Netpyne

- 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

- 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

- 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

- 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

- 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()

- 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'