Re: [Fink-devel] pymol in 10.7
Well, I am getting so senile I didn't even remember that something other than the plug-ins depended on gfortran until I tried to make a lite one. I still might, because it would be kind of cool to have one that uses the aqua-tk interface… On Jul 31, 2011, at 4:27 PM, Koen van der Drift wrote: Bill, Thanks for this explanation - with this excellent info it only seems logical to include scipy and gcc to the package, no need to make a lite version, as far as I am concerned. Sorry for the noise :) - Koen. On Jul 31, 2011, at 7:21 PM, William G. Scott wrote: Dear Koen et al: The reason for the inclusion of scipy it to support two pymol plugins: APBS (an electrostatics program that is quite popular amongst structural molecular biologists) and a py-nmr plugin (of use to NMR spectroscopists). There may be other reasons as well that I am not aware of. Please note, even if the plugins that I and other maintainers in this package's history were removed, and the dependency upon scipy, there would STILL be a required dependency on gcc46 (or some form of gfortran) because of the python gui, i.e., the tkinter python megawidgets has a dependency upon BLT (a tcltk widget), and BLT has a dependency upon a fortran component. Omitting the fortran components from BLT still allows it to compile, but it is not the fully-enabled BLT required by some other packages. So we are doomed, unless we want to create a separate set of dependencies for a slimmed-down pymol. I am willing to do this, but this does come with some overhead. Bill -- Got Input? Slashdot Needs You. Take our quick survey online. Come on, we don't ask for help often. Plus, you'll get a chance to win $100 to spend on ThinkGeek. http://p.sf.net/sfu/slashdot-survey ___ Fink-devel mailing list Fink-devel@lists.sourceforge.net List archive: http://news.gmane.org/gmane.os.apple.fink.devel Subscription management: https://lists.sourceforge.net/lists/listinfo/fink-devel
Re: [Fink-devel] pymol in 10.7
Dear Koen et al: The reason for the inclusion of scipy it to support two pymol plugins: APBS (an electrostatics program that is quite popular amongst structural molecular biologists) and a py-nmr plugin (of use to NMR spectroscopists). There may be other reasons as well that I am not aware of. Please note, even if the plugins that I and other maintainers in this package's history were removed, and the dependency upon scipy, there would STILL be a required dependency on gcc46 (or some form of gfortran) because of the python gui, i.e., the tkinter python megawidgets has a dependency upon BLT (a tcltk widget), and BLT has a dependency upon a fortran component. Omitting the fortran components from BLT still allows it to compile, but it is not the fully-enabled BLT required by some other packages. So we are doomed, unless we want to create a separate set of dependencies for a slimmed-down pymol. I am willing to do this, but this does come with some overhead. Bill -- Got Input? Slashdot Needs You. Take our quick survey online. Come on, we don't ask for help often. Plus, you'll get a chance to win $100 to spend on ThinkGeek. http://p.sf.net/sfu/slashdot-survey ___ Fink-devel mailing list Fink-devel@lists.sourceforge.net List archive: http://news.gmane.org/gmane.os.apple.fink.devel Subscription management: https://lists.sourceforge.net/lists/listinfo/fink-devel
Re: [Fink-devel] pymol in 10.7
Bill, Thanks for this explanation - with this excellent info it only seems logical to include scipy and gcc to the package, no need to make a lite version, as far as I am concerned. Sorry for the noise :) - Koen. On Jul 31, 2011, at 7:21 PM, William G. Scott wrote: Dear Koen et al: The reason for the inclusion of scipy it to support two pymol plugins: APBS (an electrostatics program that is quite popular amongst structural molecular biologists) and a py-nmr plugin (of use to NMR spectroscopists). There may be other reasons as well that I am not aware of. Please note, even if the plugins that I and other maintainers in this package's history were removed, and the dependency upon scipy, there would STILL be a required dependency on gcc46 (or some form of gfortran) because of the python gui, i.e., the tkinter python megawidgets has a dependency upon BLT (a tcltk widget), and BLT has a dependency upon a fortran component. Omitting the fortran components from BLT still allows it to compile, but it is not the fully-enabled BLT required by some other packages. So we are doomed, unless we want to create a separate set of dependencies for a slimmed-down pymol. I am willing to do this, but this does come with some overhead. Bill -- Got Input? Slashdot Needs You. Take our quick survey online. Come on, we don't ask for help often. Plus, you'll get a chance to win $100 to spend on ThinkGeek. http://p.sf.net/sfu/slashdot-survey ___ Fink-devel mailing list Fink-devel@lists.sourceforge.net List archive: http://news.gmane.org/gmane.os.apple.fink.devel Subscription management: https://lists.sourceforge.net/lists/listinfo/fink-devel
Re: [Fink-devel] pymol in 10.7
On 7/29/2011 9:52 PM, Koen van der Drift wrote: On Jul 29, 2011, at 5:27 PM, Michael Lerner wrote: Newer versions of PyMOL include several modules (scipy, numpy, matplotlib). My understanding is that this was done to make it easier to write and support plugins and extensions. I don't know how fink does things, but perhaps you could ship a lite version. You may wish to talk with Jason Vertrees directly or on the PyMOL list. Cheers, -Michael Which newer version of pymol are you referring to, the one in fink (1.4) has no mention of scipy or matplotlib in the sourcecode, only numpy. - Koen. pymol-py27 1.4-7 has a dependency on scipy-py27, which has a build dependency on gcc46. Hanspeter -- Got Input? Slashdot Needs You. Take our quick survey online. Come on, we don't ask for help often. Plus, you'll get a chance to win $100 to spend on ThinkGeek. http://p.sf.net/sfu/slashdot-survey ___ Fink-devel mailing list Fink-devel@lists.sourceforge.net List archive: http://news.gmane.org/gmane.os.apple.fink.devel Subscription management: https://lists.sourceforge.net/lists/listinfo/fink-devel
Re: [Fink-devel] pymol in 10.7
On Jul 30, 2011, at 5:13 AM, Hanspeter Niederstrasser wrote: On 7/29/2011 9:52 PM, Koen van der Drift wrote: On Jul 29, 2011, at 5:27 PM, Michael Lerner wrote: Newer versions of PyMOL include several modules (scipy, numpy, matplotlib). My understanding is that this was done to make it easier to write and support plugins and extensions. I don't know how fink does things, but perhaps you could ship a lite version. You may wish to talk with Jason Vertrees directly or on the PyMOL list. Cheers, -Michael Which newer version of pymol are you referring to, the one in fink (1.4) has no mention of scipy or matplotlib in the sourcecode, only numpy. - Koen. pymol-py27 1.4-7 has a dependency on scipy-py27, which has a build dependency on gcc46. Hanspeter I was referring to the source code, not the info file :) But why is scipy in the info file? There is no need in pymol1.4 for scipy, which was my original question. Just trying to understand why this was added. Maybe Jack Howarth can explain, since he was involved in the transfer as the maintainer explained to me? Cheers, - Koen. -- Got Input? Slashdot Needs You. Take our quick survey online. Come on, we don't ask for help often. Plus, you'll get a chance to win $100 to spend on ThinkGeek. http://p.sf.net/sfu/slashdot-survey ___ Fink-devel mailing list Fink-devel@lists.sourceforge.net List archive: http://news.gmane.org/gmane.os.apple.fink.devel Subscription management: https://lists.sourceforge.net/lists/listinfo/fink-devel
[Fink-devel] pymol in 10.7
Hi, I recently switched to Lion, and tried to install pymol through fink. I noticed that the dependency on numpy has been changed into one on scipy. Scipy pulls in a slew of additional dependencies, including gcc46, making it an elaborate install process. As far as I know, there is no need for pymol to depend on scipy, numpy works just fine as I tested on my local machine. I already contacted the maintainer, but he was not involved in the move of pymol into 10.7. Cheers, - Koen. -- Got Input? Slashdot Needs You. Take our quick survey online. Come on, we don't ask for help often. Plus, you'll get a chance to win $100 to spend on ThinkGeek. http://p.sf.net/sfu/slashdot-survey ___ Fink-devel mailing list Fink-devel@lists.sourceforge.net List archive: http://news.gmane.org/gmane.os.apple.fink.devel Subscription management: https://lists.sourceforge.net/lists/listinfo/fink-devel
Re: [Fink-devel] pymol in 10.7
Which newer version of pymol are you referring to, the one in fink (1.4) has no mention of scipy or matplotlib in the sourcecode, only numpy. - Koen. On Jul 29, 2011, at 5:27 PM, Michael Lerner wrote: Newer versions of PyMOL include several modules (scipy, numpy, matplotlib). My understanding is that this was done to make it easier to write and support plugins and extensions. I don't know how fink does things, but perhaps you could ship a lite version. You may wish to talk with Jason Vertrees directly or on the PyMOL list. Cheers, -Michael On Fri, Jul 29, 2011 at 4:16 PM, Koen van der Drift koenvanderdr...@gmail.com wrote: Hi, I recently switched to Lion, and tried to install pymol through fink. I noticed that the dependency on numpy has been changed into one on scipy. Scipy pulls in a slew of additional dependencies, including gcc46, making it an elaborate install process. As far as I know, there is no need for pymol to depend on scipy, numpy works just fine as I tested on my local machine. I already contacted the maintainer, but he was not involved in the move of pymol into 10.7. Cheers, - Koen. -- Got Input? Slashdot Needs You. Take our quick survey online. Come on, we don't ask for help often. Plus, you'll get a chance to win $100 to spend on ThinkGeek. http://p.sf.net/sfu/slashdot-survey ___ Fink-devel mailing list Fink-devel@lists.sourceforge.net List archive: http://news.gmane.org/gmane.os.apple.fink.devel Subscription management: https://lists.sourceforge.net/lists/listinfo/fink-devel -- 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) as of August 15th: Department of Physics and Astronomy Earlham College 801 National Road West Richmond, IN 47374-4095 -- Got Input? Slashdot Needs You. Take our quick survey online. Come on, we don't ask for help often. Plus, you'll get a chance to win $100 to spend on ThinkGeek. http://p.sf.net/sfu/slashdot-survey ___ Fink-devel mailing list Fink-devel@lists.sourceforge.net List archive: http://news.gmane.org/gmane.os.apple.fink.devel Subscription management: https://lists.sourceforge.net/lists/listinfo/fink-devel
