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Links to Troels' Gna! page.
* The spectrum.peak_intensities is now more robust when reading in a generic formatted file. Firstly there is a check that the intensity column number has been supplied. And then there is a checks that all relevant data could be extracted from each row of the file. This replaces traceback errors with RelaxErrors explaining the problem if the user inputs bad data or forgets the intensity column argument.
* Changed the "Execute analysis" button text back to the original "Execute" text of the old relax GUI.
* Added the 'test.seq' file from [http://gna.org/bugs/?20873 bug report #20873]. This is from [httphttps://gna.org/users/tlinnet Troels E. Linnet]. The bug report and link to http://thread.gmane.org/gmane.science.nmr.relax.user/1452 explains the contents. The file will be used to construct a system test to catch the bug.* Created the Peak_lists.test_bug_20873_peak_lists system test to catch [https://gna.org/bugs/?20873 bug #20873]. This was reported by [httphttps://gna.org/users/tlinnet Troels E. Linnet]. The test has been created by copying the user function calls from the original bug report and slightly modifying them to suite a 'relax_fit' analysis type.
* Fix for the Peak_lists.test_bug_20873_peak_lists system test. The spectrum IDs are now strings.
* Added checks of the peak intensities to the Peak_lists.test_bug_20873_peak_lists system test.
* Spacing fix in an import statement (found using the 2to3 conversion program).
* Added the relax wiki backup script for dumping the MySQL database contents locally. This is from http://article.gmane.org/gmane.science.nmr.relax.devel/4163.
* Added the script from [https://gna.org/users/tlinnet Troels Linnet ] for backing up the relax wiki via FTP. This is from the post http://article.gmane.org/gmane.science.nmr.relax.devel/4168.* Added a link to [https://gna.org/users/tlinnet Troels' ] post to the relax-devel mailing list to the relax wiki FTP backup script. The link is http://article.gmane.org/gmane.science.nmr.relax.devel/4168
* The relax info printout now works in the absence of the bmrblib module.
* Added some Oxygen icons for a boolean GUI input element. The media-record-relax-green.png files are the media-record.png files with the hue set to 117.
* Fixed the extraction of NMRPipe seriestab data in pipe_control.spectrum.read(). Progress [https://gna.org/support/?3043 sr #3043 - support for NMRPipe seriesTab format *.ser].
* Fix for handling reading spin of type heteronuc='NE1' and proton='HE1'. Progress [https://gna.org/support/?3043 sr #3043 - support for NMRPipe seriesTab format *.ser].
* Adding NMR seriesTab data file for a multiple column / multiple spectrum formatted file. This file is from https://gna.org/support/download.php?file_id=18618 attached to the support request https://gna.org/support/?3043 by [https://gna.org/users/tlinnet Troels Linnet]. This is if the command "seriesTab -in ../../peaks.dat -out seriesTab_multi.ser -list nmrfiles.list -sum -dx 1 -dy 1" where nmrfiles.list contains file reference to 10 .ft2 files.
* Fix for unit test of nmrpipe. Progress [https://gna.org/support/?3043 sr #3043 - support for NMRPipe seriesTab format *.ser].
* Replacing a pointer-reference structure to an empty creation of list of lists. Progress [https://gna.org/support/?3043 sr #3043 - support for NMRPipe seriesTab format *.ser].
* Big bug fix for the [http://www.nmr-relax.com/manual/value_copy.html value.copy user function] - it is now functional again.
* Bug fix for the [http://www.nmr-relax.com/manual/value_copy.html value.copy user function]. The user function can now handle parameter errors, and the values are set in the correct data pipe.
* Bug fix for an incorrect print statement in the N_state_model.test_paramag_centre_fit system test. This is in the script, and was uncovered using WinPython by [httphttps://gna.org/users/tlinnet Troels E. Linnet] via the relax system tests at http://thread.gmane.org/gmane.science.nmr.relax.devel/3863. The Python bug was detailed at http://thread.gmane.org/gmane.science.nmr.relax.devel/3863/focus=3867.
* Fix for the package checking as part of the unit tests. This was identified from the [https://gna.org/bugs/?20820 bug report #20820] submitted by [https://gna.org/users/tlinnet Troels E. Linnet]. The problem was that on some systems, the full path is required for checking the presence of the directories which are the sub-packages of the main package being checked. The result was that checking for the package in the __all__ list was skipped. Note that this change does not fix the bug reported.
* Fixes for the Jw.test_calc system test - the spectral density value comparison is now significant.
* Fix for [https://gna.org/bugs/?20820 bug #20820]. Solution found - 'software' was not mentioned in __init__.py, and failed at import.
* Partial fix for [https://gna.org/bugs/?20873 bug #20873]. The spectrum_id argument for the [http://www.nmr-relax.com/manual/spectrum_read_intensities.html spectrum.read_intensities user function] can now be both a string and a list of strings.
* Fix for [http://gna.org/bugs/?20873 bug #20873]. This was reported by [httphttps://gna.org/users/tlinnet Troels E. Linnet]. The ability to load multiple peak intensities from a single generic formatted file has been correctly implemented. This involves added checks to make sure that the user supplies reasonable arguments and to then loop over the intensity column argument.
* Python 3 fixes via the 2to3 program.
* Bug fix for the [http://www.nmr-relax.com/manual/value_write.html value.write user function] for list or dictionary type data. This is for the case where the variable of one spin is set to None rather than a list or dictionary type.
* Fixes for the unit tests of the lib.selection module. The contains_*() methods now should be used. And the test_Selection_ful_spin_id() unit test has been completely deleted as this way of checking the selection object is no longer valid.
* Fix for [https://gna.org/bugs/?20910 bug #20910 - the broken grace.write GUI interface]. The problem was that the Value GUI input element was not detecting list-type data returned by the wiz_combo_iter method.
* Fix for [ (https://gna.org/bugs/?20915 bug #2091 - Failure of Grace opening in MS Windows]. [https://gna.org/users/tlinnet Troels E. Linnet ] provided this patch, and was discovered during work on a Windows 7 system: telinnet aaattt bio_dot_ku_dot_dk. This is a small fix for a wrong call to "raise RelaxMissingBinaryError(binary)", when issuing an external call to xmgrace. The "path_sep" would be equal = [\/], and the RE search would not find(True) the full path specified for the xmgrace file. This is now shifted to python: os.path.isfile http://docs.python.org/2/library/os.path.html. Another fix, is that as a standard the command "xmgrace" is provided. This will work fine through windows cmd, but the true name for program in windows is "xmgrace.exe", and so an additional search for +".exe" is also performed.
* Fix for the N_state_model.test_absolute_T system test for Mac OS X. The precision of the check needed to be decreased.
* Fix for [https://gna.org/bugs/?20918 bug #20918, the hanging of the data pipe editor]. This was reported by [https://gna.org/users/tlinnet Troels Linnet] and is an MS Windows only problem. The problem is in the wxMSW part of wxPython, and it may be fixed in newer wxPython versions. The issue is nevertheless now avoided by calling the GUI user function store objects with the arguments wx_wizard_sync=True and wx_wizard_modal=True. This appears to solve the problem.
