rubyneat 0.3.5.alpha.3 → 0.3.5.alpha.5

checksums.yaml

@@ -1,7 +1,7 @@
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data/.semver

@@ -2,4 +2,4 @@
 :major: 0
 :minor: 3
 :patch: 5
-:special: ".alpha.3"
+:special: ".alpha.5"

data/Gemfile

@@ -4,30 +4,30 @@ source 'https://rubygems.org'
 
 ruby '2.1.1'
 
-gem 'mongo'
-gem 'bson_ext'
-gem 'distribution'
+gem 'mongo', '~> 1', require: false
+gem 'bson_ext', '~> 1', require: false
+gem 'distribution', '~> 0'
 
 #TODO: Check out this for a repacement of of statistics2
 #TODO: https://github.com/thirtysixthspan/descriptive_statistics
-gem 'statistics2'
+gem 'statistics2', '~> 0'
 
-gem 'debase'
-gem 'aquarium'
-gem 'thor'
-gem 'awesome_print'
-gem 'deep_dive'
+gem 'debase', '~> 0'
+gem 'aquarium', '~> 0'
+gem 'thor', '~> 0'
+gem 'awesome_print', '~> 1'
+gem 'deep_dive', '~> 0'
 
 group :development do
-  gem 'rspec'
-  gem 'yard'
-  gem 'guard'
-  gem 'guard-rspec'
-  gem 'semver'
-  gem "jeweler", "~> 1.8.7"
-  gem "simplecov"
+  gem 'rspec', '~> 2'
+  gem 'yard', '~> 0'
+  gem 'guard', '~> 2'
+  gem 'guard-rspec', '~> 4'
+  gem 'semver', '~> 1'
+  gem "jeweler", "~> 2"
+  gem "simplecov", '~> 0'
   #gem 'debugger'
-  gem 'ruby-debug-ide'
+  gem 'ruby-debug-ide', '~> 0'
 end
 
 #======================================================
@@ -35,7 +35,7 @@ end
 
 # For demo purposes, we include the gosu library, but
 # don't want this to be part of the mainstream.
-gem 'gosu', require: false
+gem 'gosu', '~> 0', require: false
 
 # So we can generate some nice graphics.
-gem 'rubyvis', require: false
+gem 'rubyvis', '~> 0', require: false

data/Gemfile.lock

@@ -19,20 +19,23 @@ GEM
     debugger-ruby_core_source (1.3.2)
     deep_dive (0.1.0)
       debase
+    descendants_tracker (0.0.4)
+      thread_safe (~> 0.3, >= 0.3.1)
     diff-lcs (1.2.5)
     distribution (0.7.0)
     docile (1.1.3)
-    faraday (0.8.9)
-      multipart-post (~> 1.2.0)
+    faraday (0.9.0)
+      multipart-post (>= 1.2, < 3)
     ffi (1.9.3)
     formatador (0.2.4)
     git (1.2.6)
-    github_api (0.10.1)
-      addressable
-      faraday (~> 0.8.1)
+    github_api (0.11.3)
+      addressable (~> 2.3)
+      descendants_tracker (~> 0.0.1)
+      faraday (~> 0.8, < 0.10)
       hashie (>= 1.2)
-      multi_json (~> 1.4)
-      nokogiri (~> 1.5.2)
+      multi_json (>= 1.7.5, < 2.0)
+      nokogiri (~> 1.6.0)
       oauth2
     gosu (0.7.50)
     guard (2.6.0)
@@ -46,13 +49,13 @@ GEM
       rspec (>= 2.14, < 4.0)
     hashie (2.1.1)
     highline (1.6.21)
-    jeweler (1.8.8)
+    jeweler (2.0.1)
       builder
-      bundler (~> 1.0)
+      bundler (>= 1.0)
       git (>= 1.2.5)
-      github_api (= 0.10.1)
+      github_api
       highline (>= 1.6.15)
-      nokogiri (= 1.5.10)
+      nokogiri (>= 1.5.10)
       rake
       rdoc
     json (1.8.1)
@@ -65,13 +68,15 @@ GEM
       rb-inotify (>= 0.9)
     lumberjack (1.0.5)
     method_source (0.8.2)
+    mini_portile (0.5.3)
     mongo (1.10.0)
       bson (~> 1.10.0)
     multi_json (1.9.2)
     multi_xml (0.5.5)
-    multipart-post (1.2.0)
+    multipart-post (2.0.0)
     nio4r (1.0.0)
-    nokogiri (1.5.10)
+    nokogiri (1.6.1)
+      mini_portile (~> 0.5.0)
     oauth2 (0.9.3)
       faraday (>= 0.8, < 0.10)
       jwt (~> 0.1.8)
@@ -83,7 +88,7 @@ GEM
       method_source (~> 0.8)
       slop (~> 3.4)
     rack (1.5.2)
-    rake (10.2.2)
+    rake (10.3.1)
     rb-fsevent (0.9.4)
     rb-inotify (0.9.3)
       ffi (>= 0.5.0)
@@ -109,6 +114,7 @@ GEM
     slop (3.5.0)
     statistics2 (0.54)
     thor (0.19.1)
+    thread_safe (0.3.3)
     timers (1.1.0)
     yard (0.8.7.4)
 
@@ -116,22 +122,22 @@ 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
-  rubyvis
-  semver
-  simplecov
-  statistics2
-  thor
-  yard
+  aquarium (~> 0)
+  awesome_print (~> 1)
+  bson_ext (~> 1)
+  debase (~> 0)
+  deep_dive (~> 0)
+  distribution (~> 0)
+  gosu (~> 0)
+  guard (~> 2)
+  guard-rspec (~> 4)
+  jeweler (~> 2)
+  mongo (~> 1)
+  rspec (~> 2)
+  ruby-debug-ide (~> 0)
+  rubyvis (~> 0)
+  semver (~> 1)
+  simplecov (~> 0)
+  statistics2 (~> 0)
+  thor (~> 0)
+  yard (~> 0)

data/README.md

@@ -0,0 +1,66 @@
+## RubyNEAT -- Neural Evolution of Augmenting Topologies
+
+For the latest docs, please see http://rubyneat.com
+
+RubyNEAT is under intense development, and then will be under intense documentation, as this is
+expected to be a full blown pure Ruby implementation of the NEAT algorithm by Kenneth Stanley:
+
+http://www.cs.ucf.edu/~kstanley/
+
+## Quick and Dirty Docs
+
+There is an (extreme) alpha RubyGEM. Just do:
+
+ gem install rubyneat --pre
+
+Then type:
+
+  neat
+
+to see the list of commands. The workflow aspect of Rails is loosely mirrored here.
+
+To generate a new NEAT project, type:
+
+  neat new PROJECTNAME
+
+and a project directory will be created. Cd into that directory, and type:
+
+  neat generate neater NEATERNAME
+
+and a scaffold Neater will be generated. Note that this generator is still
+in alpha, but improvements are coming shortly.
+
+## Also Note
+
+For now, see
+
+https://github.com/flajann2/rubyneat
+
+for the Github version, and this will probably be the better option until this
+gets out of alpha. There are a couple of example Neaters there (one of which is
+still in development). Basic, but will be a good example of how to implement your own
+Neater. Eventually all will be fully documented.
+
+## Copyright Notice
+
+This code is released under the MIT license:
+
+Copyright (c) 2014 LRCSoft.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/Rakefile

@@ -26,14 +26,31 @@ Jeweler::Tasks.new do |gem|
   gem.summary = %Q{RubyNEAT NeuralEvolution of Augmenting Topologies}
   gem.version = s_version
   gem.description = %Q{
-  NEAT Algorithm for Ruby.
+  RubyNEAT -- Neural Evolution of Augmenting Topologies for Ruby.
+  By way of an enhanced form of Genetic Algorithms -- the NEAT algorithm,
+  populations of neural nets are evolved to handle pre-defined goals.
+
+  RubyNEAT is the first implementation of the NEAT algorithm for Ruby, and
+  it leverages Ruby's power to implement the NEAT algorithm in a way that would
+  be difficult to do in other languages. The 'activation function' is largely
+  standalone. Basically, activation is achieved by functional programming.
+
+  Meaning, once your network is evolved, you can extract it as source code you
+  can then utilize without the RubyNEAT engine.
+
+  RubyNEAT can be used for nearly any Machine Learning task you can dream of,
+  because it's also extensible and modular. See http://rubyneat.com for the
+  details.
   }
   gem.email = "fred@lrcsoft.com"
   gem.authors = ["Fred Mitchell"]
   # dependencies defined in Gemfile
 
   # Exclude the Neural Docs directory
-  gem.files.exclude 'Neural_Docs/*'
+  gem.files.exclude 'Neural_Docs/*', 'foo/**/*', 'rdoc/*',
+                    '.idea/**/*', '.idea/**/.*', '.yardoc/**/*',
+                    'public/**/*', 'neater/**/*', 'doc/**/*',
+                    'public/**/.*', 'Guardfile'
 end
 Jeweler::RubygemsDotOrgTasks.new
 

data/bin/neat

@@ -1,70 +1,14 @@
 #!/usr/bin/env ruby
-=begin rdoc
-=RubyNEAT Launcher based on thor
-
-=end
 
 require 'thor'
 require 'semver'
 
 # Be sure rnlib is added to the library path
+neatpath = File.expand_path '..', File.dirname(__FILE__)
 %w{ lib neater neater/rnlib }.each do |dir|
-  $:.unshift File.join([Dir.pwd, dir])
+  $:.unshift File.join([neatpath, dir])
 end
 
-NEATER = File.join [Dir.pwd, "neater"]
-NEATGLOB = NEATER + '/*_neat.rb'
-
-require 'rubyneat'
-
-module RubyNEAT
-  module Cli
-
-    class List < Thor
-      desc 'neaters', 'List all Neaters.'
-      def neaters
-        Dir.glob(NEATGLOB).sort.each do |ne|
-          puts 'neat runeater ' + File.basename(ne).gsub(%r{_neat\.rb}, '')
-        end
-      end
-
-      desc 'neurons', 'List all Neurons.'
-      def neurons
-        puts NEAT::Neuron.neuron_types.map{|n| n.name }.sort.join "\n"
-      end
-    end
-
-    class Main < Thor
-      class_option :verbose, type: :string, banner: '[1|2|3]'
-
-      desc 'list <type>', 'List the requested type.'
-      subcommand 'list', List
-
-      desc 'version', 'Display RubyNEAT version'
-      def version
-        puts SemVer.find.format "%M.%m.%p%s"
-      end
-
-      desc 'console', 'Run RubyNEAT interactively'
-      def console
-        #TODO: Finish the console
-        puts "Not Implemented Yet."
-      end
-
-      desc 'runeater <neater> [<neater> <neater> ...] [OPTS]', 'Run a Neater'
-      option :log, type: :string, banner: 'info|warn|debug|error'
-      def runeater(*neaters)
-        NEAT::controller.verbosity = options[:verbose].to_i if options[:verbose]
-        eval %{$log.level = Logger::#{options[:log].upcase}} if options[:log]
-
-        neaters.map do |neater|
-          "#{neater}_neat.rb"
-        end.each do |file|
-          load file
-        end
-      end
-    end
-  end
-end
+require 'rubyneat/cli'
 
-RubyNEAT::Cli::Main.start(ARGV)
+RubyNEAT::Cli::Main.start

data/lib/rubyneat/cli.rb

@@ -0,0 +1,5 @@
+NEATER = File.join [Dir.pwd, "neater"]
+NEATGLOB = NEATER + '/*_neat.rb'
+
+require 'rubyneat/cli/main'
+require 'rubyneat'

data/lib/rubyneat/cli/generate.rb

@@ -0,0 +1,131 @@
+require 'ostruct'
+
+module RubyNEAT
+  module Cli
+    module Generator
+      module GenHelpers
+        def source_root
+          File.dirname(__FILE__) + "/templates/generate"
+        end
+      end
+
+      class NewProject < Thor::Group
+        include Thor::Actions
+        extend GenHelpers
+        desc "Generate a new NEAT Project."
+
+        argument :name, type: :string, desc: 'Name of the NEAT project'
+        attr_accessor :ruby
+
+        def create_project_directory
+          empty_directory name.snake
+        end
+
+        def create_project_directories
+          inside name.snake do
+            %w{neater lib config tmp log bin}.
+            each {|dir| empty_directory dir}
+          end
+        end
+
+        def create_project_root_files
+          @ruby = OpenStruct.new version: RUBY_VERSION,
+                                 engine: RUBY_ENGINE,
+                                 platform: RUBY_PLATFORM
+          %w{Gemfile README.md}.
+            map{ |pfile| [pfile, "#{name.snake}/#{pfile}"] }.
+            each{ |source, destination| template source, destination }
+        end
+      end
+
+      class Neater < Thor::Group
+        include Thor::Actions
+        extend GenHelpers
+        desc "Generate a Neater"
+
+        argument :name, type: :string, desc: 'Name of the Neater'
+        argument :nparams, type: :hash, desc: 'Neuron Parameters', default: {}
+
+        attr_accessor :description, :inputs, :outputs, :hidden, :bias
+
+        def create_neater_file
+          setup_neuron_parameters
+          @description ||= "#{name.camel_case} Neater"
+          template 'neater', "neater/#{name.snake}_neat.rb"
+        end
+
+        private
+        # We need to create the Input Neurons (including the bias neuron),
+        # the Output Neurons, and the Hidden neurons.
+        # attr:name
+        # attr:n1:t1,n2:t2,...
+        def setup_neuron_parameters
+          params = {
+                      inputs:      {in1: 'input', in2: 'input'},
+                      outputs:     {out: 'tanh'},
+                      hidden:      {tanh: nil},
+                      bias:        'bias',
+                      description: 'Neater scaffold'
+                  }.merge(nparams.inject({}) { |memo, (k,v)|
+                      memo[k.to_sym] = Hash[v.split(',').map{|q| q.split(':') }].
+                        inject({}) {|mmemo, (kk, vv)| mmemo[kk.to_sym] = vv; mmemo}
+                      memo
+                    })
+          puts params
+          params.each do |attr, o|
+            instance_variable_set("@#{attr}", case attr
+                                                when :inputs, :outputs
+                                                  o.inject({}){|memo, (ky, vl)|
+                                                    memo[ky] = unless vl.nil?
+                                                                vl.camel_case
+                                                              else
+                                                                case attr
+                                                                  when :inputs; 'Input'
+                                                                  when :outputs; 'Output'
+                                                                end
+                                                              end + 'Neuron'
+                                                    memo
+                                                  }
+                                                when :bias
+                                                  unless o.nil?
+                                                    o.camel_case
+                                                  else
+                                                    'Bias'
+                                                  end + 'Neuron'
+                                                when :hidden
+                                                  o.map{|hk, ignore| hk.to_s.camel_case + 'Neuron' }
+                                                when :description; o.keys.first
+                                                else o
+                                              end)
+            puts attr
+          end
+        end
+      end
+    end
+
+    class Generate < Thor
+      register Generator::Neater, 'neater', 'neater', 'Generates a neater'
+      register Generator::NewProject, 'new', 'new', 'Generates a new NEAT project'
+    end
+  end
+end
+
+class String
+  def camel_case
+    return self if self !~ /_| / && self =~ /[A-Z]+.*/
+    split(/_| /).map{|e| e.capitalize}.join
+  end
+
+  def camel_case_lower
+    self.split(/_| /).inject([]){ |buffer,e| buffer.push(buffer.empty? ? e : e.capitalize) }.join
+  end
+
+  def snake
+    self.gsub(/::/, '/').
+        gsub(/([A-Z]+)([A-Z][a-z])/,'\1_\2').
+        gsub(/([a-z\d])([A-Z])/,'\1_\2').
+        tr("-", "_").
+        tr(' ', '_').
+        downcase
+  end
+end