New branch to try separating build and Set/Get commands from regular queued
commands. The idea is that parser calls will be executed directly, rather
than get into the queue. This execution will happen on a single thread,
controlled by the parser. However, if the build or Set/Get calls need to
be invoked from a 'handler' function invoked by the queueing system, then
these will be buffered into a buildQ. They will again be handled by a 
single thread. MPI calls by these special commands will be done 
individually by the command, rather than go through the usual queueing.



git-svn-id: svn+ssh://svn.code.sf.net/p/moose/code/moose/branches/buildQ/python/moose@3805 d1858a74-f715-0410-99c9-c66fe9cce3d6
Ported pymoose to Python 3K. Updated makefiles to automatically configure LDFLAGS and CXXFLAGS for correct python version.
`make PYTHON=3` will compile with Python 3 support. Remember to install numpy for Python 3 also.


git-svn-id: svn+ssh://svn.code.sf.net/p/moose/code/moose/branches/buildQ/python/moose@3854 d1858a74-f715-0410-99c9-c66fe9cce3d6
Fixed le() function to throw error for non existent objects in pymoose.


git-svn-id: svn+ssh://svn.code.sf.net/p/moose/code/moose/branches/buildQ/python/moose@3857 d1858a74-f715-0410-99c9-c66fe9cce3d6
Switched to builtin wildcardFind that returns bare Ids.


git-svn-id: svn+ssh://svn.code.sf.net/p/moose/code/moose/branches/buildQ/python/moose@3864 d1858a74-f715-0410-99c9-c66fe9cce3d6
updated moose.py to deprecate some of the functions.


git-svn-id: svn+ssh://svn.code.sf.net/p/moose/code/moose/branches/buildQ/python/moose@3873 d1858a74-f715-0410-99c9-c66fe9cce3d6
another correction in the Id


git-svn-id: svn+ssh://svn.code.sf.net/p/moose/code/moose/branches/buildQ/python/moose@3875 d1858a74-f715-0410-99c9-c66fe9cce3d6
Breaking changes in pymoose: Id renamed to ematrix. ObjId renamed to element. Old element function to convert a path/Id/ObjId to appropriate class instance renamed `to_el`. Its use is discouraged as most of the functionality can be obtained from element directly.


git-svn-id: svn+ssh://svn.code.sf.net/p/moose/code/moose/branches/buildQ/python/moose@3878 d1858a74-f715-0410-99c9-c66fe9cce3d6
Bugfixes in moosemodule.cpp. Comment indentation updated in moose.py


git-svn-id: svn+ssh://svn.code.sf.net/p/moose/code/moose/branches/buildQ/python/moose@3880 d1858a74-f715-0410-99c9-c66fe9cce3d6
Updated readme file. Fixed printing docs in moose.py (the python 2k supprt stuff has to be moved to another file.


git-svn-id: svn+ssh://svn.code.sf.net/p/moose/code/moose/branches/buildQ/python/moose@3887 d1858a74-f715-0410-99c9-c66fe9cce3d6
Moved py3k support to moose_py3k.py.


git-svn-id: svn+ssh://svn.code.sf.net/p/moose/code/moose/branches/buildQ/python/moose@3888 d1858a74-f715-0410-99c9-c66fe9cce3d6
Added very preliminary implementation for saving simulator state.
Lots of problems we may need to resolve at core level: if we try to
use getField for accessing all fields in all objects, some cause
segmentation fault.

1) Elements unde /Msg 

2) HHChannel - when unitialized - possibly there is something messy
about the gates and tables. This causes segfault - which is
unacceptable.

3) TableEntry causes some weird problem where numpy cannot create
recarray from a list containing its field values.


git-svn-id: svn+ssh://svn.code.sf.net/p/moose/code/moose/branches/buildQ/python/moose@3890 d1858a74-f715-0410-99c9-c66fe9cce3d6
Several fixes to hdfutil.py missed out in last commit.


git-svn-id: svn+ssh://svn.code.sf.net/p/moose/code/moose/branches/buildQ/python/moose@3899 d1858a74-f715-0410-99c9-c66fe9cce3d6
Updated pymoose documentation.


git-svn-id: svn+ssh://svn.code.sf.net/p/moose/code/moose/branches/buildQ/python/moose@3901 d1858a74-f715-0410-99c9-c66fe9cce3d6
Started a new function in hdfutil to save only a subtree of moose elements.


git-svn-id: svn+ssh://svn.code.sf.net/p/moose/code/moose/branches/buildQ/python/moose@3919 d1858a74-f715-0410-99c9-c66fe9cce3d6
Enhanced hdfutil to save and load moose subtree starting with arbitrary root node under arbitrary node of hdf5 file.


git-svn-id: svn+ssh://svn.code.sf.net/p/moose/code/moose/branches/buildQ/python/moose@3920 d1858a74-f715-0410-99c9-c66fe9cce3d6
Added olfactory bulb (only cells -- no channels, no synapses/connections) neuroml demo. Updated MorphML.py for a reading bug. Even my smallest model with just cells is too heavy for the GUI. Takes a huge amount of time to rotate/pan/zoom the visualization.

git-svn-id: svn+ssh://svn.code.sf.net/p/moose/code/moose/branches/buildQ/python/moose@3931 d1858a74-f715-0410-99c9-c66fe9cce3d6
Had to make some modifications to MorphML.py for purkinjecell which I did not upload last.

git-svn-id: svn+ssh://svn.code.sf.net/p/moose/code/moose/branches/buildQ/python/moose@3935 d1858a74-f715-0410-99c9-c66fe9cce3d6
Fixed issue with kineticlayout.py and updated pymoose function element() to clear error flag.


git-svn-id: svn+ssh://svn.code.sf.net/p/moose/code/moose/branches/buildQ/python/moose@3936 d1858a74-f715-0410-99c9-c66fe9cce3d6
Fixed the issue with moose.doc() and cleaned up moose_ObjId_init.


git-svn-id: svn+ssh://svn.code.sf.net/p/moose/code/moose/branches/buildQ/python/moose@3952 d1858a74-f715-0410-99c9-c66fe9cce3d6
Updated moose.doc - now it will display the documentation using pager
used for diplaying Python help.


git-svn-id: svn+ssh://svn.code.sf.net/p/moose/code/moose/branches/buildQ/python/moose@3955 d1858a74-f715-0410-99c9-c66fe9cce3d6