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Various fixes and improvements for v4.0.1 - #276

Merged

RalfG merged 16 commits into

mainfrom

fix/config-defaults-4.0.1

Jul 24, 2026

Merged

Various fixes and improvements for v4.0.1#276
RalfG merged 16 commits into
mainfrom
fix/config-defaults-4.0.1

Commits on Jul 22, 2026
- fix: remove stale ms2_tolerance from ms2pip config
  RalfG
  committed
  ef5a4a2
- refactor: rename deeplc_retrain to finetune, clean up predict/finetune kwarg distribution
  RalfG
  committed
  a0c59fc
- fix: document im2deep's model_dir/reference_dataset defaults, drop dead code
  RalfG
  committed
  f990cde
- Update changelog
  RalfG
  committed
  ec448ea
- fix: remove placeholder link crashing ReadTheDocs build
  RalfG
  committed
  5d93227
- docs: add migration guide
  RalfG
  committed
  a0a0973
Commits on Jul 24, 2026
- docs: consolidate 4.0.0 alpha and stable release changelogs
  RalfG
  committed
  74259e2
- docs: backfill CHANGELOG.md with past release notes
  RalfG
  committed
  3b2298f
- Merge remote-tracking branch 'origin/worktree-changelog-history' into fix/config-defaults-4.0.1
  RalfG
  committed
  6ab0c33
- docs: add computational performance section to migration guide
  RalfG
  committed
  c8d8f68
- chore(deps): bump deeplc to stable 4.0.0
  RalfG
  committed
  9132c32
- docs: add more details to contribution guide
  RalfG
  committed
  e7b4faf
- build(deps): rely on uv.lock for installer versions, harden CI sync
  
  RalfG
  and
  Copilot
  committed
  3ba643f
- deps(lock): upgrade all locked dependencies
  RalfG
  committed
  03ddf4a
- chore: prepare for release; bump version; update changelog
  RalfG
  committed
  651c7b0
- fix(report): show missing feature-weights chart in HTML report
  RalfG
  committed
  d470e73