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Merged
merged 8 commits into from
Aug 21, 2025
Merged

compartment_set in BaseInput object #12

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test CI
cattabiani Aug 20, 2025
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cattabiani Aug 20, 2025
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cattabiani Aug 20, 2025
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final version + tests
cattabiani Aug 20, 2025
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formatting test
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remove useless files
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address comments from ilkilic
cattabiani Aug 20, 2025
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13 changes: 10 additions & 3 deletions include/bbp/sonata/config.h
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Original file line number Diff line number Diff line change
Expand Up @@ -457,8 +457,10 @@ class SONATA_API SimulationConfig
double delay{};
/// Time duration for how long input is activated (ms)
double duration{};
/// Node set which is affected by input
std::string nodeSet;
/// Node set which is affected by input. Not allowed in case of CompartmentSet
nonstd::optional<std::string> nodeSet{nonstd::nullopt};
/// CompartmentSet which is affected by the input. It has priority over nodeSet
nonstd::optional<std::string> compartmentSet{nonstd::nullopt};
};

struct InputLinear: public InputBase {
Expand Down Expand Up @@ -796,10 +798,15 @@ class SONATA_API SimulationConfig
const std::string& getCompartmentSetsFile() const noexcept;

/**
* Returns the name of node set to be instantiated for the simulation, default = None
* Returns the name of the node set to be instantiated for the simulation, default = None
*/
const nonstd::optional<std::string>& getNodeSet() const noexcept;

/**
* Returns the name of the compartment set to be instantiated for the simulation, default = None
*/
const nonstd::optional<std::string>& getCompartmentSet() const noexcept;

/**
* Returns the metadata section
*/
Expand Down
5 changes: 4 additions & 1 deletion python/bindings.cpp
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Expand Up @@ -967,7 +967,10 @@ PYBIND11_MODULE(_libsonata, m) {
DOC_SIMULATIONCONFIG(InputBase, duration))
.def_readonly("node_set",
&SimulationConfig::InputBase::nodeSet,
DOC_SIMULATIONCONFIG(InputBase, nodeSet));
DOC_SIMULATIONCONFIG(InputBase, nodeSet))
.def_readonly("compartment_set",
&SimulationConfig::InputBase::compartmentSet,
DOC_SIMULATIONCONFIG(InputBase, compartmentSet));

py::class_<SimulationConfig::InputLinear, SimulationConfig::InputBase>(simConf, "Linear")
.def_readonly("amp_start",
Expand Down
2 changes: 2 additions & 0 deletions python/generated/docstrings.h
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Expand Up @@ -893,6 +893,8 @@ static const char *__doc_bbp_sonata_SimulationConfig_InputBase_module = R"doc(Ty

static const char *__doc_bbp_sonata_SimulationConfig_InputBase_nodeSet = R"doc(Node set which is affected by input)doc";

static const char *__doc_bbp_sonata_SimulationConfig_InputBase_compartmentSet = R"doc(Compartment set which is affected by input)doc";

static const char *__doc_bbp_sonata_SimulationConfig_InputHyperpolarizing = R"doc()doc";

static const char *__doc_bbp_sonata_SimulationConfig_InputHyperpolarizing_representsPhysicalElectrode = R"doc(Whether this input represents a physical electrode. Default is false)doc";
Expand Down
45 changes: 45 additions & 0 deletions python/tests/test_config.py
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Expand Up @@ -486,6 +486,7 @@ def test_basic(self):
"ex_extracellular_stimulation",
"ex_hyperpolarizing",
"ex_linear",
"ex_linear_compartment_set",
"ex_noise_mean",
"ex_noise_meanpercent",
"ex_OU",
Expand All @@ -506,9 +507,13 @@ def test_basic(self):
self.assertEqual(self.config.input('ex_linear').delay, 0)
self.assertEqual(self.config.input('ex_linear').duration, 15)
self.assertEqual(self.config.input('ex_linear').node_set, "Column")
self.assertEqual(self.config.input('ex_linear').compartment_set, None)
self.assertEqual(self.config.input('ex_linear').amp_start, 0.15)
self.assertEqual(self.config.input('ex_linear').amp_end, 0.15)

self.assertEqual(self.config.input('ex_linear_compartment_set').node_set, None)
self.assertEqual(self.config.input('ex_linear_compartment_set').compartment_set, "cs1")

self.assertEqual(self.config.input('ex_rel_linear').input_type.name, 'current_clamp')
self.assertEqual(self.config.input('ex_rel_linear').module.name, 'relative_linear')
self.assertEqual(self.config.input('ex_rel_linear').delay, 0)
Expand Down Expand Up @@ -723,3 +728,43 @@ def test_simulation_config_failures(self):
"""
SimulationConfig(contents, "./")
self.assertEqual(e.exception.args, ('Replay spike_file should be a SONATA h5 file', ))

with self.assertRaises(SonataError) as e:
contents = """
{
"run": { "random_seed": 12345, "dt": 0.05, "tstop": 1000 },
"inputs" : {
"ex_linear": {
"input_type": "current_clamp",
"module": "linear",
"amp_start": 0.15,
"delay": 0,
"duration": 15,
"node_set":"Column",
"compartment_set":"cs1"
}
}
}
"""
SimulationConfig(contents, "./")
self.assertEqual(e.exception.args, ('`node_set` is not allowed if `compartment_set` is set in input ex_linear', ))

with self.assertRaises(SonataError) as e:
contents = """
{
"run": { "random_seed": 12345, "dt": 0.05, "tstop": 1000 },
"inputs" : {
"ex_linear": {
"input_type": "current_clamp",
"module": "linear",
"amp_start": 0.15,
"delay": 0,
"duration": 15
}
}
}
"""
SimulationConfig(contents, "./")
self.assertEqual(e.exception.args, ('One of `node_set` or `compartment_set` need to have a value in input ex_linear', ))


24 changes: 13 additions & 11 deletions src/config.cpp
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Expand Up @@ -403,7 +403,17 @@ SimulationConfig::Input parseInputModule(const nlohmann::json& valueIt,
parseMandatory(valueIt, "input_type", debugStr, input.inputType);
parseMandatory(valueIt, "delay", debugStr, input.delay);
parseMandatory(valueIt, "duration", debugStr, input.duration);
parseMandatory(valueIt, "node_set", debugStr, input.nodeSet);

parseOptional(valueIt, "node_set", input.nodeSet);
parseOptional(valueIt, "compartment_set", input.compartmentSet);

if (input.nodeSet.has_value() && input.compartmentSet.has_value()) {
throw SonataError("`node_set` is not allowed if `compartment_set` is set in " +
debugStr);
} else if (!input.nodeSet.has_value() && !input.compartmentSet.has_value()) {
throw SonataError("One of `node_set` or `compartment_set` need to have a value in " +
debugStr);
}
};

switch (module) {
Expand Down Expand Up @@ -466,16 +476,8 @@ SimulationConfig::Input parseInputModule(const nlohmann::json& valueIt,
case Module::noise: {
SimulationConfig::InputNoise ret;
parseCommon(ret);
const auto mean = valueIt.find("mean");
const auto mean_percent = valueIt.find("mean_percent");

if (mean != valueIt.end()) {
parseOptional(valueIt, "mean", ret.mean);
}

if (mean_percent != valueIt.end()) {
parseOptional(valueIt, "mean_percent", ret.meanPercent);
}
parseOptional(valueIt, "mean", ret.mean);
parseOptional(valueIt, "mean_percent", ret.meanPercent);

if (ret.mean.has_value() && ret.meanPercent.has_value()) {
throw SonataError("Both `mean` or `mean_percent` have values in " + debugStr);
Expand Down
8 changes: 8 additions & 0 deletions tests/data/config/simulation_config.json
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Expand Up @@ -73,6 +73,14 @@
"duration": 15,
"node_set":"Column"
},
"ex_linear_compartment_set": {
"input_type": "current_clamp",
"module": "linear",
"amp_start": 0.15,
"delay": 0,
"duration": 15,
"compartment_set":"cs1"
},
"ex_rel_linear": {
"input_type": "current_clamp",
"module": "relative_linear",
Expand Down
65 changes: 58 additions & 7 deletions tests/test_config.cpp
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Expand Up @@ -359,7 +359,6 @@ TEST_CASE("SimulationConfig") {
CHECK(configAllSects.sectionConfigure == "%s.gSK_E2bar_SK_E2 = 0");

CHECK_THROWS_AS(config.getReport("DoesNotExist"), SonataError);

CHECK(config.listReportNames() == std::set<std::string>{
"axonal_comp_centers",
"cell_imembrane",
Expand Down Expand Up @@ -587,6 +586,7 @@ TEST_CASE("SimulationConfig") {
"ex_extracellular_stimulation",
"ex_hyperpolarizing",
"ex_linear",
"ex_linear_compartment_set",
"ex_noise_mean",
"ex_noise_meanpercent",
"ex_OU",
Expand Down Expand Up @@ -1202,15 +1202,66 @@ TEST_CASE("SimulationConfig") {
},
"inputs": {
"linear": {
"input_type": "current_clamp",
"module": "spike_replay",
"delay": 0,
"duration": 15,
"node_set":"Column"
"input_type": "current_clamp",
"module": "linear",
"delay": 0,
"duration": 15,
"node_set":"Column"
}
}
})";
CHECK_THROWS_AS(SimulationConfig(contents, "./"), SonataError);
CHECK_THROWS_WITH(
SimulationConfig(contents, "./"),
Catch::Matchers::Contains("amp_start")
);
}
{ // Both node_set and compartment_set are given in an input object
auto contents = R"({
"run": {
"random_seed": 12345,
"dt": 0.05,
"tstop": 1000
},
"inputs": {
"linear": {
"input_type": "current_clamp",
"module": "linear",
"delay": 0,
"duration": 15,
"amp_start": 1,
"node_set":"Column",
"compartment_set":"cs1"
}
}
})";
CHECK_THROWS_WITH(
SimulationConfig(contents, "./"),
Catch::Matchers::Contains("node_set") &&
Catch::Matchers::Contains("compartment_set")
);
}
{ // Both node_set and compartment_set are missing in an input object
auto contents = R"({
"run": {
"random_seed": 12345,
"dt": 0.05,
"tstop": 1000
},
"inputs": {
"linear": {
"input_type": "current_clamp",
"module": "linear",
"delay": 0,
"duration": 15,
"amp_start": 1
}
}
})";
CHECK_THROWS_WITH(
SimulationConfig(contents, "./"),
Catch::Matchers::Contains("node_set") &&
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@ilkilic ilkilic Aug 20, 2025

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should we use Catch::Matchers::AllOf(...) here instead of &&?

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@cattabiani cattabiani Aug 20, 2025

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we are still useing catch2 v2. It does not have AllOf

Catch::Matchers::Contains("compartment_set")
);
}
{ // Both mean and mean_percent are given in a noise input object
auto contents = R"({
Expand Down
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