pyproject.toml

[build-system]
requires = ["setuptools>=45", "setuptools_scm[toml]>=6.2"]
build-backend = "setuptools.build_meta"

[project]
name = "cellxgene_census"
dynamic = ["version"]
description = "API to facilitate the use of the CZ CELLxGENE Discover Census. For more information about the API and the project visit https://github.com/chanzuckerberg/cellxgene-census/"
authors = [
    { name = "Chan Zuckerberg Initiative", email = "soma@chanzuckerberg.com" }
]
license = { text = "MIT" }
readme = "README.md"
requires-python = ">= 3.8, < 3.12"
classifiers = [
    "Development Status :: 4 - Beta",
    "Intended Audience :: Developers",
    "Intended Audience :: Information Technology",
    "Intended Audience :: Science/Research",
    "License :: OSI Approved :: MIT License",
    "Programming Language :: Python",
    "Topic :: Scientific/Engineering :: Bio-Informatics",
    "Operating System :: POSIX :: Linux",
    "Operating System :: MacOS :: MacOS X",
    "Programming Language :: Python :: 3.8",
    "Programming Language :: Python :: 3.9",
    "Programming Language :: Python :: 3.10",
    "Programming Language :: Python :: 3.11",
]
dependencies= [
    # NOTE: the tiledbsoma version must be >= to the version used in the Census builder, to
    # ensure that the assets are readable (tiledbsoma supports backward compatible reading).
    # Make sure this version does not fall behind the builder's tiledbsoma version.
    "tiledbsoma~=1.4.3",
    "anndata",
    "numpy>=1.21,<1.25",  # numpy is constrained by numba and the old pip solver
    "requests",
    "typing_extensions",
    "s3fs>=2021.06.1",
    "scipy<1.11",  # work around incompatibility between scipy and pyarrow
]

[project.optional-dependencies]
experimental = [
    "torch==2.0.1",
    "torchdata==0.6.1",
    "scikit-learn==1.2.2",
    "scikit-misc==0.2.0",
    "psutil==5.9.5",
]

[project.urls]
homepage = "https://github.com/chanzuckerberg/cellxgene-census"
repository = "https://github.com/chanzuckerberg/cellxgene-census"

[tool.setuptools.packages.find]
where = ["src"]
include = ["cellxgene_census*"]  # package names should match these glob patterns (["*"] by default)
exclude = ["tests*"]  # exclude packages matching these glob patterns (empty by default)

[tool.setuptools_scm]
root = "../../.."

[tool.black]
line-length = 120
target_version = ['py39']

[tool.mypy]
show_error_codes = true
ignore_missing_imports = true
warn_unreachable = true
strict = true
plugins = "numpy.typing.mypy_plugin"

[tool.pytest.ini_options]
markers = [
    "live_corpus: runs on the live CELLxGENE Census data corpus and small enough to run in CI",
    "expensive: too expensive to run regularly or in CI",
    "experimental: tests for the `experimental` package",
]

[tool.ruff]
select = ["E", "F", "B", "I"]
ignore = ["E501", "E402", "C408", ]
line-length = 120
target-version = "py39"

[tool.ruff.isort]
known-first-party =["cellxgene_census"]