evosynth 0.1.0

data/test/operators/mutations/tc_one_gene_flipping.rb

@@ -0,0 +1,109 @@
+#	Copyright (c) 2009, 2010 Yves Adler <yves.adler@googlemail.com>
+#
+#	Permission is hereby granted, free of charge, to any person
+#	obtaining a copy of this software and associated documentation
+#	files (the "Software"), to deal in the Software without
+#	restriction, including without limitation the rights to use,
+#	copy, modify, merge, publish, distribute, sublicense, and/or sell
+#	copies of the Software, and to permit persons to whom the
+#	Software is furnished to do so, subject to the following
+#	conditions:
+#
+#	The above copyright notice and this permission notice shall be
+#	included in all copies or substantial portions of the Software.
+#
+#	THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+#	EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+#	OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+#	NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+#	HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+#	WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+#	FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+#	OTHER DEALINGS IN THE SOFTWARE.
+
+
+require 'shoulda'
+
+require 'evosynth'
+require 'test/test_util/test_helper'
+
+
+class OneGeneFlippingTest < Test::Unit::TestCase
+
+	GENOME_SIZE = 20
+	FLIP_FUNCTION = EvoSynth::Mutations::Functions::FLIP_BOOLEAN
+
+	context "when run on binary genome (size=#{GENOME_SIZE})" do
+		setup do
+			@individual = TestArrayBinaryIndividual.new(GENOME_SIZE)
+			@individual.genome.map! { |gene| true }
+		end
+
+		context "before mutation is executed" do
+			should "all genes should be true" do
+				@individual.genome.each { |gene| assert gene }
+			end
+		end
+
+		context "after mutation is executed" do
+			setup do
+				one_gene_flipping = EvoSynth::Mutations::OneGeneFlipping.new(FLIP_FUNCTION)
+				@mutated = one_gene_flipping.mutate(@individual)
+			end
+
+			should "all genes of the parent should (still) be true" do
+				@individual.genome.each { |gene| assert gene }
+			end
+
+			should "one gene should be false" do
+				count = 0
+				@mutated.genome.each { |gene| count += 1 if !gene }
+				assert_equal 1, count
+			end
+		end
+	end
+
+	context "when run on binary genome (size=1)" do
+		setup do
+			@individual = TestArrayBinaryIndividual.new(1)
+			@individual.genome.map! { |gene| true }
+		end
+
+		context "before mutation is executed" do
+			should "the gene should be true" do
+				assert @individual.genome[0]
+			end
+		end
+
+		context "after mutation is executed" do
+			setup do
+				one_gene_flipping = EvoSynth::Mutations::OneGeneFlipping.new(FLIP_FUNCTION)
+				@mutated = one_gene_flipping.mutate(@individual)
+			end
+
+			should "the gene of the parent should (still) be true" do
+				assert @individual.genome[0]
+			end
+
+			should "the mutated gene should be false" do
+				assert !@mutated.genome[0]
+			end
+		end
+
+		context "after mutation is executed two times" do
+			setup do
+				one_gene_flipping = EvoSynth::Mutations::OneGeneFlipping.new(FLIP_FUNCTION)
+				@mutated = one_gene_flipping.mutate(@individual)
+				@mutated = one_gene_flipping.mutate(@mutated)
+			end
+
+			should "the gene of the parent should (still) be true" do
+				assert @individual.genome[0]
+			end
+
+			should "the mutated gene should be true" do
+				assert @mutated.genome[0]
+			end
+		end
+	end
+end

data/test/operators/mutations/tc_self_adaptive_gauss_mutation.rb

@@ -0,0 +1,72 @@
+#	Copyright (c) 2009, 2010 Yves Adler <yves.adler@googlemail.com>
+#
+#	Permission is hereby granted, free of charge, to any person
+#	obtaining a copy of this software and associated documentation
+#	files (the "Software"), to deal in the Software without
+#	restriction, including without limitation the rights to use,
+#	copy, modify, merge, publish, distribute, sublicense, and/or sell
+#	copies of the Software, and to permit persons to whom the
+#	Software is furnished to do so, subject to the following
+#	conditions:
+#
+#	The above copyright notice and this permission notice shall be
+#	included in all copies or substantial portions of the Software.
+#
+#	THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+#	EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+#	OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+#	NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+#	HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+#	WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+#	FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+#	OTHER DEALINGS IN THE SOFTWARE.
+
+
+require 'shoulda'
+
+require 'evosynth'
+require 'test/test_util/test_helper'
+
+# FIXME: add some meaningful test here
+
+class SelfadaptiveGaussMutationTest < Test::Unit::TestCase
+
+	VALUE = 4.0
+	DELTA = 0.1
+
+	context "when run on a float genome = #{VALUE}" do
+		setup do
+			@individual = TestArrayGenomeIndividual.new([VALUE]*5)
+		end
+
+		context "before mutation is executed" do
+			should "each gene should equal #{VALUE}" do
+				@individual.genome.each { |gene| assert_equal VALUE, gene }
+			end
+
+			should "the individual have no sigma method" do
+				assert_raise(NoMethodError) { @individual.sigma }
+			end
+		end
+
+		context "after mutation is executed" do
+			setup do
+				mutation = EvoSynth::Mutations::SelfAdaptiveGaussMutation.new
+				@mutated = mutation.mutate(@individual)
+			end
+
+			should "all genes of the parent should (still) equal #{VALUE}" do
+				@individual.genome.each { |gene| assert_equal VALUE, gene }
+			end
+
+			should "the individual have a sigma method" do
+				assert_respond_to @mutated, :sigma
+			end
+
+			should "the individual have a sigma that around 1.0 += 2.5" do
+				assert_in_delta 1.0, @mutated.sigma, 2.5
+			end
+		end
+
+	end
+end

data/test/operators/mutations/tc_shifting_muation.rb

@@ -0,0 +1,73 @@
+#	Copyright (c) 2009, 2010 Yves Adler <yves.adler@googlemail.com>
+#
+#	Permission is hereby granted, free of charge, to any person
+#	obtaining a copy of this software and associated documentation
+#	files (the "Software"), to deal in the Software without
+#	restriction, including without limitation the rights to use,
+#	copy, modify, merge, publish, distribute, sublicense, and/or sell
+#	copies of the Software, and to permit persons to whom the
+#	Software is furnished to do so, subject to the following
+#	conditions:
+#
+#	The above copyright notice and this permission notice shall be
+#	included in all copies or substantial portions of the Software.
+#
+#	THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+#	EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+#	OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+#	NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+#	HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+#	WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+#	FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+#	OTHER DEALINGS IN THE SOFTWARE.
+
+
+require 'shoulda'
+
+require 'evosynth'
+require 'test/test_util/test_helper'
+
+
+class ShiftingMutationTest < Test::Unit::TestCase
+
+	GENOME_SIZE = 20
+
+	context "a shifting mutation run on binary genome (size=#{GENOME_SIZE})" do
+
+		setup do
+			@mutation = EvoSynth::Mutations::ShiftingMutation.new
+			@individual = TestArrayBinaryIndividual.new(GENOME_SIZE)
+			GENOME_SIZE.times { |index| @individual.genome[index] = (index % 2 == 1) ? 0 : 1 }
+		end
+
+		context "before mutation is executed" do
+
+			should "genes should alternate between 0 and 1" do
+				previous = 0
+				@individual.genome.each do |gene|
+					assert_not_equal previous, gene
+					previous = gene
+				end
+			end
+
+			should "the count of 0's and 1's should be the same" do
+				count_ones, count_zeros = 0, 0
+				@individual.genome.each { |gene| gene == 0 ? count_zeros += 1 : count_ones += 1 }
+				assert_equal count_ones, count_zeros
+			end
+		end
+
+		context "after mutations is executed" do
+
+			should "the count of 0's and 1's should still be the same" do
+				mutated = @mutation.mutate(@individual)
+				count_ones, count_zeros = 0, 0
+				mutated.genome.each { |gene| gene == 0 ? count_zeros += 1 : count_ones += 1 }
+				assert_equal count_ones, count_zeros
+			end
+
+		end
+
+	end
+
+end

data/test/operators/mutations/tc_uniform_real_mutation.rb

@@ -0,0 +1,65 @@
+#	Copyright (c) 2009, 2010 Yves Adler <yves.adler@googlemail.com>
+#
+#	Permission is hereby granted, free of charge, to any person
+#	obtaining a copy of this software and associated documentation
+#	files (the "Software"), to deal in the Software without
+#	restriction, including without limitation the rights to use,
+#	copy, modify, merge, publish, distribute, sublicense, and/or sell
+#	copies of the Software, and to permit persons to whom the
+#	Software is furnished to do so, subject to the following
+#	conditions:
+#
+#	The above copyright notice and this permission notice shall be
+#	included in all copies or substantial portions of the Software.
+#
+#	THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+#	EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+#	OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+#	NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+#	HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+#	WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+#	FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+#	OTHER DEALINGS IN THE SOFTWARE.
+
+
+require 'shoulda'
+
+require 'evosynth'
+require 'test/test_util/test_helper'
+
+
+class UniformRealMutationTest < Test::Unit::TestCase
+
+	VALUE = 4.0
+	PROBABILITY = 1.0
+	DELTA = 0.4
+
+	context "when run on a float genome = #{VALUE}" do
+		setup do
+			@individual = TestArrayGenomeIndividual.new([VALUE]*5)
+		end
+
+		context "before mutation is executed" do
+			should "each gene should equal #{VALUE}" do
+				@individual.genome.each { |gene| assert_equal VALUE, gene }
+			end
+		end
+
+		context "after mutation is executed (probability = #{PROBABILITY})" do
+			setup do
+				mutation = EvoSynth::Mutations::UniformRealMutation.new(PROBABILITY, DELTA)
+				@mutated = mutation.mutate(@individual)
+			end
+
+			should "all genes of the parent should (still) equal #{VALUE}" do
+				@individual.genome.each { |gene| assert_equal VALUE, gene }
+			end
+
+			should "all genes of the child be in the around +/- #{DELTA} of #{VALUE}" do
+				@mutated.genome.each { |gene| assert_in_delta VALUE, gene, DELTA }
+			end
+
+		end
+
+	end
+end

data/test/operators/recombinations/tc_arithmetic_crossover.rb

@@ -0,0 +1,79 @@
+#	Copyright (c) 2009, 2010 Yves Adler <yves.adler@googlemail.com>
+#
+#	Permission is hereby granted, free of charge, to any person
+#	obtaining a copy of this software and associated documentation
+#	files (the "Software"), to deal in the Software without
+#	restriction, including without limitation the rights to use,
+#	copy, modify, merge, publish, distribute, sublicense, and/or sell
+#	copies of the Software, and to permit persons to whom the
+#	Software is furnished to do so, subject to the following
+#	conditions:
+#
+#	The above copyright notice and this permission notice shall be
+#	included in all copies or substantial portions of the Software.
+#
+#	THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+#	EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+#	OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+#	NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+#	HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+#	WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+#	FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+#	OTHER DEALINGS IN THE SOFTWARE.
+
+
+require 'shoulda'
+
+require 'evosynth'
+require 'test/test_util/test_helper'
+
+
+class ArithmeticCrossoverTest < Test::Unit::TestCase
+
+	GENOME_SIZE = 100
+	DELTA = 0.05
+
+	context "a arithmetic crossover run on a Fixnum genome" do
+
+		setup do
+			interpolation_function = EvoSynth::Recombinations::ArithmeticCrossover::INTERPOLATE_NUMBERS
+			@recombination = EvoSynth::Recombinations::ArithmeticCrossover.new(interpolation_function)
+
+			genome_one, genome_two = [], []
+			GENOME_SIZE.times { |i| genome_one << i; genome_two << GENOME_SIZE - i }
+			@individual_one = TestArrayGenomeIndividual.new(genome_one)
+			@individual_two = TestArrayGenomeIndividual.new(genome_two)
+		end
+
+		context "before recombination is executed" do
+
+			should "each index added should be == GENOME_SIZE" do
+				GENOME_SIZE.times { |i| assert_equal GENOME_SIZE, @individual_one.genome[i] + @individual_two.genome[i] }
+			end
+
+		end
+
+		context "after recombination is executed" do
+
+			setup do
+				@child_one, @child_two = @recombination.recombine(@individual_one, @individual_two)
+			end
+
+			should "each index of the parents added should (still) be == GENOME_SIZE" do
+				GENOME_SIZE.times { |i| assert_equal GENOME_SIZE, @individual_one.genome[i] + @individual_two.genome[i] }
+			end
+
+			should "the average value of all genes should be at #{GENOME_SIZE/2}" do
+				sum = 0
+				@child_one.genome.each { |gene| sum += gene }
+				assert_in_delta GENOME_SIZE/2, sum / GENOME_SIZE, DELTA * GENOME_SIZE
+				sum = 0
+				@child_two.genome.each { |gene| sum += gene }
+				assert_in_delta GENOME_SIZE/2, sum / GENOME_SIZE, DELTA * GENOME_SIZE
+			end
+
+		end
+
+	end
+
+end

data/test/operators/recombinations/tc_edge_recombination.rb

@@ -0,0 +1,76 @@
+#	Copyright (c) 2009, 2010 Yves Adler <yves.adler@googlemail.com>
+#
+#	Permission is hereby granted, free of charge, to any person
+#	obtaining a copy of this software and associated documentation
+#	files (the "Software"), to deal in the Software without
+#	restriction, including without limitation the rights to use,
+#	copy, modify, merge, publish, distribute, sublicense, and/or sell
+#	copies of the Software, and to permit persons to whom the
+#	Software is furnished to do so, subject to the following
+#	conditions:
+#
+#	The above copyright notice and this permission notice shall be
+#	included in all copies or substantial portions of the Software.
+#
+#	THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+#	EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+#	OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+#	NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+#	HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+#	WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+#	FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+#	OTHER DEALINGS IN THE SOFTWARE.
+
+
+require 'shoulda'
+
+require 'evosynth'
+require 'test/test_util/test_helper'
+
+class EdgeRecombinationTest < Test::Unit::TestCase
+
+	context "a edge recombination run on example genome (Weicker page 133)" do
+
+		setup do
+			@recombination = EvoSynth::Recombinations::EdgeRecombination.new
+
+			@individual_one = TestArrayGenomeIndividual.new([1,4,8,6,5,7,2,3])
+			@individual_two = TestArrayGenomeIndividual.new([1,2,3,4,8,5,6,7])
+		end
+
+		context "before the edge recombination is executed" do
+
+			should "individual one should contain all numbers from 1 to 7" do
+				[1,2,3,4,5,6,7,8].each { |item| assert @individual_one.genome.include?(item) }
+			end
+
+			should "individual two should contain all numbers from 1 to 7" do
+				[1,2,3,4,5,6,7,8].each { |item| assert @individual_two.genome.include?(item) }
+			end
+
+		end
+
+		context "after the edge recombination is executed" do
+
+			setup do
+				@child_one, @child_two = @recombination.recombine(@individual_one, @individual_two)
+			end
+
+			should "parent one should (still) contain all numbers from 1 to 7" do
+				[1,2,3,4,5,6,7,8].each { |item| assert @individual_one.genome.include?(item) }
+			end
+
+			should "parent two should (still) contain all numbers from 1 to 7" do
+				[1,2,3,4,5,6,7,8].each { |item| assert @individual_two.genome.include?(item) }
+			end
+
+			should "both children should (still) contain all numbers from 1 to 7" do
+				[1,2,3,4,5,6,7,8].each { |item| assert @child_one.genome.include?(item) }
+				[1,2,3,4,5,6,7,8].each { |item| assert @child_two.genome.include?(item) }
+			end
+
+		end
+
+	end
+
+end