copy config to output now part of core

drbergman · drbergman · commit 3a2795f3be87 · 2025-04-29T07:00:24.000-04:00
diff --git a/modules/PhysiCell_settings.cpp b/modules/PhysiCell_settings.cpp
@@ -102,9 +102,9 @@ bool load_PhysiCell_config_file( std::string filename )
 	if (!read_PhysiCell_config_file( filename ))
 	{ return false; }
 
-	PhysiCell_settings.read_from_pugixml(); 
+	PhysiCell_settings.read_from_pugixml();
 	
-	// now read the microenvironment (optional) 
+	// now read the microenvironment (optional)
 	
 	if( !setup_microenvironment_from_XML( physicell_config_root ) )
 	{
@@ -119,7 +119,9 @@ bool load_PhysiCell_config_file( std::string filename )
 
 	create_output_directory( PhysiCell_settings.folder );
 
-	return true; 	
+	copy_file_to_output( filename );
+
+	return true;
 }
 
 PhysiCell_Settings::PhysiCell_Settings()
diff --git a/sample_projects/asymmetric_division/main.cpp b/sample_projects/asymmetric_division/main.cpp
@@ -87,24 +87,18 @@ int main( int argc, char* argv[] )
 {
 	// load and parse settings file(s)
 	
-	bool XML_status = false; 
-	char copy_command [1024]; 
+	bool XML_status = false;
 	if( argc > 1 )
 	{
-		XML_status = load_PhysiCell_config_file( argv[1] ); 
-		sprintf( copy_command , "cp %s %s" , argv[1] , PhysiCell_settings.folder.c_str() ); 
+		XML_status = load_PhysiCell_config_file( argv[1] );
 	}
 	else
 	{
 		XML_status = load_PhysiCell_config_file( "./config/PhysiCell_settings.xml" );
-		sprintf( copy_command , "cp ./config/PhysiCell_settings.xml %s" , PhysiCell_settings.folder.c_str() ); 
 	}
 	if( !XML_status )
 	{ exit(-1); }
 	
-	// copy config file to output directry 
-	system( copy_command ); 
-	
 	// OpenMP setup
 	omp_set_num_threads(PhysiCell_settings.omp_num_threads);
 	
diff --git a/sample_projects/biorobots/main.cpp b/sample_projects/biorobots/main.cpp
@@ -87,24 +87,18 @@ int main( int argc, char* argv[] )
 {
 	// load and parse settings file(s)
 	
-	bool XML_status = false; 
-	char copy_command [1024]; 
+	bool XML_status = false;
 	if( argc > 1 )
 	{
-		XML_status = load_PhysiCell_config_file( argv[1] ); 
-		sprintf( copy_command , "cp %s %s" , argv[1] , PhysiCell_settings.folder.c_str() ); 
+		XML_status = load_PhysiCell_config_file( argv[1] );
 	}
 	else
 	{
 		XML_status = load_PhysiCell_config_file( "./config/PhysiCell_settings.xml" );
-		sprintf( copy_command , "cp ./config/PhysiCell_settings.xml %s" , PhysiCell_settings.folder.c_str() ); 
 	}
 	if( !XML_status )
 	{ exit(-1); }
 	
-	// copy config file to output directry 
-	system( copy_command ); 
-	
 	// OpenMP setup
 	omp_set_num_threads(PhysiCell_settings.omp_num_threads);
 	
diff --git a/sample_projects/cancer_biorobots/main.cpp b/sample_projects/cancer_biorobots/main.cpp
@@ -87,24 +87,18 @@ int main( int argc, char* argv[] )
 {
 	// load and parse settings file(s)
 	
-	bool XML_status = false; 
-	char copy_command [1024]; 
+	bool XML_status = false;
 	if( argc > 1 )
 	{
-		XML_status = load_PhysiCell_config_file( argv[1] ); 
-		sprintf( copy_command , "cp %s %s" , argv[1] , PhysiCell_settings.folder.c_str() ); 
+		XML_status = load_PhysiCell_config_file( argv[1] );
 	}
 	else
 	{
 		XML_status = load_PhysiCell_config_file( "./config/PhysiCell_settings.xml" );
-		sprintf( copy_command , "cp ./config/PhysiCell_settings.xml %s" , PhysiCell_settings.folder.c_str() ); 
 	}
 	if( !XML_status )
 	{ exit(-1); }
 	
-	// copy config file to output directry 
-	system( copy_command ); 
-	
 	// OpenMP setup
 	omp_set_num_threads(PhysiCell_settings.omp_num_threads);
 	
diff --git a/sample_projects/custom_division/main.cpp b/sample_projects/custom_division/main.cpp
@@ -87,24 +87,18 @@ int main( int argc, char* argv[] )
 {
 	// load and parse settings file(s)
 	
-	bool XML_status = false; 
-	char copy_command [1024]; 
+	bool XML_status = false;
 	if( argc > 1 )
 	{
-		XML_status = load_PhysiCell_config_file( argv[1] ); 
-		sprintf( copy_command , "cp %s %s" , argv[1] , PhysiCell_settings.folder.c_str() ); 
+		XML_status = load_PhysiCell_config_file( argv[1] );
 	}
 	else
 	{
 		XML_status = load_PhysiCell_config_file( "./config/PhysiCell_settings.xml" );
-		sprintf( copy_command , "cp ./config/PhysiCell_settings.xml %s" , PhysiCell_settings.folder.c_str() ); 
 	}
 	if( !XML_status )
 	{ exit(-1); }
 	
-	// copy config file to output directry 
-	system( copy_command ); 
-	
 	// OpenMP setup
 	omp_set_num_threads(PhysiCell_settings.omp_num_threads);
 	
diff --git a/sample_projects/heterogeneity/main.cpp b/sample_projects/heterogeneity/main.cpp
@@ -87,24 +87,18 @@ int main( int argc, char* argv[] )
 {
 	// load and parse settings file(s)
 	
-	bool XML_status = false; 
-	char copy_command [1024]; 
+	bool XML_status = false;
 	if( argc > 1 )
 	{
-		XML_status = load_PhysiCell_config_file( argv[1] ); 
-		sprintf( copy_command , "cp %s %s" , argv[1] , PhysiCell_settings.folder.c_str() ); 
+		XML_status = load_PhysiCell_config_file( argv[1] );
 	}
 	else
 	{
 		XML_status = load_PhysiCell_config_file( "./config/PhysiCell_settings.xml" );
-		sprintf( copy_command , "cp ./config/PhysiCell_settings.xml %s" , PhysiCell_settings.folder.c_str() ); 
 	}
 	if( !XML_status )
 	{ exit(-1); }
 	
-	// copy config file to output directry 
-	system( copy_command ); 
-	
 	// OpenMP setup
 	omp_set_num_threads(PhysiCell_settings.omp_num_threads);
 	
diff --git a/sample_projects/immune_function/main.cpp b/sample_projects/immune_function/main.cpp
@@ -87,24 +87,18 @@ int main( int argc, char* argv[] )
 {
 	// load and parse settings file(s)
 	
-	bool XML_status = false; 
-	char copy_command [1024]; 
+	bool XML_status = false;
 	if( argc > 1 )
 	{
-		XML_status = load_PhysiCell_config_file( argv[1] ); 
-		sprintf( copy_command , "cp %s %s" , argv[1] , PhysiCell_settings.folder.c_str() ); 
+		XML_status = load_PhysiCell_config_file( argv[1] );
 	}
 	else
 	{
 		XML_status = load_PhysiCell_config_file( "./config/PhysiCell_settings.xml" );
-		sprintf( copy_command , "cp ./config/PhysiCell_settings.xml %s" , PhysiCell_settings.folder.c_str() ); 
 	}
 	if( !XML_status )
 	{ exit(-1); }
 	
-	// copy config file to output directry 
-	system( copy_command ); 
-	
 	// OpenMP setup
 	omp_set_num_threads(PhysiCell_settings.omp_num_threads);
 	
diff --git a/sample_projects/interactions/main.cpp b/sample_projects/interactions/main.cpp
@@ -87,24 +87,18 @@ int main( int argc, char* argv[] )
 {
 	// load and parse settings file(s)
 	
-	bool XML_status = false; 
-	char copy_command [1024]; 
+	bool XML_status = false;
 	if( argc > 1 )
 	{
-		XML_status = load_PhysiCell_config_file( argv[1] ); 
-		sprintf( copy_command , "cp %s %s" , argv[1] , PhysiCell_settings.folder.c_str() ); 
+		XML_status = load_PhysiCell_config_file( argv[1] );
 	}
 	else
 	{
 		XML_status = load_PhysiCell_config_file( "./config/PhysiCell_settings.xml" );
-		sprintf( copy_command , "cp ./config/PhysiCell_settings.xml %s" , PhysiCell_settings.folder.c_str() ); 
 	}
 	if( !XML_status )
 	{ exit(-1); }
 	
-	// copy config file to output directry 
-	system( copy_command ); 
-	
 	// OpenMP setup
 	omp_set_num_threads(PhysiCell_settings.omp_num_threads);
 	
diff --git a/sample_projects/mechano/main.cpp b/sample_projects/mechano/main.cpp
@@ -87,24 +87,18 @@ int main( int argc, char* argv[] )
 {
 	// load and parse settings file(s)
 	
-	bool XML_status = false; 
-	char copy_command [1024]; 
+	bool XML_status = false;
 	if( argc > 1 )
 	{
-		XML_status = load_PhysiCell_config_file( argv[1] ); 
-		sprintf( copy_command , "cp %s %s" , argv[1] , PhysiCell_settings.folder.c_str() ); 
+		XML_status = load_PhysiCell_config_file( argv[1] );
 	}
 	else
 	{
 		XML_status = load_PhysiCell_config_file( "./config/PhysiCell_settings.xml" );
-		sprintf( copy_command , "cp ./config/PhysiCell_settings.xml %s" , PhysiCell_settings.folder.c_str() ); 
 	}
 	if( !XML_status )
 	{ exit(-1); }
 	
-	// copy config file to output directry 
-	system( copy_command ); 
-	
 	// OpenMP setup
 	omp_set_num_threads(PhysiCell_settings.omp_num_threads);
 	
diff --git a/sample_projects/physimess/main.cpp b/sample_projects/physimess/main.cpp
@@ -87,24 +87,18 @@ int main( int argc, char* argv[] )
 {
 	// load and parse settings file(s)
 	
-	bool XML_status = false; 
-	char copy_command [1024]; 
+	bool XML_status = false;
 	if( argc > 1 )
 	{
-		XML_status = load_PhysiCell_config_file( argv[1] ); 
-		sprintf( copy_command , "cp %s %s" , argv[1] , PhysiCell_settings.folder.c_str() ); 
+		XML_status = load_PhysiCell_config_file( argv[1] );
 	}
 	else
 	{
 		XML_status = load_PhysiCell_config_file( "./config/PhysiCell_settings.xml" );
-		sprintf( copy_command , "cp ./config/PhysiCell_settings.xml %s" , PhysiCell_settings.folder.c_str() ); 
 	}
 	if( !XML_status )
 	{ exit(-1); }
 	
-	// copy config file to output directry 
-	system( copy_command ); 
-	
 	// OpenMP setup
 	omp_set_num_threads(PhysiCell_settings.omp_num_threads);
 	
diff --git a/sample_projects/pred_prey_farmer/main.cpp b/sample_projects/pred_prey_farmer/main.cpp
@@ -87,24 +87,18 @@ int main( int argc, char* argv[] )
 {
 	// load and parse settings file(s)
 	
-	bool XML_status = false; 
-	char copy_command [1024]; 
+	bool XML_status = false;
 	if( argc > 1 )
 	{
-		XML_status = load_PhysiCell_config_file( argv[1] ); 
-		sprintf( copy_command , "cp %s %s" , argv[1] , PhysiCell_settings.folder.c_str() ); 
+		XML_status = load_PhysiCell_config_file( argv[1] );
 	}
 	else
 	{
 		XML_status = load_PhysiCell_config_file( "./config/PhysiCell_settings.xml" );
-		sprintf( copy_command , "cp ./config/PhysiCell_settings.xml %s" , PhysiCell_settings.folder.c_str() ); 
 	}
 	if( !XML_status )
 	{ exit(-1); }
 	
-	// copy config file to output directry 
-	system( copy_command ); 
-	
 	// OpenMP setup
 	omp_set_num_threads(PhysiCell_settings.omp_num_threads);
 	
diff --git a/sample_projects/rules_sample/main.cpp b/sample_projects/rules_sample/main.cpp
@@ -87,24 +87,18 @@ int main( int argc, char* argv[] )
 {
 	// load and parse settings file(s)
 	
-	bool XML_status = false; 
-	char copy_command [1024]; 
+	bool XML_status = false;
 	if( argc > 1 )
 	{
-		XML_status = load_PhysiCell_config_file( argv[1] ); 
-		sprintf( copy_command , "cp %s %s" , argv[1] , PhysiCell_settings.folder.c_str() ); 
+		XML_status = load_PhysiCell_config_file( argv[1] );
 	}
 	else
 	{
 		XML_status = load_PhysiCell_config_file( "./config/PhysiCell_settings.xml" );
-		sprintf( copy_command , "cp ./config/PhysiCell_settings.xml %s" , PhysiCell_settings.folder.c_str() ); 
 	}
 	if( !XML_status )
 	{ exit(-1); }
 	
-	// copy config file to output directry 
-	system( copy_command ); 
-	
 	// OpenMP setup
 	omp_set_num_threads(PhysiCell_settings.omp_num_threads);
 	
diff --git a/sample_projects/template/main.cpp b/sample_projects/template/main.cpp
@@ -87,24 +87,18 @@ int main( int argc, char* argv[] )
 {
 	// load and parse settings file(s)
 	
-	bool XML_status = false; 
-	char copy_command [1024]; 
+	bool XML_status = false;
 	if( argc > 1 )
 	{
-		XML_status = load_PhysiCell_config_file( argv[1] ); 
-		sprintf( copy_command , "cp %s %s" , argv[1] , PhysiCell_settings.folder.c_str() ); 
+		XML_status = load_PhysiCell_config_file( argv[1] );
 	}
 	else
 	{
 		XML_status = load_PhysiCell_config_file( "./config/PhysiCell_settings.xml" );
-		sprintf( copy_command , "cp ./config/PhysiCell_settings.xml %s" , PhysiCell_settings.folder.c_str() ); 
 	}
 	if( !XML_status )
 	{ exit(-1); }
 	
-	// copy config file to output directry 
-	system( copy_command ); 
-	
 	// OpenMP setup
 	omp_set_num_threads(PhysiCell_settings.omp_num_threads);
 	
diff --git a/sample_projects/virus_macrophage/main.cpp b/sample_projects/virus_macrophage/main.cpp
@@ -87,23 +87,17 @@ int main( int argc, char* argv[] )
 {
 	// load and parse settings file(s)
 	
-	bool XML_status = false; 
-	char copy_command [1024]; 
+	bool XML_status = false;
 	if( argc > 1 )
 	{
-		XML_status = load_PhysiCell_config_file( argv[1] ); 
-		sprintf( copy_command , "cp %s %s" , argv[1] , PhysiCell_settings.folder.c_str() ); 
+		XML_status = load_PhysiCell_config_file( argv[1] );
 	}
 	else
 	{
 		XML_status = load_PhysiCell_config_file( "./config/PhysiCell_settings.xml" );
-		sprintf( copy_command , "cp ./config/PhysiCell_settings.xml %s" , PhysiCell_settings.folder.c_str() ); 
 	}
 	if( !XML_status )
 	{ exit(-1); }
-	
-	// copy config file to output directry 
-	system( copy_command ); 
 
 	// OpenMP setup
 	omp_set_num_threads(PhysiCell_settings.omp_num_threads);
diff --git a/sample_projects/worm/main.cpp b/sample_projects/worm/main.cpp
@@ -87,24 +87,18 @@ int main( int argc, char* argv[] )
 {
 	// load and parse settings file(s)
 	
-	bool XML_status = false; 
-	char copy_command [1024]; 
+	bool XML_status = false;
 	if( argc > 1 )
 	{
-		XML_status = load_PhysiCell_config_file( argv[1] ); 
-		sprintf( copy_command , "cp %s %s" , argv[1] , PhysiCell_settings.folder.c_str() ); 
+		XML_status = load_PhysiCell_config_file( argv[1] );
 	}
 	else
 	{
 		XML_status = load_PhysiCell_config_file( "./config/PhysiCell_settings.xml" );
-		sprintf( copy_command , "cp ./config/PhysiCell_settings.xml %s" , PhysiCell_settings.folder.c_str() ); 
 	}
 	if( !XML_status )
 	{ exit(-1); }
 	
-	// copy config file to output directry 
-	system( copy_command ); 
-	
 	// OpenMP setup
 	omp_set_num_threads(PhysiCell_settings.omp_num_threads);
 	
diff --git a/sample_projects_intracellular/boolean/cancer_invasion/main.cpp b/sample_projects_intracellular/boolean/cancer_invasion/main.cpp
diff --git a/sample_projects_intracellular/boolean/physiboss_cell_lines/main.cpp b/sample_projects_intracellular/boolean/physiboss_cell_lines/main.cpp
diff --git a/sample_projects_intracellular/boolean/template_BM/main.cpp b/sample_projects_intracellular/boolean/template_BM/main.cpp
diff --git a/sample_projects_intracellular/boolean/tutorial/main.cpp b/sample_projects_intracellular/boolean/tutorial/main.cpp
diff --git a/sample_projects_intracellular/fba/cancer_metabolism/main.cpp b/sample_projects_intracellular/fba/cancer_metabolism/main.cpp
diff --git a/unit_tests/custom_DCs_2substrates/main.cpp b/unit_tests/custom_DCs_2substrates/main.cpp
diff --git a/unit_tests/custom_voxel_values/main.cpp b/unit_tests/custom_voxel_values/main.cpp

Original file line number	Diff line number	Diff line change
`@@ -87,24 +87,18 @@ int main( int argc, char* argv[] )`
`87`	`87`	`{`
`88`	`88`	`// load and parse settings file(s)`
`89`	`89`
`90`		`- bool XML_status = false;`
`91`		`- char copy_command [1024];`
	`90`	`+ bool XML_status = false;`
`92`	`91`	`if( argc > 1 )`
`93`	`92`	`{`
`94`		`- XML_status = load_PhysiCell_config_file( argv[1] );`
`95`		`- sprintf( copy_command , "cp %s %s" , argv[1] , PhysiCell_settings.folder.c_str() );`
	`93`	`+ XML_status = load_PhysiCell_config_file( argv[1] );`
`96`	`94`	`}`
`97`	`95`	`else`
`98`	`96`	`{`
`99`	`97`	`XML_status = load_PhysiCell_config_file( "./config/PhysiCell_settings.xml" );`
`100`		`- sprintf( copy_command , "cp ./config/PhysiCell_settings.xml %s" , PhysiCell_settings.folder.c_str() );`
`101`	`98`	`}`
`102`	`99`	`if( !XML_status )`
`103`	`100`	`{ exit(-1); }`
`104`	`101`
`105`		`- // copy config file to output directry`
`106`		`- system( copy_command );`
`107`		`-`
`108`	`102`	`// OpenMP setup`
`109`	`103`	`omp_set_num_threads(PhysiCell_settings.omp_num_threads);`
`110`	`104`