[cschanhniem]

Summary

Final hardening pass before synthesis ordering. All issues identified in audit by code-reviewer agent.

CRITICAL

• cli.py pilot-panel JSONL error handling: bare JSONDecodeError crash on any malformed line → structured JSON error with line number and 120-char preview, exit code 1. A single stray character in a multi-thousand-line ranked.jsonl file would have silently terminated the entire pilot panel selection.

HIGH

• CHANGELOG.md Unreleased section updated with PRs fix: resolve CRITICAL pre-wetlab pipeline issues (SEED-008 excluded, benchmark config mismatch) #61–66 impact summaries; stale phase3.yaml: 0.30 line corrected to 0.40 (unified in PR fix: resolve CRITICAL pre-wetlab pipeline issues (SEED-008 excluded, benchmark config mismatch) #61)

MEDIUM

• cli.py validate-scoring stdout: now includes n_positives, n_negatives, benchmark_type, auprc alongside auroc — previously required reading the --out JSON file to see these fields
• cli.py synthesis-order CSV validation: explicit header check before row iteration; missing candidate_id/sequence columns → structured error with found_columns list instead of bare KeyError
• WAVE2_PLAN.md: added SEED-008 (puroindoline-a) Trp mechanism divergence note explaining that disagreement ~0.37 is mechanistic (Boman W=−3.398 vs Wimley-White W=−1.85 kcal/mol), not prediction uncertainty — Wave 2 should expand Trp-rich scaffold confidently if SEED-008 hits

LOW

• presynth_check.py check_sequence(): validates all 20 canonical AAs before running QC; raises ValueError with bad-residue list on non-canonical input

Tests (1191 → 1200)

• TestCheckSequenceInputValidation — 6 tests: canonical accepted, lowercase normalized, non-canonical raises, error message names residues, all 20 AAs accepted
• test_validate_scoring_stdout_includes_n_and_auprc — asserts n_positives=43, n_negatives=44, benchmark_type and auprc in stdout
• test_pilot_panel_malformed_jsonl_returns_error — asserts exit code 1, structured error, "line 2" in message
• test_synthesis_order_missing_columns_returns_error — asserts exit code 1, structured error, "sequence" in message

Test plan

• pytest tests/ -q → 1200 passed
• All 4 new integration tests exercise the new error paths directly
• Existing 1191 tests unchanged

🤖 Generated with Claude Code