relax SVN archive

Fixes for the http://download.gna.org/relax/ link.

This affects the menu http://www.nmr-relax.com/menu.html used on all the main pages at
http://www.nmr-relax.com. The http://www.nmr-relax.com/download.html page also required the fix.
The original link was missing the trailing '/' so that a server redirect was required. This was
found by the W3C link checker (http://validator.w3.org/checklink).

Fixes for broken MOLMOL links.

The original site http://hugin.ethz.ch/wuthrich/software/molmol/ is now a dead link. Instead the
link http://sourceforge.net/projects/molmol/ is being used as a stop gap. This was linked from
http://www.nmr-relax.com/index.html and http://www.nmr-relax.com/features.html.

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.

The redirects are for the new pages
http://www.nmr-relax.com/manual/Comparison_dispersion_analysis_software.html,
http://www.nmr-relax.com/manual/Dispersion_script_mode_loading_data.html,
http://www.nmr-relax.com/manual/Keeping_branch_up_date_using_svnmerge_py.html,
http://www.nmr-relax.com/manual/Ri_prime_theta_Hessians.html,
http://www.nmr-relax.com/manual/clustered_relaxation_dispersion_analysis.html.

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 or from the relax API documentation.

The redirects are for the new pages
http://www.nmr-relax.com/manual/The_full_NS_2_site_3D_CPMG_model.html,
http://www.nmr-relax.com/manual/The_new_protocol_in_the_GUI.html, and
http://www.nmr-relax.com/The_relax_data_model.html.

Merged revisions 26667,26670,26679,26681,26708,26710 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r26667 | bugman | 2014-11-20 15:58:14 +0100 (Thu, 20 Nov 2014) | 9 lines

Big Python 3 bug fix for the dep_check module for the detection of the NMRPipe showApod software.

The showApod program was falsely detected as always not being present when using Python 3. This is
because the output of the program was being tested using string comparisons. However the output
from programs obtained from the subprocess module is no longer strings but rather byte-arrays in
Python 3. Therefore the byte-array is not being converted to text if Python 3 is being used,
allowing the showApod software to be detected.
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r26670 | bugman | 2014-11-20 16:39:20 +0100 (Thu, 20 Nov 2014) | 6 lines

Python 3 bug fix for the lib.spectrum.nmrpipe.show_apod_extract() function.

The subprocess module output from the showApod program, or any software, is a byte array in Python 3
rather than text. This is now detected and the byte array converted to text before any processing.
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r26679 | bugman | 2014-11-21 10:12:42 +0100 (Fri, 21 Nov 2014) | 3 lines

Fix for the unit tests to match r26656 - Python 2.5 floats do not have a 'real' property.
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r26681 | bugman | 2014-11-21 10:29:34 +0100 (Fri, 21 Nov 2014) | 9 lines

Bug fix for the lib.structure.angles.angles_*() functions for odd increments.

This affects the PDB representations of the diffusion tensor and frame order when the number of
increments in the respective user functions is set to an odd number. It really only affects the
frame_order.pdb_model user functions, as the number of increments cannot be set in any of the other
user functions (structure.create_diff_tensor_pdb, structure.create_rotor_pdb,
structure.create_vector_dist, n_state_model.cone_pdb).
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r26708 | bugman | 2014-11-24 13:37:15 +0100 (Mon, 24 Nov 2014) | 6 lines

Backported the relax 3.3.3 CHANGES file changes to trunk.

The command used was:
svn merge -r26703:r26704 svn+ssh://bugman@.../svn/relax/tags/3.3.3 .
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r26710 | bugman | 2014-11-25 10:27:00 +0100 (Tue, 25 Nov 2014) | 3 lines

Small updates for the wiki section of the release checklist document.
........

Merged revisions 26708,26710 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r26708 | bugman | 2014-11-24 13:37:15 +0100 (Mon, 24 Nov 2014) | 6 lines

Backported the relax 3.3.3 CHANGES file changes to trunk.

The command used was:
svn merge -r26703:r26704 svn+ssh://bugman@.../svn/relax/tags/3.3.3 .
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r26710 | bugman | 2014-11-25 10:27:00 +0100 (Tue, 25 Nov 2014) | 3 lines

Small updates for the wiki section of the release checklist document.
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Created two new frame order system tests for the double rotor PDB representation file.

This is the two PDB files from the frame_order.pdb_model user function. The two new system tests
are Frame_order.test_pdb_model_double_rotor_z_axis and
Frame_order.test_pdb_model_double_rotor_xz_plane_tilt.

Created two new frame order system tests for the torsionless pseudo-ellipse PDB representation file.

This is the two PDB files from the frame_order.pdb_model user function. The two new system tests
are Frame_order.test_pdb_model_pseudo_ellipse_torsionless_z_axis and
Frame_order.test_pdb_model_pseudo_ellipse_torsionless_xz_plane_tilt.

Created two new frame order system tests for the free rotor pseudo-ellipse PDB representation file.

This is the two PDB files from the frame_order.pdb_model user function. The two new system tests
are Frame_order.test_pdb_model_pseudo_ellipse_free_rotor_z_axis and
Frame_order.test_pdb_model_pseudo_ellipse_free_rotor_xz_plane_tilt.

Created two new frame order system tests for the torsionless isotropic cone PDB representation file.

This is the two PDB files from the frame_order.pdb_model user function. The two new system tests
are Frame_order.test_pdb_model_iso_cone_torsionless_z_axis and
Frame_order.test_pdb_model_iso_cone_torsionless_xz_plane_tilt.