Release 1.5.10

Snapshot before major changes in version 2.0

Bug fixing and dependencies upgrade

• Fix Windows and Linux Distributions
• Upgrade to allenSDK 0.16
• Upgrade to SqlAlchemy 1.1.14 and sql-migrate 0.11
• Bug fixes in: FFT visualizer, FCD analyzer, Brain Surface visualizer, Volumetric viewer on Safari, PSE Discreet, Phase Plane
• Bug fixes in tvb-framework flow (start/stop/show correct version) when used from Pypi package
• 2 new Epileptor model variants ([Saggioetal_2017] Fast–Slow Bursters in the Unfolding of a High Codimension Singularity and the Ultra-slow Transitions of Classes

Release Notes

* [[TVB-2465](http://req.thevirtualbrain.org/browse/TVB-2465)] - TVB_Distribution 1.5.6 won't start on Windows 10
* [[TVB-2466](http://req.thevirtualbrain.org/browse/TVB-2466)] - TVB_Distribution 1.5.6 on Linux does not run notebooks correctly
* [[TVB-2320](http://req.thevirtualbrain.org/browse/TVB-2320)] - Upgrade to sqlalchemy 1.1.14 and migrate 0.11
* [[TVB-2360](http://req.thevirtualbrain.org/browse/TVB-2360)] - Finalize TVB packages on conda-forge
* [[TVB-2255](http://req.thevirtualbrain.org/browse/TVB-2255)] - Improve upload of NII volume mapping when auto-correct
* [[TVB-2314](http://req.thevirtualbrain.org/browse/TVB-2314)] - tvb-bin vs revision number on Pypi packages
* [[TVB-2316](http://req.thevirtualbrain.org/browse/TVB-2316)] - Restart of cherrypy from tvb-framework installed with pypi does not work
* [[TVB-2301](http://req.thevirtualbrain.org/browse/TVB-2301)] - Publish TVB on conda forge 
* [[TVB-2315](http://req.thevirtualbrain.org/browse/TVB-2315)] - Wheels for gdist
* [[TVB-2318](http://req.thevirtualbrain.org/browse/TVB-2318)] - New packages 1.5.5 on Pypi
* [[TVB-2331](http://req.thevirtualbrain.org/browse/TVB-2331)] - Present TVB at SFN 2017
* [[TVB-2317](http://req.thevirtualbrain.org/browse/TVB-2317)] - Add start/stop/test helpers for Pypi installed TVB
* [[TVB-1074](http://req.thevirtualbrain.org/browse/TVB-1074)] - Extract in a table all TVB dependencies and mark the ones already on NeuroDebian
* [[TVB-2320](http://req.thevirtualbrain.org/browse/TVB-2320)] - Upgrade to sqlalchemy 1.1.14 and migrate 0.11
* [[TVB-2322](http://req.thevirtualbrain.org/browse/TVB-2322)] - Make tvb importers compatible with latest networkx version 2.0
* [[TVB-2330](http://req.thevirtualbrain.org/browse/TVB-2330)] - Upgrade AllenSDK dependency version
* [[TVB-2342](http://req.thevirtualbrain.org/browse/TVB-2342)] - Fix Mac Build after upgrade of AllenSDK, pyTables, Pillow and CherryPy
* [[TVB-2350](http://req.thevirtualbrain.org/browse/TVB-2350)] - pip install tvb-gdist on Linux fails
* [[TVB-2241](http://req.thevirtualbrain.org/browse/TVB-2241)] - octave/matlab path not automatically updated
* [[TVB-2314](http://req.thevirtualbrain.org/browse/TVB-2314)] - tvb-bin vs revision number on Pypi packages
* [[TVB-2321](http://req.thevirtualbrain.org/browse/TVB-2321)] - PSE Isocline does not correctly expand when Maximize button is pressed
* [[TVB-2324](http://req.thevirtualbrain.org/browse/TVB-2324)] - PSEDiscreet viewer can not work with a Group of TS (no measures)
* [[TVB-2325](http://req.thevirtualbrain.org/browse/TVB-2325)] - Error in FFT, when the TS sampling step is big
* [[TVB-2326](http://req.thevirtualbrain.org/browse/TVB-2326)] - Errors in FCD Analyzer
* [[TVB-2327](http://req.thevirtualbrain.org/browse/TVB-2327)] - Error in FFT Visualizer
* [[TVB-2328](http://req.thevirtualbrain.org/browse/TVB-2328)] - Brain surface viewer recently throws an exception
* [[TVB-2332](http://req.thevirtualbrain.org/browse/TVB-2332)] - Volumetric Viewer shows wrong sections on Safari
* [[TVB-2341](http://req.thevirtualbrain.org/browse/TVB-2341)] - PSE Discreet does not change sizes on size metric change
* [[TVB-2343](http://req.thevirtualbrain.org/browse/TVB-2343)] - Connectivity Measure Visualizer loads with JS error
* [[TVB-2347](http://req.thevirtualbrain.org/browse/TVB-2347)] - Integration of Epileptor Codim3 models is incomplete
* [[TVB-2355](http://req.thevirtualbrain.org/browse/TVB-2355)] - File regionMapping_16k_192.txt missing from TVB_Distribution
* [[TVB-2373](http://req.thevirtualbrain.org/browse/TVB-2373)] - Fix tvb-framework unit-tests when running in a clean env
* [[TVB-2374](http://req.thevirtualbrain.org/browse/TVB-2374)] - Off by 1 simulator current step
* [[TVB-2375](http://req.thevirtualbrain.org/browse/TVB-2375)] - tvb-framework is incompatible with latest matplotlib 2.2.0
* [[TVB-2412](http://req.thevirtualbrain.org/browse/TVB-2412)] - TVB Build Step 1 is incorrect after recent changes
* [[TVB-2414](http://req.thevirtualbrain.org/browse/TVB-2414)] - Matlab Analyzers can not be launched from recent Mac TVB_Distributions
* [[TVB-1070](http://req.thevirtualbrain.org/browse/TVB-1070)] - Prepare TVB packages for NeuroDebian
* [[TVB-1731](http://req.thevirtualbrain.org/browse/TVB-1731)] - Update some TVB dependencies
* [[TVB-2348](http://req.thevirtualbrain.org/browse/TVB-2348)] - TVB Node#6 in Berlin 26 feb 2018
* [[TVB-2358](http://req.thevirtualbrain.org/browse/TVB-2358)] - Project #2.1 Packaging TVB
* [[TVB-2359](http://req.thevirtualbrain.org/browse/TVB-2359)] - Project #2.3 Monitor Signals in 2D and 3D
* [[TVB-2377](http://req.thevirtualbrain.org/browse/TVB-2377)] - TVB Node#7 in Canada 7-8 August 2018
* [[TVB-2127](http://req.thevirtualbrain.org/browse/TVB-2127)] - Native launcher analysis
* [[TVB-1073](http://req.thevirtualbrain.org/browse/TVB-1073)] - Reorganize unit-tests
* [[TVB-2262](http://req.thevirtualbrain.org/browse/TVB-2262)] - New TVB VMs & scheduler
* [[TVB-2313](http://req.thevirtualbrain.org/browse/TVB-2313)] - Propose projects for GSOC 2018
* [[TVB-2323](http://req.thevirtualbrain.org/browse/TVB-2323)] - Support Ana during her workshop end of November
* [[TVB-2333](http://req.thevirtualbrain.org/browse/TVB-2333)] - TSV does not offer support to switch SV or Mode on complex TS signal
* [[TVB-2337](http://req.thevirtualbrain.org/browse/TVB-2337)] - Supervise students at GSOC 2018
* [[TVB-2338](http://req.thevirtualbrain.org/browse/TVB-2338)] - Write an example for Miriam
* [[TVB-2339](http://req.thevirtualbrain.org/browse/TVB-2339)] - Upgrade Anaconda Windowsx64 TVB Build Env
* [[TVB-2353](http://req.thevirtualbrain.org/browse/TVB-2353)] - After seting library profile in ipython notebook the logs from console are no longer displayed in browser
* [[TVB-2411](http://req.thevirtualbrain.org/browse/TVB-2411)] - Upgrade for allenSDK 0.16
* [[TVB-2319](http://req.thevirtualbrain.org/browse/TVB-2319)] - Topographic viewer could have ColorScheme controls
* [[TVB-2357](http://req.thevirtualbrain.org/browse/TVB-2357)] - Allow Connectivity.from_file to read either "centres" or"centers" files
* [[TVB-2378](http://req.thevirtualbrain.org/browse/TVB-2378)] - Improve the UI

Packaging and Improvements in Visualizers

• Add Structural Connectivity and Pearson Correlation Edge Bundle Viewers (circular viewers)
• Replace MPLH5 Visualizers(PSE Continous, Wavelet, Fourier, Topographic, Pearson, Complex Coherence) with new ones based on D3.JS
• Packages distributed with Pypi (tvb-library and tvb-framework)
• Bug Fixes

Release Notes - The Virtual Brain - Version 1.5.4

* [TVB-2246] - Rewrite Wavelet Viewer
* [TVB-2260] - Remove MPLH5 from Matrix Viewer
* [TVB-2266] - Rewrite the Pearson correlation coefficients visualizer
* [TVB-2268] - Rewrite Complex Coherence Viewer
* [TVB-2271] - Region Labels missing from display (lCC/rCC)
* [TVB-2272] - Ensure that size of region is correctly computed
* [TVB-2273] - Make it possible to see edges directionality in the new viewer
* [TVB-2274] - Region labels on chord not visible at extremeties
* [TVB-2275] - Fix Mac build for H5py latest version 2.7.0
* [TVB-2276] - Should we move the viewer in the Connectvity Cockpit?
* [TVB-2277] - Should we move to Ajax for handling data?
* [TVB-2278] - Can we add other kinds of data to the chord viewer?
* [TVB-2283] - Remove MPLH5 backend
* [TVB-2284] - Create documentation
* [TVB-2289] - Document involved tools
* [TVB-2301] - Publish TVB on conda forge 
* [TVB-1818] - Local connectivity and surface activity view do not expect geometry to be split in hemispheres
* [TVB-1993] - Hardcoded user home not always appropriate
* [TVB-2072] - Help bubbles from the portlets do not work any more
* [TVB-2086] - Document other datasets shipped with distribution
* [TVB-2129] - SVG TS lines too thick in MS Edge
* [TVB-2212] - LC visualizer fails for mouse cortex
* [TVB-2240] - Wrong HTML displayed when a new TVB version is announced
* [TVB-2264] - Branching a simulation fails sometimes
* [TVB-2265] - When saving Region Stimulus region indices are incorrect
* [TVB-2267] - Fix Complex Coherence Analyzer after upgrade of numpy
* [TVB-2282] - Check fft algorithm
* [TVB-2293] - PSE Discreet does not work on 1D PSE results, and sometimes not in burst preview
* [TVB-2294] - Wrong labels display in Connectivity Edge Bundle viewer
* [TVB-2295] - PSE Continous displays wrong axes when one dimension is datatype
* [TVB-2296] - Branching w/ BOLD produces too many array indices
* [TVB-2299] - PSE Discreed shows wrong IDs in the overlay messages
* [TVB-2303] - Increase resolution for PSE Isocline
* [TVB-2304] - Brain Visualizer in Burst Preview is flicking
* [TVB-2305] - When starting TVB from tvb.app Octave is not recognized
* [TVB-2306] - When trying to delete an op in error nothing happens
* [TVB-2307] - Check button has no effect in Simulator - Configure Interface
* [TVB-2308] - PSE Continuous looses the current selected metric on TAB change in Burst page
* [TVB-2309] - When clicking on "Noise Configure" from a range we get redirected to Error page
* [TVB-2310] - Y axis labels not showing completely 
* [TVB-2311] - In pse-discrete portlet hover information is not displayed
* [TVB-1974] - Rewrite TVB visualizers which are based on MPLH5 with more modern web technology
* [TVB-2258] - Implement a circular viewer in TVB
* [TVB-2084] - Rewrite continuous pse view to use canvas
* [TVB-2286] - Configure and install TVB bot
* [TVB-2114] - Update PyPI package
* [TVB-2213] - Project Planning and Discussions
* [TVB-2243] - Put TVB iPython notebook example on HBP collab
* [TVB-2253] - Investigate not aligned data from Gary
* [TVB-2279] - Upgrade Debian on TVB VM
* [TVB-2297] - Testing Release 1.5.4 Beta for the Cluster
* [TVB-2300] - Test latest version before release
* [TVB-2302] - Upgrade and prepage cm-virtbrain for Ana's presentation
* [TVB-1837] - Flexible specification of time (ms, s, minutes)
* [TVB-2242] - Remove MPLH5 from Connectivity page
* [TVB-2259] - Include server URL when sending emails about new user creation
* [TVB-2270] - Improve Pearson viewer by adding mode and SV selector
* [TVB-2287] - Check Save Figure from all Visualizers

License change from GPL v2 into GPL v3

• Update license of TVB from GPL v2 into GPL v3
• Expose in TVB_Distribution the Allen Connectivity creator
• New and improved PSE discreet viewer
• Bug fixes

[TVB-2111] - Error in the loading of PSE data now
[TVB-2137] - Create backend Python controller method for Explore
[TVB-2167] - PSE Discreet should be automatically refreshed, when operations are still in work
[TVB-2169] - Fix "Save Image" for the new PSE Viewer
[TVB-2170] - Integrate Colors Legend
[TVB-2171] - Needs to place results in the right area of canvas.
[TVB-2172] - replace the blacked out circles of incomplete results with a def svg of a cross x
[TVB-2173] - add clip paths
[TVB-2174] - scale circle radius based on zoom
[TVB-2175] - clean up contour tool
[TVB-2177] - brainstorm alternate data structure for the PSE results
[TVB-2180] - Construct API for new datastructure and experiment with function contents
[TVB-2181] - save button for filter is broken
[TVB-2182] - reintegrate the filter button
[TVB-2183] - NodeInfo made available using result coordinates
[TVB-2184] - fix contour save button
[TVB-2185] - Resolve step value issues
[TVB-2186] - create a way to have code for incoming data merge only executed once.
[TVB-2196] - Ipython is not correctly distributed after recent build machine redo
[TVB-2198] - PSE discreet no longer works for DataType ranges
[TVB-2153] - PSE viewer not loading in simulator panel
[TVB-2188] - Isocline viewer doesn't show in the simulator panel
[TVB-2190] - Fix SurfaceGainMatrix to RegionGainMatrix transformation
[TVB-2191] - UTF-8 locale not understood
[TVB-2203] - EEG monitor with reference doesn't work
[TVB-2217] - Contributor setup is incompatible with import tvb.simulator.lab
[TVB-2218] - Mistake in parameter labels for ZetterbergJansen class
[TVB-2228] - Fix TVB build on Mac
[TVB-2229] - If AllenCreator adapter becomes deprecated, it is still shown in GUI
[TVB-2233] - Phase plane does not show up in GUI
[TVB-2234] - Allen Creator with default throws KeyError
[TVB-2235] - Phase Plane is not working (Internal Server Error)
[TVB-2236] - Error in TS Viewer D3
[TVB-2083] - Convert discrete pse view to d3
[TVB-1932] - When importing a connectivity do not always throw exception when negative weights
[TVB-2165] - Finish Allen Connectivity Builder integration with TVB_Distribution
[TVB-2176] - brainstorm new structure for PSE data
[TVB-2194] - Redo TVB Mac Build machine
[TVB-2206] - Surface Viewers do not have Color scheme legend
[TVB-2207] - Integrate latest release of BCT (Version 2017-15-01)
[TVB-2221] - Integrate 2 mouse Connectivities in tvb-data and TVB_Distribution
[TVB-2222] - Change license text
[TVB-2225] - Fix TVB Build on Windows
[TVB-2230] - Change TVB License into GPLv3
[TVB-2231] - Finalize release 1.5.1
[TVB-1616] - Refactor DataTypes diamond-like inheritance
[TVB-2189] - Add stylistic changes to the discrete viewer where necessary.
[TVB-2214] - Improve ProjectionMatrices load from files
[TVB-2226] - Debug and identify performance bottlenecks in the PSE D3

New functionality related to simulation and visualizers

• New: export simulation configuration as JSON and reuse in web or console
• Volumetric Viewers extended and improved (more datatypes can be visualized in volume - e.g. TimeSeriesRegion; better performance)
• Color Scheme: allow to trim near-mean values in a color scheme
• New: tracts visualizer, FCD analyzer
• Refactored internal API for Adapters, with the purpose of simplifying console usage
• Allen SDK Creator added
• Reduced Wong-Wang default parameters updated to reflect usage in Hansen et al 2015
• Coefficients for the Stefanescu-Jirsa 3D model have been corrected
• ~5x accelerations for several models (Epileptor, Generic 2D Oscillator, Jansen-Rit, Reduced Wong-Wang)
• Epileptor state variables names updated to those used publications, (y0->x1, y1->y1, y2->z, y3->x2, y4->y2, y5->g)
• Models: new variables of interest for monitoring physiological signals e.g. LFP.
• Variable order integrators now available which can improve accuracy and execution speed for many cases.
• Conduction delays and coupling are now more efficient, especially for large and/or sparse connectivities.
• Comprehensive review to library logging, turn on useful debug info with log_debug(True).