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[PyMOL] R: Re: R: Re: plugin dependencies
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From: <rv...@li...> - 2011-03-11 04:26:28
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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: mgl...@gm... Data: 11/03/2011 4.05 A: "rv...@li..."<rv...@li...> Cc: <hon...@bi...>, <pym...@li...> 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...@li... <rv...@li...> 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: hon...@bi... >Data: 10/03/2011 12.57 >A: <pym...@li...> >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...@li... 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 (PyM...@li...) >> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >> Archives: http://www.mail-archive.com/pym...@li... > >-- >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 (PyM...@li...) >Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >Archives: http://www.mail-archive.com/pym...@li... > ------------------------------------------------------------------------------ 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 (PyM...@li...) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pym...@li... -- 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) |
