Psm-utils

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.

Changed

- `io.xtandem`: Parse double mass modifications as double modification instead of merging and
summing mass shifts into a single modification.
- `io.xtandem`: Avoid float formatting issues when parsing modification mass label.
- `io.xtandem`: Parse all proteins into `protein_list` instead of only the first one.
- `io.tsv`: Log error instead of raising exception when a TSV row cannot be parsed.

Fixed

- `io.xtandem`: Fixed bug when extracting run name (introduced in v0.7.0)