evosynth 0.1.0

data/INSTALL

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+== Installation HOWTO
+
+=== Prerequisites:
+
+- <b>Ruby 1.9.x</b>	from http://www.ruby-lang.org or http://rubyforge.org/frs/?group_id=167
+- <i>(optional)</i> <b>git</b> from http://git-scm.com (to build latest version from git repository)
+
+- optional gems (install with "gem install <gem-name>" (as root)):
+  - shoulda and rake (Rakefile, Testsuite)
+  - gruff, gnuplot and rmagick (graphs)
+  - flake, flog, roodi and rcov (code quality tools)
+
+=== Download EvoSynth:
+
+- download source package from http://github.com/yadler/EvoSynth/archives/master
+- or checkout with:
+
+	git clone git://github.com/yadler/EvoSynth.git
+
+=== Run Testcases
+
+To make sure everything is running, run the following command inside the evosynth directory:
+
+	rake test
+
+=== Get the required testdata to run the examples (copy into the "testdata" directory):
+
+- http://mat.gsia.cmu.edu/COLOR/instances/myciel4.col (graph colouring)
+- http://elib.zib.de/pub/mp-testdata/tsp/tsplib/tsp/bays29.tsp (TSP)
+
+- more testdata:
+
+  - http://mat.gsia.cmu.edu/COLOR/instances.html
+  - http://elib.zib.de/pub/mp-testdata/tsp/tsplib/tsp/index.html
+
+=== Run examples and benchmarks
+
+- run all examples with
+	rake run_examples
+
+  or run single examples with:
+
+	ruby -Ilib examples/max_ones.rb
+	ruby -Ilib examples/partition.rb
+	...
+
+- <b>Attention:</b> the exporter.rb example will only work if you've installed the gruff, gnuplot and rmagick gems!
+
+- if you are interessted in the performance of the individual components of EvoSynth, run the benchmark task:
+
+	rake run_benchmarks
+
+  or run individual benchmarks with:
+
+	ruby -Ilib test/benchmark/decoder_benchmark.rb
+	ruby -Ilib test/benchmark/mutation_benchmark.rb
+	...
+
+=== Setup Netbeans as IDE (http://netbeans.org)
+
+- download and install netbeans
+- install Ruby plugin (Tools -> Plugins -> Available Plugins ...)
+- create new project:
+  1. File -> New Project -> Ruby -> "Ruby Application with Existing Sources"
+  2. choose a name (for example "nb_evosynth")
+  3. choose a directory, this should be outside of the evosynth directory to keep the git repository clean
+  4. choose Ruby platform: Ruby 1.9.x
+  5. set source folder with "Source Folders -> Add folder" -> choose evosynth directory
+
+- right click on new created project "Properties -> Run" -> add "-Ilib" to Ruby options
+
+- test if everything is working:
+  1. open a example (examples folder in "Source Files")
+  2. run it with Shift + F6 (you might have to confirm a dialog)

data/LICENSE

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+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.

data/README

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+== EvoSynth 0.1
+
+
+Website:: http://evosynth.rubyforge.org/
+Project:: http://rubyforge.org/projects/evosynth/
+Sourcecode:: http://gitorious.org/evosynth and http://github.com/yadler/EvoSynth
+Author::    Yves Adler (http://yadler.wordpress.com/, mailto:yves.adler@googlemail.com)
+Copyright:: Copyright (c) 2009, 2010 Yves Adler <yves.adler@googlemail.com>
+License::   MIT (see LICENSE)
+
+== Description
+
+EvoSynth (Evolutionary Computation Synthesizer) is a framework for rapid development and prototyping of evolutionary algorithms.
+
+== Features (for details see docs/FEATURES)
+
+* classes for individuals, populations, algorithm profiles, genomes
+* support for custom randomizer
+
+
+* most common evolutionary algorithms:
+  * hillclimber (single individual and population based)
+  * standard genetic algorithm, steady state GA
+  * memetic algorithm
+  * evolution strategies (adaptive, selfadaptive and derandomized)
+  * local search (hillclimber, threshold acceptance, simulated annealing, great deluge, record-to-record travel)
+  * coevolutionary algorithms (round robin and balanced)
+
+* selection strategies:
+  * identity
+  * random selection
+  * best selection
+  * n-stage tournament selection
+  * tournament selection
+  * fitness proportional selection
+  * roulette wheel selection
+
+* mutations:
+  * identity
+  * one gene flipping, binary mutation, efficient binary mutation
+  * exchange mutation, inversion mutation, mixing mutation, shifting mutation
+  * uniform real mutation, gauss mutation, self-adaptive gaus mutation
+
+* recombinations:
+  * identity
+  * one-point-crossover, k-point-crossover, uniform crossover
+  * arithmetic crossover
+  * ordered recombination, partially mapped crossover, edge recombination
+  * global uniform crossover, global arithmetic crossover
+
+* meta operators: proportional, sequentional and conditional combined operators
+
+
+== Installation
+
+* gem install evosynth (as root)
+* for detailed instructions (build from source, etc.) see INSTALL

data/Rakefile

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+#	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 'rake/gempackagetask'
+require 'rake/testtask'
+require 'rake/rdoctask'
+
+
+desc "print message"
+task :default do
+	puts "You have run rake without a task - please choose one of the following:\n\n"
+	puts `rake --tasks`
+end
+
+package_specification = Gem::Specification.new do |spec|
+	spec.required_ruby_version	= '>= 1.9'
+	spec.platform				= Gem::Platform::RUBY
+	spec.name					= 'evosynth'
+	spec.version				= '0.1.0'
+
+	spec.rubyforge_project		= 'evosynth'
+	spec.homepage				= 'http://evosynth.rubyforge.org'
+	spec.summary				= 'EvoSynth (Evolutionary Computation Synthesizer) is a framework for rapid development and prototyping of evolutionary algorithms.'
+	spec.author					= 'Yves Adler'
+	spec.email					= 'yves.adler@googlemail.com'
+
+	spec.has_rdoc				= true
+	spec.rdoc_options			= ["--charset", "UTF-8", "--title", "EvoSynth Documentation", "--main", "README", "--line-numbers"]
+	spec.extra_rdoc_files		= ["README", "LICENSE", "INSTALL", "docs/FEATURES"]
+
+	# files and dependencies:
+
+	files = FileList['**/*']; files.exclude('.git*'); files.exclude('pkg/*')
+	spec.files			= files.to_a
+	spec.test_files		= FileList['test/ts_*.rb']
+	spec.require_paths	<< 'lib'
+
+	# what about gruff, gnuplot & co ? where should I mention them?
+	spec.add_development_dependency(['shoulda', 'rake'])
+end
+
+Rake::GemPackageTask.new(package_specification) do |pkg|
+	pkg.need_zip = true
+	pkg.need_tar = true
+end
+
+Rake::RDocTask.new do |rdoc|
+	rdoc.main = "README"
+	rdoc.rdoc_dir	= "docs/rdoc"
+	rdoc.title		= "EvoSynth Documentation"
+	rdoc.options	= ["--charset", "UTF-8", "--line-numbers"]
+	rdoc.rdoc_files.include("README", "LICENSE", "INSTALL", "docs/FEATURES", "lib/**/*.rb", "examples/**/*.rb")
+end
+
+
+# Test tasks and code quality stuff:
+
+task :quality => [:test, :flog, :flay, :roodi]
+
+lib_dir = File.expand_path("lib")
+examples_dir = File.expand_path("examples")
+test_dir = File.expand_path("test")
+
+Rake::TestTask.new do |test|
+	test.libs = [lib_dir, test_dir]
+	test.test_files = FileList["test/ts_*.rb"]
+	test.verbose = true
+end
+
+desc "Analyze the code with roodi (Ruby Object Oriented Design Inferometer)"
+task :roodi do
+	roodi_output = `roodi 'lib/**/*.rb' 'examples/**/*.rb'`
+	puts "ERROR: roodi not found. please install 'gems install roodi'" if $?.exitstatus == 127
+	puts roodi_output
+end
+
+desc "Analyze for code duplication"
+task :flay do
+	flay_output = `flay '#{lib_dir}' '#{examples_dir}'`
+	puts "ERROR: flay not found. please install 'gems install flay'" if $?.exitstatus != 0
+	puts flay_output
+end
+
+desc "Analyze for code complexity"
+task :flog do
+	flog_output = `find lib -name \*.rb | xargs flog -g`
+	puts "ERROR: flog not found. please install 'gems install flog'" if $?.exitstatus != 0
+	puts flog_output
+end
+
+# Shortcuts for examples and benchmark
+
+desc "Run all examples"
+task :run_examples do
+	example_files = FileList["examples/*.rb"]
+	$:.unshift File.expand_path("../lib", __FILE__)
+	example_files.each do |example_file|
+		puts "\nRunning example : #{example_file}\n\n"
+		load example_file
+	end
+end
+
+desc "Run all benchmarks"
+task :run_benchmarks do
+	$:.unshift File.expand_path("../lib", __FILE__)
+	load 'test/benchmark/decoder_benchmark.rb'
+	load 'test/benchmark/mutation_benchmark.rb'
+	load 'test/benchmark/recombination_benchmark.rb'
+	load 'test/benchmark/selection_benchmark.rb'
+end
+

data/TODO

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+============================== generelles ======================================
+
+			!!! Jeden morgen ein paar sachen Dokumentieren !!!
+				-->			aktuell ab evolvers			<--
+
+fehlende oder fehlerhafte Testfälle:
+
+	- Selektionen: Float select_count (to_i testcase)
+	- EvoSynth::Evolvers::LocalSearch::HillclimberAcceptance
+	- EvoSynth::Evolvers::LocalSearch::SimulatedAnnealingAcceptance
+	- EvoSynth::Evolvers::LocalSearch::ThresholdAcceptance
+	- EvoSynth::Evolvers::LocalSearch::GreatDelugeAcceptance
+	- EvoSynth::Evolvers::LocalSearch::RecordToRecordTravelAcceptance
+	- EvoSynth::Mutations::SelfAdaptiveGaussMutation
+
+
+============================== EvoSynth 0.2 ====================================
+
+Features:
+
+	- Algorithmen:
+		=> CMBCoevolutionary braucht ein refactoring
+
+	- Checkpointing für Evolver, Save, Stop, Restart, Continue
+		=> eventuell mit Logger verknüppern
+
+	- EvoBench: Benchmark für Evolutionäre Algorithmen
+		=> wie sollten diese Versuche ablaufen? Stichwort statistische Relevanz
+		=> mutationen, selektionen und co
+		=> diversität und co (binär, float, wie denn genau? mit lambda?)
+		=> Versuchspläne und Statistiken?!
+		=> t-test (hypothesentest)
+
+	- Logger:
+		=> mehrere "Testläufe", Durchschnittswerte
+		=> html output templates, svg outputs?
+			-> http://www.germane-software.com/software/SVG/SVG::Graph/
+		=> logger sollte auch bei fitnessänderungen (der population?) getriggert werden können,
+		   das geht aber vielleicht eher in richtung eventsystem
+
+============================== EvoSynth >0.2 ===================================
+
+Features:
+
+	- add # encoding: utf-8 to all ruby files
+	- was ist mit http://rubygems.rubyforge.org/rdoc/Gem/Security.html ?
+
+	- TSP und GraphColouring Problem generischer machen und refactorisieren
+
+	- Benchmarkfunktionen:
+		=> Matrix Multiplikationsproblem aus Paredis Paper (epistasis gut steuerbar)
+		=> C-Funktion (Weicker page 272)
+		=> sämtliche mit Randbedingungen (Weicker page 274)
+
+	- Decoder/Encoder:
+		=> RealToBinary, IntegerToBinary, BinaryToInteger
+
+	- Algorithmen:
+		=> Tabu-Suche am beispiel graph colouring (Weicker page 164)
+		=> Schwärme
+		=> neuronale Netze (gibts da ein gem für)
+
+		=> Evolutionäres Programmieren & Genetisches Programmieren (Weicker page 139--154)
+			-> Gentische Programmierung (Ruby programme wären schön)
+			-> rubytree gem nutzen: http://rubytree.rubyforge.org/rdoc/index.html
+
+		=> Mehrzieloptimierung:
+			-> NSGA selektion (204)
+			-> SPEA2, PAES (205,206)
+			-> wenigstens ein Beispiel zur Mehrzieloptimierung
+
+		=> Meta-Evolver (eventuell mittels metaprogramming alá Elistismus):
+			=> was ist mit hall-of-fame oder ähnlichem?
+
+		=> Mehrpopulationsprobleme & Koevolutionäres:
+			=> was ist da noch sinnvoll? inseln & migration?
+
+	- BinaryGenome mittels inline C optimieren
+
+	- nicht reelwertige Fitnesswerte?! Da fehlt nicht viel, aber zum Beispiel
+	  die Fitnessproportionale Selektion braucht die (einfach nach ".fitness" suchen)
+
+	- Codegenerator System (z.b. für OpenBEALE und EO) -> siehe fehler!
+
+	- Bootstrap zeugs, inspiriert von OpenBEAGLE (initializer)
+		=> braucht man das wirklich?
+		=> Breeder klingt am besten (siehe ECJ)
+		=> variable anzahl an eltern, kindern für recombinationen (siehe EO paper)

data/docs/FEATURES

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+== Core features
+
+* EvoSynth::Evaluator
+* EvoSynth::Profile
+* EvoSynth::Population
+
+* EvoSynth::Individual
+  * EvoSynth::MaximizingIndividual
+  * EvoSynth::MinimizingIndividual
+
+* EvoSynth::Randomizer
+  * EvoSynth.rand / EvoSynth.srand
+  * EvoSynth.nrand
+  * EvoSynth.rand_bool
+
+* Include "Genotypes":
+  * EvoSynth::ArrayGenome (can contain any datatype as items)
+  * EvoSynth::BinaryGenome (not optimized yet)
+
+
+== Evolution algorithms
+
+* meta features:
+  * EvoSynth::Evolvers.add_weak_elitism
+  * EvoSynth::Evolvers.add_strong_elitism
+
+* basic evolvers:
+  * EvoSynth::Evolvers::Hillclimber
+  * EvoSynth::Evolvers::PopulationHillclimber
+  * EvoSynth::Evolvers::GeneticAlgorithm
+  * EvoSynth::Evolvers::SteadyStateGA
+  * EvoSynth::Evolvers::MemeticAlgorithm
+
+* evolution strategies:
+  * EvoSynth::Evolvers::AdaptiveES
+  * EvoSynth::Evolvers::SelfAdaptiveES
+  * EvoSynth::Evolvers::DerandomizedES
+
+* local search:
+  * EvoSynth::Evolvers::LocalSearch
+  * EvoSynth::Evolvers::LocalSearch::HillclimberAcceptance
+  * EvoSynth::Evolvers::LocalSearch::SimulatedAnnealingAcceptance
+  * EvoSynth::Evolvers::LocalSearch::ThresholdAcceptance
+  * EvoSynth::Evolvers::LocalSearch::GreatDelugeAcceptance
+  * EvoSynth::Evolvers::LocalSearch::RecordToRecordTravelAcceptance
+
+* coevolutionary algorithms:
+  * EvoSynth::Evolvers::RoundRobinCoevolutionary
+  * EvoSynth::Evolvers::BalancedCoevolutionary (unfinished)
+
+== Selections
+
+* EvoSynth::Selections::Identity
+* EvoSynth::Selections::SelectBest
+* EvoSynth::Selections::NStageTournamentSelection
+* EvoSynth::Selections::TournamentSelection
+* EvoSynth::Selections::FitnessProportionalSelection
+* EvoSynth::Selections::RouletteWheelSelection
+* EvoSynth::Selections::RandomSelection
+
+
+== Meta operators
+
+* EvoSynth::MetaOperators::ProportionalCombinedOperator
+* EvoSynth::MetaOperators::SequentialCombinedOperator
+* EvoSynth::MetaOperators::ConditionalCombinedOperator
+
+== Mutations
+
+* work on every genome:
+  * EvoSynth::Mutations::Identity
+
+* work on arrays (need flip function):
+  * EvoSynth::Mutations::BinaryMutation
+  * EvoSynth::Mutations::EfficientBinaryMutation
+  * EvoSynth::Mutations::OneGeneFlipping
+
+* work on permutations:
+  * EvoSynth::Mutations::ExchangeMutation
+  * EvoSynth::Mutations::InversionMutation
+  * EvoSynth::Mutations::MixingMutation
+  * EvoSynth::Mutations::ShiftingMutation
+
+* work on (arrays of) floats:
+  * EvoSynth::Mutations::GaussMutation
+  * EvoSynth::Mutations::UniformRealMutation
+  * EvoSynth::Mutations::SelfAdaptiveGaussMutation
+
+== Recombinations
+
+* work on every genome:
+  * EvoSynth::Recombinations::Identity
+  * EvoSynth::Recombinations::OnePointCrossover
+  * EvoSynth::Recombinations::KPointCrossover
+  * EvoSynth::Recombinations::UniformCrossover
+  * EvoSynth::Recombinations::ArithmeticCrossover (needs interpolation functions)
+
+* work on permutations (no duplicates):
+  * EvoSynth::Recombinations::PartiallyMappedCrossover
+  * EvoSynth::Recombinations::OrderedRecombination
+  * EvoSynth::Recombinations::EdgeRecombination
+
+== Global recombinations
+
+* EvoSynth::GlobalRecombinations::GlobalUniformCrossover
+* EvoSynth::GlobalRecombinations::GlobalArithmeticCrossover
+
+== Adjustment strategies
+
+* EvoSynth::Adjustments::PredifinedAdjustment
+* EvoSynth::Adjustments::AdaptiveAdjustment