Author: semor
Date: Mon Nov 2 21:01:24 2009
New Revision: 9863
URL: http://svn.gna.org/viewcvs/relax?rev=9863&view=rev
Log:
Merged revisions
9248-9271,9276-9288,9290,9292,9303-9311,9314,9317-9322,9324-9405,9411-9439,9454,9457-9526,9528-9658,9696,9700,9706,9709,9747,9794,9799-9800,9829,9831,9834
via svnmerge from
svn+ssh://semor@xxxxxxxxxxx/svn/relax/1.3
Additionally, files 'prompt/grace.py' and 'specific_fns/__init__.py' were
modified manually to
solve conflicts created by the merging process...
........
r9248 | bugman | 2009-07-16 13:45:33 -0400 (Thu, 16 Jul 2009) | 5 lines
Bug fix for the write_pdb() method.
The MODEL record is now created for single structures if a model number
exists.
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r9249 | bugman | 2009-07-19 19:16:52 -0400 (Sun, 19 Jul 2009) | 11 lines
Created functions for rank-4, 3D tensor transposes (and corresponding unit
tests).
The new functions are:
maths_fns.kronecker_product.transpose_12()
maths_fns.kronecker_product.transpose_13()
maths_fns.kronecker_product.transpose_14()
maths_fns.kronecker_product.transpose_23()
maths_fns.kronecker_product.transpose_24()
maths_fns.kronecker_product.transpose_34()
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r9250 | bugman | 2009-07-20 08:02:30 -0400 (Mon, 20 Jul 2009) | 3 lines
Switched to the internal PDB reader for removal of the reliance on
Scientific python.
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r9251 | bugman | 2009-07-21 09:09:18 -0400 (Tue, 21 Jul 2009) | 3 lines
Added some MC simulation data and errors for the diffusion tensor system
tests.
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r9252 | bugman | 2009-07-21 09:19:03 -0400 (Tue, 21 Jul 2009) | 3 lines
Split the system test of structure.create_diff_tensor_pdb() into 3 tests
for each diff type.
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r9253 | bugman | 2009-07-21 09:54:30 -0400 (Tue, 21 Jul 2009) | 3 lines
Removed trailing whitespace.
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r9254 | bugman | 2009-07-21 10:28:02 -0400 (Tue, 21 Jul 2009) | 5 lines
Changed the order of setting the MC simulation data for the diffusion
tensor.
This should test things a bit better.
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r9255 | bugman | 2009-07-21 10:57:19 -0400 (Tue, 21 Jul 2009) | 3 lines
Modification of MC sim list elements is now also tested.
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r9256 | bugman | 2009-07-21 10:59:29 -0400 (Tue, 21 Jul 2009) | 6 lines
Bug fixes for the diffusion tensor MC simulation data structure updating.
The MC simulation structures were not being updated at all!!! This now
works, allowing the
diffusion tensor PDB representation to be created.
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r9257 | bugman | 2009-07-21 11:03:21 -0400 (Tue, 21 Jul 2009) | 3 lines
The MC sim vectors for the diffusion tensor axes are now being properly
created.
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r9258 | bugman | 2009-07-21 11:03:43 -0400 (Tue, 21 Jul 2009) | 3 lines
Removed some debugging code.
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r9259 | bugman | 2009-07-21 11:15:28 -0400 (Tue, 21 Jul 2009) | 5 lines
Bug fix for the creation of the ellipsoid diffusion tensor PDB
representation.
The axes are now labelled Dx, Dy, and Dz instead of all Dpar!
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r9260 | bugman | 2009-07-21 11:40:29 -0400 (Tue, 21 Jul 2009) | 5 lines
Bug fix for the creation of the spheroid diff tensor PDB representation.
The simulation vectors should be initialised to a list.
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r9261 | bugman | 2009-07-21 11:47:23 -0400 (Tue, 21 Jul 2009) | 3 lines
The ellipsoid diff tensor PDB file is now being checked, line for line.
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r9262 | bugman | 2009-07-21 15:38:43 -0400 (Tue, 21 Jul 2009) | 3 lines
The diffusion tensor MC sim data is now properly set up.
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r9263 | bugman | 2009-07-21 15:39:44 -0400 (Tue, 21 Jul 2009) | 5 lines
Bug fix for the diffusion tensor MC sim data structures.
All structures are now properly updated when a value for a single
simulation changes.
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r9264 | bugman | 2009-07-21 16:31:06 -0400 (Tue, 21 Jul 2009) | 3 lines
The spherical diffusion tensor system tests are now properly set up.
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r9265 | bugman | 2009-07-21 16:32:04 -0400 (Tue, 21 Jul 2009) | 5 lines
Bug fix for the __update_sim_append() method.
Now the diffusion tensor simulation structure appending works if the
structure doesn't already exist.
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r9266 | bugman | 2009-07-21 19:10:56 -0400 (Tue, 21 Jul 2009) | 3 lines
Extended the test_copy() system test to properly check if a copy is made,
rather than link.
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r9267 | bugman | 2009-07-21 19:20:52 -0400 (Tue, 21 Jul 2009) | 5 lines
Fix for the test_copy() system test.
The wrong indices were being checked.
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r9268 | bugman | 2009-07-21 20:00:13 -0400 (Tue, 21 Jul 2009) | 7 lines
Bug fix for the copying of diffusion tensors data structures.
The DiffTensorSimList objects in DiffTensorData were not being properly
copied! This has been fixed
by writing class specific __deepcopy__() methods for both classes. The
Element class has also been
subclassed from 'object'.
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r9269 | bugman | 2009-07-21 20:12:55 -0400 (Tue, 21 Jul 2009) | 5 lines
The test_create_diff_tensor_pdb_ellipsoid() system test has been made more
vigorous.
The copy operations are now better tested.
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r9270 | bugman | 2009-07-22 03:40:26 -0400 (Wed, 22 Jul 2009) | 3 lines
The diffusion tensor copying system test is now more comprehensive.
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r9271 | bugman | 2009-07-22 05:23:10 -0400 (Wed, 22 Jul 2009) | 5 lines
Added comprehensive checks for the creation of the diffusion tensor PDB
representations.
The sphere and spheroid PDB files are now checked, line for line.
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r9276 | bugman | 2009-08-12 07:06:51 -0400 (Wed, 12 Aug 2009) | 3 lines
Made the structure system tests more compatible with non-Unix operating
systems.
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r9277 | bugman | 2009-08-12 07:11:27 -0400 (Wed, 12 Aug 2009) | 3 lines
Made get_file_path() and mkdir_nofail() compatible with non-Unix systems.
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r9278 | bugman | 2009-08-12 07:16:06 -0400 (Wed, 12 Aug 2009) | 3 lines
Made the full_analysis.py script more compatible with non-Unix operating
systems.
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r9279 | bugman | 2009-08-12 07:18:30 -0400 (Wed, 12 Aug 2009) | 3 lines
Fix for test_load_scientific_results(). The Unix paths are used in the
results file!
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r9280 | bugman | 2009-08-12 07:23:15 -0400 (Wed, 12 Aug 2009) | 3 lines
Non-Unix os fix.
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r9281 | bugman | 2009-08-12 07:54:53 -0400 (Wed, 12 Aug 2009) | 3 lines
Modified the unit tests to be more non-Unix operating system compatible.
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r9282 | bugman | 2009-08-12 08:25:49 -0400 (Wed, 12 Aug 2009) | 3 lines
Modified the system tests to be more non-Unix operating system compatible.
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r9283 | bugman | 2009-08-12 08:38:00 -0400 (Wed, 12 Aug 2009) | 4 lines
Modified the shared data scripts to be more non-Unix operating system
compatible.
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r9284 | bugman | 2009-08-12 08:53:54 -0400 (Wed, 12 Aug 2009) | 3 lines
Removed the last '/' directory separators to be more non-Unix operating
system compatible.
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r9285 | bugman | 2009-08-12 09:02:38 -0400 (Wed, 12 Aug 2009) | 3 lines
Removed a reference to the '..' dir.
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r9286 | bugman | 2009-08-12 09:05:03 -0400 (Wed, 12 Aug 2009) | 3 lines
Redid r9279! This was accidentally reverted by hand in r9282!!!
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r9287 | bugman | 2009-08-12 09:34:50 -0400 (Wed, 12 Aug 2009) | 3 lines
Caught a NaN problem in __q_factors_rdc() causing a system test to fail in
Windows.
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r9288 | bugman | 2009-08-12 12:57:21 -0400 (Wed, 12 Aug 2009) | 7 lines
Massive clean up of the float module unit tests.
As a general clean up, the module has been converted to the relax coding
conventions. Importantly
the floating point numbers defined as constants for the tests are now
properly defined using the
packBytesAsPyFloat() function. This will allow these tests to pass on all
machines!
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r9290 | bugman | 2009-08-12 14:04:53 -0400 (Wed, 12 Aug 2009) | 8 lines
Ported the CHANGES file for relax version 1.2.15 to the 1.3 line.
This was obviously forgotten when the release was made.
The command used was:
svn merge -r8033:8034 svn+ssh://bugman@xxxxxxxxxxx/svn/relax/tags/1.2.15 .
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r9292 | bugman | 2009-08-13 09:20:47 -0400 (Thu, 13 Aug 2009) | 5 lines
Updated the _off() and _on() user function echoing methods.
The flag is now a boolean, and the message has been reworded.
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r9303 | bugman | 2009-08-14 04:49:12 -0400 (Fri, 14 Aug 2009) | 3 lines
Updated the release checklist document to reflect Gna! and Freshmeat
website changes.
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r9304 | bugman | 2009-08-14 04:51:09 -0400 (Fri, 14 Aug 2009) | 3 lines
Converted a number of flags from int to bool.
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r9305 | bugman | 2009-08-14 05:04:30 -0400 (Fri, 14 Aug 2009) | 3 lines
More changes to the release checklist document.
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r9306 | bugman | 2009-08-14 05:06:06 -0400 (Fri, 14 Aug 2009) | 3 lines
Added a script for running the full relax test suite against different
Python versions.
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r9307 | bugman | 2009-08-14 05:19:20 -0400 (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 Python 2.5.
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r9308 | bugman | 2009-08-14 05:25:29 -0400 (Fri, 14 Aug 2009) | 3 lines
Created a directory for holding miscellaneous scripts for developers.
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r9309 | bugman | 2009-08-14 05:25:55 -0400 (Fri, 14 Aug 2009) | 3 lines
Shifted the python version checking script.
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r9310 | bugman | 2009-08-14 05:28:20 -0400 (Fri, 14 Aug 2009) | 3 lines
Shifted the code validation script from the website hidden location into
the scripts directory.
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r9311 | bugman | 2009-08-14 05:37:47 -0400 (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.
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r9314 | bugman | 2009-08-14 05:44:34 -0400 (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 .
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r9317 | bugman | 2009-08-14 11:23:30 -0400 (Fri, 14 Aug 2009) | 3 lines
Docstring fix for the return_units() method.
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r9318 | bugman | 2009-08-14 11:28:03 -0400 (Fri, 14 Aug 2009) | 3 lines
Epydoc docstring fixes.
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r9319 | bugman | 2009-08-14 11:54:39 -0400 (Fri, 14 Aug 2009) | 3 lines
Converted the function into a class object variable.
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r9320 | bugman | 2009-08-14 12:44:39 -0400 (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.
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r9321 | bugman | 2009-08-14 12:55:04 -0400 (Fri, 14 Aug 2009) | 3 lines
Epydoc docstring fixes for IO.__init__().
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r9322 | bugman | 2009-08-14 13:06:31 -0400 (Fri, 14 Aug 2009) | 5 lines
Bug fix for the return_data_name() method recently introduced.
This function takes the 'index' keyword argument.
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r9324 | bugman | 2009-08-18 07:57:40 -0400 (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 08:28:08 -0400 (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.
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r9326 | bugman | 2009-08-18 08:30:03 -0400 (Tue, 18 Aug 2009) | 3 lines
Character encoding fix - cannot use umlauts.
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r9327 | bugman | 2009-08-18 08:38:38 -0400 (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 08:42:41 -0400 (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 09:00:14 -0400 (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 09:00:56 -0400 (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 09:03:43 -0400 (Tue, 18 Aug 2009) | 3 lines
Added checks for the __init_iso_cone() args.
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r9332 | bugman | 2009-08-18 09:17:37 -0400 (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>).
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r9333 | bugman | 2009-08-18 12:45:44 -0400 (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 04:19:26 -0400 (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 04:29:13 -0400 (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 04:32:35 -0400 (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 04:43:51 -0400 (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 04:45:56 -0400 (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.
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r9339 | bugman | 2009-08-19 08:19:34 -0400 (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.
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r9340 | bugman | 2009-08-19 09:37:09 -0400 (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.
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r9341 | bugman | 2009-08-19 09:48:55 -0400 (Wed, 19 Aug 2009) | 5 lines
Bug fix for the relaxation curve-fitting difference plot script.
The spin_loop blocks were missing colons!
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r9342 | bugman | 2009-08-19 10:09:33 -0400 (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.
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r9343 | bugman | 2009-08-19 11:18:47 -0400 (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.
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r9344 | bugman | 2009-08-19 11:31:11 -0400 (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 11:45:24 -0400 (Wed, 19 Aug 2009) | 3 lines
Renamed the pipe.list() user function to pipe.display().
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r9346 | bugman | 2009-08-19 12:47:50 -0400 (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.
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r9347 | bugman | 2009-08-20 11:48:36 -0400 (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.
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r9348 | bugman | 2009-08-21 04:50:08 -0400 (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 04:54:20 -0400 (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 06:07:01 -0400 (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 10:54:29 -0400 (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 10:55:01 -0400 (Fri, 21 Aug 2009) | 3 lines
Updated the 2to3 checklist for the idioms.
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r9353 | bugman | 2009-08-21 11:23:56 -0400 (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 11:25:00 -0400 (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 11:45:36 -0400 (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 12:27:29 -0400 (Fri, 21 Aug 2009) | 3 lines
Added a new error class, RelaxTupleNumError.
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r9357 | bugman | 2009-08-21 12:30:04 -0400 (Fri, 21 Aug 2009) | 3 lines
Added 2 more arg checking functions, is_float() and is_num_tuple().
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[... 2544 lines stripped ...]
r9863 - in /branches/relax_disp: ./ data/ docs/ docs/latex/ generic_fns/ generic_fns/structure/ maths_fns/ opendx/ prompt/ s...