darwinning 0.0.2 → 0.0.3

data/Gemfile

@@ -0,0 +1,12 @@
+source "http://rubygems.org"
+
+gemspec
+
+group :test do
+  gem 'rspec', '~> 2.14.0'
+end
+
+group :development, :test do
+  gem 'pry'
+  gem 'pry-nav'
+end

data/README.md

@@ -27,9 +27,9 @@ class Triple < Darwinning::Organism
 
 	@name = "Triple"
 	@genes = [
-			Darwinning::Gene.new("first digit", (0..9)),
-			Darwinning::Gene.new("second digit", (0..9)),
-			Darwinning::Gene.new("third digit", (0..9))
+			Darwinning::Gene.new(name: "first digit", value_range: (0..9)),
+			Darwinning::Gene.new(name: "second digit", value_range: (0..9)),
+			Darwinning::Gene.new(name: "third digit", value_range: (0..9))
 		]
 
 	def fitness
@@ -38,7 +38,10 @@ class Triple < Darwinning::Organism
 	end
 end 
 
-p = Darwinning::Population.new(Triple, 10, 0, 0.1, 100)
+p = Darwinning::Population.new(
+	organism: Triple, population_size: 10,
+	fitness_goal: 0, generations_limit: 100
+)
 p.evolve!
 
 p.best_member.nice_print # prints the member representing the solution
@@ -57,22 +60,25 @@ class Cookie < Darwinning::Organism
 
 	@name = "Chocolate Chip Cookie"
 	@genes = [
-			Darwinning::Gene.new("white sugar", (0..1), [], "cup"),
-			Darwinning::Gene.new("brown sugar", (0..1), [], "cup"),
-			Darwinning::Gene.new("flour", (0..3), [], "cup"),
-			Darwinning::Gene.new("eggs", (0..3)),
-			Darwinning::Gene.new("baking powder", (0..2), [], "teaspoon"),
-			Darwinning::Gene.new("salt", (0..2), [], "teaspoon"),
-			Darwinning::Gene.new("butter", (0..2), [], "cup"),
-			Darwinning::Gene.new("vanilla extract", (0..2), [], "teaspoon"),
-			Darwinning::Gene.new("chocolate chips", (0..20), [], "ounce"),
-			Darwinning::Gene.new("oven temp", (300..400), [], "degrees F"),
-			Darwinning::Gene.new("cook time", (5..20), [], "minute")
+			Darwinning::Gene.new(name: "white sugar", value_range: (0..1), units: "cup"),
+			Darwinning::Gene.new(name: "brown sugar", value_range: (0..1), units: "cup"),
+			Darwinning::Gene.new(name: "flour", value_range: (0..3), units: "cup"),
+			Darwinning::Gene.new(name: "eggs", value_range: (0..3)),
+			Darwinning::Gene.new(name: "baking powder", value_range: (0..2), units: "teaspoon"),
+			Darwinning::Gene.new(name: "salt", value_range: (0..2), units: "teaspoon"),
+			Darwinning::Gene.new(name: "butter", value_range: (0..2), units: "cup"),
+			Darwinning::Gene.new(name: "vanilla extract", value_range: (0..2), units: "teaspoon"),
+			Darwinning::Gene.new(name: "chocolate chips", value_range: (0..20), units: "ounce"),
+			Darwinning::Gene.new(name: "oven temp", value_range: (300..400), units: "degrees F"),
+			Darwinning::Gene.new(name: "cook time", value_range: (5..20), units: "minute")
 		]
 
 end
 
-p = Darwinning::Population.new(Cookie, 10, 5, 0.1, 100, true)
+p = Darwinning::Population.new(
+	organism: Cookie, population_size: 10,
+	fitness_goal: 5, generations_limit: 100
+)
 
 first_gen_ratings = [1.5, 4, 3, 3.5, 2, 1, 1.5, 3, 2.5, 0.5]
 p.set_members_fitness!(first_gen_ratings)
@@ -98,4 +104,8 @@ end
 ```
 
 ## Built by:
-* [Dave Schwantes](https://github.com/dorkrawk "dorkrawk")
+* [Dave Schwantes](https://github.com/dorkrawk "dorkrawk")
+
+### With help from:
+* [Cameron Dutro](https://github.com/camertron "camertron")
+* [Maurizio Del Corno](https://github.com/druzn3k "druzn3k")

data/lib/darwinning.rb

@@ -1,8 +1,9 @@
 require_relative 'darwinning/gene'
 require_relative 'darwinning/organism'
+require_relative 'darwinning/evolution_types'
 require_relative 'darwinning/population'
 require_relative 'darwinning/config'
 
 module Darwinning
   extend Config
-end
+end

data/lib/darwinning/config.rb

@@ -3,4 +3,4 @@ module Darwinning
     # crossover mask?
     # ordered vs weighted fitness
   end
-end
+end

data/lib/darwinning/evolution_types.rb

@@ -0,0 +1,6 @@
+module Darwinning
+  module EvolutionTypes
+    autoload :Mutation,     'darwinning/evolution_types/mutation'
+    autoload :Reproduction, 'darwinning/evolution_types/reproduction'
+  end
+end

data/lib/darwinning/evolution_types/mutation.rb

@@ -0,0 +1,41 @@
+module Darwinning
+  module EvolutionTypes
+
+    class Mutation
+      attr_reader :mutation_rate
+
+      def initialize(options = {})
+        @mutation_rate = options.fetch(:mutation_rate, 0.0)
+      end
+
+      def evolve(members)
+        mutate(members)
+      end
+
+      def pairwise?
+        false
+      end
+
+      protected
+
+      def mutate(members)
+        members.map do |member|
+          if (0..100).to_a.sample < mutation_rate * 100
+            re_express_random_genotype(member)
+          else
+            member
+          end
+        end
+      end
+
+      # Selects a random genotype from the organism and re-expresses its gene
+      def re_express_random_genotype(member)
+        random_index = (0..member.genotypes.length - 1).to_a.sample
+        new_gene = member.genes[random_index].express
+        member.genotypes[random_index] = member.genes[random_index].express
+        member
+      end
+    end
+
+  end
+end

data/lib/darwinning/evolution_types/reproduction.rb

@@ -0,0 +1,34 @@
+module Darwinning
+  module EvolutionTypes
+
+    class Reproduction
+      def evolve(organism, m1, m2)
+        sexytimes(organism, m1, m2)
+      end
+
+      def pairwise?
+        true
+      end
+
+      protected
+
+      def sexytimes(organism, m1, m2)
+        genotypes1 = []
+        genotypes2 = []
+
+        m1.genotypes.zip(m2.genotypes).each do |g|
+          if m1.genotypes.index(g[0]) % 2 == 0
+            genotypes1 << g[0]
+            genotypes2 << g[1]
+          else
+            genotypes1 << g[1]
+            genotypes2 << g[0]
+          end
+        end
+
+        [organism.new(genotypes1), organism.new(genotypes2)]
+      end
+    end
+
+  end
+end

data/lib/darwinning/gene.rb

@@ -1,21 +1,23 @@
 module Darwinning
-  class Gene
-    attr_accessor :name, :value, :value_range, :invalid_values, :units
 
-    def initialize(name = "", value_range = [], invalid_values = [], units = "")
+  class Gene
+    attr_accessor :name, :value_range, :invalid_values, :units
+    attr_accessor :value
 
-      @name = name
-      @value_range = value_range.to_a
-      @invalid_values = invalid_values.to_a
-      @units = units
+    def initialize(options = {})
+      @name = options.fetch(:name, '')
+      @value_range = Array(options.fetch(:value_range, []))
+      @invalid_values = Array(options.fetch(:invalid_values, []))
+      @units = options.fetch(:units, '')
     end
 
     def express
-      (@value_range - @invalid_values).sample
+      (value_range - invalid_values).sample
     end
 
     def is_valid_value?(value)
-      @value_range.include?(value) and not @invalid_values.include?(value)
+      value_range.include?(value) && !invalid_values.include?(value)
     end
   end
-end
+
+end

data/lib/darwinning/organism.rb

@@ -26,8 +26,8 @@ module ClassLevelInheritableAttributes
 end
 
 module Darwinning
-  class Organism
 
+  class Organism
     include ClassLevelInheritableAttributes
     inheritable_attributes :genes, :name
     attr_accessor :genotypes, :fitness, :name, :genes
@@ -45,14 +45,8 @@ module Darwinning
       else
         @genotypes = genotypes
       end
-      @fitness = -1
-    end
 
-    # Selects a random genotype from the organism and rexpresses its gene
-    def mutate!
-      random_index = (0..@genotypes.length-1).to_a.sample
-      @genotypes[random_index] = self.class.genes[random_index].express
-      self
+      @fitness = -1
     end
 
     def nice_print
@@ -69,4 +63,5 @@ module Darwinning
       self.class.genes
     end
   end
-end
+
+end

data/lib/darwinning/population.rb

@@ -1,23 +1,30 @@
 module Darwinning
 
   class Population
-    attr_accessor :members, :mutation_rate, :generations_limit, :fitness_goal, :organism, :generation
-
-    def initialize(organism, population_size, fitness_goal, mutation_rate = 0.0, generations_limit = 0, manual_fitness = false)
-      @organism = organism
-      @fitness_goal = fitness_goal
-      @mutation_rate = mutation_rate
-      @generations_limit = generations_limit
-      @manual_fitness = manual_fitness
+    attr_accessor :members, :generations_limit, :fitness_goal
+    attr_accessor :organism, :generation, :population_size
+    attr_accessor :evolution_types
+
+    DEFAULT_EVOLUTION_TYPES = [
+      Darwinning::EvolutionTypes::Reproduction.new,
+      Darwinning::EvolutionTypes::Mutation.new(mutation_rate: 0.10)
+    ]
+
+    def initialize(options = {})
+      @organism = options.fetch(:organism)
+      @population_size = options.fetch(:population_size)
+      @fitness_goal = options.fetch(:fitness_goal)
+      @generations_limit = options.fetch(:generations_limit, 0)
+      @evolution_types = options.fetch(:evolution_types, DEFAULT_EVOLUTION_TYPES)
       @members = []
       @generation = 0 # initial population is generation 0
 
-      build_population(population_size)
+      build_population(@population_size)
     end
 
     def build_population(population_size)
       population_size.times do |i|
-        @members << @organism.new
+        @members << organism.new
       end
     end
 
@@ -27,32 +34,15 @@ module Darwinning
       end
     end
 
-    def crossover(m1, m2)
-      genotypes1 = []
-      genotypes2 = []
-
-      m1.genotypes.zip(m2.genotypes).each do |g|
-        if m1.genotypes.index(g[0]) % 2 == 0
-          genotypes1 << g[0]
-          genotypes2 << g[1]
-        else
-          genotypes1 << g[1]
-          genotypes2 << g[0]
-        end
-      end
-
-      [@organism.new(genotypes1), @organism.new(genotypes2)]
-    end
-
-    def sexytimes(m1, m2)
-      crossover(m1, m2)
-    end
-
     def weighted_select(members)
       e = 0.01
       fitness_sum = members.inject(0) { |sum, m| sum + m.fitness }
 
-      weighted_members = members.sort_by { |m| (m.fitness - @fitness_goal).abs }.map { |m| [m, fitness_sum / ((m.fitness - @fitness_goal).abs + e)] }
+      weighted_members = members.sort_by do |m|
+        (m.fitness - fitness_goal).abs
+      end.map do |m|
+        [m, fitness_sum / ((m.fitness - fitness_goal).abs + e)]
+      end
 
       weight_sum = weighted_members.inject(0) { |sum, m| sum + m[1] }
       pick = (0..weight_sum).to_a.sample
@@ -65,56 +55,68 @@ module Darwinning
         pick_sum += selected_member[1]
       end
 
-      selected_member[0]
-    end
-
-    def mutate!
-      @members.map! { |m|
-        if (0..100).to_a.sample < @mutation_rate*100
-          m.mutate!
-        else
-          m
-        end
-      }
+      selected_member.first
     end
 
     def set_members_fitness!(fitness_values)
-      @members.to_enum.each_with_index { |m, i| m.fitness = fitness_values[i] }
+      members.to_enum.each_with_index { |m, i| m.fitness = fitness_values[i] }
     end
 
     def make_next_generation!
-      temp_members = @members
+      temp_members = members
       used_members = []
       new_members = []
 
-      until new_members.length == @members.length/2
-        m1 = weighted_select(@members - used_members)
+      until new_members.length == members.length / 2
+        m1 = weighted_select(members - used_members)
         used_members << m1
-        m2 = weighted_select(@members - used_members)
+        m2 = weighted_select(members - used_members)
         used_members << m2
 
-        new_members << crossover(m1,m2)
+        new_members << apply_pairwise_evolutions(organism, m1, m2)
       end
 
       new_members.flatten!
+      @members = apply_non_pairwise_evolutions(new_members)
+      @generation += 1
+    end
 
-      @members = new_members
+    def apply_pairwise_evolutions(organism, m1, m2)
+      evolution_types.inject([m1, m2]) do |ret, evolution_type|
+        if evolution_type.pairwise?
+          evolution_type.evolve(organism, *ret)
+        else
+          ret
+        end
+      end
+    end
 
-      mutate!
-      @generation += 1
+    def apply_non_pairwise_evolutions(members)
+      evolution_types.inject(members) do |ret, evolution_type|
+        if evolution_type.pairwise?
+          ret
+        else
+          evolution_type.evolve(ret)
+        end
+      end
     end
 
     def evolution_over?
       # check if the fiteness goal or generation limit has been met
-      @generation == @generations_limit or best_member.fitness == @fitness_goal
+      if generations_limit > 0
+        generation == generations_limit || best_member.fitness == fitness_goal
+      else
+        generation == generations_limit || best_member.fitness == fitness_goal
+      end
     end
 
     def best_member
-      @members.sort_by { |m| m.fitness }[0]
+      @members.sort_by { |m| m.fitness }.first
     end
 
     def size
       @members.length
     end
   end
-end
+
+end

data/lib/darwinning/version.rb

@@ -1,3 +1,3 @@
 module Darwinning
-  VERSION = "0.0.2"
-end
+  VERSION = "0.0.3"
+end

data/spec/classes/triple.rb

@@ -0,0 +1,13 @@
+class Triple < Darwinning::Organism
+  @name = "Triple"
+  @genes = [
+    Darwinning::Gene.new(name: "first digit", value_range: (0..9)),
+    Darwinning::Gene.new(name: "second digit", value_range: (0..9)),
+    Darwinning::Gene.new(name: "third digit", value_range: (0..9))
+  ]
+
+  def fitness
+    # Try to get the sum of the 3 digits to add up to 15
+    (genotypes.inject{ |sum, x| sum + x } - 15).abs
+  end
+end

data/{test → spec}/darwinning_spec.rb

@@ -1,9 +1,15 @@
 require 'darwinning'
+require './spec/classes/triple'
 
 describe Darwinning::Gene do
   before do
-    @digit = Darwinning::Gene.new("digit", (0..9))
-    @day_hour = Darwinning::Gene.new("hour", (0..23), [0,1,2,3,4,20,21,22,23], "o'clock")
+    @digit = Darwinning::Gene.new(name: "digit", value_range: (0..9))
+    @day_hour = Darwinning::Gene.new(
+      name: "hour",
+      value_range: (0..23),
+      invalid_values: [0, 1, 2, 3, 4, 20, 21, 22, 23],
+      units: "o'clock"
+    )
   end
 
   it "name should be set" do
@@ -15,43 +21,17 @@ describe Darwinning::Gene do
   end
 
   it "invalid values should be set" do
-    @day_hour.invalid_values.should == [0,1,2,3,4,20,21,22,23]
+    @day_hour.invalid_values.should == [0, 1, 2, 3, 4, 20, 21, 22, 23]
   end
 
   it "units should be set" do
     @day_hour.units.should == "o'clock"
   end
-
-  describe "#express" do
-
-    it "expressed value should be within range" do
-      (0..9).to_a.include?(@digit.express).should == true  # uncertain test
-    end
-
-    it "expressed value should not be invalid value" do
-      @day_hour.invalid_values.include?(@digit.express).should == false # uncertain test
-    end
-  end
-
 end
 
 describe Darwinning::Organism do
   before do
     @org = Darwinning::Organism.new
-
-    class Triple < Darwinning::Organism
-      @name = "Triple"
-      @genes = [
-        Darwinning::Gene.new("first digit", (0..9)),
-        Darwinning::Gene.new("second digit", (0..9)),
-        Darwinning::Gene.new("third digit", (0..9))
-      ]
-
-      def fitness
-        # Try to get the sum of the 3 digits to add up to 15
-        (genotypes.inject{ |sum, x| sum + x } - 15).abs
-      end
-    end
     @triple = Triple.new
   end
 
@@ -86,5 +66,29 @@ describe Darwinning::Organism do
 end
 
 describe Darwinning::Population do
+  before do
+    @pop_triple = Darwinning::Population.new(
+      organism: Triple, population_size: 10, fitness_goal: 0
+    )
+  end
 
-end
+  it "fitness goal should be set to 0" do
+    @pop_triple.fitness_goal.should == 0
+  end
+
+  it "population size should be 10" do
+    @pop_triple.members.length.should == 10
+  end
+
+  it "population should start on generation 0" do
+    @pop_triple.generation.should == 0
+  end
+
+  it "make_next_generation! should evolve population by one generation" do
+    old_members = @pop_triple.members
+    @pop_triple.make_next_generation!
+    @pop_triple.generation.should == 1
+    @pop_triple.members.should_not == old_members
+  end
+
+end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: darwinning
 version: !ruby/object:Gem::Version
-  version: 0.0.2
+  version: 0.0.3
   prerelease: 
 platform: ruby
 authors:
@@ -9,7 +9,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2013-05-29 00:00:00.000000000 Z
+date: 2014-12-02 00:00:00.000000000 Z
 dependencies: []
 description: Darwinning provides tools to build genetic algorithm solutions using
   a Gene, Organism, and Population structure.
@@ -19,14 +19,19 @@ extensions: []
 extra_rdoc_files: []
 files:
 - lib/darwinning/config.rb
+- lib/darwinning/evolution_types/mutation.rb
+- lib/darwinning/evolution_types/reproduction.rb
+- lib/darwinning/evolution_types.rb
 - lib/darwinning/gene.rb
 - lib/darwinning/organism.rb
 - lib/darwinning/population.rb
 - lib/darwinning/version.rb
 - lib/darwinning.rb
+- Gemfile
 - Rakefile
 - README.md
-- test/darwinning_spec.rb
+- spec/classes/triple.rb
+- spec/darwinning_spec.rb
 homepage: https://github.com/dorkrawk/darwinning
 licenses: []
 post_install_message: 
@@ -52,4 +57,5 @@ signing_key:
 specification_version: 3
 summary: A Ruby gem to aid in the use of genetic algorithms.
 test_files:
-- test/darwinning_spec.rb
+- spec/classes/triple.rb
+- spec/darwinning_spec.rb