gbanyan
34437fdf0a
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>
68 lines
2.6 KiB
Markdown
68 lines
2.6 KiB
Markdown
# 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
|
|
|
|
None yet.
|
|
|
|
## Session Continuity
|
|
|
|
Last session: 2026-02-11 - Plan execution
|
|
Stopped at: Completed 01-04-PLAN.md (Phase 01 complete)
|
|
Resume file: .planning/phases/01-data-infrastructure/01-04-SUMMARY.md
|