rput 0.1.0 → 0.1.1

data/Gemfile

@@ -13,4 +13,6 @@ group :development do
   gem "rcov", ">= 0"
   # own dependencies
   gem "rraxml", "~> 0.1.2"
+  gem "rphylip", "~> 0.1.0"
+  gem "rnewick", "~> 0.1.0"
 end

data/Gemfile.lock

@@ -12,6 +12,8 @@ GEM
     rcov (1.0.0)
     rdoc (3.12)
       json (~> 1.4)
+    rnewick (0.1.0)
+    rphylip (0.1.0)
     rraxml (0.1.2)
     shoulda (3.0.1)
       shoulda-context (~> 1.0.0)
@@ -27,5 +29,7 @@ DEPENDENCIES
   jeweler (~> 1.8.3)
   rcov
   rdoc (~> 3.12)
+  rnewick (~> 0.1.0)
+  rphylip (~> 0.1.0)
   rraxml (~> 0.1.2)
   shoulda

data/VERSION

@@ -1 +1 @@
-0.1.0
+0.1.1

data/lib/experiment.rb

@@ -1,12 +1,12 @@
 #!/usr/bin/env ruby
-#require 'rphylip'
+require 'rphylip'
 require 'fileutils'
 require 'yaml'
 
 class Experiment
-  def initialize(name)
+  def initialize(name, basedir)
     @name = name
-    @base_dir = File.join File.expand_path(File.dirname(__FILE__)), '../'
+    @base_dir = basedir
   end
   def dirname(a)
     File.join @base_dir, 'experiments', @name, a

data/lib/rput.rb

@@ -0,0 +1,3 @@
+#!/usr/bin/env ruby
+require 'experiment'
+require 'starter'

data/lib/starter.rb

@@ -1,9 +1,8 @@
 #!/usr/bin/env ruby
 #
-#gem 'rraxml','0.1.2'
-#require 'rraxml'
-#require 'rnewick'
-#require 'rphylip'
+require 'rraxml'
+require 'rnewick'
+require 'rphylip'
 require 'logger'
 
 class CycleController

data/rput.gemspec

@@ -5,7 +5,7 @@
 
 Gem::Specification.new do |s|
   s.name = %q{rput}
-  s.version = "0.1.0"
+  s.version = "0.1.1"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = [%q{Fernando Izquierdo-Carrasco}]
@@ -25,6 +25,7 @@ Gem::Specification.new do |s|
     "Rakefile",
     "VERSION",
     "lib/experiment.rb",
+    "lib/rput.rb",
     "lib/starter.rb",
     "rput.gemspec",
     "test/helper.rb",
@@ -46,6 +47,8 @@ Gem::Specification.new do |s|
       s.add_development_dependency(%q<jeweler>, ["~> 1.8.3"])
       s.add_development_dependency(%q<rcov>, [">= 0"])
       s.add_development_dependency(%q<rraxml>, ["~> 0.1.2"])
+      s.add_development_dependency(%q<rphylip>, ["~> 0.1.0"])
+      s.add_development_dependency(%q<rnewick>, ["~> 0.1.0"])
     else
       s.add_dependency(%q<shoulda>, [">= 0"])
       s.add_dependency(%q<rdoc>, ["~> 3.12"])
@@ -53,6 +56,8 @@ Gem::Specification.new do |s|
       s.add_dependency(%q<jeweler>, ["~> 1.8.3"])
       s.add_dependency(%q<rcov>, [">= 0"])
       s.add_dependency(%q<rraxml>, ["~> 0.1.2"])
+      s.add_dependency(%q<rphylip>, ["~> 0.1.0"])
+      s.add_dependency(%q<rnewick>, ["~> 0.1.0"])
     end
   else
     s.add_dependency(%q<shoulda>, [">= 0"])
@@ -61,6 +66,8 @@ Gem::Specification.new do |s|
     s.add_dependency(%q<jeweler>, ["~> 1.8.3"])
     s.add_dependency(%q<rcov>, [">= 0"])
     s.add_dependency(%q<rraxml>, ["~> 0.1.2"])
+    s.add_dependency(%q<rphylip>, ["~> 0.1.0"])
+    s.add_dependency(%q<rnewick>, ["~> 0.1.0"])
   end
 end
 

metadata

@@ -1,13 +1,13 @@
 --- !ruby/object:Gem::Specification 
 name: rput
 version: !ruby/object:Gem::Version 
-  hash: 27
+  hash: 25
   prerelease: 
   segments: 
   - 0
   - 1
-  - 0
-  version: 0.1.0
+  - 1
+  version: 0.1.1
 platform: ruby
 authors: 
 - Fernando Izquierdo-Carrasco
@@ -108,6 +108,38 @@ dependencies:
   version_requirements: *id006
   name: rraxml
   prerelease: false
+- !ruby/object:Gem::Dependency 
+  type: :development
+  requirement: &id007 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ~>
+      - !ruby/object:Gem::Version 
+        hash: 27
+        segments: 
+        - 0
+        - 1
+        - 0
+        version: 0.1.0
+  version_requirements: *id007
+  name: rphylip
+  prerelease: false
+- !ruby/object:Gem::Dependency 
+  type: :development
+  requirement: &id008 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ~>
+      - !ruby/object:Gem::Version 
+        hash: 27
+        segments: 
+        - 0
+        - 1
+        - 0
+        version: 0.1.0
+  version_requirements: *id008
+  name: rnewick
+  prerelease: false
 description: Automated iterations of raxml runs over externally-extended phylip files
 email: fer.izquierdo@gmail.com
 executables: []
@@ -126,6 +158,7 @@ files:
 - Rakefile
 - VERSION
 - lib/experiment.rb
+- lib/rput.rb
 - lib/starter.rb
 - rput.gemspec
 - test/helper.rb