smoke test for FiniteVolume and Smoldyn

.github/workflows/cd.yml

@@ -24,6 +24,8 @@ jobs:
     steps:
       - name: Checkout repository
         uses: actions/checkout@v4
+        with:
+          submodules: true
 
       - name: Log in to the Container registry
         uses: docker/login-action@v3
@@ -60,19 +62,23 @@ jobs:
     steps:
       - name: checkout vcell-solvers repo
         uses: actions/checkout@v4
+        with:
+          submodules: true
 
       - name: Install Intel MacOS dependencies
         if: matrix.platform == 'macos-13'
         shell: bash
         run: |
           brew install boost
           brew install hdf5
+          brew install libzip
           brew install ninja
 
           brew install llvm
           echo 'export PATH="/usr/local/opt/llvm/bin:$PATH"' >> /Users/runner/.bash_profile
           source /Users/runner/.bash_profile
-
+          ln -s $(which gfortran-14) /usr/local/bin/gfortran
+
           gcc --version
           gfortran --version
           cmake --version
@@ -85,6 +91,7 @@ jobs:
         run: |
           brew install boost
           brew install hdf5
+          brew install libzip
           brew install ninja
 
           brew install llvm
@@ -209,7 +216,7 @@ jobs:
           mkdir build
           cd build
 
-          PATH="/c/Program\ Files/LLVM/bin:$PATH"
+          export PATH="/c/Program\ Files/LLVM/bin:$PATH"
 
           cmake \
           -G Ninja \
@@ -232,6 +239,9 @@ jobs:
           echo "working dir is $PWD"
 
           cd build
+
+          export PATH="/d/a/_temp/msys64/clang64/bin:$PATH"
+          pacman -Sy --noconfirm diffutils
 
           ctest -VV
 
@@ -245,6 +255,7 @@ jobs:
           sudo apt-get update
           sudo apt-get install -y libboost-all-dev
           sudo apt-get install -y libhdf5-dev
+          sudo apt-get install -y libzip-dev
           sudo apt-get install -y ninja-build
 
           gcc --version

.github/workflows/conda.yml

@@ -24,6 +24,9 @@ jobs:
 
     steps:
       - uses: actions/checkout@v4
+        with:
+          submodules: true
+
 
       - name: Get conda
         uses: conda-incubator/[email protected]

.github/workflows/pip.yml

@@ -28,6 +28,8 @@ jobs:
 
     steps:
     - uses: actions/checkout@v4
+      with:
+        submodules: true
 
     - name: Install Intel MacOS dependencies
       if: matrix.platform == 'macos-13'

.github/workflows/wheels.yml

@@ -115,6 +115,7 @@ jobs:
         sudo apt-get update
         sudo apt-get install -y libboost-all-dev
         sudo apt-get install -y libhdf5-dev
+        sudo apt-get install -y libzip-dev
         sudo apt-get install -y ninja-build
 
         gcc --version

.gitignore

@@ -26,3 +26,5 @@
 tests/__pycache__/
 
 *.whl
+
+VCell/tests/testFiles/output/

.gitmodules

@@ -2,3 +2,6 @@
 	path = extern/pybind11
 	url = ../../pybind/pybind11
 	branch = stable
+[submodule "libzippp"]
+	path = libzippp
+	url = https://github.com/ctabin/libzippp.git

CMakeLists.txt

@@ -123,11 +123,14 @@ elseif (MINGW)
 endif()
 
 set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} "${CMAKE_SOURCE_DIR}/cmake/modules/")
+set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} "${CMAKE_SOURCE_DIR}/libzippp/cmake/")
 
 include(GetGitRevisionDescription)
 git_describe(GIT_DESCRIBE ALLOW_LOOKING_ABOVE_CMAKE_SOURCE_DIR)
 
 include (FindZLIB)
+include (FindLIBZIP)
+
 
 if (NOT OPTION_TARGET_PYTHON_BINDING)
 	set(CMAKE_LIBRARY_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/bin)
@@ -189,11 +192,16 @@ find_package(HDF5 COMPONENTS HL CXX C)
 set(HDF_VERSION ${HDF5_VERSION})
 ######    ${HDF5_HL_LIBRARIES} ${HDF5_CXX_LIBRARIES}
 
+if (OPTION_TARGET_TESTS)
+	enable_testing()
+	set(LIBZIPPP_BUILD_TESTS ON)
+endif ()
+
 add_subdirectory(VCellMessaging)
 
 add_subdirectory(VCellZipUtils)
 
-add_subdirectory(libzip-1.2.0)
+add_subdirectory(libzippp)
 
 add_subdirectory(ExpressionParser)
 

Dockerfile

@@ -1,8 +1,17 @@
-FROM ubuntu:22.04 as build
+FROM ubuntu:22.04
 
 RUN apt-get -y update && apt-get install -y apt-utils && \
-    apt-get install -y -qq -o=Dpkg::Use-Pty=0 build-essential gfortran zlib1g-dev \
-    libhdf5-dev ninja-build libcurl4-openssl-dev libboost-all-dev cmake wget python3
+    apt-get install -y -qq -o=Dpkg::Use-Pty=0 build-essential gfortran \
+    libhdf5-dev libzip-dev ninja-build libcurl4-openssl-dev libboost-all-dev libbz2-dev cmake python3
+
+# Install an alternative Fortran compiler
+RUN apt-get install -y gfortran-10
+
+# Set the alternative Fortran compiler as the default
+RUN update-alternatives --install /usr/bin/gfortran gfortran /usr/bin/gfortran-10 10
+
+# Fix broken dependencies and reconfigure ca-certificates
+RUN apt-get -y update && apt-get install -f && dpkg --configure -a && apt-get clean
 
 COPY . /vcellroot
 
@@ -13,10 +22,13 @@ RUN cmake \
     -G Ninja \
     -DOPTION_TARGET_PYTHON_BINDING=OFF \
     -DOPTION_TARGET_MESSAGING=ON \
-    -DOPTION_TARGET_SMOLDYN_SOLVER=OFF \
+    -DOPTION_TARGET_SMOLDYN_SOLVER=ON \
     -DOPTION_TARGET_FV_SOLVER=ON \
     -DOPTION_TARGET_DOCS=OFF \
     .. && \
     ninja
 
-#RUN ctest
+RUN ctest -VV
+
+WORKDIR /vcellroot/build/bin
+ENV PATH="/vcellroot/build/bin:${PATH}"

VCell/CMakeLists.txt

@@ -243,5 +243,18 @@ endif()
 
 # add google tests
 if (OPTION_TARGET_TESTS)
+	enable_testing()
+	if (MINGW)
+		set(test_fvsolver_exe ${CMAKE_BINARY_DIR}/bin/${EXE_FILE}.exe)
+		set(python_cmd py)
+	else (MINGW)
+		set(test_fvsolver_exe ${CMAKE_BINARY_DIR}/bin/${EXE_FILE})
+		set(python_cmd python3)
+	endif (MINGW)
+	set(test_dir ${CMAKE_CURRENT_SOURCE_DIR}/tests/smoke)
+
+	# smoke test as a python script, for bash test example, see NFsim/tests/smoke
+	add_test(NAME ${EXE_FILE}_smoke COMMAND ${python_cmd} ${test_dir}/smoke.py ${test_fvsolver_exe} WORKING_DIRECTORY ${test_dir})
+
 	add_subdirectory(tests)
 endif()

VCell/src/PostProcessingHdf5Writer.cpp

@@ -208,7 +208,7 @@ void PostProcessingHdf5Writer::writeOutput(SimTool* sim_tool) {
 
 		h5PPFile->flush(H5F_SCOPE_GLOBAL);
 	} catch(H5::Exception error ) {
-		throw error.getDetailMsg();
+		throw std::runtime_error(error.getDetailMsg());
 	}
 }
 

VCell/src/SimTool.cpp

@@ -229,25 +229,40 @@ static FILE* openFileWithRetry(const char* fileName, const char* mode) {
 	return fp;
 }
 
-static bool zipUnzipWithRetry(bool bZip, const filesystem::path& zipFileName, const filesystem::path& simFileName, std::string* errmsg) {
+static bool unzipWithRetry(const filesystem::path& zipFileName, const filesystem::path& simFileName, std::string* errmsg) {
 	bool bSuccess = false;
 	for (int attemptNum = 0; attemptNum <= numRetries; attemptNum++) {
 		try {
-			if (bZip) {
-			//	retcode = zip32(1, zipFileName, simFileName);
-				addFilesToZip(zipFileName, simFileName);
-			} else {
-			//	retcode = unzip32(zipFileName, simFileName, NULL);
-				extractFileFromZip(zipFileName, simFileName);
-			}
+			extractFileFromZip(zipFileName, simFileName);
 			bSuccess = true;
 			break;
-		} catch (const char* ziperr) {
+		} catch (runtime_error &e) {
 			errmsg->clear();
-			errmsg->append(ziperr);
-		} catch (...) {
+			errmsg->append(e.what());
+		}
+		if (attemptNum == numRetries) continue;
+		retryWait(retryWaitSeconds);
+		cout << "SimTool::updateLog(), adding .sim to .zip failed (attempt "
+			<< (attemptNum + 1) << "), trying again" << endl;
+
+	}
+	if (!bSuccess) {
+		errmsg->clear();
+		errmsg->append("Writing zip file <").append(zipFileName.string()).append("> failed.");
+	}
+	return bSuccess;
+}
+
+static bool zipWithRetry(const filesystem::path& zipFileName, const filesystem::path& simFileName, std::string* errmsg) {
+	bool bSuccess = false;
+	for (int attemptNum = 0; attemptNum <= numRetries; attemptNum++) {
+		try {
+			addFilesToZip(zipFileName, simFileName);
+			bSuccess = true;
+			break;
+		} catch (runtime_error& e) {
 			errmsg->clear();
-			errmsg->append("SimTool::updateLog(), adding .sim to .zip failed.");
+			errmsg->append(e.what());
 		}
 		if (attemptNum == numRetries) continue;
 		retryWait(retryWaitSeconds);
@@ -358,7 +373,7 @@ void SimTool::loadFinal()
 					// unzip the file (without directory) into exdir, currently we
 					// unzip the file to the current working directory
 					std::string errmsg;
-					zipUnzipWithRetry(false, zipFileAbsoluteName.string().c_str(), dataFileName.string().c_str(), &errmsg);
+					unzipWithRetry(zipFileAbsoluteName.string().c_str(), dataFileName.string().c_str(), &errmsg);
 				}
 			}
 
@@ -553,7 +568,7 @@ void SimTool::updateLog(double progress, double time, int iteration)
 					addFilesToZip(zipFileName.c_str(), simFileName.c_str(), particleFileName.c_str());
 					remove(particleFileName.c_str());
 				} else {
-					bSuccess = zipUnzipWithRetry(true, zipFileName.c_str(), simFileName.c_str(), &errorMsg);
+					bSuccess = zipWithRetry(zipFileName.c_str(), simFileName.c_str(), &errorMsg);
 				}
 				remove(simFileName.c_str());
 

VCell/src/SolverMain.cpp

@@ -40,8 +40,11 @@ std::string version()
 int solve(const std::string& inputFilename, const std::string& vcgFilename, const std::string& outputDir) {
 	// Check if output directory exists, if not create it
 	std::filesystem::path dirPath(outputDir);
-	if (!exists(dirPath)) {
-		create_directories(dirPath);
+	// converty dirPath to an absolute path and check to see if dirPath exists
+	dirPath = std::filesystem::absolute(dirPath);
+	if (!std::filesystem::exists(dirPath)) {
+		// create the directory
+		std::filesystem::create_directories(dirPath);
 	}
 
 	// Open the input file

VCell/tests/CMakeLists.txt

@@ -30,4 +30,6 @@ target_link_libraries(vcell_test vcell GTest::gtest_main)
 #        RUNTIME DESTINATION bin)
 
 include(GoogleTest)
-gtest_discover_tests(vcell_test)
+gtest_discover_tests(vcell_test)
+# copy tests files to build directory
+file(COPY ${CMAKE_CURRENT_SOURCE_DIR}/testFiles DESTINATION ${CMAKE_CURRENT_BINARY_DIR})

VCell/tests/TestVCell.cpp

@@ -1,15 +1,17 @@
 #include <gtest/gtest.h>
+#include <filesystem>
+
 
 #include <VCELL/SolverMain.h>
 
 TEST(VCellTest, BasicAssertions) {
-    std::string inputDir = "../../testFiles/input/";
-    std::string outputDir = "../../testFiles/output/";
+     std::filesystem::path inputDir = "testFiles/input/";
+    std::filesystem::path outputDir = "testFiles/output/";
 
-    std::string fvInputFile = inputDir + "SimID_11538992_0_.fvinput";
-    std::string vcgInputFile = inputDir + "SimID_11538992_0_.vcg";
-    std::string testOutputDir_1 = outputDir + "test_output_1";
-    std::string testOutputDir_2 = outputDir + "test_output_2";
+    std::filesystem::path fvInputFile = inputDir / "SimID_11538992_0_.fvinput";
+    std::filesystem::path vcgInputFile = inputDir / "SimID_11538992_0_.vcg";
+    std::string testOutputDir_1 = outputDir / "test_output_1";
+    std::string testOutputDir_2 = outputDir / "test_output_2";
 
     auto retcode_1 = solve(fvInputFile, vcgInputFile, testOutputDir_1);
     EXPECT_EQ(retcode_1, 0);

VCell/tests/smoke/SimID_1585623750_0_.functions

@@ -0,0 +1,19 @@
+##---------------------------------------------
+##  /Users/jimschaff/.vcell/simdata/temp/SimID_1585623750_0_.functions
+##---------------------------------------------
+
+subdomain1::J_flux0; (2.0 * (RanC_cyt - RanC_nuc)); ; Volume_VariableType; false
+subdomain1::J_r0; ((2.0 * RanC_cyt) - (1000.0 * Ran_cyt * C_cyt)); ; Volume_VariableType; false
+subdomain1::KFlux_nm_cyt; 1.0; ; Volume_Region_VariableType; false
+subdomain1::KFlux_nm_nuc; 1.0; ; Volume_Region_VariableType; false
+subdomain1::RanC_cyt_init_uM; (1.0 + x); ; Volume_VariableType; false
+subdomain0_subdomain1_membrane::s2; 0.0; ; Membrane_Region_VariableType; false
+subdomain1::Size_cyt; vcRegionVolume('subdomain1'); ; Volume_Region_VariableType; false
+subdomain0::Size_EC; vcRegionVolume('subdomain0'); ; Volume_Region_VariableType; false
+subdomain1::Size_nm; vcRegionVolume('subdomain1'); ; Volume_Region_VariableType; false
+subdomain1::Size_nuc; vcRegionVolume('subdomain1'); ; Volume_Region_VariableType; false
+subdomain0_subdomain1_membrane::Size_pm; vcRegionArea('subdomain0_subdomain1_membrane'); ; Membrane_Region_VariableType; false
+subdomain0_subdomain1_membrane::sobj_subdomain11_subdomain00_size; vcRegionArea('subdomain0_subdomain1_membrane'); ; Membrane_Region_VariableType; false
+subdomain0::vobj_subdomain00_size; vcRegionVolume('subdomain0'); ; Volume_Region_VariableType; false
+subdomain1::vobj_subdomain11_size; vcRegionVolume('subdomain1'); ; Volume_Region_VariableType; false
+