Latest release

.github/workflows/main.yml

@@ -1,4 +1,6 @@
 name: BuildRoadRunner
+env:
+  FORCE_JAVASCRIPT_ACTIONS_TO_NODE24: 'true' #for seanmiddleditch/gha-setup-ninja and ilammy/msvc-dev-cmd.
 
 on:
   push:
@@ -90,11 +92,11 @@ jobs:
           echo "python_v4_name=v4" >> $GITHUB_ENV
 
       - name: Checkout RoadRunner
-        uses: actions/checkout@v4
+        uses: actions/checkout@main
 
       - name: Setup Python for non-Manylinux platforms
         if: matrix.platform.build_python == 'ON' && matrix.platform.os_type != 'manylinux'
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@main
         id: four_pythons
         with:
           python-version: |
@@ -230,6 +232,7 @@ jobs:
           fi
 
       - name: Setup Ninja
+        if: matrix.platform.os_type == 'manylinux'
         uses: seanmiddleditch/gha-setup-ninja@master
 
       - name: Get Host Architecture
@@ -283,7 +286,7 @@ jobs:
 
       - name: Cache ccache files on non-Windows
         if: matrix.platform.os_type != 'windows'
-        uses: actions/cache@v4
+        uses: actions/cache@main
         with:
           path: ${RUNNER_WORKSPACE}/.ccache
           key:
@@ -300,31 +303,31 @@ jobs:
             brew install pcre pcre2
             mkdir -p ${RUNNER_WORKSPACE}/swig
             cd swig
-            curl -L https://sourceforge.net/projects/swig/files/swig/swig-4.4.0/swig-4.4.0.tar.gz/download > swig.tar.gz
+            curl -L https://sourceforge.net/projects/swig/files/swig/swig-4.4.1/swig-4.4.1.tar.gz/download > swig.tar.gz
             tar -zxf swig.tar.gz
             rm swig.tar.gz
             mkdir -p install-swig
-            cd swig-4.4.0/
+            cd swig-4.4.1/
             ./configure --prefix=${RUNNER_WORKSPACE}/swig/install-swig
             make
             make install
             echo SWIG_DIR="-DSWIG_EXECUTABLE=${RUNNER_WORKSPACE}/swig/install-swig/bin/swig" >> $GITHUB_ENV
           elif [ "${{ matrix.platform.os_type }}" == 'windows' ]; then
             mkdir -p swig
             cd swig
-            curl -L https://sourceforge.net/projects/swig/files/swigwin/swigwin-4.4.0/swigwin-4.4.0.zip/download > swig.zip
+            curl -L https://sourceforge.net/projects/swig/files/swigwin/swigwin-4.4.1/swigwin-4.4.1.zip/download > swig.zip
             unzip -q swig.zip -d install-swig
             rm swig.zip
-            echo SWIG_DIR="-DSWIG_EXECUTABLE=${RUNNER_WORKSPACE}/swig/install-swig/swigwin-4.4.0/" >> "${GITHUB_PATH}"
+            echo SWIG_DIR="-DSWIG_EXECUTABLE=${RUNNER_WORKSPACE}/swig/install-swig/swigwin-4.4.1/" >> "${GITHUB_PATH}"
           elif [ "${{ matrix.platform.os_type }}" == 'manylinux' ]; then
             dnf install -y pcre-devel pcre2-devel
             mkdir -p swig
             cd swig
-            curl -L https://sourceforge.net/projects/swig/files/swig/swig-4.4.0/swig-4.4.0.tar.gz/download > swig.tar.gz
+            curl -L https://sourceforge.net/projects/swig/files/swig/swig-4.4.1/swig-4.4.1.tar.gz/download > swig.tar.gz
             tar -zxf swig.tar.gz
             rm swig.tar.gz
             mkdir -p install-swig
-            cd swig-4.4.0/
+            cd swig-4.4.1/
             ./configure --disable-dependency-tracking --prefix=${RUNNER_WORKSPACE}/swig/install-swig
             make
             make install
@@ -334,11 +337,11 @@ jobs:
             sudo sed -i "681,684d;686d" /usr/share/swig4.0/swig.swg
             # mkdir -p swig
             # cd swig
-            # curl -L https://sourceforge.net/projects/swig/files/swig/swig-4.3.0/swig-4.3.0.tar.gz/download > swig.tar.gz
+            # curl -L https://sourceforge.net/projects/swig/files/swig/swig-4.4.1/swig-4.4.1.tar.gz/download > swig.tar.gz
             # tar -zxf swig.tar.gz
             # rm swig.tar.gz
             # mkdir -p install-swig
-            # cd swig-4.3.0/
+            # cd swig-4.4.1/
             # sed -i "677,680d;682d" Lib/swig.swg
             # ./configure --disable-dependency-tracking --prefix=${RUNNER_WORKSPACE}/swig/install-swig
             # make
@@ -451,21 +454,21 @@ jobs:
         shell: bash
         run: |
           cd ${RUNNER_WORKSPACE}/build-roadrunner
-          ctest --output-on-failure --verbose --extra-verbose --progress --exclude-regex python_tests
+          ctest --output-on-failure --verbose --extra-verbose --progress --exclude-regex ython
 
       - name: Run C RoadRunner tests (Ubuntu; skip plugins)
         if: matrix.platform.build_type == 'Release' && matrix.build_tests == 'ON' && matrix.platform.os_type == 'ubuntu'
         shell: bash
         run: |
           cd ${RUNNER_WORKSPACE}/build-roadrunner
-          ctest --output-on-failure --verbose --extra-verbose --progress --exclude-regex python_tests --exclude-regex Plugin
+          ctest --output-on-failure --verbose --extra-verbose --progress --exclude-regex "ython|Plugin"
 
       - name: Run Python Roadrunner tests (first Python version)
         if: matrix.platform.build_python == 'ON' && matrix.build_tests == 'ON'
         shell: bash
         run: |
           cd ${RUNNER_WORKSPACE}/build-roadrunner
-          ctest -C ${{ matrix.platform.build_type }} --output-on-failure --verbose --extra-verbose --progress --tests-regex python_tests
+          ctest -C ${{ matrix.platform.build_type }} --output-on-failure --verbose --extra-verbose --progress --tests-regex ython
 
       - name: Save roadrunner version
         shell: bash
@@ -483,7 +486,7 @@ jobs:
           echo "artifacts_path=${RUNNER_WORKSPACE}/install-roadrunner" >> $GITHUB_ENV
 
       - name: Upload roadrunner binaries
-        uses: actions/upload-artifact@v4
+        uses: actions/upload-artifact@main
         with:
           name: ${{ env.artifacts_name }}
           path: ${{ env.artifacts_path }}
@@ -588,7 +591,7 @@ jobs:
         shell: bash
         run: |
           cd ${RUNNER_WORKSPACE}/build-roadrunner
-          ctest -C ${{ matrix.platform.build_type }} --output-on-failure --verbose --extra-verbose --progress --tests-regex python_tests
+          ctest -C ${{ matrix.platform.build_type }} --output-on-failure --verbose --extra-verbose --progress --tests-regex ython
 
 
       - name: Create fourth Python wheel artifacts and rename
@@ -622,7 +625,7 @@ jobs:
 
       - name: Upload RoadRunner Python wheel artifacts
         if: matrix.platform.build_type == 'Release' && matrix.platform.build_python == 'ON'
-        uses: actions/upload-artifact@v4
+        uses: actions/upload-artifact@main
         with:
           name: ${{ env.roadrunner_python_wheel_artifacts_name }}
           path: ${{ env.roadrunner_python_wheel_artifacts_file }}

CMakeLists.txt

@@ -9,7 +9,7 @@ cmake_minimum_required(VERSION 3.16)
 
 set(ROADRUNNER_VERSION_MAJOR 2)
 set(ROADRUNNER_VERSION_MINOR 9)
-set(ROADRUNNER_VERSION_PATCH 0)
+set(ROADRUNNER_VERSION_PATCH 2)
 
 set(ROADRUNNER_VERSION "${ROADRUNNER_VERSION_MAJOR}.${ROADRUNNER_VERSION_MINOR}.${ROADRUNNER_VERSION_PATCH}")
 

source/llvm/LLVMExecutableModel.cpp

@@ -1246,7 +1246,7 @@ void LLVMExecutableModel::getIds(int types, std::list<std::string> &ids)
                 if (getStoichiometry(s, r) != 0)
                 {
                     string rid = getReactionId(r);
-                    ids.push_back("stoich(" + sid + ", " + rid + ")");
+                    ids.push_back(symbols->getStoichiometryIdFor(sid, rid));
                 }
             }
         }
@@ -1478,15 +1478,19 @@ double LLVMExecutableModel::getValue(const std::string& id)
     case SelectionRecord::INITIAL_GLOBAL_PARAMETER:
         getGlobalParameterInitValues(1, &index, &result);
         break;
+    case SelectionRecord::STOICHIOMETRY:
+    case SelectionRecord::INITIAL_STOICHIOMETRY:
+        result = getStoichiometry(index);
+        break;
     case SelectionRecord::EVENT:
     {
             bool trigger = getEventTrigger(index);
             result = trigger ? 1.0 : -1.0;
         }
         break;
     default:
-        rrLog(Logger::LOG_ERROR) << "A new SelectionRecord should not have this value: "
-        << sel.to_repr();
+        //rrLog(Logger::LOG_ERROR) << "A new SelectionRecord should not have this value: "
+        //<< sel.to_repr();
         throw LLVMException("Invalid selection '" + id + "' for setting value");
         break;
     }
@@ -1603,6 +1607,10 @@ const rr::SelectionRecord& LLVMExecutableModel::getSelection(const std::string&
                 sel.selectionType = SelectionRecord::INITIAL_GLOBAL_PARAMETER;
                 sel.index = index;
                 break;
+            case LLVMModelDataSymbols::STOICHIOMETRY:
+                sel.selectionType = SelectionRecord::INITIAL_STOICHIOMETRY;
+                sel.index = index;
+                break;
             default:
                 std::string msg = "Invalid Id for initial value: '" + str + "'";
                 throw LLVMException(msg);
@@ -1630,12 +1638,26 @@ const rr::SelectionRecord& LLVMExecutableModel::getSelection(const std::string&
             }
             break;
         case SelectionRecord::STOICHIOMETRY:
-            sel.index = getStoichiometryIndex(sel.p1, sel.p2);
+            if (sel.p2.empty()) {
+              sel.index = getStoichiometryIndex(sel.p1);
+              if (sel.index == -1) {
+                throw LLVMException("Invalid id '" + str + "': could not find a stoichiometry with the ID '" + sel.p1 + "'.");
+                break;
+              }
+            }
+            else {
+              sel.index = getStoichiometryIndex(sel.p1, sel.p2);
+              if (sel.index == -1) {
+                throw LLVMException("Invalid id '" + str + "': could not find a species with the ID '" + sel.p1 + "', and/or a reaction with the ID '" + sel.p2 + "'");
+                break;
+              }
+            }
+
             break;
 
         default:
-            rrLog(Logger::LOG_ERROR) << "A new SelectionRecord should not have this value: "
-                << sel.to_repr();
+            //rrLog(Logger::LOG_ERROR) << "A new SelectionRecord should not have this value: "
+            //    << sel.to_repr();
             throw LLVMException("Invalid selection '" + str + "' for setting value");
             break;
         }
@@ -1739,7 +1761,8 @@ void LLVMExecutableModel::setValue(const std::string& id, double value)
         setGlobalParameterInitValues(1, &index, &value);
         break;
     case SelectionRecord::STOICHIOMETRY:
-        setStoichiometries(1, &index, &value);
+    case SelectionRecord::INITIAL_STOICHIOMETRY:
+        setStoichiometry(index, value);
         break;
     default:
         throw LLVMException("Invalid selection '" + sel.to_string() + "' for setting value");
@@ -2314,25 +2337,73 @@ int LLVMExecutableModel::setCompartmentVolumes(size_t len, const int* indx,
     return result;
 }
 
-int LLVMExecutableModel::setStoichiometries(size_t len, const int* indx,
-                                               const double* values)
-{
-    return setStoichiometries(len, indx, values, true);
-}
+//int LLVMExecutableModel::setStoichiometries(size_t len, const int* indx,
+//                                               const double* values)
+//{
+//    return setStoichiometries(len, indx, values, true);
+//}
+
+//int LLVMExecutableModel::setStoichiometries(size_t len, const int* indx,
+//                                               const double* values, bool strict)
+//{
+//    if (len == 1) {
+//        int index = *indx;
+//        double value = *values;
+//        return setStoichiometry(index, value);
+//    }
+//
+//    return -1;
+//}
 
-int LLVMExecutableModel::setStoichiometries(size_t len, const int* indx,
-                                               const double* values, bool strict)
+int LLVMExecutableModel::setStoichiometry(int index, double value)
 {
-    if (len == 1) {
-        int index = *indx;
-        double value = *values;
-        return setStoichiometry(index, value);
-    }
+    if (std::signbit(value))
+        throw LLVMException("Invalid stoichiometry value");
+
+    if (symbols->isConservedMoietyAnalysis())
+        throw LLVMException("Unable to set stoichiometries when conserved moieties are on");
+
+    std::list <LLVMModelDataSymbols::SpeciesReferenceInfo> stoichiometryIndx = symbols->getStoichiometryList();
+    std::list<LLVMModelDataSymbols::SpeciesReferenceInfo>::const_iterator stoichiometry = stoichiometryIndx.begin();
+    for (int i = 0; i < index; i++)
+        ++stoichiometry;
+    if (stoichiometry->type == LLVMModelDataSymbols::SpeciesReferenceType::Product)
+        return setStoichiometry(stoichiometry->row, stoichiometry->column, value);
+    else if (stoichiometry->type == LLVMModelDataSymbols::SpeciesReferenceType::Reactant)
+        return setStoichiometry(stoichiometry->row, stoichiometry->column, -1 * value);
+    else if (stoichiometry->type == LLVMModelDataSymbols::SpeciesReferenceType::MultiReactantProduct)
+        throw LLVMException("Cannot set stoichiometry for a MultiReactantProduct");
+    else
+        throw LLVMException("Cannot set stoichiometry for a Modifier");
 
     return -1;
 }
 
-int LLVMExecutableModel::setStoichiometry(int index, double value)
+int LLVMExecutableModel::setStoichiometry(int speciesIndex, int reactionIndex, double value)
+{
+    double result = csr_matrix_set_nz(modelData->stoichiometry, speciesIndex, reactionIndex, value);
+    return isnan(result) ? 0 : result;
+}
+
+//int LLVMExecutableModel::setInitStoichiometries(size_t len, const int* indx,
+//                                               const double* values)
+//{
+//    return setInitStoichiometries(len, indx, values, true);
+//}
+
+//int LLVMExecutableModel::setInitStoichiometries(size_t len, const int* indx,
+//                                               const double* values, bool strict)
+//{
+//    if (len == 1) {
+//        int index = *indx;
+//        double value = *values;
+//        return setInitStoichiometry(index, value);
+//    }
+//
+//    return -1;
+//}
+
+int LLVMExecutableModel::setInitStoichiometry(int index, double value)
 {
     if (std::signbit(value))
         throw LLVMException("Invalid stoichiometry value");
@@ -2345,9 +2416,9 @@ int LLVMExecutableModel::setStoichiometry(int index, double value)
     for (int i = 0; i < index; i++)
         ++stoichiometry;
     if (stoichiometry->type == LLVMModelDataSymbols::SpeciesReferenceType::Product)
-        return setStoichiometry(stoichiometry->row, stoichiometry->column, value);
+        return setInitStoichiometry(stoichiometry->row, stoichiometry->column, value);
     else if (stoichiometry->type == LLVMModelDataSymbols::SpeciesReferenceType::Reactant)
-        return setStoichiometry(stoichiometry->row, stoichiometry->column, -1 * value);
+        return setInitStoichiometry(stoichiometry->row, stoichiometry->column, -1 * value);
     else if (stoichiometry->type == LLVMModelDataSymbols::SpeciesReferenceType::MultiReactantProduct)
         throw LLVMException("Cannot set stoichiometry for a MultiReactantProduct");
     else
@@ -2356,8 +2427,10 @@ int LLVMExecutableModel::setStoichiometry(int index, double value)
     return -1;
 }
 
-int LLVMExecutableModel::setStoichiometry(int speciesIndex, int reactionIndex, double value)
+int LLVMExecutableModel::setInitStoichiometry(int speciesIndex, int reactionIndex, double value)
 {
+    //For now, we don't store 'initStoichiometry' separately.  Essentially, every stoichiometry set is to the initial value.
+    //double result = csr_matrix_set_nz(modelData->initStoichiometry, speciesIndex, reactionIndex, value);
     double result = csr_matrix_set_nz(modelData->stoichiometry, speciesIndex, reactionIndex, value);
     return isnan(result) ? 0 : result;
 }
@@ -2389,6 +2462,35 @@ double LLVMExecutableModel::getStoichiometry(int speciesIndex, int reactionIndex
     return isnan(result) ? 0 : result;
 }
 
+double LLVMExecutableModel::getInitStoichiometry(int index)
+{
+    if (symbols->isConservedMoietyAnalysis())
+        throw LLVMException("Unable to get stoichiometries when conserved moieties are on");
+
+    if (index < 0)
+        throw LLVMException("The stoichiometry index is not valid");
+    std::list<LLVMModelDataSymbols::SpeciesReferenceInfo> stoichiometryIndx = symbols->getStoichiometryList();
+    std::list<LLVMModelDataSymbols::SpeciesReferenceInfo>::const_iterator stoichiometry = stoichiometryIndx.begin();
+    for (int i = 0; i < index; i++)
+        ++stoichiometry;
+    if (stoichiometry->type == LLVMModelDataSymbols::SpeciesReferenceType::Reactant)
+        return -1 * getInitStoichiometry(stoichiometry->row, stoichiometry->column);
+    else if (stoichiometry->type == LLVMModelDataSymbols::SpeciesReferenceType::Product)
+        return getInitStoichiometry(stoichiometry->row, stoichiometry->column);
+    else if (stoichiometry->type == LLVMModelDataSymbols::SpeciesReferenceType::MultiReactantProduct)
+        throw LLVMException("Cannot return stoichiometry for a MultiReactantProduct");
+    else
+        throw LLVMException("Cannot return stoichiometry for a Modifier");
+}
+
+double LLVMExecutableModel::getInitStoichiometry(int speciesIndex, int reactionIndex)
+{
+    //For now, we don't store 'initStoichiometry' separately.  Essentially, every stoichiometry set is to the initial value.
+    //double result = csr_matrix_get_nz(modelData->initStoichiometry, speciesIndex, reactionIndex);
+    double result = csr_matrix_get_nz(modelData->stoichiometry, speciesIndex, reactionIndex);
+    return isnan(result) ? 0 : result;
+}
+
 /******************************* Events Section *******************************/
 #if (1) /**********************************************************************/
 /******************************************************************************/