Author: bugman
Date: Fri Aug 28 12:18:00 2009
New Revision: 9410
URL: http://svn.gna.org/viewcvs/relax?rev=9410&view=rev
Log:
Merged revisions 9317-9322,9324-9405 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/1.3
........
r9317 | bugman | 2009-08-14 17:23:30 +0200 (Fri, 14 Aug 2009) | 3 lines
Docstring fix for the return_units() method.
........
r9318 | bugman | 2009-08-14 17:28:03 +0200 (Fri, 14 Aug 2009) | 3 lines
Epydoc docstring fixes.
........
r9319 | bugman | 2009-08-14 17:54:39 +0200 (Fri, 14 Aug 2009) | 3 lines
Converted the function into a class object variable.
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r9320 | bugman | 2009-08-14 18:44:39 +0200 (Fri, 14 Aug 2009) | 7 lines
Epydoc docstring improvements/fixes.
The default_value(), return_data_name() and set_doc() method docstrings
have been shifted into the
class variables default_value_doc, return_data_name_doc and set_doc, and
proper epydoc docstrings
for the methods written.
........
r9321 | bugman | 2009-08-14 18:55:04 +0200 (Fri, 14 Aug 2009) | 3 lines
Epydoc docstring fixes for IO.__init__().
........
r9322 | bugman | 2009-08-14 19:06:31 +0200 (Fri, 14 Aug 2009) | 5 lines
Bug fix for the return_data_name() method recently introduced.
This function takes the 'index' keyword argument.
........
r9324 | bugman | 2009-08-18 13:57:40 +0200 (Tue, 18 Aug 2009) | 5 lines
Credited Wikipedia and added the quaternion to rotation matrix equation.
The reason is because Wikipedia looks like it has a mistake!
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r9325 | bugman | 2009-08-18 14:28:08 +0200 (Tue, 18 Aug 2009) | 6 lines
Bug fix for the quaternion_to_R() function.
The Wikipedia page was wrong (or at least misleading). The calculation of
the rotation matrix is
now correct.
........
r9326 | bugman | 2009-08-18 14:30:03 +0200 (Tue, 18 Aug 2009) | 3 lines
Character encoding fix - cannot use umlauts.
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r9327 | bugman | 2009-08-18 14:38:38 +0200 (Tue, 18 Aug 2009) | 3 lines
Fix for the user interface of frame_order.ref_domain().
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r9328 | bugman | 2009-08-18 14:42:41 +0200 (Tue, 18 Aug 2009) | 3 lines
Implemented the back end of the frame_order.ref_domain() user function.
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r9329 | bugman | 2009-08-18 15:00:14 +0200 (Tue, 18 Aug 2009) | 3 lines
The full_in_ref_frame arg is now accepted by __init_iso_cone().
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r9330 | bugman | 2009-08-18 15:00:56 +0200 (Tue, 18 Aug 2009) | 3 lines
Fix for the kron_prod() function, due to the new transpose_14() function.
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r9331 | bugman | 2009-08-18 15:03:43 +0200 (Tue, 18 Aug 2009) | 3 lines
Added checks for the __init_iso_cone() args.
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r9332 | bugman | 2009-08-18 15:17:37 +0200 (Tue, 18 Aug 2009) | 9 lines
Applied the patch to allow compilation on Mac OS X with Python 2.6.
This patch is from Jack Howarth <howarth att bromo dot med dot uc dot edu>,
and was attached to the
post https://mail.gna.org/public/relax-users/2009-08/msg00036.html
(Message-id:
<7f080ed10908180200m27620a30x7dc64731a9e02e87@xxxxxxxxxxxxxx>). The parent
of this thread is
https://mail.gna.org/public/relax-users/2009-08/msg00017.html (Message-id:
<20090816020851.GA29683@xxxxxxxxxxxxxxxx>).
........
r9333 | bugman | 2009-08-18 18:45:44 +0200 (Tue, 18 Aug 2009) | 5 lines
Fix for the kron_prod() function.
The transpose_14() function works on the given matrix and returns None!
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r9334 | bugman | 2009-08-19 10:19:26 +0200 (Wed, 19 Aug 2009) | 3 lines
Fix for the calls to transpose_14(). This operates on the matrix rather
than returning a new one.
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r9335 | bugman | 2009-08-19 10:29:13 +0200 (Wed, 19 Aug 2009) | 3 lines
Added a unit test for the maths_fns.kronecker_product.kron_prod() function.
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r9336 | bugman | 2009-08-19 10:32:35 +0200 (Wed, 19 Aug 2009) | 3 lines
Expanded the test_kron_prod() to check all elements of the matrix.
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r9337 | bugman | 2009-08-19 10:43:51 +0200 (Wed, 19 Aug 2009) | 5 lines
Fix for the test_kron_prod() unit test.
The R2 matrix didn't match the tested real Kronecker product.
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r9338 | bugman | 2009-08-19 10:45:56 +0200 (Wed, 19 Aug 2009) | 6 lines
Bug fix for the kron_prod() function.
The T23 rather than T14 transpose should now be used! And the resultant
matrix is now returned to
the correct, original rank-2 shape.
........
r9339 | bugman | 2009-08-19 14:19:34 +0200 (Wed, 19 Aug 2009) | 7 lines
Fix for the test_opt_constr_newton_gmw_mt_S2_0_970_te_2048_Rex_0_149()
system test.
The 2 different f and g count values on 64-bit GNU/Linux are now checked.
This difference is
present even when the same Python and numpy versions are used, and is
therefore likely to be gcc
or the blas/lapack libraries causing differences.
........
r9340 | bugman | 2009-08-19 15:37:09 +0200 (Wed, 19 Aug 2009) | 10 lines
Replaced all instances of `x` with repr(x).
This was down with the python 2.x to 3.x script with the commands:
2to3 -f repr . -w
2to3 -f repr relax -w
The change is in preparation for Python 3.0, and relax still works with
Python versions 2.4, 2.5,
and 2.6.
........
r9341 | bugman | 2009-08-19 15:48:55 +0200 (Wed, 19 Aug 2009) | 5 lines
Bug fix for the relaxation curve-fitting difference plot script.
The spin_loop blocks were missing colons!
........
r9342 | bugman | 2009-08-19 16:09:33 +0200 (Wed, 19 Aug 2009) | 9 lines
Removed all usages of the has_attr() dictionary method.
This was down with the python 2.x to 3.x script with the commands:
2to3 -f has_key relax . -w
The change is in preparation for Python 3.0, and relax still works with
Python versions 2.4, 2.5,
and 2.6.
........
r9343 | bugman | 2009-08-19 17:18:47 +0200 (Wed, 19 Aug 2009) | 9 lines
Converted all print statements into print() function calls.
This was down with the python 2.x to 3.x script with the commands:
2to3 -w -f print relax .
The change is in preparation for Python 3.0, and relax still works with
Python versions 2.4, 2.5,
and 2.6.
........
r9344 | bugman | 2009-08-19 17:31:11 +0200 (Wed, 19 Aug 2009) | 9 lines
Modified the behaviour of raise statements according to
http://www.python.org/dev/peps/pep-3109/.
This was done with the python 2.x to 3.x script with the commands:
2to3 -w -f raise relax .
The change is in preparation for Python 3.0, and relax still works with
Python versions 2.4, 2.5,
and 2.6.
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r9345 | bugman | 2009-08-19 17:45:24 +0200 (Wed, 19 Aug 2009) | 3 lines
Renamed the pipe.list() user function to pipe.display().
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r9346 | bugman | 2009-08-19 18:47:50 +0200 (Wed, 19 Aug 2009) | 9 lines
The dictionary keys() return value is now converted into a list.
This was done with the python 2.x to 3.x script with the commands:
2to3 -w -f dict relax .
The change is in preparation for Python 3.0, and relax still works with
Python versions 2.4, 2.5,
and 2.6.
........
r9347 | bugman | 2009-08-20 17:48:36 +0200 (Thu, 20 Aug 2009) | 9 lines
The exec statement has been replaced with a call to the exec() function.
This was done with the python 2.x to 3.x script with the commands:
2to3 -w -f exec relax .
The change is in preparation for Python 3.0, and relax still works with
Python versions 2.4, 2.5,
and 2.6.
........
r9348 | bugman | 2009-08-21 10:50:08 +0200 (Fri, 21 Aug 2009) | 18 lines
The execfile statement has been replaced with a call to the exec(compile())
function.
This was done with the python 2.x to 3.x script with the commands:
2to3 -w -f exec relax .
The change is in preparation for Python 3.0, and relax still works with
Python versions 2.4, 2.5,
and 2.6. The syntax has changed from:
execfile(script_file, local)
to:
exec(compile(open(script_file).read(), script_file, 'exec'), local)
Hmmm, not much of a language simplification!
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r9349 | bugman | 2009-08-21 10:54:20 +0200 (Fri, 21 Aug 2009) | 3 lines
Added a text file documenting the changes in preparation for Python 3.x.
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r9350 | bugman | 2009-08-21 12:07:01 +0200 (Fri, 21 Aug 2009) | 16 lines
The Python 2.x idioms have been removed.
This was done with the python 2.x to 3.x script with the commands:
2to3 -w -f exec relax .
The change is in preparation for Python 3.0, and relax still works with
Python versions 2.4, 2.5,
and 2.6.
The changes include:
1) The call to type() has been replaced with isinstance().
2) "while 1" has been replaced with "while True".
3) list sort methods x.sort() have been replaced with a call to
sorted(x).
Booleans are instances of int, so the user function argument unit tests
will be a massive mess!
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r9351 | bugman | 2009-08-21 16:54:29 +0200 (Fri, 21 Aug 2009) | 8 lines
Added a module containing functions for checking user function args.
So far this includes:
check.is_bool()
check.is_int()
check.is_str()
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r9352 | bugman | 2009-08-21 16:55:01 +0200 (Fri, 21 Aug 2009) | 3 lines
Updated the 2to3 checklist for the idioms.
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r9353 | bugman | 2009-08-21 17:23:56 +0200 (Fri, 21 Aug 2009) | 5 lines
Created a base class for the user function classes.
This defines the __init__() method for creating the relax help string.
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r9354 | bugman | 2009-08-21 17:25:00 +0200 (Fri, 21 Aug 2009) | 3 lines
Simplified the sequence user function class by using the check and
base_class modules.
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r9355 | bugman | 2009-08-21 17:45:36 +0200 (Fri, 21 Aug 2009) | 3 lines
Removed the num_types module as this is redundant with the new check module.
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r9356 | bugman | 2009-08-21 18:27:29 +0200 (Fri, 21 Aug 2009) | 3 lines
Added a new error class, RelaxTupleNumError.
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r9357 | bugman | 2009-08-21 18:30:04 +0200 (Fri, 21 Aug 2009) | 3 lines
Added 2 more arg checking functions, is_float() and is_num_tuple().
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r9358 | bugman | 2009-08-21 18:32:25 +0200 (Fri, 21 Aug 2009) | 5 lines
Changed all the default can_be_none keywords to False.
This is so you have to explicitly say if None is allowed, rather than the
other way around.
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r9359 | bugman | 2009-08-21 18:34:29 +0200 (Fri, 21 Aug 2009) | 3 lines
Fixed the calls to checks.is_*().
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r9360 | bugman | 2009-08-21 19:07:56 +0200 (Fri, 21 Aug 2009) | 3 lines
Fixed the capitalisation of the RelaxNoneListStrError error class.
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r9361 | bugman | 2009-08-21 19:12:46 +0200 (Fri, 21 Aug 2009) | 3 lines
Added the is_num_list() function.
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r9362 | bugman | 2009-08-21 19:13:58 +0200 (Fri, 21 Aug 2009) | 3 lines
Created the RelaxNoneListNumError error class.
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r9363 | bugman | 2009-08-21 19:14:49 +0200 (Fri, 21 Aug 2009) | 3 lines
Removed a dead import of num_types.
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r9364 | bugman | 2009-08-21 19:18:32 +0200 (Fri, 21 Aug 2009) | 3 lines
Created the is_str_list() function.
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r9365 | bugman | 2009-08-21 19:22:16 +0200 (Fri, 21 Aug 2009) | 3 lines
Migrated the user function class to the new 'check' and 'base_class'
modules.
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r9366 | bugman | 2009-08-21 19:53:26 +0200 (Fri, 21 Aug 2009) | 3 lines
Bug fix for the is_str_list() function.
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r9367 | bugman | 2009-08-21 19:55:32 +0200 (Fri, 21 Aug 2009) | 3 lines
Missing imports.
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r9368 | bugman | 2009-08-21 20:20:54 +0200 (Fri, 21 Aug 2009) | 3 lines
Added the is_num() function and fixed the other number checking functions.
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r9369 | bugman | 2009-08-21 20:49:59 +0200 (Fri, 21 Aug 2009) | 3 lines
Created the crazy check.is_str_or_num_or_str_num_list() function.
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r9370 | bugman | 2009-08-21 21:07:30 +0200 (Fri, 21 Aug 2009) | 3 lines
Added the RelaxNumStrListNumStrError and RelaxNoneNumStrListNumStrError
error classes.
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r9371 | bugman | 2009-08-21 21:08:00 +0200 (Fri, 21 Aug 2009) | 3 lines
Fixes for the test_set_argfail_param() unit test.
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r9372 | bugman | 2009-08-21 21:09:53 +0200 (Fri, 21 Aug 2009) | 3 lines
Fixes for the test_set_argfail_val() unit test.
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r9373 | bugman | 2009-08-21 21:11:20 +0200 (Fri, 21 Aug 2009) | 3 lines
Removed some unused imports.
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r9374 | bugman | 2009-08-21 21:12:18 +0200 (Fri, 21 Aug 2009) | 3 lines
Added is_str_or_str_list() and fixed the is_str_or_num_or_str_num_list()
function.
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r9375 | bugman | 2009-08-21 21:19:45 +0200 (Fri, 21 Aug 2009) | 3 lines
Migrated a number of user function classes to the new 'check' and
'base_class' modules.
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r9376 | bugman | 2009-08-21 21:28:09 +0200 (Fri, 21 Aug 2009) | 3 lines
Fix for the test_set_argfail_val() unit test.
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r9377 | bugman | 2009-08-24 18:12:32 +0200 (Mon, 24 Aug 2009) | 7 lines
Converted the J(w) mapping sample script to the relax 1.3 design.
The problem of the old 1.2 line code was discovered by Leao Lagarto
<dodgy_spin att yahoo ddot co
dot uk> in the thread starting at
https://mail.gna.org/public/relax-devel/2009-08/msg00004.html
(Message-id: <44680.10570.qm@xxxxxxxxxxxxxxxxxxxxxxxxxxx>).
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r9378 | bugman | 2009-08-24 18:26:03 +0200 (Mon, 24 Aug 2009) | 5 lines
Fix for the is_num() function.
The wrong RelaxErrors were being raised.
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r9379 | bugman | 2009-08-24 19:08:12 +0200 (Mon, 24 Aug 2009) | 3 lines
Added the new function is_int_or_int_list().
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r9380 | bugman | 2009-08-24 19:08:55 +0200 (Mon, 24 Aug 2009) | 3 lines
Bug fixes for the is_num_list() and is_num_tuple() functions.
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r9381 | bugman | 2009-08-24 19:45:16 +0200 (Mon, 24 Aug 2009) | 3 lines
Added a length arg to RelaxListNumError and RelaxListStrError.
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r9382 | bugman | 2009-08-24 19:55:28 +0200 (Mon, 24 Aug 2009) | 3 lines
Added the length arg to RelaxNoneListNumError.
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r9383 | bugman | 2009-08-24 20:14:17 +0200 (Mon, 24 Aug 2009) | 3 lines
Modified is_num_list() to check for empty lists.
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r9384 | bugman | 2009-08-24 20:30:54 +0200 (Mon, 24 Aug 2009) | 3 lines
Cleaned up and simplified all the functions in prompt.check.
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r9385 | bugman | 2009-08-24 20:45:18 +0200 (Mon, 24 Aug 2009) | 3 lines
Created the RelaxNoneStrFileError error class.
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r9386 | bugman | 2009-08-24 21:02:55 +0200 (Mon, 24 Aug 2009) | 3 lines
Created the RelaxNumTupleNumError and RelaxNoneNumTupleNumError error
classes.
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r9387 | bugman | 2009-08-24 21:12:34 +0200 (Mon, 24 Aug 2009) | 5 lines
Migrated many more user function classes to the new 'check' and
'base_class' modules.
All unit tests now pass, but not all user functions use the new modules (to
be done later).
........
r9388 | bugman | 2009-08-26 10:56:29 +0200 (Wed, 26 Aug 2009) | 5 lines
The is_str_or_inst() function now checks for the DummyFileObject object as
well.
This fixes a system test.
........
r9389 | bugman | 2009-08-26 10:57:24 +0200 (Wed, 26 Aug 2009) | 5 lines
Fix for the spin.number() user function.
The number can be None to reset the values. This is used in a system test.
........
r9390 | bugman | 2009-08-26 11:12:43 +0200 (Wed, 26 Aug 2009) | 3 lines
Created the RelaxNoneStrListNumError error class.
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r9391 | bugman | 2009-08-26 11:17:47 +0200 (Wed, 26 Aug 2009) | 3 lines
Created the RelaxStrListNumError error class.
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r9392 | bugman | 2009-08-26 11:21:42 +0200 (Wed, 26 Aug 2009) | 5 lines
Wrote the is_str_or_num_list() argument checking function.
This is for arguments that can be a string or list of numbers.
........
r9393 | bugman | 2009-08-26 11:26:41 +0200 (Wed, 26 Aug 2009) | 3 lines
Wrote 5 arg unit tests for the pymol.macro_exec() user function.
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r9394 | bugman | 2009-08-26 11:28:13 +0200 (Wed, 26 Aug 2009) | 3 lines
Wrote 5 arg unit tests for the molmol.macro_exec() user function.
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r9395 | bugman | 2009-08-26 14:10:22 +0200 (Wed, 26 Aug 2009) | 3 lines
Created the RelaxNoneFunctionError error class.
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r9396 | bugman | 2009-08-26 15:32:27 +0200 (Wed, 26 Aug 2009) | 3 lines
Added the is_func() function.
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r9397 | bugman | 2009-08-26 15:44:06 +0200 (Wed, 26 Aug 2009) | 3 lines
All the user function classes have now been migrated to use the new 'check'
and 'base_class' modules.
........
r9398 | bugman | 2009-08-26 15:50:07 +0200 (Wed, 26 Aug 2009) | 3 lines
Created the Basic_class for simplifying all non-user function classes.
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r9399 | bugman | 2009-08-26 17:13:37 +0200 (Wed, 26 Aug 2009) | 3 lines
Added the is_tuple() function.
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r9400 | bugman | 2009-08-26 17:15:28 +0200 (Wed, 26 Aug 2009) | 3 lines
Fixes for the eliminate arg unit tests.
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r9401 | bugman | 2009-08-26 17:35:24 +0200 (Wed, 26 Aug 2009) | 3 lines
All the non user function classes have now been migrated to use the new
'check' and 'base_class' modules.
........
r9402 | bugman | 2009-08-26 17:38:14 +0200 (Wed, 26 Aug 2009) | 3 lines
Removed a number of now unused RelaxError imports.
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r9403 | bugman | 2009-08-26 19:28:33 +0200 (Wed, 26 Aug 2009) | 6 lines
The argument RelaxError classes have been put into relative order compared
to the previous chaos.
The RelaxNone* classes are now directly under the equivalent non-None
class, and the simple types,
lists, tuples, and mixed classes separated into subcategories.
........
r9404 | bugman | 2009-08-28 10:51:22 +0200 (Fri, 28 Aug 2009) | 3 lines
Started to redesign to simplify the argument RelaxError classes.
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r9405 | bugman | 2009-08-28 11:12:43 +0200 (Fri, 28 Aug 2009) | 3 lines
Simplified all the argument RelaxError classes using BaseArgError.
........
Added:
branches/multi_processor_merge/docs/2to3_checklist
- copied unchanged from r9405, 1.3/docs/2to3_checklist
branches/multi_processor_merge/prompt/base_class.py
- copied unchanged from r9405, 1.3/prompt/base_class.py
branches/multi_processor_merge/prompt/check.py
- copied unchanged from r9405, 1.3/prompt/check.py
branches/multi_processor_merge/test_suite/unit_tests/_prompt/test_molmol.py
- copied unchanged from r9405,
1.3/test_suite/unit_tests/_prompt/test_molmol.py
branches/multi_processor_merge/test_suite/unit_tests/_prompt/test_pymol.py
- copied unchanged from r9405,
1.3/test_suite/unit_tests/_prompt/test_pymol.py
Removed:
branches/multi_processor_merge/prompt/num_types.py
Modified:
branches/multi_processor_merge/ (props changed)
branches/multi_processor_merge/colour.py
branches/multi_processor_merge/data/__init__.py
branches/multi_processor_merge/data/align_tensor.py
branches/multi_processor_merge/data/data_classes.py
branches/multi_processor_merge/data/diff_tensor.py
branches/multi_processor_merge/data/mol_res_spin.py
branches/multi_processor_merge/data/pipe_container.py
branches/multi_processor_merge/data/prototype.py
branches/multi_processor_merge/data/relax_xml.py
branches/multi_processor_merge/docs/latex/fetch_docstrings.py
branches/multi_processor_merge/float.py
branches/multi_processor_merge/generic_fns/align_tensor.py
branches/multi_processor_merge/generic_fns/angles.py
branches/multi_processor_merge/generic_fns/dasha.py
branches/multi_processor_merge/generic_fns/diffusion_tensor.py
branches/multi_processor_merge/generic_fns/eliminate.py
branches/multi_processor_merge/generic_fns/fix.py
branches/multi_processor_merge/generic_fns/frame_order.py
branches/multi_processor_merge/generic_fns/frq.py
branches/multi_processor_merge/generic_fns/grace.py
branches/multi_processor_merge/generic_fns/minimise.py
branches/multi_processor_merge/generic_fns/model_selection.py
branches/multi_processor_merge/generic_fns/mol_res_spin.py
[... 659 lines stripped ...]
r9410 - in /branches/multi_processor_merge: ./ data/ docs/ docs/latex/ generic_fns/ generic_fns/structure/ maths_fns/ opendx...