relax SVN archive

Merged revisions 26907 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

........
r26907 | bugman | 2014-12-03 08:50:18 +0100 (Wed, 03 Dec 2014) | 3 lines

Grammar fix for a warning from the pymol.display user function.
........

Updated all frame order system tests for the frame_order.ref_domain user function requirement.

Updated the frame_order.ref_domain user function for the current branch design.

This user function was quite out of date. The alignment tensor checks have been removed, to allow
this to be used in the absence of base data. And the user function description has been updated.

Better checking for the non-moving domain setup.

The frame_order.pdb_model user function will now raise a RelaxError if the frame_order.ref_domain
user function has not been called to set up the non-moving domain.

Redesign of the pymol.frame_order user function.

This user function was still fitting to the old design in the relax trunk. It has been updated for
the frame_order_cleanup branch whereby the frame_order.pdb_model user function has been split up and
the positional distribution has been replaced by the Brownian simulation user function
frame_order.simulate.

Grammar fix for a warning from the pymol.display user function.

More redirects for the relax HTML manual at http://www.nmr-relax.com/manual/index.html.

This is required as the latex2html program used to build the manual has been modified to not
excluded the 'common words' from the page titles (see docs/devel/latex2html/). These redirects are
linked from outside of http://www.nmr-relax.com, as identified by the Google Webmaster Tools.

This is for http://www.nmr-relax.com/manual/The_NS_2_site_expanded_CPMG_model.html.

Merged revisions 26901-26902 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

........
r26901 | bugman | 2014-12-02 21:39:10 +0100 (Tue, 02 Dec 2014) | 9 lines

Created the State.test_bug_23017_ieee_754_multidim_numpy_arrays system test.

This is to catch bug #23017 (https://gna.org/bugs/?23017), the multidimensional numpy arrays are not
being stored as IEEE 754 arrays in the XML state and results files.

This test checks a rank-2 float64 numpy array stored in the current data pipe against what the IEEE
754 int list should be for it.
........
r26902 | bugman | 2014-12-02 21:42:14 +0100 (Tue, 02 Dec 2014) | 9 lines

Simple fix for bug #23017 (https://gna.org/bugs/?23017).

This is the multidimensional numpy arrays are not being stored as IEEE 754 arrays in the XML state
and results files. The problem was a relatively recent regression caused by a change to the
is_float_matrix() function of the lib.arg_check module. It was simply that the default dims keyword
argument value was changed from None to (3, 3). Therefore any call to the function without
supplying the dims argument would fail if the matrix was not of the (3, 3) shape.
........

Merged revisions 26874-26876,26885 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

........
r26874 | bugman | 2014-11-30 11:10:41 +0100 (Sun, 30 Nov 2014) | 5 lines

Updated the manual_c_module.py C module compilation development script for the recent changes.

The exponential_inv.c and exponential_sat.c files need to be compiled as well.
........
r26875 | bugman | 2014-11-30 11:11:45 +0100 (Sun, 30 Nov 2014) | 5 lines

Python 3 fix for the relax_fit_exp_3param_inv_neg.py system test script.

The xrange() function does not exist in Python 3, so was replaced by range().
........
r26876 | bugman | 2014-11-30 18:38:12 +0100 (Sun, 30 Nov 2014) | 5 lines

Updated the memory_leak_test_relax_fit.py development script for the C module changes.

This is only the docstring description which changed.
........
r26885 | bugman | 2014-12-01 20:18:24 +0100 (Mon, 01 Dec 2014) | 6 lines

Epydoc docstring fixes for the lib.io module - keyword arguments were not correctly identified.

These were identified by Troels in the post at
http://thread.gmane.org/gmane.science.nmr.relax.scm/24565/focus=7384
........

Merged revisions 26901-26902 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

........
r26901 | bugman | 2014-12-02 21:39:10 +0100 (Tue, 02 Dec 2014) | 9 lines

Created the State.test_bug_23017_ieee_754_multidim_numpy_arrays system test.

This is to catch bug #23017 (https://gna.org/bugs/?23017), the multidimensional numpy arrays are not
being stored as IEEE 754 arrays in the XML state and results files.

This test checks a rank-2 float64 numpy array stored in the current data pipe against what the IEEE
754 int list should be for it.
........
r26902 | bugman | 2014-12-02 21:42:14 +0100 (Tue, 02 Dec 2014) | 9 lines

Simple fix for bug #23017 (https://gna.org/bugs/?23017).

This is the multidimensional numpy arrays are not being stored as IEEE 754 arrays in the XML state
and results files. The problem was a relatively recent regression caused by a change to the
is_float_matrix() function of the lib.arg_check module. It was simply that the default dims keyword
argument value was changed from None to (3, 3). Therefore any call to the function without
supplying the dims argument would fail if the matrix was not of the (3, 3) shape.
........