Author: bugman
Date: Sun Sep 28 22:34:57 2008
New Revision: 7427
URL: http://svn.gna.org/viewcvs/relax?rev=7427&view=rev
Log:
Ported r7425 from the 1.3.1 tag.
The command used was:
svn merge -r7425:7426 svn+ssh://bugman@xxxxxxxxxxx/svn/relax/tags/1.3.1 .
.....
r7426 | bugman | 2008-09-28 22:32:16 +0200 (Sun, 28 Sep 2008) | 3 lines
Changed paths:
M /tags/1.3.1/docs/CHANGES
Updated the CHANGES for relax version 1.3.1.
.....
Modified:
1.3/docs/CHANGES
Modified: 1.3/docs/CHANGES
URL:
http://svn.gna.org/viewcvs/relax/1.3/docs/CHANGES?rev=7427&r1=7426&r2=7427&view=diff
==============================================================================
--- 1.3/docs/CHANGES (original)
+++ 1.3/docs/CHANGES Sun Sep 28 22:34:57 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
r7427 - /1.3/docs/CHANGES