bio-gem 1.2.2 → 1.3.0
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- data/.travis.yml +12 -0
- data/Rakefile +2 -1
- data/VERSION +1 -1
- data/bin/biogem +1 -1
- data/bio-gem.gemspec +5 -2
- data/doc/integration-testing.md +81 -0
- data/lib/bio-gem/generator/render.rb +4 -0
- data/lib/bio-gem/mod/jeweler.rb +5 -2
- data/lib/bio-gem/templates/travis.yml +12 -0
- metadata +19 -16
data/.travis.yml
ADDED
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@@ -0,0 +1,12 @@
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language: ruby
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rvm:
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- 1.9.2
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- 1.9.3
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- jruby-19mode # JRuby in 1.9 mode
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- rbx-19mode
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# - 1.8.7
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# - jruby-18mode # JRuby in 1.8 mode
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# - rbx-18mode
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# uncomment this line if your project needs to run something other than `rake`:
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# script: bundle exec rspec spec
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data/Rakefile
CHANGED
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@@ -42,7 +42,8 @@ Jeweler::RubygemsDotOrgTasks.new
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require 'rake/testtask'
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Rake::TestTask.new(:test) do |test|
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test.libs << 'lib' << 'test'
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test.pattern = 'test/**/test_*.rb'
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# test.pattern = 'test/**/test_*.rb' breaks in Ruby 1.9.3
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test.test_files = Dir.glob("test/**/test_*.rb")
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test.verbose = true
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end
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data/VERSION
CHANGED
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@@ -1 +1 @@
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1
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-
1.
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1.3.0
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data/bin/biogem
CHANGED
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@@ -19,7 +19,7 @@ if (application_exit[:exit]==0)
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Bundler::CLI.start
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#TODO: call rake directly not from shell
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# print "Note: if rake gives an error try running biogem from an installed gem\n"
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# print "Note: if rake gives an error try running biogem from an installed gem instead\n"
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print "\trake version:write\n"
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sh "rake version:write"
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print "\trake gemspec\n"
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data/bio-gem.gemspec
CHANGED
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@@ -5,11 +5,11 @@
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Gem::Specification.new do |s|
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s.name = "bio-gem"
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s.version = "1.
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s.version = "1.3.0"
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s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
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s.authors = ["Raoul J.P. Bonnal", "Pjotr Prins"]
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s.date = "2012-02-
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s.date = "2012-02-28"
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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"
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s.email = "ilpuccio.febo@gmail.com"
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s.executables = ["biogem"]
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]
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s.files = [
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".document",
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".travis.yml",
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"Gemfile",
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"Gemfile.lock",
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"LICENSE.txt",
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"bin/biogem",
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"bio-gem.gemspec",
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"doc/biogem-hacking.md",
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"doc/integration-testing.md",
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"lib/bio-gem.rb",
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"lib/bio-gem/application.rb",
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"lib/bio-gem/generator/render.rb",
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"lib/bio-gem/templates/rakefile",
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"lib/bio-gem/templates/routes",
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"lib/bio-gem/templates/seeds",
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"lib/bio-gem/templates/travis.yml",
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"test/helper.rb",
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"test/test_bio-gem.rb"
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]
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# Integration testing
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Continuous integration testing is very useful for biogems/plugins. The Ruby
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community has come up with [travis-ci](http://about.travis-ci.org/), which is
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integrated into github! Any time code is submitted to github, the automated
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testing on different platforms kicks in.
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Here we set out to set up travis-ci with a biogem. I chose my bio-gff3 gem
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for integrated testing.
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## Setting up Travis-CI
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The online documentation is rather complete. Here we just list the steps needed
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for a biogem.
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First set up an account using Github OAuth. Click the sign-in with github button in the top
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right corner of the travis-ci website. Choose the github projects you want to test for.
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Next add a .travis.yml configuration file to the repository. It lists the Rubies to
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test against. Lets test all versions:
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```yaml
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language: ruby
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rvm:
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- 1.8.7
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- 1.9.2
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- 1.9.3
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- jruby-18mode # JRuby in 1.8 mode
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- jruby-19mode # JRuby in 1.9 mode
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- rbx-18mode
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- rbx-19mode
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# uncomment this line if your project needs to run something other than `rake`:
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# script: bundle exec rspec spec
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```
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Test the file with
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```bash
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gem install travis-lint
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travis-lint
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Hooray, .travis.yml at /export/local/users/pjotr/git/opensource/ruby/bioruby-gff3/.travis.yml seems to be solid!
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```
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Pushing any changes to github should kick in all testing!
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You know what? Tests failed. Rubinius did lot like the rcov native extension,
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which got installed by older editions of biogem. So time to remove that. JRuby
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was fussy about 'NameError: uninitialized constant BIN', which was actually
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correct, and should not have passed in MRI.
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Ruby 1.9.3 complained about
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```bash
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/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)
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```
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Funny that. On my machine all tests passed. On travis all builds failed, even on the same
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Ruby interpreter. I had to disable my regression tests because Travis does not like resolving
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paths to external programs (surprise!).
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Anyway, fixing these bugs/issues made it a better gem!
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To add a status button on github, add the following to your README.md
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```
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[](http://travis-ci.org/[YOUR_GITHUB_USERNAME]/[YOUR_PROJECT_NAME])
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```
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If you check the README of
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https://github.com/pjotrp/bioruby-gff3-plugin
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You can see 'build status: passing' (as of 27/2/2012).
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Clicking on the button takes the viewer directly to the test results!
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Ready to run for all Ruby editions. We will add these buttons to
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http://biogems.info/. Also, we would like to achieve that any time a gem is
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tagged for release, the automated testing on different platforms kicks in.
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This is amazing functionality.
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# Biogem::Render contains all the logic to render Biogem specific
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# templates
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module Biogem
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module Render
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# new hook for removing stuff
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# Always do these
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output_template_in_target_generic 'README.rdoc'
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output_template_in_target_generic_append 'gitignore', '.gitignore'
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output_template_in_target_generic_append 'travis.yml', '.travis.yml'
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end
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def create_meta
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data/lib/bio-gem/mod/jeweler.rb
CHANGED
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alias original_initialize initialize
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def initialize(options = {})
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original_initialize(options)
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# RCov is not properly supported for Ruby 1.9.2, so we remove it
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# RCov is not properly supported in Ruby 1.9.2, so we remove it
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development_dependencies.delete_if { |k,v| k == "rcov" }
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# development_dependencies << ["bio-logger"]
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development_dependencies << ["bio", ">= 1.4.2"]
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# we add rdoc because of an upgrade of rake RDocTask causing errors
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development_dependencies << ["rdoc", ">= 2.4.2"]
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if options[:biogem_db]
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development_dependencies << ["activerecord", ">= 3.0.7"]
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development_dependencies << ["activesupport", ">= 3.0.7"]
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language: ruby
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rvm:
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- 1.9.2
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- 1.9.3
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- jruby-19mode # JRuby in 1.9 mode
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- rbx-19mode
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# - 1.8.7
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# - jruby-18mode # JRuby in 1.8 mode
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# - rbx-18mode
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# uncomment this line if your project needs to run something other than `rake`:
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# script: bundle exec rspec spec
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metadata
CHANGED
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--- !ruby/object:Gem::Specification
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name: bio-gem
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version: !ruby/object:Gem::Version
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version: 1.
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version: 1.3.0
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prerelease:
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platform: ruby
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authors:
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autorequire:
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bindir: bin
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cert_chain: []
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date: 2012-02-
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date: 2012-02-28 00:00:00.000000000 Z
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dependencies:
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- !ruby/object:Gem::Dependency
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name: bundler
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requirement: &
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requirement: &2152477800 !ruby/object:Gem::Requirement
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none: false
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requirements:
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- - ~>
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version: 1.0.18
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type: :runtime
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prerelease: false
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version_requirements: *
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version_requirements: *2152477800
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name: jeweler
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requirement: &
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requirement: &2152476940 !ruby/object:Gem::Requirement
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none: false
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requirements:
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- - ! '>='
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version: 1.7.0
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type: :runtime
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prerelease: false
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version_requirements: *
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version_requirements: *2152476940
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name: rdoc
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requirement: &
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requirement: &2152476160 !ruby/object:Gem::Requirement
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none: false
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requirements:
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- - ! '>='
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version: '0'
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type: :runtime
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prerelease: false
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version_requirements: *
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version_requirements: *2152476160
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- !ruby/object:Gem::Dependency
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name: shoulda
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requirement: &
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requirement: &2152490840 !ruby/object:Gem::Requirement
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none: false
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requirements:
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- - ! '>='
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version: '0'
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type: :development
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version_requirements: *
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version_requirements: *2152490840
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name: bundler
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requirement: &
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requirement: &2152488740 !ruby/object:Gem::Requirement
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none: false
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requirements:
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- - ~>
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type: :development
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prerelease: false
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name: jeweler
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requirement: &
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requirement: &2152486560 !ruby/object:Gem::Requirement
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requirements:
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- - ! '>='
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name: rdoc
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requirement: &
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requirement: &2152485000 !ruby/object:Gem::Requirement
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requirements:
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- - ! '>='
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version_requirements: *2152485000
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description: ! "Biogem is a software generator for those bioinformaticans who want
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to start coding an application or a library for using/extending BioRuby core library
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and sharing it through rubygems.org .\n The basic idea is to simplify and promote
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@@ -103,6 +103,7 @@ extra_rdoc_files:
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- Tutorial.rdoc
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files:
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- .document
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106
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+
- .travis.yml
|
|
106
107
|
- Gemfile
|
|
107
108
|
- Gemfile.lock
|
|
108
109
|
- LICENSE.txt
|
|
@@ -113,6 +114,7 @@ files:
|
|
|
113
114
|
- bin/biogem
|
|
114
115
|
- bio-gem.gemspec
|
|
115
116
|
- doc/biogem-hacking.md
|
|
117
|
+
- doc/integration-testing.md
|
|
116
118
|
- lib/bio-gem.rb
|
|
117
119
|
- lib/bio-gem/application.rb
|
|
118
120
|
- lib/bio-gem/generator/render.rb
|
|
@@ -142,6 +144,7 @@ files:
|
|
|
142
144
|
- lib/bio-gem/templates/rakefile
|
|
143
145
|
- lib/bio-gem/templates/routes
|
|
144
146
|
- lib/bio-gem/templates/seeds
|
|
147
|
+
- lib/bio-gem/templates/travis.yml
|
|
145
148
|
- test/helper.rb
|
|
146
149
|
- test/test_bio-gem.rb
|
|
147
150
|
homepage: http://github.com/helios/bioruby-gem
|