[Biopython-dev] New Biopython release - Bio.PopGen?

[Tiago Antão]

Hi

My apologies for the delay in answering, but I am traveling during a
couple of weeks as I am in the organization of a conservation genetics
course. Unit the 21st I will probably be sloppy in answering.

You can go ahead and include the code if you want (any decision that
you take is OK), please note the following:

1. Without a statistics module the functionality is limited (a good
reason to delay the release)
2. I believe that the code is in an acceptable state.
3. A diff with suggested fdist documentation is attached to the bugzilla entry.

I would lean towards a delay until statistics are in, but if it is too
much hassle please go ahead and make it public.

Tiago

On 9/10/07, Peter Cock <p.j.a.cock at warwick.ac.uk> wrote:
> Hi Tiago,
>
> I'm forwarding this email in case you had missed it on the mailing list.
>
> Basically what do you want to do with Bio.PopGen given that Michiel is
> hoping to do a Biopython release by the end of this week?
>
> Thanks
>
> Peter
>
> -------- Original Message --------
> Subject: Re: [Biopython-dev] New Biopython release
> Date: Sun, 09 Sep 2007 21:47:17 +0100
> From: Peter <biopython-dev at maubp.freeserve.co.uk>
> Reply-To: biopython-dev at lists.open-bio.org
> To: Michiel de Hoon <mdehoon at c2b2.columbia.edu>
> CC: biopython-dev at lists.open-bio.org
> References: <46E400BA.90504 at c2b2.columbia.edu>
>
> Michiel de Hoon wrote:
> > Hi everybody,
> >
> > Let's make a new release (1.44) of Biopython. Biopython has received
> > a lot of improvements and bug fixes in recent months, and the current
> > (1.43) release hangs on some platforms during the Biopython tests
> > (due to a bug in my own Bio.Cluster module, ahem). I am planning to
> > make a new release during the next weekend (around 9/15).
>
> Good idea - I was wondering about suggesting this.  By the way, I
> updated the NEWS file fairly recently.
>
> > A number of bugs in Bugzilla currently have a partial solution that
> > has not yet made it into CVS. I suggest to commit those partial
> > solutions to CVS if possible so that they can be included in the next
> > release.
>
> Some of those are enhancement bugs where things are still a little
> undecided.  I'm fairly happy with the __getitem__ method for the
> alignment, but would want to change it slightly if we added a
> __getitem__ to the SeqRecord itself.
>
> > On my machine, only test_SeqIO fails its test. The error seems to be
> > trivial, but we should fix it before making the next release.
>
> It was trivial ;)
> I had forgotten to check in a SwissProt test case. Sorry.
>
> We should get Tiago's input before making a release - see if he's happy
> for his initial Bio.PopGen code to be released yet.  If not, then it
> shouldn't be too hard to removed that module, its test cases, and
> section in the tutorial.  Just a little fiddly...
>
> I've also done a little work on writing EMBL and GenBank files (based in
> part on Howard Salis' patches on Bug 2294) but I don't think they are
> ready yet.  As part of this I am planning to making some small changed
> to the EMBL and GenBank parsers to record a few more bits of annotation.
> Rather than rush this I'll hold back until after release 1.44 is done.
>
> Peter
>
>
>


-- 
http://www.tiago.org/ps