Ok, updated the Makefile.am again to use the

make check

Command I picked up in the automake documentation (RTFM, you know)

Tagged a lot of header functions in the GnuPlot files with 'inline',
so they can be used from more than one sourcefile.

Ok, now the interesting news. Started a new library libga (not to be confused
with Matthew's GaLib). Here I suggest we put a fairly complete and configurable
genetic algorithm. Just to see how far we can stretch ourselves and also to have
a GA-componenent that can be used in other applications without having to rebuild
the entire thing. test/t-eoGA.cpp tests this library

eo/Makefile.am

@@ -4,7 +4,7 @@
 ##
 ###############################################################################
 
-SUBDIRS = src win tutorial app
+SUBDIRS = src test win tutorial app
 #Directory for documents
 DOCDIR = ~/public_html/eodocs
 #Directory for indices -- not useful for the user
@@ -17,8 +17,9 @@ EXTRA_DIST=LICENSE
 lib:	
 	pushd src; $(MAKE) all; popd
 
-test:	test/run_tests
+# The test directory should be run explicitely, to check if nothing is broken
-	pushd test; $(MAKE) all; ./run_tests; touch run_tests; popd 
+test:	test/run_tests test/Makefile
+	pushd test; touch run_tests; $(MAKE) all; ./run_tests; popd 
 
 # so that make doc always compiles the doc ...
 doc:    doc/eo.cfg

eo/src/ga/Makefile.am

@@ -4,5 +4,11 @@
 ##
 ###############################################################################
 
+INCLUDES = -I$(top_builddir)/src
+lib_LIBRARIES = libga.a
+libga_a_SOURCES = ga.cpp
+CPPFLAGS = -O2 -Wall
+
+
 libeoincdir = $(includedir)/eo/ga
-libeoinc_HEADERS = eoBit.h eoBitOp.h eoBitOpFactory.h
+libeoinc_HEADERS = eoBit.h eoBitOp.h eoBitOpFactory.h ga.h

eo/src/ga/ga.cpp

@@ -0,0 +1,91 @@
+#include <eo>
+#include <ga/ga.h>
+
+eoValueParam<float> xoverRate(0.6f, "xoverrate", "The crossover rate", 'x');
+eoValueParam<float> mutRate(1.0f, "mutationrate", "The mutation rate", 'm');
+eoValueParam<unsigned> chromSize(unsigned(10), "chromosomeSize", "The length of the bitstrings", 'n');
+eoValueParam<unsigned> popSize(unsigned(20), "PopSize", "Population Size", 'P');
+
+template <class FitT>
+eoAlgo<eoBit<FitT> >&  do_make_ga(eoParameterLoader& _parser, eoEvalFunc<eoBit<FitT> >& _eval, eoCheckPoint<eoBit<FitT> >& _checkpoint, eoState& _state)
+{
+  typedef eoBit<FitT> EOT;
+
+  _parser.processParam(xoverRate, "genetics");
+  _parser.processParam(mutRate, "genetics");
+  _parser.processParam(chromSize, "initialization");
+
+  eoBitMutation<EOT>* mutOp = new eoBitMutation<EOT>(1. / float(chromSize.value()));
+  _state.storeFunctor(mutOp);
+
+  eo1PtBitXover<EOT>* crossOp = new eo1PtBitXover<EOT>;
+  _state.storeFunctor(crossOp);
+
+  eoSelectOne<EOT>* select = new eoDetTournamentSelect<EOT>(2);
+  _state.storeFunctor(select);
+
+  eoSGA<eoBit<FitT> >* sga = new eoSGA<EOT>(*select, *crossOp, xoverRate.value(), *mutOp, mutRate.value(), _eval, _checkpoint);
+  _state.storeFunctor(sga);
+  return *sga;
+}
+
+template <class FitT>
+eoPop<eoBit<FitT> >&  do_init_ga(eoParameterLoader& _parser, eoState& _state, FitT)
+{
+  typedef eoBit<FitT> EOT;
+
+  _parser.processParam(chromSize, "initialization");
+  _parser.processParam(popSize, "initialization");
+
+  eoInitFixedLength<EOT, boolean_generator> init(chromSize.value(), boolean_generator());
+
+
+  // Let the state handle the memory
+  eoPop<EOT>& pop = _state.takeOwnership(eoPop<EOT>());
+
+  _state.registerObject(pop);
+
+  // initialize the population
+
+  pop.append(popSize.value(), init);
+
+  return pop;
+}
+
+template <class FitT>
+void do_run_ga(eoAlgo<eoBit<FitT> >& _ga, eoPop<eoBit<FitT> >& _pop)
+{
+  _ga(_pop);
+}
+
+/// The following function merely call the templatized do_* functions above
+
+eoAlgo<eoBit<double> >&  make_ga(eoParameterLoader& _parser, eoEvalFunc<eoBit<double> >& _eval, eoCheckPoint<eoBit<double> >& _checkpoint, eoState& _state)
+{
+  return do_make_ga(_parser, _eval, _checkpoint, _state);
+}
+
+eoAlgo<eoBit<eoMinimizingFitness> >&  make_ga(eoParameterLoader& _parser, eoEvalFunc<eoBit<eoMinimizingFitness> >& _eval, eoCheckPoint<eoBit<eoMinimizingFitness> >& _checkpoint, eoState& _state)
+{
+  return do_make_ga(_parser, _eval, _checkpoint, _state);
+}
+
+eoPop<eoBit<double> >&  init_ga(eoParameterLoader& _parser, eoState& _state, double _d)
+{
+  return do_init_ga(_parser, _state, _d);
+}
+
+eoPop<eoBit<eoMinimizingFitness> >&  init_ga(eoParameterLoader& _parser, eoState& _state, eoMinimizingFitness _d)
+{
+  return do_init_ga(_parser, _state, _d);
+}
+
+void run_ga(eoAlgo<eoBit<double> >& _ga, eoPop<eoBit<double> >& _pop)
+{
+  do_run_ga(_ga, _pop);
+}
+
+void run_ga(eoAlgo<eoBit<eoMinimizingFitness> >& _ga, eoPop<eoBit<eoMinimizingFitness> >& _pop)
+{
+  do_run_ga(_ga, _pop);
+}

eo/src/ga/ga.h

@@ -0,0 +1,24 @@
+#ifndef ga_h
+#define ga_h
+
+#include <eoAlgo.h>
+#include <eoScalarFitness.h>
+#include <utils/eoParser.h>
+#include <eoEvalFunc.h>
+#include <utils/eoCheckPoint.h>
+#include <eoPop.h>
+
+#include <ga/eoBit.h>
+#include <ga/eoBitOp.h>
+
+
+eoAlgo<eoBit<double> >&  make_ga(eoParameterLoader& _parser, eoEvalFunc<eoBit<double> >& _eval, eoCheckPoint<eoBit<double> >& _checkpoint, eoState& state);
+eoAlgo<eoBit<eoMinimizingFitness> >&  make_ga(eoParameterLoader& _parser, eoEvalFunc<eoBit<eoMinimizingFitness> >& _eval, eoCheckPoint<eoBit<eoMinimizingFitness> >& _checkpoint, eoState& state);
+
+eoPop<eoBit<double> >&  init_ga(eoParameterLoader& _parser, eoState& _state, double);
+eoPop<eoBit<eoMinimizingFitness> >&  init_ga(eoParameterLoader& _parser, eoState& _state, eoMinimizingFitness);
+
+void run_ga(eoAlgo<eoBit<double> >& _ga, eoPop<eoBit<double> >& _pop);
+void run_ga(eoAlgo<eoBit<eoMinimizingFitness> >& _ga, eoPop<eoBit<eoMinimizingFitness> >& _pop);
+
+#endif

eo/src/utils/Makefile.am

@@ -5,7 +5,7 @@
 ###############################################################################
 
 INCLUDES = -I$(top_builddir)/src
-CPPFLAGS = -O2
+CPPFLAGS = -O2 -Wall
 lib_LIBRARIES = libeoutils.a
 libeoutils_a_SOURCES = eoParser.cpp eoRNG.cpp eoState.cpp eoUpdater.cpp eoFileMonitor.cpp eoStdoutMonitor.cpp
 

eo/src/utils/eoGnuplot.h

@@ -91,7 +91,7 @@ private:
   static unsigned numWindow=0;
 
 ////////////////////////////////////////////////////////////
-void eoGnuplot::initGnuPlot(std::string _title, std::string _extra) 
+inline void eoGnuplot::initGnuPlot(std::string _title, std::string _extra)
   /////////////////////////////////////////////////////////
 {
   char snum[255];
@@ -129,7 +129,7 @@ void eoGnuplot::initGnuPlot(std::string _title, std::string _extra)
  * Created......: Mon Mar 13 13:50:11 1995
  * Description..: Communication par pipe bidirectionnel avec un autre process
  *
- * Ident........: $Id: eoGnuplot.h,v 1.2 2001-02-01 05:17:16 evomarc Exp $
+ * Ident........: $Id: eoGnuplot.h,v 1.3 2001-02-12 13:58:51 maartenkeijzer Exp $
  * ----------------------------------------------------------------------
  */
 
@@ -142,7 +142,7 @@ void eoGnuplot::initGnuPlot(std::string _title, std::string _extra)
 // #include "pipecom.h"
 
 
-int Check( PCom *com )
+inline int Check( PCom *com )
 {
     if( ! com ) {
 	fprintf( stderr, "PipeCom: Null pointer.\n" );
@@ -158,7 +158,7 @@ int Check( PCom *com )
 }
 
 
-PCom * PipeComOpen( char *prog )
+inline PCom * PipeComOpen( char *prog )
 {
     char	*args[2];
     args[0] = prog;
@@ -167,7 +167,7 @@ PCom * PipeComOpen( char *prog )
 }
 
 
-PCom * PipeComOpenArgv( char *prog, char *argv[] )
+inline PCom * PipeComOpenArgv( char *prog, char *argv[] )
 {
     int		toFils[2];
     int		toPere[2];
@@ -220,7 +220,7 @@ PCom * PipeComOpenArgv( char *prog, char *argv[] )
 }
 
 
-int PipeComSend( PCom *to, const char *line )
+inline int PipeComSend( PCom *to, const char *line )
 {
     int	nb = 0;
     if( ! Check(to ) )
@@ -231,7 +231,7 @@ int PipeComSend( PCom *to, const char *line )
 }
 
 
-int PipeComSendn( PCom *to, const char *data, int n )
+inline int PipeComSendn( PCom *to, const char *data, int n )
 {
     int	nb = 0;
     if( ! Check(to) )
@@ -243,7 +243,7 @@ int PipeComSendn( PCom *to, const char *data, int n )
 }
 
 
-int PipeComReceive( PCom *from, char *data, int max )
+inline int PipeComReceive( PCom *from, char *data, int max )
 {
     if( ! Check(from) )
 	return 0;
@@ -259,7 +259,7 @@ int PipeComReceive( PCom *from, char *data, int max )
 
 
 
-int PipeComClose( PCom *to )
+inline int PipeComClose( PCom *to )
 {
     if( ! Check(to) )
 	return 0;
@@ -271,7 +271,7 @@ int PipeComClose( PCom *to )
 
 
 
-int PipeComWaitFor( PCom *from, char *what )
+inline int PipeComWaitFor( PCom *from, char *what )
 {
     char	buffer[256];
     do {

eo/src/utils/eoGnuplot1DMonitor.h

@@ -73,9 +73,9 @@ private:
 };
 
 // the following should be placed in a separate eoGnuplot1DMonitor.cpp
-
+// then the inline specifier should dissappear
 ////////////////////////////////////////////////////////////
-eoMonitor&   eoGnuplot1DMonitor::operator() (void)
+inline eoMonitor&   eoGnuplot1DMonitor::operator() (void)
   /////////////////////////////////////////////////////////
 {
   // update file using the eoFileMonitor
@@ -98,7 +98,7 @@ eoMonitor&   eoGnuplot1DMonitor::operator() (void)
 }
 
 ////////////////////////////////////////////////////////////
-void  eoGnuplot1DMonitor::FirstPlot() 
+inline void  eoGnuplot1DMonitor::FirstPlot()
   ////////////////////////////////////////////////////////
 {
   if (vec.size() < 2)

eo/src/utils/eoGnuplot1DSnapshot.h

@@ -81,7 +81,7 @@ private:
 // the following should be placed in a separate eoGnuplot1DMonitor.cpp 
 
 ////////////////////////////////////////////////////////////
-eoMonitor&   eoGnuplot1DSnapshot::operator() (void)
+inline eoMonitor&   eoGnuplot1DSnapshot::operator() (void)
   /////////////////////////////////////////////////////////
 {
   // update file using the eoFileMonitor

eo/src/utils/eoState.h

@@ -32,6 +32,8 @@
 #include <map>
 #include <vector>
 
+#include <eoFunctorStore.h>
+
 class eoObject;
 class eoPersistent;
 
@@ -66,6 +68,12 @@ public :
         return static_cast<T&>(*ownedObjects.back());
     }
 
+    void storeFunctor(eoFunctorBase* _functor)
+    {
+      // add it to the functorStore, fo
+      functorStore.add(_functor);
+    }
+
     /**
     * Loading error thrown when nothing seems to work.
     */
@@ -113,9 +121,11 @@ private :
     ObjectMap objectMap;
 
     std::vector<ObjectMap::iterator> creationOrder;
-
     std::vector<eoPersistent*> ownedObjects;
 
+    // And a functor store to boot
+    eoFunctorStore functorStore;
+
     // private copy and assignment as eoState is supposed to be unique
     eoState(const eoState&);
     eoState& operator=(const eoState&);

eo/test/Makefile.am

@@ -13,16 +13,17 @@ LDADDS = $(top_builddir)/src/libeo.a $(top_builddir)/src/utils/libeoutils.a
 CXXFLAGS = -g
 ###############################################################################
 
-noinst_PROGRAMS = t-eofitness t-eobin t-eoStateAndParser t-eoCheckpointing t-eoExternalEO t-eoSymreg t-eo t-eoReplacement t-eoSelect t-eoGenOp
+check_PROGRAMS = t-eofitness t-eobin t-eoStateAndParser t-eoCheckpointing t-eoExternalEO t-eoSymreg t-eo t-eoReplacement t-eoSelect t-eoGenOp t-eoGA
+TESTS=run_tests
 # removing temporarily t-eoESFull
-# noinst_PROGRAMS = t-eofitness t-eobin t-eoStateAndParser t-eoCheckpointing t-eoExternalEO t-eoESFull t-eoSymreg t-eo t-eoReplacement t-eoSelect
+#noinst_PROGRAMS = t-eofitness t-eobin t-eoStateAndParser t-eoCheckpointing t-eoExternalEO t-eoESFull t-eoSymreg t-eo t-eoReplacement t-eoSelect t-eoGenOp t-eoGA
 
 ###############################################################################
 
-# t_eoESFull_SOURCES = t-eoESFull.cpp real_value.h
+#t_eoESFull_SOURCES = t-eoESFull.cpp real_value.h
-# t_eoESFull_DEPENDENCIES = $(DEPS)
+#t_eoESFull_DEPENDENCIES = $(DEPS)
-# t_eoESFull_LDFLAGS = -lm
+#t_eoESFull_LDFLAGS = -lm
-# t_eoESFull_LDADD = $(LDADDS)
+#t_eoESFull_LDADD = $(LDADDS)
 
 ###############################################################################
 
@@ -93,3 +94,10 @@ t_eoGenOp_LDFLAGS = -lm
 t_eoGenOp_LDADD = $(LDADDS)
 
 ###############################################################################
+
+t_eoGA_SOURCES = t-eoGA.cpp binary_value.h
+t_eoGA_DEPENDENCIES = $(DEPS) $(top_builddir)/src/ga/libga.a
+t_eoGA_LDFLAGS = -lm
+t_eoGA_LDADD = $(top_builddir)/src/ga/libga.a $(LDADDS)
+
+###############################################################################

eo/test/run_tests

@@ -33,6 +33,9 @@ echo "Testing t-eobin"
 echo "Testing t-eofitness"
 ./t-eofitness > fitness.log
 
+echo "Testing t-eoGA"
+./t-eoGA > t-eoGA.log
+
 echo "Finished"
 
 #TODO test if an error occured

eo/test/t-eoGA.cpp

@@ -0,0 +1,36 @@
+#include <iostream>
+
+#include <ga/ga.h>
+#include "binary_value.h"
+#include <apply.h>
+
+using namespace std;
+
+int main(int argc, char* argv[])
+{
+
+  try
+  {
+  typedef eoBit<double> EoType;
+
+  eoParser parser(argc, argv);
+
+  eoState state;         // keeps all things allocated, including eoEasyEA and eoPop!
+
+  eoEvalFuncPtr<EoType, float> eval( binary_value<EoType> );
+  eoGenContinue<EoType>  term(20);
+  eoCheckPoint<EoType>   checkpoint(term);
+
+  eoAlgo<EoType>& ga = make_ga(parser, eval, checkpoint, state);
+
+  eoPop<EoType>& pop   = init_ga(parser, state, double());
+
+  apply(eval, pop);
+
+  run_ga(ga, pop); // run the ga
+  }
+  catch(exception& e)
+  {
+    cout << e.what() << endl;
+  }
+}