hdmf-dev / hdmf-zarr

Zarr I/O backend for HDMF
https://hdmf-zarr.readthedocs.io/
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[Bug]: Pandas warning causing test gallery errors #156

Closed rly closed 6 months ago

rly commented 6 months ago

What happened?

A new pandas warning about not having pyarrow installed is causing test_gallery.py to fail because it is set up to raise errors on unexpected warnings. See https://github.com/hdmf-dev/hdmf-zarr/actions/runs/7676572195

The warning says:

DeprecationWarning: 
Pyarrow will become a required dependency of pandas in the next major release of pandas (pandas 3.0),
(to allow more performant data types, such as the Arrow string type, and better interoperability with other libraries)
but was not found to be installed on your system.
If this would cause problems for you,
please provide us feedback at https://github.com/pandas-dev/pandas/issues/54466

We should just add this warning to the list of ignored warnings.

Steps to Reproduce

python test_gallery.py

Traceback

2024-01-26 21:50:21,867 - INFO - Executing /Users/rly/Documents/NWB/hdmf-zarr/docs/gallery/plot_nwb_zarrio.py
Traceback (most recent call last):
  File "/Users/rly/Documents/NWB/hdmf-zarr/test_gallery.py", line 138, in run_gallery_tests
    _import_from_file(script_abs)
  File "/Users/rly/Documents/NWB/hdmf-zarr/test_gallery.py", line 23, in _import_from_file
    spec.loader.exec_module(module)
  File "<frozen importlib._bootstrap_external>", line 940, in exec_module
  File "<frozen importlib._bootstrap>", line 241, in _call_with_frames_removed
  File "/Users/rly/Documents/NWB/hdmf-zarr/docs/gallery/plot_nwb_zarrio.py", line 32, in <module>
    from pynwb import NWBFile
  File "/Users/rly/mambaforge/envs/test4/lib/python3.11/site-packages/pynwb/__init__.py", line 10, in <module>
    from hdmf.spec import NamespaceCatalog
  File "/Users/rly/mambaforge/envs/test4/lib/python3.11/site-packages/hdmf/__init__.py", line 2, in <module>
    from .backends.hdf5.h5_utils import H5Dataset, H5RegionSlicer
  File "/Users/rly/mambaforge/envs/test4/lib/python3.11/site-packages/hdmf/backends/__init__.py", line 1, in <module>
    from . import hdf5
  File "/Users/rly/mambaforge/envs/test4/lib/python3.11/site-packages/hdmf/backends/hdf5/__init__.py", line 1, in <module>
    from . import h5_utils, h5tools
  File "/Users/rly/mambaforge/envs/test4/lib/python3.11/site-packages/hdmf/backends/hdf5/h5_utils.py", line 22, in <module>
    from ...region import RegionSlicer
  File "/Users/rly/mambaforge/envs/test4/lib/python3.11/site-packages/hdmf/region.py", line 4, in <module>
    from .container import Data, DataRegion
  File "/Users/rly/mambaforge/envs/test4/lib/python3.11/site-packages/hdmf/container.py", line 11, in <module>
    import pandas as pd
  File "/Users/rly/mambaforge/envs/test4/lib/python3.11/site-packages/pandas/__init__.py", line 221, in <module>
    warnings.warn(
DeprecationWarning: 
Pyarrow will become a required dependency of pandas in the next major release of pandas (pandas 3.0),
(to allow more performant data types, such as the Arrow string type, and better interoperability with other libraries)
but was not found to be installed on your system.
If this would cause problems for you,
please provide us feedback at https://github.com/pandas-dev/pandas/issues/54466

Operating System

macOS

Python Executable

Conda

Python Version

3.8

Package Versions

No response

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