Skip to content

Latest commit

 

History

History
1443 lines (708 loc) · 45.3 KB

CHANGES.md

File metadata and controls

1443 lines (708 loc) · 45.3 KB
Raw

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)

Bug fixes

  • Fixed bug in TupleToStr function

Version 0.9.9.1

Bug fixes

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

Version 0.9.9

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

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

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

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

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

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

Version 0.9.3.1

  • Replaced deprecated imp module with importlib

  • Fix to cellsGrid cell locations with normRange

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

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

  • Added option cfg.distributeSynsUniformly to locate synapses at uniformly across section list; if false, place one syn per section in section list

  • 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

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 NetPyNE-UI)

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

Version 0.9.0

  • 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.

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

Version 0.7.8

  • 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

Version 0.7.7

  • Added LFP recording at arbitrary 3D locations

  • Added plotting of LFP time series, PSD, freq vs time and electrode locations

  • Updates to NeuroML conversion code.

  • ShapePlot now shows segment diameters as linewidths (Python version)

  • Added function to add 3D points (in NEURON+Python) from stylized geometry

  • Connection sec and loc randomly chosen from list when synsPerConn=1

  • Set default NetStim noise to 0.0

  • Fix synMech overwrite when importing multiple hoc/py cell templates

  • Fixed bug importing multiple synMechs from hoc/py cell template

  • Fixed bug using 'variable' NetStim (NSLOC)

  • Fixed save method in NetParams to use ['net']['params']

  • Fixed bug using gap junctions with mpi (multiple cores)

  • Fixed bug when creating conns afger loading json -- needed basestring instead of str

  • Fixed bug when loading json with include format ('pop', 1) -- converted to list so added exception

  • Fixed bug saving to .mat during batch sims

  • Fixed bug in order of unique cell gids in analysis funcs 'include' param

  • Fixed bug gathering data using the cfg.gatherSimOnlyData option

  • Fixed bug where empty sections where created when recording from non-existing sections

Version 0.7.6

  • Added option to order raster spike trains by multipe tags (eg. ['pop', 'y'])

  • Enable providing a 2D list of spike times to VecStim populations

  • Added exception handling to analysis functions

  • Updated saveLoadV1 examples to use compactConnFormat=True and saveCellSecs=False

  • Added cfg.rand123GlobalIndex to set global index used by all instances of the Random123 instances of Random

  • plotTraces now plots any recorded cells if 'include' is None

  • Made CVode object part of sim and simplified cvode calls

  • Added sim.rename() wrapper function

  • Added rename() method to dict class

  • Fixed bug loading from compactConnFormat

  • Fixed bug in IClamp: 'delay' -> 'del'

  • Fixed bug calculating min convergece and divergence

  • Fixed bug in plotRatePSD colors

Version 0.7.5

  • Improved NeuroML conversion support

  • Make cfg.checkErrors = True by default, but set to False if using multiple cores or batch

  • Added methods to rename netParams dict keys in a nested format (needed for GUI)

  • Added analysis.plotSpikeStats() func to plot stats of cell rates, ISI CVs and synchronies

  • Added analysis.calculateRate() func to calculate avg and peak rate of pop subset at time range

  • Added analysis.plotRates() func to plot avg and peak rate of different pop subsets at time range

  • Added option to include list of pops or cells in 'include' arguments e.g. include=[['E4','E2'], [1,3]]

  • Added cfg.compactConnFormat option to replace conns dict format with compact list format

  • Added option to plotConn() and plot2Dnet() to load data from compact format json files

  • Adapted python2 code so conversion to python3 via 2to3 command works straight away

  • Added 'instantiate' argument to sim.load function

  • Added 'dpi' argument to analysis.plotSpikeHist()

  • Replaced init()/h.stdinit() with finitialize() so h.v_init and h.dt get set properly

  • Removed call to h.stdrun() but made v_init a global in cfg.hParams and initialized h.tstop to cfg.duration

  • Fixed bug setting globals that don't exist

  • Fixed issue setting global variables when loading from json

  • Fixed issue to make convergence+divergence connections randomization more robust and efficient (issue #254)

  • Fixed bug in colors of plotSpikeHist

  • Fixed bug in replaceDictODict() that lead to wrong results when importing cells

  • Fixed bug when using sim.gatherOnlySimData

  • Fixed bugs in saveLoadV1 example

  • Fixed bug when generating subConn with createNEURONObj=False

Version 0.7.4

  • Added polarity param to analysis.plotEPSPAmp()

  • Added sim.gitChangeset() function and store netpyne_changeset in every output file

  • Added function ijsonLoad() to load faster and save tags conns to json

  • Fixed bug in convergence and divergence connectivity -- now fixed number and no self conns

  • Fixed bug by converting tuples to strings when saving Matlab; now converts to lists

  • Fixed bug use int as argument to np.full in fixedInterval variable

  • Fixed bug that removed previously existing element from path during importCellParams()

Version 0.7.3

  • Option to create section lists based on y displacement from soma (addCellParamsSecList)

  • Converted popParams, cellParams etc to object of their own class and added method to set param

  • Added 'disynapticBias' option to increase probability of B->C conns if A->B and A->C exist

  • Added function analysis.calculateDisynaptic() to count number of disynaptic conns (A->B, B->C and A->C)

  • Added 1 second between batch job submission to avoid saturating scheduler

  • Fixed bug: init randomizer so params with string-based random func are independent of cores

  • Fixed bug for newer pyplot versions: replace 'linewidths' with 'lw'

Version 0.7.2

  • Improved NeuroML importing/exporting

  • Added error checking for simConfig

  • Added popColors option to plotSpikeHist and plotRatePSD

  • Added support to load params, cfg, net and simData from .mat files

  • Made root section (with no parents) the source of spikes by default (issue #246)

  • Added option to set initial cfg in batch sims

  • Added option to set grouped params in Batch constructor

  • Added option to not record time (to reduce output file size)

  • Fixed bug: synMechFraction had no effect; replaced with synMechWeightFactor

  • Fixed bug in modifyStims for NetStim 'interval' and 'rate'

  • Fixed bug importing cell -- use h.pop_section() to avoid stack overflow

  • Fixed bug when adding stim NetStim where sec is a list

  • Fixed bug when adding stim NetStim with multiple synMechs and synsPerConn>1

Version 0.7.1

  • Updates and bug fixes of NeuroML importer/exporter

  • Added missing error checks and made error messages clearer

  • Added warning when point process mechanism (eg. VecStim) required for pop is not found

  • Added 'ylim' option to plotTraces

  • Changed 'postGid' to 'gid' in conditions of recordTraces

  • Fixed bug: threshold in conns has no effect, have to use presyn cell threshold (issue #235)

  • Fixed bug: avoid saving 't' multiple times when using multiple nodes

  • Fixed bug: removed 'propList' param in list - was replaced by 'label'

  • Fixed bug distributing cells of population with cellList (issue #235)

  • Fixed bug saving to .mat: removed h.Random object from each pop

  • Fixed bug: check if checkErrors exists in cfg before checking value

  • Fixed bug importing multiple hoc cells consecutively (removed from memory properly)

Version 0.7.0

IMPORTANT NOTE: NO BACKWARD REPRODUCIBILITY -- due to improvements in the random number generators it won't be possible to reproduce results of previous versions that required random values, e.g. random spike streams, connections or cell locations.

  • Replaced python random package methods with more robust h.Random() methods (no backward reproducibility)

  • Added netParams error checking (BETA version: set cfg.checkErrors = True to test)

  • Enabled use of VecStim spkTimes pops with individual list of cells

  • Replaced 'pop' with 'popLabel' (added fix for backward compatibility) (issue #213)

  • Can now add arbitrary set of spike times to VecStim pop

  • Dict with popColors can be passed to plotRaster() and plot2Dnet()

  • Added analysis.plotEPSPAmp()

  • readCmdLineArgs() now accepts default paths for cfg and netParams

  • Added option to customize command in batch hpc runs (e.g. 'mpirun' vs 'ibrun')

  • Added dpi param to plotRaster()

  • Added recording of h.t to simData

  • Replaced ions 'init_ext_conc' and 'init_int_conc' with 'o' and 'i' (issue #151)

  • Replaced 'globs' with 'globals'

  • Fixed bug in import of ion concentrations

  • Fixed bug in title of plotTraces()

  • Fixed bug when setting wrong num of weights or locs for synsPerConn>1

  • Fixed bug: subConn rules now update weight if different weightNorm

  • Fixed bug: missing call to noiseFromRandom() for NetStims

  • Fixed bug setting pop density with absoulute location ranges

  • Fixed missing NeuroML message so only appears in master node

  • Fixed bug in plotConn

  • Fixed bug - stimTargetParams now accepts a list of secs for 'sec' param

Version 0.6.9

  • Improved support for NeuroML export

  • Added option to skip batch job based on custom existing job filename (eg. 'skipCustom': '.run')

  • Added option to specify netParams .py file for batch

  • Modified hpc_torque batch to accept nodes and ppn

  • New option to import cell with sections not inside an object

  • plotShape now shows real diameters in interviews by default

  • Added option to set threshold when loading weightNorm

  • Added support for conditions on recordTraces

  • Fixed bug plotting NetStims (created as stims) in raster, spikeHist and ratePSD

  • Fixed bug in plotConn bar graphs

  • Fixed bug: missing hRandom for NetStim populations

  • Fixed bug: use Random123() instead of netstim.noiseFromRandom for NetStim stims

  • Fixed bug: VectStim spike generation now reproducible for different durations

  • Fixed bug in batch grouped params

  • Fixed bug: getCellsList() only checked for tuples but when load from json converted to list

  • Fixed bug so cell treshold is set by default to sim.net.defaultThreshold

  • Fixed bug plotting overlayed spikeHist over raster plot

  • Fixed bug in plotShape when includeAxon=False

Version 0.6.8

  • Keep track of last host after distributing cells of each pop (improves load balance) (issues #41 #196)

  • Added option to run batch on HPC SLURM system (eg. SDSC Comet)

  • Added cvode_atol option to cfg

  • Improved plotShape() to use matplotlib and use colormap to show num syns

  • Batch params can now have an arbitrary number of levels in structure (eg. dict of list of dicts etc)

  • Batch params can now be grouped ('group':True) so values vary together not combinatorally

  • Removed pc.done() at the end of Batch.run() method so can run multiple batches from same script

  • Added skipCfg option to batch

  • Added cfg.saveCellSecs option to reduce save time and file size (secs available via netParams)

  • Added cfg.saveCellConns option to reduce save time and file size

  • Modified code so 'cellModel' tag is optional

  • Added renameCellParamsSec() method to netParams class

  • When importing cell global 'v_init' is stored as param for each section

  • Fixed small bugs when loading saved model

  • Fixed bug when calling internal method _findPrePostCellsCondition()

  • Fixed bug in subcellConn groupedSynMechs

  • Fixed bug in subcellConn trying to add stims+conns to NetStims/VecStims

  • Fixed bug in subcellConn so syns are not placed at loc 0.0 or 1.0 (error if syn uses ion)

Version 0.6.7

  • Added gridSpacing option to create populations with cells placed in grid with fixed spacing

  • Added netParams functions: addCellParamsWeightNorm(), saveCellParamsRule() and loadCellParamsRule()

  • Added option to importCell based on instantiated cell (not just template or class)

  • Modified importCellParams to store mod mechanism global variables in cellRule['globals']

  • Added support to export gap junctions to NeuroML

  • Fixed bug during import that set section name to 'soma' if only 1 section

Version 0.6.6

  • Batch parameters can now include list or dict items

  • Added 'weightNorm' param to sections so can normalize weight based on dendritic location

  • Import cell function now has somaAtOrigin option to place the cell soma at coords 0,0,0

  • Go back to using NetStim.noiseFromRandom, since noiseFromRandom123() only available in very recent versions

  • Fixed bug in saveData option of figure plots

  • Fixed bug passing figSize param to figures

  • Fixed bug where gid only updated if cellParam rules were applied to the cell

  • Fixed bug in importCell by deleting imported modules from sys.modules

  • Fixed bug that prevented NetStim random noise generator from being initialized

Version 0.6.5

  • Added support for artificial cells (without sections) (issue #44)

  • A single NetStim (within a population) can now be connected to multiple cells (issue #113)

  • VecStim populations use same params as NetStims and allows for pulses at arbitrary times with different rates

  • NetStim and VecStim population allow for a uniformly distributed rates in the form [min,max]

  • Added option to run batch sims via mpi and bulletin board (master/slave) (issue #108)

  • netParams.shape paramter to select either 'cuboid', 'cylinder' or 'ellipsoid' network shape (issue #26)

  • analysis.plot2Dnet() 'view' param to select frontal ('xy') or top-down ('xz') view

  • analysis.plotConn() option to plot stacked bar graph, select different pre and post pops, synMech and syns vs conns

  • Made distinction between number of connections and synaptic contacts (eg. can have 5 synsPerConn)

  • New function netParams.addCellParamsSecList to create list of sections based on distance from soma

  • Removed 'plast' and 'shape' from conns when not used (issue #177)

  • Added option to center soma at origin when importing cell

  • Now using noiseFromRandom123() for NetStims() (issue #89)

  • Fixed bug in readCmdLineArgs()

  • Fixed bug in saveData option of figure plots

Version 0.6.4

  • Added analysis.nTE() function to calculate normalized transfer entropy (issue #42)

  • Added analysis.granger() function to calculate and plot Spectral Granger Causality (issue #42)

  • Added analysis.plotRatePSD() to plot firing rate power spectral density

  • Added analysis.plotShape() to plot 3D morphology of cell and synapse locations

  • Added option to fix soma depth for subcellular distributions based on 1d and 2d maps

  • Added support for gap junction (electrical synapse) connections

  • Improved import of multicompartmental cells from NeuroML2

  • Added option to turn off graphics by adding -nogui from command line

  • Added option to skip batch sims if output file already exists

  • Added option to overlay pop labels and show avg rates to plotRaster() (issue #111)

  • All section now include argument cell=self to differentiate them

  • Fixed travis script so checks all tuts and examples after each commit (issue #37)

  • Fixed bug positioning cells with 3d geom

  • Fixed bug in sim.clearAll by closing all figures instead of current (issue #168)

  • Fixed bug: cache_efficient was not being turned on

  • Fixed bug setting simConfig loaded from file

  • Fixed bug in plotRaster inverseOrder option

  • Fixed str vs basestring in analysis.py and simFuncs.py

  • Fixed bug due to not inserting ions in section

Version 0.6.3

  • Added cvode_active simConfig option to set variable time step (issue #116)

  • Added saving of avg pop rates

  • Added save method to SimConfig and NetParams class

  • Fixed bug importing 3d cell geometries

  • Fixed bug in readCmdLine func

  • Fixed bug reading from json (str vs unicode)

  • Fixed bug setting mech param values for nseg>1

Version 0.6.2

  • Added importing of cell ion parameters (eg. 'ena' or 'ek')

  • Added backupCfgFile (eg. ['cfg.py', 'backupcfg/']) to simConfig to copy cfg file after run

  • Added gatherOnlySimData to simConfig to gather only simulation data and not cells or pops

  • Added simLabel and saveFolder to simConfig (can be used instead of filename)

  • Added printRunTime to simConfig to print run time (in sec) during execution

  • Added printPopAvgRates to simConfig to print population avg firing rates after run

  • Automatic saving of netpyne and netParams version to file

  • Moved creation of fih functions to set cell vinit from setupRecording() to preRun()

  • Can now load netParams and simConfig from file without setting in sim

  • Added sim.readCmdLineArgs to read simConfig and netParams filepaths from command line

  • Can now access NEURON's h module via sim.h

  • Fixed bug so can load netParams and simConfig without initializing sim

  • Fixed bug that prevented mechanism properties with value 0.0 from being set

  • Fixed bug in code to distribute cells (converted numCells from float to int)

  • Fixe bug in plotTraces

Version 0.6.1

  • Added global boolean variable netpyne.gui to enable/disable graphics (issue #150)

  • Spike histogram fixes: axis labels only in 1st subplot, limit time range, tight_layout only if <5 subplots

  • Fixed bug so multiple traces figures are saved to separate files (issue #166)

  • Fixed bug when using point process-based cells that include synapses (eg. Izhi2007a)

  • Fixed bug where spike hist subplot didn't match raster axis

  • Fixed bug when loading data from file with multiple cores

  • Fixed bug so modify functions work with multiple cores

Version 0.6.0

  • Added option to shape conn weights dynamically to create temporal patterns (issue #33)

  • Store all params of synMechs exhaustively instead of by reference (issue #139)

  • Added netParams.importCellParamsFromNet() to import parameters of multiple cells from existing network (issue #154)

  • Added modifySynMechs function

  • Added option to record from all synMechs of a type (eg. 'AMPA')

  • Fixed bugs and improved efficiency of modify, modifyConns and modifyStims function

  • Fixed bug plotting traces

Version 0.5.9

  • Improved NeuroML2 import functions (issue #12)

  • Added support for homeostatic scaling synapse (requires self NetCon) (issue #141)

  • Added method to convert NetParams and SimConfig objects to dicts (issue #141)

  • Fixed NetParams and SimConfig constructors so arguments are converted to Dict/ODict (issue #141)

  • Added sim.loadBalance() func to calculate and print load balance information (issue #77)

Version 0.5.8

  • Fixed bug (introduced during debugging) that prevented random seeds from working properly

Version 0.5.7

  • Improved NeuroML import/export functions

  • Added option for cache_efficient (optimized load balance when many cores) (issue #77)

  • Added sim.clearAll() function to clear all objects in memory and avoid leaks

  • Cleared variables after gathering from multiple nodes to avoid memory leak

  • Separated common runSim() commands into preRun() (issue #83)

  • Fixed bugs in net.modifyStims() method

Version 0.5.6

  • Only load neuroml libraries and functions if installed to avoid error when importing sim

  • Disable subcellular connectivity since wasn't modifying the synMechs correctly.

Version 0.5.5

  • New example using Allen Institute cells showing how to save large net and reload for simulation

  • Improved export/import from/to NeuroML2 (issue #12)

  • All structures (including Dict and ODict) can now be saved and loaded via json

  • Added option to use separate simConfig when loading data from file

  • saveData() calls gatherData() if required

  • saveData() returns string with full path of saved file (issue #127)

  • Fixed bugs so its possible to create and save Python structure independently of NEURON objects

  • Fixed bug that created 2 instead of 1 NetStims per cell

  • Fixed bug regarding mutable default args in Python funcs

  • Fixed bug so NetStim stim params are set to default if missing

Version 0.5.4

  • Access to nested dictionaries via dot notation (secs.soma.geom) using new inherited classes Dict() and ODict() (issue #123)

  • 'hSection' replaced with 'hSec'

  • Added sim.popAvgRates() to calculate and optionally print population avg rates

  • Functions to modify cells, conns or stims also update sim.allCells (issue #59)

  • Fixed bug so can modify funcs now accept lists of strings (issue #59)

  • Fixed bug when recording traces of relative cell indices of populations across multiple nodes

Version 0.5.3

  • Functions to modify parameters of cells, conns and stims in an instantiated network (issue #59)

  • Added label of param rule used to create cells, conns and stims, so can modify later (issue #59)

  • Ordered sim.net.allCells by gid

  • Option to save figures with same name as data

  • Added support for VClamp list params (issue #32)

  • Fixed bug when creating pops consisiting of lists of cells

Version 0.5.2

  • Fixed bug that gave error since trying to import removed module default.py

Version 0.5.1

  • Easier and more consistent format for high-level specifications (issue #103):

    • replaced default.py with specs.py which defines classes NetParams and SimConfig

    • netParams and simConfig are now objects of class NetParams and SimConfig, respectively

    • Can use object methods to add params, eg. netParams.addPopParams(label, params)

    • All structures within netParams and simConfig are now OrderedDicts so can be referenced by label/key

    • If no label is assigned, then an increasing number is automatically used as label

    • Split netParams.stimParams into netParams.stimSourceParams and netParams.stimTargetParams (both OrderedDicts)

    • Simplified/clarified keys: 'conditions' -> 'conds', 'sections' -> 'secs', 'preTags' -> 'preConds', 'postTags' -> 'postConds'

    • Added netParams.importCellParams() to simplify

  • Added sim wrappers and modified names of existing ones to make consistent

  • Selectively save data to file: netParams, net, simConfig and/or simData (issue #30)

  • Added functions to load netParams, net, simConfig and/or simData from file (issue #30)

  • Added 'rerun' option to plotTraces()

  • Added function to get cell object by gid, sim.cellByGid(gid)

  • Fixed bug that was slowing down STDP by creating new h.Section() -- now uses existing.

  • Fixed bug so vinit gets set for all segments in a section.

  • Fixed bug related to readArgs() when running from IPYnotebook.

  • Fixed bug related to plasticity in cells with V not in section (eg. Izhi2007a)

Version 0.5.0

  • Added option 'dataSaveInclude' to select what data to save to file (issue #30)

  • Added sim.net.allPops which contains all cellGids of each when running on >1 nodes (issue #30)

  • Connectivity matrix can now be grouped by numeric tags in intervals (eg. cortical depth y in 50 um intervals) (issue #92)

  • Added support for all stims (VClamp, SEClamp, AlphaSynapse, etc) and can specify any of the stim params (amp, dur, delay,etc) as a function (eg. 'uniform(a,b)' or '2*post_ynorm') (issue #32)

  • Fixed bugs so plotRaster() is identical when running on >1 nodes, and is ordered by gid correctly

  • Fixed bug so can have multiple plot function calls even when one of them is False

Version 0.4.9

  • Modified format of simConfig analysis options to make it equivalent to calling analysis functions (issue #69)

  • Improved plotRaster() function to add customizable options (select cells, time range, order, overlay histogram, and others) (issue #39)

  • Improved plotTraces() function to add customizable options (select cells, time range, arrage by cell or trace, and others) (issue #39)

  • Improved plot2Dnet() function to add customizable options (select cells, show connections, and others) (issue #39)

  • Added spikeHist() function to plot spike histogram with customizable options (select cells, time range, bin size, and others) (issue #63)

  • Added plotConn() function to plot spike histogram with multiple customizable options (select cells, feature, order, and others) (issue #39)

  • Added option to save figure, save figure data, specify figure size, and show figure to all analysis/plotting functions (issue #39)

  • Fixed bug when generating function-based random probability values -- made random stream independent

  • Fixed bug when generating density-based random cell locations -- made random stream independent (issue #93)

Version 0.4.8

  • Removed framework and init modules, and consolidated in sim module (so just need: 'from netpyne import sim')

  • Added option to specify weight scale factor separately for each cell model, and for NetStims (issue #69)

  • Conn rules can now have list of synMechs (eg. [AMPA, NMDA]) and synMechWeightFactor (eg. [1.0, 0.1]) (issue #69)

  • Conn rules allow list of weights, delays and/or locs for each synMech in list (issue #69)

  • Conn rules allow synsPerConn and loc to be described functionally (at the cell connection level) (eg. 'uniform(5,2)') (issue #69)

  • Conn rules allow list of weights, delays, and/or locs when synsPerConn > 1 (issue #69)

  • Conn rules allow 2D list of weights, delays, and/or locs when have list of synMechs and synsPerConn > 1 (issue #69)

  • Conn rules allow list of sections or sectionList when synsPerConn > 1; synMechs distributed uniformly (loc list not allowed) (issue #69)

  • Extended fromList connectivity function so can also provide synapse locs (issue #69)

  • Added separate wrapper sim functions to create and simulate the network

  • Sim functions use simConfig and netParams from main as default (if not specified)

  • Connections between NetStims and cells are included in conn list (issue #69)

  • Fixed bug so can create Python and NEURON objects for connections independently (issue #69)

Version 0.4.7

  • Added option for random seeds for connectivity, stimulation, and cell locations (issue #49)

  • Added return pointers when create cells, pops, conns, stims, and recording (issue #48)

  • Renamed point process param labels: '_type' -> 'mod', '_loc' -> 'loc' (issue #24)

  • Added option to set h global variables (eg. celsius) (issue #31)

  • Fixed importCell() so h global variables reset after importing (issue #31)

  • Fixed importCell() so synapses stored in synMechParams (issue #25)

  • Fixed bug when pop names contained same subset of characters (issue #40)

Version 0.4.6

  • Preliminary version of exporter to NeuroML2

  • Added fromList connectivity function

  • Added new dict 'stimParams' with support for IClamps

  • Added 'start' param to NetStim populations

  • Modified izhi2007 'u' starting value to be 0 instead of 0.2

  • Modified izhi2007 'C' value and the section properties so that synaptic weights match HH

  • Renamed NMDA synapses to AMPA

  • Fixed bugs in tuts

Version 0.4.5

  • Fixed bug saving to JSON on single node

  • Fixed plotting traces from using 'all' cells option

Version 0.4.4

  • Fixed bug when plottinc synMech traces

  • Renamed 'pos' with 'loc' in recordTraces list

Version 0.4.3

  • Fixed bug in runSimWithIntervalFunc

  • Variable Netstims (NSLOCs) can now have noise > 0

Version 0.4.2

  • Placed show(block=False) in try except block since not supported by some graphic backends

  • Create parallel context before re-creating net to avoid seg fault

  • Removed unnecessary modules in analysis.py

  • Only call show() in analysis if some figure to show

Version 0.4.1

  • Fixed bug when distributing cells spatially based on xRange,yRange,zRange pop parameters

  • Added axis labels to 2D visualization, and now works when running on multiple nodes too

  • Reset Netstim random generators within runSim() so have reproducible results if working interactively

Version 0.4.0

  • Fixed bug when distributing cells spatially based on normRange pop parameter

  • Fixed bug in functional connectivity variables post_xnorm, post_ynorm, post_znorm

  • Reversed ynorm based raster so higher y values are shown at the bottom (cortical-like)

  • Added option to plot sync lines in raster and show sync measure

  • Added 2D visualization of network cells and conns

  • Fixed randomization of cell positions by adding lastGid

Version 0.3.9

  • Made synMech params independent of cell and referenced by labels (similar to NeuroML)

  • Keep Neuron objects after sim so can explore, modify and/or rerun sim.

  • Only gather data via py_alltoall if running on more than 1 node

Version 0.3.8

  • Fix recording of single cell of population when using MPI

  • Fixed raster plotting based on NCD when using MPI

  • Replaced save as .txt format with save as .csv

  • Fixed bug when importing distributed mechanisms of cells

  • importCell can use either *args or **kwargs

  • Fixed bug in secLists implementation

  • Removed mpl_toolkits.mplot3d import (unused and produced error in some Mac OS versions)

Version 0.3.7

  • Made conn functions more efficient using gid2lid and lid2gid

  • Replaced 'syn' (synapse) with 'synMech' (synaptic mechanism) to avoid confusion with synaptic connections

Version 0.3.6

  • Fixed bug: STDP objects need to be stored so it works.

  • Added support for SectionLists (modified format of importCell so also works)

  • Fixed bugs: function-based connectivity

Version 0.3.5

  • Fixed bugs: not checking connectivity rule conditions properly

  • Fixed bug: number of connections depended on number of nodes

Version 0.3.4

  • Added option to add STDP plasticity and RL to connections

  • Added option to run function at intervals during simulation, e.g. to interface with external program (such as virtual arm)

Version 0.3.3

  • Moved plot legend outside of plot area

  • Changed order of raster population colors to make separation clearer

  • Added option to select what cells to record/plot from separately; using new format with cells/pops in single list.

Version 0.3.2

  • Fixed bug: convergence connectivity produced error if used numeric value

Version 0.3.1

  • Added option to show and/or save to file the timing of initialization, cell creation, connection creation, setup recording, simulation run, data gathering, plotting, and saving.

  • Fixed bug: h.dt now set to value of simConfig.dt

Version 0.3

First version that was uploaded to pypi. Includes following features:

  • Clear separation (modularization) of parameter specifications, network instantiation and NEURON simulation code.

  • Easy-to-use, standardized, flexible, extensible and NEURON-independent format to specify parameters:

    • Populations
    • Cell property rules
    • Connectivity rules
    • Simulation configuration

  • Support for cell location (eg. cortical depth) dependence of cell density and connectivity.

  • Easy specification, importing and swapping of cell models (eg. point neuron vs multicompartment)

  • Support for hybrid networks eg. combining point and multicompartment neurons.

  • Multiple connectivity functions (eg. full, convergent, probabilistic) with optional parameters (eg. delay range)

  • Support for user-defined connectivity functions.

  • Populations, cell properties and connectivity rules can include reference to annotations (eg. for provenance).

  • NEURON-independent instantiation of network (all cells, connections, ...) using Python objects and containers.

  • NEURON-specific instantiation of network ready for simulation.

  • Enables sharing of Python-based network objects, which can then be instantiated and simulated in NEURON.

  • Easy MPI parallel simulation of network, including cell distribution across nodes an gathering of data from all nodes.

  • Analysis and visualization of network (eg. connecitivity matrix) and simulation output (eg. voltage traces, raster plot)

  • Data exporting/sharing to several formats (pickle, Matlab, JSON, HDF5) of the following:

    • Parameters/specifications
    • Instantiated networks
    • Simulation results