expanded charge range for pneuron.getLookup

updated notebooks

added sweeney lookups

updated SPIKE_MIN_VAMP to allow robust spike detection for sweeney model

parametrised Qm plot range to be neuron-specific. Solved issue with pbar update.

corrected crucial error in nbls.spatialAverage method. corrected Cm0 and Qm0…

adapted test_sims (avoiding sweeney neuron)

added sweeney lookups (ASTIM not working yet). added fixLookup to remove single…

remoed sweeney lookups (need to figure out the reason for weird profiles first).

implemented SweeneyNode class. added PointNeuron.chooseTimeStep method to…

adapted constants to enable sweeney lookups creation.

implemented pow2Search function using an incremental power of 2 search to…

added getCommonLabel method to ComparativePlot (now used to determine figure…

corrected minor mistake in getCommonLabel

harmonized peaks/spikes detection process across the package.

added figtitle and getModel as GenericPlot methods

removed paper figures folder (now in separate repo)

added iCap to plot variables. added colormap option for comparative plots even…

added VoltageClamp class with associated script and parser

corrected minor issues in timeseries

added automatic solution prepending to all simulate methods (to treat initial…

added plot_intensity_vs_amplitude.py script

fixed error in bls.filecodes

test commit.

updated README to latest changes.

set simFull, simHybrid and simSonic as private nbls methods

corrected error in getSimThresholdAmps (added default fs to 1)

corrected error in Model logNSpikes, checkTitrate and simAndSave methods.

improved QSS fixed points color labeling

interoduced derivative function to compute numerical derivatives with various…

added saddle point classification to QSS analysis.

removed all static quasiSteadyStates definition in neuron classes.

adapted findModifiedEq to work with iterables as inputs

replaced createLookupLambda by createClassLambda that can take various lambda…

added findModifiedEq function to utils, using brentq to find a new equilibrium…

modified TC neuron steadyStates method.

transformed pneuron qsState and quasiSteadyStates methods to return lambda…

cleaned up nbls

re-added file caching for QSS analysis

started implementing SonicTranslator.parseSteadyStates method. Implemented…

added more robust patterns to PointNeuronTranslator

reordered TC states. minor changes in translators.

add permeability_constant_pattern to PointNeuronTranslator

added new functionalities to Trnalsator class (now used in SonicTranslator).

added getClosure method to Translator class.

added getClosure to translator. added getConstantsDict function in constants.py

improved checkTitrate robustness

removed test lookup file

corrected TC neuron notebook

NmodlGenerator: implemented parsing of potential class attributes used as…

added option to provide simAndSave or simulate to batches. implemented addMeta…

improved SonicTranslator class

adapted methods of all classes into classmethods and staticmethods when…

created separate test module with TestBase class. renamed test_basic into…

transformed model inputs, checkInputs and simQueue into static methods

updated README

re-introduced derivatives as mandatory model method

moved lookup to core module. moved getLookup methods to nbls class.

added Model.description method. added nbls.getLookup2D method with correct fs…

defined TestBase class with smart subset handling (inherited by TestSims)

changed TimeSeries.getStimPulses to class method

rewrote test_basic into a class

moved effRates vectorization into pneuron.getEffRates method

added fs (spatially-averaged) as input to nbls model. defined SmartLookup class…

added test at bottom of lookups module

added paper url to setup.py

replaced multiprocessing import by multiprocess import in batches.py to enable…

cleaned up model classes. defined mandatory derivatives method for model…

corrected README

improved steadyStates definition in TC and STN neurons. corrected dQdt pltvar…

updated README

removed unnecessary functions from pneuron

corrected labeling error in GroupedTimeSeries

added automatic effRates function definition in pneuron.parse method. removed…

added precisions about derStates requirements in README

defined separate lookup decorator for bls.computePMparams method. updated…

finished implementing pneuron.buildDerEffStates method to automatically create…

define dLookUp class to perform lookup projections and interpolations

corrected Cinf error in ThalamoCortical neuron

added getSteadyStates and getDerStates methods to pneuron to call steadyStates…

redefined derStates and steadyStates as dictionary of lambda functions

added default output directory ("dump"). cleaned up neuron classes.

corrected error in subset parsing

refefined derEffstates construction to return a dictionary of function.

cleaned up neuron classes. redefined currents to return functions instead of…

started implementation of buildDerEffStates to contruct the derEffStates…

replaced obscur states list by explicit states dictionary in derStates and…

replaced obscur states list by explicit dictionary in all currents methods

corrected y, t order error in nbls.fullDerivatives. added custom parsing in…

added custom parsing to paper figure scripts

added custom parsing to plot_gating_kinetics.py

added custom parsing to plot_effective_variables.py

adde prettify option to timeseries plots

added colormap functionality to PhaseDiagram

defined PlotParser and TimeSeriesParser classes

moved nmodl generator to ExSONIC package

removed plotFRProfile from init file

replaced plotPhaseDiagram by PhaseDiagram class inheriting from ComparativePlot…

solved issue with ActivationMap Ascale

replaced no_offset by tbounds in plotting options. added custom parsing to…