Psm-utils

Added

- `io`: Read and write support for writing PSMs to Apache Parquet for efficient storage of PSM lists.
- `io.sage`: Support for Sage results in Parquet format (new `SageParquetReader`, renamed `SageReader` to `SageTSVReader`).

Changed

- Upgrade Pydantic dependency to v2. The PSM `spectrum_id` field is now always coerced to a string.
- `io.proteoscape`: Use pyarrow to iteratively read from Parquet instead of first reading an entire dataframe with Pandas.
- `io.sage`: Update compatibility to Sage v0.14
- Remove temporary patch for caching Proforma modification resolvers (now in Pyteomics v4.7.2).

Added

- Speed up mass calculation for large datasets by caching Proforma modification resolvers.
Temporary patch until implemented in Pyteomics (see levitsky/pyteomics147).

Added

- `io.proteoscape`: Parse filename into PSM `run` field.

Added

- `io.proteoscape`: Allow ProteoScapeReader instantiation from Pandas DataFrame and access PSM by index.

Fixed

- Remove accidental print statement.
- `io.idxml`: Fixed parenthesis in type hint

Changed

- `io.idxml`: Filter OPENMS_DATA_PATH warnings (see compomics/ms2rescore129 and OpenMS/OpenMS7418)
- `io.proteoscape`: Rename module from TIMScore to ProteoScape.
- `io.proteoscape`: Use correct search engine score (`x_corr_score` instead of `tims_score`)

Added

- `io.timscore`: Add support for TIMScore Parquet files.

Fixed

- Fixed `_csv.Error: field larger than field limit (131072)` for very large fields when reading CSV-based PSM files.
- Pinned Pyteomics version to avoid pickling issues in multithreading (to be investigated)

Added

- `Peptidoform`: Support adding and applying global terminal modifications. For now using a
workaround while waiting for official support and an implementation in Pyteomics. See
HUPO-PSI/ProForma6.