I would be cursing so much, if I had to correct someone like me... This is the second time I realise realise that the commit messages actually are used for something.
Best Troels 2014-05-22 10:13 GMT+02:00 Edward d'Auvergne <[email protected]>: > No need to read those, as you are following the format perfectly! > It's just a few capitalisation changes, spelling fixes (both git and > svn commit message editing should highlight 'systemtest' as it should > be 'system test'), and making the sentences easier to read (adding > definite articles, etc.). Just simple things that become a lot of > work when replicated in 500 commit messages. > > Cheers, > > Edward > > > On 22 May 2014 10:07, Troels Emtekær Linnet <[email protected]> wrote: >> Allright. >> >> You are handling my improper writing of English. >> That must be a tough job... >> >> I can only say, that I will really try to do this better. >> >> Maybe I should re-read: >> http://www.nmr-relax.com/manual/Format_commit_logs.html >> http://wiki.nmr-relax.com/Format_commit_logs >> >> Best >> Troels >> >> 2014-05-22 9:43 GMT+02:00 Edward d'Auvergne <[email protected]>: >>> Hi Troels, >>> >>> Just for reference, this is how I would change your commit message for >>> the release documentation, as this can make my life easier if you do >>> this for me ;) I didn't do this for all your commits in the last >>> message for relax 3.2.0 >>> (https://gna.org/forum/forum.php?forum_id=2461) because there were far >>> too many to handle :) Anyway, the main changes are to convert each >>> line into a proper sentence structure for reading: >>> >>> >>>> Implemented systemtest Relax_disp.test_cpmg_synthetic_ns3d_to_b14. >>> >>> Implemented the Relax_disp.test_cpmg_synthetic_ns3d_to_b14 system test. >>> >>> >>>> bug #22021: (https://gna.org/bugs/?22021) Model B14 shows bad fitting to >>>> data. >>> >>> Bug #22021 (https://gna.org/bugs/?22021), model B14 shows bad fitting to >>> data. >>> >>> >>>> This is to catch model B14 showing bad fitting behaviour. >>> >>> No change required :) >>> >>> Cheers, >>> >>> Edward >>> >>> >>> >>> >>> On 21 May 2014 20:36, <[email protected]> wrote: >>>> Author: tlinnet >>>> Date: Wed May 21 20:36:33 2014 >>>> New Revision: 23315 >>>> >>>> URL: http://svn.gna.org/viewcvs/relax?rev=23315&view=rev >>>> Log: >>>> Implemented systemtest Relax_disp.test_cpmg_synthetic_ns3d_to_b14. >>>> >>>> bug #22021: (https://gna.org/bugs/?22021) Model B14 shows bad fitting to >>>> data. >>>> >>>> This is to catch model B14 showing bad fitting behaviour. >>>> >>>> Modified: >>>> trunk/test_suite/system_tests/relax_disp.py >>>> >>>> Modified: trunk/test_suite/system_tests/relax_disp.py >>>> URL: >>>> http://svn.gna.org/viewcvs/relax/trunk/test_suite/system_tests/relax_disp.py?rev=23315&r1=23314&r2=23315&view=diff >>>> ============================================================================== >>>> --- trunk/test_suite/system_tests/relax_disp.py (original) >>>> +++ trunk/test_suite/system_tests/relax_disp.py Wed May 21 20:36:33 2014 >>>> @@ -1091,6 +1091,145 @@ >>>> self.assertAlmostEqual(set_val/1000, >>>> min_val/1000, 1) >>>> elif mo_param == 'pA': >>>> self.assertAlmostEqual(set_val, min_val, 3) >>>> + >>>> + >>>> + def test_cpmg_synthetic_ns3d_to_b14(self): >>>> + """Test synthetic cpmg data. >>>> + >>>> + This script will produce synthetic CPMG R2eff values according to >>>> the NS CPMG 2-site 3D model, and the fit the data with B14. >>>> + Try to catch bug #22021 U{https://gna.org/bugs/index.php?22021}: >>>> Model B14 shows bad fitting to data. >>>> + """ >>>> + >>>> + # Reset. >>>> + #self.interpreter.reset() >>>> + >>>> + ## Set Experiments. >>>> + model_create = 'NS CPMG 2-site 3D' >>>> + #model_create = 'NS CPMG 2-site expanded' >>>> + model_analyse = 'B14' >>>> + # Exp 1 >>>> + sfrq_1 = 599.8908617*1E6 >>>> + r20_key_1 = generate_r20_key(exp_type=EXP_TYPE_CPMG_SQ, >>>> frq=sfrq_1) >>>> + time_T2_1 = 0.06 >>>> + ncycs_1 = [2, 4, 8, 10, 20, 30, 40, 60] >>>> + r2eff_err_1 = [0, 0, 0, 0, 0, 0, 0, 0] >>>> + exp_1 = [sfrq_1, time_T2_1, ncycs_1, r2eff_err_1] >>>> + >>>> + sfrq_2 = 499.8908617*1E6 >>>> + r20_key_2 = generate_r20_key(exp_type=EXP_TYPE_CPMG_SQ, >>>> frq=sfrq_2) >>>> + time_T2_2 = 0.05 >>>> + ncycs_2 = [2, 4, 8, 10, 30, 35, 40, 50] >>>> + r2eff_err_2 = [0, 0, 0, 0, 0, 0, 0, 0] >>>> + exp_2 = [sfrq_2, time_T2_2, ncycs_2, r2eff_err_2] >>>> + >>>> + # Collect all exps >>>> + exps = [exp_1, exp_2] >>>> + >>>> + spins = [ >>>> + ['Ala', 1, 'N', {'r2': {r20_key_1:10., r20_key_2:10.}, 'r2a': >>>> {r20_key_1:10., r20_key_2:10.}, 'r2b': {r20_key_1:10., r20_key_2:10.}, >>>> 'kex': 1000., 'pA': 0.99, 'dw': 2.} ] >>>> + ] >>>> + >>>> + # Collect the data to be used. >>>> + ds.data = [model_create, model_analyse, spins, exps] >>>> + >>>> + # The tmp directory. None is the local directory. >>>> + ds.tmpdir = ds.tmpdir >>>> + >>>> + # The results directory. None is the local directory. >>>> + #ds.resdir = None >>>> + ds.resdir = ds.tmpdir >>>> + >>>> + # Do set_grid_r20_from_min_r2eff ?. >>>> + ds.set_grid_r20_from_min_r2eff = True >>>> + >>>> + # Remove insignificant level. >>>> + ds.insignificance = 0.0 >>>> + >>>> + # The grid search size (the number of increments per dimension). >>>> + ds.GRID_INC = 8 >>>> + >>>> + # The do clustering. >>>> + ds.do_cluster = False >>>> + >>>> + # The function tolerance. This is used to terminate minimisation >>>> once the function value between iterations is less than the tolerance. >>>> + # The default value is 1e-25. >>>> + ds.set_func_tol = 1e-9 >>>> + >>>> + # The maximum number of iterations. >>>> + # The default value is 1e7. >>>> + ds.set_max_iter = 1000 >>>> + >>>> + # The verbosity level. >>>> + ds.verbosity = 1 >>>> + >>>> + # The rel_change WARNING level. >>>> + ds.rel_change = 0.05 >>>> + >>>> + # The plot_curves. >>>> + ds.plot_curves = False >>>> + >>>> + # The conversion for ShereKhan at http://sherekhan.bionmr.org/. >>>> + ds.sherekhan_input = False >>>> + >>>> + # Make a dx map to be opened om OpenDX. To map the hypersurface >>>> of chi2, when altering kex, dw and pA. >>>> + ds.opendx = False >>>> + >>>> + # The set r2eff err. >>>> + ds.r2eff_err = 0.1 >>>> + >>>> + # The print result info. >>>> + ds.print_res = False >>>> + >>>> + # Execute the script. >>>> + self.interpreter.run(script_file=status.install_path + >>>> sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'relax_disp'+sep+'cpmg_synthetic.py') >>>> + >>>> + cur_spins = ds.data[2] >>>> + # Compare results. >>>> + for i in range(len(cur_spins)): >>>> + res_name, res_num, spin_name, params = cur_spins[i] >>>> + cur_spin_id = ":%i@%s"%(res_num, spin_name) >>>> + cur_spin = return_spin(cur_spin_id) >>>> + >>>> + grid_params = ds.grid_results[i][3] >>>> + min_params = ds.min_results[i][3] >>>> + # Now read the parameters. >>>> + print("For spin: '%s'"%cur_spin_id) >>>> + for mo_param in cur_spin.params: >>>> + # The R2 is a dictionary, depending on spectrometer >>>> frequency. >>>> + if isinstance(getattr(cur_spin, mo_param), dict): >>>> + grid_r2 = grid_params[mo_param] >>>> + min_r2 = min_params[mo_param] >>>> + set_r2 = params[mo_param] >>>> + for key, val in set_r2.items(): >>>> + grid_r2_frq = grid_r2[key] >>>> + min_r2_frq = min_r2[key] >>>> + set_r2_frq = set_r2[key] >>>> + frq = float(key.split(EXP_TYPE_CPMG_SQ+' - >>>> ')[-1].split('MHz')[0]) >>>> + rel_change = math.sqrt( (min_r2_frq - >>>> set_r2_frq)**2/(min_r2_frq)**2 ) >>>> + print("%s %s %s %s %.1f GRID=%.3f MIN=%.3f >>>> SET=%.3f RELC=%.3f"%(cur_spin.model, res_name, cur_spin_id, mo_param, frq, >>>> grid_r2_frq, min_r2_frq, set_r2_frq, rel_change) ) >>>> + if rel_change > ds.rel_change: >>>> + print("WARNING: rel change level is above >>>> %.2f, and is %.4f."%(ds.rel_change, rel_change)) >>>> + print("###################################") >>>> + >>>> + ## Make test on R2. >>>> + self.assertAlmostEqual(set_r2_frq, min_r2_frq, 2) >>>> + else: >>>> + grid_val = grid_params[mo_param] >>>> + min_val = min_params[mo_param] >>>> + set_val = params[mo_param] >>>> + rel_change = math.sqrt( (min_val - >>>> set_val)**2/(min_val)**2 ) >>>> + print("%s %s %s %s GRID=%.3f MIN=%.3f SET=%.3f >>>> RELC=%.3f"%(cur_spin.model, res_name, cur_spin_id, mo_param, grid_val, >>>> min_val, set_val, rel_change) ) >>>> + if rel_change > ds.rel_change: >>>> + print("WARNING: rel change level is above %.2f, >>>> and is %.4f."%(ds.rel_change, rel_change)) >>>> + print("###################################") >>>> + >>>> + ## Make test on parameters. >>>> + if mo_param == 'dw': >>>> + self.assertAlmostEqual(set_val/10, min_val/10, 6) >>>> + elif mo_param == 'kex': >>>> + self.assertAlmostEqual(set_val/1000, >>>> min_val/1000, 5) >>>> + elif mo_param == 'pA': >>>> + self.assertAlmostEqual(set_val, min_val, 7) >>>> >>>> >>>> def test_cpmg_synthetic_ns3d_to_cr72_noise_cluster(self): >>>> >>>> >>>> _______________________________________________ >>>> relax (http://www.nmr-relax.com) >>>> >>>> This is the relax-commits mailing list >>>> [email protected] >>>> >>>> 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 >>> [email protected] >>> >>> 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 [email protected] 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
