Author: bugman Date: Thu Jul 12 19:42:21 2012 New Revision: 17250 URL: http://svn.gna.org/viewcvs/relax?rev=17250&view=rev Log: Merged revisions 17210-17233,17236,17242-17244 via svnmerge from svn+ssh://bugman@xxxxxxxxxxx/svn/relax/trunk ........ 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/frame_order_testing/docs/latex/gpl-3.0.tex - copied unchanged from r17244, trunk/docs/latex/gpl-3.0.tex branches/frame_order_testing/sample_scripts/model_free/generate_ri.py - copied unchanged from r17244, trunk/sample_scripts/model_free/generate_ri.py branches/frame_order_testing/sample_scripts/n_state_model/stereochem_analysis.py - copied unchanged from r17244, trunk/sample_scripts/n_state_model/stereochem_analysis.py Removed: branches/frame_order_testing/sample_scripts/generate_ri.py branches/frame_order_testing/sample_scripts/stereochem_analysis.py Modified: branches/frame_order_testing/ (props changed) branches/frame_order_testing/ansi.py branches/frame_order_testing/arg_check.py branches/frame_order_testing/auto_analyses/__init__.py branches/frame_order_testing/auto_analyses/dauvergne_protocol.py branches/frame_order_testing/auto_analyses/noe.py branches/frame_order_testing/auto_analyses/relax_fit.py branches/frame_order_testing/auto_analyses/stereochem_analysis.py branches/frame_order_testing/colour.py branches/frame_order_testing/data/__init__.py branches/frame_order_testing/data/align_tensor.py branches/frame_order_testing/data/data_classes.py branches/frame_order_testing/data/diff_tensor.py branches/frame_order_testing/data/exp_info.py branches/frame_order_testing/data/gui.py branches/frame_order_testing/data/interatomic.py branches/frame_order_testing/data/mol_res_spin.py branches/frame_order_testing/data/pipe_container.py branches/frame_order_testing/data/prototype.py branches/frame_order_testing/data/relax_xml.py branches/frame_order_testing/dep_check.py branches/frame_order_testing/docs/CHANGES branches/frame_order_testing/docs/COPYING branches/frame_order_testing/docs/__init__.py branches/frame_order_testing/docs/latex/__init__.py branches/frame_order_testing/docs/latex/fetch_docstrings.py branches/frame_order_testing/docs/latex/licence.tex branches/frame_order_testing/extern/__init__.py branches/frame_order_testing/float.py branches/frame_order_testing/generic_fns/__init__.py branches/frame_order_testing/generic_fns/align_tensor.py branches/frame_order_testing/generic_fns/angles.py branches/frame_order_testing/generic_fns/bmrb.py branches/frame_order_testing/generic_fns/bruker.py branches/frame_order_testing/generic_fns/dasha.py branches/frame_order_testing/generic_fns/diffusion_tensor.py branches/frame_order_testing/generic_fns/dipole_pair.py branches/frame_order_testing/generic_fns/eliminate.py branches/frame_order_testing/generic_fns/exp_info.py branches/frame_order_testing/generic_fns/fix.py branches/frame_order_testing/generic_fns/frame_order.py branches/frame_order_testing/generic_fns/frq.py branches/frame_order_testing/generic_fns/grace.py branches/frame_order_testing/generic_fns/interatomic.py branches/frame_order_testing/generic_fns/minimise.py branches/frame_order_testing/generic_fns/model_selection.py branches/frame_order_testing/generic_fns/mol_res_spin.py branches/frame_order_testing/generic_fns/molmol.py branches/frame_order_testing/generic_fns/monte_carlo.py branches/frame_order_testing/generic_fns/noesy.py branches/frame_order_testing/generic_fns/palmer.py branches/frame_order_testing/generic_fns/paramag.py branches/frame_order_testing/generic_fns/pcs.py branches/frame_order_testing/generic_fns/pipes.py branches/frame_order_testing/generic_fns/pymol_control.py branches/frame_order_testing/generic_fns/rdc.py branches/frame_order_testing/generic_fns/relax_data.py branches/frame_order_testing/generic_fns/relax_re.py branches/frame_order_testing/generic_fns/reset.py branches/frame_order_testing/generic_fns/results.py branches/frame_order_testing/generic_fns/script.py branches/frame_order_testing/generic_fns/selection.py branches/frame_order_testing/generic_fns/sequence.py branches/frame_order_testing/generic_fns/spectrum.py branches/frame_order_testing/generic_fns/state.py branches/frame_order_testing/generic_fns/structure/__init__.py branches/frame_order_testing/generic_fns/structure/api_base.py branches/frame_order_testing/generic_fns/structure/cones.py branches/frame_order_testing/generic_fns/structure/geometric.py branches/frame_order_testing/generic_fns/structure/internal.py branches/frame_order_testing/generic_fns/structure/main.py branches/frame_order_testing/generic_fns/structure/mass.py branches/frame_order_testing/generic_fns/structure/scientific.py branches/frame_order_testing/generic_fns/structure/superimpose.py branches/frame_order_testing/generic_fns/sys_info.py branches/frame_order_testing/generic_fns/temperature.py branches/frame_order_testing/generic_fns/value.py branches/frame_order_testing/generic_fns/vmd.py branches/frame_order_testing/generic_fns/xplor.py branches/frame_order_testing/graphics/__init__.py branches/frame_order_testing/gui/__init__.py branches/frame_order_testing/gui/about.py branches/frame_order_testing/gui/analyses/__init__.py branches/frame_order_testing/gui/analyses/auto_model_free.py branches/frame_order_testing/gui/analyses/auto_noe.py branches/frame_order_testing/gui/analyses/auto_r1.py branches/frame_order_testing/gui/analyses/auto_r2.py branches/frame_order_testing/gui/analyses/auto_rx_base.py branches/frame_order_testing/gui/analyses/base.py branches/frame_order_testing/gui/analyses/elements.py branches/frame_order_testing/gui/analyses/execute.py branches/frame_order_testing/gui/analyses/results_analysis.py branches/frame_order_testing/gui/analyses/wizard.py branches/frame_order_testing/gui/base_classes.py branches/frame_order_testing/gui/components/__init__.py branches/frame_order_testing/gui/components/base_list.py branches/frame_order_testing/gui/components/citations.py branches/frame_order_testing/gui/components/conversion.py branches/frame_order_testing/gui/components/free_file_format.py branches/frame_order_testing/gui/components/grid.py branches/frame_order_testing/gui/components/menu.py branches/frame_order_testing/gui/components/molecule.py branches/frame_order_testing/gui/components/relax_data.py branches/frame_order_testing/gui/components/relax_data_meta.py branches/frame_order_testing/gui/components/scripts.py branches/frame_order_testing/gui/components/software.py branches/frame_order_testing/gui/components/spectrum.py branches/frame_order_testing/gui/controller.py branches/frame_order_testing/gui/errors.py branches/frame_order_testing/gui/export_bmrb.py branches/frame_order_testing/gui/filedialog.py branches/frame_order_testing/gui/fonts.py branches/frame_order_testing/gui/icons.py branches/frame_order_testing/gui/input_elements/__init__.py branches/frame_order_testing/gui/input_elements/bool.py branches/frame_order_testing/gui/input_elements/combo_list.py branches/frame_order_testing/gui/input_elements/dir.py branches/frame_order_testing/gui/input_elements/file.py branches/frame_order_testing/gui/input_elements/sequence.py branches/frame_order_testing/gui/input_elements/sequence_2D.py branches/frame_order_testing/gui/input_elements/spin_id.py branches/frame_order_testing/gui/input_elements/value.py branches/frame_order_testing/gui/interpreter.py branches/frame_order_testing/gui/menu.py branches/frame_order_testing/gui/message.py branches/frame_order_testing/gui/misc.py branches/frame_order_testing/gui/paths.py branches/frame_order_testing/gui/pipe_editor.py branches/frame_order_testing/gui/references.py branches/frame_order_testing/gui/relax_gui.py branches/frame_order_testing/gui/relax_prompt.py branches/frame_order_testing/gui/results_viewer.py branches/frame_order_testing/gui/spin_viewer/__init__.py branches/frame_order_testing/gui/spin_viewer/containers.py branches/frame_order_testing/gui/spin_viewer/frame.py branches/frame_order_testing/gui/spin_viewer/splitter.py branches/frame_order_testing/gui/spin_viewer/tree.py branches/frame_order_testing/gui/string_conv.py branches/frame_order_testing/gui/uf_objects.py branches/frame_order_testing/gui/wizard.py branches/frame_order_testing/info.py branches/frame_order_testing/maths_fns/__init__.py branches/frame_order_testing/maths_fns/alignment_tensor.py branches/frame_order_testing/maths_fns/c_chi2.c branches/frame_order_testing/maths_fns/c_chi2.h branches/frame_order_testing/maths_fns/chi2.py branches/frame_order_testing/maths_fns/consistency_tests.py branches/frame_order_testing/maths_fns/coord_transform.py branches/frame_order_testing/maths_fns/correlation_time.py branches/frame_order_testing/maths_fns/direction_cosine.py branches/frame_order_testing/maths_fns/exponential.c branches/frame_order_testing/maths_fns/exponential.h branches/frame_order_testing/maths_fns/frame_order.py branches/frame_order_testing/maths_fns/frame_order_matrix_ops.py branches/frame_order_testing/maths_fns/jw_mapping.py branches/frame_order_testing/maths_fns/jw_mf.py branches/frame_order_testing/maths_fns/jw_mf_comps.py branches/frame_order_testing/maths_fns/kronecker_product.py branches/frame_order_testing/maths_fns/mf.py branches/frame_order_testing/maths_fns/n_state_model.py branches/frame_order_testing/maths_fns/order_parameters.py branches/frame_order_testing/maths_fns/paramag_centre.py branches/frame_order_testing/maths_fns/pcs.py branches/frame_order_testing/maths_fns/potential.py branches/frame_order_testing/maths_fns/pseudo_ellipse.py branches/frame_order_testing/maths_fns/rdc.py branches/frame_order_testing/maths_fns/relax_fit.c branches/frame_order_testing/maths_fns/relax_fit.h branches/frame_order_testing/maths_fns/ri.py branches/frame_order_testing/maths_fns/ri_comps.py branches/frame_order_testing/maths_fns/ri_prime.py branches/frame_order_testing/maths_fns/rotation_matrix.py branches/frame_order_testing/maths_fns/weights.py branches/frame_order_testing/multi/__init__.py branches/frame_order_testing/multi/memo.py branches/frame_order_testing/multi/misc.py branches/frame_order_testing/multi/mpi4py_processor.py branches/frame_order_testing/multi/multi_processor_base.py branches/frame_order_testing/multi/processor.py branches/frame_order_testing/multi/processor_io.py branches/frame_order_testing/multi/result_commands.py branches/frame_order_testing/multi/result_queue.py branches/frame_order_testing/multi/slave_commands.py branches/frame_order_testing/multi/uni_processor.py branches/frame_order_testing/opendx/__init__.py branches/frame_order_testing/opendx/base_map.py branches/frame_order_testing/opendx/isosurface_3D.py branches/frame_order_testing/opendx/main.py branches/frame_order_testing/physical_constants.py branches/frame_order_testing/prompt/__init__.py branches/frame_order_testing/prompt/command.py branches/frame_order_testing/prompt/doc_string.py branches/frame_order_testing/prompt/gpl.py branches/frame_order_testing/prompt/help.py branches/frame_order_testing/prompt/interpreter.py branches/frame_order_testing/prompt/tab_completion.py branches/frame_order_testing/prompt/uf_docstring.py branches/frame_order_testing/prompt/uf_objects.py branches/frame_order_testing/relax.py branches/frame_order_testing/relax_errors.py branches/frame_order_testing/relax_io.py branches/frame_order_testing/relax_string.py branches/frame_order_testing/relax_warnings.py branches/frame_order_testing/sample_scripts/angles.py branches/frame_order_testing/sample_scripts/consistency_tests.py branches/frame_order_testing/sample_scripts/diff_tensor_pdb.py branches/frame_order_testing/sample_scripts/jw_mapping.py branches/frame_order_testing/sample_scripts/model_free/bmrb_deposition.py branches/frame_order_testing/sample_scripts/model_free/cv.py branches/frame_order_testing/sample_scripts/model_free/dasha.py branches/frame_order_testing/sample_scripts/model_free/dauvergne_protocol.py branches/frame_order_testing/sample_scripts/model_free/diff_min.py branches/frame_order_testing/sample_scripts/model_free/grace_S2_vs_te.py branches/frame_order_testing/sample_scripts/model_free/grace_ri_data_correlation.py branches/frame_order_testing/sample_scripts/model_free/map.py [... 1811 lines stripped ...]