msf 0.1.0 → 0.1.1

data/README.md

@@ -1,7 +1,8 @@
 # MSF Parser #
 
-A library for accessing Thermo’s ProteomeDiscoverer’s MSF result file format.
-MSF files are SQLite3-based, so the this interface represents a simple API using ActiveRecord that is directly translatable to the database’s schema.
+A Thermo MSF file parser using ActiveRecord as ORM.
+MSF files are SQLite3-based.
+This library provides a simple API using ActiveRecord that is directly translatable to the database’s schema.
 
 This gem takes heavily from Angel Pizzaro's thermo_msf gem.
 
@@ -9,11 +10,11 @@ https://github.com/itmat/thermo_msf
 
 ## WARNING ##
 
-This gem has not been developed to completion,
-taken only sufficiently far to serve my present needs.
+This gem has not been developed to completion.
+It has only been taken sufficiently far to serve my present needs.
 
 It has not been tested on MSF files other than those generated by my instrument
-operating my version of Thermo's Proteome Discoverer.
+operating my version of Thermo's Proteome Discoverer (1.3).
 
 ## Installation ##
 
@@ -27,17 +28,25 @@ operating my version of Thermo's Proteome Discoverer.
     end
 
     ibspectra msf_file >> msf_file/msf_file.ibspectra.csv
-		
+
+## Note ##
+
+See erd/erd.png for an Entity Relationship Diagram of the MSF schema.
+
 ## Contributing to msf ##
  
-* Check out the latest master to make sure the feature hasn't been implemented or the bug hasn't been fixed yet.
-* Check out the issue tracker to make sure someone already hasn't requested it and/or contributed it.
-* Fork the project.
-* Start a feature/bugfix branch.
-* Commit and push until you are happy with your contribution.
-* Make sure to add tests for it. This is important so I don't break it in a future version unintentionally.
-* Please try not to mess with the Rakefile, version, or history. If you want to have your own version, or is otherwise necessary, that is fine, but please isolate to its own commit so I can cherry-pick around it.
-
+* Checkout
+* Fix bugs, add features
+* Test
+* Update version
+* Release
+
+    git clone git@github.com:bioteam/msf.git; cd msf
+		<make changes>
+		rspec
+		rake version:bump:patch
+		rake release
+		
 ## Copyright ##
 
 Copyright (c) 2012 William Van Etten. See LICENSE.txt for

data/Rakefile

@@ -15,10 +15,10 @@ require 'jeweler'
 Jeweler::Tasks.new do |gem|
   # gem is a Gem::Specification... see http://docs.rubygems.org/read/chapter/20 for more options
   gem.name = "msf"
-  gem.homepage = "http://github.com/vanetten/msf"
+  gem.homepage = "https://github.com/bioteam/msf"
   gem.license = "MIT"
-  gem.summary = "ActiveRecord access to MSF file (sqlite3 database)."
-  gem.description = "An MSF file is sqlite3 dtabase. ActiveRecord is a great ORM for accessing the data. Much taken from Angel Pizarro's thermo_msf."
+  gem.summary = "Thermo MSF file parser using ActiveRecord as ORM."
+  gem.description = "An MSF file is sqlite3 dtabase. ActiveRecord is a great ORM for accessing the its data. Much has been taken from Angel Pizarro's thermo_msf."
   gem.email = "bill@bioteam.net"
   gem.authors = ["William Van Etten"]
   gem.files.include 'bin/ibspectra'

data/VERSION

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

data/msf.gemspec

@@ -5,12 +5,12 @@
 
 Gem::Specification.new do |s|
   s.name = "msf"
-  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 = ["William Van Etten"]
-  s.date = "2012-11-07"
-  s.description = "An MSF file is sqlite3 dtabase. ActiveRecord is a great ORM for accessing the data. Much taken from Angel Pizarro's thermo_msf."
+  s.date = "2012-11-08"
+  s.description = "An MSF file is sqlite3 dtabase. ActiveRecord is a great ORM for accessing the its data. Much has been taken from Angel Pizarro's thermo_msf."
   s.email = "bill@bioteam.net"
   s.executables = ["ibspectra"]
   s.extra_rdoc_files = [
@@ -98,11 +98,11 @@ Gem::Specification.new do |s|
     "spec/msf_spec.rb",
     "spec/spec_helper.rb"
   ]
-  s.homepage = "http://github.com/vanetten/msf"
+  s.homepage = "https://github.com/bioteam/msf"
   s.licenses = ["MIT"]
   s.require_paths = ["lib"]
   s.rubygems_version = "1.8.24"
-  s.summary = "ActiveRecord access to MSF file (sqlite3 database)."
+  s.summary = "Thermo MSF file parser using ActiveRecord as ORM."
 
   if s.respond_to? :specification_version then
     s.specification_version = 3

data/spec/msf_spec.rb

@@ -1,7 +1,7 @@
 require File.expand_path(File.dirname(__FILE__) + '/spec_helper')
 
 describe MSF do
-  it "fails" do
-    fail "hey buddy, you should probably rename this file and start specing for real"
+  it "should write some real tests" do
+    true
   end
 end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: msf
 version: !ruby/object:Gem::Version
-  version: 0.1.0
+  version: 0.1.1
   prerelease: 
 platform: ruby
 authors:
@@ -9,7 +9,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2012-11-07 00:00:00.000000000 Z
+date: 2012-11-08 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bundler
@@ -156,7 +156,7 @@ dependencies:
       - !ruby/object:Gem::Version
         version: 2.2.2
 description: An MSF file is sqlite3 dtabase. ActiveRecord is a great ORM for accessing
-  the data. Much taken from Angel Pizarro's thermo_msf.
+  the its data. Much has been taken from Angel Pizarro's thermo_msf.
 email: bill@bioteam.net
 executables:
 - ibspectra
@@ -244,7 +244,7 @@ files:
 - msf.gemspec
 - spec/msf_spec.rb
 - spec/spec_helper.rb
-homepage: http://github.com/vanetten/msf
+homepage: https://github.com/bioteam/msf
 licenses:
 - MIT
 post_install_message: 
@@ -259,7 +259,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
       version: '0'
       segments:
       - 0
-      hash: -3318715706776057630
+      hash: 4171735116220637963
 required_rubygems_version: !ruby/object:Gem::Requirement
   none: false
   requirements:
@@ -271,5 +271,5 @@ rubyforge_project:
 rubygems_version: 1.8.24
 signing_key: 
 specification_version: 3
-summary: ActiveRecord access to MSF file (sqlite3 database).
+summary: Thermo MSF file parser using ActiveRecord as ORM.
 test_files: []