Netpyne

- Removed deprecated hold function from plotConn

- Set 'pandas==0.23.4' to avoid error

- Fixed minor bug - axis font size changed from 12 to 2 by accident (change required for NetPyNE-UI)

- Updates to NeuroML converter

- Add scalebar to rxd concentration plot

- Fixed bug so comparisons to basestring work in Python 2 and 3

- Fixed bug in string-based functions representation in GUI

- 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.

- Extended metadata structure to interact with NetPyNE-UI

- Added preliminary data structures to support NEURON RxD

- Added plot RxD concentration to analysis

- Added netParams.correctBorder to compensate distance-dependent connectivity border effect

- Added option to run jobs directly on multiple mpi cores via Batch class

- Added option for custom text in PBS or SLURM scripts to submit batch jobs

- Added option to filter LFP signal before ploting PSD

- Convert 'gid' to actual cell gid when used in point process params (useful for random seeds)

- Relaxed pyneuroml requirement so just shows a warning message

- Preliminary function to save conns distributedly using HDF5

- Added function to validate string-based expressions

- Fixed bug: removed cell.\_segCoords and pop.\_morphSegCoords before saving to file

- Fixed rasterPlot pop label automated spacing

- Fixed bug: removed pandas requirement from LFP electrode module

- Fixed bug: updated rcParams text.fontsize to font.size

- Fixed bug: missing update of list-based loc in connList connections

- Fixed bug: delete sections after import cell only if section exists