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
+Johann Dreo             <johann@dreo.fr>
-==================
+
-Alexandre Quemy         <alexandre.quemy@inria.fr>
-Benjamin Bouvier        <bnjbouv@gmail.com>
-Caner Candan            <caner@candan.fr>
-Pierre Savéant          <pierre.saveant@thalesgroup.com>
 
 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

@@ -1,5 +1,6 @@
 # ParadiseO
 
+
 ######################################################################################
 ### 0) Check the CMake version
 ######################################################################################
@@ -12,13 +13,24 @@ cmake_minimum_required(VERSION 3.10 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 "${CMAKE_SOURCE_DIR}/eo"   CACHE INTERNAL "ParadisEO-EO   source directory" FORCE)
+set(  EO_SRC_DIR "${PROJECT_SOURCE_DIR}/eo"   CACHE INTERNAL "ParadisEO-EO   source directory" FORCE)
-set( EDO_SRC_DIR "${CMAKE_SOURCE_DIR}/edo"  CACHE INTERNAL "ParadisEO-EDO  source directory" FORCE)
+set( EDO_SRC_DIR "${PROJECT_SOURCE_DIR}/edo"  CACHE INTERNAL "ParadisEO-EDO  source directory" FORCE)
-set(  MO_SRC_DIR "${CMAKE_SOURCE_DIR}/mo"   CACHE INTERNAL "ParadisEO-MO   source directory" FORCE)
+set(  MO_SRC_DIR "${PROJECT_SOURCE_DIR}/mo"   CACHE INTERNAL "ParadisEO-MO   source directory" FORCE)
-set(MOEO_SRC_DIR "${CMAKE_SOURCE_DIR}/moeo" CACHE INTERNAL "ParadisEO-MOEO source directory" FORCE)
+set(MOEO_SRC_DIR "${PROJECT_SOURCE_DIR}/moeo" CACHE INTERNAL "ParadisEO-MOEO source directory" FORCE)
-set( SMP_SRC_DIR "${CMAKE_SOURCE_DIR}/smp"  CACHE INTERNAL "ParadisEO-SMP  source directory" FORCE)
+set( SMP_SRC_DIR "${PROJECT_SOURCE_DIR}/smp"  CACHE INTERNAL "ParadisEO-SMP  source directory" FORCE)
-set( MPI_SRC_DIR "${CMAKE_SOURCE_DIR}/eo/src/mpi"  CACHE INTERNAL "ParadisEO-MPI source directory" FORCE)
+set( MPI_SRC_DIR "${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

@@ -8,7 +8,9 @@ It focus on the efficiency of the implementation of solvers, by providing:
 - tools for ***automated design and selection*** of algorithms,
 - a focus on ***speed*** and several ***parallelization*** options.
 
-![Paradiseo logo](https://github.com/nojhan/paradiseo/blob/master/website/paradiseo_logo_200px_dark.png)
+<div align="center">
+  <img width="640" alt="Paradiseo logo" src="https://raw.githubusercontent.com/nojhan/paradiseo/master/docs/img/paradiseo_logo_dark.svg"/>
+</div>
 
 # Quick Start
 
@@ -166,7 +168,7 @@ It is, for instance, easy to start with a simple local search, then add multi-ob
 
 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. 
+Stable versions should however work on Windows and any Unix-like operating system with a standard-conforming C++ development system.
 
 
 # Code
@@ -193,7 +195,7 @@ The build chain uses the classical workflow of CMake. The recommended method is
 
 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.
+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).**
 
@@ -206,6 +208,13 @@ If you `ENABLE_CMAKE_TESTING` and `BUILD_TESTING`, it will be the tests, which y
 
 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).
@@ -230,3 +239,35 @@ 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:
+
+```
+@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}
+}
+```
+
+# Contact
+
+For further information about ParadisEO, help or to report any
+problem, you can either:
+
+- Chat with us on our Matrix chatroom: https://app.element.io/#/room/#paradiseo:matrix.org
+- Post an issue: https://github.com/nojhan/paradiseo/issues
+

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/index.html

@@ -28,9 +28,9 @@
             <p>Shortcuts:</p>
             <ul>
                 <li><a href="#Why">Why choosing <em class="logo">Paradis<span class="logo_eo">eo</span></em>?</a></li>
-                <li><a href="https://gforge.inria.fr/frs/?group_id=145">Downloads</a></li>
+                <li><a href="https://github.com/nojhan/paradiseo/releases">Downloads</a></li>
-                <li><a href="https://gforge.inria.fr/scm/?group_id=145">Git repository</a></li>
+                <li><a href="https://github.com/nojhan/paradiseo">Git repository</a></li>
-                <li><a href="http://irc.lc/freenode/paradiseo">Chat with us</a></li>
+                <li><a href="https://app.element.io/#/room/#paradiseo:matrix.org">Chat with us</a></li>
             </ul>
         </div>
 
@@ -61,6 +61,7 @@
                         <lh><a href="#Features">Features</a></lh>
                         <li><a href="#Component-based">Composable design</a></li>
                         <li><a href="#LargeChoice">Lot of Components</a></li>
+                        <li><a href="#AlgoSelection">Algorithm Selection</a></li>
                         <li><a href="#Portability">Portability</a></li>
                         <li><a href="#VS">VS other Frameworks</a></li>
                     </ol>
@@ -124,9 +125,9 @@
     <div id="Download">
     <h2><a name="Download"></a>Download</h2>
 
-    Download the <a href="https://gforge.inria.fr/frs/download.php/31733/Paradiseo-2.0.1.zip">latest stable release</a>.
+    Download the <a href="https://github.com/nojhan/paradiseo/releases">latest stable release</a>.
 
-    <p>Or clone the latest version: <code class="command">git clone git://scm.gforge.inria.fr/paradiseo/paradiseo.git</code></p>
+    <p>Or clone the latest version: <code class="command">git clone https://github.com/nojhan/paradiseo.git</code></p>
     </div>
 
     <div id="Build">
@@ -146,7 +147,9 @@
     <div id="Develop">
     <h2><a name="Develop"></a>Develop</h2>
 
+    <!--
     <p>Download the <a href="https://gforge.inria.fr/frs/download.php/31755/QuickStart.zip">quick start project template</a>, edit the <code>CMakeLists.txt</code> file to indicate where to find <em class="logo">Paradis<span class="logo_eo">eo</span></em> and start developing your own solver.</p>
+    -->
 
     <p>To show you how does a <em class="logo">Paradis<span class="logo_eo">eo</span></em> code look, you will find here a minimal implementation of the popular <a href="https://en.wikipedia.org/wiki/CMA-ES">CMA-ES algorithm</a>.</p>
 
@@ -235,7 +238,7 @@
     answers is to send an email to <a href='mailto:paradiseo-help@lists.gforge.inria.fr'>paradiseo-help@lists.gforge.inria.fr</a>. You can also <a href='http://lists.gforge.inria.fr/pipermail/paradiseo-help/'>consult the help archives</a>, subscribe to our <a href='http://lists.gforge.inria.fr/cgi-bin/mailman/listinfo/paradiseo-users'>(low traffic) mailing-list</a> or <a href='http://lists.gforge.inria.fr/pipermail/paradiseo-users/'>consult its archives</a>.
     </p>
 
-    <p>Alternatively, you can join us on the official chatroom. You can try our <a href="http://irc.lc/freenode/paradiseo">webchat interface</a>, or if you already use IRC, you can directly connect to the <a href="irc://irc.freenode.org/#paradiseo">irc.freenode.org/#paradiseo</a> multi-user chatroom with your favorite client.</p>
+    <p>Alternatively, you can join us on the official chatroom. You can try the <a href="https://app.element.io/#/room/#paradiseo:matrix.org">online webchat app</a>, or if you already use <a href="https://element.io">Element.io</a>, you can directly connect to the <em>#paradiseo:matrix.org</em> multi-user chatroom with your favorite client.</p>
 
     </div>
     </div>
@@ -299,7 +302,7 @@
 
     <div id="Why_efficiency">
     <h3>Efficient</h3>
-    <p class="excerpt"><em class="logo">Paradis<span class="logo_eo">eo</span></em> is <em>the fastest</em> framework on the market, which is a crucial feature for modern and robust approach to solver <em>design and validation</em>.</p>
+    <p class="excerpt"><em class="logo">Paradis<span class="logo_eo">eo</span></em> is <em>the fastest</em> framework on the market, which is a crucial feature for modern and robust approach to solver <em>design and validation</em> (especially on combinatorial problems).</p>
     </div>
 
     <div id="Why_efficiency_details">
@@ -308,6 +311,7 @@
         <p>Another classical criticism against <em class="logo">Paradis<span class="logo_eo">eo</span></em> 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.</p>
         <p>However, we argue that:
             <ul>
+                <li>The numerical optimization community often sees objective functions as monolithic “black-box”, but in combinatorial opimization, it is very often the case that the objective function can be only partially evaluated on neighbor solutions, which allows for (tremendous) speed gains. The Paradiseo-mo module is architectured around that idea, a feature that is not so often found in other frameworks.</li>
                 <li>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.</li>
                 <li>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.</li>
                 <li>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.</li>
@@ -324,7 +328,7 @@
     <p><em class="excerpt">You can expect that validating <em>an algorithm implemented with <em class="logo">Paradis<span class="logo_eo">eo</span></em></em> will be up to <strong>10 times faster</strong> than its (heavily optimized) Python counterpart.</em> </p>
     <p>To give an order of magnitude:
     <ul>
-        <li>If you use the "official" <em>vanilla implementation of <a href="https://github.com/CMA-ES/pycma">CMA-ES in Python/Numpy</a></em> solving the BBOB problem suite through the <a href="https://github.com/numbbo/coco">COCO plateform</a>, running the whole benchmark will take approximately <em>10 minutes</em> on a single Intel Core i5 @ 2.50GHz with a colid state disk.</li>
+        <li>If you use the "official" <em>vanilla implementation of <a href="https://github.com/CMA-ES/pycma">CMA-ES in Python/Numpy</a></em> solving the BBOB problem suite through the <a href="https://github.com/numbbo/coco">COCO plateform</a>, running the whole benchmark will take approximately <em>10 minutes</em> on a single Intel Core i5 @ 2.50GHz with a solid state disk.</li>
         <li>The same experiment, running <em>the <em class="logo">Paradis<span class="logo_eo">eo</span></em> implementation</em> using the seamless binding to the <a href="https://iohprofiler.github.io/">IOHprofiler</a> BBOB implementation, will take <em>1 minute</em>.</li>
     </ul>
     </p>
@@ -478,6 +482,28 @@
     </div>
     </div>
 
+    <div id="AlgoSelection">
+    <h2><a name="AlgoSelection"></a>Algorithm Selection and Configuration</h2>
+
+    <p><em class="logo">Paradis<span class="logo_eo">eo</span></em> provides meta-algorithmics features, like on-the-fly algorithm instanciation. This is useful to dynamically assemble and run an algorithm from a simple numerical encoding. This "algorithm forge" can handle a set of operators and parameter configurations, to be assembled in different "slots" to form an algorithm.</p>
+
+    <figure>
+        <img src="img/bindings_ioh_irace.png"
+             srcset="img/bindings_ioh_irace.svg"
+             width="100%"
+             style="max-width:640px;"
+             title="ParadisEO interfaced with IOHexperimenter and irace − Johann Dréo − CC-BY-SA" />
+        <figcaption>A simplified example of binding between <em class="logo">Paradis<span class="logo_eo">eo</span></em>, IOHexperimenter and irace. ParadisEO provides a on-the-fly algorithm instanciation, which is ran on an IOH problem, with performances estimated with a generic and fast module. All components figured with lego bricks forms a single, integrated, binary.</figcaption>
+    </figure>
+
+    <p>As the <em class="logo">Paradis<span class="logo_eo">eo</span></em> codebase provides generic algorithm and a large set of operators, it's easy to have access to a huge number of algorithms alternatives: there's easily millions of unique combinations.</p>
+    <p>To evaluate those algorithms, you can use bindings toward fast benchmarking tools (like <a href="https://github.com/IOHprofiler/IOHexperimenter">IOHexperimenter</a>), which allow for the fastests runs of the market.</p>
+    <p>You can then wrap this evaluation within an optimizer, to automatically search for the best algorithm instance. For instance, you can either use an optimizer made with <em class="logo">Paradis<span class="logo_eo">eo</span></em>, either plug the binary with <a href="https://iridia.ulb.ac.be/irace/">irace</a> (<em class="logo">Paradis<span class="logo_eo">eo</span></em> provides an automatic interface generation) and reach budgets of 10 000 runs in just one hour (!).</p>
+    <p>And <em>voilà</em>! You started by just designing a high-level view of a solver, and you now know which algorithm instance allow for the best performance.</p>
+    <p>Note that the binding with IOHexperimenter also allow to easily import and explore experimental results in the <a href="https://iohprofiler.liacs.nl/">IOHanalyzer HMI</a>. <em>Ohlala</em>.</p>
+    </div>
+
+
     <div id="Portability">
     <h2><a name="Portability"></a>Portability</h2>
 
@@ -785,18 +811,32 @@
 
     <ul>
         <li>
-            <p>The core EO module is described in the following scientific article:
+            <p>The latest state of the whole <em class="logo">Paradis<span class="logo_eo">eo</span></em> framework is introduced in the following article (see also <a href="https://arxiv.org/abs/2105.00420">the preprint</a>):
-            <blockquote>M. Keijzer, J.J. Merelo, G. Romero, G., M. Schoenauer,
+            <blockquote>Johann Dreo, Arnaud Liefooghe, Sébastien Verel, Marc Schoenauer, Juan J. Merelo, Alexandre Quemy, Benjamin Bouvier, and Jan Gmys,
-                <a href= "http://www.lri.fr/~marc/EO/EO-EA01.ps.gz">Evolving
+                <a href= "https://doi.org/10.1145/3449726.3463276">Paradiseo: from a modular framework for evolutionary computation to the automated design of metaheuristics —22 years of Paradiseo—</a>, <i>GECCO'21: Proceedings of the Genetic and Evolutionary Computation Conference Companion</i>, 1522–1530 (2021).</blockquote>
-                    objects: A general purpose evolutionary computation
-                    library</a>, <i>Artificial Evolution</i>, <b>2310</b>, 829--888 (2002).</blockquote>
             </p>
-
+            
-            <button class="collapsible">BiBTeX entry for citing EO…</button>
+            <button class="collapsible">BiBTeX entry for citing <em class="logo">Paradis<span class="logo_eo">eo</span></em>…</button>
             <div class="details">
-                <p>If you used EO in a study, please cite it. As of today, it has been <a href="https://scholar.google.com/scholar?cites=900770489172177244&as_sdt=2005&sciodt=0,5&hl=fr">cited more than 250 times.</a></p>
+                <p>If you used <em class="logo">Paradis<span class="logo_eo">eo</span></em> in a study, please cite the publication above:</p>
                 <figure style="text-align:left;">
                     <p>
+                        <font face="monospace">
+                        @<font color="#f917f3">inproceedings</font>{<font color="#519f50">Dreo-al_2021_Paradiseo</font>,<br>
+                        &nbsp;&nbsp;&nbsp;&nbsp;<font color="#da4939"><b>author</b></font>&nbsp;&nbsp;&nbsp;&nbsp;=&nbsp;{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},<br>
+                        &nbsp;&nbsp;&nbsp;&nbsp;<font color="#da4939"><b>title</b></font>&nbsp;&nbsp;&nbsp;&nbsp; =&nbsp;{Paradiseo: From a Modular Framework for Evolutionary Computation to the Automated Design of Metaheuristics: 22 Years of Paradiseo},<br>
+                        &nbsp;&nbsp;&nbsp;&nbsp;<font color="#da4939"><b>year</b></font>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;=&nbsp;{2021},<br>
+                        &nbsp;&nbsp;&nbsp;&nbsp;<font color="#da4939"><b>isbn</b></font>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;=&nbsp;{9781450383516},<br>
+                        &nbsp;&nbsp;&nbsp;&nbsp;<font color="#da4939"><b>publisher</b></font>&nbsp;=&nbsp;{Association for Computing Machinery},<br>
+                        &nbsp;&nbsp;&nbsp;&nbsp;<font color="#da4939"><b>address</b></font>&nbsp;&nbsp; =&nbsp;{Online conference},<br>
+                        &nbsp;&nbsp;&nbsp;&nbsp;<font color="#da4939"><b>url</b></font>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; =&nbsp;{<a href="https://doi.org/10.1145/3449726.3463276},">https://doi.org/10.1145/3449726.3463276},</a><br>
+                        &nbsp;&nbsp;&nbsp;&nbsp;<font color="#da4939"><b>booktitle</b></font>&nbsp;=&nbsp;{Proceedings of the Genetic and Evolutionary Computation Conference Companion},<br>
+                        &nbsp;&nbsp;&nbsp;&nbsp;<font color="#da4939"><b>pages</b></font>&nbsp;&nbsp;&nbsp;&nbsp; =&nbsp;{1522–1530},<br>
+                        &nbsp;&nbsp;&nbsp;&nbsp;<font color="#6d9cbe">numpages</font>&nbsp;&nbsp;=&nbsp;{9}<br>
+                        }<br>
+                        </font>
+
+                    <!--
                     <font face="monospace">
                         @<font color="#0000ff">Article</font>{<font color="#ff00ff">Keijzer2001</font>,<br/>
                         &nbsp;&nbsp;<font color="#a52a2a">title</font>&nbsp;=&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&quot;Evolving Objects: A General Purpose Evolutionary Computation Library &quot;,<br/>
@@ -808,21 +848,25 @@
                         &nbsp;&nbsp;<font color="#a020f0">keywords</font>&nbsp;=&nbsp; &quot;genetic algorithms, genetic programming, evolutionary computation, metaheuristic, computational intelligence, optimization&quot;,<br/>
                         &nbsp;&nbsp;<font color="#a020f0">URL</font>&nbsp;=&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&quot;<a href="http://www.lri.fr/~marc/EO/EO-EA01.ps.gz">http://www.lri.fr/~marc/EO/EO-EA01.ps.gz</a>&quot;,<br/>
                         &nbsp;&nbsp;<font color="#ff00ff">size</font>&nbsp;=&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &quot;12 pages&quot;,<br/>
-                        <!-- &nbsp;&nbsp;<font color="#a020f0">abstract</font>&nbsp;=&nbsp; &quot;This paper presents the evolving objects library<br/> -->
-                        <!-- &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; (EOlib), an object-oriented framework for evolutionary<br/> -->
-                        <!-- &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; computation (EC)&nbsp;that aims to provide a flexible set of<br/> -->
-                        <!-- &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; classes to build EC applications. EOlib design<br/> -->
-                        <!-- &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; objective is to be able to evolve any object in which<br/> -->
-                        <!-- &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; fitness makes sense.&quot;,<br/> -->
                         }<br/>
                         <br/>
                     </font>
+                    -->
                     </p>
                     <figcaption></figcaption>
                 </figure>
             </div>
         </li>
 
+        <li>
+            <p>The core EO module is described in the following scientific article:
+            <blockquote>M. Keijzer, J.J. Merelo, G. Romero, G., M. Schoenauer,
+                <a href= "http://www.lri.fr/~marc/EO/EO-EA01.ps.gz">Evolving
+                    objects: A general purpose evolutionary computation
+                    library</a>, <i>Artificial Evolution</i>, <b>2310</b>, 829--888 (2002).</blockquote>
+            </p>
+        </li>
+
         <!-- <li> -->
         <!--     <p>The parallelization modules have been described in: -->
         <!--     <blockquote>S. Cahon, N. Melab and E-G. Talbi, <a href="http://www.springerlink.com/content/up02m74726v1526u/"><em class="logo">Paradis<span class="logo_eo">eo</span></em>: A Framework for the Reusable Design of Parallel and Distributed Metaheuristics</a>, Journal of Heuristics, vol. 10(3), pp.357-380, May 2004.</blockquote> -->
@@ -883,10 +927,31 @@ ISBN: 978-0-470-27858-1</blockquote>
     <ul class="publications">
     </ul>
 
+<h3>Accelerator Physics</h3>
+<ul>
+    <li>E. Valetov, G. Dal Maso, P-R. Kettle, A. Knecht, A. Papa, on behalf of the HIMB Project. <a href="https://doi.org/10.3390/particles7030039">Beamline Optimisation for High-Intensity Muon Beams at PSI Using the Heterogeneous Island Model</a>. <i>Particles</i> (2024), <i>7</i>, 683-691.</li>
+</ul>
+
+<h3>Bioinformatics</h3>
+<ul>
+    <li> Emile Zakiev, Johann Dreo, Mara Santarelli, Benno Schwikowski, <a href="https://hal.science/hal-04110700">Statistical Discovery of Transcriptomic Cancer Signatures using Multimodal Local Search</a>, <i>PGMO Days</i> (2022).</li>
+</ul>
+
+<h3>Metaheuristics Design</h3>
+<ul>
+        <li>Johann Dreo, Carola Doerr, Amine Aziz-Alaoui, Alix Zheng, <a href="https://hal.science/hal-04110704/document">Using irace, paradiseo and iohprofiler for large-scale algorithm configuration</a>, <i>8th COnfiguration and SElection of ALgorithms (COSEAL) workshop</i> (2021).</li>
+        <li>Amine Aziz-Alaoui, Carola Doerr, Johann Dreo, <a href="https://arxiv.org/abs/2102.06435">Towards large scale automated algorithm design by integrating modular benchmarking frameworks</a>, <i>Proceedings of the Genetic and Evolutionary Computation Conference Companion</i> (2021).</li>
+        <li>Johann Dréo, Carola Doerr, Yann Semet, <a href="https://hal.sorbonne-universite.fr/hal-02179604/document">Coupling the design of benchmark with algorithm in landscape-aware solver design</a>, <i>Proceedings of the Genetic and Evolutionary Computation Conference Companion</i> (2019).</li>
+        <li>Johann Dreo, <a href="https://dl.acm.org/doi/10.1145/1570256.1570301">Using Performance Fronts for Parameter Setting of Stochastic Metaheuristics</a>, <i>Genetic and Evolutionary Computation Conference</i>, (2009).</li>
+</ul>
+
 <h3>Automated Planning</h3>
 <ul>
+    <li>Mostepha Redouane Khouadjia, Marc Schoenauer, Vincent Vidal, Johann Dreo, Pierre Savéant, <a href="https://arxiv.org/abs/1305.2265v1">Quality measures of parameter tuning for aggregated multi-objective temporal planning</a>, <i>7th International Conference on Learning and Intelligent Optimization (LION 7)</i> (2013).</li>
+    <li>Mostepha Redouane Khouadjia, Marc Schoenauer, Vincent Vidal, Johann Dreo, Pierre Savéant, <a href="https://arxiv.org/abs/1305.1169v1">Multi-Objective AI Planning: Comparing Aggregation and Pareto Approaches</a>, <i>Conference on Evolutionary Computation in Combinatorial Optimization (EvoCOP)</i> (2013).</li>
+    <li>Mostepha Redouane Khouadjia, Marc Schoenauer, Vincent Vidal, Johann Dreo, Pierre Savéant, <a href="https://arxiv.org/abs/1212.5276">Multi-Objective AI Planning: Evaluating DAE-YAHSP on a Tunable Benchmark</a>, <i>7th International Conference on Evolutionary Multi-Criterion Optimization</i> (2013).</li>
     <li>Jacques Bibaï, Pierre Savéant, Marc Schoenauer, Vincent Vidal, <a href="http://www.aaai.org/ocs/index.php/ICAPS/ICAPS10/paper/view/1414">An Evolutionary Metaheuristic Based on State Decomposition for Domain-Independent Satisficing Planning</a>, <i>Twentieth International Conference on Automated Planning and Scheduling </i> (2010). <strong>Winner of the International Planning Competition</strong></li>
-        <li>Jacques Bibaï, Pierre Savéant, Marc Schoenauer, Vincent Vidal, <a href="">An Evolutionary Metaheuristic for Domain-Independent Satisficing Planning</a>, <i>Genetic and Evolutionary Computation Conference</i> (2010). <strong>Silver Medal at the Human-Competitive Competition</strong></li>
+    <li>Jacques Bibaï, Pierre Savéant, Marc Schoenauer, Vincent Vidal, <a href="">An Evolutionary Metaheuristic for Domain-Independent Satisficing Planning</a>, <i>Genetic and Evolutionary Computation Conference</i> (2010). <strong>Silver Medal at the Human-Competitive Competition</strong></li>
 
 </ul>
 
@@ -950,11 +1015,6 @@ undiscovered knowledge.
             physics/0603108 (2006)</a>.</li>
 </ul>
 
-<h3>Metaheuristics Design</h3>
-<ul>
-        <li>Johann Dreo, <a href="https://dl.acm.org/doi/10.1145/1570256.1570301">Using Performance Fronts for Parameter Setting of Stochastic Metaheuristics</a>, <i>Genetic and Evolutionary Computation Conference</i>, (2009).</li>
-</ul>
-
     </div>
     </div>
 
@@ -1109,16 +1169,17 @@ undiscovered knowledge.
     <div id="Downloads">
     <h2><a name="Downloads"></a>Downloads</h2>
 
-    <p>The current stable release is version 2.0.1: <a href="https://gforge.inria.fr/frs/download.php/31733/Paradiseo-2.0.1.ziph">ParadisEO 2.0.1</a>. Some other releases (older or newer) can be found on <a href="https://github.com/nojhan/paradiseo/releases">GitHub/paradiseo/releases</a>.</p>
+    <p>The current stable release is version: <a href="https://github.com/nojhan/paradiseo/releases">Paradiseo 3.1.3</a>. Some other releases (older or newer) can be found on <a href="https://github.com/nojhan/paradiseo/tags">GitHub/paradiseo/releases</a>.</p>
 
-    <p> You can obtain the latest stable and beta version directly via the official Git repository:
+    <p> You can obtain the latest stable and beta version directly via the Git repository:
-    <code class="command">git clone git://scm.gforge.inria.fr/paradiseo/paradiseo.git</code>.
+    <code class="command">git clone https://github.com/jdreo/paradiseo.git</code>.
     The release are on the "master" branch.
     </p>
 
     <p>Or you can use (at your own risks) the development repositories of the developers:
         <ul>
-            <li>Johann Dreo's: <a href="https://github.com/nojhan/paradiseo">on GitHub</b>.</li>
+            <li>Johann Dreo's: <a href="https://github.com/jdreo/paradiseo">on GitHub</a>.</li>
+            <li>INRIA's: <a href="https://gitlab.inria.fr/paradiseo/paradiseo">on their Gitlab</a>.</li>
         </ul>
     </p>
     </div>
@@ -1160,7 +1221,7 @@ undiscovered knowledge.
     </p>
 
     <p>There is, however, several build options which you may want to switch.
-    To see them, we recommend the use of a CMake gui, like <code>ccmake</code> or <code>cmake-gui</code>.
+    To see them, we recommend the use of a CMake gui, like <code>ccmake</code> (available through the <code>cmake-curses-gui</code> package in Debian/Ubuntu) or <a href="https://cmake.org/cmake/help/latest/guide/user-interaction/index.html#cmake-gui-tool">cmake-gui</a>.
     On the command line, you can see the available options with: <code class="command">cmake -LH ..</code>.
     Those options can be set with the <code>-D&lt;option&gt;=&lt;value&gt;</code> argument to cmake.
     </p>
@@ -1191,7 +1252,7 @@ undiscovered knowledge.
     <h2><a name="Contribute"></a>Contribute</h2>
 
     <p><em class="logo">Paradis<span class="logo_eo">eo</span></em> development is open and contributions are welcomed.</p>
-    <p>The official bug tracker is available on the <a href="https://gforge.inria.fr/projects/paradiseo/">project page</a>. But you may be more confortable using the <a href="https://github.com/nojhan/paradiseo/issues">issue tracker of Johann Dreo's project page on GitHub</a>.</p>
+    <p>The official bug tracker is available on the <a href="https://github.com/nojhan/paradiseo/issues">project page</a>.</p>
     <p>If you have any question about contributing: subscribe to our <a href='http://lists.gforge.inria.fr/cgi-bin/mailman/listinfo/paradiseo-users'>(low traffic) mailing-list</a>.</p>
 
     </div>
@@ -1208,7 +1269,8 @@ undiscovered knowledge.
     <ul>
         <li><a href="https://www.inria.fr">INRIA</a> (current maintainer)</li>
         <li><a href="https://www.univ-littoral.fr/">University of the Littoral Opal Coast</a> (current maintainer)</li>
-        <li><a href="https://thalesgroup.com">Thales</a> (current maintainer)</li>
+        <li><a href="https://www.pasteur.fr/">Institut Pasteur</a> (current maintainer)</li>
+        <li><a href="https://thalesgroup.com">Thales group</a></li>
         <li><a href="https://www.polytechnique.edu/">École Polytechnique</a></li>
         <li><a href="https://www.ugr.es">University of Granada</a></li>
         <li><a href="https://www.vu.nl">Vrije Universiteit Amsterdam</a></li>
@@ -1261,7 +1323,7 @@ undiscovered knowledge.
     worked a lot on the multi-objective module and
     on the local-search one along with <a href="https://www-lisic.univ-littoral.fr/~verel/">Sébastien Verel</a>
     and Jeremy Humeau.
-    In the same team, Clive Canape and J. Boisson made significant contributions.
+    In the same team, C. C. and J. Boisson made significant contributions.
     Karima Boufaras specifically worked on (now deprecated) GPU tools.</p>
 
     <p>The (then) EO project was then taken over by <a href="http://johann.dreo.fr">Johann Dreo</a>,

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 {
+    border-top: thin solid red;
+    border-right: thin solid red;
+    border-bottom: thin solid red;
+    border-left-color: red;
+    background-color: #fee;
+}
+
+dl.warning > dt {
+    color: #500;
+}
+
+dl.note {
+    border-top:thin solid green;
+    border-right:thin solid green;
+    border-bottom:thin solid green;
+    border-left-color:green;
+    background-color: #efe;
+}
+
+dl.note > dt {
+    color: #050;
+}
+
+div.textblock {
+    padding:2em;
+    border: 2px solid var(--bgfont2);
+    box-shadow:0.5em 0.5em 0.5em var(--bgfont);
+    background-color: #fafaff;
+}
+
+div.textblock > p {
+    font-size:1.2em;
+}
+
+div.textblock > p.definition {
+    font-size:0.8em;
+}
+
+p.definition {
+    font-size: 0.8em;
+}
+
+p.reference {
+    font-size: 0.8em;
+}
+
+p {
+    background-color: transparent;
+}
+
+table {
+    margin-top:4em;
+}
+
+table.memname {
+    margin-top:0.1em;
+}
+
+table.mlabels {
+    margin-top:0.1em;
+}
+
+/***********************************/
+
+/************* fragment ************/
+
+/***********************************/
+
+h2.groupheader {
+    color: #303030;
+    font-size: 200%;
+    font-weight: bold;
+    border-bottom: thin solid var(--bgfont2);
+    padding-bottom:1px;
+    margin-top:3em;
+}
+
+h3 {
+    background-color:var(--bgfont2);
+    color: var(--bgcolor);
+    font-size: 1.5em;
+    margin:0px;
+    padding:1em;
+    margin-bottom:2em;
+    border: 2px solid var(--bgfont2);
+    box-shadow:0.5em 0.5em 0.5em var(--bgfont);
+    font-family:monospace;
+}
+
+div.fragment, pre.fragment {
+    border: none;
+    padding: 1em;
+    margin-left: 1em;
+    margin-right: 1em;
+    background-color: var(--code-bg);
+    border-left: 2px solid black;
+    border-top: 2px solid black;
+    border-right: 2px solid grey;
+    border-bottom: 2px solid grey;
+}
+
+div.fragment > div.line {
+    font-size:1em;
+    line-height:150%;
+    color: var(--code-code);
+}
+
+.textblock > div.fragment {
+    font-size: 1em;
+}
+
+.textblock > dl.section {
+    font-size: 1.2em;
+}
+
+div.line {
+    background-color: var(--code-bg);
+}
+
+span.comment {
+    color: var(--code-comment);
+}
+
+span.keyword {
+    color: var(--code-keyword);
+}
+
+span.preprocessor {
+    color: var(--code-preprocessor);
+}
+
+span.keywordtype {
+    color: var(--code-keywordtype);
+}
+
+span.stringliteral {
+    color: var(--code-text);
+}
+
+span.mlabel {
+    background-color: var(--code-text);
+    color: var(--code-bg);
+    border-top: none;
+    border-left: none;
+    border-right: none;
+    border-bottom: none;
+    padding: 10px;
+    border-radius: 0px;
+}
+
+div.fragment > div.line > a.code {
+    color: var(--code-link);
+}
+
+span.lineno, span.lineno>* {
+    color: var(--code-line);
+    border-right: none;
+    background-color: var(--code-bg);
+}
+
+span.lineno a {
+    background-color: var(--code-line-bg);
+}
+
+span.lineno a:hover {
+    color: var(--bg3font);
+    background-color: var(--code-line-bg);
+}
+
+code {
+    color:black;
+}
+
+/***********************************/
+
+/************* directory ***********/
+
+/***********************************/
+
+.directory tr.even {
+    background-color: inherit;
+}
+
+.iconfclosed {
+    background-image: url(closed-folder.png);
+    margin-right: 10px;
+}
+
+.iconfopen {
+    background-image: url(opened-folder.png);
+    margin-right: 10px;
+}
+
+.icondoc {
+    background-image: url(document.png);
+    margin-right: 10px;
+}
+
+.arrow {
+    color: #7d7d7d;
+}
+
+.icona {
+    vertical-align: middle;
+    margin-right: 5px;
+}
+
+.icon {
+    background-color: var(--icon-bg);
+    color: var(--icon-font);
+    display: table-cell;
+    vertical-align: middle;
+    height: 20px;
+    width: 20px;
+}
+
+div.ah {
+    background-color: var(--qindex-icon-bg);
+    color: var(--qindex-icon-font);
+    text-align: center;
+    background-image: none;
+    -webkit-box-shadow: none;
+    box-shadow: none;
+    -webkit-border-radius: 0px;
+    border-radius: 0px;
+    border: none;
+}
+
+div.qindex {
+    background-color: var(--qindex-menu-bg);
+    border: none;
+    padding: 20px;
+}
+
+a.qindex {
+    color: var(--qindex-menu-font);
+    font-weight: normal;
+    font-size: 20px;
+}
+
+a:hover.qindex {
+    color: var(--qindex-menu-font-hover);
+}
+
+a:visited.qindex {
+    color: var(--qindex-menu-font);
+}
+
+table.classindex {
+    margin-top: 30px;
+    margin-bottom: 30px;
+}
+
+table.classindex a.el {
+    font-weight: normal;
+}
+
+table.params {
+    margin-top:1em;
+}
+
+#titlearea > table {
+    margin-top:0px;
+}
+
+table.directory > tbody > tr {
+    border-top: thin solid var(--nav-tree-bg);
+    border-bottom: thin solid var(--nav-tree-bg);
+}
+
+/***********************************/
+
+/************** footer *************/
+
+/***********************************/
+
+div.directory {
+    border-top: 1px solid var(--bgborder);
+    border-bottom: none;
+    margin: 20px 0px;
+}
+
+div.directory a.el {
+    font-weight: normal;
+}
+
+div.directory>table {
+    margin: 20px 0px;
+}
+
+hr.footer {
+    border: none;
+}
+
+.contents>hr {
+    border-top: 0px;
+}
+
+/***********************************/
+
+/*********** memberdecls ***********/
+
+/***********************************/
+
+.memItemLeft, .memItemRight {
+    padding: 15px 30px;
+    background-color: inherit;
+}
+
+.mdescRight {
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+}
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+    background-color: inherit;
+}
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+    border-bottom: 1px solid var(--bgborder2);
+}
+
+.memTemplParams {
+    color: var(--bgfont);
+}
+
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+
+/*********** nav-tree ***********/
+
+/***********************************/
+
+#nav-tree-contents {
+    background-color: var(--nav-tree-bg);
+    margin: 0px;
+}
+
+#side-nav, #nav-tree {
+    background-image: none;
+    background-color: var(--nav-tree-bg);
+}
+
+#nav-tree .item {
+    background-color: var(--nav-tree-bg);
+    font-family: Arial;
+    text-shadow: none;
+    font-size: 14px;
+    font-weight: 700;
+    padding: 10px;
+    color: var(--nav-tree-font);
+}
+
+#nav-tree .arrow {
+    color: var(--nav-tree-font);
+}
+
+#nav-tree .selected {
+    background-image: none;
+    background-color: var(--nav-tree-bg-selected);
+}
+
+#nav-tree .selected a {
+    color: var(--nav-tree-font-selected);
+}
+
+#nav-tree .item:hover {
+    background-color: var(--nav-tree-bg-hover);
+    color: var(--nav-tree-font-hover);
+}
+
+#nav-tree .item a:hover {
+    color: var(--nav-tree-font-hover);
+}
+
+#side-nav .ui-resizable-e {
+    background-image: none;
+    background-color: var(--nav-tree-bg);
+}
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+#nav-sync {
+    background-color: transparent;
+}
+
+#nav-sync>img {
+    content: url(off_sync.png);
+}
+
+#nav-sync.sync>img {
+    content: url(on_sync.png);
+}
+
+/***********************************/
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+
+/***********************************/
+
+.plantumlgraph > img {
+    width: 80%;
+}

edo/LICENSE

@@ -0,0 +1,502 @@
+		  GNU LESSER GENERAL PUBLIC LICENSE
+		       Version 2.1, February 1999
+
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+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;
+    (void)/*ignore returned*/ system(s.c_str());
-    dummy = system(s.c_str());
     // all done
 
     _descOfFiles = new std::ofstream( std::string(dirname + "/list_of_files.txt").c_str() );

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

@@ -45,46 +45,23 @@ set(PARADISEO_LIBRARIES ga eoutils eo)
 
 # IOH
 set(IOH_ROOT "~/code/IOHexperimenter/" CACHE PATH "Where to find IOHexperimenter")
-find_path(IOH_PROBLEM_H "IOHprofiler_problem.h" PATHS ${IOH_ROOT}/src/Template/)
+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)
+# find_library(IOH_LIBRARY "IOH" PATHS ${IOH_ROOT} PATH_SUFFIXES release Release debug Debug build Build)
 
-if(EXISTS ${IOH_PROBLEM_H} AND EXISTS ${IOH_LIBRARY})
+if(EXISTS ${IOH_HPP}) # AND EXISTS ${IOH_LIBRARY})
     message(STATUS "Found IOH in ${IOH_ROOT}")
-    include_directories(${IOH_ROOT}/build/Cpp/src/)
+    include_directories(${IOH_ROOT}/include/)
-    link_directories(${IOH_ROOT}/build/Cpp/bin/)
+    include_directories(${IOH_ROOT}/external/fmt/include/)
-
+    include_directories(${IOH_ROOT}/external/clutchlog/)
-    # Workaround IOH's poorly designed headers inclusion scheme.
+    link_directories(${IOH_ROOT}/release/external/fmt/)
-    SET(PROBLEMS_BBOB_DIR "src/Problems/BBOB")
-    SET(PROBLEMS_BBOB_COMMON_DIR "src/Problems/BBOB/bbob_common_used_functions")
-    SET(PROBLEMS_COMMON_DIR "src/Problems/common_used_functions")
-    SET(PROBLEMS_PBO_DIR "src/Problems/PBO")
-    SET(PROBLEMS_WMODEL_DIR "src/Problems/WModel")
-    SET(PROBLEMS_PYTHON_DIR "src/Problems/Python")
-    SET(SUITES_DIR "src/Suites")
-    SET(TEMPLATE_DIR "src/Template")
-    SET(TEMPLATE_EXPERIMENTS_DIR "src/Template/Experiments")
-    SET(TEMPLATE_LOGGERS_DIR "src/Template/Loggers")
-    SET(IOHEXPERIMENTER_DIR
-      "${IOH_ROOT}/${PROBLEMS_COMMON_DIR}"
-      "${IOH_ROOT}/${PROBLEMS_BBOB_DIR}"
-      "${IOH_ROOT}/${PROBLEMS_BBOB_COMMON_DIR}"
-      "${IOH_ROOT}/${PROBLEMS_PBO_DIR}"
-      "${IOH_ROOT}/${PROBLEMS_WMODEL_DIR}"
-      "${IOH_ROOT}/${PROBLEMS_PYTHON_DIR}"
-      "${IOH_ROOT}/${SUITES_DIR}"
-      "${IOH_ROOT}/${TEMPLATE_DIR}"
-      "${IOH_ROOT}/${TEMPLATE_EXPERIMENTS_DIR}"
-      "${IOH_ROOT}/${TEMPLATE_LOGGERS_DIR}"
-    )
-    include_directories(${IOHEXPERIMENTER_DIR})
 
 else()
-    if(NOT EXISTS ${IOH_PROBLEM_H})
+    if(NOT EXISTS ${IOH_HPP})
-        message(FATAL_ERROR "Could not find `IOHprofiler_problem.h` in: ${IOH_ROOT}/src/Template/ (did you forget to compile it?)")
+        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()
+    # 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()
 
 
@@ -93,5 +70,9 @@ endif()
 ######################################################################################
 
 add_executable(fastga fastga.cpp)
-target_link_libraries(fastga ${PARADISEO_LIBRARIES} ${IOH_LIBRARY})
+# 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)

eo/contrib/irace/expe/beta/planO/r_iO.sh

@@ -0,0 +1,43 @@
+#!/bin/bash
+#run once each problem
+
+. /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 ${myhome}/irace_files_pO .
+
+outdir="${run}_$(date --iso-8601=seconds)_results_irace"
+echo "start a job  $(date -Iseconds)"
+
+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}/${res}
+
+    cat ./irace_files_pO/example.scen | sed "s%\".%\"${dir}/${outdir}/${res}%g" |  sed "s/maxExperiments = 0/maxExperiments=${budget_irace}/" > ${dir}/${outdir}/${res}/example.scen
+    cp ./irace_files_pO/default.instances ${dir}/${outdir}/${res}
+    cp ./irace_files_pO/fastga.param ${dir}/${outdir}/${res}
+    cat ./irace_files_pO/target-runner | sed "s/--problem=0/--problem=${pb}/" > ${dir}/${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)"
+    
+    echo "done run : ${run} pb : ${pb}"
+    date -Iseconds
+done
+
+echo "end a job $(date -Iseconds)---------------------"
+

eo/contrib/irace/expe/beta/planO/riaO.sh

@@ -0,0 +1,23 @@
+#!/bin/bash
+
+date -Iseconds
+echo "STARTS"
+myhome=$1
+scratchpath=$2
+mexp=$3
+mevals=$4
+name="dataO_maxExp=${mexp}_maxEv=${mevals}_$(date --iso-8601=seconds)"
+dir=${scratchpath}/dataFAR/dataO/${name}
+mkdir -p ${dir}
+
+for r in $(seq 2); do
+    echo "Run $r/15";
+    cmd="qsub -N iraceO_maxExp=${exp}_maxEv=${evals}_${r} -q beta -l select=1:ncpus=1 -l walltime=00:10:00 -- ${scratchpath}/planO/r_iO.sh ${dir} ${r} ${mexp} ${mevals} ${myhome}"
+    echo $cmd
+    $cmd
+    #time (p=2; while [[ ${p} > 1 ]] ; do p=$(qqueue -u $USER | wc -l); echo "$r: $p"; sleep 300; done)
+done
+
+#echo "DONE"
+#date -Iseconds
+

eo/contrib/irace/expe/beta/readme.txt

@@ -0,0 +1,167 @@
+############################################
+#Explanation of the experimental plans and the validation runs
+
+############################################
+1. INTRODUCTION
+
+The aim of all the scripts is to make the experimental plans for Algorithm Configuration for Genetic Algorithms by using a fully modular benchmarking pipeline design of this article https://arxiv.org/abs/2102.06435 . 
+
+You can upload the data in : https://zenodo.org/record/5479538#.YTaT0Bnis2w 
+
+Plan A is an experimental plan for finding an efficient algorithm for all the functions that we consider.
+
+Plan F is an experimental plan for finding an efficient algorithm for each function that we consider.
+
+Plan R is an experimental plan for getting random algorithms.
+
+Plan O is the reproduction of the experimental plan of the article.
+
+2. VOCABULARIES
+
+* maxExp : means maximum Experiments,  the budget for irace
+* maxEv : means maximum evaluation, the budget for FastGA algorithms
+
+*dataFAR : directory which we store all the experiment data of Plan F and Plan A, created when you run run_exp.sh
+
+* dataA, dataF 
+dataA is a directory which we store all the runs of an experiment plan for several budgets
+eg : /dataA/planA_maxExp=*_maxEv=**_$(data), * is a value of maxExp, and ** is a value of maxEv
+
+
+*fastga_results_all : directory which we store all the data for validation runs. It constains only 3 subdirectories (fastga_results_planF, fastga_results_planA, fastga_results_planO, fastga_results_random), created by running run_exp.sh
+
+* fastga_results_planF, fastga_results_planA, fastga_results_random, fastga_results_planO
+Each directory store the data for validation runs of each experiment plan.
+fastga_random directory are created by running run_exp.sh
+fastga_results_planF, fastag_results_planO and fastag_results_planA are created only after you have data in the dataA or dataF or dataO directories.
+
+
+* planA_*, planF_*, planO_*
+If the planA_* or planF_* or planO_* are in the dataFAR directory, the directory contains the data of experimental plan. This means that each plan contains the result of 15 runs of irace stored in irace.log file, and the data are provided by run_exp.sh.
+
+If the planA_* or planF_* or planO_* directories are in the fastga_results_planA or fastga_results_planF, these directories contain the data of 50 validation runs by running all the best algorithms of each plan stores in dataFAR. The data are provided by running run_res.sh
+
+
+*fastag_all_results : contains the directories of the validation run data.
+
+*fastga_results_planF, fastga_results_planA and fastga_results_random contain respectively the validation run data of Plan F, Plan A and Plan R.
+
+
+3. DESCRIPTION
+
+The directory which you load all the scripts contains : 
+
+ * bash files :
+	-run_res.sh : submit to the cluster all the experiment plan, get all the data we need for the plan F, plan A and plan R.
+	-run_exp.sh : submit to the cluster for getting all the data for validation runs of each data A and data F provided by running run_res.sh
+	-run_random.sh : script for getting random algorithms and the data for validation runs for each problem
+        -testrandom.sh : change the budget fastga (maxEv) in this file if you need, by running this file, you submit plan R job in the cluster
+	
+        -csv_all_bests.sh : script for getting all the best configurations of each plan in a dataF or a dataA directories
+
+        -run_elites_planA.sh : script for validation runs of plan A by giving a csv file of each best configuration. This file is provided by running parseA_irace_bests.py.
+	-run_elites_planB.sh
+	-fastga_elites_all.sh : run this file, by giving a directory csv_plan* of csv files ( must only contains the csv file of the same plan, eg : csv_planF) and a run_elites_plan*.sh (* is the name of the plan, eg run_elites_planF.sh), by running this file you get all the validation runs of each csv file. Each csv file contains the best configuration (you get these csv files by running csv_all_bests.sh) 
+
+ * python files : 
+	-parseA_irace_bests.py : for parsing the irace.log file of each data provided by running irace. By giving a bounch of directories of one experiment
+	-parseF_irace_bests.py : for the plan plan F and plan O(in the plan O csv, there are label offspringsize and popsize, but there are not values)
+
+ * 6 directories : 
+	-irace_files_pA : 
+		-default.instances
+		-example.scen
+		-fastga.param
+		-forbidden.txt
+		-target-runner
+
+	-irace_files_pF :
+		-default.instances : 
+		-example.scen
+		-fastga.param
+		-forbidden.txt
+		-target-runner
+
+	-irace_files_pO :
+		-default.instances : 
+		-example.scen
+		-fastga.param
+		-target-runner
+
+	-planA :
+		-riaA.sh : for running 15 times r_iA.sh file by submitting to the mesu cluster
+		-r_iA.sh : for running irace for all the problems
+
+	-planF :
+		-riaF.sh : for running 15 times r_iF.sh file by submitting to the mesu cluster
+		-r_iF.sh : for running irace for each problem we considered
+	-planO :
+		-riaO.sh : for running 15 times r_iO.sh file by submitting to the mesu cluster
+		-r_iO.sh : for running irace for each problem we considered
+
+
+The directories planA, planF contain the scripts to run one experiment of Plan A and Plan F.
+
+The directories irace_files_pA, irace_files_pO and irace_files_pF contain the scripts needing for calling irace for one experiment of Plan A, Plan O and Plan F. [Look at the irace package : User Guide for more information]
+
+
+5. CONCLUSION
+
+For getting all the experiment data and the validation run data run run_exp.sh file first, after run_exp.sh file finished to execute and there is all the data in the dataFAR (ie : in the cluster, all the jobs finished to execute) run_res.sh data.
+
+Warning : run_exp.sh may take few days or few weeks depending on the Budget you ask, do not run_res.sh if in dataFAR there are data which are not finished to execute in the cluster, or jobs killed. Do not forget to remove directories of plan which are not complete.
+
+
+
+
+############################################
+#Scripts for getting histograms and csv files of validation runs results.
+
+############################################
+
+get histograms or csv files for random data :
+-hist_join_random.py  : get one histogram for a plan by budget
+-dist_op_random.py  : get csv files of the distribution of operators by problems 
+
+get histograms or csv files for plan O,F,A :
+-hist_join.py
+-dist_op_all.py
+-parse_auc_average  # get the mean auc value of each problem and each irace run
+
+get histograms for plan F, A , R, O
+-hist_by_pb_budget_plan.py   : get histograms by problem
+-hist_by_FARO_pb.py  : 
+-hist_by_FARO.py
+-best_out_of_elites.py : get the best algorithm found among 15 runs of irace, for a plan
+
+
+files to call all these files : 
+-csv_all.sh : get all the csv files (average of auc, best out ..), call best_out_of_elites.py, parse_auc_average.py, dist_op_*.py
+-hist_all.sh : get all the histograms, call each hist_*.py file
+
+file for other goal :
+-mwtestU.py ; csv file for selected problems which irace algorithms gave better performances than random algorithms
+-rep_std_mean_selected.py : to get the std, mean and the distribution of operators of the selected problems 
+
+
+
+
+
+############################################
+#Summary
+
+############################################
+
+Get the experiment data :
+run : bash run_exp.sh
+
+-----------Only after you have the experiment data:
+Get the validation run data :
+run : bash run_res.sh
+
+Get histograms :
+run : bash hist_all.sh 
+
+Get csv files of validation run data :
+run : bash csv_all.sh
+

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

@@ -0,0 +1,55 @@
+#!/usr/bin/env python3
+import sys
+import os
+import numpy as np
+import matplotlib.pyplot as plt
+import pandas
+
+#eg : python3 ./rep_std_mean_selected.py ./hist_and_csv/distribution_op_fastga_results_planF
+#get the std of the selected problem
+path=sys.argv[1] # directory of each distribution by pb
+lpb={13,14,15,16,18} #set of pb selected
+#column : [operator : nbpossibilities]
+distdir=path+"/rep_std_mean"
+try:
+    os.makedirs(distdir)
+except FileExistsError:
+    pass
+
+res=[]
+for csvfile in os.listdir(os.path.join(path)):
+    if(int(csvfile.split("_")[1].split("=")[1]) in lpb):
+        print(csvfile)
+        res.append(pandas.read_csv(os.path.join(path,csvfile)))
+
+#assert(len(res[0])==len(res[1]) , "each csv file does not have the same line " #check if the number of param is eq in each csv file
+
+
+name ="std_rep_pb={}".format(str(lpb))+"".join(map(str,path.split("/")[-3].split("_")[:3]))+".csv"
+with open(os.path.join(distdir,name),'w+') as fd:
+    fd.write("Op index, "+",".join(map(str,range(0,11)))+"\n")
+globalname="rep_all_pb={}".format(str(lpb))+"".join(map(str,path.split("/")[-3].split("_")[:3]))+".csv"
+with open(os.path.join(distdir,globalname),'w+') as fd:
+    fd.write("Op index, "+",".join(map(str,range(0,11)))+"\n")
+meanname="mean_rep_pb={}".format(str(lpb))+"".join(map(str,path.split("/")[-3].split("_")[:3]))+".csv"
+with open(os.path.join(distdir,meanname),'w+') as fd:
+    fd.write("Op index, "+",".join(map(str,range(0,11)))+"\n")
+#print(res)
+limparam=[10,7,10,10,7,11,11,10,10]
+for i in range(1,10): #9 nb parameters
+    npval=np.zeros((len(res),limparam[i-1]),dtype=int)
+    for pb in range(len(res)): 
+        print(i,np.array(np.array(res[pb][i-1:i])[0]),np.array(np.array(res[pb][i-1:i])[0][1:limparam[i-1]+1]))
+        npval[pb,:]=np.array(np.array(res[pb][i-1:i])[0][1:limparam[i-1]+1],dtype=int)
+    nameparam=np.array(res[pb][i-1:i])[0][0]
+    line= ",".join(map(str,np.std(npval,0)))+",-"*(11-limparam[i-1])
+    print("ligne ",line)
+
+    with open(os.path.join(distdir,name),'a') as fd:
+        fd.write(nameparam+","+line+"\n")
+    line= ",".join(map(str,np.sum(npval,0)))+",-"*(11-limparam[i-1])
+    with open(os.path.join(distdir,globalname),'a') as fd:
+        fd.write(nameparam+","+line+"\n")
+    line= ",".join(map(str,np.mean(npval,0)))+",-"*(11-limparam[i-1])
+    with open(os.path.join(distdir,meanname),'a') as fd:
+        fd.write(nameparam+","+line+"\n")

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

@@ -0,0 +1,61 @@
+#!/bin/bash
+#instance = seed
+echo "-----------------Start $(date)"
+. /etc/profile.d/modules.sh
+export MODULEPATH=${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
+
+csv_file=$1 #contains all the configs of all the problems of one experiments
+mexp=$2
+mevals=$3
+path=$4
+# Number of runs (=seeds).
+runs=50
+
+# You most probably want to run on release builds.
+exe="/home/zhenga/fastga"
+plan=$(echo ${csv_file} | sed "s/results_irace_plan//")
+outdir="${path}/plan4_maxExp=${mexp}_maxEv=${mevals}_$(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 ${csv_file}|  sed 1,1d | cut -s -d"," -f3-11 ); do
+    a=($(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]} --pop-size=${a[7]} --offspring-size=${a[8]}"
+   
+    #perc=$(echo "scale=3;${n}/(285)*100.0" | bc)
+    #echo "${perc}% : algo ${algoid}/285"
+    # echo -n "Runs: "
+    for pb in $(seq 0 18) ; do
+        name_dir="pb=${pb}_$(echo "${algo}" | sed 's/--//g' | sed 's/ /_/g')"
+        mkdir -p ${outdir}/raw/data/${name_dir}
+        mkdir -p ${outdir}/raw/logs/${name_dir}
+        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} ${algo}"
+            cmd="${exe} --problem=${pb} --seed=${seed} --instance=${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
+            # Actually start the command.
+        
+            ${cmd} > "${outdir}/raw/data/${name_dir}/${name_run}.dat" 2> "${outdir}/raw/logs/${name_dir}/${name_run}.log"
+            # Check for the most common problem in the log file.
+            #cat "${outdir}/raw/logs/${name_run}.log" | grep "illogical performance"
+        done # seed
+        n=$(($n+1))
+     done 
+    algoid=$(($algoid+1))
+done
+
+# Move IOH logs in the results directory.
+#mv ./FastGA_* ${outdir}
+
+echo "Done $(date) -----------------------"
+#date

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

@@ -0,0 +1,59 @@
+#!/bin/bash
+#instance = seed
+echo "-----------------Start $(date)"
+. /etc/profile.d/modules.sh
+export MODULEPATH=${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
+
+csv_file=$1 #contains all the configs of all the problems of one experiments
+mexp=$2
+mevals=$3
+path=$4
+# Number of runs (=seeds).
+runs=50
+
+# You most probably want to run on release builds.
+exe="/home/${USER}/fastga"
+plan=$(echo ${csv_file} | cut -d / -f3 | sed "s/results_irace_plan//")
+outdir="${path}/plan${plan[@]:0:1}_maxExp=${mexp}_maxEv=${mevals}_$(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 ${csv_file}|  sed 1,1d ); do
+    a=($(echo $line | sed "s/,/ /g"))
+    algo="--crossover-rate=${a[3]} --cross-selector=${a[4]} --crossover=${a[5]} --mutation-rate=${a[6]} --mut-selector=${a[7]} --mutation=${a[8]} --replacement=${a[9]} --pop-size=${a[10]} --offspring-size=${a[11]}"
+   
+    #perc=$(echo "scale=3;${n}/(285)*100.0" | bc)
+    #echo "${perc}% : algo ${algoid}/285"
+    # echo -n "Runs: "
+    name_dir="pb=${a[0]}_$(echo "${algo}" | sed 's/--//g' | sed 's/ /_/g')"
+    mkdir -p ${outdir}/raw/logs/${name_dir}
+    mkdir -p ${outdir}/raw/data/${name_dir}
+    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} ${algo}"
+        cmd="${exe} --problem=${a[0]} --seed=${seed} --instance=${seed} ${algo}"
+        #echo ${cmd} # Print the command.
+            # Forge a directory/log file name
+            # (remove double dashs and replace spaces with underscore).
+        name_run="pb=${a[0]}_seed=${seed}_$(echo "${algo}" | sed 's/--//g' | sed 's/ /_/g')"
+            # echo $name_run
+            # Actually start the command.
+        ${cmd} > "${outdir}/raw/data/${name_dir}/${name_run}.dat" 2> "${outdir}/raw/logs/${name_dir}/${name_run}.log"
+            # Check for the most common problem in the log file.
+        #cat "${outdir}/raw/logs/${name_run}.log" | grep "illogical performance"
+    done # seed
+      
+        n=$(($n+1))
+    algoid=$(($algoid+1))
+done
+
+# Move IOH logs in the results directory.
+#mv ./FastGA_* ${outdir}
+
+echo "Done $(date) -----------------------"
+#date

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

@@ -0,0 +1,64 @@
+#!/bin/bash
+#instance = seed
+
+. /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
+
+
+
+
+csv_file=$1 #contains all the configs of all the problems of one experiments
+mexp=$2
+mevals=$3
+path=$4
+
+echo "-----------------Start $(date -Iseconds) "
+# Number of runs (=seeds).
+runs=50
+
+# You most probably want to run on release builds.
+exe="/home/${USER}/fastga"
+
+outdir="${path}/planO_maxExp=${mexp}_maxEv=${mevals}_$(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 ${csv_file}|  sed 1,1d ); do
+    a=($(echo $line | sed "s/,/ /g"))
+    algo="--crossover-rate=${a[3]} --cross-selector=${a[4]} --crossover=${a[5]} --mutation-rate=${a[6]} --mut-selector=${a[7]} --mutation=${a[8]} --replacement=${a[9]}"
+   
+    #perc=$(echo "scale=3;${n}/(285)*100.0" | bc)
+    #echo "${perc}% : algo ${algoid}/285"
+    # echo -n "Runs: "
+    name_dir="pb=${a[0]}_$(echo "${algo}" | sed 's/--//g' | sed 's/ /_/g')"
+    mkdir -p ${outdir}/raw/data/${name_dir}
+    mkdir -p ${outdir}/raw/logs/${name_dir}
+    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} ${algo}"
+        cmd="${exe} --problem=${a[0]} --seed=${seed} --instance=${seed} ${algo}"
+        #echo ${cmd} # Print the command.
+            # Forge a directory/log file name
+            # (remove double dashs and replace spaces with underscore).
+        name_run="pb=${a[0]}_seed=${seed}_$(echo "${algo}" | sed 's/--//g' | sed 's/ /_/g')"
+            # echo $name_run
+            # Actually start the command.
+        ${cmd} > "${outdir}/raw/data/${name_dir}/${name_run}.dat" 2> "${outdir}/raw/logs/${name_dir}/${name_run}.log"
+            # Check for the most common problem in the log file.
+        #cat "${outdir}/raw/logs/${name_run}.log" | grep "illogical performance"
+    done # seed
+      
+        n=$(($n+1))
+    algoid=$(($algoid+1))
+done
+
+# Move IOH logs in the results directory.
+#mv ./FastGA_* ${outdir}
+
+echo "Done $(date) -----------------------"
+date

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

@@ -0,0 +1,13 @@
+#!/bin/bash
+lexp=(300 600)
+levals=(100 500)
+myscratchpath=/scratchbeta/$USER
+myhome=${HOME}
+for exp in ${lexp[@]} ; do
+    for evals in ${levals[@]} ; do
+        bash ./planF/riaF.sh ${myhome} ${myscratchpath} ${exp} ${evals} 
+        bash ./planO/riaO.sh ${myhome} ${myscratchpath} ${exp} ${evals}
+        bash ./planA/riaA.sh ${myhome} ${myscratchpath} ${exp} ${evals} 
+    done
+done
+bash testrandom.sh ${myhome} ${scratchpath} ${levals[@]}    

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

@@ -0,0 +1,67 @@
+#!/bin/bash
+# Number of runs (=seeds).
+runs=5
+basename=$1
+mevals=$2
+nbAlgo=2
+echo "Start JOB maxEv= $mevals $(date -Iseconds) ----------------------"
+. /etc/profile.d/modules.sh
+export MODULEPATH=${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
+cp ${HOME}/code/paradiseo/eo/contrib/irace/release/fastga .
+# You most probably want to run on release builds.
+exe="./fastga"
+
+#outdir="/scratchbeta/$USER/$(date --iso-8601=minutes)_results_randoms"
+outdir="${basename}/maxEv=${mevals}_nbAlgo=${nbAlgo}_$(date --iso-8601=minutes)_results_randoms"
+mkdir -p ${outdir}
+n=1
+algoid=0
+for algoid in $(seq ${nbAlgo}); do
+    #date
+    r1=$(echo "scale=2 ; ${RANDOM}/32767" | bc)
+    r2=$(echo "scale=2 ; ${RANDOM}/32767" | bc)
+    a=(${r1} $((RANDOM%7)) $((RANDOM%10)) ${r2} $((RANDOM%7)) $((RANDOM%11)) $((RANDOM%11)) $((RANDOM%50 +1)) $((RANDOM%50 +1)) )
+    #condition for value of replacement, pop-size and offspringsize
+    while [[ (1 -lt ${a[6]} && ${a[7]} -lt ${a[8]}) || ( ${a[6]} -eq 1  && ${a[7]} -ne ${a[8]}) ]]
+    do
+        #echo "get in ------------------replacement ${a[6]} popsize  ${a[7]} offspringsize ${a[8]}"
+        r1=$(echo "scale=2 ; ${RANDOM}/32767" | bc)
+        r2=$(echo "scale=2 ; ${RANDOM}/32767" | bc)
+        a=(${r1} $((RANDOM%7)) $((RANDOM%10)) ${r2} $((RANDOM%7)) $((RANDOM%11)) $((RANDOM%11)) $((RANDOM%50 +1)) $((RANDOM%50 +1)))
+    done 
+    algo="--crossover-rate=${a[0]} --cross-selector=${a[1]} --crossover=${a[2]} --mutation-rate=${a[3]} --mut-selector=${a[4]} --mutation=${a[5]} --replacement=${a[6]} --pop-size=${a[7]} --offspring-size=${a[8]}"
+    echo " start algo ${a}------ $(date --iso-8601=minutes)"
+    algodir="$(echo "${algo}" | sed 's/--//g' | sed 's/ /_/g')"
+    for pb in $(seq 0 18) ; do
+        perc=$(echo "scale=3;${n}/(10*18)*10.0" | bc)
+        #echo "${perc}% : algo ${algoid}/100, problem ${pb}/18 $(date --iso-8601=minutes)"
+        # echo -n "Runs: "
+        name_dir="pb=${pb}_$(echo "${algo}" | sed 's/--//g' | sed 's/ /_/g')"
+        
+        mkdir -p ${outdir}/${algodir}/data/${name_dir}
+        mkdir -p ${outdir}/${algodir}/logs/${name_dir}
+        
+        for seed in $(seq ${runs}) ; do # Iterates over runs/seeds.
+            # This is the command to be ran.
+            cmd="${exe} --problem=${pb} --seed=${seed} --instance=${seed} ${algo} --max-evals=${mevals}"
+            name_run="pb=${pb}_seed=${seed}_$(echo "${algo}" | sed 's/--//g' | sed 's/ /_/g')"
+            # echo $name_run
+            #echo $algo
+            
+            ${cmd} > ${outdir}/${algodir}/data/${name_dir}/${name_run}.dat 2> ${outdir}/${algodir}/logs/${name_dir}/${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
+    echo "end algo $(date -Iseconds) "
+    algoid=$(($algoid+1))
+done
+
+
+
+echo "------------------------------------Done $mevals $(date -Iseconds) "
+

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

@@ -0,0 +1,26 @@
+#!/bin/bash
+
+#get csv file, parse dataF in a csv file
+dir=/scratchbeta/$USER/dataFAR
+listdir=$(echo $(ls ${dir}))
+
+for data in ${listdir[@]} ; do
+    file_py="parse${data: -1}_irace_bests.py"
+    path="${dir}/${data}"
+    cmd="bash ./csv_all_bests.sh ${path} ${file_py}"
+    echo $cmd
+    $cmd
+done
+
+#get validation run of each config 
+
+dir=/scratchbeta/$USER/csv_FAO
+listdir=$(echo $(ls ${dir}))
+echo ${listdir[@]}
+for csvdir in ${listdir[@]} ; do
+    csvpath="${dir}/${csvdir}"
+    file_py="./run_elites_plan${csvdir: -1}.sh"
+    cmd="bash ./fastga_elites_all.sh ${csvpath} ${file_py}"
+    echo $cmd
+    $cmd
+done

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

@@ -0,0 +1,18 @@
+#!/bin/bash
+
+#tab=(15000 20000 30000 40000)
+#tab=(100 500 1000 1500 2000 2500 3000 3500 4000 4500 5000 10000)
+myhome=$1
+scratchpath=$2
+tab=${@:3} 
+#echo ${tab[@]}
+outdir="/scratchbeta/$USER/fastga_results_all/fastga_results_random"
+mkdir -p ${outdir} #results of random experiment
+for evals in ${tab[@]}; do
+    #evalsdir="${name}/maxEv=${evals}"
+    #mkdir -p ${evalsdir}
+    #{ time -p bash /home/$USER/run_random.sh ${name} ${i} 50 ; } &> "${name}/sortie5_${j}_maxExp=${i}.txt"
+    #cmd="qsub -N iraceR_maxEv=${evals} -q beta -l select=1:ncpus=1 -l walltime=00:30:00 -- /scratchbeta/$USER/run_random.sh ${outdir} ${evals}"
+    $cmd
+   
+done

eo/contrib/irace/expe/gamma/irace-config/target-runner.py

@@ -0,0 +1,119 @@
+#!/usr/bin/python
+###############################################################################
+# 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:
+# argv[1] is the candidate configuration ID
+# argv[2] is the instance ID
+# argv[3] is the seed
+# argv[4] is the instance name
+# The rest (argv[5:]) 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
+###############################################################################
+
+import datetime
+import os.path
+import re
+import subprocess
+import sys
+
+exe = "../../../../release/onlymutga"
+
+problem = 19
+pop_size = 1
+offspring_size = 100
+
+fixed_parameters = ["--problem", str(problem), "--crossover-rate", "0", "--mutation-rate", "1", "--pop-size", str(pop_size), " --offspring-size", str(offspring_size)]
+
+if __name__=='__main__':
+    if len(sys.argv) < 5:
+        print("\nUsage: ./target-runner.py <configuration_id> <instance_id> <seed> <instance_path_name> <list of parameters>\n")
+        sys.exit(1)
+
+# Get the parameters as command line arguments.
+configuration_id = sys.argv[1]
+instance_id = sys.argv[2]
+seed = sys.argv[3]
+instance = sys.argv[4]
+slices_prop = sys.argv[5:]
+#print(sys.argv)
+
+exe = os.path.expanduser(exe)
+
+cmd = [exe] + fixed_parameters + ["--instance", instance, "--seed", seed]
+
+residual_prob = 1
+cl_probs = []
+residual_size = 1
+cl_sizes = []
+
+values = ""
+sizes = ""
+for i in range(len(slices_prop)):
+    cl_probs.append(residual_prob * float(slices_prop[i]))
+    cl_sizes.append(residual_size * (1-float(slices_prop[i])))
+    residual_prob -= cl_probs[-1]
+    residual_size -= cl_sizes[-1]
+    values += "%.2f,"%cl_probs[-1]
+    sizes += "%.2f,"%cl_sizes[-1]
+
+cl_probs.append(residual_prob)
+values += "%.2f"%cl_probs[-1]
+sizes += "%.2f"%cl_sizes[-1]
+
+cmd += ["--cl-probs", values, "--cl-sizes", sizes]
+
+
+# Define the stdout and stderr files.
+out_file = "c" + str(configuration_id) + "-" + str(instance_id) + str(seed) + ".stdout"
+err_file = "c" + str(configuration_id) + "-" + str(instance_id) + str(seed) + ".stderr"
+
+def target_runner_error(msg):
+    now = datetime.datetime.now()
+    print(str(now) + " error: " + msg)
+    sys.exit(1)
+
+def check_executable(fpath):
+    fpath = os.path.expanduser(fpath)
+    if not os.path.isfile(fpath):
+        target_runner_error(str(fpath) + " not found")
+    if not os.access(fpath, os.X_OK):
+        target_runner_error(str(fpath) + " is not executable")
+
+# This is an example of reading a number from the output.
+def parse_output(out):
+    match = re.search(r'Best ([-+0-9.eE]+)', out.strip())
+    if match:
+        return match.group(1);
+    else:
+        return "No match"
+        
+check_executable (exe)
+
+outf = open(out_file, "w")
+errf = open(err_file, "w")
+return_code = subprocess.call(cmd, stdout = outf, stderr = errf)
+
+outf.close()
+errf.close()
+
+if return_code != 0:
+    target_runner_error("command returned code " + str(return_code))
+
+if not os.path.isfile(out_file):
+    target_runner_error("output file " + out_file  + " not found.")
+
+cost = parse_output (open(out_file).read())
+#print(cost)
+print(open(out_file).read().strip())
+
+os.remove(out_file)
+os.remove(err_file)
+sys.exit(0)
+

eo/contrib/irace/expe/gamma/run_irace.ipynb

@@ -0,0 +1,267 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "id": "04867792",
+   "metadata": {},
+   "source": [
+    "# Imports"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 18,
+   "id": "435212a6",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import pandas as pd\n",
+    "import numpy as np\n",
+    "import seaborn as sb\n",
+    "import matplotlib.pyplot as plt\n",
+    "from matplotlib.ticker import MaxNLocator\n",
+    "import matplotlib.animation\n",
+    "from math import sqrt, log, cos, sin, pi\n",
+    "import numpy as np\n",
+    "import os\n",
+    "import shutil\n",
+    "import re\n",
+    "from subprocess import call\n",
+    "sb.set_style(\"whitegrid\")\n",
+    "#sb.set_palette(\"cubehelix\")\n",
+    "sb.set_palette(\"husl\")\n",
+    "sb.set(font_scale=1) # crazy big\n",
+    "sb.set_style('whitegrid', {'legend.frameon':True})\n",
+    "myfontsize = 12\n",
+    "titlesize = 15\n",
+    "%matplotlib notebook"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "d76bdf6b",
+   "metadata": {},
+   "source": [
+    "# Function to generate the scenario file for irace"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 19,
+   "id": "d86a9ca8",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "def scenario(filename=\"scenario.txt\", \n",
+    "             parameterFile=\"parameters.txt\", \n",
+    "             execDir=\".\", \n",
+    "             logFile=\"./irace.Rdata\", \n",
+    "             targetRunner = \"target-runner.py\", \n",
+    "             maxExperiments = 100000,\n",
+    "             digits = 2):\n",
+    "    f = open(filename, \"w\")\n",
+    "    f.write(\"parameterFile=\" + parameterFile +\"\\n\")\n",
+    "    f.write(\"execDir=\" + execDir + \"\\n\")\n",
+    "    f.write(\"logFile=\" + logFile + \"\\n\")\n",
+    "    f.write(\"targetRunner=\" + targetRunner + \"\\n\")\n",
+    "    f.write(\"maxExperiments=\" + maxExperiments + \"\\n\")\n",
+    "    f.write(\"digits=\" + digits + \"\\n\")\n",
+    "    f.close()"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "1213321a",
+   "metadata": {},
+   "source": [
+    "# Function to generate the parameter file for irace"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 20,
+   "id": "70d221c9",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Generate the param file for irace with all configuarable parameters\n",
+    "def parameters(filename=\"parameters.txt\"):\n",
+    "    f = open(\"parameters.txt\", \"w\")\n",
+    "    f.write(\"# name\\tswitch\\ttype\\tvalues\\n\") # head of the param file\n",
+    "    cl_nb_part = 10 # number of category for the custom categorial probabilistic law\n",
+    "    for i in range(cl_nb_part-1): # minus 1 slice than the number of categories\n",
+    "        f.write(\"slice_prob_%s\\t\\\"\\\"\\tr\\t(0,1)\\n\"%i) # percentage of the residual probability for the slice\n",
+    "\n",
+    "    ######################################### NOT USED YET ##########################################\n",
+    "    #for i in range(cl_nb_part-1): # minus 1 slice than the number of categories\n",
+    "    #    f.write(\"slice_size_%s\\t\\\"\\\"\\tr\\t(0,1)\\n\"%i) # percentage of the residual size for the slice\n",
+    "    #################################################################################################\n",
+    "    f.close()"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "65fcb69d",
+   "metadata": {},
+   "source": [
+    "# Fonction to generate problem dedicated target-runner.py"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 21,
+   "id": "a18ba251",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "def target_runner(origin=\"irace-config/target-runner.py\", path=\"target-runner.py\", problem=1):\n",
+    "    \n",
+    "    generalTR = open(origin, \"r\")\n",
+    "    dedicatedTR = open(path, \"w\")\n",
+    "    for line in generalTR:\n",
+    "        if re.search(\"problem = \", line, flags=0):\n",
+    "            dedicatedTR.write(\"problem = \" + str(problem) + \"\\n\")\n",
+    "        else:\n",
+    "            dedicatedTR.write(line)\n",
+    "    generalTR.close()\n",
+    "    dedicatedTR.close()"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "59421dee",
+   "metadata": {},
+   "source": [
+    "# Run script"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 28,
+   "id": "38dfec96",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "results_directory = \"results\"\n",
+    "irace_path = \"/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/irace/bin/irace\"\n",
+    "instances_file = \"instances.txt\"\n",
+    "scenario_file = \"scenario.txt\"\n",
+    "parameters_file = \"parameters.txt\"\n",
+    "target_runner_file = \"target-runner.py\"\n",
+    "\n",
+    "# create or clear the results directory\n",
+    "if not os.path.isdir(results_directory):\n",
+    "    os.mkdir(results_directory)\n",
+    "    \n",
+    "for pb in range(1,3): # for each problem\n",
+    "    # create or clear a subdirectory for the problem\n",
+    "    problem_directory = results_directory + \"/problem_%s\"%pb\n",
+    "    if os.path.isdir(problem_directory):\n",
+    "        shutil.rmtree(problem_directory)\n",
+    "    os.mkdir(problem_directory)\n",
+    "    \n",
+    "    # generate a custom target runner file for the problem\n",
+    "    target_runner(path = problem_directory + \"/\" + target_runner_file, problem = pb)\n",
+    "\n",
+    "    # copy the config files for iraces\n",
+    "    for filename in [instances_file, scenario_file, parameters_file, target_runner_file]:\n",
+    "        src = r'irace-config/' + filename\n",
+    "        dst = problem_directory + \"/\" + filename\n",
+    "        shutil.copyfile(src, dst)\n",
+    "    \n",
+    "    # run irace for\n",
+    "    cmd = [irace_path, \"--scenario\", problem_directory + \"/\" + scenario_file] #, \"&> irace.log\"\n",
+    "    call(cmd)\n",
+    "#call(cmd)\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 59,
+   "id": "b707ff3b",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "shutil.rmtree(\"results\")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 25,
+   "id": "460c588e",
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "-10"
+      ]
+     },
+     "execution_count": 25,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "call([\"../../release/onlymutga\"])"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 43,
+   "id": "eb234425",
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "'problem_1/default.instances'"
+      ]
+     },
+     "execution_count": 43,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "import shutil\n",
+    "import os\n",
+    "src = r'irace-config/default.instances'\n",
+    "dst = r'problem_1/default.instances'\n",
+    "shutil.copyfile(src, dst)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "7a62c411",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "chmod u+x script.py\n",
+    "cp -a a b"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.8.8"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}

eo/contrib/irace/expe/gamma/run_irace.py

@@ -0,0 +1,12 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+"""
+Created on Tue Dec 14 12:16:17 2021
+
+@author: labeiros
+"""
+
+import sys
+
+print('Number of arguments:', len(sys.argv), 'arguments.')
+print('Argument List:', str(sys.argv))

eo/contrib/irace/expe/gamma/target-runner.py

@@ -0,0 +1,119 @@
+#!/usr/bin/python
+###############################################################################
+# 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:
+# argv[1] is the candidate configuration ID
+# argv[2] is the instance ID
+# argv[3] is the seed
+# argv[4] is the instance name
+# The rest (argv[5:]) 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
+###############################################################################
+
+import datetime
+import os.path
+import re
+import subprocess
+import sys
+
+exe = "../../../../release/onlymutga"
+
+problem = blabla
+pop_size = 1
+offspring_size = 100
+
+fixed_parameters = ["--problem", str(problem), "--crossover-rate", "0", "--mutation-rate", "1", "--pop-size", str(pop_size), " --offspring-size", str(offspring_size)]
+
+if __name__=='__main__':
+    if len(sys.argv) < 5:
+        print("\nUsage: ./target-runner.py <configuration_id> <instance_id> <seed> <instance_path_name> <list of parameters>\n")
+        sys.exit(1)
+
+# Get the parameters as command line arguments.
+configuration_id = sys.argv[1]
+instance_id = sys.argv[2]
+seed = sys.argv[3]
+instance = sys.argv[4]
+slices_prop = sys.argv[5:]
+#print(sys.argv)
+
+exe = os.path.expanduser(exe)
+
+cmd = [exe] + fixed_parameters + ["--instance", instance, "--seed", seed]
+
+residual_prob = 1
+cl_probs = []
+residual_size = 1
+cl_sizes = []
+
+values = ""
+sizes = ""
+for i in range(len(slices_prop)):
+    cl_probs.append(residual_prob * float(slices_prop[i]))
+    cl_sizes.append(residual_size * (1-float(slices_prop[i])))
+    residual_prob -= cl_probs[-1]
+    residual_size -= cl_sizes[-1]
+    values += "%.2f,"%cl_probs[-1]
+    sizes += "%.2f,"%cl_sizes[-1]
+
+cl_probs.append(residual_prob)
+values += "%.2f"%cl_probs[-1]
+sizes += "%.2f"%cl_sizes[-1]
+
+cmd += ["--cl-probs", values, "--cl-sizes", sizes]
+
+
+# Define the stdout and stderr files.
+out_file = "c" + str(configuration_id) + "-" + str(instance_id) + str(seed) + ".stdout"
+err_file = "c" + str(configuration_id) + "-" + str(instance_id) + str(seed) + ".stderr"
+
+def target_runner_error(msg):
+    now = datetime.datetime.now()
+    print(str(now) + " error: " + msg)
+    sys.exit(1)
+
+def check_executable(fpath):
+    fpath = os.path.expanduser(fpath)
+    if not os.path.isfile(fpath):
+        target_runner_error(str(fpath) + " not found")
+    if not os.access(fpath, os.X_OK):
+        target_runner_error(str(fpath) + " is not executable")
+
+# This is an example of reading a number from the output.
+def parse_output(out):
+    match = re.search(r'Best ([-+0-9.eE]+)', out.strip())
+    if match:
+        return match.group(1);
+    else:
+        return "No match"
+        
+check_executable (exe)
+
+outf = open(out_file, "w")
+errf = open(err_file, "w")
+return_code = subprocess.call(cmd, stdout = outf, stderr = errf)
+
+outf.close()
+errf.close()
+
+if return_code != 0:
+    target_runner_error("command returned code " + str(return_code))
+
+if not os.path.isfile(out_file):
+    target_runner_error("output file " + out_file  + " not found.")
+
+cost = parse_output (open(out_file).read())
+#print(cost)
+print(open(out_file).read().strip())
+
+os.remove(out_file)
+os.remove(err_file)
+sys.exit(0)
+

eo/contrib/irace/fastga.cpp

@@ -1,33 +1,43 @@
+#include <filesystem>
 #include <iostream>
 #include <cstdlib>
 #include <string>
+#include <memory>
+
 #include <eo>
 #include <ga.h>
 #include <utils/checkpointing>
 #include <eoInt.h>
 #include <problems/eval/eoEvalIOH.h>
 
-#include <IOHprofiler_ecdf_logger.h>
+#include <ioh.hpp>
-#include <f_w_model_one_max.hpp>
+
+/*****************************************************************************
+ * ParadisEO algorithmic grammar definition.
+ *****************************************************************************/
 
-// using Particle = eoRealParticle<eoMaximizingFitness>;
-using Ints = eoInt<eoMaximizingFitnessT<int>, size_t>;
 using Bits = eoBit<eoMaximizingFitnessT<int>, int>;
 
 // by enumerating candidate operators and their parameters.
 eoAlgoFoundryFastGA<Bits>& make_foundry(
         eoFunctorStore& store,
         eoInit<Bits>& init,
-        eoEvalFunc<Bits>& eval_onemax,
+        eoEvalFunc<Bits>& eval,
         const size_t max_evals,
-        const size_t generations
+        const size_t generations,
+        const double optimum
     )
 {
     // FIXME using max_restarts>1 does not allow to honor max evals.
-    auto& foundry = store.pack< eoAlgoFoundryFastGA<Bits> >(init, eval_onemax, max_evals, /*max_restarts=*/1);
+    auto& foundry = store.pack< eoAlgoFoundryFastGA<Bits> >(init, eval, max_evals, /*max_restarts=*/1);
 
     /***** Continuators ****/
-    foundry.continuators.add< eoGenContinue<Bits> >(generations);
+    auto& fitcont = store.pack< eoFitContinue<Bits> >(optimum);
+    auto& gencont = store.pack< eoGenContinue<Bits> >(generations);
+    auto combconts = std::make_shared< std::vector<eoContinue<Bits>*> >();
+    combconts->push_back( &fitcont );
+    combconts->push_back( &gencont );
+    foundry.continuators.add< eoCombinedContinue<Bits> >( *combconts );
     // for(size_t i=1; i<10; i++) {
     //     foundry.continuators.add< eoGenContinue<Bits> >(i);
     // }
@@ -35,17 +45,17 @@ eoAlgoFoundryFastGA<Bits>& make_foundry(
     //     foundry.continuators.add< eoSteadyFitContinue<Bits> >(10,i);
     // }
 
-    for(double i=0.0; i<1.0; i+=0.2) {
+    // for(double i=0.0; i<1.0; i+=0.2) {
-        foundry.crossover_rates.add<double>(i);
+    //     foundry.crossover_rates.add<double>(i);
-        foundry.mutation_rates.add<double>(i);
+    //     foundry.mutation_rates.add<double>(i);
-    }
+    // }
 
     /***** Offsprings size *****/
     // for(size_t i=5; i<100; i+=10) {
     //     foundry.offspring_sizes.add<size_t>(i);
     // }
 
-    foundry.offspring_sizes.add<size_t>(0); // 0 = use parents fixed pop size.
+    foundry.offspring_sizes.setup(0,100); // 0 = use parents fixed pop size.
 
     /***** Crossovers ****/
     for(double i=0.1; i<1.0; i+=0.2) {
@@ -55,18 +65,25 @@ eoAlgoFoundryFastGA<Bits>& make_foundry(
 
         foundry.crossovers.add< eoNPtsBitXover<Bits> >(i); // nb of points
     }
-    foundry.crossovers.add< eo1PtBitXover<Bits> >();
+    // foundry.crossovers.add< eo1PtBitXover<Bits> >(); // Same as NPts=1
 
     /***** Mutations ****/
-    double p = 1.0; // Probability of flipping eath bit.
+    double p = 1.0; // Probability of flipping each bit.
-    foundry.mutations.add< eoUniformBitMutation<Bits> >(p); // proba of flipping k bits, k drawn in uniform distrib
+    // proba of flipping k bits, k drawn in uniform distrib
-    foundry.mutations.add< eoStandardBitMutation<Bits> >(p); // proba of flipping k bits, k drawn in binomial distrib
+    foundry.mutations.add< eoUniformBitMutation<Bits> >(p);
-    foundry.mutations.add< eoConditionalBitMutation<Bits> >(p); // proba of flipping k bits, k drawn in binomial distrib, minus zero
+    // proba of flipping k bits, k drawn in binomial distrib
-    foundry.mutations.add< eoShiftedBitMutation<Bits> >(p); // proba of flipping k bits, k drawn in binomial distrib, changing zeros to one
+    foundry.mutations.add< eoStandardBitMutation<Bits> >(p);
-    foundry.mutations.add< eoNormalBitMutation<Bits> >(p); // proba of flipping k bits, k drawn in normal distrib
+    // proba of flipping k bits, k drawn in binomial distrib, minus zero
-    foundry.mutations.add< eoFastBitMutation<Bits> >(p); // proba of flipping k bits, k drawn in powerlaw distrib
+    foundry.mutations.add< eoConditionalBitMutation<Bits> >(p);
+    // proba of flipping k bits, k drawn in binomial distrib, changing zeros to one
+    foundry.mutations.add< eoShiftedBitMutation<Bits> >(p);
+    // proba of flipping k bits, k drawn in normal distrib
+    foundry.mutations.add< eoNormalBitMutation<Bits> >(p);
+    // proba of flipping k bits, k drawn in powerlaw distrib
+    foundry.mutations.add< eoFastBitMutation<Bits> >(p);
     for(size_t i=1; i < 11; i+=2) {
-        foundry.mutations.add< eoDetSingleBitFlip<Bits> >(i); // mutate k bits without duplicates
+        // mutate k bits without duplicates
+        foundry.mutations.add< eoDetSingleBitFlip<Bits> >(i);
     }
 
     /***** Selectors *****/
@@ -100,9 +117,13 @@ eoAlgoFoundryFastGA<Bits>& make_foundry(
     return foundry;
 }
 
+/*****************************************************************************
+ * irace helper functions.
+ *****************************************************************************/
+
 Bits::Fitness fake_func(const Bits&) { return 0; }
 
-void print_param_range(const eoParam& param, const size_t slot_size, std::ostream& out = std::cout)
+void print_irace_categorical(const eoParam& param, const size_t slot_size, std::string type="c", std::ostream& out = std::cout)
 {
     // If there is no choice to be made on this operator, comment it out.
     if(slot_size - 1 <= 0) {
@@ -115,37 +136,230 @@ void print_param_range(const eoParam& param, const size_t slot_size, std::ostrea
 
     out << irace_name
         << "\t\"--" << param.longName() << "=\""
-        << "\ti";
+        << "\t" << type;
 
-    if(slot_size -1 <= 0) {
+    out << "\t(0";
-        out << "\t(0)";
+    for(size_t i=1; i<slot_size; ++i) {
+        out << "," << i;
+    }
+    out << ")" << std::endl;
+}
+
+template<class T>
+void print_irace_ranged(const eoParam& param, const T min, const T max, std::string type="r", std::ostream& out = std::cout)
+{
+    // If there is no choice to be made on this operator, comment it out.
+    if(max - min <= 0) {
+        out << "# ";
+    }
+
+    // irace doesn't support "-" in names.
+    std::string irace_name = param.longName();
+    irace_name.erase(std::remove(irace_name.begin(), irace_name.end(), '-'), irace_name.end());
+
+    out << irace_name
+        << "\t\"--" << param.longName() << "=\""
+        << "\t" << type;
+
+    if(max-min <= 0) {
+        out << "\t(?)";
     } else {
-        out << "\t(0," << slot_size-1 << ")";
+        out << "\t(" << min << "," << max << ")";
     }
     out << std::endl;
 }
 
+
+template<class ITF>
+void print_irace_oper(const eoParam& param, const eoOperatorFoundry<ITF>& op_foundry, std::ostream& out = std::cout)
+{
+    print_irace_categorical(param, op_foundry.size(), "c", out);
+}
+
+// FIXME generalize to any scalar type with enable_if
+// template<class ITF>
+void print_irace_param(
+    const eoParam& param,
+    // const eoParameterFoundry<typename std::enable_if< std::is_floating_point<ITF>::value >::type>& op_foundry,
+    const eoParameterFoundry<double>& op_foundry,
+    std::ostream& out)
+{
+    print_irace_ranged(param, op_foundry.min(), op_foundry.max(), "r", out);
+}
+
+// template<class ITF>
+void print_irace_param(
+    const eoParam& param,
+    // const eoParameterFoundry<typename std::enable_if< std::is_integral<ITF>::value >::type>& op_foundry,
+    const eoParameterFoundry<size_t>& op_foundry,
+    std::ostream& out)
+{
+    print_irace_ranged(param, op_foundry.min(), op_foundry.max(), "i", out);
+}
+
+
+template<class ITF>
+void print_irace(const eoParam& param, const eoOperatorFoundry<ITF>& op_foundry, std::ostream& out = std::cout)
+{
+    print_irace_oper<ITF>(param, op_foundry, out);
+}
+
+template<class ITF>
+void print_irace(const eoParam& param, const eoParameterFoundry<ITF>& op_foundry, std::ostream& out = std::cout)
+{
+    print_irace_param/*<ITF>*/(param, op_foundry, out);
+}
+
+void print_irace(const eoParam& param, const size_t min, const size_t max, std::ostream& out = std::cout)
+{
+    print_irace_ranged(param, min, max, "i", out);
+}
+
+void print_operator_typed(const eoFunctorBase& op, std::ostream& out)
+{
+    out << op.className();
+}
+
+void print_operator_typed(const double& op, std::ostream& out)
+{
+    out << op;
+}
+
+template<class ITF>
+void print_operators(const eoParam& param, eoOperatorFoundry<ITF>& op_foundry, std::ostream& out = std::cout, std::string indent="  ")
+{
+    out << indent << op_foundry.size() << " " << param.longName() << ":" << std::endl;
+    for(size_t i=0; i < op_foundry.size(); ++i) {
+        out << indent << indent << i << ": ";
+        auto& op = op_foundry.instantiate(i);
+        print_operator_typed(op, out);
+        out << std::endl;
+    }
+}
+
+template<class T>
+void print_operators(const eoParam& param, T min, T max, std::ostream& out = std::cout, std::string indent="  ")
+{
+    out << indent << "[" << min << "," << max << "] " << param.longName() << "." << std::endl;
+}
+
+template<class ITF>
+void print_operators(const eoParam& param, eoParameterFoundry<ITF>& op_foundry, std::ostream& out = std::cout, std::string indent="  ")
+{
+    print_operators(param, op_foundry.min(), op_foundry.max(), out, indent);
+}
+
+// Problem configuration.
+struct Problem {
+    double dummy;
+    size_t epistasis;
+    size_t neutrality;
+    size_t ruggedness;
+    size_t max_target;
+    size_t dimension;
+    friend std::ostream& operator<<(std::ostream& os, const Problem& pb);
+};
+
+std::ostream& operator<<(std::ostream& os, const Problem& pb)
+{
+    os << "u=" << pb.dummy << "_"
+       << "e=" << pb.epistasis << "_"
+       << "n=" << pb.neutrality << "_"
+       << "r=" << pb.ruggedness << "_"
+       << "t=" << pb.max_target << "_"
+       << "d=" << pb.dimension;
+    return os;
+}
+
+/*****************************************************************************
+ * IOH problem adaptation.
+ *****************************************************************************/
+
+class WModelFlat : public ioh::problem::wmodel::WModelOneMax
+{
+    public:
+        WModelFlat(const int instance, const int n_variables,
+                   const double dummy_para, const int epistasis_para, const int neutrality_para,
+                   const int ruggedness_para)
+        : WModelOneMax(instance, n_variables, dummy_para, epistasis_para, neutrality_para, ruggedness_para)
+        { }
+
+    protected:
+        double transform_objectives(const double y) override
+        { // Disable objective function shift & scaling.
+            return y;
+        }
+};
+
+/*****************************************************************************
+ * Command line interface.
+ *****************************************************************************/
+
 int main(int argc, char* argv[])
 {
     /***** Global parameters. *****/
     enum { NO_ERROR = 0, ERROR_USAGE = 100 };
 
+    std::map<size_t, Problem> benchmark {
+       /* ┌ problem index in the map
+        * │    ┌ problem ID in IOH experimenter
+        * │    │     ┌ dummy
+        * │    │     │   ┌ epistasis
+        * │    │     │   │  ┌ neutrality
+        * │    │     │   │  │    ┌ ruggedness
+        * │    │     │   │  │    │   ┌ max target
+        * │    │     │   │  │    │   │    ┌ dimension (bitstring length) */
+        { 0 /* 1*/, {0,  6, 2,  10, 10,  20 }},
+        { 1 /* 2*/, {0,  6, 2,  18, 10,  20 }},
+        { 2 /* 3*/, {0,  5, 1,  72, 16,  16 }},
+        { 3 /* 4*/, {0,  9, 3,  72, 16,  48 }},
+        { 4 /* 5*/, {0, 23, 1,  90, 25,  25 }},
+        { 5 /* 6*/, {0,  2, 1, 397, 32,  32 }},
+        { 6 /* 7*/, {0, 11, 4,   0, 32, 128 }},
+        { 7 /* 8*/, {0, 14, 4,   0, 32, 128 }},
+        { 8 /* 9*/, {0,  8, 4, 128, 32, 128 }},
+        { 9 /*10*/, {0, 36, 1, 245, 50,  50 }},
+        {10 /*11*/, {0, 21, 2, 256, 50, 100 }},
+        {11 /*12*/, {0, 16, 3, 613, 50, 150 }},
+        {12 /*13*/, {0, 32, 2, 256, 64, 128 }},
+        {13 /*14*/, {0, 21, 3,  16, 64, 192 }},
+        {14 /*15*/, {0, 21, 3, 256, 64, 192 }},
+        {15 /*16*/, {0, 21, 3, 403, 64, 192 }},
+        {16 /*17*/, {0, 52, 4,   2, 64, 256 }},
+        {17 /*18*/, {0, 60, 1,  16, 75,  75 }},
+        {18 /*19*/, {0, 32, 2,   4, 75, 150 }}
+    };
+
     eoFunctorStore store;
 
     eoParser parser(argc, argv, "FastGA interface for iRace");
 
-    const size_t dimension = parser.getORcreateParam<size_t>(1000,
+    /***** Problem parameters *****/
-            "dimension", "Dimension size",
+    auto problem_p = parser.getORcreateParam<size_t>(0,
-            'd', "Problem").value();
+            "problem", "Problem ID",
+            'p', "Problem", /*required=*/true);
+    const size_t problem = problem_p.value();
+    assert(problem < benchmark.size());
 
-    const size_t max_evals = parser.getORcreateParam<size_t>(2 * dimension,
+    // const size_t dimension = parser.getORcreateParam<size_t>(1000,
-            "max-evals", "Maximum number of evaluations",
+    //         "dimension", "Dimension size",
+    //         'd', "Problem").value();
+    const size_t dimension = benchmark[problem].dimension;
+
+    auto instance_p = parser.getORcreateParam<size_t>(0,
+            "instance", "Instance ID",
+            'i', "Instance", /*required=*/false);
+    const size_t instance = instance_p.value();
+
+    const size_t max_evals = parser.getORcreateParam<size_t>(5 * dimension,
+            "max-evals", "Maximum number of evaluations (default: 5*dim, else the given value)",
             'e', "Stopping criterion").value();
 
     const size_t buckets = parser.getORcreateParam<size_t>(100,
             "buckets", "Number of buckets for discretizing the ECDF",
             'b', "Performance estimation").value();
 
+    /***** Generic options *****/
     uint32_t seed =
         parser.getORcreateParam<uint32_t>(0,
             "seed", "Random number seed (0 = epoch)",
@@ -156,33 +370,52 @@ int main(int argc, char* argv[])
     // rng is a global
     rng.reseed(seed);
 
+    bool full_log =
+        parser.getORcreateParam<bool>(0,
+            "full-log", "Log the full search in CSV files"/* (using the IOH profiler format)"*/,
+            'F').value();
 
-    auto problem_p = parser.getORcreateParam<size_t>(0,
+    bool output_mat =
-            "problem", "Problem ID",
+        parser.getORcreateParam<bool>(0,
-            'p', "Problem", /*required=*/true);
+            "output-mat", "Output the aggregated attainment matrix instead of its scalar sum (fancy colormap on stderr, parsable CSV on stdout).",
-    const size_t problem = problem_p.value();
+            'A').value();
 
-
+    /***** populations sizes *****/
-    auto pop_size_p = parser.getORcreateParam<size_t>(1,
+    auto pop_size_p = parser.getORcreateParam<size_t>(5,
             "pop-size", "Population size",
             'P', "Operator Choice", /*required=*/false);
     const size_t pop_size = pop_size_p.value();
+    const size_t pop_size_max = 200;
 
-    auto instance_p = parser.getORcreateParam<size_t>(0,
+    auto offspring_size_p = parser.getORcreateParam<size_t>(0,
-            "instance", "Instance ID",
+            "offspring-size", "Offsprings size (0 = same size than the parents pop, see --pop-size)",
-            'i', "Instance", /*required=*/false);
+            'O', "Operator Choice", /*required=*/false); // Single alternative, not required.
-    const size_t instance = instance_p.value();
+    const size_t offspring_size = offspring_size_p.value();
 
+    size_t generations = static_cast<size_t>(std::floor(
+                static_cast<double>(max_evals) / static_cast<double>(pop_size)));
+    // const size_t generations = std::numeric_limits<size_t>::max();
+    if(generations < 1) {
+        generations = 1;
+    }
+
+    /***** metric parameters *****/
+    auto crossover_rate_p = parser.getORcreateParam<double>(0.5,
+            "crossover-rate", "",
+            'C', "Operator Choice", /*required=*/true);
+    const double crossover_rate = crossover_rate_p.value();
+
+    auto mutation_rate_p = parser.getORcreateParam<double>(0,
+            "mutation-rate", "",
+            'M', "Operator Choice", /*required=*/true);
+    const double mutation_rate = mutation_rate_p.value();
+
+    /***** operators *****/
     auto continuator_p = parser.getORcreateParam<size_t>(0,
             "continuator", "Stopping criterion",
             'o', "Operator Choice", /*required=*/false); // Single alternative, not required.
     const size_t continuator = continuator_p.value();
 
-    auto crossover_rate_p = parser.getORcreateParam<size_t>(0,
-            "crossover-rate", "",
-            'C', "Operator Choice", /*required=*/true);
-    const size_t crossover_rate = crossover_rate_p.value();
-
     auto crossover_selector_p = parser.getORcreateParam<size_t>(0,
             "cross-selector", "How to selects candidates for cross-over",
             's', "Operator Choice", /*required=*/true);
@@ -198,11 +431,6 @@ int main(int argc, char* argv[])
             'a', "Operator Choice", /*required=*/false); // Single alternative, not required.
     const size_t aftercross_selector = aftercross_selector_p.value();
 
-    auto mutation_rate_p = parser.getORcreateParam<size_t>(0,
-            "mutation-rate", "",
-            'M', "Operator Choice", /*required=*/true);
-    const size_t mutation_rate = mutation_rate_p.value();
-
     auto mutation_selector_p = parser.getORcreateParam<size_t>(0,
             "mut-selector", "How to selects candidate for mutation",
             'u', "Operator Choice", /*required=*/true);
@@ -218,12 +446,6 @@ int main(int argc, char* argv[])
             'r', "Operator Choice", /*required=*/true);
     const size_t replacement = replacement_p.value();
 
-    auto offspring_size_p = parser.getORcreateParam<size_t>(0,
-            "offspring-size", "Offsprings size (0 = same size than the parents pop, see --pop-size)",
-            'O', "Operator Choice", /*required=*/false); // Single alternative, not required.
-    const size_t offspring_size = offspring_size_p.value();
-
-
     // Help + Verbose routines
     make_verbose(parser);
     make_help(parser, /*exit_after*/false, std::clog);
@@ -235,36 +457,56 @@ int main(int argc, char* argv[])
         eoEvalFuncPtr<Bits> fake_eval(fake_func);
         eoUniformGenerator<int> fake_gen(0, 1);
         eoInitFixedLength<Bits> fake_init(/*bitstring size=*/1, fake_gen);
-        auto fake_foundry = make_foundry(store, fake_init, fake_eval, max_evals, /*generations=*/ 1);
+        auto fake_foundry = make_foundry(store, fake_init, fake_eval, max_evals, /*generations=*/ 1, 0);
 
+        std::clog << std::endl << "Available operators:" << std::endl;
+        print_operators(        continuator_p, fake_foundry.continuators        , std::clog);
+        print_operators(     crossover_rate_p, fake_foundry.crossover_rates     , std::clog);
+        print_operators( crossover_selector_p, fake_foundry.crossover_selectors , std::clog);
+        print_operators(aftercross_selector_p, fake_foundry.aftercross_selectors, std::clog);
+        print_operators(          crossover_p, fake_foundry.crossovers          , std::clog);
+        print_operators(      mutation_rate_p, fake_foundry.mutation_rates      , std::clog);
+        print_operators(  mutation_selector_p, fake_foundry.mutation_selectors  , std::clog);
+        print_operators(           mutation_p, fake_foundry.mutations           , std::clog);
+        print_operators(        replacement_p, fake_foundry.replacements        , std::clog);
+        print_operators(     offspring_size_p, fake_foundry.offspring_sizes     , std::clog);
+        print_operators(           pop_size_p, (size_t)1, pop_size_max          , std::clog);
+        std::clog << std::endl;
+
+        // If we were to make a DoE sampling numeric parameters,
+        // we would use that many samples:
+        size_t fake_sample_size = 10;
+        std::clog << "With " << fake_sample_size << " samples for numeric parameters..." << std::endl;
         size_t n =
-              fake_foundry.crossover_rates.size()
+              fake_sample_size //crossover_rates
             * fake_foundry.crossover_selectors.size()
             * fake_foundry.crossovers.size()
             * fake_foundry.aftercross_selectors.size()
-            * fake_foundry.mutation_rates.size()
+            * fake_sample_size //mutation_rates
             * fake_foundry.mutation_selectors.size()
             * fake_foundry.mutations.size()
             * fake_foundry.replacements.size()
             * fake_foundry.continuators.size()
-            * fake_foundry.offspring_sizes.size();
+            * fake_sample_size //offspring_sizes
-        std::clog << std::endl;
+            * fake_sample_size //pop_size
-        std::clog << n << " possible algorithms configurations." << std::endl;
+            ;
+        std::clog << "~" << n << " possible algorithms configurations." << std::endl;
 
         std::clog << "Ranges of configurable parameters (redirect the stdout in a file to use it with iRace): " << std::endl;
 
         // Do not print problem and instances, as they are managed separately by irace.
         std::cout << "# name\tswitch\ttype\trange" << std::endl;
-        print_param_range(        continuator_p, fake_foundry.continuators        .size(), std::cout);
+        print_irace(        continuator_p, fake_foundry.continuators        , std::cout);
-        print_param_range(     crossover_rate_p, fake_foundry.crossover_rates     .size(), std::cout);
+        print_irace(     crossover_rate_p, fake_foundry.crossover_rates     , std::cout);
-        print_param_range( crossover_selector_p, fake_foundry.crossover_selectors .size(), std::cout);
+        print_irace( crossover_selector_p, fake_foundry.crossover_selectors , std::cout);
-        print_param_range(aftercross_selector_p, fake_foundry.aftercross_selectors.size(), std::cout);
+        print_irace(aftercross_selector_p, fake_foundry.aftercross_selectors, std::cout);
-        print_param_range(          crossover_p, fake_foundry.crossovers          .size(), std::cout);
+        print_irace(          crossover_p, fake_foundry.crossovers          , std::cout);
-        print_param_range(      mutation_rate_p, fake_foundry.mutation_rates      .size(), std::cout);
+        print_irace(      mutation_rate_p, fake_foundry.mutation_rates      , std::cout);
-        print_param_range(  mutation_selector_p, fake_foundry.mutation_selectors  .size(), std::cout);
+        print_irace(  mutation_selector_p, fake_foundry.mutation_selectors  , std::cout);
-        print_param_range(           mutation_p, fake_foundry.mutations           .size(), std::cout);
+        print_irace(           mutation_p, fake_foundry.mutations           , std::cout);
-        print_param_range(        replacement_p, fake_foundry.replacements        .size(), std::cout);
+        print_irace(        replacement_p, fake_foundry.replacements        , std::cout);
-        print_param_range(     offspring_size_p, fake_foundry.offspring_sizes     .size(), std::cout);
+        print_irace(     offspring_size_p, fake_foundry.offspring_sizes     , std::cout);
+        print_irace(           pop_size_p, 1, pop_size_max                  , std::cout);
 
         // std::ofstream irace_param("fastga.params");
         // irace_param << "# name\tswitch\ttype\tvalues" << std::endl;
@@ -272,91 +514,105 @@ int main(int argc, char* argv[])
         exit(NO_ERROR);
     }
 
-    const size_t generations = static_cast<size_t>(std::floor(
+    eo::log << eo::debug << "Maximum number of evaluations: " << max_evals << std::endl;
-                static_cast<double>(max_evals) / static_cast<double>(pop_size)));
-    // const size_t generations = std::numeric_limits<size_t>::max();
     eo::log << eo::debug << "Number of generations: " << generations << std::endl;
 
-    // Problem configuration code.
-    struct Problem {
-        double dummy;
-        size_t epistasis;
-        size_t neutrality;
-        size_t ruggedness;
-        size_t max_target;
-    };
 
-    std::map<size_t, Problem> problem_config_mapping {
+    /*****************************************************************************
-        { 0, {0,   0, 1, 0, 1000}},
+     * IOH stuff.
-        { 1, {0,   0, 3, 0,  333}},
+     *****************************************************************************/
-        { 2, {0,   0, 5, 0,  200}},
-        { 3, {0,   2, 1, 0, 1000}},
-        { 4, {0,   2, 3, 0,  333}},
-        { 5, {0,   2, 3, 0,  200}},
-        { 6, {0,   4, 1, 0, 1000}},
-        { 7, {0,   4, 3, 0,  333}},
-        { 8, {0,   4, 5, 0,  200}},
-        { 9, {0.5, 0, 1, 0,  500}},
-        {10, {0.5, 0, 3, 0,  166}},
-        {11, {0.5, 0, 5, 0,  100}},
-        {12, {0.5, 2, 1, 0,  500}},
-        {13, {0.5, 2, 3, 0,  166}},
-        {14, {0.5, 2, 5, 0,  100}},
-        {15, {0.5, 4, 1, 0,  500}},
-        {16, {0.5, 4, 3, 0,  166}},
-        {17, {0.5, 4, 5, 0,  100}},
-    };
-
-    assert(0 <= problem and problem < problem_config_mapping.size());
 
     /***** IOH logger *****/
-    auto max_target_para = problem_config_mapping[problem].max_target;
+    auto max_target = benchmark[problem].max_target;
-    IOHprofiler_RangeLinear<size_t> target_range(0, max_target_para, buckets);
+    ioh::logger::eah::Log10Scale<double> target_range(0, max_target, buckets);
-    IOHprofiler_RangeLinear<size_t> budget_range(0, max_evals, buckets);
+    ioh::logger::eah::Log10Scale<size_t> budget_range(0, max_evals, buckets);
-    IOHprofiler_ecdf_logger<int, size_t, size_t> logger(
+    ioh::logger::EAH eah_logger(target_range, budget_range);
-            target_range, budget_range,
-            /*use_known_optimum*/false);
 
-    logger.set_complete_flag(true);
+    ioh::logger::Combine loggers(eah_logger);
-    logger.set_interval(0);
+
-    logger.activate_logger();
+    std::shared_ptr<ioh::logger::FlatFile> csv_logger = nullptr;
+    if(full_log) {
+        // Build up an algorithm name from main parameters.
+        std::ostringstream name;
+        name << "FastGA";
+        for(auto& p : {
+                crossover_selector_p,
+                crossover_p,
+                aftercross_selector_p,
+                mutation_selector_p,
+                mutation_p,
+                replacement_p }) {
+            name << "_" << p.shortName() << "=" << p.getValue();
+        }
+        for(auto& p : {
+                crossover_rate_p,
+                mutation_rate_p }) {
+            name << "_" << p.shortName() << "=" << p.getValue();
+        }
+        for(auto& p : {pop_size_p,
+                offspring_size_p }) {
+            name << "_" << p.shortName() << "=" << p.getValue();
+        }
+        std::clog << name.str() << std::endl;
+
+        // Build up a problem description.
+        std::ostringstream desc;
+        desc << "pb=" << problem << "_";
+        desc << benchmark[problem]; // Use the `operator<<` above.
+        std::clog << desc.str() << std::endl;
+
+        std::filesystem::path folder = desc.str();
+        std::filesystem::create_directories(folder);
+
+        ioh::trigger::OnImprovement on_improvement;
+        ioh::watch::Evaluations evaluations;
+        ioh::watch::TransformedYBest transformed_y_best;
+        std::vector<std::reference_wrapper<ioh::logger::Trigger >> t = {on_improvement};
+        std::vector<std::reference_wrapper<ioh::logger::Property>> w = {evaluations,transformed_y_best};
+        csv_logger = std::make_shared<ioh::logger::FlatFile>(
+            // {std::ref(on_improvement)},
+            // {std::ref(evaluations),std::ref(transformed_y_best)},
+            t, w,
+            name.str(),
+            folder
+        );
+        loggers.append(*csv_logger);
+    }
 
     /***** IOH problem *****/
-    double w_model_suite_dummy_para   = problem_config_mapping[problem].dummy;
+    double w_dummy   = benchmark[problem].dummy;
-    int w_model_suite_epitasis_para   = problem_config_mapping[problem].epistasis;
+    int w_epitasis   = benchmark[problem].epistasis;
-    int w_model_suite_neutrality_para = problem_config_mapping[problem].neutrality;
+    int w_neutrality = benchmark[problem].neutrality;
-    int w_model_suite_ruggedness_para = problem_config_mapping[problem].ruggedness;
+    int w_ruggedness = benchmark[problem].ruggedness;
 
-    W_Model_OneMax w_model_om;
+    // std::string problem_name = "OneMax";
-    std::string problem_name = "OneMax";
+    // problem_name = problem_name
-    problem_name = problem_name
+    //                 + "_D" + std::to_string((int)(w_dummy * dimension))
-                    + "_D" + std::to_string((int)(w_model_suite_dummy_para * dimension))
+    //                 + "_E" + std::to_string(w_epitasis)
-                    + "_E" + std::to_string(w_model_suite_epitasis_para)
+    //                 + "_N" + std::to_string(w_neutrality)
-                    + "_N" + std::to_string(w_model_suite_neutrality_para)
+    //                 + "_R" + std::to_string(w_ruggedness);
-                    + "_R" + std::to_string(w_model_suite_ruggedness_para);
 
-
+    // ioh::problem::wmodel::WModelOneMax w_model_om(
-    /// This must be called to configure the w-model to be tested.
+    WModelFlat w_model_om(
-    w_model_om.set_w_setting(w_model_suite_dummy_para,w_model_suite_epitasis_para,
+        instance,
-                                    w_model_suite_neutrality_para,w_model_suite_ruggedness_para);
+        dimension, 
-
+        w_dummy,
-    /// Set problem_name based on the configuration.
+        w_epitasis,
-    w_model_om.IOHprofiler_set_problem_name(problem_name);
+        w_neutrality,
-
+        w_ruggedness);
-    /// Set problem_id as 1
-    w_model_om.IOHprofiler_set_problem_id(problem); // FIXME check what that means
-    // w_model_om.IOHprofiler_set_instance_id(instance); // FIXME changing the instance seems to change the target upper bound.
-
-    /// Set dimension.
-    w_model_om.IOHprofiler_set_number_of_variables(dimension);
 
     /***** Bindings *****/
-    logger.track_problem(w_model_om);
+    w_model_om.attach_logger(loggers);
 
-    eoEvalIOHproblem<Bits> onemax_pb(w_model_om, logger);
+    /*****************************************************************************
+     * Binding everything together.
+     *****************************************************************************/
+
+    eoEvalIOHproblem<Bits> onemax_pb(w_model_om, loggers);
 
     // eoEvalPrint<Bits> eval_print(onemax_pb, std::clog, "\n");
-    eoEvalFuncCounter<Bits> eval_count(onemax_pb);
+    // eoEvalFuncCounter<Bits> eval_count(onemax_pb);
+    eoEvalCounterThrowException<Bits> eval_count(onemax_pb, max_evals);
 
     eoPopLoopEval<Bits> onemax_eval(eval_count);
 
@@ -364,9 +620,9 @@ int main(int argc, char* argv[])
 
     eoBooleanGenerator<int> bgen;
     eoInitFixedLength<Bits> onemax_init(/*bitstring size=*/dimension, bgen);
-    auto& foundry = make_foundry(store, onemax_init, eval_count, max_evals - pop_size, generations);
+    auto& foundry = make_foundry(store, onemax_init, eval_count, max_evals, generations, max_target);
 
-    Ints encoded_algo(foundry.size());
+    eoAlgoFoundry<Bits>::Encodings encoded_algo(foundry.size());
 
     encoded_algo[foundry.crossover_rates     .index()] = crossover_rate;
     encoded_algo[foundry.crossover_selectors .index()] = crossover_selector;
@@ -379,39 +635,55 @@ int main(int argc, char* argv[])
     encoded_algo[foundry.continuators        .index()] = continuator;
     encoded_algo[foundry.offspring_sizes     .index()] = offspring_size;
 
-    std::clog << "Encoded algorithm:" << std::endl;
+    // std::clog << "Encoded algorithm:" << std::endl;
     foundry.select(encoded_algo);
     std::clog << foundry.name() << std::endl;
 
-    // // Evaluation of a forged encoded_algo on the sub-problem
+    /*****************************************************************************
-    // eoEvalFoundryFastGA<Ints, Bits> eval_foundry(
+     * Run and output results.
-    //         foundry, pop_size,
+     *****************************************************************************/
-    //         onemax_init, onemax_eval,
-    //         /*penalization=*/ dimension, // Worst case penalization.
-    //         /*normalized=*/ false); // Use direct integer encoding.
-    //
-    // // Actually instanciate and run the algorithm.
-    // eval_foundry(encoded_algo);
 
     eoPop<Bits> pop;
     pop.append(pop_size, onemax_init);
-    onemax_eval(pop,pop);
+    try {
-    foundry(pop); // Actually run the selected algorithm.
+        onemax_eval(pop,pop);
+        foundry(pop); // Actually run the selected algorithm.
+        
+    } catch(eoMaxEvalException & e) {
+        eo::log << eo::debug << "Reached maximum evaluations: " << eval_count.getValue() << " / " << max_evals << std::endl;
+    }
 
     /***** IOH perf stats *****/
-    IOHprofiler_ecdf_sum ecdf_sum;
+    double perf = ioh::logger::eah::stat::under_curve::volume(eah_logger);
-    // iRace expects minimization
-    long perf = ecdf_sum(logger.data());
 
-    // assert(0 < perf and perf <= buckets*buckets);
+    if(perf == 0 or perf > max_target * max_evals * 1.0) {
-    if(perf <= 0 or buckets*buckets < perf) {
+        std::cerr << "WARNING: illogical performance? " << perf
-        std::cerr << "WARNING: illogical performance: " << perf
+                  << " Check the bounds or the algorithm." << std::endl;
-                  << ", check the bounds or the algorithm." << std::endl;
     }
 
     // std::clog << "After " << eval_count.getValue() << " / " << max_evals << " evaluations" << std::endl;
 
-    // Output
+    if(output_mat) {
-    std::cout << -1 * perf << std::endl;
+        std::vector<std::vector<double>> mat = ioh::logger::eah::stat::distribution(eah_logger);
 
+        // Fancy color map on clog.
+        std::clog << ioh::logger::eah::colormap(mat) << std::endl;
+
+        // Parsable CSV on cout.
+        std::clog << "Attainment matrix distribution: " << std::endl;
+        assert(mat.size() > 0);
+        assert(mat[0].size() > 1);
+        for(size_t i = mat.size()-1; i > 0; --i) {
+            assert(mat[i].size() >= 1);
+            std::cout << mat[i][0];
+            for(size_t j = 1; j < mat[i].size(); ++j) {
+                std::cout << "," << mat[i][j];
+            }
+            std::cout << std::endl;
+        }
+
+    } else {
+        // iRace expects minimization
+        std::cout << -1 * perf << std::endl;
+    }
 }

eo/contrib/irace/fastga.sindef

@@ -0,0 +1,64 @@
+https://github.com/drbild/json2yaml.gitBootstrap: library
+From: ubuntu:20.04
+
+%post
+
+    # Dependencies
+    apt -y update
+    apt -y install software-properties-common
+    add-apt-repository universe
+    apt -y update
+    apt -y dist-upgrade
+    apt -y install git clang-9 cmake make libeigen3-dev
+    apt clean
+    update-alternatives --install /usr/bin/c++ c++ /usr/bin/clang++-9 90
+    update-alternatives --set c++ /usr/bin/clang++-9
+
+    # Temporary directory where we are going to build everything.
+    tmpdir=$(mktemp -d)
+    mkdir -p ${tmpdir}/fastga/
+
+    # Build IOH
+    cd ${tmpdir}/fastga/
+    git clone --branch feat+EAF --single-branch --recurse-submodules https://github.com/jdreo/IOHexperimenter.git
+    cd IOHexperimenter
+    mkdir -p release
+    cd release
+    cmake -D CMAKE_BUILD_TYPE=Release -D BUILD_TESTS=OFF -D BUILD_EXAMPLE=OFF -D BUILD_GMOCK=OFF ..
+    make
+
+    # Build Paradiseo
+    cd ${tmpdir}/fastga/
+    git clone --branch feat+num_foundry --single-branch https://github.com/jdreo/paradiseo.git
+    cd paradiseo
+    touch LICENSE
+    mkdir -p release
+    cd release
+    cmake -D CMAKE_BUILD_TYPE=Release -EDO=ON -EDO_USE_LIB=Eigen3 ..
+    make
+
+    # Build FastGA
+    cd ${tmpdir}/fastga/paradiseo/eo/contrib/irace/
+    mkdir -p release
+    cd release
+    cmake -D CMAKE_BUILD_TYPE=Release -D IOH_ROOT=${tmpdir}/fastga/IOHexperimenter/ -D PARADISEO_ROOT=${tmpdir}/fastga/paradiseo/ -D PARADISEO_BUILD=${tmpdir}/fastga/paradiseo/release/ ..
+    make
+
+    # Install FastGA
+    cp fastga /usr/local/bin/
+
+    # Clean-up
+    rm -rf ${tmpdir}
+    apt -y purge software-properties-common git clang-9 cmake make libeigen3-dev
+    apt -y --purge autoremove
+    apt -y autoclean
+    apt clean
+
+%environment
+
+%runscript
+    /usr/local/bin/fastga $*
+    
+%labels
+    Author Quentin Renau
+    Author Johann Dreo

eo/contrib/irace/irace-config/example.scen

@@ -15,7 +15,7 @@ execDir = "."
 
 ## File to save tuning results as an R dataset, either absolute path or
 ## relative to execDir.
-# logFile = "./irace.Rdata"
+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,
@@ -62,8 +62,8 @@ targetRunner = "./target-runner"
 
 ## Maximum number of runs (invocations of targetRunner) that will be
 ## performed. It determines the maximum budget of experiments for the
-## tuning.
+## tuning. (minimum: 180)
-maxExperiments = 2000
+maxExperiments = 100000
 
 ## Maximum total execution time in seconds for the executions of
 ## targetRunner. targetRunner must return two values: cost and time.
@@ -129,13 +129,13 @@ digits = 2
 
 ## Number of calls to targetRunner to execute in parallel. Values 0 or 1
 ## mean no parallelization.
-# parallel = 0
+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
+loadBalancing = 0
 
 ## Enable/disable MPI. Use Rmpi to execute targetRunner in parallel
 ## (parameter parallel is the number of slaves).

eo/contrib/irace/irace-config/target-runner

@@ -25,7 +25,7 @@ error() {
 EXE="./fastga"
 LOG_DIR="irace_logs"
 
-FIXED_PARAMS="--problem=0"
+FIXED_PARAMS="--problem={{PROBLEM}}"
 
 CONFIG_ID=$1
 INSTANCE_ID=$2

eo/contrib/irace/onlymutga.cpp

@@ -0,0 +1,770 @@
+#include <filesystem>
+#include <iostream>
+#include <cstdlib>
+#include <string>
+#include <memory>
+
+#include <eo>
+#include <ga.h>
+#include <utils/checkpointing>
+#include <eoInt.h>
+#include <problems/eval/eoEvalIOH.h>
+
+#include <ioh.hpp>
+
+/*****************************************************************************
+ * ParadisEO algorithmic grammar definition.
+ *****************************************************************************/
+
+// using Particle = eoRealParticle<eoMaximizingFitness>;
+using Ints = eoInt<eoMaximizingFitnessT<int>, size_t>;
+using Bits = eoBit<eoMaximizingFitnessT<int>, int>;
+
+// by enumerating candidate operators and their parameters.
+eoAlgoFoundryFastGA<Bits>& make_foundry(
+        eoFunctorStore& store,
+        eoInit<Bits>& init,
+        eoEvalFunc<Bits>& eval,
+        const size_t max_evals,
+        const size_t generations,
+        const double optimum,
+        const size_t pop_size,
+        const size_t offspring_size,
+        std::vector<double> cl_sizes,
+        std::vector<double> cl_values
+    )
+{
+    // FIXME using max_restarts>1 does not allow to honor max evals.
+    auto& foundry = store.pack< eoAlgoFoundryFastGA<Bits> >(init, eval, max_evals, /*max_restarts=*/1);
+
+    /***** Continuators ****/
+    auto& fitcont = store.pack< eoFitContinue<Bits> >(optimum);
+    auto& gencont = store.pack< eoGenContinue<Bits> >(generations);
+    auto combconts = std::make_shared< std::vector<eoContinue<Bits>*> >();
+    combconts->push_back( &fitcont );
+    combconts->push_back( &gencont );
+    foundry.continuators.add< eoCombinedContinue<Bits> >( *combconts );
+    // for(size_t i=1; i<10; i++) {
+    //     foundry.continuators.add< eoGenContinue<Bits> >(i);
+    // }
+    // for(size_t i=10; i < 100; i+=2 ) {
+    //     foundry.continuators.add< eoSteadyFitContinue<Bits> >(10,i);
+    // }
+
+    // for(double i=0.0; i<1.0; i+=0.2) {
+    //     foundry.crossover_rates.add<double>(i);
+    //     foundry.mutation_rates.add<double>(i);
+    // }
+
+    /***** Offsprings size *****/
+    // for(size_t i=5; i<100; i+=10) {
+    //     foundry.offspring_sizes.add<size_t>(i);
+    // }
+
+    foundry.offspring_sizes.setup(0,offspring_size); // 0 = use parents fixed pop size.
+
+    /***** Crossovers ****/
+    for(double i=0.1; i<1.0; i+=0.2) {
+        foundry.crossovers.add< eoUBitXover<Bits> >(i); // preference over 1
+    }
+    for(size_t i=1; i < 10; i+=2) {
+
+        foundry.crossovers.add< eoNPtsBitXover<Bits> >(i); // nb of points
+    }
+    // foundry.crossovers.add< eo1PtBitXover<Bits> >(); // Same as NPts=1
+
+    /***** Mutations ****/
+    /* ######################## Removed by Alexis ######################## */
+    /*
+    double p = 1.0; // Probability of flipping each bit.
+    // proba of flipping k bits, k drawn in uniform distrib
+    foundry.mutations.add< eoUniformBitMutation<Bits> >(p);
+    // proba of flipping k bits, k drawn in binomial distrib
+    foundry.mutations.add< eoStandardBitMutation<Bits> >(p);
+    // proba of flipping k bits, k drawn in binomial distrib, minus zero
+    foundry.mutations.add< eoConditionalBitMutation<Bits> >(p);
+    // proba of flipping k bits, k drawn in binomial distrib, changing zeros to one
+    foundry.mutations.add< eoShiftedBitMutation<Bits> >(p);
+    // proba of flipping k bits, k drawn in normal distrib
+    foundry.mutations.add< eoNormalBitMutation<Bits> >(p);
+    // proba of flipping k bits, k drawn in powerlaw distrib
+    foundry.mutations.add< eoFastBitMutation<Bits> >(p);
+    for(size_t i=1; i < 11; i+=2) {
+        // mutate k bits without duplicates
+        foundry.mutations.add< eoDetSingleBitFlip<Bits> >(i);
+    }
+    */
+    /* ######################## RbA END ######################## */
+    
+    /* ######################## Add by Alexis ######################## */
+    foundry.mutations.add< eoBucketBitMutation<Bits> >(cl_sizes, cl_values);
+    /* ######################## AbA END ######################## */
+
+    /***** Selectors *****/
+    for(eoOperatorFoundry<eoSelectOne<Bits>>& ops :
+        {std::ref(foundry.crossover_selectors),
+         std::ref(foundry.mutation_selectors) }) {
+
+        ops.add< eoRandomSelect<Bits> >();
+        ops.add< eoStochTournamentSelect<Bits> >(0.5);
+        ops.add< eoSequentialSelect<Bits> >();
+        ops.add< eoProportionalSelect<Bits> >();
+        for(size_t i=2; i < 11; i+=4) {
+            ops.add< eoDetTournamentSelect<Bits> >(i);
+        }
+    }
+
+    foundry.aftercross_selectors.add< eoRandomSelect<Bits> >();
+
+
+    /***** Replacements ****/
+    /* ######################## Removed by Alexis ######################## */
+    /*
+    foundry.replacements.add< eoPlusReplacement<Bits> >();
+    foundry.replacements.add< eoCommaReplacement<Bits> >();
+    foundry.replacements.add< eoSSGAWorseReplacement<Bits> >();
+    for(double i=0.51; i<0.92; i+=0.2) {
+        foundry.replacements.add< eoSSGAStochTournamentReplacement<Bits> >(i);
+    }
+    for(size_t i=2; i < 11; i+=2) {
+        foundry.replacements.add< eoSSGADetTournamentReplacement<Bits> >(i);
+    }
+     */
+     /* ######################## RbA END ######################## */
+     
+     /* ######################## Add by Alexis ######################## */
+    //foundry.replacements.add< eoSSGADetTournamentReplacement<Bits> >(1);
+    foundry.replacements.add< eoCommaReplacement<Bits> >();
+     /* ######################## AbA END ######################## */
+    
+    return foundry;
+}
+
+/*****************************************************************************
+ * irace helper functions.
+ *****************************************************************************/
+
+Bits::Fitness fake_func(const Bits&) { return 0; }
+
+void print_irace_categorical(const eoParam& param, const size_t slot_size, std::string type="c", std::ostream& out = std::cout)
+{
+    // If there is no choice to be made on this operator, comment it out.
+    if(slot_size - 1 <= 0) {
+        out << "# ";
+    }
+
+    // irace doesn't support "-" in names.
+    std::string irace_name = param.longName();
+    irace_name.erase(std::remove(irace_name.begin(), irace_name.end(), '-'), irace_name.end());
+
+    out << irace_name
+        << "\t\"--" << param.longName() << "=\""
+        << "\t" << type;
+
+    out << "\t(0";
+    for(size_t i=1; i<slot_size; ++i) {
+        out << "," << i;
+    }
+    out << ")" << std::endl;
+}
+
+template<class T>
+void print_irace_ranged(const eoParam& param, const T min, const T max, std::string type="r", std::ostream& out = std::cout)
+{
+    // If there is no choice to be made on this operator, comment it out.
+    if(max - min <= 0) {
+        out << "# ";
+    }
+
+    // irace doesn't support "-" in names.
+    std::string irace_name = param.longName();
+    irace_name.erase(std::remove(irace_name.begin(), irace_name.end(), '-'), irace_name.end());
+
+    out << irace_name
+        << "\t\"--" << param.longName() << "=\""
+        << "\t" << type;
+
+    if(max-min <= 0) {
+        out << "\t(?)";
+    } else {
+        out << "\t(" << min << "," << max << ")";
+    }
+    out << std::endl;
+}
+
+
+template<class ITF>
+void print_irace_oper(const eoParam& param, const eoOperatorFoundry<ITF>& op_foundry, std::ostream& out = std::cout)
+{
+    print_irace_categorical(param, op_foundry.size(), "c", out);
+}
+
+// FIXME generalize to any scalar type with enable_if
+// template<class ITF>
+void print_irace_param(
+    const eoParam& param,
+    // const eoParameterFoundry<typename std::enable_if< std::is_floating_point<ITF>::value >::type>& op_foundry,
+    const eoParameterFoundry<double>& op_foundry,
+    std::ostream& out)
+{
+    print_irace_ranged(param, op_foundry.min(), op_foundry.max(), "r", out);
+}
+
+// template<class ITF>
+void print_irace_param(
+    const eoParam& param,
+    // const eoParameterFoundry<typename std::enable_if< std::is_integral<ITF>::value >::type>& op_foundry,
+    const eoParameterFoundry<size_t>& op_foundry,
+    std::ostream& out)
+{
+    print_irace_ranged(param, op_foundry.min(), op_foundry.max(), "i", out);
+}
+
+
+template<class ITF>
+void print_irace(const eoParam& param, const eoOperatorFoundry<ITF>& op_foundry, std::ostream& out = std::cout)
+{
+    print_irace_oper<ITF>(param, op_foundry, out);
+}
+
+template<class ITF>
+void print_irace(const eoParam& param, const eoParameterFoundry<ITF>& op_foundry, std::ostream& out = std::cout)
+{
+    print_irace_param/*<ITF>*/(param, op_foundry, out);
+}
+
+void print_irace(const eoParam& param, const size_t min, const size_t max, std::ostream& out = std::cout)
+{
+    print_irace_ranged(param, min, max, "i", out);
+}
+
+void print_operator_typed(const eoFunctorBase& op, std::ostream& out)
+{
+    out << op.className();
+}
+
+void print_operator_typed(const double& op, std::ostream& out)
+{
+    out << op;
+}
+
+template<class ITF>
+void print_operators(const eoParam& param, eoOperatorFoundry<ITF>& op_foundry, std::ostream& out = std::cout, std::string indent="  ")
+{
+    out << indent << op_foundry.size() << " " << param.longName() << ":" << std::endl;
+    for(size_t i=0; i < op_foundry.size(); ++i) {
+        out << indent << indent << i << ": ";
+        auto& op = op_foundry.instantiate(i);
+        print_operator_typed(op, out);
+        out << std::endl;
+    }
+}
+
+template<class T>
+void print_operators(const eoParam& param, T min, T max, std::ostream& out = std::cout, std::string indent="  ")
+{
+    out << indent << "[" << min << "," << max << "] " << param.longName() << "." << std::endl;
+}
+
+template<class ITF>
+void print_operators(const eoParam& param, eoParameterFoundry<ITF>& op_foundry, std::ostream& out = std::cout, std::string indent="  ")
+{
+    print_operators(param, op_foundry.min(), op_foundry.max(), out, indent);
+}
+
+// Problem configuration.
+struct Problem {
+    double dummy;
+    size_t epistasis;
+    size_t neutrality;
+    size_t ruggedness;
+    size_t max_target;
+    size_t dimension;
+    friend std::ostream& operator<<(std::ostream& os, const Problem& pb);
+};
+
+std::ostream& operator<<(std::ostream& os, const Problem& pb)
+{
+    os << "u=" << pb.dummy << "_"
+       << "e=" << pb.epistasis << "_"
+       << "n=" << pb.neutrality << "_"
+       << "r=" << pb.ruggedness << "_"
+       << "t=" << pb.max_target << "_"
+       << "d=" << pb.dimension;
+    return os;
+}
+
+/*****************************************************************************
+ * IOH problem adaptation.
+ *****************************************************************************/
+
+class WModelFlat : public ioh::problem::wmodel::WModelOneMax
+{
+    public:
+        WModelFlat(const int instance, const int n_variables,
+                   const double dummy_para, const int epistasis_para, const int neutrality_para,
+                   const int ruggedness_para)
+        : WModelOneMax(instance, n_variables, dummy_para, epistasis_para, neutrality_para, ruggedness_para)
+        { }
+
+    protected:
+        double transform_objectives(const double y) override
+        { // Disable objective function shift & scaling.
+            return y;
+        }
+};
+
+/*****************************************************************************
+ * Command line interface.
+ *****************************************************************************/
+
+int main(int argc, char* argv[])
+{
+    /***** Global parameters. *****/
+    enum { NO_ERROR = 0, ERROR_USAGE = 100 };
+
+    std::map<size_t, Problem> benchmark {
+       /* ┌ problem index in the map
+        * │    ┌ problem ID in IOH experimenter
+        * │    │     ┌ dummy
+        * │    │     │   ┌ epistasis
+        * │    │     │   │  ┌ neutrality
+        * │    │     │   │  │    ┌ ruggedness
+        * │    │     │   │  │    │   ┌ max target
+        * │    │     │   │  │    │   │    ┌ dimension (bitstring length) */
+        { 0 /* 1*/, {0,  6, 2,  10, 10,  20 }},
+        { 1 /* 2*/, {0,  6, 2,  18, 10,  20 }},
+        { 2 /* 3*/, {0,  5, 1,  72, 16,  16 }},
+        { 3 /* 4*/, {0,  9, 3,  72, 16,  48 }},
+        { 4 /* 5*/, {0, 23, 1,  90, 25,  25 }},
+        { 5 /* 6*/, {0,  2, 1, 397, 32,  32 }},
+        { 6 /* 7*/, {0, 11, 4,   0, 32, 128 }},
+        { 7 /* 8*/, {0, 14, 4,   0, 32, 128 }},
+        { 8 /* 9*/, {0,  8, 4, 128, 32, 128 }},
+        { 9 /*10*/, {0, 36, 1, 245, 50,  50 }},
+        {10 /*11*/, {0, 21, 2, 256, 50, 100 }},
+        {11 /*12*/, {0, 16, 3, 613, 50, 150 }},
+        {12 /*13*/, {0, 32, 2, 256, 64, 128 }},
+        {13 /*14*/, {0, 21, 3,  16, 64, 192 }},
+        {14 /*15*/, {0, 21, 3, 256, 64, 192 }},
+        {15 /*16*/, {0, 21, 3, 403, 64, 192 }},
+        {16 /*17*/, {0, 52, 4,   2, 64, 256 }},
+        {17 /*18*/, {0, 60, 1,  16, 75,  75 }},
+        {18 /*19*/, {0, 32, 2,   4, 75, 150 }},
+        {19 /*20?*/, {0,  0, 0,   0,  0,  64 }} // Add by Alexis
+    };
+
+    eoFunctorStore store;
+
+    eoParser parser(argc, argv, "OnlymutGA interface for iRace");
+
+    /***** Problem parameters *****/
+    auto problem_p = parser.getORcreateParam<size_t>(0,
+            "problem", "Problem ID",
+            'p', "Problem", /*required=*/true);
+    const size_t problem = problem_p.value();
+    assert(0 <= problem and problem < benchmark.size());
+
+    // const size_t dimension = parser.getORcreateParam<size_t>(1000,
+    //         "dimension", "Dimension size",
+    //         'd', "Problem").value();
+    const size_t dimension = benchmark[problem].dimension;
+
+    auto instance_p = parser.getORcreateParam<size_t>(0,
+            "instance", "Instance ID",
+            'i', "Instance", /*required=*/false);
+    const size_t instance = instance_p.value();
+
+    const size_t max_evals = parser.getORcreateParam<size_t>(5 * dimension,
+            "max-evals", "Maximum number of evaluations (default: 5*dim, else the given value)",
+            'e', "Stopping criterion").value();
+
+    const size_t buckets = parser.getORcreateParam<size_t>(100,
+            "buckets", "Number of buckets for discretizing the ECDF",
+            'b', "Performance estimation").value();
+
+    /***** Generic options *****/
+    uint32_t seed =
+        parser.getORcreateParam<uint32_t>(0,
+            "seed", "Random number seed (0 = epoch)",
+            'S').value();
+    if(seed == 0) {
+        seed = time(0);
+    }
+    // rng is a global
+    rng.reseed(seed);
+
+    bool full_log =
+        parser.getORcreateParam<bool>(0,
+            "full-log", "Log the full search in CSV files"/* (using the IOH profiler format)"*/,
+            'F').value();
+
+    bool output_mat =
+        parser.getORcreateParam<bool>(0,
+            "output-mat", "Output the aggregated attainment matrix instead of its scalar sum (fancy colormap on stderr, parsable CSV on stdout).",
+            'A').value();
+
+    /***** populations sizes *****/
+    auto pop_size_p = parser.getORcreateParam<size_t>(1,
+            "pop-size", "Population size",
+            'P', "Operator Choice", /*required=*/false); // Changed by Alexis: 5 -> 1
+    const size_t pop_size = pop_size_p.value();
+    const size_t pop_size_max = 10;
+
+    auto offspring_size_p = parser.getORcreateParam<size_t>(10,
+            "offspring-size", "Offsprings size (0 = same size than the parents pop, see --pop-size)",
+            'O', "Operator Choice", /*required=*/false); // Single alternative, not required. // Changed by Alexis: 0 -> 10
+    const size_t offspring_size = offspring_size_p.value();
+
+    size_t generations = static_cast<size_t>(std::floor(
+                static_cast<double>(max_evals) / static_cast<double>(pop_size)));
+    // const size_t generations = std::numeric_limits<size_t>::max();
+    if(generations < 1) {
+        generations = 1;
+    }
+
+    /***** metric parameters *****/
+    auto crossover_rate_p = parser.getORcreateParam<double>(0,
+            "crossover-rate", "",
+            'C', "Operator Choice", /*required=*/false); // Changed by Alexis: 0.5 -> 0 | true -> false
+    const double crossover_rate = crossover_rate_p.value();
+
+    auto mutation_rate_p = parser.getORcreateParam<double>(1,
+            "mutation-rate", "",
+            'M', "Operator Choice", /*required=*/false); // Changed by Alexis: 0 -> 1 | true -> false
+    const double mutation_rate = mutation_rate_p.value();
+
+    /***** operators *****/
+    auto continuator_p = parser.getORcreateParam<size_t>(0,
+            "continuator", "Stopping criterion",
+            'o', "Operator Choice", /*required=*/false); // Single alternative, not required.
+    const size_t continuator = continuator_p.value();
+
+    auto crossover_selector_p = parser.getORcreateParam<size_t>(0,
+            "cross-selector", "How to selects candidates for cross-over",
+            's', "Operator Choice", /*required=*/false); // Changed by Alexis: true -> false
+    const size_t crossover_selector = crossover_selector_p.value();
+
+    auto crossover_p = parser.getORcreateParam<size_t>(0,
+            "crossover", "",
+            'c', "Operator Choice", /*required=*/false); // Changed by Alexis: true -> false
+    const size_t crossover = crossover_p.value();
+
+    auto aftercross_selector_p = parser.getORcreateParam<size_t>(0,
+            "aftercross-selector", "How to selects between the two individuals altered by cross-over which one will mutate",
+            'a', "Operator Choice", /*required=*/false); // Single alternative, not required.
+    const size_t aftercross_selector = aftercross_selector_p.value();
+
+    auto mutation_selector_p = parser.getORcreateParam<size_t>(0,
+            "mut-selector", "How to selects candidate for mutation",
+            'u', "Operator Choice", /*required=*/false); // Changed by Alexis: true -> false
+    const size_t mutation_selector = mutation_selector_p.value();
+
+    auto mutation_p = parser.getORcreateParam<size_t>(0,
+            "mutation", "",
+            'm', "Operator Choice", /*required=*/false); // Changed by Alexis: true -> false
+    const size_t mutation = mutation_p.value();
+
+    auto replacement_p = parser.getORcreateParam<size_t>(0,
+            "replacement", "",
+            'r', "Operator Choice", /*required=*/false); // Changed by Alexis: true -> false
+    const size_t replacement = replacement_p.value();
+    
+    /* ######################## Add by Alexis ######################## */
+    
+    auto cl_values_p = parser.getORcreateParam<std::string>("0.8,0.2",
+            "cl-probs", "Probabilities of each part for the custom law (sum = 1)",
+            'y', "Operator Choice", false);
+    
+    std::string cl_v = cl_values_p.value();
+    std::vector<double> cl_probs = std::vector<double>();
+    
+    std::string sep = ",";
+
+    size_t pos = 0;
+    std::string token;
+    while ((pos = cl_v.find(sep)) != std::string::npos) {
+        token = cl_v.substr(0, pos);
+        cl_probs.push_back(std::stod(token));
+        cl_v.erase(0, pos + sep.length());
+    }
+    cl_probs.push_back(std::stod(cl_v));
+
+    auto cl_sizes_p = parser.getORcreateParam<std::string>("0.5,0.5",
+            "cl-sizes", "Proportion sizes of each part for the custom law (sum = 1)",
+            'x', "Operator Choice", false);
+    std::string cl_s = cl_sizes_p.value();
+    std::vector<double> cl_sizes = std::vector<double>();
+    
+    pos = 0;
+    while ((pos = cl_s.find(sep)) != std::string::npos) {
+        token = cl_s.substr(0, pos);
+        cl_sizes.push_back(std::stod(token));
+        cl_s.erase(0, pos + sep.length());
+    }
+    cl_sizes.push_back(std::stod(cl_s));
+    /* ######################## AbA END ######################## */
+    
+    // Help + Verbose routines
+    make_verbose(parser);
+    make_help(parser, /*exit_after*/false, std::clog);
+
+    if(parser.userNeedsHelp()) {
+
+        // Fake operators, just to be able to call make_foundry
+        // to get the configured operators slots.
+        eoEvalFuncPtr<Bits> fake_eval(fake_func);
+        eoUniformGenerator<int> fake_gen(0, 1);
+        eoInitFixedLength<Bits> fake_init(/*bitstring size=*/1, fake_gen);
+        auto fake_foundry = make_foundry(store, fake_init, fake_eval, max_evals, /*generations=*/ 1, 0, pop_size_max, offspring_size, cl_sizes, cl_probs);
+
+        std::clog << std::endl << "Available operators:" << std::endl;
+        
+        print_operators(        continuator_p, fake_foundry.continuators        , std::clog);
+        print_operators(     crossover_rate_p, fake_foundry.crossover_rates     , std::clog);
+        print_operators( crossover_selector_p, fake_foundry.crossover_selectors , std::clog);
+        print_operators(aftercross_selector_p, fake_foundry.aftercross_selectors, std::clog);
+        print_operators(          crossover_p, fake_foundry.crossovers          , std::clog);
+        print_operators(      mutation_rate_p, fake_foundry.mutation_rates      , std::clog);
+        print_operators(  mutation_selector_p, fake_foundry.mutation_selectors  , std::clog);
+        print_operators(           mutation_p, fake_foundry.mutations           , std::clog);
+        print_operators(        replacement_p, fake_foundry.replacements        , std::clog);
+        print_operators(     offspring_size_p, fake_foundry.offspring_sizes     , std::clog);
+        print_operators(           pop_size_p, (size_t)1, pop_size_max          , std::clog);
+        /* ######################## Add by Alexis ######################## */
+        print_operators(           cl_values_p, "(1)", "(0.01,...,0.99)"        , std::clog);
+        print_operators(           cl_sizes_p,  "(1)", "(0.01,...,0.99)"        , std::clog);
+        /* ######################## AbA END ######################## */
+        std::clog << std::endl;
+
+        
+
+        // If we were to make a DoE sampling numeric parameters,
+        // we would use that many samples:
+        size_t fake_sample_size = 10;
+        std::clog << "With " << fake_sample_size << " samples for numeric parameters..." << std::endl;
+        size_t n =
+              fake_sample_size //crossover_rates
+            * fake_foundry.crossover_selectors.size()
+            * fake_foundry.crossovers.size()
+            * fake_foundry.aftercross_selectors.size()
+            * fake_sample_size //mutation_rates
+            * fake_foundry.mutation_selectors.size()
+            * fake_foundry.mutations.size()
+            * fake_foundry.replacements.size()
+            * fake_foundry.continuators.size()
+            * fake_sample_size //offspring_sizes
+            * fake_sample_size //pop_size
+            ;
+        std::clog << "~" << n << " possible algorithms configurations." << std::endl;
+
+        std::clog << "Ranges of configurable parameters (redirect the stdout in a file to use it with iRace): " << std::endl;
+
+        // Do not print problem and instances, as they are managed separately by irace.
+        std::cout << "# name\tswitch\ttype\trange" << std::endl;
+        /* ######################## Removed by Alexis ######################## */
+        /*
+        print_irace(        continuator_p, fake_foundry.continuators        , std::cout);
+        print_irace(     crossover_rate_p, fake_foundry.crossover_rates     , std::cout);
+        print_irace( crossover_selector_p, fake_foundry.crossover_selectors , std::cout);
+        print_irace(aftercross_selector_p, fake_foundry.aftercross_selectors, std::cout);
+        print_irace(          crossover_p, fake_foundry.crossovers          , std::cout);
+        print_irace(      mutation_rate_p, fake_foundry.mutation_rates      , std::cout);
+        print_irace(  mutation_selector_p, fake_foundry.mutation_selectors  , std::cout);
+        print_irace(           mutation_p, fake_foundry.mutations           , std::cout);
+        print_irace(        replacement_p, fake_foundry.replacements        , std::cout);
+        print_irace(     offspring_size_p, fake_foundry.offspring_sizes     , std::cout);
+        print_irace(           pop_size_p, 1, pop_size_max                  , std::cout);
+        */
+        /* ######################## RbA END ######################## */
+        
+        //std::ofstream irace_param("fastga.params");
+        //irace_param << "# name\tswitch\ttype\tvalues" << std::endl;
+
+        exit(NO_ERROR);
+    }
+
+    eo::log << eo::debug << "Maximum number of evaluations: " << max_evals << std::endl;
+    eo::log << eo::debug << "Number of generations: " << generations << std::endl;
+
+
+    /*****************************************************************************
+     * IOH stuff.
+     *****************************************************************************/
+
+    /***** IOH logger *****/
+    auto max_target = benchmark[problem].max_target;
+    ioh::logger::eah::Log10Scale<double> target_range(0, max_target, buckets);
+    ioh::logger::eah::Log10Scale<size_t> budget_range(0, max_evals, buckets);
+    ioh::logger::EAH eah_logger(target_range, budget_range);
+
+    ioh::logger::Combine loggers(eah_logger);
+
+    std::shared_ptr<ioh::logger::FlatFile> csv_logger = nullptr;
+    if(full_log) {
+        // Build up an algorithm name from main parameters.
+        std::ostringstream name;
+        name << "OnlymutGA";
+        for(auto& p : {
+                crossover_selector_p,
+                crossover_p,
+                aftercross_selector_p,
+                mutation_selector_p,
+                mutation_p,
+                replacement_p }) {
+            name << "_" << p.shortName() << "=" << p.getValue();
+        }
+        for(auto& p : {
+                crossover_rate_p,
+                mutation_rate_p }) {
+            name << "_" << p.shortName() << "=" << p.getValue();
+        }
+        for(auto& p : {pop_size_p,
+                offspring_size_p }) {
+            name << "_" << p.shortName() << "=" << p.getValue();
+        }
+        std::clog << name.str() << std::endl;
+
+        // Build up a problem description.
+        std::ostringstream desc;
+        desc << "pb=" << problem << "_";
+        desc << benchmark[problem]; // Use the `operator<<` above.
+        std::clog << desc.str() << std::endl;
+
+        std::filesystem::path folder = desc.str();
+        std::filesystem::create_directories(folder);
+
+        ioh::trigger::OnImprovement on_improvement;
+        ioh::watch::Evaluations evaluations;
+        ioh::watch::TransformedYBest transformed_y_best;
+        std::vector<std::reference_wrapper<ioh::logger::Trigger >> t = {on_improvement};
+        std::vector<std::reference_wrapper<ioh::logger::Property>> w = {evaluations,transformed_y_best};
+        csv_logger = std::make_shared<ioh::logger::FlatFile>(
+            // {std::ref(on_improvement)},
+            // {std::ref(evaluations),std::ref(transformed_y_best)},
+            t, w,
+            name.str(),
+            folder
+        );
+        loggers.append(*csv_logger);
+    }
+
+    /***** IOH problem *****/
+    double w_dummy   = benchmark[problem].dummy;
+    int w_epitasis   = benchmark[problem].epistasis;
+    int w_neutrality = benchmark[problem].neutrality;
+    int w_ruggedness = benchmark[problem].ruggedness;
+
+    // std::string problem_name = "OneMax";
+    // problem_name = problem_name
+    //                 + "_D" + std::to_string((int)(w_dummy * dimension))
+    //                 + "_E" + std::to_string(w_epitasis)
+    //                 + "_N" + std::to_string(w_neutrality)
+    //                 + "_R" + std::to_string(w_ruggedness);
+
+    // ioh::problem::wmodel::WModelOneMax w_model_om(
+    WModelFlat w_model_om(
+        instance,
+        dimension, 
+        w_dummy,
+        w_epitasis,
+        w_neutrality,
+        w_ruggedness);
+
+    /***** Bindings *****/
+    w_model_om.attach_logger(loggers);
+
+    /*****************************************************************************
+     * Binding everything together.
+     *****************************************************************************/
+
+    eoEvalIOHproblem<Bits> onemax_pb(w_model_om, loggers);
+
+    // eoEvalPrint<Bits> eval_print(onemax_pb, std::clog, "\n");
+    // eoEvalFuncCounter<Bits> eval_count(onemax_pb);
+    eoEvalCounterThrowException<Bits> eval_count(onemax_pb, max_evals);
+
+    eoPopLoopEval<Bits> onemax_eval(eval_count);
+
+    /***** Instanciate and run the algo *****/
+
+    eoBooleanGenerator<int> bgen;
+    eoInitFixedLength<Bits> onemax_init(/*bitstring size=*/dimension, bgen);
+    auto& foundry = make_foundry(store, onemax_init, eval_count, max_evals, generations, max_target, pop_size_max, offspring_size, cl_sizes, cl_probs);
+
+    Ints encoded_algo(foundry.size());
+
+    encoded_algo[foundry.crossover_rates     .index()] = crossover_rate;
+    encoded_algo[foundry.crossover_selectors .index()] = crossover_selector;
+    encoded_algo[foundry.crossovers          .index()] = crossover;
+    encoded_algo[foundry.aftercross_selectors.index()] = aftercross_selector;
+    encoded_algo[foundry.mutation_rates      .index()] = mutation_rate;
+    encoded_algo[foundry.mutation_selectors  .index()] = mutation_selector;
+    encoded_algo[foundry.mutations           .index()] = mutation;
+    encoded_algo[foundry.replacements        .index()] = replacement;
+    encoded_algo[foundry.continuators        .index()] = continuator;
+    encoded_algo[foundry.offspring_sizes     .index()] = offspring_size;
+
+    // std::clog << "Encoded algorithm:" << std::endl;
+    foundry.select(encoded_algo);
+
+    std::clog << foundry.name() << std::endl;
+
+    // // Evaluation of a forged encoded_algo on the sub-problem
+    // eoEvalFoundryFastGA<Ints, Bits> eval_foundry(
+    //         foundry, pop_size,
+    //         onemax_init, onemax_eval,
+    //         /*penalization=*/ dimension, // Worst case penalization.
+    //         /*normalized=*/ false); // Use direct integer encoding.
+    //
+    // // Actually instanciate and run the algorithm.
+    // eval_foundry(encoded_algo);
+
+    /*****************************************************************************
+     * Run and output results.
+     *****************************************************************************/
+
+    eoPop<Bits> pop;
+    pop.append(pop_size, onemax_init);
+    try {
+        onemax_eval(pop,pop);
+        foundry(pop); // Actually run the selected algorithm.
+        
+    } catch(eoMaxEvalException e) {
+        eo::log << eo::debug << "Reached maximum evaluations: " << eval_count.getValue() << " / " << max_evals << std::endl;
+    }
+
+    /***** IOH perf stats *****/
+    double perf = ioh::logger::eah::stat::under_curve::volume(eah_logger);
+
+    if(perf == 0 or perf > max_target * max_evals * 1.0) {
+        std::cerr << "WARNING: illogical performance? " << perf
+                  << " Check the bounds or the algorithm." << std::endl;
+    }
+
+    // std::clog << "After " << eval_count.getValue() << " / " << max_evals << " evaluations" << std::endl;
+
+    if(output_mat) {
+        std::vector<std::vector<double>> mat = ioh::logger::eah::stat::distribution(eah_logger);
+
+        // Fancy color map on clog.
+        std::clog << ioh::logger::eah::colormap(mat) << std::endl;
+
+        // Parsable CSV on cout.
+        std::clog << "Attainment matrix distribution: " << std::endl;
+        assert(mat.size() > 0);
+        assert(mat[0].size() > 1);
+        for(size_t i = mat.size()-1; i > 0; --i) {
+            assert(mat[i].size() >= 1);
+            std::cout << mat[i][0];
+            for(size_t j = 1; j < mat[i].size(); ++j) {
+                std::cout << "," << mat[i][j];
+            }
+            std::cout << std::endl;
+        }
+
+    } else {
+        // iRace expects minimization
+        std::cout << -1 * perf << std::endl;
+    }
+}

eo/contrib/irace/run_irace.sh

@@ -1,19 +0,0 @@
-#!/bin/bash
-
-if [[ $# != 1 ]] ; then
-    echo "ERROR: build dir not indicated"
-    exit 1
-fi
-
-cd $1
-pwd
-
-# Fore some reason, irace absolutely need those files...
-cp ../irace-config/example.scen .
-cp ../irace-config/target-runner .
-cp ../irace-config/default.instances .
-
-# 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
-

eo/doc/CMakeLists.txt

@@ -32,8 +32,9 @@ IF (DOXYGEN_FOUND)
   ENDIF (DOXYGEN_EXECUTABLE)
 
   # configure cfg file
+    # "${CMAKE_CURRENT_SOURCE_DIR}/${EO_DOC_CONFIG_FILE}.cmake"
   CONFIGURE_FILE(
-    "${CMAKE_CURRENT_SOURCE_DIR}/${EO_DOC_CONFIG_FILE}.cmake"
+    "${DOXYGEN_CONFIG_DIR}/doxyfile.cmake"
     "${CMAKE_CURRENT_BINARY_DIR}/${EO_DOC_CONFIG_FILE}"
     )
 

eo/src/EO.h

@@ -64,6 +64,8 @@ template<class F = double> class EO: public eoObject, public eoPersistent
 public:
   typedef F Fitness;
 
+  static constexpr const char* invalidTag = "INVALID";
+
   /** Default constructor.
   */
   EO(): repFitness(Fitness()), invalidFitness(true) { }
@@ -72,7 +74,9 @@ public:
   virtual ~EO() {};
 
   /// Return fitness value.
-  const Fitness& fitness() const {
+  // virtual const Fitness& fitness() const { // This would be impossible with MOEO.
+  // virtual Fitness fitness() const { // Cannot do that either, MOEO changes the interface.
+  Fitness fitness() const {
     if (invalid())
         throw eoInvalidFitnessError("Cannot retrieve unevaluated fitness");
     return repFitness;
@@ -86,7 +90,7 @@ public:
   }
 
   // Set fitness as invalid.
-  void invalidate() { invalidFitness = true; repFitness = Fitness(); }
+  virtual void invalidate() { invalidFitness = true; repFitness = Fitness(); }
 
   /** Set fitness. At the same time, validates it.
    *  @param _fitness New fitness value.
@@ -122,25 +126,21 @@ public:
    * The read and print methods should be compatible and have the same format.
    * In principle, format is "plain": they just print a number
    * @param _is a std::istream.
-   * @throw eoInvalidFitnessError If a valid object can't be read.
    */
-  virtual void readFrom(std::istream& _is) {
+  virtual void readFrom(std::istream& _is)
-
+  {
-        // the new version of the reafFrom function.
-        // It can distinguish between valid and invalid fitness values.
         std::string fitness_str;
-        int pos = _is.tellg();
         _is >> fitness_str;
 
-        if (fitness_str == "INVALID")
+        if (fitness_str == invalidTag)
         {
                 invalidFitness = true;
         }
         else
         {
                 invalidFitness = false;
-                _is.seekg(pos); // rewind
+                std::istringstream iss(fitness_str);
-                _is >> repFitness;
+                iss >> repFitness;
         }
   }
 
@@ -148,12 +148,11 @@ public:
    * Write object. Called printOn since it prints the object _on_ a stream.
    * @param _os A std::ostream.
    */
-  virtual void printOn(std::ostream& _os) const {
+  virtual void printOn(std::ostream& _os) const
-
+  {
-
+    if (invalid())
-    // the latest version of the code. Very similar to the old code
+    {
-    if (invalid()) {
+        _os << invalidTag << ' ';
-        _os << "INVALID ";
     }
     else
     {

eo/src/do/make_checkpoint.h

@@ -65,7 +65,7 @@ eoCheckPoint<EOT>& do_make_checkpoint(eoParser& _parser, eoState& _state, eoValu
 
 #ifndef _MSC_VER
     // the CtrlC monitoring interception
-    eoSignal<EOT> *mon_ctrlCCont;
+    eoSignal<EOT> *mon_ctrlCCont = nullptr;
     eoValueParam<bool>& mon_ctrlCParam = _parser.createParam(false, "monitor-with-CtrlC", "Monitor current generation upon Ctrl C",0, "Stopping criterion");
     if (mon_ctrlCParam.value())
       {