Merge remote-tracking branch 'origin/development' into sk/test-rate-r…

…ule-converter-rigorously

.github/workflows/store-artefact.yml

@@ -276,47 +276,40 @@ jobs:
         package_option: ["-DWITH_ALL_PACKAGES=ON", "-DWITH_STABLE_PACKAGES=ON"]
         cpp_standard: [98]
         language_bindings:
-          ["-DWITH_JAVA=True -DWITH_PYTHON=True -DWITH_CSHARP=True -DWITH_R=True"]
+          ["-DWITH_JAVA=True -DWITH_PYTHON=True"]
         container: ["quay.io/pypa/manylinux_2_28_x86_64"]
     runs-on: ${{ matrix.platform }}
     container: ${{ matrix.container}}
 
     steps:
       - uses: actions/checkout@v4
-      - name: install Swig 4 from source
-        run: |
-          yum install -y pcre-devel
-          echo "SWIG_DIR=/usr/local/swig/" >> "${GITHUB_ENV}"
-          curl -L https://sourceforge.net/projects/swig/files/swig/swig-4.0.2/swig-4.0.2.tar.gz/download > swig.tar.gz
-          tar -zxvf swig.tar.gz
-          cd swig-4.0.2/
-          ./configure --disable-dependency-tracking --prefix=$SWIG_DIR
-          make clean
-          make -j 2
-          make install
-          swig -version
 
-      - name: install CMake using pip
+      - name: install CMake, ninja and swig using pip
         run: |
-          /opt/python/cp38-cp38/bin/pip install cmake
+          /opt/python/cp38-cp38/bin/pip install cmake swig ninja
           ln -s /opt/python/cp38-cp38/bin/cmake /usr/bin/cmake
           ln -s /opt/python/cp38-cp38/bin/ctest /usr/bin/ctest
+          ln -s /opt/python/cp38-cp38/bin/swig /usr/bin/swig
+          ln -s /opt/python/cp38-cp38/bin/ninja /usr/bin/ninja
           cmake --version
           ctest --version
+          swig -version
+          ninja --version
 
       - name: Install dependencies, configure, build
         run: |
-          yum install -y libxml2-devel check-devel java-devel mono-devel R
+          yum install -y libxml2-devel check-devel java-devel
           git clone https://github.com/libexpat/libexpat
-          cmake -DCMAKE_BUILD_TYPE=$BUILD_TYPE -DCMAKE_POSITION_INDEPENDENT_CODE=ON -DEXPAT_BUILD_TESTS=OFF -DEXPAT_BUILD_TOOLS=OFF -DEXPAT_BUILD_EXAMPLES=OFF -DEXPAT_SHARED_LIBS=OFF -DCMAKE_INSTALL_PREFIX=./dependencies -B libexpat -S libexpat/expat 
+          export DEPENDENCY_DIR=$PWD/dependencies
+          export INSTALL_DIR=$PWD/install
+          cmake -G Ninja -DCMAKE_BUILD_TYPE=$BUILD_TYPE -DCMAKE_POSITION_INDEPENDENT_CODE=ON -DEXPAT_BUILD_TESTS=OFF -DEXPAT_BUILD_TOOLS=OFF -DEXPAT_BUILD_EXAMPLES=OFF -DEXPAT_SHARED_LIBS=OFF -DCMAKE_INSTALL_PREFIX=$DEPENDENCY_DIR -B libexpat -S libexpat/expat 
           cmake --build libexpat
           cmake --install libexpat
           cd ..
           mkdir build
           cd build
-          mkdir ../install
-          cmake ../libsbml \
-          -DCMAKE_INSTALL_PREFIX=../install \
+          cmake ../libsbml -G Ninja \
+          -DCMAKE_INSTALL_PREFIX=$INSTALL_DIR \
           -DCMAKE_BUILD_TYPE=$BUILD_TYPE \
           -DCMAKE_CXX_STANDARD=${{matrix.cpp_standard}} \
           -DWITH_CHECK=True \
@@ -327,15 +320,14 @@ jobs:
           ${{matrix.xml_parser_option}} \
           ${{matrix.package_option}} \
           ${{matrix.language_bindings}} \
-          -DWITH_CREATE_R_SOURCE=ON \
-          -DWITH_SKIP_R_BINARY=ON \
           -DPYTHON_EXECUTABLE=/opt/python/cp38-cp38/bin/python \
           -DPYTHON_INCLUDE_DIR=/opt/python/cp38-cp38/include/python3.8/ \
           -DWITH_STATIC_RUNTIME=ON \
+          -DLIBSBML_DEPENDENCY_DIR=$DEPENDENCY_DIR \
+          -DEXPAT_LIBRARY=$DEPENDENCY_DIR/lib64/libexpat.a \
+          -DEXPAT_INCLUDE_DIR=$DEPENDENCY_DIR/include \
           -DPYTHON_USE_DYNAMIC_LOOKUP=ON
           cmake --build . --config $BUILD_TYPE
-          # mkdir r-binaries
-          # R CMD INSTALL -l r-binaries --build ./src/bindings/r/out/libSBML_5.19.3.tar.gz
 
       - name: Test
         run: |
@@ -369,4 +361,5 @@ jobs:
           name:
             Manylinux nightly (zip, libSBML ${{env.LIBSBML_VERSION}},
             ${{env.ARTIFACT_NAME_SUFFIX}})-${{ strategy.job-index }}
-          path: ../install
+          path:
+            install/

src/sbml/SBMLTransforms.cpp

@@ -553,7 +553,9 @@ SBMLTransforms::clearComponentValues(const Model* m)
   }
 
   // otherwise remove only specific set
-	mModelValues.erase(m);
+  if (!mModelValues.empty()) {
+      mModelValues.erase(m);
+  }
 }
 
 

src/sbml/packages/render/sbml/ListOfGlobalRenderInformation.cpp

@@ -789,6 +789,8 @@ ListOfGlobalRenderInformation::getAllElements(ElementFilter* filter)
 {
   List* ret = new List();
   List* sublist = ListOf::getAllElements(filter);
+  ret->transferFrom(sublist);
+  delete sublist;
 
   ADD_FILTERED_POINTER(ret, sublist, mDefaultValues, filter);
 

src/sbml/packages/render/sbml/ListOfLocalRenderInformation.cpp

@@ -760,6 +760,8 @@ ListOfLocalRenderInformation::getAllElements(ElementFilter* filter)
 {
   List* ret = new List();
   List* sublist = ListOf::getAllElements(filter);
+  ret->transferFrom(sublist);
+  delete sublist;
 
   ADD_FILTERED_POINTER(ret, sublist, mDefaultValues, filter);
 

src/sbml/packages/render/sbml/RenderCurve.cpp

@@ -1142,7 +1142,7 @@ RenderCurve::createObject(XMLInputStream& stream)
 
   const std::string& name = stream.peek().getName();
 
-  if (name == "listOfCurveElements")
+  if (name == "listOfCurveElements" || name == "listOfElements")
   {
     if (mRenderPoints.size() != 0 && getErrorLog() != NULL)
     {

src/sbml/packages/render/sbml/Style.cpp

@@ -601,6 +601,7 @@ Style::createGroup()
 
   delete renderns;
   this->setGroup(g);
+  delete g;
 
   connectToChild();
 
@@ -1280,6 +1281,7 @@ Style::createObject(XMLInputStream& stream)
     RenderGroup* g = new RenderGroup(renderns);
     g->setElementName(name);
     setGroup(g);
+    delete g;
     obj = &mGroup;
   }
 

src/sbml/packages/render/sbml/Transformation2D.cpp

@@ -714,65 +714,72 @@ Transformation2D::addExpectedAttributes(ExpectedAttributes& attributes)
  */
 void
 Transformation2D::readAttributes(const XMLAttributes& attributes,
-                                 const ExpectedAttributes& expectedAttributes)
-{
-  unsigned int level = getLevel();
-  unsigned int version = getVersion();
-  unsigned int pkgVersion = getPackageVersion();
-  unsigned int numErrs;
-  SBMLErrorLog* log = getErrorLog();
-
-  if (log && getParentSBMLObject() &&
-    static_cast<ListOfDrawables*>(getParentSBMLObject())->size() < 2)
-  {
-    numErrs = log->getNumErrors();
-    for (int n = numErrs-1; n >= 0; n--)
-    {
-      if (log->getError(n)->getErrorId() == UnknownPackageAttribute)
-      {
-        const std::string details = log->getError(n)->getMessage();
-        log->remove(UnknownPackageAttribute);
-        log->logPackageError("render", RenderUnknown, pkgVersion, level,
-          version, details, getLine(), getColumn());
-      }
-      else if (log->getError(n)->getErrorId() == UnknownCoreAttribute)
-      {
-        const std::string details = log->getError(n)->getMessage();
-        log->remove(UnknownCoreAttribute);
-        log->logPackageError("render", RenderUnknown, pkgVersion, level,
-          version, details, getLine(), getColumn());
-      }
+    const ExpectedAttributes& expectedAttributes)
+{
+    unsigned int level = getLevel();
+    unsigned int version = getVersion();
+    unsigned int pkgVersion = getPackageVersion();
+    unsigned int numErrs;
+    SBMLErrorLog* log = getErrorLog();
+
+    if (log && getParentSBMLObject()) {
+        bool isSizeOne = false;
+        int type = getParentSBMLObject()->getTypeCode();
+        switch (type) {
+        case SBML_LIST_OF:
+            if (static_cast<ListOf*>(getParentSBMLObject())->size() < 2)
+            {
+                isSizeOne = true;
+            }
+            break;
+        case SBML_RENDER_LINEENDING:
+        case SBML_RENDER_STYLE_BASE:
+        case SBML_RENDER_LOCALSTYLE:
+        case SBML_RENDER_GLOBALSTYLE:
+            // These objects all have a single RenderGroup child, so the size can never be greater than 2.
+            isSizeOne = true;
+            break;
+        case SBML_RENDER_GROUP:
+        {
+            //A RenderGroup can have multiple Transformation2D children.
+            RenderGroup* rg = static_cast<RenderGroup*>(getParentSBMLObject());
+            if (rg->getNumElements() < 2)
+            {
+                isSizeOne = false;
+            }
+            break;
+        }
+        default:
+            assert(false); //Some situation we didn't think through; could be anything.
+            isSizeOne = true;
+        }
+        if (isSizeOne) {
+            numErrs = log->getNumErrors();
+            for (int n = numErrs - 1; n >= 0; n--)
+            {
+                if (log->getError(n)->getErrorId() == UnknownPackageAttribute)
+                {
+                    const std::string details = log->getError(n)->getMessage();
+                    log->remove(UnknownPackageAttribute);
+                    log->logPackageError("render", RenderUnknown, pkgVersion, level,
+                        version, details, getLine(), getColumn());
+                }
+                else if (log->getError(n)->getErrorId() == UnknownCoreAttribute)
+                {
+                    const std::string details = log->getError(n)->getMessage();
+                    log->remove(UnknownCoreAttribute);
+                    log->logPackageError("render", RenderUnknown, pkgVersion, level,
+                        version, details, getLine(), getColumn());
+                }
+            }
+        }
     }
-  }
 
-  Transformation::readAttributes(attributes, expectedAttributes);
-
-  //if (log)
-  //{
-  //  numErrs = log->getNumErrors();
-
-  //  for (int n = numErrs-1; n >= 0; n--)
-  //  {
-  //    if (log->getError(n)->getErrorId() == UnknownPackageAttribute)
-  //    {
-  //      const std::string details = log->getError(n)->getMessage();
-  //      log->remove(UnknownPackageAttribute);
-  //      log->logPackageError("render", RenderUnknown, pkgVersion, level,
-  //        version, details);
-  //    }
-  //    else if (log->getError(n)->getErrorId() == UnknownCoreAttribute)
-  //    {
-  //      const std::string details = log->getError(n)->getMessage();
-  //      log->remove(UnknownCoreAttribute);
-  //      log->logPackageError("render",
-  //        RenderTransformation2DAllowedCoreAttributes, pkgVersion, level,
-  //          version, details);
-  //    }
-  //  }
-  //}
+    Transformation::readAttributes(attributes, expectedAttributes);
+
     std::string s;
     attributes.readInto("transform", s);
-    if(!s.empty())
+    if (!s.empty())
     {
         this->parseTransformation(s);
     }