SimulationConfig: set the default value of random_seed in inputs to None

include/bbp/sonata/config.h

@@ -464,8 +464,8 @@ class SONATA_API SimulationConfig
         double riseTime{};
         /// The decay time of the bi-exponential shots (ms)
         double decayTime{};
-        /// Override the random seed to introduce correlations between cells
-        int randomSeed{};
+        /// Override the random seed to introduce correlations between cells, default = None
+        nonstd::optional<int> randomSeed{nonstd::nullopt};
         /// Timestep of generated signal in ms. Default is 0.25 ms
         double dt{};
         /// Rate of Poisson events (Hz)
@@ -482,8 +482,8 @@ class SONATA_API SimulationConfig
         double riseTime{};
         /// The decay time of the bi-exponential shots (ms)
         double decayTime{};
-        /// Override the random seed to introduce correlations between cells
-        int randomSeed{};
+        /// Override the random seed to introduce correlations between cells, default = None
+        nonstd::optional<int> randomSeed{nonstd::nullopt};
         /// Timestep of generated signal in ms. Default is 0.25 ms
         double dt{};
         /// The coefficient of variation (sd/mean) of gamma-distributed amplitudes
@@ -501,8 +501,8 @@ class SONATA_API SimulationConfig
         double riseTime{};
         /// The decay time of the bi-exponential shots (ms)
         double decayTime{};
-        /// Override the random seed to introduce correlations between cells
-        int randomSeed{};
+        /// Override the random seed to introduce correlations between cells, default = None
+        nonstd::optional<int> randomSeed{nonstd::nullopt};
         /// Timestep of generated signal in ms. Default is 0.25 ms
         double dt{};
         /// The coefficient of variation (sd/mean) of gamma-distributed amplitudes
@@ -520,8 +520,8 @@ class SONATA_API SimulationConfig
         double reversal{};
         /// Timestep of generated signal in ms. Default is 0.25 ms
         double dt{};
-        /// Override the random seed to introduce correlations between cells
-        int randomSeed{};
+        /// Override the random seed to introduce correlations between cells, default = None
+        nonstd::optional<int> randomSeed{nonstd::nullopt};
         /// Signal mean in nA (current_clamp) or uS (conductance)
         double mean{};
         /// Signal std dev in nA (current_clamp) or uS (conductance)
@@ -535,8 +535,8 @@ class SONATA_API SimulationConfig
         double reversal{};
         /// Timestep of generated signal in ms. Default is 0.25 ms
         double dt{};
-        /// Override the random seed to introduce correlations between cells
-        int randomSeed{};
+        /// Override the random seed to introduce correlations between cells, default = None
+        nonstd::optional<int> randomSeed{nonstd::nullopt};
         /// Signal mean as percentage of a cell’s threshold current (current_clamp) or inverse input
         /// resistance (conductance)
         double meanPercent{};

python/generated/docstrings.h

@@ -235,6 +235,8 @@ static const char *__doc_bbp_sonata_NodeSets_NodeSets_2 = R"doc()doc";
 
 static const char *__doc_bbp_sonata_NodeSets_NodeSets_3 = R"doc()doc";
 
+static const char *__doc_bbp_sonata_NodeSets_NodeSets_4 = R"doc()doc";
+
 static const char *__doc_bbp_sonata_NodeSets_fromFile = R"doc(Open a SONATA `node sets` file from a path */)doc";
 
 static const char *__doc_bbp_sonata_NodeSets_impl = R"doc()doc";
@@ -652,7 +654,9 @@ static const char *__doc_bbp_sonata_SimulationConfig_InputAbsoluteShotNoise_dt =
 
 static const char *__doc_bbp_sonata_SimulationConfig_InputAbsoluteShotNoise_mean = R"doc(Signal mean in nA (current_clamp) or uS (conductance).)doc";
 
-static const char *__doc_bbp_sonata_SimulationConfig_InputAbsoluteShotNoise_randomSeed = R"doc(Override the random seed to introduce correlations between cells)doc";
+static const char *__doc_bbp_sonata_SimulationConfig_InputAbsoluteShotNoise_randomSeed =
+R"doc(Override the random seed to introduce correlations between cells,
+default = None)doc";
 
 static const char *__doc_bbp_sonata_SimulationConfig_InputAbsoluteShotNoise_riseTime = R"doc(The rise time of the bi-exponential shots (ms))doc";
 
@@ -740,7 +744,9 @@ static const char *__doc_bbp_sonata_SimulationConfig_InputOrnsteinUhlenbeck_dt =
 
 static const char *__doc_bbp_sonata_SimulationConfig_InputOrnsteinUhlenbeck_mean = R"doc(Signal mean in nA (current_clamp) or uS (conductance))doc";
 
-static const char *__doc_bbp_sonata_SimulationConfig_InputOrnsteinUhlenbeck_randomSeed = R"doc(Override the random seed to introduce correlations between cells)doc";
+static const char *__doc_bbp_sonata_SimulationConfig_InputOrnsteinUhlenbeck_randomSeed =
+R"doc(Override the random seed to introduce correlations between cells,
+default = None)doc";
 
 static const char *__doc_bbp_sonata_SimulationConfig_InputOrnsteinUhlenbeck_reversal = R"doc(Reversal potential for conductance injection in mV. Default is 0)doc";
 
@@ -772,7 +778,9 @@ static const char *__doc_bbp_sonata_SimulationConfig_InputRelativeOrnsteinUhlenb
 R"doc(Signal mean as percentage of a cell’s threshold current
 (current_clamp) or inverse input resistance (conductance))doc";
 
-static const char *__doc_bbp_sonata_SimulationConfig_InputRelativeOrnsteinUhlenbeck_randomSeed = R"doc(Override the random seed to introduce correlations between cells)doc";
+static const char *__doc_bbp_sonata_SimulationConfig_InputRelativeOrnsteinUhlenbeck_randomSeed =
+R"doc(Override the random seed to introduce correlations between cells,
+default = None)doc";
 
 static const char *__doc_bbp_sonata_SimulationConfig_InputRelativeOrnsteinUhlenbeck_reversal = R"doc(Reversal potential for conductance injection in mV. Default is 0)doc";
 
@@ -794,7 +802,9 @@ static const char *__doc_bbp_sonata_SimulationConfig_InputRelativeShotNoise_mean
 R"doc(Signal mean as percentage of a cell’s threshold current
 (current_clamp) or inverse input resistance (conductance))doc";
 
-static const char *__doc_bbp_sonata_SimulationConfig_InputRelativeShotNoise_randomSeed = R"doc(Override the random seed to introduce correlations between cells)doc";
+static const char *__doc_bbp_sonata_SimulationConfig_InputRelativeShotNoise_randomSeed =
+R"doc(Override the random seed to introduce correlations between cells,
+default = None)doc";
 
 static const char *__doc_bbp_sonata_SimulationConfig_InputRelativeShotNoise_riseTime = R"doc(The rise time of the bi-exponential shots (ms))doc";
 
@@ -822,7 +832,9 @@ static const char *__doc_bbp_sonata_SimulationConfig_InputShotNoise_decayTime =
 
 static const char *__doc_bbp_sonata_SimulationConfig_InputShotNoise_dt = R"doc(Timestep of generated signal in ms. Default is 0.25 ms)doc";
 
-static const char *__doc_bbp_sonata_SimulationConfig_InputShotNoise_randomSeed = R"doc(Override the random seed to introduce correlations between cells)doc";
+static const char *__doc_bbp_sonata_SimulationConfig_InputShotNoise_randomSeed =
+R"doc(Override the random seed to introduce correlations between cells,
+default = None)doc";
 
 static const char *__doc_bbp_sonata_SimulationConfig_InputShotNoise_rate = R"doc(Rate of Poisson events (Hz))doc";
 

python/tests/test_config.py

@@ -449,6 +449,7 @@ def test_basic(self):
         self.assertEqual(self.config.input('ex_subthreshold').percent_less, 80)
         self.assertEqual(self.config.input('ex_shotnoise').rise_time, 0.4)
         self.assertEqual(self.config.input('ex_shotnoise').amp_mean, 70)
+        self.assertEqual(self.config.input('ex_shotnoise').random_seed, None)
 
         self.assertEqual(self.config.input('ex_hyperpolarizing').duration, 1000)
 
@@ -468,7 +469,7 @@ def test_basic(self):
         self.assertEqual(self.config.input('ex_rel_shotnoise').delay, 0)
         self.assertEqual(self.config.input('ex_rel_shotnoise').duration, 1000)
         self.assertEqual(self.config.input('ex_rel_shotnoise').node_set, "L5E")
-        self.assertEqual(self.config.input('ex_rel_shotnoise').random_seed, self.config.run.random_seed)
+        self.assertEqual(self.config.input('ex_rel_shotnoise').random_seed, 230522)
         self.assertEqual(self.config.input('ex_rel_shotnoise').dt, 0.25)
 
         self.assertEqual(self.config.input('ex_replay').input_type.name, 'spikes')
@@ -485,19 +486,22 @@ def test_basic(self):
         self.assertEqual(self.config.input('ex_abs_shotnoise').amp_cv, 0.63)
         self.assertEqual(self.config.input('ex_abs_shotnoise').mean, 50)
         self.assertEqual(self.config.input('ex_abs_shotnoise').sigma, 5)
+        self.assertEqual(self.config.input('ex_abs_shotnoise').random_seed, None)
 
         self.assertEqual(self.config.input('ex_OU').module.name, "ornstein_uhlenbeck")
         self.assertEqual(self.config.input('ex_OU').input_type.name, "conductance")
         self.assertEqual(self.config.input('ex_OU').tau, 2.8)
         self.assertEqual(self.config.input('ex_OU').reversal, 10)
         self.assertEqual(self.config.input('ex_OU').mean, 50)
         self.assertEqual(self.config.input('ex_OU').sigma, 5)
+        self.assertEqual(self.config.input('ex_OU').random_seed, None)
 
         self.assertEqual(self.config.input('ex_rel_OU').input_type.name, "current_clamp")
         self.assertEqual(self.config.input('ex_rel_OU').tau, 2.8)
         self.assertEqual(self.config.input('ex_rel_OU').reversal, 0)
         self.assertEqual(self.config.input('ex_rel_OU').mean_percent, 70)
         self.assertEqual(self.config.input('ex_rel_OU').sd_percent, 10)
+        self.assertEqual(self.config.input('ex_rel_OU').random_seed, 230522)
 
         self.assertEqual(self.config.input('ex_seclamp').voltage, 1.1)
         self.assertEqual(self.config.input('ex_seclamp').series_resistance, 0.5)

src/config.cpp

@@ -344,7 +344,6 @@ void parseVariantType(const nlohmann::json& it, variantValueType& var) {
 SimulationConfig::Input parseInputModule(const nlohmann::json& valueIt,
                                          const SimulationConfig::InputBase::Module module,
                                          const std::string& basePath,
-                                         int randomSeed,
                                          const std::string& debugStr) {
     using Module = SimulationConfig::InputBase::Module;
 
@@ -415,7 +414,7 @@ SimulationConfig::Input parseInputModule(const nlohmann::json& valueIt,
         parseCommon(ret);
         parseMandatory(valueIt, "rise_time", debugStr, ret.riseTime);
         parseMandatory(valueIt, "decay_time", debugStr, ret.decayTime);
-        parseOptional(valueIt, "random_seed", ret.randomSeed, {randomSeed});
+        parseOptional(valueIt, "random_seed", ret.randomSeed);
         parseOptional(valueIt, "dt", ret.dt, {0.25});
         parseMandatory(valueIt, "rate", debugStr, ret.rate);
         parseMandatory(valueIt, "amp_mean", debugStr, ret.ampMean);
@@ -428,7 +427,7 @@ SimulationConfig::Input parseInputModule(const nlohmann::json& valueIt,
 
         parseMandatory(valueIt, "rise_time", debugStr, ret.riseTime);
         parseMandatory(valueIt, "decay_time", debugStr, ret.decayTime);
-        parseOptional(valueIt, "random_seed", ret.randomSeed, {randomSeed});
+        parseOptional(valueIt, "random_seed", ret.randomSeed);
         parseOptional(valueIt, "dt", ret.dt, {0.25});
         parseMandatory(valueIt, "amp_cv", debugStr, ret.ampCv);
         parseMandatory(valueIt, "mean_percent", debugStr, ret.meanPercent);
@@ -441,7 +440,7 @@ SimulationConfig::Input parseInputModule(const nlohmann::json& valueIt,
 
         parseMandatory(valueIt, "rise_time", debugStr, ret.riseTime);
         parseMandatory(valueIt, "decay_time", debugStr, ret.decayTime);
-        parseOptional(valueIt, "random_seed", ret.randomSeed, {randomSeed});
+        parseOptional(valueIt, "random_seed", ret.randomSeed);
         parseOptional(valueIt, "dt", ret.dt, {0.25});
         parseMandatory(valueIt, "amp_cv", debugStr, ret.ampCv);
         parseMandatory(valueIt, "mean", debugStr, ret.mean);
@@ -473,7 +472,7 @@ SimulationConfig::Input parseInputModule(const nlohmann::json& valueIt,
         parseCommon(ret);
         parseMandatory(valueIt, "tau", debugStr, ret.tau);
         parseOptional(valueIt, "reversal", ret.reversal);
-        parseOptional(valueIt, "random_seed", ret.randomSeed, {randomSeed});
+        parseOptional(valueIt, "random_seed", ret.randomSeed);
         parseOptional(valueIt, "dt", ret.dt, {0.25});
 
         parseMandatory(valueIt, "mean", debugStr, ret.mean);
@@ -485,7 +484,7 @@ SimulationConfig::Input parseInputModule(const nlohmann::json& valueIt,
         parseCommon(ret);
         parseMandatory(valueIt, "tau", debugStr, ret.tau);
         parseOptional(valueIt, "reversal", ret.reversal);
-        parseOptional(valueIt, "random_seed", ret.randomSeed, {randomSeed});
+        parseOptional(valueIt, "random_seed", ret.randomSeed);
         parseOptional(valueIt, "dt", ret.dt, {0.25});
 
         parseMandatory(valueIt, "mean_percent", debugStr, ret.meanPercent);
@@ -1016,8 +1015,7 @@ class SimulationConfig::Parser
             InputBase::Module module;
             parseMandatory(valueIt, "module", debugStr, module);
 
-            const auto input =
-                parseInputModule(valueIt, module, _basePath, parseRun().randomSeed, debugStr);
+            const auto input = parseInputModule(valueIt, module, _basePath, debugStr);
             result[it.key()] = input;
 
             auto mismatchingModuleInputType = [&it]() {

tests/data/config/simulation_config.json

@@ -148,7 +148,8 @@
             "amp_cv": 0.63,
             "mean_percent": 70,
             "sd_percent": 40,
-            "node_set": "L5E"
+            "node_set": "L5E",
+            "random_seed": 230522
         },
         "ex_abs_shotnoise": {
             "input_type": "conductance",
@@ -198,7 +199,8 @@
             "tau": 2.8,
             "mean_percent": 70,
             "sd_percent": 10,
-            "node_set": "Column"
+            "node_set": "Column",
+            "random_seed": 230522
         }
     },
     "connection_overrides": [

tests/test_config.cpp

@@ -466,7 +466,7 @@ TEST_CASE("SimulationConfig") {
             CHECK(input.ampMean == 70);
             CHECK(input.ampVar == 40);
             CHECK(input.rate == 4);
-            CHECK(input.randomSeed == 201506);
+            CHECK(input.randomSeed == nonstd::nullopt);
             CHECK(input.riseTime == 0.4);
             CHECK(input.decayTime == 4);
         }
@@ -480,7 +480,7 @@ TEST_CASE("SimulationConfig") {
             CHECK(input.ampCv == 0.63);
             CHECK(input.meanPercent == 70);
             CHECK(input.sdPercent == 40);
-            CHECK(input.randomSeed == 201506);
+            CHECK(input.randomSeed == 230522);
             CHECK(input.riseTime == 0.4);
             CHECK(input.decayTime == 4);
         }
@@ -520,6 +520,7 @@ TEST_CASE("SimulationConfig") {
             CHECK(input.ampCv == 0.63);
             CHECK(input.mean == 50);
             CHECK(input.sigma == 5);
+            CHECK(input.randomSeed == nonstd::nullopt);
         }
         {
             const auto input = nonstd::get<SimulationConfig::InputOrnsteinUhlenbeck>(
@@ -530,6 +531,7 @@ TEST_CASE("SimulationConfig") {
             CHECK(input.reversal == 10);
             CHECK(input.mean == 50);
             CHECK(input.sigma == 5);
+            CHECK(input.randomSeed == nonstd::nullopt);
         }
         {
             const auto input = nonstd::get<SimulationConfig::InputRelativeOrnsteinUhlenbeck>(
@@ -540,6 +542,7 @@ TEST_CASE("SimulationConfig") {
             CHECK(input.reversal == 0);
             CHECK(input.meanPercent == 70);
             CHECK(input.sdPercent == 10);
+            CHECK(input.randomSeed == 230522);
         }
 
         CHECK(config.listInputNames() == std::set<std::string>{"ex_abs_shotnoise",