darwinning 0.1.0 → 0.1.1

data/README.md

@@ -123,6 +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:
-* [Cameron Dutro](https://github.com/camertron "camertron")
-* [Maurizio Del Corno](https://github.com/druzn3k "druzn3k")
-* [Evan Brynne](https://github.com/ebrynne "ebrynne")
+[lots of great contributers](https://github.com/dorkrawk/darwinning/graphs/contributors)

data/lib/darwinning/evolution_types/mutation.rb

@@ -31,8 +31,14 @@ 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
-        new_gene = member.genes[random_index].express
-        member.genotypes[random_index] = member.genes[random_index].express
+        gene = member.genes[random_index]
+
+        if member.class.superclass == Darwinning::Organism
+          member.genotypes[gene] = gene.express
+        else
+          member.send("#{gene.name}=", gene.express)
+        end
+
         member
       end
     end

data/lib/darwinning/evolution_types/reproduction.rb

@@ -33,7 +33,7 @@ module Darwinning
 
       def new_member_from_genotypes(organism_klass, genotypes)
         new_member = organism_klass.new
-        if organism_klass.superclass.to_s == "Darwinning::Organism"
+        if organism_klass.superclass == Darwinning::Organism
           new_member.genotypes = genotypes
         else
           new_member.genes.each do |gene|
@@ -60,7 +60,7 @@ module Darwinning
         [genotypes1, genotypes2]
       end
 
-      def random_swap(m1, m2)        
+      def random_swap(m1, m2)
         genotypes1 = {}
         genotypes2 = {}
 
@@ -69,7 +69,7 @@ module Darwinning
           g2_parent = [m1,m2].sample
 
           genotypes1[gene] = g1_parent.genotypes[gene]
-          genotypes2[gene] = g2_parent.genotypes[gene]          
+          genotypes2[gene] = g2_parent.genotypes[gene]
         end
 
         [genotypes1, genotypes2]

data/lib/darwinning/population.rb

@@ -44,16 +44,20 @@ module Darwinning
     end
 
     def make_next_generation!
-      temp_members = members
+      verify_population_size_is_positive!
+
       new_members = []
 
-      until new_members.length == members.length
+      until new_members.length >= members.length
         m1 = weighted_select(members)
         m2 = weighted_select(members)
 
         new_members += apply_pairwise_evolutions(m1, m2)
       end
 
+      # In the case of an odd population size, we likely added one too many members.
+      new_members.pop if new_members.length > members.length
+
       @members = apply_non_pairwise_evolutions(new_members)
       @history << @members
       @generation += 1
@@ -87,9 +91,15 @@ module Darwinning
 
     private
 
+    def verify_population_size_is_positive!
+      unless @population_size.positive?
+        raise "Population size must be a positive number!"
+      end
+    end
+
     def build_member
       member = organism.new
-      unless member.class.superclass.to_s == "Darwinning::Organism"
+      unless member.class.superclass == Darwinning::Organism
         member.class.genes.each do |gene|
           gene_expression = gene.express
           member.send("#{gene.name}=", gene_expression)

data/lib/darwinning/version.rb

@@ -1,3 +1,3 @@
 module Darwinning
-  VERSION = "0.1.0"
+  VERSION = "0.1.1"
 end

data/spec/classes/new_single.rb

@@ -0,0 +1,14 @@
+class NewSingle
+  include Darwinning
+
+  GENE_RANGES = {
+    first_digit: (0..9)
+  }
+
+  attr_accessor :first_digit
+
+  def fitness
+    # Try to get the digit to equal 15
+    (first_digit - 15).abs
+  end
+end

data/spec/classes/single.rb

@@ -0,0 +1,11 @@
+class Single < Darwinning::Organism
+  @name = "Single"
+  @genes = [
+    Darwinning::Gene.new(name: "first digit", value_range: (0..9))
+  ]
+
+  def fitness
+    # Try to get the digit to equal 15
+    (genotypes.values.inject{ |sum, x| sum + x } - 15).abs
+  end
+end

data/spec/evolution_types/mutation_spec.rb

@@ -0,0 +1,45 @@
+require 'spec_helper'
+
+describe Darwinning::EvolutionTypes::Mutation do
+
+  describe '#evolve' do
+    context 'when the mutation is triggered' do
+      # Use a mutation_rate of 1 ... which means a 100% chance of mutation.
+      subject { described_class.new(mutation_rate: 1.0) }
+      let(:new_gene_variant) { double }
+
+      before do
+        allow(gene).to receive(:express).and_return(new_gene_variant)
+      end
+
+      shared_examples_for 'a mutation that updates the genotype of the member' do
+        before { subject.evolve([member]) }
+
+        it "modifies the member's genotype to be the new expression of the gene" do
+          expect(member.genotypes[gene]).to eq(new_gene_variant)
+        end
+      end
+
+      context 'with a subclass of Organism' do
+        let(:member) { Single.new }
+        let(:gene) { member.genes[0] }
+
+        it_behaves_like 'a mutation that updates the genotype of the member'
+      end
+
+      context 'with a class that includes Darwinning' do
+        let(:member) { NewSingle.new }
+        let(:gene) { Darwinning::Gene.new(name: :first_digit, value_range: (0..9)) }
+
+        before do
+          allow(Darwinning::Gene).to receive(:new)
+            .with(name: :first_digit, value_range: (0..9))
+            .and_return(gene)
+        end
+
+        it_behaves_like 'a mutation that updates the genotype of the member'
+      end
+    end
+  end
+
+end

data/spec/population_spec.rb

@@ -6,7 +6,7 @@ describe Darwinning::Population do
       organism: Triple, population_size: 10, fitness_goal: 0
     )
   }
-  
+
   it "fitness goal should be set to 0" do
     expect(pop_triple.fitness_goal).to eq 0
   end
@@ -27,6 +27,28 @@ describe Darwinning::Population do
     expect(pop_triple.members).not_to eq old_members
   end
 
+  describe "#make_next_generation!" do
+    context "with a specified odd-number for population size" do
+      it "does not change the member count" do
+        population = Darwinning::Population.new(
+          organism: Triple, fitness_goal: 0, population_size: 3
+        )
+
+        expect { population.make_next_generation! }.not_to change{ population.members.length }
+      end
+    end
+
+    context "with a specified not-positive number for population size" do
+      it "raises an exception" do
+        population = Darwinning::Population.new(
+          organism: Triple, fitness_goal: 0, population_size: 0
+        )
+
+        expect { population.make_next_generation! }.to raise_error(RuntimeError)
+      end
+    end
+  end
+
   describe "#history" do
 
     it "should be generations + 1 in size" do

data/spec/spec_helper.rb

@@ -1,4 +1,5 @@
 require 'darwinning'
-require './spec/classes/triple'
-require './spec/classes/new_triple'
-require './spec/classes/chimps'
+
+Dir[
+  File.join(File.dirname(__FILE__), './classes/*.rb'),
+].each { |file| require file }

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: darwinning
 version: !ruby/object:Gem::Version
-  version: 0.1.0
+  version: 0.1.1
   prerelease: 
 platform: ruby
 authors:
@@ -9,7 +9,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2015-09-27 00:00:00.000000000 Z
+date: 2016-10-26 00:00:00.000000000 Z
 dependencies: []
 description: Darwinning provides tools to build genetic algorithm solutions using
   a Gene, Organism, and Population structure.
@@ -31,9 +31,12 @@ files:
 - Rakefile
 - README.md
 - spec/classes/chimps.rb
+- spec/classes/new_single.rb
 - spec/classes/new_triple.rb
+- spec/classes/single.rb
 - spec/classes/triple.rb
 - spec/darwinning_spec.rb
+- spec/evolution_types/mutation_spec.rb
 - spec/gene_spec.rb
 - spec/organism_spec.rb
 - spec/population_spec.rb
@@ -64,9 +67,12 @@ specification_version: 3
 summary: A Ruby gem to aid in the use of genetic algorithms.
 test_files:
 - spec/classes/chimps.rb
+- spec/classes/new_single.rb
 - spec/classes/new_triple.rb
+- spec/classes/single.rb
 - spec/classes/triple.rb
 - spec/darwinning_spec.rb
+- spec/evolution_types/mutation_spec.rb
 - spec/gene_spec.rb
 - spec/organism_spec.rb
 - spec/population_spec.rb