darwinning 0.0.1 → 0.0.2

data/README.md

@@ -1,7 +1,18 @@
 Darwinning
 ==========
+[![Gem Version](https://badge.fury.io/rb/darwinning.png)](http://badge.fury.io/rb/darwinning)
+
+[gem]: https://rubygems.org/gems/darwinning
+
 A Ruby gem to aid in the use of genetic algorithms.
 
+Installation
+--------
+
+```
+gem install darwinning
+```
+
 Examples
 --------
 
@@ -28,7 +39,7 @@ class Triple < Darwinning::Organism
 end 
 
 p = Darwinning::Population.new(Triple, 10, 0, 0.1, 100)
-p.evolve
+p.evolve!
 
 p.best_member.nice_print # prints the member representing the solution
 ```

data/lib/darwinning.rb

@@ -4,5 +4,5 @@ require_relative 'darwinning/population'
 require_relative 'darwinning/config'
 
 module Darwinning
-	extend Config
+  extend Config
 end

data/lib/darwinning/config.rb

@@ -1,6 +1,6 @@
 module Darwinning
-	module Config
-		# crossover mask?
-		# ordered vs weighted fitness
-	end
+  module Config
+    # crossover mask?
+    # ordered vs weighted fitness
+  end
 end

data/lib/darwinning/gene.rb

@@ -1,21 +1,21 @@
 module Darwinning
-	class Gene
-		attr_accessor :name, :value, :value_range, :invalid_values, :units
+  class Gene
+    attr_accessor :name, :value, :value_range, :invalid_values, :units
 
-		def initialize(name = "", value_range = [], invalid_values = [], units = "")
+    def initialize(name = "", value_range = [], invalid_values = [], units = "")
 
-			@name = name
-			@value_range = value_range.to_a
-			@invalid_values = invalid_values.to_a
-			@units = units
-		end
+      @name = name
+      @value_range = value_range.to_a
+      @invalid_values = invalid_values.to_a
+      @units = units
+    end
 
-		def express
-			(@value_range - @invalid_values).sample
-		end
+    def express
+      (@value_range - @invalid_values).sample
+    end
 
-		def is_valid_value?(value)
-			@value_range.include?(value) and not @invalid_values.include?(value)
-		end
-	end
+    def is_valid_value?(value)
+      @value_range.include?(value) and not @invalid_values.include?(value)
+    end
+  end
 end

data/lib/darwinning/organism.rb

@@ -1,9 +1,9 @@
 # Found from http://www.railstips.org/blog/archives/2006/11/18/class-and-instance-variables-in-ruby/
 module ClassLevelInheritableAttributes
   def self.included(base)
-    base.extend(ClassMethods)    
+    base.extend(ClassMethods)
   end
-  
+
   module ClassMethods
     def inheritable_attributes(*args)
       @inheritable_attributes ||= [:inheritable_attributes]
@@ -15,7 +15,7 @@ module ClassLevelInheritableAttributes
       end
       @inheritable_attributes
     end
-    
+
     def inherited(subclass)
       @inheritable_attributes.each do |inheritable_attribute|
         instance_var = "@#{inheritable_attribute}"
@@ -26,47 +26,47 @@ module ClassLevelInheritableAttributes
 end
 
 module Darwinning
-	class Organism
+  class Organism
 
-		include ClassLevelInheritableAttributes
-		inheritable_attributes :genes, :name
-		attr_accessor :genotypes, :fitness, :name, :genes
+    include ClassLevelInheritableAttributes
+    inheritable_attributes :genes, :name
+    attr_accessor :genotypes, :fitness, :name, :genes
 
-		@genes = []  # Gene instances
-		@name = ""
+    @genes = []  # Gene instances
+    @name = ""
 
-		def initialize(genotypes = [])
-			#TODO: catch errors if genotype.length != @genotypes.length
-			# catch if genotype[x] is not a valid value for @gene[x]
+    def initialize(genotypes = [])
+      #TODO: catch errors if genotype.length != @genotypes.length
+      # catch if genotype[x] is not a valid value for @gene[x]
 
-			if genotypes == []
-				# fill genotypes with expressed Genes
-				@genotypes = self.class.genes.map { |g| g.express } # Gene expressions
-			else
-				@genotypes = genotypes
-			end
-			@fitness = -1
-		end
+      if genotypes == []
+        # fill genotypes with expressed Genes
+        @genotypes = self.class.genes.map { |g| g.express } # Gene expressions
+      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
-		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
+    end
 
-		def nice_print
-			puts self.class.name == "" ? "[no name]" : self.class.name
-			self.class.genes.to_enum.each_with_index { |g, i| puts "  #{g.name}: #{@genotypes[i]} #{g.units}" }
-			puts "    fitness: #{fitness}"
-		end
+    def nice_print
+      puts self.class.name == "" ? "[no name]" : self.class.name
+      self.class.genes.to_enum.each_with_index { |g, i| puts "  #{g.name}: #{@genotypes[i]} #{g.units}" }
+      puts "    fitness: #{fitness}"
+    end
 
-		def name
-			self.class.name
-		end
+    def name
+      self.class.name
+    end
 
-		def genes
-			self.class.genes
-		end
-	end
+    def genes
+      self.class.genes
+    end
+  end
 end

data/lib/darwinning/population.rb

@@ -1,120 +1,120 @@
 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
-			@members = []
-			@generation = 0 # initial population is generation 0
-			
-			build_population(population_size)
-		end
-
-		def build_population(population_size)
-			population_size.times do |i|
-				@members << @organism.new 
-			end
-		end
-
-		def evolve
-			until evolution_over?
-				make_next_generation!
-			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)] }
-		
-			weight_sum = weighted_members.inject(0) { |sum, m| sum + m[1] }
-			pick = (0..weight_sum).to_a.sample
-			
-			weighted_members.reverse! # In order to pop from the end we need the lowest ranked first
-			pick_sum = 0
-
-			until pick_sum > pick do
-				selected_member = weighted_members.pop 
-				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
-			}
-		end
-
-		def set_members_fitness!(fitness_values)
-			@members.to_enum.each_with_index { |m, i| m.fitness = fitness_values[i] }
-		end
-
-		def make_next_generation!			
-			temp_members = @members
-			used_members = []
-			new_members = []
-
-			until new_members.length == @members.length/2
-				m1 = weighted_select(@members - used_members)
-				used_members << m1
-				m2 = weighted_select(@members - used_members)
-				used_members << m2
-
-				new_members << crossover(m1,m2)
-			end
-
-			new_members.flatten!
-
-			@members = new_members
-
-			mutate!
-			@generation += 1
-		end
-
-		def evolution_over?
-			# check if the fiteness goal or generation limit has been met
-			@generation == @generations_limit or best_member.fitness == @fitness_goal
-		end
-
-		def best_member
-			@members.sort_by { |m| m.fitness }[0]
-		end
-
-		def size
-			@members.length
-		end
-	end
+  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
+      @members = []
+      @generation = 0 # initial population is generation 0
+
+      build_population(population_size)
+    end
+
+    def build_population(population_size)
+      population_size.times do |i|
+        @members << @organism.new
+      end
+    end
+
+    def evolve!
+      until evolution_over?
+        make_next_generation!
+      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)] }
+
+      weight_sum = weighted_members.inject(0) { |sum, m| sum + m[1] }
+      pick = (0..weight_sum).to_a.sample
+
+      weighted_members.reverse! # In order to pop from the end we need the lowest ranked first
+      pick_sum = 0
+
+      until pick_sum > pick do
+        selected_member = weighted_members.pop
+        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
+      }
+    end
+
+    def set_members_fitness!(fitness_values)
+      @members.to_enum.each_with_index { |m, i| m.fitness = fitness_values[i] }
+    end
+
+    def make_next_generation!
+      temp_members = @members
+      used_members = []
+      new_members = []
+
+      until new_members.length == @members.length/2
+        m1 = weighted_select(@members - used_members)
+        used_members << m1
+        m2 = weighted_select(@members - used_members)
+        used_members << m2
+
+        new_members << crossover(m1,m2)
+      end
+
+      new_members.flatten!
+
+      @members = new_members
+
+      mutate!
+      @generation += 1
+    end
+
+    def evolution_over?
+      # check if the fiteness goal or generation limit has been met
+      @generation == @generations_limit or best_member.fitness == @fitness_goal
+    end
+
+    def best_member
+      @members.sort_by { |m| m.fitness }[0]
+    end
+
+    def size
+      @members.length
+    end
+  end
 end

data/lib/darwinning/version.rb

@@ -1,3 +1,3 @@
 module Darwinning
-  VERSION = "0.0.1"
+  VERSION = "0.0.2"
 end

data/test/darwinning_spec.rb

@@ -1,87 +1,87 @@
 require 'darwinning'
 
 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")
-	end
+  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")
+  end
 
-	it "name should be set" do
-		@digit.name.should == "digit"
-	end
+  it "name should be set" do
+    @digit.name.should == "digit"
+  end
 
-	it "value range should be set" do
-		@digit.value_range.should == (0..9).to_a
-	end
+  it "value range should be set" do
+    @digit.value_range.should == (0..9).to_a
+  end
 
-	it "invalid values should be set" do
-		@day_hour.invalid_values.should == [0,1,2,3,4,20,21,22,23]
-	end
+  it "invalid values should be set" do
+    @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
+  it "units should be set" do
+    @day_hour.units.should == "o'clock"
+  end
 
-	describe "#express" do
+  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 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
+    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
-
-	it "name should default to blank" do
-		@org.name.should == ""
-	end
-
-	it "genes should default to empty array" do
-		@org.genes.should == []
-	end
-
-	it "genotypes should initialize to empty array if genes is empty" do
-		@org.genotypes.should == []
-	end
-
-	it "fitness should default to -1" do
-		@org.fitness.should == -1
-	end
-
-	it "child class should set name" do
-		@triple.name.should == "Triple"
-	end
-
-	it "child class should set genes" do
-		@triple.genes.length.should == 3 # not the best test...
-	end
-
-	it "child class should initialize genotypes from genes" do
-		@triple.genotypes.length.should == 3 # not the best test...
-	end
+  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
+
+  it "name should default to blank" do
+    @org.name.should == ""
+  end
+
+  it "genes should default to empty array" do
+    @org.genes.should == []
+  end
+
+  it "genotypes should initialize to empty array if genes is empty" do
+    @org.genotypes.should == []
+  end
+
+  it "fitness should default to -1" do
+    @org.fitness.should == -1
+  end
+
+  it "child class should set name" do
+    @triple.name.should == "Triple"
+  end
+
+  it "child class should set genes" do
+    @triple.genes.length.should == 3 # not the best test...
+  end
+
+  it "child class should initialize genotypes from genes" do
+    @triple.genotypes.length.should == 3 # not the best test...
+  end
 
 end
 

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: darwinning
 version: !ruby/object:Gem::Version
-  version: 0.0.1
+  version: 0.0.2
   prerelease: 
 platform: ruby
 authors:
@@ -9,7 +9,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2013-05-23 00:00:00.000000000 Z
+date: 2013-05-29 00:00:00.000000000 Z
 dependencies: []
 description: Darwinning provides tools to build genetic algorithm solutions using
   a Gene, Organism, and Population structure.