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docs(04-03): complete CLI score command and tests plan

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- SUMMARY.md: CLI orchestration with checkpoint-restart + 10 comprehensive tests
- STATE.md: Updated position (Phase 4 complete), progress (75%), velocity, decisions
- Duration: 3 minutes, 2 tasks, 4 files (3 created, 1 modified)
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gbanyan
2026-02-11 20:56:31 +08:00
parent a6ad6c6d19
commit 386fbf51b2
2 changed files with 247 additions and 10 deletions
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.planning/STATE.md
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@@ -10,17 +10,17 @@ See: .planning/PROJECT.md (updated 2026-02-11)
## Current Position
Phase: 4 of 6 (Scoring and Integration)
Plan: 2 of 3 in current phase (in progress)
Status: Plan 04-02 complete — quality control and positive control validation
Last activity: 2026-02-11 — Completed 04-02-PLAN.md
Plan: 3 of 3 in current phase (complete)
Status: Phase 04 complete — CLI score command and comprehensive test coverage
Last activity: 2026-02-11 — Completed 04-03-PLAN.md
Progress: [███████░░░] 70.0% (14/20 plans complete across all phases)
Progress: [████████░░] 75.0% (15/20 plans complete across all phases)
## Performance Metrics
**Velocity:**
- Total plans completed: 14
- Average duration: 5.4 min
- Total plans completed: 15
- Average duration: 5.1 min
- Total execution time: 1.3 hours
**By Phase:**
@@ -30,17 +30,17 @@ Progress: [███████░░░] 70.0% (14/20 plans complete across al
| 01 - Data Infrastructure | 4/4 | 14 min | 3.5 min/plan |
| 02 - Prototype Evidence Layer | 2/2 | 8 min | 4.0 min/plan |
| 03 - Core Evidence Layers | 6/6 | 52 min | 8.7 min/plan |
| 04 - Scoring Integration | 2/3 | 7 min | 3.5 min/plan |
| 04 - Scoring Integration | 3/3 | 10 min | 3.3 min/plan |
**Recent Plan Details:**
| Plan | Duration | Tasks | Files |
|------|----------|-------|-------|
| Phase 03 P03 | 11 min | 2 tasks | 7 files |
| Phase 03 P04 | 8 min | 2 tasks | 8 files |
| Phase 03 P05 | 10 min | 2 tasks | 8 files |
| Phase 03 P06 | 13 min | 2 tasks | 10 files |
| Phase 04 P01 | 4 min | 2 tasks | 4 files |
| Phase 04 P02 | 3 min | 2 tasks | 4 files |
| Phase 04 P03 | 3 min | 2 tasks | 4 files |
## Accumulated Context
@@ -107,6 +107,10 @@ Recent decisions affecting current work:
- [04-02]: Missing data thresholds: 50% warn, 80% error for graduated QC feedback
- [04-02]: PERCENT_RANK validation computed before known gene exclusion (validates scoring system)
- [04-02]: Top quartile validation criterion (median percentile >= 0.75 for known genes)
- [04-03]: Score command follows evidence_cmd.py pattern for consistency
- [04-03]: Separate --skip-qc and --skip-validation flags for flexible iteration
- [04-03]: Tests use tmp_path fixtures for isolated DuckDB instances
- [04-03]: Synthetic test data designed to ensure known genes rank highly (0.8-0.95 scores across all layers)
### Pending Todos
@@ -119,5 +123,5 @@ None yet.
## Session Continuity
Last session: 2026-02-11 - Plan execution
Stopped at: Completed 04-02-PLAN.md (Quality control and positive control validation)
Resume file: .planning/phases/04-scoring-integration/04-02-SUMMARY.md
Stopped at: Completed 04-03-PLAN.md (CLI score command and comprehensive tests)
Resume file: .planning/phases/04-scoring-integration/04-03-SUMMARY.md