To add to the list of trivialities to fix: - The 'chi2_sum' initialisation in func_ns_mmq_2site() should go.
Cheers, Edward On 27 June 2014 17:23, Edward d'Auvergne <edw...@nmr-relax.com> wrote: > Let me see. You've covered most of the running list, there's just one > or two things left. I'll add a few more trivial things as well. > > - Some modules have "=" operators outside of functions that need > spaces around them. > > - Trailing whitespace, most of it is in the trunk, but there are some > new ones. Just run: grep " $" lib/dispersion/* | grep -v "\\\\ " > > - There are some empty lines straight after a 'for' loop in many places. > > - Your copyright in the tsmfk01.py file needs to be extended to 2014. > > - There are some FIXME comments in the lib.dispersion package. > > - In some places, comment lines require empty lines before them (in > target_functions.relax_disp and lib.dispersion). > > - Not very important, but the target function calc_ns_mmq_3site_chi2() > can have the "Once off parameter conversions" shifted into the > lib.dispersion module to simplify this. > > - The newline spacing between target function methods needs some fixes. > > > I'll keep looking. I'm guessing you will not be tackling the numeric > models to speed them up to match 'NS CPMG 2-site expanded' model via > the ultimate solution of brute-force expansion > (http://www.mail-archive.com/relax-users@gna.org/msg01641.html) any > time soon. This will have a similar effect as the ultimate speed up > at http://www.mail-archive.com/relax-devel%40gna.org/msg05691.html > which you have so successfully achieved in this branch. Can you > remember if there were any other changes required? I will create a > new timings file just before tagging the relax release. > > Cheers, > > Edward > > On 27 June 2014 16:53, Troels Emtekær Linnet <tlin...@nmr-relax.com> wrote: >> This sounds good. >> >> What is needed to be done, to merge disp_spin_speed in trunk now? >> >> Best >> Troels >> >> 2014-06-27 15:53 GMT+02:00 Edward d'Auvergne <edw...@nmr-relax.com>: >>> Hmmm: >>> >>> $ grep -c "out=\|einsum" lib/dispersion/* >>> lib/dispersion/b14.py:0 >>> lib/dispersion/cr72.py:2 >>> lib/dispersion/dpl94.py:0 >>> lib/dispersion/__init__.py:0 >>> lib/dispersion/it99.py:0 >>> lib/dispersion/lm63_3site.py:0 >>> lib/dispersion/lm63.py:0 >>> lib/dispersion/m61b.py:0 >>> lib/dispersion/m61.py:0 >>> lib/dispersion/matrix_exponential.py:5 >>> lib/dispersion/matrix_power.py:0 >>> lib/dispersion/mmq_cr72.py:0 >>> lib/dispersion/mp05.py:0 >>> lib/dispersion/ns_cpmg_2site_3d.py:6 >>> lib/dispersion/ns_cpmg_2site_expanded.py:0 >>> lib/dispersion/ns_cpmg_2site_star.py:3 >>> lib/dispersion/ns_matrices.py:0 >>> lib/dispersion/ns_mmq_2site.py:12 >>> lib/dispersion/ns_mmq_3site.py:12 >>> lib/dispersion/ns_r1rho_2site.py:3 >>> lib/dispersion/ns_r1rho_3site.py:3 >>> lib/dispersion/tap03.py:0 >>> lib/dispersion/tp02.py:0 >>> lib/dispersion/tsmfk01.py:0 >>> lib/dispersion/two_point.py:0 >>> >>> >>> What do you think of the idea of making this a hard dependency: >>> >>> """ >>> Index: dep_check.py >>> =================================================================== >>> --- dep_check.py (revision 24343) >>> +++ dep_check.py (working copy) >>> @@ -37,6 +37,9 @@ >>> # numpy. >>> try: >>> import numpy >>> + if float(numpy.version.version[:3]) < 1.6: >>> + sys.stderr.write("Version %s of the 'numpy' dependency is not >>> supported, numpy >= 1.6 is required.\n" % numpy.version.version) >>> + sys.exit() >>> except ImportError: >>> sys.stderr.write("The dependency 'numpy' has not been installed.\n") >>> sys.exit() >>> """ >>> >>> This might be the easiest way, just forcing users to upgrade. I've >>> used the out argument a lot with the frame order analysis as well and >>> plan to use it more often, so maybe we just have to put our foot down >>> and make this a hard dependency. That will make everyone's life >>> easier, and simplify what we as developers have to do to handle this. >>> I can apply this to the trunk and release relax 3.2.3 with all the >>> current fixes and this hard numpy version dependency, and then in a >>> few weeks when you are ready, merge the disp_spin_speed branch and >>> release relax 3.2.4. What do you think? >>> >>> Regards, >>> >>> Edward >>> >>> >>> >>> >>> >>> On 27 June 2014 14:40, Troels Emtekær Linnet <tlin...@nmr-relax.com> wrote: >>>> Hi Ed. >>>> >>>> You can just grep for "out" or "einsum" in lib/dispersion. >>>> >>>> Best >>>> Troels >>>> >>>> 2014-06-27 14:15 GMT+02:00 Edward d'Auvergne <edw...@nmr-relax.com>: >>>>> Hi Troels, >>>>> >>>>> I think if would be better if we caught this earlier, specifically the >>>>> select_model() method of the specific_analyses.relax_disp.uf module if >>>>> the user chooses a model which is not supported by their numpy >>>>> version. Such a check with a RelaxError would only be two lines of >>>>> code, plus a comment (which could include the current version in >>>>> numpy.version.version). It would be very useful to add the models to >>>>> a list variable in specific_analyses.relax_disp.variables so that I >>>>> can replicate the checks in the GUI. Even better would be to add the >>>>> 2 line check to a function in specific_analyses.relax_disp.checks to >>>>> allow for consistent checking in all user interfaces. There could >>>>> even be two separate tests, one for the numpy.einsum and one for the >>>>> numpy out argument, each with their own model lists, if you wish. >>>>> >>>>> Cheers, >>>>> >>>>> Edward >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> On 27 June 2014 12:58, <tlin...@nmr-relax.com> wrote: >>>>>> Author: tlinnet >>>>>> Date: Fri Jun 27 12:58:22 2014 >>>>>> New Revision: 24336 >>>>>> >>>>>> URL: http://svn.gna.org/viewcvs/relax?rev=24336&view=rev >>>>>> Log: >>>>>> Added to target function that experiment_type_setup() should not be >>>>>> initiated, if numpy.einsum is missing. >>>>>> >>>>>> Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion >>>>>> models for Clustered analysis. >>>>>> >>>>>> Modified: >>>>>> branches/disp_spin_speed/target_functions/relax_disp.py >>>>>> >>>>>> Modified: branches/disp_spin_speed/target_functions/relax_disp.py >>>>>> URL: >>>>>> http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/target_functions/relax_disp.py?rev=24336&r1=24335&r2=24336&view=diff >>>>>> ============================================================================== >>>>>> --- branches/disp_spin_speed/target_functions/relax_disp.py >>>>>> (original) >>>>>> +++ branches/disp_spin_speed/target_functions/relax_disp.py Fri Jun >>>>>> 27 12:58:22 2014 >>>>>> @@ -365,8 +365,10 @@ >>>>>> # This is to make sure, that the chi2 values is not affected by >>>>>> missing values. >>>>>> self.mask_replace_blank = masked_equal(self.missing, 1.0) >>>>>> >>>>>> - # Check the experiment types, simplifying the data structures >>>>>> as needed. >>>>>> - self.experiment_type_setup() >>>>>> + # Check if eisum is available for numerical models. >>>>>> + if dep_check.einsum_module: >>>>>> + # Check the experiment types, simplifying the data >>>>>> structures as needed. >>>>>> + self.experiment_type_setup() >>>>>> >>>>>> # Scaling initialisation. >>>>>> self.scaling_flag = False >>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> relax (http://www.nmr-relax.com) >>>>>> >>>>>> This is the relax-commits mailing list >>>>>> relax-comm...@gna.org >>>>>> >>>>>> To unsubscribe from this list, get a password >>>>>> reminder, or change your subscription options, >>>>>> visit the list information page at >>>>>> https://mail.gna.org/listinfo/relax-commits >>>>> >>>>> _______________________________________________ >>>>> relax (http://www.nmr-relax.com) >>>>> >>>>> This is the relax-devel mailing list >>>>> relax-devel@gna.org >>>>> >>>>> To unsubscribe from this list, get a password >>>>> reminder, or change your subscription options, >>>>> visit the list information page at >>>>> https://mail.gna.org/listinfo/relax-devel _______________________________________________ relax (http://www.nmr-relax.com) This is the relax-devel mailing list relax-devel@gna.org To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-devel
