A quick patch to make such changes is attached.
On May 13, 2008, at 1:57 PM, Friedrich Foerster wrote:
> could anyone also create a simple README/directory explaining, which > packages (including supported versions) are needed and where to get > them? the file should be be in the root IMP directory to maximize > visibility. > that would make the installation way simpler and avoid things like > frank's hassle with boost. > > thanks > > frido > > Daniel Russel wrote: >> Since by now things are a bit mixed up, here is a monster diff. >> >> The changes that I remember are: >> API Changes: >> - There are now just AllNonbondedListScoreState and >> BipartiteNonbondedListScoreState. The default algorithm should be the >> best currently available in your build. >> >> - The level of checks can now be set at runtime using the methods >> set_check_level and get_check_level. Valid values for the levels are >> NONE, CHEAP, EXPENSIVE. NDEBUG works as before in that it >> permentantly >> turns off various checks but the speed difference compared to running >> with NONE appears to be small. I suggest that python code be run with >> cheap checks and interactive python run with expensive checks. >> >> - The ChainBondedList went away as the speed advantage didn't seem to >> be worth having an extra class. >> >> - A new class BondCoverScoreState is added which adds x,y,z,r to >> bonds >> passed to it in order cover the bonds with spheres for collision >> detection purposes. >> >> - there is now BD optimizer. The tests for it suck and occasionally >> fail. I am not sure of a good way to test such stochastic things. >> >> - the previously mentioned WLCEnergy unary function has been added >> >> >> Internal API changes: >> - ScoreStates should now implement do_before_evaluate and >> do_after_evaluate instead of update and after_evaluate. Model calls >> before_evaluate and after_evaluate which check the iteration numbers >> as mentioned before and calls the internal methods if appropriate. >> >> - I tried to roll back Ben's disabling of some tests which had been >> failing, but didn't try very hard, so they might not all be back. >> >> - The default check level should probably always be cheap and the >> unit >> test should turn on expensive tests. I don't know how to add code to >> all IMP unit tests. >> >> - there is code in restraints and things to return how much memory >> they used. I added that when I was having problems with running out >> of >> memory (due to, as it turned out, the nonbonded lists growing too >> large). Having something like that in our code is great. >> Unfortunately, I'll bet that it will slowly atrophy with time. >> Anyway, >> it is there for now as it doesn't hurt anything. >> >> >> I am sure there are other changes which I forgot. >> >> >> >> >> On May 12, 2008, at 3:42 PM, Ben Webb wrote: >> >>> Andrej would prefer to avoid commercial-license code in IMP, and it >>> would surely be a pain to remove this code in future if it became >>> incompatible with our license. But he prefers more to save time >>> now, so >>> he's OK with linking against something like CGAL. So I can commit >>> this >>> patch in essentially its current form, provided that it applies >>> against >>> current SVN (it doesn't right now, e.g. because it's missing some >>> files). >>> >>> Ben >>> -- >>> ben@salilab.org http://salilab.org/~ben/ >>> "It is a capital mistake to theorize before one has data." >>> - Sir Arthur Conan Doyle >>> _______________________________________________ >>> IMP-dev mailing list >>> IMP-dev@salilab.org >>> https://salilab.org/mailman/listinfo/imp-dev >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> IMP-dev mailing list >> IMP-dev@salilab.org >> https://salilab.org/mailman/listinfo/imp-dev > > > -- > -- > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > % Friedrich Foerster % > % Andrej Sali Lab % > % University of California at San Francisco % > # MC 2552 % > % Byers Hall Room 501 % > % 1700 4th Street % > % San Francisco, CA 94158-2330, USA % > % % > % phone: +1 (415) 514-4258 % > % fax: +1 (415) 514-4231 % > % % > % www.salilab.org/~frido % > % % > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > _______________________________________________ > IMP-dev mailing list > IMP-dev@salilab.org > https://salilab.org/mailman/listinfo/imp-dev