Changelog

2.1.3 - Green Kakapo

Fixed

  • Create output directory in the translate-igblast command if it doesn’t exist.

  • Allow different prefixes and organism names for igblast germline reference files.

  • Pinned version of transformers to avoid incompatibility with Antiberty.

2.1.2 - Green Weka hotfix II

Fixed

  • Improved TCRT5 and AbLang parallelization.

  • Minor doc fixes.

  • Added multithread processing for translate-igblast.

2.1.1 - Green Weka hotfix

Fixed

  • Fixed automatic locus determination.

  • Fixed example command in documentation.

2.1 - Green Weka

Added

  • Added fine-tuning tutorial

Fixed

  • Make locus uppercase to avoid missmatches.

  • Fixed bug on translation when sequence_vdj column was empty.

  • Fix compatibility for Python 3.14 (does not support AbLang).

2.0 - Brown Kiwi

Added

  • Allow calling Python API as well as CLI.

  • Allow choosing sequence column for translation.

  • Added PROTT5, TCRT5 and TCRbert embeddings.

  • Added Ablang embeddings.

  • Added AnnData export

  • Added possibility to store residue-level embeddings for all models that support them.

Fixed

  • Refactored code to allow extending to TCR embeddings.

  • Used lazy imports to decrease the response time to load help message.

1.1 - Blue Tui

Added

  • Added explicit command for BALM-paired embedding

  • Added Tutorial

  • Added better docs on included embeddings

Fixed

  • When multiple heavy or light chains are present, pick the one with highest duplicate count, not consensus count.

  • Consider IGH, TRB and TRD as heavy chains.

1.0 - Green kea

  • First release on PyPI of amulety