rubyneat 0.3.5.alpha.2

data/.semver

@@ -0,0 +1,5 @@
+---
+:major: 0
+:minor: 3
+:patch: 5
+:special: ".alpha.2"

data/.yardoc/checksums

@@ -0,0 +1,11 @@
+lib/rubyneat.rb 1da1fbcf4887eff825e525710f40a9c4a13814a4
+lib/rubyneat/dsl.rb 537a8cb3bfed4911e3b2a25040131d0acbd6eb13
+lib/rubyneat/graph.rb b1b6605698590438ade2bed11f76fbb46f1758a0
+lib/rubyneat/neuron.rb bed0637d2b668d328bdbe5c65a8400e0b73bb65b
+lib/rubyneat/critter.rb 6caffc41daa1c6f78e0abf46246a2f6e9eb04d39
+lib/rubyneat/evolver.rb fc45db30b5915c03becf11dbd9a10fe64888f866
+lib/rubyneat/rubyneat.rb e21b5035d4e8acdec8c1833c0ec57a1a01745830
+lib/rubyneat/expressor.rb 3b729ffb27f7fd8c92cd897ec3c4ed882cedc3eb
+lib/rubyneat/evaluator.rb f77384c83d266062790bffa6966ceb0e9e3da208
+lib/rubyneat/population.rb b1fcede0e71da3192ae1584952413d3eb54ca4d2
+lib/rubyneat/default_neat.rb df2d106cdf3bf6f6b707b4f2997bb326f23e5cd5

data/Gemfile

@@ -0,0 +1,32 @@
+source 'https://rubygems.org'
+
+#gemspec
+
+ruby '2.1.1'
+
+gem 'mongo'
+gem 'bson_ext'
+gem 'distribution'
+#gem 'gsl'
+gem 'statistics2'
+gem 'debase'
+gem 'aquarium'
+gem 'slop'
+gem 'awesome_print'
+gem 'deep_dive'
+
+group :development do
+  gem 'rspec'
+  gem 'yard'
+  gem 'guard'
+  gem 'guard-rspec'
+  gem 'semver'
+  gem "jeweler", "~> 1.8.7"
+  gem "simplecov"
+  #gem 'debugger'
+  gem 'ruby-debug-ide'
+end
+
+# For demo purposes, we include the gosu library, but
+# don't want this to be part of the mainstream.
+gem 'gosu', require: false

data/Gemfile.lock

@@ -0,0 +1,135 @@
+GEM
+  remote: https://rubygems.org/
+  specs:
+    addressable (2.3.6)
+    aquarium (0.5.1)
+    awesome_print (1.2.0)
+    bson (1.10.0)
+    bson_ext (1.10.0)
+      bson (~> 1.10.0)
+    builder (3.2.2)
+    celluloid (0.15.2)
+      timers (~> 1.1.0)
+    celluloid-io (0.15.0)
+      celluloid (>= 0.15.0)
+      nio4r (>= 0.5.0)
+    coderay (1.1.0)
+    debase (0.0.9)
+      debugger-ruby_core_source
+    debugger-ruby_core_source (1.3.2)
+    deep_dive (0.1.0)
+      debase
+    diff-lcs (1.2.5)
+    distribution (0.7.0)
+    docile (1.1.3)
+    faraday (0.8.9)
+      multipart-post (~> 1.2.0)
+    ffi (1.9.3)
+    formatador (0.2.4)
+    git (1.2.6)
+    github_api (0.10.1)
+      addressable
+      faraday (~> 0.8.1)
+      hashie (>= 1.2)
+      multi_json (~> 1.4)
+      nokogiri (~> 1.5.2)
+      oauth2
+    gosu (0.7.50)
+    guard (2.6.0)
+      formatador (>= 0.2.4)
+      listen (~> 2.7)
+      lumberjack (~> 1.0)
+      pry (>= 0.9.12)
+      thor (>= 0.18.1)
+    guard-rspec (4.2.8)
+      guard (~> 2.1)
+      rspec (>= 2.14, < 4.0)
+    hashie (2.1.1)
+    highline (1.6.21)
+    jeweler (1.8.8)
+      builder
+      bundler (~> 1.0)
+      git (>= 1.2.5)
+      github_api (= 0.10.1)
+      highline (>= 1.6.15)
+      nokogiri (= 1.5.10)
+      rake
+      rdoc
+    json (1.8.1)
+    jwt (0.1.11)
+      multi_json (>= 1.5)
+    listen (2.7.1)
+      celluloid (>= 0.15.2)
+      celluloid-io (>= 0.15.0)
+      rb-fsevent (>= 0.9.3)
+      rb-inotify (>= 0.9)
+    lumberjack (1.0.5)
+    method_source (0.8.2)
+    mongo (1.10.0)
+      bson (~> 1.10.0)
+    multi_json (1.9.2)
+    multi_xml (0.5.5)
+    multipart-post (1.2.0)
+    nio4r (1.0.0)
+    nokogiri (1.5.10)
+    oauth2 (0.9.3)
+      faraday (>= 0.8, < 0.10)
+      jwt (~> 0.1.8)
+      multi_json (~> 1.3)
+      multi_xml (~> 0.5)
+      rack (~> 1.2)
+    pry (0.9.12.6)
+      coderay (~> 1.0)
+      method_source (~> 0.8)
+      slop (~> 3.4)
+    rack (1.5.2)
+    rake (10.2.2)
+    rb-fsevent (0.9.4)
+    rb-inotify (0.9.3)
+      ffi (>= 0.5.0)
+    rdoc (4.1.1)
+      json (~> 1.4)
+    rspec (2.14.1)
+      rspec-core (~> 2.14.0)
+      rspec-expectations (~> 2.14.0)
+      rspec-mocks (~> 2.14.0)
+    rspec-core (2.14.8)
+    rspec-expectations (2.14.5)
+      diff-lcs (>= 1.1.3, < 2.0)
+    rspec-mocks (2.14.6)
+    ruby-debug-ide (0.4.22)
+      rake (>= 0.8.1)
+    semver (1.0.1)
+    simplecov (0.8.2)
+      docile (~> 1.1.0)
+      multi_json
+      simplecov-html (~> 0.8.0)
+    simplecov-html (0.8.0)
+    slop (3.5.0)
+    statistics2 (0.54)
+    thor (0.19.1)
+    timers (1.1.0)
+    yard (0.8.7.4)
+
+PLATFORMS
+  ruby
+
+DEPENDENCIES
+  aquarium
+  awesome_print
+  bson_ext
+  debase
+  deep_dive
+  distribution
+  gosu
+  guard
+  guard-rspec
+  jeweler (~> 1.8.7)
+  mongo
+  rspec
+  ruby-debug-ide
+  semver
+  simplecov
+  slop
+  statistics2
+  yard

data/Gemfile.lock.orig

@@ -0,0 +1,147 @@
+GEM
+  remote: https://rubygems.org/
+  specs:
+    addressable (2.3.6)
+    aquarium (0.5.1)
+    awesome_print (1.2.0)
+    bson (1.10.0)
+    bson_ext (1.10.0)
+      bson (~> 1.10.0)
+    builder (3.2.2)
+    celluloid (0.15.2)
+      timers (~> 1.1.0)
+    celluloid-io (0.15.0)
+      celluloid (>= 0.15.0)
+      nio4r (>= 0.5.0)
+    coderay (1.1.0)
+    debase (0.0.9)
+      debugger-ruby_core_source
+    debugger-ruby_core_source (1.3.2)
+    deep_dive (0.1.0)
+      debase
+    diff-lcs (1.2.5)
+    distribution (0.7.0)
+    docile (1.1.3)
+    faraday (0.8.9)
+      multipart-post (~> 1.2.0)
+    ffi (1.9.3)
+    formatador (0.2.4)
+    git (1.2.6)
+    github_api (0.10.1)
+      addressable
+      faraday (~> 0.8.1)
+      hashie (>= 1.2)
+      multi_json (~> 1.4)
+      nokogiri (~> 1.5.2)
+      oauth2
+    gosu (0.7.50)
+<<<<<<< HEAD
+    guard (2.4.0)
+=======
+    guard (2.6.0)
+>>>>>>> utility
+      formatador (>= 0.2.4)
+      listen (~> 2.7)
+      lumberjack (~> 1.0)
+      pry (>= 0.9.12)
+      thor (>= 0.18.1)
+<<<<<<< HEAD
+    guard-rspec (4.2.6)
+=======
+    guard-rspec (4.2.8)
+>>>>>>> utility
+      guard (~> 2.1)
+      rspec (>= 2.14, < 4.0)
+    hashie (2.1.1)
+    highline (1.6.21)
+    jeweler (1.8.8)
+      builder
+      bundler (~> 1.0)
+      git (>= 1.2.5)
+      github_api (= 0.10.1)
+      highline (>= 1.6.15)
+      nokogiri (= 1.5.10)
+      rake
+      rdoc
+    json (1.8.1)
+    jwt (0.1.11)
+      multi_json (>= 1.5)
+<<<<<<< HEAD
+    listen (2.5.0)
+=======
+    listen (2.7.1)
+>>>>>>> utility
+      celluloid (>= 0.15.2)
+      celluloid-io (>= 0.15.0)
+      rb-fsevent (>= 0.9.3)
+      rb-inotify (>= 0.9)
+    lumberjack (1.0.5)
+    method_source (0.8.2)
+    mongo (1.10.0)
+      bson (~> 1.10.0)
+    multi_json (1.9.2)
+    multi_xml (0.5.5)
+    multipart-post (1.2.0)
+    nio4r (1.0.0)
+    nokogiri (1.5.10)
+    oauth2 (0.9.3)
+      faraday (>= 0.8, < 0.10)
+      jwt (~> 0.1.8)
+      multi_json (~> 1.3)
+      multi_xml (~> 0.5)
+      rack (~> 1.2)
+    pry (0.9.12.6)
+      coderay (~> 1.0)
+      method_source (~> 0.8)
+      slop (~> 3.4)
+    rack (1.5.2)
+    rake (10.2.2)
+    rb-fsevent (0.9.4)
+    rb-inotify (0.9.3)
+      ffi (>= 0.5.0)
+    rdoc (4.1.1)
+      json (~> 1.4)
+    rspec (2.14.1)
+      rspec-core (~> 2.14.0)
+      rspec-expectations (~> 2.14.0)
+      rspec-mocks (~> 2.14.0)
+    rspec-core (2.14.8)
+    rspec-expectations (2.14.5)
+      diff-lcs (>= 1.1.3, < 2.0)
+    rspec-mocks (2.14.6)
+    ruby-debug-ide (0.4.22)
+      rake (>= 0.8.1)
+    semver (1.0.1)
+    simplecov (0.8.2)
+      docile (~> 1.1.0)
+      multi_json
+      simplecov-html (~> 0.8.0)
+    simplecov-html (0.8.0)
+    slop (3.5.0)
+    statistics2 (0.54)
+    thor (0.19.1)
+    timers (1.1.0)
+    yard (0.8.7.4)
+
+PLATFORMS
+  ruby
+
+DEPENDENCIES
+  aquarium
+  awesome_print
+  bson_ext
+  debase
+  deep_dive
+  distribution
+  gosu
+  guard
+  guard-rspec
+  jeweler (~> 1.8.7)
+  mongo
+  rspec
+  ruby-debug-ide
+  semver
+  simplecov
+  slop
+  statistics2
+  yard

data/Guardfile

@@ -0,0 +1,8 @@
+# A sample Guardfile
+# More info at https://github.com/guard/guard#readme
+
+guard 'rspec' do
+  watch(%r{^spec/.+_spec\.rb$})
+  watch(%r{^rnlib/(.+)\.rb$})     { |m| "spec/rnlib/#{m[1]}_spec.rb" }
+  watch('spec/spec_helper.rb')  { "spec" }
+end

data/Rakefile

@@ -0,0 +1,61 @@
+# encoding: utf-8
+
+require 'rubygems'
+require 'bundler'
+require 'semver'
+
+def s_version
+  SemVer.find.format "%M.%m.%p%s"
+end
+
+begin
+  Bundler.setup(:default, :development)
+rescue Bundler::BundlerError => e
+  $stderr.puts e.message
+  $stderr.puts "Run `bundle install` to install missing gems"
+  exit e.status_code
+end
+require 'rake'
+
+require 'jeweler'
+Jeweler::Tasks.new do |gem|
+  # gem is a Gem::Specification... see http://docs.rubygems.org/read/chapter/20 for more options
+  gem.name = "rubyneat"
+  gem.homepage = "http://rubyneat.com"
+  gem.license = "MIT"
+  gem.summary = %Q{RubyNEAT NeuralEvolution of Augmenting Topologies}
+  gem.version = s_version
+  gem.description = %Q{
+  NEAT Algorithm for Ruby.
+  }
+  gem.email = "fred@lrcsoft.com"
+  gem.authors = ["Fred Mitchell"]
+  # dependencies defined in Gemfile
+
+  # Exclude the Neural Docs directory
+  gem.files.exclude 'Neural_Docs/*'
+end
+Jeweler::RubygemsDotOrgTasks.new
+
+require 'rspec/core'
+require 'rspec/core/rake_task'
+RSpec::Core::RakeTask.new(:spec) do |spec|
+  spec.pattern = FileList['spec/**/*_spec.rb']
+end
+
+RSpec::Core::RakeTask.new(:rcov) do |spec|
+  spec.pattern = 'spec/**/*_spec.rb'
+  spec.rcov = true
+end
+
+task :default => :spec
+
+require 'rdoc/task'
+Rake::RDocTask.new do |rdoc|
+  version = s_version
+
+  rdoc.rdoc_dir = 'rdoc'
+  rdoc.title = "rubyneat #{version}"
+  rdoc.rdoc_files.include('README*')
+  rdoc.rdoc_files.include('rnlib/**/*.rb')
+end

data/bin/neat

@@ -0,0 +1,83 @@
+#!/usr/bin/env ruby
+=begin rdoc
+=RubyNEAT Launcher
+
+=end
+require 'semver'
+
+# Be sure rnlib is added to the library path
+%w{ lib neater neater/rnlib }.each do |dir|
+  $:.unshift File.join([Dir.pwd, dir])
+end
+
+NEATER = File.join [Dir.pwd, "neater"]
+NEATGLOB = NEATER + '/*_neat.rb'
+
+require 'slop'
+require 'rubyneat'
+
+def list_neaters
+  Dir.glob(NEATGLOB).sort.each do |ne|
+    puts 'neat run ' + File.basename(ne).gsub(%r{_neat\.rb}, '')
+  end
+end
+
+def list_neurons
+  puts NEAT::Neuron.neuron_types.map{|n| n.name }.sort.join "\n"
+end
+
+opts = Slop.parse(strict: true, help: true) do
+  banner 'Usage: neat [commands] [options] ...'
+
+  on :version, 'Version information' do
+    run do |opts, args|
+      puts SemVer.find.format "%M.%m.%p%s"
+    end
+  end
+
+  command :console do
+    banner 'Usage: neat console [options]'
+    run do
+      # TODO Implement an interactive console
+      puts "Interactive Console NIY"
+    end
+  end
+
+  command :list do
+    banner 'Usage: neat list options'
+    on :n, :neaters, 'list available neaters (default)'
+    on :u, :neurons, 'list available Neuron types'
+    run do |opts, args|
+      opts.to_hash.map { |k, v| k }.reject{ |o| opts[o].nil? }.each do |o|
+        case o
+          when :neurons
+            list_neurons
+          when :neaters
+            list_neaters
+        end
+      end
+
+    end
+  end
+
+  command :run do
+    banner "Usage: neat run [options] neater_module ...\nFor a list of neater modules: neat list"
+    on :log=, 'Debugging level [info|warn|error|debug]'
+    on :v, :verbose=, 'Verbose mode', as: Integer
+
+    run do |opts, args|
+      NEAT::controller.verbosity = opts[:v].to_i unless opts[:v].nil?
+      eval %{$log.level = Logger::#{opts[:log].upcase}} unless opts[:log].nil?
+
+      args.map do |proj|
+        "#{proj}_neat.rb"
+      end.each do |file|
+        load file
+      end
+    end
+  end
+
+  run do |opts, args|
+    puts opts
+  end
+end

data/config/application.rb

@@ -0,0 +1,5 @@
+module RubyNEAT
+  class Application
+
+  end
+end

data/doc/ControllerPoint.html

@@ -0,0 +1,125 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+  "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
+  <head>
+    <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+<title>
+  Class: ControllerPoint
+  
+    &mdash; Documentation by YARD 0.8.7.3
+  
+</title>
+
+  <link rel="stylesheet" href="css/style.css" type="text/css" charset="utf-8" />
+
+  <link rel="stylesheet" href="css/common.css" type="text/css" charset="utf-8" />
+
+<script type="text/javascript" charset="utf-8">
+  hasFrames = window.top.frames.main ? true : false;
+  relpath = '';
+  framesUrl = "frames.html#!" + escape(window.location.href);
+</script>
+
+
+  <script type="text/javascript" charset="utf-8" src="js/jquery.js"></script>
+
+  <script type="text/javascript" charset="utf-8" src="js/app.js"></script>
+
+
+  </head>
+  <body>
+    <div id="header">
+      <div id="menu">
+  
+    <a href="_index.html">Index (C)</a> &raquo;
+    
+    
+    <span class="title">ControllerPoint</span>
+  
+
+  <div class="noframes"><span class="title">(</span><a href="." target="_top">no frames</a><span class="title">)</span></div>
+</div>
+
+      <div id="search">
+  
+    <a class="full_list_link" id="class_list_link"
+        href="class_list.html">
+      Class List
+    </a>
+  
+    <a class="full_list_link" id="method_list_link"
+        href="method_list.html">
+      Method List
+    </a>
+  
+    <a class="full_list_link" id="file_list_link"
+        href="file_list.html">
+      File List
+    </a>
+  
+</div>
+      <div class="clear"></div>
+    </div>
+
+    <iframe id="search_frame"></iframe>
+
+    <div id="content"><h1>Class: ControllerPoint
+  
+  
+  
+</h1>
+
+<dl class="box">
+  
+    <dt class="r1">Inherits:</dt>
+    <dd class="r1">
+      <span class="inheritName">Object</span>
+      
+        <ul class="fullTree">
+          <li>Object</li>
+          
+            <li class="next">ControllerPoint</li>
+          
+        </ul>
+        <a href="#" class="inheritanceTree">show all</a>
+      
+      </dd>
+    
+  
+  
+    
+  
+    
+      <dt class="r2">Includes:</dt>
+      <dd class="r2">Aquarium::DSL</dd>
+      
+    
+  
+  
+  
+    <dt class="r1 last">Defined in:</dt>
+    <dd class="r1 last">lib/rubyneat/foo.rb</dd>
+  
+</dl>
+<div class="clear"></div>
+
+
+
+
+
+
+
+
+
+  
+
+</div>
+
+    <div id="footer">
+  Generated on Mon Jan  6 11:16:36 2014 by
+  <a href="http://yardoc.org" title="Yay! A Ruby Documentation Tool" target="_parent">yard</a>
+  0.8.7.3 (ruby-2.0.0).
+</div>
+
+  </body>
+</html>