darwinning 0.1.1 → 0.1.2

checksums.yaml

@@ -0,0 +1,7 @@
+---
+SHA1:
+  metadata.gz: 00597c08fc47e731a886be9e68771c1e5a1d5ddc
+  data.tar.gz: d6f8e46f456c6c9734fef044cada94ebe951b8f4
+SHA512:
+  metadata.gz: 8e0963dc3e6dd57ad76aa25565f1714cfcd74449c01d72bd9dadc9161715c4395b16bef6ee92e6c452fe79ea7ab1ba2c539a55127397264fd823f5081e6b8dbd
+  data.tar.gz: 5fdf2aa0bebd1bed384489440e415611f3560711913ccf7c140a0c4651e703ad4b86f6b88334fd45abae32e3ae47016567b744b926bef2d2b809932b212a783c

data/README.md

@@ -123,4 +123,4 @@ Check out the `/examples` folder for more examples. That seems like a good place
 * [Dave Schwantes](https://github.com/dorkrawk "dorkrawk")
 
 ### With help from:
-[lots of great contributers](https://github.com/dorkrawk/darwinning/graphs/contributors)
+[lots of great contributers](https://github.com/dorkrawk/darwinning/graphs/contributors) and work based on forks from: [Nanosim-LIG](https://github.com/Nanosim-LIG)

data/darwinning.gemspec

@@ -0,0 +1,18 @@
+require "./lib/darwinning/version"
+
+Gem::Specification.new do |s|
+	s.name = 'darwinning'
+	s.version = Darwinning::VERSION
+
+	s.authors = ['Dave Schwantes']
+	s.email = 'dave.schwantes@gmail.com'
+	s.summary = 'A Ruby gem to aid in the use of genetic algorithms.'
+	s.description = 'Darwinning provides tools to build genetic algorithm solutions using a Gene, Organism, and Population structure.'
+	s.homepage = 'https://github.com/dorkrawk/darwinning'
+
+
+	s.files = Dir["{lib}/**/*", "[A-Z]*"] - ["Gemfile.lock"]
+	s.require_paths = ["lib"]
+
+	s.test_files  = Dir.glob("{test,spec,features}/**/*.rb")
+end

data/lib/darwinning.rb

@@ -4,6 +4,8 @@ require_relative 'darwinning/evolution_types/mutation'
 require_relative 'darwinning/evolution_types/reproduction'
 require_relative 'darwinning/population'
 require_relative 'darwinning/config'
+require_relative 'darwinning/monkey_patch'
+
 
 module Darwinning
   extend Config
@@ -13,7 +15,7 @@ module Darwinning
       gene_ranges.map { |k,v| Gene.new(name: k, value_range: v) }
     end
 
-    def base.build_population(fitness_goal, population_size = 10, generations_limit = 100, 
+    def base.build_population(fitness_goal, population_size = 10, generations_limit = 100,
                          evolution_types = Population::DEFAULT_EVOLUTION_TYPES)
       Population.new(organism: self, population_size: population_size,
                      generations_limit: generations_limit, fitness_goal: fitness_goal,
@@ -61,4 +63,4 @@ module Darwinning
     end
     gt
   end
-end
+end

data/lib/darwinning/evolution_types/mutation.rb

@@ -20,7 +20,7 @@ module Darwinning
 
       def mutate(members)
         members.map do |member|
-          if (0..100).to_a.sample < mutation_rate * 100
+          if rand < mutation_rate
             re_express_random_genotype(member)
           else
             member
@@ -30,7 +30,7 @@ module Darwinning
 
       # 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
+        random_index = rand(member.genotypes.length - 1)
         gene = member.genes[random_index]
 
         if member.class.superclass == Darwinning::Organism

data/lib/darwinning/monkey_patch.rb

@@ -0,0 +1,7 @@
+unless 42.respond_to? :positive?
+  class Numeric
+    def positive?
+      self > 0
+    end
+  end
+end

data/lib/darwinning/organism.rb

@@ -46,9 +46,9 @@ module Darwinning
         @genotypes = genotypes
       end
 
-      @fitness = -1
+      @fitness = nil
     end
-    
+
     def name
       self.class.name
     end

data/lib/darwinning/population.rb

@@ -1,9 +1,7 @@
 module Darwinning
   class Population
 
-    EPSILON = 0.01
-
-    attr_reader :members, :generations_limit, :fitness_goal,
+    attr_reader :members, :generations_limit, :fitness_goal, :fitness_objective,
                 :organism, :population_size, :generation,
                 :evolution_types, :history
 
@@ -16,6 +14,7 @@ module Darwinning
       @organism = options.fetch(:organism)
       @population_size = options.fetch(:population_size)
       @fitness_goal = options.fetch(:fitness_goal)
+      @fitness_objective = options.fetch(:fitness_objective, :nullify) # :nullify, :maximize, :minimize
       @generations_limit = options.fetch(:generations_limit, 0)
       @evolution_types = options.fetch(:evolution_types, DEFAULT_EVOLUTION_TYPES)
       @members = []
@@ -23,7 +22,6 @@ module Darwinning
       @history = []
 
       build_population(@population_size)
-      @history << @members
     end
 
     def build_population(population_size)
@@ -41,16 +39,19 @@ module Darwinning
     def set_members_fitness!(fitness_values)
       throw "Invaid number of fitness values for population size" if fitness_values.size != members.size
       members.to_enum.each_with_index { |m, i| m.fitness = fitness_values[i] }
+      sort_members
     end
 
     def make_next_generation!
       verify_population_size_is_positive!
+      sort_members
+      @history << @members
 
       new_members = []
 
       until new_members.length >= members.length
-        m1 = weighted_select(members)
-        m2 = weighted_select(members)
+        m1 = weighted_select
+        m2 = weighted_select
 
         new_members += apply_pairwise_evolutions(m1, m2)
       end
@@ -59,6 +60,7 @@ module Darwinning
       new_members.pop if new_members.length > members.length
 
       @members = apply_non_pairwise_evolutions(new_members)
+      sort_members
       @history << @members
       @generation += 1
     end
@@ -66,14 +68,18 @@ module Darwinning
     def evolution_over?
       # check if the fitness goal or generation limit has been met
       if generations_limit > 0
-        generation == generations_limit || best_member.fitness == fitness_goal
+        generation == generations_limit || goal_attained?
       else
-        best_member.fitness == fitness_goal
+        goal_attained?
       end
     end
 
     def best_member
-      @members.sort_by { |m| m.fitness }.first
+      @members.first
+    end
+
+    def best_each_generation
+      @history.map(&:first)
     end
 
     def size
@@ -91,6 +97,28 @@ module Darwinning
 
     private
 
+    def goal_attained?
+      case @fitness_objective
+      when :nullify
+        best_member.fitness.abs <= fitness_goal
+      when :maximize
+        best_member.fitness >= fitness_goal
+      else
+        best_member.fitness <= fitness_goal
+      end
+    end
+
+    def sort_members
+      case @fitness_objective
+      when :nullify
+        @members = @members.sort_by { |m| m.fitness ? m.fitness.abs : m.fitness }
+      when :maximize
+        @members = @members.sort_by { |m| m.fitness }.reverse
+      else
+        @members = @members.sort_by { |m| m.fitness }
+      end
+    end
+
     def verify_population_size_is_positive!
       unless @population_size.positive?
         raise "Population size must be a positive number!"
@@ -99,7 +127,7 @@ module Darwinning
 
     def build_member
       member = organism.new
-      unless member.class.superclass == Darwinning::Organism
+      unless member.class < Darwinning::Organism
         member.class.genes.each do |gene|
           gene_expression = gene.express
           member.send("#{gene.name}=", gene_expression)
@@ -108,27 +136,49 @@ module Darwinning
       member
     end
 
-    def weighted_select(members)
-      fitness_sum = members.inject(0) { |sum, m| sum + m.fitness }
-
-      weighted_members = members.sort_by do |m|
-        (m.fitness - fitness_goal).abs
-      end.map do |m|
-        [m, fitness_sum / ((m.fitness - fitness_goal).abs + EPSILON)]
+    def compute_normalized_fitness(membs=members)
+      normalized_fitness = nil
+      return membs.collect { |m| [1.0/membs.length, m] } if membs.first.fitness == membs.last.fitness
+      if @fitness_objective == :nullify
+        normalized_fitness = membs.collect { |m| [ m.fitness.abs <= fitness_goal ? Float::INFINITY : 1.0/(m.fitness.abs - fitness_goal), m] }
+      else
+        if @fitness_objective == :maximize
+          if fitness_goal == Float::INFINITY then
+            #assume goal to be at twice the maximum distance between fitness
+            goal = membs.first.fitness + ( membs.first.fitness - membs.last.fitness )
+          else
+            goal = fitness_goal
+          end
+          normalized_fitness  = membs.collect { |m| [ m.fitness >= goal ? Float::INFINITY : 1.0/(goal - m.fitness), m] }
+        else
+          if fitness_goal == -Float::INFINITY then
+            goal = membs.first.fitness - ( membs.last.fitness - membs.first.fitness )
+          else
+            goal = fitness_goal
+          end
+          normalized_fitness  = membs.collect { |m| [ m.fitness <= goal ? Float::INFINITY : 1.0/(m.fitness - goal), m] }
+        end
       end
-
-      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]
+      if normalized_fitness.first[0] == Float::INFINITY then
+        normalized_fitness.collect! { |m|
+          m[0] == Float::INFINITY ? [1.0, m[1]] : [0.0, m[1]]
+        }
       end
+      sum = normalized_fitness.collect(&:first).inject(0.0, :+)
+      normalized_fitness.collect { |m| [m[0]/sum, m[1]] }
+    end
 
-      selected_member.first
+    def weighted_select(membs=members)
+      normalized_fitness = compute_normalized_fitness
+      normalized_cumulative_sums = []
+      normalized_cumulative_sums[0] = normalized_fitness[0]
+      (1...normalized_fitness.length).each { |i|
+        normalized_cumulative_sums[i] = [ normalized_cumulative_sums[i-1][0] + normalized_fitness[i][0], normalized_fitness[i][1] ]
+      }
+
+      normalized_cumulative_sums.last[0] = 1.0
+      cut = rand
+      return normalized_cumulative_sums.find { |e| cut < e[0] }[1]
     end
 
     def apply_pairwise_evolutions(m1, m2)

data/lib/darwinning/version.rb

@@ -1,3 +1,3 @@
 module Darwinning
-  VERSION = "0.1.1"
+  VERSION = "0.1.2"
 end

data/spec/darwinning_spec.rb

@@ -1,4 +1,4 @@
-require 'spec_helper'
+require_relative 'spec_helper'
 
 describe Darwinning do
   let(:triple_pop) { NewTriple.build_population(0, 20, 1000) }
@@ -18,7 +18,7 @@ describe Darwinning do
       manual_fitness = (a_triple.first_digit + a_triple.second_digit + a_triple.third_digit - 15).abs
 
       expect(a_triple.fitness).to eq manual_fitness
-    end 
+    end
   end
 
   describe '#genes' do
@@ -53,7 +53,7 @@ describe Darwinning do
     end
   end
 
-  describe 'population member' do 
+  describe 'population member' do
     it 'is of the parent class' do
       expect(triple_pop_member.class.name).to eq "NewTriple"
     end

data/spec/gene_spec.rb

@@ -1,4 +1,4 @@
-require 'spec_helper'
+require_relative 'spec_helper'
 
 describe Darwinning::Gene do
   let(:digit) { Darwinning::Gene.new(name: "digit", value_range: (0..9)) }
@@ -10,7 +10,7 @@ describe Darwinning::Gene do
       units: "o'clock"
     )
   }
-  
+
   it "name should be set" do
     expect(digit.name).to eq "digit"
   end
@@ -26,4 +26,4 @@ describe Darwinning::Gene do
   it "units should be set" do
     expect(day_hour.units).to eq "o'clock"
   end
-end
+end

data/spec/organism_spec.rb

@@ -1,4 +1,4 @@
-require 'spec_helper'
+require_relative 'spec_helper'
 
 describe Darwinning::Organism do
   let(:org) { Darwinning::Organism.new }
@@ -16,8 +16,8 @@ describe Darwinning::Organism do
     expect(org.genotypes).to be {}
   end
 
-  it "fitness should default to -1" do
-    expect(org.fitness).to eq -1
+  it "fitness should default to nil" do
+    expect(org.fitness).to eq nil
   end
 
   it "child class should set name" do
@@ -32,4 +32,4 @@ describe Darwinning::Organism do
     expect(triple.genotypes.length).to eq 3
   end
 
-end
+end

data/spec/population_spec.rb

@@ -1,4 +1,4 @@
-require 'spec_helper'
+require_relative 'spec_helper'
 
 describe Darwinning::Population do
   let(:pop_triple) {
@@ -58,4 +58,12 @@ describe Darwinning::Population do
 
   end
 
+  describe "#best_each_generation" do
+
+    it "should show the best member from each generations members" do
+      pop_triple.evolve!
+      expect(pop_triple.best_each_generation.last).to eq pop_triple.best_member
+    end
+  end
+
 end

metadata

@@ -1,15 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: darwinning
 version: !ruby/object:Gem::Version
-  version: 0.1.1
-  prerelease: 
+  version: 0.1.2
 platform: ruby
 authors:
 - Dave Schwantes
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2016-10-26 00:00:00.000000000 Z
+date: 2017-09-15 00:00:00.000000000 Z
 dependencies: []
 description: Darwinning provides tools to build genetic algorithm solutions using
   a Gene, Organism, and Population structure.
@@ -18,18 +17,25 @@ executables: []
 extensions: []
 extra_rdoc_files: []
 files:
+- Gemfile
+- README.md
+- Rakefile
+- darwinning-0.0.1.gem
+- darwinning-0.0.2.gem
+- darwinning-0.0.3.gem
+- darwinning-0.1.0.gem
+- darwinning-0.1.1.gem
+- darwinning.gemspec
+- lib/darwinning.rb
 - lib/darwinning/config.rb
+- lib/darwinning/evolution_types.rb
 - lib/darwinning/evolution_types/mutation.rb
 - lib/darwinning/evolution_types/reproduction.rb
-- lib/darwinning/evolution_types.rb
 - lib/darwinning/gene.rb
+- lib/darwinning/monkey_patch.rb
 - lib/darwinning/organism.rb
 - lib/darwinning/population.rb
 - lib/darwinning/version.rb
-- lib/darwinning.rb
-- Gemfile
-- Rakefile
-- README.md
 - spec/classes/chimps.rb
 - spec/classes/new_single.rb
 - spec/classes/new_triple.rb
@@ -43,27 +49,26 @@ files:
 - spec/spec_helper.rb
 homepage: https://github.com/dorkrawk/darwinning
 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'
 required_rubygems_version: !ruby/object:Gem::Requirement
-  none: false
   requirements:
-  - - ! '>='
+  - - ">="
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 1.8.24
+rubygems_version: 2.4.5
 signing_key: 
-specification_version: 3
+specification_version: 4
 summary: A Ruby gem to aid in the use of genetic algorithms.
 test_files:
 - spec/classes/chimps.rb