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chore(tools): pin protein-prep 11 - #658

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Summary

  • Pin deeporigin.protein-prep to "11" (was "10") in TOOL_KEYS_AND_VERSIONS.
  • 11.0.0 adds the mark_prepared action (platform-toolbox #1143, DDOS-8072); existing inputs are unchanged.
  • Update "v10" wording in docstrings, CONTEXT.md, protein-prep docs and notebook.

Test plan

  • uv run pytest tests/test_protein_prep.py tests/test_results.py --env local: 115 passed
  • Protein Prep recommend + run() on staging (serves 10.0.2, 11.0.4 since platform-gitops#762)

🤖 Generated with Claude Code

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
@ASinanSaglam
ASinanSaglam requested a review from a team as a code owner October 6, 2026 23:38

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docs — 0775e8c5 Deployed Oct 6, 2026 by ASinanSaglam via build-docs #853
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