relax SVN archive

Merged revisions 9314-9407 via svnmerge from
svn+ssh://bugman@.../svn/relax/1.3

........
r9314 | bugman | 2009-08-14 11:44:34 +0200 (Fri, 14 Aug 2009) | 6 lines

Merged the relax 1.3.4 CHANGES file into the 1.3 line.

The command used was:
svn merge -r9296:9297 svn+ssh://bugman@.../svn/relax/tags/1.3.4 .
........
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.
........
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!
........
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.
........
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().
........
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.
........
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().
........
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.
........
r9331 | bugman | 2009-08-18 15:03:43 +0200 (Tue, 18 Aug 2009) | 3 lines

Added checks for the __init_iso_cone() args.
........
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@...>). The parent of this thread is
https://mail.gna.org/public/relax-users/2009-08/msg00017.html (Message-id:
<20090816020851.GA29683@...>).
........
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!
........
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.
........
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.
........
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.
........
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.
........
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.
........
r9345 | bugman | 2009-08-19 17:45:24 +0200 (Wed, 19 Aug 2009) | 3 lines

Renamed the pipe.list() user function to pipe.display().
........
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!
........
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.
........
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!
........
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()
........
r9352 | bugman | 2009-08-21 16:55:01 +0200 (Fri, 21 Aug 2009) | 3 lines

Updated the 2to3 checklist for the idioms.
........
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.
........
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.
........
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.
........
r9356 | bugman | 2009-08-21 18:27:29 +0200 (Fri, 21 Aug 2009) | 3 lines

Added a new error class, RelaxTupleNumError.
........
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().
........
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.
........
r9359 | bugman | 2009-08-21 18:34:29 +0200 (Fri, 21 Aug 2009) | 3 lines

Fixed the calls to checks.is_*().
........
r9360 | bugman | 2009-08-21 19:07:56 +0200 (Fri, 21 Aug 2009) | 3 lines

Fixed the capitalisation of the RelaxNoneListStrError error class.
........
r9361 | bugman | 2009-08-21 19:12:46 +0200 (Fri, 21 Aug 2009) | 3 lines

Added the is_num_list() function.
........
r9362 | bugman | 2009-08-21 19:13:58 +0200 (Fri, 21 Aug 2009) | 3 lines

Created the RelaxNoneListNumError error class.
........
r9363 | bugman | 2009-08-21 19:14:49 +0200 (Fri, 21 Aug 2009) | 3 lines

Removed a dead import of num_types.
........
r9364 | bugman | 2009-08-21 19:18:32 +0200 (Fri, 21 Aug 2009) | 3 lines

Created the is_str_list() function.
........
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.
........
r9366 | bugman | 2009-08-21 19:53:26 +0200 (Fri, 21 Aug 2009) | 3 lines

Bug fix for the is_str_list() function.
........
r9367 | bugman | 2009-08-21 19:55:32 +0200 (Fri, 21 Aug 2009) | 3 lines

Missing imports.
........
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.
........
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.
........
r9370 | bugman | 2009-08-21 21:07:30 +0200 (Fri, 21 Aug 2009) | 3 lines

Added the RelaxNumStrListNumStrError and RelaxNoneNumStrListNumStrError error classes.
........
r9371 | bugman | 2009-08-21 21:08:00 +0200 (Fri, 21 Aug 2009) | 3 lines

Fixes for the test_set_argfail_param() unit test.
........
r9372 | bugman | 2009-08-21 21:09:53 +0200 (Fri, 21 Aug 2009) | 3 lines

Fixes for the test_set_argfail_val() unit test.
........
r9373 | bugman | 2009-08-21 21:11:20 +0200 (Fri, 21 Aug 2009) | 3 lines

Removed some unused imports.
........
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.
........
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.
........
r9376 | bugman | 2009-08-21 21:28:09 +0200 (Fri, 21 Aug 2009) | 3 lines

Fix for the test_set_argfail_val() unit test.
........
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@...>).
........
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.
........
r9379 | bugman | 2009-08-24 19:08:12 +0200 (Mon, 24 Aug 2009) | 3 lines

Added the new function is_int_or_int_list().
........
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.
........
r9381 | bugman | 2009-08-24 19:45:16 +0200 (Mon, 24 Aug 2009) | 3 lines

Added a length arg to RelaxListNumError and RelaxListStrError.
........
r9382 | bugman | 2009-08-24 19:55:28 +0200 (Mon, 24 Aug 2009) | 3 lines

Added the length arg to RelaxNoneListNumError.
........
r9383 | bugman | 2009-08-24 20:14:17 +0200 (Mon, 24 Aug 2009) | 3 lines

Modified is_num_list() to check for empty lists.
........
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.
........
r9385 | bugman | 2009-08-24 20:45:18 +0200 (Mon, 24 Aug 2009) | 3 lines

Created the RelaxNoneStrFileError error class.
........
r9386 | bugman | 2009-08-24 21:02:55 +0200 (Mon, 24 Aug 2009) | 3 lines

Created the RelaxNumTupleNumError and RelaxNoneNumTupleNumError error classes.
........
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.
........
r9391 | bugman | 2009-08-26 11:17:47 +0200 (Wed, 26 Aug 2009) | 3 lines

Created the RelaxStrListNumError error class.
........
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.
........
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.
........
r9395 | bugman | 2009-08-26 14:10:22 +0200 (Wed, 26 Aug 2009) | 3 lines

Created the RelaxNoneFunctionError error class.
........
r9396 | bugman | 2009-08-26 15:32:27 +0200 (Wed, 26 Aug 2009) | 3 lines

Added the is_func() function.
........
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.
........
r9399 | bugman | 2009-08-26 17:13:37 +0200 (Wed, 26 Aug 2009) | 3 lines

Added the is_tuple() function.
........
r9400 | bugman | 2009-08-26 17:15:28 +0200 (Wed, 26 Aug 2009) | 3 lines

Fixes for the eliminate arg unit tests.
........
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.
........
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.
........
r9405 | bugman | 2009-08-28 11:12:43 +0200 (Fri, 28 Aug 2009) | 3 lines

Simplified all the argument RelaxError classes using BaseArgError.
........

Docstring fix.

Merged revisions 9313-9405 via svnmerge from
svn+ssh://bugman@.../svn/relax/1.3

........
r9314 | bugman | 2009-08-14 11:44:34 +0200 (Fri, 14 Aug 2009) | 6 lines

Merged the relax 1.3.4 CHANGES file into the 1.3 line.

The command used was:
svn merge -r9296:9297 svn+ssh://bugman@.../svn/relax/tags/1.3.4 .
........
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.
........
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!
........
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.
........
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().
........
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.
........
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().
........
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.
........
r9331 | bugman | 2009-08-18 15:03:43 +0200 (Tue, 18 Aug 2009) | 3 lines

Added checks for the __init_iso_cone() args.
........
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@...>). The parent of this thread is
https://mail.gna.org/public/relax-users/2009-08/msg00017.html (Message-id:
<20090816020851.GA29683@...>).
........
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!
........
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.
........
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.
........
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.
........
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.
........
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.
........
r9345 | bugman | 2009-08-19 17:45:24 +0200 (Wed, 19 Aug 2009) | 3 lines

Renamed the pipe.list() user function to pipe.display().
........
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!
........
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.
........
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!
........
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()
........
r9352 | bugman | 2009-08-21 16:55:01 +0200 (Fri, 21 Aug 2009) | 3 lines

Updated the 2to3 checklist for the idioms.
........
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.
........
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.
........
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.
........
r9356 | bugman | 2009-08-21 18:27:29 +0200 (Fri, 21 Aug 2009) | 3 lines

Added a new error class, RelaxTupleNumError.
........
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().
........
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.
........
r9359 | bugman | 2009-08-21 18:34:29 +0200 (Fri, 21 Aug 2009) | 3 lines

Fixed the calls to checks.is_*().
........
r9360 | bugman | 2009-08-21 19:07:56 +0200 (Fri, 21 Aug 2009) | 3 lines

Fixed the capitalisation of the RelaxNoneListStrError error class.
........
r9361 | bugman | 2009-08-21 19:12:46 +0200 (Fri, 21 Aug 2009) | 3 lines

Added the is_num_list() function.
........
r9362 | bugman | 2009-08-21 19:13:58 +0200 (Fri, 21 Aug 2009) | 3 lines

Created the RelaxNoneListNumError error class.
........
r9363 | bugman | 2009-08-21 19:14:49 +0200 (Fri, 21 Aug 2009) | 3 lines

Removed a dead import of num_types.
........
r9364 | bugman | 2009-08-21 19:18:32 +0200 (Fri, 21 Aug 2009) | 3 lines

Created the is_str_list() function.
........
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.
........
r9366 | bugman | 2009-08-21 19:53:26 +0200 (Fri, 21 Aug 2009) | 3 lines

Bug fix for the is_str_list() function.
........
r9367 | bugman | 2009-08-21 19:55:32 +0200 (Fri, 21 Aug 2009) | 3 lines

Missing imports.
........
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.
........
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.
........
r9370 | bugman | 2009-08-21 21:07:30 +0200 (Fri, 21 Aug 2009) | 3 lines

Added the RelaxNumStrListNumStrError and RelaxNoneNumStrListNumStrError error classes.
........
r9371 | bugman | 2009-08-21 21:08:00 +0200 (Fri, 21 Aug 2009) | 3 lines

Fixes for the test_set_argfail_param() unit test.
........
r9372 | bugman | 2009-08-21 21:09:53 +0200 (Fri, 21 Aug 2009) | 3 lines

Fixes for the test_set_argfail_val() unit test.
........
r9373 | bugman | 2009-08-21 21:11:20 +0200 (Fri, 21 Aug 2009) | 3 lines

Removed some unused imports.
........
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.
........
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.
........
r9376 | bugman | 2009-08-21 21:28:09 +0200 (Fri, 21 Aug 2009) | 3 lines

Fix for the test_set_argfail_val() unit test.
........
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@...>).
........
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.
........
r9379 | bugman | 2009-08-24 19:08:12 +0200 (Mon, 24 Aug 2009) | 3 lines

Added the new function is_int_or_int_list().
........
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.
........
r9381 | bugman | 2009-08-24 19:45:16 +0200 (Mon, 24 Aug 2009) | 3 lines

Added a length arg to RelaxListNumError and RelaxListStrError.
........
r9382 | bugman | 2009-08-24 19:55:28 +0200 (Mon, 24 Aug 2009) | 3 lines

Added the length arg to RelaxNoneListNumError.
........
r9383 | bugman | 2009-08-24 20:14:17 +0200 (Mon, 24 Aug 2009) | 3 lines

Modified is_num_list() to check for empty lists.
........
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.
........
r9385 | bugman | 2009-08-24 20:45:18 +0200 (Mon, 24 Aug 2009) | 3 lines

Created the RelaxNoneStrFileError error class.
........
r9386 | bugman | 2009-08-24 21:02:55 +0200 (Mon, 24 Aug 2009) | 3 lines

Created the RelaxNumTupleNumError and RelaxNoneNumTupleNumError error classes.
........
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.
........
r9391 | bugman | 2009-08-26 11:17:47 +0200 (Wed, 26 Aug 2009) | 3 lines

Created the RelaxStrListNumError error class.
........
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.
........
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.
........
r9395 | bugman | 2009-08-26 14:10:22 +0200 (Wed, 26 Aug 2009) | 3 lines

Created the RelaxNoneFunctionError error class.
........
r9396 | bugman | 2009-08-26 15:32:27 +0200 (Wed, 26 Aug 2009) | 3 lines

Added the is_func() function.
........
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.
........
r9399 | bugman | 2009-08-26 17:13:37 +0200 (Wed, 26 Aug 2009) | 3 lines

Added the is_tuple() function.
........
r9400 | bugman | 2009-08-26 17:15:28 +0200 (Wed, 26 Aug 2009) | 3 lines

Fixes for the eliminate arg unit tests.
........
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.
........
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.
........
r9405 | bugman | 2009-08-28 11:12:43 +0200 (Fri, 28 Aug 2009) | 3 lines

Simplified all the argument RelaxError classes using BaseArgError.
........

Merged revisions 9311-9405 via svnmerge from
svn+ssh://bugman@.../svn/relax/1.3

........
r9311 | bugman | 2009-08-14 11:37:47 +0200 (Fri, 14 Aug 2009) | 3 lines

Fix for the test_opt_constr_newton_gmw_mt_S2_0_970_te_2048_Rex_0_149() system test for all Python version.
........
r9314 | bugman | 2009-08-14 11:44:34 +0200 (Fri, 14 Aug 2009) | 6 lines

Merged the relax 1.3.4 CHANGES file into the 1.3 line.

The command used was:
svn merge -r9296:9297 svn+ssh://bugman@.../svn/relax/tags/1.3.4 .
........
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.
........
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!
........
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.
........
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().
........
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.
........
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().
........
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.
........
r9331 | bugman | 2009-08-18 15:03:43 +0200 (Tue, 18 Aug 2009) | 3 lines

Added checks for the __init_iso_cone() args.
........
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@...>). The parent of this thread is
https://mail.gna.org/public/relax-users/2009-08/msg00017.html (Message-id:
<20090816020851.GA29683@...>).
........
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!
........
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.
........
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.
........
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.
........
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.
........
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.
........
r9345 | bugman | 2009-08-19 17:45:24 +0200 (Wed, 19 Aug 2009) | 3 lines

Renamed the pipe.list() user function to pipe.display().
........
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!
........
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.
........
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!
........
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()
........
r9352 | bugman | 2009-08-21 16:55:01 +0200 (Fri, 21 Aug 2009) | 3 lines

Updated the 2to3 checklist for the idioms.
........
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.
........
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.
........
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.
........
r9356 | bugman | 2009-08-21 18:27:29 +0200 (Fri, 21 Aug 2009) | 3 lines

Added a new error class, RelaxTupleNumError.
........
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().
........
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.
........
r9359 | bugman | 2009-08-21 18:34:29 +0200 (Fri, 21 Aug 2009) | 3 lines

Fixed the calls to checks.is_*().
........
r9360 | bugman | 2009-08-21 19:07:56 +0200 (Fri, 21 Aug 2009) | 3 lines

Fixed the capitalisation of the RelaxNoneListStrError error class.
........
r9361 | bugman | 2009-08-21 19:12:46 +0200 (Fri, 21 Aug 2009) | 3 lines

Added the is_num_list() function.
........
r9362 | bugman | 2009-08-21 19:13:58 +0200 (Fri, 21 Aug 2009) | 3 lines

Created the RelaxNoneListNumError error class.
........
r9363 | bugman | 2009-08-21 19:14:49 +0200 (Fri, 21 Aug 2009) | 3 lines

Removed a dead import of num_types.
........
r9364 | bugman | 2009-08-21 19:18:32 +0200 (Fri, 21 Aug 2009) | 3 lines

Created the is_str_list() function.
........
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.
........
r9366 | bugman | 2009-08-21 19:53:26 +0200 (Fri, 21 Aug 2009) | 3 lines

Bug fix for the is_str_list() function.
........
r9367 | bugman | 2009-08-21 19:55:32 +0200 (Fri, 21 Aug 2009) | 3 lines

Missing imports.
........
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.
........
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.
........
r9370 | bugman | 2009-08-21 21:07:30 +0200 (Fri, 21 Aug 2009) | 3 lines

Added the RelaxNumStrListNumStrError and RelaxNoneNumStrListNumStrError error classes.
........
r9371 | bugman | 2009-08-21 21:08:00 +0200 (Fri, 21 Aug 2009) | 3 lines

Fixes for the test_set_argfail_param() unit test.
........
r9372 | bugman | 2009-08-21 21:09:53 +0200 (Fri, 21 Aug 2009) | 3 lines

Fixes for the test_set_argfail_val() unit test.
........
r9373 | bugman | 2009-08-21 21:11:20 +0200 (Fri, 21 Aug 2009) | 3 lines

Removed some unused imports.
........
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.
........
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.
........
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@...>).
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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).
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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Simplified all the argument RelaxError classes using BaseArgError.

Started to redesign to simplify the argument RelaxError classes.

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.

Removed a number of now unused RelaxError imports.

All the non user function classes have now been migrated to use the new 'check' and 'base_class' modules.

Fixes for the eliminate arg unit tests.