61 lines
2.0 KiB
Markdown
61 lines
2.0 KiB
Markdown
# Project State
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## Project Reference
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See: .planning/PROJECT.md (updated 2026-02-11)
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**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.
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**Current focus:** Phase 1 - Data Infrastructure
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## Current Position
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Phase: 1 of 6 (Data Infrastructure)
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Plan: 3 of 4 in current phase
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Status: Executing
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Last activity: 2026-02-11 — Completed 01-03-PLAN.md (DuckDB persistence and provenance tracking)
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Progress: [███░░░░░░░] 25.0% (1/6 phases planned, 2/4 plans in phase 1 complete)
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## Performance Metrics
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**Velocity:**
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- Total plans completed: 2
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- Average duration: 2.5 min
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- Total execution time: 0.08 hours
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**By Phase:**
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| Phase | Plans | Total | Avg/Plan |
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|-------|-------|-------|----------|
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| 01 - Data Infrastructure | 2/4 | 5 min | 2.5 min/plan |
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## Accumulated Context
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### Decisions
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Decisions are logged in PROJECT.md Key Decisions table.
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Recent decisions affecting current work:
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- Python over R/Bioconductor for rich data integration ecosystem
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- Weighted rule-based scoring over ML for explainability
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- Public data only for reproducibility
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- Modular CLI scripts for flexibility during development
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- Virtual environment required for dependency isolation (01-01: PEP 668 externally-managed Python)
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- Auto-creation of directories on config load (01-01: data_dir, cache_dir field validators)
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- [Phase 01-data-infrastructure]: DuckDB over SQLite for DataFrame storage (native polars/pandas integration, better analytics)
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- [Phase 01-data-infrastructure]: Provenance sidecar files alongside outputs (co-located metadata, bioinformatics standard pattern)
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### Pending Todos
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None yet.
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### Blockers/Concerns
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None yet.
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## Session Continuity
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Last session: 2026-02-11 - Plan execution
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Stopped at: Completed 01-03-PLAN.md
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Resume file: .planning/phases/01-data-infrastructure/01-03-SUMMARY.md
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