Merge pull request #835 from ICB-DCM/develop

Release 0.10.13

* BREAKING CHANGE: Renaming {get|set}tNewtonPreequilibration to {get|set}Preequilibration (Closes #720)
* Make wurlitzer non-optional requirement for AMICI python package (Fixes missing AMICI errors when running from jupyter notebooks)
* Compute initial state for Model::getInitialStates if not already set (Fixes #818)
* Make swig generate pydoc comments from doxygen comments #830 (Closes #745) to provide Python docstrings for C++ wrapper functions
* feature(cmake) Add option to disable compiler optimizations for wrapfunctions.cpp (Fixes #828) (#829)
* Change SBML test suite to pytest to allow for parallel test execution… (#824)
* Fix(cmake): -E option is not available in all sed versions. Neither is the equivalent -r. Use --regexp-extended instead (Closes #826)
* Refactor(python) Move PEtab import code from command line script… (#825)
* Fix(core) Fix regular expressions for intel compiler (Closes #754) (#822)
* Update workflow figure to include PySB (Closes #799)
* Fix compiler warnings

Author: dweindl

cmake/version.cmake

@@ -1,6 +1,6 @@
 find_package(Git)
 if(Git_FOUND)
-    execute_process(COMMAND sh -c "${GIT_EXECUTABLE} describe --abbrev=4 --dirty=-dirty --always --tags  | cut -c 2- | tr -d '\n' | sed -E s/-/./"
+    execute_process(COMMAND sh -c "${GIT_EXECUTABLE} describe --abbrev=4 --dirty=-dirty --always --tags  | cut -c 2- | tr -d '\n' | sed --regexp-extended s/-/./"
         WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}
         OUTPUT_VARIABLE PROJECT_VERSION_GIT
         )

documentation/gfx/amici_workflow.png

@@ -13,22 +13,22 @@
 namespace amici {
 
 /*!
- * @brief printErrMsgIdAndTxt prints a specified error message associated to the
- * specified identifier
+ * @brief Prints a specified error message associated to the specified
+ * identifier
  *
- * @param[in] identifier error identifier @type char
- * @param[in] format string with error message printf-style format
+ * @param identifier error identifier
+ * @param format string with error message printf-style format
  * @param ... arguments to be formatted
  */
 void
 printErrMsgIdAndTxt(const char* identifier, const char* format, ...);
 
 /*!
- * @brief printErrMsgIdAndTxt prints a specified warning message associated to
- * the specified identifier
+ * @brief Prints a specified warning message associated to the specified
+ * identifier
  *
- * @param[in] identifier warning identifier @type char
- * @param[in] format string with error message printf-style format
+ * @param identifier warning identifier
+ * @param format string with error message printf-style format
  * @param ... arguments to be formatted
  */
 void

documentation/gfx/amici_workflow.svg

@@ -7,6 +7,7 @@
 #include <algorithm>
 #include <vector>
 #include <memory>
+#include <regex>
 
 #include <gsl/gsl-lite.hpp>
 
@@ -84,6 +85,12 @@ void scaleParameters(gsl::span<const realtype> bufferUnscaled,
  */
 std::string backtraceString(int maxFrames);
 
+/**
+ * @brief Convert std::regex_constants::error_type to string
+ * @param err_type error type
+ * @return Error type as string
+ */
+std::string regexErrorToString(std::regex_constants::error_type err_type);
 
 } // namespace amici
 

include/amici/amici.h

@@ -588,19 +588,25 @@ class Model : public AbstractModel {
      * @brief Get the initial states
      * @return initial state vector
      */
-    std::vector<realtype> const &getInitialStates() const;
+    std::vector<realtype> getInitialStates();
 
     /**
      * @brief Set the initial states
      * @param x0 initial state vector
      */
     void setInitialStates(std::vector<realtype> const &x0);
 
+    /**
+     * @brief Returns whether custom initial states have been set
+     * @return True if has custom initial states, otherwise false
+     */
+    bool hasCustomInitialStates() const;
+
     /**
      * @brief Get the initial states sensitivities
      * @return vector of initial state sensitivities
      */
-    std::vector<realtype> const &getInitialStateSensitivities() const;
+    std::vector<realtype> getInitialStateSensitivities();
 
     /**
      * @brief Set the initial state sensitivities
@@ -609,6 +615,12 @@ class Model : public AbstractModel {
      */
     void setInitialStateSensitivities(std::vector<realtype> const &sx0);
 
+    /**
+     * @brief Returns whether custom initial state sensitivitiess have been set
+     * @return True if has custom initial state sensitivitiess, otherwise false
+     */
+    bool hasCustomInitialStateSensitivities() const;
+
     /**
      * @brief Set the initial state sensitivities
      * @param sx0 vector of initial state sensitivities without chainrule
@@ -1046,7 +1058,7 @@ class Model : public AbstractModel {
 
     /**
      * @brief Sets only those initial states sensitivities that are affected
-     *from fx0 fixedParmeters
+     * from fx0 fixedParmeters
      * @param sx pointer to state sensitivity variables
      * @param x pointer to state variables
      **/

include/amici/misc.h

@@ -147,7 +147,7 @@ class Model_DAE : public Model {
              realtype cj) override;
 
     /** Matrix vector product of J with a vector v (for iterative solvers)
-     * @param t timepoint @type realtype
+     * @param t timepoint
      * @param cj scaling factor, inverse of the step size
      * @param x Vector with the states
      * @param dx Vector with the derivative states

include/amici/model.h

@@ -54,7 +54,7 @@ void serialize(Archive &ar, amici::Solver &u, const unsigned int version) {
     ar &u.ss_rtol_sensi;
     ar &u.maxsteps;
     ar &u.maxstepsB;
-    ar &u.newton_preeq;
+    ar &u.requires_preequilibration;
     ar &u.newton_maxsteps;
     ar &u.newton_maxlinsteps;
     ar &u.ism;

include/amici/model_dae.h

@@ -194,16 +194,16 @@ class Solver {
     void setNewtonMaxSteps(int newton_maxsteps);
 
     /**
-     * @brief Get if preequilibration of model via Newton solver is enabled
+     * @brief Get if model preequilibration is enabled
      * @return
      */
-    bool getNewtonPreequilibration() const;
+    bool getPreequilibration() const;
 
     /**
-     * @brief Enable/disable preequilibration of model via Newton solver
-     * @param newton_preeq
+     * @brief Enable/disable model preequilibration
+     * @param require_preequilibration
      */
-    void setNewtonPreequilibration(bool newton_preeq);
+    void setPreequilibration(bool require_preequilibration);
 
     /**
      * @brief Get maximum number of allowed linear steps per Newton step for
@@ -1381,8 +1381,8 @@ class Solver {
      * computation */
     long int newton_maxlinsteps = 0;
 
-    /** Preequilibration of model via Newton solver? */
-    bool newton_preeq = false;
+    /** Enable model preequilibration */
+    bool requires_preequilibration = false;
 
     /** linear solver specification */
     LinearSolver linsol = LinearSolver::KLU;
@@ -1464,8 +1464,7 @@ bool operator==(const Solver &a, const Solver &b);
  *
  * @param error_code error identifier
  * @param module name of the module in which the error occured
- * @param function name of the function in which the error occured @type
- * char
+ * @param function name of the function in which the error occured
  * @param msg error message
  * @param eh_data unused input
  */