Seb, To fix this, I have manually copied over the changes from the 1.3 line into the relax_fit_exp_2param_neg.py script. For the relax_fit_exp_3param_inv_neg.py script, there would need to be a few small changes to make this work. Though I don't know if it will reach this part of the script, as I think the C code is not functional at the moment.
Regards, Edward On 20 January 2012 15:22, Edward d'Auvergne <[email protected]> wrote: > Hi Seb, > > I'm in the process of updating all of the branches using svnmerge.py > and have noticed that there is a problem with your inversion-recovery > branch. It seems to be that the system test script > branches/inversion-recovery/test_suite/system_tests/scripts/relax_fit.py > was renamed to relax_fit_exp_2param_neg.py. Have you had problems > with svnmerge.py before? And if so, how did you resolved the problem? > > Cheers, > > Edward > > > On 17 June 2011 17:23, <[email protected]> wrote: >> Author: semor >> Date: Fri Jun 17 17:23:14 2011 >> New Revision: 13114 >> >> URL: http://svn.gna.org/viewcvs/relax?rev=13114&view=rev >> Log: >> >> Added '_exp_2param_neg' in the name for the tests currently using the >> function 'exp_2param_neg'. >> >> This is the first step before making a test for the 'inversion-recovery' >> function 'exp_3param_inv_neg'. >> >> >> Added: >> >> branches/inversion-recovery/test_suite/system_tests/scripts/relax_fit_exp_2param_neg.py >> - copied unchanged from r13113, >> branches/inversion-recovery/test_suite/system_tests/scripts/relax_fit.py >> Removed: >> branches/inversion-recovery/test_suite/system_tests/scripts/relax_fit.py >> Modified: >> branches/inversion-recovery/test_suite/system_tests/relax_fit.py >> >> Modified: branches/inversion-recovery/test_suite/system_tests/relax_fit.py >> URL: >> http://svn.gna.org/viewcvs/relax/branches/inversion-recovery/test_suite/system_tests/relax_fit.py?rev=13114&r1=13113&r2=13114&view=diff >> ============================================================================== >> --- branches/inversion-recovery/test_suite/system_tests/relax_fit.py >> (original) >> +++ branches/inversion-recovery/test_suite/system_tests/relax_fit.py Fri Jun >> 17 17:23:14 2011 >> @@ -127,27 +127,27 @@ >> self.assertEqual(lines[index][1], '487178.0') >> >> >> - def test_curve_fitting_height(self): >> + def test_curve_fitting_height_exp_2param_neg(self): >> """Test the relaxation curve fitting C modules.""" >> >> # The intensity type. >> ds.int_type = 'height' >> >> # Execute the script. >> - self.interpreter.run(script_file=status.install_path + >> sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'relax_fit.py') >> + self.interpreter.run(script_file=status.install_path + >> sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'relax_fit_exp_2param_neg.py') >> >> # Check the curve-fitting results. >> self.check_curve_fitting() >> >> >> - def test_curve_fitting_volume(self): >> + def test_curve_fitting_volume_exp_2param_neg(self): >> """Test the relaxation curve fitting C modules.""" >> >> # The intensity type. >> ds.int_type = 'volume' >> >> # Execute the script. >> - self.interpreter.run(script_file=status.install_path + >> sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'relax_fit.py') >> + self.interpreter.run(script_file=status.install_path + >> sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'relax_fit_exp_2param_neg.py') >> >> # Check the curve-fitting results. >> self.check_curve_fitting() >> >> Removed: >> branches/inversion-recovery/test_suite/system_tests/scripts/relax_fit.py >> URL: >> http://svn.gna.org/viewcvs/relax/branches/inversion-recovery/test_suite/system_tests/scripts/relax_fit.py?rev=13113&view=auto >> ============================================================================== >> --- branches/inversion-recovery/test_suite/system_tests/scripts/relax_fit.py >> (original) >> +++ branches/inversion-recovery/test_suite/system_tests/scripts/relax_fit.py >> (removed) >> @@ -1,107 +1,0 @@ >> -# Script for relaxation curve fitting. >> - >> -# Python module imports. >> -from os import sep >> -import sys >> - >> -# relax module imports. >> -from data import Relax_data_store; ds = Relax_data_store() >> -from status import Status; status = Status() >> - >> - >> -# Missing intensity type (allow this script to run outside of the system >> test framework). >> -if not hasattr(ds, 'int_type'): >> - ds.int_type = 'height' >> - >> - >> -# Create the data pipe. >> -pipe.create('rx', 'relax_fit') >> - >> -# The path to the data files. >> -data_path = status.install_path + >> sep+'test_suite'+sep+'shared_data'+sep+'curve_fitting' >> - >> -# Load the sequence. >> -sequence.read('Ap4Aase.seq', dir=status.install_path + >> sep+'test_suite'+sep+'shared_data', res_num_col=1, res_name_col=2) >> - >> -# Name the spins so they can be matched to the assignments. >> -spin.name(name='N') >> - >> -# Spectrum names. >> -names = [ >> - 'T2_ncyc1_ave', >> - 'T2_ncyc1b_ave', >> - 'T2_ncyc2_ave', >> - 'T2_ncyc4_ave', >> - 'T2_ncyc4b_ave', >> - 'T2_ncyc6_ave', >> - 'T2_ncyc9_ave', >> - 'T2_ncyc9b_ave', >> - 'T2_ncyc11_ave', >> - 'T2_ncyc11b_ave' >> -] >> - >> -# Relaxation times (in seconds). >> -times = [ >> - 0.0176, >> - 0.0176, >> - 0.0352, >> - 0.0704, >> - 0.0704, >> - 0.1056, >> - 0.1584, >> - 0.1584, >> - 0.1936, >> - 0.1936 >> -] >> - >> -# Loop over the spectra. >> -for i in xrange(len(names)): >> - # Load the peak intensities. >> - spectrum.read_intensities(file=names[i]+'.list', dir=data_path, >> spectrum_id=names[i], int_method=ds.int_type) >> - >> - # Set the relaxation times. >> - relax_fit.relax_time(time=times[i], spectrum_id=names[i]) >> - >> -# Specify the duplicated spectra. >> -spectrum.replicated(spectrum_ids=['T2_ncyc1_ave', 'T2_ncyc1b_ave']) >> -spectrum.replicated(spectrum_ids=['T2_ncyc4_ave', 'T2_ncyc4b_ave']) >> -spectrum.replicated(spectrum_ids=['T2_ncyc9_ave', 'T2_ncyc9b_ave']) >> -spectrum.replicated(spectrum_ids=['T2_ncyc11_ave', 'T2_ncyc11b_ave']) >> - >> -# Peak intensity error analysis. >> -spectrum.error_analysis() >> - >> -# Deselect unresolved spins. >> -deselect.read(file='unresolved', dir=data_path, res_num_col=1) >> - >> -# Set the relaxation curve type. >> -relax_fit.select_model('exp_2param_neg') >> - >> -# Grid search. >> -grid_search(inc=11) >> - >> -# Minimise. >> -minimise('simplex', constraints=False) >> - >> -# Monte Carlo simulations. >> -monte_carlo.setup(number=3) >> -monte_carlo.create_data() >> -monte_carlo.initial_values() >> -minimise('simplex', constraints=False) >> -monte_carlo.error_analysis() >> - >> -# Save the relaxation rates. >> -value.write(param='rx', file='devnull', force=True) >> - >> -# Save the results. >> -results.write(file='devnull', force=True) >> - >> -# Create Grace plots of the data. >> -grace.write(y_data_type='chi2', file='devnull', force=True) # Minimised >> chi-squared value. >> -grace.write(y_data_type='i0', file='devnull', force=True) # Initial peak >> intensity. >> -grace.write(y_data_type='rx', file='devnull', force=True) # Relaxation >> rate. >> -grace.write(x_data_type='relax_times', y_data_type='int', file='devnull', >> force=True) # Average peak intensities. >> -grace.write(x_data_type='relax_times', y_data_type='int', norm=True, >> file='devnull', force=True) # Average peak intensities (normalised). >> - >> -# Save the program state. >> -state.save('devnull', force=True) >> >> >> _______________________________________________ >> relax (http://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://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
