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* Changed the RelaxError for missing relaxation times in the relaxation curve-fitting analyses.
* Modified the test_bug_20152_read_dc_file() GUI test to catch the RelaxError. This error is because of the old PDC format.
* Created the test_bug_20152_read_dc_file() GUI test for catching bug #20152 ([https://gna.org/bugs/?20152)bug #20152]. This includes truncated data taken from the bug report (with data for only the first 3 residues).* Set up the Bruker Dynamics Center system tests as GUI tests. This is in preparation for catching bug #20152 ([https://gna.org/bugs/?20152)bug #20152].
* Re-added Dominique Marion's solvent suppression to the NMRPipe script in the curve-fitting chapter.
* A few small edits of the relaxation curve-fitting chapter. This is to reinforce the exact time of the relaxation time period.
* Created the GUI wizard _apply() method for executing the current page's _apply() method. This is for the GUI tests to simulate a click on the 'Apply' button.
* Removed a debugging print out.
* Modified the NOE system test to catch bug #20120 ([https://gna.org/bugs/?20120)bug #20120].
* Lots of editing of the NOE chapter of the user manual.
* Significant update of the NOE chapter of the user manual. The sample script used in this chapter was incredibly out of date.
* Modified the NOE system test to test the usage of Trp indole <sup>15</sup>N data. This is to catch bug #20119 ([https://gna.org/bugs/?20119)bug #20119].* Added some Trp peak data (backbone and indole N) to the Sparky steady-state NOE peak lists. This is in preparation for the modification of the NOE system test to catch bug #20119([https://gna.org/bugs/?20119)bug #20119].
* Modified the NOE sample script to include Trp indole NH data.
* Added a step-by-step tutorial for the GUI NOE auto-analysis to the user manual. This includes 22 screenshots of all the steps.
<section begin=bugfixes/>
* Fix for bug #20189 ([https://gna.org/bugs/?20189)bug #20189]. The Sequence GUI element can not handle values of None.
* The citations chapter is now included in the HTML version of the user manual. For some reason, a file named 'cite.tex' cannot be handled by latex2html.
* The latex2html compilation of the user manual now ignores the \bibitem{} commands. This is needed for the HTML version of the user manual.
* Removed the text '.eps.gz' from all of the LaTeX included graphics in the user manual. This allows latex2html to select and use the PNG images instead, producing much better graphics for the online manual (http://www.nmr-relax.com/manual/index.html).
* Fix for the graphics.fetch_icon() function for when no file format is specified.
* Elimination of all duplicated chapter, section and subsection titles in the user manual. This fixes bug #20185 ([https://gna.org/bugs/?20185)bug #20185].
* The HTML files for the user manual now have longer names - this is needed for removing the duplicates.
* Fix for the duplicate title finding script - the LaTeX and HTML mode alternatives are no longer mixed up.
* Fix for bug #20177 ([https://gna.org/bugs/?20177)bug #20177]. This was simply a lower precision OS/Python/numpy combination causing a test suite failure - there are no practical effects and only the precision of the system/GUI test has been lowered.
* Another bug fix for the sequence GUI editor window. This bug was being triggered by the User_functions.test_structure_pdb_read() GUI test which now passes.
* Small fix for the User_functions.test_structure_pdb_read() GUI test.
* Fix for bug #20184 ([https://gna.org/bugs/?20184)bug #20184]. The behaviour of the gui.string_conv.gui_to_int() and related functions has changed in the last few months and the Sequence_window() GUI element has not changed to match. This has been fixed and the User_functions.test_structure_pdb_read() GUI test now passes.
* Fixes for the User_functions.test_structure_pdb_read() GUI test.
* Fix for bug #20183 ([https://gna.org/bugs/?20183) bug #20183 - the failure of the sequence editor window]. The problem was that fields which could be either single values or lists (or tuples) of values were not properly handled.* Fix for bug #20182 ([https://gna.org/bugs/?20182) bug #20182 - the sequence element window ordering issue]. The sequence element window now has the parent wx.Window element set. This prevents the main relax window from being set as the parent and hence coming to the front after the sequence element window is launched from a user function window.* Fix for bug #20181 ([https://gna.org/bugs/?20181) bug #20181 - the GUI sequence editor window TypeError problem].
* Window ordering bug fix for the user function windows launched from the spin viewer window. The spin viewer window no longer hides behind the main relax window after the launch of the user function.
* Bug fix for the repetition of Monte Carlo simulations in the relaxation curve-fitting analyses. This is in the specific analysis API, so will allow all analysis types to repeat Monte Carlo simulations for error analysis.
* MS Windows fix - the NOE system and GUI tests are now less strict in checking the errors.
* Proper bug fix for storing the execution status of wizard and user function pages. This allows the test suite to pass again. The execution status is now properly returned from the wizard pages run synchronously (and always set to True for asynchronous calls).
* Fix for bug #20173 ([https://gna.org/bugs/?20173)bug #20173]. The palmer.create user function should have been checking that the diffusion tensor had been initialised. This is now being performed.* Bug fix for the execution of wizard pages - the execution status is now observed. This fixes bug #20152 ([https://gna.org/bugs/?20152)bug #20152]. The problem was that the execution status was being lost in the protected_exec() function. However as relax errors are caught in the GUI interpreter anyway and the status is returned normally, the protected_exec() wrapper was removed.
* Bug fix for the creation of the user function GUI pages - the (a)synchronous arg is now observed. This argument was being ignored, which in some wizards was causing user function calls to be asynchronous. This can result in racing related crashes.
* The bruker.read user function now throws a RelaxError when old PDC files are detected. This is a partial fix for bug #20152 ([https://gna.org/bugs/?20152)bug #20152].
* Fixed the newlines in the sample script in the consistency testing chapter.
* Fixed the bounding box for the consistency testing figure and also fixed some Latex unfriendly code. Problems were spotted by [https://gna.org/users/bugman Edward d'Auvergne] in a post at https://mail.gna.org/public/relax-devel/2012-09/msg00039.html.
* Fixed a bibliography entry label problem. This was spotted by [https://gna.org/users/bugman Edward d'Auvergne] in a post at:https://mail.gna.org/public/relax-devel/2012-09/msg00040.html.
* Bug fix for the creation of 2D graphs via grace.write for when many data sets exist. The algorithm for setting the Grace symbol number to be between 1 and 10 was broken!
* Fix for bug #20133 ([https://gna.org/bugs/?20133) bug #20133] - this was simply a missing import.
* Fix for the spin.create user function documentation - the prompt examples were wrong.
* Bug fix for the generic_fns.grace.get_data() function. This was just recently introduced and was triggered by the Relax_fit.test_bug_12670_12679 system test.
* Fix for bug #20120 ([https://gna.org/bugs/?20120)bug #20120, the bad Grace plots with multiple spin types]. The grace data assembly function was not setting the correct index for when a spin type changes to a preexisting type.
* Bug fix for the reading of Sparky peak lists. Spin names with numbers at the end were not being correctly identified. This fix allows Trp indole NE1-HE1 data to be loaded.
* Bug fix for the loading of peak intensities via spectrum.read_intensities. The user function could not be applied twice, preventing the loading of data from different spin systems such as Trp indole NH data.