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
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
|
import os
import sys
import glob
import tarfile
import zipfile
import urllib.request
from setuptools import setup, Extension
from setuptools.command import build_ext
root_dir = os.path.dirname(os.path.abspath(__file__))
sources = glob.glob(os.path.join(root_dir, 'src', '*.c'))
link_args = ['-lsqlite3']
link_args.extend(os.environ['LDFLAGS'].split(' '))
comp_args = []
comp_args.extend(os.environ['CPPFLAGS'].split(' '))
comp_args.extend(os.environ['CFLAGS'].split(' '))
include_dirs = []
def prepare_zlib():
global include_dirs
global sources
zlib_dir = os.path.join(root_dir, "zlib-1.3.1")
zlib_file = os.path.join(root_dir, "zlib-1.3.1.zip")
url = "https://github.com/madler/zlib/releases/download/v1.3.1/zlib131.zip"
if not os.path.exists(zlib_dir):
if not os.path.isfile(zlib_file):
urllib.request.urlretrieve(url, zlib_file)
with zipfile.ZipFile(zlib_file) as _zip:
_zip.extractall()
include_dirs.append(zlib_dir)
sources.extend(glob.glob(os.path.join(zlib_dir, '*.c')))
def prepare_sqlite3():
global include_dirs
global sources
sqlite_dir = os.path.join(root_dir, "sqlite-amalgamation-3470200")
sqlite_file = os.path.join(root_dir, "sqlite-amalgamation-3470200.zip")
url = "https://www.sqlite.org/2024/sqlite-amalgamation-3470200.zip"
if not os.path.exists(sqlite_dir):
if not os.path.isfile(sqlite_file):
urllib.request.urlretrieve(url, sqlite_file)
with zipfile.ZipFile(sqlite_file) as _zip:
_zip.extractall()
include_dirs.append(sqlite_dir)
sources.append(os.path.join(sqlite_dir, 'sqlite3.c'))
def prepare_indexed_gzip():
global include_dirs
global sources
igzip_dir = os.path.join(root_dir, "indexed_gzip-1.9.4", "indexed_gzip")
igzip_file = os.path.join(root_dir, "indexed_gzip-1.9.4.zip")
url = "https://github.com/pauldmccarthy/indexed_gzip/archive/refs/tags/v1.9.4.zip"
if not os.path.exists(igzip_dir):
if not os.path.isfile(igzip_file):
urllib.request.urlretrieve(url, igzip_file)
with zipfile.ZipFile(igzip_file) as _zip:
_zip.extractall()
include_dirs.append(igzip_dir)
sources.extend(glob.glob(os.path.join(igzip_dir, 'zran*.c')))
if sys.platform.startswith('win'):
comp_args.extend([
'/D_LFS64_LARGEFILE',
'/D_LARGEFILE64_SOURCE',
'/D_FILE_OFFSET_BITS=64'
])
else:
comp_args.extend([
'-Wno-unused-result',
'-D_FILE_OFFSET_BITS=64'
])
if sys.platform.startswith('darwin'):
comp_args.append('-DHAVE_UNISTD_H')
else:
comp_args.extend([
'-D_LFS64_LARGEFILE',
'-D_LARGEFILE64_SOURCE'
])
class CustomBuildExt(build_ext.build_ext):
def build_extensions(self):
if not sys.platform.startswith(('win', 'darwin')):
if '--debug' in sys.argv:
self.compiler.compiler_so = [
opt
for opt in self.compiler.compiler_so
if opt != '-O2'
]
self.compiler.compiler_so.append('-O0')
self.compiler.compiler_so.append('--coverage')
self.compiler.linker_so = [
opt
for opt in self.compiler.linker_so
if opt != '-O2'
]
self.compiler.linker_so.append('-O0')
self.compiler.linker_so.append('--coverage')
else:
self.compiler.compiler_so = [
opt
for opt in self.compiler.compiler_so
if opt != '-g'
]
self.compiler.linker_so = [
opt
for opt in self.compiler.linker_so
if opt != '-g'
]
super().build_extensions()
#if not sys.platform.startswith('linux'):
#prepare_sqlite3()
#prepare_zlib()
#prepare_indexed_gzip()
extension = Extension('pyfastx',
sources = sources,
include_dirs = include_dirs,
extra_compile_args = comp_args,
extra_link_args = link_args
)
description = (
"pyfastx is a python module for fast random "
"access to sequences from plain and gzipped "
"FASTA/Q file"
)
with open(os.path.join(root_dir, 'README.rst')) as fh:
long_description = fh.read()
with open(os.path.join(root_dir, 'src', 'version.h')) as fh:
version = fh.read().split()[2].strip('"')
setup(
name = 'pyfastx',
version = version,
ext_modules = [extension],
description = description,
long_description = long_description,
#long_description_content_type = 'text/x-rst',
author = 'Lianming Du',
author_email = 'adullb@qq.com',
url = 'https://github.com/lmdu/pyfastx',
license = 'MIT',
keywords = 'fasta fastq sequence bioinformatics',
classifiers = [
"Development Status :: 5 - Production/Stable",
"Intended Audience :: Developers",
"Intended Audience :: Education",
"Intended Audience :: Science/Research",
"Natural Language :: English",
"License :: OSI Approved :: MIT License",
"Programming Language :: C",
"Programming Language :: Python :: 3.6",
"Programming Language :: Python :: 3.7",
"Programming Language :: Python :: 3.8",
"Programming Language :: Python :: 3.9",
"Programming Language :: Python :: 3.10",
"Programming Language :: Python :: 3.11",
"Programming Language :: Python :: 3.12",
"Programming Language :: Python :: 3.13",
"Operating System :: Microsoft :: Windows",
"Operating System :: POSIX :: Linux",
"Operating System :: Unix",
"Topic :: Scientific/Engineering :: Bio-Informatics"
],
entry_points = {
'console_scripts': ['pyfastx = pyfastxcli:main']
},
py_modules = ["pyfastxcli"],
test_suite = "tests",
cmdclass = {
'build_ext': CustomBuildExt
}
)
|
