answer-factory 0.0.9 → 0.0.10

data/Rakefile

@@ -15,6 +15,7 @@ begin
     gemspec.add_dependency('nudge', '>= 0.2')
     gemspec.add_dependency('thor', '>= 0.13')
     gemspec.add_dependency('couchrest', '>= 0.33')
+    gemspec.add_dependency('configatron', '>= 2.6.2')
     gemspec.add_dependency('fakeweb', '>= 0.33')
     gemspec.add_dependency('sinatra', '>= 0.9.4')
     gemspec.add_dependency('activesupport', '>= 2.3.5')

data/Thorfile

@@ -33,25 +33,28 @@ class New_Nudge_Type < Thor::Group
   
   def create_lib_file
     filename = "#{camelcased_type_name}.rb"
-    template("#{nudge_gem_path}/templates/nudge_type_class.erb", "#{New_Nudge_Type.source_root}/lib/nudge/types/#{filename}")
+    template("#{nudge_gem_path}/templates/nudge_type_class.erb",
+      "#{New_Nudge_Type.source_root}/lib/nudge/types/#{filename}")
   end
-  
+
   def create_lib_spec
     filename = "#{camelcased_type_name}_spec.rb"
-    template("#{nudge_gem_path}/templates/nudge_type_spec.erb", "#{New_Nudge_Type.source_root}/spec/#{filename}")
+    template("#{nudge_gem_path}/templates/nudge_type_spec.erb",
+      "#{New_Nudge_Type.source_root}/spec/#{filename}")
   end  
-  
+
   def create_instructions
     suite = ["define", "equal_q", "duplicate", "flush", "pop",
       "random", "rotate", "shove", "swap", "yank", "yankdup"]
-    
+  
     suite.each do |inst|
       @core = "#{typename_root}_#{inst}"
       filename = "#{@core}.rb"
       @instname = "#{@core.camelize}Instruction"
       @type = typename_root
       @camelized_type = New_Nudge_Type.type_name(typename_root)
-      template("#{nudge_gem_path}/templates/nudge_#{inst}_instruction.erb", "#{New_Nudge_Type.source_root}/lib/nudge/instructions/#{filename}")
+      template("#{nudge_gem_path}/templates/nudge_#{inst}_instruction.erb",
+        "#{New_Nudge_Type.source_root}/lib/nudge/instructions/#{filename}")
     end
   end
 end

data/VERSION

@@ -1 +1 @@
-0.0.9
+0.0.10

data/answer-factory.gemspec

@@ -5,11 +5,11 @@
 
 Gem::Specification.new do |s|
   s.name = %q{answer-factory}
-  s.version = "0.0.9"
+  s.version = "0.0.10"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["Bill Tozier", "Trek Glowacki", "Jesse Sielaff"]
-  s.date = %q{2010-05-02}
+  s.date = %q{2010-05-06}
   s.default_executable = %q{answer-factory}
   s.description = %q{The pragmaticgp gem provides a simple framework for building, running and managing genetic programming experiments which automatically discover algorithms and equations to solve user-defined problems.}
   s.email = %q{bill@vagueinnovation.com}
@@ -32,9 +32,21 @@ Gem::Specification.new do |s|
      "lib/answers/batch.rb",
      "lib/factories/factory.rb",
      "lib/factories/workstation.rb",
-     "lib/operators/basic_operators.rb",
-     "lib/operators/evaluators.rb",
-     "lib/operators/samplers_and_selectors.rb",
+     "lib/operators/all_duplicated_genomes_sampler.rb",
+     "lib/operators/any_one_sampler.rb",
+     "lib/operators/dominated_quantile_selector.rb",
+     "lib/operators/infrastructure.rb",
+     "lib/operators/most_dominated_subset_sampler.rb",
+     "lib/operators/nondominated_subset_selector.rb",
+     "lib/operators/point_crossover_operator.rb",
+     "lib/operators/point_delete_operator.rb",
+     "lib/operators/point_mutation_operator.rb",
+     "lib/operators/program_point_count_evaluator.rb",
+     "lib/operators/random_guess_operator.rb",
+     "lib/operators/resample_and_clone_operator.rb",
+     "lib/operators/resample_values_operator.rb",
+     "lib/operators/test_case_evaluator.rb",
+     "lib/operators/uniform_backbone_crossover_operator.rb",
      "pkg/nudgegp-0.0.1.gem",
      "readme.md",
      "spec/answer_spec.rb",
@@ -102,6 +114,7 @@ Gem::Specification.new do |s|
       s.add_runtime_dependency(%q<nudge>, [">= 0.2"])
       s.add_runtime_dependency(%q<thor>, [">= 0.13"])
       s.add_runtime_dependency(%q<couchrest>, [">= 0.33"])
+      s.add_runtime_dependency(%q<configatron>, [">= 2.6.2"])
       s.add_runtime_dependency(%q<fakeweb>, [">= 0.33"])
       s.add_runtime_dependency(%q<sinatra>, [">= 0.9.4"])
       s.add_runtime_dependency(%q<activesupport>, [">= 2.3.5"])
@@ -109,6 +122,7 @@ Gem::Specification.new do |s|
       s.add_dependency(%q<nudge>, [">= 0.2"])
       s.add_dependency(%q<thor>, [">= 0.13"])
       s.add_dependency(%q<couchrest>, [">= 0.33"])
+      s.add_dependency(%q<configatron>, [">= 2.6.2"])
       s.add_dependency(%q<fakeweb>, [">= 0.33"])
       s.add_dependency(%q<sinatra>, [">= 0.9.4"])
       s.add_dependency(%q<activesupport>, [">= 2.3.5"])
@@ -117,6 +131,7 @@ Gem::Specification.new do |s|
     s.add_dependency(%q<nudge>, [">= 0.2"])
     s.add_dependency(%q<thor>, [">= 0.13"])
     s.add_dependency(%q<couchrest>, [">= 0.33"])
+    s.add_dependency(%q<configatron>, [">= 2.6.2"])
     s.add_dependency(%q<fakeweb>, [">= 0.33"])
     s.add_dependency(%q<sinatra>, [">= 0.9.4"])
     s.add_dependency(%q<activesupport>, [">= 2.3.5"])

data/lib/answer-factory.rb

@@ -8,9 +8,21 @@ require 'couchrest'
 require 'answers/answer'
 require 'answers/batch'
 
-require 'operators/basic_operators'
+require 'operators/infrastructure'
+require 'operators/random_guess_operator'
+require 'operators/resample_and_clone_operator'
+require 'operators/resample_values_operator'
+require 'operators/uniform_backbone_crossover_operator'
+require 'operators/point_crossover_operator'
+require 'operators/point_delete_operator'
+require 'operators/point_mutation_operator'
+
+require 'operators/test_case_evaluator'
+require 'operators/program_point_count_evaluator'
+
+
+
 require 'operators/samplers_and_selectors'
-require 'operators/evaluators'
 
 require 'factories/factory'
 require 'factories/workstation'

data/lib/answers/answer.rb

@@ -4,7 +4,7 @@ module AnswerFactory
   class Answer
     attr_accessor :scores, :tags
     attr_reader :draft_blueprint, :program, :timestamp, :ancestors
-    attr_reader :initialization_options, :progress
+    attr_reader :initialization_options, :progress, :couch_id
     
     
     def initialize(blueprint, options = {})
@@ -12,11 +12,12 @@ module AnswerFactory
         blueprint.kind_of?(String) || blueprint.kind_of?(NudgeProgram)
       build_from_blueprint!(blueprint)
       
-      @scores = Hash.new do |hash, key|
+      @scores = options[:scores] || Hash.new do |hash, key|
         raise ArgumentError, "scores must use symbols as keys" unless key.kind_of?(Symbol)
         nil
       end
       @timestamp = Time.now
+      @couch_id = options[:couch_id] || ""
       @initialization_options = options
       @progress = options[:progress] || 0
       @ancestors = options[:ancestors] || []
@@ -121,6 +122,19 @@ module AnswerFactory
   
   
   def data
-    {'blueprint' => self.blueprint, 'tags' => self.tags, 'scores' => self.scores, 'timestamp' => @timestamp}
+    {'blueprint' => self.blueprint, 'tags' => self.tags, 'scores' => self.scores, 'progress' => @progress, 'timestamp' => @timestamp}
+  end
+  
+  
+  def from_serial_hash(hash)
+    value_hash = hash["value"]
+    tag_set = Set.new(value_hash["tags"].collect {|t| t.to_sym})
+    symbolized_scores = value_hash["scores"].inject({}) {|memo,(k,v)| memo[k.to_sym] = v; memo }
+    
+    Answer.new(value_hash["blueprint"],
+      couch_id:value_hash["_id"],
+      tags:tag_set,
+      scores:symbolized_scores,
+      progress:value_hash["progress"])
   end
 end

data/lib/answers/batch.rb

@@ -34,11 +34,23 @@ module AnswerFactory
     end
     
     
-    def self.load_tagged_answers(couchdb_uri, tag)
+    def self.load_from_couch(couchdb_uri, design_doc)
       raise ArgumentError, "#{couchdb_uri} is not a String" unless couchdb_uri.kind_of?(String)
-      raise ArgumentError, "#{tag} is not a String" unless tag.kind_of?(String)
+      raise ArgumentError, "#{design_doc} is not a String" unless design_doc.kind_of?(String)
+      
+      batch = Batch.new
+      
       db = CouchRest.database(couchdb_uri) # add the view document and key here
-      return Batch.new
+      begin
+        response = db.view(design_doc)
+        response["rows"].each do |hash|
+          puts hash["values"]
+          batch << Answer.from_serial_hash(hash)
+        end
+      rescue JSON::ParserError => e
+        puts "Batch not read due to JSON ParserError: '#{e.message}'"
+      end
+      return batch
     end
     
     

data/lib/factories/workstation.rb

@@ -1,8 +1,10 @@
 module AnswerFactory
+  
   class Workstation
     attr_reader :name, :capacity, :couchdb_uri, :factory_name
     attr_accessor :downstream_stations
     attr_accessor :answers
+    attr_accessor :build_sequence
     
     
     def initialize(name, options = {})
@@ -11,8 +13,9 @@ module AnswerFactory
       @factory_name = options[:factory_name] || 'factory_name'
       @couchdb_uri = options[:couchdb_uri] || "http://127.0.0.1:5984/#{@factory_name}"
       @capacity = options[:capacity] || 100
+      @build_sequence = options[:build_sequence] || Array.new
       @downstream_stations = Array.new
-      @answers = Array.new
+      @answers = Batch.new
     end
     
     
@@ -23,6 +26,52 @@ module AnswerFactory
     end
     
     
+    def gather_mine
+      @answers += Batch.load_from_couch(@couchdb_uri, "#{name}/current")
+    end
+    
+    
+    def build!
+      # Workstation is a superclass; the default behavior (doing nothing)
+      # should be overridden in a subclass definition
+    end
+    
+    
+    def process_with(operator)
+      raise ArgumentError, "Workstation#process_with cannot process with a #{operator.class}" unless
+        operator.kind_of?(SearchOperator)
+      operator.generate(@answers)
+    end
+    
+    
+    def ship!
+      # Workstation is a superclass; the default behavior (doing nothing)
+      # should be overridden in a subclass definition
+    end
+    
+    
+    def ship_to(where, &filter)
+      raise ArgumentError, "Workstation#ship_to cannot ship to a #{where.class}" unless
+        where.kind_of?(Symbol)
+      (@answers.find_all &filter).each {|a| a.add_tag where; a.remove_tag @name}
+    end
+    
+    
+    def scrap!
+      # Workstation is a superclass; the default behavior (doing nothing)
+      # should be overridden in a subclass definition
+    end
+    
+    
+    def scrap_if(why, &filter)
+      (@answers.find_all &filter).each {|a| a.add_tag :SCRAP; a.remove_tag @name}
+    end
+    
+    def scrap_everything
+      scrap_if("everything dies") {|x| true}
+    end
+    
+    
     def cycle
       self.receive!
       self.build!

data/lib/operators/all_duplicated_genomes_sampler.rb

@@ -0,0 +1,14 @@
+module AnswerFactory
+  class AllDuplicatedGenomesSampler < Sampler
+    def generate(crowd)
+      result = Batch.new
+      clustered = diversity_classes(crowd)
+      clustered.each do |blueprint, array|
+        if array.length > 1
+          result.concat array
+        end
+      end
+      return result
+    end
+  end
+end

data/lib/operators/any_one_sampler.rb

@@ -0,0 +1,7 @@
+module AnswerFactory
+  class AnyOneSampler < Sampler
+    def generate(crowd)
+      result = Batch[crowd.sample]
+    end
+  end
+end

data/lib/operators/dominated_quantile_selector.rb

@@ -0,0 +1,16 @@
+module AnswerFactory
+  class DominatedQuantileSampler < Sampler
+    def generate(crowd, proportion = 0.5, template = all_shared_scores(crowd))
+      classified = domination_classes(crowd, template)
+      increasing_grades = classified.keys.sort {|a,b| b <=> a}
+      partial_ordering = []
+      increasing_grades.each {|grade| partial_ordering += classified[grade]}
+      how_many = (crowd.length * proportion).ceil
+      
+      result = Batch.new
+      partial_ordering[0...how_many].each {|dude| result << dude} unless how_many == 0
+      return result
+    end
+  end
+  
+end

data/lib/operators/infrastructure.rb

@@ -0,0 +1,74 @@
+module AnswerFactory
+  
+  # Abstract class that from which specific SearchOperator subclasses inherit initialization
+  
+  class SearchOperator
+    attr_accessor :incoming_options
+    
+     def initialize(options={})
+       @incoming_options = options
+     end
+  end
+  
+  
+  class Evaluator < SearchOperator
+    attr_accessor :score_label
+    
+    def initialize(params = {})
+      raise(ArgumentError, "Evaluators must have a score_label") if params[:score_label] == nil
+      @score_label = params[:score_label]
+    end
+  end
+  
+  
+  class Sampler < SearchOperator
+    def initialize (params = {})
+      super
+    end
+    
+    def all_known_criteria(crowd)
+      union = []
+      crowd.each do |dude|
+        union |= dude.known_criteria
+      end
+      return union
+    end
+    
+    
+    def all_shared_scores(crowd)
+      intersection = self.all_known_criteria(crowd)
+      crowd.each do |dude|
+        intersection = intersection & dude.known_criteria
+      end
+      return intersection
+    end
+    
+    
+    def domination_classes(crowd, template = all_shared_scores(crowd))
+      result = Hash.new()
+      
+      crowd.each_index do |i|
+        dominated_by = 0
+        
+        crowd.each_index do |j|
+          dominated_by += 1 if crowd[i].dominated_by?(crowd[j], template)
+        end
+        
+        result[dominated_by] ||= []
+        result[dominated_by].push crowd[i]
+      end
+      
+      return result
+    end
+    
+    
+    def diversity_classes(crowd)
+      result = Hash.new()
+      crowd.each do |dude|
+        result[dude.program.tidy] ||= []
+        result[dude.program.tidy] << dude
+      end
+      return result
+    end
+  end
+end

data/lib/operators/most_dominated_subset_sampler.rb

@@ -0,0 +1,13 @@
+module AnswerFactory
+  
+  class MostDominatedSubsetSampler < Sampler
+    def generate(crowd, template = all_shared_scores(crowd))
+      result = Batch.new
+      classified = domination_classes(crowd, template)
+      worst_key = classified.keys.sort[-1]
+      classified[worst_key].each {|bad_dude| result.push bad_dude}
+      return result
+    end
+  end
+  
+end

data/lib/operators/nondominated_subset_selector.rb

@@ -0,0 +1,17 @@
+module AnswerFactory
+  class NondominatedSubsetSelector < Sampler
+    
+    def generate(crowd, template = all_shared_scores(crowd))
+      result = Batch.new
+      crowd.each do |answer|
+        dominated = false
+        crowd.each do |other_answer|
+          dominated ||= answer.dominated_by?(other_answer, template)
+        end
+        result << answer unless dominated
+      end
+      return result
+    end
+  end
+  
+end

data/lib/operators/point_crossover_operator.rb

@@ -0,0 +1,24 @@
+module AnswerFactory
+  class PointCrossoverOperator < SearchOperator
+    def generate(crowd, howManyBabies = 1)
+      raise(ArgumentError) if !crowd.kind_of?(Array)
+      raise(ArgumentError) if crowd.empty?
+      crowd.each {|dude| raise(ArgumentError) if !dude.kind_of?(Answer) }
+      
+      result = Batch.new
+      production = crowd.length*howManyBabies
+      production.times do
+        mom = crowd.sample
+        dad = crowd.sample
+        mom_receives = rand(mom.points) + 1
+        dad_donates = rand(dad.points) + 1
+        
+        baby_blueprint = mom.replace_point_or_clone(mom_receives,dad.program[dad_donates])
+        baby = Answer.new(baby_blueprint,
+          progress:[mom.progress,dad.progress].max + 1)
+        result << baby
+      end
+      return result
+    end
+  end
+end