Author: bugman
Date: Mon Oct 15 14:54:26 2012
New Revision: 17807
URL: http://svn.gna.org/viewcvs/relax?rev=17807&view=rev
Log:
Merged revisions 17687,17689-17691,17693,17697-17737,17776-17778,17780-17806
via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/trunk
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r17687 | bugman | 2012-10-02 18:55:31 +0200 (Tue, 02 Oct 2012) | 5 lines
Another Python 3 fix for the relax_io.extract_data() function.
Sometimes this function sees byte types, sometimes string types. The
function can now handle both.
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r17689 | bugman | 2012-10-02 23:51:32 +0200 (Tue, 02 Oct 2012) | 3 lines
Python 3 bug fix for the geometric structure module - another integer
division to float problem.
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r17690 | bugman | 2012-10-03 00:09:30 +0200 (Wed, 03 Oct 2012) | 3 lines
The Python 3 dictionary values() method no longer returns a list, so a
list() call is needed.
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r17691 | bugman | 2012-10-03 01:26:26 +0200 (Wed, 03 Oct 2012) | 6 lines
Bug fix for wxPython 2.9.4.0 - the unsetting of the alpha mask for all
bitmap images should now work.
The wx.Bitmap.SetMaskColour(None) call does not work, so instead a
wx.Colour() instance is passed in
instead.
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r17693 | bugman | 2012-10-03 22:46:34 +0200 (Wed, 03 Oct 2012) | 6 lines
Fix to the DummyFileObject to allow Python 2.5 and lower to run relax.
The byte arrays are now placed in eval() statements to allow the 2.5 and
lower interpreters to parse
the code.
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r17697 | bugman | 2012-10-04 18:20:51 +0200 (Thu, 04 Oct 2012) | 7 lines
Added the Mf.test_bug_20213_asn_sidechain() system test to catch bug #20213.
The data and script comes from the files 'sh3-47.2.zip' and 'run.py'
attached to the bug report
https://gna.org/bugs/?20213. The PDB now only contains Asp47, the
optimisation parameters have been
made almost insignificant, and all models but 'tm0' have been removed from
the analysis.
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r17698 | bugman | 2012-10-04 18:23:16 +0200 (Thu, 04 Oct 2012) | 3 lines
The Mf.test_bug_20213_asn_sidechain() system test now uses a temporary
directory for output.
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r17699 | bugman | 2012-10-04 18:37:56 +0200 (Thu, 04 Oct 2012) | 5 lines
Created the simple Sequence.test_sequence_copy() system test to catch bug
#20213.
https://gna.org/bugs/?20213.
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r17700 | bugman | 2012-10-04 19:02:08 +0200 (Thu, 04 Oct 2012) | 8 lines
Fix for bug #20213 (https://gna.org/bugs/?20213).
The problem was that the generic_fns.sequence.generate() function was
searching for a spin based on
its spin ID generated from the spin name and not spin number. Hence two
spins with the same name
but different numbers were treated as the same spin, and only data from one
was being generated via
the copy() function.
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r17701 | bugman | 2012-10-05 18:42:15 +0200 (Fri, 05 Oct 2012) | 8 lines
Created the relax_io.readlines method for handling the bz2 and gzip module
byte strings in Python 3.
The bz2.BZ2File and gzip.GzipFile classes now return lists of bytes strings
from their readlines()
methods in Python 3. This causes failures all over relax. This behaviour
is probably a bug in
these classes. The relax_io.readlines method is a workaround for this
problem, to have a list of
standard strings returned.
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r17702 | bugman | 2012-10-05 18:43:11 +0200 (Fri, 05 Oct 2012) | 3 lines
Python 3 bug fix for the internal PDB and XYZ 3D structure readers by using
relax_io.readlines().
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r17703 | bugman | 2012-10-05 19:39:17 +0200 (Fri, 05 Oct 2012) | 3 lines
First attempt at making the relaxation curve-fitting C module Python 3
compatible.
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r17704 | bugman | 2012-10-05 19:45:46 +0200 (Fri, 05 Oct 2012) | 3 lines
The relaxation curve-fitting C module now supports compilation on both
Python 2 and 3.
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r17705 | bugman | 2012-10-05 19:48:03 +0200 (Fri, 05 Oct 2012) | 6 lines
The relax_fit specific analysis module now supports both Python 2 and 3.
The command used was:
2to3 -w specific_fns/relax_fit.py
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r17706 | bugman | 2012-10-07 15:00:19 +0200 (Sun, 07 Oct 2012) | 3 lines
Added a script for testing out the C module compilation on multiple python
targets.
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r17707 | bugman | 2012-10-07 15:13:52 +0200 (Sun, 07 Oct 2012) | 3 lines
Finished off the C module compilation testing script.
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r17708 | bugman | 2012-10-07 15:16:28 +0200 (Sun, 07 Oct 2012) | 3 lines
Renamed the 'scripts' directory to 'devel_scripts' so that users are less
likely to ask about the scripts.
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r17709 | bugman | 2012-10-07 15:26:15 +0200 (Sun, 07 Oct 2012) | 3 lines
The manual C module compilation script is now executable.
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r17710 | bugman | 2012-10-07 15:37:52 +0200 (Sun, 07 Oct 2012) | 3 lines
Added the IO module to the relax information print out and dependency
checks.
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r17711 | bugman | 2012-10-07 15:40:50 +0200 (Sun, 07 Oct 2012) | 7 lines
The relax_io.open_read_file() now supports all Python versions over 2.4.
This required some really nasty hacks for Python 3.0, 3.1 and 3.2 with the
Bzip2Fixed and GzipFixed
classes overriding the incomplete and buggy bz2.BZ2File and gzip.GzipFile
modules, and being wrapped
around io.TextIOWrapper().
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r17712 | bugman | 2012-10-07 15:50:10 +0200 (Sun, 07 Oct 2012) | 11 lines
Reverted revisions r17702, r17701, r17693, r17687, r17685, r17684, and
r17669.
The command used were:
svn merge -r17702:17669 relax_io.py
svn merge -r17702:r17701
/data/relax/relax-trunk/generic_fns/structure/internal.py
The relax_io module should now handle all files as text, independent of
compression. These reverted
revisions were attempts at fixing the buggy behaviour of Python 3.0, 3.1
and 3.2. But now the
io.TextIOWrapper() class is being used to eliminate the byte streams, which
should be text streams.
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r17713 | bugman | 2012-10-07 15:56:44 +0200 (Sun, 07 Oct 2012) | 3 lines
The C module compilation testing script now accepts the Python version as a
first argument.
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r17714 | bugman | 2012-10-07 16:15:02 +0200 (Sun, 07 Oct 2012) | 6 lines
Reverted r17681 as file objects in relax are now always treated as text, so
byte streams are not needed.
The command used was:
svn merge -r17681:r17680 .
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r17715 | bugman | 2012-10-07 16:29:56 +0200 (Sun, 07 Oct 2012) | 5 lines
Python 3 fix for the Pipes.test_pipe_bundle() system test.
The order of bundle names returned by generic_fns.pipes.bundle_names() is
not guaranteed in Python 3.
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r17716 | bugman | 2012-10-07 16:38:01 +0200 (Sun, 07 Oct 2012) | 5 lines
For consistency between Python 2 and 3, the grace.write user function
outputs to 15 decimal places.
This increased precision will only be of use in the relax test suite.
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r17717 | bugman | 2012-10-07 16:38:43 +0200 (Sun, 07 Oct 2012) | 3 lines
Python 3 fix for the Noe.test_noe_analysis() system test for the
grace.write precision changes.
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r17718 | bugman | 2012-10-07 18:12:33 +0200 (Sun, 07 Oct 2012) | 8 lines
Python 3 fix for the relax_io.open_write_file() function.
This now matches the behaviour of open_read_file() in that there are three
different behaviours for
opening bz2 and gz files for writing to for the different Python versions
(one for Python 2, one for
Python 3.0 to 3.2, and one for Python 3.3+). All byte streams have been
eliminated as
open_write_file() is for creating text files.
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r17719 | bugman | 2012-10-07 18:45:38 +0200 (Sun, 07 Oct 2012) | 3 lines
Fix for the Relax_fit.test_bug_12670_12679() system test for the changes to
Grace files at r17716.
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r17720 | bugman | 2012-10-07 18:53:30 +0200 (Sun, 07 Oct 2012) | 3 lines
Python 3 fix - removed the use of the string module from
generic_fns.spectrum.
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r17721 | bugman | 2012-10-07 18:59:12 +0200 (Sun, 07 Oct 2012) | 6 lines
Removed the ability to save and restore states using the pickle module.
A pickled state is of no use to relax anymore. It's removal is needed for
Python 3 support. So now
everything defaults to the XML formatted output.
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r17722 | bugman | 2012-10-07 18:59:43 +0200 (Sun, 07 Oct 2012) | 3 lines
Eliminated the State.test_state_pickle() system test as pickled states are
no longer supported.
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r17723 | bugman | 2012-10-07 19:12:26 +0200 (Sun, 07 Oct 2012) | 3 lines
Removed the pickle format information and arguments from the state user
function definitions.
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r17724 | bugman | 2012-10-07 19:21:06 +0200 (Sun, 07 Oct 2012) | 6 lines
Python 3 support for Modelfree4 and Dasha.
The subprocess.Popen class works with byte arrays rather than strings in
Python 3+. The Python
objects are now interconverted when the Python 3 encode() and decode()
methods are detected.
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r17725 | bugman | 2012-10-07 19:22:04 +0200 (Sun, 07 Oct 2012) | 3 lines
Small comment edit.
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r17726 | bugman | 2012-10-07 20:56:21 +0200 (Sun, 07 Oct 2012) | 6 lines
Python 3 fix for the Mf.test_latex_table system test.
The latex_mf_table.py model-free system test script docstring contains
backslashes, so the raw
string format r"""Text""" is now used.
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r17727 | bugman | 2012-10-07 20:59:22 +0200 (Sun, 07 Oct 2012) | 3 lines
The OMP model-free results file generation script now outputs for any relax
version.
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r17728 | bugman | 2012-10-07 21:54:24 +0200 (Sun, 07 Oct 2012) | 6 lines
Removed the Python 3 byte array hack which should have been removed earlier.
This code is from r17669 which should have been removed at r17712 but was
accidentally left out.
Instead of reverting, the code has been deleted as r17669 contained another
useful change.
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r17729 | bugman | 2012-10-07 21:58:58 +0200 (Sun, 07 Oct 2012) | 5 lines
Added a Python 3 version of the truncated OMP model-free results file.
This was created with trunk which is during the 2.1 relax releases.
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r17730 | bugman | 2012-10-07 22:06:49 +0200 (Sun, 07 Oct 2012) | 6 lines
The messsage about skipping the GUI tests due to wxPython being missing is
now more specific.
This was being shown for all runs of the test suite when it only needs to
appear if GUI tests have
been run.
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r17731 | bugman | 2012-10-07 22:11:43 +0200 (Sun, 07 Oct 2012) | 6 lines
The relaxation curve-fitting system tests are now skipped if the module is
missing or broken.
This improves the printouts from the test suite and shows a summary of
skipped tests rather than a
pile of traceback messages and errors.
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r17732 | bugman | 2012-10-08 00:11:32 +0200 (Mon, 08 Oct 2012) | 7 lines
Python 3 fix for the model-free results file reading tests.
The ordering of dictionaries is different in Python 3, so now these are
properly converted from
strings to dictionaries before comparison. This was not happening because
of the XML changes from
Python 2.7.3 onwards.
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r17733 | bugman | 2012-10-08 00:34:46 +0200 (Mon, 08 Oct 2012) | 5 lines
Python 3 fix for the setting of diffusion and alignment tensor simulation
values.
The previous code somehow worked in Python 2 but was not formally correct
and broke in Python 3.
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r17734 | bugman | 2012-10-08 00:41:24 +0200 (Mon, 08 Oct 2012) | 5 lines
The fix of r17733 actually broke Python 2.
The list.__setattr__() method is fundamentally different between Python 2
and 3!
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r17735 | bugman | 2012-10-08 00:47:19 +0200 (Mon, 08 Oct 2012) | 3 lines
Removed some debugging printouts accidentally committed in r17734.
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r17736 | bugman | 2012-10-08 00:48:50 +0200 (Mon, 08 Oct 2012) | 5 lines
Fix for the fix of r17734 which attempted to fix r17733.
The Python version is now being detected.
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r17737 | bugman | 2012-10-08 11:04:32 +0200 (Mon, 08 Oct 2012) | 6 lines
Updated the relax version numbers and 'trunk' used relax user manual.
For example the information about checking out the main development line
was still talking about 1.3
rather than the trunk.
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r17776 | bugman | 2012-10-09 00:59:53 +0200 (Tue, 09 Oct 2012) | 3 lines
Initialized merge tracking via "svnmerge" with revisions "1-17738" from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/tensor_data
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r17777 | bugman | 2012-10-09 01:01:34 +0200 (Tue, 09 Oct 2012) | 180 lines
Merged revisions 17739-17774 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/tensor_data
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r17739 | bugman | 2012-10-08 11:36:44 +0200 (Mon, 08 Oct 2012) | 6 lines
The diffusion tensor data structure has been completely converted into a
read-only structure.
The __setattr__() method now will always raise a RelaxError, and the
diffusion tensor simulation
data structure objects __setitem__() method will raise the same error.
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r17740 | bugman | 2012-10-08 11:37:18 +0200 (Mon, 08 Oct 2012) | 3 lines
Fix for the initialisation of the diffusion tensor data structure, now
that it is read-only.
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r17741 | bugman | 2012-10-08 11:37:54 +0200 (Mon, 08 Oct 2012) | 3 lines
The new diffusion tensor fixed() method has been created to allow the
fixed flag to be changed.
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r17742 | bugman | 2012-10-08 11:42:23 +0200 (Mon, 08 Oct 2012) | 6 lines
Created the diffusion tensor data structure type() method for setting the
tensor type.
This is to remove the "cdp.diff_tensor.type = 'x'" code from the core of
relax, as the structure is
now read only.
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r17743 | bugman | 2012-10-08 11:44:02 +0200 (Mon, 08 Oct 2012) | 5 lines
Renamed the diffusion tensor data structure type() method to set_type().
This is because the type is stored as the 'type' object, clashing with
the method name.
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r17744 | bugman | 2012-10-08 14:04:54 +0200 (Mon, 08 Oct 2012) | 5 lines
Converted the old diffusion tensor __setattr__() method into the set()
method.
This is the only way in which diffusion tensor parameters, errors and
simulations can be set.
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r17745 | bugman | 2012-10-08 14:13:34 +0200 (Mon, 08 Oct 2012) | 5 lines
Improvements to the diffusion tensor set() method.
The parameters, errors and simulations are now properly differentiated
and stored.
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r17746 | bugman | 2012-10-08 14:19:03 +0200 (Mon, 08 Oct 2012) | 3 lines
A number of private diffusion tensor objects and methods have switched to
the single leading '_' format.
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r17747 | bugman | 2012-10-08 16:32:48 +0200 (Mon, 08 Oct 2012) | 3 lines
Removed all the unused imports from specific_fns.model_free.main.
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r17748 | bugman | 2012-10-08 17:16:25 +0200 (Mon, 08 Oct 2012) | 5 lines
Redesigned how diffusion tensor simulation structures are handled.
The design is now much cleaner and works with all Python versions.
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r17749 | bugman | 2012-10-08 17:17:08 +0200 (Mon, 08 Oct 2012) | 3 lines
Modified the setUp() method for the diffusion tensor system tests to use
the new design.
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r17750 | bugman | 2012-10-08 17:22:42 +0200 (Mon, 08 Oct 2012) | 3 lines
The model-free specific analysis _disassemble_param_vector() method now
uses the new diffusion tensor design.
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r17751 | bugman | 2012-10-08 17:57:50 +0200 (Mon, 08 Oct 2012) | 3 lines
Fix for the diffusion tensor __deepcopy__() replacement method for the
new design.
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r17752 | bugman | 2012-10-08 18:00:05 +0200 (Mon, 08 Oct 2012) | 6 lines
The setting of list values for the DiffTensorSimList object now works
correctly.
The private _set() method now works correctly by calling the base class
method, and the normal
setting of diffusion tensor simulation values produces a RelaxError.
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r17753 | bugman | 2012-10-08 18:01:36 +0200 (Mon, 08 Oct 2012) | 5 lines
Fix for the Diffusion_tensor.test_copy system test - the simulation
parameters are now read-only.
Instead, the diffusion tensor set() method needs to be called.
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r17754 | bugman | 2012-10-08 18:27:08 +0200 (Mon, 08 Oct 2012) | 3 lines
Converted the diffusion tensor data structure from_xml() method to the
new tensor design.
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r17755 | bugman | 2012-10-08 18:44:12 +0200 (Mon, 08 Oct 2012) | 5 lines
Fix for the diffusion tensor to_xml() method for the new design.
For some reason the methods of the Element class are no longer
blacklisted.
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r17756 | bugman | 2012-10-08 18:46:31 +0200 (Mon, 08 Oct 2012) | 5 lines
Fix for the model-free specific analysis duplicate_data() method for the
new design.
The diffusion tensor __mod_attr__ object is now called _mod_attr.
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r17757 | bugman | 2012-10-08 18:50:29 +0200 (Mon, 08 Oct 2012) | 3 lines
Renamed the diffusion tensor fixed() method to set_fixed() to avoid
clashing with the 'fixed' object.
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r17758 | bugman | 2012-10-08 18:50:46 +0200 (Mon, 08 Oct 2012) | 3 lines
The fix user function now uses the diffusion tensor set_fixed() method.
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r17759 | bugman | 2012-10-08 18:54:29 +0200 (Mon, 08 Oct 2012) | 3 lines
The diffusion tensor bmrb_read() function now uses the set_fixed() method
instead of fixed().
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r17760 | bugman | 2012-10-08 19:00:43 +0200 (Mon, 08 Oct 2012) | 3 lines
Converted the palmer.extract user function to use the new diffusion
tensor design.
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r17761 | bugman | 2012-10-08 19:15:40 +0200 (Mon, 08 Oct 2012) | 5 lines
Fix for the XML output of the diffusion tensor - only the modifiable
parameters are output.
This was the previous behaviour and is needed for the test suite to pass.
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r17762 | bugman | 2012-10-08 19:16:25 +0200 (Mon, 08 Oct 2012) | 5 lines
Fix for the fixing of parameters in the model-free analyses.
The diffusion tensor set_fixed() method is now used.
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r17763 | bugman | 2012-10-08 19:20:38 +0200 (Mon, 08 Oct 2012) | 3 lines
Another fix for the diffusion_tensor.init user function - it was not
completely converted.
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r17764 | bugman | 2012-10-08 19:27:45 +0200 (Mon, 08 Oct 2012) | 3 lines
Fix for the setup of the model-free Monte Carlo simulations for the new
diffusion tensor design.
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r17765 | bugman | 2012-10-08 19:30:25 +0200 (Mon, 08 Oct 2012) | 3 lines
Fix for the setting of the diffusion tensor parameter errors in the
model-free specific analysis code.
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r17766 | bugman | 2012-10-08 19:36:16 +0200 (Mon, 08 Oct 2012) | 3 lines
Another fix for the fold_angles() diffusion tensor function - again an
incomplete design conversion.
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r17767 | bugman | 2012-10-08 19:56:55 +0200 (Mon, 08 Oct 2012) | 3 lines
Fix for the reading of relax 1.2 model-free results files for the
diffusion tensor structure redesign.
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r17768 | bugman | 2012-10-08 20:04:53 +0200 (Mon, 08 Oct 2012) | 3 lines
Fix for the reading of model-free results files from relax 1.2 when
simulation data is missing.
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r17769 | bugman | 2012-10-08 22:21:31 +0200 (Mon, 08 Oct 2012) | 3 lines
Updated all of the diffusion tensor unit tests to the new design.
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[... 496 lines stripped ...]
r17807 - in /branches/cst: ./ auto_analyses/ data/ devel_scripts/ docs/latex/ generic_fns/ generic_fns/structure/ gui/ maths...