a0388cf4e1
docs(02-02): complete gnomAD evidence layer integration plan
...
- DuckDB persistence: gnomad_constraint table with CREATE OR REPLACE (idempotent)
- CLI evidence command: usher-pipeline evidence gnomad with checkpoint-restart
- Provenance tracking: records processing steps, saves sidecar JSON
- Query helpers: query_constrained_genes validates GCON-03 interpretation
- 12 integration tests: end-to-end pipeline, checkpoint, provenance, CLI
- Phase 2 complete: Evidence layer pattern established for future sources
- Duration: 4 min, 2 tasks, 5 files, 70 tests passing
Phase 2 (Prototype Evidence Layer) complete.
2026-02-11 18:23:32 +08:00
c6198122ac
docs(02-01): complete gnomAD constraint data pipeline plan
2026-02-11 18:16:35 +08:00
c7753e7b1c
docs(02): create phase plan
2026-02-11 17:47:23 +08:00
d328467737
docs(phase-02): research prototype evidence layer
2026-02-11 17:41:35 +08:00
34437fdf0a
docs(phase-01): complete phase execution
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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
102dcdbe84
docs(01-04): complete CLI integration and end-to-end testing plan
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- CLI entry point with setup and info commands
- Full infrastructure integration verified
- 6 integration tests with mocked APIs
- Phase 01 Data Infrastructure complete
2026-02-11 16:45:12 +08:00
e29d39d1dc
docs(01-02): complete gene ID mapping and validation plan
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- Gene universe definition with mygene protein-coding gene retrieval
- Batch Ensembl->HGNC+UniProt mapping with edge case handling
- Validation gates with configurable success rate thresholds
- 15 comprehensive tests with mocked API responses
2026-02-11 16:35:57 +08:00
92322b1d7c
docs(01-03): complete DuckDB persistence and provenance tracking plan
...
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com >
2026-02-11 16:34:00 +08:00
9ee3ec2e84
docs(01-01): complete project scaffold and config system plan
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- Created comprehensive SUMMARY.md with all execution details
- Updated STATE.md: 1/4 plans in phase 1 complete, 16.7% overall progress
- Documented deviation (venv creation) and decisions
- Verified all files and commits exist (self-check passed)
2026-02-11 16:28:03 +08:00
cab2f5fc66
docs(01-data-infrastructure): create phase plan
2026-02-11 16:04:42 +08:00
982f7f5a9b
docs(01-data-infrastructure): research phase domain
2026-02-11 15:56:40 +08:00
f80f384a61
docs: create roadmap (6 phases)
2026-02-11 15:47:36 +08:00
0fb1a9581f
docs: define v1 requirements
2026-02-11 15:31:05 +08:00
bb7bfaedab
docs: complete project research
2026-02-11 14:52:06 +08:00
c0abe8bc6c
chore: add project config
2026-02-11 14:41:35 +08:00
e2c202d689
docs: initialize project
2026-02-11 14:40:36 +08:00
