how to submit upgraded biopython spkg for python-2.6?

[tkeller]

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.

[Marshall Hampton]

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

[Marshall Hampton]

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

[bbarker]

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

[tkeller]

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

[Minh Nguyen]

Hi Thomas,

On Tue, Jul 28, 2009 at 3:30 AM, tkeller<Thomas....@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?

If you haven't done so, you might want to have a look at the
Developer's Guide at

http://www.sagemath.org/doc/developer/

You don't need to read through all of it. But in particular, you
should consider the section "Producing New Sage Packages"

http://www.sagemath.org/doc/developer/producing_spkgs.html

which discusses how to put together a package for Sage. It's good to
know about this even if you won't be producing an SPKG yourself. The
knowledge would serve you well when reviewing SPKG's. The section "The
Sage Trac Server: Submitting Patches and Packages"

http://www.sagemath.org/doc/developer/trac.html

contains some guidelines about reviewing patches and SPKG's. If you're
going to review tickets or SPKG's, that section is highly recommended.
If in doubt, there are always sage-support and sage-devel :-)

--
Regards
Minh Van Nguyen

[Marshall Hampton]

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

[Marshall Hampton]

Biopython 1.51 has been released, and I have a spkg up at

http://sage.math.washington.edu/home/mhampton/biopython-1.51.spkg

which I also posted on the ticket:

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

Since the biopython-1.51b spkg never got reviewed, and biopython-1.49b
is broken, it would be great if someone could review this!

-Marshall Hampton


On Jul 28, 10:44 am, Marshall Hampton <hampto...@gmail.com> wrote:
> Well,biopythondevelopment 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,biopythonis pretty simple to install now so

> > > > >biopythoncan be made a standard part of sage, but that will require a