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test: 12 new CLI tests, 99% coverage; docs sync PRs #93-#98 (#99) - #90
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(#99) Test coverage: - generate-batch: missing seeds file error + successful CSV generation - batch-pack: full success path with JSON and markdown output - pilot-panel: ranked file not found + blank-line skipping + success path (lines 521–571) - novelty-check-broad: empty panel, missing refs, empty refs, empty sequence skip, CLOSE_RELATIVE classification and report output - diversity-check: family structural warnings (TRYPSIN_STABILITY, ≥4 sites × 3 members), redundancy warning section, optimal-cluster-representatives section (optimal ≠ minimal) CLI coverage: 86% → 99% (576 lines, 6 remaining structurally unreachable) Total coverage: 96% → 99% (2171 lines, 14 remaining) Test count: 1292 → 1304 Docs: - ROADMAP.md v0.7.x extended to include PRs #93–#99 - DISCOVERY_PREDICTION.md tracking line extended through PR #99, bottom-line tag updated
…ports - test_diversity_check_family_structural_warning: remove vacuous OR fallback; assert 'Family-Level Structural' directly (reviewer HIGH finding) - test_pilot_panel_blank_lines: n_panel <= 2 → == 2, deterministic with --n 2 and 3 distinct-seed candidates (reviewer MEDIUM finding) - open() calls → context managers / Path.write_text throughout (reviewer LOW finding: Windows-safe file handling)
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Summary
cli.py:generate-batch(missing seeds + success),batch-pack(success + markdown),pilot-panel(file not found + blank-line skip + full success path),novelty-check-broad(empty panel, missing refs, empty refs, empty-sequence skip, CLOSE_RELATIVE classification),diversity-check(family structural warnings, redundancy section, optimal-cluster-representatives section)__main__guard)post-PR #95→post-PR #99Test plan
python3 -m pytest -q— 1304 passed in ~1.3s--cov=src --cov-report=term-missing— TOTAL 99% (14 uncovered lines)🤖 Generated with Claude Code