3350 tool to automatically convert obsolete variables from input file

process/main.py

@@ -197,6 +197,11 @@ def parse_args(self, args):
             action="store_true",
             help="Print the version of PROCESS to the terminal",
         )
+        parser.add_argument(
+            "--update-obsolete",
+            action="store_true",
+            help="Automatically update obsolete variables in the IN.DAT file",
+        )
 
         # If args is not None, then parse the supplied arguments. This is likely
         # to come from the test suite when testing command-line arguments; the
@@ -215,7 +220,11 @@ def run_mode(self):
         if self.args.varyiterparams:
             self.run = VaryRun(self.args.varyiterparamsconfig, self.args.solver)
         else:
-            self.run = SingleRun(self.args.input, self.args.solver)
+            self.run = SingleRun(
+                self.args.input,
+                self.args.solver,
+                update_obsolete=self.args.update_obsolete,
+            )
         self.run.run()
 
     def post_process(self):
@@ -355,17 +364,16 @@ def run(self):
 class SingleRun:
     """Perform a single run of PROCESS."""
 
-    def __init__(self, input_file, solver="vmcon"):
+    def __init__(self, input_file, solver="vmcon", *, update_obsolete=False):
         """Read input file and initialise variables.
-
         :param input_file: input file named <optional_name>IN.DAT
         :type input_file: str
         :param solver: which solver to use, as specified in solver.py
         :type solver: str, optional
         """
         self.input_file = input_file
 
-        self.validate_input()
+        self.validate_input(update_obsolete)
         self.init_module_vars()
         self.set_filenames()
         self.initialise()
@@ -524,49 +532,103 @@ def append_input(self):
             mfile_file.write("***********************************************")
             mfile_file.writelines(input_lines)
 
-    def validate_input(self):
-        """Checks the input IN.DAT file for any obsolete variables in the OBS_VARS dict contained
-        within obsolete_variables.py.
-        Then will print out what the used obsolete variables are (if any) before continuing the proces run.
+    def validate_input(self, replace_obsolete=False):
+        """
+        Checks the input IN.DAT file for any obsolete variables in the OBS_VARS dict contained
+        within obsolete_variables.py. If obsolete variables are found, and if `replace_obsolete`
+        is set to True, they are either removed or replaced by their updated names as specified
+        in the OBS_VARS dictionary.
+
+        Parameters:
+            replace_obsolete (bool): If True, modifies the IN.DAT file to replace or comment out
+                                    obsolete variables. If False, only reports obsolete variables.
         """
 
         obsolete_variables = ov.OBS_VARS
         obsolete_vars_help_message = ov.OBS_VARS_HELP
 
         filename = self.input_file
-
         variables_in_in_dat = []
+        modified_lines = []
+        changes_made = []  # To store details of the changes
+
         with open(filename, "r") as file:
             for line in file:
-                if line[0] == "*" or "=" not in line:
+                # Skip comment lines or lines without an assignment
+                if line.startswith("*") or "=" not in line:
+                    modified_lines.append(line)
                     continue
 
+                # Extract the variable name before the separator
+                variable_name = line.split("=", 1)[0].strip()
+                variables_in_in_dat.append(variable_name)
+
+                # Check if the variable is obsolete and needs replacing
+                if variable_name in obsolete_variables:
+                    replacement = obsolete_variables.get(variable_name)
+
+                    if replace_obsolete:
+                        # Prepare replacement or removal
+                        if replacement is None:
+                            # If no replacement is defined, comment out the line
+                            modified_lines.append(f"* Obsolete: {line}")
+                            changes_made.append(
+                                f"Commented out obsolete variable: {variable_name}"
+                            )
+                        else:
+                            if isinstance(replacement, list):
+                                # Raise an error if replacement is a list
+                                replacement_str = ", ".join(replacement)
+                                raise ValueError(
+                                    f"The variable '{variable_name}' is obsolete and should be replaced by the following variables: {replacement_str}. "
+                                    "Please set their values accordingly."
+                                )
+                            else:
+                                # Replace obsolete variable with updated variable
+                                modified_line = line.replace(
+                                    variable_name, replacement, 1
+                                )
+                                modified_lines.append(
+                                    f"* Replaced '{variable_name}' with '{replacement}'\n{modified_line}"
+                                )
+                                changes_made.append(
+                                    f"Replaced '{variable_name}' with '{replacement}'"
+                                )
+                    else:
+                        # If replacement is False, add the line as-is
+                        modified_lines.append(line)
                 else:
-                    sep = " "
-                    variables = line.strip().split(sep, 1)[0]
-                    variables_in_in_dat.append(variables)
-
-        obs_vars_in_in_dat = []
-        replace_hints = {}
-        for var in variables_in_in_dat:
-            if var in obsolete_variables:
-                obs_vars_in_in_dat.append(var)
-                replace_hints[var] = obsolete_variables.get(var)
-
-        if len(obs_vars_in_in_dat) > 0:
-            message = (
-                "The IN.DAT file contains obsolete variables from the OBS_VARS dictionary. The obsolete variables in your IN.DAT file are: "
-                f"{obs_vars_in_in_dat}. "
-                "Either remove these or replace them with their updated variable names. "
-            )
-            for obs_var in obs_vars_in_in_dat:
-                if replace_hints[obs_var] is None:
-                    message += f"\n\n {obs_var} is an obsolete variable and needs to be removed. "
-                else:
-                    message += f"\n \n {obs_var} is an obsolete variable and needs to be replaced by {str(replace_hints[obs_var])}. "
-                message += f"{obsolete_vars_help_message.get(obs_var, '')}"
-
-            raise ValueError(message)
+                    modified_lines.append(line)
+
+        obs_vars_in_in_dat = [
+            var for var in variables_in_in_dat if var in obsolete_variables
+        ]
+        if obs_vars_in_in_dat:
+            if replace_obsolete:
+                # If replace_obsolete is True, write the modified content to the file
+                with open(filename, "w") as file:
+                    file.writelines(modified_lines)
+                print(
+                    "The IN.DAT file has been updated to replace or comment out obsolete variables."
+                )
+                print("Summary of changes made:")
+                for change in changes_made:
+                    print(f" - {change}")
+            else:
+                # Only print the report if replace_obsolete is False
+                message = (
+                    "The IN.DAT file contains obsolete variables from the OBS_VARS dictionary. "
+                    f"The obsolete variables in your IN.DAT file are: {obs_vars_in_in_dat}. "
+                    "Either remove these or replace them with their updated variable names. "
+                )
+                for obs_var in obs_vars_in_in_dat:
+                    replacement = obsolete_variables.get(obs_var)
+                    if replacement is None:
+                        message += f"\n\n{obs_var} is an obsolete variable and needs to be removed."
+                    else:
+                        message += f"\n\n{obs_var} is an obsolete variable and needs to be replaced by {replacement}."
+                    message += f" {obsolete_vars_help_message.get(obs_var, '')}"
+                raise ValueError(message)
 
         else:
             print("The IN.DAT file does not contain any obsolete variables.")

tests/unit/test_main.py

@@ -102,6 +102,8 @@ def test_run_mode(process_obj, monkeypatch):
     monkeypatch.setattr(process_obj, "args", argparse.Namespace(), raising=False)
     monkeypatch.setattr(process_obj.args, "varyiterparams", True, raising=False)
     monkeypatch.setattr(process_obj.args, "version", False, raising=False)
+    monkeypatch.setattr(process_obj.args, "update_obsolete", False, raising=False)
+
     monkeypatch.setattr(
         process_obj.args, "varyiterparamsconfig", "file.conf", raising=False
     )