Author: bugman Date: Wed Jun 6 09:38:50 2012 New Revision: 16679 URL: http://svn.gna.org/viewcvs/relax?rev=16679&view=rev Log: Merged revisions 15670,15688-15797,15799-15801,15803-15817,15820,15825-15826,15828-15829,15832-15903,15906-15907,16041,16126-16130,16135-16137,16144,16203-16204,16222,16226-16229,16236,16246,16312-16313,16321,16323,16356,16451-16454,16666,16668,16672-16673 via svnmerge from svn+ssh://bugman@xxxxxxxxxxx/svn/relax/1.3 ........ r15670 | bugman | 2012-04-03 21:00:02 +0200 (Tue, 03 Apr 2012) | 5 lines Fix for the scons binary_dist target on Mac OS X systems with multiple Python versions. Now the py2app program is called with the same python version as used by scons. ........ r15688 | bugman | 2012-04-05 11:38:29 +0200 (Thu, 05 Apr 2012) | 5 lines The scons binary_dist target on Mac OS X can now overwrite a pre-existing DMG file. This is just an argument to the Mac hdiutil program. ........ r15689 | bugman | 2012-04-05 12:16:43 +0200 (Thu, 05 Apr 2012) | 15 lines Bug fix for Mac OS X - attempt at killing the Carbon.Evt.TickCount problem by removing argv emulation. See https://mail.gna.org/public/relax-users/2012-04/msg00004.html (Message-id: <CAED9pY9U7fqqj=Oq6UyCKV-+zw-Py-9kkq-X-eUnmpseegk9vQ@xxxxxxxxxxxxxx>), https://mail.gna.org/public/relax-users/2012-03/msg00047.html (Message-id: <15983F01-ECC5-4C70-BC56-5D07A903C489@xxxxxxxxxxxxx>) and other messages in these threads. The suggestion from http://stackoverflow.com/questions/3461983/evt-tickcount-not-found-with-python2-6-on-osx-10-6-3 was used, where the py2app 'argv_emulation' option is set to false. For this to work in relax, the command line argument parsing had to be turned off and default values set in the Relax() instance namespace. ........ r15690 | bugman | 2012-04-05 12:39:02 +0200 (Thu, 05 Apr 2012) | 6 lines The DMG image file is now being sent to the parent directory '..' rather than the base directory. This fixes the problem of the DMG file packaging itself into relax.app/Contents/Resources, creating a 120 Mb file rather than a 60 Mb file!!! ........ r15691 | bugman | 2012-04-05 12:45:20 +0200 (Thu, 05 Apr 2012) | 6 lines Removed the ppc64 build target for the relax C modules on Mac OS X. This architecture is not supported by the recent Xcode frameworks, so it has been dropped. ppc64 users can manually compile the modules, if desired. ........ r15692 | bugman | 2012-04-10 18:34:29 +0200 (Tue, 10 Apr 2012) | 6 lines Improved the relax info print out for the installed python packages. This now shows more information for the wxPython version, and formats the output based on maximum widths to handle different situations. ........ r15693 | bugman | 2012-04-10 19:51:37 +0200 (Tue, 10 Apr 2012) | 6 lines The relax Mac OS X dock icon is now turned off when using the wxGTK build of wxPython. This prevents a little grey frameless window appearing with the largest of the relax Ulysses butterfly icons in the centre. ........ r15694 | bugman | 2012-04-11 17:44:21 +0200 (Wed, 11 Apr 2012) | 3 lines Added a script which is used to validate the binary architecture of Mac OS X Frameworks. ........ r15695 | bugman | 2012-04-11 18:26:32 +0200 (Wed, 11 Apr 2012) | 5 lines Added a document describing how to build a 3-way (i386, pcc, x86_64) Mac OS X Python framework. This is needed to create the DMG distribution file. ........ r15696 | bugman | 2012-04-12 09:23:54 +0200 (Thu, 12 Apr 2012) | 3 lines Updates to the instructions for building a Mac OS X Python+modules framework. ........ r15697 | bugman | 2012-04-12 09:29:42 +0200 (Thu, 12 Apr 2012) | 3 lines Updates and clean up of the Mac OS X framework building document. ........ r15698 | bugman | 2012-04-12 14:54:48 +0200 (Thu, 12 Apr 2012) | 5 lines Fix for the building of the relax C modules as universal binaries on Mac OS X. The linking was not functioning correctly, and the resultant module was build only for i386. ........ r15699 | bugman | 2012-04-12 15:26:50 +0200 (Thu, 12 Apr 2012) | 6 lines Bug fix for the relax GUI spin viewer window. When right clicking on nothing in the tree view, an error would occur. Now, instead, a special menu pops up with a single entry for loading spins. ........ r15700 | bugman | 2012-04-12 15:53:59 +0200 (Thu, 12 Apr 2012) | 3 lines Bug fix for the spectrum.replicated user function for when it is called twice with the same IDs. ........ r15701 | bugman | 2012-04-12 15:57:04 +0200 (Thu, 12 Apr 2012) | 5 lines Fix for the text on the 'finish' button of the GUI wizard. This was accidentally changed to 'apply' at r15427 when it should say 'finish'. ........ r15702 | bugman | 2012-04-13 09:45:51 +0200 (Fri, 13 Apr 2012) | 5 lines Updated the multi-processor package __all__ list. This allows the relax unit tests to pass. ........ r15703 | bugman | 2012-04-13 14:16:36 +0200 (Fri, 13 Apr 2012) | 6 lines Fix for the spin viewer window for wxPython 2.9.3.1. This 2.9 fix is for when you right click in the tree view panel on nothing, and is compatible with wxPython 2.8. This fix will be required for the Mac application which will use this version. ........ r15704 | bugman | 2012-04-13 16:09:35 +0200 (Fri, 13 Apr 2012) | 6 lines Created a dictionary object containing wxPython version info within the status singleton object. This is being used to construct the Mac dock icon, when the Carbon and Cocoa builds and not GTK are being used. ........ r15705 | bugman | 2012-04-13 16:31:23 +0200 (Fri, 13 Apr 2012) | 10 lines Bug fix for Mac OS X - the main window is no longer started maximised. This was reported by Jack Howarth at https://mail.gna.org/public/relax-users/2012-03/msg00053.html (Message-id: <20120326161412.GA30924@xxxxxxxxxxxxxxxx>). The thread continues at https://mail.gna.org/public/relax-users/2012-04/msg00003.html (Message-id: <CAED9pY9uuVyYSBP+9E2yPE7AydnP=BK6JBsmWw61gqo5zj+rzw@xxxxxxxxxxxxxx>). This maximisation is a problem for certain, though not all, Mac OS X systems. ........ r15706 | bugman | 2012-04-13 16:32:40 +0200 (Fri, 13 Apr 2012) | 3 lines Missing import fix. ........ r15707 | bugman | 2012-04-13 16:44:37 +0200 (Fri, 13 Apr 2012) | 5 lines The maximize calls for the spin viewer window are now turned off for Mac OS X systems. This is to fix certain Mac systems when the wxPython install is compiled for wxGTK. ........ r15708 | bugman | 2012-04-13 18:00:49 +0200 (Fri, 13 Apr 2012) | 6 lines wxPython 2.9 fix for the spin viewer window (at least for Mac OS X). The FlexGridSizer now requires the number of elements to be exact or set to zero to expand on demand! ........ r15709 | bugman | 2012-04-16 00:01:36 +0200 (Mon, 16 Apr 2012) | 5 lines Improved details of relax and the compiled C modules from the info print out. The relax introduction has also been removed so it is not printed from the sys_info user function. ........ r15710 | bugman | 2012-04-16 00:03:06 +0200 (Mon, 16 Apr 2012) | 6 lines Reintroduced the relax intro print out when running in info mode (relax --info). This was removed from the info print out in the last commit, and this reintroduces it at the start up level. ........ r15711 | bugman | 2012-04-16 00:03:55 +0200 (Mon, 16 Apr 2012) | 3 lines Small print out fix for the Mac OS X framework checking script. ........ r15712 | bugman | 2012-04-16 00:05:04 +0200 (Mon, 16 Apr 2012) | 5 lines Converted the structure.read_xyz user function front end to the new design. This will be used later for introducing this into the GUI. ........ r15713 | bugman | 2012-04-16 00:06:32 +0200 (Mon, 16 Apr 2012) | 5 lines Introduced the empty() method into the structure API to check if structural data is loaded. This will be used in the spin loading wizard of the spin viewer window. ........ r15714 | bugman | 2012-04-16 00:09:08 +0200 (Mon, 16 Apr 2012) | 6 lines The relax controller now shows the relax intro text to mimic the prompt/scripting modes. Previously the text was being printed prior to the initialisation of the controller and was being lost. ........ r15715 | bugman | 2012-04-16 00:10:35 +0200 (Mon, 16 Apr 2012) | 5 lines Fix for the relax controller find dialog on Mac OS X with wxPython 2.9. The dialog Show() method now needs to be called. This should not affect wxPython 2.8 behaviour. ........ r15716 | bugman | 2012-04-16 00:11:09 +0200 (Mon, 16 Apr 2012) | 3 lines The relax controller now accepts Ctrl-A to select all text. ........ r15717 | bugman | 2012-04-16 00:12:23 +0200 (Mon, 16 Apr 2012) | 3 lines Created the GUI front end to the structure.read_xyz user function. ........ r15718 | bugman | 2012-04-16 00:14:07 +0200 (Mon, 16 Apr 2012) | 3 lines Created the Tools->System Information menu entry, which is simply the sys_info user function front end. ........ r15719 | bugman | 2012-04-16 00:14:54 +0200 (Mon, 16 Apr 2012) | 3 lines Added the structure.read_xyz user function to the menus. ........ r15720 | bugman | 2012-04-16 00:17:49 +0200 (Mon, 16 Apr 2012) | 8 lines Redesigned the spin loading wizard. Now the starting screen allows the choice of the sequence.read, structure.read_pdb, and structure.read_xyz user functions. If structural data is already loaded, then the option to use the pre-loaded structures is also given (which skips to the structure.load_spins user function wizard page). ........ r15721 | bugman | 2012-04-16 00:18:37 +0200 (Mon, 16 Apr 2012) | 3 lines The maths_fns.relax_fit module is now stored in the dep_check module for the info print out. ........ r15722 | bugman | 2012-04-16 14:43:50 +0200 (Mon, 16 Apr 2012) | 6 lines Fix for the about relax window. On some GTK systems, the font is larger and hence the window will be resized to being bigger than original hight of 600 px, resulting in the bottom of the window not being rendered. ........ r15723 | bugman | 2012-04-16 14:54:57 +0200 (Mon, 16 Apr 2012) | 7 lines Fix for the spin loading wizard of the spin window. The RadioButtons of the first page for selecting the spin loading method are now fixed. With the new 2.9.3.1 wxPython version, all options were selected. Now using the wx.RB_GROUP style, the first option is the only one initially selected. ........ r15724 | bugman | 2012-04-16 15:13:23 +0200 (Mon, 16 Apr 2012) | 3 lines Modified the spin loading wizard so that preloaded structures are the default. ........ r15725 | bugman | 2012-04-16 15:15:55 +0200 (Mon, 16 Apr 2012) | 3 lines Improved the user feedback during a state save by just sleeping a little to show the busy cursor. ........ r15726 | bugman | 2012-04-16 15:18:59 +0200 (Mon, 16 Apr 2012) | 3 lines Increased the dialog heights for the deletion of spin data via the spin viewer window. ........ r15727 | bugman | 2012-04-16 15:22:50 +0200 (Mon, 16 Apr 2012) | 3 lines Improved the spin data deletion messages from the spin viewer window. ........ r15728 | bugman | 2012-04-16 15:45:31 +0200 (Mon, 16 Apr 2012) | 5 lines Fix for the radiobutton group in the Spectral_error_type_page of the peak intensity wizard. The first element of a RadioButton group needs the wx.RB_GROUP style! ........ r15729 | bugman | 2012-04-16 16:00:19 +0200 (Mon, 16 Apr 2012) | 5 lines Increased the loading state warning dialog size. This is to accommodate for larger text on wxPython 2.9 on GNU/Linux with GTK. ........ r15730 | bugman | 2012-04-16 16:06:34 +0200 (Mon, 16 Apr 2012) | 3 lines Added the document-preview.png Oxygen icons. ........ r15731 | bugman | 2012-04-16 16:10:18 +0200 (Mon, 16 Apr 2012) | 3 lines Added the document_preview Oxygen icon to the graphic paths. ........ r15732 | bugman | 2012-04-16 16:13:16 +0200 (Mon, 16 Apr 2012) | 3 lines Increased the incomplete set up dialogs for wxPython 2.9 on GNU/Linux. ........ r15733 | bugman | 2012-04-16 17:17:59 +0200 (Mon, 16 Apr 2012) | 5 lines Added a file preview button to the file selection GUI element of the wizards. This is currently activated for the sequence.read user function. ........ r15734 | bugman | 2012-04-16 17:22:39 +0200 (Mon, 16 Apr 2012) | 3 lines Added a file preview button for the spectrum.read_intensities user function GUI page. ........ r15735 | bugman | 2012-04-16 17:45:55 +0200 (Mon, 16 Apr 2012) | 3 lines Double clicking on a file in the results view window now opens it. ........ r15736 | bugman | 2012-04-16 18:06:03 +0200 (Mon, 16 Apr 2012) | 3 lines The file selection wizard GUI element now has the preview button turned on by default. ........ r15737 | bugman | 2012-04-16 18:16:23 +0200 (Mon, 16 Apr 2012) | 3 lines Increased the size of the model-free model change warning dialog for wxPython 2.9 on GNU/Linux. ........ r15738 | bugman | 2012-04-16 18:30:38 +0200 (Mon, 16 Apr 2012) | 3 lines Missing import. ........ r15739 | bugman | 2012-04-16 19:24:42 +0200 (Mon, 16 Apr 2012) | 5 lines The analysis deletion buttons now do nothing if the notebook is not created yet. This avoids problems on the new wxPython 2.9 versions. ........ r15740 | bugman | 2012-04-16 19:38:39 +0200 (Mon, 16 Apr 2012) | 5 lines Converted the pipe switching with GUI tab switching to synchronous to avoid rare races. This racing is triggered by wxPython 2.9. This change should not affect wxPython 2.8 installs. ........ r15741 | bugman | 2012-04-16 19:54:00 +0200 (Mon, 16 Apr 2012) | 6 lines Fix for a bug triggered by wxPython 2.9 when deleting the last analysis tab. The self.notebook object is now deleted when the set_init_state() method is called, allowing it to be properly accessed and recreated. ........ r15742 | bugman | 2012-04-16 23:21:24 +0200 (Mon, 16 Apr 2012) | 8 lines Bug fix for the GUI when deleting analysis tabs. The deletion of analysis tabs was previously failing in certain cases. The problem was the generic_fns.pipes.delete() call in the middle of the delete_analysis() method causing a notification to be sent to the pipe_deletion GUI observer object, which would then handle the pipe deletion prior to the completion of the delete_analysis() call causing things to get out of sync. ........ r15743 | bugman | 2012-04-17 10:40:56 +0200 (Tue, 17 Apr 2012) | 5 lines Added some heavy debugging code to the GUI analysis delete_analysis() method. This will hopefully allow the analysis deletion problems to be finally solved. ........ r15744 | bugman | 2012-04-17 11:03:29 +0200 (Tue, 17 Apr 2012) | 3 lines More advanced debugging print outs for the delete_analysis() method. ........ r15745 | bugman | 2012-04-17 11:06:57 +0200 (Tue, 17 Apr 2012) | 3 lines Added debugging print outs to the delete_all() analysis method. ........ r15746 | bugman | 2012-04-17 11:43:18 +0200 (Tue, 17 Apr 2012) | 6 lines Created observer_register() for all GUI analyses for method registration and unregistration. This method allows for external calls to observer_register() to pre-remove the methods from the observer objects. ........ r15747 | bugman | 2012-04-17 11:48:24 +0200 (Tue, 17 Apr 2012) | 6 lines Multiple unregistrations of observer methods are now possible without a RelaxError. This allows multiple code paths to unregister methods to allow for pre-removal of methods to avoid queued wx events in wxGTK from occurring on dead or missing objects. ........ r15748 | bugman | 2012-04-17 11:49:03 +0200 (Tue, 17 Apr 2012) | 3 lines The GUI analyses delete_all() method now unregisters all observer methods prior to deletion. ........ r15749 | bugman | 2012-04-17 14:35:13 +0200 (Tue, 17 Apr 2012) | 9 lines Big bug fix for the deletion of analyses tabs from the GUI! This affects wxGTK users on Macs and Linux. Now the spectrum and relaxation data list GUI elements have observer_register() methods, allowing the analysis delete_all() method to unregister all analysis specific methods from the observer objects. This prevents queued wx calls to be made on dead or non-existent GUI objects after the analysis has been deleted. wx.Yield() calls were not sufficient to solve this issue. ........ r15750 | bugman | 2012-04-17 15:27:22 +0200 (Tue, 17 Apr 2012) | 6 lines Bug fix for the spin.create user function GUI interface for when molecules or residues are not named. Unnamed molecules are now properly handled in the GUI page, and the residue name of None is properly converted into a NoneType prior to executing the back end. ........ r15751 | bugman | 2012-04-17 15:27:49 +0200 (Tue, 17 Apr 2012) | 3 lines Copyright updates. ........ r15752 | bugman | 2012-04-17 15:29:27 +0200 (Tue, 17 Apr 2012) | 3 lines Removal of a debugging print out. ........ r15753 | bugman | 2012-04-17 15:31:34 +0200 (Tue, 17 Apr 2012) | 5 lines Clean up of the Create_page.on_execute() method. The gui_to_*() functions are now being used for the spin information. ........ r15754 | bugman | 2012-04-17 15:35:14 +0200 (Tue, 17 Apr 2012) | 3 lines Fix for the gui_to_int() function for when a text instead of an int is given by the user. ........ r15755 | bugman | 2012-04-17 15:50:47 +0200 (Tue, 17 Apr 2012) | 6 lines Fix for the residue.create user function GUI front end along the same lines as the spin.create fn. The unnamed molecules are now properly handled, and the gui_to_*() methods are now used for data conversion. ........ r15756 | bugman | 2012-04-17 16:33:03 +0200 (Tue, 17 Apr 2012) | 6 lines Added a flag to the status singleton object to signal if text output can be coloured. This is only activated when sys.stdout has not been changed. Unix redirection and pipes will need to be handled later (http://mail.python.org/pipermail/python-list/2012-April/1291044.html). ........ r15757 | bugman | 2012-04-17 16:35:38 +0200 (Tue, 17 Apr 2012) | 6 lines Fix for the initialisation of the Exec_info class for the prompt/script output. The class was not being initialised at all! Thought the variables were class rather than instance variables, so the problem was hidden. ........ r15758 | bugman | 2012-04-17 16:36:41 +0200 (Tue, 17 Apr 2012) | 3 lines If the status.text_colouring flag is set, then the relax prompts will be coloured blue! ........ r15759 | bugman | 2012-04-17 16:37:19 +0200 (Tue, 17 Apr 2012) | 3 lines All RelaxErrors are now coloured red if the status.text_colouring flag is set. ........ r15760 | bugman | 2012-04-17 16:40:01 +0200 (Tue, 17 Apr 2012) | 5 lines All RelaxWarnings are now coloured yellow if the status.text_colouring flag is set. Though this looks more like orange on the Konsole terminal under GNU/Linux. ........ r15761 | bugman | 2012-04-17 16:40:20 +0200 (Tue, 17 Apr 2012) | 3 lines Copyright update. ........ r15762 | bugman | 2012-04-17 16:50:34 +0200 (Tue, 17 Apr 2012) | 8 lines The sys.std*.isatty() methods are now being used to determine if text output should be coloured. This removes the need for the status.text_colouring flag, and can handle changes in IO redirection occurring at any point. This was suggested at both http://mail.python.org/pipermail/python-list/2012-April/1291046.html and http://mail.python.org/pipermail/python-list/2012-April/1291048.html. ........ r15763 | bugman | 2012-04-17 17:01:00 +0200 (Tue, 17 Apr 2012) | 18 lines Reverted r15756 as the status.text_colouring flag is no longer needed. The command used was: svn merge -r15756:r15755 . ..... r15756 | bugman | 2012-04-17 16:33:03 +0200 (Tue, 17 Apr 2012) | 6 lines Changed paths: [... 1559 lines stripped ...]