Simulation: have simulation tasks run in their own thread

.github/workflows/buildThirdPartyLibrary.yml

@@ -72,6 +72,16 @@ jobs:
         uses: ilammy/msvc-dev-cmd@v1
         with:
           arch: ${{ matrix.arch }}
+      - name: Install (latest) GCC
+        if: ${{ runner.os == 'Linux' }}
+        run: |
+          sudo add-apt-repository -y ppa:ubuntu-toolchain-r/test
+          sudo apt-get update
+          GCC_LATEST=$(apt-cache search ^gcc-[0-9]+$ | sort -V | tail -1 | awk '{print $1}')
+          GXX_LATEST=$(echo "$GCC_LATEST" | sed 's/gcc/g++/')
+          sudo apt-get install -y "$GCC_LATEST" "$GXX_LATEST"
+          sudo ln -sf "/usr/bin/$GCC_LATEST" /usr/local/bin/cc
+          sudo ln -sf "/usr/bin/$GXX_LATEST" /usr/local/bin/c++
       - name: Configure libOpenCOR (for LLVM+Clang)
         if: ${{ inputs.third_party_library_name == 'LLVMClang' }}
         shell: bash
@@ -129,4 +139,4 @@ jobs:
         uses: actions/upload-artifact@v4
         with:
           name: WebAssembly
-          path: ./build/*.wasm.tar.gz
+          path: ./build/*.tar.gz

.github/workflows/cd.yml

@@ -104,6 +104,16 @@ jobs:
         uses: ilammy/msvc-dev-cmd@v1
         with:
           arch: ${{ matrix.arch }}
+      - name: Install (latest) GCC
+        if: ${{ runner.os == 'Linux' }}
+        run: |
+          sudo add-apt-repository -y ppa:ubuntu-toolchain-r/test
+          sudo apt-get update
+          GCC_LATEST=$(apt-cache search ^gcc-[0-9]+$ | sort -V | tail -1 | awk '{print $1}')
+          GXX_LATEST=$(echo "$GCC_LATEST" | sed 's/gcc/g++/')
+          sudo apt-get install -y "$GCC_LATEST" "$GXX_LATEST"
+          sudo ln -sf "/usr/bin/$GCC_LATEST" /usr/local/bin/cc
+          sudo ln -sf "/usr/bin/$GXX_LATEST" /usr/local/bin/c++
       - name: Configure libOpenCOR
         run: cmake -G Ninja -S . -B build -DBUILD_TYPE=${{ matrix.build_type }} -DCODE_ANALYSIS=OFF -DCODE_COVERAGE=OFF -DDOCUMENTATION=OFF -DJAVASCRIPT_BINDINGS=OFF -DMEMORY_CHECKS=OFF -DPYTHON_BINDINGS=OFF -DPYTHON_UNIT_TESTING=OFF -DSHARED_LIBS=${{ matrix.shared_libs }} -DUNIT_TESTING=OFF
       - name: Build libOpenCOR

.github/workflows/ci.yml

@@ -357,25 +357,29 @@ jobs:
         uses: ilammy/msvc-dev-cmd@v1
         with:
           arch: ${{ matrix.arch }}
+      - name: Install (latest) GCC
+        if: ${{ runner.os == 'Linux' }}
+        run: |
+          sudo add-apt-repository -y ppa:ubuntu-toolchain-r/test
+          sudo apt-get update
+          GCC_LATEST=$(apt-cache search ^gcc-[0-9]+$ | sort -V | tail -1 | awk '{print $1}')
+          GXX_LATEST=$(echo "$GCC_LATEST" | sed 's/gcc/g++/')
+          sudo apt-get install -y "$GCC_LATEST" "$GXX_LATEST"
+          sudo ln -sf "/usr/bin/$GCC_LATEST" /usr/local/bin/cc
+          sudo ln -sf "/usr/bin/$GXX_LATEST" /usr/local/bin/c++
       - name: Install LLVM
         if: ${{ matrix.code_coverage == 'ON' }}
         run: brew install llvm
-      - name: Install Clang
+      - name: Install LLVM+Clang tools
         if: ${{ matrix.code_analysis == 'ON' }}
         run: |
           wget https://github.com/opencor/gha/releases/download/gha/clang.tar.gz -O - | tar -xz
           sudo mv clang /usr/local/bin
           sudo cp /usr/local/bin/clang /usr/local/bin/clang++
           wget https://github.com/opencor/gha/releases/download/gha/clang-include.tar.gz -O - | tar -xz
           sudo mv include/* /usr/local/include
-      - name: Install ClangFormat
-        if: ${{ matrix.target == 'check_code_formatting' }}
-        run: |
           wget https://github.com/opencor/gha/releases/download/gha/clang-format.tar.gz -O - | tar -xz
           sudo mv clang-format /usr/local/bin
-      - name: Install Clang-Tidy
-        if: ${{ matrix.name == 'Code analysis' }}
-        run: |
           wget https://github.com/opencor/gha/releases/download/gha/clang-tidy.tar.gz -O - | tar -xz
           sudo mv clang-tidy /usr/local/bin
       - name: Install Emscripten
@@ -399,6 +403,9 @@ jobs:
       - name: Install Sphinx and some Sphinx packages
         if: ${{ matrix.documentation == 'ON' }}
         run: uv pip install --system sphinx~=8.0 sphinx-copybutton sphinx-inline-tabs
+      - name: Install NumPy
+        if: ${{ matrix.python_support == 'ON' }}
+        run: uv pip install --system numpy
       - name: Install Doxygen
         if: ${{ matrix.documentation == 'ON' }}
         run: |

.gitignore

@@ -1,3 +1,4 @@
+.omo/
 .vscode/
 build/
 _skbuild/

VERSION.txt

@@ -1 +1 @@
-0.20260623.0
+1.20260707.0

cmake/buildpackage.cmake.in

@@ -18,4 +18,4 @@ project(@PACKAGE_NAME@)
 
 include(ExternalProject)
 
-ExternalProject_Add(@PACKAGE_NAME@ @ARGN@)
+ExternalProject_Add(@PACKAGE_NAME@ @ARGN_QUOTED@)

cmake/common.cmake

@@ -108,6 +108,7 @@ function(configure_target TARGET)
                 -Wno-global-constructors
                 -Wno-padded
                 -Wno-switch-enum
+                -Wno-thread-safety-negative
                 -Wno-unsafe-buffer-usage
                 -Wno-weak-vtables
             )

cmake/packages.cmake

@@ -57,6 +57,21 @@ function(build_package PACKAGE_NAME)
 
     message(STATUS "Building ${PACKAGE_NAME}")
 
+    set(ARGN_QUOTED)
+
+    foreach(ARG ${ARGN})
+        string(REPLACE "\\" "\\\\" ARG_ESCAPED "${ARG}")
+        string(REPLACE "\"" "\\\"" ARG_ESCAPED "${ARG_ESCAPED}")
+
+        if(NOT WIN32)
+            string(REPLACE " " "\\ " ARG_ESCAPED "${ARG_ESCAPED}")
+        endif()
+
+        list(APPEND ARGN_QUOTED "\"${ARG_ESCAPED}\"")
+    endforeach()
+
+    string(REPLACE ";" " " ARGN_QUOTED "${ARGN_QUOTED}")
+
     configure_file(${CMAKE_SOURCE_DIR}/cmake/buildpackage.cmake.in ${CMAKE_CURRENT_BINARY_DIR}/CMakeLists.txt)
 
     if(EMSCRIPTEN)
@@ -263,8 +278,15 @@ function(retrieve_package PACKAGE_NAME PACKAGE_VERSION PACKAGE_REPOSITORY RELEAS
     add_custom_target(${PACKAGE_NAME})
 endfunction()
 
-function(escape_path OLD_PATH NEW_PATH)
-    # Escape spaces and parentheses in a path.
+function(safe_path OLD_PATH NEW_PATH)
+    # Make a path safe for use in CMake arguments by double quoting it on Windows and by escaping spaces and parentheses
+    # on Linux and macOS.
+
+    if(WIN32)
+        set(${NEW_PATH} "${OLD_PATH}" PARENT_SCOPE)
+
+        return()
+    endif()
 
     string(REPLACE " " "\\ " NEW_PATH_VALUE "${OLD_PATH}")
     string(REPLACE "(" "\\(" NEW_PATH_VALUE "${NEW_PATH_VALUE}")
@@ -276,7 +298,7 @@ endfunction()
 # Determine the platform on which we are and the architecture on which we want to build.
 
 if(EMSCRIPTEN)
-    set(TARGET_PLATFORM_ARCHITECTURE wasm)
+    set(TARGET_PLATFORM_ARCHITECTURE wasm-threaded) #---GRY--- This should eventually be renamed to just "wasm" once we are done with running simulations in their own thread.
 else()
     if(WIN32)
         if(RELEASE_MODE)
@@ -336,8 +358,8 @@ if(APPLE)
 endif()
 
 if(CMAKE_C_COMPILER_LAUNCHER AND CMAKE_CXX_COMPILER_LAUNCHER)
-    escape_path(${CMAKE_C_COMPILER_LAUNCHER} EP_CMAKE_C_COMPILER_LAUNCHER)
-    escape_path(${CMAKE_CXX_COMPILER_LAUNCHER} EP_CMAKE_CXX_COMPILER_LAUNCHER)
+    safe_path(${CMAKE_C_COMPILER_LAUNCHER} EP_CMAKE_C_COMPILER_LAUNCHER)
+    safe_path(${CMAKE_CXX_COMPILER_LAUNCHER} EP_CMAKE_CXX_COMPILER_LAUNCHER)
 
     list(APPEND CMAKE_ARGS
         -DCMAKE_C_COMPILER_LAUNCHER=${EP_CMAKE_C_COMPILER_LAUNCHER}
@@ -346,13 +368,20 @@ if(CMAKE_C_COMPILER_LAUNCHER AND CMAKE_CXX_COMPILER_LAUNCHER)
 endif()
 
 if(EMSCRIPTEN)
+    # Note: we are using the same CMake variables that we used to build libOpenCOR so that we can build our third-party
+    #       libraries in the same way that we built libOpenCOR.
+
     list(APPEND CMAKE_ARGS
         -DCMAKE_TOOLCHAIN_FILE=${CMAKE_TOOLCHAIN_FILE}
         -DCMAKE_CROSSCOMPILING_EMULATOR=${CMAKE_CROSSCOMPILING_EMULATOR}
+        -DCMAKE_C_FLAGS=${CMAKE_C_FLAGS}
+        -DCMAKE_CXX_FLAGS=${CMAKE_CXX_FLAGS}
+        -DCMAKE_EXE_LINKER_FLAGS=${CMAKE_EXE_LINKER_FLAGS}
+        -DCMAKE_SHARED_LINKER_FLAGS=${CMAKE_SHARED_LINKER_FLAGS}
     )
 else()
-    escape_path(${CMAKE_C_COMPILER} EP_CMAKE_C_COMPILER)
-    escape_path(${CMAKE_CXX_COMPILER} EP_CMAKE_CXX_COMPILER)
+    safe_path(${CMAKE_C_COMPILER} EP_CMAKE_C_COMPILER)
+    safe_path(${CMAKE_CXX_COMPILER} EP_CMAKE_CXX_COMPILER)
 
     list(APPEND CMAKE_ARGS
         -DCMAKE_C_COMPILER=${EP_CMAKE_C_COMPILER}

cmake/staticarchiveextractor.cpp

@@ -176,9 +176,9 @@ int main(int pArgC, char *pArgV[])
         // Parse the size field (right-justified decimal, 10 characters).
 
         long memberSize {};
+        auto [_, ec] = std::from_chars(header.size, header.size + 10, memberSize);
 
-        if (auto [ptr, ec] = std::from_chars(header.size, header.size + 10, memberSize);
-            ec != std::errc {}) {
+        if (ec != std::errc {}) {
             break;
         }
 
@@ -210,9 +210,9 @@ int main(int pArgC, char *pArgV[])
             // BSD ar format (#1/N): the first N bytes of the data area contain the member name.
 
             long nameSize {};
+            auto [_, ec] = std::from_chars(nameBuf + 3, nameBuf + nameEnd, nameSize);
 
-            if (auto [ptr, ec] = std::from_chars(nameBuf + 3, nameBuf + nameEnd, nameSize);
-                ec != std::errc {}) {
+            if (ec != std::errc {}) {
                 nameSize = 0;
             }
 
@@ -274,9 +274,9 @@ int main(int pArgC, char *pArgV[])
 
             if (allDigits) {
                 long offset {};
+                auto [_, ec] = std::from_chars(memberName.data() + 1, memberName.data() + memberName.size(), offset);
 
-                if (auto [ptr, ec] = std::from_chars(memberName.data() + 1, memberName.data() + memberName.size(), offset);
-                    (ec == std::errc {}) && (offset >= 0) && (static_cast<size_t>(offset) < stringTable.size())) {
+                if ((ec == std::errc {}) && (offset >= 0) && (static_cast<size_t>(offset) < stringTable.size())) {
                     auto end {static_cast<size_t>(offset)};
 
                     while ((end < stringTable.size()) && (stringTable[end] != '/') && (stringTable[end] != '\n') && (stringTable[end] != '\0')) {

extern/README.md

@@ -2,4 +2,4 @@
 
 - [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 [5068510](https://chromium.googlesource.com/chromium/src/third_party/modp_b64/+/50685101d51ef9aabbd60c94f52d9e026d39c509)
-- [nanobind](https://github.com/wjakob/nanobind) [2.12.0](https://github.com/wjakob/nanobind/releases/tag/v2.12.0)
+- [nanobind](https://github.com/wjakob/nanobind) [2.13.0](https://github.com/wjakob/nanobind/releases/tag/v2.13.0)

extern/nanobind/.github/workflows/ci.yml

@@ -108,18 +108,18 @@ jobs:
         python3 -m pytest
 
   free-threaded:
-    name: "Python 3.14-dev / ubuntu.latest [free-threaded]"
+    name: "Python 3.14t / ubuntu-latest [free-threaded]"
     runs-on: ubuntu-latest
 
     steps:
     - uses: actions/checkout@v4
       with:
         submodules: true
 
-    - uses: deadsnakes/action@v3.1.0
+    - name: Setup Python 3.14t (free-threaded)
+      uses: actions/setup-python@v5
       with:
-        python-version: 3.14-dev
-        nogil: true
+        python-version: '3.14t'
 
     - name: Install the latest CMake
       uses: lukka/get-cmake@latest
@@ -177,6 +177,18 @@ jobs:
           mingw-w64-x86_64-python-pip
           mingw-w64-x86_64-python-pytest
 
+    # The GCC 16.1 compiler that rolled out in MSYS2 in June 2026 produces
+    # objects with unresolvable references to std::string's move constructor
+    # (a re-run of a previously green master commit fails identically).
+    # Downgrade the compiler only: the GCC 16 runtime (gcc-libs) must stay,
+    # since the other MSYS2 packages were rebuilt against it, and it is
+    # backward-compatible with GCC 15-compiled code.
+    - name: Downgrade GCC to 15.2
+      shell: msys2 {0}
+      run: |
+        pacman -U --noconfirm --nodeps --nodeps \
+          https://repo.msys2.org/mingw/mingw64/mingw-w64-x86_64-gcc-15.2.0-13-any.pkg.tar.zst
+
     - name: Install Python packages
       shell: msys2 {0}
       run: |

extern/nanobind/CMakeLists.txt

@@ -64,9 +64,6 @@ endif()
 # Installation rules
 # ---------------------------------------------------------------------------
 if(NB_CREATE_INSTALL_RULES AND NOT CMAKE_SKIP_INSTALL_RULES)
-  # Silence warning in GNUInstallDirs due to no enabled languages
-  set(CMAKE_INSTALL_LIBDIR "")
-  include(GNUInstallDirs)
   set(NB_INSTALL_DATADIR "nanobind"
     CACHE PATH "Installation path for read-only architecture-independent nanobind data files")
 
@@ -136,7 +133,7 @@ endif()
 # Find the Python interpreter and development libraries
 # ---------------------------------------------------------------------------
 
-if (NOT TARGET Python::Module OR NOT TARGET Python::Interpreter)
+if (NOT TARGET Python::Module AND NOT TARGET Python::Interpreter)
   set(Python_FIND_FRAMEWORK LAST) # Prefer Brew/Conda to Apple framework python
 
   if (CMAKE_VERSION VERSION_LESS 3.18)

extern/nanobind/cmake/darwin-ld-cpython.sym

@@ -122,6 +122,7 @@
 -U _PyDict_Type
 -U _PyDict_Update
 -U _PyDict_Values
+-U _PyFrozenDict_Type
 -U _PyEllipsis_Type
 -U _PyEnum_Type
 -U _PyErr_BadArgument
@@ -942,6 +943,7 @@
 -U __PyTrash_destroy_chain
 -U __PyTrash_thread_deposit_object
 -U __PyTrash_thread_destroy_chain
+-U __PyType_Lookup
 -U __PyWeakref_CallableProxyType
 -U __PyWeakref_ProxyType
 -U __PyWeakref_RefType
@@ -969,6 +971,7 @@
 -U __Py_DecRefSharedDebug
 -U __Py_DECREF_DecRefTotal
 -U __Py_INCREF_IncRefTotal
+-U __Py_NewReference
 -U __PyObject_GetDictPtr
 -U _PyList_GetItemRef
 -U _PyDict_GetItemRef