3 Commits

Author	SHA1	Message	Date
gbanyan	a88b0eea60	feat(02-01): add gnomAD constraint data models and download module ... - Create evidence layer package structure - Define ConstraintRecord Pydantic model with NULL preservation - Implement streaming download with httpx and tenacity retry - Add lazy TSV parser with column name variant handling - Add httpx and structlog dependencies	2026-02-11 18:11:49 +08:00
gbanyan	f33b048635	feat(01-04): add CLI entry point with setup and info commands ... - Create click-based CLI with command group (--config, --verbose options) - Add 'info' command displaying pipeline version, config hash, data source versions - Add 'setup' command orchestrating full infrastructure flow: - Load config -> create store/provenance - Fetch gene universe (with checkpoint-restart) - Map Ensembl IDs to HGNC + UniProt - Validate mapping quality gates - Save to DuckDB with provenance sidecar - Update pyproject.toml entry point to usher_pipeline.cli.main:cli - Add .gitignore for data/, *.duckdb, build artifacts, provenance files	2026-02-11 16:39:50 +08:00
gbanyan	4a80a0398e	feat(01-01): create Python package scaffold with config system ... - pyproject.toml: installable package with bioinformatics dependencies - Pydantic config schema with validation (ensembl_release >= 100, directory creation) - YAML config loader with override support - Default config with Ensembl 113, gnomAD v4.1 - 5 passing tests for config validation and hashing	2026-02-11 16:24:35 +08:00