genomer 0.0.5 → 0.0.6

data/.travis.yml

@@ -0,0 +1,4 @@
+language: ruby
+rvm:
+  - 1.8.7
+  - 1.9.3

data/Gemfile

@@ -1,2 +1,4 @@
 source :rubygems
 gemspec
+
+gem "md2man", :git => "git://github.com/sunaku/md2man.git", :ref => "c87dab11"

data/bin/genomer

@@ -4,7 +4,6 @@ $:.unshift File.join(File.dirname(__FILE__), '..', 'lib')
 require 'rubygems'
 require 'configliere'
 require 'genomer'
-require 'ronn'
 
 Settings.use :commandline
 Settings.resolve!

data/genomer-plugin-simple/man/genomer-simple-subcommand.ronn

@@ -1,5 +1,8 @@
+# GENOMER-SIMPLE-SUBCOMMAND 1
+
+## NAME
+
 genomer-simple-subcommand(1) -- A test plugin subcommand
-========================================================
 
 ## SYNOPSIS
 

data/genomer-plugin-simple/man/genomer-simple.ronn

@@ -1,5 +1,8 @@
+# GENOMER-SIMPLE 1
+
+## NAME
+
 genomer-simple(1) -- A test plugin for genomer
-==============================================
 
 ## SYNOPSIS
 

data/genomer.gemspec

@@ -19,9 +19,9 @@ Gem::Specification.new do |s|
   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", ">= 0.1.2"
+  s.add_dependency "scaffolder-annotation-locator", ">= 0.1.4"
   s.add_dependency "unindent",                      "~> 1.0.0"
-  s.add_dependency "ronn",                          "~> 0.7.3"
+  s.add_dependency "md2man",                        "~> 1.2.0"
 
   # Specs
   s.add_development_dependency "rspec",                   "~> 2.7.0"

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'
+    YAML::ENGINE.yamler = 'syck' if defined?(YAML::ENGINE)
     Scaffolder.new(YAML.load(File.read(scaffold_file)),sequence_file)
   end
 
@@ -90,9 +90,7 @@ class Genomer::Plugin
     attns = Scaffolder::AnnotationLocator.new(
       scaffold_file,sequence_file,annotation_file)
 
-    attns.sort_by! do |attn|
-      [attn.start,attn.end]
-    end
+    attns = attns.sort_by{|attn| [attn.start,attn.end] }
 
     if value = options[:reset]
       start = value.to_s =~ /^[-+]?[0-9]+$/ ? value.to_i : 1

data/lib/genomer/runtime.rb

@@ -1,7 +1,6 @@
 require 'unindent'
 require 'tempfile'
-require 'ronn/index'
-require 'ronn/document'
+require 'md2man'
 
 class Genomer::Runtime
 
@@ -79,7 +78,7 @@ class Genomer::Runtime
   def groffed_man_file(original_man_file)
     converted_man = Tempfile.new("genome-manpage-")
     File.open(converted_man.path,'w') do |out|
-      out.puts Ronn::Document.new(original_man_file).convert('roff')
+      out.puts Md2Man::ENGINE.render(File.read(original_man_file))
     end
     converted_man
   end

data/lib/genomer/version.rb

@@ -1,3 +1,3 @@
 module Genomer
-  VERSION = "0.0.5"
+  VERSION = "0.0.6"
 end

data/man/genomer-init.1.ronn

@@ -1,9 +1,12 @@
+# GENOMER-INIT 1
+
+## NAME
+
 genomer-init(1) -- create a new genomer project
-===============================================
 
 ## SYNOPSIS
 
-`genomer init` <project-name>
+`genomer init` *project-name*
 
 ## DESCRIPTION
 

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: genomer
 version: !ruby/object:Gem::Version
-  version: 0.0.5
+  version: 0.0.6
   prerelease: 
 platform: ruby
 authors:
@@ -9,7 +9,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2012-05-28 00:00:00.000000000 Z
+date: 2012-05-31 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake
@@ -82,7 +82,7 @@ dependencies:
     requirements:
     - - ! '>='
       - !ruby/object:Gem::Version
-        version: 0.1.2
+        version: 0.1.4
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
@@ -90,7 +90,7 @@ dependencies:
     requirements:
     - - ! '>='
       - !ruby/object:Gem::Version
-        version: 0.1.2
+        version: 0.1.4
 - !ruby/object:Gem::Dependency
   name: unindent
   requirement: !ruby/object:Gem::Requirement
@@ -108,13 +108,13 @@ dependencies:
       - !ruby/object:Gem::Version
         version: 1.0.0
 - !ruby/object:Gem::Dependency
-  name: ronn
+  name: md2man
   requirement: !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
-        version: 0.7.3
+        version: 1.2.0
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
@@ -122,7 +122,7 @@ dependencies:
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
-        version: 0.7.3
+        version: 1.2.0
 - !ruby/object:Gem::Dependency
   name: rspec
   requirement: !ruby/object:Gem::Requirement
@@ -229,6 +229,7 @@ extra_rdoc_files: []
 files:
 - .document
 - .gitignore
+- .travis.yml
 - Gemfile
 - LICENSE.txt
 - README.rdoc
@@ -274,7 +275,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
       version: '0'
       segments:
       - 0
-      hash: 4331820328226072819
+      hash: -2849054132154778027
 required_rubygems_version: !ruby/object:Gem::Requirement
   none: false
   requirements: