Patch/pq memory opt

[singjc]

• Update parquet export to use duckdb views and copy for more efficient streaming and memory use.
• Added the option to split the osw parquet into a directory of separate precursor data parquet and transition data parquet.
• Update scoring, ipf and level contexts for directory of split parquet inputs

Example

## Original OSW with 50 runs
merged.osw (275G)

## Conversion to split parquet
pyprophet export-parquet --in merged.osw --out merged.pq --scoring_format --split_transition_data

merged.pq (150G)
|-- precursors_features.parquet (7.7G)
|-- transition_features.parquet (143G)

## Scoring (pass the directory with split parquet)
pyprophet score --level ms1ms2 --in merged.pq
pyprophet score --level transition --in merged.pq

## IPF
pyprophet ipf --in merged.pq

## Context level scoring
pyprophet peptide --in merged.pq --context global
pyprophet protein --in merged.pq --context global

Enhancements to Parquet File Handling:

• Added a new utility function is_valid_split_parquet_dir to validate directories containing split Parquet files (precursors_features.parquet and transition_features.parquet). This ensures that both required files exist and are valid Parquet files. (pyprophet/data_handling.py, pyprophet/data_handling.pyR139-R161)
• Introduced new methods read_pyp_parquet_dir_peakgroup_precursor and read_pyp_parquet_dir_transition to handle reading data from split Parquet directories. These methods support precursor-level and transition-level data processing. (pyprophet/ipf.py, [1] [2]

Export Functionality Improvements:

• Added a --split_transition_data option to the export_parquet command, allowing users to export data into separate Parquet files for precursors and transitions. This provides better organization and compatibility with downstream tools. (pyprophet/main.py, pyprophet/main.pyR571-R672)
• Updated the Parquet file export logic to handle existing SCORE_IPF_ columns by dropping them before writing new scores, ensuring data consistency. (pyprophet/ipf.py, pyprophet/ipf.pyR1048-R1090)