kemal/SimurgArray
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P0: project setup (packaging, CI, licences, data/oracle scripts)

Browse Source 
- 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
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kemalandClaude Opus 5.5 committed 2026-09-27 16:56:39 +01:00
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README.md
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Personal research toolkit for Illumina Infinium genotyping BeadChip data
(IDAT → normalization → genotype calling → BAF/LRR → QC → VCF/PLINK; later CN/LOH, PGx, cluster training).
Start with **SIMURGARRAY_MASTER_PLAN.md** (architecture, algorithms, roadmap) and
**SIMURGARRAY_FUNCTIONAL_SPEC.md** (416 itemised requirements: CLI, inputs, outputs, QC, CN, PGx, methylation, edge cases).
- **SIMURGARRAY_MASTER_PLAN.md** — architecture, algorithms, roadmap
- **SIMURGARRAY_FUNCTIONAL_SPEC.md** — 416 itemised requirements (CLI, inputs, outputs, QC, CN, PGx, methylation, edge cases)
- `docs/validation/` — per-phase validation reports · `docs/known_unknowns.md` — findings log · `docs/research/` — background
## Status
Phases **P0 (setup)** and **P1 (file parsers)** are complete — see `docs/validation/P1.md`.
Available commands: `simurg version`, `simurg inspect <files…> [--json]`.
## Quick start
```bash
bash scripts/bootstrap_refs.sh # clone reference open-source repos into refs/
bash scripts/fetch_data.sh p0 # download small test datasets into data/
uv venv && uv pip install -e ".[dev]"
uv run pytest tests/unit # no downloads needed
bash scripts/bootstrap_refs.sh # reference open-source repos → refs/ (oracles)
bash scripts/fetch_data.sh p0 # ~1.4 GB of public test data → data/
bash scripts/make_oracle_gtcs.sh # builds gtc2vcf, writes oracle GTCs
uv run pytest tests/oracle # real-data acceptance tests (add -m "not slow" to skip the long ones)
uv run simurg inspect data/p0/gsa_v4_pgx/idats_Demo_36/idats_Demo_36/207895980019/207895980019_R03C01_Grn.idat
```
Vendor data files are downloaded for personal research use only and are never committed. See `THIRD_PARTY_NOTICES.md`.