Merge branch 'master' of ssh://eodev.git.sourceforge.net/gitroot/eodev/eodev

edo/src/edoNormalMulti.h

@@ -1,4 +1,24 @@
-// (c) Thales group, 2010
+/*
+The Evolving Distribution Objects framework (EDO) is a template-based,
+ANSI-C++ evolutionary computation library which helps you to write your
+own estimation of distribution algorithms.
+
+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 2.1 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., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
+
+Copyright (C) 2010 Thales group
+*/
 /*
     Authors:
 	     Johann Dreo <johann.dreo@thalesgroup.com>

eo/CMakeLists.txt

@@ -1,3 +1,4 @@
+CMAKE_MINIMUM_REQUIRED(VERSION 2.6)
 
 ######################################################################################
 ### 0) If you want to set your variables in eo-conf.cmake and avoid the cmd line

eo/eo-conf.cmake

@@ -5,3 +5,4 @@ SET(PROJECT_VERSION_MINOR 3)
 SET(PROJECT_VERSION_PATCH 0)
 SET(PROJECT_VERSION_MISC "-edge")
 
+# ADD_DEFINITIONS(-DDEPRECATED_MESSAGES) # disable warning deprecated function messages

eo/install_symlink.py.cmake

@@ -21,19 +21,19 @@ import os, sys
 
 def isroot():
     if os.getuid() != 0:
-	print '[WARNING] you have to be root'
+        print('[WARNING] you have to be root')
         return False
     return True
 
 def uninstall():
     for dummy, link in DATA['links']: os.remove(link)
     for dirname in DATA['dirs']: os.rmdir(dirname)
-    print 'All symlinks have been removed.'
+    print('All symlinks have been removed.')
 
 def install():
     for dirname in DATA['dirs']: os.mkdir(dirname)
     for src, dst in DATA['links']: os.symlink(src, dst)
-    print 'All symlinks have been installed.'
+    print('All symlinks have been installed.')
 
 def data():
     from pprint import pprint
@@ -44,7 +44,7 @@ if __name__ == '__main__':
         sys.exit()
 
     if len(sys.argv) < 2:
-	print 'Usage: %s [install|uninstall|data]' % sys.argv[0]
+        print(('Usage: %s [install|uninstall|data]' % sys.argv[0]))
         sys.exit()
 
     if sys.argv[1] == 'install': install()

eo/src/do/make_checkpoint.h

@@ -1,13 +1,8 @@
 // -*- mode: c++; c-indent-level: 4; c++-member-init-indent: 8; comment-column: 35; -*-
 
-
-
 //-----------------------------------------------------------------------------
-
 // make_checkpoint.h
-
 // (c) Maarten Keijzer, Marc Schoenauer and GeNeura Team, 2000
-
 /*
   This library is free software; you can redistribute it and/or
   modify it under the terms of the GNU Lesser General Public
@@ -24,22 +19,14 @@
   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 _make_checkpoint_h
-
 #define _make_checkpoint_h
 
-
 #ifdef HAVE_CONFIG_H
 #include <config.h>
 #endif
@@ -52,521 +39,315 @@
 #include <eoEvalFuncCounter.h>
 #include <utils/checkpointing>
 
-
-
 // at the moment, in utils/make_help.cpp
-
 // this should become some eoUtils.cpp with corresponding eoUtils.h
-
 bool testDirRes(std::string _dirName, bool _erase);
-
 /////////////////// The checkpoint and other I/O //////////////
 
-
-
-
 /**
  *
  * CHANGE (March 2008): now receiving an eoValueParam instead of an eoEvalFuncCounter. This function is just interested
  * in the value of the parameter calculated on the evaluation function, not in the actual function itself!!
  *
  * @ingroup Builders
-*/
+ */
 template <class EOT>
 eoCheckPoint<EOT>& do_make_checkpoint(eoParser& _parser, eoState& _state, eoValueParam<unsigned long>& _eval, eoContinue<EOT>& _continue)
 {
-
     // first, create a checkpoint from the eoContinue
     eoCheckPoint<EOT> *checkpoint = new eoCheckPoint<EOT>(_continue);
 
     _state.storeFunctor(checkpoint);
 
+    ////////////////////
+    // Signal monitoring
+    ////////////////////
 
+#ifndef _MSC_VER
+    // the CtrlC monitoring interception
+    eoSignal<EOT> *mon_ctrlCCont;
+    eoValueParam<bool>& mon_ctrlCParam = _parser.createParam(false, "monitor-with-CtrlC", "Monitor current generation upon Ctrl C",0, "Stopping criterion");
+    if (mon_ctrlCParam.value())
+      {
+        mon_ctrlCCont = new eoSignal<EOT>;
+        // store
+        _state.storeFunctor(mon_ctrlCCont);
+        // add to checkpoint
+	checkpoint->add(*mon_ctrlCCont);
+      }
+#endif
 
     ///////////////////
-
     // Counters
-
     //////////////////
 
     // is nb Eval to be used as counter?
-
     eoValueParam<bool>& useEvalParam = _parser.createParam(true, "useEval", "Use nb of eval. as counter (vs nb of gen.)", '\0', "Output");
-
     eoValueParam<bool>& useTimeParam = _parser.createParam(true, "useTime", "Display time (s) every generation", '\0', "Output");
-
-
-
     // if we want the time, we need an eoTimeCounter
-
     eoTimeCounter * tCounter = NULL;
 
-
-
     // Create anyway a generation-counter
-
     // Recent change (03/2002): it is now an eoIncrementorParam, both
-
     // a parameter AND updater so you can store it into the eoState
-
     eoIncrementorParam<unsigned> *generationCounter = new eoIncrementorParam<unsigned>("Gen.");
 
     // store it in the state
-
     _state.storeFunctor(generationCounter);
 
     // And add it to the checkpoint,
-
     checkpoint->add(*generationCounter);
 
-
-
     // dir for DISK output
-
     eoValueParam<std::string>& dirNameParam =  _parser.createParam(std::string("Res"), "resDir", "Directory to store DISK outputs", '\0', "Output - Disk");
 
     // shoudl we empty it if exists
-
     eoValueParam<bool>& eraseParam = _parser.createParam(true, "eraseDir", "erase files in dirName if any", '\0', "Output - Disk");
 
     bool dirOK = false;            // not tested yet
 
-
-
     /////////////////////////////////////////
-
     // now some statistics on the population:
-
     /////////////////////////////////////////
 
     /**
-
      * existing stats as of today, April 10. 2001
-
      *
-
      * eoBestFitnessStat : best value in pop - type EOT::Fitness
-
      * eoAverageStat     : average value in pop - type EOT::Fitness
-
      * eoSecondMomentStat: average + stdev - type std::pair<double, double>
-
      * eoSortedPopStat   : whole population - type std::string (!!)
-
      * eoScalarFitnessStat: the fitnesses - type std::vector<double>
-
      */
 
-
-
     // Best fitness in population
-
     //---------------------------
-
     eoValueParam<bool>& printBestParam = _parser.createParam(true, "printBestStat", "Print Best/avg/stdev every gen.", '\0', "Output");
-
     eoValueParam<bool>& plotBestParam = _parser.createParam(false, "plotBestStat", "Plot Best/avg Stat", '\0', "Output - Graphical");
-
     eoValueParam<bool>& fileBestParam = _parser.createParam(false, "fileBestStat", "Output bes/avg/std to file", '\0', "Output - Disk");
 
-
-
     eoBestFitnessStat<EOT> *bestStat = NULL;
-
     if ( printBestParam.value() || plotBestParam.value() || fileBestParam.value() )
-
 	// we need the bestStat for at least one of the 3 above
-
 	{
-
 	    bestStat = new eoBestFitnessStat<EOT>;
-
 	    // store it
-
 	    _state.storeFunctor(bestStat);
-
 	    // add it to the checkpoint
-
 	    checkpoint->add(*bestStat);
-
+	    // check if monitoring with signal
+	    if ( mon_ctrlCParam.value() )
+		mon_ctrlCCont->add(*bestStat);
 	}
 
-
-
     // Average fitness alone
-
     //----------------------
-
     eoAverageStat<EOT> *averageStat = NULL; // do we need averageStat?
-
+    if ( printBestParam.value() || plotBestParam.value() || fileBestParam.value() ) // we need it for gnuplot output
-    if ( plotBestParam.value() ) // we need it for gnuplot output
-
 	{
-
 	    averageStat = new eoAverageStat<EOT>;
-
 	    // store it
-
 	    _state.storeFunctor(averageStat);
-
 	    // add it to the checkpoint
-
 	    checkpoint->add(*averageStat);
-
+	    // check if monitoring with signal
+	    if ( mon_ctrlCParam.value() )
+		mon_ctrlCCont->add(*averageStat);
 	}
 
-
-
     // Second moment stats: average and stdev
-
     //---------------------------------------
-
     eoSecondMomentStats<EOT> *secondStat = NULL;
-
     if ( printBestParam.value() || fileBestParam.value() ) // we need it for screen output or file output
-
 	{
-
 	    secondStat = new eoSecondMomentStats<EOT>;
-
 	    // store it
-
 	    _state.storeFunctor(secondStat);
-
 	    // add it to the checkpoint
-
 	    checkpoint->add(*secondStat);
-
+	    // check if monitoring with signal
+	    if ( mon_ctrlCParam.value() )
+		mon_ctrlCCont->add(*secondStat);
 	}
 
-
-
-
-
     // Dump of the whole population
-
     //-----------------------------
-
     eoSortedPopStat<EOT> *popStat = NULL;
-
     eoValueParam<bool>& printPopParam = _parser.createParam(false, "printPop", "Print sorted pop. every gen.", '\0', "Output");
 
     if ( printPopParam.value() ) // we do want pop dump
-
 	{
-
 	    popStat = new eoSortedPopStat<EOT>;
-
 	    // store it
-
 	    _state.storeFunctor(popStat);
-
 	    // add it to the checkpoint
-
 	    checkpoint->add(*popStat);
-
+	    // check if monitoring with signal
+	    if ( mon_ctrlCParam.value() )
+		mon_ctrlCCont->add(*popStat);
 	}
 
-
-
-
-
     // do we wnat some histogram of fitnesses snpashots?
-
     eoValueParam<bool> plotHistogramParam = _parser.createParam(false, "plotHisto", "Plot histogram of fitnesses", '\0', "Output - Graphical");
 
-
-
     ///////////////
-
     // The monitors
-
     ///////////////
 
     // do we want an eoStdoutMonitor?
-
     bool needStdoutMonitor = printBestParam.value()
-
         || printPopParam.value() ;
 
-
-
     // The Stdout monitor will print parameters to the screen ...
-
     if ( needStdoutMonitor )
-
 	{
-
 	    eoStdoutMonitor *monitor = new eoStdoutMonitor(false);
-
 	    _state.storeFunctor(monitor);
 
-
-
 	    // when called by the checkpoint (i.e. at every generation)
-
+	    // check if monitoring with signal
+	    if ( ! mon_ctrlCParam.value() )
 		checkpoint->add(*monitor);
-
+	    else
-
+		mon_ctrlCCont->add(*monitor);
 
 	    // the monitor will output a series of parameters: add them
-
 	    monitor->add(*generationCounter);
 
 	    if (useEvalParam.value()) // we want nb of evaluations
-
 		monitor->add(_eval);
-
 	    if (useTimeParam.value()) // we want time
-
 		{
-
 		    tCounter = new eoTimeCounter;
-
 		    _state.storeFunctor(tCounter);
-
+		    // check if monitoring with signal
+		    if ( ! mon_ctrlCParam.value() )
 			checkpoint->add(*tCounter);
-
+		    else
+			mon_ctrlCCont->add(*tCounter);
 		    monitor->add(*tCounter);
-
 		}
 
 	    if (printBestParam.value())
-
 		{
-
 		    monitor->add(*bestStat);
-
 		    monitor->add(*secondStat);
-
 		}
 
 	    if ( printPopParam.value())
-
 		monitor->add(*popStat);
-
 	}
 
-
-
     // first handle the dir test - if we need at least one file
-
     if ( ( fileBestParam.value() || plotBestParam.value() ||
-
            plotHistogramParam.value() )
-
          && !dirOK )               // just in case we add something before
-
 	dirOK = testDirRes(dirNameParam.value(), eraseParam.value()); // TRUE
 
-
-
     if (fileBestParam.value())    // A file monitor for best & secondMoment
-
 	{
-
 #ifdef _MSVC
-
 	    std::string stmp = dirNameParam.value() + "\best.xg";
-
 #else
-
 	    std::string stmp = dirNameParam.value() + "/best.xg";
-
 #endif
-
 	    eoFileMonitor *fileMonitor = new eoFileMonitor(stmp);
-
 	    // save and give to checkpoint
-
 	    _state.storeFunctor(fileMonitor);
-
 	    checkpoint->add(*fileMonitor);
-
 	    // and feed with some statistics
-
 	    fileMonitor->add(*generationCounter);
-
 	    fileMonitor->add(_eval);
-
 	    if (tCounter)              // we want the time as well
-
 		{
-
 		    //      std::cout << "On met timecounter\n";
-
 		    fileMonitor->add(*tCounter);
-
 		}
-
 	    fileMonitor->add(*bestStat);
-
 	    fileMonitor->add(*secondStat);
-
 	}
 
-
-
 #if defined(HAVE_GNUPLOT)
-
     if (plotBestParam.value())    // an eoGnuplot1DMonitor for best & average
-
 	{
-
 	    std::string stmp = dirNameParam.value() + "/gnu_best.xg";
-
 	    eoGnuplot1DMonitor *gnuMonitor = new eoGnuplot1DMonitor(stmp,minimizing_fitness<EOT>());
-
 	    // save and give to checkpoint
-
 	    _state.storeFunctor(gnuMonitor);
-
 	    checkpoint->add(*gnuMonitor);
-
 	    // and feed with some statistics
-
 	    if (useEvalParam.value())  // do we want eval as X coordinate
-
 		gnuMonitor->add(_eval);
-
 	    else if (tCounter)         // or time?
-
 		gnuMonitor->add(*tCounter);
-
 	    else                       // default: generation
-
 		gnuMonitor->add(*generationCounter);
-
 	    gnuMonitor->add(*bestStat);
-
 	    gnuMonitor->add(*averageStat);
-
 	}
 
-
-
     // historgram?
-
     if (plotHistogramParam.value()) // want to see how the fitness is spread?
-
 	{
-
 	    eoScalarFitnessStat<EOT> *fitStat = new eoScalarFitnessStat<EOT>;
-
 	    _state.storeFunctor(fitStat);
-
 	    checkpoint->add(*fitStat);
-
 	    // a gnuplot-based monitor for snapshots: needs a dir name
-
 	    eoGnuplot1DSnapshot *fitSnapshot = new eoGnuplot1DSnapshot(dirNameParam.value());
-
 	    _state.storeFunctor(fitSnapshot);
-
 	    // add any stat that is a std::vector<double> to it
-
 	    fitSnapshot->add(*fitStat);
-
 	    // and of course add it to the checkpoint
-
 	    checkpoint->add(*fitSnapshot);
-
 	}
 
 #endif
 
     //////////////////////////////////
-
     // State savers
-
     //////////////////////////////
 
-
-
     // feed the state to state savers
-
     // save state every N  generation
-
     eoValueParam<unsigned>& saveFrequencyParam = _parser.createParam(unsigned(0), "saveFrequency", "Save every F generation (0 = only final state, absent = never)", '\0', "Persistence" );
 
-
-
     if (_parser.isItThere(saveFrequencyParam))
-
 	{
-
 	    // first make sure dirName is OK
-
 	    if (! dirOK )
-
 		dirOK = testDirRes(dirNameParam.value(), eraseParam.value()); // TRUE
 
-
-
 	    unsigned freq = (saveFrequencyParam.value()>0 ? saveFrequencyParam.value() : UINT_MAX );
-
 #ifdef _MSVC
-
 	    std::string stmp = dirNameParam.value() + "\generations";
-
 #else
-
 	    std::string stmp = dirNameParam.value() + "/generations";
-
 #endif
-
 	    eoCountedStateSaver *stateSaver1 = new eoCountedStateSaver(freq, _state, stmp);
-
 	    _state.storeFunctor(stateSaver1);
-
 	    checkpoint->add(*stateSaver1);
-
 	}
 
-
-
     // save state every T seconds
-
     eoValueParam<unsigned>& saveTimeIntervalParam = _parser.createParam(unsigned(0), "saveTimeInterval", "Save every T seconds (0 or absent = never)", '\0',"Persistence" );
-
     if (_parser.isItThere(saveTimeIntervalParam) && saveTimeIntervalParam.value()>0)
-
 	{
-
 	    // first make sure dirName is OK
-
 	    if (! dirOK )
-
 		dirOK = testDirRes(dirNameParam.value(), eraseParam.value()); // TRUE
 
-
-
 #ifdef _MSVC
-
 	    std::string stmp = dirNameParam.value() + "\time";
-
 #else
-
 	    std::string stmp = dirNameParam.value() + "/time";
-
 #endif
-
 	    eoTimedStateSaver *stateSaver2 = new eoTimedStateSaver(saveTimeIntervalParam.value(), _state, stmp);
-
 	    _state.storeFunctor(stateSaver2);
-
 	    checkpoint->add(*stateSaver2);
-
 	}
 
-
-
     // and that's it for the (control and) output
-
     return *checkpoint;
-
 }
 
-
-
 #endif

eo/src/eoCombinedContinue.h

@@ -61,7 +61,9 @@ public:
   eoCombinedContinue( eoContinue<EOT>& _cont1, eoContinue<EOT>& _cont2)
     : eoContinue<EOT>(), std::vector<eoContinue<EOT>* >()
   {
+#ifndef DEPRECATED_MESSAGES
 #pragma message "The double continuators constructor of eocombinedContinue is deprecated and will be removed in the next release."
+#endif // !DEPRECATED_MESSAGES
 
     this->push_back(&_cont1);
     this->push_back(&_cont2);
@@ -74,7 +76,10 @@ public:
 
   void removeLast(void)
   {
+#ifndef DEPRECATED_MESSAGES
 #pragma message "The removeLast method of eocombinedContinue is deprecated and will be removed in the next release, use pop_back instead."
+#endif // !DEPRECATED_MESSAGES
+
     this->pop_back();
   }
 

eo/src/eoCtrlCContinue.h

@@ -30,7 +30,7 @@
 #ifndef eoCtrlCContinue_h
 #define eoCtrlCContinue_h
 
-#include <signal.h>
+#include <csignal>
 #include <eoContinue.h>
 
 /**

eo/src/eoFlight.h

@@ -46,7 +46,7 @@ public:
     {
         for (unsigned i = 0; i < _pop.size (); i++)
         {
-            operator  ()(_pop[i]);
+            this->operator  ()(_pop[i]);
         }
 
     }

eo/src/eoInitializer.h

@@ -129,7 +129,7 @@ private :
 class eoDummyEval : public eoPopEvalFunc<POT>
     {
     public:
-        void operator()(eoPop<POT> &,eoPop<POT> &_pop)
+        void operator()(eoPop<POT> &,eoPop<POT> &/*_pop*/)
         {}
     }
     dummyEval;

eo/src/eoParticleBestInit.h

@@ -46,7 +46,7 @@ public:
     {
         for (unsigned i = 0; i < _pop.size (); i++)
         {
-            operator  ()(_pop[i]);
+            this->operator  ()(_pop[i]);
         }
 
     }

eo/src/eoPeriodicContinue.h

@@ -39,7 +39,7 @@ public:
 
   /** It returns 'true' only if the current number of generations modulo
       the period doen't equal to zero. */
-  bool operator () (const eoPop <EOT> & pop)
+  bool operator () (const eoPop <EOT> & /*pop*/)
   {
     return ((++ counter) % period) != 0 ;
   }

eo/src/eoProportionalCombinedOp.h

@@ -188,8 +188,11 @@ public:
 
   virtual void add(eoQuadOp<EOT> & _op, const double _rate, bool _verbose)
   {
+#ifndef DEPRECATED_MESSAGES
 #pragma message "The use of the verbose parameter in eoPropCombinedQuadOp::add is deprecated and will be removed in the next release."
     eo::log << eo::warnings << "WARNING: the use of the verbose parameter in eoPropCombinedQuadOp::add is deprecated and will be removed in the next release." << std::endl;
+#endif // !DEPRECATED_MESSAGES
+
     add(_op,_rate);
   }
 

eo/src/eoProportionalSelect.h

@@ -46,7 +46,7 @@ template <class EOT> class eoProportionalSelect: public eoSelectOne<EOT>
 {
 public:
   /// Sanity check
-  eoProportionalSelect(const eoPop<EOT>& pop = eoPop<EOT>())
+  eoProportionalSelect(const eoPop<EOT>& /*pop*/ = eoPop<EOT>())
   {
     if (minimizing_fitness<EOT>())
       throw std::logic_error("eoProportionalSelect: minimizing fitness");

eo/src/eoReduceSplit.h

@@ -104,7 +104,7 @@ public:
     unsigned eliminated = howMany(popSize);
     if (!eliminated)   // nothing to do
       return ;
-    unsigned newsize = popSize - eliminated;
+    long newsize = static_cast<long>(popSize) - static_cast<long>(eliminated);
     if (newsize < 0)
       throw std::logic_error("eoLinearTruncateSplit: Cannot truncate to a larger size!\n");
 

eo/src/eoScalarFitnessAssembled.h

@@ -212,7 +212,7 @@ public:
   //! Print term values and descriptions
   void printAll(std::ostream& os) const {
     for (size_type i=0; i < size(); ++i )
-      os << FitnessTraits::getDescription(i) << " = " << operator[](i) << " ";
+      os << FitnessTraits::getDescription(i) << " = " << this->operator[](i) << " ";
   }
 
   //! Comparison, using less by default

eo/src/eoSelectFromWorth.h

@@ -217,7 +217,7 @@ public:
 
 #ifndef NDEBUG
   // check whether the stuff is still in sync
-  check_sync(index, _pop[index]);
+  this->check_sync(index, _pop[index]);
 #endif
 
     return _pop[index];

eo/src/eoSyncEasyPSO.h

@@ -241,7 +241,7 @@ private:
         {
                 public:
         eoDummyFlight () {}
-        void operator  () (POT & _po) {}
+	void operator  () (POT & /*_po*/) {}
         }dummyFlight;
 
         // if the initializer does not need to be used, use the dummy one instead

eo/src/eoVelocity.h

@@ -49,7 +49,7 @@ public:
     {
         for (unsigned i = 0; i < _pop.size (); i++)
         {
-            operator  ()(_pop[i],i);
+            this->operator  ()(_pop[i],i);
         }
 
     }
@@ -57,7 +57,7 @@ public:
     /**
      * Update the neighborhood of the given particle.
      */
-    virtual void updateNeighborhood(POT & ,unsigned _indice){}
+    virtual void updateNeighborhood(POT & ,unsigned /*_indice*/){}
 
 
     /**

eo/src/ga/eoBitOp.h

@@ -56,7 +56,7 @@ template<class Chrom> class eoOneBitFlip: public eoMonOp<Chrom>
   bool operator()(Chrom& chrom)
     {
       unsigned i = eo::rng.random(chrom.size());
-      chrom[i] = (chrom[i]) ? false : true;
+      chrom[i] = !chrom[i];
       return true;
     }
 };
@@ -85,11 +85,11 @@ template<class Chrom> class eoDetBitFlip: public eoMonOp<Chrom>
    */
   bool operator()(Chrom& chrom)
     {
-      // does not check for duplicate: if someone volunteers ....
+      // for duplicate checking see eoDetSingleBitFlip
       for (unsigned k=0; k<num_bit; k++)
         {
           unsigned i = eo::rng.random(chrom.size());
-          chrom[i] = (chrom[i]) ? false : true;
+          chrom[i] = !chrom[i];
         }
       return true;
     }
@@ -98,6 +98,58 @@ template<class Chrom> class eoDetBitFlip: public eoMonOp<Chrom>
 };
 
 
+/** eoDetSingleBitFlip --> changes exactly k bits with checking for duplicate
+\class eoDetSingleBitFlip eoBitOp.h ga/eoBitOp.h
+\ingroup bitstring
+*/
+
+template<class Chrom> class eoDetSingleBitFlip: public eoMonOp<Chrom>
+{
+ public:
+  /**
+   * (Default) Constructor.
+   * @param _num_bit The number of bits to change
+   * default is one - equivalent to eoOneBitFlip then
+   */
+  eoDetSingleBitFlip(const unsigned& _num_bit = 1): num_bit(_num_bit) {}
+
+  /// The class name.
+  virtual std::string className() const { return "eoDetSingleBitFlip"; }
+
+  /**
+   * Change num_bit bits.
+   * @param chrom The cromosome which one bit is going to be changed.
+   */
+  bool operator()(Chrom& chrom)
+    {
+      std::vector< unsigned > selected;
+
+      // check for duplicate
+      for (unsigned k=0; k<num_bit; k++)
+        {
+	    unsigned temp;
+
+	    do
+		{
+		    temp = eo::rng.random( chrom.size() );
+		}
+	    while ( find( selected.begin(), selected.end(), temp ) != selected.end() );
+
+	    selected.push_back(temp);
+        }
+
+	for ( size_t i = 0; i < selected.size(); ++i )
+	    {
+		chrom[i] = !chrom[i];
+	    }
+
+      return true;
+    }
+ private:
+  unsigned num_bit;
+};
+
+
 /** eoBitMutation --> classical mutation
 \class eoBitMutation eoBitOp.h ga/eoBitOp.h
 \ingroup bitstring

eo/src/ga/make_continue_ga.cpp

@@ -37,7 +37,7 @@
  *
  * The corresponding ***INSTANCIATED DECLARATIONS*** are contained
  *       in ga.h
- * while the TEMPLATIZED code is define in make_contninue.h in the src/do dir
+ * while the TEMPLATIZED code is define in make_continue.h in the src/do dir
  *
  * Unlike most EO .h files, it does not (and should not) contain any code,
  * just declarations

eo/src/ga/make_ga.h

@@ -57,8 +57,8 @@
  */
 
 // the genotypes
-eoInit<eoBit<double> > & make_genotype(eoParser& _parser, eoState& _state, eoBit<double> _eo);
+eoInit<eoBit<double> > & make_genotype(eoParser& _parser, eoState& _state, eoBit<double> _eo, float _bias=0.5);
-  eoInit<eoBit<eoMinimizingFitness> > & make_genotype(eoParser& _parser, eoState& _state, eoBit<eoMinimizingFitness> _eo);
+  eoInit<eoBit<eoMinimizingFitness> > & make_genotype(eoParser& _parser, eoState& _state, eoBit<eoMinimizingFitness> _eo, float _bias=0.5);
 
 // the operators
 eoGenOp<eoBit<double> >&  make_op(eoParser& _parser, eoState& _state, eoInit<eoBit<double> >& _init);

eo/src/ga/make_genotype_ga.cpp

@@ -45,11 +45,11 @@
 
 /// The following function merely call the templatized do_* functions above
 
-eoInit<eoBit<double> > & make_genotype(eoParser& _parser, eoState& _state, eoBit<double> _eo)
+eoInit<eoBit<double> > & make_genotype(eoParser& _parser, eoState& _state, eoBit<double> _eo, float _bias)
 {
-  return do_make_genotype(_parser, _state, _eo);
+    return do_make_genotype(_parser, _state, _eo, _bias);
 }
-eoInit<eoBit<eoMinimizingFitness> > & make_genotype(eoParser& _parser, eoState& _state, eoBit<eoMinimizingFitness> _eo)
+eoInit<eoBit<eoMinimizingFitness> > & make_genotype(eoParser& _parser, eoState& _state, eoBit<eoMinimizingFitness> _eo, float _bias)
 {
-  return do_make_genotype(_parser, _state, _eo);
+    return do_make_genotype(_parser, _state, _eo, _bias);
 }

eo/src/ga/make_genotype_ga.h

@@ -60,7 +60,7 @@
  * @ingroup Builders
 */
 template <class EOT>
-eoInit<EOT> & do_make_genotype(eoParser& _parser, eoState& _state, EOT)
+eoInit<EOT> & do_make_genotype(eoParser& _parser, eoState& _state, EOT, float _bias=0.5)
 {
   // for bitstring, only thing needed is the size
   // but it might have been already read in the definition fo the performance
@@ -68,7 +68,7 @@ eoInit<EOT> & do_make_genotype(eoParser& _parser, eoState& _state, EOT)
 
   // Then we can built a bitstring random initializer
   // based on boolean_generator class (see utils/rnd_generator.h)
-  eoBooleanGenerator * gen = new eoBooleanGenerator;
+  eoBooleanGenerator * gen = new eoBooleanGenerator(_bias);
   _state.storeFunctor(gen);
   eoInitFixedLength<EOT>* init = new eoInitFixedLength<EOT>(theSize, *gen);
   // store in state

eo/src/ga/make_op.h

@@ -115,11 +115,11 @@ eoGenOp<EOT> & do_make_op(eoParser& _parser, eoState& _state, eoInit<EOT>& _init
       throw std::runtime_error("Invalid uRate");
 
     // minimum check
-    bool bCross = true;
+    // bool bCross = true; // not used ?
     if (onePointRateParam.value()+twoPointsRateParam.value()+uRateParam.value()==0)
       {
         std::cerr << "Warning: no crossover" << std::endl;
-        bCross = false;
+        // bCross = false;
       }
 
     // Create the CombinedQuadOp
@@ -156,17 +156,29 @@ eoGenOp<EOT> & do_make_op(eoParser& _parser, eoState& _state, eoInit<EOT>& _init
     if ( (bitFlipRateParam.value() < 0) )
       throw std::runtime_error("Invalid bitFlipRate");
 
+    // oneBitFlip
     eoValueParam<double> & oneBitRateParam = _parser.createParam(0.01, "oneBitRate", "Relative rate for deterministic bit-flip mutation", 'd', "Variation Operators" );
     // minimum check
     if ( (oneBitRateParam.value() < 0) )
       throw std::runtime_error("Invalid oneBitRate");
 
+    // kBitFlip
+    eoValueParam<unsigned> & kBitParam = _parser.createParam((unsigned)1, "kBit", "Number of bit for deterministic k bit-flip mutation", 0, "Variation Operators" );
     // minimum check
-    bool bMut = true;
+    if ( ! kBitParam.value() )
+      throw std::runtime_error("Invalid kBit");
+
+    eoValueParam<double> & kBitRateParam = _parser.createParam(0.0, "kBitRate", "Relative rate for deterministic k bit-flip mutation", 0, "Variation Operators" );
+    // minimum check
+    if ( (kBitRateParam.value() < 0) )
+      throw std::runtime_error("Invalid kBitRate");
+
+    // minimum check
+    // bool bMut = true; // not used ?
     if (bitFlipRateParam.value()+oneBitRateParam.value()==0)
       {
         std::cerr << "Warning: no mutation" << std::endl;
-        bMut = false;
+        // bMut = false;
       }
 
     // Create the CombinedMonOp
@@ -184,6 +196,11 @@ eoGenOp<EOT> & do_make_op(eoParser& _parser, eoState& _state, eoInit<EOT>& _init
   _state.storeFunctor(ptMon);
   ptCombinedMonOp->add(*ptMon, oneBitRateParam.value());
 
+  // mutate exactly k bit per individual
+  ptMon = new eoDetBitFlip<EOT>(kBitParam.value());
+  _state.storeFunctor(ptMon);
+  ptCombinedMonOp->add(*ptMon, kBitRateParam.value());
+
   _state.storeFunctor(ptCombinedMonOp);
 
   // now build the eoGenOp:

eo/src/gp/eoParseTree.h

@@ -94,7 +94,7 @@ public:
 
         while (size() > _size)
         {
-            back() = operator[](size()-2);
+            back() = this->operator[](size()-2);
         }
     }
 
@@ -150,7 +150,7 @@ public:
             v[i] = node;
         }
         parse_tree<Node> tmp(v.begin(), v.end());
-        swap(tmp);
+        this->swap(tmp);
 
         /*
          * old code which caused problems for paradisEO

eo/src/pyeo/test/run_tests.sh

@@ -2,6 +2,6 @@
 
 for i in *.py
 do
-    python $i > /dev/null
+    python2 $i > /dev/null
 
 done

eo/src/utils/CMakeLists.txt

@@ -29,6 +29,7 @@ SET(EOUTILS_SOURCES
   pipecom.cpp
   eoLogger.cpp
   eoParallel.cpp
+  eoSignal.cpp
   )
 
 ADD_LIBRARY(eoutils STATIC ${EOUTILS_SOURCES})

eo/src/utils/checkpointing

@@ -1,3 +1,29 @@
+/*
+  -----------------------------------------------------------------------------
+  checkpointing
+
+ (c) Maarten Keijzer (mak@dhi.dk) and GeNeura Team, 1999, 2000
+
+    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
+ */
+
+#ifndef _CHECKPOINTING_
+#define _CHECKPOINTING_
+
 #include <utils/eoParser.h>
 #include <utils/eoState.h>
 #include <utils/eoUpdater.h>
@@ -10,6 +36,7 @@
 #include <utils/eoGnuplot1DSnapshot.h>
 #endif
 #include <utils/eoCheckPoint.h>
+#include <utils/eoSignal.h>
 #include <utils/eoStat.h>
 #include <utils/eoScalarFitnessStat.h>
 #include <utils/eoAssembledFitnessStat.h>
@@ -21,3 +48,9 @@
 
 // and make_help - any better suggestion to include it?
 void make_help(eoParser & _parser);
+
+#endif // !_CHECKPOINTING_
+
+// Local Variables:
+// mode: C++
+// End:

eo/src/utils/eoFuncPtrStat.h

@@ -4,6 +4,8 @@
 #include <eoFunctorStore.h>
 #include <utils/eoStat.h>
 
+
+
 /** Wrapper to turn any stand-alone function and into an eoStat.
  *
  * The function should take an eoPop as argument.
@@ -41,4 +43,38 @@ eoFuncPtrStat<EOT, T>& makeFuncPtrStat( T (*func)(const eoPop<EOT>&), eoFunctorS
         );
 }
 
+/** Wrapper to turn any stand-alone function and into an eoStat.
+ *
+ * The function should take an eoPop as argument.
+ *
+ * @ingroup Stats
+ */
+template <class EOT, class T>
+class eoFunctorStat : public eoStat<EOT, T>
+{
+public :
+    eoFunctorStat(eoUF< const eoPop<EOT>&, T >& f, std::string _description = "functor")
+        : eoStat<EOT, T>(T(), _description), func(f)
+        {}
+
+    using eoStat<EOT, T>::value;
+
+    void operator()(const eoPop<EOT>& pop) {
+        value() = func(pop);
+    }
+
+private:
+    eoUF< const eoPop<EOT>&, T >& func;
+};
+
+/**
+ * @ingroup Stats
+ */
+template <class EOT, class T>
+eoFunctorStat<EOT, T>& makeFunctorStat( eoUF< const eoPop<EOT>&, T >& func, eoFunctorStore& store, std::string description = "func") {
+    return store.storeFunctor(
+        new eoFunctorStat<EOT, T>( func, description)
+        );
+}
+
 #endif

eo/src/utils/eoLogger.cpp

@@ -194,8 +194,7 @@ int eoLogger::outbuf::overflow(int_type c)
       {
         if (_fd >= 0 && c != EOF)
           {
-              size_t num;
+              ::write(_fd, &c, 1);
-              num = ::write(_fd, &c, 1);
           }
       }
     return c;

eo/src/utils/eoOStreamMonitor.h

@@ -44,12 +44,13 @@ Authors:
 class eoOStreamMonitor : public eoMonitor
 {
 public :
-    eoOStreamMonitor( std::ostream & _out, bool _verbose=true, std::string _delim = "\t", unsigned int _width=20, char _fill=' ' ) :
+    eoOStreamMonitor( std::ostream & _out, bool /*_verbose*/=true, std::string _delim = "\t", unsigned int _width=20, char _fill=' ' ) :
         out(_out), delim(_delim), width(_width), fill(_fill), firsttime(true)
     {
-        (void)_verbose;
+#ifndef DEPRECATED_MESSAGES
         eo::log << eo::warnings << "WARNING: the use of the verbose parameter in eoOStreamMonitor constructor is deprecated and will be removed in the next release" << std::endl;
 #pragma message "WARNING: the use of the verbose parameter in eoOStreamMonitor constructor is deprecated and will be removed in the next release"
+#endif // !DEPRECATED_MESSAGES
     }
 
     eoOStreamMonitor( std::ostream & _out, std::string _delim = "\t", unsigned int _width=20, char _fill=' ' ) :

eo/src/utils/eoSignal.cpp

@@ -0,0 +1,36 @@
+// -*- mode: c++; c-indent-level: 4; c++-member-init-indent: 8; comment-column: 35; -*-
+
+/**
+   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: http://eodev.sourceforge.net
+
+   Autors: todos@geneura.ugr.es, http://geneura.ugr.es
+	   Marc.Schoenauer@polytechnique.fr
+	   mak@dhi.dk
+	   Caner.Candan@univ-angers.fr
+*/
+
+#include <utils/eoSignal.h>
+
+/**
+ * @addtogroup Continuators
+ * @{
+ */
+
+// --- Global variables - but don't know what else to do - MS ---
+std::map< int, bool > signals_called;
+
+/** @} */

eo/src/utils/eoSignal.h

@@ -0,0 +1,106 @@
+// -*- mode: c++; c-indent-level: 4; c++-member-init-indent: 8; comment-column: 35; -*-
+
+/**
+   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: http://eodev.sourceforge.net
+
+   Authors: todos@geneura.ugr.es, http://geneura.ugr.es
+	    Marc.Schoenauer@polytechnique.fr
+	    mak@dhi.dk
+	    Caner.Candan@univ-angers.fr
+*/
+
+#ifndef _eoSignal_h
+#define _eoSignal_h
+
+#include <csignal>
+#include <utils/eoCheckPoint.h>
+#include <utils/eoLogger.h>
+
+#include <map>
+#include <vector>
+
+/**
+ * @addtogroup Continuators
+ * @{
+ */
+
+extern std::map< int, bool > signals_called;
+
+/** eoSignal inherits from eoCheckPoint including signals handling (see signal(7))
+ *
+ * @ingroup Utilities
+ */
+template <class EOT>
+class eoSignal : public eoCheckPoint<EOT>
+{
+public :
+
+    eoSignal( int sig = SIGINT ) : eoCheckPoint<EOT>( _dummyContinue ), _sig( sig )
+    {
+	::signals_called[_sig] = false;
+
+#ifndef _WINDOWS
+#ifdef SIGQUIT
+	::signal( _sig, handler );
+#endif // !SIGQUIT
+#endif // !_WINDOWS
+    }
+
+    eoSignal( eoContinue<EOT>& _cont, int sig = SIGINT ) : eoCheckPoint<EOT>( _cont ), _sig( sig )
+    {
+	::signals_called[_sig] = false;
+
+#ifndef _WINDOWS
+#ifdef SIGQUIT
+	::signal( _sig, handler );
+#endif // !SIGQUIT
+#endif // !_WINDOWS
+    }
+
+    bool operator()( const eoPop<EOT>& _pop )
+    {
+	bool& called = ::signals_called[_sig];
+	if ( called )
+	    {
+		eo::log << eo::logging << "Signal granted…" << std::endl ;
+		called = false;
+		return this->eoCheckPoint<EOT>::operator()( _pop );
+	    }
+	return true;
+    }
+
+    virtual std::string className(void) const { return "eoSignal"; }
+
+    static void handler( int sig )
+    {
+	::signals_called[sig] = true;
+	eo::log << eo::logging << "Signal wished…" << std::endl ;
+    }
+
+private:
+    class DummyContinue : public eoContinue<EOT>
+    {
+    public:
+	bool operator() ( const eoPop<EOT>& ) { return true; }
+    } _dummyContinue;
+
+    int _sig;
+};
+
+/** @} */
+
+#endif // !_eoSignal_h

eo/src/utils/eoStdoutMonitor.h

@@ -46,7 +46,9 @@ public :
     eoStdoutMonitor(bool _verbose, std::string _delim = "\t", unsigned int _width=20, char _fill=' ' ) :
        eoOStreamMonitor( std::cout, _verbose, _delim, _width, _fill)
     {
-        eo::log << eo::warnings << "WARNING: the use of the verbose parameter in eoStdutMonitor constructor is deprecated and will be removed in the next release" << std::endl;
+#ifndef DEPRECATED_MESSAGES
+        eo::log << eo::warnings << "WARNING: the use of the verbose parameter in eoStdoutMonitor constructor is deprecated and will be removed in the next release" << std::endl;
+#endif // !DEPRECATED_MESSAGES
     }
 
     eoStdoutMonitor(std::string _delim = "\t", unsigned int _width=20, char _fill=' ' ) :

eo/test/CMakeLists.txt

@@ -66,7 +66,7 @@ SET (TEST_LIST
   t-eoLogger
   t-eoIQRStat
   t-eoParallel
-  t-openmp
+  #t-openmp # does not work anymore since functions used in this test were removed from EO
   #t-eoDualFitness
   t-eoParser
   )

eo/test/t-openmp.cpp

@@ -39,6 +39,8 @@ Caner Candan <caner.candan@thalesgroup.com>
 
 #include <omp.h>
 
+#include <unistd.h>
+
 #include "real_value.h"
 
 //-----------------------------------------------------------------------------