kemal
7767a596bb
Wheels (pure + manylinux_2_28 kernels), sdist, Docker image and conda packages built and installed on fresh Ubuntu 24.04 machines; 225 unit tests pass against the installed package; the tutorial runs with pip (with and without kernels); GTC/VCF content digests are identical across pip, Docker and conda on both architectures and equal to the Pi's run. docs/validation/P10.md; guide: install from wheels, Docker, conda; exit code 141.
2.9 KiB
Phase P10 validation — packaging and fresh-machine acceptance
Date: 2026-09-28. Artifacts built and tested on fresh AWS Ubuntu 24.04 VMs (4 vCPU): aarch64 c7g.xlarge and x86_64 m6a.xlarge / c6a.xlarge (one x86 spot instance was reclaimed by AWS after 4 min and relaunched). Cloud cost ≈ $0.10.
Artifacts
| Artifact | How | Notes |
|---|---|---|
simurg-1.0.0-py3-none-any.whl, simurg-1.0.0.tar.gz |
uv build (hatchling) |
QC report assets, profiles, LICENSE and THIRD_PARTY_NOTICES.md inside |
simurg_core-1.0.0-cp312-abi3-manylinux_2_28_{aarch64,x86_64}.whl |
maturin --zig --compatibility manylinux_2_28 (both built on either machine) |
one wheel per architecture for every Python ≥ 3.12; glibc ≥ 2.28 |
Docker image (Dockerfile) |
multi-stage, python:3.12-slim-bookworm, non-root user |
545 MB (x86_64), 551 MB (aarch64) |
conda packages (packaging/conda/) |
conda build -c conda-forge |
simurg (noarch) + simurg-core (Rust compiler from conda-forge) |
scripts/build_dist.sh builds the wheels and sdist and writes dist/SHA256SUMS. A wheel built on the Pi is not
portable (glibc 2.41 symbols such as exp@GLIBC_2.29), hence the zig-linked manylinux build.
Acceptance (plan §18 P10: clean install + tutorial works on a fresh VM)
scripts/cloud/tasks/p10.sh (and p10t.sh, the same without Docker/conda) on each architecture:
| Step | aarch64 | x86_64 |
|---|---|---|
| Build sdist, pure wheel, both kernel wheels | ok | ok |
pip install into a new venv of the system Python 3.12.3 (with / without kernels) |
ok / ok | ok / ok |
| Unit tests against the installed package (225) | pass | pass |
Tutorial examples/gsa_demo.sh on 6 demo samples, pip install with kernels |
ok (506 s) | ok (521 s) |
| Tutorial, pure-Python install | ok (539 s) | ok (494 s) |
Docker build + genotype + gtc-to-vcf |
ok | ok |
conda build + install + genotype |
ok | ok |
Content digests (scripts/p10/digest.py: every numeric GTC field and sample statistic with NaNs canonicalised, all
VCF data lines) of the 6 GTCs and 6 VCFs are identical across all of them: pip with kernels, pip pure, Docker and
conda, on aarch64 and on x86_64, and equal to the Raspberry Pi's own run of the same tutorial. The x86_64 results come
from AMD EPYC (m6a/c6a) machines; bit-exactness had so far only been shown on ARM.
Found and fixed
simurg inspect … | headmade the CLI reportE_INTERNAL: BrokenPipeErrorand exit 1, which stopped the tutorial underset -o pipefail(it passed on the Pi only by timing luck). A closed stdout now exits with 141 (like a tool killed by SIGPIPE) and prints nothing; the tutorial reads withsedinstead ofhead; unit test added.- The
fastextra (simurg[fast]→simurg-core) was dropped:uvmust resolve every extra, andsimurg-coreis not on a package index. The kernels are installed as their own wheel.