usher-exploring

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gbanyan e4d71d0790 test(01-04): add integration tests verifying module wiring

- test_config_to_store_roundtrip: config -> PipelineStore -> save/load
- test_config_to_provenance: config -> ProvenanceTracker -> sidecar
- test_full_setup_flow_mocked: full setup with mocked mygene (fetch, map, validate, save, provenance)
- test_checkpoint_skip_flow: verify checkpoint-restart skips re-fetch
- test_setup_cli_help: CLI help output verification
- test_info_cli: info command with config display

All tests pass with mocked API calls (no external dependencies).

2026-02-11 16:42:13 +08:00

.planning

docs(01-02): complete gene ID mapping and validation plan

2026-02-11 16:35:57 +08:00

config

feat(01-01): create Python package scaffold with config system

2026-02-11 16:24:35 +08:00

src/usher_pipeline

feat(01-04): add CLI entry point with setup and info commands

2026-02-11 16:39:50 +08:00

tests

test(01-04): add integration tests verifying module wiring