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 complete — ready for Phase 2

Current Position

Phase: 2 of 6 (Prototype Evidence Layer) Plan: 1 of 2 in current phase Status: In progress Last activity: 2026-02-11 — Completed 02-01: gnomAD constraint data pipeline (fetch->filter->normalize pattern established)

Progress: [█████░░░░░] 20.8% (1/6 phases complete, 1/2 plans in phase 2 complete)

Performance Metrics

Velocity:

Total plans completed: 5
Average duration: 3.6 min
Total execution time: 0.30 hours

By Phase:

Phase	Plans	Total	Avg/Plan
01 - Data Infrastructure	4/4	14 min	3.5 min/plan
02 - Prototype Evidence Layer	1/2	4 min	4.0 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)
[01-02]: Warn on gene count outside 19k-22k range but don't fail (allows for Ensembl version variations)
[01-02]: HGNC success rate is primary validation gate (UniProt mapping tracked but not used for pass/fail)
[01-02]: Take first UniProt accession when multiple exist (simplifies data model)
[01-02]: Mock mygene in tests (avoids rate limits, ensures reproducibility)
[01-03]: DuckDB over SQLite for DataFrame storage (native polars/pandas integration, better analytics)
[01-03]: Provenance sidecar files alongside outputs (co-located metadata, bioinformatics standard pattern)
[01-04]: Click for CLI framework (standard Python CLI library with excellent UX)
[01-04]: Setup command uses checkpoint-restart pattern (gene universe fetch can take minutes)
[01-04]: Mock mygene in integration tests (avoids external API dependency, reproducible)
[02-01]: httpx over requests for streaming downloads (async-native, cleaner API)
[02-01]: structlog for structured logging (JSON-formatted, context-aware)
[02-01]: LOEUF normalization with inversion (lower LOEUF = more constrained = higher 0-1 score)
[02-01]: Quality flags instead of filtering (preserve all genes with measured/incomplete_coverage/no_data categorization)
[02-01]: NULL preservation pattern (unknown constraint != zero constraint, must not be conflated)
[02-01]: Lazy polars evaluation (LazyFrame until final collect() for query optimization)

Pending Todos

None yet.

Blockers/Concerns