Updated makefiles, updated the moo stuff and cleaned up some stuff that refused to compile

eo/contrib/mathsym/README

@@ -94,7 +94,7 @@ To add two values, do
 
 Sym sym = var + const;
 
-This will create a tree with tree nodes. All other operations work identically.
+This will create a tree with three nodes. Other operators are overloaded similarily.
 
 === Evaluation (eval/) ===
 

eo/doc/eo.cfg

@@ -17,20 +17,20 @@
 # The PROJECT_NAME tag is a single word (or a sequence of words surrounded 
 # by quotes) that should identify the project.
 
-PROJECT_NAME           = EO
+PROJECT_NAME           = Evolving Objects
 
 # 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         = 1.0.2-cvs
+PROJECT_NUMBER         = 1.02-cvs1
 
 # The OUTPUT_DIRECTORY tag is used to specify the (relative or absolute) 
 # base path where the generated documentation will be put. 
 # If a relative path is entered, it will be relative to the location 
 # where doxygen was started. If left blank the current directory will be used.
 
-OUTPUT_DIRECTORY       = 
+OUTPUT_DIRECTORY       = /home/mkeijzer/projects/eo/doc 
 
 # The OUTPUT_LANGUAGE tag is used to specify the language in which all 
 # documentation generated by doxygen is written. Doxygen will use this 
@@ -104,7 +104,7 @@ FULL_PATH_NAMES        = NO
 # If left blank the directory from which doxygen is run is used as the 
 # path to strip.
 
-STRIP_FROM_PATH        = 
+STRIP_FROM_PATH        = /home/mkeijzer/projects/eo 
 
 # If the SHORT_NAMES tag is set to YES, doxygen will generate much shorter 
 # (but less readable) file names. This can be useful is your file systems 
@@ -391,7 +391,7 @@ WARN_LOGFILE           =
 # directories like "/usr/src/myproject". Separate the files or directories 
 # with spaces.
 
-INPUT                  = ..
+INPUT                  = /home/mkeijzer/projects/eo
 
 # If the value of the INPUT tag contains directories, you can use the 
 # FILE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp 
@@ -414,7 +414,7 @@ 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                = ../src/obsolete
+EXCLUDE                = /home/mkeijzer/projects/eo/src/obsolete
 
 # The EXCLUDE_SYMLINKS tag can be used select whether or not files or directories 
 # that are symbolic links (a Unix filesystem feature) are excluded from the input.

eo/src/EO.h

@@ -47,11 +47,8 @@ public:
   typedef F Fitness;
 
   /** Default constructor.
-      Fitness must have a ctor which takes 0 as a value; we can not use void
-      ctors here since default types like float have no void initializer.
-      VC++ allows it, but gcc does not
   */
-  EO(): repFitness(Fitness()), invalidFitness(true) {}
+  EO(): repFitness(Fitness()), invalidFitness(true) { }
 
   /// Virtual dtor
   virtual ~EO() {};

eo/src/Makefile.am

@@ -143,6 +143,7 @@ pkginclude_HEADERS 	= eo \
 			eoWeightUpdater.h \
 			es.h \
 			ga.h \
-			PO.h
+			PO.h \
+			eoTimeContinue.h
 
 AM_CXXFLAGS		= -I$(top_srcdir)/src

eo/src/eo

@@ -127,6 +127,7 @@
 #include <eoParetoRanking.h>
 #include <eoNDSorting.h>
 
+
 // Algorithms
 #include <eoEasyEA.h>
 #include <eoSGA.h>

eo/src/eoEasyEA.h

@@ -185,7 +185,7 @@ public:
          breed(_pop, offspring);
 
          popEval(_pop, offspring); // eval of parents + offspring if necessary
-
+         
          replace(_pop, offspring); // after replace, the new pop. is in _pop
 
          if (pSize > _pop.size())

eo/src/eoPop.h

@@ -51,7 +51,7 @@
  */
 
 template<class EOT>
-class eoPop: public std::vector<EOT>, public eoObject, public eoPersistent 
+class eoPop: public std::vector<EOT>, public eoObject, public eoPersistent
 {
 
  public:
@@ -295,7 +295,6 @@ class eoPop: public std::vector<EOT>, public eoObject, public eoPersistent
       this->operator[](i).invalidate();
   }
 
-
  protected:
 
 };

eo/src/eoSGA.h

@@ -89,7 +89,7 @@ public :
       }
 	  }
 
-	for (i=0; i < _pop.size(); i++)
+	for (i=0; i < offspring.size(); i++)
 	  {
 	    if (rng.flip(mutationRate) )
 	    {

eo/src/es/eoCMABreed.h

@@ -47,7 +47,9 @@ class eoCMABreed : public eoBreed< eoVector<FitT, double> > {
 	
 	// two temporary arrays of pointers to store the sorted population
 	std::vector<const EOT*> sorted(parents.size());
-	std::vector<const std::vector<double>* > mu(parents.size());
+	
+        // mu stores population as vector (instead of eoPop)
+        std::vector<const std::vector<double>* > mu(parents.size());
 	
 	parents.sort(sorted);
 	for (unsigned i = 0; i < sorted.size(); ++i) {
@@ -55,7 +57,6 @@ class eoCMABreed : public eoBreed< eoVector<FitT, double> > {
 	}
 	
 	// learn
-	
 	state.reestimate(mu, sorted[0]->fitness(), sorted.back()->fitness());
 	
 	if (!state.updateEigenSystem(10)) {

eo/src/moo/Makefile.am

@@ -5,7 +5,14 @@ libeomoo_a_SOURCES 	= 	eoFrontSorter.cpp \
 				eoNSGA_IIa_Eval.cpp \
 				eoNSGA_II_Eval.cpp
 
-pkginclude_HEADERS 	= 	eoFrontSorter.h \
+pkginclude_HEADERS 	=\
-				eoMOFitness.h 
+eoEpsilonArchive.h\
+eoEpsMOEA.h\
+eoFrontSorter.h\
+eoMOEval.h\
+eoMOFitness.h\
+eoNSGA_I_Eval.h\
+eoNSGA_IIa_Eval.h\
+eoNSGA_II_Eval.h
 
 AM_CXXFLAGS		= -I$(top_srcdir)/src

eo/src/moo/eoEpsMOEA.h

@@ -16,7 +16,7 @@ class eoEpsMOEA : public eoAlgo<EOT> {
          eoEvalFunc<EOT>& _eval,
          eoGenOp<EOT>& _op,
          const std::vector<double>& eps,
-         unsigned max_archive_size
+         unsigned max_archive_size = std::numeric_limits<unsigned>::max()
      ) : continuator(_continuator),
 	 eval (_eval),
 	 loopEval(_eval),

eo/src/moo/eoEpsilonArchive.h

@@ -114,26 +114,6 @@ exitLoop:
             }
         }
         
-        /*
-        static unsigned counter = 0;
-        if (++counter % 500 == 0) {
-            std::vector<long> mins(archive[0].discretized.size(), std::numeric_limits<long>::max());
-            std::vector<long> maxs(archive[0].discretized.size(), std::numeric_limits<long>::min());
-            for (unsigned i = 0; i < archive.size(); ++i) {
-                for (unsigned dim = 0; dim < archive[i].discretized.size(); ++dim) {
-                    mins[dim] = std::min( mins[dim], archive[i].discretized[dim] );
-                    maxs[dim] = std::max( maxs[dim], archive[i].discretized[dim] );
-                }
-            }
-            
-            std::cout << "Range ";
-            for (unsigned dim = 0; dim < mins.size(); ++dim) {
-                std::cout << (maxs[dim] - mins[dim]) << ' ';
-            }
-            std::cout << archive.size() << std::endl;
-
-        }*/
-
         if (archive.size() > max_size) {
             unsigned idx = rng.random(archive.size());
             if (idx != archive.size()-1) std::swap(archive[idx], archive.back());

eo/src/moo/eoNSGA_II_Eval.cpp

@@ -1,6 +1,5 @@
-
 #include <limits>
-#include <eoNSGA_II_Eval.h>
+#include <moo/eoNSGA_II_Eval.h>
 
 namespace nsga2 {
     

eo/src/moo/eoNSGA_II_Eval.h

@@ -25,7 +25,7 @@ class eoNSGA_II_Eval : public eoMOEval<EOT>
   eoNSGA_II_Eval(eoPopEvalFunc<EOT>& eval) : eoMOEval<EOT>(eval) {}
     
     virtual void operator()(eoPop<EOT>& parents, eoPop<EOT>& offspring) {
-        eval(parents, offspring);
+        this->eval(parents, offspring);
 
         std::vector<EOT*> pop;
         pop.reserve(parents.size() + offspring.size());

eo/src/pyeo/Makefile

@@ -16,7 +16,9 @@ OBJECTS=eoFunctorStore.o PyEO.o abstract1.o algos.o \
 	random_numbers.o geneticOps.o selectOne.o continuators.o\
 	reduce.o replacement.o selectors.o breeders.o\
 	mergers.o valueParam.o perf2worth.o monitors.o\
-	statistics.o
+	statistics.o 
+
+LIB=../libeo.a ../utils/libeoutils.a
 
 all: PyEO/PyEO.so
 
@@ -24,7 +26,7 @@ clean:
 	rm PyEO/*.so *.o test/*.pyc
 
 PyEO/PyEO.so: $(OBJECTS)
-	$(LINK) -o PyEO/PyEO.so $(OBJECTS) -lboost_python -lpython2.4 -shared #-lstlport
+	$(LINK) -o PyEO/PyEO.so $(OBJECTS) -lboost_python -lpython2.4 ${LIB} -shared #-lstlport
 
 eoFunctorStore.o: ../eoFunctorStore.h ../eoFunctorStore.cpp
 	$(COMPILE) -o eoFunctorStore.o ../eoFunctorStore.cpp $(INC)

eo/src/pyeo/PyEO.cpp

@@ -180,7 +180,7 @@ BOOST_PYTHON_MODULE(PyEO)
 
     boost::python::class_<eoPop<PyEO> >("eoPop", init<>() )
 	.def( init< unsigned, eoInit<PyEO>& >()[with_custodian_and_ward<1,3>()] )
-	.def("append", &eoPop<PyEO>::append)
+	.def("append", &eoPop<PyEO>::append, "docstring?")
 	.def("__str__", to_string<eoPop<PyEO> >)
 	.def("__len__", pop_size)
 	.def("sort",    pop_sort )

eo/test/Makefile.am

@@ -108,4 +108,10 @@ t_eoEasyPSO_SOURCES		= t-eoEasyPSO.cpp
 t_eoNSGA_SOURCES		= t-eoNSGA.cpp
 t_eoFrontSorter_SOURCES		= t-eoFrontSorter.cpp
 t_eoEpsMOEA_SOURCES		= t-eoEpsMOEA.cpp
+t_eoInt_SOURCES			= t-eoInt.cpp
+t_eoInitPermutation_SOURCES	= t-eoInitPermutation.cpp
+t_eoSwapMutation_SOURCES        = t-eoSwapMutation.cpp
+t_eoShiftMutation_SOURCES	= t-eoShiftMutation.cpp
+t_eoTwoOptMutation_SOURCES	= t-eoTwoOptMutation.cpp
+t_eoRingTopology_SOURCES	= t-eoRingTopology.cpp
 

eo/test/t-eo.cpp

@@ -9,7 +9,6 @@
 typedef EO<float> Chrom;
 
 //-----------------------------------------------------------------------------
-
 int main()
 {
   Chrom chrom1, chrom2;
@@ -17,6 +16,7 @@ int main()
   std::cout << "chrom1 = " << chrom1 << std::endl
        << "chrom2 = " << chrom2 << std::endl;
 
+    
   return 0;
 }
 

eo/test/t-eoEpsMOEA.cpp

@@ -2,6 +2,7 @@
 #include <eo>
 
 #include <moo/eoEpsMOEA.h>
+#include <utils/eoFuncPtrStat.h>
 
 using namespace std;
 
@@ -133,6 +134,17 @@ class Init : public eoInit<eoDouble>
   }
 };
 
+template <class EOT>
+unsigned get_size(const eoPop<EOT>& pop) { 
+    return pop.size(); 
+}
+
+template <class EOT>
+unsigned counter(const eoPop<EOT>& pop) { 
+    static unsigned c = 0; 
+    return c++; 
+}
+
 // Test pareto dominance and perf2worth, and while you're at it, test the eoGnuPlot monitor as well
 void the_main(int argc, char* argv[])
 {
@@ -174,7 +186,20 @@ void the_main(int argc, char* argv[])
 
   snapshot.add(fitness0);
   snapshot.add(fitness1);
+    
+  eoGnuplot1DMonitor monitor("sizemon");
+    
+  cp.add(monitor);
+ 
+  eoFuncPtrStat<eoDouble, unsigned> size(get_size<eoDouble>);
+  eoFuncPtrStat<eoDouble, unsigned> counterStat(counter<eoDouble>);
+  
+  monitor.add(counterStat);
+  monitor.add(size);
 
+  cp.add(size);
+  cp.add(counterStat);
+    
   // the algo
   eoEpsMOEA<eoDouble> ea(cp, eval, opsel, MinimizingFitnessTraits::eps );