[BioPython] Deprecating Bio.PubMed and some of Bio.GenBank

[Peter]

On Thu, Oct 9, 2008 at 4:48 PM, Peter <biopython at maubp.freeserve.co.uk> wrote:
> Dear Biopythoneers,
>
> Those of you who looked at the release notes for Biopython 1.48 might
> have read this bit:
>
>>> Bio.PubMed and the online code in Bio.GenBank are now considered
>>> obsolete, and we intend to deprecate them after the next release.
>>> For accessing PubMed and GenBank, please use Bio.Entrez instead.
>
> These bits of code are effectively simple wrappers for Bio.Entrez.
> While they may be simple to use, they cannot take advantage of the
> NCBI's Entrez utils history functionality.  This means they discourage
> users from following the NCBI's preferred usage patterns.
>
> We're already trying to encouraging the use of Bio.Entrez by
> documenting it prominently in the tutorial (which seems to be working
> given the recent questions on the mailing list), but for Biopython
> 1.49 I'm suggesting we go further and deprecate Bio.PubMed and the
> online code in Bio.GenBank.  This would mean a warning message would
> appear when this code is used, and (barring feedback) after a couple
> of releases this code would be removed completely.
>
> Any comments or objections?  In particular, is anyone using this
> "obsolete" functionality now?

I've just deprecated Bio.PubMed in CVS - meaning for the next release
of Biopython you'll see a warning message when you import the PubMed
module.  If you are using this module please say something sooner rather
than later.  This can still be undone.

Thanks,

Peter