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