genomer 0.0.10 → 0.1.0

checksums.yaml

@@ -0,0 +1,15 @@
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data/.gitignore

@@ -44,3 +44,5 @@ pkg
 #
 # For vim:
 #*.swp
+
+Gemfile.lock

data/.travis.yml

@@ -1,4 +1,6 @@
 language: ruby
 rvm:
   - 1.8.7
+  - 1.9.2
   - 1.9.3
+  - 2.0.0

data/CHANGELOG.mkd

@@ -1,4 +1,4 @@
-== 0.0.9 ==
+## 0.0.9
 
   * Genomer now has different behaviour dependent on whether inside or outside
     a genomer project directory. These differences are as follows: 

data/Gemfile

@@ -1,2 +1,2 @@
-source :rubygems
+source 'https://rubygems.org'
 gemspec

data/README.mkd

@@ -54,6 +54,15 @@ be made there.
 
 [github]: https://github.com/michaelbarton/genomer
 
+## Troubleshooting
+
+Genomer specifically requires the 1.2.x version of md2man. This is because
+later versions are not compatible with ruby 1.8.7 and I aim to keep genomer
+backwards compatible for as long as possible. If you find that there are errors
+running or developing genomer related to md2man please remove all versions from
+the systems and try reinstalling genomer. If you have further problems please
+contact the genomer mailing list found at the http://next.gs site.
+
 ## Copyright
 
 Genomer copyright (c) 2010 by Michael Barton. Genomer is licensed under the MIT

data/features/cli/error.feature

@@ -6,6 +6,10 @@ Feature: Reporting genomer errors
   Scenario: Calling a non-specified genomer plugin
     Given I run the genomer command with the arguments "init project"
       And I cd to "project"
+      And I overwrite "Gemfile" with:
+      """
+      gem 'genomer',               :path => '../../../'
+      """
      When I run the genomer command with the arguments "simple"
      Then the exit status should be 1
       And the output should contain:

data/features/cli/help.feature

@@ -26,6 +26,10 @@ Feature: Listing available commands
   Scenario: Running genomer with no commands inside a project
     Given I run the genomer command with the arguments "init project"
       And I cd to "project"
+      And I overwrite "Gemfile" with:
+      """
+      gem 'genomer',               :path => '../../../'
+      """
      When I run the genomer command with no arguments
      Then the exit status should be 0
       And the output should contain:
@@ -39,6 +43,10 @@ Feature: Listing available commands
   Scenario: Running genomer with the --version flag inside a project
     Given I run the genomer command with the arguments "init project"
       And I cd to "project"
+      And I overwrite "Gemfile" with:
+      """
+      gem 'genomer',               :path => '../../../'
+      """
      When I run the genomer command with the arguments "--version"
      Then the exit status should be 0
       And the output should match:
@@ -50,6 +58,10 @@ Feature: Listing available commands
   Scenario: Running the genomer help command inside a genomer project
     Given I run the genomer command with the arguments "init project"
       And I cd to "project"
+      And I overwrite "Gemfile" with:
+      """
+      gem 'genomer',               :path => '../../../'
+      """
      When I run the genomer command with the arguments "help"
      Then the exit status should be 0
       And the output should contain:
@@ -73,6 +85,7 @@ Feature: Listing available commands
       And I cd to "project"
       And I overwrite "Gemfile" with:
       """
+      gem 'genomer',               :path => '../../../'
       gem 'genomer-plugin-simple', :path => '../../../genomer-plugin-simple'
       """
      When I run the genomer command with the arguments "help"

data/features/cli/init.feature

@@ -51,9 +51,9 @@ Feature: Creating a new genomer project
     And a file named "project/Gemfile" should exist
     And the file "project/Gemfile" should contain exactly:
     """
-    source :rubygems
+    source "https://rubygems.org"
 
-    gem 'genomer',    '~> 0.0.0'
+    gem 'genomer',    '~> 0.1.0'
 
     """
 

data/features/cli/man.feature

@@ -18,6 +18,7 @@ Feature: Showing man pages for available commands
       And I cd to "project"
       And I overwrite "Gemfile" with:
       """
+      gem 'genomer',               :path => '../../../'
       gem 'genomer-plugin-simple', :path => '../../../genomer-plugin-simple'
       """
      When I run the genomer command with the arguments "man simple"
@@ -30,6 +31,7 @@ Feature: Showing man pages for available commands
       And I cd to "project"
       And I overwrite "Gemfile" with:
       """
+      gem 'genomer',               :path => '../../../'
       gem 'genomer-plugin-simple', :path => '../../../genomer-plugin-simple'
       """
      When I run the genomer command with the arguments "man simple subcommand"
@@ -42,6 +44,7 @@ Feature: Showing man pages for available commands
       And I cd to "project"
       And I overwrite "Gemfile" with:
       """
+      gem 'genomer',               :path => '../../../'
       gem 'genomer-plugin-simple', :path => '../../../genomer-plugin-simple'
       """
      When I run the genomer command with the arguments "man unknown"
@@ -59,6 +62,7 @@ Feature: Showing man pages for available commands
       And I cd to "project"
       And I overwrite "Gemfile" with:
       """
+      gem 'genomer',               :path => '../../../'
       gem 'genomer-plugin-simple', :path => '../../../genomer-plugin-simple'
       """
      When I run the genomer command with the arguments "man simple unknown"

data/features/cli/plugins.feature

@@ -9,6 +9,7 @@ Feature: Calling genomer plugins in a genomer project
       And I cd to "project"
       And I overwrite "Gemfile" with:
       """
+      gem 'genomer',               :path => '../../../'
       gem 'genomer-plugin-simple', :path => '../../../genomer-plugin-simple'
       """
      When I run the genomer command with the arguments "simple"
@@ -24,6 +25,7 @@ Feature: Calling genomer plugins in a genomer project
       And I cd to "project"
       And I overwrite "Gemfile" with:
       """
+      gem 'genomer',               :path => '../../../'
       gem 'genomer-plugin-simple', :path => '../../../genomer-plugin-simple'
       """
      When I run the genomer command with the arguments "simple echo some words"

data/genomer.gemspec

@@ -7,7 +7,7 @@ Gem::Specification.new do |s|
   s.platform    = Gem::Platform::RUBY
   s.authors     = ["Michael Barton"]
   s.email       = ["mail@michaelbarton.me.uk"]
-  s.homepage    = "http://github.com/michaelbarton/genomer"
+  s.homepage    = "http://next.gs"
   s.summary     = %Q{Build genome output files}
   s.description = %Q{Turns scaffolded contigs and annotations into a genome.}
   s.license     = "MIT"
@@ -15,18 +15,18 @@ Gem::Specification.new do |s|
   s.required_rubygems_version = ">= 1.8.0"
   s.rubyforge_project         = "genomer"
 
-  s.add_dependency "rake",                          "~> 0.9.0"
-  s.add_dependency "bundler",                        "> 1.1.0"
-  s.add_dependency "configliere",                   "~> 0.4.8"
-  s.add_dependency "scaffolder",                    "~> 0.4.0"
-  s.add_dependency "scaffolder-annotation-locator", ">= 0.1.4"
+  s.add_dependency "rake",                          "~> 10.1.0"
+  s.add_dependency "bundler",                       "~> 1.3.0"
+  s.add_dependency "configliere",                   "~> 0.4.0"
+  s.add_dependency "scaffolder",                    "~> 0.5.0"
+  s.add_dependency "scaffolder-annotation-locator", "~> 0.2.0"
   s.add_dependency "unindent",                      "~> 1.0.0"
   s.add_dependency "md2man",                        "~> 1.2.0"
 
   # Specs
-  s.add_development_dependency "rspec",                   "~> 2.7.0"
+  s.add_development_dependency "rspec",                   "~> 2.14.0"
   s.add_development_dependency "fakefs",                  "~> 0.4.0"
-  s.add_development_dependency "rr",                      "~> 1.0.4"
+  s.add_development_dependency "rr",                      "~> 1.1.0"
   s.add_development_dependency "scaffolder-test-helpers", "~> 0.4.0"
 
   # Features

data/lib/genomer.rb

@@ -1,4 +1,5 @@
 module Genomer
+  require 'yaml'
   require 'genomer/error'
 
   autoload :Runtime, 'genomer/runtime'

data/lib/genomer/files.rb

@@ -6,7 +6,7 @@ class Genomer::Files
     def gemfile
       version = Genomer::VERSION.split('.')[0..1].<<(0).join('.')
       <<-EOF.unindent
-        source :rubygems
+        source "https://rubygems.org"
 
         gem 'genomer',    '~> #{version}'
       EOF

data/lib/genomer/plugin.rb

@@ -82,7 +82,7 @@ class Genomer::Plugin
   #
   # @return [Array] An array of Scaffolder::Region instances
   def scaffold
-    YAML::ENGINE.yamler = 'syck' if defined?(YAML::ENGINE)
+    YAML::ENGINE.yamler = 'syck' if defined?(YAML::ENGINE) and Gem::Version.new(RUBY_VERSION.dup) < Gem::Version.new('2.0.0')
     Scaffolder.new(YAML.load(File.read(scaffold_file)),sequence_file)
   end
 

data/lib/genomer/runtime.rb

@@ -1,6 +1,6 @@
 require 'unindent'
 require 'tempfile'
-require 'md2man'
+require 'md2man/engine'
 
 require 'genomer/version'
 
@@ -103,10 +103,14 @@ class Genomer::Runtime
     File.join(Genomer::Plugin.fetch(plugin).full_gem_path, 'man', page)
   end
 
+  def render_man(input)
+    Md2Man::ENGINE.render input
+  end
+
   def groffed_man_file(original_man_file)
     converted_man = Tempfile.new("genome-manpage-")
     File.open(converted_man.path,'w') do |out|
-      out.puts Md2Man::ENGINE.render(File.read(original_man_file))
+      out.puts render_man(File.read(original_man_file))
     end
     converted_man
   end

data/lib/genomer/version.rb

@@ -1,3 +1,3 @@
 module Genomer
-  VERSION = "0.0.10"
+  VERSION = "0.1.0"
 end

data/spec/genomer/runtime_spec.rb

@@ -300,7 +300,7 @@ describe Genomer::Runtime do
 
           File.exists?(file).should be_true
           File.read(file).should == <<-EOF.unindent
-            source :rubygems
+            source "https://rubygems.org"
 
             gem 'genomer',    '~> #{version.join('.')}'
           EOF
@@ -340,6 +340,14 @@ describe Genomer::Runtime do
 
   end
 
+  describe "#render_man" do
+
+    it "should render markdown to man page" do
+      subject.render_man("##Title").should_not be_nil
+    end
+
+  end
+
   describe "#man_file" do
 
     before do

metadata

@@ -1,100 +1,88 @@
 --- !ruby/object:Gem::Specification
 name: genomer
 version: !ruby/object:Gem::Version
-  version: 0.0.10
-  prerelease: 
+  version: 0.1.0
 platform: ruby
 authors:
 - Michael Barton
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2013-03-04 00:00:00.000000000 Z
+date: 2013-08-13 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
-        version: 0.9.0
+        version: 10.1.0
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
-        version: 0.9.0
+        version: 10.1.0
 - !ruby/object:Gem::Dependency
   name: bundler
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>'
+    - - ~>
       - !ruby/object:Gem::Version
-        version: 1.1.0
+        version: 1.3.0
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>'
+    - - ~>
       - !ruby/object:Gem::Version
-        version: 1.1.0
+        version: 1.3.0
 - !ruby/object:Gem::Dependency
   name: configliere
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
-        version: 0.4.8
+        version: 0.4.0
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
-        version: 0.4.8
+        version: 0.4.0
 - !ruby/object:Gem::Dependency
   name: scaffolder
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
-        version: 0.4.0
+        version: 0.5.0
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
-        version: 0.4.0
+        version: 0.5.0
 - !ruby/object:Gem::Dependency
   name: scaffolder-annotation-locator
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - ~>
       - !ruby/object:Gem::Version
-        version: 0.1.4
+        version: 0.2.0
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - ~>
       - !ruby/object:Gem::Version
-        version: 0.1.4
+        version: 0.2.0
 - !ruby/object:Gem::Dependency
   name: unindent
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
@@ -102,7 +90,6 @@ dependencies:
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
@@ -110,7 +97,6 @@ dependencies:
 - !ruby/object:Gem::Dependency
   name: md2man
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
@@ -118,7 +104,6 @@ dependencies:
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
@@ -126,23 +111,20 @@ dependencies:
 - !ruby/object:Gem::Dependency
   name: rspec
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
-        version: 2.7.0
+        version: 2.14.0
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
-        version: 2.7.0
+        version: 2.14.0
 - !ruby/object:Gem::Dependency
   name: fakefs
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
@@ -150,7 +132,6 @@ dependencies:
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
@@ -158,23 +139,20 @@ dependencies:
 - !ruby/object:Gem::Dependency
   name: rr
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
-        version: 1.0.4
+        version: 1.1.0
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
-        version: 1.0.4
+        version: 1.1.0
 - !ruby/object:Gem::Dependency
   name: scaffolder-test-helpers
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
@@ -182,7 +160,6 @@ dependencies:
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
@@ -190,7 +167,6 @@ dependencies:
 - !ruby/object:Gem::Dependency
   name: cucumber
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
@@ -198,7 +174,6 @@ dependencies:
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
@@ -206,7 +181,6 @@ dependencies:
 - !ruby/object:Gem::Dependency
   name: aruba
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
@@ -214,7 +188,6 @@ dependencies:
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
@@ -260,32 +233,28 @@ files:
 - spec/genomer/plugin_spec.rb
 - spec/genomer/runtime_spec.rb
 - spec/spec_helper.rb
-homepage: http://github.com/michaelbarton/genomer
+homepage: http://next.gs
 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: -2033630129832100244
 required_rubygems_version: !ruby/object:Gem::Requirement
-  none: false
   requirements:
   - - ! '>='
     - !ruby/object:Gem::Version
       version: 1.8.0
 requirements: []
 rubyforge_project: genomer
-rubygems_version: 1.8.25
+rubygems_version: 2.0.3
 signing_key: 
-specification_version: 3
+specification_version: 4
 summary: Build genome output files
 test_files: []