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setup.py
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setup.py
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#!/usr/bin/env python
from __future__ import division, print_function
import os.path
import numpy
from setuptools import Extension, setup
from BioExt import __version__ as _bioext_version
from BioExt.references._factory import _installrefdirs
np_inc = [os.path.join(os.path.dirname(numpy.__file__), 'core', 'include')]
ext_modules = [
Extension(
'BioExt.align._align',
sources=[
os.path.join('BioExt', 'align', '_align.c'),
os.path.join('BioExt', 'align', 'alignment.c')
],
include_dirs=np_inc,
libraries=['m'],
extra_compile_args=['-O3']
),
Extension(
'BioExt.graphing._count',
sources=[os.path.join('BioExt', 'graphing', '_count.c')],
include_dirs=np_inc,
extra_compile_args=['-O3']
),
Extension(
'BioExt.merge._merge',
sources=[
os.path.join('BioExt', 'merge', '_merge.c'),
os.path.join('BioExt', 'merge', 'merge.cpp')
],
extra_compile_args=['-O3']
),
Extension(
'BioExt.rateclass._rateclass',
sources=[
os.path.join('BioExt', 'rateclass', '_rateclass.cpp'),
os.path.join('BioExt', 'rateclass', 'rateclass.cpp')
],
extra_compile_args=['-O3']
)
]
setup(
name='bioext',
version=_bioext_version,
description='Misc utilities and definitions not included or hidden in BioPython',
author='N Lance Hepler',
author_email='[email protected]',
url='http://github.com/nlhepler/bioext',
license='GNU GPL version 3',
packages=[
'BioExt',
'BioExt.align',
'BioExt.args',
'BioExt.collections',
'BioExt.errorize',
'BioExt.freetype',
'BioExt.freetype.ft_enums',
'BioExt.graphing',
'BioExt.io',
'BioExt.io.BamIO',
'BioExt.io.LazyAlignIO',
'BioExt.io.SamIO',
'BioExt.joblib',
'BioExt.joblib.test',
'BioExt.merge',
'BioExt.misc',
'BioExt.ndarray',
'BioExt.optimize',
'BioExt.orflist',
'BioExt.phylo',
'BioExt.quiver',
'BioExt.rateclass',
'BioExt.references',
'BioExt.scorematrices',
'BioExt.stats',
'BioExt.uds',
'BioExt.untranslate'
],
package_dir={
'BioExt': 'BioExt',
'BioExt.align': 'BioExt/align',
'BioExt.args': 'BioExt/args',
'BioExt.collections': 'BioExt/collections',
'BioExt.errorize': 'BioExt/errorize',
'BioExt.freetype': 'BioExt/freetype',
'BioExt.freetype.ft_enums': 'BioExt/freetype/ft_enums',
'BioExt.graphing': 'BioExt/graphing',
'BioExt.io': 'BioExt/io',
'BioExt.io.BamIO': 'BioExt/io/BamIO',
'BioExt.io.LazyAlignIO': 'BioExt/io/LazyAlignIO',
'BioExt.io.SamIO': 'BioExt/io/SamIO',
'BioExt.joblib': 'BioExt/joblib',
'BioExt.joblib.test': 'BioExt/joblib/test',
'BioExt.merge': 'BioExt/merge',
'BioExt.misc': 'BioExt/misc',
'BioExt.ndarray': 'BioExt/ndarray',
'BioExt.optimize': 'BioExt/optimize',
'BioExt.orflist': 'BioExt/orflist',
'BioExt.phylo': 'BioExt/phylo',
'BioExt.quiver': 'BioExt/quiver',
'BioExt.rateclass': 'BioExt/rateclass',
'BioExt.references': 'BioExt/references',
'BioExt.scorematrices': 'BioExt/scorematrices',
'BioExt.stats': 'BioExt/stats',
'BioExt.uds': 'BioExt/uds',
'BioExt.untranslate': 'BioExt/untranslate'
},
package_data={
'BioExt': [
'data/fonts/ttf/*.ttf',
'data/scorematrices/*.txt'
] + _installrefdirs
},
scripts=[
'scripts/bam2fna',
'scripts/bam2msa',
'scripts/bamclip',
'scripts/bealign',
'scripts/begraph',
'scripts/clipedge',
'scripts/consensus',
'scripts/msa2bam',
'scripts/seqmerge',
'scripts/translate'
# 'scripts/variants'
],
ext_modules=ext_modules,
requires=[
'Bio (>=1.58)',
'matplotlib (>=1.2.1)',
'numpy (>=1.6)',
'pysam (>=0.7.5)',
]
)