clan-lib: Move nix_options from Machine class to Flake class

pkgs/clan-cli/clan_cli/__init__.py

@@ -35,20 +35,27 @@ with contextlib.suppress(ImportError):
     import argcomplete  # type: ignore[no-redef]
 
 
-def flake_path(arg: str) -> Flake:
+def flake_path(arg: str) -> str:
     flake_dir = Path(arg).resolve()
     if flake_dir.exists() and flake_dir.is_dir():
-        return Flake(str(flake_dir))
-    return Flake(arg)
+        return str(flake_dir)
+    return arg
 
 
-def default_flake() -> Flake | None:
+def default_flake() -> str | None:
     val = get_clan_flake_toplevel_or_env()
     if val:
-        return Flake(str(val))
+        return str(val)
     return None
 
 
+def create_flake_from_args(args: argparse.Namespace) -> Flake:
+    """Create a Flake object from parsed arguments, including nix_options."""
+    flake_path_str = args.flake
+    nix_options = getattr(args, "option", [])
+    return Flake(flake_path_str, nix_options=nix_options)
+
+
 def add_common_flags(parser: argparse.ArgumentParser) -> None:
     def argument_exists(parser: argparse.ArgumentParser, arg: str) -> bool:
         """
@@ -450,6 +457,10 @@ def main() -> None:
     if not hasattr(args, "func"):
         return
 
+    # Convert flake path to Flake object with nix_options if flake argument exists
+    if hasattr(args, "flake") and args.flake is not None:
+        args.flake = create_flake_from_args(args)
+
     try:
         args.func(args)
     except ClanError as e:

pkgs/clan-cli/clan_cli/machines/install.py

@@ -42,7 +42,7 @@ def install_command(args: argparse.Namespace) -> None:
         else:
             password = None
 
-        machine = Machine(name=args.machine, flake=args.flake, nix_options=args.option)
+        machine = Machine(name=args.machine, flake=args.flake)
         host_key_check = args.host_key_check
 
         if target_host_str is not None:

pkgs/clan-cli/clan_cli/machines/update.py

@@ -46,9 +46,7 @@ def update_command(args: argparse.Namespace) -> None:
             raise ClanError(msg)
 
         for machine_name in selected_machines:
-            machine = Machine(
-                name=machine_name, flake=args.flake, nix_options=args.option
-            )
+            machine = Machine(name=machine_name, flake=args.flake)
             machines.append(machine)
 
         if args.target_host is not None and len(machines) > 1:

pkgs/clan-cli/clan_cli/tests/helpers/cli.py

@@ -2,7 +2,7 @@ import argparse
 import logging
 import shlex
 
-from clan_cli import create_parser
+from clan_cli import create_flake_from_args, create_parser
 from clan_lib.custom_logger import print_trace
 
 log = logging.getLogger(__name__)
@@ -13,6 +13,10 @@ def run(args: list[str]) -> argparse.Namespace:
     parsed = parser.parse_args(args)
     cmd = shlex.join(["clan", *args])
 
+    # Convert flake path to Flake object with nix_options if flake argument exists
+    if hasattr(parsed, "flake") and parsed.flake is not None:
+        parsed.flake = create_flake_from_args(parsed)
+
     print_trace(f"$ {cmd}", log, "localhost")
     if hasattr(parsed, "func"):
         parsed.func(parsed)

pkgs/clan-cli/clan_cli/vars/generate.py

@@ -511,7 +511,7 @@ def generate_command(args: argparse.Namespace) -> None:
         msg = "Could not find clan flake toplevel directory"
         raise ClanError(msg)
 
-    machines: list[Machine] = list(list_full_machines(args.flake, args.option).values())
+    machines: list[Machine] = list(list_full_machines(args.flake).values())
 
     if len(args.machines) > 0:
         machines = list(