Author: bugman
Date: Mon Jan 25 20:50:37 2010
New Revision: 10327
URL: http://svn.gna.org/viewcvs/relax?rev=10327&view=rev
Log:
Merged revisions 10304-10326 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/1.3
........
r10304 | bugman | 2010-01-25 14:25:32 +0100 (Mon, 25 Jan 2010) | 11 lines
Redesign of the setup of the names spaces for the user functions.
All the user functions and other objects located in the run() method
namespace have been shifted
into the interpreter self._locals dictionary. These are then placed into
the run() method namespace
by looping over the keys and using the 'locals()[key] = object' syntax.
There may be better ways to
do this.
This has no visible effect on the prompt or script based interfaces. It
will change how this is
seen by other modules though, and will allow the namespace to be more
easily accessed.
........
r10305 | bugman | 2010-01-25 14:26:57 +0100 (Mon, 25 Jan 2010) | 3 lines
Removed some unused and commented out code.
........
r10306 | bugman | 2010-01-25 14:31:09 +0100 (Mon, 25 Jan 2010) | 5 lines
Eliminated the dummy mode.
This is only used by the fetch_docstrings script and will soon not be
necessary.
........
r10307 | bugman | 2010-01-25 15:55:49 +0100 (Mon, 25 Jan 2010) | 7 lines
The relax base object is no longer passed into the class namespace of the
user functions.
This was only being used for access to the intro flag (a few other cases
exist, but these should be
fixed). Now a new container object with this flag is being passed in.
This significantly
simplifies the code paths and removes the need for the test suite to create
'fake' relax instances.
........
r10308 | bugman | 2010-01-25 16:08:41 +0100 (Mon, 25 Jan 2010) | 7 lines
Modified how the Exec_info data container is handled.
The class was shifted from prompt.interpreter to prompt.base_class. In
addition if not container
is passed into the user function classes, then one is created with the
intro flag set to a default
of True.
........
r10309 | bugman | 2010-01-25 16:34:44 +0100 (Mon, 25 Jan 2010) | 8 lines
The prompt info has been shifted into the execution info container.
The sys.ps1, sys.ps2, and sys.ps3 prompts are still set, but these strings
are hardcoded into the
execution info container. This allows the user functions to be imported
and operate outside of the
prompt/scripting based interface, as the no longer require sys.ps3 to be
set or the relax main
instance passed into them.
........
r10310 | bugman | 2010-01-25 16:39:34 +0100 (Mon, 25 Jan 2010) | 5 lines
Eliminated the fake_relax instance dependence.
This is no longer necessary as the user functions can be initialised
without relax.
........
r10311 | bugman | 2010-01-25 16:53:14 +0100 (Mon, 25 Jan 2010) | 3 lines
Created the populate_self() method to place all user functions into the
interpreter namespace.
........
r10312 | bugman | 2010-01-25 16:58:57 +0100 (Mon, 25 Jan 2010) | 5 lines
The relax main instance is no longer passed into the test suite.
This can be done as the prompt/script interface has been detached from
relax.
........
r10313 | bugman | 2010-01-25 17:00:12 +0100 (Mon, 25 Jan 2010) | 5 lines
The relax main instance is no longer passed into the prompt/script
interface.
This can be done as the prompt/script interface has been detached from
relax.
........
r10314 | bugman | 2010-01-25 17:06:28 +0100 (Mon, 25 Jan 2010) | 3 lines
The relax main instance is no longer handled by the system test
initialisation code.
........
r10315 | bugman | 2010-01-25 18:04:17 +0100 (Mon, 25 Jan 2010) | 5 lines
Created the SystemTestCase base class for all the system tests to use.
This base class initialises the relax interpreter within the TestCase class
instances.
........
r10316 | bugman | 2010-01-25 18:13:12 +0100 (Mon, 25 Jan 2010) | 3 lines
The interpreter _on() method does not need to be called as user fn intros
are turned on by default.
........
r10317 | bugman | 2010-01-25 18:52:04 +0100 (Mon, 25 Jan 2010) | 5 lines
Fixed all the calls to the user functions located in the interpreter class.
self.relax is no longer referenced and the user functions are now directly
called.
........
r10318 | bugman | 2010-01-25 18:52:38 +0100 (Mon, 25 Jan 2010) | 3 lines
Fixed the script user function.
........
r10319 | bugman | 2010-01-25 18:54:20 +0100 (Mon, 25 Jan 2010) | 3 lines
Removed redundant and now non-functional code from interact_script().
........
r10320 | bugman | 2010-01-25 19:04:45 +0100 (Mon, 25 Jan 2010) | 3 lines
Comment fix.
........
r10321 | bugman | 2010-01-25 19:11:25 +0100 (Mon, 25 Jan 2010) | 6 lines
Update the user function print out functions.
_off() and _on() are no longer private, and accept the verbose keyword arg
to allow the print out to
be suppressed.
........
r10322 | bugman | 2010-01-25 19:11:59 +0100 (Mon, 25 Jan 2010) | 3 lines
Alphabetical ordering of methods.
........
r10323 | bugman | 2010-01-25 19:21:05 +0100 (Mon, 25 Jan 2010) | 3 lines
The dAuvergne_protocol class now calls the user functions from the
self.interpreter instance directly.
........
r10324 | bugman | 2010-01-25 19:26:36 +0100 (Mon, 25 Jan 2010) | 5 lines
Fix for the automatic model-free protocol in dAuvergne_protocol.
The sequence.read() and relax_data.read() user functions args are now sent
in as keywords.
........
r10325 | bugman | 2010-01-25 20:31:25 +0100 (Mon, 25 Jan 2010) | 3 lines
Created the RelaxFileEmptyWarning class.
........
r10326 | bugman | 2010-01-25 20:36:30 +0100 (Mon, 25 Jan 2010) | 3 lines
Modified read_spin_data() to throw a warning rather than error when an
empty file is encountered.
........
Added:
branches/bieri_gui/test_suite/system_tests/base_classes.py
- copied unchanged from r10326,
1.3/test_suite/system_tests/base_classes.py
Removed:
branches/bieri_gui/test_suite/unit_tests/_prompt/fake_relax.py
Modified:
branches/bieri_gui/ (props changed)
branches/bieri_gui/auto_analyses/dauvergne_protocol.py
branches/bieri_gui/prompt/__init__.py
branches/bieri_gui/prompt/align_tensor.py
branches/bieri_gui/prompt/angles.py
branches/bieri_gui/prompt/base_class.py
branches/bieri_gui/prompt/command.py
branches/bieri_gui/prompt/consistency_tests.py
branches/bieri_gui/prompt/dasha.py
branches/bieri_gui/prompt/deselect.py
branches/bieri_gui/prompt/diffusion_tensor.py
branches/bieri_gui/prompt/doc_string.py
branches/bieri_gui/prompt/dx.py
branches/bieri_gui/prompt/eliminate.py
branches/bieri_gui/prompt/fix.py
branches/bieri_gui/prompt/frame_order.py
branches/bieri_gui/prompt/frq.py
branches/bieri_gui/prompt/grace.py
branches/bieri_gui/prompt/interpreter.py
branches/bieri_gui/prompt/jw_mapping.py
branches/bieri_gui/prompt/minimisation.py
branches/bieri_gui/prompt/model_free.py
branches/bieri_gui/prompt/model_selection.py
branches/bieri_gui/prompt/molecule.py
branches/bieri_gui/prompt/molmol.py
branches/bieri_gui/prompt/monte_carlo.py
branches/bieri_gui/prompt/n_state_model.py
branches/bieri_gui/prompt/noe.py
branches/bieri_gui/prompt/palmer.py
branches/bieri_gui/prompt/pcs.py
branches/bieri_gui/prompt/pipe.py
branches/bieri_gui/prompt/pymol.py
branches/bieri_gui/prompt/rdc.py
branches/bieri_gui/prompt/relax_data.py
branches/bieri_gui/prompt/relax_fit.py
branches/bieri_gui/prompt/residue.py
branches/bieri_gui/prompt/results.py
branches/bieri_gui/prompt/select.py
branches/bieri_gui/prompt/sequence.py
branches/bieri_gui/prompt/spectrum.py
branches/bieri_gui/prompt/spin.py
branches/bieri_gui/prompt/state.py
branches/bieri_gui/prompt/structure.py
branches/bieri_gui/prompt/temperature.py
branches/bieri_gui/prompt/value.py
branches/bieri_gui/prompt/view.py
branches/bieri_gui/prompt/vmd.py
branches/bieri_gui/relax
branches/bieri_gui/relax_io.py
branches/bieri_gui/relax_warnings.py
branches/bieri_gui/test_suite/system_tests/__init__.py
branches/bieri_gui/test_suite/system_tests/align_tensor.py
branches/bieri_gui/test_suite/system_tests/angles.py
branches/bieri_gui/test_suite/system_tests/consistency_tests.py
branches/bieri_gui/test_suite/system_tests/dasha.py
branches/bieri_gui/test_suite/system_tests/diffusion_tensor.py
branches/bieri_gui/test_suite/system_tests/frame_order.py
branches/bieri_gui/test_suite/system_tests/generic.py
branches/bieri_gui/test_suite/system_tests/jw_mapping.py
branches/bieri_gui/test_suite/system_tests/load_spins.py
branches/bieri_gui/test_suite/system_tests/model_elimination.py
branches/bieri_gui/test_suite/system_tests/model_free.py
branches/bieri_gui/test_suite/system_tests/model_selection.py
branches/bieri_gui/test_suite/system_tests/n_state_model.py
branches/bieri_gui/test_suite/system_tests/noe.py
branches/bieri_gui/test_suite/system_tests/noe_restraints.py
branches/bieri_gui/test_suite/system_tests/palmer.py
branches/bieri_gui/test_suite/system_tests/peak_lists.py
branches/bieri_gui/test_suite/system_tests/pipes.py
branches/bieri_gui/test_suite/system_tests/relax_fit.py
branches/bieri_gui/test_suite/system_tests/results.py
branches/bieri_gui/test_suite/system_tests/scripts/omp_model_free.py
branches/bieri_gui/test_suite/system_tests/sequence.py
branches/bieri_gui/test_suite/system_tests/state.py
branches/bieri_gui/test_suite/system_tests/structure.py
branches/bieri_gui/test_suite/system_tests/unit_vectors.py
branches/bieri_gui/test_suite/test_suite_runner.py
branches/bieri_gui/test_suite/unit_tests/_prompt/test_align_tensor.py
branches/bieri_gui/test_suite/unit_tests/_prompt/test_dasha.py
branches/bieri_gui/test_suite/unit_tests/_prompt/test_deselect.py
branches/bieri_gui/test_suite/unit_tests/_prompt/test_diffusion_tensor.py
branches/bieri_gui/test_suite/unit_tests/_prompt/test_eliminate.py
branches/bieri_gui/test_suite/unit_tests/_prompt/test_minimisation.py
branches/bieri_gui/test_suite/unit_tests/_prompt/test_model_free.py
branches/bieri_gui/test_suite/unit_tests/_prompt/test_molecule.py
branches/bieri_gui/test_suite/unit_tests/_prompt/test_molmol.py
branches/bieri_gui/test_suite/unit_tests/_prompt/test_n_state_model.py
branches/bieri_gui/test_suite/unit_tests/_prompt/test_noe.py
branches/bieri_gui/test_suite/unit_tests/_prompt/test_pymol.py
branches/bieri_gui/test_suite/unit_tests/_prompt/test_relax_data.py
branches/bieri_gui/test_suite/unit_tests/_prompt/test_relax_fit.py
branches/bieri_gui/test_suite/unit_tests/_prompt/test_residue.py
branches/bieri_gui/test_suite/unit_tests/_prompt/test_select.py
branches/bieri_gui/test_suite/unit_tests/_prompt/test_sequence.py
branches/bieri_gui/test_suite/unit_tests/_prompt/test_spectrum.py
branches/bieri_gui/test_suite/unit_tests/_prompt/test_spin.py
branches/bieri_gui/test_suite/unit_tests/_prompt/test_state.py
branches/bieri_gui/test_suite/unit_tests/_prompt/test_structure.py
branches/bieri_gui/test_suite/unit_tests/_prompt/test_value.py
[This mail would be too long, it was shortened to contain the URLs only.]
Modified: branches/bieri_gui/auto_analyses/dauvergne_protocol.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bieri_gui/auto_analyses/dauvergne_protocol.py?rev=10327&r1=10326&r2=10327&view=diff
Modified: branches/bieri_gui/prompt/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bieri_gui/prompt/__init__.py?rev=10327&r1=10326&r2=10327&view=diff
Modified: branches/bieri_gui/prompt/align_tensor.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bieri_gui/prompt/align_tensor.py?rev=10327&r1=10326&r2=10327&view=diff
Modified: branches/bieri_gui/prompt/angles.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bieri_gui/prompt/angles.py?rev=10327&r1=10326&r2=10327&view=diff
Modified: branches/bieri_gui/prompt/base_class.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bieri_gui/prompt/base_class.py?rev=10327&r1=10326&r2=10327&view=diff
Modified: branches/bieri_gui/prompt/command.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bieri_gui/prompt/command.py?rev=10327&r1=10326&r2=10327&view=diff
Modified: branches/bieri_gui/prompt/consistency_tests.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bieri_gui/prompt/consistency_tests.py?rev=10327&r1=10326&r2=10327&view=diff
Modified: branches/bieri_gui/prompt/dasha.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bieri_gui/prompt/dasha.py?rev=10327&r1=10326&r2=10327&view=diff
Modified: branches/bieri_gui/prompt/deselect.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bieri_gui/prompt/deselect.py?rev=10327&r1=10326&r2=10327&view=diff
Modified: branches/bieri_gui/prompt/diffusion_tensor.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bieri_gui/prompt/diffusion_tensor.py?rev=10327&r1=10326&r2=10327&view=diff
Modified: branches/bieri_gui/prompt/doc_string.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bieri_gui/prompt/doc_string.py?rev=10327&r1=10326&r2=10327&view=diff
Modified: branches/bieri_gui/prompt/dx.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bieri_gui/prompt/dx.py?rev=10327&r1=10326&r2=10327&view=diff
Modified: branches/bieri_gui/prompt/eliminate.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bieri_gui/prompt/eliminate.py?rev=10327&r1=10326&r2=10327&view=diff
Modified: branches/bieri_gui/prompt/fix.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bieri_gui/prompt/fix.py?rev=10327&r1=10326&r2=10327&view=diff
Modified: branches/bieri_gui/prompt/frame_order.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bieri_gui/prompt/frame_order.py?rev=10327&r1=10326&r2=10327&view=diff
Modified: branches/bieri_gui/prompt/frq.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bieri_gui/prompt/frq.py?rev=10327&r1=10326&r2=10327&view=diff
Modified: branches/bieri_gui/prompt/grace.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bieri_gui/prompt/grace.py?rev=10327&r1=10326&r2=10327&view=diff
Modified: branches/bieri_gui/prompt/interpreter.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bieri_gui/prompt/interpreter.py?rev=10327&r1=10326&r2=10327&view=diff
Modified: branches/bieri_gui/prompt/jw_mapping.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bieri_gui/prompt/jw_mapping.py?rev=10327&r1=10326&r2=10327&view=diff
Modified: branches/bieri_gui/prompt/minimisation.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bieri_gui/prompt/minimisation.py?rev=10327&r1=10326&r2=10327&view=diff
Modified: branches/bieri_gui/prompt/model_free.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bieri_gui/prompt/model_free.py?rev=10327&r1=10326&r2=10327&view=diff
Modified: branches/bieri_gui/prompt/model_selection.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bieri_gui/prompt/model_selection.py?rev=10327&r1=10326&r2=10327&view=diff
Modified: branches/bieri_gui/prompt/molecule.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bieri_gui/prompt/molecule.py?rev=10327&r1=10326&r2=10327&view=diff
Modified: branches/bieri_gui/prompt/molmol.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bieri_gui/prompt/molmol.py?rev=10327&r1=10326&r2=10327&view=diff
Modified: branches/bieri_gui/prompt/monte_carlo.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bieri_gui/prompt/monte_carlo.py?rev=10327&r1=10326&r2=10327&view=diff
Modified: branches/bieri_gui/prompt/n_state_model.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bieri_gui/prompt/n_state_model.py?rev=10327&r1=10326&r2=10327&view=diff
Modified: branches/bieri_gui/prompt/noe.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bieri_gui/prompt/noe.py?rev=10327&r1=10326&r2=10327&view=diff
Modified: branches/bieri_gui/prompt/palmer.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bieri_gui/prompt/palmer.py?rev=10327&r1=10326&r2=10327&view=diff
Modified: branches/bieri_gui/prompt/pcs.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bieri_gui/prompt/pcs.py?rev=10327&r1=10326&r2=10327&view=diff
Modified: branches/bieri_gui/prompt/pipe.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bieri_gui/prompt/pipe.py?rev=10327&r1=10326&r2=10327&view=diff
Modified: branches/bieri_gui/prompt/pymol.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bieri_gui/prompt/pymol.py?rev=10327&r1=10326&r2=10327&view=diff
Modified: branches/bieri_gui/prompt/rdc.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bieri_gui/prompt/rdc.py?rev=10327&r1=10326&r2=10327&view=diff
Modified: branches/bieri_gui/prompt/relax_data.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bieri_gui/prompt/relax_data.py?rev=10327&r1=10326&r2=10327&view=diff
Modified: branches/bieri_gui/prompt/relax_fit.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bieri_gui/prompt/relax_fit.py?rev=10327&r1=10326&r2=10327&view=diff
Modified: branches/bieri_gui/prompt/residue.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bieri_gui/prompt/residue.py?rev=10327&r1=10326&r2=10327&view=diff
Modified: branches/bieri_gui/prompt/results.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bieri_gui/prompt/results.py?rev=10327&r1=10326&r2=10327&view=diff
Modified: branches/bieri_gui/prompt/select.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bieri_gui/prompt/select.py?rev=10327&r1=10326&r2=10327&view=diff
Modified: branches/bieri_gui/prompt/sequence.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bieri_gui/prompt/sequence.py?rev=10327&r1=10326&r2=10327&view=diff
Modified: branches/bieri_gui/prompt/spectrum.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bieri_gui/prompt/spectrum.py?rev=10327&r1=10326&r2=10327&view=diff
Modified: branches/bieri_gui/prompt/spin.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bieri_gui/prompt/spin.py?rev=10327&r1=10326&r2=10327&view=diff
Modified: branches/bieri_gui/prompt/state.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bieri_gui/prompt/state.py?rev=10327&r1=10326&r2=10327&view=diff
Modified: branches/bieri_gui/prompt/structure.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bieri_gui/prompt/structure.py?rev=10327&r1=10326&r2=10327&view=diff
Modified: branches/bieri_gui/prompt/temperature.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bieri_gui/prompt/temperature.py?rev=10327&r1=10326&r2=10327&view=diff
Modified: branches/bieri_gui/prompt/value.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bieri_gui/prompt/value.py?rev=10327&r1=10326&r2=10327&view=diff
Modified: branches/bieri_gui/prompt/view.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bieri_gui/prompt/view.py?rev=10327&r1=10326&r2=10327&view=diff
Modified: branches/bieri_gui/prompt/vmd.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bieri_gui/prompt/vmd.py?rev=10327&r1=10326&r2=10327&view=diff
Modified: branches/bieri_gui/relax
URL:
http://svn.gna.org/viewcvs/relax/branches/bieri_gui/relax?rev=10327&r1=10326&r2=10327&view=diff
Modified: branches/bieri_gui/relax_io.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bieri_gui/relax_io.py?rev=10327&r1=10326&r2=10327&view=diff
Modified: branches/bieri_gui/relax_warnings.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bieri_gui/relax_warnings.py?rev=10327&r1=10326&r2=10327&view=diff
Modified: branches/bieri_gui/test_suite/system_tests/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bieri_gui/test_suite/system_tests/__init__.py?rev=10327&r1=10326&r2=10327&view=diff
Modified: branches/bieri_gui/test_suite/system_tests/align_tensor.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bieri_gui/test_suite/system_tests/align_tensor.py?rev=10327&r1=10326&r2=10327&view=diff
Modified: branches/bieri_gui/test_suite/system_tests/angles.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bieri_gui/test_suite/system_tests/angles.py?rev=10327&r1=10326&r2=10327&view=diff
[... 141 lines stripped ...]
r10327 - in /branches/bieri_gui: ./ auto_analyses/ prompt/ test_suite/ test_suite/system_tests/ test_suite/system_tests/scri...