Mark development version as such

cmake/version.cmake

@@ -11,5 +11,13 @@ endif()
 # get project root directory
 get_filename_component(CMAKE_PARENT_LIST_DIR ${CMAKE_CURRENT_LIST_DIR}
                        DIRECTORY)
-file(STRINGS "${CMAKE_PARENT_LIST_DIR}/version.txt" PROJECT_VERSION)
+file(STRINGS "${CMAKE_PARENT_LIST_DIR}/version.txt" PROJECT_VERSION_RAW)
+
+# try to extract major.minor.patch
+# (ignore any Python .dev, .post, etc. suffixes)
+string(REGEX MATCH "([0-9]+\\.[0-9]+\\.[0-9]+)" PROJECT_VERSION "${PROJECT_VERSION_RAW}")
+if(NOT PROJECT_VERSION)
+  message(FATAL_ERROR "Could not extract version number from version.txt")
+endif()
+
 message(DEBUG "Version number: ${PROJECT_VERSION}")

doc/development.rst

@@ -163,6 +163,14 @@ To create a new release, please follow these steps:
    create and deploy the new release on Zenodo and PyPI.
    Verify that this was successful.
 
+7. Bump the version number in `version.txt` back to a development
+   version (e.g., after release "1.1.0", set the version to "1.2.0-dev")
+   and commit this change to ``main``.
+   This ensures that documentation at https://amici.readthedocs.io/en/latest/
+   will show the correct development version and won't be confused with the
+   latest release, and that models imported with a development version
+   will be marked as such.
+
 In rare cases, it might be necessary to create a hotfix release for a
 critical bug in an existing release. In this case, create a new branch
 from the respective tag, apply the fix (usually a backport from ``main``),

models/model_calvetti_py/CMakeLists.txt

@@ -36,7 +36,7 @@ if(DEFINED ENV{AMICI_LDFLAGS})
   link_libraries("$ENV{AMICI_LDFLAGS}")
 endif()
 
-find_package(Amici 0.34.2 REQUIRED HINTS
+find_package(Amici 1.0.0 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 "0.34.2";
+        return "1.0.0.dev";
     }
 
     /**
      * @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 "c4a395b6462dc1f26ad1472e6b2fa71fe0d54382";
+        return "a8dfd6e0963f32c1ce4647a652e93a271b14a053";
     }
 
     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==0.34.2"],
+    install_requires=["amici==1.0.0.dev"],
     python_requires=">=3.11",
     package_data={},
     zip_safe=False,

models/model_dirac_py/CMakeLists.txt

@@ -36,7 +36,7 @@ if(DEFINED ENV{AMICI_LDFLAGS})
   link_libraries("$ENV{AMICI_LDFLAGS}")
 endif()
 
-find_package(Amici 0.34.2 REQUIRED HINTS
+find_package(Amici 1.0.0 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 "0.34.2";
+        return "1.0.0.dev";
     }
 
     /**
      * @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 "c4a395b6462dc1f26ad1472e6b2fa71fe0d54382";
+        return "a8dfd6e0963f32c1ce4647a652e93a271b14a053";
     }
 
     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==0.34.2"],
+    install_requires=["amici==1.0.0.dev"],
     python_requires=">=3.11",
     package_data={},
     zip_safe=False,

models/model_events_py/CMakeLists.txt

@@ -36,7 +36,7 @@ if(DEFINED ENV{AMICI_LDFLAGS})
   link_libraries("$ENV{AMICI_LDFLAGS}")
 endif()
 
-find_package(Amici 0.34.2 REQUIRED HINTS
+find_package(Amici 1.0.0 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

@@ -571,15 +571,15 @@ class Model_model_events_py : public amici::Model_ODE {
      * @return AMICI version string
      */
     std::string get_amici_version() const override {
-        return "0.34.2";
+        return "1.0.0.dev";
     }
 
     /**
      * @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 "c4a395b6462dc1f26ad1472e6b2fa71fe0d54382";
+        return "a8dfd6e0963f32c1ce4647a652e93a271b14a053";
     }
 
     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==0.34.2"],
+    install_requires=["amici==1.0.0.dev"],
     python_requires=">=3.11",
     package_data={},
     zip_safe=False,

models/model_jakstat_adjoint_py/CMakeLists.txt

@@ -36,7 +36,7 @@ if(DEFINED ENV{AMICI_LDFLAGS})
   link_libraries("$ENV{AMICI_LDFLAGS}")
 endif()
 
-find_package(Amici 0.34.2 REQUIRED HINTS
+find_package(Amici 1.0.0 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

@@ -544,15 +544,15 @@ class Model_model_jakstat_adjoint_py : public amici::Model_ODE {
      * @return AMICI version string
      */
     std::string get_amici_version() const override {
-        return "0.34.2";
+        return "1.0.0.dev";
     }
 
     /**
      * @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 "c4a395b6462dc1f26ad1472e6b2fa71fe0d54382";
+        return "a8dfd6e0963f32c1ce4647a652e93a271b14a053";
     }
 
     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==0.34.2"],
+    install_requires=["amici==1.0.0.dev"],
     python_requires=">=3.11",
     package_data={},
     zip_safe=False,

models/model_nested_events_py/CMakeLists.txt

@@ -36,7 +36,7 @@ if(DEFINED ENV{AMICI_LDFLAGS})
   link_libraries("$ENV{AMICI_LDFLAGS}")
 endif()
 
-find_package(Amici 0.34.2 REQUIRED HINTS
+find_package(Amici 1.0.0 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

@@ -544,15 +544,15 @@ class Model_model_nested_events_py : public amici::Model_ODE {
      * @return AMICI version string
      */
     std::string get_amici_version() const override {
-        return "0.34.2";
+        return "1.0.0.dev";
     }
 
     /**
      * @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 "c4a395b6462dc1f26ad1472e6b2fa71fe0d54382";
+        return "a8dfd6e0963f32c1ce4647a652e93a271b14a053";
     }
 
     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==0.34.2"],
+    install_requires=["amici==1.0.0.dev"],
     python_requires=">=3.11",
     package_data={},
     zip_safe=False,

models/model_neuron_py/CMakeLists.txt

@@ -36,7 +36,7 @@ if(DEFINED ENV{AMICI_LDFLAGS})
   link_libraries("$ENV{AMICI_LDFLAGS}")
 endif()
 
-find_package(Amici 0.34.2 REQUIRED HINTS
+find_package(Amici 1.0.0 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

@@ -566,15 +566,15 @@ class Model_model_neuron_py : public amici::Model_ODE {
      * @return AMICI version string
      */
     std::string get_amici_version() const override {
-        return "0.34.2";
+        return "1.0.0.dev";
     }
 
     /**
      * @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 "c4a395b6462dc1f26ad1472e6b2fa71fe0d54382";
+        return "a8dfd6e0963f32c1ce4647a652e93a271b14a053";
     }
 
     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==0.34.2"],
+    install_requires=["amici==1.0.0.dev"],
     python_requires=">=3.11",
     package_data={},
     zip_safe=False,

models/model_robertson_py/CMakeLists.txt

@@ -36,7 +36,7 @@ if(DEFINED ENV{AMICI_LDFLAGS})
   link_libraries("$ENV{AMICI_LDFLAGS}")
 endif()
 
-find_package(Amici 0.34.2 REQUIRED HINTS
+find_package(Amici 1.0.0 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

@@ -528,15 +528,15 @@ class Model_model_robertson_py : public amici::Model_DAE {
      * @return AMICI version string
      */
     std::string get_amici_version() const override {
-        return "0.34.2";
+        return "1.0.0.dev";
     }
 
     /**
      * @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 "c4a395b6462dc1f26ad1472e6b2fa71fe0d54382";
+        return "a8dfd6e0963f32c1ce4647a652e93a271b14a053";
     }
 
     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==0.34.2"],
+    install_requires=["amici==1.0.0.dev"],
     python_requires=">=3.11",
     package_data={},
     zip_safe=False,

models/model_steadystate_py/CMakeLists.txt

@@ -36,7 +36,7 @@ if(DEFINED ENV{AMICI_LDFLAGS})
   link_libraries("$ENV{AMICI_LDFLAGS}")
 endif()
 
-find_package(Amici 0.34.2 REQUIRED HINTS
+find_package(Amici 1.0.0 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

@@ -528,15 +528,15 @@ class Model_model_steadystate_py : public amici::Model_ODE {
      * @return AMICI version string
      */
     std::string get_amici_version() const override {
-        return "0.34.2";
+        return "1.0.0.dev";
     }
 
     /**
      * @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 "c4a395b6462dc1f26ad1472e6b2fa71fe0d54382";
+        return "a8dfd6e0963f32c1ce4647a652e93a271b14a053";
     }
 
     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 "0.34.2" != amici.__version__:
+if "1.0.0.dev" != amici.__version__:
     raise amici.AmiciVersionError(
         f"Cannot use model `model_steadystate_py` in {Path(__file__).parent}, "
-        "generated with amici==0.34.2, "
+        "generated with amici==1.0.0.dev, "
         f"together with amici=={amici.__version__} "
         "which is currently installed. To use this model, install "
-        "amici==0.34.2 or re-import the model with the amici "
+        "amici==1.0.0.dev 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==0.34.2"],
+    install_requires=["amici==1.0.0.dev"],
     python_requires=">=3.11",
     package_data={},
     zip_safe=False,

python/sdist/amici/exporters/sundials/de_export.py

@@ -1235,7 +1235,9 @@ def _write_c_make_file(self):
         template_data = {
             "MODELNAME": self.model_name,
             "SOURCES": sources,
-            "AMICI_VERSION": __version__,
+            # Use major.minor.patch for find_package compatibility.
+            # CMake version only has number components, no ".dev", ".post", ...
+            "AMICI_VERSION": ".".join(__version__.split(".")[:3]),
         }
         apply_template(
             MODEL_CMAKE_TEMPLATE_FILE,

version.txt

@@ -1 +1 @@
-0.34.2
+1.0.0.dev