biopsy 0.1.6.alpha → 0.1.7

checksums.yaml

@@ -0,0 +1,7 @@
+---
+SHA1:
+  metadata.gz: 64634183ae77fe731606799110dad261a5e65ac3
+  data.tar.gz: c0f9775091fde41e4856c2109a910ef7d4b31f7d
+SHA512:
+  metadata.gz: 487ea9c1efa2d5447eec05293e4f6673459828a7f9e08918112893898dfe9fe65daa3675c36f07269fdb4376281c24fc2e62bf3350e58cd81496f89d1fac70c6
+  data.tar.gz: e04fc594a7b60fc4fbd2098421cdd7f99f83fe2c58542a37a7fe0bed4dc7fb2369fa96d8221a0c4a64cfaf6a146fd0e700d71e94d0f944691813cf28aad021fc

data/README.md

@@ -5,7 +5,7 @@ An automatic optimisation framework for programs and pipelines.
 
 Biopsy is a framework for optimising any program or pipeline which produces a measurable output. By reducing the settings of one or more programs to a parameter space, and by carefully choosing objective functions with which to measure the output of the program(s), biopsy can use a range of optimisation strategies to rapidly find the settings that perform the best. Combined with a strategy for subsampling the input data, this can lead to vast time and performance improvements.
 
-A simple example of the power of this approach is *de-novo* transcriptome assembly. Typically, the assembly process takes many GB of data as input, uses many GB of RAM and takes many hours to complete. This prevents researchers from performing full parameter sweeps, and they are therefore forced to use word-of-mouth and very basic optimisation to choose assembler settings. Assemblotron, which uses the Biopsy framework, can fully optimise any *de-novo* assembler to produce the optimal assembly possible given a particular input. This typically takes little more time than running a single assembly.
+A simple example of the power of this approach is *de-novo* transcriptome assembly. Typically, the assembly process takes many GB of data as input, uses many GB of RAM and takes many hours to complete. This prevents researchers from performing full parameter sweeps, and they are therefore forced to use word-of-mouth and very basic optimisation to choose assembler settings. [Assemblotron](https://github.com/Blahah/assemblotron), which uses the Biopsy framework, can fully optimise any *de-novo* assembler to produce the optimal assembly possible given a particular input. This typically takes little more time than running a single assembly.
 
 ## Installation
 
@@ -15,8 +15,6 @@ Make sure you have Ruby installed, then:
 
 ## Usage
 
-[]
-
 Detailed usage instructions are on the wiki. Here's a quick overview:
 
 1. Define your optimisation target. This is a program or pipeline you want to optimise, and you define it by filling in a template [YAML file](http://en.wikipedia.org/wiki/YAML). Easy!
@@ -59,8 +57,6 @@ Please don't report issues or request documentation until we are ready for beta
 | ObjectiveHandler | DONE   | DONE    | DONE   |
 
 * ~ 20/24 tasks completed, ~83% done overall
-* alpha released: 6th September 2013
-* planned beta release date: 17th September 2013
 
 ### Documentation
 
@@ -69,4 +65,6 @@ Documentation is in development and will be released with the beta.
 ### Citation
 
 This is *pre-release*, *pre-publication* academic software. In lieu of a paper to cite, please cite this Github repo and/or the [Figshare DOI (http://dx.doi.org/10.6084/m9.figshare.790660
-)](http://dx.doi.org/10.6084/m9.figshare.790660) if your use of the software leads to a publication.
+)](http://dx.doi.org/10.6084/m9.figshare.790660) if your use of the software leads to a publication.
+
+[![Analytics](https://ga-beacon.appspot.com/UA-46900280-1/Blahah/biopsy)](https://github.com/Blahah/biopsy)

data/lib/biopsy.rb

@@ -5,7 +5,6 @@ require "biopsy/experiment"
 require "biopsy/target"
 require "biopsy/objective_handler"
 require "biopsy/objective_function"
-require "biopsy/opt_algorithm"
 require "biopsy/optimisers/genetic_algorithm"
 require "biopsy/optimisers/tabu_search"
 require "biopsy/optimisers/parameter_sweeper"

data/lib/biopsy/experiment.rb

@@ -1,4 +1,4 @@
-# Optimisation Framework: Experiment
+1# Optimisation Framework: Experiment
 #
 # == Description
 #
@@ -19,7 +19,8 @@ module Biopsy
     attr_reader :inputs, :outputs, :retain_intermediates, :target, :start, :algorithm
 
     # Returns a new Experiment
-    def initialize(target, options={}, start=nil, algorithm=nil)
+    def initialize(target, options={}, threads=4, start=nil, algorithm=nil)
+      @threads = threads
       @start = start
       @algorithm = algorithm
       if target.is_a? Target
@@ -77,10 +78,16 @@ module Biopsy
       while in_progress do
         run_iteration
         # update the best result
+        best = @best
         @best = @algorithm.best
+        ptext = @best[:parameters].each_pair.map{ |k, v| "#{k}:#{v}" }.join(", ")
+        if (@best && @best.has_key?(:score) && best && best.has_key?(:score) && @best[:score] > best[:score])
+          puts "found a new best score: #{@best[:score]} for parameters #{ptext}"
+        end
         # have we finished?
         in_progress = !@algorithm.finished?
       end
+      @algorithm.write_data if @algorithm.respond_to? :write_data
       puts "found optimum score: #{@best[:score]} for parameters #{@best[:parameters]} in #{@iteration_count} iterations."
       return @best
     end
@@ -99,8 +106,9 @@ module Biopsy
         if @scores.has_key? param_key
           result = @scores[param_key]
         else
-          result = @objective.run_for_output raw_output
+          result = @objective.run_for_output(raw_output, @threads)
           @iteration_count += 1
+          self.print_progress(@iteration_count, @current_params, result, @best)
         end
         @scores[@current_params.to_s] = result
         # get next steps from optimiser
@@ -109,6 +117,13 @@ module Biopsy
       self.cleanup
     end
 
+    def print_progress(iteration, params, score, best)
+      ptext = params.each_pair.map{ |k, v| "#{k}:#{v}" }.join(", ")
+      msg = "run #{iteration}. parameters: #{ptext} | score: #{score}"
+      msg += " | best #{best[:score]}" if (best && best.has_key?(:score))
+      puts msg
+    end
+    
     def cleanup
       # TODO: make this work
       # remove all but essential files
@@ -116,6 +131,8 @@ module Biopsy
         @objectives.values.each{ |objective| essential_files += objective.essential_files }
       end
       Dir["*"].each do |file|
+        next
+        # TODO: implement this
         next if File.directory? file
         if essential_files && essential_files.include?(file)
           `gzip #{file}` if Settings.instance.gzip_intermediates
@@ -141,4 +158,4 @@ module Biopsy
 
   end # end of class RunHandler
 
-end # end of module Biopsy
+end # end of module Biopsy

data/lib/biopsy/objective_handler.rb

@@ -113,8 +113,7 @@ module Biopsy
         files = Dir[glob]
         zerosize = files.reduce(false) { |empty, f| File.size(f) == 0 }
         if files.empty? || zerosize
-          puts Dir.pwd
-          raise ObjectiveHandlerError.new "output files for #{key} matching #{glob} do not exist or are empty"
+          puts ObjectiveHandlerError.new "output files for #{key} matching #{glob} do not exist or are empty"
           return nil
         end
         output_files[key] = files.map { |f| File.expand_path(f) }
@@ -130,8 +129,8 @@ module Biopsy
         return {:results => results,
                 :reduced => self.dimension_reduce(results)}
       else
-        results.each do |key, value|
-          return value[:result]
+        results.each_pair do |key, value|
+          return value.kind_of?(Hash) ? value[:result] : value
         end
       end
     end

data/lib/biopsy/optimisers/spea2.rb

@@ -0,0 +1,297 @@
+require 'csv'
+require 'pp'
+
+module Biopsy
+	class SPEA2
+		attr_reader :current, :probability_of_cross
+		attr_writer :probability_of_cross
+		attr_accessor :population_size, :archive_size, :probability_of_cross
+		def initialize(parameter_ranges, threads=8)
+			@parameter_ranges = parameter_ranges
+			@currently_mating = false
+			@probability_of_cross = 0.94
+			@population_size = 50
+			@archive_size = 15
+			@mutation_rate = 0.20
+			@generation_handler = Generation.new(@population_size, @archive_size)
+			@mating_handler = MatingHandler.new(@population_size, @probability_of_cross, @parameter_ranges, @mutation_rate)
+		end
+		def setup start_point
+			@current = {:parameters => start_point, :score => nil}
+			@best = @current
+		end
+		# accepts a parameter set and a score (which are added to population)
+		# returns another parameter set to be scored which is then accepted next iteration
+	  def run_one_iteration(parameters, score)
+	  	self.run_one_mating_iteration(parameters, score) if @currently_mating == true
+	    @current = {:parameters => parameters, :score => score}
+	    # update best score?
+	    self.update_best?
+	    # push new parameter set into generation
+	    @currently_mating = @generation_handler.add_new_individual(@current)
+	    if @currently_mating == true
+	    	# begin mating process
+	    	# empty current population
+	    	@generation_handler.population_array = []
+	    	selected_to_mate = @mating_handler.select_mating_population(@generation_handler.archive_array)
+	    	self.get_children_to_score(selected_to_mate)
+	    	@children_to_score.pop[:parameters]
+	    else
+	    	# get next parameter set to score
+	    	self.random_parameter_set
+	    end
+	  end
+	  def get_children_to_score selected_to_mate
+	  	@children_to_score = @mating_handler.run(selected_to_mate)
+	  end
+	  def run_one_mating_iteration(parameters, score)
+	  	@generation_handler.add_new_individual({:parameters => parameters, :score => score})
+	  	if @children_to_score.length == 1
+	  		@currently_mating = false
+	  	end
+	  	@children_to_score.pop
+	  end
+		# return true if algorithm knows its own starting point
+		def knows_starting_point?
+			return true
+		end
+		def update_best?
+	    if @best[:score].nil? || @current[:score] > @best[:score]
+	      @best = @current.clone
+	      @iterations_since_best = 0
+	    else
+	      @iterations_since_best += 1
+	    end
+	  end
+		# returns a parameter set to be used as the starting point
+		def select_starting_point
+			self.random_parameter_set
+		end
+		# generates a random parameter set
+		def random_parameter_set
+			Hash[@parameter_ranges.map { |k, v| [k, v.sample] }]
+		end
+		# check if termination conditions are met
+		def finished?
+			true if rand < 0.00025
+		end
+		def best
+			@best
+		end
+	end # Algorithm
+
+	class Generation
+		attr_accessor :population_array, :archive_array
+		def initialize(population_size, archive_size)
+			@archive_generation = ArchiveGeneration.new
+			@population_size = population_size
+			@archive_size = archive_size
+			@population_array = []
+			@archive_array = []
+		end
+		def add_new_individual individual
+			@population_array << Individual.new(individual)
+			# run generation
+			if @population_array.length == @population_size
+				self.run_generation
+				true
+			else
+				false
+			end
+		end
+		def run_generation
+			@pop_and_archive = @population_array + @archive_array
+			FitnessAssignment.run(@pop_and_archive)
+			@archive_array = @archive_generation.run(@pop_and_archive, 10)
+		end
+	end # Generation
+
+	class Individual
+		attr_reader :parameters, :score, :fitness, :raw_fitness, :density, :distance_to_kth_point, :distance_to_origin
+		attr_writer :parameters, :fitness, :raw_fitness, :density, :distance_to_kth_point
+		def initialize(individual)
+			@parameters = individual[:parameters]
+			@score = individual[:score]
+			@distance_to_origin = FitnessAssignment.distance_to_origin(@score)
+		end
+	end # Individual
+
+	class FitnessAssignment
+		def self.run generation
+			self.score_raw_fitness(generation)
+			self.score_density(generation)
+			generation.each do |individual|
+				individual.fitness = individual.density + individual.raw_fitness
+			end
+		end
+		def self.distance_to_origin coordinates
+			# coordinates is a hash of coordinates
+			return rand(coordinates)
+		end
+		def self.distance_between_points(individual_one, individual_two)
+			if (individual_one.score - individual_two.score) < 0
+				return (individual_one.score - individual_two.score)*-1
+			else
+				return (individual_one.score - individual_two.score)
+			end
+		end
+		def self.score_density generation
+			generation_hash = map_points_distance(generation)
+
+			find_distance_to_kth_point(generation_hash)
+
+			generation_hash.each do |key,value|
+				value[0].density = (1.to_f/(value[0].distance_to_kth_point+2))
+			end
+		end
+		def self.map_points_distance generation
+			generation_clone = generation.clone
+			generation_hash = {}
+			generation_length = generation.length
+			(1..generation_length).each do |num|
+				generation_hash[num.to_s] = [generation_clone.pop, {}]
+			end
+			generation_hash.each do |key, value|
+				(1..generation_length).each do |num|
+					next if key.to_i == num or generation_hash[key][1].has_key?(num.to_s)
+					generation_hash[key][1][num.to_s] = distance_between_points(generation_hash[key][0], generation_hash[num.to_s][0])
+					generation_hash[num.to_s][1][key] = distance_between_points(generation_hash[key][0], generation_hash[num.to_s][0])
+				end
+			end
+			return generation_hash
+		end
+		def self.score_raw_fitness generation
+			generation.sort! { |a, b| a.distance_to_origin <=> b.distance_to_origin }.reverse!
+			counter = 0
+			previous_distance = +1.0/0.0
+			generation.each do |individual|
+				if previous_distance > individual.distance_to_origin
+					individual.raw_fitness = counter
+				else
+					individual.raw_fitness = counter - 1
+				end
+				previous_distance = individual.distance_to_origin
+				counter += 1
+			end
+		end
+		def self.find_distance_to_kth_point generation_hash
+			kth_point = Math.sqrt(generation_hash.length).round(0)
+			generation_hash.each do |key, value|
+				sorted_distances_array = value[1].sort_by {|k,v| v}
+				(1..sorted_distances_array.length).each do |num|
+					if num == (kth_point-1)
+						value[0].distance_to_kth_point = sorted_distances_array[num][1]
+					end
+				end
+			end
+		end
+	end # FitnessAssignment
+
+	class ArchiveGeneration
+		def run(generation, archive_size)
+			@generation = generation
+			archive = fill_archive(@generation)
+			
+			if archive.length < archive_size
+				archive = self.further_archive_selection(archive, archive_size)
+			elsif archive.length > archive_size
+				archive = self.archive_truncation(archive)
+			end
+			return archive
+		end
+		def fill_archive generation
+			archive = []
+			@generation.clone.each do |individual|
+				if individual.fitness < 1
+					archive << individual 
+					@generation.delete(individual)
+				end
+			end
+			return archive
+		end
+		def archive_truncation archive
+			return archive
+		end
+		def further_archive_selection archive, archive_size
+			@generation.sort!{|a, b| a.fitness <=> b.fitness}
+			@generation.clone.each do |individual|
+				if archive.length < archive_size
+					archive << individual 
+					@generation.delete(individual)
+				else
+					break
+				end
+			end
+			return archive
+		end
+	end # ArchiveGeneration
+
+	class MatingHandler
+		def initialize(population_size, probability_of_cross, parameter_ranges, mutation_rate)
+			@probability_of_cross = probability_of_cross
+			@parameter_ranges = parameter_ranges
+			@population_size = population_size
+			@mutation_rate = mutation_rate
+		end
+		def run selected_to_mate
+			new_population = reproduce(selected_to_mate)
+			return new_population
+		end
+		def select_mating_population archive
+			Array.new(@population_size) {self.binary_tournament(archive)}
+		end
+		def binary_tournament(archive)
+			individual_one = rand(archive.size)
+			individual_two = rand(archive.size)
+			individual_two = rand(archive.size) while individual_one == individual_two
+			if archive[individual_one].fitness > archive[individual_two].fitness
+				return archive[individual_one]
+			else
+				return archive[individual_two]
+			end
+		end
+		def reproduce selected_to_mate
+			# loop through selected
+			# mate first with last
+			# mate index 1 with index 2
+			# mate index 2 with index 1
+			# mate index 3 with index 4
+			children = []
+			selected_to_mate.each_with_index do |parent_one, index|
+				if index == selected_to_mate.size+1
+					parent_two = selected_to_mate[0]
+				elsif index.modulo(2) == 1
+					parent_two = selected_to_mate[index-1]
+				else
+					parent_two = selected_to_mate[index+1]
+				end
+				children << self.mate(parent_one, parent_two)
+			end
+			return children
+		end
+		def mate(parent_one, parent_two)
+			child = self.crossover(parent_one, parent_two)
+			child = self.mutation(child)
+			return child
+		end
+		def crossover(parent_one, parent_two)
+			return {:parameters => parent_one.parameters} if rand >= @probability_of_cross
+			# create the hash if parameter_ranges that can be passed to the +:Individual:+ class
+			child_parameters = {}
+			parent_one.parameters.each do |parent_one_key, parent_one_value|
+				if rand < 0.5
+					child_parameters[parent_one_key.to_sym] = parent_one_value
+				else
+					child_parameters[parent_one_key.to_sym] = parent_two.parameters[parent_one_key.to_sym]
+				end
+			end
+			return {:parameters => child_parameters}
+		end
+		def mutation child
+			child[:parameters].each do |key, value|
+				child[:parameters][key.to_sym] = @parameter_ranges[key.to_sym].sample(1)[0] if rand < @mutation_rate
+			end
+			return child
+		end
+	end # MatingHandler
+end # Biopsy

data/lib/biopsy/optimisers/tabu_search.rb

@@ -165,7 +165,8 @@ module Biopsy
     Thread = Struct.new(:best, :tabu, :distributions, 
                         :standard_deviations, :recent_scores, 
                         :iterations_since_best, :backtracks,
-                        :current, :current_hood, :loaded)
+                        :current, :current_hood, :loaded,
+                        :score_history, :best_history)
 
     def initialize(parameter_ranges, threads=8, limit=nil)
 
@@ -191,6 +192,8 @@ module Biopsy
       @jump_cutoff = 10
 
       # logging
+      @score_history = []
+      @best_history = []
       @log_data = false
       @logfiles = {}
       self.log_setup
@@ -241,6 +244,8 @@ module Biopsy
         @best = @current
         @standard_deviations = {}
         @recent_scores = []
+        @score_history = []
+        @best_history = []
         @tabu = Set.new
         self.define_neighbourhood_structure
         @current_hood = Biopsy::Hood.new(@distributions, @max_hood_size, @tabu)
@@ -434,6 +439,10 @@ module Biopsy
     end
 
     def log
+      if @current[:score]
+        @score_history << @current[:score]
+        @best_history << @best[:score]
+      end
       if @log_data
         @logfiles[:standard_deviations] << @distributions.map { |k, d| d.sd }
         @logfiles[:best] << [@best[:score]]
@@ -460,6 +469,23 @@ module Biopsy
       Hash[@ranges.map { |p, r| [p, r.sample] }] 
     end
 
+    def write_data
+      require 'csv'
+      now = Time.now.to_i
+      CSV.open("../#{now}_scores.csv", "w") do |c|
+        c << %w(iteration thread score best)
+        @threads.each_with_index do |t, t_idx|
+          sh = t.score_history
+          bh = t.best_history
+          sh.zip(bh).each_with_index do |pair, i|
+            c << [i, t_idx] + pair
+          end
+        end
+      end
+      path = File.expand_path("../#{now}_scores.csv")
+      puts "wrote TabuSearch run data to #{path}"
+    end
+
   end # TabuSearch
 
-end # Biopsy
+end # Biopsy

data/lib/biopsy/version.rb

@@ -4,9 +4,8 @@ module Biopsy
   module VERSION
     MAJOR = 0
     MINOR = 1
-    PATCH = 6
-    BUILD = 'alpha'
+    PATCH = 7
 
-    STRING = [MAJOR, MINOR, PATCH, BUILD].compact.join('.')
+    STRING = [MAJOR, MINOR, PATCH].compact.join('.')
   end
 end # Biopsy

data/test/helper.rb

@@ -7,7 +7,7 @@ SimpleCov.formatter = SimpleCov::Formatter::MultiFormatter[
 ]
 SimpleCov.start
 
-require 'test/unit'
+require 'minitest/autorun'
 begin; require 'turn/autorun'; rescue LoadError; end
 require 'shoulda-context'
 require 'biopsy'
@@ -161,4 +161,4 @@ end
     end
   end
 
-end
+end

data/test/test_experiment.rb

@@ -47,7 +47,7 @@ class TestExperiment < Test::Unit::TestCase
 
     should "respect user's choice of starting point" do
       s = {:a => 2, :b => 4}
-      e = Biopsy::Experiment.new('target_test', s)
+      e = Biopsy::Experiment.new('target_test', start=s)
       assert_equal s, e.start
     end
 

metadata

@@ -1,142 +1,125 @@
 --- !ruby/object:Gem::Specification
 name: biopsy
 version: !ruby/object:Gem::Version
-  version: 0.1.6.alpha
-  prerelease: 6
+  version: 0.1.7
 platform: ruby
 authors:
 - Richard Smith
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2013-09-19 00:00:00.000000000 Z
+date: 2014-04-22 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
         version: 10.1.0
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
         version: 10.1.0
 - !ruby/object:Gem::Dependency
   name: threach
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: '0'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: '0'
 - !ruby/object:Gem::Dependency
   name: rubystats
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: '0'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: '0'
 - !ruby/object:Gem::Dependency
   name: statsample
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: '0'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: '0'
 - !ruby/object:Gem::Dependency
   name: turn
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: '0'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: '0'
 - !ruby/object:Gem::Dependency
   name: simplecov
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: '0'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: '0'
 - !ruby/object:Gem::Dependency
   name: shoulda-context
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: '0'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: '0'
 - !ruby/object:Gem::Dependency
   name: coveralls
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
         version: 0.6.7
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
         version: 0.6.7
 description: 
@@ -146,51 +129,50 @@ extensions: []
 extra_rdoc_files: []
 files:
 - Rakefile
-- lib/biopsy/base_extensions.rb
-- lib/biopsy/experiment.rb
-- lib/biopsy/objective_function.rb
+- lib/biopsy.rb
+- lib/biopsy/version.rb
 - lib/biopsy/objective_handler.rb
 - lib/biopsy/objectives/fastest_optimum.rb
-- lib/biopsy/opt_algorithm.rb
+- lib/biopsy/settings.rb
+- lib/biopsy/optimisers/tabu_search.rb
 - lib/biopsy/optimisers/genetic_algorithm.rb
+- lib/biopsy/optimisers/spea2.rb
 - lib/biopsy/optimisers/parameter_sweeper.rb
-- lib/biopsy/optimisers/tabu_search.rb
-- lib/biopsy/settings.rb
+- lib/biopsy/objective_function.rb
 - lib/biopsy/target.rb
-- lib/biopsy/version.rb
-- lib/biopsy.rb
-- test/helper.rb
-- test/test_experiment.rb
-- test/test_file.rb
+- lib/biopsy/base_extensions.rb
+- lib/biopsy/experiment.rb
+- test/test_target.rb
 - test/test_hash.rb
+- test/test_string.rb
+- test/helper.rb
 - test/test_objective_handler.rb
+- test/test_file.rb
 - test/test_settings.rb
-- test/test_string.rb
-- test/test_target.rb
+- test/test_experiment.rb
 - README.md
 - LICENSE.txt
 homepage: https://github.com/Blahah/biopsy
 licenses: []
+metadata: {}
 post_install_message: 
 rdoc_options: []
 require_paths:
 - lib
 required_ruby_version: !ruby/object:Gem::Requirement
-  none: false
   requirements:
-  - - ! '>='
+  - - ">="
     - !ruby/object:Gem::Version
       version: '0'
 required_rubygems_version: !ruby/object:Gem::Requirement
-  none: false
   requirements:
-  - - ! '>'
+  - - ">="
     - !ruby/object:Gem::Version
-      version: 1.3.1
+      version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 1.8.24
+rubygems_version: 2.1.4
 signing_key: 
-specification_version: 3
+specification_version: 4
 summary: framework for optimising any computational pipeline or program
 test_files: []