Fix: calibration refactoring and bug fixes#221

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JemmaLDaniel wants to merge 25 commits into

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fix/calibration-bugfixes

Commits on Jul 16, 2026

Merge branch 'fix/calibration-bugfixes' into fix-tokenised-dataset-contract
JemmaLDaniel
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fix: restore predict metadata and FDR CSV split without mutating input
JemmaLDaniel
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docs: update DatabaseGroundedFDRControl required columns
JemmaLDaniel
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chore: small docstring changes and function naming changes
JemmaLDaniel
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chore: prefer raising ValueErrors over AssertionErrors
JemmaLDaniel
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fix: estimate FDR on labelled-only set in calibration diagnostics
JemmaLDaniel
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Merge pull request #227 from instadeepai/fix-tokenised-dataset-contract
JemmaLDaniel
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fix: filter out None prediction in RetentionTimeFeature
JemmaLDaniel
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fix: require 'correct' column and re-check after possible feature-level filtering
JemmaLDaniel
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docs: note how users can extrapolate database-grounded FDR to unlabelled datasets
JemmaLDaniel
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fix: remap leucine to isoleucine at token level only, leave prediction_untokenised as untouched source
JemmaLDaniel
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