Author: bugman Date: Fri Aug 28 11:42:12 2009 New Revision: 9409 URL: http://svn.gna.org/viewcvs/relax?rev=9409&view=rev Log: Merged revisions 9314-9407 via svnmerge from svn+ssh://bugman@xxxxxxxxxxx/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@xxxxxxxxxxx/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@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! ........ 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@xxxxxxxxxxxxxxxxxxxxxxxxxxx>). ........ 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. ........ Added: branches/j_couplings/docs/2to3_checklist - copied unchanged from r9405, 1.3/docs/2to3_checklist branches/j_couplings/prompt/base_class.py - copied unchanged from r9405, 1.3/prompt/base_class.py branches/j_couplings/prompt/check.py - copied unchanged from r9405, 1.3/prompt/check.py branches/j_couplings/test_suite/unit_tests/_prompt/test_molmol.py - copied unchanged from r9405, 1.3/test_suite/unit_tests/_prompt/test_molmol.py branches/j_couplings/test_suite/unit_tests/_prompt/test_pymol.py - copied unchanged from r9405, 1.3/test_suite/unit_tests/_prompt/test_pymol.py Removed: branches/j_couplings/prompt/num_types.py Modified: branches/j_couplings/ (props changed) branches/j_couplings/colour.py branches/j_couplings/data/__init__.py branches/j_couplings/data/align_tensor.py branches/j_couplings/data/data_classes.py branches/j_couplings/data/diff_tensor.py branches/j_couplings/data/mol_res_spin.py branches/j_couplings/data/pipe_container.py branches/j_couplings/data/prototype.py branches/j_couplings/data/relax_xml.py branches/j_couplings/docs/CHANGES branches/j_couplings/docs/latex/fetch_docstrings.py branches/j_couplings/float.py branches/j_couplings/generic_fns/align_tensor.py branches/j_couplings/generic_fns/angles.py branches/j_couplings/generic_fns/dasha.py branches/j_couplings/generic_fns/diffusion_tensor.py branches/j_couplings/generic_fns/eliminate.py branches/j_couplings/generic_fns/fix.py branches/j_couplings/generic_fns/frame_order.py branches/j_couplings/generic_fns/frq.py branches/j_couplings/generic_fns/grace.py branches/j_couplings/generic_fns/minimise.py branches/j_couplings/generic_fns/model_selection.py branches/j_couplings/generic_fns/mol_res_spin.py [... 662 lines stripped ...]