fix: typecheck and fix errors

Run typecheck and fix errors. There are many errors so make a plan about which module to do first based on dependencies.

```git-revs
cbc5d78  (Base revision)
3e0e7f2  Fix return type of run_command to specify CompletedProcess type parameters
7c760d1  Add type parameter to CompletedProcess instantiation
d66377f  Fix type issue with wait_time in TimeoutExpired constructor by ensuring it's a float
688b278  Remove unnecessary isinstance check since input is already typed as Optional[str]
5069fc5  Add necessary imports and type definitions for anyio file operations
60cc81f  Fix the mode type parameter in async_open_text function
e658af6  Fix the mode type parameter in async_open_binary function
96e35cc  Fix the mode type parameter in async_write_text function
263feed  Fix the mode type parameter in async_write_binary function and remove the unnecessary newline parameter for binary mode
5208044  Update the async_readlines function to use OpenTextMode
9520770  Expand OpenTextMode and OpenBinaryMode literals to include write and append modes
dc10140  Add proper imports including type definitions
24b253e  Update async_open_text to use OpenTextMode
c495c2d  Update write_text_content to use Optional instead of union type
5eb7591  Fix the write mode by using an explicit OpenTextMode variable
7d8a50d  Update return type annotation in check_file_path_and_permissions
f02bdae  Fix returncode handling to avoid None value
121b4d9  Remove unused Any import
bea7686  Remove unused imports
07dd0c8  Fix async_readlines by using string literal for mode
f020f12  Remove unused imports from file_utils.py
6202623  Cast stdout to str in get_head_commit_message function
350e6ed  Cast stdout to str in get_head_commit_hash function
6683f1b  Cast stdout to str in get_repository_root function
ed6d8c0  Cast stdout to str in get_ref_commit_chat_id function
e214ad5  Cast tree_hash to str in create_commit_reference
672df85  Cast head_hash to str
1664682  Cast commit_hash to str
5d39ae8  Cast tree_hash and ref_message to str
5eb976c  Cast new_commit_hash to str
5e4e2bc  Fix chat_id parameter using Optional type
75fc0b2  Add Union to imports in code_command.py
9eb3519  Add necessary imports to common.py
572f0c3  Update truncate_output_content to handle bytes input
1f7c76a  Add type annotation for the result list in get_edit_snippet
ab4cd32  Add type annotation for processed_lines list in truncate_output_content
24e0ea9  Convert chat_id to string to fix type error in commit_changes call
c5a765a  Convert chat_id to string for earlier commit_changes call
HEAD     Auto-commit format changes
```

codemcp-id: 220-fix-typecheck-and-fix-errors
ghstack-source-id: c4b2f88
Pull-Request-resolved: #211

Author: ezyang

codemcp/async_file_utils.py

@@ -1,16 +1,73 @@
 #!/usr/bin/env python3
 
 import os
-from typing import List
+from typing import List, Literal
 
 import anyio
 
 from .line_endings import detect_line_endings
 
+# Define OpenTextMode and OpenBinaryMode similar to what anyio uses
+OpenTextMode = Literal[
+    "r",
+    "r+",
+    "+r",
+    "rt",
+    "rt+",
+    "r+t",
+    "+rt",
+    "tr",
+    "tr+",
+    "t+r",
+    "w",
+    "w+",
+    "+w",
+    "wt",
+    "wt+",
+    "w+t",
+    "+wt",
+    "tw",
+    "tw+",
+    "t+w",
+    "a",
+    "a+",
+    "+a",
+    "at",
+    "at+",
+    "a+t",
+    "+at",
+    "ta",
+    "ta+",
+    "t+a",
+]
+OpenBinaryMode = Literal[
+    "rb",
+    "rb+",
+    "r+b",
+    "+rb",
+    "br",
+    "br+",
+    "b+r",
+    "wb",
+    "wb+",
+    "w+b",
+    "+wb",
+    "bw",
+    "bw+",
+    "b+w",
+    "ab",
+    "ab+",
+    "a+b",
+    "+ab",
+    "ba",
+    "ba+",
+    "b+a",
+]
+
 
 async def async_open_text(
     file_path: str,
-    mode: str = "r",
+    mode: OpenTextMode = "r",
     encoding: str = "utf-8",
     errors: str = "replace",
 ) -> str:
@@ -31,7 +88,7 @@ async def async_open_text(
         return await f.read()
 
 
-async def async_open_binary(file_path: str, mode: str = "rb") -> bytes:
+async def async_open_binary(file_path: str, mode: OpenBinaryMode = "rb") -> bytes:
     """Asynchronously open and read a binary file.
 
     Args:
@@ -67,7 +124,7 @@ async def async_readlines(
 async def async_write_text(
     file_path: str,
     content: str,
-    mode: str = "w",
+    mode: OpenTextMode = "w",
     encoding: str = "utf-8",
 ) -> None:
     """Asynchronously write text to a file.
@@ -84,15 +141,17 @@ async def async_write_text(
         await f.write(content)
 
 
-async def async_write_binary(file_path: str, content: bytes, mode: str = "wb") -> None:
+async def async_write_binary(
+    file_path: str, content: bytes, mode: OpenBinaryMode = "wb"
+) -> None:
     """Asynchronously write binary data to a file.
 
     Args:
         file_path: The path to the file
         content: The binary content to write
         mode: The file open mode (default: 'wb')
     """
-    async with await anyio.open_file(file_path, mode, newline="") as f:
+    async with await anyio.open_file(file_path, mode) as f:
         await f.write(content)
 
 

codemcp/code_command.py

@@ -3,7 +3,7 @@
 import logging
 import os
 import subprocess
-from typing import List, Optional
+from typing import List, Optional, Union
 
 import tomli
 
@@ -92,7 +92,7 @@ async def run_code_command(
     command_name: str,
     command: List[str],
     commit_message: str,
-    chat_id: str = None,
+    chat_id: Optional[str] = None,
 ) -> str:
     """Run a code command (lint, format, etc.) and handle git operations.
 
@@ -131,10 +131,11 @@ async def run_code_command(
         # If it's a git repo, commit any pending changes before running the command
         if is_git_repo:
             logging.info(f"Committing any pending changes before {command_name}")
+            chat_id_str = str(chat_id) if chat_id is not None else ""
             commit_result = await commit_changes(
                 full_dir_path,
                 f"Snapshot before auto-{command_name}",
-                chat_id,
+                chat_id_str,
                 commit_all=True,
             )
             if not commit_result[0]:
@@ -160,8 +161,9 @@ async def run_code_command(
                 has_changes = await check_for_changes(full_dir_path)
                 if has_changes:
                     logging.info(f"Changes detected after {command_name}, committing")
+                    chat_id_str = str(chat_id) if chat_id is not None else ""
                     success, commit_result_message = await commit_changes(
-                        full_dir_path, commit_message, chat_id, commit_all=True
+                        full_dir_path, commit_message, chat_id_str, commit_all=True
                     )
 
                     if success:

codemcp/common.py

@@ -1,6 +1,7 @@
 #!/usr/bin/env python3
 
 import os
+from typing import List, Union
 
 # Constants
 MAX_LINES_TO_READ = 1000
@@ -78,15 +79,15 @@ def get_edit_snippet(
     snippet_lines = edited_lines[start_line:end_line]
 
     # Format with line numbers
-    result = []
+    result: List[str] = []
     for i, line in enumerate(snippet_lines):
         line_num = start_line + i + 1
         result.append(f"{line_num:4d} | {line}")
 
     return "\n".join(result)
 
 
-def truncate_output_content(content: str, prefer_end: bool = True) -> str:
+def truncate_output_content(content: Union[str, bytes], prefer_end: bool = True) -> str:
     """Truncate command output content to a reasonable size.
 
     When prefer_end is True, this function prioritizes keeping content from the end
@@ -101,15 +102,22 @@ def truncate_output_content(content: str, prefer_end: bool = True) -> str:
         The truncated content with appropriate indicators
     """
     if not content:
-        return content
+        return "" if content is None else str(content)
+
+    # Convert bytes to str if needed
+    if isinstance(content, bytes):
+        try:
+            content = content.decode("utf-8")
+        except UnicodeDecodeError:
+            return "[Binary content cannot be displayed]"
 
     lines = content.splitlines()
     total_lines = len(lines)
 
     # If number of lines is within the limit, check individual line lengths
     if total_lines <= MAX_LINES_TO_READ:
         # Process line lengths
-        processed_lines = []
+        processed_lines: List[str] = []
         for line in lines:
             if len(line) > MAX_LINE_LENGTH:
                 processed_lines.append(line[:MAX_LINE_LENGTH] + "... (line truncated)")

codemcp/file_utils.py

@@ -2,12 +2,14 @@
 
 import logging
 import os
+from typing import Optional, Tuple
 
 import anyio
 
 from .access import check_edit_permission
 from .git import commit_changes
 from .line_endings import apply_line_endings, normalize_to_lf
+from .async_file_utils import OpenTextMode
 
 __all__ = [
     "check_file_path_and_permissions",
@@ -18,7 +20,7 @@
 ]
 
 
-async def check_file_path_and_permissions(file_path: str) -> tuple[bool, str | None]:
+async def check_file_path_and_permissions(file_path: str) -> Tuple[bool, Optional[str]]:
     """Check if the file path is valid and has the necessary permissions.
 
     Args:
@@ -110,7 +112,7 @@ def ensure_directory_exists(file_path: str) -> None:
 
 async def async_open_text(
     file_path: str,
-    mode: str = "r",
+    mode: OpenTextMode = "r",
     encoding: str = "utf-8",
     errors: str = "replace",
 ) -> str:
@@ -135,7 +137,7 @@ async def write_text_content(
     file_path: str,
     content: str,
     encoding: str = "utf-8",
-    line_endings: str | None = None,
+    line_endings: Optional[str] = None,
 ) -> None:
     """Write text content to a file with specified encoding and line endings.
 
@@ -156,7 +158,8 @@ async def write_text_content(
     ensure_directory_exists(file_path)
 
     # Write the content using anyio
+    write_mode: OpenTextMode = "w"
     async with await anyio.open_file(
-        file_path, "w", encoding=encoding, newline=""
+        file_path, write_mode, encoding=encoding, newline=""
     ) as f:
         await f.write(final_content)

codemcp/git_commit.py

@@ -91,7 +91,7 @@ async def create_commit_reference(
             text=True,
             check=True,
         )
-        tree_hash = tree_result.stdout.strip()
+        tree_hash = str(tree_result.stdout.strip())
     else:
         # Create an empty tree if no HEAD exists
         empty_tree_result = await run_command(
@@ -102,7 +102,7 @@ async def create_commit_reference(
             text=True,
             check=True,
         )
-        tree_hash = empty_tree_result.stdout.strip()
+        tree_hash = str(empty_tree_result.stdout.strip())
 
     commit_message = commit_msg
 
@@ -116,7 +116,7 @@ async def create_commit_reference(
             text=True,
             check=True,
         )
-        head_hash = head_hash_result.stdout.strip()
+        head_hash = str(head_hash_result.stdout.strip())
         parent_arg = ["-p", head_hash]
 
     # Create the commit object (with GPG signing explicitly disabled)
@@ -135,7 +135,7 @@ async def create_commit_reference(
         text=True,
         check=True,
     )
-    commit_hash = commit_result.stdout.strip()
+    commit_hash = str(commit_result.stdout.strip())
 
     ref_name = f"refs/codemcp/{chat_id}"
 
@@ -309,7 +309,7 @@ async def commit_changes(
                 text=True,
                 check=True,
             )
-            tree_hash = tree_result.stdout.strip()
+            tree_hash = str(tree_result.stdout.strip())
 
             # Get the commit message from the reference
             ref_message_result = await run_command(
@@ -319,7 +319,7 @@ async def commit_changes(
                 text=True,
                 check=True,
             )
-            ref_message = ref_message_result.stdout.strip()
+            ref_message = str(ref_message_result.stdout.strip())
 
             # Create a new commit with the same tree as HEAD but message from the reference
             # This effectively creates the commit without changing the working tree
@@ -339,7 +339,7 @@ async def commit_changes(
                 text=True,
                 check=True,
             )
-            new_commit_hash = new_commit_result.stdout.strip()
+            new_commit_hash = str(new_commit_result.stdout.strip())
 
             # Update HEAD to point to the new commit
             await run_command(

codemcp/git_query.py

@@ -42,7 +42,7 @@ async def get_head_commit_message(directory: str) -> str:
         text=True,
     )
 
-    return result.stdout.strip()
+    return str(result.stdout.strip())
 
 
 async def get_head_commit_hash(directory: str, short: bool = True) -> str:
@@ -73,7 +73,7 @@ async def get_head_commit_hash(directory: str, short: bool = True) -> str:
         text=True,
     )
 
-    return result.stdout.strip()
+    return str(result.stdout.strip())
 
 
 async def get_head_commit_chat_id(directory: str) -> str | None:
@@ -150,7 +150,7 @@ async def get_repository_root(path: str) -> str:
         text=True,
     )
 
-    return result.stdout.strip()
+    return str(result.stdout.strip())
 
 
 async def is_git_repository(path: str) -> bool:
@@ -207,7 +207,7 @@ async def get_ref_commit_chat_id(directory: str, ref_name: str) -> str | None:
             capture_output=True,
             text=True,
         )
-        commit_message = message_result.stdout.strip()
+        commit_message = str(message_result.stdout.strip())
 
         # Use regex to find the last occurrence of codemcp-id: XXX
         # The pattern looks for "codemcp-id: " followed by any characters up to a newline or end of string