opentox-ruby 2.0.1 → 2.1.0

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Files changed (19) hide show
  1. data/Rakefile +39 -46
  2. data/VERSION +1 -1
  3. data/lib/algorithm.rb +797 -80
  4. data/lib/compound.rb +40 -0
  5. data/lib/config/config_ru.rb +2 -0
  6. data/lib/dataset.rb +57 -18
  7. data/lib/environment.rb +3 -3
  8. data/lib/feature.rb +15 -13
  9. data/lib/helper.rb +1 -2
  10. data/lib/model.rb +185 -82
  11. data/lib/opentox-ruby.rb +1 -1
  12. data/lib/overwrite.rb +2 -1
  13. data/lib/parser.rb +247 -69
  14. data/lib/rest_client_wrapper.rb +3 -2
  15. data/lib/serializer.rb +24 -10
  16. data/lib/task.rb +10 -3
  17. data/lib/to-html.rb +66 -41
  18. data/lib/validation.rb +93 -29
  19. metadata +206 -117
metadata CHANGED
@@ -1,13 +1,13 @@
1
1
  --- !ruby/object:Gem::Specification
2
2
  name: opentox-ruby
3
3
  version: !ruby/object:Gem::Version
4
- hash: 13
4
+ hash: 11
5
5
  prerelease:
6
6
  segments:
7
7
  - 2
8
- - 0
9
8
  - 1
10
- version: 2.0.1
9
+ - 0
10
+ version: 2.1.0
11
11
  platform: ruby
12
12
  authors:
13
13
  - Christoph Helma, Martin Guetlein, Andreas Maunz, Micha Rautenberg, David Vorgrimmler
@@ -15,7 +15,7 @@ autorequire:
15
15
  bindir: bin
16
16
  cert_chain: []
17
17
 
18
- date: 2011-06-15 00:00:00 +02:00
18
+ date: 2011-08-08 00:00:00 +02:00
19
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  default_executable:
20
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  dependencies:
21
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  - !ruby/object:Gem::Dependency
@@ -24,12 +24,14 @@ dependencies:
24
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  requirement: &id001 !ruby/object:Gem::Requirement
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  none: false
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  requirements:
27
- - - ">="
27
+ - - "="
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  - !ruby/object:Gem::Version
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- hash: 3
29
+ hash: 19
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  segments:
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- - 0
32
- version: "0"
31
+ - 1
32
+ - 2
33
+ - 6
34
+ version: 1.2.6
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  type: :runtime
34
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  version_requirements: *id001
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  - !ruby/object:Gem::Dependency
@@ -38,12 +40,14 @@ dependencies:
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  requirement: &id002 !ruby/object:Gem::Requirement
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  none: false
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  requirements:
41
- - - ">="
43
+ - - "="
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  - !ruby/object:Gem::Version
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- hash: 3
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+ hash: 21
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  segments:
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  - 0
46
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+ version: 0.2.1
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  type: :runtime
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  version_requirements: *id002
49
53
  - !ruby/object:Gem::Dependency
@@ -52,12 +56,14 @@ dependencies:
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  requirement: &id003 !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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  hash: 3
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  segments:
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  - 0
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- version: "0"
64
+ - 7
65
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66
+ version: 0.7.0
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  type: :runtime
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68
  version_requirements: *id003
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69
  - !ruby/object:Gem::Dependency
@@ -66,12 +72,14 @@ dependencies:
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  requirement: &id004 !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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- hash: 3
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+ hash: 11
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  segments:
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  - 0
74
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+ - 5
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82
+ version: 0.5.0
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  type: :runtime
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  version_requirements: *id004
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  - !ruby/object:Gem::Dependency
@@ -80,12 +88,14 @@ dependencies:
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  requirement: &id005 !ruby/object:Gem::Requirement
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  none: false
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  requirements:
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- - - ">="
91
+ - - "="
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  - !ruby/object:Gem::Version
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- hash: 3
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+ hash: 13
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  segments:
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+ - 1
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+ - 1
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+ version: 1.6.1
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  type: :runtime
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  version_requirements: *id005
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  - !ruby/object:Gem::Dependency
@@ -94,12 +104,14 @@ dependencies:
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  requirement: &id006 !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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- hash: 3
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+ hash: 25
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  segments:
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+ version: 1.3.1
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  type: :runtime
104
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  version_requirements: *id006
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  - !ruby/object:Gem::Dependency
@@ -108,12 +120,14 @@ dependencies:
108
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  requirement: &id007 !ruby/object:Gem::Requirement
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  none: false
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  requirements:
111
- - - ">="
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+ - - "="
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  - !ruby/object:Gem::Version
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- hash: 3
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+ hash: 19
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  segments:
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  - 0
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+ version: 1.1.0
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  type: :runtime
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  version_requirements: *id007
119
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  - !ruby/object:Gem::Dependency
@@ -122,12 +136,14 @@ dependencies:
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  requirement: &id008 !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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+ hash: 25
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  segments:
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  - 0
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- version: "0"
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+ - 1
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+ version: 0.1.1
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  type: :runtime
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  version_requirements: *id008
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  - !ruby/object:Gem::Dependency
@@ -136,12 +152,14 @@ dependencies:
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  requirement: &id009 !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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- hash: 3
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+ hash: 15
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  segments:
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+ version: 1.4.4
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  type: :runtime
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  version_requirements: *id009
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  - !ruby/object:Gem::Dependency
@@ -150,12 +168,14 @@ dependencies:
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  requirement: &id010 !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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+ hash: 51
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  segments:
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  - 0
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+ version: 0.9.4
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  type: :runtime
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  version_requirements: *id010
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  - !ruby/object:Gem::Dependency
@@ -164,12 +184,14 @@ dependencies:
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  requirement: &id011 !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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- hash: 3
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+ hash: 53
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  segments:
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- - 0
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- version: "0"
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+ - 1
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+ - 3
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+ version: 1.9.3
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  type: :runtime
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  version_requirements: *id011
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  - !ruby/object:Gem::Dependency
@@ -178,12 +200,15 @@ dependencies:
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  requirement: &id012 !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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- hash: 3
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+ hash: 99
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  segments:
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  - 0
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- version: "0"
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+ - 6
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+ - 4
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+ version: 0.6.5.4
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  type: :runtime
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  version_requirements: *id012
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  - !ruby/object:Gem::Dependency
@@ -192,12 +217,14 @@ dependencies:
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  requirement: &id013 !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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- hash: 3
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+ hash: 17
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  segments:
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  - 0
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+ - 1
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+ - 5
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+ version: 0.1.5
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  type: :runtime
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  version_requirements: *id013
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  - !ruby/object:Gem::Dependency
@@ -206,208 +233,238 @@ dependencies:
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  requirement: &id014 !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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- hash: 3
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+ hash: 59
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  segments:
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  - 0
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+ - 8
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+ version: 0.8.2
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  type: :runtime
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  version_requirements: *id014
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  - !ruby/object:Gem::Dependency
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- name: tmail
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+ name: rinruby
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  prerelease: false
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  requirement: &id015 !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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- hash: 3
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+ hash: 11
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  segments:
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+ - 2
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  - 0
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- version: "0"
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+ - 2
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+ version: 2.0.2
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  type: :runtime
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  version_requirements: *id015
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  - !ruby/object:Gem::Dependency
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- name: rinruby
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+ name: ohm
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  prerelease: false
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  requirement: &id016 !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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- hash: 3
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+ hash: 29
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  segments:
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  - 0
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+ - 1
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+ - 3
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+ version: 0.1.3
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  type: :runtime
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  version_requirements: *id016
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  - !ruby/object:Gem::Dependency
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- name: ohm
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+ name: ohm-contrib
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  prerelease: false
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  requirement: &id017 !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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- hash: 3
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+ hash: 25
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  segments:
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  - 0
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+ - 1
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+ version: 0.1.1
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  type: :runtime
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  version_requirements: *id017
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  - !ruby/object:Gem::Dependency
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- name: ohm-contrib
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+ name: SystemTimer
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  prerelease: false
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  requirement: &id018 !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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- hash: 3
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+ hash: 25
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  segments:
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- - 0
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- version: "0"
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+ - 1
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+ - 2
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+ - 3
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+ version: 1.2.3
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  type: :runtime
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  version_requirements: *id018
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  - !ruby/object:Gem::Dependency
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- name: SystemTimer
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+ name: rjb
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  prerelease: false
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  requirement: &id019 !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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- hash: 3
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+ hash: 19
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  segments:
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- - 0
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- version: "0"
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+ - 1
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+ - 3
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+ - 4
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+ version: 1.3.4
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  type: :runtime
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  version_requirements: *id019
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  - !ruby/object:Gem::Dependency
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- name: rjb
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+ name: haml
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  prerelease: false
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  requirement: &id020 !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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- hash: 3
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+ hash: 1
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  segments:
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- - 0
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+ - 3
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+ version: 3.1.1
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  type: :runtime
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  version_requirements: *id020
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  - !ruby/object:Gem::Dependency
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- name: dm-core
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+ name: akephalos
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  prerelease: false
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  requirement: &id021 !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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- hash: 3
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+ hash: 29
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  segments:
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  - 0
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+ - 2
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+ version: 0.2.5
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  type: :runtime
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  version_requirements: *id021
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  - !ruby/object:Gem::Dependency
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- name: dm-serializer
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+ name: dm-core
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  prerelease: false
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  requirement: &id022 !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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  segments:
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  - 0
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+ version: 1.1.0
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  type: :runtime
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  version_requirements: *id022
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  - !ruby/object:Gem::Dependency
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- name: dm-timestamps
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+ name: dm-serializer
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  prerelease: false
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  requirement: &id023 !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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- hash: 3
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  segments:
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  - 0
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+ version: 1.1.0
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  type: :runtime
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  version_requirements: *id023
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  - !ruby/object:Gem::Dependency
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- name: dm-types
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+ name: dm-timestamps
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  prerelease: false
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  requirement: &id024 !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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- hash: 3
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+ hash: 19
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  segments:
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  - 0
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+ version: 1.1.0
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  type: :runtime
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  version_requirements: *id024
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  - !ruby/object:Gem::Dependency
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- name: dm-migrations
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+ name: dm-types
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  prerelease: false
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  requirement: &id025 !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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- hash: 3
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+ hash: 19
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  segments:
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+ - 1
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  - 0
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+ version: 1.1.0
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  type: :runtime
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  version_requirements: *id025
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  - !ruby/object:Gem::Dependency
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- name: dm-validations
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+ name: dm-migrations
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  prerelease: false
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  requirement: &id026 !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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- hash: 3
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  segments:
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+ - 1
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  - 0
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- version: "0"
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+ version: 1.1.0
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  type: :runtime
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  version_requirements: *id026
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  - !ruby/object:Gem::Dependency
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- name: dm-sqlite-adapter
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+ name: dm-validations
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  prerelease: false
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  requirement: &id027 !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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- hash: 3
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+ hash: 19
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  segments:
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  - 0
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+ version: 1.1.0
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  type: :runtime
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  version_requirements: *id027
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  - !ruby/object:Gem::Dependency
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- name: haml
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+ name: dm-sqlite-adapter
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  prerelease: false
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  requirement: &id028 !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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- hash: 5
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+ hash: 19
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  segments:
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- - 3
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+ - 1
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+ version: 1.1.0
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  type: :runtime
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  version_requirements: *id028
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  - !ruby/object:Gem::Dependency
@@ -416,20 +473,52 @@ dependencies:
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  requirement: &id029 !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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- hash: 15
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+ hash: 11
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  segments:
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  - 0
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+ - 5
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  - 0
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- version: 0.4.0
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+ version: 0.5.0
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  type: :runtime
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  version_requirements: *id029
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  - !ruby/object:Gem::Dependency
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- name: jeweler
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+ name: gsl
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  prerelease: false
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  requirement: &id030 !ruby/object:Gem::Requirement
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+ none: false
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+ requirements:
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+ - - "="
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+ hash: 33
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+ segments:
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+ type: :runtime
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+ version_requirements: *id030
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+ - !ruby/object:Gem::Dependency
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+ name: statsample
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+ prerelease: false
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+ requirement: &id031 !ruby/object:Gem::Requirement
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+ none: false
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+ requirements:
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+ - - "="
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+ hash: 19
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+ segments:
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+ - 1
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+ type: :runtime
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+ version_requirements: *id031
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+ - !ruby/object:Gem::Dependency
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+ name: jeweler
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+ prerelease: false
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+ requirement: &id032 !ruby/object:Gem::Requirement
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  none: false
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  requirements:
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524
  - - ">="
@@ -439,7 +528,7 @@ dependencies:
439
528
  - 0
440
529
  version: "0"
441
530
  type: :development
442
- version_requirements: *id030
531
+ version_requirements: *id032
443
532
  description: Ruby wrapper for the OpenTox REST API (http://www.opentox.org)
444
533
  email: helma@in-silico.ch
445
534
  executables:
@@ -483,7 +572,7 @@ files:
483
572
  - lib/to-html.rb
484
573
  - lib/validation.rb
485
574
  has_rdoc: true
486
- homepage: http://github.com/helma/opentox-ruby
575
+ homepage: http://github.com/opentox/opentox-ruby
487
576
  licenses: []
488
577
 
489
578
  post_install_message: