P10 (WIP): release build script, Dockerfile, conda recipes, fresh-VM acceptance task
scripts/build_dist.sh: sdist + pure wheel + manylinux_2_28 kernel wheels (maturin --zig,
both architectures). Dockerfile (multi-stage, kernels included, non-root user).
packaging/conda/{simurg,simurg-core}. scripts/p10/digest.py: platform-independent content
digests of GTC/VCF/summary outputs. Cloud task p10 installs the artifacts on a fresh
Ubuntu VM and runs the tutorial with pip, Docker and conda installs. trial.sh picks the
arm64/amd64 image from the instance type and can run instances in parallel (PARALLEL=1).
Licence files ship in both wheels; Rust crate notices added.
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@@ -12,6 +12,7 @@ used only as external subprocess oracles and are not copied or linked.
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| [klib `ksort.h`](https://github.com/attractivechaos/klib) as shipped in htslib — Copyright (c) 2008, 2012-2013, 2017-2019 Genome Research Ltd | MIT | Quickselect `ks_ksmall` partition order, ported to `simurg/qc/contamination.py` (`ks_ksmall`) to reproduce BAFregress medians |
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| [Illumina GTCtoVCF](https://github.com/Illumina/GTCtoVCF) — Copyright Illumina, Inc. | Apache-2.0 | Indel source-sequence handling ported to `simurg/harmonize/sites.py` (design-strand orientation, left shift, IUPAC flank matching, deletion/insertion context score); multi-probe consistency idea in `simurg/harmonize/combine.py`; test oracle (run under Python 3 with two local compatibility patches, never shipped) |
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| [Picard `picard.arrays`](https://github.com/broadinstitute/picard) | MIT | Second format reference |
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| [PyO3](https://github.com/PyO3/pyo3), [rust-numpy](https://github.com/PyO3/rust-numpy), [ndarray](https://github.com/rust-ndarray/ndarray) and their Rust dependencies | MIT / Apache-2.0 / BSD-2-Clause | Compiled into the optional `simurg_core` extension (`rust/simurg-core`); list with `cargo tree` |
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| [illuminaio](https://github.com/HenrikBengtsson/illuminaio) | GPL-2 | Documentation of IDAT field codes only; oracle via subprocess |
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## BSD-2-Clause (BeadArrayFiles, verbatim from its README)
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