Author: bugman
Date: Thu Oct 4 10:16:28 2012
New Revision: 17694
URL: http://svn.gna.org/viewcvs/relax?rev=17694&view=rev
Log:
Merged revisions
17254-17255,17272,17274,17295,17332,17337-17359,17361-17365,17367-17376,17378-17389,17391-17538,17540,17542,17552-17687
via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/trunk
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r17254 | bugman | 2012-07-16 12:02:30 +0200 (Mon, 16 Jul 2012) | 6 lines
Bug fix for the RDC Q factor calculations for when the dipolar constants
are not all the same.
Now instead of a RelaxError, a warning is given and the Q factor normalised
by 2Da^2(4 + 3R)/5 is
skipped. This allows long range and mixed nuclear pairs to be supported.
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r17255 | bugman | 2012-07-16 15:26:11 +0200 (Mon, 16 Jul 2012) | 5 lines
Added the 'unit' argument to the dipole_pair.read_dist and
dipole_pair.set_dist user functions.
This is to allow distances in Angstroms to be read into relax and converted
to meters.
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r17272 | bugman | 2012-07-17 16:46:28 +0200 (Tue, 17 Jul 2012) | 3 lines
Import clean ups for the N-state model specific module.
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r17274 | bugman | 2012-07-17 16:50:29 +0200 (Tue, 17 Jul 2012) | 3 lines
Removed an unused import.
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r17295 | bugman | 2012-07-23 15:44:47 +0200 (Mon, 23 Jul 2012) | 3 lines
Alphabetical ordering of the imports.
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r17332 | bugman | 2012-08-15 16:38:48 +0200 (Wed, 15 Aug 2012) | 7 lines
Redesign of how the GPL license is presented to the user.
The old prompt.gpl module with the version 2 of the license has been
deleted. Now the text form the
docs/COPYING file is passed through pydoc.pager for the './relax --licence'
and the prompt mode GPL
object, and is simply printed to STDOUT for the GUI help system.
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r17337 | bugman | 2012-08-27 11:05:17 +0200 (Mon, 27 Aug 2012) | 5 lines
Rewrote the relaxation curve-fitting chapter of the relax manual.
This chapter was quite out of date and was of no use to modern relax
versions!
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r17338 | bugman | 2012-08-27 11:09:07 +0200 (Mon, 27 Aug 2012) | 3 lines
Small fix for the sample script in the NOE chapter of the relax manual.
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r17339 | bugman | 2012-08-27 11:11:23 +0200 (Mon, 27 Aug 2012) | 3 lines
Small fix for the sample script in the relaxation curve-fitting chapter of
the relax manual.
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r17340 | bugman | 2012-08-27 11:43:17 +0200 (Mon, 27 Aug 2012) | 6 lines
The fetch_docstrings.py now adds LaTeX labels to each user function section.
This has the form of 'uf: ' followed by the user function name, and is for
referencing purposes
within the main text.
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r17341 | bugman | 2012-08-27 11:55:55 +0200 (Mon, 27 Aug 2012) | 3 lines
Added screenshots of Xmgrace displaying relaxation curves.
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r17342 | bugman | 2012-08-27 11:58:38 +0200 (Mon, 27 Aug 2012) | 5 lines
Improvements to the final section of the relaxation curve-fitting chapter.
The Xmgrace screenshot and page references for the user functions have been
added.
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r17343 | bugman | 2012-08-27 12:06:44 +0200 (Mon, 27 Aug 2012) | 3 lines
Small fix for the model-free chapter of the relax manual.
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r17344 | bugman | 2012-08-27 12:25:29 +0200 (Mon, 27 Aug 2012) | 5 lines
Modified the graphics.fetch_icon function to return different file formats.
This will be used for the relax manual where eps.gz files are required.
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r17345 | bugman | 2012-08-27 16:32:14 +0200 (Mon, 27 Aug 2012) | 6 lines
Large expansion of the Oxygen icons within relax.
All 128x128 versions of the icons used by the user functions have been
added as both PNG and gzipped
EPS files. A number of gzipped SVG icons has been added as well.
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r17346 | bugman | 2012-08-27 16:35:03 +0200 (Mon, 27 Aug 2012) | 6 lines
Large expansion of the relax icon set.
All 128x128 versions of the icons used by the user functions have been
added as both PNG and gzipped
EPS files. A few gzipped SVG and non-sized icons have been added as well.
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r17347 | bugman | 2012-08-27 19:10:54 +0200 (Mon, 27 Aug 2012) | 9 lines
Redesigned the formatting of the user function chapter of the relax manual.
The fetch_docstrings.py now forces each user function to start in a new
column. This increases the
size of the manual, but makes the reading of the user function
documentation much easier. The user
function class and function icons (128x128 format) are now placed between
the top bar and the
subsection title and are left and right justified. This prettification
simply allows the user
functions to be more quickly identified.
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r17348 | bugman | 2012-08-27 19:59:38 +0200 (Mon, 27 Aug 2012) | 3 lines
Removed some now useless whitespace from the top of each user function
subsection of the manual.
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r17349 | bugman | 2012-08-28 14:01:17 +0200 (Tue, 28 Aug 2012) | 3 lines
Created EPS versions of a number of wizard graphics for use in the user
manual.
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r17350 | bugman | 2012-08-28 14:21:35 +0200 (Tue, 28 Aug 2012) | 3 lines
Updated the screenshot of the pipe editor window.
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r17351 | bugman | 2012-08-28 14:50:55 +0200 (Tue, 28 Aug 2012) | 3 lines
Updates to the generic_fns.mol_res_spin.id_string_doc documentation
structure.
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r17352 | bugman | 2012-08-28 14:51:57 +0200 (Tue, 28 Aug 2012) | 5 lines
The user manual now specifies the repository revision if a non-tagged
version is built.
This enables easier tracking and editing of the manual.
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r17353 | bugman | 2012-08-28 14:52:30 +0200 (Tue, 28 Aug 2012) | 3 lines
Updates and small expansion of the intro chapter of the relax user manual.
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r17354 | bugman | 2012-08-28 15:20:27 +0200 (Tue, 28 Aug 2012) | 3 lines
Converted some more wizard graphics to the EPS format for the user manual.
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r17355 | bugman | 2012-08-28 15:23:43 +0200 (Tue, 28 Aug 2012) | 3 lines
Fix for the pipe editor window screenshot width in the relax manual.
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r17356 | bugman | 2012-08-28 15:32:04 +0200 (Tue, 28 Aug 2012) | 3 lines
Created a new chapter for the relax user manual titled 'The relax data
model'.
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r17357 | bugman | 2012-08-28 15:32:31 +0200 (Tue, 28 Aug 2012) | 3 lines
Added some more abbreviations to the relax user manual.
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r17358 | bugman | 2012-08-28 15:59:16 +0200 (Tue, 28 Aug 2012) | 3 lines
Added the Morin and Gagne 2009 reference for the consistency testing.
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r17359 | bugman | 2012-08-28 16:03:18 +0200 (Tue, 28 Aug 2012) | 5 lines
Improvements to the 'Supported NMR theories' section of the user manual
introduction.
This includes the addition of the Morin and Gagne 2009 reference!!!
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r17361 | bugman | 2012-08-28 17:28:52 +0200 (Tue, 28 Aug 2012) | 3 lines
Added the Fushman 1999 reference and a few formatting fixes in other
references.
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r17362 | bugman | 2012-08-28 17:29:48 +0200 (Tue, 28 Aug 2012) | 5 lines
Created the new 'Citations' chapter of the relax user manual.
This is to clearly outline to the user the citations required for the
various components of relax.
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r17363 | bugman | 2012-08-28 18:46:56 +0200 (Tue, 28 Aug 2012) | 5 lines
Modified the relax LaTeX bibliography style file relax.bst to convert DOI
numbers to hyperlinks.
This is to add links to the references within the relax user manual.
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r17364 | bugman | 2012-08-28 18:57:01 +0200 (Tue, 28 Aug 2012) | 3 lines
Slight modification of the DOI hyperlink formatting bibliography style for
the user manual.
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r17365 | bugman | 2012-08-28 19:14:29 +0200 (Tue, 28 Aug 2012) | 5 lines
The LaTeX bibliography style for PhD theses now includes the DOI hyperlink.
This is for the user manual.
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r17367 | bugman | 2012-08-28 19:33:25 +0200 (Tue, 28 Aug 2012) | 3 lines
Added and fixed DOI numbers for many bibliographic entries.
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r17368 | bugman | 2012-08-28 20:40:27 +0200 (Tue, 28 Aug 2012) | 5 lines
Added a tonne of DOI numbers to the relax user manual bibliography.
This will simplify accessing these references for the user.
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r17369 | bugman | 2012-08-28 21:12:06 +0200 (Tue, 28 Aug 2012) | 3 lines
Expansion of the abbreviations chapter of the relax user manual.
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r17370 | bugman | 2012-08-28 21:13:59 +0200 (Tue, 28 Aug 2012) | 3 lines
Added another abbreviation.
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r17371 | bugman | 2012-08-28 22:05:23 +0200 (Tue, 28 Aug 2012) | 3 lines
Edits to the abbreviations chapter of the relax user manual.
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r17372 | bugman | 2012-08-28 22:13:48 +0200 (Tue, 28 Aug 2012) | 3 lines
Small edits of the relax user manual.
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r17373 | bugman | 2012-08-29 10:55:20 +0200 (Wed, 29 Aug 2012) | 5 lines
Shortened the Literature subsection of the intro chapter to point to the
citations chapter.
This part of the user manual is now redundant.
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r17374 | bugman | 2012-08-29 10:55:58 +0200 (Wed, 29 Aug 2012) | 3 lines
Added the Horne 2007 paper to the 'Supported NMR theories' subsection of
the user manual intro.
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r17375 | bugman | 2012-08-29 10:57:22 +0200 (Wed, 29 Aug 2012) | 5 lines
Added the Horne 2007 paper to the 'Citations' chapter of the user manual.
Whitespace has also been cleaned up, and a chapter label added.
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r17376 | bugman | 2012-08-29 11:03:26 +0200 (Wed, 29 Aug 2012) | 3 lines
More chapter cross referencing in the relax user manual.
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r17378 | bugman | 2012-08-29 11:17:10 +0200 (Wed, 29 Aug 2012) | 3 lines
Added the Fushman et al., 1999 reference for consistency testing to the
intro chapter of the user manual.
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r17379 | bugman | 2012-08-29 11:29:30 +0200 (Wed, 29 Aug 2012) | 3 lines
Added EPS versions of the specific analysis graphics for use in the user
manual.
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r17380 | bugman | 2012-08-29 11:58:31 +0200 (Wed, 29 Aug 2012) | 3 lines
Small edit of the 'Citations' chapter of the relax user manual.
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r17381 | bugman | 2012-08-29 11:59:17 +0200 (Wed, 29 Aug 2012) | 3 lines
Added the specific analysis graphics to the start of each chapter of the
relax user manual.
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r17382 | bugman | 2012-08-29 11:59:32 +0200 (Wed, 29 Aug 2012) | 3 lines
Expanded the size of the specific analysis graphics - mainly for use in the
relax user manual.
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r17383 | bugman | 2012-08-29 12:28:44 +0200 (Wed, 29 Aug 2012) | 3 lines
Added more high resolution graphics for use in the relax user manual.
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r17384 | bugman | 2012-08-29 12:35:45 +0200 (Wed, 29 Aug 2012) | 3 lines
Some more high quality graphics.
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r17385 | bugman | 2012-08-29 12:36:12 +0200 (Wed, 29 Aug 2012) | 3 lines
The relax data model chapter of the user manual now uses the higher quality
graphics.
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r17386 | bugman | 2012-08-29 12:36:38 +0200 (Wed, 29 Aug 2012) | 3 lines
Better figure layout in the NOE chapter of the user manual.
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r17387 | bugman | 2012-08-29 15:33:21 +0200 (Wed, 29 Aug 2012) | 3 lines
Created an initial rough version of the RSDM chapter of the user manual.
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r17388 | bugman | 2012-08-29 15:33:44 +0200 (Wed, 29 Aug 2012) | 3 lines
Added a label to the data model chapter of the user manual.
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r17389 | bugman | 2012-08-29 16:46:41 +0200 (Wed, 29 Aug 2012) | 3 lines
Fixed a bunch of links in the development chapter of the user manual.
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r17391 | bugman | 2012-08-30 11:02:04 +0200 (Thu, 30 Aug 2012) | 3 lines
Added a paragraph to the model-free chapter of the user manual explaining
the J(w) equation forms.
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r17392 | bugman | 2012-08-30 11:03:23 +0200 (Thu, 30 Aug 2012) | 3 lines
Fixed some citations in the newly introduced model-free J(w) paragraph.
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r17393 | bugman | 2012-08-30 11:13:54 +0200 (Thu, 30 Aug 2012) | 3 lines
Added a LaTeX label to the NOE chapter of the user manual.
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r17394 | bugman | 2012-08-30 11:14:21 +0200 (Thu, 30 Aug 2012) | 3 lines
Fixes for the referencing in the J(w) mapping chapter of the user manual.
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r17395 | bugman | 2012-08-30 16:40:40 +0200 (Thu, 30 Aug 2012) | 3 lines
Small description edit for the relax_data.temp_control user function.
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r17396 | bugman | 2012-08-30 16:42:48 +0200 (Thu, 30 Aug 2012) | 3 lines
Spell fix for the relax_data.temp_calibration user function description.
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r17397 | bugman | 2012-08-30 16:49:41 +0200 (Thu, 30 Aug 2012) | 3 lines
Fix for the incomplete relax_data.temp_control user function description.
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r17398 | bugman | 2012-08-30 16:50:46 +0200 (Thu, 30 Aug 2012) | 3 lines
Another fix for the relax_data.temp_control description.
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r17399 | bugman | 2012-08-30 17:43:09 +0200 (Thu, 30 Aug 2012) | 3 lines
Added the Viles et al., 2001 reference.
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r17400 | bugman | 2012-08-30 18:07:51 +0200 (Thu, 30 Aug 2012) | 5 lines
Added a new section called 'From spectra to peak intensities' to the Rx
fitting chapter of the manual.
This adds a number of recommendations for high quality relaxation rates.
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r17401 | bugman | 2012-08-30 18:11:27 +0200 (Thu, 30 Aug 2012) | 3 lines
The NOE chapter now points to the recommendations in the Rx fitting chapter.
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r17402 | bugman | 2012-08-30 18:11:49 +0200 (Thu, 30 Aug 2012) | 3 lines
Added the nth package for the user manual LaTeX compilation.
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r17403 | bugman | 2012-08-31 22:05:56 +0200 (Fri, 31 Aug 2012) | 6 lines
Bug fix for the loading of peak intensities via spectrum.read_intensities.
The user function could not be applied twice, preventing the loading of
data from different spin
systems such as Trp indole NH data.
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r17404 | bugman | 2012-08-31 22:16:37 +0200 (Fri, 31 Aug 2012) | 6 lines
Bug fix for the reading of Sparky peak lists.
Spin names with numbers at the end were not being correctly identified.
This fix allows Trp indole
NE1-HE1 data to be loaded.
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r17405 | bugman | 2012-08-31 23:35:22 +0200 (Fri, 31 Aug 2012) | 3 lines
Allowed the raggedbottom LaTeX setting as this is better for the screenshot
layout in the user manual.
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r17406 | bugman | 2012-08-31 23:36:07 +0200 (Fri, 31 Aug 2012) | 3 lines
Added some Sparky info to the Rx curve-fitting chapter of the user manual.
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r17407 | bugman | 2012-08-31 23:36:17 +0200 (Fri, 31 Aug 2012) | 3 lines
Added a section label.
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r17408 | bugman | 2012-08-31 23:42:01 +0200 (Fri, 31 Aug 2012) | 5 lines
Added a step-by-step tutorial for the GUI NOE auto-analysis to the user
manual.
This includes 22 screenshots of all the steps!
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r17409 | bugman | 2012-08-31 23:53:41 +0200 (Fri, 31 Aug 2012) | 3 lines
Modified the NOE sample script to include Trp indole NH data.
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r17410 | bugman | 2012-09-01 10:09:08 +0200 (Sat, 01 Sep 2012) | 6 lines
Added some Trp peak data (backbone and indole N) to the Sparky steady-state
NOE peak lists.
This is in preparation for the modification of the NOE system test to catch
bug #20119
(https://gna.org/bugs/index.php?20119).
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r17411 | bugman | 2012-09-01 10:17:30 +0200 (Sat, 01 Sep 2012) | 5 lines
Modified the NOE system test to test the usage of Trp indole 15N data.
This is to catch bug #20119 (https://gna.org/bugs/index.php?20119).
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r17412 | bugman | 2012-09-01 10:18:22 +0200 (Sat, 01 Sep 2012) | 5 lines
Significant update of the NOE chapter of the user manual.
The sample script used in this chapter was incredibly out of date!
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r17413 | bugman | 2012-09-01 11:05:16 +0200 (Sat, 01 Sep 2012) | 3 lines
Lots of editing of the NOE chapter of the user manual.
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r17414 | bugman | 2012-09-01 11:20:30 +0200 (Sat, 01 Sep 2012) | 3 lines
Modified the NOE system test to catch bug #20120
(https://gna.org/bugs/?20120).
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r17415 | bugman | 2012-09-01 11:21:54 +0200 (Sat, 01 Sep 2012) | 3 lines
Removed a debugging print out.
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r17416 | bugman | 2012-09-01 11:27:10 +0200 (Sat, 01 Sep 2012) | 6 lines
Fix for bug #20120 (https://gna.org/bugs/?20120), the bad Grace plots with
multiple spin types.
The grace data assembly function was not setting the correct index for when
a spin type changes to a
preexisting type.
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r17417 | bugman | 2012-09-01 13:13:01 +0200 (Sat, 01 Sep 2012) | 6 lines
Bug fix for the generic_fns.grace.get_data() function.
This was just recently introduced and was triggered by the
Relax_fit.test_bug_12670_12679 system
test.
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r17418 | bugman | 2012-09-01 14:58:49 +0200 (Sat, 01 Sep 2012) | 5 lines
Created the GUI wizard _apply() method for executing the current page's
_apply() method.
This is for the GUI tests to simulate a click on the 'Apply' button.
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r17419 | bugman | 2012-09-01 15:13:43 +0200 (Sat, 01 Sep 2012) | 5 lines
The spectrum.read_intensities user function now prints out a list of the
intensities read in.
This is for better user feedback as to what the user function has actually
done.
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r17420 | bugman | 2012-09-01 15:14:32 +0200 (Sat, 01 Sep 2012) | 3 lines
The NOE auto-analysis GUI test now checks the support for Trp indole N data
as well.
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r17421 | bugman | 2012-09-03 10:19:35 +0200 (Mon, 03 Sep 2012) | 3 lines
Fix for the spin.create user function documentation - the prompt examples
were wrong.
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r17422 | bugman | 2012-09-03 10:23:39 +0200 (Mon, 03 Sep 2012) | 3 lines
Created a directory for screenshots of the spin viewer window operation.
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r17423 | bugman | 2012-09-03 10:48:57 +0200 (Mon, 03 Sep 2012) | 3 lines
Changed the "View->Spin view" menu item to "View->Spin viewer".
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r17424 | bugman | 2012-09-03 11:11:48 +0200 (Mon, 03 Sep 2012) | 3 lines
Shifted the spin viewer screenshots into their own directory.
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r17425 | bugman | 2012-09-03 11:16:01 +0200 (Mon, 03 Sep 2012) | 5 lines
Redesign of the data model chapter of the user manual.
This includes the moving of all of the spin viewer window text and
screenshots from the NOE chapter.
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r17426 | bugman | 2012-09-03 11:28:42 +0200 (Mon, 03 Sep 2012) | 3 lines
Added screenshots of the spin viewer spin loading wizard sequence.read page.
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r17427 | bugman | 2012-09-03 11:43:36 +0200 (Mon, 03 Sep 2012) | 6 lines
More rearrangements of data model and NOE chapters of the relax manual.
The GUI spin deselection part of the NOE chapter has been shifted into the
data model chapter. And
the GUI loading of spins from a sequence file section has been completed.
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r17428 | bugman | 2012-09-03 12:06:00 +0200 (Mon, 03 Sep 2012) | 6 lines
Defined a new set of LaTeX commands for prompt/script/GUI strings and
elements for the user manual.
These will be used to regularize the text throughout the manual, as this is
currently quite mixed
up.
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r17429 | bugman | 2012-09-03 12:16:00 +0200 (Mon, 03 Sep 2012) | 3 lines
Added some more LaTeX functions for formatting consistency.
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r17430 | bugman | 2012-09-03 13:29:09 +0200 (Mon, 03 Sep 2012) | 3 lines
Removed some '()' text from the end of the user functions in the user
function documentation.
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r17431 | bugman | 2012-09-03 14:13:37 +0200 (Mon, 03 Sep 2012) | 6 lines
Improved the consistency on the user manual by using the new LaTeX commands.
These changes are throughout the manual and affect all the text of user
functions, menu items,
prompt examples, GUI elements, files, directories, etc.
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r17432 | bugman | 2012-09-03 14:22:16 +0200 (Mon, 03 Sep 2012) | 3 lines
Clean up of a paragraph of the data model chapter of the user manual.
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r17433 | bugman | 2012-09-03 14:24:13 +0200 (Mon, 03 Sep 2012) | 6 lines
[... 2803 lines stripped ...]
r17694 - in /branches/inversion-recovery: ./ auto_analyses/ data/ docs/ docs/html/ docs/latex/ extern/scientific_python/Geom...