relax SVN archive

Added the checklist file describing the steps required for releasing stable versions of relax.

Merge of r2329 from 1.0 branch

Shifted the program version number to its own file so it can be read by the Makefile.

Relaxation curve fitting and error analysis is now fully functional!

The ability to execute Monte Carlo simulations has been added, as well as Grace plotting
capabilities. Now all parts of relaxation curve fitting data analysis are functional. However, the
'dfunc()' and 'd2func()' C functions have not be implemented and therefore only simplex minimisation
without constraints is supported.

The standard deviation in the relaxation curve fitting C module is now a Python array rather than
a double. The data structure called 'intensities' has been changed to 'values' so that the
'maths_fns/c_chi2.c' chi-squared function is made more generic.

In the common functions of 'specific_fns/base_class.py', the 'set_error()', 'sim_init_values()',
'sim_return_param()', and 'sim_return_selected()' functions have been added for Monte Carlo
simulation functionality. The function 'sim_pack_data()' which was moved from
'specific_fns/model_free.py' to 'specific_fns/base_class.py' has been returned as it is not
generalisable.

A few bugs have been removed from 'specific_fns/relax_fit.py'. In the function
'assemble_param_vector()', Monte Carlo simulations are now properly supported. The
'create_mc_data()' function has also been improved. The function 'set_error()' has been removed
from the file. This function was a relic as the origin of 'specific_fns/relax_fit.py' was from
'specific_fns/noe.py'. It hides the function of the same name in 'specific_fns/base_class.py' and
hence causes Monte Carlo simulations to fail.

The functions 'read_columnar_results()', 'write()', 'write_columnar_line()', and
'write_columnar_results()' have been deleted out of 'specific_fns/relax_fit.py'. These too were
relics from the file's origin from 'specific_fns/noe.py'.

The calculation of the peak intensity errors has been modified. The docstring in
'prompt/relax_fit.py' has been rewritten and significantly improved. Now if all spectra have been
replicated, each relaxation time point will have its own error (which is averaged across all
residues). If there are time points with only a single spectrum, then the standard deviations are
averaged for all time points.

In the data analysis chapter of the manual, the section on relaxation curve fitting has been half
completed.

Fix the noe_ri_table bug introduced in r2324

Fixed the loops in the two C functions to go to '(int)num_times' rather than the temp value of '6'.

The 'back_calc_I' C function now works by returning a Python list instead of a Numeric array!

An attempt at making the 'back_calc_I' C function return a Numeric array.

Completion of the C code for the fitting of relaxation curves and preparation for Monte Carlo sims.

The 'chi2()' C function is now declared in the 'func()' function as returning a double. Previously
it was interpreting it the result as an int!

The exponential back calculation function has been debugged. The function is I0 * exp(-t * Rx) and
not I0 * exp(-t / Rx)!

In 'maths_fns/c_chi2.c' the function 'square()' has been defined.

The makefile 'maths_fns/Makefile' has been modified so that changes to 'maths_fns/relax_fit.h' will
now cause recompilation of all C code.

The spectral density function 'num_instances()' in 'specific_fns/jw_mapping.py' has been debugged.

In 'specific_fns/relax_fit.py', the function 'ave_and_sd()' has been renamed to 'mean_and_error()'.
The user function 'mean_and_error()' has been added to 'prompt/relax_fit.py'. Previously this was
being called by the minimise function of 'specific_fns/relax_fit.py', ie both during the grid search
and the minimisation. This function has to be called prior to optimisation.

For Monte Carlo simulations, the function 'back_calc_I()' has been added to 'maths_fns/relax_fit.c'.
This simply converts the C external variable 'back_calc[]' to a Numeric array and returns it. The
code isn't fully functional yet. In addition, in the file 'specific_fns/relax_fit.py', the
functions 'num_instances()', 'return_data()', 'set_selected_sim()', and 'sim_pack_data()' have been
added for MC sims.

The error function 'RelaxNoMfModelError' has been changed to 'RelaxNoModelError' to generalise it
for both model-free analysis and relaxation curve fitting.

The function 'sim_set_selected()' has been renamed to 'set_selected_sim()' in
'specific_fns/model_free.py'.

Fix bug where Ri values of None were read from results files