VERSION RELEASES

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salvadord
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VERSION RELEASES

Post by salvadord » Fri Jun 09, 2017 10:41 pm

NetPyNE releases will be published in this topic

salvadord
Posts: 57
Joined: Tue Aug 18, 2015 3:49 pm

Version 0.7.0

Post by salvadord » Fri Jun 09, 2017 10:41 pm

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. Also, the 'gauss()' method used in string-based functions should be replaced with 'normal()'.

- 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

ted
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Re: VERSION RELEASES

Post by ted » Wed Jun 14, 2017 10:39 am

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 value
Is it technically not feasible to offer backward compatibility as an option? Without that, how can model developers (let alone participants in NetPyNE development) verify correctness from one version of their own models (or of NetPyNE itself) to the next?

salvadord
Posts: 57
Joined: Tue Aug 18, 2015 3:49 pm

Re: VERSION RELEASES

Post by salvadord » Wed Jun 14, 2017 11:08 am

This applies only to version 0.7.0. We understand this is a big issue and we will avoid it in the future; however, we are still at a relatively early stage of development and this change was necessary to ensure proper randomization of multiple features.

Please also note that all previous versions were backward compatible with the preceding ones; and all new versions from now onwards will be backward compatible down to 0.7.0.

salvadord
Posts: 57
Joined: Tue Aug 18, 2015 3:49 pm

Version 0.7.1

Post by salvadord » Sat Jul 08, 2017 3:03 pm

# Version 0.7.1
https://github.com/Neurosim-lab/netpyne ... tag/v0.7.1

- 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)

salvadord
Posts: 57
Joined: Tue Aug 18, 2015 3:49 pm

Re: VERSION RELEASES

Post by salvadord » Mon Aug 14, 2017 11:29 am

Version 0.7.2

https://github.com/Neurosim-lab/netpyne ... tag/v0.7.2

- 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

salvadord
Posts: 57
Joined: Tue Aug 18, 2015 3:49 pm

Re: VERSION RELEASES

Post by salvadord » Wed Aug 30, 2017 8:18 pm

Version 0.7.3

https://github.com/Neurosim-lab/netpyne ... tag/v0.7.3

- 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'

salvadord
Posts: 57
Joined: Tue Aug 18, 2015 3:49 pm

Re: VERSION RELEASES

Post by salvadord » Thu Oct 05, 2017 6:20 pm

# Version 0.7.4

https://github.com/Neurosim-lab/netpyne ... tag/v0.7.4

- 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()

salvadord
Posts: 57
Joined: Tue Aug 18, 2015 3:49 pm

Re: VERSION RELEASES

Post by salvadord » Sun Dec 03, 2017 3:17 pm

# Version 0.7.5

https://github.com/Neurosim-lab/netpyne ... tag/v0.7.5

- 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

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