bugrelax - Bugs: bug #20119, The loading of...

 
 
Show feedback again

bug #20119: The loading of spectrum.peak_intensities user function is restricted to one spin type.

Submitted by:  Edward d Auvergne <bugman>
Submitted on:  Sat 01 Sep 2012 07:33:15 AM UTC  
 
Category: relax's source codeSpecific analysis category: None
Priority: 5 - NormalSeverity: 3 - Normal
Status: FixedAssigned to: Edward d Auvergne <bugman>
Originator Name: Open/Closed: Closed
Release: 2.1.0Operating System: All systems

Add a New Comment (Rich MarkupRich Markup):
   

You are not logged in

Please log in, so followups can be emailed to you.

 

Tue 16 Oct 2012 08:19:57 AM UTC, SVN revision 17828:

Merged revisions 17391-17538 via svnmerge from
svn+ssh://bugman@svn.gna.org/svn/relax/trunk

........
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.
........
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.
........
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.
........
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.
........
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.
........
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.
........
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.
........
r17398 | bugman | 2012-08-30 16:50:46 +0200 (Thu, 30 Aug 2012) | 3 lines

Another fix for the relax_data.temp_control description.
........
r17399 | bugman | 2012-08-30 17:43:09 +0200 (Thu, 30 Aug 2012) | 3 lines

Added the Viles et al., 2001 reference.
........
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.
........
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.
........
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.

[...]........

[...] 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.

[...]........

[...] 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.

[...]........

[...] 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.

[...]........

[...] 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.

[...]........

[...] r17407 | bugman | 2012-08-31 23:36:17 +0200 (Fri, 31 Aug 2012) | 3 lines

[...]

[...] Added a section label.

[...]........

[...] 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!

[...]........

[...] 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.

[...]........

[...] 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).

[...]........

[...] 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).

[...]........

[...] 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!

[...]........

[...] 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.

[...]........

[...] 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).

[...]........

[...] r17415 | bugman | 2012-09-01 11:21:54 +0200 (Sat, 01 Sep 2012) | 3 lines

[...]

[...] Removed a debugging print out.

[...]........

[...] 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.

[...]........

[...] 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.

[...]........

[...] 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.

[...]........

[...] 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.

[...]........

[...] 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.

[...]........

[...] 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.

[...]........

[...] 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.

[...]........

[...] 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".

[...]........

[...] r17424 | bugman | 2012-09-03 11:11:48 +0200 (Mon, 03 Sep 2012) | 3 lines

[...]

[...] Shifted the spin viewer screenshots into their own directory.

[...]........

[...] 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.

[...]........

[...] 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.

[...]........

[...] 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.

[...]........

[...] 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.

[...]........

[...] r17429 | bugman | 2012-09-03 12:16:00 +0200 (Mon, 03 Sep 2012) | 3 lines

[...]

[...] Added some more LaTeX functions for formatting consistency.

[...]........

[...] 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.

[...]........

[...] 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.

[...]........

[...] 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.

[...]........

[...] 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.

[...]........

[...] r17434 | bugman | 2012-09-03 14:51:11 +0200 (Mon, 03 Sep 2012) | 3 lines

[...]

[...] Fix for the Farrow et al., 1995 DOI number.

[...]........

[...] r17435 | bugman | 2012-09-03 15:03:36 +0200 (Mon, 03 Sep 2012) | 3 lines

[...]

[...] Added the Fushman et al., 1998 reference.

[...]........

[...] 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.

[...]........

[...] 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.

[...]........

[...] r17438 | bugman | 2012-09-03 15:13:16 +0200 (Mon, 03 Sep 2012) | 3 lines

[...]

[...] Activated the consistency testing chapter of the user manual.

[...]........

[...] 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.

[...]........

[...] 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.

[...]........

[...] 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.

[...]........

[...] 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.

[...]........

[...] 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.

[...]........

[...] 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.

[...]........

[...] 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.

[...]........

[...] 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.

[...]........

[...] 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.

[...]........

[...] 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.

[...]........

[...] 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.

[...]........

[...] 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.

[...]........

[...] 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: )

[...]........

[...] 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!

[...]........

[...] 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: )

[...]........

[...] 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.

[...]........

[...] 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: )

[...]........

[...] 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.

[...]........

[...] 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: )

[...]........

[...] 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: )

[...]........

[...] 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: )

[...]........

[...] 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: )

[...]........

[...] 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: )

[...]

[...] This also follows a discussion started by Edward d'Auvergne at:

[...] https://mail.gna.org/public/relax-devel/2012-09/msg00019.html

[...] (Message-id: )

[...]........

[...] 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: )

[...]

[...] The command used was:

[...] svn merge -r17456:17455 .

[...]

[...] Then, the file was manually adjusted since there were apparently conflicts with svn...

[...]........

[...] 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: )

[...]

[...] and

[...]

[...] https://mail.gna.org/public/relax-devel/2012-09/msg00032.html

[...] (Message-id: )

[...]........

[...] 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.

[...]........

[...] 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: )

[...]........

[...] 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: )

[...]........

[...] 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.

[...]........

[...] 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.

[...]........

[...] 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.

[...]........

[...] 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.

[...]........

[...] 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.

[...]........

[...] 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: )

[...]........

[...] 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.

[...]........

[...] 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.

[...]........

[...] 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).

[...]........

[...] 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).

[...]........

[...] 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).

[...]........

[...] 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!

[...]........

[...] 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.

[...]........

[...] 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.

[...]........

[...] r17481 | bugman | 2012-09-17 10:51:37 +0200 (Mon, 17 Sep 2012) | 3 lines

[...]

[...] Comment spelling fix.

[...]........

[...] 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.

[...]........

[...] 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.

[...]........

[...] 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).

[...]........

[...] 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@C2", ":A@C8", ":G@N1",

[...] ":G@C8", ":C@C5", ":C@C5", ":U@N3", ":U@C5", ":U@C6".

[...]........

[...] 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.

[...]........

[...] 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@gna.org/msg01253.html and bug #20174

[...] (http://gna.org/bugs/?20174).

[...]........

[...] 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.

[...]........

[...] 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.

[...]........

[...] 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.

[...]........

[...] 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.

[...]........

[...] 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.

[...]........

[...] 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.

[...]........

[...] 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.

[...]........

[...] 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.

[...]........

[...] 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.

[...]........

[...] 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.

[...]........

[...] 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.

[...]........

[...] 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.

[...]........

[...] 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.

[...]........

[...] 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.

[...]........

[...] 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.

[...]........

[...] 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.

[...]........

[...] 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.

[...]........

[...] 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.

[...]........

[...] 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.

[...]........

[...] 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.

[...]........

[...] 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.

[...]........

[...] 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.

[...]........

[...] 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.

[...]........

[...] 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.

[...]........

[...] 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!

[...]........

[...] r17513 | bugman | 2012-09-19 17:03:20 +0200 (Wed, 19 Sep 2012) | 3 lines

[...]

[...] Improvements to the duplicate user manual title finding script.

[...]........

[...] 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.

[...]........

[...] 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.

[...]........

[...] 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).

[...]........

[...] 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.

[...]........

[...] 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.

[...]........

[...] 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).

[...]........

[...] 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.

[...]........

[...] 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.

[...]........

[...] 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.

[...]........

[...] 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.

[...]........

[...] 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.

[...]........

[...] 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.

[...]........

[...] 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.

[...]........

[...] 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!.

[...]........

[...] r17528 | bugman | 2012-09-20 12:14:31 +0200 (Thu, 20 Sep 2012) | 3 lines

[...]

[...] Spacing fix.

[...]........

[...] 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.

[...]........

[...] 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.

[...]........

[...] 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.

[...]........

[...] 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!

[...]........

[...] 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.

[...]........

[...] 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.

[...]........

[...] 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.

[...]........

[...] 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.

[...]........

[...] 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.

[...]........

[...] 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.

[...]........

[...]

[...]

(Browse SVN revision 17828)

Edward d Auvergne <bugman>
Project AdministratorIn charge of this item.
Sat 01 Sep 2012 08:17:30 AM UTC, SVN revision 17411:

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).

(Browse SVN revision 17411)

Edward d Auvergne <bugman>
Project AdministratorIn charge of this item.
Sat 01 Sep 2012 08:09:09 AM UTC, SVN revision 17410:

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).

(Browse SVN revision 17410)

Edward d Auvergne <bugman>
Project AdministratorIn charge of this item.
Sat 01 Sep 2012 07:33:15 AM UTC, original submission:

This appears to be a recently introduced bug which prevents, for example, both the protein backbone and Trp indole NH data from being simultaneously loaded via the spectrum.peak_intensities user function. This affects the Rx exponential curve-fitting and the steady-state NOE calculation. This is more annoying than fatal, as a sequent execution of these analyses on the different spin types can be performed and then all the data loaded into relax later for J(w) mapping and model-free analyses.

Edward d Auvergne <bugman>
Project AdministratorIn charge of this item.

 

(Note: upload size limit is set to 1024 kB, after insertion of the required escape characters.)

Attach File(s):
   
   
Comment:
   

No files currently attached

 

Depends on the following items: None found

Items that depend on this one: None found

 

Carbon-Copy List
  • -unavailable- added by bugman (Submitted the item)
  •  

    Do you think this task is very important?
    If so, you can click here to add your encouragement to it.
    This task has 0 encouragements so far.

    Only logged-in users can vote.

     

    Please enter the title of George Orwell's famous dystopian book (it's a date):

     

     

    Follow 2 latest changes.

    Date Changed By Updated Field Previous Value => Replaced By
    Sat 01 Sep 2012 07:43:46 AM UTCbugmanStatusNone=>Fixed
      Open/ClosedOpen=>Closed
    Show feedback again

    Back to the top


    Powered by Savane 3.1-cleanup