relax SVN archive

Large improvement for the GUI test tearDown() clean up method, fixing the tests on wxPython 2.8.

The user function window destruction has been shifted into a new clean_up_windows() method which is
executed via wx.CallAfter() to avoid racing conditions. In addition, the spin viewer window is
destroyed between tests.

The spin viewer window change allows the GUI tests to pass on wxPython 2.8 again. This also allows
the GUI tests to progress much further on Mac OS X systems before they crash again for some other
reason. This could simply be hiding a problem in the spin viewer window. However it is likely to
be a racing problem only triggered by the super fast speed of the GUI tests and a normal user would
never be able to operate the GUI on the millisecond timescale and hence may never see it.

Big bug fix for the GUI tests on MS Windows systems.

On MS Windows systems, the GUI tests were unable to complete without crashing. This is because each
GUI element requires one 'User object', and MS Windows has a maximum limit of 10,000 of these
objects. The GUI tests were taking more than 10,000 and then Windows would say - relax, you die
now.

The solution is that after each GUI test, all user function windows are destroyed. The user
function page is a wx.Panel object, so this requires a Destroy() call. But the window is a Uf_page
instance which inherits from Wiz_page which inherits from wx.Dialog. Calling Destroy() on MS
Windows and Linux works fine, but is fatal on Mac OS X systems. So the solution is to call Close()
instead.

Updates for many of the Diffusion_tensor system tests.

This is due to the changed directory names in test_suite/shared_data/diffusion_tensor/. The
ds.diff_dir variable has been introduced to point to the correct data directory.

More fixes for the Structure.test_create_diff_tensor_pdb_oblate system test.

The initial Diso value is now set to the real final Diso, and the PDB file contents have been
updated for the fixed oblate spheroidal diffusion relaxation data.

Fix for the oblate spheroid diffusion relaxation data.

The diffusion parameters are constrained as Dx <= Dy <= Dz.

Copyright update.

The Structure.test_create_diff_tensor_pdb_oblate now uses oblate diffusion relaxation data.

This fixes bug #23232 (https://gna.org/bugs/?23232), the failure of this system test on Mac OS X.
The problem was that the system test was previously using relaxation data for prolate spheroidal
diffusion and fitting an oblate tensor to that data. This caused the solution to be slightly
different on different CPUs, operating systems, Python versions, etc. and hence the PDB file
representation of the diffusion would be slightly different.

Creation of oblate spheroid diffusion relaxation data.

This will be used in the Structure.test_create_diff_tensor_pdb_oblate system test.

Test data directory renaming.

The test_suite/shared_data/diffusion_tensor/spheroid directory has been renamed to spheroid_prolate.
This is in preparation for creating oblate spheroid diffusion relaxation data.

Fix for the internal structural object atomic coordinate assembly function.

This is the pipe_control.structure.main.assemble_structural_coordinates() function. The case of no
sequence alignment being required as only models are being handled is now functional. The strings
and gaps data structures passed into the lib.sequence_alignment.msa.msa_residue_skipping() function
for generating the residue skipping data structure are now set to the one letter codes and an empty
structure of zeros respectively.