v0.9.4

Version 0.9.4

• Added option to avoid creating connections with weight=0

• Made recording of dipoles optional with attribute cfg.recordDipoles

• Rotated conn matrix x-axis labels so can fit large matrices

• Added 'removeWeightNorm' argument to plotConn() function

• Added cfg option 'oneSynPerNetcon' to conn rules to create one synapse object per Netcon

• Added first version of Contributors Guide

• Fixed file write permissions for evol optim batches

• Fixed bug calculating normally distributed rhythmic inputs - was using variance instead of std

• Fixed bug in iplotDipole when smoothing window size = 0

• Fixed bug in plotSpikeStats pop order

• Fixed bug is plots with scalebars

• Fixed bug in grid lines of plotConn

• Fixed bug in subConnParams by sorting conns to ensure reproducibility on different number of cores

• Fixed bug so uses 'Agg' backend if no display env variable e.g. in clusters

v0.9.3.1

Note: release to fix wrong v0.9.3 files in PyPi

Version 0.9.3.1

• Replaced deprecated imp module with importlib

• Fix to cellsGrid cell locations with normRange

v0.9.3

Version 0.9.3

• Improved conversion from SONATA format, including 300 biophys cell example

• Added saveCellConns, pt3dRelativeToCellLocation and invertedYCoord cfg options

• Added lineWidth as argument of plotRatePSD() and plotLFP()

• Modified plotLFP and plotRatePSD to use Morlet wavelet for PSD calculation

• Added lineWidth argument to some raster and LFP plots

• Added shuffling test to granger causality functions

• Fixed bug plotting traces with one fig per trace

• Fixed bug in granger functions - required conversion to int

• Fixed bug in plotShape when cells sections not available

• Return meaningful cell info via 'repr' and 'str' for pointCell, compartCell

• Fixed spelling typos in documentation

v0.9.2

Version 0.9.2

• Support for saving simulation at intervals

• Improved Python cell template import so can read section names from a Python list or dict of sections

• Fixed replicability issue across different number of cores when using 'connList' connectivity rules

• Improved speed performance of 'connList' connectivity rules

• Updated RxD calcium buffering example

• Added netClamp example to re-simulate activity of single cell from network data

• Added support for recording and plotting variable time step

• Replaced spectrogram FFT method with Morlet wavelet method

• Updated installation instructions

• Added 'fontSize' argument to several plots

• Fixed issue completing batches in Python 3

• Fixed bug saving evolutionary optimization batch output file

• Fixed bug in plotShape()

• Fixed bug in plotSpikeStats()

• Fixed bug loading files with colons

• Fixed issue sorting raster by population and y coord

v0.9.1.3

Version 0.9.1.3

• Removed deprecated hold function from plotConn

Version 0.9.1.2

• Set 'pandas==0.23.4' to avoid error

Version 0.9.1.1

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

v0.9.1.1

Version 0.9.1.1

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

v0.9.1

Version 0.9.1

• 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

v0.9.0

Version 0.9.0

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

• Improved performance (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.

v0.7.9

Version 0.7.9

• 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

v0.7.8

• Added netParams.rotateCellsRandomly option to rotate cells randomly around y-axis

• Added netParams.defineCellShapes option to convert stylized cell geometries to 3d points

• Added 'histogram' option to plotSpikeStats

• Improved shapePlot so generates 3d pts for stylized morphs and plots all cells by default

• Added showElectrodes and bkgColor options to shapePlot

• Adapted so can set cfg.createPyStruct=0 before creating conns to save memory on large nets

• Added option cfg.connRandomSecFromList=True to set if sec and loc are randomly chosen from list when synsPerConn=1

• Added cfg.printSynsAfterRule to print total connections after each conn rule is applied

• Fixed bug to ensure VecStim random streams are independent of simulation duration

• Fixed bug calculating avg pop rate in plotRaster when using subsets of pops

• Fixed bug LFP recording only applied to compartmental cells

• Fixed bug when using conn 'threshold' in verbose -- removed all since has no effect

• Fixed bug when deleting sections -- needed sec.push() before

• Fixed bug in shapePlot figSize option

• Fixed format of git changeset stored -- removed 'g' prefix

• Fixed bug in Windows trying to get git changeset

• Fixed bug gathering LFP data

• Fixed bug importing global v_init from multiple cell files

• Fixed bug so gitChangeset() returns to orig folder even when git not installed

• Fixed bugs in plotConn -- missing rounding func and grouping by y interval