Add: Full parquet support for scoring and inference#137
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singjc merged 20 commits intoPyProphet:masterfrom Apr 28, 2025
Merged
Add: Full parquet support for scoring and inference#137singjc merged 20 commits intoPyProphet:masterfrom
singjc merged 20 commits intoPyProphet:masterfrom
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The commit updates the PyProphet CLI options for input and output files. It adds information about valid file formats and clarifies that the output file must be in the same format as the input file.
This commit updates the `numpy` dependency to version 1.26.4 (currently pyopenms needs <= 1.26.4) and adds a new dependency `polars` with version 1.28.1 to the `pyproject.toml` file.
…OSW files that have missing Gene tables and IM related columns
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This pull request introduces updates for handling of Parquet files. Added a method to convert OSW files to parquet files, and updated scoring, ipf inference and level context inference modules to take parquet as inputs.
Parquet File Handling:
is_parquet_fileandget_parquet_column_namesutility functions inpyprophet/data_handling.pyto validate Parquet files and retrieve column names without reading the entire file.polarsin multiple files (pyprophet/export_parquet.py,pyprophet/ipf.py) to leverage its high-performance DataFrame capabilities. [1] [2]Export and Conversion Enhancements:
export_to_parquetmethod inpyprophet/export_parquet.pyto handle missing DuckDB extensions by attempting installation and loading with error handling.convert_osw_to_parquetmethod inpyprophet/export_parquet.pyto convert OSW SQLite files to Parquet format. This method supports advanced compression options and ensures compatibility with PyProphet scoring.