pandas 2.2.3 import fails with RuntimeError on GraalPy 25.0.2

[timfel]

Description

On Linux with GraalPy 25.0.2, a pandas wheel built from source installs successfully but fails on import with:

RuntimeError: dictionary changed size during iteration

The reporter used:

• GraalPy 25.0.2
• Linux x86_64
• numpy 2.2.6
• pandas 2.2.3

Traceback

Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "/home/user/Desktop/venv/lib/python3.12/site-packages/pandas/__init__.py", line 49, in <module>
    from pandas.core.api import (
  File "/home/user/Desktop/venv/lib/python3.12/site-packages/pandas/core/api.py", line 1, in <module>
    from pandas._libs import (
  File "/home/user/Desktop/venv/lib/python3.12/site-packages/pandas/_libs/__init__.py", line 18, in <module>
    from pandas._libs.interval import Interval
  File "interval.pyx", line 1, in init pandas._libs.interval
  File "hashtable.pyx", line 1, in init pandas._libs.hashtable
  File "missing.pyx", line 1, in init pandas._libs.missing
  File "/home/user/Desktop/venv/lib/python3.12/site-packages/pandas/_libs/tslibs/__init__.py", line 39, in <module>
    from pandas._libs.tslibs import dtypes  # pylint: disable=import-self
  File "dtypes.pyx", line 172, in init pandas._libs.tslibs.dtypes
RuntimeError: dictionary changed size during iteration

Dockerfile Used To Build Wheels

FROM --platform=linux/amd64 amazonlinux:2023
USER root
ARG GRAALPY_VERSION=25.0.2
ARG ARCH=amd64
RUN dnf update -y && \
    dnf install -y \
    wget tar gzip unzip patchelf gcc gcc-c++ patch git \
    gcc-gfortran openblas-devel zlib-devel libjpeg-turbo-devel \
    libxml2-devel libxslt-devel && \
    dnf clean all
RUN wget https://github.com/oracle/graalpython/releases/download/graal-${GRAALPY_VERSION}/graalpy-${GRAALPY_VERSION}-linux-${ARCH}.tar.gz && \
    tar -xzf graalpy-${GRAALPY_VERSION}-linux-${ARCH}.tar.gz -C /opt/ && \
    rm graalpy-${GRAALPY_VERSION}-linux-${ARCH}.tar.gz
ENV PATH="/opt/graalpy-${GRAALPY_VERSION}-linux-${ARCH}/bin:$PATH"
RUN graalpy -m ensurepip --default-pip && \
    graalpy -m pip install --upgrade pip auditwheel setuptools wheel && \
    graalpy -m pip install meson-python ninja cython pyproject-metadata setuptools-scm pybind11
WORKDIR /workspace
CMD ["/bin/bash", "-c", "\
    graalpy -m pip wheel numpy --no-binary numpy -w /workspace && \
    graalpy -m auditwheel repair /workspace/numpy-*.whl -w /workspace/wheelhouse && \
    graalpy -m pip install /workspace/wheelhouse/numpy-*.whl && \
    graalpy -m pip wheel pandas --no-binary pandas --find-links /workspace/wheelhouse -w /workspace && \
    graalpy -m auditwheel repair /workspace/pandas-*.whl -w /workspace/wheelhouse && \
    cp /workspace/wheelhouse/*.whl /out \
"]
# docker build -t libs .
# docker run --rm -v "$PWD":/out --cpus="2" --memory="15g" --memory-swap="15g" libs

Steps To Reproduce

graalpy -m venv venv
source venv/bin/activate
docker build -t libs .
docker run --rm -v "$PWD":/out --cpus="2" --memory="15g" --memory-swap="15g" libs
pip install numpy*.whl pandas*.whl
python -c "import pandas"

Expected Behavior

import pandas succeeds.

Actual Behavior

import pandas raises RuntimeError: dictionary changed size during iteration during initialization of pandas._libs.tslibs.dtypes.

[timfel]

Seems to only happen on 25.0.2 & 25.0.3, not on master. I pushed a new patch

[timfel]

Via Slack:

graalpy -c "import pandas as pd; print(pd.DataFrame({'a':[1,2,3],'b':[4,5,6]}))"

Traceback:
Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "/home/user/Desktop/graal-error/venv/lib/python3.12/site-packages/pandas/core/frame.py", line 1214, in __repr__
    return self.to_string(**repr_params)
  File "/home/user/Desktop/graal-error/venv/lib/python3.12/site-packages/pandas/util/_decorators.py", line 333, in wrapper
    return func(*args, **kwargs)
  File "/home/user/Desktop/graal-error/venv/lib/python3.12/site-packages/pandas/core/frame.py", line 1394, in to_string
    return fmt.DataFrameRenderer(formatter).to_string(
  File "/home/user/Desktop/graal-error/venv/lib/python3.12/site-packages/pandas/io/formats/format.py", line 962, in to_string
    string = string_formatter.to_string()
  File "/home/user/Desktop/graal-error/venv/lib/python3.12/site-packages/pandas/io/formats/string.py", line 29, in to_string
    text = self._get_string_representation()
  File "/home/user/Desktop/graal-error/venv/lib/python3.12/site-packages/pandas/io/formats/string.py", line 53, in _get_string_representation
    return self._fit_strcols_to_terminal_width(strcols)
  File "/home/user/Desktop/graal-error/venv/lib/python3.12/site-packages/pandas/io/formats/string.py", line 157, in _fit_strcols_to_terminal_width
    max_len = Series(lines).str.len().max()
  File "/home/user/Desktop/graal-error/venv/lib/python3.12/site-packages/pandas/core/strings/accessor.py", line 3094, in len
    result = self._data.array._str_len()
  File "/home/user/Desktop/graal-error/venv/lib/python3.12/site-packages/pandas/core/strings/object_array.py", line 302, in _str_len
    return self._str_map(len, dtype="int64")
  File "/home/user/Desktop/graal-error/venv/lib/python3.12/site-packages/pandas/core/strings/object_array.py", line 78, in _str_map
    result = lib.map_infer_mask(arr, f, mask.view(np.uint8), map_convert)
  File "lib.pyx", line 2895, in pandas._libs.lib.map_infer_mask
  File "lib.pyx", line 2908, in pandas._libs.lib.__pyx_fused_cpdef
RuntimeError: dictionary changed size during iteration