Author: bugman
Date: Fri Sep 5 09:16:32 2014
New Revision: 25657
URL: http://svn.gna.org/viewcvs/relax?rev=25657&view=rev
Log:
Merged revisions
25617-25626,25628,25631-25632,25634,25636,25638,25640-25643,25649,25651,25655
via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/trunk
........
r25617 | bugman | 2014-09-04 11:13:35 +0200 (Thu, 04 Sep 2014) | 9 lines
Merged the profiling_cr72.py and profiling_dpl94.py scripts into base.py.
These dispersion model profiling scripts have been merged into one base
script, and the code in
profiling_cr72.py and profiling_dpl94.py minimised to imports, two class
initialisation lines, and
the execution of the main() function. This removes a huge amount of code
duplication and allows the
profiling scripts to be more easily modified, for example for compatibility
with new relax versions.
All of the other profiling scripts will be updated to use this base script.
........
r25618 | bugman | 2014-09-04 14:30:22 +0200 (Thu, 04 Sep 2014) | 7 lines
Merged all dispersion model profiling scripts into the base.py module.
The test_suite/shared_data/dispersion/profiling/profiling_*.py scripts are
now extremely minimal.
The change removes huge amounts of duplicated code. This will allow for
much easier maintenance of
these profiling scripts as changes will only need to be made to the base.py
script.
........
r25619 | bugman | 2014-09-04 14:34:50 +0200 (Thu, 04 Sep 2014) | 7 lines
Copied the dep_check.version_comparison() function into the dispersion
model profiling base script.
This will be used to provide compatibility between different relax versions
by allowing the version
numbers to be compared. The function needs to be copied here as older
relax versions do not provide
this function.
........
r25620 | bugman | 2014-09-04 14:48:20 +0200 (Thu, 04 Sep 2014) | 3 lines
Import fix for the dispersion model profiling base script.
........
r25621 | bugman | 2014-09-04 14:49:54 +0200 (Thu, 04 Sep 2014) | 6 lines
The IT99 dispersion model profiling script can now handle the clustering
bug.
For relax versions <= 3.2.2, the clustering is turned off as there was a
bug in the IT99 model
target function. The script will print out a warning when this occurs.
........
r25622 | bugman | 2014-09-04 14:51:17 +0200 (Thu, 04 Sep 2014) | 6 lines
The dispersion model super profiling script now handles the IT99 bug
differently.
Instead of printing out a comment within the table of results, the warnings
from the
profiling_it99.py script will be printed out when it occurs.
........
r25623 | bugman | 2014-09-04 15:17:56 +0200 (Thu, 04 Sep 2014) | 7 lines
Updated the dispersion model profiling scripts to handle new relax versions.
The relaxation time data structure is now being set up differently if relax
3.2.3 or earlier
versions are being used compared to the trunk or new versions. This allows
the scripts to run on
all relax versions.
........
r25624 | bugman | 2014-09-04 15:23:11 +0200 (Thu, 04 Sep 2014) | 5 lines
Fix for the relaxation time data structure compatibility with different
relax versions.
This is for the dispersion model profiling base script.
........
r25625 | bugman | 2014-09-04 15:25:22 +0200 (Thu, 04 Sep 2014) | 5 lines
Another fix for the relaxation time data structure compatibility with
different relax versions.
This is for the dispersion model profiling base script.
........
r25626 | bugman | 2014-09-04 15:35:36 +0200 (Thu, 04 Sep 2014) | 6 lines
Created the user_functions.uf_translation_table list.
The elements of this list are the names of user functions before and after
a renaming. The list is
provided for backwards compatibility for relax scripts, though it is not
used yet.
........
r25628 | bugman | 2014-09-04 16:25:48 +0200 (Thu, 04 Sep 2014) | 13 lines
Ported r25627 from the 3.3.0 tag.
The command used was:
svn merge -r25626:25627 svn+ssh://bugman@xxxxxxxxxxx/svn/relax/tags/3.3.0 .
.....
Python 3 fixes via the 2to3 compatibility script.
The command used was:
2to3 -w -f buffer -f idioms -f set_literal -f ws_comma -x except -x
import -x imports -x long -x numliterals -x xrange .
.....
........
r25631 | bugman | 2014-09-04 16:35:35 +0200 (Thu, 04 Sep 2014) | 20 lines
Ported r25629 from the 3.3.0 tag.
The command used was:
svn merge -r25628:25629 svn+ssh://bugman@xxxxxxxxxxx/svn/relax/tags/3.3.0 .
.....
r25629 | bugman | 2014-09-04 16:31:00 +0200 (Thu, 04 Sep 2014) | 6 lines
Changed paths:
M
/tags/3.3.0/test_suite/shared_data/curve_fitting/numeric_topology/estimate_errors.py
M
/tags/3.3.0/test_suite/shared_data/curve_fitting/numeric_topology/estimate_errors_analyse.py
M
/tags/3.3.0/test_suite/shared_data/curve_fitting/numeric_topology/estimate_errors_analyse_relax.py
M /tags/3.3.0/test_suite/system_tests/relax_disp.py
Python 3 fixes via the 2to3 compatibility script.
The command used was:
2to3 -w -f except -f import -f imports -f long -f numliterals -f xrange .
.....
........
r25632 | bugman | 2014-09-04 16:36:36 +0200 (Thu, 04 Sep 2014) | 20 lines
Ported r25630 from the 3.3.0 tag.
The command used was:
svn merge -r25629:25630 svn+ssh://bugman@xxxxxxxxxxx/svn/relax/tags/3.3.0 .
.....
r25630 | bugman | 2014-09-04 16:33:24 +0200 (Thu, 04 Sep 2014) | 7 lines
Changed paths:
M
/tags/3.3.0/test_suite/shared_data/curve_fitting/numeric_topology/estimate_errors.py
M
/tags/3.3.0/test_suite/shared_data/curve_fitting/numeric_topology/estimate_errors_analyse.py
M
/tags/3.3.0/test_suite/shared_data/curve_fitting/numeric_topology/estimate_errors_analyse_relax.py
Python 2 vs. 3 compatibility fix for the pickle module.
This is for the estimate_errors*.py scripts in the directory
test_suite/shared_data/curve_fitting/numeric_topology/. The
lib.compat.pickle module is now used to
allow both Python versions to run relax.
.....
........
r25634 | bugman | 2014-09-04 16:41:28 +0200 (Thu, 04 Sep 2014) | 17 lines
Ported r25633 from the 3.3.0 tag.
The command used was:
svn merge -r25632:25633 svn+ssh://bugman@xxxxxxxxxxx/svn/relax/tags/3.3.0 .
.....
r25633 | bugman | 2014-09-04 16:40:11 +0200 (Thu, 04 Sep 2014) | 6 lines
Changed paths:
M /tags/3.3.0/dep_check.py
Python 3 fix.
The cmp(v1, v2) notation in the dep_check.version_comparison() function
has been replaced with
(v1 > v2) - (v1 < v2). This allows relax to run on Python 3.
.....
........
r25636 | bugman | 2014-09-04 16:45:05 +0200 (Thu, 04 Sep 2014) | 6 lines
Backported the relax 3.3.0 CHANGES file changes to trunk.
The command used was:
svn merge -r25634:25635 svn+ssh://bugman@xxxxxxxxxxx/svn/relax/tags/3.3.0 .
........
r25638 | bugman | 2014-09-04 16:49:29 +0200 (Thu, 04 Sep 2014) | 12 lines
Ported r25637 from the 3.3.0 tag.
The command used was:
svn merge -r25636:25637 svn+ssh://bugman@xxxxxxxxxxx/svn/relax/tags/3.3.0 .
.....
Python 3 fix for the lib.periodic_table module.
The Python string module does not exist in Python 3.
.....
........
r25640 | bugman | 2014-09-04 16:56:24 +0200 (Thu, 04 Sep 2014) | 6 lines
Backported the relax 3.3.0 CHANGES file changes to trunk.
The command used was:
svn merge -r25638:25639 svn+ssh://bugman@xxxxxxxxxxx/svn/relax/tags/3.3.0 .
........
r25641 | bugman | 2014-09-04 17:13:38 +0200 (Thu, 04 Sep 2014) | 5 lines
Converted the user_functions.uf_translation_table object to a dictionary.
This is for faster access which does not require looping.
........
r25642 | bugman | 2014-09-04 17:18:08 +0200 (Thu, 04 Sep 2014) | 10 lines
The prompt UI now uses the user_functions.uf_translation_table dictionary.
The modified runcode() function will now check if the command typed by the
user is a function or
method call and then will raise a RelaxError if the command name is in the
user_functions.uf_translation_table dictionary, telling the user that the
user function has been
renamed to the new name in the translation table.
This appears to have no effect in the script UI however.
........
r25643 | bugman | 2014-09-04 17:44:58 +0200 (Thu, 04 Sep 2014) | 10 lines
Hack in the script UI for handling missing user functions due to it being
renamed.
This script UI requires a different solution as the prompt UI. The script
is executed via the runpy
Python module and there appears to be no clean way of catching each command
before it is executed.
So instead, prior to executing the script, the contents of the script are
read and old user
functions are searched for using re.search(). The old user function name
has "(" appended to it in
the search so that it is sure that it is a user function call. And the old
function must have a
space or newline character preceding it.
........
r25649 | bugman | 2014-09-04 18:13:46 +0200 (Thu, 04 Sep 2014) | 6 lines
Backported the relax 3.3.0 CHANGES file changes to trunk.
The command used was:
svn merge -r25647:25648 svn+ssh://bugman@xxxxxxxxxxx/svn/relax/tags/3.3.0 .
........
r25651 | bugman | 2014-09-04 18:42:53 +0200 (Thu, 04 Sep 2014) | 3 lines
Epydoc docstring fix for the dep_check.version_comparison() function.
........
r25655 | bugman | 2014-09-04 18:56:18 +0200 (Thu, 04 Sep 2014) | 5 lines
Removed ZZ and HD exchange from the dispersion chapter of the relax manual.
These would probably require completely new analysis types added to relax
to analyse such data.
........
Added:
branches/frame_order_cleanup/test_suite/shared_data/dispersion/profiling/base.py
- copied unchanged from r25655,
trunk/test_suite/shared_data/dispersion/profiling/base.py
Modified:
branches/frame_order_cleanup/ (props changed)
branches/frame_order_cleanup/dep_check.py
branches/frame_order_cleanup/docs/CHANGES
branches/frame_order_cleanup/docs/latex/dispersion.tex
branches/frame_order_cleanup/docs/latex/dispersion_software.tex
branches/frame_order_cleanup/gui/components/spectrum.py
branches/frame_order_cleanup/lib/periodic_table.py
branches/frame_order_cleanup/prompt/interpreter.py
branches/frame_order_cleanup/specific_analyses/relax_disp/estimate_r2eff.py
branches/frame_order_cleanup/specific_analyses/relax_fit/optimisation.py
branches/frame_order_cleanup/test_suite/shared_data/curve_fitting/numeric_topology/estimate_errors.py
branches/frame_order_cleanup/test_suite/shared_data/curve_fitting/numeric_topology/estimate_errors_analyse.py
branches/frame_order_cleanup/test_suite/shared_data/curve_fitting/numeric_topology/estimate_errors_analyse_relax.py
branches/frame_order_cleanup/test_suite/shared_data/dispersion/profiling/disp_profile_all.py
branches/frame_order_cleanup/test_suite/shared_data/dispersion/profiling/profiling_b14.py
branches/frame_order_cleanup/test_suite/shared_data/dispersion/profiling/profiling_b14_full.py
branches/frame_order_cleanup/test_suite/shared_data/dispersion/profiling/profiling_cr72.py
branches/frame_order_cleanup/test_suite/shared_data/dispersion/profiling/profiling_cr72_full.py
branches/frame_order_cleanup/test_suite/shared_data/dispersion/profiling/profiling_dpl94.py
branches/frame_order_cleanup/test_suite/shared_data/dispersion/profiling/profiling_it99.py
branches/frame_order_cleanup/test_suite/shared_data/dispersion/profiling/profiling_lm63.py
branches/frame_order_cleanup/test_suite/shared_data/dispersion/profiling/profiling_lm63_3site.py
branches/frame_order_cleanup/test_suite/shared_data/dispersion/profiling/profiling_m61.py
branches/frame_order_cleanup/test_suite/shared_data/dispersion/profiling/profiling_mmq_cr72.py
branches/frame_order_cleanup/test_suite/shared_data/dispersion/profiling/profiling_mp05.py
branches/frame_order_cleanup/test_suite/shared_data/dispersion/profiling/profiling_norex.py
branches/frame_order_cleanup/test_suite/shared_data/dispersion/profiling/profiling_ns_cpmg_2site_3D.py
branches/frame_order_cleanup/test_suite/shared_data/dispersion/profiling/profiling_ns_cpmg_2site_3D_full.py
branches/frame_order_cleanup/test_suite/shared_data/dispersion/profiling/profiling_ns_cpmg_2site_expanded.py
branches/frame_order_cleanup/test_suite/shared_data/dispersion/profiling/profiling_ns_cpmg_2site_star.py
branches/frame_order_cleanup/test_suite/shared_data/dispersion/profiling/profiling_ns_cpmg_2site_star_full.py
branches/frame_order_cleanup/test_suite/shared_data/dispersion/profiling/profiling_ns_mmq_2site.py
branches/frame_order_cleanup/test_suite/shared_data/dispersion/profiling/profiling_ns_mmq_3site.py
branches/frame_order_cleanup/test_suite/shared_data/dispersion/profiling/profiling_ns_mmq_3site_linear.py
branches/frame_order_cleanup/test_suite/shared_data/dispersion/profiling/profiling_ns_r1rho_2site.py
branches/frame_order_cleanup/test_suite/shared_data/dispersion/profiling/profiling_ns_r1rho_3site.py
branches/frame_order_cleanup/test_suite/shared_data/dispersion/profiling/profiling_ns_r1rho_3site_linear.py
branches/frame_order_cleanup/test_suite/shared_data/dispersion/profiling/profiling_tap03.py
branches/frame_order_cleanup/test_suite/shared_data/dispersion/profiling/profiling_tp02.py
branches/frame_order_cleanup/test_suite/shared_data/dispersion/profiling/profiling_tsmfk01.py
branches/frame_order_cleanup/test_suite/system_tests/relax_disp.py
branches/frame_order_cleanup/user_functions/__init__.py
[This mail would be too long, it was shortened to contain the URLs only.]
Modified: branches/frame_order_cleanup/dep_check.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/dep_check.py?rev=25657&r1=25656&r2=25657&view=diff
Modified: branches/frame_order_cleanup/docs/CHANGES
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/docs/CHANGES?rev=25657&r1=25656&r2=25657&view=diff
Modified: branches/frame_order_cleanup/docs/latex/dispersion.tex
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/docs/latex/dispersion.tex?rev=25657&r1=25656&r2=25657&view=diff
Modified: branches/frame_order_cleanup/docs/latex/dispersion_software.tex
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/docs/latex/dispersion_software.tex?rev=25657&r1=25656&r2=25657&view=diff
Modified: branches/frame_order_cleanup/gui/components/spectrum.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/gui/components/spectrum.py?rev=25657&r1=25656&r2=25657&view=diff
Modified: branches/frame_order_cleanup/lib/periodic_table.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/lib/periodic_table.py?rev=25657&r1=25656&r2=25657&view=diff
Modified: branches/frame_order_cleanup/prompt/interpreter.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/prompt/interpreter.py?rev=25657&r1=25656&r2=25657&view=diff
Modified:
branches/frame_order_cleanup/specific_analyses/relax_disp/estimate_r2eff.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/specific_analyses/relax_disp/estimate_r2eff.py?rev=25657&r1=25656&r2=25657&view=diff
Modified:
branches/frame_order_cleanup/specific_analyses/relax_fit/optimisation.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/specific_analyses/relax_fit/optimisation.py?rev=25657&r1=25656&r2=25657&view=diff
Modified:
branches/frame_order_cleanup/test_suite/shared_data/curve_fitting/numeric_topology/estimate_errors.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/shared_data/curve_fitting/numeric_topology/estimate_errors.py?rev=25657&r1=25656&r2=25657&view=diff
Modified:
branches/frame_order_cleanup/test_suite/shared_data/curve_fitting/numeric_topology/estimate_errors_analyse.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/shared_data/curve_fitting/numeric_topology/estimate_errors_analyse.py?rev=25657&r1=25656&r2=25657&view=diff
Modified:
branches/frame_order_cleanup/test_suite/shared_data/curve_fitting/numeric_topology/estimate_errors_analyse_relax.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/shared_data/curve_fitting/numeric_topology/estimate_errors_analyse_relax.py?rev=25657&r1=25656&r2=25657&view=diff
Modified:
branches/frame_order_cleanup/test_suite/shared_data/dispersion/profiling/disp_profile_all.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/shared_data/dispersion/profiling/disp_profile_all.py?rev=25657&r1=25656&r2=25657&view=diff
Modified:
branches/frame_order_cleanup/test_suite/shared_data/dispersion/profiling/profiling_b14.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/shared_data/dispersion/profiling/profiling_b14.py?rev=25657&r1=25656&r2=25657&view=diff
Modified:
branches/frame_order_cleanup/test_suite/shared_data/dispersion/profiling/profiling_b14_full.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/shared_data/dispersion/profiling/profiling_b14_full.py?rev=25657&r1=25656&r2=25657&view=diff
Modified:
branches/frame_order_cleanup/test_suite/shared_data/dispersion/profiling/profiling_cr72.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/shared_data/dispersion/profiling/profiling_cr72.py?rev=25657&r1=25656&r2=25657&view=diff
Modified:
branches/frame_order_cleanup/test_suite/shared_data/dispersion/profiling/profiling_cr72_full.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/shared_data/dispersion/profiling/profiling_cr72_full.py?rev=25657&r1=25656&r2=25657&view=diff
Modified:
branches/frame_order_cleanup/test_suite/shared_data/dispersion/profiling/profiling_dpl94.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/shared_data/dispersion/profiling/profiling_dpl94.py?rev=25657&r1=25656&r2=25657&view=diff
Modified:
branches/frame_order_cleanup/test_suite/shared_data/dispersion/profiling/profiling_it99.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/shared_data/dispersion/profiling/profiling_it99.py?rev=25657&r1=25656&r2=25657&view=diff
Modified:
branches/frame_order_cleanup/test_suite/shared_data/dispersion/profiling/profiling_lm63.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/shared_data/dispersion/profiling/profiling_lm63.py?rev=25657&r1=25656&r2=25657&view=diff
Modified:
branches/frame_order_cleanup/test_suite/shared_data/dispersion/profiling/profiling_lm63_3site.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/shared_data/dispersion/profiling/profiling_lm63_3site.py?rev=25657&r1=25656&r2=25657&view=diff
Modified:
branches/frame_order_cleanup/test_suite/shared_data/dispersion/profiling/profiling_m61.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/shared_data/dispersion/profiling/profiling_m61.py?rev=25657&r1=25656&r2=25657&view=diff
Modified:
branches/frame_order_cleanup/test_suite/shared_data/dispersion/profiling/profiling_mmq_cr72.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/shared_data/dispersion/profiling/profiling_mmq_cr72.py?rev=25657&r1=25656&r2=25657&view=diff
Modified:
branches/frame_order_cleanup/test_suite/shared_data/dispersion/profiling/profiling_mp05.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/shared_data/dispersion/profiling/profiling_mp05.py?rev=25657&r1=25656&r2=25657&view=diff
Modified:
branches/frame_order_cleanup/test_suite/shared_data/dispersion/profiling/profiling_norex.py
[... 50 lines stripped ...]
r25657 - in /branches/frame_order_cleanup: ./ docs/ docs/latex/ gui/components/ lib/ prompt/ specific_analyses/relax_disp/ s...