Author: bugman
Date: Wed Feb 13 15:15:49 2013
New Revision: 18458
URL: http://svn.gna.org/viewcvs/relax?rev=18458&view=rev
Log:
Merged revisions 18443-18444 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/trunk
........
r18443 | bugman | 2013-02-12 21:42:25 +0100 (Tue, 12 Feb 2013) | 6 lines
Merged the relax version 2.2.2 CHANGES file back to trunk.
The command used was:
svn merge -r18441:18442 svn+ssh://bugman@xxxxxxxxxxx/svn/relax/tags/2.2.2 .
........
r18444 | bugman | 2013-02-12 21:43:15 +0100 (Tue, 12 Feb 2013) | 3 lines
Training whitespace removal in the CHANGES document.
........
Modified:
branches/frame_order_testing/ (props changed)
branches/frame_order_testing/docs/CHANGES
Propchange: branches/frame_order_testing/
------------------------------------------------------------------------------
--- svnmerge-integrated (original)
+++ svnmerge-integrated Wed Feb 13 15:15:49 2013
@@ -1,1 +1,1 @@
-/trunk:1-18437
+/trunk:1-18457
Modified: branches/frame_order_testing/docs/CHANGES
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/docs/CHANGES?rev=18458&r1=18457&r2=18458&view=diff
==============================================================================
--- branches/frame_order_testing/docs/CHANGES (original)
+++ branches/frame_order_testing/docs/CHANGES Wed Feb 13 15:15:49 2013
@@ -1,3 +1,49 @@
+Version 2.2.2
+(12 February 2013, from /trunk)
+http://svn.gna.org/svn/relax/tags/2.2.2
+
+ Features:
+ * Improvements to the relax API documentation
(http://www.nmr-relax.com/api/).
+
+
+ Changes:
+ * Updated the release checklist to include the
devel_scripts/log_converter.py script usage.
+ * Modified the relax manual subtitle as this is no longer only for
relaxation analysis.
+ * Docstring fix for the maths_fns.vectors.random_unit_vector()
function (this is for the API documentation at http://www.nmr-relax.com/api/).
+ * Epydoc docstring fix for the dfunc_standard() N-state model target
function (this is for the API documentation at http://www.nmr-relax.com/api/).
+ * Epydoc docstring fixes for the diffusion tensor objects of the
relax data store.
+ * Added and edited a number of module docstrings.
+ * Module and package docstrings additions/improvements for the SCons
scripts.
+ * Lots of module and package docstring updates for the analysis
specific code.
+ * Module docstring additions and improvements for the relax data
store modules.
+ * Addition of the generic_fns package docstring.
+ * Added a module docstring for the main relax module.
+ * Created the State.test_bug_20480 system test to catch bug #20480,
the failure to load a saved relax model-free state in the GUI
(https://gna.org/bugs/?20480). This bug was reported by Stanislava Panova
(https://gna.org/users/stacy).
+ * Created the Mf.test_bug_20479_gui_final_pipe GUI test to catch bug
#20479, the model-free analysis failure in the GUI after setting the protocol
mode to local tm. (https://gna.org/bugs/?20479). This bug was reported by
Stanislava Panova (https://gna.org/users/stacy).
+ * Added a printout to the GUI test case base check_exceptions()
method to explain what is happening.
+ * Large expansion of the Mf.test_bug_20479_gui_final_pipe GUI test.
Instead of loading the bug #20480 state file, now the entire GUI analysis
starting from scratch and using the relaxation data files is performed
remotely by the test. This is necessary because the result of the bug is
present in the state file.
+ * Added spherical diffusion to the optimisation in the
Mf.test_bug_20479_gui_final_pipe GUI test.
+ * Added a global model print out to the
Mf.test_bug_20479_gui_final_pipe GUI test. This is to help identify where
failures occur.
+ * Proper handling of the dipole interaction wizard in the
Mf.test_bug_20479_gui_final_pipe GUI test. This was causing the subsequent
GUI tests to fail as the observer objects from the wizard were not all being
unregistered.
+ * Added skips for some GUI tests when wxPython version '2.9.4.1 gtk2
(classic)' is used. There are a number of bugs in this version which cannot
be worked around in certain GUI tests, so they must be skipped.
+ * More wxPython version '2.9.4.1 gtk2 (classic)' bug avoidances in
the GUI tests. Now the auto-analyses do not check the gauges in the relax
controller at the end of the auto NOE, Rx, and model-free analyses, as
reading gauge values is faulty in this version. The Rx test is no longer
skipped for this wxPython version.
+ * Improved the printout from the align_tensor.matrix_angles user
function. The relax_io.write_data() function is being used and the tensors
are now identified by name rather than index.
+ * Improved the printouts from the align_tensor.svd user function.
+ * The relax program introduction now includes the revision number
for subversion checked out copied. This allows for better identification of
the code base being used.
+ * Fixes for the Pcs.test_structural_noise system test. As this is
based on random functions, sometimes, though rarely, the test fails. Now the
simulation accuracy has been increased and the tests are less rigorous.
+ * Spacing fixes as identified by the Python 2to3 conversion program.
+
+
+ Bugfixes:
+ * Epydoc documentation fix - a circular import in the GUI code paths
has been broken. This affects the API documentation at
http://www.nmr-relax.com/api/.
+ * Fix for the failed loading of states in the GUI. This problem was
caught by the State.test_bug_20480 GUI test. If the loading of a state file
fails,sometimes the relax data store can contain partial information from
that file. Now if the loading fails in the GUI, relax is reset.
+ * Fix for bug #20480, the failure to load a saved relax model-free
state in the GUI (https://gna.org/bugs/?20480). This was reported by
Stanislava Panova (https://gna.org/users/stacy). The problem was that the
state file was saved after a RelaxError occurred during the model-free
analysis. The GUI data store information states that the active data pipe is
called 'final'. But an error occurred prior to the 'final' data pipe being
created. The fix was to allow the state to be loaded even if the GUI data
store information has been corrupted.
+ * Fix for bug #20479 - the failure of non-fully automated model-free
analyses in the GUI. This bug was reported by Stanislava Panova
(https://gna.org/users/stacy) at https://gna.org/bugs/?20479. The problem is
GUI specific and was when running each diffusion model one after the other.
The GUI was setting the base data pipe to the 'final' data pipe, which is a
clear error.
+ * Fix for bug #20481 (https://gna.org/bugs/?20481). This is the bug
where the dauvergne_protocol model-free auto-analysis expects the prolate and
oblate spheroids and ellipsoid to be optimised. It was caught by the
Mf.test_bug_20479_gui_final_pipe GUI test.
+ * Bug fix for the diffusion tensor PDB creation in the
dauvergne_protocol model-free auto-analysis. The call to the
structure.create_diff_tensor_pdb user function now only occurs if structural
data is present.
+
+
+
Version 2.2.1
(01 February 2013, from /trunk)
http://svn.gna.org/svn/relax/tags/2.2.1
@@ -7,8 +53,8 @@
Changes:
- * Replaced a reference to freshmeat with Freecode in the Release
checklist document. Freshmeat no longer exists and is now called Freecode
(http://freecode.com/projects/nmr-relax).
- * Created the Mf.test_bug_20464_missing_ri_data system test to catch
bug #20464. The data comes from the bug report submitted by Stanislava
Panova (stpanova att gmail dot com) at https://gna.org/bugs/?20464.
+ * Replaced a reference to freshmeat with Freecode in the Release
checklist document. Freshmeat no longer exists and is now called Freecode
(http://freecode.com/projects/nmr-relax).
+ * Created the Mf.test_bug_20464_missing_ri_data system test to catch
bug #20464. The data comes from the bug report submitted by Stanislava
Panova (stpanova att gmail dot com) at https://gna.org/bugs/?20464.
* Created the Structure.test_bug_sr_2998_broken_conect_records
system test. This is to catch the bug reported as service request #2998
(https://gna.org/support/?2998) and is for corrupted PDB files with broken
CONECT records.
* Created the
Structure.test_bug_20469_scientific_parser_xray_records system test. This is
to catch bug #20469 (https://gna.org/bugs/?20469).
* Created the Structure.test_bug_20470_alternate_location_indicator
system test to catch bug #20470. This report is at
https://gna.org/bugs/?20470.
@@ -18,11 +64,11 @@
Bugfixes:
- * Python 3 fix for a print statement in the metal_pos_opt.py N-state
model system test script.
- * Python 3 fix for the part of ScientificPython distributed with
relax (for the PDB parser).
- * Python 3 import fixes for the GUI.
- * Python 3 fixes for the list sort() method - this has been replaced
by the builtin sorted() function.
- * Fix for bug #20464 (https://gna.org/bugs/?20464) - the model-free
analysis failure with missing relaxation data. The problem was the
previously missing data had a value of None whereas now the dictionary
element can be missing. Checks have been added to make sure the spin
specific relaxation data structures have the key corresponding to the data.
+ * Python 3 fix for a print statement in the metal_pos_opt.py N-state
model system test script.
+ * Python 3 fix for the part of ScientificPython distributed with
relax (for the PDB parser).
+ * Python 3 import fixes for the GUI.
+ * Python 3 fixes for the list sort() method - this has been replaced
by the builtin sorted() function.
+ * Fix for bug #20464 (https://gna.org/bugs/?20464) - the model-free
analysis failure with missing relaxation data. The problem was the
previously missing data had a value of None whereas now the dictionary
element can be missing. Checks have been added to make sure the spin
specific relaxation data structures have the key corresponding to the data.
* Fix for the N_state_model.test_monte_carlo_sims system test. On
certain systems, the chi2 check is too stringent.
* Fix for the bug reported as the support request #2998
(https://gna.org/support/?2998). CONECT records pointing to non-existent
atoms can now be handled.
* Fix for bug #20469 (https://gna.org/bugs/?20469). This is the
Failure in reading X-ray PDB files using the ScientificPython parser. The
ScientificPython Geometry.Transformation module is now distributed with
relax. Some linear algebra imports in the Geometry.TensorModule in newly
used code paths have been fixed as well.
@@ -159,7 +205,7 @@
* Modified the initial testing of the rdc.set_errors and
pcs.set_errors user functions. This is to better indicate to the user what
the problem is and why the user function cannot operate.
* Fixes for the align_fit.py N-state model system test script. The
recently introduced Monte Carlo simulations and associated RDC and PCS error
setting was failing when RDC or PCS data was missing. The script now checks
the mode of operation and only sets errors if the corresponding data is
present.
* The N_state_model.test_align_fit system test now checks the
simulation PCS values.
- * Fix for the metal_pos_opt.py N-state model system test script.
The moving interatomic data containers are now also deselected.
+ * Fix for the metal_pos_opt.py N-state model system test script.
The moving interatomic data containers are now also deselected.
* Added extensive data checks to the
N_state_model.test_metal_pos_opt system test script.
* Added new checks in the N_state_model.test_metal_pos_opt system
test. These are for structures which should not be in the deselected spins
and interatomic containers
* The N-state model _check_rdcs() method now skips deselected
interatomic data containers. A FIXME comment has also been added to
highlight a possible future problem.
r18458 - in /branches/frame_order_testing: ./ docs/CHANGES