Author: bugman
Date: Sun Mar 17 11:21:49 2013
New Revision: 18838
URL: http://svn.gna.org/viewcvs/relax?rev=18838&view=rev
Log:
Updated the CHANGES file for relax 2.2.4.
Modified:
tags/2.2.4/docs/CHANGES
Modified: tags/2.2.4/docs/CHANGES
URL:
http://svn.gna.org/viewcvs/relax/tags/2.2.4/docs/CHANGES?rev=18838&r1=18837&r2=18838&view=diff
==============================================================================
--- tags/2.2.4/docs/CHANGES (original)
+++ tags/2.2.4/docs/CHANGES Sun Mar 17 11:21:49 2013
@@ -1,3 +1,47 @@
+Version 2.2.4
+(17 March 2013, from /trunk)
+http://svn.gna.org/svn/relax/tags/2.2.4
+
+ Features:
+ * Creation of the structure.create_rotor_pdb user function for
creating representations of the rotor frame order model.
+
+
+ Changes:
+ * Updated the release checklist document to include the correct
instructions for minfx and bmrblib. These are the packages bundled with
relax (http://gna.org/projects/minfx/ and http://gna.org/projects/bmrblib/)
+ * Improvements for Python 2 and 3 compatibility. Much of the Python
2 verses 3 compatibility, as well as different Python 2 version compatibility
and different Python 3 version compatibility, code has been shifted into the
compat module. The different parts of relax now import from the compat
module for modules/packages with different import semantics for different
Python versions. In addition the different handling of the bz2 and gzip
module for reading and writing files has been shifted from 'relax_io' into
'compat'.
+ * Updated the 2to3 checklist document to include multiple threads
for faster operation.
+ * Eliminated the os.devnull import flag dep_check.devnull_import.
This is not needed as the compat relax module defines os.devnull for Python
<= 2.3. The devnull module is no longer part of the relax information
printout.
+ * Added a more informative error message if the platform module is
missing. This is for Python <= 2.2. The file from
http://hg.python.org/cpython/file/2.3/Lib/platform.py can simply be copied
into the lib/pythonX.X/ directory to fix this.
+ * Slight change to the message printed if the platform module is
missing.
+ * Modified the script for running the relax test-suite on multiple
Python versions. The pre-2.2 Python versions are now commented out as well
as the abortive Python 3.0.
+ * Created the Mf.test_bug_20613_auto_mf_diff_tensor_pdb system test
to catch bug #20613. This was reported by Angelo Miguel Figueiredo <am dott
figueiredo att fct dot unl dot pt> at https://gna.org/bugs/?20613. This test
is a direct copy of the Mf.test_bug_20563_missing_ri_error system test. The
only change is that the local tm global model results file (in the
local_tm/aic/ directory) has been modified. This results were read into
relax, the file test_suite/shared_data/structures/Ap4Aase_res1-12.pdb loaded
into the data pipe, and the results saved again. This triggers the bug as
the problem is the presence of structural data with the local tm global model
being selected in the auto-analysis.
+ * Shifted all of the model-free specific analysis class
documentation variables to the top. This is simply for better organisation
of the code.
+ * Created the model-free write_doc class variable talking about the
field strength independent Rex value. This has been added to the
value.display and value.write user functions to explain that Rex values are
very small and that the user needs to scale them up.
+ * Shifted all of the documentation variables to the top of the
specific API_base class. This is for better organisation.
+ * Added the write_doc class variable to the specific analysis API
class as a empty string. This is to fix the unit tests.
+ * Created the front end for the new structure.create_rotor_pdb user
function. This will be used to create a PDB representation of a rotor
motional model.
+ * Added file, directory and overwrite force arguments to the
structure.create_rotor_pdb user function.
+ * Started to implement the backend of the structure.create_rotor_pdb
user function.
+ * The internal structural object MolContainer.add_atom() method now
returns the index of the new atom.
+ * Created the internal structural object MolContainer.last_residue()
method.
+ * Fully implemented the structure.create_rotor_pdb user function.
For this, the generic_fns.structure.geometric.create_rotor_propellers()
function was created.
+
+
+ Bugfixes:
+ * Fix for the system tests in the Mac OS X application binary. The
Mf.test_bug_20563_missing_ri_error system test fails in the Mac OS X
application binary. The problem is that the py2app extension used to build
the Mac application decides that empty directories are not to be included in
the app, so naturally the test fails when checking for these. Now empty
results files have been added to these directories to trick py2app to include
them.
+ * Fixes for the unit test package __all__ list checking. Now only
*.py files and directories are checked. In some cases other files could be
present in the packages, for example the object files when compiling the C
modules. These would cause the unit tests to fail unnecessarily.
+ * Fixes for the unit test __all__ list checking for the lib package
for the Mac OS X application. For some reason the py2app extension which
creates the app merges the Python installation directory
Resources/lib/python2.7 and the relax lib package into Resources/lib. Now
'python2.7' is blacklisted when checking the lib package so that the
parasitic Python install location is ignored.
+ * Bug fix for the structure RMSD function for when old numpy
versions are present. Older numpy versions do not have the ddof argument for
the std() standard deviation function,therefore relax now catches this,
calculates the biased standard deviation formula, and then multiplies the
value by a correction factor to obtain the non-biased estimator.
+ * Bug fix for the info relax system information module for when
spaces are present in the relax path. If relax is placed into a directory
containing spaces, then the determination of the architecture of the compiled
C modules fails.
+ * Python 3 fixes for the model-free analysis specific code. This
was causing errors "AttributeError: 'dict_values' object has no attribute
'sort'".
+ * Python 3 updates and fixes using the 2to3 program.
+ * Bug fix for the external Scientific Python Geometry package. This
is a strange Python 3 issue only triggered when the epydoc Python package is
installed.
+ * Fix for bug #20613 (https://gna.org/bugs/?20613), the failure of
the diffusion tensor PDB creation. This was reported by Angelo Miguel
Figueiredo <am dott figueiredo att fct dot unl dot pt>. The problem was that
the diffusion tensor PDB representation structure.create_diff_tensor_pdb user
function was being called even when the local tm global model was selected.
This naturally failed as there is no global diffusion tensor. Now this user
function is avoided for the local tm global model.
+ * Fix for the value.write user function for very small parameter
values (Rex for example). This was reported by Martin Ballaschk <ballaschk
att fmp-berlin dott de> in the thread
http://thread.gmane.org/gmane.science.nmr.relax.user/1397/focus=1402 and by
by Angelo Miguel Figueiredo <am dott figueiredo att fct dot unl dot pt> in
the unrelated bug report at https://gna.org/bugs/?20613. The formatting
string "20.15f" has been changed to "20.15g" to allow Python to decide if the
normal decimal or exponential form of the number should be printed.
+ * Fix for a strange and extremely rare typo bug in the model-free
specific analysis code. This was identified by Manish Chaubey <manish dott
chaubey att tuebingen dott mpg dott de> in the message at
http://thread.gmane.org/gmane.science.nmr.relax.user/1422. This only occurs
if a relaxation data error of zero is encountered and is a bug in the
RelaxError message explaining the problem with the data.
+
+
+
Version 2.2.3
(11 March 2013, from /trunk)
http://svn.gna.org/svn/relax/tags/2.2.3
r18838 - /tags/2.2.4/docs/CHANGES