[BioPython] Martel problems and MS-Windows

[Jeffrey Chang]

This was my doing.  At the time (and still now, I believe), Andrew 
wanted also to distribute Martel as a separate package, that people can 
use outside of Biopython.  So thus, the CVS version, and possible 
distributions, were ahead of Biopython.  But now that it appears that 
Martel development is stabilizing, perhaps it is time to revisit that 
decision.

Jeff


On Mar 2, 2004, at 8:43 PM, Michiel Jan Laurens de Hoon wrote:

> You are right, Martel did get skipped because it was already present 
> on my machine. Why is it necessary to check version number of Martel? 
> Is it possible that a version of Martel is already present that is 
> newer than the one included with Biopython?
>
> --Michiel.
>
> Brad Chapman wrote:
>
>> Hello;
>>> I have tried to install biopython. It seem to works propertly, but 
>>> when
>>> trying the example of the cookbook the Martel module fails (or this 
>>> is what
>>> I think).
>>>
>>> When typing: GenBank.FeatureParser() I get the error: "ImportError: 
>>> No
>>> module named Martel".
>> It looks like you did everything perfectly find -- I believe the
>> problem is that Martel (the underlying parsing engine) was
>> accidentally left out of the windows installer.
>> Michiel kindly provided the installers, so maybe he'd be willing to
>> double-check if the might have been left out -- since I'm not much
>> of a Windows person myself.
>> (As an aside to Michiel -- I think this problem is caused by the way
>> that the setup.py works. Specifically, only installing Martel if the
>> version number of the "distributed Martel" is bigger than the
>> "installed Martel." I put a note in the release instructions and
>> will fix this in the future by bumping the Martel version on each
>> release. This also ensures that any fixes/changes to Martel get
>> installed).
>> So yes, it looks like a problem on our part, and hopefully we can
>> get it sorted for you. Thanks for reporting it and sorry for any
>> confusion.
>> Brad
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>
> -- 
> Michiel de Hoon, Assistant Professor
> University of Tokyo, Institute of Medical Science
> Human Genome Center
> 4-6-1 Shirokane-dai, Minato-ku
> Tokyo 108-8639
> Japan
> http://bonsai.ims.u-tokyo.ac.jp/~mdehoon
>
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