Neurosim-lab/netpyne: v0.9.0

• Added support for reaction-diffusion (RxD) and usage examples

• Improved performanced (speed) of connectivity algorithms

• Major code refactor to split functions across modules and subpackages

• Switched to Python 3 as the default development environment

• Optimized implementation of raster and spikeHist plotting using Pandas

• Added support for recording spikes from only a subset of cells using e.g. cfg.recordCellsSpikes = ['E2']

• Support for exporting to SONATA standardized network format (Beta)

• Support for Human Neocortical Neurosolver (HNN) dipole mechanisms

• Added option for filename to saveData()

• Removed pop cellModelClass when saving

• Removed cell h object keys when saving

• Added support for evolutionary algorithm optimization (via Inspyred) and usage example

• cfg.popAvgRates now accepts a time range to calculate rates (e.g. to discard initial period)

• All NEURON objects now accessible via ['hObj'] key within Python network structure

• Fixed bug in batch to allow having only grouped params

• Fixed bug initalizing batch 'mpi_bulletin' and batch tutorial example

• Fixed bug: removed '_labelid' from netParams when saving

• Fixed bug: made self.scaleConnWeightModels False when not used (avoids saving weird dict in json)

• Fixed bug in Pickle file encoding so works in Python3

• Fixed bug in convergence and divergence conn when repicking a value if postGid=preGid is randomly selected

• Fixed bug in rand initialization for string-based func with div conn

• Fixed issue in probabilistic connectivity random number generation to ensure replicability in Python 2 and 3.

NOTE on backward replicability: Due to several performance improvements and bug fixes to ensure future replicability in both Python 2 and 3, it won't be possible to replicate results of previous versions.