Pyrefly crash with `Internal error: a variable has leaked from one module to another.`

[HellConnector]

I was able to crash pyrefly but didn't really get why it happened.

The error is in title — Internal error: a variable has leaked from one module to another.
It happens only with this particular SQL Alchemy query

item_type_spent = (
    select(
        Client.id.label("client_id"),
        SearchItem.item_type.label("item_type"),
        Item.count.label("item_count"),
        (
            func.round(
                (
                    func.sum(Deal.price * Deal.volume)
                    / func.sum(Deal.volume)
                ),
                2,
            )
            * Item.count
        ).label("current_spent"),
    )
    .select_from(Item)
    .join(Client, Client.id == Item.client_id)
    .join(Deal, Deal.item_id == Item.id)
    .join(SearchItem, SearchItem.name == Item.name)
    .where(
        Deal.deal_currency == Client.currency,
        Deal.deal_type == "buy",
        Deal.closed == False,  # noqa: E712
        Item.count > 0,
    )
    .group_by(Client.id, Item.name, Item.count, SearchItem.item_type)
).cte("item_type_spent")

query = select(
    item_type_spent.c.client_id,
    item_type_spent.c.item_type,
    func.sum(item_type_spent.c.item_count),
    func.sum(item_type_spent.c.current_spent),
).group_by(item_type_spent.c.client_id, item_type_spent.c.item_type)

When I type dot . after the group_by section Pyrefly just crashes every time with the Internal Error.
The models are defined in another database-specific package and imported from there.

I also noticed that despite my pyproject.toml configuration for Pyrefly I always see in LSP logs these lines:

Could not decode LspConfig from Null, skipping client configuration request: invalid type: null, expected struct LspConfig.
Populating up to 2000 files in the workspace ...
Prepare to check 2469 files.

And sometimes it leads to oserror 24 with too many files open.

[kinto0]

Thanks for the report!! I'm looking into the first panic now.

re: Prepare to check 2469 files, how many files is your project itself (not including site-packages / pip-installed python stuff)? and how big is your python env (site-packages, pip-installed stuff)

[kinto0]

I can't reproduce this with importing only sqlalchemy. Can you show me the imports to see which versions of libraries you are using? And can you confirm you are on the newest version of pyrefly?

[HellConnector]

Thanks for the report!! I'm looking into the first panic now.

re: Prepare to check 2469 files, how many files is your project itself (not including site-packages / pip-installed python stuff)? and how big is your python env (site-packages, pip-installed stuff)

Here is the pyrefly configuration I use in the pyproject.toml

[tool.pyrefly]
python-interpreter = ".venv/bin/python"
python-version = "3.13"
project-includes = [
  "bot",
  "mini_app_api",
  "price_worker",
  "search_items_worker"
]
site-package-path = [".venv/lib/python3.13/site-packages"]

search-path = [
  ".",
  "bot",
  "bot/db",
  "mini_app_api",
  "price_worker",
  "search_items_worker"
]

project-excludes = [
  "**/.[!/.]*",
  "**/*venv/**",
  ".venv",
  "**/__pycache__",
  "./telegram-mini-app"
]

ignore-errors-in-generated-code = true

Basically the project is a monorepo with several independent packages. But the db package in bot/db/ is shared and can be imported where it is needed.
Codebase contains about 50 python files.

Here are the dependencies I use

dependencies = [
    "python-telegram-bot==22.1",
    "asyncpg==0.30",
    "apscheduler==3.11.0",
    "alembic==1.16.2",
    "python-dotenv==1.1.1",
    "sqlalchemy[asyncio, mypy]==2.0.41",
    "httpx==0.28.1",
    "hatchling==1.27.0",
    "fastapi==0.115.12",
    "uvicorn[standard]==0.34.2",
    "python-multipart==0.0.9",
    "sentry-sdk[fastapi]==2.35.0",
]

[HellConnector]

I can't reproduce this with importing only sqlalchemy. Can you show me the imports to see which versions of libraries you are using? And can you confirm you are on the newest version of pyrefly?

Here is the exact file that crashes Pyrefly (0.36) every time.

from sqlalchemy import func, select
from sqlalchemy.dialects import postgresql

from bot.db import get_async_session
from bot.db.models import Client, Deal, Item, SearchItem


async def get_diversity_by_item_type_spent():
    item_type_spent = (
        select(
            Client.id.label("client_id"),
            SearchItem.item_type.label("item_type"),
            Item.count.label("item_count"),
            (
                func.round(
                    (
                        func.sum(Deal.price * Deal.volume)
                        / func.sum(Deal.volume)
                    ),
                    2,
                )
                * Item.count
            ).label("current_spent"),
        )
        .select_from(Item)
        .join(Client, Client.id == Item.client_id)
        .join(Deal, Deal.item_id == Item.id)
        .join(SearchItem, SearchItem.name == Item.name)
        .where(
            Deal.deal_currency == Client.currency,
            Deal.deal_type == "buy",
            Deal.closed == False,  # noqa: E712
            Item.count > 0,
        )
        .group_by(Client.id, Item.name, Item.count, SearchItem.item_type)
    ).cte("item_type_spent")

    query = select(
        item_type_spent.c.client_id,
        item_type_spent.c.item_type,
        func.sum(item_type_spent.c.item_count),
        func.sum(item_type_spent.c.current_spent),
    ).group_by(item_type_spent.c.client_id, item_type_spent.c.item_type)
    
    # For query debugging
    async with get_async_session() as session:
        string_query = str(
            query.compile(
                dialect=postgresql.dialect(),
                compile_kwargs={"literal_binds": True},
                bind=session.get_bind(),
            )
        )
        print(string_query)
        results = (await session.execute(query)).all()

    return results


if __name__ == "__main__":
    import asyncio

    spent_diversity = asyncio.run(get_diversity_by_item_type_spent())
    for client_id, item_type, item_count, spent in spent_diversity:
        if client_id == 1:
            print(client_id)

Folders structure

bot/
├─ db/
mini_app_api/
price_worker/
search_items_worker/
.venv/

[kinto0]

Thanks for the detailed info! I'm able to reproduce it now.