gga4r 0.9.2 → 0.9.3

checksums.yaml

@@ -0,0 +1,15 @@
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data/Manifest.txt

@@ -1,12 +1,7 @@
 Rakefile
-README.txt
-CHANGELOG.txt
+README.md
 Manifest.txt
-setup.rb
-lib/gga4r/version.rb
-lib/gga4r/array_helper.rb
-lib/gga4r/gga4r_main.rb
 lib/gga4r.rb
 test/test_helper.rb
 test/gga4r_test.rb
-examples/ga_fitness_all_1s.rb
+examples/ga_fitness_all_1s.rb

data/README.md

@@ -0,0 +1,87 @@
+# gga4r - General Genetic Algorithm for Ruby
+
+##Introduction
+
+General Genetic Algorithm for Ruby is a Ruby Genetic Algorithm that is very simple to use:
+
+1) Take a class to evolve it and define fitness, recombine and mutate methods.
+
+```ruby
+class StringPopulation < Array
+  def fitness
+    self.select { |pos| pos == 1 }.size.to_f / self.size.to_f
+  end
+
+  def recombine(c2)
+    cross_point = (rand * c2.size).to_i
+    c1_a, c1_b = self.separate(cross_point)
+    c2_a, c2_b = c2.separate(cross_point)
+    StringPopulation.new(c1_a + c2_b)
+  end
+
+  def mutate
+    mutate_point = (rand * self.size).to_i
+    self[mutate_point] = 1
+  end
+end
+```
+
+2) Create a GeneticAlgorithm object with the population.
+
+```ruby
+def create_population_with_fit_all_1s(s_long = 10, num = 10)
+    population = []
+    num.times  do
+      chromosome = StringPopulation.new(Array.new(s_long).collect { (rand > 0.2) ? 0:1 })
+      population << chromosome
+    end
+    population
+end
+
+ga = GeneticAlgorithm.new(create_population_with_fit_all_1s)
+```
+
+3) Call the evolve method as many times as you want and see the best evolution.
+
+```ruby
+100.times { |i|  ga.evolve }
+p ga.best_fit[0]
+```
+
+##Install
+
+1. Execute:
+```
+gem install gga4r
+```
+
+2. Add require in your code headers:
+```
+require "rubygems"
+require "gga4r"
+```
+
+##Documentation
+
+Documentation can be generated using rdoc tool under the source code with:
+```
+rdoc README lib
+```
+
+##Contributors
+
+- Ben Prew https://github.com/benprew
+- Rory O'Kane
+- Sergio Espeja https://github.com/spejman
+
+
+##Copying
+
+This work is developed by Sergio Espeja ( www.upf.edu/pdi/iula/sergio.espeja, sergio.espeja at gmail.com )
+mainly in Institut Universitari de Lingüística Aplicada of Universitat Pompeu Fabra ( www.iula.upf.es ),
+and also in bee.com.es ( bee.com.es ).
+
+It is free software, and may be redistributed under GPL license.
+
+
+

data/Rakefile

@@ -1,19 +1,11 @@
 require 'rubygems'
-require 'rake'
-require 'rake/clean'
-require 'rake/testtask'
-require 'rake/packagetask'
-require 'rake/gempackagetask'
-require 'rake/rdoctask'
-require 'rake/contrib/rubyforgepublisher'
-require 'fileutils'
 require 'hoe'
+
 include FileUtils
-require File.join(File.dirname(__FILE__), 'lib', 'gga4r', 'version')
 
 AUTHOR = "Sergio Espeja"
 EMAIL = "sergio.espeja@gmail.com"
-DESCRIPTION = "A Ruby Genetic Algorithm. So simple to use: 1, take a class to evolve it and define fitness, recombine and mutate methods. 2, create a GeneticAlgorithm object with the population. 3, call evolve method as many times as you want.description of gem"
+DESCRIPTION = "A Ruby Genetic Algorithm. Very simple to use: 1, take a class to evolve it and define fitness, recombine and mutate methods. 2, create a GeneticAlgorithm object with the population. 3, call the evolve method as many times as you want.description of gem"
 GEM_NAME = "gga4r" # what ppl will type to install your gem
 RUBYFORGE_PROJECT = "gga4r" # The unix name for your project
 HOMEPATH = "http://#{RUBYFORGE_PROJECT}.rubyforge.org"
@@ -21,32 +13,30 @@ HOMEPATH = "http://#{RUBYFORGE_PROJECT}.rubyforge.org"
 
 NAME = "gga4r"
 REV = nil # UNCOMMENT IF REQUIRED: File.read(".svn/entries")[/committed-rev="(d+)"/, 1] rescue nil
-VERS = ENV['VERSION'] || (Gga4r::VERSION::STRING + (REV ? ".#{REV}" : ""))
-                          CLEAN.include ['**/.*.sw?', '*.gem', '.config']
 RDOC_OPTS = ['--quiet', '--title', "gga4r documentation",
     "--opname", "index.html",
-    "--line-numbers", 
+    "--line-numbers",
     "--main", "README",
     "--inline-source"]
 
 class Hoe
-  def extra_deps 
-    @extra_deps.reject { |x| Array(x).first == 'hoe' } 
-  end 
+  def extra_deps
+    @extra_deps.reject { |x| Array(x).first == 'hoe' }
+  end
 end
 
 # Generate all the Rake tasks
 # Run 'rake -T' to see list of generated tasks (from gem root directory)
-hoe = Hoe.new(GEM_NAME, VERS) do |p|
-  p.author = AUTHOR 
+hoe = Hoe.spec GEM_NAME do |p|
+  p.author = AUTHOR
   p.description = DESCRIPTION
   p.email = EMAIL
   p.summary = DESCRIPTION
-  p.url = HOMEPATH
+  p.urls = [HOMEPATH]
   p.rubyforge_name = RUBYFORGE_PROJECT if RUBYFORGE_PROJECT
   p.test_globs = ["test/**/*_test.rb"]
-  p.clean_globs = CLEAN  #An array of file patterns to delete on clean.
-  
+  p.readme_file = 'README.md'
+
   # == Optional
   #p.changes        - A description of the release's latest changes.
   #p.extra_deps     - An array of rubygem dependencies.

data/lib/gga4r.rb

@@ -1 +1,142 @@
-Dir[File.join(File.dirname(__FILE__), 'gga4r/**/*.rb')].sort.each { |lib| require lib }
+require 'logger'
+
+class GeneticAlgorithm
+  VERSION = '0.9.3'
+
+  # Must be initialized with a Array of chromosomes
+  # To be a chomosome the object must implement the next methods:
+  #  - fitness
+  #  - recombine
+  #  - mutate
+  #  - distance (only for multi-modal optimization)
+  #  Accepts the next properties:
+  #   - max_population: maximum number of individuals that are allowed to form a generation.
+  #   - logger: logger to write messages if given.
+  #   - multi_recombination: set to true if the result of a chromosome's #recombination method
+  #     returns an array. Default to false
+  #   - multi_modal: set to true to use a multi-modal algorithm using deterministic crowding and a distance-derated fitness.
+  #   - share_radius: in multi-modal optimization, determines the niche radius for derated fitness calculation. 
+  def initialize(in_pop, prop = {})
+    @max_population =  prop[:max_population]
+    @logger = prop[:logger] || Logger.new('/dev/null')
+    @population = in_pop
+    @multi_recombination = prop[:multi_recombination] || false
+    @generations = []
+    @multi_modal = prop[:multi_modal] || false
+    @share_radius = prop[:share_radius] or 3
+  end
+
+  # Returns an array with the best fitted individuals for last generation
+  def best_fit
+    @population.max_by(&:fitness)
+  end
+
+  # Returns an array with the best fitted n individuals from the population (might include local optima)
+  def best_fitted(n)
+    @population.uniq.sort_by{|c| -c.fitness}.first(n)
+  end
+
+   # Returns an array with the best fitted n individuals from the population (might include local optima)
+   # Uses a distance-derated fitness metric
+  def best_fitted_derated(n)
+    @population.uniq.sort_by{|c| -(derated_fitness(c,@population))}.first(n)
+  end
+
+  # Returns a GeneticAlgorithm object with the generations
+  # loaded from given files and with properties prop.
+  # Files must contain the chromosomes in YAML format.
+  def self.populate_from_file(filename, prop = {})
+    GeneticAlgorithm.new(YAML.load(File.open(filename, 'r')), prop)
+  end
+
+  # Saves into filename and in yaml format the generation that matchs with given
+  # generation number ( by default from last generation ).
+  def save_population(filename)
+    f = File.new(filename, "w")
+    f.write(@population.to_yaml)
+    f.close
+  end
+
+# EVOLUTION METHODS
+
+  # Evolves the actual generation num_steps steps (1 by default).
+  def evolve(num_steps = 1)
+    num_steps.times do |t|
+      @population = selection(@population)
+      new_gen = @population.map { |chromosome| chromosome.dup }
+      if !@multi_modal
+        @population += recombination(new_gen) + mutation(new_gen)
+      else
+        @population = deterministic_crowding(@population)
+        @population = mutation(@population)
+      end
+    end
+  end
+
+  private
+
+  # Selects population to survive and recombine
+  def selection(g)
+      @max_population && g.length > @max_population ? g.sort_by{|c| -c.fitness}.first(@max_population) : g
+  end
+
+  # Recombines population
+  def recombination(g)
+    @logger.debug "Recombination " + g.size.to_s + " chromosomes." if @logger
+    new_generation = g.dup.shuffle!
+    @logger.debug "Shuffled!" if @logger
+    new_children = []
+    new_generation.each_slice(2) do |chromosome1, chromosome2|
+      next if chromosome2.nil?
+      @logger.debug "Recombining" if @logger
+      new_children << chromosome1.recombine(chromosome2)
+    end
+    new_children.flatten!(1) if @multi_recombination
+    new_generation + new_children
+  end
+
+  def deterministic_crowding(g)
+    groups = g.shuffle
+    group1 = groups.first(g.length/2)
+    group2 = groups[g.length/2..-1]
+
+    new_gen = []
+
+    group1.each_with_index do |p1,i|
+      p2 = group2[i]
+
+      if p2
+
+        c1, c2 = p1.recombine(p2)
+
+        if p1.distance(c1) + p2.distance(c2) <= p1.distance(c2) + p2.distance(c1)
+          new_gen << [p1,c1].max_by{|c| derated_fitness(c,g)}
+          new_gen << [p2,c2].max_by{|c| derated_fitness(c,g)}
+        else 
+          new_gen << [p1,c2].max_by{|c| derated_fitness(c,g)}
+          new_gen << [p2,c1].max_by{|c| derated_fitness(c,g)}
+        end
+      else
+        new_gen << p1
+      end
+    end
+    new_gen
+  end
+
+  def derated_fitness(c,g)
+    share_count = g.map{|c2| [(1-c.distance(c2)/@share_radius),0].max }.sum
+    share_count = Float::EPSILON if share_count==0
+    c.fitness/share_count
+  end
+
+  # Mutates population
+  def mutation(g)
+    @logger.debug "Mutation " + g.size.to_s + " chromosomes." if @logger
+    new_generation = g.dup
+    new_generation.each do |chromosome|
+      @logger.debug "Mutate" if @logger
+      chromosome.mutate
+    end
+    new_generation
+  end
+end

data/test/gga4r_test.rb

@@ -1,37 +1,73 @@
 require File.dirname(__FILE__) + '/test_helper.rb'
 
 class IndividualStub < Array
+
+  def mutate
+  end
+
+  def fitness
+  end
+
   def recombine(a)
     self * 2
   end
+
   def self.create_random_population(num_population = 30)
     population = []
     num_population.times do
-      population << IndividualStub.new
+      population << IndividualStub.new([1,2,3])
     end
     return population
   end
 end
 
-class Gga4rTest < Test::Unit::TestCase
+class StringPopulation < Array
+  def fitness
+    fitness = self.select { |pos| pos == 1 }.size.to_f / self.size.to_f
+    fitness
+  end
+
+  def recombine(c2)
+    cross_point = rand([self.size, c2.size].min) + 1
+    c1_a, c1_b = self.slice(0,cross_point), self.slice(cross_point, 0)
+    c2_a, c2_b = c2.slice(0,cross_point), c2.slice(cross_point, 0)
+    [StringPopulation.new(c1_a + c2_b), StringPopulation.new(c2_a + c1_b)]
+  end
 
-  def setup
+  def mutate
+    mutate_point = (rand * self.size).to_i
+    self[mutate_point] = 1
   end
-  
-  def test_truth
-    assert true
+
+  def self.create_population(s_long = 10, num = 10)
+    population = []
+    num.times  do
+      chromosome = self.new(Array.new(s_long).collect { (rand > 0.2) ? 0:1 })
+      population << chromosome
+    end
+    population
   end
-  
-  def test_recombine
+end
+
+class Gga4rTest < Test::Unit::TestCase
+  def test_single_recombination_result
     first_pop_even = IndividualStub.create_random_population(30)
     ga = GeneticAlgorithm.new(first_pop_even)
-    new_pop = ga.recombination!
-    assert true, first_pop_even.size < new_pop.size
-    
-    first_pop_odd = IndividualStub.create_random_population(31)
-    ga = GeneticAlgorithm.new(first_pop_odd)
-    new_pop = ga.recombination!
-    assert true, first_pop_odd.size < new_pop.size
-    
+    5.times do |i|
+      ga.evolve
+      new_pop = ga.instance_variable_get(:@population)
+      assert first_pop_even.size < new_pop.size
+    end
+  end
+
+  def test_multiple_recombination
+    opts = {multi_recombination: true}
+    ga = GeneticAlgorithm.new(StringPopulation.create_population, opts)
+    assert ga.instance_variable_get(:@multi_recombination)
+    4.times do |i|
+      assert_nothing_raised do
+        ga.evolve
+      end
+    end
   end
 end

metadata

@@ -1,60 +1,90 @@
---- !ruby/object:Gem::Specification 
-rubygems_version: 0.9.4
-specification_version: 1
+--- !ruby/object:Gem::Specification
 name: gga4r
-version: !ruby/object:Gem::Version 
-  version: 0.9.2
-date: 2007-11-30 00:00:00 +01:00
-summary: "A Ruby Genetic Algorithm. So simple to use: 1, take a class to evolve it and define fitness, recombine and mutate methods. 2, create a GeneticAlgorithm object with the population. 3, call evolve method as many times as you want.description of gem"
-require_paths: 
-- lib
-email: sergio.espeja@gmail.com
-homepage: http://gga4r.rubyforge.org
-rubyforge_project: gga4r
-description: "A Ruby Genetic Algorithm. So simple to use: 1, take a class to evolve it and define fitness, recombine and mutate methods. 2, create a GeneticAlgorithm object with the population. 3, call evolve method as many times as you want.description of gem"
-autorequire: 
-default_executable: 
-bindir: bin
-has_rdoc: true
-required_ruby_version: !ruby/object:Gem::Version::Requirement 
-  requirements: 
-  - - ">"
-    - !ruby/object:Gem::Version 
-      version: 0.0.0
-  version: 
+version: !ruby/object:Gem::Version
+  version: 0.9.3
 platform: ruby
-signing_key: 
-cert_chain: 
-post_install_message: 
-authors: 
+authors:
 - Sergio Espeja
-files: 
+autorequire: 
+bindir: bin
+cert_chain: []
+date: 2013-12-16 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: rdoc
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '4.0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '4.0'
+- !ruby/object:Gem::Dependency
+  name: hoe
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '3.7'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '3.7'
+description: ! 'A Ruby Genetic Algorithm. Very simple to use: 1, take a class to evolve
+  it and define fitness, recombine and mutate methods. 2, create a GeneticAlgorithm
+  object with the population. 3, call the evolve method as many times as you want.description
+  of gem'
+email: sergio.espeja@gmail.com
+executables: []
+extensions: []
+extra_rdoc_files:
+- README.md
+- Manifest.txt
+files:
 - Rakefile
-- README.txt
-- CHANGELOG.txt
+- README.md
 - Manifest.txt
-- setup.rb
-- lib/gga4r/version.rb
-- lib/gga4r/array_helper.rb
-- lib/gga4r/gga4r_main.rb
 - lib/gga4r.rb
 - test/test_helper.rb
 - test/gga4r_test.rb
 - examples/ga_fitness_all_1s.rb
-test_files: 
-- test/gga4r_test.rb
-rdoc_options: 
+- .gemtest
+homepage: http://gga4r.rubyforge.org
+licenses:
+- MIT
+metadata: {}
+post_install_message: 
+rdoc_options:
 - --main
-- README.txt
-extra_rdoc_files: 
-- README.txt
-- CHANGELOG.txt
-- Manifest.txt
-executables: []
-
-extensions: []
-
+- README.md
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+required_rubygems_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
 requirements: []
-
-dependencies: []
-
+rubyforge_project: gga4r
+rubygems_version: 2.1.10
+signing_key: 
+specification_version: 4
+summary: ! 'A Ruby Genetic Algorithm. Very simple to use: 1, take a class to evolve
+  it and define fitness, recombine and mutate methods. 2, create a GeneticAlgorithm
+  object with the population. 3, call the evolve method as many times as you want.description
+  of gem'
+test_files:
+- test/gga4r_test.rb