# 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: 1 of 4 in current phase
Status: Executing
Last activity: 2026-02-11 — Completed 01-01-PLAN.md (Project scaffold, config system, base API client)

Progress: [██░░░░░░░░] 16.7% (1/6 phases planned, 1/4 plans in phase 1 complete)

## Performance Metrics

**Velocity:**
- Total plans completed: 1
- Average duration: 3 min
- Total execution time: 0.05 hours

**By Phase:**

| Phase | Plans | Total | Avg/Plan |
|-------|-------|-------|----------|
| 01 - Data Infrastructure | 1/4 | 3 min | 3 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)

### Pending Todos

None yet.

### Blockers/Concerns

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