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edits
Changes
User function HTML manual links.
* Added a BMRB section to the end of the model-free chapter of the user manual.
* Massive expansion of the model-free chapter of the user manual including script and GUI tutorials. The model-free chapter now has step-by-step tutorials for both the prompt/script mode and GUI mode for the new automated model-free protocol (the d'Auvergne protocol)[d'Auvergne and Gooley, 2007][d'Auvergne and Gooley, 2008]. This includes a large set of screenshots for the GUI mode.
* Created the User_functions.test_value_set GUI test demonstrating the failure of the [http://www.nmr-relax.com/manual/value.set user function].
* Modified the dauvergne_protocol sample script[d'Auvergne and Gooley, 2007][d'Auvergne and Gooley, 2008] to handle tryptophan indole NE1 data.
* The graphics.fetch_icon() function argument 'format' can now be set to None. This will return the file path without the extension.
* Created the User_functions.test_structure_pdb_read GUI test for checking the sequence editor window. This new user function GUI testing class is to be used for testing out the special GUI elements not invoked within the unit testing. The test_structure_pdb_read() test specifically shows a number of failures of the sequence editor window.
* Modified the operation of the sequence GUI element to have access to the sequence editor window. This is to allow this GUI element to be blasted within the test suite.
* Improvements to the descriptions of the [http://www.nmr-relax.com/manual/structure.read_xyz user function ] arguments.* Improvements to the descriptions of the [http://www.nmr-relax.com/manual/structure.read_pdb user function ] arguments.* Added @HE1 to the spin ID list of the [http://www.nmr-relax.com/manual/structure.load_spins user function]. This is only seen in the GUI.
* Created the new generic_fns.result_files for standardising the handling of results files. This fixes the bug where results files are repetitively added to the list. All of the code touching cdp.result_files now uses this module instead.
* Updated the scripting section of the intro chapter of the user manual for non-technical users.
* Expanded the spin ID list for the [http://www.nmr-relax.com/manual/structure.load_spins user function]. This now includes the spins "@N", "@NE1", "@C", "@H", "@O", "@P", ":A@C2", ":A@C8", ":G@N1",":G@C8", ":C@C5", ":C@C5", ":U@N3", ":U@C5", ":U@C6".
* 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 a directory for screenshots of the spin viewer window operation.
* The NOE auto-analysis GUI test now checks the support for Trp indole N data as well.
* The [http://www.nmr-relax.com/manual/spectrum.read_intensities user function ] now prints out a list of the intensities read in. This is for better user feedback as to what the user function has actually done.
* 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.
* Added a new section called 'From spectra to peak intensities' to the Rx fitting chapter of the manual. This adds a number of recommendations for high quality relaxation rates.
* Added the Viles et al., 2001 reference.
* Small description edit for the [http://www.nmr-relax.com/manual/relax_data.temp_control user function].
* Added a LaTeX label to the NOE chapter of the user manual.
* Added a paragraph to the model-free chapter of the user manual explaining the J(w) equation forms.
* Redesign of how the GPL license is presented to the user. The old prompt.gpl module with the version 2 of the license has been deleted. Now the text form the docs/COPYING file is passed through pydoc.pager for the './relax --licence' and the prompt mode GPL object, and is simply printed to STDOUT for the GUI help system.
* Import clean ups for the N-state model specific module.
* Added the 'unit' argument to the [http://www.nmr-relax.com/manual/dipole_pair.read_dist.html dipole_pair.read_dist ] and [http://www.nmr-relax.com/manual/dipole_pair.set_dist.html dipole_pair.set_dist ] user functions. This is to allow distances in Angstroms to be read into relax and converted to meters.
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* 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 [https://gna.org/bugs/?20173 bug #20173]. The [http://www.nmr-relax.com/manual/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 [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 [http://www.nmr-relax.com/manual/bruker.read user function ] now throws a RelaxError when old PDC files are detected. This is a partial fix for [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 Edward d'Auvergne in a post at https://mail.gna.org/public/relax-devel/2012-09/msg00039.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 [https://gna.org/bugs/?20133 bug #20133] - this was simply a missing import.
* Fix for the [http://www.nmr-relax.com/manual/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 [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 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.
* Another fix for the relax_data.temp_control description.
* Fix for the incomplete [http://www.nmr-relax.com/manual/relax_data.temp_control user function description].* Spell fix for the [http://www.nmr-relax.com/manual/relax_data.temp_calibration user function description].
* Fixes for the referencing in the J(w) mapping chapter of the user manual.
* Fixed some citations in the newly introduced model-free J(w) paragraph.