Netpyne

- 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

- 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)

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

- 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

- 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)

- 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