Re: [PyMOL] plugin dependencies

2011-03-10 Thread Hongbo Zhu 
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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Re: [PyMOL] plugin dependencies

2011-03-10 Thread Jason Vertrees 
Hi Roberto,

This has always been a stumbling block for PyMOL.  Either you compile
from source and add any modules you want, or you use what we provide
in the Incentive or Academic builds.

In the past, to keep PyMOL light Warren always shipped a stripped
Python version.  Because of PyMOL's utility as a platform for
scripting, I think it's better to increase the size a bit and add more
modules that expands its basic functionality.

As a note, the new PyMOL builds will be quite a bit larger because
we're adding more useful Python modules and some other libraries to
the default install.  Along with Numpy, PIL and friends, we'll also be
distributing BioPython.

Cheers,

-- Jason


On Thu, Mar 10, 2011 at 12:17 AM, rv...@libero.it 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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 A question and answer guide to determining the best fit
 for your organization - today and in the future.
 http://p.sf.net/sfu/internap-sfd2d
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-- 
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC

(e) jason.vertr...@schrodinger.com
(o) +1 (603) 374-7120

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