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Changes
Formatting of all symbols/parameters.
* Created the Ct.test_bug_20674_ct_analysis_failure system test for catching bug #20674. This was reported by Mengjun Xue <mengjun dott xue att mailbox dott tu-berlin dot de> at https://gna.org/bugs/?20674.
* Decreased the number of Monte Carlo simulations in the Ct.test_bug_20674_ct_analysis_failure system test.
* Created the Jw.bug_20674_jw_mapping system test. This is a modification of the Ct.test_bug_20674_ct_analysis_failure system test for catching [https://gna.org/bugs/?20674 bug #20674]. The test script was duplicated and the small modifications made to convert it into the J(wω) mapping analysis. This now reveals the same bug but for the J(wω) mapping analysis.
* System test speed ups - decreased the number of Monte Carlo simulations in many tests. Running 500 simulation optimisations in a system test is a total waste of time!
* Converted the bug_20674_jw_mapping.py system test script to use the self._execute_uf() interface. This allows the script to be used in the GUI.
* Created the Mf.test_bug_20683_bdc_inf_values system test. This is for catching [https://gna.org/bugs/?20683 bug #20683] reported by Mengjun Xue <mengjun dott xue att mailbox dott tu-berlin dot de>. The problem is due to infinite and NaN values in the Bruker Dynamics Centre file.
* Ported the changes of r19302 to the consistency testing and J(wω) mapping analyses. This is the code for checking for infinite relaxation rates imported from Bruker Dynamics Centre files.
* Missing imports of the lib.float.isInf() function.
* Modified the bug_20674_ct_analysis_failure.py system test script to use self._execute_uf(). This allows the test to operate as a GUI test, which was failing.
* Converted all of the relaxation curve-fitting chapter of the user manual to the lstlisting environment. This is for all parts of the script UI section of the chapter.
* Converted all of the model-free chapter of the user manual to the lstlisting environment. This is for all parts of the script UI section of the chapter.
* Converted all of the J(wω) mapping chapter of the user manual to the lstlisting environment. This is for all parts of the script UI section of the chapter.
* Converted all of the Consistency testing chapter of the user manual to the lstlisting environment. This is for all parts of the script UI section of the chapter.
* Created a new listings language definition for relax for the user manual. This is for better highlighting of relax scripts and code in the relax manual.
* Fix for [https://gna.org/bugs/?20674 bug #20674 - the failure of the consistency testing analysis]. This was reported by Mengjun Xue <mengjun dott xue att mailbox dott tu-berlin dot de>. The problem was that the first residue did not have a single proton 'H' in the PDB file, and therefore the dipolar relaxation interaction was not set up. The overfit_deselect() method of the consistency testing specific API was not checking for this. The method is now much more like that of the model-free specific analysis.
* Fix for the model-free analysis specific overfit_deselect() method. The tests for the presence of dipolar relaxation was not correct and was non-functional.
* Fix for the J(wω) mapping analysis matching that for the consistency testing. The overfit_deselect() method is now identical to that of the consistency testing analysis.
* Fix for [https://gna.org/bugs/?20683 bug #20683 - the infinite and NaN data in Bruker DC files]. This was reported by Mengjun Xue <mengjun dott xue att mailbox dott tu-berlin dot de>. The model-free specific overfit_deselect() method now checks for infinite relaxation data and deselects the spin if such data is encountered.
* Fix for the analysis specific API common method _data_init_spin(). The data types are now correctly checked - they are not strings but types.
* Fixes for the value.write user function for simple parameter values of None. This is a recently introduced bug which causes a complete failure of the user function is the parameter for any spin is None.
* Fix for [https://gna.org/bugs/?20888 bug #20888, the autoscaling of Grace graphs]. This solution was mentioned in the post at http://thread.gmane.org/gmane.science.nmr.relax.devel/3920/focus=3930. Instead of using minimum and maximum values for the axes in the Grace graphs produced by the lib.software.grace module, which was the old solution for having the graphs scaled to reasonable values, instead the '@autoscale' command is appended to the end of all graphs. This is performed by the write_xy_data() function.
* Bug fix for the running of the test suite in the relax GUI. The fix of r19727 was extended to apply to the GUI as well. Too many arguments were being sent into TextTestRunner Python class on certain Python versions (3.1 and <= ≤ 2.6).
* Big bug fix - the relax execution lock now truly supports nesting. This fixes [https://gna.org/bugs/?20891 bug #20891] reported by [https://gna.org/users/tlinnet Troels Linnet]. Scripts can now be executed from the GUI. Note that this is a very dangerous fix.
* Completed the fix for [https://gna.org/bugs/?20889 bug #20889]. The problem was that the spectrum.read_intensities user function was incorrectly updating the cdp.spectrum_ids list when the spectrum_id argument is set to a list. The list of IDs was being set as a single element of cdp.spectrum_ids, causing problems with the GUI when updating the ComboBox choices and then subsequent setting of the spectrum IDs. This bug and fix is independent of the relax_disp branch, despite being uncovered there and being caught by the Relax_disp.test_bug_20889_multi_col_peak_list GUI test in that branch.