relax version 2.2.2.
Posted by Edward d'Auvergne on February 13, 2013 - 00:37:
This is a minor bug fix release which resolves an important issue,
introduced somewhere within the last few relax releases, whereby
missing relaxation data is not handled properly in a model-free
analysis. A number of other small bugs have also been fixed - please
see below for details. If you plan on performing a new model-free
analysis, upgrading to this version is recommended.
The new relax versions can be downloaded from
http://www.nmr-relax.com/download.html. If binary distributions are
not yet available for your platform and you manage to compile the
binary modules, please consider contributing these to the relax
project (described in section 3.6 of the relax manual,
The full list of changes is:
* Improvements to the relax API documentation
* 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
* Epydoc docstring fix for the dfunc_standard() N-state model
target function (this is for the API documentation at
* 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
* 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
* 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
* 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
'18.104.22.168 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 '22.214.171.124 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.
* Epydoc documentation fix - a circular import in the GUI code
paths has been broken. This affects the API documentation at
* 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
* 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.
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, Updated Thu Feb 14 01:40:03 2013