Author: bugman
Date: Sun Aug 18 15:53:34 2013
New Revision: 20627
URL: http://svn.gna.org/viewcvs/relax?rev=20627&view=rev
Log:
Merged revisions 20582-20584,20587-20588,20590-20596,20620-20621,20623-20625
via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/trunk
................
r20582 | bugman | 2013-08-13 17:58:03 +0200 (Tue, 13 Aug 2013) | 8 lines
Large change to the free file format GUI element for the user functions.
The GUI element used in the user function wizard windows has been modified
to have both a 'default'
form, which is the previous design, and a 'mini' form which is now used for
the user functions.
This mini form only uses 1 row, rather than the default of 6 or 8. It is a
read only text element
with a button that launches the free file format window. The amount of
space saved is huge.
................
r20583 | bugman | 2013-08-13 18:03:42 +0200 (Tue, 13 Aug 2013) | 3 lines
Improved the text for the mini free file format GUI element.
................
r20584 | bugman | 2013-08-13 18:12:04 +0200 (Tue, 13 Aug 2013) | 5 lines
Updated all of the user function GUI window sizes for the 'mini' free file
format GUI element.
This allows much more text of the description to be displayed.
................
r20587 | bugman | 2013-08-14 15:49:57 +0200 (Wed, 14 Aug 2013) | 5 lines
Fixes for the Palmer.test_palmer_omp system test for Modelfree4 version
4.20 gcc.
The gcc and pgf results were somehow switched!
................
r20588 | bugman | 2013-08-14 16:11:51 +0200 (Wed, 14 Aug 2013) | 6 lines
Another fix for the Palmer.test_palmer_omp system test for Modelfree4.
The gcc and pgf compiled i386 Linux binaries of Modelfree4 version 4.20
actually give identical
results. Therefore the checks have been merged.
................
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.
"""
................
r20620 | bugman | 2013-08-16 20:15:58 +0200 (Fri, 16 Aug 2013) | 3 lines
Initialized merge tracking via "svnmerge" with revisions "1-20577" from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/peak_intensities
................
r20621 | bugman | 2013-08-16 20:19:19 +0200 (Fri, 16 Aug 2013) | 15 lines
Reverted r20620 as the checked out trunk copy was not up to date.
The command used was:
svn merge -r20620:r20619 .
.....
r20620 | bugman | 2013-08-16 20:15:58 +0200 (Fri, 16 Aug 2013) | 3 lines
Changed paths:
M /trunk
Initialized merge tracking via "svnmerge" with revisions "1-20577" from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/peak_intensities
.....
................
r20623 | bugman | 2013-08-16 20:20:23 +0200 (Fri, 16 Aug 2013) | 3 lines
Initialized merge tracking via "svnmerge" with revisions "1-20577" from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/peak_intensities
................
r20624 | bugman | 2013-08-16 20:30:10 +0200 (Fri, 16 Aug 2013) | 112 lines
Merged revisions 20579,20598-20619 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/peak_intensities
........
r20579 | bugman | 2013-08-13 11:58:38 +0200 (Tue, 13 Aug 2013) | 6 lines
Modification of the spectrum.read_intensities user function front end.
The heteronuc and proton arguments have been eliminated. Instead the new
dim argument is used to
associate the data with the spins of any dimension in the peak list.
........
r20598 | bugman | 2013-08-15 12:01:52 +0200 (Thu, 15 Aug 2013) | 3 lines
Replaced the 'heteronuc' and 'proton' arguments of the
spectrum.read_intensities user function backend with 'dim'.
........
r20599 | bugman | 2013-08-16 17:15:24 +0200 (Fri, 16 Aug 2013) | 6 lines
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.
........
r20600 | bugman | 2013-08-16 17:18:21 +0200 (Fri, 16 Aug 2013) | 3 lines
Started to shift the spectrum.read_intensities user function backend to
use lib.spectrum.peak_list.
........
r20601 | bugman | 2013-08-16 17:49:45 +0200 (Fri, 16 Aug 2013) | 3 lines
The pipe_control.spectrum.read_intensities() function now works with the
Peak_list object.
........
r20602 | bugman | 2013-08-16 17:50:26 +0200 (Fri, 16 Aug 2013) | 3 lines
The Peak_list object is now used by the
lib.spectrum.peak_list.read_peak_list() function.
........
r20603 | bugman | 2013-08-16 18:28:25 +0200 (Fri, 16 Aug 2013) | 3 lines
Fix for the lib.spectrum.objects.Peak_list object - the Assignment object
was not initialised.
........
r20604 | bugman | 2013-08-16 18:31:04 +0200 (Fri, 16 Aug 2013) | 3 lines
Small fix for how pipe_control.spectrum.read() uses the Peak_list object.
........
r20605 | bugman | 2013-08-16 18:31:40 +0200 (Fri, 16 Aug 2013) | 3 lines
The lib.software.sparky.read_list_intensity() function now operates on
the Peak_list object.
........
r20606 | bugman | 2013-08-16 18:42:46 +0200 (Fri, 16 Aug 2013) | 3 lines
Changed the spectrum.read_intensities dim argument default to w2 and
improved the long description.
........
r20607 | bugman | 2013-08-16 18:44:54 +0200 (Fri, 16 Aug 2013) | 5 lines
Fix for the assignment handling in the
lib.software.sparky.read_peak_list() function.
The first element is usually the indirect dimension or w2.
........
r20608 | bugman | 2013-08-16 18:48:15 +0200 (Fri, 16 Aug 2013) | 5 lines
Fix for many of the Peak_list system tests for the user function argument
changes.
The heteronuc and proton arguments have been replaced by the dim argument.
........
r20609 | bugman | 2013-08-16 18:57:15 +0200 (Fri, 16 Aug 2013) | 3 lines
The lib.software.xeasy.read_list_intensity() function now operates on the
Peak_list object.
........
r20610 | bugman | 2013-08-16 18:58:58 +0200 (Fri, 16 Aug 2013) | 3 lines
Small docstring change for lib.software.sparky.read_list_intensity().
........
r20611 | bugman | 2013-08-16 19:02:03 +0200 (Fri, 16 Aug 2013) | 3 lines
The lib.software.nmrview.read_list_intensity() function now operates on
the Peak_list object.
........
r20612 | bugman | 2013-08-16 19:14:57 +0200 (Fri, 16 Aug 2013) | 3 lines
The lib.spectrum.peak_list.intensity_generic() function now operates on
the Peak_list object.
........
r20613 | bugman | 2013-08-16 19:16:39 +0200 (Fri, 16 Aug 2013) | 5 lines
Fixes for the pipe_control.spectrum.read() function.
An error was referencing a now non-existent variable and the docstring
has been fixed.
........
r20614 | bugman | 2013-08-16 19:17:01 +0200 (Fri, 16 Aug 2013) | 3 lines
Removal of a now unused list variable.
........
r20615 | bugman | 2013-08-16 19:34:45 +0200 (Fri, 16 Aug 2013) | 6 lines
The Peak_list object can now store peak intensity names.
This is for peak lists such as from NMRPipe seriersTab files where the
peak list covers multiple
spectra.
........
r20616 | bugman | 2013-08-16 19:42:56 +0200 (Fri, 16 Aug 2013) | 3 lines
The NMRPipe seriesTab peak lists are now supported through the Peak_list
object.
........
r20617 | bugman | 2013-08-16 19:54:36 +0200 (Fri, 16 Aug 2013) | 3 lines
Unit test fixes for the spectrum.read_intensities user function argument
changes.
........
r20618 | bugman | 2013-08-16 19:56:45 +0200 (Fri, 16 Aug 2013) | 3 lines
Fixes for a few system tests for the spectrum.read_intensities user
function argument changes.
........
r20619 | bugman | 2013-08-16 20:11:07 +0200 (Fri, 16 Aug 2013) | 3 lines
Fixes for a few GUI tests for the spectrum.read_intensities user function
argument changes.
........
................
r20625 | bugman | 2013-08-16 20:30:34 +0200 (Fri, 16 Aug 2013) | 3 lines
Removed merge tracking for "svnmerge" for
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/peak_intensities
................
Added:
branches/relax_disp/lib/spectrum/objects.py
- copied unchanged from r20625, trunk/lib/spectrum/objects.py
Modified:
branches/relax_disp/ (props changed)
branches/relax_disp/devel_scripts/python_seek.py
branches/relax_disp/docs/Mac_framework_build_3way
branches/relax_disp/gui/components/free_file_format.py
branches/relax_disp/gui/uf_objects.py
branches/relax_disp/lib/software/nmrpipe.py
branches/relax_disp/lib/software/nmrview.py
branches/relax_disp/lib/software/sparky.py
branches/relax_disp/lib/software/xeasy.py
branches/relax_disp/lib/spectrum/__init__.py
branches/relax_disp/lib/spectrum/peak_list.py
branches/relax_disp/pipe_control/spectrum.py
branches/relax_disp/test_suite/gui_tests/noe.py
branches/relax_disp/test_suite/gui_tests/rx.py
branches/relax_disp/test_suite/shared_data/frame_order/cam/pseudo_ellipse_free_rotor/frame_order_pseudo_ellipse.py
branches/relax_disp/test_suite/system_tests/palmer.py
branches/relax_disp/test_suite/system_tests/peak_lists.py
branches/relax_disp/test_suite/system_tests/scripts/1UBQ_relax_fit.py
branches/relax_disp/test_suite/system_tests/scripts/noe.py
branches/relax_disp/test_suite/unit_tests/_prompt/test_spectrum.py
branches/relax_disp/user_functions/deselect.py
branches/relax_disp/user_functions/pcs.py
branches/relax_disp/user_functions/relax_data.py
branches/relax_disp/user_functions/select.py
branches/relax_disp/user_functions/sequence.py
branches/relax_disp/user_functions/spectrum.py
branches/relax_disp/user_functions/value.py
[This mail would be too long, it was shortened to contain the URLs only.]
Modified: branches/relax_disp/devel_scripts/python_seek.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/devel_scripts/python_seek.py?rev=20627&r1=20626&r2=20627&view=diff
Modified: branches/relax_disp/docs/Mac_framework_build_3way
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/docs/Mac_framework_build_3way?rev=20627&r1=20626&r2=20627&view=diff
Modified: branches/relax_disp/gui/components/free_file_format.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/gui/components/free_file_format.py?rev=20627&r1=20626&r2=20627&view=diff
Modified: branches/relax_disp/gui/uf_objects.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/gui/uf_objects.py?rev=20627&r1=20626&r2=20627&view=diff
Modified: branches/relax_disp/lib/software/nmrpipe.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/lib/software/nmrpipe.py?rev=20627&r1=20626&r2=20627&view=diff
Modified: branches/relax_disp/lib/software/nmrview.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/lib/software/nmrview.py?rev=20627&r1=20626&r2=20627&view=diff
Modified: branches/relax_disp/lib/software/sparky.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/lib/software/sparky.py?rev=20627&r1=20626&r2=20627&view=diff
Modified: branches/relax_disp/lib/software/xeasy.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/lib/software/xeasy.py?rev=20627&r1=20626&r2=20627&view=diff
Modified: branches/relax_disp/lib/spectrum/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/lib/spectrum/__init__.py?rev=20627&r1=20626&r2=20627&view=diff
Modified: branches/relax_disp/lib/spectrum/peak_list.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/lib/spectrum/peak_list.py?rev=20627&r1=20626&r2=20627&view=diff
Modified: branches/relax_disp/pipe_control/spectrum.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/pipe_control/spectrum.py?rev=20627&r1=20626&r2=20627&view=diff
Modified: branches/relax_disp/test_suite/gui_tests/noe.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/test_suite/gui_tests/noe.py?rev=20627&r1=20626&r2=20627&view=diff
Modified: branches/relax_disp/test_suite/gui_tests/rx.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/test_suite/gui_tests/rx.py?rev=20627&r1=20626&r2=20627&view=diff
Modified:
branches/relax_disp/test_suite/shared_data/frame_order/cam/pseudo_ellipse_free_rotor/frame_order_pseudo_ellipse.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/test_suite/shared_data/frame_order/cam/pseudo_ellipse_free_rotor/frame_order_pseudo_ellipse.py?rev=20627&r1=20626&r2=20627&view=diff
Modified: branches/relax_disp/test_suite/system_tests/palmer.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/test_suite/system_tests/palmer.py?rev=20627&r1=20626&r2=20627&view=diff
Modified: branches/relax_disp/test_suite/system_tests/peak_lists.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/test_suite/system_tests/peak_lists.py?rev=20627&r1=20626&r2=20627&view=diff
Modified:
branches/relax_disp/test_suite/system_tests/scripts/1UBQ_relax_fit.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/test_suite/system_tests/scripts/1UBQ_relax_fit.py?rev=20627&r1=20626&r2=20627&view=diff
Modified: branches/relax_disp/test_suite/system_tests/scripts/noe.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/test_suite/system_tests/scripts/noe.py?rev=20627&r1=20626&r2=20627&view=diff
Modified: branches/relax_disp/test_suite/unit_tests/_prompt/test_spectrum.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/test_suite/unit_tests/_prompt/test_spectrum.py?rev=20627&r1=20626&r2=20627&view=diff
Modified: branches/relax_disp/user_functions/deselect.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/user_functions/deselect.py?rev=20627&r1=20626&r2=20627&view=diff
Modified: branches/relax_disp/user_functions/pcs.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/user_functions/pcs.py?rev=20627&r1=20626&r2=20627&view=diff
Modified: branches/relax_disp/user_functions/relax_data.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/user_functions/relax_data.py?rev=20627&r1=20626&r2=20627&view=diff
Modified: branches/relax_disp/user_functions/select.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/user_functions/select.py?rev=20627&r1=20626&r2=20627&view=diff
Modified: branches/relax_disp/user_functions/sequence.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/user_functions/sequence.py?rev=20627&r1=20626&r2=20627&view=diff
Modified: branches/relax_disp/user_functions/spectrum.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/user_functions/spectrum.py?rev=20627&r1=20626&r2=20627&view=diff
Modified: branches/relax_disp/user_functions/value.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/user_functions/value.py?rev=20627&r1=20626&r2=20627&view=diff
r20627 - in /branches/relax_disp: ./ devel_scripts/ docs/ gui/ gui/components/ lib/software/ lib/spectrum/ pipe_control/ tes...