harmonypy/pyproject.toml at master · slowkow/harmonypy · GitHub

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[build-system]
requires = ["scikit-build-core>=0.10", "nanobind>=2.0"]
build-backend = "scikit_build_core.build"

[project]
name = "harmonypy"
version = "2.0.0"
description = "Batch correction for single-cell data using the Harmony algorithm with a C++ Armadillo backend."
readme = "README.md"
license = "GPL-3.0-or-later"
requires-python = ">=3.9"
authors = [
    { name = "Kamil Slowikowski", email = "kslowikowski@gmail.com" },
    { name = "John Arevalo", email = "johnarevalo@gmail.com" }
]
keywords = ["harmony", "batch-correction", "integration", "single-cell", "bioinformatics"]
classifiers = [
    "Development Status :: 5 - Production/Stable",
    "Intended Audience :: Science/Research",
    "Natural Language :: English",
    "Operating System :: MacOS",
    "Operating System :: POSIX :: Linux",
    "Programming Language :: Python :: 3",
    "Programming Language :: Python :: 3.9",
    "Programming Language :: Python :: 3.10",
    "Programming Language :: Python :: 3.11",
    "Programming Language :: Python :: 3.12",
    "Programming Language :: Python :: 3.13",
    "Programming Language :: Python :: 3.14",
    "Programming Language :: C++",
    "Topic :: Scientific/Engineering :: Bio-Informatics",
]
dependencies = [
    "numpy",
]

[project.optional-dependencies]
test = [
    "pandas",
    "pytest>=8.4.2",
    "scipy",
]

[project.urls]
Homepage = "https://github.com/slowkow/harmonypy"
Repository = "https://github.com/slowkow/harmonypy"
Issues = "https://github.com/slowkow/harmonypy/issues"
Changelog = "https://github.com/slowkow/harmonypy/blob/master/CHANGELOG.md"

[tool.scikit-build]
wheel.packages = ["harmonypy"]
sdist.exclude = ["scripts", "figures", "data", "tests", ".claude", ".cursor", ".github"]
build.verbose = true
build-dir = "/tmp/harmonypy-build/{wheel_tag}"
ninja.make-fallback = true

[tool.scikit-build.cmake.define]
CMAKE_BUILD_TYPE = "Release"

[tool.cibuildwheel]
build = "cp39-* cp310-* cp311-* cp312-* cp313-* cp314-*"
skip = "*-musllinux_* *-win32 *-manylinux_i686"
test-requires = ["pytest"]
test-command = "mkdir -p /tmp/hptest/data && cp -r {project}/tests /tmp/hptest/ && cp {project}/data/pbmc_3500_*.tsv.gz /tmp/hptest/data/ && cd /tmp/hptest && pytest tests/test_harmony.py::test_run_harmony_small -v"

[tool.cibuildwheel.linux]
archs = ["x86_64", "aarch64"]
before-all = "yum install -y epel-release && yum install -y openblas-devel lapack-devel || apk add openblas-dev lapack-dev"

[tool.cibuildwheel.macos]
archs = ["x86_64", "arm64"]

[tool.cibuildwheel.macos.environment]
MACOSX_DEPLOYMENT_TARGET = "11.0"