Author: bugman
Date: Mon Sep 8 20:56:34 2014
New Revision: 25708
URL: http://svn.gna.org/viewcvs/relax?rev=25708&view=rev
Log:
Merged revisions 25658-25672,25674-25679,25681-25707 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/trunk
........
r25658 | bugman | 2014-09-05 09:47:22 +0200 (Fri, 05 Sep 2014) | 8 lines
Updated the 'Announcement' section of the release checklist document.
This now includes details about initially composing the message using the
relax wiki
(http://wiki.nmr-relax.com), and then how that text and the CHANGES file
are used for the email
announcement (http://news.gmane.org/gmane.science.nmr.relax.announce) and
the Gna! news item
(https://gna.org/news/?group=relax).
........
r25659 | bugman | 2014-09-05 09:59:13 +0200 (Fri, 05 Sep 2014) | 3 lines
Small changes for the Gna! news item in the release checklist document.
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r25660 | bugman | 2014-09-05 10:19:34 +0200 (Fri, 05 Sep 2014) | 5 lines
Modified the announcement section of the release checklist document.
Text about removing wiki markup has been added.
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r25661 | bugman | 2014-09-05 11:06:31 +0200 (Fri, 05 Sep 2014) | 5 lines
More expansion of the release checklist document.
Added text about creating internal and external links for the wiki release
notes.
........
r25662 | tlinnet | 2014-09-05 11:09:45 +0200 (Fri, 05 Sep 2014) | 1 line
Modified systemtest Relax_disp.test_show_apod_extract that test output from
showApod. The output can be different according to NMRPipe version. The
'Noise Std Dev' is though the same.
........
r25663 | tlinnet | 2014-09-05 11:09:47 +0200 (Fri, 05 Sep 2014) | 1 line
Fix for comments to dependency check of showApod.
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r25664 | tlinnet | 2014-09-05 11:09:49 +0200 (Fri, 05 Sep 2014) | 1 line
Fix for raising error when calling showApod, and subprocess module not
available.
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r25665 | tlinnet | 2014-09-05 11:09:51 +0200 (Fri, 05 Sep 2014) | 1 line
Fix for the dependency check for showApod in systemtests.
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r25666 | tlinnet | 2014-09-05 11:09:53 +0200 (Fri, 05 Sep 2014) | 3 lines
Further extended the protocol for repeated dispersion analysis.
Task #7826 (https://gna.org/task/index.php?7826): Write an python class for
the repeated analysis of dispersion data.
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r25667 | tlinnet | 2014-09-05 11:09:54 +0200 (Fri, 05 Sep 2014) | 3 lines
Extended the systemtest for the protocol for repeated dispersion analysis.
Task #7826 (https://gna.org/task/index.php?7826): Write an python class for
the repeated analysis of dispersion data.
........
r25668 | bugman | 2014-09-05 11:31:06 +0200 (Fri, 05 Sep 2014) | 6 lines
Added a relaxation dispersion model profiling log file for relax version
3.3.0 vs. 3.2.3.
This is the output from the dispersion model profiling master script.
These numbers will be used
for the relax 3.3.0 release notes (http://wiki.nmr-relax.com/Relax_3.3.0).
........
r25669 | bugman | 2014-09-05 11:37:50 +0200 (Fri, 05 Sep 2014) | 5 lines
Fixes for the relax 3.3.0 vs. 3.2.3 dispersion model profiling log file.
The numeric model numbers were incorrectly scaled and a factor of 10 too
high.
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r25670 | bugman | 2014-09-05 11:39:06 +0200 (Fri, 05 Sep 2014) | 3 lines
Fixes for the scaling factors in the dispersion model super profiling
script.
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r25671 | bugman | 2014-09-05 11:51:53 +0200 (Fri, 05 Sep 2014) | 5 lines
Editing of the relax 3.3.0 features section of the CHANGES file.
This will be used for the release notes.
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r25672 | tlinnet | 2014-09-05 12:00:19 +0200 (Fri, 05 Sep 2014) | 3 lines
Added more test data for the repeated analysis.
task #7826(https://gna.org/task/index.php?7826): Write an python class for
the repeated analysis of dispersion data.
........
r25674 | bugman | 2014-09-05 17:37:16 +0200 (Fri, 05 Sep 2014) | 6 lines
Updated the Baldwin 2014 reference in the relax manual.
The pybliographic software was used to format this BibTeX entry
(http://pybliographer.org/). This
was updated as volume and page number information is now available.
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r25675 | bugman | 2014-09-05 17:40:32 +0200 (Fri, 05 Sep 2014) | 5 lines
Updated the Morin et al, 2014 paper (the relax relaxation dispersion paper)
reference in the manual.
The paper now has volume and page information.
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r25676 | bugman | 2014-09-06 13:04:31 +0200 (Sat, 06 Sep 2014) | 6 lines
Added some more user function ranamings to the translation table.
These were identified while preparing the release notes on the wiki
(http://wiki.nmr-relax.com/Category:Release_Notes,
http://wiki.nmr-relax.com/Release_notes).
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r25677 | tlinnet | 2014-09-07 19:31:24 +0200 (Sun, 07 Sep 2014) | 5 lines
Stored a frequency dependent dictionary with spectrum ids and reÃpeatead
PMG frequencies in setup pipe.
This information will progress out through children pipes.
Task #7826 (https://gna.org/task/index.php?7826): Write an python class for
the repeated analysis of dispersion data.
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r25678 | tlinnet | 2014-09-07 19:31:30 +0200 (Sun, 07 Sep 2014) | 3 lines
Further extended methods in the tclass for repeated analysis of dispersion
data.
Task #7826 (https://gna.org/task/index.php?7826): Write an python class for
the repeated analysis of dispersion data.
........
r25679 | bugman | 2014-09-08 08:59:39 +0200 (Mon, 08 Sep 2014) | 5 lines
Updated the release checklist document, including adding a section about
cross-linking.
The cross-linking is important for search engine indexing.
........
r25681 | bugman | 2014-09-08 17:53:44 +0200 (Mon, 08 Sep 2014) | 3 lines
Created a simple script for printing out the names of all user functions.
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r25682 | bugman | 2014-09-08 18:40:48 +0200 (Mon, 08 Sep 2014) | 5 lines
Added listings of all user functions from relax version 2.0.0 all the way
to relax 3.3.0.
This will be used to look at how the user function names have changed with
time.
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r25683 | bugman | 2014-09-08 18:41:45 +0200 (Mon, 08 Sep 2014) | 3 lines
Added a script and log file for comparing relax user function differences
between versions.
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r25684 | bugman | 2014-09-08 18:46:12 +0200 (Mon, 08 Sep 2014) | 3 lines
Created a document for relax users which follows the changes to the user
function names.
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r25685 | tlinnet | 2014-09-08 18:49:34 +0200 (Mon, 08 Sep 2014) | 5 lines
For the user function, spin.display(), added the print out of spin id, and
status for selection.
This is to help with showing the spin id string for selection, and the
current status of selection.
task #7826(https://gna.org/task/index.php?7826): Write an python class for
the repeated analysis of dispersion data.
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r25686 | tlinnet | 2014-09-08 18:49:41 +0200 (Mon, 08 Sep 2014) | 7 lines
To the back-end of display pipes, added functionality to sort the pipe
names before printing.
Also added the return of the list of pipes, with its associated information
about pipe type, and pipe_bundle.
This is to help with getting a better overview for multiple pipes in data
store.
task #7826(https://gna.org/task/index.php?7826): Write an python class for
the repeated analysis of dispersion data.
........
r25687 | tlinnet | 2014-09-08 18:49:43 +0200 (Mon, 08 Sep 2014) | 3 lines
Parsed the force flag from front end of value.set to back end.
Bug #22598 (https://gna.org/bugs/index.php?22598). Back end of value.set
does not respect force=False flag.
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r25688 | tlinnet | 2014-09-08 18:49:45 +0200 (Mon, 08 Sep 2014) | 5 lines
Broke optimisation function into smaller functions.
This is to help selecting spins, do particular grid search and minimise.
Task #7826 (https://gna.org/task/index.php?7826): Write an python class for
the repeated analysis of dispersion data.
........
r25689 | tlinnet | 2014-09-08 18:49:47 +0200 (Mon, 08 Sep 2014) | 3 lines
Modified system test to follow the new functions in the auto analysis.
Task #7826 (https://gna.org/task/index.php?7826): Write an python class for
the repeated analysis of dispersion data.
........
r25690 | bugman | 2014-09-08 18:55:05 +0200 (Mon, 08 Sep 2014) | 3 lines
Shifted the user function listing script into the test suite directory
where the results are.
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r25691 | bugman | 2014-09-08 18:56:52 +0200 (Mon, 08 Sep 2014) | 3 lines
Created a script for printing out relax 1.3 user functions.
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r25692 | bugman | 2014-09-08 19:01:01 +0200 (Mon, 08 Sep 2014) | 3 lines
Fix for the relax 1.3 user function extraction script.
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r25693 | bugman | 2014-09-08 19:08:46 +0200 (Mon, 08 Sep 2014) | 5 lines
Stripped out all of the relax intro and script printouts from the user
function listing files.
This allows the diff.py script to be simplified.
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r25694 | bugman | 2014-09-08 19:27:08 +0200 (Mon, 08 Sep 2014) | 6 lines
Updated the relax 1.3 user function printout script and added many
printouts.
The printouts are for relax versions 1.3.5 to 1.3.16. The earlier relax
versions used the relax 1.2
user function setup.
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r25695 | bugman | 2014-09-08 19:54:58 +0200 (Mon, 08 Sep 2014) | 5 lines
Created a script for printing out all user functions for relax 1.2 versions.
This also includes the relax 1.3.0 to 1.3.4 versions.
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r25696 | bugman | 2014-09-08 19:55:20 +0200 (Mon, 08 Sep 2014) | 3 lines
Added the relax 1.3.0 to 1.3.4 user function printouts.
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r25697 | bugman | 2014-09-08 19:59:40 +0200 (Mon, 08 Sep 2014) | 6 lines
Changed the behaviour of the script for showing user function difference
between relax versions.
The relax versions are now reversed so the oldest version is at the bottom
of the difference
printout.
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r25698 | bugman | 2014-09-08 20:14:12 +0200 (Mon, 08 Sep 2014) | 5 lines
Added the relax 1.0.1 to 1.2.15 user function printouts.
The diff.log file has also been updated with all of these versions.
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r25699 | bugman | 2014-09-08 20:15:35 +0200 (Mon, 08 Sep 2014) | 6 lines
Updated the user_function_changes.txt document.
This now lists all changes in the user function naming from relax version
1.0.1 all the way to relax
3.3.0.
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r25700 | bugman | 2014-09-08 20:21:53 +0200 (Mon, 08 Sep 2014) | 5 lines
Added all remaining user function ranamings since relax 2.0.0 to the
translation table.
These were taken directly from the docs/user_function_changes.txt document.
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r25701 | bugman | 2014-09-08 20:29:43 +0200 (Mon, 08 Sep 2014) | 9 lines
Added all user function ranamings since relax 1.3.1 to the translation
table.
These were taken directly from the docs/user_function_changes.txt document.
Earlier relax versions
are far too different, so this will be the earliest relax version for this
translation table. The
relax 1.2 and earlier (and 1.3.0) versions used the run argument throughout
and the scripting was so
different, that telling the user how to upgrade to new user functions is
pointless. And the release
date of relax 1.2.15, the last of these old designs was in November 2008.
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r25702 | bugman | 2014-09-08 20:35:02 +0200 (Mon, 08 Sep 2014) | 5 lines
Changed the order of the two relax versions being compared for user
function changes.
This is in the diff.py script and log file and the
user_function_changes.txt document.
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r25703 | bugman | 2014-09-08 20:35:35 +0200 (Mon, 08 Sep 2014) | 3 lines
Spacing fix in the user_function_changes.txt document.
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r25704 | bugman | 2014-09-08 20:39:52 +0200 (Mon, 08 Sep 2014) | 8 lines
Changed the organisation of the files in the docs/ directory.
A new docs/devel directory has been created and the 2to3_checklist,
Mac_framework_build_3way,
package_layout, and prompt_screenshot.txt documents shifted into it. This
is to hide or abstract
away the development documents so that relax users do not see them when
looking into docs/. This
should make the directory less intimidating.
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r25705 | bugman | 2014-09-08 20:40:59 +0200 (Mon, 08 Sep 2014) | 3 lines
Shifted the Release_Checklist document into docs/devel/ to hide it from
users.
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r25706 | bugman | 2014-09-08 20:42:54 +0200 (Mon, 08 Sep 2014) | 3 lines
Editing of the user_function_changes.txt document.
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r25707 | bugman | 2014-09-08 20:48:17 +0200 (Mon, 08 Sep 2014) | 5 lines
Correction for the noe.read to spectrum.read_intensities user function
change.
This is for the translation table used to catch old user function calls.
........
Added:
branches/frame_order_cleanup/docs/devel/
- copied from r25707, trunk/docs/devel/
branches/frame_order_cleanup/docs/user_function_changes.txt
- copied unchanged from r25707, trunk/docs/user_function_changes.txt
branches/frame_order_cleanup/test_suite/shared_data/dispersion/profiling/disp_profile_all_3.3.0_vs_3.2.3.log
- copied unchanged from r25707,
trunk/test_suite/shared_data/dispersion/profiling/disp_profile_all_3.3.0_vs_3.2.3.log
branches/frame_order_cleanup/test_suite/shared_data/dispersion/repeated_analysis/SOD1/cpmg_disp_sod1d90a_060518/cpmg_disp_sod1d90a_060518_normal.fid/analysis_FT/ser_files/FT/4_FT.ser
- copied unchanged from r25707,
trunk/test_suite/shared_data/dispersion/repeated_analysis/SOD1/cpmg_disp_sod1d90a_060518/cpmg_disp_sod1d90a_060518_normal.fid/analysis_FT/ser_files/FT/4_FT.ser
branches/frame_order_cleanup/test_suite/shared_data/dispersion/repeated_analysis/SOD1/cpmg_disp_sod1d90a_060518/cpmg_disp_sod1d90a_060518_normal.fid/analysis_FT/ser_files/FT/6_FT.ser
- copied unchanged from r25707,
trunk/test_suite/shared_data/dispersion/repeated_analysis/SOD1/cpmg_disp_sod1d90a_060518/cpmg_disp_sod1d90a_060518_normal.fid/analysis_FT/ser_files/FT/6_FT.ser
branches/frame_order_cleanup/test_suite/shared_data/dispersion/repeated_analysis/SOD1/cpmg_disp_sod1d90a_060518/cpmg_disp_sod1d90a_060518_normal.fid/analysis_FT/ser_files/MDD/
- copied from r25707,
trunk/test_suite/shared_data/dispersion/repeated_analysis/SOD1/cpmg_disp_sod1d90a_060518/cpmg_disp_sod1d90a_060518_normal.fid/analysis_FT/ser_files/MDD/
branches/frame_order_cleanup/test_suite/shared_data/dispersion/repeated_analysis/SOD1/cpmg_disp_sod1d90a_060518/cpmg_disp_sod1d90a_060518_normal.fid/ft2_data/126_0_MDD.rmsd
- copied unchanged from r25707,
trunk/test_suite/shared_data/dispersion/repeated_analysis/SOD1/cpmg_disp_sod1d90a_060518/cpmg_disp_sod1d90a_060518_normal.fid/ft2_data/126_0_MDD.rmsd
branches/frame_order_cleanup/test_suite/shared_data/dispersion/repeated_analysis/SOD1/cpmg_disp_sod1d90a_060518/cpmg_disp_sod1d90a_060518_normal.fid/ft2_data/126_10_MDD.rmsd
- copied unchanged from r25707,
trunk/test_suite/shared_data/dispersion/repeated_analysis/SOD1/cpmg_disp_sod1d90a_060518/cpmg_disp_sod1d90a_060518_normal.fid/ft2_data/126_10_MDD.rmsd
branches/frame_order_cleanup/test_suite/shared_data/dispersion/repeated_analysis/SOD1/cpmg_disp_sod1d90a_060518/cpmg_disp_sod1d90a_060518_normal.fid/ft2_data/126_11_MDD.rmsd
- copied unchanged from r25707,
trunk/test_suite/shared_data/dispersion/repeated_analysis/SOD1/cpmg_disp_sod1d90a_060518/cpmg_disp_sod1d90a_060518_normal.fid/ft2_data/126_11_MDD.rmsd
branches/frame_order_cleanup/test_suite/shared_data/dispersion/repeated_analysis/SOD1/cpmg_disp_sod1d90a_060518/cpmg_disp_sod1d90a_060518_normal.fid/ft2_data/126_12_MDD.rmsd
- copied unchanged from r25707,
trunk/test_suite/shared_data/dispersion/repeated_analysis/SOD1/cpmg_disp_sod1d90a_060518/cpmg_disp_sod1d90a_060518_normal.fid/ft2_data/126_12_MDD.rmsd
branches/frame_order_cleanup/test_suite/shared_data/dispersion/repeated_analysis/SOD1/cpmg_disp_sod1d90a_060518/cpmg_disp_sod1d90a_060518_normal.fid/ft2_data/126_13_MDD.rmsd
- copied unchanged from r25707,
trunk/test_suite/shared_data/dispersion/repeated_analysis/SOD1/cpmg_disp_sod1d90a_060518/cpmg_disp_sod1d90a_060518_normal.fid/ft2_data/126_13_MDD.rmsd
branches/frame_order_cleanup/test_suite/shared_data/dispersion/repeated_analysis/SOD1/cpmg_disp_sod1d90a_060518/cpmg_disp_sod1d90a_060518_normal.fid/ft2_data/126_14_MDD.rmsd
- copied unchanged from r25707,
trunk/test_suite/shared_data/dispersion/repeated_analysis/SOD1/cpmg_disp_sod1d90a_060518/cpmg_disp_sod1d90a_060518_normal.fid/ft2_data/126_14_MDD.rmsd
branches/frame_order_cleanup/test_suite/shared_data/dispersion/repeated_analysis/SOD1/cpmg_disp_sod1d90a_060518/cpmg_disp_sod1d90a_060518_normal.fid/ft2_data/126_15_MDD.rmsd
- copied unchanged from r25707,
trunk/test_suite/shared_data/dispersion/repeated_analysis/SOD1/cpmg_disp_sod1d90a_060518/cpmg_disp_sod1d90a_060518_normal.fid/ft2_data/126_15_MDD.rmsd
branches/frame_order_cleanup/test_suite/shared_data/dispersion/repeated_analysis/SOD1/cpmg_disp_sod1d90a_060518/cpmg_disp_sod1d90a_060518_normal.fid/ft2_data/126_16_MDD.rmsd
- copied unchanged from r25707,
trunk/test_suite/shared_data/dispersion/repeated_analysis/SOD1/cpmg_disp_sod1d90a_060518/cpmg_disp_sod1d90a_060518_normal.fid/ft2_data/126_16_MDD.rmsd
branches/frame_order_cleanup/test_suite/shared_data/dispersion/repeated_analysis/SOD1/cpmg_disp_sod1d90a_060518/cpmg_disp_sod1d90a_060518_normal.fid/ft2_data/126_17_MDD.rmsd
- copied unchanged from r25707,
trunk/test_suite/shared_data/dispersion/repeated_analysis/SOD1/cpmg_disp_sod1d90a_060518/cpmg_disp_sod1d90a_060518_normal.fid/ft2_data/126_17_MDD.rmsd
branches/frame_order_cleanup/test_suite/shared_data/dispersion/repeated_analysis/SOD1/cpmg_disp_sod1d90a_060518/cpmg_disp_sod1d90a_060518_normal.fid/ft2_data/126_18_MDD.rmsd
- copied unchanged from r25707,
trunk/test_suite/shared_data/dispersion/repeated_analysis/SOD1/cpmg_disp_sod1d90a_060518/cpmg_disp_sod1d90a_060518_normal.fid/ft2_data/126_18_MDD.rmsd
branches/frame_order_cleanup/test_suite/shared_data/dispersion/repeated_analysis/SOD1/cpmg_disp_sod1d90a_060518/cpmg_disp_sod1d90a_060518_normal.fid/ft2_data/126_1_MDD.rmsd
- copied unchanged from r25707,
trunk/test_suite/shared_data/dispersion/repeated_analysis/SOD1/cpmg_disp_sod1d90a_060518/cpmg_disp_sod1d90a_060518_normal.fid/ft2_data/126_1_MDD.rmsd
branches/frame_order_cleanup/test_suite/shared_data/dispersion/repeated_analysis/SOD1/cpmg_disp_sod1d90a_060518/cpmg_disp_sod1d90a_060518_normal.fid/ft2_data/126_2_MDD.rmsd
- copied unchanged from r25707,
trunk/test_suite/shared_data/dispersion/repeated_analysis/SOD1/cpmg_disp_sod1d90a_060518/cpmg_disp_sod1d90a_060518_normal.fid/ft2_data/126_2_MDD.rmsd
branches/frame_order_cleanup/test_suite/shared_data/dispersion/repeated_analysis/SOD1/cpmg_disp_sod1d90a_060518/cpmg_disp_sod1d90a_060518_normal.fid/ft2_data/126_3_MDD.rmsd
- copied unchanged from r25707,
trunk/test_suite/shared_data/dispersion/repeated_analysis/SOD1/cpmg_disp_sod1d90a_060518/cpmg_disp_sod1d90a_060518_normal.fid/ft2_data/126_3_MDD.rmsd
branches/frame_order_cleanup/test_suite/shared_data/dispersion/repeated_analysis/SOD1/cpmg_disp_sod1d90a_060518/cpmg_disp_sod1d90a_060518_normal.fid/ft2_data/126_4_MDD.rmsd
- copied unchanged from r25707,
trunk/test_suite/shared_data/dispersion/repeated_analysis/SOD1/cpmg_disp_sod1d90a_060518/cpmg_disp_sod1d90a_060518_normal.fid/ft2_data/126_4_MDD.rmsd
branches/frame_order_cleanup/test_suite/shared_data/dispersion/repeated_analysis/SOD1/cpmg_disp_sod1d90a_060518/cpmg_disp_sod1d90a_060518_normal.fid/ft2_data/126_5_MDD.rmsd
- copied unchanged from r25707,
trunk/test_suite/shared_data/dispersion/repeated_analysis/SOD1/cpmg_disp_sod1d90a_060518/cpmg_disp_sod1d90a_060518_normal.fid/ft2_data/126_5_MDD.rmsd
[... 352 lines stripped ...]
r25708 - in /branches/frame_order_cleanup: ./ auto_analyses/ docs/ docs/devel/ docs/latex/ lib/spectrum/ pipe_control/ test_...