[BioPython] will BioSQL work with psycopg2?

[Peter]

On Mon, Dec 1, 2008 at 2:59 AM, Alex Lancaster wrote:
> Hi there,
>
> I am maintaining the Fedora package for Biopython and we are doing a
> complete rebuild of all Python packages for Python 2.6.

Excellent.  Biopython 1.49 onwards should be fine on Python 2.6, but
please do let us know if you find anything amiss or any deprecations
we've missed.

Slightly off topic, but If you want any clarification on things like
the deprecation of Martel (with its dependency on mxTextTools), or the
switch from Numeric to NumPy please ask.

> Currently I have a dependency on psycopg (version 1.1.21) but since
> that is so old pyscopg won't rebuild against the new mx, meaning that
> I can't rebuild Biopython because the dependencies aren't there.
>
> So my question is, will the Biopython BioSQL work with the newer
> psycopg2 (currently version 2.0.8)?  See:
> http://www.initd.org/pub/software/psycopg/

Yes, psycopg2 should work with Biopython 1.49 onwards (including
Biopython 1.49 beta) thanks to a patch from Cymon Cox, see Bug 2616:

http://bugzilla.open-bio.org/show_bug.cgi?id=2616

> Does it require the 1.x API or will it work with 2.x?  The BioSQL page:
> http://biopython.org/wiki/BioSQL
> isn't clear on this.

I'm not sure, having not used psycopg or psycopg2 myself.  Hopefully
Cymon can clarify this (CC'd).

Peter