Author: bugman
Date: Sun Jun 10 15:35:38 2012
New Revision: 16814
URL: http://svn.gna.org/viewcvs/relax?rev=16814&view=rev
Log:
Merged revisions
15670,15688-15797,15799-15801,15803-15817,15820,15825-15826,15828-15829,15832-15903,15906-15907,16041,16126-16130,16135-16137,16144,16203-16204,16222,16226-16229,16236,16246,16312-16313,16321,16323,16356,16451-16454,16666,16668,16672-16673,16684,16728
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
[... 1577 lines stripped ...]
r16814 - in /branches/inversion-recovery: ./ data/ docs/ docs/latex/ docs/latex/images/ generic_fns/ generic_fns/structure/ ...