Author: bugman
Date: Tue Feb 23 19:27:22 2010
New Revision: 10873
URL: http://svn.gna.org/viewcvs/relax?rev=10873&view=rev
Log:
Merged revisions
10117,10157,10178-10188,10197,10204-10205,10240,10242-10245,10267,10296-10302,10304-10326,10330,10404,10431-10435,10443,10450,10461-10462,10611-10612,10626-10631,10645,10652,10668-10671,10674,10676,10680,10684,10688-10689,10691,10694,10699,10703-10704,10708-10754,10766-10789,10794-10829,10838,10841-10842,10845-10860,10862,10865
via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/1.3
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r10117 | bugman | 2010-01-06 18:57:55 +0100 (Wed, 06 Jan 2010) | 6 lines
Modified the IO redirection methods.
The original IO streams are stored and then restore instead of
sys.__stdout__ and sys.__stderr__.
This might help in the multi-processor branch where IO redirection has gone
haywire.
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r10157 | bugman | 2010-01-08 10:57:41 +0100 (Fri, 08 Jan 2010) | 6 lines
Big bug fix for the model-free grid search!!!
The lower and upper bounds were being scaled iteratively for each spin
causing the values to be
ridiculously bigger and bigger. This caused a total failure of the grid
search.
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r10178 | bugman | 2010-01-12 13:20:36 +0100 (Tue, 12 Jan 2010) | 3 lines
Modified the import of euler_zyz_to_R to allow easy switching later on to a
different notation.
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r10179 | bugman | 2010-01-12 13:21:01 +0100 (Tue, 12 Jan 2010) | 3 lines
Copyright notice update.
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r10180 | bugman | 2010-01-12 13:32:12 +0100 (Tue, 12 Jan 2010) | 3 lines
Renamed all euler_ijk_to_R() functions to euler_to_R_ijk().
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r10181 | bugman | 2010-01-12 13:35:04 +0100 (Tue, 12 Jan 2010) | 3 lines
Ordered the euler angle conversion functions.
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r10182 | bugman | 2010-01-12 13:40:33 +0100 (Tue, 12 Jan 2010) | 3 lines
Fixes for all the euler angle to rotation matrix unit tests.
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r10183 | bugman | 2010-01-12 13:42:00 +0100 (Tue, 12 Jan 2010) | 3 lines
Fix for reverse_euler_zyz() due to the function renaming.
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r10184 | bugman | 2010-01-12 14:22:09 +0100 (Tue, 12 Jan 2010) | 3 lines
Created a unit test to check all hard-coded conversion functions for all 12
static axis rotations.
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r10185 | bugman | 2010-01-12 14:22:52 +0100 (Tue, 12 Jan 2010) | 3 lines
Fix for the euler_to_axis_angle_xzx() function.
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r10186 | bugman | 2010-01-12 15:10:54 +0100 (Tue, 12 Jan 2010) | 5 lines
Improvements to the test_euler_cycle_1() unit test.
This includes verbose printing of data structures and checking of the
rotation matrix at each cycle.
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r10187 | bugman | 2010-01-12 15:36:01 +0100 (Tue, 12 Jan 2010) | 5 lines
Added 12 unit tests for all notations of R -> Euler -> R.
This uses a random rotation matrix and sees if the matrix is returned.
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r10188 | bugman | 2010-01-12 15:39:31 +0100 (Tue, 12 Jan 2010) | 6 lines
Important bug fix for the R_to_euler() function.
The special angle wrapping when beta was negative is only for the ijk Euler
notation when i == k!
When i != k, another type of wrapping will be required.
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r10197 | bugman | 2010-01-13 15:15:37 +0100 (Wed, 13 Jan 2010) | 3 lines
Removed the alpha Euler angle from the isotropic code frame order model.
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r10204 | bugman | 2010-01-13 17:33:24 +0100 (Wed, 13 Jan 2010) | 5 lines
Bug fix for the frame order isotropic cone target function.
The optimised rotation matrix for the alignment tensor orientations was
being applied in reverse!!!
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r10205 | bugman | 2010-01-13 19:21:19 +0100 (Wed, 13 Jan 2010) | 6 lines
Reverted r10204 as this was a not a bug and the revision introduced a bug!!!
The command used was:
svn merge -r10204:10203 .
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r10240 | bugman | 2010-01-15 15:35:22 +0100 (Fri, 15 Jan 2010) | 5 lines
Bug fixes for the code validator script.
The 4 character spacing check was faulty.
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r10242 | bugman | 2010-01-18 17:15:33 +0100 (Mon, 18 Jan 2010) | 5 lines
Shifted the target function initialisation into _target_fn_setup().
This will be shared by the calculate() method.
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r10243 | bugman | 2010-01-18 17:20:45 +0100 (Mon, 18 Jan 2010) | 3 lines
The calculate() method now uses _target_fn_setup() and stores the chi2 in
the cdp.
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r10244 | bugman | 2010-01-18 17:34:19 +0100 (Mon, 18 Jan 2010) | 3 lines
The number of elements in the atomic position arg is now checked to be 3.
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r10245 | bugman | 2010-01-18 18:07:36 +0100 (Mon, 18 Jan 2010) | 5 lines
Removed the print out from _overfit_deselect_dummy().
This was totally unnecessary!
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r10267 | bugman | 2010-01-20 12:01:00 +0100 (Wed, 20 Jan 2010) | 3 lines
Removed the beta angle folding from the frame order module as it was
failing.
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r10296 | bugman | 2010-01-25 11:13:06 +0100 (Mon, 25 Jan 2010) | 14 lines
Spun out the automatic model-free protocol code from the full_analysis.py
script.
This is discussed in the post
https://mail.gna.org/public/relax-devel/2010-01/msg00075.html.
The aim is to have a single code base for the automatic protocols for all
UI designs (prompt,
script, GUI, web interface, etc.). The API interface will be via class
initialisations. The
automatic model-free protocol has been placed into the dAuvergne_protocol
class.
Future aims of this code is to have the UI fill a single data pipe with all
the data required for
the analysis, and then to pass in this pipe into the protocol. Then the
auto-analysis will copy
this info into any other data pipes it requires. This will allow for
better GUI interaction, data
display, etc.
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r10297 | bugman | 2010-01-25 11:33:22 +0100 (Mon, 25 Jan 2010) | 3 lines
Removed all the now unused imports and a useless comment.
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r10298 | bugman | 2010-01-25 11:34:54 +0100 (Mon, 25 Jan 2010) | 3 lines
Updated the copyright notice.
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r10299 | bugman | 2010-01-25 11:37:25 +0100 (Mon, 25 Jan 2010) | 3 lines
Fixed the import of the dAuvergne_protocol class.
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r10300 | bugman | 2010-01-25 12:13:59 +0100 (Mon, 25 Jan 2010) | 3 lines
Modifications to the phthalic_acid_noes.py system test script to allow for
standalone operation.
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r10301 | bugman | 2010-01-25 12:40:54 +0100 (Mon, 25 Jan 2010) | 5 lines
Fixes for the N-state model for when only NOEs are present.
This fixes a bug introduced at r10243.
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r10302 | bugman | 2010-01-25 12:54:34 +0100 (Mon, 25 Jan 2010) | 5 lines
Bug fix for the bug fix of r10301!
The bug fix actually introduced a bug, and this commit fixes that!
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r10304 | bugman | 2010-01-25 14:25:32 +0100 (Mon, 25 Jan 2010) | 11 lines
Redesign of the setup of the names spaces for the user functions.
All the user functions and other objects located in the run() method
namespace have been shifted
into the interpreter self._locals dictionary. These are then placed into
the run() method namespace
by looping over the keys and using the 'locals()[key] = object' syntax.
There may be better ways to
do this.
This has no visible effect on the prompt or script based interfaces. It
will change how this is
seen by other modules though, and will allow the namespace to be more
easily accessed.
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r10305 | bugman | 2010-01-25 14:26:57 +0100 (Mon, 25 Jan 2010) | 3 lines
Removed some unused and commented out code.
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r10306 | bugman | 2010-01-25 14:31:09 +0100 (Mon, 25 Jan 2010) | 5 lines
Eliminated the dummy mode.
This is only used by the fetch_docstrings script and will soon not be
necessary.
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r10307 | bugman | 2010-01-25 15:55:49 +0100 (Mon, 25 Jan 2010) | 7 lines
The relax base object is no longer passed into the class namespace of the
user functions.
This was only being used for access to the intro flag (a few other cases
exist, but these should be
fixed). Now a new container object with this flag is being passed in.
This significantly
simplifies the code paths and removes the need for the test suite to create
'fake' relax instances.
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r10308 | bugman | 2010-01-25 16:08:41 +0100 (Mon, 25 Jan 2010) | 7 lines
Modified how the Exec_info data container is handled.
The class was shifted from prompt.interpreter to prompt.base_class. In
addition if not container
is passed into the user function classes, then one is created with the
intro flag set to a default
of True.
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r10309 | bugman | 2010-01-25 16:34:44 +0100 (Mon, 25 Jan 2010) | 8 lines
The prompt info has been shifted into the execution info container.
The sys.ps1, sys.ps2, and sys.ps3 prompts are still set, but these strings
are hardcoded into the
execution info container. This allows the user functions to be imported
and operate outside of the
prompt/scripting based interface, as the no longer require sys.ps3 to be
set or the relax main
instance passed into them.
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r10310 | bugman | 2010-01-25 16:39:34 +0100 (Mon, 25 Jan 2010) | 5 lines
Eliminated the fake_relax instance dependence.
This is no longer necessary as the user functions can be initialised
without relax.
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r10311 | bugman | 2010-01-25 16:53:14 +0100 (Mon, 25 Jan 2010) | 3 lines
Created the populate_self() method to place all user functions into the
interpreter namespace.
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r10312 | bugman | 2010-01-25 16:58:57 +0100 (Mon, 25 Jan 2010) | 5 lines
The relax main instance is no longer passed into the test suite.
This can be done as the prompt/script interface has been detached from
relax.
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r10313 | bugman | 2010-01-25 17:00:12 +0100 (Mon, 25 Jan 2010) | 5 lines
The relax main instance is no longer passed into the prompt/script
interface.
This can be done as the prompt/script interface has been detached from
relax.
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r10314 | bugman | 2010-01-25 17:06:28 +0100 (Mon, 25 Jan 2010) | 3 lines
The relax main instance is no longer handled by the system test
initialisation code.
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r10315 | bugman | 2010-01-25 18:04:17 +0100 (Mon, 25 Jan 2010) | 5 lines
Created the SystemTestCase base class for all the system tests to use.
This base class initialises the relax interpreter within the TestCase class
instances.
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r10316 | bugman | 2010-01-25 18:13:12 +0100 (Mon, 25 Jan 2010) | 3 lines
The interpreter _on() method does not need to be called as user fn intros
are turned on by default.
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r10317 | bugman | 2010-01-25 18:52:04 +0100 (Mon, 25 Jan 2010) | 5 lines
Fixed all the calls to the user functions located in the interpreter class.
self.relax is no longer referenced and the user functions are now directly
called.
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r10318 | bugman | 2010-01-25 18:52:38 +0100 (Mon, 25 Jan 2010) | 3 lines
Fixed the script user function.
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r10319 | bugman | 2010-01-25 18:54:20 +0100 (Mon, 25 Jan 2010) | 3 lines
Removed redundant and now non-functional code from interact_script().
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r10320 | bugman | 2010-01-25 19:04:45 +0100 (Mon, 25 Jan 2010) | 3 lines
Comment fix.
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r10321 | bugman | 2010-01-25 19:11:25 +0100 (Mon, 25 Jan 2010) | 6 lines
Update the user function print out functions.
_off() and _on() are no longer private, and accept the verbose keyword arg
to allow the print out to
be suppressed.
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r10322 | bugman | 2010-01-25 19:11:59 +0100 (Mon, 25 Jan 2010) | 3 lines
Alphabetical ordering of methods.
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r10323 | bugman | 2010-01-25 19:21:05 +0100 (Mon, 25 Jan 2010) | 3 lines
The dAuvergne_protocol class now calls the user functions from the
self.interpreter instance directly.
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r10324 | bugman | 2010-01-25 19:26:36 +0100 (Mon, 25 Jan 2010) | 5 lines
Fix for the automatic model-free protocol in dAuvergne_protocol.
The sequence.read() and relax_data.read() user functions args are now sent
in as keywords.
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r10325 | bugman | 2010-01-25 20:31:25 +0100 (Mon, 25 Jan 2010) | 3 lines
Created the RelaxFileEmptyWarning class.
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r10326 | bugman | 2010-01-25 20:36:30 +0100 (Mon, 25 Jan 2010) | 3 lines
Modified read_spin_data() to throw a warning rather than error when an
empty file is encountered.
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r10330 | bugman | 2010-01-25 21:01:23 +0100 (Mon, 25 Jan 2010) | 3 lines
As a precaution, the spins will always be named in the automatic model-free
protocol.
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r10404 | bugman | 2010-01-26 18:38:14 +0100 (Tue, 26 Jan 2010) | 3 lines
The generic_fns.state.save_state() pickle arg now defaults to False.
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r10431 | bugman | 2010-01-27 12:54:10 +0100 (Wed, 27 Jan 2010) | 7 lines
Epydoc is now documenting everything!
The whitelist system of selected what to document was not working! Too
many packages are changing,
especially in the branches. Therefore absolutely everything is now being
documented, including the
test suite. This will allow all new packages to be automatically
documented.
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r10432 | bugman | 2010-01-27 13:01:21 +0100 (Wed, 27 Jan 2010) | 3 lines
Epydoc fixes for the dauvergne_protocol module docstring.
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r10433 | bugman | 2010-01-27 13:32:04 +0100 (Wed, 27 Jan 2010) | 3 lines
Epydoc fixes throughout the 'data' package.
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r10434 | bugman | 2010-01-27 13:33:11 +0100 (Wed, 27 Jan 2010) | 3 lines
Epydoc fixes for the 'opendx' package.
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r10435 | bugman | 2010-01-27 13:42:02 +0100 (Wed, 27 Jan 2010) | 3 lines
Epydoc fixes throughout the test suite.
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r10443 | bugman | 2010-01-27 17:22:00 +0100 (Wed, 27 Jan 2010) | 3 lines
The generic_fns.state.save_state() function can now have the verbosity
level changed.
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r10450 | bugman | 2010-01-27 18:24:53 +0100 (Wed, 27 Jan 2010) | 5 lines
Variable name fix for the from_xml() method.
relax_node should have been called pipe_node!
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r10461 | bugman | 2010-01-28 09:37:58 +0100 (Thu, 28 Jan 2010) | 3 lines
The generic_fns.state.load_state() function can now have the verbosity
level changed.
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r10462 | bugman | 2010-01-28 09:38:30 +0100 (Thu, 28 Jan 2010) | 3 lines
Epydoc fix for generic_fns.state.save_state(). Verbosity is a keyword arg!
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r10611 | bugman | 2010-02-01 23:36:57 +0100 (Mon, 01 Feb 2010) | 5 lines
Bug fix for the running of the test suite.
The interpreter _on() and _off() methods are now called on() and off()!
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r10612 | bugman | 2010-02-02 00:19:55 +0100 (Tue, 02 Feb 2010) | 3 lines
Switched from using a cone angle to using an order parameter in the
isotropic cone frame order model.
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r10626 | bugman | 2010-02-03 11:22:00 +0100 (Wed, 03 Feb 2010) | 5 lines
Added the stub function
maths_fns.order_parameters.iso_cone_S_to_cos_theta().
This will be used to convert the order parameter S into the cosine of the
cone angle.
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r10627 | bugman | 2010-02-03 18:00:17 +0100 (Wed, 03 Feb 2010) | 16 lines
Redesigned get_intro_string() to return a container of different strings.
The method is now called get_intro_text() and returns a container with the
following str objects:
- title: The program title 'relax'
- version: For example 'repository checkout' or '1.3.8'.
- desc: The short program description.
- copyright: A list of copyright statements.
- licence: Text pertaining to the licencing.
- errors: A list of import errors.
This is being abstracted so that the different UIs can use this
differently. The prompt/script can
word wrap to 100 char (80 char in Windows), and print this to stdout. The
GUI can use this in the
about prompt and not print to stdout. Other interfaces can use this in any
other way. And the
information content can be expanded for different purposes.
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r10628 | bugman | 2010-02-03 18:09:01 +0100 (Wed, 03 Feb 2010) | 6 lines
Shifted the introductory text object into its own module.
This makes the use of this object more flexible as anything and any part of
the program can import
it.
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r10629 | bugman | 2010-02-03 18:15:59 +0100 (Wed, 03 Feb 2010) | 5 lines
Shifted the spacing() method from relax to the intro module and renamed it
to centre().
The docstring has also been expanded to include epydoc tags.
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r10630 | bugman | 2010-02-03 18:26:28 +0100 (Wed, 03 Feb 2010) | 6 lines
The introductory text for the prompt/script based interface is now
recreated.
The _build_intro_text() method has been added to replicate the formatting
of the deleted
get_intro_text() method of the main relax class. This formatting is only
to be used in these 2 UIs.
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r10631 | bugman | 2010-02-03 18:28:49 +0100 (Wed, 03 Feb 2010) | 7 lines
Changed the program description again.
The program is now described as "Molecular dynamics by NMR data analysis".
This takes into account
that this is for proteins, RNA, DNA, organic molecules, sugars, etc., and
for relaxation data, RDCs,
PCSs, NOEs, and all NMR data.
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r10645 | bugman | 2010-02-04 17:33:24 +0100 (Thu, 04 Feb 2010) | 3 lines
Added the website and a long description to the Intro_text container.
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r10652 | bugman | 2010-02-04 18:31:37 +0100 (Thu, 04 Feb 2010) | 7 lines
Better UI separation in the Intro_text descriptions.
The 'help' assistance message has been shifted directly into
prompt.interpreter as it is only part
of the prompt/script interface. The GPL message has been changed to
specify that it is at the
prompt that you type GPL.
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r10668 | bugman | 2010-02-05 17:54:15 +0100 (Fri, 05 Feb 2010) | 5 lines
Renamed the intro.Intro_text class to info.Info_box.
This is used for introduction strings, but can be used at any point in
relax as well.
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r10669 | bugman | 2010-02-05 18:14:30 +0100 (Fri, 05 Feb 2010) | 3 lines
Updated the d'Auvergne and Gooley, 2008 references to have the full medline
info.
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r10670 | bugman | 2010-02-05 19:56:18 +0100 (Fri, 05 Feb 2010) | 3 lines
Fixes for the d'Auvergne and Gooley, 2008 references.
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r10671 | bugman | 2010-02-05 19:58:02 +0100 (Fri, 05 Feb 2010) | 5 lines
References pertaining to relax have been added to the info box container.
Each reference is a container placed within the 'bib' dictionary of the
info box class.
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r10674 | bugman | 2010-02-06 01:15:52 +0100 (Sat, 06 Feb 2010) | 3 lines
Created the reference base class 'Ref' and added cite_short() to build a
short citation.
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r10676 | bugman | 2010-02-06 01:34:06 +0100 (Sat, 06 Feb 2010) | 3 lines
Fixes for some journal titles. Periods have been added.
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r10680 | bugman | 2010-02-06 02:16:35 +0100 (Sat, 06 Feb 2010) | 6 lines
Created the module for the automatic relaxation curve fitting protocol.
This should better help define the API interface between the UIs and the
core, allowing all UIs to
benefit from advances in this code base.
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r10684 | bugman | 2010-02-06 02:52:44 +0100 (Sat, 06 Feb 2010) | 5 lines
A couple of fixes for the Relax_fit auto analysis class.
The interpreter was not being imported and a class variable was missing the
'self.' part!
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r10688 | bugman | 2010-02-09 11:36:44 +0100 (Tue, 09 Feb 2010) | 5 lines
Added support for using Me pseudo-atom RDCs.
This follows the method of Verdier, et al., JMR, 2003, 163, 353-359.
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r10689 | bugman | 2010-02-11 14:26:13 +0100 (Thu, 11 Feb 2010) | 3 lines
Added the cite_html() method to the citation base class to produce a HTML
formatted citation.
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r10691 | bugman | 2010-02-11 15:03:14 +0100 (Thu, 11 Feb 2010) | 5 lines
Fix for the cite_html() method.
The hyperlinks were incorrectly formed.
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r10694 | bugman | 2010-02-12 10:50:17 +0100 (Fri, 12 Feb 2010) | 5 lines
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r10873 - in /branches/cst: ./ auto_analyses/ data/ docs/latex/ generic_fns/ maths_fns/ opendx/ prompt/ sample_scripts/ scons...