[BioRuby] GSOC: phyloXML for BioRuby: Code Review

[Naohisa GOTO]

Hi,

On Mon, 22 Jun 2009 12:27:11 -0400
Diana Jaunzeikare <rozziite at gmail.com> wrote:

> Hi all,
> 
> In the Google Summer of Code project I have reached a stage where most of
> the code has been written for PhyloXML parser and I would like to ask for
> code review.
> 
> I would like to know answers to these questions:
> 
> * What parts should have more documentation?

For each attribute and methods, not only the return value's class
but also description for the attribute will be needed,
although it will be nearly the same as the phyloxml's description.

> * Are there any places where code could be made more rubyish?

Currently, no problem.

> 
> * Are the structure of unit tests fine, or there are some conventions which
> my code doesn't follow?

It is good that the module TestPhyloXMLData is defined inside
the module Bio namespace.

> 
> * Is code readable?

Yes.

> 
> * Are there any conventions that I don't follow? (like lines should strictly
> fit into 80 columns)?

There are no strict conventions, especially for tests
which may depend on test data variety.

> 
> Any comments would be appreciated.
> 
> Code is available on github
> http://github.com/latvianlinuxgirl/bioruby/tree/dev  in *
> lib/bio/db/phyloxml.rb* and *test/unit/bio/db/test_phyloxml.rb* files.
> 
> 
> Diana
> 

In my environment,
(Debian lenny i386, Ruby 1.8.7-p160, libxml-ruby 1.1.3)

% ruby -r rubygems test/unit/bio/db/test_phyloxml.rb
Loaded suite test/unit/bio/db/test_phyloxml
Started
............................
Finished in 1.375441 seconds.

28 tests, 91 assertions, 0 failures, 0 errors

-- 
Naohisa Goto
ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org