[Biopython-dev] [Bug 2866] SQLite support for BioSQL

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http://bugzilla.open-bio.org/show_bug.cgi?id=2866





------- Comment #18 from biopython-bugzilla at maubp.freeserve.co.uk  2009-12-12 14:41 EST -------
(In reply to comment #16)
> 
> Yep, no problems, although I only tried the psycopg2 driver (with and
> without rules deletion).
> 
> Psycopg version 1 support has had a deprecation warning since version 1.53
> http://bugzilla.open-bio.org/show_bug.cgi?id=2851#c4 - when can we drop it?
> 
> C.
> 

Minor typo - Psycopg v1 support was deprecated in Biopython 1.51 (August 2009).
In line with the current deprecation policy, we aim for two releases with the
warning (which has happened already, 1.51 and 1.52) plus at least one year -
which means we can drop Psycopg v1 in summer 2010. Given in this case its a
fairly simple task for someone to just install Psycopg v2, we might look at
dropping the Psycopg v1 support a little quicker (say Biopython 1.54?).

See: http://www.biopython.org/wiki/Deprecation_policy

(In reply to comment #17)
> Thanks Cymon -- glad nothing is broken on Postgres. 
> 
> The in memory database (:memory:) doesn't work for the tests, because they
> assume a database created by previous test cases. Since the memory one keeps
> going away, they will get plenty of errors about non-existing tables. It would
> work in theory with some test re-writing, but it's not too necessary.
> 
> Sorry, should have added a note about this. Thanks again for double checking
> that everything works.

OK then - Brad, would you like to merge this to the trunk now (or in the next
few days), add a note about not using :memory: in Tests/setup_BioSQL.py, and
something to the NEWS file (with a proviso about the SQLite schema not yet
being official)?

Thanks,

Peter


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