Moving example and tests, fixing a major bug that didn't drop previou…

…s fitness computation on mutation
frantzmiccoli · Mar 30, 2014 · 3895efe13769299a21cc8f090d22bbf599c4b6cc · 3895efe
1 parent b6dca86
commit 3895efe13769299a21cc8f090d22bbf599c4b6cc
diff --git a/example/getting_started_1.rb → examples/getting_started_1.rb b/example/getting_started_1.rb → examples/getting_started_1.rb
@@ -12,10 +12,6 @@
 # STEP 1: First we define a solution
 class SampleProblemSolution < FunctionBasedSolution
 
-  def initialize(x_values = nil)
-    super(x_values)
-  end
-
   def evaluate
     product = 1.0
     @x_values.each do |x_value|
@@ -52,6 +48,10 @@ def get_dimension_number
 end
 
 # STEP 3: We get back the found solution
+r = optimizer.get_best_solution.get_solution_representation
+e = [-2.46835042100562,1.88147457884558,-0.467589756441865]
+
+
 puts '[' + optimizer.get_best_solution.get_solution_representation.join(',') + ']'
 puts optimizer.get_best_fitness
 
diff --git a/example/getting_started_2.rb → examples/getting_started_2.rb b/example/getting_started_2.rb → examples/getting_started_2.rb
diff --git a/examples/manual_instantiation.rb b/examples/manual_instantiation.rb
@@ -0,0 +1,41 @@
+require 'gimuby/genetic/archipelago/archipelago'
+require 'gimuby/genetic/archipelago/connect_strategy/fully_connected_connect_strategy'
+
+require 'gimuby/genetic/population/population'
+require 'gimuby/genetic/population/pick_strategy/tournament_pick_strategy'
+require 'gimuby/genetic/population/replace_strategy/replace_worst_replace_strategy'
+
+require 'gimuby/problem/step/step_solution'
+
+# Manual archipelago creation
+archipelago = Archipelago.new
+archipelago.connect_strategy = FullyConnectedConnectStrategy.new
+archipelago.migration_rate = 10.0 / 100.0
+archipelago.migration_symmetric = true
+archipelago.migration_type = :synchronized
+
+10.times do
+  # Manual population creation
+  population = Population.new
+  population.pick_strategy = TournamentPickStrategy.new
+  population.replace_strategy = ReplaceWorstReplaceStrategy.new
+
+  # We add solution of the relevant problem
+  30.times do
+    solution = StepSolution.new
+    population.add_solution(solution)
+  end
+
+  # The current population is attached to the archipelago
+  archipelago.add_population(population)
+end
+
+# Every population is here, we connect them together
+archipelago.connect_all
+
+# We run the algorithm
+100.times do
+  archipelago.generation_step
+end
+
+puts archipelago.get_best_fitness
diff --git a/example/population_vs_archipelago.rb → examples/population_vs_archipelago.rb b/example/population_vs_archipelago.rb → examples/population_vs_archipelago.rb
@@ -4,9 +4,6 @@
 
 SolutionClass = StepSolution
 
-srand(ARGV[0].to_i)
-puts ARGV[0]
-
 # Let's test the following configurations, the optimizer is either population
 # for a standard genetic algorithm, either archipelago for a "distributed"
 # version of the algorithm (nothing is distributed in Gimuby)

diff --git a/gimuby.gemspec b/gimuby.gemspec
@@ -14,7 +14,7 @@ Gem::Specification.new do |spec|
       'algorithm (named population) and distributed genetic algorithm or ' +
       'island model (named archipelago).' + "\n" +
       'The presented archipelago are NOT distributed (nor with threads, ' +
-      'process, or physical machine). However they let the user benefits of' +
+      'processes, or physical machines). However they let the user benefits of' +
       'the leverage they represent to obtain a better solution with the same ' +
       'amount of resources spent.' + "\n" +
       'Similar to: AI4R, gga4r and darwinning'
@@ -27,4 +27,4 @@ Gem::Specification.new do |spec|
   spec.required_ruby_version = '~> 1.8'
   spec.license = 'MIT'
 
-end
+end
diff --git a/lib/gimuby/genetic/population/population.rb b/lib/gimuby/genetic/population/population.rb
@@ -78,9 +78,10 @@ def get_best_fitness
   end
 
   def get_best_solution
-    @solutions.min_by do |solution|
+    best_solution = @solutions.min_by do |solution|
       solution.get_fitness
     end
+    best_solution
   end
 
   protected

diff --git a/lib/gimuby/genetic/solution/mutation_strategy/mutation_strategy.rb b/lib/gimuby/genetic/solution/mutation_strategy/mutation_strategy.rb
@@ -11,6 +11,7 @@ def initialize(mutation_rate = 0.01)
   def mutate(solution)
     if rand < @mutation_rate
       perform_mutation(solution)
+      solution.reset_fitness_state
     end
   end
 

diff --git a/lib/gimuby/genetic/solution/solution.rb b/lib/gimuby/genetic/solution/solution.rb
@@ -33,6 +33,10 @@ def get_fitness
     @fitness
   end
 
+  def reset_fitness_state
+    @fitness = nil
+  end
+
   def mutate
     @mutation_strategy.mutate(self)
   end

diff --git a/rakefile b/rakefile
@@ -1,8 +1,7 @@
 require 'rake/testtask'
 
 Rake::TestTask.new do |test|
-  Dir.chdir './test'
-  test.libs << "./test"
+  Dir.chdir './tests'
   test.libs << "../lib"
   test.test_files = FileList['**/test*.rb']
   test.verbose = true

diff --git a/test/abstract_test_case.rb → tests/abstract_test_case.rb b/test/abstract_test_case.rb → tests/abstract_test_case.rb
diff --git a/test/genetic/archipelago/test_archipelago.rb → ...s/genetic/archipelago/test_archipelago.rb b/test/genetic/archipelago/test_archipelago.rb → ...s/genetic/archipelago/test_archipelago.rb
diff --git a/.../test_barabasi_albert_connect_strategy.rb → .../test_barabasi_albert_connect_strategy.rb b/.../test_barabasi_albert_connect_strategy.rb → .../test_barabasi_albert_connect_strategy.rb
diff --git a/...chipelago/test_circle_connect_strategy.rb → ...chipelago/test_circle_connect_strategy.rb b/...chipelago/test_circle_connect_strategy.rb → ...chipelago/test_circle_connect_strategy.rb
diff --git a/...go/test_clustering_coefficient_measure.rb → ...go/test_clustering_coefficient_measure.rb b/...go/test_clustering_coefficient_measure.rb → ...go/test_clustering_coefficient_measure.rb
diff --git a/...tic/archipelago/test_connected_measure.rb → ...tic/archipelago/test_connected_measure.rb b/...tic/archipelago/test_connected_measure.rb → ...tic/archipelago/test_connected_measure.rb
diff --git a/.../test_constant_degree_connect_strategy.rb → .../test_constant_degree_connect_strategy.rb b/.../test_constant_degree_connect_strategy.rb → .../test_constant_degree_connect_strategy.rb
diff --git a/...etic/archipelago/test_diameter_measure.rb → ...etic/archipelago/test_diameter_measure.rb b/...etic/archipelago/test_diameter_measure.rb → ...etic/archipelago/test_diameter_measure.rb
diff --git a/.../test_fully_connected_connect_strategy.rb → .../test_fully_connected_connect_strategy.rb b/.../test_fully_connected_connect_strategy.rb → .../test_fully_connected_connect_strategy.rb
diff --git a/...chipelago/test_random_connect_strategy.rb → ...chipelago/test_random_connect_strategy.rb b/...chipelago/test_random_connect_strategy.rb → ...chipelago/test_random_connect_strategy.rb
diff --git a/...rchipelago/test_shortest_paths_measure.rb → ...rchipelago/test_shortest_paths_measure.rb b/...rchipelago/test_shortest_paths_measure.rb → ...rchipelago/test_shortest_paths_measure.rb
diff --git a/...o/test_watts_strogatz_connect_strategy.rb → ...o/test_watts_strogatz_connect_strategy.rb b/...o/test_watts_strogatz_connect_strategy.rb → ...o/test_watts_strogatz_connect_strategy.rb
diff --git a/...ic/population/test_bests_pick_strategy.rb → ...ic/population/test_bests_pick_strategy.rb b/...ic/population/test_bests_pick_strategy.rb → ...ic/population/test_bests_pick_strategy.rb
diff --git a/test/genetic/population/test_population.rb → tests/genetic/population/test_population.rb b/test/genetic/population/test_population.rb → tests/genetic/population/test_population.rb
diff --git a/...lation/test_random_wheel_pick_strategy.rb → ...lation/test_random_wheel_pick_strategy.rb b/...lation/test_random_wheel_pick_strategy.rb → ...lation/test_random_wheel_pick_strategy.rb
diff --git a/...on/test_replace_worst_replace_strategy.rb → ...on/test_replace_worst_replace_strategy.rb b/...on/test_replace_worst_replace_strategy.rb → ...on/test_replace_worst_replace_strategy.rb
diff --git a/...pulation/test_tournament_pick_strategy.rb → ...pulation/test_tournament_pick_strategy.rb b/...pulation/test_tournament_pick_strategy.rb → ...pulation/test_tournament_pick_strategy.rb
diff --git a/...pulation/test_uniform_replace_strategy.rb → ...pulation/test_uniform_replace_strategy.rb b/...pulation/test_uniform_replace_strategy.rb → ...pulation/test_uniform_replace_strategy.rb
diff --git a/...n/test_average_new_generation_strategy.rb → ...n/test_average_new_generation_strategy.rb b/...n/test_average_new_generation_strategy.rb → ...n/test_average_new_generation_strategy.rb
diff --git a/.../test_combined_new_generation_strategy.rb → .../test_combined_new_generation_strategy.rb b/.../test_combined_new_generation_strategy.rb → .../test_combined_new_generation_strategy.rb
diff --git a/...est_cross_over_new_generation_strategy.rb → ...est_cross_over_new_generation_strategy.rb b/...est_cross_over_new_generation_strategy.rb → ...est_cross_over_new_generation_strategy.rb
diff --git a/...t_parent_range_new_generation_strategy.rb → ...t_parent_range_new_generation_strategy.rb b/...t_parent_range_new_generation_strategy.rb → ...t_parent_range_new_generation_strategy.rb
diff --git a/...lution/test_permutation_check_strategy.rb → ...lution/test_permutation_check_strategy.rb b/...lution/test_permutation_check_strategy.rb → ...lution/test_permutation_check_strategy.rb
diff --git a/...ion/test_permutation_mutation_strategy.rb → ...ion/test_permutation_mutation_strategy.rb b/...ion/test_permutation_mutation_strategy.rb → ...ion/test_permutation_mutation_strategy.rb
diff --git a/...ion/test_solution_space_check_strategy.rb → ...ion/test_solution_space_check_strategy.rb b/...ion/test_solution_space_check_strategy.rb → ...ion/test_solution_space_check_strategy.rb
diff --git a/.../test_solution_space_mutation_strategy.rb → .../test_solution_space_mutation_strategy.rb b/.../test_solution_space_mutation_strategy.rb → .../test_solution_space_mutation_strategy.rb
diff --git a/test/mock/population_mock.rb → tests/mock/population_mock.rb b/test/mock/population_mock.rb → tests/mock/population_mock.rb
diff --git a/test/mock/solution_mock.rb → tests/mock/solution_mock.rb b/test/mock/solution_mock.rb → tests/mock/solution_mock.rb
diff --git a/...problem/abstract_test_problem_solution.rb → ...problem/abstract_test_problem_solution.rb b/...problem/abstract_test_problem_solution.rb → ...problem/abstract_test_problem_solution.rb
diff --git a/test/problem/foxholes/test_foxholes.rb → tests/problem/foxholes/test_foxholes.rb b/test/problem/foxholes/test_foxholes.rb → tests/problem/foxholes/test_foxholes.rb
diff --git a/...roblem/foxholes/test_foxholes_solution.rb → ...roblem/foxholes/test_foxholes_solution.rb b/...roblem/foxholes/test_foxholes_solution.rb → ...roblem/foxholes/test_foxholes_solution.rb
diff --git a/...oblem/lennard_jones/test_lennard_jones.rb → ...oblem/lennard_jones/test_lennard_jones.rb b/...oblem/lennard_jones/test_lennard_jones.rb → ...oblem/lennard_jones/test_lennard_jones.rb
diff --git a/...nard_jones/test_lennard_jones_solution.rb → ...nard_jones/test_lennard_jones_solution.rb b/...nard_jones/test_lennard_jones_solution.rb → ...nard_jones/test_lennard_jones_solution.rb
diff --git a/test/problem/rastrigin/test_rastrigin.rb → tests/problem/rastrigin/test_rastrigin.rb b/test/problem/rastrigin/test_rastrigin.rb → tests/problem/rastrigin/test_rastrigin.rb
diff --git a/...blem/rastrigin/test_rastrigin_solution.rb → ...blem/rastrigin/test_rastrigin_solution.rb b/...blem/rastrigin/test_rastrigin_solution.rb → ...blem/rastrigin/test_rastrigin_solution.rb
diff --git a/...em/rosenbrock/test_rosenbrock_solution.rb → ...em/rosenbrock/test_rosenbrock_solution.rb b/...em/rosenbrock/test_rosenbrock_solution.rb → ...em/rosenbrock/test_rosenbrock_solution.rb
diff --git a/...roblem/schaffer/test_schaffer_solution.rb → ...roblem/schaffer/test_schaffer_solution.rb b/...roblem/schaffer/test_schaffer_solution.rb → ...roblem/schaffer/test_schaffer_solution.rb
diff --git a/test/problem/sphere/test_sphere.rb → tests/problem/sphere/test_sphere.rb b/test/problem/sphere/test_sphere.rb → tests/problem/sphere/test_sphere.rb
diff --git a/test/problem/sphere/test_sphere_solution.rb → tests/problem/sphere/test_sphere_solution.rb b/test/problem/sphere/test_sphere_solution.rb → tests/problem/sphere/test_sphere_solution.rb
diff --git a/test/problem/step/test_step.rb → tests/problem/step/test_step.rb b/test/problem/step/test_step.rb → tests/problem/step/test_step.rb
diff --git a/test/problem/step/test_step_solution.rb → tests/problem/step/test_step_solution.rb b/test/problem/step/test_step_solution.rb → tests/problem/step/test_step_solution.rb
diff --git a/test/problem/tsp/test_tsp.rb → tests/problem/tsp/test_tsp.rb b/test/problem/tsp/test_tsp.rb → tests/problem/tsp/test_tsp.rb
diff --git a/test/problem/tsp/test_tsp_solution.rb → tests/problem/tsp/test_tsp_solution.rb b/test/problem/tsp/test_tsp_solution.rb → tests/problem/tsp/test_tsp_solution.rb
diff --git a/test/test_event_manager.rb → tests/test_event_manager.rb b/test/test_event_manager.rb → tests/test_event_manager.rb