Author: bugman
Date: Thu Jul 20 06:52:05 2006
New Revision: 2518
URL: http://svn.gna.org/viewcvs/relax?rev=2518&view=rev
Log:
Added an entry to the changes file for relax version 1.2.5 (r2490-r2518).
Modified:
1.2/docs/CHANGES
Modified: 1.2/docs/CHANGES
URL:
http://svn.gna.org/viewcvs/relax/1.2/docs/CHANGES?rev=2518&r1=2517&r2=2518&view=diff
==============================================================================
--- 1.2/docs/CHANGES (original)
+++ 1.2/docs/CHANGES Thu Jul 20 06:52:05 2006
@@ -1,3 +1,32 @@
+Version 1.2.5
+(20 July 2006, from /1.2)
+http://svn.gna.org/svn/relax/tags/1.2.5
+
+ Features:
+ * The data analysis chapter has been split into four: The NOE,
relaxation curve-fitting, model-free, and reduced spectral density mapping
chapters.
+ * A section called the 'The core design of relax' has been added to
the the development chapter of the manual.
+ * The 'Values, gradients, and Hessians' chapter of the manual is now
complete. These are all the equations used during optimisation.
+ * The Hessian kite diagram and the gradient construction diagram
have been added to the 'Values, gradients, and Hessians' chapter of the
manual.
+
+ Changes:
+ * The distribution archives now unpack to the directory
'relax-x.x.x' rather than just 'relax', where x.x.x is the version number.
+ * All chapters of the manual have been edited and proofed.
+ * The Sparky and XEasy peak intensity reading functions have been
split to allow the easy addition of new peak intensity file types.
+ * Test of AIC model selection between diffusion tensors added to the
test suite. (To catch bug #5746)
+ * Changing of the local tm parameter name of 'tm' to 'local_tm' to
distinguish it from the global tumbling time 'tm'. (Preparation for fixing
bug #6384)
+
+ Bugfixes:
+ * Fix of bug where self.relax.data.select_sim was treated as a list.
(bug #5977)
+ * The value.copy() function now handles the value of None. (bug
#6288)
+ * The global flag is now set by the relax_data.delete() function.
(bug #6383)
+ * The model-free model_statistics() function now tests for the
presence of relaxation data. (bug #5806)
+ * Sorting of global from local parameters in 'generic_fns/value.py'
simplified and fixed by changing the parameter name 'tm' to 'local_tm'. (bug
#6384)
+ * Model-free parameters now set in the OpenDX mapping test of the
test-suite. (bug #6388)
+ * Failure of model elimination because of a 'local_tm' and 'tm' mix
up. (bug #6389)
+ * Modification of the model-free calculate() function and
elimination of the 'combined' flag from the self.model_statistics() function.
(bug #5746)
+
+
+
Version 1.2.4
(2 May 2006, from /1.2)
http://svn.gna.org/svn/relax/tags/1.2.4
@@ -10,53 +39,40 @@
* Addition of a chapter called 'Open source infrastructure'.
* Rewrite of the 'Development of relax' chapter.
* Addition of the user function 'run.hybridise()'. (task #3122)
- * The user function 'relax_data.read()' no longer deselects residues
when no data is
- encountered. (bug #5501)
- * Residues are deselected by the user functions 'grid_search()',
'calc()', and 'minimise()'
- if k > n or if there is less than 3 data sets. (bug #5501)
+ * The user function 'relax_data.read()' no longer deselects residues
when no data is encountered. (bug #5501)
+ * Residues are deselected by the user functions 'grid_search()',
'calc()', and 'minimise()' if k > n or if there is less than 3 data sets.
(bug #5501)
* Mapping parameter values onto the structure through Molmol macros.
(task #3146)
* Added support for arbitrary colour gradients in the Molmol macros.
(task #3146)
- * Addition of a file for colour operations. All X11 colours and all
Molmol colours can be
- selected by name. (task #3146)
+ * Addition of a file for colour operations. All X11 colours and all
Molmol colours can be selected by name. (task #3146)
Changes:
- * The 'full_analysis.py' sample script now only searches over 6^6
rather than 11^6 grid
- points for the ellipsoid diffusion tensor to speed up the analysis.
+ * The 'full_analysis.py' sample script now only searches over 6^6
rather than 11^6 grid points for the ellipsoid diffusion tensor to speed up
the analysis.
* Updated the manual to replace the references to 'make' with
'sconstruct'.
* Extension of the installation chapter.
- * Changed the square and round brackets to curly brackets and
replaced ':' with '=' in the
- user function docstrings.
+ * Changed the square and round brackets to curly brackets and
replaced ':' with '=' in the user function docstrings.
* All the model-free Molmol functions have been moved into their own
class Molmol.
- * The null device can now be opened instead of a file for writing by
passing 'devnull' as
- the name.
- * Updated the release checklist so that the directory 'relax-x.x.x'
is included in the
- distributions rather than just 'relax'.
+ * The null device can now be opened instead of a file for writing by
passing 'devnull' as the name.
+ * Updated the release checklist so that the directory 'relax-x.x.x'
is included in the distributions rather than just 'relax'.
* Removed the bugs file 'docs/BUGS'.
Bugfixes:
* Small bugs in the sconstruct script have been removed.
* The value reading function can now handle rows which contain no
data.
- * The ellipsoid diffusion tensor was being incorrectly initialised
in the 'full_analysis.py'
- script.
- * Another Numeric version issue. The model m0 with no parameters
which used to be handled
- okay by the grid search and minimisation code was failing due to
changes in Numeric.
- * In certain situations, the angle folding function which is called
after model-free
- minimisation used the wrong run name.
+ * The ellipsoid diffusion tensor was being incorrectly initialised
in the 'full_analysis.py' script.
+ * Another Numeric version issue. The model m0 with no parameters
which used to be handled okay by the grid search and minimisation code was
failing due to changes in Numeric.
+ * In certain situations, the angle folding function which is called
after model-free minimisation used the wrong run name.
* Fixed the -fPIC option segfault problem on some Linux systems.
(bug #5473)
* Changed the tm grid search which was between 6-12 ns to be between
1-12ns.
* Fixed some grammar in the intro chapter of the manual.
* Fixed a bug in the model-free sample script in the spheroid
diffusion tensor function.
* Removed the spaces in front of the \index{} commands from the
manual LaTeX source files.
- * The diffusion parameters 'Diso', 'Dper', 'Dpar', 'Dratio', 'Dx',
'Dy', and 'Dz' are
- generated on the fly. (bug #5559)
+ * The diffusion parameters 'Diso', 'Dper', 'Dpar', 'Dratio', 'Dx',
'Dy', and 'Dz' are generated on the fly. (bug #5559)
* Fixed the spacing after 'Gna!' in the manual.
* The 'grace.write()' user function now plots the associated errors.
(bug #5659)
- * Fix to the parameter errors not being scaled in the value.read()
user function.
- (bug #5670)
+ * Fix to the parameter errors not being scaled in the value.read()
user function. (bug #5670)
* Parameter errors were not always included in the results file.
(bug #5660)
* Removed the memory leak in the relaxation curve-fitting C modules.
(bug #5602)
- * The user function 'value.set()' no longer raises RelaxError in
spectral density mapping
- runs. (bug #5698)
+ * The user function 'value.set()' no longer raises RelaxError in
spectral density mapping runs. (bug #5698)
* Fix to the broken Molmol pipe. (bug #5752)
* Fix of the failure of molmol.view() when the PDB is missing. (bug
#5753)
* Fix to the failure of relax_data.read() when relaxation data is
missing. (bug #5805)
r2518 - /1.2/docs/CHANGES