Issues

• Drop Python 3.10 support (end of life October 2026)

  instadeepai/winnow#300 · Filter by author BioGeek opened on Nov 2, 2026

• feat: score every beam candidate and emit the best, not only the top-ranked one

  enhancement
  instadeepai/winnow#299 · Filter by author BioGeek opened on Nov 1, 2026

• fix: winnow predict exits 1 when feature computation legitimately removes every spectrum

  bug
  instadeepai/winnow#298 · Filter by author BioGeek opened on Nov 1, 2026

• processed_peptide_for_match re-implements strip_modifications -- and is the only version that handles N-terminal mods

  instadeepai/winnow#296 · Filter by author BioGeek opened on Oct 29, 2026

• koina.constraints.max_peptide_length / max_precursor_charge and feature learn_from_missing have no effect when a pretrained calibrator is loaded

  instadeepai/winnow#295 · Filter by author BioGeek opened on Oct 29, 2026

• refactor: vectorise per-PSM FDR and q-value assignment in FDRControl

  refactor
  instadeepai/winnow#293 · Filter by author BioGeek opened on Oct 26, 2026

• Refined InstaNovo predictions cannot be loaded: the beam columns move under an instanovo_ prefix

  instadeepai/winnow#292 · Filter by author BioGeek opened on Oct 25, 2026

• build: ship a py.typed marker so downstream type checkers use winnow's annotations

  build
  instadeepai/winnow#288 · Filter by author JemmaLDaniel opened on Oct 21, 2026

• feat: keep the original score columns when a loader transforms their values

  enhancement
  instadeepai/winnow#287 · Filter by author JemmaLDaniel opened on Oct 20, 2026

• fix: loaders silently discard predictions columns that clash with spectrum columns

  bug
  instadeepai/winnow#286 · Filter by author JemmaLDaniel opened on Oct 20, 2026

• refactor: give every type: ignore a reason and tidy duplicated imports

  refactor
  instadeepai/winnow#285 · Filter by author JemmaLDaniel opened on Oct 19, 2026

• docs: remove em dashes and emoji, add missing scope sentence, fix American spellings

  documentation
  instadeepai/winnow#284 · Filter by author JemmaLDaniel opened on Oct 19, 2026

• refactor: modernise type annotations to Python 3.10 syntax

  refactor
  instadeepai/winnow#283 · Filter by author JemmaLDaniel opened on Oct 19, 2026

• ci: replace flake8 and pydocstyle with Ruff rules

  cirefactor
  instadeepai/winnow#282 · Filter by author JemmaLDaniel opened on Oct 19, 2026

• ci: cache pre-commit environments in the lint workflow

  ci
  instadeepai/winnow#281 · Filter by author JemmaLDaniel opened on Oct 19, 2026

• chore: remove GCP credentials script and Google Cloud CLI install

  refactor
  instadeepai/winnow#280 · Filter by author JemmaLDaniel opened on Oct 19, 2026

• docs: generate the API reference from docstrings

  documentation
  instadeepai/winnow#279 · Filter by author JemmaLDaniel opened on Oct 19, 2026

• docs: convert the examples notebook to marimo

  documentation
  instadeepai/winnow#278 · Filter by author JemmaLDaniel opened on Oct 19, 2026

• ci: remove PR-Agent configuration

  ci
  instadeepai/winnow#277 · Filter by author JemmaLDaniel opened on Oct 19, 2026

• docs: restructure documentation to one purpose per page

  documentation
  instadeepai/winnow#276 · Filter by author JemmaLDaniel opened on Oct 19, 2026

• docs: add an Explanation page

  documentation
  instadeepai/winnow#275 · Filter by author JemmaLDaniel opened on Oct 19, 2026

• Greedy-decoded predictions: accept a single candidate, and flag that beam features are then constant

  instadeepai/winnow#270 · Filter by author BioGeek opened on Oct 19, 2026

• Publish which fragment ions matched, not only the predicted ones

  instadeepai/winnow#269 · Filter by author BioGeek opened on Oct 19, 2026

• Train calibrators on AlphaPeptDeep and MS2PIP/DeepLC features: the general model is fitted on Prosit's

  enhancement
  instadeepai/winnow#263 · Filter by author BioGeek opened on Oct 12, 2026

• Train a calibrator on InstaNovo v1.3.0 predictions: the general model is fitted on v1.2.0's

  enhancement
  instadeepai/winnow#262 · Filter by author BioGeek opened on Oct 12, 2026
  1