gbanyan/usher-exploring
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  • dc36730cb4 docs: update gitignore to track report results, add README cross-links master gbanyan 2026-02-13 05:57:27 +08:00
  • 674a9ae845 docs: add project README (zh/en) and CLAUDE.md gbanyan 2026-02-13 04:50:02 +08:00
  • 6605ff0f2b fix: resolve runtime bugs for pipeline execution on Python 3.14 + latest deps gbanyan 2026-02-13 03:44:01 +08:00
  • a2ef2125ba chore: complete v1.0 MVP milestone gbanyan 2026-02-12 21:31:43 +08:00
  • c284804493 docs: milestone v1.0 audit — passed (40/40 requirements) gbanyan 2026-02-12 10:28:53 +08:00
  • 294b4defbb docs(phase-06): complete phase execution gbanyan 2026-02-12 04:57:56 +08:00
  • c97592d629 docs(06-03): complete comprehensive validation report & CLI plan gbanyan 2026-02-12 04:53:05 +08:00
  • 5879ae9768 test(06-03): unit tests for all validation modules gbanyan 2026-02-12 04:50:17 +08:00
  • 10f19f89f4 feat(06-03): comprehensive validation report and CLI validate command gbanyan 2026-02-12 04:48:25 +08:00
  • 2d29f43848 docs(06-02): complete sensitivity analysis plan gbanyan 2026-02-12 04:44:13 +08:00
  • a2d6e97acf docs(06-01): complete negative controls and recall@k validation plan gbanyan 2026-02-12 04:43:59 +08:00
  • 0084a67fba feat(06-02): export sensitivity analysis module from scoring package gbanyan 2026-02-12 04:41:27 +08:00
  • 0f615c0d53 feat(06-01): add recall@k metrics and extended positive control validation gbanyan 2026-02-12 04:41:00 +08:00
  • a7589d9bf1 feat(06-02): implement sensitivity analysis module with weight perturbation and Spearman correlation gbanyan 2026-02-12 04:40:21 +08:00
  • e488ff2d7a feat(06-01): add negative control validation with housekeeping genes gbanyan 2026-02-12 04:39:48 +08:00
  • 844295c681 docs(06): create phase plan gbanyan 2026-02-12 04:33:17 +08:00
  • ca2b715d8e docs(phase-06): research validation domain with controls and sensitivity analysis gbanyan 2026-02-12 04:27:26 +08:00
  • 964c1cebe8 docs(phase-05): complete phase execution gbanyan 2026-02-12 04:15:50 +08:00
  • 00e2836eb9 docs(05-03): complete CLI report command plan gbanyan 2026-02-12 04:09:26 +08:00
  • c10d59548f test(05-03): add CliRunner integration tests for report command gbanyan 2026-02-12 04:07:34 +08:00
  • 2ab25ef5c2 feat(05-03): implement CLI report command gbanyan 2026-02-12 04:05:52 +08:00
  • 5f14dc2e64 docs(05-02): complete visualization and reproducibility report plan gbanyan 2026-02-12 04:03:08 +08:00
  • 434c79c0a8 docs(05-01): complete output generation core plan gbanyan 2026-02-12 04:01:24 +08:00
  • 5af63eab46 feat(05-02): implement reproducibility report module with JSON and Markdown output gbanyan 2026-02-12 04:00:21 +08:00
  • 4e46b488f1 feat(05-01): add dual-format writer with provenance and tests gbanyan 2026-02-12 03:59:26 +08:00
  • 150417ffcc feat(05-02): implement visualization module with matplotlib/seaborn plots gbanyan 2026-02-12 03:57:50 +08:00
  • d2ef3a2b84 feat(05-01): implement tiering logic and evidence summary module gbanyan 2026-02-12 03:56:42 +08:00
  • 6ab7fd1378 docs(05-output-cli): create phase plan gbanyan 2026-02-11 21:14:37 +08:00
  • 1799906138 docs(05): research phase output-cli domain gbanyan 2026-02-11 21:07:56 +08:00
  • de678858cd docs(phase-04): complete phase execution gbanyan 2026-02-11 21:01:50 +08:00
  • 386fbf51b2 docs(04-03): complete CLI score command and tests plan gbanyan 2026-02-11 20:56:31 +08:00
  • a6ad6c6d19 test(04-03): add unit and integration tests for scoring module gbanyan 2026-02-11 20:54:39 +08:00
  • d57a5f2826 feat(04-03): add CLI score command with checkpoint-restart gbanyan 2026-02-11 20:52:37 +08:00
  • c501951b0f docs(04-02): complete QC and validation plan gbanyan 2026-02-11 20:50:00 +08:00
  • 70a5d6eff8 feat(04-02): implement positive control validation gbanyan 2026-02-11 20:47:59 +08:00
  • ba2f97ac55 feat(04-02): implement QC checks for scoring results gbanyan 2026-02-11 20:46:57 +08:00
  • 71c4e8f736 docs(04-01): complete known gene compilation and weighted scoring plan gbanyan 2026-02-11 20:44:09 +08:00
  • f441e8c1ad feat(04-01): implement multi-evidence weighted scoring integration gbanyan 2026-02-11 20:41:44 +08:00
  • 0cd2f7c9dd feat(04-01): implement known gene compilation and ScoringWeights validation gbanyan 2026-02-11 20:41:31 +08:00
  • ed21f18a98 fix(03-05): handle NULL columns and deprecated polars API in animal models gbanyan 2026-02-11 20:38:36 +08:00
  • a52724aff4 docs(04): create phase plan for scoring and integration gbanyan 2026-02-11 20:31:55 +08:00
  • 32988c631f docs(04): research multi-evidence weighted scoring with NULL preservation gbanyan 2026-02-11 20:24:42 +08:00
  • 190bedaa80 docs(phase-03): complete phase execution gbanyan 2026-02-11 19:18:12 +08:00
  • e72c516669 docs(03-06): complete literature evidence layer gbanyan 2026-02-11 19:13:26 +08:00
  • 0e89bf0dd6 docs(03-02): complete expression evidence layer plan gbanyan 2026-02-11 19:12:18 +08:00
  • cfe4b830e6 docs(03-03): complete protein features plan with SUMMARY and STATE updates gbanyan 2026-02-11 19:10:03 +08:00
  • 053f0d926b docs(03-05): complete animal model phenotype evidence layer plan gbanyan 2026-02-11 19:08:45 +08:00
  • d8009f1236 docs(03-04): complete subcellular localization evidence layer gbanyan 2026-02-11 19:08:01 +08:00
  • 46059874f2 feat(03-03): implement protein evidence layer with UniProt/InterPro integration gbanyan 2026-02-11 19:07:30 +08:00
  • bcd3c4ffbe feat(03-05): add animal model DuckDB loader, CLI, and comprehensive tests gbanyan 2026-02-11 19:06:49 +08:00
  • 99bc975a2c docs(03-01): complete annotation completeness plan gbanyan 2026-02-11 19:05:56 +08:00
  • 942aaf2ec3 feat(03-04): add localization CLI command and comprehensive tests gbanyan 2026-02-11 19:05:22 +08:00
  • d70239c4ce feat(03-01): add annotation DuckDB loader, CLI command, and tests gbanyan 2026-02-11 19:03:10 +08:00
  • 0e389c7e41 feat(03-05): implement animal model evidence fetch and transform gbanyan 2026-02-11 19:00:24 +08:00
  • 8aa66987f8 feat(03-06): implement literature evidence models, PubMed fetch, and scoring gbanyan 2026-02-11 19:00:20 +08:00
  • 6645c59b0b feat(03-04): create localization evidence data model and processing gbanyan 2026-02-11 19:00:09 +08:00
  • adbb74b965 feat(03-01): implement annotation evidence fetch and transform modules gbanyan 2026-02-11 18:58:45 +08:00
  • 0d252da348 docs(03): create phase plan gbanyan 2026-02-11 18:46:28 +08:00
  • 3354cfe006 docs(phase-03): research core evidence layers domain gbanyan 2026-02-11 18:37:14 +08:00
  • ffb4963d2b docs(phase-02): complete phase execution gbanyan 2026-02-11 18:28:13 +08:00
  • a0388cf4e1 docs(02-02): complete gnomAD evidence layer integration plan gbanyan 2026-02-11 18:23:32 +08:00
  • 56e04e68c2 test(02-02): add comprehensive gnomAD integration tests gbanyan 2026-02-11 18:20:59 +08:00
  • ee27f3ad2f feat(02-02): add DuckDB loader and CLI evidence command for gnomAD gbanyan 2026-02-11 18:19:07 +08:00
  • c6198122ac docs(02-01): complete gnomAD constraint data pipeline plan gbanyan 2026-02-11 18:16:35 +08:00
  • 174c4af02d feat(02-01): add gnomAD transform pipeline and comprehensive tests gbanyan 2026-02-11 18:14:41 +08:00
  • a88b0eea60 feat(02-01): add gnomAD constraint data models and download module gbanyan 2026-02-11 18:11:49 +08:00
  • c7753e7b1c docs(02): create phase plan gbanyan 2026-02-11 17:47:23 +08:00
  • d328467737 docs(phase-02): research prototype evidence layer gbanyan 2026-02-11 17:41:35 +08:00
  • 34437fdf0a docs(phase-01): complete phase execution gbanyan 2026-02-11 16:50:30 +08:00
  • 102dcdbe84 docs(01-04): complete CLI integration and end-to-end testing plan gbanyan 2026-02-11 16:45:12 +08:00
  • e4d71d0790 test(01-04): add integration tests verifying module wiring gbanyan 2026-02-11 16:42:13 +08:00
  • f33b048635 feat(01-04): add CLI entry point with setup and info commands gbanyan 2026-02-11 16:39:50 +08:00
  • e29d39d1dc docs(01-02): complete gene ID mapping and validation plan gbanyan 2026-02-11 16:35:57 +08:00
  • 92322b1d7c docs(01-03): complete DuckDB persistence and provenance tracking plan gbanyan 2026-02-11 16:34:00 +08:00
  • 0200395d9e feat(01-02): create mapping validation gates with tests gbanyan 2026-02-11 16:33:36 +08:00
  • 98a1a750dd feat(01-03): create provenance tracker with comprehensive tests gbanyan 2026-02-11 16:31:51 +08:00
  • d51141f7d5 feat(01-03): create DuckDB persistence layer with checkpoint-restart gbanyan 2026-02-11 16:30:25 +08:00
  • 9ee3ec2e84 docs(01-01): complete project scaffold and config system plan gbanyan 2026-02-11 16:28:03 +08:00
  • 4204116772 feat(01-01): create base API client with retry and caching gbanyan 2026-02-11 16:25:46 +08:00
  • 4a80a0398e feat(01-01): create Python package scaffold with config system gbanyan 2026-02-11 16:24:35 +08:00
  • cab2f5fc66 docs(01-data-infrastructure): create phase plan gbanyan 2026-02-11 16:04:42 +08:00
  • 982f7f5a9b docs(01-data-infrastructure): research phase domain gbanyan 2026-02-11 15:56:40 +08:00
  • f80f384a61 docs: create roadmap (6 phases) gbanyan 2026-02-11 15:47:36 +08:00
  • 0fb1a9581f docs: define v1 requirements gbanyan 2026-02-11 15:31:05 +08:00
  • bb7bfaedab docs: complete project research gbanyan 2026-02-11 14:52:06 +08:00
  • c0abe8bc6c chore: add project config gbanyan 2026-02-11 14:41:35 +08:00
  • e2c202d689 docs: initialize project gbanyan 2026-02-11 14:40:36 +08:00