relax SVN archive

Added a redirect for http://www.nmr-relax.com/api/bmrblib-module.html.

This is pointed to by some old Bmrblib news items, so now this redirects to the newer link of
http://www.nmr-relax.com/api/4.0/bmrblib-module.html.

Increased the Gna! news item sectioning depth in the release checklist document.

Updated the minfx and bmrblib versions in the release checklist document to 1.0.12 and 1.0.4.

This is to remove the numpy FutureWarning messages about the '== None' and '=! None' comparisons to
numpy data structures, which in the future will change in behaviour.

Updated the Mf.test_bug_23933_relax_data_read_ids system test to catch the RelaxMultiSpinIDError.

This allows the system test to pass, as a RelaxMultiSpinIDError is expected.

Fix for bug #23933 (https://gna.org/bugs/?23933).

This is the "NameError: global name 'ids' is not defined" problem when loading relaxation data.

The bug was introduced back in November 2014 (r26588), and is due to some incomplete error handling
code. The problem is that the spin type that the relaxation data belongs to (@N vs. @H) has not
been specified. Now the correct RelaxMultiSpinIDError is raised. The 'ids' variable did not exist
- it was code that was planned to be added, but never was and was forgotten.

Created the Mf.test_bug_23933_relax_data_read_ids system test.

This is designed to catch bug #23933 (https://gna.org/bugs/?23933), the "NameError: global name
'ids' is not defined" problem when loading relaxation data.

A truncated version of the PDB file and relaxation data, the full versions of which are attached to
the bug report, consisting solely of residues 329, 330, and 331 have been added to the test suite
shared data directories, and the system test written to catch the NameError.

More future protection against numpy changes.

The FutureWarning is "`rank` is deprecated; use the `ndim` attribute or function instead. To find
the rank of a matrix see `numpy.linalg.matrix_rank`." Therefore the N-state model target function
method paramag_info() has been updated to use the .ndim attribute and longer use numpy.rank()
function.

Updated all of relax to protect against future changes occurring in the numpy Python package.

From numpy version 1.9, the FutureWarning "__main__:1: FutureWarning: comparison to `None` will
result in an elementwise object comparison in the future." is seen in a large percentage of all
relax's user functions. This is caught and turned into a RelaxWarning with the same message.

The issue is that the behaviour of the comparison operators '==' and '!=' will change with future
numpy versions. These have been replaced with 'is' and 'is not' throughout the relax code base.
Changes have also been made to the minfx and bmrblib packages to match.

Replicated title fix for the HTML version of the manual.

The replicated titles were causing the sections with the same name to all point to a single HTML
page with the title name, resulting in a mess in the contents and in the flow of following the
manual sections sequentially. The relax 4.0.0 documentation has therefore been especially updated
with these fixes, even though the release does not contain the title name changes.

Ported r28058 and r28059 from trunk to fix the live HTML manual at http://www.nmr-relax.com .

The command used was:
svn merge -r28057:28059 svn+ssh://bugman@.../svn/relax/trunk/ .

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r28059 | bugman | 2015-10-15 11:55:30 +0200 (Thu, 15 Oct 2015) | 7 lines

Removal of an old replicated title in the LaTeX sources for the manual.

This is the title 'Model-free analysis' which is used for the entire specific analysis chapter as
well as for the model-free analysis section of the values, gradients, and Hessians for optimisation
chapter.


r28058 | bugman | 2015-10-15 11:51:00 +0200 (Thu, 15 Oct 2015) | 3 lines

Elimination of replicated titles in the LaTeX sources that the new frame order chapters introduced.
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