setup.py

# 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',
          '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',
                               # Note that we intentionally include the top-level `test` package for
                               # functionality like the @experimental and @integrative decorators:
                               exclude=['*.test.*']),
        package_data={
            '': ['*.yml', '*.yaml', 'cloud-config'],
        },
        # 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_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()