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Merge release branch for v2.0.0 - #23

Merged

RalfG merged 64 commits into

mainfrom

release/2.0

Jul 13, 2026

Commits on Jan 8, 2026
- Add core module, outline core functionality
  rodvrees
  committed
  1f206d6
- model_ops and calibration
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  committed
  9735019
Commits on Jan 9, 2026
- Calibration refactoring done
  rodvrees
  committed
  52a6b0e
- CLI functionality start
  rodvrees
  committed
  7c12fc5
- Implement prediction logic
  rodvrees
  committed
  e2f69d0
Commits on Jan 12, 2026
- New model
  rodvrees
  committed
  07428d7
- get_default_reference in Calibration class
  rodvrees
  committed
  3ff0946
- Do not use PSMList during calibration
  rodvrees
  committed
  436fb18
- Fix calibration logic
  rodvrees
  committed
  8943fb1
- Fix calibration for multiconformer prediction
  rodvrees
  committed
  1e2a027
- delete outdated modules and model files
  rodvrees
  committed
  8206671
- add tests + adapt code where needed
  rodvrees
  committed
  dca3582
- Add test workflow
  rodvrees
  committed
  b9e1fb4
- update dependencies
  rodvrees
  committed
  e99a871
- pytorch-lightning -> lightning
  rodvrees
  committed
  49bc58f
- update pyproject and README.md
  rodvrees
  committed
  35ccac0
- Remove non-optional optional dependencies
  rodvrees
  committed
  1a4c5ce
Commits on Jan 13, 2026
- Add profiling + use dataframes for calibration
  rodvrees
  committed
  52e1999
- Fix tests
  rodvrees
  committed
  8902973
- Fix error if CCS is directly in df
  rodvrees
  committed
  35f4451
- Fix tests
  rodvrees
  committed
  10b7c32
- Fix if CCS is directly in df
  rodvrees
  committed
  e3c0a18
- Further fixes
  rodvrees
  committed
  074cb9c
- Fix general shift allocation
  rodvrees
  committed
  e3c39eb
Commits on Jan 14, 2026
- throw out im2deeptrainer dependency
  rodvrees
  committed
  40ca412
- update pyproject.toml
  rodvrees
  committed
  ddd62ef
- wandb optional
  rodvrees
  committed
  be33db8
Commits on Jan 19, 2026
- update version
  rodvrees
  committed
  681998e
Commits on Feb 17, 2026
- update __init__.,py
  rodvrees
  committed
  112c5c3
Commits on Mar 16, 2026
- Ruff Ruff
  rodvrees
  committed
  74ff2cb
Commits on Mar 17, 2026
- Update CI workflows:
  RalfG
  committed
  ed966f7
- Merge branch 'new-api' of https://github.com/CompOmics/IM2Deep into new-api
  RalfG
  committed
  84e63c9
- Split up architecture module into subpackage
  RalfG
  committed
  0e4ab37
- Consolidate pytest config to pyproject.toml; fix test workflow; move optional dependencies to dependency groups
  RalfG
  committed
  874fc9f
- Make exceptions public
  RalfG
  committed
  e0efbc9
- Fix linting and formatting issues
  RalfG
  committed
  f6e349b
- Split utils module into public utils and private _io_helpers; fix remaining typing issues; add some to-do's.
  RalfG
  committed
  d7a016a
- Change version to alpha.1
  RalfG
  committed
  c9fdc43
- Add type checking to CI
  RalfG
  committed
  888db74
- Move type checking to separate job with installed package
  RalfG
  committed
  da16941
Commits on Mar 18, 2026
- Use uv build system
  RalfG
  committed
  8157bdd
- Apply suggestions from code review
  
  RalfG
  and
  Copilot
  authored
  1626bec
- Fix remaining issues from code review
  RalfG
  committed
  6e60ff2
- Add module config for uv build backend
  RalfG
  committed
  5be8f47
- Fix linting
  RalfG
  committed
  dd6b1cc
- Update dev dependencies
  RalfG
  committed
  50e39cf
- Fix remaining typing issues
  RalfG
  committed
  9103fa5
- Fix remaining formatting issues
  RalfG
  committed
  140d3cf
- Fix remaining test issues
  RalfG
  committed
  9c4c354
- Fix formatting
  RalfG
  committed
  81ff852
- Merge pull request #18 from CompOmics/new-api
  RalfG
  authored
  51cb69b
- Fix calibration logic by removing error, do not output array in csv when multiconformer prediction
  rodvrees
  committed
  3e98325
- Merge pull request #19 from CompOmics/fix-calibration-logic
  RalfG
  authored
  5191751
Commits on Apr 8, 2026
- deps: Allow newer alpha versions of deeplc
  RalfG
  committed
  4e91e94
- Merge branch 'release/2.0' of https://github.com/CompOmics/IM2Deep into release/2.0
  RalfG
  committed
  8fc2fb4
Commits on Apr 14, 2026
- Add num_threads argument to predict controlling Torch CPU parallelization
  RalfG
  committed
  69ad629
- Fix type checking issues by removing unnecessary type: ignore comments
  RalfG
  committed
  86e1cad
- Merge pull request #20 from CompOmics/feat/control-torch-parallelization
  RalfG
  authored
  696e4b5
- Bump version and update changelog
  RalfG
  committed
  474d6f5
- Add Sphinx documentation
  RalfG
  committed
  f9359c4
- Add readthedocs config
  RalfG
  committed
  58ed69c
- Merge pull request #21 from CompOmics/feat/docs
  RalfG
  authored
  5795b8e
Commits on Jul 13, 2026
- feat: add dependency version constraints; update changelog; bump to stable 2.0 release
  RalfG
  committed
  95f2f77
- Merge pull request #22 from CompOmics/feat/bumps-and-versions
  RalfG
  authored
  363c3e9

Commits

Commits on Jan 8, 2026

Commits on Jan 9, 2026

Commits on Jan 12, 2026

Commits on Jan 13, 2026

Commits on Jan 14, 2026

Commits on Jan 19, 2026

Commits on Feb 17, 2026

Commits on Mar 16, 2026

Commits on Mar 17, 2026

Commits on Mar 18, 2026

Commits on Apr 8, 2026

Commits on Apr 14, 2026

Commits on Jul 13, 2026