Author: bugman Date: Sun Sep 28 22:32:16 2008 New Revision: 7426 URL: http://svn.gna.org/viewcvs/relax?rev=7426&view=rev Log: Updated the CHANGES for relax version 1.3.1. Modified: tags/1.3.1/docs/CHANGES Modified: tags/1.3.1/docs/CHANGES URL: http://svn.gna.org/viewcvs/relax/tags/1.3.1/docs/CHANGES?rev=7426&r1=7425&r2=7426&view=diff ============================================================================== --- tags/1.3.1/docs/CHANGES (original) +++ tags/1.3.1/docs/CHANGES Sun Sep 28 22:32:16 2008 @@ -1,3 +1,64 @@ +Version 1.3.1 +(28 September 2008, from /1.3) +http://svn.gna.org/svn/relax/tags/1.3.1 + + Features: + * Complete redesign of relax (https://mail.gna.org/public/relax-devel/2006-10/msg00053.html). + * Extension of the Grace plotting abilities to include series data such as relaxation exponential curves. + * For easy reference, all physical constants have been shifted to the 'physical_constants.py' module. + * Complete overhaul of the handling of structures with the introduction of a structural object API. + * An internal structural object has been created, complete with PDB reading and writing methods, to optionally replace the Scientific python PDB object. + * Large improvements to the API documentation by the use of epydoc formatted docstrings. + * All spins can be looped over simply by using the spin_loop() generator function. + * Molecules, residues, and spins are now selected by the new syntax of the spin identification string. + * Improvements and simplifications to the 'full_analysis.py' script with all user modifiable variables shifted to the top of the script as global variables. + * Automatic looping until convergence has been added to the 'full_analysis.py' script to further simplify usage. + * Setting the type of nucleus is now done with the value.set() user function on a spin-by-spin basis. This is important for RNA, small molecules and protein analyses with Ca and N data. + * A new analysis type, the N-state model for interpreting domain motions using RDC and PCS data, is now supported. + * The mechanical pivot-CoM analysis of the N-state model and associated cone image construction is included. + * The consistency testing code has been ported from the 1.2 line. + * The results file has been converted to the versatile XML format. + * All analysis types, present and future, are automatically supported through the reading and writing of the XML results file. + * The XML results file stores floats at full 64 bit precision in an XML attribute using the IEEE-754 byte array. + + Changes: + * The RelaxError and RelaxWarning systems have been redesigned. The objects are no longer placed into __builtin__ but must now be imported. + * The unit and system test frameworks have been expanded to 1046 and 55 tests respectively covering most aspects of relax usage. + * The inclusion of headers in the sample scripts to identify the author and age of the script. + * Conversion of the relax data storage object into a singleton. Rather than accessing 'self.relax.data', the singleton is now imported as needed. + * Unit tests can now be run individually. + * The optimisation code has been spun out into its own project, minfx (https://gna.org/projects/minfx/). This is now a dependency. + * The Boolean values True and False are now used instead of 1 and 0 for user function arguments. + * The class methods of the 'generic_fns' package have been converted to module functions for greater API flexibility. + * Complete redesign of the diffusion tensor object in the relax data store. Many diffusion tensor attributes are calculated on the fly when accessed. + * The 'specific_fns' package has been redesigned with the API for retrieving analysis specific methods tidied up. + * The inevitable switch from Numeric python to numpy has occurred. + * The system tests and unit tests can be run separately. + * All STDOUT and STDERR output is caught by the test suite and only printed if the test fails. + * The system tests use the unit test framework to significantly simplify the addition of new tests. + * User scripts can now be used directly as system tests. + * All threading code has been eliminated in preparation for replacement by the multi_processor code. + * The precision of the 15N gyromagnetic ratio input into Art Palmer's Modelfree4 program has been increased. + * Scientific python is no longer an essential dependency. + * The 'unselect' user function class has been renamed to 'deselect'. + * Big updates to the relax manual. + * PDB files can be specified without the '.pdb' ending. + + Bugfixes: + * The unit test and system test frameworks are now functional. + * The failure of reduced spectral density mapping has been identified and fixed (bug #9238, bug #9562). + * The second set of extended model-free formulae were accessing undefined functions (bug #9189). + * Docstring fetching issues with Python 2.5 have been fixed (bug #9390). + * The sample script for placing model-free results into a LaTeX table now works (bug #10189). + * The default parameter values for relaxation curve fitting were incorrectly set. + * Security: Replaced the insecure os.tempnam() with tempfile.mktemp(). + * ZeroDivisionError fix for model elimination and Monte Carlo simulation elimination (bug #11004). + * The handling of spins with missing XH bond vectors has been fixed (bug #11378). + * The relax_data.display() user function is now functional again (bug #11383). + * MS Windows with Python 2.5 is now supported. + + + Version 1.3.0 (19 February 2007, from /1.3) http://svn.gna.org/svn/relax/tags/1.3.0