bugrelax - Bugs: bug #22035, The dx.map user function is broken...

 
 
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bug #22035: The dx.map user function is broken in the GUI.

Submitted by:  Edward d Auvergne <bugman>
Submitted on:  Mon 12 May 2014 07:42:45 AM UTC  
 
Category: GUISpecific analysis category: None
Priority: 7 - HighSeverity: 5 - Blocker
Status: FixedAssigned to: Troels E. Linnet <tlinnet>
Originator Name: Open/Closed: Closed
Release: Repository: trunkOperating System: All systems

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(Jump to the original submission Jump to the original submission)

Wed 28 May 2014 05:26:49 PM UTC, comment #8:

The 'point' argument for the dx.map user function is now correctly handled in the GUI Sequence_2D window. This is extensively tested via the User_functions.test_dx_map GUI test so this regression can now never return.

Edward d Auvergne <bugman>
Project Administrator
Wed 28 May 2014 07:01:54 AM UTC, SVN revision 23489:

Merged revisions 23480-23481,23488 via svnmerge from
svn+ssh://bugman@svn.gna.org/svn/relax/trunk

........
r23480 | tlinnet | 2014-05-27 18:47:25 +0200 (Tue, 27 May 2014) | 3 lines

Modified py_type from "list" to "float_array" in uf_object type in user function dx.map.

Bug #22035: (https://gna.org/bugs/?22035) The dx.map user function is broken in the GUI.
........
r23481 | tlinnet | 2014-05-27 18:47:30 +0200 (Tue, 27 May 2014) | 3 lines

Added py_type "list_val_or_list_of_list_val" to be handled in GUI uf_objects.

Bug #22035: (https://gna.org/bugs/?22035) The dx.map user function is broken in the GUI.
........
r23488 | bugman | 2014-05-28 08:59:22 +0200 (Wed, 28 May 2014) | 5 lines

Modified the frame order constraints so that cone_theta_x <= cone_theta_y.

The linear_constraints() function docstring has been updated to include this constraint.
........

(Browse SVN revision 23489)

Edward d Auvergne <bugman>
Project Administrator
Tue 27 May 2014 04:52:22 PM UTC, SVN revision 23482:

Merged revisions 23474-23478,23480-23481 via svnmerge from
svn+ssh://tlinnet@svn.gna.org/svn/relax/trunk

........
r23474 | bugman | 2014-05-27 17:06:23 +0200 (Tue, 27 May 2014) | 6 lines

Deletion of the pipe_control.structure.main.create_cone_pdb() function.

This is only used in the frame order analysis, but has been made redundant by the
lib.structure.represent.cone.cone() function.
........
r23475 | bugman | 2014-05-27 17:08:55 +0200 (Tue, 27 May 2014) | 6 lines

Fix for the heterogen section of the internal structural object write_pdb() method.

A number of checks were performed to see if the PDB heterogen records were the same for all
structures, but this is meaningless as the structures can of course be different.
........
r23476 | bugman | 2014-05-27 17:17:56 +0200 (Tue, 27 May 2014) | 13 lines

Completed the frame_order.pdb_model user function backend for the frame order PDB representation.

Most of this backend, including the axes and cone representations, had been broken for quite a while
and were being skipped with an early return statement. This has now been made functional and a few
fixes have been made.

For the 'rotor' and 'free rotor' model, the neg_cone argument is now ignored so that only one model
is produced in the final frame order PDB representation file. For all other models, the rotor
representation is no longer centred to the point on axis closest to the centre of mass, as the pivot
is unambiguously defined. The rotor representation has also been made larger in these models so
that it is outside of the cone, and the propeller blades are now staggered.
........
r23477 | bugman | 2014-05-27 17:19:16 +0200 (Tue, 27 May 2014) | 6 lines

Fixes for the lib.structure.represent.cone module.

The function arguments named 'cone' have been renamed to 'cone_obj' so that they do not clash with
the cone() function in the module namespace.
........
r23478 | bugman | 2014-05-27 17:21:53 +0200 (Tue, 27 May 2014) | 7 lines

Fix for the lib.structure.geometric.generate_vector_residues() function.

The atom numbers are no longer read from the internal structural object, as these are not reliable.
If another geometric representation exists in the object, then the atom numbers could be None. Or
loading structures from multiple PDB files can cause the numbering to be repeated or out of order.
........
r23480 | tlinnet | 2014-05-27 18:47:25 +0200 (Tue, 27 May 2014) | 3 lines

Modified py_type from "list" to "float_array" in uf_object type in user function dx.map.

[...] Bug #22035: (https://gna.org/bugs/?22035) The dx.map user function is broken in the GUI.

[...]........

[...] r23481 | tlinnet | 2014-05-27 18:47:30 +0200 (Tue, 27 May 2014) | 3 lines

[...]

[...] Added py_type "list_val_or_list_of_list_val" to be handled in GUI uf_objects.

[...]

[...] Bug #22035: (https://gna.org/bugs/?22035) The dx.map user function is broken in the GUI.

[...]........

[...]

[...]

(Browse SVN revision 23482)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Tue 27 May 2014 04:47:30 PM UTC, SVN revision 23481:

Added py_type "list_val_or_list_of_list_val" to be handled in GUI uf_objects.

Bug #22035: (https://gna.org/bugs/?22035) The dx.map user function is broken in the GUI.

(Browse SVN revision 23481)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Tue 27 May 2014 04:47:25 PM UTC, SVN revision 23480:

Modified py_type from "list" to "float_array" in uf_object type in user function dx.map.

Bug #22035: (https://gna.org/bugs/?22035) The dx.map user function is broken in the GUI.

(Browse SVN revision 23480)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Wed 21 May 2014 08:01:27 AM UTC, SVN revision 23284:

Merged revisions 23260,23262-23264,23267 via svnmerge from
svn+ssh://bugman@svn.gna.org/svn/relax/trunk

........
r23260 | bugman | 2014-05-20 16:19:30 +0200 (Tue, 20 May 2014) | 6 lines

Converted the Mf.test_opendx_s2_te_rex system test into a GUI test.

This is to demonstrate bug #22035 (https://gna.org/bugs/?22035), the dx.map user function being
broken in the GUI.
........
r23262 | bugman | 2014-05-20 17:50:10 +0200 (Tue, 20 May 2014) | 5 lines

Python 3 fixes for the extern.numpy_future module.

These changes are necessary to allow relax to even run.
........
r23263 | bugman | 2014-05-20 18:02:55 +0200 (Tue, 20 May 2014) | 20 lines

Python 3 fixes for all of the relax code base.

The command used was:
2to3 -j 4 -w \
-f buffer \
-f idioms \
-f set_literal \
-f ws_comma \
-x except \
-x import \
-x imports \
-x long \
-x numliterals \
-x xrange \
.

The lib.compat and multi.processor module changes were fatal, not useful for Python 3, and hence
reverted.
........
r23264 | bugman | 2014-05-20 19:06:02 +0200 (Tue, 20 May 2014) | 8 lines

Python >= 3.2 fix for the Relax_disp.test_sod1wt_t25_to_sherekhan_input system test.

The B0 field value of the ShereKhan input files created by the relax_disp.sherekhan_input user
function was formatted as "%s". However in Python >= 3.2, floats are now converted to have 14
decimal places whereas previous Python versions only had 10 places. The user function backend now
forces only 10 decimal places to be written to the input files.
........
r23267 | bugman | 2014-05-20 19:21:49 +0200 (Tue, 20 May 2014) | 5 lines

Update for the release checklist.

[...] The log_converter.py script instructions should now work on more systems.

[...]........

[...]

[...]

(Browse SVN revision 23284)

Edward d Auvergne <bugman>
Project Administrator
Tue 20 May 2014 03:40:13 PM UTC, SVN revision 23261:

Merged revisions 23254,23260 via svnmerge from
svn+ssh://tlinnet@svn.gna.org/svn/relax/trunk

........
r23254 | bugman | 2014-05-20 13:37:32 +0200 (Tue, 20 May 2014) | 12 lines

Fix for the chain-reaction failures in the test suite.

This fixes bug #22055 (https://gna.org/bugs/?22055), the processor.run_queue() not cleaning up in
uni_processor - chain-reaction failures in the test suite.

The fix was insanely simple, just implementing what was mentioned Gary's FIXME comment in the
run_queue() method of the uni-processor object. The queue execution code has been placed inside a
'try' statement and the queue cleaning up code in a 'finally' statement.

This closes a painfully difficult to find bug that has been in relax since 2006.
........
r23260 | bugman | 2014-05-20 16:19:30 +0200 (Tue, 20 May 2014) | 6 lines

Converted the Mf.test_opendx_s2_te_rex system test into a GUI test.

This is to demonstrate bug #22035 (https://gna.org/bugs/?22035), the dx.map user function being
broken in the GUI.
........

(Browse SVN revision 23261)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Tue 20 May 2014 02:19:30 PM UTC, SVN revision 23260:

Converted the Mf.test_opendx_s2_te_rex system test into a GUI test.

This is to demonstrate bug #22035 (https://gna.org/bugs/?22035), the dx.map user function being
broken in the GUI.

(Browse SVN revision 23260)

Edward d Auvergne <bugman>
Project Administrator
Mon 12 May 2014 07:42:45 AM UTC, original submission:

To reproduce, simply click on the 'User functions->dx->map' menu item. You will see:

Traceback (most recent call last):
File "/data/relax/relax-trunk2/gui/relax_gui.py", line 906, in uf_call
uf_store[name](event=event, wx_parent=self)
File "/data/relax/relax-trunk2/gui/uf_objects.py", line 201, in _call_
status = self.create_wizard(wx_parent)
File "/data/relax/relax-trunk2/gui/uf_objects.py", line 293, in create_wizard
self.page = self.create_page(self.wizard, sync=self._sync)
File "/data/relax/relax-trunk2/gui/uf_objects.py", line 272, in create_page
return Uf_page(self._name, parent=wizard, height_desc=self._height_desc, sync=self._sync, execute=execute)
File "/data/relax/relax-trunk2/gui/uf_objects.py", line 352, in _init_
super(Uf_page, self).__init__(parent, height_desc=height_desc)
File "/data/relax/relax-trunk2/gui/wizards/wiz_objects.py", line 127, in _init_
self.add_contents(main_sizer)
File "/data/relax/relax-trunk2/gui/uf_objects.py", line 617, in add_contents
raise RelaxError("The Python object type '%s' cannot be handled." % arg['py_type'])
lib.errors.RelaxError: RelaxError: The Python object type 'list_val_or_list_of_list_val' cannot be handled.

This bug will block the release of relax 3.2.0.

Edward d Auvergne <bugman>
Project Administrator

 

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  • -unavailable- added by tlinnet (Updated the item)
  • -unavailable- added by bugman (Submitted the item)
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    Follow 3 latest changes.

    Date Changed By Updated Field Previous Value => Replaced By
    Tue 27 May 2014 04:48:16 PM UTCtlinnetStatusNone=>Fixed
      Open/ClosedOpen=>Closed
    Tue 27 May 2014 08:49:01 AM UTCbugmanAssigned toNone=>tlinnet
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