Skip to content

standardize file copy to output #372

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
drbergman wants to merge 3 commits into
base: development
Choose a base branch
from
Open

standardize file copy to output #372

Show file tree
Hide file tree
Changes from 2 commits
Commits
Show all changes
3 commits
Select commit Hold shift + click to select a range
0c7b54b
copy config to output now part of core
drbergman Apr 29, 2025
ae0c2b7
copy files with default name to output as well
drbergman Apr 29, 2025
6a1895f
add error handling for file copy command in copy_file_to_output
drbergman Aug 20, 2026
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
6 changes: 4 additions & 2 deletions core/PhysiCell_rules.cpp
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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; }
Expand Down
13 changes: 11 additions & 2 deletions core/PhysiCell_utilities.cpp
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand All @@ -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());
Comment thread
drbergman marked this conversation as resolved.
(void)system(copy_command); // make it explicit that we are ignoring the return value
Comment thread
drbergman marked this conversation as resolved.
Outdated
return;
}

};
2 changes: 1 addition & 1 deletion core/PhysiCell_utilities.h
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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
3 changes: 2 additions & 1 deletion modules/PhysiCell_geometry.cpp
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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;
}

Expand Down
12 changes: 8 additions & 4 deletions modules/PhysiCell_settings.cpp
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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 ) )
{
Expand All @@ -119,7 +119,10 @@ bool load_PhysiCell_config_file( std::string filename )

create_output_directory( PhysiCell_settings.folder );

return true;
std::string default_basename = "PhysiCell_settings.xml";
copy_file_to_output( filename, default_basename ); // copy the settings file to the output folder

return true;
}

PhysiCell_Settings::PhysiCell_Settings()
Expand Down Expand Up @@ -961,7 +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);
}
}

Expand Down
10 changes: 2 additions & 8 deletions sample_projects/asymmetric_division/main.cpp
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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);

Expand Down
10 changes: 2 additions & 8 deletions sample_projects/biorobots/main.cpp
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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);

Expand Down
10 changes: 2 additions & 8 deletions sample_projects/cancer_biorobots/main.cpp
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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);

Expand Down
6 changes: 0 additions & 6 deletions sample_projects/cancer_immune/main-cancer_immune_3D.cpp
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -88,23 +88,17 @@ int main( int argc, char* argv[] )
// load and parse settings file(s)

bool XML_status = false;
char copy_command [1024];
if( argc > 1 )
{
XML_status = load_PhysiCell_config_file( argv[1] );
sprintf( copy_command , "cp %s %s" , argv[1] , PhysiCell_settings.folder.c_str() );
}
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);

Expand Down
10 changes: 2 additions & 8 deletions sample_projects/custom_division/main.cpp
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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);

Expand Down
10 changes: 2 additions & 8 deletions sample_projects/heterogeneity/main.cpp
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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);

Expand Down
10 changes: 2 additions & 8 deletions sample_projects/immune_function/main.cpp
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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);

Expand Down
10 changes: 2 additions & 8 deletions sample_projects/interactions/main.cpp
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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);

Expand Down
10 changes: 2 additions & 8 deletions sample_projects/mechano/main.cpp
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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);

Expand Down
10 changes: 2 additions & 8 deletions sample_projects/physimess/main.cpp
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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);

Expand Down
10 changes: 2 additions & 8 deletions sample_projects/pred_prey_farmer/main.cpp
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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);

Expand Down
Loading