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Commit db218ef

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author
Weina Ji
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generate docstrings
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-24
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‎include/bbp/sonata/config.h

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Original file line numberDiff line numberDiff line change
@@ -368,7 +368,7 @@ class SONATA_API SimulationConfig
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mechanisms;
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/// List of modifications that mimics experimental manipulations to the circuit.
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std::vector<Modification> modifications;
371-
// Method to return the full list of modifications in the Conditions section
371+
/// Method to return the full list of modifications in the Conditions section.
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const std::vector<Modification>& getModifications() const noexcept;
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};
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/**

‎python/generated/docstrings.h

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Original file line numberDiff line numberDiff line change
@@ -713,22 +713,18 @@ R"doc(Extracellular calcium concentration, being applied to the synapse
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uHill parameter in order to scale the U parameter of synapses. Default
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is None.)doc";
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static const char *__doc_bbp_sonata_SimulationConfig_Conditions_getModification =
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R"doc(Returns the given modification parameters
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719-
Throws:
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SonataError if the given modification name does not exist)doc";
721-
722-
static const char *__doc_bbp_sonata_SimulationConfig_Conditions_listModificationNames = R"doc(Returns the names of the modifications)doc";
716+
static const char *__doc_bbp_sonata_SimulationConfig_Conditions_getModifications =
717+
R"doc(Method to return the full list of modifications in the Conditions
718+
section.)doc";
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static const char *__doc_bbp_sonata_SimulationConfig_Conditions_mechanisms =
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R"doc(Properties to assign values to variables in synapse MOD files. The
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format is a dictionary with keys being the SUFFIX names and values
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being dictionaries of variables' names and values.)doc";
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static const char *__doc_bbp_sonata_SimulationConfig_Conditions_modifications =
730-
R"doc(Collection of dictionaries with each member decribing a modification
731-
that mimics experimental manipulations to the circuit.)doc";
726+
R"doc(List of modifications that mimics experimental manipulations to the
727+
circuit.)doc";
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static const char *__doc_bbp_sonata_SimulationConfig_Conditions_randomizeGabaRiseTime =
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R"doc(Enable legacy behavior to randomize the GABA_A rise time in the helper
@@ -794,14 +790,14 @@ static const char *__doc_bbp_sonata_SimulationConfig_InputAbsoluteShotNoise_rand
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R"doc(Override the random seed to introduce correlations between cells,
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default = None)doc";
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793+
static const char *__doc_bbp_sonata_SimulationConfig_InputAbsoluteShotNoise_representsPhysicalElectrode = R"doc(Whether this input represents a physical electrode. Default is false)doc";
794+
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static const char *__doc_bbp_sonata_SimulationConfig_InputAbsoluteShotNoise_reversal = R"doc(Reversal potential for conductance injection in mV. Default is 0)doc";
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static const char *__doc_bbp_sonata_SimulationConfig_InputAbsoluteShotNoise_riseTime = R"doc(The rise time of the bi-exponential shots (ms))doc";
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static const char *__doc_bbp_sonata_SimulationConfig_InputAbsoluteShotNoise_sigma = R"doc(signal std dev in nA (current_clamp) or uS (conductance).)doc";
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803-
static const char *__doc_bbp_sonata_SimulationConfig_InputAbsoluteShotNoise_representsPhysicalElectrode = R"doc(Whether this input represents a physical electrode. Default is false)doc";
804-
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static const char *__doc_bbp_sonata_SimulationConfig_InputBase = R"doc()doc";
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static const char *__doc_bbp_sonata_SimulationConfig_InputBase_InputType = R"doc()doc";
@@ -878,12 +874,12 @@ static const char *__doc_bbp_sonata_SimulationConfig_InputNoise_meanPercent =
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R"doc(The mean value of current to inject as a percentage of threshold
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current, default = None)doc";
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877+
static const char *__doc_bbp_sonata_SimulationConfig_InputNoise_representsPhysicalElectrode = R"doc(Whether this input represents a physical electrode. Default is false)doc";
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static const char *__doc_bbp_sonata_SimulationConfig_InputNoise_variance =
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R"doc(State var to track whether the value of injected noise current is mean
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or mean_percent)doc";
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static const char *__doc_bbp_sonata_SimulationConfig_InputNoise_representsPhysicalElectrode = R"doc(Whether this input represents a physical electrode. Default is false)doc";
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static const char *__doc_bbp_sonata_SimulationConfig_InputOrnsteinUhlenbeck = R"doc()doc";
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static const char *__doc_bbp_sonata_SimulationConfig_InputOrnsteinUhlenbeck_dt = R"doc(Timestep of generated signal in ms. Default is 0.25 ms)doc";
@@ -894,14 +890,14 @@ static const char *__doc_bbp_sonata_SimulationConfig_InputOrnsteinUhlenbeck_rand
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R"doc(Override the random seed to introduce correlations between cells,
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default = None)doc";
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static const char *__doc_bbp_sonata_SimulationConfig_InputOrnsteinUhlenbeck_representsPhysicalElectrode = R"doc(Whether this input represents a physical electrode. Default is false)doc";
894+
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static const char *__doc_bbp_sonata_SimulationConfig_InputOrnsteinUhlenbeck_reversal = R"doc(Reversal potential for conductance injection in mV. Default is 0)doc";
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static const char *__doc_bbp_sonata_SimulationConfig_InputOrnsteinUhlenbeck_sigma = R"doc(Signal std dev in nA (current_clamp) or uS (conductance))doc";
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static const char *__doc_bbp_sonata_SimulationConfig_InputOrnsteinUhlenbeck_tau = R"doc(Relaxation time constant in ms)doc";
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903-
static const char *__doc_bbp_sonata_SimulationConfig_InputOrnsteinUhlenbeck_representsPhysicalElectrode = R"doc(Whether this input represents a physical electrode. Default is false)doc";
904-
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static const char *__doc_bbp_sonata_SimulationConfig_InputPulse = R"doc()doc";
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907903
static const char *__doc_bbp_sonata_SimulationConfig_InputPulse_ampEnd = R"doc(The final current when a stimulus concludes (nA))doc";
@@ -910,10 +906,10 @@ static const char *__doc_bbp_sonata_SimulationConfig_InputPulse_ampStart = R"doc
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911907
static const char *__doc_bbp_sonata_SimulationConfig_InputPulse_frequency = R"doc(The frequency of pulse trains (Hz))doc";
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913-
static const char *__doc_bbp_sonata_SimulationConfig_InputPulse_width = R"doc(The length of time each pulse lasts (ms))doc";
914-
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static const char *__doc_bbp_sonata_SimulationConfig_InputPulse_representsPhysicalElectrode = R"doc(Whether this input represents a physical electrode. Default is false)doc";
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911+
static const char *__doc_bbp_sonata_SimulationConfig_InputPulse_width = R"doc(The length of time each pulse lasts (ms))doc";
912+
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static const char *__doc_bbp_sonata_SimulationConfig_InputRelativeLinear = R"doc()doc";
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static const char *__doc_bbp_sonata_SimulationConfig_InputRelativeLinear_percentEnd = R"doc(The percentage of a cell's threshold current to inject at the end)doc";
@@ -934,6 +930,8 @@ static const char *__doc_bbp_sonata_SimulationConfig_InputRelativeOrnsteinUhlenb
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R"doc(Override the random seed to introduce correlations between cells,
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default = None)doc";
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933+
static const char *__doc_bbp_sonata_SimulationConfig_InputRelativeOrnsteinUhlenbeck_representsPhysicalElectrode = R"doc(Whether this input represents a physical electrode. Default is false)doc";
934+
937935
static const char *__doc_bbp_sonata_SimulationConfig_InputRelativeOrnsteinUhlenbeck_reversal = R"doc(Reversal potential for conductance injection in mV. Default is 0)doc";
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939937
static const char *__doc_bbp_sonata_SimulationConfig_InputRelativeOrnsteinUhlenbeck_sdPercent =
@@ -942,8 +940,6 @@ R"doc(Signal std dev as percentage of a cell’s threshold current
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943941
static const char *__doc_bbp_sonata_SimulationConfig_InputRelativeOrnsteinUhlenbeck_tau = R"doc(Relaxation time constant in ms)doc";
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945-
static const char *__doc_bbp_sonata_SimulationConfig_InputRelativeOrnsteinUhlenbeck_representsPhysicalElectrode = R"doc(Whether this input represents a physical electrode. Default is false)doc";
946-
947943
static const char *__doc_bbp_sonata_SimulationConfig_InputRelativeShotNoise = R"doc()doc";
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949945
static const char *__doc_bbp_sonata_SimulationConfig_InputRelativeShotNoise_ampCv = R"doc(The coefficient of variation (sd/mean) of gamma-distributed amplitudes)doc";
@@ -960,6 +956,8 @@ static const char *__doc_bbp_sonata_SimulationConfig_InputRelativeShotNoise_rand
960956
R"doc(Override the random seed to introduce correlations between cells,
961957
default = None)doc";
962958

959+
static const char *__doc_bbp_sonata_SimulationConfig_InputRelativeShotNoise_representsPhysicalElectrode = R"doc(Whether this input represents a physical electrode. Default is false)doc";
960+
963961
static const char *__doc_bbp_sonata_SimulationConfig_InputRelativeShotNoise_reversal = R"doc(Reversal potential for conductance injection in mV. Default is 0)doc";
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965963
static const char *__doc_bbp_sonata_SimulationConfig_InputRelativeShotNoise_riseTime = R"doc(The rise time of the bi-exponential shots (ms))doc";
@@ -968,8 +966,6 @@ static const char *__doc_bbp_sonata_SimulationConfig_InputRelativeShotNoise_sdPe
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R"doc(signal std dev as percentage of a cell’s threshold current
969967
(current_clamp) or inverse input resistance (conductance).)doc";
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971-
static const char *__doc_bbp_sonata_SimulationConfig_InputRelativeShotNoise_representsPhysicalElectrode = R"doc(Whether this input represents a physical electrode. Default is false)doc";
972-
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static const char *__doc_bbp_sonata_SimulationConfig_InputSeclamp = R"doc()doc";
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975971
static const char *__doc_bbp_sonata_SimulationConfig_InputSeclamp_seriesResistance = R"doc(The series resistance (Mohm), default is 0.01 Mohm)doc";
@@ -996,12 +992,12 @@ default = None)doc";
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997993
static const char *__doc_bbp_sonata_SimulationConfig_InputShotNoise_rate = R"doc(Rate of Poisson events (Hz))doc";
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995+
static const char *__doc_bbp_sonata_SimulationConfig_InputShotNoise_representsPhysicalElectrode = R"doc(Whether this input represents a physical electrode. Default is false)doc";
996+
999997
static const char *__doc_bbp_sonata_SimulationConfig_InputShotNoise_reversal = R"doc(Reversal potential for conductance injection in mV. Default is 0)doc";
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1001999
static const char *__doc_bbp_sonata_SimulationConfig_InputShotNoise_riseTime = R"doc(The rise time of the bi-exponential shots (ms))doc";
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1003-
static const char *__doc_bbp_sonata_SimulationConfig_InputShotNoise_representsPhysicalElectrode = R"doc(Whether this input represents a physical electrode. Default is false)doc";
1004-
10051001
static const char *__doc_bbp_sonata_SimulationConfig_InputSubthreshold = R"doc()doc";
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10071003
static const char *__doc_bbp_sonata_SimulationConfig_InputSubthreshold_percentLess = R"doc(A percentage adjusted from 100 of a cell's threshold current)doc";
@@ -1024,6 +1020,8 @@ static const char *__doc_bbp_sonata_SimulationConfig_ModificationBase_Modificati
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static const char *__doc_bbp_sonata_SimulationConfig_ModificationBase_ModificationType_invalid = R"doc()doc";
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1023+
static const char *__doc_bbp_sonata_SimulationConfig_ModificationBase_name = R"doc(Name of the modification setting.)doc";
1024+
10271025
static const char *__doc_bbp_sonata_SimulationConfig_ModificationBase_nodeSet = R"doc(Node set which receives the manipulation)doc";
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static const char *__doc_bbp_sonata_SimulationConfig_ModificationBase_type =

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