Releases: MannLabs/alphadia
Releases · MannLabs/alphadia
v1.9.0
What's Changed
Bug fixes
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
Contributors
GeorgWa, mschwoer, and vbrennsteiner
Assets 6
v1.8.2
What's Changed
Bug fixes
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
Contributors
GeorgWa
Assets 6
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
Contributors
GeorgWa and mschwoer
Assets 6
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
Full Changelog: v1.7.2...v1.8.0
Contributors
GeorgWa, odespard, and 2 other contributors
Assets 6
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
Contributors
GeorgWa, mo-sameh, and mschwoer
Assets 4
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
Full Changelog: v1.7.0...v1.7.1
Contributors
dnusinow, GeorgWa, and 2 other contributors
Assets 4
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
Contributors
GeorgWa, mschwoer, and vbrennsteiner
Assets 4
v1.6.2
What's Changed
Breaking changes
New features
Bug fixes
Improvements
- Several improvements of the documentation
Full Changelog: v1.6.1...v1.6.2
Contributors
mschwoer
Assets 4
v1.6.1
Contributors
GeorgWa and mschwoer
Assets 4
v1.6.0
What's Changed
- Release 1.5.5 by @GeorgWa in #116
- DOCS include slurm install instructions by @GeorgWa in #123
- BUG allow empty modification string by @GeorgWa in #121
- FEAT allow to specify custom DL weights by @GeorgWa in #120
- BUG allow space in binary path by @GeorgWa in #119
- FEAT Accumulator for transfer learning by @mo-sameh in #106
- #125 restart cd workflow after hf bug by @GeorgWa in #126
- CHORE updated configuration of directLFQ by @ammarcsj in #128
- CHORE pre-commit hook & code formatting by @GeorgWa in #129
- FIX bump action version by @GeorgWa in #131
- FEAT allow custom fragment types by @GeorgWa in #136
- FEAT improve interaction with file input by @GeorgWa in #134
- FEAT extraction of fragment intensities for transfer learning by @GeorgWa in #133
- Updated Readme on on main by @GeorgWa in #139
- Add docker by @mschwoer in #137
- FEAT small alphadia logo by @GeorgWa in #141
- FEAT DIA transfer learning by @mo-sameh in #130
- FIX file ending matching by @GeorgWa in #148
- CHORE move code to finetuning subpackage by @GeorgWa in #145
- CHORE move calibration to subpackage by @GeorgWa in #147
- 140 automated e2e tests by @mschwoer in #143
- 156 migrate to pyprojectstoml by @mschwoer in #158
- Pip cache and concurrency by @mschwoer in #159
- 140 e2e self hosted by @mschwoer in #150
- #140: run only on labeled PRs by @mschwoer in #163
- FIX numerical stabilty for small intensities by @GeorgWa in #161
- Update ms2 prediction by @mo-sameh in #151
- FIX install instructions by @GeorgWa in #160
- 140 e2e more test cases by @mschwoer in #162
- 169 fixed dependency versions by @mschwoer in #170
- FEAT SILAC & multiplexing support by @GeorgWa in #149
- Pypi project info by @mschwoer in #177
- #174: enable releasing tags by @mschwoer in #179
- #174: enable releasing tags by @mschwoer in #180
- #174: bump version to 1.6.0 by @mschwoer in #181
New Contributors
Full Changelog: v1.5.5...v1.6.0
Contributors
GeorgWa, mo-sameh, and 2 other contributors