Merge branch 'develop' into gha_split_macos

include/amici/edata.h

@@ -14,24 +14,24 @@ class ReturnData;
 
 /**
  * @brief ExpData carries all information about experimental or
- * condition-specific data
+ * condition-specific data.
  */
 class ExpData : public SimulationParameters {
 
   public:
     /**
-     * @brief default constructor
+     * @brief Default constructor.
      */
     ExpData() = default;
 
     /**
-     * @brief Copy constructor, needs to be declared to be generated in
-     * swig
+     * @brief Copy constructor.
      */
+    // needs to be declared to be wrapped by SWIG
     ExpData(ExpData const&) = default;
 
     /**
-     * @brief constructor that only initializes dimensions
+     * @brief Constructor that only initializes dimensions.
      *
      * @param nytrue Number of observables
      * @param nztrue Number of event outputs
@@ -154,6 +154,16 @@ class ExpData : public SimulationParameters {
     /**
      * @brief Set output timepoints.
      *
+     * If the number of timepoint increases, this will grow the
+     * observation/sigma matrices and fill new entries with NaN.
+     * If the number of timepoints decreases, this will shrink the
+     * observation/sigma matrices.
+     *
+     * Note that the mapping from timepoints to measurements will not be
+     * preserved. E.g., say there are measurements at t = 2, and this
+     * function is called with [1, 2], then the old measurements will belong to
+     * t = 1.
+     *
      * @param ts timepoints
      */
     void setTimepoints(std::vector<realtype> const& ts);
@@ -225,7 +235,7 @@ class ExpData : public SimulationParameters {
     void setObservedDataStdDev(std::vector<realtype> const& observedDataStdDev);
 
     /**
-     * @brief Set indentical standard deviation for all measurements.
+     * @brief Set identical standard deviation for all measurements.
      *
      * @param stdDev standard deviation (dimension: scalar)
      */
@@ -278,26 +288,23 @@ class ExpData : public SimulationParameters {
     realtype const* getObservedDataStdDevPtr(int it) const;
 
     /**
-     * @brief set function that copies observed event data from input to
-     * ExpData::observedEvents
+     * @brief Set observed event data.
      *
      * @param observedEvents observed data (dimension: nmaxevent x nztrue,
      * row-major)
      */
     void setObservedEvents(std::vector<realtype> const& observedEvents);
 
     /**
-     * @brief set function that copies observed event data for specific event
-     * observable
+     * @brief Set observed event data for specific event observable.
      *
      * @param observedEvents observed data (dimension: nmaxevent)
      * @param iz observed event data index
      */
     void setObservedEvents(std::vector<realtype> const& observedEvents, int iz);
 
     /**
-     * @brief get function that checks whether event data at specified indices
-     * has been set
+     * @brief Check whether event data at specified indices has been set.
      *
      * @param ie event index
      * @param iz event observable index
@@ -306,42 +313,38 @@ class ExpData : public SimulationParameters {
     bool isSetObservedEvents(int ie, int iz) const;
 
     /**
-     * @brief get function that copies data from ExpData::mz to output
+     * @brief Get observed event data.
      *
      * @return observed event data
      */
     std::vector<realtype> const& getObservedEvents() const;
 
     /**
-     * @brief get function that returns a pointer to observed data at ieth
-     * occurrence
+     * @brief Get pointer to observed data at ie-th occurrence.
      *
      * @param ie event occurrence
      *
-     * @return pointer to observed event data at ieth occurrence
+     * @return pointer to observed event data at ie-th occurrence
      */
     realtype const* getObservedEventsPtr(int ie) const;
 
     /**
-     * @brief set function that copies data from input to
-     * ExpData::observedEventsStdDev
+     * @brief Set standard deviation of observed event data.
      *
      * @param observedEventsStdDev standard deviation of observed event data
      */
     void
     setObservedEventsStdDev(std::vector<realtype> const& observedEventsStdDev);
 
     /**
-     * @brief set function that sets all ExpData::observedDataStdDev to the
-     * input value
+     * @brief Set standard deviation of observed event data.
      *
      * @param stdDev standard deviation (dimension: scalar)
      */
     void setObservedEventsStdDev(realtype stdDev);
 
     /**
-     * @brief set function that copies standard deviation of observed data for
-     * specific observable
+     * @brief Set standard deviation of observed data for a specific observable.
      *
      * @param observedEventsStdDev standard deviation of observed data
      * (dimension: nmaxevent)
@@ -352,17 +355,16 @@ class ExpData : public SimulationParameters {
     );
 
     /**
-     * @brief set function that sets all standard deviation of a specific
-     * observable to the input value
+     * @brief Set all standard deviations of a specific event-observable.
      *
      * @param stdDev standard deviation (dimension: scalar)
      * @param iz observed data index
      */
     void setObservedEventsStdDev(realtype stdDev, int iz);
 
     /**
-     * @brief get function that checks whether standard deviation of even data
-     * at specified indices has been set
+     * @brief Check whether standard deviation of event data
+     * at specified indices has been set.
      *
      * @param ie event index
      * @param iz event observable index
@@ -371,16 +373,15 @@ class ExpData : public SimulationParameters {
     bool isSetObservedEventsStdDev(int ie, int iz) const;
 
     /**
-     * @brief get function that copies data from ExpData::observedEventsStdDev
-     * to output
+     * @brief Get standard deviation of observed event data.
      *
      * @return standard deviation of observed event data
      */
     std::vector<realtype> const& getObservedEventsStdDev() const;
 
     /**
-     * @brief get function that returns a pointer to standard deviation of
-     * observed event data at ie-th occurrence
+     * @brief Get pointer to standard deviation of
+     * observed event data at ie-th occurrence.
      *
      * @param ie event occurrence
      *

include/amici/logging.h

@@ -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;

include/amici/model.h

@@ -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)

include/amici/simulation_parameters.h

@@ -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
@@ -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

src/steadystateproblem.cpp

@@ -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;
@@ -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
@@ -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;