[Biopython-dev] [BioPython] Bio.MultiProc

[Michiel De Hoon]

> Would it be possible to include the module, comment out the unworkable
> source code and print a deprecation warning when it is imported?

That is what I did.

> 3) Leave an option of fixing and commenting the code back in (i.e. it is
not
> lost forever).

Even after removing the code in some future release, the code will not be
lost forever. It can always be retrieved from CVS and from older Biopython
releases.

> Also, is it possible to track down the original author?

That would be Jeff Chang.

--Michiel.


Michiel de Hoon
Center for Computational Biology and Bioinformatics
Columbia University
1150 St Nicholas Avenue
New York, NY 10032



-----Original Message-----
From: Iddo Friedberg [mailto:idoerg at gmail.com]
Sent: Tue 10/2/2007 12:00 PM
To: Michiel De Hoon
Cc: BioPython Developers List; biopython at biopython.org
Subject: Re: [Biopython-dev] [BioPython] Bio.MultiProc
 
Would it be possible to include the module, comment out the unworkable
source code and print a deprecation warning when it is imported? That was
we:

1) Don't have a clunky module BUT
2) we warn anyone who uses it (but didn't happen to read your post) that it
is deprecated when they install a new biopython version AND
3) Leave an option of fixing and commenting the code back in (i.e. it is not
lost forever).

Also, is it possible to track down the original author?

./I

On 10/2/07, Michiel De Hoon <mdehoon at c2b2.columbia.edu> wrote:
>
> Hi everybody,
>
> Since no users of Bio.MultiProc came forward, I deprecated it for the
> upcoming release.
>
> --Michiel.
>
> Michiel de Hoon
> Center for Computational Biology and Bioinformatics
> Columbia University
> 1150 St Nicholas Avenue
> New York, NY 10032
>
>
>
> -----Original Message-----
> From: biopython-bounces at lists.open-bio.org on behalf of Michiel De Hoon
> Sent: Tue 9/11/2007 10:37 AM
> To: BioPython Developers List; biopython at biopython.org
> Subject: [BioPython] Bio.MultiProc
>
> Hi everybody,
>
> In preparation for the upcoming release, I was running the Biopython
> test suite and found that test_copen.py hangs on Cygwin. It doesn't
> fail, it just sits there forever. This may be related to the use of
> fork() instead of select() in Bio/MultiProc/copen.py. Anyway, while it
> is probably possible to fix this, I'd have to dig fairly deep into the
> code, and I am not sure if it is worth it. It looks like the copen
> functions are used only in Bio/config, which is needed for Bio.db. A
> description of the functionality of thia module can be found in the
> tutorial section 4.7.2.
>
> Now, I don't remember users asking about this module on the mailing
> list. From the tutorial documentation, it seems to be a nice piece of
> code, but I doubt that it is being used often in practice.
>
> So I was wondering:
> 1) Is anybody on this list using this code?
> 2) If not, can I mark it as deprecated for the upcoming release?
> Hopefully, people who are using this code will notice, and let us know
> that they need it.
>
> --Michiel.
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-- 

I. Friedberg

"The only problem with troubleshooting is that
sometimes trouble shoots back."