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

[lisphilar]

Checkbox

• I agree to follow code of conduct and to engage in discussion actively.
• I agree to create a new issue with the other templates if this is not a bug.
• I used the latest version of covsirphy.

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

No response

Expected outputs

No response

Environment

- CovsirPhy version: 3.0.0
- Python version: 3.11.0

Package manager (required if installation issue)

No response

Platform (required if installation issue)

No response

Additional Context

No response