Added unit tests for NeuroNode. Clears.



git-svn-id: svn+ssh://svn.code.sf.net/p/moose/code@3862 d1858a74-f715-0410-99c9-c66fe9cce3d6
Updated makefile to handle systems where python-config is not installed.


git-svn-id: svn+ssh://svn.code.sf.net/p/moose/code@3863 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@3864 d1858a74-f715-0410-99c9-c66fe9cce3d6
Fixed toplevel Makefiel.


git-svn-id: svn+ssh://svn.code.sf.net/p/moose/code@3865 d1858a74-f715-0410-99c9-c66fe9cce3d6
Fixed richcompart of Id in pymoose. Added support for getting Id and ObjId attributes in Id class.


git-svn-id: svn+ssh://svn.code.sf.net/p/moose/code@3866 d1858a74-f715-0410-99c9-c66fe9cce3d6

test file

git-svn-id: svn+ssh://svn.code.sf.net/p/moose/code@3867 d1858a74-f715-0410-99c9-c66fe9cce3d6
PyMOOSE bug with getting Id.class_ fixed. Need to find why Python is sending 'class' to the getter when we are asking for 'class_'


git-svn-id: svn+ssh://svn.code.sf.net/p/moose/code@3868 d1858a74-f715-0410-99c9-c66fe9cce3d6
first stage of clean up in kineticlayout.py for loading the models

git-svn-id: svn+ssh://svn.code.sf.net/p/moose/code@3869 d1858a74-f715-0410-99c9-c66fe9cce3d6
Added code comments in pymoose about `class_` field access
optimization bug. In summary, when a MOOSE field name clashes with a
python keyword, an '_' is added to the field name in Python
interface. `class_`, which is a field of both ObjId and Id is accessed
this way. There is a static function to lookup the original MOOSE
field name for such fields. But this check was not done in Id and
class_ being a special field, it was being handled directly. Now when
a python script calls the getter for ObjId.class_ several times, which
substitutes `class_` with its alias `class`, some optimization by the
OS/gcc takes place and when the getter for Id.class_ is called, it
looks for the attribute `class` instead. I came to this conclusion as
(1) gdb showed that the getter for Id was receiving `class` as
attribute name and this was a direct call from Python. (2) this went
away as I removed the access to ObjId.class_ and (3) when compiled
with -O0 flag to disable optimization, the error also disappears.


git-svn-id: svn+ssh://svn.code.sf.net/p/moose/code@3870 d1858a74-f715-0410-99c9-c66fe9cce3d6
traub 2005 model: Single compartment test with channel settings of spiny stellate cell's soma updated. Plots almost identical.


git-svn-id: svn+ssh://svn.code.sf.net/p/moose/code@3871 d1858a74-f715-0410-99c9-c66fe9cce3d6
traub 2005 model: Updated test_tcr.py to use hsolve optionally. But hsolve somehow is missing out the compartments.


git-svn-id: svn+ssh://svn.code.sf.net/p/moose/code@3872 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@3873 d1858a74-f715-0410-99c9-c66fe9cce3d6
corrections incorporating the new changes in calling Id's


git-svn-id: svn+ssh://svn.code.sf.net/p/moose/code@3874 d1858a74-f715-0410-99c9-c66fe9cce3d6
another correction in the Id


git-svn-id: svn+ssh://svn.code.sf.net/p/moose/code@3875 d1858a74-f715-0410-99c9-c66fe9cce3d6
Put a temporary fix in Wildcrad.cpp:matchName to avoid an assertion failure. But need to check kkit reader to find why it is skipping one Id value.


git-svn-id: svn+ssh://svn.code.sf.net/p/moose/code@3876 d1858a74-f715-0410-99c9-c66fe9cce3d6
Some clean up in kineticlayout

git-svn-id: svn+ssh://svn.code.sf.net/p/moose/code@3877 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@3878 d1858a74-f715-0410-99c9-c66fe9cce3d6
incorporating the to_el for /tick change


git-svn-id: svn+ssh://svn.code.sf.net/p/moose/code@3879 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@3880 d1858a74-f715-0410-99c9-c66fe9cce3d6
subha: Updated Id.__repr__. Now Id/ematrix objects will be printed as: <moose.ematrix: class={classname}, id={number}, path={pathstring}>


git-svn-id: svn+ssh://svn.code.sf.net/p/moose/code@3881 d1858a74-f715-0410-99c9-c66fe9cce3d6