refactor VCellStoch into separate lib/exe, add unit test

Stochastic/CMakeLists.txt

@@ -1,12 +1,22 @@
-project(Stochastic)		
-
-set (SRC_FILES 
-	VCellStoch/Gibson.cpp
-	VCellStoch/IndexedTree.cpp
-	VCellStoch/Jump.cpp
-	VCellStoch/StochModel.cpp
-	VCellStoch/StochVar.cpp
-	VCellStoch/VCellStoch.cpp
+cmake_minimum_required (VERSION 3.0)
+project(Stochastic)
+
+set (SRC_FILES
+		VCellStoch/src/Gibson.cpp
+		VCellStoch/src/IndexedTree.cpp
+		VCellStoch/src/Jump.cpp
+		VCellStoch/src/StochModel.cpp
+		VCellStoch/src/StochVar.cpp
+)
+
+set (SRC_MAIN_FILE VCellStoch/src/VCellStoch.cpp)
+
+set (HEADER_FILES
+		VCellStoch/include/Gibson.h
+		VCellStoch/include/IndexedTree.h
+		VCellStoch/include/Jump.h
+		VCellStoch/include/StochModel.h
+		VCellStoch/include/StochVar.h
 )
 
 set(EXE_FILE VCellStoch)
@@ -33,8 +43,19 @@ if (DEFINED ENV{PETSC_ARCH})
         link_directories("/usr/lib/x86_64-linux-gnu/hdf5/serial")
 endif()
 
-add_executable(${EXE_FILE} ${SRC_FILES})
+add_library(VCellStochLib ${SRC_FILES} ${HEADER_FILES})
+target_link_libraries(VCellStochLib ExpressionParser vcommons vcellmessaging hdf5)
+target_include_directories(VCellStochLib PUBLIC
+		$<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/VCellStoch/include>
+		$<INSTALL_INTERFACE:VCellStoch/include>  # <prefix>/VCellStoch/include
+		)
+
+
+add_executable(${EXE_FILE} ${SRC_MAIN_FILE} ${SRC_FILES} ${HEADER_FILES})
 #target_link_libraries(${EXE_FILE} ExpressionParser vcommons vcellmessaging ${CMAKE_SOURCE_DIR}/mylibs/libhdf5_serial.so.10)
-target_link_libraries(${EXE_FILE} ExpressionParser vcommons vcellmessaging hdf5)
+target_link_libraries(${EXE_FILE} VCellStochLib)
 #add_dependencies(${EXE_FILE} ExpressionParser)
-install(TARGETS ${EXE_FILE} RUNTIME DESTINATION ${OPTION_EXE_DIRECTORY})
+install(TARGETS VCellStochLib ${EXE_FILE} RUNTIME DESTINATION ${OPTION_EXE_DIRECTORY})
+
+enable_testing()
+add_subdirectory(Tests)

Stochastic/Tests/CMakeLists.txt

@@ -0,0 +1,26 @@
+cmake_minimum_required (VERSION 3.0)
+project(MovingBoundaryTest)
+set (CMAKE_CXX_STANDARD 11)
+cmake_policy(SET CMP0046 OLD)
+enable_testing()
+
+set(SRC_FILES
+		statstest.cpp
+)
+
+file(GLOB HDR_FILES *h)
+
+set(EXE_FILE Test TestVCellStoch)
+
+set_source_files_properties( ${SRC_FILES} PROPERTIES LANGUAGE CXX)
+
+message(STATUS "HDF5 VERSION IS ${HDF5_VERSION}, LIBS = ${HDF5_LIBRARIES}, HL_LIBS = ${HDF5_HL_LIBRARIES}")
+
+add_executable(TestVCellStoch ${SRC_FILES} ${HDR_FILES})
+add_dependencies(TestVCellStoch VCellStochLib gtest)
+target_link_libraries(TestVCellStoch VCellStochLib GTest::gtest_main)
+install(TARGETS TestVCellStoch
+	RUNTIME DESTINATION bin)
+
+include(GoogleTest)
+gtest_discover_tests(TestVCellStoch)

Stochastic/Tests/statstest.cpp

@@ -0,0 +1,82 @@
+//
+// Created by Jim Schaff on 4/25/23.
+//
+#include <stdexcept>
+#include "gtest/gtest.h"
+#include "../VCellStoch/include/Gibson.h"
+#include <iostream>
+#include <cstdio>
+
+const char* input_file_contents = R"INPUT_FILE(
+<control>
+STARTING_TIME	0.0
+ENDING_TIME 	20.0
+TOLERANCE 	1.0E-9
+SAVE_PERIOD	0.02
+MAX_SAVE_POINTS	1001.0
+NUM_TRIAL	50000
+SEED	566564762
+BMULTIBUTNOTHISTO	1
+</control>
+
+<model>
+<discreteVariables>
+        TotalVars	3
+s0_Count	1
+s1_Count	0
+s2_Count	1
+</discreteVariables>
+
+<jumpProcesses>
+        TotalProcesses	2
+r0
+        r0_reverse
+        </jumpProcesses>
+
+<processDesc>
+        TotalDescriptions	2
+JumpProcess	r0
+Propensity	(0.9996443474639611 * s0_Count * s2_Count)
+Effect	3
+s0_Count	inc	-1.0
+
+s2_Count	inc	-1.0
+
+s1_Count	inc	1.0
+
+DependentProcesses	0
+
+JumpProcess	r0_reverse
+Propensity	0.0
+Effect	3
+s0_Count	inc	1.0
+
+s2_Count	inc	1.0
+
+s1_Count	inc	-1.0
+
+DependentProcesses	1
+r0
+
+</processDesc>
+</model>
+)INPUT_FILE";
+
+
+TEST(statstest,test1) {
+    std::string temp_input_file_name = std::tmpnam(nullptr);
+    std::ofstream input_file (temp_input_file_name);
+    bool bWroteFile = false;
+    if (input_file.is_open()){
+        input_file << input_file_contents;
+        input_file.close();
+        bWroteFile = true;
+    }
+    ASSERT_TRUE(bWroteFile);
+
+    std::string temp_output_file_name = std::tmpnam(nullptr);
+
+    Gibson *gb= new Gibson(temp_input_file_name.c_str(), temp_output_file_name.c_str());
+    gb->march();
+    delete gb;
+}

Stochastic/VCellStoch/Gibson.h → Stochastic/VCellStoch/include/Gibson.h

@@ -23,7 +23,7 @@ class IndexedTree;
 class Gibson : public StochModel{
 public:
 	Gibson();
-	Gibson(char*, char*);
+	Gibson(const char*, const char*);
 	~Gibson();
 	int core();
 	void march();
@@ -37,7 +37,7 @@ class Gibson : public StochModel{
 	IndexedTree *Tree; //the data structure(binary tree) to store all the processes and make each parent smaller than it's children.
 	double* currvals;//array of variable values to be used by expression parser. variables are stored in vector listOfVars.
 	ofstream outfile; //the output file stream where the results are saved.
-	char* outfilename;//the output file name.
+	const char* outfilename;//the output file name.
 	bool flag_savePeriod;//the flag for using save period.
 	int finalizeSampleRow(int,double);//central location to call to complete 1 output sample to file
 	int savedSampleCount; //saved sample counter that survives certain iterations to keep overall count

Stochastic/VCellStoch/Jump.h → Stochastic/VCellStoch/include/Jump.h

@@ -3,7 +3,7 @@
 
 #include <string>
 #include <vector>
-#include <SymbolTable.h>
+#include "../../../ExpressionParser/SymbolTable.h"
 
 using std::string;
 using std::vector;

Stochastic/VCellStoch/Gibson.cpp → Stochastic/VCellStoch/src/Gibson.cpp

@@ -1,7 +1,7 @@
 //#define DEBUG //enable it when debug is needed.
 #include <limits>
 #include <stdexcept>
-#include "Gibson.h"
+#include "../include/Gibson.h"
 #ifdef __APPLE__
 	#include "/usr/local/opt/[email protected]/include/hdf5.h"
 #else
@@ -32,14 +32,14 @@ using namespace std;
 #include <sys/types.h>
 #include <sys/timeb.h>
 #include <time.h>
-#include "Jump.h"
-#include "StochVar.h"
-#include "IndexedTree.h"
+#include "../include/Jump.h"
+#include "../include/StochVar.h"
+#include "../include/IndexedTree.h"
 
 #ifdef USE_MESSAGING
 #include <VCELL/SimulationMessaging.h>
 #endif
-#include <VCellException.h>
+#include "VCellException.h"
 const double double_infinity = numeric_limits<double>::infinity();
 const double EPSILON = 1E-12;
 const string Gibson::MY_T_STR = "t";
@@ -61,7 +61,7 @@ Gibson::Gibson()
  *Input para: srting, the input file(name), where the model info. is read.
  *            string, the output file(name), where the results are saved.
  */
-Gibson::Gibson(char* arg_infilename, char* arg_outfilename)
+Gibson::Gibson(const char* arg_infilename, const char* arg_outfilename)
 	:StochModel(),
 	savedSampleCount(1),
 	lastTime (std::numeric_limits<long>::min( ))

Stochastic/VCellStoch/IndexedTree.cpp → Stochastic/VCellStoch/src/IndexedTree.cpp

@@ -1,6 +1,6 @@
 #include <assert.h>
 #include <math.h>
-#include "IndexedTree.h"
+#include "../include/IndexedTree.h"
 
 /*
  *The constructor of IndexedTree.

Stochastic/VCellStoch/Jump.cpp → Stochastic/VCellStoch/src/Jump.cpp

@@ -1,8 +1,8 @@
-#include "Jump.h"
+#include "../include/Jump.h"
 
-#include <SimpleSymbolTable.h>
-#include <Exception.h>
-#include <Expression.h>
+#include "SimpleSymbolTable.h"
+#include "Exception.h"
+#include "Expression.h"
 using VCell::Exception;
 using VCell::Expression;