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[codex] Add optional ESM embedding helpers - #6

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Axfff wants to merge 1 commit into
2003100127:mainfrom
unibio-hkust-gz-sunnylab:codex/pypropel-esm-feature
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[codex] Add optional ESM embedding helpers#6
Axfff wants to merge 1 commit into
2003100127:mainfrom
unibio-hkust-gz-sunnylab:codex/pypropel-esm-feature

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@Axfff

@Axfff Axfff commented Jun 19, 2026

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Summary

  • Add pypropel.esm helpers for optional ESM model loading, sequence embedding, batch embedding, metadata, and NPZ save/load workflows.
  • Expose the ESM helper module through the public package namespace.
  • Add optional Poetry/setuptools extras for torch and fair-esm.
  • Add documentation for ESM embedding usage.
  • Add tests using fake torch/esm dependencies so the optional heavy packages are not required for the test suite.

Validation

  • /Users/zhaoj/Project/TMInter/.venv/bin/python -m unittest discover -s tests
  • ESM worktree result: Ran 6 tests ... OK

Created as a draft for maintainer review.

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