[BioRuby] BioRuby API

Anthony Underwood email2ants at gmail.com
Thu Oct 6 09:27:55 UTC 2011

Hello Naohisa

Thanks for the advice. Thaks to rvm I have regenerated the 1.4.2 rdoc using rdoc version 2.2.1 (the last  version before the new 'darkfish' look beccame standard).
This is publically available at

Thanks again,


On Thursday, 6 October 2011 at 05:53, Naohisa GOTO wrote:

> Hi,
> The change is due to the change of RDoc default html generator.
> The new pages are generated by using RDoc bundled in Ruby 1.9.2,
> with its default style. Old style, which was the default of
> older RDoc, seems to be no longer maintained by anyone, and
> is dropped from current RDoc.
> It is easy to generate API html pages locally.
> "rake rdoc" in the top of bioruby source tree.
> Old style pages may be generated by using Ruby 1.9.1-p431
> (or Ruby 1.8.x with older version of RDoc).
> Naohisa Goto
> ngoto at gen-info.osaka-u.ac.jp (mailto:ngoto at gen-info.osaka-u.ac.jp) / ng at bioruby.org (mailto:ng at bioruby.org)
> On Wed, 5 Oct 2011 15:57:44 +0100
> Anthony Underwood <email2ants at gmail.com (mailto:email2ants at gmail.com)> wrote:
> >  Hi all
> > 
> > Does anyone else find the new API docs more difficult to navigate than the old api?
> > It looks prettier but I find it harder to find what I'm after. OK frames may be very 1990s but in the case of the API having all the Methods and Classes in scrollable frames worked well.
> > Does anybody have 
> > any tips on how to navigate around?
> > a URL where the old form of presenting the API is still accessible?
> > the command to generate the old API locally?
> > 
> > Many thanks in advance
> > 
> > Anthony 
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