Author: bugman
Date: Thu Jul 28 17:00:23 2011
New Revision: 13963
URL: http://svn.gna.org/viewcvs/relax?rev=13963&view=rev
Log:
Merged revisions
12840-12851,12854-12888,12891-12897,12899-12935,12937-12941,12943-12945,12947-12952,12954-12957,12959-12960,12965-12967,12969-12975,12982-13022,13028-13029,13045-13046,13153,13258,13357-13359,13411,13510-13512,13577,13631-13632,13641,13655,13660,13683,13686,13706,13742-13743,13748-13749,13780,13835-13836,13845-13857,13904-13906,13909,13919,13926-13927,13929,13932,13951,13956,13958
via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/1.3
........
r12840 | bugman | 2011-05-31 14:47:37 +0200 (Tue, 31 May 2011) | 7 lines
Updates for the Dasha sample script.
The problem was identified by Shantanu Bhattacharyya <shantanu01 att cmu
dott edu> in the post at
https://mail.gna.org/public/relax-users/2011-05/msg00018.html (Message-id:
<7a068ac7a9e90b8e8d374b334a20d4be.squirrel@xxxxxxxxxxxxxxxxxxxxxx>).
........
r12841 | semor | 2011-05-31 16:29:49 +0200 (Tue, 31 May 2011) | 7 lines
Updates for the diffusion tensor optimization sample script.
The problem was identified (for sample script "dasha.py")
by Shantanu Bhattacharyya <shantanu01 att cmu dott edu> in the post at
https://mail.gna.org/public/relax-users/2011-05/msg00018.html (Message-id:
<7a068ac7a9e90b8e8d374b334a20d4be.squirrel@xxxxxxxxxxxxxxxxxxxxxx>).
........
r12842 | bugman | 2011-05-31 18:43:18 +0200 (Tue, 31 May 2011) | 3 lines
Some fixes for the subprocess.Popen() calls on MS Windows.
........
r12843 | bugman | 2011-06-03 17:46:57 +0200 (Fri, 03 Jun 2011) | 7 lines
Added the PDB reading parts of Scientific python to relax.
This is allowed as the CeCILL licence is GPL compatible. The Scientific
python website is
https://sourcesup.cru.fr/projects/scientific-py/, but it hasn't been
updated in a long time and
might be a dying project. Therefore the code is now part of relax so it
can be used in the future.
........
r12844 | bugman | 2011-06-03 17:48:05 +0200 (Fri, 03 Jun 2011) | 3 lines
The Scientific python PDB reading tests are no longer skipped if the module
is not installed.
........
r12845 | bugman | 2011-06-03 17:48:41 +0200 (Fri, 03 Jun 2011) | 3 lines
Removed Scientific python from the information printout from 'relax --info'.
........
r12846 | bugman | 2011-06-03 17:51:24 +0200 (Fri, 03 Jun 2011) | 3 lines
Modified the Scientific python PDB reader relax module to use the internal
module.
........
r12847 | bugman | 2011-06-03 17:52:10 +0200 (Fri, 03 Jun 2011) | 3 lines
Removed Scientific python from the dependency checking.
........
r12848 | bugman | 2011-06-03 17:54:51 +0200 (Fri, 03 Jun 2011) | 3 lines
The 'extern' package is now a proper package - the __init__.py file has
been added!
........
r12849 | bugman | 2011-06-03 17:57:07 +0200 (Fri, 03 Jun 2011) | 3 lines
Fixes for the Scientific python parts included with relax for the module
path.
........
r12850 | bugman | 2011-06-03 17:57:55 +0200 (Fri, 03 Jun 2011) | 3 lines
The dep_check.scientific_pdb_module flag was still being checked.
........
r12851 | bugman | 2011-06-03 18:00:15 +0200 (Fri, 03 Jun 2011) | 3 lines
Removed the dep_check checks and test disabling for the Scientific python
system and unit tests.
........
r12854 | bugman | 2011-06-03 18:34:07 +0200 (Fri, 03 Jun 2011) | 5 lines
Removed Scientific python and Numeric from the blacklisted modules.
This is for the docstring fetching script to generate the user function
section of the user manual.
........
r12855 | bugman | 2011-06-03 18:34:53 +0200 (Fri, 03 Jun 2011) | 3 lines
Removed Scientific python from the dependency list in the user manual.
........
r12856 | michaelbieri | 2011-06-07 01:12:19 +0200 (Tue, 07 Jun 2011) | 2
lines
relax icon is not shown in window title if running on a Mac.
........
r12857 | michaelbieri | 2011-06-07 01:14:31 +0200 (Tue, 07 Jun 2011) | 2
lines
Included copyright be the relax development team to main window.
........
r12858 | michaelbieri | 2011-06-07 01:50:39 +0200 (Tue, 07 Jun 2011) | 2
lines
Peak lists and relaxation times are collected in data grid.
........
r12859 | michaelbieri | 2011-06-07 01:55:37 +0200 (Tue, 07 Jun 2011) | 2
lines
Renamed load_peaklists() to add_pleaklists().
........
r12860 | michaelbieri | 2011-06-07 02:10:21 +0200 (Tue, 07 Jun 2011) | 2
lines
Add peaklist button was added.
........
r12861 | michaelbieri | 2011-06-07 02:42:27 +0200 (Tue, 07 Jun 2011) | 2
lines
Peak lists can be loaded into peak list grid.
........
r12862 | michaelbieri | 2011-06-07 02:43:01 +0200 (Tue, 07 Jun 2011) | 2
lines
Allowed to load 50 peaklists.
........
r12863 | michaelbieri | 2011-06-07 02:44:15 +0200 (Tue, 07 Jun 2011) | 2
lines
Added R1 and R2 label to peak list title.
........
r12864 | michaelbieri | 2011-06-07 02:52:01 +0200 (Tue, 07 Jun 2011) | 2
lines
Button in R1 to read relaxation delays from VD lists.
........
r12865 | michaelbieri | 2011-06-07 02:53:18 +0200 (Tue, 07 Jun 2011) | 2
lines
Removed event.skip due to conflict with Windows.
........
r12866 | michaelbieri | 2011-06-07 03:04:13 +0200 (Tue, 07 Jun 2011) | 2
lines
R1 delays can be imported from VD lists.
........
r12867 | michaelbieri | 2011-06-07 03:12:32 +0200 (Tue, 07 Jun 2011) | 2
lines
Added import VC (variable counter) list function incl. space to sepcify
counter time.
........
r12868 | michaelbieri | 2011-06-07 03:38:15 +0200 (Tue, 07 Jun 2011) | 2
lines
R2 delax can be imported from variable counter (VC) list.
........
r12869 | michaelbieri | 2011-06-07 04:29:04 +0200 (Tue, 07 Jun 2011) | 2
lines
Peak lists and relaxation delays are synchronized with relax data storage.
........
r12870 | michaelbieri | 2011-06-07 06:17:52 +0200 (Tue, 07 Jun 2011) | 2
lines
Peak lists and relaxation times can be opened.
........
r12871 | bugman | 2011-06-07 12:03:03 +0200 (Tue, 07 Jun 2011) | 5 lines
Copied all of Michael's code from the auto_rx_base module committed
yesterday into the spectrum module.
This is to keep a clear code separation of the different elements in the R1
and R2 frames.
........
r12872 | bugman | 2011-06-07 12:43:45 +0200 (Tue, 07 Jun 2011) | 3 lines
Partially reverted r12870 as the commenting out of link_data() broke the
loading of the relax state!
........
r12873 | bugman | 2011-06-07 12:44:36 +0200 (Tue, 07 Jun 2011) | 3 lines
Redesigned sync_ds() to handle the new wx.grid.Grid() object.
........
r12874 | bugman | 2011-06-07 14:15:03 +0200 (Tue, 07 Jun 2011) | 3 lines
Capitalisation fix.
........
r12875 | bugman | 2011-06-07 14:15:13 +0200 (Tue, 07 Jun 2011) | 3 lines
Spacing fix.
........
r12876 | bugman | 2011-06-07 14:49:40 +0200 (Tue, 07 Jun 2011) | 3 lines
Double clicking on the peak list cells in the Rx frames now runs openfile().
........
r12877 | bugman | 2011-06-07 15:47:04 +0200 (Tue, 07 Jun 2011) | 3 lines
Removed some unused variables.
........
r12878 | bugman | 2011-06-07 16:19:42 +0200 (Tue, 07 Jun 2011) | 3 lines
Added a title and nicer spacing for the relaxation peak lists GUI element.
........
r12879 | bugman | 2011-06-07 16:20:44 +0200 (Tue, 07 Jun 2011) | 3 lines
The 'Rx peak lists' column name is no longer plural.
........
r12880 | bugman | 2011-06-07 16:41:43 +0200 (Tue, 07 Jun 2011) | 3 lines
Not selecting a peak list file also vetos the event so the cell is not
editable.
........
r12881 | bugman | 2011-06-07 16:46:06 +0200 (Tue, 07 Jun 2011) | 3 lines
Comment fix.
........
r12882 | bugman | 2011-06-07 16:46:46 +0200 (Tue, 07 Jun 2011) | 5 lines
Fixes for the spin.copy() GUI user function element.
This still had remnants of the residue.copy() window.
........
r12883 | bugman | 2011-06-07 17:22:47 +0200 (Tue, 07 Jun 2011) | 6 lines
Fix for the CSA value in the value.set() GUI wizard image.
This was reported by Seb at
https://mail.gna.org/public/relax-devel/2011-06/msg00040.html
(Message-id: <4DEE3D12.4000406@xxxxxxxxx>).
........
r12884 | bugman | 2011-06-07 17:32:07 +0200 (Tue, 07 Jun 2011) | 3 lines
Updated the Bieri et al., 2011 reference as the relax GUI paper is now
published.
........
r12885 | bugman | 2011-06-07 17:56:24 +0200 (Tue, 07 Jun 2011) | 6 lines
Changed the "Help->Contact relaxGUI" to "Help->Mailing list contact".
This is because this sends an email to the relax users mailing list, and
the user needs to be aware
that this is a public mailing list.
........
r12886 | bugman | 2011-06-07 19:53:09 +0200 (Tue, 07 Jun 2011) | 6 lines
Renamed the "Relaxation time [s]" column to "Relaxation delay [s]" as this
is a more correct desc.
Relaxation times are the inverse of the rates, not the delays causing
relaxation in the pulse
sequence.
........
r12887 | bugman | 2011-06-07 19:54:51 +0200 (Tue, 07 Jun 2011) | 3 lines
Widened the "Relaxation delay" column for the Rx tabs.
........
r12888 | bugman | 2011-06-07 21:35:08 +0200 (Tue, 07 Jun 2011) | 3 lines
Deleted my ancient Melbourne Uni email address from the MEDLINE info!
........
r12891 | bugman | 2011-06-08 12:13:37 +0200 (Wed, 08 Jun 2011) | 5 lines
Implemented the deletion of cell contents in the wx.grid element for Rx
peak lists.
This requires a complex algorithm for handling wx.grid selections!
........
r12892 | bugman | 2011-06-08 12:50:24 +0200 (Wed, 08 Jun 2011) | 3 lines
Better behaviour for the addition of peak list files to the Rx grid element.
........
r12893 | semor | 2011-06-08 13:46:03 +0200 (Wed, 08 Jun 2011) | 3 lines
Fixed an alignment.
........
r12894 | bugman | 2011-06-08 13:52:30 +0200 (Wed, 08 Jun 2011) | 3 lines
Shifted the button code into the add_buttons() method.
........
r12895 | bugman | 2011-06-08 13:56:48 +0200 (Wed, 08 Jun 2011) | 3 lines
Shifted the grid construction code into the add_grid() method.
........
r12896 | bugman | 2011-06-08 13:57:31 +0200 (Wed, 08 Jun 2011) | 3 lines
Renamed peak_list_header() to add_header().
........
r12897 | bugman | 2011-06-08 13:58:59 +0200 (Wed, 08 Jun 2011) | 3 lines
Abstracted the grid GUI element by renaming self.peaklist to self.grid.
........
r12899 | semor | 2011-06-08 14:49:50 +0200 (Wed, 08 Jun 2011) | 12 lines
relax icon is not shown in "Global relax settings" window if running on a
Mac.
This is as in revision 12856:
http://svn.gna.org/viewcvs/relax?rev=12856&view=rev),
but for the button "Settings" / "Global relax settings".
This change creates a bug, as the opened window upon clicking this button,
when closed, will have relax gui crash (with no button responding). This
needs to be fixed...
........
r12900 | bugman | 2011-06-08 20:44:28 +0200 (Wed, 08 Jun 2011) | 10 lines
Implemented the delay time TextCtrl and added the number of cycles column
to the Rx peak list grid.
This implements what was discussed in
https://mail.gna.org/public/relax-devel/2011-06/msg00036.html
(Message-id: <BANLkTi=8v-S=rO4NBcFVrxHorWaq34J5Jw@xxxxxxxxxxxxxx>).
This is a big change. The changing of the number of cycles values or the
delay time automatically
updates the relaxation times. These times are now read only cells. And
the +, +VD, and +VC buttons
are gone as they are no longer needed.
........
r12901 | bugman | 2011-06-08 20:55:02 +0200 (Wed, 08 Jun 2011) | 3 lines
Better spacing of the Rx tab elements.
........
r12902 | bugman | 2011-06-09 08:43:04 +0200 (Thu, 09 Jun 2011) | 5 lines
Fixed the behaviour of the number of cycles column in the Rx tab grid.
Deleting or not entering a number was causing '1' to appear in the cell!
........
r12903 | bugman | 2011-06-09 08:43:52 +0200 (Thu, 09 Jun 2011) | 3 lines
Fix for the Delay_num_cell_editor.Clone() method for cloning the grid
editor class.
........
r12904 | bugman | 2011-06-09 10:22:10 +0200 (Thu, 09 Jun 2011) | 3 lines
The delay time textctrl can now only have a single '.' char in the peak
list grid.
........
r12905 | bugman | 2011-06-09 10:28:03 +0200 (Thu, 09 Jun 2011) | 3 lines
Navigation keys are now allowed in the Rx tab delay time text field.
........
r12906 | bugman | 2011-06-09 10:45:42 +0200 (Thu, 09 Jun 2011) | 5 lines
Better behaviour of the deletion of single cells in the Rx peak list grids.
The relaxation time is now cleared, rather than set to 0.0.
........
r12907 | bugman | 2011-06-09 11:45:07 +0200 (Thu, 09 Jun 2011) | 6 lines
Normalisation of the text in the auto model-free analysis GUI tab.
The font sizes are now all the same, the text is not right aligned (not
seen under Linux but very
ugly in Windows), and semicolon usage and capitalisation is normalised.
........
r12908 | bugman | 2011-06-09 11:53:58 +0200 (Thu, 09 Jun 2011) | 5 lines
Shifted the model-free tab font formatting to be interface wide in self.gui.
This will help regularise the font throughout the GUI.
........
r12909 | bugman | 2011-06-09 12:16:38 +0200 (Thu, 09 Jun 2011) | 3 lines
Regularisation of the font formatting in the steady-state NOE GUI tab.
........
r12910 | bugman | 2011-06-09 12:29:21 +0200 (Thu, 09 Jun 2011) | 5 lines
Shifted the title and subtitle creation for the NOE frame into a base class
for all frames to use.
The formatting has also been regularised to improve the look of the GUI
across operating systems.
........
r12911 | bugman | 2011-06-09 12:29:52 +0200 (Thu, 09 Jun 2011) | 3 lines
Removal of empty lines.
........
r12912 | bugman | 2011-06-09 12:32:27 +0200 (Thu, 09 Jun 2011) | 3 lines
Removed some unused imports.
........
r12913 | bugman | 2011-06-09 12:41:15 +0200 (Thu, 09 Jun 2011) | 3 lines
Spacing cleanup.
........
r12914 | bugman | 2011-06-09 12:41:41 +0200 (Thu, 09 Jun 2011) | 3 lines
Regularisation of the fonts, titles, and subtitles in the Rx auto-analysis
frames.
........
r12915 | bugman | 2011-06-09 12:52:56 +0200 (Thu, 09 Jun 2011) | 3 lines
The auto model-free frame is now using the add_title() base class method.
........
r12916 | bugman | 2011-06-09 12:54:05 +0200 (Thu, 09 Jun 2011) | 3 lines
Rearrangement of the import statements.
........
r12917 | bugman | 2011-06-09 13:05:45 +0200 (Thu, 09 Jun 2011) | 3 lines
Created the add_subsubtitle() base class method for creating a
sub-sub-title.
........
r12918 | bugman | 2011-06-09 13:06:06 +0200 (Thu, 09 Jun 2011) | 3 lines
Regularised the text in the results tab.
........
r12919 | bugman | 2011-06-09 13:08:58 +0200 (Thu, 09 Jun 2011) | 3 lines
Regularised the "Single delay cycle time [s]" text in the model-free frame.
........
r12920 | bugman | 2011-06-09 13:10:19 +0200 (Thu, 09 Jun 2011) | 3 lines
Attempt to regularise the text in the text controls.
........
r12921 | bugman | 2011-06-09 13:32:22 +0200 (Thu, 09 Jun 2011) | 3 lines
Created the add_text_control() base class method for standardising the text
controls.
........
r12922 | bugman | 2011-06-09 13:33:48 +0200 (Thu, 09 Jun 2011) | 3 lines
Regularised all the stead-state NOE frame text controls.
........
r12923 | bugman | 2011-06-09 13:57:46 +0200 (Thu, 09 Jun 2011) | 3 lines
Fix for the base class add_text_control() method, the parent object is
passed into the method!
........
r12924 | bugman | 2011-06-09 13:58:24 +0200 (Thu, 09 Jun 2011) | 3 lines
Created the add_static_text() base class method for all the GUI frames to
use.
........
r12925 | bugman | 2011-06-09 13:58:47 +0200 (Thu, 09 Jun 2011) | 3 lines
The NOE auto-analysis now uses the add_static_text() base class method for
text.
........
r12926 | bugman | 2011-06-09 14:35:27 +0200 (Thu, 09 Jun 2011) | 3 lines
Added the add_button_open() base class method for regularising the buttons
across frames.
........
r12927 | bugman | 2011-06-09 14:39:25 +0200 (Thu, 09 Jun 2011) | 3 lines
Regularised all of the auto NOE analysis frame buttons.
........
r12928 | bugman | 2011-06-09 15:28:44 +0200 (Thu, 09 Jun 2011) | 5 lines
Added the add_text_sel_element() base class method for creating one of the
basic frame elements.
This element consists of text, a text control, and an optional button.
........
r12929 | bugman | 2011-06-09 15:45:25 +0200 (Thu, 09 Jun 2011) | 3 lines
Large simplification of the NOE frame code by the use of the
add_text_sel_element() base method.
........
r12930 | bugman | 2011-06-09 15:53:09 +0200 (Thu, 09 Jun 2011) | 3 lines
Large simplification of the Rx frame code by the use of the
add_text_sel_element() base method.
........
r12931 | bugman | 2011-06-09 15:59:58 +0200 (Thu, 09 Jun 2011) | 3 lines
The Rx peak list grid GUI element now also uses the add_text_sel_element()
base method.
........
r12932 | bugman | 2011-06-09 16:13:13 +0200 (Thu, 09 Jun 2011) | 3 lines
Large simplification of the model-free frame code by the use of the
add_text_sel_element() base method.
........
r12933 | bugman | 2011-06-09 16:32:40 +0200 (Thu, 09 Jun 2011) | 3 lines
With debugging turned on, the size of the GUI main frame can be changed.
........
r12934 | bugman | 2011-06-09 17:15:10 +0200 (Thu, 09 Jun 2011) | 6 lines
Added a simple XYZ structure file for the test suite.
This was attached to task #7404 (https://gna.org/task/?7404) by Han. The
directory for the file was
given at https://mail.gna.org/public/relax-devel/2011-06/msg00083.html.
........
r12935 | bugman | 2011-06-09 17:18:10 +0200 (Thu, 09 Jun 2011) | 5 lines
Eliminated the __set_properties() and __do_layout() methods.
The code has been shifted into __init__() and some variables shifted to
hardcoded class variables.
........
r12937 | bugman | 2011-06-09 17:52:04 +0200 (Thu, 09 Jun 2011) | 3 lines
Removed a duplicated self.SetSize() call for the main GUI window.
........
r12938 | bugman | 2011-06-09 17:53:10 +0200 (Thu, 09 Jun 2011) | 3 lines
Changed the Frame.SetSize() call to SetMinSize() to prevent the main GUI
window becoming too small.
........
r12939 | bugman | 2011-06-09 17:54:12 +0200 (Thu, 09 Jun 2011) | 5 lines
Both SetSize() and SetMinSize() are now used for the main GUI window.
This allows for a proper layout.
........
r12940 | bugman | 2011-06-09 18:19:37 +0200 (Thu, 09 Jun 2011) | 3 lines
Simplified and localised a variable.
........
r12941 | bugman | 2011-06-09 18:31:46 +0200 (Thu, 09 Jun 2011) | 3 lines
Added a hard coded variable for the size of the graphical part of the
analysis frames.
........
r12943 | bugman | 2011-06-09 19:06:49 +0200 (Thu, 09 Jun 2011) | 3 lines
The text controls are now horizontally expandable.
........
r12944 | bugman | 2011-06-09 19:11:05 +0200 (Thu, 09 Jun 2011) | 3 lines
The model-free, Rx, and NOE frame main box sizers all expand horizontally
now.
........
r12945 | bugman | 2011-06-09 19:33:23 +0200 (Thu, 09 Jun 2011) | 3 lines
A spacer is now used for add_text_sel_element() if no button is present to
fill the button space.
........
r12947 | bugman | 2011-06-09 20:10:45 +0200 (Thu, 09 Jun 2011) | 5 lines
Big simplification by shifting the widths of the text selection GUI element
to hard coded variables.
These hard coded class variables are located in the base class.
........
r12948 | bugman | 2011-06-09 20:16:10 +0200 (Thu, 09 Jun 2011) | 3 lines
Added some horizontal spacing between the elements of the text selection
GUI element.
........
r12949 | bugman | 2011-06-10 09:42:25 +0200 (Fri, 10 Jun 2011) | 5 lines
Created the setup_analysis_element() base method for laying out the main
analysis GUI element.
This currently adds a border of 10 px around each analysis.
........
[... 870 lines stripped ...]
r13963 - in /branches/multi_processor_merge: ./ auto_analyses/ data/ docs/latex/ extern/ generic_fns/ generic_fns/structure/...