Unify predict_peptides_dataframe schema with predict_proteins_dataframe (fixes #193) - #197
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predict_peptides_dataframe (deprecated) returned the legacy BindingPrediction schema — missing predictor_version, kind, value, and using prediction_method_name instead of predictor_name. Meanwhile predict_proteins_dataframe / predict_dataframe emit the canonical mhctools.pred.COLUMNS schema. The asymmetry forced downstream consumers that treat predictions from either path uniformly (e.g. topiary's CachedPredictor design) to None-fill the missing identity columns. Fix: predict_peptides_dataframe now delegates to predict_dataframe, so both batch-dataframe paths emit the same columns. This is a schema change on an already-deprecated method. Callers that relied on the old legacy columns (affinity, prediction_method_name, length) should migrate to the canonical names (value, predictor_name) and add predictor_version / kind.
iskandr
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Apr 15, 2026
predict_peptides_dataframe now emits the canonical COLUMNS schema (matching predict_proteins_dataframe / predict_dataframe). This is a schema change on a deprecated method, hence the minor-version bump.
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Fixes #193.
Summary
`predict_peptides_dataframe` (deprecated) emitted the legacy `BindingPrediction` schema — missing `predictor_version`, `kind`, `value` and using `prediction_method_name` instead of `predictor_name`. `predict_proteins_dataframe` and `predict_dataframe` already emit the canonical `mhctools.pred.COLUMNS` schema.
Fix: `predict_peptides_dataframe` now delegates to `predict_dataframe`, so both batch-dataframe paths emit identical columns.
Schema before → after
Before (peptides path):
```
source_sequence_name, offset, peptide, allele,
score, affinity, percentile_rank,
prediction_method_name, length
```
After (peptides path, matches proteins path):
```
sample_name, peptide, n_flank, c_flank,
source_sequence_name, offset,
predictor_name, predictor_version,
allele, kind, score, value, percentile_rank
```
Breaking change
This is a schema change on an already-deprecated method. Downstream callers that relied on the old column names need to migrate:
New columns (`sample_name`, `n_flank`, `c_flank`, `predictor_version`, `kind`) populate with empty strings or inherited values, as they already do in the proteins path.
Requires a minor bump — I'll tag this 3.13.0.
Test plan