relax SVN archive

Removed the estimate_rx_err module from the specific_analyses.relax_fit.__all__ list.

This module was deleted after merger into the api module.

Modified the frame order sim_init_values() API method to handle missing optimisation data.

The monte_carlo.initial_values user function was failing if optimisation had not been performed.
This is now caught and handled correctly.

Fix for the Frame_order.test_frame_order_pdb_model_ensemble system test.

More needed to be done to set up the Monte Carlo simulations - the monte_carlo.initial_values user
function call was required.

Added support for the model argument for the frame_order.pdb_model user function.

This argument is used to specify which of the models in an ensemble will be used to represent the
average domain position Monte Carlo simulations, as each simulation is encoded as a model, as well
as for the distribution of structures simulating the motion of the system. The argument is
therefore passed into the create_ave_pos() and create_distribution() functions of the
specific_analyses.frame_order.geometric module.

To handle all models being used in the non Monte Carlo simulation PDB file and only one in this
file, the internal structural object is copied twice. The second copy for the MC sims has all but
the chosen model deleted out of it.

Fix for the pipe_control.error_analysis.covariance_matrix() function.

The set_errors() API method is parameter specific, so a loop over the parameters using the
get_param_names() API method has been added.

Removed the specific_analyses.relax_fit.estimate_rx_err module import.

The module has been merged into the specific API module.

Shifted the contents of the specific_analysis.relax_fit.estimate_rx_err module into the API.

The estimate_rx_err() function is now the covariance_matrix() method of the specific API. The code
for calculating the covariance matrix and errors are now in the function
pipe_control.error_analysis.covariance_matrix(), so this has been removed. And the error setting is
performed by the set_errors() API method, so that code has been deleted as well.

Missing imports in the pipe_control.error_analysis module for the covariance matrix function.

Modified pipe_control.error_analysis.covariance_matrix().

The call to the API covariance_matrix() method now has the model_info argument passed into it. For
the relaxation curve-fitting, this allows the loop over spin systems to be skipped.

Created the specific analysis base API method covariance_matrix().

This defines the arguments required and what is returned by the method. It raises the
RelaxImplementError for all analyses which do not implement this method.