doc: bump version + clean authors list

* Adds eoRankingCached with better documentation
* Optimize eoRanking with caching and index vector
* Adds t-eoRankingCached.cpp

.github/workflows/build_ubuntu_debug.yml

@@ -0,0 +1,47 @@
+name: Build Debug (Ubuntu)
+on: [push, pull_request]
+
+env:
+  # Customize the CMake build type here (Release, Debug, RelWithDebInfo, etc.)
+  BUILD_TYPE: Debug
+
+jobs:
+  build:
+    # The CMake configure and build commands are platform agnostic and should work equally well on Windows or Mac.
+    # You can convert this to a matrix build if you need cross-platform coverage.
+    # See: https://docs.github.com/en/free-pro-team@latest/actions/learn-github-actions/managing-complex-workflows#using-a-build-matrix
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        compiler: [g++-10, g++-9, g++-8, g++-7, clang-6, clang-7, clang-8, clang-9, clang-10, clang-11, clang-12] 
+
+    steps:
+    - uses: actions/checkout@v4
+    
+    - name: Caching objects
+      id: cache-objects
+      uses: actions/cache@v4
+      with:
+        path: ~/.cache/ccache
+        key: ${{ runner.os }}-${{env.BUILD_TYPE}}-${{ matrix.compiler }}-objects
+
+    - name: Install Dependencies
+      shell: bash
+      run: |
+        sudo apt-get install libeigen3-dev libboost-dev
+
+    - name: Configure
+      # Configure CMake in a 'build' subdirectory. `CMAKE_BUILD_TYPE` is only required if you are using a single-configuration generator such as make.
+      # See https://cmake.org/cmake/help/latest/variable/CMAKE_BUILD_TYPE.html?highlight=cmake_build_type
+      run: cmake -B ${{github.workspace}}/build -DCMAKE_BUILD_TYPE=${{env.BUILD_TYPE}} -DEDO=ON -DEDO_USE_LIB=Eigen3 -DENABLE_CMAKE_EXAMPLE=ON -DENABLE_CMAKE_TESTING=ON
+
+    - name: Build
+      # Build your program with the given configuration
+      run: cmake --build ${{github.workspace}}/build --config ${{env.BUILD_TYPE}}
+
+    - name: Test
+      working-directory: ${{github.workspace}}/build
+      # Execute tests defined by the CMake configuration.  
+      # See https://cmake.org/cmake/help/latest/manual/ctest.1.html for more detail
+      run: ctest -C ${{env.BUILD_TYPE}}
+      

.gitignore

@@ -1,11 +1,20 @@
-# ignore html files
+# ignore generated files
 *.html
+*.pdf
 
 # ignore all textual files
 *.txt
+*.swp
+*.swo
+.kak_history
+*.log
+*.csv
+*.ods
 
 # ignore object and archive files
 *.[oa]
+*.bak
+*.tar*
 tags
 
 # ignore auto-saved files
@@ -29,4 +38,7 @@ debug/*
 build/*
 website/EO_star.png
 website/paradiseo_logo.png
+Release/*
+Debug/*
+Build/*
 

AUTHORS

@@ -1,41 +1,52 @@
 Current maintainers
 ===================
-Arnaud Liefooghe        <arnaud.liefooghe@univ-lille1.fr>
-Clive Canape            <clive.canape@inria.fr>
-Johann Dreo             <johann@dreo.fr>
-Sébastien Verel         <sebastien.verel@inria.fr>
 
-Active developpers
-==================
-Alexandre Quemy         <alexandre.quemy@inria.fr>
-Benjamin Bouvier        <bnjbouv@gmail.com>
-Caner Candan            <caner@candan.fr>
-Pierre Savéant          <pierre.saveant@thalesgroup.com>
+Johann Dreo             <johann@dreo.fr>
+
 
 Past contributors
 =================
+
 atantar
+Alesandro Sidero
+Alexandre Quemy
+Alix Zheng
+Amine Aziz-Alaoui
+Arnaud Liefooghe
+Benjamin Bouvier
+Bahri
+Caner Candan
+Clive Canape
 fatene
 Gustavo Romero Lopez
 jboisson
 Jeroen Eggermont
 Jochen Küpper
-Joost                   <joost@dsj.nl>
+Joost
 Juan Julian Merelo Guervos
 Jérémie Humeau
+Jxtopher
 Karima Boufaras
-legillon
+legillono
+Leo Bertheas
 Louis Da Costa
 Loïc Jean David Arjanen
 Maarten Keijzer
+Mammar Amara
+Manu
 Marc Schoenauer
 Marie-Éleonore
 Mostepha Khouadjia
 Olivier König
+Pierre Savéant
 Pedro Angel Castillo Valdivieso
+Potalas
+Ronald Pinho
 Steve Madere
 Sébastien Cahon
+Sébastien Verel
 Thomas Legrand
+Thibault Lasnier
 Victor Manuel Rivas Santos
 wcancino
 xohm

CMakeLists.txt

@@ -1,10 +1,11 @@
 # ParadiseO
 
+
 ######################################################################################
 ### 0) Check the CMake version
 ######################################################################################
 
-cmake_minimum_required(VERSION 3.0 FATAL_ERROR)
+cmake_minimum_required(VERSION 3.10 FATAL_ERROR)
 
 ######################################################################################
 ### 1) Define the project
@@ -12,13 +13,24 @@ cmake_minimum_required(VERSION 3.0 FATAL_ERROR)
 
 ## Name
 project("ParadisEO"
-    VERSION 3.0.0
+    VERSION 3.1.3
     DESCRIPTION "Evolutionary optimization framework"
     LANGUAGES C CXX)
 
 ## Language
 set(CMAKE_CXX_STANDARD 17)
 
+## ccache
+find_program(CCACHE_PROGRAM ccache)
+
+if (CCACHE_PROGRAM)
+    message(NOTICE "-- ccache is enabled (found here: ${CCACHE_PROGRAM})")
+    set_property(GLOBAL PROPERTY RULE_LAUNCH_COMPILE "\"${CCACHE_PROGRAM}\"")
+    set_property(GLOBAL PROPERTY RULE_LAUNCH_LINK "\"${CCACHE_PROGRAM}\"")
+else ()
+    message(NOTICE "-- ccache has not been found")
+endif ()
+
 
 ######################################################################################
 ### 2) Check dependencies
@@ -51,16 +63,16 @@ include(${CMAKE_CURRENT_SOURCE_DIR}/cmake/Target.cmake)
 ######################################################################################
 
 ## Paths to sources of modules
-set(  EO_SRC_DIR "${CMAKE_SOURCE_DIR}/eo"   CACHE INTERNAL "ParadisEO-EO   source directory" FORCE)
-set( EDO_SRC_DIR "${CMAKE_SOURCE_DIR}/edo"  CACHE INTERNAL "ParadisEO-EDO  source directory" FORCE)
-set(  MO_SRC_DIR "${CMAKE_SOURCE_DIR}/mo"   CACHE INTERNAL "ParadisEO-MO   source directory" FORCE)
-set(MOEO_SRC_DIR "${CMAKE_SOURCE_DIR}/moeo" CACHE INTERNAL "ParadisEO-MOEO source directory" FORCE)
-set( SMP_SRC_DIR "${CMAKE_SOURCE_DIR}/smp"  CACHE INTERNAL "ParadisEO-SMP  source directory" FORCE)
-set( MPI_SRC_DIR "${CMAKE_SOURCE_DIR}/eo/src/mpi"  CACHE INTERNAL "ParadisEO-MPI source directory" FORCE)
+set(  EO_SRC_DIR "${PROJECT_SOURCE_DIR}/eo"   CACHE INTERNAL "ParadisEO-EO   source directory" FORCE)
+set( EDO_SRC_DIR "${PROJECT_SOURCE_DIR}/edo"  CACHE INTERNAL "ParadisEO-EDO  source directory" FORCE)
+set(  MO_SRC_DIR "${PROJECT_SOURCE_DIR}/mo"   CACHE INTERNAL "ParadisEO-MO   source directory" FORCE)
+set(MOEO_SRC_DIR "${PROJECT_SOURCE_DIR}/moeo" CACHE INTERNAL "ParadisEO-MOEO source directory" FORCE)
+set( SMP_SRC_DIR "${PROJECT_SOURCE_DIR}/smp"  CACHE INTERNAL "ParadisEO-SMP  source directory" FORCE)
+set( MPI_SRC_DIR "${PROJECT_SOURCE_DIR}/eo/src/mpi"  CACHE INTERNAL "ParadisEO-MPI source directory" FORCE)
 
-set(PROBLEMS_SRC_DIR "${CMAKE_SOURCE_DIR}/problems" CACHE INTERNAL "Problems dependant source directory" FORCE)
+set(PROBLEMS_SRC_DIR "${PROJECT_SOURCE_DIR}/problems" CACHE INTERNAL "Problems dependant source directory" FORCE)
 
-set(CMAKE_BASE_SOURCE_DIR ${CMAKE_SOURCE_DIR})
+set(CMAKE_BASE_SOURCE_DIR ${PROJECT_SOURCE_DIR})
 
 # All libraries are built in <build_dir>/lib/
 set(  EO_BIN_DIR "${CMAKE_BINARY_DIR}" CACHE INTERNAL "ParadisEO-EO   binary directory" FORCE)
@@ -80,31 +92,34 @@ set(SMP "false" CACHE BOOL "Build the SMP module")
 set(MPI "false" CACHE BOOL "Build the MPI module")
 
 ## EO Module
-set(EO_MODULE_NAME "Evolving Object")
+set(MODULE_NAME "Paradiseo")
+set(DOXYGEN_CONFIG_DIR ${CMAKE_CURRENT_SOURCE_DIR}/doxygen)
+# set(EO_MODULE_NAME "Evolving Objects")
 set(CMAKE_SOURCE_DIR ${EO_SRC_DIR})
 add_subdirectory(${EO_SRC_DIR})
 
 if(NOT EO_ONLY)
     ## MO Module
-    set(MO_MODULE_NAME "Moving objects")
+    # set(MO_MODULE_NAME "Moving Objects")
+    # set(MODULE_NAME "Moving Objects")
     set(CMAKE_SOURCE_DIR ${MO_SRC_DIR})
     add_subdirectory(${MO_SRC_DIR})
 
     ## EDO Module
     if(EDO)
-        set(EDO_MODULE_NAME "Evolving Distribution Objects")
+        # set(EDO_MODULE_NAME "Evolving Distribution Objects")
         set(CMAKE_SOURCE_DIR ${EDO_SRC_DIR})
         add_subdirectory(${EDO_SRC_DIR})
     endif()
 
     ## MOEO Module
-    set(MOEO_MODULE_NAME "Multi-Objectives EO")
+    # set(MOEO_MODULE_NAME "Multi-Objectives EO")
     set(CMAKE_SOURCE_DIR ${MOEO_SRC_DIR})
     add_subdirectory(${MOEO_SRC_DIR})
 
     ## SMP Module
     if(SMP)
-        set(SMP_MODULE_NAME "Symmetric Multi-Processing")
+        # set(SMP_MODULE_NAME "Symmetric Multi-Processing")
         set(CMAKE_SOURCE_DIR ${SMP_SRC_DIR})
         add_subdirectory(${SMP_SRC_DIR})
     endif()

CONTRIBUTING.md

@@ -0,0 +1,84 @@
+
+Licenses
+========
+
+ParadisEO modules are using free software licenses,
+any contribution should be licensed under the same license.
+
+| Module | License | Version | Copyleft | Patent-left |
+|--------|---------|---------|----------|-------------|
+| EO     | LGPL    |  2      | Lib only | No          |
+| EDO    | LGPL    |  2      | Lib only | No          |
+| MO     | CeCILL  |  2.1    | Yes      | No          |
+| MOEO   | CeCILL  |  2.1    | Yes      | No          |
+| SMP    | CeCILL  |  2.1    | Yes      | No          |
+
+
+Contribution Workflow
+=====================
+
+The maintainer(s) will try to answer under a couple of weeks, if not, do not hesitate to send an e-mail.
+
+If you're not familiar with Git and merge requests, start by cloning one of the main repository:
+- `git clone https://github.com/nojhan/paradiseo.git`
+- `git clone https://scm.gforge.inria.fr/anonscm/git/paradiseo/paradiseo.git`
+
+
+Git workflow
+------------
+
+ParadisEO follows a classical Git workflow using merge requests.
+In order to fix a bug or add a feature yourself, you would follow this process.
+
+```bash
+cd paradiseo
+git pull origin master # Always start with an up-to-date version.
+git checkout -b <my_feature> # Always work on a dedicated branch.
+# [ make some modifications… ]
+git commit <whatever>
+mkdir build
+cd build
+cmake -DCMAKE_BUILD_TYPE=Debug -BUILD_TESTING=ON -DENABLE_CMAKE_TESTING=ON .. && make && ctest # Always test.
+cd ..
+git pull origin master # Always check that your modification still merges.
+```
+
+If everything went without error, you can either send the patch or submit a merge request.
+To do so, you can either:
+- submit a "pull request" on Github: [nojhan/paradiseo](https://github.com/nojhan/paradiseo),
+- or send a patch on the [ParadisEO mailing list](https://lists.gforge.inria.fr/cgi-bin/mailman/listinfo/paradiseo-users).
+
+See below for the details.
+
+
+Github pull request
+-------------------
+
+Once logged in Github, go to the [maintainer repository](https://github.com/nojhan/paradiseo) and click the "fork" button.
+You should have your own copy of the ParadisEO project under your own name.
+Then add it as an additional "remote" to your ParadisEO Git tree: `git remote add me <your own URL>`.
+Then, checkout the branch holding the modifications you want to propose, check that it merges with the main repository
+and push it on your own repository:
+```bash
+git checkout <my_feature>
+git pull origin master
+git push me <my_feature>
+```
+
+Then go to the maintainer's repository page, click on the "Pull request" tab, and on the "New pull request" button.
+You should then select the maintainer's master branch on the left dropdown list, and your own `my_feature` on the right one.
+Explain why the maintainer should merge your modifications and click the "Submit" button.
+
+
+E-mail your patch
+-----------------
+
+Generate a patch file from the difference between your branch and a fresh master:
+```bash
+git pull origin master
+git diff master <my_feature> > my_feature.patch
+```
+
+Then send the `my_feature.patch` (along with your explanations about why the maintainer should merge your modifications)
+to the [mailing list](https://lists.gforge.inria.fr/cgi-bin/mailman/listinfo/paradiseo-users).
+

INSTALL

@@ -1,200 +0,0 @@
-
-==========================================================================================
-                       INSTALLING PARADISEO		
-==========================================================================================
-
-There is several ways to install ParadisEO, according to your needs.
-
-==========================================================================================
-                       WINDOWS		
-==========================================================================================
-
-On Windows, and for compatibility reason, ParadisEO supply support only for MinGW.
-Feel free to test with another compiler and to send us you report.
-
-------------------------------------------------------------------------------------------
-1) WITH EXE
-------------------------------------------------------------------------------------------
-
-The simpliest way ton install ParadisEO on Windows is to use the NSIS installer. 
-We would like to draw your attention on the fact that the PATH variable will not 
-be affected by the installation in order to allow anybody to install ParadisEO 
-without administration right. To have further information about how to use ParadisEO 
-in your project, see the tutorial on ParadisEO website (http://paradiseo.gforge.inria.fr/).
-
-------------------------------------------------------------------------------------------
-2) WITH CMAKE
-------------------------------------------------------------------------------------------
-
-You can also install ParadisEO using CMake. For that you must have a compiler installed, 
-and obviously cmake.
-Then, follow UNIX instructions.
-
-==========================================================================================
-                       UNIX		
-==========================================================================================
-------------------------------------------------------------------------------------------
-1. WITH CMAKE
-------------------------------------------------------------------------------------------
-1.0 DEPENDENCIES
-------------------------------------------------------------------------------------------
-Optionnal
-- Doxygen for documentation
-- lcov for coverage
-
-------------------------------------------------------------------------------------------
-1.1 FAST INSTALLATION
-------------------------------------------------------------------------------------------
-
-After getting ParadisEO sources from repository, you have to create a build directory in order to keep your file tree clean.
-
-> mkdir build
-> cd build
-
-To make the installation easier, ParadisEO propose you two installation types which are "Full" and "Min".
-Full corresponds examples / lessons, tests and obviously libraries. 
-Min corresponds to libraries and headers and it is the standard behavior.
-
-You can specified an installation type by adding the following declaration to cmake :
-
-> cmake .. -DINSTALL_TYPE=full
-> cmake .. -DINSTALL_TYPE=min
-which is equivalent to
-> cmake ..
-
-Actually, by default the generator will be "Unix Makefiles" and cmake will try to look for a C++ compiler. 
-Be sure you have make installed, or choose an alternative according to your configuration. 
-To know available generators on your computer, type cmake -help. If you are on Windows and you use MinGW, you have to specify it explicitly by adding -G "MinGW Makefiles".
-
-To compile ParadisEO simply compile sources using your generator. For instance, if you are using Unix Makefiles, type make.
-
-------------------------------------------------------------------------------------------
-1.2 BUILD TYPE
-------------------------------------------------------------------------------------------
-
-There are 2 types of build : Release or Debug.
-To explicitly change the type, add -DDEBUG=true, otherwise, it will be the Release type.
-
-------------------------------------------------------------------------------------------
-1.3 COMPILERS
-------------------------------------------------------------------------------------------
-
-You can change the compiler used by CMake with the following options :
-
->-DCMAKE_C_COMPILER=/path/to/your/c/compiler
-
->-DCMAKE_CXX_COMPILER=/path/to/your/c++/compiler
-
-------------------------------------------------------------------------------------------
-1.4 INSTALLATION
-------------------------------------------------------------------------------------------
-
-WARNING : This require administration rights.
-
-To install ParadisEO in standard paths (such as /usr/lib for lib and /usr/include for headers on UNIX-like) :
-
-> make install
-
-------------------------------------------------------------------------------------------
-2. SPECIFIC MODULE
-------------------------------------------------------------------------------------------
-2.1 EO MODULE ONLY
-------------------------------------------------------------------------------------------
-
-If you want to compile and install only the Evolving Objects module, you can add to CMake the following option :
-
-> cmake .. -DEO_ONLY
-
-------------------------------------------------------------------------------------------
-2.1 SMP MODULE
-------------------------------------------------------------------------------------------
-
-WARNING : The SMP module requires gcc 4.7 or higher. This is due to the fact that it uses the new C++ standard.
-
-WARNING : At the moment, the SMP module does not work on Windows or Mac OS X since MinGW does not provide support for std::thread 
-          and Apple does not supply a recent version of gcc (but you can try to compile gcc 4.7 by yourself).
-
-To enable the compilation of the SMP module, just add -DSMP=true to CMake :
-
-> cmake .. -DSMP=true
-
-Depending on your distribution, you might have to give to CMake the path of gcc and g++ 4.7.
-This is the case for Ubuntu 12.04 LTS for instance. Please, check installation guide on ParadisEO website for more details.
-
-If you are in that case and assuming you have a standard path for gcc et g++ 4.7 :
-
-> cmake .. -DSMP=true -DCMAKE_C_COMPILER=/usr/bin/gcc-4.7 -DCMAKE_CXX_COMPILER=/usr/bin/g++-4.7
-
-------------------------------------------------------------------------------------------
-2.2 PEO MODULE
-------------------------------------------------------------------------------------------
-
-WARNING : The PEO module requires libXML 2 and a MPI implementation such as MPICH2.
-
-To enable the compilation of the PEO module, just add -DPEO=true to CMake :
-
-> cmake .. -DPEO=true
-
-------------------------------------------------------------------------------------------
-2.3 EDO MODULE
-------------------------------------------------------------------------------------------
-
-WARNING : The EDO module requires either the Boost::ublas or the Eigen3 library.
-
-To enable the compilation of the EDO module, just add -DEDO=true to CMake :
-
-> cmake .. -DEDO=true
-
-
-------------------------------------------------------------------------------------------
-3. DOCUMENTATION
-------------------------------------------------------------------------------------------
-
-There is 2 ways to build ParadisEO documentation : module by module, or all the documentation.
-
-Targets are :
-doc for all documentations
-doc-eo for building EO documentation
-doc-mo for MO
-doc-edo for MO
-doc-moeo for MOEO
-doc-smp for SMP
-
-Each documentation are generated separatly in the module build folder. 
-For instance, after the generation of the MO documentation, you will find it in build/paradise-mo/doc.
-
-------------------------------------------------------------------------------------------
-4. LESSONS / EXAMPLES
-------------------------------------------------------------------------------------------
-
-Examples and lessons are generated by default. 
-If you want to disable lessons manually, you have to specify -DENABLE_CMAKE_TESTING=false to CMake.
-If you want to build a specific lesson or example, you can check the list of available targets with make help. 
-
-All lessons are build on the same pattern : <module>Lesson<number>.
-For instance, make moLesson4 will build the Lesson 4 from the MO module. 
-Easy, isn't it ?
-
-------------------------------------------------------------------------------------------
-5. TESTS
-------------------------------------------------------------------------------------------
-5.1 CTESTS
-------------------------------------------------------------------------------------------
-
-By performing tests, you can check your installation. 
-Testing is disable by default, except if you build with the full install type.
-To enable testing, define -DENABLE_CMAKE_TESTING=true when you launch cmake.
-
-To perform tests simply type ctest or make test.
-
-------------------------------------------------------------------------------------------
-5.2 REPORTING
-------------------------------------------------------------------------------------------
-
-Feel free to send us reports about building, installation, tests and profiling in order to help us to improve compatibilty and installation process. Sending reports is very simple :
-
-> ctest -D Experimental
-
-WARNING : Reports are anonymous. CTest will also send informations about your configuration such as OS, CPU frequency, etc.
-
-

INSTALL.md

@@ -0,0 +1,217 @@
+
+Summary
+=======
+
+As Paradiseo is a development framework, you do not really need to install it on all your systems.
+Just put it somewhere on your development computer, compile it from here and indicate where to find it to your favorite build system.
+
+
+Build
+-----
+
+Paradiseo is mainly developed for Linux, on which it is straightforward to install a C++ build chain. For example, on Ubuntu 18.04:
+```bash
+sudo apt install g++-8 cmake make libeigen3-dev libopenmpi-dev doxygen graphviz libgnuplot-iostream-dev
+```
+
+Paradiseo use the CMake build system, so building it should be as simple as:
+```bash
+mkdir build ; cd build ; cmake -DEDO=ON .. && make -j
+```
+
+The file `howto_build_paradiseo.apptainer.def` shows you how to install and build from scratch.
+It is a definition file for the [Apptainer](https://apptainer.org/) container system,
+which is often used on HPC clusters.
+
+
+Develop
+-------
+
+Download the quick start project template, edit the `CMakeLists.txt` file to indicate where to find Paradiseo and start developing your own solver.
+
+If you don't know CMake or a modern build system, you should still be able to build a stand-alone code from a `paradiseo/build` directory with something like:
+```bash
+ c++ ../solver.cpp -I../eo/src -I../edo/src -DWITH_EIGEN=1 -I/usr/include/eigen3 -std=c++17 -L./lib/ -leo -leoutils -les -lga -o solver
+```
+
+
+Install
+-------
+
+If you want to install ParadisEO system-wide anyway:
+```bash
+cmake -D CMAKE_BUILD_TYPE=Release .. && sudo make install
+```
+
+
+More details
+============
+
+As a templated framework, most of the ParadisEO code rely within headers and is thus compiled
+by you when you build your own solver.
+
+However, in order to save some compilation time,
+the EO and EDO modules are compiled within static libraries by the default build system.
+
+If you believe you have a working build chain and want to test if it works with ParadisEO,
+you can try to build the tests and the examples.
+Note that if some of them failed (but not all), you may still be able to build your own solver,
+as you will most probably not use all ParadisEO features anyway.
+
+
+Windows
+-------
+
+Last time we checked, ParadisEO could only be built with MinGW.
+Feel free to test with another compiler and to send us your report.
+
+As of today, we cannot guarantee that it will be easy to
+install ParadisEO under Windows if you're a beginner.
+There is still some (possibly outdated) help about oldest version on the [Website](http://paradiseo.gforge.inria.fr/).
+
+If you know how to install a working compiler and the dependencies,
+you may follow the same steps than the Linux process below.
+
+If you are a beginner, we strongly suggest you install a Linux distribution
+(either as an OS, as a virtual machine or using the Windows 10 compatibility layer).
+
+
+Linux
+-----
+
+### Dependencies
+
+In order to build the latest version of Paradiseo, you will need a C++ compiler supporting C++17.
+So far, GCC and CLANG gave good results under Linux. You will also need the CMake and make build tools.
+
+Some features are only available if some dependencies are installed:
+- Most of the EDO module depends on either uBlas or Eigen3. The recommended package is Eigen3, which enables the adaptive algorithms.
+- Doxygen is needed to build the API documentation, and you should also install graphviz if you want the class relationship diagrams.
+- GNUplot is needed to have the… GNUplot graphs at checkpoints.
+
+To install all those dependencies at once under Ubuntu (18.04), just type:
+```bash
+sudo apt install g++-8 cmake make libeigen3-dev libopenmpi-dev doxygen graphviz libgnuplot-iostream-dev.
+```
+
+
+### Build
+
+The build chain uses the classical workflow of CMake.
+The recommended method is to build in a specific, separated directory and call `cmake ..` from here.
+CMake will prepare the compilation script for your system of choice which you can change with the `-G <generator-name>` option (see your CMake doc for the list of available generators).
+
+Under Linux, the default is `make`, and a build command is straitghtforward:
+```bash
+mkdir build ; cd build ; cmake .. && make -j
+```
+
+There is, however, several build options which you may want to switch.
+To see them, we recommend the use of a CMake gui, like ccmake or cmake-gui.
+On the command line, you can see the available options with: `cmake -LH ..`.
+Those options can be set with the `-D<option>=<value>` argument to cmake.
+
+The first option to consider is `CMAKE_BUILD_TYPE`,
+which you most probably want to set to "Debug" (during development/tests)
+or "Release" (for production/validation).
+
+
+### More compilation options
+
+Other important options are: `EDO` (which is false by default)
+and parallelization options: `ENABLE_OPENMP`, `MPI`, `SMP`.
+
+By default, the build script will build the Paradiseo libraries only.
+
+If you `ENABLE_CMAKE_TESTING` and `BUILD_TESTING`, it will build the tests,
+which you can run with the `ctest` command.
+
+If you `ENABLE_CMAKE_EXAMPLE`, it will also build the examples.
+
+You can change the compiler used by CMake with the following options:
+`CMAKE_CXX_COMPILER=/path/to/your/c++/compiler`.
+
+
+Even more details
+=================
+
+Evolving Objects (EO) module
+----------------------------
+
+If you want to compile and install only the core EO module, set `EO_ONLY`,
+this can be helpful if you don't need other modules with more complex dependencies.
+
+Shared Memory Processing (SMP) module
+-------------------------------------
+
+The SMP module requires gcc 4.7 or higher. This is due to the fact that it uses the new C++ standard.
+
+At the moment, the SMP module does not work on Windows or Mac OS X since MinGW does not provide support for std::thread and Apple does not supply a recent version of gcc (but you can try to compile gcc 4.7 by yourself).  
+
+To enable the compilation of the SMP module, just set the `SMP` option.
+
+Depending on your distribution, you might have to give to CMake the path of gcc and g++ 4.7.
+This is the case for Ubuntu 12.04 LTS for instance.
+
+If you are in that case and assuming you have a standard path for gcc et g++ 4.7:
+```bash
+cmake .. -DSMP=true -DCMAKE_C_COMPILER=/usr/bin/gcc-4.7 -DCMAKE_CXX_COMPILER=/usr/bin/g++-4.7
+```
+
+Estimating Distribution Objects (EDO) module
+--------------------------------------------
+
+To enable the compilation of the EDO module, just set the `EDO` option.
+
+The EDO module requires a linear algebra library.
+So far the core features are implemented in either [Boost::ublas](https://www.boost.org/doc/libs/release/libs/numeric/ublas) or the [Eigen3 library](https://eigen.tuxfamily.org).
+
+The adaptive algorithms are only implemented with Eigen3, which is thus the recommended package.
+
+
+Documentation
+-------------
+
+There is 2 ways to build ParadisEO documentation: module by module, or all the documentation.
+
+Targets for the build system (usually `make`) are:
+- `doc` for all documentations,
+- `doc-eo` for building EO documentation,
+- `doc-mo` for MO,
+- `doc-edo` for MO,
+- `doc-moeo` for MOEO,
+- `doc-smp` for SMP.
+
+Each documentation are generated separatly in the module build folder.
+For instance, after the generation of the MO documentation, you will find it in `build/paradise-mo/doc`.
+
+Examples
+--------
+
+Examples and lessons are generated when `ENABLE_CMAKE_EXAMPLE` is set.
+
+If you want to build a specific lesson or example, you can check the list of available targets with `make help`.
+
+All lessons are build on the same pattern: `<module>Lesson<number>`.
+For instance, make `moLesson4` will build the Lesson 4 from the MO module.
+Easy, isn't it ?
+
+Tests
+-----
+
+By performing tests, you can check your installation.
+Testing is disable by default, except if you build with the full install type.
+To enable testing, define `ENABLE_CMAKE_TESTING` when you run cmake.
+
+To perform tests simply type `ctest` or `make test`.
+
+Reporting
+---------
+
+Feel free to send us reports about building, installation, tests and profiling in order to help us to improve compatibilty and installation process. Generate reports is very simple:
+```bash
+ctest -D Experimental
+```
+
+NOTE: Reports are anonymous, but CTest will also send informations about your configuration such as OS, CPU frequency, etc.
+

README.md

@@ -1,69 +1,273 @@
-# ParadisEO: A C++ evolutionary computation framework to build parallel stochastic optimization solvers
+# Paradiseo: a Heuristic Optimization Framework
 
-## Release
+Paradiseo is an open-source ***full-featured evolutionary computation framework*** which main purpose is to help you write ***your own stochastic optimization algorithms***, insanely fast.
 
-The actual release is paradiseo-2.0
+It focus on the efficiency of the implementation of solvers, by providing:
+- a ***modular design*** for several types of paradigms,
+- the ***largest codebase*** of existing components,
+- tools for ***automated design and selection*** of algorithms,
+- a focus on ***speed*** and several ***parallelization*** options.
 
-## Installation
+<div align="center">
+  <img width="640" alt="Paradiseo logo" src="https://raw.githubusercontent.com/nojhan/paradiseo/master/docs/img/paradiseo_logo_dark.svg"/>
+</div>
 
-The basic installation procedure must be done in a separatly folder in order to keep your file tree clean.
+# Quick Start
 
-Create a directory to build and access it:
+# Very Quick Start
 
-```
-$ mkdir build && cd build
+1. Use a recent Linux, like an Ubuntu.
+2. `sudo apt install g++-8 cmake make libeigen3-dev libopenmpi-dev doxygen graphviz libgnuplot-iostream-dev`
+3. From the Paradiseo directory: `mkdir build ; cd build ; cmake -D CMAKE_BUILD_TYPE=Release -DEDO=ON .. && make -j`
+4. Copy-paste this CMA-ES code in `cmaes.cpp`:
+```cpp
+#include <eo>
+#include <edo>
+#include <es.h>
+#include <do/make_pop.h>
+#include <do/make_run.h>
+#include <do/make_continue.h>
+#include <do/make_checkpoint.h>
+
+using R = eoReal<eoMinimizingFitness>;
+using CMA = edoNormalAdaptive<R>;
+
+R::FitnessType sphere(const R& sol) {
+    double sum = 0;
+    for(auto x : sol) { sum += x * x; }
+    return sum;
+}
+
+int main(int argc, char** argv) {
+    eoParser parser(argc, argv);
+    eoState state;
+
+    size_t dim = parser.createParam<size_t>(10,
+            "dimension", "Dimension", 'd',
+            "Problem").value();
+
+    size_t max_eval = parser.getORcreateParam<size_t>(100 * dim,
+            "maxEval", "Maximum number of evaluations", 'E',
+            "Stopping criterion").value();
+
+    edoNormalAdaptive<R> gaussian(dim);
+
+    auto& obj_func = state.pack< eoEvalFuncPtr<R> >(sphere);
+    auto& eval     = state.pack< eoEvalCounterThrowException<R> >(obj_func, max_eval);
+    auto& pop_eval = state.pack< eoPopLoopEval<R> >(eval);
+
+    auto& gen  = state.pack< eoUniformGenerator<R::AtomType> >(-5, 5);
+    auto& init = state.pack< eoInitFixedLength<R> >(dim, gen);
+    auto& pop = do_make_pop(parser, state, init);
+    pop_eval(pop,pop);
+
+    auto& eo_continue  = do_make_continue(  parser, state, eval);
+    auto& pop_continue = do_make_checkpoint(parser, state, eval, eo_continue);
+    auto& best = state.pack< eoBestIndividualStat<R> >();
+    pop_continue.add( best );
+    auto& distrib_continue = state.pack< edoContAdaptiveFinite<CMA> >();
+
+    auto& selector  = state.pack< eoRankMuSelect<R> >(dim/2);
+    auto& estimator = state.pack< edoEstimatorNormalAdaptive<R> >(gaussian);
+    auto& bounder   = state.pack< edoBounderRng<R> >(R(dim, -5), R(dim, 5), gen);
+    auto& sampler   = state.pack< edoSamplerNormalAdaptive<R> >(bounder);
+    auto& replacor  = state.pack< eoCommaReplacement<R> >();
+
+    make_verbose(parser);
+    make_help(parser);
+
+    auto& algo = state.pack< edoAlgoAdaptive<CMA> >(
+         gaussian , pop_eval, selector,
+         estimator, sampler , replacor,
+         pop_continue, distrib_continue);
+
+    try {
+        algo(pop);
+    } catch (eoMaxEvalException& e) {
+        eo::log << eo::progress << "STOP" << std::endl;
+    }
+
+    std::cout << best.value() << std::endl;
+    return 0;
+}
 ```
 
-Compile the project into the directory with ```cmake```:
+5. Compile it with: `c++ cmaes.cpp -I../eo/src -I../edo/src -DWITH_EIGEN=1 -I/usr/include/eigen3 -std=c++17 -L./lib/ -leo -leoutils -les -o cmaes`
+6. `./cmaes -h`
+
+
+## Not-so-quick Start
+
+1. Use your system of choice, as soon as you know how to operate a C++ buildchain on it.
+2. Dependencies are: `libeigen3-dev libopenmpi-dev doxygen graphviz libgnuplot-iostream-dev` (or similar packagesnames, depending on your system)
+3. From the Paradiseo directory, within a `build` directory, call the equivalent of `cmake -D CMAKE_BUILD_TYPE=Release -DEDO=ON ..`, then call your system's favorite generator (see cmake's documentation for the `-G` option).
+4. Code your own algorithm, starting from one of the numerous examples (or tests) available around ParadisEO
+   (see the source code in `<module>/test/` or `<module>/tutorial/`, or see the website).
+5. Build it, indicating where to include the needed ParadisEO `<module>/src/` directories, and the `build/lib` directory for the library linker.
+
+
+# Rationale
+
+## Black-box and Gray-box Optimization Problems
+
+Paradiseo targets the development of solvers for mathematical optimization
+problems for which you cannot compute gradients.
+The classical use case is the automated design or configuration of
+some system which is simulated.
+
+## Metaheuristics / Evolutionary Algorithms
+
+Paradiseo targets the design of metaheuristics solvers using
+computational intelligence methods, a subdomain of artificial intelligence.
+
+## Why choosing Paradiseo?
+
+Learning a full-featured framework like Paradiseo very often seems overkill.
+However, we would like to stress out that you may forget some points
+while jumping to this conclusion.
+
+**Paradiseo provides the *largest mature codebase* of state-of-the-art algorithms, and is focused on (automatically) find the *most efficient solvers*.**
+
+The most classical impediment to the use of Paradiseo is that you just want to check if your problem can actually be solved with heuristics. You feel that it would be a loss of time to learn complex stuff if it ends being useless.
+
+However, you should keep in mind that:
+
+- Metaheuristics do seem very easy to implement in textbooks, but the state-of-the art versions of efficient algorithms can be a lot more complex.
+- It is usually easy to get something to actually run, but it is far more difficult to get an efficient solver.
+- Metaheuristics performances on a given problem are very sensitive to small variations in the parameter setting or the choice of some operators. Which render large experimental plans and algorithm selection compulsory to attain peak efficiency.
+
+**Fortunately, Paradiseo have the *largest codebase* of the market, hardened along 20 years of development of tens of solvers. Additionally, it provides the tools to rapidly search for the best combination of algorithms to solve your problem, even searching for this combination *automatically*.**
+
+Paradiseo is the fastest framework on the market, which is a crucial feature for modern and robust approach to solver design and validation.
+
+Another classical criticism against Paradiseo is that C++ is hard and that a fast language is useless because speed is not a concern when your objective function is dominating all the runtime.
+
+However, we argue that:
+
+- During the design phase of your solver, you will need to estimate its performance against synthetic benchmarks that are fast to compute. In that case, fast computation means fast design iterations. And it's even more true if you plan to use automated design to find the best solver for your problem.
+- Modern C++ makes use of the very same high-level abstractions you would find in more accepted languages like Python. Sure, the syntax is cumbersome, but you will not see it after a while, given that you will work at the algorithm level.
+- C++ provides full type checking and the largest set of tooling for any modern language, which are your first line of defense against long-term bugs. Sure, it sometimes gives you the impression that you fight against the compiler, but chasing subtle interface bugs across a complex Python code is even harder.
+
+# Features
+
+## Component-based Design
+
+Designing an algorithm with Paradiseo consists in choosing what components (called operators) 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 operators to form an algorithm and connect it to your evaluation 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 encodes how solutions to your problem are represented, and perhaps a few more. For instance, you may want ad-hoc variations operators, but most of the other operators (selection, replacement, stopping criteria, command-line interface, etc.) are already available in Paradiseo.
+
+## Large Choice of Components
+
+Paradiseo is organized in several modules, either providing different "grammars" for different algorithms, either providing high-level features. All modules follows the same architecture design and are interoperable with the others, so that you can easily choose the subset of features you need.
+
+It is, for instance, easy to start with a simple local search, then add multi-objective capabilities, then shared-memory parallelization, then hybridization with an evolutionary algorithm and finally plug everything in an objective function so as to optimize the parameters with a particle swarm optimizer.
+
+## Portability
+
+Paradiseo is mainly developed under Linux operating systems, where its dependencies and the C++ toolchain are easy to install. Recent versions have been tested with gcc and clang compilers.
+
+Stable versions should however work on Windows and any Unix-like operating system with a standard-conforming C++ development system.
+
+
+# Code
+
+The latest stable version is on the official Git repository of INRIA: `git clone git://scm.gforge.inria.fr/paradiseo/paradiseo.git`
+
+## Dependencies
+
+In order to build the latest version of Paradiseo, you will need a C++ compiler supporting C++17. So far, GCC and CLANG gave good results under Linux. You will also need the CMake and make build tools.
+
+A free working build chain under Windows seems always difficult to find. Paradiseo 2.0.1 was successfully tested with MinGW (minus the PEO module), but it's unsure if it still work for recent versions. If you managed to build under Windows, your feedback would be appreciated.
+
+Some features are only available if some dependencies are installed:
+
+- Most of the EDO module depends on either uBlas or Eigen3. The recommended package is Eigen3, which enables the adaptive algorithms.
+- Doxygen is needed to build the API documentation, and you should also install graphviz if you want the class relationship diagrams.
+- GNUplot is needed to have the… GNUplot graphs at checkpoints.
+
+To install all those dependencies at once under Ubuntu (18.04), just type: `sudo apt install g++-8 cmake make libeigen3-dev libopenmpi-dev doxygen graphviz libgnuplot-iostream-dev`.
+
+## Compilation
+
+The build chain uses the classical workflow of CMake. The recommended method is to build in a specific, separated directory and call `cmake ..` from here. CMake will prepare the compilation script for your system of choice which you can change with the `-G <generator-name>` option (see the CMake doc for the list of available generators).
+
+Under Linux, the default is make, and a build command is straitghtforward: `mkdir build ; cd build ; cmake .. && make -j`.
+
+There is, however, several build options which you may want to switch. To see them, we recommend the use of a CMake gui, like ccmake or cmake-gui. On the command line, you can see the available options with: `cmake -LH ..` . Those options can be set with the `-D<option>=<value>` argument to cmake.
+
+**The first option to consider is `CMAKE_BUILD_TYPE`, which you most probably want to set to `Debug` (during development/tests) or `Release` (for production/validation).**
+
+
+Other important options are: `EDO` (which is false by default) and parallelization options: `ENABLE_OPENMP`, `MPI`, `SMP`.
+
+By default, the build script will build the Paradiseo libraries only.
+
+If you `ENABLE_CMAKE_TESTING` and `BUILD_TESTING`, it will be the tests, which you can run with the `ctest` command.
+
+If you `ENABLE_CMAKE_EXAMPLE`, it will also build the examples.
+
+If may want to make build scripts more verbose (especially when building the
+doc) by enabling `CMAKE_VERBOSE_MAKEFILE`.
+
+If `ccache` installed in your environment, it will try its best to re-use other compilations,
+which may speed-up your builds if you manage several compatible builds at the same time.
+To clear all cached objects, execute `ccache -C`.
+
+## Licenses
+
+Paradiseo is distributed under the GNU Lesser General Public License and the CeCILL license (depending on the modules).
+
+Note that those licenses places copyleft restrictions on a program created with Paradiseo, but does not apply these restrictions to other software that would links with the program.
+
+
+# Documentation
+
+Paradiseo has a lot of documentation! You will find in the source repository
+a lot of examples, the tutorials and you can generate the API documentation
+(`make doc`, then open
+`paradiseo/<build>/<module>/doc/html/index.html`).
+
+Tutorials are located in each module's directory. For example for the EO module:
+`paradiseo/eo/tutorial`.
+A lot of examples for (almost) each class are available in the test directories
+(e.g. `paradiseo/eo/test`). Example problems and bindings to external
+benchmark libraries are in `paradiseo/problems`.
+
+For academic articles, books, more tutorials, presentations slides,
+real life example of solvers and contact information,
+please see the web site (available in `paradiseo/website/index.html`).
+
+
+# Citing Paradiseo
+
+If you use Paradiseo, please cite the following publication:
+
+Johann Dreo, Arnaud Liefooghe, Sébastien Verel, Marc Schoenauer, Juan J. Merelo, Alexandre Quemy, Benjamin Bouvier, and Jan Gmys, [Paradiseo: from a modular framework for evolutionary computation to the automated design of metaheuristics —22 years of Paradiseo—](https://doi.org/10.1145/3449726.3463276), GECCO'21: Proceedings of the Genetic and Evolutionary Computation Conference Companion, 1522–1530 (2021).
+
+BiBTeX entry:
+
 ```
-$ cmake ..
-$ make
+@inproceedings{Dreo-al_2021_Paradiseo,
+    author    = {Dreo, Johann and Liefooghe, Arnaud and Verel, S\'{e}bastien and Schoenauer, Marc and Merelo, Juan J. and Quemy, Alexandre and Bouvier, Benjamin and Gmys, Jan},
+    title     = {Paradiseo: From a Modular Framework for Evolutionary Computation to the Automated Design of Metaheuristics: 22 Years of Paradiseo},
+    year      = {2021},
+    isbn      = {9781450383516},
+    publisher = {Association for Computing Machinery},
+    address   = {Online conference},
+    url       = {https://doi.org/10.1145/3449726.3463276},
+    booktitle = {Proceedings of the Genetic and Evolutionary Computation Conference Companion},
+    pages     = {1522–1530},
+    numpages  = {9}
+}
 ```
 
-Take a coffee ;)
+# Contact
 
-<font size=3>**Congratulations!! ParadiseEO is installed!**</font>
+For further information about ParadisEO, help or to report any
+problem, you can either:
 
-Please refer to paradisEO website or INSTALL file for further information about installation types and options.
+- Chat with us on our Matrix chatroom: https://app.element.io/#/room/#paradiseo:matrix.org
+- Post an issue: https://github.com/nojhan/paradiseo/issues
 
----
-
-## Directory Structure
-
-* __AUTHORS__:    Authors list;
-
-* __cmake__:  Directory of cmake files;
-
-* __CMakeLists.txt__: Definitions for building process;
-
-* __CTestConfig.cmake__:  Definitions for testing process;
-
-* __INSTALL__:    Steps and options of the installation process;
-
-* __LICENSE__: License contents;
-
-* __eo__: Specific directory of the EO (Evolving Objects) module;
-
-* __mo__: Specific directory of the MO (Moving Objects) module;
-
-* __moeo__: Specific directory of the MOEO (Multi-Objective Optimization) module;
-
-* __problems__: classical problems evaluation functions.
-
----
-## Notes
-
-ParadisEO uses EO, 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. 
-
-EO Website: http://eodev.sourceforge.net/.
-
-ParadisEO Website: http://paradiseo.gforge.inria.fr/
-
-EO is distributed under the GNU Lesser General Public License: http://www.gnu.org/copyleft/lesser.html
-
-Please read README file of each extracted directory if you have problems for the installation.
-
----
-<font size=3>**Contact**</font>
-
-<font size=2>For further information about ParadisEO, help or to report any problem : paradiseo-help@lists.gforge.inria.fr</font>

cmake/Target.cmake

@@ -27,7 +27,7 @@ if(DOXYGEN_FOUND AND DOXYGEN_EXECUTABLE)
     #         set(DOC_SMP "")
     #     endif()
     #     if(MPI)
-    #         set(DOC_MPI "make doc-mpi")
+            # set(DOC_MPI "make doc-mpi")
     #     else()
     #         set(DOC_MPI "")
     #     endif()
@@ -78,7 +78,7 @@ if(DOXYGEN_FOUND AND DOXYGEN_EXECUTABLE)
                 COMMAND make doc-eo
                 COMMAND make doc-mo
                 COMMAND make doc-moeo
-                COMMAND make doc-mpi
+                # COMMAND make doc-mpi
             )
         endif()
 
@@ -89,7 +89,7 @@ if(DOXYGEN_FOUND AND DOXYGEN_EXECUTABLE)
                 COMMAND make doc-mo
                 COMMAND make doc-moeo
                 COMMAND make doc-smp
-                COMMAND make doc-mpi
+                # COMMAND make doc-mpi
             )
         endif()
         if(EDO AND NOT SMP AND MPI)
@@ -98,7 +98,7 @@ if(DOXYGEN_FOUND AND DOXYGEN_EXECUTABLE)
                 COMMAND make doc-mo
                 COMMAND make doc-moeo
                 COMMAND make doc-edo
-                COMMAND make doc-mpi
+                # COMMAND make doc-mpi
             )
         endif()
         if(EDO AND SMP AND NOT MPI)
@@ -119,7 +119,7 @@ if(DOXYGEN_FOUND AND DOXYGEN_EXECUTABLE)
                 COMMAND make doc-moeo
                 COMMAND make doc-edo
                 COMMAND make doc-smp
-                COMMAND make doc-mpi
+                # COMMAND make doc-mpi
             )
         endif()
 
@@ -131,7 +131,7 @@ endif(DOXYGEN_FOUND AND DOXYGEN_EXECUTABLE)
 ######################################################################################
 
 if(PROFILING)
-    find_program(LCOV 
+    find_program(LCOV
         NAMES lcov
         PATHS
         "/usr/local/bin /usr/bin [HKEY_LOCAL_MACHINE\\SOFTWARE\\Rational Software\\Purify\\Setup;InstallFolder] [HKEY_CURRENT_USER\\Software]"

docs/lightblue.css

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+}
+
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+    display:block;
+    margin:1em;
+    box-shadow: 10px 10px 15px #074198;
+}
+
+.excerpt em {
+    font-weight: bold;
+}
+
+.excerpt a {
+    color:white;
+    text-decoration:underline;
+}
+
+ul#menu {
+    clear:both;
+    margin: 0;
+    padding: 0;
+    list-style: none;
+/*width:650px;*/
+}
+
+ul#menu li {
+    margin: 0;
+    padding:0;
+    float: left;
+    width:16.5%;
+    text-align: center;
+}
+
+ul#menu li a {
+    display: block;
+    font-size: 0.75em;
+    color: #FFFFFF;
+    font-weight: bold;
+    text-decoration: none;
+    background: #5588CC;
+    padding: 2px 0px 2px 0px;
+    padding: 0em 1em 0em 1em;
+}
+
+ul#menu li a:hover { background: #3366CC; color: #FFFFFF; }
+ul#menu a.selected:link { background: #3366CC; color: #FFFFFF; }
+ul#menu a.selected:visited { background: #3366CC; color: #FFFFFF; }
+
+.collapsible {
+    background-color: #eee;
+    color:#36C;
+    cursor: pointer;
+    padding: 0.2em;
+    border: thin solid #ccc;
+    text-align: left;
+    outline: none;
+    font-size: 0.75em;
+    margin-left:2em;
+    max-width:50%;
+}
+
+.active, .collapsible:hover {
+    background-color: #ddd;
+    color:#03C;
+    /* text-decoration: underline; */
+}
+
+.collapsible:after {
+    content: "\002B  ";
+    font-weight: bold;
+    float: left;
+    margin-left: 5px;
+}
+
+.active:after {
+    content: "\2212  ";
+}
+
+.details {
+    padding: 0 18px;
+    max-height: 0;
+    overflow: hidden;
+    transition: max-height 0.2s ease-out;
+    background-color: #fbfbfb;
+    border: thin solid #ccc;
+    margin-left:2em;
+}
+
+figure {
+    text-align:center;
+    padding:1em;
+    border:thin solid lightgray;
+    box-shadow: 5px 10px 18px #ddd;
+    /* min-width:400px; */
+    max-width: 60%;
+    margin:1em;
+    margin-left:20%
+}
+
+figcaption {
+    font-size: 0.75em;
+    max-width: 90%;
+    margin-left:5%;
+}
+
+.code {
+    width:95%;
+    height:70ch;
+    resize:vertical;
+    overflow-y:scroll;
+    box-shadow: 10px 10px 10px #888;
+    background-color:#2b2b2b;
+    color: #d4cfc9; 
+    border:thin solid black;
+    white-space: pre;
+}
+
+.vimCodeElement { /* white-space: pre-wrap; */ font-family: monospace; color: #d4cfc9; background-color: #2b2b2b; }
+.String { color: #cc7844; background-color: #272935; padding-bottom: 1px; }
+.Character { color: #da4939; }
+.Number { color: #519f50; }
+.LineNr { color: #6b758f; background-color: #272935; padding-bottom: 1px; }
+.Statement { color: #da4939; font-weight: bold; }
+.Type { color: #6d9cbe; }
+.Repeat { color: #da4939; }
+.Include { color: #6d9cbe; }
+.Exception { color: #da4939; }
+.StorageClass { color: #ffc66d; }
+.cppOperator { color: #b6b3eb; }
+.cppSTL { color: #f4f1ed; }
+.cppBraces { color: #ffc66d; }
+.cppStatement { color: #ffc66d; }
+.cppEndline { color: #6b758f; }
+
+.table {
+    padding:1em;
+    border:thin solid lightgray;
+    box-shadow: 5px 10px 18px #ddd;
+    width:60%;
+    max-width: 40em;
+    margin-left:20%
+}
+
+figure.table table {
+    width:100%;
+}
+
+a.comment-indicator:hover + comment { background:#ffd; position:absolute; display:block; border:1px solid black; padding:0.5em;  } 
+a.comment-indicator { background:red; display:inline-block; border:1px solid black; width:0.5em; height:0.5em;  } 
+comment { display:none;  } 
+
+@media (min-resolution: 192dpi) {
+    body {
+        font-size:1.5em;
+    }
+    #alt {
+        font-size:1em;
+    }
+}
+
+@media only screen and (max-width: 50em), screen and (min-resolution: 192dpi) and (max-width: 75em)  {
+    #alt {
+        clear:left;
+        width:100%;
+        max-width:100%;
+        height:auto;
+        text-align:left;
+        position:relative;
+    }
+
+    #shortcuts {
+        margin-left:30%;
+    }
+
+    #toc_header {
+        width:100%;
+        display:block;
+    }
+
+    #toc ol {
+        counter-reset: LIST-ITEMS 0;
+    }
+
+    .toc_section:before
+    {
+        float:left;
+        content: counter( LIST-ITEMS ) ".";
+        counter-increment: LIST-ITEMS;
+    }
+    .toc_section {
+        display:inline-block;
+        vertical-align:top;
+        *display:list-item;
+    }
+
+    #main {
+        clear:left;
+        width:95%;
+        padding-left:1em;
+        padding-right:1em;
+        text-align:justify;
+    }
+
+    pre {
+        text-align:left;
+    }
+
+    figure {
+        max-width:90%;
+        margin-left:5%;
+    }
+
+    .table {
+        padding:1em;
+        border:thin solid lightgray;
+        box-shadow: 5px 10px 18px #ddd;
+        width:80%;
+        max-width: 30em;
+        margin-left:5%
+    }
+}
+
+@media only screen and (min-width: 90em) {
+    #main {
+    }
+
+    .details {
+        font-size:0.80em;
+        color:gray;
+        box-shadow: inset 5px 5px 5px #ddd;
+    }
+
+    #Plan .excerpt {
+        width:80%;
+        margin-left:5%;
+    }
+
+    /* QUICKSTART */
+
+    #Quickstart {
+        text-align:justify;
+        display:grid;
+        grid-template-columns:1fr 1fr;
+        grid-gap:2em;
+    }
+
+    #Quickstart h1 {
+        grid-row:1;
+        grid-column-start:1;
+        grid-column-end:3;
+    }
+
+    #Quickstart #Download {
+        grid-row:2;
+        grid-column:1;
+    }
+
+    #Quickstart #Build {
+        grid-row:3;
+        grid-column:1;
+    }
+
+    #Quickstart #Develop {
+        grid-row:4;
+        grid-column:1;
+    }
+
+    #Quickstart #Gethelp {
+        grid-row:5;
+        grid-column:1;
+    }
+
+    #Quickstart .code {
+        grid-row-start:2;
+        grid-row-end:6;
+        grid-column:2;
+        height:110ch;
+        max-height:95vh;
+    }
+
+    /* RATIONALE */
+
+    #Rationale {
+        display:grid;
+        grid-template-columns:1fr 1fr;
+        grid-gap:2em;
+        text-align:justify;
+    }
+
+    #Rationale .collapsible {
+        display:none;
+    }
+
+    #Rationale .details {
+        max-height:100%;
+        width:80%;
+    }
+
+    #Rationale h1 {
+        grid-row:1;
+        grid-column-start:1;
+        grid-column-end:3;
+    }
+
+    #Rationale #Optimization {
+        grid-row:2;
+        grid-column:1;
+    }
+
+    #Rationale #Optimization_details {
+        grid-row:2;
+        grid-column:2;
+    }
+
+    #Rationale #Metaheuristics {
+        grid-row:3;
+        grid-column:1;
+    }
+
+    #Rationale #Metaheuristics_details {
+        grid-row:3;
+        grid-column:2;
+    }
+
+    #Rationale #Why {
+        grid-row:4;
+        grid-column-start:1;
+        grid-column-end:3;
+    }
+
+    #Rationale #Why_fullfeatured {
+        grid-row:5;
+        grid-column:1;
+    }
+
+    #Rationale #Why_fullfeatured_details {
+        grid-row:5;
+        grid-column:2;
+    }
+
+    #Rationale #Why_efficiency {
+        grid-row:6;
+        grid-column:1;
+    }
+
+    #Rationale #Why_efficiency_details {
+        grid-row:6;
+        grid-column:2;
+    }
+
+    #Rationale #Fast {
+        grid-row:7;
+        grid-column:1;
+    }
+
+    #Rationale #Fast_details {
+        grid-row:7;
+        grid-column:2;
+        margin-top:15ch;
+    }
+
+    /* FEATURES */
+
+    #Features {
+        display:grid;
+        grid-template-columns:1fr 1fr;
+        grid-gap:2em;
+        text-align:justify;
+    }
+
+    #Features .collapsible {
+        display:none;
+    }
+
+    #Features .details {
+        max-height:100%;
+        width:80%;
+    }
+
+    #Features figure {
+        max-width:100%;
+        margin-left:1em;
+    }
+
+    #Features h1 {
+        grid-row:1;
+        grid-column-start:1;
+        grid-column-end:3;
+    }
+
+    #Features #ComponentBased {
+        grid-row:2;
+        grid-column:1;
+    }
+
+    #Features #ComponentBased_details {
+        grid-row:2;
+        grid-column:2;
+    }
+
+    #Features #LargeChoice {
+        grid-row:3;
+        grid-column:1;
+    }
+
+    #Features #LargeChoice_details {
+        grid-row:3;
+        grid-column:2;
+    }
+
+    #Features #Portability {
+        grid-row:4;
+        grid-column:1;
+    }
+ 
+    #Features #Portability_details {
+        grid-row:4;
+        grid-column:2;
+    }
+
+    #Features #VS {
+        grid-row:5;
+        grid-column-start:1;
+        grid-column-end:3;
+    }
+
+    #Features #VS figure {
+        margin-left:15%;
+    }
+
+    /* DOCUMENTATION */
+
+    #Documentation {
+        display:flex;
+        flex-wrap: wrap;
+    }
+
+    #Documentation div {
+        margin:1em;
+    }
+
+    #Documentation #Articles {
+        flex: 1 1 25em;
+    }
+
+    #Documentation #Presentations {
+        flex: 1 1 25em;
+    }
+
+    #Documentation #Tutorials {
+        flex: 1 1 30em;
+    }
+
+    #Documentation #API {
+        flex: 1 1 25em;
+    }
+
+    #Documentation #Examples {
+        flex: 1 1 25em;
+    }
+
+    /* DOCUMENTATION */
+
+    #Code {
+        display:flex;
+        flex-wrap: wrap;
+    }
+
+    #Code div {
+        margin:1em;
+    }
+
+    #Code #Downloads {
+        flex: 1 1 20em;
+        text-align:justify;
+    }
+
+    #Code #Dependencies {
+        flex: 1 1 40em;
+        text-align:justify;
+    }
+
+    #Code #Compilation {
+        flex: 1 1 40em;
+        text-align:justify;
+    }
+
+    #Code #Licenses_Contribute {
+        flex: 1 1 20em;
+    }
+
+    /* HISTORY */
+
+    #History {
+        display:grid;
+        grid-template-columns:1fr 2fr;
+        grid-gap:2em;
+    }
+
+    #History h1 {
+        grid-row:1;
+        grid-column-start:1;
+        grid-column-end:3;
+    }
+
+    #History #Institution {
+        grid-row:2;
+        grid-column:1;
+    }
+
+    #History #Authors {
+        grid-row:2;
+        grid-column:2;
+    }
+
+}
+
+@media only print {
+
+    #header_logo {
+        background-image:none;
+        height:100%;
+    }
+    #header_logo em.logo {
+        display:block;
+        font-size:5em;
+    }
+
+    body {
+        background:none;
+        font-size:11pt;
+    }
+
+    a {
+        color:black;
+        font-style:italic;
+    }
+
+    #main a::after{
+        content: " [" attr(href) "] ";
+        color:#888;
+    }
+
+    h1 a {
+        display:none;
+    }
+
+    h2 a {
+        display:none;
+    }
+
+    h2 {
+        border-bottom:thin solid black;
+        margin-top:2ch;
+    }
+
+    h3 {
+        margin:2ch 0;
+    }
+
+    #alt {
+        clear:left;
+        width:100%;
+        max-width:100%;
+        height:auto;
+        text-align:left;
+        position:relative;
+        background-color:transparent;
+        color:black;
+    }
+
+    #alt * {
+        color:black;
+    }
+
+    #shortcuts {
+        display:none;
+    }
+
+    #toc_header {
+        display:none;
+    }
+
+    #main {
+        counter-reset: heading;
+        clear:left;
+        width:95%;
+        padding-left:1em;
+        padding-right:1em;
+        text-align:justify;
+    }
+
+    h1:before {
+        content: counter(heading)". ";
+        counter-increment: heading;
+    }
+    h1 {
+        counter-reset: subheading;
+    }
+    h2:before {
+        content: counter(heading)"." counter(subheading)". ";
+        counter-increment: subheading;
+    }
+
+    .excerpt {
+        box-shadow:none;
+        border:2pt solid #3771c8;
+        background-color:white;
+        color: #3771c8;
+        page-break-inside:avoid;
+    }
+
+    .command {
+        background-color:white;
+        color:black;
+        border:none;
+    }
+
+    .collapsible {
+        color:gray;
+    }
+
+    .details {
+        background-color:white;
+        color:gray;
+        font-size:0.8em;
+        max-height:100%;
+    }
+
+    figure {
+        max-width:90%;
+        margin-left:5%;
+        box-shadow:none;
+    }
+
+    .table {
+        padding:1em;
+        border:thin solid lightgray;
+        box-shadow: 5px 10px 18px #ddd;
+        width:80%;
+        max-width: 30em;
+        margin-left:5%
+    }
+
+    #cmaes * {
+        background-color:white;
+    }
+
+    .vimCodeElement {
+        background-color:white;
+        color:#444;
+    }
+
+    .code  {
+        background-color:white;
+        color:black;
+        height:100%;
+        overflow-y:auto;
+        white-space: pre-wrap;
+        box-shadow:none;
+    }
+
+    .cppSTL {color:black;}
+    .cppStatement {color:#dfa64d;}
+    .StorageClass {color:#dfa64d;}
+
+    .table {
+        margin-left:20%;
+        box-shadow:none;
+    }
+
+    .comment-indicator {
+        display:none;
+    }
+
+    comment {
+        display:none;
+    }
+}

doxygen/DoxygenLayout.xml

@@ -0,0 +1,226 @@
+<doxygenlayout version="1.0">
+  <!-- Generated by doxygen 1.8.17 -->
+  <!-- Navigation index tabs for HTML output -->
+  <navindex>
+    <tab type="mainpage" visible="yes" title=""/>
+    <tab type="pages" visible="yes" title="" intro=""/>
+    <tab type="modules" visible="yes" title="" intro=""/>
+    <tab type="namespaces" visible="yes" title="">
+      <tab type="namespacelist" visible="yes" title="" intro=""/>
+      <tab type="namespacemembers" visible="yes" title="" intro=""/>
+    </tab>
+    <tab type="interfaces" visible="yes" title="">
+      <tab type="interfacelist" visible="yes" title="" intro=""/>
+      <tab type="interfaceindex" visible="$ALPHABETICAL_INDEX" title=""/> 
+      <tab type="interfacehierarchy" visible="yes" title="" intro=""/>
+    </tab>
+    <tab type="classes" visible="yes" title="">
+      <tab type="classlist" visible="yes" title="" intro=""/>
+      <tab type="classindex" visible="$ALPHABETICAL_INDEX" title=""/> 
+      <tab type="hierarchy" visible="yes" title="" intro=""/>
+      <tab type="classmembers" visible="yes" title="" intro=""/>
+    </tab>
+    <tab type="structs" visible="yes" title="">
+      <tab type="structlist" visible="yes" title="" intro=""/>
+      <tab type="structindex" visible="$ALPHABETICAL_INDEX" title=""/> 
+    </tab>
+    <tab type="exceptions" visible="yes" title="">
+      <tab type="exceptionlist" visible="yes" title="" intro=""/>
+      <tab type="exceptionindex" visible="$ALPHABETICAL_INDEX" title=""/> 
+      <tab type="exceptionhierarchy" visible="yes" title="" intro=""/>
+    </tab>
+    <tab type="files" visible="yes" title="">
+      <tab type="filelist" visible="yes" title="" intro=""/>
+      <tab type="globals" visible="yes" title="" intro=""/>
+    </tab>
+    <tab type="examples" visible="yes" title="" intro=""/>  
+  </navindex>
+
+  <!-- Layout definition for a class page -->
+  <class>
+    <briefdescription visible="yes"/>
+    <includes visible="$SHOW_INCLUDE_FILES"/>
+    <inheritancegraph visible="$CLASS_GRAPH"/>
+    <collaborationgraph visible="$COLLABORATION_GRAPH"/>
+    <detaileddescription title=""/>
+    <memberdecl>
+      <publicmethods title=""/>
+      <publicstaticmethods title=""/>
+      <publicattributes title=""/>
+      <publicstaticattributes title=""/>
+      <protectedtypes title=""/>
+      <protectedslots title=""/>
+      <protectedmethods title=""/>
+      <protectedstaticmethods title=""/>
+      <protectedattributes title=""/>
+      <protectedstaticattributes title=""/>
+      <nestedclasses visible="yes" title=""/>
+      <publictypes title=""/>
+      <services title=""/>
+      <interfaces title=""/>
+      <publicslots title=""/>
+      <signals title=""/>
+      <packagetypes title=""/>
+      <packagemethods title=""/>
+      <packagestaticmethods title=""/>
+      <packageattributes title=""/>
+      <packagestaticattributes title=""/>
+      <properties title=""/>
+      <events title=""/>
+      <privatetypes title=""/>
+      <privateslots title=""/>
+      <privatemethods title=""/>
+      <privatestaticmethods title=""/>
+      <privateattributes title=""/>
+      <privatestaticattributes title=""/>
+      <friends title=""/>
+      <related title="" subtitle=""/>
+      <membergroups visible="yes"/>
+    </memberdecl>
+    <memberdef>
+      <constructors title=""/>
+      <functions title=""/>
+      <related title=""/>
+      <variables title=""/>
+      <properties title=""/>
+      <inlineclasses title=""/>
+      <typedefs title=""/>
+      <enums title=""/>
+      <services title=""/>
+      <interfaces title=""/>
+      <events title=""/>
+    </memberdef>
+    <allmemberslink visible="yes"/>
+    <usedfiles visible="$SHOW_USED_FILES"/>
+    <authorsection visible="yes"/>
+  </class>
+
+  <!-- Layout definition for a namespace page -->
+  <namespace>
+    <briefdescription visible="yes"/>
+    <detaileddescription title=""/>
+    <memberdecl>
+      <nestednamespaces visible="yes" title=""/>
+      <constantgroups visible="yes" title=""/>
+      <interfaces visible="yes" title=""/>
+      <classes visible="yes" title=""/>
+      <structs visible="yes" title=""/>
+      <exceptions visible="yes" title=""/>
+      <typedefs title=""/>
+      <sequences title=""/>
+      <dictionaries title=""/>
+      <enums title=""/>
+      <functions title=""/>
+      <variables title=""/>
+      <membergroups visible="yes"/>
+    </memberdecl>
+    <memberdef>
+      <inlineclasses title=""/>
+      <typedefs title=""/>
+      <sequences title=""/>
+      <dictionaries title=""/>
+      <enums title=""/>
+      <functions title=""/>
+      <variables title=""/>
+    </memberdef>
+    <authorsection visible="yes"/>
+  </namespace>
+
+  <!-- Layout definition for a file page -->
+  <file>
+    <briefdescription visible="yes"/>
+    <includes visible="$SHOW_INCLUDE_FILES"/>
+    <includegraph visible="$INCLUDE_GRAPH"/>
+    <includedbygraph visible="$INCLUDED_BY_GRAPH"/>
+    <sourcelink visible="yes"/>
+    <detaileddescription title=""/>
+    <memberdecl>
+      <interfaces visible="yes" title=""/>
+      <classes visible="yes" title=""/>
+      <structs visible="yes" title=""/>
+      <exceptions visible="yes" title=""/>
+      <namespaces visible="yes" title=""/>
+      <constantgroups visible="yes" title=""/>
+      <defines title=""/>
+      <typedefs title=""/>
+      <sequences title=""/>
+      <dictionaries title=""/>
+      <enums title=""/>
+      <functions title=""/>
+      <variables title=""/>
+      <membergroups visible="yes"/>
+    </memberdecl>
+    <memberdef>
+      <inlineclasses title=""/>
+      <defines title=""/>
+      <typedefs title=""/>
+      <sequences title=""/>
+      <dictionaries title=""/>
+      <enums title=""/>
+      <functions title=""/>
+      <variables title=""/>
+    </memberdef>
+    <authorsection/>
+  </file>
+
+  <!-- Layout definition for a group page -->
+  <group>
+    <briefdescription visible="yes"/>
+    <groupgraph visible="$GROUP_GRAPHS"/>
+    <detaileddescription title=""/>
+    <memberdecl>
+      <nestedgroups visible="yes" title=""/>
+      <namespaces visible="yes" title=""/>
+      <functions title=""/>
+      <classes visible="yes" title=""/>
+      <defines title=""/>
+      <typedefs title=""/>
+      <dirs visible="yes" title=""/>
+      <files visible="yes" title=""/>
+      <sequences title=""/>
+      <dictionaries title=""/>
+      <enums title=""/>
+      <enumvalues title=""/>
+      <variables title=""/>
+      <signals title=""/>
+      <publicslots title=""/>
+      <protectedslots title=""/>
+      <privateslots title=""/>
+      <events title=""/>
+      <properties title=""/>
+      <friends title=""/>
+      <membergroups visible="yes"/>
+    </memberdecl>
+    <memberdef>
+      <pagedocs/>
+      <inlineclasses title=""/>
+      <defines title=""/>
+      <typedefs title=""/>
+      <sequences title=""/>
+      <dictionaries title=""/>
+      <enums title=""/>
+      <enumvalues title=""/>
+      <functions title=""/>
+      <variables title=""/>
+      <signals title=""/>
+      <publicslots title=""/>
+      <protectedslots title=""/>
+      <privateslots title=""/>
+      <events title=""/>
+      <properties title=""/>
+      <friends title=""/>
+    </memberdef>
+    <authorsection visible="yes"/>
+  </group>
+
+  <!-- Layout definition for a directory page -->
+  <directory>
+    <briefdescription visible="yes"/>
+    <directorygraph visible="yes"/>
+    <detaileddescription title=""/>
+    <memberdecl>
+      <dirs visible="yes"/>
+      <files visible="yes"/>
+    </memberdecl>
+  </directory>
+</doxygenlayout>

doxygen/doxyfile.cmake

@@ -25,13 +25,21 @@ DOXYFILE_ENCODING      = UTF-8
 # The PROJECT_NAME tag is a single word (or a sequence of words surrounded
 # by quotes) that should identify the project.
 
-PROJECT_NAME           = @PACKAGE_NAME@
+PROJECT_NAME           = @MODULE_NAME@
+
+# With the PROJECT_LOGO tag one can specify a logo or an icon
+# that is included in the documentation.
+# The maximum height of the logo should not exceed 55 pixels
+# and the maximum width should not exceed 200 pixels.
+# Doxygen will copy the logo to the output directory.
+
+PROJECT_LOGO           = @CMAKE_SOURCE_DIR@/docs/img/paradiseo_logo.svg
 
 # The PROJECT_NUMBER tag can be used to enter a project or revision number.
 # This could be handy for archiving the generated documentation or
 # if some version control system is used.
 
-PROJECT_NUMBER         = @PACKAGE_VERSION@
+PROJECT_NUMBER         = @PROJECT_VERSION@
 
 # The OUTPUT_DIRECTORY tag is used to specify the (relative or absolute)
 # base path where the generated documentation will be put.
@@ -272,22 +280,6 @@ SUBGROUPING            = YES
 
 TYPEDEF_HIDES_STRUCT   = NO
 
-# The SYMBOL_CACHE_SIZE determines the size of the internal cache use to
-# determine which symbols to keep in memory and which to flush to disk.
-# When the cache is full, less often used symbols will be written to disk.
-# For small to medium size projects (<1000 input files) the default value is
-# probably good enough. For larger projects a too small cache size can cause
-# doxygen to be busy swapping symbols to and from disk most of the time
-# causing a significant performance penality.
-# If the system has enough physical memory increasing the cache will improve the
-# performance by keeping more symbols in memory. Note that the value works on
-# a logarithmic scale so increasing the size by one will rougly double the
-# memory usage. The cache size is given by this formula:
-# 2^(16+SYMBOL_CACHE_SIZE). The valid range is 0..9, the default is 0,
-# corresponding to a cache size of 2^16 = 65536 symbols
-
-SYMBOL_CACHE_SIZE      = 0
-
 #---------------------------------------------------------------------------
 # Build related configuration options
 #---------------------------------------------------------------------------
@@ -500,7 +492,7 @@ FILE_VERSION_FILTER    =
 # file name after the option, if omitted DoxygenLayout.xml will be used as the name
 # of the layout file.
 
-LAYOUT_FILE            =
+LAYOUT_FILE            = @CMAKE_SOURCE_DIR@/doxygen/DoxygenLayout.xml
 
 #---------------------------------------------------------------------------
 # configuration options related to warning and progress messages
@@ -594,7 +586,7 @@ RECURSIVE              = YES
 # excluded from the INPUT source files. This way you can easily exclude a
 # subdirectory from a directory tree whose root is specified with the INPUT tag.
 
-EXCLUDE                = @CMAKE_SOURCE_DIR@/src/obsolete @CMAKE_SOURCE_DIR@/test @CMAKE_SOURCE_DIR@/tutorial @CMAKE_SOURCE_DIR@/contrib @CMAKE_SOURCE_DIR@/app  
+EXCLUDE                = @CMAKE_SOURCE_DIR@/deprecated @CMAKE_SOURCE_DIR@/eo/contrib @CMAKE_SOURCE_DIR@/eo/app  @CMAKE_SOURCE_DIR@/eo/tutorial @CMAKE_SOURCE_DIR@/mo/tutorial @CMAKE_SOURCE_DIR@/moeo/tutorial @CMAKE_SOURCE_DIR@/smp/tutorial 
 
 # The EXCLUDE_SYMLINKS tag can be used select whether or not files or
 # directories that are symbolic links (a Unix filesystem feature) are excluded
@@ -608,7 +600,7 @@ EXCLUDE_SYMLINKS       = NO
 # against the file with absolute path, so to exclude all test directories
 # for example use the pattern */test/*
 
-EXCLUDE_PATTERNS       =
+EXCLUDE_PATTERNS       = *.sif/*
 
 # The EXCLUDE_SYMBOLS tag can be used to specify one or more symbol names
 # (namespaces, classes, functions, etc.) that should be excluded from the
@@ -622,7 +614,7 @@ EXCLUDE_SYMBOLS        =
 # directories that contain example code fragments that are included (see
 # the \include command).
 
-EXAMPLE_PATH           = @CMAKE_SOURCE_DIR@/test
+EXAMPLE_PATH           = @CMAKE_SOURCE_DIR@/eo/test @CMAKE_SOURCE_DIR@/edo/test @CMAKE_SOURCE_DIR@/mo/test @CMAKE_SOURCE_DIR@/moeo/test @CMAKE_SOURCE_DIR@/smp/test 
 
 # If the value of the EXAMPLE_PATH tag contains directories, you can use the
 # EXAMPLE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp
@@ -784,14 +776,14 @@ HTML_HEADER            =
 
 HTML_FOOTER            =
 
-# The HTML_STYLESHEET tag can be used to specify a user-defined cascading
+# The HTML_EXTRA_STYLESHEET tag can be used to specify a user-defined cascading
 # style sheet that is used by each HTML page. It can be used to
 # fine-tune the look of the HTML output. If the tag is left blank doxygen
 # will generate a default style sheet. Note that doxygen will try to copy
 # the style sheet file to the HTML output directory, so don't put your own
 # stylesheet in the HTML output directory as well, or it will be erased!
 
-HTML_STYLESHEET        =
+HTML_EXTRA_STYLESHEET        = @CMAKE_SOURCE_DIR@/doxygen/doxygen-style.css
 
 
 # If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
@@ -800,7 +792,7 @@ HTML_STYLESHEET        =
 # JavaScript and DHTML is required (for instance Mozilla 1.0+, Firefox
 # Netscape 6.0+, Internet explorer 5.0+, Konqueror, or Safari).
 
-HTML_DYNAMIC_SECTIONS  = NO
+HTML_DYNAMIC_SECTIONS  = YES
 
 # If the GENERATE_DOCSET tag is set to YES, additional index files
 # will be generated that can be used as input for Apple's Xcode 3
@@ -970,7 +962,7 @@ SEARCHENGINE           = YES
 # If the GENERATE_LATEX tag is set to YES (the default) Doxygen will
 # generate Latex output.
 
-GENERATE_LATEX         = YES
+GENERATE_LATEX         = NO
 
 # The LATEX_OUTPUT tag is used to specify where the LaTeX docs will be put.
 # If a relative path is entered the value of OUTPUT_DIRECTORY will be
@@ -1129,18 +1121,6 @@ GENERATE_XML           = NO
 
 XML_OUTPUT             = xml
 
-# The XML_SCHEMA tag can be used to specify an XML schema,
-# which can be used by a validating XML parser to check the
-# syntax of the XML files.
-
-XML_SCHEMA             =
-
-# The XML_DTD tag can be used to specify an XML DTD,
-# which can be used by a validating XML parser to check the
-# syntax of the XML files.
-
-XML_DTD                =
-
 # If the XML_PROGRAMLISTING tag is set to YES Doxygen will
 # dump the program listings (including syntax highlighting
 # and cross-referencing information) to the XML output. Note that
@@ -1301,11 +1281,6 @@ ALLEXTERNALS           = NO
 
 EXTERNAL_GROUPS        = YES
 
-# The PERL_PATH should be the absolute path and name of the perl script
-# interpreter (i.e. the result of `which perl').
-
-PERL_PATH              = /usr/bin/perl
-
 #---------------------------------------------------------------------------
 # Configuration options related to the dot tool
 #---------------------------------------------------------------------------
@@ -1319,15 +1294,6 @@ PERL_PATH              = /usr/bin/perl
 
 CLASS_DIAGRAMS         = YES
 
-# You can define message sequence charts within doxygen comments using the \msc
-# command. Doxygen will then run the mscgen tool (see
-# http://www.mcternan.me.uk/mscgen/) to produce the chart and insert it in the
-# documentation. The MSCGEN_PATH tag allows you to specify the directory where
-# the mscgen tool resides. If left empty the tool is assumed to be found in the
-# default search path.
-
-MSCGEN_PATH            =
-
 # If set to YES, the inheritance and collaboration graphs will hide
 # inheritance and usage relations if the target is undocumented
 # or is not a class.
@@ -1350,7 +1316,7 @@ HAVE_DOT               = YES
 # DOTFONTPATH environment variable or by setting DOT_FONTPATH to the directory
 # containing the font.
 
-DOT_FONTNAME           = FreeSans
+DOT_FONTNAME           = 
 
 # The DOT_FONTSIZE tag can be used to set the size of the font of dot graphs.
 # The default size is 10pt.
@@ -1392,7 +1358,7 @@ UML_LOOK               = NO
 # If set to YES, the inheritance and collaboration graphs will show the
 # relations between templates and their instances.
 
-TEMPLATE_RELATIONS     = NO
+TEMPLATE_RELATIONS     = YES
 
 # If the ENABLE_PREPROCESSING, SEARCH_INCLUDES, INCLUDE_GRAPH, and HAVE_DOT
 # tags are set to YES then doxygen will generate a graph for each documented
@@ -1440,7 +1406,18 @@ DIRECTORY_GRAPH        = YES
 # generated by dot. Possible values are png, jpg, or gif
 # If left blank png will be used.
 
-DOT_IMAGE_FORMAT       = png
+DOT_IMAGE_FORMAT       = svg
+
+# If DOT_IMAGE_FORMAT is set to svg, then this option can be set to YES
+# to enable generation of interactive SVG images that allow zooming and panning.
+# Note that this requires a modern browser other than Internet Explorer.
+# Tested and working are Firefox, Chrome, Safari, and Opera.
+# Note: For IE 9+ you need to set HTML_FILE_EXTENSION to xhtml
+#       in order to make the SVG files visible.
+#        Older versions of IE do not have SVG support.
+# This tag requires that the tag HAVE_DOT is set to YES. 
+
+INTERACTIVE_SVG = YES
 
 # The tag DOT_PATH can be used to specify the path where the dot tool can be
 # found. If left blank, it is assumed the dot tool can be found in the path.
@@ -1486,7 +1463,7 @@ DOT_TRANSPARENT        = NO
 # makes dot run faster, but since only newer versions of dot (>1.8.10)
 # support this, this feature is disabled by default.
 
-DOT_MULTI_TARGETS      = NO
+DOT_MULTI_TARGETS      = YES
 
 # If the GENERATE_LEGEND tag is set to YES (the default) Doxygen will
 # generate a legend page explaining the meaning of the various boxes and

doxygen/doxygen-style.css

@@ -0,0 +1,791 @@
+/* This doxygen theme is free to use. If you like this, please Star https://github.com/kcwongjoe/doxygen_theme_flat_design */
+
+/* Color Pattern. You can change this pattern to design your theme. */
+
+:root {
+    /* Content */
+    --bgcolor: #ffffff;
+    --bgfont: #303030;
+    --bgfont2: #3771c8;
+    --bgfont-hover: #3771c8;
+    --bgfont-hover-text-decoration: underline solid #3771c8;
+    --bgborder: #7d7d7d;
+    --bgborder2: #f6f6f6;
+    --bgfont-link:#1751a8;
+    /* Main Header */
+    --bg1color: #303030;
+    --bg1font: #ffffff;
+    --bg1font2: #3771c8;
+    /* Second header */
+    --bg2color: #E2E2E2;
+    --bg2font: #7D7D7D;
+    --bg2-hover-bg: #ffffff;
+    --bg2-hover-font: #303030;
+    --bg2-hover-topborder: #3771c8;
+    /* Third header */
+    --bg3color: #f6f6f6;
+    --bg3font: #303030;
+    --bg3font2: #7D7D7D;
+    /* Code */
+    --code-bg: #232323;
+    --code-comment: #a5c261;
+    --code-keyword: #db4939;
+    --code-preprocessor: #efcd45;
+    --code-keywordtype: #87bbff;
+    --code-text: #b1cfb1;
+    --code-code: #d3d0cc;
+    --code-line: #73707c;
+    --code-line-bg: #232323;
+    --code-link: #b7dbff;
+    /* Namespace List, Class List icon */
+    --icon-bg: #303030
+    --icon-font: #3771c8;
+    /* Class Index */
+    --qindex-menu-bg: #303030;
+    --qindex-menu-font: #ffffff;
+    --qindex-menu-font-hover: #3771c8;
+    --qindex-icon-bg: #3771c8;
+    --qindex-icon-font: #303030;
+    /* Member table */
+    --mem-title-bg: #3771c8;
+    --mem-title-font: #ffffff;
+    --mem-subtitle-bg: #77b1f8;
+    --mem-subtitle-font: #303030;
+    --mem-subtitle-font-hover: #303030;
+    --mem-content-bg: #ffffff;
+    --mem-content-font: #303030;
+    --mem-content-border: grey;
+    --mem-content-highlighted:#3771c8;
+    /* Nav Tree */
+    --nav-tree-bg: #E2E2E2;
+    --nav-tree-bg-hover: #ffffff;
+    --nav-tree-font: #7D7D7D;
+    --nav-tree-font-hover: #303030;
+    --nav-tree-bg-selected: #3771c8;
+    --nav-tree-font-selected: white;
+}
+
+body, table, div, p, dl {
+    color: var(--bgfont);
+    background-color: var(--bgcolor);
+    line-height: 150%;
+    font: 14px/22px, Roboto, Arial;
+}
+
+div.contents {
+    margin: 20px 40px;
+}
+
+div.contents ul {
+    line-height: 200%;
+}
+
+/***********************************/
+
+/********** Project header *********/
+
+/***********************************/
+
+#titlearea {
+    border-bottom: none;
+    padding-bottom: 20px;
+    padding-top: 20px;
+}
+
+#titlearea, #titlearea * {
+    color: var(--bg1font);
+    background-color: var(--bg1color);
+}
+
+#projectname {
+    padding: 0px 40px !important;
+}
+
+#projectbrief {
+    padding: 0px 40px !important;
+}
+
+#projectalign {
+    padding: 0px !important;
+    vertical-align: bottom;
+}
+
+/***********************************/
+
+/************ Main Menu ************/
+
+/***********************************/
+
+/* Margin */
+
+#main-menu {
+    padding: 0px 30px;
+}
+
+#main-menu a, #main-menu a:hover {
+    padding-top: 10px;
+    padding-bottom: 10px;
+}
+
+/* Menu button */
+
+#main-menu li a {
+    background-image: none;
+    font-family: Arial;
+    text-shadow: none;
+    font-size: 14px;
+    font-weight: 700;
+}
+
+#main-menu, #main-menu>li>a {
+    background-image: none;
+    background-color: var(--bg2color);
+    color: var(--bg2font);
+    transition: 0.2s;
+}
+
+/* hover Effect */
+
+#main-menu>li {
+    border-top: 5px solid var(--bg2color);
+}
+
+#main-menu>li:hover {
+    color: var(--bg2-hover-font);
+    background-color: var(--bg2-hover-bg);
+    border-top: 5px solid var(--bg2-hover-topborder);
+    font-width: bold;
+}
+
+#main-menu>li:hover, #main-menu>li>a:hover, #main-menu>li>a.highlighted {
+    color: var(--bg2-hover-font);
+    background-color: var(--bg2-hover-bg);
+    font-width: bold;
+}
+
+/* Search Bar */
+
+#MSearchBox {
+    border-radius: 0;
+    box-shadow: none;
+}
+
+#MSearchBox>span {
+    margin: 10px;
+}
+
+#main-menu>li:last-child {
+    padding: 25px 0px;
+}
+
+/* Reset search hover color*/
+
+#main-menu>li:last-child:hover {
+    color: var(--bg2font);
+    background-color: var(--bg2color);
+    border-top: 5px solid var(--bg2color);
+}
+
+#MSearchResultsWindow {
+    border: 1px solid var(--bg3font2);
+    background-color: var(--bg3color);
+    padding: 10px;
+}
+
+body.SRPage, body.SRPage * {
+    font-family: Arial;
+}
+
+/* Sub Menu  */
+
+#main-menu>li ul {
+    transition: max-height 0.2s ease-in-out;
+    padding: 0px;
+    border-radius: 0px !important;
+}
+
+#main-menu>li ul:before, #main-menu>li ul:after {
+    border-width: 0px;
+}
+
+#main-menu>li>ul li a, #main-menu>li>ul li {
+    background-color: var(--bgcolor);
+    color: var(--bgfont);
+    background-image: none;
+}
+
+#main-menu>li>ul li a:hover, #main-menu>li>ul li:hover {
+    background-color: var(--bgfont2);
+    /*color: var(--bgfont);*/
+    color: white;
+    font-width: bold;
+}
+
+/***********************************/
+
+/************** Header *************/
+
+/***********************************/
+
+div.headertitle {
+    padding: 5px 40px;
+}
+
+div.header, div.header * {
+    color: var(--bg3font);
+    background-color: var(--bg3color);
+    border-bottom: none;
+}
+
+div.summary {
+    padding-right: 40px;
+}
+
+/***********************************/
+
+/************** Link *************/
+
+/***********************************/
+
+a, a:visited, a:active, .contents a:visited, body.SRPage a, body.SRPage a:visited, body.SRPage a:active {
+    color: var(--bgfont-link);
+    text-decoration: none;
+}
+
+a:hover, .contents a:hover, body.SRPage a:hover {
+    color: var(--bgfont-hover);
+    text-decoration: var(--bgfont-hover-text-decoration);
+    
+}
+
+.dynheader {
+    color: var(--bgfont-link);
+    text-decoration: none;
+}
+
+.dynheader:hover {
+    color: var(--bgfont-hover);
+    text-decoration: var(--bgfont-hover-text-decoration);
+}
+
+/***********************************/
+
+/************ Nav-path ************/
+
+/***********************************/
+
+#nav-path, #nav-path ul {
+    background-image: none;
+}
+
+#nav-path ul {
+    padding: 5px 30px;
+}
+
+#nav-path, #nav-path * {
+    color: var(--bg3font2);
+    background-color: var(--bg3color);
+    border: none;
+    font-family: Arial;
+}
+
+li.navelem {
+    background-image: url(data:image/svg+xml;base64,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);
+    background-size: 9px;
+}
+
+li.navelem a {
+    margin-right: 20px;
+}
+
+/***********************************/
+
+/*************** mem ***************/
+
+/***********************************/
+
+.memtitle {
+    padding: 15px;
+    margin-top: 30px;
+    border-top-left-radius: 0px;
+    border-top-right-radius: 0px;
+}
+
+.memtitle, .memtitle *, .memtitle a:visited {
+    border: none;
+    background-image: none;
+    color: var(--mem-title-font);
+    background-color: var(--mem-title-bg);
+}
+
+.memproto {
+    padding: 2em;
+    text-shadow: none;
+    border-top-right-radius: 0px;
+    -moz-border-radius-topright: 0px;
+    -webkit-border-top-right-radius: 0px;
+}
+
+.memproto, .memproto *, .memproto a:visited {
+    border: none;
+    background-image: none;
+    background-color: var(--mem-subtitle-bg);
+    color: var(--mem-subtitle-font);
+    font-size: inherit;
+    line-height: 100%
+}
+
+.memproto a:hover {
+    color: var(--mem-subtitle-font-hover);
+}
+
+.memdoc {
+    border-bottom: 1px solid var(--mem-content-border);
+    border-left: 1px solid var(--mem-content-border);
+    border-right: 1px solid var(--mem-content-border);
+    background-color: var(--mem-content-bg);
+    color: var(--mem-content-font);
+    border-bottom-left-radius: 0px;
+    border-bottom-right-radius: 0px;
+    -moz-border-radius-bottomleft: 0px;
+    -moz-border-radius-bottomright: 0px;
+    -webkit-border-bottom-left-radius: 0px;
+    -webkit-border-bottom-right-radius: 0px;
+    padding:1em;
+}
+
+.memdoc p, .memdoc dt {
+    /*padding: 0px 20px;*/
+}
+
+.memdoc > p {
+    font-size:1em;
+}
+
+.paramname {
+    color:black;
+}
+
+td.memItemRight > a:first-of-type {
+    font-size:1.3em;
+}
+
+/***********************************/
+
+/************* Contents ************/
+
+/***********************************/
+
+a.anchor {
+    padding-top: 20px;
+}
+
+dl {
+    border-left: 5px solid;
+    padding:1em;
+}
+
+dt {
+    font-variant-caps: small-caps;
+}
+
+dl.warning {
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edo/LICENSE

@@ -0,0 +1,502 @@
+		  GNU LESSER GENERAL PUBLIC LICENSE
+		       Version 2.1, February 1999
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+  10. Each time you redistribute the Library (or any work based on the
+Library), the recipient automatically receives a license from the
+original licensor to copy, distribute, link with or modify the Library
+subject to these terms and conditions.  You may not impose any further
+restrictions on the recipients' exercise of the rights granted herein.
+You are not responsible for enforcing compliance by third parties with
+this License.
+
+  11. If, as a consequence of a court judgment or allegation of patent
+infringement or for any other reason (not limited to patent issues),
+conditions are imposed on you (whether by court order, agreement or
+otherwise) that contradict the conditions of this License, they do not
+excuse you from the conditions of this License.  If you cannot
+distribute so as to satisfy simultaneously your obligations under this
+License and any other pertinent obligations, then as a consequence you
+may not distribute the Library at all.  For example, if a patent
+license would not permit royalty-free redistribution of the Library by
+all those who receive copies directly or indirectly through you, then
+the only way you could satisfy both it and this License would be to
+refrain entirely from distribution of the Library.
+
+If any portion of this section is held invalid or unenforceable under any
+particular circumstance, the balance of the section is intended to apply,
+and the section as a whole is intended to apply in other circumstances.
+
+It is not the purpose of this section to induce you to infringe any
+patents or other property right claims or to contest validity of any
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+integrity of the free software distribution system which is
+implemented by public license practices.  Many people have made
+generous contributions to the wide range of software distributed
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+system; it is up to the author/donor to decide if he or she is willing
+to distribute software through any other system and a licensee cannot
+impose that choice.
+
+This section is intended to make thoroughly clear what is believed to
+be a consequence of the rest of this License.
+
+  12. If the distribution and/or use of the Library is restricted in
+certain countries either by patents or by copyrighted interfaces, the
+original copyright holder who places the Library under this License may add
+an explicit geographical distribution limitation excluding those countries,
+so that distribution is permitted only in or among countries not thus
+excluded.  In such case, this License incorporates the limitation as if
+written in the body of this License.
+
+  13. The Free Software Foundation may publish revised and/or new
+versions of the Lesser General Public License from time to time.
+Such new versions will be similar in spirit to the present version,
+but may differ in detail to address new problems or concerns.
+
+Each version is given a distinguishing version number.  If the Library
+specifies a version number of this License which applies to it and
+"any later version", you have the option of following the terms and
+conditions either of that version or of any later version published by
+the Free Software Foundation.  If the Library does not specify a
+license version number, you may choose any version ever published by
+the Free Software Foundation.
+
+  14. If you wish to incorporate parts of the Library into other free
+programs whose distribution conditions are incompatible with these,
+write to the author to ask for permission.  For software which is
+copyrighted by the Free Software Foundation, write to the Free
+Software Foundation; we sometimes make exceptions for this.  Our
+decision will be guided by the two goals of preserving the free status
+of all derivatives of our free software and of promoting the sharing
+and reuse of software generally.
+
+			    NO WARRANTY
+
+  15. BECAUSE THE LIBRARY IS LICENSED FREE OF CHARGE, THERE IS NO
+WARRANTY FOR THE LIBRARY, TO THE EXTENT PERMITTED BY APPLICABLE LAW.
+EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR
+OTHER PARTIES PROVIDE THE LIBRARY "AS IS" WITHOUT WARRANTY OF ANY
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+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+PURPOSE.  THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE
+LIBRARY IS WITH YOU.  SHOULD THE LIBRARY PROVE DEFECTIVE, YOU ASSUME
+THE COST OF ALL NECESSARY SERVICING, REPAIR OR CORRECTION.
+
+  16. IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN
+WRITING WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY
+AND/OR REDISTRIBUTE THE LIBRARY AS PERMITTED ABOVE, BE LIABLE TO YOU
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+LIBRARY (INCLUDING BUT NOT LIMITED TO LOSS OF DATA OR DATA BEING
+RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD PARTIES OR A
+FAILURE OF THE LIBRARY TO OPERATE WITH ANY OTHER SOFTWARE), EVEN IF
+SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH
+DAMAGES.
+
+		     END OF TERMS AND CONDITIONS
+
+	   How to Apply These Terms to Your New Libraries
+
+  If you develop a new library, and you want it to be of the greatest
+possible use to the public, we recommend making it free software that
+everyone can redistribute and change.  You can do so by permitting
+redistribution under these terms (or, alternatively, under the terms of the
+ordinary General Public License).
+
+  To apply these terms, attach the following notices to the library.  It is
+safest to attach them to the start of each source file to most effectively
+convey the exclusion of warranty; and each file should have at least the
+"copyright" line and a pointer to where the full notice is found.
+
+    <one line to give the library's name and a brief idea of what it does.>
+    Copyright (C) <year>  <name of author>
+
+    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; either
+    version 2 of the License, or (at your option) any later version.
+
+    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
+
+Also add information on how to contact you by electronic and paper mail.
+
+You should also get your employer (if you work as a programmer) or your
+school, if any, to sign a "copyright disclaimer" for the library, if
+necessary.  Here is a sample; alter the names:
+
+  Yoyodyne, Inc., hereby disclaims all copyright interest in the
+  library `Frob' (a library for tweaking knobs) written by James Random Hacker.
+
+  <signature of Ty Coon>, 1 April 1990
+  Ty Coon, President of Vice
+
+That's all there is to it!

edo/doc/CMakeLists.txt

@@ -22,7 +22,8 @@ if(DOXYGEN_FOUND)
                               )
         endif(UNIX AND NOT ${CMAKE_VERBOSE_MAKEFILE})
     endif(DOXYGEN_EXECUTABLE)
-    configure_file("${CMAKE_CURRENT_SOURCE_DIR}/${EDO_DOC_CONFIG_FILE}.cmake"
+    # configure_file("${CMAKE_CURRENT_SOURCE_DIR}/${EDO_DOC_CONFIG_FILE}.cmake"
+    configure_file("${DOXYGEN_CONFIG_DIR}/doxyfile.cmake"
         "${EDO_DOC_DIR}/${EDO_DOC_CONFIG_FILE}")
     install(
         DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}

edo/doc/edo.doxyfile.cmake

@@ -25,13 +25,13 @@ DOXYFILE_ENCODING      = UTF-8
 # The PROJECT_NAME tag is a single word (or a sequence of words surrounded
 # by quotes) that should identify the project.
 
-PROJECT_NAME           = @PACKAGE_NAME@
+PROJECT_NAME           = @EDO_MODULE_NAME@
 
 # The PROJECT_NUMBER tag can be used to enter a project or revision number.
 # This could be handy for archiving the generated documentation or
 # if some version control system is used.
 
-PROJECT_NUMBER         = @PACKAGE_VERSION@
+PROJECT_NUMBER         = @PROJECT_VERSION@
 
 # The OUTPUT_DIRECTORY tag is used to specify the (relative or absolute)
 # base path where the generated documentation will be put.
@@ -1030,7 +1030,7 @@ SERVER_BASED_SEARCH    = NO
 # If the GENERATE_LATEX tag is set to YES (the default) Doxygen will
 # generate Latex output.
 
-GENERATE_LATEX         = YES
+GENERATE_LATEX         = NO
 
 # The LATEX_OUTPUT tag is used to specify where the LaTeX docs will be put.
 # If a relative path is entered the value of OUTPUT_DIRECTORY will be

edo/src/edoEstimatorAdaptive.h

@@ -45,7 +45,7 @@ class edoEstimatorAdaptive : public edoEstimator<D>
 public:
     typedef typename D::EOType EOType;
 
-    edoEstimatorAdaptive<D>( D& distrib ) : _distrib(distrib) {}
+    edoEstimatorAdaptive( D& distrib ) : _distrib(distrib) {}
 
     // virtual D operator() ( eoPop< EOT >& )=0 (provided by eoUF< A1, R >)
 

edo/src/edoEstimatorAdaptiveReset.h

@@ -41,12 +41,12 @@ class edoEstimatorAdaptiveReset : public edoEstimatorAdaptive<D>
 public:
     typedef typename D::EOType EOType;
 
-    edoEstimatorAdaptiveReset<D>( D& distrib ) :
+    edoEstimatorAdaptiveReset( D& distrib ) :
         edoEstimatorAdaptive<D>(distrib),
         _dim(0)
     { }
 
-    edoEstimatorAdaptiveReset<D>( D& distrib, size_t dim ) :
+    edoEstimatorAdaptiveReset( D& distrib, size_t dim ) :
         edoEstimatorAdaptive<D>(distrib),
         _dim(dim)
     { }

edo/src/edoEstimatorCombined.h

@@ -43,12 +43,12 @@ class edoEstimatorCombinedAdaptive : public edoEstimatorAdaptive<D>, public std:
 public:
     typedef typename D::EOType EOType;
 
-    edoEstimatorCombinedAdaptive<D>( D& distrib, edoEstimator<D>& estim) :
+    edoEstimatorCombinedAdaptive( D& distrib, edoEstimator<D>& estim) :
         edoEstimatorAdaptive<D>(distrib),
         std::vector<edoEstimator<D>*>(1,&estim)
     {}
 
-    edoEstimatorCombinedAdaptive<D>( D& distrib, std::vector<edoEstimator<D>*> estims) :
+    edoEstimatorCombinedAdaptive( D& distrib, std::vector<edoEstimator<D>*> estims) :
         edoEstimatorAdaptive<D>(distrib),
         std::vector<edoEstimator<D>*>(estims)
     {}
@@ -78,11 +78,11 @@ class edoEstimatorCombinedStateless : public edoEstimatorCombinedAdaptive<D>
 public:
     typedef typename D::EOType EOType;
 
-    edoEstimatorCombinedStateless<D>( edoEstimator<D>& estim ) :
+    edoEstimatorCombinedStateless( edoEstimator<D>& estim ) :
         edoEstimatorCombinedAdaptive<D>(*(new D), estim)
     {}
 
-    edoEstimatorCombinedStateless<D>( std::vector<edoEstimator<D>*> estims) :
+    edoEstimatorCombinedStateless( std::vector<edoEstimator<D>*> estims) :
         edoEstimatorCombinedAdaptive<D>(*(new D), estims)
     {}
 

edo/src/edoEstimatorNormalAdaptive.h

@@ -233,7 +233,7 @@ public:
             Matrix mD = eigensolver.eigenvalues().asDiagonal();
 
             // from variance to standard deviations
-            mD.cwiseSqrt();
+            mD=mD.cwiseSqrt();
             d.scaling( mD.diagonal() );
 
             d.coord_sys( eigensolver.eigenvectors() );

edo/src/edoRepairerModulo.h

@@ -39,7 +39,7 @@ template < typename EOT >
 class edoRepairerModulo: public edoRepairerApplyBinary<EOT>
 {
 public:
-    edoRepairerModulo<EOT>( double denominator ) : edoRepairerApplyBinary<EOT>( std::fmod, denominator ) {}
+    edoRepairerModulo( double denominator ) : edoRepairerApplyBinary<EOT>( std::fmod, denominator ) {}
 };
 
 

edo/src/utils/edoFileSnapshot.cpp

@@ -76,8 +76,7 @@ edoFileSnapshot::edoFileSnapshot(std::string dirname,
 	    s = " ";
 	}
 
-    int dummy;
-    dummy = system(s.c_str());
+    (void)/*ignore returned*/ system(s.c_str());
     // all done
 
     _descOfFiles = new std::ofstream( std::string(dirname + "/list_of_files.txt").c_str() );

edo/test/CMakeLists.txt

@@ -42,6 +42,7 @@ set(SOURCES
   t-repairer-modulo
   t-binomial
   t-binomialmulti
+  t-minimal-cmaes
   )
 
 foreach(current ${SOURCES})

edo/test/t-minimal-cmaes.cpp

@@ -0,0 +1,69 @@
+#include <eo>
+#include <edo>
+#include <es.h>
+#include <do/make_pop.h>
+#include <do/make_run.h>
+#include <do/make_continue.h>
+#include <do/make_checkpoint.h>
+
+using R = eoReal<eoMinimizingFitness>;
+using CMA = edoNormalAdaptive<R>;
+
+R::FitnessType sphere(const R& sol) {
+    double sum = 0;
+    for(auto x : sol) { sum += x * x; }
+    return sum;
+}
+
+int main(int argc, char** argv) {
+    eoParser parser(argc, argv);
+    eoState state;
+
+    size_t dim = parser.createParam<size_t>(10,
+            "dimension", "Dimension", 'd',
+            "Problem").value();
+
+    size_t max_eval = parser.getORcreateParam<size_t>(100 * dim,
+            "maxEval", "Maximum number of evaluations", 'E',
+            "Stopping criterion").value();
+
+    edoNormalAdaptive<R> gaussian(dim);
+
+    auto& obj_func = state.pack< eoEvalFuncPtr<R> >(sphere);
+    auto& eval     = state.pack< eoEvalCounterThrowException<R> >(obj_func, max_eval);
+    auto& pop_eval = state.pack< eoPopLoopEval<R> >(eval);
+
+    auto& gen  = state.pack< eoUniformGenerator<R::AtomType> >(-5, 5);
+    auto& init = state.pack< eoInitFixedLength<R> >(dim, gen);
+    auto& pop = do_make_pop(parser, state, init);
+    pop_eval(pop,pop);
+
+    auto& eo_continue  = do_make_continue(  parser, state, eval);
+    auto& pop_continue = do_make_checkpoint(parser, state, eval, eo_continue);
+    auto& best = state.pack< eoBestIndividualStat<R> >();
+    pop_continue.add( best );
+    auto& distrib_continue = state.pack< edoContAdaptiveFinite<CMA> >();
+
+    auto& selector  = state.pack< eoRankMuSelect<R> >(dim/2);
+    auto& estimator = state.pack< edoEstimatorNormalAdaptive<R> >(gaussian);
+    auto& bounder   = state.pack< edoBounderRng<R> >(R(dim, -5), R(dim, 5), gen);
+    auto& sampler   = state.pack< edoSamplerNormalAdaptive<R> >(bounder);
+    auto& replacor  = state.pack< eoCommaReplacement<R> >();
+
+    make_verbose(parser);
+    make_help(parser);
+
+    auto& algo = state.pack< edoAlgoAdaptive<CMA> >(
+         gaussian , pop_eval, selector,
+         estimator, sampler , replacor,
+         pop_continue, distrib_continue);
+
+    try {
+        algo(pop);
+    } catch (eoMaxEvalException& e) {
+        eo::log << eo::progress << "STOP" << std::endl;
+    }
+
+    std::cout << best.value() << std::endl;
+    return 0;
+}

eo/contrib/MGE/eoVirus.h

@@ -108,7 +108,12 @@ public:
         if (is) {
             virus.resize(bits.size());
             std::transform(bits.begin(), bits.end(), virus.begin(),
+#if __cplusplus >= 201103L
+                           std::bind(std::equal_to<char>(), std::placeholders::_1, '1'));
+#else
+                           // Deprecated since C++11.
                            std::bind2nd(std::equal_to<char>(), '1'));
+#endif
         }
     }
 

eo/contrib/irace/CMakeLists.txt

@@ -0,0 +1,78 @@
+
+######################################################################################
+# Project settings
+######################################################################################
+
+cmake_minimum_required(VERSION 3.10 FATAL_ERROR)
+
+project("paradiseo-irace")
+
+enable_language(CXX) # C++
+set(CMAKE_CXX_STANDARD 17)
+
+## Current version
+set(VERSION_MAJOR 0 CACHE STRING "Major version number" )
+set(VERSION_MINOR 1 CACHE STRING "Minor version number" )
+set(VERSION_PATCH 0 CACHE STRING "Patch version number" )
+mark_as_advanced(VERSION_MAJOR VERSION_MINOR VERSION_PATCH)
+
+
+######################################################################################
+# Configurable user settings
+######################################################################################
+
+set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wall -Wextra -Wpedantic")
+
+# put binaries in the build directory
+set(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR})
+
+# Dump used compiler flags.
+set(CMAKE_EXPORT_COMPILE_COMMANDS ON)
+
+
+######################################################################################
+# Dependencies
+######################################################################################
+
+# ParadisEO
+set(PARADISEO_ROOT "../../../../paradiseo" CACHE PATH "Where to find ParadisEO")
+set(PARADISEO_BUILD "${PARADISEO_ROOT}/build" CACHE PATH "Build dir of ParadisEO")
+
+include_directories(${PARADISEO_ROOT})
+include_directories(${PARADISEO_ROOT}/eo/src)
+link_directories(${PARADISEO_BUILD}/lib)
+set(PARADISEO_LIBRARIES ga eoutils eo)
+
+# IOH
+set(IOH_ROOT "~/code/IOHexperimenter/" CACHE PATH "Where to find IOHexperimenter")
+find_path(IOH_HPP "ioh.hpp" PATHS ${IOH_ROOT}/include/)
+# find_library(IOH_LIBRARY "IOH" PATHS ${IOH_ROOT} PATH_SUFFIXES release Release debug Debug build Build)
+
+if(EXISTS ${IOH_HPP}) # AND EXISTS ${IOH_LIBRARY})
+    message(STATUS "Found IOH in ${IOH_ROOT}")
+    include_directories(${IOH_ROOT}/include/)
+    include_directories(${IOH_ROOT}/external/fmt/include/)
+    include_directories(${IOH_ROOT}/external/clutchlog/)
+    link_directories(${IOH_ROOT}/release/external/fmt/)
+
+else()
+    if(NOT EXISTS ${IOH_HPP})
+        message(FATAL_ERROR "Could not find `ioh.hpp` in: ${IOH_ROOT}/include/")
+    endif()
+    # if(NOT EXISTS ${IOH_LIBRARIES})
+    #     message(FATAL_ERROR "Could not find `libIOH` in: ${IOH_ROOT}/[release|debug|build] (did you forget to compile it?)")
+    # endif()
+endif()
+
+
+######################################################################################
+# Start building
+######################################################################################
+
+add_executable(fastga fastga.cpp)
+# Link to stdc++fs at the end because of an Ubuntu bug, see:  https://stackoverflow.com/a/57760267
+target_link_libraries(fastga ${PARADISEO_LIBRARIES} fmt stdc++fs)
+
+add_executable(onlymutga onlymutga.cpp)
+target_link_libraries(onlymutga ${PARADISEO_LIBRARIES} fmt)
+

eo/contrib/irace/build_fastga.sh

@@ -0,0 +1,80 @@
+#!/bin/sh
+
+########################################################################
+# This is an example of how to deal with complex builds,
+# for instance on clusters with compilers provided as side modules.
+########################################################################
+
+# Run this script in a separate dir, e.g.
+# mkdir -p code ; cd code ; ../build_fastga.sh
+
+# exit when any command fails
+set -e
+
+# We need recent clang and cmake
+module load LLVM/clang-llvm-10.0
+module load cmake/3.18
+
+# We are going to use a specific compiler, different from the system's one.
+# Path toward the compiler:
+C="/opt/dev/Compilers/LLVM/10.0.1/bin"
+# Path toward the include for the std lib:
+I="/opt/dev/Compilers/LLVM/10.0.1/include/c++/v1/"
+# Path toward the compiled std lib:
+L="/opt/dev/Compilers/LLVM/10.0.1/lib"
+
+# As we use clang, we use its std lib (instead of gcc's "libstdc++")
+S="libc++"
+
+# Gather all those into a set of flags:
+flags="-I${I} -stdlib=${S} -L${L}"
+
+# Current dir, for further reference.
+here=$(pwd)
+
+# Compiler selection
+export CC=${C}/clang
+export CXX=${C}/clang++
+
+# If the dir already exists
+if cd IOHexperimenter ; then
+    # Just update the code
+    git pull
+else
+    # Clone the repo
+    git clone --branch feat+EAF --single-branch --recurse-submodules https://github.com/jdreo/IOHexperimenter.git
+    cd IOHexperimenter
+fi
+# Clean build from scratch
+rm -rf release
+mkdir -p release
+cd release
+cmake -DCMAKE_CXX_FLAGS="${flags}" -D CMAKE_BUILD_TYPE=Release -D BUILD_TESTS=OFF -D BUILD_EXAMPLE=OFF ..
+make -j
+# Get back to the root dir
+cd ${here}
+
+
+if cd paradiseo ; then
+    git pull
+else
+    git clone --branch feat+num_foundry --single-branch --recurse-submodules https://github.com/jdreo/paradiseo.git
+    cd paradiseo
+    touch LICENSE
+fi
+rm -rf release
+mkdir -p release
+cd release
+cmake -DCMAKE_CXX_FLAGS="${flags}" -D CMAKE_BUILD_TYPE=Release ..
+make -j
+cd ${here}
+
+
+cd paradiseo/eo/contrib/irace
+rm -rf release
+mkdir -p release
+cd release
+cmake -DCMAKE_CXX_FLAGS="${flags}" -D CMAKE_BUILD_TYPE=Release -D IOH_ROOT=${here}/IOHexperimenter/ -D PARADISEO_ROOT=${here}/paradiseo/ -D PARADISEO_BUILD=${here}/paradiseo/release/ ..
+make -j
+cd ${here}
+

eo/contrib/irace/expe/alpha/parse_baseline.py

@@ -0,0 +1,28 @@
+#!/usr/bin/env python3
+
+import sys
+
+print("algo,problem,seed,ECDF_AUC")
+
+algos_names = {
+    str({"crossover-rate":0, "cross-selector":0, "crossover":0, "mutation-rate":0, "mut-selector":0, "mutation":1, "replacement":0}) : "EA",
+    str({"crossover-rate":0, "cross-selector":0, "crossover":0, "mutation-rate":0, "mut-selector":0, "mutation":5, "replacement":0}) : "fEA",
+    str({"crossover-rate":2, "cross-selector":2, "crossover":2, "mutation-rate":2, "mut-selector":2, "mutation":1, "replacement":0}) : "xGA",
+    str({"crossover-rate":2, "cross-selector":2, "crossover":5, "mutation-rate":2, "mut-selector":2, "mutation":1, "replacement":0}) : "1ptGA",
+}
+
+for fname in sys.argv[1:]:
+
+    run = {}
+    for f in fname.strip(".dat").split("_"):
+        kv = f.split("=")
+        assert(len(kv)==2),str(kv)+" "+str(len(kv))
+        key,idx = kv[0], int(kv[1])
+        run[key] = idx
+
+    with open(fname) as fd:
+        auc = int(fd.readlines()[0]) * -1
+
+    algo = str({"crossover-rate":run["crossover-rate"], "cross-selector":run["cross-selector"], "crossover":run["crossover"], "mutation-rate":run["mutation-rate"], "mut-selector":run["mut-selector"], "mutation":run["mutation"], "replacement":run["replacement"]})
+
+    print(algos_names[algo], run["pb"], run["seed"], auc, sep=",")

eo/contrib/irace/expe/alpha/parse_baseline_average.py

@@ -0,0 +1,49 @@
+#!/usr/bin/env python3
+
+import sys
+
+print("problem,EA,fEA,xGA,1ptGA")
+
+algos_names = {
+    str({"crossover-rate":0, "cross-selector":0, "crossover":0, "mutation-rate":0, "mut-selector":0, "mutation":1, "replacement":0}) : "EA",
+    str({"crossover-rate":0, "cross-selector":0, "crossover":0, "mutation-rate":0, "mut-selector":0, "mutation":5, "replacement":0}) : "fEA",
+    str({"crossover-rate":2, "cross-selector":2, "crossover":2, "mutation-rate":2, "mut-selector":2, "mutation":1, "replacement":0}) : "xGA",
+    str({"crossover-rate":2, "cross-selector":2, "crossover":5, "mutation-rate":2, "mut-selector":2, "mutation":1, "replacement":0}) : "1ptGA",
+}
+
+data = {}
+
+# Parse
+for fname in sys.argv[1:]:
+
+    run = {}
+    for f in fname.strip(".dat").split("_"):
+        kv = f.split("=")
+        assert(len(kv)==2),str(kv)+" "+str(len(kv))
+        key,idx = kv[0], int(kv[1])
+        run[key] = idx
+
+    with open(fname) as fd:
+        auc = int(fd.readlines()[0]) * -1
+
+    algo = str({"crossover-rate":run["crossover-rate"], "cross-selector":run["cross-selector"], "crossover":run["crossover"], "mutation-rate":run["mutation-rate"], "mut-selector":run["mut-selector"], "mutation":run["mutation"], "replacement":run["replacement"]})
+
+    if run["pb"] in data:
+        data[run["pb"]][algos_names[algo]].append(auc)
+    else:
+        data[run["pb"]] = {
+                "EA"   : [],
+                "fEA"  : [],
+                "xGA"  : [],
+                "1ptGA": [],
+            }
+        data[run["pb"]][algos_names[algo]].append(auc)
+
+
+# Print CSV
+for pb in sorted(data.keys()):
+    print(pb, end="")
+    for algo in ["EA","fEA","xGA","1ptGA"]:
+        res = data[pb][algo]
+        print(",", sum(res)/len(res), end="", sep="")
+    print()

eo/contrib/irace/expe/alpha/parse_elites.py

@@ -0,0 +1,21 @@
+#!/usr/bin/env python3
+
+import sys
+
+print("algo,problem,seed,ECDF_AUC")
+
+for fname in sys.argv[1:]:
+
+    run = {}
+    for f in fname.strip(".dat").split("_"):
+        kv = f.split("=")
+        assert(len(kv)==2),str(kv)+" "+str(len(kv))
+        key,idx = kv[0], int(kv[1])
+        run[key] = idx
+
+    with open(fname) as fd:
+        auc = int(fd.readlines()[0]) * -1
+
+    algo = "pc={}_c={}_C={}_pm={}_m={}_M={}_R={}".format(run["crossover-rate"],run["cross-selector"],run["crossover"],run["mutation-rate"],run["mut-selector"],run["mutation"],run["replacement"])
+
+    print(algo, run["pb"], run["seed"], auc, sep=",")

eo/contrib/irace/expe/alpha/parse_irace_bests.py

@@ -0,0 +1,30 @@
+#!/usr/bin/env python3
+
+import os
+import re
+import sys
+
+print("pb,ecdf,id,crossover-rate,cross-selector,crossover,mutation-rate,mut-selector,mutation,replacement")
+for datadir in sys.argv[1:]:
+
+    for pb_dir in os.listdir(datadir):
+        if "results_problem" in pb_dir:
+            pb_id=pb_dir.replace("results_problem_","")
+            with open(os.path.join("./",datadir,pb_dir,"irace.log")) as fd:
+                data = fd.readlines()
+
+                # Find the last best configuration
+                bests = [line.strip() for line in data if "Best-so-far" in line]
+                best = bests[-1].split()
+                best_id, best_perf = best[2], best[5]
+                # print(best_id,best_perf)
+
+                # Filter the config detail
+                configs = [line.strip() for line in data if "--crossover-rate=" in line and best_id in line]
+                # print(configs)
+
+                # Format as CSV
+                for config in configs:
+                    algo = re.sub("\-\-\S*=", ",", config)
+                    csv_line = pb_id + "," + best_perf + "," + algo
+                    print(csv_line.replace(" ",""))

eo/contrib/irace/expe/alpha/plot_attain_mat.py

@@ -0,0 +1,44 @@
+#!/usr/bin/env python3
+
+import os
+import numpy as np
+import matplotlib.pyplot as plt
+
+for p in range(18):
+
+    print("Pb",p,end=": ")
+    datadir="attain_mat_{pb}".format(pb=p)
+
+    try:
+        os.mkdir(datadir)
+    except FileExistsError:
+        pass
+
+    for i in range(50):
+        cmd="./release/fastga --seed={i} \
+            --crossover-rate=2 --cross-selector=2 --crossover=5 --mutation-rate=2 --mut-selector=2 --mutation=1 --replacement=0 \
+            --problem={pb} --buckets=20 --output-mat 2>/dev/null > {dir}/output_mat_{i}.csv"\
+            .format(dir=datadir, i=i, pb=p)
+        # print(cmd)
+        print(i,end=" ",flush=True)
+        os.system(cmd)
+
+
+    matrices=[]
+    for root, dirs, files in os.walk(datadir):
+        for filename in files:
+            matrices.append( np.genfromtxt(datadir+"/"+filename,delimiter=',') )
+
+    agg = matrices[0]
+    for mat in matrices[1:]:
+        agg += mat
+
+    # print(agg)
+
+    plt.rcParams["figure.figsize"] = (3,3)
+    plt.gca().pcolor(agg, edgecolors='grey', cmap="Blues")
+    plt.gca().set_xlabel("Time budget")
+    plt.gca().set_ylabel("Target")
+    plt.savefig("aittain_map_{pb}.png".format(pb=p), bbox_inches='tight')
+
+    print(".")

eo/contrib/irace/expe/alpha/run_algo.sh

@@ -0,0 +1,43 @@
+#!/bin/bash
+
+# Number of runs (=seeds).
+runs=50
+
+# Array of problems.
+# You may set something like: (0 2 5 17)
+problems=($(seq 0 18))
+
+# Capture anything passed to the script
+outdir="$1"
+algo="${@:2}"
+
+# You most probably want to run on release builds.
+exe="./release/fastga"
+
+i=1 # Loop counter.
+for pb in "${problems[@]}" ; do # Iterate over the problems array.
+    for seed in $(seq ${runs}) ; do # Iterates over runs/seeds.
+        # Forge a directory/log file name
+        # (remove double dashs and replace spaces with underscore).
+        name="pb=${pb}_seed=${seed}_$(echo "${algo}" | sed 's/--//g' | sed 's/ /_/g')"
+
+        # This is the command to be ran.
+        cmd="${exe} --problem=${pb} --seed=${seed} ${algo}"
+        echo ${cmd} # Print the command.
+
+        # Progress print.
+        echo -n "problem ${pb}, run ${seed}"
+
+        # Actually start the command.
+        ${cmd} > "${outdir}/${name}.dat" 2> "${outdir}/${name}.log"
+
+        # Check for the most common problem in the log file.
+        cat "${outdir}/${name}.log" | grep "illogical performance"
+
+        perc=$(echo "scale=2;${i}/(${#problems[@]}*${runs})*100" | bc)
+        echo -e " -- ${perc}%"
+        i=$((i+1))
+    done
+done
+
+echo "Done $((${#problems[@]}*${runs})) runs, results in ${outdir}"

eo/contrib/irace/expe/alpha/run_baseline.sh

@@ -0,0 +1,30 @@
+#!/bin/bash
+
+outdir="$(date --iso-8601=minutes)_results_baselines"
+mkdir ${outdir}
+
+algos=(
+# (λ+λ)EA
+"--full-log=1 --crossover-rate=0 --cross-selector=0 --crossover=0 --mutation-rate=0 --mut-selector=0 --mutation=1 --replacement=0"
+# (λ+λ)fEA
+"--full-log=1 --crossover-rate=0 --cross-selector=0 --crossover=0 --mutation-rate=0 --mut-selector=0 --mutation=5 --replacement=0"
+# (λ+λ)xGA
+"--full-log=1 --crossover-rate=2 --cross-selector=2 --crossover=2 --mutation-rate=2 --mut-selector=2 --mutation=1 --replacement=0"
+# (λ+λ)1ptGA
+"--full-log=1 --crossover-rate=2 --cross-selector=2 --crossover=5 --mutation-rate=2 --mut-selector=2 --mutation=1 --replacement=0"
+)
+
+
+i=1 # Loop counter.
+for algo in "${algos[@]}" ; do
+    echo "${algo}"
+
+    name="$(echo "${algo}" | sed 's/--//g' | sed 's/ /_/g')"
+    ./run_algo.sh ${outdir} ${algo} &> "expe_${name}.log"
+
+    perc=$(echo "scale=2;${i}/${#algos[@]}*100" | bc)
+    echo -e "${perc}%\n"
+    i=$((i+1))
+done
+
+echo "Done"

eo/contrib/irace/expe/alpha/run_elite.sh

@@ -0,0 +1,67 @@
+#!/bin/bash
+
+# Number of runs (=seeds).
+runs=50
+
+# You most probably want to run on release builds.
+exe="./release/fastga"
+
+outdir="$(date --iso-8601=minutes)_results_elites"
+mkdir ${outdir}
+
+# FIXME
+algos=(
+"--crossover-rate=1 --cross-selector=2 --crossover=1  --mutation-rate=2 --mut-selector=2 --mutation=8  --replacement=8"
+"--crossover-rate=4 --cross-selector=5 --crossover=2  --mutation-rate=3 --mut-selector=4 --mutation=9  --replacement=9"
+"--crossover-rate=1 --cross-selector=3 --crossover=8  --mutation-rate=2 --mut-selector=6 --mutation=3  --replacement=2"
+"--crossover-rate=2 --cross-selector=1 --crossover=1  --mutation-rate=2 --mut-selector=6 --mutation=9  --replacement=0"
+"--crossover-rate=4 --cross-selector=2 --crossover=2  --mutation-rate=4 --mut-selector=3 --mutation=7  --replacement=0"
+"--crossover-rate=0 --cross-selector=3 --crossover=2  --mutation-rate=4 --mut-selector=2 --mutation=6  --replacement=0"
+"--crossover-rate=3 --cross-selector=0 --crossover=3  --mutation-rate=4 --mut-selector=3 --mutation=10 --replacement=0"
+"--crossover-rate=0 --cross-selector=1 --crossover=0  --mutation-rate=3 --mut-selector=2 --mutation=10 --replacement=0"
+"--crossover-rate=2 --cross-selector=2 --crossover=2  --mutation-rate=4 --mut-selector=5 --mutation=10 --replacement=0"
+"--crossover-rate=4 --cross-selector=2 --crossover=2  --mutation-rate=4 --mut-selector=5 --mutation=9  --replacement=0"
+"--crossover-rate=3 --cross-selector=2 --crossover=10 --mutation-rate=4 --mut-selector=2 --mutation=10 --replacement=0"
+"--crossover-rate=2 --cross-selector=2 --crossover=5  --mutation-rate=4 --mut-selector=3 --mutation=9  --replacement=0"
+"--crossover-rate=3 --cross-selector=6 --crossover=2  --mutation-rate=4 --mut-selector=1 --mutation=10 --replacement=0"
+"--crossover-rate=1 --cross-selector=5 --crossover=9  --mutation-rate=4 --mut-selector=2 --mutation=8  --replacement=0"
+"--crossover-rate=2 --cross-selector=5 --crossover=2  --mutation-rate=4 --mut-selector=6 --mutation=8  --replacement=0"
+"--crossover-rate=2 --cross-selector=2 --crossover=10 --mutation-rate=4 --mut-selector=6 --mutation=10 --replacement=0"
+"--crossover-rate=3 --cross-selector=2 --crossover=2  --mutation-rate=4 --mut-selector=5 --mutation=10 --replacement=0"
+"--crossover-rate=4 --cross-selector=2 --crossover=2  --mutation-rate=4 --mut-selector=1 --mutation=8  --replacement=0"
+"--crossover-rate=4 --cross-selector=2 --crossover=2  --mutation-rate=4 --mut-selector=6 --mutation=9  --replacement=0"
+)
+
+pb=0 # Loop counter.
+for algo in "${algos[@]}" ; do
+    echo "Problem ${pb}"
+    echo -n "Runs: "
+
+    for seed in $(seq ${runs}) ; do # Iterates over runs/seeds.
+        # This is the command to be ran.
+        cmd="${exe} --full-log=1 --problem=${pb} --seed=${seed} ${algo}"
+        # echo ${cmd} # Print the command.
+
+        # Forge a directory/log file name
+        # (remove double dashs and replace spaces with underscore).
+        name_run="pb=${pb}_seed=${seed}_$(echo "${algo}" | sed 's/--//g' | sed 's/ /_/g')"
+        # echo $name_run
+
+        # Progress print.
+        echo -n "${seed} "
+
+        # Actually start the command.
+        ${cmd} > "${outdir}/${name_run}.dat" 2> "${outdir}/${name_run}.log"
+
+        # Check for the most common problem in the log file.
+        cat "${outdir}/${name_run}.log" | grep "illogical performance"
+    done
+
+    echo ""
+    perc=$(echo "scale=2;${pb}/${#algos[@]}*100" | bc)
+    echo -e "${perc}%\n"
+    pb=$((pb+1))
+
+done
+
+echo "Done"

eo/contrib/irace/expe/alpha/run_elites_all.sh

@@ -0,0 +1,61 @@
+
+#!/bin/bash
+
+# Number of runs (=seeds).
+runs=50
+
+# You most probably want to run on release builds.
+exe="./release/fastga"
+
+outdir="$(date --iso-8601=minutes)_results_elites_all"
+mkdir -p ${outdir}
+mkdir -p ${outdir}/raw
+mkdir -p ${outdir}/raw/data
+mkdir -p ${outdir}/raw/logs
+
+n=0
+algoid=0
+for line in $(cat results_irace_100k.csv|cut -s -d"," -f4-10); do
+    echo ""
+    date
+
+    a=($(echo $line | sed "s/,/ /g"))
+    algo="--crossover-rate=${a[0]} --cross-selector=${a[1]} --crossover=${a[2]}  --mutation-rate=${a[3]} --mut-selector=${a[4]} --mutation=${a[5]}  --replacement=${a[6]}"
+
+    for pb in $(seq 0 18) ; do
+        perc=$(echo "scale=3;${n}/(285*18)*100.0" | bc)
+        echo "${perc}% : algo ${algoid}/285, problem ${pb}/18"
+        # echo -n "Runs: "
+
+        for seed in $(seq ${runs}) ; do # Iterates over runs/seeds.
+            # This is the command to be ran.
+            cmd="${exe} --full-log=1 --problem=${pb} --seed=${seed} ${algo}"
+            # echo ${cmd} # Print the command.
+
+            # Forge a directory/log file name
+            # (remove double dashs and replace spaces with underscore).
+            name_run="pb=${pb}_seed=${seed}_$(echo "${algo}" | sed 's/--//g' | sed 's/ /_/g')"
+            # echo $name_run
+
+            # Progress print.
+            # echo -n "${seed} "
+
+            # Actually start the command.
+            ${cmd} > "${outdir}/raw/data/${name_run}.dat" 2> "${outdir}/raw/logs/${name_run}.log"
+
+            # Check for the most common problem in the log file.
+            cat "${outdir}/raw/logs/${name_run}.log" | grep "illogical performance"
+        done # seed
+        # echo ""
+
+        n=$(($n+1))
+    done # pb
+
+    algoid=$(($algoid+1))
+done
+
+# Move IOH logs in the results directory.
+mv ./FastGA_* ${outdir}
+
+echo "Done"
+date

eo/contrib/irace/expe/alpha/run_irace.sh

@@ -0,0 +1,27 @@
+#!/bin/bash
+
+outdir="$(date --iso-8601=minutes)_results_irace"
+mkdir ${outdir}
+cd ${outdir}
+
+for p in $(seq 0 18) ; do
+    echo -n "Problem ${p}... "
+    res="results_problem_${p}"
+    mkdir ${res}
+    cd ${res}
+
+    # Fore some reason, irace absolutely need those files...
+    cp ../../irace-config/example.scen .
+    cp ../../irace-config/default.instances .
+    cp ../../release/fastga .
+    cat ../../irace-config/target-runner | sed "s/{{PROBLEM}}/${p}/" > ./target-runner
+    chmod u+x target-runner
+
+    # Generate the parameter list file.
+    ./fastga -h > fastga.param 2>/dev/null
+    # /usr/lib/R/site-library/irace/bin/irace --scenario example.scen 2>&1 | tee irace.log
+    /usr/lib/R/site-library/irace/bin/irace --scenario example.scen &> irace.log
+
+    cd ..
+    echo " done"
+done

eo/contrib/irace/expe/alpha/run_irace_all.sh

@@ -0,0 +1,14 @@
+#!/bin/bash
+
+date -Iseconds
+echo "STARTS"
+
+for r in $(seq 15); do
+    echo "Run $r/15";
+    date -Iseconds
+    ./run_irace_parallel-batch.sh
+    date -Iseconds
+done
+
+echo "DONE"
+date -Iseconds

eo/contrib/irace/expe/alpha/run_irace_parallel-batch.sh

@@ -0,0 +1,38 @@
+#!/bin/bash
+
+outdir="$(date --iso-8601=ns)_results_irace"
+mkdir ${outdir}
+cd ${outdir}
+
+run(){
+    p="$1"
+
+    echo "Problem ${p}"
+    res="results_problem_${p}"
+    mkdir ${res}
+    cd ${res}
+
+    # Fore some reason, irace absolutely need those files...
+    cp ../../irace-config/example.scen .
+    cp ../../irace-config/default.instances .
+    cp ../../release/fastga .
+    cat ../../irace-config/target-runner | sed "s/{{PROBLEM}}/${p}/" > ./target-runner
+    chmod u+x target-runner
+
+    # Generate the parameter list file.
+    ./fastga -h > fastga.param 2>/dev/null
+    # /usr/lib/R/site-library/irace/bin/irace --scenario example.scen 2>&1 | tee irace.log
+    /usr/lib/R/site-library/irace/bin/irace --scenario example.scen &> irace.log
+
+    cd ..
+    echo "Done problem ${p}"
+}
+
+N=5 # Somehow 5 is the fastest on my 4-cores machine.
+(
+for pb in $(seq 0 18); do 
+    ((i=i%N)); ((i++==0)) && wait
+    run "$pb" &
+done
+wait
+)

eo/contrib/irace/expe/alpha/run_randoms.sh

@@ -0,0 +1,61 @@
+
+#!/bin/bash
+
+# Number of runs (=seeds).
+runs=50
+
+# You most probably want to run on release builds.
+exe="./release/fastga"
+
+outdir="$(date --iso-8601=minutes)_results_randoms"
+mkdir -p ${outdir}
+mkdir -p ${outdir}/raw
+mkdir -p ${outdir}/raw/data
+mkdir -p ${outdir}/raw/logs
+
+n=1
+algoid=0
+for algoid in $(seq 0 100); do
+    echo ""
+    date
+
+    a=( $((RANDOM%5)) $((RANDOM%7)) $((RANDOM%11)) $((RANDOM%5)) $((RANDOM%7)) $((RANDOM%11)) $((RANDOM%11)) )
+    algo="--crossover-rate=${a[0]} --cross-selector=${a[1]} --crossover=${a[2]}  --mutation-rate=${a[3]} --mut-selector=${a[4]} --mutation=${a[5]}  --replacement=${a[6]}"
+
+    for pb in $(seq 0 18) ; do
+        perc=$(echo "scale=3;${n}/(100*18)*100.0" | bc)
+        echo "${perc}% : algo ${algoid}/100, problem ${pb}/18"
+        # echo -n "Runs: "
+
+        for seed in $(seq ${runs}) ; do # Iterates over runs/seeds.
+            # This is the command to be ran.
+            cmd="${exe} --full-log=1 --problem=${pb} --seed=${seed} ${algo}"
+            # echo ${cmd} # Print the command.
+
+            # Forge a directory/log file name
+            # (remove double dashs and replace spaces with underscore).
+            name_run="pb=${pb}_seed=${seed}_$(echo "${algo}" | sed 's/--//g' | sed 's/ /_/g')"
+            # echo $name_run
+
+            # Progress print.
+            # echo -n "${seed} "
+
+            # Actually start the command.
+            ${cmd} > "${outdir}/raw/data/${name_run}.dat" 2> "${outdir}/raw/logs/${name_run}.log"
+
+            # Check for the most common problem in the log file.
+            cat "${outdir}/raw/logs/${name_run}.log" | grep "illogical performance"
+        done # seed
+        # echo ""
+
+        n=$(($n+1))
+    done # pb
+
+    algoid=$(($algoid+1))
+done
+
+# Move IOH logs in the results directory.
+mv ./FastGA_* ${outdir}
+
+echo "Done"
+date

eo/contrib/irace/expe/beta/best_out_of_elites.py

@@ -0,0 +1,86 @@
+#!/usr/bin/env python3
+import sys
+import os
+import numpy as np
+import matplotlib.pyplot as plt
+#cmd eg : 
+#python3 best_out_of_elites.py ./fastga_results_all/fastga_results_planO/planO_maxExp=50000_maxEv=5n_2021-08-13T19:16+02:00_results_elites_all
+#python3 best_out_of_elites.py ./fastga_results_all/fastga_results_random/maxEv=10000_nbAlgo=15_2021-08-21T20:53+02:00_results_randoms
+
+
+#get the configuration of the best out of the elite
+# recommendation suggested by 15 independant runs of irace
+
+figdir=sys.argv[1] # directory of a result of one experiment
+#eg : ./fastga_results_all/fastga_results_plan1/plan1_maxExp\=100000_maxEv\=5n_2021-08-13T19\:04+02\:00_results_elites_all/
+#print(figdir.split('/')[-2], figdir.split('/'))
+if("plan" in figdir.split('/')[-2]):
+    print("Operator,","op. ,",",".join(map(str,range(1,20))))
+
+    column={"pc" : 101, "SelectC": 7, "Crossover" : 10, "pm": 101,"SelectM" : 7, "Mutation": 11, "Replacement" : 11, "pop-size": 50, "offspring-size" : 50}
+    nbparam=(len(os.listdir(os.path.join(figdir,"raw/data"))[0].split("_"))-1) #-1 car il y a le pb
+
+    if( nbparam<len(column)):
+        del column["pop-size"]
+        del column["offspring-size"]
+    configs=[(-1,-1)]*19 #tuple(auc,config)
+    res=np.zeros((nbparam,19))
+    for fastgadir in os.listdir(os.path.join(figdir,"raw/data")): #fastgadir : directory of 50 runs of an elite configuration
+        #cum=np.cumsum([0.1]*10)
+        average=[]
+        for fname in os.listdir(os.path.join(figdir,"raw/data",fastgadir)):
+            with open(os.path.join(figdir,"raw/data",fastgadir,fname)) as fd:
+                auc = float(fd.readlines()[0]) * -1
+            average.append(auc)
+        pb=int(fastgadir.split("_")[0].split("=")[1])
+        new_auc=np.mean(average)
+        if(configs[pb][0]<new_auc):
+            configs[pb]=(new_auc,fastgadir)
+
+
+    for pb in range(19):
+        config=configs[pb][1].split("_")
+        configparam=[p.split("=")[1] for p in config[1:]]
+        res[:,pb]=configparam
+
+    ind=0 #index of param_name
+    for param_name in column.keys():
+        #print(map(str,res[ind]),res[ind], ",".join(map(str,res[ind])))
+        print(param_name+","+str(column[param_name])+",", ",".join(map(str,res[ind])))
+        ind+=1
+        #print(str(i)+",",",".join(map(str,np.mean(aucs[i],1))))
+
+if("maxEv" in figdir.split('/')[-2]):
+    print("Operator,","op. ,",",".join(map(str,range(1,20))))
+
+    column={"pc" : 101, "SelectC": 7, "Crossover" : 10, "pm": 101,"SelectM" : 7, "Mutation": 11, "Replacement" : 11, "pop-size": 50, "offspring-size" : 50}
+    nbparam=(len(os.listdir(figdir)[0].split("_")))
+    if( nbparam<len(column)):
+        del column["pop-size"]
+        del column["offspring-size"]
+    configs=[(-1,-1)]*19 #tuple(auc,config)
+    bests=np.zeros((nbparam,19))
+    
+    for algodir in os.listdir(figdir): #algodir : directory of one random algo
+        for fname in os.listdir(os.path.join(figdir,algodir,"data")): #fname : directory of 50 runs of fastga for one pb
+            average=[]
+            for res in os.listdir(os.path.join(figdir,algodir,"data",fname)):
+                with open(os.path.join(figdir,algodir,"data",fname,res)) as fd:
+                    auc = float(fd.readlines()[0]) * -1
+                average.append(auc)
+            pb=int(fname.split("_")[0].split("=")[1])
+            new_auc=np.mean(average)
+            if(configs[pb][0]<new_auc):
+                configs[pb]=(new_auc,algodir)
+
+
+    for pb in range(19):
+        config=configs[pb][1].split("_")
+        configparam=[p.split("=")[1] for p in config]
+        bests[:,pb]=configparam
+
+    ind=0 #index of param_name
+    for param_name in column.keys():
+        #print(map(str,res[ind]),res[ind], ",".join(map(str,res[ind])))
+        print(param_name+","+str(column[param_name])+",", ",".join(map(str,bests[ind])))
+        ind+=1

eo/contrib/irace/expe/beta/csv_all.sh

@@ -0,0 +1,40 @@
+#!/bin/bash
+
+ldata="./fastga_results_all/"  #fastga_results_all
+figpath="./hist_and_csv/"  #hist_and_csv
+
+#get distribution of operators variants of all problems of each plan of fastga_results_all
+#fastga_results_all contains all experiments of all plans 
+
+ldir=$(echo $(ls ${ldata})) #list of directory of each plan
+for plan in ${ldir[@]} ; do #get the directory of each plan
+    lexperiment=$(echo $(ls ${ldata}/${plan}))
+
+    for experiments in ${lexperiment[@]} ; do
+        path="${ldata}/${plan}/${experiments}"
+
+        #----------------average aucs of each algo for each pb only for plan A,F,O ---------------
+        #myfig=${figpath}/auc_average_${plan}
+        #mkdir -p ${myfig}
+        #cmd="python3 parse_auc_average.py ${path} "
+        #$cmd > "${myfig}/auc_average_${experiments}.csv"
+        #--------------distribution of operators by pb and for all pb only for plan A,F,O ------
+        #myfig=${figpath}/distribution_op_${plan}
+        #mkdir -p ${myfig}
+        #cmd="python3 distribution_op_all.py ${path} ${myfig} "
+        #$cmd 
+        #--------------best out csv--------
+        cmd="python3 best_out_of_elites.py ${path}"
+        myfig=${figpath}/best_out_${plan}
+        mkdir -p ${myfig}
+        $cmd > ${myfig}/best_out_all_pb_${experiments}.csv
+        echo ${cmd}
+
+    done
+done
+
+#---------------distribution of operators of randoma algo------------------
+#rpath=${ldata}/fastga_results_random
+#cmd="python3 dist_op_random.py ${rpath} ${figpath}"
+#$cmd
+#---------------random---------------

eo/contrib/irace/expe/beta/csv_all_bests.sh

@@ -0,0 +1,16 @@
+#!/bin/bash
+ldata=$1
+file_py=$2
+csvdir="csv_FAO"
+ldir=$(echo $(ls ${ldata}))
+for data in ${ldir[@]} ; do 
+    path="${ldata}/${data}"
+    cmd="python3 ${file_py} ${path}"
+    plan_name=$(echo ${data} | sed "s/data//")
+    mexp=$(echo ${data[@]} | cut -d _ -f2)
+    mevals=$(echo ${data[@]} | cut -d _ -f3)
+    ddate=$(echo ${data[@]} | cut -d _ -f4)
+    name="results_irace_plan${plan_name[@]:0:1}_${mexp}_${mevals}_${ddate}"
+    mkdir -p "${csvdir}/csv_plan${plan_name[@]:0:1}"
+    ${cmd} > "${csvdir}/csv_plan${plan_name[@]:0:1}/${name}.csv"
+done

eo/contrib/irace/expe/beta/dist_op_random.py

@@ -0,0 +1,78 @@
+#!/usr/bin/env python3
+import sys
+import os
+import numpy as np
+import matplotlib.pyplot as plt
+
+#cmd eg : python3 ./dist_op_random.py ./fastga_results_all/fastga_results_random/ ./hist_and_csv/
+#get the distribution of operators variants recommended by 15 random algo for each maxEv 
+#pc and pm 10 possibilities :   [0-0.1[  [0.1-0.2[ [0.2-0.3[  [0.3-0.4[  [0-0.5[  [0.5-0.6[ ...[0.9-1[
+#pop-size and offspring-size 10 possibilities : 0-5 5-10, 10-15 15-20  20-25  25-30 30-35- 35-40 40-45 45-50
+
+path=sys.argv[1] # directory of a result of one experiment
+#eg : ./fastga_results_all/fastga_results_random/
+figdir=sys.argv[2] #directory of where you want to store the data
+if("random" in path):
+    #column : [operator : nbpossibilities]
+    distdir=figdir+"/distribution_random"
+    try:
+        os.makedirs(distdir)
+    except FileExistsError:
+        pass
+
+    nbparam=9 #-1 car il y a le pb
+
+    res=[]
+            
+    for maxEvdir in os.listdir(path):
+        res.append({"crossover-rate":["pc" , np.zeros(10, dtype=int)], 
+    "cross-selector":["SelectC", np.zeros(7, dtype=int)],
+    "crossover":["Crossover" , np.zeros(10, dtype=int)],
+    "mutation-rate":["pm",np.zeros(10, dtype=int)], 
+    "mut-selector":["SelectM",np.zeros(10, dtype=int)],
+    "mutation":["Mutation", np.zeros(11, dtype=int)],
+    "replacement":["Replacement" , np.zeros(11, dtype=int)],
+    "pop-size":["pop-size", np.zeros(10, dtype=int)], 
+    "offspring-size":["offspring-size" , np.zeros(10, dtype=int)]})
+        for algodir in os.listdir(os.path.join(path,maxEvdir)): #fastgadir : directory of 50 runs of an elite configuration
+            algo=algodir.split("_")
+            for param in algo:
+                name,val=param.split("=")[0],float(param.split("=")[1])
+                if(name in {"pop-size" ,"offspring-size"}):
+                    if(val%5==0):
+                        res[-1][name][1][int(val//5) -1]+=1
+                    else:
+                        #print(res[-1][name][1],val//5)
+                        res[-1][name][1][int(val//5)]+=1
+                        
+                elif(name in {"crossover-rate","mutation-rate"} ):
+                    if(int(val*10)==10): #case of val=1
+                        res[-1][name][1][-1]+=1
+                    else :
+                        #print(int(float(val)*10), name,pb,val)
+                        res[-1][name][1][int(val*10)]+=1
+                else :
+                    res[-1][name][1][int(val)]+=1
+
+
+    ind=0
+    for maxEvdir in os.listdir(path):
+        name="distribution_random_"+maxEvdir.split("_")[0]+".csv" #the end of the path must be /
+        with open(os.path.join(distdir,name),"w+") as csvfile:
+            csvfile.write("Op index, "+",".join(map(str,range(0,11)))+"\n")
+        with open(os.path.join(distdir,name),"a") as csvfile:
+            for param_name in res[ind].keys():
+                #print(map(str,res[ind]),res[ind], ",".join(map(str,res[ind])))
+                csvfile.write(res[ind][param_name][0]+","+ ",".join(map(str,res[ind][param_name][1]))+",-"*(11-len(res[ind][param_name][1])) +"\n")
+                #print(str(i)+",",",".join(map(str,np.mean(aucs[i],1))))
+        ind+=1
+    #all problems
+    name ="distribution_all_random_"+path.split("/")[-1]+".csv"
+    with open(os.path.join(distdir,name),'w+') as csvfile:
+        csvfile.write("Op index, "+",".join(map(str,range(0,11)))+"\n")
+
+    with open(os.path.join(distdir,name),'a') as csvfile:
+        for param_name in res[0].keys():
+            #print(map(str,res[ind]),res[ind], ",".join(map(str,res[ind])))
+            csvfile.write(res[0][param_name][0]+","+ ",".join(map(str,np.sum([res[i][param_name][1] for i in range(ind-1)],0)))+",-"*(11-len(res[0][param_name][1])) +"\n") #res[0] only for getting the name of parameters
+            #print(str(i)+",",",".join(map(str,np.mean(aucs[i],1)))) 

eo/contrib/irace/expe/beta/distribution_op_all.py

@@ -0,0 +1,87 @@
+#!/usr/bin/env python3
+import sys
+import os
+import numpy as np
+import matplotlib.pyplot as plt
+
+#get the distribution of operators variants recommended by 15 runs of irace for all problems and each problem
+#also get an csv file
+#pc and pm 10 possibilities :   [0-0.1[  [0.1-0.2[ [0.2-0.3[  [0.3-0.4[  [0-0.5[  [0.5-0.6[ ...[0.9-1[
+#pop-size and offspring-size 10 possibilities : 0-5 5-10, 10-15 15-20  20-25  25-30 30-35- 35-40 40-45 45-50
+
+path=sys.argv[1] # directory of a result of one experiment
+#eg : ./fastga_results_all/fastga_results_planO/planO_maxExp\=100000_maxEv\=5n_2021-08-13T19\:04+02\:00_results_elites_all/
+
+if("fastga_results_plan" in path):
+        #column : [operator : nbpossibilities]
+    distdir=sys.argv[2]
+    try:
+        os.makedirs(distdir)
+    except FileExistsError:
+        pass
+
+    nbparam=(len(os.listdir(os.path.join(path,"raw/data"))[0].split("_"))-1)
+
+    if( nbparam==7):
+        res=[{"crossover-rate":["pc" , np.zeros(10, dtype=int)], 
+        "cross-selector":["SelectC", np.zeros(7, dtype=int)],
+        "crossover":["Crossover" , np.zeros(10, dtype=int)],
+        "mutation-rate":["pm",np.zeros(10, dtype=int)], 
+        "mut-selector":["SelectM",np.zeros(7, dtype=int)],
+        "mutation":["Mutation", np.zeros(11, dtype=int)],
+        "replacement":["Replacement" ,np.zeros(11, dtype=int)]} for i in range(19)]
+    else:
+        res=[{"crossover-rate":["pc" , np.zeros(10, dtype=int)], 
+        "cross-selector":["SelectC", np.zeros(7, dtype=int)],
+        "crossover":["Crossover" , np.zeros(10, dtype=int)],
+        "mutation-rate":["pm",np.zeros(10, dtype=int)], 
+        "mut-selector":["SelectM",np.zeros(7, dtype=int)],
+        "mutation":["Mutation", np.zeros(11, dtype=int)],
+        "replacement":["Replacement" , np.zeros(11, dtype=int)],
+        "pop-size":["pop-size", np.zeros(10, dtype=int)], 
+        "offspring-size":["offspring-size" , np.zeros(10, dtype=int)]} for i in range(19)]
+        
+
+    for fastgadir in os.listdir(os.path.join(path,"raw/data")): #fastgadir : directory of 50 runs of an elite configuration
+        algo=fastgadir.split("_")
+        pb=int(fastgadir.split("_")[0].split("=")[1])
+        for param in algo[1:]:
+            name,val=param.split("=")[0],float(param.split("=")[1])
+            if(name in {"pop-size" ,"offspring-size"}):
+                if(val%5==0):
+                    res[pb][name][1][int(val//5) -1]+=1
+                else:
+                    #print(res[pb][name][1],val//5)
+                    res[pb][name][1][int(val//5)]+=1
+                    
+            elif(name in {"crossover-rate","mutation-rate"} ):
+                if(int(val*10)==10): #case of val=1
+                    res[pb][name][1][-1]+=1
+                else :
+                    #print(int(float(val)*10), name,pb,val)
+                    res[pb][name][1][int(val*10)]+=1
+            else :
+                res[pb][name][1][int(val)]+=1
+
+
+
+    for pb in range(19):
+        name="distribution_pb="+str(pb)+"_"+path.split("/")[-2]+".csv" #the end of the path must be /
+        with open(os.path.join(distdir,name),"w+") as csvfile:
+            csvfile.write("Op index, "+",".join(map(str,range(0,11)))+"\n")
+        with open(os.path.join(distdir,name),"a") as csvfile:
+            for param_name in res[pb].keys():
+                #print(map(str,res[ind]),res[ind], ",".join(map(str,res[ind])))
+                csvfile.write(res[pb][param_name][0]+","+ ",".join(map(str,res[pb][param_name][1]))+",-"*(11-len(res[pb][param_name][1])) +"\n")
+                #print(str(i)+",",",".join(map(str,np.mean(aucs[i],1))))
+
+    #all problems
+    name ="distribution_all_pb_"+path.split("/")[-1]+".csv"
+    with open(os.path.join(path,"raw",name),'w+') as csvfile:
+        csvfile.write("Op index, "+",".join(map(str,range(0,11)))+"\n")
+
+    with open(os.path.join(path,"raw",name),'a') as csvfile:
+        for param_name in res[0].keys():
+            #print(map(str,res[ind]),res[ind], ",".join(map(str,res[ind])))
+            csvfile.write(res[0][param_name][0]+","+ ",".join(map(str,np.sum([res[i][param_name][1] for i in range(19)],0)))+",-"*(11-len(res[0][param_name][1])) +"\n") #res[0] only for getting the name of parameters
+            #print(str(i)+",",",".join(map(str,np.mean(aucs[i],1)))) 

eo/contrib/irace/expe/beta/fastga_elites_all.sh

@@ -0,0 +1,23 @@
+#!/bin/bash
+ldata=$1 
+file_sh=$2
+ldir=$(echo $(ls ${ldata}))
+fastga_dir="fastga_results_all"
+mkdir -p /scratchbeta/${USER}/${fatga_dir}
+#mkdir -p "/home/${USER}/${fastga_dir}/fastga_results_plan1"
+mkdir -p "/scratchbeta/${USER}/${fastga_dir}/fastga_results_planF"
+mkdir -p "/scratchbeta/${USER}/${fastga_dir}/fastga_results_planA"
+mkdir -p "/scratchbeta/${USER}/${fastga_dir}/fastga_results_planO"
+
+for data in ${ldir[@]} ; do 
+    path_csv="${ldata}/${data}"
+    plan_name=$(echo ${data} | sed "s/results_irace_plan//")
+    mexp=$(echo ${data[@]} | cut -d _ -f4)
+    mexp_id=$(echo ${mexp} | cut -d = -f2)
+    mevals=$(echo ${data[@]} | cut -d _ -f5)
+    mevals_id=$(echo ${mevals} | cut -d = -f2)
+    path="/scratchbeta/${USER}/${fastga_dir}/fastga_results_plan${plan_name[@]:0:1}"
+    cmd="bash ${file_sh} ${path_csv} ${mexp_id} ${mevals_id} ${path}"
+    name="fastga${plan_name[@]:0:1}_${mexp}_${mevals}_$(date -Iseconds)_results_elites_all"
+    ${cmd} &> "${path}/output${plan_name[@]:0:1}_fastga_${mexp}_${mevals}_$(date -Iseconds).txt"
+done

eo/contrib/irace/expe/beta/hist_all.sh

@@ -0,0 +1,34 @@
+#!/bin/bash
+
+ldata="./fastga_results_all"  #fastga_results_all
+figpath="./hist_and_csv"  #hist_and_csv
+
+ldir=$(echo $(ls ${ldata})) #list of directory of each plan
+for plan in ${ldir[@]} ; do #get the directory of each plan
+    #------------hist by budget of a Plan (O,R or F)
+    #path="${ldata}/${plan}"   
+    #cmd="python3 hist_join.py ${path} ${figpath}"
+    #echo $cmd
+    #$cmd
+
+    #---------------------------hist by pb by budget---------------
+    path="${ldata}/${plan}"   
+    cmd="python3 hist_by_pb_budget_plan.py ${path} ${figpath}"
+    echo $cmd
+    $cmd
+done
+
+#---------------random------------------
+#rpath=${ldata}/fastga_results_random
+#cmd="python3 hist_join_random.py ${rpath} ${figpath}"
+#---------------random---------------
+
+#--------------------Choose a Budget irace and a budget fastga
+mexp=100000
+mevals=1000
+#-------------------histogram join each plan F,A,R,O and join all algorithms for the budget chosen
+cmd="python3 hist_by_FARO.py ${ldata} ${figdir} ${mexp} ${mevals}"
+$cmd
+#-------------------histogram by pb join each plan F,A,R,O and join all algorithms for the budget chosen
+cmd="python3 hist_by_FARO_pb.py ${ldata} ${figdir} ${mexp} ${mevals}"
+$cmd

eo/contrib/irace/expe/beta/hist_by_FARO.py

@@ -0,0 +1,71 @@
+#!/usr/bin/env python3
+import sys
+import os
+import numpy as np
+import matplotlib.pyplot as plt
+from scipy.stats import mannwhitneyu
+
+##python3 hist_by_FARO.py ./fastga_results_all/ ./hist_and_csv/ 100000 1000
+#one plot for one experiment plan for the same budget fastga, and the same budget irace if there is a budget irace (A,F)
+path=sys.argv[1]
+figpath=sys.argv[2]
+maxExp=sys.argv[3]
+maxEv=sys.argv[4]
+
+indF=-1
+indFO=-1
+averageConfigs=[]
+name=[]
+for fastga in os.listdir(path): #ddir : directory of fastga_plan
+    if(fastga in {"fastga_results_planA","fastga_results_planF","fastga_results_planO"}):
+        for plan in os.listdir(os.path.join(path,fastga)):
+            print("maxExp="+str(maxExp)+"_maxEv="+str(maxEv) in plan,plan,"maxExp="+str(maxExp)+"_maxEv="+str(maxEv))
+            if("maxExp="+str(maxExp)+"_maxEv="+str(maxEv) in plan):
+                average=[]
+                
+                for fastgadir in os.listdir(os.path.join(path,fastga,plan,"raw","data")): #fastgadir : directory of 50 runs of a configuration
+                    for fname in os.listdir(os.path.join(path,fastga,plan,"raw","data",fastgadir)):
+                        with open(os.path.join(path,fastga,plan,"raw","data",fastgadir,fname)) as fd:
+                            auc = float(fd.readlines()[0]) *(-1)
+                        average.append(auc)
+                averageConfigs.append(average)
+                nameid=plan.split("_")[0][-1]
+                name.append("plan"+nameid+"_"+"_".join(plan.split("_")[1:3]))
+    if("random" in fastga):
+        for randir in os.listdir(os.path.join(path,fastga)):
+            #eg path: maxEv=100_nbAlgo=15_2021-08-20T1511+0200_results_randoms
+            average=[]
+            if("maxEv="+str(maxEv)+"_" in randir):
+                for ddir in os.listdir(os.path.join(path,fastga,randir)): #ddir : directory of one run_elites_all or more
+                    if("crossover" in ddir):
+                        #name.append("_".join(ddir.split("_")[1:3]))
+                        for fastgadir in os.listdir(os.path.join(path,fastga,randir,ddir,"data")): #fastgadir : directory of 50 runs of a configuration
+                            for fname in os.listdir(os.path.join(path,fastga,randir,ddir,"data",fastgadir)):
+                                with open(os.path.join(path,fastga,randir,ddir,"data",fastgadir,fname)) as fd:
+                                    auc = float(fd.readlines()[0]) *(-1)
+                                average.append(auc)
+                                #hist[belonging(auc,cum)]+=1
+                averageConfigs.append(average)
+                name.append(randir.split("_")[0]+"_random")
+
+
+figdir=os.path.join(figpath,"hist_FARO_by_budget")
+try:
+    os.makedirs(figdir)
+except FileExistsError:
+    pass
+
+#_,pv=mannwhitneyu(averageConfigs[indFO],averageConfigs[indF])
+#print(name,len(averageConfigs))
+plt.figure()
+plt.hist(averageConfigs,bins=10,range=(0,1),align="mid",rwidth=0.9,label=name) #no label
+plt.xlabel("performances")
+plt.ylabel("Number of runs")
+plt.xlim(0,1)
+plt.ylim(0,8000)
+plt.yticks(range(0,8000,500))
+#plt.title("pvalue="+str(pv)+"\n medianeF="+str(np.median(averageConfigs[indF]))+", medianeFO="+str(np.median(averageConfigs[indFO])))
+plt.legend()
+plt.savefig(figdir+"/hist_planFARO"+"_maxExp="+str(maxExp)+"_maxEv="+str(maxEv)+".png")
+plt.close()
+    

eo/contrib/irace/expe/beta/hist_by_FARO_pb.py

@@ -0,0 +1,88 @@
+#!/usr/bin/env python3
+import sys
+import os
+import numpy as np
+import matplotlib.pyplot as plt
+
+##python3 hist_by_FARO_pb.py ./fastga_results_all/ ./hist_and_csv/ 100000 1000
+#19 histograms by plan F,A ,R O
+path=sys.argv[1]
+figpath=sys.argv[2]
+maxExp=sys.argv[3]
+maxEv=sys.argv[4]
+
+hist_pb=[[] for i in range(19)]
+name=[]
+for fastga in os.listdir(path): #ddir : directory of fastga_plan
+    if(fastga in {"fastga_results_planA", "fastga_results_planF","fastga_results_planO"}):
+        for plan in os.listdir(os.path.join(path,fastga)):
+            #print("maxExp="+str(maxExp)+"_maxEv="+str(maxEv)+"_" in plan,plan,"maxExp="+str(maxExp)+"_maxEv="+str(maxEv))
+            #print("maxExp="+str(maxExp)+"_maxEv="+str(maxEv) in plan,plan,"maxExp="+str(maxExp)+"_maxEv="+str(maxEv))
+            if("maxExp="+str(maxExp)+"_maxEv="+str(maxEv)+"_" in plan):
+                nameid=fastga[-1]
+                name.append("plan"+nameid+"_".join(plan.split("_")[1:3]))
+                for fastgadir in os.listdir(os.path.join(path,fastga,plan,"raw","data")): #fastgadir : directory of 50 runs of a configuration
+                    pb=int(fastgadir.split("_")[0].split("=")[1])
+                    average_pb=[]
+                    for fname in os.listdir(os.path.join(path,fastga,plan,"raw","data",fastgadir)):
+                        with open(os.path.join(path,fastga,plan,"raw","data",fastgadir,fname)) as fd:
+                            auc = float(fd.readlines()[0]) *(-1)
+                        average_pb.append(auc)
+                    if(hist_pb[pb]==[]): #first algo
+                        hist_pb[pb].append(average_pb)
+                    elif(len(hist_pb[pb])!=len(name)):
+                        hist_pb[pb].append(average_pb)
+                    else:
+                        hist_pb[pb][len(name)-1]+=average_pb #another algo for the same plan
+
+    if("random" in fastga):
+        for randir in os.listdir(os.path.join(path,fastga)):
+            #eg path: maxEv=100_nbAlgo=15_2021-08-20T1511+0200_results_randoms
+            if(("maxEv="+str(maxEv)+"_") in randir):
+                #print("maxEv="+str(maxEv) in randir,randir)
+                name.append(randir.split("_")[0]+"_random")
+                for ddir in os.listdir(os.path.join(path,fastga,randir)): #ddir : directory of one run_elites_all or more
+                    if("crossover" in ddir):
+                        #name.append("_".join(ddir.split("_")[1:3]))
+                        for fastgadir in os.listdir(os.path.join(path,fastga,randir,ddir,"data")): #fastgadir : directory of 50 runs of a configuration
+                            average_pb=[]
+                            pb=int(fastgadir.split("_")[0].split("=")[1])
+                            for fname in os.listdir(os.path.join(path,fastga,randir,ddir,"data",fastgadir)):
+                                with open(os.path.join(path,fastga,randir,ddir,"data",fastgadir,fname)) as fd:
+                                    auc = float(fd.readlines()[0]) *(-1)
+                                average_pb.append(auc)
+                            #print(len(hist_pb[pb]),len(name), pb)
+                            if(hist_pb[pb]==[]): #first algo
+                                #print("entrer random vide")
+                                hist_pb[pb].append(average_pb)
+                            elif(len(hist_pb[pb])!=len(name)):
+                                #print("entrer random !=")
+                                hist_pb[pb].append(average_pb)
+                            else:
+                                hist_pb[pb][len(name)-1]+=average_pb #another algo for the same plan
+
+
+figdir=os.path.join(figpath,"hist_by_FARO_pb_maxExp={}_maxEv={}".format(maxExp,maxEv))
+try:
+    os.makedirs(figdir)
+except FileExistsError:
+    pass
+#colors=['yellow', 'green',"blue","pink","purple","orange","magenta","gray","darkred","cyan","brown","olivedrab","thistle","stateblue"]
+print(name)
+for pb in range(19):
+    print(pb, len(hist_pb[pb]))
+    for i in hist_pb[pb]:
+        print(len(i))
+    plt.figure()
+    plt.hist(hist_pb[pb],bins=10,range=(0,1),align="mid",rwidth=0.9,edgecolor="red",label=name) #no label color=colors[:len(name)]
+    #for aucs in range(len(hist_pb[pb])):
+        #plt.hist(hist_pb[pb][aucs],bins=10,range=(0,1),align="mid",rwidth=0.9,edgecolor="red",label=name[aucs]) #no label
+    plt.xlabel("performances")
+    plt.ylabel("Number of runs")
+    plt.ylim(0,800)
+    plt.xlim(0,1)
+    plt.yticks(range(0,800,50))
+    #plt.xticks(np.cumsum([0.1]*10))
+    plt.legend()
+    plt.savefig(figdir+"/hist_FARO_pb={}_maxExp={}_maxEv={}.png".format(pb,maxExp,maxEv))
+    plt.close()

eo/contrib/irace/expe/beta/hist_by_pb_budget_plan.py

@@ -0,0 +1,90 @@
+#!/usr/bin/env python3
+import sys
+import os
+import numpy as np
+import matplotlib.pyplot as plt
+
+# python3 hist_by_pb_budget_plan.py ./fastga_results_all/fastga_results_planF/ ./hist_and_csv/
+#python3 hist_by_pb_budget_plan.py ./fastga_results_all/fastga_results_planO ./hist_and_csv
+#get 19 histograms with number of budget bars, same as hist_join but now is by pb
+
+#argv : list of elite results
+path=sys.argv[1]
+figpath=sys.argv[2]
+#plan_name=sys.argv[3]
+hist_pb=[[] for i in range(19)]
+name=[]
+if("random" in path):
+    plan_name="R"
+else:
+    plan_name=path.strip("/").split("/")[-1][-1]
+
+
+for plandir in os.listdir(path): #plandir: directory of an experiment of elite results 
+    if("results_elites_all" in plandir):
+        #eg : plan2_maxExp=10000_maxEv=1000_2021-08-20T1347+0200_results_elites_all
+        budget_irace=plandir.split("_")[1].split("=")[1]
+        budget_fastga=plandir.split("_")[2].split("=")[1]
+        name.append("plan="+plan_name+"_"+"".join(plandir.split("_")[1:3])) #plan=*_maxExp=*_maxEv=*
+        
+        for algodir in os.listdir(os.path.join(path,plandir,"raw","data")):
+            average_pb=[]
+            pb=int(algodir.split("_")[0].split("=")[1])
+            for algo in os.listdir(os.path.join(path,plandir,"raw","data",algodir)):
+                with open(os.path.join(path,plandir,"raw","data",algodir,algo)) as fd:
+                    auc = float(fd.readlines()[0]) *(-1)
+                average_pb.append(auc)
+            if(hist_pb[pb]==[]): #first algo
+                hist_pb[pb].append(average_pb)
+            elif(len(hist_pb[pb])!=len(name)):
+                hist_pb[pb].append(average_pb)
+            else:
+                hist_pb[pb][len(name)-1]+=average_pb #another algo for the same plan
+
+    if("results_randoms" in plandir):
+        #eg : maxEv=1000_2021-08-20T1347+0200_results_random
+        budget_fastga=plandir.split("_")[0].split("=")[1]
+        name.append("plan="+plan_name+"_"+"".join(plandir.split("_")[0])) #plan=*_maxExp=*_maxEv=*
+        for algodir in os.listdir(os.path.join(path,plandir)):
+            
+            for algo in os.listdir(os.path.join(path,plandir,algodir,"data")):
+                pb=int(algo.split("_")[0].split("=")[1])
+                average_pb=[]
+                for fname in os.listdir(os.path.join(path,plandir,algodir,"data",algo)):
+                    with open(os.path.join(path,plandir,algodir,"data",algo,fname)) as fd:
+                        auc = float(fd.readlines()[0]) *(-1)
+                    average_pb.append(auc)
+                if(hist_pb[pb]==[]): #first algo
+                    print("entrer")
+                    hist_pb[pb].append(average_pb)
+                elif(len(hist_pb[pb])!=len(name)):
+                    hist_pb[pb].append(average_pb)
+                else:
+                    hist_pb[pb][len(name)-1]+=average_pb #another algo for the same plan
+        
+
+
+print(path.split("/")[-1][-1])
+
+figdir=os.path.join(figpath,"hist_by_{}_pb_budget_plan".format(plan_name))
+#figdir=os.path.join(figpath,"hist_by_{}_pb_irace_maxEv={}".format(plan_name,1000))
+try:
+    os.makedirs(figdir)
+except FileExistsError:
+    pass
+
+
+for pb in range(19):
+    print(pb, len(hist_pb[pb]))
+    plt.figure()
+    plt.hist(hist_pb[pb],bins=10,range=(0,1),align="mid",rwidth=0.9,edgecolor="red",label=name) #no label color=colors[:len(name)]
+    #for aucs in range(len(hist_pb[pb])):
+        #plt.hist(hist_pb[pb][aucs],bins=10,range=(0,1),align="mid",rwidth=0.9,edgecolor="red",label=name[aucs]) #no label
+    plt.xlabel("performances")
+    plt.ylabel("Number of runs")
+    plt.ylim(0,750)
+    plt.yticks(range(0,750,50))
+    plt.xlim(0,1)
+    plt.legend()
+    plt.savefig(figdir+"/hist_plan={}_pb={}_budget.png".format(plan_name,pb))
+    plt.close()

eo/contrib/irace/expe/beta/hist_join.py

@@ -0,0 +1,68 @@
+#!/usr/bin/env python3
+import sys
+import os
+import numpy as np
+import matplotlib.pyplot as plt
+from scipy.stats import mannwhitneyu
+
+#cmd : python3 hist_join.py ./fastga_results_all/fastga_results_planO/ ./hist_and_csv/
+#histogram by plan for the budgets (irace and fastag)
+
+
+path=sys.argv[1] #argv : directory of a Plan (O, A, F)
+figpath=sys.argv[2] #path to store the histograms
+averageConfigs=[]
+name=[]
+if("fastga_results_plan" in path):
+    for ddir in os.listdir(path): #ddir : directory of one run_elites_all or more
+        if("plan" in ddir):
+            average=[]
+            name.append("_".join(ddir.split("_")[1:3]))
+            for fastgadir in os.listdir(os.path.join(path,ddir,"raw","data")): #fastgadir : directory of 50 runs of a configuration
+                for fname in os.listdir(os.path.join(path,ddir,"raw","data",fastgadir)):
+                    with open(os.path.join(path,ddir,"raw","data",fastgadir,fname)) as fd:
+                        auc = float(fd.readlines()[0]) *(-1)
+                    average.append(auc)
+                    #hist[belonging(auc,cum)]+=1
+            averageConfigs.append(average)
+                #print(hist)
+                #print(average)
+
+    figdir=os.path.join(figpath,"hist_join")
+    try:
+        os.makedirs(figdir)
+    except FileExistsError:
+        pass
+
+
+    print(name,len(averageConfigs))
+
+    """
+    idd0=name[0].split("_")[0].split("=")[1][:-3]+"k"
+    idd1=name[1].split("_")[0].split("=")[1][:-3]+"k"
+    idd2=name[2].split("_")[0].split("=")[1][:-3]+"k"
+
+    #only for Budget irace 10000, 50000, 100000 ie: only three experiment results
+    titlename="median"+idd0+"={:.3f}".format(np.median(averageConfigs[0]))+" , median"+idd1+"={:.3f}".format(np.median(averageConfigs[1]))+" , median"+idd2+"={:.3f}".format(np.median(averageConfigs[2]))
+    _,pv=mannwhitneyu(averageConfigs[0],averageConfigs[1])
+    titlename+="\n pvalue{}={:.3f}".format(idd0+idd1,pv)
+    _,pv=mannwhitneyu(averageConfigs[0],averageConfigs[2])
+    titlename+=" ,pvalue{}={:.3f}".format(idd0+idd2,pv)
+    _,pv=mannwhitneyu(averageConfigs[1],averageConfigs[2])
+    titlename+=" ,pvalue{}={:.3f}".format(idd1+idd2,pv)
+    print(titlename)
+    """
+    plt.figure()
+    plt.hist(averageConfigs,bins=10,range=(0,1),align="mid",rwidth=0.9,label=name) #no label
+    plt.xlabel("performances")
+    plt.ylabel("Number of runs")
+    plt.xlim(0,1)
+    plt.ylim(0,7000)
+    plt.yticks(range(0,7000,500))
+    #plt.title(titlename)
+    plt.legend()
+    plt.savefig(figdir+"/hist_plan"+path.strip("/")[-1]+"_by_budget.png")
+    #plt.savefig(figpath+"/hist_plan"+path.strip("/")[-1]+"_by_budgetI.png")
+    plt.close()
+    
+

eo/contrib/irace/expe/beta/hist_join_random.py

@@ -0,0 +1,46 @@
+#!/usr/bin/env python3
+import sys
+import os
+import numpy as np
+import matplotlib.pyplot as plt
+
+##python3 hist_random.py ./dastga_results_all/fastga_results_random ./hist_and_csv/
+#argv : list of elite results
+data=sys.argv[1]
+figpath=sys.argv[2]
+averageConfigs=[]
+name=[]
+for path in os.listdir(data):
+    #eg path: maxEv=100_nbAlgo=15_2021-08-20T1511+0200_results_randoms
+    average=[]
+    if("maxEv" in path):
+        for ddir in os.listdir(os.path.join(data,path)): #ddir : directory of one run_elites_all or more
+            if("crossover" in ddir):
+                #name.append("_".join(ddir.split("_")[1:3]))
+                for fastgadir in os.listdir(os.path.join(data,path,ddir,"data")): #fastgadir : directory of 50 runs of a configuration
+                    for fname in os.listdir(os.path.join(data,path,ddir,"data",fastgadir)):
+                        with open(os.path.join(data,path,ddir,"data",fastgadir,fname)) as fd:
+                            auc = float(fd.readlines()[0]) *(-1)
+                        average.append(auc)
+                        #hist[belonging(auc,cum)]+=1
+        averageConfigs.append(average)
+        name.append(path.split("_")[0])
+
+figdir=os.path.join(figpath,"hist_join")
+try:
+    os.makedirs(figdir)
+except FileExistsError:
+    pass
+
+colors=['yellow', 'green',"blue","pink","purple","orange","magenta","gray","darkred","cyan","brown","olivedrab","thistle","stateblue"]
+plt.figure()
+plt.hist(averageConfigs,bins=10,range=(0,1),align="mid",rwidth=0.5,label=name) #no label
+plt.xlabel("performances")
+plt.ylabel("Number of runs")
+plt.ylim([0,8000])
+plt.xlim(0,1)
+plt.yticks(range(0,8000,500))
+#plt.xticks(np.cumsum([0.1]*10))
+plt.legend()
+plt.savefig(figdir+"/hist_random_by_budget.png")
+plt.close()

eo/contrib/irace/expe/beta/irace_files_pA/default.instances

@@ -0,0 +1,27 @@
+## This is an example of specifying instances with a file.
+
+# Each line is an instance relative to trainInstancesDir
+# (see scenario.txt.tmpl) and an optional sequence of instance-specific
+# parameters that will be passed to target-runnerx when invoked on that
+# instance.
+
+0
+1
+2
+3
+4
+5
+6
+7
+8
+9
+10
+11
+12
+13
+14
+15
+16
+17
+18
+

eo/contrib/irace/expe/beta/irace_files_pA/example.scen

@@ -0,0 +1,227 @@
+###################################################### -*- mode: r -*- #####
+## Scenario setup for Iterated Race (irace).
+############################################################################
+
+## To use the default value of a parameter of iRace, simply do not set
+## the parameter (comment it out in this file, and do not give any
+## value on the command line).
+
+## File that contains the description of the parameters of the target
+## algorithm.
+parameterFile = "./fastga.param"
+
+## Directory where the programs will be run.
+execDir = "."
+
+## File to save tuning results as an R dataset, either absolute path or
+## relative to execDir.
+# logFile = "./irace.Rdata"
+
+## Previously saved log file to recover the execution of irace, either
+## absolute path or relative to the current directory.  If empty or NULL,
+## recovery is not performed.
+# recoveryFile = ""
+
+## Directory where training instances are located; either absolute path or
+## relative to current directory. If no trainInstancesFiles is provided,
+## all the files in trainInstancesDir will be listed as instances.
+trainInstancesDir = "."
+
+## File that contains a list of training instances and optionally
+## additional parameters for them. If trainInstancesDir is provided, irace
+## will search for the files in this folder.
+trainInstancesFile = "./default.instances"
+
+## File that contains a table of initial configurations. If empty or NULL,
+## all initial configurations are randomly generated.
+# configurationsFile = ""
+
+## File that contains a list of logical expressions that cannot be TRUE
+## for any evaluated configuration. If empty or NULL, do not use forbidden
+## expressions.
+forbiddenFile = "./forbidden.txt"
+
+## Script called for each configuration that executes the target algorithm
+## to be tuned. See templates.
+targetRunner = "./target-runner"
+
+## Number of times to retry a call to targetRunner if the call failed.
+# targetRunnerRetries = 0
+
+## Optional data passed to targetRunner. This is ignored by the default
+## targetRunner function, but it may be used by custom targetRunner
+## functions to pass persistent data around.
+# targetRunnerData = ""
+
+## Optional R function to provide custom parallelization of targetRunner.
+# targetRunnerParallel = ""
+
+## Optional script or R function that provides a numeric value for each
+## configuration. See templates/target-evaluator.tmpl
+# targetEvaluator = ""
+
+## Maximum number of runs (invocations of targetRunner) that will be
+## performed. It determines the maximum budget of experiments for the
+## tuning.
+maxExperiments = 0 #100000
+
+## Maximum total execution time in seconds for the executions of
+## targetRunner. targetRunner must return two values: cost and time.
+# maxTime = 60
+
+## Fraction (smaller than 1) of the budget used to estimate the mean
+## computation time of a configuration. Only used when maxTime > 0
+# budgetEstimation = 0.02
+
+## Maximum number of decimal places that are significant for numerical
+## (real) parameters.
+digits = 2
+
+## Debug level of the output of irace. Set this to 0 to silence all debug
+## messages. Higher values provide more verbose debug messages.
+# debugLevel = 0
+
+## Number of iterations.
+# nbIterations = 0
+
+## Number of runs of the target algorithm per iteration.
+# nbExperimentsPerIteration = 0
+
+## Randomly sample the training instances or use them in the order given.
+# sampleInstances = 1
+
+## Statistical test used for elimination. Default test is always F-test
+## unless capping is enabled, in which case the default test is t-test.
+## Valid values are: F-test (Friedman test), t-test (pairwise t-tests with
+## no correction), t-test-bonferroni (t-test with Bonferroni's correction
+## for multiple comparisons), t-test-holm (t-test with Holm's correction
+## for multiple comparisons).
+# testType = "F-test"
+
+## Number of instances evaluated before the first elimination test. It
+## must be a multiple of eachTest.
+# firstTest = 5
+
+## Number of instances evaluated between elimination tests.
+# eachTest = 1
+
+## Minimum number of configurations needed to continue the execution of
+## each race (iteration).
+# minNbSurvival = 0
+
+## Number of configurations to be sampled and evaluated at each iteration.
+# nbConfigurations = 0
+
+## Parameter used to define the number of configurations sampled and
+## evaluated at each iteration.
+# mu = 5
+
+## Confidence level for the elimination test.
+# confidence = 0.95
+
+## If the target algorithm is deterministic, configurations will be
+## evaluated only once per instance.
+# deterministic = 0
+
+## Seed of the random number generator (by default, generate a random
+## seed).
+# seed = NA
+
+## Number of calls to targetRunner to execute in parallel. Values 0 or 1
+## mean no parallelization.
+# parallel = 0
+
+## Enable/disable load-balancing when executing experiments in parallel.
+## Load-balancing makes better use of computing resources, but increases
+## communication overhead. If this overhead is large, disabling
+## load-balancing may be faster.
+# loadBalancing = 1
+
+## Enable/disable MPI. Use Rmpi to execute targetRunner in parallel
+## (parameter parallel is the number of slaves).
+# mpi = 0
+
+## Specify how irace waits for jobs to finish when targetRunner submits
+## jobs to a batch cluster: sge, pbs, torque or slurm. targetRunner must
+## submit jobs to the cluster using, for example, qsub.
+# batchmode = 0
+
+## Enable/disable the soft restart strategy that avoids premature
+## convergence of the probabilistic model.
+# softRestart = 1
+
+## Soft restart threshold value for numerical parameters. If NA, NULL or
+## "", it is computed as 10^-digits.
+# softRestartThreshold = ""
+
+## Directory where testing instances are located, either absolute or
+## relative to current directory.
+# testInstancesDir = ""
+
+## File containing a list of test instances and optionally additional
+## parameters for them.
+# testInstancesFile = ""
+
+## Number of elite configurations returned by irace that will be tested if
+## test instances are provided.
+# testNbElites = 1
+
+## Enable/disable testing the elite configurations found at each
+## iteration.
+# testIterationElites = 0
+
+## Enable/disable elitist irace.
+# elitist = 1
+
+## Number of instances added to the execution list before previous
+## instances in elitist irace.
+# elitistNewInstances = 1
+
+## In elitist irace, maximum number per race of elimination tests that do
+## not eliminate a configuration. Use 0 for no limit.
+# elitistLimit = 2
+
+## User-defined R function that takes a configuration generated by irace
+## and repairs it.
+# repairConfiguration = ""
+
+## Enable the use of adaptive capping, a technique designed for minimizing
+## the computation time of configurations. This is only available when
+## elitist is active.
+# capping = 0
+
+## Measure used to obtain the execution bound from the performance of the
+## elite configurations: median, mean, worst, best.
+# cappingType = "median"
+
+## Method to calculate the mean performance of elite configurations:
+## candidate or instance.
+# boundType = "candidate"
+
+## Maximum execution bound for targetRunner. It must be specified when
+## capping is enabled.
+# boundMax = 0
+
+## Precision used for calculating the execution time. It must be specified
+## when capping is enabled.
+# boundDigits = 0
+
+## Penalization constant for timed out executions (executions that reach
+## boundMax execution time).
+# boundPar = 1
+
+## Replace the configuration cost of bounded executions with boundMax.
+# boundAsTimeout = 1
+
+## Percentage of the configuration budget used to perform a postselection
+## race of the best configurations of each iteration after the execution
+## of irace.
+# postselection = 0
+
+## Enable/disable AClib mode. This option enables compatibility with
+## GenericWrapper4AC as targetRunner script.
+# aclib = 0
+
+## END of scenario file
+############################################################################
+

eo/contrib/irace/expe/beta/irace_files_pA/fastga.param

@@ -0,0 +1,12 @@
+# name	switch	type	range
+# continuator	"--continuator="	c	(0)
+crossoverrate	"--crossover-rate="	r	(0,1)
+crossselector	"--cross-selector="	c	(0,1,2,3,4,5,6)
+# aftercrossselector	"--aftercross-selector="	c	(0)
+crossover	"--crossover="	c	(0,1,2,3,4,5,6,7,8,9)
+mutationrate	"--mutation-rate="	r	(0,1)
+mutselector	"--mut-selector="	c	(0,1,2,3,4,5,6)
+mutation	"--mutation="	c	(0,1,2,3,4,5,6,7,8,9,10)
+replacement "--replacement=" c (0,1,2,3,4,5,6,7,8,9,10)
+popsize         "--pop-size="           i	(1,50)
+offspringsize	"--offspring-size="	i	(1,50)

eo/contrib/irace/expe/beta/irace_files_pA/forbidden.txt

@@ -0,0 +1,13 @@
+## Template for specifying forbidden parameter configurations in irace.
+##
+## This filename must be specified via the --forbidden-file command-line option
+## (or forbiddenFile in scenario.txt).
+##
+## The format is one constraint per line. Each constraint is a logical
+## expression (in R syntax). If a parameter configuration
+## is generated that makes the logical expression evaluate to TRUE,
+## then the configuration is discarded.
+##
+## Examples of valid logical operators are: ==  !=  >=  <=  >  <  &  |  !  %in%
+(replacement %in% c(2,3,4,5,6,7,8,9,10)) & (offspringsize > popsize)
+(replacement %in% c(1)) & (offspringsize < popsize)

eo/contrib/irace/expe/beta/irace_files_pA/target-runner

@@ -0,0 +1,89 @@
+#!/bin/bash
+###############################################################################
+# This script is the command that is executed every run.
+# Check the examples in examples/
+#
+# This script is run in the execution directory (execDir, --exec-dir).
+#
+# PARAMETERS:
+# $1 is the candidate configuration number
+# $2 is the instance ID
+# $3 is the seed
+# $4 is the instance name
+# The rest ($* after `shift 4') are parameters to the run
+#
+# RETURN VALUE:
+# This script should print one numerical value: the cost that must be minimized.
+# Exit with 0 if no error, with 1 in case of error
+###############################################################################
+error() {
+    echo "`TZ=UTC date`: $0: error: $@"
+    exit 1
+}
+
+
+EXE="./fastga"
+LOG_DIR="irace_logs"
+
+#FIXED_PARAMS="--problem=0"
+#
+CONFIG_ID=$1
+INSTANCE_ID=$2 
+SEED=$3
+INSTANCE=$(echo $4 | sed 's/\//\n/g'|tail -n 1)
+CROSSOVER_RATE=$5
+CROSSOVER_SELECTOR=$6
+CROSSOVER=$7
+MUTATION_RATE=$8
+MUT_SELECTOR=$9
+MUTATION=${10}
+REPLACEMENT=${11}
+POPSIZE=${12}
+OFFSPRINGSIZE=${13}
+shift 13 || error "Not enough parameters"
+
+INSTANCE_PARAMS=$*
+buckets=0
+# STDOUT=${LOG_DIR}/c${CONFIG_ID}_i${INSTANCE_ID}_s${SEED}.stdout
+# STDERR=${LOG_DIR}/c${CONFIG_ID}_i${INSTANCE_ID}_s${SEED}.stderr
+STDOUT="/dev/null"
+STDERR="/dev/null"
+
+if [ ! -x "${EXE}" ]; then
+    error "${EXE}: not found or not executable (pwd: $(pwd))"
+fi
+
+# If the program just prints a number, we can use 'exec' to avoid
+# creating another process, but there can be no other commands after exec.
+#exec $EXE ${FIXED_PARAMS} -i $INSTANCE ${INSTANCE_PARAMS} 
+# exit 1
+# 
+# Otherwise, save the output to a file, and parse the result from it.
+# (If you wish to ignore segmentation faults you can use '{}' around
+# the command.)
+cmd="$EXE --problem=${INSTANCE} --instance=${INSTANCE} --seed=${SEED} ${CROSSOVER_RATE} ${CROSSOVER_SELECTOR} ${CROSSOVER} ${MUTATION_RATE} ${MUT_SELECTOR} ${MUTATION} ${REPLACEMENT} ${POPSIZE} ${OFFSPRINGSIZE} --max-evals=${buckets}"
+# NOTE: irace seems to capture both stderr and stdout, so you should not output to stderr
+echo ${cmd} > ${STDERR}
+$cmd 2> ${STDERR} | tee ${STDOUT}
+
+# The following code is useless if the binary only output a single number on stdout.
+
+# This may be used to introduce a delay if there are filesystem
+# issues.
+# SLEEPTIME=1
+# while [ ! -s "${STDOUT}" ]; do
+#     sleep $SLEEPTIME
+#     let "SLEEPTIME += 1"
+# done
+
+# This is an example of reading a number from the output.
+# It assumes that the objective value is the first number in
+# the first column of the last line of the output.
+# if [ -s "${STDOUT}" ]; then
+#     COST=$(tail -n 1 ${STDOUT} | grep -e '^[[:space:]]*[+-]\?[0-9]' | cut -f1)
+#     echo "$COST"
+#     rm -f "${STDOUT}" "${STDERR}"
+#     exit 0
+# else
+#     error "${STDOUT}: No such file or directory"
+# fi

eo/contrib/irace/expe/beta/irace_files_pF/default.instances

@@ -0,0 +1,48 @@
+## This is an example of specifying instances with a file.
+
+# Each line is an instance relative to trainInstancesDir
+# (see scenario.txt.tmpl) and an optional sequence of instance-specific
+# parameters that will be passed to target-runnerx when invoked on that
+# instance.
+
+0
+1
+2
+3
+4
+5
+6
+7
+8
+9
+10
+11
+12
+13
+14
+15
+16
+17
+18
+19
+20
+21
+22
+23
+24
+25
+26
+27
+28
+29
+30
+31
+32
+33
+34
+35
+36
+37
+38
+39
+40

eo/contrib/irace/expe/beta/irace_files_pF/example.scen

@@ -0,0 +1,227 @@
+###################################################### -*- mode: r -*- #####
+## Scenario setup for Iterated Race (irace).
+############################################################################
+
+## To use the default value of a parameter of iRace, simply do not set
+## the parameter (comment it out in this file, and do not give any
+## value on the command line).
+
+## File that contains the description of the parameters of the target
+## algorithm.
+parameterFile = "./fastga.param"
+
+## Directory where the programs will be run.
+execDir = "."
+
+## File to save tuning results as an R dataset, either absolute path or
+## relative to execDir.
+# logFile = "./irace.Rdata"
+
+## Previously saved log file to recover the execution of irace, either
+## absolute path or relative to the current directory.  If empty or NULL,
+## recovery is not performed.
+# recoveryFile = ""
+
+## Directory where training instances are located; either absolute path or
+## relative to current directory. If no trainInstancesFiles is provided,
+## all the files in trainInstancesDir will be listed as instances.
+trainInstancesDir = "."
+
+## File that contains a list of training instances and optionally
+## additional parameters for them. If trainInstancesDir is provided, irace
+## will search for the files in this folder.
+trainInstancesFile = "./default.instances"
+
+## File that contains a table of initial configurations. If empty or NULL,
+## all initial configurations are randomly generated.
+# configurationsFile = ""
+
+## File that contains a list of logical expressions that cannot be TRUE
+## for any evaluated configuration. If empty or NULL, do not use forbidden
+## expressions.
+forbiddenFile = "./forbidden.txt"
+
+## Script called for each configuration that executes the target algorithm
+## to be tuned. See templates.
+targetRunner = "./target-runner"
+
+## Number of times to retry a call to targetRunner if the call failed.
+# targetRunnerRetries = 0
+
+## Optional data passed to targetRunner. This is ignored by the default
+## targetRunner function, but it may be used by custom targetRunner
+## functions to pass persistent data around.
+# targetRunnerData = ""
+
+## Optional R function to provide custom parallelization of targetRunner.
+# targetRunnerParallel = ""
+
+## Optional script or R function that provides a numeric value for each
+## configuration. See templates/target-evaluator.tmpl
+# targetEvaluator = ""
+
+## Maximum number of runs (invocations of targetRunner) that will be
+## performed. It determines the maximum budget of experiments for the
+## tuning.
+maxExperiments = 0 #100000
+
+## Maximum total execution time in seconds for the executions of
+## targetRunner. targetRunner must return two values: cost and time.
+# maxTime = 60
+
+## Fraction (smaller than 1) of the budget used to estimate the mean
+## computation time of a configuration. Only used when maxTime > 0
+# budgetEstimation = 0.02
+
+## Maximum number of decimal places that are significant for numerical
+## (real) parameters.
+digits = 2
+
+## Debug level of the output of irace. Set this to 0 to silence all debug
+## messages. Higher values provide more verbose debug messages.
+# debugLevel = 0
+
+## Number of iterations.
+# nbIterations = 0
+
+## Number of runs of the target algorithm per iteration.
+# nbExperimentsPerIteration = 0
+
+## Randomly sample the training instances or use them in the order given.
+# sampleInstances = 1
+
+## Statistical test used for elimination. Default test is always F-test
+## unless capping is enabled, in which case the default test is t-test.
+## Valid values are: F-test (Friedman test), t-test (pairwise t-tests with
+## no correction), t-test-bonferroni (t-test with Bonferroni's correction
+## for multiple comparisons), t-test-holm (t-test with Holm's correction
+## for multiple comparisons).
+# testType = "F-test"
+
+## Number of instances evaluated before the first elimination test. It
+## must be a multiple of eachTest.
+# firstTest = 5
+
+## Number of instances evaluated between elimination tests.
+# eachTest = 1
+
+## Minimum number of configurations needed to continue the execution of
+## each race (iteration).
+# minNbSurvival = 0
+
+## Number of configurations to be sampled and evaluated at each iteration.
+# nbConfigurations = 0
+
+## Parameter used to define the number of configurations sampled and
+## evaluated at each iteration.
+# mu = 5
+
+## Confidence level for the elimination test.
+# confidence = 0.95
+
+## If the target algorithm is deterministic, configurations will be
+## evaluated only once per instance.
+# deterministic = 0
+
+## Seed of the random number generator (by default, generate a random
+## seed).
+# seed = NA
+
+## Number of calls to targetRunner to execute in parallel. Values 0 or 1
+## mean no parallelization.
+# parallel = 0
+
+## Enable/disable load-balancing when executing experiments in parallel.
+## Load-balancing makes better use of computing resources, but increases
+## communication overhead. If this overhead is large, disabling
+## load-balancing may be faster.
+# loadBalancing = 1
+
+## Enable/disable MPI. Use Rmpi to execute targetRunner in parallel
+## (parameter parallel is the number of slaves).
+# mpi = 0
+
+## Specify how irace waits for jobs to finish when targetRunner submits
+## jobs to a batch cluster: sge, pbs, torque or slurm. targetRunner must
+## submit jobs to the cluster using, for example, qsub.
+# batchmode = 0
+
+## Enable/disable the soft restart strategy that avoids premature
+## convergence of the probabilistic model.
+# softRestart = 1
+
+## Soft restart threshold value for numerical parameters. If NA, NULL or
+## "", it is computed as 10^-digits.
+# softRestartThreshold = ""
+
+## Directory where testing instances are located, either absolute or
+## relative to current directory.
+# testInstancesDir = ""
+
+## File containing a list of test instances and optionally additional
+## parameters for them.
+# testInstancesFile = ""
+
+## Number of elite configurations returned by irace that will be tested if
+## test instances are provided.
+# testNbElites = 1
+
+## Enable/disable testing the elite configurations found at each
+## iteration.
+# testIterationElites = 0
+
+## Enable/disable elitist irace.
+# elitist = 1
+
+## Number of instances added to the execution list before previous
+## instances in elitist irace.
+# elitistNewInstances = 1
+
+## In elitist irace, maximum number per race of elimination tests that do
+## not eliminate a configuration. Use 0 for no limit.
+# elitistLimit = 2
+
+## User-defined R function that takes a configuration generated by irace
+## and repairs it.
+# repairConfiguration = ""
+
+## Enable the use of adaptive capping, a technique designed for minimizing
+## the computation time of configurations. This is only available when
+## elitist is active.
+# capping = 0
+
+## Measure used to obtain the execution bound from the performance of the
+## elite configurations: median, mean, worst, best.
+# cappingType = "median"
+
+## Method to calculate the mean performance of elite configurations:
+## candidate or instance.
+# boundType = "candidate"
+
+## Maximum execution bound for targetRunner. It must be specified when
+## capping is enabled.
+# boundMax = 0
+
+## Precision used for calculating the execution time. It must be specified
+## when capping is enabled.
+# boundDigits = 0
+
+## Penalization constant for timed out executions (executions that reach
+## boundMax execution time).
+# boundPar = 1
+
+## Replace the configuration cost of bounded executions with boundMax.
+# boundAsTimeout = 1
+
+## Percentage of the configuration budget used to perform a postselection
+## race of the best configurations of each iteration after the execution
+## of irace.
+# postselection = 0
+
+## Enable/disable AClib mode. This option enables compatibility with
+## GenericWrapper4AC as targetRunner script.
+# aclib = 0
+
+## END of scenario file
+############################################################################
+

eo/contrib/irace/expe/beta/irace_files_pF/fastga.param

@@ -0,0 +1,12 @@
+# name	switch	type	range
+# continuator	"--continuator="	c	(0)
+crossoverrate	"--crossover-rate="	r	(0,1)
+crossselector	"--cross-selector="	c	(0,1,2,3,4,5,6)
+# aftercrossselector	"--aftercross-selector="	c	(0)
+crossover	"--crossover="	        c	(0,1,2,3,4,5,6,7,8,9)
+mutationrate	"--mutation-rate="	r	(0,1)
+mutselector	"--mut-selector="       c	(0,1,2,3,4,5,6)
+mutation	"--mutation="	        c	(0,1,2,3,4,5,6,7,8,9,10)
+replacement     "--replacement="        c       (0,1,2,3,4,5,6,7,8,9,10)
+popsize         "--pop-size="           i	(1,50)
+offspringsize	"--offspring-size="	i	(1,50)

eo/contrib/irace/expe/beta/irace_files_pF/forbidden.txt

@@ -0,0 +1,15 @@
+## Template for specifying forbidden parameter configurations in irace.
+##
+## This filename must be specified via the --forbidden-file command-line option
+## (or forbiddenFile in scenario.txt).
+##
+## The format is one constraint per line. Each constraint is a logical
+## expression (in R syntax). If a parameter configuration
+## is generated that makes the logical expression evaluate to TRUE,
+## then the configuration is discarded.
+##
+## Examples of valid logical operators are: ==  !=  >=  <=  >  <  &  |  !  %in%
+(replacement %in% c(2,3,4,5,6,7,8,9,10)) & (offspringsize > popsize)
+(replacement %in% c(1)) & (offspringsize < popsize)
+#(as.numeric(replacement) == 2) & (offspringsize > popsize)
+#(as.numeric(replacement) == 3) & (offspringsize > popsize)

eo/contrib/irace/expe/beta/irace_files_pF/target-runner

@@ -0,0 +1,96 @@
+#!/bin/bash
+###############################################################################
+# This script is the command that is executed every run.
+# Check the examples in examples/
+#
+# This script is run in the execution directory (execDir, --exec-dir).
+#
+# PARAMETERS:
+# $1 is the candidate configuration number
+# $2 is the instance ID
+# $3 is the seed
+# $4 is the instance name
+# The rest ($* after `shift 4') are parameters to the run
+#
+# RETURN VALUE:
+# This script should print one numerical value: the cost that must be minimized.
+# Exit with 0 if no error, with 1 in case of error
+###############################################################################
+error() {
+    echo "`TZ=UTC date`: $0: error: $@"
+    exit 1
+}
+
+
+EXE="./fastga"
+LOG_DIR="irace_logs"
+
+FIXED_PARAMS="--problem=0"
+#MAX_EVALS=2
+#
+CONFIG_ID=$1
+INSTANCE_ID=$2 
+SEED=$3
+INSTANCE=$(echo $4 | sed 's/\//\n/g'|tail -n 1)
+CROSSOVER_RATE=$5
+CROSSOVER_SELECTOR=$6
+CROSSOVER=$7
+MUTATION_RATE=$8
+MUT_SELECTOR=$9
+MUTATION=${10}
+REPLACEMENT=${11}
+POPSIZE=${12}
+OFFSPRINGSIZE=${13}
+shift 13 || error "Not enough parameters"
+
+INSTANCE_PARAMS=$*
+
+buckets=0
+#dim=(20 20 16 48 25 32 128 128 128 50 100 150 128 192 192 192 256 75 150)
+#size= $( echo $(echo $13 | cut -d'=' -f2))
+#pb=$(echo $(echo $13 | cut -d'=' -f2))
+#maxevals=$( echo ${dim[$pb]})
+# STDOUT=${LOG_DIR}/c${CONFIG_ID}_i${INSTANCE_ID}_s${SEED}.stdout
+# STDERR=${LOG_DIR}/c${CONFIG_ID}_i${INSTANCE_ID}_s${SEED}.stderr
+STDOUT="/dev/null"
+STDERR="/dev/null"
+
+if [ ! -x "${EXE}" ]; then
+    error "${EXE}: not found or not executable (pwd: $(pwd))"
+fi
+
+# If the program just prints a number, we can use 'exec' to avoid
+# creating another process, but there can be no other commands after exec.
+#exec $EXE ${FIXED_PARAMS} -i $INSTANCE ${INSTANCE_PARAMS} 
+# exit 1
+# 
+# Otherwise, save the output to a file, and parse the result from it.
+# (If you wish to ignore segmentation faults you can use '{}' around
+# the command.)
+
+cmd="$EXE ${FIXED_PARAMS} --instance=${INSTANCE} --seed=${SEED} ${CROSSOVER_RATE} ${CROSSOVER_SELECTOR} ${CROSSOVER} ${MUTATION_RATE} ${MUT_SELECTOR} ${MUTATION} ${REPLACEMENT} ${POPSIZE} ${OFFSPRINGSIZE} --max-evals=${buckets}"
+# NOTE: irace seems to capture both stderr and stdout, so you should not output to stderr
+echo ${cmd} > ${STDERR}
+$cmd 2> ${STDERR} | tee ${STDOUT}
+
+# The following code is useless if the binary only output a single number on stdout.
+
+# This may be used to introduce a delay if there are filesystem
+# issues.
+# SLEEPTIME=1
+# while [ ! -s "${STDOUT}" ]; do
+#     sleep $SLEEPTIME
+#     let "SLEEPTIME += 1"
+# done
+
+# This is an example of reading a number from the output.
+# It assumes that the objective value is the first number in
+# the first column of the last line of the output.
+# if [ -s "${STDOUT}" ]; then
+#     COST=$(tail -n 1 ${STDOUT} | grep -e '^[[:space:]]*[+-]\?[0-9]' | cut -f1)
+#     echo "$COST"
+#     rm -f "${STDOUT}" "${STDERR}"
+#     exit 0
+# else
+#     error "${STDOUT}: No such file or directory"
+# fi

eo/contrib/irace/expe/beta/irace_files_pO/default.instances

@@ -0,0 +1,48 @@
+## This is an example of specifying instances with a file.
+
+# Each line is an instance relative to trainInstancesDir
+# (see scenario.txt.tmpl) and an optional sequence of instance-specific
+# parameters that will be passed to target-runnerx when invoked on that
+# instance.
+
+0
+1
+2
+3
+4
+5
+6
+7
+8
+9
+10
+11
+12
+13
+14
+15
+16
+17
+18
+19
+20
+21
+22
+23
+24
+25
+26
+27
+28
+29
+30
+31
+32
+33
+34
+35
+36
+37
+38
+39
+40

eo/contrib/irace/expe/beta/irace_files_pO/example.scen

@@ -0,0 +1,228 @@
+###################################################### -*- mode: r -*- #####
+## Scenario setup for Iterated Race (irace).
+############################################################################
+
+## To use the default value of a parameter of iRace, simply do not set
+## the parameter (comment it out in this file, and do not give any
+## value on the command line).
+
+## File that contains the description of the parameters of the target
+## algorithm.
+parameterFile = "./fastga.param"
+
+## Directory where the programs will be run.
+execDir = "."
+
+## File to save tuning results as an R dataset, either absolute path or
+## relative to execDir.
+# logFile = "./irace.Rdata"
+
+## Previously saved log file to recover the execution of irace, either
+## absolute path or relative to the current directory.  If empty or NULL,
+## recovery is not performed.
+# recoveryFile = ""
+
+## Directory where training instances are located; either absolute path or
+## relative to current directory. If no trainInstancesFiles is provided,
+## all the files in trainInstancesDir will be listed as instances.
+trainInstancesDir = "."
+
+## File that contains a list of training instances and optionally
+## additional parameters for them. If trainInstancesDir is provided, irace
+## will search for the files in this folder.
+trainInstancesFile = "./default.instances"
+
+## File that contains a table of initial configurations. If empty or NULL,
+## all initial configurations are randomly generated.
+# configurationsFile = ""
+
+## File that contains a list of logical expressions that cannot be TRUE
+## for any evaluated configuration. If empty or NULL, do not use forbidden
+## expressions.
+# forbiddenFile = ""
+
+## Script called for each configuration that executes the target algorithm
+## to be tuned. See templates.
+targetRunner = "./target-runner"
+
+## Number of times to retry a call to targetRunner if the call failed.
+# targetRunnerRetries = 0
+
+## Optional data passed to targetRunner. This is ignored by the default
+## targetRunner function, but it may be used by custom targetRunner
+## functions to pass persistent data around.
+# targetRunnerData = ""
+
+## Optional R function to provide custom parallelization of targetRunner.
+# targetRunnerParallel = ""
+
+## Optional script or R function that provides a numeric value for each
+## configuration. See templates/target-evaluator.tmpl
+# targetEvaluator = ""
+
+## Maximum number of runs (invocations of targetRunner) that will be
+## performed. It determines the maximum budget of experiments for the
+## tuning.
+maxExperiments = 0 #100000
+
+
+## Maximum total execution time in seconds for the executions of
+## targetRunner. targetRunner must return two values: cost and time.
+# maxTime = 60
+
+## Fraction (smaller than 1) of the budget used to estimate the mean
+## computation time of a configuration. Only used when maxTime > 0
+# budgetEstimation = 0.02
+
+## Maximum number of decimal places that are significant for numerical
+## (real) parameters.
+digits = 2
+
+## Debug level of the output of irace. Set this to 0 to silence all debug
+## messages. Higher values provide more verbose debug messages.
+# debugLevel = 0
+
+## Number of iterations.
+# nbIterations = 0
+
+## Number of runs of the target algorithm per iteration.
+# nbExperimentsPerIteration = 0
+
+## Randomly sample the training instances or use them in the order given.
+# sampleInstances = 1
+
+## Statistical test used for elimination. Default test is always F-test
+## unless capping is enabled, in which case the default test is t-test.
+## Valid values are: F-test (Friedman test), t-test (pairwise t-tests with
+## no correction), t-test-bonferroni (t-test with Bonferroni's correction
+## for multiple comparisons), t-test-holm (t-test with Holm's correction
+## for multiple comparisons).
+# testType = "F-test"
+
+## Number of instances evaluated before the first elimination test. It
+## must be a multiple of eachTest.
+# firstTest = 5
+
+## Number of instances evaluated between elimination tests.
+# eachTest = 1
+
+## Minimum number of configurations needed to continue the execution of
+## each race (iteration).
+# minNbSurvival = 0
+
+## Number of configurations to be sampled and evaluated at each iteration.
+# nbConfigurations = 0
+
+## Parameter used to define the number of configurations sampled and
+## evaluated at each iteration.
+# mu = 5
+
+## Confidence level for the elimination test.
+# confidence = 0.95
+
+## If the target algorithm is deterministic, configurations will be
+## evaluated only once per instance.
+# deterministic = 0
+
+## Seed of the random number generator (by default, generate a random
+## seed).
+# seed = NA
+
+## Number of calls to targetRunner to execute in parallel. Values 0 or 1
+## mean no parallelization.
+# parallel = 0
+
+## Enable/disable load-balancing when executing experiments in parallel.
+## Load-balancing makes better use of computing resources, but increases
+## communication overhead. If this overhead is large, disabling
+## load-balancing may be faster.
+# loadBalancing = 1
+
+## Enable/disable MPI. Use Rmpi to execute targetRunner in parallel
+## (parameter parallel is the number of slaves).
+# mpi = 0
+
+## Specify how irace waits for jobs to finish when targetRunner submits
+## jobs to a batch cluster: sge, pbs, torque or slurm. targetRunner must
+## submit jobs to the cluster using, for example, qsub.
+# batchmode = 0
+
+## Enable/disable the soft restart strategy that avoids premature
+## convergence of the probabilistic model.
+# softRestart = 1
+
+## Soft restart threshold value for numerical parameters. If NA, NULL or
+## "", it is computed as 10^-digits.
+# softRestartThreshold = ""
+
+## Directory where testing instances are located, either absolute or
+## relative to current directory.
+# testInstancesDir = ""
+
+## File containing a list of test instances and optionally additional
+## parameters for them.
+# testInstancesFile = ""
+
+## Number of elite configurations returned by irace that will be tested if
+## test instances are provided.
+# testNbElites = 1
+
+## Enable/disable testing the elite configurations found at each
+## iteration.
+# testIterationElites = 0
+
+## Enable/disable elitist irace.
+# elitist = 1
+
+## Number of instances added to the execution list before previous
+## instances in elitist irace.
+# elitistNewInstances = 1
+
+## In elitist irace, maximum number per race of elimination tests that do
+## not eliminate a configuration. Use 0 for no limit.
+# elitistLimit = 2
+
+## User-defined R function that takes a configuration generated by irace
+## and repairs it.
+# repairConfiguration = ""
+
+## Enable the use of adaptive capping, a technique designed for minimizing
+## the computation time of configurations. This is only available when
+## elitist is active.
+# capping = 0
+
+## Measure used to obtain the execution bound from the performance of the
+## elite configurations: median, mean, worst, best.
+# cappingType = "median"
+
+## Method to calculate the mean performance of elite configurations:
+## candidate or instance.
+# boundType = "candidate"
+
+## Maximum execution bound for targetRunner. It must be specified when
+## capping is enabled.
+# boundMax = 0
+
+## Precision used for calculating the execution time. It must be specified
+## when capping is enabled.
+# boundDigits = 0
+
+## Penalization constant for timed out executions (executions that reach
+## boundMax execution time).
+# boundPar = 1
+
+## Replace the configuration cost of bounded executions with boundMax.
+# boundAsTimeout = 1
+
+## Percentage of the configuration budget used to perform a postselection
+## race of the best configurations of each iteration after the execution
+## of irace.
+# postselection = 0
+
+## Enable/disable AClib mode. This option enables compatibility with
+## GenericWrapper4AC as targetRunner script.
+# aclib = 0
+
+## END of scenario file
+############################################################################
+

eo/contrib/irace/expe/beta/irace_files_pO/fastga.param

@@ -0,0 +1,10 @@
+# name	switch	type	range
+# continuator	"--continuator="	c	(0)
+crossoverrate	"--crossover-rate="	r	(0,1)
+crossselector	"--cross-selector="	c	(0,1,2,3,4,5,6)
+# aftercrossselector	"--aftercross-selector="	c	(0)
+crossover	"--crossover="	        c	(0,1,2,3,4,5,6,7,8,9)
+mutationrate	"--mutation-rate="	r	(0,1)
+mutselector	"--mut-selector="	c	(0,1,2,3,4,5,6)
+mutation	"--mutation="	        c	(0,1,2,3,4,5,6,7,8,9,10)
+replacement     "--replacement="        c	(0,1,2,3,4,5,6,7,8,9,10)

eo/contrib/irace/expe/beta/irace_files_pO/target-runner

@@ -0,0 +1,88 @@
+#!/bin/bash
+###############################################################################
+# This script is the command that is executed every run.
+# Check the examples in examples/
+#
+# This script is run in the execution directory (execDir, --exec-dir).
+#
+# PARAMETERS:
+# $1 is the candidate configuration number
+# $2 is the instance ID
+# $3 is the seed
+# $4 is the instance name
+# The rest ($* after `shift 4') are parameters to the run
+#
+# RETURN VALUE:
+# This script should print one numerical value: the cost that must be minimized.
+# Exit with 0 if no error, with 1 in case of error
+###############################################################################
+error() {
+    echo "`TZ=UTC date`: $0: error: $@"
+    exit 1
+}
+
+
+EXE="./fastga"
+LOG_DIR="irace_logs"
+
+FIXED_PARAMS="--problem=0"
+MAX_EVALS=100
+#
+CONFIG_ID=$1
+INSTANCE_ID=$2 
+SEED=$3
+INSTANCE=$(echo $4 | sed 's/\//\n/g'|tail -n 1)
+CROSSOVER_RATE=$5
+CROSSOVER_SELECTOR=$6
+CROSSOVER=$7
+MUTATION_RATE=$8
+MUT_SELECTOR=$9
+MUTATION=${10}
+REPLACEMENT=${11}
+shift 11 || error "Not enough parameters"
+
+INSTANCE_PARAMS=$*
+
+# STDOUT=${LOG_DIR}/c${CONFIG_ID}_i${INSTANCE_ID}_s${SEED}.stdout
+# STDERR=${LOG_DIR}/c${CONFIG_ID}_i${INSTANCE_ID}_s${SEED}.stderr
+STDOUT="/dev/null"
+STDERR="/dev/null"
+
+if [ ! -x "${EXE}" ]; then
+    error "${EXE}: not found or not executable (pwd: $(pwd))"
+fi
+
+# If the program just prints a number, we can use 'exec' to avoid
+# creating another process, but there can be no other commands after exec.
+#exec $EXE ${FIXED_PARAMS} -i $INSTANCE ${INSTANCE_PARAMS} 
+# exit 1
+# 
+# Otherwise, save the output to a file, and parse the result from it.
+# (If you wish to ignore segmentation faults you can use '{}' around
+# the command.)
+cmd="$EXE ${FIXED_PARAMS} --instance=${INSTANCE} --seed=${SEED} ${CROSSOVER_RATE} ${CROSSOVER_SELECTOR} ${CROSSOVER} ${MUTATION_RATE} ${MUT_SELECTOR} ${MUTATION} ${REPLACEMENT}"
+# NOTE: irace seems to capture both stderr and stdout, so you should not output to stderr
+echo ${cmd} > ${STDERR}
+$cmd 2> ${STDERR} | tee ${STDOUT}
+
+# The following code is useless if the binary only output a single number on stdout.
+
+# This may be used to introduce a delay if there are filesystem
+# issues.
+# SLEEPTIME=1
+# while [ ! -s "${STDOUT}" ]; do
+#     sleep $SLEEPTIME
+#     let "SLEEPTIME += 1"
+# done
+
+# This is an example of reading a number from the output.
+# It assumes that the objective value is the first number in
+# the first column of the last line of the output.
+# if [ -s "${STDOUT}" ]; then
+#     COST=$(tail -n 1 ${STDOUT} | grep -e '^[[:space:]]*[+-]\?[0-9]' | cut -f1)
+#     echo "$COST"
+#     rm -f "${STDOUT}" "${STDERR}"
+#     exit 0
+# else
+#     error "${STDOUT}: No such file or directory"
+# fi

eo/contrib/irace/expe/beta/mwtestU.py

@@ -0,0 +1,140 @@
+#!/usr/bin/env python3
+import sys
+import os
+import numpy as np
+import matplotlib.pyplot as plt
+from scipy.stats import mannwhitneyu
+
+##cmd eg : 
+# python3 hist_by_2_4_5.py ./fastga_results_all/ ./hist_and_csv/ 100000 1000
+
+#get the Mann Whitney test U results between the plan F and plan R
+#  (change ligne 23 and 44 for other plan, and the maxExp, maxEv for other budget)
+
+path=sys.argv[1] 
+figpath=sys.argv[2] #directory to store the data
+maxExp=sys.argv[3]
+maxEv=sys.argv[4]
+
+hist_pb=[[] for i in range(19)]
+name=[]
+randind=-1
+for fastga in os.listdir(path): #ddir : directory of fastga_plan
+    if(fastga in {"fastga_results_planF"}):
+        for plan in os.listdir(os.path.join(path,fastga)):
+            print("maxExp="+str(maxExp)+"_maxEv="+str(maxEv)+"_" in plan,plan,"maxExp="+str(maxExp)+"_maxEv="+str(maxEv))
+            #print("maxExp="+str(maxExp)+"_maxEv="+str(maxEv) in plan,plan,"maxExp="+str(maxExp)+"_maxEv="+str(maxEv))
+            if("maxExp="+str(maxExp)+"_maxEv="+str(maxEv)+"_" in plan):
+                name.append("_".join(plan.split("_")[:3]))
+                for fastgadir in os.listdir(os.path.join(path,fastga,plan,"raw","data")): #fastgadir : directory of 50 runs of a configuration
+                    pb=int(fastgadir.split("_")[0].split("=")[1])
+                    average_pb=[]
+                    for fname in os.listdir(os.path.join(path,fastga,plan,"raw","data",fastgadir)):
+                        with open(os.path.join(path,fastga,plan,"raw","data",fastgadir,fname)) as fd:
+                            auc = float(fd.readlines()[0]) 
+                        average_pb.append(auc)
+                    if(hist_pb[pb]==[]): #first algo
+                        hist_pb[pb].append(average_pb)
+                    elif(len(hist_pb[pb])!=len(name)):
+                        hist_pb[pb].append(average_pb)
+                    else:
+                        hist_pb[pb][len(name)-1]+=average_pb #another algo for the same plan
+
+
+    if("random" in fastga):
+        for randir in os.listdir(os.path.join(path,fastga)):
+            #eg path: maxEv=100_nbAlgo=15_2021-08-20T1511+0200_results_randoms
+            if(("maxEv="+str(maxEv)+"_") in randir):
+                print("maxEv="+str(maxEv) in randir,randir)
+                name.append(randir.split("_")[0]+"_random")
+                randind=len(name)-1
+                print(randind,name)
+                for ddir in os.listdir(os.path.join(path,fastga,randir)): #ddir : directory of one run_elites_all or more
+                    if("crossover" in ddir):
+                        for fastgadir in os.listdir(os.path.join(path,fastga,randir,ddir,"data")): #fastgadir : directory of 50 runs of a configuration
+                            average_pb=[]
+                            pb=int(fastgadir.split("_")[0].split("=")[1])
+                            for fname in os.listdir(os.path.join(path,fastga,randir,ddir,"data",fastgadir)):
+                                with open(os.path.join(path,fastga,randir,ddir,"data",fastgadir,fname)) as fd:
+                                    auc = float(fd.readlines()[0]) 
+                                average_pb.append(auc)
+                            #print(len(hist_pb[pb]),len(name), pb)
+                            if(hist_pb[pb]==[]): #first algo
+                                #print("entrer random vide")
+                                hist_pb[pb].append(average_pb)
+                            elif(len(hist_pb[pb])!=len(name)):
+                                #print("entrer random !=")
+                                hist_pb[pb].append(average_pb)
+                            else:
+                                hist_pb[pb][len(name)-1]+=average_pb #another algo for the same plan
+
+
+figdir=os.path.join(figpath,"mwtestU_FR")
+try:
+    os.makedirs(figdir)
+except FileExistsError:
+    pass
+#colors=['yellow', 'green',"blue","pink","purple","orange","magenta","gray","darkred","cyan","brown","olivedrab","thistle","stateblue"]
+print(name)
+
+filename="mwtestU_maxExp={}_maxEv={}_FR.csv".format(maxExp,maxEv)
+with open(os.path.join(figdir,filename),'w+') as csvfile:
+    csvfile.write(" ,"+",".join(map(str,range(0,19)))+"\n")
+meanvalue=[]
+pvalue=[]
+meanR=[]
+meanF=[]
+mdianR=[]
+mdianF=[]
+mdianvalue=[]
+iqrR=[]
+iqrF=[]
+stdR=[]
+stdF=[]
+iqrvalue=[]
+pstd=[]
+
+for pb in range(19):
+    #hR,lR,_=plt.hist(hist_pb[pb][randind],bins=10,range=(-1,0),align="mid",label=name) #no label color=colors[:len(name)]
+    #hF,lF,_=plt.hist(hist_pb[pb][np.abs(1-randind)],bins=10,range=(-1,0),align="mid",label=name) #no label color=colors[:len(name)]
+    _,pv=mannwhitneyu(hist_pb[pb][np.abs(1-randind)],hist_pb[pb][randind])
+    print(_,pv)
+    #meanvalue.append(np.mean(np.array(hF)*np.array(lF[:len(lF)-1]))-np.mean(np.array(hR)*np.array(lR[:len(lR)-1])))
+    pstd.append(np.std(hist_pb[pb][np.abs(1-randind)])-np.std(hist_pb[pb][randind]))
+    stdF.append(np.std(hist_pb[pb][np.abs(1-randind)]))
+    stdR.append(np.std(hist_pb[pb][randind]))
+    meanF.append(np.mean(hist_pb[pb][np.abs(1-randind)]))
+    meanR.append(np.mean(hist_pb[pb][randind]))
+    mdianF.append(np.median(hist_pb[pb][np.abs(1-randind)]))
+    mdianR.append(np.median(hist_pb[pb][randind]))
+    mdianvalue.append(np.median(hist_pb[pb][np.abs(1-randind)])-np.median(hist_pb[pb][randind]))
+    meanvalue.append(np.mean(hist_pb[pb][np.abs(1-randind)])-np.mean(hist_pb[pb][randind]))
+    pvalue.append(pv)
+    Q1 = np.percentile(hist_pb[pb][np.abs(1-randind)], 25, interpolation = 'midpoint')
+    # Third quartile (Q3)
+    Q3 = np.percentile(hist_pb[pb][np.abs(1-randind)], 75, interpolation = 'midpoint')
+    # Interquaritle range (IQR)
+    iqrF.append( Q3 - Q1)
+    Q1 = np.percentile(hist_pb[pb][randind], 25, interpolation = 'midpoint')
+    # Third quartile (Q3)
+    Q3 = np.percentile(hist_pb[pb][randind], 75, interpolation = 'midpoint')
+    # Interquaritle range (IQR)
+    iqrR.append( Q3 - Q1)
+    print(_,pv)
+iqrvalue=np.array(iqrF)-np.array(iqrR)
+with open(os.path.join(figdir,filename),'a') as csvfile:
+    csvfile.write("mF-mR,"+",".join(map(str,meanvalue))+"\n")
+    csvfile.write("p_value,"+",".join(map(str,pvalue))+"\n")
+    csvfile.write("mF,"+",".join(map(str,meanF))+"\n")
+    csvfile.write("mR,"+",".join(map(str,meanR))+"\n")
+    csvfile.write("medianF-medianR,"+",".join(map(str,mdianvalue))+"\n")
+    csvfile.write("medianF,"+",".join(map(str,mdianF))+"\n")
+    csvfile.write("medianR,"+",".join(map(str,mdianR))+"\n")
+    csvfile.write("stdF-stdR,"+",".join(map(str,mdianvalue))+"\n")
+    csvfile.write("stdF,"+",".join(map(str,stdF))+"\n")
+    csvfile.write("stdR,"+",".join(map(str,stdR))+"\n")
+    csvfile.write("iqrF,"+",".join(map(str,iqrF))+"\n")
+    csvfile.write("iqrR,"+",".join(map(str,iqrR))+"\n")
+    csvfile.write("iqrF-iqrR,"+",".join(map(str,iqrvalue))+"\n")
+
+    

eo/contrib/irace/expe/beta/parseA_irace_bests.py

@@ -0,0 +1,31 @@
+#!/usr/bin/env python3
+#parse data1
+import os
+import re
+import sys
+
+print("ecdf,id,crossover-rate,cross-selector,crossover,mutation-rate,mut-selector,mutation,replacement,pop-size,offspring-size")
+
+
+#give the path of one experiment
+argv=sys.argv[1]
+for datadir in os.listdir(argv):
+    #if(os.path.isdir(os.path.join(argv,datadir))): check if argv/datadir is a directory
+    if(datadir.find("results_irace")>=0): #check if the directory is one JOB
+        with open(os.path.join("./",argv,datadir,"irace.log")) as fd:
+            data = fd.readlines()
+
+                    # Find the last best configuration
+            bests = [line.strip() for line in data if "Best-so-far" in line]
+                    #print(datadir,bests)
+            best = bests[-1].split()
+            best_id, best_perf = best[2], best[5]
+                    # print(best_id,best_perf)
+
+                    # Filter the config detail
+            configs = [line.strip() for line in data if "--crossover-rate=" in line and best_id in line]
+                    # print(configs)
+                    # Format as CSV
+            algo = re.sub("\-\-\S*=", ",", configs[0])
+            csv_line = best_perf + "," + algo
+            print(csv_line.replace(" ",""))

eo/contrib/irace/expe/beta/parseF_irace_bests.py

@@ -0,0 +1,35 @@
+#!/usr/bin/env python3
+#parse data1
+import os
+import re
+import sys
+#print("pb,ecdf,id,crossover-rate,cross-selector,crossover,mutation-rate,mut-selector,mutation,replacement") #plan1
+print("pb,ecdf,id,crossover-rate,cross-selector,crossover,mutation-rate,mut-selector,mutation,replacement,pop-size,offspring-size")
+
+
+#give the path of one experiment 
+argv=sys.argv[1]
+for datadir in os.listdir(argv):
+    #if(os.path.isdir(os.path.join(argv,datadir))): check if argv/datadir is a directory
+    if(datadir.find("results_irace")>=0): #check if the directory is one JOB
+        for pb_dir in os.listdir(os.path.join(argv,datadir)):
+            if "results_problem" in pb_dir:
+                pb_id=pb_dir.replace("results_problem_","")
+                with open(os.path.join("./",argv,datadir,pb_dir,"irace.log")) as fd:
+                    data = fd.readlines()
+
+                    # Find the last best configuration
+                    bests = [line.strip() for line in data if "Best-so-far" in line]
+                    #print(datadir,bests)
+                    best = bests[-1].split()
+                    best_id, best_perf = best[2], best[5]
+                    # print(best_id,best_perf)
+
+                    # Filter the config detail
+                    configs = [line.strip() for line in data if "--crossover-rate=" in line and best_id in line]
+                    # print(configs)
+
+                    # Format as CSV
+                    algo = re.sub("\-\-\S*=", ",", configs[0])
+                    csv_line = pb_id + "," + best_perf + "," + algo
+                    print(csv_line.replace(" ",""))

eo/contrib/irace/expe/beta/parseO_irace_bests.py

@@ -0,0 +1,35 @@
+#!/usr/bin/env python3
+#parse data1
+import os
+import re
+import sys
+#print("pb,ecdf,id,crossover-rate,cross-selector,crossover,mutation-rate,mut-selector,mutation,replacement") #plan1
+print("pb,ecdf,id,crossover-rate,cross-selector,crossover,mutation-rate,mut-selector,mutation,replacement")
+
+
+#give the path of one experiment 
+argv=sys.argv[1]
+for datadir in os.listdir(argv):
+    #if(os.path.isdir(os.path.join(argv,datadir))): check if argv/datadir is a directory
+    if(datadir.find("results_irace")>=0): #check if the directory is one JOB
+        for pb_dir in os.listdir(os.path.join(argv,datadir)):
+            if "results_problem" in pb_dir:
+                pb_id=pb_dir.replace("results_problem_","")
+                with open(os.path.join("./",argv,datadir,pb_dir,"irace.log")) as fd:
+                    data = fd.readlines()
+
+                    # Find the last best configuration
+                    bests = [line.strip() for line in data if "Best-so-far" in line]
+                    #print(datadir,bests)
+                    best = bests[-1].split()
+                    best_id, best_perf = best[2], best[5]
+                    # print(best_id,best_perf)
+
+                    # Filter the config detail
+                    configs = [line.strip() for line in data if "--crossover-rate=" in line and best_id in line]
+                    # print(configs)
+
+                    # Format as CSV
+                    algo = re.sub("\-\-\S*=", ",", configs[0])
+                    csv_line = pb_id + "," + best_perf + "," + algo
+                    print(csv_line.replace(" ",""))

eo/contrib/irace/expe/beta/parse_auc_average.py

@@ -0,0 +1,34 @@
+#!/usr/bin/env python3
+import sys
+import os
+import numpy as np
+import matplotlib.pyplot as plt
+
+#get the auc average values of one experiment
+figdir=sys.argv[1] # directory of a result of one experiment
+#eg : ./fastga_results_all/fastga_results_planO/planO_maxExp\=100000_maxEv\=5n_2021-08-13T19\:04+02\:00_results_elites_all/raw
+
+if("fastga_results_plan" in figdir):
+    print("FID,",",".join(map(str,range(1,16))))
+    aucs=[[] for i in range(19)]
+    for fastgadir in os.listdir(os.path.join(figdir,"raw/data")): #fastgadir : directory of 50 runs of an elite configuration
+        #cum=np.cumsum([0.1]*10)
+        average=[]
+        for fname in os.listdir(os.path.join(figdir,"raw/data",fastgadir)):
+            with open(os.path.join(figdir,"raw/data",fastgadir,fname)) as fd:
+                auc = float(fd.readlines()[0]) * -1
+            average.append(auc)
+        aucs[int(fastgadir.split("_")[0].split("=")[1])].append(average)
+    #print(np.shape(aucs))
+
+
+
+    for i in range(19):
+        print(str(i)+",",",".join(map(str,np.mean(aucs[i],1))))
+
+        
+        
+        
+
+
+

eo/contrib/irace/expe/beta/planA/r_iA.sh

@@ -0,0 +1,34 @@
+#!/bin/bash
+#run once each problem
+
+echo "-------------------------Start the JOB : $(date --iso-8601=seconds)"
+. /etc/profile.d/modules.sh
+export MODULEPATH=${MODULEPATH}${MODULEPATH:+:}/opt/dev/Modules/Anaconda:/opt/dev/Modules/Compilers:/opt/dev/Modules/Frameworks:/opt/dev/Modules/Libraries:/opt/dev/Modules/Tools:/opt/dev/Modules/IDEs:/opt/dev/Modules/MPI
+module load LLVM/clang-llvm-10.0
+module load R
+
+dir=$1
+run=$2
+budget_irace=$3
+buckets=$4
+myhome=$5
+cp -r ${myhome}/R .
+cp -r ${myhome}/irace_files_pA .
+#cp -r /scratchbeta/zhenga/irace_files .
+#chmod u+x ./fastga
+outdir="${run}_$(date --iso-8601=seconds)_results_irace"
+rundir=${dir}/${outdir}
+mkdir -p ${rundir}
+# Fore some reason, irace absolutely need those files...
+cp ${myhome}/code/paradiseo/eo/contrib/irace/release/fastga  ${rundir}
+cat ./irace_files_pA/example.scen | sed "s%\".%\"${rundir}%g" | sed "s/maxExperiments = 0/maxExperiments=${budget_irace}/" > ${rundir}/example.scen
+cp ./irace_files_pA/default.instances ${rundir}
+cp ./irace_files_pA/fastga.param ${rundir}
+cp ./irace_files_pA/forbidden.txt ${rundir}
+cat ./irace_files_pA/target-runner | sed "s/buckets=0/buckets=${buckets}/" > ${rundir}/target-runner
+chmod u+x ${rundir}/target-runner
+
+echo "---start $(date)"
+time -p ./R/x86_64-pc-linux-gnu-library/3.6/irace/bin/irace --scenario ${rundir}/example.scen  > ${rundir}/irace.log 
+echo "---end $(date)"
+echo "End the JOB : $(date --iso-8601=seconds)------------------------------"

eo/contrib/irace/expe/beta/planA/riaA.sh

@@ -0,0 +1,25 @@
+#!/bin/bashi
+myhome=$1
+scratchpath=$2
+mexp=$3
+mevals=$4
+date -Iseconds
+echo "STARTS"
+dir=${scratchpath}/dataFAR/dataA
+#dir=${HOME}/plan4/${name}
+#cat ${HOME}/irace_files_pA/example.scen |sed "s/maxExperiments = 0/maxExperiments = ${mexp}/" > ${HOME}/irace_files_pA/example.scen
+
+mkdir -p ${dir}
+outdir="${dir}/dataA_maxExp=${mexp}_maxEv=${mevals}_$(date --iso-8601=seconds)"
+mkdir -p ${outdir}
+for r in $(seq 2); do
+    echo "Run $r/15";
+    cmd="qsub -N iraceA_maxEv_${r} -q beta -l select=1:ncpus=1 -l walltime=00:25:00 -- ${scratchpath}/planA/r_iA.sh ${outdir} ${r} ${mexp} ${mevals} ${myhome}"
+    #cmd="bash ./r_iA_buckets.sh ${outdir} ${r} ${mexp} ${mevals}"
+    echo $cmd
+    time -p $cmd 
+done
+echo "DONE"
+#cat ${HOME}/irace_files_pA/example.scen |sed "s/maxExperiments = ${mexp}/maxExperiments = 0/" > ${HOME}/irace_files_pA/example.scen
+date -Iseconds
+

eo/contrib/irace/expe/beta/planF/r_iF.sh

@@ -0,0 +1,37 @@
+#!/bin/bash
+#run once each problem
+dir=$1
+run=$2
+budget_irace=$3
+buckets=$4
+myhome=$5
+
+echo "---------------start JOB ${run} $(date --iso-8601=seconds)"
+. /etc/profile.d/modules.sh
+export MODULEPATH=${MODULEPATH}${MODULEPATH:+:}/opt/dev/Modules/Anaconda:/opt/dev/Modules/Compilers:/opt/dev/Modules/Frameworks:/opt/dev/Modules/Libraries:/opt/dev/Modules/Tools:/opt/dev/Modules/IDEs:/opt/dev/Modules/MPI
+module load LLVM/clang-llvm-10.0
+module load R
+
+cp -r ${myhome}/R .
+cp -r ${myhome}/irace_files_pF .
+#cp -r /scratchbeta/zhenga/irace_files .
+#chmod u+x ./fastga
+outdir="${run}_$(date --iso-8601=seconds)_results_irace"
+for pb in $(seq 0 18) ; do
+    echo "Problem ${pb}... "
+    res="results_problem_${pb}"
+    mkdir -p ${dir}/${outdir}/${res}
+    # Fore some reason, irace absolutely need those files...
+    cp ${myhome}/code/paradiseo/eo/contrib/irace/release/fastga  ${dir}/${outdir}/${res}
+    cat ./irace_files_pF/example.scen | sed "s%\".%\"${dir}/${outdir}/${res}%g" |  sed "s/maxExperiments = 0/maxExperiments=${budget_irace}/" > ${dir}/${outdir}/${res}/example.scen
+    cp ./irace_files_pF/default.instances ${dir}/${outdir}/${res}
+    cp ./irace_files_pF/fastga.param ${dir}/${outdir}/${res}
+    cp ./irace_files_pF/forbidden.txt ${dir}/${outdir}/${res}
+    cat ./irace_files_pF/target-runner | sed "s/--problem=0/--problem=${p}/" |  sed "s/buckets=0/buckets=${buckets}/" > ${dir}/${outdir}/${res}/target-runner
+    chmod u+x ${dir}/${outdir}/${res}/target-runner
+
+    echo "---start $(date)"
+    time -p ./R/x86_64-pc-linux-gnu-library/3.6/irace/bin/irace --scenario ${dir}/${outdir}/${res}/example.scen  > ${dir}/${outdir}/${res}/irace.log 
+    echo "---end $(date)"
+done
+echo "end JOB ${run} $(date --iso-8601=seconds)---------------"

eo/contrib/irace/expe/beta/planF/riaF.sh

@@ -0,0 +1,28 @@
+#!/bin/bash
+
+date -Iseconds
+echo "STARTS"
+myhome=$1
+scratchpath=$2
+#dir=${HOME}/plan2/${name}
+mexp=$3 #budget irace
+mevals=$4 #budget fastga
+name="dataF_maxExp=${mexp}_maxEv=${mevals}_$(date --iso-8601=seconds)"
+dir=${scratchpath}/dataFAR/dataF/${name}
+mkdir -p ${dir}
+
+for r in $(seq 2); do
+    echo "Run $r/15";
+    #date -Iseconds 
+    #cmd="qsub -N irace_${runs}_${buckets}" -q beta -l select=1:ncpus=1 -l walltime=00:04:00 --${HOME}/run_irace.sh ${dir}
+    cmd="qsub -N iraceF_${mevals}_run=${r} -q beta -l select=1:ncpus=1 -l walltime=00:25:00 -- ${scratchpath}/planF/r_iF.sh ${dir} ${r} ${mexp} ${mevals} ${myhome}"
+    #time -p bash ${HOME}/plan2/run_irace2.sh ${dir} ${r} &> ${dir}/erreur_${r}.txt
+    #bash ${HOME}/test/r_i.sh
+    echo $cmd
+    $cmd
+    #date -Iseconds
+done
+
+#echo "DONE"
+#date -Iseconds
+#echo $(pwd)