rput 0.1.5 → 0.2.0

data/Gemfile

@@ -2,17 +2,18 @@ source "http://rubygems.org"
 # Add dependencies required to use your gem here.
 # Example:
 #   gem "activesupport", ">= 2.3.5"
+  # own dependencies
+  gem "rraxml", "~> 0.1.2"
+  gem "rphylip", "~> 0.1.0"
+  gem "rnewick", "~> 0.1.0"
 
 # 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 "bundler", "~> 1.0.0"
+  gem "bundler", "~> 1.1.3"
   gem "jeweler", "~> 1.8.3"
+  gem "simplecov", ">= 0"
   gem "rcov", ">= 0"
-  # own dependencies
-  gem "rraxml", "~> 0.1.2"
-  gem "rphylip", "~> 0.1.0"
-  gem "rnewick", "~> 0.1.0"
 end

data/Gemfile.lock

@@ -8,8 +8,9 @@ GEM
       rake
       rdoc
     json (1.6.6)
+    multi_json (1.3.4)
     rake (0.9.2.2)
-    rcov (1.0.0)
+    rcov (0.9.9)
     rdoc (3.12)
       json (~> 1.4)
     rnewick (0.1.0)
@@ -20,12 +21,16 @@ GEM
       shoulda-matchers (~> 1.0.0)
     shoulda-context (1.0.0)
     shoulda-matchers (1.0.0)
+    simplecov (0.6.2)
+      multi_json (~> 1.3)
+      simplecov-html (~> 0.5.3)
+    simplecov-html (0.5.3)
 
 PLATFORMS
   ruby
 
 DEPENDENCIES
-  bundler (~> 1.0.0)
+  bundler (~> 1.1.3)
   jeweler (~> 1.8.3)
   rcov
   rdoc (~> 3.12)
@@ -33,3 +38,4 @@ DEPENDENCIES
   rphylip (~> 0.1.0)
   rraxml (~> 0.1.2)
   shoulda
+  simplecov

data/VERSION

@@ -1 +1 @@
-0.1.5
+0.2.0

data/rput.gemspec

@@ -5,11 +5,11 @@
 
 Gem::Specification.new do |s|
   s.name = %q{rput}
-  s.version = "0.1.5"
+  s.version = "0.2.0"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = [%q{Fernando Izquierdo-Carrasco}]
-  s.date = %q{2012-04-13}
+  s.date = %q{2012-05-08}
   s.description = %q{Automated iterations of raxml runs over externally-extended phylip files}
   s.email = %q{fer.izquierdo@gmail.com}
   s.extra_rdoc_files = [
@@ -24,7 +24,6 @@ Gem::Specification.new do |s|
     "README.rdoc",
     "Rakefile",
     "VERSION",
-    "lib/experiment.rb",
     "lib/rput.rb",
     "lib/starter.rb",
     "rput.gemspec",
@@ -41,33 +40,36 @@ Gem::Specification.new do |s|
     s.specification_version = 3
 
     if Gem::Version.new(Gem::VERSION) >= Gem::Version.new('1.2.0') then
+      s.add_runtime_dependency(%q<rraxml>, ["~> 0.1.2"])
+      s.add_runtime_dependency(%q<rphylip>, ["~> 0.1.0"])
+      s.add_runtime_dependency(%q<rnewick>, ["~> 0.1.0"])
       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<bundler>, ["~> 1.1.3"])
       s.add_development_dependency(%q<jeweler>, ["~> 1.8.3"])
+      s.add_development_dependency(%q<simplecov>, [">= 0"])
       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<rraxml>, ["~> 0.1.2"])
+      s.add_dependency(%q<rphylip>, ["~> 0.1.0"])
+      s.add_dependency(%q<rnewick>, ["~> 0.1.0"])
       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<bundler>, ["~> 1.1.3"])
       s.add_dependency(%q<jeweler>, ["~> 1.8.3"])
+      s.add_dependency(%q<simplecov>, [">= 0"])
       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<rraxml>, ["~> 0.1.2"])
+    s.add_dependency(%q<rphylip>, ["~> 0.1.0"])
+    s.add_dependency(%q<rnewick>, ["~> 0.1.0"])
     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<bundler>, ["~> 1.1.3"])
     s.add_dependency(%q<jeweler>, ["~> 1.8.3"])
+    s.add_dependency(%q<simplecov>, [">= 0"])
     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

@@ -1,155 +1,123 @@
---- !ruby/object:Gem::Specification 
+--- !ruby/object:Gem::Specification
 name: rput
-version: !ruby/object:Gem::Version 
-  hash: 17
+version: !ruby/object:Gem::Version
+  version: 0.2.0
   prerelease: 
-  segments: 
-  - 0
-  - 1
-  - 5
-  version: 0.1.5
 platform: ruby
-authors: 
+authors:
 - Fernando Izquierdo-Carrasco
 autorequire: 
 bindir: bin
 cert_chain: []
-
-date: 2012-04-13 00:00:00 Z
-dependencies: 
-- !ruby/object:Gem::Dependency 
-  type: :development
-  requirement: &id001 !ruby/object:Gem::Requirement 
+date: 2012-05-08 00:00:00.000000000Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: rraxml
+  requirement: &23178960 !ruby/object:Gem::Requirement
     none: false
-    requirements: 
-    - - ">="
-      - !ruby/object:Gem::Version 
-        hash: 3
-        segments: 
-        - 0
-        version: "0"
-  version_requirements: *id001
-  name: shoulda
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 0.1.2
+  type: :runtime
   prerelease: false
-- !ruby/object:Gem::Dependency 
-  type: :development
-  requirement: &id002 !ruby/object:Gem::Requirement 
+  version_requirements: *23178960
+- !ruby/object:Gem::Dependency
+  name: rphylip
+  requirement: &23178400 !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
+      - !ruby/object:Gem::Version
+        version: 0.1.0
+  type: :runtime
   prerelease: false
-- !ruby/object:Gem::Dependency 
-  type: :development
-  requirement: &id003 !ruby/object:Gem::Requirement 
+  version_requirements: *23178400
+- !ruby/object:Gem::Dependency
+  name: rnewick
+  requirement: &23177880 !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
+      - !ruby/object:Gem::Version
+        version: 0.1.0
+  type: :runtime
   prerelease: false
-- !ruby/object:Gem::Dependency 
+  version_requirements: *23177880
+- !ruby/object:Gem::Dependency
+  name: shoulda
+  requirement: &23177360 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
   type: :development
-  requirement: &id004 !ruby/object:Gem::Requirement 
+  prerelease: false
+  version_requirements: *23177360
+- !ruby/object:Gem::Dependency
+  name: rdoc
+  requirement: &23176800 !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: '3.12'
   type: :development
-  requirement: &id005 !ruby/object:Gem::Requirement 
-    none: false
-    requirements: 
-    - - ">="
-      - !ruby/object:Gem::Version 
-        hash: 3
-        segments: 
-        - 0
-        version: "0"
-  version_requirements: *id005
-  name: rcov
   prerelease: false
-- !ruby/object:Gem::Dependency 
-  type: :development
-  requirement: &id006 !ruby/object:Gem::Requirement 
+  version_requirements: *23176800
+- !ruby/object:Gem::Dependency
+  name: bundler
+  requirement: &23176180 !ruby/object:Gem::Requirement
     none: false
-    requirements: 
+    requirements:
     - - ~>
-      - !ruby/object:Gem::Version 
-        hash: 31
-        segments: 
-        - 0
-        - 1
-        - 2
-        version: 0.1.2
-  version_requirements: *id006
-  name: rraxml
-  prerelease: false
-- !ruby/object:Gem::Dependency 
+      - !ruby/object:Gem::Version
+        version: 1.1.3
   type: :development
-  requirement: &id007 !ruby/object:Gem::Requirement 
+  prerelease: false
+  version_requirements: *23176180
+- !ruby/object:Gem::Dependency
+  name: jeweler
+  requirement: &23175580 !ruby/object:Gem::Requirement
     none: false
-    requirements: 
+    requirements:
     - - ~>
-      - !ruby/object:Gem::Version 
-        hash: 27
-        segments: 
-        - 0
-        - 1
-        - 0
-        version: 0.1.0
-  version_requirements: *id007
-  name: rphylip
+      - !ruby/object:Gem::Version
+        version: 1.8.3
+  type: :development
   prerelease: false
-- !ruby/object:Gem::Dependency 
+  version_requirements: *23175580
+- !ruby/object:Gem::Dependency
+  name: simplecov
+  requirement: &23174700 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
   type: :development
-  requirement: &id008 !ruby/object:Gem::Requirement 
+  prerelease: false
+  version_requirements: *23174700
+- !ruby/object:Gem::Dependency
+  name: rcov
+  requirement: &23174140 !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
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
   prerelease: false
+  version_requirements: *23174140
 description: Automated iterations of raxml runs over externally-extended phylip files
 email: fer.izquierdo@gmail.com
 executables: []
-
 extensions: []
-
-extra_rdoc_files: 
+extra_rdoc_files:
 - LICENSE.txt
 - README.rdoc
-files: 
+files:
 - .document
 - Gemfile
 - Gemfile.lock
@@ -157,44 +125,37 @@ files:
 - README.rdoc
 - Rakefile
 - VERSION
-- lib/experiment.rb
 - lib/rput.rb
 - lib/starter.rb
 - rput.gemspec
 - test/helper.rb
 - test/test_rput.rb
 homepage: http://github.com/fizquierdo/rput
-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: 1995023676577088386
+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: Raxml-based perpetually updated tree
 test_files: []
-

data/lib/experiment.rb

@@ -1,113 +0,0 @@
-#!/usr/bin/env ruby
-require 'rphylip'
-require 'fileutils'
-require 'yaml'
-
-class Experiment
-  def initialize(name, basedir)
-    @name = name
-    @base_dir = basedir
-  end
-  def dirname(a)
-    File.join @base_dir, 'experiments', @name, a
-  end
-  def last_bunch_dir
-    dirs = Dir.entries(dirname("output")).select{|f| f =~ /^bunch/}
-    dirs.sort_by{|s| s.split("_").last.to_i}.last
-  end
-  def setup_dirs
-    setup_ready = true
-    %w(alignment output).map{|n| self.dirname n}.each do |dir|
-      if File.exist?(dir)
-        puts "Exists #{dir}"
-        setup_ready = false # to avoid overwrite
-      else
-        FileUtils.mkdir_p dir
-      end
-    end
-    setup_ready
-  end
-  def expand_with_updates(opts, updates_are_full_alignments = true)
-    ali = self.dirname("alignment")
-    phy = opts[:phylip]
-    raise "phylip file not available" if phy.nil? or not File.exist?(phy)
-    FileUtils.copy phy, ali 
-    p = Phylip.new(File.join ali, File.basename(phy))
-    p.subdivide_random opts 
-  end
-end
-
-class ExperimentList
-  # Persistent storage in .yml file of the experiment status
-  attr_accessor :name, :date
-  def initialize(expfile)
-    @expfile = expfile
-    File.open(expfile, "w"){|f| f.puts "---"} unless File.exist?(expfile)
-    @list = YAML.load_file(expfile) || Array.new
-  end
-  def add(opts)
-    name_available = self.name_available?(opts[:name]) 
-    if name_available
-      #newexp = {:name => opts[:name], :date => Time.now, :fake_phy => opts[:fake_phy]}
-      newexp = {:name => opts[:name], :date => Time.now}
-      newexp.merge!({:fake_phy => opts[:fake_phy]}) unless opts[:fake_phy].nil?
-      newexp.merge!({:initial_phy => opts[:initial_phy]}) unless opts[:initial_phy].nil?
-      @list.push newexp
-      self.save
-      true
-    end
-  end
-  def update(name, step, state)
-    e = self.find_by_name(name) 
-    unless e.nil?
-      @list.each do |item|
-        if item[:name] == name
-          if item[step].nil?
-            item[step] = state
-          else
-            item[step] += " " + state
-          end
-        end
-      end
-    end
-    self.save
-  end
-  def show
-    puts "Current Experiments"
-    puts "ID\tname"
-    @list.each_with_index  do |item, i|
-      fake_name = item[:fake_phy].nil? ? "-" : File.basename(item[:fake_phy]) 
-      initial_name = item[:initial_phy].nil? ? "-" : File.basename(item[:initial_phy]) 
-      puts "#{i}\t#{item[:name]}\t fake: #{fake_name} \t init: #{initial_name} Best LH: #{item["bestLH"]}"
-      item.keys.select{|k| k =~ /^u\d+$/}.sort.each do |update_key|
-        puts "  #{update_key}: #{item[update_key]}"
-      end
-    end
-  end
-  def remove(name)
-    item = find_by_name(name)
-    unless item.nil?
-      @list.delete(item) 
-      self.save
-    end
-  end
-  def save
-    File.open(@expfile, "w"){|f| f.write @list.to_yaml}
-    puts "Experiment list updated"
-  end
-  def name_available?(name)
-    existing_items = find_by_name(name)
-    unless existing_items.nil?
-       if existing_items.size >= 1
-         puts "A expremient with this name exists already"
-         p existing_items
-         return false
-       end
-    end
-    return true
-  end
-  protected
-  def find_by_name(name)
-    @list.find{|e| e[:name] == name}
-  end
-end