v1.7.5 🌈

Highlights ✨

• Optimized some inputs in the GUI to be more responsive with streamlit forms
• Added support for older xiFDR input files by falling back to the run column if a PeakListFileName is not available
• Fixed a bug in the PyXlinkViewer export that did allow matching of regex patterns to sequences

What's Changed

🚀 Features

• Feat/Optimize GUI inputs by @michabirklbauer in #191
• V1.7.5 by @michabirklbauer in #192

Full Changelog: v1.7.4...v1.7.5

v1.7.4 🌈

Highlights ✨

• The AlphaLink2 exporter now supports output of the required crosslinks pickled file for running AlphaLink2 locally
• Various smaller improvements of the GUI

What's Changed

🚀 Features

• Feat/AlphaLink2 pickle export by @michabirklbauer in #187
• V1.7.4 by @michabirklbauer in #188

📖 Documentation

• Docs/Add Examples ReadMe by @michabirklbauer in #184
• Docs/Add ReadMe for Examples by @michabirklbauer in #185

🧰 Maintenance

• Misc/Add GitHub actions workflow for pages deployment by @michabirklbauer in #189
• Misc/Add GitHub actions workflow for pages deployment by @michabirklbauer in #190

Full Changelog: v1.7.3...v1.7.4

v1.7.3 🌈

Highlights ✨

• Adapted the Scout parser for modification changes introduced in the newest Scout release
• Removed support for reading decoy matches from pdResult files for XlinkX due to the limited available information

What's Changed

🐛 Bug Fixes

• Fix/Adapt parser for Scout v2 modification changes by @michabirklbauer in #181
• V1.7.3 by @michabirklbauer in #182

Full Changelog: v1.7.2...v1.7.3

v1.7.2 🌈

Highlights ✨

• Fixed a bug that prevented reading of n-terminal crosslink modifications in XlinkX result files

What's Changed

🐛 Bug Fixes

• Fix/Handle N-Term Crosslink Protein Positions in XlinkX by @michabirklbauer in #179
• V1.7.2 by @michabirklbauer in #180

Full Changelog: v1.7.1...v1.7.2

v1.7.1 🌈

Highlights ✨

• Fixed a bug that prevented reading of unfiltered crosslink-spectrum-matches from the newest Scout release
• Added documentation to all parsers for which scores are being used, see example here

What's Changed

📖 Documentation

• V1.7.1 by @michabirklbauer in #177

🐛 Bug Fixes

• Fix/Support for Scout v2.0.0 by @michabirklbauer in #176

🧰 Maintenance

• Misc/Update help domain by @michabirklbauer in #172
• Misc/Update help domain by @michabirklbauer in #173

Full Changelog: v1.7.0...v1.7.1

v1.7.0 🌈

Highlights ✨

• Added function to export crosslink-spectrum-matches to ProXL via exporter.to_proxl() link
• Fixed a bug in the source data serialization of result files, e.g. in ➡️item["additional_information"]["source"]
• Various improvements in the GUI

What's Changed

🚀 Features

• Feat/Export to ProXL by @michabirklbauer in #168
• V1.7.0 by @michabirklbauer in #169
• Feat/GUI export to ProXL by @michabirklbauer in #170
• GUI V1.3.0 by @michabirklbauer in #171

Full Changelog: v1.6.1...v1.7.0

v1.6.1 🌈

Highlights ✨

• Added function to annotate FDR for crosslink-spectrum-matches and crosslinks via transform.annotate_fdr() link
• Added function to export crosslinks to AlphaLink2 via exporter.to_alphalink2() link
• Added support for non-standard and placeholder amino acids
• Added the AlphaLink2 exporter to the GUI
• The GUI now also supports multiple result files as input

What's Changed

🚀 Features

• Feat/Add AlphaLink2 exporter, annotate FDR functionality, and various improvements by @michabirklbauer in #160
• V1.6.0 by @michabirklbauer in #161
• Feat/GUI export to AlphaLink2 by @michabirklbauer in #164
• Feat/Support for permissive matching in AlphaLink2 exporter by @michabirklbauer in #165
• V1.6.1 by @michabirklbauer in #166

📖 Documentation

• Docs/Examples - Update 6 by @michabirklbauer in #149
• Docs/Examples - Update 6 by @michabirklbauer in #150
• Docs/Examples - Update 7 by @michabirklbauer in #156
• Docs/Examples - Update 7 by @michabirklbauer in #157
• Docs/Examples - Update 8 by @michabirklbauer in #162
• Docs/Examples - Update 8 by @michabirklbauer in #163

🐛 Bug Fixes

• Fix/GUI: Reset st.session_state on file read by @michabirklbauer in #151
• Fix/GUI: Reset st.session_state on file read by @michabirklbauer in #153

Full Changelog: v1.5.3...v1.6.1

v1.5.3 🌈

Highlights ✨

• All parsers now add the serialized source data to crosslink-spectrum-matches and crosslinks:
  • ➡️ source data can be accessed via item["additional_information"]["source"]
  • ➡️ source data is always a dictionary with str keys
  • ➡️ the exact source data structure, e.g. keys and values, is dynamic due to the different data sources
  • ➡️ recommendation: check source data via item["additional_information"]["source"].keys()

What's Changed

🚀 Features

• Feat/Keep data source when parsing information by @michabirklbauer in #144
• Feat/GUI usability improvements by @michabirklbauer in #147
• V1.5.3 by @michabirklbauer in #148

📖 Documentation

• Docs/Examples - Update 5 by @michabirklbauer in #146

Full Changelog: v1.5.2...v1.5.3

v1.5.2 🌈

Highlights ✨

• Fixed a bug in the xiVIEW exporter which resulted in wrong formatted decoy labels for ambiguous peptides

What's Changed

🚀 Features

• V1.5.2 by @michabirklbauer in #139

📖 Documentation

• update nb formatting by @michabirklbauer in #133
• Docs/Examples - Update 2 by @s48r1n4 in #134
• Docs/Examples - Update 3 by @michabirklbauer in #137
• Docs/Examples - Update 4 by @michabirklbauer in #138

🐛 Bug Fixes

• Fix/Set correct xiView decoy label length by @michabirklbauer in #136

🧰 Maintenance

• Misc/Update codeowners by @michabirklbauer in #140
• Misc/Change MPL backend for pytest by @michabirklbauer in #142
• Misc/Change MPL backend for pytest by @michabirklbauer in #143

New Contributors

• @s48r1n4 made their first contribution in #134

Full Changelog: v1.5.1...v1.5.2

v1.5.1 🌈

Highlights ✨

• Support for reading CSMs and crosslinks directly from dataframes via transform.from_dataframe() link
• Support for parquet files in parser.read_custom() link
• Support for using uv for the streamlit GUI link
• Added DSG to list of pre-defined crosslinkers in data.constants.CROSSLINKERS link

What's Changed

🚀 Features

• Feat/transform/from_dataframe by @michabirklbauer in #123
• Feat/custom_parser/parquet by @michabirklbauer in #124
• Feat/uv support by @michabirklbauer in #126
• Feat/Add Crosslinkers by @michabirklbauer in #127
• V1.5.0 by @michabirklbauer in #129

📖 Documentation

• Docs/[Auto] format examples by @michabirklbauer in #125
• Docs/Update contribution guidelines by @michabirklbauer in #128
• Docs/Add param names in data examples by @michabirklbauer in #130

🐛 Bug Fixes

• Fix/Explicitly require parquet engine by @michabirklbauer in #131
• V1.5.1 by @michabirklbauer in #132

Full Changelog: v1.4.3...v1.5.1