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setup.py
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setup.py
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from __future__ import print_function
from setuptools import setup, find_packages, Command
from setuptools.command.sdist import sdist
from setuptools.command.build_py import build_py
from setuptools.command.egg_info import egg_info
from subprocess import check_call
import os
import sys
import platform
from distutils import log
here = os.path.dirname(os.path.abspath(__file__))
node_root = os.path.join(here, 'js')
is_repo = os.path.exists(os.path.join(here, '.git'))
npm_path = os.pathsep.join([
os.path.join(node_root, 'node_modules', '.bin'),
os.environ.get('PATH', os.defpath),
])
log.set_verbosity(log.DEBUG)
log.info('setup.py entered')
log.info('$PATH=%s' % os.environ['PATH'])
name = 'vitessce'
LONG_DESCRIPTION = 'Jupyter widget facilitating interactive visualization of spatial single-cell data with Vitessce'
def js_prerelease(command, strict=False):
"""Decorator for building minified js/css prior to another command."""
class DecoratedCommand(command):
def run(self):
jsdeps = self.distribution.get_command_obj('jsdeps')
if not is_repo and all(os.path.exists(t) for t in jsdeps.targets):
# sdist, nothing to do
command.run(self)
return
try:
self.distribution.run_command('jsdeps')
except Exception as e:
missing = [t for t in jsdeps.targets if not os.path.exists(t)]
if strict or missing:
log.warn('rebuilding js and css failed')
if missing:
log.error('missing files: %s' % missing)
raise e
else:
log.warn('rebuilding js and css failed (not a problem)')
log.warn(str(e))
command.run(self)
update_package_data(self.distribution)
return DecoratedCommand
def update_package_data(distribution):
"""Update package_data to catch changes during setup."""
build_py = distribution.get_command_obj('build_py')
# distribution.package_data = find_package_data()
# re-init build_py options which load package_data
build_py.finalize_options()
class NPM(Command):
description = 'install package.json dependencies using npm'
user_options = []
node_modules = os.path.join(node_root, 'node_modules')
targets = [
os.path.join(here, 'vitessce', 'static', 'extension.js'),
os.path.join(here, 'vitessce', 'static', 'index.js')
]
def initialize_options(self):
pass
def finalize_options(self):
pass
def get_npm_name(self):
npm_name = 'npm'
if platform.system() == 'Windows':
npm_name = 'npm.cmd'
return npm_name
def has_npm(self):
npm_name = self.get_npm_name()
try:
check_call([npm_name, '--version'])
return True
except:
return False
def should_run_npm_install(self):
return self.has_npm()
def run(self):
has_npm = self.has_npm()
if not has_npm:
log.error("`npm` unavailable. If you're running this command using sudo, make sure `npm` is available to sudo")
env = os.environ.copy()
env['PATH'] = npm_path
if self.should_run_npm_install():
log.info("Installing build dependencies with npm. This may take a while...")
npm_name = self.get_npm_name()
check_call([npm_name, 'install'], cwd=node_root, stdout=sys.stdout, stderr=sys.stderr)
os.utime(self.node_modules, None)
npm_name = self.get_npm_name()
check_call([npm_name, 'run', 'build'], cwd=node_root, stdout=sys.stdout, stderr=sys.stderr)
for t in self.targets:
if not os.path.exists(t):
msg = 'Missing file: %s' % t
if not has_npm:
msg += '\nnpm is required to build a development version of a widget extension'
raise ValueError(msg)
# update package data in case this created new files
update_package_data(self.distribution)
version_ns = {}
with open(os.path.join(here, 'vitessce', '_version.py')) as f:
exec(f.read(), {}, version_ns)
setup_args = dict(
name=name,
version=version_ns['__version__'],
description='Jupyter widget facilitating interactive visualization of spatial single-cell data with Vitessce',
long_description=LONG_DESCRIPTION,
include_package_data=True,
data_files=[
# like `jupyter nbextension install --sys-prefix`
('share/jupyter/nbextensions/vitessce-jupyter', [
'vitessce/static/extension.js',
'vitessce/static/index.js',
'vitessce/static/index.js.map',
]),
# like `jupyter nbextension enable --sys-prefix`
('etc/jupyter/nbconfig/notebook.d' ,['vitessce-jupyter.json'])
],
install_requires=[
'ipywidgets>=7.0.0',
'hypercorn>=0.11.0',
'ujson>=4.0.1',
'aiofiles>=0.6.0',
'starlette==0.14.0',
'zarr>=2.5.0',
'numcodecs>=0.5.7',
'scipy>=1.2.1',
'negspy>=0.2.24',
'generate-tiff-offsets>=0.1.7'
],
packages=find_packages(),
zip_safe=False,
cmdclass={
'build_py': js_prerelease(build_py),
'egg_info': js_prerelease(egg_info),
'sdist': js_prerelease(sdist, strict=True),
'jsdeps': NPM,
},
author='Gehlenborg Lab',
author_email='',
url='https://github.com/vitessce/vitessce-python',
keywords=[
'ipython',
'jupyter',
'widgets',
],
classifiers=[
'Development Status :: 4 - Beta',
'Framework :: IPython',
'Intended Audience :: Developers',
'Intended Audience :: Science/Research',
'Topic :: Multimedia :: Graphics',
'Programming Language :: Python :: 3.7',
'Programming Language :: Python :: 3.8',
],
)
setup(**setup_args)