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chore(tools): pin docking 4, mol-props 2, secondary-pharma 3 - #652
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- docking "3" -> "4": staging drops 3.6.8 in platform-gitops#759. - secondary-pharma "2" -> "3": 2.1.8 is disabled on dev; 3.0.1 is the only enabled version. - mol-props-combined "1" -> "2": 2.0.0 only makes molprops optional with self_test; outputs unchanged. - Drop ABFEParams.annihilate: abfe 2.x / rbfe 2.x removed it from both simulation blocks, and "latest" resolves to 2.x. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
"latest" resolves to 1.x wherever 1.x is the newest enabled version, and 1.x requires the annihilate field the SDK no longer sends. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
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… Admet batch_size (#653) ## Summary - New `src/drug_discovery/ligand_list_file.py`: one inline-vs-file path for Admet, Metabolism, Docking, SecondaryPharmacology (>100 ligands → UFA Ligand list file + `ligands_file`/`ligands_count`); `from_dto` rehydrates both. - Fix: SecondaryPharmacology ligand-ml with >100 unsynced ligands sent file rows without `id`, which preflight rejects; now syncs above the cap. - `Admet(batch_size=...)`: sets `batchSize` (ligands per pod, min 50) on file/project runs. - Needed now that #652 pins docking 4 / secondary-pharma 3, which reject >100 inline ligands. ## Test plan - [x] `uv run pytest tests --env local -p no:xdist`: 1643 passed, 1 failed (`test_pairwise_pose_rmsd_lv0`, fails on main too) - [x] New: `test_secondary_pharma_make_inputs_ligand_ml_above_cap_uses_synced_file`, `test_admet_batch_size_sent_on_workflow_paths_only` - [ ] Dev run: Admet 150 ligands with `batch_size=50` → 3 chunk pods 🤖 Generated with [Claude Code](https://claude.com/claude-code) --------- Co-authored-by: Claude Opus 5.5 <noreply@anthropic.com>
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Summary
"3"→"4": staging drops 3.x in platform-gitops#759."2"→"3": 2.1.8 disabled on dev."1"→"2": additive change only.ABFEParams.annihilate: dropped in abfe/rbfe 2.x (public API break).Test plan
pytest --env local: 1642 passed; 1 failure also onmain(test_pairwise_pose_rmsd_lv0)test_platform_constants.py --env dev: 6 passed🤖 Generated with Claude Code