Author: bugman
Date: Mon Jul 2 12:21:45 2012
New Revision: 17120
URL: http://svn.gna.org/viewcvs/relax?rev=17120&view=rev
Log:
Merged revisions
16833-16839,16847,16866,16879,16884,16887,16889,16891,16900-16916,16957,16959,16992,16998,17009,17017-17021,17028,17030,17039-17040,17044,17114-17116
via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/trunk
........
r16833 | bugman | 2012-06-11 09:27:38 +0200 (Mon, 11 Jun 2012) | 5 lines
The Missing_data dialog can now have the parent wx element specified.
This is needed when launched from a child window such as the BMRB export
window.
........
r16834 | bugman | 2012-06-11 09:30:51 +0200 (Mon, 11 Jun 2012) | 3 lines
Removed the word 'used' from the software and scripts GUI list element
titles.
........
r16835 | bugman | 2012-06-11 09:31:41 +0200 (Mon, 11 Jun 2012) | 5 lines
Added checks to the BMRB export to make sure all necessary data has been
input.
If not, then the Missing_data dialog will be presented to the user to
explain what is required.
........
r16836 | bugman | 2012-06-11 10:05:58 +0200 (Mon, 11 Jun 2012) | 3 lines
The completion of the test suite in the GUI mode now sets the controller
main gauge to 100%.
........
r16837 | bugman | 2012-06-11 10:15:21 +0200 (Mon, 11 Jun 2012) | 17 lines
Python 3 updates for the entire relax code base.
The command used was:
2to3 -w \
-f buffer \
-f idioms \
-f set_literal \
-f ws_comma \
-x except \
-x import \
-x imports \
-x long \
-x numliterals \
-x xrange \
relax .
........
r16838 | bugman | 2012-06-11 10:19:08 +0200 (Mon, 11 Jun 2012) | 3 lines
Used some colour for the relax GUI terminating print out asking for
citations.
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r16839 | bugman | 2012-06-11 11:48:27 +0200 (Mon, 11 Jun 2012) | 3 lines
Updated the release checklist document for the relax 2.0 development series.
........
r16847 | bugman | 2012-06-11 19:55:17 +0200 (Mon, 11 Jun 2012) | 6 lines
Spun out the automatic column width formatting code from
relax_io.write_spin_data() to write_data().
The write_data() will be useful for many other columnar data printouts, and
will write out to any
file handles given to it.
........
r16866 | bugman | 2012-06-11 21:05:16 +0200 (Mon, 11 Jun 2012) | 6 lines
Bug fix for a segmentation fault occurring during the model-free GUI test.
Flushing of the interpreter queue object is needed as some parts of the
interface use asynchronous
user function calls.
........
r16879 | bugman | 2012-06-12 11:34:42 +0200 (Tue, 12 Jun 2012) | 6 lines
Reverted the 2to3 changes of r16837 as these are deadly for Python 2.6!
The command used was:
svn merge -r16837:16836 .
........
r16884 | bugman | 2012-06-12 17:56:04 +0200 (Tue, 12 Jun 2012) | 3 lines
Bug fix for the Sequence GUI input element - the Sequence_list_ctrl class
was in the wrong module!
........
r16887 | bugman | 2012-06-12 21:12:00 +0200 (Tue, 12 Jun 2012) | 3 lines
Created a script for converting svn logs into the format for release
messages.
........
r16889 | bugman | 2012-06-12 23:39:44 +0200 (Tue, 12 Jun 2012) | 6 lines
Merged the changes to the CHANGES file from the 2.0.0 tag back into the
trunk.
The command used was:
svn merge -r16887:r16888 svn+ssh://bugman@xxxxxxxxxxx/svn/relax/tags/2.0.0
........
r16891 | bugman | 2012-06-12 23:52:04 +0200 (Tue, 12 Jun 2012) | 6 lines
Merged the remainder of the 2.0.0 tag CHANGES file changes back to trunk.
The command used was:
svn merge -r16889:r16890 svn+ssh://bugman@xxxxxxxxxxx/svn/relax/tags/2.0.0
........
r16900 | bugman | 2012-06-13 17:06:56 +0200 (Wed, 13 Jun 2012) | 3 lines
Hack for the relax_fit C module compilation to detect supported CPUs for
Mac OS X cross compilation.
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r16901 | bugman | 2012-06-13 20:36:49 +0200 (Wed, 13 Jun 2012) | 3 lines
Improved the debugging drawing for the about GUI elements.
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r16902 | bugman | 2012-06-13 21:10:14 +0200 (Wed, 13 Jun 2012) | 7 lines
Bug fix for sizing of the GUI about dialogs - the virtual sizes are now
accurately calculated.
To do this, the window contents (a wx.BufferedDC instance) is created
twice, with the virtual window
size exactly calculated in the first pass, and then used to set up the
device context in the second.
A space is also now added to the end to ensure the border is there.
........
r16903 | bugman | 2012-06-13 21:11:44 +0200 (Wed, 13 Jun 2012) | 5 lines
Bug fix for the model-free analysis tab about window - sometimes a grey
region would appear at the bottom.
This is a problem in at least GTK+ as scrolling is in increments of 20!
........
r16904 | bugman | 2012-06-13 21:45:56 +0200 (Wed, 13 Jun 2012) | 5 lines
Bug fix for the grey about windows on MS Windows!
All the about windows were grey. The temporary wxPython 2.9.3.1 fix was
breaking the Windows GUI!
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r16905 | bugman | 2012-06-13 21:51:27 +0200 (Wed, 13 Jun 2012) | 6 lines
The about model-free dialog no longer has grey at the bottom in MS Windows.
The wx.ScrolledWindow.GetScrollPixelsPerUnit() function is now used to
determine how many pixels the
y scrolling is, and rounds up the virtual size based on that.
........
r16906 | bugman | 2012-06-13 22:47:51 +0200 (Wed, 13 Jun 2012) | 3 lines
Added the status/weather-snow-scattered-night Oxygen icon as a wizard
graphic for the temperature uf.
........
r16907 | bugman | 2012-06-14 00:05:46 +0200 (Thu, 14 Jun 2012) | 7 lines
Created the gui.misc.bitmap_setup() function for handling bitmap alpha
correctly on operating systems.
This function is required to handle alpha in bitmap on MS Windows so that
regions with partial
transparency are not blended into the default dark grey colour of Windows'
windows.
........
r16908 | bugman | 2012-06-14 14:38:37 +0200 (Thu, 14 Jun 2012) | 6 lines
Initialised a look up table in the cdp.mol structure for faster spin access.
This look up table will be slowly transitioned to, and should significantly
speed up certain
operations.
........
r16909 | bugman | 2012-06-14 14:54:56 +0200 (Thu, 14 Jun 2012) | 8 lines
Started to fill up the spin ID look up table.
The index_molecule() and index_residue() functions have been added to
determine the MoleculeList and
ResidueList indices of given molecules and residues. These are used by the
create_spin for
efficiency and to allow the indices (together with the spin index and spin
ID string) to be
assembled into the look up table. This table is not used anywhere yet.
........
r16910 | bugman | 2012-06-14 15:40:44 +0200 (Thu, 14 Jun 2012) | 6 lines
generic_fns.mol_res_spin.create_pseudo_spin() is now adding data to the
spin ID look up table.
To support this, the return_residue() method now takes the 'indices'
argument and returns the
molecule and residue indices.
........
r16911 | bugman | 2012-06-14 16:07:52 +0200 (Thu, 14 Jun 2012) | 3 lines
Created generic_fns.mol_res_spin.return_spin_from_id() for returning spin
containers from spin IDs.
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r16912 | bugman | 2012-06-14 16:14:08 +0200 (Thu, 14 Jun 2012) | 3 lines
Fix for return_residue() for a bug introduced at r16910.
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r16913 | bugman | 2012-06-14 16:24:16 +0200 (Thu, 14 Jun 2012) | 3 lines
Fix for the gui.misc.bitmap_setup() function for Mac OS X - all bitmaps
with alpha had black backgrounds!
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r16914 | bugman | 2012-06-14 16:27:58 +0200 (Thu, 14 Jun 2012) | 5 lines
Added the 'pipe' argument to generic_fns.mol_res_spin.return_spin_from_id().
This is to mimic the return_spin() function.
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r16915 | bugman | 2012-06-14 16:34:52 +0200 (Thu, 14 Jun 2012) | 5 lines
return_spin_from_id() now defaults to return_spin() when the spin ID is not
in the lookup table.
The slower return_spin() method will allow return_spin_from_id() to always
be functional.
........
r16916 | bugman | 2012-06-14 17:38:57 +0200 (Thu, 14 Jun 2012) | 6 lines
Renamed return_spin_from_id() to return_spin(), and return_spin() to
return_spin_from_selection().
This shaves off a number of seconds from the system test - the look up
table speed ups will come
with support in the other mol_res_spin module functions.
........
r16957 | bugman | 2012-06-19 14:55:38 +0200 (Tue, 19 Jun 2012) | 3 lines
The generate_spin_id() function now choses to use the spin name instead of
number by default.
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r16959 | bugman | 2012-06-19 16:06:30 +0200 (Tue, 19 Jun 2012) | 5 lines
Created the generic_fns.mol_res_spin.return_spin_indices() function to
return the index triplet.
This allows a spin ID to be converted into the molecule, residue and spin
indices.
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r16992 | bugman | 2012-06-20 01:33:02 +0200 (Wed, 20 Jun 2012) | 3 lines
Bug fix for the relax_data.copy user function - it can now handle spins
without relaxation data.
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r16998 | bugman | 2012-06-20 11:19:32 +0200 (Wed, 20 Jun 2012) | 3 lines
Update and clean up of the model-free LaTeX table generation script.
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r17009 | bugman | 2012-06-21 10:01:59 +0200 (Thu, 21 Jun 2012) | 6 lines
Bug fox for the generic_fns.mol_res_spin.return_spin_indices() function.
The selection object was using the wrong variable name, and the look up
table fallback was always
on!
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r17017 | bugman | 2012-06-21 10:36:48 +0200 (Thu, 21 Jun 2012) | 3 lines
The spin ID lookup table has been made private so that it is not included
in the save files.
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r17018 | bugman | 2012-06-21 21:49:43 +0200 (Thu, 21 Jun 2012) | 5 lines
Fix for reading of BMRB CSA saveframe data - spin IDs generated from the
data now have molecule info.
This is problematic only in certain edge cases, for example a
multi-molecule entry.
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r17019 | bugman | 2012-06-21 22:05:06 +0200 (Thu, 21 Jun 2012) | 6 lines
Removal of a hack from the generic_fns.bmrb.generate_sequence() function.
This hack was for naming unnamed spins. But this is not needed as the
generic_fns.mol_res_spin.create_spin() function already does this but with
many more safety checks.
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r17020 | bugman | 2012-06-21 22:18:14 +0200 (Thu, 21 Jun 2012) | 6 lines
Removed a hack from the generic_fns.relax_data.pack_data() function for the
BMRB support.
This calls the generic_fns.bmrb.generate_sequence() function! As non-BMRB
code paths access the
pack_data() function, this is a nasty hack which would have caused problems
in the future.
........
r17021 | bugman | 2012-06-22 13:41:40 +0200 (Fri, 22 Jun 2012) | 26 lines
Creation of a fast molecule, residue and spin data lookup framework using
private metadata.
This consists of two elements: The already existing private lookup table
now at
cdp.mol._spin_id_lookup which is a dictionary with spin IDs as keys and a
list of molecule, residue
and spin indices as values; and a set of private variables within the
molecule, residue and spin
containers which identify the parent container names, numbers and indices.
As all data is private,
it will not be visible to the user or be saved in the XML results and save
files and should be
considered volatile.
All this private metadata is kept up to date via the two new
generic_fns.mol_res_spin functions
metadata_prune() and metadata_update(). For fast operation, these methods
can update specific
container subsets via the mol_index, res_index and spin_index arguments.
All parts of relax which
modify the data pipe's molecule, residue and spin data structure (the
generic_fns.mol_res_spin
functions and test suite) call these two functions as needed. Two
auxiliary functions
spin_id_variants() and spin_id_variants_elim() have been added to create
all possible matching spin
ID strings for a given spin (the second created IDs strings which should no
longer exist).
The speed ups from this change are significant. On one system, the system
and unit tests decrease
from 492.8s/26.4s to 434.3s/25.1s. On another the decrease is from
330.7s/17.4s to 258.9s/15.4s.
In addition, the pipe argument has been added to the
generic_fns.mol_res_spin functions
create_molecule(), create_residue(), create_pseudo_spin() and
create_spin(). Also, the molecule
name will now always be a string! Previously this was allowed to be an
integer. This is needed for
the private metadata functions to operate correctly. A number of unit
tests have been updated for
the changes.
........
r17028 | bugman | 2012-06-22 15:15:56 +0200 (Fri, 22 Jun 2012) | 5 lines
The sequence.read user function now fails with a RelaxError if no sequence
data was loaded.
This is for better user feedback.
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r17030 | bugman | 2012-06-22 16:12:48 +0200 (Fri, 22 Jun 2012) | 7 lines
Fix for the sequence.read user function for a problem with r17028.
The sequence.generate() function was not returning the correct result as it
didn't take into account
the renaming and renumbering of empty spin containers. Now sequence.read
will always print out the
generated sequence and not result in a RelaxError for most of the system
tests.
........
r17039 | bugman | 2012-06-22 18:21:16 +0200 (Fri, 22 Jun 2012) | 5 lines
Converted the consistency testing documentation strings to the Uf_tables
and Desc_container design.
This is needed to use the consistency testing documentation within the user
function help system.
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r17040 | bugman | 2012-06-22 18:23:31 +0200 (Fri, 22 Jun 2012) | 3 lines
Added the consistency testing documentation to the grace.write and value.*
user functions.
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r17044 | bugman | 2012-06-25 09:34:49 +0200 (Mon, 25 Jun 2012) | 6 lines
Modified the working of the n_state_model.elim_no_prob backend.
This user function is not functional anyway and is not tested by the relax
test suite, but will
remain as it might be useful in the future.
........
r17114 | bugman | 2012-07-02 11:14:28 +0200 (Mon, 02 Jul 2012) | 5 lines
Created a system test to replicate Romel Bobby's bug #19887.
This is the bug report at https://gna.org/bugs/?19887.
........
r17115 | bugman | 2012-07-02 12:03:02 +0200 (Mon, 02 Jul 2012) | 11 lines
Partial fix for bug #19887 (https://gna.org/bugs/?19887).
The problem is that the number of peak height values was not the same for
all spins!
The error message was being caused by the math_fns.relax_fit C object
'setup' function being feed in
incorrect values, causing relax to fail directly after the setup() call in
specific_fns.relax_fit.minimise(). The number of points was being taken
from cdp.relax_times, but
in the Relax_fit.test_bug_19887_curvefit_fail system test, one of the 3
spins has 4 points rather
than 5. Now the correct number is sent into setup().
........
r17116 | bugman | 2012-07-02 12:17:23 +0200 (Mon, 02 Jul 2012) | 6 lines
A final fix for bug #19887 (https://gna.org/bugs/?19887).
Now a RelaxError is raised if the number of peak intensities is not the
same for all spins. This
occurs in the relaxation curve-fitting overfit_deselect() method.
........
Added:
branches/frame_order_testing/graphics/wizards/oxygen-icon-weather-snow-scattered-night.png
- copied unchanged from r17116,
trunk/graphics/wizards/oxygen-icon-weather-snow-scattered-night.png
branches/frame_order_testing/scripts/log_converter.py
- copied unchanged from r17116, trunk/scripts/log_converter.py
branches/frame_order_testing/test_suite/shared_data/peak_lists/bug_19887/
- copied from r17116, trunk/test_suite/shared_data/peak_lists/bug_19887/
branches/frame_order_testing/test_suite/system_tests/scripts/curve_fitting/bug_19887_curvefit_fail.py
- copied unchanged from r17116,
trunk/test_suite/system_tests/scripts/curve_fitting/bug_19887_curvefit_fail.py
Modified:
branches/frame_order_testing/ (props changed)
branches/frame_order_testing/data/__init__.py
branches/frame_order_testing/data/mol_res_spin.py
branches/frame_order_testing/docs/CHANGES
branches/frame_order_testing/docs/Release_Checklist
branches/frame_order_testing/generic_fns/bmrb.py
branches/frame_order_testing/generic_fns/mol_res_spin.py
branches/frame_order_testing/generic_fns/relax_data.py
branches/frame_order_testing/generic_fns/sequence.py
branches/frame_order_testing/gui/about.py
branches/frame_order_testing/gui/analyses/auto_model_free.py
branches/frame_order_testing/gui/analyses/base.py
branches/frame_order_testing/gui/analyses/wizard.py
branches/frame_order_testing/gui/components/free_file_format.py
branches/frame_order_testing/gui/components/scripts.py
branches/frame_order_testing/gui/components/software.py
branches/frame_order_testing/gui/controller.py
branches/frame_order_testing/gui/export_bmrb.py
branches/frame_order_testing/gui/input_elements/sequence.py
branches/frame_order_testing/gui/input_elements/sequence_2D.py
branches/frame_order_testing/gui/message.py
branches/frame_order_testing/gui/misc.py
branches/frame_order_testing/gui/pipe_editor.py
branches/frame_order_testing/gui/relax_gui.py
branches/frame_order_testing/gui/spin_viewer/containers.py
branches/frame_order_testing/gui/wizard.py
branches/frame_order_testing/relax_io.py
branches/frame_order_testing/sample_scripts/model_free/table_latex.py
branches/frame_order_testing/sconstruct
branches/frame_order_testing/specific_fns/consistency_tests.py
branches/frame_order_testing/specific_fns/model_free/bmrb.py
branches/frame_order_testing/specific_fns/n_state_model.py
branches/frame_order_testing/specific_fns/relax_fit.py
branches/frame_order_testing/test_suite/gui_tests/model_free.py
branches/frame_order_testing/test_suite/system_tests/relax_fit.py
branches/frame_order_testing/test_suite/unit_tests/_generic_fns/test_mol_res_spin.py
branches/frame_order_testing/test_suite/unit_tests/molecule_testing_base.py
branches/frame_order_testing/test_suite/unit_tests/spin_testing_base.py
branches/frame_order_testing/user_functions/grace.py
branches/frame_order_testing/user_functions/temperature.py
branches/frame_order_testing/user_functions/value.py
[This mail would be too long, it was shortened to contain the URLs only.]
Modified: branches/frame_order_testing/data/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/data/__init__.py?rev=17120&r1=17119&r2=17120&view=diff
Modified: branches/frame_order_testing/data/mol_res_spin.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/data/mol_res_spin.py?rev=17120&r1=17119&r2=17120&view=diff
Modified: branches/frame_order_testing/docs/CHANGES
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/docs/CHANGES?rev=17120&r1=17119&r2=17120&view=diff
Modified: branches/frame_order_testing/docs/Release_Checklist
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/docs/Release_Checklist?rev=17120&r1=17119&r2=17120&view=diff
Modified: branches/frame_order_testing/generic_fns/bmrb.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/generic_fns/bmrb.py?rev=17120&r1=17119&r2=17120&view=diff
Modified: branches/frame_order_testing/generic_fns/mol_res_spin.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/generic_fns/mol_res_spin.py?rev=17120&r1=17119&r2=17120&view=diff
Modified: branches/frame_order_testing/generic_fns/relax_data.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/generic_fns/relax_data.py?rev=17120&r1=17119&r2=17120&view=diff
Modified: branches/frame_order_testing/generic_fns/sequence.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/generic_fns/sequence.py?rev=17120&r1=17119&r2=17120&view=diff
Modified: branches/frame_order_testing/gui/about.py
[... 95 lines stripped ...]
r17120 - in /branches/frame_order_testing: ./ data/ docs/ generic_fns/ graphics/wizards/ gui/ gui/analyses/ gui/components/ ...