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)
59 lines
1.7 KiB
Markdown
59 lines
1.7 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: 1 of 4 in current phase
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Status: Executing
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Last activity: 2026-02-11 — Completed 01-01-PLAN.md (Project scaffold, config system, base API client)
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Progress: [██░░░░░░░░] 16.7% (1/6 phases planned, 1/4 plans in phase 1 complete)
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## Performance Metrics
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**Velocity:**
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- Total plans completed: 1
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- Average duration: 3 min
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- Total execution time: 0.05 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 | 1/4 | 3 min | 3 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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### 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 01-01-PLAN.md
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Resume file: .planning/phases/01-data-infrastructure/01-01-SUMMARY.md
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