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setup.py
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setup.py
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"""Setuptools magic to install antiSMASH."""
import glob
import os
from setuptools import setup, find_packages
from setuptools.command.test import test as TestCommand
import subprocess
import sys
def read(fname):
"""Read a file from the current directory."""
return open(os.path.join(os.path.dirname(__file__), fname)).read()
long_description = read('README.md')
install_requires = [
'numpy',
'biopython >= 1.71',
'helperlibs',
'jinja2',
'pysvg-py3',
'bcbio-gff',
'pyScss',
'matplotlib',
'scipy',
'scikit-learn == 0.19.0', # until pickles are rebuilt automatically
]
tests_require = [
'pytest >= 3.3.0',
'minimock',
'coverage',
'pylint == 1.8.4', # until pylint handles ignore lines the same way
]
def read_version():
"""Read the version fromt he appropriate place in the library."""
for line in open(os.path.join('antismash', 'main.py'), 'r'):
if line.startswith('__version__'):
return line.split('=')[-1].strip().strip('"')
def find_data_files():
"""Setuptools package_data globbing is stupid, so make this work ourselves."""
data_files = []
for pathname in glob.glob("antismash/**/*", recursive=True):
if pathname.endswith('.pyc'):
continue
if pathname.endswith('.py'):
continue
if '__pycache__' in pathname:
continue
if pathname[:-1].endswith('.hmm.h3'):
continue
if pathname.endswith('bgc_seeds.hmm'):
continue
pathname = glob.escape(pathname)
pathname = pathname[10:]
data_files.append(pathname)
if "HARDCODE_ANTISMASH_GIT_VERSION" in os.environ:
version_file = os.path.join('antismash', 'git_hash')
with open(version_file, 'wt') as handle:
try:
git_version = subprocess.check_output(['git', 'rev-parse', '--short', 'HEAD'],
universal_newlines=True).strip()
changes = subprocess.check_output(['git', 'status', '--porcelain'],
universal_newlines=True).splitlines()
if len(changes) != 0:
git_version += "(changed)"
handle.write(git_version)
except (OSError, subprocess.CalledProcessError):
pass
data_files.append(version_file)
return data_files
class PyTest(TestCommand):
"""Allow running tests via python setup.py test."""
def finalize_options(self):
"""Test command magic."""
TestCommand.finalize_options(self)
self.test_args = []
self.test_suite = True
def run_tests(self):
"""Run tests."""
import pytest
errcode = pytest.main(self.test_args)
sys.exit(errcode)
setup(
name="antismash",
python_requires='>=3.5',
version=read_version(),
packages=find_packages(exclude=["*.tests", "*.tests.*", "tests.*", "tests"]),
package_data={
'antismash': find_data_files(),
},
author='antiSMASH development team',
author_email='antismash@secondarymetabolites.org',
description='The antibiotics and Secondary Metabolites Analysis Shell.',
long_description=long_description,
long_description_content_type='text/markdown',
install_requires=install_requires,
tests_require=tests_require,
entry_points={
'console_scripts': [
'download-antismash-databases=antismash.download_databases:_main',
'antismash=antismash.__main__:entrypoint',
],
},
cmdclass={'test': PyTest},
url='https://github.com/antismash/antismash',
license='GNU Affero General Public License v3 or later (AGPLv3+)',
classifiers=[
'Programming Language :: Python',
'Programming Language :: Python :: 3',
'Development Status :: 3 - Alpha',
'Intended Audience :: Science/Research',
'Topic :: Scientific/Engineering :: Bio-Informatics',
'License :: OSI Approved :: GNU Affero General Public License v3 or later (AGPLv3+)',
'Operating System :: OS Independent',
],
extras_require={
'testing': tests_require,
},
)