update templates, regenerate test models

Author: dweindl

models/model_calvetti_py/main.cpp

@@ -38,7 +38,7 @@ int main() {
     solver->set_relative_tolerance(1e-8);
 
     // Run the simulation using default parameters set during model import
-    // (can be changed using model->setParameters() or model->setParameterBy*())
+    // (can be changed using model->set_free_parameters() or model->set_free_parameter_by*())
     auto rdata = run_simulation(*solver, nullptr, *model);
 
     // Print observable time course
@@ -69,7 +69,7 @@ int main() {
     // Print state sensitivities sx...
     // ... for the first timepoint...
     int i_time = 0;
-    // ... with respect to the first parameter
+    // ... with respect to the first free parameter
     int i_nplist = 0;
 
     // get identifiers from model

models/model_calvetti_py/model_calvetti_py.cpp

@@ -5,7 +5,7 @@ namespace amici::model_model_calvetti_py {
 
 // clang-format off
 
-std::array<const char*, 0> parameter_names = {
+std::array<const char*, 0> free_parameter_names = {
 
 };
 
@@ -65,7 +65,7 @@ std::array<const char*, 17> expression_names = {
 "flux_r0", // w[16]
 };
 
-std::array<const char*, 0> parameter_ids = {
+std::array<const char*, 0> free_parameter_ids = {
 
 };
 

models/model_calvetti_py/model_calvetti_py.h

@@ -144,7 +144,7 @@ class Model_model_calvetti_py : public amici::Model_DAE {
               },
               amici::SimulationParameters(
                   std::vector<realtype>{0.28999999999999998, 0.73999999999999999, 0.44, 0.080000000000000002, 0.27000000000000002, 0.17999999999999999}, // fixedParameters
-                  std::vector<realtype>{}        // dynamic parameters
+                  std::vector<realtype>{}        // free parameters
               ),
               amici::SecondOrderMode::none,                                  // o2mode
               std::vector<realtype>{1.0, 1.0, 1.0, 0.0, 0.0, 0.0},   // idlist
@@ -421,7 +421,7 @@ class Model_model_calvetti_py : public amici::Model_DAE {
     }
 
     /**
-     * @brief Get names of the model parameters
+     * @brief Get names of the free model parameters
      * @return the names
      */
     std::vector<std::string> get_free_parameter_names() const override {
@@ -478,7 +478,7 @@ class Model_model_calvetti_py : public amici::Model_DAE {
     }
 
     /**
-     * @brief Get ids of the model parameters
+     * @brief Get ids of the free model parameters
      * @return the ids
      */
     std::vector<std::string> get_free_parameter_ids() const override {
@@ -557,7 +557,7 @@ class Model_model_calvetti_py : public amici::Model_DAE {
      * @return AMICI git commit hash
      */
     std::string get_amici_commit() const override {
-        return "f005fac9e2de7c3c90be2ac55d4ad165471ed1e7";
+        return "40190b46b1b398e321314ded4169fe910b37c484";
     }
 
     bool has_quadratic_llh() const override {

models/model_calvetti_py/setup.py

@@ -1,5 +1,6 @@
 """AMICI model package setup"""
 
+import importlib.metadata
 import os
 import sys
 from pathlib import Path
@@ -8,7 +9,6 @@
 from amici.custom_commands import AmiciBuildCMakeExtension
 from cmake_build_extension import CMakeExtension
 from setuptools import find_namespace_packages, setup
-import importlib.metadata
 
 
 def get_extension() -> CMakeExtension:

models/model_calvetti_py/swig/model_calvetti_py.i

@@ -8,10 +8,11 @@ import sysconfig
 from pathlib import Path
 
 ext_suffix = sysconfig.get_config_var('EXT_SUFFIX')
+extension_path = Path(__file__).parent / f'_model_calvetti_py{ext_suffix}'
 _model_calvetti_py = amici._module_from_path(
     'model_calvetti_py._model_calvetti_py' if __package__ or '.' in __name__
     else '_model_calvetti_py',
-    Path(__file__).parent / f'_model_calvetti_py{ext_suffix}',
+    extension_path,
 )
 
 def _get_import_time():
@@ -36,6 +37,28 @@ if t_imported < t_modified:
 
 %module(package="model_calvetti_py",moduleimport=MODULEIMPORT) model_calvetti_py
 
+// store swig version
+%constant int SWIG_VERSION_MAJOR = (SWIG_VERSION >> 16);
+%constant int SWIG_VERSION_MINOR = ((SWIG_VERSION >> 8) & 0xff);
+%constant int SWIG_VERSION_PATCH = (SWIG_VERSION & 0xff);
+
+%pythoncode %{
+# SWIG version used to build the model extension as `(major, minor, patch)`
+_SWIG_VERSION = (SWIG_VERSION_MAJOR, SWIG_VERSION_MINOR, SWIG_VERSION_PATCH)
+
+if (amici_swig := amici.amici._SWIG_VERSION) != (model_swig := _SWIG_VERSION):
+    import warnings
+    warnings.warn(
+        f"SWIG version mismatch between amici ({amici_swig}) and model "
+        f"({model_swig}). This may lead to unexpected behavior. "
+        "In that case, please recompile the model with swig=="
+        f"{amici_swig[0]}.{amici_swig[1]}.{amici_swig[2]} or rebuild amici "
+        f"with swig=={model_swig[0]}.{model_swig[1]}.{model_swig[2]}.",
+        RuntimeWarning,
+        stacklevel=2,
+    )
+%}
+
 %pythoncode %{
 # the model-package __init__.py module (will be set during import)
 _model_module = None
@@ -56,7 +79,7 @@ using namespace amici;
 // store the time a module was imported
 %{
 #include <chrono>
-static std::chrono::time_point<std::chrono::system_clock> _module_import_time;
+static std::chrono::time_point<std::chrono::system_clock> _module_import_time = std::chrono::system_clock::now();
 
 static double _get_import_time() {
     auto epoch = _module_import_time.time_since_epoch();
@@ -67,7 +90,9 @@ static double _get_import_time() {
 static double _get_import_time();
 
 %init %{
-    _module_import_time = std::chrono::system_clock::now();
+    // NOTE: from SWIG 4.4.0 onwards, %init code is executed every time the
+    // module is executed - not only on first import
+    // This code ends up in `SWIG_mod_exec`.
 %}
 
 

models/model_dirac_py/main.cpp

@@ -38,7 +38,7 @@ int main() {
     solver->set_relative_tolerance(1e-8);
 
     // Run the simulation using default parameters set during model import
-    // (can be changed using model->setParameters() or model->setParameterBy*())
+    // (can be changed using model->set_free_parameters() or model->set_free_parameter_by*())
     auto rdata = run_simulation(*solver, nullptr, *model);
 
     // Print observable time course
@@ -69,7 +69,7 @@ int main() {
     // Print state sensitivities sx...
     // ... for the first timepoint...
     int i_time = 0;
-    // ... with respect to the first parameter
+    // ... with respect to the first free parameter
     int i_nplist = 0;
 
     // get identifiers from model

models/model_dirac_py/model_dirac_py.cpp

@@ -5,7 +5,7 @@ namespace amici::model_model_dirac_py {
 
 // clang-format off
 
-std::array<const char*, 4> parameter_names = {
+std::array<const char*, 4> free_parameter_names = {
     "p1", // p[0]
 "p2", // p[1]
 "p3", // p[2]
@@ -33,7 +33,7 @@ std::array<const char*, 1> expression_names = {
     "flux_r0", // w[0]
 };
 
-std::array<const char*, 4> parameter_ids = {
+std::array<const char*, 4> free_parameter_ids = {
     "p1", // p[0]
 "p2", // p[1]
 "p3", // p[2]

models/model_dirac_py/model_dirac_py.h

@@ -14,7 +14,7 @@ class Solver;
 
 namespace model_model_dirac_py {
 
-extern std::array<const char*, 4> parameter_names;
+extern std::array<const char*, 4> free_parameter_names;
 extern std::array<const char*, 0> fixed_parameter_names;
 extern std::array<const char*, 2> state_names;
 extern std::array<const char*, 1> observable_names;
@@ -144,7 +144,7 @@ class Model_model_dirac_py : public amici::Model_ODE {
               },
               amici::SimulationParameters(
                   std::vector<realtype>{}, // fixedParameters
-                  std::vector<realtype>{1.0, 0.5, 2.0, 3.0}        // dynamic parameters
+                  std::vector<realtype>{1.0, 0.5, 2.0, 3.0}        // free parameters
               ),
               amici::SecondOrderMode::none,                                  // o2mode
               std::vector<realtype>{1.0, 1.0},   // idlist
@@ -408,12 +408,12 @@ class Model_model_dirac_py : public amici::Model_ODE {
     }
 
     /**
-     * @brief Get names of the model parameters
+     * @brief Get names of the free model parameters
      * @return the names
      */
-    std::vector<std::string> get_parameter_names() const override {
-        return std::vector<std::string>(parameter_names.begin(),
-                                        parameter_names.end());
+    std::vector<std::string> get_free_parameter_names() const override {
+        return std::vector<std::string>(free_parameter_names.begin(),
+                                        free_parameter_names.end());
     }
 
     /**
@@ -465,7 +465,7 @@ class Model_model_dirac_py : public amici::Model_ODE {
     }
 
     /**
-     * @brief Get ids of the model parameters
+     * @brief Get ids of the free model parameters
      * @return the ids
      */
     std::vector<std::string> get_free_parameter_ids() const override {
@@ -544,7 +544,7 @@ class Model_model_dirac_py : public amici::Model_ODE {
      * @return AMICI git commit hash
      */
     std::string get_amici_commit() const override {
-        return "f005fac9e2de7c3c90be2ac55d4ad165471ed1e7";
+        return "40190b46b1b398e321314ded4169fe910b37c484";
     }
 
     bool has_quadratic_llh() const override {

models/model_dirac_py/model_dirac_py/model_dirac_py.py

@@ -1,5 +1,5 @@
 # This file was automatically generated by SWIG (https://www.swig.org).
-# Version 4.3.1
+# Version 4.4.0
 #
 # Do not make changes to this file unless you know what you are doing - modify
 # the SWIG interface file instead.
@@ -14,10 +14,11 @@
 from pathlib import Path
 
 ext_suffix = sysconfig.get_config_var('EXT_SUFFIX')
+extension_path = Path(__file__).parent / f'_model_dirac_py{ext_suffix}'
 _model_dirac_py = amici._module_from_path(
     'model_dirac_py._model_dirac_py' if __package__ or '.' in __name__
     else '_model_dirac_py',
-    Path(__file__).parent / f'_model_dirac_py{ext_suffix}',
+    extension_path,
 )
 
 def _get_import_time():
@@ -86,6 +87,25 @@ class _SwigNonDynamicMeta(type):
     __setattr__ = _swig_setattr_nondynamic_class_variable(type.__setattr__)
 
 
+SWIG_VERSION_MAJOR = _model_dirac_py.SWIG_VERSION_MAJOR
+SWIG_VERSION_MINOR = _model_dirac_py.SWIG_VERSION_MINOR
+SWIG_VERSION_PATCH = _model_dirac_py.SWIG_VERSION_PATCH
+
+# SWIG version used to build the model extension as `(major, minor, patch)`
+_SWIG_VERSION = (SWIG_VERSION_MAJOR, SWIG_VERSION_MINOR, SWIG_VERSION_PATCH)
+
+if (amici_swig := amici.amici._SWIG_VERSION) != (model_swig := _SWIG_VERSION):
+    import warnings
+    warnings.warn(
+        f"SWIG version mismatch between amici ({amici_swig}) and model "
+        f"({model_swig}). This may lead to unexpected behavior. "
+        "In that case, please recompile the model with swig=="
+        f"{amici_swig[0]}.{amici_swig[1]}.{amici_swig[2]} or rebuild amici "
+        f"with swig=={model_swig[0]}.{model_swig[1]}.{model_swig[2]}.",
+        RuntimeWarning,
+        stacklevel=2,
+    )
+
 
 # the model-package __init__.py module (will be set during import)
 _model_module = None

models/model_dirac_py/setup.py

@@ -1,5 +1,6 @@
 """AMICI model package setup"""
 
+import importlib.metadata
 import os
 import sys
 from pathlib import Path
@@ -8,7 +9,6 @@
 from amici.custom_commands import AmiciBuildCMakeExtension
 from cmake_build_extension import CMakeExtension
 from setuptools import find_namespace_packages, setup
-import importlib.metadata
 
 
 def get_extension() -> CMakeExtension: