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