add tests interfaces as examples in the doc ; remove unused test binaries ; some code formating

eo/src/EO.h

@@ -55,6 +55,8 @@
     @ref Operators that effectively modify EO objects must invalidate them.
 
     The fitness object must have, besides an void ctor, a copy ctor.
+
+    @example t-eo.cpp
 */
 template<class F = double> class EO: public eoObject, public eoPersistent
 {

eo/src/do/make_algo_scalar.h

@@ -307,5 +307,7 @@ eoAlgo<EOT> & do_make_algo_scalar(eoParser& _parser, eoState& _state, eoEvalFunc
   // that's it!
   return *algo;
 }
+/** @example t-eoGA.cpp
+ */
 
 #endif

eo/src/eoEasyEA.h

@@ -273,9 +273,11 @@ template<class EOT> class eoEasyEA: public eoAlgo<EOT>
     // Friend classes
     friend class eoIslandsEasyEA <EOT> ;
     friend class eoDistEvalEasyEA <EOT> ;
-  };
-
-//-----------------------------------------------------------------------------
+};
+/**
+@example t-eoEasyEA.cpp
+Example of a test program building an EA algorithm.
+*/
 
 #endif
 

eo/src/eoEasyPSO.h

@@ -188,6 +188,9 @@ protected:
 	}dummyInit;
 	
 };
-
+/**
+ * @example t-eoEasyPSO.cpp
+ * Example of a test program building a PSO algorithm.
+ */
 
 #endif /*_EOEASYPSO_H*/

eo/src/eoExtendedVelocity.h

@@ -35,7 +35,9 @@
 //-----------------------------------------------------------------------------
 
 
-/** Extended velocity performer for particle swarm optimization. Derivated from abstract eoVelocity,
+/** Extended velocity performer for particle swarm optimization. 
+ *
+ *  Derivated from abstract eoVelocity,
 *   At step t: v(t+1)= w * v(t) + c1 * r1 * ( xbest(t)-x(t) ) + c2 * r2 * ( lbest(t) - x(t) )  + c3 * r3 * ( gbest(t) - x(t) )
 *   It includes both a "topology" best and a global best in the social knowledge. Each topology
 *   provides a method to retrieve the global best <=> the best of all the neighborhood the topology contains.
@@ -60,7 +62,7 @@ public:
     * @param _c3 - Learning factor used for the global best 
     * @param _bounds - An eoRealBaseVectorBounds: real bounds for real velocities. 
     * If the velocities are not real, they won't be bounded by default. Should have a eoBounds ?
-    * @param _boundsModifier - An eoRealBoundModifier used to modify the bounds (for real bounds only).
+    * @param _bndsModifier - An eoRealBoundModifier used to modify the bounds (for real bounds only).
     * @param _gen - The eo random generator, default=rng
     */
     eoExtendedVelocity (eoTopology < POT > & _topology,
@@ -204,7 +206,9 @@ protected:
     // If the bound modifier doesn't need to be used, use the dummy instance
     eoDummyRealBoundModifier dummyModifier;
 };
-
-
+/** @todo this example does not appear in the doc for an unknown reason
+ * @example t-eoExtendedVelocity.cpp
+ * Example of a test program using this class:
+*/
 #endif /*eoExtendedVelocity_H */
 

eo/src/eoFunctor.h

@@ -60,6 +60,8 @@ public :
     /// tag to identify a binary function in compile time function selection @see functor_category
     struct binary_function_tag {};
 };
+/** @example t-eoFunctop.cpp
+ */
 
 /**
     Basic Function. Derive from this class when defining

eo/src/eoGenOp.h

@@ -81,6 +81,8 @@ class eoGenOp : public eoOp<EOT>, public eoUF<eoPopulator<EOT> &, void>
    */
     virtual void apply(eoPopulator<EOT>& _pop) = 0;
 };
+/** @example t-eoGenOp.cpp
+ */
 
 
 /** Wrapper for eoMonOp */

eo/src/eoInit.h

@@ -183,6 +183,8 @@ class eoInitPermutation: public eoInit<EOT>
         unsigned startFrom;
         UF_random_generator<unsigned int> gen;
 };
+/** @example t-eoInitPermutation.cpp
+ */
 
 
 /**

eo/src/eoInt.h

@@ -54,6 +54,8 @@ template <class FitT> class eoInt: public eoVector<FitT, int>
     }
 
 };
+/** @example t-eoInt.cpp
+ */
 
 //-----------------------------------------------------------------------------
 

eo/src/eoOp.h

@@ -63,10 +63,16 @@ Variators are operators that modify individuals.
 
 Selectors are operators that select a subset of a population.
 
+Example:
+@include t-eoSelect.cpp
+
 
 @defgroup Replacors Replacement operators
 
 Replacors are operators that replace a subset of a population by another set of individuals.
+
+Here is an example with several replacement operators:
+@include t-eoReplacement.cpp
 */
 
 /** Abstract data types for EO operators.

eo/src/eoOrderXover.h

@@ -84,5 +84,7 @@ template<class Chrom> class eoOrderXover: public eoQuadOp<Chrom>
 	 }
 	 	
 };
+/** @example t-eoOrderXover.cpp
+ */
 
 #endif

eo/src/eoProportionalSelect.h

@@ -81,5 +81,7 @@ private :
   typedef std::vector<typename EOT::Fitness> FitVec;
   FitVec cumulative;
 };
+/** @example t-eoRoulette.cpp
+ */
 
 #endif

eo/src/eoRingTopology.h

@@ -188,5 +188,7 @@ protected:
     unsigned neighborhoodSize; 
     bool isSetup;
 };
+/** @example t-eoRingTopology.cpp
+ */
 
 #endif /*EORINGTOPOLOGY_H_*/

eo/src/eoScalarFitness.h

@@ -79,6 +79,9 @@ class eoScalarFitness
     private :
         ScalarType value;
 };
+/** @example t-eofitness.cpp
+ *
+ */
 
 /**
 Typedefs for fitness comparison, Maximizing Fitness compares with less,

eo/src/eoScalarFitnessAssembled.h

@@ -77,6 +77,8 @@ public:
 private:
   static std::vector<std::string> TermDescriptions;
 };
+/** @example t-eoFitnessAssembled.cpp
+ */
 
 //! Implements fitness as std::vector, storing all values that might occur during fitness assembly
 /*! Properties:
@@ -237,6 +239,10 @@ public:
   bool operator>=(const eoScalarFitnessAssembled<ScalarType, Compare, FitnessTraits>& y ) const { return !(*this < y); }
 
 };
+/** 
+ * @example t-eoFitnessAssembledEA.cpp
+*/
+
 
 /**
 Typedefs for fitness comparison, Maximizing Fitness compares with less,

eo/src/eoSecondsElapsedContinue.h

@@ -64,6 +64,8 @@ public:
   }
 
 };
+/** @example t-eoSecondsElapsedContinue.cpp
+ */
 
 #endif
 

eo/src/eoSelectOne.h

@@ -53,6 +53,8 @@ class eoSelectOne : public eoUF<const eoPop<EOT>&, const EOT&>
 	  (void)_pop;
       }
 };
+/** @example t-eoSelectOne.cpp
+ */
 
 
 #endif

eo/src/eoSharingSelect.h

@@ -53,5 +53,7 @@ public:
 private :
   eoSharing<EOT> sharing;	   // derived from eoPerf2Worth
 };
+/** @example t-eoSharing.cpp
+ */
 
 #endif

eo/src/eoShiftMutation.h

@@ -83,6 +83,8 @@ template<class EOT> class eoShiftMutation: public eoMonOp<EOT>
     }
     
 };
+/** @example t-eoShiftMutation.cpp
+ */ 
 
 
 //-----------------------------------------------------------------------------

eo/src/eoStochasticUniversalSelect.h

@@ -104,5 +104,7 @@ private :
   typedef std::vector<unsigned> IndexVec;
   IndexVec indices;
 };
+/** @example t-eoRoulette.cpp
+ */
 
 #endif

eo/src/eoSwapMutation.h

@@ -75,6 +75,8 @@ template<class Chrom> class eoSwapMutation: public eoMonOp<Chrom>
    private:
    	unsigned int howManySwaps;
 };
+/** @example t-eoSwapMutation.cpp
+ */
 
 //-----------------------------------------------------------------------------
 #endif

eo/src/eoSyncEasyPSO.h

@@ -253,6 +253,8 @@ private:
 	}dummyInit;
 	
 };
+/** @example t-eoSyncEasyPSO.cpp
+ */
 
 
 #endif /*_EOSYNCEASYPSO_H*/

eo/src/eoTwoOptMutation.h

@@ -69,6 +69,8 @@ public:
     }
 
 };
+/** @example t-eoTwoOptMutation.cpp
+ */
 
 
 //-----------------------------------------------------------------------------

eo/src/eoVariableInertiaWeightedVelocity.h

@@ -60,7 +60,7 @@ public:
     * @param _c2 - The second learning factor used for the local/global best(s). Type must be POT::ParticleVelocityType 
     * @param _bounds - An eoRealBaseVectorBounds: real bounds for real velocities. 
     * If the velocities are not real, they won't be bounded by default. Should have a eoBounds ?
-    * @param _boundsModifier - An eoRealBoundModifier used to modify the bounds (for real bounds only).
+    * @param _bndsModifier - An eoRealBoundModifier used to modify the bounds (for real bounds only).
     * @param _gen - The eo random generator, default=rng
     */
     eoVariableInertiaWeightedVelocity (eoTopology < POT > & _topology,

eo/src/eoVariableLengthMutation.h

@@ -56,7 +56,7 @@ public :
 
   /** default ctor
 
-   * @param nMax      max number of atoms
+   * @param _nMax      max number of atoms
    * @param _atomInit an Atom initializer
    */
   eoVlAddMutation(unsigned _nMax, eoInit<AtomType> & _atomInit) :
@@ -118,15 +118,15 @@ public :
 
   /** ctor with an external gene chooser
 
-   * @param nMin      min number of atoms to leave in the individual
-   * @param _geneChooser an eoGeneCHooser to choose which one to delete
+   * @param _nMin      min number of atoms to leave in the individual
+   * @param _chooser   an eoGeneCHooser to choose which one to delete
    */
   eoVlDelMutation(unsigned _nMin, eoGeneDelChooser<EOT> & _chooser) :
     nMin(_nMin), uChooser(), chooser(_chooser) {}
 
   /** ctor with uniform gene chooser - the default
 
-   * @param nMin      min number of atoms to leave in the individual
+   * @param _nMin      min number of atoms to leave in the individual
    */
   eoVlDelMutation(unsigned _nMin) :
     nMin(_nMin), uChooser(), chooser(uChooser) {}

eo/src/eoVector.h

@@ -66,8 +66,8 @@ public:
 
     /** default constructor
 
-    @param size Length of vector (default is 0)
-    @param value Initial value of all elements (default is default value of type GeneType)
+    @param _size Length of vector (default is 0)
+    @param _value Initial value of all elements (default is default value of type GeneType)
     */
     eoVector(unsigned _size = 0, GeneType _value = GeneType())
         : EO<FitT>(), std::vector<GeneType>(_size, _value)
@@ -129,6 +129,8 @@ public:
             }
         }
 };
+/** @example t-eoVector.cpp
+ */
 
 /** Less than
 

eo/src/eoVectorParticle.h

@@ -66,9 +66,9 @@ public:
 
     /** Default constructor.
     *  @param _size Length of the tree vectors (we expect the same size), default is 0
-    *  @param position
-    *  @param velocity
-    *  @param  bestPositions
+    *  @param _position
+    *  @param _velocity
+    *  @param _bestPositions
     */
     eoVectorParticle (unsigned _size = 0,PositionType _position = PositionType (), VelocityType _velocity = VelocityType (), PositionType _bestPositions = PositionType ()):PO < FitT > (),std::vector < PositionType > (_size, _position), bestPositions (_size, _bestPositions), velocities (_size,
                     _velocity)

eo/src/es/eoReal.h

@@ -54,6 +54,8 @@ template <class FitT> class eoReal: public eoVector<FitT, double>
     }
 
 };
+/** @example t-eoReal.cpp
+ */
 
 //-----------------------------------------------------------------------------
 

eo/src/ga/eoBit.h

@@ -44,7 +44,10 @@
 
 /** @defgroup bitstring Bit strings
 
-Various functions for a bitstring representation
+Various functions for a bitstring representation.
+
+Example of a complete test program that use various bitstrings operators:
+@include t-eobin.cpp
 
 @ingroup Representations
 */

eo/src/gp/eoParseTree.h

@@ -41,6 +41,9 @@ using namespace gp_parse_tree;
 
 Various functions for tree-based Genetic Programming
 
+Example:
+@include t-eoSymreg.cpp
+
 @ingroup Representations
 */
 
@@ -166,6 +169,8 @@ public:
 	*/
     }
 };
+/** @example t-eoSymreg.cpp
+ */
 
 // friend function to print eoParseTree
 template <class FType, class Node>

eo/src/gp/parse_tree.h

@@ -22,8 +22,9 @@
   class Node (your node in the tree) must have the following implemented:
 
   ******      Arity      ******
-
+    \code
 	int arity(void) const
+    \endcode
 
 	Note:	the default constructor of a Node should provide a
 			Node with arity 0!
@@ -36,7 +37,9 @@
 
 	   is the simplest evaluation, it will call
 
+    \code
 	   RetVal Node::operator()(RetVal, subtree<Node, RetVal>::const_iterator)
+    \endcode
 
        (Unfortunately the first RetVal argument is mandatory (although you
        might not need it. This is because MSVC does not support member template
@@ -50,7 +53,9 @@
 
        will call:
 
+    \code
        RetVal Node::operator()(RetVal, subtree<... , It values)
+    \endcode
 
        where It is whatever type you desire (most of the time
 	   this will be a std::vector containing the values of your
@@ -60,7 +65,9 @@
 
        will call:
 
+    \code
        RetVal Node::operator()(RetVal, subtree<... , It values, It2 moreValues)
+    \endcode
 
 	   although I do not see the immediate use of this, however...
 
@@ -68,7 +75,9 @@
 
 		that calls:
 
+    \code
        RetVal Node::operator()(subtree<... , It values, It2 args, It3 adfs)
+    \endcode
 
 		can be useful for implementing adfs.
 
@@ -77,8 +86,10 @@
 	arguments open so that different ways of evaluation remain
 	possible. Implement the simplest eval as:
 
+    \code
 	template <class It>
 		RetVal operator()(RetVal dummy, It begin) const
+    \endcode
 
   ******	Internal Structure    ******
 
@@ -144,7 +155,9 @@
 
   or from an std::istream:
 
-  copy(std::istream_iterator<T>(my_stream), std::istream_iterator<T>(), back_inserter(tree));
+\code
+    copy(std::istream_iterator<T>(my_stream), std::istream_iterator<T>(), back_inserter(tree));
+\endcode
 
   Note that the back_inserter must be used as there is no
   resize member in the parse_tree. back_inserter will use

eo/src/other/eoExternalEO.h

@@ -74,6 +74,8 @@ public :
   }
 
 };
+/** @example t-eoExternalEO.cpp
+ */
 
 /** To remove ambiguities between EO<F> and External, streaming operators are defined yet again
  * @ingroup Utilities

eo/src/utils/eoCheckPoint.h

@@ -39,10 +39,13 @@
  *
  * Use them with eoStats, eoUpdater and eoMonitor to get statistics at each generation.
  *
- * @see eoStats
+ * @see eoStat
  * @see eoMonitor
  * @see eoUpdater
  *
+ * Example of a test program using checkpointing:
+ * @include t-eoCheckpointing.cpp
+ *
  * @ingroup Utilities
  *
  * @{

eo/src/utils/eoLogger.h

@@ -247,6 +247,8 @@ private:
      */
     std::map< std::ostream*, int >	_standard_io_streams;
 };
+/** @example t-eoLogger.cpp
+ */
 
 namespace	eo
 {

eo/src/utils/eoRNG.h

@@ -438,6 +438,8 @@ private:
     */
     eoRng& operator=(const eoRng&);
 };
+/** @example t-eoRNG.cpp
+ */
 
 
 

eo/src/utils/eoRealBounds.h

@@ -33,6 +33,12 @@
 /**
 \defgroup Real Vector of reals
 
+Set of classes related to continuous black-box optimization problems.
+
+Here are several examples of test programs using eoReal, eoEsSimple, eoEsStdev or eoEsFull to build an Evoution Strategies algorithm:
+@include t-eoESAll.cpp
+@include t-eoESFull.cpp
+
 @ingroup Representations
 
 */

eo/src/utils/eoRndGenerators.h

@@ -88,12 +88,16 @@ template <class T = double> class eoUniformGenerator : public eoRndGenerator<T>
   for ints and unsigneds
   */
   T operator()(void) { return minim+static_cast<T>(uniform.uniform(range)); }
+  /** @example t-eoUniform.cpp
+   */
 
 private :
   T minim;
   T range;
   eoRng& uniform;
 };
+/** @example t-eoRandom.cpp
+ */
 
 
 /// Specialization for bool, does an unbiased coin flip

eo/src/utils/eoStat.h

@@ -407,6 +407,8 @@ private :
     }
 
 };
+/** @example t-eoSSGA.cpp
+ */
 
 template <class EOT>
 class eoDistanceStat : public eoStat<EOT, double>

eo/src/utils/eoState.h

@@ -132,5 +132,7 @@ private :
     eoState& operator=(const eoState&);
 
 };
+/** @example t-eoStateAndParser.cpp
+ */
 
 #endif