relax SVN archive

Converted the spectra list GUI element to behave the same way as the relaxation data list element.

The size is now fixed, and the entire thing is packed into a single panel.

Merged revisions 13153,13258,13357-13359,13411,13510-13512,13577,13631-13632,13641,13655,13660,13683,13686,13706,13742-13743,13748-13749,13780 via svnmerge from
svn+ssh://semor@.../svn/relax/1.3

........
r13153 | bugman | 2011-06-21 19:18:15 +0200 (Tue, 21 Jun 2011) | 5 lines

Removed a test for the sequence in the user function structure.create_diff_tensor_pdb() backend.

The sequence data is not needed for this.
........
r13258 | bugman | 2011-06-28 12:37:30 +0200 (Tue, 28 Jun 2011) | 6 lines

Bug fix for the NOE auto-analysis - the column numbers for the deselected spins file are now assumed.

The residue number is assumed to be in the first column. This is a hack until the spin selection
part is better designed.
........
r13357 | bugman | 2011-07-01 13:33:41 +0200 (Fri, 01 Jul 2011) | 3 lines

Added support for old save files in the Peak_intensity.sync_ds() method.
........
r13358 | bugman | 2011-07-01 13:35:09 +0200 (Fri, 01 Jul 2011) | 6 lines

Fix for the bug reported as sr #2764 (https://gna.org/support/index.php?2764).

The problem was that the sequence file is now in the variable sequence_file.
........
r13359 | bugman | 2011-07-01 13:36:36 +0200 (Fri, 01 Jul 2011) | 5 lines

Another fix for the bug of sr #2764 (https://gna.org/support/?2764).

The sequence file variable is in self.data!!!
........
r13411 | michaelbieri | 2011-07-04 01:15:43 +0200 (Mon, 04 Jul 2011) | 2 lines

Argument change_all for deselecting residues in the d'Auvergne protocol has to be boolean.
........
r13510 | bugman | 2011-07-08 08:58:14 +0200 (Fri, 08 Jul 2011) | 3 lines

Bug fix for the sequence.read() user function - the force flag is now being passed on.
........
r13511 | bugman | 2011-07-08 09:00:06 +0200 (Fri, 08 Jul 2011) | 5 lines

Another fix for the sequence.write() user function - the force flag is passed to open_write_file().

This is from the relax_io.write_spin_data() function.
........
r13512 | bugman | 2011-07-08 09:01:05 +0200 (Fri, 08 Jul 2011) | 5 lines

Bug fix for the sequence.write() user function when the column separator is not whitespace.

The column widths are no longer fixed is the separator is not whitespace.
........
r13577 | bugman | 2011-07-13 11:44:38 +0200 (Wed, 13 Jul 2011) | 5 lines

Many bug fixes for the functions of the generic_fns.mol_res_spin module.

These fixes are for when a data pipe other than the current data pipe is used.
........
r13631 | bugman | 2011-07-14 18:38:10 +0200 (Thu, 14 Jul 2011) | 5 lines

Bug fix for the relax save states - the current data pipe is now saved and restored.

The info about the cdp was being blacklisted, so was not stored in the relax save file.
........
r13632 | bugman | 2011-07-14 20:09:47 +0200 (Thu, 14 Jul 2011) | 7 lines

Fix for the loading of saved state files prior to r13631 - the cdp is now set to the last pipe.

The earlier saved state files did not store the current data pipe info, so the current data pipe was
set by default to the last data pipe. This behaviour was broken with r13631 but is now restored for
the old state files.
........
r13641 | bugman | 2011-07-15 12:25:21 +0200 (Fri, 15 Jul 2011) | 3 lines

Fix for the new relax save state with current pipe info - the cdp ojbect is now set after loading.
........
r13655 | bugman | 2011-07-15 16:37:34 +0200 (Fri, 15 Jul 2011) | 3 lines

Bug fix for the atomic position check in the spin.create_pseudo user function.
........
r13660 | bugman | 2011-07-15 19:50:44 +0200 (Fri, 15 Jul 2011) | 6 lines

Bug fix for pseudo-atom support when only a single structure is loaded.

Pseudo-atom support was only working correctly for when multiple models were loaded and atomic
positions were not averaged.
........
r13683 | bugman | 2011-07-18 14:00:29 +0200 (Mon, 18 Jul 2011) | 6 lines

Bug fix for the spectrum.read_intensities int_method argument for volumes.

Volume integration should be called 'point sum', but the back end code was checking against the
string 'volume'.
........
r13686 | bugman | 2011-07-18 14:24:00 +0200 (Mon, 18 Jul 2011) | 3 lines

Bug fix in one of the relaxation curve-fitting system tests - 'volume' should have been 'point sum'.
........
r13706 | bugman | 2011-07-18 20:13:04 +0200 (Mon, 18 Jul 2011) | 6 lines

Fix for the PCS back-calculation function - divide by zero is now avoided.

The PCS back-calculation function was calculating the normalised bond vector between the lanthanide
atom and itself. The normalisation in this case is now avoided.
........
r13742 | bugman | 2011-07-19 17:02:29 +0200 (Tue, 19 Jul 2011) | 6 lines

Changed the order of some of the replicated spectra in the test_curve_fitting_height system test.

This triggers a bug in the spectra.error_analysis user function which looks like the replicated
spectra list is order dependent (when it shouldn't be).
........
r13743 | bugman | 2011-07-19 17:18:49 +0200 (Tue, 19 Jul 2011) | 7 lines

Bug fix for the spectrum user functions for when the ID order does not match those loaded.

If the order of IDs sent to spectrum.replicated did not match the order they were loaded by
spectrum.read_intensities, then the spectrum.error_analysis user function would fail. The order is
no longer important.
........
r13748 | bugman | 2011-07-19 17:58:00 +0200 (Tue, 19 Jul 2011) | 5 lines

The relax_fit overfit_deselect() method now skips deselected spins.

This prevents unnecessary warnings about missing data for deselected spins.
........
r13749 | bugman | 2011-07-19 18:00:13 +0200 (Tue, 19 Jul 2011) | 3 lines

All of the overfit_deselect() methods now skip deselected spins, avoiding confusing warnings.
........
r13780 | bugman | 2011-07-20 15:56:27 +0200 (Wed, 20 Jul 2011) | 6 lines

Bug fix - the pipe switching flag is now propagated all the way to the data store add() method.

The flag was previously not sent to the method so that the creation of a new data pipe always
resulted in a switch to that pipe. This bug is normally harmless.
........

The virtual width of the analysis GUI elements now matches the real width.

The horizontal scrollbar has also been disabled.

Initialized merge tracking via "svnmerge" with revisions "1-13061" from
svn+ssh://semor@.../svn/relax/1.3

Converted all of the analysis objects into instances of wx.lib.scrolledpanel.ScrolledPanel.

This is instead of just having the right hand panel as a scrolled panel, as was tested in the
model-free auto-analysis. The setup of the GUI element has also shifted into the base class in
gui.analyses.base, whereas the analysis specific setup still occurs in the specific classes.

Attempted to put the model-free auto-analysis into a scrolled panel.

The idea is that the analysis panels might be larger than the main app window, so scrolling would be
needed to see it all. This will be important in the custom analysis.

Improvements to the relaxation data list GUI element.

These include having a fixed height for the element, fixes for the setting of the cell data, and a
global panel instead of a panel for just the buttons.

Missing import.

The ds.relax_gui data structure is initialised if absent when associating a pipe with a new tab.

The test_load_state_no_gui() GUI test is now more advanced, using the pipe editor to associate a tab.