v1.11.0

Algorithmic changes

• Fdr memopt by @mschwoer in #544
  => reduced memory requirements and runtime

These changes should avoid certain algorithmic failures:

• Filter fragments df by @mschwoer in #551
• Fix nonconverged estimators by @mschwoer in #681
• Correct tolerances in transfer lib req handler by @mschwoer in #684

Other relevant changes

• disable MBR step in default configuration by @mschwoer in #644
  => in the CLI only, this confused many people

Some expert features aiming for speed & reproducibity:

• test_numba_caching by @mschwoer in #543
• Allow fixed random seed 2 by @mschwoer in #670

Improved usability, logging and error messages:

• Improve usability by @mschwoer in #655
• Allow saving flat library by @mschwoer in #657
• fix inconsistent output paths by @mschwoer in #683
• Improve config handling by @mschwoer in #521
• Speed up -v and -h by @mschwoer in #539
• Invalid dia data error by @mschwoer in #552
• Wrap train test split error by @mschwoer in #553
• Re enable plotting by @mschwoer in #555

Non-functional changes / Refactoring

The backend has been refactored for modularity and readability.

• Slimmer utils by @mschwoer in #542
• Documentation by @mschwoer in #519
• Fix #546 by @jalew188 in #547
• small improvements of README.md by @mschwoer in #550
• Remove neptune from code by @mschwoer in #554
• Split plexscoring by @mschwoer in #556
• Refactor workflow paths by @mschwoer in #558
• Split features by @mschwoer in #559
• Split outputtransform by @mschwoer in #560
• Split workflow by @mschwoer in #561
• Split workflow ii by @mschwoer in #562
• More splitting by @mschwoer in #563
• update documentation configuration and add autosummary for modules by @mschwoer in #567
• add nb-clean pre-commit hook and apply by @mschwoer in #571
• Fix nbs by @mschwoer in #572
• Minor refactorings by @mschwoer in #573
• move quadrupole.py to plexscoring by @mschwoer in #574
• splitting_IV by @mschwoer in #575
• split_fdr_I by @mschwoer in #576
• split_fdr_II by @mschwoer in #577
• Lint fdr by @mschwoer in #578
• make_e2e_order_deterministic by @mschwoer in #583
• Remove unused methods from quadrupole by @mschwoer in #584
• split_fragcomp by @mschwoer in #585
• lint_fragcomp by @mschwoer in #586
• more_splitting_2 by @mschwoer in #587
• Split validate by @mschwoer in #588
• simplify validation by @mschwoer in #589
• Refactor numba by @mschwoer in #591
• Refactor workflow by @mschwoer in #592
• minor update in distributed search documentation by @vbrennsteiner in #605
• fix a test failing on windows runners by @mschwoer in #599
• Fix neptune in e2e by @mschwoer in #610
• Split containers by @mschwoer in #594
• Split peakgroups by @mschwoer in #595
• Split peakgroups ii by @mschwoer in #596
• Split peakgroups iii by @mschwoer in #597
• Split peakgroups iv by @mschwoer in #598
• inlinee _select_candidates, switch order of arguments by @mschwoer in #601
• Split peptidecentric i by @mschwoer in #602
• Split peptidecentric ii by @mschwoer in #603
• move out requantification_handler.pyi by @mschwoer in #604
• Split peptidecentric iv by @mschwoer in #606
• Split peptidecentric v by @mschwoer in #607
• Split peptidecentric vi by @mschwoer in #608
• Simplify init library by @mschwoer in #609
• split_peptidecentric_VII by @mschwoer in #611
• Misc refactorings by @mschwoer in #612
• Refactor managers i by @mschwoer in #613
• Refactor managers ii by @mschwoer in #614
• inline logic of disable_mobility_calibration() by @mschwoer in #615
• Refactor managers iv by @mschwoer in #616
• split optimizers by @mschwoer in #617
• Refactor managers vi by @mschwoer in #618
• Refactor managers vii by @mschwoer in #619
• Refactor data by @mschwoer in #620
• Misc refactorings ii by @mschwoer in #621
• Misc refactorings iii by @mschwoer in #622
• Refactor fdr manager by @mschwoer in #623
• Misc refactorings iv by @mschwoer in #624
• fix candidate index data type to int64 by @mschwoer in #634
• run also slow tests on every PR by @mschwoer in #627
• restrict output files to specific types in calc_metrics.py by @mschwoer in #642
• More timings by @mschwoer in #628
• Refactor search step by @mschwoer in #629
• remove previously removed classifier from fdr performance test by @mschwoer in #632
• Refactor raw data by @mschwoer in #635
• refactor extraction handler to prepare for multiple strategies by @mschwoer in #636
• Misc feedback by @mschwoer in #637
• reverting fd86f3f by @mschwoer in #645
• Add ng extraction handler by @mschwoer in #643
• Refactor plexscoring by @mschwoer in #647
• Introduce string constants by @mschwoer in #650
• Refactor calibration by @mschwoer in #651
• Refactor calibration ii by @mschwoer in #652
• Refactor calibration iii by @mschwoer in #653
• Refactor calibration iv by @mschwoer in #654
• Refactor calibration v by @mschwoer in #656
• Ng fixes by @mschwoer in #658
• disable norm and use batch norm by @mschwoer in #665
• Refactor search by @mschwoer in #660
• change classifier in to legacy_new_batching in fdr_test.py by @mschwoer in #667
• Refactor misc by @mschwoer in #662
• Improve gui 2 by @mschwoer in #674
• Dont repeat fdr for plotting 2 by @mschwoer in #671
• Improve logging by @mschwoer in #672
• Generify batch plan by @mschwoer in #685
• Misc changes by @mschwoer in #679
• manually bump alphabase version by @mschwoer in #682
• Dedicated ng defaults 2 by @mschwoer in #680

Full Changelog: v1.10.3...v1.11.0