From b611a07297aea1bef2cea7e739cbad8ae23c5e24 Mon Sep 17 00:00:00 2001
From: Daniel Weindl <daniel.weindl@uni-bonn.de>
Date: Wed, 11 Mar 2026 21:32:27 +0100
Subject: [PATCH] Release 1.0.1

bump version, update changelog
---
 CHANGELOG.md                                                | 4 ++++
 models/model_calvetti_py/model_calvetti_py.h                | 4 ++--
 models/model_calvetti_py/setup.py                           | 2 +-
 models/model_dirac_py/model_dirac_py.h                      | 4 ++--
 models/model_dirac_py/setup.py                              | 2 +-
 models/model_events_py/model_events_py.h                    | 4 ++--
 models/model_events_py/setup.py                             | 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/model_nested_events_py.h      | 4 ++--
 models/model_nested_events_py/setup.py                      | 2 +-
 models/model_neuron_py/model_neuron_py.h                    | 4 ++--
 models/model_neuron_py/setup.py                             | 2 +-
 models/model_robertson_py/model_robertson_py.h              | 4 ++--
 models/model_robertson_py/setup.py                          | 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 +-
 version.txt                                                 | 2 +-
 19 files changed, 32 insertions(+), 28 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index f71549bc94..c6a72aca4b 100644
--- a/CHANGELOG.md
+++ b/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+* Fixed various broken links and outdated function names in the documentation.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
 
diff --git a/models/model_calvetti_py/model_calvetti_py.h b/models/model_calvetti_py/model_calvetti_py.h
index 7c730c9350..710a86c39f 100644
--- a/models/model_calvetti_py/model_calvetti_py.h
+++ b/models/model_calvetti_py/model_calvetti_py.h
@@ -533,7 +533,7 @@ 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";
     }
 
     /**
@@ -541,7 +541,7 @@ class Model_model_calvetti_py : public amici::Model_DAE {
      * @return AMICI git commit hash
      */
     std::string get_amici_commit() const override {
-        return "39afcefa103c861d4efecc0d15196bab302eba69";
+        return "33affbfd8bca2bd5e82a10cc6b764a63e292cc6f";
     }
 
     bool has_quadratic_llh() const override {
diff --git a/models/model_calvetti_py/setup.py b/models/model_calvetti_py/setup.py
index ae00dac43a..77e2fdc351 100644
--- a/models/model_calvetti_py/setup.py
+++ b/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,
diff --git a/models/model_dirac_py/model_dirac_py.h b/models/model_dirac_py/model_dirac_py.h
index 5da41a1617..b76538a1fc 100644
--- a/models/model_dirac_py/model_dirac_py.h
+++ b/models/model_dirac_py/model_dirac_py.h
@@ -520,7 +520,7 @@ 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";
     }
 
     /**
@@ -528,7 +528,7 @@ class Model_model_dirac_py : public amici::Model_ODE {
      * @return AMICI git commit hash
      */
     std::string get_amici_commit() const override {
-        return "39afcefa103c861d4efecc0d15196bab302eba69";
+        return "33affbfd8bca2bd5e82a10cc6b764a63e292cc6f";
     }
 
     bool has_quadratic_llh() const override {
diff --git a/models/model_dirac_py/setup.py b/models/model_dirac_py/setup.py
index da19b64c80..0d2d71f75d 100644
--- a/models/model_dirac_py/setup.py
+++ b/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,
diff --git a/models/model_events_py/model_events_py.h b/models/model_events_py/model_events_py.h
index 980a378564..25ba0cdd33 100644
--- a/models/model_events_py/model_events_py.h
+++ b/models/model_events_py/model_events_py.h
@@ -555,7 +555,7 @@ 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";
     }
 
     /**
@@ -563,7 +563,7 @@ class Model_model_events_py : public amici::Model_ODE {
      * @return AMICI git commit hash
      */
     std::string get_amici_commit() const override {
-        return "39afcefa103c861d4efecc0d15196bab302eba69";
+        return "33affbfd8bca2bd5e82a10cc6b764a63e292cc6f";
     }
 
     bool has_quadratic_llh() const override {
diff --git a/models/model_events_py/setup.py b/models/model_events_py/setup.py
index cedf22c40a..a4260fc198 100644
--- a/models/model_events_py/setup.py
+++ b/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,
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 74a9edfd1c..14e929295e 100644
--- a/models/model_jakstat_adjoint_py/model_jakstat_adjoint_py.h
+++ b/models/model_jakstat_adjoint_py/model_jakstat_adjoint_py.h
@@ -528,7 +528,7 @@ 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";
     }
 
     /**
@@ -536,7 +536,7 @@ class Model_model_jakstat_adjoint_py : public amici::Model_ODE {
      * @return AMICI git commit hash
      */
     std::string get_amici_commit() const override {
-        return "39afcefa103c861d4efecc0d15196bab302eba69";
+        return "33affbfd8bca2bd5e82a10cc6b764a63e292cc6f";
     }
 
     bool has_quadratic_llh() const override {
diff --git a/models/model_jakstat_adjoint_py/setup.py b/models/model_jakstat_adjoint_py/setup.py
index 204c0ceb71..57b74e6b3c 100644
--- a/models/model_jakstat_adjoint_py/setup.py
+++ b/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,
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 442bd18e77..38c5c6350f 100644
--- a/models/model_nested_events_py/model_nested_events_py.h
+++ b/models/model_nested_events_py/model_nested_events_py.h
@@ -528,7 +528,7 @@ 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";
     }
 
     /**
@@ -536,7 +536,7 @@ class Model_model_nested_events_py : public amici::Model_ODE {
      * @return AMICI git commit hash
      */
     std::string get_amici_commit() const override {
-        return "39afcefa103c861d4efecc0d15196bab302eba69";
+        return "33affbfd8bca2bd5e82a10cc6b764a63e292cc6f";
     }
 
     bool has_quadratic_llh() const override {
diff --git a/models/model_nested_events_py/setup.py b/models/model_nested_events_py/setup.py
index 61ef32792b..0a8b17d1fa 100644
--- a/models/model_nested_events_py/setup.py
+++ b/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,
diff --git a/models/model_neuron_py/model_neuron_py.h b/models/model_neuron_py/model_neuron_py.h
index 92eb42d972..efff344ce7 100644
--- a/models/model_neuron_py/model_neuron_py.h
+++ b/models/model_neuron_py/model_neuron_py.h
@@ -550,7 +550,7 @@ 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";
     }
 
     /**
@@ -558,7 +558,7 @@ class Model_model_neuron_py : public amici::Model_ODE {
      * @return AMICI git commit hash
      */
     std::string get_amici_commit() const override {
-        return "39afcefa103c861d4efecc0d15196bab302eba69";
+        return "33affbfd8bca2bd5e82a10cc6b764a63e292cc6f";
     }
 
     bool has_quadratic_llh() const override {
diff --git a/models/model_neuron_py/setup.py b/models/model_neuron_py/setup.py
index f3365e0aa3..85d33ac8c4 100644
--- a/models/model_neuron_py/setup.py
+++ b/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,
diff --git a/models/model_robertson_py/model_robertson_py.h b/models/model_robertson_py/model_robertson_py.h
index e9455fdf73..e71591cdab 100644
--- a/models/model_robertson_py/model_robertson_py.h
+++ b/models/model_robertson_py/model_robertson_py.h
@@ -512,7 +512,7 @@ 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";
     }
 
     /**
@@ -520,7 +520,7 @@ class Model_model_robertson_py : public amici::Model_DAE {
      * @return AMICI git commit hash
      */
     std::string get_amici_commit() const override {
-        return "39afcefa103c861d4efecc0d15196bab302eba69";
+        return "33affbfd8bca2bd5e82a10cc6b764a63e292cc6f";
     }
 
     bool has_quadratic_llh() const override {
diff --git a/models/model_robertson_py/setup.py b/models/model_robertson_py/setup.py
index 88cc50b14f..ee56bb32cf 100644
--- a/models/model_robertson_py/setup.py
+++ b/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,
diff --git a/models/model_steadystate_py/model_steadystate_py.h b/models/model_steadystate_py/model_steadystate_py.h
index f52f3d05ba..cdc35f003c 100644
--- a/models/model_steadystate_py/model_steadystate_py.h
+++ b/models/model_steadystate_py/model_steadystate_py.h
@@ -512,7 +512,7 @@ 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";
     }
 
     /**
@@ -520,7 +520,7 @@ class Model_model_steadystate_py : public amici::Model_ODE {
      * @return AMICI git commit hash
      */
     std::string get_amici_commit() const override {
-        return "39afcefa103c861d4efecc0d15196bab302eba69";
+        return "33affbfd8bca2bd5e82a10cc6b764a63e292cc6f";
     }
 
     bool has_quadratic_llh() 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 aecdb1d126..bd034a4166 100644
--- a/models/model_steadystate_py/model_steadystate_py/__init__.py
+++ b/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."
     )
 
diff --git a/models/model_steadystate_py/setup.py b/models/model_steadystate_py/setup.py
index 3777f11e79..555f2cd35e 100644
--- a/models/model_steadystate_py/setup.py
+++ b/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,
diff --git a/version.txt b/version.txt
index 7784ef8c9a..7dea76edb3 100644
--- a/version.txt
+++ b/version.txt
@@ -1 +1 @@
-1.0.1.dev
+1.0.1