.travis-tox.ini

# This is a configuration file for tox, used to test
# Biopython on various versions of Python etc under
# the Travis Continous 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
    {py27,py34,py35,py36,pypy,pypy3}-cover
    {py27,py34,py35,py36,pypy,pypy3}-nocov

[testenv]
# TODO: Try tox default sdist based install instead:
skip_install = True
sitepackages = True
passenv =
    CI
    TRAVIS
    TRAVIS_*
    TOXENV
    CODECOV_*
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 =
    #Lines startings xxx: are filtered by the environment.
    #Leaving py34 without any soft dependencies (just numpy)
    cover: coverage
    cover: codecov
    {py27}: unittest2
    {py27}: mysql-python
    {py27,py36}: mmtf-python
    {py27,py35}: reportlab
    {py27,py34,py35,py36}: psycopg2-binary
    {py27,py34,py35,py35}: mysql-connector-python-rf
    {py27,py35,pypy}: rdflib
    {pypy,pypy3}: numpy==1.12.1
    {py27,py34,py35,py36}: numpy
    {py36}: scipy
    {py27}: networkx
    {py36}: 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
    rst-lint
    bash
deps =
    flake8
    flake8-docstrings
    flake8-blind-except
    flake8-rst-docstrings
    restructuredtext_lint
commands =
    # These folders each have their own .flake8 file:
    flake8 BioSQL/
    flake8 Scripts/
    flake8 Doc/examples/
    flake8 Bio/
    flake8 Tests/
    # 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\'
    # 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 use NumPy while compiling our C code...
skip_install = True
deps =
    numpy
commands =
    python setup.py bdist_wheel