SimurgArray

4 Commits

Include renames

Author	SHA1	Message	Date
kemalandClaude Opus 5.5	150650424c	Lint fixes in validate_p1_large.py ci / test (3.12) (push) Failing after 10s Details ci / test (3.13) (push) Failing after 12s Details Co-Authored-By: Claude Opus 5.5 <[email protected]> Claude-Session: https://claude.ai/code/session_01814GKVzZVL3FuF3DeiZXhv	2026-09-27 19:30:37 +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	f10c651f0f	P0: project setup (packaging, CI, licences, data/oracle scripts) - pyproject (uv/hatch, ruff, mypy strict, pytest markers), MIT LICENSE, THIRD_PARTY_NOTICES with verbatim BSD-2 (BeadArrayFiles) and MIT (gtc2vcf) - CI workflow for Gitea/GitHub Actions: lint, type check, unit tests - fetch_data.sh p0 now fetches the GSA v4 PGx demo IDATs (the GDA "Demo 36" bundle is a GenomeStudio project), unpacks archives, fixes pipefail bug - make_oracle_gtcs.sh builds bcftools + gtc2vcf and writes oracle GTCs - plan §17: corrected P0 dataset table Co-Authored-By: Claude Opus 5.5 <[email protected]> Claude-Session: https://claude.ai/code/session_01814GKVzZVL3FuF3DeiZXhv	2026-09-27 16:56:39 +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