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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 os
import sys
import types
from importlib.machinery import SourceFileLoader
from tempfile import NamedTemporaryFile
from setuptools import find_packages, setup
SETUP_DIR = os.path.dirname(__file__)
README = os.path.join(SETUP_DIR, "README.rst")
def get_requirements(extra=None):
"""
Load the requirements for the given extra.
Uses 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, dropping comments
return [
l.split("#")[0].strip() for l in fp.readlines() if l.split("#")[0].strip()
]
def run_setup():
"""
Call 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",
"wdl",
"server",
]
for extra in non_htcondor_extras:
extras_require[extra] = get_requirements(extra)
all_reqs += 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["mesos"] = get_requirements("mesos")
all_reqs += get_requirements("mesos")
extras_require["all"] = all_reqs
setup(
name="toil",
version=version.distVersion,
long_description=open(README).read(),
long_description_content_type="text/x-rst",
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 :: 3.9",
"Programming Language :: Python :: 3.10",
"Programming Language :: Python :: 3.11",
"Programming Language :: Python :: 3.12",
"Programming Language :: Python :: 3.13",
"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=">=3.9",
install_requires=install_requires,
extras_require=extras_require,
package_dir={"": "src"},
packages=find_packages(where="src"),
include_package_data=True,
# 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.wdltoil:main [wdl]",
"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
# First make sure we can find it (in case we're happening during an
# install where the source tree isn't on the path already).
# See <https://github.com/pypa/setuptools/discussions/3909#discussioncomment-5718455>
sys.path.append(os.path.dirname(__file__))
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")
loader = SourceFileLoader("toil.version", "src/toil/version.py")
mod = types.ModuleType(loader.name)
loader.exec_module(mod)
return mod
version = import_version()
run_setup()
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