[Biopython-dev] New release

Michiel de Hoon mjldehoon at yahoo.com
Thu Jun 26 23:16:23 UTC 2008

OK, then let's make a new release as soon as possible, and perhaps another one soon after that. Tentative date is this Sunday, around noon GMT. All biopython unit tests pass (at least, on my machine), so it should be straightforward to build a release.


--- On Thu, 6/26/08, Peter <biopython at maubp.freeserve.co.uk> wrote:
From: Peter <biopython at maubp.freeserve.co.uk>
Subject: Re: [Biopython-dev] New release
To: mjldehoon at yahoo.com
Cc: biopython-dev at biopython.org
Date: Thursday, June 26, 2008, 4:32 PM

On Thu, Jun 26, 2008 at 1:50 PM, Michiel de Hoon <mjldehoon at yahoo.com>
> Hi everybody,
> I think we should make a new Biopython release within the next couple of
> to solve the issues with NCBI and to get the fixed Blast parser out (for
> from Blast 2.2.18). There are a few outstanding issues that hopefully can
> fixed before the next release:
> 1) NCBI access from Bio.GenBank
> 2) Bug #2454 (Iterators can't use file-like objects), which affects a
number of parsers in Biopython
> 3) Martel-based parsers.

Given the updates to Bio.EUtils to enforce the 3 second rule, the
urgent part of issue (1) is now resolved, and any futher refinements
needn't hold up the release.

>From a technical viewpoint, none of these are very complicated. 2) is
almost finished.

While there are still outstanding parsers affected by issue (2) (Bug
2454), I don't think this need hold up the release.

> With respect to 3), a small number of parsers in Biopython are based on
> Martel (none of the major ones as far as I can tell). For some of these
> parsers, it is not quite clear if they are still useful. For the remaining
>  it would be nice if they could be rewritten without using Martel -- that
> let us get rid of the dependency on mxTextTools.

Again, while removing the dependency on mxTextTools is a worthwhile
aim, I don't think this should hold up the release.

> Any other urgent issues that need to be resolved before a release?

There is an AlignInfo alphabet issue I'm currently working on, and
expect to have fixed tomorrow.



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