relax SVN archive

Fix for the Test_value.test_value_set_r1_rit test of the _pipe_control.test_value unit test module.

This is a general fix for all unit test modules which use the
test_suite.unit_tests.value_testing_base.Value_testing_base base class. After the molecules,
residues and spins are manually created, the pipe_control.mol_res_spin.metadata_update() function is
called to make sure that all of the private and volatile metadata have been correctly created, so
that the other pipe_control.mol_res_spin module functions can operate correctly.

Fix for the Bmrb.test_bug_22704_corrupted_state_file GUI test.

This was failing because the setUp() method in the inherited Bmrb system test module was being
overwritten by the default Unittest.setUp() method. Therefore the system test setUp() method has
been copied into the GUI test class.

Modified the help strings for the test suite options shown when 'relax -h' is run.

The ability to specify individual tests (or modules of tests for the unit tests) is now documented.
The '--time' option help string has also been edited.

Modified the printouts for the unit tests when running with the --time command line option.

The test name is now being processed. The leading 'test_suite.unit_tests.' text is now stripped
out. And the remaining text is split into the module name and the test name. This is to allow the
unit test module name to be more easily identifiable, so it can then be used as a command line
option to allow only a subset of tests to be performed.

Big improvement for running the relax unit tests via the relax command line options.

The unit test module path is now accepted as a command line option. This brings more capabilities
of Gary Thompson's test_suite/unit_tests/unit_test_runner.py script into the relax command line.
The _pipe_control/test_value unit test module path can be specified as, for example, one of
'test_suite.unit_tests._pipe_control.test_value', 'test_suite/unit_tests/_pipe_control/test_value',
'_pipe_control.test_value', '_pipe_control/test_value'. This allows individual modules of tests to
be run, rather than having to execute all unit tests, which is very useful for debugging.

Added some test pymol script, to create dx maps and chi2 surface plot.

These will go to the wiki: http://wiki.nmr-relax.com/Chi2_surface_plot

Epydoc change for DOI reference in systemtests.

Bug #22754 (https://gna.org/bugs/index.php?22754): The minimise.calculate() does not calculate chi2 value for clustered residues.

Merged revisions 26176 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r26176 | bugman | 2014-10-06 18:20:25 +0200 (Mon, 06 Oct 2014) | 7 lines

Updated all of the Relax_disp.test_korzhnev_2005_*_data system tests.

These now have slightly changed parameter values due to the fix of bug #22563
(https://gna.org/bugs/?22563), the NS MMQ 2-site dispersion model running at 32-bit precision and
not 64-bit as it should be.
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Merged revisions 26175 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r26175 | tlinnet | 2014-10-06 18:11:05 +0200 (Mon, 06 Oct 2014) | 1 line

Fix for epydoc in systemtest Relax_disp.test_dx_map_clustered.
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Merged revisions 26167-26174 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r26167 | tlinnet | 2014-10-06 17:07:49 +0200 (Mon, 06 Oct 2014) | 3 lines

In the dispersion API calculate(), used the API function model_loop() to loop over the clusters instead.

Bug #22754 (https://gna.org/bugs/index.php?22754): The minimise.calculate() does not calculate chi2 value for clustered residues.
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r26168 | tlinnet | 2014-10-06 17:07:54 +0200 (Mon, 06 Oct 2014) | 5 lines

Removed then function loop_cluster_ids() from dispersion API().

This should be implemented elsewhere.

Bug #22754 (https://gna.org/bugs/index.php?22754): The minimise.calculate() does not calculate chi2 value for clustered residues.
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r26169 | tlinnet | 2014-10-06 17:07:55 +0200 (Mon, 06 Oct 2014) | 3 lines

Updated the API set_param_values() function to use model_loop() to get the spin_ids from the cluster.

Bug #22754 (https://gna.org/bugs/index.php?22754): The minimise.calculate() does not calculate chi2 value for clustered residues.
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r26170 | tlinnet | 2014-10-06 17:07:57 +0200 (Mon, 06 Oct 2014) | 11 lines

Initial try to fix unit test test_value_set_r1_rit().

The problem is, that no spin-id can be generated, since the spins are created manually,

"
File "/sbinlab2/tlinnet/software/NMR-relax/relax_trunk/pipe_control/mol_res_spin.py", line 1498, in generate_spin_id_unique
if res and res.name != None and mol._res_name_count[res.name] > 1:
AttributeError: 'MoleculeContainer' object has no attribute '_res_name_count'
"

Bug #22754 (https://gna.org/bugs/index.php?22754): The minimise.calculate() does not calculate chi2 value for clustered residues.
........
r26171 | tlinnet | 2014-10-06 17:21:32 +0200 (Mon, 06 Oct 2014) | 3 lines

Removed the checking of MODEL_LIST_MMQ, and spin.isotope from optimisation.back_calc_r2eff(), since this check is already covered.

Bug #22754 (https://gna.org/bugs/index.php?22754): The minimise.calculate() does not calculate chi2 value for clustered residues.
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r26172 | tlinnet | 2014-10-06 18:03:28 +0200 (Mon, 06 Oct 2014) | 3 lines

Fix for references to "spin" in optimisation.back_calc_r2eff().

Bug #22754 (https://gna.org/bugs/index.php?22754): The minimise.calculate() does not calculate chi2 value for clustered residues.
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r26173 | tlinnet | 2014-10-06 18:03:30 +0200 (Mon, 06 Oct 2014) | 3 lines

Fix for looping performed twice in relax_disp API model_loop().

Bug #22754 (https://gna.org/bugs/index.php?22754): The minimise.calculate() does not calculate chi2 value for clustered residues.
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r26174 | tlinnet | 2014-10-06 18:03:32 +0200 (Mon, 06 Oct 2014) | 10 lines

Removed unused proton reference in relax_disp API calculate().

There is though some problems with these tests:
F 1.93 s for Relax_disp.test_korzhnev_2005_15n_dq_data
F 2.01 s for Relax_disp.test_korzhnev_2005_1h_mq_data
F 1.93 s for Relax_disp.test_korzhnev_2005_1h_sq_data

It is unsure where these comes from.

Bug #22754 (https://gna.org/bugs/index.php?22754): The minimise.calculate() does not calculate chi2 value for clustered residues.
........