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
