v1.8.8 🌈

Highlights ✨

• Added support for reading files exported from xiNET via parser.read_xinet() link
• Added support for reading files exported from xiVIEW via parser.read_xiview() link
• Added support for xiNET and xiVIEW parsing in the generic parser via parser.read(..., engine="xiNET/xiVIEW") link
• Added support for result files from the newest Scout version
• Added full support for mzIdentML versions 1.2 and 1.3
• Added a new function to reannotate decoy labels via transform.reannotate_decoy_labels() link
• Added a new function to filter by residue pair via transform.filter_residue_pair_distribution() link
• Added a new function to plot the residue pair distribution via plotting.plot_residue_pair_distribution() link
• Added a new function to annotate STRING scores for inter-links via transform.annotate_string_scores() link
• Added support for passing additional **kwargs to parsers
• Added a function to pretty print pyXLMS data structures via transform.display() link
• Various bug fixes (see changelog below)
• Upgraded the GUI to v1.4.0 using pyXLMS v1.8.8

What's Changed

🚀 Features

• Feat/xiNET and xiVIEW parser by @michabirklbauer in #205
• Feat/Update Scout parser by @michabirklbauer in #211
• Feat/Update mzIdentML parser by @michabirklbauer in #212
• Feat/Reannotate Decoy Labels by @michabirklbauer in #214
• Feat/Add Residue Pair Distribution Filter & Plot by @michabirklbauer in #218
• Feat/STRING integration by @michabirklbauer in #221
• Feat/Support for *kwargs in parser.read by @michabirklbauer in #222
• V1.8.7 by @michabirklbauer in #223
• V1.8.8 by @michabirklbauer in #225
• GUI/Feature Update for pyXLMS v1.8.8 by @michabirklbauer in #228
• GUI V1.4.0 by @michabirklbauer in #230

📖 Documentation

• Fix/Tool naming by @michabirklbauer in #193
• fix: FDR documentation by @michabirklbauer in #195
• Update FDR documentation & upgrade CI by @michabirklbauer in #197
• Documentation and small QOL updates by @michabirklbauer in #224

🐛 Bug Fixes

• Fix/Modification parsing for MS Annika and XlinkX by @michabirklbauer in #206
• Fix/Account for Target and Decoy Labels in XL Grouping by @michabirklbauer in #209
• Fix/Reset File Pointer on Sequential Reads by @michabirklbauer in #216
• Fix/Add xiVIEW Parser to Pipeline by @michabirklbauer in #219

🧰 Maintenance

• misc: upgrade workflows by @michabirklbauer in #196
• misc: add code coverage to pytest by @michabirklbauer in #198
• misc: upgrade python packages in gui lockfile by @michabirklbauer in #199
• misc: code coverage, gui package upgrades by @michabirklbauer in #200
• Misc/Type Checking with ty by @michabirklbauer in #210
• Misc/Upgrade GitHub Actions by @michabirklbauer in #217
• Misc/Fix Python Package Test CI by @michabirklbauer in #226
• Misc/Fix Python Package Test CI by @michabirklbauer in #227
• Misc/Upgrade GitHub Actions Workflows by @michabirklbauer in #229

Full Changelog: v1.7.5...v1.8.8