Author: bugman
Date: Thu Sep 3 14:21:48 2009
New Revision: 9440
URL: http://svn.gna.org/viewcvs/relax?rev=9440&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/bmrb/scripts/optimisation_testing.py
- copied unchanged from r9439, 1.3/scripts/optimisation_testing.py
branches/bmrb/test_suite/system_tests/frame_order.py
- copied unchanged from r9439,
1.3/test_suite/system_tests/frame_order.py
branches/bmrb/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/bmrb/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/bmrb/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/bmrb/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/bmrb/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/bmrb/test_suite/unit_tests/_opendx/test___init__.py
- copied unchanged from r9439,
1.3/test_suite/unit_tests/_opendx/test___init__.py
branches/bmrb/test_suite/unit_tests/_prompt/test___init__.py
- copied unchanged from r9439,
1.3/test_suite/unit_tests/_prompt/test___init__.py
branches/bmrb/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/bmrb/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/bmrb/test_suite/unit_tests/package_checking.py
- copied unchanged from r9439,
1.3/test_suite/unit_tests/package_checking.py
Modified:
branches/bmrb/ (props changed)
branches/bmrb/data/__init__.py
branches/bmrb/dep_check.py
branches/bmrb/docs/2to3_checklist
branches/bmrb/docs/latex/develop.tex
branches/bmrb/float.py
branches/bmrb/generic_fns/__init__.py
branches/bmrb/generic_fns/align_tensor.py
branches/bmrb/generic_fns/angles.py
branches/bmrb/generic_fns/dasha.py
branches/bmrb/generic_fns/diffusion_tensor.py
branches/bmrb/generic_fns/eliminate.py
branches/bmrb/generic_fns/fix.py
branches/bmrb/generic_fns/frq.py
branches/bmrb/generic_fns/grace.py
branches/bmrb/generic_fns/minimise.py
branches/bmrb/generic_fns/model_selection.py
branches/bmrb/generic_fns/mol_res_spin.py
branches/bmrb/generic_fns/molmol.py
branches/bmrb/generic_fns/monte_carlo.py
branches/bmrb/generic_fns/noesy.py
branches/bmrb/generic_fns/palmer.py
branches/bmrb/generic_fns/pcs.py
branches/bmrb/generic_fns/pipes.py
branches/bmrb/generic_fns/pymol.py
branches/bmrb/generic_fns/rdc.py
branches/bmrb/generic_fns/relax_data.py
branches/bmrb/generic_fns/results.py
branches/bmrb/generic_fns/spectrum.py
branches/bmrb/generic_fns/structure/__init__.py
branches/bmrb/generic_fns/structure/api_base.py
branches/bmrb/generic_fns/structure/geometric.py
branches/bmrb/generic_fns/structure/internal.py
branches/bmrb/generic_fns/structure/main.py
branches/bmrb/generic_fns/structure/mass.py
branches/bmrb/generic_fns/structure/scientific.py
branches/bmrb/generic_fns/temperature.py
branches/bmrb/generic_fns/vmd.py
branches/bmrb/maths_fns/__init__.py
branches/bmrb/maths_fns/alignment_tensor.py
branches/bmrb/maths_fns/chi2.py
branches/bmrb/maths_fns/frame_order_matrix_ops.py
branches/bmrb/maths_fns/frame_order_models.py
branches/bmrb/maths_fns/mf.py
branches/bmrb/maths_fns/n_state_model.py
branches/bmrb/maths_fns/rdc.py
branches/bmrb/maths_fns/rotation_matrix.py
branches/bmrb/opendx/base_map.py
branches/bmrb/opendx/isosurface_3D.py
branches/bmrb/prompt/__init__.py
branches/bmrb/prompt/base_class.py
branches/bmrb/prompt/help.py
branches/bmrb/prompt/interpreter.py
branches/bmrb/prompt/tab_completion.py
branches/bmrb/relax
branches/bmrb/relax_io.py
branches/bmrb/sample_scripts/full_analysis.py
branches/bmrb/sample_scripts/latex_mf_table.py
branches/bmrb/sample_scripts/modsel.py
branches/bmrb/sample_scripts/palmer.py
branches/bmrb/sample_scripts/relax_curve_diff.py
branches/bmrb/scons/distrib.py
branches/bmrb/scons/install.py
branches/bmrb/scons/manuals.py
branches/bmrb/scripts/test_python_versions.py
branches/bmrb/specific_fns/__init__.py
branches/bmrb/specific_fns/base_class.py
branches/bmrb/specific_fns/consistency_tests.py
branches/bmrb/specific_fns/frame_order.py
branches/bmrb/specific_fns/hybrid.py
branches/bmrb/specific_fns/jw_mapping.py
branches/bmrb/specific_fns/model_free/main.py
branches/bmrb/specific_fns/model_free/mf_minimise.py
branches/bmrb/specific_fns/model_free/molmol.py
branches/bmrb/specific_fns/model_free/results.py
branches/bmrb/specific_fns/n_state_model.py
branches/bmrb/specific_fns/noe.py
branches/bmrb/specific_fns/relax_fit.py
branches/bmrb/test_suite/shared_data/align_data/CaM/generate_data.py
branches/bmrb/test_suite/shared_data/align_data/CaM/pre_bleach.py
branches/bmrb/test_suite/system_tests/__init__.py
branches/bmrb/test_suite/system_tests/angles.py
branches/bmrb/test_suite/system_tests/diffusion_tensor.py
branches/bmrb/test_suite/system_tests/load_spins.py
branches/bmrb/test_suite/system_tests/model_free.py
branches/bmrb/test_suite/system_tests/n_state_model.py
branches/bmrb/test_suite/system_tests/noe_restraints.py
branches/bmrb/test_suite/system_tests/palmer.py
branches/bmrb/test_suite/system_tests/peak_lists.py
branches/bmrb/test_suite/system_tests/scripts/align_fit.py
branches/bmrb/test_suite/system_tests/scripts/latex_mf_table.py
branches/bmrb/test_suite/system_tests/scripts/palmer.py
branches/bmrb/test_suite/system_tests/scripts/palmer_omp.py
branches/bmrb/test_suite/system_tests/sequence.py
branches/bmrb/test_suite/system_tests/structure.py
branches/bmrb/test_suite/system_tests/unit_vectors.py
branches/bmrb/test_suite/unit_tests/_data/test___init__.py
branches/bmrb/test_suite/unit_tests/_data/test_diff_tensor.py
branches/bmrb/test_suite/unit_tests/_generic_fns/test_mol_res_spin.py
branches/bmrb/test_suite/unit_tests/_generic_fns/test_selection.py
branches/bmrb/test_suite/unit_tests/_maths_fns/test_chi2.py
branches/bmrb/test_suite/unit_tests/_maths_fns/test_kronecker_product.py
branches/bmrb/test_suite/unit_tests/_prompt/test_sequence.py
branches/bmrb/test_suite/unit_tests/_specific_fns/test_n_state_model.py
branches/bmrb/test_suite/unit_tests/align_tensor_testing_base.py
branches/bmrb/test_suite/unit_tests/relax_data_testing_base.py
branches/bmrb/test_suite/unit_tests/spin_testing_base.py
branches/bmrb/test_suite/unit_tests/state_testing_base.py
branches/bmrb/test_suite/unit_tests/unit_test_runner.py
branches/bmrb/test_suite/unit_tests/value_testing_base.py
[This mail would be too long, it was shortened to contain the URLs only.]
Modified: branches/bmrb/data/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/data/__init__.py?rev=9440&r1=9439&r2=9440&view=diff
Modified: branches/bmrb/dep_check.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/dep_check.py?rev=9440&r1=9439&r2=9440&view=diff
Modified: branches/bmrb/docs/2to3_checklist
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/docs/2to3_checklist?rev=9440&r1=9439&r2=9440&view=diff
Modified: branches/bmrb/docs/latex/develop.tex
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/docs/latex/develop.tex?rev=9440&r1=9439&r2=9440&view=diff
Modified: branches/bmrb/float.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/float.py?rev=9440&r1=9439&r2=9440&view=diff
Modified: branches/bmrb/generic_fns/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/generic_fns/__init__.py?rev=9440&r1=9439&r2=9440&view=diff
Modified: branches/bmrb/generic_fns/align_tensor.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/generic_fns/align_tensor.py?rev=9440&r1=9439&r2=9440&view=diff
Modified: branches/bmrb/generic_fns/angles.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/generic_fns/angles.py?rev=9440&r1=9439&r2=9440&view=diff
Modified: branches/bmrb/generic_fns/dasha.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/generic_fns/dasha.py?rev=9440&r1=9439&r2=9440&view=diff
Modified: branches/bmrb/generic_fns/diffusion_tensor.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/generic_fns/diffusion_tensor.py?rev=9440&r1=9439&r2=9440&view=diff
Modified: branches/bmrb/generic_fns/eliminate.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/generic_fns/eliminate.py?rev=9440&r1=9439&r2=9440&view=diff
Modified: branches/bmrb/generic_fns/fix.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/generic_fns/fix.py?rev=9440&r1=9439&r2=9440&view=diff
Modified: branches/bmrb/generic_fns/frq.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/generic_fns/frq.py?rev=9440&r1=9439&r2=9440&view=diff
Modified: branches/bmrb/generic_fns/grace.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/generic_fns/grace.py?rev=9440&r1=9439&r2=9440&view=diff
Modified: branches/bmrb/generic_fns/minimise.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/generic_fns/minimise.py?rev=9440&r1=9439&r2=9440&view=diff
Modified: branches/bmrb/generic_fns/model_selection.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/generic_fns/model_selection.py?rev=9440&r1=9439&r2=9440&view=diff
Modified: branches/bmrb/generic_fns/mol_res_spin.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/generic_fns/mol_res_spin.py?rev=9440&r1=9439&r2=9440&view=diff
Modified: branches/bmrb/generic_fns/molmol.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/generic_fns/molmol.py?rev=9440&r1=9439&r2=9440&view=diff
Modified: branches/bmrb/generic_fns/monte_carlo.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/generic_fns/monte_carlo.py?rev=9440&r1=9439&r2=9440&view=diff
Modified: branches/bmrb/generic_fns/noesy.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/generic_fns/noesy.py?rev=9440&r1=9439&r2=9440&view=diff
Modified: branches/bmrb/generic_fns/palmer.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/generic_fns/palmer.py?rev=9440&r1=9439&r2=9440&view=diff
Modified: branches/bmrb/generic_fns/pcs.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/generic_fns/pcs.py?rev=9440&r1=9439&r2=9440&view=diff
Modified: branches/bmrb/generic_fns/pipes.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/generic_fns/pipes.py?rev=9440&r1=9439&r2=9440&view=diff
Modified: branches/bmrb/generic_fns/pymol.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/generic_fns/pymol.py?rev=9440&r1=9439&r2=9440&view=diff
Modified: branches/bmrb/generic_fns/rdc.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/generic_fns/rdc.py?rev=9440&r1=9439&r2=9440&view=diff
Modified: branches/bmrb/generic_fns/relax_data.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/generic_fns/relax_data.py?rev=9440&r1=9439&r2=9440&view=diff
Modified: branches/bmrb/generic_fns/results.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/generic_fns/results.py?rev=9440&r1=9439&r2=9440&view=diff
Modified: branches/bmrb/generic_fns/spectrum.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/generic_fns/spectrum.py?rev=9440&r1=9439&r2=9440&view=diff
Modified: branches/bmrb/generic_fns/structure/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/generic_fns/structure/__init__.py?rev=9440&r1=9439&r2=9440&view=diff
Modified: branches/bmrb/generic_fns/structure/api_base.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/generic_fns/structure/api_base.py?rev=9440&r1=9439&r2=9440&view=diff
Modified: branches/bmrb/generic_fns/structure/geometric.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/generic_fns/structure/geometric.py?rev=9440&r1=9439&r2=9440&view=diff
Modified: branches/bmrb/generic_fns/structure/internal.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/generic_fns/structure/internal.py?rev=9440&r1=9439&r2=9440&view=diff
Modified: branches/bmrb/generic_fns/structure/main.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/generic_fns/structure/main.py?rev=9440&r1=9439&r2=9440&view=diff
Modified: branches/bmrb/generic_fns/structure/mass.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/generic_fns/structure/mass.py?rev=9440&r1=9439&r2=9440&view=diff
Modified: branches/bmrb/generic_fns/structure/scientific.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/generic_fns/structure/scientific.py?rev=9440&r1=9439&r2=9440&view=diff
Modified: branches/bmrb/generic_fns/temperature.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/generic_fns/temperature.py?rev=9440&r1=9439&r2=9440&view=diff
Modified: branches/bmrb/generic_fns/vmd.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/generic_fns/vmd.py?rev=9440&r1=9439&r2=9440&view=diff
Modified: branches/bmrb/maths_fns/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/maths_fns/__init__.py?rev=9440&r1=9439&r2=9440&view=diff
Modified: branches/bmrb/maths_fns/alignment_tensor.py
[... 212 lines stripped ...]
r9440 - in /branches/bmrb: ./ data/ docs/ docs/latex/ generic_fns/ generic_fns/structure/ maths_fns/ opendx/ prompt/ sample_...