Add force_overwrite_tools flag

expts_manager/Expts_manager.py

@@ -82,6 +82,7 @@ class Expts_manager(object):
 
     def __init__(
         self,
+        force_overwrite_tools: bool = False,
         MOM_prefix: str = "MOM_list",
         CONFIG_prefix: str = "config_list",
         runconfig_suffix1: str = "_attributes",
@@ -93,6 +94,7 @@ def __init__(
     ):
 
         self.dir_manager = self.DIR_MANAGER
+        self.force_overwrite_tools = force_overwrite_tools
         self.MOM_prefix = MOM_prefix
         self.CONFIG_prefix = CONFIG_prefix
         self.runconfig_suffix1 = runconfig_suffix1
@@ -127,6 +129,7 @@ def load_variables(self, yamlfile):
         self.indata = self._read_ryaml(yamlfile)
 
         self.model = self.indata["model"]
+        self.force_overwrite_tools = self.indata.get("force_overwrite_tools", False)
         self.utils_url = self.indata.get("utils_url", None)
         self.utils_dir_name = self.indata.get("utils_dir_name", None)
         self.utils_branch_name = self.indata.get("utils_branch_name", None)
@@ -183,18 +186,23 @@ def load_tools(self):
         """
         Loads external tools required for the experiments.
         """
-
         # currently import from a fork: https://github.com/minghangli-uni/om3-utils
         # will update the tool when it is merged to COSIMA/om3-utils
-        def _clone_repo(branch_name, url, path, tool_name):
-            if not os.path.isdir(path):
-                command = (
-                    f"git clone --branch {branch_name} {url} {path} --single-branch"
-                )
-                subprocess.run(command, shell=True, check=True)
-                print(f"Cloning {tool_name} for use!")
+        def _clone_repo(branch_name, url, path, tool_name, force_overwrite_tools):
+            if os.path.exists(path) and os.path.isdir(path):
+                if force_overwrite_tools:
+                    print(f"-- Force_overwrite_tools is activated, hence removing existing {tool_name}: {path}")
+                    shutil.rmtree(path)
+                    print(f"Cloning {tool_name} for use!")
+                    command = (f"git clone --branch {branch_name} {url} {path} --single-branch")
+                    subprocess.run(command, shell=True, check=True)
+                else:
+                    print(f"{tool_name} already exists, hence skips cloning!")
             else:
-                print(f"{path} already exists!")
+                print(f"Cloning {tool_name} for use!")
+                command = (f"git clone --branch {branch_name} {url} {path} --single-branch")
+                subprocess.run(command, shell=True, check=True)
+            print(f"Finished cloning {tool_name}!")
 
         # om3-utils is a must for om3 but not required for access-om2.
         utils_path = (
@@ -214,7 +222,7 @@ def _clone_repo(branch_name, url, path, tool_name):
 
         if self.model == "access-om3":
             _clone_repo(
-                self.utils_branch_name, self.utils_url, utils_path, self.utils_dir_name
+                self.utils_branch_name, self.utils_url, utils_path, self.utils_dir_name, self.force_overwrite_tools
             )
 
         # make_diag_table is [optional]
@@ -226,7 +234,7 @@ def _clone_repo(branch_name, url, path, tool_name):
 
         if self.diag_path is not None:
             _clone_repo(
-                self.diag_branch_name, self.diag_url, self.diag_path, self.diag_dir_name
+                self.diag_branch_name, self.diag_url, self.diag_path, self.diag_dir_name, self.force_overwrite_tools
             )
             sys.path.extend([utils_path, self.diag_path])
         else:

expts_manager/Expts_manager.yaml

@@ -17,6 +17,7 @@ model: access-om3  # Specify the model to be used. Options: 'access-om2', 'acces
 # 1. Parse parameters and comments from `MOM_input` in MOM6.
 # 2. Read and write the `nuopc.runconfig` file.
 
+force_overwrite_tools: False
 utils_url: git@github.com:minghangli-uni/om3-utils.git  # Git URL for the utility tool repository
 utils_branch_name: main  # The branch for which the utility tool will be checked out
 utils_dir_name: om3-utils  # Directory name for the utility tool (user-defined)

expts_manager/write_Expts_manager_yaml.py

@@ -87,6 +87,10 @@ def write_value(key, value, file, comment=None, indent=0):
 # 2. Read and write the `nuopc.runconfig` file.
 """
     config_util = [
+        {
+            "key": "force_overwrite_tools",
+            "value": "False",
+        },
         {
             "key": "utils_url",
             "value": "git@github.com:minghangli-uni/om3-utils.git",