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setup.py
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setup.py
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#!/usr/bin/env python
# vim: set fileencoding=<utf-8> :
from setuptools import setup, find_packages
from codecs import open
from os import path
import os, sys
import re
import io
import platform
import subprocess
from setuptools import setup, find_packages, Extension
from setuptools.command.build_ext import build_ext
from setuptools.command.install import install
from distutils.version import LooseVersion
def read(*names, **kwargs):
with io.open(
os.path.join(os.path.dirname(__file__), *names),
encoding=kwargs.get("encoding", "utf8")
) as fp:
return fp.read()
def find_version(*file_paths):
version_file = read(*file_paths)
version_match = re.search(r"^__version__ = ['\"]([^'\"]*)['\"]",
version_file, re.M)
if version_match:
return version_match.group(1)
raise RuntimeError("Unable to find version string.")
class CMakeExtension(Extension):
def __init__(self, name, sourcedir=''):
Extension.__init__(self, name, sources=[])
self.sourcedir = os.path.abspath(sourcedir)
class CMakeBuild(build_ext):
def run(self):
try:
out = subprocess.check_output(['cmake', '--version'])
except OSError:
raise RuntimeError("CMake must be installed to build the following extensions: " +
", ".join(e.name for e in self.extensions))
if platform.system() == "Windows":
cmake_version = LooseVersion(re.search(r'version\s*([\d.]+)', out.decode()).group(1))
if cmake_version < '3.1.0':
raise RuntimeError("CMake >= 3.1.0 is required on Windows")
for ext in self.extensions:
self.build_extension(ext)
def build_extension(self, ext):
extdir = os.path.abspath(os.path.dirname(self.get_ext_fullpath(ext.name)))
cmake_args = ['-DCMAKE_LIBRARY_OUTPUT_DIRECTORY=' + extdir,
'-DPYTHON_EXECUTABLE=' + sys.executable,
'-DCMAKE_VERBOSE_MAKEFILE:BOOL=ON']
cfg = 'Debug' if self.debug else 'Release'
build_args = ['--config', cfg]
if platform.system() == "Windows":
cmake_args += ['-DCMAKE_LIBRARY_OUTPUT_DIRECTORY_{}={}'.format(cfg.upper(), extdir)]
if sys.maxsize > 2**32:
cmake_args += ['-A', 'x64']
build_args += ['--', '/m']
else:
cmake_args += ['-DCMAKE_BUILD_TYPE=' + cfg]
build_args += ['--', '-j2']
env = os.environ.copy()
env['CXXFLAGS'] = '{} -DVERSION_INFO=\\"{}\\"'.format(env.get('CXXFLAGS', ''),
self.distribution.get_version())
if not os.path.exists(self.build_temp):
os.makedirs(self.build_temp)
subprocess.check_call(['cmake', ext.sourcedir] + cmake_args, cwd=self.build_temp, env=env)
subprocess.check_call(['cmake', '--build', '.'] + build_args, cwd=self.build_temp)
here = path.abspath(path.dirname(__file__))
with open(path.join(here, 'README.md'), encoding='utf-8') as f:
long_description = f.read()
setup(
name='poppunk',
version=find_version("PopPUNK/__init__.py"),
description='PopPUNK (POPulation Partitioning Using Nucleotide Kmers)',
long_description=long_description,
long_description_content_type='text/markdown',
url='https://github.com/johnlees/PopPUNK',
author='John Lees, Nicholas Croucher, Marie Gronemeyer, Richard Fitzjohn',
license='Apache Software License',
classifiers=[
'Development Status :: 4 - Beta',
'Intended Audience :: Science/Research',
'Topic :: Scientific/Engineering :: Bio-Informatics',
'License :: OSI Approved :: Apache Software License',
'Programming Language :: Python :: 3.8',
],
python_requires='>=3.8.0',
install_requires=['biopython',
'h5py',
'hdbscan',
'matplotlib',
# 'mandrake', #uncomment when on PyPI
'networkx',
'pandas',
'pp-sketchlib',
'requests',
'scikit-learn',
'tqdm',
'treeswift',
],
keywords='bacteria genomics population-genetics k-mer',
packages=['PopPUNK'],
entry_points={
"console_scripts": [
'poppunk = PopPUNK.__main__:main',
'poppunk_assign = PopPUNK.assign:main',
'poppunk_visualise = PopPUNK.visualise:main',
'poppunk_mst = PopPUNK.sparse_mst:main',
'poppunk_references = PopPUNK.reference_pick:main',
'poppunk_mandrake = PopPUNK.mandrake:main',
'poppunk_info = PopPUNK.info:main',
'poppunk_lineages_from_strains = PopPUNK.lineages:main'
]
},
scripts=['scripts/poppunk_calculate_rand_indices.py',
'scripts/poppunk_extract_components.py',
'scripts/poppunk_calculate_silhouette.py',
'scripts/poppunk_batch_mst.py',
'scripts/poppunk_extract_distances.py',
'scripts/poppunk_iterate.py',
'scripts/poppunk_add_weights.py',
'scripts/poppunk_easy_run.py',
'scripts/poppunk_distribute_fit.py'],
ext_modules=[CMakeExtension('poppunk_refine')],
test_suite="test",
cmdclass=dict(build_ext=CMakeBuild),
zip_safe=False,
include_package_data=True,
package_data={'': ['PopPUNK/data/*.json.gz',
'PopPUNK/data/microreact_example.pkl']}
)