v0.0.40 - FragPipe Support

What's Changed

• Add logo by @yueqixuan in #442
• update dev branch by @ypriverol in #443
• update logo of pmultiqc by @ypriverol in #444
• minor changes in the CI/CD by @ypriverol in #445
• Fix logo issue by @yueqixuan in #449
• Update the logo for all the examples. by @ypriverol in #450
• Add citation information for bioRxiv preprint by @Copilot in #453
• citation added to the project by @ypriverol in #454
• Standardize service branding to lowercase "pmultiqc" by @Copilot in #457
• Add option to disable plot tooltips by @yueqixuan in #467
• Solve issue tooltips by @ypriverol in #468
• fix bug by @yueqixuan in #469
• update dev branch by @ypriverol in #471
• Minor bug fixed by @ypriverol in #472
• Add initial support for SDRF integration by @yueqixuan in #476
• minor changes by @ypriverol in #477
• Optimize CodeRabbitAI code suggestions by @yueqixuan in #479
• First iteration about supporting some SDRF-based plots by @ypriverol in #478
• Add support for SDRF integration by @yueqixuan in #483
• SDRF integration in more plots by @ypriverol in #484
• Minor update by @yueqixuan in #487
• fix by @yueqixuan in #489
• Security: Fix path traversal, zip bombs, command injection, and CORS vulnerabilities by @Copilot in #458
• Minor changes in the code and refactoring by @ypriverol in #488
• minor bug fixed. by @ypriverol in #490
• Add FragPipe plugin by @yueqixuan in #494
• FragPipe first implementation by @ypriverol in #495
• Add new features to the FragPipe plugin by @yueqixuan in #498
• FragPipe second iteration by @ypriverol in #499
• Add new features to the FragPipe plugin by @yueqixuan in #502
• Update dev branch by @ypriverol in #504
• Minor update by @yueqixuan in #506
• Third iteration of FragPipe support by @ypriverol in #505
• Add heatmap support to the FragPipe plugin by @yueqixuan in #509
• Heatmap for FragPipe by @ypriverol in #510
• Add Longitudinal Trends module by @yueqixuan in #513
• Update dev by @ypriverol in #514
• fix by @yueqixuan in #516
• First iteration of longitudinal trends module by @ypriverol in #515
• Optimize longitudinal trends by @yueqixuan in #519
• Minor changes in the FragPipe support by @ypriverol in #520
• Auto-update examples by @github-actions[bot] in #521
• Claude Review codebase for performance and bugs by @ypriverol in #523
• fix by @yueqixuan in #525
• Dev by @ypriverol in #524
• Add dataset download links to example reports by @ypriverol in #527
• fix: Dockerfile procps dependency by @selvaebi in #530
• Add intensity-based QC plots to FragPipe by @ypriverol in #532
• Fix by @yueqixuan in #534
• Adding Quant plots to FragPipe based on ion.tsv by @ypriverol in #533
• Refactor pmultiqc service to support FragPipe by @ypriverol in #538
• Tus - transfer improvement using Tus framework by @ypriverol in #539
• Tus implementation to resume transfer by @ypriverol in #540
• Improve FragPipe support and file handling by @ypriverol in #543
• Fix duplicate reports for ion and psm files by @ypriverol in #545
• Minor update by @yueqixuan in #547
• Fix security issue in RAR file extraction by @ypriverol in #548
• fix by @yueqixuan in #549
• Fix by @yueqixuan in #550
• Improving FragPipe by @ypriverol in #544
• Add peptide length distribution by @yueqixuan in #553
• Peptide level distributions by @ypriverol in #554
• fix by @yueqixuan in #555
• Dev by @ypriverol in #556
• Performance improvements and test verification by @ypriverol in #559
• Performance improvements by @claude by @ypriverol in #560

Full Changelog: v0.0.39...v0.0.40

v0.0.39

What's Changed

• Fix boxplot crash by @cbielow in #422
• Update dev branch by @ypriverol in #423
• Fix delta mass ppm by @yueqixuan in #427
• Fix bugs by @yueqixuan in #429
• Link and coding style fix by @cbielow in #428
• Dev by @ypriverol in #431
• Fix contaminant_affix help text to match default value by @Copilot in #435
• Fix the bug in quantms contaminants by @yueqixuan in #436
• Bug fixing when no contaminants in found in quantms by @ypriverol in #437
• Auto-update examples by @github-actions[bot] in #439

Full Changelog: v0.0.37...v0.0.39

v0.0.37 - MultiQC v1.32

What's Changed

• Add Tübingen University pmultiqc service to documentation by @Copilot in #407
• add the service from Tubingen to the documentation by @ypriverol in #408
• Fix psutil dependency issue by removing it completely by @Copilot in #409
• Fix bugs by @yueqixuan in #415
• support multiqc 1.32 by @yueqixuan in #416
• Add FU Berlin University Service to README by @cbielow in #417
• fix: pride visibility by @selvaebi in #414
• Minor changes by @ypriverol in #419
• Auto-update examples by @github-actions[bot] in #420

Full Changelog: v0.0.36...v0.0.37

v0.0.36 - pmultiqc plugin design

What's Changed

During the release of 0.0.35 we introduced l bug in MQ generation report.

• Fix minor bug by @yueqixuan in #401
• Minor change in bug introduced for MaxQuant by @ypriverol in #402

Full Changelog: v0.0.35...v0.0.36

v0.0.35 - pmultiqc plugin design

What's Changed

• elaborate modification table by @cbielow in #363
• fix: docker compose by @selvaebi in #362
• minor changes in docker compose. by @ypriverol in #365
• Fix help text related to MaxQuant by @cbielow in #369
• Dev by @selvaebi in #370
• Dev by @selvaebi in #371
• Added MaxQuant mass recalibration correction by @yueqixuan in #374
• Dev by @ypriverol in #375
• Add configurable BASE_URL and port support for Docker Compose deployments by @Copilot in #373
• Updated the docker compose. by @ypriverol in #379
• Improve the issue reporting. by @ypriverol in #381
• minor changes in the issues templates by @ypriverol in #382
• Refactor modules by @yueqixuan in #386
• Rename DIA-NN command-line argument by @yueqixuan in #387
• Unify CLI formats across modules by @yueqixuan in #388
• Code optimization by @yueqixuan in #391
• Implement Reader and clean up code by @yueqixuan in #392
• first iteration refactoring by @ypriverol in #390
• add plots to mzid_mzml by @yueqixuan in #393
• update test dataset by @yueqixuan in #395
• Refactoring by @ypriverol in #396
• Apply some AI suggestions by @yueqixuan in #397
• minor change by @yueqixuan in #398
• Major refactoring and cleaning of the code. by @ypriverol in #394

New Contributors

• @Copilot made their first contribution in #373

Full Changelog: v0.0.34...v0.0.35

v0.0.34 - DIANN and MaxDIA support

What's Changed

• fix bugs and add plots for mzid by @yueqixuan in #295
• Multiple fix in mzidentml by @ypriverol in #296
• MaxQuant: Fix NaN intensity errors by @cbielow in #304
• Fix bug in proteobench_utils by @yueqixuan in #310
• Update dev branch by @ypriverol in #311
• Fix bugs and add features for DIA-NN by @yueqixuan in #315
• Major changes in DIANN by @ypriverol in #316
• Build final by @selvaebi in #319
• Fix GitHub Actions workflow: remove duplicate ghcr-push.yml and fix i… by @selvaebi in #321
• Build final by @selvaebi in #322
• Update dev branch by @ypriverol in #325
• Fix bugs and add heatmap in DIA by @yueqixuan in #324
• Dev by @ypriverol in #326
• Build final by @selvaebi in #332
• update by @ypriverol in #333
• fix intensity score when all is NaN (2nd attempt) by @cbielow in #331
• minor update by @ypriverol in #336
• Fix nan2 by @cbielow in #341
• Fix bugs and add features in MaxQuant by @yueqixuan in #343
• Major changes added MaxDIA by @ypriverol in #344
• Build by @selvaebi in #352
• Dev by @selvaebi in #354
• Fix bugs in DIANN by @yueqixuan in #357
• Major improvements in DIA by @ypriverol in #358

New Contributors

• @cbielow made their first contribution in #304

Full Changelog: v0.0.33...v0.0.34

v0.0.33 - Major release with bug fixing and service creation

What's Changed

• major changes in index.html by @ypriverol in #269
• feat: GitHub action to push images by @selvaebi in #268
• Auto-update examples by @github-actions[bot] in #270
• support SDRF for DIA-NN by @yueqixuan in #272
• Update DIANN support for SDRF. by @ypriverol in #273
• Auto-update examples by @github-actions[bot] in #275
• support quant table for DIA-NN and MaxQuant by @yueqixuan in #280
• Better Docker Service, handling errors by @ypriverol in #279
• Auto-update examples by @github-actions[bot] in #281
• minor changes by @ypriverol in #282
• Auto-update examples by @github-actions[bot] in #283
• fix bugs and optimize read_mzid by @yueqixuan in #285
• Dev by @ypriverol in #286
• Auto-update examples by @github-actions[bot] in #287
• fix bugs and add features for mzid by @yueqixuan in #291
• Dev by @ypriverol in #292
• Auto-update examples by @github-actions[bot] in #293

New Contributors

• @selvaebi made their first contribution in #268

Full Changelog: v0.0.32...v0.0.33

v0.0.32

What's Changed

• major changes to add service by @ypriverol in #251
• minor changes web by @ypriverol in #253
• Auto-update examples by @github-actions[bot] in #254
• Update to the service by @yueqixuan in #256
• Dev by @ypriverol in #257
• Auto-update examples by @github-actions[bot] in #258
• adding information about the service. by @ypriverol in #260
• SSL proteobench updated by @ypriverol in #261
• Auto-update examples by @github-actions[bot] in #262
• fix for MaxQuant and DIA-NN by @yueqixuan in #264
• Major Bug fixing for MAxQuant and DIANN datasets in PRIDE by @ypriverol in #265
• Auto-update examples by @github-actions[bot] in #266

Full Changelog: v0.0.31...v0.0.32

v0.0.31

What's Changed

• 🔧 see if Python 3.13 works by @enryH in #244
• Auto-update examples by @github-actions[bot] in #245
• Fix github actions by @ypriverol in #246
• Auto-update examples by @github-actions[bot] in #248

Full Changelog: v0.0.30...v0.0.31

v0.0.30

What's Changed

• [Fix] the issue in MaxQuant by @yueqixuan in #228
• Dev by @ypriverol in #229
• [Fix] avoid NaN conversion by @yueqixuan in #232
• Bug fix with NaN handling issue #231 by @ypriverol in #233
• Auto-update examples by @github-actions[bot] in #234
• add support for DIA-NN report.parquet by @yueqixuan in #236
• Dev by @ypriverol in #237
• Auto-update examples by @github-actions[bot] in #238
• add support for quantms DIA-NN 2.0 by @yueqixuan in #240
• refactoring of multiple plugin pmultiqc by @ypriverol in #241
• Auto-update examples by @github-actions[bot] in #242

Full Changelog: v0.0.29...v0.0.30