bio-gem 1.2.2 → 1.3.0

data/.travis.yml

@@ -0,0 +1,12 @@
+language: ruby
+rvm:
+  - 1.9.2
+  - 1.9.3
+  - jruby-19mode # JRuby in 1.9 mode
+  - rbx-19mode
+#  - 1.8.7
+#  - jruby-18mode # JRuby in 1.8 mode
+#  - rbx-18mode
+
+# uncomment this line if your project needs to run something other than `rake`:
+# script: bundle exec rspec spec

data/Rakefile

@@ -42,7 +42,8 @@ Jeweler::RubygemsDotOrgTasks.new
 require 'rake/testtask'
 Rake::TestTask.new(:test) do |test|
   test.libs << 'lib' << 'test'
-  test.pattern = 'test/**/test_*.rb'
+  # test.pattern = 'test/**/test_*.rb' breaks in Ruby 1.9.3
+  test.test_files = Dir.glob("test/**/test_*.rb")
   test.verbose = true
 end
 

data/VERSION

@@ -1 +1 @@
-1.2.2
+1.3.0

data/bin/biogem

@@ -19,7 +19,7 @@ if (application_exit[:exit]==0)
 
   Bundler::CLI.start
   #TODO: call rake directly not from shell
-  # print "Note: if rake gives an error try running biogem from an installed gem\n"
+  # print "Note: if rake gives an error try running biogem from an installed gem instead\n"
   print "\trake version:write\n"
   sh "rake version:write"
   print "\trake gemspec\n"

data/bio-gem.gemspec

@@ -5,11 +5,11 @@
 
 Gem::Specification.new do |s|
   s.name = "bio-gem"
-  s.version = "1.2.2"
+  s.version = "1.3.0"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["Raoul J.P. Bonnal", "Pjotr Prins"]
-  s.date = "2012-02-16"
+  s.date = "2012-02-28"
   s.description = "Biogem is a software generator for those bioinformaticans who want to start coding an application or a library for using/extending BioRuby core library and sharing it through rubygems.org .\n  The basic idea is to simplify and promote a modular approach to bioinformatics software development"
   s.email = "ilpuccio.febo@gmail.com"
   s.executables = ["biogem"]
@@ -20,6 +20,7 @@ Gem::Specification.new do |s|
   ]
   s.files = [
     ".document",
+    ".travis.yml",
     "Gemfile",
     "Gemfile.lock",
     "LICENSE.txt",
@@ -30,6 +31,7 @@ Gem::Specification.new do |s|
     "bin/biogem",
     "bio-gem.gemspec",
     "doc/biogem-hacking.md",
+    "doc/integration-testing.md",
     "lib/bio-gem.rb",
     "lib/bio-gem/application.rb",
     "lib/bio-gem/generator/render.rb",
@@ -59,6 +61,7 @@ Gem::Specification.new do |s|
     "lib/bio-gem/templates/rakefile",
     "lib/bio-gem/templates/routes",
     "lib/bio-gem/templates/seeds",
+    "lib/bio-gem/templates/travis.yml",
     "test/helper.rb",
     "test/test_bio-gem.rb"
   ]

data/doc/integration-testing.md

@@ -0,0 +1,81 @@
+# Integration testing
+
+Continuous integration testing is very useful for biogems/plugins. The Ruby
+community has come up with [travis-ci](http://about.travis-ci.org/), which is
+integrated into github!  Any time code is submitted to github, the automated
+testing on different platforms kicks in. 
+
+Here we set out to set up travis-ci with a biogem. I chose my bio-gff3 gem 
+for integrated testing.
+
+## Setting up Travis-CI
+
+The online documentation is rather complete. Here we just list the steps needed
+for a biogem.
+
+First set up an account using Github OAuth. Click the sign-in with github button in the top
+right corner of the travis-ci website. Choose the github projects you want to test for.
+
+Next add a .travis.yml configuration file to the repository. It lists the Rubies to
+test against. Lets test all versions:
+
+```yaml
+language: ruby
+rvm:
+  - 1.8.7
+  - 1.9.2
+  - 1.9.3
+  - jruby-18mode # JRuby in 1.8 mode
+  - jruby-19mode # JRuby in 1.9 mode
+  - rbx-18mode
+  - rbx-19mode
+# uncomment this line if your project needs to run something other than `rake`:
+# script: bundle exec rspec spec
+```
+
+Test the file with
+
+```bash
+gem install travis-lint
+travis-lint 
+Hooray, .travis.yml at /export/local/users/pjotr/git/opensource/ruby/bioruby-gff3/.travis.yml seems to be solid!
+```
+
+Pushing any changes to github should kick in all testing!
+
+You know what? Tests failed. Rubinius did lot like the rcov native extension,
+which got installed by older editions of biogem. So time to remove that. JRuby
+was fussy about 'NameError: uninitialized constant BIN', which was actually
+correct, and should not have passed in MRI.
+
+Ruby 1.9.3 complained about
+  
+```bash
+  /home/vagrant/.rvm/rubies/ruby-1.9.3-p125/lib/ruby/1.9.1/test/unit.rb:167:in 'block in non_options': file not found: test/**/test_*.rb (ArgumentError)
+```
+
+Funny that. On my machine all tests passed. On travis all builds failed, even on the same 
+Ruby interpreter. I had to disable my regression tests because Travis does not like resolving
+paths to external programs (surprise!).
+
+Anyway, fixing these bugs/issues made it a better gem!
+
+To add a status button on github, add the following to your README.md
+
+```
+  [![Build Status](https://secure.travis-ci.org/[YOUR_GITHUB_USERNAME]/[YOUR_PROJECT_NAME].png)](http://travis-ci.org/[YOUR_GITHUB_USERNAME]/[YOUR_PROJECT_NAME])
+```
+
+If you check the README of
+
+  https://github.com/pjotrp/bioruby-gff3-plugin
+
+You can see 'build status: passing' (as of 27/2/2012).
+
+Clicking on the button takes the viewer directly to the test results!
+
+Ready to run for all Ruby editions. We will add these buttons to
+http://biogems.info/.  Also, we would like to achieve that any time a gem is
+tagged for release, the automated testing on different platforms kicks in. 
+
+This is amazing functionality. 

data/lib/bio-gem/generator/render.rb

@@ -1,3 +1,6 @@
+# Biogem::Render contains all the logic to render Biogem specific 
+# templates
+
 module Biogem
   module Render
     # new hook for removing stuff
@@ -60,6 +63,7 @@ module Biogem
       # Always do these
       output_template_in_target_generic 'README.rdoc'
       output_template_in_target_generic_append 'gitignore', '.gitignore'
+      output_template_in_target_generic_append 'travis.yml', '.travis.yml'
     end
 
     def create_meta

data/lib/bio-gem/mod/jeweler.rb

@@ -17,9 +17,12 @@ class Jeweler
     alias original_initialize initialize
     def initialize(options = {})
       original_initialize(options)
-      development_dependencies << ["bio", ">= 1.4.2"]
-      # RCov is not properly supported for Ruby 1.9.2, so we remove it
+      # RCov is not properly supported in Ruby 1.9.2, so we remove it
       development_dependencies.delete_if { |k,v| k == "rcov" }
+      # development_dependencies << ["bio-logger"]
+      development_dependencies << ["bio", ">= 1.4.2"]
+      # we add rdoc because of an upgrade of rake RDocTask causing errors
+      development_dependencies << ["rdoc", ">= 2.4.2"]
       if options[:biogem_db]
         development_dependencies << ["activerecord", ">= 3.0.7"]
         development_dependencies << ["activesupport", ">= 3.0.7"]

data/lib/bio-gem/templates/travis.yml

@@ -0,0 +1,12 @@
+language: ruby
+rvm:
+  - 1.9.2
+  - 1.9.3
+  - jruby-19mode # JRuby in 1.9 mode
+  - rbx-19mode
+#  - 1.8.7
+#  - jruby-18mode # JRuby in 1.8 mode
+#  - rbx-18mode
+
+# uncomment this line if your project needs to run something other than `rake`:
+# script: bundle exec rspec spec

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: bio-gem
 version: !ruby/object:Gem::Version
-  version: 1.2.2
+  version: 1.3.0
   prerelease: 
 platform: ruby
 authors:
@@ -10,11 +10,11 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2012-02-16 00:00:00.000000000 Z
+date: 2012-02-28 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bundler
-  requirement: &2164358520 !ruby/object:Gem::Requirement
+  requirement: &2152477800 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -22,10 +22,10 @@ dependencies:
         version: 1.0.18
   type: :runtime
   prerelease: false
-  version_requirements: *2164358520
+  version_requirements: *2152477800
 - !ruby/object:Gem::Dependency
   name: jeweler
-  requirement: &2164357900 !ruby/object:Gem::Requirement
+  requirement: &2152476940 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -33,10 +33,10 @@ dependencies:
         version: 1.7.0
   type: :runtime
   prerelease: false
-  version_requirements: *2164357900
+  version_requirements: *2152476940
 - !ruby/object:Gem::Dependency
   name: rdoc
-  requirement: &2164357060 !ruby/object:Gem::Requirement
+  requirement: &2152476160 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -44,10 +44,10 @@ dependencies:
         version: '0'
   type: :runtime
   prerelease: false
-  version_requirements: *2164357060
+  version_requirements: *2152476160
 - !ruby/object:Gem::Dependency
   name: shoulda
-  requirement: &2164355560 !ruby/object:Gem::Requirement
+  requirement: &2152490840 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -55,10 +55,10 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *2164355560
+  version_requirements: *2152490840
 - !ruby/object:Gem::Dependency
   name: bundler
-  requirement: &2164355000 !ruby/object:Gem::Requirement
+  requirement: &2152488740 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -66,10 +66,10 @@ dependencies:
         version: 1.0.18
   type: :development
   prerelease: false
-  version_requirements: *2164355000
+  version_requirements: *2152488740
 - !ruby/object:Gem::Dependency
   name: jeweler
-  requirement: &2164354440 !ruby/object:Gem::Requirement
+  requirement: &2152486560 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -77,10 +77,10 @@ dependencies:
         version: 1.7.0
   type: :development
   prerelease: false
-  version_requirements: *2164354440
+  version_requirements: *2152486560
 - !ruby/object:Gem::Dependency
   name: rdoc
-  requirement: &2164353960 !ruby/object:Gem::Requirement
+  requirement: &2152485000 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -88,7 +88,7 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *2164353960
+  version_requirements: *2152485000
 description: ! "Biogem is a software generator for those bioinformaticans who want
   to start coding an application or a library for using/extending BioRuby core library
   and sharing it through rubygems.org .\n  The basic idea is to simplify and promote
@@ -103,6 +103,7 @@ extra_rdoc_files:
 - Tutorial.rdoc
 files:
 - .document
+- .travis.yml
 - Gemfile
 - Gemfile.lock
 - LICENSE.txt
@@ -113,6 +114,7 @@ files:
 - bin/biogem
 - bio-gem.gemspec
 - doc/biogem-hacking.md
+- doc/integration-testing.md
 - lib/bio-gem.rb
 - lib/bio-gem/application.rb
 - lib/bio-gem/generator/render.rb
@@ -142,6 +144,7 @@ files:
 - lib/bio-gem/templates/rakefile
 - lib/bio-gem/templates/routes
 - lib/bio-gem/templates/seeds
+- lib/bio-gem/templates/travis.yml
 - test/helper.rb
 - test/test_bio-gem.rb
 homepage: http://github.com/helios/bioruby-gem