short name for the system
type, such as `sun4', or a canonical name which has the form:
CPU-COMPANY-SYSTEM
where SYSTEM can have one of these forms:
OS KERNEL-OS
See the file `config.sub' for the possible values of each field. If
`config.sub' isn't included in this package, then this package doesn't
need to know the machine type.
If you are _building_ compiler tools for cross-compiling, you should
use the `--target=TYPE' option to select the type of system they will
produce code for.
If you want to _use_ a cross compiler, that generates code for a
platform different from the build platform, you should specify the
"host" platform (i.e., that on which the generated programs will
eventually be run) with `--host=TYPE'.
Sharing Defaults
================
If you want to set default values for `configure' scripts to share,
you can create a site shell script called `config.site' that gives
default values for variables like `CC', `cache_file', and `prefix'.
`configure' looks for `PREFIX/share/config.site' if it exists, then
`PREFIX/etc/config.site' if it exists. Or, you can set the
`CONFIG_SITE' environment variable to the location of the site script.
A warning: not all `configure' scripts look for a site script.
Defining Variables
==================
Variables not defined in a site shell script can be set in the
environment passed to `configure'. However, some packages may run
configure again during the build, and the customized values of these
variables may be lost. In order to avoid this problem, you should set
them in the `configure' command line, using `VAR=value'. For example:
./configure CC=/usr/local2/bin/gcc
will cause the specified gcc to be used as the C compiler (unless it is
overridden in the site shell script).
`configure' Invocation
======================
`configure' recognizes the following options to control how it
operates.
`--help'
`-h'
Print a summary of the options to `configure', and exit.
`--version'
`-V'
Print the version of Autoconf used to generate the `configure'
script, and exit.
`--cache-file=FILE'
Enable the cache: use and save the results of the tests in FILE,
traditionally `config.cache'. FILE defaults to `/dev/null' to
disable caching.
`--config-cache'
`-C'
Alias for `--cache-file=config.cache'.
`--quiet'
`--silent'
`-q'
Do not print messages saying which checks are being made. To
suppress all normal output, redirect it to `/dev/null' (any error
messages will still be shown).
`--srcdir=DIR'
Look for the package's source code in directory DIR. Usually
`configure' can determine that directory automatically.
`configure' also accepts some other, not widely useful, options. Run
`configure --help' for more details.

15
eo/NEWS
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@ -1,7 +1,16 @@
* current * release 1.2 (10. May. 2011)
- evaluators that throw an exception if a maximum time has en reached (wallclock and CPU user time for POSIX systems), independently of the number of generations - fixed the incremental allocation issue in the variation operator which were
taking too much time for big population sizes
- new class eoParallel enabling parallelization in EO using OpenMP. At this
time, it only concerns the evaluation operator, for advanced details go to
the file test/t-eoParallel.cpp. The default parallelization mode is off, to
switch it on, see the parameters prefixed by --parallelize-*
- pyeo compatible with the last version of Boost and Python libraries
- script installing EO manually in using symbolic links
- evaluators that throw an exception if a maximum time has been reached
(wallclock and CPU user time for POSIX systems), independently of the number of generations
* release 1.1 * release 1.1 (8. Nov. 2010)
- provide cmake build system, remove the old autotools one - provide cmake build system, remove the old autotools one
- package generation system - package generation system
- GCC 4.3 compatibility - GCC 4.3 compatibility

33
eo/README
View file

@ -10,7 +10,7 @@ The latest news about EO can be found on the sourceforge repository at
http://eodev.sourceforge.net/ http://eodev.sourceforge.net/
In case of any problem, please e-mail us at In case of any problem, please e-mail us at
eodev-help@lists.sourceforge.net, eodev@egroups.com eodev-main@lists.sourceforge.net
To get started, take a look at the tutorial, starting with To get started, take a look at the tutorial, starting with
./tutorial/html/eoTutorial.html ./tutorial/html/eoTutorial.html
@ -18,7 +18,7 @@ To get started, take a look at the tutorial, starting with
The easiest way to start programming a new genome with all EO The easiest way to start programming a new genome with all EO
evolution engines handy is to create a new standalone EO project from evolution engines handy is to create a new standalone EO project from
the tutorial/Templates/ directory. Read Lesson 5 of the tutorial for the tutorial/Templates/ directory. Read Lesson 5 of the tutorial for
an introduction;) an introduction ;)
================================================================== ==================================================================
@ -26,27 +26,15 @@ an introduction;)
================================================================== ==================================================================
The basic installation procedure goes the following: The basic installation procedure goes the following:
Go to your build-directory and run Go to the "eo/" and run one of the "build_*" script. 
$(SRCDIR)/configure
make
make check
make install
where $(SRCDIR) is the top-level source directory of EO, i.e. where
the sources where unpacked.
Run "$(SRCDIR)/configure --help" for possible options. You can specify Using the "build_gcc_linux_release" script is generally what you want. The
to not build example applications, the tutorial, or to build the binaries are then located in the "release/" directory.
ParadisEO tutorial. You may also change the installation directory
that way.
Now you should probably go to the tutorial and start learning about EO Now you should probably go to the tutorial and start learning about EO
features and programming. features and programming.
In case of problems or if you want advanced options, you can read the INSTALL file.
In case of problems, you can read the INSTALL file - but remember this
is a standard installation file from GNU and that it contains nothing
specific about EO.
=================================================================== ===================================================================
DIRECTORY STRUCTURE DIRECTORY STRUCTURE
@ -99,12 +87,3 @@ structure:
| |
+-- win WINDOWS dir: project files for MS/VC5+ +-- win WINDOWS dir: project files for MS/VC5+
===================================================================
NOTES
===================================================================
If you extracted a fresh snapshot from the cvs-repository, remember
to run
./autogen.sh
in the source-directory before building the libraries.

2
eo/app/.cvsignore
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@ -1,2 +0,0 @@
Makefile.in
Makefile

4
eo/app/gprop/.cvsignore
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@ -1,4 +0,0 @@
Makefile.in
Makefile
gprop
.deps

3
eo/app/gpsymreg/.cvsignore
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@ -1,3 +0,0 @@
Makefile.in
.deps
Makefile

4
eo/app/mastermind/.cvsignore
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@ -1,4 +0,0 @@
Makefile.in
Makefile
mastermind
.deps

7
eo/build_gcc_linux_pyeo Executable file
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@ -0,0 +1,7 @@
#!/usr/bin/env sh
mkdir -p release
cd release
cmake -DENABLE_PYEO=1 ..
make
cd ..

7
eo/build_gcc_linux_stl_parallel Executable file
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@ -0,0 +1,7 @@
#!/usr/bin/env sh
mkdir -p release
cd release
cmake -D_GLIBCXX_PARALLEL=1 ..
make
cd ..

2
eo/build_gcc_linux_tutorial
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@ -1,6 +1,6 @@
#!/usr/bin/env sh #!/usr/bin/env sh
mkdir release mkdir -p release
cd release cd release
cmake -DENABLE_EO_TUTORIAL=1 .. cmake -DENABLE_EO_TUTORIAL=1 ..
make make

2
eo/build_gcc_linux_unittest
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@ -1,6 +1,6 @@
#!/usr/bin/env sh #!/usr/bin/env sh
mkdir debug mkdir -p debug
cd debug cd debug
cmake -DCMAKE_BUILD_TYPE=Debug -DENABLE_CMAKE_TESTING=1 .. cmake -DCMAKE_BUILD_TYPE=Debug -DENABLE_CMAKE_TESTING=1 ..
make make

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File diff suppressed because it is too large Load diff

2
eo/contrib/.cvsignore
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@ -1,2 +0,0 @@
Makefile.in
Makefile

6
eo/doc/.cvsignore
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@ -1,6 +0,0 @@
Makefile
Makefile.in
eo.doxytag
html
latex
man

7
eo/eo-conf.cmake Normal file
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@ -0,0 +1,7 @@
# Current version
SET(PROJECT_VERSION_MAJOR 1)
SET(PROJECT_VERSION_MINOR 3)
SET(PROJECT_VERSION_PATCH 0)
SET(PROJECT_VERSION_MISC "-edge")

6
eo/src/.cvsignore
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@ -1,6 +0,0 @@
*.lo
*.la
.deps
.libs
Makefile
Makefile.in

5
eo/src/CMakeLists.txt
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@ -43,6 +43,9 @@ ADD_SUBDIRECTORY(ga)
ADD_SUBDIRECTORY(gp) ADD_SUBDIRECTORY(gp)
ADD_SUBDIRECTORY(other) ADD_SUBDIRECTORY(other)
ADD_SUBDIRECTORY(utils) ADD_SUBDIRECTORY(utils)
ADD_SUBDIRECTORY(pyeo)
IF(ENABLE_PYEO)
ADD_SUBDIRECTORY(pyeo)
ENDIF(ENABLE_PYEO)
###################################################################################### ######################################################################################

6
eo/src/apply.h
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@ -19,7 +19,7 @@
Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
Contact: todos@geneura.ugr.es, http://geneura.ugr.es Contact: todos@geneura.ugr.es, http://geneura.ugr.es
mak@dhi.dk mak@dhi.dk
*/ */
//----------------------------------------------------------------------------- //-----------------------------------------------------------------------------
@ -94,7 +94,7 @@ void omp_apply(eoUF<EOT&, void>& _proc, std::vector<EOT>& _pop)
//default(none) shared(_proc, _pop, size) //default(none) shared(_proc, _pop, size)
for (size_t i = 0; i < size; ++i) for (size_t i = 0; i < size; ++i)
{ {
_proc(_pop[i]); _proc(_pop[i]);
} }
} }
@ -112,7 +112,7 @@ void omp_dynamic_apply(eoUF<EOT&, void>& _proc, std::vector<EOT>& _pop)
//default(none) shared(_proc, _pop, size) //default(none) shared(_proc, _pop, size)
for (size_t i = 0; i < size; ++i) for (size_t i = 0; i < size; ++i)
{ {
_proc(_pop[i]); _proc(_pop[i]);
} }
} }

2
eo/src/do/.cvsignore
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@ -1,2 +0,0 @@
Makefile.in
Makefile

3
eo/src/eo
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@ -199,8 +199,7 @@
#include <eoLinearDecreasingWeightUp.h> #include <eoLinearDecreasingWeightUp.h>
#include <eoGaussRealWeightUp.h> #include <eoGaussRealWeightUp.h>
#include <utils/eoParserLogger.h> #include <utils/eoLogger.h>
#include <utils/eoParallel.h> #include <utils/eoParallel.h>
#endif #endif

9
eo/src/eoDualFitness.h
View file

@ -132,7 +132,6 @@ public:
return *this; return *this;
} }
//! Comparison that separate feasible individuals from unfeasible ones. Feasible are always better //! Comparison that separate feasible individuals from unfeasible ones. Feasible are always better
/*! /*!
* Use less as a default comparison operator * Use less as a default comparison operator
@ -160,14 +159,16 @@ public:
} }
//! Greater: if the other is lesser than me //! Greater: if the other is lesser than me
bool operator>( const eoDualFitness<BaseType, Compare>& other ) const { return other < *this; } bool operator>( const eoDualFitness& other ) const { return other < *this; }
//! Less or equal: if the other is not lesser than me //! Less or equal: if the other is not lesser than me
bool operator<=( const eoDualFitness<BaseType, Compare>& other ) const { return !(other < *this); } bool operator<=( const eoDualFitness& other ) const { return !(other < *this); }
//! Greater or equal: if the other is not greater than me //! Greater or equal: if the other is not greater than me
bool operator>=(const eoDualFitness<BaseType, Compare>& other ) const { return !(*this < other); } bool operator>=(const eoDualFitness& other ) const { return !(*this < other); }
//! Equal: if the other is equal to me
bool operator==(const eoDualFitness& other) const { return ( _is_feasible == other._is_feasible ) && ( _value == other._value ); }
public: public:

35
eo/src/eoEasyEA.h
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@ -78,7 +78,8 @@ template<class EOT> class eoEasyEA: public eoAlgo<EOT>
selectTransform(dummySelect, dummyTransform), selectTransform(dummySelect, dummyTransform),
breed(_breed), breed(_breed),
mergeReduce(dummyMerge, dummyReduce), mergeReduce(dummyMerge, dummyReduce),
replace(_replace) replace(_replace),
isFirstCall(true)
{} {}
/** Ctor taking a breed and merge, an overload of ctor to define an offspring size */ /** Ctor taking a breed and merge, an overload of ctor to define an offspring size */
@ -95,7 +96,8 @@ template<class EOT> class eoEasyEA: public eoAlgo<EOT>
selectTransform(dummySelect, dummyTransform), selectTransform(dummySelect, dummyTransform),
breed(_breed), breed(_breed),
mergeReduce(dummyMerge, dummyReduce), mergeReduce(dummyMerge, dummyReduce),
replace(_replace) replace(_replace),
isFirstCall(true)
{ {
offspring.reserve(_offspringSize); // This line avoids an incremental resize of offsprings. offspring.reserve(_offspringSize); // This line avoids an incremental resize of offsprings.
} }
@ -113,7 +115,9 @@ template<class EOT> class eoEasyEA: public eoAlgo<EOT>
selectTransform (dummySelect, dummyTransform), selectTransform (dummySelect, dummyTransform),
breed (_breed), breed (_breed),
mergeReduce (dummyMerge, dummyReduce), mergeReduce (dummyMerge, dummyReduce),
replace (_replace) { replace (_replace),
isFirstCall(true)
{
} }
*/ */
@ -131,7 +135,8 @@ template<class EOT> class eoEasyEA: public eoAlgo<EOT>
selectTransform(dummySelect, dummyTransform), selectTransform(dummySelect, dummyTransform),
breed(_breed), breed(_breed),
mergeReduce(dummyMerge, dummyReduce), mergeReduce(dummyMerge, dummyReduce),
replace(_replace) replace(_replace),
isFirstCall(true)
{} {}
@ -149,7 +154,8 @@ template<class EOT> class eoEasyEA: public eoAlgo<EOT>
selectTransform(_select, _transform), selectTransform(_select, _transform),
breed(selectTransform), breed(selectTransform),
mergeReduce(dummyMerge, dummyReduce), mergeReduce(dummyMerge, dummyReduce),
replace(_replace) replace(_replace),
isFirstCall(true)
{} {}
/// Ctor eoBreed, eoMerge and eoReduce. /// Ctor eoBreed, eoMerge and eoReduce.
@ -166,7 +172,8 @@ template<class EOT> class eoEasyEA: public eoAlgo<EOT>
selectTransform(dummySelect, dummyTransform), selectTransform(dummySelect, dummyTransform),
breed(_breed), breed(_breed),
mergeReduce(_merge, _reduce), mergeReduce(_merge, _reduce),
replace(mergeReduce) replace(mergeReduce),
isFirstCall(true)
{} {}
/// Ctor eoSelect, eoTransform, and eoReplacement /// Ctor eoSelect, eoTransform, and eoReplacement
@ -183,7 +190,8 @@ template<class EOT> class eoEasyEA: public eoAlgo<EOT>
selectTransform(_select, _transform), selectTransform(_select, _transform),
breed(selectTransform), breed(selectTransform),
mergeReduce(dummyMerge, dummyReduce), mergeReduce(dummyMerge, dummyReduce),
replace(_replace) replace(_replace),
isFirstCall(true)
{} {}
/// Ctor eoSelect, eoTransform, eoMerge and eoReduce. /// Ctor eoSelect, eoTransform, eoMerge and eoReduce.
@ -201,7 +209,8 @@ template<class EOT> class eoEasyEA: public eoAlgo<EOT>
selectTransform(_select, _transform), selectTransform(_select, _transform),
breed(selectTransform), breed(selectTransform),
mergeReduce(_merge, _reduce), mergeReduce(_merge, _reduce),
replace(mergeReduce) replace(mergeReduce),
isFirstCall(true)
{} {}
@ -210,7 +219,13 @@ template<class EOT> class eoEasyEA: public eoAlgo<EOT>
/// Apply a few generation of evolution to the population. /// Apply a few generation of evolution to the population.
virtual void operator()(eoPop<EOT>& _pop) virtual void operator()(eoPop<EOT>& _pop)
{ {
_pop.reserve(offspring.capacity()); if (isFirstCall)
{
size_t total_capacity = _pop.capacity() + offspring.capacity();
_pop.reserve(total_capacity);
offspring.reserve(total_capacity);
isFirstCall = false;
}
eoPop<EOT> empty_pop; eoPop<EOT> empty_pop;
@ -293,6 +308,8 @@ template<class EOT> class eoEasyEA: public eoAlgo<EOT>
eoPop<EOT> offspring; eoPop<EOT> offspring;
bool isFirstCall;
// Friend classes // Friend classes
friend class eoIslandsEasyEA <EOT> ; friend class eoIslandsEasyEA <EOT> ;
friend class eoDistEvalEasyEA <EOT> ; friend class eoDistEvalEasyEA <EOT> ;

110
eo/src/eoReduce.h
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@ -90,81 +90,87 @@ Softer selective pressure than pure truncate
template <class EOT> class eoEPReduce : public eoReduce<EOT> template <class EOT> class eoEPReduce : public eoReduce<EOT>
{ {
public: public:
typedef typename EOT::Fitness Fitness; typedef typename EOT::Fitness Fitness;
eoEPReduce(unsigned _t_size ): eoEPReduce(unsigned _t_size ):
t_size(_t_size) t_size(_t_size)
{
if (t_size < 2)
{
eo::log << eo::warnings << "Warning: EP tournament size should be >= 2. Adjusted" << std::endl;
t_size = 2;
}
}
/// helper struct for comparing on std::pairs
// compares the scores
// uses the fitness if scores are equals ????
typedef std::pair<float, typename eoPop<EOT>::iterator> EPpair;
struct Cmp {
bool operator()(const EPpair a, const EPpair b) const
{ {
if (b.first == a.first) if (t_size < 2)
return (*b.second < *a.second); {
return b.first < a.first; eo::log << eo::warnings << "Warning: EP tournament size should be >= 2. Adjusted" << std::endl;
t_size = 2;
}
} }
};
/// helper struct for comparing on std::pairs
// compares the scores
// uses the fitness if scores are equals ????
typedef std::pair<float, typename eoPop<EOT>::iterator> EPpair;
struct Cmp {
bool operator()(const EPpair a, const EPpair b) const
{
if (b.first == a.first)
return (*b.second < *a.second);
return b.first < a.first;
}
};
void operator()(eoPop<EOT>& _newgen, unsigned _newsize) void operator()(eoPop<EOT>& _newgen, unsigned _newsize)
{ {
unsigned int presentSize = _newgen.size(); unsigned int presentSize = _newgen.size();
if (presentSize == _newsize) if (presentSize == _newsize)
return; return;
if (presentSize < _newsize) if (presentSize < _newsize)
throw std::logic_error("eoTruncate: Cannot truncate to a larger size!\n"); throw std::logic_error("eoTruncate: Cannot truncate to a larger size!\n");
std::vector<EPpair> scores(presentSize); std::vector<EPpair> scores(presentSize);
for (unsigned i=0; i<presentSize; i++) for (unsigned i=0; i<presentSize; i++)
{ {
scores[i].second = _newgen.begin()+i; scores[i].second = _newgen.begin()+i;
Fitness fit = _newgen[i].fitness(); Fitness fit = _newgen[i].fitness();
for (unsigned itourn = 0; itourn < t_size; ++itourn) for (unsigned itourn = 0; itourn < t_size; ++itourn)
{ {
const EOT & competitor = _newgen[rng.random(presentSize)]; const EOT & competitor = _newgen[rng.random(presentSize)];
if (fit > competitor.fitness()) if (fit > competitor.fitness())
scores[i].first += 1; scores[i].first += 1;
else if (fit == competitor.fitness()) else if (fit == competitor.fitness())
scores[i].first += 0.5; scores[i].first += 0.5;
} }
} }
// now we have the scores // now we have the scores
typename std::vector<EPpair>::iterator it = scores.begin() + _newsize; typename std::vector<EPpair>::iterator it = scores.begin() + _newsize;
std::nth_element(scores.begin(), it, scores.end(), Cmp()); std::nth_element(scores.begin(), it, scores.end(), Cmp());
// sort(scores.begin(), scores.end(), Cmp()); // sort(scores.begin(), scores.end(), Cmp());
unsigned j; unsigned j;
// std::cout << "Les scores apres tri\n"; // std::cout << "Les scores apres tri\n";
// for (j=0; j<scores.size(); j++) // for (j=0; j<scores.size(); j++)
// { // {
// std::cout << scores[j].first << " " << *scores[j].second << std::endl; // std::cout << scores[j].first << " " << *scores[j].second << std::endl;
// } // }
eoPop<EOT> tmPop;
tmPop.reserve(presentSize);
tmPop.clear();
for (j=0; j<_newsize; j++) for (j=0; j<_newsize; j++)
{ {
tmPop.push_back(*scores[j].second); tmPop.push_back(*scores[j].second);
} }
_newgen.swap(tmPop); _newgen.swap(tmPop);
// erase does not work, but I'm sure there is a way in STL to mark // erase does not work, but I'm sure there is a way in STL to mark
// and later delete all inside a std::vector ?????? // and later delete all inside a std::vector ??????
// this would avoid all copies here // this would avoid all copies here
// it = scores.begin() + _newsize; // it = scores.begin() + _newsize;
// while (it < scores.end()) // while (it < scores.end())
// _newgen.erase(it->second); // _newgen.erase(it->second);
} }
private: private:
unsigned t_size; unsigned t_size;
eoPop<EOT> tmPop;
}; };
/** a truncate class that does not sort, but repeatidely kills the worse. /** a truncate class that does not sort, but repeatidely kills the worse.
@ -220,7 +226,9 @@ public:
if (oldSize < _newsize) if (oldSize < _newsize)
throw std::logic_error("eoDetTournamentTruncate: Cannot truncate to a larger size!\n"); throw std::logic_error("eoDetTournamentTruncate: Cannot truncate to a larger size!\n");
// Now OK to erase some losers // Now OK to erase some losers
std::cout << "oldSize - _newsize: " << oldSize - _newsize << std::endl;
for (unsigned i=0; i<oldSize - _newsize; i++) for (unsigned i=0; i<oldSize - _newsize; i++)
{ {
//OLDCODE EOT & eo = inverse_deterministic_tournament<EOT>(_newgen, t_size); //OLDCODE EOT & eo = inverse_deterministic_tournament<EOT>(_newgen, t_size);

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eo/src/es/.cvsignore
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@ -1,8 +0,0 @@
*.lo
*.la
.deps
.libs
Makefile
Makefile.in
libcma.a
libes.a

40
eo/src/es/CMakeLists.txt
View file

@ -14,25 +14,28 @@ SET(CMA_LIB_OUTPUT_PATH ${EO_BINARY_DIR}/lib)
SET(LIBRARY_OUTPUT_PATH ${ES_LIB_OUTPUT_PATH}) # the same output for the two libs SET(LIBRARY_OUTPUT_PATH ${ES_LIB_OUTPUT_PATH}) # the same output for the two libs
SET (ES_SOURCES make_algo_scalar_es.cpp SET(ES_SOURCES
make_algo_scalar_real.cpp make_algo_scalar_es.cpp
make_checkpoint_es.cpp make_algo_scalar_real.cpp
make_checkpoint_real.cpp make_checkpoint_es.cpp
make_continue_es.cpp make_checkpoint_real.cpp
make_continue_real.cpp make_continue_es.cpp
make_genotype_es.cpp make_continue_real.cpp
make_genotype_real.cpp make_genotype_es.cpp
make_op_es.cpp make_genotype_real.cpp
make_op_real.cpp make_op_es.cpp
make_pop_es.cpp make_op_real.cpp
make_pop_real.cpp make_pop_es.cpp
make_run_es.cpp make_pop_real.cpp
make_run_real.cpp) make_run_es.cpp
make_run_real.cpp
SET (CMA_SOURCES eig.cpp )
CMAState.cpp
CMAParams.cpp)
SET(CMA_SOURCES
eig.cpp
CMAState.cpp
CMAParams.cpp
)
ADD_LIBRARY(es STATIC ${ES_SOURCES}) ADD_LIBRARY(es STATIC ${ES_SOURCES})
INSTALL(TARGETS es ARCHIVE DESTINATION lib COMPONENT libraries) INSTALL(TARGETS es ARCHIVE DESTINATION lib COMPONENT libraries)
@ -54,4 +57,3 @@ SET(CMA_VERSION ${GLOBAL_VERSION})
SET_TARGET_PROPERTIES(cma PROPERTIES VERSION "${CMA_VERSION}") SET_TARGET_PROPERTIES(cma PROPERTIES VERSION "${CMA_VERSION}")
###################################################################################### ######################################################################################

7
eo/src/ga/.cvsignore
View file

@ -1,7 +0,0 @@
*.lo
*.la
.deps
.libs
Makefile
Makefile.in
libga.a

18
eo/src/ga/CMakeLists.txt
View file

@ -12,14 +12,15 @@ INCLUDE_DIRECTORIES(${CMAKE_CURRENT_SOURCE_DIR})
SET(GA_LIB_OUTPUT_PATH ${EO_BINARY_DIR}/lib) SET(GA_LIB_OUTPUT_PATH ${EO_BINARY_DIR}/lib)
SET(LIBRARY_OUTPUT_PATH ${GA_LIB_OUTPUT_PATH}) SET(LIBRARY_OUTPUT_PATH ${GA_LIB_OUTPUT_PATH})
SET (GA_SOURCES make_algo_scalar_ga.cpp SET(GA_SOURCES
make_checkpoint_ga.cpp make_algo_scalar_ga.cpp
make_continue_ga.cpp make_checkpoint_ga.cpp
make_genotype_ga.cpp make_continue_ga.cpp
make_op_ga.cpp make_genotype_ga.cpp
make_pop_ga.cpp make_op_ga.cpp
make_run_ga.cpp) make_pop_ga.cpp
make_run_ga.cpp
)
ADD_LIBRARY(ga STATIC ${GA_SOURCES}) ADD_LIBRARY(ga STATIC ${GA_SOURCES})
INSTALL(TARGETS ga ARCHIVE DESTINATION lib COMPONENT libraries) INSTALL(TARGETS ga ARCHIVE DESTINATION lib COMPONENT libraries)
@ -35,4 +36,3 @@ SET(GA_VERSION ${GLOBAL_VERSION})
SET_TARGET_PROPERTIES(ga PROPERTIES VERSION "${GA_VERSION}") SET_TARGET_PROPERTIES(ga PROPERTIES VERSION "${GA_VERSION}")
###################################################################################### ######################################################################################

6
eo/src/gp/.cvsignore
View file

@ -1,6 +0,0 @@
*.lo
*.la
.deps
.libs
Makefile
Makefile.in

1
eo/src/gp/CMakeLists.txt
View file

@ -1,3 +1,2 @@
FILE(GLOB HDRS *.h) FILE(GLOB HDRS *.h)
INSTALL(FILES ${HDRS} DESTINATION include/eo/gp COMPONENT headers) INSTALL(FILES ${HDRS} DESTINATION include/eo/gp COMPONENT headers)

6
eo/src/other/.cvsignore
View file

@ -1,6 +0,0 @@
*.lo
*.la
.deps
.libs
Makefile
Makefile.in

7
eo/src/utils/.cvsignore
View file

@ -1,7 +0,0 @@
*.lo
*.la
.deps
.libs
Makefile
Makefile.in
libeoutils.a

36
eo/src/utils/CMakeLists.txt
View file

@ -12,24 +12,24 @@ INCLUDE_DIRECTORIES(${CMAKE_CURRENT_SOURCE_DIR})
SET(EOUTILS_LIB_OUTPUT_PATH ${EO_BINARY_DIR}/lib) SET(EOUTILS_LIB_OUTPUT_PATH ${EO_BINARY_DIR}/lib)
SET(LIBRARY_OUTPUT_PATH ${EOUTILS_LIB_OUTPUT_PATH}) SET(LIBRARY_OUTPUT_PATH ${EOUTILS_LIB_OUTPUT_PATH})
SET (EOUTILS_SOURCES eoData.cpp SET(EOUTILS_SOURCES
eoFileMonitor.cpp eoData.cpp
eoGnuplot.cpp eoFileMonitor.cpp
eoGnuplot1DMonitor.cpp eoGnuplot.cpp
eoGnuplot1DSnapshot.cpp eoGnuplot1DMonitor.cpp
eoIntBounds.cpp eoGnuplot1DSnapshot.cpp
eoParser.cpp eoIntBounds.cpp
eoRealBounds.cpp eoParser.cpp
eoRNG.cpp eoRealBounds.cpp
eoState.cpp eoRNG.cpp
eoOStreamMonitor.cpp eoState.cpp
eoUpdater.cpp eoOStreamMonitor.cpp
make_help.cpp eoUpdater.cpp
pipecom.cpp make_help.cpp
eoLogger.cpp pipecom.cpp
eoParserLogger.cpp eoLogger.cpp
eoParallel.cpp) eoParallel.cpp
)
ADD_LIBRARY(eoutils STATIC ${EOUTILS_SOURCES}) ADD_LIBRARY(eoutils STATIC ${EOUTILS_SOURCES})
INSTALL(TARGETS eoutils ARCHIVE DESTINATION lib COMPONENT libraries) INSTALL(TARGETS eoutils ARCHIVE DESTINATION lib COMPONENT libraries)

93
eo/src/utils/eoLogger.cpp
View file

@ -26,30 +26,31 @@ Authors:
*/ */
#ifdef _INTERIX #ifdef _WIN32
#include <io.h> #include <io.h>
#else // _INTERIX #else // _WIN32
#include <unistd.h> #include <unistd.h>
#endif // ! _INTERIX #endif // ! _WIN32
#include <fcntl.h> #include <fcntl.h>
#include <cstdlib> #include <cstdlib>
#include <cstdio> // used to define EOF #include <cstdio> // used to define EOF
#include <iostream> #include <iostream>
#include <sstream>
#include <exception>
#include <stdexcept>
#include <locale>
#include "eoLogger.h" #include "eoLogger.h"
eoLogger eo::log; eoLogger::eoLogger() :
std::ostream(&_obuf),
eoLogger::eoLogger() _verbose("quiet", "verbose", "Set the verbose level", 'v'),
: std::ostream(&_obuf), _printVerboseLevels(false, "print-verbose-levels", "Print verbose levels", 'l'),
_selectedLevel(eo::progress), _contextLevel(eo::quiet), _output("", "output", "Redirect a standard output to a file", 'o'),
_fd(2), _obuf(_fd, _contextLevel, _selectedLevel)
_selectedLevel(eo::progress),
_contextLevel(eo::quiet),
_fd(2),
_obuf(_fd, _contextLevel, _selectedLevel)
{ {
_standard_io_streams[&std::cout] = 1; _standard_io_streams[&std::cout] = 1;
_standard_io_streams[&std::clog] = 2; _standard_io_streams[&std::clog] = 2;
@ -71,18 +72,56 @@ eoLogger::~eoLogger()
if (_fd > 2) { ::close(_fd); } if (_fd > 2) { ::close(_fd); }
} }
std::string eoLogger::className() const void eoLogger::_createParameters( eoParser& parser )
{
//------------------------------------------------------------------
// we are saying to eoParser to create the parameters created above.
//------------------------------------------------------------------
std::string section("Logger");
parser.processParam(_verbose, section);
parser.processParam(_printVerboseLevels, section);
parser.processParam(_output, section);
//------------------------------------------------------------------
//------------------------------------------------------------------
// we're gonna redirect the log to the given filename if -o is used.
//------------------------------------------------------------------
if ( ! _output.value().empty() )
{
eo::log << eo::file( _output.value() );
}
//------------------------------------------------------------------
//------------------------------------------------------------------
// // we're gonna print the list of levels if -l parameter is used.
//------------------------------------------------------------------
if ( _printVerboseLevels.value() )
{
eo::log.printLevels();
}
//------------------------------------------------------------------
}
std::string eoLogger::className() const
{ {
return ("eoLogger"); return ("eoLogger");
} }
void eoLogger::addLevel(std::string name, eo::Levels level) void eoLogger::addLevel(std::string name, eo::Levels level)
{ {
_levels[name] = level; _levels[name] = level;
_sortedLevels.push_back(name); _sortedLevels.push_back(name);
} }
void eoLogger::printLevels() const void eoLogger::printLevels() const
{ {
std::cout << "Available verbose levels:" << std::endl; std::cout << "Available verbose levels:" << std::endl;
@ -95,25 +134,25 @@ void eoLogger::printLevels() const
::exit(0); ::exit(0);
} }
eoLogger& operator<<(eoLogger& l, const eo::Levels lvl) eoLogger& operator<<(eoLogger& l, const eo::Levels lvl)
{ {
l._contextLevel = lvl; l._contextLevel = lvl;
return l; return l;
} }
eoLogger& operator<<(eoLogger& l, eo::file f) eoLogger& operator<<(eoLogger& l, eo::file f)
{ {
l._fd = ::open(f._f.c_str(), O_WRONLY | O_APPEND | O_CREAT, 0644); l._fd = ::open(f._f.c_str(), O_WRONLY | O_APPEND | O_CREAT, 0644);
return l; return l;
} }
eoLogger& operator<<(eoLogger& l, eo::setlevel v) eoLogger& operator<<(eoLogger& l, eo::setlevel v)
{ {
l._selectedLevel = (v._lvl < 0 ? l._levels[v._v] : v._lvl); l._selectedLevel = (v._lvl < 0 ? l._levels[v._v] : v._lvl);
return l; return l;
} }
eoLogger& operator<<(eoLogger& l, std::ostream& os) eoLogger& operator<<(eoLogger& l, std::ostream& os)
{ {
if (l._standard_io_streams.find(&os) != l._standard_io_streams.end()) if (l._standard_io_streams.find(&os) != l._standard_io_streams.end())
{ {
@ -128,20 +167,20 @@ eoLogger::outbuf::outbuf(const int& fd,
: _fd(fd), _contextLevel(contexlvl), _selectedLevel(selectedlvl) : _fd(fd), _contextLevel(contexlvl), _selectedLevel(selectedlvl)
{} {}
int eoLogger::outbuf::overflow(int_type c) int eoLogger::outbuf::overflow(int_type c)
{ {
if (_selectedLevel >= _contextLevel) if (_selectedLevel >= _contextLevel)
{ {
if (_fd >= 0 && c != EOF) if (_fd >= 0 && c != EOF)
{ {
ssize_t num; size_t num;
num = ::write(_fd, &c, 1); num = ::write(_fd, &c, 1);
} }
} }
return c; return c;
} }
namespace eo namespace eo
{ {
file::file(const std::string f) file::file(const std::string f)
: _f(f) : _f(f)
@ -155,3 +194,13 @@ namespace eo
: _v(std::string("")), _lvl(lvl) : _v(std::string("")), _lvl(lvl)
{} {}
} }
//! make_verbose gets level of verbose and sets it in eoLogger
void make_verbose(eoParser& parser)
{
eo::log._createParameters( parser );
eo::log << eo::setlevel(eo::log._verbose.value());
}
eoLogger eo::log;

95
eo/src/utils/eoLogger.h
View file

@ -32,15 +32,12 @@ Caner Candan <caner.candan@thalesgroup.com>
Here's an example explaning how to use eoLogger: Here's an example explaning how to use eoLogger:
\code \code
#include <iostream> #include <eo>
#include <utils/eoLogger.h>
#include <utils/eoParserLogger.h>
int main(int ac, char** av) int main(int ac, char** av)
{ {
// We are declaring first an overload of eoParser class using Logger // We are declaring the usual eoParser class
// component. eoParser parser(ac, av);
eoParserLogger parser(ac, av);
// This call is important to allow -v parameter to change user level. // This call is important to allow -v parameter to change user level.
make_verbose(parser); make_verbose(parser);
@ -88,17 +85,17 @@ Caner Candan <caner.candan@thalesgroup.com>
*/ */
#ifndef eoLogger_h #ifndef eoLogger_h
# define eoLogger_h #define eoLogger_h
# include <map> #include <map>
# include <vector> #include <vector>
# include <string> #include <string>
# include <iosfwd> #include <iosfwd>
# include "eoObject.h" #include "eoObject.h"
#include "eoParser.h"
namespace eo
namespace eo
{ {
/** /**
* Levels contents all the available levels in eoLogger * Levels contents all the available levels in eoLogger
@ -117,7 +114,7 @@ namespace eo
* file * file
* this structure combined with the friend operator<< below is an easy way to select a file as output. * this structure combined with the friend operator<< below is an easy way to select a file as output.
*/ */
struct file struct file
{ {
file(const std::string f); file(const std::string f);
const std::string _f; const std::string _f;
@ -127,7 +124,7 @@ namespace eo
* setlevel * setlevel
* this structure combined with the friend operator<< below is an easy way to set a verbose level. * this structure combined with the friend operator<< below is an easy way to set a verbose level.
*/ */
struct setlevel struct setlevel
{ {
setlevel(const std::string v); setlevel(const std::string v);
setlevel(const Levels lvl); setlevel(const Levels lvl);
@ -141,14 +138,14 @@ namespace eo
* Class providing a verbose management through EO * Class providing a verbose management through EO
* Use of a global variable eo::log to easily use the logger like std::cout * Use of a global variable eo::log to easily use the logger like std::cout
*/ */
class eoLogger : public eoObject, class eoLogger : public eoObject,
public std::ostream public std::ostream
{ {
public: public:
eoLogger(); eoLogger();
~eoLogger(); ~eoLogger();
virtual std::string className() const; virtual std::string className() const;
//! Print the available levels on the standard output //! Print the available levels on the standard output
void printLevels() const; void printLevels() const;
@ -158,107 +155,115 @@ public:
* Use this function if you want to be able to compare selected levels to a given one, like: * Use this function if you want to be able to compare selected levels to a given one, like:
* if( eo::log.getLevelSelected() >= eo::progress ) {...} * if( eo::log.getLevelSelected() >= eo::progress ) {...}
*/ */
eo::Levels getLevelSelected() const { return _selectedLevel; } inline eo::Levels getLevelSelected() const { return _selectedLevel; }
/*! Returns the current level of the context /*! Returns the current level of the context
* the one given when you output message with the logger * the one given when you output message with the logger
*/ */
eo::Levels getLevelContext() const { return _contextLevel; } inline eo::Levels getLevelContext() const { return _contextLevel; }
protected: protected:
void addLevel(std::string name, eo::Levels level); void addLevel(std::string name, eo::Levels level);
private:
void _createParameters( eoParser& );
private: private:
/** /**
* outbuf * outbuf
* this class inherits from std::streambuf which is used by eoLogger to write the buffer in an output stream * this class inherits from std::streambuf which is used by eoLogger to write the buffer in an output stream
*/ */
class outbuf : public std::streambuf class outbuf : public std::streambuf
{ {
public: public:
outbuf(const int& fd, outbuf(const int& fd, const eo::Levels& contexlvl, const eo::Levels& selectedlvl);
const eo::Levels& contexlvl,
const eo::Levels& selectedlvl);
protected: protected:
virtual int overflow(int_type c); virtual int overflow(int_type c);
private: private:
const int& _fd; const int& _fd;
const eo::Levels& _contextLevel; const eo::Levels& _contextLevel;
const eo::Levels& _selectedLevel; const eo::Levels& _selectedLevel;
}; };
private: private:
/** /**
* MapLevel is the type used by the map member _levels. * MapLevel is the type used by the map member _levels.
*/ */
typedef std::map<std::string, eo::Levels> MapLevel; typedef std::map<std::string, eo::Levels> MapLevel;
public: public:
/** /**
* operator<< used there to set a verbose mode. * operator<< used there to set a verbose mode.
*/ */
friend eoLogger& operator<<(eoLogger&, const eo::Levels); friend eoLogger& operator<<(eoLogger&, const eo::Levels);
/** /**
* operator<< used there to set a filename through the class file. * operator<< used there to set a filename through the class file.
*/ */
friend eoLogger& operator<<(eoLogger&, eo::file); friend eoLogger& operator<<(eoLogger&, eo::file);
/** /**
* operator<< used there to set a verbose level through the class setlevel. * operator<< used there to set a verbose level through the class setlevel.
*/ */
friend eoLogger& operator<<(eoLogger&, eo::setlevel); friend eoLogger& operator<<(eoLogger&, eo::setlevel);
/** /**
* operator<< used there to be able to use std::cout to say that we wish to redirect back the buffer to a standard output. * operator<< used there to be able to use std::cout to say that we wish to redirect back the buffer to a standard output.
*/ */
friend eoLogger& operator<<(eoLogger&, std::ostream&); friend eoLogger& operator<<(eoLogger&, std::ostream&);
private: private:
friend void make_verbose(eoParser&);
eoValueParam<std::string> _verbose;
eoValueParam<bool> _printVerboseLevels;
eoValueParam<std::string> _output;
/** /**
* _selectedLevel is the member storing verbose level setted by the user thanks to operator() * _selectedLevel is the member storing verbose level setted by the user thanks to operator()
*/ */
eo::Levels _selectedLevel; eo::Levels _selectedLevel;
eo::Levels _contextLevel; eo::Levels _contextLevel;
/** /**
* _fd in storing the file descriptor at this place we can disable easily the buffer in * _fd in storing the file descriptor at this place we can disable easily the buffer in
* changing the value at -1. It is used by operator <<. * changing the value at -1. It is used by operator <<.
*/ */
int _fd; int _fd;
/** /**
* _obuf std::ostream mandates to use a buffer. _obuf is a outbuf inheriting of std::streambuf. * _obuf std::ostream mandates to use a buffer. _obuf is a outbuf inheriting of std::streambuf.
*/ */
outbuf _obuf; outbuf _obuf;
/** /**
* _levels contains all the existing level order by position * _levels contains all the existing level order by position
*/ */
MapLevel _levels; MapLevel _levels;
/** /**
* _levelsOrder is just a list to keep the order of levels * _levelsOrder is just a list to keep the order of levels
*/ */
std::vector<std::string> _sortedLevels; std::vector<std::string> _sortedLevels;
/** /**
* _standard_io_streams * _standard_io_streams
*/ */
std::map< std::ostream*, int > _standard_io_streams; std::map< std::ostream*, int > _standard_io_streams;
}; };
/** @example t-eoLogger.cpp /** @example t-eoLogger.cpp
*/ */
namespace eo void make_verbose(eoParser&);
namespace eo
{ {
/** /**
* log is an external global variable defined to easily use a same way than std::cout to write a log. * log is an external global variable defined to easily use a same way than std::cout to write a log.
*/ */
extern eoLogger log; extern eoLogger log;
} }
/** @} */ /** @} */
#endif // !eoLogger_h #endif // !eoLogger_h

80
eo/src/utils/eoParserLogger.cpp
View file

@ -1,80 +0,0 @@
/*
(c) Thales group, 2010
This library is free software; you can redistribute it and/or modify it under
the terms of the GNU Lesser General Public License as published by the Free
Software Foundation; version 2 of the license.
This library is distributed in the hope that it will be useful, but WITHOUT ANY
WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A
PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details.
You should have received a copy of the GNU Lesser General Public License along
with this library; if not, write to the Free Software Foundation, Inc., 59
Temple Place, Suite 330, Boston, MA 02111-1307 USA
Contact: http://eodev.sourceforge.net
Authors:
Johann Dreo <johann.dreo@thalesgroup.com>
Caner Candan <caner.candan@thalesgroup.com>
*/
#include "eoParserLogger.h"
eoParserLogger::eoParserLogger(unsigned _argc, char** _argv,
std::string _programDescription /*= ""*/
,
std::string _lFileParamName /*= "param-file"*/,
char _shortHand /*= 'p'*/)
: eoParser(_argc, _argv, _programDescription, _lFileParamName, _shortHand),
_verbose("quiet", "verbose", "Set the verbose level", 'v'),
_printVerboseLevels(false, "print-verbose-levels", "Print verbose levels", 'l'),
_output("", "output", "Redirect a standard output to a file", 'o')
{
//------------------------------------------------------------------
// we are saying to eoParser to create the parameters created above.
//------------------------------------------------------------------
processParam(_verbose);
processParam(_printVerboseLevels);
processParam(_output);
//------------------------------------------------------------------
//------------------------------------------------------------------
// we're gonna redirect the log to the given filename if -o is used.
//------------------------------------------------------------------
if ( ! _output.value().empty() )
{
eo::log << eo::file( _output.value() );
}
//------------------------------------------------------------------
//------------------------------------------------------------------
// // we're gonna print the list of levels if -l parameter is used.
//------------------------------------------------------------------
if ( _printVerboseLevels.value() )
{
eo::log.printLevels();
}
//------------------------------------------------------------------
}
eoParserLogger::~eoParserLogger()
{}
//! make_verbose gets level of verbose and sets it in eoLogger
void make_verbose(eoParserLogger& _parser)
{
eo::log << eo::setlevel(_parser._verbose.value());
}

60
eo/src/utils/eoParserLogger.h
View file

@ -1,62 +1,36 @@
/* // -*- mode: c++; c-indent-level: 4; c++-member-init-indent: 8; comment-column: 35; -*-
/*
(c) Thales group, 2010 (c) Thales group, 2010
This library is free software; you can redistribute it and/or modify it under This library is free software; you can redistribute it and/or
the terms of the GNU Lesser General Public License as published by the Free modify it under the terms of the GNU Lesser General Public
Software Foundation; version 2 of the license. License as published by the Free Software Foundation;
version 2 of the License.
This library is distributed in the hope that it will be useful, but WITHOUT ANY This library is distributed in the hope that it will be useful,
WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A but WITHOUT ANY WARRANTY; without even the implied warranty of
PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details. MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
Lesser General Public License for more details.
You should have received a copy of the GNU Lesser General Public License along You should have received a copy of the GNU Lesser General Public
with this library; if not, write to the Free Software Foundation, Inc., 59 License along with this library; if not, write to the Free Software
Temple Place, Suite 330, Boston, MA 02111-1307 USA Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
Contact: http://eodev.sourceforge.net Contact: http://eodev.sourceforge.net
Authors: Authors:
Johann Dréo <johann.dreo@thalesgroup.com> Caner Candan <caner.candan@thalesgroup.com>
Caner Candan <caner.candan@thalesgroup.com>
*/ */
#ifndef EO_PARSER_LOGGER_H #ifndef EO_PARSER_LOGGER_H
#define EO_PARSER_LOGGER_H #define EO_PARSER_LOGGER_H
#include "eoParser.h" #include "eoParser.h"
#include "eoLogger.h"
/** #warning "[eoParserLogger] is deprecated"
* A parser that use the advanced logging system (@see eoLogger)
*
* @ingroup Parameters
* @ingroup Logging
*/
class eoParserLogger : public eoParser
{
public:
eoParserLogger(unsigned _argc, char** _argv,
std::string _programDescription = "",
std::string _lFileParamName = "param-file",
char _shortHand = 'p');
~eoParserLogger();
private: typedef eoParser eoParserLogger;
friend void make_verbose(eoParserLogger&);
eoValueParam<std::string> _verbose;
eoValueParam<bool> _printVerboseLevels;
eoValueParam<std::string> _output;
};
void make_verbose(eoParserLogger&);
#endif // !EO_PARSER_LOGGER_H #endif // !EO_PARSER_LOGGER_H
// Local Variables:
// coding: iso-8859-1
// mode: C++
// c-file-offsets: ((c . 0))
// c-file-style: "Stroustrup"
// fill-column: 80
// End:

30
eo/test/.cvsignore
View file

@ -1,30 +0,0 @@
*.o
*.csv
*.sav
*.status
.deps
Makefile
Makefile.in
t-eo
t-eobin
t-eobreeder
t-eofitness
t-eoinclusion
t-eoinsertion
t-eolottery
t-eoproblem
t-eogeneration
t-eoNonUniform
t-eo2dVector
t-eoEasyEA
t-eoUniform
t-eoRandom
t-eoCheckpointing
t-eoVector
t-eoAtomOps
t-selectOne
t-eoStateAndParser
t-eoGOpSel
t-eoExternalEO
t-eoESFull
t-eoSymreg

8
eo/test/t-eoLogger.cpp
View file

@ -2,17 +2,13 @@
// t-eoLogger.cpp // t-eoLogger.cpp
//----------------------------------------------------------------------------- //-----------------------------------------------------------------------------
#include <iostream>
#include <utils/eoLogger.h>
#include <utils/eoParserLogger.h>
#include <eo> #include <eo>
//----------------------------------------------------------------------------- //-----------------------------------------------------------------------------
int main(int ac, char** av) int main(int ac, char** av)
{ {
eoParserLogger parser(ac, av); eoParser parser(ac, av);
if (parser.userNeedsHelp()) if (parser.userNeedsHelp())
{ {

5
eo/test/t-openmp.cpp
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@ -32,9 +32,6 @@ Caner Candan <caner.candan@thalesgroup.com>
#include <sstream> #include <sstream>
#include <climits> #include <climits>
#include <utils/eoLogger.h>
#include <utils/eoParserLogger.h>
#include <eo> #include <eo>
#include <es/make_real.h> #include <es/make_real.h>
@ -114,7 +111,7 @@ void measure( size_t p,
int main(int ac, char** av) int main(int ac, char** av)
{ {
eoParserLogger parser(ac, av); eoParser parser(ac, av);
unsigned int popMin = parser.getORcreateParam((unsigned int)1, "popMin", "Population Min", 'p', "Evolution Engine").value(); unsigned int popMin = parser.getORcreateParam((unsigned int)1, "popMin", "Population Min", 'p', "Evolution Engine").value();
unsigned int popStep = parser.getORcreateParam((unsigned int)1, "popStep", "Population Step", 0, "Evolution Engine").value(); unsigned int popStep = parser.getORcreateParam((unsigned int)1, "popStep", "Population Step", 0, "Evolution Engine").value();

2
eo/tutorial/.cvsignore
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@ -1,2 +0,0 @@
Makefile.in
Makefile

6
eo/tutorial/Lesson1/.cvsignore
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@ -1,6 +0,0 @@
Makefile.in
.deps
FirstBitGA
Makefile
exercise1.3
FirstRealGA

6
eo/tutorial/Lesson2/.cvsignore
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@ -1,6 +0,0 @@
Makefile.in
.deps
FirstBitEA
FirstRealEA
exercise2.3
Makefile

3
eo/tutorial/Lesson3/.cvsignore
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@ -1,3 +0,0 @@
Makefile.in
.deps
Makefile

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eo/tutorial/Lesson4/.cvsignore
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@ -1,3 +0,0 @@
Makefile.in
.deps
Makefile

3
eo/tutorial/Lesson5/.cvsignore
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@ -1,3 +0,0 @@
Makefile.in
.deps
Makefile

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eo/tutorial/Lesson6/.cvsignore
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@ -1 +0,0 @@
Makefile.in

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eo/tutorial/Templates/.cvsignore
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@ -1,2 +0,0 @@
Makefile.in
Makefile

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eo/tutorial/html/.cvsignore
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@ -1,2 +0,0 @@
Makefile.in
Makefile

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eo/tutorial/pdf/.cvsignore
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@ -1,2 +0,0 @@
Makefile.in
Makefile

6
website/index.html
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@ -138,7 +138,9 @@
<p>EO is <em>a template-based, ANSI-C++ evolutionary computation library</em> which helps you to write your own stochastic optimization algorithms insanely fast.</p> <p>EO is <em>a template-based, ANSI-C++ evolutionary computation library</em> which helps you to write your own stochastic optimization algorithms insanely fast.</p>
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<p>Evolutionary algorithms forms a family of algorithms inspired by the theory of evolution, that solve various problems. <p>Evolutionary algorithms forms a family of algorithms inspired by the theory of evolution, that solve various problems.
They evolve a set of solutions to a given problem, in order to produce the best results. They evolve a set of solutions to a given problem, in order to produce the best results.
@ -175,6 +177,9 @@
<p>If you need immediate support or have any question, you can join us on the official chatroom. Just go on our <a href="http://chat.jabberfr.org/muckl_int/index.php?room=eo">webchat interface</a> and enter your nick. If you already have an XMPP account (Jabber or Google Talk, for example), you can directly connect to the <a href="xmpp:eo@chat.jabberfr.org">eo@chat.jabberfr.org</a> MUC with your favorite client.</p> <p>If you need immediate support or have any question, you can join us on the official chatroom. Just go on our <a href="http://chat.jabberfr.org/muckl_int/index.php?room=eo">webchat interface</a> and enter your nick. If you already have an XMPP account (Jabber or Google Talk, for example), you can directly connect to the <a href="xmpp:eo@chat.jabberfr.org">eo@chat.jabberfr.org</a> MUC with your favorite client.</p>
<div style="font-size:1.5em;color:red;border:thin solid blue; background-color:#eef;margin:1em;padding:0.5em;text-align:center;-moz-border-radius:1em;"><a href="http://sourceforge.net/projects/eodev/files/">Download</a></div>
<h1><a name="Features"></a>Features <a href="#Plan">⤒</a></h1> <h1><a name="Features"></a>Features <a href="#Plan">⤒</a></h1>
<h2><a name="Component-based"></a>Component-based framework</h2> <h2><a name="Component-based"></a>Component-based framework</h2>
@ -184,7 +189,6 @@
<p>If your problem is a bit more exotic, you will have to code a class that represents how your <em>individuals</em> (a solution to your problem) are represented, and perhaps some <em>variations operators</em>, but most of the other operators (selection, replacement, stopping criteria, command-line interface, etc.) are already available in EO.</p> <p>If your problem is a bit more exotic, you will have to code a class that represents how your <em>individuals</em> (a solution to your problem) are represented, and perhaps some <em>variations operators</em>, but most of the other operators (selection, replacement, stopping criteria, command-line interface, etc.) are already available in EO.</p>
<p><img src="Evolutionary_algorithm.png" title="A typical Evolutionary Algorithm, as seen from the EO point of vue − Johann Dréo − CC-BY-SA" /></p> <p><img src="Evolutionary_algorithm.png" title="A typical Evolutionary Algorithm, as seen from the EO point of vue − Johann Dréo − CC-BY-SA" /></p>
<h2><a name="Main-Features"></a>Main Features</h2> <h2><a name="Main-Features"></a>Main Features</h2>
<!-- <img src="http://upload.wikimedia.org/wikipedia/en/timeline/3f507249a36a4a38020e7fc0a5f448df.png" title="Metaheuristics that can be implemented with EO and ParadisEO, ordered by date of invention − Johann Dréo/Wikipédia − CC-BY-SA" style="float:right;" /> --> <!-- http://en.wikipedia.org/wiki/Metaheuristic --> <!-- <img src="http://upload.wikimedia.org/wikipedia/en/timeline/3f507249a36a4a38020e7fc0a5f448df.png" title="Metaheuristics that can be implemented with EO and ParadisEO, ordered by date of invention − Johann Dréo/Wikipédia − CC-BY-SA" style="float:right;" /> --> <!-- http://en.wikipedia.org/wiki/Metaheuristic -->