Check for being free not only the cherryPy port, but also the MPLH5 port.
From app.py, make sure MPLH5 is gets not started.
Add 'onerror' for mplh5 socket client in JS.


git-svn-id: https://repo.thevirtualbrain.org/svn/tvb/trunk/scientific_library@6706 1c0e02f0-7929-43c0-8fb3-3293bf43b0d1
cleanup imports

git-svn-id: https://repo.thevirtualbrain.org/svn/tvb/trunk/scientific_library@6716 1c0e02f0-7929-43c0-8fb3-3293bf43b0d1
Fully vectorized angle computation

git-svn-id: https://repo.thevirtualbrain.org/svn/tvb/trunk/scientific_library@6717 1c0e02f0-7929-43c0-8fb3-3293bf43b0d1
TVB-1594
Increase speed to load Surface DataType overlay, by caching all info in summary and not  reading from H5 each time.
On big surfaces (80k vertices) the loading time for the overlay was reduced with 30%.

git-svn-id: https://repo.thevirtualbrain.org/svn/tvb/trunk/scientific_library@6730 1c0e02f0-7929-43c0-8fb3-3293bf43b0d1
Improved region viewer performance.  Computing region boundaries from 2sec to 1sec.

git-svn-id: https://repo.thevirtualbrain.org/svn/tvb/trunk/scientific_library@6740 1c0e02f0-7929-43c0-8fb3-3293bf43b0d1
Improved region viewer performance.  Computing region boundaries from 1s to 0.6s

git-svn-id: https://repo.thevirtualbrain.org/svn/tvb/trunk/scientific_library@6741 1c0e02f0-7929-43c0-8fb3-3293bf43b0d1
TVB-1568 speed up Heun integrators by computing common subexpression once

git-svn-id: https://repo.thevirtualbrain.org/svn/tvb/trunk/scientific_library@6785 1c0e02f0-7929-43c0-8fb3-3293bf43b0d1
TVB-1568 speed up Heun stochastic by computing common subexpression once

git-svn-id: https://repo.thevirtualbrain.org/svn/tvb/trunk/scientific_library@6786 1c0e02f0-7929-43c0-8fb3-3293bf43b0d1
TVB-1626 Improve surface simulation performance by using a row sparse matrix for the  vertex mapping.

git-svn-id: https://repo.thevirtualbrain.org/svn/tvb/trunk/scientific_library@6788 1c0e02f0-7929-43c0-8fb3-3293bf43b0d1
TVB-1626 Amend last commit.

git-svn-id: https://repo.thevirtualbrain.org/svn/tvb/trunk/scientific_library@6789 1c0e02f0-7929-43c0-8fb3-3293bf43b0d1
TVB-1627 Prealocate arrays in Generic2dOscilator.

git-svn-id: https://repo.thevirtualbrain.org/svn/tvb/trunk/scientific_library@6790 1c0e02f0-7929-43c0-8fb3-3293bf43b0d1
TVB-1626 Surface sim speed. use sparse matrices for region average.

git-svn-id: https://repo.thevirtualbrain.org/svn/tvb/trunk/scientific_library@6793 1c0e02f0-7929-43c0-8fb3-3293bf43b0d1
Fix Animated time series view for surface time series

git-svn-id: https://repo.thevirtualbrain.org/svn/tvb/trunk/scientific_library@6795 1c0e02f0-7929-43c0-8fb3-3293bf43b0d1
Merge branch 'trunk' of https://github.com/the-virtual-brain/tvb-library into trunk
Fix problem in decoding GRAPH JSON, due to special characters in DataType.user_tag fields.

git-svn-id: https://repo.thevirtualbrain.org/svn/tvb/trunk/scientific_library@6805 1c0e02f0-7929-43c0-8fb3-3293bf43b0d1
TVB-1629
Split Simulator.configure() in two parts (the light one before memory estimate, and the full configure, before execution).
PEP8: cleanup simulator module.

git-svn-id: https://repo.thevirtualbrain.org/svn/tvb/trunk/scientific_library@6809 1c0e02f0-7929-43c0-8fb3-3293bf43b0d1
TVB-1629 fix

git-svn-id: https://repo.thevirtualbrain.org/svn/tvb/trunk/scientific_library@6810 1c0e02f0-7929-43c0-8fb3-3293bf43b0d1
Improve documentation on FullGraphStructure class.
Set session timeout to 10 hours.

git-svn-id: https://repo.thevirtualbrain.org/svn/tvb/trunk/scientific_library@6813 1c0e02f0-7929-43c0-8fb3-3293bf43b0d1
Prepare for release 1.3

git-svn-id: https://repo.thevirtualbrain.org/svn/tvb/trunk/scientific_library@6814 1c0e02f0-7929-43c0-8fb3-3293bf43b0d1
Update simulator diagrams from api-documentation as generated with the latest code version.

git-svn-id: https://repo.thevirtualbrain.org/svn/tvb/trunk/scientific_library@6816 1c0e02f0-7929-43c0-8fb3-3293bf43b0d1