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setup.py
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setup.py
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#!/usr/bin/env python3
import io
import re
import os
import sys
from setuptools import setup, find_packages
from setuptools.command.develop import develop
from setuptools.command.install import install
from subprocess import check_call
def read(*names, **kwargs):
with io.open(
os.path.join(os.path.dirname(__file__), *names),
encoding=kwargs.get("encoding", "utf8"),
) as fp:
return fp.read()
def find_version(*file_paths):
version_file = read(*file_paths)
version_match = re.search(r"^__version__ = ['\"]([^'\"]*)['\"]", version_file, re.M)
if version_match:
return version_match.group(1)
raise RuntimeError("Unable to find version string.")
def install_apsw(method="pip", version="3.27.2", tag="-r1"):
try:
import apsw
assert apsw
except ImportError:
try:
print(f"Installing apsw from GitHub using {method}")
version = "3.27.2"
tag = "-r1"
check_call(
f"""\
pip install \
https://github.com/rogerbinns/apsw/releases/download/{version}{tag}/apsw-{version}{tag}.zip \
--global-option=fetch \
--global-option=--version \
--global-option={version} \
--global-option=--all \
--global-option=build \
--global-option=--enable=rtree \
""".split()
)
except Exception:
raise ValueError(
f"Unable to automatically install APSW using {method}. Please install apsw manually"
f" and re-run minus80 installation process.\n"
"https://rogerbinns.github.io/apsw/build.html#recommended",
)
class DevelopCommand(develop):
"""
Installation (develop) command that pre-installs APSW since its not on pypi
"""
def run(self):
try:
install_apsw()
develop.run(self)
except ValueError as e:
print(e, file=sys.stderr)
sys.exit(1)
class InstallCommand(install):
"""
Installation command that pre-installs APSW since its not on pypi
"""
def run(self):
try:
install_apsw()
install.run(self)
except ValueError as e:
print(e, file=sys.stderr)
sys.exit(1)
setup(
name="minus80",
version=find_version("minus80", "__init__.py"), # +'-dev3',
description="A library for freezing, unfreezing and storing biological data.",
url="http://linkage.io",
author="Rob Schaefer",
author_email="rob@linkage.io",
license="Copyright Linkage Analytics 2016-2018. Available under the MIT License",
classifiers=[
# How mature is this project? Common values are
# 3 - Alpha
# 4 - Beta
# 5 - Production/Stable
"Development Status :: 4 - Beta",
# Indicate who your project is intended for
"Intended Audience :: Developers",
"Topic :: Software Development :: Build Tools",
# Pick your license as you wish (should match "license" above)
"License :: OSI Approved :: MIT License",
# Specify the Python versions you support here. In particular, ensure
# that you indicate whether you support Python 2, Python 3 or both.
"Programming Language :: Python :: 3",
"Programming Language :: Python :: 3.6",
],
keywords="data storage biology freeze",
project_urls={
"Documentation": "https://minus80.readthedocs.io/en/latest/",
"Source": "https://github.com/LinkageIO/Minus80",
"Tracker": "https://github.com/LinkageIO/Minus80/issues",
},
packages=find_packages(),
scripts=[],
ext_modules=[],
cmdclass={"develop": DevelopCommand, "install": InstallCommand},
package_data={"": ["*.cyx"]},
install_requires=[
"aiosqlite>=0.16.1",
"google-cloud >= 0.34.0",
"google-cloud-storage >= 1.17.0",
"google-cloud-kms >= 1.2.1",
"pandas>=0.23.4",
"tinydb>=3.13.0",
"tables >= 3.5.2",
"h5py >= 2.9.0",
"termcolor >= 1.1.0",
"pyyaml >= 5.1.2",
"click >= 7.0",
"asyncssh >= 1.17.1",
"aiohttp >= 3.6.1",
"aiofiles >= 0.4.0",
"networkx == 1.11",
"urllib3 >= 1.24.2",
"requests >= 2.11.1",
"pyrebase4 >=4.3.0",
"fuzzywuzzy >= 0.17.0",
"python-Levenshtein >= 0.12.0",
"tqdm >= 4.32.2",
"backoff >= 1.8.0",
],
extras_require={
"docs": ["ipython>=6.5.0", "matplotlib>=2.2.3"],
"local_install": [
"flask>=1.1.1",
"firebase-admin>=3.1.0",
"flask-cors>=3.0.8",
],
},
# dependency_links = [
# 'git+https://github.com/rogerbinns/apsw'
# ],
include_package_data=True,
entry_points="""
[console_scripts]
minus80=minus80.cli.minus80:cli
""",
)