Hi Ed. I wont change anymore.
This development line is way overdue. Best Troels 2014-06-27 18:03 GMT+02:00 Edward d'Auvergne <edw...@nmr-relax.com>: > Here is one more point. For the DPL94 model, the denominator is > "kex**2 + spin_lock_fields**2". This can only be zero when kex is > zero, and then there should be no exchange. Therefore we can add a > kex == 0 check at the start to return R1_R2 and then delete the > mask_denom_zero logic. This should slightly speed things up by > removing one 'if' statement. Also, kex**2 is not a repetitive > operation. > > Cheers, > > Edward > > > On 27 June 2014 17:33, Edward d'Auvergne <edw...@nmr-relax.com> wrote: >> There are also a number of double spacing issues. You can find these >> by running: >> >> $ ./devel_scripts/code_validator lib/dispersion/b14.py >> $ ./devel_scripts/code_validator lib/dispersion/cr72.py >> >> Etc. Some things can be ignored, like the capitals in the function >> name and double spacing or trailing spacing for equations in >> docstrings. This script will identify most formatting problems >> remaining. >> >> Cheers, >> >> Edward >> >> >> >> On 27 June 2014 17:28, Edward d'Auvergne <edw...@nmr-relax.com> wrote: >>> Also the documentation in the get_back_calc() method of the target >>> function needs a little polish - it is not a float that is returned. >>> So, the running list: >>> >>> - 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. >>> >>> - The 'chi2_sum' initialisation in func_ns_mmq_2site() should go. >>> >>> - The get_back_calc() method of the target function needs a little >>> polish - it is not a float that is returned. >>> >>> Cheers, >>> >>> Edward >>> >>> >>> >>> On 27 June 2014 17:26, Edward d'Auvergne <edw...@nmr-relax.com> wrote: >>>> 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
