forked from biopython/biopython
-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy path.travis-tox.ini
180 lines (173 loc) · 5.6 KB
/
.travis-tox.ini
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
# This is a configuration file for tox, used to test
# Biopython on various versions of Python etc under
# the Travis Continuous Integration service which is
# configured in the file .travis.yml
#
# By default tox will look for tox.ini, so this file
# will not conflict with any personal tox setup.
#
# You can explicitly use this tox configuration on your
# own machine (via the -c setting), PROVIDED you have
# all the relevant versions of Python installed. e.g.
# specifying a specific target envronment (via -e):
#
# $ pip install tox
# $ tox -c .travis-tox.ini -e py35-nocov
#
# Or with test coverage:
#
# $ pip install tox coverage
# $ tox -c .travis-tox.ini -e py35-cover
#
# Or to run the pep8/flake8 etc Python coding style checks:
#
# $ pip install tox flake8 pydocstyle restructuredtext_lint
# $ tox -c .travis-tox.ini -e style
#
# See the envlist setting for other valid arguments.
[tox]
minversion = 2.0
skipsdist = True
envlist =
style
flake8
sdist
bdist_wheel
api
{py36,py37,py38,pypy3}-cover
{py36,py37,py38,pypy3}-nocov
[testenv]
# TODO: Try tox default sdist based install instead:
skip_install = True
sitepackages = True
passenv =
CI
TRAVIS
TRAVIS_*
TOXENV
CODECOV_*
HOME_4_TCOFFEE
whitelist_externals =
bash
echo
# Want to avoid overhead of compiling numpy or scipy:
# (But must compile numpy for PyPy right now)
install_command = pip install --only-binary=scipy {opts} {packages}
deps =
setuptools
wheel
py36,py37,py38: numpy
pypy3: numpy<1.18.0
#Lines startings xxx: are filtered by the environment.
#Leaving py36 without any dependencies (except numpy)
cover: coverage
cover: codecov
py37: mmtf-python
# https://bitbucket.org/rptlab/reportlab/issues/176/incompatibility-with-pillow-600
py38: reportlab
py38: pillow==5.4
py37: psycopg2-binary
py37: mysql-connector-python-rf
py37: mysqlclient
py38: rdflib
pypy3: mysqlclient
py37: scipy
py38: networkx
py37: matplotlib
commands =
#The bash call is a work around for special characters
#The /dev/null is to hide the verbose output but leave warnings
bash -c \'python setup.py install > /dev/null\'
#The bash call is a work around for the cd command
nocov: bash -c \'cd Tests && python run_tests.py --offline\'
#See https://codecov.io/ and https://github.com/codecov/example-python
cover: bash -c \'rm -rf Tests/coverage.xml\'
cover: bash -c \'cd Tests && coverage run run_tests.py --offline && coverage xml\'
cover: codecov --file Tests/coverage.xml -X pycov -X gcov
[testenv:flake8]
# Doing this separately from and in parallel with black etc
# This does not need to install Biopython or any of its dependencies
skip_install = True
whitelist_externals =
flake8
deps =
flake8
flake8-docstrings
flake8-blind-except
flake8-rst-docstrings
flake8-comprehensions
flake8-bugbear
flake8-implicit-str-concat
flake8-quotes
# pydocstyle v4 had false positives with D413, need v5
pydocstyle>=5.0.0
commands =
flake8
[testenv:style]
# This does not need to install Biopython or any of its dependencies
skip_install = True
whitelist_externals =
black
doc8
rst-lint
bash
deps =
black
restructuredtext_lint
doc8
pygments
# doc8 needs docutils, but docutils==0.15 has an import order bug
# https://bugs.launchpad.net/doc8/+bug/1837515
# https://sourceforge.net/p/docutils/bugs/366/
docutils==0.14
commands =
# Now do various checks on our RST files:
# Calling via bash to get it to expand the wildcard for us
bash -c \'rst-lint --level warning *.rst\'
# Check sort order (bash call work around for pipe character)
bash -c \'grep "^- " CONTRIB.rst | LC_ALL=C sort -u -c -f\'
# Check copyright date
bash -c \'grep "1999-`date +'%Y'`" LICENSE.rst\'
# Would like to tell doc8 to just check *.rst but does *.txt too:
bash -c "doc8 --ignore-path 'Doc/examples/ec_*.txt' 'Doc/doc.rst' *.rst Doc/"
# Check no __docformat__ lines
bash -c "if grep --include '*.py' -rn '^__docformat__ ' Bio BioSQL Tests Scripts Doc ; then echo 'Remove __docformat__ line(s), we assume restructuredtext.'; false; fi"
# Check DOI link style, see https://www.crossref.org/display-guidelines/
bash -c "if grep --include '*.py' --include '*.rst' --include '*.tex' -rni 'doi:' Bio BioSQL Scripts Doc ; then echo 'Please use https://doi.org/... not the doi: or DOI: style.'; false; fi"
bash -c "if grep --include '*.py' --include '*.rst' --include '*.tex' -rn 'dx\.doi\.org' Bio BioSQL Tests Scripts Doc ; then echo 'Please use https://doi.org/... not the dx.doi.org style.'; false; fi"
bash -c "if grep --include '*.py' --include '*.rst' --include '*.tex' -rn 'http://doi\.org' Bio BioSQL Tests Scripts Doc ; then echo 'Please use https://doi.org/... not http://doi.org/...'; false; fi"
# Black style check:
black --diff .
[testenv:sdist]
# This does not need to install Biopython or any of its dependencies
skip_install = True
deps =
commands =
python setup.py sdist --formats=gztar,zip
[testenv:bdist_wheel]
# This should not require NumPy while compiling our C code...
skip_install = True
deps =
commands =
python setup.py bdist_wheel
[testenv:api]
# Note Sphinx likes to have the code installed so can import it
skip_install = False
whitelist_externals =
bash
sphinx-apidoc
make
deps =
mmtf-python
mysql-connector-python-rf
numpy
rdflib
reportlab
scipy
sphinx>=1.8.0
numpydoc==1.0.0
pygments
sphinx_rtd_theme
commands =
bash -c \'python setup.py install > /dev/null\'
make -C Doc/api/ html