SimurgArray

6 Commits

Include renames

Author	SHA1	Message	Date
kemal	ab92c6ec20	Plan: drop the assistant-specific appendices; numeric helpers become Appendix A ci / test (3.12) (push) Failing after 8s Details ci / test (3.13) (push) Failing after 10s Details	2026-09-30 08:13:07 +01:00
kemal	6ab7a72935	Keep Claude Code files local: untrack CLAUDE.md, ignore CLAUDE.md, CLAUDE.local.md and .claude/ ci / test (3.12) (push) Failing after 9s Details ci / test (3.13) (push) Failing after 10s Details	2026-09-30 08:10:57 +01:00
kemal	14ed32f03a	Tidy the repository: remove docs/research and bench, fix references ci / test (3.12) (push) Failing after 11s Details ci / test (3.13) (push) Failing after 13s Details	2026-09-30 08:07:35 +01:00
kemal	705138d70b	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	2026-09-27 16:56:39 +01:00
kemal	336a6b8226	Add functional specification (416 items) and link it from plan/docs SIMURGARRAY_FUNCTIONAL_SPEC.md defines externally visible behaviour: CLI, inputs, genotyping outputs, QC and report, cytogenetics CNV/LOH, targeted PGx copy number, star alleles, methylation control QC, edge-case catalogue, performance targets, open questions and a traceability table.	2026-09-27 16:13:40 +01:00
kemal	631c1d030d	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.	2026-09-27 15:20:06 +01:00