[BioRuby] [GSoC][NeXML and RDF API] Code Review.

[Anurag Priyam]

On Fri, Jun 25, 2010 at 12:38 PM, Pjotr Prins <pjotr.public14 at thebird.nl>wrote:

> > >  http://github.com/tablatom/rubydoctest
> > >
> > >
> > Hey, I did not know that doctests existed for Ruby too. I will have a
> look
> > into it.
>
> They are good, however finding bugs is a bit problematic as the stack
> traces are lengthy and often not descriptive. So with troubling code
> I tend to write extra unit tests. Also, with BioRuby we have not
> settled on doctests yet, so you need to reach coverage with unit
> tests and/or Specs.
>
> I really think it is good for validating documentation.
>
> > > I used these in bio/appl/paml/codeml/report.rb - these are examples
> > > that double as tests. Kill two birds with one stone! The BioRuby
> > > tutorial also uses doctests - i.e. the code in the Tutorial can be
> > > validated against the installed bioruby. If you want to use this you
> > > need an extra conversion - I have that tool.
> > >
> >
> > I will check out the examples. What tool? I would like to know more.
>
> It simply parses out commented code in the source headers, and turns
> them over to rubydoctest. The tool is in my bioruby-support tree on
> github - see
>
>
> http://github.com/pjotrp/bioruby-support/blob/master/bin/uncomment_doctest
>
> you can see it uses an environment variable.
>
>
Perfect. I will use it when expanding the documentation.


> > I am missing Rspec too from my Rails and Merb days. I picked up unit
> tests
> > because much of the framework had used the same and also because I wanted
> to
> > try it out :).
> >
> >
> > > I am interested to see what you want to do for RDF support. Maybe you
> > > can write out the API as an RSpec? That would be a good start.
> > >
> > >
> > That sounds like a nice idea.
>
> RSpec is new for BioRuby. Since you have experience you are the right
> one to introduce it to us ;). If it is convincing to the others we
> may accept it as standard use (personally I think it is a step
> forward from unit testing - unit tests are not very good as
> documentation).
>
>
I am willing to use Rspec for the RDF API part. Converting the already
existing unit tests I have written to Rspec does not sound a good idea?

-- 
Anurag Priyam,
2nd Year Undergraduate,
Department of Mechanical Engineering,
IIT Kharagpur.
+91-9775550642