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Message from discussion how to submit upgraded biopython spkg for python-2.6?
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Marshall Hampton  
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 More options Jul 28 2009, 11:44 am
From: Marshall Hampton <hampto...@gmail.com>
Date: Tue, 28 Jul 2009 08:44:44 -0700 (PDT)
Local: Tues, Jul 28 2009 11:44 am
Subject: Re: how to submit upgraded biopython spkg for python-2.6?
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Well, biopython development is pretty active right now, so 1.51 will
have quite a few changes from the beta.  There is still quite a lot of
discussion about what will be in 1.51 on their mailing list (http://
lists.open-bio.org/pipermail/biopython-dev/2009-July/).

If you search on trac for "biopython", you can see all the previous
rounds of reviews for package updates. That may be helpful in addition
to what Minh suggested.  But with the recent changes away from
mxtexttools and Numeric, biopython is pretty simple to install now so
its a relatively easy package to maintain.

-Marshall

On Jul 27, 12:30 pm, tkeller <Thomas.E.Kel...@gmail.com> wrote:

> Sounds like a good plan. I downloaded your spkg and it installs fine
> and works as expected. I have added this information to your ticket,
> is there something else I should do for reviewing?

> Do you know what the proposed differences between the beta and 1.51
> final are?

> Thomas

> On Jul 27, 12:30 am, bbarker <Brandon.Bar...@gmail.com> wrote:

> > Great, glad to see this!  Thanks for the updated spkg.

> > On Jul 26, 9:47 pm, Marshall Hampton <hampto...@gmail.com> wrote:

> > > Ok, I posted my spkg at:

> > >http://trac.sagemath.org/sage_trac/ticket/6634

> > > It would be great if you (tkeller) got a trac account, since currently
> > > I don't know any other sage developers who have any real interest in
> > > this (partial exception of William Stein but clearly he has a lot on
> > > his plate).

> > > -Marshall

> > > On Jul 26, 12:25 pm, Marshall Hampton <hampto...@gmail.com> wrote:

> > > > Hi,

> > > > Thanks for pointing that out.  I have made a 1.51b spkg, but decided
> > > > to wait a week or two for the final 1.51 to come out.  But I didn't
> > > > realize that the 1.49b install was broken.

> > > > Anyway if you have any interest in helping out, you should get a trac
> > > > account.  Just email William Stein for one.

> > > > I am excited about their cleanup too, I think with a little more work
> > > > biopython can be made a standard part of sage, but that will require a
> > > > developer vote.

> > > > -Marshall Hampton

> > > > On Jul 26, 12:05 pm, tkeller <Thomas.E.Kel...@gmail.com> wrote:

> > > > > Thanks for all the recent work upgrading the base python distribution
> > > > > to 2.6, I imagine it was quite a task. I noticed that installing the
> > > > > biopython-1.49b spkg is broken from the upgrade . I have upgraded the
> > > > > spkg to 1.51b and it installs and works fine on my sage-4.1
> > > > > installation. Is there a place to upload supplemental spkg's , or
> > > > > should I get a trac account?

> > > > > A side benefit to upgrading the spkg is that the last few patches
> > > > > finally removed the mxText dependency, so it is now a clean install
> > > > > aside from requiring Numpy.


 
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