SED-ML: add support for initialTime

VERSION.txt

@@ -1 +1 @@
-0.20260529.1
+0.20260604.0

src/api/libopencor/seduniformtimecourse.h

@@ -68,9 +68,6 @@ class LIBOPENCOR_EXPORT SedUniformTimeCourse: public SedSimulation
      * Return the initial time used by this simulation.
      *
      * @return The initial time used by this simulation.
-     *
-     * @warning ---GRY--- The initial time of a simulation is currently ignored. We currently assume that the initial
-     * time is always the same as the output start time.
      */
 
     double initialTime() const;
@@ -81,9 +78,6 @@ class LIBOPENCOR_EXPORT SedUniformTimeCourse: public SedSimulation
      * Set the initial time to be used by this simulation.
      *
      * @param pInitialTime The initial time to be used by this simulation.
-     *
-     * @warning ---GRY--- The initial time of a simulation is currently ignored. We currently assume that the initial
-     * time is always the same as the output start time.
      */
 
     void setInitialTime(double pInitialTime);

src/bindings/javascript/file.cpp

@@ -32,57 +32,62 @@ void fileApi()
         .property("fileName", &libOpenCOR::File::fileName)
         .property("url", &libOpenCOR::File::url)
         .property("path", &libOpenCOR::File::path)
+        // clang-format off
         .function("contents", emscripten::optional_override([](const libOpenCOR::FilePtr &pThis) {
-                      const auto &contents {pThis->contents()};
-                      auto size = contents.size();
-
-                      if (size == 0) {
-                          return emscripten::val::global("Uint8Array").new_(0);
-                      }
-
-                      // Note: we avoid using emscripten::typed_memory_view() as an intermediate step since it creates a
-                      //       JavaScript's TypedArray view directly backed by wasmMemory.buffer. This is fragile and
-                      //       would break if ALLOW_MEMORY_GROWTH was to be enabled or if pthreads/SharedArrayBuffer
-                      //       support were to be added. By performing the copy entirely within a single EM_ASM() block,
-                      //       HEAPU8 is fetched and used atomically.
-
-                      return emscripten::val::take_ownership(
-                          static_cast<emscripten::EM_VAL>(EM_ASM_PTR({
-                              var jsArray = new Uint8Array(HEAPU8.subarray($0, $0 + $1));
-
-                              return Emval.toHandle(jsArray); }, contents.data(), size)));
-                  }))
+            const auto &contents {pThis->contents()};
+            auto size = contents.size();
+
+            if (size == 0) {
+                return emscripten::val::global("Uint8Array").new_(0);
+            }
+
+            // Note: we avoid using emscripten::typed_memory_view() as an intermediate step since it creates a
+            //       JavaScript's TypedArray view directly backed by wasmMemory.buffer. This is fragile and would break
+            //       if ALLOW_MEMORY_GROWTH was to be enabled or if pthreads/SharedArrayBuffer support were to be added.
+            //       By performing the copy entirely within a single EM_ASM() block, HEAPU8 is fetched and used
+            //       atomically.
+
+            return emscripten::val::take_ownership(static_cast<emscripten::EM_VAL>(
+                EM_ASM_PTR({
+                    let jsArray = new Uint8Array(HEAPU8.subarray($0, $0 + $1));
+
+                    return Emval.toHandle(jsArray);
+                }, contents.data(), size)));
+        }))
         .function("setContents", emscripten::optional_override([](const libOpenCOR::FilePtr &pThis, emscripten::val pContents) {
-                      if (pContents.isNull() || pContents.isUndefined()) {
-                          pThis->setContents(libOpenCOR::UnsignedChars {});
+            if (pContents.isNull() || pContents.isUndefined()) {
+                pThis->setContents(libOpenCOR::UnsignedChars {});
 
-                          return;
-                      }
+                return;
+            }
 
-                      // Note: avoid using emscripten::vecFromJSArray() since it internally uses typed_memory_view (see
-                      //       the note in the contents() binding above).
+            // Note: avoid using emscripten::vecFromJSArray() since it internally uses typed_memory_view (see the note
+            //       in the contents() binding above).
 
-                      auto length = pContents["length"].as<size_t>();
-                      libOpenCOR::UnsignedChars contents(length);
+            auto length = pContents["length"].as<size_t>();
+            libOpenCOR::UnsignedChars contents(length);
 
-                      if (length > 0) {
-                          EM_ASM({ HEAPU8.set(Emval.toValue($0).subarray(0, $2), $1); }, pContents.as_handle(), contents.data(), length);
-                      }
+            if (length > 0) {
+                EM_ASM({
+                    HEAPU8.set(Emval.toValue($0).subarray(0, $2), $1);
+                }, pContents.as_handle(), contents.data(), length);
+            }
 
-                      pThis->setContents(std::move(contents));
-                  }))
+            pThis->setContents(std::move(contents));
+        })) // clang-format on
         .property("hasChildFiles", &libOpenCOR::File::hasChildFiles)
         .property("childFileCount", &libOpenCOR::File::childFileCount)
         .property("childFileNames", &libOpenCOR::File::childFileNames)
         .property("childFiles", &libOpenCOR::File::childFiles)
         .function("childFile", &libOpenCOR::File::childFile)
         .function("childFileFromFileName", &libOpenCOR::File::childFileFromFileName);
 
+    // clang-format off
     EM_ASM({
         Module["File"]["Type"] = Module["File.Type"];
 
         delete Module["File.Type"];
-    });
+    }); // clang-format on
 
     // FileManager API.
 

src/bindings/javascript/logger.cpp

@@ -46,14 +46,14 @@ void loggerApi()
         .property("typeAsString", &libOpenCOR::Issue::typeAsString)
         .property("description", &libOpenCOR::Issue::description);
 
+    // clang-format off
     EM_ASM({
         Module["Issue"]["Type"] = Module["Issue.Type"];
 
         delete Module["Issue.Type"];
 
-        Module["Issue"].prototype.toString = function()
-        {
+        Module["Issue"].prototype.toString = function() {
             return this.description;
         };
-    });
+    }); // clang-format on
 }

src/bindings/javascript/main.cpp

@@ -55,39 +55,59 @@ EMSCRIPTEN_BINDINGS(libOpenCOR)
     //       those commas can get interpreted as macro argument separators by the C++ preprocessor, which causes
     //       compilation errors.
 
+    // clang-format off
     EM_ASM({
         let vectorNames = 'Doubles|FilePtrs|IssuePtrs|SedAbstractTaskPtrs|SedChangePtrs|SedDataDescriptionPtrs|SedDataGeneratorPtrs|SedInstanceTaskPtrs|SedModelPtrs|SedOutputPtrs|SedSimulationPtrs|SedStylePtrs|Strings'.split('|');
 
-        vectorNames.forEach(function(name) {
+        vectorNames.forEach((name) => {
             let prototype = Module[name].prototype;
 
             Object.defineProperty(prototype, 'length', {
-                get: function() { return this.size(); }
-    });
-
-    prototype[Symbol.iterator] = function()
-    {
-        let i = 0;
-        let n = this.size();
-        let iterator = {};
-
-        iterator.next = () =>
-        {
-            let result = {};
-
-            if (i < n) {
-                result.value = this.get(i++);
-                result.done = false;
-            } else {
-                result.value = undefined;
-                result.done = true;
-            }
-
-            return result;
-        };
-
-        return iterator;
-    };
-});
-});
+                get: function() {
+                    return this.size();
+                }
+            });
+
+            prototype[Symbol.iterator] = function() {
+                let i = 0;
+                let n = this.size();
+                let iterator = {};
+
+                iterator.next = () => {
+                    let result = {};
+
+                    if (i < n) {
+                        result.value = this.get(i++);
+                        result.done = false;
+                    } else {
+                        result.value = undefined;
+                        result.done = true;
+                    }
+
+                    return result;
+                };
+
+                return iterator;
+            };
+
+            Object.setPrototypeOf(prototype, new Proxy(Object.getPrototypeOf(prototype), {
+                get: (target, prop, receiver) => {
+                    if (typeof prop === 'string' && /^[0-9]+$/.test(prop)) {
+                        return receiver.get(parseInt(prop));
+                    }
+
+                    return Reflect.get(target, prop, receiver);
+                },
+                set: (target, prop, value, receiver) => {
+                    if (typeof prop === 'string' && /^[0-9]+$/.test(prop)) {
+                        receiver.set(parseInt(prop), value);
+
+                        return true;
+                    }
+
+                    return Reflect.set(target, prop, value, receiver);
+                }
+            }));
+        });
+    }); // clang-format on
 }

src/bindings/javascript/solver.cpp

@@ -31,16 +31,16 @@ void solverApi()
         .property("id", &libOpenCOR::Solver::id)
         .property("name", &libOpenCOR::Solver::name);
 
+    // clang-format off
     EM_ASM({
         Module["Solver"]["Type"] = Module["Solver.Type"];
 
         delete Module["Solver.Type"];
 
-        Module["Solver"].prototype.toString = function()
-        {
+        Module["Solver"].prototype.toString = function() {
             return this.name;
         };
-    });
+    }); // clang-format on
 
     // SolverOde API.
 
@@ -59,9 +59,10 @@ void solverApi()
                                                   reinterpret_cast<double *>(pU), pN, reinterpret_cast<void *>(pData));
                          }));
 
+    // clang-format off
     EM_ASM({
         Module["nlaSolve"] = Module["nlaSolve"];
-    });
+    }); // clang-format on
 
     emscripten::class_<libOpenCOR::SolverNla, emscripten::base<libOpenCOR::Solver>>("SolverNla")
         .smart_ptr<libOpenCOR::SolverNlaPtr>("SolverNla");
@@ -102,6 +103,7 @@ void solverApi()
         .property("absoluteTolerance", &libOpenCOR::SolverCvode::absoluteTolerance, &libOpenCOR::SolverCvode::setAbsoluteTolerance)
         .property("interpolateSolution", &libOpenCOR::SolverCvode::interpolateSolution, &libOpenCOR::SolverCvode::setInterpolateSolution);
 
+    // clang-format off
     EM_ASM({
         Module["SolverCvode"]["IntegrationMethod"] = Module["SolverCvode.IntegrationMethod"];
         Module["SolverCvode"]["IterationType"] = Module["SolverCvode.IterationType"];
@@ -112,7 +114,7 @@ void solverApi()
         delete Module["SolverCvode.IterationType"];
         delete Module["SolverCvode.LinearSolver"];
         delete Module["SolverCvode.Preconditioner"];
-    });
+    }); // clang-format on
 
     // SolverForwardEuler API.
 
@@ -145,11 +147,12 @@ void solverApi()
         .property("upperHalfBandwidth", &libOpenCOR::SolverKinsol::upperHalfBandwidth, &libOpenCOR::SolverKinsol::setUpperHalfBandwidth)
         .property("lowerHalfBandwidth", &libOpenCOR::SolverKinsol::lowerHalfBandwidth, &libOpenCOR::SolverKinsol::setLowerHalfBandwidth);
 
+    // clang-format off
     EM_ASM({
         Module["SolverKinsol"]["LinearSolver"] = Module["SolverKinsol.LinearSolver"];
 
         delete Module["SolverKinsol.LinearSolver"];
-    });
+    }); // clang-format on
 
     // SolverSecondOrderRungeKutta API.