Author: bugman
Date: Thu Jul 12 19:25:43 2012
New Revision: 17247
URL: http://svn.gna.org/viewcvs/relax?rev=17247&view=rev
Log:
Merged revisions 17206,17210-17233,17236,17242-17244 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/trunk
........
r17206 | bugman | 2012-07-04 14:22:00 +0200 (Wed, 04 Jul 2012) | 5 lines
Fixes for the tooltips and activation/deactivation of the GUI model-free
analysis buttons.
This is for the buttons for setting up the relaxation mechanisms and the
nuclear isotopes.
........
r17210 | bugman | 2012-07-04 17:43:04 +0200 (Wed, 04 Jul 2012) | 7 lines
Bug fix for the GUI tests on MS Windows.
The GuiTestCase._execute_uf() method now prevents the wizard from running
when calling the GUI
user function by setting the wx_wizard_run argument to False. This allows
the wizard _ok() call to
function on Windows.
........
r17211 | bugman | 2012-07-09 10:52:01 +0200 (Mon, 09 Jul 2012) | 5 lines
Bug fix for the Dead_uf_pages.test_mol_create() GUI test for MS Windows.
The _execute_uf() method is now used instead of simulating _ok() calls.
........
r17212 | bugman | 2012-07-09 16:06:34 +0200 (Mon, 09 Jul 2012) | 3 lines
Bug fix for the running of the GUI tests on Mac OS X - the relax GUI 'app'
needs to be deleted after each test.
........
r17213 | bugman | 2012-07-09 16:20:57 +0200 (Mon, 09 Jul 2012) | 6 lines
Bug fix for the GUI test suite setUp() method.
The observer objects are reset at the start to get around a bug when the
setUp() method fails for a
previous test.
........
r17214 | bugman | 2012-07-10 08:11:40 +0200 (Tue, 10 Jul 2012) | 9 lines
Redesign of the setUp() and tearDown() methods of the GUI tests.
This is needed as the current design does not work under MS Windows!
Instead of created a new wx
app for each test (this dies in Windows as it looks like only a limited
number of toolbars can be
created), only one app is created and is recycled. This design better
mimics GUI usage anyway.
This change uncovers a few GUI bugs not caught by the previous design.
........
r17215 | bugman | 2012-07-10 08:50:40 +0200 (Tue, 10 Jul 2012) | 6 lines
Removed the notebook tab deletion from the GUI tests tearDown() method.
This should be performed when a relax reset happens, so it is not needed in
the tearDown() method
just before the reset() call. This change reveals another set of GUI bugs!
........
r17216 | bugman | 2012-07-10 09:33:26 +0200 (Tue, 10 Jul 2012) | 5 lines
Improved debugging print outs for the observer objects.
The method name is now stored and included in all the observer 'debug>'
printouts.
........
r17217 | bugman | 2012-07-10 10:43:04 +0200 (Tue, 10 Jul 2012) | 3 lines
Bug fix for the GUI tests setUp() method - the observer objects must no be
reset!
........
r17218 | bugman | 2012-07-10 11:52:31 +0200 (Tue, 10 Jul 2012) | 3 lines
Shifted all of the observer registration and unregistration to
observer_setup() in the pipe editor.
........
r17219 | bugman | 2012-07-10 11:55:00 +0200 (Tue, 10 Jul 2012) | 6 lines
The GUI show_pipe_editor() method is now the place where the methods are
registered with the observers.
This is a partial bug fix for the GUI tests. The hiding mechanism of the
window with unregistration
requires this.
........
r17220 | bugman | 2012-07-10 12:24:49 +0200 (Tue, 10 Jul 2012) | 6 lines
Fix for the State.test_load_state_no_gui() for handling pipe bundles.
Though not caught by the test, the pipe needs to be associated with a pipe
bundle to be able to
cleanly associate with a model-free analysis tab.
........
r17221 | bugman | 2012-07-10 12:26:41 +0200 (Tue, 10 Jul 2012) | 7 lines
Bug fix for the pipe editor window hiding and restoring.
All of the Pipe_editor.Show() method has been shifted into the GUI
show_pipe_editor() method. This
is needed for the technique of unregistering with the observer objects when
the window is closed via
a Hide() call.
........
r17222 | bugman | 2012-07-10 14:14:07 +0200 (Tue, 10 Jul 2012) | 6 lines
Improvements to the skipped test printout from the test suite.
Now all test categories (system, unit and GUI) are printed if a
module/package is missing. This
allows for better debugging.
........
r17223 | bugman | 2012-07-10 14:37:33 +0200 (Tue, 10 Jul 2012) | 6 lines
Fix for the reporting of skipped GUI tests.
The Frame_order tests skipped because of the missing Scipy module were been
labelled as system
rather than GUI tests.
........
r17224 | bugman | 2012-07-10 17:39:28 +0200 (Tue, 10 Jul 2012) | 7 lines
Bug fix for MS Windows for the deletion of temporary files in the system
tests.
For certain Windows/Python combinations, a WindowsError was being raised
saying that the file cannot
be deleted as it is being used by another process. This happens when the
XML file from a
results.write or state.save user function call is deleted by the system
test tearDown() method.
........
r17225 | bugman | 2012-07-10 20:16:55 +0200 (Tue, 10 Jul 2012) | 3 lines
Updated relax to the GNU General Public License version 3.
........
r17226 | bugman | 2012-07-10 20:43:53 +0200 (Tue, 10 Jul 2012) | 3 lines
More GPL v3 license updates.
........
r17227 | bugman | 2012-07-11 11:18:44 +0200 (Wed, 11 Jul 2012) | 7 lines
Bug fix for the model-free GUI auto-analysis GUI test on MS Windows.
The wizards for the CSA value and nuclear isotopes were experiencing racing
conditions on MS Windows
with the _ok() calls. These have been replaced with _go_next() calls which
do not have the same
issue.
........
r17228 | bugman | 2012-07-11 12:23:50 +0200 (Wed, 11 Jul 2012) | 3 lines
Increased the size of the test suite warning dialog for MS Windows.
........
r17229 | bugman | 2012-07-11 15:31:08 +0200 (Wed, 11 Jul 2012) | 3 lines
Shifted some of the sample scripts into the analysis specific
sub-directories.
........
r17230 | bugman | 2012-07-11 16:59:51 +0200 (Wed, 11 Jul 2012) | 3 lines
Updated the journal reference for the published lactose conformational
search scripts.
........
r17231 | bugman | 2012-07-11 17:06:20 +0200 (Wed, 11 Jul 2012) | 3 lines
Fixes for the prompt examples in the dipole_pair.read_dist user function
documentation.
........
r17232 | bugman | 2012-07-11 17:24:52 +0200 (Wed, 11 Jul 2012) | 3 lines
Expanded RelaxNoInteratomError to handle the spin IDs as arguments,
including these in the message.
........
r17233 | bugman | 2012-07-11 18:00:45 +0200 (Wed, 11 Jul 2012) | 3 lines
Fixes for the dipole_pair.read_dist user function.
........
r17236 | bugman | 2012-07-12 11:35:20 +0200 (Thu, 12 Jul 2012) | 6 lines
Merged the CHANGES file from the relax 2.1.0 tag back to the trunk.
The command used was:
svn merge -r17234:17235 svn+ssh://bugman@xxxxxxxxxxx/svn/relax/tags/2.1.0
........
r17242 | bugman | 2012-07-12 17:29:44 +0200 (Thu, 12 Jul 2012) | 3 lines
Import fix for the epydoc building of the API documentation.
........
r17243 | bugman | 2012-07-12 17:30:02 +0200 (Thu, 12 Jul 2012) | 3 lines
Epydoc docstring fixes for the API documentation.
........
r17244 | bugman | 2012-07-12 17:36:04 +0200 (Thu, 12 Jul 2012) | 3 lines
Import additions to fix the epydoc import of the 'sconstruct' script for
the API documentation.
........
Added:
branches/relax_disp/docs/latex/gpl-3.0.tex
- copied unchanged from r17244, trunk/docs/latex/gpl-3.0.tex
branches/relax_disp/sample_scripts/model_free/generate_ri.py
- copied unchanged from r17244,
trunk/sample_scripts/model_free/generate_ri.py
branches/relax_disp/sample_scripts/n_state_model/stereochem_analysis.py
- copied unchanged from r17244,
trunk/sample_scripts/n_state_model/stereochem_analysis.py
Removed:
branches/relax_disp/sample_scripts/generate_ri.py
branches/relax_disp/sample_scripts/stereochem_analysis.py
Modified:
branches/relax_disp/ (props changed)
branches/relax_disp/ansi.py
branches/relax_disp/arg_check.py
branches/relax_disp/auto_analyses/__init__.py
branches/relax_disp/auto_analyses/dauvergne_protocol.py
branches/relax_disp/auto_analyses/noe.py
branches/relax_disp/auto_analyses/relax_fit.py
branches/relax_disp/auto_analyses/stereochem_analysis.py
branches/relax_disp/colour.py
branches/relax_disp/data/__init__.py
branches/relax_disp/data/align_tensor.py
branches/relax_disp/data/data_classes.py
branches/relax_disp/data/diff_tensor.py
branches/relax_disp/data/exp_info.py
branches/relax_disp/data/gui.py
branches/relax_disp/data/interatomic.py
branches/relax_disp/data/mol_res_spin.py
branches/relax_disp/data/pipe_container.py
branches/relax_disp/data/prototype.py
branches/relax_disp/data/relax_xml.py
branches/relax_disp/dep_check.py
branches/relax_disp/docs/CHANGES
branches/relax_disp/docs/COPYING
branches/relax_disp/docs/__init__.py
branches/relax_disp/docs/latex/__init__.py
branches/relax_disp/docs/latex/fetch_docstrings.py
branches/relax_disp/docs/latex/licence.tex
branches/relax_disp/extern/__init__.py
branches/relax_disp/float.py
branches/relax_disp/generic_fns/__init__.py
branches/relax_disp/generic_fns/align_tensor.py
branches/relax_disp/generic_fns/angles.py
branches/relax_disp/generic_fns/bmrb.py
branches/relax_disp/generic_fns/bruker.py
branches/relax_disp/generic_fns/dasha.py
branches/relax_disp/generic_fns/diffusion_tensor.py
branches/relax_disp/generic_fns/dipole_pair.py
branches/relax_disp/generic_fns/eliminate.py
branches/relax_disp/generic_fns/exp_info.py
branches/relax_disp/generic_fns/fix.py
branches/relax_disp/generic_fns/frame_order.py
branches/relax_disp/generic_fns/frq.py
branches/relax_disp/generic_fns/grace.py
branches/relax_disp/generic_fns/interatomic.py
branches/relax_disp/generic_fns/minimise.py
branches/relax_disp/generic_fns/model_selection.py
branches/relax_disp/generic_fns/mol_res_spin.py
branches/relax_disp/generic_fns/molmol.py
branches/relax_disp/generic_fns/monte_carlo.py
branches/relax_disp/generic_fns/noesy.py
branches/relax_disp/generic_fns/palmer.py
branches/relax_disp/generic_fns/paramag.py
branches/relax_disp/generic_fns/pcs.py
branches/relax_disp/generic_fns/pipes.py
branches/relax_disp/generic_fns/pymol_control.py
branches/relax_disp/generic_fns/rdc.py
branches/relax_disp/generic_fns/relax_data.py
branches/relax_disp/generic_fns/relax_re.py
branches/relax_disp/generic_fns/reset.py
branches/relax_disp/generic_fns/results.py
branches/relax_disp/generic_fns/script.py
branches/relax_disp/generic_fns/selection.py
branches/relax_disp/generic_fns/sequence.py
branches/relax_disp/generic_fns/spectrum.py
branches/relax_disp/generic_fns/state.py
branches/relax_disp/generic_fns/structure/__init__.py
branches/relax_disp/generic_fns/structure/api_base.py
branches/relax_disp/generic_fns/structure/cones.py
branches/relax_disp/generic_fns/structure/geometric.py
branches/relax_disp/generic_fns/structure/internal.py
branches/relax_disp/generic_fns/structure/main.py
branches/relax_disp/generic_fns/structure/mass.py
branches/relax_disp/generic_fns/structure/scientific.py
branches/relax_disp/generic_fns/structure/superimpose.py
branches/relax_disp/generic_fns/sys_info.py
branches/relax_disp/generic_fns/temperature.py
branches/relax_disp/generic_fns/value.py
branches/relax_disp/generic_fns/vmd.py
branches/relax_disp/generic_fns/xplor.py
branches/relax_disp/graphics/__init__.py
branches/relax_disp/gui/__init__.py
branches/relax_disp/gui/about.py
branches/relax_disp/gui/analyses/__init__.py
branches/relax_disp/gui/analyses/auto_model_free.py
branches/relax_disp/gui/analyses/auto_noe.py
branches/relax_disp/gui/analyses/auto_r1.py
branches/relax_disp/gui/analyses/auto_r2.py
branches/relax_disp/gui/analyses/auto_rx_base.py
branches/relax_disp/gui/analyses/base.py
branches/relax_disp/gui/analyses/elements.py
branches/relax_disp/gui/analyses/execute.py
branches/relax_disp/gui/analyses/results_analysis.py
branches/relax_disp/gui/analyses/wizard.py
branches/relax_disp/gui/base_classes.py
branches/relax_disp/gui/components/__init__.py
branches/relax_disp/gui/components/base_list.py
branches/relax_disp/gui/components/citations.py
branches/relax_disp/gui/components/conversion.py
branches/relax_disp/gui/components/free_file_format.py
branches/relax_disp/gui/components/grid.py
branches/relax_disp/gui/components/menu.py
branches/relax_disp/gui/components/molecule.py
branches/relax_disp/gui/components/relax_data.py
branches/relax_disp/gui/components/relax_data_meta.py
branches/relax_disp/gui/components/scripts.py
branches/relax_disp/gui/components/software.py
branches/relax_disp/gui/components/spectrum.py
branches/relax_disp/gui/controller.py
branches/relax_disp/gui/errors.py
branches/relax_disp/gui/export_bmrb.py
branches/relax_disp/gui/filedialog.py
branches/relax_disp/gui/fonts.py
branches/relax_disp/gui/icons.py
branches/relax_disp/gui/input_elements/__init__.py
branches/relax_disp/gui/input_elements/bool.py
branches/relax_disp/gui/input_elements/combo_list.py
branches/relax_disp/gui/input_elements/dir.py
branches/relax_disp/gui/input_elements/file.py
branches/relax_disp/gui/input_elements/sequence.py
branches/relax_disp/gui/input_elements/sequence_2D.py
branches/relax_disp/gui/input_elements/spin_id.py
branches/relax_disp/gui/input_elements/value.py
branches/relax_disp/gui/interpreter.py
branches/relax_disp/gui/menu.py
branches/relax_disp/gui/message.py
branches/relax_disp/gui/misc.py
branches/relax_disp/gui/paths.py
branches/relax_disp/gui/pipe_editor.py
branches/relax_disp/gui/references.py
branches/relax_disp/gui/relax_gui.py
branches/relax_disp/gui/relax_prompt.py
branches/relax_disp/gui/results_viewer.py
branches/relax_disp/gui/spin_viewer/__init__.py
branches/relax_disp/gui/spin_viewer/containers.py
branches/relax_disp/gui/spin_viewer/frame.py
branches/relax_disp/gui/spin_viewer/splitter.py
branches/relax_disp/gui/spin_viewer/tree.py
branches/relax_disp/gui/string_conv.py
branches/relax_disp/gui/uf_objects.py
branches/relax_disp/gui/wizard.py
branches/relax_disp/info.py
branches/relax_disp/maths_fns/__init__.py
branches/relax_disp/maths_fns/alignment_tensor.py
branches/relax_disp/maths_fns/c_chi2.c
branches/relax_disp/maths_fns/c_chi2.h
branches/relax_disp/maths_fns/chi2.py
branches/relax_disp/maths_fns/consistency_tests.py
branches/relax_disp/maths_fns/coord_transform.py
branches/relax_disp/maths_fns/correlation_time.py
branches/relax_disp/maths_fns/direction_cosine.py
branches/relax_disp/maths_fns/exponential.c
branches/relax_disp/maths_fns/exponential.h
branches/relax_disp/maths_fns/frame_order.py
branches/relax_disp/maths_fns/frame_order_matrix_ops.py
branches/relax_disp/maths_fns/jw_mapping.py
branches/relax_disp/maths_fns/jw_mf.py
branches/relax_disp/maths_fns/jw_mf_comps.py
branches/relax_disp/maths_fns/kronecker_product.py
branches/relax_disp/maths_fns/mf.py
branches/relax_disp/maths_fns/n_state_model.py
branches/relax_disp/maths_fns/order_parameters.py
branches/relax_disp/maths_fns/paramag_centre.py
branches/relax_disp/maths_fns/pcs.py
branches/relax_disp/maths_fns/potential.py
branches/relax_disp/maths_fns/pseudo_ellipse.py
branches/relax_disp/maths_fns/rdc.py
branches/relax_disp/maths_fns/relax_fit.c
branches/relax_disp/maths_fns/relax_fit.h
branches/relax_disp/maths_fns/ri.py
branches/relax_disp/maths_fns/ri_comps.py
branches/relax_disp/maths_fns/ri_prime.py
branches/relax_disp/maths_fns/rotation_matrix.py
branches/relax_disp/maths_fns/weights.py
branches/relax_disp/multi/__init__.py
branches/relax_disp/multi/memo.py
branches/relax_disp/multi/misc.py
branches/relax_disp/multi/mpi4py_processor.py
branches/relax_disp/multi/multi_processor_base.py
branches/relax_disp/multi/processor.py
branches/relax_disp/multi/processor_io.py
branches/relax_disp/multi/result_commands.py
branches/relax_disp/multi/result_queue.py
branches/relax_disp/multi/slave_commands.py
branches/relax_disp/multi/uni_processor.py
branches/relax_disp/opendx/__init__.py
branches/relax_disp/opendx/base_map.py
branches/relax_disp/opendx/isosurface_3D.py
branches/relax_disp/opendx/main.py
branches/relax_disp/physical_constants.py
branches/relax_disp/prompt/__init__.py
branches/relax_disp/prompt/command.py
branches/relax_disp/prompt/doc_string.py
branches/relax_disp/prompt/gpl.py
branches/relax_disp/prompt/help.py
branches/relax_disp/prompt/interpreter.py
branches/relax_disp/prompt/tab_completion.py
branches/relax_disp/prompt/uf_docstring.py
branches/relax_disp/prompt/uf_objects.py
branches/relax_disp/relax.py
branches/relax_disp/relax_errors.py
branches/relax_disp/relax_io.py
branches/relax_disp/relax_string.py
branches/relax_disp/relax_warnings.py
branches/relax_disp/sample_scripts/angles.py
branches/relax_disp/sample_scripts/consistency_tests.py
branches/relax_disp/sample_scripts/diff_tensor_pdb.py
branches/relax_disp/sample_scripts/jw_mapping.py
branches/relax_disp/sample_scripts/model_free/bmrb_deposition.py
branches/relax_disp/sample_scripts/model_free/cv.py
branches/relax_disp/sample_scripts/model_free/dasha.py
branches/relax_disp/sample_scripts/model_free/dauvergne_protocol.py
branches/relax_disp/sample_scripts/model_free/diff_min.py
branches/relax_disp/sample_scripts/model_free/grace_S2_vs_te.py
branches/relax_disp/sample_scripts/model_free/grace_ri_data_correlation.py
branches/relax_disp/sample_scripts/model_free/map.py
branches/relax_disp/sample_scripts/model_free/mf_multimodel.py
branches/relax_disp/sample_scripts/model_free/modsel.py
branches/relax_disp/sample_scripts/model_free/molmol_plot.py
branches/relax_disp/sample_scripts/model_free/palmer.py
branches/relax_disp/sample_scripts/model_free/remap.py
branches/relax_disp/sample_scripts/model_free/single_model.py
branches/relax_disp/sample_scripts/model_free/table_csv.py
branches/relax_disp/sample_scripts/model_free/table_latex.py
branches/relax_disp/sample_scripts/n_state_model/conformation_analysis_rdc+pcs.py
branches/relax_disp/sample_scripts/n_state_model/local_min_search.py
branches/relax_disp/sample_scripts/n_state_model/two_domain.py
branches/relax_disp/sample_scripts/noe.py
branches/relax_disp/sample_scripts/relax_curve_diff.py
branches/relax_disp/sample_scripts/relax_fit.py
branches/relax_disp/sample_scripts/xh_vector_dist.py
branches/relax_disp/scons/__init__.py
branches/relax_disp/scons/distrib.py
branches/relax_disp/scons/install.py
branches/relax_disp/scons/manuals.py
branches/relax_disp/sconstruct
branches/relax_disp/scripts/gui/about_gui.py
branches/relax_disp/scripts/gui/about_model_free.py
branches/relax_disp/scripts/gui/about_relax.py
branches/relax_disp/scripts/gui/refs.py
branches/relax_disp/scripts/gui/spin_create.py
branches/relax_disp/scripts/gui/uf_sequence_read.py
branches/relax_disp/setup.py
branches/relax_disp/specific_fns/__init__.py
branches/relax_disp/specific_fns/api_base.py
branches/relax_disp/specific_fns/api_common.py
branches/relax_disp/specific_fns/api_objects.py
[... 1780 lines stripped ...]
r17247 - in /branches/relax_disp: ./ auto_analyses/ data/ docs/ docs/latex/ extern/ generic_fns/ generic_fns/structure/ grap...