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.travis-tox.ini
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.travis-tox.ini
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# 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
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:style]
# This does not need to install Biopython or any of its dependencies
skip_install = True
whitelist_externals =
flake8
doc8
rst-lint
bash
deps =
flake8
flake8-docstrings
flake8-blind-except
flake8-rst-docstrings
flake8-comprehensions
flake8-bugbear
flake8-implicit-str-concat
flake8-black
flake8-quotes
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
# pydocstyle v4 had false positives with D413, need v5
pydocstyle>=5.0.0
commands =
# PEP-8 and PEP-257 style checks:
flake8
# 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' *.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"
[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
pygments
sphinx_rtd_theme
commands =
bash -c \'python setup.py install > /dev/null\'
make -C Doc/api/ html