kemal/SimurgArray
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Author SHA1 Message Date
kemal 3ed0503bdf Jev maintenance tools: shared client, spec coverage audit, voice check, nightly triage
ci / test (3.13) (push) Successful in 4m32s
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ci / test (3.12) (push) Successful in 4m36s
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2026-10-01 13:21:36 +01:00
kemal 0ff888e41b Ignore the local claim checker report
ci / test (3.13) (push) Successful in 3m41s
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ci / test (3.12) (push) Successful in 3m43s
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2026-10-01 13:10:03 +01:00
kemal 783e2a0039 Claim checker for public texts (TypeSafe), measured manifest load times, corrected README timings
ci / test (3.13) (push) Successful in 3m59s
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ci / test (3.12) (push) Successful in 4m1s
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2026-10-01 13:05:37 +01:00
kemal 21e63089b9 Guard against committed credentials: ignore secret files, secret scan in CI 2026-09-30 08:37:18 +01:00
kemal deb8e263b2 Ignore editor lock files (.~lock.*#) 2026-09-30 07:52:07 +01:00
kemal b8e3cf233a 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 3bfb7b5757 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