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Tracker link improvements.
* Modified the Sequence GUI input element used for the user function list arguments. The first column is now of fixed with when titles are supplied. Previously when supplying titles, the width would be tiny and no text would be visible.
* Added titles for all 3D coordinate user function arguments. This is for the Sequence GUI input element, and affects the frame_order.average_position, n_state_model.CoM and paramag.centre user functions.
* The compilation of the C modules now respects the user defined environment. This is the patch from Justin (https://gna.org/users/jlec) attached to bug #22145 ([https://gna.org/bugs/?22145)bug #22145]. It has been modified to include a comment and remove a double empty line.
* Bug fix for the compilation of the C modules now respects the user defined environment. The problem was that on Mac OS X (as well as other systems), that these environmental variables were not defined and hence the scons commands would all fail with a KeyError and traceback. Now the keys in the os.environ dictionary are being searched for before they are set.
* Fix for the wxPython link in the installation chapter of the manual. This was pointing to the scipy website for some reason.
* Changed the Python readline link for MS Windows in the installation chapter of the manual. This now points to https://pypi.python.org/pypi/pyreadline as the iPython link is broken.
* Implemented system test Relax_disp.test_bug_22146_unpacking_r2a_r2b_cluster. This is to catch the wrong unpacking of R2A and R2B when performing a clustered full dispersion model analysis. Bug #22146: ([https://gna.org/bugs/?22146) Bug #22146] Unpacking of R2A and R2B is performed wrong for clustered "full" dispersion models.* Extended system test Relax_disp.test_bug_22146_unpacking_r2a_r2b_cluster for B14 full model. This is to catch the wrong unpacking of R2A and R2B when performing a clustered full dispersion model analysis. Bug #22146: ([https://gna.org/bugs/?22146) Bug #22146] Unpacking of R2A and R2B is performed wrong for clustered "full" dispersion models.* Extended system test Relax_disp.test_bug_22146_unpacking_r2a_r2b_cluster for NS CPMG 2SITE 3D full model. This is to catch the wrong unpacking of R2A and R2B when performing a clustered full dispersion model analysis. Bug #22146: ([https://gna.org/bugs/?22146) Bug #22146] Unpacking of R2A and R2B is performed wrong for clustered "full" dispersion models.* Extended system test Relax_disp.test_bug_22146_unpacking_r2a_r2b_cluster for NS CPMG 2SITE STAR full model. This is to catch the wrong unpacking of R2A and R2B when performing a clustered full dispersion model analysis. Bug #22146: ([https://gna.org/bugs/?22146) Bug #22146] Unpacking of R2A and R2B is performed wrong for clustered "full" dispersion models.* Added synthetic data generator script which created the data to test against. Bug #22146: ([https://gna.org/bugs/?22146) Bug #22146] Unpacking of R2A and R2B is performed wrong for clustered "full" dispersion models.* Split system test Relax_disp.test_bug_22146_unpacking_r2a_r2b_cluster up in different tests. A setup function which is: setup_bug_22146_unpacking_r2a_r2b_cluster(self, folder=None, model_analyse=None): And then the tests: test_bug_22146_unpacking_r2a_r2b_cluster_B14 test_bug_22146_unpacking_r2a_r2b_cluster_CR72 test_bug_22146_unpacking_r2a_r2b_cluster_NS_3D test_bug_22146_unpacking_r2a_r2b_cluster_NS_STAR. Bug #22146: ([https://gna.org/bugs/?22146) Bug #22146] Unpacking of R2A and R2B is performed wrong for clustered "full" dispersion models.* Modified profiling script to get closer to the implementation in relax. An additional test function is setup to figure out how to reshape the numpy arrays in the target function. Bug #22146: ([https://gna.org/bugs/?22146) Bug #22146] Unpacking of R2A and R2B is performed wrong for clustered "full" dispersion models.* Updated profiling text for CR72 model. Now it is tested for 3 fields. This is related to: Task #7807 ([https://gna.org/task/index.php?7807)Task #7807]: Speed-up of dispersion models for Clustered analysis.
* Added searching for environment variable PYTHON_INCLUDE_DIR if Python.h is not found in standard Python library. This can be very handsome, if one has a Python virtual environment for multiple users. This relates to the wiki page: http://wiki.nmr-relax.com/Epd_canopy.
* The lib.compat.norm() replacement function for numpy.linalg.norm() now handles no axis argument. This is to allow the function to be used in all cases where numpy.linalg.norm() is used, while providing compatibility with the axis argument and all numpy versions.
== Bugfixes ==
* Fix for the wrong unpacking of R20A and R20B in model CR72 full. Bug #22146: ([https://gna.org/bugs/?22146) Bug #22146] Unpacking of R2A and R2B is performed wrong for clustered "full" dispersion models.* Fix for the wrong unpacking of R20A and R20B in model B14 full. Bug #22146: ([https://gna.org/bugs/?22146) Bug #22146] Unpacking of R2A and R2B is performed wrong for clustered "full" dispersion models.* Fix for the wrong unpacking of R20A and R20B in model NS CPMG 2SITE 3D full model. Bug #22146: ([https://gna.org/bugs/?22146) Bug #22146] Unpacking of R2A and R2B is performed wrong for clustered "full" dispersion models.* Fix for the wrong unpacking of R20A and R20B in model NS CPMG 2SITE STAR full model. Bug #22146: ([https://gna.org/bugs/?22146) Bug #22146] Unpacking of R2A and R2B is performed wrong for clustered "full" dispersion models.
* Bug fix for the lib.io.file_root() function for multiple file extensions. The function will now strip off all file extensions.
* Fix for bug #22210 ([https://gna.org/bugs/?22210)bug #22210], the failure of the 'LM63 3-site' dispersion model. The problem is described in the bug report - the multiplication in the tanh() function is a mistake, it must be a division.
* Fix for the Library.test_library_independence verification test on MS Windows. The tearDown() method now uses the error handling test_suite.clean_up.deletion() function to remove the copied version of the relax library.
* Fixed the packing out of parameter tex for global analysis in model IT99. Bug #22220 ([https://gna.org/bugs/index.php?22220)Bug #22220]: Unpacking of parameters for global analysis in model IT99, is performed wrong.* Fix for [https://gna.org/bugs/?22257 bug #22257], the freezing of the GUI after using the free file format window on Mac OS X. This is reported at https://gna.org/bugs/?22257. This is a recurring problem in Mac OS X as it cannot be tested in the relax test suite. The problem is with wxPython. The modal dialogs, such as the free file format window, cannot be destroyed on Mac OS X using wx.Dialog.Destroy() - this kills wxPython and hence kills relax. The problem does not exist on any other operating system. To fix this, all wx.Dialog.Destroy() calls have been replaced with wx.Dialog.Close().
