SimurgArray

6 Commits

Include renames

Author	SHA1	Message	Date
kemal	ab92c6ec20	Plan: drop the assistant-specific appendices; numeric helpers become Appendix A ci / test (3.12) (push) Failing after 8s Details ci / test (3.13) (push) Failing after 10s Details	2026-09-30 08:13:07 +01:00
kemal	6ab7a72935	Keep Claude Code files local: untrack CLAUDE.md, ignore CLAUDE.md, CLAUDE.local.md and .claude/ ci / test (3.12) (push) Failing after 9s Details ci / test (3.13) (push) Failing after 10s Details	2026-09-30 08:10:57 +01:00
kemal	3ff38e6009	Remove an editor lock file committed by mistake; ignore .~lock.*# files	2026-09-30 07:52:07 +01:00
kemal	efe781fbe0	Track the packaged CN data files (the data/ ignore rule matched src/simurg/cn/data) Found by the CN cloud validation: mask_GRCh3{7,8}.bed and cytoBand_GRCh3{7,8}.txt.gz were never committed nor shipped in the wheel. The ignore rule now covers only the top-level data/.	2026-09-29 07:06:47 +01:00
kemal	6bea6c4930	Add self-destructing AWS trial and large-scale P1 validation script scripts/cloud/trial.sh launches one spot instance that validates the parsers on the 1000 Genomes Omni2.5 set (2141 samples, vendor GTCs) streamed from the public S3 bucket, uploads the summary and terminates itself. Cost guards: spot price cap, hard time limit (shutdown = terminate), EXIT-trap shutdown, CloudWatch idle alarm that terminates from outside, disk deleted with the instance, monthly budget alert, and an `audit` command listing anything still billable. scripts/validate_p1_large.py compares every GTC with BeadArrayFiles, checks byte-identical round-trips, IDAT pairs and BPM/EGT/CSV.	2026-09-27 19:30:27 +01:00
kemal	631c1d030d	SimurgArray: master plan, repo scaffolding and data/ref fetch scripts Phase 0 deliverables: full technical specification and roadmap (SIMURGARRAY_MASTER_PLAN.md), CLAUDE.md, bootstrap script for reference open-source repos and tiered dataset fetch script with checksums.	2026-09-27 15:20:06 +01:00