vdjtools 3.12.0

The docs tell you where the signature is

The signature pages were written, committed and live, and nobody could find them: the left sidebar was a flat wall of page titles in source order, so signature sat in it indistinguishable from everything else. index.rst now carries captioned toctrees -- Start here, Repertoire signatures, Models and single cell, Worked examples, Reference -- and the theme renders that structure rather than flattening it, matching seqtree and mhcmatch.

The end-to-end recipe

docs/signature.rst now answers the question people actually ask: a directory of per-sample AIRR TSVs plus your own metadata sheet, to one table you can join.

vdjtools signature --preset classify samples/*.tsv -o vsig.tsv

sample_id is the file name up to the first dot, so naming files after the key your metadata already uses means the join needs no mapping table. For both halves of the signature in one command, mir signature (mirpy) emits the same sample_id and the same column names.

docs/notebooks.rst links the example notebooks, which the docs did not reference at all.

Also

CLAUDE.md records that this repo uses branches, not worktrees: work committed under a gitignored .claude/worktrees/ is invisible from the repo root and effectively unbacked.

1,181 tests pass, 11 skipped.