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docs(01-03): complete DuckDB persistence and provenance tracking plan

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Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
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gbanyan
2026-02-11 16:34:00 +08:00
parent 0200395d9e
commit 92322b1d7c
2 changed files with 265 additions and 9 deletions
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.planning/STATE.md
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@@ -10,24 +10,24 @@ See: .planning/PROJECT.md (updated 2026-02-11)
## Current Position
Phase: 1 of 6 (Data Infrastructure)
Plan: 1 of 4 in current phase
Plan: 3 of 4 in current phase
Status: Executing
Last activity: 2026-02-11 — Completed 01-01-PLAN.md (Project scaffold, config system, base API client)
Last activity: 2026-02-11 — Completed 01-03-PLAN.md (DuckDB persistence and provenance tracking)
Progress: [██░░░░░░░░] 16.7% (1/6 phases planned, 1/4 plans in phase 1 complete)
Progress: [███░░░░░░░] 25.0% (1/6 phases planned, 2/4 plans in phase 1 complete)
## Performance Metrics
**Velocity:**
- Total plans completed: 1
- Average duration: 3 min
- Total execution time: 0.05 hours
- Total plans completed: 2
- Average duration: 2.5 min
- Total execution time: 0.08 hours
**By Phase:**
| Phase | Plans | Total | Avg/Plan |
|-------|-------|-------|----------|
| 01 - Data Infrastructure | 1/4 | 3 min | 3 min/plan |
| 01 - Data Infrastructure | 2/4 | 5 min | 2.5 min/plan |
## Accumulated Context
@@ -42,6 +42,8 @@ Recent decisions affecting current work:
- Modular CLI scripts for flexibility during development
- Virtual environment required for dependency isolation (01-01: PEP 668 externally-managed Python)
- Auto-creation of directories on config load (01-01: data_dir, cache_dir field validators)
- [Phase 01-data-infrastructure]: DuckDB over SQLite for DataFrame storage (native polars/pandas integration, better analytics)
- [Phase 01-data-infrastructure]: Provenance sidecar files alongside outputs (co-located metadata, bioinformatics standard pattern)
### Pending Todos
@@ -54,5 +56,5 @@ None yet.
## Session Continuity
Last session: 2026-02-11 - Plan execution
Stopped at: Completed 01-01-PLAN.md
Resume file: .planning/phases/01-data-infrastructure/01-01-SUMMARY.md
Stopped at: Completed 01-03-PLAN.md
Resume file: .planning/phases/01-data-infrastructure/01-03-SUMMARY.md