relax SVN archive

Added printouts to the determine_rnd() function of the dauvergne_protocol model-free auto-analysis.

This is for better user feedback in the log files as to what is happening. It may help in debugging
bug #22730 (https://gna.org/bugs/?22730): Model-free auto-analysis - relax stops and quits at the
polate step.

Added an additional check to determine_rnd() of the dauvergne_protocol model-free auto-analysis.

This is to try to catch bizarre situations such as bug #22730 (https://gna.org/bugs/?22730),
model-free auto-analysis - relax stops and quits at the polate step.

The additional check is that if the base model directory is not executable, a RelaxError is raised.

Added more checks to the determine_rnd() of the dauvergne_protocol model-free auto-analysis.

This is to try to catch bizarre situations such as bug #22730 (https://gna.org/bugs/?22730),
model-free auto-analysis - relax stops and quits at the polate step.

The following additional fatal conditions are now checked for: A file with the same name as the
base model directory already exists; The base model directory is not readable; The base model
directory is not writable. The last two could be caused by file system corruptions. In addition,
the presence of the base model directory is checked for using os.path.isdir() rather than catching
errors coming out of the os.listdir() function. These changes should make the analysis more robust
in the presence of 'strangeness'.

Renaming of the 'dx' user function class to 'mapping'.

In addition, the dx.map user function is now called mapping.setup and the dx.execute user function
is now mapping.dx_execute.

Initialized merge tracking via "svnmerge" with revisions "1-26279" from
svn+ssh://bugman@.../svn/relax/trunk

Creating a quick branch for refactoring the space mapping code.

This follows from the discussion in the thread at
http://thread.gmane.org/gmane.science.nmr.relax.scm/24009/focus=7228.

The idea is to create a number of software independent and dependent user functions for setting up
the space mapping (the map.setup user function), creating the map, storing all data in the current
data pipe, and having user functions for outputting the data for OpenDX, matplotlib and plain text.

Merged revisions 26261-26267 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r26261 | tlinnet | 2014-10-13 18:19:34 +0200 (Mon, 13 Oct 2014) | 1 line

Inserted a z_axis limit for the plotting of 2D surfaces in matplotlib.
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r26262 | tlinnet | 2014-10-13 18:19:36 +0200 (Mon, 13 Oct 2014) | 1 line

Added better figure control of chi2 values on z-axis for surface plots.
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r26263 | tlinnet | 2014-10-13 18:19:38 +0200 (Mon, 13 Oct 2014) | 5 lines

Narrowed in dx_map in systemtest Relax_disp.test_dx_map_clustered_create_par_file()

This is to illustrate the failure of relax finding the global minimum.

It seems there is a shallow barrier, which relax failed to climb over, in order to find the minimum value.
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r26264 | bugman | 2014-10-13 19:07:30 +0200 (Mon, 13 Oct 2014) | 3 lines

Removed a debugging printout.
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r26265 | bugman | 2014-10-13 22:57:11 +0200 (Mon, 13 Oct 2014) | 6 lines

Added the verbosity argument to the pipe_control.minimise.reset_min_stats() function.

All of the minimisation code which calls this now send in their verbosity arguments. This allows
the text "Resetting the minimisation statistics." to be suppressed.
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r26266 | bugman | 2014-10-13 22:58:22 +0200 (Mon, 13 Oct 2014) | 6 lines

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.
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r26267 | bugman | 2014-10-13 22:59:51 +0200 (Mon, 13 Oct 2014) | 6 lines

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.
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Merged revisions 26260 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r26260 | tlinnet | 2014-10-13 17:19:00 +0200 (Mon, 13 Oct 2014) | 5 lines

Fix for testing the raise of expected errors in systemtests.

The systemtest will not be tested, if python version is under version 2.7.

Bug #22801 (https://gna.org/bugs/?22801): Failure of the relax test suite on Python 2.5.
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Merged revisions 26259 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r26259 | tlinnet | 2014-10-13 17:18:58 +0200 (Mon, 13 Oct 2014) | 7 lines

Removal the use of OrderecDict().

OrderedDict is first available in python 2.7, and is not essential functionality.

The functionality is replaced with looping over a list of dictionary keys instead, which is picked up under analysis.

Bug #22798 (https://gna.org/bugs/?22798): Failure of relax to start due to an OrderedDict ImportError on Python 2.6 and earlier.
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Merged revisions 26256-26258 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r26256 | bugman | 2014-10-13 16:30:13 +0200 (Mon, 13 Oct 2014) | 6 lines

The devel_scripts/python_multiversion_test_suite.py script now runs relax with the --time flag.

This is for quicker identification of failure points. It will also force the sys.stdout buffer to
be flushed more often on Python 2.5 so that it does not appear as if the tests have frozen.
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r26257 | tlinnet | 2014-10-13 17:18:50 +0200 (Mon, 13 Oct 2014) | 1 line

Added check to systemtest Relax_disp.test_cpmg_synthetic_dx_map_points() for the creation of a matplotlib surface command plot file.
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r26258 | tlinnet | 2014-10-13 17:18:56 +0200 (Mon, 13 Oct 2014) | 10 lines

Added the write out of a matplotlib command file, to plot surfaces of a dx map.

It uses the minimum chi2 value in the map space, to define surface defitions.

It creates a X,Y; X,Z; Y,Z map, where the values in the missing dimension has been cut at the minimum chi2 value.
For each map, it creates a projected 3d map of the parameters and the chi2 value, and a heat map for the contours.

It also scatters the minimum chi2 value, the 4 smallest chi2 values, and maps any points in the point file, to a scatter point.

Mapping the points from file to map points, is done by finding the shortest Euclidean distance in the space from the points to any map points.
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