Merge

--HG-- branch : dev
falconzyx · Jan 7, 2013 · e414441 · e414441
2 parents 83b59b0 + d596e72
commit e414441
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Showing 5 changed files with 37 additions and 31 deletions.
diff --git a/MANIFEST.in b/MANIFEST.in
@@ -1,4 +1,5 @@
 include *.txt
-recursive-include examples *.py *.csv *.json
+recursive-include deap *.cpp
+recursive-include examples *.py *.csv *.json 
 recursive-include doc *
 prune doc/_build
diff --git a/deap/benchmarks/tools.py b/deap/benchmarks/tools.py
@@ -253,6 +253,9 @@ def diversity(first_front, first, last):
                 first.fitness.values[1] - second.fitness.values[1])
           for first, second in zip(first_front[:-1], first_front[1:])]
 
+    if len(first_front) == 1:
+        return df + dl
+
     dm = sum(dt)/len(dt)
     di = sum(abs(d_i - dm) for d_i in dt)
     delta = (df + dl + di)/(df + dl + len(dt) * dm )

diff --git a/deap/tools.py b/deap/tools.py
@@ -1630,17 +1630,19 @@ def assignCrowdingDist(individuals):
         return
 
     distances = [0.0] * len(individuals)
-    crowding = [(ind.fitness.values, i) for i, ind in enumerate(individuals)]
-
-    number_objectives = len(individuals[0].fitness.values)
-
-    for i in xrange(number_objectives):
-        crowding.sort(key=lambda element: element[0][i])
-        distances[crowding[0][1]] = float("inf")
-        distances[crowding[-1][1]] = float("inf")
-        for j in xrange(1, len(crowding) - 1):
-            distances[crowding[j][1]] += crowding[j + 1][0][i] - \
-                                         crowding[j - 1][0][i]
+    crowd = [(ind.fitness.values, i) for i, ind in enumerate(individuals)]
+
+    nobj = len(individuals[0].fitness.values)
+
+    for i in xrange(nobj):
+        crowd.sort(key=lambda element: element[0][i])
+        distances[crowd[0][1]] = float("inf")
+        distances[crowd[-1][1]] = float("inf")
+        if crowd[-1][0][i] == crowd[0][0][i]:
+            continue
+        norm = nobj * float(crowd[-1][0][i] - crowd[0][0][i])
+        for prev, cur, next in zip(crowd[:-2], crowd[1:-1], crowd[2:]):
+            distances[cur[1]] += (next[0][i] - prev[0][i]) / norm
 
     for i, dist in enumerate(distances):
         individuals[i].fitness.crowding_dist = dist

diff --git a/doc/api/algo.rst b/doc/api/algo.rst
@@ -11,16 +11,16 @@ basic evolutionary computation concepts. All algorithms accept, in addition to
 their arguments, an initialized :class:`~deap.tools.Statistics` object to
 maintain stats of the evolution, an initialized
 :class:`~deap.tools.HallOfFame` to hold the best individual(s) to appear in
-the population, and/or an initialized :class:`~deap.tools.EvolutionLogger` to
-log what is happening during the evolution.
+the population, and a boolean `verbose` to specify wether to
+log what is happening during the evolution or not.
 
-.. autofunction:: deap.algorithms.eaSimple(population, toolbox, cxpb, mutpb, ngen[, stats, halloffame, logger])
+.. autofunction:: deap.algorithms.eaSimple(population, toolbox, cxpb, mutpb, ngen[, stats, halloffame, verbose])
 
-.. autofunction:: deap.algorithms.eaMuPlusLambda(population, toolbox, mu, lambda_, cxpb, mutpb, ngen[, stats, halloffame, logger])
+.. autofunction:: deap.algorithms.eaMuPlusLambda(population, toolbox, mu, lambda_, cxpb, mutpb, ngen[, stats, halloffame, verbose])
 
-.. autofunction:: deap.algorithms.eaMuCommaLambda(population, toolbox, mu, lambda_, cxpb, mutpb, ngen[, stats, halloffame, logger])
+.. autofunction:: deap.algorithms.eaMuCommaLambda(population, toolbox, mu, lambda_, cxpb, mutpb, ngen[, stats, halloffame, verbose])
 
-.. autofunction:: deap.algorithms.eaGenerateUpdate(toolbox, ngen[, stats, halloffame, logger])
+.. autofunction:: deap.algorithms.eaGenerateUpdate(toolbox, ngen[, stats, halloffame, verbose])
 
 Variations
 ----------
@@ -39,5 +39,5 @@ Covariance Matrix Adaptation Evolution Strategy
 .. autoclass:: deap.cma.Strategy(centroid, sigma[, **kargs])
    :members:
 
-.. .. autoclass:: deap.cma.StrategyOnePlusLambda(parent, sigma[, **kargs])
-..    :members:
+.. autoclass:: deap.cma.StrategyOnePlusLambda(parent, sigma[, **kargs])
+   :members:
diff --git a/doc/api/tools.rst b/doc/api/tools.rst
@@ -20,9 +20,9 @@ Here is a list of the implemented operators in DEAP,
  :func:`initRepeat`           :func:`cxOnePoint`                          :func:`mutGaussian`                       :func:`selTournament`     :func:`migRing`
  :func:`initIterate`          :func:`cxTwoPoints`                         :func:`mutShuffleIndexes`                 :func:`selRoulette`       ..             
  :func:`initCycle`            :func:`cxUniform`                           :func:`mutFlipBit`                        :func:`selNSGA2`          ..             
- :func:`~deap.gp.genFull`     :func:`cxPartialyMatched`                   :func:`mutPolynomialBounded`              :func:`selSPEA2`          ..             
- :func:`~deap.gp.genGrow`     :func:`cxUniformPartialyMatched`            :func:`mutUniformInt`                     :func:`selRandom`         ..             
- :func:`~deap.gp.genRamped`   :func:`cxOrdered`                           :func:`mutESLogNormal`                    :func:`selBest`           ..             
+ ..                           :func:`cxPartialyMatched`                   :func:`mutPolynomialBounded`              :func:`selSPEA2`          ..             
+ ..                           :func:`cxUniformPartialyMatched`            :func:`mutUniformInt`                     :func:`selRandom`         ..             
+ ..                           :func:`cxOrdered`                           :func:`mutESLogNormal`                    :func:`selBest`           ..             
  ..                           :func:`cxBlend`                             ..                                        :func:`selWorst`          ..             
  ..                           :func:`cxESBlend`                           ..                                        :func:`selTournamentDCD`  ..             
  ..                           :func:`cxESTwoPoints`                       ..                                        ..                        ..             
@@ -33,14 +33,14 @@ Here is a list of the implemented operators in DEAP,
 
 and genetic programming specific operators.
 
-=========================================== =========================================
- Crossover                                   Mutation                                
-=========================================== =========================================
- :func:`~deap.gp.cxOnePoint`                 :func:`~deap.gp.mutUniform`             
- :func:`~deap.gp.cxOnePointLeafBiased`       :func:`~deap.gp.mutNodeReplacement`     
- ..                                          :func:`~deap.gp.mutEphemeral`           
- ..                                          :func:`~deap.gp.mutInsert`
-=========================================== =========================================
+============================ =========================================== =========================================
+ Initialization               Crossover                                   Mutation                                
+============================ =========================================== =========================================
+ :func:`~deap.gp.genFull`     :func:`~deap.gp.cxOnePoint`                 :func:`~deap.gp.mutUniform`             
+ :func:`~deap.gp.genGrow`     :func:`~deap.gp.cxOnePointLeafBiased`       :func:`~deap.gp.mutNodeReplacement`     
+ :func:`~deap.gp.genRamped`   ..                                          :func:`~deap.gp.mutEphemeral`           
+ ..                           ..                                          :func:`~deap.gp.mutInsert`
+============================ =========================================== =========================================
 
 
 Initialization