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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# conda recipe for the optional compiled kernels of SimurgArray (Rust, PyO3; abi3 for Python >= 3.12).
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# conda build packaging/conda/simurg-core -c conda-forge
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{% set version = load_file_regex(load_file="Cargo.toml", regex_pattern='version = "([^"]+)"', from_recipe_dir=False).group(1) %}
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package:
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name: simurg-core
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version: {{ version }}
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source:
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path: ../../../rust/simurg-core
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build:
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number: 0
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skip: true # [win]
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script: {{ PYTHON }} -m pip install . --no-deps -vv
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requirements:
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build:
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- {{ compiler('c') }}
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- {{ compiler('rust') }}
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host:
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- python >=3.12
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- pip
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- maturin >=1.7,<2
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run:
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- python >=3.12
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- numpy >=1.26
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test:
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imports:
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- simurg_core
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commands:
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- python -c "import simurg_core, numpy as np; assert simurg_core.log10(np.array([0.0]))[0] == -np.inf"
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about:
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summary: Optional compiled kernels of SimurgArray (results identical to the pure-Python paths)
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license: MIT
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license_file:
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- LICENSE
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- NOTICE
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# conda recipe for SimurgArray (pure Python). Build from a checkout:
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# conda build packaging/conda/simurg -c conda-forge
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{% set version = load_file_regex(load_file="src/simurg/__init__.py", regex_pattern='__version__ = "([^"]+)"', from_recipe_dir=False).group(1) %}
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package:
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name: simurg
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version: {{ version }}
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source:
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path: ../../..
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build:
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noarch: python
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number: 0
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script: {{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vv
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entry_points:
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- simurg = simurg.cli.main:app
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requirements:
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host:
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- python >=3.12
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- pip
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- hatchling >=1.27
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run:
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- python >=3.12
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- numpy >=1.26
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- typer >=0.12
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- rich >=13
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- pyyaml >=6
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- pyarrow >=15
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- openpyxl >=3.1
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run_constrained:
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- simurg-core =={{ version }}
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test:
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imports:
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- simurg
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- simurg.cli.main
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commands:
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- simurg --version
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- simurg --help
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about:
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summary: Research toolkit for Illumina Infinium genotyping BeadChip data (IDAT to GTC, QC, VCF, PLINK)
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license: MIT
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license_file:
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- LICENSE
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- THIRD_PARTY_NOTICES.md
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