v1.1.1

Version 1.1.1

Bug fixes

• Fixed ignored synMech[Weight/Delay/Loc]Factor
• Fixed issue with SSH based searches
• Fixed issue with data and trial logging file creation

v1.1.0

Version 1.1.0

New features

• Added extracellular stimulation with a supporting xtra.mod (which includes a global variable defining the temporal modulation and a pointer to link the extracellular mechanism in NEURON). Useful for large networks

• Improved netParams validation (mechs validation, improved error messages)

• added ability to save transmembrane current for each segment

• Updated options for batch communication (see netpyne documentation: "running a batch job (beta)")

Bug fixes

• Solve minor bug in the uniform field for extracelular stimulation (sign). Deposited the xtra.mod in support module.

• Fixed batch SGE example (credit: Adam Newton)

• Solved small bug when plotting colorbar in the raster plot colored by the LFP phase

• Solved conflict between diversity and segment coordinates (per population), used in LFP setups

• Added extracellular stimulation (option: without compiling an additional .mod file - large memory requirements-)

• Update of documentation (stimSourceParams and stimTargetParams) incorporating how to define extracellular stimulations

• Fixed ODict in examples/batchCell (credit: Hyunsu Lee)

• Fix in RxD to support NEURON 9 (credit: Adam Newton)

• Fixed recording from variables of Point process

• Fixed time slicing on pre-loaded data in plotCSD() (credit: Nikita Novikov)

• Fixed sbi deprecation error. Fixes in docs formatting

• Fixes, refactoring and fail-fast checks in multisinaptic connections

• Fix verbatim function defs in mod files (credit: Ankur Sinha)

v1.0.7

Version 1.0.7

New features

• Introducing batchtools subpackage for parameters exploration and optimization

• Added progress-bar indicating network creation progress. Toggle the progress bar with cfg.progressBar

• cfg.connRandomSecFromList and cfg.distributeSynsUniformly can now be overriden in individual conn rule

• Added ability to use sec, loc, preSec and preLoc from list in connList-type connParams

• Updated tests.examples.utils to allow for dynamic pathing

• Dropped python2 support

Bug fixes

• Better handling of exceptions in importCellParams() (incl. h.load_file() - issue 782)

• Pandas deprecated parameter fix

• Fixed pointer id overflow on MPI (e.g. for gap junctions)

• preSec and preLoc are no longer lost for inverse pointer connection

• Fixed crash due to use of matplotlib.TextArea deprecated param (credit: Christian O'Reilly)

• syncLines in rasterPlot restored

• Fixed a bug in gatherDataFromFiles() where cellGids for node 0 were lost

• Fixed generating rhythmic spiking pattern with 'uniform' option

• Fixed misleading console output when cfg.recordStims is On

• The colors in CSD plots are now properly aligned vertically with the CSD time-series overlays (credit: Sam Neymotin)

• Update mkdir to makedirs (credit: Jacob Sprouse)

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