P10 complete: packaging verified on fresh x86_64 and aarch64 VMs
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.
This commit is contained in:
1 parent
522429b731
commit
0b05b0d346
4 files changed
+80
-3
No files matched your search
+27
-1
@@ -28,6 +28,31 @@ uv pip install ./rust/simurg-core
|
||||
```
|
||||
|
||||
Without them the same code runs in pure Python/NumPy; `SIMURG_PURE_PYTHON=1` forces that path.
|
||||
|
||||
**From release files** (`bash scripts/build_dist.sh` writes them to `dist/`: a pure wheel, an sdist and
|
||||
`manylinux_2_28` kernel wheels for x86_64 and aarch64, glibc ≥ 2.28):
|
||||
|
||||
```bash
|
||||
python3 -m venv simurg-env && simurg-env/bin/pip install simurg-1.0.0-py3-none-any.whl \
|
||||
simurg_core-1.0.0-cp312-abi3-manylinux_2_28_$(uname -m).whl # the second wheel is optional
|
||||
```
|
||||
|
||||
**Docker** (image ≈ 550 MB, kernels included, runs as a non-root user; data stay in the mounted folder):
|
||||
|
||||
```bash
|
||||
docker build -t simurg:1.0.0 .
|
||||
docker run --rm --user "$(id -u):$(id -g)" -v "$PWD":/work simurg:1.0.0 \
|
||||
genotype --bpm M.bpm --egt C.egt --idats idats --out run/gtc
|
||||
```
|
||||
|
||||
**conda** (recipes in `packaging/conda/`):
|
||||
|
||||
```bash
|
||||
conda build -c conda-forge --output-folder conda-bld packaging/conda/simurg-core packaging/conda/simurg
|
||||
conda create -n simurg -c ./conda-bld -c conda-forge simurg simurg-core
|
||||
```
|
||||
|
||||
All four installs give identical results on x86_64 and aarch64 (`docs/validation/P10.md`).
|
||||
Only pure-Python dependencies are needed (numpy, pyarrow, typer, rich, pyyaml, openpyxl). VCF/BCF, tabix/CSI
|
||||
indexes and PLINK files are written by SimurgArray itself; bcftools/plink2 are not required (they are used only
|
||||
as test oracles).
|
||||
@@ -167,5 +192,6 @@ A nightly differential run (`scripts/nightly.py`) re-checks these against the or
|
||||
Errors and warnings carry a stable code (`E_…`, `W_…`) — all are listed in `docs/messages.md` with their spec item.
|
||||
Add `--debug` for a traceback or `--log-json` for machine-readable logs. Exit codes (CLI-014): 0 success,
|
||||
1 internal error, 2 usage or pre-flight validation error (nothing processed), 3 some samples failed (or
|
||||
`compare --fail-on-discrepancy` found discrepancies), 4 no sample succeeded, 130/143 interrupted. Findings about vendor behaviour that SimurgArray reproduces
|
||||
`compare --fail-on-discrepancy` found discrepancies), 4 no sample succeeded, 130/143 interrupted, 141 the reader of
|
||||
stdout went away (e.g. `simurg inspect … | head`; nothing is reported). Findings about vendor behaviour that SimurgArray reproduces
|
||||
(or deliberately does not) are in `docs/known_unknowns.md`.
|
||||
Reference in new issue
Block a user