Migration guide

Old spellings that still work, and what replaces them.

Prediction types

Old	New
BindingPrediction, BindingPredictionCollection	Prediction and PeptideResult (see results)
Pred, PeptidePreds	Aliases of Prediction and PeptideResult; use the new names
predict_peptides(peptides)	predict(peptides)
predict_subsequences(sequences, peptide_lengths)	predict_proteins(sequences, peptide_lengths=...)
predict_peptides_dataframe()	predict_dataframe(); now returns the canonical mhctools.pred.COLUMNS schema rather than the legacy columns (prediction_method_name, length, ...)

Convert legacy results with collection.to_preds() (a list of Prediction) or collection.to_peptide_preds() (a list of PeptideResult). The standalone to_peptide_preds() conversion groups by (peptide, offset, source_sequence_name) because it has no input list, so unlike predict() it does not preserve repeated input peptides.

collection = predictor.predict_subsequences({"1L2Y": "NLYIQWLKDGGPSSGRPPPS"},
                                            peptide_lengths=[9])
df = collection.to_dataframe()
preds = collection.to_preds()

Predictor names

Old	New
IedbNetMHCpan, IedbNetMHCcons, IedbNetMHCIIpan, IedbSMM, IedbSMM_PMBEC and their *-iedb CLI names	Still work as local wrappers. Prefer the explicit local names (NetMHCpan41_BA, NetMHCcons, NetMHCIIpan43_BA, SMM, SMMPMBEC) when recording provenance. See compatibility names.
IEDB HTTP constructor arguments url, request_timeout, raise_on_error and the CLI option --do-not-raise-on-error	Removed. There is no HTTP fallback; missing installations and unsupported inputs raise errors.

Commands and options

Old	New
mhctools integrations	mhctools predictors (the old spelling is an alias)
--mhc-epitope-lengths	--mhc-peptide-lengths (deprecated name still accepted)

Kinds

serum_half_life, plasma_half_life, blood_half_life and systemic_elimination_half_life are accepted as input and canonicalized to peptide_half_life, with the matrix kept in the measurement context. canonical_kind() performs the mapping.