Author: bugman
Date: Mon Mar 19 18:44:20 2012
New Revision: 15563
URL: http://svn.gna.org/viewcvs/relax?rev=15563&view=rev
Log:
Merged the CHANGES file for relax version 1.3.14 back into the main 1.3 line.
The command used was:
svn merge -r15561:15562 svn+ssh://bugman@xxxxxxxxxxx/svn/relax/tags/1.3.14
Modified:
1.3/docs/CHANGES
Modified: 1.3/docs/CHANGES
URL:
http://svn.gna.org/viewcvs/relax/1.3/docs/CHANGES?rev=15563&r1=15562&r2=15563&view=diff
==============================================================================
--- 1.3/docs/CHANGES (original)
+++ 1.3/docs/CHANGES Mon Mar 19 18:44:20 2012
@@ -1,3 +1,87 @@
+Version 1.3.14
+(19 March 2012, from /1.3)
+http://svn.gna.org/svn/relax/tags/1.3.14
+
+ Features:
+ * An expanded system information printout (from 'relax -i').
+ * Improvements to the multi-processor implementation, including
creation of a public API and a reference implementation.
+ * Overhaul of the multi-processor stream capture design - the slave
IO streams are now properly redirected to the master processor and the master
no longer overrides stream capture by the relax user interfaces.
+ * Numpy data structures are now supported in relax save files.
+ * Implemented the rdc.delete and pcs.delete user functions.
+ * Speed ups of a number of user functions involved in looping over
atomic or spin specific data - this can be significant if a lot of structural
operations are performed, or a large number of structures are required.
+ * Redesigned how spin parameters are handled in the specific
analyses (which includes parameter name changes).
+
+
+ Changes:
+ * The MS Windows text wrapping width has been changed from 80 to 79
- this now fits the cmd prompt.
+ * The program intro print out and prompt UI help system is using the
new Status.text_width variable to wrap text.
+ * The model-free constraint matrix A is now of numpy.int8 type -
this is to decrease virtual memory usage and increase the scaling efficiency
on clusters.
+ * Changed all relax website links to http://www.nmr-relax.com for
consistency.
+ * The setup.py script can now be imported for the epydoc API
documentation system.
+ * The extern and minfx.scipy_subset relax packages are excluded form
the API documentation.
+ * Added the ability to skip scripts in the package __all__ list unit
test checks.
+ * Added some code to detect the bit version of MS Windows in the
information print out (to better distinguish 32 vs. 64-bit versions).
+ * Added some documentation about master processors on Linux 2.6
eating 100% of one CPU core (in the mpi4py multi-processor fabric).
+ * Added a reference implementation to the multi-processor package -
this is to demonstrate to users of the package how an implementation is
created via the public API.
+ * Elimination of all relax dependencies from the multi-processor
package.
+ * Added support for the memory size on MS Windows to the relax info
print out.
+ * Updated the value.set user function unknown parameter error
message to list the known ones.
+ * For Unix and GNU/Linux systems, the relax info printout now shows
the ram and swap size.
+ * Expansion and improvement of the information printed out by 'relax
--info'.
+ * Expansion of the multi-processor API documentation.
+ * Expansion of the multi-processor package documentation with a step
by step usage guide - this should increase the usability of the package by
clarifying how one should use it.
+ * Expansion and improvements to the multi-processor package and
module docstrings.
+ * The finish button in the new analysis wizard has been renamed to
"Start".
+ * Created a special Verbosity singleton for controlling the
multi-processor package print outs.
+ * Future proofed the relax codebase by replacing all ''' with """ in
the docstrings.
+ * Removed the unnecessary try statement in the model-free
Slave_command.run() method as exception handling is correctly performed on
the slave and master.
+ * Shifted the Memo object into its own module (multi package).
+ * Simplification and abstraction of the Slave_command.run() method
to shift all exception handling into the package. Therefore program code no
longer needs to handle the multi-processor specific errors.
+ * Created a new module 'multi.misc' for holding miscellaneous
functions used throughout the multi package.
+ * Created a public API for the multi-processor package, available
via multi.__init__.
+ * The load_multiprocessor() function is no longer a static method of
the Processor base class. This function loads the correct Processor class,
so doesn't need to be a method of the base class and operates cleanly and
more clearly as a stand alone function.
+ * Clean up of the processor IO module (multi package).
+ * Eliminated all usage of sys.__stdout__ and sys.__stderr__ in the
multi-processor package - this returns full control of IO streams to the
parent program.
+ * The float arg checks now checks against all the numpy float types
(float16, float32, float64, float128).
+ * Added value.write user function calls to the J(w) mapping system
test script.
+ * Added some value.write user functions to the J(w) mapping sample
script.
+ * Modified the J(w) mapping test data to include relaxation values
of None to trigger bug #19329.
+ * Speed up for the generic_fns.relax_re.search() function.
+ * More speed ups for the
Selection.__contains_mol_res_spin_containers() method.
+ * Reordered the checks in
Selection.__contains_mol_res_spin_containers() - this cuts the number of
function calls down by avoiding relax_re.search() calls if residue or spin
numbers match.
+ * Simplified the generic_fns.relax_re.search() function - this is to
minimise the number of isinstance() calls when dealing with the relax
mol-res-spin sequence data.
+ * Updates for Python 3.0 using 2to3.
+ * Removal of a number of debugging print out statements.
+ * Significant speed ups of the return_spin() and return_residue()
functions.
+ * Added a print out for the diffusion_tensor.init user function to
inform the user of an angle unit change - this is in response to bug #19323
to make it clearer that a parameter conversion has occurred.
+ * Created a special specific API object called SPIN_PARAMS - this
will be used to handle all operations to do with model parameters. The
object Param_list has methods for parameter initialisation and handling
(where all info is specified such as Grace string, units, default value, etc)
and for determining if a parameter exists.
+ * Mass conversion to the new GLOBAL_PARAMS and SPIN_PARAMS specific
API data structures. The parameters are now all lowercase, for example
['S2', 'te', 'Rex'] is now ['s2', 'te', 'rex']. The follow parameters are
now converted throughout relax: 'bond_length' to 'r', 'CSA' to 'csa',
'heteronucleus' to 'heteronuc_type', 'proton' to 'proton_type'.
+ * Created a new algorithm for finding the pivot of motion between
different structural models - this is available through the
structure.find_pivot user function.
+ * Added the validate_models() method to the structural API - this is
used to check that the models are 100% consistent.
+ * Added the centroid argument to the structure.superimpose user
function - this allows for the superimposition of structures assuming a
pivoted motion.
+
+
+ Bugfixes:
+ * Fix for the title of the analysis selection wizard GUI element.
+ * Fix for the MemoryError during the "final" run of d'Auvergne
Protocol affecting 32-bit systems (bug #19528).
+ * Epydoc docstring fixes for the API documentation.
+ * Bug fix for old numpy versions missing the float16 object.
+ * The relax prompt mode now prints the intro message to sys.stdout -
this fixes this mode with the logging option or in the mpi4py multiprocessor
mode.
+ * Fix for the storage of numpy data structures in the relax save
files - if special structures are created by the user, these were not
correctly stored. The precision was often too low (printed at the numpy
default of a precision of 8), and if one dimension had more than 1000
elements, ellipses would be stored instead (the ellipses would cause the save
file to be unreadable by relax).
+ * Created the SplitIO.flush() method so that a flush() call now
works with the -t and -l command line args - this simply calls the flush()
methods of both streams.
+ * The relax data store __repr__() method now prints out all objects
within the base object.
+ * Fix for a rare bug in the model-free analysis for when relaxation
data of None is encountered.
+ * Fixes for the Dasha system test for the bug #19332 fix.
+ * Fixes for the Dasha use functions for file creation and data
extraction - this should now handle relaxation data values of None, and also
set the parameter values of deselected spins using the Dasha output files.
+ * Big bugfix for the value.read user function - the wrong spin ID
string was being used to set the parameter value so that all spins have the
same value set for the parameter(bug #19332).
+ * Bug fix for the consistency testing analysis for when relaxation
data of None is encountered.
+ * The spin is now deselected if there is really less than three data
points, excluding data points of None (bug #19329).
+ * Bug fix for the arg_check.is_none() function - the RelaxNoneError
was not imported!
+ * Fix for the numbering of the TER record and subsequence HETATM
records in the PDB file creation. The structure.write_pdb user function now
creates the correct TER record after the ATOM records, and the HETATM records
are renumbered if needed.
+ * Bug fix for the compilation of the user manual. The molecule user
function class used the temporary variable i, which was causing the
fetch_docstrings script to fail.
+
+
+
Version 1.3.13
(10 November 2011, from /1.3)
http://svn.gna.org/svn/relax/tags/1.3.13
r15563 - /1.3/docs/CHANGES