Hi Troels, When I run:
$ scons api_manual_html I see: +------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | File /data/relax/relax-trunk/test_suite/system_tests/relax_disp.py, line 2990, in test_suite.system_tests.relax_disp.Relax_disp.test_dx_map_clustered | Warning: Line 2994: Improper paragraph indentation. | +------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- You will need to use better epydoc formatting. For the reference, add a '- ' to the front, i.e. use the list formatting as described at http://epydoc.sourceforge.net/epytext.html. I would also recommend you use the U{text<link>} format for the DOI number. This will add link to Kaare's paper in the relax API documentation, and hence help this paper appear higher in the Google and other search engine search results. The more links from diverse websites, the better ;) Regards, Edward P. S. If you run the 'scons api_manual_html' command yourself, you will see 5-6 more places where you have introduced epydoc formatting errors into the docstrings. These are all simple fixes though. On 5 October 2014 22:22, <[email protected]> wrote: > Author: tlinnet > Date: Sun Oct 5 22:22:35 2014 > New Revision: 26149 > > URL: http://svn.gna.org/viewcvs/relax?rev=26149&view=rev > Log: > Implemented systemtest Relax_disp.test_dx_map_clustered to cath the missing > creation of a point file. > > Bug #22753 (https://gna.org/bugs/index.php?22753): dx.map does not work when > only 1 point is used. > > 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=26149&r1=26148&r2=26149&view=diff > ============================================================================== > --- trunk/test_suite/system_tests/relax_disp.py (original) > +++ trunk/test_suite/system_tests/relax_disp.py Sun Oct 5 22:22:35 2014 > @@ -2984,6 +2984,122 @@ > > # Increment the spin index. > spin_index += 1 > + > + > + def test_dx_map_clustered(self): > + """Test making dx_map for residues under clustered calculation. > + > + This uses CPMG data from: > + > + Webb H, Tynan-Connolly BM, Lee GM, Farrell D, O'Meara F, > Soendergaard CR, Teilum K, Hewage C, McIntosh LP, Nielsen JE > + Remeasuring HEWL pK(a) values by NMR spectroscopy: methods, > analysis, accuracy, and implications for theoretical pK(a) calculations. > + (2011), Proteins: Struct, Funct, Bioinf 79(3):685-702, DOI > 10.1002/prot.22886 > + """ > + > + # Define path to data > + prev_data_path = status.install_path + > sep+'test_suite'+sep+'shared_data'+sep+'dispersion'+sep+'HWebb_KTeilum_Proteins_Struct_Funct_Bioinf_2011' > + > + # Read data. > + self.interpreter.results.read(prev_data_path + sep + > 'FT_-_CR72_-_min_-_128_-_free_spins') > + > + # Define temporary folder. > + result_dir = self.tmpdir > + #result_dir = None > + > + # Get residue of interest. > + cur_spin_id = ":%i@%s"%(52, 'N') > + cur_spin_id_str = cur_spin_id .replace('#', '_').replace(':', > '_').replace('@', '_') > + > + # Get the spin container. > + cur_spin = return_spin(cur_spin_id) > + > + # Get the chi2 value > + pre_chi2 = cur_spin.chi2 > + > + # Then do a local minimisation. > + self.interpreter.minimise.calculate() > + > + # Get the chi2 value after calculation. > + calc_chi2 = cur_spin.chi2 > + > + # Assert calculation is equal. > + #self.assertAlmostEqual(pre_chi2, calc_chi2) > + > + # Define dx.map settings. > + dx_inc = 2 > + dx_inc_sides = dx_inc / 2 > + > + dx_params = ['dw', 'pA', 'kex'] > + dx_point_clustered_min = [cur_spin.dw, cur_spin.pA, cur_spin.kex] > + > + print("Params for dx map is") > + print(dx_params) > + print("Point param for dx map is, with chi2=%3.3f"%pre_chi2) > + print(dx_point_clustered_min) > + > + # Define file_names. > + cur_model = 'CR72' > + file_name_map = "%s_map%s" % (cur_model, cur_spin_id_str) > + file_name_point = "%s_point%s" % (cur_model, cur_spin_id_str) > + > + # Step-size of parameter is 10 % > + param_delta = 0.1 > + > + # Determine bounds for lower and upper > + lower = [] > + upper = [] > + for i, param_val in enumerate(dx_point_clustered_min): > + param = dx_params[0] > + step_val = param_delta * param_val > + step_length = step_val * dx_inc_sides > + > + # Calculate value > + low_val = param_val - step_length > + lower.append(low_val) > + > + upp_val = param_val + step_length > + upper.append(upp_val) > + > + print("For param %s, lower=%3.3f, upper=%3.3f, step_value=%3.3f, > steps=%i, centered at=%3.3f"% (param, low_val, upp_val, step_val, dx_inc, > param_val)) > + > + # If the number of increments are 2, there will be 3 point > calculations per parameter. > + # Since we have ordered the lower and upper limits on sides of the > parameter, the middle index should give us the expected global value. > + dx_param_indexes = dx_inc + 1 > + dx_point_index = dx_inc_sides + 1 > + > + # Find the line number. > + line = 1 > + for i in range(1, dx_param_indexes + 1): > + for j in range(1, dx_param_indexes + 1): > + for k in range(1, dx_param_indexes + 1): > + if i == dx_point_index and j == dx_point_index and k == > dx_point_index: > + line_chi2 = line > + # Add to line counter. > + line += 1 > + > + # Then do the map. > + self.interpreter.dx.map(params=dx_params, map_type='Iso3D', > spin_id=cur_spin_id, inc=dx_inc, lower=lower, upper=upper, axis_incs=10, > file_prefix=file_name_map, dir=result_dir, point=dx_point_clustered_min, > point_file=file_name_point) > + > + # Print where to locate values. > + nr_chi2_val = dx_param_indexes**3 > + print("Nr of chi2 calculations are=%i"%nr_chi2_val) > + print("Global chi2=%3.3f, Calc_chi=%3.3f, map_line_chi2=%i" % > (pre_chi2, calc_chi2, line_chi2) ) > + > + ## Check for file creation > + # Set filepaths. > + map_cfg = get_file_path(file_name=file_name_map+".cfg", > dir=result_dir) > + map_net = get_file_path(file_name=file_name_map+".net", > dir=result_dir) > + map_general = get_file_path(file_name=file_name_map+".general", > dir=result_dir) > + > + point_general = get_file_path(file_name=file_name_point+".general", > dir=result_dir) > + point_point = get_file_path(file_name=file_name_point, > dir=result_dir) > + > + # Test the files exists. > + self.assert_(access(map_cfg, F_OK)) > + self.assert_(access(map_net, F_OK)) > + self.assert_(access(map_general, F_OK)) > + self.assert_(access(point_general, F_OK)) > + self.assert_(access(point_point, F_OK)) > > > def test_estimate_r2eff_err(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
