Author: bugman
Date: Fri Sep 25 14:01:36 2015
New Revision: 27867
URL: http://svn.gna.org/viewcvs/relax?rev=27867&view=rev
Log:
Merged revisions 27800-27805,27807,27816,27818-27820,27822,27827 via svnmerge
from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/trunk
........
r27800 | bugman | 2015-03-10 10:05:25 +0100 (Tue, 10 Mar 2015) | 7 lines
Fix for the lib.sequence.check_sequence checking object.
Although rarely used, the check for the spin number was incorrect and half
of the checks were
instead for the residue number. This is a classic copy and paste error
where the residue name and
number checks were copied but not completely converted to spin name and
numbers.
........
r27801 | bugman | 2015-03-10 10:13:33 +0100 (Tue, 10 Mar 2015) | 5 lines
Added the raise_flag argument to the lib.sequence.read_spin_data() function.
This is to allow the missing data RelaxError to be deactivated.
........
r27802 | bugman | 2015-03-10 10:15:35 +0100 (Tue, 10 Mar 2015) | 7 lines
Modified the spectrum.read_intensities user function backend to be more
robust.
This affects the generic formatted peak lists, via the
lib.spectrum.peak_list.intensity_generic()
function. The peak list reading will now continue reading the file after
corrupted lines have been
encountered.
........
r27803 | bugman | 2015-03-10 18:00:53 +0100 (Tue, 10 Mar 2015) | 7 lines
Python 3 improvement for the rdc.corr_plot and pcs.corr_plot user functions.
The world view is now set in floating point numbers. In Python 2, the
math.ceil() and math.floor()
functions return floats, whereas in Python 3 these functions return
integers. The behaviour is now
consistent in both Python versions, fixing a few system tests.
........
r27804 | bugman | 2015-03-10 18:36:55 +0100 (Tue, 10 Mar 2015) | 7 lines
Improvements for the pcs.structural_noise user function.
The check for the presence of PCS data for points to skip now includes
checking for PCS values of
None. And the output Grace file now also includes the spin ID string as a
string or comment value
which can be displayed in the plot when desired.
........
r27805 | bugman | 2015-03-10 18:58:41 +0100 (Tue, 10 Mar 2015) | 9 lines
Modified the internal formatting of the data section of the Grace 2D graph
files.
This affects the lib.plotting.grace.write_xy_data() function. The
formatting is now more
consistent, with the X value now set to a fixed number of decimal places,
and hence will no longer
change between Python 2 and 3. The data is now all right justified as
well, for easier reading.
All affected system tests have been updated for the new format.
........
r27807 | bugman | 2015-03-13 11:39:16 +0100 (Fri, 13 Mar 2015) | 3 lines
Epydoc documentation fix for the lib.structure.pdb_write_handle_atom_name()
function.
........
r27816 | bugman | 2015-03-13 15:42:37 +0100 (Fri, 13 Mar 2015) | 6 lines
Backported the relax 3.3.7 CHANGES file changes to trunk.
The command used was:
svn merge -r27810:r27811 svn+ssh://bugman@xxxxxxxxxxx/svn/relax/tags/3.3.7 .
........
r27818 | bugman | 2015-03-13 17:55:09 +0100 (Fri, 13 Mar 2015) | 3 lines
Spacing fixes in the CHANGES document.
........
r27819 | bugman | 2015-03-17 11:12:55 +0100 (Tue, 17 Mar 2015) | 6 lines
Fix for the pipe_control.reset.reset() function when resetting the GUI in
non-standard contexts.
This is mainly for debugging scripts when simulating a GUI and hence the
GUI reset() method does not
exist.
........
r27820 | bugman | 2015-03-17 12:21:57 +0100 (Tue, 17 Mar 2015) | 7 lines
Created a GUI memory management debugging script for the align_tensor.init
user function.
This repetitively calls the reset, pipe.create and align_tensor.init user
functions, and opening the
GUI element for setting alignment tensor elements (the Sequence window).
The pympler muppy_log file
shows no memory leaks for these user functions on Linux systems.
........
r27822 | bugman | 2015-04-02 09:14:10 +0200 (Thu, 02 Apr 2015) | 10 lines
Resized all fixed-sized GUI wizards to fit on 1024x768 pixel wide displays.
The problem was reported by Lora Picton in the thread starting at
http://thread.gmane.org/gmane.science.nmr.relax.user/1813 .
Both the spin loading wizard of the spin viewer window and the relaxation
data loading wizard used
currently in the model-free analysis tab and BMRB export page were fixed.
These both had the
y-dimension set to 800 pixels, hence parts of the window would be out of
view.
........
r27827 | bugman | 2015-04-02 09:41:52 +0200 (Thu, 02 Apr 2015) | 6 lines
Backported the relax 3.3.8 CHANGES file changes to trunk.
The command used was:
svn merge -r27825:r27826 svn+ssh://bugman@xxxxxxxxxxx/svn/relax/tags/3.3.8 .
........
Added:
branches/frame_order_cleanup/devel_scripts/memory_management/GUI_uf_align_tensor_init.py
- copied unchanged from r27827,
trunk/devel_scripts/memory_management/GUI_uf_align_tensor_init.py
Modified:
branches/frame_order_cleanup/ (props changed)
branches/frame_order_cleanup/docs/CHANGES
branches/frame_order_cleanup/gui/components/relax_data.py
branches/frame_order_cleanup/gui/spin_viewer/frame.py
branches/frame_order_cleanup/lib/plotting/grace.py
branches/frame_order_cleanup/lib/sequence.py
branches/frame_order_cleanup/lib/spectrum/peak_list.py
branches/frame_order_cleanup/lib/structure/pdb_write.py
branches/frame_order_cleanup/pipe_control/pcs.py
branches/frame_order_cleanup/pipe_control/rdc.py
branches/frame_order_cleanup/pipe_control/reset.py
branches/frame_order_cleanup/test_suite/system_tests/noe.py
branches/frame_order_cleanup/test_suite/system_tests/pcs.py
branches/frame_order_cleanup/test_suite/system_tests/rdc.py
branches/frame_order_cleanup/test_suite/system_tests/relax_fit.py
[This mail would be too long, it was shortened to contain the URLs only.]
Modified: branches/frame_order_cleanup/docs/CHANGES
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/docs/CHANGES?rev=27867&r1=27866&r2=27867&view=diff
Modified: branches/frame_order_cleanup/gui/components/relax_data.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/gui/components/relax_data.py?rev=27867&r1=27866&r2=27867&view=diff
Modified: branches/frame_order_cleanup/gui/spin_viewer/frame.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/gui/spin_viewer/frame.py?rev=27867&r1=27866&r2=27867&view=diff
Modified: branches/frame_order_cleanup/lib/plotting/grace.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/lib/plotting/grace.py?rev=27867&r1=27866&r2=27867&view=diff
Modified: branches/frame_order_cleanup/lib/sequence.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/lib/sequence.py?rev=27867&r1=27866&r2=27867&view=diff
Modified: branches/frame_order_cleanup/lib/spectrum/peak_list.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/lib/spectrum/peak_list.py?rev=27867&r1=27866&r2=27867&view=diff
Modified: branches/frame_order_cleanup/lib/structure/pdb_write.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/lib/structure/pdb_write.py?rev=27867&r1=27866&r2=27867&view=diff
Modified: branches/frame_order_cleanup/pipe_control/pcs.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/pipe_control/pcs.py?rev=27867&r1=27866&r2=27867&view=diff
Modified: branches/frame_order_cleanup/pipe_control/rdc.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/pipe_control/rdc.py?rev=27867&r1=27866&r2=27867&view=diff
Modified: branches/frame_order_cleanup/pipe_control/reset.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/pipe_control/reset.py?rev=27867&r1=27866&r2=27867&view=diff
Modified: branches/frame_order_cleanup/test_suite/system_tests/noe.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/system_tests/noe.py?rev=27867&r1=27866&r2=27867&view=diff
Modified: branches/frame_order_cleanup/test_suite/system_tests/pcs.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/system_tests/pcs.py?rev=27867&r1=27866&r2=27867&view=diff
Modified: branches/frame_order_cleanup/test_suite/system_tests/rdc.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/system_tests/rdc.py?rev=27867&r1=27866&r2=27867&view=diff
Modified: branches/frame_order_cleanup/test_suite/system_tests/relax_fit.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/system_tests/relax_fit.py?rev=27867&r1=27866&r2=27867&view=diff
r27867 - in /branches/frame_order_cleanup: ./ devel_scripts/memory_management/ docs/ gui/components/ gui/spin_viewer/ lib/ l...