4 Commits

Include renames

Author	SHA1	Message	Date
kemal	76851b20a6	Release 2.0.0: v2 modules (ArrayTrain, CN/LOH, PGx, methylation QC) ... User guide: ArrayTrain section, v2 commands in the table, v2 accuracy rows, updated limitations. README status for v2.0.0. Version 2.0.0 (Python package); the Rust kernels are unchanged and stay simurg_core 1.1.0. uv.lock committed (uv lock --check clean). Full suite on the Pi, file by file under the memory guard: 29 files exit 0 (unit: 282 passed), ruff and mypy clean.	2026-09-30 06:24:12 +01:00
kemal	26c8a0cf40	Release 1.1.0: compiled kernels (P9) and packaging (P10)	2026-09-28 23:56:39 +01:00
kemal	f11b39b5a3	v1.0.0: user guide, examples, changelog ... docs/user_guide.md (install, inputs, complete run, commands, presets, QC, outputs, accuracy, limitations, troubleshooting), examples/gsa_demo.sh (end-to-end run on the public GSA demo, verified on the Pi), examples/sample_sheet.csv, CHANGELOG.md; version 1.0.0.	2026-09-28 20:38:24 +01:00
kemal	e518ea03d5	P1: file parsers, sample sheet, discovery, CLI inspect ... Readers for IDAT v3, BPM (locus entries v4-v8), CSV manifest, EGT (data blocks 5-9) and GTC v3-v5 (plus a layout-preserving GTC writer); sample-sheet validation (IN-001..IN-014), IDAT discovery and pairing (IN-020..IN-022), message catalogue and exit codes (CLI-014/016), JSON Lines logging (CLI-007/008), atomic writes (CLI-011), run manifest, and `simurg inspect`. Validation (docs/validation/P1.md): GTC, BPM and EGT readers agree exactly with Illumina BeadArrayFiles on GSA v4 / GDA v1 files; GTCs round-trip byte-identically; BPM and CSV manifests are consistent.	2026-09-27 16:56:39 +01:00