Releases: suny-downstate-medical-center/netpyne
Releases · suny-downstate-medical-center/netpyne
v0.6.7
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['globs']
- Added support to export gap junctions to NeuroML
- Fixed bug during import that set section name to 'soma' if only 1 section
v0.6.6
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
v0.6.5
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
v0.6.4
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
v0.6.3
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
v0.6.2
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
v0.6.1
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
v0.6.0
- 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
v0.5.9
- 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)