answer-factory 0.0.14 → 0.0.15

data/VERSION

@@ -1 +1 @@
-0.0.14
+0.0.15

data/answer-factory.gemspec

@@ -5,11 +5,11 @@
 
 Gem::Specification.new do |s|
   s.name = %q{answer-factory}
-  s.version = "0.0.14"
+  s.version = "0.0.15"
 
   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{2010-05-07}
+  s.date = %q{2010-05-10}
   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}
@@ -31,44 +31,24 @@ Gem::Specification.new do |s|
      "lib/answers/batch.rb",
      "lib/factories/factory.rb",
      "lib/factories/workstation.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",
+     "lib/machines/any_one.rb",
+     "lib/machines/build_random.rb",
+     "lib/machines/evaluate_simple_score.rb",
+     "lib/machines/infrastructure.rb",
+     "lib/machines/mutate_footnotes.rb",
+     "lib/machines/select_nondominated.rb",
      "readme.md",
      "spec/answer_spec.rb",
      "spec/batch_spec.rb",
      "spec/factories/factory_spec.rb",
      "spec/factories/workstation_spec.rb",
-     "spec/integration_specs/activate_integration.rb",
-     "spec/integration_specs/build_integration.rb",
-     "spec/integration_specs/thor_integration.rb",
-     "spec/operators/any_one_sampler_spec.rb",
-     "spec/operators/dominated_quantile_spec.rb",
-     "spec/operators/duplicate_genomes_spec.rb",
-     "spec/operators/evaluators/program_point_evaluator_spec.rb",
-     "spec/operators/evaluators/test_case_evaluator_spec.rb",
-     "spec/operators/infrastructure_spec.rb",
-     "spec/operators/most_dominated_subset_spec.rb",
-     "spec/operators/nondominated_subset_spec.rb",
-     "spec/operators/pointCrossover_spec.rb",
-     "spec/operators/pointDeletion_spec.rb",
-     "spec/operators/pointMutation_spec.rb",
-     "spec/operators/random_guess_spec.rb",
-     "spec/operators/resample_and_clone_spec.rb",
-     "spec/operators/resample_values_spec.rb",
-     "spec/operators/uniformBackboneCrossover_spec.rb",
+     "spec/integration_specs/couch_db_integration.rb",
+     "spec/machines/any_one_spec.rb",
+     "spec/machines/build_random_spec.rb",
+     "spec/machines/evaluate_simple_score_spec.rb",
+     "spec/machines/infrastructure_spec.rb",
+     "spec/machines/mutate_footnotes_spec.rb",
+     "spec/machines/select_nondominated_spec.rb",
      "spec/spec_helper.rb",
      "tasks/setup_factory.thor",
      "templates/answer_factory_activate_template.erb",
@@ -85,24 +65,13 @@ Gem::Specification.new do |s|
      "spec/batch_spec.rb",
      "spec/factories/factory_spec.rb",
      "spec/factories/workstation_spec.rb",
-     "spec/integration_specs/activate_integration.rb",
-     "spec/integration_specs/build_integration.rb",
-     "spec/integration_specs/thor_integration.rb",
-     "spec/operators/any_one_sampler_spec.rb",
-     "spec/operators/dominated_quantile_spec.rb",
-     "spec/operators/duplicate_genomes_spec.rb",
-     "spec/operators/evaluators/program_point_evaluator_spec.rb",
-     "spec/operators/evaluators/test_case_evaluator_spec.rb",
-     "spec/operators/infrastructure_spec.rb",
-     "spec/operators/most_dominated_subset_spec.rb",
-     "spec/operators/nondominated_subset_spec.rb",
-     "spec/operators/pointCrossover_spec.rb",
-     "spec/operators/pointDeletion_spec.rb",
-     "spec/operators/pointMutation_spec.rb",
-     "spec/operators/random_guess_spec.rb",
-     "spec/operators/resample_and_clone_spec.rb",
-     "spec/operators/resample_values_spec.rb",
-     "spec/operators/uniformBackboneCrossover_spec.rb",
+     "spec/integration_specs/couch_db_integration.rb",
+     "spec/machines/any_one_spec.rb",
+     "spec/machines/build_random_spec.rb",
+     "spec/machines/evaluate_simple_score_spec.rb",
+     "spec/machines/infrastructure_spec.rb",
+     "spec/machines/mutate_footnotes_spec.rb",
+     "spec/machines/select_nondominated_spec.rb",
      "spec/spec_helper.rb"
   ]
 

data/lib/answer-factory.rb

@@ -9,22 +9,14 @@ require 'couchrest'
 require 'answers/answer'
 require 'answers/batch'
 
-require 'operators/infrastructure'
-
-require 'operators/all_duplicated_genomes_sampler'
-require 'operators/any_one_sampler'
-require 'operators/dominated_quantile_selector'
-require 'operators/most_dominated_subset_sampler'
-require 'operators/nondominated_subset_selector'
-require 'operators/point_crossover_operator'
-require 'operators/point_delete_operator'
-require 'operators/point_mutation_operator'
-require 'operators/program_point_count_evaluator'
-require 'operators/random_guess_operator'
-require 'operators/resample_and_clone_operator'
-require 'operators/resample_values_operator'
-require 'operators/test_case_evaluator'
-require 'operators/uniform_backbone_crossover_operator'
+require 'machines/infrastructure'
+require 'machines/any_one'
+require 'machines/build_random'
+require 'machines/evaluate_simple_score'
+require 'machines/select_nondominated'
+require 'machines/mutate_footnotes'
+
+
 
 require 'factories/factory'
 require 'factories/workstation'

data/lib/answers/answer.rb

@@ -4,11 +4,12 @@ module AnswerFactory
   class Answer
     attr_accessor :scores, :tags
     attr_reader :draft_blueprint, :program, :timestamp, :ancestors
-    attr_reader :initialization_options, :progress, :couch_id
+    attr_reader :initialization_options, :progress
+    attr_accessor :couch_id, :couch_rev
     
     
     def initialize(blueprint, options = {})
-      raise ArgumentError unless
+      raise ArgumentError, "Answer cannot be initialized with a #{blueprint.class}" unless
         blueprint.kind_of?(String) || blueprint.kind_of?(NudgeProgram)
       build_from_blueprint!(blueprint)
       
@@ -18,6 +19,7 @@ module AnswerFactory
       end
       @timestamp = Time.now
       @couch_id = options[:couch_id] || ""
+      @couch_rev = options[:couch_rev] || ""
       @progress = options[:progress] || 0
       @ancestors = options[:ancestors] || []
       @tags = Set.new(options[:tags]) || Set.new
@@ -123,11 +125,16 @@ module AnswerFactory
   
   
   def data
-    {'blueprint' => self.blueprint,
-      'tags' => self.tags, 
+    basics = Hash.new
+    basics["_id"] = self.couch_id unless self.couch_id.empty? 
+    basics["_rev"] = self.couch_rev unless self.couch_rev.empty? 
+    
+    basics.merge!({'blueprint' => self.blueprint,
+      'tags' => self.tags.to_a, 
       'scores' => self.scores,
       'progress' => self.progress,
-      'timestamp' => self.timestamp}
+      'timestamp' => self.timestamp})
+    return basics
   end
   
   
@@ -135,11 +142,13 @@ module AnswerFactory
     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"],
+      couch_id:value_hash['id'],
+      couch_rev:value_hash['rev'],
       tags:tag_set,
       scores:symbolized_scores,
-      progress:value_hash["progress"])
+      progress:value_hash["progress"],
+      timestamp:value_hash["timestamp"])
   end
 end

data/lib/answers/batch.rb

@@ -15,13 +15,15 @@ module AnswerFactory
     
     
     def <<(obj)
-      raise ArgumentError unless obj.kind_of?(Answer)
+      raise ArgumentError, "Batch.<< cannot append class #{obj.class}" unless
+        obj.kind_of?(Answer)
       super
     end
     
     
     def initialize(*args)
-      raise ArgumentError unless args.inject(true) {|anded, a| anded & a.kind_of?(Answer)}
+      raise ArgumentError, "Batches can only contain Answers" unless
+        args.inject(true) {|anded, a| anded & a.kind_of?(Answer)}
       super
     end
     
@@ -30,7 +32,11 @@ module AnswerFactory
       raise ArgumentError, "#{couchdb_uri} is not a String" unless couchdb_uri.kind_of?(String)
       
       db = CouchRest.database!(couchdb_uri)
-      db.bulk_save(self.data)
+      response = db.bulk_save(self.data)
+      response.each_index do |idx|
+        self[idx].couch_id = response[idx]["id"]
+        self[idx].couch_rev = response[idx]["rev"]
+      end
     end
     
     

data/lib/factories/workstation.rb

@@ -35,7 +35,6 @@ module AnswerFactory
     
     def gather_mine
       gathered = Batch.load_from_couch(couchdb_uri, "#{name}/current")
-      puts "gathered: #{gathered.class}"
       @answers = gathered
     end
     
@@ -48,7 +47,7 @@ module AnswerFactory
     
     def process_with(operator)
       raise ArgumentError, "Workstation#process_with cannot process with a #{operator.class}" unless
-        operator.kind_of?(SearchOperator)
+        operator.kind_of?(Machines::Machine)
       operator.generate(@answers)
     end
     

data/lib/machines/any_one.rb

@@ -0,0 +1,38 @@
+module AnswerFactory
+  module Machines
+    
+    
+    
+    
+    class SampleAnyOne < Machine
+      
+      def screen(batch)
+        raise ArgumentError, "SampleAnyOne#screen: argument is not a Batch" unless
+          batch.kind_of?(Batch)
+        one = batch.sample
+        return one.nil? ? Batch.new : Batch.[](one)
+      end
+      
+      alias :generate :screen
+    end
+    
+    
+    
+    
+    class RemoveAnyOne < Machine
+      
+      def screen(batch)
+        raise ArgumentError, "RemoveAnyOne#screen: argument is not a Batch" unless
+          batch.kind_of?(Batch)
+        working_copy = batch.dup
+        where = rand(working_copy.length)
+        working_copy.delete_at(where)
+        return working_copy
+      end
+      
+      alias :generate :screen
+    end
+    
+    
+  end
+end

data/lib/machines/build_random.rb

@@ -0,0 +1,21 @@
+module AnswerFactory
+  module Machines
+    
+    
+    
+    
+    class BuildRandom < Machine
+      
+      
+      def build(batch = nil, overridden_options = {})
+        all_options = @options.merge(overridden_options)
+        how_many = all_options[:how_many] || 1
+        result = Batch.new
+        how_many.times {result << Answer.new(NudgeProgram.random(all_options))}
+        return result
+      end
+      
+      alias generate build
+    end
+  end
+end

data/lib/machines/evaluate_simple_score.rb

@@ -0,0 +1,32 @@
+module AnswerFactory
+  module Machines
+    
+    
+    
+    
+    class EvaluateSimpleScore < Machine
+      
+      def score(batch, overridden_options = {}, &score_block)
+        all_options = @options.merge(overridden_options)
+        name = all_options[:name]
+        scorer = score_block || all_options[:scorer]
+        
+        raise ArgumentError, "EvaluateSimpleScore#score cannot process a #{batch.class}" unless
+          batch.kind_of?(Batch)
+        raise ArgumentError, "EvaluateSimpleScore: Undefined #name attribute" if
+          name.nil?
+        raise ArgumentError, "EvaluateSimpleScore: No scoring block available" if
+          scorer.nil?
+        
+        batch.each do |answer|
+          all_options[:static_score?] ?
+            (answer.scores[name] ||= scorer.call(answer)) :
+            (answer.scores[name] = scorer.call(answer))
+        end
+        return batch
+      end
+      
+      alias :generate :score
+    end
+  end
+end

data/lib/machines/infrastructure.rb

@@ -0,0 +1,14 @@
+module AnswerFactory
+  module Machines
+    
+    class Machine
+      
+      attr_reader :options
+      
+      def initialize(options = {})
+        @options = options
+      end
+    end
+    
+  end
+end

data/lib/machines/mutate_footnotes.rb

@@ -0,0 +1,61 @@
+#encoding: utf-8
+module AnswerFactory
+  module Machines
+    
+    
+    
+    
+    class MutateFootnotesUniform < Machine
+      
+      def build(batch, overridden_options={})
+        raise ArgumentError, "MutateFootnotesUniform#build cannot process a #{batch.class}" unless
+          batch.kind_of?(Batch)
+        
+        all_options = @options.merge(overridden_options)
+          
+        fraction = all_options[:proportion_changed] || 0.5
+        fraction = 0.0 if fraction < 0.0
+        fraction = 1.0 if fraction > 1.0
+        
+        replicates = all_options[:replicates] || 1
+        
+        result = Batch.new
+        
+        batch.each do |orig|
+          
+          codeblock = orig.program.code_section.strip
+          fn = orig.program.footnote_section.split(/^(?=«)/)
+          fn_count = fn.length
+          
+          replicates.times do
+            changes = (fraction*fn_count).ceil
+            which_fns_change = (0...fn_count).to_a.sample(changes)
+            new_blueprint = "#{codeblock} \n"
+            (0...fn_count).each do |f|
+              new_fn = which_fns_change.include?(f) ? mutated_footnote_value(fn[f],all_options) : fn[f]
+              new_blueprint << "\n#{new_fn.strip}"
+            end
+            result << Answer.new(new_blueprint, progress:(orig.progress+1))
+          end
+        end
+        
+        return result
+      end
+      
+      
+      def mutated_footnote_value(footnote_string, options = {})
+        type = /^«([\p{Alpha}][_\p{Alnum}]*)(?=»)/.match(footnote_string)[1]
+        nudgified = "#{type}_type".camelize
+        Nudge.const_defined?(nudgified) ? 
+          "«#{type}» #{nudgified.constantize.any_value(options)}" : 
+          footnote_string
+      end
+      
+      
+      
+      alias :generate :build
+      
+      
+    end
+  end
+end

data/lib/machines/select_nondominated.rb

@@ -0,0 +1,32 @@
+module AnswerFactory
+  module Machines
+    
+    
+    
+    
+    class SelectNondominated < Machine
+
+      def screen(batch, overriden_options={})
+        raise ArgumentError, "SelectNondominated#screen cannot process class #{batch.class}" unless
+          batch.kind_of?(Batch)
+        all_options = @options.merge(overriden_options)
+        
+        criteria = all_options[:comparison_criteria]
+        result = Batch.new
+        
+        batch.each do |a|
+          if criteria.nil?
+            winner = batch.inject(true) {|anded, b| anded && (!a.dominated_by?(b))}
+          else
+            winner = batch.inject(true) {|anded, b| anded && (!a.dominated_by?(b, criteria))}
+          end
+          result << a if winner
+        end
+        
+        return result
+      end
+      
+      alias :generate :screen
+    end
+  end
+end