v1.10.0

What's Changed

Breaking Changes

The config file has been changed to improve clarity and readability. Some parameters have been renamed, others have been dropped.
See here for the changes to the config:
v1.9.2...v1.10.0#diff-673bd31fc26e28495eb9c2d8712bcfb7d8752dca4308217d40737cfd7d1cbe76

• Details:
  • Misc fixes 2 by @mschwoer in #391
  • Refactor config by @mschwoer in #411
  • Change config handling by @mschwoer in #410
  • Simplify config by @mschwoer in #417
  • Improved config for fragment types by @GeorgWa in #424
  • Simplify config file and GUI by @GeorgWa in #479
  • Update prediction config to use enabled pattern by @GeorgWa in #495

New Features

• Multistep search by @mschwoer in #399
• GUI for multistep searches by @GeorgWa in #494

Bug fixes

• fix fdr bug by @mschwoer in #418
• add dynamic hyperparameter scaling by @GeorgWa in #435
• restrict num threads by @GeorgWa in #452
• Add option to write fragment level quant by @ammarcsj in #443
• Adapt transfer library building to diverse fragment types in alphabase 1.5.0 by @GeorgWa in #423
• quant window bug by @GeorgWa in #488

Other Changes / unlabeled

• Remove wsl by @mschwoer in #400
• Refactoring by @mschwoer in #398
• Minor fixes by @mschwoer in #401
• install mono in CI by @mschwoer in #416
• Refactor multistep search by @mschwoer in #402
• renaming Plan -> SearchStep by @mschwoer in #403
• add more unit tests for config by @mschwoer in #414
• Refactor config2 by @mschwoer in #415
• no mono for windows by @mschwoer in #420
• add code review workflow by @mschwoer in #428
• renaming parent path by @mschwoer in #427
• fix search plan tests for windows by @mschwoer in #426
• add speclib file info to docs by @mschwoer in #430
• Hotfix for alphaBase bug by @GeorgWa in #434
• Minor improvementes by @mschwoer in #436
• Fix output path by @mschwoer in #437
• fix actions by @mschwoer in #438
• Replace bumpversion with bump-my-version by @mschwoer in #429
• run also slow tests by @mschwoer in #439
• fix running e2e tests manually by @mschwoer in #440
• fix bug in multistep config output dir by @mschwoer in #445
• Add two step classifier by @anna-charlotte in #431
• Adapt hyperparameter scaling by @GeorgWa in #447
• Fix fasta in cli by @mschwoer in #448
• add stricter linting by @mschwoer in #446
• Adjust config and gui for max_iter parameter by @anna-charlotte in #449
• Adjust two-step-classifier files for stricter linting by @anna-charlotte in #451
• Add missing max iterations parameter by @anna-charlotte in #453
• Add more logging statements to the two step classifier by @anna-charlotte in #456
• UI fixes by @mschwoer in #457
• keep old log files by @mschwoer in #459
• Run test nightly by @mschwoer in #454
• fix tests by adapting to changes in pytorch 2.6 by @anna-charlotte in #463
• Fix updating of the TwoStepClassifier.first_classifier and add logging by @anna-charlotte in #455
• UI improvements by @mschwoer in #461
• Highlight non default by @mschwoer in #471
• Ci improvements by @mschwoer in #469
• Config simplifications by @mschwoer in #466
• Improve multistep docs by @mschwoer in #470
• Add additional unittests for outputaccumulator by @mo-sameh in #450
• Fix config refactoring bug by @GeorgWa in #490
• Save advanced parameters from GUI by @GeorgWa in #492

New Contributors

• @anna-charlotte made their first contribution in #431

Full Changelog: v1.9.2...v1.10.0