nanobind: leaked ... when a DuckDB type is referenced in overload signature and numpy is imported

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Bewertung

Schwierigkeit
4/5
Geschätzter Aufwand
3-5 Tage
Anfängerfreundlichkeit
25/100
Issue-Typ
Bug
Klarheit
Größtenteils klar
Aktivitätsstatus
Aktiv
Tech-Stack
numpy, python
Bereich
databases

Rechercherichtung

Start with the reproduction script in the issue: it needs only typing.overload referencing duckdb.DuckDBPyConnection plus import numpy, and the leak appears at interpreter exit. Run it with uv run --script to confirm the nanobind warnings. The cause is a reference-counting problem in the nanobind binding code, so the work is tracing which type or function objects are not released, which needs familiarity with nanobind. Done means the script exits without the leak warnings.

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Beschreibung

needs triage
What happens?

When the interpreter exits, duckdb 2.0.0 prints nanobind leak warnings if both of these are true:

  • a DuckDB type (e.g. DuckDBPyConnection) is referenced from a typing.overload signature, which typing keeps in its module-level overload registry until shutdown
  • numpy is imported (torch 2.6.0 triggers it the same way)
nanobind: leaked 27 instances!
nanobind: leaked 6 types!
 - leaked type "_duckdb._sqltypes.DuckDBPyType"
 - leaked type "_duckdb.DuckDBPyConnection"
 - leaked type "FunctionNullHandling"
 - leaked type "PythonUDFType"
 - leaked type "ExplainType"
 - leaked type "PythonExceptionHandling"
nanobind: leaked 84 functions!
 - leaked function "fetchone"
 - leaked function "fetch_df"
 - leaked function "__exit__"
 - leaked function "_result_as_arrow"
 - leaked function ""
 - leaked function "abort"
 - leaked function "append"
 - leaked function "interrupt"
 - leaked function "dtype"
 - leaked function "_register_values"
 - ... skipped remainder
nanobind: this is likely caused by a reference counting issue in the binding code.
See https://nanobind.readthedocs.io/en/latest/refleaks.html%
To Reproduce

with duckdb_nanobind_leak.py as follows

# /// script
# requires-python = ">=3.13"
# dependencies = ["duckdb==2.0.0", "numpy==2.5.2"]
# ///
"""duckdb 2.0.0 prints "nanobind: leaked ..." at interpreter exit.

Run: uv run --script duckdb_nanobind_leak.py

Triggered when a DuckDB type is referenced from a `typing.overload` signature (typing keeps overloads in a
module-level registry until shutdown) and numpy is imported. Without the overload, or without numpy, exit is clean.
torch (2.6.0) triggers it the same way as numpy.
"""

from typing import overload

import duckdb
import numpy


@overload
def connect(database: str) -> duckdb.DuckDBPyConnection: ...
@overload
def connect(database: None) -> None: ...
def connect(database):
    return None if database is None else duckdb.connect(database)

run uv run --script duckdb_nanobind_leak.py

OS:

x86_64

DuckDB Version:

2.0.0

DuckDB Client:

Python

Hardware:

No response

Full Name:

Bartosz Marcinkowski

Affiliation:

MIM Fertility

Did you include all relevant configuration (e.g., CPU architecture, Linux distribution) to reproduce the issue?
  • Yes, I have
Did you include all code required to reproduce the issue?
  • Yes, I have
Did you include all relevant data sets for reproducing the issue?

Not applicable - the reproduction does not require a data set

Vorherrschende Sprache
Python
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Ø Merge
13 Std. 36 Min.
Gemergte PRs (30 T.)
61

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