make output folder if it does not exist

.github/workflows/tests.yml

@@ -18,22 +18,23 @@ jobs:
           {name: "Windows", os: "windows-latest", shell: "msys2", compiler: "g++"},
         ]
         projects: [
-          {project: "template", name: "PhysiCell Template", binary: "project", max_time: 120, config: "config/PhysiCell_settings.xml", output_folder: "output"},
-          {project: "template_BM", name: "PhysiBoSS Template", binary: "project", max_time: 120, config: "config/PhysiCell_settings.xml", output_folder: "output"},
-          {project: "physiboss-cell-lines-sample", name: "PhysiBoSS Cell Lines", binary: "PhysiBoSS_Cell_Lines", max_time: 120, config: "config/PhysiCell_settings.xml", output_folder: "output"},
-          {project: "physimess-sample", name: "PhysiMeSS Sample", binary: "project", config: "config/Fibre_Degradation/mymodel_matrix_degradation.xml", max_time: 120, output_folder: ""},
-          {project: "physiboss-tutorial", name: "PhysiBoSS Tutorial", binary: "project", config: "config/cell_cycle/PhysiCell_settings.xml", max_time: 300, output_folder: "output"},
-          {project: "worm-sample", name: "PhysiCell worm", binary: "worm", config: "config/PhysiCell_settings.xml", max_time: 120, output_folder: "output"},
-          {project: "virus-macrophage-sample", name: "Virus Macrophage", binary: "virus-sample", config: "config/PhysiCell_settings.xml", max_time: 120, output_folder: "output"},
-          {project: "mechano-sample", name: "PhysiCell Mechano", binary: "project", config: "config/PhysiCell_settings.xml", max_time: 120, output_folder: "output"},
-          {project: "cancer-biorobots-sample", name: "PhysiCell Cancer Biorobots", binary: "cancer_biorobots", config: "config/PhysiCell_settings.xml", max_time: 120, output_folder: ""},
-          {project: "biorobots-sample", name: "PhysiCell Biorobots", binary: "biorobots", config: "config/PhysiCell_settings.xml", max_time: 120, output_folder: ""},
-          {project: "celltypes3-sample", name: "PhysiCell Celltypes3", binary: "celltypes3", config: "config/PhysiCell_settings.xml", max_time: 120, output_folder: ""},
-          {project: "custom-division-sample", name: "PhysiCell custom division", binary: "project", config: "config/PhysiCell_settings.xml", max_time: 120, output_folder: ""},
-          {project: "interaction-sample", name: "PhysiCell interactions", binary: "interaction_demo", config: "config/PhysiCell_settings.xml", max_time: 120, output_folder: ""},
-          {project: "pred-prey-farmer", name: "PhysiCell prey predator", binary: "pred_prey", config: "config/PhysiCell_settings.xml", max_time: 120, output_folder: ""},
-          {project: "rules-sample", name: "PhysiCell rules sample", binary: "rules_sample", config: "config/PhysiCell_settings.xml", max_time: 120, output_folder: ""},
-          {project: "asymmetric-division-sample", name: "PhysiCell asymmetric division", binary: "project", config: "config/PhysiCell_settings.xml", max_time: 120, output_folder: ""}
+          {project: "template", name: "PhysiCell Template", binary: "project", max_time: 120, config: "config/PhysiCell_settings.xml", compare_svgs: true, output_folder: "output"},
+          {project: "template_BM", name: "PhysiBoSS Template", binary: "project", max_time: 120, config: "config/PhysiCell_settings.xml", compare_svgs: true, output_folder: "output"},
+          {project: "physiboss-cell-lines-sample", name: "PhysiBoSS Cell Lines", binary: "PhysiBoSS_Cell_Lines", max_time: 120, config: "config/PhysiCell_settings.xml", compare_svgs: true, output_folder: "output"},
+          {project: "physimess-sample", name: "PhysiMeSS Sample", binary: "project", config: "config/Fibre_Degradation/mymodel_matrix_degradation.xml", max_time: 120, compare_svgs: false, output_folder: "output"},
+          {project: "physiboss-tutorial", name: "PhysiBoSS Tutorial", binary: "project", config: "config/cell_cycle/PhysiCell_settings.xml", max_time: 300, compare_svgs: true, output_folder: "output"},
+          {project: "worm-sample", name: "PhysiCell worm", binary: "worm", config: "config/PhysiCell_settings.xml", max_time: 120, compare_svgs: true, output_folder: "output"},
+          {project: "virus-macrophage-sample", name: "Virus Macrophage", binary: "virus-sample", config: "config/PhysiCell_settings.xml", max_time: 120, compare_svgs: true, output_folder: "output"},
+          {project: "mechano-sample", name: "PhysiCell Mechano", binary: "project", config: "config/PhysiCell_settings.xml", max_time: 120, compare_svgs: true, output_folder: "output"},
+          {project: "cancer-biorobots-sample", name: "PhysiCell Cancer Biorobots", binary: "cancer_biorobots", config: "config/PhysiCell_settings.xml", max_time: 120, compare_svgs: false, output_folder: "output"},
+          {project: "biorobots-sample", name: "PhysiCell Biorobots", binary: "biorobots", config: "config/PhysiCell_settings.xml", max_time: 120, compare_svgs: false, output_folder: "output"},
+          {project: "celltypes3-sample", name: "PhysiCell Celltypes3", binary: "celltypes3", config: "config/PhysiCell_settings.xml", max_time: 120, compare_svgs: false, output_folder: "output"},
+          {project: "custom-division-sample", name: "PhysiCell custom division", binary: "project", config: "config/PhysiCell_settings.xml", max_time: 120, compare_svgs: false, output_folder: "output"},
+          {project: "interaction-sample", name: "PhysiCell interactions", binary: "interaction_demo", config: "config/PhysiCell_settings.xml", max_time: 120, compare_svgs: false, output_folder: "output"},
+          {project: "pred-prey-farmer", name: "PhysiCell prey predator", binary: "pred_prey", config: "config/PhysiCell_settings.xml", max_time: 120, compare_svgs: false, output_folder: "output"},
+          {project: "template", name: "PhysiCell Template - make output folder", binary: "project", config: "config/PhysiCell_settings.xml", max_time: 120, compare_svgs: false, "output_folder": "test/create/output/folder"},
+          {project: "rules-sample", name: "PhysiCell rules sample", binary: "rules_sample", config: "config/PhysiCell_settings.xml", max_time: 120, compare_svgs: false, output_folder: "output"},
+          {project: "asymmetric-division-sample", name: "PhysiCell asymmetric division", binary: "project", config: "config/PhysiCell_settings.xml", max_time: 120, compare_svgs: false, output_folder: "output"}
         ]
 
     name: Testing ${{ matrix.projects.name }} on ${{ matrix.os.name }}
@@ -59,9 +60,9 @@ jobs:
 
     - name: Run ${{ matrix.projects.name }} project
       run: |
-        python beta/test_run_sample.py ${{ matrix.projects.binary }} ${{ matrix.projects.config }} ${{ matrix.projects.max_time }}
+        python beta/test_run_sample.py ${{ matrix.projects.binary }} ${{ matrix.projects.config }} ${{ matrix.projects.max_time }} ${{ matrix.projects.output_folder }}
 
     - name: Check ${{ matrix.projects.name }} project simulation results
-      if: matrix.projects.output_folder != ''
+      if: matrix.projects.compare_svgs
       run: |
-        python beta/test_diff_svg.py ${{ matrix.projects.output_folder }} tests/cases/output_${{ matrix.projects.project }}
+        python beta/test_diff_svg.py output tests/cases/output_${{ matrix.projects.project }}

beta/test_run_sample.py

@@ -29,7 +29,12 @@ def disable_automated_spring_adhesions(root):
     if spring_adhesion is not None:
         spring_adhesion.text = "true"
 
-def run_sample(myexec, xml_file, max_time):
+def set_output_folder(root, folder):
+    if folder == "":
+        return
+    root.find(".//save//folder").text = folder
+
+def run_sample(myexec, xml_file, max_time, output_folder):
 
     print("\n\n------------   ",myexec, "   ----------------------------------")
     # update max_time and omp_num_threads (=1)
@@ -42,6 +47,7 @@ def run_sample(myexec, xml_file, max_time):
     make_deathmodel_deterministic(root)
     make_chemotaxis_deterministic(root)   
     disable_automated_spring_adhesions(root)
+    set_output_folder(root, output_folder)
 
     tree.write(xml_file)
     subprocess.run(["cat", xml_file])

modules/PhysiCell_settings.cpp

@@ -65,6 +65,7 @@
 ###############################################################################
 */
 
+#include <sys/stat.h>
 #include "./PhysiCell_settings.h"
 
 using namespace BioFVM; 
@@ -108,6 +109,8 @@ bool load_PhysiCell_config_file( std::string filename )
 
 	parameters.read_from_pugixml( physicell_config_root ); 
 
+	create_output_directory( PhysiCell_settings.folder );
+
 	return true; 	
 }
 
@@ -320,6 +323,45 @@ void PhysiCell_Settings::read_from_pugixml( void )
 	return; 
 }
 
+bool create_directories(const std::string &path)
+{
+	std::vector<std::string> directories;
+	size_t pos = 0;
+    std::string currentPath;
+
+    while ((pos = path.find_first_of("/\\", pos)) != std::string::npos) {
+        currentPath = path.substr(0, pos++);
+        if (!create_directory(currentPath)) {
+            return false;
+        }
+    }
+    return create_directory(path);
+}
+
+bool create_directory(const std::string &path)
+{
+#if defined(__MINGW32__) || defined(__MINGW64__)
+	bool success = mkdir(path.c_str()) == 0;
+#else
+	bool success = mkdir(path.c_str(), 0755) == 0;
+#endif
+	return success || errno == EEXIST;
+}
+
+void create_output_directory(const std::string& path)
+{
+	if (!create_directories(path))
+	{
+		std::cout << "ERROR: Could not create output directory " << path << " ! Quitting." << std::endl;
+		exit(-1);
+	}
+}
+
+void create_output_directory(void)
+{
+	create_output_directory(PhysiCell_settings.folder);
+}
+
 PhysiCell_Globals PhysiCell_globals; 
 
 /* parameters functions */ 

modules/PhysiCell_settings.h

@@ -137,6 +137,12 @@ class PhysiCell_Settings
 	void read_from_pugixml( void ); 
 };
 
+bool create_directories(const std::string &path);
+bool create_directory(const std::string &path);
+
+void create_output_directory(const std::string& path);
+void create_output_directory(void);
+
 class PhysiCell_Globals
 {
  private:

sample_projects/cancer_biorobots/main.cpp

@@ -101,7 +101,7 @@ int main( int argc, char* argv[] )
 	}
 	if( !XML_status )
 	{ exit(-1); }
-
+		
 	// copy config file to output directry 
 	system( copy_command ); 
 

sample_projects/cancer_immune/main-cancer_immune_3D.cpp

@@ -101,7 +101,7 @@ int main( int argc, char* argv[] )
 	}
 	if( !XML_status )
 	{ exit(-1); }
-
+		
 	// copy config file to output directry 
 	system( copy_command ); 
 

sample_projects/heterogeneity/main.cpp

@@ -101,7 +101,7 @@ int main( int argc, char* argv[] )
 	}
 	if( !XML_status )
 	{ exit(-1); }
-
+		
 	// copy config file to output directry 
 	system( copy_command ); 
 

sample_projects/interactions/main.cpp

@@ -101,7 +101,7 @@ int main( int argc, char* argv[] )
 	}
 	if( !XML_status )
 	{ exit(-1); }
-
+		
 	// copy config file to output directry 
 	system( copy_command ); 
 

sample_projects/mechano/main.cpp

@@ -101,7 +101,7 @@ int main( int argc, char* argv[] )
 	}
 	if( !XML_status )
 	{ exit(-1); }
-
+		
 	// copy config file to output directry 
 	system( copy_command ); 
 

sample_projects/pred_prey_farmer/main.cpp

@@ -101,7 +101,7 @@ int main( int argc, char* argv[] )
 	}
 	if( !XML_status )
 	{ exit(-1); }
-
+		
 	// copy config file to output directry 
 	system( copy_command ); 
 

sample_projects/rules_sample/main.cpp

@@ -101,7 +101,7 @@ int main( int argc, char* argv[] )
 	}
 	if( !XML_status )
 	{ exit(-1); }
-
+		
 	// copy config file to output directry 
 	system( copy_command ); 
 

sample_projects/template/main.cpp

@@ -101,7 +101,7 @@ int main( int argc, char* argv[] )
 	}
 	if( !XML_status )
 	{ exit(-1); }
-
+		
 	// copy config file to output directry 
 	system( copy_command ); 
 

sample_projects/virus_macrophage/main.cpp

@@ -101,7 +101,7 @@ int main( int argc, char* argv[] )
 	}
 	if( !XML_status )
 	{ exit(-1); }
-
+		
 	// copy config file to output directry 
 	system( copy_command ); 
 

sample_projects/worm/main.cpp

@@ -101,7 +101,7 @@ int main( int argc, char* argv[] )
 	}
 	if( !XML_status )
 	{ exit(-1); }
-
+		
 	// copy config file to output directry 
 	system( copy_command ); 
 

sample_projects_intracellular/boolean/cancer_invasion/main.cpp

@@ -104,7 +104,7 @@ int main( int argc, char* argv[] )
 	}
 	if( !XML_status )
 	{ exit(-1); }
-
+		
 	// copy config file to output directry 
 	system( copy_command ); 
 

sample_projects_intracellular/boolean/physiboss_cell_lines/main.cpp

@@ -101,7 +101,7 @@ int main( int argc, char* argv[] )
 	}
 	if( !XML_status )
 	{ exit(-1); }
-
+		
 	// copy config file to output directry 
 	system( copy_command ); 
 

sample_projects_intracellular/boolean/template_BM/main.cpp

@@ -102,7 +102,7 @@ int main( int argc, char* argv[] )
 	}
 	if( !XML_status )
 	{ exit(-1); }
-
+		
 	// copy config file to output directry 
 	system( copy_command ); 
 

sample_projects_intracellular/boolean/tutorial/main.cpp

@@ -104,7 +104,7 @@ int main( int argc, char* argv[] )
 	}
 	if( !XML_status )
 	{ exit(-1); }
-
+		
 	// copy config file to output directry 
 	system( copy_command ); 
 

sample_projects_intracellular/fba/cancer_metabolism/main.cpp

@@ -101,7 +101,7 @@ int main( int argc, char* argv[] )
 	}
 	if( !XML_status )
 	{ exit(-1); }
-
+		
 	// copy config file to output directry 
 	system( copy_command ); 
 

unit_tests/custom_DCs_2substrates/main.cpp

@@ -101,7 +101,7 @@ int main( int argc, char* argv[] )
 	}
 	if( !XML_status )
 	{ exit(-1); }
-
+		
 	// copy config file to output directry 
 	system( copy_command ); 
 

unit_tests/custom_voxel_values/main.cpp

@@ -101,7 +101,7 @@ int main( int argc, char* argv[] )
 	}
 	if( !XML_status )
 	{ exit(-1); }
-
+		
 	// copy config file to output directry 
 	system( copy_command );