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use poetry
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‎docs/conf.py

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# If your documentation needs a minimal Sphinx version, state it here.
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#
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needs_sphinx = "2.0" # Nicer param docs
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needs_sphinx = "3.0" # Nicer param docs
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# Add any Sphinx extension module names here, as strings. They can be
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# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom ones.

‎pyproject.toml

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[tool.poetry]
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authors = ["Romain Lopez <[email protected]>", "Adam Gayoso <[email protected]", "Galen Xing <[email protected]>"]
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classifiers = [
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"Development Status :: 4 - Beta",
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"Intended Audience :: Science/Research",
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"License :: OSI Approved :: MIT License",
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"Natural Language :: English",
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"Programming Language :: Python :: 3.6",
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"Programming Language :: Python :: 3.7",
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"Operating System :: MacOS :: MacOS X",
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"Operating System :: Microsoft :: Windows",
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"Operating System :: POSIX :: Linux",
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"Topic :: Scientific/Engineering :: Bio-Informatics",
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]
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description = "Deep generative models for end-to-end analysis of single-cell omics data."
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documentation = "https://scvi.readthedocs.io/en/stable/"
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homepage = "https://github.com/YosefLab/scvi-tools"
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license = "MIT"
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name = "scvi-tools"
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packages = [
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{include = "scvi"},
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]
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readme = "README.rst"
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version = "0.6.7"
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[tool.poetry.dependencies]
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anndata = "^0.7.4"
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black = {version = "^20.8b1", optional = true}
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codecov = {version = "^2.0.8", optional = true}
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flake8 = {version = "^3.7.7", optional = true}
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h5py = "^2.9.0"
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hyperopt = "^0.1.2"
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ipython = {version = "^7.1.1", optional = true}
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ipywidgets = "*"
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jupyter = {version = "^1.0", optional = true}
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leidenalg = {version = "*", optional = true}
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loompy = {version = "^3.0.6", optional = true}
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nbconvert = {version = "^5.4.0", optional = true}
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nbformat = {version = "^4.4.0", optional = true}
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nbsphinx = {version = "*", optional = true}
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nbsphinx-link = {version = "*", optional = true}
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numba = "^0.41.0"
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numpy = "^1.17.0"
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pandas = "^1.0"
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pre-commit = {version = "^2.7.1", optional = true}
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pydata-sphinx-theme = {version = "^0.4.0", optional = true}
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pytest = {version = "^4.4", optional = true}
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python = "^3.6"
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python-igraph = {version = "*", optional = true}
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rich = "^6.2.0"
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scanpy = {version = "^1.6", optional = true}
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scanpydoc = {version = "^0.5", optional = true}
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scikit-learn = "^0.21.2"
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sphinx = {version = "^3.0", optional = true}
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torch = "^1.3"
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tqdm = "^4.31.1"
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typing_extensions = {version = "*", python = "<3.8"}
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xlrd = "^1.2.0"
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[tool.poetry.extras]
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dev = ["black", "pytest", "flake8", "codecov", "scanpy", "loompy", "jupyter", "nbformat", "nbconvert", "pre-commit"]
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docs = ["sphinx", "scanpydoc", "nbsphinx", "nbsphinx-link", "ipython", "pydata-sphinx-theme", "typing_extensions"]
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tutorials = ["scanpy", "leidenalg", "python-igraph", "loompy"]
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[tool.poetry.dev-dependencies]
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[build-system]
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build-backend = "poetry.masonry.api"
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requires = ["poetry>=1.0"]

‎scvi/__init__.py

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__author__ = "Romain Lopez"
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__email__ = "[email protected]"
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__version__ = "0.6.8"
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"""scvi-tools."""
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# Set default logging handler to avoid logging with logging.lastResort logger.
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import logging

‎setup.py

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#!/usr/bin/env python
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# -*- coding: utf-8 -*-
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from setuptools import setup, find_packages
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# This is a shim to hopefully allow Github to detect the package, build is done with poetry
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with open("README.rst") as readme_file:
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readme = readme_file.read()
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import setuptools
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requirements = [
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"numpy>=1.17.0",
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"torch>=1.3",
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"matplotlib>=3.1.2",
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"scikit-learn>=0.20.3",
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"h5py>=2.9.0",
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"pandas>=0.25",
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"tqdm>=4.31.1",
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"xlrd>=1.2.0",
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"hyperopt==0.1.2",
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"anndata>=0.7",
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'dataclasses; python_version < "3.7"', # for `dataclass`
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"scikit-misc>=0.1.3",
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"tables>=3.6.1", # read_hdf pandas in load_posterior
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"rich[jupyter]",
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"numba>=0.41.0",
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]
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setup_requirements = ["pip>=18.1"]
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test_requirements = [
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"pytest>=4.4",
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"pytest-runner>=5.0",
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"flake8>=3.7.7",
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"coverage>=4.5.1",
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"codecov>=2.0.8",
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"black>=19.3b0",
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"nbconvert>=5.4.0",
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"nbformat>=4.4.0",
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"jupyter>=1.0.0",
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"ipython>=7.1.1",
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"loompy>=3.0.6",
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"scanpy>=1.6",
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]
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extras_requirements = {
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"notebooks": [
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"louvain>=0.6.1",
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"leidenalg>=0.7.0",
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"python-igraph>=0.7.1.post6",
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"colour>=0.1.5",
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"umap-learn>=0.3.10",
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"seaborn>=0.9.0",
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"leidenalg>=0.7.0",
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"loompy>=3.0.6",
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"scanpy>=1.6",
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],
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"docs": [
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"sphinx>=2.0.1",
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"nbsphinx",
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"sphinx_autodoc_typehints",
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"sphinx-rtd-theme>=0.3.1",
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"nbsphinx-link",
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"scanpydoc",
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"pydata-sphinx-theme>=0.4.0",
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'typing_extensions; python_version < "3.8"', # for `Literal`
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"ipython>=7.1.1",
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],
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"test": test_requirements,
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}
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author = (
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"Romain Lopez, "
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"Jeffrey Regier, "
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"Maxime Langevin, "
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"Edouard Mehlman, "
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"Yining Liu, "
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"Achille Nazaret, "
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"Gabriel Misrachi, "
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"Oscar Clivio, "
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"Pierre Boyeau, "
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"Adam Gayoso"
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)
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setup(
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author=author,
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author_email="[email protected]",
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classifiers=[
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"Development Status :: 4 - Beta",
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"Intended Audience :: Science/Research",
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"License :: OSI Approved :: MIT License",
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"Natural Language :: English",
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"Programming Language :: Python :: 3.6",
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"Programming Language :: Python :: 3.7",
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"Operating System :: MacOS :: MacOS X",
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"Operating System :: Microsoft :: Windows",
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"Operating System :: POSIX :: Linux",
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"Topic :: Scientific/Engineering :: Bio-Informatics",
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],
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description="Single-cell Variational Inference",
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install_requires=requirements,
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license="MIT license",
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long_description=readme,
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include_package_data=True,
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keywords="scvi",
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name="scvi",
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python_requires=">=3.6",
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packages=find_packages(),
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setup_requires=setup_requirements,
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test_suite="tests",
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tests_require=test_requirements,
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extras_require=extras_requirements,
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url="https://github.com/YosefLab/scVI",
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version="0.6.8",
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zip_safe=False,
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)
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if __name__ == "__main__":
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setuptools.setup(name="scvi-tools")

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