relax SVN archive

The verbosity argument for the N-state model optimisation is now propagated for more printouts.

The argument for the calculate() and minimise() API methods is now sent into
specific_analyses.n_state_model.optimisation.target_fn_setup(), and from there into the
pipe_control.pcs.return_pcs_data() and pipe_control.rdc.return_rdc_data() functions. That way the
number of RDCs and PCSs used in the N-state model is reported back to the user for better feedback.

Added printouts to pipe_control.pcs.return_pcs_data() and pipe_control.rdc.return_rdc_data().

These functions now accept the verbosity argument which if greater than 0 will activate printouts of
how many RDCs or PCSs have been assembled for each alignment. This will be useful for user feedback
as the spin verses interatomic data container selections can be difficult to understand.

Speed up of the N_state_model.test_CaM_IQ_tensor_fit system test.

This test is however still far too slow.

Added spacing after the minimise.grid_search user function setup printouts.

This is for better spacing for the next messages from the specific analysis.

Lists of lists containing rows of None are now better supported by the lib.xml functions.

The object_to_xml() function will now convert the float parts to IEEE-754 byte arrays, and the None
parts will be stored as None in the <ieee_754_byte_array> list node. The matching xml_to_object()
method has also been modified to read in this new node format. This affects the results.write and
state.save user functions (as well as the results.read and state.load user functions).

Expanded the lib.arg_check.is_float_matrix() function by adding the none_elements argument.

This matches a number of the other module functions, and allows for entire rows of the matrix to be
None.

Bug fix for the lib.arg_check.is_float_matrix() function.

The check for a numpy.ndarray data structure type was incorrect so that lists of numpy arrays were
failing in this function. Rank-2 arrays were not affected.

Clean up and speed up of the N_state_model.test_CaM_IQ_tensor_fit system test.

All output files are now set to 'devnull' so that the system test no longer creates any files within
the relax source directories. And the optimisation settings have been decreased to hugely speed up
the system test.

The structure.load_spins user function now stores the number of states in cdp.N.

This is to help the specific analyses which handle ensembles of structures. With the introduction
of the from_mols argument to the structure.load_spins user function, the number of states is now not
equal to the number of structural models, as the states can now come from different structures of
the same model. Therefore the user function will now explicitly set cdp.N to the number of states
depending on how the spins were loaded.

Fix for the atomic position handling in pipe_control.structure.main.load_spins_multi_mol().

The dimensionality of the position structure returned by the structural object atom_loop() method
needed to be reduced.