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pyproject.toml
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pyproject.toml
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[build-system]
build-backend = "hatchling.build"
requires = ["hatchling", "hatch-vcs"]
[project]
name = "anndata"
description = "Annotated data."
requires-python = ">=3.9"
license = "BSD-3-Clause"
authors = [
{ name = "Philipp Angerer" },
{ name = "Alex Wolf" },
{ name = "Isaac Virshup" },
{ name = "Sergei Rybakov" },
]
maintainers = [
{ name = "Isaac Virshup", email = "ivirshup@gmail.com" },
{ name = "Philipp Angerer", email = "philipp.angerer@helmholtz-munich.de" },
{ name = "Alex Wolf", email = "f.alex.wolf@gmx.de" },
]
readme = "README.md"
classifiers = [
"Environment :: Console",
"Framework :: Jupyter",
"Intended Audience :: Developers",
"Intended Audience :: Science/Research",
"Natural Language :: English",
"Operating System :: MacOS :: MacOS X",
"Operating System :: Microsoft :: Windows",
"Operating System :: POSIX :: Linux",
"Programming Language :: Python :: 3",
"Programming Language :: Python :: 3.9",
"Programming Language :: Python :: 3.10",
"Programming Language :: Python :: 3.11",
"Topic :: Scientific/Engineering :: Bio-Informatics",
"Topic :: Scientific/Engineering :: Visualization",
]
dependencies = [
# pandas <1.1.1 has pandas/issues/35446
# pandas 2.1.0rc0 has pandas/issues/54622
"pandas >=1.1.1, !=2.1.0rc0",
"numpy>=1.16.5", # required by pandas 1.x
"scipy>1.4",
"h5py>=3",
"exceptiongroup; python_version<'3.11'",
"natsort",
"packaging>=20",
"array_api_compat",
]
dynamic = ["version"]
[project.urls]
Documentation = "https://anndata.readthedocs.io/"
Source = "https://github.com/scverse/anndata"
Home-page = "https://github.com/scverse/anndata"
[project.optional-dependencies]
dev = [
# dev version generation
"setuptools_scm",
# test speedups
"pytest-xdist",
]
doc = [
"sphinx>=4.4",
"sphinx-book-theme>=1.0.1",
"sphinx-autodoc-typehints>=1.11.0",
"sphinx-issues",
"sphinx-copybutton",
"sphinxext.opengraph",
"nbsphinx",
"scanpydoc>=0.9",
"zarr",
"awkward>=2.0.7",
"IPython", # For syntax highlighting in notebooks
"myst_parser",
"sphinx_design>=0.5.0",
]
test = [
"loompy>=3.0.5",
"pytest>=6.0",
"pytest-cov>=2.10",
"zarr",
"matplotlib",
"scikit-learn",
"openpyxl",
"joblib",
"boltons",
"scanpy",
"httpx", # For data downloading
"dask[array,distributed]",
"awkward>=2.3",
"pytest_memray",
]
gpu = ["cupy"]
[tool.hatch.build]
exclude = ["anndata/tests/test_*.py", "anndata/tests/data"]
[tool.hatch.version]
source = "vcs"
[tool.hatch.build.hooks.vcs]
version-file = "anndata/_version.py"
[tool.coverage.run]
source = ["anndata"]
omit = ["setup.py", "versioneer.py", "anndata/_version.py", "**/test_*.py"]
[tool.pytest.ini_options]
addopts = "--doctest-modules"
python_files = "test_*.py"
testpaths = ["anndata", "docs/concatenation.rst"]
filterwarnings = ['ignore:X\.dtype being converted to np.float32:FutureWarning']
# For some reason this effects how logging is shown when tests are run
xfail_strict = true
markers = ["gpu: mark test to run on GPU"]
[tool.ruff]
ignore = [
# line too long -> we accept long comment lines; black gets rid of long code lines
"E501",
# Do not assign a lambda expression, use a def -> AnnData allows lambda expression assignments,
"E731",
# allow I, O, l as variable names -> I is the identity matrix, i, j, k, l is reasonable indexing notation
"E741",
]
select = [
"E", # Error detected by Pycodestyle
"F", # Errors detected by Pyflakes
"W", # Warning detected by Pycodestyle
"UP", # pyupgrade
"I", # isort
"TCH", # manage type checking blocks
"ICN", # Follow import conventions
"PTH", # Pathlib instead of os.path
]
[tool.ruff.per-file-ignores]
# E721 comparing types, but we specifically are checking that we aren't getting subtypes (views)
"anndata/tests/test_readwrite.py" = ["E721"]
[tool.ruff.isort]
known-first-party = ["anndata"]
required-imports = ["from __future__ import annotations"]
[tool.codespell]
skip = ".git,*.pdf,*.svg"
ignore-words-list = "theis,coo,homogenous"