relax SVN archive

Fixes for the unit tests of the package __all__ lists for Python 3.

When Python 3 generates byte-compiled *.pyc files, these are stored in __pycache__ directories.
These directories are now skipped for the package content unit tests, allowing the test to pass.

Fix for the test_suite/system_tests/scripts/noe/bug_21562_noe_replicate_fail.py system test script.

There was some invisible binary junk at the start of the file which as causing the
Noe.test_bug_21562_noe_replicate_fail system test to fail, as the script could not load. This was
only affecting one 32-bit test system using Python 3.1 and Python 3.2 (Mageia 4 i586 VM).

Decreased the precision of the Relax_disp.test_hansen_cpmg_data_to_cr72 system test.

This is to allow the test to pass on a 32-bit test system using Python 2.5 and Python 3.1 (Mageia 4
i586 VM).

Decreased the precision of the Relax_disp.test_hansen_cpmg_data_auto_analysis_r2eff system test.

This is to allow the test to pass on a 32-bit test system using Python 2.5 and Python 3.1 (Mageia 4
i586 VM).

Decreased the precision of the Relax_disp.test_hansen_cpmg_data_auto_analysis system test.

This is to allow the test to pass on a 32-bit test system using Python 2.5 and Python 3.1 (Mageia 4
i586 VM).

Decreased the accuracy of the Relax_disp.test_korzhnev_2005_15n_dq_data system test.

This is to allow the test to pass on a 32-bit test system (Mageia 4 i586 VM).

Merged revisions 22139,22143-22144 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r22139 | bugman | 2014-02-06 16:17:49 +0100 (Thu, 06 Feb 2014) | 6 lines

Small improvement for the devel_scripts/python_seek.py script.

The list of detected Python binaries files are now sorted prior to determining the installed
modules.
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r22143 | bugman | 2014-02-07 11:11:55 +0100 (Fri, 07 Feb 2014) | 8 lines

Updated the N_state_model.5_state_xz system test to allow it to complete on i586 Linux systems.

The optimisation would continue for a huge amount of time on a test system (Mageia 4 i586 VM) and
would make it appear as though the test suite has hung. By limiting the maximum number of
iterations in the optimisation to 1000, the test will complete successfully and the parameters
optimised to the same precision.
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r22144 | bugman | 2014-02-07 11:17:55 +0100 (Fri, 07 Feb 2014) | 5 lines

Loosened the checks for the Frame_order.test_korzhnev_2005_15n_zq_data system test.

This is to allow the test to pass on a 32-bit test system (Mageia 4 i586 VM).
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Merged revisions 22138 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r22138 | bugman | 2014-02-06 12:33:29 +0100 (Thu, 06 Feb 2014) | 7 lines

Fix for bug #21605, the failure of the Frame_order.test_generate_rotor2_distribution system test.

The bug at http://gna.org/bugs/?21605 is due to the fact that numpy.float16 is not defined on all
systems. Older numpy versions do not have this. Therefore the float16 value is now imported from
lib.check_types where it is aliased to float32 when not defined.
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Merged revisions 22125-22127,22135-22137 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r22125 | bugman | 2014-02-04 16:25:58 +0100 (Tue, 04 Feb 2014) | 3 lines

Improvements for the devel_scripts/log_converter.py script - trailing whitespace is now stripped.
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r22126 | bugman | 2014-02-04 16:26:50 +0100 (Tue, 04 Feb 2014) | 3 lines

Removed tailing whitespace from the CHANGES file.
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r22127 | bugman | 2014-02-04 16:28:19 +0100 (Tue, 04 Feb 2014) | 6 lines

Backported the relax 3.1.5 CHANGES file addition to trunk.

The command used was:
svn merge -r22123:22124 svn+ssh://bugman@.../svn/relax/tags/3.1.5 .
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r22135 | bugman | 2014-02-05 17:16:11 +0100 (Wed, 05 Feb 2014) | 3 lines

Converted the chain ID list in the internal structural object to the CHAIN_ID_LIST module variable.
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r22136 | bugman | 2014-02-05 17:33:42 +0100 (Wed, 05 Feb 2014) | 5 lines

The internal structure object method _pdb_chain_id_to_mol_index() now uses the CHAIN_ID_LIST string.

This allows for the full PDB chain ID range to be supported.
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r22137 | bugman | 2014-02-05 17:38:36 +0100 (Wed, 05 Feb 2014) | 7 lines

Minor bugfix for the internal structural object add_model() method.

The internal structural object was being called with self as an argument, which would default to the
chain_id keyword argument. The result would be relax state files with multiple copies of the
internal structural object embedded in the structural XML section.
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Loosened the checks for the Frame_order.test_korzhnev_2005_15n_zq_data system test.

This is to allow the test to pass on a 32-bit test system (Mageia 4 i586 VM).