biopsy 0.1.5.alpha → 0.1.6.alpha

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (4) hide show
  1. data/lib/biopsy/experiment.rb +3 -2
  2. data/lib/biopsy/version.rb +1 -1
  3. metadata +50 -32
  4. checksums.yaml +0 -7
data/lib/biopsy/experiment.rb CHANGED
@@ -19,7 +19,7 @@ module Biopsy
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  attr_reader :inputs, :outputs, :retain_intermediates, :target, :start, :algorithm
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  # Returns a new Experiment
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- def initialize(target, start=nil, algorithm=nil)
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+ def initialize(target, options={}, start=nil, algorithm=nil)
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  @start = start
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  @algorithm = algorithm
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  if target.is_a? Target
@@ -27,6 +27,7 @@ module Biopsy
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  else
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  self.load_target target
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  end
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+ @options = options
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  @objective = ObjectiveHandler.new @target
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  self.select_algorithm
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  self.select_starting_point
@@ -91,7 +92,7 @@ module Biopsy
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  # create temp dir
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  Dir.chdir(self.create_tempdir) do
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  # run the target
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- raw_output = @target.run @current_params
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+ raw_output = @target.run @current_params.merge(@options)
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  # evaluate with objectives
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  param_key = @current_params.to_s
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  result = nil
data/lib/biopsy/version.rb CHANGED
@@ -4,7 +4,7 @@ module Biopsy
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  module VERSION
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  MAJOR = 0
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  MINOR = 1
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- PATCH = 5
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+ PATCH = 6
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  BUILD = 'alpha'
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  STRING = [MAJOR, MINOR, PATCH, BUILD].compact.join('.')
metadata CHANGED
@@ -1,18 +1,20 @@
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  --- !ruby/object:Gem::Specification
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  name: biopsy
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  version: !ruby/object:Gem::Version
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- version: 0.1.5.alpha
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+ version: 0.1.6.alpha
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+ prerelease: 6
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  platform: ruby
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  authors:
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  - Richard Smith
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  autorequire:
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  bindir: bin
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  cert_chain: []
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- date: 2013-09-18 00:00:00.000000000 Z
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+ date: 2013-09-19 00:00:00.000000000 Z
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  dependencies:
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  - !ruby/object:Gem::Dependency
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  name: rake
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  requirement: !ruby/object:Gem::Requirement
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+ none: false
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  requirements:
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  - - ~>
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  - !ruby/object:Gem::Version
@@ -20,6 +22,7 @@ dependencies:
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  type: :runtime
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  prerelease: false
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  version_requirements: !ruby/object:Gem::Requirement
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+ none: false
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  requirements:
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  - - ~>
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  - !ruby/object:Gem::Version
@@ -27,90 +30,103 @@ dependencies:
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  - !ruby/object:Gem::Dependency
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  name: threach
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  requirement: !ruby/object:Gem::Requirement
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+ none: false
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  requirements:
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- - - '>='
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+ - - ! '>='
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  - !ruby/object:Gem::Version
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  version: '0'
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  type: :runtime
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  prerelease: false
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  version_requirements: !ruby/object:Gem::Requirement
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+ none: false
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  requirements:
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- - - '>='
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+ - - ! '>='
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  - !ruby/object:Gem::Version
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  version: '0'
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  - !ruby/object:Gem::Dependency
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  name: rubystats
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  requirement: !ruby/object:Gem::Requirement
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+ none: false
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  requirements:
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- - - '>='
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+ - - ! '>='
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  - !ruby/object:Gem::Version
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  version: '0'
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  type: :runtime
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  prerelease: false
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  version_requirements: !ruby/object:Gem::Requirement
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+ none: false
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  requirements:
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- - - '>='
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+ - - ! '>='
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  - !ruby/object:Gem::Version
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  version: '0'
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  - !ruby/object:Gem::Dependency
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  name: statsample
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  requirement: !ruby/object:Gem::Requirement
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+ none: false
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  requirements:
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- - - '>='
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+ - - ! '>='
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  - !ruby/object:Gem::Version
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  version: '0'
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  type: :runtime
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  prerelease: false
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  version_requirements: !ruby/object:Gem::Requirement
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+ none: false
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  requirements:
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- - - '>='
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+ - - ! '>='
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  - !ruby/object:Gem::Version
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  version: '0'
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  - !ruby/object:Gem::Dependency
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  name: turn
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  requirement: !ruby/object:Gem::Requirement
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+ none: false
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  requirements:
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- - - '>='
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+ - - ! '>='
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  - !ruby/object:Gem::Version
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  version: '0'
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  type: :development
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  prerelease: false
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  version_requirements: !ruby/object:Gem::Requirement
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+ none: false
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  requirements:
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- - - '>='
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+ - - ! '>='
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  - !ruby/object:Gem::Version
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  version: '0'
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  - !ruby/object:Gem::Dependency
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  name: simplecov
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  requirement: !ruby/object:Gem::Requirement
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+ none: false
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  requirements:
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- - - '>='
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+ - - ! '>='
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  - !ruby/object:Gem::Version
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  version: '0'
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  type: :development
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  prerelease: false
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  version_requirements: !ruby/object:Gem::Requirement
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+ none: false
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  requirements:
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- - - '>='
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+ - - ! '>='
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  - !ruby/object:Gem::Version
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  version: '0'
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  - !ruby/object:Gem::Dependency
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  name: shoulda-context
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  requirement: !ruby/object:Gem::Requirement
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+ none: false
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  requirements:
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- - - '>='
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+ - - ! '>='
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  - !ruby/object:Gem::Version
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  version: '0'
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  type: :development
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  prerelease: false
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  version_requirements: !ruby/object:Gem::Requirement
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+ none: false
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  requirements:
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- - - '>='
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+ - - ! '>='
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  - !ruby/object:Gem::Version
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  version: '0'
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  - !ruby/object:Gem::Dependency
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  name: coveralls
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  requirement: !ruby/object:Gem::Requirement
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+ none: false
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  requirements:
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  - - ~>
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  - !ruby/object:Gem::Version
@@ -118,6 +134,7 @@ dependencies:
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  type: :development
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  prerelease: false
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  version_requirements: !ruby/object:Gem::Requirement
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+ none: false
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  requirements:
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  - - ~>
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  - !ruby/object:Gem::Version
@@ -129,50 +146,51 @@ extensions: []
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  extra_rdoc_files: []
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  files:
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  - Rakefile
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- - lib/biopsy/version.rb
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- - lib/biopsy/objective_handler.rb
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- - lib/biopsy/settings.rb
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  - lib/biopsy/base_extensions.rb
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- - lib/biopsy/target.rb
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- - lib/biopsy/objectives/fastest_optimum.rb
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  - lib/biopsy/experiment.rb
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- - lib/biopsy/opt_algorithm.rb
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  - lib/biopsy/objective_function.rb
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- - lib/biopsy/optimisers/tabu_search.rb
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- - lib/biopsy/optimisers/parameter_sweeper.rb
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+ - lib/biopsy/objective_handler.rb
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+ - lib/biopsy/objectives/fastest_optimum.rb
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+ - lib/biopsy/opt_algorithm.rb
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  - lib/biopsy/optimisers/genetic_algorithm.rb
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+ - lib/biopsy/optimisers/parameter_sweeper.rb
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+ - lib/biopsy/optimisers/tabu_search.rb
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+ - lib/biopsy/settings.rb
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+ - lib/biopsy/target.rb
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+ - lib/biopsy/version.rb
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  - lib/biopsy.rb
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- - test/test_settings.rb
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- - test/test_string.rb
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  - test/helper.rb
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- - test/test_objective_handler.rb
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+ - test/test_experiment.rb
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  - test/test_file.rb
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- - test/test_target.rb
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  - test/test_hash.rb
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- - test/test_experiment.rb
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+ - test/test_objective_handler.rb
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+ - test/test_settings.rb
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+ - test/test_string.rb
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+ - test/test_target.rb
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  - README.md
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  - LICENSE.txt
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  homepage: https://github.com/Blahah/biopsy
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  licenses: []
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- metadata: {}
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  post_install_message:
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  rdoc_options: []
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  require_paths:
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  - lib
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  required_ruby_version: !ruby/object:Gem::Requirement
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+ none: false
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  requirements:
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- - - '>='
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+ - - ! '>='
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  - !ruby/object:Gem::Version
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  version: '0'
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  required_rubygems_version: !ruby/object:Gem::Requirement
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+ none: false
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  requirements:
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- - - '>'
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+ - - ! '>'
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  - !ruby/object:Gem::Version
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  version: 1.3.1
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  requirements: []
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  rubyforge_project:
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- rubygems_version: 2.0.3
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+ rubygems_version: 1.8.24
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  signing_key:
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- specification_version: 4
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+ specification_version: 3
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  summary: framework for optimising any computational pipeline or program
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  test_files: []
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