relax SVN archive

Merged revisions 26255 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r26255 | bugman | 2014-10-13 15:16:28 +0200 (Mon, 13 Oct 2014) | 10 lines

Updated the Palmer.test_palmer_omp system test for the 64-bit Linux Modelfree 4.20 GCC binary file.

This fixes the second part and last part of the bug #22772 (https://gna.org/bugs/?22772), the
modelfree4 binary issue and the User_functions GUI tests with wxPython 2.9 failures of the test
suite.

The problem is that the 64-bit GNU/Linux GCC compiled binary of Modelfree 4.20 produces different
results as previous versions. These are now caught by the system test and correctly checked.
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Merged revisions 26254 via svnmerge from
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r26254 | bugman | 2014-10-13 14:25:26 +0200 (Mon, 13 Oct 2014) | 9 lines

Fix for the poorly written User_functions.test_structure_add_atom GUI test.

This fixes one part of 2 of the bug #22772 (https://gna.org/bugs/?22772), the modelfree4 binary
issue and the User_functions GUI tests with wxPython 2.9 failures of the test suite.

The problem was that a list element was being set in the GUI test, but that element did not exist
yet. Somehow this worked in wxPython 2.8. But the bad code failed on wxPython 2.9.
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Merged revisions 26249-26253 via svnmerge from
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r26249 | tlinnet | 2014-10-11 17:38:24 +0200 (Sat, 11 Oct 2014) | 1 line

Added example save state for more surface plotting.
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r26250 | tlinnet | 2014-10-13 10:47:40 +0200 (Mon, 13 Oct 2014) | 3 lines

Added boolean argument to dx.map() function, to specify the creation of a parameter and associated chi2 values file.

For very very special situtaions, the creation of this file is not desired.
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r26251 | tlinnet | 2014-10-13 11:48:03 +0200 (Mon, 13 Oct 2014) | 1 line

Modified that structure of points in dx.map() is always a list of numpy arrays with 3 values.
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r26252 | tlinnet | 2014-10-13 11:48:05 +0200 (Mon, 13 Oct 2014) | 1 line

When issuing dx.map() function with points, implemented the writing out of parameter file, with associated calculated chi2 values.
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r26253 | bugman | 2014-10-13 14:11:03 +0200 (Mon, 13 Oct 2014) | 5 lines

Improved the feedback in the User_functions.test_structure_add_atom system test.

It is now clearer what the input and output data is.
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Merged revisions 26248 via svnmerge from
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r26248 | tlinnet | 2014-10-11 17:35:48 +0200 (Sat, 11 Oct 2014) | 3 lines

Added example surface chi2 values for plots.

Task #7826 (https://gna.org/task/index.php?7826): Write an python class for the repeated analysis of dispersion data.
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Merged revisions 26245-26247 via svnmerge from
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r26245 | tlinnet | 2014-10-11 17:35:41 +0200 (Sat, 11 Oct 2014) | 1 line

Renamed test scripts and files for producing surface chi2 plots.
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r26246 | tlinnet | 2014-10-11 17:35:44 +0200 (Sat, 11 Oct 2014) | 1 line

Renamed sample scripts making surface maps.
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r26247 | tlinnet | 2014-10-11 17:35:46 +0200 (Sat, 11 Oct 2014) | 1 line

Added scripts to make surface plots of spin independents parameters dw and r2a.
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Merged revisions 26244 via svnmerge from
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r26244 | tlinnet | 2014-10-10 17:05:39 +0200 (Fri, 10 Oct 2014) | 10 lines

Created systemtest Relax_disp.test_dx_map_clustered_create_par_file, which must show that relax is not able to find the local minimum under clustered conditions.

When creating the map, the map contain chi2 values, which are lower than the clustered fitted values.

This should not be the case.

I am running a larger map with larger bounds and more increements, which should show that there exist a minimum in the minimisation space with a lower chi2 value.

Bug #22754 (https://gna.org/bugs/index.php?22754): The minimise.calculate() does not calculate chi2 value for clustered residues.
Task #7860(https://gna.org/task/index.php?7860): When dx_map is issued, create a parameter file which maps parameters to chi2 value.
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Merged revisions 26243 via svnmerge from
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r26243 | tlinnet | 2014-10-10 17:05:25 +0200 (Fri, 10 Oct 2014) | 3 lines

Added the write out of parameters and chi2 values, when creating a dx_map.

Task #7860(https://gna.org/task/index.php?7860): When dx_map is issued, create a parameter file which maps parameters to chi2 value.
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Merged revisions 26208,26214-26216,26221-26228,26232-26234,26237-26238,26241-26242 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r26208 | bugman | 2014-10-09 08:50:07 +0200 (Thu, 09 Oct 2014) | 7 lines

Expanded the list of global dispersion parameters in the set_param_values() API method.

This is a quick expansion of Troels' fix of r26197, to allow for the release of relax 3.3.1. This
is a small part of the discussion at
http://thread.gmane.org/gmane.science.nmr.relax.scm/23948/focus=7188.
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r26214 | bugman | 2014-10-09 11:13:39 +0200 (Thu, 09 Oct 2014) | 6 lines

Backported the relax 3.3.1 CHANGES file changes to trunk.

The command used was:
svn merge -r26211:r26213 svn+ssh://bugman@.../svn/relax/tags/3.3.1 .
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r26215 | bugman | 2014-10-09 11:14:59 +0200 (Thu, 09 Oct 2014) | 3 lines

Updated the minfx version in the release checklist document to version 1.0.11.
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r26216 | bugman | 2014-10-09 11:31:51 +0200 (Thu, 09 Oct 2014) | 3 lines

Updated the relax version in the release checklist document to be more modern.
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r26221 | bugman | 2014-10-09 17:15:26 +0200 (Thu, 09 Oct 2014) | 3 lines

Spelling fixes for the CHANGES file.
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r26222 | bugman | 2014-10-09 17:16:27 +0200 (Thu, 09 Oct 2014) | 6 lines

Updates for the release checklist document.

This is mainly because the main release notes are now the relax wiki, for example for the current
version at http://wiki.nmr-relax.com/Relax_3.3.1.
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r26223 | bugman | 2014-10-09 17:32:01 +0200 (Thu, 09 Oct 2014) | 3 lines

Spelling fixed throughout the CHANGES document.
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r26224 | bugman | 2014-10-09 17:32:59 +0200 (Thu, 09 Oct 2014) | 3 lines

Removed a few triple spaces in the CHANGES document.
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r26225 | bugman | 2014-10-09 17:34:40 +0200 (Thu, 09 Oct 2014) | 3 lines

Added periods to the end of all items in the CHANGES document.
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r26226 | bugman | 2014-10-09 17:35:11 +0200 (Thu, 09 Oct 2014) | 3 lines

Fix for an 'N/A' in the CHANGES document.
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r26227 | bugman | 2014-10-09 17:38:40 +0200 (Thu, 09 Oct 2014) | 3 lines

Converted a number of single spaces between sentences to double spaces in the CHANGES document.
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r26228 | bugman | 2014-10-10 10:20:36 +0200 (Fri, 10 Oct 2014) | 3 lines

More updates for the announcement section of the release checklist document.
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r26232 | bugman | 2014-10-10 10:52:28 +0200 (Fri, 10 Oct 2014) | 6 lines

Fix for the latex2html tags in the model-free chapter of the relax manual.

This bug may affect the compilation of both the PDF and HTML version
(http://www.nmr-relax.com/manual/) of the manual.
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r26233 | bugman | 2014-10-10 10:55:58 +0200 (Fri, 10 Oct 2014) | 10 lines

Formatting improvements for the user function chapter of the HTML manual.

This is for http://www.nmr-relax.com/manual/Alphabetical_listing_user_functions.html. This will
hopefully fix the horrible formatting whereby all text is wrapped in the HTML tags <SMALL
CLASS="FOOTNOTESIZE"><SMALL CLASS="FOOTNOTESIZE"><SMALL CLASS="FOOTNOTESIZE"><SMALL
CLASS="FOOTNOTESIZE"><SMALL CLASS="FOOTNOTESIZE"><SMALL CLASS="FOOTNOTESIZE"><SMALL
CLASS="FOOTNOTESIZE"><SMALL CLASS="FOOTNOTESIZE"><SMALL CLASS="FOOTNOTESIZE"><SMALL
CLASS="SCRIPTSIZE">text</SMALL></SMALL></SMALL></SMALL></SMALL></SMALL></SMALL></SMALL></SMALL></SMALL>.
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r26234 | bugman | 2014-10-10 11:50:20 +0200 (Fri, 10 Oct 2014) | 12 lines

Big bug fix for the text size formatting of the HTML manual.

The previous fix for the user function chapter of the HTML manual
(http://www.nmr-relax.com/manual/Alphabetical_listing_user_functions.html) did not fix the problem.

The issue was with the {exampleenv} defined using a \newenvironment command in the preamble. The
command \footnotesize was bing used in the start, but nothing was changing the font size at the end.
In LaTeX, the ending of the environment appears to reset the font size, whereas in latex2html it
does not. Therefore all text after this environment is prepended by <SMALL CLASS="FOOTNOTESIZE"> in
the HTML manual and this keeps adding to the text after each new exampleenv environment.
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r26237 | bugman | 2014-10-10 13:26:14 +0200 (Fri, 10 Oct 2014) | 7 lines

The HTML version of the manual is now compiled with Unicode character support.

This is for the manual at http://www.nmr-relax.com/manual/index.html. It allows Greek symbols, for
example, to be represented as text rather than LaTeX generated PNG images. This fixes titles and
massively decreases the number of images required by the HTML pages.
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r26238 | bugman | 2014-10-10 13:37:01 +0200 (Fri, 10 Oct 2014) | 9 lines

Removal of many dual LaTeX and latex2html section titles in the manual.

As the HTML manual (http://www.nmr-relax.com/manual/index.html) is now compiled with Unicode
support, the Greek characters in the titles are now supported. Therefore in the model-free and the
values, gradients, and Hessians chapters, the dual LaTeX and latex2html section titles could be
collapsed to the standard LaTeX section title. This will result in better formatting of the manual
and its links.
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r26241 | bugman | 2014-10-10 16:54:59 +0200 (Fri, 10 Oct 2014) | 9 lines

Added instructions and a build script for creating a useful version of latex2html.

This version is essential for building the HTML version of the manual at
http://www.nmr-relax.com/manual/. The build script downloads the Debian latex2html-2008 sources as
well as all Debian patches for latex2html. It then applies a number of patches for fixing and
improving the relax documentation. The program is then compiled and can be installed as the root
user into /usr/local/.
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r26242 | bugman | 2014-10-10 17:00:52 +0200 (Fri, 10 Oct 2014) | 5 lines

Extended the number of words used in the HTML webpage file names.

This is to hopefully prevent files from being overwritten by multiple files having the same name.
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The pipe_control.opendx space mapping code now calls the value.set() function with verbosity=0.

This is to silence the very repetitive statistics resetting messages when executing the dx.map user
function.

Added the verbosity argument to the pipe_control.value.set() function.

This is passed into the pipe_control.minimise.reset_min_stats() function so its printouts can be
silenced.