
Hi, Have you considered distributing chimera through fink? Payam ------ "...who search the reason of things Are those who bring the most sorrow on themselves." --Euripides, The Medea ------ "...who search the reason of things Are those who bring the most sorrow on themselves." --Euripides, The Medea

We haven't really seriously considered it, no. One stumbling block is that Chimera really isn't completely open source yet. We distribute the source to the Python part of Chimera but not the C++ part. We plan on distributing the C++ part once we have organized it enough that outside developers would have a prayer of compiling it, but we haven't put in the work to do that yet -- always so many things to do! The other problem is that we need to track our downloads so that we can report those statistics to our funding agency (NIH). Perhaps fink allows for that, I don't know. Eric Pettersen UCSF Computer Graphics Lab pett@cgl.ucsf.edu http://www.cgl.ucsf.edu On Sep 13, 2004, at 1:29 PM, Ersatz Sophist wrote:
Hi,
Have you considered distributing chimera through fink?
Payam ------ "...who search the reason of things Are those who bring the most sorrow on themselves." --Euripides, The Medea
------ "...who search the reason of things Are those who bring the most sorrow on themselves." --Euripides, The Medea
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users

FWIW, I prefer the .dmg style installer, or at least single package, one click installers. Its also useful to have the application relocatable to any folder within /Applications. Fink is useful in that it provides a lot of "raw" Unix stuff to OSX, but I find having "yet another" location for software (/sw) a bit irritating (yes, I know why its that way). Its another hierarchy to maintain, backup, consider each time you're sorting out a software issue, etc. I prefer that GUI-oriented applications go to /Applications and only command-line level only applications be in /sw as a sort-of hack to add command-line level stuff that is extra to BSD. Another criteria would be that any application that you can open from Finder should be in /Applications. This follows Apple's logical divide of GUI apps and the Unix/BSD level. Having written all this (!), can fink look after applications belonging in /Applications, rather than /sw? I suppose I should have asked this first I... Grant
We haven't really seriously considered it, no. One stumbling block is that Chimera really isn't completely open source yet. We distribute the source to the Python part of Chimera but not the C++ part. We plan on distributing the C++ part once we have organized it enough that outside developers would have a prayer of compiling it,
:-) For my money I'd be more concerned about good documentation of the APIs (etc) so that people can build on what already exists without having to decipher someone else's code base. Just my 2c - my pet peeve about open source is that poor or non-existant documentation forces everyone up the same time-wasting learning curves.
but we haven't put in the work to do that yet -- always so many things to do! The other problem is that we need to track our downloads so that we can report those statistics to our funding agency (NIH). Perhaps fink allows for that, I don't know.
Eric Pettersen UCSF Computer Graphics Lab pett@cgl.ucsf.edu http://www.cgl.ucsf.edu
On Sep 13, 2004, at 1:29 PM, Ersatz Sophist wrote:
Hi,
Have you considered distributing chimera through fink?
Payam
-- ------------------------------------------------------------------- Grant Jacobs Ph.D. BioinfoTools ph. +64 3 478 0095 (office, after 10am) PO Box 6129, or +64 25 601 5917 (mobile) Dunedin, gjacobs@bioinfotools.com NEW ZEALAND. Bioinformatics tools: deriving knowledge from biological data Bioinformatics tools - software development - consulting - training Check out the website for more details: http://www.bioinfotools.com The information contained in this mail message is confidential and may be legally privileged. Readers of this message who are not the intended recipient are hereby notified that any use, dissemination, distribution or reproduction of this message is prohibited. If you have received this message in error please notify the sender immed- iately and destroy the original message. This applies also to any attached documents.

On Sep 14, 2004, at 4:42 PM, Grant Jacobs wrote:
FWIW, I prefer the .dmg style installer, or at least single package, one click installers. Its also useful to have the application relocatable to any folder within /Applications.
Certainly if you're _not_ using fink, the .dmg is almost certainly what you want. I find it highly convenient too. If you're using fink, perhaps you'd like to be able to do everything through that mechanism, but as you point out sometimes even fink users prefer the .dmg install. And given the work we would need to do before we could even try to have Chimera available via fink, it won't be happening soon.
We haven't really seriously considered it, no. One stumbling block is that Chimera really isn't completely open source yet. We distribute the source to the Python part of Chimera but not the C++ part. We plan on distributing the C++ part once we have organized it enough that outside developers would have a prayer of compiling it,
:-)
For my money I'd be more concerned about good documentation of the APIs (etc) so that people can build on what already exists without having to decipher someone else's code base. Just my 2c - my pet peeve about open source is that poor or non-existant documentation forces everyone up the same time-wasting learning curves.
but we haven't put in the work to do that yet -- always so many things to do!
Yes, better documentation would be part of "organizing" the C++ part. Right now, the only comprehensive API documentation we have is the programmer's reference guide, which amounts to simply a dump of all APIs with some doc strings thrown in -- barely more useful that using 'dir' on Python objects of interest. The best documentation we have is the programmer's examples, which do a good job of explaining how to do various commonly-desired tasks in Chimera, such as getting your extension into the menus, using molecular data, and saving into sessions. Once you want to go beyond the realm of the examples, we trust that people will look at other Chimera extensions that do similar things to what they want to do and figure things out. It's the best we have until we get that "organizing" done. Of course, we do answer any development-related questions we get on chimera-dev@cgl.ucsf.edu. The other thing about a documented API is that you can expect that it won't disappear from one release to the next -- at least not without a migration path being provided. Eric Pettersen UCSF Computer Graphics Lab pett@cgl.ucsf.edu http://www.cgl.ucsf.edu
participants (3)
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Eric Pettersen
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Ersatz Sophist
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Grant Jacobs