v0.5.3

What's Changed

• Update quant_base_module.py by @RobbinBouwmeester in #462

Full Changelog: v0.5.2...v0.5.3

Issues with storing submitted data

What's Changed

• Add protein columns to alphadia and spectronaut TOMLs by @rodvrees in #445
• Change saving from intermediate to raw input by @RobbinBouwmeester in #461

Full Changelog: v0.5.1...v0.5.2

v0.5.1

What's Changed

• Documentation dda peptidoforms by @mlocardpaulet in #441
• fix param parsing for diann issue #447 by @wolski in #448
• Fix link to fasta by @rodvrees in #450
• homogenise peptidoform strings in DDA result files by @Cajac102 in #446

Full Changelog: v0.5.0...v0.5.1

v0.5.0

What's Changed

• constrain dependency st-pages to <1.0 by @bfurtwa in #420
• Fix alphadia params parsing by @rodvrees in #428
• Provide fasta and raws, correct docu by @julianu in #431
• MSAID output compatibility by @rodvrees in #430
• Fix proforma parsing for FragpipeDIA and AlphaDIA by @rodvrees in #435
• Rem unused functions, part rename by @RobbinBouwmeester in #432
• Update 4-DIA-Quantification.md to provide info about DIA-NN log level setting by @rodvrees in #433
• 🐛 temporay file alwas opened as text object, even if it's binary by @enryH in #425
• ✨ Update Proline Studio parameter parsing by @enryH in #422
• Spectronaut params by @wolski in #437
• Show peptidoform DDA quant module by @RobbinBouwmeester in #440

New Contributors

• @bfurtwa made their first contribution in #420

Full Changelog: v0.4.0...v0.5.0

v0.4.0

What's Changed

• Update input_file_description.md by @brvpuyve in #358
• Added new sample file for i2MassChroQ by @scaramonche in #362
• Update 2-DDA-Quantification-ion-level.md by @brvpuyve in #365
• fragpipe v22 params file can now be parsed by @scaramonche in #367
• Created DIA quant ion beta page by @Alirezak2n in #364
• Update 2-DDA-Quantification-ion-level.md by @brvpuyve in #368
• Dia by @Alirezak2n in #375
• added a container to download the raw data by @julianu in #369
• Renamed Proline to Proline Studio by @scaramonche in #376
• Rename sample files by @scaramonche in #363
• Change color by @scaramonche in #381
• Delete duplicated plot file in utils/plotting/ by @scaramonche in #379
• Show submission comment instead of additional comment for public runs. by @scaramonche in #382
• added small helper to get info for all submitted datasets by @julianu in #383
• Remove additional params except for comments by @scaramonche in #384
• Add documentation and docstrings, improve DIA-NN parsing, refactoring by @Cajac102 in #378
• Added information about dataset download by @julianu in #391
• Show the corrrect comment fields and information depending on whether they are private of public submissions by @scaramonche in #392
• Proline fix by @scaramonche in #398
• Added back the parameter parsing dict and fixed the gh body message. by @scaramonche in #397
• Add support for maxdia parameter parsing by @Alirezak2n in #394
• Redesign landing page by @RalfG in #390
• Add support for spectronaut by @rodvrees in #399
• Add support for FraggerDIA by @rodvrees in #395
• Support for non-DIANN quant Fragpipe DIA output by @rodvrees in #402
• Enhance plot by @RobbinBouwmeester in #405
• Enhance plot by @Cajac102 in #401
• Merge pull request #405 from Proteobench/enhance_plot by @RobbinBouwmeester in #406
• Fragpipe params by @rodvrees in #408
• Spectronaut: allow comma as decimal separators by @rodvrees in #409
• Update logos by @mlocardpaulet in #411
• Changed tab descriptions by @RobbinBouwmeester in #413
• Change reading of params by @RobbinBouwmeester in #414
• Update index.srt to add the module proposed for the Dev. Meet. by @mlocardpaulet in #410

New Contributors

• @Alirezak2n made their first contribution in #364
• @Cajac102 made their first contribution in #378
• @rodvrees made their first contribution in #399

Full Changelog: v0.3.3...v0.4.0

v0.3.3

What's Changed

• Fix GH by @RobbinBouwmeester in #351

Full Changelog: v0.3.2...v0.3.3

Allow for additional modules

What's Changed

• server update by webhook by @julianu in #342
• New Peptidoform module by @RobbinBouwmeester in #343

Full Changelog: v0.3.1...v0.3.2

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