[Biopython-dev] Bio.Ndb obsolete?

[Peter]

On Thu, Oct 9, 2008 at 5:22 PM, Peter <biopython at maubp.freeserve.co.uk> wrote:
> Hi all,
>
> I just had a very superficial look at the Bio.Ndb module.  This is an
> HTML parser written six years ago, with its last real update five
> years ago.  The given URL doesn't work, but the server is still up -
> however from first glance the whole page layout has changed.
>
> For example, compare the old HTML example under Bio/Ndb/PR0004.html to
> what seems to be the current equivalent:
> http://ndbserver.rutgers.edu/servlet/IDSearch.NDBSearch1?id=PR0004
>
> I think it is safe to say Bio.Ndb stopped working some time ago due to
> the website's HTML changing.  Does anyone here use this database?
> Maybe we should ask on the mailing list, and assuming no one is
> interested, just deprecate this code.

If we do drop Bio.Ndb, then I wonder if the related Bio.Crystal module
is still relevant?

> For future, should we have a statement
> http://www.biopython.org/wiki/Contributing and in the tutorial that we
> don't want to add any HTML parsers to Biopython?

I've made some fairly small changes to the wiki "Contributing" page,
which includes this and also mentioning unit tests and documentation
for code contributions.

Peter