Mark developement version as such (#3087)

Append `.dev` suffix to development versions.
To show the right version on RTD/latest and to mark models imported with a development version as such.

Author: dweindl

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 {