- Revised .gitignore to ignore raw data/cache but track data/report/ (candidates TSV/Parquet, plots, reproducibility metadata) - Added zh↔en cross-links between README.md and README.en.md Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
- 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
