biopsy 0.1.0.alpha
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- data/LICENSE.txt +7 -0
- data/README.md +49 -0
- data/Rakefile +8 -0
- data/lib/biopsy/base_extensions.rb +64 -0
- data/lib/biopsy/domain.rb +156 -0
- data/lib/biopsy/experiment.rb +103 -0
- data/lib/biopsy/objective_function.rb +38 -0
- data/lib/biopsy/objective_handler.rb +170 -0
- data/lib/biopsy/objectives/fastest_optimum.rb +26 -0
- data/lib/biopsy/opt_algorithm.rb +0 -0
- data/lib/biopsy/optimisers/genetic_algorithm.rb +244 -0
- data/lib/biopsy/optimisers/parameter_sweeper.rb +66 -0
- data/lib/biopsy/optimisers/tabu_search.rb +437 -0
- data/lib/biopsy/settings.rb +110 -0
- data/lib/biopsy/target.rb +113 -0
- data/lib/biopsy/version.rb +12 -0
- data/lib/biopsy.rb +13 -0
- data/test/helper.rb +187 -0
- data/test/test_domain.rb +61 -0
- data/test/test_experiment.rb +84 -0
- data/test/test_file.rb +20 -0
- data/test/test_hash.rb +55 -0
- data/test/test_objective_handler.rb +99 -0
- data/test/test_settings.rb +74 -0
- data/test/test_string.rb +14 -0
- data/test/test_target.rb +89 -0
- metadata +198 -0
metadata
ADDED
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@@ -0,0 +1,198 @@
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--- !ruby/object:Gem::Specification
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2
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name: biopsy
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3
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version: !ruby/object:Gem::Version
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4
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version: 0.1.0.alpha
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5
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prerelease: 6
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6
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platform: ruby
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7
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authors:
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8
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- Richard Smith
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9
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autorequire:
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10
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bindir: bin
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11
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+
cert_chain: []
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12
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date: 2013-09-06 00:00:00.000000000 Z
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13
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dependencies:
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14
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+
- !ruby/object:Gem::Dependency
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15
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name: rake
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16
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requirement: !ruby/object:Gem::Requirement
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17
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none: false
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18
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requirements:
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19
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+
- - ~>
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20
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+
- !ruby/object:Gem::Version
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21
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+
version: 10.1.0
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22
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+
type: :runtime
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23
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+
prerelease: false
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24
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version_requirements: !ruby/object:Gem::Requirement
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25
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none: false
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26
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requirements:
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27
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+
- - ~>
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28
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+
- !ruby/object:Gem::Version
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29
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version: 10.1.0
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30
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+
- !ruby/object:Gem::Dependency
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31
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+
name: threach
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32
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+
requirement: !ruby/object:Gem::Requirement
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33
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none: false
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34
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requirements:
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35
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+
- - ! '>='
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36
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+
- !ruby/object:Gem::Version
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37
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version: '0'
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38
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+
type: :runtime
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39
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+
prerelease: false
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40
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+
version_requirements: !ruby/object:Gem::Requirement
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41
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none: false
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42
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requirements:
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43
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+
- - ! '>='
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44
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+
- !ruby/object:Gem::Version
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45
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version: '0'
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46
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+
- !ruby/object:Gem::Dependency
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47
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+
name: rubystats
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48
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+
requirement: !ruby/object:Gem::Requirement
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49
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+
none: false
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50
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+
requirements:
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51
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+
- - ! '>='
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52
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+
- !ruby/object:Gem::Version
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53
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+
version: '0'
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54
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+
type: :runtime
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55
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+
prerelease: false
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56
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+
version_requirements: !ruby/object:Gem::Requirement
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57
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+
none: false
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58
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+
requirements:
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59
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+
- - ! '>='
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60
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+
- !ruby/object:Gem::Version
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61
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+
version: '0'
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62
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+
- !ruby/object:Gem::Dependency
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63
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+
name: statsample
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64
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+
requirement: !ruby/object:Gem::Requirement
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65
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+
none: false
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66
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+
requirements:
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67
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+
- - ! '>='
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68
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+
- !ruby/object:Gem::Version
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69
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+
version: '0'
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70
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+
type: :runtime
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71
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+
prerelease: false
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72
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+
version_requirements: !ruby/object:Gem::Requirement
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|
73
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+
none: false
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|
74
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+
requirements:
|
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75
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+
- - ! '>='
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76
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+
- !ruby/object:Gem::Version
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77
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+
version: '0'
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78
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+
- !ruby/object:Gem::Dependency
|
|
79
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+
name: turn
|
|
80
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+
requirement: !ruby/object:Gem::Requirement
|
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81
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+
none: false
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82
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+
requirements:
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83
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+
- - ! '>='
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84
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+
- !ruby/object:Gem::Version
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85
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+
version: '0'
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86
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+
type: :development
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87
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+
prerelease: false
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88
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+
version_requirements: !ruby/object:Gem::Requirement
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89
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+
none: false
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90
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+
requirements:
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91
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+
- - ! '>='
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92
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+
- !ruby/object:Gem::Version
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93
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version: '0'
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94
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+
- !ruby/object:Gem::Dependency
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|
95
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+
name: simplecov
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96
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+
requirement: !ruby/object:Gem::Requirement
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97
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none: false
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98
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requirements:
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99
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+
- - ! '>='
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100
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+
- !ruby/object:Gem::Version
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101
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version: '0'
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|
102
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type: :development
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103
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+
prerelease: false
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104
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version_requirements: !ruby/object:Gem::Requirement
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|
105
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none: false
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106
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requirements:
|
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107
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+
- - ! '>='
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108
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+
- !ruby/object:Gem::Version
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109
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version: '0'
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110
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+
- !ruby/object:Gem::Dependency
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111
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name: shoulda-context
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112
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requirement: !ruby/object:Gem::Requirement
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113
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none: false
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|
114
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requirements:
|
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115
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+
- - ! '>='
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116
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+
- !ruby/object:Gem::Version
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117
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version: '0'
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118
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type: :development
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119
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prerelease: false
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120
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version_requirements: !ruby/object:Gem::Requirement
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|
121
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none: false
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122
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requirements:
|
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123
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+
- - ! '>='
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124
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+
- !ruby/object:Gem::Version
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125
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version: '0'
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126
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+
- !ruby/object:Gem::Dependency
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127
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+
name: coveralls
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128
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+
requirement: !ruby/object:Gem::Requirement
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|
129
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none: false
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130
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requirements:
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131
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+
- - ~>
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132
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+
- !ruby/object:Gem::Version
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133
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version: 0.6.7
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134
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type: :development
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135
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prerelease: false
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136
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version_requirements: !ruby/object:Gem::Requirement
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137
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+
none: false
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|
138
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+
requirements:
|
|
139
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+
- - ~>
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140
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+
- !ruby/object:Gem::Version
|
|
141
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version: 0.6.7
|
|
142
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+
description:
|
|
143
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+
email: rds45@cam.ac.uk
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|
144
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+
executables: []
|
|
145
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+
extensions: []
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|
146
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+
extra_rdoc_files: []
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147
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+
files:
|
|
148
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+
- Rakefile
|
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149
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+
- lib/biopsy/base_extensions.rb
|
|
150
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+
- lib/biopsy/domain.rb
|
|
151
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+
- lib/biopsy/experiment.rb
|
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152
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+
- lib/biopsy/objective_function.rb
|
|
153
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+
- lib/biopsy/objective_handler.rb
|
|
154
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+
- lib/biopsy/objectives/fastest_optimum.rb
|
|
155
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+
- lib/biopsy/opt_algorithm.rb
|
|
156
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+
- lib/biopsy/optimisers/genetic_algorithm.rb
|
|
157
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+
- lib/biopsy/optimisers/parameter_sweeper.rb
|
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158
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+
- lib/biopsy/optimisers/tabu_search.rb
|
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159
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+
- lib/biopsy/settings.rb
|
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160
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+
- lib/biopsy/target.rb
|
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161
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+
- lib/biopsy/version.rb
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162
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+
- lib/biopsy.rb
|
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163
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+
- test/helper.rb
|
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164
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+
- test/test_domain.rb
|
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165
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+
- test/test_experiment.rb
|
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166
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+
- test/test_file.rb
|
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167
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+
- test/test_hash.rb
|
|
168
|
+
- test/test_objective_handler.rb
|
|
169
|
+
- test/test_settings.rb
|
|
170
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+
- test/test_string.rb
|
|
171
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+
- test/test_target.rb
|
|
172
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+
- README.md
|
|
173
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+
- LICENSE.txt
|
|
174
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+
homepage: https://github.com/Blahah/biopsy
|
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175
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licenses: []
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176
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+
post_install_message:
|
|
177
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+
rdoc_options: []
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178
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+
require_paths:
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179
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+
- lib
|
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180
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required_ruby_version: !ruby/object:Gem::Requirement
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181
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none: false
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182
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requirements:
|
|
183
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+
- - ! '>='
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|
184
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+
- !ruby/object:Gem::Version
|
|
185
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+
version: '0'
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|
186
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+
required_rubygems_version: !ruby/object:Gem::Requirement
|
|
187
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+
none: false
|
|
188
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requirements:
|
|
189
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+
- - ! '>'
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190
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+
- !ruby/object:Gem::Version
|
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191
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version: 1.3.1
|
|
192
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requirements: []
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|
193
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rubyforge_project:
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194
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rubygems_version: 1.8.24
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195
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signing_key:
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196
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specification_version: 3
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197
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summary: framework for optimising any computational pipeline or program
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198
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test_files: []
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