Compiler: add JavaScript support

cmake/base64encoder.cpp

@@ -25,7 +25,7 @@ int main(int pArgC, char *pArgV[])
     // Convert the given file to a base64-encoded string.
 
     if (pArgC != 2) {
-        std::cerr << "Usage: " << pArgV[0] << " <file>" << std::endl;
+        std::cerr << "Usage: " << pArgV[0] << " <file>\n";
 
         return 1;
     }
@@ -37,7 +37,7 @@ int main(int pArgC, char *pArgV[])
     file.read(buffer, fileSize);
 
     if (!file) {
-        std::cerr << "Error: the file could not be read." << std::endl;
+        std::cerr << "Error: the file could not be read.\n";
 
         return 1;
     }
@@ -48,7 +48,7 @@ int main(int pArgC, char *pArgV[])
 
     modp_b64_encode(base64, buffer, fileSize);
 
-    std::cout << base64 << std::endl;
+    std::cout << base64 << "\n";
 
     delete[] base64;
     delete[] buffer;

cmake/packages.cmake

@@ -193,9 +193,9 @@ function(retrieve_package PACKAGE_NAME PACKAGE_VERSION PACKAGE_REPOSITORY RELEAS
         set(PACKAGE_URL "https://github.com/opencor/${PACKAGE_REPOSITORY}/releases/download/${RELEASE_TAG}/${PACKAGE_FILE}")
 
         if("${PACKAGE_NAME}" STREQUAL "libCellML")
-            #---GRY--- THIS IS TEMPORARY UNTIL libCellML HAS AN OFFICIAL RELEASE WITH THE INTERPRETER.
+            #---GRY--- USE THIS VERSION OF libCellML WHICH CORRESPONDS TO PR #1256 UNTIL IT GETS MERGED IN.
 
-            set(PACKAGE_URL "https://github.com/agarny/${PACKAGE_REPOSITORY}/releases/download/707e211/${PACKAGE_FILE}")
+            set(PACKAGE_URL "https://github.com/agarny/${PACKAGE_REPOSITORY}/releases/download/04d8d15/${PACKAGE_FILE}")
         endif()
 
         set(ATTEMPT 1)

scripts/genericclean

@@ -8,11 +8,8 @@ fi
 
 appDir=$(cd $(dirname $0); pwd)/..
 
-for i in _skbuild build src/bindings/python/libopencor.egg-info tests/install/build; do
-    rm -fr $appDir/$i
-done
-
-find $appDir -name .DS_Store -exec rm -f {} \;
+find $appDir -type f -name .DS_Store -exec rm -f {} \; 2> /dev/null
+find $appDir -type d \( -name .pytest_cache -o -name __pycache__ -o -name _skbuild -o -name build \) -exec rm -fr {} \; 2> /dev/null
 
 if [ "$1" = "all" ]; then
     rm -fr $appDir/prebuilt/* > /dev/null 2>&1

scripts/genericclean.bat

@@ -11,7 +11,9 @@ IF "%1" == "all" (
 SET AppDir=%~dp0..\
 SET OrigDir=!CD!
 
-FOR /D %%I IN (_skbuild build src\bindings\python\libopencor.egg-info tests\install\build) DO IF EXIST !AppDir!%%I RMDIR /S /Q !AppDir!%%I
+FOR /R "%AppDir%" %%d IN (.pytest_cache __pycache__ _skbuild build) DO (
+    IF EXIST "%%d" RMDIR /S /Q "%%d"
+)
 
 IF "%1" == "all" (
     IF EXIST !AppDir!prebuilt (

src/3rdparty/libCellML/CMakeLists.txt

@@ -34,49 +34,49 @@ if(LIBOPENCOR_PREBUILT_LIBCELLML OR ONLY_BUILD_JAVASCRIPT_THIRD_PARTY_LIBRARIES)
     if(EMSCRIPTEN)
         retrieve_package(${PACKAGE_NAME} ${PACKAGE_VERSION}
                          ${PACKAGE_REPOSITORY} ${RELEASE_TAG}
-                         e6e9bfdc883280289aa6131598b617b54672ae72)
+                         13a93a71d210b4ec3af336180f5d386b1e6d44c9)
     else()
         if(WIN32)
             if(RELEASE_MODE)
                 if(INTEL_MODE)
                     retrieve_package(${PACKAGE_NAME} ${PACKAGE_VERSION}
                                      ${PACKAGE_REPOSITORY} ${RELEASE_TAG}
-                                     c688813b383c5759cb4982c1d6737f0fa0d68462)
+                                     25c2e2dd016a47e9fff6a81b610de7be6cdb6bbc)
                 else()
                     retrieve_package(${PACKAGE_NAME} ${PACKAGE_VERSION}
                                      ${PACKAGE_REPOSITORY} ${RELEASE_TAG}
-                                     a1cab436551c576ab8d1bd16b6156e246134b733)
+                                     bb4b2e898776d03abd0644e2662d97034725f8d7)
                 endif()
             else()
                 if(INTEL_MODE)
                     retrieve_package(${PACKAGE_NAME} ${PACKAGE_VERSION}
                                      ${PACKAGE_REPOSITORY} ${RELEASE_TAG}
-                                     9623a3a236f4eadd9a9e7614b66fad916f07ea1d)
+                                     526cfc4d623af35081c37e865f37b856cd39fe0a)
                 else()
                     retrieve_package(${PACKAGE_NAME} ${PACKAGE_VERSION}
                                      ${PACKAGE_REPOSITORY} ${RELEASE_TAG}
-                                     d486630d09a245f8b35670304f259019afb70fc9)
+                                     770ac1735960bf4d01564fee6a09ff33a62486ab)
                 endif()
             endif()
         elseif(APPLE)
             if(INTEL_MODE)
                 retrieve_package(${PACKAGE_NAME} ${PACKAGE_VERSION}
                                  ${PACKAGE_REPOSITORY} ${RELEASE_TAG}
-                                 62768aa55bea80757378c706cb190043173991fb)
+                                 836e28f4bce436fbee88f109a4f050b9e4dd68f6)
             else()
                 retrieve_package(${PACKAGE_NAME} ${PACKAGE_VERSION}
                                  ${PACKAGE_REPOSITORY} ${RELEASE_TAG}
-                                 c80100db4e298acc5a1e2ea06c71c7b2766e49d4)
+                                 555c258f6541ca7c51c54445a02386c5a619d754)
             endif()
         else()
             if(INTEL_MODE)
                 retrieve_package(${PACKAGE_NAME} ${PACKAGE_VERSION}
                                  ${PACKAGE_REPOSITORY} ${RELEASE_TAG}
-                                 1ce868ce9918deb8972f869f63817cbfbf6a411e)
+                                 0842347a0a7abf4c6350aa44a6142ad5ba22a397)
             else()
                 retrieve_package(${PACKAGE_NAME} ${PACKAGE_VERSION}
                                  ${PACKAGE_REPOSITORY} ${RELEASE_TAG}
-                                 deb06fa9adcae7a786f8150e3fa77aafa175e297)
+                                 235fb4aa20bc3dde6ad28483775f2e41e9a093ef)
             endif()
         endif()
     endif()

src/CMakeLists.txt

@@ -131,6 +131,7 @@ set(API_MODULE_FILE ${GIT_API_MODULE_FILE})
 
 set(INTERNAL_SOURCE_FILES
     ${CMAKE_CURRENT_SOURCE_DIR}/file/filemanager.cpp
+    ${CMAKE_CURRENT_SOURCE_DIR}/misc/compiler.cpp
     ${CMAKE_CURRENT_SOURCE_DIR}/misc/utils.cpp
     ${CMAKE_CURRENT_SOURCE_DIR}/solver/solver.cpp
     ${CMAKE_CURRENT_SOURCE_DIR}/solver/solvercvode.cpp
@@ -148,12 +149,6 @@ set(INTERNAL_SOURCE_FILES
     ${CMAKE_CURRENT_SOURCE_DIR}/support/sedml/sedmlfile.cpp
 )
 
-if(NOT EMSCRIPTEN)
-    list(APPEND INTERNAL_SOURCE_FILES
-        ${CMAKE_CURRENT_SOURCE_DIR}/misc/compiler.cpp
-    )
-endif()
-
 set(GIT_API_SOURCE_FILES
     ${CMAKE_CURRENT_SOURCE_DIR}/file/file.cpp
     ${CMAKE_CURRENT_SOURCE_DIR}/file/filemanager.cpp
@@ -214,6 +209,8 @@ set(SOURCE_FILES
 )
 
 set(INTERNAL_HEADER_FILES
+    ${CMAKE_CURRENT_SOURCE_DIR}/misc/compiler_p.h
+    ${CMAKE_CURRENT_SOURCE_DIR}/misc/compiler.h
     ${CMAKE_CURRENT_SOURCE_DIR}/misc/utils.h
     ${CMAKE_CURRENT_SOURCE_DIR}/solver/solver_p.h
     ${CMAKE_CURRENT_SOURCE_DIR}/solver/solvercvode_p.h
@@ -236,13 +233,6 @@ set(INTERNAL_HEADER_FILES
     ${CMAKE_CURRENT_SOURCE_DIR}/unittestingexport.h
 )
 
-if(NOT EMSCRIPTEN)
-    list(APPEND INTERNAL_HEADER_FILES
-        ${CMAKE_CURRENT_SOURCE_DIR}/misc/compiler_p.h
-        ${CMAKE_CURRENT_SOURCE_DIR}/misc/compiler.h
-    )
-endif()
-
 set(GIT_HEADER_FILES
     ${INTERNAL_HEADER_FILES}
     ${THIRD_PARTY_HEADER_FILES}
@@ -281,9 +271,10 @@ if(EMSCRIPTEN)
 
     # Set the flags for our generated .js file.
     # Note #1: we use -O3 to get the best performance, -sALLOW_MEMORY_GROWTH to allow the memory to grow dynamically,
-    #          -sEXPORT_ES6=1 to export ES6 classes, -sEXPORTED_FUNCTIONS to export the functions we need,
-    #          -sINLINING_LIMIT to increase the inlining limit, -sSINGLE_FILE=1 to generate a single file, -sSTACK_SIZE
-    #          to increase the stack size, and --bind to generate the necessary bindings.
+    #          -sASSERTIONS=0 to disable assertions (which are not needed in production), -sEXPORT_ES6=1 to export ES6
+    #          classes, -sEXPORTED_FUNCTIONS to export the functions we need, -sINLINING_LIMIT to increase the inlining
+    #          limit, -sSINGLE_FILE=1 to generate a single file, -sSTACK_SIZE to increase the stack size, and --bind to
+    #          generate the necessary bindings.
     # Note #2: by default, Emscripten uses 64KB of stack, but this is not enough for "complex" models such as the Zhang
     #          et al. model (see https://github.com/agarny/COR/blob/master/Models/zhang_SAN_model_2000_all.cellml). For
     #          that model, we need about 108KB of stack. However, Emscripten originally used to use 5MB of stack (see
@@ -301,7 +292,7 @@ if(EMSCRIPTEN)
 
     set_target_properties(${CMAKE_PROJECT_NAME} PROPERTIES
                           COMPILE_FLAGS "-O3"
-                          LINK_FLAGS "-O3 -sALLOW_MEMORY_GROWTH -sEXPORT_ES6=1 -sEXPORTED_FUNCTIONS=[_malloc,_free] -sEXPORTED_RUNTIME_METHODS=HEAPU8 -sINLINING_LIMIT -sSINGLE_FILE=1 -sSTACK_SIZE=4MB --bind")
+                          LINK_FLAGS "-O3 -sALLOW_MEMORY_GROWTH -sASSERTIONS=0 -sEXPORT_ES6=1 -sEXPORTED_FUNCTIONS=[_malloc,_free] -sEXPORTED_RUNTIME_METHODS=HEAPU8 -sINLINING_LIMIT -sSINGLE_FILE=1 -sSTACK_SIZE=4MB --bind")
 
     # Create a .tgz file for our generated .js file that can be used to distribute our JavaScript bindings.
 

src/api/libopencor/seddocument.h

@@ -320,17 +320,10 @@ class LIBOPENCOR_EXPORT SedDocument: public Logger
      *
      * Create an instance of this simulation experiment description.
      *
-     * @param pCompiled Whether the instance of this simulation experiment description is to be compiled (as opposed to
-     * being interpreted).
-     *
      * @return A smart pointer to a @ref SedInstance object.
      */
 
-#ifdef __EMSCRIPTEN__
     SedInstancePtr instantiate();
-#else
-    SedInstancePtr instantiate(bool pCompiled = true);
-#endif
 
 private:
     class Impl; /**< Forward declaration of the implementation class, @private. */

src/api/libopencor/sedinstance.h

@@ -98,7 +98,7 @@ class LIBOPENCOR_EXPORT SedInstance: public Logger
 private:
     class Impl; /**< Forward declaration of the implementation class, @private. */
 
-    explicit SedInstance(const SedDocumentPtr &pDocument, bool pCompiled); /**< Constructor @private. */
+    explicit SedInstance(const SedDocumentPtr &pDocument); /**< Constructor @private. */
 
     Impl *pimpl(); /**< Private implementation pointer, @private. */
     const Impl *pimpl() const; /**< Constant private implementation pointer, @private. */

src/api/libopencor/sedinstancetask.h

@@ -335,7 +335,7 @@ class LIBOPENCOR_EXPORT SedInstanceTask: public Logger
 private:
     class Impl; /**< Forward declaration of the implementation class, @private. */
 
-    explicit SedInstanceTask(const SedAbstractTaskPtr &pTask, bool pCompiled); /**< Constructor @private. */
+    explicit SedInstanceTask(const SedAbstractTaskPtr &pTask); /**< Constructor @private. */
 
     Impl *pimpl(); /**< Private implementation pointer, @private. */
     const Impl *pimpl() const; /**< Constant private implementation pointer, @private. */

src/api/libopencor/solvernla.h

@@ -33,7 +33,7 @@ class LIBOPENCOR_EXPORT SolverNla: public Solver
     friend class SedSimulation;
 
 public:
-    using ComputeSystem = void (*)(double *pU, double *pF, void *pUserData); /**< Signature of the method that computes the system of NLA equations. */
+    using ComputeObjectiveFunction = void (*)(double *pU, double *pF, void *pUserData); /**< Signature of the method that computes the objective function of the NLA system. */
 
     /**
      * Constructors, destructor, and assignment operators.
@@ -54,15 +54,19 @@ class LIBOPENCOR_EXPORT SolverNla: public Solver
      *
      * Solve the NLA system.
      *
-     * @param pComputeSystem The method that computes the system of NLA equations.
+     * @param pComputeObjectiveFunction The method that computes the objective function of the NLA system.
      * @param pU The initial guess for the solution of the NLA system.
      * @param pN The number of variables in the NLA system.
-     * @param pUserData Some user data that may be passed to @p pComputeSystem.
+     * @param pUserData User data, if any, that are passed to @p pComputeObjectiveFunction.
      *
      * @return @c true if the NLA system could be solved, @c false otherwise.
      */
 
-    bool solve(ComputeSystem pComputeSystem, double *pU, size_t pN, void *pUserData);
+#ifdef __EMSCRIPTEN__
+    bool solve(size_t pComputeObjectiveFunctionIndex, double *pU, size_t pN, void *pUserData);
+#else
+    bool solve(ComputeObjectiveFunction pComputeObjectiveFunction, double *pU, size_t pN, void *pUserData);
+#endif
 
 protected:
     class Impl; /**< Forward declaration of the implementation class, @private. */

src/bindings/javascript/solver.cpp

@@ -14,6 +14,8 @@ See the License for the specific language governing permissions and
 limitations under the License.
 */
 
+#include "solvernla_p.h"
+
 #include <libopencor>
 
 void solverApi()
@@ -47,6 +49,11 @@ void solverApi()
 
     // SolverNla API.
 
+    emscripten::function("nlaSolve", emscripten::optional_override([](uintptr_t pNlaSolverAddress, size_t pObjectiveFunctionIndex, uintptr_t pU, size_t pN, uintptr_t pData) {
+                             libOpenCOR::nlaSolve(pNlaSolverAddress, pObjectiveFunctionIndex,
+                                                  reinterpret_cast<double *>(pU), pN, reinterpret_cast<void *>(pData));
+                         }));
+
     emscripten::class_<libOpenCOR::SolverNla, emscripten::base<libOpenCOR::Solver>>("SolverNla")
         .smart_ptr<libOpenCOR::SolverNlaPtr>("SolverNla");
 

src/bindings/python/sed.cpp

@@ -89,7 +89,7 @@ void sedApi(nb::module_ &m)
         .def("add_task", &libOpenCOR::SedDocument::addTask, "Add a task.", nb::arg("task").none())
         .def("remove_task", &libOpenCOR::SedDocument::removeTask, "Remove a task.", nb::arg("task").none())
         .def("remove_all_tasks", &libOpenCOR::SedDocument::removeAllTasks, "Remove all tasks.")
-        .def("instantiate", &libOpenCOR::SedDocument::instantiate, "Instantiate this SedDocument object.", nb::arg("compiled") = true);
+        .def("instantiate", &libOpenCOR::SedDocument::instantiate, "Instantiate this SedDocument object.");
 
     // SedInstance API.