From 11ce87f50d4d122d1dc0e7db3aef3ee8e655bbb9 Mon Sep 17 00:00:00 2001 From: Daniel Weindl Date: Tue, 26 Aug 2025 11:18:29 +0200 Subject: [PATCH 1/2] Prepare release 0.34.1 --- CHANGELOG.md | 8 ++++++++ version.txt | 2 +- 2 files changed, 9 insertions(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 408034d3ab..a84ed524f3 100644 --- a/CHANGELOG.md +++ b/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. diff --git a/version.txt b/version.txt index 85e60ed180..cd46610fe4 100644 --- a/version.txt +++ b/version.txt @@ -1 +1 @@ -0.34.0 +0.34.1 From 0bff04860d1c24b0b4c6cb5b35390b497253e7f2 Mon Sep 17 00:00:00 2001 From: Daniel Weindl Date: Tue, 26 Aug 2025 11:27:02 +0200 Subject: [PATCH 2/2] maint: regenerate test models --- models/model_calvetti_py/CMakeLists.txt | 2 +- models/model_calvetti_py/model_calvetti_py.h | 4 ++-- models/model_calvetti_py/setup.py | 2 +- models/model_dirac_py/CMakeLists.txt | 2 +- models/model_dirac_py/model_dirac_py.h | 4 ++-- models/model_dirac_py/setup.py | 2 +- models/model_events_py/CMakeLists.txt | 2 +- models/model_events_py/model_events_py.h | 4 ++-- models/model_events_py/setup.py | 2 +- models/model_jakstat_adjoint_py/CMakeLists.txt | 2 +- models/model_jakstat_adjoint_py/model_jakstat_adjoint_py.h | 4 ++-- models/model_jakstat_adjoint_py/setup.py | 2 +- models/model_nested_events_py/CMakeLists.txt | 2 +- models/model_nested_events_py/model_nested_events_py.h | 4 ++-- models/model_nested_events_py/setup.py | 2 +- models/model_neuron_py/CMakeLists.txt | 2 +- models/model_neuron_py/model_neuron_py.h | 4 ++-- models/model_neuron_py/setup.py | 2 +- models/model_robertson_py/CMakeLists.txt | 2 +- models/model_robertson_py/model_robertson_py.h | 4 ++-- models/model_robertson_py/setup.py | 2 +- models/model_steadystate_py/CMakeLists.txt | 2 +- models/model_steadystate_py/model_steadystate_py.h | 4 ++-- .../model_steadystate_py/model_steadystate_py/__init__.py | 6 +++--- models/model_steadystate_py/setup.py | 2 +- 25 files changed, 35 insertions(+), 35 deletions(-) diff --git a/models/model_calvetti_py/CMakeLists.txt b/models/model_calvetti_py/CMakeLists.txt index 86a65c5442..d4e0a7b5ea 100644 --- a/models/model_calvetti_py/CMakeLists.txt +++ b/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 ${Amici_DIR}") set_target_properties(Upstream::amici PROPERTIES diff --git a/models/model_calvetti_py/model_calvetti_py.h b/models/model_calvetti_py/model_calvetti_py.h index 55f63d810f..a0e20af341 100644 --- a/models/model_calvetti_py/model_calvetti_py.h +++ b/models/model_calvetti_py/model_calvetti_py.h @@ -550,7 +550,7 @@ class Model_model_calvetti_py : public amici::Model_DAE { * @return AMICI version string */ std::string getAmiciVersion() const override { - return "0.34.0"; + return "0.34.1"; } /** @@ -558,7 +558,7 @@ class Model_model_calvetti_py : public amici::Model_DAE { * @return AMICI git commit hash */ std::string getAmiciCommit() const override { - return "08d0c9533715453de60b684970751c6de07ffd9b"; + return "b12c68a7a02f1cbd33de59d47cbc0c4d77d30d6f"; } bool hasQuadraticLLH() const override { diff --git a/models/model_calvetti_py/setup.py b/models/model_calvetti_py/setup.py index 8cfb7c56ce..8396442dc5 100644 --- a/models/model_calvetti_py/setup.py +++ b/models/model_calvetti_py/setup.py @@ -87,7 +87,7 @@ def get_extension() -> CMakeExtension: author_email="model-author-todo", ext_modules=[MODEL_EXT], packages=find_namespace_packages(), - install_requires=["amici==0.34.0"], + install_requires=["amici==0.34.1"], python_requires=">=3.11", package_data={}, zip_safe=False, diff --git a/models/model_dirac_py/CMakeLists.txt b/models/model_dirac_py/CMakeLists.txt index ddeb462b7e..98212ecd3a 100644 --- a/models/model_dirac_py/CMakeLists.txt +++ b/models/model_dirac_py/CMakeLists.txt @@ -30,7 +30,7 @@ if(DEFINED ENV{AMICI_LDFLAGS}) link_libraries("$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 ${Amici_DIR}") set_target_properties(Upstream::amici PROPERTIES diff --git a/models/model_dirac_py/model_dirac_py.h b/models/model_dirac_py/model_dirac_py.h index a554a47f2d..7a7d4a1119 100644 --- a/models/model_dirac_py/model_dirac_py.h +++ b/models/model_dirac_py/model_dirac_py.h @@ -537,7 +537,7 @@ class Model_model_dirac_py : public amici::Model_ODE { * @return AMICI version string */ std::string getAmiciVersion() const override { - return "0.34.0"; + return "0.34.1"; } /** @@ -545,7 +545,7 @@ class Model_model_dirac_py : public amici::Model_ODE { * @return AMICI git commit hash */ std::string getAmiciCommit() const override { - return "08d0c9533715453de60b684970751c6de07ffd9b"; + return "b12c68a7a02f1cbd33de59d47cbc0c4d77d30d6f"; } bool hasQuadraticLLH() const override { diff --git a/models/model_dirac_py/setup.py b/models/model_dirac_py/setup.py index 82990687e6..96a986db12 100644 --- a/models/model_dirac_py/setup.py +++ b/models/model_dirac_py/setup.py @@ -87,7 +87,7 @@ def get_extension() -> CMakeExtension: author_email="model-author-todo", ext_modules=[MODEL_EXT], packages=find_namespace_packages(), - install_requires=["amici==0.34.0"], + install_requires=["amici==0.34.1"], python_requires=">=3.11", package_data={}, zip_safe=False, diff --git a/models/model_events_py/CMakeLists.txt b/models/model_events_py/CMakeLists.txt index aac7f01360..5f8dafbecd 100644 --- a/models/model_events_py/CMakeLists.txt +++ b/models/model_events_py/CMakeLists.txt @@ -30,7 +30,7 @@ if(DEFINED ENV{AMICI_LDFLAGS}) link_libraries("$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 ${Amici_DIR}") set_target_properties(Upstream::amici PROPERTIES diff --git a/models/model_events_py/model_events_py.h b/models/model_events_py/model_events_py.h index 305ff09fde..114369a530 100644 --- a/models/model_events_py/model_events_py.h +++ b/models/model_events_py/model_events_py.h @@ -572,7 +572,7 @@ class Model_model_events_py : public amici::Model_ODE { * @return AMICI version string */ std::string getAmiciVersion() const override { - return "0.34.0"; + return "0.34.1"; } /** @@ -580,7 +580,7 @@ class Model_model_events_py : public amici::Model_ODE { * @return AMICI git commit hash */ std::string getAmiciCommit() const override { - return "08d0c9533715453de60b684970751c6de07ffd9b"; + return "b12c68a7a02f1cbd33de59d47cbc0c4d77d30d6f"; } bool hasQuadraticLLH() const override { diff --git a/models/model_events_py/setup.py b/models/model_events_py/setup.py index 2a16c2a2f2..0b7665b708 100644 --- a/models/model_events_py/setup.py +++ b/models/model_events_py/setup.py @@ -87,7 +87,7 @@ def get_extension() -> CMakeExtension: author_email="model-author-todo", ext_modules=[MODEL_EXT], packages=find_namespace_packages(), - install_requires=["amici==0.34.0"], + install_requires=["amici==0.34.1"], python_requires=">=3.11", package_data={}, zip_safe=False, diff --git a/models/model_jakstat_adjoint_py/CMakeLists.txt b/models/model_jakstat_adjoint_py/CMakeLists.txt index 1f9cd62dda..f5403df754 100644 --- a/models/model_jakstat_adjoint_py/CMakeLists.txt +++ b/models/model_jakstat_adjoint_py/CMakeLists.txt @@ -30,7 +30,7 @@ if(DEFINED ENV{AMICI_LDFLAGS}) link_libraries("$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 ${Amici_DIR}") set_target_properties(Upstream::amici PROPERTIES diff --git a/models/model_jakstat_adjoint_py/model_jakstat_adjoint_py.h b/models/model_jakstat_adjoint_py/model_jakstat_adjoint_py.h index 1a6eaefb58..6dbcb93a04 100644 --- a/models/model_jakstat_adjoint_py/model_jakstat_adjoint_py.h +++ b/models/model_jakstat_adjoint_py/model_jakstat_adjoint_py.h @@ -545,7 +545,7 @@ class Model_model_jakstat_adjoint_py : public amici::Model_ODE { * @return AMICI version string */ std::string getAmiciVersion() const override { - return "0.34.0"; + return "0.34.1"; } /** @@ -553,7 +553,7 @@ class Model_model_jakstat_adjoint_py : public amici::Model_ODE { * @return AMICI git commit hash */ std::string getAmiciCommit() const override { - return "08d0c9533715453de60b684970751c6de07ffd9b"; + return "b12c68a7a02f1cbd33de59d47cbc0c4d77d30d6f"; } bool hasQuadraticLLH() const override { diff --git a/models/model_jakstat_adjoint_py/setup.py b/models/model_jakstat_adjoint_py/setup.py index 95ec992582..34f6a26701 100644 --- a/models/model_jakstat_adjoint_py/setup.py +++ b/models/model_jakstat_adjoint_py/setup.py @@ -87,7 +87,7 @@ def get_extension() -> CMakeExtension: author_email="model-author-todo", ext_modules=[MODEL_EXT], packages=find_namespace_packages(), - install_requires=["amici==0.34.0"], + install_requires=["amici==0.34.1"], python_requires=">=3.11", package_data={}, zip_safe=False, diff --git a/models/model_nested_events_py/CMakeLists.txt b/models/model_nested_events_py/CMakeLists.txt index 869b44e495..0c65a1a636 100644 --- a/models/model_nested_events_py/CMakeLists.txt +++ b/models/model_nested_events_py/CMakeLists.txt @@ -30,7 +30,7 @@ if(DEFINED ENV{AMICI_LDFLAGS}) link_libraries("$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 ${Amici_DIR}") set_target_properties(Upstream::amici PROPERTIES diff --git a/models/model_nested_events_py/model_nested_events_py.h b/models/model_nested_events_py/model_nested_events_py.h index ef1e36a67d..4f5c25497a 100644 --- a/models/model_nested_events_py/model_nested_events_py.h +++ b/models/model_nested_events_py/model_nested_events_py.h @@ -545,7 +545,7 @@ class Model_model_nested_events_py : public amici::Model_ODE { * @return AMICI version string */ std::string getAmiciVersion() const override { - return "0.34.0"; + return "0.34.1"; } /** @@ -553,7 +553,7 @@ class Model_model_nested_events_py : public amici::Model_ODE { * @return AMICI git commit hash */ std::string getAmiciCommit() const override { - return "08d0c9533715453de60b684970751c6de07ffd9b"; + return "b12c68a7a02f1cbd33de59d47cbc0c4d77d30d6f"; } bool hasQuadraticLLH() const override { diff --git a/models/model_nested_events_py/setup.py b/models/model_nested_events_py/setup.py index f9af7829de..a3f550259e 100644 --- a/models/model_nested_events_py/setup.py +++ b/models/model_nested_events_py/setup.py @@ -87,7 +87,7 @@ def get_extension() -> CMakeExtension: author_email="model-author-todo", ext_modules=[MODEL_EXT], packages=find_namespace_packages(), - install_requires=["amici==0.34.0"], + install_requires=["amici==0.34.1"], python_requires=">=3.11", package_data={}, zip_safe=False, diff --git a/models/model_neuron_py/CMakeLists.txt b/models/model_neuron_py/CMakeLists.txt index 84f809898f..fa74dafbb9 100644 --- a/models/model_neuron_py/CMakeLists.txt +++ b/models/model_neuron_py/CMakeLists.txt @@ -30,7 +30,7 @@ if(DEFINED ENV{AMICI_LDFLAGS}) link_libraries("$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 ${Amici_DIR}") set_target_properties(Upstream::amici PROPERTIES diff --git a/models/model_neuron_py/model_neuron_py.h b/models/model_neuron_py/model_neuron_py.h index 3a8ae3fc06..5b95c92f8d 100644 --- a/models/model_neuron_py/model_neuron_py.h +++ b/models/model_neuron_py/model_neuron_py.h @@ -567,7 +567,7 @@ class Model_model_neuron_py : public amici::Model_ODE { * @return AMICI version string */ std::string getAmiciVersion() const override { - return "0.34.0"; + return "0.34.1"; } /** @@ -575,7 +575,7 @@ class Model_model_neuron_py : public amici::Model_ODE { * @return AMICI git commit hash */ std::string getAmiciCommit() const override { - return "08d0c9533715453de60b684970751c6de07ffd9b"; + return "b12c68a7a02f1cbd33de59d47cbc0c4d77d30d6f"; } bool hasQuadraticLLH() const override { diff --git a/models/model_neuron_py/setup.py b/models/model_neuron_py/setup.py index f13fd72d33..ea902ab899 100644 --- a/models/model_neuron_py/setup.py +++ b/models/model_neuron_py/setup.py @@ -87,7 +87,7 @@ def get_extension() -> CMakeExtension: author_email="model-author-todo", ext_modules=[MODEL_EXT], packages=find_namespace_packages(), - install_requires=["amici==0.34.0"], + install_requires=["amici==0.34.1"], python_requires=">=3.11", package_data={}, zip_safe=False, diff --git a/models/model_robertson_py/CMakeLists.txt b/models/model_robertson_py/CMakeLists.txt index 90b22dd4e0..f1f97144c3 100644 --- a/models/model_robertson_py/CMakeLists.txt +++ b/models/model_robertson_py/CMakeLists.txt @@ -30,7 +30,7 @@ if(DEFINED ENV{AMICI_LDFLAGS}) link_libraries("$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 ${Amici_DIR}") set_target_properties(Upstream::amici PROPERTIES diff --git a/models/model_robertson_py/model_robertson_py.h b/models/model_robertson_py/model_robertson_py.h index d46970792e..64f015a80c 100644 --- a/models/model_robertson_py/model_robertson_py.h +++ b/models/model_robertson_py/model_robertson_py.h @@ -529,7 +529,7 @@ class Model_model_robertson_py : public amici::Model_DAE { * @return AMICI version string */ std::string getAmiciVersion() const override { - return "0.34.0"; + return "0.34.1"; } /** @@ -537,7 +537,7 @@ class Model_model_robertson_py : public amici::Model_DAE { * @return AMICI git commit hash */ std::string getAmiciCommit() const override { - return "08d0c9533715453de60b684970751c6de07ffd9b"; + return "b12c68a7a02f1cbd33de59d47cbc0c4d77d30d6f"; } bool hasQuadraticLLH() const override { diff --git a/models/model_robertson_py/setup.py b/models/model_robertson_py/setup.py index b201a0616b..db4c2f0b85 100644 --- a/models/model_robertson_py/setup.py +++ b/models/model_robertson_py/setup.py @@ -87,7 +87,7 @@ def get_extension() -> CMakeExtension: author_email="model-author-todo", ext_modules=[MODEL_EXT], packages=find_namespace_packages(), - install_requires=["amici==0.34.0"], + install_requires=["amici==0.34.1"], python_requires=">=3.11", package_data={}, zip_safe=False, diff --git a/models/model_steadystate_py/CMakeLists.txt b/models/model_steadystate_py/CMakeLists.txt index 315be705ba..fbc93d9f04 100644 --- a/models/model_steadystate_py/CMakeLists.txt +++ b/models/model_steadystate_py/CMakeLists.txt @@ -30,7 +30,7 @@ if(DEFINED ENV{AMICI_LDFLAGS}) link_libraries("$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 diff --git a/models/model_steadystate_py/model_steadystate_py.h b/models/model_steadystate_py/model_steadystate_py.h index 989937c1db..04ee22b23e 100644 --- a/models/model_steadystate_py/model_steadystate_py.h +++ b/models/model_steadystate_py/model_steadystate_py.h @@ -529,7 +529,7 @@ 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"; } /** @@ -537,7 +537,7 @@ class Model_model_steadystate_py : public amici::Model_ODE { * @return AMICI git commit hash */ std::string getAmiciCommit() const override { - return "08d0c9533715453de60b684970751c6de07ffd9b"; + return "b12c68a7a02f1cbd33de59d47cbc0c4d77d30d6f"; } bool hasQuadraticLLH() const override { diff --git a/models/model_steadystate_py/model_steadystate_py/__init__.py b/models/model_steadystate_py/model_steadystate_py/__init__.py index fad121c291..e5db4754f2 100644 --- a/models/model_steadystate_py/model_steadystate_py/__init__.py +++ b/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." ) diff --git a/models/model_steadystate_py/setup.py b/models/model_steadystate_py/setup.py index d517ffeab5..2741e047ae 100644 --- a/models/model_steadystate_py/setup.py +++ b/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,