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@.../svn/relax/1.3
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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.
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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.
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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@...>),
https://mail.gna.org/public/relax-users/2012-03/msg00047.html
(Message-id: <15983F01-ECC5-4C70-BC56-5D07A903C489@...>) 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.
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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!!!
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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'.
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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.
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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.
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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.
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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@...>). The thread continues at
https://mail.gna.org/public/relax-users/2012-04/msg00003.html (Message-id:
<CAED9pY9uuVyYSBP+9E2yPE7AydnP=BK6JBsmWw61gqo5zj+rzw@...>).
This maximisation is a problem for certain, though not all, Mac OS X systems.
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r15706 | bugman | 2012-04-13 16:32:40 +0200 (Fri, 13 Apr 2012) | 3 lines
Missing import fix.
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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.
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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!
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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).
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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!
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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.
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r15730 | bugman | 2012-04-16 16:06:34 +0200 (Mon, 16 Apr 2012) | 3 lines
Added the document-preview.png Oxygen icons.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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r15738 | bugman | 2012-04-16 18:30:38 +0200 (Mon, 16 Apr 2012) | 3 lines
Missing import.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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r15751 | bugman | 2012-04-17 15:27:49 +0200 (Tue, 17 Apr 2012) | 3 lines
Copyright updates.
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r15752 | bugman | 2012-04-17 15:29:27 +0200 (Tue, 17 Apr 2012) | 3 lines
Removal of a debugging print out.
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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.
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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.
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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.
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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).
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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.
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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!
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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.
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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.
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r15761 | bugman | 2012-04-17 16:40:20 +0200 (Tue, 17 Apr 2012) | 3 lines
Copyright update.
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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.
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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 .
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r15756 | bugman | 2012-04-17 16:33:03 +0200 (Tue, 17 Apr 2012) | 6 lines
Changed paths:
M /1.3/relax.py
M /1.3/status.py
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).
.....
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r15764 | bugman | 2012-04-17 17:41:06 +0200 (Tue, 17 Apr 2012) | 8 lines
ANSI escape characters are now turned off forcibly when in GUI mode.
The prompt.interpreter.Interpreter class was being initialised during the import startup phase due to
the gui.interpreter.Interpreter singleton class. This meant that sys.stdout had not been redirected
to the relax controller yet and was still set to the terminal TTY. This hack turns off the relax
prompt colouring forcibly.
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r15765 | bugman | 2012-04-17 18:18:35 +0200 (Tue, 17 Apr 2012) | 5 lines
Added isatty() methods to all of the dummy file objects within relax.
This fixes a number of errors caused by the recent introduction of coloured text.
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r15766 | bugman | 2012-04-17 18:23:53 +0200 (Tue, 17 Apr 2012) | 3 lines
The script print out in scripting mode is now in green if sys.stdout is a TTY.
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r15767 | bugman | 2012-04-17 18:27:46 +0200 (Tue, 17 Apr 2012) | 6 lines
The import of the gui package now only occurs in GUI mode.
This will speed up the program start up. It also has the side effect of bypassing the hack of the
GUI resetting the ANSI escape characters of the relax prompt.
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r15768 | bugman | 2012-04-17 18:32:17 +0200 (Tue, 17 Apr 2012) | 5 lines
The test suite is now only imported in the test modes of operation.
This should also speed up program initialisation.
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r15769 | bugman | 2012-04-17 18:49:22 +0200 (Tue, 17 Apr 2012) | 5 lines
Shifted the terminal colouring ANSI escape sequences into their own 'ansi' module.
This will allow the colours to be easily changed.
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r15770 | bugman | 2012-04-17 18:50:11 +0200 (Tue, 17 Apr 2012) | 3 lines
Fix for a typo in r15769.
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r15771 | bugman | 2012-04-17 19:04:04 +0200 (Tue, 17 Apr 2012) | 3 lines
Shifted the script colouring ANSI escape sequences into the 'ansi' module.
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r15772 | bugman | 2012-04-17 19:30:16 +0200 (Tue, 17 Apr 2012) | 7 lines
Better control of the relax prompt colouring via ANSI escape sequences.
The new Exec_info.prompt_colour_on() and Exec_info.prompt_colour_off() methods are now used to turn
the colours on and off by aliasing the coloured or non-colours prompts to both the class instance
namespace and to the sys module.
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r15773 | bugman | 2012-04-17 19:33:56 +0200 (Tue, 17 Apr 2012) | 3 lines
Fix for the GUI interpreter when turning off the ANSI codes of the relax prompt.
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r15774 | bugman | 2012-04-17 19:45:41 +0200 (Tue, 17 Apr 2012) | 3 lines
The script ANSI colour is now cyan to fit better into the relax blue/black colour theme.
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r15775 | bugman | 2012-04-17 19:50:21 +0200 (Tue, 17 Apr 2012) | 5 lines
The ANSI ending escape sequence is now always placed before the last newline.
This fixes some weirdness of the cursor or other parts being coloured when they should not be.
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r15776 | bugman | 2012-04-17 20:08:34 +0200 (Tue, 17 Apr 2012) | 6 lines
The relax GUI is now robust and able to withstand a call to the reset user function.
This could have occurred if the user ran a script with a reset() call, or if reset() was typed at
the GUI version of the relax prompt.
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r15777 | bugman | 2012-04-17 20:14:28 +0200 (Tue, 17 Apr 2012) | 3 lines
Added the larger sized application-x-executable-script Oxygen icons.
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r15778 | bugman | 2012-04-17 20:16:17 +0200 (Tue, 17 Apr 2012) | 3 lines
Added the relax prompt icon to the main GUI window toolbar.
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r15779 | bugman | 2012-04-18 14:39:49 +0200 (Wed, 18 Apr 2012) | 3 lines
The py2app part of the setup.py script now throws a RelaxError if the setuptools module is missing.
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r15780 | bugman | 2012-04-18 17:58:36 +0200 (Wed, 18 Apr 2012) | 9 lines
Complete redesign of the py2app setup.py script for building Mac OS X applications.
The script has been converted into a class called Setup which performs all the actions. All files,
source or otherwise, are now stated as data files to be included in relax.app/Contents/Resources.
All relax modules are specified by the py2app 'includes' option so that they are all included within
the relax.app/Contents/Resources/lib/python2.X/site-packages.zip as *.pyc files. These changes are
needed for the newer versions of the py2app and setuptools Python packages.
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r15781 | bugman | 2012-04-18 18:14:16 +0200 (Wed, 18 Apr 2012) | 6 lines
Shifted the build and dist directories out of the relax base directory.
This is for the Mac OS X application building, and is to prevent the 'dist' directory from being
recursively copied into itself. This seems to be a recently introduced bug.
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r15782 | bugman | 2012-04-18 19:40:46 +0200 (Wed, 18 Apr 2012) | 5 lines
Fix for the py2app setup.py script for Mac OS X application creation.
The list of data files to include with the app is now properly formatted.
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r15783 | bugman | 2012-04-18 22:25:11 +0200 (Wed, 18 Apr 2012) | 6 lines
Prepared the multi-processor package for the import mechanisms of Python 3.
This new mechanism is present in Python 2.7 now, and the code falls back to the old method when not
present.
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r15784 | bugman | 2012-04-19 00:21:06 +0200 (Thu, 19 Apr 2012) | 17 lines
Reverted r15781, as this is no longer required.
The command used was:
$ svn merge -r15781:r15780 .
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r15781 | bugman | 2012-04-18 18:14:16 +0200 (Wed, 18 Apr 2012) | 6 lines
Changed paths:
M /1.3/setup.py
Shifted the build and dist directories out of the relax base directory.
This is for the Mac OS X application building, and is to prevent the 'dist' directory from being
recursively copied into itself. This seems to be a recently introduced bug.
.....
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r15785 | bugman | 2012-04-19 23:08:59 +0200 (Thu, 19 Apr 2012) | 6 lines
Created the _det_install_path() status singleton method for better determining the install path.
This will be used for the Mac OS X applications whereby the current logic of using sys.path[0]
fails miserably!
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r15786 | bugman | 2012-04-20 00:31:03 +0200 (Fri, 20 Apr 2012) | 7 lines
Big bug fix for the installation path for the relax Mac OS X application.
The path to the application Resources folder, where all the relax data files are located, is now set
to the install path. The relax.py module was also overwriting the value set in the status singleton
and now this no longer occurs.
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r15787 | bugman | 2012-04-20 22:41:12 +0200 (Fri, 20 Apr 2012) | 5 lines
The 'Tools->Test suite' menu item has been converted into a sub-menu.
Now there are entries for running all tests, or the individual categories.
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r15788 | bugman | 2012-04-20 22:42:44 +0200 (Fri, 20 Apr 2012) | 3 lines
Missing RelaxError import!
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r15789 | bugman | 2012-04-20 22:44:11 +0200 (Fri, 20 Apr 2012) | 6 lines
The relax test-suite runner code can now handle the different categories from the GUI menus.
This runs very differently to the command line mode of the test-suite, so needs a different
solution.
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r15790 | bugman | 2012-04-23 09:08:25 +0200 (Mon, 23 Apr 2012) | 6 lines
The ds.relax_gui GUI data object is now a permanent feature of the relax data store.
This is in preparation for attempting the almost impossible task of making the GUI tests work within
the GUI!
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r15791 | bugman | 2012-04-23 09:36:12 +0200 (Mon, 23 Apr 2012) | 3 lines
Renamed 'Tools->Test suite->All tests' to 'Tools->Test suite->Full test suite'.
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r15792 | bugman | 2012-04-23 09:38:27 +0200 (Mon, 23 Apr 2012) | 3 lines
Added a separator between the 'Tools->Test suite->Full test suite' menu item and the individual categories.
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r15793 | bugman | 2012-04-23 09:54:26 +0200 (Mon, 23 Apr 2012) | 6 lines
The relax mode (i.e. prompt, script, GUI, test suite, etc.) is now stored in the status object.
This will be used to activate and deactivate certain parts of the GUI tests within the GUI and
normal test suite modes.
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r15794 | bugman | 2012-04-23 10:10:22 +0200 (Mon, 23 Apr 2012) | 12 lines
The GUI tests now work in the GUI!!
This is thanks to a lot of GUI black magic. The tests' tearDown() method now carefully deconstructs
the GUI element prior to the next test being run. In the normal 'relax --gui-test' mode, the GUI
object is destroyed and recreated for each test. However when run from the GUI, the GUI object is
always there and must remain intact. Some of the careful deconstruction includes the deletion of
each analysis tab, the selective destruction of all non-main windows (excluding the controller which
shows the test suite progress). The relax data store GUI object is also reconstructed in the
tearDown() method, and all wx events flushed at the very end to prevent clashes with the next GUI
test.
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r15795 | bugman | 2012-04-23 11:41:40 +0200 (Mon, 23 Apr 2012) | 5 lines
Fix for the information print out on MS Windows.
The 'file' command is not present on Windows systems.
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r15796 | bugman | 2012-04-23 12:36:12 +0200 (Mon, 23 Apr 2012) | 7 lines
ANSI control characters are now suppressed on MS Windows.
The characters are useless in both the PowerShell and cmd. Therefore the
ansi.enable_control_chars() helper function has been created to replace the sys.std*.isatty() calls
throughout relax.
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r15797 | bugman | 2012-04-23 12:37:57 +0200 (Mon, 23 Apr 2012) | 3 lines
Docstring completion for the ansi.enable_control_chars() function.
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r15799 | bugman | 2012-04-23 13:58:43 +0200 (Mon, 23 Apr 2012) | 3 lines
Fix for the setuptools RelaxError for when the extension is unknown.
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r15800 | bugman | 2012-04-24 09:12:24 +0200 (Tue, 24 Apr 2012) | 8 lines
Added a new version of the truncated OMP results relax state file.
From Python version 2.7.3 (and the equivalent 3.x versions), the XML toprettyxml() output has been
changed to not wrap the value in newline characters! See line 258 of the Python change log at
http://hg.python.org/cpython/file/d46c1973d3c4/Misc/NEWS#l276. This change affects one of the relax
system tests.
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r15801 | bugman | 2012-04-24 09:46:57 +0200 (Tue, 24 Apr 2012) | 7 lines
The Mf.test_write_results system test now works with the newer Python 2.7.3 version.
The final_results_trunc_1.3_new.bz2 file was updated to be a results file rather than save state,
and the system test itself now checks the Python version and then loads the correct results file for
that version.
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r15803 | bugman | 2012-04-24 13:04:11 +0200 (Tue, 24 Apr 2012) | 5 lines
The relax controller now stays on top of all windows when the GUI tests are being run.
This improves the running of the GUI tests in GUI mode on Mac OS X and MS Windows.
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r15804 | bugman | 2012-04-24 13:50:36 +0200 (Tue, 24 Apr 2012) | 3 lines
Shifted the code of r15803 from the test suite into the GUI method for running the test suite.
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r15805 | bugman | 2012-04-24 13:59:45 +0200 (Tue, 24 Apr 2012) | 5 lines
During the GUI tests from the GUI, the relax controller is now modal.
This is to stop users from doing silly things!
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r15806 | bugman | 2012-04-24 14:32:41 +0200 (Tue, 24 Apr 2012) | 5 lines
The relax controller can now not be closed while the test suite is running.
This presents uses from doing silly things, and then reporting it as a bug!
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r15807 | bugman | 2012-04-24 14:36:27 +0200 (Tue, 24 Apr 2012) | 6 lines
Exiting the GUI now only warns about data loss only if there is data to loose.
The relax data store is_empty() method is being used to skip the question dialog, allowing relax to
be shut quickly.
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r15808 | bugman | 2012-04-24 14:58:56 +0200 (Tue, 24 Apr 2012) | 3 lines
All open relax windows are now closed prior to running the test suite within the GUI.
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r15809 | bugman | 2012-04-24 15:11:15 +0200 (Tue, 24 Apr 2012) | 3 lines
The pipe editor window is no longer centred, now matching the behaviour all other windows.
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r15810 | bugman | 2012-04-24 18:50:03 +0200 (Tue, 24 Apr 2012) | 3 lines
Updated the ancient COMMITTERS which hasn't been changed in over 4 years!
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r15811 | bugman | 2012-04-24 20:03:06 +0200 (Tue, 24 Apr 2012) | 7 lines
Fix for the HTML user manual at http://www.nmr-relax.com/manual/relax.html.
The document splitting has been restored to a split depth of 5. This had been changed to make the
main chapters of the text more readable, but the user function document is now far, far too long and
is a massive strain on browsers, so the behaviour has been reverted.
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r15812 | bugman | 2012-04-24 21:27:57 +0200 (Tue, 24 Apr 2012) | 7 lines
Fix for the HTML user manual at http://www.nmr-relax.com/manual/relax.html.
The ignore_commands function is now being used to force latex2html to ignore \linebreak[0] commands.
These were previously putting the text '[0]' throughout all the HTML pages, and were especially bad
in the user function section.
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r15813 | bugman | 2012-04-24 21:31:52 +0200 (Tue, 24 Apr 2012) | 7 lines
Fix for the fetch_docstrings.py script.
The number of \linebreak[0] commands inserted was far too great. However there is still a problem
in that all \linebreak[0] commands are doubled. This is for the latex2html generated user manual at
http://www.nmr-relax.com/manual/relax.html.
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r15814 | bugman | 2012-04-25 12:27:14 +0200 (Wed, 25 Apr 2012) | 9 lines
Improvements to the HTML version of the user manual.
The latex2html configuration script now allows for more maths in the HTML with the HTML_VERSION math
extension. The section numbers are now removed from the HTML pages to allow for more static pages
for the user functions which don't disappear as new user functions are added, changing the section
numbering. The title page has also been renamed to "The relax user manual" for better search engine
indexing.
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r15815 | bugman | 2012-04-25 12:29:10 +0200 (Wed, 25 Apr 2012) | 6 lines
Changed all of the maths in the HTML page titles.
The latexonly and htmlonly environments are now being used to produce different section titles.
The LaTeX version still uses the full maths, whereas the HTML version now has pure text output.
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r15816 | bugman | 2012-04-25 16:45:11 +0200 (Wed, 25 Apr 2012) | 7 lines
Fixes for the HTML user manual (http://www.nmr-relax.com/manual/relax_user_manual.html).
The \widehat maths command in titles (which were only for LaTeX and not latex2html) was causing
latex2html to fail in the generation of certain images, causing the image numbers to no longer
match the text, resulting in all the images being mixed up!
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r15817 | bugman | 2012-04-25 16:52:52 +0200 (Wed, 25 Apr 2012) | 6 lines
Fix for the about dialogs in the GUI when combined with a scrolling window.
This is only a problem for the wxPython 2.9 series, and the fix was suggested by Robin Dunn at
http://groups.google.com/group/wxpython-users/browse_thread/thread/7dff3f5d7ca24985.
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r15820 | bugman | 2012-04-25 18:51:56 +0200 (Wed, 25 Apr 2012) | 6 lines
Merged the CHANGES file for relax version 1.3.15 back into the main 1.3 line.
The command used was:
svn merge -r15818:15819 svn+ssh://bugman@.../svn/relax/tags/1.3.15
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r15825 | bugman | 2012-04-25 20:12:40 +0200 (Wed, 25 Apr 2012) | 3 lines
Fix for the creation of the HTML user manual http://www.nmr-relax.com/manual/index.html file.
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r15826 | bugman | 2012-04-25 20:45:39 +0200 (Wed, 25 Apr 2012) | 6 lines
Fix for the ANSI escape sequences for colouring text for when an isatty() method does not exist.
This is needed for the epydoc constructed API documentation as the redirection is a special epydoc
_Devnull object which has not isatty() method!
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r15828 | bugman | 2012-04-26 09:30:19 +0200 (Thu, 26 Apr 2012) | 5 lines
Removed more maths from the HTML user manual section titles.
This is using the \latexonly and \htmlonly constructs to toggle titles.
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r15829 | bugman | 2012-04-26 11:15:21 +0200 (Thu, 26 Apr 2012) | 3 lines
Some small edits to the release checklist document.
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r15832 | bugman | 2012-04-26 15:46:36 +0200 (Thu, 26 Apr 2012) | 6 lines
Expansion and completion of the model-free chapter of the relax user manual.
A large number of changes have been made to complete the chapter and description of all model-free
sample scripts. The dauvernge_protocol.py script is now fully described.
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r15833 | bugman | 2012-04-26 15:51:45 +0200 (Thu, 26 Apr 2012) | 3 lines
Fix for the chi2 references in the maths chapter of the relax user manual.
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r15834 | bugman | 2012-04-26 16:16:17 +0200 (Thu, 26 Apr 2012) | 6 lines
Fix for the scons 'install' target for the byte-compilation of the *.pyc files.
Running 'relax --test' no longer byte-compiles the files, so instead 'python -m compileall .' is
being used instead.
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r15835 | bugman | 2012-04-26 16:41:08 +0200 (Thu, 26 Apr 2012) | 5 lines
Updated and completed the installation chapter of the relax user manual.
A lot of the text was 4-6 years out of date.
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r15836 | bugman | 2012-04-26 16:44:32 +0200 (Thu, 26 Apr 2012) | 3 lines
Added colons to all entries of the abbreviation chapter in the relax user manual.
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r15837 | bugman | 2012-04-27 10:20:01 +0200 (Fri, 27 Apr 2012) | 5 lines
Added a number of GUI screenshots for use in the relax user manual.
These were taken from http://www.nmr-relax.com/screenshots.html.
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r15838 | bugman | 2012-04-27 10:30:19 +0200 (Fri, 27 Apr 2012) | 5 lines
The alignment tensor user functions can now all handle the situation whereby no tensors exist.
This was previously giving non-informative Python tracebacks.
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r15839 | bugman | 2012-04-27 10:51:23 +0200 (Fri, 27 Apr 2012) | 7 lines
Significant updates to the introduction chapter of the relax user manual.
The text has been updated to match the current relax versions. All mention of the dead SRLS theory
has been eliminated. Screenshots of all the GUI windows and analyses have been added to prettify
the chapter, and the text for the GUI has been rewritten for the new GUI design.
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r15840 | bugman | 2012-04-27 10:52:42 +0200 (Fri, 27 Apr 2012) | 5 lines
Added a screenshot of the new relax 1.3.15 version in script mode.
This adds the ANSI text colouring and makes the screenshot more interesting.
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r15841 | bugman | 2012-04-27 10:58:28 +0200 (Fri, 27 Apr 2012) | 5 lines
Updated the open source infrastructure chapter of the relax user manual.
The relax 1.2 versions used as examples in the chapter are far too ancient!
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r15842 | bugman | 2012-04-27 11:03:09 +0200 (Fri, 27 Apr 2012) | 3 lines
The list of figures in the relax user manual is now on a new page.
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r15843 | bugman | 2012-04-27 11:46:34 +0200 (Fri, 27 Apr 2012) | 7 lines
The GUI and logging/teeing modes are now compatible with each other.
The relax controller now uses the relax_io.SplitIO class to allow the STDOUT and STDERR messages to
be both directed to the log file and the controller. The controller will capture both streams,
rather than splitting the IO, if no IO redirection has been set up.
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r15844 | bugman | 2012-04-27 12:30:01 +0200 (Fri, 27 Apr 2012) | 5 lines
Added GUI sections to the end of the NOE, R1+R2 and model-free chapters of the user manual.
The screenshots of each of the GUI analyses have been shifted into the specific analysis chapters.
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r15845 | bugman | 2012-04-27 12:42:53 +0200 (Fri, 27 Apr 2012) | 3 lines
Added mpi4py to the list of relax dependencies.
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r15846 | bugman | 2012-04-27 14:43:23 +0200 (Fri, 27 Apr 2012) | 8 lines
Added a new section to the intro chapter of the user manual for the multi-processor framework.
This is just a light description and pointer to Gary's official announcement at
https://mail.gna.org/public/relax-devel/2007-05/msg00000.html (Message-id:
<463B2E31.30503@...>). In the future this should be expanded into its own chapter and
include an extensive description with most of the text of the mailing list message.
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r15847 | bugman | 2012-04-27 17:01:29 +0200 (Fri, 27 Apr 2012) | 5 lines
Updated the development chapter of the relax user manual to be more current.
This includes removing the text saying that the GUI is yet to be coded!
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r15848 | bugman | 2012-04-30 12:25:17 +0200 (Mon, 30 Apr 2012) | 8 lines
Renamed the 'pdc' user function class to 'bruker' and removed all references to 'protein'.
This is due to the Bruker absorption of the Protein Dynamics Centre into the Bruker Dynamics Centre
announced at https://mail.gna.org/public/relax-users/2012-04/msg00011.html (Message-id:
<4F7AE13B.6010309@...>) by Dr. Klaus-Peter Neidig (peter dott neidig att bruker-biospin dott
de).
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r15849 | bugman | 2012-04-30 12:43:05 +0200 (Mon, 30 Apr 2012) | 9 lines
Renamed the PDC to Bruker DC in the test suite.
This is due to the Bruker absorption of the Protein Dynamics Centre into the Bruker Dynamics Centre
announced at https://mail.gna.org/public/relax-users/2012-04/msg00011.html (Message-id:
<4F7AE13B.6010309@...>) by Dr. Klaus-Peter Neidig (peter dott neidig att bruker-biospin dott
de).
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r15850 | bugman | 2012-04-30 12:48:28 +0200 (Mon, 30 Apr 2012) | 5 lines
Converted the bruker.read user function prompt interface to the new design.
This will be required for implementation in the GUI.
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r15851 | bugman | 2012-04-30 13:13:40 +0200 (Mon, 30 Apr 2012) | 5 lines
Added the Bruker logo in various formats for use in the relax GUI.
This will be used for the bruker.read user function.
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r15852 | bugman | 2012-04-30 13:14:25 +0200 (Mon, 30 Apr 2012) | 3 lines
Added the Bruker logos to the image and icon paths.
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r15853 | bugman | 2012-04-30 13:15:20 +0200 (Mon, 30 Apr 2012) | 3 lines
Created the bruker.read GUI user function page and menu entry.
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r15854 | bugman | 2012-04-30 13:15:48 +0200 (Mon, 30 Apr 2012) | 3 lines
Improved the bruker.read user function docstring.
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r15855 | bugman | 2012-04-30 14:33:07 +0200 (Mon, 30 Apr 2012) | 5 lines
Added a button to the relaxation data GUI element for calling the bruker.read user function.
This is not functional yet.
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r15856 | bugman | 2012-04-30 14:58:03 +0200 (Mon, 30 Apr 2012) | 3 lines
The relaxation data list GUI element 'bruker' button now launches the bruker.read user function.
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r15857 | bugman | 2012-04-30 15:18:31 +0200 (Mon, 30 Apr 2012) | 3 lines
Fixed the size of the 22x22 Bruker icon.
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r15858 | bugman | 2012-04-30 15:19:00 +0200 (Mon, 30 Apr 2012) | 3 lines
Created a special Bruker add icon for use in the relaxation data GUI element.
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r15859 | bugman | 2012-04-30 15:24:23 +0200 (Mon, 30 Apr 2012) | 3 lines
Edit of the 'Add' button help in the relaxation data GUI element.
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r15860 | bugman | 2012-04-30 16:11:02 +0200 (Mon, 30 Apr 2012) | 3 lines
Updated all the BMRB user function front ends to the modern docstring design.
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r15861 | bugman | 2012-04-30 16:29:49 +0200 (Mon, 30 Apr 2012) | 3 lines
Added the BMRB icon in various sizes to the graphics directory and icon paths.
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r15862 | bugman | 2012-04-30 20:52:39 +0200 (Mon, 30 Apr 2012) | 5 lines
Added an initial but far from complete bmrb.citation user function page and menu element.
This user function will require a new type of wizard element to handle the list of authors!
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r15863 | bugman | 2012-05-02 11:11:09 +0200 (Wed, 02 May 2012) | 3 lines
The relax system information print out now includes information about the XML modules.
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r15864 | bugman | 2012-05-02 11:16:55 +0200 (Wed, 02 May 2012) | 3 lines
Improved the XML module system information print out.
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r15865 | bugman | 2012-05-02 11:42:43 +0200 (Wed, 02 May 2012) | 6 lines
Added the xml module import tests to the dep_check module.
This also adds some code to differentiate between the ancient and dead PyXML which should be
eliminated for Python 2.7.3 onwards and the Python internal XML module.
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r15866 | bugman | 2012-05-02 11:43:09 +0200 (Wed, 02 May 2012) | 3 lines
The XML system information print out now uses the dep_check module XML data.
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r15867 | bugman | 2012-05-02 11:46:30 +0200 (Wed, 02 May 2012) | 6 lines
The Mf.test_write_results system test now checks for the ancient PyXML.
This ancient version from 2004 which should be eliminated, if installed, causes the toprettyxml()
changes in Python 2.7.3 to be overridden.
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r15868 | bugman | 2012-05-02 12:12:30 +0200 (Wed, 02 May 2012) | 7 lines
Created a new infrastructure in the wizards for handling more advanced GUI elements.
The _elements dictionary has been created to store the full GUI elements within the wizard. The
GetValue() and SetValue() methods have been created as a front end to the specific GUI element's
equivalent methods.
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r15869 | bugman | 2012-05-02 13:54:19 +0200 (Wed, 02 May 2012) | 8 lines
Created a new String_list wizard GUI element class and associated element_string_list() method.
This special object is currently very similar to the input_field() object, but is set up as a class
in the gui.wizard_elements module. The wizard page element_string_list() method has been added as
the interface for adding this element to a wizard page. This method stores the String_list element
in the wizard page _element dictionary.
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r15870 | bugman | 2012-05-02 16:37:02 +0200 (Wed, 02 May 2012) | 3 lines
Added the edit-rename Oxygen icons.
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r15871 | bugman | 2012-05-02 16:38:06 +0200 (Wed, 02 May 2012) | 3 lines
Added the edit-rename Oxygen icons to the paths module.
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r15872 | bugman | 2012-05-02 16:53:41 +0200 (Wed, 02 May 2012) | 6 lines
Completed the wizard string list GUI element.
This control opens a dialog consisting of an editable ListCtrl that the user can input the text
into.
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r15873 | bugman | 2012-05-02 16:54:24 +0200 (Wed, 02 May 2012) | 3 lines
The bmrb.citation GUI user function now uses the new wizard page string list GUI element.
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r15874 | bugman | 2012-05-02 16:55:36 +0200 (Wed, 02 May 2012) | 5 lines
Fix for the wizard GetValue() and SetValue() methods.
The GUI elements are in the self._elements dictionary!
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r15875 | bugman | 2012-05-02 17:12:19 +0200 (Wed, 02 May 2012) | 5 lines
Abstracted out most of the String_list wizard element into the List base class.
This will allow different list types to be easily added.
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r15876 | bugman | 2012-05-02 17:14:22 +0200 (Wed, 02 May 2012) | 3 lines
The element_string_list() wizard method now has all arguments converted to keyword args.
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r15877 | bugman | 2012-05-02 17:58:23 +0200 (Wed, 02 May 2012) | 6 lines
Created a new wizard GUI element for lists of lists of strings.
This is similar to the list of strings GUI element, but has been extended for list of lists. It is
now used by the bmrb.citation user function.
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r15878 | bugman | 2012-05-02 17:58:41 +0200 (Wed, 02 May 2012) | 3 lines
Debugging print out removal.
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r15879 | bugman | 2012-05-02 18:36:42 +0200 (Wed, 02 May 2012) | 5 lines
Fix for the bmrb.citation user function documentation.
The 'type' argument was not being described.
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r15880 | bugman | 2012-05-02 18:36:59 +0200 (Wed, 02 May 2012) | 3 lines
Completed the GUI interface for the bmrb.citation user function.
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r15881 | bugman | 2012-05-02 20:42:08 +0200 (Wed, 02 May 2012) | 5 lines
Created the Bmrb.test_bmrb_rw GUI test.
This incomplete test is based on the bmrb_rw.py system test script.
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r15882 | bugman | 2012-05-02 21:01:53 +0200 (Wed, 02 May 2012) | 7 lines
Created a new wizard element for inputting strings.
This will be used for user function args which should be strings. The wizard page element_string()
method creates the element from the wizard_elements.String class. This class inherits from
wizard_elements.Base_value which contains most of the executable code.
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r15883 | bugman | 2012-05-02 21:08:06 +0200 (Wed, 02 May 2012) | 7 lines
Created a new wizard element for inputting integers.
This will be used for user function args which should be integers. This is based on the string
element. The wizard page element_int() method creates the element from the wizard_elements.Integer
class.
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r15884 | bugman | 2012-05-02 21:12:13 +0200 (Wed, 02 May 2012) | 3 lines
The bmrb.citation GUI user function now uses the new wizard page element_*() methods for the GUI elements.
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r15885 | bugman | 2012-05-02 21:26:54 +0200 (Wed, 02 May 2012) | 8 lines
Created the GUI test base method execute_uf() for executing a user function.
This is an interface which will massively simplify the creation of GUI tests, so that they can be
almost the same as normal relax scripts. This will allow for the porting of most of the system test
scripts into GUI tests. This however requires the use of the new wizard page element_*() methods
to create the GUI elements.
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r15886 | bugman | 2012-05-02 21:27:35 +0200 (Wed, 02 May 2012) | 3 lines
The Bmrb.test_bmrb_rw GUI test now uses the new execute_uf() method for the bmrb.citation uf.
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r15887 | bugman | 2012-05-02 21:44:22 +0200 (Wed, 02 May 2012) | 6 lines
Modified the wizard_elements.Base_value base GUI element class to handle combo boxes.
This class can now choose between a wx.TextCtrl or a wx.ComboBox element with the element_type
keyword arg.
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r15888 | bugman | 2012-05-03 09:04:54 +0200 (Thu, 03 May 2012) | 6 lines
Better ComboBox support in wizard_elements.Base_value class.
Now strings and data are separate (if the data is supplied), and the GetValue() method now returns
the client data rather than the string value.
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r15889 | bugman | 2012-05-03 09:31:12 +0200 (Thu, 03 May 2012) | 5 lines
Created generic_fns.pipes.PIPE_DESC_LIST which is the PIPE_DESC as a list, sorted by VALID_TYPES.
This will be used in the GUI user functions.
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r15890 | bugman | 2012-05-03 09:45:01 +0200 (Thu, 03 May 2012) | 3 lines
The wizard page element_string() method now accepts all the combo box args (and a read_only arg).
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r15891 | bugman | 2012-05-03 09:45:33 +0200 (Thu, 03 May 2012) | 3 lines
The wizard_elements.Base_value class now can set the element to be read only.
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r15892 | bugman | 2012-05-03 10:00:09 +0200 (Thu, 03 May 2012) | 3 lines
The wizard_elements.Base_value.SetValue() method now works properly with the ComboBox.
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r15893 | bugman | 2012-05-03 10:04:14 +0200 (Thu, 03 May 2012) | 3 lines
The read_only=True flag to wizard_elements.Base_value now sets a TextCtrl to the background colour.
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r15894 | bugman | 2012-05-03 10:05:29 +0200 (Thu, 03 May 2012) | 3 lines
The wizard page element_string() GUI element creator read_only flag now defaults to False.
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r15895 | bugman | 2012-05-03 10:44:27 +0200 (Thu, 03 May 2012) | 5 lines
Created a Clear() wizard page method for clearing a specific GUI element.
This is currently only implemented for the wizard_elements.Base_value class.
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r15896 | bugman | 2012-05-03 10:59:06 +0200 (Thu, 03 May 2012) | 5 lines
Created the wizard page ResetChoices() method for resetting the list of values in a ComboBox.
This is currently implemented for the wizard_elements.Base_value class.
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r15897 | bugman | 2012-05-03 12:04:00 +0200 (Thu, 03 May 2012) | 7 lines
The wizard page element_string_list() method can now create the special Combo_list objects.
The element_type argument is used to select between the default element and the Combo_list object.
This allows this one element to be used for all string list user function arguments, independent of
the GUI element type.
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r15898 | bugman | 2012-05-03 15:19:17 +0200 (Thu, 03 May 2012) | 3 lines
The scons 'install' target now creates both *.pyc and *.pyo files during installation.
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r15899 | bugman | 2012-05-03 15:20:24 +0200 (Thu, 03 May 2012) | 5 lines
A number of the pipe GUI user function front ends now use the wizard page element_*() methods.
This is to simplify the code base.
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r15900 | bugman | 2012-05-03 15:21:42 +0200 (Thu, 03 May 2012) | 5 lines
The Bmrb.test_bmrb_rw GUI test now uses the base execute_uf() method for the pipe.create call.
This is part of the simplification of the user function interfaces.
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r15901 | bugman | 2012-05-03 15:40:04 +0200 (Thu, 03 May 2012) | 3 lines
Updated the generic_fns package __all__ list for the 'pdc' to 'bruker' module renaming.
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r15902 | bugman | 2012-05-03 15:42:48 +0200 (Thu, 03 May 2012) | 5 lines
Fix for the align_tensor.fix user function caused by recent changes.
The tensor checking code was not suitable for this function and needed modification.
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r15903 | bugman | 2012-05-03 16:05:22 +0200 (Thu, 03 May 2012) | 5 lines
Simplified the wizard_elements.Base_value ResetChoices() method.
This is an attempt to fix some racing conditions under wxGTK, triggered in the test suite.
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r15906 | bugman | 2012-05-03 16:29:16 +0200 (Thu, 03 May 2012) | 6 lines
Fix for the Base_value ResetChoices() method.
The recent simplification was failing as the ComboBox.Insert() method could not handle the position
being set to sys.maxint, unlike most other of its methods.
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r15907 | bugman | 2012-05-03 18:14:11 +0200 (Thu, 03 May 2012) | 8 lines
Big bug fix for the test suite!
One of the state system tests was removing the frame order analysis from the
generic_fns.pipes.VALID_TYPES list with a pop() call. But this change is permanent. So in the
later Bmrb.test_bmrb_rw GUI test, the GUI fails as this list is used in the pipe.create GUI user
function interface and it no longer matches the corresponding PIPE_DESC_LIST structure!
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r16041 | bugman | 2012-05-07 12:26:56 +0200 (Mon, 07 May 2012) | 3 lines
Missing import.
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r16126 | bugman | 2012-05-09 09:14:08 +0200 (Wed, 09 May 2012) | 6 lines
Improved the error message system for the spin ID matching multiple spins
This is a partial response to bug #19717 (http://gna.org/bugs/?19717) reported by Martin Ballaschk
(http://gna.org/users/mab).
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r16127 | bugman | 2012-05-09 09:16:59 +0200 (Wed, 09 May 2012) | 6 lines
The relax_fit.py sample script deselect.read user function now has all columns specified.
This is a partial response to bug #19717 (http://gna.org/bugs/?19717) reported by Martin Ballaschk
(http://gna.org/users/mab).
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r16128 | bugman | 2012-05-09 09:20:42 +0200 (Wed, 09 May 2012) | 3 lines
Updated the copyright statement.
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r16129 | bugman | 2012-05-09 09:22:17 +0200 (Wed, 09 May 2012) | 5 lines
Updated the deselect.read user function call in the noe.py sample script to match relax_fit.py.
All the column args are now specified.
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r16130 | bugman | 2012-05-09 09:45:24 +0200 (Wed, 09 May 2012) | 8 lines
Improved error reporting for multiple vectors in a model-free analysis.
This was reported by Vitaly Vostrikov (vvostri att uark.edu) at
http://www.mail-archive.com/relax-users@.../msg00991.html (Message-ID:
<CAO2iSXE1ycB4KX1vxqk15CxbW1rpWczZAyR_bX1g6j+yA2PCTQ@...>) and reported at bug #18807
(https://gna.org/bugs/?18807).
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r16135 | bugman | 2012-05-09 10:22:44 +0200 (Wed, 09 May 2012) | 3 lines
Fix for the call to arg_check.is_list() in the model-free code.
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r16136 | bugman | 2012-05-09 10:44:24 +0200 (Wed, 09 May 2012) | 7 lines
Changed the behaviour of the arg_check module so that the functions can return answers.
The raise_error flag is now accepted by all is_*() functions. If this is False, then the functions
will return either True or False, answering the question. This should allow the functions to be
used more extensively.
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r16137 | bugman | 2012-05-09 10:46:11 +0200 (Wed, 09 May 2012) | 5 lines
Fix for the arg_check.is_list call used in the fix at r16130.
This now will return the answer rather than raising a RelaxError.
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r16144 | bugman | 2012-05-09 11:33:44 +0200 (Wed, 09 May 2012) | 3 lines
Fix for the test_name_molecule_many_fail() unit test - RelaxMultiMolIDError is now raised.
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r16203 | bugman | 2012-05-10 20:01:40 +0200 (Thu, 10 May 2012) | 3 lines
Debugging print out fix.
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r16204 | bugman | 2012-05-10 20:04:30 +0200 (Thu, 10 May 2012) | 6 lines
Improved debugging of the observers in the status singleton object.
The Status_container has been renamed to Observer_container and the info() method added to print out
everything about the observer objects. This has to be called in temporary debugging code.
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r16222 | bugman | 2012-05-11 11:04:48 +0200 (Fri, 11 May 2012) | 6 lines
Merged the CHANGES file for relax version 1.3.16 back into the main 1.3 line.
The command used was:
svn merge -r16220:16221 svn+ssh://bugman@.../svn/relax/tags/1.3.16
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r16226 | bugman | 2012-05-11 14:28:12 +0200 (Fri, 11 May 2012) | 12 lines
Ported the HTML user manual fix of r16225 from the 1.3.16 tag.
The command used was:
svn merge -r16224:r16225 svn+ssh://bugman@.../svn/relax/tags/1.3.16 .
.....
Removed more maths from the section titles of the HTML user manual.
This is an attempt at fixing the image brokenness of the HTML manual!
.....
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r16227 | bugman | 2012-05-11 14:30:26 +0200 (Fri, 11 May 2012) | 6 lines
Fix for the creation of the HTML user manual (http://www.nmr-relax.com/manual).
The shell command for renaming the relax_user_manual.html file to index.html had a typo and was not
working!
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r16228 | bugman | 2012-05-11 15:04:08 +0200 (Fri, 11 May 2012) | 7 lines
Fix for the HTML version of the relax user manual (http://www.nmr-relax.com/manual/).
The model-free chapter subsection on the universal solution was causing Latex2html to die! This is
the same as the fixes of r15816, but the \widehat maths command was recently reintroduced into this
new section.
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r16229 | bugman | 2012-05-11 15:06:24 +0200 (Fri, 11 May 2012) | 5 lines
A small edit of the "The universal solution" subsection title of the model-free chapter.
This is for the relax HTML user manual (http://www.nmr-relax.com/manual/Model_free_analysis.html).
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r16236 | bugman | 2012-05-11 17:25:36 +0200 (Fri, 11 May 2012) | 3 lines
The scons 'clean' target now removes *.pyo files as well.
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r16246 | bugman | 2012-05-11 20:29:02 +0200 (Fri, 11 May 2012) | 3 lines
Fixes for most of the structure user functions - the pipe check is now performed at the start.
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r16312 | bugman | 2012-05-16 12:25:52 +0200 (Wed, 16 May 2012) | 5 lines
Created a system test Mol_res_spin.test_residue_delete() demonstrating a failure of the user function.
Deleting the first residue removes the entire sequence!
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r16313 | bugman | 2012-05-16 17:11:02 +0200 (Wed, 16 May 2012) | 10 lines
Changed the behaviour of the generate_spin_id() and generate_spin_id_data_array() functions.
This is a large change affecting many parts of the code base. The problem that this solves is the
incorrect usage of the '&' character in spin IDs, tripping up on the powerful Selection object of
Chris MacRaild.
For example, the spin ID ':2&:Glu' cannot be correctly handled. This actually matches all residues
with the number 2, and all residues with the name 'Glu'. It is very strange that this has not been
noticed before!
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r16321 | bugman | 2012-05-16 19:02:48 +0200 (Wed, 16 May 2012) | 3 lines
The relax data store is_empty() method now only prints to STDERR if the verbosity flag is set.
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r16323 | bugman | 2012-05-18 09:09:55 +0200 (Fri, 18 May 2012) | 7 lines
Fix for the relax controller SplitIO() setup for logging and teeing modes.
The SplitIO() usage is now disabled for the test suite. This prevents a doubling of the print outs
in the GUI tests. The problem was introduced at r15843 with the accommodation for the logging and
teeing modes with the GUI.
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r16356 | bugman | 2012-05-21 09:37:25 +0200 (Mon, 21 May 2012) | 3 lines
Created a sample script for BMRB data deposition.
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r16451 | bugman | 2012-05-25 09:23:58 +0200 (Fri, 25 May 2012) | 9 lines
Made the bond vector extraction print out from structure.vectors more informative.
This is in response to James Nyirenda's <jamesn7414 att yahoo dott com> post at
https://mail.gna.org/public/relax-users/2012-05/msg00023.html (Message-id:
<1337916876.99384.YahooMailNeo@...>).
The number of vectors extracted is now being printed out.
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r16452 | bugman | 2012-05-25 09:32:17 +0200 (Fri, 25 May 2012) | 3 lines
A small change for the structure.vectors print out.
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r16453 | bugman | 2012-05-25 09:47:49 +0200 (Fri, 25 May 2012) | 10 lines
The model-free minimisation is now checking for multiple vectors per spin, and raises a RelaxError.
This is in response to James Nyirenda's <jamesn7414 att yahoo dott com> post at
https://mail.gna.org/public/relax-users/2012-05/msg00023.html (Message-id:
<1337916876.99384.YahooMailNeo@...>).
The RelaxMultiVectorError has been modified to accept a spin ID. This error is now raised if
multiple vectors exist per spin, as model-free analysis cannot handle this.
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r16454 | bugman | 2012-05-25 11:30:38 +0200 (Fri, 25 May 2012) | 7 lines
Fix for a bug introduced at r16453.
The structure.vectors user function will now store single vectors as a 3D, rank-1 array. In some
cases this was being stored as a list of 3D, rank-1 arrays which was then failing in with the
RelaxMultipleVectorError in the model-free code.
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r16666 | bugman | 2012-06-05 14:27:34 +0200 (Tue, 05 Jun 2012) | 3 lines
Missing import.
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r16668 | bugman | 2012-06-05 15:17:58 +0200 (Tue, 05 Jun 2012) | 9 lines
Added checks for the proton frq for the relax_data.read and relax_data.back_calc user functions.
This is in response to the problems seen by Martin Ballaschk <ballaschk att fmp-berlin dott de> and
reported at http://www.mail-archive.com/relax-users@.../msg01179.html (Message-Id:
<533CDA92-36FE-4E36-8925-7536EFF2608E@...>).
If the frequency is not exact or is less than 1 MHz, warnings are now given to the user.
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r16672 | bugman | 2012-06-05 17:52:56 +0200 (Tue, 05 Jun 2012) | 3 lines
Created a system test for catching bug #19785 (https://gna.org/bugs/?19785).
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r16673 | bugman | 2012-06-05 18:04:02 +0200 (Tue, 05 Jun 2012) | 11 lines
The relax_data.delete user function is now finally properly implemented!
This was reported by Martin Ballaschk <ballaschk att fmp-berlin dott de> as bug #19785
(https://gna.org/bugs/?19785), and the mail message at
http://www.mail-archive.com/relax-users@.../msg01183.html (Message-Id:
<EED32F2B-B78F-4D23-9E0B-3DDE8B661F48@...>).
The problem was that this was not being checked by the test suite, and no one had tried to delete
relaxation data before (well, at least it was never reported).
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