genetica 0.0.1.beta.2 → 0.0.1

checksums.yaml

@@ -0,0 +1,7 @@
+---
+SHA1:
+  metadata.gz: 9b8e281a009a9819b4c780b57560498e4561a38a
+  data.tar.gz: a1f2c7977d9b164a39aa04faf27e93b66ad4daf7
+SHA512:
+  metadata.gz: 66c0b5c5b0dfe9fc2080e2a7acc5103be24e452b2ad13df46a67e9ccfbe12cc053e93bbd5ce8a2b48d53ade3180d58c32a57c4b30d3fffc20892f76b669376bc
+  data.tar.gz: 982f38678edc5df1205f3f9d7da574a4d2bceddbbbda389694499a1a23280b0941dc4724384dd759d6cf0116d1a2f4d0a17cddb991d9497880dae1355431295c

data/lib/genetica/chromosome.rb

@@ -1,25 +1,42 @@
 module Genetica
-  class Chromosome
+  class Chromosome < Array
+    def crossover(crossover_method, crossover_probability, chromosome)
+      if crossover_probability > 0 && rand.between?(0, crossover_probability)
+        self.send(crossover_method, crossover_probability, chromosome)
+      else
+        # There is no crossover, return chromosomes without changes
+        return self, chromosome
+      end
+    end
 
-    attr_reader :chromosome
+    def single_point_crossover(crossover_probability, chromosome)
+      locus = rand(chromosome.size) + 1
 
-    def initialize(chromosome)
-      @chromosome = chromosome
+      offspring_a = take(locus) + chromosome.last(size - locus)
+      offspring_b = chromosome.take(locus) + last(size - locus)
+
+      return Chromosome.new(offspring_a), Chromosome.new(offspring_b)
     end
 
-    def single_point_crossover(chromosome)
-      other_chromosome = chromosome.chromosome
-      locus = rand(other_chromosome.size) + 1
+    def uniform_crossover(crossover_probability, chromosome)
+      offspring_a, offspring_b = Array.new, Array.new
 
-      offspring_a = @chromosome.take(locus) + other_chromosome.last(@chromosome.size - locus)
-      offspring_b = other_chromosome.take(locus) + @chromosome.last(@chromosome.size - locus)
+      chromosome.size.times do |i|
+        if rand(2) == 0
+          offspring_a << self[i]
+          offspring_b << chromosome[i]
+        else
+          offspring_a << chromosome[i]
+          offspring_b << self[i]
+        end
+      end
 
       return Chromosome.new(offspring_a), Chromosome.new(offspring_b)
     end
 
     def mutate!(mutation_probability, alleles)
       if mutation_probability > 0
-        @chromosome.collect! do |gene|
+        map! do |gene|
           if rand.between? 0, mutation_probability
             # Mutated Gene, we select a different gene from the alleles
             (alleles - [gene]).sample
@@ -32,9 +49,7 @@ module Genetica
     end
 
     def to_s
-      return @chromosome.join
+      join
     end
-
   end
 end
-

data/lib/genetica/chromosome_builder.rb

@@ -1,20 +1,22 @@
 module Genetica
   class ChromosomeBuilder
-
-    attr_accessor :length
-    attr_accessor :alleles
+    attr_accessor :length, :alleles
 
     def initialize
-      # Default Chromosome values
-      @length = 8
-      @alleles = [0, 1]
+      set_default_chromosome_attributes
     end
-    
+
     def chromosome
-      chromosome = Array.new
-      @length.times { chromosome << @alleles.sample }
-      return Chromosome.new(chromosome)
+      Chromosome.new.tap do |chromosome|
+        length.times { chromosome << alleles.sample }
+      end
     end
 
+    private
+
+    def set_default_chromosome_attributes
+      @length = 8
+      @alleles = [0, 1]
+    end
   end
 end

data/lib/genetica/population.rb

@@ -1,113 +1,109 @@
 module Genetica
-  class Population
-
-    attr_reader :population
-    attr_reader :generation
-
-    attr_accessor :alleles
-    attr_accessor :elitism
-    attr_accessor :crossover_probability
-    attr_accessor :mutation_probability
-    attr_accessor :fitness_function
+  class Population < Array
+    attr_reader   :generation, :population_fitness
+    attr_accessor :alleles, :elitism, :crossover_method, :crossover_probability, :mutation_probability
 
     def initialize(population)
+      super population
+
       @generation = 0
-      @population = population
+    end
+
+    def fitness
+      raise NotImplementedError, "Your class should implement #{__method__} class method"
     end
 
     def best_chromosome
-      @population.at @population_fitness.index(self.best_fitness)
+      @best_chromosome ||= at(population_fitness.index(best_fitness))
     end
 
-    def best_chromosomes(quantity=1)
-      self.best_fitnesses(quantity).collect { |fitness| @population.at(@population_fitness.index fitness) }     
+    def best_chromosomes(quantity = 1)
+      @best_chromosomes ||= best_fitnesses(quantity).map do |fitness|
+        at population_fitness.index(fitness)
+      end
     end
 
     def best_fitness
-      @population_fitness.max
+      @best_fitness ||= population_fitness.max
     end
 
-    def best_fitnesses(quantity=1)
-      @population_fitness.sort.reverse.take(quantity)      
-    end    
+    def best_fitnesses(quantity = 1)
+      @best_fitnesses ||= population_fitness.sort.reverse.first(quantity)
+    end
 
     def average_fitness
-      @population_fitness.inject(:+) / @population_fitness.size.to_f
+      @average_fitness ||= population_fitness.inject(:+) / population_fitness.size.to_f
     end
 
     def population_fitness
-      @population.collect { |chromosome| @fitness_function.call(chromosome) }
-    end
-
-    def fitness_function=(new_fitness_function)
-      @fitness_function = new_fitness_function
-      @population_fitness = self.population_fitness
-    end
-
-    def population=(new_population)
-      @population = new_population
-      @population_fitness = self.population_fitness
+      @population_fitness ||= map { |chromosome| fitness(chromosome) }
     end
 
-    def fitness_proportionate_selection
-      # FUTURE: With Ruby 1.9.3 you can use rand with ranges, e.g. rand 0.0..3.4
-      # Get random number
-      random_generator = Random.new
-      random_number = random_generator.rand 0.0..@population_fitness.inject(:+)
-
-      # Chromosome selection
-      fitness_counter = 0
-      @population.each_with_index do |chromosome, i|
-        fitness_counter += @population_fitness[i]
-        if fitness_counter >= random_number
-          return chromosome
-        end
-      end
-    end
-
-    def run(generations=1)
+    def run(generations = 1)
       generations.times do
         # Generate a new chromosome population
         population = Array.new
 
         # If elitism if greater than 0 then we save the same number of chromosomes to the next generation
-        population += self.best_chromosomes(quantity=@elitism) if @elitism > 0
+        population += best_chromosomes(quantity = elitism) if elitism > 0
 
-        while population.size < @population.size
+        while population.size < size
           # 1. Selection Step
           # Select a pair of parent chromosomes from the current population.
           # This selection is 'with replacement', the same chromosome can be selected
           # more than once to become a parent.
-          chromosome_a = self.fitness_proportionate_selection
-          chromosome_b = self.fitness_proportionate_selection
+          chromosome_a = fitness_proportionate_selection
+          chromosome_b = fitness_proportionate_selection
 
           # 2. Crossover Step
-          # TODO: Maybe crossover probability check would be in the single_point_crossover of
-          # Chromosome class.
-          if @crossover_probability > 0 and rand.between? 0, @crossover_probability
-            offspring_a, offspring_b = chromosome_a.single_point_crossover chromosome_b
-          else
-            offspring_a, offspring_b = chromosome_a, chromosome_b
-          end
+          offspring_a, offspring_b = chromosome_a.crossover(crossover_method, crossover_probability,
+            chromosome_b)
 
           # 3. Mutation Step
-          offspring_a.mutate! @mutation_probability, @alleles
-          offspring_b.mutate! @mutation_probability, @alleles
+          offspring_a.mutate!(mutation_probability, alleles)
+          offspring_b.mutate!(mutation_probability, alleles)
 
           # 4. Adding offsprings to new chromosome population
-          population << offspring_a << offspring_b          
+          population << offspring_a << offspring_b
         end
 
         # If original population size is odd discard a random chromosome
-        population.delete_at rand population.size if @population.size.odd?
+        population.delete_at rand population.size if size.odd?
 
         # Replacing chromosome population with the new one
-        self.population = population
+        replace population
 
         # A new generation has been created
         @generation += 1
       end
     end
 
+    private
+
+    def fitness_proportionate_selection
+      random_number = rand 0.0..population_fitness.inject(:+)
+
+      # Chromosome selection
+      fitness_counter = 0
+      each_with_index do |chromosome, i|
+        fitness_counter += population_fitness[i]
+        return chromosome if fitness_counter >= random_number
+      end
+    end
+
+    def replace(other_ary)
+      super other_ary
+
+      reset_memoizes
+    end
+
+    def reset_memoizes
+      @population_fitness = nil
+      @average_fitness = nil
+      @best_fitnesses = nil
+      @best_fitness = nil
+      @best_chromosomes = nil
+      @best_chromosome = nil
+    end
   end
 end

data/lib/genetica/population_builder.rb

@@ -1,47 +1,58 @@
 module Genetica
   class PopulationBuilder
+    class PopulationClassError < StandardError; end
 
     # Population attributes
-    attr_accessor :size
-    attr_accessor :elitism
-    attr_accessor :crossover_probability
-    attr_accessor :mutation_probability
-    attr_accessor :fitness_function
+    attr_accessor :size, :elitism, :crossover_method, :crossover_probability, :mutation_probability,
+      :population_class
+
     # Chromosome attributes
-    attr_accessor :chromosome_length
-    attr_accessor :chromosome_alleles
+    attr_accessor :chromosome_length, :chromosome_alleles
 
     def initialize
-      # Default Population values
+      set_default_population_attributes
+      set_default_chromosome_attributes
+    end
+
+    def population
+      raise PopulationClassError, 'You must assign a population class' if population_class.nil?
+
+      population_class.new(chromosome_population).tap do |population|
+        population.alleles = chromosome_alleles
+        population.elitism = elitism
+        population.crossover_method = crossover_method
+        population.crossover_probability = crossover_probability
+        population.mutation_probability = mutation_probability
+      end
+    end
+
+    private
+
+    def set_default_population_attributes
       @size = 20
       @elitism = 0
+      @crossover_method = :uniform_crossover
       @crossover_probability = 0.7
       @mutation_probability = 0.001
-      @fitness_function = nil
-      # Default Chromosome values
+      @population_class = nil
+    end
+
+    def set_default_chromosome_attributes
       @chromosome_length = 8
       @chromosome_alleles = [0, 1]
     end
 
-    def population
-      # Generating Chromosome population
-      chromosome_builder = ChromosomeBuilder.new
-      chromosome_builder.length = @chromosome_length
-      chromosome_builder.alleles = @chromosome_alleles
-
-      chromosome_population = Array.new
-      @size.times { chromosome_population << chromosome_builder.chromosome }
-
-      # Generating Population 
-      population = Population.new chromosome_population
-      population.alleles = @chromosome_alleles
-      population.elitism = @elitism
-      population.crossover_probability = @crossover_probability
-      population.mutation_probability = @mutation_probability
-      population.fitness_function = @fitness_function
-      
-      return population
+    def chromosome_population
+      Array.new.tap do |chromosome_population|
+        size.times { chromosome_population << chromosome_builder.chromosome }
+      end
     end
 
+    def chromosome_builder
+      ChromosomeBuilder.new.tap do |chromosome_builder|
+        chromosome_builder.length = chromosome_length
+        chromosome_builder.alleles = chromosome_alleles
+      end
+    end
   end
 end

data/spec/chromosome_builder_spec.rb

@@ -0,0 +1,34 @@
+require 'spec_helper'
+
+shared_examples 'correct chromosome attribute values' do
+  its('chromosome') { should be_an_instance_of Genetica::Chromosome }
+  its('chromosome.size') { should be == subject.length }
+
+  it 'should have correct alleles' do
+    subject.chromosome.each do |allele|
+      subject.alleles.include?(allele).should be_true
+    end
+  end
+end
+
+describe Genetica::ChromosomeBuilder do
+  subject { described_class.new }
+
+  describe '#chromosome' do
+    context 'build chromosome with default values' do
+      it_behaves_like 'correct chromosome attribute values'
+    end
+
+    context 'build chromosome with custom values' do
+      let(:length) { 120 }
+      let(:alleles) { ('a'..'z').to_a }
+
+      before do
+        subject.length = length
+        subject.alleles = alleles
+      end
+
+      it_behaves_like 'correct chromosome attribute values'
+    end
+  end
+end

data/spec/population_builder_spec.rb

@@ -0,0 +1,62 @@
+require 'spec_helper'
+
+class PopulationClass < Genetica::Population
+  def fitness(chromosome)
+  end
+end
+
+shared_examples 'correct population attribute values' do
+  its(:population_class) { should be == PopulationClass }
+  its(:population) { should be_an_instance_of PopulationClass }
+  its('population.size') { should be == subject.size }
+  its('population.elitism') { should be == subject.elitism }
+  its('population.crossover_method') { should be == subject.crossover_method }
+  its('population.crossover_probability') { should be == subject.crossover_probability }
+  its('population.mutation_probability') { should be == subject.mutation_probability }
+  its('population.first.size') { should be == subject.chromosome_length }
+  its('population.alleles') { should be == subject.chromosome_alleles }
+end
+
+describe Genetica::PopulationBuilder do
+  subject { described_class.new }
+
+  describe '#population' do
+    context 'assigned population class' do
+      before { subject.population_class = PopulationClass }
+
+      context 'build population with default values' do
+        it_behaves_like 'correct population attribute values'
+      end
+
+      context 'build population with custom values' do
+        let(:size) { 12 }
+        let(:elitism) { 2 }
+        let(:crossover_method) { :single_point_crossover }
+        let(:crossover_probability) { 1.0 }
+        let(:mutation_probability) { 0.5 }
+        let(:chromosome_length) { 7 }
+        let(:chromosome_alleles) { ['a', 'b', 'c'] }
+
+        before do
+          subject.size = size
+          subject.elitism = elitism
+          subject.crossover_method = :single_point_crossover
+          subject.crossover_probability = crossover_probability
+          subject.mutation_probability = mutation_probability
+          subject.chromosome_length = chromosome_length
+          subject.chromosome_alleles = chromosome_alleles
+        end
+
+        it_behaves_like 'correct population attribute values'
+      end
+    end
+
+    context 'not assigned population class' do
+      it 'should raise an error when trying to build population' do
+        expect do
+          subject.population
+        end.to raise_error(described_class::PopulationClassError)
+      end
+    end
+  end
+end

data/spec/spec_helper.rb

@@ -0,0 +1,3 @@
+$: << File.expand_path(File.join(File.dirname(__FILE__), '..', 'lib'))
+
+require 'genetica'

metadata

@@ -1,17 +1,29 @@
 --- !ruby/object:Gem::Specification
 name: genetica
 version: !ruby/object:Gem::Version
-  version: 0.0.1.beta.2
-  prerelease: 6
+  version: 0.0.1
 platform: ruby
 authors:
 - José Francisco Calvo
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2011-11-23 00:00:00.000000000 +01:00
-default_executable: 
-dependencies: []
+date: 2015-03-22 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: rspec
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '3.0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '3.0'
 description: Genetica is a library to create and use Genetics Algorithms with Ruby.
 email: josefranciscocalvo@gmail.com
 executables: []
@@ -23,29 +35,33 @@ files:
 - lib/genetica/chromosome_builder.rb
 - lib/genetica/population.rb
 - lib/genetica/population_builder.rb
-has_rdoc: true
+- spec/chromosome_builder_spec.rb
+- spec/population_builder_spec.rb
+- spec/spec_helper.rb
 homepage: http://dev.monsterzen.com/projects/genetica.html
 licenses: []
+metadata: {}
 post_install_message: 
 rdoc_options: []
 require_paths:
 - lib
 required_ruby_version: !ruby/object:Gem::Requirement
-  none: false
   requirements:
-  - - ! '>='
+  - - ">="
     - !ruby/object:Gem::Version
-      version: '0'
+      version: 2.0.0
 required_rubygems_version: !ruby/object:Gem::Requirement
-  none: false
   requirements:
-  - - ! '>'
+  - - ">="
     - !ruby/object:Gem::Version
-      version: 1.3.1
+      version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 1.6.2
+rubygems_version: 2.4.5
 signing_key: 
-specification_version: 3
+specification_version: 4
 summary: The Ruby Genetic Algorithms Gem.
-test_files: []
+test_files:
+- spec/chromosome_builder_spec.rb
+- spec/population_builder_spec.rb
+- spec/spec_helper.rb