Prepare release 0.34.1

CHANGELOG.md

@@ -4,6 +4,14 @@ See also our [versioning policy](https://amici.readthedocs.io/en/latest/versioni
 
 ## v0.X Series
 
+### v0.34.1 (2025-08-25)
+
+Bugfix release.
+
+* Fixed a bug that would lead to incorrect model initialization in SBML models
+  with initial assignments that depend on dynamic entities
+  (by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2939)
+
 ### v0.34.0 (2025-07-29)
 
 This will probably be the last release to include the MATLAB interface.

models/model_calvetti_py/CMakeLists.txt

@@ -30,7 +30,7 @@ if(DEFINED ENV{AMICI_LDFLAGS})
   link_libraries("$ENV{AMICI_LDFLAGS}")
 endif()
 
-find_package(Amici 0.34.0 REQUIRED HINTS
+find_package(Amici 0.34.1 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

@@ -550,15 +550,15 @@ class Model_model_calvetti_py : public amici::Model_DAE {
      * @return AMICI version string
      */
     std::string getAmiciVersion() const override {
-        return "0.34.0";
+        return "0.34.1";
     }
 
     /**
      * @brief returns the amici version that was used to generate the model
      * @return AMICI git commit hash
      */
     std::string getAmiciCommit() const override {
-        return "08d0c9533715453de60b684970751c6de07ffd9b";
+        return "b12c68a7a02f1cbd33de59d47cbc0c4d77d30d6f";
     }
 
     bool hasQuadraticLLH() const override {

models/model_calvetti_py/setup.py

@@ -87,7 +87,7 @@ def get_extension() -> CMakeExtension:
     author_email="model-author-todo",
     ext_modules=[MODEL_EXT],
     packages=find_namespace_packages(),
-    install_requires=["amici==0.34.0"],
+    install_requires=["amici==0.34.1"],
     python_requires=">=3.11",
     package_data={},
     zip_safe=False,

models/model_dirac_py/CMakeLists.txt

@@ -30,7 +30,7 @@ if(DEFINED ENV{AMICI_LDFLAGS})
   link_libraries("$ENV{AMICI_LDFLAGS}")
 endif()
 
-find_package(Amici 0.34.0 REQUIRED HINTS
+find_package(Amici 0.34.1 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

@@ -537,15 +537,15 @@ class Model_model_dirac_py : public amici::Model_ODE {
      * @return AMICI version string
      */
     std::string getAmiciVersion() const override {
-        return "0.34.0";
+        return "0.34.1";
     }
 
     /**
      * @brief returns the amici version that was used to generate the model
      * @return AMICI git commit hash
      */
     std::string getAmiciCommit() const override {
-        return "08d0c9533715453de60b684970751c6de07ffd9b";
+        return "b12c68a7a02f1cbd33de59d47cbc0c4d77d30d6f";
     }
 
     bool hasQuadraticLLH() const override {

models/model_dirac_py/setup.py

@@ -87,7 +87,7 @@ def get_extension() -> CMakeExtension:
     author_email="model-author-todo",
     ext_modules=[MODEL_EXT],
     packages=find_namespace_packages(),
-    install_requires=["amici==0.34.0"],
+    install_requires=["amici==0.34.1"],
     python_requires=">=3.11",
     package_data={},
     zip_safe=False,

models/model_events_py/CMakeLists.txt

@@ -30,7 +30,7 @@ if(DEFINED ENV{AMICI_LDFLAGS})
   link_libraries("$ENV{AMICI_LDFLAGS}")
 endif()
 
-find_package(Amici 0.34.0 REQUIRED HINTS
+find_package(Amici 0.34.1 REQUIRED HINTS
              ${CMAKE_CURRENT_LIST_DIR}/../../build)
 message(STATUS "Found AMICI ${Amici_DIR}")
 set_target_properties(Upstream::amici PROPERTIES

models/model_events_py/model_events_py.h

@@ -572,15 +572,15 @@ class Model_model_events_py : public amici::Model_ODE {
      * @return AMICI version string
      */
     std::string getAmiciVersion() const override {
-        return "0.34.0";
+        return "0.34.1";
     }
 
     /**
      * @brief returns the amici version that was used to generate the model
      * @return AMICI git commit hash
      */
     std::string getAmiciCommit() const override {
-        return "08d0c9533715453de60b684970751c6de07ffd9b";
+        return "b12c68a7a02f1cbd33de59d47cbc0c4d77d30d6f";
     }
 
     bool hasQuadraticLLH() const override {

models/model_events_py/setup.py

@@ -87,7 +87,7 @@ def get_extension() -> CMakeExtension:
     author_email="model-author-todo",
     ext_modules=[MODEL_EXT],
     packages=find_namespace_packages(),
-    install_requires=["amici==0.34.0"],
+    install_requires=["amici==0.34.1"],
     python_requires=">=3.11",
     package_data={},
     zip_safe=False,

models/model_jakstat_adjoint_py/CMakeLists.txt

@@ -30,7 +30,7 @@ if(DEFINED ENV{AMICI_LDFLAGS})
   link_libraries("$ENV{AMICI_LDFLAGS}")
 endif()
 
-find_package(Amici 0.34.0 REQUIRED HINTS
+find_package(Amici 0.34.1 REQUIRED HINTS
              ${CMAKE_CURRENT_LIST_DIR}/../../build)
 message(STATUS "Found AMICI ${Amici_DIR}")
 set_target_properties(Upstream::amici PROPERTIES

models/model_jakstat_adjoint_py/model_jakstat_adjoint_py.h

@@ -545,15 +545,15 @@ class Model_model_jakstat_adjoint_py : public amici::Model_ODE {
      * @return AMICI version string
      */
     std::string getAmiciVersion() const override {
-        return "0.34.0";
+        return "0.34.1";
     }
 
     /**
      * @brief returns the amici version that was used to generate the model
      * @return AMICI git commit hash
      */
     std::string getAmiciCommit() const override {
-        return "08d0c9533715453de60b684970751c6de07ffd9b";
+        return "b12c68a7a02f1cbd33de59d47cbc0c4d77d30d6f";
     }
 
     bool hasQuadraticLLH() const override {

models/model_jakstat_adjoint_py/setup.py

@@ -87,7 +87,7 @@ def get_extension() -> CMakeExtension:
     author_email="model-author-todo",
     ext_modules=[MODEL_EXT],
     packages=find_namespace_packages(),
-    install_requires=["amici==0.34.0"],
+    install_requires=["amici==0.34.1"],
     python_requires=">=3.11",
     package_data={},
     zip_safe=False,

models/model_nested_events_py/CMakeLists.txt

@@ -30,7 +30,7 @@ if(DEFINED ENV{AMICI_LDFLAGS})
   link_libraries("$ENV{AMICI_LDFLAGS}")
 endif()
 
-find_package(Amici 0.34.0 REQUIRED HINTS
+find_package(Amici 0.34.1 REQUIRED HINTS
              ${CMAKE_CURRENT_LIST_DIR}/../../build)
 message(STATUS "Found AMICI ${Amici_DIR}")
 set_target_properties(Upstream::amici PROPERTIES

models/model_nested_events_py/model_nested_events_py.h

@@ -545,15 +545,15 @@ class Model_model_nested_events_py : public amici::Model_ODE {
      * @return AMICI version string
      */
     std::string getAmiciVersion() const override {
-        return "0.34.0";
+        return "0.34.1";
     }
 
     /**
      * @brief returns the amici version that was used to generate the model
      * @return AMICI git commit hash
      */
     std::string getAmiciCommit() const override {
-        return "08d0c9533715453de60b684970751c6de07ffd9b";
+        return "b12c68a7a02f1cbd33de59d47cbc0c4d77d30d6f";
     }
 
     bool hasQuadraticLLH() const override {

models/model_nested_events_py/setup.py

@@ -87,7 +87,7 @@ def get_extension() -> CMakeExtension:
     author_email="model-author-todo",
     ext_modules=[MODEL_EXT],
     packages=find_namespace_packages(),
-    install_requires=["amici==0.34.0"],
+    install_requires=["amici==0.34.1"],
     python_requires=">=3.11",
     package_data={},
     zip_safe=False,

models/model_neuron_py/CMakeLists.txt

@@ -30,7 +30,7 @@ if(DEFINED ENV{AMICI_LDFLAGS})
   link_libraries("$ENV{AMICI_LDFLAGS}")
 endif()
 
-find_package(Amici 0.34.0 REQUIRED HINTS
+find_package(Amici 0.34.1 REQUIRED HINTS
              ${CMAKE_CURRENT_LIST_DIR}/../../build)
 message(STATUS "Found AMICI ${Amici_DIR}")
 set_target_properties(Upstream::amici PROPERTIES

models/model_neuron_py/model_neuron_py.h

@@ -567,15 +567,15 @@ class Model_model_neuron_py : public amici::Model_ODE {
      * @return AMICI version string
      */
     std::string getAmiciVersion() const override {
-        return "0.34.0";
+        return "0.34.1";
     }
 
     /**
      * @brief returns the amici version that was used to generate the model
      * @return AMICI git commit hash
      */
     std::string getAmiciCommit() const override {
-        return "08d0c9533715453de60b684970751c6de07ffd9b";
+        return "b12c68a7a02f1cbd33de59d47cbc0c4d77d30d6f";
     }
 
     bool hasQuadraticLLH() const override {

models/model_neuron_py/setup.py

@@ -87,7 +87,7 @@ def get_extension() -> CMakeExtension:
     author_email="model-author-todo",
     ext_modules=[MODEL_EXT],
     packages=find_namespace_packages(),
-    install_requires=["amici==0.34.0"],
+    install_requires=["amici==0.34.1"],
     python_requires=">=3.11",
     package_data={},
     zip_safe=False,

models/model_robertson_py/CMakeLists.txt

@@ -30,7 +30,7 @@ if(DEFINED ENV{AMICI_LDFLAGS})
   link_libraries("$ENV{AMICI_LDFLAGS}")
 endif()
 
-find_package(Amici 0.34.0 REQUIRED HINTS
+find_package(Amici 0.34.1 REQUIRED HINTS
              ${CMAKE_CURRENT_LIST_DIR}/../../build)
 message(STATUS "Found AMICI ${Amici_DIR}")
 set_target_properties(Upstream::amici PROPERTIES

models/model_robertson_py/model_robertson_py.h

@@ -529,15 +529,15 @@ class Model_model_robertson_py : public amici::Model_DAE {
      * @return AMICI version string
      */
     std::string getAmiciVersion() const override {
-        return "0.34.0";
+        return "0.34.1";
     }
 
     /**
      * @brief returns the amici version that was used to generate the model
      * @return AMICI git commit hash
      */
     std::string getAmiciCommit() const override {
-        return "08d0c9533715453de60b684970751c6de07ffd9b";
+        return "b12c68a7a02f1cbd33de59d47cbc0c4d77d30d6f";
     }
 
     bool hasQuadraticLLH() const override {

models/model_robertson_py/setup.py

@@ -87,7 +87,7 @@ def get_extension() -> CMakeExtension:
     author_email="model-author-todo",
     ext_modules=[MODEL_EXT],
     packages=find_namespace_packages(),
-    install_requires=["amici==0.34.0"],
+    install_requires=["amici==0.34.1"],
     python_requires=">=3.11",
     package_data={},
     zip_safe=False,

models/model_steadystate_py/CMakeLists.txt

@@ -30,7 +30,7 @@ if(DEFINED ENV{AMICI_LDFLAGS})
   link_libraries("$ENV{AMICI_LDFLAGS}")
 endif()
 
-find_package(Amici 0.34.0 REQUIRED HINTS
+find_package(Amici 0.34.1 REQUIRED HINTS
              ${CMAKE_CURRENT_LIST_DIR}/../../build)
 message(STATUS "Found AMICI ${Amici_DIR}")
 set_target_properties(Upstream::amici PROPERTIES

models/model_steadystate_py/model_steadystate_py.h

@@ -529,15 +529,15 @@ class Model_model_steadystate_py : public amici::Model_ODE {
      * @return AMICI version string
      */
     std::string getAmiciVersion() const override {
-        return "0.34.0";
+        return "0.34.1";
     }
 
     /**
      * @brief returns the amici version that was used to generate the model
      * @return AMICI git commit hash
      */
     std::string getAmiciCommit() const override {
-        return "08d0c9533715453de60b684970751c6de07ffd9b";
+        return "b12c68a7a02f1cbd33de59d47cbc0c4d77d30d6f";
     }
 
     bool hasQuadraticLLH() const override {

models/model_steadystate_py/model_steadystate_py/__init__.py

@@ -6,13 +6,13 @@
 import warnings
 
 # Ensure we are binary-compatible, see #556
-if "0.34.0" != amici.__version__:
+if "0.34.1" != amici.__version__:
     raise amici.AmiciVersionError(
         f"Cannot use model `model_steadystate_py` in {Path(__file__).parent}, "
-        "generated with amici==0.34.0, "
+        "generated with amici==0.34.1, "
         f"together with amici=={amici.__version__} "
         "which is currently installed. To use this model, install "
-        "amici==0.34.0 or re-import the model with the amici "
+        "amici==0.34.1 or re-import the model with the amici "
         "version currently installed."
     )
 

models/model_steadystate_py/setup.py

@@ -87,7 +87,7 @@ def get_extension() -> CMakeExtension:
     author_email="model-author-todo",
     ext_modules=[MODEL_EXT],
     packages=find_namespace_packages(),
-    install_requires=["amici==0.34.0"],
+    install_requires=["amici==0.34.1"],
     python_requires=">=3.11",
     package_data={},
     zip_safe=False,

version.txt

@@ -1 +1 @@
-0.34.0
+0.34.1