relax SVN archive

relax version 1.2.3.

This is a bug fix release which fixes segfault crashes of the exponential relaxation curve-fitting
modules introduced by the shift from the makefile to Sconstruct build system. The full
descriptions of all bug fixes are:

Sconstruct now does not use the '-fPIC' option during compilation which caused the exponential
relaxation curve-fitting modules to segfault.

The distribution binary and source file creation Sconstruct functions now properly compress the
archives.

The printout of the 'relax_fit.select_model()' function has been fixed.

The sconstruct script can now execute the fetch_docstrings code. The path previously did not
include the current working directory and hence the module could not be imported.

Unselected residues are now properly ignored for the value.read() function as well as all the Dasha
functions.

The value.read() function contained a bug where the residue number from the file was not being read.
Instead the integer position within the file was being used as the residue number.

The model-free spectral density function 'calc_S2f_S2s_ts_djw_dS2s' does not exist. Therefore when
using the model with the parameters {S2f, S2s, ts}, the program would throw an error and stop. The
function is actually 'calc_S2f_tf_S2s_ts_djw_dS2s'. The factor 'data.s2f_s2' also had to be
calculated in 'maths_fns/jw_mf_comps.py'.

Bug fixes:

Sconstruct now does not use the '-fPIC' option during compilation which caused the exponential
relaxation curvefitting modules to segfault.

The distribution binary and source file creation Sconstruct functions now properly compress the
archives.

The printout of the 'relax_fit.select_model()' function has been fixed.

A number of bug fixes:

The sconstruct script can now execute the fetch_docstrings code. The path previously did not
include the current working directory and hence the module could not be imported.

Unselected residues are now properly ignored for the value.read() function as well as all the Dasha
functions.

The value.read() function contained a bug where the residue number from the file was not being read.
Instead the integer position within the file was being used as the residue number.

The model-free spectal density function 'calc_S2f_S2s_ts_djw_dS2s' does not exist. Therefore when
using the model with the parameters {S2f, S2s, ts}, the program would throw an error and stop. The
function is actually 'calc_S2f_tf_S2s_ts_djw_dS2s'. The factor 'data.s2f_s2' also had to be
calculated in 'maths_fns/jw_mf_comps.py'.

Updated the manual and version number to 1.2.2.

relax version 1.2.2.

This release improves compatibility for different operating systems including Unix, Mac OS X, and
Windows. To achieve this, the make system has been replaced by the Sconstruct system. Both the
Dasha and Modelfree4 functions have been significantly improved. A number of bugs have also been
fixed including:

The automatically generated Dasha script has been fixed. Previously the optimise command used was
'min all' or 'lmin all'. This is incorrect and the proper syntax is 'min m n' or 'lmin m n' where m
is the first residue number while n is the last.

The code of 'generic_fns/value.py', 'generic_fns/diffusion_tensor.py', and
'specific_fns/model_free.py' has been fixed to properly handle the local tm parameter as well as the
global tm parameter.

The local tm parameter can now also be part of the parameter set for an OpenDX map of the
chi-squared space.

The optimisation code has been fixed to handle the unstable, broken Numeric Python packages so that
the Cholesky Hessian modification works again and the eigenvalue decomposition (which now freezes
Python) is avoided.

The file 'generic_fns/palmer.py' has been modified to gracefully handle a Modelfree4 bug whereby the
'mfout' output file has been corrupted due to the fusion of columns.

A bug fix and a few added features:

The Dasha execute function has been updated to follow the lead of the Modelfree4 equivalent function
whereby a non-standary binary executable Dasha file can be specified.

The Dasha sample script has been significantly modified to optimise a series of model-free models.

The OpenDX surfaces have had their opacity levels changed to better veiw the curvature of the space.

The automatically generated Dasha script has been fixed. Previously the optimise command used was
'min all' or 'lmin all'. This is incorrect and the proper syntax is 'min m n' or 'lmin m n' where
m is the first residue number while n is the last.

Bug fixes:

The code of 'generic_fns/value.py', 'generic_fns/diffusion_tensor.py', and
'specific_fns/model_free.py' has been fixed to properly handle the local tm parameter as well as the
global tm parameter.

The local tm parameter can now also be part of the parameter set for an OpenDX map of the
chi-squared space.

Modified the Sconstruct script to load the entire program only when fetching the docstrings.

Bug fixes due to unstable, broken Numeric Python packages:

Fixed a bug in the minimisation code. The Cholesky Hessian modification was failing due to the
Numeric Python package instability. The code should catch if the Cholesky factorisation fails and
then modify the factor tau and repeat the steps until the factorisation is succesful. Previously
the Numeric 'cholesky_decomposition()' function would throw out the "LinearAlgebraError" error, but
now something else is thrown out! The code now handles any error.

A bug fix to the Newton minimisation code has also been added. When the print flag is set above 3,
the code tries to calculate the eigenvalues of the Hessian. However the Numeric function
'eigenvectors()' is completely broken and causes any code which calls it to hang infinitely. The
code has been commented out.

A complete shift from the make build system to the scons build system (and a bug fix).

All the targets of all makefiles have been rewritten into python functions within the Sconstruct
file 'sconstruct'. Now instead of typing 'make install', you type 'scons install'. Hence, all
makefiles have been deleted.

The executable python script 'docs/latex/fetch_docstrings' has been moved to the non-executable file
'docs/latex/fetch_docstrings.py'. It is now imported into the Scons python script 'sconstruct' and
hence '__init__.py' files have been added to the 'docs' and 'docs/latex' directories.

The script 'docs/latex/version' has been shifted completely into the 'sconstruct' file and has been
deleted.

The file 'docs/release_checklist' has been modified to use the scons rather than make commands.

The script 'package' which was made redundant by the original shift to the make system has been
deleted.

Bug fix: The file 'generic_fns/palmer.py' has been modified to gracefully handle a Modelfree4 bug
whereby the 'mfout' output file has been corrupted due to the fusion of columns.