bio-tm_hmm 0.2.2 → 0.2.3

checksums.yaml

@@ -0,0 +1,7 @@
+---
+SHA1:
+  metadata.gz: a63ec466bfd78426f0c588a4fa930cc83ef1b017
+  data.tar.gz: 016f3310e83507e7a8c43d5f4980495990299ee9
+SHA512:
+  metadata.gz: cab26f0526b1d1858251b9c7db940b0b79aa8d9f2e1a051060d24463337d63124ccdcaddbbcf550f01fc041afa160f3df19eba5449b424decdd4397a5c2d5d16
+  data.tar.gz: 68a9f82aaafb5723ee217405872bababd8c458a7ecb77e09c704f4a5303ba3033be3d1127deb3ff66642d4e5f7259fe201f0bbfd01ad94841b3e963776af45e2

data/Gemfile

@@ -2,13 +2,14 @@ source "http://rubygems.org"
 # Add dependencies required to use your gem here.
 # Example:
 #   gem "activesupport", ">= 2.3.5"
+gem "bio", ">= 1.4.2"
+gem "test-unit", "~>3.2"
 
 # Add dependencies to develop your gem here.
 # Include everything needed to run rake, tests, features, etc.
 group :development do
   gem "shoulda", ">= 0"
   gem "rdoc", "~> 3.12"
-  gem "jeweler", "~> 1.8.3"
+  gem "jeweler", "~> 2.3"
   gem "bundler", ">= 1.0.21"
-  gem "bio", ">= 1.4.2"
 end

data/VERSION

@@ -1 +1 @@
-0.2.2
+0.2.3

data/bin/bio-tm_hmm

@@ -45,7 +45,6 @@ Bio::FlatFile.auto(ARGF).each do |seq|
 
   # Default output - a description of the TMDs for each input aaseq
   if options[:filter_in] == false and options[:filter_out] == false
-    p result
     if result.has_domain?
       # At least one TMD found. Output each on a separate line
       result.transmembrane_domains.each do |tmd|

data/bio-tm_hmm.gemspec

@@ -2,17 +2,19 @@
 # DO NOT EDIT THIS FILE DIRECTLY
 # Instead, edit Jeweler::Tasks in Rakefile, and run 'rake gemspec'
 # -*- encoding: utf-8 -*-
+# stub: bio-tm_hmm 0.2.3 ruby lib
 
 Gem::Specification.new do |s|
-  s.name = "bio-tm_hmm"
-  s.version = "0.2.2"
+  s.name = "bio-tm_hmm".freeze
+  s.version = "0.2.3"
 
-  s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
-  s.authors = ["Ben J. Woodcroft"]
-  s.date = "2012-12-01"
-  s.description = "A bioruby plugin for interaction with the transmembrane predictor TMHMM"
-  s.email = "donttrustben@gmail.com"
-  s.executables = ["bio-tm_hmm"]
+  s.required_rubygems_version = Gem::Requirement.new(">= 0".freeze) if s.respond_to? :required_rubygems_version=
+  s.require_paths = ["lib".freeze]
+  s.authors = ["Ben J. Woodcroft".freeze]
+  s.date = "2017-04-06"
+  s.description = "A bioruby plugin for interaction with the transmembrane predictor TMHMM".freeze
+  s.email = "donttrustben@gmail.com".freeze
+  s.executables = ["bio-tm_hmm".freeze]
   s.extra_rdoc_files = [
     "LICENSE.txt",
     "README.md"
@@ -36,34 +38,36 @@ Gem::Specification.new do |s|
     "test/test_tm_hmm_wrapper.rb",
     "test/test_transmembrane.rb"
   ]
-  s.homepage = "http://github.com/wwood/bioruby-tm_hmm"
-  s.licenses = ["MIT"]
-  s.require_paths = ["lib"]
-  s.rubygems_version = "1.8.24"
-  s.summary = "A bioruby plugin for interaction with the transmembrane predictor TMHMM"
+  s.homepage = "http://github.com/wwood/bioruby-tm_hmm".freeze
+  s.licenses = ["MIT".freeze]
+  s.rubygems_version = "2.5.2".freeze
+  s.summary = "A bioruby plugin for interaction with the transmembrane predictor TMHMM".freeze
 
   if s.respond_to? :specification_version then
-    s.specification_version = 3
+    s.specification_version = 4
 
     if Gem::Version.new(Gem::VERSION) >= Gem::Version.new('1.2.0') then
-      s.add_development_dependency(%q<shoulda>, [">= 0"])
-      s.add_development_dependency(%q<rdoc>, ["~> 3.12"])
-      s.add_development_dependency(%q<jeweler>, ["~> 1.8.3"])
-      s.add_development_dependency(%q<bundler>, [">= 1.0.21"])
-      s.add_development_dependency(%q<bio>, [">= 1.4.2"])
+      s.add_runtime_dependency(%q<bio>.freeze, [">= 1.4.2"])
+      s.add_runtime_dependency(%q<test-unit>.freeze, ["~> 3.2"])
+      s.add_development_dependency(%q<shoulda>.freeze, [">= 0"])
+      s.add_development_dependency(%q<rdoc>.freeze, ["~> 3.12"])
+      s.add_development_dependency(%q<jeweler>.freeze, ["~> 2.3"])
+      s.add_development_dependency(%q<bundler>.freeze, [">= 1.0.21"])
     else
-      s.add_dependency(%q<shoulda>, [">= 0"])
-      s.add_dependency(%q<rdoc>, ["~> 3.12"])
-      s.add_dependency(%q<jeweler>, ["~> 1.8.3"])
-      s.add_dependency(%q<bundler>, [">= 1.0.21"])
-      s.add_dependency(%q<bio>, [">= 1.4.2"])
+      s.add_dependency(%q<bio>.freeze, [">= 1.4.2"])
+      s.add_dependency(%q<test-unit>.freeze, ["~> 3.2"])
+      s.add_dependency(%q<shoulda>.freeze, [">= 0"])
+      s.add_dependency(%q<rdoc>.freeze, ["~> 3.12"])
+      s.add_dependency(%q<jeweler>.freeze, ["~> 2.3"])
+      s.add_dependency(%q<bundler>.freeze, [">= 1.0.21"])
     end
   else
-    s.add_dependency(%q<shoulda>, [">= 0"])
-    s.add_dependency(%q<rdoc>, ["~> 3.12"])
-    s.add_dependency(%q<jeweler>, ["~> 1.8.3"])
-    s.add_dependency(%q<bundler>, [">= 1.0.21"])
-    s.add_dependency(%q<bio>, [">= 1.4.2"])
+    s.add_dependency(%q<bio>.freeze, [">= 1.4.2"])
+    s.add_dependency(%q<test-unit>.freeze, ["~> 3.2"])
+    s.add_dependency(%q<shoulda>.freeze, [">= 0"])
+    s.add_dependency(%q<rdoc>.freeze, ["~> 3.12"])
+    s.add_dependency(%q<jeweler>.freeze, ["~> 2.3"])
+    s.add_dependency(%q<bundler>.freeze, [">= 1.0.21"])
   end
 end
 

metadata

@@ -1,96 +1,99 @@
 --- !ruby/object:Gem::Specification
 name: bio-tm_hmm
 version: !ruby/object:Gem::Version
-  version: 0.2.2
-  prerelease: 
+  version: 0.2.3
 platform: ruby
 authors:
 - Ben J. Woodcroft
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2012-12-01 00:00:00.000000000 Z
+date: 2017-04-06 00:00:00.000000000 Z
 dependencies:
+- !ruby/object:Gem::Dependency
+  name: bio
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 1.4.2
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 1.4.2
+- !ruby/object:Gem::Dependency
+  name: test-unit
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '3.2'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '3.2'
 - !ruby/object:Gem::Dependency
   name: shoulda
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: '0'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: '0'
 - !ruby/object:Gem::Dependency
   name: rdoc
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
         version: '3.12'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
         version: '3.12'
 - !ruby/object:Gem::Dependency
   name: jeweler
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: 1.8.3
+        version: '2.3'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: 1.8.3
+        version: '2.3'
 - !ruby/object:Gem::Dependency
   name: bundler
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: 1.0.21
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: 1.0.21
-- !ruby/object:Gem::Dependency
-  name: bio
-  requirement: !ruby/object:Gem::Requirement
-    none: false
-    requirements:
-    - - ! '>='
-      - !ruby/object:Gem::Version
-        version: 1.4.2
-  type: :development
-  prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    none: false
-    requirements:
-    - - ! '>='
-      - !ruby/object:Gem::Version
-        version: 1.4.2
 description: A bioruby plugin for interaction with the transmembrane predictor TMHMM
 email: donttrustben@gmail.com
 executables:
@@ -100,8 +103,8 @@ extra_rdoc_files:
 - LICENSE.txt
 - README.md
 files:
-- .document
-- .travis.yml
+- ".document"
+- ".travis.yml"
 - Gemfile
 - LICENSE.txt
 - README.md
@@ -120,29 +123,25 @@ files:
 homepage: http://github.com/wwood/bioruby-tm_hmm
 licenses:
 - MIT
+metadata: {}
 post_install_message: 
 rdoc_options: []
 require_paths:
 - lib
 required_ruby_version: !ruby/object:Gem::Requirement
-  none: false
   requirements:
-  - - ! '>='
+  - - ">="
     - !ruby/object:Gem::Version
       version: '0'
-      segments:
-      - 0
-      hash: 24340783
 required_rubygems_version: !ruby/object:Gem::Requirement
-  none: false
   requirements:
-  - - ! '>='
+  - - ">="
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 1.8.24
+rubygems_version: 2.5.2
 signing_key: 
-specification_version: 3
+specification_version: 4
 summary: A bioruby plugin for interaction with the transmembrane predictor TMHMM
 test_files: []