Release 1.0.1

CHANGELOG.md

@@ -12,6 +12,10 @@ See also our [versioning policy](https://amici.readthedocs.io/en/latest/versioni
   the jax-dependencies weren't installed.
 * Fixed a pandas>=3.0 compatibility issue in the PEtab importer which resulted
   in incorrect selection of fixed parameters.
+* Fixed logger configuration for simulation warnings/errors, such that users
+  can adjust the log level or simulations with, e.g.,
+  `logging.getLogger("amici.sim.sundials").setLevel(logging.ERROR)`
+* Fixed various broken links and outdated function names in the documentation.
 
 ### v1.0.0
 

models/model_calvetti_py/model_calvetti_py.h

@@ -533,15 +533,15 @@ class Model_model_calvetti_py : public amici::Model_DAE {
      * @return AMICI version string
      */
     std::string get_amici_version() const override {
-        return "1.0.1.dev";
+        return "1.0.1";
     }
 
     /**
      * @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 "39afcefa103c861d4efecc0d15196bab302eba69";
+        return "33affbfd8bca2bd5e82a10cc6b764a63e292cc6f";
     }
 
     bool has_quadratic_llh() const override {

models/model_calvetti_py/setup.py

@@ -89,7 +89,7 @@ def get_extension() -> CMakeExtension:
     author_email="model-author-todo",
     ext_modules=[MODEL_EXT],
     packages=find_namespace_packages(),
-    install_requires=["amici==1.0.1.dev"],
+    install_requires=["amici==1.0.1"],
     python_requires=">=3.11",
     package_data={},
     zip_safe=False,

models/model_dirac_py/model_dirac_py.h

@@ -520,15 +520,15 @@ class Model_model_dirac_py : public amici::Model_ODE {
      * @return AMICI version string
      */
     std::string get_amici_version() const override {
-        return "1.0.1.dev";
+        return "1.0.1";
     }
 
     /**
      * @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 "39afcefa103c861d4efecc0d15196bab302eba69";
+        return "33affbfd8bca2bd5e82a10cc6b764a63e292cc6f";
     }
 
     bool has_quadratic_llh() const override {

models/model_dirac_py/setup.py

@@ -89,7 +89,7 @@ def get_extension() -> CMakeExtension:
     author_email="model-author-todo",
     ext_modules=[MODEL_EXT],
     packages=find_namespace_packages(),
-    install_requires=["amici==1.0.1.dev"],
+    install_requires=["amici==1.0.1"],
     python_requires=">=3.11",
     package_data={},
     zip_safe=False,

models/model_events_py/model_events_py.h

@@ -555,15 +555,15 @@ class Model_model_events_py : public amici::Model_ODE {
      * @return AMICI version string
      */
     std::string get_amici_version() const override {
-        return "1.0.1.dev";
+        return "1.0.1";
     }
 
     /**
      * @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 "39afcefa103c861d4efecc0d15196bab302eba69";
+        return "33affbfd8bca2bd5e82a10cc6b764a63e292cc6f";
     }
 
     bool has_quadratic_llh() const override {

models/model_events_py/setup.py

@@ -89,7 +89,7 @@ def get_extension() -> CMakeExtension:
     author_email="model-author-todo",
     ext_modules=[MODEL_EXT],
     packages=find_namespace_packages(),
-    install_requires=["amici==1.0.1.dev"],
+    install_requires=["amici==1.0.1"],
     python_requires=">=3.11",
     package_data={},
     zip_safe=False,

models/model_jakstat_adjoint_py/model_jakstat_adjoint_py.h

@@ -528,15 +528,15 @@ class Model_model_jakstat_adjoint_py : public amici::Model_ODE {
      * @return AMICI version string
      */
     std::string get_amici_version() const override {
-        return "1.0.1.dev";
+        return "1.0.1";
     }
 
     /**
      * @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 "39afcefa103c861d4efecc0d15196bab302eba69";
+        return "33affbfd8bca2bd5e82a10cc6b764a63e292cc6f";
     }
 
     bool has_quadratic_llh() const override {

models/model_jakstat_adjoint_py/setup.py

@@ -89,7 +89,7 @@ def get_extension() -> CMakeExtension:
     author_email="model-author-todo",
     ext_modules=[MODEL_EXT],
     packages=find_namespace_packages(),
-    install_requires=["amici==1.0.1.dev"],
+    install_requires=["amici==1.0.1"],
     python_requires=">=3.11",
     package_data={},
     zip_safe=False,

models/model_nested_events_py/model_nested_events_py.h

@@ -528,15 +528,15 @@ class Model_model_nested_events_py : public amici::Model_ODE {
      * @return AMICI version string
      */
     std::string get_amici_version() const override {
-        return "1.0.1.dev";
+        return "1.0.1";
     }
 
     /**
      * @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 "39afcefa103c861d4efecc0d15196bab302eba69";
+        return "33affbfd8bca2bd5e82a10cc6b764a63e292cc6f";
     }
 
     bool has_quadratic_llh() const override {

models/model_nested_events_py/setup.py

@@ -89,7 +89,7 @@ def get_extension() -> CMakeExtension:
     author_email="model-author-todo",
     ext_modules=[MODEL_EXT],
     packages=find_namespace_packages(),
-    install_requires=["amici==1.0.1.dev"],
+    install_requires=["amici==1.0.1"],
     python_requires=">=3.11",
     package_data={},
     zip_safe=False,

models/model_neuron_py/model_neuron_py.h

@@ -550,15 +550,15 @@ class Model_model_neuron_py : public amici::Model_ODE {
      * @return AMICI version string
      */
     std::string get_amici_version() const override {
-        return "1.0.1.dev";
+        return "1.0.1";
     }
 
     /**
      * @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 "39afcefa103c861d4efecc0d15196bab302eba69";
+        return "33affbfd8bca2bd5e82a10cc6b764a63e292cc6f";
     }
 
     bool has_quadratic_llh() const override {

models/model_neuron_py/setup.py

@@ -89,7 +89,7 @@ def get_extension() -> CMakeExtension:
     author_email="model-author-todo",
     ext_modules=[MODEL_EXT],
     packages=find_namespace_packages(),
-    install_requires=["amici==1.0.1.dev"],
+    install_requires=["amici==1.0.1"],
     python_requires=">=3.11",
     package_data={},
     zip_safe=False,

models/model_robertson_py/model_robertson_py.h

@@ -512,15 +512,15 @@ class Model_model_robertson_py : public amici::Model_DAE {
      * @return AMICI version string
      */
     std::string get_amici_version() const override {
-        return "1.0.1.dev";
+        return "1.0.1";
     }
 
     /**
      * @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 "39afcefa103c861d4efecc0d15196bab302eba69";
+        return "33affbfd8bca2bd5e82a10cc6b764a63e292cc6f";
     }
 
     bool has_quadratic_llh() const override {

models/model_robertson_py/setup.py

@@ -89,7 +89,7 @@ def get_extension() -> CMakeExtension:
     author_email="model-author-todo",
     ext_modules=[MODEL_EXT],
     packages=find_namespace_packages(),
-    install_requires=["amici==1.0.1.dev"],
+    install_requires=["amici==1.0.1"],
     python_requires=">=3.11",
     package_data={},
     zip_safe=False,

models/model_steadystate_py/model_steadystate_py.h

@@ -512,15 +512,15 @@ class Model_model_steadystate_py : public amici::Model_ODE {
      * @return AMICI version string
      */
     std::string get_amici_version() const override {
-        return "1.0.1.dev";
+        return "1.0.1";
     }
 
     /**
      * @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 "39afcefa103c861d4efecc0d15196bab302eba69";
+        return "33affbfd8bca2bd5e82a10cc6b764a63e292cc6f";
     }
 
     bool has_quadratic_llh() const override {

models/model_steadystate_py/model_steadystate_py/__init__.py

@@ -7,13 +7,13 @@
 import amici
 
 # Ensure we are binary-compatible, see #556
-if "1.0.1.dev" != amici.__version__:
+if "1.0.1" != amici.__version__:
     raise amici.AmiciVersionError(
         f"Cannot use model `model_steadystate_py` in {Path(__file__).parent}, "
-        "generated with amici==1.0.1.dev, "
+        "generated with amici==1.0.1, "
         f"together with amici=={amici.__version__} "
         "which is currently installed. To use this model, install "
-        "amici==1.0.1.dev or re-import the model with the amici "
+        "amici==1.0.1 or re-import the model with the amici "
         "version currently installed."
     )
 

models/model_steadystate_py/setup.py

@@ -89,7 +89,7 @@ def get_extension() -> CMakeExtension:
     author_email="model-author-todo",
     ext_modules=[MODEL_EXT],
     packages=find_namespace_packages(),
-    install_requires=["amici==1.0.1.dev"],
+    install_requires=["amici==1.0.1"],
     python_requires=">=3.11",
     package_data={},
     zip_safe=False,

version.txt

@@ -1 +1 @@
-1.0.1.dev
+1.0.1