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# Copyright (C) 2015-2021 Regents of the University of California
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
import imp
import os
from tempfile import NamedTemporaryFile
from setuptools import find_packages, setup
def get_requirements(extra=None):
"""
Load the requirements for the given extra from the appropriate
requirements-extra.txt, or the main requirements.txt if no extra is
specified.
"""
filename = f"requirements-{extra}.txt" if extra else "requirements.txt"
with open(filename) as fp:
# Parse out as one per line
return [l.strip() for l in fp.readlines() if l.strip()]
def run_setup():
"""
Calls setup(). This function exists so the setup() invocation preceded more internal
functionality. The `version` module is imported dynamically by import_version() below.
"""
install_requires = get_requirements()
extras_require = {}
# htcondor is not supported by apple
# this is tricky to conditionally support in 'all' due
# to how wheels work, so it is not included in all and
# must be explicitly installed as an extra
all_reqs = ""
non_htcondor_extras = [
"aws",
"cwl",
"encryption",
"google",
"kubernetes",
"mesos",
"wdl",
"server"
]
for extra in non_htcondor_extras:
extras_require[extra] = get_requirements(extra)
all_reqs += "\n" + "\n".join(extras_require[extra])
# We exclude htcondor from "all" because it can't be on Mac
extras_require['htcondor:sys_platform!="darwin"'] = get_requirements("htcondor")
extras_require["all"] = all_reqs
setup(
name='toil',
version=version.distVersion,
description='Pipeline management software for clusters.',
author='Benedict Paten and the Toil community',
author_email='toil-community@googlegroups.com',
url="https://github.com/DataBiosphere/toil",
classifiers=[
'Development Status :: 5 - Production/Stable',
'Environment :: Console',
'Intended Audience :: Developers',
'Intended Audience :: Science/Research',
'Intended Audience :: Healthcare Industry',
'License :: OSI Approved :: Apache Software License',
'Natural Language :: English',
'Operating System :: MacOS :: MacOS X',
'Operating System :: POSIX',
'Operating System :: POSIX :: Linux',
'Programming Language :: Python :: 3.7',
'Programming Language :: Python :: 3.8',
'Programming Language :: Python :: 3.9',
'Programming Language :: Python :: 3.10',
'Topic :: Scientific/Engineering',
'Topic :: Scientific/Engineering :: Bio-Informatics',
'Topic :: Scientific/Engineering :: Astronomy',
'Topic :: Scientific/Engineering :: Atmospheric Science',
'Topic :: Scientific/Engineering :: Information Analysis',
'Topic :: Scientific/Engineering :: Medical Science Apps.',
'Topic :: System :: Distributed Computing',
'Topic :: Utilities'],
license="Apache License v2.0",
python_requires=">=3.7",
install_requires=install_requires,
extras_require=extras_require,
package_dir={'': 'src'},
packages=find_packages(where='src'),
package_data={
'': ['*.yml', '*.yaml', 'cloud-config', '*.cwl'],
},
# Unfortunately, the names of the entry points are hard-coded elsewhere in the code base so
# you can't just change them here. Luckily, most of them are pretty unique strings, and thus
# easy to search for.
entry_points={
'console_scripts': [
'toil = toil.utils.toilMain:main',
'_toil_worker = toil.worker:main',
'cwltoil = toil.cwl.cwltoil:cwltoil_was_removed [cwl]',
'toil-cwl-runner = toil.cwl.cwltoil:main [cwl]',
'toil-wdl-runner = toil.wdl.toilwdl:main',
'toil-wes-cwl-runner = toil.server.cli.wes_cwl_runner:main [server]',
'_toil_mesos_executor = toil.batchSystems.mesos.executor:main [mesos]',
'_toil_contained_executor = toil.batchSystems.contained_executor:executor']})
def import_version():
"""Return the module object for src/toil/version.py, generate from the template if required."""
if not os.path.exists('src/toil/version.py'):
for req in get_requirements("cwl"):
# Determine cwltool version from requirements file
if req.startswith("cwltool=="):
cwltool_version = req[len("cwltool=="):]
break
# Use the template to generate src/toil/version.py
import version_template
with NamedTemporaryFile(mode='w', dir='src/toil', prefix='version.py.', delete=False) as f:
f.write(version_template.expand_(others={
# expose the dependency versions that we may need to access in Toil
'cwltool_version': cwltool_version,
}))
os.rename(f.name, 'src/toil/version.py')
# Unfortunately, we can't use a straight import here because that would also load the stuff
# defined in "src/toil/__init__.py" which imports modules from external dependencies that may
# yet to be installed when setup.py is invoked.
#
# This is also the reason we cannot switch from the "deprecated" imp library
# and use:
# from importlib.machinery import SourceFileLoader
# return SourceFileLoader('toil.version', path='src/toil/version.py').load_module()
#
# Because SourceFileLoader will error and load "src/toil/__init__.py" .
return imp.load_source('toil.version', 'src/toil/version.py')
version = import_version()
run_setup()
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