2014-06-27 17:28 GMT+02:00 Edward d'Auvergne <edw...@nmr-relax.com>: > 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.
Done > - Trailing whitespace, most of it is in the trunk, but there are some > new ones. Just run: grep " $" lib/dispersion/* | grep -v "\\\\ " Done > - There are some empty lines straight after a 'for' loop in many places. Done > - Your copyright in the tsmfk01.py file needs to be extended to 2014. Done > - There are some FIXME comments in the lib.dispersion package. They are not critical, and are in module which is not used yet. > - In some places, comment lines require empty lines before them (in > target_functions.relax_disp and lib.dispersion). Where? Can you give example? > - 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. Done > - The newline spacing between target function methods needs some fixes. Done? > - The 'chi2_sum' initialisation in func_ns_mmq_2site() should go. Done > - The get_back_calc() method of the target function needs a little > polish - it is not a float that is returned. Done Best Troels > 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
