Bug fix to atomeye.py for case with opening AtomEye without an Atoms object

git-svn-id: svn+ssh://cvs/home/jrk33/repo/trunk/AtomEye@9906 9aeadc09-fa51-0410-b5d8-e5c65b1e449c
Added AtomEyeView.get_visible() method - returns indices of visible atoms

git-svn-id: svn+ssh://cvs/home/jrk33/repo/trunk/AtomEye@9931 9aeadc09-fa51-0410-b5d8-e5c65b1e449c
Bug fix to reference counting

git-svn-id: svn+ssh://cvs/home/jrk33/repo/trunk/AtomEye@9935 9aeadc09-fa51-0410-b5d8-e5c65b1e449c
Correct duplicate atom indices when small_cell_err_handler=1

git-svn-id: svn+ssh://cvs/home/jrk33/repo/trunk/AtomEye@9936 9aeadc09-fa51-0410-b5d8-e5c65b1e449c
Added debugging print statements

git-svn-id: svn+ssh://cvs/home/jrk33/repo/trunk/AtomEye@9943 9aeadc09-fa51-0410-b5d8-e5c65b1e449c
Allow compilation without NetCDF. Update read_xyz() args

git-svn-id: svn+ssh://cvs/home/jrk33/repo/trunk/AtomEye@9947 9aeadc09-fa51-0410-b5d8-e5c65b1e449c
Corrected include order of Makefiles

git-svn-id: svn+ssh://cvs/home/jrk33/repo/trunk/AtomEye@9949 9aeadc09-fa51-0410-b5d8-e5c65b1e449c
Remove mutex locks during call to atomeyelib_on_advance()

git-svn-id: svn+ssh://cvs/home/jrk33/repo/trunk/AtomEye@9950 9aeadc09-fa51-0410-b5d8-e5c65b1e449c
Increase pthread stack size - eliminates segmentation fault on Mac OS X

git-svn-id: svn+ssh://cvs/home/jrk33/repo/trunk/AtomEye@9978 9aeadc09-fa51-0410-b5d8-e5c65b1e449c
Bugfixes and stability enhancements to quippy AtomEye plugin

Main change is that new Atoms are now "pulled" from AtomEye thread,
rather than "pushed" from Python GIL thread.

git-svn-id: svn+ssh://cvs/home/jrk33/repo/trunk/AtomEye@9979 9aeadc09-fa51-0410-b5d8-e5c65b1e449c
Minor bug fix to AtomEye window_ids

git-svn-id: svn+ssh://cvs/home/jrk33/repo/trunk/AtomEye@9984 9aeadc09-fa51-0410-b5d8-e5c65b1e449c
Remove set_title() method

git-svn-id: svn+ssh://cvs/home/jrk33/repo/trunk/AtomEye@9986 9aeadc09-fa51-0410-b5d8-e5c65b1e449c
Added default_commands list and hooks for entry, exit, redraw and atom-click

git-svn-id: svn+ssh://cvs/home/jrk33/repo/trunk/AtomEye@9987 9aeadc09-fa51-0410-b5d8-e5c65b1e449c
Move remainder of quippy-specific functionality out of atomeye.py

Also improved documentation strings.

git-svn-id: svn+ssh://cvs/home/jrk33/repo/trunk/AtomEye@9991 9aeadc09-fa51-0410-b5d8-e5c65b1e449c
Fix handling of fortran_indexing in atomeye quippy plugin

git-svn-id: svn+ssh://cvs/home/jrk33/repo/trunk/AtomEye@10004 9aeadc09-fa51-0410-b5d8-e5c65b1e449c
Renamed set() to setp() to avoid clashes with set builtin. Removed 'default' viewers entry.

git-svn-id: svn+ssh://cvs/home/jrk33/repo/trunk/AtomEye@10018 9aeadc09-fa51-0410-b5d8-e5c65b1e449c
Fix update of window title

git-svn-id: svn+ssh://cvs/home/jrk33/repo/trunk/AtomEye@10019 9aeadc09-fa51-0410-b5d8-e5c65b1e449c
Store counter as MultipleExtMod class attribute

git-svn-id: svn+ssh://cvs/home/jrk33/repo/trunk/AtomEye@10020 9aeadc09-fa51-0410-b5d8-e5c65b1e449c
Added saving and loading of state to pickles

git-svn-id: svn+ssh://cvs/home/jrk33/repo/trunk/AtomEye@10080 9aeadc09-fa51-0410-b5d8-e5c65b1e449c
Rename sca() and gca() to scat() and gcat() to avoid name clash with pylab

git-svn-id: svn+ssh://cvs/home/jrk33/repo/trunk/AtomEye@10848 9aeadc09-fa51-0410-b5d8-e5c65b1e449c