v0.7.7

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

v0.7.6

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

v0.7.5

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

v0.7.4

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()

v0.7.3

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'

v0.7.2

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

v0.7.1

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)

v0.7.0

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

v0.6.9

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

v0.6.8

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)