rnewick 0.1.1 → 0.1.2

data/Gemfile

@@ -8,7 +8,7 @@ source "http://rubygems.org"
 group :development do
   gem "shoulda", ">= 0"
   gem "rdoc", "~> 3.12"
-  gem "bundler", "~> 1.0.0"
-  gem "jeweler", "~> 1.8.3"
-  gem "rcov", ">= 0"
+  gem "bundler", "~> 1.1.3"
+  gem "jeweler", "~> 1.6.4"
+  gem "rcov", "0.9.9"
 end

data/Gemfile.lock

@@ -2,14 +2,13 @@ GEM
   remote: http://rubygems.org/
   specs:
     git (1.2.5)
-    jeweler (1.8.3)
+    jeweler (1.6.4)
       bundler (~> 1.0)
       git (>= 1.2.5)
       rake
-      rdoc
     json (1.6.6)
     rake (0.9.2.2)
-    rcov (1.0.0)
+    rcov (0.9.9)
     rdoc (3.12)
       json (~> 1.4)
     shoulda (3.0.1)
@@ -22,8 +21,8 @@ PLATFORMS
   ruby
 
 DEPENDENCIES
-  bundler (~> 1.0.0)
-  jeweler (~> 1.8.3)
-  rcov
+  bundler (~> 1.1.3)
+  jeweler (~> 1.6.4)
+  rcov (= 0.9.9)
   rdoc (~> 3.12)
   shoulda

data/Rakefile

@@ -1,6 +1,5 @@
 # encoding: utf-8
 
-require 'rubygems'
 require 'bundler'
 begin
   Bundler.setup(:default, :development)

data/VERSION

@@ -1 +1 @@
-0.1.1
+0.1.2

data/lib/rnewick.rb

@@ -74,11 +74,15 @@ class NewickFile
     # assume nw_prune and nw_reroot are in the PATH
     nw_pruner = "nw_prune"
     nw_unrooter = "nw_reroot"
-    [nw_pruner, nw_unrooter].each do |nw_util|
+    #required_utils = [nw_pruner, nw_unrooter] 
+    required_utils = [nw_pruner] 
+    required_utils.each do |nw_util|
       raise "#{nw_util} from newick utilities not available" unless binary_available(nw_util)
     end
-    # prune a list of taxa and unroot resulting tree(s) with these nice and fast newick utilities
-    system "#{nw_pruner} #{@filename} #{taxa.join ' '} | #{nw_unrooter} -d - > #{pruned_tree}"
+    # prune a list of taxa and unroot resulting tree with these nice and fast newick utilities
+    # on the first tree of the file or all of them?
+    #system "#{nw_pruner} #{@filename} #{taxa.join ' '} | #{nw_unrooter} -d - > #{pruned_tree}"
+    system "#{nw_pruner} #{@filename} #{taxa.join ' '} > #{pruned_tree}"
     puts "removed #{taxa.join ','} and saved in #{pruned_tree}" if verbose
   end
 end

data/rnewick.gemspec

@@ -5,11 +5,11 @@
 
 Gem::Specification.new do |s|
   s.name = %q{rnewick}
-  s.version = "0.1.1"
+  s.version = "0.1.2"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = [%q{Fernando Izquierdo-Carrasco}]
-  s.date = %q{2012-04-11}
+  s.date = %q{2012-06-08}
   s.description = %q{newick utilities}
   s.email = %q{fer.izquierdo@gmail.com}
   s.extra_rdoc_files = [
@@ -45,22 +45,22 @@ Gem::Specification.new do |s|
     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<bundler>, ["~> 1.0.0"])
-      s.add_development_dependency(%q<jeweler>, ["~> 1.8.3"])
-      s.add_development_dependency(%q<rcov>, [">= 0"])
+      s.add_development_dependency(%q<bundler>, ["~> 1.1.3"])
+      s.add_development_dependency(%q<jeweler>, ["~> 1.6.4"])
+      s.add_development_dependency(%q<rcov>, ["= 0.9.9"])
     else
       s.add_dependency(%q<shoulda>, [">= 0"])
       s.add_dependency(%q<rdoc>, ["~> 3.12"])
-      s.add_dependency(%q<bundler>, ["~> 1.0.0"])
-      s.add_dependency(%q<jeweler>, ["~> 1.8.3"])
-      s.add_dependency(%q<rcov>, [">= 0"])
+      s.add_dependency(%q<bundler>, ["~> 1.1.3"])
+      s.add_dependency(%q<jeweler>, ["~> 1.6.4"])
+      s.add_dependency(%q<rcov>, ["= 0.9.9"])
     end
   else
     s.add_dependency(%q<shoulda>, [">= 0"])
     s.add_dependency(%q<rdoc>, ["~> 3.12"])
-    s.add_dependency(%q<bundler>, ["~> 1.0.0"])
-    s.add_dependency(%q<jeweler>, ["~> 1.8.3"])
-    s.add_dependency(%q<rcov>, [">= 0"])
+    s.add_dependency(%q<bundler>, ["~> 1.1.3"])
+    s.add_dependency(%q<jeweler>, ["~> 1.6.4"])
+    s.add_dependency(%q<rcov>, ["= 0.9.9"])
   end
 end
 

data/test/testdata/20start.nw

@@ -1,2 +1 @@
 ((Seq14,Seq10),((Seq18,((Seq20,Seq19),(Seq17,(Seq15,Seq16)))),((Seq13,(Seq11,Seq12)),((Seq5,(Seq4,(Seq2,(Seq7,(Seq3,Seq6))))),(Seq9,Seq8)))),Seq1);
-((Seq14,Seq10),((Seq18,((Seq20,Seq19),(Seq17,(Seq15,Seq16)))),((Seq13,(Seq11,Seq12)),((Seq5,(Seq4,(Seq2,(Seq7,(Seq3,Seq6))))),(Seq9,Seq8)))),Seq1);

metadata

@@ -1,107 +1,79 @@
---- !ruby/object:Gem::Specification 
+--- !ruby/object:Gem::Specification
 name: rnewick
-version: !ruby/object:Gem::Version 
-  hash: 25
+version: !ruby/object:Gem::Version
+  version: 0.1.2
   prerelease: 
-  segments: 
-  - 0
-  - 1
-  - 1
-  version: 0.1.1
 platform: ruby
-authors: 
+authors:
 - Fernando Izquierdo-Carrasco
 autorequire: 
 bindir: bin
 cert_chain: []
-
-date: 2012-04-11 00:00:00 Z
-dependencies: 
-- !ruby/object:Gem::Dependency 
-  type: :development
-  requirement: &id001 !ruby/object:Gem::Requirement 
-    none: false
-    requirements: 
-    - - ">="
-      - !ruby/object:Gem::Version 
-        hash: 3
-        segments: 
-        - 0
-        version: "0"
-  version_requirements: *id001
+date: 2012-06-08 00:00:00.000000000Z
+dependencies:
+- !ruby/object:Gem::Dependency
   name: shoulda
-  prerelease: false
-- !ruby/object:Gem::Dependency 
+  requirement: &13618960 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
   type: :development
-  requirement: &id002 !ruby/object:Gem::Requirement 
+  prerelease: false
+  version_requirements: *13618960
+- !ruby/object:Gem::Dependency
+  name: rdoc
+  requirement: &13618480 !ruby/object:Gem::Requirement
     none: false
-    requirements: 
+    requirements:
     - - ~>
-      - !ruby/object:Gem::Version 
-        hash: 31
-        segments: 
-        - 3
-        - 12
-        version: "3.12"
-  version_requirements: *id002
-  name: rdoc
-  prerelease: false
-- !ruby/object:Gem::Dependency 
+      - !ruby/object:Gem::Version
+        version: '3.12'
   type: :development
-  requirement: &id003 !ruby/object:Gem::Requirement 
+  prerelease: false
+  version_requirements: *13618480
+- !ruby/object:Gem::Dependency
+  name: bundler
+  requirement: &13617980 !ruby/object:Gem::Requirement
     none: false
-    requirements: 
+    requirements:
     - - ~>
-      - !ruby/object:Gem::Version 
-        hash: 23
-        segments: 
-        - 1
-        - 0
-        - 0
-        version: 1.0.0
-  version_requirements: *id003
-  name: bundler
-  prerelease: false
-- !ruby/object:Gem::Dependency 
+      - !ruby/object:Gem::Version
+        version: 1.1.3
   type: :development
-  requirement: &id004 !ruby/object:Gem::Requirement 
+  prerelease: false
+  version_requirements: *13617980
+- !ruby/object:Gem::Dependency
+  name: jeweler
+  requirement: &13617480 !ruby/object:Gem::Requirement
     none: false
-    requirements: 
+    requirements:
     - - ~>
-      - !ruby/object:Gem::Version 
-        hash: 49
-        segments: 
-        - 1
-        - 8
-        - 3
-        version: 1.8.3
-  version_requirements: *id004
-  name: jeweler
-  prerelease: false
-- !ruby/object:Gem::Dependency 
+      - !ruby/object:Gem::Version
+        version: 1.6.4
   type: :development
-  requirement: &id005 !ruby/object:Gem::Requirement 
-    none: false
-    requirements: 
-    - - ">="
-      - !ruby/object:Gem::Version 
-        hash: 3
-        segments: 
-        - 0
-        version: "0"
-  version_requirements: *id005
+  prerelease: false
+  version_requirements: *13617480
+- !ruby/object:Gem::Dependency
   name: rcov
+  requirement: &13616960 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - =
+      - !ruby/object:Gem::Version
+        version: 0.9.9
+  type: :development
   prerelease: false
+  version_requirements: *13616960
 description: newick utilities
 email: fer.izquierdo@gmail.com
 executables: []
-
 extensions: []
-
-extra_rdoc_files: 
+extra_rdoc_files:
 - LICENSE.txt
 - README.rdoc
-files: 
+files:
 - .document
 - Gemfile
 - Gemfile.lock
@@ -118,37 +90,31 @@ files:
 - test/testdata/20start.nw.pruned_to.9
 - test/testdata/9
 homepage: http://github.com/fizquierdo/rnewick
-licenses: 
+licenses:
 - MIT
 post_install_message: 
 rdoc_options: []
-
-require_paths: 
+require_paths:
 - lib
-required_ruby_version: !ruby/object:Gem::Requirement 
+required_ruby_version: !ruby/object:Gem::Requirement
   none: false
-  requirements: 
-  - - ">="
-    - !ruby/object:Gem::Version 
-      hash: 3
-      segments: 
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+      segments:
       - 0
-      version: "0"
-required_rubygems_version: !ruby/object:Gem::Requirement 
+      hash: -697700823016450153
+required_rubygems_version: !ruby/object:Gem::Requirement
   none: false
-  requirements: 
-  - - ">="
-    - !ruby/object:Gem::Version 
-      hash: 3
-      segments: 
-      - 0
-      version: "0"
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
 requirements: []
-
 rubyforge_project: 
 rubygems_version: 1.8.6
 signing_key: 
 specification_version: 3
 summary: newick utilities
 test_files: []
-