[BioRuby] doctests for BioRuby

Pjotr Prins pjotr2008 at thebird.nl
Sun Feb 3 10:05:51 UTC 2008

I have a doctest.rb program that works with BioRuby. Basically you can run

doctest.rb [-v] sourcefilename(s) e.g.

ruby doctest.rb -v Tutorial.rd
Looking for doctests in 1 files
Processing 'Tutorial.rd'Testing 'Testing bioruby'...OK
Total tests: 1; assertions 2; succeeded: 2

Where in this case the Tutorial.rd contains bioruby shell type (you
can check it!):

  bioruby> seq = Bio::Sequence::NA.new("atgcatgcaaaa")
  ==> "atgcatgcaaaa"

  bioruby> seq.complement
  ==> "ttttgcatgcat"

The cool thing is allows writing tests in documentation - doubling as
a unit or regression test and ascertaining the examples in the
documentation are still valid. doctest is big in the Python
community, and I think it is a very good idea. See

Question: where should I store this functionality? Should the script
go into:

./bin/extra/   (my preference)

or even


At this point doctest.rb is not a module - though that may be useful
when people start using doctests in place of unit tests.


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