# 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