Author: bugman
Date: Thu Jul 3 14:54:46 2014
New Revision: 24430
URL: http://svn.gna.org/viewcvs/relax?rev=24430&view=rev
Log:
Merged revisions 24407,24412,24418-24419,24421-24422,24425 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/trunk
........
r24407 | bugman | 2014-07-02 14:42:51 +0200 (Wed, 02 Jul 2014) | 6 lines
Created the new lib.structure.files module.
This currently contains the single find_pdb_files() function which will be
used to find all *.pdb,
*.pdb.gz and *.pdb.bz2 versions of the PDB file in a given path.
........
r24412 | bugman | 2014-07-02 15:38:13 +0200 (Wed, 02 Jul 2014) | 11 lines
Fix for the breakage of the relax help system.
This was reported at
http://thread.gmane.org/gmane.science.nmr.relax.devel/6481.
The problem was that the TERM environmental variable was turned off to
avoid the GNU readline
library on Linux systems emitting the ^[[?1034h escape code. See the
message at
http://thread.gmane.org/gmane.science.nmr.relax.devel/6481/focus=6489 for
more details. However the
Python help system obviously requires this environmental variable. Now
only if the TERM variable is
set to 'xterm' will it be reset, and to 'linux' instead of the blank string
''.
........
r24418 | bugman | 2014-07-02 16:48:30 +0200 (Wed, 02 Jul 2014) | 6 lines
Backported the relax 3.2.3 CHANGES file changes to trunk.
The command used was:
svn merge -r24416:24417 svn+ssh://bugman@xxxxxxxxxxx/svn/relax/tags/3.2.3 .
........
r24419 | bugman | 2014-07-02 17:45:14 +0200 (Wed, 02 Jul 2014) | 6 lines
MS Windows fixes to allow relax to run again.
The code for eliminating the GNU readline ^[[?1034h escape code emission on
Linux systems fails on
Windows as the 'TERM' environmental variable does not exist in os.environ.
........
r24421 | bugman | 2014-07-03 08:54:26 +0200 (Thu, 03 Jul 2014) | 8 lines
Better tab completion support in the prompt UI for Mac OS X users.
For some Python versions, the Mac supplied libedit library is used rather
than GNU readline. But
this library uses a completely different language and hence tab completion
was non-functional on
these systems. The library difference is now detected and the correct
language sent into libedit to
activate tab completion.
........
r24422 | bugman | 2014-07-03 11:35:50 +0200 (Thu, 03 Jul 2014) | 13 lines
Improved model handling for the internal structural object.
The set_model() method has been added to allow either a model number to be
set to the first
unnumbered model (in preparation for adding new models) or to allow models
to be renumbered.
The logic of the add_model() has also been changed. Rather than looping
over all atoms of the first
model and copying them, which does not work due to the model validity
checks, the entire MolList
(molecule list) data structure is copied using copy.deepcopy() to make a
perfect copy of the
structural data.
The ModelList.add_item() method has also been modified to return the newly
added or numbered model.
This is used by the add_model() structural object method to obtain the
model object.
........
r24425 | bugman | 2014-07-03 13:25:59 +0200 (Thu, 03 Jul 2014) | 10 lines
Updated the Mac OS X framework setting up instruction document.
New sections have been added for the nose and matplotlib Python packages,
as nose is needed for the
numpy and scipy testing frameworks and matplotlib might be a useful
optional dependency in the
future.
The mpy4py section has been updated to avoid the non-framework fink version
of mpicc which cannot
produce universal binaries. A few other parts also have small edits.
........
Added:
branches/disp_spin_speed/lib/structure/files.py
- copied unchanged from r24425, trunk/lib/structure/files.py
Modified:
branches/disp_spin_speed/ (props changed)
branches/disp_spin_speed/dep_check.py
branches/disp_spin_speed/docs/CHANGES
branches/disp_spin_speed/docs/Mac_framework_build_3way
branches/disp_spin_speed/lib/structure/__init__.py
branches/disp_spin_speed/lib/structure/internal/models.py
branches/disp_spin_speed/lib/structure/internal/object.py
branches/disp_spin_speed/prompt/interpreter.py
branches/disp_spin_speed/relax.py
[This mail would be too long, it was shortened to contain the URLs only.]
Modified: branches/disp_spin_speed/dep_check.py
URL:
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/dep_check.py?rev=24430&r1=24429&r2=24430&view=diff
Modified: branches/disp_spin_speed/docs/CHANGES
URL:
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/docs/CHANGES?rev=24430&r1=24429&r2=24430&view=diff
Modified: branches/disp_spin_speed/docs/Mac_framework_build_3way
URL:
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/docs/Mac_framework_build_3way?rev=24430&r1=24429&r2=24430&view=diff
Modified: branches/disp_spin_speed/lib/structure/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/lib/structure/__init__.py?rev=24430&r1=24429&r2=24430&view=diff
Modified: branches/disp_spin_speed/lib/structure/internal/models.py
URL:
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/lib/structure/internal/models.py?rev=24430&r1=24429&r2=24430&view=diff
Modified: branches/disp_spin_speed/lib/structure/internal/object.py
URL:
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/lib/structure/internal/object.py?rev=24430&r1=24429&r2=24430&view=diff
Modified: branches/disp_spin_speed/prompt/interpreter.py
URL:
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/prompt/interpreter.py?rev=24430&r1=24429&r2=24430&view=diff
Modified: branches/disp_spin_speed/relax.py
URL:
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/relax.py?rev=24430&r1=24429&r2=24430&view=diff
r24430 - in /branches/disp_spin_speed: ./ docs/ lib/structure/ lib/structure/internal/ prompt/