snf2/pyproject.toml at main · bhklab/snf2 · GitHub

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#:tombi toml-version = "v1.0.0"

[project]
name = "snf2"
version = "0.2.0"
description = "Modern Python implementation of Similarity Network Fusion"
readme = "README.md"
requires-python = ">=3.12"
license = "MIT"
license-files = ["LICENSE", "NOTICE"]
authors = [
    { name = "Michael Tran", email = "bhklab.michaeltran@gmail.com" },
    { name = "James Bannon", email = "bhklab.jamesbannon@gmail.com" },
]
keywords = [
    "bioinformatics",
    "data integration",
    "multi-omics",
    "network fusion",
    "similarity network fusion",
]
classifiers = [
    "Intended Audience :: Science/Research",
    "Operating System :: OS Independent",
    "Programming Language :: Python :: 3",
    "Programming Language :: Python :: 3 :: Only",
    "Programming Language :: Python :: 3.12",
    "Programming Language :: Python :: 3.13",
    "Programming Language :: Python :: 3.14",
    "Programming Language :: Python :: Implementation :: CPython",
    "Topic :: Scientific/Engineering :: Bio-Informatics",
    "Typing :: Typed",
]
dependencies = [
    "numpy>=2.0,<3",
    "scipy>=1.18,<2",
]

[project.urls]
Changelog = "https://github.com/bhklab/snf2/releases"
Documentation = "https://bhklab.github.io/snf2/"
Issues = "https://github.com/bhklab/snf2/issues"
Repository = "https://github.com/bhklab/snf2"

[build-system]
requires = ["hatchling>=1.27,<2"]
build-backend = "hatchling.build"

[tool.hatch.build.targets.wheel]
packages = ["src/snf2"]

[tool.hatch.build.targets.sdist]
include = [
    "/CHANGELOG.md",
    "/LICENSE",
    "/NOTICE",
    "/README.md",
    "/docs",
    "/mkdocs.yml",
    "/pyproject.toml",
    "/src",
    "/tests",
]

[tool.ruff]
src = ["src"]

[tool.ruff.lint]
select = ["E4", "E7", "E9", "F", "I", "B", "UP"]

[tool.ty.environment]
root = ["./src"]

[tool.pixi.workspace]
name = "snf2"
description = "Development workspace for the SNF2 Python package"
authors = [
    "Michael Tran <bhklab.michaeltran@gmail.com>",
    "James Bannon <bhklab.jamesbannon@gmail.com>",
]
channels = ["conda-forge"]
platforms = ["osx-arm64", "linux-64", "win-64"]
requires-pixi = ">=0.78.0,<0.79"

[tool.pixi.dependencies]
python = "3.14.*"
numpy = ">=2.0,<3"
scipy = ">=1.18,<2"

[tool.pixi.pypi-dependencies]
snf2 = { path = ".", editable = true }

[tool.pixi.environments]
dev = { features = ["dev"], solve-group = "default" }
docs = { features = ["docs"], solve-group = "default" }

[tool.pixi.feature.dev.dependencies]
python-build = ">=1.3,<2"
pytest = ">=9.0,<10"
ruff = ">=0.16,<0.17"
ty = ">=0.0.72,<0.1"

[tool.pixi.feature.dev.tasks]
format = { cmd = ["ruff", "format", "."], description = "Format Python files" }
format-check = { cmd = ["ruff", "format", "--check", "."], description = "Check Python formatting" }
lint = { cmd = ["ruff", "check", "."], description = "Lint Python files" }
typecheck = { cmd = ["ty", "check"], description = "Type-check Python files" }
test = { cmd = ["pytest"], description = "Run the test suite" }
build = { cmd = ["python", "-m", "build"], description = "Build the source and wheel distributions" }
check = { depends-on = ["format-check", "lint", "typecheck", "test", "build"], description = "Run all development checks" }

[tool.pixi.feature.docs.dependencies]
mkdocs = ">=1.6,<2"

[tool.pixi.feature.docs.tasks]
docs-build = { cmd = ["mkdocs", "build"], description = "Build documentation" }
docs-serve = { cmd = ["mkdocs", "serve"], description = "Serve documentation locally" }
docs-deploy = { cmd = ["mkdocs", "gh-deploy", "--force"], description = "Deploy documentation to GitHub Pages" }