opencor · agarny · Dec 4, 2025 · Dec 3, 2025 · Dec 3, 2025 · Dec 3, 2025
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -399,7 +399,7 @@ jobs:
         run: uv pip install --system pytest pytest-html
       - name: Install Sphinx and some Sphinx packages
         if: ${{ matrix.documentation == 'ON' }}
-        run: uv pip install --system sphinx sphinx-copybutton sphinx-inline-tabs
+        run: uv pip install --system sphinx~=8.0 sphinx-copybutton sphinx-inline-tabs
       - name: Install Doxygen
         if: ${{ matrix.documentation == 'ON' }}
         run: |

diff --git a/VERSION.txt b/VERSION.txt
@@ -1 +1 @@
-0.20251030.0
+0.20251204.0
diff --git a/cmake/environmentchecks.cmake b/cmake/environmentchecks.cmake
@@ -281,9 +281,19 @@ endif()
 
 if(DOXYGEN_EXE AND PATCH_EXE AND PYTHON_EXE AND SPHINX_EXE)
     set(EXPECTED_DOXYGEN_VERSION 1.9.3)
+    set(UNSUPPORTED_SPHINX_VERSION 9.0.0)
+
+    execute_process(COMMAND ${SPHINX_EXE} --version
+                    OUTPUT_VARIABLE SPHINX_VERSION_OUTPUT
+                    OUTPUT_STRIP_TRAILING_WHITESPACE
+                    ERROR_QUIET)
+
+    string(REGEX REPLACE "^sphinx-build ([0-9]+\\.[0-9]+\\.[0-9]+).*$" "\\1" SPHINX_VERSION "${SPHINX_VERSION_OUTPUT}")
 
     if(NOT DOXYGEN_VERSION VERSION_EQUAL EXPECTED_DOXYGEN_VERSION)
         set(DOCUMENTATION_AVAILABLE_ERROR_MESSAGE "Documentation is requested and Doxygen ${DOXYGEN_VERSION} was found, but version ${EXPECTED_DOXYGEN_VERSION} is needed.")
+    elseif(SPHINX_VERSION VERSION_GREATER_EQUAL UNSUPPORTED_SPHINX_VERSION)
+        set(DOCUMENTATION_AVAILABLE_ERROR_MESSAGE "Documentation is requested and Sphinx ${SPHINX_VERSION} was found, but version ${UNSUPPORTED_SPHINX_VERSION}+ is not supported." )
     else()
         check_python_package(sphinx-copybutton PYTHON_SPHINX_COPY_BUTTON_AVAILABLE)
         check_python_package(sphinx-inline-tabs PYTHON_SPHINX_INLINE_TABS_AVAILABLE)

diff --git a/cmake/packages.cmake b/cmake/packages.cmake
@@ -195,7 +195,7 @@ function(retrieve_package PACKAGE_NAME PACKAGE_VERSION PACKAGE_REPOSITORY RELEAS
         if("${PACKAGE_NAME}" STREQUAL "libCellML")
             #---GRY--- USE THIS VERSION OF libCellML WHICH CORRESPONDS TO PR #1256 UNTIL IT GETS MERGED IN.
 
-            set(PACKAGE_URL "https://github.com/agarny/${PACKAGE_REPOSITORY}/releases/download/6d27883/${PACKAGE_FILE}")
+            set(PACKAGE_URL "https://github.com/agarny/${PACKAGE_REPOSITORY}/releases/download/7cc5bea/${PACKAGE_FILE}")
         endif()
 
         set(ATTEMPT 1)

diff --git a/extern/README.md b/extern/README.md
@@ -1,5 +1,5 @@
 [libOpenCOR](https://opencor.ws/libopencor/index.html) relies on the following external projects:
 
 - [GoogleTest](https://github.com/google/googletest) [1.17.0](https://github.com/google/googletest/releases/tag/v1.17.0)
-- [modp_b64](https://chromium.googlesource.com/chromium/src/third_party/modp_b64/) at commit [bcb074f](https://chromium.googlesource.com/chromium/src/third_party/modp_b64/+/bcb074f6614b4cbda45c9f87f968f6743266a52a)
+- [modp_b64](https://chromium.googlesource.com/chromium/src/third_party/modp_b64/) at commit [5068510](https://chromium.googlesource.com/chromium/src/third_party/modp_b64/+/50685101d51ef9aabbd60c94f52d9e026d39c509)
 - [nanobind](https://github.com/wjakob/nanobind) [2.9.2](https://github.com/wjakob/nanobind/releases/tag/v2.9.2)
diff --git a/extern/modp_b64/README.chromium b/extern/modp_b64/README.chromium
@@ -3,6 +3,7 @@ Short Name: stringencoders
 URL: https://github.com/client9/stringencoders
 Version: 2.0.0
 Revision: 26701a1c1fcb98ae43eefcaee23abc58459a6e59
+Update Mechanism: Static.HardFork (https://crbug.com/422922180)
 License: BSD-3-Clause
 License File: LICENSE
 Security Critical: yes

diff --git a/src/3rdparty/libCellML/CMakeLists.txt b/src/3rdparty/libCellML/CMakeLists.txt
@@ -34,49 +34,49 @@ if(LIBOPENCOR_PREBUILT_LIBCELLML)
     if(EMSCRIPTEN)
         retrieve_package(${PACKAGE_NAME} ${PACKAGE_VERSION}
                          ${PACKAGE_REPOSITORY} ${RELEASE_TAG}
-                         f3087749522fb85a72d440180b9b4c3b5bf77eb4)
+                         5bee3b3c508fb274e084468243b43d9f83647beb)
     else()
         if(WIN32)
             if(RELEASE_MODE)
                 if(INTEL_MODE)
                     retrieve_package(${PACKAGE_NAME} ${PACKAGE_VERSION}
                                      ${PACKAGE_REPOSITORY} ${RELEASE_TAG}
-                                     b1bfb0c9d197e7b858f5f27f305bda5ae40a9ad7)
+                                     d277ce028be3806aa2514ba27ec4bed352faf069)
                 else()
                     retrieve_package(${PACKAGE_NAME} ${PACKAGE_VERSION}
                                      ${PACKAGE_REPOSITORY} ${RELEASE_TAG}
-                                     4d06110bb96f71cff8f1fb0e0e463f94920f8fa9)
+                                     388a936417a5681fbcf835bdda20e8ed0fbf3382)
                 endif()
             else()
                 if(INTEL_MODE)
                     retrieve_package(${PACKAGE_NAME} ${PACKAGE_VERSION}
                                      ${PACKAGE_REPOSITORY} ${RELEASE_TAG}
-                                     214b685fbaf9c616739ad8786800b75d59a47f8b)
+                                     c768d8c59db5ee4a07baa0fc61d7a8ccac4ea6db)
                 else()
                     retrieve_package(${PACKAGE_NAME} ${PACKAGE_VERSION}
                                      ${PACKAGE_REPOSITORY} ${RELEASE_TAG}
-                                     0d6d70f9fdf7443d82016216a78be7d2acea2e7e)
+                                     2fd521abaf83b480e5b07c746ae310be529faa7e)
                 endif()
             endif()
         elseif(APPLE)
             if(INTEL_MODE)
                 retrieve_package(${PACKAGE_NAME} ${PACKAGE_VERSION}
                                  ${PACKAGE_REPOSITORY} ${RELEASE_TAG}
-                                 8ccd4a8a95a3b4b243d900746340f167d9f31075)
+                                 055181384ac2e4e942603c6b1f3d0c20f439b523)
             else()
                 retrieve_package(${PACKAGE_NAME} ${PACKAGE_VERSION}
                                  ${PACKAGE_REPOSITORY} ${RELEASE_TAG}
-                                 72b1e4f2e4a2b76a0d45efced9ef96cbba263d66)
+                                 847c024d893e3a1f73172e8f6d2e55136e46dd86)
             endif()
         else()
             if(INTEL_MODE)
                 retrieve_package(${PACKAGE_NAME} ${PACKAGE_VERSION}
                                  ${PACKAGE_REPOSITORY} ${RELEASE_TAG}
-                                 623866e3cf071f652fe778a22868b5c6917db6f9)
+                                 f8d847dffd74264a3074e742149dca0ab4c57653)
             else()
                 retrieve_package(${PACKAGE_NAME} ${PACKAGE_VERSION}
                                  ${PACKAGE_REPOSITORY} ${RELEASE_TAG}
-                                 9742ef210ca1cc88549b802c6f0fc5d1c0670f25)
+                                 674bb536a67cc7e7d4afef553c843ac38d44d43f)
             endif()
         endif()
     endif()
@@ -86,7 +86,7 @@ elseif(NOT ONLY_BUILD_JAVASCRIPT_THIRD_PARTY_LIBRARIES)
     build_package(${PACKAGE_NAME}
         URL
             # https://github.com/opencor/${PACKAGE_REPOSITORY}/archive/refs/tags/${RELEASE_TAG}.tar.gz
-            https://github.com/agarny/${PACKAGE_REPOSITORY}/archive/refs/tags/6d27883.tar.gz
+            https://github.com/agarny/${PACKAGE_REPOSITORY}/archive/refs/tags/7cc5bea.tar.gz
         DOWNLOAD_NO_PROGRESS ON
         CMAKE_ARGS
             -DBINDINGS_PYTHON=OFF

diff --git a/src/api/libopencor/sedinstancetask.h b/src/api/libopencor/sedinstancetask.h
@@ -288,7 +288,7 @@ class LIBOPENCOR_EXPORT SedInstanceTask: public Logger
      * @return The number of algebraic variables.
      */
 
-    size_t algebraicCount() const;
+    size_t algebraicVariableCount() const;
 
     /**
      * @brief Get the values of the algebraic variable at the given index.
@@ -300,10 +300,10 @@ class LIBOPENCOR_EXPORT SedInstanceTask: public Logger
      * @return The values of the algebraic variable, as a @c Doubles, if the index is valid, an empty vector otherwise.
      */
 
-    Doubles algebraic(size_t pIndex) const;
+    Doubles algebraicVariable(size_t pIndex) const;
 
 #ifdef __EMSCRIPTEN__
-    emscripten::val algebraicAsArray(size_t pIndex) const;
+    emscripten::val algebraicVariableAsArray(size_t pIndex) const;
 #endif
 
     /**
@@ -317,7 +317,7 @@ class LIBOPENCOR_EXPORT SedInstanceTask: public Logger
      * otherwise.
      */
 
-    std::string algebraicName(size_t pIndex) const;
+    std::string algebraicVariableName(size_t pIndex) const;
 
     /**
      * @brief Get the unit of the algebraic variable.
@@ -330,7 +330,7 @@ class LIBOPENCOR_EXPORT SedInstanceTask: public Logger
      * otherwise.
      */
 
-    std::string algebraicUnit(size_t pIndex) const;
+    std::string algebraicVariableUnit(size_t pIndex) const;
 
 private:
     class Impl; /**< Forward declaration of the implementation class, @private. */

diff --git a/src/bindings/javascript/sed.cpp b/src/bindings/javascript/sed.cpp
@@ -120,11 +120,11 @@ void sedApi()
         .function("computedConstantAsArray", &libOpenCOR::SedInstanceTask::computedConstantAsArray)
         .function("computedConstantName", &libOpenCOR::SedInstanceTask::computedConstantName)
         .function("computedConstantUnit", &libOpenCOR::SedInstanceTask::computedConstantUnit)
-        .property("algebraicCount", &libOpenCOR::SedInstanceTask::algebraicCount)
-        .function("algebraic", &libOpenCOR::SedInstanceTask::algebraic)
-        .function("algebraicAsArray", &libOpenCOR::SedInstanceTask::algebraicAsArray)
-        .function("algebraicName", &libOpenCOR::SedInstanceTask::algebraicName)
-        .function("algebraicUnit", &libOpenCOR::SedInstanceTask::algebraicUnit);
+        .property("algebraicVariableCount", &libOpenCOR::SedInstanceTask::algebraicVariableCount)
+        .function("algebraicVariable", &libOpenCOR::SedInstanceTask::algebraicVariable)
+        .function("algebraicVariableAsArray", &libOpenCOR::SedInstanceTask::algebraicVariableAsArray)
+        .function("algebraicVariableName", &libOpenCOR::SedInstanceTask::algebraicVariableName)
+        .function("algebraicVariableUnit", &libOpenCOR::SedInstanceTask::algebraicVariableUnit);
 
     // SedModel API.
 

diff --git a/src/bindings/python/sed.cpp b/src/bindings/python/sed.cpp
@@ -124,10 +124,10 @@ void sedApi(nb::module_ &m)
         .def("computed_constant", &libOpenCOR::SedInstanceTask::computedConstant, "Return the values of a computed constant.")
         .def("computed_constant_name", &libOpenCOR::SedInstanceTask::computedConstantName, "Return the name of a computed constant.")
         .def("computed_constant_unit", &libOpenCOR::SedInstanceTask::computedConstantUnit, "Return the unit of a computed constant.")
-        .def_prop_ro("algebraic_count", &libOpenCOR::SedInstanceTask::algebraicCount, "Return the number of algebraic variables.")
-        .def("algebraic", &libOpenCOR::SedInstanceTask::algebraic, "Return the values of an algebraic variable.")
-        .def("algebraic_name", &libOpenCOR::SedInstanceTask::algebraicName, "Return the name of an algebraic variable.")
-        .def("algebraic_unit", &libOpenCOR::SedInstanceTask::algebraicUnit, "Return the unit of an algebraic variable.");
+        .def_prop_ro("algebraic_variable_count", &libOpenCOR::SedInstanceTask::algebraicVariableCount, "Return the number of algebraic variables.")
+        .def("algebraic_variable", &libOpenCOR::SedInstanceTask::algebraicVariable, "Return the values of an algebraic variable.")
+        .def("algebraic_variable_name", &libOpenCOR::SedInstanceTask::algebraicVariableName, "Return the name of an algebraic variable.")
+        .def("algebraic_variable_unit", &libOpenCOR::SedInstanceTask::algebraicVariableUnit, "Return the unit of an algebraic variable.");
 
     // SedModel API.
 

diff --git a/src/sed/sedchangeattribute.cpp b/src/sed/sedchangeattribute.cpp
@@ -95,7 +95,7 @@ void SedChangeAttribute::Impl::apply(const SedInstanceTaskPtr &pInstanceTask,
         auto voiVariable {pAnalyserModel->voi()->variable()};
         auto voiComponent {owningComponent(voiVariable)};
 
-        addWarning(std::string("The variable of integration '").append(voiVariable->name()).append("' in component '").append(voiComponent->name()).append("'cannot be changed. Only state variables and constants can be changed."));
+        addWarning(std::string("The variable of integration '").append(voiVariable->name()).append("' in component '").append(voiComponent->name()).append("' cannot be changed. Only state variables and constants can be changed."));
 
         return;
     }
@@ -140,9 +140,9 @@ void SedChangeAttribute::Impl::apply(const SedInstanceTaskPtr &pInstanceTask,
     }
 
     if (!isParameterSet) {
-        for (size_t i {0}; i < pAnalyserModel->algebraicCount(); ++i) {
-            if (instanceTaskPimpl->algebraicName(i) == changeName) {
-                auto algebraicVariable {pAnalyserModel->algebraic()[i]->variable()};
+        for (size_t i {0}; i < pAnalyserModel->algebraicVariableCount(); ++i) {
+            if (instanceTaskPimpl->algebraicVariableName(i) == changeName) {
+                auto algebraicVariable {pAnalyserModel->algebraicVariables()[i]->variable()};
                 auto algebraicComponent {owningComponent(algebraicVariable)};
 
                 addWarning(std::string("The algebraic variable '").append(algebraicVariable->name()).append("' in component '").append(algebraicComponent->name()).append("' cannot be changed. Only state variables and constants can be changed."));
@@ -155,7 +155,7 @@ void SedChangeAttribute::Impl::apply(const SedInstanceTaskPtr &pInstanceTask,
     }
 
     if (!isParameterSet) {
-        addWarning(std::string("The variable '").append(mComponentName).append("' in component '").append(mVariableName).append("'could not be found and therefore could not be changed."));
+        addWarning(std::string("The variable '").append(mVariableName).append("' in component '").append(mComponentName).append("' could not be found and therefore could not be changed."));
     }
 }
 

diff --git a/src/sed/sedinstancetask.cpp b/src/sed/sedinstancetask.cpp
@@ -96,15 +96,15 @@ SedInstanceTask::Impl::Impl(const SedAbstractTaskPtr &pTask)
 
     mConstantDoubles.resize(mAnalyserModel->constantCount(), NAN);
     mComputedConstantDoubles.resize(mAnalyserModel->computedConstantCount(), NAN);
-    mAlgebraicDoubles.resize(mAnalyserModel->algebraicCount(), NAN);
+    mAlgebraicDoubles.resize(mAnalyserModel->algebraicVariableCount(), NAN);
 
     mConstants = mConstantDoubles.data();
     mComputedConstants = mComputedConstantDoubles.data();
     mAlgebraic = mAlgebraicDoubles.data();
 
     mResults.constants.resize(mAnalyserModel->constantCount(), {});
     mResults.computedConstants.resize(mAnalyserModel->computedConstantCount(), {});
-    mResults.algebraic.resize(mAnalyserModel->algebraicCount(), {});
+    mResults.algebraic.resize(mAnalyserModel->algebraicVariableCount(), {});
 }
 
 void SedInstanceTask::Impl::trackResults(size_t pIndex)
@@ -124,7 +124,7 @@ void SedInstanceTask::Impl::trackResults(size_t pIndex)
         mResults.computedConstants[i][pIndex] = mComputedConstants[i]; // NOLINT
     }
 
-    for (size_t i {0}; i < mAnalyserModel->algebraicCount(); ++i) {
+    for (size_t i {0}; i < mAnalyserModel->algebraicVariableCount(); ++i) {
         mResults.algebraic[i][pIndex] = mAlgebraic[i]; // NOLINT
     }
 }
@@ -157,15 +157,15 @@ void SedInstanceTask::Impl::initialise()
         mVoi = mSedUniformTimeCourse->pimpl()->mOutputStartTime;
 
 #ifdef __EMSCRIPTEN__
-        mRuntime->initialiseVariablesForDifferentialModel(mStates, mRates, mConstants, mComputedConstants, mAlgebraic);
+        mRuntime->initialiseArraysForDifferentialModel(mStates, mRates, mConstants, mComputedConstants, mAlgebraic);
 #else
-        mRuntime->initialiseVariablesForDifferentialModel()(mStates, mRates, mConstants, mComputedConstants, mAlgebraic);
+        mRuntime->initialiseArraysForDifferentialModel()(mStates, mRates, mConstants, mComputedConstants, mAlgebraic);
 #endif
     } else {
 #ifdef __EMSCRIPTEN__
-        mRuntime->initialiseVariablesForAlgebraicModel(mConstants, mComputedConstants, mAlgebraic);
+        mRuntime->initialiseArraysForAlgebraicModel(mConstants, mComputedConstants, mAlgebraic);
 #else
-        mRuntime->initialiseVariablesForAlgebraicModel()(mConstants, mComputedConstants, mAlgebraic);
+        mRuntime->initialiseArraysForAlgebraicModel()(mConstants, mComputedConstants, mAlgebraic);
 #endif
     }
 
@@ -245,7 +245,7 @@ double SedInstanceTask::Impl::run()
             mResults.computedConstants[i].resize(resultsSize, NAN);
         }
 
-        for (size_t i {0}; i < mAnalyserModel->algebraicCount(); ++i) {
+        for (size_t i {0}; i < mAnalyserModel->algebraicVariableCount(); ++i) {
             mResults.algebraic[i].resize(resultsSize, NAN);
         }
 
@@ -302,7 +302,7 @@ double SedInstanceTask::Impl::run()
             mResults.computedConstants[i].resize(1, mComputedConstants[i]); // NOLINT
         }
 
-        for (size_t i {0}; i < mAnalyserModel->algebraicCount(); ++i) {
+        for (size_t i {0}; i < mAnalyserModel->algebraicVariableCount(); ++i) {
             mResults.algebraic[i].resize(1, mAlgebraic[i]); // NOLINT
         }
     }
@@ -467,36 +467,36 @@ std::string SedInstanceTask::Impl::computedConstantUnit(size_t pIndex) const
     return mAnalyserModel->computedConstants()[pIndex]->variable()->units()->name();
 }
 
-size_t SedInstanceTask::Impl::algebraicCount() const
+size_t SedInstanceTask::Impl::algebraicVariableCount() const
 {
-    return mAnalyserModel->algebraicCount();
+    return mAnalyserModel->algebraicVariableCount();
 }
 
-Doubles SedInstanceTask::Impl::algebraic(size_t pIndex) const
+Doubles SedInstanceTask::Impl::algebraicVariable(size_t pIndex) const
 {
-    if (pIndex >= mAnalyserModel->algebraicCount()) {
+    if (pIndex >= mAnalyserModel->algebraicVariableCount()) {
         return {};
     }
 
     return mResults.algebraic[pIndex];
 }
 
-std::string SedInstanceTask::Impl::algebraicName(size_t pIndex) const
+std::string SedInstanceTask::Impl::algebraicVariableName(size_t pIndex) const
 {
-    if (pIndex >= mAnalyserModel->algebraicCount()) {
+    if (pIndex >= mAnalyserModel->algebraicVariableCount()) {
         return {};
     }
 
-    return name(mAnalyserModel->algebraic()[pIndex]->variable());
+    return name(mAnalyserModel->algebraicVariables()[pIndex]->variable());
 }
 
-std::string SedInstanceTask::Impl::algebraicUnit(size_t pIndex) const
+std::string SedInstanceTask::Impl::algebraicVariableUnit(size_t pIndex) const
 {
-    if (pIndex >= mAnalyserModel->algebraicCount()) {
+    if (pIndex >= mAnalyserModel->algebraicVariableCount()) {
         return {};
     }
 
-    return mAnalyserModel->algebraic()[pIndex]->variable()->units()->name();
+    return mAnalyserModel->algebraicVariables()[pIndex]->variable()->units()->name();
 }
 
 SedInstanceTask::SedInstanceTask(const SedAbstractTaskPtr &pTask)
@@ -649,31 +649,31 @@ std::string SedInstanceTask::computedConstantUnit(size_t pIndex) const
     return pimpl()->computedConstantUnit(pIndex);
 }
 
-size_t SedInstanceTask::algebraicCount() const
+size_t SedInstanceTask::algebraicVariableCount() const
 {
-    return pimpl()->algebraicCount();
+    return pimpl()->algebraicVariableCount();
 }
 
-Doubles SedInstanceTask::algebraic(size_t pIndex) const
+Doubles SedInstanceTask::algebraicVariable(size_t pIndex) const
 {
-    return pimpl()->algebraic(pIndex);
+    return pimpl()->algebraicVariable(pIndex);
 }
 
 #ifdef __EMSCRIPTEN__
-emscripten::val SedInstanceTask::algebraicAsArray(size_t pIndex) const
+emscripten::val SedInstanceTask::algebraicVariableAsArray(size_t pIndex) const
 {
-    return emscripten::val::array(algebraic(pIndex));
+    return emscripten::val::array(algebraicVariable(pIndex));
 }
 #endif
 
-std::string SedInstanceTask::algebraicName(size_t pIndex) const
+std::string SedInstanceTask::algebraicVariableName(size_t pIndex) const
 {
-    return pimpl()->algebraicName(pIndex);
+    return pimpl()->algebraicVariableName(pIndex);
 }
 
-std::string SedInstanceTask::algebraicUnit(size_t pIndex) const
+std::string SedInstanceTask::algebraicVariableUnit(size_t pIndex) const
 {
-    return pimpl()->algebraicUnit(pIndex);
+    return pimpl()->algebraicVariableUnit(pIndex);
 }
 
 } // namespace libOpenCOR
diff --git a/src/sed/sedinstancetask_p.h b/src/sed/sedinstancetask_p.h
@@ -99,10 +99,10 @@ class SedInstanceTask::Impl: public Logger::Impl
     std::string computedConstantName(size_t pIndex) const;
     std::string computedConstantUnit(size_t pIndex) const;
 
-    size_t algebraicCount() const;
-    Doubles algebraic(size_t pIndex) const;
-    std::string algebraicName(size_t pIndex) const;
-    std::string algebraicUnit(size_t pIndex) const;
+    size_t algebraicVariableCount() const;
+    Doubles algebraicVariable(size_t pIndex) const;
+    std::string algebraicVariableName(size_t pIndex) const;
+    std::string algebraicVariableUnit(size_t pIndex) const;
 };
 
 } // namespace libOpenCOR