Webserver deployment issues

What's Changed

• Update DDA_Quant_ion.py by @RobbinBouwmeester in #341

Full Changelog: v0.3.0...v0.3.1

Issue fixes and refactoring

What's Changed

• Remove dependencies on secrets by @RobbinBouwmeester in #322
• Catch GH error by @RobbinBouwmeester in #323
• New parsing for variety of MQ versions by @RobbinBouwmeester in #324
• Add proteobench version for parsing and calc metric by @RobbinBouwmeester in #325
• Test MQ by @RobbinBouwmeester in #326
• Add exceptions by @RobbinBouwmeester in #327
• Update DDA_Quant_ion.py by @RobbinBouwmeester in #329
• Test proline #153 by @wolski in #331
• Nox and notebooks by @wolski in #319
• Refactor gh py 276 by @wolski in #332
• Add pre-commit checks to ProteoBench by @wolski in #334
• add file for testing custom format by @mlocardpaulet in #337
• add i2MassChroQ file for testing by @mlocardpaulet in #336
• Start changing webpage texts by @RobbinBouwmeester in #330
• 🐛 Close 338 parsing MQ 2.6 (minPepLen) by @enryH in #340

Full Changelog: v0.2.10...v0.3.0

Support FragPipe, improve docs, dynamic versioning and Proline parsing updates

What's Changed

• add comments and doc regarding FragPipe protein groups parsing by @mlocardpaulet in #306
• Fix double brackets and C-terminal mods by @RobbinBouwmeester in #307
• 🐛 Fix FragPipe parameter parsing by @enryH in #302
• 🐛 Allow local use and UploadFile use in streamlit. Fix #310 by @enryH in #311
• ✨ support dynamic version (identify version by latest tag+co… by @enryH in #312
• 📝 Add current proteobench version to landing page of UI by @enryH in #313
• adding gdpr notices if provided by @julianu in #314
• refactoring the sidebar and general configs by @julianu in #317
• Documentation by @mlocardpaulet in #278
• 📝 harmonize version in CHANGELOG.md by @enryH in #315
• 🐛 update publishing workflow by @enryH in #318
• 🐛 fix "-" as psm-fdr setting by @enryH in #320

Full Changelog: v0.2.9...v0.2.10

v0.2.8

• modify documentation and website by @mlocardpaulet in #304

Full Changelog: v0.2.8...v0.2.9

v0.2.7

New

• Update documentation

v0.2.6

• Refactor module
• Handle parameter input for FragPipe outputs public upload
• Add i2MassChroQ

v0.2.5

What's Changed

• Refactor module
• Handle parameter input for FragPipe outputs public upload
• Add i2MassChroQ

Full Changelog: v0.2.4...v0.2.5

v0.2.4

New

• Analysis notebooks
• start contribution page
• clean up contribution
• Update index.rst
• add tolerance unit of alphapept search
• update ProteoBench on server after update
• Fragpipe params upload

v0.2.3

New

• Fixed removing column highlights

v0.2.2

New

• Fixed parsing proline
• Added initial stages of peptidoform module