relax SVN archive

Fix for the lib.spectrum.objects.Peak_list object - the Assignment object was not initialised.

The Peak_list object is now used by the lib.spectrum.peak_list.read_peak_list() function.

The pipe_control.spectrum.read_intensities() function now works with the Peak_list object.

Started to shift the spectrum.read_intensities user function backend to use lib.spectrum.peak_list.

Created the new lib.spectrum.objects module.

This will hold temporary data structures for representing peak lists and other spectral data. The
module currently contains the Peak_list class which is used to hold peak list data.

Replaced the 'heteronuc' and 'proton' arguments of the spectrum.read_intensities user function backend with 'dim'.

Merged revisions 20590-20596 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

........
r20590 | bugman | 2013-08-14 16:48:43 +0200 (Wed, 14 Aug 2013) | 8 lines

Reverted r20587 and r20588 as these were rubbish!

The command used was:
svn merge -rHEAD:r20586 .

There are gcc verses pdf Modelfree4 binary results for version 4.20.
........
r20591 | bugman | 2013-08-14 18:19:38 +0200 (Wed, 14 Aug 2013) | 6 lines

Proper fix for the Palmer.test_palmer_omp for the different Modelfree4 binaries.

The gcc and pdf binaries are now properly detected and the slightly different results are now
correctly checked for.
........
r20592 | bugman | 2013-08-14 18:53:13 +0200 (Wed, 14 Aug 2013) | 3 lines

Updated the Mac Framework setup document to help with scipy compilation problems.
........
r20593 | bugman | 2013-08-14 18:54:19 +0200 (Wed, 14 Aug 2013) | 5 lines

Improved the Python seeking and module version print out script for symlinks.

This should now be much more capable of finding all Python versions on a system.
........
r20594 | bugman | 2013-08-14 19:52:39 +0200 (Wed, 14 Aug 2013) | 8 lines

Added support for the Mac OS X Modelfree4 binary results to the Palmer.* system tests.

The Mac OS X Modelfree 4.20 binary produces different results than the Linux binaries, mainly due to
a compilation problem. In the Linux binaries, the results are written out to 4 decimal places. In
the Mac binaries, the results are instead written out to 4 significant figures. Therefore the
number of decimal places are much less than the Linux results.
........
r20595 | bugman | 2013-08-14 19:55:57 +0200 (Wed, 14 Aug 2013) | 5 lines

Fix for the Palmer.test_palmer system test for older Python versions.

This is a problem introduced in the previous commit (r20594).
........
r20596 | bugman | 2013-08-15 09:10:12 +0200 (Thu, 15 Aug 2013) | 24 lines

Syntax error fix for one of the unused scripts in the relax test suite shared data directories.

This problem was encountered by Jack Howarth <howarth att bromo dott med dott uc dott edu> and
communicated in a private message. The issue was found by fink. This script is never used and will
never be used again - it is only there for reference. How a syntax error was introduced is a
mystery. For reference, the full message is:

"""
While preparing fink packaging for the new relax 3.0.0 release, I noticed an error
in the python scripts. When installing relax-py27-3.0.0, I get the following error as
the the frame_order_pseudo_ellipse.py python script is compiled. What is the correct
syntax for that particular call to pymol.command?

Setting up relax-py27 (3.0.0-1) ...
Compiling /sw/lib/relax-py27/test_suite/shared_data/frame_order/cam/pseudo_ellipse_free_rotor/frame_order_pseudo_ellipse.py ...
File "/sw/lib/relax-py27/test_suite/shared_data/frame_order/cam/pseudo_ellipse_free_rotor/frame_order_pseudo_ellipse.py", line 154
pymol.command('show spheres'_pseudo_ellipse)
^
SyntaxError: invalid syntax

Thanks in advance for any clarification.
"""
........

Syntax error fix for one of the unused scripts in the relax test suite shared data directories.

This problem was encountered by Jack Howarth <howarth att bromo dott med dott uc dott edu> and
communicated in a private message. The issue was found by fink. This script is never used and will
never be used again - it is only there for reference. How a syntax error was introduced is a
mystery. For reference, the full message is:

"""
While preparing fink packaging for the new relax 3.0.0 release, I noticed an error
in the python scripts. When installing relax-py27-3.0.0, I get the following error as
the the frame_order_pseudo_ellipse.py python script is compiled. What is the correct
syntax for that particular call to pymol.command?

Setting up relax-py27 (3.0.0-1) ...
Compiling /sw/lib/relax-py27/test_suite/shared_data/frame_order/cam/pseudo_ellipse_free_rotor/frame_order_pseudo_ellipse.py ...
File "/sw/lib/relax-py27/test_suite/shared_data/frame_order/cam/pseudo_ellipse_free_rotor/frame_order_pseudo_ellipse.py", line 154
pymol.command('show spheres'_pseudo_ellipse)
^
SyntaxError: invalid syntax

Thanks in advance for any clarification.
"""

Fix for the Palmer.test_palmer system test for older Python versions.

This is a problem introduced in the previous commit (r20594).

Added support for the Mac OS X Modelfree4 binary results to the Palmer.* system tests.

The Mac OS X Modelfree 4.20 binary produces different results than the Linux binaries, mainly due to
a compilation problem. In the Linux binaries, the results are written out to 4 decimal places. In
the Mac binaries, the results are instead written out to 4 significant figures. Therefore the
number of decimal places are much less than the Linux results.