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
