evosynth 0.1.0

data/test/operators/recombinations/tc_identity_recombination.rb

@@ -0,0 +1,81 @@
+#	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 IdentityRecombinationTest < Test::Unit::TestCase
+
+	GENOME_SIZE = 100
+
+	context "a identity recombination run on binary genome" do
+
+		setup do
+			@recombination = EvoSynth::Recombinations::Identity.new
+
+			@individual_one = TestArrayBinaryIndividual.new(GENOME_SIZE)
+			@individual_one.genome.map! { |gene| true }
+			@individual_two = TestArrayBinaryIndividual.new(GENOME_SIZE)
+			@individual_two.genome.map! { |gene| false }
+		end
+
+		context "before recombination is executed" do
+
+			should "all genes of individual one should be true" do
+				@individual_one.genome.each { |gene| assert_equal true, gene }
+			end
+
+			should "all genes of individual two should be false" do
+				@individual_two.genome.each { |gene| assert_equal false, gene }
+			end
+
+		end
+
+		context "after recombination is executed" do
+
+			setup do
+				@child_one, @child_two = @recombination.recombine(@individual_one, @individual_two)
+			end
+
+			should "all genes of the parent one should (still) be true" do
+				@individual_one.genome.each { |gene| assert_equal true, gene }
+			end
+
+			should "all genes of the parent two should (still) be false" do
+				@individual_two.genome.each { |gene| assert_equal false, gene }
+			end
+
+			should "the childrens genomes should be equal to their parents genomes" do
+				@child_one.genome.each_with_index { |gene, index| assert_equal gene, @individual_one.genome[index] }
+				@child_two.genome.each_with_index { |gene, index| assert_equal gene, @individual_two.genome[index] }
+			end
+
+		end
+
+	end
+
+end

data/test/operators/recombinations/tc_k_point_crossover.rb

@@ -0,0 +1,81 @@
+#	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 KPointCrossoverTest < Test::Unit::TestCase
+
+	GENOME_SIZE = 2000
+	K = 4
+
+	context "a k-point-crossover (k=#{K}) run on binary genome" do
+
+		setup do
+			@recombination = EvoSynth::Recombinations::KPointCrossover.new(K)
+
+			@individual_one = TestArrayBinaryIndividual.new(GENOME_SIZE)
+			@individual_one.genome.map! { |gene| true }
+			@individual_two = TestArrayBinaryIndividual.new(GENOME_SIZE)
+			@individual_two.genome.map! { |gene| false }
+		end
+
+		context "before k-point-crossover is executed" do
+
+			should "all genes of individual one should be true" do
+				@individual_one.genome.each { |gene| assert_equal true, gene }
+			end
+
+			should "all genes of individual two should be false" do
+				@individual_two.genome.each { |gene| assert_equal false, gene }
+			end
+
+		end
+
+		context "after k-point-crossover is executed" do
+
+			setup do
+				@child_one, @child_two = @recombination.recombine(@individual_one, @individual_two)
+			end
+
+			should "all genes of the parent one should (still) be true" do
+				@individual_one.genome.each { |gene| assert_equal true, gene }
+			end
+
+			should "all genes of the parent two should (still) be false" do
+				@individual_two.genome.each { |gene| assert_equal false, gene }
+			end
+
+			should "the genes of the childrens should always be different at the same index" do
+				@child_one.genome.each_with_index { |gene, index| assert_equal !gene, @child_two.genome[index] }
+			end
+
+		end
+
+	end
+
+end

data/test/operators/recombinations/tc_one_point_crossover.rb

@@ -0,0 +1,80 @@
+#	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 OnePointCrossoverTest < Test::Unit::TestCase
+
+	GENOME_SIZE = 2000
+
+	context "a one-point-crossover run on binary genome" do
+
+		setup do
+			@recombination = EvoSynth::Recombinations::OnePointCrossover.new
+
+			@individual_one = TestArrayBinaryIndividual.new(GENOME_SIZE)
+			@individual_one.genome.map! { |gene| true }
+			@individual_two = TestArrayBinaryIndividual.new(GENOME_SIZE)
+			@individual_two.genome.map! { |gene| false }
+		end
+
+		context "before one-point-crossover is executed" do
+
+			should "all genes of individual one should be true" do
+				@individual_one.genome.each { |gene| assert_equal true, gene }
+			end
+
+			should "all genes of individual two should be false" do
+				@individual_two.genome.each { |gene| assert_equal false, gene }
+			end
+
+		end
+
+		context "after one-point-crossover is executed" do
+
+			setup do
+				@child_one, @child_two = @recombination.recombine(@individual_one, @individual_two)
+			end
+
+			should "all genes of the parent one should (still) be true" do
+				@individual_one.genome.each { |gene| assert_equal true, gene }
+			end
+
+			should "all genes of the parent two should (still) be false" do
+				@individual_two.genome.each { |gene| assert_equal false, gene }
+			end
+
+			should "the genes of the childrens should always be different at the same index" do
+				@child_one.genome.each_with_index { |gene, index| assert_equal !gene, @child_two.genome[index] }
+			end
+
+		end
+
+	end
+
+end

data/test/operators/recombinations/tc_ordered_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 OrderedRecombinationTest < Test::Unit::TestCase
+
+	context "a ordered recombination run on example genome (Weicker page 29)" do
+
+		setup do
+			@recombination = EvoSynth::Recombinations::OrderedRecombination.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 ordered 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 ordered 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

data/test/operators/recombinations/tc_partially_mapped_crossover.rb

@@ -0,0 +1,91 @@
+#	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 PartiallyMappedCrossoverTest < Test::Unit::TestCase
+
+	context "a partially mapped crossover run on genome's with duplicates" do
+
+		setup do
+			@recombination = EvoSynth::Recombinations::PartiallyMappedCrossover.new
+
+			@individual_one = TestArrayGenomeIndividual.new([0,1,0,1,0,1,0])
+			@individual_two = TestArrayGenomeIndividual.new([1,0,1,0,1,0,1])
+		end
+
+		should "raise a exception" do
+			assert_raise(RuntimeError) { @child_one, @child_two = @recombination.recombine(@individual_one, @individual_two) }
+		end
+
+	end
+
+	context "a partially mapped crossover run on example genome (Weicker page 133)" do
+
+		setup do
+			@recombination = EvoSynth::Recombinations::PartiallyMappedCrossover.new
+
+			@individual_one = TestArrayGenomeIndividual.new([1,4,6,5,7,2,3])
+			@individual_two = TestArrayGenomeIndividual.new([1,2,3,4,5,6,7])
+		end
+
+		context "before the partially mapped crossover is executed" do
+
+			should "individual one should contain all numbers from 1 to 7" do
+				[1,2,3,4,5,6,7].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].each { |item| assert @individual_two.genome.include?(item) }
+			end
+
+		end
+
+		context "after the partially mapped crossover 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].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].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].each { |item| assert @child_one.genome.include?(item) }
+				[1,2,3,4,5,6,7].each { |item| assert @child_two.genome.include?(item) }
+			end
+
+		end
+
+	end
+
+end

data/test/operators/recombinations/tc_uniform_crossover.rb

@@ -0,0 +1,84 @@
+#	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 UniformCrossoverTest < Test::Unit::TestCase
+
+	GENOME_SIZE = 100
+	PROBABILITY = 0.5
+	TIMES = 1000
+	DELTA = 0.05
+	EXPECTED = PROBABILITY * GENOME_SIZE * TIMES
+
+	context "when run on binary genome (size=#{GENOME_SIZE})" do
+		setup do
+			@individual_one = TestArrayBinaryIndividual.new(GENOME_SIZE)
+			@individual_one.genome.map! { |gene| true }
+			@individual_two = TestArrayBinaryIndividual.new(GENOME_SIZE)
+			@individual_two.genome.map! { |gene| false }
+		end
+
+		context "before recombination is executed" do
+			should "all genes of individual one should be true" do
+				@individual_one.genome.each { |gene| assert gene }
+			end
+
+			should "all genes of individual two should be false" do
+				@individual_two.genome.each { |gene| assert !gene }
+			end
+		end
+
+		context "after recombination is executed #{TIMES} times" do
+			setup do
+				uniform_crossover = EvoSynth::Recombinations::UniformCrossover.new
+				@count = [0, 0]
+				TIMES.times do
+					child_one, child_two = uniform_crossover.recombine(@individual_one, @individual_two)
+					child_one.genome.each { |gene| @count[0] += 1 if !gene }
+					child_two.genome.each { |gene| @count[1] += 1 if !gene }
+				end
+			end
+
+			should "all genes of the parent one should (still) be true" do
+				@individual_one.genome.each { |gene| assert gene }
+			end
+
+			should "all genes of the parent two should (still) be false" do
+				@individual_two.genome.each { |gene| assert !gene }
+			end
+
+			should "around #{EXPECTED} genes should have mutated to false (in both children)" do
+				assert_in_delta EXPECTED, @count[0], DELTA * EXPECTED
+				assert_in_delta EXPECTED, @count[1], DELTA * EXPECTED
+			end
+		end
+
+	end
+
+end