[cschanhniem]

Summary

• New CLI subcommand synthesis-order (make synthesis-order)
• New module src/openamp_foundry/qc/order_generator.py
• 54 new tests; 1036 total passing

What it does

Reads a confident panel CSV, runs pre-synthesis QC on every candidate, and outputs two files:

1. synthesis_order.csv — GenScript-compatible order form with:

   • pilot_rank, candidate_id, sequence, length, mol_weight_da
   • n_modification — Ac- when interior trypsin sites exist (N-terminal acetylation), Free otherwise
   • c_modification — NH2 when c_amidation_recommended, OH otherwise
   • purity_spec — always >95% HPLC
   • quantity_mg — 2× for HIGH-difficulty, default (5 mg) for LOW/MODERATE
   • synthesis_difficulty, special_handling (condensed, vendor-readable notes)

2. synthesis_checklist.md — human-facing per-candidate brief with:

   • Order summary table (total mg, n Ac-, n NH2, difficulty counts)
   • Pre-order checklist (CoA requirements, Cys/Trp handling, vendor discussion)
   • Per-candidate N-Ac and C-amide rationale
   • Wave 2 D-amino substitution guide

Downstream changes

• cli.py: added synthesis-order subparser + _run_synthesis_order() handler with file-not-found guard
• Makefile: added synthesis-order target (depends on confident_panel.csv)

Test plan

• 54 unit tests in tests/test_order_generator.py
  • _extract_handling flag-to-note mapping (11 tests)
  • Order row structure, N/C modification logic, quantity logic, special handling
  • write_order_csv — creates files, roundtrip, parent dir creation
  • write_synthesis_checklist — content checks, disclaimer, Wave 2 section
  • CLI integration tests — missing-file returns rc=1, outputs created, HIGH 2× qty
  • End-to-end: realistic 4-candidate mixed panel
• python3 -m pytest tests/ -q → 1036 passed

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