v1.0.6

Version 1.0.6

New features

• Raster plot colored by phase

• Examples based on the CA3 model using the 'colorbyPhase' option in the plotRaster

• API for loading .mod files selectively

• Ability to specify custom executor to run batch with (defaults to sh)

Bug fixes

• Fixed loading point cell params from legacy models (issue 607)

• Fix voltage movie tutorial

• Fix to automatically include netstims in the sim.allSimData object when plotRaster 'include' selects 'all'

• Fixed loading netParams in some scenarios (bug caused by srting functions pre-processing)

• Fix of plotRaster pops coloring if ordered not by gid

• Made cells diversity work with popParams based on cellsList and gridSpacing

• Fixed handling of output of sim.create() - was wrong order (credit: Kate Doxey)

• Fixed undeclared var dpi in plotShape()

• Fixes in batch utils

• Added some missing math functions to use with 'Functions as string' functionality

• Switch file copying method to shutil to be compatible over all operating systems (credit: Henrik Podeus)

v1.0.5

Version 1.0.5

New features

• Time series and PSD plots for current source density (CSD)

• Added colorbar to CSD plot

• Support for Sun Grid Engine HPC

• Extended sim.gatherData() with more optional arguments for flexibility

• Specify linear/log scale in plotRatePSD()

• Print more info about exceptions in plotting functions

• Check RxD specification for potential syntax issues

• Prevent zero population size in scaled-down models

• Better messages for validation errors

Bug fixes

• Fixed errors in plotting with sim.cfg.gatherOnlySimData=True

• Support saving and loading data in .mat and .hdf5 formats

• Multiple fixes in plotRatePSD() - popColors, fft, minFreq

• Fixed sync lines in plotRaster()

• Fixed performance issue in plotConn() with groupBy='pop' (default)

• Fixed recordTraces to not require more presicion than segment size (for stim and synMech)

v1.0.4.2

Version 1.0.4.2

Bug fixes

• Unpin matplotlib version (params copying issue fixed)

v1.0.4.1

Version 1.0.4.1

New features

• Added env variable to define head model placement

v1.0.4

Version 1.0.4

New features

• Added 'linewidth' as argument of plotting.plotSpikeHist()

• More detailed validation of netParams

• Save and load model in native NetPyNE format

• Converted most of examples to new NetPyNE model structure

• Complex stimulation ('rhythmic', 'evoked', 'poisson' and 'gauss') for VecStim created as pointCell (as a population rule)

• Codebase brought into compliance with PEP8 conventions

• Updates in NeuroML examples and tests

Bug fixes

• fixed handling filenames with multiple dots in MetaFigure.saveFig()

• Fixed readCmdLimeArgs() default arguments for backward-compatibility

• Cleaned up example models to drop some legacy/irrelevant params

• RxD module: Parameters defined before reactions + names given by default when missing (by the key)

• Analysis: try ... except call in plotDipole

• Save hObj of gap junction to connParams

• Removed duplicated or unused code from gridSearch()

• Fixes in batch utilities to make OS-agnostic

v1.0.3.1

Version 1.0.3.1

• Hotfix to support new GUI functionality

v1.0.3

Version 1.0.3

New features

• Added ability to load PointCell from saved network

• Added MultiPlotter class to allow plotting line data on multiple axes

• Added option to use separate axis for each PSD trace (set axis='multi')

• Added new Batch method named SBI (Simulation Based Inference) with example folder (sbiOptim)

• Added support for string functions in properties of cell mechanism, in cell geometry (in netParams.cellParams)

• Added support for string functions in synMech parameters

• Massive update of schemas (validator.py and setup.py)

• More control over POINTER variables through synMechParams (e.g. for gap junctions)

• Introduced cell variables in cellParams

• Added plotRateSpectrogram to utils.py

• Functions prepareCSD() and plotCSD() are now available

• Updated documentation on install and about

Bug fixes

• Fixed bug with loading CompartCell with custom mechanisms from saved network

• Fixed bug with accessing proper sim data file during batch parameters optimization

• Fixed bug where most batch optimization methods used to misname simulation output file

• Fixed bug in pop.py: "gridSpacing" is in the list of excludeTags

• Fixed bug in network.py: in the list "stimStringFuncParams" --> 'del' instead of 'delay', and removed 'i'

• Fixed bug in conn.py: included "params['preSec'] = connParam.get('preSec')" in gapJunctions

• Fixed bug in stim.py: 'Loc' with capital letter, for making 'synMechLocFactor'

• Fixed some misinformation in reference.rst about the subconn

• Fixed bug in dipole calculation units - changed from mA to uA

• Fixed bug in conditional logic when gathering LFP / dipoles

• Allow tuples to specify population's cells in 'include' for plotSpike

• Cleaned up optuna optim tutorial

v1.0.2.1

Version 1.0.2.1

New features

• Added axis sharing and twinning capability

• Updated metadata with dipole specs

• Updated some LFP examples

• Added clearAll argument to sim.create()

• Changed ordering of documentation to “by source”

Bug fixes

• Fixed bug in plotting when overlaying axis

• Fixed bug with syncLines option in plotter

• Fixed bugs in MultiFigs (2D subplots, bug in LFP with multi axis)

• Fixed bug in checkAvailablePlots()

• Fixed gathering dipoleSum and LFPPops data from nodes

v1.0.2

Version 1.0.2

New features

• Added back the syncLines argument to plotRaster()

• Updated conversion to/from NeuroML 2

• Added RxD-based spreading depression example model

Bug fixes

• Avoid exception in plotSpikeHist() and plotSpikeFreq() when pop has no spikes

v1.0.1

Version 1.0.1

New features

• Added new plotting module with custom plotters

• Separated analysis.plotSpikeRaster into analysis.prepareRaster and plotting.plotRaster

• Separated analysis.plotSpikeHist into analysis.prepareSpikeData, analysis.prepareSpikeHist, plotting.plotSpikeHist and plotting.plotSpikeFreq

• Separated analysis.plotLFP into analysis.prepareLFP, analysis.preparePSD, analysis.prepareSpectrogram, plotting.plotLFPTimeSeries, plotting.plotLFPPSD, plotting.plotLFPSpectrogram, and plotting.plotLFPLocations

• Mapped old analysis.plots onto new ones

• Interfaced with LFPkit to enable recording/plotting of dipole current moments and EEG signals

• Added Current Source Density (CSD) analysis and plots

• Enabled selecting a subset of cells to save individual LFP signal from via cfg.saveLFPCells = [...]

• Added cfg.saveLFPPops to store LFP generated individually by each population

• Function to return batch parameter combinations (used for GUI)

• Added jupyter nb tutorials

• Added hippocampus CA3 model example

• Updated SONATA importing

• Improved distributed saving and interval saving (more robust)

• Added mapping of netParams values within cfg (used for batch sims in GUI)

• Extended Action tests to pull requests (not just push)

Bug fixes

• Fixed setting cfgMapping nested params when not string

• Fixed defineCellShapes when sec['hObj'] is not a h.Section()

• Fixed bug when using lognormal in string functions

• Added rxdmath to avoid RxD error

• Fixed bug in Tutorial 8 (batch)

• When saving to JSON wait until file exists before returning (to avoid exiting before saving finished)