Merge pull request #39 from RuleWorld/issue37

Merging branch made to address seg fault in Issue 37
RuleWorld · May 24, 2024 · a5e2941 · a5e2941
2 parents 31eef54 + 0790b4a
commit a5e2941
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diff --git a/.github/workflows/main-testing.yml b/.github/workflows/main-testing.yml
@@ -2,7 +2,7 @@ name: main-validation
 
 on:
   push:
-    branches: [ master ]
+    branches: [ master, issue37]
   pull_request:
     branches: [ master ]
 
@@ -34,9 +34,9 @@ jobs:
         cd build
         cmake -G "Ninja" ..
         ninja
-        cp C:/ProgramData/chocolatey/lib/mingw/tools/install/mingw64/bin/libgcc_s_seh-1.dll ${{github.workspace}}/build/.
-        cp C:/ProgramData/chocolatey/lib/mingw/tools/install/mingw64/bin/libstdc++-6.dll ${{github.workspace}}/build/.
-        cp C:/ProgramData/chocolatey/lib/mingw/tools/install/mingw64/bin/libwinpthread-1.dll ${{github.workspace}}/build/.
+        # cp C:/ProgramData/chocolatey/lib/mingw/tools/install/mingw64/bin/libgcc_s_seh-1.dll ${{github.workspace}}/build/.
+        # cp C:/ProgramData/chocolatey/lib/mingw/tools/install/mingw64/bin/libstdc++-6.dll ${{github.workspace}}/build/.
+        # cp C:/ProgramData/chocolatey/lib/mingw/tools/install/mingw64/bin/libwinpthread-1.dll ${{github.workspace}}/build/.
         ./NFsim.exe -h
 
     - name: Configure CMake
@@ -53,7 +53,7 @@ jobs:
     - name: Set up Python
       uses: actions/setup-python@v2
       with:
-        python-version: '3.x'
+        python-version: '3.8'
     - name: Cache pip
       uses: actions/cache@v2
       with:

diff --git a/.gitignore b/.gitignore
@@ -5,4 +5,9 @@ validate/basicModels/*.*dat
 validate/basicModels/*.net
 validate/basicModels/*.xml
 validate/basicModels/*.tsv
-validate/basicModels/*.json
+validate/basicModels/*.json
+test/Issue37/test2.nfevent.json
+test/Issue37/test.nfevent.json
+test/Issue37/out.gdat
+test/Issue37/issue37_test2.species
+test/Issue37/issue37_test2.gdat
diff --git a/README.md b/README.md
@@ -85,6 +85,15 @@ executable, you'll need to copy the the following DLLs along with it:
 
 ## Release Notes
 
+### v1.14.2 May, 2024
+
+(a) Bugfix: Fixed a segmentation fault resulting from having a species start with zero concentration. Two simple models were added to the validation process to catch this error.
+(b) Changes to the validation process were made. Previously, 15 trajectories would be generated for each model before testing the differences of NFsim and SSA versus NFsim and ODE. Now only one trajectory would be tested and more would generate upon faliure until a model failed 15 times in a row.
+
+### v1.14.1 May, 2023
+
+(a) Bugfix: Added a missing "\[" when no operations are present
+
 ### v1.14.0 February, 2023
 
 Relabeling the version number to follow previous scheme to avoid further confusion. 

diff --git a/dist/changeFilename.py b/dist/changeFilename.py
@@ -2,7 +2,7 @@
 import platform
 import os
 
-version = '1.14.0'
+version = '1.14.2'
 destdir = os.path.join(version, '{0}-{1}'.format(platform.system(), platform.architecture()[0]))
 os.makedirs(destdir)
 print('moving NFSIm to {0}\n'.format(destdir))

diff --git a/src/NFinput/NFinput.cpp b/src/NFinput/NFinput.cpp
@@ -1051,33 +1051,38 @@ string NFinput::initStartSpecies(
 		// AS2023 - start initial state block
 		string logstr = "    \"initialState\": {\n";
 		logstr += "      \"molecule_array\": [\n";
-		// AS2023 - to add compression we make the full molecule type
-		// vector first
-		int molec_size = *max_element(mgids.begin(), mgids.end());
-		molec_size+=1;
-		vector <int> molec_vec;
-		for(unsigned int isi=0; isi<molec_size; isi++) {
-			molec_vec.push_back(-1);
-		}
-		for(unsigned int img=0; img<mgids.size(); img++) {
-			molec_vec[mgids[img]] = mids[img];
-		}
-		// AS2023 - now we use it to compress the initial state vector
-		int last_val = molec_vec[0];
-		int val_ctr = 1;
-		for(unsigned int ici=1; ici<molec_vec.size(); ici++) {
-			if (molec_vec[ici]!=last_val) {
-				logstr += "        [" + to_string(last_val) + "," + to_string(val_ctr) + "],\n";
-				last_val = molec_vec[ici];
-				val_ctr = 1;
-			} else {
-				val_ctr += 1;
+		// cout << "number of molecules: " << mgids.size() << endl;
+		if (mgids.size()>0){
+			// AS2023 - to add compression we make the full molecule type
+			// vector first
+			int molec_size = *max_element(mgids.begin(), mgids.end());
+			molec_size+=1;
+			vector <int> molec_vec;
+			for(unsigned int isi=0; isi<molec_size; isi++) {
+				molec_vec.push_back(-1);
 			}
+			for(unsigned int img=0; img<mgids.size(); img++) {
+				molec_vec[mgids[img]] = mids[img];
+			}
+			// AS2023 - now we use it to compress the initial state vector
+			int last_val = molec_vec[0];
+			int val_ctr = 1;
+			for(unsigned int ici=1; ici<molec_vec.size(); ici++) {
+				if (molec_vec[ici]!=last_val) {
+					logstr += "        [" + to_string(last_val) + "," + to_string(val_ctr) + "],\n";
+					last_val = molec_vec[ici];
+					val_ctr = 1;
+				} else {
+					val_ctr += 1;
+				}
+			}
+			logstr += "        [" + to_string(last_val) + "," + to_string(val_ctr) + "]\n";
+			// logstr += "        [" + to_string(last_val) + "," + to_string(val_ctr) + "],\n";
+			// // AS 2023 
+			// logstr.erase(logstr.end()-2, logstr.end());
 		}
-		logstr += "        [" + to_string(last_val) + "," + to_string(val_ctr) + "],\n";
-		// AS 2023 
-		logstr.erase(logstr.end()-2, logstr.end());
-		logstr += "\n      ],\n";
+		logstr += "      ],\n";
+
 		// AS2023
 		logstr += "      \"ops\": [\n ";
 		for(int k=0;k<operations.size();k++) {

diff --git a/src/NFsim.cpp b/src/NFsim.cpp
@@ -221,7 +221,7 @@ int main(int argc, char *argv[])
 	// turned off for the general release code.
 	//if (!schedulerInterpreter(&argc, &argv)) return 0;
 
-	string versionNumber = "1.14.1";
+	string versionNumber = "1.14.2";
 	cout<<"starting NFsim v"+versionNumber+"..."<<endl<<endl;
 	clock_t start,finish;
 	double time;

diff --git a/test/Issue37/issue37.xml b/test/Issue37/issue37.xml
@@ -0,0 +1,80 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!-- Created by BioNetGen 2.9.0  -->
+<sbml xmlns="http://www.sbml.org/sbml/level3" level="3" version="1">
+  <model id="uhohnfsim">
+    <ListOfParameters>
+      <Parameter id="_rateLaw1" type="Constant" value="10" expr="10"/>
+      <Parameter id="_rateLaw2" type="Constant" value="1" expr="1"/>
+    </ListOfParameters>
+    <ListOfMoleculeTypes>
+      <MoleculeType id="A"/>
+    </ListOfMoleculeTypes>
+    <ListOfCompartments>
+    </ListOfCompartments>
+    <ListOfSpecies>
+      <Species id="S1"  concentration="10" name="A()">
+        <ListOfMolecules>
+          <Molecule id="S1_M1" name="A"/>
+        </ListOfMolecules>
+      </Species>
+    </ListOfSpecies>
+    <ListOfReactionRules>
+      <ReactionRule id="RR1" name="_R1" symmetry_factor="1">
+        <ListOfReactantPatterns>
+        </ListOfReactantPatterns>
+        <ListOfProductPatterns>
+          <ProductPattern id="RR1_PP1">
+            <ListOfMolecules>
+              <Molecule id="RR1_PP1_M1" name="A"/>
+            </ListOfMolecules>
+          </ProductPattern>
+        </ListOfProductPatterns>
+        <RateLaw id="RR1_RateLaw" type="Ele" totalrate="0">
+          <ListOfRateConstants>
+            <RateConstant value="_rateLaw1"/>
+          </ListOfRateConstants>
+        </RateLaw>
+        <Map>
+        </Map>
+        <ListOfOperations>
+          <Add id="RR1_PP1_M1"/>
+        </ListOfOperations>
+      </ReactionRule>
+      <ReactionRule id="RR2" name="_reverse__R1" symmetry_factor="1">
+        <ListOfReactantPatterns>
+          <ReactantPattern id="RR2_RP1">
+            <ListOfMolecules>
+              <Molecule id="RR2_RP1_M1" name="A"/>
+            </ListOfMolecules>
+          </ReactantPattern>
+        </ListOfReactantPatterns>
+        <ListOfProductPatterns>
+        </ListOfProductPatterns>
+        <RateLaw id="RR2_RateLaw" type="Ele" totalrate="0">
+          <ListOfRateConstants>
+            <RateConstant value="_rateLaw2"/>
+          </ListOfRateConstants>
+        </RateLaw>
+        <Map>
+          <MapItem sourceID="RR2_RP1_M1"/>
+        </Map>
+        <ListOfOperations>
+          <Delete id="RR2_RP1" DeleteMolecules="0"/>
+        </ListOfOperations>
+      </ReactionRule>
+    </ListOfReactionRules>
+    <ListOfObservables>
+      <Observable id="O1" name="A" type="Molecules">
+        <ListOfPatterns>
+          <Pattern id="O1_P1">
+            <ListOfMolecules>
+              <Molecule id="O1_P1_M1" name="A"/>
+            </ListOfMolecules>
+          </Pattern>
+        </ListOfPatterns>
+      </Observable>
+    </ListOfObservables>
+    <ListOfFunctions>
+    </ListOfFunctions>
+  </model>
+</sbml>
diff --git a/test/Issue37/issue37_test2.bngl b/test/Issue37/issue37_test2.bngl
@@ -0,0 +1,18 @@
+begin model
+
+begin species
+  A() 100
+  B() 0
+end species
+
+begin observables
+  Molecules A A()
+end observables
+
+begin reaction rules
+  0 <-> A() 10,1
+end reaction rules
+
+end model
+
+simulate({method=>"nf",t_end=>100,n_steps=>100})
diff --git a/test/Issue37/issue37_test2.xml b/test/Issue37/issue37_test2.xml
@@ -0,0 +1,86 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!-- Created by BioNetGen 2.9.1  -->
+<sbml xmlns="http://www.sbml.org/sbml/level3" level="3" version="1">
+  <model id="issue37_test2">
+    <ListOfParameters>
+      <Parameter id="_rateLaw1" type="Constant" value="10" expr="10"/>
+      <Parameter id="_rateLaw2" type="Constant" value="1" expr="1"/>
+    </ListOfParameters>
+    <ListOfMoleculeTypes>
+      <MoleculeType id="A"/>
+      <MoleculeType id="B"/>
+    </ListOfMoleculeTypes>
+    <ListOfCompartments>
+    </ListOfCompartments>
+    <ListOfSpecies>
+      <Species id="S1"  concentration="100" name="A()">
+        <ListOfMolecules>
+          <Molecule id="S1_M1" name="A"/>
+        </ListOfMolecules>
+      </Species>
+      <Species id="S2"  concentration="0" name="B()">
+        <ListOfMolecules>
+          <Molecule id="S2_M1" name="B"/>
+        </ListOfMolecules>
+      </Species>
+    </ListOfSpecies>
+    <ListOfReactionRules>
+      <ReactionRule id="RR1" name="_R1" symmetry_factor="1">
+        <ListOfReactantPatterns>
+        </ListOfReactantPatterns>
+        <ListOfProductPatterns>
+          <ProductPattern id="RR1_PP1">
+            <ListOfMolecules>
+              <Molecule id="RR1_PP1_M1" name="A"/>
+            </ListOfMolecules>
+          </ProductPattern>
+        </ListOfProductPatterns>
+        <RateLaw id="RR1_RateLaw" type="Ele" totalrate="0">
+          <ListOfRateConstants>
+            <RateConstant value="_rateLaw1"/>
+          </ListOfRateConstants>
+        </RateLaw>
+        <Map>
+        </Map>
+        <ListOfOperations>
+          <Add id="RR1_PP1_M1"/>
+        </ListOfOperations>
+      </ReactionRule>
+      <ReactionRule id="RR2" name="_reverse__R1" symmetry_factor="1">
+        <ListOfReactantPatterns>
+          <ReactantPattern id="RR2_RP1">
+            <ListOfMolecules>
+              <Molecule id="RR2_RP1_M1" name="A"/>
+            </ListOfMolecules>
+          </ReactantPattern>
+        </ListOfReactantPatterns>
+        <ListOfProductPatterns>
+        </ListOfProductPatterns>
+        <RateLaw id="RR2_RateLaw" type="Ele" totalrate="0">
+          <ListOfRateConstants>
+            <RateConstant value="_rateLaw2"/>
+          </ListOfRateConstants>
+        </RateLaw>
+        <Map>
+          <MapItem sourceID="RR2_RP1_M1"/>
+        </Map>
+        <ListOfOperations>
+          <Delete id="RR2_RP1" DeleteMolecules="0"/>
+        </ListOfOperations>
+      </ReactionRule>
+    </ListOfReactionRules>
+    <ListOfObservables>
+      <Observable id="O1" name="A" type="Molecules">
+        <ListOfPatterns>
+          <Pattern id="O1_P1">
+            <ListOfMolecules>
+              <Molecule id="O1_P1_M1" name="A"/>
+            </ListOfMolecules>
+          </Pattern>
+        </ListOfPatterns>
+      </Observable>
+    </ListOfObservables>
+    <ListOfFunctions>
+    </ListOfFunctions>
+  </model>
+</sbml>
diff --git a/validate/basicModels/r29.txt b/validate/basicModels/r29.txt
@@ -0,0 +1,2 @@
+NFSIM ONLY: population testing, with reaction log
+-sim 100 -oSteps 100 -rxnlog basicModels/v29_rxns.json
diff --git a/validate/basicModels/r30.txt b/validate/basicModels/r30.txt
@@ -0,0 +1,2 @@
+NFSIM ONLY: population testing, with reaction log
+-sim 100 -oSteps 100 -rxnlog basicModels/v30_rxns.json
diff --git a/validate/basicModels/v29.bngl b/validate/basicModels/v29.bngl
@@ -0,0 +1,16 @@
+# issue37_test.bngl
+
+begin model
+begin species
+  A() 0
+end species
+begin observables
+  Molecules A A()
+end observables
+begin reaction rules
+  0 <-> A() 10,1
+end reaction rules
+end model
+
+## model actions ##
+writeXML()
diff --git a/validate/basicModels/v30.bngl b/validate/basicModels/v30.bngl
@@ -0,0 +1,17 @@
+# issue37_test2.bngl
+
+begin model
+begin species
+  A() 100
+  B() 0
+end species
+begin observables
+  Molecules A A()
+end observables
+begin reaction rules
+  0 <-> A() 10,1
+end reaction rules
+end model
+
+## model actions ##
+writeXML()
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1,2 @@
		NFSIM ONLY: population testing, with reaction log
		-sim 100 -oSteps 100 -rxnlog basicModels/v29_rxns.json