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, [email protected] <[email protected]> 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: [email protected]
> >Data: 10/03/2011 12.57
> >A: <[email protected]>
> >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, [email protected] 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
> >>
> >>
>
> ------------------------------------------------------------------------------
> >> Colocation vs. Managed Hosting
> >> 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
> >> _______________________________________________
> >> PyMOL-users mailing list ([email protected])
> >> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> >> Archives: http://www.mail-archive.com/[email protected]
> >
> >--
> >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
> >
>
>
> >------------------------------------------------------------------------------
> >Colocation vs. Managed Hosting
> >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
> >_______________________________________________
> >PyMOL-users mailing list ([email protected])
> >Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> >Archives: http://www.mail-archive.com/[email protected]
> >
>
>
>
>
> ------------------------------------------------------------------------------
> Colocation vs. Managed Hosting
> 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
> _______________________________________________
> PyMOL-users mailing list ([email protected])
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/[email protected]
>
--
Michael Lerner, Ph.D.
IRTA Postdoctoral Fellow
Laboratory of Computational Biology NIH/NHLBI
5635 Fishers Lane, Room T909, MSC 9314
Rockville, MD 20852 (UPS/FedEx/Reality)
Bethesda MD 20892-9314 (USPS)
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