Hangs when instantiating a simulation

.github/workflows/ci.yml

@@ -184,7 +184,7 @@ jobs:
             install_uninstall_and_package: ON
             use_install_prefix: ON
           - name: 'JavaScript bindings'
-            os: macos-15
+            os: ubuntu-22.04
             build_type: Release
             code_analysis: OFF
             code_coverage: OFF
@@ -251,7 +251,7 @@ jobs:
             context: PATH=$GITHUB_WORKSPACE:$PATH
             target: check_code_formatting
           - name: 'JavaScript code formatting'
-            os: macos-15
+            os: ubuntu-22.04
             build_type: Release
             code_analysis: OFF
             code_coverage: OFF
@@ -376,10 +376,13 @@ jobs:
           sudo mv clang-tidy /usr/local/bin
       - name: Install Emscripten
         if: ${{ matrix.javascript_support == 'ON' }}
-        run: brew install --overwrite emscripten
+        uses: mymindstorm/setup-emsdk@v14
       - name: Install Biome
         if: ${{ matrix.target == 'javascript_check_code_formatting' }}
-        run: brew install --overwrite biome
+        run: |
+          curl -L https://github.com/biomejs/biome/releases/latest/download/biome-linux-x64 -o biome
+          chmod +x biome
+          mv biome /usr/local/bin
       - name: Install uv
         if: ${{ matrix.documentation == 'ON' || matrix.python_support == 'ON' || matrix.target == 'python_check_code_formatting' }}
         uses: astral-sh/setup-uv@v6

VERSION.txt

@@ -1 +1 @@
-0.20251027.0
+0.20251030.0

cmake/base64encoder.cpp

@@ -30,8 +30,8 @@ int main(int pArgC, char *pArgV[])
         return 1;
     }
 
-    std::uintmax_t fileSize = std::filesystem::file_size(pArgV[1]);
-    char *buffer = new char[fileSize];
+    std::uintmax_t fileSize {std::filesystem::file_size(pArgV[1])};
+    char *buffer {new char[fileSize]};
     std::ifstream file(pArgV[1], std::ios::binary);
 
     file.read(buffer, fileSize);
@@ -44,7 +44,7 @@ int main(int pArgC, char *pArgV[])
 
     file.close();
 
-    char *base64 = new char[modp_b64_encode_len(fileSize)];
+    char *base64 {new char[modp_b64_encode_len(fileSize)]};
 
     modp_b64_encode(base64, buffer, fileSize);
 

extern/nanobind/src/implicit.cpp

@@ -15,13 +15,13 @@ NAMESPACE_BEGIN(detail)
 
 void implicitly_convertible(const std::type_info *src,
                             const std::type_info *dst) noexcept {
-    nb_internals *internals_ = internals;
-    type_data *t = nb_type_c2p(internals_, dst);
+    nb_internals *internals_ {internals};
+    type_data *t {nb_type_c2p(internals_, dst)};
     check(t, "nanobind::detail::implicitly_convertible(src=%s, dst=%s): "
              "destination type unknown!", type_name(src), type_name(dst));
 
     lock_internals guard(internals_);
-    size_t size = 0;
+    size_t size {0};
 
     if (t->flags & (uint32_t) type_flags::has_implicit_conversions) {
         while (t->implicit.cpp && t->implicit.cpp[size])
@@ -45,13 +45,13 @@ void implicitly_convertible(const std::type_info *src,
 void implicitly_convertible(bool (*predicate)(PyTypeObject *, PyObject *,
                                               cleanup_list *),
                             const std::type_info *dst) noexcept {
-    nb_internals *internals_ = internals;
-    type_data *t = nb_type_c2p(internals_, dst);
+    nb_internals *internals_ {internals};
+    type_data *t {nb_type_c2p(internals_, dst)};
     check(t, "nanobind::detail::implicitly_convertible(src=<predicate>, dst=%s): "
              "destination type unknown!", type_name(dst));
 
     lock_internals guard(internals_);
-    size_t size = 0;
+    size_t size {0};
 
     if (t->flags & (uint32_t) type_flags::has_implicit_conversions) {
         while (t->implicit.py && t->implicit.py[size])

src/api/libopencor/file.h

@@ -79,8 +79,8 @@ class LIBOPENCOR_EXPORT File: public Logger
      * Factory method to create a @ref File object:
      *
      * ```
-     * auto localFile = libOpenCOR::File::create("/some/path/file.txt");
-     * auto remoteFile = libOpenCOR::File::create("https://some.domain.com/file.txt");
+     * auto localFile {libOpenCOR::File::create("/some/path/file.txt")};
+     * auto remoteFile {libOpenCOR::File::create("https://some.domain.com/file.txt")};
      * ```
      *
      * Note: if there is already a @ref File object for the given file name or URL then we return it after having reset

src/api/libopencor/sedanalysis.h

@@ -50,8 +50,8 @@ class LIBOPENCOR_EXPORT SedAnalysis: public SedSimulation
      * Factory method to create a @ref SedAnalysis object:
      *
      * ```
-     * auto document = libOpenCOR::SedDocument::create();
-     * auto simulation = libOpenCOR::SedAnalysis::create(document);
+     * auto document {libOpenCOR::SedDocument::create()};
+     * auto simulation {libOpenCOR::SedAnalysis::create(document)};
      * ```
      *
      * @param pDocument The @ref SedDocument object to which the @ref SedAnalysis object is to belong.

src/api/libopencor/sedchangeattribute.h

@@ -50,7 +50,7 @@ class LIBOPENCOR_EXPORT SedChangeAttribute: public SedChange
      * Factory method to create a @ref SedChangeAttribute object:
      *
      * ```
-     * auto simulation = libOpenCOR::SedChangeAttribute::create(component, variable, newValue);
+     * auto simulation {libOpenCOR::SedChangeAttribute::create(component, variable, newValue)};
      * ```
      *
      * @param pComponentName The name of the component, as a @c std::string, where the target is located.

src/api/libopencor/seddocument.h

@@ -53,7 +53,7 @@ class LIBOPENCOR_EXPORT SedDocument: public Logger
      * Factory method to create a @ref SedDocument object:
      *
      * ```
-     * auto document = libOpenCOR::SedDocument::create();
+     * auto document {libOpenCOR::SedDocument::create()};
      * ```
      *
      * @param pFile The @ref File, if any, used to initialise this @ref SedDocument object.

src/api/libopencor/sedmodel.h

@@ -53,9 +53,9 @@ class LIBOPENCOR_EXPORT SedModel: public SedBase
      * Factory method to create a @ref SedModel object:
      *
      * ```
-     * auto document = libOpenCOR::SedDocument::create();
-     * auto file = libOpenCOR::File::create("/some/path/file.txt");
-     * auto model = libOpenCOR::SedModel::create(document, file);
+     * auto document {libOpenCOR::SedDocument::create()};
+     * auto file {libOpenCOR::File::create("/some/path/file.txt")};
+     * auto model {libOpenCOR::SedModel::create(document, file)};
      * ```
      *
      * @param pDocument The @ref SedDocument object to which the @ref SedModel object is to belong.

src/api/libopencor/sedonestep.h

@@ -49,8 +49,8 @@ class LIBOPENCOR_EXPORT SedOneStep: public SedSimulation
      * Factory method to create a @ref SedOneStep object:
      *
      * ```
-     * auto document = libOpenCOR::SedDocument::create();
-     * auto simulation = libOpenCOR::SedOneStep::create(document);
+     * auto document {libOpenCOR::SedDocument::create()};
+     * auto simulation {libOpenCOR::SedOneStep::create(document)};
      * ```
      *
      * @param pDocument The @ref SedDocument object to which the @ref SedOneStep object is to belong.

src/api/libopencor/sedrepeatedtask.h

@@ -47,8 +47,8 @@ class LIBOPENCOR_EXPORT SedRepeatedTask: public SedAbstractTask
      * Factory method to create a @ref SedRepeatedTask object:
      *
      * ```
-     * auto document = libOpenCOR::SedDocument::create();
-     * auto task = libOpenCOR::SedRepeatedTask::create(document);
+     * auto document {libOpenCOR::SedDocument::create()};
+     * auto task {libOpenCOR::SedRepeatedTask::create(document)};
      * ```
      *
      * @param pDocument The @ref SedDocument object to which the @ref SedRepeatedTask object is to belong.

src/api/libopencor/sedsteadystate.h

@@ -50,8 +50,8 @@ class LIBOPENCOR_EXPORT SedSteadyState: public SedSimulation
      * Factory method to create a @ref SedSteadyState object:
      *
      * ```
-     * auto document = libOpenCOR::SedDocument::create();
-     * auto simulation = libOpenCOR::SedSteadyState::create(document);
+     * auto document {libOpenCOR::SedDocument::create()};
+     * auto simulation {libOpenCOR::SedSteadyState::create(document)};
      * ```
      *
      * @param pDocument The @ref SedDocument object to which the @ref SedSteadyState object is to belong.

src/api/libopencor/sedtask.h

@@ -49,8 +49,8 @@ class LIBOPENCOR_EXPORT SedTask: public SedAbstractTask
      * Factory method to create a @ref SedTask object:
      *
      * ```
-     * auto document = libOpenCOR::SedDocument::create();
-     * auto task = libOpenCOR::SedTask::create(document);
+     * auto document {libOpenCOR::SedDocument::create()};
+     * auto task {libOpenCOR::SedTask::create(document)};
      * ```
      *
      * @param pDocument The @ref SedDocument object to which the @ref SedTask object is to belong.

src/api/libopencor/seduniformtimecourse.h

@@ -50,8 +50,8 @@ class LIBOPENCOR_EXPORT SedUniformTimeCourse: public SedSimulation
      * Factory method to create a @ref SedUniformTimeCourse object:
      *
      * ```
-     * auto document = libOpenCOR::SedDocument::create();
-     * auto simulation = libOpenCOR::SedUniformTimeCourse::create(document);
+     * auto document {libOpenCOR::SedDocument::create()};
+     * auto simulation {libOpenCOR::SedUniformTimeCourse::create(document)};
      * ```
      *
      * @param pDocument The @ref SedDocument object to which the @ref SedUniformTimeCourse object is to

src/api/libopencor/solvercvode.h

@@ -99,7 +99,7 @@ class LIBOPENCOR_EXPORT SolverCvode: public SolverOde
      * Factory method to create a @ref SolverCvode object:
      *
      * ```
-     * auto solver = libOpenCOR::SolverCvode::create();
+     * auto solver {libOpenCOR::SolverCvode::create()};
      * ```
      *
      * @return A smart pointer to a @ref SolverCvode object.

src/api/libopencor/solverforwardeuler.h

@@ -47,7 +47,7 @@ class LIBOPENCOR_EXPORT SolverForwardEuler: public SolverOdeFixedStep
      * Factory method to create a @ref SolverForwardEuler object:
      *
      * ```
-     * auto solver = libOpenCOR::SolverForwardEuler::create();
+     * auto solver {libOpenCOR::SolverForwardEuler::create()};
      * ```
      *
      * @return A smart pointer to a @ref SolverForwardEuler object.

src/api/libopencor/solverfourthorderrungekutta.h

@@ -47,7 +47,7 @@ class LIBOPENCOR_EXPORT SolverFourthOrderRungeKutta: public SolverOdeFixedStep
      * Factory method to create a @ref SolverFourthOrderRungeKutta object:
      *
      * ```
-     * auto solver = libOpenCOR::SolverFourthOrderRungeKutta::create();
+     * auto solver {libOpenCOR::SolverFourthOrderRungeKutta::create()};
      * ```
      *
      * @return A smart pointer to a @ref SolverFourthOrderRungeKutta object.

src/api/libopencor/solverheun.h

@@ -47,7 +47,7 @@ class LIBOPENCOR_EXPORT SolverHeun: public SolverOdeFixedStep
      * Factory method to create a @ref SolverHeun object:
      *
      * ```
-     * auto solver = libOpenCOR::SolverHeun::create();
+     * auto solver {libOpenCOR::SolverHeun::create()};
      * ```
      *
      * @return A smart pointer to a @ref SolverHeun object.

src/api/libopencor/solverkinsol.h

@@ -62,7 +62,7 @@ class LIBOPENCOR_EXPORT SolverKinsol: public SolverNla
      * Factory method to create a @ref SolverKinsol object:
      *
      * ```
-     * auto solver = libOpenCOR::SolverKinsol::create();
+     * auto solver {libOpenCOR::SolverKinsol::create()};
      * ```
      *
      * @return A smart pointer to a @ref SolverKinsol object.

src/api/libopencor/solversecondorderrungekutta.h

@@ -47,7 +47,7 @@ class LIBOPENCOR_EXPORT SolverSecondOrderRungeKutta: public SolverOdeFixedStep
      * Factory method to create a @ref SolverSecondOrderRungeKutta object:
      *
      * ```
-     * auto solver = libOpenCOR::SolverSecondOrderRungeKutta::create();
+     * auto solver {libOpenCOR::SolverSecondOrderRungeKutta::create()};
      * ```
      *
      * @return A smart pointer to a @ref SolverSecondOrderRungeKutta object.

src/bindings/javascript/file.cpp

@@ -32,17 +32,17 @@ void fileApi()
         .property("fileName", &libOpenCOR::File::fileName)
         .property("url", &libOpenCOR::File::url)
         .property("path", &libOpenCOR::File::path)
-        .function("contents", emscripten::optional_override([](libOpenCOR::FilePtr &pThis) {
-                      auto contents = pThis->contents();
-                      auto view = emscripten::typed_memory_view(contents.size(), contents.data());
-                      auto res = emscripten::val::global("Uint8Array").new_(contents.size());
+        .function("contents", emscripten::optional_override([](const libOpenCOR::FilePtr &pThis) {
+                      auto contents {pThis->contents()};
+                      auto view {emscripten::typed_memory_view(contents.size(), contents.data())};
+                      auto res {emscripten::val::global("Uint8Array").new_(contents.size())};
 
                       res.call<void>("set", view);
 
                       return res;
                   }))
-        .function("setContents", emscripten::optional_override([](libOpenCOR::FilePtr &pThis, uintptr_t pContents, size_t pSize) {
-                      auto contents = reinterpret_cast<unsigned char *>(pContents);
+        .function("setContents", emscripten::optional_override([](const libOpenCOR::FilePtr &pThis, uintptr_t pContents, size_t pSize) {
+                      auto contents {reinterpret_cast<unsigned char *>(pContents)};
 
                       pThis->setContents(libOpenCOR::UnsignedChars(contents, contents + pSize));
                   }))

src/file/file.cpp

@@ -27,7 +27,7 @@ File::Impl::Impl(const std::string &pFileNameOrUrl, bool pRetrieveContents)
 {
     // Check whether we are dealing with a local file or a URL.
 
-    auto [isLocalFile, fileNameOrUrl] = retrieveFileInfo(decodeUrl(pFileNameOrUrl));
+    auto [isLocalFile, fileNameOrUrl] {retrieveFileInfo(decodeUrl(pFileNameOrUrl))};
 
     if (isLocalFile) {
         mFilePath = stringToPath(fileNameOrUrl);
@@ -40,7 +40,7 @@ File::Impl::Impl(const std::string &pFileNameOrUrl, bool pRetrieveContents)
 
     if (mFilePath.empty()) {
         if (pRetrieveContents) {
-            auto [res, filePath] = downloadFile(mUrl);
+            auto [res, filePath] {downloadFile(mUrl)};
 
             if (res) {
                 mFilePath = filePath;
@@ -258,21 +258,21 @@ FilePtr File::create(const std::string &pFileNameOrUrl, bool pRetrieveContents)
     // Check whether the given file name or URL is already managed and if so then return it otherwise create, manage,
     // and return a new file object.
 
-    auto fileManager = FileManager::instance();
+    auto fileManager {FileManager::instance()};
 #ifdef __EMSCRIPTEN__
-    auto file = fileManager.fileFromFileNameOrUrl(pFileNameOrUrl);
+    auto file {fileManager.fileFromFileNameOrUrl(pFileNameOrUrl)};
 #else
-    auto file = fileManager.file(pFileNameOrUrl);
+    auto file {fileManager.file(pFileNameOrUrl)};
 #endif
 
     if (file != nullptr) {
         return file;
     }
 
 #ifdef __EMSCRIPTEN__
-    auto res = FilePtr {new File {pFileNameOrUrl, false}};
+    auto res {FilePtr {new File {pFileNameOrUrl, false}}};
 #else
-    auto res = FilePtr {new File {pFileNameOrUrl, pRetrieveContents}};
+    auto res {FilePtr {new File {pFileNameOrUrl, pRetrieveContents}}};
 #endif
 
     res->pimpl()->checkType(res);

src/file/file_p.h

@@ -31,15 +31,15 @@ namespace libOpenCOR {
 class File::Impl: public Logger::Impl
 {
 public:
-    Type mType = Type::UNKNOWN_FILE;
+    Type mType {Type::UNKNOWN_FILE};
 
     std::filesystem::path mFilePath;
     std::string mUrl;
 
-    bool mTypeChecked = false;
+    bool mTypeChecked {false};
 
-    bool mRetrieveContents = true;
-    bool mContentsRetrieved = false;
+    bool mRetrieveContents {true};
+    bool mContentsRetrieved {false};
     UnsignedChars mContents;
 
     CellmlFilePtr mCellmlFile;

src/file/filemanager.cpp

@@ -47,7 +47,7 @@ void FileManager::Impl::unmanage(File *pFile)
     while (!files.empty()) {
         // Retrieve the file at the top of the stack.
 
-        File *file = files.top();
+        auto *file {files.top()};
 
         files.pop();
 
@@ -59,7 +59,7 @@ void FileManager::Impl::unmanage(File *pFile)
 
         // Unmanage the current file.
 
-        auto iter = std::ranges::find(mFiles, file);
+        auto iter {std::ranges::find(mFiles, file)};
 
         if (iter != mFiles.cend()) {
             mFiles.erase(iter);
@@ -109,17 +109,17 @@ FilePtr FileManager::Impl::file(const std::string &pFileNameOrUrl) const
 #endif
 {
 #if __clang_major__ < 16
-    auto [tIsLocalFile, tFileNameOrUrl] = retrieveFileInfo(pFileNameOrUrl);
-    auto isLocalFile = tIsLocalFile;
-    auto fileNameOrUrl = tFileNameOrUrl;
+    auto [tIsLocalFile, tFileNameOrUrl] {retrieveFileInfo(pFileNameOrUrl)};
+    auto isLocalFile {tIsLocalFile};
+    auto fileNameOrUrl {tFileNameOrUrl};
 #else
-    auto [isLocalFile, fileNameOrUrl] = retrieveFileInfo(pFileNameOrUrl);
+    auto [isLocalFile, fileNameOrUrl] {retrieveFileInfo(pFileNameOrUrl)};
 #endif
-    auto res = std::ranges::find_if(mFiles, [&](const auto &file) {
+    auto res {std::ranges::find_if(mFiles, [&](const auto &file) {
         return isLocalFile ?
                    file->fileName() == fileNameOrUrl :
                    file->url() == fileNameOrUrl;
-    });
+    })};
 
     if (res != mFiles.end()) {
         return (*res)->shared_from_this();