[BioRuby] alignment.rb

Naohisa Goto ngoto at gen-info.osaka-u.ac.jp
Sat Sep 24 11:51:38 EDT 2005


> I added this to the Tutorial.

I backported into Japanese Tutorial.rd.ja.
I also made little changes to the Tutorial.rd. Please refer to
cvs commit log. (I'm sorry not updated Wiki yet.)

> Again, can I ask everyone - how do we plan to maintain unit tests and
> make sure the code in the documentation is *not* broken? The code
> should be only *once* in the source repository for a dual purpose -
> and I would like to be sure it is correct.
> If I were to write something I would like to have these code snippets
> in the unit tests and parse them into the rd documentation when
> generating documents with rdoc. Is there already something for this in
> Ruby space? I know you can do an include in rd, but would need to do
> some preparsing to lift only the interesting code out of the unit
> test.
> Anyway if I were to experiment with this would you welcome it - or
> reject it?

I think this may be very good for algorithmic or mathematical methods.
I fear this might not be so good for database parsers, especially
for complex structured data, because they depend on original
data's structure and I think we can hardly describe every location in
original data in every method's unittest where the method's
return value is based on.

Naohisa GOTO
ngoto at gen-info.osaka-u.ac.jp
Department of Genome Informatics, Genome Information Research Center,
Research Institute for Microbial Diseases, Osaka University, Japan

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