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pyproject.toml
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pyproject.toml
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[tool.isort]
include_trailing_comma = true
multi_line_output = 3
profile = "black"
skip_glob = ["docs/*", "scvi/__init__.py"]
[tool.poetry]
authors = ["Romain Lopez <romain_lopez@gmail.com>", "Adam Gayoso <adamgayoso@berkeley.edu>", "Galen Xing <gx2113@columbia.edu>"]
classifiers = [
"Development Status :: 4 - Beta",
"Intended Audience :: Science/Research",
"Natural Language :: English",
"Programming Language :: Python :: 3.7",
"Programming Language :: Python :: 3.8",
"Programming Language :: Python :: 3.9",
"Operating System :: MacOS :: MacOS X",
"Operating System :: Microsoft :: Windows",
"Operating System :: POSIX :: Linux",
"Topic :: Scientific/Engineering :: Bio-Informatics",
]
description = "Deep probabilistic analysis of single-cell omics data."
documentation = "https://scvi-tools.org"
homepage = "https://github.com/YosefLab/scvi-tools"
license = "BSD-3-Clause"
name = "scvi-tools"
packages = [
{include = "scvi"},
]
readme = "README.md"
version = "0.13.0"
[tool.poetry.dependencies]
anndata = ">=0.7.5"
black = {version = ">=20.8b1", optional = true}
codecov = {version = ">=2.0.8", optional = true}
flake8 = {version = ">=3.7.7", optional = true}
h5py = ">=2.9.0"
importlib-metadata = {version = "^1.0", python = "<3.8"}
ipython = {version = ">=7.20", optional = true, python = ">=3.7"}
ipywidgets = "*"
isort = {version = ">=5.7", optional = true}
jupyter = {version = ">=1.0", optional = true}
leidenalg = {version = "*", optional = true}
loompy = {version = ">=3.0.6", optional = true}
nbconvert = {version = ">=5.4.0", optional = true}
nbformat = {version = ">=4.4.0", optional = true}
nbsphinx = {version = "*", optional = true}
nbsphinx-link = {version = "*", optional = true}
numba = ">=0.41.0"
numpy = ">=1.17.0"
openpyxl = ">=3.0"
pandas = ">=1.0"
pre-commit = {version = ">=2.7.1", optional = true}
pydata-sphinx-theme = {version = ">=0.4.3", optional = true}
pyro-ppl = ">=1.6.0"
pytest = {version = ">=4.4", optional = true}
python = ">=3.7,<4.0"
python-igraph = {version = "*", optional = true}
pytorch-lightning = "~1.3"
rich = ">=9.1.0"
scanpy = {version = ">=1.6", optional = true}
scanpydoc = {version = ">=0.5", optional = true}
scikit-learn = ">=0.21.2"
scikit-misc = {version = ">=0.1.3", optional = true}
sphinx = {version = ">=3.4", optional = true}
sphinx-autodoc-typehints = {version = "*", optional = true}
sphinx-gallery = {version = ">0.6", optional = true}
sphinx-tabs = {version = "*", optional = true}
sphinx_copybutton = {version = "<=0.3.1", optional = true}
torch = ">=1.8.0"
tqdm = ">=4.56.0"
typing_extensions = {version = "*", python = "<3.8", optional = true}
[tool.poetry.extras]
dev = ["black", "pytest", "flake8", "codecov", "scanpy", "loompy", "jupyter", "nbformat", "nbconvert", "pre-commit", "isort"]
docs = [
"sphinx",
"scanpydoc",
"nbsphinx",
"nbsphinx-link",
"ipython",
"pydata-sphinx-theme",
"typing_extensions",
"sphinx-autodoc-typehints",
"sphinx_copybutton",
"sphinx_gallery",
"sphinx-tabs",
]
tutorials = ["scanpy", "leidenalg", "python-igraph", "loompy", "scikit-misc"]
[tool.poetry.dev-dependencies]
[tool.tox]
legacy_tox_ini = """
[tox]
envlist = py37
[testenv]
deps = pytest
extras =
dev
commands = pytest {posargs}
"""
[build-system]
build-backend = "poetry.masonry.api"
requires = [
"poetry>=1.0",
"setuptools", # keep it here or "pip install -e" would fail
]