Fix contributor setup after recent changes in profiles.

git-svn-id: https://repo.thevirtualbrain.org/svn/tvb/trunk/scientific_library@6679 1c0e02f0-7929-43c0-8fb3-3293bf43b0d1
Remove an extra way of loading defaults Connectivity.default() and Cortex.default().
We do not want to have too many ways of loading defaults, as that could become confusing and difficult to maintain and test.

git-svn-id: https://repo.thevirtualbrain.org/svn/tvb/trunk/scientific_library@6680 1c0e02f0-7929-43c0-8fb3-3293bf43b0d1
TVB-1604
Improve the way Cortex objects gets populated from data-files.

git-svn-id: https://repo.thevirtualbrain.org/svn/tvb/trunk/scientific_library@6681 1c0e02f0-7929-43c0-8fb3-3293bf43b0d1
TVB-1604
Fix tests after recent changes.

git-svn-id: https://repo.thevirtualbrain.org/svn/tvb/trunk/scientific_library@6682 1c0e02f0-7929-43c0-8fb3-3293bf43b0d1
TVB-1591
Make sure in db_events that the H5 file is always created before DT.configure() gets called
TimeSeriesFramework.read_data_shape throws an explicit exception if the 'data' field in H5 is empty.

git-svn-id: https://repo.thevirtualbrain.org/svn/tvb/trunk/scientific_library@6683 1c0e02f0-7929-43c0-8fb3-3293bf43b0d1
TVB-1607
Set flags IN_OPERATION,  before ProfileSettings.initialize** calls, to avoid LoggingBuilder being created there.

git-svn-id: https://repo.thevirtualbrain.org/svn/tvb/trunk/scientific_library@6685 1c0e02f0-7929-43c0-8fb3-3293bf43b0d1
TVB-1604: update Tutorial after recent changes in readers for the library profile

git-svn-id: https://repo.thevirtualbrain.org/svn/tvb/trunk/scientific_library@6686 1c0e02f0-7929-43c0-8fb3-3293bf43b0d1
TVB-1607
When no profile if set and we are trying to use TVB, fail to default LIBRARY_PROFILE.


git-svn-id: https://repo.thevirtualbrain.org/svn/tvb/trunk/scientific_library@6687 1c0e02f0-7929-43c0-8fb3-3293bf43b0d1
TVB-1607
Revert part of the previous change, to fix build.


git-svn-id: https://repo.thevirtualbrain.org/svn/tvb/trunk/scientific_library@6688 1c0e02f0-7929-43c0-8fb3-3293bf43b0d1
TVB-1607
Fix build


git-svn-id: https://repo.thevirtualbrain.org/svn/tvb/trunk/scientific_library@6689 1c0e02f0-7929-43c0-8fb3-3293bf43b0d1
TVB-1607
Compromise between build and console requests.


git-svn-id: https://repo.thevirtualbrain.org/svn/tvb/trunk/scientific_library@6690 1c0e02f0-7929-43c0-8fb3-3293bf43b0d1
TVB-1607
Correctly set library_test


git-svn-id: https://repo.thevirtualbrain.org/svn/tvb/trunk/scientific_library@6691 1c0e02f0-7929-43c0-8fb3-3293bf43b0d1
TVB-1590 introduced a surfaces.validate. Renamed MappedType.validate to _validate_before_store. Surface validation no longer called by configure.

git-svn-id: https://repo.thevirtualbrain.org/svn/tvb/trunk/scientific_library@6692 1c0e02f0-7929-43c0-8fb3-3293bf43b0d1
TVB-1590 Surface validate methods can return warning results not just fail with exceptions or pass. Fixed failing test.

git-svn-id: https://repo.thevirtualbrain.org/svn/tvb/trunk/scientific_library@6693 1c0e02f0-7929-43c0-8fb3-3293bf43b0d1
TVB-1609 Reduce redundant allocation

git-svn-id: https://repo.thevirtualbrain.org/svn/tvb/trunk/scientific_library@6696 1c0e02f0-7929-43c0-8fb3-3293bf43b0d1
TVB-1609 _find_vertex_triangles 3 times faster; Angle computation  1.4 times

git-svn-id: https://repo.thevirtualbrain.org/svn/tvb/trunk/scientific_library@6697 1c0e02f0-7929-43c0-8fb3-3293bf43b0d1
TVB-1609 Reduce attr lookup

git-svn-id: https://repo.thevirtualbrain.org/svn/tvb/trunk/scientific_library@6698 1c0e02f0-7929-43c0-8fb3-3293bf43b0d1
TVB-1609 Fixed a typo. Angle computation 3 times faster

git-svn-id: https://repo.thevirtualbrain.org/svn/tvb/trunk/scientific_library@6699 1c0e02f0-7929-43c0-8fb3-3293bf43b0d1
TVB-1298 TVB-1609 Vectorized part of the _find_triangle_angles: run time  5 times faster.

git-svn-id: https://repo.thevirtualbrain.org/svn/tvb/trunk/scientific_library@6701 1c0e02f0-7929-43c0-8fb3-3293bf43b0d1
Merge branch 'trunk' of https://github.com/the-virtual-brain/tvb-library into trunk