Include functionality for rearranging algebraic loops to turn certain DAEs into ODEs

.github/workflows/ci.yml

@@ -21,29 +21,39 @@ jobs:
           - name: 'Windows static - C++'
             os: windows-latest
             python_bindings: OFF
-            additional_cmake_options: -DLibXml2_DIR="C:\libxml2\libxml2-2.9.10\CMake" -DZLIB_DIR="C:\zlib\lib\cmake\ZLIB-1.2.12"
+            additional_cmake_options: -DLibXml2_DIR=C:\libxml2\libxml2-2.9.10\CMake -DZLIB_DIR=C:\zlib\lib\cmake\ZLIB-1.2.12 -DSymEngine_DIR=C:\symengine\debug\CMake
           - name: 'Windows shared - C++/Python'
             os: windows-latest
             python_bindings: ON
-            additional_cmake_options: -DLibXml2_DIR="C:\libxml2\libxml2-2.9.10\CMake" -DZLIB_DIR="C:\zlib\lib\cmake\ZLIB-1.2.12"
+            additional_cmake_options: -DLibXml2_DIR=C:\libxml2\libxml2-2.9.10\CMake -DZLIB_DIR=C:\zlib\lib\cmake\ZLIB-1.2.12 -DSymEngine_DIR=C:\symengine\debug\CMake
           - name: 'Linux static - C++'
             os: ubuntu-latest
             python_bindings: OFF
+            additional_cmake_options: -DCMAKE_PREFIX_PATH=$HOME
           - name: 'Linux shared - C++/Python'
             os: ubuntu-latest
             python_bindings: ON
+            additional_cmake_options: -DCMAKE_PREFIX_PATH=$HOME
           - name: 'macOS static - C++ (Intel)'
             os: macos-15-intel
             python_bindings: OFF
+            architecture: Intel
+            additional_cmake_options: -DCMAKE_PREFIX_PATH=$HOME
           - name: 'macOS shared - C++/Python (Intel)'
             os: macos-15-intel
             python_bindings: ON
+            architecture: Intel
+            additional_cmake_options: -DCMAKE_PREFIX_PATH=$HOME
           - name: 'macOS static - C++ (ARM)'
             os: macos-latest
             python_bindings: OFF
+            architecture: ARM
+            additional_cmake_options: -DCMAKE_PREFIX_PATH=$HOME
           - name: 'macOS shared - C++/Python (ARM)'
             os: macos-latest
             python_bindings: ON
+            architecture: ARM
+            additional_cmake_options: -DCMAKE_PREFIX_PATH=$HOME
     steps:
       - name: Check out libCellML
         uses: actions/checkout@v6
@@ -61,18 +71,30 @@ jobs:
         uses: TheMrMilchmann/setup-msvc-dev@v4
         with:
           arch: x64
-      - name: Install libxml2 (Windows only)
+      - name: Install dependencies (Windows only)
         if: ${{ runner.os == 'Windows' }}
         run: |
           cd C:\
           curl -L https://github.com/cellml/gha/releases/download/gha/libxml2-Windows.tar.gz -o libxml2.tar.gz -s
           tar -xzf libxml2.tar.gz
-      - name: Install zlib (Windows only)
-        if: ${{ runner.os == 'Windows' }}
-        run: |
-          cd C:\
+          curl -L https://github.com/cellml/gha/releases/download/gha/symengine-Windows.tar.gz -o symengine.tar.gz -s
+          tar -xzf symengine.tar.gz
           curl -L https://github.com/cellml/gha/releases/download/gha/zlib-Windows.tar.gz -o zlib.tar.gz -s
           tar -xzf zlib.tar.gz
+      - name: Install dependencies (Linux only)
+        if: ${{ runner.os == 'Linux' }}
+        run: |
+          cd $HOME
+          wget https://github.com/cellml/gha/releases/download/gha/libxml2-Linux.tar.gz -O - | tar -xz
+          wget https://github.com/cellml/gha/releases/download/gha/symengine-Linux.tar.gz -O - | tar -xz
+          wget https://github.com/cellml/gha/releases/download/gha/zlib-Linux.tar.gz -O - | tar -xz
+      - name: Install dependencies (macOS only)
+        if: ${{ runner.os == 'macOS' }}
+        run: |
+          cd $HOME
+          wget https://github.com/cellml/gha/releases/download/gha/libxml2-macOS-${{ matrix.architecture }}.tar.gz -O - | tar -xz
+          wget https://github.com/cellml/gha/releases/download/gha/symengine-macOS-${{ matrix.architecture }}.tar.gz -O - | tar -xz
+          wget https://github.com/cellml/gha/releases/download/gha/zlib-macOS-${{ matrix.architecture }}.tar.gz -O - | tar -xz
       - name: Install SWIG (macOS only and if needed)
         if: ${{ runner.os == 'macOS' && matrix.python_bindings == 'ON' }}
         run: brew install swig
@@ -96,17 +118,14 @@ jobs:
         uses: lukka/get-cmake@latest
       - name: Install Emscripten
         run: brew install --overwrite emscripten
-      - name: Install libxml2
+      - name: Install dependencies
         run: |
           cd $HOME
           wget https://github.com/cellml/gha/releases/download/gha/libxml2-WASM.tar.gz -O - | tar -xz
-      - name: Install zlib
-        run: |
-          cd $HOME
+          wget https://github.com/cellml/gha/releases/download/gha/symengine-WASM.tar.gz -O - | tar -xz
           wget https://github.com/cellml/gha/releases/download/gha/zlib-WASM.tar.gz -O - | tar -xz
       - name: Configure libCellML
-        run: |
-          emcmake cmake -G Ninja -S . -B build-wasm -DBUILD_TYPE=Release -DLIBXML2_INCLUDE_DIR=$HOME/libxml2/include/libxml2 -DLIBXML2_LIBRARY=$HOME/libxml2/lib/libxml2.a -DZLIB_INCLUDE_DIR=$HOME/zlib/include -DZLIB_LIBRARY=$HOME/zlib/lib/libz.a
+        run: emcmake cmake -G Ninja -S . -B build-wasm -DBUILD_TYPE=Release -DCMAKE_PREFIX_PATH=$HOME
       - name: Build libCellML
         run: cmake --build build-wasm
       - name: Unit testing
@@ -127,15 +146,16 @@ jobs:
           sudo apt install clang-format
       - name: Install CMake and Ninja
         uses: lukka/get-cmake@latest
-      - name: Configure libCellML
+      - name: Install dependencies
         run: |
-          mkdir build
-          cd build
-          cmake -G Ninja ..
+          cd $HOME
+          wget https://github.com/cellml/gha/releases/download/gha/libxml2-Linux.tar.gz -O - | tar -xz
+          wget https://github.com/cellml/gha/releases/download/gha/symengine-Linux.tar.gz -O - | tar -xz
+          wget https://github.com/cellml/gha/releases/download/gha/zlib-Linux.tar.gz -O - | tar -xz
+      - name: Configure libCellML
+        run: cmake -G Ninja -S . -B build -DCMAKE_PREFIX_PATH=$HOME
       - name: Code formatting
-        run: |
-          cd build
-          ninja test_clang_format
+        run: cmake --build build --target test_clang_format
   coverage:
     name: Code coverage
     runs-on: macos-latest
@@ -152,19 +172,20 @@ jobs:
         run: |
           brew install --overwrite llvm
           echo 'export PATH="/opt/homebrew/opt/llvm/bin:$PATH"' >> ~/.bash_profile
-      - name: Configure libCellML
+      - name: Install dependencies
         run: |
-          mkdir build
-          cd build
-          cmake -G Ninja -DBINDINGS_PYTHON=OFF ..
+          cd $HOME
+          wget https://github.com/cellml/gha/releases/download/gha/libxml2-macOS-ARM.tar.gz -O - | tar -xz
+          wget https://github.com/cellml/gha/releases/download/gha/symengine-macOS-ARM.tar.gz -O - | tar -xz
+          wget https://github.com/cellml/gha/releases/download/gha/zlib-macOS-ARM.tar.gz -O - | tar -xz
+      - name: Configure libCellML
+        run: cmake -G Ninja -S . -B build -DBINDINGS_PYTHON=OFF -DCMAKE_PREFIX_PATH=$HOME
       - name: Code coverage
         run: |
-          cd build
-          ninja llvm_coverage
-          if [ `ninja llvm_coverage | grep TOTAL | sed 's/ /\n/g' | grep "100.00%" | wc -l | sed 's/ //g'` -eq 4 ]; then exit 0; else exit 1; fi
+          cmake --build build --target llvm_coverage
+          if [ `cmake --build build --target llvm_coverage | grep TOTAL | sed 's/ /\n/g' | grep "100.00%" | wc -l | sed 's/ //g'` -eq 4 ]; then exit 0; else exit 1; fi
   memory_leaks:
     name: Memory leaks
-    if: false # Temporarily disabled.
     runs-on: ubuntu-latest
     strategy:
       fail-fast: false
@@ -179,15 +200,16 @@ jobs:
         run: |
           sudo apt update
           sudo apt install valgrind
-      - name: Configure libCellML
+      - name: Install dependencies
         run: |
-          mkdir build
-          cd build
-          cmake -G Ninja -DBINDINGS_PYTHON=OFF ..
+          cd $HOME
+          wget https://github.com/cellml/gha/releases/download/gha/libxml2-Linux.tar.gz -O - | tar -xz
+          wget https://github.com/cellml/gha/releases/download/gha/symengine-Linux.tar.gz -O - | tar -xz
+          wget https://github.com/cellml/gha/releases/download/gha/zlib-Linux.tar.gz -O - | tar -xz
+      - name: Configure libCellML
+        run: cmake -G Ninja -S . -B build -DBINDINGS_PYTHON=OFF -DCMAKE_PREFIX_PATH=$HOME
       - name: Memory leaks
-        run: |
-          cd build
-          ninja memcheck
+        run: cmake --build build --target memcheck
   documentation:
     name: Documentation
     runs-on: ubuntu-latest
@@ -207,12 +229,13 @@ jobs:
       - name: Install Sphinx
         run: |
           pip3 install sphinx
-      - name: Configure libCellML
+      - name: Install dependencies
         run: |
-          mkdir build
-          cd build
-          cmake -G Ninja -DBINDINGS_PYTHON=OFF ..
+          cd $HOME
+          wget https://github.com/cellml/gha/releases/download/gha/libxml2-Linux.tar.gz -O - | tar -xz
+          wget https://github.com/cellml/gha/releases/download/gha/symengine-Linux.tar.gz -O - | tar -xz
+          wget https://github.com/cellml/gha/releases/download/gha/zlib-Linux.tar.gz -O - | tar -xz
+      - name: Configure libCellML
+        run: cmake -G Ninja -S . -B build -DBINDINGS_PYTHON=OFF -DCMAKE_PREFIX_PATH=$HOME
       - name: Documentation
-        run: |
-          cd build
-          ninja docs
+        run: cmake --build build --target docs

CMakeLists.txt

@@ -15,13 +15,13 @@
 cmake_minimum_required(VERSION 3.18.0)
 
 if(APPLE)
-  set(CMAKE_OSX_DEPLOYMENT_TARGET 10.15 CACHE STRING "Minimum OS X deployment version.")
+  set(CMAKE_OSX_DEPLOYMENT_TARGET 14 CACHE STRING "Minimum OS X deployment version.")
 endif()
 
 set(PROJECT_NAME libCellML)
 set(PROJECT_URL https://libcellml.org)
 set(_PROJECT_VERSION 0.7.0)
-set(PROJECT_DEVELOPER_VERSION -rc.1.post)
+set(PROJECT_DEVELOPER_VERSION)
 project(${PROJECT_NAME} VERSION ${_PROJECT_VERSION} LANGUAGES CXX)
 
 # Set policies that affect the build.

cmake/common.cmake

@@ -312,6 +312,19 @@ function(redhat_based _RESULT)
   set(${_RESULT} ${_REDHAT_BASED} PARENT_SCOPE)
 endfunction()
 
+function(apply_dependency_settings _TARGET)
+  if(HAVE_ZLIB_TARGET)
+    target_link_libraries(${_TARGET} PUBLIC zlib)
+  else()
+    target_link_libraries(${_TARGET} PUBLIC ${ZLIB_LIBRARIES})
+    target_include_directories(${_TARGET} PUBLIC ${ZLIB_INCLUDE_DIRS})
+  endif()
+
+  target_include_directories(${_TARGET} SYSTEM PUBLIC ${SYMENGINE_INCLUDE_DIRS}
+                                        PRIVATE $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/3rdparty/symengine>)
+  target_link_libraries(${_TARGET} PUBLIC ${LIBXML2_TARGET} ${SYMENGINE_LIBRARIES} ${ZLIB_TARGET})
+endfunction()
+
 function(get_runtime_dlls_from_target target target_property out_var)
   set(_result "")
   get_target_property(_items ${target} INTERFACE_LINK_LIBRARIES)

cmake/environmentchecks.cmake

@@ -114,6 +114,19 @@ resolve_zlib(${LIBXML2_TARGET} ZLIB_TARGET)
 get_target_property(ZLIB_TARGET_TYPE ${ZLIB_TARGET} TYPE)
 get_target_property(LIBXML2_TARGET_TYPE ${LIBXML2_TARGET} TYPE)
 
+# Set the minimum policy version to work around SymEngine's outdated CMake requirements.
+if(NOT DEFINED CMAKE_POLICY_VERSION_MINIMUM OR CMAKE_POLICY_VERSION_MINIMUM VERSION_LESS "3.10")
+  set(CMAKE_POLICY_VERSION_MINIMUM 3.10)
+endif()
+
+# Find SymEngine.
+find_package(SymEngine REQUIRED CONFIG)
+if(TARGET symengine)
+  set(HAVE_SYMENGINE_TARGET TRUE)
+  get_target_property(SYMENGINE_TARGET_TYPE symengine TYPE)
+  message(STATUS "Found SymEngine: ${SYMENGINE_LIBRARIES} (found version \"${SymEngine_VERSION}\").")
+endif()
+
 if(BUILDCACHE_EXE OR CLCACHE_EXE OR CCACHE_EXE)
   set(COMPILER_CACHE_AVAILABLE TRUE CACHE INTERNAL "Executable required to cache compilations.")
 endif()

src/CMakeLists.txt

@@ -41,6 +41,7 @@ set(SOURCE_FILES
   ${CMAKE_CURRENT_SOURCE_DIR}/analyserequationast.cpp
   ${CMAKE_CURRENT_SOURCE_DIR}/analyserexternalvariable.cpp
   ${CMAKE_CURRENT_SOURCE_DIR}/analysermodel.cpp
+  ${CMAKE_CURRENT_SOURCE_DIR}/analysersymengine.cpp
   ${CMAKE_CURRENT_SOURCE_DIR}/analyservariable.cpp
   ${CMAKE_CURRENT_SOURCE_DIR}/annotator.cpp
   ${CMAKE_CURRENT_SOURCE_DIR}/commonutils.cpp
@@ -194,14 +195,7 @@ target_include_directories(cellml
   ${CMAKE_CURRENT_BINARY_DIR}
 )
 
-if(HAVE_ZLIB_TARGET)
-  target_link_libraries(cellml PUBLIC zlib)
-else()
-  target_link_libraries(cellml PUBLIC ${ZLIB_LIBRARIES})
-  target_include_directories(cellml PUBLIC ${ZLIB_INCLUDE_DIRS})
-endif()
-
-target_link_libraries(cellml PUBLIC ${LIBXML2_TARGET} ${ZLIB_TARGET})
+apply_dependency_settings(cellml)
 
 # Use target compile features to propagate features to consuming projects.
 target_compile_features(cellml PUBLIC cxx_std_20)
@@ -237,7 +231,7 @@ target_include_directories(cellml_debug_utilities
   $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/api>
 )
 
-target_link_libraries(cellml_debug_utilities PUBLIC ${LIBXML2_TARGET})
+apply_dependency_settings(cellml_debug_utilities)
 
 set_target_properties(cellml_debug_utilities PROPERTIES
   CXX_VISIBILITY_PRESET hidden
@@ -282,7 +276,7 @@ endfunction()
 
 if(LIBCELLML_COVERAGE)
   append_target_property(cellml COMPILE_FLAGS "-fprofile-arcs -ftest-coverage")
-  append_target_property(cellml LINK_FLAGS "-fprofile-arcs -ftest-coverage")
+  target_link_options(cellml PUBLIC $<BUILD_INTERFACE:-fprofile-arcs> $<BUILD_INTERFACE:-ftest-coverage>)
 
   # Share some paths with interested parties (tests)
   set(GCOV_ANALYSIS_PATH "${CMAKE_CURRENT_BINARY_DIR}${CMAKE_FILES_DIRECTORY}/cellml.dir" PARENT_SCOPE)
@@ -300,7 +294,7 @@ endif()
 
 if(LIBCELLML_LLVM_COVERAGE)
   append_target_property(cellml COMPILE_FLAGS "-fprofile-instr-generate -fcoverage-mapping")
-  append_target_property(cellml LINK_FLAGS "-fprofile-instr-generate")
+  target_link_options(cellml PUBLIC $<BUILD_INTERFACE:-fprofile-instr-generate>)
 endif()
 
 install(TARGETS cellml EXPORT libcellml-targets