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gbanyan 34437fdf0a docs(phase-01): complete phase execution

Phase 1 (Data Infrastructure) verified: 5/5 must-haves, 12/12 artifacts,
9/9 key links, 7/7 requirements satisfied. All 4 plans executed across
3 waves with 49 tests passing.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

2026-02-11 16:50:30 +08:00

2.6 KiB

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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: 1 of 6 (Data Infrastructure) Plan: 4 of 4 in current phase Status: Phase complete — verified Last activity: 2026-02-11 — Phase 1 verified (5/5 must-haves, 12/12 artifacts, 7/7 requirements)

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

Performance Metrics

Velocity:

Total plans completed: 4
Average duration: 3.5 min
Total execution time: 0.23 hours

By Phase:

Phase	Plans	Total	Avg/Plan
01 - Data Infrastructure	4/4	14 min	3.5 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)

Pending Todos

None yet.

Blockers/Concerns