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)

v1.0.0.2

Release for use with GUI

New features

• Added guiBlack and guiWhite themes, streamlined theming

• Updated iplots to avoid Bokeh deprecation

v1.0.0.1

Updated iplots to avoid Bokeh deprecation

v1.0.0

Version 1.0.0

New features

• Added wrapper for distributed saving; can now simply replace 'sim.gatherData()' with 'sim.gatherDataFromNodes()'

• Added distributed saving/loading ability (save/load data by MPI node)

• Allowed to specify 'cellModel' and point neuron params in netParams.cellParams (not only in netParams.popParams)

• Added cellsVisualizationSpacingMultiplier property to netParams

• Improved Granger plot, renamed it plotGranger

• Added interactive Granger plot (iplotGranger)

• Implemented testing in GitHub Actions with pytest (thanks Daniel!)

• Improved sim.clearAll such that it works even before a sim is run

• Properly formatted all module docstrings

Bug fixes

• Fixed bug in TupleToStr function

• Fixed broken links in tutorials

• Bokeh update required changing options from None to 'auto'

v0.9.9.1

Bug fixes

• Fixed gathering of dipoles when running on multiple cores (uncommented lines that had been commented for debugging)

v0.9.9

New features

• Plot current source density (CSD) from local field potential (LFP) simulated data

• Additional customization of 3D shape plot: show voltage as color, change proportions, include axis labels

• Enable modifyConns based on properties of presynaptic neurons

• Replaced -np with -n so compatible for all commands: mpiexec/mpirun/srun

• Updated netrxd.py and network.py to include RxD's Parameter class, naming of States and Regions, and specification of Region geometries that do not require arguments like 'membrane' and 'inside'

• Improved recordTraces such that the cond 'gid' can accept a list of numbers as well as a single number

• Added a new tutorial going through use of NetPyNE with virtual environments and Jupyter notebooks

• Added cfg.use_fast_imem to enable recording membrane voltage via seg.i_membrane_

• Added swc import ability to importCell (and thus importCellParams)

• Batch now polls processes, prints their output and terminates them once completed

• Updated web documentation to explain importing SWC files and add Recording Configuration section

• Added link to Jupyter notebook tutorial and video to website front page

Bug fixes

• Made rate_b be positional instead of keyword argument in rxd multiCompartmentReaction

• Check if _morphSegCoords exists in population before using

• Fixed bug to avoid recursive creating of synMechs when loading with cfg.oneSynPerNetcon=True

• Fixed an issue with running rxd code twice

• Wait until all subprocesses have ended before completing mpi_bulletin batches

• Fixed repeated rxd simulation issue for rates and reactions

• Fixed pointNeuron spikePattern 'sync' option

v0.9.8

Version 0.9.8

New features

• analysis.plotLFP can now be applied to external data

• Evolutionary and Optuna optimization can now read results from .pkl files

• Enabled recording of stimulus variables (e.g. SEClamp i)

• Added options in load func to avoid instantiating cells, conns, stims and/or rxd

• Analysis and plotting of rate vs current (f-I) curve for single cell tuning

• Recording and plotting of current dipoles in arbitrary subset of populations

• Added option to plot LFP spectrogram with log y-axis

• Added option to plot the log of connectivity in plotConn

• Enabled random distribution of multiple synapses with synsPerConn>1 and connRandomSecFromList=True

• Added lineWidth option to plot2Dnet (thanks Eric!)

• Updated Travis Continuous Integration to use NEURON 7.8.1 (from 7.6.2)

• Removed trailing white space from all Python files in the repository

Bug fixes

• Fixed bug when using index with recordTraces

• Fixed axes values in plotRxDConcentration and iplotRxDConcentration

• Added links to necessary mod files in the importing cell models tutorial

• Added aux_fun.inc to doc/source/code/mod as it's needed for some examples

• Blocked terminal output from Git when no repository is found (i.e. with pip install netpyne)

• Avoid adding section-based weightNorm values to point neurons (was affecting tut_import.py)

• Prevent error when loading pointCell params from json by converting Dict to dict

• Fixed bug in plotShape (thanks Eric!)

• Updated setup.py so PyPI website renders the README as markdown

• Fixed expected numSpikes in test of M1detailed example

• Merged GUI branch into development branch

• Fixed bug in iplotConn

• Fixed bug and coloring in iplotSpikeStats with different themes

v0.9.7

Version 0.9.7

New features

• Added optimization using Optuna (optuna.org)

• Simplified cellParams to use dict key as 'cellType' and make 'conds' optional

• Added netParams method addCellParamsTemplate() to create predefined cell templates

• Calculation of population avg rates now accepts multiple time intervals

• Optional index argument to record from synMech

• Added scale bar location option to plotTraces scalebar

• Added evolutionary optimization for cell

• Added support for reading pkl files in evol batches

• Added plotfI func to netpyne

• Added calculation of fI to gather.py

• Added module imports to netpyne import

• Added adaptive stochastic descent (ASD)

• Added ability to set theme and palette for iplots

• Added netParams method addCellParamsTemplate() to create predefined cell templates

• Added sizing-mode to iplots

• Added Bokeh to NetPyNE requirements

• Added theme for gui to analysis/utils, iplots can now use custom theme

• Added t variable to plotLFP output data

• Cleaned up plotRxD, added saving, added plot options, scalebar

• Added interactive plot: iplotRxDConcentration

• Added interactive plot: iplot2Dnet

• Added interactive plot: iplotRatePSD

• Added interactive plot: iplotSpikeStats

• Cleaned up iplotLFP and improved color-handling with themes

Documentation improvements

• Updated and tested online tutorials

• Changed all triple single-quoted docstrings to triple double-quoted

• Improved many docstrings

• Created a complete package index (http://netpyne.org/package_index.html) which is automatically generated from the human-readable docstrings in the codebase

• Documented the process to release a new version and automated the html building process

• Removed old unused Makefile for docs

Bug fixes

• Fixed bug importing cells (avoid reading docstring)

• Fixed bug when recording LFP with recordStep <1.0ms

• Fixed net_lfp.py example

• Fixed bug in plotSpikeStats

• Fixed bug in plotSpikeHist

• Fixed bugs in plotTraces scalebar

• Fixed travis test issues

• Fixed tut3 travis issue

• Fixed bug in spikes.py

• Fixed bug in plotRaster

• Fix minor bug in iplotRaster()

• Fixed problems with NeuroML

v0.9.6

Version 0.9.6

• Added useful hover information to iplots

• Improvements to iplotTraces

• Added interactive plot for connectivity (iplotConn)

• Added 'dynamicRates' option for NetStim populations

• Added option to have a uniform distribution of rates for Vecstim pulses

• Added function for distributed saving at intervals

• Added issue templates for GitHub

• Overhaul of contribution guide (CONTRIBUTING.md)

• Improved documentation

• Fixed bugs and improved exception handling in plotConn

• Fixed loadSave V1 example model

• Fixed bug calculating popRates when no spikes

• Fixed bug in _distributeSynsUniformly()

• Fixed bug in saveCellParamsRule()

• Fixed bug in batch.py: initCfg params were not being updated for evol optim

• Fixed bug in subconn.py: missing initialization of newWeightNorm

• Fixed bug in run.py: print run time with 2 significant figures

• Fixed output stat filenames of evolutionary optim: .cvs to .csv

• Fixed bug in interval saving

• Fixed bug in spikes.py in plotSpikeStats

v0.9.5

Version 0.9.5

• Print start and end date/time

• Avoid removing batch folder so can rerun and complete batch simulations

• Added loadBalance option to print individual node computer times

• Initialize hoc events recursivley to reduce event queue overhead

• Added plotRateSpectrogram analysis function

• Added option to save at intervals

• Fixed bug: wrong indentation for initializing fixedInterval in batch.py

• Fixed bug in _distributeSynsUniformly function

• Fixed bug in subConnParams grouped synapses

• Fixed bug in analysis.granger figure save name

• Fixed bug in printRunTime function