More protections for editing files.

Now check if the lines to be added are already present before adding them. In Makefile and main.cpp, just check if the first line to be added is present and then assume the rest are the same. Warnings are issued if it is found and the rest are being skipped.

Author: drbergman

helpers_for_get_and_add.py

@@ -140,101 +140,126 @@ def update_physicell_files(DIR, project_loaded=False):
     if project_loaded:
         makefile = f'{DIR}/Makefile'
         makefile_temp = append_suffix(f'{DIR}/Makefile-TEMP')
+        add_to_makefile = True
         with open(makefile, 'r') as f:
             lines = f.readlines()
             for line_number, line in enumerate(lines):
-                if "PhysiCell_custom_module_OBJECTS :=" in line:
-                    lines.insert(line_number,"PhysiPKPD_OBJECTS := PhysiPKPD_PK.o PhysiPKPD_PD.o\n\n")
+                if "PhysiPKPD_OBJECTS := PhysiPKPD_PK.o PhysiPKPD_PD.o" in line:
+                    print(f"WARNING: Found PhysiPKPD_OBJECTS already defined in {makefile}. Skipping the rest of Makefile additions.")
+                    print(f"\tIf compilation errors occur, make sure PhysiPKPD_PK.o and PhysiPKPD_PD.o are defined")
+                    print(f"\tAnd make sure that $(PhysiPKPD_OBJECTS) is added to PhysiCell_OBJECTS.")
+                    add_to_makefile = False
                     break
+            if add_to_makefile:
+                for line_number, line in enumerate(lines):
+                    if "PhysiCell_custom_module_OBJECTS :=" in line:
+                        lines.insert(line_number,"PhysiPKPD_OBJECTS := PhysiPKPD_PK.o PhysiPKPD_PD.o\n\n")
+                        break
+        
+        if add_to_makefile:
+            source_file = f'{DIR}/addons/PhysiPKPD/Makefile-PhysiPKPD-Objects.txt'
+            with open(source_file, 'r') as sf:
+                new_lines = sf.readlines()
 
-        source_file = f'{DIR}/addons/PhysiPKPD/Makefile-PhysiPKPD-Objects.txt'
-        with open(source_file, 'r') as sf:
-            new_lines = sf.readlines()
-
-        for line_number, line in enumerate(lines):
-            if "custom_modules/custom.cpp" in line:
-                break
-
-        with open(makefile_temp,'w') as f:
-            for i in range(line_number):
-                print(lines[i].rstrip('\n'), file=f)
-            for new_line in new_lines:
-                print(new_line.rstrip('\n'), file=f)
-            print("\n", file=f)
-            for i in range(i+1,len(lines)):
-                print(lines[i].rstrip('\n'), file=f)
-
-        with open(makefile_temp,'r+') as f:
-            lines = f.readlines()
+            for line_number, line in enumerate(lines):
+                if "custom_modules/custom.cpp" in line:
+                    break
 
-        for i, line in enumerate(lines):
-            if "PhysiCell_OBJECTS :=" in line:
-                line = line.rstrip('\n') + ' $(PhysiPKPD_OBJECTS)\n'
-                break
-        lines[i] = line
+            with open(makefile_temp,'w') as f:
+                for i in range(line_number):
+                    print(lines[i].rstrip('\n'), file=f)
+                for new_line in new_lines:
+                    print(new_line.rstrip('\n'), file=f)
+                print("\n", file=f)
+                for i in range(i+1,len(lines)):
+                    print(lines[i].rstrip('\n'), file=f)
+
+            with open(makefile_temp,'r+') as f:
+                lines = f.readlines()
+
+            for i, line in enumerate(lines):
+                if "PhysiCell_OBJECTS :=" in line:
+                    line = line.rstrip('\n') + ' $(PhysiPKPD_OBJECTS)\n'
+                    break
+            lines[i] = line
 
-        with open(makefile_temp,'w') as f:
-            f.writelines(lines)
+            with open(makefile_temp,'w') as f:
+                f.writelines(lines)
 
-        print(f"{makefile_temp} is ready for PhysiPKPD. Editing other files first before overwriting {makefile}")
+            print(f"{makefile_temp} is ready for PhysiPKPD. Editing other files first before overwriting {makefile}")
 
-        def get_line_number(s, lines):
+        def get_line_number(s, lines, print_missing_message=True):
             for line_number, line in enumerate(lines):
                 if s in line:
                     return line_number
-            print(f"{f.name} does not have a line containing {s}")
+            if print_missing_message:
+                print(f"{f.name} does not have a line containing {s}")
             return None
 
+        add_to_main = True
         main_temp = append_suffix(f'{DIR}/main','.cpp')
         with open(main_file, 'r+') as f:
             lines = f.readlines()
-            line_number = get_line_number("setup_tissue", lines)
-            if line_number is not None:
-                lines.insert(line_number+1, "\n\tsetup_pharmacodynamics();\n")  # new_string should end in a newline
-                with open(main_temp,'w') as f_temp:
-                    f_temp.writelines(lines)  # No need to truncate as we are increasing filesize
+            if get_line_number("setup_pharmacodynamics", lines, print_missing_message=False) is not None:
+                print(f"WARNING: Found setup_pharmacodynamics already defined in {main_file}. Skipping the rest of main.cpp additions.")
+                print(f"\tIf errors occur, make sure PK_model(PhysiCell_globals.current_time); and PD_model(PhysiCell_globals.current_time); are on either side of microenvironment.simulate_diffusion_decay.")
+                add_to_main = False
             else:
-                print(f"{DIR}/main.cpp does not include `setup_tissue();`???")
-                exit()
+                line_number = get_line_number("setup_tissue", lines)
+                if line_number is not None:
+                    lines.insert(line_number+1, "\n\tsetup_pharmacodynamics();\n")  # new_string should end in a newline
+                    with open(main_temp,'w') as f_temp:
+                        f_temp.writelines(lines)  # No need to truncate as we are increasing filesize
+                else:
+                    print(f"{DIR}/main.cpp does not include `setup_tissue();`???")
+                    exit()
 
-        with open(main_temp, 'r+') as f:
-            lines = f.readlines()
-            line_number = get_line_number("microenvironment.simulate_diffusion_decay", lines)
-            if line_number is not None:
-                lines.insert(line_number+1, "\n\t\t\tPD_model( PhysiCell_globals.current_time );\n")  # new_string should end in a newline
-                lines.insert(line_number, "\t\t\tPK_model( PhysiCell_globals.current_time );\n\n")  # new_string should end in a newline
-                f.seek(0)  # readlines consumes the iterator, so we need to start over
-                f.writelines(lines)  # No need to truncate as we are increasing filesize
-            else:
-                print(f"{DIR}/main.cpp does not include `microenvironment.simulate_diffusion_decay(diffusion_dt);`???")
-                exit()
-
-        print(f"{main_temp} is ready for PhysiPKPD. Editing other files first before overwriting {main_file}")
+        if add_to_main:
+            with open(main_temp, 'r+') as f:
+                lines = f.readlines()
+                line_number = get_line_number("microenvironment.simulate_diffusion_decay", lines)
+                if line_number is not None:
+                    lines.insert(line_number+1, "\n\t\t\tPD_model( PhysiCell_globals.current_time );\n")  # new_string should end in a newline
+                    lines.insert(line_number, "\t\t\tPK_model( PhysiCell_globals.current_time );\n\n")  # new_string should end in a newline
+                    f.seek(0)  # readlines consumes the iterator, so we need to start over
+                    f.writelines(lines)  # No need to truncate as we are increasing filesize
+                else:
+                    print(f"{DIR}/main.cpp does not include `microenvironment.simulate_diffusion_decay(diffusion_dt);`???")
+                    exit()
+
+            print(f"{main_temp} is ready for PhysiPKPD. Editing other files first before overwriting {main_file}")
 
         with open(f"{DIR}/custom_modules/custom.h", "r+") as f:
             lines = f.readlines()
-            line_number = get_line_number("#include", lines)
-            if line_number is not None:
-                lines.insert(line_number,'#include "../addons/PhysiPKPD/src/PhysiPKPD.h"\n')
-                f.seek(0)
-                f.writelines(lines)
+            if get_line_number("addons/PhysiPKPD/src/PhysiPKPD.h", lines, print_missing_message=False):
+                print("Found addons/PhysiPKPD/src/PhysiPKPD.h in {DIR}/custom_modules/custom.h. Not going to add it again here.")
             else:
-                print(f"{DIR}/custom_modules/custom.h does not have any `#include` statements???")
-                exit()
-
-        with open(makefile, 'w') as f:
-            with open(makefile_temp, 'r') as f_temp:
-                lines = f_temp.readlines()
-                f.writelines(lines)
-
-        with open(main_file, 'w') as f:
-            with open(main_temp, 'r') as f_temp:
-                lines = f_temp.readlines()
-                f.writelines(lines)
+                line_number = get_line_number("#include", lines)
+                if line_number is not None:
+                    lines.insert(line_number,'#include "../addons/PhysiPKPD/src/PhysiPKPD.h"\n')
+                    f.seek(0)
+                    f.writelines(lines)
+                else:
+                    print(f"{DIR}/custom_modules/custom.h does not have any `#include` statements???")
+                    exit()
+
+        if add_to_makefile:
+            with open(makefile, 'w') as f:
+                with open(makefile_temp, 'r') as f_temp:
+                    lines = f_temp.readlines()
+                    f.writelines(lines)
+
+        if add_to_main:
+            with open(main_file, 'w') as f:
+                with open(main_temp, 'r') as f_temp:
+                    lines = f_temp.readlines()
+                    f.writelines(lines)
 
         print(f"All files (Makefile, main.cpp, and custom_modules/custom.h) updated and overwritten now. Removing temporary files...")
-        os.remove(makefile_temp)
-        os.remove(main_temp)
+        if os.path.exists(makefile):
+            os.remove(makefile_temp)
+        if os.path.exists(main_temp):
+            os.remove(main_temp)
     else:
         with open(f'{DIR}/addons/PhysiPKPD/Makefile-PhysiPKPD-Samples.txt', "r") as f:
             add_samples_to_makefile(f, f"{DIR}/Makefile")