Merge branch 'master' into double-ctest

BlueBrain · Nov 13, 2024 · 9ed998d · 9ed998d
2 parents c4e7144 + a9650ad
commit 9ed998d
Show file tree

Hide file tree

Showing 7 changed files with 19 additions and 17 deletions.
diff --git a/include/bbp/sonata/config.h b/include/bbp/sonata/config.h
@@ -263,7 +263,7 @@ class SONATA_API SimulationConfig
      * Parameters defining global simulation settings for spike reports
      */
     struct Run {
-        enum class IntegrationMethod { invalid = -1, euler, nicholson, nicholson_ion };
+        enum class IntegrationMethod { invalid = -1, euler, crank_nicolson, crank_nicolson_ion };
 
         static constexpr double DEFAULT_spikeThreshold = -30.0;
         static constexpr IntegrationMethod DEFAULT_IntegrationMethod = IntegrationMethod::euler;
@@ -281,7 +281,7 @@ class SONATA_API SimulationConfig
         /// The spike detection threshold. Default is -30mV
         double spikeThreshold = DEFAULT_spikeThreshold;
         /// Selects the NEURON/CoreNEURON integration method. This parameter sets the NEURON
-        /// global variable h.secondorder. Default 0 ('euler')
+        /// global variable h.secondorder, default is "euler".
         IntegrationMethod integrationMethod = DEFAULT_IntegrationMethod;
         /// A non-negative integer used for seeding noise stimuli and any other future stochastic
         /// stimuli, default is 0.

diff --git a/python/bindings.cpp b/python/bindings.cpp
@@ -646,8 +646,8 @@ PYBIND11_MODULE(_libsonata, m) {
 
     py::enum_<SimulationConfig::Run::IntegrationMethod>(run, "IntegrationMethod")
         .value("euler", SimulationConfig::Run::IntegrationMethod::euler)
-        .value("nicholson", SimulationConfig::Run::IntegrationMethod::nicholson)
-        .value("nicholson_ion", SimulationConfig::Run::IntegrationMethod::nicholson_ion);
+        .value("crank_nicolson", SimulationConfig::Run::IntegrationMethod::crank_nicolson)
+        .value("crank_nicolson_ion", SimulationConfig::Run::IntegrationMethod::crank_nicolson_ion);
 
     py::class_<SimulationConfig::Output> output(simConf,
                                                 "Output",

diff --git a/python/generated/docstrings.h b/python/generated/docstrings.h
@@ -1157,21 +1157,21 @@ static const char *__doc_bbp_sonata_SimulationConfig_Run = R"doc(Parameters defi
 
 static const char *__doc_bbp_sonata_SimulationConfig_Run_IntegrationMethod = R"doc()doc";
 
-static const char *__doc_bbp_sonata_SimulationConfig_Run_IntegrationMethod_euler = R"doc()doc";
+static const char *__doc_bbp_sonata_SimulationConfig_Run_IntegrationMethod_crank_nicolson = R"doc()doc";
 
-static const char *__doc_bbp_sonata_SimulationConfig_Run_IntegrationMethod_invalid = R"doc()doc";
+static const char *__doc_bbp_sonata_SimulationConfig_Run_IntegrationMethod_crank_nicolson_ion = R"doc()doc";
 
-static const char *__doc_bbp_sonata_SimulationConfig_Run_IntegrationMethod_nicholson = R"doc()doc";
+static const char *__doc_bbp_sonata_SimulationConfig_Run_IntegrationMethod_euler = R"doc()doc";
 
-static const char *__doc_bbp_sonata_SimulationConfig_Run_IntegrationMethod_nicholson_ion = R"doc()doc";
+static const char *__doc_bbp_sonata_SimulationConfig_Run_IntegrationMethod_invalid = R"doc()doc";
 
 static const char *__doc_bbp_sonata_SimulationConfig_Run_dt = R"doc(Integration step duration in milliseconds)doc";
 
 static const char *__doc_bbp_sonata_SimulationConfig_Run_electrodesFile = R"doc(Filename that contains the weights for the LFP calculation.)doc";
 
 static const char *__doc_bbp_sonata_SimulationConfig_Run_integrationMethod =
 R"doc(Selects the NEURON/CoreNEURON integration method. This parameter sets
-the NEURON global variable h.secondorder. Default 0 ('euler'))doc";
+the NEURON global variable h.secondorder, default is "euler".)doc";
 
 static const char *__doc_bbp_sonata_SimulationConfig_Run_ionchannelSeed =
 R"doc(A non-negative integer used for seeding stochastic ion channels,

diff --git a/python/tests/test_config.py b/python/tests/test_config.py
@@ -413,7 +413,7 @@ def test_basic(self):
         self.assertEqual(self.config.run.random_seed, 201506)
         self.assertEqual(self.config.run.spike_threshold, -35.5)
         self.assertEqual(self.config.run.integration_method,
-                         SimulationConfig.Run.IntegrationMethod.nicholson_ion)
+                         SimulationConfig.Run.IntegrationMethod.crank_nicolson_ion)
         self.assertEqual(self.config.run.stimulus_seed, 111)
         self.assertEqual(self.config.run.ionchannel_seed, 222)
         self.assertEqual(self.config.run.minis_seed, 333)

diff --git a/src/config.cpp b/src/config.cpp
@@ -58,11 +58,12 @@ NLOHMANN_JSON_SERIALIZE_ENUM(SimulationConfig::Conditions::SpikeLocation,
                               {SimulationConfig::Conditions::SpikeLocation::soma, "soma"},
                               {SimulationConfig::Conditions::SpikeLocation::AIS, "AIS"}})
 
-NLOHMANN_JSON_SERIALIZE_ENUM(SimulationConfig::Run::IntegrationMethod,
-                             {{SimulationConfig::Run::IntegrationMethod::invalid, nullptr},
-                              {SimulationConfig::Run::IntegrationMethod::euler, 0},
-                              {SimulationConfig::Run::IntegrationMethod::nicholson, 1},
-                              {SimulationConfig::Run::IntegrationMethod::nicholson_ion, 2}})
+NLOHMANN_JSON_SERIALIZE_ENUM(
+    SimulationConfig::Run::IntegrationMethod,
+    {{SimulationConfig::Run::IntegrationMethod::invalid, nullptr},
+     {SimulationConfig::Run::IntegrationMethod::euler, "euler"},
+     {SimulationConfig::Run::IntegrationMethod::crank_nicolson, "crank_nicolson"},
+     {SimulationConfig::Run::IntegrationMethod::crank_nicolson_ion, "crank_nicolson_ion"}})
 
 NLOHMANN_JSON_SERIALIZE_ENUM(SimulationConfig::Output::SpikesSortOrder,
                              {{SimulationConfig::Output::SpikesSortOrder::invalid, nullptr},

diff --git a/tests/data/config/simulation_config.json b/tests/data/config/simulation_config.json
@@ -25,7 +25,7 @@
          "ionchannel_seed": 222,
          "minis_seed": 333,
          "synapse_seed": 444,
-         "integration_method" : 2,
+         "integration_method" : "crank_nicolson_ion",
          "forward_skip": 500,
          "electrodes_file": "$ELECTRODES_DIR/electrode_weights.h5",
          "spike_threshold": -35.5

diff --git a/tests/test_config.cpp b/tests/test_config.cpp
@@ -310,7 +310,8 @@ TEST_CASE("SimulationConfig") {
         CHECK(config.getRun().dt == 0.025);
         CHECK(config.getRun().randomSeed == 201506);
         CHECK(config.getRun().spikeThreshold == -35.5);
-        CHECK(config.getRun().integrationMethod == SimulationConfig::Run::IntegrationMethod::nicholson_ion);
+        CHECK(config.getRun().integrationMethod ==
+              SimulationConfig::Run::IntegrationMethod::crank_nicolson_ion);
         CHECK(config.getRun().stimulusSeed == 111);
         CHECK(config.getRun().ionchannelSeed == 222);
         CHECK(config.getRun().minisSeed == 333);