kemal/SimurgArray
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4 Commits
Author SHA1 Message Date
kemalandClaude Opus 5.5 dfe477787f Remove an editor lock file committed by mistake; ignore .~lock.*# files
ci / test (3.12) (push) Failing after 9s
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ci / test (3.13) (push) Failing after 10s
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Co-Authored-By: Claude Opus 5.5 <[email protected]>
Claude-Session: https://claude.ai/code/session_01814GKVzZVL3FuF3DeiZXhv
 2026-09-30 07:52:07 +01:00
kemalandClaude Opus 5.5 b2e0c09f2a Track the packaged CN data files (the data/ ignore rule matched src/simurg/cn/data)
ci / test (3.12) (push) Failing after 10s
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ci / test (3.13) (push) Failing after 11s
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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/.

Co-Authored-By: Claude Opus 5.5 <[email protected]>
Claude-Session: https://claude.ai/code/session_01814GKVzZVL3FuF3DeiZXhv
 2026-09-29 07:06:47 +01:00
kemalandClaude Opus 5.5 a9aa6dc080 Add self-destructing AWS trial and large-scale P1 validation script
ci / test (3.12) (push) Failing after 9s
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ci / test (3.13) (push) Failing after 13s
Details 
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.

Co-Authored-By: Claude Opus 5.5 <[email protected]>
Claude-Session: https://claude.ai/code/session_01814GKVzZVL3FuF3DeiZXhv
 2026-09-27 19:30:27 +01:00
kemalandClaude Opus 5.5 ee4ebaaa1e 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.

Co-Authored-By: Claude Opus 5.5 <[email protected]>
Claude-Session: https://claude.ai/code/session_01814GKVzZVL3FuF3DeiZXhv
 2026-09-27 15:20:06 +01:00