[BioRuby] Proposal: Bioruby modules (the bazaar)

Thu Jan 21 16:20:49 UTC 2010

Dear Toshiaki,

On Thu, Jan 21, 2010 at 11:05:42PM +0900, Toshiaki Katayama wrote:
> I looked your code and had a feeling that we should use some
> template system.  If HTML tags are hard coded in the library as you
> did, it will be very hard to modify them by the user.

Aren't we trying to overcomplicate things? This is an HTML generator
- in fact it is embedded HTML as I don't provide the <html>, header or
body parts. It can just be inserted into Rails, or whatever HTML
framework that is out there.

Templating is just another abstraction. I don't intend to template
engines like Rails.

Or, are you here merely referring to using the CGI class (or something
like that).  I guess I could do that, though I have trouble seeing the
benefits. It is just another way of writing HTML statements.

> Besides, what version of the HTML specification did you have in
> mind?
> This is my first time to see the <p> tag is used in the form of <p />. Is it valid?

Yes. It is, in fact, XHTML.

> I also think decorations should be separated to the CSS layer and you should avoid to use the <font> tag, especially when you are trying to distribute your code as a part of the library.

We use hard coded colors. I could use CSS, but then you need to
provide a CSS file (or I need to hard code the header of the file).
That makes it (again) more complicated than necessary. Where do we
store the CSS file, how do we make sure the browser finds it? CSS is
really to adapt look and feel. If the output is meant to be fixed, why
make it flexible?  Besides all (future) browsers support the font tag,
as used. If that stops we could always adapt that source code.

> As for the file location, I still like the way Naohisa has
> suggested.

Alright. I can move the files, if that was all.

However, my colored alignment is not going to make it into Bioruby
this way. There is always something wrong with my code, it appears.
Now I need to move file locations that have not really been decided
on; I need to template HTML - but we haven't decided how and it is
questionable; I need to use CSS, though I think it makes things worse
for users.

Are we really sure you want to reject this code just because it does
not live up to everyone's current and future expectations? It may
still be useful to someone else, you know, it does not break anything
else, and can be improved in the future. Once we decide what we want
to achieve.

The same really holds to my PAML branch and my GEO branch. Both
contain useful utilities for others to use. And now the alignment is
the third pending Bioruby branch.

Can you imagine my growing frustration? Should this go into Bioruby,
or should I start another project, like others have done? Or stick it
into my existing biotools or bigbio projects? Just, so I don't have
the hassle?

The way the Perl people handle it is by having independent modules.
Everyone owns his, or her, own module and Perl's CPAN acts more as an
aggragator. The advantage is that the environment is more dynamic. And
you really don't care what is inside a module. That is up to the
maintainer and his/her users.

We could create independent BioRuby modules, which have their own git
repositories. When a module is nice enough to include in Bioruby make
it a git submodule - I use this technique for biolib - it will
register in the BioRuby repository. That way Bioruby still controls
what goes in a release. However, modules can be maintained for
experimental setups or private use. So my modules would go in

  lib/bio/modules/paml
  lib/bio/modules/geo
  lib/bio/modules/htmlalignment

each its own git repository.

When one of those is 'strong' enough for main line you move it into a
different location in the main repository. Modules could even be
included in Bioruby releases.

What hurts me now is that no one is going to use my code, since I
don't have the time to make it perfect, and it is hidden in my
experimental Bioruby branches. We should find a way to make
'experimental code' available to the rest of the community. That way
we may also 'recruit' help to make the code more perfect. 

Make it easy to allow external modules to become visible through
Bioruby - that is a win-win, as well as a more bazaar-like approach
to OSS development.

I wonder how many people on this list would contribute code if it was
more loosely organised.

Pj.