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docs(01-04): complete CLI integration and end-to-end testing plan

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- CLI entry point with setup and info commands
- Full infrastructure integration verified
- 6 integration tests with mocked APIs
- Phase 01 Data Infrastructure complete
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gbanyan
2026-02-11 16:45:12 +08:00
parent e4d71d0790
commit 102dcdbe84
2 changed files with 305 additions and 10 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: 3 of 4 in current phase
Status: Executing
Last activity: 2026-02-11 — Completed 01-02-PLAN.md (Gene ID mapping and validation)
Plan: 4 of 4 in current phase
Status: Complete
Last activity: 2026-02-11 — Completed 01-04-PLAN.md (CLI integration and end-to-end testing)
Progress: [███░░░░░░░] 25.0% (1/6 phases planned, 2/4 plans in phase 1 complete)
Progress: [█████░░░░░] 16.7% (1/6 phases complete, 4/4 plans in phase 1 complete)
## Performance Metrics
**Velocity:**
- Total plans completed: 2
- Average duration: 3 min
- Total execution time: 0.12 hours
- Total plans completed: 4
- Average duration: 3.5 min
- Total execution time: 0.23 hours
**By Phase:**
| Phase | Plans | Total | Avg/Plan |
|-------|-------|-------|----------|
| 01 - Data Infrastructure | 2/4 | 7 min | 3.5 min/plan |
| 01 - Data Infrastructure | 4/4 | 14 min | 3.5 min/plan |
## Accumulated Context
@@ -48,6 +48,9 @@ Recent decisions affecting current work:
- [01-02]: Mock mygene in tests (avoids rate limits, ensures reproducibility)
- [01-03]: DuckDB over SQLite for DataFrame storage (native polars/pandas integration, better analytics)
- [01-03]: Provenance sidecar files alongside outputs (co-located metadata, bioinformatics standard pattern)
- [01-04]: Click for CLI framework (standard Python CLI library with excellent UX)
- [01-04]: Setup command uses checkpoint-restart pattern (gene universe fetch can take minutes)
- [01-04]: Mock mygene in integration tests (avoids external API dependency, reproducible)
### Pending Todos
@@ -60,5 +63,5 @@ None yet.
## Session Continuity
Last session: 2026-02-11 - Plan execution
Stopped at: Completed 01-02-PLAN.md
Resume file: .planning/phases/01-data-infrastructure/01-02-SUMMARY.md
Stopped at: Completed 01-04-PLAN.md (Phase 01 complete)
Resume file: .planning/phases/01-data-infrastructure/01-04-SUMMARY.md