Author: bugman
Date: Tue Nov 11 12:02:16 2014
New Revision: 26515
URL: http://svn.gna.org/viewcvs/relax?rev=26515&view=rev
Log:
Merged revisions 26498-26513 via svnmerge from
svn+ssh://bug...@svn.gna.org/svn/relax/trunk
r26498 | bugman | 2014-11-10 19:56:07 +0100 (Mon, 10 Nov 2014) |
Author: bugman
Date: Tue Nov 11 12:02:14 2014
New Revision: 26514
URL: http://svn.gna.org/viewcvs/relax?rev=26514&view=rev
Log:
Merged revisions 26498-26513 via svnmerge from
svn+ssh://bug...@svn.gna.org/svn/relax/trunk
r26498 | bugman | 2014-11-10 19:56:07 +0100 (Mon, 10 Nov 2014) |
Author: bugman
Date: Tue Nov 11 12:13:52 2014
New Revision: 26516
URL: http://svn.gna.org/viewcvs/relax?rev=26516&view=rev
Log:
The ImportErrors in unit tests are now correctly handled by the relax test
suite.
If an ImportError occurred, this was previously killing the entire test suite.
Modif
Author: bugman
Date: Tue Nov 11 13:39:57 2014
New Revision: 26517
URL: http://svn.gna.org/viewcvs/relax?rev=26517&view=rev
Log:
The target_function.relax_fit module unit tests are now skipped if the C module
is not compiled.
Modified:
trunk/test_suite/unit_tests/_target_functions/test_relax
Author: bugman
Date: Tue Nov 11 14:10:47 2014
New Revision: 26518
URL: http://svn.gna.org/viewcvs/relax?rev=26518&view=rev
Log:
Expanded the Python 2 to 3 conversion document.
Modified:
trunk/docs/devel/2to3_checklist
Modified: trunk/docs/devel/2to3_checklist
URL:
http://svn.gna.org/viewcv
Author: bugman
Date: Tue Nov 11 14:26:23 2014
New Revision: 26519
URL: http://svn.gna.org/viewcvs/relax?rev=26519&view=rev
Log:
Manual Python 3 fixes for the dict.key() function which returns a list or
iterator in Python 2 or 3.
This involves a number of changes. The biggest is the conversion o
Author: bugman
Date: Tue Nov 11 14:34:56 2014
New Revision: 26521
URL: http://svn.gna.org/viewcvs/relax?rev=26521&view=rev
Log:
Small update to the 2to3_checklist document - the print statement conversion
has been added.
Modified:
trunk/docs/devel/2to3_checklist
Modified: trunk/docs/devel/
Author: bugman
Date: Tue Nov 11 14:34:12 2014
New Revision: 26520
URL: http://svn.gna.org/viewcvs/relax?rev=26520&view=rev
Log:
Python 3 fixes via 2to3 - elimination of all apply() calls.
This only affects the GUI which cannot run in Python 3 yet as wxPython is not
Python 3 compatible
yet.
The
Author: bugman
Date: Tue Nov 11 14:43:25 2014
New Revision: 26522
URL: http://svn.gna.org/viewcvs/relax?rev=26522&view=rev
Log:
Python 3 fixes via 2to3 - proper handling of the dict.items() and dict.values()
functions.
These are now all wrapped in list() function calls to ensure that the Python
Author: bugman
Date: Tue Nov 11 14:55:38 2014
New Revision: 26523
URL: http://svn.gna.org/viewcvs/relax?rev=26523&view=rev
Log:
Python 3 fixes via 2to3 - the execfile() function does not exist in Python 3.
The command used was:
2to3 -j 4 -w -f execfile .
Modified:
trunk/test_suite/shared_d
Author: bugman
Date: Tue Nov 11 15:52:43 2014
New Revision: 26524
URL: http://svn.gna.org/viewcvs/relax?rev=26524&view=rev
Log:
The lib.errors module is now importing lib.compat.pickle for better Python 2
and 3 support.
This shifts the compatibility code from lib.errors into lib.compat so that t
014
@@ -3,6 +3,7 @@
###
# #
# Copyright (C) 2014 Troels E. Linnet #
+# Copyright (C) 2014 E
Author: bugman
Date: Tue Nov 11 16:06:36 2014
New Revision: 26526
URL: http://svn.gna.org/viewcvs/relax?rev=26526&view=rev
Log:
Unicode fixes for the "\u" string in "\usepackage" in the module docstring.
This requires escaping as "\\usepackage" to avoid the unicode character '\u'.
Modified:
Author: bugman
Date: Tue Nov 11 16:13:25 2014
New Revision: 26527
URL: http://svn.gna.org/viewcvs/relax?rev=26527&view=rev
Log:
The lib.check_types now imports io.IOBase from the lib.compat module.
This is to shift more Python 2 vs. 3 compatibility into lib.compat and out of
all other modules.
Author: bugman
Date: Tue Nov 11 16:21:12 2014
New Revision: 26528
URL: http://svn.gna.org/viewcvs/relax?rev=26528&view=rev
Log:
Python 3 improvements - changed how the Python 3 absent builtins.unicode()
function is handled.
The aliased builtins.str() function is now referenced as lib.compat.unic
Author: bugman
Date: Tue Nov 11 16:31:32 2014
New Revision: 26529
URL: http://svn.gna.org/viewcvs/relax?rev=26529&view=rev
Log:
Merged revisions 26516-26528 via svnmerge from
svn+ssh://bug...@svn.gna.org/svn/relax/trunk
r26516 | bugman | 2014-11-11 12:13:52 +0100 (Tue, 11 Nov 2014) |
Author: bugman
Date: Tue Nov 11 16:31:33 2014
New Revision: 26530
URL: http://svn.gna.org/viewcvs/relax?rev=26530&view=rev
Log:
Merged revisions 26516-26528 via svnmerge from
svn+ssh://bug...@svn.gna.org/svn/relax/trunk
r26516 | bugman | 2014-11-11 12:13:52 +0100 (Tue, 11 Nov 2014) |
Author: bugman
Date: Tue Nov 11 16:37:13 2014
New Revision: 26531
URL: http://svn.gna.org/viewcvs/relax?rev=26531&view=rev
Log:
Python 3 fixes via 2to3 - the filter() function in Python 3 now returns an
iterator.
The command used was:
2to3 -j 4 -w -f filter .
Modified:
trunk/lib/sequence.p
Author: bugman
Date: Tue Nov 11 16:38:42 2014
New Revision: 26533
URL: http://svn.gna.org/viewcvs/relax?rev=26533&view=rev
Log:
Merged revisions 26531 via svnmerge from
svn+ssh://bug...@svn.gna.org/svn/relax/trunk
r26531 | bugman | 2014-11-11 16:37:13 +0100 (Tue, 11 Nov 2014) | 6 line
Author: bugman
Date: Tue Nov 11 16:38:39 2014
New Revision: 26532
URL: http://svn.gna.org/viewcvs/relax?rev=26532&view=rev
Log:
Merged revisions 26531 via svnmerge from
svn+ssh://bug...@svn.gna.org/svn/relax/trunk
r26531 | bugman | 2014-11-11 16:37:13 +0100 (Tue, 11 Nov 2014) | 6 line
Author: bugman
Date: Tue Nov 11 16:41:51 2014
New Revision: 26534
URL: http://svn.gna.org/viewcvs/relax?rev=26534&view=rev
Log:
Manual Python 3 fixes for the dict.key() function which returns a list or
iterator in Python 2 or 3.
This matches r26519 in trunk.
Modified:
branches/frame_order_
Author: bugman
Date: Tue Nov 11 16:51:21 2014
New Revision: 26535
URL: http://svn.gna.org/viewcvs/relax?rev=26535&view=rev
Log:
Python 3 fixes via 2to3 - the "while 1" construct has been replaces with "while
True".
The command used was:
2to3 -j 4 -w -f idioms .
Modified:
branches/frame_ord
Author: bugman
Date: Tue Nov 11 17:37:03 2014
New Revision: 26537
URL: http://svn.gna.org/viewcvs/relax?rev=26537&view=rev
Log:
Python 3 fixes via 2to3 - the xrange() function has been replaced by range().
The command used was:
2to3 -j 4 -w -f xrange .
Modified:
branches/frame_order_cleanu
Author: bugman
Date: Tue Nov 11 17:57:37 2014
New Revision: 26538
URL: http://svn.gna.org/viewcvs/relax?rev=26538&view=rev
Log:
Missing import of lib.compat.unicode in lib.check_types.
Modified:
trunk/lib/check_types.py
Modified: trunk/lib/check_types.py
URL:
http://svn.gna.org/viewcvs/rel
Author: bugman
Date: Tue Nov 11 17:28:08 2014
New Revision: 26536
URL: http://svn.gna.org/viewcvs/relax?rev=26536&view=rev
Log:
Python 3 fixes via 2to3 - the spacing around commas has been fixed.
The command used was:
2to3 -j 4 -w -f ws_comma .
Modified:
branches/frame_order_cleanup/test_s
Author: bugman
Date: Wed Nov 12 09:11:08 2014
New Revision: 26540
URL: http://svn.gna.org/viewcvs/relax?rev=26540&view=rev
Log:
Merged revisions 26538 via svnmerge from
svn+ssh://bug...@svn.gna.org/svn/relax/trunk
r26538 | bugman | 2014-11-11 17:57:37 +0100 (Tue, 11 Nov 2014) | 3 line
Author: bugman
Date: Wed Nov 12 09:11:04 2014
New Revision: 26539
URL: http://svn.gna.org/viewcvs/relax?rev=26539&view=rev
Log:
Merged revisions 26538 via svnmerge from
svn+ssh://bug...@svn.gna.org/svn/relax/trunk
r26538 | bugman | 2014-11-11 17:57:37 +0100 (Tue, 11 Nov 2014) | 3 line
Author: bugman
Date: Wed Nov 12 10:51:25 2014
New Revision: 26541
URL: http://svn.gna.org/viewcvs/relax?rev=26541&view=rev
Log:
Removed the writable base directory check in the dauvergne_protocol
auto-analysis.
This check was causing the system test to fail if the user does not have write
acces
Author: bugman
Date: Wed Nov 12 10:57:44 2014
New Revision: 26542
URL: http://svn.gna.org/viewcvs/relax?rev=26542&view=rev
Log:
Expanded the Mac_framework_build_3way document to include matplotlib.
Modified:
trunk/docs/devel/Mac_framework_build_3way
Modified: trunk/docs/devel/Mac_framework_
Author: bugman
Date: Wed Nov 12 11:45:54 2014
New Revision: 26543
URL: http://svn.gna.org/viewcvs/relax?rev=26543&view=rev
Log:
Important bug fix for racing causing the GUI to freeze.
This is really only seen in the GUI tests on MS Windows systems, as a user
could never be fast
enough with the m
Author: bugman
Date: Wed Nov 12 11:47:40 2014
New Revision: 26544
URL: http://svn.gna.org/viewcvs/relax?rev=26544&view=rev
Log:
Bug fix for the Mf.test_bug_21615_incomplete_setup_failure GUI test on MS
Windows systems.
The GUI interpreter flush() method needs to be called between the two
struct
Author: bugman
Date: Wed Nov 12 17:28:42 2014
New Revision: 26545
URL: http://svn.gna.org/viewcvs/relax?rev=26545&view=rev
Log:
Shifted a number of wx.NewId() calls to the module namespace to conserve IDs.
These are for the menus in the main window and in the spin view window.
Modified:
tru
Author: bugman
Date: Wed Nov 12 17:38:25 2014
New Revision: 26546
URL: http://svn.gna.org/viewcvs/relax?rev=26546&view=rev
Log:
Shifted the wx.NewId() calls for the spectrum list GUI element to the module
namespace.
These IDs are used for the pop up menus. The change avoids repetitive calls to
pyright (C) 2009-2011 Michael Bieri #
-# Copyright (C) 2010-2013 Edward d'Auvergne #
+# Copyright (C) 2010-2
Author: bugman
Date: Wed Nov 12 17:54:31 2014
New Revision: 26548
URL: http://svn.gna.org/viewcvs/relax?rev=26548&view=rev
Log:
Converted all of the GUI wizard button IDs to -1, as they are currently unused.
This should conserve wx IDs, especially in the test suite.
Modified:
trunk/gui/wiza
Author: bugman
Date: Wed Nov 12 17:58:30 2014
New Revision: 26549
URL: http://svn.gna.org/viewcvs/relax?rev=26549&view=rev
Log:
Shifted the main GUI window toolbar button wx IDs to the module namespace.
This has no effect apart from better organising the code.
Modified:
trunk/gui/relax_gui.
Author: bugman
Date: Wed Nov 12 18:01:11 2014
New Revision: 26550
URL: http://svn.gna.org/viewcvs/relax?rev=26550&view=rev
Log:
Shifted the relax controller window popup menu wx IDs to the module namespace.
This is simply to better organise the code to match the other GUI module
changes.
Modif
014
@@ -1,7 +1,7 @@
###
# #
# Copyright (C) 2009 Michael Bieri#
-# Copyright (C) 2010-2011 Edward d'Auvergne #
+# Copyright (C) 2010-2
014
@@ -1,6 +1,6 @@
###
# #
-# Copyright (C) 2010-2013 Edward d'Auvergne #
+# Copyright (C) 2010-2014 Edward d'Auvergne #
# Copyright (C)
014
@@ -1,6 +1,6 @@
###
# #
-# Copyright (C) 2011-2013 Edward d'Auvergne #
+# Copyright (C) 2011-2
Author: bugman
Date: Wed Nov 12 18:30:47 2014
New Revision: 26554
URL: http://svn.gna.org/viewcvs/relax?rev=26554&view=rev
Log:
Another large wx ID saving change.
The ID associated with the special accelerator table that allows the ESC button
to close relax
wizards is now initialised once in the
ght (C) 2009 Michael Bieri#
-# Copyright (C) 2010-2013 Edward d'Auvergne #
+# Copyright (C) 2010-2014 Edward d'Auvergne #
# #
# This file is part
Author: bugman
Date: Wed Nov 12 18:36:23 2014
New Revision: 26556
URL: http://svn.gna.org/viewcvs/relax?rev=26556&view=rev
Log:
The user function class menus no longer have unique wx IDs, as these are
unnecessary.
This conserves the small pool of unique wx IDs, as the spin viewer window is
crea
Author: bugman
Date: Wed Nov 12 19:57:54 2014
New Revision: 26557
URL: http://svn.gna.org/viewcvs/relax?rev=26557&view=rev
Log:
Bug fix for the structure.load_spins user function new from_mols argument.
This was incorrectly using the pipe_control.pipes.pipe_names() function to
obtain its default
Author: bugman
Date: Thu Nov 13 10:20:43 2014
New Revision: 26558
URL: http://svn.gna.org/viewcvs/relax?rev=26558&view=rev
Log:
Added a debugging Python version check to the
devel_scripts/memory_leak_test_relax_fit.py script.
This prevents the script from being executed with a normal Python bina
Author: bugman
Date: Thu Nov 13 11:34:01 2014
New Revision: 26560
URL: http://svn.gna.org/viewcvs/relax?rev=26560&view=rev
Log:
Added a printout to the Noe.test_noe_analysis_memory_leaks GUI test to help
with debugging.
Modified:
trunk/test_suite/gui_tests/noe.py
Modified: trunk/test_suite
Author: bugman
Date: Thu Nov 13 11:36:22 2014
New Revision: 26561
URL: http://svn.gna.org/viewcvs/relax?rev=26561&view=rev
Log:
Improved debugging printouts for the Noe.test_noe_analysis_memory_leaks GUI
test.
Modified:
trunk/test_suite/gui_tests/noe.py
Modified: trunk/test_suite/gui_tests
Author: bugman
Date: Thu Nov 13 13:31:57 2014
New Revision: 26564
URL: http://svn.gna.org/viewcvs/relax?rev=26564&view=rev
Log:
Created the General.test_new_analysis_wizard_memory_leak blacklisted GUI test.
This will be used to check for memory leaks in the new analysis wizard.
Modified:
tr
Author: bugman
Date: Thu Nov 13 13:37:23 2014
New Revision: 26565
URL: http://svn.gna.org/viewcvs/relax?rev=26565&view=rev
Log:
Removed an unused dictionary from the GUI wizard object.
Modified:
trunk/gui/wizards/wiz_objects.py
Modified: trunk/gui/wizards/wiz_objects.py
URL:
http://svn.gna
Author: bugman
Date: Thu Nov 13 14:27:02 2014
New Revision: 26566
URL: http://svn.gna.org/viewcvs/relax?rev=26566&view=rev
Log:
Added a wx.Yield() before destroying the new analysis wizard via menu_new().
This is to avoid racing which can be triggered in the test suite.
Modified:
trunk/gui/
Author: bugman
Date: Thu Nov 13 15:53:52 2014
New Revision: 26567
URL: http://svn.gna.org/viewcvs/relax?rev=26567&view=rev
Log:
Merged revisions 26541-26566 via svnmerge from
svn+ssh://bug...@svn.gna.org/svn/relax/trunk
r26541 | bugman | 2014-11-12 10:51:25 +0100 (Wed, 12 Nov 2014) |
Author: bugman
Date: Thu Nov 13 17:51:57 2014
New Revision: 26569
URL: http://svn.gna.org/viewcvs/relax?rev=26569&view=rev
Log:
relax version 3.3.2.
This is a minor feature and bugfix release.
Added:
tags/3.3.2/
- copied from r26568, trunk/
__
Author: bugman
Date: Thu Nov 13 17:54:03 2014
New Revision: 26570
URL: http://svn.gna.org/viewcvs/relax?rev=26570&view=rev
Log:
Updated the version number to relax 3.3.2.
Modified:
tags/3.3.2/version.py
Modified: tags/3.3.2/version.py
URL:
http://svn.gna.org/viewcvs/relax/tags/3.3.2/versio
Author: bugman
Date: Thu Nov 13 18:08:54 2014
New Revision: 26571
URL: http://svn.gna.org/viewcvs/relax?rev=26571&view=rev
Log:
Added the relax 3.3.2 manual to the repository.
Added:
tags/3.3.2/docs/relax.pdf (with props)
Added: tags/3.3.2/docs/relax.pdf
URL:
http://svn.gna.org/viewcvs/r
Author: bugman
Date: Thu Nov 13 18:14:27 2014
New Revision: 26572
URL: http://svn.gna.org/viewcvs/relax?rev=26572&view=rev
Log:
Updated the CHANGES file for relax 3.3.2.
Modified:
tags/3.3.2/docs/CHANGES
[This mail would be too long, it was shortened to contain the URLs only.]
Modified: ta
Author: bugman
Date: Fri Nov 14 09:19:08 2014
New Revision: 26573
URL: http://svn.gna.org/viewcvs/relax?rev=26573&view=rev
Log:
Updated the http://www.nmr-relax.com/download.html webpage for relax 3.3.2.
Modified:
website/download.html
[This mail would be too long, it was shortened to conta
Author: bugman
Date: Fri Nov 14 09:59:43 2014
New Revision: 26574
URL: http://svn.gna.org/viewcvs/relax?rev=26574&view=rev
Log:
Updated the relax HTML manual at http://www.nmr-relax.com/manual/index.html to
version 3.3.2.
The HTML file names are now very different due to the latex2html changes i
Author: bugman
Date: Fri Nov 14 10:04:51 2014
New Revision: 26575
URL: http://svn.gna.org/viewcvs/relax?rev=26575&view=rev
Log:
Small expansion and editing of the
http://www.nmr-relax.com/download_request.html webpage.
Modified:
website/download_request.html
Modified: website/download_requ
Author: bugman
Date: Fri Nov 14 10:09:53 2014
New Revision: 26576
URL: http://svn.gna.org/viewcvs/relax?rev=26576&view=rev
Log:
Removed the old relax 2.2.5 API documentation files from
http://www.nmr-relax.com/api/.
These were shifted into http://www.nmr-relax.com/api/2.2. The files were left
Author: bugman
Date: Fri Nov 14 10:24:21 2014
New Revision: 26577
URL: http://svn.gna.org/viewcvs/relax?rev=26577&view=rev
Log:
Basic Epydoc fix for the data_store.exp_info module.
Modified:
trunk/data_store/exp_info.py
Modified: trunk/data_store/exp_info.py
URL:
http://svn.gna.org/viewcvs
Author: bugman
Date: Fri Nov 14 10:26:00 2014
New Revision: 26578
URL: http://svn.gna.org/viewcvs/relax?rev=26578&view=rev
Log:
Epydoc fix for the name_pipe() method of the relaxation dispersion
auto-analysis for repeated data.
Modified:
trunk/auto_analyses/relax_disp_repeat_cpmg.py
Modifi
Author: bugman
Date: Fri Nov 14 10:29:29 2014
New Revision: 26579
URL: http://svn.gna.org/viewcvs/relax?rev=26579&view=rev
Log:
Updated the relax API documentation at http://www.nmr-relax.com/api/3.3/ to
version 3.3.2.
Removed:
website/api/3.3/pipe_control.monte_carlo-module.html
websit
Author: bugman
Date: Fri Nov 14 10:40:20 2014
New Revision: 26580
URL: http://svn.gna.org/viewcvs/relax?rev=26580&view=rev
Log:
Updated the relax version number to 3.3.2 on the
http://www.nmr-relax.com/api/index.html webpage.
Modified:
website/api/index.html
Modified: website/api/index.htm
Author: bugman
Date: Fri Nov 14 10:50:36 2014
New Revision: 26581
URL: http://svn.gna.org/viewcvs/relax?rev=26581&view=rev
Log:
Restored the http://www.nmr-relax.com/manual/index.html file accidentally
deleted in r26574.
The command used was:
svn cp svn+ssh://bug...@svn.gna.org/svn/relax/website
Author: bugman
Date: Fri Nov 14 10:51:58 2014
New Revision: 26582
URL: http://svn.gna.org/viewcvs/relax?rev=26582&view=rev
Log:
Updated the http://www.nmr-relax.com/manual/index.html file to the current
relax 3.3.2 version.
Modified:
website/manual/index.html
[This mail would be too long,
Author: bugman
Date: Fri Nov 14 11:52:51 2014
New Revision: 26583
URL: http://svn.gna.org/viewcvs/relax?rev=26583&view=rev
Log:
Fixes for the HTML user manual compilation.
The index.html file was not being created as the main page has changed from
'relax_user_manual.html'
to 'The_relax_user_manu
Author: bugman
Date: Fri Nov 14 11:55:36 2014
New Revision: 26584
URL: http://svn.gna.org/viewcvs/relax?rev=26584&view=rev
Log:
Added a line to the release checklist document about updating the wiki release
links.
These are for the combined release notes pages at
http://wiki.nmr-relax.com/Relax
Author: bugman
Date: Fri Nov 14 16:45:49 2014
New Revision: 26585
URL: http://svn.gna.org/viewcvs/relax?rev=26585&view=rev
Log:
Updates for the release announcement section of the release checklist document.
Modified:
trunk/docs/devel/Release_Checklist
Modified: trunk/docs/devel/Release_Che
Author: bugman
Date: Sun Nov 16 14:57:22 2014
New Revision: 26586
URL: http://svn.gna.org/viewcvs/relax?rev=26586&view=rev
Log:
Created a system test to catch a rare relaxation data loading problem.
Modified:
trunk/test_suite/system_tests/model_free.py
Modified: trunk/test_suite/system_test
Author: bugman
Date: Mon Nov 17 10:16:29 2014
New Revision: 26587
URL: http://svn.gna.org/viewcvs/relax?rev=26587&view=rev
Log:
Merged revisions 26577-26578,26583-26586 via svnmerge from
svn+ssh://bug...@svn.gna.org/svn/relax/trunk
r26577 | bugman | 2014-11-14 10:24:21 +0100 (Fri, 14
Author: bugman
Date: Mon Nov 17 10:20:31 2014
New Revision: 26588
URL: http://svn.gna.org/viewcvs/relax?rev=26588&view=rev
Log:
Fix for bug #22961 (https://gna.org/bugs/?22961)
This is the failure of relaxation data loading with the message "IndexError:
list index out of
range". The bug was fou
Author: bugman
Date: Mon Nov 17 10:20:46 2014
New Revision: 26589
URL: http://svn.gna.org/viewcvs/relax?rev=26589&view=rev
Log:
Merged revisions 26577-26578,26583-26586 via svnmerge from
svn+ssh://bug...@svn.gna.org/svn/relax/trunk
r26577 | bugman | 2014-11-14 10:24:21 +0100 (Fri, 14
Author: bugman
Date: Mon Nov 17 10:28:11 2014
New Revision: 26591
URL: http://svn.gna.org/viewcvs/relax?rev=26591&view=rev
Log:
Merged revisions 26588 via svnmerge from
svn+ssh://bug...@svn.gna.org/svn/relax/trunk
r26588 | bugman | 2014-11-17 10:20:31 +0100 (Mon, 17 Nov 2014) | 13 lin
Author: bugman
Date: Mon Nov 17 10:28:10 2014
New Revision: 26590
URL: http://svn.gna.org/viewcvs/relax?rev=26590&view=rev
Log:
Merged revisions 26588 via svnmerge from
svn+ssh://bug...@svn.gna.org/svn/relax/trunk
r26588 | bugman | 2014-11-17 10:20:31 +0100 (Mon, 17 Nov 2014) | 13 lin
Author: bugman
Date: Mon Nov 17 11:12:16 2014
New Revision: 26592
URL: http://svn.gna.org/viewcvs/relax?rev=26592&view=rev
Log:
Created the Mf.test_dauvergne_protocol_sphere system test.
This catches bug #22963 (https://gna.org/bugs/?22963): Using '@N*' to define
the interatomic
interactions fo
Author: bugman
Date: Mon Nov 17 11:12:44 2014
New Revision: 26594
URL: http://svn.gna.org/viewcvs/relax?rev=26594&view=rev
Log:
Merged revisions 26592 via svnmerge from
svn+ssh://bug...@svn.gna.org/svn/relax/trunk
r26592 | bugman | 2014-11-17 11:12:16 +0100 (Mon, 17 Nov 2014) | 6 line
Author: bugman
Date: Mon Nov 17 11:12:42 2014
New Revision: 26593
URL: http://svn.gna.org/viewcvs/relax?rev=26593&view=rev
Log:
Merged revisions 26592 via svnmerge from
svn+ssh://bug...@svn.gna.org/svn/relax/trunk
r26592 | bugman | 2014-11-17 11:12:16 +0100 (Mon, 17 Nov 2014) | 6 line
Author: bugman
Date: Mon Nov 17 11:56:50 2014
New Revision: 26595
URL: http://svn.gna.org/viewcvs/relax?rev=26595&view=rev
Log:
Set more reasonable default values for the lib.structure.pdb_write functions
atom() and hetatm().
The occupancy now defaults to 1.0 instead of '', and the temperature f
Author: bugman
Date: Mon Nov 17 11:57:19 2014
New Revision: 26596
URL: http://svn.gna.org/viewcvs/relax?rev=26596&view=rev
Log:
Removed an accidentally committed debugging printout.
Modified:
trunk/lib/structure/pdb_write.py
Modified: trunk/lib/structure/pdb_write.py
URL:
http://svn.gna.or
odel_free/sphere/create_sphere.py
(original)
+++ trunk/test_suite/shared_data/model_free/sphere/create_sphere.py Mon Nov
17 12:04:25 2014
@@ -1,35 +1,11 @@
-#!/usr/bin/python
+# relax script for creating the spherical PDB file.
+# Copyright 2004-2014, Edward d'Auvergne
-# Copyright 2004-20
Author: bugman
Date: Mon Nov 17 12:17:22 2014
New Revision: 26598
URL: http://svn.gna.org/viewcvs/relax?rev=26598&view=rev
Log:
Converted all ATOM records to HETATM in the sphere.pdb file.
Modified:
trunk/test_suite/shared_data/model_free/sphere/create_sphere.py
trunk/test_suite/shared_d
p_factor=0.0,
element='', charge=''):
"""Generate the HETATM record.
The following is the PDB v3.3 documentation
U{http://www.wwpdb.org/documentation/format33/sect9.html#HETATM}.
Modified:
branches/frame_order_cleanup/test_suite/shared_data/model_free/sphe
hared_data/model_free/sphere/create_sphere.py
URL:
http://svn.gna.org/viewcvs/relax/branches/space_mapping_refactor/test_suite/shared_data/model_free/sphere/create_sphere.py?rev=26599&r1=26598&r2=26599&view=diff
===
Author: bugman
Date: Mon Nov 17 17:12:44 2014
New Revision: 26601
URL: http://svn.gna.org/viewcvs/relax?rev=26601&view=rev
Log:
Implemented the lib.geometry.vectors.vector_angle_atan2() function.
This is for calculating the inter-vector angle using the more numerically
stable atan2() formula.
Author: bugman
Date: Mon Nov 17 17:16:36 2014
New Revision: 26603
URL: http://svn.gna.org/viewcvs/relax?rev=26603&view=rev
Log:
Missing import.
Modified:
trunk/lib/geometry/vectors.py
Modified: trunk/lib/geometry/vectors.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/geometry/vectors.p
Author: bugman
Date: Mon Nov 17 17:16:23 2014
New Revision: 26602
URL: http://svn.gna.org/viewcvs/relax?rev=26602&view=rev
Log:
Implemented the lib.geometry.vectors.vector_angle_acos() function.
This is used to calculate the inter-vector angle using the arccos of the dot
product formula. The
fu
Author: bugman
Date: Mon Nov 17 17:23:30 2014
New Revision: 26604
URL: http://svn.gna.org/viewcvs/relax?rev=26604&view=rev
Log:
Renamed vector_angle() to vector_angle_normal() in the lib.geometry.vectors
module.
This is to standardise the naming as there are now the standard vector angle
formul
Author: bugman
Date: Mon Nov 17 17:29:14 2014
New Revision: 26605
URL: http://svn.gna.org/viewcvs/relax?rev=26605&view=rev
Log:
Added 6 unit tests for the lib.geometry.vectors.vector_angle_acos() function.
These are similar to those of the vector_angle_normal() function but unsigned
angles are c
Author: bugman
Date: Mon Nov 17 17:30:43 2014
New Revision: 26606
URL: http://svn.gna.org/viewcvs/relax?rev=26606&view=rev
Log:
Created 6 unit tests for the lib.geometry.vectors.vector_angle_atan2() function.
Modified:
trunk/test_suite/unit_tests/_lib/_geometry/test_vectors.py
Modified: tru
vn/relax/trunk
+
+ Molecular dynamics by NMR data analysis
+
+ Copyright (C) 2001-2006 Edward d'Auvergne
+ Copyright (C) 2006-2014 the relax development team
+
+This is free software which you are welcome to modify and
Author: bugman
Date: Mon Nov 17 18:20:05 2014
New Revision: 26608
URL: http://svn.gna.org/viewcvs/relax?rev=26608&view=rev
Log:
Improved the printouts from the align_tensor.svd user function by including the
basis set text.
Modified:
trunk/pipe_control/align_tensor.py
Modified: trunk/pipe_
Author: bugman
Date: Mon Nov 17 18:22:18 2014
New Revision: 26609
URL: http://svn.gna.org/viewcvs/relax?rev=26609&view=rev
Log:
Updated the log file for comparing different alignment tensor basis sets for
align_tensor.svd changes.
Modified:
trunk/test_suite/shared_data/align_data/basis_sets
Author: bugman
Date: Tue Nov 18 09:26:29 2014
New Revision: 26610
URL: http://svn.gna.org/viewcvs/relax?rev=26610&view=rev
Log:
Fix for the 64-bit Linux distribution file md5sum placement.
This is for http://www.nmr-relax.com/download.html.
Modified:
website/download.html
Modified: website
Author: bugman
Date: Tue Nov 18 11:54:21 2014
New Revision: 26611
URL: http://svn.gna.org/viewcvs/relax?rev=26611&view=rev
Log:
Implemented a new default basis set for the align_tensor.matrix_angles user
function.
This is uses standard definition of the inter-matrix angle using the Euclidean
in
Author: bugman
Date: Tue Nov 18 13:46:26 2014
New Revision: 26612
URL: http://svn.gna.org/viewcvs/relax?rev=26612&view=rev
Log:
Improvements to the description of the align_tensor.matrix_angles user function.
Modified:
trunk/user_functions/align_tensor.py
Modified: trunk/user_functions/alig
Author: bugman
Date: Tue Nov 18 14:08:58 2014
New Revision: 26613
URL: http://svn.gna.org/viewcvs/relax?rev=26613&view=rev
Log:
Import fix for the frame order CaM system test base script.
The vector_angle() function of the lib.geometry.vectors module is now called
vector_angle_normal().
Modifi
014
@@ -1,6 +1,6 @@
###
# #
-# Copyright (C) 2007-2013 Edward d'Auvergne #
+# Copyright (C) 2007-2014 Edward d'Auvergne #
# #
# This file is part of the pro
Author: bugman
Date: Tue Nov 18 15:14:45 2014
New Revision: 26616
URL: http://svn.gna.org/viewcvs/relax?rev=26616&view=rev
Log:
Added a check for the values of the basis_set argument.
This is to the align_tensor.matrix_angles user function backend.
Modified:
trunk/pipe_control/align_tensor.
Author: bugman
Date: Tue Nov 18 15:12:41 2014
New Revision: 26615
URL: http://svn.gna.org/viewcvs/relax?rev=26615&view=rev
Log:
Conversion of the basis_set argument for the align_tensor.matrix_angles user
function.
The argument is now a string that accepts the values of 'matrix', 'unitary 5D',
Author: bugman
Date: Tue Nov 18 15:30:36 2014
New Revision: 26617
URL: http://svn.gna.org/viewcvs/relax?rev=26617&view=rev
Log:
Printout improvements clarifying the align_tensor.matrix_angles user function.
Modified:
trunk/pipe_control/align_tensor.py
Modified: trunk/pipe_control/align_tens
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