rubyneat 0.3.5.alpha.2

data/rubyneat.gemspec.orig

@@ -0,0 +1,375 @@
+# Generated by jeweler
+# DO NOT EDIT THIS FILE DIRECTLY
+# Instead, edit Jeweler::Tasks in Rakefile, and run 'rake gemspec'
+# -*- encoding: utf-8 -*-
+<<<<<<< HEAD
+# stub: rubyneat 0.3.5.alpha ruby lib
+
+Gem::Specification.new do |s|
+  s.name = "rubyneat"
+  s.version = "0.3.5.alpha"
+=======
+# stub: rubyneat 0.3.5 ruby lib
+
+Gem::Specification.new do |s|
+  s.name = "rubyneat"
+  s.version = "0.3.5"
+>>>>>>> utility
+
+  s.required_rubygems_version = Gem::Requirement.new("> 1.3.1") if s.respond_to? :required_rubygems_version=
+  s.require_paths = ["lib"]
+  s.authors = ["Fred Mitchell"]
+<<<<<<< HEAD
+  s.date = "2014-04-13"
+=======
+  s.date = "2014-03-30"
+>>>>>>> utility
+  s.description = "\n  NEAT Algorithm for Ruby.\n  "
+  s.email = "fred@lrcsoft.com"
+  s.executables = ["neat"]
+  s.files = [
+    ".directory",
+    ".gitignore.orig",
+    ".idea/.name",
+    ".idea/.rakeTasks",
+    ".idea/dictionaries/trader.xml",
+    ".idea/encodings.xml",
+    ".idea/misc.xml",
+    ".idea/modules.xml",
+    ".idea/rubyneat.iml",
+    ".idea/runConfigurations/invpend_neat.xml",
+    ".idea/runConfigurations/sigdebug_neat.xml",
+    ".idea/runConfigurations/xor_neat.xml",
+    ".idea/runConfigurations/xordebug_neat.xml",
+    ".idea/runConfigurations/xorsin_neat.xml",
+    ".idea/scopes/scope_settings.xml",
+    ".idea/vcs.xml",
+    ".idea/workspace.xml",
+    ".semver",
+    ".yardoc/checksums",
+    ".yardoc/object_types",
+    ".yardoc/objects/root.dat",
+    ".yardoc/proxy_types",
+    "Gemfile",
+    "Gemfile.lock",
+    "Guardfile",
+    "Rakefile",
+    "bin/neat",
+    "config/application.rb",
+    "doc/ControllerPoint.html",
+    "doc/CuteA.html",
+    "doc/CuteB.html",
+    "doc/DSL.html",
+    "doc/NEAT.html",
+    "doc/NEAT/BasicNeuronTypes.html",
+    "doc/NEAT/BasicNeuronTypes/BiasNeuron.html",
+    "doc/NEAT/BasicNeuronTypes/CosineNeuron.html",
+    "doc/NEAT/BasicNeuronTypes/InputNeuron.html",
+    "doc/NEAT/BasicNeuronTypes/SigmoidNeuron.html",
+    "doc/NEAT/BasicNeuronTypes/SineNeuron.html",
+    "doc/NEAT/BasicNeuronTypes/TanhNeuron.html",
+    "doc/NEAT/Controller.html",
+    "doc/NEAT/Controller/NeatSettings.html",
+    "doc/NEAT/Critter.html",
+    "doc/NEAT/Critter/Genotype.html",
+    "doc/NEAT/Critter/Genotype/Gene.html",
+    "doc/NEAT/Critter/Phenotype.html",
+    "doc/NEAT/DSL.html",
+    "doc/NEAT/Evaluator.html",
+    "doc/NEAT/Evolver.html",
+    "doc/NEAT/Evolver/CritterOp.html",
+    "doc/NEAT/Expressor.html",
+    "doc/NEAT/Graph.html",
+    "doc/NEAT/Graph/DependencyResolver.html",
+    "doc/NEAT/Graph/GraphException.html",
+    "doc/NEAT/NeatException.html",
+    "doc/NEAT/NeatOb.html",
+    "doc/NEAT/Neuron.html",
+    "doc/NEAT/Operator.html",
+    "doc/NEAT/Population.html",
+    "doc/NEAT/Trait.html",
+    "doc/_index.html",
+    "doc/class_list.html",
+    "doc/css/common.css",
+    "doc/css/full_list.css",
+    "doc/css/style.css",
+    "doc/file_list.html",
+    "doc/frames.html",
+    "doc/index.html",
+    "doc/js/app.js",
+    "doc/js/full_list.js",
+    "doc/js/jquery.js",
+    "doc/method_list.html",
+    "doc/top-level-namespace.html",
+    "foo/foo_aquarium_example.rb",
+    "foo/foo_gosu.rb",
+    "foo/foo_rubygoo.rb",
+    "foo/foo_sdl.rb",
+    "foo/icon.png",
+    "lib/rubyneat.rb",
+    "lib/rubyneat/critter.rb",
+    "lib/rubyneat/default_neat.rb",
+    "lib/rubyneat/dsl.rb",
+    "lib/rubyneat/evaluator.rb",
+    "lib/rubyneat/evolver.rb",
+    "lib/rubyneat/expressor.rb",
+    "lib/rubyneat/graph.rb",
+    "lib/rubyneat/neuron.rb",
+    "lib/rubyneat/population.rb",
+    "lib/rubyneat/rubyneat.rb",
+    "neater/invpend_neat.rb",
+    "neater/rnlib/inverted_pendulum.rb",
+    "neater/rnlib/xor.rb",
+    "neater/sigdebug_neat.rb",
+    "neater/xor_neat.rb",
+    "neater/xoranalog_neat.rb",
+    "neater/xorsin_neat.rb",
+<<<<<<< HEAD
+=======
+    "pkg/rubyneat-0.0.7.gem",
+    "pkg/rubyneat-0.1.4.gem",
+    "pkg/rubyneat-0.1.7.gem",
+    "pkg/rubyneat-0.1.8.gem",
+    "pkg/rubyneat-0.2.1.gem",
+    "pkg/rubyneat-0.3.1.gem",
+    "pkg/rubyneat-0.3.3.gem",
+    "pkg/rubyneat-0.3.4.gem",
+>>>>>>> utility
+    "projectFilesBackup/.idea/rubyneat.iml",
+    "public/.directory",
+    "public/background.png",
+    "public/background.xcf",
+    "public/cart.png",
+    "public/cart.xcf",
+    "public/metalpoles_molton_ball_l.jpg",
+<<<<<<< HEAD
+=======
+    "public/old_background.png",
+>>>>>>> utility
+    "public/pointer.png",
+    "public/pointer.xcf",
+    "public/pole.kra",
+    "public/pole.png",
+    "public/pole.xcf",
+    "public/wheel-of-year-stone-DD-131-WOYS.jpg",
+    "public/wheel.png",
+    "public/wheel.xcf",
+    "public/wood-planks-texture.jpg",
+    "rdoc/ControllerPoint.html",
+    "rdoc/CuteA.html",
+    "rdoc/CuteB.html",
+    "rdoc/DSLSetup.html",
+    "rdoc/GameTestWindow.html",
+    "rdoc/GameWindow.html",
+    "rdoc/Gemfile.html",
+    "rdoc/Gemfile_lock.html",
+    "rdoc/GraphTest.html",
+    "rdoc/Guardfile.html",
+    "rdoc/InvertedPendulum.html",
+    "rdoc/InvertedPendulum/Cart.html",
+    "rdoc/InvertedPendulum/DSL.html",
+    "rdoc/InvertedPendulum/InvPendWindow.html",
+    "rdoc/Logger.html",
+    "rdoc/NEAT.html",
+    "rdoc/NEAT/BasicNeuronTypes.html",
+    "rdoc/NEAT/BasicNeuronTypes/BiasNeuron.html",
+    "rdoc/NEAT/BasicNeuronTypes/CosineNeuron.html",
+    "rdoc/NEAT/BasicNeuronTypes/InputNeuron.html",
+    "rdoc/NEAT/BasicNeuronTypes/SigmoidNeuron.html",
+    "rdoc/NEAT/BasicNeuronTypes/SineNeuron.html",
+    "rdoc/NEAT/BasicNeuronTypes/TanhNeuron.html",
+    "rdoc/NEAT/Controller.html",
+    "rdoc/NEAT/Controller/NeatSettings.html",
+    "rdoc/NEAT/Critter.html",
+    "rdoc/NEAT/Critter/Genotype.html",
+    "rdoc/NEAT/Critter/Genotype/Gene.html",
+    "rdoc/NEAT/Critter/Phenotype.html",
+    "rdoc/NEAT/DSL.html",
+    "rdoc/NEAT/Evaluator.html",
+    "rdoc/NEAT/Evolver.html",
+    "rdoc/NEAT/Evolver/CritterOp.html",
+    "rdoc/NEAT/Expressor.html",
+    "rdoc/NEAT/Graph.html",
+    "rdoc/NEAT/Graph/DependencyResolver.html",
+    "rdoc/NEAT/Graph/GraphException.html",
+    "rdoc/NEAT/NeatException.html",
+    "rdoc/NEAT/NeatOb.html",
+    "rdoc/NEAT/Neuron.html",
+    "rdoc/NEAT/Operator.html",
+    "rdoc/NEAT/Population.html",
+    "rdoc/NEAT/Trait.html",
+    "rdoc/Object.html",
+    "rdoc/Phi.html",
+    "rdoc/Player.html",
+    "rdoc/Rakefile.html",
+    "rdoc/RubyNEAT.html",
+    "rdoc/RubyNEAT/Application.html",
+    "rdoc/SDL.html",
+    "rdoc/SDL/Event2.html",
+    "rdoc/Vector.html",
+    "rdoc/created.rid",
+    "rdoc/doc/ControllerPoint_html.html",
+    "rdoc/doc/CuteA_html.html",
+    "rdoc/doc/CuteB_html.html",
+    "rdoc/doc/DSL_html.html",
+    "rdoc/doc/NEAT/BasicNeuronTypes/BiasNeuron_html.html",
+    "rdoc/doc/NEAT/BasicNeuronTypes/CosineNeuron_html.html",
+    "rdoc/doc/NEAT/BasicNeuronTypes/InputNeuron_html.html",
+    "rdoc/doc/NEAT/BasicNeuronTypes/SigmoidNeuron_html.html",
+    "rdoc/doc/NEAT/BasicNeuronTypes/SineNeuron_html.html",
+    "rdoc/doc/NEAT/BasicNeuronTypes/TanhNeuron_html.html",
+    "rdoc/doc/NEAT/BasicNeuronTypes_html.html",
+    "rdoc/doc/NEAT/Controller/NeatSettings_html.html",
+    "rdoc/doc/NEAT/Controller_html.html",
+    "rdoc/doc/NEAT/Critter/Genotype/Gene_html.html",
+    "rdoc/doc/NEAT/Critter/Genotype_html.html",
+    "rdoc/doc/NEAT/Critter/Phenotype_html.html",
+    "rdoc/doc/NEAT/Critter_html.html",
+    "rdoc/doc/NEAT/DSL_html.html",
+    "rdoc/doc/NEAT/Evaluator_html.html",
+    "rdoc/doc/NEAT/Evolver/CritterOp_html.html",
+    "rdoc/doc/NEAT/Evolver_html.html",
+    "rdoc/doc/NEAT/Expressor_html.html",
+    "rdoc/doc/NEAT/Graph/DependencyResolver_html.html",
+    "rdoc/doc/NEAT/Graph/GraphException_html.html",
+    "rdoc/doc/NEAT/Graph_html.html",
+    "rdoc/doc/NEAT/NeatException_html.html",
+    "rdoc/doc/NEAT/NeatOb_html.html",
+    "rdoc/doc/NEAT/Neuron_html.html",
+    "rdoc/doc/NEAT/Operator_html.html",
+    "rdoc/doc/NEAT/Population_html.html",
+    "rdoc/doc/NEAT/Trait_html.html",
+    "rdoc/doc/NEAT_html.html",
+    "rdoc/doc/_index_html.html",
+    "rdoc/doc/class_list_html.html",
+    "rdoc/doc/css/common_css.html",
+    "rdoc/doc/css/full_list_css.html",
+    "rdoc/doc/css/style_css.html",
+    "rdoc/doc/file_list_html.html",
+    "rdoc/doc/frames_html.html",
+    "rdoc/doc/index_html.html",
+    "rdoc/doc/js/app_js.html",
+    "rdoc/doc/js/full_list_js.html",
+    "rdoc/doc/js/jquery_js.html",
+    "rdoc/doc/method_list_html.html",
+    "rdoc/doc/top-level-namespace_html.html",
+    "rdoc/fonts.css",
+    "rdoc/fonts/Lato-Light.ttf",
+    "rdoc/fonts/Lato-LightItalic.ttf",
+    "rdoc/fonts/Lato-Regular.ttf",
+    "rdoc/fonts/Lato-RegularItalic.ttf",
+    "rdoc/fonts/SourceCodePro-Bold.ttf",
+    "rdoc/fonts/SourceCodePro-Regular.ttf",
+    "rdoc/images/add.png",
+    "rdoc/images/arrow_up.png",
+    "rdoc/images/brick.png",
+    "rdoc/images/brick_link.png",
+    "rdoc/images/bug.png",
+    "rdoc/images/bullet_black.png",
+    "rdoc/images/bullet_toggle_minus.png",
+    "rdoc/images/bullet_toggle_plus.png",
+    "rdoc/images/date.png",
+    "rdoc/images/delete.png",
+    "rdoc/images/find.png",
+    "rdoc/images/loadingAnimation.gif",
+    "rdoc/images/macFFBgHack.png",
+    "rdoc/images/package.png",
+    "rdoc/images/page_green.png",
+    "rdoc/images/page_white_text.png",
+    "rdoc/images/page_white_width.png",
+    "rdoc/images/plugin.png",
+    "rdoc/images/ruby.png",
+    "rdoc/images/tag_blue.png",
+    "rdoc/images/tag_green.png",
+    "rdoc/images/transparent.png",
+    "rdoc/images/wrench.png",
+    "rdoc/images/wrench_orange.png",
+    "rdoc/images/zoom.png",
+    "rdoc/index.html",
+    "rdoc/js/darkfish.js",
+    "rdoc/js/jquery.js",
+    "rdoc/js/navigation.js",
+    "rdoc/js/search.js",
+    "rdoc/js/search_index.js",
+    "rdoc/js/searcher.js",
+    "rdoc/rdoc.css",
+    "rdoc/rubyneat_gemspec.html",
+    "rdoc/table_of_contents.html",
+    "rdoc/xordebug_log.html",
+    "rdoc/xorsin_log.html",
+    "rubyneat.gemspec",
+    "spec/lib/rubyneat/rubyneat_spec.rb"
+  ]
+  s.homepage = "http://rubyneat.com"
+  s.licenses = ["MIT"]
+  s.rubygems_version = "2.2.2"
+<<<<<<< HEAD
+  s.summary = "RubyNEAT NeuralEvolution of Augmenting Topologies"
+=======
+  s.summary = "RubyNEAT NeuralEvolution by Augmented Topologies"
+>>>>>>> utility
+
+  if s.respond_to? :specification_version then
+    s.specification_version = 4
+
+    if Gem::Version.new(Gem::VERSION) >= Gem::Version.new('1.2.0') then
+      s.add_runtime_dependency(%q<mongo>, [">= 0"])
+      s.add_runtime_dependency(%q<bson_ext>, [">= 0"])
+      s.add_runtime_dependency(%q<distribution>, [">= 0"])
+      s.add_runtime_dependency(%q<statistics2>, [">= 0"])
+      s.add_runtime_dependency(%q<debase>, [">= 0"])
+      s.add_runtime_dependency(%q<aquarium>, [">= 0"])
+      s.add_runtime_dependency(%q<slop>, [">= 0"])
+      s.add_runtime_dependency(%q<awesome_print>, [">= 0"])
+      s.add_runtime_dependency(%q<deep_dive>, [">= 0"])
+      s.add_runtime_dependency(%q<gosu>, [">= 0"])
+      s.add_development_dependency(%q<rspec>, [">= 0"])
+      s.add_development_dependency(%q<yard>, [">= 0"])
+      s.add_development_dependency(%q<guard>, [">= 0"])
+      s.add_development_dependency(%q<guard-rspec>, [">= 0"])
+      s.add_development_dependency(%q<semver>, [">= 0"])
+      s.add_development_dependency(%q<jeweler>, ["~> 1.8.7"])
+      s.add_development_dependency(%q<simplecov>, [">= 0"])
+      s.add_development_dependency(%q<ruby-debug-ide>, [">= 0"])
+    else
+      s.add_dependency(%q<mongo>, [">= 0"])
+      s.add_dependency(%q<bson_ext>, [">= 0"])
+      s.add_dependency(%q<distribution>, [">= 0"])
+      s.add_dependency(%q<statistics2>, [">= 0"])
+      s.add_dependency(%q<debase>, [">= 0"])
+      s.add_dependency(%q<aquarium>, [">= 0"])
+      s.add_dependency(%q<slop>, [">= 0"])
+      s.add_dependency(%q<awesome_print>, [">= 0"])
+      s.add_dependency(%q<deep_dive>, [">= 0"])
+      s.add_dependency(%q<gosu>, [">= 0"])
+      s.add_dependency(%q<rspec>, [">= 0"])
+      s.add_dependency(%q<yard>, [">= 0"])
+      s.add_dependency(%q<guard>, [">= 0"])
+      s.add_dependency(%q<guard-rspec>, [">= 0"])
+      s.add_dependency(%q<semver>, [">= 0"])
+      s.add_dependency(%q<jeweler>, ["~> 1.8.7"])
+      s.add_dependency(%q<simplecov>, [">= 0"])
+      s.add_dependency(%q<ruby-debug-ide>, [">= 0"])
+    end
+  else
+    s.add_dependency(%q<mongo>, [">= 0"])
+    s.add_dependency(%q<bson_ext>, [">= 0"])
+    s.add_dependency(%q<distribution>, [">= 0"])
+    s.add_dependency(%q<statistics2>, [">= 0"])
+    s.add_dependency(%q<debase>, [">= 0"])
+    s.add_dependency(%q<aquarium>, [">= 0"])
+    s.add_dependency(%q<slop>, [">= 0"])
+    s.add_dependency(%q<awesome_print>, [">= 0"])
+    s.add_dependency(%q<deep_dive>, [">= 0"])
+    s.add_dependency(%q<gosu>, [">= 0"])
+    s.add_dependency(%q<rspec>, [">= 0"])
+    s.add_dependency(%q<yard>, [">= 0"])
+    s.add_dependency(%q<guard>, [">= 0"])
+    s.add_dependency(%q<guard-rspec>, [">= 0"])
+    s.add_dependency(%q<semver>, [">= 0"])
+    s.add_dependency(%q<jeweler>, ["~> 1.8.7"])
+    s.add_dependency(%q<simplecov>, [">= 0"])
+    s.add_dependency(%q<ruby-debug-ide>, [">= 0"])
+  end
+end
+

data/spec/lib/rubyneat/rubyneat_spec.rb

@@ -0,0 +1,132 @@
+require 'rubyneat'
+
+module DSLSetup
+  include DSL
+
+  # The number of inputs to the xor function
+  XOR_INPUTS=2
+
+  # Basic xor function we shall evolve a net for. Only goes true
+  # on one and only one true input, false otherwise.
+  def xor(*inp)
+    p = 0
+    inp.each {|i| p += 1 if i}
+    return p == 1
+  end
+
+  # This defines the controller
+  define "Default Setup" do
+    # Define the IO neurons
+    inputs {
+      cinv = Hash[(1..XOR_INPUTS).map{|i| [("i%s" % i).to_sym, InputNeuron]}]
+      cinv[:bias] = BiasNeuron
+      cinv
+    }
+    outputs out: SigmoidNeuron
+    
+    # Hidden neuron specification is optional. 
+    # The name given here is largely meaningless, but may be useful as some sort
+    # of unique flag.
+    hidden sig: SigmoidNeuron
+    
+    # Settings
+    hash_on_fitness = false
+    start_population_size 10
+    population_size 100
+    max_generations 50
+
+    start_sequence_at 0
+    end_sequence_at 10
+  end
+  
+  evolve do
+    query { |seq|
+      puts "Query called with seq %s" % seq
+    }
+    
+    fitness { |vin, vout, seq|
+      puts "Fitness called with vin=%s, vout=%s, seq=%s" % [vin, vout, seq]
+      return 0.0
+    }
+  end
+
+  report do
+  end
+
+  # The block here is called upon the completion of each generation
+  run_engine do |c|
+    log.info { "Run of generation %s completed, history count %d" % [c.generation_num, 
+                                                                     c.population_history.size] }
+  end
+end
+
+
+class GraphTest
+  include NEAT::Graph
+  def initialize(i)
+    @i = i
+  end
+  
+  def to_s
+    "node[%s]" % @i
+  end
+end
+
+
+def pgraph(a, mess)
+  puts "\n\n" + mess
+  a.each{|g|
+    puts "  %s ->" % g
+    g.inputs.each{|h|
+      puts "    %s" % h
+    }
+  }
+end
+
+def create_nodes(n)
+  nodes = (1..n).map{ |i| GraphTest.new i }
+  n.times {|i|
+    nodes[i].clear_graph
+    i.times {|j| nodes[i] << nodes[j] }}
+  nodes
+end
+
+describe NEAT do
+  describe "::random_name_generator" do
+    it "returns a random string" do
+      s = NEAT::random_name_generator
+      s.size.should > 0
+    end
+  end
+
+  describe "::Graph::DependencyResolver" do
+
+    nodes_ff = create_nodes 5
+    pgraph nodes_ff, "Feed Forward"
+
+    it "resolves depedencies" do
+      depres = NEAT::Graph::DependencyResolver.new([nodes_ff.last])
+      dr, cl = depres.resolve
+
+      log.debug { "\n**** dr=%s\n**** cl=%s" % [dr, cl] }
+
+      dr.size.should == 5
+      cl.nil?.should == true
+    end
+
+    # we add a circular dependency between the first and last.
+    nodes_c = create_nodes 5
+    nodes_c.first << nodes_c.last
+    pgraph nodes_c, "Circluar Dependency"
+
+    it "detects circular dependencies" do
+      depres = NEAT::Graph::DependencyResolver.new([nodes_c.last])
+      dr, cl = depres.resolve
+
+      log.debug { "\nxxxx dr=%s\nxxxx cl=%s" % [dr, cl] }
+
+      dr.size.should == 5
+      cl.nil?.should_not == true
+    end
+  end
+end