.travis.yml

# Special configuration file to run tests on Travis-CI via GitHub notifications
# See https://travis-ci.org/biopython/biopython/builds for results
#
# Using TravisCI's configuration alone became too complicated once we wanted
# to cover more than just running the unit tests on different versions of
# Python, so this now does all the complicated test configuration via TOX
# See file .travis-tox.ini
#
# Environment variables setup here:
# - TOXENV = environment used in Tox (conventionally uses py35 etc)
#

language: python
matrix:
  include:
    - env: TOXENV=style
    - env: TOXENV=sdist
    - env: TOXENV=bdist_wheel
    - python: 2.7
      env: TOXENV=py27-cover
    - python: 3.3
      env: TOXENV=py33-cover
    - python: 3.4
      env: TOXENV=py34-cover
    - python: 3.5
      env: TOXENV=py35-cover
    - python: 3.6
      env: TOXENV=py36-cover
    - python: pypy
      env: TOXENV=pypy-nocov
    - python: pypy3
      env: TOXENV=pypy3-nocov

sudo: false
addons:
  apt:
    packages:
    - bwa
    - clustalo
    - clustalw
    - emboss
    - mafft
    - muscle
    - paml
    - phyml
    - probcons
    - samtools
    - wise

# We setup $HOME/bin and add it to the $PATH for extra binaries we're using.
#
# There is a phyml Ubuntu package, but currently too old.
#
# There are TravisCI provided versions of PyPy and PyPy3, but currently too old.
# We therefore deactivate that, and download and unzip portable PyPy binaries.
#
# We also need DSSP for testing but it is not available in the repositories.
# Try to download the binary for Linux and place it in $HOME/bin
# 
before_install:
  - cd $HOME
  - mkdir bin
  - export PATH=$HOME/bin:$PATH
  - curl -L -O http://www.atgc-montpellier.fr/download/binaries/phyml/PhyML-3.1.zip
  - unzip PhyML-3.1.zip
  - mv PhyML-3.1/PhyML-3.1_linux64 bin/phyml
  - cd $HOME
  - "if [[ $TRAVIS_PYTHON_VERSION == 'pypy' ]]; then deactivate && wget https://bitbucket.org/squeaky/portable-pypy/downloads/pypy-5.6-linux_x86_64-portable.tar.bz2 && tar -jxvf pypy-5.6-linux_x86_64-portable.tar.bz2 && echo 'Setting up aliases...' && export PATH=$HOME/pypy-5.6-linux_x86_64-portable/bin/:$PATH && ln -s ~/pypy-5.6-linux_x86_64-portable/bin/pypy ~/bin/python && echo 'Setting up pip...' && pypy-5.6-linux_x86_64-portable/bin/pypy -m ensurepip ; fi"
  - "if [[ $TRAVIS_PYTHON_VERSION == 'pypy3' ]]; then deactivate && wget https://bitbucket.org/squeaky/portable-pypy/downloads/pypy3.3-5.5-alpha-20161013-linux_x86_64-portable.tar.bz2 && tar -jxvf pypy3.3-5.5-alpha-20161013-linux_x86_64-portable.tar.bz2 && echo 'Setting up aliases...' && export PATH=$HOME/pypy3.3-5.5-alpha-20161013-linux_x86_64-portable/bin/:$PATH && ln -s ~/pypy3.3-5.5-alpha-20161013-linux_x86_64-portable/bin/pypy3.3 ~/bin/python && echo 'Setting up pip...' && pypy3.3-5.5-alpha-20161013-linux_x86_64-portable/bin/pypy -m ensurepip && ln -s ~/pypy3.3-5.5-alpha-20161013-linux_x86_64-portable/bin/pip3.3 ~/bin/pip ; fi"
  - cd $HOME
  - curl -L -O ftp://ftp.cmbi.ru.nl/pub/software/dssp/dssp-2.0.4-linux-amd64
  - mv dssp-2.0.4-linux-amd64 bin/dssp
  - chmod a+x bin/dssp
  - cd $TRAVIS_BUILD_DIR

install:
  - "cp Tests/biosql.ini.sample Tests/biosql.ini"
  - "pip install --upgrade pip setuptools"
  - "pip install tox"
  - "tox -c .travis-tox.ini -e $TOXENV --notest"

script:
  - "tox -c .travis-tox.ini -e $TOXENV"

notifications:
  email: false