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35cfa6da »
2011-10-30 minimal setup to get into pythonpath
1 from setuptools import setup
618988f0 »
2012-06-27 Add cython code #25
2 from distutils.core import setup
3 from distutils.extension import Extension
1d6918d0 »
2012-06-27 cython support with pure python fallback, pypy tests
4
5 try:
6 from Cython.Distutils import build_ext
7 CYTHON = True
8 except:
9 CYTHON = False
bc8c85ed »
2012-01-16 use ordered dict for samples, fixes #2
10
11 requires = []
12
49e2e570 »
2012-02-03 fix argparse requirement for python < 2.6
13 # python 2.6 does not have argparse
14 try:
15 import argparse
16 except ImportError:
b59b6f72 »
2012-01-17 argparse for python < 2.7
17 requires.append('argparse')
35cfa6da »
2011-10-30 minimal setup to get into pythonpath
18
ad9d9a20 »
2012-06-10 use ordereddict for headers
19
20 try:
21 import collections
22 collections.OrderedDict
23 except AttributeError:
24 requires.append('ordereddict')
25
89daaa9a »
2012-03-14 setup.py without import
26 # get the version without an import
27 VERSION = "Undefined"
28 DOC = ""
29 inside_doc = False
30 for line in open('vcf/__init__.py'):
31 if "'''" in line:
32 inside_doc = not inside_doc
33 if inside_doc:
34 DOC += line.replace("'''", "")
35
36 if (line.startswith('VERSION')):
37 exec(line.strip())
38
1d6918d0 »
2012-06-27 cython support with pure python fallback, pypy tests
39 extras = {}
40 if CYTHON:
41 extras['cmdclass'] = {'build_ext': build_ext}
42 extras['ext_modules'] = [Extension("vcf.cparse", ["vcf/cparse.pyx"])]
49e2e570 »
2012-02-03 fix argparse requirement for python < 2.6
43
35cfa6da »
2011-10-30 minimal setup to get into pythonpath
44 setup(
45 name='PyVCF',
c240e10e »
2012-05-22 convert tests so they are runnable with 2to3, need to include test da…
46 packages=['vcf', 'vcf.test'],
cd8c710c »
2012-02-08 introduce vcf package structure
47 scripts=['scripts/vcf_melt', 'scripts/vcf_filter.py'],
9fcf4f66 »
2012-01-20 add FILTERS.md
48 author='James Casbon and @jdoughertyii',
60625baf »
2012-01-12 add meta to setup.py, note about fork to README
49 author_email='casbon@gmail.com',
cb00f477 »
2012-05-18 use_2to3 in setup.py, mostly completing Python 3 support.
50 description='Variant Call Format (VCF) parser for Python',
89daaa9a »
2012-03-14 setup.py without import
51 long_description=DOC,
c240e10e »
2012-05-22 convert tests so they are runnable with 2to3, need to include test da…
52 test_suite='vcf.test.test_vcf.suite',
cb00f477 »
2012-05-18 use_2to3 in setup.py, mostly completing Python 3 support.
53 install_requires=['distribute'],
7f7b7bdd »
2012-01-17 initial work on an extensible VCF filter
54 requires=requires,
55 entry_points = {
56 'vcf.filters': [
cd8c710c »
2012-02-08 introduce vcf package structure
57 'site_quality = vcf.filters:SiteQuality',
58 'vgq = vcf.filters:VariantGenotypeQuality',
8a79f574 »
2012-06-25 Add error bias filter
59 'eb = vcf.filters:ErrorBiasFilter',
8eece3f2 »
2012-06-26 add filters from @libor-m
60 'dps = vcf.filters:DepthPerSample',
61 'avg-dps = vcf.filters:AvgDepthPerSample',
62 'snp-only = vcf.filters:SnpOnly',
7f7b7bdd »
2012-01-17 initial work on an extensible VCF filter
63 ]
9fcf4f66 »
2012-01-20 add FILTERS.md
64 },
c0c7d16f »
2012-01-20 version bump
65 url='https://github.com/jamescasbon/PyVCF',
89daaa9a »
2012-03-14 setup.py without import
66 version=VERSION,
3811a816 »
2012-02-08 update version to 0.3.0, doc improvements, fixes issue #16
67 classifiers = [
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2012-06-10 use ordereddict for headers
68 'Development Status :: 4 - Beta',
3811a816 »
2012-02-08 update version to 0.3.0, doc improvements, fixes issue #16
69 'Intended Audience :: Developers',
70 'Intended Audience :: Science/Research',
71 'Operating System :: OS Independent',
72 'Programming Language :: Python',
cb00f477 »
2012-05-18 use_2to3 in setup.py, mostly completing Python 3 support.
73 'Programming Language :: Python :: 3',
3811a816 »
2012-02-08 update version to 0.3.0, doc improvements, fixes issue #16
74 'Topic :: Scientific/Engineering',
75 ],
76 keywords='bioinformatics',
cb00f477 »
2012-05-18 use_2to3 in setup.py, mostly completing Python 3 support.
77 use_2to3=True,
c240e10e »
2012-05-22 convert tests so they are runnable with 2to3, need to include test da…
78 include_package_data=True,
79 package_data = {
1b29ce70 »
2012-05-22 include tabix index for tests
80 '': ['*.vcf', '*.gz', '*.tbi'],
618988f0 »
2012-06-27 Add cython code #25
81 },
1d6918d0 »
2012-06-27 cython support with pure python fallback, pypy tests
82 **extras
35cfa6da »
2011-10-30 minimal setup to get into pythonpath
83 )
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