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Peter Cock | 3 Mar 2011 11:37
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Biopython 1.57 release plans

Hi all,

It is probably about time to do the Biopython 1.57 release.

Thanks to Tiago's work on the buildbot, see http://testing.open-bio.org
for this, we can be reasonably confident that all the offline unit tests
are passing on the main platforms and different versions of Python.
However, it would be a good idea for people to run the full test suite
on their machines now.

What (minor) issues need to be addressed?

Note I don't want this to be an excuse to land any big units of code (but
now would be a good time to discuss preparations for merging after the
release is done).

Would anyone like to proof read the current tutorial? You don't need to
mess about with LaTeX since there should be a nightly update here:
http://biopython.org/DIST/docs/tutorial/Tutorial-dev.html
http://biopython.org/DIST/docs/tutorial/Tutorial-dev.pdf

Regards,

Peter
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João Rodrigues | 3 Mar 2011 12:35
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Re: Biopython 1.57 release plans

Hey Peter, should we include the Bio.PDB things we've been discussing for a
while now? That has been a bit quiet lately so I dunno how it stands with
you guys.

Cheers,

João

On Thu, Mar 3, 2011 at 11:37 AM, Peter Cock <p.j.a.cock <at> googlemail.com>wrote:

> Hi all,
>
> It is probably about time to do the Biopython 1.57 release.
>
> Thanks to Tiago's work on the buildbot, see http://testing.open-bio.org
> for this, we can be reasonably confident that all the offline unit tests
> are passing on the main platforms and different versions of Python.
> However, it would be a good idea for people to run the full test suite
> on their machines now.
>
> What (minor) issues need to be addressed?
>
> Note I don't want this to be an excuse to land any big units of code (but
> now would be a good time to discuss preparations for merging after the
> release is done).
>
> Would anyone like to proof read the current tutorial? You don't need to
> mess about with LaTeX since there should be a nightly update here:
> http://biopython.org/DIST/docs/tutorial/Tutorial-dev.html
> http://biopython.org/DIST/docs/tutorial/Tutorial-dev.pdf
(Continue reading)

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Peter Cock | 3 Mar 2011 12:41
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Re: Biopython 1.57 release plans

On Thu, Mar 3, 2011 at 11:35 AM, João Rodrigues <anaryin <at> gmail.com> wrote:
> Hey Peter, should we include the Bio.PDB things we've been discussing for a
> while now? That has been a bit quiet lately so I dunno how it stands with
> you guys.

I'm tempted to say no, try and get the release out within a week, and
then work with you and Eric to merge the code. I'm worried the merge
might push the release back, and I would like to get it out this month.
What's your impression Eric?

Also which github branch are you considering merging? I can do a trial
merge (offline) and run some tests here (I have access to all the main
platforms).

Peter
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Eric Talevich | 3 Mar 2011 21:10
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Re: Biopython 1.57 release plans

On Thu, Mar 3, 2011 at 6:41 AM, Peter Cock <p.j.a.cock <at> googlemail.com>wrote:

> On Thu, Mar 3, 2011 at 11:35 AM, João Rodrigues <anaryin <at> gmail.com> wrote:
> > Hey Peter, should we include the Bio.PDB things we've been discussing for
> a
> > while now? That has been a bit quiet lately so I dunno how it stands with
> > you guys.
>
> I'm tempted to say no, try and get the release out within a week, and
> then work with you and Eric to merge the code. I'm worried the merge
> might push the release back, and I would like to get it out this month.
> What's your impression Eric?
>

João, I'm sorry to put this off again -- but I think we should do that merge
after the 1.57 release. The API for the functions renumber_residues and
remove_disordered_atoms is tricky to get right, because they have to support
so many variations on the same concept. I'd like to give dev-version testers
some time with it before locking down the API with a stable release.

I'm looking at the NEWS file and I don't see any mention of the GSoC work
that we already merged -- was that in time for the 1.56 release, or just
after?

Here's what's already in 1.57 (pre-release):

 - index_db(), which I think people will really like
 - Blast+ support: blast_formatter
 - Some improvements to SeqiO and SeqRecord
 - Last release to support Python 2.4, for real this time
(Continue reading)

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Peter Cock | 3 Mar 2011 21:16
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Testing examples in the Tutorial

Hi all,

In part prompted by recent discussions on the BioPerl and BioRuby
mailing lists about documentation and testing, I was inspired to try
and code up something I'd been thinking about doing for some time:
treat the embedded examples in our tutorial as doctests.

This required adding a little extra markup to the LaTeX file since
I wanted the tests to be "opt in" (some examples will not make
good tests, for example random outputs or command line tool
dependencies). I've gone for a special comment line, %doctest
(which can include an optional name for the test) to mark the
the following verbatim block is a doctest. Likewise, %cont-doctest
indicates the following verbatim block is a continuation of the
previous doctest - important when there is text in the middle
so variable definitions or import statements would otherwise
need to be repeated.

Then I wrote test_Tutorial.py which parses Tutorial.tex to find
these examples, and turn them into doctests. It is a bit hacky
but appears to do the job. Running it like this:

python run_tests.py test_Tutorial.py

you can very minimal output from failures. For more details,
use this:

python test_Tutorial.py

I've already marked up some basic Seq examples (and in the
(Continue reading)

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Peter Cock | 3 Mar 2011 21:22
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Re: Biopython 1.57 release plans

2011/3/3 Eric Talevich <eric.talevich <at> gmail.com>:
> On Thu, Mar 3, 2011 at 6:41 AM, Peter Cock wrote:
>>
>> On Thu, Mar 3, 2011 at 11:35 AM, João Rodrigues <anaryin <at> gmail.com> wrote:
>> > Hey Peter, should we include the Bio.PDB things we've been discussing
>> > for a
>> > while now? That has been a bit quiet lately so I dunno how it stands
>> > with
>> > you guys.
>>
>> I'm tempted to say no, try and get the release out within a week, and
>> then work with you and Eric to merge the code. I'm worried the merge
>> might push the release back, and I would like to get it out this month.
>> What's your impression Eric?
>
> João, I'm sorry to put this off again -- but I think we should do that merge
> after the 1.57 release. The API for the functions renumber_residues and
> remove_disordered_atoms is tricky to get right, because they have to support
> so many variations on the same concept. I'd like to give dev-version testers
> some time with it before locking down the API with a stable release.

OK then.

> I'm looking at the NEWS file and I don't see any mention of the GSoC work
> that we already merged -- was that in time for the 1.56 release, or just
> after?
>
> Here's what's already in 1.57 (pre-release):
>
>  - index_db(), which I think people will really like
(Continue reading)

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Tiago Antão | 4 Mar 2011 00:27
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Re: buildbot failure in Biopython on Linux 64 - Jython 2.5.2

On Thu, Mar 3, 2011 at 8:00 PM,  <biopython-dev <at> biopython.org> wrote:
>  http://testing.open-bio.org:8010/buildbotbuilders/Linux%2064%20-%20Jython%202.5.2/builds/61

Argh... these links are wrong. I will have a look.
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bugzilla-daemon | 7 Mar 2011 16:48

[Bug 2968] Modifications to Emboss eprimer3 parser and associated files

http://bugzilla.open-bio.org/show_bug.cgi?id=2968

------- Comment #3 from biopython-bugzilla <at> maubp.freeserve.co.uk  2011-03-07 10:48 EST -------
I've committed some fixes based on Leighton's ideas,
https://github.com/biopython/biopython/commit/b550da19d1749bb160711d240074010ebbd7252f

--

-- 
Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email
------- You are receiving this mail because: -------
You are the assignee for the bug, or are watching the assignee.
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Komal S | 8 Mar 2011 08:58
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Biopython Projects

Hi everyone,

I'm Komal, a Junior Undergraduate Student from India studying
Bioengineering. I'm a fan of Python and I love Computational Biology and I
plan to do my further studies in the same.
I went through the projects on the Biopython page. I was very much
interested in the RNA Structure project mentioned. Any contribution which I
make will help me a lot and the organisation too. In fact, I am currently
doing a project on RNA Editing. I'll be very happy to integrate my
knowledge.

Please help me on how I should proceed.

Komal
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Komal S | 9 Mar 2011 11:49
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::Biopython Project

Hi everyone,

I'm Komal, a Junior Undergraduate Student from India
studying Bioengineering. I'm a fan of Python and I love Computational
Biology and I plan to do my further studies in the same.
I went through the projects on the Biopython page. I was very
much interested in the RNA Structure project mentioned. Any contribution
which I make will help me a lot and the organisation too. In fact, I am
currently doing a project on RNA Editing. I'll be very happy to integrate
my knowledge.

In fact, I have been trying to contact people on #obf-soc IRC. I think there
is no separate IRC for Biopython.

Please help me on how I should proceed.

Komal
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Gmane