forked from Clinical-Genomics/cgbeacon
-
Notifications
You must be signed in to change notification settings - Fork 0
/
setup.py
137 lines (109 loc) · 4.11 KB
/
setup.py
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# Note: To use the 'upload' functionality of this file, you must:
# $ pip install twine
import io
import os
import sys
from shutil import rmtree
from setuptools import find_packages, setup, Command
# Package meta-data.
NAME = 'cgbeacon'
DESCRIPTION = 'Extracts variants from a VCF file and inserts them into a Beacon MySQL database'
URL = 'https://github.com/Clinical-Genomics/cgbeacon'
EMAIL = 'chiara.rasi@scilifelab.se'
AUTHOR = 'Chiara Rasi'
here = os.path.abspath(os.path.dirname(__file__))
def parse_reqs(req_path='./requirements.txt'):
"""Recursively parse requirements from nested pip files."""
install_requires = []
with io.open(os.path.join(here, 'requirements.txt'), encoding='utf-8') as handle:
# remove comments and empty lines
lines = (line.strip() for line in handle
if line.strip() and not line.startswith('#'))
for line in lines:
# check for nested requirements files
if line.startswith('-r'):
# recursively call this function
install_requires += parse_reqs(req_path=line[3:])
else:
# add the line as a new requirement
install_requires.append(line)
return install_requires
# What packages are required for this module to be executed?
REQUIRED = parse_reqs()
# The rest you shouldn't have to touch too much :)
# ------------------------------------------------
# Except, perhaps the License and Trove Classifiers!
# If you do change the License, remember to change the Trove Classifier for that!
# Import the README and use it as the long-description.
# Note: this will only work if 'README.rst' is present in your MANIFEST.in file!
with io.open(os.path.join(here, 'README.md'), encoding='utf-8') as f:
long_description = '\n' + f.read()
# Load the package's __version__.py module as a dictionary.
about = {}
with open(os.path.join(here, NAME, '__version__.py')) as f:
exec(f.read(), about)
class UploadCommand(Command):
"""Support setup.py upload."""
description = 'Build and publish the package.'
user_options = []
@staticmethod
def status(s):
"""Prints things in bold."""
print('\033[1m{0}\033[0m'.format(s))
def initialize_options(self):
pass
def finalize_options(self):
pass
def run(self):
try:
self.status('Removing previous builds…')
rmtree(os.path.join(here, 'dist'))
except OSError:
pass
self.status('Building Source and Wheel (universal) distribution…')
os.system('{0} setup.py sdist bdist_wheel --universal'.format(sys.executable))
self.status('Uploading the package to PyPi via Twine…')
os.system('twine upload dist/*')
sys.exit()
# Where the magic happens:
setup(
name=NAME,
version=about['__version__'],
description=DESCRIPTION,
long_description=long_description,
author=AUTHOR,
author_email=EMAIL,
url=URL,
packages=find_packages(exclude=('tests',)),
# If your package is a single module, use this instead of 'packages':
# py_modules=['mypackage'],
entry_points={
'console_scripts': [
'cgbeacon = cgbeacon.cli.root:cli'
],
},
install_requires=REQUIRED,
include_package_data=True,
license='MIT',
classifiers=[
# Trove classifiers
# Full list: https://pypi.python.org/pypi?%3Aaction=list_classifiers
'License :: OSI Approved :: MIT License',
'Programming Language :: Python',
'Programming Language :: Python :: 2.6',
'Programming Language :: Python :: 2.7',
'Programming Language :: Python :: 3',
'Programming Language :: Python :: 3.3',
'Programming Language :: Python :: 3.4',
'Programming Language :: Python :: 3.5',
'Programming Language :: Python :: 3.6',
'Programming Language :: Python :: Implementation :: CPython',
'Programming Language :: Python :: Implementation :: PyPy'
],
# $ setup.py publish support.
cmdclass={
'upload': UploadCommand,
},
)