Author: bugman
Date: Fri May 23 16:11:51 2014
New Revision: 23386
URL: http://svn.gna.org/viewcvs/relax?rev=23386&view=rev
Log:
Merged revisions 23379 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/trunk
........
r23379 | bugman | 2014-05-23 14:45:43 +0200 (Fri, 23 May 2014) | 6 lines
Backported the relax 3.2.1 CHANGES file changes to trunk.
The command used was:
svn merge -r23376:23377 svn+ssh://bugman@xxxxxxxxxxx/svn/relax/tags/3.2.1 .
........
Modified:
branches/frame_order_cleanup/ (props changed)
branches/frame_order_cleanup/docs/CHANGES
Propchange: branches/frame_order_cleanup/
------------------------------------------------------------------------------
--- svnmerge-integrated (original)
+++ svnmerge-integrated Fri May 23 16:11:51 2014
@@ -1 +1 @@
-/trunk:1-23374
+/trunk:1-23385
Modified: branches/frame_order_cleanup/docs/CHANGES
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/docs/CHANGES?rev=23386&r1=23385&r2=23386&view=diff
==============================================================================
--- branches/frame_order_cleanup/docs/CHANGES (original)
+++ branches/frame_order_cleanup/docs/CHANGES Fri May 23 16:11:51 2014
@@ -1,3 +1,45 @@
+Version 3.2.1
+(23 May 2014, from /trunk)
+http://svn.gna.org/svn/relax/tags/3.2.1
+
+ Features:
+ * N/A
+
+
+ Changes:
+ * Punctuation fixes throughout the CHANGES document.
+ * Modified system test Relax_disp.test_cpmg_synthetic_ns3d_to_cr72
to catch bug #22017: (https://gna.org/bugs/index.php?22017) LinAlgError, for
all numerical CPMG models. System test was renamed from
test_cpmg_synthetic_cr72 to test_cpmg_synthetic_ns3d_to_cr72, to reflect
which model create the data and which model fits the data.
+ * Modified cpmg_synthetic script to first create all time structures
before doing back-calculation. Bug #22017:
(https://gna.org/bugs/index.php?22017) LinAlgError, for all numerical CPMG
models. The numerical models need all time points which are defined in setup
to be present when calculating.
+ * Renamed system test to
test_cpmg_synthetic_ns3d_to_cr72_noise_cluster. The model that creates the
data has been changed to numerical model. Bug #22017:
(https://gna.org/bugs/index.php?22017) LinAlgError, for all numerical CPMG
models.
+ * Implemented system test
Relax_disp.test_cpmg_synthetic_ns3d_to_b14. Bug #22021:
(https://gna.org/bugs/?22021) model B14 shows bad fitting to data. This is
to catch model B14 showing bad fitting behaviour.
+ * Parameter precision increase for system test
Relax_disp.test_baldwin_synthetic. The correct implementation of the
trigonometric functions allow for higher precision. Bug #22021:
(https://gna.org/bugs/?22021) model B14 shows bad fitting to data. Duplicate
line codes were also removed.
+ * Code cleanup in system test
Relax_disp.test_baldwin_synthetic_full. Bug #22021:
(https://gna.org/bugs/?22021) model B14 shows bad fitting to data. The
precision could also be increased by 1 digit.
+ * Code cleanup in system test Relax_disp.test_baldwin_synthetic.
Bug #22021: (https://gna.org/bugs/?22021) model B14 shows bad fitting to
data. Removing many unnecessary lines of code.
+ * Added 7 unit tests demonstrating edge case 'no Rex' failures of
the 'NS CPMG 2-site expanded' model. This follows from the ideas in the post
http://article.gmane.org/gmane.science.nmr.relax.devel/5858. These tests
cover all parameter value combinations which result in no exchange: dw = 0.0;
pA = 1.0; kex = 0.0; dw = 0.0 and pA = 1.0; dw = 0.0 and kex = 0.0; pA = 1.0
and kex = 0.0; dw = 0.0, pA = 1.0, and kex = 0.0. Such tests should be
replicated for all dispersion models.
+ * Created the
Structure.test_bug_22069_structure_delete_helix_attribute system test. This
is to catch bug #22069 (https://gna.org/bugs/index.php?22069), the failure of
the structure.delete user function with "AttributeError: Internal instance
has no attribute 'helices'".
+ * Created the
Structure.test_bug_22070_structure_superimpose_after_deletion system test.
This is to catch bug #22070 (https://gna.org/bugs/index.php?22070), the
failure of the structure.superimpose user function after deleting atoms with
structure.delete.
+ * Added some checks to the
Structure.test_bug_22070_structure_superimpose_after_deletion system test.
These tests reveal the real problem - that the atoms of the second model have
not been removed by the structure.delete user function.
+ * Added git-svn support for the relax version information module.
This allows the subversion revision number and repository URL to be displayed
on program startup, so that it is stored in log files. This is very useful
for debugging purposes.
+ * Improvements for the git-svn support in the relax version module.
Python 3 is now correctly handled and the URL is properly extracted from the
git repository.
+ * Improvement for the unit test printouts when run with the --time
command line option. The full unit test name is now printed out, reverting
to the old behaviour. However the shortened test names are preserved for the
other test suite categories.
+ * Created the test_ns_cpmg_2site_expanded_no_rex8() relaxation
dispersion unit test. This is a demonstration, showing the 'NS CPMG 2-site
expanded' model with no exchange when kex = 1e5. I.e. when the motion is too
fast for exchange to be observed. This test should be used for all
dispersion models to make sure that they model this edge case correctly as
well. This follows from
http://article.gmane.org/gmane.science.nmr.relax.devel/5906.
+ * Attempt at fixing bug #22071, the relax unit test and system test
not functioning. This is reported at https://gna.org/bugs/?22071. The fix
here is that the git commands to show the current subversion revision number
only works when run from the relax base directory, or one of the
subdirectories. This should now be fixed, as the pipe running the command
will first 'cd' to the relax base directory.
+ * Another attempt at fixing bug #22071, the relax unit test and
system test not functioning. This is reported at
https://gna.org/bugs/?22071. This time the complicated shell command "cd %s;
git svn find-rev $(git rev-parse HEAD)" has been replaced with "cd %s; git
svn info".
+ * Changed most default dispersion parameter values to avoid edge
cases where there is no exchange. The dw parameters were all 0.0 and kex
1e5, both of which result in no exchange. If this is ever used for an
optimisation starting point - which it never should, apart from development,
test suite, and debugging purposes - then the optimisation algorithm will
have a very hard time recovering. The pA parameter has been changed to 0.90
to set it to a reasonable value while still staying far away from the no
exchange condition of pA = 1.0. This follows from
http://article.gmane.org/gmane.science.nmr.relax.devel/5917.
+ * Fixes for 3 dispersion system tests for the change in default
parameter values. The default values are used in the auto-analysis in the
test suite to avoid the grid search. The changed values affected the
optimisation of two spins from Flemming Hansen's data located at
test_suite/shared_data/dispersion/Hansen/, residue 4 used as an example of no
exchange and residue 70 used as an example where data is only available at
one field. The system test Relax_disp.test_set_grid_r20_from_min_r2eff_cpmg
was also modified as it was directly checking these default values.
+ * Fix for the Relax_disp.test_cpmg_synthetic_dx_map_points system
test. This uses the default parameter values to start the optimisation,
therefore the recent change away from edge case 'no Rex' values allows the
parameter values stored in ds.dx_clust_val to be correctly optimised.
+ * Speed up for the version module when using a repository copy of
the code. The repository revision and URL and now stored as module
variables, so that the 'svn info' and 'git svn info' commands are only run
twice, once for the revision() function and once for the url() function.
+ * Large speed up for the relax start up times for svn and git-svn
copies of the relax repository. The 'svn info' and 'git svn info' commands
are now only executed once when the version module is first imported. The
revision() and url() functions have been merged into the repo_info() function
and this is called when the module is imported. This repo_info() function
stores the repository revision and URL as the version.repo_revision and
version.repo_url module variables. It also catches if these variables are
already set, so that multiple imports of the module do not cause the
repository information to be looked up each time. Previously the revision()
and url() functions where called every time a relax state or result file was
created, hence for repository copies the 'svn info' or 'git svn info'
commands were being called each time. The functions were also called for
each interpreter object instantiated, and for each import of the version
module.
+
+
+ Bugfixes:
+ * Extremely important fix for the model B14. This was discovered by
author Andrew Baldwin by inspecting his code in relax. Bug #22021:
(https://gna.org/bugs/?22021) model B14 shows bad fitting to data. The
implementation was performed wrong for calculation of g3 and g4. The
implementations should be performed by trigonometric functions. The model
B14 was previously in a state of non-functioning. The B14 model now shows
excellent performance.
+ * Fix for bug #22069 by only deleting helix and sheet data with
structure.delete when it exists. This is bug #22069
(https://gna.org/bugs/index.php?22069), the failure of the structure.delete
user function with "AttributeError: Internal instance has no attribute
'helices'".
+ * Fix for all edge case 'no Rex' failures of the 'NS CPMG 2-site
expanded' model. This uses the no exchange checking idea, modified to
function in the relax trunk, from
http://article.gmane.org/gmane.science.nmr.relax.devel/5847. This is
importantly on line 1 of the function. The recently introduced set of 7 unit
tests comprehensively showing these failures now all pass.
+ * Important bug fix for the structure.delete user function when
multiple models are present. This is to fix bug #22070
(https://gna.org/bugs/index.php?22070), the failure of the
structure.superimpose user function after deleting atoms with
structure.delete. The problem is that structure.delete was removing the
atoms from the first model but none of the others. This is because it was
using the structural object atom_loop() method to find the atoms to be
deleted, but this method operates on the first model. So when the second
model is reached, the atoms are already gone.
+
+
+
Version 3.2.0
(20 May 2014, from /trunk)
http://svn.gna.org/svn/relax/tags/3.2.0
r23386 - in /branches/frame_order_cleanup: ./ docs/CHANGES