mspire 0.8.3 → 0.8.4

data/Rakefile

@@ -19,7 +19,7 @@ Jeweler::Tasks.new do |gem|
   gem.add_dependency "obo", ">= 0.1.0"
   gem.add_dependency "builder", "~> 3.0.0"
   gem.add_dependency "bio", "~> 1.4.2"
-  gem.add_dependency "trollop", "~> 1.16.2"
+  gem.add_dependency "trollop", "~> 2.0.0"
   gem.add_dependency "uuid", ">= 2.3.5"
   # this should be a real dependency, but need to document getting this
   # working on windows first!

data/VERSION

@@ -1 +1 @@
-0.8.3
+0.8.4

data/lib/mspire/molecular_formula.rb

@@ -123,6 +123,10 @@ module Mspire
       mss
     end
 
+    def avg_mass
+      inject(0.0) {|sum,(el,cnt)| sum + (Mspire::Mass::AVG[el]*cnt) }
+    end
+
     # returns nil if the charge == 0
     def mz(consider_electron_masses = true)
       if charge == 0

data/spec/mspire/mzml_spec.rb

@@ -87,7 +87,9 @@ describe Mspire::Mzml do
         mzml.write(outfile)
       end
       # this output was checked to be accurate with TOPPView
-      file_check(outfile)
+      file_check(outfile) do |string|
+        sanitize_mspire_version_xml(string)
+      end
     end
   end
 

data/spec/mspire/readme_spec.rb

@@ -69,7 +69,9 @@ describe 'performing what is on the readme' do
         mzml.run.spectrum_list = Mspire::Mzml::SpectrumList.new(normalize_processing, spectra)
         mzml.write(outfile)
       end
-      file_check(outfile)
+      file_check(outfile) do |string|
+        sanitize_mspire_version_xml(string)
+      end
     end
 
   end

data/spec/spec_helper.rb

@@ -45,6 +45,7 @@ end
 
 def sanitize_mspire_version_xml(string)
   string.gsub(/"mspire(_[\d\.]+)?" version="([\.\d]+)"/, %Q{"mspire" version="X.X.X"})
+  .gsub(/softwareRef="mspire_[\d\.]+/, 'softwareRef="mspire_X.X.X')
 end
 
 require 'stringio'

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: mspire
 version: !ruby/object:Gem::Version
-  version: 0.8.3
+  version: 0.8.4
   prerelease: 
 platform: ruby
 authors:
@@ -10,7 +10,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2012-09-18 00:00:00.000000000 Z
+date: 2012-09-20 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: nokogiri
@@ -115,7 +115,7 @@ dependencies:
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
-        version: 1.16.2
+        version: 2.0.0
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
@@ -123,7 +123,7 @@ dependencies:
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
-        version: 1.16.2
+        version: 2.0.0
 - !ruby/object:Gem::Dependency
   name: uuid
   requirement: !ruby/object:Gem::Requirement