pg_gpu/pyproject.toml at main · kr-colab/pg_gpu · GitHub

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[build-system]
requires = ["hatchling", "hatch-vcs"]
build-backend = "hatchling.build"

# The package version is derived from the latest git tag (e.g. tag v0.1.0 ->
# version 0.1.0), so a release is cut by tagging -- there is no version string
# to bump by hand. Untagged builds get a setuptools-scm dev version.
[tool.hatch.version]
source = "vcs"

# Restrict the source distribution to the package and its tests. Without an
# explicit allowlist hatchling sweeps in everything not git-ignored -- stray
# PDFs, scratch data, and local .claude/ config -- which should not ship to
# PyPI. pyproject.toml, README.md, and LICENSE are always included via project
# metadata.
[tool.hatch.build.targets.sdist]
include = [
    "/pg_gpu",
    "/tests",
]

[project]
name = "pg_gpu"
dynamic = ["version"]
description = "GPU-accelerated population genetics statistics"
readme = "README.md"
requires-python = ">=3.12"
license = "MIT"
license-files = ["LICENSE"]
authors = [
    { name = "Andrew Kern", email = "adkern@uoregon.edu" },
]
maintainers = [
    { name = "Andrew Kern", email = "adkern@uoregon.edu" },
]
keywords = [
    "population genetics",
    "popgen",
    "genomics",
    "bioinformatics",
    "GPU",
    "CUDA",
    "CuPy",
]
classifiers = [
    "Development Status :: 3 - Alpha",
    "Intended Audience :: Science/Research",
    "Topic :: Scientific/Engineering :: Bio-Informatics",
    "Programming Language :: Python :: 3",
    "Programming Language :: Python :: 3.12",
    "Programming Language :: Python :: 3.13",
    "Operating System :: POSIX :: Linux",
    "Environment :: GPU :: NVIDIA CUDA :: 12",
]

# pg_gpu is GPU-first: cupy and the kvikio/nvcomp GPU-decompression stack are
# hard runtime requirements, not optional extras. The cupy [ctk] extra pulls
# the CUDA toolkit headers (nvrtc + runtime) from PyPI -- cupy 14 stopped
# bundling them, and they are needed at runtime because cupy JIT-compiles its
# kernels with NVRTC. With [ctk], a plain `pip install` works given only an
# NVIDIA CUDA-12 driver; no separate conda/system CUDA toolkit is required.
# matplotlib/seaborn back the plotting module (imported from __init__); tskit
# is imported directly by HaplotypeMatrix (otherwise only transitive via msprime).
dependencies = [
    "numpy>=2.0",
    "scipy>=1.12",
    "pandas>=2.0",
    "matplotlib>=3.7",
    "seaborn>=0.12",
    "scikit-allel>=1.3",
    "msprime>=1.0",
    "tskit>=0.5",
    "h5py>=3.0",
    "tqdm>=4.0",
    "zarr>=2.16",
    "bio2zarr[vcf]>=0.1",
    "cupy-cuda12x[ctk]>=13.0",
    "kvikio-cu12>=25.0",
    "nvidia-nvcomp-cu12>=4.0",
]

[project.optional-dependencies]
dev = [
    "pytest>=7.0",
    "pytest-xdist>=3.0",
    "ipython>=8.0",
    "ipykernel>=6.0",
    "ruff>=0.4",
]
docs = [
    "sphinx>=4.0",
    "sphinx-rtd-theme>=1.0",
    "nbsphinx>=0.9.8",
]
moments = [
    "moments-popgen",
    "demes",
    "demesdraw",
]

[project.urls]
Homepage = "https://github.com/kr-colab/pg_gpu"
Documentation = "https://pg-gpu.readthedocs.io"
Repository = "https://github.com/kr-colab/pg_gpu"
Issues = "https://github.com/kr-colab/pg_gpu/issues"

[tool.pytest.ini_options]
pythonpath = [
    "pg_gpu"
]
markers = [
    "slow: marks tests as slow (deselected by default, run with --slow)",
    "requires_r: developer-local test that shells out to R (skipped when R is unavailable; never run in CI)",
]
filterwarnings = [
    "ignore::DeprecationWarning:cupyx",
    "ignore::DeprecationWarning:moments",
    "ignore::DeprecationWarning:allel",
    "ignore:No invariant site information:UserWarning",
    "ignore:__array__ implementation:DeprecationWarning",
    "ignore:.*FORMAT header not found:UserWarning",
    "ignore::zarr.errors.UnstableSpecificationWarning",
    "ignore::zarr.errors.ZarrDeprecationWarning",
    "ignore:The `compressor` argument is deprecated:UserWarning:zarr",
    # A multiallelic drop must be expected by the test that triggers it; any
    # other drop fails the test. Matched by message, not category, so pytest's
    # warnings plugin does not import pg_gpu before pytest-cov starts measuring
    # (which would drop module-level coverage); a test pins the phrase.
    "error:.* is defined on biallelic sites:UserWarning",
]

[tool.coverage.run]
source = ["pg_gpu"]
# Record repo-relative file paths in .coverage / coverage.xml instead of
# absolute ones, so the reports are portable across checkouts and CI (and
# diff-cover can map the files).
relative_files = true
# Measure example scripts that tests launch in a child interpreter; pytest-cov 7
# no longer instruments subprocesses automatically.
patch = ["subprocess"]

[tool.ruff]
line-length = 120
target-version = "py312"

[tool.ruff.lint]
select = ["E", "F", "W"]
ignore = [
    "E501",   # line too long (handled by formatter)
    "E711",   # comparison to None (existing codebase style)
    "E712",   # comparison to True/False (existing codebase style)
    "E721",   # type comparison (existing codebase style)
    "E741",   # ambiguous variable name (common in pop gen: l, n, p)
    "F401",   # unused import (some re-exports are intentional)
    "F811",   # redefined unused name (test fixtures)
    "F841",   # unused variable (sometimes used for GPU sync)
    "W605",   # invalid escape sequence (in CUDA kernel strings)
]