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MAINT: address all deprecation warnings in test suite #3066

@connortann

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@connortann

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At present, there are several deprecation warnings in the test suite logs. If left unaddressed, these will turn into future failures.

We've had two a few cases of breaking issues, which were previously deprecation warnings. For example, a breaking change in numpy 0.24 delayed our most recent release. Let's fix these issues whilst they're still just warnings!

As an aside, it will also be useful to explicitly ignore warnings that are not within our control or that are false positives. That will keep the pytest output concise, and mean we're more likely to spot any new important warnings. This can be done by adding a line to the filterwarnings setting in pyproject.toml.

Where are the warnings?

Look at the most recent test run on the master branch, on the job called ubuntu-latest, 3.12, test. Example screenshot:

Image

TODO

Completed

  • typing.io
  • distutils
  • sentencepiece
  • tf.keras
  • xgboost
  • LightGBM
  • sklearn (column names)
  • Unable to determine axes for colorbar
  • default value of n_init
  • Numba types scheduled for deprecation
  • pytorch Using a non-full backward hook
  • Pyspark check_additivity
  • No data for colormapping

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    ciRelating to Continuous Integration / GitHub Actionsgood first issueThis is a fix that might be easier for someone to do as a first contribution

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