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docs(05-01): complete output generation core plan

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- Add 05-01-SUMMARY.md with performance metrics and decisions
- Update STATE.md to Phase 5, Plan 1 of 3 (80% overall progress)
- Record key decisions: configurable tiers, dual-format output, YAML provenance
- Document deviation: pl.count() -> pl.len() deprecation fix

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
This commit is contained in:
gbanyan
2026-02-12 04:01:24 +08:00
parent 5af63eab46
commit 434c79c0a8
2 changed files with 170 additions and 12 deletions
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31
.planning/STATE.md
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@@ -9,19 +9,19 @@ See: .planning/PROJECT.md (updated 2026-02-11)
## Current Position
Phase: 4 of 6 (Scoring & Integration)
Plan: 3 of 3 in current phase (phase complete)
Status: Phase 4 complete — verified (14/14 must-haves, 5/5 requirements)
Last activity: 2026-02-11 — Phase 4 verified and complete
Phase: 5 of 6 (Output & CLI)
Plan: 1 of 3 in current phase (plan 05-01 complete)
Status: Phase 5 in progress — 05-01 complete
Last activity: 2026-02-11 — Plan 05-01 executed and verified
Progress: [████████░░] 75.0% (15/20 plans complete across all phases)
Progress: [████████░░] 80.0% (16/20 plans complete across all phases)
## Performance Metrics
**Velocity:**
- Total plans completed: 15
- Average duration: 5.1 min
- Total execution time: 1.3 hours
- Total plans completed: 16
- Average duration: 5.0 min
- Total execution time: 1.4 hours
**By Phase:**
@@ -31,16 +31,17 @@ Progress: [████████░░] 75.0% (15/20 plans complete across al
| 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 | 3/3 | 10 min | 3.3 min/plan |
| 05 - Output & CLI | 1/3 | 4 min | 4.0 min/plan |
**Recent Plan Details:**
| Plan | Duration | Tasks | 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 |
| Phase 05 P01 | 4 min | 2 tasks | 5 files |
## Accumulated Context
@@ -111,6 +112,12 @@ Recent decisions affecting current work:
- [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)
- [05-01]: Configurable tier thresholds (HIGH: score>=0.7 and evidence>=3, MEDIUM: score>=0.4 and evidence>=2, LOW: score>=0.2)
- [05-01]: EXCLUDED genes filtered out (below LOW threshold or NULL composite_score)
- [05-01]: Deterministic sorting (composite_score DESC, gene_id ASC) for reproducible output
- [05-01]: Dual-format TSV+Parquet with identical data for downstream tool compatibility
- [05-01]: YAML provenance sidecar includes statistics (tier counts) and column metadata
- [05-01]: Fixed deprecated pl.count() -> pl.len() usage for polars 0.20.5+ compatibility
### Pending Todos
@@ -122,6 +129,6 @@ None yet.
## Session Continuity
Last session: 2026-02-11 - Phase 4 execution
Stopped at: Phase 4 complete and verified — all 3 plans executed, 14/14 must-haves verified
Resume file: .planning/phases/04-scoring-integration/04-VERIFICATION.md
Last session: 2026-02-11 - Phase 5 execution
Stopped at: Plan 05-01 complete — tiering, evidence summary, and dual-format writer implemented with tests
Resume file: .planning/phases/05-output-cli/05-01-SUMMARY.md