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
