Post-Development Cleanup

virtualcell · Jan 26, 2024 · c4b18cf · c4b18cf
1 parent c7b7847
commit c4b18cf
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Showing 7 changed files with 9 additions and 32 deletions.
diff --git a/Stochastic/Tests/statstest.cpp b/Stochastic/Tests/statstest.cpp
@@ -7,8 +7,6 @@
 #include <iostream>
 #include <cstdio>
 
-#include "VCELL/SimulationMessaging.h"
-
 const char* input_file_contents = R"INPUT_FILE(
 <control>
 STARTING_TIME	0.0
@@ -103,13 +101,13 @@ TEST(statstest,test1) {
 	std::string outputFileName = std::tmpnam(nullptr);
 	std::map<int,double> results;
 	std::fstream inputFileStream;
-	inputFileStream.open(inputFileName, fstream::out);
+	inputFileStream.open(inputFileName, std::fstream::out);
 	if (inputFileStream.fail()) {
 		std::perror(("File <" + inputFileName + "> could not be created.").c_str());
 		ASSERT_FALSE(inputFileStream.fail());
 	}
 	std::fstream outputFileStream;
-	outputFileStream.open(outputFileName, fstream::out);
+	outputFileStream.open(outputFileName, std::fstream::out);
 	if (outputFileStream.fail()) {
 		std::perror(("File <" + inputFileName + "> could not be created.").c_str());
 		ASSERT_FALSE(outputFileStream.fail());
@@ -127,7 +125,7 @@ TEST(statstest,test1) {
     gb->march();
 
 	// Verify file contents
-    outputFileStream.open(outputFileName, fstream::in);
+    outputFileStream.open(outputFileName, std::fstream::in);
     std::string line;
     std::getline(outputFileStream, line); // remove header line
 	for (int i = 0; !outputFileStream.eof(); i++) {

diff --git a/Stochastic/VCellStoch/src/Gibson.cpp b/Stochastic/VCellStoch/src/Gibson.cpp
@@ -15,7 +15,6 @@
 #include <cstdlib>
 #include <iostream>
 #include <random>
-using namespace std;
 
 #include <ctime>
 #include "../include/IndexedTree.h"

diff --git a/VCell/include/VCELL/PostProcessingHdf5Writer.h b/VCell/include/VCELL/PostProcessingHdf5Writer.h
@@ -20,7 +20,6 @@ namespace H5 {
 class PostProcessingHdf5Writer
 {
 public:
-	PostProcessingHdf5Writer(char* fileName, PostProcessingBlock* postProcessingBlock);
 	PostProcessingHdf5Writer(std::string fileName, PostProcessingBlock* postProcessingBlock);
 	virtual ~PostProcessingHdf5Writer();
 

diff --git a/VCell/src/PostProcessingHdf5Writer.cpp b/VCell/src/PostProcessingHdf5Writer.cpp
@@ -11,23 +11,13 @@
 #include <H5Cpp.h>
 #include <iostream>
 #include <fstream>
-#include <utility>
-using std::cout;
-using std::endl;
 #include <sys/stat.h>
 
 #define POST_PROCESSING_ROOT "/PostProcessing"
 
 const char* PostProcessingHdf5Writer::PPGroupName  = POST_PROCESSING_ROOT;
 const char* PostProcessingHdf5Writer::TimesDataSetName  = POST_PROCESSING_ROOT"/Times";
 
-PostProcessingHdf5Writer::PostProcessingHdf5Writer(char* fileName, PostProcessingBlock* ppb) {
-	this->h5PPFileName = fileName;
-	this->postProcessingBlock = ppb;
-	h5PPFile = NULL;
-	timesDataSet = NULL;
-}
-
 PostProcessingHdf5Writer::PostProcessingHdf5Writer(std::string fileName, PostProcessingBlock* ppb) {
 	this->h5PPFileName = std::move(fileName);
 	this->postProcessingBlock = ppb;
@@ -75,7 +65,7 @@ bool PostProcessingHdf5Writer::loadFinal(int numTimes) {
 		// the max time in log file is numTimes
 		// hdf5 is missing times
 		if (timesDim < numTimes) {
-			cout << "post processing hdf5 times don't match" << endl;
+			std::cout << "post processing hdf5 times don't match" << std::endl;
 			return false;
 		}		
 		double* times = new double[int(timesDim)];
@@ -109,7 +99,7 @@ bool PostProcessingHdf5Writer::loadFinal(int numTimes) {
 		}
 		hdf5Copy.close();
 	} catch(H5::Exception error ) {
-		cout << "failed to reload post processing block: " << error.getDetailMsg() << endl;
+		std::cout << "failed to reload post processing block: " << error.getDetailMsg() << std::endl;
 		// recreate the file later
 	}
 

diff --git a/VCellMessaging/include/VCELL/SimulationMessaging.h b/VCellMessaging/include/VCELL/SimulationMessaging.h
@@ -10,7 +10,6 @@
 
 #endif
 #include <iostream>
-using namespace std;
 
 #if (defined(WIN32) || defined(WIN64) )
 #include <windows.h>

diff --git a/VCellMessaging/src/SimulationMessaging.cpp b/VCellMessaging/src/SimulationMessaging.cpp
@@ -1,13 +1,9 @@
 #include <VCELL/SimulationMessaging.h>
-#include <utility>
 #include <iostream>
 #include <algorithm>
 #include <sstream>
-using std::cerr;
-using std::cout;
-using std::endl;
 
-#include <stdio.h>
+#include <cstdio>
 #ifdef USE_MESSAGING
 #if ( !defined(WIN32) && !defined(WIN64) ) // UNIX
 #include <curl/curl.h>
@@ -173,13 +169,13 @@ void SimulationMessaging::sendStatus() {
 				fflush(stdout);
 				break;
 			case JOB_STARTING:
-				cout<< workerEvent->eventMessage << endl;
+				std::cout<< workerEvent->eventMessage << std::endl;
 				break;
 			case JOB_COMPLETED:
-				cerr << "Simulation Complete in Main() ... " << endl;
+				std::cerr << "Simulation Complete in Main() ... " << std::endl;
 				break;
 			case JOB_FAILURE:
-				cerr << workerEvent->eventMessage << endl;
+				std::cerr << workerEvent->eventMessage << std::endl;
 				break;
 			}
 			return;

diff --git a/smoldyn-2.38/CMakeLists.txt b/smoldyn-2.38/CMakeLists.txt
@@ -119,10 +119,6 @@ set_source_files_properties(${MAIN_FILES} PROPERTIES LANGUAGE CXX )
 
 include_directories(source/lib source/Smoldyn source/NextSubVolume source/vtk ${CMAKE_CURRENT_BINARY_DIR})
 
-# The following command is to signal we need to link "szip", which hdf5 uses. We should look into
-# how to disable this, or at least control it via an option.
-# add_link_options("${CMAKE_LINK_LIBRARY_FLAG}sz")
-
 ####### Build for debugging or release ##########
 
 if("${CMAKE_CXX_COMPILER_ID}" STREQUAL "Clang")