Psm-utils

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)

Added

- Tests: Added tests for \_format_number_as_string function
- Tests: Added more test cases for `peptidoform.rename_modifications` for mass modifications
- `io.xtandem`: To parse `run` value, fall back to PSM file name if run name cannot be parsed from `label` field

Fixed

- `peptidoform.rename_modifications`: Fixed mapping of negative mass modifications
- `io.xtandem`: Fixed regular expression to parse `run` value fom XML `label` field
- `io.idxml`: Fix handling multiple types in `rescoring_features` when writing (fixes 60)

Added

- `io.idxml`: Write support for idXML files, including merging an existing idXML with a `PSMList` 🎉
- `io.xtandem`: New argument `score_key` to select which score to parse as `PSM.score`.
- `io.xtandem`: Parse `run` name from X!Tandem PSM files
- Docs: Add intersphinx links to other package documentation pages.

Changed

- `io.idxml`: Use pyOpenMS instead of Pyteomics for reading idXML (~5x faster⚡)

Fixed

- Fix reading of pepXML files without RT
- Fixed Black formatting throughout project

Fixed

- `io.pepxml`: Fix reading pepXML files without retention time information.

Added

- `io`: Added new `io.pepxml` reader

Fixed

- Docs: Add ionbot to README.rst, fix order in API docs