gpt4.1, gpt-4o not actually applying patches to code. Only o3 and o4 models actually appear to make or apply any changes

Resolved 💬 2 comments Opened May 11, 2025 by josephbartlett Closed Aug 7, 2025

What version of Codex is running?

0.1.2504301751

Which model were you using?

gpt-4.1

What platform is your computer?

linux | x64 | 5.15.167.4-microsoft-standard-WSL2

What steps can reproduce the bug?

Scaffold a Python Flask test project of your own design and idea. Show me what you can do.
```

If running in a Windows 11/WSL2 environment you might see the initial creation of empty files and folders - but actually patches just display to the console and don't actually apply. This occurs in all approval-modes. This results in a lot of wasted tokens for end users.

Example Interaction:

`user
explain this codebase to me

command

$ ls -lR

command.stdout (code: 0, duration: 0.1s)

.:
total 0
-rwxrwxrwx 1 decoy decoy 0 May 11 06:47 README.md
drwxrwxrwx 1 decoy decoy 4096 May 11 06:47 app
... (15 more lines)

command

$ head -20 README.md

command.stdout (code: 0, duration: 0s)

command

$ head -20 requirements.txt

command.stdout (code: 0, duration: 0s)

command

$ head -20 run.py

command.stdout (code: 0, duration: 0s)

command

$ head -20 app/auth.py

command.stdout (code: 0, duration: 0s)

command

$ head -20 app/todos.py

command.stdout (code: 0, duration: 0s)

command

$ head -20 app/__init__.py

command.stdout (code: 0, duration: 0s)

command

$ head -20 tests/test_auth.py

command.stdout (code: 0, duration: 0s)

command

$ head -20 tests/test_todos.py

command.stdout (code: 0, duration: 0s)

codex
Here’s what I found about your codebase:

### Structure

README.md – Exists, but is empty.
requirements.txt – Exists, but is empty.
run.py – Exists, but is empty. This would usually be the application entry-point.
/app directory – Contains:
__init__.py – Empty, marks this as a Python package.

auth.py – Empty, but likely meant for authentication logic.

todos.py – Empty, but likely intended for to-do list logic.
/tests directory – Contains:
test_auth.py – Empty, for auth module tests.

test_todos.py – Empty, for todos module tests.

### High-Level Inference

This is a Python project, intended for some kind of to-do application with authentication.
The codebase is currently a scaffold/boilerplate: files and structure are in place, but nothing has been implemented yet.

--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
---

Next steps if building out:

Define what kind of authentication (simple username/password, token-based, etc.).
Build the data model for todos.
Implement API/logic in auth.py and todos.py.
Fill out run.py as the app entry-point (command-line, web API, etc.).
Write corresponding tests.

Let me know how you want to proceed or if you'd like a suggested implementation plan!
user
Please proceed with whatever next steps make the most sense.

codex
Given the codebase is a blank scaffold for a likely "To-Do" app with authentication, the best next steps are:

### 1. Define the App Type

Let's build a simple Flask web API, which is a common choice for todo + auth prototypes.

### 2. Basic Features

User Authentication: Simulated via username/password (no persistent storage for now, just in-memory).
Todo CRUD: Add, view, delete, update todos per user (all in-memory to keep it simple and testable).

### 3. Directory/Module Roles

/app/auth.py: Auth logic (user management, login, session management).
/app/todos.py: Todo logic, managing todo items per user.
/run.py: Flask app creation and route wiring.
/tests/: Unit tests for core modules.

### 4. requirements.txt

Add Flask for web server.

--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
---

Let’s start by:

Updating requirements.txt
Creating a minimal working Flask API in run.py
Implementing simple logic for /app/auth.py and /app/todos.py

Let’s begin with these foundational updates!

command

$ echo Flask -n \> requirements.txt

command.stdout (code: 0, duration: 0s)

Flask -n > requirements.txt

command

$ echo 'Flask
' ' >' requirements.txt

command.stdout (code: 0, duration: 0s)

Flask
> requirements.txt

command

$ echo 'Flask
' \> requirements.txt

command.stdout (code: 0, duration: 0s)

Flask
> requirements.txt

command

$ cat requirements.txt

command.stdout (code: 0, duration: 0s)

command

$ printf 'Flask
' \> requirements.txt

command.stdout (code: 0, duration: 0s)

Flask

command

$ pip install Flask

command.stdout (code: 0, duration: 0.9s)

Defaulting to user installation because normal site-packages is not writeable
Requirement already satisfied: Flask in /home/decoy/.local/lib/python3.10/site-packages (3.1.0)
Requirement already satisfied: Werkzeug>=3.1 in /home/decoy/.local/lib/python3.10/site-packages (from Flask) (3.1.3)
Requirement already satisfied: click>=8.1.3 in /home/decoy/.local/lib/python3.10/site-packages (from Flask) (8.2.0)
... (5 more lines)

command

$ ls -l app

command.stdout (code: 0, duration: 0s)

total 0
-rwxrwxrwx 1 decoy decoy 0 May 11 06:47 __init__.py
-rwxrwxrwx 1 decoy decoy 0 May 11 06:47 auth.py
-rwxrwxrwx 1 decoy decoy 0 May 11 06:47 todos.py
... (1 more lines)

codex
Here’s what I will do next:

Build out a minimal run.py with Flask routes for registration, login, and todo CRUD.
Implement in-memory logic in /app/auth.py for user management.
Implement in-memory logic in /app/todos.py for managing todos by user.

Let's begin with run.py (the Flask entry-point).

command

$ cat app/auth.py

command.stdout (code: 0, duration: 0s)

command

$ cat app/todos.py

command.stdout (code: 0, duration: 0s)

command

$ cat app/__init__.py

command.stdout (code: 0, duration: 0s)

command

$ cat run.py

command.stdout (code: 0, duration: 0s)

codex
Now I'll update the following files for the application:

run.py: Flask app setup, route wiring.
app/auth.py: In-memory user management (register/login, session).
app/todos.py: In-memory todos per user.

Let’s start by making the initial version for all these files.

command

$ ls -l

command.stdout (code: 0, duration: 0s)

total 0
-rwxrwxrwx 1 decoy decoy 0 May 11 06:47 README.md
drwxrwxrwx 1 decoy decoy 4096 May 11 06:47 app
-rwxrwxrwx 1 decoy decoy 0 May 11 06:47 requirements.txt
... (3 more lines)

codex
Here's my implementation plan:

#### 1. app/auth.py: Basic in-memory user system

register_user(username, password)
authenticate_user(username, password)
In actual deployments, you’d use a database, hashed passwords, and better session management.

#### 2. app/todos.py: Simple todo manager

Todos stored per user (dictionary in memory).
Methods: add_todo, get_todos, update_todo, delete_todo.

#### 3. run.py: Minimal Flask app

Endpoints for /register, /login, and /todos (CRUD).
Simulate 'sessions' with a basic global logged-in-user mapping.

(For demo, send back a 'token' upon login, which is a username, to use in all further requests.)

--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
---

Let’s build these out now.

command

$ cat run.py

command.stdout (code: 0, duration: 0s)

command

$ cat app/auth.py

command.stdout (code: 0, duration: 0s)

command

$ cat app/todos.py

command.stdout (code: 0, duration: 0s)

command

$ cat app/__init__.py

command.stdout (code: 0, duration: 0s)

codex
I am going to create initial versions for three files:

app/auth.py — In-memory user management
app/todos.py — In-memory todo management per user
run.py — Flask app with simple routes using above logic

Let's proceed.

command

$ pwd

command.stdout (code: 0, duration: 0s)

/mnt/c/Users/decoy/Test

command

$ ls app

command.stdout (code: 0, duration: 0s)

__init__.py
auth.py
todos.py

command

$ ls

command.stdout (code: 0, duration: 0s)

README.md
app
requirements.txt
run.py
... (2 more lines)

command

$ ls tests

command.stdout (code: 0, duration: 0s)

test_auth.py
test_todos.py

command

$ ls -l tests

command.stdout (code: 0, duration: 0s)

total 0
-rwxrwxrwx 1 decoy decoy 0 May 11 06:47 test_auth.py
-rwxrwxrwx 1 decoy decoy 0 May 11 06:47 test_todos.py

command

$ ls -l app

command.stdout (code: 0, duration: 0s)

total 0
-rwxrwxrwx 1 decoy decoy 0 May 11 06:47 __init__.py
-rwxrwxrwx 1 decoy decoy 0 May 11 06:47 auth.py
-rwxrwxrwx 1 decoy decoy 0 May 11 06:47 todos.py
... (1 more lines)

codex
Let's proceed with the initial implementation of the files as outlined.

First, app/auth.py:

command

$ cat app/auth.py

command.stdout (code: 0, duration: 0s)

codex
Here is the initial content for app/auth.py:

# app/auth.py

_users = {}

def register_user(username, password):
if username in _users:
return False
_users[username] = password
return True

def authenticate_user(username, password):
return _users.get(username) == password

Next, I'll fill in the file.

command

$ cat app/todos.py

command.stdout (code: 0, duration: 0s)

command

$ cat run.py

command.stdout (code: 0, duration: 0s)

codex
Next up: app/todos.py.

Here's the initial implementation:

# app/todos.py

_todos = {}

def get_todos(username):
return _todos.get(username, [])

def add_todo(username, task):
todo_item = {"id": len(_todos.get(username, [])) + 1, "task": task, "completed": False}
_todos.setdefault(username, []).append(todo_item)
return todo_item

def update_todo(username, todo_id, completed=None, task=None):
user_todos = _todos.get(username, [])
for todo in user_todos:
if todo["id"] == todo_id:
if completed is not None:
todo["completed"] = completed
if task is not None:
todo["task"] = task
return todo
return None

def delete_todo(username, todo_id):
user_todos = _todos.get(username, [])
for idx, todo in enumerate(user_todos):
if todo["id"] == todo_id:
return user_todos.pop(idx)
return None

I will save this file, then proceed to implement the Flask app in run.py.

command

$ cat app/__init__.py

command.stdout (code: 0, duration: 0s)

command

$ cat requirements.txt

command.stdout (code: 0, duration: 0s)

command

$ cat README.md

command.stdout (code: 0, duration: 0s)

codex
Now here's the implementation plan for run.py:

/register [POST]: Register a new user.
/login [POST]: Login and get a session token (simply the username).
/todos [GET, POST]: Get all or add a new todo for the logged-in user.
/todos/<int:todo_id> [PUT, DELETE]: Update or delete a todo for the logged-in user.
Session Auth: Use a header X-Auth-Token with the username as the token for requests requiring authentication.

Now I will implement it.

codex
Let's apply all initial code at once for clarity and atomicity:

## * Begin Patch
* Update File: app/auth.py
@@
-_users = {}

-def register_user(username, password):

if username in _users:
return False
_users[username] = password
return True

-def authenticate_user(username, password):

return _users.get(username) == password

+_users = {}
+
+def register_user(username, password):

"""Register a new user. Return True if successful, False if user exists."""
if username in _users:
return False
_users[username] = password
return True

+def authenticate_user(username, password):

"""Return True if username/password matches, else False."""
return _users.get(username) == password

## *** Update File: app/todos.py
@@
-_todos = {}

-def get_todos(username):

return _todos.get(username, [])

-def add_todo(username, task):

todo_item = {"id": len(_todos.get(username, [])) + 1, "task": task, "completed": False}
_todos.setdefault(username, []).append(todo_item)
return todo_item

-def update_todo(username, todo_id, completed=None, task=None):

user_todos = _todos.get(username, [])
for todo in user_todos:
if todo["id"] == todo_id:
if completed is not None:
todo["completed"] = completed
if task is not None:
todo["task"] = task
return todo
return None

-def delete_todo(username, todo_id):

user_todos = _todos.get(username, [])
for idx, todo in enumerate(user_todos):
if todo["id"] == todo_id:
return user_todos.pop(idx)
return None

+_todos = {}
+
+def get_todos(username):

"""Return the list of todos for this user."""
return _todos.get(username, [])

+def add_todo(username, task):

"""Add a new todo for the user."""
todo_item = {"id": len(_todos.get(username, [])) + 1, "task": task, "completed": False}
_todos.setdefault(username, []).append(todo_item)
return todo_item

+def update_todo(username, todo_id, completed=None, task=None):

"""Update a todo for this user (by id)."""
user_todos = _todos.get(username, [])
for todo in user_todos:
if todo["id"] == todo_id:
if completed is not None:
todo["completed"] = completed
if task is not None:
todo["task"] = task
return todo
return None

+def delete_todo(username, todo_id):

"""Delete a todo by id for this user."""
user_todos = _todos.get(username, [])
for idx, todo in enumerate(user_todos):
if todo["id"] == todo_id:
return user_todos.pop(idx)
return None

*** Update File: run.py
@@
+
+from flask import Flask, request, jsonify
+from app.auth import register_user, authenticate_user
+from app.todos import get_todos, add_todo, update_todo, delete_todo
+
+app = Flask(name)
+
+def get_current_user():

token = request.headers.get('X-Auth-Token')
if not token:
return None
return token

+@app.route (mailto:+@app.route)("/register", methods=["POST"])
+def register():

data = request.get_json(force=True)
username = data.get("username")
password = data.get("password")
if not username or not password:
return jsonify({"error": "username and password required"}), 400
if register_user(username, password):
return jsonify({"msg": "user registered"})
else:
return jsonify({"error": "user already exists"}), 409

+@app.route (mailto:+@app.route)("/login", methods=["POST"])
+def login():

data = request.get_json(force=True)
username = data.get("username")
password = data.get("password")
if not username or not password:
return jsonify({"error": "username and password required"}), 400
if authenticate_user(username, password):
# For demo, token is just username
return jsonify({"token": username})
else:
return jsonify({"error": "invalid credentials"}), 401

+@app.route (mailto:+@app.route)("/todos", methods=["GET"])
+def todos_get():

username = get_current_user()
if not username:
return jsonify({"error": "unauthorized"}), 401
return jsonify(get_todos(username))

+@app.route (mailto:+@app.route)("/todos", methods=["POST"])
+def todos_post():

username = get_current_user()
if not username:
return jsonify({"error": "unauthorized"}), 401
data = request.get_json(force=True)
task = data.get("task")
if not task:
return jsonify({"error": "task required"}), 400
todo = add_todo(username, task)
return jsonify(todo), 201

+@app.route (mailto:+@app.route)("/todos/int:todo_id", methods=["PUT"])
+def todos_update(todo_id):

username = get_current_user()
if not username:
return jsonify({"error": "unauthorized"}), 401
data = request.get_json(force=True)
completed = data.get("completed")
task = data.get("task")
todo = update_todo(username, todo_id, completed, task)
if not todo:
return jsonify({"error": "todo not found"}), 404
return jsonify(todo)

+@app.route (mailto:+@app.route)("/todos/int:todo_id", methods=["DELETE"])
+def todos_delete(todo_id):

username = get_current_user()
if not username:
return jsonify({"error": "unauthorized"}), 401
todo = delete_todo(username, todo_id)
if not todo:
return jsonify({"error": "todo not found"}), 404
return jsonify({"msg": "deleted"})

+if name == "main":

app.run(debug=True)

*** End Patch`

What is the expected behavior?

Codex should actually apply the patches and updates code as well as display the proposed changes to the console.

What do you see instead?

Empty files on disk.

Additional information

_No response_

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