[Bug] DeprecationWarning: DataFrameGroupBy.apply operated on the grouping columns

[lisphilar]

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Summary

Tests failed with the following warning.

DeprecationWarning: DataFrameGroupBy.apply operated on the grouping columns. This behavior is deprecated, and in a future version of pandas the grouping columns will be excluded from the operation. Either pass `include_groups=False` to exclude the groupings or explicitly select the grouping columns after groupby to silence this warning.

Reproducible example script

NA

The current outputs

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Expected outputs

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Environment

- CovsirPhy version: 3.0.0
- Python version: 3.11.0

Package manager (required if installation issue)

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Platform (required if installation issue)

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Additional Context

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