setup.py

from glob import glob
import os
import re
from setuptools import setup, find_packages
from setuptools import Distribution
from setuptools.command.install import install
import shutil
import sys

__pkg_name__ = 'pomoxis'
__author__ = 'cwright'
__description__ = 'Assembly, consensensus, and analysis tools by ONT research.'

# Use readme as long description and say its github-flavour markdown
from os import path
this_directory = path.abspath(path.dirname(__file__))
kwargs = {'encoding':'utf-8'} if sys.version_info.major == 3 else {}
with open(path.join(this_directory, 'README.md'), **kwargs) as f:
    __long_description__ = f.read()
__long_description_content_type__ = 'text/markdown'

__path__ = os.path.dirname(__file__)
__pkg_path__ = os.path.join(os.path.join(__path__, __pkg_name__))

# Get the version number from __init__.py, and exe_path
verstrline = open(os.path.join(__pkg_name__, '__init__.py'), 'r').read()
vsre = r"^__version__ = ['\"]([^'\"]*)['\"]"
mo = re.search(vsre, verstrline, re.M)
if mo:
    __version__ = mo.group(1)
else:
    raise RuntimeError('Unable to find version string in "{}/__init__.py".'.format(__pkg_name__))

dir_path = os.path.dirname(__file__)
install_requires = []
with open(os.path.join(dir_path, 'requirements.txt')) as fh:
    reqs = (
        r.split('#')[0].strip()
        for r in fh.read().splitlines() if not r.startswith('#')
    )
    for req in reqs:
        if req == '':
            continue
        if req.startswith('git+https'):
            req = req.split('/')[-1].split('@')[0]
        install_requires.append(req)

data_files = []
extensions = []
extra_requires={}

# Read these from Makefile in the event someone modified list there
exes = []
if os.environ.get("POMO_BINARIES") is not None:
    with open(os.path.join(dir_path, 'Makefile')) as fh:
        for line in fh.readlines():
            tokens = line.split('=')
            if tokens[0] == 'BINARIES':
                exes = tokens[1].split()
                break
    #place binaries as package data, below we'll copy them to standard path in dist
    data_files.append(
        ('exes', [
            'bincache/{}'.format(x, x) for x in exes
        ])
    )

setup(
    name=__pkg_name__,
    version=__version__,
    author=__author__,
    author_email='{}@nanoporetech.com'.format(__author__),
    description=__description__,
    long_description=__long_description__,
    long_description_content_type=__long_description_content_type__,
    dependency_links=[],
    ext_modules=extensions,
    install_requires=install_requires,
    tests_require=[].extend(install_requires),
    extras_require=extra_requires,
    python_requires='>=3.6',
    packages=find_packages(exclude=['*.test', '*.test.*', 'test.*', 'test']),
    package_data={},
    zip_safe=False,
    test_suite='discover_tests',
    data_files=data_files,
    entry_points={
        'console_scripts': [
            'catalogue_errors = {}.catalogue_errors:main'.format(__pkg_name__),
            'common_errors_from_bam = {}.common_errors_from_bam:main'.format(__pkg_name__),
            'assess_homopolymers = {}.assess_homopolymers:main'.format(__pkg_name__),
            'coverage_from_bam = {}.coverage_from_bam:main'.format(__pkg_name__),
            'coverage_from_fastx = {}.util:coverage_from_fastx'.format(__pkg_name__),
            'fast_convert = {}.util:fast_convert'.format(__pkg_name__),
            'long_fastx = {}.util:extract_long_reads'.format(__pkg_name__),
            'pomoxis_path = {}:show_prog_path'.format(__pkg_name__),
            'qscores_from_summary = {}.qscores_from_summary:main'.format(__pkg_name__),
            'reverse_bed = {}.util:reverse_bed'.format(__pkg_name__),
            'split_fastx = {}.util:split_fastx_cmdline'.format(__pkg_name__),
            'stats_from_bam = {}.stats_from_bam:main'.format(__pkg_name__),
            'subsample_bam = {}.subsample_bam:main'.format(__pkg_name__),
            'filter_bam = {}.filter_bam:main'.format(__pkg_name__),
            'summary_from_stats = {}.summary_from_stats:main'.format(__pkg_name__),
            'tag_bam = {}.util:tag_bam'.format(__pkg_name__),
            'trim_alignments = {}.trim_alignments:main'.format(__pkg_name__),
            'ref_seqs_from_bam = {}.ref_seqs_from_bam:main'.format(__pkg_name__),
            'find_indels = {}.find_indels:main'.format(__pkg_name__),
        ] # leave this here
    },
    scripts=[
        'scripts/assess_assembly',
        'scripts/intersect_assembly_errors',
        'scripts/mini_align',
        'scripts/mini_assemble']
)


# Nasty hack to get binaries into bin path
class GetPaths(install):
    def run(self):
        self.distribution.install_scripts = self.install_scripts
        self.distribution.install_libbase = self.install_libbase

def get_setuptools_script_dir():
    # Run the above class just to get paths
    dist = Distribution({'cmdclass': {'install': GetPaths}})
    dist.dry_run = True
    dist.parse_config_files()
    command = dist.get_command_obj('install')
    command.ensure_finalized()
    command.run()

    src_dir = glob(os.path.join(dist.install_libbase, 'pomoxis-*', 'exes'))[0]
    for exe in (os.path.join(src_dir, x) for x in os.listdir(src_dir)):
        print("Copying", os.path.basename(exe), '->', dist.install_scripts)
        shutil.copy(exe, dist.install_scripts)
    return dist.install_libbase, dist.install_scripts

if os.environ.get("POMO_BINARIES") is not None:
    print("\nCopying utility binaries to your path.")
    get_setuptools_script_dir()