relax SVN archive

relax version 3.3.7.

This is a major feature and bugfix release. New features include the statistics.aic and
statistics.model user functions, plotting API advancements, huge speed ups for the assembly of
atomic coordinates from a large number of structures, the sorting of sequence data in the internal
structural object for better structural consistency, conversion of the structure.mean user function
to the new pipe/model/molecule/atom_id design, and improvements to the rdc.copy and pcs.copy user
functions. Bugs fixed include the incorrect pre-scanning of old scripts identifying the
minimise.calculate user function as the old minimise user function, Python 3 fixes, and the failure
in reading CSV files in the sequence.read user function.

Epydoc documentation fix for the lib.structure.pdb_write_handle_atom_name() function.

Bug fix for the frame order target function (introduced recently in r27715).

The copy.deepcopy() function is now used for all numpy input data to avoid the data from being
modified between function calls. This is important for missing RDC and PCS data which is sent in as
NaN values. In the target function __init__() method, the NaN values are replaced by 0.0 after the
self.missing_rdc and self.missing_pcs structures have been by checking for NaN values. However the
recent specific_analyses.frame_order.optimisation change in the Frame_order_minimise_command slave
command to printout the number of integration points resulted in the target function being
initialised twice, causing all NaN values to be 0.0 in the second initialisation. Hence all missing
data was being treated as real data with values of 0.0.

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.

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.

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.

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.

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

This is to allow the missing data RelaxError to be deactivated.

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.

Merged revisions 27797 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r27797 | bugman | 2015-03-10 09:50:16 +0100 (Tue, 10 Mar 2015) | 6 lines

Fix for bug #23372 (https://gna.org/bugs/?23372), the sequence.read failure with CSV files.

The problem was that the sep argument was not being passed all the way to the backend
lib.io.extract_data() function.
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