relax SVN archive

Python 3 fixes for the entire codebase using the 2to3 script.

The command used was:
2to3 -j 4 -w -f xrange .

Merged revisions 24390-24391 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

........
r24390 | bugman | 2014-07-02 09:37:42 +0200 (Wed, 02 Jul 2014) | 17 lines

General Python 3 fixes via the 2to3 script.

The command used was:
2to3 -j 4 -w \
-f buffer \
-f idioms \
-f set_literal \
-f ws_comma \
-x except \
-x import \
-x imports \
-x long \
-x numliterals \
-x xrange \
.
........
r24391 | bugman | 2014-07-02 09:42:01 +0200 (Wed, 02 Jul 2014) | 7 lines

Removed the lib.compat.sorted() function which was providing Python2.3 compatibility.

For a while now, relax has been unable to run on Python versions less than 2.5. Therefore there is
no use for having this replacement function for Python <= 2.3 which was being placed into the
builtins module.
........

Merged revisions 24390-24391 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

........
r24390 | bugman | 2014-07-02 09:37:42 +0200 (Wed, 02 Jul 2014) | 17 lines

General Python 3 fixes via the 2to3 script.

The command used was:
2to3 -j 4 -w \
-f buffer \
-f idioms \
-f set_literal \
-f ws_comma \
-x except \
-x import \
-x imports \
-x long \
-x numliterals \
-x xrange \
.
........
r24391 | bugman | 2014-07-02 09:42:01 +0200 (Wed, 02 Jul 2014) | 7 lines

Removed the lib.compat.sorted() function which was providing Python2.3 compatibility.

For a while now, relax has been unable to run on Python versions less than 2.5. Therefore there is
no use for having this replacement function for Python <= 2.3 which was being placed into the
builtins module.
........

Merged revisions 24387 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

........
r24387 | bugman | 2014-07-02 09:22:04 +0200 (Wed, 02 Jul 2014) | 11 lines

Fix for 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().
........

Merged revisions 24354-24355,24361,24365,24380-24383,24386 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

........
r24354 | bugman | 2014-06-27 18:13:27 +0200 (Fri, 27 Jun 2014) | 16 lines

Numpy version 1.6 or higher is now required to be able to run relax.

This follows from the series of messages:

- http://www.mail-archive.com/relax-devel@.../msg06288.html,
- http://www.mail-archive.com/relax-devel@.../msg06289.html,
- http://www.mail-archive.com/relax-devel@.../msg06327.html,
- http://www.mail-archive.com/relax-devel@.../msg06335.html.

If too many users complain, maybe this change can be reverted later. This minimal numpy version is
needed for many of the speed ups going in the relaxation dispersion and frame order analyses. It is
required for the numpy ufunc out arguments and for the numpy.eigsum() function. These will likely
be used in other analyses in the future for improving the speed of relax, so it might affect users
of other analyses later on.
........
r24355 | bugman | 2014-06-27 18:14:26 +0200 (Fri, 27 Jun 2014) | 3 lines

Updated the numpy minimal dependency in the installation chapter of the manual to version 1.6.
........
r24361 | bugman | 2014-06-30 10:16:57 +0200 (Mon, 30 Jun 2014) | 5 lines

Added better epydoc sectioning to the lib.dispersion.ns_cpmg_2site_expanded module docstring.

This is to better separate the original scripts used to document the code evolution.
........
r24365 | bugman | 2014-06-30 18:10:09 +0200 (Mon, 30 Jun 2014) | 6 lines

Created the very basic structure.com user function for calculating the centre of mass.

This is to simply allow an easy interface to the pipe_control.structure.mass.pipe_centre_of_mass()
function.
........
r24380 | bugman | 2014-07-01 17:04:41 +0200 (Tue, 01 Jul 2014) | 6 lines

Empty lines are now handled by the lib.structure.pdb_write.record() function.

By supplying the remark as None, empty lines can now be created in the REMARK section of a PDB file.
This can be used for nicer formatting.
........
r24381 | bugman | 2014-07-01 17:08:16 +0200 (Tue, 01 Jul 2014) | 8 lines

Expansion of the REMARK section of the PDB file created for the internal structural object.

This is visible when using the structure.write_pdb user function, as well as the many other user
functions which create PDB files. The relax version as well as the file creation date are now
recorded in the PDB file. This extra information should be very useful. Empty lines in the REMARK
section improve the formatting.
........
r24382 | bugman | 2014-07-01 17:16:30 +0200 (Tue, 01 Jul 2014) | 5 lines

Fixes for the Diffusion_tensor system tests due to the recent PDB file changes.

Prior to the comparison of the generated PDB files, all REMARK PDB lines are now stripped out.
........
r24383 | bugman | 2014-07-01 17:30:56 +0200 (Tue, 01 Jul 2014) | 6 lines

Fixes for all system tests failing due to the expanded and improved PDB REMARK section.

The system tests now remove all REMARK records prior to comparing file contents. The special
strip_remarks() system test method has been created to simplify the stripping process.
........
r24386 | bugman | 2014-07-02 09:06:16 +0200 (Wed, 02 Jul 2014) | 10 lines

Fix for the software verification tests.

The recent expansion and improvements of the REMARK records created by the internal structural
object PDB writing method imported the relax version to place this information into the PDB files.
However this breaks the relax library design, as shown by the verification tests. Instead the relax
version information is being taken from the lib.structure.internal.object.RELAX_VERSION variable.
This defaults to None, however the version module now sets this variable directly when it is
imported so that it is always set to the current relax version when running relax.
........

Removed the lib.compat.sorted() function which was providing Python2.3 compatibility.

For a while now, relax has been unable to run on Python versions less than 2.5. Therefore there is
no use for having this replacement function for Python <= 2.3 which was being placed into the
builtins module.

General Python 3 fixes via the 2to3 script.

The command used was:
2to3 -j 4 -w \
-f buffer \
-f idioms \
-f set_literal \
-f ws_comma \
-x except \
-x import \
-x imports \
-x long \
-x numliterals \
-x xrange \
.

Merged revisions 24387 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

........
r24387 | bugman | 2014-07-02 09:22:04 +0200 (Wed, 02 Jul 2014) | 11 lines

Fix for 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().
........

Merged revisions 24386 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

........
r24386 | bugman | 2014-07-02 09:06:16 +0200 (Wed, 02 Jul 2014) | 10 lines

Fix for the software verification tests.

The recent expansion and improvements of the REMARK records created by the internal structural
object PDB writing method imported the relax version to place this information into the PDB files.
However this breaks the relax library design, as shown by the verification tests. Instead the relax
version information is being taken from the lib.structure.internal.object.RELAX_VERSION variable.
This defaults to None, however the version module now sets this variable directly when it is
imported so that it is always set to the current relax version when running relax.
........

Fix for 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().