copy files with default name to output as well

- default names:
  - config: PhysiCell_settings.xml
  - rules: cell_rules.csv
  - ic cells: cells.csv
  - ic substrates: substrates.csv or substrates.mat

Author: drbergman

core/PhysiCell_rules.cpp

@@ -1934,8 +1934,10 @@ void parse_rules_from_pugixml( void )
 			if( done == false )
 			{ std::cout << "\tWarning: Ruleset had unknown format (" << format << "). Skipping!" << std::endl; }
 			else
-			{ copy_file_to_output( input_filename ); }
-
+			{
+				std::string default_basename = "cell_rules.csv";
+				copy_file_to_output(input_filename, default_basename);
+			}
 		}
 		else
 		{ std::cout << "\tRuleset disabled ... " << std::endl; }

core/PhysiCell_utilities.cpp

@@ -365,7 +365,7 @@ int choose_event( std::vector<double>& probabilities )
 	return probabilities.size(); 
 }
 
-void copy_file_to_output(std::string filename)
+void copy_file_to_output(const std::string &filename, const std::string &default_basename)
 {
 	std::cout << "Copying " << filename << " to output folder." << std::endl;
 	// copy the file to the output folder
@@ -381,8 +381,17 @@ void copy_file_to_output(std::string filename)
 	// copy filename to output_filename
 	char copy_command[1024];
 	sprintf(copy_command, "cp %s %s", filename.c_str(), output_filename.c_str());
-	std::cout << "Copy command: " << copy_command << std::endl;
 	(void)system(copy_command); // make it explicit that we are ignoring the return value
+
+	if (default_basename.empty() || default_basename == basename) {
+		return;
+	}
+
+	// copy the file to the output folder with the default basename
+	std::string default_output_filename = PhysiCell_settings.folder + "/" + default_basename;
+	sprintf(copy_command, "cp %s %s", filename.c_str(), default_output_filename.c_str());
+	(void)system(copy_command); // make it explicit that we are ignoring the return value
+	return;
 }
 
 };

core/PhysiCell_utilities.h

@@ -111,7 +111,7 @@ void add_software_citation( std::string name , std::string version, std::string
 
 int choose_event( std::vector<double>& probabilities ); 
 
-void copy_file_to_output( std::string filename );
+void copy_file_to_output(const std::string &filename, const std::string &default_basename = "");
 };
 
 #endif

modules/PhysiCell_geometry.cpp

@@ -395,7 +395,8 @@ bool load_cells_from_pugixml( pugi::xml_node root )
 		exit(-1);
 	}
 
-	copy_file_to_output(input_filename);
+	std::string default_basename = "cells.csv";
+	copy_file_to_output(input_filename, default_basename);
 	return true; 
 }
 

modules/PhysiCell_settings.cpp

@@ -119,7 +119,8 @@ bool load_PhysiCell_config_file( std::string filename )
 
 	create_output_directory( PhysiCell_settings.folder );
 
-	copy_file_to_output( filename );
+	std::string default_basename = "PhysiCell_settings.xml";
+	copy_file_to_output( filename, default_basename ); // copy the settings file to the output folder
 
 	return true;
 }
@@ -963,7 +964,8 @@ bool setup_microenvironment_from_XML( pugi::xml_node root_node )
 			default_microenvironment_options.initial_condition_file_type = node.attribute("type").as_string();
 			default_microenvironment_options.initial_condition_file = xml_get_string_value(node, "filename");
 
-			copy_file_to_output(default_microenvironment_options.initial_condition_file);
+			std::string default_basename = default_microenvironment_options.initial_condition_file_type == "matlab" ? "substrates.mat" : "substrates.csv"; // when loading the file, we check that it is one of these two types
+			copy_file_to_output(default_microenvironment_options.initial_condition_file, default_basename);
 		}
 	}