gbanyan
9ee3ec2e84
- Created comprehensive SUMMARY.md with all execution details - Updated STATE.md: 1/4 plans in phase 1 complete, 16.7% overall progress - Documented deviation (venv creation) and decisions - Verified all files and commits exist (self-check passed)
1.7 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: 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