Hi Roberto,
The Biopython license is really permissive (
http://biopython.org/wiki/Biopython). Support for multi-file plugins is on
the table (http://pymolwiki.org/index.php/PluginArchitecture), but not
implemented yet. I wanted to make things as easy as possible on the user, so
I just distributed my plugin as one gigantic file that contained the plugin
code as well as code from a few (~3 if I recall correctly) Biopython files.
I'm certainly not claiming it was pretty, but it worked quite well.
Cheers,
-Michael
On Thu, Mar 10, 2011 at 11:26 PM, [email protected] <[email protected]> wrote:
> 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: [email protected]
> Data: 11/03/2011 4.05
> A: "[email protected]"<[email protected]>
> Cc: <[email protected]>, <[email protected]>
> 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, [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%2F10%2F2011>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: <%2B49%20%280%29%20351%20463-40083>+49 (0) 351 463-40083
>> >Fax: <%2B49%20%280%29%20351%20463-40087>+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)
>
>
>
--
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)
------------------------------------------------------------------------------
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
_______________________________________________
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Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
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