biopsy 0.1.0.alpha → 0.1.1.alpha

data/test/helper.rb

@@ -11,9 +11,10 @@ require 'test/unit'
 begin; require 'turn/autorun'; rescue LoadError; end
 require 'shoulda-context'
 require 'biopsy'
+require 'yaml'
 
 Turn.config.format = :pretty
-Turn.config.trace = 10
+Turn.config.trace = 5
 
 Biopsy::Settings.instance.set_defaults
 
@@ -24,8 +25,6 @@ class Helper
 
   attr_reader :tmp_dir
   attr_reader :target_dir
-  attr_reader :domain_dir
-  attr_reader :domain_path
   attr_reader :target_path
   attr_reader :objective_dir
   attr_reader :objective_path
@@ -48,18 +47,32 @@ class Helper
   # Return a hash of valid target data
   def target_data
     {
-      :input_files => {
-        :in => 'input.txt'
+      :name => 'target_test',
+      :output => {
+        :onlyfile => 'output.txt'
       },
-      :output_files => {
-        :params => 'output.txt'
-      },
-      :parameter_ranges => {
-        :a => (-40..40).step(2).to_a,
-        :b => (0..100).step(2).to_a,
-        :c => (-50..50).to_a
+      :parameters => {
+        :a => {
+          type: 'integer',
+          opt: true,
+          min: -40,
+          max: 40,
+          step: 2
+        },
+        :b => {
+          type: 'integer',
+          opt: true,
+          min: 0,
+          max: 40,
+          step: 2
+        },
+        :c => {
+          type: 'integer',
+          opt: true,
+          min: -20,
+          max: 20
+        }
       },
-      :constructor_path => 'test_constructor.rb'
     }
   end
 
@@ -73,12 +86,15 @@ class Helper
   # Create a valid target definition in the target dir
   def create_valid_target
     data = self.target_data
-    name = 'test_target'
+    name = 'target_test'
     @target_path = File.join(@target_dir, name + '.yml')
     self.yaml_dump data, @target_path
-    File.open(File.join(@target_dir, data[:constructor_path]), 'w') do |f|
+    File.open(File.join(@target_dir, name + '.rb'), 'w') do |f|
       f.puts %Q{
-class TestConstructor
+class TargetTest
+
+  def initialize
+  end
 
   require 'yaml'
 
@@ -86,7 +102,7 @@ class TestConstructor
     File.open('output.txt', 'w') do |f|
       f.puts(params.to_yaml)
     end
-    { :params => File.expand_path('output.txt') }
+    nil
   end
 
 end
@@ -95,45 +111,6 @@ end
     name
   end
 
-  # Return a hash of valid domain data
-  def domain_data
-    {
-      :input_filetypes => [
-        {
-          :n => 1,
-          :allowed_extensions => [
-            '.txt'
-          ]
-        }
-      ],
-      :output_filetypes => [
-        {
-          :n => 1,
-          :allowed_extensions => [
-            '.txt'
-          ]
-        }
-      ],
-      :objectives => [
-        'test1', 'test2'
-      ]
-    }
-  end
-
-  def setup_domain
-    @domain_dir = File.join(@tmp_dir, 'domains')
-    Dir.mkdir @domain_dir
-    Biopsy::Settings.instance.domain_dir = [@domain_dir]
-  end
-
-  def create_valid_domain
-    data = domain_data
-    name = 'test_domain'
-    @domain_path = File.join(@domain_dir, name + '.yml')
-    self.yaml_dump data, @domain_path
-    name
-  end
-
   def setup_objective
     @objective_dir = File.join(@tmp_dir, 'objectives')
     Dir.mkdir @objective_dir
@@ -152,8 +129,8 @@ class TestObjective < Biopsy::ObjectiveFunction
     @weighting = 1
   end
 
-  def run(input, threads)
-    file = input[:params]
+  def run(raw_output, output_files, threads)
+    file = output_files[:onlyfile].first
     input = YAML::load_file(file)
     a = input[:a].to_i
     b = input[:b].to_i

data/test/test_experiment.rb

@@ -8,15 +8,10 @@ class TestExperiment < Test::Unit::TestCase
       @h = Helper.new
       @h.setup_tmp_dir
 
-      # we need a domain
-      @h.setup_domain
-      domain_name = @h.create_valid_domain
-      @domain = Biopsy::Domain.new domain_name
-
       # and a target
       @h.setup_target
       target_name = @h.create_valid_target
-      @target = Biopsy::Target.new @domain
+      @target = Biopsy::Target.new
       @target.load_by_name target_name
 
       # and an objective
@@ -30,53 +25,45 @@ class TestExperiment < Test::Unit::TestCase
 
     should "fail to init when passed a non existent target" do
       assert_raise Biopsy::TargetLoadError do
-        Biopsy::Experiment.new('fake_target', 'test_domain')
-      end
-    end
-
-    should "fail to init when passed a non existent domain" do
-      assert_raise Biopsy::DomainLoadError do
-        Biopsy::Experiment.new('test_target', 'fake_domain')
+        Biopsy::Experiment.new('fake_target')
       end
     end
 
     should "be able to select a valid point from the parameter space" do
-      e = Biopsy::Experiment.new('test_target', 'test_domain')
+      e = Biopsy::Experiment.new('target_test')
       start_point = e.random_start_point
       start_point.each_pair do |param, value|
-        assert @h.target_data[:parameter_ranges][param].include? value
+        assert @target.parameters[param].include?(value), "#{value} not in #{@target.parameters[param]}"
       end
     end
 
     should "be able to select a starting point" do
-      e = Biopsy::Experiment.new('test_target', 'test_domain')
+      e = Biopsy::Experiment.new('target_test')
       start_point = e.start
       start_point.each_pair do |param, value|
-        assert @h.target_data[:parameter_ranges][param].include? value
+        assert @target.parameters[param].include?(value), "#{value} not in #{@target.parameters[param]}"
       end
     end
 
     should "respect user's choice of starting point" do
       s = {:a => 2, :b => 4}
-      e = Biopsy::Experiment.new('test_target', 'test_domain', s)
+      e = Biopsy::Experiment.new('target_test', s)
       assert_equal s, e.start
     end
 
     should "automatically select an optimiser if none is specified" do
-      e = Biopsy::Experiment.new('test_target', 'test_domain')
+      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
       # Kernel.srand 123
-      e = Biopsy::Experiment.new('test_target', 'test_domain')
-      known_best = {
-        :a => 4,
-        :b => 4,
-        :c => 4
-      }
-      best_found = e.run[:parameters]
-      assert_equal known_best, best_found
+      Dir.chdir @h.tmp_dir do
+        e = Biopsy::Experiment.new('target_test')
+        known_best = -4
+        best_found = e.run[:score]
+        assert known_best < best_found
+      end
     end
 
   end # Experiment context

data/test/test_objective_handler.rb

@@ -8,20 +8,15 @@ class TestObjectiveHandler < Test::Unit::TestCase
       @h = Helper.new
       @h.setup_tmp_dir
 
-      # we need a domain
-      @h.setup_domain
-      domain_name = @h.create_valid_domain
-      @domain = Biopsy::Domain.new domain_name
-
       # and a target
       @h.setup_target
       target_name = @h.create_valid_target
-      @target = Biopsy::Target.new @domain
+      @target = Biopsy::Target.new
       @target.load_by_name target_name
       
       # and an objective
       @h.setup_objective
-      objective_name = @h.create_valid_objective
+      @h.create_valid_objective
     end
 
     teardown do
@@ -29,7 +24,7 @@ class TestObjectiveHandler < Test::Unit::TestCase
     end
 
     should "return loaded objectives on init" do
-      oh = Biopsy::ObjectiveHandler.new @domain, @target
+      oh = Biopsy::ObjectiveHandler.new @target
       refute oh.objectives.empty?
     end
 
@@ -49,13 +44,13 @@ class TestObjectiveHandler < Test::Unit::TestCase
           f.puts 'another_objective'
         end
       end
-      oh = Biopsy::ObjectiveHandler.new @domain, @target
+      oh = Biopsy::ObjectiveHandler.new @target
       assert_equal 1, oh.objectives.length
       assert_equal 'AnotherObjective', oh.objectives.keys.first
     end
 
     should "run an objective and return the result" do
-      oh = Biopsy::ObjectiveHandler.new @domain, @target
+      oh = Biopsy::ObjectiveHandler.new @target
       values = {
         :a => 4,
         :b => 4,
@@ -65,12 +60,14 @@ class TestObjectiveHandler < Test::Unit::TestCase
       File.open(file, 'w') do |f|
         f.puts values.to_yaml
       end
-      result = oh.run_for_output({:params => file}, 0, 1, allresults=true)
-      assert_equal 0, result[:results]["TestObjective"][:result]
+      Dir.chdir(@h.tmp_dir) do
+        result = oh.run_for_output(nil, {:onlyfile => file})
+        assert_equal 0, result
+      end
     end
 
     should "perform euclidean distance dimension reduction" do
-      oh = Biopsy::ObjectiveHandler.new @domain, @target
+      oh = Biopsy::ObjectiveHandler.new @target
       results = {
         :a => {
           :optimum => 100,

data/test/test_settings.rb

@@ -6,8 +6,7 @@ class TestSettings < Test::Unit::TestCase
 
     setup do
       @data = {
-        :domain => 'test_domain',
-        :objectives_dir => './objectives',
+        :objectives_dir => './objectives'
       }
       @config_file = File.expand_path 'testconfig.yml'
       @settings = Biopsy::Settings.instance
@@ -22,7 +21,6 @@ class TestSettings < Test::Unit::TestCase
     end
 
     should "load the specified config file" do
-      assert @settings.domain == @data[:domain]
       assert @settings.objectives_dir == @data[:objectives_dir]
     end
 
@@ -50,25 +48,18 @@ class TestSettings < Test::Unit::TestCase
     end
 
     should "make loaded settings available as methods" do
-      assert @settings.domain == @data[:domain], 'domain 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)
-      @data.each_pair do |key, value|
+      h.each_pair do |key, value|
         varname = "@#{key.to_s}".to_sym
         assert_equal value, @settings.instance_variable_get(varname)
       end
     end
 
-    should "error when a non-existent config is requested" do
-      assert_raise Biopsy::SettingsError do
-        @settings.locate_config :fake_key, 'blah'
-      end
-    end
-
   end # RunHandler context
 
 end # TestRunHandler

data/test/test_target.rb

@@ -10,15 +10,10 @@ class TestTarget < Test::Unit::TestCase
       @h = Helper.new
       @h.setup_tmp_dir
 
-      # we need a domain
-      @h.setup_domain
-      domain_name = @h.create_valid_domain
-      @domain = Biopsy::Domain.new domain_name
-
       # and a target
       @h.setup_target
       target_name = @h.create_valid_target
-      @target = Biopsy::Target.new @domain
+      @target = Biopsy::Target.new
       @target.load_by_name target_name
     end
 
@@ -36,7 +31,9 @@ class TestTarget < Test::Unit::TestCase
     end
 
     should "fail to find a non-existent definition" do
-      assert_equal nil, @target.locate_definition('not_real')
+      assert_raise Biopsy::TargetLoadError do
+        @target.locate_definition('not_real')
+      end
     end
 
     should "reject any invalid config" do
@@ -57,17 +54,29 @@ class TestTarget < Test::Unit::TestCase
       end
     end
 
-    should "reject a config that doesn't match the domain spec" do
-      d = @h.target_data
-      d[:input_files][:fake] = 'another.file'
-      assert @target.validate_config(d).length > 0
-    end
-
     should "be able to store a loaded config file" do
       config = YAML::load_file(@h.target_path).deep_symbolize
       @target.store_config config
       @h.target_data.each_pair do |key, value|
-        assert_equal value, @target.instance_variable_get('@' + key.to_s)
+        if key == :parameters
+          parsed = {}
+          value.each_pair do |param, spec|
+            if spec[:min] && spec[:max]
+              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"
+            end
+          end
+          parsed.each_pair do |param, spec|
+            assert_equal spec, @target.parameters[param]
+          end
+        else
+          assert_equal value, @target.instance_variable_get('@' + key.to_s)
+        end
       end
     end
 
@@ -75,13 +84,15 @@ class TestTarget < Test::Unit::TestCase
       config = YAML::load_file(@h.target_path).deep_symbolize
       @target.store_config config
 
-      assert !@target.check_constructor, "missing constructor is invalid"
+      assert_raise Biopsy::TargetLoadError do
+        @target.check_constructor('target_missing')
+      end
 
-      File.open(@h.target_data[:constructor_path], 'w') do |f|
+      File.open(@target.constructor_path, 'w') do |f|
         f.puts '[x**2 for x in range(10)]' # python :)
       end
-      assert !@target.check_constructor, "invalid ruby is invalid"
-      File.delete @h.target_data[:constructor_path]
+      assert !@target.check_constructor('target_test'), "invalid ruby is invalid"
+      File.delete @target.constructor_path
     end
 
   end # Target context

metadata

@@ -1,20 +1,18 @@
 --- !ruby/object:Gem::Specification
 name: biopsy
 version: !ruby/object:Gem::Version
-  version: 0.1.0.alpha
-  prerelease: 6
+  version: 0.1.1.alpha
 platform: ruby
 authors:
 - Richard Smith
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2013-09-06 00:00:00.000000000 Z
+date: 2013-09-18 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
@@ -22,7 +20,6 @@ dependencies:
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
@@ -30,103 +27,90 @@ dependencies:
 - !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
@@ -134,7 +118,6 @@ dependencies:
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
@@ -146,53 +129,50 @@ extensions: []
 extra_rdoc_files: []
 files:
 - Rakefile
-- lib/biopsy/base_extensions.rb
-- lib/biopsy/domain.rb
-- lib/biopsy/experiment.rb
-- lib/biopsy/objective_function.rb
+- lib/biopsy/version.rb
 - lib/biopsy/objective_handler.rb
+- lib/biopsy/settings.rb
+- lib/biopsy/base_extensions.rb
+- lib/biopsy/target.rb
 - lib/biopsy/objectives/fastest_optimum.rb
+- lib/biopsy/experiment.rb
 - lib/biopsy/opt_algorithm.rb
-- lib/biopsy/optimisers/genetic_algorithm.rb
-- lib/biopsy/optimisers/parameter_sweeper.rb
+- lib/biopsy/objective_function.rb
 - lib/biopsy/optimisers/tabu_search.rb
-- lib/biopsy/settings.rb
-- lib/biopsy/target.rb
-- lib/biopsy/version.rb
+- lib/biopsy/optimisers/parameter_sweeper.rb
+- lib/biopsy/optimisers/genetic_algorithm.rb
 - lib/biopsy.rb
-- test/helper.rb
-- test/test_domain.rb
-- test/test_experiment.rb
-- test/test_file.rb
-- test/test_hash.rb
-- test/test_objective_handler.rb
 - test/test_settings.rb
 - test/test_string.rb
+- test/helper.rb
+- test/test_objective_handler.rb
+- test/test_file.rb
 - test/test_target.rb
+- test/test_hash.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
 requirements: []
 rubyforge_project: 
-rubygems_version: 1.8.24
+rubygems_version: 2.0.3
 signing_key: 
-specification_version: 3
+specification_version: 4
 summary: framework for optimising any computational pipeline or program
 test_files: []