Merge branch 'trunk' of https://github.com/the-virtual-brain/tvb-library into trunk

git-svn-id: https://repo.thevirtualbrain.org/svn/tvb/trunk/scientific_library@6286 1c0e02f0-7929-43c0-8fb3-3293bf43b0d1
TVB-1405
Code review:
- avoid storing temporary sparse matrix in H5, as it will be replaced soon anyway (in theory improves performance of this op)
- compute_sparse_matrix should really compute the matrix, not just the gdist and require a second compute step to be called

git-svn-id: https://repo.thevirtualbrain.org/svn/tvb/trunk/scientific_library@6300 1c0e02f0-7929-43c0-8fb3-3293bf43b0d1
TVB-1405
Replace temporary attribute with the usage of a local variable (to avoid memory allocation).

git-svn-id: https://repo.thevirtualbrain.org/svn/tvb/trunk/scientific_library@6303 1c0e02f0-7929-43c0-8fb3-3293bf43b0d1
Fix logger created from library profile.

git-svn-id: https://repo.thevirtualbrain.org/svn/tvb/trunk/scientific_library@6304 1c0e02f0-7929-43c0-8fb3-3293bf43b0d1
Revert Github commit by @maedoc or we won't have logs from tvb-library profile.

git-svn-id: https://repo.thevirtualbrain.org/svn/tvb/trunk/scientific_library@6305 1c0e02f0-7929-43c0-8fb3-3293bf43b0d1
Add range over Noise parameters at Tim's suggestion.

git-svn-id: https://repo.thevirtualbrain.org/svn/tvb/trunk/scientific_library@6306 1c0e02f0-7929-43c0-8fb3-3293bf43b0d1
Fix recent wrong change in Cortex.compute_LC

git-svn-id: https://repo.thevirtualbrain.org/svn/tvb/trunk/scientific_library@6308 1c0e02f0-7929-43c0-8fb3-3293bf43b0d1
Fix LocalConnectivity related test after recent code change.

git-svn-id: https://repo.thevirtualbrain.org/svn/tvb/trunk/scientific_library@6309 1c0e02f0-7929-43c0-8fb3-3293bf43b0d1
Make tests run faster, by modifying the input parameters in scientific computations and simulation lengths.

git-svn-id: https://repo.thevirtualbrain.org/svn/tvb/trunk/scientific_library@6310 1c0e02f0-7929-43c0-8fb3-3293bf43b0d1
Merge pull request #28 from quiuquio/tsv_vis

Tsv vis
Merge branch 'trunk' of https://github.com/the-virtual-brain/tvb-library into trunk
Merge branch 'trunk' of https://github.com/the-virtual-brain/tvb-library into trunk

git-svn-id: https://repo.thevirtualbrain.org/svn/tvb/trunk/scientific_library@6316 1c0e02f0-7929-43c0-8fb3-3293bf43b0d1
Add Robert to the list of TVB authors.

git-svn-id: https://repo.thevirtualbrain.org/svn/tvb/trunk/scientific_library@6318 1c0e02f0-7929-43c0-8fb3-3293bf43b0d1
Merge branch 'trunk' of https://github.com/the-virtual-brain/tvb-library into trunk
TVB-1405
Revert refactor, as it seems to be breaking un-committed code.

git-svn-id: https://repo.thevirtualbrain.org/svn/tvb/trunk/scientific_library@6326 1c0e02f0-7929-43c0-8fb3-3293bf43b0d1
Merge branch 'trunk' of https://github.com/the-virtual-brain/tvb-library into trunk
Coupling:

+ Added a new coupling function for the Jansen and Rit model.
* Coupling desesperately needs to be reviewed.  
* The couplings Datatypes are currently unused.
* Currently there is almost one coupling per model. 
? Consider linking a model to a coupling function.
? Make the coupling aware of the models coupling variables and which operations should be performed. 



git-svn-id: https://repo.thevirtualbrain.org/svn/tvb/trunk/scientific_library@6344 1c0e02f0-7929-43c0-8fb3-3293bf43b0d1
Models:

+ Updated Jansen and Rit model. The long range coupling term was somewhat incorrect.
+ With the recently introduced SigmoidalJansenRit coupling function it should be safe to use this model.
+ See demos/region_stochastic_jansen.py


git-svn-id: https://repo.thevirtualbrain.org/svn/tvb/trunk/scientific_library@6345 1c0e02f0-7929-43c0-8fb3-3293bf43b0d1
region-stochastic_jansen.py:
----------------------------
+ Updated demo
   
   *The noise scaling has been corrected
   *It makes use of the right coupling function  



git-svn-id: https://repo.thevirtualbrain.org/svn/tvb/trunk/scientific_library@6346 1c0e02f0-7929-43c0-8fb3-3293bf43b0d1
Merge branch 'trunk' of https://github.com/the-virtual-brain/tvb-library into trunk