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Jun 2, 2025
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use clang 20.1.5 #5

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2 changes: 1 addition & 1 deletion ci/check_clang_format.sh
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Expand Up @@ -8,7 +8,7 @@ DIRS_TO_FORMAT='src include python'
set -euo pipefail

VENV=build/venv-clang-format
CLANG_FORMAT_VERSION=9.0.0
CLANG_FORMAT_VERSION=20.1.5

if [[ ! -d $VENV ]]; then
python3 -mvenv "$VENV"
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1 change: 1 addition & 0 deletions ci/check_generated_docstrings.sh
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Expand Up @@ -18,6 +18,7 @@ set -euo pipefail

if [[ -z $LIBCLANG_PATH ]]; then
echo "Expect a \$LIBCLANG_PATH in the environment, it should have the path to the libclang.so"
echo "see .github/workflows/docstring_check.yaml for the version currrently used"
exit -1
fi

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3 changes: 2 additions & 1 deletion include/bbp/sonata/config.h
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Expand Up @@ -328,7 +328,8 @@ class SONATA_API SimulationConfig
std::string name;
};

struct ModificationTTX: public ModificationBase {};
struct ModificationTTX: public ModificationBase {
};

struct ModificationConfigureAllSections: public ModificationBase {
/// For “ConfigureAllSections” manipulation, a snippet of python code to perform one or more
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33 changes: 19 additions & 14 deletions python/bindings.cpp
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Expand Up @@ -326,13 +326,16 @@ py::class_<Storage> bindStorageClass(py::module& m, const char* clsName, const c
namespace pybind11 {
namespace detail {
template <typename T>
struct type_caster<nonstd::optional<T>>: optional_caster<nonstd::optional<T>> {};
struct type_caster<nonstd::optional<T>>: optional_caster<nonstd::optional<T>> {
};

template <>
struct type_caster<nonstd::nullopt_t>: public void_caster<nonstd::nullopt_t> {};
struct type_caster<nonstd::nullopt_t>: public void_caster<nonstd::nullopt_t> {
};

template <typename... Ts>
struct type_caster<nonstd::variant<Ts...>>: variant_caster<nonstd::variant<Ts...>> {};
struct type_caster<nonstd::variant<Ts...>>: variant_caster<nonstd::variant<Ts...>> {
};
} // namespace detail
} // namespace pybind11

Expand All @@ -345,17 +348,19 @@ void bindReportReader(py::module& m, const std::string& prefix) {
// .ids, .data and .time members are owned by the c++ object. We can't do std::move.
// To avoid copies, we must declare the owner of the data as the current Python
// object. Numpy will adjust owner reference count according to returned arrays
.def_property_readonly("ids", [](const DataFrame<KeyType>& dframe) {
std::array<ssize_t, 1> dims { ssize_t(dframe.ids.size()) };
return managedMemoryArray(dframe.ids.data(), dims, dframe);
})
.def_property_readonly("data", [](const DataFrame<KeyType>& dframe) {
std::array<ssize_t, 2> dims {0l, ssize_t(dframe.ids.size())};
if (dims[1] > 0) {
dims[0] = dframe.data.size() / dims[1];
}
return managedMemoryArray(dframe.data.data(), dims, dframe);
})
.def_property_readonly("ids",
[](const DataFrame<KeyType>& dframe) {
std::array<ssize_t, 1> dims{ssize_t(dframe.ids.size())};
return managedMemoryArray(dframe.ids.data(), dims, dframe);
})
.def_property_readonly("data",
[](const DataFrame<KeyType>& dframe) {
std::array<ssize_t, 2> dims{0l, ssize_t(dframe.ids.size())};
if (dims[1] > 0) {
dims[0] = dframe.data.size() / dims[1];
}
return managedMemoryArray(dframe.data.data(), dims, dframe);
})
.def_property_readonly("times", [](DataFrame<KeyType>& dframe) {
return managedMemoryArray(dframe.times.data(), dframe.times.size(), dframe);
});
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2 changes: 1 addition & 1 deletion src/common.cpp
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Expand Up @@ -13,6 +13,6 @@ namespace bbp {
namespace sonata {

SonataError::SonataError(const std::string& what)
: std::runtime_error(what) {}
: std::runtime_error(what) { }
} // namespace sonata
} // namespace bbp
29 changes: 16 additions & 13 deletions src/config.cpp
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Expand Up @@ -341,7 +341,7 @@ template <typename Type>
void raiseIfInvalidEnum(const char* /*unused*/,
const Type& /*unused*/,
const std::string& /*unused*/,
std::false_type /* tag */) {}
std::false_type /* tag */) { }

template <typename Type>
void parseMandatory(const nlohmann::json& it,
Expand Down Expand Up @@ -923,10 +923,11 @@ class CircuitConfig::Parser
"node",
status,
[&](NodePopulationProperties& popProperties, const nlohmann::json& popData) {
popProperties.spatialSegmentIndexDir = getJSONPath(popData, "spatial_segment_index_dir");
popProperties.vasculatureFile = getOptionalJSONPath(popData, "vasculature_file");
popProperties.vasculatureMesh = getOptionalJSONPath(popData, "vasculature_mesh");
popProperties.microdomainsFile = getOptionalJSONPath(popData, "microdomains_file");
popProperties.spatialSegmentIndexDir = getJSONPath(popData,
"spatial_segment_index_dir");
popProperties.vasculatureFile = getOptionalJSONPath(popData, "vasculature_file");
popProperties.vasculatureMesh = getOptionalJSONPath(popData, "vasculature_mesh");
popProperties.microdomainsFile = getOptionalJSONPath(popData, "microdomains_file");
});
}

Expand All @@ -936,10 +937,12 @@ class CircuitConfig::Parser
"edge",
status,
[&](EdgePopulationProperties& popProperties, const nlohmann::json& popData) {
popProperties.spatialSynapseIndexDir = getJSONPath(popData, "spatial_synapse_index_dir");
popProperties.endfeetMeshesFile = getOptionalJSONPath(popData, "endfeet_meshes_file");
popProperties.spineMorphologiesDir = getOptionalJSONPath(popData,
"spine_morphologies_dir");
popProperties.spatialSynapseIndexDir = getJSONPath(popData,
"spatial_synapse_index_dir");
popProperties.endfeetMeshesFile = getOptionalJSONPath(popData,
"endfeet_meshes_file");
popProperties.spineMorphologiesDir = getOptionalJSONPath(popData,
"spine_morphologies_dir");
});
}

Expand Down Expand Up @@ -1458,13 +1461,13 @@ const nonstd::optional<std::string>& SimulationConfig::getNodeSet() const noexce
return _nodeSet;
}

const std::unordered_map<std::string, variantValueType>& SimulationConfig::getMetaData() const
noexcept {
const std::unordered_map<std::string, variantValueType>& SimulationConfig::getMetaData()
const noexcept {
return _metaData;
}

const std::unordered_map<std::string, variantValueType>& SimulationConfig::getBetaFeatures() const
noexcept {
const std::unordered_map<std::string, variantValueType>& SimulationConfig::getBetaFeatures()
const noexcept {
return _betaFeatures;
}

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4 changes: 2 additions & 2 deletions src/edges.cpp
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Expand Up @@ -37,13 +37,13 @@ namespace sonata {
EdgePopulation::EdgePopulation(const std::string& h5FilePath,
const std::string& csvFilePath,
const std::string& name)
: Population(h5FilePath, csvFilePath, name, ELEMENT, Hdf5Reader()) {}
: Population(h5FilePath, csvFilePath, name, ELEMENT, Hdf5Reader()) { }

EdgePopulation::EdgePopulation(const std::string& h5FilePath,
const std::string& csvFilePath,
const std::string& name,
const Hdf5Reader& hdf5_reader)
: Population(h5FilePath, csvFilePath, name, ELEMENT, hdf5_reader) {}
: Population(h5FilePath, csvFilePath, name, ELEMENT, hdf5_reader) { }


std::string EdgePopulation::source() const {
Expand Down
4 changes: 2 additions & 2 deletions src/hdf5_reader.cpp
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Expand Up @@ -8,11 +8,11 @@ namespace sonata {

Hdf5Reader::Hdf5Reader()
: impl(std::make_shared<
Hdf5PluginDefault<Hdf5Reader::supported_1D_types, supported_2D_types>>()) {}
Hdf5PluginDefault<Hdf5Reader::supported_1D_types, supported_2D_types>>()) { }

Hdf5Reader::Hdf5Reader(
std::shared_ptr<Hdf5PluginInterface<supported_1D_types, supported_2D_types>> impl)
: impl(std::move(impl)) {}
: impl(std::move(impl)) { }

HighFive::File Hdf5Reader::openFile(const std::string& filename) const {
return impl->openFile(filename);
Expand Down
30 changes: 15 additions & 15 deletions src/node_sets.cpp
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Expand Up @@ -93,15 +93,15 @@ class NodeSets
}

explicit NodeSets(const fs::path& path)
: NodeSets(json::parse(std::ifstream(validate_path(path)))) {}
: NodeSets(json::parse(std::ifstream(validate_path(path)))) { }

static std::unique_ptr<NodeSets> fromFile(const std::string& path_) {
fs::path path(path_);
return std::make_unique<detail::NodeSets>(path);
}

explicit NodeSets(const std::string& content)
: NodeSets(json::parse(content)) {}
: NodeSets(json::parse(content)) { }

Selection materialize(const std::string& name, const NodePopulation& population) const;

Expand Down Expand Up @@ -168,7 +168,7 @@ class NodeSetBasicRule: public NodeSetRule
public:
NodeSetBasicRule(std::string attribute, const std::vector<T>& values)
: attribute_(std::move(attribute))
, values_(values) {}
, values_(values) { }

Selection materialize(const detail::NodeSets& /* unused */,
const NodePopulation& np) const final {
Expand Down Expand Up @@ -200,7 +200,7 @@ class NodeSetBasicPopulation: public NodeSetRule
{
public:
explicit NodeSetBasicPopulation(const std::vector<std::string>& values)
: values_(values) {}
: values_(values) { }

Selection materialize(const detail::NodeSets& /* unused */,
const NodePopulation& np) const final {
Expand Down Expand Up @@ -228,7 +228,7 @@ class NodeSetBasicNodeIds: public NodeSetRule
{
public:
explicit NodeSetBasicNodeIds(Selection::Values values)
: values_(std::move(values)) {}
: values_(std::move(values)) { }

Selection materialize(const detail::NodeSets& /* unused */,
const NodePopulation& np) const final {
Expand Down Expand Up @@ -256,7 +256,7 @@ class NodeSetBasicMultiClause: public NodeSetRule
{
public:
explicit NodeSetBasicMultiClause(std::vector<NodeSetRulePtr>&& clauses)
: clauses_(std::move(clauses)) {}
: clauses_(std::move(clauses)) { }

Selection materialize(const detail::NodeSets& ns, const NodePopulation& np) const final {
Selection ret = np.selectAll();
Expand Down Expand Up @@ -302,14 +302,14 @@ class NodeSetBasicOperatorString: public NodeSetRule
std::string value)
: op_(string2op(op))
, attribute_(std::move(attribute))
, value_(std::move(value)) {}
, value_(std::move(value)) { }

Selection materialize(const detail::NodeSets& /* unused */,
const NodePopulation& np) const final {
switch (op_) {
case Op::regex:
return np.regexMatch(attribute_, value_);
default: // LCOV_EXCL_LINE
default: // LCOV_EXCL_LINE
LIBSONATA_THROW_IF_REACHED // LCOV_EXCL_LINE
}
}
Expand All @@ -333,7 +333,7 @@ class NodeSetBasicOperatorString: public NodeSetRule
switch (op) {
case Op::regex:
return "$regex";
default: // LCOV_EXCL_LINE
default: // LCOV_EXCL_LINE
LIBSONATA_THROW_IF_REACHED // LCOV_EXCL_LINE
}
}
Expand All @@ -357,7 +357,7 @@ class NodeSetBasicOperatorNumeric: public NodeSetRule
explicit NodeSetBasicOperatorNumeric(std::string name, const std::string& op, double value)
: name_(std::move(name))
, value_(value)
, op_(string2op(op)) {}
, op_(string2op(op)) { }

Selection materialize(const detail::NodeSets& /* unused */,
const NodePopulation& np) const final {
Expand All @@ -372,7 +372,7 @@ class NodeSetBasicOperatorNumeric: public NodeSetRule
case Op::lte:
return np.filterAttribute<double>(name_,
[this](const double v) { return v <= value_; });
default: // LCOV_EXCL_LINE
default: // LCOV_EXCL_LINE
LIBSONATA_THROW_IF_REACHED // LCOV_EXCL_LINE
}
}
Expand Down Expand Up @@ -411,7 +411,7 @@ class NodeSetBasicOperatorNumeric: public NodeSetRule
return "$gte";
case Op::lte:
return "$lte";
default: // LCOV_EXCL_LINE
default: // LCOV_EXCL_LINE
LIBSONATA_THROW_IF_REACHED // LCOV_EXCL_LINE
}
}
Expand All @@ -432,7 +432,7 @@ class NodeSetCompoundRule: public NodeSetRule
public:
NodeSetCompoundRule(std::string name, CompoundTargets targets)
: name_(std::move(name))
, targets_(std::move(targets)) {}
, targets_(std::move(targets)) { }

Selection materialize(const detail::NodeSets& ns, const NodePopulation& np) const final {
Selection ret{{}};
Expand Down Expand Up @@ -727,10 +727,10 @@ Selection NodeSets::materialize(const std::string& name, const NodePopulation& p
} // namespace detail

NodeSets::NodeSets(const std::string& content)
: impl_(new detail::NodeSets(content)) {}
: impl_(new detail::NodeSets(content)) { }

NodeSets::NodeSets(std::unique_ptr<detail::NodeSets>&& impl)
: impl_(std::move(impl)) {}
: impl_(std::move(impl)) { }

NodeSets::NodeSets(NodeSets&&) noexcept = default;
NodeSets& NodeSets::operator=(NodeSets&&) noexcept = default;
Expand Down
4 changes: 2 additions & 2 deletions src/nodes.cpp
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Expand Up @@ -92,13 +92,13 @@ Selection _filterStringAttribute(const NodePopulation& population,
NodePopulation::NodePopulation(const std::string& h5FilePath,
const std::string& csvFilePath,
const std::string& name)
: NodePopulation(h5FilePath, csvFilePath, name, Hdf5Reader()) {}
: NodePopulation(h5FilePath, csvFilePath, name, Hdf5Reader()) { }

NodePopulation::NodePopulation(const std::string& h5FilePath,
const std::string& csvFilePath,
const std::string& name,
const Hdf5Reader& hdf5_reader)
: Population(h5FilePath, csvFilePath, name, ELEMENT, hdf5_reader) {}
: Population(h5FilePath, csvFilePath, name, ELEMENT, hdf5_reader) { }

Selection NodePopulation::regexMatch(const std::string& attribute, const std::string& regex) const {
std::regex re(regex);
Expand Down
2 changes: 1 addition & 1 deletion src/population.cpp
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Expand Up @@ -64,7 +64,7 @@ Population::Population(const std::string& h5FilePath,
: impl_([h5FilePath, csvFilePath, name, prefix, hdf5_reader] {
HDF5_LOCK_GUARD
return new Population::Impl(h5FilePath, csvFilePath, name, prefix, hdf5_reader);
}()) {}
}()) { }


Population::Population(Population&&) noexcept = default;
Expand Down
12 changes: 6 additions & 6 deletions src/population.hpp
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Expand Up @@ -169,10 +169,10 @@ struct Population::Impl {
template <typename Population>
struct PopulationStorage<Population>::Impl {
Impl(const std::string& _h5FilePath)
: Impl(_h5FilePath, Hdf5Reader()) {}
: Impl(_h5FilePath, Hdf5Reader()) { }

Impl(const std::string& _h5FilePath, const Hdf5Reader& hdf5_reader)
: Impl(_h5FilePath, std::string(), hdf5_reader) {}
: Impl(_h5FilePath, std::string(), hdf5_reader) { }

Impl(const std::string& _h5FilePath,
const std::string& _csvFilePath,
Expand All @@ -196,17 +196,17 @@ struct PopulationStorage<Population>::Impl {

template <typename Population>
PopulationStorage<Population>::PopulationStorage(const std::string& h5FilePath)
: PopulationStorage(h5FilePath, Hdf5Reader()) {}
: PopulationStorage(h5FilePath, Hdf5Reader()) { }

template <typename Population>
PopulationStorage<Population>::PopulationStorage(const std::string& h5FilePath,
const Hdf5Reader& hdf5_reader)
: PopulationStorage(h5FilePath, std::string(), hdf5_reader) {}
: PopulationStorage(h5FilePath, std::string(), hdf5_reader) { }

template <typename Population>
PopulationStorage<Population>::PopulationStorage(const std::string& h5FilePath,
const std::string& csvFilePath)
: PopulationStorage(h5FilePath, csvFilePath, Hdf5Reader()) {}
: PopulationStorage(h5FilePath, csvFilePath, Hdf5Reader()) { }

template <typename Population>
PopulationStorage<Population>::PopulationStorage(const std::string& h5FilePath,
Expand All @@ -215,7 +215,7 @@ PopulationStorage<Population>::PopulationStorage(const std::string& h5FilePath,
: impl_([h5FilePath, csvFilePath, hdf5_reader] {
HDF5_LOCK_GUARD
return new PopulationStorage::Impl(h5FilePath, csvFilePath, hdf5_reader);
}()) {}
}()) { }


template <typename Population>
Expand Down
2 changes: 1 addition & 1 deletion src/read_canonical_selection.hpp
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@@ -1,7 +1,7 @@
#pragma once

#include <vector>
#include <highfive/H5File.hpp>
#include <vector>

#include "read_bulk.hpp"

Expand Down
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