v1.9.2

What's Changed

Other Changes / unlabeled

• Misc improvements by @mschwoer in #390
• fix: zero predictions for ms2 by @mo-sameh in #409
• Bump version: 1.9.1 → 1.9.2 by @mschwoer in #412
• fix dask version by @GeorgWa in #413
• fix the nans in accumulated transferlib bug by @mo-sameh in #419

Full Changelog: v1.9.1...v1.9.2

v1.9.1

What's Changed

Bug fixes

• fix bug in get_frame_indices by @mschwoer in #389
  This causes AlphaDIA to stall at the "Starting candidate selection" step in some cases. Was introduced in v1.9.0

Other Changes / unlabeled

• update alphabase to 1.4.2 by @mschwoer in #389
• Bump version: 1.9.0 → 1.9.1 by @mschwoer in #392
• Development by @mschwoer in #393

Full Changelog: v1.9.0...v1.9.1

v1.9.0

What's Changed

Bug fixes

• Zero slice bug by @GeorgWa in #374
• Transfer Library Bug by @GeorgWa in #382

New Features

• Improved calibration and optimization stats by @GeorgWa in #369
• Distributed Search by @vbrennsteiner in #364
• alpharaw hdf reader by @GeorgWa in #381

Other Changes / unlabeled

• autofixes for linting by @mschwoer in #366
• add notes how to debug with vscode by @mschwoer in #370
• Rename progress folder by @mschwoer in #371
• introduce rawfilemanager by @mschwoer in #372
• Add rt length to output ii by @mschwoer in #373
• update and layout docs by @GeorgWa in #386
• Bump version: 1.8.2 → 1.9.0 by @GeorgWa in #387
• release 1.9.0 by @GeorgWa in #388

Full Changelog: v1.8.2...v1.9.0

v1.8.2

What's Changed

Bug fixes

• BUG zero division on zero intensity detector events by @GeorgWa in #358

Other Changes / unlabeled

• libfree gui tutorial by @GeorgWa in #354
• Dimethyl tutorial by @GeorgWa in #355
• update debug notebook by @GeorgWa in #357
• Guid for evaluation transfer learning performance by @GeorgWa in #359
• Prepare 1.8.2 by @GeorgWa in #361
• Release 1.8.2 by @GeorgWa in #360

Full Changelog: v1.8.1...v1.8.2

v1.8.1

What's Changed

Bug fixes

• BUG optimization lock, fix #347 by @GeorgWa in #348
• Allow correct processing of empty files by @GeorgWa in #349

Other Changes / unlabeled

• Bump alphaX dependencies by @GeorgWa in #346
• Remove old release workflow by @mschwoer in #345
• Bump version: 1.8.0 → 1.8.1 by @GeorgWa in #350
• Change modlayout default by @GeorgWa in #352
• release 1.8.1 by @GeorgWa in #351

Full Changelog: v1.8.0...v1.8.1

v1.8.0

What's Changed

Bug fixes

• BUG in timstof transpose function by @GeorgWa in #307
• BUG multiplexing fails due to missing column by @GeorgWa in #314
• BUG max-lr not used correctly by @GeorgWa in #311

New Features

• Add unknown mods by @GeorgWa in #291
• Add automatic calibration by @odespard in #293
• timing manager by @odespard in #306
• Multiplex spectral library by @GeorgWa in #292
• FEAT enable selection of alternative peptdeep models by @GeorgWa in #312

Other Changes / unlabeled

• Selecting classifier version by @odespard in #282
• MS2 Optimizer by @odespard in #283
• Getting the right classifier version in the optimizer by @odespard in #287
• Transfer learning documentation by @mo-sameh in #266
• make error handling automation-friendly by @mschwoer in #279
• raise on missing checkpoint path by @GeorgWa in #290
• add parameters to stat.tsv by @odespard in #302
• Fix slurm install instructions by @mschwoer in #294
• fix test case data by @mschwoer in #298
• #299: add slurm e2e script by @mschwoer in #300
• 296 reduce alphadia output by @mschwoer in #297
• Calibrate optimization lock only during optimization by @odespard in #301
• extend transfer-learning to include mobility by @mo-sameh in #303
• New dynamic lock with RT proportion by @odespard in #316
• New dynamic optimization lock by @odespard in #309
• Calibrate relevant subset in dynamic lock by @odespard in #317
• Make optimization configurable by @odespard in #318
• Refactor parameter proposal by @odespard in #319
• Fix timing manager by @odespard in #321
• Make convergence configurable by @odespard in #322
• Make fragment calibration configurable by @odespard in #323
• New RT convergence criteria by @odespard in #320
• Fix optimizer plotting by @odespard in #325
• Refactor search parameter optimization by @odespard in #324
• allow definition of target RT as fraction by @odespard in #328
• fix error with config by @odespard in #327
• Use batch index at optimum by @odespard in #329
• Additional convergence criterion by @odespard in #330
• Refactor convergence rules by @odespard in #331
• make automatic default by @odespard in #336
• updated documentation by @odespard in #334
• Proceed if insufficient precursors by @odespard in #333
• feat: save stats of transfer learning to disk by @mo-sameh in #338
• Fix incorrect mobility outputaccumulator by @mo-sameh in #337
• Refactor Finetune Manager by @mo-sameh in #310
• Adapt to new release workflow by @mschwoer in #326
• bump version to 1.8.0 by @mschwoer in #342
• GUI fixes by @GeorgWa in #343
• Release 1.8.0 by @GeorgWa in #344

New Contributors

• @odespard made their first contribution in #282

Full Changelog: v1.7.2...v1.8.0

v1.7.2

What's Changed

Bug fixes

• Bugfixes in GUI by @GeorgWa in #275
• Fail transparently for failed output accumulation by @GeorgWa in #278
• Fix out of bounds segfault by @GeorgWa in #272

Other Changes / unlabeled

• Development by @mschwoer in #199
• Simplified pyinstaller script by @GeorgWa in #265
• change plotting to use seaborn by @mo-sameh in #267
• 268 divisionbyzeroerror by @mschwoer in #269
• Update Badges in README.md by @GeorgWa in #271
• update debug notebook by @GeorgWa in #274
• Cleanup unused numba functions by @GeorgWa in #273
• release 1.7.2 by @GeorgWa in #276

Full Changelog: v1.7.1...v1.7.2

v1.7.1

What's Changed

Bug fixes

• fix warnings for scheduler step and early stopping by @mo-sameh in #252
• FIX remove numba strict true by @GeorgWa in #259
• FIX Overwrite old profile by @GeorgWa in #255

New Features

• FEAT Change transferlearning metrics datastructure by @mo-sameh in #232
• FEAT modular FDR core implementation by @GeorgWa in #229
• Include raw name in transfer lib by @GeorgWa in #254

Other Changes / unlabeled

• 230 basic linting by @mschwoer in #231
• 230 basic linting rule e by @mschwoer in #233
• 230 basic linting rule f by @mschwoer in #235
• 230 basic linting rule f remove unused by @mschwoer in #236
• CHORE fix supported python version 3.10 - 3.12 by @GeorgWa in #239
• 230 basic linting rule up by @mschwoer in #237
• 230 basic linting rule sim by @mschwoer in #238
• 230 basic linting rule b2 by @mschwoer in #241
• #230: ruff rule B006: auto fixes by @mschwoer in #242
• 230 basic linting rule i2 by @mschwoer in #244
• Add conda to docu by @mschwoer in #245
• Add test split by @mo-sameh in #243
• #230: ruff rule B905: add strict keyword to zip by @mschwoer in #246
• FIX Readme by @GeorgWa in #256
• CHORE: raise on output error by @mschwoer in #253
• BUG: fix issue with zip strict & numba by @mschwoer in #258
• #261 install MANIFEST.in in docker container by @dnusinow in #262
• Fix loose tests and Docker issues by @mschwoer in #263
• BUG: fix release building by @mschwoer in #264

New Contributors

• @dnusinow made their first contribution in #262

Full Changelog: v1.7.0...v1.7.1

v1.7.0

What's Changed

• Development by @mschwoer in #199
• Fix uname issue by @mschwoer in #201
• DOCS Improved installation and method section by @GeorgWa in #203
• Add readthedocs link and badge by @mschwoer in #206
• DOCS update readme by @GeorgWa in #210
• release 1.6.2 by @GeorgWa in #204
• CHORE fixed alphabase requirement by @GeorgWa in #193
• FIX fasta for Bruker by @GeorgWa in #213
• Added features to grouping.py and update tutorial notebook to heuristic grouping by @vbrennsteiner in #171
• FIX Pip no cache by @GeorgWa in #220
• FEAT update plotting utils by @GeorgWa in #219
• FEAT logging raw file stats by @GeorgWa in #216
• 140 plot history by @mschwoer in #172
• FEAT Set log level from config by @GeorgWa in #215
• FIX transfer learning bug by @GeorgWa in #218
• FEAT Use parquet files as output by @GeorgWa in #222
• FEAT automatic transfer learning in consensus pipeline by @GeorgWa in #223
• Fix logger issue by @mschwoer in #227
• FEAT transfer learning controls in GUI by @GeorgWa in #226
• CHORE raise alphabase version by @GeorgWa in #228
• Release 1.7.0 by @GeorgWa in #217

Full Changelog: v1.6.2...v1.7.0

v1.6.2

What's Changed

Breaking changes

New features

Bug fixes

• FIX fix issue with windows uname by @mschwoer in #201

Improvements

• Several improvements of the documentation

Full Changelog: v1.6.1...v1.6.2