Author: bugman
Date: Wed Jul 2 16:47:32 2014
New Revision: 24417
URL: http://svn.gna.org/viewcvs/relax?rev=24417&view=rev
Log:
Updated the CHANGES file for relax 3.2.3.
Modified:
tags/3.2.3/docs/CHANGES
Modified: tags/3.2.3/docs/CHANGES
URL:
http://svn.gna.org/viewcvs/relax/tags/3.2.3/docs/CHANGES?rev=24417&r1=24416&r2=24417&view=diff
==============================================================================
--- tags/3.2.3/docs/CHANGES (original)
+++ tags/3.2.3/docs/CHANGES Wed Jul 2 16:47:32 2014
@@ -1,3 +1,80 @@
+Version 3.2.3
+(1 July 2014, from /trunk)
+http://svn.gna.org/svn/relax/tags/3.2.3
+
+ Features:
+ * Improvements for a number of GUI elements used in the user
function windows.
+ * The ^[[?1034h escape code should now no longer be emitted by GNU
readline on Linux systems.
+ * Created the very basic structure.com user function for calculating
the centre of mass. This is to simply allow an easy interface to the
pipe_control.structure.mass.pipe_centre_of_mass() function.
+ * Expansion of the REMARK section of the PDB file created for the
internal structural object. This is visible when using the
structure.write_pdb user function, as well as the many other user functions
which create PDB files. The relax version as well as the file creation date
are now recorded in the PDB file. This extra information should be very
useful. Empty lines in the REMARK section improve the formatting.
+
+
+ Changes:
+ * Added proper sectioning to the release checklist document.
+ * Added the upload script to the release checklist document.
+ * Modified the Sequence GUI input element used for the user function
list arguments. The first column is now of fixed with when titles are
supplied. Previously when supplying titles, the width would be tiny and no
text would be visible.
+ * Added titles for all 3D coordinate user function arguments. This
is for the Sequence GUI input element, and affects the
frame_order.average_position, n_state_model.CoM and paramag.centre user
functions.
+ * The compilation of the C modules now respects the user defined
environment. This is the patch from Justin (https://gna.org/users/jlec)
attached to bug #22145 (https://gna.org/bugs/?22145). It has been modified
to include a comment and remove a double empty line.
+ * Bug fix for the compilation of the C modules now respects the user
defined environment. The problem was that on Mac OS X (as well as other
systems), that these environmental variables were not defined and hence the
scons commands would all fail with a KeyError and traceback. Now the keys in
the os.environ dictionary are being searched for before they are set.
+ * Fix for the wxPython link in the installation chapter of the
manual. This was pointing to the scipy website for some reason.
+ * Changed the Python readline link for MS Windows in the
installation chapter of the manual. This now points to
https://pypi.python.org/pypi/pyreadline as the iPython link is broken.
+ * Implemented system test
Relax_disp.test_bug_22146_unpacking_r2a_r2b_cluster. This is to catch the
wrong unpacking of R2A and R2B when performing a clustered full dispersion
model analysis. Bug #22146: (https://gna.org/bugs/?22146) Unpacking of R2A
and R2B is performed wrong for clustered "full" dispersion models.
+ * Extended system test
Relax_disp.test_bug_22146_unpacking_r2a_r2b_cluster for B14 full model. This
is to catch the wrong unpacking of R2A and R2B when performing a clustered
full dispersion model analysis. Bug #22146: (https://gna.org/bugs/?22146)
Unpacking of R2A and R2B is performed wrong for clustered "full" dispersion
models.
+ * Extended system test
Relax_disp.test_bug_22146_unpacking_r2a_r2b_cluster for NS CPMG 2SITE 3D full
model. This is to catch the wrong unpacking of R2A and R2B when performing a
clustered full dispersion model analysis. Bug #22146:
(https://gna.org/bugs/?22146) Unpacking of R2A and R2B is performed wrong for
clustered "full" dispersion models.
+ * Extended system test
Relax_disp.test_bug_22146_unpacking_r2a_r2b_cluster for NS CPMG 2SITE STAR
full model. This is to catch the wrong unpacking of R2A and R2B when
performing a clustered full dispersion model analysis. Bug #22146:
(https://gna.org/bugs/?22146) Unpacking of R2A and R2B is performed wrong for
clustered "full" dispersion models.
+ * Added synthetic data generator script which created the data to
test against. Bug #22146: (https://gna.org/bugs/?22146) Unpacking of R2A and
R2B is performed wrong for clustered "full" dispersion models.
+ * Split system test
Relax_disp.test_bug_22146_unpacking_r2a_r2b_cluster up in different tests. A
setup function which is: setup_bug_22146_unpacking_r2a_r2b_cluster(self,
folder=None, model_analyse=None): And then the tests:
test_bug_22146_unpacking_r2a_r2b_cluster_B14
test_bug_22146_unpacking_r2a_r2b_cluster_CR72
test_bug_22146_unpacking_r2a_r2b_cluster_NS_3D
test_bug_22146_unpacking_r2a_r2b_cluster_NS_STAR. Bug #22146:
(https://gna.org/bugs/?22146) Unpacking of R2A and R2B is performed wrong for
clustered "full" dispersion models.
+ * Modified profiling script to get closer to the implementation in
relax. An additional test function is setup to figure out how to reshape the
numpy arrays in the target function. Bug #22146:
(https://gna.org/bugs/?22146) Unpacking of R2A and R2B is performed wrong for
clustered "full" dispersion models.
+ * Updated profiling text for CR72 model. Now it is tested for 3
fields. This is related to: Task #7807
(https://gna.org/task/index.php?7807): Speed-up of dispersion models for
Clustered analysis.
+ * Added searching for environment variable PYTHON_INCLUDE_DIR if
Python.h is not found in standard Python library. This can be very handsome,
if one has a Python virtual environment for multiple users. This relates to
the wiki page: http://wiki.nmr-relax.com/Epd_canopy.
+ * The lib.compat.norm() replacement function for numpy.linalg.norm()
now handles no axis argument. This is to allow the function to be used in
all cases where numpy.linalg.norm() is used, while providing compatibility
with the axis argument and all numpy versions.
+ * Fix for the scons target for compiling the relax manual when using
a repository checkout copy. The method for compiling the relax manual was
calling the version.revision() function, however this has been replaced a
while ago by the version.repo_revision variable.
+ * Created two unit tests for the lib.io.file_root() function. The
second of the tests demonstrate a failure of the function if multiple file
extensions are present.
+ * Lowered chi2 value test in system test
Relax_disp.test_bug_22146_unpacking_r2a_r2b_cluster_NS_STAR. This is due to
the data produced on 32 bit machine, and tested on 64 bit machines. The
error was: AssertionError: 2.4659455670347743e-05 != 0.0 within 7 places.
The reason for this is due to truncation artifacts.
+ * Fix for wrong path testing of Python.h. Python.h would be in
PYTHON_PREFIX/include/pythonX.Y/Python.h and not in
PYTHON_PREFIX/include/Python.h.
+ * Better handling of the control-C keyboard interrupt signal in the
relax test suite. This includes two changes. The Python 2.7 and higher
unittest.installHandler() function is now called, when present, to terminate
all tests using the unittest module control-C handler. The second change is
that the keyboard interrupt signal is caught in a try-except statement, a
message printed out, and the tests terminated. This should be an improvement
for all systems.
+ * Adding last profiling information for model CR72.
+ * Added system test for model LM63 3 site. According to results
folder in test_suite/shared_data/dispersion/Hansen/relax_results/LM63 3-site.
This should pass, but it doesn't.
+ * Created an initial Relax_disp.test_lm63_3site_synthetic system
test. This should have been set up a long time ago. It uses the synthetic
noise-free data in the test_suite/shared_data/dispersion/lm63_3site directory
which was created for a system test but never converted into one. The test
still needs modifications to allow it to pass.
+ * Modifications for the Relax_disp.test_lm63_3site_synthetic system
test. The r2eff_values.bz2 saved state file has been updated, as it was too
old to use in the test. The test has also had a typo bug fixed and the data
pipe name updated. The test now also checks all of the optimised values.
+ * Removed system test test_hansen_cpmg_data_to_lm63_3site. This was
a temporary implementation and has been replaced with system test
Relax_disp.test_lm63_3site_synthetic.
+ * Fixes for all of the relaxation dispersion system tests which were
failing with the new minfx code. Due to the tuning of the log barrier
constraint algorithm in minfx in the commit at
http://article.gmane.org/gmane.science.mathematics.minfx.scm/25, many system
tests needed to be slightly adjusted. Two of the
Relax_disp.test_tp02_data_to_* system tests were also failing as the
optimisation can no longer move out of the minimum at pA = 0.5 for one spin
(due to the low quality grid search in the auto-analysis).
+ * Updated the release checklist document for the new 1.0.7 release
of minfx.
+ * Fixes for the
Relax_disp.test_hansen_cpmg_data_missing_auto_analysis system test. The pA
parameter is no longer tested for one spin as it moves to random values on
different operating systems and 32 vs. 64-bit systems. This is because this
spin experiences no exchange, both dw and kex are zero.
+ * Decreased the value checking precision in the
Relax_disp.test_hansen_cpmg_data_to_lm63 system test. This is to allow the
test to pass on certain operating systems and 32-bit systems.
+ * Modified the precision of the output from the
relax_disp.sherekhan_input user function. This is simply to allow the
Relax_disp.test_sod1wt_t25_to_sherekhan_input system test to pass on certain
32-bit systems, as the float output to 15 decimal places is not always the
same. This system test has been updated for the change.
+ * Modified the Relax_disp.test_sprangers_data_to_mmq_cr72 system
test to pass on certain systems. This test fails on 32-bit Linux (and
probably other systems as well). To fix the test, the kex values are all
divided by 100 before checking them to 4 decimal places of accuracy.
+ * Improved how the relax installation path is determined in the
status object. If the path cannot be found, the current working directory is
then checked if it is where relax is installed. This is needed when
importing modules outside of relax.
+ * Hack to permanently eliminate the ^[[?1034h escape code being
produced on Linux systems. This is produced by importing the readline
module. The escape code will be sent to STDOUT every time relax is executed,
so it will be present in all log files. The problem is the TERM
environmental variable being set to 'xterm'. The hack simply sets TERM to an
empty string.
+ * More hacks for permanently eliminating the ^[[?1034h escape code
being produced on Linux systems. This is a nasty feature of the GNU readline
library. It is now also turned off in the dep_check module, suppressing
^[[?1034h in Python scripts which import only parts of relax.
+ * Numpy version 1.6 or higher is now required to be able to run
relax. This follows from the series of messages:
http://www.mail-archive.com/relax-devel@xxxxxxx/msg06288.html,
http://www.mail-archive.com/relax-devel@xxxxxxx/msg06289.html,
http://www.mail-archive.com/relax-devel@xxxxxxx/msg06327.html, and
http://www.mail-archive.com/relax-devel@xxxxxxx/msg06335.html. If too many
users complain, maybe this change can be reverted later. This minimal numpy
version is needed for many of the speed ups going in the relaxation
dispersion and frame order analyses. It is required for the numpy ufunc out
arguments and for the numpy.eigsum() function. These will likely be used in
other analyses in the future for improving the speed of relax, so it might
affect users of other analyses later on.
+ * Updated the numpy minimal dependency in the installation chapter
of the manual to version 1.6.
+ * Added better epydoc sectioning to the
lib.dispersion.ns_cpmg_2site_expanded module docstring. This is to better
separate the original scripts used to document the code evolution.
+ * Empty lines are now handled by the
lib.structure.pdb_write.record() function. By supplying the remark as None,
empty lines can now be created in the REMARK section of a PDB file. This can
be used for nicer formatting.
+ * Fixes for the Diffusion_tensor system tests due to the recent PDB
file changes. Prior to the comparison of the generated PDB files, all REMARK
PDB lines are now stripped out.
+ * Fixes for all system tests failing due to the expanded and
improved PDB REMARK section. The system tests now remove all REMARK records
prior to comparing file contents. The special strip_remarks() system test
method has been created to simplify the stripping process.
+ * Fix for the software verification tests. The recent expansion and
improvements of the REMARK records created by the internal structural object
PDB writing method imported the relax version to place this information into
the PDB files. However this breaks the relax library design, as shown by the
verification tests. Instead the relax version information is being taken
from the lib.structure.internal.object.RELAX_VERSION variable. This defaults
to None, however the version module now sets this variable directly when it
is imported so that it is always set to the current relax version when
running relax.
+ * General Python 3 fixes via the 2to3 script.
+ * Removed the lib.compat.sorted() function which was providing
Python2.3 compatibility. For a while now, relax has been unable to run on
Python versions less than 2.5. Therefore there is no use for having this
replacement function for Python <= 2.3 which was being placed into the
builtins module.
+ * Python 3 fixes for the entire codebase using the 2to3 script. The
command used was: 2to3 -j 4 -w -f xrange .
+ * The internal structural object add_molecule() and has_molecule()
methods are now model specific. This allows for finer control of structural
object.
+ * Created the new lib.structure.files module. This currently
contains the single find_pdb_files() function which will be used to find all
*.pdb, *.pdb.gz and *.pdb.bz2 versions of the PDB file in a given path.
+ * Fix for the breakage of the relax help system. This was reported
at http://thread.gmane.org/gmane.science.nmr.relax.devel/6481. The problem
was that the TERM environmental variable was turned off to avoid the GNU
readline library on Linux systems emitting the ^[[?1034h escape code. See
the message at
http://thread.gmane.org/gmane.science.nmr.relax.devel/6481/focus=6489 for
more details. However the Python help system obviously requires this
environmental variable. Now only if the TERM variable is set to 'xterm' will
it be reset, and to 'linux' instead of the blank string ''. This does not
affect any relax releases.
+
+
+ Bugfixes:
+ * Fix for the wrong unpacking of R20A and R20B in model CR72 full.
Bug #22146: (https://gna.org/bugs/?22146) Unpacking of R2A and R2B is
performed wrong for clustered "full" dispersion models.
+ * Fix for the wrong unpacking of R20A and R20B in model B14 full.
Bug #22146: (https://gna.org/bugs/?22146) Unpacking of R2A and R2B is
performed wrong for clustered "full" dispersion models.
+ * Fix for the wrong unpacking of R20A and R20B in model NS CPMG
2SITE 3D full model. Bug #22146: (https://gna.org/bugs/?22146) Unpacking of
R2A and R2B is performed wrong for clustered "full" dispersion models.
+ * Fix for the wrong unpacking of R20A and R20B in model NS CPMG
2SITE STAR full model. Bug #22146: (https://gna.org/bugs/?22146) Unpacking
of R2A and R2B is performed wrong for clustered "full" dispersion models.
+ * Bug fix for the lib.io.file_root() function for multiple file
extensions. The function will now strip off all file extensions.
+ * Fix for bug #22210 (https://gna.org/bugs/?22210), the failure of
the 'LM63 3-site' dispersion model. The problem is described in the bug
report - the multiplication in the tanh() function is a mistake, it must be a
division.
+ * Fix for the Library.test_library_independence verification test on
MS Windows. The tearDown() method now uses the error handling
test_suite.clean_up.deletion() function to remove the copied version of the
relax library.
+ * Fixed the packing out of parameter tex for global analysis in
model IT99. Bug #22220 (https://gna.org/bugs/index.php?22220): Unpacking of
parameters for global analysis in model IT99, is performed wrong.
+ * Fix for bug #22257, the freezing of the GUI after using the free
file format window on Mac OS X. This is reported at
https://gna.org/bugs/?22257. This is a recurring problem in Mac OS X as it
cannot be tested in the relax test suite. The problem is with wxPython. The
modal dialogs, such as the free file format window, cannot be destroyed on
Mac OS X using wx.Dialog.Destroy() - this kills wxPython and hence kills
relax. The problem does not exist on any other operating system. To fix
this, all wx.Dialog.Destroy() calls have been replaced with wx.Dialog.Close().
+
+
+
Version 3.2.2
(5 June 2014, from /trunk)
http://svn.gna.org/svn/relax/tags/3.2.2
r24417 - /tags/3.2.3/docs/CHANGES