biocore / kl-metapool / 39500419094

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Update to Python 3.11 (#368)

* build: require Python 3.11 and pandas 3

* fix: preserve behavior under pandas 3 string dtype and Copy-on-Write

- validate_plate_df no longer treats undescribed samples as controls
- astype(str) -> map(str) so missing values still render as 'nan'
- make_replicates accepts all-empty text columns
- text placeholders take the str dtype
- replace deprecated set_index(verify_integrity=True)

* test: adapt tests to pandas 3 and make them checkout-independent

* fix: keep missing values and blank names version-independent under pandas 3

Write missing section values as empty cells, reject a blank Sample_ID
explicitly, and report blank sample names in read counts. The trimmed/raw
split moves from three notebooks into split_trimmed_read_counts.

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