[BioRuby] tutorial

Raoul Bonnal bonnalraoul at ingm.it
Thu Mar 3 20:29:15 UTC 2011

Dear All,
a) this discussion is a good starting point for a workgroup during Codefest 2011 and/or BOSC (can't post to bopen-bio list cause I don't have the addr here, sorry)
a.idea) why not create a common "machine" on the cloud for testing our projects ?! It would be fun to see all the bio* with stats about testing etc...
b) testing is very important and new contributes should be accepted only with tests, which implies a problem how to check fake tests? :-)
c) usually ruby's community relies a lot on doc==tests that's completely wrong, because the newbies can't read fluently the code, also because there are different tools and sometimes a lot of mocking.
c.a) recently i had an idea, but I have no time to do that: establish a relationship between a mock and a real object and validate the mock or enable it only if the real object has been tested before. That would make mocking more sens to me, but i think this is another story.
d) I agree with Toshiaki, after this very useful brain storming start working (Impressed to see all this traffic :-) )


From: Peter Cock [mailto:p.j.a.cock at googlemail.com]
To: Pjotr Prins [mailto:pjotr.public14 at thebird.nl]
Cc: BioRuby [mailto:bioruby at lists.open-bio.org]
Sent: Thu, 03 Mar 2011 20:51:09 +0100
Subject: Re: [BioRuby] tutorial

On Thu, Mar 3, 2011 at 7:12 PM, Pjotr Prins <pjotr.public14 at thebird.nl> wrote:
  > Thanks Peter and Chris. I am glad we can learn from your experience.
  > Toshiaki had a very cool idea today (on IRC). The implications
  > carry beyond BioRuby gems.
  > My wish is to see whether BioRuby and plugins are running well on
  > different Ruby implementations, and operating systems.
  > The reality is that developers won't test every possibility.
  > On the other hand, users do ;)
  > Also, for every plugin and BioRuby we create tests.
  > Users can run those tests.
  > So, what we need is a tool to report test results to some central DB
  > ...
  > This would be interesting to rubygems in general. Debian uses
  > something similar for packages. What do you think? I don't think
  > BioPerl or BioPython has that, correct?
  > Pj.
  No, but Biopython is now using Buildbot on http://testing.open-bio.org
  with a small number of buildslaves belonging to Biopython developers
  running nightly unit tests on our latest code in github.
  This is a very recent setup (having been prototyped on another OBF
  machine late last year), and in theory other build systems could be
  used too. I think BioPerl is interested in using smoke server.
  Having end users submit tests would be useful too...
  BioRuby Project - http://www.bioruby.org/
  BioRuby mailing list
  BioRuby at lists.open-bio.org

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