[BioRuby] bioruby documentation

[Toshiaki Katayama]

Hi,

Thanks for a lot of discussions.

* format of RDoc and level of detail - still need discussion

For readability in terminal, please fold docs within 79 columns
(example code in doc would break this principle).
Please use "#" prefixed style and don't use =begin rdoc/=end pairs
as it makes impossible to read the code without coloring.

Basically agreed to have standardized format as Jan suggested.
It will make clear what should be documented at least,
especially for the non-native developers.

Also agreed with Ryan's comparison

  - standardized format can be repetitive
  - simple methods are simply documented, complex methods
    are documented in detail

It looks ideal to have adequate dose of documentation and
it will also require some writing skill.  I'm really happy
if some of you could lead to fill BioRuby with nice level
of documentation.

* license - please change to Ruby's

Core Japanese developers are agreed to change license from LGPL to Ruby's
to make everyone who use Ruby can use BioRuby (re-writing of header is
not yet completed in some modules, though).

We need to ask other contributors to follow this change - ask their
permission that we can change the license whenever BioRuby staff needs.

* where and how to include data (enzyme.yaml for REBASE)

This is under discussion with Trevor but I think all discussions should
be done on this list to have audience (to tell the truth, reading/writing
English mails require time for me, so wants to share them without posting
summary in addition:).

Toshiaki