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#!/usr/bin/env python3
"""Setup for the reference implementation of the CWL standards."""
import os
import sys
import setuptools.command.egg_info as egg_info_cmd
from setuptools import setup
SETUP_DIR = os.path.dirname(__file__)
README = os.path.join(SETUP_DIR, "README.rst")
try:
import gittaggers
Tagger = gittaggers.EggInfoFromGit
except ImportError:
Tagger = egg_info_cmd.egg_info
NEEDS_PYTEST = {"pytest", "test", "ptr"}.intersection(sys.argv)
PYTEST_RUNNER = ["pytest-runner", "pytest-cov"] if NEEDS_PYTEST else []
USE_MYPYC = False
# To compile with mypyc, a mypyc checkout must be present on the PYTHONPATH
if len(sys.argv) > 1 and sys.argv[1] == "--use-mypyc":
sys.argv.pop(1)
USE_MYPYC = True
if os.getenv("CWLTOOL_USE_MYPYC", None) == "1":
USE_MYPYC = True
if USE_MYPYC:
mypyc_targets = [
"cwltool/argparser.py",
"cwltool/builder.py",
"cwltool/checker.py",
"cwltool/command_line_tool.py",
# "cwltool/context.py", # monkeypatching
"cwltool/cwlrdf.py",
"cwltool/docker_id.py",
"cwltool/docker.py",
"cwltool/udocker.py",
"cwltool/errors.py",
"cwltool/executors.py",
"cwltool/expression.py",
"cwltool/factory.py",
"cwltool/flatten.py",
# "cwltool/__init__.py",
"cwltool/job.py",
"cwltool/load_tool.py",
# "cwltool/loghandler.py", # so we can monkeypatch the logger from tests
# "cwltool/__main__.py",
"cwltool/main.py",
"cwltool/mutation.py",
"cwltool/pack.py",
# "cwltool/pathmapper.py", # class PathMapper needs to be subclassable
"cwltool/process.py",
"cwltool/procgenerator.py",
# "cwltool/provenance.py", # WritableBag is having issues
"cwltool/resolver.py",
# "cwltool/sandboxjs.py", # probably not speed critical, tests need to mock components
"cwltool/secrets.py",
"cwltool/singularity.py",
"cwltool/software_requirements.py",
"cwltool/stdfsaccess.py",
"cwltool/subgraph.py",
"cwltool/update.py",
"cwltool/utils.py",
"cwltool/validate_js.py",
"cwltool/workflow.py",
]
from mypyc.build import mypycify
opt_level = os.getenv("MYPYC_OPT_LEVEL", "3")
ext_modules = mypycify(mypyc_targets, opt_level=opt_level)
else:
ext_modules = []
setup(
name="cwltool",
version="3.0",
description="Common workflow language reference implementation",
long_description=open(README).read(),
long_description_content_type="text/x-rst",
author="Common workflow language working group",
author_email="common-workflow-language@googlegroups.com",
url="https://github.com/common-workflow-language/cwltool",
download_url="https://github.com/common-workflow-language/cwltool",
ext_modules=ext_modules,
# platforms='', # empty as is conveyed by the classifier below
# license='', # empty as is conveyed by the classifier below
packages=["cwltool", "cwltool.tests"],
package_dir={"cwltool.tests": "tests"},
include_package_data=True,
install_requires=[
"setuptools",
"requests >= 2.6.1", # >= 2.6.1 to workaround
# https://github.com/ionrock/cachecontrol/issues/137
"ruamel.yaml >= 0.12.4",
"rdflib >= 4.2.2, < 5.1.0",
"shellescape >= 3.4.1, < 3.5",
"schema-salad >= 7.0.20210124093443, < 8",
"mypy-extensions",
"psutil",
"prov >= 1.5.1",
"typing-extensions",
"coloredlogs",
"pydot >= 1.4.1",
"argcomplete",
],
extras_require={
"deps": ["galaxy-tool-util"],
"docs": [
"sphinx >= 2.2",
"sphinx-rtd-theme",
"sphinx-autoapi",
"sphinx-autodoc-typehints",
"typed_ast;python_version<'3.8'",
],
},
python_requires=">=3.6, <4",
setup_requires=PYTEST_RUNNER,
test_suite="tests",
tests_require=[
"pytest == 6.0.2",
"mock >= 2.0.0",
"pytest-mock >= 1.10.0",
"arcp >= 0.2.0",
"rdflib-jsonld >= 0.4.0",
],
entry_points={"console_scripts": ["cwltool=cwltool.main:run"]},
zip_safe=True,
cmdclass={"egg_info": Tagger},
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",
"Operating System :: OS Independent",
"Operating System :: Microsoft :: Windows",
"Operating System :: Microsoft :: Windows :: Windows 10",
"Operating System :: Microsoft :: Windows :: Windows 8.1",
# 'Operating System :: Microsoft :: Windows :: Windows 8', # not tested
# 'Operating System :: Microsoft :: Windows :: Windows 7', # not tested
"Programming Language :: Python :: 3",
"Programming Language :: Python :: 3.6",
"Programming Language :: Python :: 3.7",
"Programming Language :: Python :: 3.8",
"Programming Language :: Python :: 3.9",
"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",
],
)
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