* New tree configuration of the project:

.../
   ...           + -- EO
   |             |
   |             |
   +-- src ----- + -- EDO
   |             |
   |             |
   +-- test      + -- MO
   |             |
   |             |
   +-- tutorial  + -- MOEO
   |             |
   |             |
   +-- doc       + -- SMP
   |             |
   |             |
   ...           + -- EOMPI
                 |
                 |
                 + -- EOSERIAL

Question for current maintainers: ./README: new release?

Also:

* Moving out eompi & eoserial modules (issue #2).

* Correction of the errors when executing "make doc" command.

* Adding a solution for the conflicting headers problem (see the two CMake Cache
 Values: PROJECT_TAG & PROJECT_HRS_INSTALL_SUBPATH) (issue #1)

* Header inclusions:
        ** src: changing absolute paths into relative paths ('#include <...>' -> '#include "..."')
        ** test, tutorial: changing relative paths into absolute paths ('#include "..."' -> '#include <...>')

* Moving out some scripts from EDO -> to the root

* Add a new script for compilation and installation (see build_gcc_linux_install)

* Compilation with uBLAS library or EDO module: now ok

* Minor modifications on README & INSTALL files

* Comment eompi failed tests with no end

*** TODO: CPack (debian (DEB) & RedHat (RPM) packages) (issues #6 & #7) ***

tutorial/mo/Lesson7/hybridAlgo.cpp

@@ -0,0 +1,222 @@
+//-----------------------------------------------------------------------------
+/** testILS.cpp
+ *
+ * SV - 12/01/10
+ * JH - 06/05/10
+ *
+ */
+//-----------------------------------------------------------------------------
+
+// standard includes
+#define HAVE_SSTREAM
+
+#include <stdexcept>  // runtime_error
+#include <iostream>   // cout
+#include <sstream>  // ostrstream, istrstream
+#include <fstream>
+#include <string.h>
+
+// the general include for eo
+#include <paradiseo/eo.h>
+#include <paradiseo/eo/ga.h>
+#include <paradiseo/eo/ga/eoBitOp.h>
+
+using namespace std;
+
+//-----------------------------------------------------------------------------
+//Representation and initializer
+#include <paradiseo/eo/eoInt.h>
+#include <paradiseo/eo/eoInit.h>
+#include <paradiseo/eo/eoScalarFitness.h>
+
+// fitness function
+#include <paradiseo/problems/eval/queenEval.h>
+#include <paradiseo/mo/eval/moFullEvalByModif.h>
+#include <paradiseo/mo/eval/moFullEvalByCopy.h>
+
+//Neighbors and Neighborhoods
+#include <paradiseo/mo/problems/permutation/moShiftNeighbor.h>
+#include <paradiseo/mo/neighborhood/moOrderNeighborhood.h>
+
+//Mutation
+#include <paradiseo/eo/eoSwapMutation.h>
+#include <paradiseo/eo/eoOrderXover.h>
+
+//Algorithm and its components
+#include <paradiseo/mo/algo/moFirstImprHC.h>
+
+//mo eval
+#include <paradiseo/mo/eval/moFullEvalByCopy.h>
+
+#include <paradiseo/mo/continuator/moTrueContinuator.h>
+
+// REPRESENTATION
+//-----------------------------------------------------------------------------
+typedef eoInt<eoMinimizingFitness> Queen; //Permutation (Queen's problem representation)
+
+typedef moShiftNeighbor<Queen> shiftNeighbor; //shift Neighbor
+typedef moOrderNeighborhood<shiftNeighbor> orderShiftNeighborhood; //order shift Neighborhood (Indexed)
+
+void main_function(int argc, char **argv)
+{
+    /* =========================================================
+    *
+    * Parameters
+    *
+    * ========================================================= */
+
+    // First define a parser from the command-line arguments
+    eoParser parser(argc, argv);
+
+    // For each parameter, define Parameter, read it through the parser,
+    // and assign the value to the variable
+
+    eoValueParam<uint32_t> seedParam(time(0), "seed", "Random number seed", 'S');
+    parser.processParam( seedParam );
+    unsigned seed = seedParam.value();
+
+    // description of genotype
+    eoValueParam<unsigned int> vecSizeParam(8, "vecSize", "Genotype size", 'V');
+    parser.processParam( vecSizeParam, "Representation" );
+    unsigned vecSize = vecSizeParam.value();
+
+    // the name of the "status" file where all actual parameter values will be saved
+    string str_status = parser.ProgramName() + ".status"; // default value
+    eoValueParam<string> statusParam(str_status.c_str(), "status", "Status file");
+    parser.processParam( statusParam, "Persistence" );
+
+    // do the following AFTER ALL PARAMETERS HAVE BEEN PROCESSED
+    // i.e. in case you need parameters somewhere else, postpone these
+    if (parser.userNeedsHelp()) {
+        parser.printHelp(cout);
+        exit(1);
+    }
+    if (statusParam.value() != "") {
+        ofstream os(statusParam.value().c_str());
+        os << parser;// and you can use that file as parameter file
+    }
+
+    /* =========================================================
+     *
+     * Random seed
+     *
+     * ========================================================= */
+
+    //reproducible random seed: if you don't change SEED above,
+    // you'll aways get the same result, NOT a random run
+    rng.reseed(seed);
+
+    /* =========================================================
+     *
+     * Full evaluation fitness function
+     *
+     * ========================================================= */
+
+    queenEval<Queen> fullEval;
+
+
+    /* =========================================================
+     *
+     * Initializer of a solution
+     *
+     * ========================================================= */
+
+    eoInitPermutation<Queen> init(vecSize);
+
+    /* =========================================================
+     *
+     * Declare and init a population
+     *
+     * ========================================================= */
+
+    eoPop<Queen> pop;
+
+    Queen tmp;
+
+    for (unsigned int i=0; i<20; i++) {
+        init(tmp);
+        fullEval(tmp);
+        pop.push_back(tmp);
+    }
+
+    /* =========================================================
+     *
+     * evaluation of a neighbor solution
+     *
+     * ========================================================= */
+
+    moFullEvalByCopy<shiftNeighbor> shiftEval(fullEval);
+
+    /* =========================================================
+     *
+     * the neighborhood of a solution
+     *
+     * ========================================================= */
+
+    orderShiftNeighborhood orderShiftNH((vecSize-1) * (vecSize-1));
+
+    /* =========================================================
+     *
+     * the local search algorithm
+     *
+     * ========================================================= */
+
+    //Basic Constructor a first improvement hill climber
+    moFirstImprHC<shiftNeighbor> hc(orderShiftNH, fullEval, shiftEval);
+
+    /* =========================================================
+     *
+     * the evolutionary algorithm
+     *
+     * ========================================================= */
+
+    //continuator
+    eoGenContinue<Queen> EAcont(50);
+
+    //selection
+    eoDetTournamentSelect<Queen> selectOne(2);
+    eoSelectMany<Queen> select(selectOne, 1);
+
+    //crossover
+    eoOrderXover<Queen> cross;
+
+    //transform operator (the hill climber replace the mutation operator)
+    eoSGATransform<Queen> transform(cross, 0.3, hc, 0.7);
+
+    //replacement
+    eoGenerationalReplacement<Queen> repl;
+
+    //easyEA
+    eoEasyEA<Queen> hybridAlgo(EAcont, fullEval, select, transform, repl);
+
+
+    std::cout << "INITIAL POPULATION:" << std::endl;
+    std::cout << "-------------------" << std::endl;
+
+    for (unsigned int i=0; i<pop.size(); i++)
+        std::cout << pop[i] << std::endl;
+
+    hybridAlgo(pop);
+
+    std::cout << std::endl;
+    std::cout << "FINAL POPULATION:" << std::endl;
+    std::cout << "-------------------" << std::endl;
+    for (unsigned int i=0; i<pop.size(); i++)
+        std::cout << pop[i] << std::endl;
+
+
+}
+
+
+// A main that catches the exceptions
+
+int main(int argc, char **argv)
+{
+    try {
+        main_function(argc, argv);
+    }
+    catch (exception& e) {
+        cout << "Exception: " << e.what() << '\n';
+    }
+    return 1;
+}