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DDOS-7952: normalize Pose provenance in do-dd-client - #654
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Canonicalize legacy crystal_extract to cocrystal on every Pose instance, accept both spellings in Protein Prep crystal-pose filtering, extend the public origin vocabulary with manual, and add compatibility tests/docs.
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Copilot review overview
🟢 Approval recommended
The implementation is consistent and well tested, with only minor documentation wording to correct.
Review effort: Balanced
Findings: 1
What changed in this PR
Normalizes legacy Pose provenance while preserving forward compatibility.
Changes:
- Maps
crystal_extracttococrystalacross Pose creation and assignment. - Adds
manualprovenance and Protein Prep compatibility. - Adds tests and provenance documentation.
| File | Description |
|---|---|
src/drug_discovery/structures/pose.py |
Implements origin normalization. |
src/drug_discovery/protein_prep.py |
Accepts legacy cocrystal rows. |
tests/test_pose.py |
Tests normalization paths. |
tests/test_protein_prep.py |
Tests Protein Prep compatibility. |
docs/dd/ref/pose.md |
Documents Pose origins. |
CONTEXT.md |
Records provenance terminology. |
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Align pose.md with the forward-compat contract so callers do not treat the known origins as a closed set.
Retigger required Test Python Code checks after a docs-only push that did not match the workflow path filters.
Capture path-filter retrigger, required-check watcher pitfalls, and the non-exhaustive Pose origin docs nit for future cycles.
docs/agents-only pushes skip Test Python Code path filters; nudge a .py file so formatting and Ubuntu functionality re-run on the tip.
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Summary
Completes the remaining do-dd-client work for DDOS-7952 after toolbox provenance landed in DDOS-7925.
normalize_pose_origin()and enforce it on everyPose(__post_init__/originsetter) so legacycrystal_extractreads as canonicalcocrystalwhile unknown future values pass through.PoseOriginwithmanual._crystal_pose_output_rows()accepts legacy and canonical cocrystal rows before buildingPoseobjects.origin,ligand_name,selection_names) was already shipped; no Pocket code changes.Merge-ready status
Auto-updated — cycle 2, last updated: 2026-10-05T21:35:33Z
mainbd3f9fa56a91bd56a91bd, 0 open threadsmerge-readyRecent activity
docs/agents/merge-ready-lessons.md.Test plan
uv run --extra test --extra core --extra tools pytest tests/test_pose.py tests/test_protein_prep.py -q --env local(138 passed)pytest ... -k 'origin or crystal_poses_from_output'(10 passed)Notes
Depends on toolbox contract from DDOS-7925; this PR is client read/compatibility only.