5 Commits

Include renames

Author	SHA1	Message	Date
kemal	7cffb67e18	Guard against committed credentials: ignore secret files, secret scan in CI	2026-09-30 08:37:18 +01:00
kemal	aea1d459d9	Ignore editor lock files (.~lock.*#)	2026-09-30 07:52:07 +01:00
kemal	e4be579bfe	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	46e46037cd	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	b63852e775	SimurgArray: master plan, repo scaffolding and data/ref fetch scripts ... Phase 0 deliverables: full technical specification and roadmap (SIMURGARRAY_MASTER_PLAN.md), bootstrap script for reference open-source repos and tiered dataset fetch script with checksums.	2026-09-27 15:20:06 +01:00