SimurgArray

63 Commits 1 Branch 3 Tags

3 Commits

Include renames

Author	SHA1	Message	Date
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 Details ci / test (3.13) (push) Failing after 11s Details 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 Details 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

Author

SHA1

Message

Date

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

Details

ci / test (3.13) (push) Failing after 11s

Details

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

Details

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