Added many template files, and totally modified the comments in most other.

This was when preparing Evonet Summer School - though it finally was not used there!

eo/tutorial/Templates/README

@@ -0,0 +1,125 @@
+This directory contains sample files that should make it easy to
+create an EO algorithm to evolve any type of structure 
+(EO comes with two examples, bitstrings and vector of real variables,
+so you'll need this qs soon as you want to evolve something else).
+
+At the moment, only algorithms involving a scalar fitness (double)
+are implemented (see test dir for Pareto optimization of multiple-
+objective fitness - or be patient :-)
+
+This file will help you to build the same algorithm than the ones 
+in the Lesson4 of the tutorial, but with YOUR genotype instead of
+*bitstrings or vector<double>
+
+It is assumed in the following that you have read the first part of
+the tutorial (Lessons 1 to 4).
+
+Creating the algorithm for your genotype
+----------------------------------------
+In what follows, we will suppose that you want to evolve some data
+structure, and that you have enough programming skills to be able to
+write C code for its random initilialization, its crossover, its
+mutation and the computation of its fitness.
+
+The helper script create.sh will create for you the files you need
+from teh examples in tutorial/Templates dir, and all you'll have to do
+is to include the actual code where indicated in those files (between
+keywords START and END). 
+
+First, let's choose a name: let's call the new EO class eoAppli.
+All newly created classes will be named eoApplicationXXX (in the file
+eoApplicationXXX)
+
+1- create a directory for your application in the tutorial dir, "parallel" to
+the LessonX dirs (though any name can do, of course, we will suppose
+its full name, from the / root dir, is APPLICATION in what follows)
+
+2- cd to the tutorial/Templates dir
+
+3- run the helper script create.sh with the following arguments
+            create.sh Appli APPLICATION
+
+4- cd to the APPLICATION dir. You should see there the following
+files:
+   Makefile               with default target eoAppliEA
+   eoAppli.h              class eoAppli<FitT>, FitT = template fitness
+   eoAppliEA.cpp          the main file, includes all other, to be compiled
+   eoAppliEvalFunc.h      class for the computation of fotness
+   eoAppliInit.h          class for genotype initlialization
+   eoAppliMutation.h      class for mutation 
+   eoAppliQuadCrossover.h class for (quadratic) crossover
+
+Note: You can go directly to step 6 and 7: you'll get a lot of
+warnings, but will be able to run an EA that does nothing!
+
+5- Edit those files one after the other and add you code where
+indicated (look for keywords START and END and modify code in
+between).
+
+Note: If your APPLICATION dir is in the tutorial dir, you don't need
+to modify Makefile.
+
+6- Compile eoAppliEA.cpp:
+
+               % make
+
+7- Run the resulting program:
+
+               % eoAppliEA
+
+The default output is one line per generation with the generation
+number, the number of evaluations performed, the best and average
+fitnesses in the population.
+The algorithm stops by default after 100 generations.
+
+8- Customize the parameters: copy eoAppliEA.status into
+e.g. eoAppliEA.param, edit eoAppliEA.param (uncomment the lines you
+want to become active), and run
+
+               % eoAppliEA @eoAppliEA.param
+
+(see the Lesson 4 of the tutorial for more details now).
+
+HINTS
+-----
+
+1- All new classes you will create probably require some parameters in
+the constructor, and some (if not all) thoses parameters are likele to
+be user parameter: you can either read them in the main file (as is
+done in the sample eoAppliEA.cpp) or pass the eoParser to the
+constructor of the class, and read the parameter from the parser.
+
+2- If you stick to privacy for the data in your EO class, you will
+probably need to write accessors to those data, as well as some public
+methods to modify them.
+
+3- The sample eoAppliEA.cpp supposes that you ony have one crossover
+and one mutation operator. However, the code for multiple operators
+is there: you can have for instance 2 crossover operators, and choose
+among them according to relative weights (proportional choice) - same
+for mutation. Look at the operator section in eoAppliEA.cpp
+In particular, the user parameter mutationRate is totally useless for
+a single operator, and is there only as a provision for using more
+than one.
+
+To add another operator, you have to create another class by mimicking
+what has been done for the first operator.
+For instance, let's suppose you want to create another mutation.
+
+* duplicate the code for eoAppliMutation class 
+* in the second version, change the class name (eoAppliMutation) into
+another name (let's say eoAppliBetterMutation) - you must change the
+name in the class declaration, in the constructor and in the
+className() method.
+* in the new eoAppliBetterMutation class, change the code for the
+operator() - and eventually the code for the constructor.
+* in the eoAppliEA.cpp file, in the mutation section, uncomment the
+lines 
+      eoMyStructSecondMutation<Indi> mut2(varType  _anyVariable);
+      double mut2Rate = parser.createParam(1.0, "mut2Rate", "Relative rate for mutation 2", '2', "Variation Operators").value(); 
+       propMutation.add(mut2, mut2Rate); 
+
+and change the name of the class from eoAppliSecondMutation to your
+name eoAppliBetterMutation (you can also change the keyword from
+mut2Rate to something more meaningful like BetterMutationRate).
+You're done!