SimulationConfig: remove amp_end from pulse input (#358)

To follow the change in SONATA specs: BlueBrain/sonata-extension#56
BlueBrain · Jul 2, 2024 · bcdcaeb · bcdcaeb
1 parent c1e6f17
commit bcdcaeb
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Showing 4 changed files with 14 additions and 22 deletions.
diff --git a/include/bbp/sonata/config.h b/include/bbp/sonata/config.h
@@ -476,8 +476,6 @@ class SONATA_API SimulationConfig
  struct InputPulse: public InputBase {
  /// The amount of current initially injected (nA)
  double ampStart{};
- /// The final current when a stimulus concludes (nA)
- double ampEnd{};
  /// The length of time each pulse lasts (ms)
  double width{};
  /// The frequency of pulse trains (Hz)

diff --git a/python/bindings.cpp b/python/bindings.cpp
@@ -844,9 +844,6 @@ PYBIND11_MODULE(_libsonata, m) {
  .def_readonly("amp_start",
  &SimulationConfig::InputPulse::ampStart,
  DOC_SIMULATIONCONFIG(InputPulse, ampStart))
- .def_readonly("amp_end",
- &SimulationConfig::InputPulse::ampEnd,
- DOC_SIMULATIONCONFIG(InputPulse, ampEnd))
  .def_readonly("width",
  &SimulationConfig::InputPulse::width,
  DOC_SIMULATIONCONFIG(InputPulse, width))

diff --git a/python/generated/docstrings.h b/python/generated/docstrings.h
@@ -794,14 +794,14 @@ static const char *__doc_bbp_sonata_SimulationConfig_InputAbsoluteShotNoise_rand
 R"doc(Override the random seed to introduce correlations between cells,
 default = None)doc";
 
+static const char *__doc_bbp_sonata_SimulationConfig_InputAbsoluteShotNoise_representsPhysicalElectrode = R"doc(Whether this input represents a physical electrode. Default is false)doc";
+
 static const char *__doc_bbp_sonata_SimulationConfig_InputAbsoluteShotNoise_reversal = R"doc(Reversal potential for conductance injection in mV. Default is 0)doc";
 
 static const char *__doc_bbp_sonata_SimulationConfig_InputAbsoluteShotNoise_riseTime = R"doc(The rise time of the bi-exponential shots (ms))doc";
 
 static const char *__doc_bbp_sonata_SimulationConfig_InputAbsoluteShotNoise_sigma = R"doc(signal std dev in nA (current_clamp) or uS (conductance).)doc";
 
-static const char *__doc_bbp_sonata_SimulationConfig_InputAbsoluteShotNoise_representsPhysicalElectrode = R"doc(Whether this input represents a physical electrode. Default is false)doc";
-
 static const char *__doc_bbp_sonata_SimulationConfig_InputBase = R"doc()doc";
 
 static const char *__doc_bbp_sonata_SimulationConfig_InputBase_InputType = R"doc()doc";
@@ -878,12 +878,12 @@ static const char *__doc_bbp_sonata_SimulationConfig_InputNoise_meanPercent =
 R"doc(The mean value of current to inject as a percentage of threshold
 current, default = None)doc";
 
+static const char *__doc_bbp_sonata_SimulationConfig_InputNoise_representsPhysicalElectrode = R"doc(Whether this input represents a physical electrode. Default is false)doc";
+
 static const char *__doc_bbp_sonata_SimulationConfig_InputNoise_variance =
 R"doc(State var to track whether the value of injected noise current is mean
 or mean_percent)doc";
 
-static const char *__doc_bbp_sonata_SimulationConfig_InputNoise_representsPhysicalElectrode = R"doc(Whether this input represents a physical electrode. Default is false)doc";
-
 static const char *__doc_bbp_sonata_SimulationConfig_InputOrnsteinUhlenbeck = R"doc()doc";
 
 static const char *__doc_bbp_sonata_SimulationConfig_InputOrnsteinUhlenbeck_dt = R"doc(Timestep of generated signal in ms. Default is 0.25 ms)doc";
@@ -894,26 +894,24 @@ static const char *__doc_bbp_sonata_SimulationConfig_InputOrnsteinUhlenbeck_rand
 R"doc(Override the random seed to introduce correlations between cells,
 default = None)doc";
 
+static const char *__doc_bbp_sonata_SimulationConfig_InputOrnsteinUhlenbeck_representsPhysicalElectrode = R"doc(Whether this input represents a physical electrode. Default is false)doc";
+
 static const char *__doc_bbp_sonata_SimulationConfig_InputOrnsteinUhlenbeck_reversal = R"doc(Reversal potential for conductance injection in mV. Default is 0)doc";
 
 static const char *__doc_bbp_sonata_SimulationConfig_InputOrnsteinUhlenbeck_sigma = R"doc(Signal std dev in nA (current_clamp) or uS (conductance))doc";
 
 static const char *__doc_bbp_sonata_SimulationConfig_InputOrnsteinUhlenbeck_tau = R"doc(Relaxation time constant in ms)doc";
 
-static const char *__doc_bbp_sonata_SimulationConfig_InputOrnsteinUhlenbeck_representsPhysicalElectrode = R"doc(Whether this input represents a physical electrode. Default is false)doc";
-
 static const char *__doc_bbp_sonata_SimulationConfig_InputPulse = R"doc()doc";
 
-static const char *__doc_bbp_sonata_SimulationConfig_InputPulse_ampEnd = R"doc(The final current when a stimulus concludes (nA))doc";
-
 static const char *__doc_bbp_sonata_SimulationConfig_InputPulse_ampStart = R"doc(The amount of current initially injected (nA))doc";
 
 static const char *__doc_bbp_sonata_SimulationConfig_InputPulse_frequency = R"doc(The frequency of pulse trains (Hz))doc";
 
-static const char *__doc_bbp_sonata_SimulationConfig_InputPulse_width = R"doc(The length of time each pulse lasts (ms))doc";
-
 static const char *__doc_bbp_sonata_SimulationConfig_InputPulse_representsPhysicalElectrode = R"doc(Whether this input represents a physical electrode. Default is false)doc";
 
+static const char *__doc_bbp_sonata_SimulationConfig_InputPulse_width = R"doc(The length of time each pulse lasts (ms))doc";
+
 static const char *__doc_bbp_sonata_SimulationConfig_InputRelativeLinear = R"doc()doc";
 
 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 +932,8 @@ static const char *__doc_bbp_sonata_SimulationConfig_InputRelativeOrnsteinUhlenb
 R"doc(Override the random seed to introduce correlations between cells,
 default = None)doc";
 
+static const char *__doc_bbp_sonata_SimulationConfig_InputRelativeOrnsteinUhlenbeck_representsPhysicalElectrode = R"doc(Whether this input represents a physical electrode. Default is false)doc";
+
 static const char *__doc_bbp_sonata_SimulationConfig_InputRelativeOrnsteinUhlenbeck_reversal = R"doc(Reversal potential for conductance injection in mV. Default is 0)doc";
 
 static const char *__doc_bbp_sonata_SimulationConfig_InputRelativeOrnsteinUhlenbeck_sdPercent =
@@ -942,8 +942,6 @@ R"doc(Signal std dev as percentage of a cell’s threshold current
 
 static const char *__doc_bbp_sonata_SimulationConfig_InputRelativeOrnsteinUhlenbeck_tau = R"doc(Relaxation time constant in ms)doc";
 
-static const char *__doc_bbp_sonata_SimulationConfig_InputRelativeOrnsteinUhlenbeck_representsPhysicalElectrode = R"doc(Whether this input represents a physical electrode. Default is false)doc";
-
 static const char *__doc_bbp_sonata_SimulationConfig_InputRelativeShotNoise = R"doc()doc";
 
 static const char *__doc_bbp_sonata_SimulationConfig_InputRelativeShotNoise_ampCv = R"doc(The coefficient of variation (sd/mean) of gamma-distributed amplitudes)doc";
@@ -960,6 +958,8 @@ static const char *__doc_bbp_sonata_SimulationConfig_InputRelativeShotNoise_rand
 R"doc(Override the random seed to introduce correlations between cells,
 default = None)doc";
 
+static const char *__doc_bbp_sonata_SimulationConfig_InputRelativeShotNoise_representsPhysicalElectrode = R"doc(Whether this input represents a physical electrode. Default is false)doc";
+
 static const char *__doc_bbp_sonata_SimulationConfig_InputRelativeShotNoise_reversal = R"doc(Reversal potential for conductance injection in mV. Default is 0)doc";
 
 static const char *__doc_bbp_sonata_SimulationConfig_InputRelativeShotNoise_riseTime = R"doc(The rise time of the bi-exponential shots (ms))doc";
@@ -968,8 +968,6 @@ static const char *__doc_bbp_sonata_SimulationConfig_InputRelativeShotNoise_sdPe
 R"doc(signal std dev as percentage of a cell’s threshold current
 (current_clamp) or inverse input resistance (conductance).)doc";
 
-static const char *__doc_bbp_sonata_SimulationConfig_InputRelativeShotNoise_representsPhysicalElectrode = R"doc(Whether this input represents a physical electrode. Default is false)doc";
-
 static const char *__doc_bbp_sonata_SimulationConfig_InputSeclamp = R"doc()doc";
 
 static const char *__doc_bbp_sonata_SimulationConfig_InputSeclamp_seriesResistance = R"doc(The series resistance (Mohm), default is 0.01 Mohm)doc";
@@ -996,12 +994,12 @@ default = None)doc";
 
 static const char *__doc_bbp_sonata_SimulationConfig_InputShotNoise_rate = R"doc(Rate of Poisson events (Hz))doc";
 
+static const char *__doc_bbp_sonata_SimulationConfig_InputShotNoise_representsPhysicalElectrode = R"doc(Whether this input represents a physical electrode. Default is false)doc";
+
 static const char *__doc_bbp_sonata_SimulationConfig_InputShotNoise_reversal = R"doc(Reversal potential for conductance injection in mV. Default is 0)doc";
 
 static const char *__doc_bbp_sonata_SimulationConfig_InputShotNoise_riseTime = R"doc(The rise time of the bi-exponential shots (ms))doc";
 
-static const char *__doc_bbp_sonata_SimulationConfig_InputShotNoise_representsPhysicalElectrode = R"doc(Whether this input represents a physical electrode. Default is false)doc";
-
 static const char *__doc_bbp_sonata_SimulationConfig_InputSubthreshold = R"doc()doc";
 
 static const char *__doc_bbp_sonata_SimulationConfig_InputSubthreshold_percentLess = R"doc(A percentage adjusted from 100 of a cell's threshold current)doc";

diff --git a/src/config.cpp b/src/config.cpp
@@ -432,7 +432,6 @@ SimulationConfig::Input parseInputModule(const nlohmann::json& valueIt,
  parseMandatory(valueIt, "amp_start", debugStr, ret.ampStart);
  parseMandatory(valueIt, "width", debugStr, ret.width);
  parseMandatory(valueIt, "frequency", debugStr, ret.frequency);
- parseOptional(valueIt, "amp_end", ret.ampEnd, {ret.ampStart});
  parseOptional(valueIt,
  "represents_physical_electrode",
  ret.representsPhysicalElectrode,