2.0 KiB
Project State
Project Reference
See: .planning/PROJECT.md (updated 2026-02-11)
Core value: Produce a high-confidence, multi-evidence-backed ranked list of under-studied cilia/Usher candidate genes that is fully traceable — every gene's inclusion is explainable by specific evidence, and every gap is documented. Current focus: Phase 1 - Data Infrastructure
Current Position
Phase: 1 of 6 (Data Infrastructure) Plan: 3 of 4 in current phase Status: Executing Last activity: 2026-02-11 — Completed 01-03-PLAN.md (DuckDB persistence and provenance tracking)
Progress: [███░░░░░░░] 25.0% (1/6 phases planned, 2/4 plans in phase 1 complete)
Performance Metrics
Velocity:
- 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 | 2/4 | 5 min | 2.5 min/plan |
Accumulated Context
Decisions
Decisions are logged in PROJECT.md Key Decisions table. Recent decisions affecting current work:
- Python over R/Bioconductor for rich data integration ecosystem
- Weighted rule-based scoring over ML for explainability
- Public data only for reproducibility
- 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
None yet.
Blockers/Concerns
None yet.
Session Continuity
Last session: 2026-02-11 - Plan execution Stopped at: Completed 01-03-PLAN.md Resume file: .planning/phases/01-data-infrastructure/01-03-SUMMARY.md