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Fix swig shadow warning + other linting issues #2261

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merged 1 commit into from
Jan 6, 2024
Merged

Fix swig shadow warning + other linting issues #2261

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2 changes: 1 addition & 1 deletion include/amici/logging.h
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Original file line number Diff line number Diff line change
Expand Up @@ -83,7 +83,7 @@ struct LogItem {
, message(message){};

/** Severity level */
LogSeverity severity;
LogSeverity severity = LogSeverity::error;

/** Short identifier for the logged event */
std::string identifier;
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2 changes: 1 addition & 1 deletion include/amici/model.h
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Expand Up @@ -1437,7 +1437,7 @@ class Model : public AbstractModel, public ModelDimensions {
std::vector<int> const& getReinitializationStateIdxs() const;

/** Flag indicating Matlab- or Python-based model generation */
bool pythonGenerated;
bool pythonGenerated = false;

/**
* @brief getter for dxdotdp (matlab generated)
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6 changes: 6 additions & 0 deletions include/amici/simulation_parameters.h
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Expand Up @@ -35,6 +35,11 @@ class SimulationParameters {
this->parameters.size(), ParameterScaling::none
)) {}

#ifndef SWIGPYTHON
/*
* include/amici/simulation_parameters.h:71: Warning 509: Overloaded method amici::SimulationParameters::SimulationParameters(std::vector< amici::realtype,std::allocator< amici::realtype > >,std::vector< amici::realtype,std::allocator< amici::realtype > >,std::vector< amici::realtype,std::allocator< amici::realtype > >) effectively ignored,
* include/amici/simulation_parameters.h:54: Warning 509: as it is shadowed by amici::SimulationParameters::SimulationParameters(std::vector< amici::realtype,std::allocator< amici::realtype > >,std::vector< amici::realtype,std::allocator< amici::realtype > >,std::vector< int,std::allocator< int > >).
*/
/**
* @brief Constructor
* @param fixedParameters Model constants
Expand Down Expand Up @@ -69,6 +74,7 @@ class SimulationParameters {
this->parameters.size(), ParameterScaling::none
))
, ts_(std::move(timepoints)) {}
#endif

/**
* @brief Set reinitialization of all states based on model constants for
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6 changes: 3 additions & 3 deletions src/steadystateproblem.cpp
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Expand Up @@ -601,8 +601,6 @@ void SteadystateProblem::applyNewtonsMethod(Model& model, bool newton_retry) {
int& i_newtonstep = numsteps_.at(newton_retry ? 2 : 0);
i_newtonstep = 0;
gamma_ = 1.0;
bool update_direction = true;
bool step_successful = false;

if (model.nx_solver == 0)
return;
Expand All @@ -613,6 +611,8 @@ void SteadystateProblem::applyNewtonsMethod(Model& model, bool newton_retry) {
bool converged = false;
wrms_ = getWrms(model, SensitivityMethod::none);
converged = newton_retry ? false : wrms_ < conv_thresh;
bool update_direction = true;

while (!converged && i_newtonstep < max_steps_) {

/* If Newton steps are necessary, compute the initial search
Expand All @@ -634,7 +634,7 @@ void SteadystateProblem::applyNewtonsMethod(Model& model, bool newton_retry) {
/* Compute new xdot and residuals */
realtype wrms_tmp = getWrms(model, SensitivityMethod::none);

step_successful = wrms_tmp < wrms_;
bool step_successful = wrms_tmp < wrms_;
if (step_successful) {
/* If new residuals are smaller than old ones, update state */
wrms_ = wrms_tmp;
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