relax SVN archive

Critical fix, for k_AB not belonging to list of global parameters.

k_AB was only changed to the spin of interest, but not for the rest of the cluster.
When the parameter vector is assembled, "assemble_param_vector(spins=spins)" it takes the global parameter from spin 0.

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

Added script to simulate dispersion profiles at different settings.

This shows that something is wrong.

The back-calculated values in the graphs are not equal to the interpolated values.
There must be something wrong somewhere.

This list shows the chi2 values, and judging from the dispersion graphs, this simply cannot be True.

10.405 2.414 6722.833
9.900 1.000 6722.159
9.900 2.333 6722.159
9.900 3.667 6722.159
9.900 5.000 6722.159
10.300 1.000 6722.156
10.300 2.333 6722.156
10.300 3.667 6722.156
10.300 5.000 6722.156
10.700 1.000 6726.040
10.700 2.333 6726.040
10.700 3.667 6726.040
10.700 5.000 6726.040
11.100 1.000 6732.256
11.100 2.333 6732.256
11.100 3.667 6732.256
11.100 5.000 6732.256

Removal of repetitive code in the relaxation dispersion model_loop() API method.

The spin loop does not need to be called twice, instead the if statements have been modified to
better direct the code execution.

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.