relax SVN archive

Merged revisions 27841-27843 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r27841 | tlinnet | 2015-05-27 03:09:50 +0200 (Wed, 27 May 2015) | 2 lines

Adding to user function minimise.execute() the keyword "mp_verbosity", to control the amount
of information to print when running multi processors.
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r27842 | tlinnet | 2015-05-27 03:09:52 +0200 (Wed, 27 May 2015) | 1 line

In multi.processor(), moving up the debugging print-out of running sets of calculatation.
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r27843 | tlinnet | 2015-05-27 03:09:55 +0200 (Wed, 27 May 2015) | 1 line

In pipe_control of minimise, adding the possibility to control verbosity in multi processor mode.
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Merged revisions 27834-27840 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r27834 | tlinnet | 2015-05-27 03:09:35 +0200 (Wed, 27 May 2015) | 8 lines

Wrote a method to store parameter data and dispersion curves, for the protocol of repeated analysis.

This is to prepare for analysis in other programs.
The method loops throug the data pipes, and write the data out.

It then write a bash script, that will concatenate the data in an matrix array style, for reading and processing in other programs.

Task #7826 (https://gna.org/task/?7826): Write an python class for the repeated analysis of dispersion data.
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r27835 | tlinnet | 2015-05-27 03:09:38 +0200 (Wed, 27 May 2015) | 3 lines

Added to write out a collection script for chi2 and rate parameters.

Task #7826 (https://gna.org/task/?7826): Write an python class for the repeated analysis of dispersion data.
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r27836 | tlinnet | 2015-05-27 03:09:40 +0200 (Wed, 27 May 2015) | 3 lines

In the collection bash script, removes spins which have not been fitted.

Task #7826 (https://gna.org/task/?7826): Write an python class for the repeated analysis of dispersion data.
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r27837 | tlinnet | 2015-05-27 03:09:42 +0200 (Wed, 27 May 2015) | 3 lines

Fix for use of " instead of ' in bash script.

Task #7826 (https://gna.org/task/?7826): Write an python class for the repeated analysis of dispersion data.
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r27838 | tlinnet | 2015-05-27 03:09:44 +0200 (Wed, 27 May 2015) | 3 lines

Adding option to minimise class function, to perform monte carlo error analysis.

Task #7826 (https://gna.org/task/?7826): Write an python class for the repeated analysis of dispersion data.
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r27839 | tlinnet | 2015-05-27 03:09:46 +0200 (Wed, 27 May 2015) | 3 lines

Printout when minimising monte-carlo simulations.

Task #7826 (https://gna.org/task/?7826): Write an python class for the repeated analysis of dispersion data.
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r27840 | tlinnet | 2015-05-27 03:09:48 +0200 (Wed, 27 May 2015) | 3 lines

Adding keyword for verbosity for multi processor mode.

Task #7826 (https://gna.org/task/?7826): Write an python class for the repeated analysis of dispersion data.
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Merged revisions 27800-27805,27807,27816,27818-27820,27822,27827 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r27800 | bugman | 2015-03-10 10:05:25 +0100 (Tue, 10 Mar 2015) | 7 lines

Fix for the lib.sequence.check_sequence checking object.

Although rarely used, the check for the spin number was incorrect and half of the checks were
instead for the residue number. This is a classic copy and paste error where the residue name and
number checks were copied but not completely converted to spin name and numbers.
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r27801 | bugman | 2015-03-10 10:13:33 +0100 (Tue, 10 Mar 2015) | 5 lines

Added the raise_flag argument to the lib.sequence.read_spin_data() function.

This is to allow the missing data RelaxError to be deactivated.
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r27802 | bugman | 2015-03-10 10:15:35 +0100 (Tue, 10 Mar 2015) | 7 lines

Modified the spectrum.read_intensities user function backend to be more robust.

This affects the generic formatted peak lists, via the lib.spectrum.peak_list.intensity_generic()
function. The peak list reading will now continue reading the file after corrupted lines have been
encountered.
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r27803 | bugman | 2015-03-10 18:00:53 +0100 (Tue, 10 Mar 2015) | 7 lines

Python 3 improvement for the rdc.corr_plot and pcs.corr_plot user functions.

The world view is now set in floating point numbers. In Python 2, the math.ceil() and math.floor()
functions return floats, whereas in Python 3 these functions return integers. The behaviour is now
consistent in both Python versions, fixing a few system tests.
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r27804 | bugman | 2015-03-10 18:36:55 +0100 (Tue, 10 Mar 2015) | 7 lines

Improvements for the pcs.structural_noise user function.

The check for the presence of PCS data for points to skip now includes checking for PCS values of
None. And the output Grace file now also includes the spin ID string as a string or comment value
which can be displayed in the plot when desired.
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r27805 | bugman | 2015-03-10 18:58:41 +0100 (Tue, 10 Mar 2015) | 9 lines

Modified the internal formatting of the data section of the Grace 2D graph files.

This affects the lib.plotting.grace.write_xy_data() function. The formatting is now more
consistent, with the X value now set to a fixed number of decimal places, and hence will no longer
change between Python 2 and 3. The data is now all right justified as well, for easier reading.

All affected system tests have been updated for the new format.
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r27807 | bugman | 2015-03-13 11:39:16 +0100 (Fri, 13 Mar 2015) | 3 lines

Epydoc documentation fix for the lib.structure.pdb_write_handle_atom_name() function.
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r27816 | bugman | 2015-03-13 15:42:37 +0100 (Fri, 13 Mar 2015) | 6 lines

Backported the relax 3.3.7 CHANGES file changes to trunk.

The command used was:
svn merge -r27810:r27811 svn+ssh://bugman@.../svn/relax/tags/3.3.7 .
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r27818 | bugman | 2015-03-13 17:55:09 +0100 (Fri, 13 Mar 2015) | 3 lines

Spacing fixes in the CHANGES document.
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r27819 | bugman | 2015-03-17 11:12:55 +0100 (Tue, 17 Mar 2015) | 6 lines

Fix for the pipe_control.reset.reset() function when resetting the GUI in non-standard contexts.

This is mainly for debugging scripts when simulating a GUI and hence the GUI reset() method does not
exist.
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r27820 | bugman | 2015-03-17 12:21:57 +0100 (Tue, 17 Mar 2015) | 7 lines

Created a GUI memory management debugging script for the align_tensor.init user function.

This repetitively calls the reset, pipe.create and align_tensor.init user functions, and opening the
GUI element for setting alignment tensor elements (the Sequence window). The pympler muppy_log file
shows no memory leaks for these user functions on Linux systems.
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r27822 | bugman | 2015-04-02 09:14:10 +0200 (Thu, 02 Apr 2015) | 10 lines

Resized all fixed-sized GUI wizards to fit on 1024x768 pixel wide displays.

The problem was reported by Lora Picton in the thread starting at
http://thread.gmane.org/gmane.science.nmr.relax.user/1813 .

Both the spin loading wizard of the spin viewer window and the relaxation data loading wizard used
currently in the model-free analysis tab and BMRB export page were fixed. These both had the
y-dimension set to 800 pixels, hence parts of the window would be out of view.
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r27827 | bugman | 2015-04-02 09:41:52 +0200 (Thu, 02 Apr 2015) | 6 lines

Backported the relax 3.3.8 CHANGES file changes to trunk.

The command used was:
svn merge -r27825:r27826 svn+ssh://bugman@.../svn/relax/tags/3.3.8 .
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Made a summarize function to compare results.

Task #7826 (https://gna.org/task/?7826): Write an python class for the repeated analysis of dispersion data.

Added a unit test for the new lib.statistics.geometric_std() function.

Addition of the file which should have been committed in the last commit (r27863).

Created a simple unit test for the new lib.statistics.geometric_mean() function.

Removed some rubbish text from the new lib.statistics.geometric_*() function docstrings.

Added functions for calculating the geometric mean and standard deviation to the relax library.

These are the geometric_mean() and geometric_std() functions of the lib.statistics module. The
implementation is designed to be fast, using numpy array arithmetic rather than Python loops.

Huge speed up for the Monte Carlo simulations in the N-state model analyses.

This speed up is also for Bootstrap simulations and the frame order analysis. The change affects
the monte_carlo.initial_values user function. The alignment tensor _update_object() method was very
inefficient when updating the Monte Carlo simulation data structures. For each simulation, each of
the alignment tensor data structures were being updated for all simulations. Now only the current
simulations is being updated. This speeds up the user function by many orders of magnitude.