forked from ga4gh/vrs-python
-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathsetup.cfg
135 lines (118 loc) · 3.01 KB
/
setup.cfg
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
# See here:
# https://setuptools.readthedocs.io/en/latest/setuptools.html#configuring-setup-using-setup-cfg-files
# https://gist.github.com/althonos/6914b896789d3f2078d1e6237642c35c
# https://github.com/pyscaffold/pyscaffold/blob/master/setup.cfg
[metadata]
name = ga4gh.vrs
home_page = https://github.com/ga4gh/vrs-python
long_description = file:README.rst
long_description_content_type = text/x-rst; charset=UTF-8
description = "GA4GH Variation Representation Specification (VRS) reference implementation (https://github.com/ga4gh/vrs-python/)"
#description-content-type = text/x-rst; charset=UTF-8
license_file = LICENSE
author = Reece Hart
author_email = [email protected]
platform = any
# version is pulled from tags by setuptools_scm
classifiers =
Development Status :: 3 - Alpha
Intended Audience :: Developers
Intended Audience :: Healthcare Industry
Intended Audience :: Science/Research
License :: OSI Approved :: Apache Software License
Operating System :: OS Independent
Programming Language :: Python
Programming Language :: Python :: 3
Programming Language :: Python :: 3.6
Programming Language :: Python :: 3.7
Topic :: Scientific/Engineering :: Bio-Informatics
Topic :: Scientific/Engineering :: Medical Science Apps.
keywords =
bioinformatics
ga4gh
genomics
hgvs
spdi
variation
[options]
packages = find_namespace:
include_package_data = True
python_requires = >= 3.6
zip_safe = True
package_dir =
= src
install_requires =
bioutils
canonicaljson
coloredlogs
jsonschema<4
numpy
python-jsonschema-objects>=0.4.0
pyyaml
setup_requires =
cython
pytest-runner
setuptools_scm
wheel
tests_require =
pytest
pytest-cov
pytest-vcr
vcrpy
[options.packages.find]
where = src
exclude =
__pycache__
*.pyc
[options.package_data]
ga4gh.vrs =
_internal/data/schema/vrs.*
ga4gh.core =
_internal/data/schema/ga4gh.*
# Jedi pinned https://github.com/ipython/ipython/issues/12677#issuecomment-752258403
[options.extras_require]
dev =
ipython
jedi<0.18
pylint
pytest
pytest-cov
pytest-vcr
pyyaml
restview
smart_open
sphinx
sphinx_rtd_theme
tox
vcrpy
yapf
extras =
psycopg2-binary
biocommons.seqrepo>=0.5.1
bioutils>=0.5.2
hgvs>=1.4
requests
click
notebooks =
ipython
jupyter
tabulate
[aliases]
test = pytest
[bdist_wheel]
universal = 1
[build_sphinx]
all_files = 1
# http://pep8.readthedocs.org/en/latest/intro.html#error-codes
[flake8]
max-line-length = 120
exclude = tests/*
max-complexity = 10
ignore = E129,E221,E241,E251,E303,W291
[tool:pytest]
# TODO: add src to testpaths to trigger doctests. However, this
# requires injecting fixtures, which requires conftest.py in src/,
# which requires packaging changes. Deferred.
testpaths = src tests
doctest_optionflags = ALLOW_UNICODE ALLOW_BYTES ELLIPSIS IGNORE_EXCEPTION_DETAIL NORMALIZE_WHITESPACE
addopts = --cov-config=setup.cfg --cov-report=term-missing --cov=ga4gh