Fixes using a stoichiometry name as an ID on a roadrunner object.

.github/workflows/main.yml

@@ -454,21 +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
@@ -591,7 +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

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 1)
+set(ROADRUNNER_VERSION_PATCH 2)
 
 set(ROADRUNNER_VERSION "${ROADRUNNER_VERSION_MAJOR}.${ROADRUNNER_VERSION_MINOR}.${ROADRUNNER_VERSION_PATCH}")
 

source/llvm/LLVMExecutableModel.cpp

@@ -1478,6 +1478,10 @@ 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);
@@ -1634,10 +1638,19 @@ const rr::SelectionRecord& LLVMExecutableModel::getSelection(const std::string&
             }
             break;
         case SelectionRecord::STOICHIOMETRY:
-            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;
+            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;

source/rrRoadRunner.cpp

@@ -1353,12 +1353,7 @@ namespace rr {
                 break;
             case SelectionRecord::STOICHIOMETRY:
             case SelectionRecord::INITIAL_STOICHIOMETRY: {
-                // in case it is entered in the form of stoich(SpeciesId, ReactionId)
-                if (impl->model->getFloatingSpeciesIndex(record.p1) != -1 && impl->model->getReactionIndex(record.p2) != -1)
-                    dResult = impl->model->getStoichiometry(impl->model->getStoichiometryIndex(record.p1, record.p2));
-                // in case it is entered in the form of a stoichiometry parameter
-                else
-                    dResult = impl->model->getStoichiometry(impl->model->getStoichiometryIndex(record.p1));
+                dResult = impl->model->getStoichiometry(record.index);
                 break;
             }
             case SelectionRecord::TIME:
@@ -4914,14 +4909,26 @@ namespace rr {
                 }
                 break;
             case SelectionRecord::STOICHIOMETRY:
-                if (impl->model->getFloatingSpeciesIndex(sel.p1) >= 0) {
-                    if (impl->model->getReactionIndex(sel.p2) >= 0) {
-                        break;
+                if (sel.p2.empty()) {
+                  if (impl->model->getStoichiometryIndex(sel.p1) < 0) {
+                    throw Exception("The id '" + sel.p1 + "' is not the id of a stoichiometry (speciesReference).");
+                  }
+                  break;
+                }
+                else {
+                    if (impl->model->getFloatingSpeciesIndex(sel.p1) >= 0) {
+                        if (impl->model->getReactionIndex(sel.p2) >= 0) {
+                            sel.index = impl->model->getStoichiometryIndex(sel.p1, sel.p2);
+                            if (sel.index < 0) {
+                              throw Exception("The species id '" + sel.p1 + "' and reaction id '" + sel.p2 + "' does not lead to a valid stoichiometry.");
+                            }
+                            break;
+                        } else {
+                            throw Exception("second argument to stoich '" + sel.p2 + "' is not a reaction id.");
+                        }
                     } else {
-                        throw Exception("second argument to stoich '" + sel.p2 + "' is not a reaction id.");
+                        throw Exception("first argument to stoich '" + sel.p1 + "' is not a floating species id.");
                     }
-                } else {
-                    throw Exception("first argument to stoich '" + sel.p1 + "' is not a floating species id.");
                 }
             case SelectionRecord::INITIAL_CONCENTRATION:
                 if ((sel.index = impl->model->getFloatingSpeciesIndex(sel.p1)) >= 0) {

test/cxx_api_tests/SelectionRecordTests.cpp

@@ -301,7 +301,7 @@ TEST_F(SelectionRecordTests, STOICHIOMETRY){
     SelectionRecord record = rr.createSelection("stoich(S1, _J1)");
     EXPECT_EQ(record.selectionType, SelectionRecord::STOICHIOMETRY);
     EXPECT_STREQ(record.to_string().c_str(), "stoich(S1, _J1)");
-    EXPECT_EQ(record.index, -1);
+    EXPECT_EQ(record.index, 3);
     EXPECT_EQ(record.p1, "S1");
     EXPECT_EQ(record.p2, "_J1");
     delete testModel;

test/python/named_stoic_in_kinetic_law.xml

@@ -0,0 +1,45 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!-- Created by libAntimony version v3.1.2 with libSBML version 5.21.1. -->
+<sbml xmlns="http://www.sbml.org/sbml/level3/version2/core" xmlns:comp="http://www.sbml.org/sbml/level3/version1/comp/version1" level="3" version="2" comp:required="true">
+  <model metaid="__main" id="__main">
+    <listOfCompartments>
+      <compartment sboTerm="SBO:0000410" id="default_compartment" spatialDimensions="3" size="1" constant="true"/>
+    </listOfCompartments>
+    <listOfSpecies>
+      <species id="A" compartment="default_compartment" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
+      <species id="B" compartment="default_compartment" initialConcentration="7" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
+      <species id="C" compartment="default_compartment" initialConcentration="0" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
+      <species id="D" compartment="default_compartment" initialConcentration="0" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
+    </listOfSpecies>
+    <listOfParameters>
+      <parameter id="k1" value="0.1" constant="true"/>
+      <parameter id="k2" value="0.04" constant="true"/>
+    </listOfParameters>
+    <listOfReactions>
+      <reaction id="J0" reversible="true">
+        <listOfReactants>
+          <speciesReference species="A" stoichiometry="1" constant="true"/>
+          <speciesReference id="n" species="B" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference id="m" species="C" stoichiometry="2" constant="true"/>
+          <speciesReference id="q" species="D" stoichiometry="3" constant="true"/>
+        </listOfProducts>
+        <kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">
+            <apply>
+              <times/>
+              <apply>
+                <plus/>
+                <ci> n </ci>
+                <ci> m </ci>
+                <ci> q </ci>
+              </apply>
+              <ci> A </ci>
+            </apply>
+          </math>
+        </kineticLaw>
+      </reaction>
+    </listOfReactions>
+  </model>
+</sbml>

test/python/test_python_api.py

@@ -397,6 +397,23 @@ def test_getFullStoichiometryMatrix(self):
 
     def test_getGlobalParameterByName(self):
         self.assertEqual(self.rr.getGlobalParameterByName("kf"), 0.1)
+
+    def test_getSetNamedStoichiometries(self):
+        rr = RoadRunner("named_stoic_in_kinetic_law.xml")
+        self.assertEqual(rr.n, 1)
+        self.assertEqual(rr.m, 2)
+        self.assertEqual(rr.q, 3)
+        self.assertEqual(rr['q'], 3)
+        self.assertEqual(rr.model['q'], 3)
+        self.assertEqual(rr.getValue('q'), 3)
+        rr.n = 3
+        rr.m = 5
+        rr.q = 7
+        self.assertEqual(rr['n'], 3)
+        self.assertEqual(rr['m'], 5)
+        self.assertEqual(rr['q'], 7)
+        self.assertEqual(rr.model['q'], 7)
+        self.assertEqual(rr.getValue('q'), 7)
 
     @unittest.skip("No way to use this method from Python - it "
                    "requires an out parameter as input")

test/sbml_features/named_stoich.cpp

@@ -9,6 +9,7 @@
 #include <filesystem>
 #include "RoadRunnerTest.h"
 #include "llvm/LLVMException.h"
+#include "llvm/LLVMExecutableModel.h"
 
 using namespace testing;
 using namespace rr;
@@ -85,7 +86,21 @@ TEST_F(SBMLFeatures, named_stoich_init_value) {
 }
 
 
-TEST_F(SBMLFeatures, variable_named_stoich) {
+TEST_F(SBMLFeatures, named_stoich_values) {
+  rr::RoadRunner rr((SBMLFeaturesDir / "named_stoic_in_kinetic_law.xml").string());
+  rr.setValue("n", 3);
+  rr.setValue("m", 5);
+  rr.setValue("q", 7);
+  EXPECT_EQ(rr.getModel()->getValue("n"), 3.0);
+  EXPECT_EQ(rr.getModel()->getValue("m"), 5.0);
+  EXPECT_EQ(rr.getModel()->getValue("q"), 7.0);
+  EXPECT_EQ(rr.getModel()->getValue("init(n)"), 3.0);
+  EXPECT_EQ(rr.getModel()->getValue("init(m)"), 5.0);
+  EXPECT_EQ(rr.getModel()->getValue("init(q)"), 7.0);
+}
+
+
+TEST_F(SBMLFeatures, no_variable_named_stoich) {
   rr::RoadRunner rr((SBMLFeaturesDir / "named_stoic_in_kinetic_law.xml").string());
   EXPECT_THROW(rr.addAssignmentRule("n", "5", true), rrllvm::LLVMException);
 
@@ -94,3 +109,36 @@ TEST_F(SBMLFeatures, variable_named_stoich) {
 }
 
 
+TEST_F(SBMLFeatures, named_stoich_selectors) {
+  rr::RoadRunner rr((SBMLFeaturesDir / "named_stoic_in_kinetic_law.xml").string());
+  SelectionRecord record = rr.createSelection("n");
+  EXPECT_EQ(record.selectionType, SelectionRecord::STOICHIOMETRY);
+  EXPECT_STREQ(record.to_string().c_str(), "n");
+  EXPECT_EQ(record.index, 1);
+  EXPECT_EQ(record.p1, "n");
+  EXPECT_EQ(record.p2, "");
+
+  record = rr.createSelection("stoich(A, J0)");
+  EXPECT_EQ(record.selectionType, SelectionRecord::STOICHIOMETRY);
+  EXPECT_STREQ(record.to_string().c_str(), "stoich(A, J0)");
+  EXPECT_EQ(record.index, 0);
+  EXPECT_EQ(record.p1, "A");
+  EXPECT_EQ(record.p2, "J0");
+}
+
+
+TEST_F(SBMLFeatures, get_named_stoich_value_from_model) {
+  rr::RoadRunner rr((SBMLFeaturesDir / "named_stoic_in_kinetic_law.xml").string());
+  ExecutableModel* em = rr.getModel();
+  rrllvm::LLVMExecutableModel* llem = static_cast<rrllvm::LLVMExecutableModel*>(em);
+
+  EXPECT_EQ(llem->getValue("n"), 1);
+  llem->setValue("n", 3);
+  EXPECT_EQ(llem->getValue("n"), 3);
+
+  EXPECT_EQ(llem->getValue("stoich(A, J0)"), 1);
+  llem->setValue("stoich(A, J0)", 5);
+  EXPECT_EQ(llem->getValue("stoich(A, J0)"), 5);
+}
+
+

wrappers/Python/roadrunner/roadrunner.i

@@ -1401,6 +1401,10 @@ namespace std { class ostream{}; }
             for s in model.getGlobalParameterIds() + model.getCompartmentIds() + model.getReactionIds() + model.getConservedMoietyIds():
                 makeProperty(s, s)
 
+            for s in model.getStoichiometryIds():
+                if "(" not in s:
+                    makeProperty(s, s)
+
         def __getstate__(self):
             return self.saveStateS()
 
@@ -2498,6 +2502,10 @@ namespace std { class ostream{}; }
         return rr_ExecutableModel_getIds($self, rr::SelectionRecord::REACTION_RATE);
     }
 
+    PyObject *getStoichiometryIds() {
+        return rr_ExecutableModel_getIds($self, rr::SelectionRecord::STOICHIOMETRY);
+    }
+
     PyObject *getFloatingSpeciesInitAmountIds() {
         return rr_ExecutableModel_getIds($self, rr::SelectionRecord::INITIAL_FLOATING_AMOUNT);
     }

wrappers/Python/roadrunner/rr_docstrings.txt

@@ -508,9 +508,22 @@ ExecutableModel.getConservedMoietyIds([index])
 Returns a vector of conserved moiety identifier symbols.
 
 
-:param index: A array of compartment indices indicating which compartment ids to return.
+:param index: A array of conserved moiety indices indicating which conserved moiety ids to return.
 :type index: None or numpy.ndarray
-:returns: a list of compartment ids.
+:returns: a list of conserved moiety ids.
+";
+
+
+
+%feature("docstring") rr::ExecutableModel::getStoichiometryIds "
+ExecutableModel.getStoichiometryIds([index])
+
+Returns a vector of stoichiometry identifier symbols.
+
+
+:param index: A array of stoichiometry indices indicating which stoichiometry ids to return.
+:type index: None or numpy.ndarray
+:returns: a list of stoichiometry ids.
 ";