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pyproject.toml
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[build-system]
build-backend = "hatchling.build"
requires = ["hatchling"]
[project]
name = "scvi-tools"
version = "0.20.0b0"
description = "Deep probabilistic analysis of single-cell omics data."
readme = "README.md"
requires-python = ">=3.8"
license = {file = "LICENSE"}
authors = [
{name = "The scvi-tools development team"},
]
maintainers = [
{name = "The scvi-tools development team", email = "adamgayoso@berkeley.edu"},
]
urls.Documentation = "https://scvi-tools.org"
urls.Source = "https://github.com/scverse/scvi-tools"
urls.Home-page = "https://scvi-tools.org"
classifiers = [
"Development Status :: 4 - Beta",
"Intended Audience :: Science/Research",
"Natural Language :: English",
"Programming Language :: Python :: 3.8",
"Programming Language :: Python :: 3.9",
"Programming Language :: Python :: 3.10",
"Operating System :: MacOS :: MacOS X",
"Operating System :: Microsoft :: Windows",
"Operating System :: POSIX :: Linux",
"Topic :: Scientific/Engineering :: Bio-Informatics",
]
dependencies = [
"anndata>=0.7.5",
"chex",
"docrep>=0.3.2",
"flax",
"jax>=0.3",
"jaxlib",
"optax",
"numpy>=1.17.0",
"pandas>=1.0",
"scipy",
"scikit-learn>=0.21.2",
"openpyxl>=3.0",
"rich>=9.1.0",
"h5py>=2.9.0",
"torch>=1.8.0",
"pytorch-lightning>=1.8.0,<1.9.0",
"torchmetrics>=0.6.0",
"pyro-ppl>=1.6.0",
"tqdm>=4.56.0",
"scikit-learn>=0.21.2",
"numpyro",
"ml-collections>=0.1.1",
"mudata>=0.1.2",
]
[project.optional-dependencies]
dev = ["black", "pytest", "flake8", "codecov", "scanpy>=1.6", "loompy>=3.0.6", "jupyter", "nbformat", "nbconvert", "pre-commit", "isort", "pymde", "genomepy"]
docs = [
"sphinx>=4.1",
"nbsphinx",
"ipython",
"furo",
"sphinx-autodoc-typehints<1.21.4",
"sphinx_copybutton",
"sphinx-design",
"sphinxext-opengraph",
"sphinx-hoverxref",
"sphinxcontrib-bibtex>=1.0.0",
"myst-parser",
]
autotune = [
"hyperopt>=0.2",
"ray[tune]>=2.2.0",
"ipython",
"scib-metrics>=0.1.1",
]
pymde = ["pymde"]
tutorials = ["scanpy", "leidenalg", "python-igraph", "loompy", "scikit-misc", "pynndescent", "pymde", "huggingface_hub", "genomepy"]
hub = ["huggingface_hub"]
[tool.hatch.build.targets.wheel]
packages = ['scvi']
[tool.coverage.run]
source = ["scvi"]
omit = [
"**/test_*.py",
]
[tool.pytest.ini_options]
testpaths = ["tests"]
xfail_strict = true
[tool.isort]
include_trailing_comma = true
multi_line_output = 3
profile = "black"
skip_glob = ["docs/*", "scvi/__init__.py"]
[tool.black]
target-version = ['py38']
include = '\.pyi?$'
exclude = '''
(
/(
\.eggs
| \.git
| \.hg
| \.mypy_cache
| \.tox
| \.venv
| _build
| buck-out
| build
| dist
)/
)
'''
[tool.jupytext]
formats = "ipynb,md"