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35cfa6d minimal setup to get into pythonpath
James Casbon authored Oct 30, 2011
1 from setuptools import setup
bc8c85e use ordered dict for samples, fixes #2
James Casbon authored Jan 16, 2012
2
3 requires = []
4
49e2e57 fix argparse requirement for python < 2.6
James Casbon authored Feb 3, 2012
5 # python 2.6 does not have argparse
6 try:
7 import argparse
8 except ImportError:
b59b6f7 argparse for python < 2.7
James Casbon authored Jan 17, 2012
9 requires.append('argparse')
35cfa6d minimal setup to get into pythonpath
James Casbon authored Oct 30, 2011
10
ad9d9a2 use ordereddict for headers
James Casbon authored Jun 10, 2012
11
12 try:
13 import collections
14 collections.OrderedDict
15 except AttributeError:
16 requires.append('ordereddict')
17
89daaa9 setup.py without import
James Casbon authored Mar 14, 2012
18 # get the version without an import
19 VERSION = "Undefined"
20 DOC = ""
21 inside_doc = False
22 for line in open('vcf/__init__.py'):
23 if "'''" in line:
24 inside_doc = not inside_doc
25 if inside_doc:
26 DOC += line.replace("'''", "")
27
28 if (line.startswith('VERSION')):
29 exec(line.strip())
30
49e2e57 fix argparse requirement for python < 2.6
James Casbon authored Feb 3, 2012
31
35cfa6d minimal setup to get into pythonpath
James Casbon authored Oct 30, 2011
32 setup(
33 name='PyVCF',
c240e10 convert tests so they are runnable with 2to3, need to include test da…
James Casbon authored May 22, 2012
34 packages=['vcf', 'vcf.test'],
cd8c710 introduce vcf package structure
James Casbon authored Feb 8, 2012
35 scripts=['scripts/vcf_melt', 'scripts/vcf_filter.py'],
9fcf4f6 add FILTERS.md
James Casbon authored Jan 20, 2012
36 author='James Casbon and @jdoughertyii',
60625ba add meta to setup.py, note about fork to README
James Casbon authored Jan 12, 2012
37 author_email='casbon@gmail.com',
cb00f47 @marcelm use_2to3 in setup.py, mostly completing Python 3 support.
marcelm authored May 18, 2012
38 description='Variant Call Format (VCF) parser for Python',
89daaa9 setup.py without import
James Casbon authored Mar 14, 2012
39 long_description=DOC,
c240e10 convert tests so they are runnable with 2to3, need to include test da…
James Casbon authored May 22, 2012
40 test_suite='vcf.test.test_vcf.suite',
cb00f47 @marcelm use_2to3 in setup.py, mostly completing Python 3 support.
marcelm authored May 18, 2012
41 install_requires=['distribute'],
7f7b7bd initial work on an extensible VCF filter
James Casbon authored Jan 17, 2012
42 requires=requires,
43 entry_points = {
44 'vcf.filters': [
cd8c710 introduce vcf package structure
James Casbon authored Feb 8, 2012
45 'site_quality = vcf.filters:SiteQuality',
46 'vgq = vcf.filters:VariantGenotypeQuality',
8a79f57 Add error bias filter
James Casbon authored Jun 25, 2012
47 'eb = vcf.filters:ErrorBiasFilter',
8eece3f add filters from @libor-m
James Casbon authored Jun 26, 2012
48 'dps = vcf.filters:DepthPerSample',
49 'avg-dps = vcf.filters:AvgDepthPerSample',
50 'snp-only = vcf.filters:SnpOnly',
7f7b7bd initial work on an extensible VCF filter
James Casbon authored Jan 17, 2012
51 ]
9fcf4f6 add FILTERS.md
James Casbon authored Jan 20, 2012
52 },
c0c7d16 version bump
James Casbon authored Jan 20, 2012
53 url='https://github.com/jamescasbon/PyVCF',
89daaa9 setup.py without import
James Casbon authored Mar 14, 2012
54 version=VERSION,
3811a81 update version to 0.3.0, doc improvements, fixes issue #16
James Casbon authored Feb 8, 2012
55 classifiers = [
ad9d9a2 use ordereddict for headers
James Casbon authored Jun 10, 2012
56 'Development Status :: 4 - Beta',
3811a81 update version to 0.3.0, doc improvements, fixes issue #16
James Casbon authored Feb 8, 2012
57 'Intended Audience :: Developers',
58 'Intended Audience :: Science/Research',
59 'Operating System :: OS Independent',
60 'Programming Language :: Python',
cb00f47 @marcelm use_2to3 in setup.py, mostly completing Python 3 support.
marcelm authored May 18, 2012
61 'Programming Language :: Python :: 3',
3811a81 update version to 0.3.0, doc improvements, fixes issue #16
James Casbon authored Feb 8, 2012
62 'Topic :: Scientific/Engineering',
63 ],
64 keywords='bioinformatics',
cb00f47 @marcelm use_2to3 in setup.py, mostly completing Python 3 support.
marcelm authored May 18, 2012
65 use_2to3=True,
c240e10 convert tests so they are runnable with 2to3, need to include test da…
James Casbon authored May 22, 2012
66 include_package_data=True,
67 package_data = {
1b29ce7 include tabix index for tests
James Casbon authored May 22, 2012
68 '': ['*.vcf', '*.gz', '*.tbi'],
c240e10 convert tests so they are runnable with 2to3, need to include test da…
James Casbon authored May 22, 2012
69 }
35cfa6d minimal setup to get into pythonpath
James Casbon authored Oct 30, 2011
70 )
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