biopsy 0.1.7 → 0.1.9

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
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-  data.tar.gz: c0f9775091fde41e4856c2109a910ef7d4b31f7d
+  metadata.gz: cd71d61a677d1be5a428a38587f2a81a2215f3ef
+  data.tar.gz: ce06d5dd2fadae096a852560cff2093fc5db249c
 SHA512:
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+  metadata.gz: d400127139fdd1c30a39e1304fd23ebe87cc95bbb2ac0f304de3492057a5b27069f038dfe7940ecc03c89a5311ccdf2d234a5420d3e9d8b1530607f053023e2b
+  data.tar.gz: 3145eb5f5826d1e90745986e1305eff1f10eb327a74107077dee0807d1f8735281ce056edf9e43b9e567442afa94122b0dcc512264ca4877f2e28f31f92f3fdd

data/lib/biopsy/experiment.rb

@@ -1,4 +1,4 @@
-1# Optimisation Framework: Experiment
+# Optimisation Framework: Experiment
 #
 # == Description
 #
@@ -12,6 +12,8 @@
 # cycle. It takes user input, runs the target program, the objective function(s)
 # and the optimisation algorithm, looping through the optimisation cycle until
 # completion and then returning the output.
+require 'logger'
+
 module Biopsy
 
   class Experiment
@@ -19,10 +21,11 @@ module Biopsy
     attr_reader :inputs, :outputs, :retain_intermediates, :target, :start, :algorithm
 
     # Returns a new Experiment
-    def initialize(target, options={}, threads=4, start=nil, algorithm=nil)
+    def initialize(target, options:{}, threads:4, start:nil, algorithm:nil, verbosity: :quiet)
       @threads = threads
       @start = start
       @algorithm = algorithm
+      @verbosity = verbosity
       if target.is_a? Target
         @target = target
       else
@@ -38,7 +41,7 @@ module Biopsy
 
     # return the set of parameters to evaluate first
     def select_starting_point
-      return unless @start.nil?
+      return if !@start.nil?
       if @algorithm && @algorithm.knows_starting_point?
         @start = @algorithm.select_starting_point
       else
@@ -53,6 +56,7 @@ module Biopsy
 
     # select the optimisation algorithm to use
     def select_algorithm
+      return if !algorithm.nil?
       max = Settings.instance.sweep_cutoff
       n = @target.count_parameter_permutations
       if n < max
@@ -82,13 +86,15 @@ module Biopsy
         @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}"
+          puts "found a new best score: #{@best[:score]} for parameters #{ptext}" unless @verbosity == :silent
         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."
+      unless @verbosity == :silent
+        puts "found optimum score: #{@best[:score]} for parameters #{@best[:parameters]} in #{@iteration_count} iterations."
+      end
       return @best
     end
 
@@ -118,10 +124,12 @@ module Biopsy
     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
+      unless [:silent, :quiet].include? @verbosity
+        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
     end
     
     def cleanup

data/lib/biopsy/objectives/fastest_optimum.rb

@@ -3,7 +3,7 @@
 
 class FastestOptimum < Biopsy::ObjectiveFunction
 
-  def run(optdata, threads=6)
+  def run(optdata, threads:6)
     info "running objective: FastestOptimum"
     t0 = Time.now
     @threads = threads

data/lib/biopsy/optimisers/parameter_sweeper.rb

@@ -24,7 +24,7 @@ module Biopsy
 
     attr_reader :combinations
 
-    def initialize(ranges, threads=8, limit=nil)
+    def initialize(ranges, threads:1, limit:1000)
       @ranges = ranges
       # parameter_counter: a count of input parameters to be used
       @parameter_counter = 1
@@ -32,29 +32,41 @@ module Biopsy
       @combinations = []
       # if the number of threads is set, update the global variable, if not default to 1
       @threads = threads
+      # set the limit to the number of parameters
+      @limit = limit
       # convert all options to an array so it can be handled by the generate_combinations() method
       # ..this is for users entering single values e.g 4 as a parameter
       @ranges.each { |key, value| value = [value] unless value.kind_of? Array }
-      self.generate_combinations
+      self.generate_combinations(0, {})
       # restrict to a subsample?
-      unless limit.nil?
-        @combinations = @combinations.sample limit
+      
+      if @limit < @combinations.size
+        @combinations = @combinations.sample @limit
       end
     end
 
     def setup *args
-      nil 
+      @best = {
+        :parameters => nil,
+        :score => nil
+      }
     end
 
     # return the next parameter set to evaluate
-    def run_one_iteration *args
-      @combinations.pop
-    rescue
-      nil
+    def run_one_iteration(parameters, score)
+      @current = {:parameters => parameters, :score => score}
+      self.update_best?
+      @combinations.pop rescue nil
+    end
+
+    def update_best?
+      if @best[:score].nil? || @current[:score] > @best[:score]
+        @best = @current.clone
+      end
     end
 
     # generate all the parameter combinations to be applied
-    def generate_combinations(index=0, opts={})
+    def generate_combinations(index, opts)
       if index == @ranges.length
         @combinations << opts.clone  
         return
@@ -67,13 +79,29 @@ module Biopsy
       end
     end
 
+    def best
+      @best
+    end
+
     def knows_starting_point?
       true
     end
 
     def select_starting_point
-      self.run_one_iteration
+      return @combinations.pop
+    end
+
+    def random_start_point
+      return @combinations.pop
+    end
+
+    def finished?
+      return @combinations.empty?
     end
 
+    # True if this algorithm chooses its own starting point
+    def knows_starting_point?
+      true
+    end
   end
 end

data/lib/biopsy/settings.rb

@@ -51,7 +51,8 @@ module Biopsy
     # specified, the default location ('~/.biopsyrc') is used.
     # Settings loaded from the file are merged into any
     # previously loaded settings.
-    def load(config_file=@config_file)
+    def load config_file
+      config_file ||= @config_file
       newsets = YAML::load_file(config_file)
       raise 'Config file was not valid YAML' if newsets == false
       newsets.deep_symbolize.each_pair do |key, value|
@@ -65,7 +66,8 @@ module Biopsy
 
     # Saves the settings to a YAML config file. If no file is
     # specified, the default location ('~/.biopsyrc') is used.
-    def save(config_file=@config_file)
+    def save config_file
+      config_file ||= @config_file
       File.open(config_file, 'w') do |f|
         f.puts self.to_s
       end

data/lib/biopsy/target.rb

@@ -126,6 +126,28 @@ module Biopsy
       @parameters.each_pair.map{ |k, v| v }.reduce(1) { |n, arr| n * arr.size }
     end
 
-  end # end of class Domain
+    # pass calls to missing methods to the constructor iff
+    # the constructor's class directly defines that method
+    def method_missing(meth, *args, &block)
+      const_methods = @constructor.class.instance_methods(false)
+      if const_methods.include? meth
+        @constructor
+      else
+        super
+      end
+    end
+
+    # accurately report ability to respond to methods passed
+    # to constructor
+    def method_missing(meth, *args, &block)
+      const_methods = @constructor.class.instance_methods(false)
+      if const_methods.include? meth
+        true
+      else
+        super
+      end
+    end
+
+  end # end of class Target
 
 end # end of module Biopsy

data/lib/biopsy/version.rb

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

data/test/helper.rb

@@ -105,6 +105,10 @@ class TargetTest
     nil
   end
 
+  def fake_method
+    true
+  end
+
 end
       }
     end

data/test/test_experiment.rb

@@ -5,6 +5,7 @@ class TestExperiment < Test::Unit::TestCase
   context "Experiment" do
 
     setup do
+      # create a target called 'target_test'
       @h = Helper.new
       @h.setup_tmp_dir
 
@@ -46,8 +47,8 @@ class TestExperiment < Test::Unit::TestCase
     end
 
     should "respect user's choice of starting point" do
-      s = {:a => 2, :b => 4}
-      e = Biopsy::Experiment.new('target_test', start=s)
+      s = {:a => 4, :b => 2} 
+      e = Biopsy::Experiment.new('target_test', start: s, verbosity: :silent)
       assert_equal s, e.start
     end
 
@@ -57,15 +58,32 @@ class TestExperiment < Test::Unit::TestCase
     end
 
     should "return an optimal set of parameters and score when run" do
-      # Kernel.srand 123
       Dir.chdir @h.tmp_dir do
-        e = Biopsy::Experiment.new('target_test')
+        e = Biopsy::Experiment.new('target_test', verbosity: :silent)
         known_best = -4
         best_found = e.run[:score]
         assert known_best < best_found
       end
     end
 
+    should "run really quickly when starting from the optimal parameters" do
+      Dir.chdir @h.tmp_dir do
+        s = {:a => 4, :b => 4, :c => 4} 
+        e = Biopsy::Experiment.new('target_test', start: s, verbosity: :silent)
+        known_best = -4
+        best_found = e.run[:score]
+        assert known_best < best_found
+      end
+    end
+
+    should "run using the parameter sweeper (with limit)" do
+      Dir.chdir @h.tmp_dir do
+        p = Biopsy::ParameterSweeper.new(@target.parameters, limit: 250)
+        e = Biopsy::Experiment.new('target_test', algorithm: p, verbosity: :silent)
+        best_found = e.run[:score]
+        assert best_found != nil
+      end
+    end
   end # Experiment context
 
 end # TestExperiment

data/test/test_target.rb

@@ -95,6 +95,15 @@ class TestTarget < Test::Unit::TestCase
       File.delete @target.constructor_path
     end
 
+    should "pass missing method calls to constructor iff it directly defines them" do
+      # this method is defined on the constructor in helper.rb
+      assert_send([@target, :fake_method],
+                  'valid method not passed to constructor')
+      assert_raise NoMethodError do
+        @target.totes_fake_method
+      end
+    end
+
   end # Target context
 
 end # TestTarget context

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: biopsy
 version: !ruby/object:Gem::Version
-  version: 0.1.7
+  version: 0.1.9
 platform: ruby
 authors:
 - Richard Smith
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-04-22 00:00:00.000000000 Z
+date: 2014-04-24 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake
@@ -16,14 +16,14 @@ dependencies:
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: 10.1.0
+        version: '10.3'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: 10.1.0
+        version: '10.3'
 - !ruby/object:Gem::Dependency
   name: threach
   requirement: !ruby/object:Gem::Requirement
@@ -66,6 +66,20 @@ dependencies:
     - - ">="
       - !ruby/object:Gem::Version
         version: '0'
+- !ruby/object:Gem::Dependency
+  name: minitest
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
 - !ruby/object:Gem::Dependency
   name: turn
   requirement: !ruby/object:Gem::Requirement
@@ -128,30 +142,30 @@ executables: []
 extensions: []
 extra_rdoc_files: []
 files:
+- LICENSE.txt
+- README.md
 - Rakefile
 - lib/biopsy.rb
-- lib/biopsy/version.rb
+- lib/biopsy/base_extensions.rb
+- lib/biopsy/experiment.rb
+- lib/biopsy/objective_function.rb
 - lib/biopsy/objective_handler.rb
 - lib/biopsy/objectives/fastest_optimum.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/objective_function.rb
+- lib/biopsy/optimisers/spea2.rb
+- lib/biopsy/optimisers/tabu_search.rb
+- lib/biopsy/settings.rb
 - lib/biopsy/target.rb
-- lib/biopsy/base_extensions.rb
-- lib/biopsy/experiment.rb
-- test/test_target.rb
-- test/test_hash.rb
-- test/test_string.rb
+- lib/biopsy/version.rb
 - test/helper.rb
-- test/test_objective_handler.rb
+- test/test_experiment.rb
 - test/test_file.rb
+- test/test_hash.rb
+- test/test_objective_handler.rb
 - test/test_settings.rb
-- test/test_experiment.rb
-- README.md
-- LICENSE.txt
+- test/test_string.rb
+- test/test_target.rb
 homepage: https://github.com/Blahah/biopsy
 licenses: []
 metadata: {}
@@ -171,8 +185,9 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 2.1.4
+rubygems_version: 2.2.2
 signing_key: 
 specification_version: 4
 summary: framework for optimising any computational pipeline or program
 test_files: []
+has_rdoc: