Netpyne

- Batch parameters can now include list or dict items

- Added 'weightNorm' param to sections so can normalize weight based on dendritic location

- Import cell function now has somaAtOrigin option to place the cell soma at coords 0,0,0

- Go back to using NetStim.noiseFromRandom, since noiseFromRandom123() only available in very recent versions

- Fixed bug in saveData option of figure plots

- Fixed bug passing figSize param to figures

- Fixed bug where gid only updated if cellParam rules were applied to the cell

- Fixed bug in importCell by deleting imported modules from sys.modules

- Fixed bug that prevented NetStim random noise generator from being initialized

- Added support for artificial cells (without sections) (issue 44)

- A single NetStim (within a population) can now be connected to multiple cells (issue 113)

- VecStim populations use same params as NetStims and allows for pulses at arbitrary times with different rates

- NetStim and VecStim population allow for a uniformly distributed rates in the form [min,max]

- Added option to run batch sims via mpi and bulletin board (master/slave) (issue 108)

- netParams.shape paramter to select either 'cuboid', 'cylinder' or 'ellipsoid' network shape (issue 26)

- analysis.plot2Dnet() 'view' param to select frontal ('xy') or top-down ('xz') view

- analysis.plotConn() option to plot stacked bar graph, select different pre and post pops, synMech and syns vs conns

- Made distinction between number of connections and synaptic contacts (eg. can have 5 synsPerConn)

- New function netParams.addCellParamsSecList to create list of sections based on distance from soma

- Removed 'plast' and 'shape' from conns when not used (issue 177)

- Added option to center soma at origin when importing cell

- Now using noiseFromRandom123() for NetStims() (issue 89)

- Fixed bug in readCmdLineArgs()

- Fixed bug in saveData option of figure plots

- Added analysis.nTE() function to calculate normalized transfer entropy (issue 42)

- Added analysis.granger() function to calculate and plot Spectral Granger Causality (issue 42)

- Added analysis.plotRatePSD() to plot firing rate power spectral density

- Added analysis.plotShape() to plot 3D morphology of cell and synapse locations

- Added option to fix soma depth for subcellular distributions based on 1d and 2d maps

- Added support for gap junction (electrical synapse) connections

- Improved import of multicompartmental cells from NeuroML2

- Added option to turn off graphics by adding -nogui from command line

- Added option to skip batch sims if output file already exists

- Added option to overlay pop labels and show avg rates to plotRaster() (issue 111)

- All section now include argument cell=self to differentiate them

- Fixed travis script so checks all tuts and examples after each commit (issue 37)

- Fixed bug positioning cells with 3d geom

- Fixed bug in sim.clearAll by closing all figures instead of current (issue 168)

- Fixed bug: cache_efficient was not being turned on

- Fixed bug setting simConfig loaded from file

- Fixed bug in plotRaster inverseOrder option

- Fixed str vs basestring in analysis.py and simFuncs.py

- Fixed bug due to not inserting ions in section

- Added cvode_active simConfig option to set variable time step (issue 116)

- Added saving of avg pop rates

- Added save method to SimConfig and NetParams class

- Fixed bug importing 3d cell geometries

- Fixed bug in readCmdLine func

- Fixed bug reading from json (str vs unicode)

- Fixed bug setting mech param values for nseg>1

- Added importing of cell ion parameters (eg. 'ena' or 'ek')

- Added backupCfgFile (eg. ['cfg.py', 'backupcfg/']) to simConfig to copy cfg file after run

- Added gatherOnlySimData to simConfig to gather only simulation data and not cells or pops

- Added simLabel and saveFolder to simConfig (can be used instead of filename)

- Added printRunTime to simConfig to print run time (in sec) during execution

- Added printPopAvgRates to simConfig to print population avg firing rates after run

- Automatic saving of netpyne and netParams version to file

- Moved creation of fih functions to set cell vinit from setupRecording() to preRun()

- Can now load netParams and simConfig from file without setting in sim

- Added sim.readCmdLineArgs to read simConfig and netParams filepaths from command line

- Can now access NEURON's h module via sim.h

- Fixed bug so can load netParams and simConfig without initializing sim

- Fixed bug that prevented mechanism properties with value 0.0 from being set

- Fixed bug in code to distribute cells (converted numCells from float to int)

- Fixe bug in plotTraces

- Added global boolean variable netpyne.__gui__ to enable/disable graphics (issue 150)

- Spike histogram fixes: axis labels only in 1st subplot, limit time range, tight_layout only if <5 subplots

- Fixed bug so multiple traces figures are saved to separate files (issue 166)

- Fixed bug when using point process-based cells that include synapses (eg. Izhi2007a)

- Fixed bug where spike hist subplot didn't match raster axis

- Fixed bug when loading data from file with multiple cores

- Fixed bug so modify functions work with multiple cores