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Merged
RalfG merged 1 commit into from
Oct 27, 2025
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Update changelog #133

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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -15,6 +15,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
### Changed

- ♻️ `stats.qvalues`: Set the **regular target–decoy formula** explicitly in Pyteomics when `remove_decoy=False` and apply the **+1 correction** (probability that the first excluded decoy out-scores the threshold PSM). This produces less overly conservative q-values (e.g., on `example_files/msms.txt`). (#128)
- ♻️ `io.pepxml`: Refactor spectrum naming logic to prefer `spectrumNativeID` when available
- 🏷️ **Typing**: Adopted full **MyPy** typing across the codebase. (#125)
- 👷 **CI**: Replaced file-hash–based tests for `io.idxml` with unit tests; added formatting checks. (#125)

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