[codex] fix unit test setup

src/graph_sitter/compiled/autocommit.pyx

@@ -1,6 +1,6 @@
 import functools
 from collections.abc import Callable
-from typing import Any, ParamSpec, TypeVar, Union, overload
+from typing import Any, ParamSpec, TypeVar, Union
 
 import wrapt
 
@@ -20,14 +20,6 @@ def is_outdated(c) -> bool:
     return False
 
 
-@overload
-def reader(wrapped: Callable[P, T]) -> Callable[P, T]: ...
-
-
-@overload
-def reader(wrapped: None = None, *, cache: bool | None = ...) -> Callable[[Callable[P, T]], Callable[P, T]]: ...
-
-
 def reader(wrapped: Callable[P, T] | None = None, *, cache: bool | None = None) -> Callable[P, T] | Callable[[Callable[P, T]], Callable[P, T]]:
     """Indicates this method is a read
 
@@ -176,14 +168,6 @@ def update_dict(seen: set["Editable"], obj: "Editable", new_obj: "Editable"):
     assert not obj.is_outdated
 
 
-@overload
-def commiter(wrapped: Callable[P, T]) -> Callable[P, T]: ...
-
-
-@overload
-def commiter(wrapped: None = None, *, reset: bool = ...) -> Callable[[Callable[P, T]], Callable[P, T]]: ...
-
-
 def commiter(wrapped: Callable[P, T] | None = None, *, reset: bool = False) -> Callable[P, T] | Callable[[Callable[P, T]], Callable[P, T]]:
     """Indicates this method is part of a commit. There should be no writes within this method and reads will not be updated
 

src/graph_sitter/git/repo_operator/repo_operator.py

@@ -142,7 +142,7 @@
         email_level = None
         levels = ["system", "global", "user", "repository"]
         for level in levels:
             with git_cli.config_reader(level) as reader:
                 if reader.has_option("user", "name") and not username:
                     username = username or reader.get("user", "name")
                     user_level = user_level or level
@@ -170,8 +170,8 @@
         try:
             return self.git_cli.head.commit
         except ValueError as e:
             if (f"Reference at {self.git_cli.head.ref.path!r} does not exist") in str(e):
                 logger.info(f"Ref: {self.git_cli.head.ref.name} has no commits")
                 return None
             raise
 
@@ -479,7 +479,7 @@
 
     def _get_username_email(self) -> tuple[str, str] | None:
         for level in ["user", "global", "system"]:
             with self.git_cli.config_reader(level) as reader:
                 if reader.has_section("user"):
                     user, email = reader.get_value("user", "name"), reader.get_value("user", "email")
                     if isinstance(user, str) and isinstance(email, str) and user != CODEGEN_BOT_NAME and email != CODEGEN_BOT_EMAIL:
@@ -488,7 +488,7 @@
 
     def commit_changes(self, message: str, verify: bool = False) -> bool:
         """Returns True if a commit was made and False otherwise."""
-        staged_changes = self.git_cli.git.diff("--staged")
+        staged_changes = self.git_cli.git.diff("--no-ext-diff", "--staged")
         if staged_changes:
             if self.bot_commit and (info := self._get_username_email()):
                 user, email = info
@@ -580,7 +580,7 @@
                     return content
             except UnicodeDecodeError:
                 print(f"Warning: Unable to decode file {file_path}. Skipping.")
                 return None
 
     def write_file(self, relpath: str, content: str) -> None:
         """Writes file content to disk"""
@@ -652,7 +652,7 @@
         filepaths = self.get_filepaths_for_repo(ignore_list)
         # Iterate through files and yield contents
         for rel_filepath in filepaths:
             rel_filepath: str
             filepath = os.path.join(self.repo_path, rel_filepath)
 
             # Filter by subdirectory (includes full filenames)
@@ -689,7 +689,7 @@
         list_files = []
 
         for rel_filepath in self.git_cli.git.ls_files().split("\n"):
             rel_filepath: str
             if subdirs and not any(d in rel_filepath for d in subdirs):
                 continue
             if extensions is None or any(rel_filepath.endswith(e) for e in extensions):
@@ -713,7 +713,7 @@
 
     def get_modified_files_in_last_n_days(self, days: int = 1) -> tuple[list[str], list[str]]:
         """Returns a list of files modified and deleted in the last n days"""
         modified_files = []
         deleted_files = []
         allowed_extensions = [".py"]
 
@@ -729,9 +729,9 @@
                     if file in modified_files:
                         modified_files.remove(file)
                 else:
                     if file not in modified_files and file[-3:] in allowed_extensions:
                         modified_files.append(file)
         return modified_files, deleted_files
 
     @cached_property
     def base_url(self) -> str | None: