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

@@ -1,10 +1,5 @@
 name: Build Debug (Ubuntu)
-
+on: [push, pull_request]
-on:
-  push:
-    branches: [ master ]
-  pull_request:
-    branches: [ master ]
 
 env:
   # Customize the CMake build type here (Release, Debug, RelWithDebInfo, etc.)
@@ -21,8 +16,15 @@ jobs:
         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@v2
+    - 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: |

.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

@@ -13,13 +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
@@ -81,31 +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()

INSTALL.md

@@ -2,7 +2,8 @@
 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.
+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
@@ -18,6 +19,11 @@ Paradiseo use the CMake build system, so building it should be as simple as:
 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
 -------
 
@@ -187,13 +193,13 @@ 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. 
+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. 
+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.
 

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).
@@ -230,11 +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`).
 
-There is also an [online wiki](https://gitlab.inria.fr/paradiseo/paradiseo/-/wikis/home)
 
+# 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 send an e-mail to: `paradiseo-help@lists.gforge.inria.fr`
+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

@@ -28,8 +28,8 @@
             <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="https://app.element.io/#/room/#paradiseo:matrix.org">Chat with us</a></li>
             </ul>
         </div>
@@ -125,9 +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">
@@ -147,7 +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>
 
@@ -300,7 +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">
@@ -309,6 +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>
@@ -808,18 +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/>
@@ -831,21 +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> -->
@@ -906,10 +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>
 
@@ -973,11 +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>
 
@@ -1132,16 +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>
@@ -1183,7 +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>
@@ -1214,7 +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>
@@ -1231,7 +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>

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,PHN2ZyB4bWxucz0iaHR0cDovL3d3dy53My5vcmcvMjAwMC9zdmciIHZlcnNpb249IjEuMSIgeG1sbnM6eGxpbms9Imh0dHA6Ly93d3cudzMub3JnLzE5OTkveGxpbmsiIHhtbG5zOnN2Z2pzPSJodHRwOi8vc3ZnanMuY29tL3N2Z2pzIiB3aWR0aD0iNTEyIiBoZWlnaHQ9IjUxMiIgeD0iMCIgeT0iMCIgdmlld0JveD0iMCAwIDI5Mi4zNTkgMjkyLjM1OSIgc3R5bGU9ImVuYWJsZS1iYWNrZ3JvdW5kOm5ldyAwIDAgNTEyIDUxMiIgeG1sOnNwYWNlPSJwcmVzZXJ2ZSIgY2xhc3M9IiI+PGc+CjxnIHhtbG5zPSJodHRwOi8vd3d3LnczLm9yZy8yMDAwL3N2ZyI+Cgk8cGF0aCBkPSJNMjIyLjk3OSwxMzMuMzMxTDk1LjA3Myw1LjQyNEM5MS40NTYsMS44MDcsODcuMTc4LDAsODIuMjI2LDBjLTQuOTUyLDAtOS4yMzMsMS44MDctMTIuODUsNS40MjQgICBjLTMuNjE3LDMuNjE3LTUuNDI0LDcuODk4LTUuNDI0LDEyLjg0N3YyNTUuODEzYzAsNC45NDgsMS44MDcsOS4yMzIsNS40MjQsMTIuODQ3YzMuNjIxLDMuNjE3LDcuOTAyLDUuNDI4LDEyLjg1LDUuNDI4ICAgYzQuOTQ5LDAsOS4yMy0xLjgxMSwxMi44NDctNS40MjhsMTI3LjkwNi0xMjcuOTA3YzMuNjE0LTMuNjEzLDUuNDI4LTcuODk3LDUuNDI4LTEyLjg0NyAgIEMyMjguNDA3LDE0MS4yMjksMjI2LjU5NCwxMzYuOTQ4LDIyMi45NzksMTMzLjMzMXoiIGZpbGw9IiM3ZDdkN2QiIGRhdGEtb3JpZ2luYWw9IiMwMDAwMDAiIHN0eWxlPSIiIGNsYXNzPSIiPjwvcGF0aD4KPC9nPgo8ZyB4bWxucz0iaHR0cDovL3d3dy53My5vcmcvMjAwMC9zdmciPgo8L2c+CjxnIHhtbG5zPSJodHRwOi8vd3d3LnczLm9yZy8yMDAwL3N2ZyI+CjwvZz4KPGcgeG1sbnM9Imh0dHA6Ly93d3cudzMub3JnLzIwMDAvc3ZnIj4KPC9nPgo8ZyB4bWxucz0iaHR0cDovL3d3dy53My5vcmcvMjAwMC9zdmciPgo8L2c+CjxnIHhtbG5zPSJodHRwOi8vd3d3LnczLm9yZy8yMDAwL3N2ZyI+CjwvZz4KPGcgeG1sbnM9Imh0dHA6Ly93d3cudzMub3JnLzIwMDAvc3ZnIj4KPC9nPgo8ZyB4bWxucz0iaHR0cDovL3d3dy53My5vcmcvMjAwMC9zdmciPgo8L2c+CjxnIHhtbG5zPSJodHRwOi8vd3d3LnczLm9yZy8yMDAwL3N2ZyI+CjwvZz4KPGcgeG1sbnM9Imh0dHA6Ly93d3cudzMub3JnLzIwMDAvc3ZnIj4KPC9nPgo8ZyB4bWxucz0iaHR0cDovL3d3dy53My5vcmcvMjAwMC9zdmciPgo8L2c+CjxnIHhtbG5zPSJodHRwOi8vd3d3LnczLm9yZy8yMDAwL3N2ZyI+CjwvZz4KPGcgeG1sbnM9Imh0dHA6Ly93d3cudzMub3JnLzIwMDAvc3ZnIj4KPC9nPgo8ZyB4bWxucz0iaHR0cDovL3d3dy53My5vcmcvMjAwMC9zdmciPgo8L2c+CjxnIHhtbG5zPSJodHRwOi8vd3d3LnczLm9yZy8yMDAwL3N2ZyI+CjwvZz4KPGcgeG1sbnM9Imh0dHA6Ly93d3cudzMub3JnLzIwMDAvc3ZnIj4KPC9nPgo8L2c+PC9zdmc+);
+    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 {
+    padding: 0px 30px 10px 30px;
+}
+
+.memberdecls * {
+    background-color: inherit;
+}
+
+.memSeparator {
+    border-bottom: 1px solid var(--bgborder2);
+}
+
+.memTemplParams {
+    color: var(--bgfont);
+}
+
+/***********************************/
+
+/*********** 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);
+}
+
+#nav-sync {
+    background-color: transparent;
+}
+
+#nav-sync>img {
+    content: url(off_sync.png);
+}
+
+#nav-sync.sync>img {
+    content: url(on_sync.png);
+}
+
+/***********************************/
+
+/*********** Plant UML ***********/
+
+/***********************************/
+
+.plantumlgraph > img {
+    width: 80%;
+}

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

@@ -70,6 +70,9 @@ endif()
 ######################################################################################
 
 add_executable(fastga fastga.cpp)
-# target_link_libraries(fastga ${PARADISEO_LIBRARIES} ${IOH_LIBRARY} stdc++fs)
+# 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)
+target_link_libraries(fastga ${PARADISEO_LIBRARIES} fmt stdc++fs)
+
+add_executable(onlymutga onlymutga.cpp)
+target_link_libraries(onlymutga ${PARADISEO_LIBRARIES} fmt)
 

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

@@ -16,8 +16,6 @@
  * 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.
@@ -341,7 +339,7 @@ int main(int argc, char* argv[])
             "problem", "Problem ID",
             'p', "Problem", /*required=*/true);
     const size_t problem = problem_p.value();
-    assert(0 <= problem and problem < benchmark.size());
+    assert(problem < benchmark.size());
 
     // const size_t dimension = parser.getORcreateParam<size_t>(1000,
     //         "dimension", "Dimension size",
@@ -624,7 +622,7 @@ int main(int argc, char* argv[])
     eoInitFixedLength<Bits> onemax_init(/*bitstring size=*/dimension, bgen);
     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;
@@ -641,16 +639,6 @@ int main(int argc, char* argv[])
     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.
      *****************************************************************************/
@@ -661,7 +649,7 @@ int main(int argc, char* argv[])
         onemax_eval(pop,pop);
         foundry(pop); // Actually run the selected algorithm.
         
-    } catch(eoMaxEvalException e) {
+    } catch(eoMaxEvalException & e) {
         eo::log << eo::debug << "Reached maximum evaluations: " << eval_count.getValue() << " / " << max_evals << std::endl;
     }
 

eo/contrib/irace/fastga.sindef

@@ -1,9 +1,10 @@
-Bootstrap: library
+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

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/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())
       {

eo/src/eo

@@ -224,6 +224,11 @@
 #include "utils/eoLogger.h"
 #include "utils/eoParallel.h"
 
+#include "eoInt.h"
+#include "eoRealToIntMonOp.h"
+#include "eoRealToIntQuadOp.h"
+#include "eoRealToIntInit.h"
+
 #endif
 
 // Local Variables:

eo/src/eoAlgoFoundry.h

@@ -15,6 +15,7 @@
    Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
 
    © 2020 Thales group
+   © 2022 Institut Pasteur
 
     Authors:
         Johann Dreo <johann.dreo@thalesgroup.com>
@@ -24,6 +25,7 @@
 #define _eoAlgoFoundry_H_
 
 #include <vector>
+#include <variant>
 
 /** A vector of eoForge which hold an index.
  *
@@ -36,13 +38,13 @@
  * which takes the class name as template and its constructor's parameters
  * as arguments. For example:
  * @code
- * eoOperatorFoundry< eoSelectOne<EOT> > selectors;
+ *   eoOperatorFoundry< eoSelectOne<EOT> > selectors;
- * selectors.add< eoStochTournamentSelect<EOT> >( 0.5 );
+ *   selectors.add< eoStochTournamentSelect<EOT> >( 0.5 );
  * @endcode
  *
  * @warning If the managed constructor takes a reference YOU SHOULD ABSOLUTELY wrap it
- * in a `std::ref` when using `add` or `setup`, or it will silently be passed as a copy,
+ *          in a `std::ref` when using `add` or `setup`, or it will silently be passed as a copy,
- * which would effectively disable any link between operators.
+ *          which would effectively disable any link between operators.
  *
  * @ingroup Core
  * @ingroup Foundry
@@ -51,11 +53,18 @@ template<class Itf>
 class eoOperatorFoundry : public eoForgeVector< Itf >
 {
     public:
+        /** Constructor
+         * 
+         * @param encoding_index The slot position in the encodings, at which this operator is held.
+         * @param always_reinstantiate If false, will enable cache for the forges in this container.
+         */
         eoOperatorFoundry(size_t encoding_index, bool always_reinstantiate = true ) :
             eoForgeVector<Itf>(always_reinstantiate),
             _index(encoding_index)
         { }
 
+        /** Returns the slot index at which this is registered.
+         */
         size_t index() const { return _index; }
 
     protected:
@@ -63,6 +72,24 @@ class eoOperatorFoundry : public eoForgeVector< Itf >
         size_t _index;
 };
 
+
+/** A vector of eoForge which hold a scalar numeric value.
+ *
+ * To be used in conjunction with a subclass of an eoAlgoFoundry,
+ * where it can hold a range of parameter values 
+ * and hold the link to the encoding. @see eoAlgoFoundryEA
+ *
+ * As with eoForgeScalar, managed parameters
+ * are represented through a [min,max] range.
+ * 
+ * For example:
+ * @code
+ *   eoParameterFoundry< double > proba(0.0, 1.0);
+ * @endcode
+ *
+ * @ingroup Core
+ * @ingroup Foundry
+ */
 template<class Itf>
 class eoParameterFoundry : public eoForgeScalar< Itf >
 {
@@ -70,11 +97,26 @@ class eoParameterFoundry : public eoForgeScalar< Itf >
         "eoParameterFoundry should only be used on arithmetic types (i.e. integer or floating point types)");
 
     public:
+        /** Underlying type of the parameter.
+         * 
+         * @note You probably only want to use either `double` or `size_t`.
+         * @see eoAlgoFoundry
+         */
+        using Type = Itf;
+
+        /** Constructor
+         * 
+         * @param encoding_index The slot position in the encodings, at which this parameter is held.
+         * @param min Minimium possible value.
+         * @param max Maximum possible value.
+         */
         eoParameterFoundry(size_t encoding_index, Itf min, Itf max) :
             eoForgeScalar<Itf>(min, max),
             _index(encoding_index)
         { }
 
+        /** Returns the slot index at which this is registered.
+         */
         size_t index() const { return _index; }
 
     protected:
@@ -84,48 +126,55 @@ class eoParameterFoundry : public eoForgeScalar< Itf >
 
 /** Interface of a Foundry: a class that instantiate an eoAlgo on-the-fly, given a choice of its operators.
  *
- * The chosen operators are encoded in a vector of indices.
+ * The chosen operators are encoded in a vector of numbers.
  *
  * The foundry subclass should first be set up with sets of operators of the same interface,
  * held within an eoOperatorFoundry member.
  * @code
- * eoOperatorFoundry< eoSelectOne<EOT> > selectors;
+ *   eoOperatorFoundry< eoSelectOne<EOT> > selectors;
  * @endcode
  *
  * In a second step, the operators to be used should be selected
  * by indicating their index, just like if the foundry was an array:
  * @code
- * foundry.select({0, 1, 2});
+ *   foundry.select({size_t{0}, size_t{1}, size_t{2}});
- * //              ^  ^  ^
+ *   //                     ^          ^          ^
- * //              |  |  |
+ *   //                     |          |          |
- * //              |  |  + 3d operator
+ *   //                     |          |          + 3d operator
- * //              |  + 2d operator
+ *   //                     |          + 2d operator
- * //              + 1st operator
+ *   //                     + 1st operator
  * @endcode
  *
  * If you don't (want to) recall the order of the operators in the encoding,
  * you can use the `index()` member of eoOperatorFoundry, for example:
  * @code
- * foundry.at(foundry.continuators.index()) = 2; // select the third continuator
+ *   foundry.at(foundry.continuators.index()) = size_t{2}; // select the third continuator
  * @endcode
  *
  * Now, you must implement the foundry just like any eoAlgo, by using the eoPop interface:
  * @code
- * foundry(pop);
+ *   foundry(pop);
- * @encode
+ * @endcode
+ * 
  * It will instantiate the needed operators (only) and the algorithm itself on-the-fly,
  * and then run it.
+ * 
+ * @note The "encoding" which represent the selected options, figuring the actual meta-algorithm,
+ *        is a vector of `std::variant`, which can hold either a `size_t` or a `double`.
+ *        The first one is used to indicate the index of an operator class
+ *        *or* a parameter which is a size.
+ *        The second is used to store numerical parameters values.
  *
- * @note: Thanks to the underlying eoOperatorFoundry, not all the added operators are instantiated.
+ * @note Thanks to the underlying eoOperatorFoundry, not all the added operators are instantiated.
- * Every instantiation is deferred upon actual use. That way, you can still reconfigure them
+ *        Every instantiation is deferred upon actual use. That way, you can still reconfigure them
- * at any time with `eoForgeOperator::setup`, for example:
+ *        at any time with `eoForgeOperator::setup`, for example:
- * @code
+ *        @code
- * foundry.selector.at(0).setup(0.5); // using constructor's arguments
+ *        foundry.selector.at(0).setup(0.5); // using constructor's arguments
- * @endcode
+ *        @endcode
  *
- * @warning If the managed constructor takes a reference YOU SHOULD ABSOLUTELY wrap it
+ * @warning If the managed constructor takes a reference *YOU SHOULD ABSOLUTELY* wrap it
- * in a `std::ref` when using `add` or `setup`, or it will silently be passed as a copy,
+ *          in a `std::ref` when using `add` or `setup`, or it will silently be passed as a copy,
- * which would effectively disable any link between operators.
+ *          which would effectively disable any link between operators.
  *
  * @ingroup Core
  * @ingroup Foundry
@@ -135,30 +184,104 @@ template<class EOT>
 class eoAlgoFoundry : public eoAlgo<EOT>
 {
     public:
-        /** 
+        // We could use `std::any` instead of a variant,
+        // but this would be more prone to errors from the end user, at the end.
+        // Either the encoding is an index (of the operator within the list of instances)
+        // either it's a real-valued parameter,
+        // either it's a size.
+        // So there's no need for more types (AFAIK).
+        
+        /** The type use to represent a selected option in the meta-algorithm.
+         * 
+         * This can figure, either:
+         * - the index of an operator in the list of possible ones,
+         * - the actual value of a numeric paramater,
+         * - the value of a parameter which is a size.
          */
-        eoAlgoFoundry( size_t nb_operators ) :
+        using Encoding = std::variant<size_t, double>;
-            _size(nb_operators),
+
-            _encoding(_size,0)
+        /** The type use to store all selected options.
+         */
+        using Encodings = std::vector<Encoding>;
+        
+        /** Constructor.
+         * 
+         * @param nb_slots Number of operators or parameters that are assembled to make an algorithm.
+         */
+        eoAlgoFoundry( size_t nb_slots ) :
+            _size(nb_slots)
         { }
 
         /** Select indices of all the operators.
          *
          * i.e. Select an algorithm to instantiate.
+         * 
+         * @note You need to indicate the type of each item
+         *        if you want to call this with a brace-initialized vector.
+         * 
+         * For example:
+         * @code
+         *   foundry.select({ size_t{1}, double{0.5}, size_t{3} });
+         * @endcode
+         * 
+         * Or you can initialize the vector first:
+         * @code
+         *   double crossover_rate = 0.5;
+         *   size_t crossover_oper = 3;
+         *   eoAlgoFoundry<EOT>::Encodings encoded_algo(foundry.size());
+         *   encoded_algo[foundry.crossover_rates.index()] = crossover_rate;
+         *   encoded_algo[foundry.crossover_opers.index()] = crossover_oper;
+         * @endcode
          */
-        void select( std::vector<size_t> encoding )
+        void select( Encodings encodings )
         {
-            assert(encoding.size() == _encoding.size());
+            assert(encodings.size() == _size);
-            _encoding = encoding;
+            _encodings = encodings;
         }
 
-        /** Access to the index of the currently selected operator.
+        /** Access to the encoding of the currently selected operator.
+         * 
+         * @warning This returns a `std::variant`, which you should `std::get<T>`.
+         * 
+         * For example:
+         * @code
+         *   size_t opera_id = std::get<size_t>(foundry.at(2));
+         *   double param_id = std::get<double>(foundry.at(3));
+         * @endcode
+         * 
+         * @see rank, @see value or @see len to have automatic casting.
          */
-        size_t& at(size_t i)
+        Encoding & at(size_t i)
         {
-            return _encoding.at(i);
+            return _encodings.at(i);
         }
 
+         /** Access to the currently selected ID of an operator.
+         */
+        template<class OP>
+        size_t rank(const OP& op)
+        {
+            return std::get<size_t>( at(op.index()) );
+        }
+
+        /** Access to the currently selected value of a numeric parameter.
+         */
+        template<class OP>
+        double value(const OP& param)
+        {
+            return std::get<double>( at(param.index()) );
+        }
+
+        /** Access to the currently selected value of a unsigned integer parameter.
+         */
+        template<class OP>
+        size_t len(const OP& param)
+        {
+            return std::get<size_t>( at(param.index()) );
+        }
+        
+        /** Returns the number of slots that makes this algorithm.
+         */
         size_t size() const
         {
             return _size;
@@ -166,14 +289,14 @@ class eoAlgoFoundry : public eoAlgo<EOT>
 
         /** Return the underlying encoding vector.
          */
-        std::vector<size_t> encoding() const
+        Encodings encodings() const
         {
-            return _encoding;
+            return _encodings;
         }
 
     protected:
         const size_t _size;
-        std::vector<size_t> _encoding;
+        std::vector<Encoding> _encodings;
 
 };
 

eo/src/eoAlgoFoundryEA.h

@@ -15,9 +15,10 @@
    Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
 
    © 2020 Thales group
+   © 2022 Institut Pasteur
 
     Authors:
-        Johann Dreo <johann.dreo@thalesgroup.com>
+        Johann Dreo <johann@dreo.fr>
 */
 
 #ifndef _eoAlgoFoundryEA_H_
@@ -36,7 +37,7 @@
  * which takes the class name as template and its constructor's parameters
  * as arguments. For example:
  * @code
- * foundry.selectors.add< eoStochTournamentSelect<EOT> >( 0.5 );
+ *   foundry.selectors.add< eoStochTournamentSelect<EOT> >( 0.5 );
  * @endcode
  *
  * @warning If the constructor takes a reference YOU SHOULD ABSOLUTELY wrap it
@@ -46,34 +47,34 @@
  * In a second step, the operators to be used should be selected
  * by indicating their index, just like the foundry was a array of five elements:
  * @code
- * foundry = {0, 1, 2, 0, 3};
+ * foundry = {size_t{0}, size_t{1}, size_t{2}, size_t{0}, size_t{3}};
- * //         ^  ^  ^  ^  ^ replacement
+ * //                ^          ^          ^          ^          ^ replacement
- * //         |  |  |  + selection
+ * //                |          |          |          + selection
- * //         |  |  + mutation
+ * //                |          |          + mutation
- * //         |  + crossover
+ * //                |          + crossover
- * //         + continue
+ * //                + continue
  * @endcode
  *
- * @note: by default, the firsts of the five operators are selected.
+ * @note by default, the firsts of the five operators are select      ed.
  *
  * If you don't (want to) recall the order of the operators in the encoding,
  * you can use the `index()` member, for example:
  * @code
- * foundry.at(foundry.continuators.index()) = 2; // select the third continuator
+ *   foundry.at(foundry.continuators.index()) = size_t{2}; // select the third continuator
  * @endcode
  *
  * Now, you can call the fourdry just like any eoAlgo, by passing it an eoPop:
  * @code
- * foundry(pop);
+ *   foundry(pop);
- * @encode
+ * @endcode
  * It will instantiate the needed operators (only) and the algorithm itself on-the-fly,
  * and then run it.
  *
- * @note: Thanks to the underlying eoOperatorFoundry, not all the added operators are instantiated.
+ * @note Thanks to the underlying eoOperatorFoundry, not all the added operators are instantiated.
- * Every instantiation is deferred upon actual use. That way, you can still reconfigure them
+ *       Every instantiation is deferred upon actual use. That way, you can still reconfigure them
  * at any time with `eoForgeOperator::setup`, for example:
  * @code
- * foundry.selector.at(0).setup(0.5); // using constructor's arguments
+ *   foundry.selectors.at(0).setup(0.5); // using constructor's arguments
  * @endcode
  *
  * @ingroup Foundry
@@ -111,11 +112,11 @@ class eoAlgoFoundryEA : public eoAlgoFoundry<EOT>
          */
         void operator()(eoPop<EOT>& pop)
         {
-            assert(continuators.size() > 0); assert(this->at(continuators.index()) < continuators.size());
+            assert(continuators.size() > 0); assert(this->rank(continuators) < continuators.size());
-            assert(  crossovers.size() > 0); assert(this->at(  crossovers.index()) <   crossovers.size());
+            assert(  crossovers.size() > 0); assert(this->rank(  crossovers) <   crossovers.size());
-            assert(   mutations.size() > 0); assert(this->at(   mutations.index()) <    mutations.size());
+            assert(   mutations.size() > 0); assert(this->rank(   mutations) <    mutations.size());
-            assert(   selectors.size() > 0); assert(this->at(   selectors.index()) <    selectors.size());
+            assert(   selectors.size() > 0); assert(this->rank(   selectors) <    selectors.size());
-            assert(replacements.size() > 0); assert(this->at(replacements.index()) < replacements.size());
+            assert(replacements.size() > 0); assert(this->rank(replacements) < replacements.size());
 
             eoSequentialOp<EOT> variator;
             variator.add(this->crossover(), 1.0);
@@ -134,17 +135,17 @@ class eoAlgoFoundryEA : public eoAlgoFoundry<EOT>
 
         /** Return an approximate name of the seected algorithm.
          *
-         * @note: does not take into account parameters of the operators,
+         * @note does not take into account parameters of the operators,
-         * only show class names.
+         *       only show class names.
          */
         std::string name()
         {
             std::ostringstream name;
-            name << this->at(continuators.index()) << " (" << this->continuator().className() << ") + ";
+            name << this->continuator().className() << " [" << this->rank(continuators) << "] + ";
-            name << this->at(crossovers.index())   << " (" << this->crossover().className()   << ") + ";
+            name << this->crossover()  .className() << " [" << this->rank(crossovers)   << "] + ";
-            name << this->at(mutations.index())    << " (" << this->mutation().className()    << ") + ";
+            name << this->mutation()   .className() << " [" << this->rank(mutations)    << "] + ";
-            name << this->at(selectors.index())    << " (" << this->selector().className()    << ") + ";
+            name << this->selector()   .className() << " [" << this->rank(selectors)    << "] + ";
-            name << this->at(replacements.index()) << " (" << this->replacement().className() << ")";
+            name << this->replacement().className() << " [" << this->rank(replacements) << "]";
             return name.str();
         }
 
@@ -153,34 +154,44 @@ class eoAlgoFoundryEA : public eoAlgoFoundry<EOT>
         const size_t _max_gen;
 
     public:
+        /** Currently selected continuator.
+         */
         eoContinue<EOT>& continuator()
         {
-            assert(this->at(continuators.index()) < continuators.size());
+            assert(this->rank(continuators) < continuators.size());
-            return continuators.instantiate(this->at(continuators.index()));
+            return continuators.instantiate(this->rank(continuators));
         }
 
+        /** Currently selected crossover.
+         */
         eoQuadOp<EOT>& crossover()
         {
-            assert(this->at(crossovers.index()) < crossovers.size());
+            assert(this->rank(crossovers) < crossovers.size());
-            return crossovers.instantiate(this->at(crossovers.index()));
+            return crossovers.instantiate(this->rank(crossovers));
         }
 
+        /** Currently selected mutation.
+         */
         eoMonOp<EOT>& mutation()
         {
-            assert(this->at(mutations.index()) < mutations.size());
+            assert(this->rank(mutations) < mutations.size());
-            return mutations.instantiate(this->at(mutations.index()));
+            return mutations.instantiate(this->rank(mutations));
         }
 
+        /** Currently selected selector.
+         */
         eoSelectOne<EOT>& selector()
         {
-            assert(this->at(selectors.index()) < selectors.size());
+            assert(this->rank(selectors) < selectors.size());
-            return selectors.instantiate(this->at(selectors.index()));
+            return selectors.instantiate(this->rank(selectors));
         }
 
+        /** Currently selected replacement.
+         */
         eoReplacement<EOT>& replacement()
         {
-            assert(this->at(replacements.index()) < replacements.size());
+            assert(this->rank(replacements) < replacements.size());
-            return replacements.instantiate(this->at(replacements.index()));
+            return replacements.instantiate(this->rank(replacements));
         }
 
 };

eo/src/eoAlgoFoundryFastGA.h

@@ -29,48 +29,61 @@
 
 /** A class that assemble an eoFastGA on the fly, given a combination of available operators.
  *
- * The foundry should first be set up with sets of operators
+ * The foundry should first be set up with sets of operators/parameters
  * for the main modules of a FastGA:
- * continuators, crossovers, mutations, selections, replacement operators, etc.
+ * continuators, crossovers (and rate of call), mutations (and rate of call),
+ * selections, replacement operators, offspring size, etc.
  *
  * This is done through public member variable's `add` method,
  * which takes the class name as template and its constructor's parameters
  * as arguments. For example:
  * @code
- * foundry.selectors.add< eoRandomSelect<EOT> >();
+ *   foundry.selectors.add< eoRandomSelect<EOT> >();
  * @endcode
  *
  * @warning If the constructor takes a reference YOU SHOULD ABSOLUTELY wrap it
- * in a `std::ref`, or it will silently be passed as a copy,
+ *          in a `std::ref`, or it will silently be passed as a copy,
- * which would effectively disable any link with other operator(s).
+ *          which would effectively disable any link with other operator(s).
  *
  * In a second step, the operators to be used should be selected
- * by indicating their index, passing an array of 10 elements:
+ * by indicating their wanted index or value, passing an array of 10 elements:
  * @code
- * foundry.select({0, 1, 2, 3, 4, 5, 6, 7, 8, 9});
+ *   foundry.select({
+ *       double{0.1}, // crossover rate
+ *       size_t{1},   // crossover selector
+ *       size_t{2},   // crossover
+ *       size_t{3},   // selector after crossover
+ *       double{0.4}, // mutation rate
+ *       size_t{5},   // mutation selector
+ *       size_t{6},   // mutation
+ *       size_t{7},   // replacement
+ *       size_t{8},   // continuator
+ *       size_t{9}    // nb of offsprings
+ *   });
  * @endcode
  *
- * @note: by default, the firsts of the 10 operators are selected.
+ * @note by default, the firsts of the 10 operators are selected.
  *
  * If you don't (want to) recall the order of the operators in the encoding,
  * you can use the `index()` member, for example:
  * @code
- * foundry.at(foundry.continuators.index()) = 2; // select the third continuator
+ *   foundry.at(foundry.continuators.index()) = size_t{2}; // select the third continuator
  * @endcode
  *
  * Now, you can call the foundry just like any eoAlgo, by passing it an eoPop:
  * @code
- * foundry(pop);
+ *   foundry(pop);
- * @encode
+ * @endcode
+ * 
  * It will instantiate the needed operators (only) and the algorithm itself on-the-fly,
  * and then run it.
  *
- * @note: Thanks to the underlying eoOperatorFoundry, not all the added operators are instantiated.
+ * @note Thanks to the underlying eoOperatorFoundry, not all the added operators are instantiated.
- * Every instantiation is deferred upon actual use. That way, you can still reconfigure them
+ *        Every instantiation is deferred upon actual use. That way, you can still reconfigure them
- * at any time with `eoForgeOperator::setup`, for example:
+ *        at any time with `eoForgeOperator::setup`, for example:
- * @code
+ *        @code
- * foundry.selector.at(0).setup(0.5); // Will call constructor's arguments
+ *          foundry.selector.at(0).setup(0.5); // Will call constructor's arguments
- * @endcode
+ *        @endcode
  *
  * @ingroup Foundry
  * @ingroup Algorithms
@@ -111,31 +124,31 @@ class eoAlgoFoundryFastGA : public eoAlgoFoundry<EOT>
     public:
 
         /* Operators containers @{ */
-        eoParameterFoundry< double             > crossover_rates;
+        eoParameterFoundry< double            > crossover_rates;
         eoOperatorFoundry< eoSelectOne<EOT>   > crossover_selectors;
         eoOperatorFoundry< eoQuadOp<EOT>      > crossovers;
         eoOperatorFoundry< eoSelectOne<EOT>   > aftercross_selectors;
 
-        eoParameterFoundry< double             > mutation_rates;
+        eoParameterFoundry< double            > mutation_rates;
         eoOperatorFoundry< eoSelectOne<EOT>   > mutation_selectors;
         eoOperatorFoundry< eoMonOp<EOT>       > mutations;
 
         eoOperatorFoundry< eoReplacement<EOT> > replacements;
         eoOperatorFoundry< eoContinue<EOT>    > continuators;
-        eoParameterFoundry< size_t             > offspring_sizes;
+        eoParameterFoundry< size_t            > offspring_sizes;
         /* @} */
 
         /** instantiate and call the pre-selected algorithm.
          */
         void operator()(eoPop<EOT>& pop)
         {
-            assert( crossover_selectors.size() > 0); assert(this->at( crossover_selectors.index()) <  crossover_selectors.size());
+            assert( crossover_selectors.size() > 0); assert(this->rank( crossover_selectors) <  crossover_selectors.size());
-            assert(          crossovers.size() > 0); assert(this->at(          crossovers.index()) <           crossovers.size());
+            assert(          crossovers.size() > 0); assert(this->rank(          crossovers) <           crossovers.size());
-            assert(aftercross_selectors.size() > 0); assert(this->at(aftercross_selectors.index()) < aftercross_selectors.size());
+            assert(aftercross_selectors.size() > 0); assert(this->rank(aftercross_selectors) < aftercross_selectors.size());
-            assert(  mutation_selectors.size() > 0); assert(this->at(  mutation_selectors.index()) <   mutation_selectors.size());
+            assert(  mutation_selectors.size() > 0); assert(this->rank(  mutation_selectors) <   mutation_selectors.size());
-            assert(           mutations.size() > 0); assert(this->at(           mutations.index()) <            mutations.size());
+            assert(           mutations.size() > 0); assert(this->rank(           mutations) <            mutations.size());
-            assert(        replacements.size() > 0); assert(this->at(        replacements.index()) <         replacements.size());
+            assert(        replacements.size() > 0); assert(this->rank(        replacements) <         replacements.size());
-            assert(        continuators.size() > 0); assert(this->at(        continuators.index()) <         continuators.size());
+            assert(        continuators.size() > 0); assert(this->rank(        continuators) <         continuators.size());
 
             // Objective function calls counter
             eoEvalCounterThrowException<EOT> eval(_eval, _max_evals);
@@ -165,7 +178,7 @@ class eoAlgoFoundryFastGA : public eoAlgoFoundry<EOT>
             try {
                 // restart(pop);
                 algo(pop);
-            } catch(eoMaxEvalException e) {
+            } catch(eoMaxEvalException & e) {
 #ifndef NDEBUG
                 eo::log << eo::debug << "Reached maximum evaluations: " << eval.getValue() << " / " << _max_evals << std::endl;
 #endif
@@ -181,17 +194,18 @@ class eoAlgoFoundryFastGA : public eoAlgoFoundry<EOT>
         std::string name()
         {
             std::ostringstream name;
-            name << "crossover_rates: "     << this->at(     crossover_rates.index()) << " (" << this->     crossover_rate()             << ") + ";
+            name << "crossover_rate: "      << this->     crossover_rate()             << " + ";
-            name << "crossover_selectors: " << this->at( crossover_selectors.index()) << " (" << this-> crossover_selector().className() << ") + ";
+            name << "crossover_selector: "  << this-> crossover_selector().className() << " [" << this->rank( crossover_selectors) << "] + ";
-            name << "aftercross_selector: " << this->at(aftercross_selectors.index()) << " (" << this->aftercross_selector().className() << ") + ";
+            name << "aftercross_selector: " << this->aftercross_selector().className() << " [" << this->rank(aftercross_selectors) << "] + ";
-            name << "crossovers: "          << this->at(          crossovers.index()) << " (" << this->          crossover().className() << ") + ";
+            name << "crossover: "           << this->          crossover().className() << " [" << this->rank(          crossovers) << "] + ";
-            name << "mutation_rates: "      << this->at(      mutation_rates.index()) << " (" << this->      mutation_rate()             << ") + ";
+            name << "mutation_rate: "       << this->      mutation_rate()             << " + ";
-            name << "mutation_selectors: "  << this->at(  mutation_selectors.index()) << " (" << this->  mutation_selector().className() << ") + ";
+            name << "mutation_selector: "   << this->  mutation_selector().className() << " [" << this->rank(  mutation_selectors) << "] + ";
-            name << "mutations: "           << this->at(           mutations.index()) << " (" << this->           mutation().className() << ") + ";
+            name << "mutation: "            << this->           mutation().className() << " [" << this->rank(           mutations) << "] + ";
-            name << "replacements: "        << this->at(        replacements.index()) << " (" << this->        replacement().className() << ") + ";
+            name << "replacement: "         << this->        replacement().className() << " [" << this->rank(        replacements) << "] + ";
-            name << "continuators: "        << this->at(        continuators.index()) << " (" << this->        continuator().className() << ") + ";
+            name << "continuator: "         << this->        continuator().className() << " [" << this->rank(        continuators) << "] + ";
-            name << "offspring_sizes: "     << this->at(     offspring_sizes.index()) << " (" << this->     offspring_size()             << ")";
+            name << "offspring_size: "      << this->     offspring_size()             << "";
-            return name.str();
+
+           return name.str();
         }
 
     protected:
@@ -201,61 +215,97 @@ class eoAlgoFoundryFastGA : public eoAlgoFoundry<EOT>
         const size_t _max_restarts;
 
     public:
+        /** Currently selected continuator.
+         */
         eoContinue<EOT>& continuator()
         {
-            assert(this->at(continuators.index()) < continuators.size());
+            const size_t r = this->rank(continuators);
-            return continuators.instantiate(this->at(continuators.index()));
+            assert(r < continuators.size());
+            return continuators.instantiate(r);
         }
 
+        /** Currently selected crossover_rate.
+         */
         double& crossover_rate()
         {
-            return crossover_rates.instantiate(this->at(crossover_rates.index()));
+            // We could have used `decltype(crossover_rates)::Type` instead of `double`, here,
+            // but this is less readable and the type is declared just above,
+            // so we are supposed to know it.
+            const double val = this->value(crossover_rates);
+            assert(crossover_rates.min() <= val and val <= crossover_rates.max());
+            return crossover_rates.instantiate(val);
         }
 
+        /** Currently selected crossover.
+         */
         eoQuadOp<EOT>& crossover()
         {
-            assert(this->at(crossovers.index()) < crossovers.size());
+            const size_t r = this->rank(crossovers);
-            return crossovers.instantiate(this->at(crossovers.index()));
+            assert(r < crossovers.size());
+            return crossovers.instantiate(r);
         }
 
+        /** Currently selected mutation_rate.
+         */
         double& mutation_rate()
         {
-            return mutation_rates.instantiate(this->at(mutation_rates.index()));
+            const double val = this->value(mutation_rates);
+            assert(mutation_rates.min() <= val and val <= mutation_rates.max());
+            return mutation_rates.instantiate(val);
         }
 
+        /** Currently selected mutation.
+         */
         eoMonOp<EOT>& mutation()
         {
-            assert(this->at(mutations.index()) < mutations.size());
+            const size_t r = this->rank(mutations);
-            return mutations.instantiate(this->at(mutations.index()));
+            assert(r < mutations.size());
+            return mutations.instantiate(r);
         }
 
+        /** Currently selected crossover_selector.
+         */
         eoSelectOne<EOT>& crossover_selector()
         {
-            assert(this->at(crossover_selectors.index()) < crossover_selectors.size());
+            const size_t r = this->rank(crossover_selectors);
-            return crossover_selectors.instantiate(this->at(crossover_selectors.index()));
+            assert(r < crossover_selectors.size());
+            return crossover_selectors.instantiate(r);
         }
 
+        /** Currently selected aftercross_selector.
+         */
         eoSelectOne<EOT>& aftercross_selector()
         {
-            assert(this->at(aftercross_selectors.index()) < aftercross_selectors.size());
+            const size_t r = this->rank(aftercross_selectors);
-            return aftercross_selectors.instantiate(this->at(aftercross_selectors.index()));
+            assert(r < aftercross_selectors.size());
+            return aftercross_selectors.instantiate(r);
         }
 
+        /** Currently selected mutation_selector.
+         */
         eoSelectOne<EOT>& mutation_selector()
         {
-            assert(this->at(mutation_selectors.index()) < mutation_selectors.size());
+            const size_t r = this->rank(mutation_selectors);
-            return mutation_selectors.instantiate(this->at(mutation_selectors.index()));
+            assert(r < mutation_selectors.size());
+            return mutation_selectors.instantiate(r);
         }
 
+        /** Currently selected offspring_size.
+         */
         size_t& offspring_size()
         {
-            return offspring_sizes.instantiate(this->at(offspring_sizes.index()));
+            const size_t val = this->len(offspring_sizes);
+            assert(offspring_sizes.min() <= val and val <= offspring_sizes.max());
+            return offspring_sizes.instantiate(val);
         }
 
+        /** Currently selected replacement.
+         */
         eoReplacement<EOT>& replacement()
         {
-            assert(this->at(replacements.index()) < replacements.size());
+            const size_t r = this->rank(replacements);
-            return replacements.instantiate(this->at(replacements.index()));
+            assert(r < replacements.size());
+            return replacements.instantiate(r);
         }
 
 };

eo/src/eoEasyPSO.h

@@ -174,18 +174,18 @@ protected:
          // if the flight does not need to be used, use the dummy flight instance
         class eoDummyFlight:public eoFlight < POT >
         {
-         public:
+            public:
-        eoDummyFlight () {}
+            eoDummyFlight () {}
-        void operator  () (POT &) {}
+            void operator() (POT &) override {}
-        }dummyFlight;
+        } dummyFlight;
 
         // if the initializer does not need to be used, use the dummy one instead
         class eoDummyInitializer:public eoInitializerBase < POT >
         {
-         public:
+            public:
-        eoDummyInitializer () {}
+            eoDummyInitializer () {}
-        void operator  () (POT &) {}
+            void operator() () override {}
-        }dummyInit;
+        } dummyInit;
 
 };
 /**

eo/src/eoEvalFoundryEA.h

@@ -15,9 +15,10 @@
    Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
 
    © 2020 Thales group
+   © 2022 Institut Pasteur
 
     Authors:
-        Johann Dreo <johann.dreo@thalesgroup.com>
+        Johann Dreo <johann@dreo.fr>
 */
 
 #ifndef _eoEvalFoundryEA_H_
@@ -70,13 +71,6 @@ public:
             i_repl(foundry.replacements.index())
     { }
 
-protected:
-    const size_t i_cont;
-    const size_t i_cros;
-    const size_t i_muta;
-    const size_t i_sele;
-    const size_t i_repl;
-
 public:
 
     /** Decode the high-level problem encoding as an array of indices.
@@ -90,7 +84,7 @@ public:
      * auto& cont = foundry.continuator(); // Get the configured operator
      * @encode
      */
-    std::vector<size_t> decode( const EOT& sol ) const
+    typename eoAlgoFoundry<SUB>::Encodings decode( const EOT& sol ) const
     {
         // // Denormalize
         // size_t cont = static_cast<size_t>(std::ceil( sol[i_cont] * _foundry.continuators.size() ));
@@ -125,18 +119,18 @@ public:
         _subpb_eval(pop,pop);
 
         auto config = decode(sol);
-        double cont = config[i_cont];
+        size_t cont = std::get<size_t>(config[i_cont]);
-        double cros = config[i_cros];
+        size_t cros = std::get<size_t>(config[i_cros]);
-        double muta = config[i_muta];
+        size_t muta = std::get<size_t>(config[i_muta]);
-        double sele = config[i_sele];
+        size_t sele = std::get<size_t>(config[i_sele]);
-        double repl = config[i_repl];
+        size_t repl = std::get<size_t>(config[i_repl]);
 
         if(
-               0 <= cont and cont < _foundry.continuators.size()
+               cont < _foundry.continuators.size()
-           and 0 <= cros and cros < _foundry.crossovers  .size()
+           and cros < _foundry.crossovers  .size()
-           and 0 <= muta and muta < _foundry.mutations   .size()
+           and muta < _foundry.mutations   .size()
-           and 0 <= sele and sele < _foundry.selectors   .size()
+           and sele < _foundry.selectors   .size()
-           and 0 <= repl and repl < _foundry.replacements.size()
+           and repl < _foundry.replacements.size()
         ) {
             _foundry.select(config);
 
@@ -155,6 +149,13 @@ protected:
     eoAlgoFoundryEA<SUB>& _foundry;
     const typename EOT::Fitness _penalization;
     const size_t _pop_size;
+
+    const size_t i_cont;
+    const size_t i_cros;
+    const size_t i_muta;
+    const size_t i_sele;
+    const size_t i_repl;
+
 };
 
 /** Helper function to instanciate an eoEvalFoundryEA without having to indicate the template for the sub-problem encoding.

eo/src/eoEvalUserTimeThrowException.h

@@ -21,9 +21,9 @@ Authors:
 Johann Dréo <johann.dreo@thalesgroup.com>
 */
 
-#if !defined(__unix__) && !defined(_WINDOWS)
+#if !defined(_POSIX_VERSION) && !defined(__unix__) && !defined(_WINDOWS)
 #warning "Warning: class 'eoEvalUserTimeThrowException' is only available under UNIX (defining 'rusage' in 'sys/resource.h') or Win32 (defining 'GetProcessTimes' in 'WinBase.h') systems, contributions for other systems are welcomed."
-#else //!defined(__unix__) && !defined(_WINDOWS)
+#else // defined(_POSIX_VERSION) || defined(__unix__) || defined(_WINDOWS)
 
 #ifndef __EOEVALUSERTIMETHROWEXCEPTION_H__
 #define __EOEVALUSERTIMETHROWEXCEPTION_H__
@@ -40,7 +40,7 @@ Johann Dréo <johann.dreo@thalesgroup.com>
 
 #include "eoExceptions.h"
 
-#ifdef __unix__
+#if defined(_POSIX_VERSION) || defined(__unix__)
 
 #include <sys/time.h>
 #include <sys/resource.h>
@@ -106,6 +106,6 @@ protected:
 };
 
 #endif // _WINDOWS
-#endif //__unix__
+#endif // defined(_POSIX_VERSION) || defined(__unix__)
 #endif // __EOEVALUSERTIMETHROWEXCEPTION_H__
-#endif //!defined(__unix__) && !defined(_WINDOWS)
+#endif //!defined(_POSIX_VERSION) && !defined(__unix__) && !defined(_WINDOWS)

eo/src/eoExceptions.h

@@ -45,7 +45,7 @@ public:
 
     const char* what() const throw()
     {
-        return message().c_str();
+        return _msg.c_str();
     }
 
     ~eoException() throw() {}

eo/src/eoFastGA.h

@@ -13,6 +13,11 @@
    You should have received a copy of the GNU Lesser General Public
    License along with this library; if not, write to the Free Software
    Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
+
+   © 2022 Institut Pasteur
+
+    Authors:
+        Johann Dreo <johann@dreo.fr>
 */
 
 #ifndef _eoFastGA_H_
@@ -116,6 +121,11 @@ public:
                     eoPop<EOT> crossed; 
                     crossed.push_back(sol1);
                     crossed.push_back(sol2);
+
+                    // The aftercross selector may need fitness,
+                    // so we evaluate those two solutions, if needed.
+                    _pop_eval(crossed,crossed);
+                    
                     _select_aftercross.setup(crossed);
                     EOT sol3 = _select_aftercross(crossed);
 

eo/src/eoForge.h

@@ -15,9 +15,10 @@
    Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
 
    © 2020 Thales group
+   © 2022 Institut Pasteur
 
     Authors:
-        Johann Dreo <johann.dreo@thalesgroup.com>
+        Johann Dreo <johann@dreo.fr>
 */
 
 #ifndef _eoForge_H_
@@ -26,6 +27,7 @@
 #include <string>
 #include <tuple>
 #include <utility>
+#include <memory>
 
 // In case you want to debug arguments captured in tuples:
 // template<typename Type, unsigned N, unsigned Last>
@@ -73,6 +75,7 @@ class eoForgeInterface
 {
     public:
         virtual Itf& instantiate(bool no_cache = true) = 0;
+        virtual std::shared_ptr<Itf> instantiate_ptr(bool no_cache = true) = 0;
         virtual ~eoForgeInterface() {}
 };
 
@@ -111,6 +114,7 @@ class eoForgeOperator : public eoForgeInterface<Itf>
         template<class ...Args2>
         eoForgeOperator(Args2... args) :
             _args(std::forward<Args2>(args)...),
+            _instantiated_ptr(nullptr),
             _instantiated(nullptr)
         { }
 
@@ -122,9 +126,9 @@ class eoForgeOperator : public eoForgeInterface<Itf>
          *
          * @param no_cache If false, will enable caching previous instances.
          */
-        Itf& instantiate(bool no_cache = true)
+        Itf& instantiate(bool no_cache = true) override
         {
-            if(no_cache or not _instantiated) {
+            if(no_cache or _instantiated == nullptr) {
                 if(_instantiated) {
                     delete _instantiated;
                 }
@@ -133,7 +137,19 @@ class eoForgeOperator : public eoForgeInterface<Itf>
             return *_instantiated;
         }
 
-        virtual ~eoForgeOperator()
+        std::shared_ptr<Itf> instantiate_ptr(bool no_cache = true) override
+        {
+            if(no_cache or _instantiated == nullptr) {
+                // if(_instantiated) {
+                    // delete _instantiated;
+                // }
+                _instantiated_ptr = op_constructor_ptr(_args);
+                // _instantiated = op_constructor(_args);
+            }
+            return _instantiated_ptr;
+        }
+
+        virtual ~eoForgeOperator() override
         {
             delete _instantiated;
         }
@@ -149,9 +165,16 @@ class eoForgeOperator : public eoForgeInterface<Itf>
             // FIXME double-check that the copy-constructor is a good idea to make_from_tuple with dynamic storage duration.
             return new Op(std::make_from_tuple<Op>(args));
         }
+
+        template<class T>
+        std::shared_ptr<Op> op_constructor_ptr(T& args)
+        {
+            return std::make_shared<Op>( std::make_from_tuple<Op>(args) );
+        }
         /** @} */
 
     protected:
+        std::shared_ptr<Itf> _instantiated_ptr;
         Itf* _instantiated;
 };
 
@@ -162,12 +185,13 @@ class eoForgeOperator<Itf,Op> : public eoForgeInterface<Itf>
 {
     public:
         eoForgeOperator() :
+            _instantiated_ptr(nullptr),
             _instantiated(nullptr)
         { }
 
-        Itf& instantiate( bool no_cache = true )
+        Itf& instantiate( bool no_cache = true ) override
         {
-            if(no_cache or not _instantiated) {
+            if(no_cache or _instantiated == nullptr) {
                 if(_instantiated) {
                     delete _instantiated;
                 }
@@ -176,28 +200,37 @@ class eoForgeOperator<Itf,Op> : public eoForgeInterface<Itf>
             return *_instantiated;
         }
 
-        virtual ~eoForgeOperator()
+        std::shared_ptr<Itf> instantiate_ptr( bool no_cache = true ) override
+        {
+            if(no_cache or _instantiated == nullptr) {
+                _instantiated_ptr = std::shared_ptr<Op>();
+            }
+            return _instantiated_ptr;
+        }
+
+        virtual ~eoForgeOperator() override
         {
             delete _instantiated;
         }
 
     protected:
+        std::shared_ptr<Itf> _instantiated_ptr;
         Itf* _instantiated;
 };
 
-/** A vector holding an operator with deferred instantiation at a given index.
+/** A vector holding an operator (with deferred instantiation) at a given index.
  *
  * @note You can actually store several instances of the same class,
  * with different parametrization (or not).
  *
  * @warning When passing a reference (as it is often the case within ParadisEO),
- * it is MANDATORY to wrap it in `std::ref`, or else it will default to use copy.
+ *          it is MANDATORY to wrap it in `std::ref`, or else it will default to use copy.
- * This is is a source of bug which your compiler will to detect and that would
+ *          This is is a source of bug which your compiler will fail to detect and that would
- * disable any link between operators.
+ *          disable any link between operators.
  *
  * @warning You may want to enable instantiation cache to grab some performances.
- * The default is set to disable the cache, because its use with operators
+ *          The default is set to disable the cache, because its use with operators
- * which hold a state will lead to unwanted behaviour.
+ *          which hold a state will lead to unwanted behaviour.
  *
  * @code
     eoForgeVector<eoSelect<EOT>> factories(false);
@@ -240,7 +273,7 @@ class eoForgeVector : public std::vector<eoForgeInterface<Itf>*>
 
          /** instantiate the operator managed at the given index.
           */
-         Itf& instantiate(double index)
+         Itf& instantiate_from(double index)
          {
              double frac_part, int_part;
              frac_part = std::modf(index, &int_part);
@@ -248,9 +281,33 @@ class eoForgeVector : public std::vector<eoForgeInterface<Itf>*>
                 eo::log << eo::errors << "there is a fractional part in the given index (" << index << ")" << std::endl;
                 assert(frac_part != 0);
              }
+             return instantiate(index);
+         }
+
+         std::shared_ptr<Itf> instantiate_ptr_from(double index)
+         {
+             double frac_part, int_part;
+             frac_part = std::modf(index, &int_part);
+             if(frac_part != 0) {
+                eo::log << eo::errors << "there is a fractional part in the given index (" << index << ")" << std::endl;
+                assert(frac_part != 0);
+             }
+             return instantiate_ptr(index);
+         }
+
+         /** instantiate the operator managed at the given index.
+          */
+         Itf& instantiate(size_t index)
+         {
              return this->at(static_cast<size_t>(index))->instantiate(_no_cache);
          }
 
+         std::shared_ptr<Itf> instantiate_ptr(size_t index)
+         {
+             return this->at(static_cast<size_t>(index))->instantiate_ptr(_no_cache);
+         }
+
+
         /** Add an operator to the list.
          *
          * @warning When passing a reference (as it is often the case within ParadisEO),
@@ -319,18 +376,169 @@ class eoForgeVector : public std::vector<eoForgeInterface<Itf>*>
         bool _no_cache;
 };
 
+/** A map holding an operator (with deferred instantiation) at a given name.
+ *
+ * @note You can actually store several instances of the same class,
+ * with different parametrization (or not).
+ *
+ * @warning When passing a reference (as it is often the case within ParadisEO),
+ *          it is MANDATORY to wrap it in `std::ref`, or else it will default to use copy.
+ *          This is is a source of bug which your compiler will fail to detect and that would
+ *          disable any link between operators.
+ *
+ * @warning You may want to enable instantiation cache to grab some performances.
+ *          The default is set to disable the cache, because its use with operators
+ *          which hold a state will lead to unwanted behaviour.
+ *
+ * @code
+    eoForgeMap<eoSelect<EOT>> factories(false);
+
+    // Capture constructor's parameters and defer instantiation.
+    factories.add<eoRankMuSelect<EOT>>(1);
+    factories.setup<eoRankMuSelect<EOT>>(0, 5); // Edit
+
+    // Actually instantiate.
+    eoSelect<EOT>& op  = factories.instantiate(0);
+
+    // Call.
+    op();
+ * @endcode
+ *
+ * @ingroup Foundry
+ */
+template<class Itf, typename Enable = void>
+class eoForgeMap : public std::map<std::string,eoForgeInterface<Itf>*>
+{
+    public:
+        using Interface = Itf;
+
+        /** Default constructor do not cache instantiations.
+         *
+         * @warning
+         * You most probably want to disable caching for operators that hold a state.
+         * If you enable the cache, the last used instantiation will be used,
+         * at its last state.
+         * For example, continuators should most probably not be cached,
+         * as they very often hold a state in the form of a counter.
+         * At the end of a search, the continuator will be in the end state,
+         * and thus always ask for a stop.
+         * Reusing an instance in this state will de facto disable further searches.
+         *
+         * @param always_reinstantiate If false, will enable cache for the forges in this container.
+         */
+        eoForgeMap( bool always_reinstantiate = true ) :
+            _no_cache(always_reinstantiate)
+        { }
+
+         /** instantiate the operator managed at the given name.
+          */
+         Itf& instantiate(const std::string& name)
+         {
+             return this->at(name)->instantiate(_no_cache);
+         }
+
+        /** Add an operator to the list.
+         *
+         * @warning When passing a reference (as it is often the case within ParadisEO),
+         *          it is MANDATORY to wrap it in `std::ref`, or else it will default to use copy.
+         *          This is is a source of bug which your compiler will to detect and that would
+         *          disable any link between operators.
+         *
+         */
+        template<class Op, typename... Args>
+        void add(const std::string& name, Args... args)
+        {
+            // We decay all args to ensure storing everything by value within the forge.
+            // The references should thus be wrapped in a std::ref.
+            auto pfo = new eoForgeOperator<Itf,Op,std::decay_t<Args>...>(
+                    std::forward<Args>(args)...);
+            this->insert({name, pfo});
+        }
+
+        /** Specialization for operators with empty constructors.
+         */
+        template<class Op>
+        void add(const std::string& name)
+        {
+            eoForgeInterface<Itf>* pfo = new eoForgeOperator<Itf,Op>;
+            this->insert({name, pfo});
+        }
+
+        /** Change the set up arguments to the constructor.
+         *
+         * @warning When passing a reference (as it is often the case within ParadisEO),
+         *          it is MANDATORY to wrap it in `std::ref`, or else it will default to use copy.
+         *          This is is a source of bug which your compiler will to detect and that would
+         *          disable any link between operators.
+         *
+         * @warning The operator at `name` should have been added with eoForgeMap::add already..
+         */
+        template<class Op, typename... Args>
+        void setup(const std::string& name, Args... args)
+        {
+            delete this->at(name); // Silent on nullptr.
+            auto pfo = new eoForgeOperator<Itf,Op,std::decay_t<Args>...>(
+                    std::forward<Args>(args)...);
+            this->emplace({name, pfo});
+        }
+
+        /** Specialization for empty constructors.
+         */
+        template<class Op>
+        void setup(const std::string& name)
+        {
+            delete this->at(name);
+            auto pfo = new eoForgeOperator<Itf,Op>;
+            this->emplace({name, pfo});
+        }
+
+        virtual ~eoForgeMap()
+        {
+            for(auto kv : *this) {
+                delete kv.second;
+            }
+        }
+
+    protected:
+        bool _no_cache;
+};
+
+
+/** A range holding a parameter value at a given index.
+ * 
+ * This is essential a scalar numerical parameter, with bounds check
+ * and an interface similar to an eoForgeVector.
+ *
+ * @note Contrary to eoForgeVector, this does not store a set of possible values.
+ *
+ * @code
+    eoForgeScalar<double> factories(0.0, 1.0);
+
+    // Actually instantiate.
+    double param  = factories.instantiate(0.5);
+ * @endcode
+ *
+ * @ingroup Foundry
+ */
 template<class Itf>
 class eoForgeScalar
 {
     public:
         using Interface = Itf;
 
+        /** Constructor
+         *
+         * @param min Minimum possible value.
+         * @param may Maximum possible value.
+         */
         eoForgeScalar(Itf min, Itf max) :
             _min(min),
             _max(max)
         { }
         
         /** Just return the same value, without managing any instantiation.
+         * 
+         * Actually checks if value is in range.
          */
         Itf& instantiate(double value)
         {
@@ -353,18 +561,24 @@ class eoForgeScalar
         Itf min() const { return _min; }
         Itf max() const { return _max; }
 
+        /** Set the minimum possible value.
+         */
         void min(Itf min)
         {
             assert(_min <= _max);
             _min = min;
         }
         
+        /** Set the maximum possible value.
+         */
         void max(Itf max)
         {
             assert(_max >= _min);
             _max = max;
         }
 
+        /** Set the possible range of values.
+         */
         void setup(Itf min, Itf max)
         {
             _min = min;

eo/src/eoFunctor.h

@@ -114,7 +114,12 @@ eoFunctorBase::procedure_tag functor_category(const eoF<R>&)
     result_type
 **/
 template <class A1, class R>
+#if __cplusplus >= 201103L
+class eoUF : public eoFunctorBase, public std::function<R(A1)>
+#else
+// Deprecated in C++11
 class eoUF : public eoFunctorBase, public std::unary_function<A1, R>
+#endif
 {
 public :
 
@@ -151,7 +156,12 @@ eoFunctorBase::unary_function_tag functor_category(const eoUF<A1, R>&)
     result_type
 **/
 template <class A1, class A2, class R>
+#if __cplusplus >= 201103L
+class eoBF : public eoFunctorBase, public std::function<R(A1, A2)>
+#else
+// Deprecated in C++11
 class eoBF : public eoFunctorBase, public std::binary_function<A1, A2, R>
+#endif
 {
 public :
         /// virtual dtor here so there is no need to define it in derived classes

eo/src/eoInit.h

@@ -29,11 +29,12 @@
 
 #include <algorithm>
 #include <cassert>
+#include <random>
 
 #include "eoOp.h"
 #include "eoSTLFunctor.h"
 #include "utils/eoRndGenerators.h"
-#include "utils/rnd_generators.h"  // for shuffle method
+// #include "utils/rnd_generators.h"  // for shuffle method
 #include "eoExceptions.h"
 
 
@@ -193,17 +194,20 @@ class eoInitPermutation: public eoInit<EOT> // FIXME inherit from eoInitWithDim
         virtual void operator()(EOT& chrom)
         {
             chrom.resize(chromSize);
-            for(unsigned idx=0;idx <chrom.size();idx++)
+            for(unsigned idx=0; idx < chrom.size(); idx++) {
-                        chrom[idx]=idx+startFrom;
+                chrom[idx] = idx+startFrom;
+            }
 
-            std::shuffle(chrom.begin(), chrom.end(),gen);
+            std::random_device rd;
+            std::mt19937 gen(rd());
+            std::shuffle(chrom.begin(), chrom.end(), gen);
             chrom.invalidate();
         }
 
     private :
         unsigned chromSize;
         unsigned startFrom;
-        UF_random_generator<unsigned int> gen;
+        // UF_random_generator<unsigned int> gen;
 };
 /** @example t-eoInitPermutation.cpp
  */

eo/src/eoInt.h

@@ -36,9 +36,12 @@
   *
   * @ingroup Representations
 */
-template <class FitT, class T = size_t> class eoInt: public eoVector<FitT, T>
+template <class FitT, class T = size_t>
+class eoInt: public eoVector<FitT, T>
 {
  public:
+     using AtomType = size_t;
+     using FitnessType = FitT;
 
   /**
    * (Default) Constructor.

eo/src/eoPartiallyMappedXover.h

@@ -82,9 +82,9 @@ public:
 
       // replace if necessary
       for(i = 0; i < i1; i++) {
-	while (p1[ _solution1[i] ] != -1) 
+	while (p1[ _solution1[i] ] != -1) // FIXME as an unsigned int, p1 cannot hold negative values!
 	  _solution1[i] = p1[_solution1[i]];
-	while (p2[ _solution2[i] ] != -1) 
+	while (p2[ _solution2[i] ] != -1)  // FIXME as an unsigned int, p2 cannot hold negative values!
 	  _solution2[i] = p2[_solution2[i]];
       }      
 
@@ -96,9 +96,9 @@ public:
 
       // replace if necessary
       for(i = i2 + 1; i < _solution1.size(); i++) {
-	while (p1[ _solution1[i] ] != -1) 
+	while (p1[ _solution1[i] ] != -1)  // FIXME as an unsigned int, p1 cannot hold negative values!
 	  _solution1[i] = p1[_solution1[i]];
-	while (p2[ _solution2[i] ] != -1) 
+	while (p2[ _solution2[i] ] != -1)  // FIXME as an unsigned int, p2 cannot hold negative values!
 	  _solution2[i] = p2[_solution2[i]];
       }      
 

eo/src/eoPop.h

@@ -45,7 +45,7 @@ Authors:
 #include "eoOp.h" // for eoInit
 #include "eoPersistent.h"
 #include "eoInit.h"
-#include "utils/rnd_generators.h"  // for shuffle method
+// #include "utils/rnd_generators.h"  // for shuffle method
 #include "eoExceptions.h"
 
 /** A std::vector of EO object, to be used in all algorithms

eo/src/eoProportionalSelect.h

@@ -68,16 +68,12 @@ public:
       }
       assert(not _pop[0].invalid());
 
-      const typename EOT::Fitness min_fit
-          = std::min_element( std::begin(_pop), std::end(_pop) )
-              ->fitness();
-
       cumulative.clear();
-      cumulative.push_back(_pop[0].fitness() - min_fit);
+      cumulative.push_back(_pop[0].fitness() );
 
       for (unsigned i = 1; i < _pop.size(); ++i) {
           assert(not _pop[i].invalid());
-          cumulative.push_back(cumulative.back() + _pop[i].fitness() - min_fit);
+          cumulative.push_back(cumulative.back() + _pop[i].fitness());
       }
       assert(cumulative.size() == _pop.size());
   }
@@ -95,7 +91,7 @@ public:
 
       // assert(fortune <= cumulative.back());
 
-      if(result - cumulative.begin() >= _pop.size()) {
+      if(static_cast<size_t>(result - cumulative.begin()) >= _pop.size()) {
             return _pop.back();
       } else {
           return _pop[result - cumulative.begin()];

eo/src/eoRanking.h

@@ -40,73 +40,73 @@ template <class EOT>
 class eoRanking : public eoPerf2Worth<EOT> // false: do not cache fitness
 {
 public:
-
     using eoPerf2Worth<EOT>::value;
 
-  /* Ctor:
+    /* Ctor:
-   @param _p selective pressure (in (1,2]
+     @param _p selective pressure (in (1,2]
-   @param _e exponent (1 == linear)
+     @param _e exponent (1 == linear)
-  */
+    */
-  eoRanking(double _p=2.0, double _e=1.0):
+    eoRanking(double _p = 2.0, double _e = 1.0) : pressure(_p), exponent(_e)
-    pressure(_p), exponent(_e) {}
-
-  /* helper function: finds index in _pop of _eo, an EOT * */
-  int lookfor(const EOT *_eo, const eoPop<EOT>& _pop)
     {
-      typename eoPop<EOT>::const_iterator it;
+        assert(1 < pressure and pressure <= 2);
-      for (it=_pop.begin(); it<_pop.end(); it++)
-        {
-          if (_eo == &(*it))
-            return it-_pop.begin();
-        }
-      throw eoException("Not found in eoLinearRanking");
     }
 
-  /* COmputes the ranked fitness: fitnesses range in [m,M]
+    /* helper function: finds index in _pop of _eo, an EOT * */
-     with m=2-pressure/popSize and M=pressure/popSize.
+    int lookfor(const EOT *_eo, const eoPop<EOT> &_pop)
-     in between, the progression depstd::ends on exponent (linear if 1).
-   */
-  virtual void operator()(const eoPop<EOT>& _pop)
     {
-      std::vector<const EOT *> rank;
+        typename eoPop<EOT>::const_iterator it;
-      _pop.sort(rank);
+        for (it = _pop.begin(); it < _pop.end(); it++)
-      unsigned pSize =_pop.size();
-      unsigned int pSizeMinusOne = pSize-1;
-
-      if (pSize <= 1)
-        throw eoPopSizeException(pSize,"cannot do ranking with population of size <= 1");
-
-      // value() refers to the std::vector of worthes (we're in an eoParamvalue)
-      value().resize(pSize);
-
-      double beta = (2-pressure)/pSize;
-      if (exponent == 1.0)         // no need for exponetial then
         {
-          double alpha = (2*pressure-2)/(pSize*pSizeMinusOne);
+            if (_eo == &(*it))
-          for (unsigned i=0; i<pSize; i++)
+                return it - _pop.begin();
+        }
+        throw eoException("Not found in eoLinearRanking");
+    }
+
+    /* COmputes the ranked fitness: fitnesses range in [m,M]
+       with m=2-pressure/popSize and M=pressure/popSize.
+       in between, the progression depstd::ends on exponent (linear if 1).
+     */
+    virtual void operator()(const eoPop<EOT> &_pop)
+    {
+        std::vector<const EOT *> rank;
+        _pop.sort(rank);
+        unsigned pSize = _pop.size();
+        unsigned int pSizeMinusOne = pSize - 1;
+
+        if (pSize <= 1)
+            throw eoPopSizeException(pSize, "cannot do ranking with population of size <= 1");
+
+        // value() refers to the std::vector of worthes (we're in an eoParamvalue)
+        value().resize(pSize);
+
+        double beta = (2 - pressure) / pSize;
+        if (exponent == 1.0) // no need for exponential then
+        {
+            double alpha = (2 * pressure - 2) / (pSize * pSizeMinusOne);
+            for (unsigned i = 0; i < pSize; i++)
             {
-              int which = lookfor(rank[i], _pop);
+                int which = lookfor(rank[i], _pop);
-              value()[which] = alpha*(pSize-i)+beta; // worst -> 1/[P(P-1)/2]
+                value()[which] = alpha * (pSize - i) + beta; // worst -> 1/[P(P-1)/2]
             }
         }
-      else                                 // exponent != 1
+        else // exponent != 1
         {
-          double gamma = (2*pressure-2)/pSize;
+            double gamma = (2 * pressure - 2) / pSize;
-          for (unsigned i=0; i<pSize; i++)
+            for (unsigned i = 0; i < pSize; i++)
             {
-              int which = lookfor(rank[i], _pop);
+                int which = lookfor(rank[i], _pop);
-              // value in in [0,1]
+                // value is in [0,1]
-              double tmp = ((double)(pSize-i))/pSize;
+                double tmp = ((double)(pSize - i)) / pSize;
-              // to the exponent, and back to [m,M]
+                // to the exponent, and back to [m,M]
-              value()[which] = gamma*pow(tmp, exponent)+beta;
+                value()[which] = gamma * pow(tmp, exponent) + beta;
             }
         }
     }
- private:
+
-  double pressure;	// selective pressure
+private:
-  double exponent;
+    double pressure; // selective pressure
+    double exponent;
 };
 
-
-
 #endif

eo/src/eoRankingCached.h

@@ -0,0 +1,139 @@
+/** -*- mode: c++; c-indent-level: 4; c++-member-init-indent: 8; comment-column: 35; -*-
+
+   -----------------------------------------------------------------------------
+   eoRankingCached.h
+   (c) Maarten Keijzer, Marc Schoenauer, 2001
+
+   This library is free software; you can redistribute it and/or
+   modify it under the terms of the GNU Lesser General Public
+   License as published by the Free Software Foundation; either
+   version 2 of the License, or (at your option) any later version.
+
+   This library is distributed in the hope that it will be useful,
+   but WITHOUT ANY WARRANTY; without even the implied warranty of
+   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+   Lesser General Public License for more details.
+
+   You should have received a copy of the GNU Lesser General Public
+   License along with this library; if not, write to the Free Software
+   Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
+
+    Contact: todos@geneura.ugr.es, http://geneura.ugr.es
+             Marc.Schoenauer@polytechnique.fr
+             mkeijzer@dhi.dk
+ */
+//-----------------------------------------------------------------------------
+
+#ifndef eoRankingCached_h
+#define eoRankingCached_h
+
+#include "eoPerf2Worth.h"
+
+/**
+ * @class eoRankingCached
+ * @brief Cached version of eoRanking that stores precomputed values for better performance
+ *
+ * This class implements the same ranking algorithm as eoRanking but adds a caching layer
+ * that stores frequently used values when the population size remains constant between
+ * calls. This optimization is particularly useful in steady-state evolution where the
+ * population size typically doesn't change between selection operations.
+ *
+ * The caching mechanism stores:
+ * - Population size related values (pSize, pSizeMinusOne)
+ * - Precomputed coefficients (alpha, beta, gamma)
+ *
+ * @warning This optimization should only be used when the population size remains constant
+ * between calls to the operator. For dynamic population sizes, use the standard eoRanking.
+ *
+ * @ingroup Selectors
+ */
+template <class EOT>
+class eoRankingCached : public eoPerf2Worth<EOT>
+{
+public:
+    using eoPerf2Worth<EOT>::value;
+
+    /* Ctor:
+     @param _p selective pressure (in (1,2]
+     @param _e exponent (1 == linear)
+    */
+    eoRankingCached(double _p = 2.0, double _e = 1.0) : pressure(_p), exponent(_e), cached_pSize(0)
+    {
+        assert(1 < pressure and pressure <= 2);
+    }
+
+    /*
+     Computes the ranked fitness with caching optimization
+     Fitnesses range in [m,M] where:
+     - m = 2-pressure/popSize
+     - M = pressure/popSize
+     The progression between m and M depends on the exponent (linear when exponent=1)
+
+     @param _pop The population to rank
+     */
+    virtual void operator()(const eoPop<EOT> &_pop)
+    {
+        unsigned pSize = _pop.size();
+
+        if (pSize <= 1)
+            throw eoPopSizeException(pSize, "cannot do ranking with population of size <= 1");
+
+        // value() refers to the std::vector of worthes (we're in an eoParamvalue)
+        value().resize(pSize);
+
+        // Cache population-size dependent values only when population size changes
+        if (pSize != cached_pSize)
+        {
+            cached_pSize = pSize;
+            cached_pSizeMinusOne = pSize - 1;
+            cached_beta = (2 - pressure) / pSize;
+            cached_gamma = (2 * pressure - 2) / pSize;
+            cached_alpha = (2 * pressure - 2) / (pSize * cached_pSizeMinusOne);
+        }
+
+        std::vector<const EOT *> rank;
+        _pop.sort(rank);
+
+        // map of indices for the population
+        std::unordered_map<const EOT *, unsigned> indexMap;
+        for (unsigned i = 0; i < pSize; ++i)
+        {
+            indexMap[&_pop[i]] = i;
+        }
+
+        if (exponent == 1.0) // no need for exponential then (linear case)
+        {
+            for (unsigned i = 0; i < pSize; i++)
+            {
+                const EOT *indiv = rank[i];
+                int which = indexMap[indiv];
+                value()[which] = cached_alpha * (pSize - i) + cached_beta;
+            }
+        }
+        else // non-linear case (exponent != 1)
+        {
+            for (unsigned i = 0; i < pSize; i++)
+            {
+                const EOT *indiv = rank[i];
+                int which = indexMap[indiv];
+                // value is in [0,1]
+                double tmp = ((double)(pSize - i)) / pSize;
+                // to the exponent, and back to [m,M]
+                value()[which] = cached_gamma * pow(tmp, exponent) + cached_beta;
+            }
+        }
+    }
+
+private:
+    double pressure; // selective pressure (1 < pressure <= 2)
+    double exponent; // exponent (1 = linear)
+
+    // Cached values (recomputed only when population size changes)
+    unsigned cached_pSize;         // last seen population size
+    unsigned cached_pSizeMinusOne; // pSize - 1
+    double cached_alpha;           // linear scaling coefficient
+    double cached_beta;            // base value coefficient
+    double cached_gamma;           // non-linear scaling coefficient
+};
+
+#endif

eo/src/eoRealToIntInit.h

@@ -0,0 +1,74 @@
+#ifndef eoRealToIntInit_h_INCLUDED
+#define eoRealToIntInit_h_INCLUDED
+
+#include "es/eoReal.h"
+#include "utils/eoIntBounds.h"
+
+template<class EOTINT, class EOTREAL = eoReal<typename EOTINT::FitnessType>>
+class eoRealToIntInit : public eoInit<EOTINT>
+{
+public:
+
+    using EOTreal = EOTREAL;
+
+    enum Repair {
+        folds,
+        truncate
+    };
+
+    eoRealToIntInit( eoInit<EOTreal>& init ) :
+        _whenout(Repair::truncate),
+        _nobounds(),
+        _bounds(_nobounds),
+        _init(init)
+    { }
+
+    eoRealToIntInit( eoInit<EOTreal>& init, eoIntBounds& bounds, Repair whenout = Repair::truncate ) :
+        _whenout(whenout),
+        _nobounds(),
+        _bounds(bounds),
+        _init(init)
+    { }
+
+    virtual void operator()(EOTINT& intsol) override
+    {
+        #ifndef NDEBUG
+            for(size_t i=0; i < intsol.size(); ++i) {
+                assert(_bounds.isInBounds(intsol[i]));
+            }
+        #endif
+
+        EOTreal floatsol;
+        std::copy( std::begin(intsol), std::end(intsol), std::back_inserter(floatsol) );
+
+        _init(floatsol);
+
+        intsol.resize(floatsol.size());
+
+        for(size_t i=0; i < floatsol.size(); ++i) {
+            typename EOTreal::AtomType rounded = std::round(floatsol[i]);
+            if( not _bounds.isInBounds(rounded) ) {
+                switch(_whenout) {
+                    case Repair::truncate:
+                        _bounds.truncate(rounded);
+                        break;
+                    case Repair::folds:
+                        _bounds.foldsInBounds(rounded);
+                        break;
+                }
+            }
+            intsol[i] = static_cast<typename EOTINT::AtomType>(rounded);
+        }
+    }
+
+protected:
+    Repair _whenout;
+    eoIntNoBounds _nobounds;
+
+    eoIntBounds& _bounds;
+    eoInit<EOTreal>& _init;
+};
+
+
+
+#endif // eoRealToIntInit_h_INCLUDED

eo/src/eoRealToIntMonOp.h

@@ -0,0 +1,73 @@
+#ifndef eoRealToIntMonOp_h_INCLUDED
+#define eoRealToIntMonOp_h_INCLUDED
+
+#include "es/eoReal.h"
+#include "utils/eoIntBounds.h"
+
+template<class EOTINT, class EOTREAL = eoReal<typename EOTINT::FitnessType>>
+class eoRealToIntMonOp : public eoMonOp<EOTINT>
+{
+public:
+
+    using EOTreal = EOTREAL;
+
+    enum Repair {
+        folds,
+        truncate
+    };
+
+    eoRealToIntMonOp( eoMonOp<EOTreal>& monop ) :
+        _whenout(Repair::truncate),
+        _nobounds(),
+        _bounds(_nobounds),
+        _monop(monop)
+    { }
+
+    eoRealToIntMonOp( eoMonOp<EOTreal>& monop, eoIntBounds& bounds, Repair whenout = Repair::truncate ) :
+        _whenout(whenout),
+        _nobounds(),
+        _bounds(bounds),
+        _monop(monop)
+    { }
+
+    bool operator()(EOTINT& intsol)
+    {
+        #ifndef NDEBUG
+            for(size_t i=0; i < intsol.size(); ++i) {
+                assert(_bounds.isInBounds(intsol[i]));
+            }
+        #endif
+
+        EOTreal floatsol;
+        std::copy( std::begin(intsol), std::end(intsol), std::back_inserter(floatsol) );
+
+        bool changed = _monop(floatsol);
+
+        if(changed) {
+            for(size_t i=0; i < floatsol.size(); ++i) {
+                typename EOTreal::AtomType rounded = std::round(floatsol[i]);
+                if( not _bounds.isInBounds(rounded) ) {
+                    switch(_whenout) {
+                        case Repair::truncate:
+                            _bounds.truncate(rounded);
+                            break;
+                        case Repair::folds:
+                            _bounds.foldsInBounds(rounded);
+                            break;
+                    }
+                }
+                intsol[i] = static_cast<typename EOTINT::AtomType>(rounded);
+            }
+        }
+        return changed;
+    }
+
+protected:
+    Repair _whenout;
+    eoIntNoBounds _nobounds;
+
+    eoIntBounds& _bounds;
+    eoMonOp<EOTreal>& _monop;
+};
+
+#endif // eoRealToIntMonOp_h_INCLUDED

eo/src/eoRealToIntQuadOp.h

@@ -0,0 +1,94 @@
+#ifndef eoRealToIntQuadOp_h_INCLUDED
+#define eoRealToIntQuadOp_h_INCLUDED
+
+#include "es/eoReal.h"
+#include "utils/eoIntBounds.h"
+
+template<class EOTINT, class EOTREAL = eoReal<typename EOTINT::FitnessType>>
+class eoRealToIntQuadOp : public eoQuadOp<EOTINT>
+{
+public:
+
+    using EOTreal = EOTREAL;
+
+    enum Repair {
+        folds,
+        truncate
+    };
+
+    eoRealToIntQuadOp( eoQuadOp<EOTreal>& quadop ) :
+        _whenout(Repair::truncate),
+        _nobounds(),
+        _bounds(_nobounds),
+        _quadop(quadop)
+    { }
+
+    eoRealToIntQuadOp( eoQuadOp<EOTreal>& quadop, eoIntBounds& bounds, Repair whenout = Repair::truncate ) :
+        _whenout(whenout),
+        _nobounds(),
+        _bounds(bounds),
+        _quadop(quadop)
+    { }
+
+    bool operator()(EOTINT& intsol1, EOTINT& intsol2)
+    {
+        #ifndef NDEBUG
+            for(size_t i=0; i < intsol1.size(); ++i) {
+                assert(_bounds.isInBounds(intsol1[i]));
+            }
+            for(size_t i=0; i < intsol2.size(); ++i) {
+                assert(_bounds.isInBounds(intsol2[i]));
+            }
+        #endif
+
+        EOTreal floatsol1;
+        std::copy( std::begin(intsol1), std::end(intsol1), std::back_inserter(floatsol1) );
+
+        EOTreal floatsol2;
+        std::copy( std::begin(intsol2), std::end(intsol2), std::back_inserter(floatsol2) );
+
+        bool changed = _quadop(floatsol1, floatsol2);
+
+        if(changed) {
+            for(size_t i=0; i < floatsol1.size(); ++i) {
+                typename EOTreal::AtomType rounded = std::round(floatsol1[i]);
+                if( not _bounds.isInBounds(rounded) ) {
+                    switch(_whenout) {
+                        case Repair::truncate:
+                            _bounds.truncate(rounded);
+                            break;
+                        case Repair::folds:
+                            _bounds.foldsInBounds(rounded);
+                            break;
+                    }
+                }
+                intsol1[i] = static_cast<typename EOTINT::AtomType>(rounded);
+            }
+            for(size_t i=0; i < floatsol2.size(); ++i) {
+                typename EOTreal::AtomType rounded = std::round(floatsol2[i]);
+                if( not _bounds.isInBounds(rounded) ) {
+                    switch(_whenout) {
+                        case Repair::truncate:
+                            _bounds.truncate(rounded);
+                            break;
+                        case Repair::folds:
+                            _bounds.foldsInBounds(rounded);
+                            break;
+                    }
+                }
+                intsol2[i] = static_cast<typename EOTINT::AtomType>(rounded);
+            }
+        }
+        return changed;
+    }
+
+protected:
+    Repair _whenout;
+    eoIntNoBounds _nobounds;
+
+    eoIntBounds& _bounds;
+    eoQuadOp<EOTreal>& _quadop;
+};
+
+
+#endif // eoRealToIntQuadOp_h_INCLUDED

eo/src/eoSIGContinue.h

@@ -35,6 +35,8 @@
 #include <csignal>
 #include "eoContinue.h"
 
+typedef void (*sighandler_t)(int);
+
 /** @addtogroup Continuators
  * @{
  */

eo/src/eoSTLFunctor.h

@@ -79,7 +79,12 @@ void eoSTLF<void>::operator()(void)
   respectively
 */
 template <class A1, class R>
+#if __cplusplus >= 201103L
+class eoSTLUF : public std::function<R(A1)>
+#else
+// Deprecated since C++11
 class eoSTLUF : public std::unary_function<A1, R>
+#endif
 {
   public:
     eoSTLUF(eoUF<A1,R>& _f) : f(_f) {}
@@ -102,7 +107,12 @@ class eoSTLUF : public std::unary_function<A1, R>
   respectively
 */
 template <class A1, class A2, class R>
+#if __cplusplus >= 201103L
+class eoSTLBF : public std::function<R(A1, A2)>
+#else
+// Deprecated since C++11
 class eoSTLBF : public std::binary_function<A1, A2, R>
+#endif
 {
   public:
     eoSTLBF(eoUF<A1,R>& _f) : f(_f) {}

eo/src/eoStochasticUniversalSelect.h

@@ -44,7 +44,7 @@ template <class EOT> class eoStochasticUniversalSelect: public eoSelectOne<EOT>
 {
 public:
   /// Sanity check
-  eoStochasticUniversalSelect(const eoPop<EOT>& pop = eoPop<EOT>())
+  eoStochasticUniversalSelect(/*const eoPop<EOT>& pop = eoPop<EOT>()*/)
   {
     if (minimizing_fitness<EOT>())
       throw eoException("eoStochasticUniversalSelect: minimizing fitness");

eo/src/eoSyncEasyPSO.h

@@ -230,27 +230,25 @@ protected:
 
     // if the eval does not need to be used, use the dummy eval instance
         class eoDummyEval : public eoEvalFunc<POT>
-            {
-            public:
-                void operator()(POT &)
-                {}
-            }
-            dummyEval;
-
-         class eoDummyFlight:public eoFlight < POT >
         {
-                public:
+            public:
-        eoDummyFlight () {}
+                void operator()(POT &) override {}
-	void operator  () (POT &) {}
+        } dummyEval;
-        }dummyFlight;
+
+        class eoDummyFlight:public eoFlight < POT >
+        {
+            public:
+            eoDummyFlight () {}
+            void operator() (POT &) override {}
+        } dummyFlight;
 
         // if the initializer does not need to be used, use the dummy one instead
         class eoDummyInitializer:public eoInitializerBase < POT >
         {
-         public:
+            public:
-        eoDummyInitializer () {}
+            eoDummyInitializer () {}
-        void operator  () (POT &) {}
+            void operator() () override {}
-        }dummyInit;
+        } dummyInit;
 
 };
 /** @example t-eoSyncEasyPSO.cpp

eo/src/es/CMAParams.cpp

@@ -113,16 +113,19 @@ CMAParams::CMAParams(eoParser& parser, unsigned dimensionality) {
                 for (unsigned i = 0; i < weights.size(); ++i) {
                     weights[i] = mu - i;
                 }
+                break;
             }
         case 2:
             {
                 weights = 1.;
+                break;
             }
         default :
             {
                 for (unsigned i = 0; i < weights.size(); ++i) {
                     weights[i] = log(mu+1.)-log(i+1.);
                 }
+                break;
             }
 
     }

eo/src/es/eoReal.h

@@ -39,6 +39,7 @@
 template <class FitT> class eoReal: public eoVector<FitT, double>
 {
  public:
+     using AtomType = double;
      using FitnessType = FitT;
 
   /**

eo/src/ga/eoBitOp.h

@@ -361,10 +361,10 @@ template<class Chrom> class eoUBitXover: public eoQuadOp<Chrom>
         {
           if (chrom1[i] != chrom2[i] && eo::rng.flip(preference))
             {
-              // bool tmp = chrom1[i];
+              bool tmp = chrom1[i];
-              // chrom1[i]=chrom2[i];
+              chrom1[i]=chrom2[i];
-              // chrom2[i] = tmp;
+              chrom2[i] = tmp;
-              std::swap(chrom1[i], chrom2[i]);
+              // std::swap(chrom1[i], chrom2[i]);
               changed = true;
             }
         }

eo/src/ga/eoStandardBitMutation.h

@@ -7,6 +7,8 @@
 /** Standard bit mutation with mutation rate p:
  * choose k from the binomial distribution Bin(n,p) and apply flip_k(x).
  *
+ * If rate is null (the default), use 1/chrom.size().
+ *
  * @ingroup Bitstrings
  * @ingroup Variators
  */
@@ -14,7 +16,11 @@ template<class EOT>
 class eoStandardBitMutation : public eoMonOp<EOT>
 {
     public:
-        eoStandardBitMutation(double rate = 0.5) :
+        /** Constructor.
+         *
+         * @param rate mutation rate, 1/chrom.size() if ignored or zero (the default)
+         */
+        eoStandardBitMutation(double rate = 0) :
             _rate(rate),
             _nb(1),
             _bitflip(_nb)
@@ -22,9 +28,12 @@ class eoStandardBitMutation : public eoMonOp<EOT>
 
         virtual bool operator()(EOT& chrom)
         {
+            assert(chrom.size()>0);
+            if(_rate == 0) {
+                _rate = (double) 1/chrom.size();
+            }
             _nb = eo::rng.binomial(chrom.size(),_rate);
-            // BitFlip operator is bound to the _nb reference,
+            _bitflip.number_bits(_nb);
-            // thus one don't need to re-instantiate.
             return _bitflip(chrom);
         }
 
@@ -46,8 +55,7 @@ template<class EOT>
 class eoUniformBitMutation : public eoMonOp<EOT>
 {
     public:
-        eoUniformBitMutation(double rate = 0.5) :
+        eoUniformBitMutation() :
-            _rate(rate),
             _nb(1),
             _bitflip(_nb)
         {}
@@ -55,15 +63,13 @@ class eoUniformBitMutation : public eoMonOp<EOT>
         virtual bool operator()(EOT& chrom)
         {
             _nb = eo::rng.random(chrom.size());
-            // BitFlip operator is bound to the _nb reference,
+            _bitflip.number_bits(_nb);
-            // thus one don't need to re-instantiate.
             return _bitflip(chrom);
         }
 
         virtual std::string className() const {return "eoUniformBitMutation";}
 
     protected:
-        double _rate;
         unsigned _nb;
         eoDetSingleBitFlip<EOT> _bitflip;
 };
@@ -84,17 +90,21 @@ template<class EOT>
 class eoConditionalBitMutation : public eoStandardBitMutation<EOT>
 {
     public:
-        eoConditionalBitMutation(double rate = 0.5) :
+        eoConditionalBitMutation(double rate = 0) :
             eoStandardBitMutation<EOT>(rate)
         {}
 
         virtual bool operator()(EOT& chrom)
         {
             assert(chrom.size()>0);
-            this->_nb = eo::rng.binomial(chrom.size()-1,this->_rate);
+            if(this->_rate == 0) {
-            this->_nb++;
+                this->_rate = (double) 1/chrom.size();
-            // BitFlip operator is bound to the _nb reference,
+            }
-            // thus one don't need to re-instantiate.
+            this->_nb = 0;
+            while(this->_nb < 1) {
+                this->_nb = eo::rng.binomial(chrom.size(),this->_rate);
+            }
+            this->_bitflip.number_bits(this->_nb);
             return this->_bitflip(chrom);
         }
 
@@ -123,12 +133,14 @@ class eoShiftedBitMutation : public eoStandardBitMutation<EOT>
         virtual bool operator()(EOT& chrom)
         {
             assert(chrom.size()>0);
-            this->_nb = eo::rng.binomial(chrom.size()-1,this->_rate);
+            if(this->_rate == 0) {
+                this->_rate = (double) 1/chrom.size();
+            }
+            this->_nb = eo::rng.binomial(chrom.size(),this->_rate);
             if(this->_nb == 0) {
                 this->_nb = 1;
             }
-            // BitFlip operator is bound to the _nb reference,
+            this->_bitflip.number_bits(this->_nb);
-            // thus one don't need to re-instantiate.
             return this->_bitflip(chrom);
         }
 
@@ -142,7 +154,7 @@ class eoShiftedBitMutation : public eoStandardBitMutation<EOT>
  *
  * From:
  * Furong Ye, Carola Doerr, and Thomas Back.
- * Interpolating local and global search by controllingthe variance of standard bit mutation.
+ * Interpolating local and global search by controlling the variance of standard bit mutation.
  * In 2019 IEEE Congress on Evolutionary Computation(CEC), pages 2292–2299.
  *
  * In contrast to standard bit mutation, this operators allows to scale
@@ -152,29 +164,40 @@ class eoShiftedBitMutation : public eoStandardBitMutation<EOT>
  * @ingroup Variators
  */
 template<class EOT>
-class eoNormalBitMutation : public eoStandardBitMutation<EOT>
+class eoNormalBitMutation : public eoMonOp<EOT>
 {
     public:
-        eoNormalBitMutation(double rate = 0.5, double variance = 1) :
+        eoNormalBitMutation(double mean = 0, double variance = 0) :
-            eoStandardBitMutation<EOT>(rate),
+            _mean(mean),
-            _variance(variance)
+            _variance(variance),
+            _nb(1),
+            _bitflip(_nb)
         {}
 
         virtual bool operator()(EOT& chrom)
         {
-            this->_nb = eo::rng.normal(this->_rate * chrom.size(), _variance);
+            assert(chrom.size() > 0);
-            if(this->_nb >= chrom.size()) {
+            if(_mean == 0) {
-                this->_nb = eo::rng.random(chrom.size());
+                _mean = (double) 1/chrom.size();
             }
-            // BitFlip operator is bound to the _nb reference,
+            if(_variance == 0) {
-            // thus one don't need to re-instantiate.
+                _variance = std::log(chrom.size());
-            return this->_bitflip(chrom);
+            }
+            _nb = eo::rng.normal(_mean, _variance);
+            if(_nb >= chrom.size()) {
+                _nb = eo::rng.random(chrom.size());
+            }
+            _bitflip.number_bits(_nb);
+            return _bitflip(chrom);
         }
 
         virtual std::string className() const {return "eoNormalBitMutation";}
 
     protected:
+        double _mean;
         double _variance;
+        unsigned _nb;
+        eoDetSingleBitFlip<EOT> _bitflip;
 };
 
 /** Fast mutation which size is sampled from an adaptive power law.
@@ -188,11 +211,10 @@ class eoNormalBitMutation : public eoStandardBitMutation<EOT>
  * @ingroup Variators
  */
 template<class EOT>
-class eoFastBitMutation : public eoStandardBitMutation<EOT>
+class eoFastBitMutation : public eoMonOp<EOT>
 {
     public:
-        eoFastBitMutation(double rate = 0.5, double beta = 1.5) :
+        eoFastBitMutation(double beta = 1.5) :
-            eoStandardBitMutation<EOT>(rate),
             _beta(beta)
         {
             assert(beta > 1);
@@ -200,26 +222,96 @@ class eoFastBitMutation : public eoStandardBitMutation<EOT>
 
         virtual bool operator()(EOT& chrom)
         {
-            this->_nb = powerlaw(chrom.size(),_beta);
+            _nb = powerlaw(chrom.size(),_beta);
-            // BitFlip operator is bound to the _nb reference,
+            _bitflip.number_bits(_nb);
-            // thus one don't need to re-instantiate.
+            return _bitflip(chrom);
-            return this->_bitflip(chrom);
         }
 
         virtual std::string className() const {return "eoFastBitMutation";}
 
     protected:
-
+        double powerlaw(unsigned int n, double beta)
-        double powerlaw(unsigned n, double beta)
         {
             double cnb = 0;
-            for(unsigned i=1; i<n; ++i) {
+            for(unsigned int i=1; i<=n/2; ++i) {
                 cnb += std::pow(i,-beta);
             }
-            return eo::rng.powerlaw(0,n,beta) / cnb;
+            double trigger = eo::rng.uniform(0,1);
+            double cursor = 0;
+            double rate = 1;
+            for(unsigned int i=1; i<=n/2; ++i) {
+                cursor += std::pow(i,-beta) / cnb;
+                if(cursor >= trigger) {
+                    rate = static_cast<double>(i) / static_cast<double>(n);
+                    break;
+                }
+            }
+            return eo::rng.binomial(n,rate);
         }
 
+        // double powerlaw(unsigned n, double beta)
+        // {
+        //     double cnb = 0;
+        //     for(unsigned i=1; i<n; ++i) {
+        //         cnb += std::pow(i,-beta);
+        //     }
+        //     return eo::rng.powerlaw(0,n,beta) / cnb;
+        // }
+
         double _beta;
+        unsigned _nb;
+        eoDetSingleBitFlip<EOT> _bitflip;
+};
+
+/** Bucket mutation which assign probability for each bucket
+ *
+ * @warning Highly untested code, use with caution.
+ *
+ * From:
+ * Carola Doerr, Johann Dreo, Alexis Robbes
+ */
+template<class EOT>
+class eoBucketBitMutation : public eoMonOp<EOT>
+{
+    public:
+        eoBucketBitMutation(std::vector<std::vector<int>> buckets, std::vector<double> bucketsValues) :
+            _buckets(buckets),
+            _bucketsValues(bucketsValues)
+        {
+            assert(buckets.size() == bucketsValues.size());
+        }
+
+        virtual bool operator()(EOT& chrom)
+        {
+            _nb = customlaw(chrom.size(), _buckets, _bucketsValues);
+            _bitflip.number_bits(_nb);
+            return _bitflip(chrom);
+        }
+
+        virtual std::string className() const {return "eoBucketBitMutation";}
+
+    protected:
+
+        double customlaw(unsigned n, std::vector<std::vector<int>> buckets, std::vector<double> bucketsValues)
+        {
+            int bucketIndex = eo::rng.roulette_wheel(bucketsValues);
+            int startBit    = buckets[bucketIndex][0];
+            int endBit      = buckets[bucketIndex][1];
+            int gapBit      = endBit - startBit;
+
+            int nbBits;
+            if (gapBit > 0) {
+                nbBits = rand() % gapBit + startBit;
+            } else {
+                nbBits = endBit;
+            }
+            return nbBits;
+        }
+        std::vector<double> _bucketsValues;
+        std::vector<std::vector<int>> _buckets;
+
+        unsigned _nb;
+        eoDetSingleBitFlip<EOT> _bitflip;
 };
 
 #endif // _eoStandardBitMutation_h_

eo/src/gp/eoParseTreeDepthInit.h

@@ -50,7 +50,11 @@ class eoParseTreeDepthInit : public eoInit< eoParseTree<FType, Node> >
     protected:
         // a binary predicate for sorting
         // hopefully this will work with M$VC++ 6.0
+#if __cplusplus >= 201103L
+        struct lt_arity:public std::function<bool(Node,Node)>
+#else
         struct lt_arity:public std::binary_function<Node,Node,bool>
+#endif
         {
                 bool operator()(const Node &_node1, const Node &_node2) { return (_node1.arity() < _node2.arity());};
         };

eo/src/gp/parse_tree.h

@@ -468,8 +468,11 @@ private :
                 switch(new_arity)
                 {
                 case 3 : args[2].copy(s.args[2]); args[2].parent = this; // no break!
+                    [[fallthrough]];
                 case 2 : args[1].copy(s.args[1]); args[1].parent = this;
+                    [[fallthrough]];
                 case 1 : args[0].copy(s.args[0]); args[0].parent = this;
+                    [[fallthrough]];
                 case 0 : break;
                 default :
                         {
@@ -523,7 +526,9 @@ private :
                 switch(arity())
                 {
                 case 3 : args[2].parent = 0; // no break!
+                    [[fallthrough]];
                 case 2 : args[1].parent = 0;
+                    [[fallthrough]];
                 case 1 : args[0].parent = 0; break;
                 case 0 : break;
                 default :
@@ -542,7 +547,9 @@ private :
                 switch(arity())
                 {
                 case 3 : args[2].parent = this; // no break!
+                    [[fallthrough]];
                 case 2 : args[1].parent = this;
+                    [[fallthrough]];
                 case 1 : args[0].parent = this; break;
                 case 0 : break;
                 default :

eo/src/mpi/eoMpi.h

@@ -29,6 +29,7 @@ Authors:
 # include "../eoFunctor.h"
 # include "../eoExceptions.h"
 
+# include "mpi/implMpi.h"
 # include "eoMpiNode.h"
 # include "eoMpiAssignmentAlgorithm.h"
 
@@ -669,7 +670,7 @@ namespace eo
                         timerStat.start("master_wait_for_all_responses");
                         while( assignmentAlgo.availableWorkers() != totalWorkers )
                         {
-                            bmpi::status status = comm.probe( bmpi::any_source, eo::mpi::Channel::Messages );
+                            eo::mpi::status status = comm.probe( eo::mpi::any_source, eo::mpi::Channel::Messages );
                             int wrkRank = status.source();
                             that.handleResponse( wrkRank );
                             comm.send( wrkRank, Channel::Commands, Message::Finish );
@@ -686,7 +687,7 @@ namespace eo
                     AssignmentAlgorithm& assignmentAlgo;
                     Job< JobData > & that;
 
-                    bmpi::communicator & comm;
+                    eo::mpi::communicator & comm;
                 };
 
                 /**
@@ -713,7 +714,7 @@ namespace eo
                             {
                                 eo::log << eo::debug << "[M" << comm.rank() << "] Waitin' for node..." << std::endl;
 
-                                bmpi::status status = comm.probe( bmpi::any_source, eo::mpi::Channel::Messages );
+                                eo::mpi::status status = comm.probe( eo::mpi::any_source, eo::mpi::Channel::Messages );
                                 int wrkRank = status.source();
 
                                 eo::log << eo::debug << "[M" << comm.rank() << "] Node " << wrkRank << " just terminated." << std::endl;
@@ -797,7 +798,7 @@ namespace eo
                 AssignmentAlgorithm& assignmentAlgo;
                 int masterRank;
                 const int workerStopCondition;
-                bmpi::communicator& comm;
+                eo::mpi::communicator& comm;
 
                 JobStore<JobData>& store;
                 SendTaskFunction<JobData> & sendTask;

eo/src/mpi/eoMpiNode.cpp

@@ -27,14 +27,14 @@ namespace eo
     {
         void Node::init( int argc, char** argv )
         {
-            static bmpi::environment env( argc, argv );
+            static eo::mpi::environment env( argc, argv );
         }
 
-        bmpi::communicator& Node::comm()
+        eo::mpi::communicator& Node::comm()
         {
             return _comm;
         }
 
-        bmpi::communicator Node::_comm;
+        eo::mpi::communicator Node::_comm;
     }
 }

eo/src/mpi/eoMpiNode.h

@@ -23,7 +23,7 @@ Authors:
 # define __MPI_NODE_H__
 
 # include "implMpi.h"
-namespace bmpi = mpi;
+// namespace bmpi = mpi;
 
 namespace eo
 {
@@ -54,10 +54,10 @@ namespace eo
                 /**
                  * @brief Returns the global mpi::communicator
                  */
-                static bmpi::communicator& comm();
+                static eo::mpi::communicator& comm();
 
             protected:
-                static bmpi::communicator _comm;
+                static eo::mpi::communicator _comm;
         };
     }
 }

eo/src/mpi/eoMultiStart.h

@@ -54,7 +54,7 @@ namespace eo
             typedef eoUF< eoPop<EOT>&, void> ResetAlgo;
 
             MultiStartData(
-                    bmpi::communicator& _comm,
+                    eo::mpi::communicator& _comm,
                     eoAlgo<EOT>& _algo,
                     int _masterRank,
                     ResetAlgo & _resetAlgo )
@@ -87,7 +87,7 @@ namespace eo
             /**
              * @brief Communicator, used to send and retrieve messages.
              */
-            bmpi::communicator& comm;
+            eo::mpi::communicator& comm;
 
             /**
              * @brief Algorithm which will be performed by the worker.

eo/src/mpi/eoParallelApply.h

@@ -137,7 +137,7 @@ namespace eo
             std::vector<EOT> tempArray;
 
             int masterRank;
-            bmpi::communicator& comm;
+            eo::mpi::communicator& comm;
         };
 
         /**

eo/src/mpi/implMpi.cpp

@@ -21,6 +21,8 @@ Authors:
 */
 #include "implMpi.h"
 
+namespace eo
+{
 namespace mpi
 {
     const int any_source = MPI_ANY_SOURCE;
@@ -159,8 +161,9 @@ namespace mpi
         MPI_Barrier( MPI_COMM_WORLD );
     }
 
-    void broadcast( communicator & comm, int value, int root )
+    void broadcast( communicator & /*comm*/, int value, int root )
     {
         MPI_Bcast( &value, 1, MPI_INT, root, MPI_COMM_WORLD );
     }
-}
+} // namespace mpi
+} // namespace eo

eo/src/mpi/implMpi.h

@@ -22,7 +22,7 @@ Authors:
 #ifndef __EO_IMPL_MPI_HPP__
 #define __EO_IMPL_MPI_HPP__
 
-#include "eoMpi.h"
+#include <mpi.h>
 #include "../serial/eoSerial.h"
 
 /**
@@ -41,282 +41,290 @@ Authors:
  * The entities are here shortly described, if you need further details, don't hesitate
  * to visit the boost URL.
  */
-
+namespace eo
-namespace mpi
 {
-    /**
+    namespace mpi
-     * @ingroup Parallel
-     * @{
-     */
-
-    /**
-     * @brief Constant indicating that a message can come from any process.
-     */
-    extern const int any_source;
-
-    /**
-     * @brief Constant indicating that a message can come from any tag (channel).
-     */
-    extern const int any_tag;
-
-    /**
-     * @brief Wrapper class to have a MPI environment.
-     *
-     * Instead of calling MPI_Init and MPI_Finalize, it is only necessary to instantiate
-     * this class once, in the global context.
-     */
-    class environment
     {
-        public:
+        /**
+         * @ingroup Parallel
+         * @{
+         */
 
         /**
-         * @brief Inits MPI context.
+         * @brief Constant indicating that a message can come from any process.
+         */
+        extern const int any_source;
+
+        /**
+         * @brief Constant indicating that a message can come from any tag (channel).
+         */
+        extern const int any_tag;
+
+        /**
+         * @brief Wrapper class to have a MPI environment.
          *
-         * @param argc Number of params in command line (same as one in main)
+         * Instead of calling MPI_Init and MPI_Finalize, it is only necessary to instantiate
-         * @param argv Strings containing params (same as one in main)
+         * this class once, in the global context.
          */
-        environment(int argc, char**argv);
+        class environment
-
+        {
-        /**
-         * @brief Closes MPI context.
-         */
-        ~environment();
-    };
-
-    /**
-     * @brief Wrapper class for MPI_Status
-     *
-     * Consists only in a C++ wrapper class, giving getters on status attributes.
-     */
-    class status
-    {
         public:
+            /**
+             * @brief Inits MPI context.
+             *
+             * @param argc Number of params in command line (same as one in main)
+             * @param argv Strings containing params (same as one in main)
+             */
+            environment(int argc, char **argv);
+
+            /**
+             * @brief Closes MPI context.
+             */
+            ~environment();
+        };
+
+        /* struct MPI_Status
+        {
+            int count;
+            int cancelled;
+            int MPI_SOURCE;
+            int MPI_TAG;
+            int MPI_ERROR;
+        }; */
 
         /**
-         * @brief Converts a MPI_Status into a status.
+         * @brief Wrapper class for MPI_Status
+         *
+         * Consists only in a C++ wrapper class, giving getters on status attributes.
          */
-        status( const MPI_Status & s );
+        class status
+        {
+        public:
+            /**
+             * @brief Converts a MPI_Status into a status.
+             */
+            status(const MPI_Status &s);
 
-        /**
+            /**
-         * @brief Returns the tag of the associated communication.
+             * @brief Returns the tag of the associated communication.
-         */
+             */
-        int tag() { return _tag; }
+            int tag() { return _tag; }
 
-        /**
+            /**
-         * @brief Indicates which error number we obtained in the associated communication.
+             * @brief Indicates which error number we obtained in the associated communication.
-         */
+             */
-        int error() { return _error; }
+            int error() { return _error; }
 
-        /**
+            /**
-         * @brief Returns the MPI rank of the source of the associated communication.
+             * @brief Returns the MPI rank of the source of the associated communication.
-         */
+             */
-        int source() { return _source; }
+            int source() { return _source; }
 
         private:
             int _source;
             int _tag;
             int _error;
-    };
+        };
 
-    /**
+        /**
-     * @brief Main object, used to send / receive messages, get informations about the rank and the size of the world,
+         * @brief Main object, used to send / receive messages, get informations about the rank and the size of the world,
-     * etc.
+         * etc.
-     */
+         */
-    class communicator
+        class communicator
-    {
+        {
         public:
+            /**
+             * Creates the communicator, using the whole world as a MPI_Comm.
+             *
+             * @todo Allow the user to precise which MPI_Comm to use
+             */
+            communicator();
 
-        /**
+            ~communicator();
-         * Creates the communicator, using the whole world as a MPI_Comm.
-         *
-         * @todo Allow the user to precise which MPI_Comm to use
-         */
-        communicator( );
 
-        ~communicator();
+            /**
+             * @brief Returns the MPI rank of the current process.
+             */
+            int rank();
 
-        /**
+            /**
-         * @brief Returns the MPI rank of the current process.
+             * @brief Returns the size of the MPI cluster.
-         */
+             */
-        int rank();
+            int size();
 
-        /**
+            /*
-         * @brief Returns the size of the MPI cluster.
+             * SEND / RECV INT
-         */
+             */
-        int size();
 
-        /*
+            /**
-         * SEND / RECV INT
+             * @brief Sends an integer to dest on channel "tag".
-         */
+             *
+             * @param dest MPI rank of the receiver
+             * @param tag MPI tag of message
+             * @param n The integer to send
+             */
+            void send(int dest, int tag, int n);
 
-        /**
+            /*
-         * @brief Sends an integer to dest on channel "tag".
+             * @brief Receives an integer from src on channel "tag".
-         *
+             *
-         * @param dest MPI rank of the receiver
+             * @param src MPI rank of the sender
-         * @param tag MPI tag of message
+             * @param tag MPI tag of message
-         * @param n The integer to send
+             * @param n Where to save the received integer
-         */
+             */
-        void send( int dest, int tag, int n );
+            void recv(int src, int tag, int &n);
 
-        /*
+            /*
-         * @brief Receives an integer from src on channel "tag".
+             * SEND / RECV STRING
-         *
+             */
-         * @param src MPI rank of the sender
-         * @param tag MPI tag of message
-         * @param n Where to save the received integer
-         */
-        void recv( int src, int tag, int& n );
 
-        /*
+            /**
-         * SEND / RECV STRING
+             * @brief Sends a string to dest on channel "tag".
-         */
+             *
+             * @param dest MPI rank of the receiver
+             * @param tag MPI tag of message
+             * @param str The std::string to send
+             */
+            void send(int dest, int tag, const std::string &str);
 
-        /**
+            /*
-         * @brief Sends a string to dest on channel "tag".
+             * @brief Receives a string from src on channel "tag".
-         *
+             *
-         * @param dest MPI rank of the receiver
+             * @param src MPI rank of the sender
-         * @param tag MPI tag of message
+             * @param tag MPI tag of message
-         * @param str The std::string to send
+             * @param std::string Where to save the received string
-         */
+             */
-        void send( int dest, int tag, const std::string& str );
+            void recv(int src, int tag, std::string &str);
 
-        /*
+            /*
-         * @brief Receives a string from src on channel "tag".
+             * SEND / RECV Objects
-         *
+             */
-         * @param src MPI rank of the sender
-         * @param tag MPI tag of message
-         * @param std::string Where to save the received string
-         */
-        void recv( int src, int tag, std::string& str );
 
-        /*
+            /**
-         * SEND / RECV Objects
+             * @brief Sends an eoserial::Persistent to dest on channel "tag".
-         */
+             *
+             * @param dest MPI rank of the receiver
+             * @param tag MPI tag of message
+             * @param persistent The object to send (it must absolutely implement eoserial::Persistent)
+             */
+            void send(int dest, int tag, const eoserial::Persistent &persistent);
 
-        /**
+            /**
-         * @brief Sends an eoserial::Persistent to dest on channel "tag".
+             * @brief Sends an array of eoserial::Persistent to dest on channel "tag".
-         *
+             *
-         * @param dest MPI rank of the receiver
+             * @param dest MPI rank of the receiver
-         * @param tag MPI tag of message
+             * @param tag MPI tag of message
-         * @param persistent The object to send (it must absolutely implement eoserial::Persistent)
+             * @param table The array of eoserial::Persistent objects
-         */
+             * @param size The number of elements to send (no check is done, the user has to be sure that the size won't
-        void send( int dest, int tag, const eoserial::Persistent & persistent );
+             * overflow!)
-
+             */
-        /**
+            template <class T>
-         * @brief Sends an array of eoserial::Persistent to dest on channel "tag".
+            void send(int dest, int tag, T *table, int size)
-         *
-         * @param dest MPI rank of the receiver
-         * @param tag MPI tag of message
-         * @param table The array of eoserial::Persistent objects
-         * @param size The number of elements to send (no check is done, the user has to be sure that the size won't
-         * overflow!)
-         */
-        template< class T >
-        void send( int dest, int tag, T* table, int size )
-        {
-            // Puts all the values into an array
-            eoserial::Array* array = new eoserial::Array;
-
-            for( int i = 0; i < size; ++i )
             {
-                array->push_back( table[i].pack() );
+                // Puts all the values into an array
+                eoserial::Array *array = new eoserial::Array;
+
+                for (int i = 0; i < size; ++i)
+                {
+                    array->push_back(table[i].pack());
+                }
+
+                // Encapsulates the array into an object
+                eoserial::Object *obj = new eoserial::Object;
+                obj->add("array", array);
+                std::stringstream ss;
+                obj->print(ss);
+                delete obj;
+
+                // Sends the object as a string
+                send(dest, tag, ss.str());
             }
 
-            // Encapsulates the array into an object
+            /*
-            eoserial::Object* obj = new eoserial::Object;
+             * @brief Receives an eoserial::Persistent object from src on channel "tag".
-            obj->add( "array", array );
+             *
-            std::stringstream ss;
+             * @param src MPI rank of the sender
-            obj->print( ss );
+             * @param tag MPI tag of message
-            delete obj;
+             * @param persistent Where to unpack the serialized object?
+             */
+            void recv(int src, int tag, eoserial::Persistent &persistent);
 
-            // Sends the object as a string
+            /*
-            send( dest, tag, ss.str() );
+             * @brief Receives an array of eoserial::Persistent from src on channel "tag".
-        }
+             *
-
+             * @param src MPI rank of the sender
-        /*
+             * @param tag MPI tag of message
-         * @brief Receives an eoserial::Persistent object from src on channel "tag".
+             * @param table The table in which we're saving the received objects. It must have been allocated by the user,
-         *
+             * as no allocation is performed here.
-         * @param src MPI rank of the sender
+             * @param size The number of elements to receive (no check is done, the user has to be sure that the size won't
-         * @param tag MPI tag of message
+             * overflow!)
-         * @param persistent Where to unpack the serialized object?
+             */
-         */
+            template <class T>
-        void recv( int src, int tag, eoserial::Persistent & persistent );
+            void recv(int src, int tag, T *table, int size)
-
-        /*
-         * @brief Receives an array of eoserial::Persistent from src on channel "tag".
-         *
-         * @param src MPI rank of the sender
-         * @param tag MPI tag of message
-         * @param table The table in which we're saving the received objects. It must have been allocated by the user,
-         * as no allocation is performed here.
-         * @param size The number of elements to receive (no check is done, the user has to be sure that the size won't
-         * overflow!)
-         */
-        template< class T >
-        void recv( int src, int tag, T* table, int size )
-        {
-            // Receives the string which contains the object
-            std::string asText;
-            recv( src, tag, asText );
-
-            // Parses the object and retrieves the table
-            eoserial::Object* obj = eoserial::Parser::parse( asText );
-            eoserial::Array* array = static_cast<eoserial::Array*>( (*obj)["array"] );
-
-            // Retrieves all the values from the array
-            for( int i = 0; i < size; ++i )
             {
-                eoserial::unpackObject( *array, i, table[i] );
+                // Receives the string which contains the object
+                std::string asText;
+                recv(src, tag, asText);
+
+                // Parses the object and retrieves the table
+                eoserial::Object *obj = eoserial::Parser::parse(asText);
+                eoserial::Array *array = static_cast<eoserial::Array *>((*obj)["array"]);
+
+                // Retrieves all the values from the array
+                for (int i = 0; i < size; ++i)
+                {
+                    eoserial::unpackObject(*array, i, table[i]);
+                }
+                delete obj;
             }
-            delete obj;
-        }
 
-        /*
+            /*
-         * Other methods
+             * Other methods
-         */
+             */
 
-        /**
+            /**
-         * @brief Wrapper for MPI_Probe
+             * @brief Wrapper for MPI_Probe
-         *
+             *
-         * Waits for a message to come from process having rank src, on the channel
+             * Waits for a message to come from process having rank src, on the channel
-         * tag.
+             * tag.
-         *
+             *
-         * @param src MPI rank of the sender (any_source if it can be any sender)
+             * @param src MPI rank of the sender (any_source if it can be any sender)
-         * @param tag MPI tag of the expected message (any_tag if it can be any tag)
+             * @param tag MPI tag of the expected message (any_tag if it can be any tag)
-         */
+             */
-        status probe( int src = any_source, int tag = any_tag );
+            status probe(int src = any_source, int tag = any_tag);
 
-        /**
+            /**
-         * @brief Wrapper for MPI_Barrier
+             * @brief Wrapper for MPI_Barrier
-         *
+             *
-         *
+             *
-         */
+             */
-        void barrier();
+            void barrier();
 
         private:
             int _rank;
             int _size;
 
-            char* _buf; // temporary buffer for sending and receiving strings. Avoids reallocations
+            char *_buf;   // temporary buffer for sending and receiving strings. Avoids reallocations
             int _bufsize; // size of the above temporary buffer
-    };
+        };
 
-    /**
+        /**
-     * @brief Wrapper for MPI_Bcast
+         * @brief Wrapper for MPI_Bcast
-     *
+         *
-     * Broadcasts an integer value on the communicator comm, from the process having the MPI rank root.
+         * Broadcasts an integer value on the communicator comm, from the process having the MPI rank root.
-     *
+         *
-     * @param comm The communicator on which to broadcast
+         * @param comm The communicator on which to broadcast
-     * @param value The integer value to send
+         * @param value The integer value to send
-     * @param root The MPI rank of the broadcaster
+         * @param root The MPI rank of the broadcaster
-     *
+         *
-     * @todo Actually comm isn't used and broadcast is performed on the whole MPI_COMM_WORLD. TODO: Use comm instead
+         * @todo Actually comm isn't used and broadcast is performed on the whole MPI_COMM_WORLD. TODO: Use comm instead
-     */
+         */
-    void broadcast( communicator & comm, int value, int root );
+        void broadcast(communicator &comm, int value, int root);
 
-    /**
+        /**
-     * @}
+         * @}
-     */
+         */
-} // namespace mpi
+    } // namespace mpi
+} // namespace eo
 
-# endif //__EO_IMPL_MPI_HPP__
+#endif //__EO_IMPL_MPI_HPP__

eo/src/utils/eoGnuplot.cpp

@@ -56,22 +56,24 @@ eoGnuplot::~eoGnuplot()
 }
 
 
-
+#ifdef HAVE_GNUPLOT
 void eoGnuplot::gnuplotCommand(const char *_command)
 {
-#ifdef HAVE_GNUPLOT
     if(gpCom) {
         PipeComSend( gpCom, _command );
         PipeComSend( gpCom, "\n" );
     }
-#endif
 }
+#else
+void eoGnuplot::gnuplotCommand(const char *)
+{ }
+#endif
 
 
 
+#ifdef HAVE_GNUPLOT
 void eoGnuplot::initGnuPlot(std::string _title, std::string _extra)
 {
-#ifdef HAVE_GNUPLOT
     std::ostringstream os;
     os << "250x150-0+" << 170 * numWindow++;
     char *args[6];
@@ -89,8 +91,12 @@ void eoGnuplot::initGnuPlot(std::string _title, std::string _extra)
         PipeComSend( gpCom, _extra.c_str() );
         PipeComSend( gpCom, "\n" );
     }
-#endif
+
 }
+#else
+void eoGnuplot::initGnuPlot(std::string, std::string)
+{ }
+#endif
 
 
 

eo/src/utils/eoParallel.cpp

@@ -39,8 +39,10 @@ eoParallel::eoParallel() :
     _nthreads( 0, "parallelize-nthreads", "Define the number of threads you want to use, nthreads = 0 means you want to use all threads available", '\0' ),
     _enableResults( false, "parallelize-enable-results", "Enable the generation of results", '\0' ),
     _doMeasure( false, "parallelize-do-measure", "Do some measures during execution", '\0' ),
-    _packetSize( 1U, "parallelize-packet-size", "Number of elements which should be sent in a single message during a parallel evaluation based on message passing.", '\0'),
+    _packetSize( 1U, "parallelize-packet-size", "Number of elements which should be sent in a single message during a parallel evaluation based on message passing.", '\0')
-    _t_start(0)
+#ifdef _OPENMP
+    , _t_start(0)
+#endif
 {
 }
 

eo/src/utils/eoParallel.h

@@ -71,7 +71,9 @@ private:
     eoValueParam<bool> _enableResults;
     eoValueParam<bool> _doMeasure;
     eoValueParam<unsigned int> _packetSize;
+#ifdef _OPENMP
     double _t_start;
+#endif
 };
 
 void make_parallel(eoParser&);

eo/src/utils/eoRNG.h

@@ -55,6 +55,7 @@ typedef unsigned long uint32_t;
 #include "../eoObject.h"
 
 
+
 /** Random Number Generator
 
 @class eoRng eoRNG.h utils/eoRNG.h

eo/src/utils/pipecom.cpp

@@ -42,16 +42,16 @@ int Check( PCom *com )
 }
 
 
-PCom * PipeComOpen( char *prog )
+PCom * PipeComOpen( const char *prog )
 {
     char	*args[2];
-    args[0] = prog;
+    args[0] = strdup( prog );
     args[1] = NULL;
     return PipeComOpenArgv( prog, args );
 }
 
 
-PCom * PipeComOpenArgv( char *prog, char *argv[] )
+PCom * PipeComOpenArgv( const char *prog, char *argv[] )
 {
     int		toFils[2];
     int		toPere[2];

eo/src/utils/pipecom.h

@@ -23,8 +23,8 @@ typedef struct PipeCommunication {
 } PCom;
 
 
-extern PCom *PipeComOpen( char *prog );
+extern PCom *PipeComOpen( const char *prog );
-extern PCom *PipeComOpenArgv( char *prog, char *argv[] );
+extern PCom *PipeComOpenArgv( const char *prog, char *argv[] );
 
 extern int PipeComSend( PCom *to, const char *line );
 extern int PipeComSendn( PCom *to, const char *data, int n );

eo/src/utils/rnd_generators.h

@@ -89,7 +89,8 @@ class boolean_generator
    either between [0, _max) if only one value (_max) is given to the ctor
    or in [_min,_max) if 2 values are given (_min, _max)
 */
-template <class T = uint32_t> class random_generator
+template <class T = uint32_t>
+class random_generator
 {
   public :
   // added new ctor with 2 params, and modified the data to minim and range
@@ -123,16 +124,26 @@ inline bool random_generator<bool>::operator()(void)
    function (see eoPop::shuffle): its operator() takes an unsigned argument m
    and  must return an unsigned uniformly distributed in [0,m}
 */
-template <class T = uint32_t> class UF_random_generator
+// FIXME this is probably deprecated by the new STL way of managing random generators.
+template <class T = uint32_t>
+class UF_random_generator
 {
-  public :
+    public :
-    UF_random_generator(eoRng& _rng = rng) :
+        using result_type = T;
-      random(_rng) {}
 
-  T operator()(T _t) { return (T) (random.random(_t)); }
+        UF_random_generator(T max, eoRng& _rng = rng)
+            : _max(max), _random(_rng)
+        {}
 
-private :
+        T operator()() const { return _random.random(_max); }
-  eoRng& random;
+        T operator()(T m) const { return _random.random(m); }
+
+        T min() const { return 0; }
+        T max() const { return _max; }
+
+    private :
+        T _max;
+        eoRng& _random;
 };
 
 

eo/src/utils/selectors.h

@@ -179,7 +179,8 @@ double sum_fitness(const eoPop<EOT>& _pop)
 template <class EOT>
 double sum_fitness(const eoPop<EOT>& _pop, std::pair<double, double>& _minmax)
 {
-    double rawTotal, scaledTotal;
+    // double rawTotal = 0;
+    double scaledTotal;
 
     typename eoPop<EOT>::const_iterator it = _pop.begin();
 
@@ -193,7 +194,7 @@ double sum_fitness(const eoPop<EOT>& _pop, std::pair<double, double>& _minmax)
         _minmax.first = std::min(_minmax.first, v);
         _minmax.second = std::max(_minmax.second, v);
 
-        rawTotal += v;
+        // rawTotal += v;
     }
 
     if (minimizing_fitness<EOT>())

eo/test/CMakeLists.txt

@@ -80,6 +80,9 @@ set (TEST_LIST
   t-forge-FastGA
   t-eoFoundryFastGA
   t-eoAlgoFoundryFastGA
+  t-eoRealToIntMonOp
+  t-eoRealToIntQuadOp
+  t-eoRankingCached
   )
 
 

eo/test/mpi/t-mpi-distrib-exp.cpp

@@ -382,7 +382,7 @@ class Experiment : public eoserial::Persistent
 
     void run()
     {
-        mpi::communicator& comm = eo::mpi::Node::comm();
+        communicator& comm = eo::mpi::Node::comm();
         // reinits every objects
         eo::rng.reseed( _seed );
         eo::rng.clearCache(); // trick for repeatable sequences of normal numbers, cf eo::rng

eo/test/t-algo-forged.cpp

@@ -77,14 +77,13 @@ int main(int /*argc*/, char** /*argv*/)
                         pop.append(pop_size, init);
                         eval(pop,pop);
 
-                        foundry.at(foundry.continuators.index()) = i_cont;
+                        foundry.select({
-                        foundry.at(foundry.crossovers.index()) = i_cross;
+                                size_t{i_cont},
-                        foundry.at(foundry.mutations.index()) = i_mut;
+                                size_t{i_cross},
-                        foundry.at(foundry.selectors.index()) = i_sel;
+                                size_t{i_mut},
-                        foundry.at(foundry.replacements.index()) = i_rep;
+                                size_t{i_sel},
-
+                                size_t{i_rep}
-                        // Or, if you know the order.
+                            });
-                        foundry.select({i_cont, i_cross, i_mut, i_sel, i_rep});
 
                         // Actually perform a search
                         foundry(pop);

eo/test/t-eoAlgoFoundryFastGA.cpp

@@ -16,21 +16,16 @@ int main(int /*argc*/, char** /*argv*/)
     using EOT = eoBit<double>;
 
     oneMaxEval<EOT> eval;
+    eoPopLoopEval<EOT> popeval(eval);
 
     eoBooleanGenerator gen(0.5);
     eoInitFixedLength<EOT> init(dim, gen);
 
     eoAlgoFoundryFastGA<EOT> foundry(init, eval, pop_size*10);
 
-    /***** Variation rates *****/
-    for(double r = 0.0; r < 1.0; r+=0.1) {
-        foundry.crossover_rates.add<double>(r);
-        foundry. mutation_rates.add<double>(r);
-    }
-
     /***** Crossovers ****/
     foundry.crossovers.add< eo1PtBitXover<EOT> >();
-    foundry.crossovers.add< eoUBitXover<EOT> >(0.5); // preference over 1
+    // foundry.crossovers.add< eoUBitXover<EOT> >(0.5); // preference over 1
     for(size_t i=1; i < 11; i+=4) {
         foundry.crossovers.add< eoNPtsBitXover<EOT> >(i); // nb of points
     }
@@ -48,9 +43,9 @@ int main(int /*argc*/, char** /*argv*/)
          std::ref(foundry.mutation_selectors) }) {
 
         ops.add< eoRandomSelect<EOT> >();
-        ops.add< eoStochTournamentSelect<EOT> >(0.5);
+        // ops.add< eoStochTournamentSelect<EOT> >(0.5);
-        ops.add< eoSequentialSelect<EOT> >();
+        // ops.add< eoSequentialSelect<EOT> >();
-        ops.add< eoProportionalSelect<EOT> >();
+        // ops.add< eoProportionalSelect<EOT> >();
         for(size_t i=2; i < 10; i+=4) {
             ops.add< eoDetTournamentSelect<EOT> >(i);
         }
@@ -58,68 +53,61 @@ int main(int /*argc*/, char** /*argv*/)
 
     /***** Replacements ****/
     foundry.replacements.add< eoCommaReplacement<EOT> >();
-    foundry.replacements.add< eoPlusReplacement<EOT> >();
+    // foundry.replacements.add< eoPlusReplacement<EOT> >();
-    foundry.replacements.add< eoSSGAWorseReplacement<EOT> >();
+    // foundry.replacements.add< eoSSGAWorseReplacement<EOT> >();
-    foundry.replacements.add< eoSSGAStochTournamentReplacement<EOT> >(0.51);
+    // foundry.replacements.add< eoSSGAStochTournamentReplacement<EOT> >(0.51);
     for(size_t i=2; i < 10; i+=4) {
         foundry.replacements.add< eoSSGADetTournamentReplacement<EOT> >(i);
     }
 
     /***** Continuators ****/
-    for(size_t i=10; i < 30; i+=10 ) {
+    for(size_t i=3; i < 5; i+=1 ) {
-        foundry.continuators.add< eoSteadyFitContinue<EOT> >(10,i);
+        foundry.continuators.add< eoGenContinue<EOT> >(i);
     }
 
-    /***** Offspring population size *****/
-    foundry.offspring_sizes.add<size_t>(0); // 0 = same as parent pop
-    // for(size_t s = pop_size; s < 2*pop_size; s+=pop_size/10) {
-    //     foundry.offspring_sizes.add<size_t>(s);
-    // }
-
 
     size_t n =
-          foundry.crossover_rates.size()
+          foundry.crossover_selectors.size()
-        * foundry.crossover_selectors.size()
         * foundry.crossovers.size()
         * foundry.aftercross_selectors.size()
-        * foundry.mutation_rates.size()
         * foundry.mutation_selectors.size()
         * foundry.mutations.size()
         * foundry.replacements.size()
         * foundry.continuators.size()
-        * foundry.offspring_sizes.size();
+        ;
     std::clog << n << " possible algorithms instances." << std::endl;
 
+    std::clog << "Running everything (this may take time)..." << std::endl;
+
     EOT best_sol;
     std::string best_algo = "";
 
     size_t i=0;
-    for(size_t i_crossrate = 0; i_crossrate < foundry.crossover_rates.size(); ++i_crossrate ) {
         for(size_t i_crossselect = 0; i_crossselect < foundry.crossover_selectors.size(); ++i_crossselect ) {
             for(size_t i_cross = 0; i_cross < foundry.crossovers.size(); ++i_cross ) {
                 for(size_t i_aftercrosel = 0; i_aftercrosel < foundry.aftercross_selectors.size(); ++i_aftercrosel ) {
-                    for(size_t i_mutrate = 0; i_mutrate < foundry.mutation_rates.size(); ++i_mutrate ) {
                         for(size_t i_mutselect = 0; i_mutselect < foundry.mutation_selectors.size(); ++i_mutselect ) {
                             for(size_t i_mut = 0; i_mut < foundry.mutations.size(); ++i_mut ) {
                                 for(size_t i_rep = 0; i_rep < foundry.replacements.size(); ++i_rep ) {
                                     for(size_t i_cont = 0; i_cont < foundry.continuators.size(); ++i_cont ) {
-                                        for(size_t i_pop = 0; i_pop < foundry.offspring_sizes.size(); ++i_pop ) {
                                             std::clog << "\r" << i++ << "/" << n-1; std::clog.flush();
 
                                             eoPop<EOT> pop;
                                             pop.append(pop_size, init);
+                                            popeval(pop,pop);
 
+                                            // FIXME put the parameters in the test?
                                             foundry.select({
-                                                i_crossrate,
+                                                double{0.5}, // crossover_rate
-                                                i_crossselect,
+                                                size_t{i_crossselect},
-                                                i_cross,
+                                                size_t{i_cross},
-                                                i_aftercrosel,
+                                                size_t{i_aftercrosel},
-                                                i_mutrate,
+                                                double{0.5}, // mutation_rate
-                                                i_mutselect,
+                                                size_t{i_mutselect},
-                                                i_mut,
+                                                size_t{i_mut},
-                                                i_rep,
+                                                size_t{i_rep},
-                                                i_cont,
+                                                size_t{i_cont},
-                                                i_pop
+                                                size_t{pop_size} // offspring_size
                                             });
 
                                             // Actually perform a search
@@ -132,16 +120,13 @@ int main(int /*argc*/, char** /*argv*/)
                                                 best_sol = pop.best_element();
                                                 best_algo = foundry.name();
                                             }
-                                        }
                                     }
                                 }
                             }
                         }
-                    }
                 }
             }
         }
-    }
     std::cout << std::endl << "Best algo: " << best_algo << ", with " << best_sol << std::endl;
 
 }

eo/test/t-eoCheckpointing.cpp

@@ -31,8 +31,6 @@ public :
 int the_main(int argc, char **argv)
 { // ok, we have a command line parser and a state
 
-    typedef eoBit<float> Chrom;
-
     eoParser parser(argc, argv);
 
     // Define Parameters

eo/test/t-eoESAll.cpp

@@ -101,7 +101,7 @@ in test dir)
 template <class EOT>
 void runAlgorithm(EOT, eoParser& _parser, eoState& _state)
 {
-    typedef typename EOT::Fitness FitT;
+    // typedef typename EOT::Fitness FitT;
 
     ///// FIRST, problem or representation dependent stuff
     //////////////////////////////////////////////////////

eo/test/t-eoFoundryFastGA.cpp

@@ -20,15 +20,6 @@ eoAlgoFoundryFastGA<Bits>& make_foundry(eoFunctorStore& store, eoInit<Bits>& ini
         foundry.continuators.add< eoSteadyFitContinue<Bits> >(10,i);
     }
 
-    for(double i=0.1; i<1.0; i+=0.1) {
-        foundry.crossover_rates.add<double>(i);
-        foundry.mutation_rates.add<double>(i);
-    }
-
-    for(size_t i=5; i<100; i+=10) {
-        foundry.offspring_sizes.add<size_t>(i);
-    }
-
     /***** Crossovers ****/
     for(double i=0.1; i<0.9; i+=0.1) {
         foundry.crossovers.add< eoUBitXover<Bits> >(i); // preference over 1
@@ -39,13 +30,13 @@ eoAlgoFoundryFastGA<Bits>& make_foundry(eoFunctorStore& store, eoInit<Bits>& ini
     foundry.crossovers.add< eo1PtBitXover<Bits> >();
 
     /***** Mutations ****/
-    double p = 1.0; // Probability of flipping eath bit.
+    // Use defaults for all operators (usually falls back to p=1/chrom.size()).
-    foundry.mutations.add< eoUniformBitMutation<Bits> >(p); // proba of flipping k bits, k drawn in uniform distrib
+    foundry.mutations.add< eoUniformBitMutation<Bits> >(); // 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< eoStandardBitMutation<Bits> >(); // proba of flipping k bits, k drawn in binomial distrib
-    foundry.mutations.add< eoConditionalBitMutation<Bits> >(p); // proba of flipping k bits, k drawn in binomial distrib, minus zero
+    foundry.mutations.add< eoConditionalBitMutation<Bits> >(); // proba of flipping k bits, k drawn in binomial distrib, minus zero
-    foundry.mutations.add< eoShiftedBitMutation<Bits> >(p); // proba of flipping k bits, k drawn in binomial distrib, changing zeros to one
+    foundry.mutations.add< eoShiftedBitMutation<Bits> >(); // proba of flipping k bits, k drawn in binomial distrib, changing zeros to one
-    foundry.mutations.add< eoNormalBitMutation<Bits> >(p); // proba of flipping k bits, k drawn in normal distrib
+    foundry.mutations.add< eoNormalBitMutation<Bits> >(); // proba of flipping k bits, k drawn in normal distrib
-    foundry.mutations.add< eoFastBitMutation<Bits> >(p); // proba of flipping k bits, k drawn in powerlaw distrib
+    foundry.mutations.add< eoFastBitMutation<Bits> >(); // proba of flipping k bits, k drawn in powerlaw distrib
     for(size_t i=1; i < 11; i+=1) {
         foundry.mutations.add< eoDetSingleBitFlip<Bits> >(i); // mutate k bits without duplicates
     }
@@ -65,12 +56,6 @@ eoAlgoFoundryFastGA<Bits>& make_foundry(eoFunctorStore& store, eoInit<Bits>& ini
         }
     }
 
-    /***** Variation rates *****/
-    for(double r = 0.0; r < 1.0; r+=0.1) {
-        foundry.crossover_rates.add<double>(r);
-        foundry. mutation_rates.add<double>(r);
-    }
-
     /***** Replacements ****/
     foundry.replacements.add< eoPlusReplacement<Bits> >();
     foundry.replacements.add< eoCommaReplacement<Bits> >();
@@ -100,16 +85,13 @@ int main(int /*argc*/, char** /*argv*/)
 
 
     size_t n =
-          foundry.crossover_rates.size()
+          foundry.crossover_selectors.size()
-        * foundry.crossover_selectors.size()
-        * foundry.crossovers.size()
         * foundry.aftercross_selectors.size()
-        * foundry.mutation_rates.size()
         * foundry.mutation_selectors.size()
         * foundry.mutations.size()
         * foundry.replacements.size()
         * foundry.continuators.size()
-        * foundry.offspring_sizes.size();
+        ;
 
         std::clog << n << " possible algorithms instances." << std::endl;
 
@@ -117,7 +99,18 @@ int main(int /*argc*/, char** /*argv*/)
     pop.append(5,init);
     ::apply(onemax_eval,pop);
 
-    foundry.select({0,0,0,0,0,0,0,0});
+    foundry.select({
+            /*crossover_rates     */ double{0.8},
+            /*crossover_selectors */ size_t{0},
+            /*crossovers          */ size_t{0},
+            /*aftercross_selectors*/ size_t{0},
+            /*mutation_rates      */ double{0.9},
+            /*mutation_selectors  */ size_t{0},
+            /*mutations           */ size_t{0},
+            /*replacements        */ size_t{0},
+            /*continuators        */ size_t{0},
+            /*offspring_sizes     */ size_t{1},
+        });
     foundry(pop);
 
     std::cout << "Done" << std::endl;

eo/test/t-eoInitPermutation.cpp

@@ -43,7 +43,7 @@ int main()
   unsigned i;
 
    // a chromosome randomizer
-  eoInitPermutation <Chrom> random(CHROM_SIZE);
+  eoInitPermutation <Chrom> randomize(CHROM_SIZE);
 
    // the population:
   eoPop<Chrom> pop;
@@ -55,7 +55,7 @@ int main()
     {
       Chrom chrom(CHROM_SIZE);
       std::cout << " Initial chromosome n°" << i << " : " << chrom << "..." <<  std::endl;
-      random(chrom);
+      randomize(chrom);
       eval(chrom);
       std::cout << " ... becomes : " << chrom << " after initialization" << std::endl;
       check_permutation(chrom);

eo/test/t-eoRankingCached.cpp

@@ -0,0 +1,219 @@
+#include <apply.h>
+#include <eo>
+#include <eoRanking.h>
+#include <eoRankingCached.h>
+#include <es/eoReal.h>
+#include <utils/eoRNG.h>
+#include "real_value.h"
+
+class RankingTest
+{
+public:
+    RankingTest(eoParser &parser, eoEvalFuncCounter<eoReal<double>> &_eval, unsigned size = 100)
+        : rng(0),
+          popSize(size),
+          seedParam(parser.createParam(uint32_t(time(0)), "seed", "Random seed", 'S')),
+          pressureParam(parser.createParam(1.5, "pressure", "Selective pressure", 'p')),
+          exponentParam(parser.createParam(1.0, "exponent", "Ranking exponent", 'e')),
+          eval(_eval)
+    {
+        rng.reseed(seedParam.value());
+        initPopulation();
+    }
+
+    void initPopulation()
+    {
+        pop.clear();
+        for (unsigned i = 0; i < popSize; ++i)
+        {
+            eoReal<double> ind;
+            ind.resize(1);
+            ind[0] = rng.uniform();
+            pop.push_back(ind);
+        }
+        apply<eoReal<double>>(eval, pop);
+    }
+
+    const unsigned popSize;
+    eoPop<eoReal<double>> pop;
+    eoRng rng;
+    double pressure() const { return pressureParam.value(); }
+    double exponent() const { return exponentParam.value(); }
+
+private:
+    eoValueParam<uint32_t> &seedParam;
+    eoValueParam<double> &pressureParam;
+    eoValueParam<double> &exponentParam;
+    eoEvalFuncCounter<eoReal<double>> eval;
+};
+
+// Test case 1: Verify both implementations produce identical results
+void test_Consistency(eoParser &parser)
+{
+    eoEvalFuncPtr<eoReal<double>, double, const std::vector<double> &> mainEval(real_value);
+    eoEvalFuncCounter<eoReal<double>> eval(mainEval);
+    RankingTest fixture(parser, eval);
+
+    eoRanking<eoReal<double>> ranking(fixture.pressure(), fixture.exponent());
+    eoRankingCached<eoReal<double>> rankingCached(fixture.pressure(), fixture.exponent());
+
+    ranking(fixture.pop);
+    rankingCached(fixture.pop);
+
+    const std::vector<double> &values = ranking.value();
+    const std::vector<double> &cachedValues = rankingCached.value();
+
+    for (unsigned i = 0; i < fixture.pop.size(); ++i)
+    {
+        if (abs(values[i] - cachedValues[i]) > 1e-9)
+        {
+            throw std::runtime_error("Inconsistent ranking values between implementations");
+        }
+    }
+    std::clog << "Test 1 passed: Both implementations produce identical results" << std::endl;
+}
+
+// Test case 2: Test edge case with minimum population size
+void test_MinPopulationSize(eoParser &parser)
+{
+    eoPop<eoReal<double>> smallPop;
+    eoReal<double> ind1, ind2;
+    ind1.resize(1);
+    ind1[0] = 0.5;
+    ind2.resize(1);
+    ind2[0] = 1.0;
+    smallPop.push_back(ind1);
+    smallPop.push_back(ind2);
+    eoEvalFuncPtr<eoReal<double>, double, const std::vector<double> &> mainEval(real_value);
+    eoEvalFuncCounter<eoReal<double>> eval(mainEval);
+
+    RankingTest fixture(parser, eval, 2); // Use fixture to get parameters
+    eoRanking<eoReal<double>> ranking(fixture.pressure(), fixture.exponent());
+    eoRankingCached<eoReal<double>> rankingCached(fixture.pressure(), fixture.exponent());
+
+    apply<eoReal<double>>(eval, smallPop);
+
+    ranking(smallPop);
+    rankingCached(smallPop);
+
+    if (ranking.value()[0] >= ranking.value()[1] ||
+        rankingCached.value()[0] >= rankingCached.value()[1])
+    {
+        throw std::runtime_error("Invalid ranking for population size 2");
+    }
+    std::clog << "Test 2 passed: Minimum population size handled correctly" << std::endl;
+}
+
+// Test case 3: Verify caching actually works
+void test_CachingEffectiveness(eoParser &parser)
+{
+    eoEvalFuncPtr<eoReal<double>, double, const std::vector<double> &> mainEval(real_value);
+    eoEvalFuncCounter<eoReal<double>> eval(mainEval);
+    RankingTest fixture(parser, eval, 50); // Fixed size for cache test
+
+    eoRankingCached<eoReal<double>> rankingCached(fixture.pressure(), fixture.exponent());
+
+    // First run - should compute all values
+    rankingCached(fixture.pop);
+    const auto firstValues = rankingCached.value();
+
+    // Modify fitness values but keep same population size
+    for (auto &ind : fixture.pop)
+    {
+        ind[0] = fixture.rng.uniform();
+    }
+
+    apply<eoReal<double>>(eval, fixture.pop);
+
+    // Second run - should use cached coefficients
+    rankingCached(fixture.pop);
+
+    // Add one individual to invalidate cache
+    eoReal<double> newInd;
+    newInd.resize(1);
+    newInd[0] = fixture.rng.uniform();
+    fixture.pop.push_back(newInd);
+
+    apply<eoReal<double>>(eval, fixture.pop);
+
+    // Third run - should recompute coefficients
+    rankingCached(fixture.pop);
+
+    std::clog << "Test 3 passed: Caching mechanism properly invalidated" << std::endl;
+}
+
+// Helper function to test constructor assertions
+bool testRankingConstructor(double pressure, double exponent)
+{
+    try
+    {
+        eoRanking<eoReal<double>> ranking(pressure, exponent);
+        return true; // Constructor succeeded
+    }
+    catch (...)
+    {
+        return false; // Assertion failed
+    }
+}
+
+// Helper function to test constructor assertions
+bool testRankingCachedConstructor(double pressure, double exponent)
+{
+    try
+    {
+        eoRankingCached<eoReal<double>> ranking(pressure, exponent);
+        return true;
+    }
+    catch (...)
+    {
+        return false;
+    }
+}
+
+// Test case 4: Verify assertions on invalid parameters
+void test_Assertions(eoParser &parser)
+{
+    // Test valid parameters (should succeed)
+    bool valid_ok = true;
+    valid_ok &= testRankingConstructor(1.1, 1.0);       // Valid pressure
+    valid_ok &= testRankingCachedConstructor(1.1, 1.0); // Valid pressure
+
+    // Test invalid parameters (should fail)
+    bool invalid_ok = true;
+    invalid_ok &= !testRankingConstructor(1.0, 1.0);       // pressure = 1 (invalid)
+    invalid_ok &= !testRankingConstructor(0.5, 1.0);       // pressure < 1 (invalid)
+    invalid_ok &= !testRankingConstructor(2.1, 1.0);       // pressure > 2 (invalid)
+    invalid_ok &= !testRankingCachedConstructor(1.0, 1.0); // pressure = 1 (invalid)
+    invalid_ok &= !testRankingCachedConstructor(0.5, 1.0); // pressure < 1 (invalid)
+    invalid_ok &= !testRankingCachedConstructor(2.1, 1.0); // pressure > 2 (invalid)
+
+    if (!valid_ok)
+    {
+        throw std::runtime_error("Valid parameter tests failed");
+    }
+
+    if (!invalid_ok)
+    {
+        throw std::runtime_error("Invalid parameter tests failed - some invalid values were accepted");
+    }
+
+    std::clog << "Test 4 passed: All parameter assertions working correctly\n";
+}
+
+int main(int argc, char **argv)
+{
+    try
+    {
+        eoParser parser(argc, argv);
+        test_Consistency(parser);
+        test_MinPopulationSize(parser);
+        test_CachingEffectiveness(parser);
+        // test_Assertions(parser);
+        return 0;
+    }
+    catch (std::exception &e)
+    {
+        std::clog << "Exception: " << e.what() << std::endl;
+        return 1;
+    }
+}

eo/test/t-eoRealToIntMonOp.cpp

@@ -0,0 +1,28 @@
+#include <iostream>
+
+#include <eo>
+#include <es.h>
+
+using namespace std;
+
+int main(int, char**)
+{
+    eoIntInterval bounds(1,5);
+
+    using Chrom = eoInt<double>;
+    using MutWrapper = eoRealToIntMonOp<Chrom>;
+
+    eoDetUniformMutation< typename MutWrapper::EOTreal > mutreal(/*range*/6, /*nb*/5);
+
+    MutWrapper mutint(mutreal, bounds);
+
+    Chrom sol({1,2,3,4,5});
+
+    bool changed = mutint(sol);
+    assert(changed);
+
+    for(auto& x : sol) {
+        assert(bounds.isInBounds(x));
+    }
+}
+

eo/test/t-eoRealToIntQuadOp.cpp

@@ -0,0 +1,35 @@
+#include <iostream>
+
+#include <eo>
+#include <es.h>
+
+using namespace std;
+
+int main(int, char**)
+{
+    eoIntInterval intbounds(1,5);
+    eoRealInterval rb(1,5);
+    eoRealVectorBounds realbounds(5, rb);
+
+    using Chrom = eoInt<double>;
+    using CrossWrapper = eoRealToIntQuadOp<Chrom>;
+
+    eoSegmentCrossover< typename CrossWrapper::EOTreal > crossreal(realbounds, /*alpha*/0);
+
+    CrossWrapper crossint(crossreal, intbounds);
+
+    Chrom sol1({1,2,3,4,5});
+    Chrom sol2({1,2,3,4,5});
+
+    bool changed = crossint(sol1, sol2);
+    assert(changed);
+
+    for(auto& x : sol1) {
+        assert(intbounds.isInBounds(x));
+    }
+    for(auto& x : sol2) {
+        assert(intbounds.isInBounds(x));
+    }
+}
+
+

eo/test/t-eoSelect.cpp

@@ -126,7 +126,7 @@ eoValueParam<unsigned> tournamentSizeParam = parser.createParam(unsigned(2), "to
       }
 
     // hard-coded directory name ...
-    system("mkdir ResSelect");
+    (void) system("mkdir ResSelect");
     std::cout << "Testing the Selections\nParents size = " << pSize
 	 << ", offspring rate = " << oRate;
     std::cout << " and putting rsulting files in dir ResSelect" << std::endl;

eo/test/t-eoSharing.cpp

@@ -193,7 +193,7 @@ int the_main(int argc, char **argv)
 
       std::cout << "The resulting file (in dir ResSelect), contains \n";
     std::cout << " the empirical proba. for each indi to be selected." << std::endl;
-    system("mkdir ResSelect");
+    (void) system("mkdir ResSelect");
 
     // initialize parent population
     parentsOrg.resize(pSize);

eo/test/t-eoStateAndParser.cpp

@@ -37,8 +37,6 @@ struct Dummy : public EO<double>
 int the_main(int argc, char **argv)
 { // ok, we have a command line parser and a state
 
-    typedef eoBit<float> Chrom;
-
     eoParser parser(argc, argv);
 
     // Define Parameters

eo/test/t-eobin.cpp

@@ -123,17 +123,17 @@ void main_function()
 	   << chrom << " " << chrom2 << std::endl;
     }
 
-  for (i = 1; i < SIZE / 2; i++)
+  for (i = 1; i < SIZE / 2; i++) {
-    for (j = 1; j < SIZE / 2; j++)
+    for (j = 1; j < SIZE / 2; j++) {
-      {
+        eoBitGxOver<Chrom> gxover(i, j);
-	eoBitGxOver<Chrom> gxover(i, j);
+        std::fill(chrom.begin(), chrom.end(), false);
-	std::fill(chrom.begin(), chrom.end(), false);
+        std::fill(chrom2.begin(), chrom2.end(), true);
-	std::fill(chrom2.begin(), chrom2.end(), true);
+        gxover(chrom, chrom2);
-	gxover(chrom, chrom2);
+        chrom.fitness(binary_value(chrom)); chrom2.fitness(binary_value(chrom2));
-	chrom.fitness(binary_value(chrom)); chrom2.fitness(binary_value(chrom2));
+        std::cout  << "eoBinGxOver(" << i << ", " << j << ") ..... "
-	std::cout  << "eoBinGxOver(" << i << ", " << j << ") ..... "
+              << chrom << " " << chrom2 << std::endl;
-	      << chrom << " " << chrom2 << std::endl;
       }
+  }
 
     // test SGA algorithm
     eoGenContinue<Chrom> continuator1(50);

eo/test/t-forge-FastGA.cpp

@@ -19,7 +19,7 @@ int main(int /*argc*/, char** /*argv*/)
     eoBooleanGenerator gen(0.5);
     eoInitFixedLength<EOT> init(dim, gen);
 
-    eoGenContinue<EOT> common_cont(100);
+    eoGenContinue<EOT> common_cont(5);
 
     eoForgeVector< eoContinue<EOT> > continuators;
     continuators.add< eoSteadyFitContinue<EOT> >(10,10);

eo/tutorial/Lesson4/ESEA.cpp

@@ -87,7 +87,7 @@ int main(int argc, char **argv)
 template <class EOT>
 void runAlgorithm(EOT, eoParser& _parser, eoState& _state)
 {
-  typedef typename EOT::Fitness FitT;
+  // typedef typename EOT::Fitness FitT;
 
   ///// FIRST, problem or representation dependent stuff
   //////////////////////////////////////////////////////

howto_build_paradiseo.apptainer.def

@@ -0,0 +1,54 @@
+Bootstrap: docker
+From: ubuntu:24.04
+
+%post
+    # Update the available packages list.
+    apt -y update
+    # And add the "universe" repository (allow to install many more software).
+    apt -y install software-properties-common
+    add-apt-repository universe
+    apt -y update
+    # Update the operating systems (install last versions with bugfixes).
+    apt -y dist-upgrade
+
+    # Install dependencies for your project.
+    apt -y install git g++ cmake ccache make libeigen3-dev libopenmpi-dev doxygen graphviz libgnuplot-iostream-dev
+
+    # Download sources.
+    git clone --branch master --single-branch --recurse-submodules https://github.com/nojhan/paradiseo
+    cd paradiseo
+
+    # Build directory that holds built binaries and cache.
+    mkdir -p build
+    cd build
+
+    # Example of minimum build:
+    # Use that if you want the minimal set of libraries needed to build a simple solver.
+    # cmake -DCMAKE_BUILD_TYPE=Release -DEDO=ON .. && make
+
+    # Example of trying to build everything:
+    # Use that to test if everything can be built with your setup,
+    # or if you modified something in Paradiseo and want to test it.
+    cmake -DCMAKE_BUILD_TYPE=Release -DEDO=ON -DENABLE_CMAKE_EXAMPLE=ON -DENABLE_CMAKE_TESTING=ON -DENABLE_GNUPLOT=ON -DENABLE_OPENMP=ON -DMPI=ON -DSMP=ON .. && make
+
+    # You may run the tests, to check if everything works:
+    ctest
+
+    # Make the documentation:
+    make doc
+
+    # Clean-up of the APT cache (will lighten the container).
+    apt -y purge software-properties-common git g++ cmake ccache make libeigen3-dev libopenmpi-dev doxygen graphviz libgnuplot-iostream-dev
+    apt -y --purge autoremove
+    apt -y autoclean
+    apt clean
+
+%environment
+
+%runscript
+    # When executing the container, this will be called,
+    # and pass all the command line arguments.
+    ./paradiseo/build/edo/application/cmaes/cmaes $*
+
+%labels
+    Author Johann Dreo

mo/doc/CMakeLists.txt

@@ -19,7 +19,8 @@ if(DOXYGEN_FOUND)
                 WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR})
         endif(UNIX AND NOT ${CMAKE_VERBOSE_MAKEFILE})
     endif(DOXYGEN_EXECUTABLE)
-    configure_file("${CMAKE_CURRENT_SOURCE_DIR}/${MO_DOC_CONFIG_FILE}.cmake"
+    # configure_file("${CMAKE_CURRENT_SOURCE_DIR}/${MO_DOC_CONFIG_FILE}.cmake"
+    configure_file("${DOXYGEN_CONFIG_DIR}/doxyfile.cmake"
                    "${MO_DOC_DIR}/${MO_DOC_CONFIG_FILE}")
     install(
         DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}

mo/doc/mo.doxyfile.cmake

@@ -31,7 +31,7 @@ PROJECT_NAME           = @MO_MODULE_NAME@
 # 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. 
@@ -987,7 +987,7 @@ FORMULA_FONTSIZE       = 10
 # 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 

mo/src/acceptCrit/moAlwaysAcceptCrit.h

@@ -48,7 +48,7 @@ public:
      * @param _sol2 the new solution after local search
      * @return always true
      */
-    bool operator()(EOT& _sol1, EOT& _sol2) {
+    bool operator()(EOT& /*_sol1*/, EOT& /*_sol2*/) {
         return true;
     }
 

mo/src/algo/eoDummyMonOp.h

@@ -47,7 +47,7 @@ public:
    * Do nothing on the solution
    * @param _solution the related solution
    */
-  virtual bool operator()(EOT & _solution) {
+  virtual bool operator()(EOT & /*_solution*/) {
     return true;
   }
 };

mo/src/algo/moSA.h

@@ -79,6 +79,20 @@ public:
             explorer(_neighborhood, _eval, defaultSolNeighborComp, _cool)
     {}
 
+    /**
+     * Constructor without cooling schedule, but with a continuator.
+     *
+     * @param _neighborhood the neighborhood
+     * @param _fullEval the full evaluation function
+     * @param _eval neighbor's evaluation function
+     * @param _cont an external continuator
+     */
+    moSA(Neighborhood& _neighborhood, eoEvalFunc<EOT>& _fullEval, moEval<Neighbor>& _eval, moContinuator<Neighbor>& _cont):
+            moLocalSearch<Neighbor>(explorer, _cont, _fullEval),
+            defaultCool(0, 0, 0, 0),
+            explorer(_neighborhood, _eval, defaultSolNeighborComp, defaultCool)
+    {}
+
     /**
      * General constructor for a simulated annealing
      * @param _neighborhood the neighborhood