added LogBatch class

added isPickable function. corrected install_requires list in setup file.

added gaussian function to utils.

updated README (added instructions for git-lfs install)

added copy method to all model classes. added TI US notebook. updated…

adapted simAndSave function to work also with source-based titration cases.

changed erroneous calls to parseAmp to parseAmplitude in parsers module

replaced erroneous "return NotImplementedError" statements by "raise…

renamed ElectricDrive A to I

correctd mismatch in ElectricDrive

introduced properties in classes of drives and protocols modules.

added xkey property to XDrive class and Arange property to pneuron and nbls…

Created Drive objects inheritance scheme (now used in all model classes).

corrected docstring errors in pneuron Cm0 and Qm0

added FH fs lookups

Initialized LFS. deleted lookup files from neuron folder.

added lookups files in separate lookups folder using LFS.

Created AcousticSource class to be used for US simulations.

added sundt fs lookups. adapted RS fs lookups. adapted nbls.getLookup2D method…

Modified Lookup class (new properties, corrected methods).

added interp_method Lookup attribute to enable choice of lookup interpolation…

added DQ_LOOKUP constant (used in run_lookups.py)

added toDict, toJson, fromDict and fromJson methods to Lookup class.

added membrane area attributes to IB and STN neurons

improved modularity of TestBase class

Automated getModel using automatically generated dictionary of models with…

removed plotVarQSSDynamics function from QSS and plot_QSS

Merge branch 'master' of https://c4science.ch/diffusion/4670/pysonic

updated STN neuron notebook with correct model parameters and enabled…

added boundDataframe method to postpro module

re-ran and completed STN notebook

updated README with instructions on how to cite.

changed Lookup repr method. added test_lkp test file.

corrected nbls fullDerivatives, simFull and simHybrid methods (removed phi…

added threshold module with isolated threshold function (now used for all…

mofified SPIKE_MIN_QAMP and SPIKE_MIN_VAMP from 5 (nC/cm2 - mV) to 3

added sundt lookups

commented useless parameters in Sundt class

moved pushbullet key file to package root

added internal bls.simUntilConvergence method (without decorators) to enable…

added Eleak logging upon Sundt class creation.

cleaned up Sundt class

corrected borg-graham formalism methods

corrected Astim factor error in pneuron desc. added extra parsing methods

added qss_vars and pulse-avg run options to nbls simSonic method.

implemented GenericPlot.wraptitle method

updated titrations log

moved model.simAndSave to utils to facilitate use in ExSONIC

moved filecode function to utils

Major update:

added equality operators to TimeProtocol and PulsedProtocol classes.

improved filecodes generation from meta dictionary in Model.filecode

created Timeprotocol and PulsedProtocol classes, now used in pneuron, nbls and…

checked iM taup against ref. (Yamada 1989)

added PointNeuron alphaBorgGaham and betaBorgGraham methods, now used for sundt…

renamed PhaseDiagram to SpikePlot (more appropriate). simplified Sundt model…

modified nbls.QSSderivatives and nbls.__simQSS to work with any specified…

renamed iKm to iM and kmk gate to p in Sundt to match formalism ot Cortical…

parametrized Caiinf in sundt model (checked for correct equivalence at Vm0)

corrected error in effvars for plotGatingKinetics

corrected Ikd kinetics (n and l zeta signs matching those of Borg-Graham 1991…

debugged sundt class (estim now running)

added time step reduction to sundt class. code is running but simulations and…

further corrections to the sundt class, and implementation of Eleak computation…

identified parameters in Sundt expressions and highlighted discrepancies with…

modified README

Merge branch 'master' of https://c4science.ch/diffusion/4670/pysonic

corrected errors in sundt class (now compiling). minf and taum both seem off…

added sundt import to neurons. corrected pushbullet requirement in setup

added Lookup.tile and modified SmartLookup.projectDC. modified nbls.

defined Lookup algorihtmic operators. defined OnOffSimulator class. defined…

commented out numdifftools import. updated README.md

corrected addThresholdCurve. updated astim_titrations.log with latest batch

updated ActivationMap (removed correctAmp method). corrected TimeSeriesPlot.

changed TimeSeriesPlot.addLegend from static method to instance method

corrected unwanted changes to sublime-project file

added rotAroundPoint2D function to utils

added nan return in pow2Search if x > xmax. added getPow10 to utils

changed log level for logCache found entry

added fillLine function to utils. added Parser.addOverwrite method (opposite of…

added method type in nbls.simulate logging

corrected tirations log file

in PWSimulator.compute: added division of offset interval in several slices if…

abstracted Model.simQueue method (now defined in children classes). changed…

changed outputdir to keyword argument in queue items in Model.checkOutputDir…

add handling of positional and keyword arguments in Batch queues. added…

added Parser.addCheckForOutput method, now used in run_*** scripts to…

replaced hypersampling error by warning message PWSimulator.downsample

updated titrations log

Merge branch 'master' of https://c4science.ch/diffusion/4670/pysonic

added vsteprange to VlcampParser. changed timeseries default onset from…

re-computed lookups of FH, FS, IB, LTS, RE, RS, STN and TC neurons

Merge branch 'master' of https://c4science.ch/diffusion/4670/pointnice

implemmented inheritance scheme for PointNeuron.chooseTimeStep method

added sweeney neuron lookups

corrected SweeneyNode alpham equation according to Basser and Roth, 1991.

added prependDataframe method to postpro module.

renamed Simulator.resample method to downsample in order to avoid confusion…

corrected minor issues in spike detection functions (dt bounding for resampling…

modified find_tpeaks to work with irregular time vectors.