Merged revisions 17254-17255,17272,17274,17295,17332,17337-17359,17361-17365,17367-17376,17378-17389,17391-17538,17540,17542,17552-17686 via svnmerge from
svn+ssh://bugman@.../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This chapter was quite out of date and was of no use to modern relax versions!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
Changed the order of the Rx curve-fitting and NOE chapters in the relax manual.
This is because the NOE chapter references passages from the Rx curve-fitting chapter, so it's more
logical to have the Rx curve-fitting chapter first.
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r17434 | bugman | 2012-09-03 14:51:11 +0200 (Mon, 03 Sep 2012) | 3 lines
Fix for the Farrow et al., 1995 DOI number.
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r17435 | bugman | 2012-09-03 15:03:36 +0200 (Mon, 03 Sep 2012) | 3 lines
Added the Fushman et al., 1998 reference.
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r17436 | bugman | 2012-09-03 15:06:25 +0200 (Mon, 03 Sep 2012) | 3 lines
Added the other consistency testing references to the citation chapter of the manual.
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r17437 | bugman | 2012-09-03 15:06:52 +0200 (Mon, 03 Sep 2012) | 3 lines
Added a LaTeX label to the J(w) mapping chapter.
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r17438 | bugman | 2012-09-03 15:13:16 +0200 (Mon, 03 Sep 2012) | 3 lines
Activated the consistency testing chapter of the user manual.
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r17439 | bugman | 2012-09-03 15:13:38 +0200 (Mon, 03 Sep 2012) | 3 lines
Large edits of the consistency testing chapter of the user manual.
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r17440 | bugman | 2012-09-03 17:37:14 +0200 (Mon, 03 Sep 2012) | 3 lines
Added trp indole NH loading into the relaxation curve-fitting sample script.
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r17441 | bugman | 2012-09-03 22:34:03 +0200 (Mon, 03 Sep 2012) | 6 lines
Editing of the relaxation curve-fitting and NOE chapters of the user manual.
This is to synchronise the format of the two chapters, and includes the swapping of text between
them.
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r17442 | bugman | 2012-09-03 23:07:07 +0200 (Mon, 03 Sep 2012) | 3 lines
Small edits of the relax data model chapter of the user manual.
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r17443 | bugman | 2012-09-04 11:52:07 +0200 (Tue, 04 Sep 2012) | 3 lines
Added some Grace plots from an NOE analysis for use in the user manual.
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r17444 | bugman | 2012-09-04 16:51:24 +0200 (Tue, 04 Sep 2012) | 5 lines
Added a tonne of GUI screenshots of an R1 analysis.
These will be used in the relaxation curve-fitting chapter of the user manual.
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r17445 | bugman | 2012-09-04 16:51:25 +0200 (Tue, 04 Sep 2012) | 7 lines
Large expansion and lots of editing of the relaxation curve-fitting chapter of the user manual.
The GUI section has been added which includes step-by-step instructions on how to use relax,
illustrated with screenshots at each step. There has been general editing of the whole of the
chapter as well.
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r17446 | bugman | 2012-09-04 16:52:00 +0200 (Tue, 04 Sep 2012) | 3 lines
Editing of the relax data model chapter of the user manual.
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r17447 | bugman | 2012-09-04 16:52:34 +0200 (Tue, 04 Sep 2012) | 3 lines
The old R1 and R2 analysis screenshots have been shifted to the intro chapter.
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r17448 | bugman | 2012-09-04 16:53:06 +0200 (Tue, 04 Sep 2012) | 3 lines
Some editing of the NOE chapter of the relax user manual.
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r17449 | bugman | 2012-09-04 17:11:43 +0200 (Tue, 04 Sep 2012) | 3 lines
Fix for bug #20133 (https://gna.org/bugs/?20133) - this was simply a missing import.
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r17450 | bugman | 2012-09-05 12:12:02 +0200 (Wed, 05 Sep 2012) | 3 lines
Editing of the nmrPipe script in the Rx curve-fitting chapter of the manual.
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r17451 | semor | 2012-09-05 13:52:36 +0200 (Wed, 05 Sep 2012) | 6 lines
Added some text and a reference to the consistency testing chapter.
This follows a discussion started by Edward d'Auvergne at:
https://mail.gna.org/public/relax-devel/2012-09/msg00019.html
(Message-id: <CAED9pY8XhmmvyfBS7mZA8XZ=4mJZe9TuGjARHoV2tVcjjV9SrQ@...>)
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r17452 | bugman | 2012-09-05 13:52:45 +0200 (Wed, 05 Sep 2012) | 5 lines
Bug fix for the creation of 2D graphs via grace.write for when many data sets exist.
The algorithm for setting the Grace symbol number to be between 1 and 10 was broken!
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r17453 | semor | 2012-09-05 14:16:17 +0200 (Wed, 05 Sep 2012) | 8 lines
Added text to detail the usage of the consistency testing script.
This text was modified from the corresponding text for jw_mapping.
This follows a discussion started by Edward d'Auvergne at:
https://mail.gna.org/public/relax-devel/2012-09/msg00019.html
(Message-id: <CAED9pY8XhmmvyfBS7mZA8XZ=4mJZe9TuGjARHoV2tVcjjV9SrQ@...>)
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r17454 | bugman | 2012-09-05 14:18:38 +0200 (Wed, 05 Sep 2012) | 3 lines
Deletion of the relax version LaTeX file - this is automatically created anyway.
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r17455 | semor | 2012-09-05 14:20:52 +0200 (Wed, 05 Sep 2012) | 8 lines
Added the DOI to reference Morin11 and fixed indentation.
10.1016/j.pnmrs.2010.12.003
This follows a comment by Edward d'Auvergne at:
https://mail.gna.org/public/relax-devel/2012-09/msg00022.html
(Message-id: <CAED9pY-ikjPvGaRPADHRJpLGFGnoeu+yNp5D1hLLm1U70maAwA@...>)
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r17456 | semor | 2012-09-05 14:25:48 +0200 (Wed, 05 Sep 2012) | 3 lines
Made some corrections to the formatting of math symbols in Latex.
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r17457 | semor | 2012-09-05 14:48:42 +0200 (Wed, 05 Sep 2012) | 8 lines
Corrected the bibliography entries whih were still in plain text and not as a Latex \cite call...
Also renamed the MorinGagne09 entry to MorinGagne09a as there is now also MorinGagne09b.
This was proposed by Edward d'Auvergne in a post at:
https://mail.gna.org/public/relax-devel/2012-09/msg00025.html
(Message-id: <CAED9pY9uKUd_OesCvDLqv2fGPoLDHB4ftrbW1-y6df4oQtbWyg@...>)
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r17458 | semor | 2012-09-05 15:08:57 +0200 (Wed, 05 Sep 2012) | 6 lines
Added a directory for placing consistency testing graphics.
This follows a discussion started by Edward d'Auvergne at:
https://mail.gna.org/public/relax-devel/2012-09/msg00019.html
(Message-id: <CAED9pY8XhmmvyfBS7mZA8XZ=4mJZe9TuGjARHoV2tVcjjV9SrQ@...>)
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r17459 | semor | 2012-09-05 15:23:32 +0200 (Wed, 05 Sep 2012) | 10 lines
Added a modified version of figure 1 from Morin and Gagne (JBNMR, 2009).
http://dx.doi.org/10.1007/s10858-009-9381-4
File formats are .agr (xmgrace), eps (gzipped), and png.
This follows a discussion started by Edward d'Auvergne at:
https://mail.gna.org/public/relax-devel/2012-09/msg00019.html
(Message-id: <CAED9pY8XhmmvyfBS7mZA8XZ=4mJZe9TuGjARHoV2tVcjjV9SrQ@...>)
........
r17460 | semor | 2012-09-05 15:33:12 +0200 (Wed, 05 Sep 2012) | 6 lines
Added some text to describe the consistency testing example figure.
This follows a discussion started by Edward d'Auvergne at:
https://mail.gna.org/public/relax-devel/2012-09/msg00019.html
(Message-id: <CAED9pY8XhmmvyfBS7mZA8XZ=4mJZe9TuGjARHoV2tVcjjV9SrQ@...>)
........
r17461 | semor | 2012-09-05 16:00:48 +0200 (Wed, 05 Sep 2012) | 12 lines
Added more text to describe the consistency testing approach.
Also includes a very basic point by point protocol for consistency testing.
This was proposed by by Edward d'Auvergne at:
https://mail.gna.org/public/relax-devel/2012-09/msg00028.html
(Message-id: <CAED9pY_YTDj8SX8crQu9on4LqA=pLzQwwyaz9kMLWD96xg-d0g@...>)
This also follows a discussion started by Edward d'Auvergne at:
https://mail.gna.org/public/relax-devel/2012-09/msg00019.html
(Message-id: <CAED9pY8XhmmvyfBS7mZA8XZ=4mJZe9TuGjARHoV2tVcjjV9SrQ@...>)
........
r17462 | semor | 2012-09-05 17:02:41 +0200 (Wed, 05 Sep 2012) | 12 lines
Reverted r17456.
This follows a remark by Edward d'Auvergne at:
https://mail.gna.org/public/relax-devel/2012-09/msg00029.html
(Message-id: <CAED9pY9jMXUyUsRv_FDcoen-_3SOu3oyrYK_egyw89dgH5-ESQ@...>)
The command used was:
svn merge -r17456:17455 .
Then, the file was manually adjusted since there were apparently conflicts with svn...
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r17463 | semor | 2012-09-05 17:09:25 +0200 (Wed, 05 Sep 2012) | 13 lines
Added the bounding box and a centerline command to the code for the figure for consistency testing...
This follows two remark by Edward d'Auvergne at:
https://mail.gna.org/public/relax-devel/2012-09/msg00030.html
(Message-id: <CAED9pY_DzNvTcCjD0NzzkW_Zy-xdHrUe4q6ooqrSF17ySnj_Tg@...>)
and
https://mail.gna.org/public/relax-devel/2012-09/msg00032.html
(Message-id: <CAED9pY-aymMGvmo=JMC_nWYSeLd-HAsCirv7so5P3OhJBNFY5Q@...>)
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r17464 | semor | 2012-09-05 17:15:23 +0200 (Wed, 05 Sep 2012) | 3 lines
Made a small correction to a reference such that a superscript is correctly displayed.
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r17465 | semor | 2012-09-05 21:07:58 +0200 (Wed, 05 Sep 2012) | 7 lines
Fixed a bibliography entry label problem.
This was spotted by Edward d'Auvergne in a post at:
https://mail.gna.org/public/relax-devel/2012-09/msg00040.html
(Message-id: <CAED9pY-pvtpE69tqXqb30fj9aWL1_wU8yaM4u44rMXY1LEQbag@...>)
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r17466 | semor | 2012-09-05 21:11:24 +0200 (Wed, 05 Sep 2012) | 6 lines
Fixed the bounding box for the consistency testing figure and also fixed some Latex unfriendly code...
Problems were spotted by Edward d'Auvergne in a post at:
https://mail.gna.org/public/relax-devel/2012-09/msg00039.html
(Message-id: <CAED9pY9pucoVrGzDvKs0u6hdUb94-Db8ixvno7MFN1QZsQDonA@...>)
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r17467 | bugman | 2012-09-06 08:17:08 +0200 (Thu, 06 Sep 2012) | 3 lines
Fixed the newlines in the sample script in the consistency testing chapter.
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r17468 | bugman | 2012-09-06 10:59:01 +0200 (Thu, 06 Sep 2012) | 7 lines
Editing of the "Values, gradients, and Hessians" chapter of the user manual to make it fit better.
The context of this chapter has been specified by changing the title to "Optimisation of relaxation
data -- values, gradients, and Hessians" and the intro text has been updated. As this chapter is no
longer straight after the model-free chapter, this is needed.
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r17469 | bugman | 2012-09-06 11:19:43 +0200 (Thu, 06 Sep 2012) | 3 lines
Editing and a number of fixes/cleanups for the consistency testing chapter of the user manual.
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r17470 | bugman | 2012-09-06 11:30:04 +0200 (Thu, 06 Sep 2012) | 3 lines
Small edits of the consistency testing figure caption in the relax user manual.
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r17471 | bugman | 2012-09-06 11:47:49 +0200 (Thu, 06 Sep 2012) | 3 lines
Big clean up of the Bibtex bibliography file for the relax user manual.
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r17472 | semor | 2012-09-06 11:48:22 +0200 (Thu, 06 Sep 2012) | 6 lines
Added some text to explain why test only J(0) is discussed whereas the script also calculated F_R2 and F_eta.
This was suggested by Edward d'Auvergne in a post at:
https://mail.gna.org/public/relax-devel/2012-09/msg00044.html
(Message-id: <CAED9pY9U46ga6_j245peX1ETNZc_Lw0f5cz+5xx5rGVhee29YA@...>)
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r17473 | bugman | 2012-09-06 16:07:04 +0200 (Thu, 06 Sep 2012) | 5 lines
A few small edits of the relaxation curve-fitting chapter.
This is to reinforce the exact time of the relaxation time period.
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r17474 | bugman | 2012-09-06 17:14:43 +0200 (Thu, 06 Sep 2012) | 3 lines
Re-added Dominique Marion's solvent suppression to the NMRPipe script in the curve-fitting chapter.
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r17475 | bugman | 2012-09-07 08:59:17 +0200 (Fri, 07 Sep 2012) | 5 lines
Set up the Bruker Dynamics Center system tests as GUI tests.
This is in preparation for catching bug #20152 (https://gna.org/bugs/?20152).
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r17476 | bugman | 2012-09-07 09:29:57 +0200 (Fri, 07 Sep 2012) | 5 lines
Created the test_bug_20152_read_dc_file() GUI test for catching bug #20152 (https://gna.org/bugs/?20152).
This includes truncated data taken from the bug report (with data for only the first 3 residues).
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r17477 | bugman | 2012-09-07 10:21:46 +0200 (Fri, 07 Sep 2012) | 5 lines
The bruker.read user function now throws a RelaxError when old PDC files are detected.
This is a partial fix for bug #20152 (https://gna.org/bugs/?20152).
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r17478 | bugman | 2012-09-07 10:46:18 +0200 (Fri, 07 Sep 2012) | 6 lines
Bug fix for the creation of the user function GUI pages - the (a)synchronous arg is now observed.
This argument was being ignored, which in some wizards was causing user function calls to be
asynchronous. This can result in racing related crashes!
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r17479 | bugman | 2012-09-07 10:48:15 +0200 (Fri, 07 Sep 2012) | 9 lines
Bug fix for the execution of wizard pages - the execution status is now observed.
This fixes bug #20152 (https://gna.org/bugs/?20152).
The problem was that the execution status was being lost in the protected_exec() function. However
as relax errors are caught in the GUI interpreter anyway and the status is returned normally, the
protected_exec() wrapper was removed.
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r17480 | bugman | 2012-09-07 11:03:10 +0200 (Fri, 07 Sep 2012) | 5 lines
Modified the test_bug_20152_read_dc_file() GUI test to catch the RelaxError!
This error is because of the old PDC format.
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r17481 | bugman | 2012-09-17 10:51:37 +0200 (Mon, 17 Sep 2012) | 3 lines
Comment spelling fix.
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r17482 | bugman | 2012-09-17 13:35:40 +0200 (Mon, 17 Sep 2012) | 3 lines
Changed the RelaxError for missing relaxation times in the relaxation curve-fitting analyses.
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r17483 | bugman | 2012-09-17 13:58:27 +0200 (Mon, 17 Sep 2012) | 6 lines
Fix for bug #20173 (https://gna.org/bugs/?20173).
The palmer.create user function should have been checking that the diffusion tensor had been
initialised. This is now being performed.
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r17484 | bugman | 2012-09-17 16:44:01 +0200 (Mon, 17 Sep 2012) | 6 lines
Proper bug fix for storing the execution status of wizard and user function pages.
This allows the test suite to pass again. The execution status is now properly returned from the
wizard pages run synchronously (and always set to True for asynchronous calls).
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r17485 | bugman | 2012-09-17 18:05:56 +0200 (Mon, 17 Sep 2012) | 6 lines
Expanded the spin ID list for the structure.load_spins user function.
This now includes the spins "@N", "@NE1", "@C", "@H", "@O", "@P", ":A@...", ":A@...", ":G@...",
":G@...", ":C@...", ":C@...", ":U@...", ":U@...", ":U@...".
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r17486 | bugman | 2012-09-18 10:51:49 +0200 (Tue, 18 Sep 2012) | 3 lines
MS Windows fix - the NOE system and GUI tests are now less strict in checking the errors.
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r17487 | bugman | 2012-09-18 12:11:17 +0200 (Tue, 18 Sep 2012) | 6 lines
Updated the scripting section of the intro chapter of the user manual for non-technical users.
See http://www.mail-archive.com/relax-users@.../msg01253.html and bug #20174
(http://gna.org/bugs/?20174).
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r17488 | bugman | 2012-09-18 15:19:03 +0200 (Tue, 18 Sep 2012) | 6 lines
Bug fix for the repetition of Monte Carlo simulations in the relaxation curve-fitting analyses.
This is in the specific analysis API, so will allow all analysis types to repeat Monte Carlo
simulations for error analysis.
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r17489 | bugman | 2012-09-18 16:15:01 +0200 (Tue, 18 Sep 2012) | 6 lines
Created the new generic_fns.result_files for standardising the handling of results files.
This fixes the bug where results files are repetitively added to the list. All of the code touching
cdp.result_files now uses this module instead.
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r17490 | bugman | 2012-09-18 18:15:51 +0200 (Tue, 18 Sep 2012) | 6 lines
Window ordering bug fix for the user function windows launched from the spin viewer window.
The spin viewer window no longer hides behind the main relax window after the launch of the user
function.
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r17491 | bugman | 2012-09-18 19:23:14 +0200 (Tue, 18 Sep 2012) | 5 lines
Added @HE1 to the spin ID list of the structure.load_spins user function.
This is only seen in the GUI.
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r17492 | bugman | 2012-09-18 19:44:54 +0200 (Tue, 18 Sep 2012) | 6 lines
Updated the model-free GUI auto-analysis buttons for multiple spin name types.
The @H and @N names in the wizards behind the 'Dipolar relaxation', 'X isotope', and 'H isotope'
buttons have been changed to @H* and @N* to support Trp NE1-HE1 atom pairs.
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r17493 | bugman | 2012-09-19 09:19:54 +0200 (Wed, 19 Sep 2012) | 5 lines
Fix for bug #20181 - the GUI sequence editor window TypeError problem.
This is the fix for the bug reported at https://gna.org/bugs/?20181.
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r17494 | bugman | 2012-09-19 09:35:49 +0200 (Wed, 19 Sep 2012) | 3 lines
Improvements to the descriptions of the structure.read_pdb user function arguments.
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r17495 | bugman | 2012-09-19 09:37:07 +0200 (Wed, 19 Sep 2012) | 3 lines
Improvements to the descriptions of the structure.read_xyz user function arguments.
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r17496 | bugman | 2012-09-19 09:43:30 +0200 (Wed, 19 Sep 2012) | 7 lines
Fix for bug #20182 (https://gna.org/bugs/?20182) - the sequence element window ordering issue.
The sequence element window now has the parent wx.Window element set. This prevents the main relax
window from being set as the parent and hence coming to the front after the sequence element window
is launched from a user function window.
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r17497 | bugman | 2012-09-19 10:02:13 +0200 (Wed, 19 Sep 2012) | 6 lines
Fix for bug #20183 (https://gna.org/bugs/?20183) - the failure of the sequence editor window.
The problem was that fields which could be either single values or lists (or tuples) of values were
not properly handled.
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r17498 | bugman | 2012-09-19 10:53:11 +0200 (Wed, 19 Sep 2012) | 5 lines
Modified the operation of the sequence GUI element to have access to the sequence editor window.
This is to allow this GUI element to be blasted within the test suite.
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r17499 | bugman | 2012-09-19 10:55:30 +0200 (Wed, 19 Sep 2012) | 7 lines
Created the User_functions.test_structure_pdb_read GUI test for checking the sequence editor window.
This new user function GUI testing class is to be used for testing out the special GUI elements not
invoked within the unit testing. The test_structure_pdb_read() test specifically shows a number of
failures of the sequence editor window.
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r17500 | bugman | 2012-09-19 11:22:35 +0200 (Wed, 19 Sep 2012) | 3 lines
Fixes for the User_functions.test_structure_pdb_read() GUI test.
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r17501 | bugman | 2012-09-19 11:24:21 +0200 (Wed, 19 Sep 2012) | 7 lines
Fix for bug #20184 (https://gna.org/bugs/?20184).
The behaviour of the gui.string_conv.gui_to_int() and related functions has changed in the last few
months and the Sequence_window() GUI element has not changed to match. This has been fixed and the
User_functions.test_structure_pdb_read() GUI test now passes.
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r17502 | bugman | 2012-09-19 11:27:52 +0200 (Wed, 19 Sep 2012) | 5 lines
Modified the User_functions.test_structure_pdb_read() GUI test to catch another bug.
This is a bug recently introduced with the fixes to the other sequence editor GUI window problems.
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r17503 | bugman | 2012-09-19 11:38:56 +0200 (Wed, 19 Sep 2012) | 3 lines
Small fix for the User_functions.test_structure_pdb_read() GUI test.
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r17504 | bugman | 2012-09-19 11:40:28 +0200 (Wed, 19 Sep 2012) | 6 lines
Another bug fix for the sequence GUI editor window.
This bug was being triggered by the User_functions.test_structure_pdb_read() GUI test which now
passes.
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r17505 | bugman | 2012-09-19 14:16:04 +0200 (Wed, 19 Sep 2012) | 6 lines
Fix for bug #20177 (https://gna.org/bugs/?20177).
This was simply a lower precision OS/Python/numpy combination causing a test suite failure - there
are no practical effects and only the precision of the system/GUI test has been lowered.
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r17506 | bugman | 2012-09-19 14:55:33 +0200 (Wed, 19 Sep 2012) | 5 lines
All of the GUI strings and text are now formatted with a small sans serif font in the user manual.
This is because in the GUI, a sans serif font is almost always used be default.
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r17507 | bugman | 2012-09-19 14:57:03 +0200 (Wed, 19 Sep 2012) | 6 lines
Updated the data model chapter of the user manual to cover the handling of protons.
This change includes the modification of the PDB reading screenshot to demonstrate the reading of a
specific model and the naming of the molecule.
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r17508 | bugman | 2012-09-19 15:42:33 +0200 (Wed, 19 Sep 2012) | 6 lines
A number of updates and edits to the intro chapter of the user manual.
The model-free GUI screenshot has been shifted to the intro chapter in preparation for a full
tutorial with screenshots in the model-free chapter.
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r17509 | bugman | 2012-09-19 15:43:04 +0200 (Wed, 19 Sep 2012) | 3 lines
Added some labelling to the infrastructure chapter of the user manual for referencing.
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r17510 | bugman | 2012-09-19 15:49:35 +0200 (Wed, 19 Sep 2012) | 3 lines
A small edit to the intro chapter for the multi-processor operation and logging.
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r17511 | bugman | 2012-09-19 16:19:47 +0200 (Wed, 19 Sep 2012) | 3 lines
Additions to the scripting section of the relaxation curve-fitting chapter of the user manual.
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r17512 | bugman | 2012-09-19 16:57:35 +0200 (Wed, 19 Sep 2012) | 7 lines
Created a simple shell script to find duplicate titles in the relax user manual.
This is important for the HTML version of the manual as duplicated titles causes HTML pages to be
overwritten. For example all chapters, sections and subsections titled "Introduction" will load the
introduction.html file which will contain the text of the last section with that title!
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r17513 | bugman | 2012-09-19 17:03:20 +0200 (Wed, 19 Sep 2012) | 3 lines
Improvements to the duplicate user manual title finding script.
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r17514 | bugman | 2012-09-19 17:22:47 +0200 (Wed, 19 Sep 2012) | 3 lines
Fix for the duplicate title finding script - the LaTeX and HTML mode alternatives are no longer mixed up.
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r17515 | bugman | 2012-09-19 17:25:16 +0200 (Wed, 19 Sep 2012) | 3 lines
The HTML files for the user manual now have longer names - this is needed for removing the duplicates.
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r17516 | bugman | 2012-09-19 17:33:55 +0200 (Wed, 19 Sep 2012) | 5 lines
Elimination of all duplicated chapter, section and subsection titles in the user manual.
This fixes bug #20185 (https://gna.org/bugs/?20185).
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r17517 | bugman | 2012-09-19 18:41:08 +0200 (Wed, 19 Sep 2012) | 5 lines
The graphics.fetch_icon() function argument 'format' can now be set to None.
This will return the file path without the extension.
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r17518 | bugman | 2012-09-19 19:03:48 +0200 (Wed, 19 Sep 2012) | 3 lines
Fix for the graphics.fetch_icon() function for when no file format is specified.
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r17519 | bugman | 2012-09-19 21:49:04 +0200 (Wed, 19 Sep 2012) | 6 lines
Removed the text '.eps.gz' from all of the LaTeX included graphics in the user manual.
This allows latex2html to select and use the PNG images instead, producing much better graphics for
the online manual (http://www.nmr-relax.com/manual/index.html).
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r17520 | bugman | 2012-09-19 22:29:43 +0200 (Wed, 19 Sep 2012) | 5 lines
Fixes for the user function icons in the HTML version of the user manual.
These icons are now placed on the correct HTML page.
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r17521 | bugman | 2012-09-19 22:30:27 +0200 (Wed, 19 Sep 2012) | 3 lines
Fixed a section titled 'Introduction' clashing with the intro chapter of the user manual.
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r17522 | bugman | 2012-09-19 22:46:36 +0200 (Wed, 19 Sep 2012) | 5 lines
The latex2html compilation of the user manual now ignores the \bibitem{} commands.
This is needed for the HTML version of the user manual.
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r17523 | bugman | 2012-09-19 22:47:29 +0200 (Wed, 19 Sep 2012) | 5 lines
The citations chapter is now included in the HTML version of the user manual.
For some reason, a file named 'cite.tex' cannot be handled by latex2html.
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r17524 | bugman | 2012-09-20 11:41:19 +0200 (Thu, 20 Sep 2012) | 3 lines
Modified the dauvergne_protocol sample script to handle tryptophan indole NE1 data.
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r17525 | bugman | 2012-09-20 12:08:11 +0200 (Thu, 20 Sep 2012) | 3 lines
Added a section label to the intro chapter of the user manual.
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r17526 | bugman | 2012-09-20 12:09:59 +0200 (Thu, 20 Sep 2012) | 5 lines
Removed \verb from the \newcommand definitions as that is forbidden in LaTeX.
Now Python code is formatted using a small TT font.
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r17527 | bugman | 2012-09-20 12:11:11 +0200 (Thu, 20 Sep 2012) | 6 lines
Removed the \pycodestar{} references in the development chapter.
This command has been deleted as \newcommand cannot have \verb inside it! The \pycodestar{x}
references have been changed to \verb*!x!.
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r17528 | bugman | 2012-09-20 12:14:31 +0200 (Thu, 20 Sep 2012) | 3 lines
Spacing fix.
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r17529 | bugman | 2012-09-20 12:21:46 +0200 (Thu, 20 Sep 2012) | 3 lines
Added a subsubsection label to the data model chapter of the user manual.
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r17530 | bugman | 2012-09-20 16:34:18 +0200 (Thu, 20 Sep 2012) | 3 lines
Created the User_functions.test_value_set GUI test demonstrating the failure of the value.set user function.
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r17531 | bugman | 2012-09-20 17:21:44 +0200 (Thu, 20 Sep 2012) | 5 lines
Fix for bug #20189 (https://gna.org/bugs/?20189).
The Sequence GUI element can no handle values of None.
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r17532 | bugman | 2012-09-20 17:39:30 +0200 (Thu, 20 Sep 2012) | 6 lines
The GUI model-free auto-analysis dipole_pair.define field values have been changed again.
These now default to @N and @H, as @N* and @H* will connect @N spins to @HE1 spins and @H spins to
@NE1 spins!
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r17533 | bugman | 2012-09-20 17:46:26 +0200 (Thu, 20 Sep 2012) | 5 lines
Fixed the dipole_pair.define user function calls in the dauvergne_protocol.py sample script.
This is a recently introduced problem only present in the trunk.
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r17534 | bugman | 2012-09-20 20:32:32 +0200 (Thu, 20 Sep 2012) | 7 lines
Massive expansion of the model-free chapter of the user manual including script and GUI tutorials.
The model-free chapter now has step-by-step tutorials for both the prompt/script mode and GUI mode
for the new automated model-free protocol (the d'Auvergne protocol). This includes a large set of
screenshots for the GUI mode.
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r17535 | bugman | 2012-09-20 20:47:09 +0200 (Thu, 20 Sep 2012) | 3 lines
Added a BMRB section to the end of the model-free chapter of the user manual.
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r17536 | bugman | 2012-09-20 20:49:02 +0200 (Thu, 20 Sep 2012) | 3 lines
Removed the out of date and useless README file for the HTML version of the user manual.
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r17537 | bugman | 2012-09-21 10:22:46 +0200 (Fri, 21 Sep 2012) | 3 lines
Added the use of the program 'nice' to the model-free GUI tutorial in the user manual.
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r17538 | bugman | 2012-09-21 11:09:52 +0200 (Fri, 21 Sep 2012) | 6 lines
Modified the model-free optimisation final printout to be more multi-processor friendly.
The message saying that the optimised chi2 is an improvement or not now includes the spin ID string
if present. This is more informative for the multi-processor mpi4py printouts.
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r17540 | bugman | 2012-09-21 11:51:25 +0200 (Fri, 21 Sep 2012) | 6 lines
Fix for the SVN log converter script for the relax release process.
All SVN messages beginning with "Changed" were being skipped. The skipping of the "Changed paths:"
SVN log lines is now more explicit.
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r17542 | bugman | 2012-09-21 12:04:23 +0200 (Fri, 21 Sep 2012) | 6 lines
Merged the CHANGES file from the relax 2.1.1 tag back to the trunk.
The command used was:
svn merge -r17540:17541 svn+ssh://bugman@.../svn/relax/tags/2.1.1
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r17552 | bugman | 2012-09-25 13:42:50 +0200 (Tue, 25 Sep 2012) | 7 lines
Fix for bug #20198 (https://gna.org/bugs/?20198) - the relaxation data back-calculation error.
The problem was that the call to the model-free overfit_deselect() method was deselecting any spins
lacking relaxation data! This should not happen, as no spins need to have relaxation data for this
calculation.
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r17553 | bugman | 2012-09-25 14:03:50 +0200 (Tue, 25 Sep 2012) | 5 lines
Added the data_check Boolean argument to all of the specific analysis overfit_deselect() methods.
This allows the unit tests to pass.
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r17554 | bugman | 2012-09-25 14:05:41 +0200 (Tue, 25 Sep 2012) | 7 lines
Added a tryptophan NE1 data set to the sphere model-free model test data.
This is in preparation to catch bug #20197 (https://gna.org/bugs/?20197).
The scripts have also been updated for the newer relax designs.
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r17555 | bugman | 2012-09-25 14:38:21 +0200 (Tue, 25 Sep 2012) | 6 lines
Improved the model-free overfitting deselection printouts prior to optimisation.
Only a single message per spin is now given when the spin is deselected, minimising the amount of
output.
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r17556 | bugman | 2012-09-25 14:53:03 +0200 (Tue, 25 Sep 2012) | 3 lines
More improvements to the model-free over-fitting deselection printouts.
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r17557 | bugman | 2012-09-25 14:58:22 +0200 (Tue, 25 Sep 2012) | 5 lines
Printouts for the over-fitting deselection of spins are suppressed for the back-calculation of relaxation data.
This affects the model-free Monte Carlo simulations, simplifying the output.
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r17558 | bugman | 2012-09-25 15:01:37 +0200 (Tue, 25 Sep 2012) | 3 lines
All overfit_deselect() methods now accept and use the verbose argument.
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r17559 | bugman | 2012-09-25 15:06:25 +0200 (Tue, 25 Sep 2012) | 3 lines
The overfit_deselect() printouts are now regularised and match the model-free printouts.
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r17560 | bugman | 2012-09-25 15:18:23 +0200 (Tue, 25 Sep 2012) | 6 lines
Small change to the sphere model model-free test suite data.
The trptophan indole data is now merged into the last residue (a glycine) to catch bug #20197
(https://gna.org/bugs/?20197).
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r17561 | bugman | 2012-09-25 15:21:43 +0200 (Tue, 25 Sep 2012) | 5 lines
Modified the Mf.test_dauvergne_protocol system test to catch bug #20197 (https://gna.org/bugs/?20197).
The sphere test data NE1 and HE1 data is now being used in this system test, triggering the bug.
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r17562 | bugman | 2012-09-25 16:37:03 +0200 (Tue, 25 Sep 2012) | 3 lines
Relaxation data is no longer loaded by relax_data.read if the values and errors are both None.
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r17563 | bugman | 2012-09-25 16:41:25 +0200 (Tue, 25 Sep 2012) | 3 lines
Fix for the N_state_model.test_monte_carlo_sims due to the changed sphere.pdb test suite file.
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r17564 | bugman | 2012-09-25 16:42:04 +0200 (Tue, 25 Sep 2012) | 3 lines
Fix to the Dasha system test needed for the changes to the relax_data.read user function.
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r17565 | bugman | 2012-09-25 17:02:49 +0200 (Tue, 25 Sep 2012) | 3 lines
Fix for the Relax_data.test_read unit tests for the relax_data.read user function changes.
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r17566 | bugman | 2012-09-25 17:07:18 +0200 (Tue, 25 Sep 2012) | 3 lines
Fix for the Relax_data.test_delete system test for the changes to the relax_data.read user function.
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r17567 | bugman | 2012-09-25 18:46:03 +0200 (Tue, 25 Sep 2012) | 6 lines
Fix for bug #20197 (https://gna.org/bugs/?20197) - the PyMOL and Molmol macro failure.
The macro creation now only operates on spins called 'N' and assumes these are the backbone
nitrogens. The sidechain tryptophan indole NH data will need to be detected and added later.
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r17568 | bugman | 2012-09-27 10:03:08 +0200 (Thu, 27 Sep 2012) | 3 lines
Lots of editing of the model-free GUI section of the user manual.
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r17569 | bugman | 2012-09-27 10:04:04 +0200 (Thu, 27 Sep 2012) | 3 lines
Fix for the comment on the 'Export' button in the BMRB export window.
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r17570 | bugman | 2012-09-27 10:04:22 +0200 (Thu, 27 Sep 2012) | 3 lines
Removed some debugging printouts.
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r17571 | bugman | 2012-09-27 10:05:14 +0200 (Thu, 27 Sep 2012) | 3 lines
Added star versions of the standard spin IDs to the spin ID GUI element (e.g. '@N*', '@H*').
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r17572 | bugman | 2012-09-27 10:07:03 +0200 (Thu, 27 Sep 2012) | 6 lines
The CSA setting in the model-free auto GUI analysis now defaults to the '@N*' spin ID.
Previously no spin ID was being used so that the protons where also having their CSA values set to
that of the nitrogens. Now the execution checking code skips the proton CSA check.
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r17573 | bugman | 2012-09-27 10:08:12 +0200 (Thu, 27 Sep 2012) | 3 lines
Fixes for the checks in the Mf.test_mf_auto_analysis() GUI test for the recent test suite data changes.
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r17574 | bugman | 2012-09-27 16:14:47 +0200 (Thu, 27 Sep 2012) | 6 lines
Removed the 'force flag' text from the RelaxWarning messages output by the bruker.read user function.
The force flag arguments of the generic_fns.mol_res_spin.name_spin() and
generic_fns.mol_res_spin.set_spin_isotope() functions can now be set to None to suppress the text.
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r17575 | bugman | 2012-09-27 16:29:40 +0200 (Thu, 27 Sep 2012) | 7 lines
Fix for bug #20201 (https://gna.org/bugs/?20201).
The bruker.read user function can now handle the situation where multiple spins per residue are
already loaded prior to the user function call. The isotope value from the DC file is now
translated to the element name and this is used as part of the spin ID string.
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r17576 | bugman | 2012-09-27 19:19:13 +0200 (Thu, 27 Sep 2012) | 3 lines
Some changes in preparation for Python 3.
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r17577 | bugman | 2012-09-28 10:02:02 +0200 (Fri, 28 Sep 2012) | 3 lines
Fix for a fatal bug introduced in the last revision (r17576).
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r17578 | bugman | 2012-09-28 10:49:08 +0200 (Fri, 28 Sep 2012) | 5 lines
Removed all of the xrange() calls from the system tests as these are not necessary.
This is in preparation for Python 3.
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r17579 | bugman | 2012-09-28 10:55:55 +0200 (Fri, 28 Sep 2012) | 3 lines
Python 3 preparation - changed the import of SystemTestCase to use the absolute module path.
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r17580 | bugman | 2012-09-28 10:57:54 +0200 (Fri, 28 Sep 2012) | 3 lines
Python 3 preparation - the test_suite.system_tests package now uses the absolute module path for imports.
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r17581 | bugman | 2012-09-28 10:58:47 +0200 (Fri, 28 Sep 2012) | 13 lines
Last Python 3 compatibility update for the system tests - they are now both Python 2 and 3 compatible!
The command used was:
2to3 -w \
-f except \
-f import \
-f imports \
-f long \
-f numliterals \
-f xrange \
.
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r17582 | bugman | 2012-09-28 11:00:34 +0200 (Fri, 28 Sep 2012) | 3 lines
Python 3 preparation - removed all xrange() calls from the unit tests, these are not needed.
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r17583 | bugman | 2012-09-28 11:06:47 +0200 (Fri, 28 Sep 2012) | 3 lines
Python 3 preparations - all the _prompt unit tests now use absolute module imports.
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r17584 | bugman | 2012-09-28 11:08:34 +0200 (Fri, 28 Sep 2012) | 3 lines
Python 3 preparation - all of the _generic_fns unit tests now use absolute module imports.
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r17585 | bugman | 2012-09-28 11:09:41 +0200 (Fri, 28 Sep 2012) | 6 lines
Python 3 preparations - the unit tests are now fully Python 2 and 3 compatible.
The command used was:
2to3 -w -f except -f import -f imports -f long -f numliterals -f xrange .
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r17586 | bugman | 2012-09-28 11:32:12 +0200 (Fri, 28 Sep 2012) | 5 lines
Bug fix for the BMRB system test initialisation for when the bmrblib module is missing.
The base __init__() method needs to be initialised first.
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r17587 | bugman | 2012-09-28 11:32:41 +0200 (Fri, 28 Sep 2012) | 3 lines
Removed some temporary debugging code.
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r17588 | bugman | 2012-09-28 11:34:04 +0200 (Fri, 28 Sep 2012) | 3 lines
Python 3 preparations - the test_suite.gui_tests package now uses absolute module path imports.
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r17589 | bugman | 2012-09-28 11:42:00 +0200 (Fri, 28 Sep 2012) | 3 lines
Python 3 preparations - the queue modules for both Python versions are now supported in the GUI tests.
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r17590 | bugman | 2012-09-28 11:43:29 +0200 (Fri, 28 Sep 2012) | 6 lines
Python 3 preparations - the GUI tests are now fully Python 2 and 3 compatible.
The command used was:
2to3 -w -f except -f import -f imports -f long -f numliterals -f xrange .
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r17591 | bugman | 2012-09-28 11:45:14 +0200 (Fri, 28 Sep 2012) | 3 lines
Python 3 preparations - the use of the queue module in the status module is now compatible with 2 and 3.
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r17592 | bugman | 2012-09-28 11:49:34 +0200 (Fri, 28 Sep 2012) | 3 lines
Python 3 preparation - the auto_analyses package now uses absolute paths for the module imports.
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r17593 | bugman | 2012-09-28 11:50:34 +0200 (Fri, 28 Sep 2012) | 6 lines
Python 3 preparations - the auto_analyses package is now fully Python 2 and 3 compatible.
The command used was:
2to3 -w -f except -f import -f imports -f long -f numliterals -f xrange .
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r17594 | bugman | 2012-09-28 13:28:49 +0200 (Fri, 28 Sep 2012) | 3 lines
Python 3 preparation - the use of an absolute module path for import.
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r17595 | bugman | 2012-09-28 13:29:29 +0200 (Fri, 28 Sep 2012) | 3 lines
Python 3 preparation - eliminated the unneeded use of xrange().
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r17596 | bugman | 2012-09-28 13:36:50 +0200 (Fri, 28 Sep 2012) | 6 lines
Python 3 preparations - removed all usage of the xrange() in the generic_fns package as none are needed.
The command used was:
2to3 -w -f xrange .
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r17597 | bugman | 2012-09-28 14:23:58 +0200 (Fri, 28 Sep 2012) | 3 lines
Updated the Python 2 to 3 checklist document for the shifting of the 'relax' file to 'relax.py'.
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r17598 | bugman | 2012-09-28 16:40:50 +0200 (Fri, 28 Sep 2012) | 17 lines
Python 3 conversions using 2to3.
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 \
.
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r17599 | bugman | 2012-09-28 16:57:03 +0200 (Fri, 28 Sep 2012) | 6 lines
Reverted r17598 for the multi.processor module as this breaks in Python 2.
The command used was:
svn merge -r17598:r17597 processor.py
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r17600 | bugman | 2012-09-28 16:58:29 +0200 (Fri, 28 Sep 2012) | 3 lines
Python 3 preparations - exception handling fix to be Python 2.4+ compatible.
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r17601 | bugman | 2012-09-28 17:17:05 +0200 (Fri, 28 Sep 2012) | 3 lines
More exception handling changes to be Python 2.4+ compatible.
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r17602 | bugman | 2012-09-28 17:22:32 +0200 (Fri, 28 Sep 2012) | 3 lines
Python 3 preparations - eliminated the use of the os.popen3 function from the info module.
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r17603 | bugman | 2012-09-28 17:28:11 +0200 (Fri, 28 Sep 2012) | 3 lines
Python 3 preparations - all os.popen3() instances in relax have been replaced by the subprocess module.
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r17604 | bugman | 2012-09-28 17:28:56 +0200 (Fri, 28 Sep 2012) | 3 lines
Removed an unused import (which was breaking relax in Python 3).
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r17605 | bugman | 2012-09-28 17:55:25 +0200 (Fri, 28 Sep 2012) | 3 lines
Removed the completely unused gui.components.conversion module.
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r17606 | bugman | 2012-09-28 18:08:24 +0200 (Fri, 28 Sep 2012) | 3 lines
Python 3 preparations - all usage of string.split() and string.strip() has been eliminated.
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r17607 | bugman | 2012-09-28 18:11:48 +0200 (Fri, 28 Sep 2012) | 3 lines
Python 3 preparations - compatibility for both the Python 2 cPickle and Python 3 pickle modules.
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r17608 | bugman | 2012-09-28 18:20:48 +0200 (Fri, 28 Sep 2012) | 3 lines
Python 3 preparations - removed the use of the types.ClassType object.
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r17609 | bugman | 2012-09-28 18:32:10 +0200 (Fri, 28 Sep 2012) | 3 lines
Python 3 preparations - converted the relax prompt/script interpreter to be Python 2 and 3 compatible.
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r17610 | bugman | 2012-09-28 18:34:49 +0200 (Fri, 28 Sep 2012) | 3 lines
Python 3 preparations - error handling is now Python 2 and 3 compatible in the relax_io module.
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r17611 | bugman | 2012-09-28 18:50:32 +0200 (Fri, 28 Sep 2012) | 3 lines
Python 3 preparation - all raising of RelaxErrors is now Python 2.4+ compatible.
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r17612 | bugman | 2012-09-28 18:52:10 +0200 (Fri, 28 Sep 2012) | 3 lines
Python 3 preparations - more exception handling updates for all Python 2.4+ versions.
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r17613 | bugman | 2012-09-28 18:55:04 +0200 (Fri, 28 Sep 2012) | 3 lines
Python 3 preparations - absolute module path fix.
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r17614 | bugman | 2012-09-28 18:57:45 +0200 (Fri, 28 Sep 2012) | 3 lines
Python 3 preparations - support for both Python 2 __builtin__ and Python 3 builtins modules.
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r17615 | bugman | 2012-09-28 18:58:47 +0200 (Fri, 28 Sep 2012) | 3 lines
Bug fix for a problem introduced in the last commit.
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r17616 | bugman | 2012-09-28 19:02:02 +0200 (Fri, 28 Sep 2012) | 3 lines
Python 3 preparations - absolute module path fixes.
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r17617 | bugman | 2012-09-28 19:04:46 +0200 (Fri, 28 Sep 2012) | 3 lines
Python 3 preparations - eliminated the use of the types.ListType object.
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r17618 | bugman | 2012-09-28 19:06:23 +0200 (Fri, 28 Sep 2012) | 3 lines
Python 3 preparations - the data package now uses absolute imports for all its modules.
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r17619 | bugman | 2012-09-28 19:13:09 +0200 (Fri, 28 Sep 2012) | 3 lines
Python 3 preparations - the data package now really does use the absolute path for its module imports.
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r17620 | bugman | 2012-09-28 19:13:30 +0200 (Fri, 28 Sep 2012) | 3 lines
Python 3 preparations - removal of some unneeded xrange() calls.
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r17621 | bugman | 2012-10-01 14:04:16 +0200 (Mon, 01 Oct 2012) | 3 lines
Fix for bug #20210 (https://gna.org/bugs/?20210) - relax now runs again without having wxPython installed.
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r17622 | bugman | 2012-10-01 18:13:20 +0200 (Mon, 01 Oct 2012) | 5 lines
Improvements for the relax test suite synopsis for when the wxPython module is missing or broken.
This is simply a printout improvement.
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r17623 | bugman | 2012-10-01 18:48:11 +0200 (Mon, 01 Oct 2012) | 5 lines
Python 3 preparations - removed all of the string module functions which no longer exist in Python 3.
These functions are part of the strings themselves now.
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r17624 | bugman | 2012-10-01 21:33:21 +0200 (Mon, 01 Oct 2012) | 5 lines
Python 3 - removed the use of the types module from generic_fns.sequence.
The relax arg_check module is now being used instead.
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r17625 | bugman | 2012-10-01 21:34:01 +0200 (Mon, 01 Oct 2012) | 3 lines
Python 3 - a pile of relative path fixes for many relax modules.
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r17626 | bugman | 2012-10-01 21:44:20 +0200 (Mon, 01 Oct 2012) | 5 lines
Python 3 - Fix for an os.chmod() call by using the stat module rather than the number 0775.
The number 0755 is no longer valid in Python 3.
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r17627 | bugman | 2012-10-01 21:48:28 +0200 (Mon, 01 Oct 2012) | 3 lines
Python 3 - converted some print statements to function calls in the ScientificPython modules.
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r17628 | bugman | 2012-10-01 21:52:19 +0200 (Mon, 01 Oct 2012) | 3 lines
Python 3 - modified some except statements to be Python 2.4+ compatible in a ScientificPython module.
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r17629 | bugman | 2012-10-01 22:12:24 +0200 (Mon, 01 Oct 2012) | 6 lines
Python 3 - a number of fixes for running the ScientificPython modules in relax on Python 2 and 3.
This includes relative imports, converting raise statements to function calls, removal of the use of
many string module functions which do not exist in Python 3, etc.
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r17630 | bugman | 2012-10-01 22:15:43 +0200 (Mon, 01 Oct 2012) | 6 lines
Python 3 - removal of the use of the string.atoi and string.atof functions.
These have been depreciated since Python 2.0!! They have been replace by the int and float
functions.
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r17631 | bugman | 2012-10-01 22:22:34 +0200 (Mon, 01 Oct 2012) | 3 lines
Python 3 - converted the last of the except error catching statements to be Python 2.4+ compatible.
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r17632 | bugman | 2012-10-01 22:27:00 +0200 (Mon, 01 Oct 2012) | 3 lines
Python 3 - fixes for the renaming of the Queue package.
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r17633 | bugman | 2012-10-01 22:41:26 +0200 (Mon, 01 Oct 2012) | 3 lines
Python 3 fix - ensure an integer is actually an integer (division now converts ints to floats).
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r17634 | bugman | 2012-10-01 22:43:38 +0200 (Mon, 01 Oct 2012) | 3 lines
Python 3 fixes for the version module for catching empty lists.
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r17635 | bugman | 2012-10-01 22:51:12 +0200 (Mon, 01 Oct 2012) | 3 lines
Debugging printout removal.
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r17636 | bugman | 2012-10-01 22:54:43 +0200 (Mon, 01 Oct 2012) | 3 lines
Python 3 - relative module paths are now used for the test suite runner.
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r17637 | bugman | 2012-10-01 22:55:29 +0200 (Mon, 01 Oct 2012) | 3 lines
Python 3 - The cStringIO.StringIO import switches to io.StringIO if missing.
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r17638 | bugman | 2012-10-01 23:06:27 +0200 (Mon, 01 Oct 2012) | 3 lines
Python 2 fixes - the Python 3 fixes for the ScientificPython module imports broke Python 2.
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r17639 | bugman | 2012-10-01 23:19:57 +0200 (Mon, 01 Oct 2012) | 5 lines
Python 3 fix for the relax information print out.
The try blocks seem to now operate slightly differently in Python 3.
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r17640 | bugman | 2012-10-01 23:34:08 +0200 (Mon, 01 Oct 2012) | 3 lines
Python 3 - removed the use of the string.lower() function as it is missing in Python 3.
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r17641 | bugman | 2012-10-01 23:34:42 +0200 (Mon, 01 Oct 2012) | 3 lines
Python 3 - eliminated the use of the map() function, as this behaves differently in Python 3.
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r17642 | bugman | 2012-10-01 23:40:37 +0200 (Mon, 01 Oct 2012) | 3 lines
Python 3 - Eliminated an unneeded xrange call.
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r17643 | bugman | 2012-10-02 00:37:08 +0200 (Tue, 02 Oct 2012) | 3 lines
Created the special check_types.is_filetype() function for checking for files in all Python versions.
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r17644 | bugman | 2012-10-02 01:16:44 +0200 (Tue, 02 Oct 2012) | 5 lines
Fix for a bug introduced at r17624 in the generic_fns.sequence.validate_sequence() function.
The is_none() function call doesn't seem to be working correctly.
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r17645 | bugman | 2012-10-02 10:23:28 +0200 (Tue, 02 Oct 2012) | 3 lines
Python 3 preparations - mass conversion of all xrange() calls to range().
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r17646 | bugman | 2012-10-02 10:26:09 +0200 (Tue, 02 Oct 2012) | 6 lines
Python 3 fixes - the list() function is now used in combination with range() to generate the ordered list.
range() in Python 3 is an iterator object (just as xrange was), so now the list() function has to be
called.
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r17647 | bugman | 2012-10-02 10:35:22 +0200 (Tue, 02 Oct 2012) | 3 lines
Created a new module for simultaneous Python 2 and 3 support in relax called 'compat'.
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r17648 | bugman | 2012-10-02 10:45:46 +0200 (Tue, 02 Oct 2012) | 9 lines
Converted the ScientificPython PDB reader to support both Python 2 and 3.
The command used was:
2to3 extern/scientific_python/IO/PDB.py -w
The __repr__() method was manually modified due to the 'list' variable clashing with the 'list'
type.
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r17649 | bugman | 2012-10-02 10:47:48 +0200 (Tue, 02 Oct 2012) | 3 lines
Converted some raise() function calls to raise statements in preparation for the 2to3 conversion.
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r17650 | bugman | 2012-10-02 10:49:09 +0200 (Tue, 02 Oct 2012) | 3 lines
Another raise() function call to statement change for 2to3 preparations.
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r17651 | bugman | 2012-10-02 10:52:35 +0200 (Tue, 02 Oct 2012) | 5 lines
Created the check_types.is_unicode() function for Python 2+3 compatibility.
This is used in the generic_fns.mol_res_spin module.
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r17652 | bugman | 2012-10-02 10:53:34 +0200 (Tue, 02 Oct 2012) | 3 lines
More usage of the is_unicode() function in the generic_fns.mol_res_spin module.
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r17653 | bugman | 2012-10-02 10:54:58 +0200 (Tue, 02 Oct 2012) | 3 lines
Import fix for the OpenDX mapping package, recently broken with the relative import for Python 3 change.
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r17654 | bugman | 2012-10-02 11:04:51 +0200 (Tue, 02 Oct 2012) | 3 lines
The compat module now has the py_version variable specifying if this is Python 2 or 3.
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r17655 | bugman | 2012-10-02 11:39:17 +0200 (Tue, 02 Oct 2012) | 7 lines
For running relax with Python 2, the __builtin__.range() function has been replaced with xrange.
This causes large speed ups (speed that was lost with the earlier xrange() to range() conversions),
and memory decreases. For example on one system, the system test time decreased from 513.029s to
487.586s.
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r17656 | bugman | 2012-10-02 11:47:15 +0200 (Tue, 02 Oct 2012) | 6 lines
Automatically converted the generic_fns.mol_res_spin module to support both Python 2 and 3.
The command used was:
2to3 -w generic_fns/mol_res_spin.py
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r17657 | bugman | 2012-10-02 11:53:17 +0200 (Tue, 02 Oct 2012) | 5 lines
Python 3 fix for the generic_fns.mol_res_spin.parse_token() function.
Mixed lists for int and string can no longer be sorted. This sort call is not needed anyway.
........
r17658 | bugman | 2012-10-02 13:35:59 +0200 (Tue, 02 Oct 2012) | 3 lines
Fix for the test_parse_token_multi_element_name() unit test, as parse_token() no longer sorts.
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r17659 | bugman | 2012-10-02 14:05:17 +0200 (Tue, 02 Oct 2012) | 6 lines
Fix for the running of the test suite under Python 3.
The zip() function used in the loadTestsFromTestCase() function is now an iterator, so it needs to
be passed through the list() function to generate a list.
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r17660 | bugman | 2012-10-02 14:05:50 +0200 (Tue, 02 Oct 2012) | 3 lines
Copyright update.
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r17661 | bugman | 2012-10-02 14:08:22 +0200 (Tue, 02 Oct 2012) | 5 lines
Fix for the test suite summary for Python 3.
The test suite now runs, but fails miserably, under Python 3.
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r17662 | bugman | 2012-10-02 14:16:02 +0200 (Tue, 02 Oct 2012) | 3 lines
Python 3 fixes - the character '\' is now properly escaped as '\\' in the stereochemistry auto-analysis.
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r17663 | bugman | 2012-10-02 14:18:41 +0200 (Tue, 02 Oct 2012) | 6 lines
Python 3 fix - the relax_errors.AllRelaxErrors object is now a proper tuple.
Due to bad coding, it was previously a nested tuple. This nested tuple worked in Python 2, but is
fatal for Python 3.
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r17664 | bugman | 2012-10-02 14:23:43 +0200 (Tue, 02 Oct 2012) | 6 lines
Python 3 preparation - the relax data store (the data package) now supports both Python 2 and 3.
The command used was:
2to3 -w data/__init__.py
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r17665 | bugman | 2012-10-02 14:25:52 +0200 (Tue, 02 Oct 2012) | 5 lines
Better support for both Python 2 and 3 in the relax data store.
The 2to3 script was used on all of the files in the data package.
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r17666 | bugman | 2012-10-02 14:37:01 +0200 (Tue, 02 Oct 2012) | 7 lines
Python 3 bug fix for the state.load user function.
The header line of pickled states (rather than the standard XML states) is of the b'' byte format.
This is now converted to a string, and the search expression is comparing it to the raw string
r"<\?xml".
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r17667 | bugman | 2012-10-02 15:18:32 +0200 (Tue, 02 Oct 2012) | 6 lines
Python 3 bug fix for the relax_io.read_spin_data() function.
The built in max() function cannot handle the value of None, therefore the filter() function is used
to remove all instances of None from the list.
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r17668 | bugman | 2012-10-02 15:19:32 +0200 (Tue, 02 Oct 2012) | 3 lines
Python 3 fix for the results.read user function matching that of state.load at r17666.
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r17669 | bugman | 2012-10-02 15:42:37 +0200 (Tue, 02 Oct 2012) | 6 lines
Python 3 fix for the reading of text from a bz2 file.
In Python 3, the readlines() function was returning a list of bytes types, not a list of strings.
The relax_io.extract_data() function now detects this and converts to string when possible.
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r17670 | bugman | 2012-10-02 15:44:24 +0200 (Tue, 02 Oct 2012) | 5 lines
Python 3 bug fix for the N-state model target function setup.
The num_tensors variable needs to be an integer, but the Python 3 division will create a float type.
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r17671 | bugman | 2012-10-02 15:48:31 +0200 (Tue, 02 Oct 2012) | 5 lines
Python 3 fix for the user function docstring creation in the prompt UI mode.
Again this is the problem of a division now returning a float rather than an int.
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r17672 | bugman | 2012-10-02 16:05:11 +0200 (Tue, 02 Oct 2012) | 5 lines
Python 3 fix for the test_write_protein_sequence() unit test.
This is again a string verses byte verses unicode problem.
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r17673 | bugman | 2012-10-02 16:09:58 +0200 (Tue, 02 Oct 2012) | 5 lines
Python 3 bug fix for the Structure.test_read_pdb_mol_2_model_scientific system tests.
This is again an integer division problem returning a float.
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r17674 | bugman | 2012-10-02 16:12:01 +0200 (Tue, 02 Oct 2012) | 5 lines
Python 2 and 3 support in the generic_fns.relax_data module using 2to3.
One print call was fixed after running 2to3.
........
r17675 | bugman | 2012-10-02 16:24:58 +0200 (Tue, 02 Oct 2012) | 3 lines
Python 3 fixes - eliminated all usage of the dictionary has_key() calls as they are no longer present.
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r17676 | bugman | 2012-10-02 16:30:46 +0200 (Tue, 02 Oct 2012) | 3 lines
Python 3 bug fix for the frame order analysis - another int division problem.
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r17677 | bugman | 2012-10-02 16:35:26 +0200 (Tue, 02 Oct 2012) | 3 lines
Python 3 integer division to float fix for the frame order analysis.
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r17678 | bugman | 2012-10-02 16:54:57 +0200 (Tue, 02 Oct 2012) | 5 lines
Python 3 fix for the frame order system tests - float to string conversions behave differently.
Now the explicit %.1f formatting is used to force only a single decimal place float.
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r17679 | bugman | 2012-10-02 16:58:40 +0200 (Tue, 02 Oct 2012) | 6 lines
Python 3 fix for the frame order system tests matching r17678.
As float to string conversions behave differently, the %.1f formatting is used to force only a
single decimal place float.
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r17680 | bugman | 2012-10-02 16:59:22 +0200 (Tue, 02 Oct 2012) | 3 lines
Python 3 fix - removed the use of the string.lower() function in the OpenDX mapping code.
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r17681 | bugman | 2012-10-02 17:47:23 +0200 (Tue, 02 Oct 2012) | 6 lines
Python 3 fix for the writing out of XML formatted state and results files.
In Python 3, the xmldoc.toprettyxml() returns a string object which needs to be 'encoded' prior to
writing out to file.
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r17682 | bugman | 2012-10-02 17:58:04 +0200 (Tue, 02 Oct 2012) | 3 lines
Python 3 import fixes for the generic_fns.structure package using relative paths.
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r17683 | bugman | 2012-10-02 18:29:25 +0200 (Tue, 02 Oct 2012) | 3 lines
Python 3 fix for the format detection of results and save files.
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r17684 | bugman | 2012-10-02 18:34:02 +0200 (Tue, 02 Oct 2012) | 3 lines
Python 2 fix for the relax_io.extract_data() function for a bug introduced at r17669.
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r17685 | bugman | 2012-10-02 18:46:16 +0200 (Tue, 02 Oct 2012) | 5 lines
The relax_io.DummyFileObject now mimics a file object for both Python 2 and 3.
In Python 3, everything from a file is of byte type and no longer string type.
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r17686 | bugman | 2012-10-02 18:48:25 +0200 (Tue, 02 Oct 2012) | 6 lines
The Mf.test_write_results system test can now select the correct file to compare against in Python 3.
The algorithm for determining if the 'final_results_trunc_1.3_v2' or
'final_results_trunc_1.3_pre_py2.7.3_v2' file should be used could not handle Python 3.
........
