relax SVN archive

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.

Modified the interatom.unit_vectors user function backend to handle missing atomic positions.

This is to match the structure.load_spins user function change whereby missing atomic positions are
now set to the value of None.

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

The multiple molecule merging functionality of the structure.load_spins user function now handles
missing atomic positions differently. The aim is that the length of the spin container position
variable is fixed for all spins to the number of structures, as the N-state model analysis assumes
this equal length for all spins. When data is missing, the atomic position for that structure is
now set to None. This will require other modifications in relax to support this new design.

Final fix for bug #22849 (https://gna.org/bugs/?22849).

This is the failure of the N-state model analysis when optimising only alignment tensors using RDCs
and/or PCSs. The alignment tensor is no longer initialised to zero values. This is to allow the
skip_preset argument for the minimise.grid_search user function to be operational for the N-state
model, a feature introduced with the zooming grid search. The solution was to check for the
uninitialised tensor in the minimise_setup_fixed_tensors() method of the
specific_analyses.n_state_model.optimisation module.

Created the N_state_model.test_CaM_IQ_tensor_fit system test.

This is for catching bug #22849 (https://gna.org/bugs/?22849), the failure of the N-state model
analysis when optimising only alignment tensors using RDCs and/or PCSs.

This new test checks code paths unchecked in the rest of the test suite, and is therefore of high
value.