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Add docstrings to some python initializers #11

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merged 1 commit into from
Jun 26, 2025
Merged

Add docstrings to some python initializers #11

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32 changes: 24 additions & 8 deletions python/bindings.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -182,7 +182,12 @@ py::class_<Population, std::shared_ptr<Population>> bindPopulationClass(py::modu
return fmt::format(msg, fmt::arg("element", Population::ELEMENT));
};
return py::class_<Population, std::shared_ptr<Population>>(m, clsName, docString)
.def(py::init<const std::string&, const std::string&, const std::string&>())
.def(py::init([](py::object h5_filepath, py::object csv_filepath, std::string name) {
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@cattabiani cattabiani Jun 26, 2025

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I thought these methods did not need a docstring

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@mgeplf mgeplf Jun 26, 2025

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I thought you wanted them :)

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@cattabiani cattabiani Jun 26, 2025

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(I approved already :D)

return Population(py::str(h5_filepath), py::str(csv_filepath), name);
}),
"h5_filepath"_a,
"csv_filepath"_a,
"name"_a)
.def_property_readonly("name", &Population::name, DOC_POP(name))
.def_property_readonly("size", &Population::size, imbueElementName(DOC_POP(size)).c_str())
.def_property_readonly("attribute_names",
Expand Down Expand Up @@ -541,8 +546,11 @@ PYBIND11_MODULE(_libsonata, m) {
bindStorageClass<NodeStorage>(m, "NodeStorage", "NodePopulation");

py::class_<NodeSets>(m, "NodeSets", "NodeSets")
.def(py::init<const std::string&>())
.def_static("from_file", [](py::object path) { return NodeSets::fromFile(py::str(path)); })
.def(py::init<const std::string&>(), "string of NodeSets JSON"_a)
.def_static(
"from_file",
[](py::object path) { return NodeSets::fromFile(py::str(path)); },
"path"_a)
.def_property_readonly("names", &NodeSets::names, DOC_NODESETS(names))
.def("materialize", &NodeSets::materialize, DOC_NODESETS(materialize))
.def("update", &NodeSets::update, "other"_a, DOC_NODESETS(update))
Expand Down Expand Up @@ -571,7 +579,7 @@ PYBIND11_MODULE(_libsonata, m) {
.def_readonly("offset", &CompartmentLocation::offset, DOC_COMPARTMENTLOCATION(offset));

py::class_<CompartmentSet>(m, "CompartmentSet")
.def(py::init<const std::string&>())
.def(py::init<const std::string&>(), "string of CompartmentSet JSON"_a)
.def_property_readonly("population",
&CompartmentSet::population,
DOC_COMPARTMENTSET(population))
Expand Down Expand Up @@ -635,8 +643,11 @@ PYBIND11_MODULE(_libsonata, m) {
[](const CompartmentSet& self) { return py::str(py::repr(py::cast(self))); });

py::class_<CompartmentSets>(m, "CompartmentSets")
.def(py::init<const std::string&>())
.def_static("from_file", &CompartmentSets::fromFile, py::arg("path"))
.def(py::init<const std::string&>(), "string of CompartmentSets JSON"_a)
.def_static(
"from_file",
[](py::object path) { return CompartmentSets::fromFile(py::str(path)); },
"path"_a)
.def("__contains__",
&CompartmentSets::contains,
py::arg("key"),
Expand Down Expand Up @@ -724,7 +735,9 @@ PYBIND11_MODULE(_libsonata, m) {
.value("partial", CircuitConfig::ConfigStatus::partial);

py::class_<CircuitConfig>(m, "CircuitConfig", "Circuit Configuration")
.def(py::init<const std::string&, const std::string&>())
.def(py::init<const std::string&, const std::string&>(),
"string of CircuitConfig JSON"_a,
"base_path"_a)
.def_static("from_file",
[](py::object path) { return CircuitConfig::fromFile(py::str(path)); })
.def_property_readonly("config_status", &CircuitConfig::getCircuitConfigStatus, "ibid")
Expand Down Expand Up @@ -1252,7 +1265,10 @@ PYBIND11_MODULE(_libsonata, m) {
&SimulationConfig::ConnectionOverride::neuromodulationStrength,
DOC_SIMULATIONCONFIG(ConnectionOverride, neuromodulationStrength));

simConf.def(py::init<const std::string&, const std::string&>())
simConf
.def(py::init<const std::string&, const std::string&>(),
"string of SimulationConfig JSON"_a,
"base_path"_a)
.def_static(
"from_file",
[](py::object path) { return SimulationConfig::fromFile(py::str(path)); },
Expand Down
29 changes: 18 additions & 11 deletions python/tests/test_population.py
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Original file line number Diff line number Diff line change
Expand Up @@ -4,17 +4,21 @@

import numpy as np

from libsonata import (CircuitConfig,
ElementReportReader,
NodeSets,
NodeStorage,
Selection,
SimulationConfig,
SomaReportReader,
SonataError,
SpikeReader,
EdgeStorage,
)
from libsonata import (
CircuitConfig,
CompartmentSets,
EdgePopulation,
EdgeStorage,
ElementReportReader,
NodePopulation,
NodeSets,
NodeStorage,
Selection,
SimulationConfig,
SomaReportReader,
SonataError,
SpikeReader,
)


PATH = os.path.join(os.path.dirname(os.path.realpath(__file__)),
Expand Down Expand Up @@ -296,3 +300,6 @@ def test_path_ctor(self):
NodeSets.from_file(path / 'node_sets.json')
CircuitConfig.from_file(path / 'config/circuit_config.json')
SimulationConfig.from_file(path / 'config/simulation_config.json')
NodePopulation(path / 'nodes1.h5', csv_filepath="", name="nodes-A")
EdgePopulation(path / 'edges1.h5', csv_filepath="", name="edges-AB")
CompartmentSets.from_file(path / 'compartment_sets.json')
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