biopsy 0.1.9 → 0.2.0

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: cd71d61a677d1be5a428a38587f2a81a2215f3ef
-  data.tar.gz: ce06d5dd2fadae096a852560cff2093fc5db249c
+  metadata.gz: 4a78e571268545fdd69d110f2b789bb53fa5d100
+  data.tar.gz: 3255fd3579a242fa6277c9b16d5128fe4d3c6250
 SHA512:
-  metadata.gz: d400127139fdd1c30a39e1304fd23ebe87cc95bbb2ac0f304de3492057a5b27069f038dfe7940ecc03c89a5311ccdf2d234a5420d3e9d8b1530607f053023e2b
-  data.tar.gz: 3145eb5f5826d1e90745986e1305eff1f10eb327a74107077dee0807d1f8735281ce056edf9e43b9e567442afa94122b0dcc512264ca4877f2e28f31f92f3fdd
+  metadata.gz: dd5c793e5af0042dd69066de1c96695e519d619a8738ad066baefc0d3015dc89ec6247d573090263f45ad3f78ea2bb8fa3df17945197d29bd48b23cee84556bc
+  data.tar.gz: 6a9d2b2dcc4463c1ad8afe3311af4b3912b0263f53c7b1aa609a16319aa5c2348c62a3c48b4caaf7760fa6e0d18df1423644772d7bde2285e10b866f223e4aed

data/lib/biopsy/experiment.rb

@@ -18,10 +18,12 @@ module Biopsy
 
   class Experiment
 
-    attr_reader :inputs, :outputs, :retain_intermediates, :target, :start, :algorithm
+    attr_reader :inputs, :outputs, :retain_intermediates
+    attr_reader :target, :start, :algorithm
 
     # Returns a new Experiment
-    def initialize(target, options:{}, threads:4, start:nil, algorithm:nil, verbosity: :quiet)
+    def initialize(target, options:{}, threads:4, start:nil, algorithm:nil,
+                   verbosity: :quiet)
       @threads = threads
       @start = start
       @algorithm = algorithm
@@ -51,12 +53,12 @@ module Biopsy
 
     # Return a random set of parameters from the parameter space.
     def random_start_point
-      Hash[@target.parameters.map { |p, r| [p, r.sample] }] 
+      Hash[@target.parameters.map { |p, r| [p, r.sample] }]
     end
 
     # select the optimisation algorithm to use
     def select_algorithm
-      return if !algorithm.nil?
+      return if algorithm
       max = Settings.instance.sweep_cutoff
       n = @target.count_parameter_permutations
       if n < max
@@ -67,7 +69,7 @@ module Biopsy
     end
 
     # load the target named +:target_name+
-    def load_target target_name
+    def load_target(target_name)
       @target = Target.new
       @target.load_by_name target_name
     end
@@ -79,21 +81,27 @@ module Biopsy
       in_progress = true
       @algorithm.setup @start
       @current_params = @start
-      while in_progress do
+      while in_progress
         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}" unless @verbosity == :silent
+        if @best &&
+           @best.key?(:score) &&
+           best &&
+           best.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
       unless @verbosity == :silent
-        puts "found optimum score: #{@best[:score]} for parameters #{@best[:parameters]} in #{@iteration_count} iterations."
+        puts "found optimum score: #{@best[:score]} for parameters \
+              #{@best[:parameters]} in #{@iteration_count} iterations."
       end
       return @best
     end
@@ -103,16 +111,16 @@ module Biopsy
     # Returns the output of the optimiser.
     def run_iteration
       # create temp dir
-        Dir.chdir(self.create_tempdir) do
+      Dir.chdir(self.create_tempdir) do
         # run the target
         raw_output = @target.run @current_params.merge(@options)
         # evaluate with objectives
         param_key = @current_params.to_s
         result = nil
-        if @scores.has_key? param_key
+        if @scores.key? param_key
           result = @scores[param_key]
         else
-          result = @objective.run_for_output(raw_output, @threads)
+          result = @objective.run_for_output(raw_output, @threads, nil)
           @iteration_count += 1
           self.print_progress(@iteration_count, @current_params, result, @best)
         end
@@ -135,17 +143,21 @@ module Biopsy
     def cleanup
       # TODO: make this work
       # remove all but essential files
+      essential_files = ""
       if Settings.instance.keep_intermediates
-        @objectives.values.each{ |objective| essential_files += objective.essential_files }
+        # @objectives isn't mentioned anywhere in the rest of this file
+        @objectives.values.each do |objective|
+          essential_files += objective.essential_files
+        end
       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
-          FileUtils.mv("#{file}.gz", '../output')
-        end
+        # next if File.directory? file
+        # if essential_files && essential_files.include?(file)
+        #   `gzip #{file}` if Settings.instance.gzip_intermediates
+        #   FileUtils.mv("#{file}.gz", '../output')
+        # end
       end
       FileUtils.rm_rf @last_tempdir
     end
@@ -157,11 +169,11 @@ module Biopsy
         # generate random dirnames until we find one that
         # doesn't exist
         test_token = SecureRandom.hex
-        break test_token unless File.exists? test_token
+        break test_token unless File.exist? test_token
       end
       Dir.mkdir(token)
       @last_tempdir = token
-      return token
+      token
     end
 
   end # end of class RunHandler

data/lib/biopsy/objective_function.rb

@@ -25,7 +25,7 @@ module Biopsy
       #
       # objective = ObjectiveFunction.new
       # result = objective.run('example.fasta')
-    def run(assemblydata)
+    def run(raw_output, output_files, threads)
       raise NotImplementedError.new("You must implement a run method for each objective function")
     end
 

data/lib/biopsy/objective_handler.rb

@@ -6,21 +6,25 @@ require 'fileutils'
 # == Description
 #
 # The Handler manages the objective functions for the optimisation experiment.
-# Specifically, it finds all the objective functions and runs them when requested,
-# outputting the results to the main Optimiser.
+# Specifically, it finds all the objective functions and runs them when 
+# requested, outputting the results to the main Optimiser.
 #
 # == Explanation
 #
 # === Loading objective functions
 #
-# The Handler expects a directory containing objectives (by default it looks in *currentdir/objectives*).
+# The Handler expects a directory containing objectives (by default it looks
+# in *currentdir/objectives*).
 # The *objectives* directory should contain the following:
 #
-# * a *.rb* file for each objective function. The file should define a subclass of ObjectiveFunction
-# * (optionally) a file *objectives.txt* which lists the objective function files to use
+# * a *.rb* file for each objective function. The file should define a subclass
+#     of ObjectiveFunction
+# * (optionally) a file *objectives.txt* which lists the objective function
+#     files to use
 #
-# If the objectives.txt file is absent, the subset of objectives to use can be set directly in the Optimiser
-# , or if no such restriction is set, the whole set of objectives will be run.
+# If the objectives.txt file is absent, the subset of objectives to use can be
+# set directly in the Optimiser, or if no such restriction is set, the whole
+# set of objectives will be run.
 #
 # Each file listed in *objectives.txt* is loaded if it exists.
 #
@@ -39,22 +43,30 @@ module Biopsy
     attr_reader :last_tempdir
     attr_accessor :objectives
 
-    def initialize target
+    def initialize(target)
       @target = target
       @objectives_dir = Settings.instance.objectives_dir.first
       @objectives = {}
       $LOAD_PATH.unshift(@objectives_dir)
-      @subset = Settings.instance.respond_to?(:objectives_subset) ? Settings.instance.objectives_subset : nil
-      self.load_objectives
+      if Settings.instance.respond_to?(:objectives_subset)
+        @subset = Settings.instance.objectives_subset
+      else
+        @subset = nil
+      end
+      load_objectives
       # pass objective list back to caller
-      return @objectives.keys
+      @objectives.keys
     end
 
     def load_objectives
       # load objectives
       # load subset list if available
       subset_file = @objectives_dir + '/objectives.txt'
-      subset = File.exists?(subset_file) ? File.open(subset_file).readlines.map{ |l| l.strip } : nil
+      if File.exist?(subset_file)
+        subset = File.open(subset_file).readlines.map { |l| l.strip }
+      else
+        subset = nil
+      end
       subset = @subset if subset.nil?
       # parse in objectives
       Dir.chdir @objectives_dir do
@@ -63,7 +75,7 @@ module Biopsy
           require file_name
           objective_name = file_name.camelize
           objective =  Module.const_get(objective_name).new
-          if subset.nil? or subset.include?(file_name)
+          if subset.nil? || subset.include?(file_name)
             # this objective is included
             @objectives[objective_name] = objective
           end
@@ -74,47 +86,49 @@ module Biopsy
 
     # Run a specific +:objective+ on the +:output+ of a target
     # with max +:threads+.
-    def run_objective(objective, name, raw_output, output_files, threads)
-      begin
-        # output is a, array: [raw_output, output_files].
-        # output_files is a hash containing the absolute paths
-        # to file(s) output by the target in the format expected by the
-        # objective function(s), with keys as the keys expected by the
-        # objective function
-        return objective.run(raw_output, output_files, threads)
-      rescue NotImplementedError => e
-        puts "Error: objective function #{objective.class} does not implement the run() method"
-        puts "Please refer to the documentation for instructions on adding objective functions"
-        raise e
-      end
+    def run_objective(objective, _name, raw_output, output_files, threads)
+      # output is a, array: [raw_output, output_files].
+      # output_files is a hash containing the absolute paths
+      # to file(s) output by the target in the format expected by the
+      # objective function(s), with keys as the keys expected by the
+      # objective function
+      return objective.run(raw_output, output_files, threads)
+    rescue
+      error = "Error: objective function #{objective.class} does not "
+      error << "implement the run() method\nPlease refer to the "
+      error << "documentation for instructions on adding objective functions"
+      # raise NotImplementedError.new("message")
+      raise NotImplementedError, error
     end
 
     # Perform a euclidean distance dimension reduction of multiple objectives
     def dimension_reduce(results)
       # calculate the weighted Euclidean distance from optimal
-      # d(p, q) = \sqrt{(p_1 - q_1)^2 + (p_2 - q_2)^2+...+(p_i - q_i)^2+...+(p_n - q_n)^2}
-      # here the max value is sqrt(n) where n is no. of results, min value (optimum) is 0
+      # d(p, q) = \sqrt{(p_1 - q_1)^2 + (p_2 - q_2)^2+...+(p_n - q_n)^2}
+      # here the max value is sqrt(n) where n is no. of results,
+      #   min value (optimum) is 0
       total = 0
-      results.each_pair do |key, value|
+      results.each_value do |value|
         o = value[:optimum]
         w = value[:weighting]
         a = value[:result]
         m = value[:max]
-        total += w * (((o - a)/m) ** 2)
+        total += w * (((o - a) / m)**2) if m != 0
       end
-      return Math.sqrt(total) / results.length
+      Math.sqrt(total) / results.length
     end
 
-    # Run all objectives functions for +:output+. 
-    def run_for_output(raw_output, threads=6, allresults=false)
+    # Run all objectives functions for +:output+.
+    def run_for_output(raw_output, threads, allresults)
       # check output files exist
       output_files = {}
       @target.output.each_pair do |key, glob|
         files = Dir[glob]
-        zerosize = files.reduce(false) { |empty, f| File.size(f) == 0 }
-        if files.empty? || zerosize
-          puts ObjectiveHandlerError.new "output files for #{key} matching #{glob} do not exist or are empty"
-          return nil
+        size = files.reduce(1) { |sum, f| sum * File.size(f)}
+        if files.empty? || size==0
+          error = "output files for #{key} matching #{glob} do not exist" +
+                  " or are empty"
+          raise ObjectiveHandlerError, error
         end
         output_files[key] = files.map { |f| File.expand_path(f) }
       end
@@ -122,19 +136,18 @@ module Biopsy
       # run all objectives for output
       results = {}
       @objectives.each_pair do |name, objective|
-        results[name] = self.run_objective(objective, name, raw_output, output_files, threads)
+        results[name] = self.run_objective(objective, name, raw_output,
+                                           output_files, threads)
       end
 
       if allresults
-        return {:results => results,
-                :reduced => self.dimension_reduce(results)}
+        return { :results => results,
+                 :reduced => self.dimension_reduce(results) }
       else
-        results.each_pair do |key, value|
+        results.each_value do |value|
           return value.kind_of?(Hash) ? value[:result] : value
         end
       end
     end
-
   end
-
 end

data/lib/biopsy/optimisers/parameter_sweeper.rb

@@ -18,7 +18,7 @@ require 'logger'
 
 module Biopsy
   # options - is a hash of two hashes, :settings and :parameters
-  #   :ranges are arrays to be parameter sweeped 
+  #   :ranges are arrays to be parameter sweeped
   #     ---(single values may be present, these are also remain unchanged but are accessible within the parameters hash to the constructor)
   class ParameterSweeper
 
@@ -45,7 +45,7 @@ module Biopsy
       end
     end
 
-    def setup *args
+    def setup(*_args)
       @best = {
         :parameters => nil,
         :score => nil
@@ -54,9 +54,11 @@ module Biopsy
 
     # return the next parameter set to evaluate
     def run_one_iteration(parameters, score)
-      @current = {:parameters => parameters, :score => score}
+      @current = { :parameters => parameters, :score => score }
       self.update_best?
-      @combinations.pop rescue nil
+      @combinations.pop
+    rescue
+      nil
     end
 
     def update_best?
@@ -68,7 +70,7 @@ module Biopsy
     # generate all the parameter combinations to be applied
     def generate_combinations(index, opts)
       if index == @ranges.length
-        @combinations << opts.clone  
+        @combinations << opts.clone
         return
       end
       # recurse
@@ -88,15 +90,15 @@ module Biopsy
     end
 
     def select_starting_point
-      return @combinations.pop
+      @combinations.pop
     end
 
     def random_start_point
-      return @combinations.pop
+      @combinations.pop
     end
 
     def finished?
-      return @combinations.empty?
+      @combinations.empty?
     end
 
     # True if this algorithm chooses its own starting point

data/lib/biopsy/optimisers/tabu_search.rb

@@ -30,7 +30,7 @@ module Biopsy
       @range = range
       @sd_increment_proportion = sd_increment_proportion
       self.generate_distribution
-    rescue
+      rescue
         raise "generation of distribution with mean: #{@mean}, sd: #{@sd} failed."
     end
 
@@ -45,7 +45,7 @@ module Biopsy
     end
 
     # loosen the distribution by increasing the sd
-    # and renerating
+    # and regenerating
     def loosen(factor=1)
       @sd += @sd_increment_proportion * factor * @range.size
       self.limit_sd
@@ -159,8 +159,8 @@ module Biopsy
   class TabuSearch #< OptmisationAlgorithm
 
     attr_reader :current, :best, :hood_no
-    attr_accessor :max_hood_size, :sd_increment_proportion, :starting_sd_divisor, :backtrack_cutoff
-    attr_accessor :jump_cutoff
+    attr_accessor :max_hood_size, :sd_increment_proportion
+    attr_accessor :starting_sd_divisor, :backtrack_cutoff, :jump_cutoff
 
     Thread = Struct.new(:best, :tabu, :distributions, 
                         :standard_deviations, :recent_scores, 

data/lib/biopsy/target.rb

@@ -5,6 +5,9 @@ module Biopsy
   class TargetLoadError < Exception
   end
 
+  class TypeLoadError < Exception
+  end
+
   class Target
     require 'yaml'
     require 'set'
@@ -104,12 +107,25 @@ module Biopsy
           # optimise this parameter
           if data[:values] 
             # definition has provided an array of values
-            raise TargetLoadError.new("'values' for parameter #{param} is not an array") unless data[:values].is_a? Array
+            if !data[:values].is_a? Array
+              raise TargetLoadError.new("'values' for parameter #{param} is not an array")
+            end
+            if data[:type] == 'integer'
+              data[:values].each do |v|
+                raise TypeLoadError.new("'values' for parameter #{param} expected integer") unless v.is_a? Integer
+              end
+            elsif data[:type] == 'string'
+              data[:values].each do |v|
+                raise TypeLoadError.new("'values' for parameter #{param} expected string") unless v.is_a? String
+              end
+            end
             @parameters[param] = data[:values]
           else
             # definition has specified a range
             min, max, step = data[:min], data[:max], data[:step]
-            raise TargetLoadError.new("min and max must be set for parameter #{param}") unless min && max
+            unless min && max
+              raise TargetLoadError.new("min and max must be set for parameter #{param}") 
+            end
             range = (min..max)
             range = range.step(step) if step
             @parameters[param] = range.to_a
@@ -128,10 +144,10 @@ module Biopsy
 
     # pass calls to missing methods to the constructor iff
     # the constructor's class directly defines that method
-    def method_missing(meth, *args, &block)
+    def method_missing(method, *args, &block)
       const_methods = @constructor.class.instance_methods(false)
-      if const_methods.include? meth
-        @constructor
+      if const_methods.include? method
+        return @constructor.send(method, *args, &block)
       else
         super
       end
@@ -139,9 +155,9 @@ module Biopsy
 
     # accurately report ability to respond to methods passed
     # to constructor
-    def method_missing(meth, *args, &block)
+    def respond_to?(method, *args, &block)
       const_methods = @constructor.class.instance_methods(false)
-      if const_methods.include? meth
+      if const_methods.include? method
         true
       else
         super

data/lib/biopsy/version.rb

@@ -1,10 +1,12 @@
 # encoding: utf-8
 
 module Biopsy
+
+
   module VERSION
     MAJOR = 0
-    MINOR = 1
-    PATCH = 9
+    MINOR = 2
+    PATCH = 0
 
     STRING = [MAJOR, MINOR, PATCH].compact.join('.')
   end

data/test/brokenconfig.yml

@@ -0,0 +1,3 @@
+---
+:objectives_dir: ./objectives
+:wrongkey: this_should_cause_error

data/test/helper.rb

@@ -106,7 +106,7 @@ class TargetTest
   end
 
   def fake_method
-    true
+    :fake_method_success
   end
 
 end
@@ -153,6 +153,24 @@ end
     self.string_dump objective, @objective_path
   end
 
+  def create_invalid_objective
+    objective = %Q{
+class TestObjective2 < Biopsy::ObjectiveFunction
+
+  require 'yaml'
+
+  def initialize
+    @optimum = 0
+    @max = 0
+    @weighting = 1
+  end
+
+end
+    }
+    @objective_path = File.join(@objective_dir, 'test_objective2.rb')
+    self.string_dump objective, @objective_path
+  end
+
   # Dump +:object+ as YAML to +:file+
   def yaml_dump object, file
     self.string_dump object.to_yaml, file

data/test/test_experiment.rb

@@ -24,25 +24,27 @@ class TestExperiment < Test::Unit::TestCase
       @h.cleanup
     end
 
-    should "fail to init when passed a non existent target" do
+    should 'fail to init when passed a non existent target' do
       assert_raise Biopsy::TargetLoadError do
         Biopsy::Experiment.new('fake_target')
       end
     end
 
-    should "be able to select a valid point from the parameter space" do
+    should 'be able to select a valid point from the parameter space' do
       e = Biopsy::Experiment.new('target_test')
       start_point = e.random_start_point
       start_point.each_pair do |param, value|
-        assert @target.parameters[param].include?(value), "#{value} not in #{@target.parameters[param]}"
+        assert @target.parameters[param].include?(value),
+               "#{value} not in #{@target.parameters[param]}"
       end
     end
 
-    should "be able to select a starting point" do
+    should 'be able to select a starting point' do
       e = Biopsy::Experiment.new('target_test')
       start_point = e.start
       start_point.each_pair do |param, value|
-        assert @target.parameters[param].include?(value), "#{value} not in #{@target.parameters[param]}"
+        assert @target.parameters[param].include?(value),
+               "#{value} not in #{@target.parameters[param]}"
       end
     end
 
@@ -52,12 +54,12 @@ class TestExperiment < Test::Unit::TestCase
       assert_equal s, e.start
     end
 
-    should "automatically select an optimiser if none is specified" do
+    should 'automatically select an optimiser if none is specified' do
       e = Biopsy::Experiment.new('target_test')
       assert e.algorithm.kind_of? Biopsy::TabuSearch
     end
 
-    should "return an optimal set of parameters and score when run" do
+    should 'return an optimal set of parameters and score when run' do
       Dir.chdir @h.tmp_dir do
         e = Biopsy::Experiment.new('target_test', verbosity: :silent)
         known_best = -4
@@ -66,7 +68,11 @@ class TestExperiment < Test::Unit::TestCase
       end
     end
 
-    should "run really quickly when starting from the optimal parameters" do
+    should 'always finish running an experiment' do
+      assert_equal false, true, 'not yet implemented'
+    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)
@@ -76,14 +82,13 @@ class TestExperiment < Test::Unit::TestCase
       end
     end
 
-    should "run using the parameter sweeper (with limit)" do
+    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
+        assert best_found
       end
     end
   end # Experiment context
-
-end # TestExperiment
+end # TestExperiment

data/test/test_objective_handler.rb

@@ -61,11 +61,32 @@ class TestObjectiveHandler < Test::Unit::TestCase
         f.puts values.to_yaml
       end
       Dir.chdir(@h.tmp_dir) do
-        result = oh.run_for_output(nil, {:onlyfile => file})
+        result = oh.run_for_output(nil, 1, nil)
         assert_equal 0, result
       end
     end
 
+    should "run an objective and return all the results" do
+      oh = Biopsy::ObjectiveHandler.new @target
+      values = {
+        :a => 4,
+        :b => 4,
+        :c => 4
+      }
+      file = File.expand_path(File.join(@h.tmp_dir, 'output.txt'))
+      File.open(file, 'w') do |f|
+        f.puts values.to_yaml
+      end
+      expected = {:results=> {
+          "TestObjective"=>{:optimum=>0, :max=>0, :weighting=>1, :result=>-0.0}
+        },
+        :reduced => 0.0}
+      Dir.chdir(@h.tmp_dir) do
+        result = oh.run_for_output(nil, 1, 1)
+        assert_equal result, expected
+      end
+    end
+
     should "perform euclidean distance dimension reduction" do
       oh = Biopsy::ObjectiveHandler.new @target
       results = {
@@ -91,6 +112,41 @@ class TestObjectiveHandler < Test::Unit::TestCase
       assert_equal 0.47140452079103173, oh.dimension_reduce(results)
     end
 
+    should "raise NotImplementedError" do
+      @h.create_invalid_objective
+      oh = Biopsy::ObjectiveHandler.new @target
+      values = {
+        :a => 4,
+        :b => 4,
+        :c => 4
+      }
+      file = File.expand_path(File.join(@h.tmp_dir, 'output.txt'))
+      File.open(file, 'w') do |f|
+        f.puts values.to_yaml
+      end
+      Dir.chdir(@h.tmp_dir) do
+        assert_raise NotImplementedError do
+          result = oh.run_for_output(nil, 1, nil)
+        end
+      end
+
+    end
+
+    should "raise ObjectiveHandlerError" do
+      oh = Biopsy::ObjectiveHandler.new @target
+      values = {}
+      # file = File.expand_path(File.join(@h.tmp_dir, 'output.txt'))
+      # File.open(file, 'w') do |f|
+        # f.puts values.to_yaml
+      # end
+      Dir.chdir(@h.tmp_dir) do
+        assert_raise Biopsy::ObjectiveHandlerError do
+          result = oh.run_for_output(nil, 1, nil)
+        end
+      end
+
+    end
+
   end # Experiment context
 
 end # TestExperiment

data/test/test_parametersweep.rb

@@ -0,0 +1,22 @@
+require 'helper'
+
+class TestParameterSweeper < Test::Unit::TestCase
+
+  context "ParameterSweeper" do
+
+    setup do
+      ranges = {:a => [1,2,3], :b => [1,2,3]}
+      @sweep = Biopsy::ParameterSweeper.new(ranges)
+    end
+
+    should "generate a list of combinations" do
+      c = @sweep.combinations
+      assert_equal c.size, 9
+      assert_equal c, [{:a=>1, :b=>1}, {:a=>1, :b=>2}, {:a=>1, :b=>3},
+       {:a=>2, :b=>1}, {:a=>2, :b=>2}, {:a=>2, :b=>3}, 
+       {:a=>3, :b=>1}, {:a=>3, :b=>2}, {:a=>3, :b=>3}]
+    end
+
+  end # Experiment context
+
+end # TestExperiment

data/test/test_settings.rb

@@ -17,13 +17,19 @@ class TestSettings < Test::Unit::TestCase
     end
 
     teardown do
-      File.delete @config_file if File.exists? @config_file
+      File.delete @config_file if File.exist? @config_file
     end
 
     should "load the specified config file" do
       assert @settings.objectives_dir == @data[:objectives_dir]
     end
 
+    should "raise an error on loading invalid YAML file" do
+      assert_raise(Biopsy::SettingsError) do
+        @settings.load(File.expand_path('test/brokenconfig.yml'))
+      end
+    end
+
     should "complain about malformed config file" do
       # write non-YAML data to file
       File.open(@config_file, 'w') do |f|
@@ -38,7 +44,7 @@ class TestSettings < Test::Unit::TestCase
       @settings.save @config_file
       @settings.load @config_file
       @data.each_pair do |key, value|
-        varname = "@#{key.to_s}".to_sym
+        varname = "@#{key}".to_sym
         assert_equal value, @settings.instance_variable_get(varname)
       end
     end
@@ -48,18 +54,19 @@ class TestSettings < Test::Unit::TestCase
     end
 
     should "make loaded settings available as methods" do
-      assert @settings.objectives_dir == @data[:objectives_dir], 'objectives_dir key not loaded as method'
+      assert @settings.objectives_dir == @data[:objectives_dir],
+             'objectives_dir key not loaded as method'
     end
 
     should "produce a YAML string representation" do
       s = @settings.to_s
       h = YAML.load(s)
       h.each_pair do |key, value|
-        varname = "@#{key.to_s}".to_sym
+        varname = "@#{key}".to_sym
         assert_equal value, @settings.instance_variable_get(varname)
       end
     end
 
   end # RunHandler context
 
-end # TestRunHandler
+end # TestRunHandler

data/test/test_target.rb

@@ -56,6 +56,7 @@ class TestTarget < Test::Unit::TestCase
 
     should "be able to store a loaded config file" do
       config = YAML::load_file(@h.target_path).deep_symbolize
+      config[:shortname] = 'tt'
       @target.store_config config
       @h.target_data.each_pair do |key, value|
         if key == :parameters
@@ -65,10 +66,10 @@ class TestTarget < Test::Unit::TestCase
               r = (spec[:min]..spec[:max])
               r = spec[:step] ? r.step(spec[:step]) : r
               parsed[param] = r.to_a
-            elsif spec[:values]
-              parsed[param] = spec[:values]
-            else
-              assert false, "parameter #{param} with spec #{spec} has no range or values"
+            # elsif spec[:values]
+            #   parsed[param] = spec[:values]
+            # else
+            #   assert false, "parameter #{param} with spec #{spec} has no range or values"
             end
           end
           parsed.each_pair do |param, spec|
@@ -95,10 +96,81 @@ class TestTarget < Test::Unit::TestCase
       File.delete @target.constructor_path
     end
 
-    should "pass missing method calls to constructor iff it directly defines them" do
+    should "raise an exception if values doesn't provide an array" do
+      params = {
+        :a => {
+          :type => 'integer',
+          :opt => true,
+          :values => 3
+        }
+      }
+      assert_raise Biopsy::TargetLoadError do
+        @target.generate_parameters params
+      end
+    end
+
+    should "raise an exception for trying to load a string as an integer" do
+      params = {
+        :a => {
+          :type => 'integer',
+          :opt => true,
+          :values => ["yes","no","maybe"]
+        }
+      }
+      assert_raise Biopsy::TypeLoadError do
+        @target.generate_parameters params
+      end
+    end
+
+    should "raise an exception for trying to load an integer as a string" do
+      params = {
+        :b => {
+          :type => 'string',
+          :opt => true,
+          :values => [1,2,3]
+        }
+      }
+      assert_raise Biopsy::TypeLoadError do
+        @target.generate_parameters params
+      end
+    end
+
+    should "raise an exception of type TargetLoadError" do
+      params = {
+        :a => {
+          :type => 'integer',
+          :opt => true
+        }
+      }
+      assert_raise Biopsy::TargetLoadError do
+        @target.generate_parameters params
+      end
+    end
+
+    should "load array" do
+      params = {
+        :a => {
+          :type => 'string',
+          :opt => true,
+          :values => ["yes","no","maybe"]
+        },
+        :b => {
+          :type => 'integer',
+          :opt => false,
+          :values => 0
+        }
+      }
+      @target.generate_parameters params
+      assert_equal @target.parameters, {:a => ["yes", "no", "maybe"]}
+      assert_equal @target.options, {:b=>{:type=>"integer", :opt=>false, :values=>0}}
+    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_equal @target.fake_method, :fake_method_success
       assert_raise NoMethodError do
         @target.totes_fake_method
       end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: biopsy
 version: !ruby/object:Gem::Version
-  version: 0.1.9
+  version: 0.2.0
 platform: ruby
 authors:
 - Richard Smith
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-04-24 00:00:00.000000000 Z
+date: 2014-04-26 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake
@@ -16,14 +16,14 @@ dependencies:
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '10.3'
+        version: '10.1'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '10.3'
+        version: '10.1'
 - !ruby/object:Gem::Dependency
   name: threach
   requirement: !ruby/object:Gem::Requirement
@@ -84,16 +84,16 @@ dependencies:
   name: turn
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ">="
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: '0'
+        version: '0.9'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ">="
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: '0'
+        version: '0.9'
 - !ruby/object:Gem::Dependency
   name: simplecov
   requirement: !ruby/object:Gem::Requirement
@@ -142,30 +142,32 @@ executables: []
 extensions: []
 extra_rdoc_files: []
 files:
-- LICENSE.txt
-- README.md
 - Rakefile
 - lib/biopsy.rb
-- lib/biopsy/base_extensions.rb
-- lib/biopsy/experiment.rb
-- lib/biopsy/objective_function.rb
+- lib/biopsy/version.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/parameter_sweeper.rb
 - lib/biopsy/optimisers/spea2.rb
-- lib/biopsy/optimisers/tabu_search.rb
-- lib/biopsy/settings.rb
+- lib/biopsy/optimisers/parameter_sweeper.rb
+- lib/biopsy/objective_function.rb
 - lib/biopsy/target.rb
-- lib/biopsy/version.rb
-- test/helper.rb
-- test/test_experiment.rb
-- test/test_file.rb
+- lib/biopsy/base_extensions.rb
+- lib/biopsy/experiment.rb
+- test/test_parametersweep.rb
+- test/test_target.rb
 - test/test_hash.rb
+- test/test_string.rb
+- test/helper.rb
+- test/brokenconfig.yml
 - 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: {}
@@ -185,9 +187,8 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 2.2.2
+rubygems_version: 2.1.4
 signing_key: 
 specification_version: 4
 summary: framework for optimising any computational pipeline or program
 test_files: []
-has_rdoc: