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Refactor: snake case #3017

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Merged
dweindl merged 1 commit into from
Nov 10, 2025
Merged

Refactor: snake case #3017

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2 changes: 1 addition & 1 deletion include/amici/abstract_model.h
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Original file line number Diff line number Diff line change
Expand Up @@ -101,7 +101,7 @@ class AbstractModel {
* @param dxB Vector with the adjoint derivative states
* @param xBdot Vector with the adjoint state right hand side
*/
virtual void writeSteadystateJB(
virtual void write_steady_state_JB(
realtype t, realtype cj, AmiVector const& x, AmiVector const& dx,
AmiVector const& xB, AmiVector const& dxB, AmiVector const& xBdot
) = 0;
Expand Down
4 changes: 2 additions & 2 deletions include/amici/edata.h
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Expand Up @@ -507,7 +507,7 @@ inline bool operator==(ExpData const& lhs, ExpData const& rhs) {
* @param sigmaVector vector input to be checked
* @param vectorName name of the input
*/
void checkSigmaPositivity(
void check_sigma_positivity(
std::vector<realtype> const& sigmaVector, char const* vectorName
);

Expand All @@ -517,7 +517,7 @@ void checkSigmaPositivity(
* @param sigma input to be checked
* @param sigmaName name of the input
*/
void checkSigmaPositivity(realtype sigma, char const* sigmaName);
void check_sigma_positivity(realtype sigma, char const* sigmaName);

/**
* @brief The ConditionContext class applies condition-specific amici::Model
Expand Down
2 changes: 1 addition & 1 deletion include/amici/model_dae.h
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Expand Up @@ -284,7 +284,7 @@ class Model_DAE : public Model {
* @param dxB Vector with the adjoint derivative states
* @param xBdot Vector with the adjoint state right hand side
*/
void writeSteadystateJB(
void write_steady_state_JB(
realtype t, realtype cj, AmiVector const& x, AmiVector const& dx,
AmiVector const& xB, AmiVector const& dxB, AmiVector const& xBdot
) override;
Expand Down
2 changes: 1 addition & 1 deletion include/amici/model_ode.h
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Expand Up @@ -254,7 +254,7 @@ class Model_ODE : public Model {
* @param dxB Vector with the adjoint derivative states
* @param xBdot Vector with the adjoint state right hand side
*/
void writeSteadystateJB(
void write_steady_state_JB(
realtype t, realtype cj, AmiVector const& x, AmiVector const& dx,
AmiVector const& xB, AmiVector const& dxB, AmiVector const& xBdot
) override;
Expand Down
2 changes: 1 addition & 1 deletion include/amici/rdata.h
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Expand Up @@ -546,7 +546,7 @@ class ReturnData : public ModelDimensions {
* @param quadratic_llh whether model defines a quadratic nllh and computing
* res, sres and FIM makes sense.
*/
void initializeObservablesLikelihoodReporting(bool quadratic_llh);
void initialize_observables_likelihood_reporting(bool quadratic_llh);

/**
* @brief initializes storage for residual reporting mode
Expand Down
26 changes: 13 additions & 13 deletions src/edata.cpp
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Expand Up @@ -103,8 +103,8 @@ ExpData::ExpData(

realtype sigma;

checkSigmaPositivity(sigma_y, "sigma_y");
checkSigmaPositivity(sigma_z, "sigma_z");
check_sigma_positivity(sigma_y, "sigma_y");
check_sigma_positivity(sigma_z, "sigma_z");

for (int iy = 0; iy < nytrue_; ++iy) {
for (int it = 0; it < nt(); ++it) {
Expand Down Expand Up @@ -195,7 +195,7 @@ void ExpData::set_observed_data_std_dev(
std::vector<realtype> const& observedDataStdDev
) {
check_data_dimension(observedDataStdDev, "observedDataStdDev");
checkSigmaPositivity(observedDataStdDev, "observedDataStdDev");
check_sigma_positivity(observedDataStdDev, "observedDataStdDev");

if (observedDataStdDev.size() == static_cast<unsigned>(nt()) * nytrue_)
observed_data_std_dev_ = observedDataStdDev;
Expand All @@ -204,7 +204,7 @@ void ExpData::set_observed_data_std_dev(
}

void ExpData::set_observed_data_std_dev(realtype const stdDev) {
checkSigmaPositivity(stdDev, "stdDev");
check_sigma_positivity(stdDev, "stdDev");
std::ranges::fill(observed_data_std_dev_, stdDev);
}

Expand All @@ -216,15 +216,15 @@ void ExpData::set_observed_data_std_dev(
"Input observedDataStdDev did not match dimensions nt (%i), was %i",
nt(), observedDataStdDev.size()
);
checkSigmaPositivity(observedDataStdDev, "observedDataStdDev");
check_sigma_positivity(observedDataStdDev, "observedDataStdDev");

for (int it = 0; it < nt(); ++it)
observed_data_std_dev_.at(iy + it * nytrue_)
= observedDataStdDev.at(it);
}

void ExpData::set_observed_data_std_dev(realtype const stdDev, int const iy) {
checkSigmaPositivity(stdDev, "stdDev");
check_sigma_positivity(stdDev, "stdDev");
for (int it = 0; it < nt(); ++it)
observed_data_std_dev_.at(iy + it * nytrue_) = stdDev;
}
Expand Down Expand Up @@ -289,7 +289,7 @@ void ExpData::set_observed_events_std_dev(
std::vector<realtype> const& observedEventsStdDev
) {
check_events_dimension(observedEventsStdDev, "observedEventsStdDev");
checkSigmaPositivity(observedEventsStdDev, "observedEventsStdDev");
check_sigma_positivity(observedEventsStdDev, "observedEventsStdDev");

if (observedEventsStdDev.size() == (unsigned)nmaxevent_ * nztrue_)
observed_events_std_dev_ = observedEventsStdDev;
Expand All @@ -298,7 +298,7 @@ void ExpData::set_observed_events_std_dev(
}

void ExpData::set_observed_events_std_dev(realtype const stdDev) {
checkSigmaPositivity(stdDev, "stdDev");
check_sigma_positivity(stdDev, "stdDev");
std::ranges::fill(observed_events_std_dev_, stdDev);
}

Expand All @@ -311,15 +311,15 @@ void ExpData::set_observed_events_std_dev(
"(%i), was %i",
nmaxevent_, observedEventsStdDev.size()
);
checkSigmaPositivity(observedEventsStdDev, "observedEventsStdDev");
check_sigma_positivity(observedEventsStdDev, "observedEventsStdDev");

for (int ie = 0; ie < nmaxevent_; ++ie)
observed_events_std_dev_.at(iz + ie * nztrue_)
= observedEventsStdDev.at(ie);
}

void ExpData::set_observed_events_std_dev(realtype const stdDev, int const iz) {
checkSigmaPositivity(stdDev, "stdDev");
check_sigma_positivity(stdDev, "stdDev");

for (int ie = 0; ie < nmaxevent_; ++ie)
observed_events_std_dev_.at(iz + ie * nztrue_) = stdDev;
Expand Down Expand Up @@ -386,14 +386,14 @@ void ExpData::check_events_dimension(
);
}

void checkSigmaPositivity(
void check_sigma_positivity(
std::vector<realtype> const& sigmaVector, char const* vectorName
) {
for (auto&& sigma : sigmaVector)
checkSigmaPositivity(sigma, vectorName);
check_sigma_positivity(sigma, vectorName);
}

void checkSigmaPositivity(realtype const sigma, char const* sigmaName) {
void check_sigma_positivity(realtype const sigma, char const* sigmaName) {
if (sigma <= 0.0)
throw AmiException(
"Encountered sigma <= 0 in %s! value: %f", sigmaName, sigma
Expand Down
12 changes: 6 additions & 6 deletions src/hdf5.cpp
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Expand Up @@ -25,7 +25,7 @@ namespace amici::hdf5 {
* @param n
* @param model
*/
void checkMeasurementDimensionsCompatible(
void check_measurement_dimensions_compatible(
hsize_t const m, hsize_t const n, Model const& model
) {
bool compatible = true;
Expand Down Expand Up @@ -54,7 +54,7 @@ void checkMeasurementDimensionsCompatible(
* @param n
* @param model
*/
void checkEventDimensionsCompatible(
void check_event_dimensions_compatible(
hsize_t const m, hsize_t const n, Model const& model
) {
bool compatible = true;
Expand Down Expand Up @@ -126,7 +126,7 @@ std::unique_ptr<ExpData> read_exp_data_from_hdf5(
if (model.ny * model.nt() > 0) {
if (location_exists(file, hdf5Root + "/Y")) {
auto const my = get_double_2d_dataset(file, hdf5Root + "/Y", m, n);
checkMeasurementDimensionsCompatible(m, n, model);
check_measurement_dimensions_compatible(m, n, model);
edata->set_observed_data(my);
} else {
throw AmiException(
Expand All @@ -137,7 +137,7 @@ std::unique_ptr<ExpData> read_exp_data_from_hdf5(
if (location_exists(file, hdf5Root + "/Sigma_Y")) {
auto const sigmay
= get_double_2d_dataset(file, hdf5Root + "/Sigma_Y", m, n);
checkMeasurementDimensionsCompatible(m, n, model);
check_measurement_dimensions_compatible(m, n, model);
edata->set_observed_data_std_dev(sigmay);
} else {
throw AmiException(
Expand All @@ -150,7 +150,7 @@ std::unique_ptr<ExpData> read_exp_data_from_hdf5(
if (model.nz * model.n_max_event() > 0) {
if (location_exists(file, hdf5Root + "/Z")) {
auto const mz = get_double_2d_dataset(file, hdf5Root + "/Z", m, n);
checkEventDimensionsCompatible(m, n, model);
check_event_dimensions_compatible(m, n, model);
edata->set_observed_events(mz);
} else {
throw AmiException(
Expand All @@ -161,7 +161,7 @@ std::unique_ptr<ExpData> read_exp_data_from_hdf5(
if (location_exists(file, hdf5Root + "/Sigma_Z")) {
auto sigmaz
= get_double_2d_dataset(file, hdf5Root + "/Sigma_Z", m, n);
checkEventDimensionsCompatible(m, n, model);
check_event_dimensions_compatible(m, n, model);
edata->set_observed_events_std_dev(sigmaz);
} else {
throw AmiException(
Expand Down
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