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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
57 changed files with 2012 additions and 2662 deletions
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221
eo/.cproject
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@ -1,221 +0,0 @@
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25
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 @@
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1664
eo/CHANGELOG
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13
eo/CMakeLists.txt
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@ -14,12 +14,11 @@ INCLUDE(eo-conf.cmake OPTIONAL)
# set the project name and other variables
PROJECT(EO)
SET(PROJECT_VERSION_MAJOR 1)
SET(PROJECT_VERSION_MINOR 1)
SET(PROJECT_VERSION_PATCH 1)
#SET(PROJECT_VERSION_MAJOR 1)
#SET(PROJECT_VERSION_MINOR 1)
#SET(PROJECT_VERSION_PATCH 1)
SET(PROJECT_VERSION "${PROJECT_VERSION_MAJOR}.${PROJECT_VERSION_MINOR}.${PROJECT_VERSION_PATCH}" CACHE STRING "Package version" FORCE)
#SET(VERSION "${PROJECT_VERSION_MAJOR}.${PROJECT_VERSION_MINOR}" CACHE STRING "Global version" FORCE)
SET(VERSION "1.1.1-edge" CACHE STRING "Global version" FORCE)
SET(VERSION "${PROJECT_VERSION_MAJOR}.${PROJECT_VERSION_MINOR}${PROJECT_VERSION_MISC}" CACHE STRING "Global version" FORCE)
SET(GLOBAL_VERSION "${VERSION}")
SET(PACKAGE_BUGREPORT "eodev-help@sourceforge.net" CACHE STRING "Package bug report" FORCE)
@ -58,7 +57,9 @@ INCLUDE(FindGnuplot)
INCLUDE(CheckLibraryExists)
INCLUDE(ConfigureChecks.cmake)
IF(UNIX)
INCLUDE(ConfigureChecks.cmake)
ENDIF(UNIX)
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
include(CheckIncludeFile)
include(CheckIncludeFiles)
include(CheckSymbolExists)
include(CheckFunctionExists)
include(CheckLibraryExists)
INCLUDE(CheckIncludeFile)
INCLUDE(CheckIncludeFiles)
INCLUDE(CheckSymbolExists)
INCLUDE(CheckFunctionExists)
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(stdio.h "stdio.h" HAVE_STDIO_H)
check_include_files(stdlib.h "stdlib.h" HAVE_STDLIB_H)
check_include_files(string.h "string.h" HAVE_STRING_H)
check_include_files(strings.h "strings.h" HAVE_STRINGS_H)
check_include_files(malloc.h "malloc.h" HAVE_MALLOC_H)
check_include_files(limits.h "limits.h" HAVE_LIMITS_H)
check_include_files(unistd.h "unistd.h" HAVE_UNISTD_H)
check_include_files(stdint.h "stdint.h" HAVE_STDINT_H)
CHECK_INCLUDE_FILES(math.h "math.h" HAVE_MATH_H)
CHECK_INCLUDE_FILES(stdio.h "stdio.h" HAVE_STDIO_H)
CHECK_INCLUDE_FILES(stdlib.h "stdlib.h" HAVE_STDLIB_H)
CHECK_INCLUDE_FILES(string.h "string.h" HAVE_STRING_H)
CHECK_INCLUDE_FILES(strings.h "strings.h" HAVE_STRINGS_H)
CHECK_INCLUDE_FILES(malloc.h "malloc.h" HAVE_MALLOC_H)
CHECK_INCLUDE_FILES(limits.h "limits.h" HAVE_LIMITS_H)
CHECK_INCLUDE_FILES(unistd.h "unistd.h" HAVE_UNISTD_H)
CHECK_INCLUDE_FILES(stdint.h "stdint.h" HAVE_STDINT_H)
# 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
# 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:
- 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.
- Run `make check && make dist`
- Test distribution (unpack, configure, make check)
- Tag released code in cvs, in order to allow a branch to be created at that
version if the necessity will arise later
- Put distribution files at SourceForge
- use the "archive_current.sh" script to create the source archive
- Build the packages
- Put source archive and packages files at SourceForge
- Post news on SourceForge project-page
- 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
==================
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 do this, run the shell script sh ./autogen.sh.
To compile EO you will need CMake and a compiler for your system.
The `configure' shell script attempts to guess correct values for
various system-dependent variables used during compilation. It uses
those values to create a `Makefile' in each directory of the package.
It may also create one or more `.h' files containing system-dependent
definitions. Finally, it creates a shell script `config.status' that
you can run in the future to recreate the current configuration, and a
file `config.log' containing compiler output (useful mainly for
debugging `configure').
So far the available scripts for posix systems using g++ are the following:
* build_gcc_linux_release : the most usefull script, build the core libraries in release mode
* build_gcc_linux_debug : build the core libraries with debugging informations in the binaries
* build_gcc_linux_tutorial : build the core libraries and the tutorials
* build_gcc_linux_unittest : build the core libraries and the tests executables
* build_gcc_linux_stl_parallel : build the core libraries enabling STL parallel algorithms (like sorting)
* build_gcc_linux_pyeo : build the core libraries and the python module
* 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'
and enabled with `--cache-file=config.cache' or simply `-C') that saves
the results of its tests to speed up reconfiguring. (Caching is
disabled by default to prevent problems with accidental use of stale
cache files.)
For Windows systems using Visual Studio:
* build_vs2008_release.bat
You may need to adapt the ID to your version of Visual Studio, edit
the "Visual Studio 9 2008" string accordingly.
If you need to do unusual things to compile the package, please try
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 libraries are in the "release/lib/" or "debug/lib/" directories.
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
=====================
Some systems require unusual options for compilation or linking that
the `configure' script does not know about. Run `./configure --help'
for details on some of the pertinent environment variables.
The build scripts are really simple, take a look at them to see how to use the
build system.
You can give `configure' initial values for configuration parameters
by setting variables in the command line or in the environment. Here
is an example:
Basically, the steps are:
0. remove any old build directory that's on the way:
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
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 `..'.
Installation using packages
===========================
If you have to use a `make' that does not support the `VPATH'
variable, you have to compile the package for one architecture at a
time in the source code directory. After you have installed the
package for one architecture, use `make distclean' before reconfiguring
for another architecture.
To construct a dummy template of the EO package you will need CPack. Be warned
that those do not guarantee correct dependencies and version management.
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
`/usr/local/bin', `/usr/local/man', etc. You can specify an
installation prefix other than `/usr/local' by giving `configure' the
option `--prefix=PATH'.
To install the framework system-wide, copy the "eo/" directory somewhere in your
path. The "lib/" directory should be reachable for the linker and the "src/"
directory must be in the compiler include 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
- 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
* release 1.2 (10. May. 2011)
- 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
- package generation system
- 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/
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
./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
evolution engines handy is to create a new standalone EO project from
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:
Go to your build-directory and run
$(SRCDIR)/configure
make
make check
make install
where $(SRCDIR) is the top-level source directory of EO, i.e. where
the sources where unpacked.
Go to the "eo/" and run one of the "build_*" script. 
Run "$(SRCDIR)/configure --help" for possible options. You can specify
to not build example applications, the tutorial, or to build the
ParadisEO tutorial. You may also change the installation directory
that way.
Using the "build_gcc_linux_release" script is generally what you want. The
binaries are then located in the "release/" directory.
Now you should probably go to the tutorial and start learning about EO
features and programming.
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.
In case of problems or if you want advanced options, you can read the INSTALL file.
===================================================================
DIRECTORY STRUCTURE
@ -99,12 +87,3 @@ structure:
|
+-- 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
mkdir release
mkdir -p release
cd release
cmake -DENABLE_EO_TUTORIAL=1 ..
make

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

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

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