Biopython Developers List

Peter | 4 Nov 2010 18:13

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Biopython 1.56 release plans

Hi all,

I've mentioned in recent threads that I think we should try and
release Biopython 1.56 this month (November 2010).

I think the NEWS file is pretty up to date, and covers important
new functionality like Andrea Pierleoni's UniProt XML parser
and the IMGT support (with Uri Laserson).

Is there any other functionality which is ready for merging?

For example, Tiago - you've been doing lots of work on your
branch with the PopGen code. Is that code ready? I'm willing
to do the git merge/rebase.

Is there any reason to bother with a beta release this time?

If there are no pressing additions, I may be able to do the
release tomorrow - otherwise how about aiming for Thursday
or Friday next week (11 or 12 November)?

Regards,

Peter

Michiel de Hoon | 5 Nov 2010 10:40

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Re: Biopython 1.56 release plans

I think the following should be removed before the release:

Bio/SwissProt/SProt.py
Bio/Transcribe.py
Bio/Translate.py

as well as the Iterator class in Bio/SCOP/Dom.py.

These have been deprecated since Biopython 1.52.

Best,
--Michiel.

--- On Thu, 11/4/10, Peter <biopython <at> maubp.freeserve.co.uk> wrote:

> From: Peter <biopython <at> maubp.freeserve.co.uk>
> Subject: [Biopython-dev] Biopython 1.56 release plans
> To: "Biopython-Dev Mailing List" <biopython-dev <at> biopython.org>
> Date: Thursday, November 4, 2010, 1:13 PM
> Hi all,
> 
> I've mentioned in recent threads that I think we should try
> and
> release Biopython 1.56 this month (November 2010).
> 
> I think the NEWS file is pretty up to date, and covers
> important
> new functionality like Andrea Pierleoni's UniProt XML
> parser
> and the IMGT support (with Uri Laserson).

(Continue reading)

Peter | 5 Nov 2010 11:23

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Re: Biopython 1.56 release plans

On Fri, Nov 5, 2010 at 9:40 AM, Michiel de Hoon <mjldehoon <at> yahoo.com> wrote:
> I think the following should be removed before the release:
>
> Bio/SwissProt/SProt.py
> Bio/Transcribe.py
> Bio/Translate.py
>
> as well as the Iterator class in Bio/SCOP/Dom.py.
>
> These have been deprecated since Biopython 1.52.

According to the DEPRECATED file, those modules were
deprecated in Biopython 1.51, so they are definitely due for
removal. In any case Biopython 1.52 was very nearly a year
ago [1] as it was released 22 September 2009.

Please go ahead and tidy this up.

Thanks,

Peter

[1] http://www.biopython.org/wiki/Deprecation_policy

Michiel de Hoon | 5 Nov 2010 12:52

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Re: Biopython 1.56 release plans

> > Bio/SwissProt/SProt.py
> > the Iterator class in Bio/SCOP/Dom.py

I have removed these.

> > Bio/Transcribe.py
> > Bio/Translate.py

These are still imported from Bio/Encodings/IUPACEncoding.py, which is imported from
Bio/Alphabet/IUPAC.py. I have no idea what this code is doing. Does anybody know?

--Michiel.

Peter | 5 Nov 2010 13:01

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Re: Biopython 1.56 release plans

On Fri, Nov 5, 2010 at 11:52 AM, Michiel de Hoon <mjldehoon <at> yahoo.com> wrote:
>
>> > Bio/SwissProt/SProt.py
>> > the Iterator class in Bio/SCOP/Dom.py
>
> I have removed these.
>
>> > Bio/Transcribe.py
>> > Bio/Translate.py
>
> These are still imported from Bio/Encodings/IUPACEncoding.py, which
> is imported from Bio/Alphabet/IUPAC.py. I have no idea what this code
> is doing. Does anybody know?

Ah right - sorry, that had slipped my mind:
http://lists.open-bio.org/pipermail/biopython-dev/2010-September/008255.html

I had suggested we leave Bio.Transcribe and Bio.Translate in for
Biopython 1.56 and remove them (and Bio.utils, Bio.PropertyManager,
and Bio.Encodings.IUPACEncoding) for Biopython 1.57

Peter

Peter | 26 Nov 2010 17:25

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Re: Biopython 1.56 release plans

On Fri, Nov 5, 2010 at 12:01 PM, Peter <biopython <at> maubp.freeserve.co.uk> wrote:
> On Fri, Nov 5, 2010 at 11:52 AM, Michiel de Hoon <mjldehoon <at> yahoo.com> wrote:
>>
>> Bio/Transcribe.py
>> Bio/Translate.py
>>
>> These are still imported from Bio/Encodings/IUPACEncoding.py, which
>> is imported from Bio/Alphabet/IUPAC.py. I have no idea what this code
>> is doing. Does anybody know?
>
> Ah right - sorry, that had slipped my mind:
> http://lists.open-bio.org/pipermail/biopython-dev/2010-September/008255.html
>
> I had suggested we leave Bio.Transcribe and Bio.Translate in for
> Biopython 1.56 and remove them (and Bio.utils, Bio.PropertyManager,
> and Bio.Encodings.IUPACEncoding) for Biopython 1.57

Hi Michiel,

Now Biopython 1.56 is out, would you like to remove those modules?

Thanks

Peter

Michiel de Hoon | 30 Nov 2010 14:14

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Re: Biopython 1.56 release plans

OK, I have removed these modules:
  	Bio.Encodings
 	Bio.PropertyManager
 	Bio.Transcribe
 	Bio.Translate
 	Bio.utils

--Michiel.

--- On Fri, 11/26/10, Peter <biopython <at> maubp.freeserve.co.uk> wrote:

> From: Peter <biopython <at> maubp.freeserve.co.uk>
> Subject: Re: [Biopython-dev] Biopython 1.56 release plans
> To: "Michiel de Hoon" <mjldehoon <at> yahoo.com>
> Cc: "Biopython-Dev Mailing List" <biopython-dev <at> biopython.org>
> Date: Friday, November 26, 2010, 11:25 AM
> On Fri, Nov 5, 2010 at 12:01 PM,
> Peter <biopython <at> maubp.freeserve.co.uk>
> wrote:
> > On Fri, Nov 5, 2010 at 11:52 AM, Michiel de Hoon
> <mjldehoon <at> yahoo.com>
> wrote:
> >>
> >> Bio/Transcribe.py
> >> Bio/Translate.py
> >>
> >> These are still imported from
> Bio/Encodings/IUPACEncoding.py, which
> >> is imported from Bio/Alphabet/IUPAC.py. I have no
> idea what this code

(Continue reading)

Tiago Antão | 5 Nov 2010 11:13

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Re: Biopython 1.56 release plans

On Thu, Nov 4, 2010 at 5:13 PM, Peter <biopython <at> maubp.freeserve.co.uk> wrote:
> For example, Tiago - you've been doing lots of work on your
> branch with the PopGen code. Is that code ready? I'm willing
> to do the git merge/rebase.

I was hoping that would offer to do a merge ;) . <sarcasm> Though we
need a broken repository to test the integration server, so maybe I
could do it myself </sarcasm>.
Yes, the code is ready.
After the merge I will still add a couple of functions (also ready,
but not committed) and make sure the test cases are fully ready. But
it should be a day only and better done after the merge.
This is mainly new code that does much faster GENEPOP parsing and
supports AFLP processing.

Tiago

Peter | 5 Nov 2010 11:19

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Re: Biopython 1.56 release plans

2010/11/5 Tiago Antão <tiagoantao <at> gmail.com>:
> On Thu, Nov 4, 2010 at 5:13 PM, Peter <biopython <at> maubp.freeserve.co.uk> wrote:
>> For example, Tiago - you've been doing lots of work on your
>> branch with the PopGen code. Is that code ready? I'm willing
>> to do the git merge/rebase.
>
> I was hoping that would offer to do a merge ;) . <sarcasm> Though we
> need a broken repository to test the integration server, so maybe I
> could do it myself </sarcasm>.
> Yes, the code is ready.

OK - I'll try to get your code, rebase it onto the current master,
then post it as a new branch for you to check. Once that is OK,
I'll rebase it again if the master has changed, then fast-forward
merge it to the master (that way we don't get a split and join on
the master history - just a sudden batch of commits).

> After the merge I will still add a couple of functions (also ready,
> but not committed) and make sure the test cases are fully ready.
> But it should be a day only and better done after the merge.
> This is mainly new code that does much faster GENEPOP
> parsing and supports AFLP processing.

Hopefully we can get that part done early next week.

Peter

Peter | 5 Nov 2010 11:47

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Re: Biopython 1.56 release plans

2010/11/5 Peter <biopython <at> maubp.freeserve.co.uk>:
> 2010/11/5 Tiago Antão <tiagoantao <at> gmail.com>:
>> On Thu, Nov 4, 2010 at 5:13 PM, Peter <biopython <at> maubp.freeserve.co.uk> wrote:
>>> For example, Tiago - you've been doing lots of work on your
>>> branch with the PopGen code. Is that code ready? I'm willing
>>> to do the git merge/rebase.
>>
>> I was hoping that would offer to do a merge ;) . <sarcasm> Though we
>> need a broken repository to test the integration server, so maybe I
>> could do it myself </sarcasm>.
>> Yes, the code is ready.
>
> OK - I'll try to get your code, rebase it onto the current master,
> then post it as a new branch for you to check.

Notes on how I did this:

$ git remote add tiago https://github.com/tiagoantao/biopython.git
$ git fetch tiago
...
>From https://github.com/tiagoantao/biopython
 * [new branch]      buildbot   -> tiago/buildbot
 * [new branch]      master     -> tiago/master

Now I want your "master" branch, but that name clashes with
my "master" branch... the following worked here:

$ git checkout tiago/master
Note: moving to "tiago/master" which isn't a local branch
If you want to create a new branch from this checkout, you may do so

(Continue reading)

Tiago Antão | 5 Nov 2010 11:50

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Re: Biopython 1.56 release plans

2010/11/5 Peter <biopython <at> maubp.freeserve.co.uk>:
> If you agree the rebased branch is sane, it should be trivial to
> now merge that onto the master as a fast-forward merge.
> (But I would check first that the master hasn't changed, and
> if it has, repeat the rebase).

Many thanks for the guide, maybe in the future I will have the courage
to do it myself.

Go ahead and commit the changes. I will make sure the module is sane
this Sunday.

Peter | 5 Nov 2010 12:08

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Re: Biopython 1.56 release plans

2010/11/5 Tiago Antão <tiagoantao <at> gmail.com>:
> 2010/11/5 Peter <biopython <at> maubp.freeserve.co.uk>:
>> If you agree the rebased branch is sane, it should be trivial to
>> now merge that onto the master as a fast-forward merge.
>> (But I would check first that the master hasn't changed, and
>> if it has, repeat the rebase).
>
> Many thanks for the guide, maybe in the future I will have the
> courage to do it myself.
>
> Go ahead and commit the changes. I will make sure the module
> is sane this Sunday.

Done. The master hadn't changed in the meantime so I didn't
have to re-rebase:

$ git checkout master
Switched to branch "master"
$ git merge tiago-pop-gen
Updating 065e235..4f318a4
Fast forward
 Bio/PopGen/FDist/Async.py            |   21 +-
 Bio/PopGen/FDist/Controller.py       |  125 +-
 Bio/PopGen/FDist/Utils.py            |   68 +-
 Bio/PopGen/FDist/__init__.py         |    1 -
 Bio/PopGen/GenePop/EasyController.py |   10 +-
 Bio/PopGen/GenePop/FileParser.py     |   69 +-
 Tests/PopGen/data_dfst_outfile       |  300 +
 Tests/PopGen/dfdist1                 | 1204 +
 Tests/PopGen/dout.cpl                |  300 +

(Continue reading)

Michiel de Hoon | 5 Nov 2010 13:08

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Re: Biopython 1.56 release plans

I'd like to suggest also that we deprecate Bio.Prosite.Prodoc; this functionality moved to
Bio.ExPASy.Prodoc at least since release 1.50, and the module has been labeled as obsolete since then.
The enclosing module Bio.Prosite itself is already deprecated.

--Michiel.

Peter | 5 Nov 2010 13:19

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Re: Biopython 1.56 release plans

On Fri, Nov 5, 2010 at 12:08 PM, Michiel de Hoon <mjldehoon <at> yahoo.com> wrote:
> I'd like to suggest also that we deprecate Bio.Prosite.Prodoc; this
> functionality moved to Bio.ExPASy.Prodoc at least since release 1.50,
> and the module has been labeled as obsolete since then. The enclosing
> module Bio.Prosite itself is already deprecated.

Since Bio.Prosite is deprecated that means Bio.Prosite.Prodoc (and any
other child modules) is too. If you try "from Bio.Prosite import Prodoc"
you get a deprecation warning. Feel free to add "(DEPRECATED)" to
the Bio.Prosite.Prodoc docstrings if you think it would be clearer.

Peter

Peter | 12 Nov 2010 18:47

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Re: Biopython 1.56 release plans

On Thu, Nov 4, 2010 at 5:13 PM, Peter <biopython <at> maubp.freeserve.co.uk> wrote:
> Hi all,
>
> I've mentioned in recent threads that I think we should try and
> release Biopython 1.56 this month (November 2010).
>
> I think the NEWS file is pretty up to date, and covers important
> new functionality like Andrea Pierleoni's UniProt XML parser
> and the IMGT support (with Uri Laserson).
>
> Is there any other functionality which is ready for merging?
>
> For example, Tiago - you've been doing lots of work on your
> branch with the PopGen code. Is that code ready? I'm willing
> to do the git merge/rebase.
>
> Is there any reason to bother with a beta release this time?
>
> If there are no pressing additions, I may be able to do the
> release tomorrow - otherwise how about aiming for Thursday
> or Friday next week (11 or 12 November)?

As people will have noticed, the release didn't happen this week.

Tiago has been doing some excellent work with the prototype
buildbot server (see http://events.open-bio.org:8010/grid for
the current temporary home), and as part of this we've set
up a few machines as buildslaves. See this thread:
http://lists.open-bio.org/pipermail/biopython-dev/2010-November/008376.html

(Continue reading)

Peter | 15 Nov 2010 18:05

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Re: Biopython 1.56 release plans

On Fri, Nov 12, 2010 at 5:47 PM, Peter <biopython <at> maubp.freeserve.co.uk> wrote:
> On Thu, Nov 4, 2010 at 5:13 PM, Peter <biopython <at> maubp.freeserve.co.uk> wrote:
>> Hi all,
>>
>> I've mentioned in recent threads that I think we should try and
>> release Biopython 1.56 this month (November 2010).
>>
>> ...
>
> As people will have noticed, the release didn't happen this week.
>
> ...
>
> Unfortunately running under Jython on Windows XP has
> revealed several new problems, e.g.
> http://lists.open-bio.org/pipermail/biopython-dev/2010-November/008431.html
>
> ...
>
> Hopefully we can address these three test failures (or
> at least understand them) and do Biopython 1.56 at
> the end of next week instead.

Two of the problems on Jython on Windows were down
to the Windows specific command line tool detection
not being used, now fixed:

https://github.com/biopython/biopython/commit/db41d7e4bfd8f5d4ea44bf8254334fcd7b76474f
https://github.com/biopython/biopython/commit/7e5b71093c8408de140de1937480e26aaaa5daf1

(Continue reading)

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