Regenerate test models, update version (#3032)

* update version number - missed update on `main`
* regenerate test models - missed updating after recent changes to the templates

Author: dweindl

models/model_calvetti_py/CMakeLists.txt

@@ -4,6 +4,12 @@ cmake_policy(VERSION 3.22...3.31)
 
 project(model_calvetti_py)
 
+message(STATUS "CMAKE_CURRENT_SOURCE_DIR: ${CMAKE_CURRENT_SOURCE_DIR}")
+message(STATUS "CMAKE_BINARY_DIR: ${CMAKE_BINARY_DIR}")
+message(STATUS "CMAKE_INSTALL_PREFIX: ${CMAKE_INSTALL_PREFIX}")
+message(STATUS "CMAKE_VERSION: ${CMAKE_VERSION}")
+message(STATUS "CMAKE_COMMAND: ${CMAKE_COMMAND}")
+
 set(CMAKE_CXX_STANDARD 20)
 set(CMAKE_CXX_STANDARD_REQUIRED ON)
 set(CMAKE_POSITION_INDEPENDENT_CODE ON)
@@ -30,7 +36,7 @@ if(DEFINED ENV{AMICI_LDFLAGS})
   link_libraries("$ENV{AMICI_LDFLAGS}")
 endif()
 
-find_package(Amici 0.34.1 REQUIRED HINTS
+find_package(Amici 0.34.2 REQUIRED HINTS
              ${CMAKE_CURRENT_LIST_DIR}/../../build)
 message(STATUS "Found AMICI ${Amici_DIR}")
 set_target_properties(Upstream::amici PROPERTIES

models/model_calvetti_py/model_calvetti_py.h

@@ -549,15 +549,15 @@ class Model_model_calvetti_py : public amici::Model_DAE {
      * @return AMICI version string
      */
     std::string get_amici_version() const override {
-        return "0.34.1";
+        return "0.34.2";
     }
 
     /**
      * @brief returns the amici version that was used to generate the model
      * @return AMICI git commit hash
      */
     std::string get_amici_commit() const override {
-        return "f005fac9e2de7c3c90be2ac55d4ad165471ed1e7";
+        return "b0b2684b4b67db9eadf5e47d4f87f8fe74dd9070";
     }
 
     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:
@@ -87,7 +87,7 @@ def get_extension() -> CMakeExtension:
     author_email="model-author-todo",
     ext_modules=[MODEL_EXT],
     packages=find_namespace_packages(),
-    install_requires=["amici==0.34.1"],
+    install_requires=["amici==0.34.2"],
     python_requires=">=3.11",
     package_data={},
     zip_safe=False,

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/CMakeLists.txt

@@ -4,6 +4,12 @@ cmake_policy(VERSION 3.22...3.31)
 
 project(model_dirac_py)
 
+message(STATUS "CMAKE_CURRENT_SOURCE_DIR: ${CMAKE_CURRENT_SOURCE_DIR}")
+message(STATUS "CMAKE_BINARY_DIR: ${CMAKE_BINARY_DIR}")
+message(STATUS "CMAKE_INSTALL_PREFIX: ${CMAKE_INSTALL_PREFIX}")
+message(STATUS "CMAKE_VERSION: ${CMAKE_VERSION}")
+message(STATUS "CMAKE_COMMAND: ${CMAKE_COMMAND}")
+
 set(CMAKE_CXX_STANDARD 20)
 set(CMAKE_CXX_STANDARD_REQUIRED ON)
 set(CMAKE_POSITION_INDEPENDENT_CODE ON)
@@ -30,7 +36,7 @@ if(DEFINED ENV{AMICI_LDFLAGS})
   link_libraries("$ENV{AMICI_LDFLAGS}")
 endif()
 
-find_package(Amici 0.34.1 REQUIRED HINTS
+find_package(Amici 0.34.2 REQUIRED HINTS
              ${CMAKE_CURRENT_LIST_DIR}/../../build)
 message(STATUS "Found AMICI ${Amici_DIR}")
 set_target_properties(Upstream::amici PROPERTIES

models/model_dirac_py/model_dirac_py.h

@@ -536,15 +536,15 @@ class Model_model_dirac_py : public amici::Model_ODE {
      * @return AMICI version string
      */
     std::string get_amici_version() const override {
-        return "0.34.1";
+        return "0.34.2";
     }
 
     /**
      * @brief returns the amici version that was used to generate the model
      * @return AMICI git commit hash
      */
     std::string get_amici_commit() const override {
-        return "f005fac9e2de7c3c90be2ac55d4ad165471ed1e7";
+        return "b0b2684b4b67db9eadf5e47d4f87f8fe74dd9070";
     }
 
     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:
@@ -87,7 +87,7 @@ def get_extension() -> CMakeExtension:
     author_email="model-author-todo",
     ext_modules=[MODEL_EXT],
     packages=find_namespace_packages(),
-    install_requires=["amici==0.34.1"],
+    install_requires=["amici==0.34.2"],
     python_requires=">=3.11",
     package_data={},
     zip_safe=False,

models/model_dirac_py/swig/model_dirac_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_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():
@@ -36,6 +37,28 @@ if t_imported < t_modified:
 
 %module(package="model_dirac_py",moduleimport=MODULEIMPORT) model_dirac_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_events_py/CMakeLists.txt

@@ -4,6 +4,12 @@ cmake_policy(VERSION 3.22...3.31)
 
 project(model_events_py)
 
+message(STATUS "CMAKE_CURRENT_SOURCE_DIR: ${CMAKE_CURRENT_SOURCE_DIR}")
+message(STATUS "CMAKE_BINARY_DIR: ${CMAKE_BINARY_DIR}")
+message(STATUS "CMAKE_INSTALL_PREFIX: ${CMAKE_INSTALL_PREFIX}")
+message(STATUS "CMAKE_VERSION: ${CMAKE_VERSION}")
+message(STATUS "CMAKE_COMMAND: ${CMAKE_COMMAND}")
+
 set(CMAKE_CXX_STANDARD 20)
 set(CMAKE_CXX_STANDARD_REQUIRED ON)
 set(CMAKE_POSITION_INDEPENDENT_CODE ON)
@@ -30,7 +36,7 @@ if(DEFINED ENV{AMICI_LDFLAGS})
   link_libraries("$ENV{AMICI_LDFLAGS}")
 endif()
 
-find_package(Amici 0.34.1 REQUIRED HINTS
+find_package(Amici 0.34.2 REQUIRED HINTS
              ${CMAKE_CURRENT_LIST_DIR}/../../build)
 message(STATUS "Found AMICI ${Amici_DIR}")
 set_target_properties(Upstream::amici PROPERTIES