adata-cli/pyproject.toml at main · cellgeni/adata-cli · GitHub

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[project]
# The short name `adata-cli` was taken on PyPI by an unrelated project,
# so the distribution is published as `pyadata-cli`. The import package
# and the command are both still `adata`.
name = "pyadata-cli"
version = "0.7.1"
description = "Streaming CLI for exploring and editing large AnnData .h5ad and .zarr stores"
readme = "README.md"
requires-python = ">=3.12"
license = "MIT"
license-files = ["LICENSE"]
authors = [
    { name = "Aljes Binkevich", email = "ab76@sanger.ac.uk" },
]
maintainers = [
    { name = "Aljes Binkevich", email = "ab76@sanger.ac.uk" },
]
keywords = [
    "anndata",
    "h5ad",
    "zarr",
    "bioinformatics",
    "single-cell",
    "cli",
]
classifiers = [
    "Development Status :: 4 - Beta",
    "Environment :: Console",
    "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",
    "Topic :: Scientific/Engineering :: Bio-Informatics",
    "Typing :: Typed",
]

dependencies = [
    "h5py>=3.15.1",
    "numpy>=2.3.5",
    "pillow>=12.1.0",
    "rich>=14.2.0",
    "typer>=0.20.0",
    "zarr>=3.1.5",
]

[project.urls]
Homepage = "https://github.com/cellgeni/adata-cli"
Repository = "https://github.com/cellgeni/adata-cli"
Documentation = "https://cellgeni.github.io/adata-cli/"
Issues = "https://github.com/cellgeni/adata-cli/issues"
Changelog = "https://github.com/cellgeni/adata-cli/blob/main/CHANGELOG.md"

[project.optional-dependencies]
dev = [
    "pytest>=8.3.4",
    "pytest-cov>=6.0.0",
    # Turns a hang into a failure with a traceback. Without it a stuck test
    # burns the CI job's whole timeout and reports nothing useful.
    "pytest-timeout>=2.3.0",
    # Used only by tests/test_anndata_roundtrip.py, to check that what this
    # tool reads and writes matches what anndata itself produces.
    "anndata>=0.13",
]

[build-system]
requires = ["uv_build>=0.8.0,<0.9.0"]
build-backend = "uv_build"

[tool.uv.build-backend]
module-name = "adata"


[project.scripts]
adata = "adata.cli:main"
# Deprecated alias, removed in 1.0.0
h5ad = "adata.cli:main_deprecated"

[tool.coverage.run]
source = ["src/adata"]
omit = [
    "*/tests/*",
    "*/__pycache__/*",
]

[tool.coverage.report]
precision = 2
show_missing = true
skip_covered = false