Hi Michael,
did you install each scattered file as a plugin?I am considering this option
although looks quite tricky for disinstallation.
If I don't fail the authors of Biopython allow this scattered use of their code
(a citation of course is needed).
Cheers, roberto
----Messaggio originale----
Da: mgler...@gmail.com
Data: 11/03/2011 4.05
A: "rv...@libero.it"<rv...@libero.it>
Cc: <hongbo....@biotec.tu-dresden.de>, <pymol-users@lists.sourceforge.net>
Ogg: Re: [PyMOL] R: Re: plugin dependencies
I really like the fact that Jason will be including more libraries with PyMOL
in the future.
I once needed to distribute a library that depended on BioPython. It turned out
that, in my case, I only cared about a few specific files from BioPython, so I
was able to strip out the necessary functionality and just ship that with my
plugin. I don't know exactly what you're doing, but that might be an option.
Cheers,
-Michael
On Thu, Mar 10, 2011 at 9:25 PM, rv...@libero.it <rv...@libero.it> wrote:
Hi Hongbo,
thanks for your reply.
>So, how about ship all the BioPython packages you need in your python
>code together with your plugin? Of course all dependencies should be
>included.
Is not so simple. A library like Biopython can't be installed as a plugin. An
installer (OS specific) program is needed: the official windows installer I
checked doesn't allow the user to choose the folder (this way the interpreter)
where to install. Installing manually is still tricky for a not experienced
user.
Cheers,
roberto
>----Messaggio originale----
>Da: hongbo....@biotec.tu-dresden.de
>Data: 10/03/2011 12.57
>A: <pymol-users@lists.sourceforge.net>
>Ogg: Re: [PyMOL] plugin dependencies
>
>Just another reminder:
>
>If the version of the "external" python and the python shipped with
>PyMOL are different enough on the user's computer, the package might
>still fail to work in PyMOL even if the user has installed the package
>using the external python and edited the PYTHONPATH.
>
>
>So, how about ship all the BioPython packages you need in your python
>code together with your plugin? Of course all dependencies should be
>included.
>
>On 03/10/2011 06:17 AM, rv...@libero.it wrote:
>> Hello everyone,
>>
>> my plugin needs Biopython.
>> I wish check the Biopython installation by
>>
>> try:
>> from Bio import AlignIO # or similar
>> except ImportError:
>> .. prompt the user with a msg ..
>>
>> The problem is:
>> what the msg to the user?
>>
>> Downloading and installing Biopython is not enough:
>> If the user downloads and installs Biopython in the external python
>> interpreter still Biopython continues to be unavailable for the internal
python
>> interpreter in pyMOL.
>>
>> Of course the user could edit the PYTHONPATH environment variable and so
all
>> the python interpreters can read Biopython but working with environment
>> variables could be too difficult for a not experienced user.
>>
>> Is there a simpler way?
>>
>> Cheers,
>> roberto
>>
>>
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>--
>Hongbo ZHU
>Postdoctoral Researcher
>Structural Bioinformatics
>
>Technische Universität Dresden
>Biotechnology Center
>Tatzberg 47/49
>01307 Dresden, Germany
>
>Tel: +49 (0) 351 463-40083
>Fax: +49 (0) 351 463-40087
>E-Mail: hongbo.zhu at biotec
>Webpage: www.biotec.tu-dresden.de
>
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IRTA Postdoctoral Fellow
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