Author: bugman
Date: Wed Sep 3 15:30:54 2014
New Revision: 25579
URL: http://svn.gna.org/viewcvs/relax?rev=25579&view=rev
Log:
Ported the CHANGES file changes from trunk to the 3.3.0 tag.
The command used was:
svn merge -r25577:25578 svn+ssh://bugman@xxxxxxxxxxx/svn/relax/trunk .
Modified:
tags/3.3.0/docs/CHANGES
Modified: tags/3.3.0/docs/CHANGES
URL:
http://svn.gna.org/viewcvs/relax/tags/3.3.0/docs/CHANGES?rev=25579&r1=25578&r2=25579&view=diff
==============================================================================
--- tags/3.3.0/docs/CHANGES (original)
+++ tags/3.3.0/docs/CHANGES Wed Sep 3 15:30:54 2014
@@ -676,7 +676,7 @@
* 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.
+ * Updated profiling text for CR72 model. Now it is tested for 3
fields. This is related to: Task #7807 (https://gna.org/task/?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.
@@ -721,7 +721,7 @@
* 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.
+ * Fixed the packing out of parameter tex for global analysis in
model IT99. Bug #22220 (https://gna.org/bugs/?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().
@@ -933,16 +933,16 @@
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.
+ * Modified system test Relax_disp.test_cpmg_synthetic_ns3d_to_cr72
to catch bug #22017: (https://gna.org/bugs/?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/?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/?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.
+ * Created the
Structure.test_bug_22069_structure_delete_helix_attribute system test. This
is to catch bug #22069 (https://gna.org/bugs/?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/?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.
@@ -959,9 +959,9 @@
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 bug #22069 by only deleting helix and sheet data with
structure.delete when it exists. This is bug #22069
(https://gna.org/bugs/?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.
+ * Important bug fix for the structure.delete user function when
multiple models are present. This is to fix bug #22070
(https://gna.org/bugs/?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.
r25579 - /tags/3.3.0/docs/CHANGES