Author: bugman Date: Thu Sep 3 14:23:17 2009 New Revision: 9441 URL: http://svn.gna.org/viewcvs/relax?rev=9441&view=rev Log: Merged revisions 9411-9439 via svnmerge from svn+ssh://bugman@xxxxxxxxxxx/svn/relax/1.3 ........ r9411 | bugman | 2009-08-28 12:24:03 +0200 (Fri, 28 Aug 2009) | 3 lines Added a check for the unimplemented constraints in the frame order code. ........ r9412 | bugman | 2009-08-28 18:01:25 +0200 (Fri, 28 Aug 2009) | 3 lines Created the 'rigid' frame order model. ........ r9413 | bugman | 2009-08-31 17:49:38 +0200 (Mon, 31 Aug 2009) | 5 lines Constraints are now automatically turned off, if the minimisation option is set to True. These are not yet implemented! ........ r9414 | bugman | 2009-08-31 17:52:41 +0200 (Mon, 31 Aug 2009) | 5 lines Bug fix for the ref_domain() method. This method now works if no domain names have been associated with the tensors. ........ r9415 | bugman | 2009-08-31 18:08:22 +0200 (Mon, 31 Aug 2009) | 5 lines Fix for the turning off of minimisation constraints. The algorithm needs to also change. ........ r9416 | bugman | 2009-08-31 18:08:39 +0200 (Mon, 31 Aug 2009) | 3 lines Changed a flag to a bool type. ........ r9417 | bugman | 2009-08-31 19:07:18 +0200 (Mon, 31 Aug 2009) | 6 lines Added __description__ strings to the user function class relax help strings. The __strip_lead() method has been added to User_fn_class to remove leading whitespace from the __description__ strings. ........ r9418 | bugman | 2009-09-01 10:15:08 +0200 (Tue, 01 Sep 2009) | 6 lines Rearrangement of the handling of frame order models. The tensor rotation Euler angles are now model independent, the 'rigid' model is better supported, and a clear isolation of the isotropic cone model has been made. ........ r9419 | bugman | 2009-09-01 11:15:17 +0200 (Tue, 01 Sep 2009) | 3 lines Added a missing alias for the current data pipe. ........ r9420 | bugman | 2009-09-01 11:52:51 +0200 (Tue, 01 Sep 2009) | 3 lines Added a system test for the frame order 'rigid' model with no tensor rotations and no motion. ........ r9421 | bugman | 2009-09-01 13:48:39 +0200 (Tue, 01 Sep 2009) | 5 lines Large code refactorisation - the current data pipe is now in __builtin__.cdp. The result is the removal of 484 calls to generic_fns.pipes.get_pipe() to get the current data pipe. ........ r9422 | bugman | 2009-09-01 16:02:48 +0200 (Tue, 01 Sep 2009) | 3 lines Created the new maths_fns.rotation_matrix.R_to_euler_zyz() function and associated unit test. ........ r9423 | bugman | 2009-09-01 16:38:26 +0200 (Tue, 01 Sep 2009) | 3 lines The frame order minimisation now first checks if the tensor reductions have been specified. ........ r9424 | bugman | 2009-09-01 16:40:49 +0200 (Tue, 01 Sep 2009) | 5 lines Fix for the script() user function. The function intro flag at the end of executing an external script was not being restored. ........ r9425 | bugman | 2009-09-01 16:44:00 +0200 (Tue, 01 Sep 2009) | 3 lines Added a function intro text for the script() user function. ........ r9426 | bugman | 2009-09-02 14:09:02 +0200 (Wed, 02 Sep 2009) | 8 lines Improvements to the optimisation tests and fixes for bug #14173, bug #14174, bug #14175, bug #14176, bug #14177, bug #14182. The bugs were reported by Jack Howarth (https://gna.org/users/jhowarth) and Seb (https://gna.org/users/semor). The architecture info and optimisation stats for a number of systems have been added to the file for reference. ........ r9427 | bugman | 2009-09-02 14:10:30 +0200 (Wed, 02 Sep 2009) | 6 lines Created a script to test optimisation on various systems. This just runs the optimisation system tests, collecting and printing the architecture info and optimisation stats. ........ r9428 | bugman | 2009-09-02 15:15:13 +0200 (Wed, 02 Sep 2009) | 3 lines Added a unit test checking the generic_fns.structure.__all__ list. ........ r9429 | bugman | 2009-09-02 15:21:46 +0200 (Wed, 02 Sep 2009) | 3 lines Tidying up of the docstrings and printouts of the Test___init__ test class. ........ r9430 | bugman | 2009-09-02 15:37:30 +0200 (Wed, 02 Sep 2009) | 3 lines Shifted the test___all__() method into the PackageTestCase base class. ........ r9431 | bugman | 2009-09-02 15:43:16 +0200 (Wed, 02 Sep 2009) | 3 lines Added many more checks for the package __all__ lists. ........ r9432 | bugman | 2009-09-02 15:48:17 +0200 (Wed, 02 Sep 2009) | 3 lines Added a check for the __all__ list of the data package. ........ r9433 | bugman | 2009-09-02 19:53:15 +0200 (Wed, 02 Sep 2009) | 3 lines Comment fixes. ........ r9434 | bugman | 2009-09-02 20:15:21 +0200 (Wed, 02 Sep 2009) | 3 lines Updated the package __all__ lists. ........ r9435 | bugman | 2009-09-02 20:24:47 +0200 (Wed, 02 Sep 2009) | 3 lines Added a check for non-existent modules, and updated the __all__ lists. ........ r9436 | bugman | 2009-09-02 22:11:08 +0200 (Wed, 02 Sep 2009) | 7 lines Made the profile module optional, removing the dependency on the Python development packages. This was in response to Tiago Pais's <tpais att itqb dot unl dot pt> message at https://mail.gna.org/public/relax-users/2009-08/msg00040.html (Message-id: <A3A9E765436240CDA75B3045C405BED6@Mercurio>). ........ r9437 | bugman | 2009-09-03 13:42:16 +0200 (Thu, 03 Sep 2009) | 11 lines The whitespace after commas has been enforced (for Python 3.x). This was done with the python 2.x to 3.x script with the command: 2to3 -w -f ws_comma relax . The change is in preparation for Python 3.0, and relax still works with Python versions 2.4, 2.5, and 2.6. All commas now have whitespace after them. The docs/2to3_checklist file has also been updated with all the 2to3 changes. ........ r9438 | bugman | 2009-09-03 13:52:25 +0200 (Thu, 03 Sep 2009) | 3 lines Removed some debugging code. ........ r9439 | bugman | 2009-09-03 14:06:49 +0200 (Thu, 03 Sep 2009) | 9 lines Some more print statement updates for Python 3.x. 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. ........ Added: branches/cst/scripts/optimisation_testing.py - copied unchanged from r9439, 1.3/scripts/optimisation_testing.py branches/cst/test_suite/system_tests/frame_order.py - copied unchanged from r9439, 1.3/test_suite/system_tests/frame_order.py branches/cst/test_suite/system_tests/scripts/frame_order_rigid_no_rot.py - copied unchanged from r9439, 1.3/test_suite/system_tests/scripts/frame_order_rigid_no_rot.py branches/cst/test_suite/unit_tests/_generic_fns/_structure/test___init__.py - copied unchanged from r9439, 1.3/test_suite/unit_tests/_generic_fns/_structure/test___init__.py branches/cst/test_suite/unit_tests/_generic_fns/test___init__.py - copied unchanged from r9439, 1.3/test_suite/unit_tests/_generic_fns/test___init__.py branches/cst/test_suite/unit_tests/_maths_fns/test___init__.py - copied unchanged from r9439, 1.3/test_suite/unit_tests/_maths_fns/test___init__.py branches/cst/test_suite/unit_tests/_maths_fns/test_rotation_matrix.py - copied unchanged from r9439, 1.3/test_suite/unit_tests/_maths_fns/test_rotation_matrix.py branches/cst/test_suite/unit_tests/_opendx/test___init__.py - copied unchanged from r9439, 1.3/test_suite/unit_tests/_opendx/test___init__.py branches/cst/test_suite/unit_tests/_prompt/test___init__.py - copied unchanged from r9439, 1.3/test_suite/unit_tests/_prompt/test___init__.py branches/cst/test_suite/unit_tests/_specific_fns/_model_free/test___init__.py - copied unchanged from r9439, 1.3/test_suite/unit_tests/_specific_fns/_model_free/test___init__.py branches/cst/test_suite/unit_tests/_specific_fns/test___init__.py - copied unchanged from r9439, 1.3/test_suite/unit_tests/_specific_fns/test___init__.py branches/cst/test_suite/unit_tests/package_checking.py - copied unchanged from r9439, 1.3/test_suite/unit_tests/package_checking.py Modified: branches/cst/ (props changed) branches/cst/data/__init__.py branches/cst/dep_check.py branches/cst/docs/2to3_checklist branches/cst/docs/latex/develop.tex branches/cst/float.py 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branches/cst/sample_scripts/modsel.py branches/cst/sample_scripts/palmer.py branches/cst/sample_scripts/relax_curve_diff.py branches/cst/scons/distrib.py branches/cst/scons/install.py branches/cst/scons/manuals.py branches/cst/scripts/test_python_versions.py branches/cst/specific_fns/__init__.py branches/cst/specific_fns/base_class.py branches/cst/specific_fns/consistency_tests.py branches/cst/specific_fns/frame_order.py branches/cst/specific_fns/hybrid.py branches/cst/specific_fns/jw_mapping.py branches/cst/specific_fns/model_free/main.py branches/cst/specific_fns/model_free/mf_minimise.py branches/cst/specific_fns/model_free/molmol.py branches/cst/specific_fns/model_free/results.py branches/cst/specific_fns/n_state_model.py branches/cst/specific_fns/noe.py branches/cst/specific_fns/relax_fit.py branches/cst/test_suite/shared_data/align_data/CaM/generate_data.py branches/cst/test_suite/shared_data/align_data/CaM/pre_bleach.py branches/cst/test_suite/system_tests/__init__.py branches/cst/test_suite/system_tests/angles.py branches/cst/test_suite/system_tests/diffusion_tensor.py branches/cst/test_suite/system_tests/load_spins.py branches/cst/test_suite/system_tests/model_free.py branches/cst/test_suite/system_tests/n_state_model.py branches/cst/test_suite/system_tests/noe_restraints.py branches/cst/test_suite/system_tests/palmer.py branches/cst/test_suite/system_tests/peak_lists.py branches/cst/test_suite/system_tests/scripts/align_fit.py branches/cst/test_suite/system_tests/scripts/latex_mf_table.py branches/cst/test_suite/system_tests/scripts/palmer.py branches/cst/test_suite/system_tests/scripts/palmer_omp.py branches/cst/test_suite/system_tests/sequence.py branches/cst/test_suite/system_tests/structure.py branches/cst/test_suite/system_tests/unit_vectors.py branches/cst/test_suite/unit_tests/_data/test___init__.py branches/cst/test_suite/unit_tests/_data/test_diff_tensor.py branches/cst/test_suite/unit_tests/_generic_fns/test_mol_res_spin.py branches/cst/test_suite/unit_tests/_generic_fns/test_selection.py branches/cst/test_suite/unit_tests/_maths_fns/test_chi2.py branches/cst/test_suite/unit_tests/_maths_fns/test_kronecker_product.py branches/cst/test_suite/unit_tests/_prompt/test_sequence.py branches/cst/test_suite/unit_tests/_specific_fns/test_n_state_model.py branches/cst/test_suite/unit_tests/align_tensor_testing_base.py branches/cst/test_suite/unit_tests/relax_data_testing_base.py branches/cst/test_suite/unit_tests/spin_testing_base.py branches/cst/test_suite/unit_tests/state_testing_base.py branches/cst/test_suite/unit_tests/unit_test_runner.py branches/cst/test_suite/unit_tests/value_testing_base.py [This mail would be too long, it was shortened to contain the URLs only.] Modified: branches/cst/data/__init__.py URL: http://svn.gna.org/viewcvs/relax/branches/cst/data/__init__.py?rev=9441&r1=9440&r2=9441&view=diff Modified: branches/cst/dep_check.py URL: 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Modified: branches/cst/generic_fns/dasha.py URL: http://svn.gna.org/viewcvs/relax/branches/cst/generic_fns/dasha.py?rev=9441&r1=9440&r2=9441&view=diff Modified: branches/cst/generic_fns/diffusion_tensor.py URL: http://svn.gna.org/viewcvs/relax/branches/cst/generic_fns/diffusion_tensor.py?rev=9441&r1=9440&r2=9441&view=diff Modified: branches/cst/generic_fns/eliminate.py URL: http://svn.gna.org/viewcvs/relax/branches/cst/generic_fns/eliminate.py?rev=9441&r1=9440&r2=9441&view=diff Modified: branches/cst/generic_fns/fix.py URL: http://svn.gna.org/viewcvs/relax/branches/cst/generic_fns/fix.py?rev=9441&r1=9440&r2=9441&view=diff Modified: branches/cst/generic_fns/frq.py URL: http://svn.gna.org/viewcvs/relax/branches/cst/generic_fns/frq.py?rev=9441&r1=9440&r2=9441&view=diff Modified: branches/cst/generic_fns/grace.py URL: http://svn.gna.org/viewcvs/relax/branches/cst/generic_fns/grace.py?rev=9441&r1=9440&r2=9441&view=diff Modified: branches/cst/generic_fns/minimise.py URL: 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