updated documentation in basic and framework classes and tests

git-svn-id: https://repo.thevirtualbrain.org/svn/tvb/trunk/scientific_library@4942 1c0e02f0-7929-43c0-8fb3-3293bf43b0d1
Add notes about the Jansen and Rit model. This models does not have local couplings terms ... Consider to implement the modified model used by Andreas

git-svn-id: https://repo.thevirtualbrain.org/svn/tvb/trunk/scientific_library@4945 1c0e02f0-7929-43c0-8fb3-3293bf43b0d1
Modification to plort_connectivity3d. It now uses mlab points3d. Some visualization modules should be added

git-svn-id: https://repo.thevirtualbrain.org/svn/tvb/trunk/scientific_library@4946 1c0e02f0-7929-43c0-8fb3-3293bf43b0d1
Added method to obtain the corresponding  binary matrix

git-svn-id: https://repo.thevirtualbrain.org/svn/tvb/trunk/scientific_library@4947 1c0e02f0-7929-43c0-8fb3-3293bf43b0d1
Modified lower bound of tau in the Generic2dOscillator

git-svn-id: https://repo.thevirtualbrain.org/svn/tvb/trunk/scientific_library@4948 1c0e02f0-7929-43c0-8fb3-3293bf43b0d1
It's like the Stephen Wright joke about how one night, 
someone snuck into your house and replaced everything with
an exact copy. Traits started replacing attributes with
deepcopies and so the device_info instances had lonely 
orphan objects without names. Literally. Now they are 
given as strings, which allow the device_info objects to
retrieve by name at runtime after the parent objects have
been initialized. multo bene



git-svn-id: https://repo.thevirtualbrain.org/svn/tvb/trunk/scientific_library@4949 1c0e02f0-7929-43c0-8fb3-3293bf43b0d1
demos/debug_device now successfully runs 512 parallel Heun stochastic
integrations on the GPU, with quite reasonable error with respect to
pure Python simulation.


git-svn-id: https://repo.thevirtualbrain.org/svn/tvb/trunk/scientific_library@4950 1c0e02f0-7929-43c0-8fb3-3293bf43b0d1
start simulator.backend refactoring

This begins refactoring the C and CUDA backends, and completely
breaks the code that was just working. Bug fixes follow tomorrow.

- driver.py had a terrible mix of if using_gpu: X else: Y
- common code regrouped in base classes
- cee.py and cuda.py respectively provide subclasses taht
  extend the base classes with specific code 
- outside user just needs to import tvb.simulator.backend.cee for example




git-svn-id: https://repo.thevirtualbrain.org/svn/tvb/trunk/scientific_library@4951 1c0e02f0-7929-43c0-8fb3-3293bf43b0d1
Continue refactoring of the backend



git-svn-id: https://repo.thevirtualbrain.org/svn/tvb/trunk/scientific_library@4952 1c0e02f0-7929-43c0-8fb3-3293bf43b0d1
Fix wrong indentation

git-svn-id: https://repo.thevirtualbrain.org/svn/tvb/trunk/scientific_library@4953 1c0e02f0-7929-43c0-8fb3-3293bf43b0d1
updated documentation in basic and framework classes and tests

git-svn-id: https://repo.thevirtualbrain.org/svn/tvb/trunk/scientific_library@4959 1c0e02f0-7929-43c0-8fb3-3293bf43b0d1
Add preliminary MATLAB bridge

This updates old(er) work on providing a pure Cython
MEX function interface *from* MATLAB *to* Python and
TVB. There's a lot to do before it's as usuable as
other MATLAB toolboxes, but the basics are there:

- initialize Python & TVB libraries
- setup & run simulations
- transfer data back and forth between MATLAB & Python
- use other Python libraries as needed

git-svn-id: https://repo.thevirtualbrain.org/svn/tvb/trunk/scientific_library@4960 1c0e02f0-7929-43c0-8fb3-3293bf43b0d1
Sync merge.

git-svn-id: https://repo.thevirtualbrain.org/svn/tvb/trunk/scientific_library@4961 1c0e02f0-7929-43c0-8fb3-3293bf43b0d1