biopsy 0.1.5.alpha → 0.1.6.alpha

data/lib/biopsy/experiment.rb

@@ -19,7 +19,7 @@ module Biopsy
     attr_reader :inputs, :outputs, :retain_intermediates, :target, :start, :algorithm
 
     # Returns a new Experiment
-    def initialize(target, start=nil, algorithm=nil)
+    def initialize(target, options={}, start=nil, algorithm=nil)
       @start = start
       @algorithm = algorithm
       if target.is_a? Target
@@ -27,6 +27,7 @@ module Biopsy
       else
         self.load_target target
       end
+      @options = options
       @objective = ObjectiveHandler.new @target
       self.select_algorithm
       self.select_starting_point
@@ -91,7 +92,7 @@ module Biopsy
       # create temp dir
         Dir.chdir(self.create_tempdir) do
         # run the target
-        raw_output = @target.run @current_params
+        raw_output = @target.run @current_params.merge(@options)
         # evaluate with objectives
         param_key = @current_params.to_s
         result = nil

data/lib/biopsy/version.rb

@@ -4,7 +4,7 @@ module Biopsy
   module VERSION
     MAJOR = 0
     MINOR = 1
-    PATCH = 5
+    PATCH = 6
     BUILD = 'alpha'
 
     STRING = [MAJOR, MINOR, PATCH, BUILD].compact.join('.')

metadata

@@ -1,18 +1,20 @@
 --- !ruby/object:Gem::Specification
 name: biopsy
 version: !ruby/object:Gem::Version
-  version: 0.1.5.alpha
+  version: 0.1.6.alpha
+  prerelease: 6
 platform: ruby
 authors:
 - Richard Smith
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2013-09-18 00:00:00.000000000 Z
+date: 2013-09-19 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake
   requirement: !ruby/object:Gem::Requirement
+    none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
@@ -20,6 +22,7 @@ dependencies:
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
+    none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
@@ -27,90 +30,103 @@ 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
@@ -118,6 +134,7 @@ dependencies:
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
+    none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
@@ -129,50 +146,51 @@ extensions: []
 extra_rdoc_files: []
 files:
 - Rakefile
-- 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/objective_function.rb
-- lib/biopsy/optimisers/tabu_search.rb
-- lib/biopsy/optimisers/parameter_sweeper.rb
+- lib/biopsy/objective_handler.rb
+- lib/biopsy/objectives/fastest_optimum.rb
+- lib/biopsy/opt_algorithm.rb
 - lib/biopsy/optimisers/genetic_algorithm.rb
+- lib/biopsy/optimisers/parameter_sweeper.rb
+- lib/biopsy/optimisers/tabu_search.rb
+- lib/biopsy/settings.rb
+- lib/biopsy/target.rb
+- lib/biopsy/version.rb
 - lib/biopsy.rb
-- test/test_settings.rb
-- test/test_string.rb
 - test/helper.rb
-- test/test_objective_handler.rb
+- test/test_experiment.rb
 - test/test_file.rb
-- test/test_target.rb
 - test/test_hash.rb
-- test/test_experiment.rb
+- test/test_objective_handler.rb
+- test/test_settings.rb
+- test/test_string.rb
+- test/test_target.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: 2.0.3
+rubygems_version: 1.8.24
 signing_key: 
-specification_version: 4
+specification_version: 3
 summary: framework for optimising any computational pipeline or program
 test_files: []

checksums.yaml

@@ -1,7 +0,0 @@
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