[BioRuby] [Open-bio Board] Buildbot on testing.open-bio.org

[Pjotr Prins]

On Thu, Nov 03, 2011 at 09:23:17AM +0000, Peter Cock wrote:
> On Thu, Nov 3, 2011 at 6:18 AM, Pjotr Prins <pjotr.public14 at thebird.nl> wrote:
> > On Wed, Nov 02, 2011 at 09:01:40PM +0000, Peter Cock wrote:
> >> Have you decided which versions of Ruby should be tested?
> >> For example, do you just need two targets, 1.8.x and 1.9.x?
> >
> > My feeling is that 1.9 is relevant for default testing. In the wild
> > there may be versions running 1.8 - and if someone feels like it,
> > they can set up the buildbot too. Right?
> 
> Yes, but we need to know the planned matrix to setup the server.
> So both Ruby 1.8.x and Ruby 1.9.x as two targets then, potentially
> on the usual Windows 32 bit, Linux 32bit, Linux 64bit and Mac OS X?
> So that could be 8 targets.

OK, sounds good. It makes sense, also for other languages, to have 
two versions of compiler or interpreter for testing.

> > It is more important to test plugins. Raoul and I will set that up,
> > as soon as we grasp the infrastructure.
> 
> Right, we hear you. Essentially that will require knowing the
> commands to call. Right now we have (roughly - Tiago can
> correct me) the following to do an in-situ test (no installation):

> (1) Get BioRuby from github (usually the latest, but you can
> ask for a specific revision via the buildbot web interface)
> (2) Run: ruby test/runner.rb (or similar)
> 
> If it possible to have Ruby 1.8 and 1.9 installed at the same
> time, is there a convention for calling them? I'd guess ruby1.8
> and ruby1.9 if the same style as Python is used. Then we'd
> have two versions of the above:
> 
> (1) Get BioRuby from github
> (2) Run: ruby1.8 test/runner.rb (or similar)
> 
> or,
> 
> (1) Get BioRuby from github
> (2) Run: ruby1.9 test/runner.rb (or similar)
> 
> The server configuration tells it which "recipe" to call on
> which slaves, so if one machine only has Ruby 1.9, it will
> not be asked to test on Ruby 1.8.
> 
> We may also need slight variants for Windows vs Linux
> vs Mac.
> 
> So what we'll need is an extended recipe which also gets the
> appropriate gem versions for that revision, and tests them.
> This could be a shell script, but if given as a list of commands
> you can see the progress, output and success/failure of each
> on the buildbot web interface.

We don't have a protocol just yet. The important containers are bio-core,
bio-core-ext and bio-biolinux. Each of these installs all important plugins.

For testing you'd want a test of each *released* plugin on
rubygems.org. The plugins to test are listed inside above containers
- for example in

  https://github.com/helios/bioruby-core/blob/master/Rakefile

and can also be queried on rubygems (REST interface). I do that to
generate http://biogems.info/.

The install of a released plugin is simple:

  gem install plugin

installs the gem in 

  cd ~/.gems/gems/plugin-0.7

and the tests should run with

  rake test

Some dependencies may be needed at test time. These can (in principle)
be run with

  cd ~/.gems/gems/plugin-0.7
  bundle
  rake test

Note1: all plugins should support 'rake test' - though now they don't.

Note2: plugins require ruby 1.9.x - on Debian install ruby-1.9.1-dev

Pj.