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4 Commits
Author SHA1 Message Date
kemalandClaude Opus 5.5 6a483cdf5c Release 2.0.0: v2 modules (ArrayTrain, CN/LOH, PGx, methylation QC)
ci / test (3.13) (push) Failing after 30s
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ci / test (3.12) (push) Failing after 31s
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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.

Co-Authored-By: Claude Opus 5.5 <[email protected]>
Claude-Session: https://claude.ai/code/session_01814GKVzZVL3FuF3DeiZXhv
 2026-09-30 06:24:12 +01:00
kemalandClaude Opus 5.5 7c0e348033 Release 1.1.0: compiled kernels (P9) and packaging (P10)
ci / test (3.13) (push) Failing after 9s
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ci / test (3.12) (push) Failing after 8s
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Co-Authored-By: Claude Opus 5.5 <[email protected]>
Claude-Session: https://claude.ai/code/session_01814GKVzZVL3FuF3DeiZXhv
 2026-09-28 23:56:39 +01:00
kemalandClaude Opus 5.5 874aeaef61 v1.0.0: user guide, examples, changelog
ci / test (3.13) (push) Failing after 9s
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ci / test (3.12) (push) Failing after 10s
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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.

Co-Authored-By: Claude Opus 5.5 <[email protected]>
Claude-Session: https://claude.ai/code/session_01814GKVzZVL3FuF3DeiZXhv
 2026-09-28 20:38:24 +01:00
kemalandClaude Opus 5.5 4357d3deef P1: file parsers, sample sheet, discovery, CLI inspect
ci / test (3.12) (push) Failing after 11s
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ci / test (3.13) (push) Failing after 12s
Details 
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.

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