[MNT] Remove pandas 3 warnings

[phoeenniixx]

pandas 3 introduced some deprecations which were clogging up the CI. This PR tries to remove these warnings
Currently removed warnings:

• In a future version, the keys of `groups` will be a tuple with a single element, e.g. (group_id,) , instead of a scalar, e.g. group_id, when grouping by a list with a single element. Use ``df.groupby(by='a').groups`` instead of ``df.groupby(by=['a']).groups`` to avoid this warning
• For backward compatibility, 'str' dtypes are included by select_dtypes when 'object' dtype is specified. This behavior is deprecated and will be removed in a future version. Explicitly pass 'str' to `include` to select them, or to `exclude` to remove them and silence this warning.
• The 'mode.copy_on_write' option is deprecated. Copy-on-Write can no longer be disabled (it is always enabled with pandas >= 3.0), and setting the option has no impact. This option will be removed in pandas 4.0.

[phoeenniixx]

Not sure about the LeafSpec() warning, but I think that is coming from upstream? maybe torch or lightning? See Lightning-AI/pytorch-lightning#21326

[codecov]

Codecov Report

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Additional details and impacted files

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pytest	86.63% <100.00%> (?)

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