setup.py

import os
import sys
import shutil
from subprocess import call
from setuptools import setup
from warnings import warn
import py_compile


# Replace py_compile.compile with a function that calls it with doraise=True
# so stop when there is a syntax error
orig_py_compile = py_compile.compile


def doraise_py_compile(file, cfile=None, dfile=None, doraise=False):
    orig_py_compile(file, cfile=cfile, dfile=dfile, doraise=True)


py_compile.compile = doraise_py_compile

if sys.version_info.major != 3:
    raise RuntimeError('SEQC requires Python 3')
if sys.version_info.minor < 5:
    warn('Multiprocessing analysis methods may not function on Python versions < 3.5')

# install phenograph if pip3 is installed
if shutil.which('pip3'):
    call(['pip3', 'install', 'git+https://github.com/jacoblevine/phenograph.git'])
    call(['pip3', 'install', 'git+https://github.com/pkathail/magic.git'])

# get version
with open('src/seqc/version.py') as f:
    exec(f.read())

setup(
    name='seqc',
    version=__version__,  # read in from the exec of version.py; ignore error
    description='Single Cell Sequencing Processing and QC Suite',
    author='Ambrose J. Carr',
    author_email='mail@ambrosejcarr.com',
    package_dir={'': 'src'},
    package_data={'': ['*.r', '*.R']},
    packages=['seqc', 'seqc.sequence', 'seqc.alignment', 'seqc.core', 'seqc.stats',
              'seqc.summary', 'seqc.notebooks'],
    install_requires=[
      'numpy>=1.10.0',
      'bhtsne',
      'wikipedia',
      'awscli',
      'Cython>0.14',
      'numexpr>=2.4',
      'pandas>=0.18.1',
      'paramiko>=2.0.2',
      'regex',
      'requests',
      'nose2',
      'scipy>=0.14.0',
      'boto3',
      'intervaltree',
      'matplotlib',
      'tinydb',
      'tables',
      'fastcluster',
      'statsmodels',
      'ecdsa',
      'dill',
      'jupyter',
      'multiprocessing_on_dill',
      'jinja2',
      'pycrypto',
      'cairocffi>=0.8.0',
      'weasyprint',
      'scikit_learn>=0.17'],
    scripts=['src/scripts/SEQC'],
    extras_require={
      'GSEA_XML': ['html5lib', 'lxml', 'BeautifulSoup4'],
    },
    include_package_data=True
)

# look for star
if not shutil.which('STAR'):
    warn('SEQC: STAR is not installed. SEQC will not be able to align files.')

# get location of setup.py
setup_dir = os.path.dirname(os.path.realpath(__file__))
seqc_dir = os.path.expanduser('~/.seqc/seqc')

print('setup_dir: {}'.format(setup_dir))
print('seqc_dir: {}'.format(seqc_dir))

if os.path.isdir(seqc_dir):
    shutil.rmtree(seqc_dir)


def ignore_test_and_tools(dir_, files):
    """Filter files to be moved by shutil.copytree. Ignore any hidden file and the
    test and tools directories, which are not needed by the remote instance.
    :param dir_: dummy variable, must be present to be passed to shutil.copytree()
    :param files: output of os.listdir(), files to be subjected to filtering
    :return list: list of files that should be filtered, and not copied.
    """
    return [f for f in files if (f == 'test' or f.startswith('.'))]


# install tools and a local copy of seqc.
shutil.copytree(setup_dir, seqc_dir, ignore=ignore_test_and_tools)  # copy seqc repository
shutil.make_archive(base_name=seqc_dir, format='gztar', root_dir=seqc_dir)