File: .travis.yml

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augur 11.0.0-1
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version: ~> 1.0
language: generic

# See <https://docs.travis-ci.com/user/build-stages/> for more information on
# how build stages work.
stages:
  - test

  # See <https://docs.travis-ci.com/user/conditions-v1> for more on the "if" syntax.
  - name: deploy
    if: branch = release and type != pull_request

jobs:
  include:
    - &test
      stage: test
      language: python
      python: 3.6
      before_install:
        - wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh;
        - bash miniconda.sh -b -p $HOME/miniconda
        - export PATH="$HOME/miniconda/bin:$PATH"
        - hash -r
        - conda config --set always_yes yes --set changeps1 no
        - conda update -q conda
        - conda info -a
        - conda create -n augur -c bioconda python=$TRAVIS_PYTHON_VERSION mafft raxml fasttree iqtree vcftools pip
        - source activate augur
      install:
        - pip install -e .[dev]
      script:
        - (pytest -c pytest.python3.ini  --cov-report= --cov=augur)
        - (cram --shell=/bin/bash tests/functional/*.t tests/builds/*.t)
        - (bash tests/builds/runner.sh)
      after_success:
        # upload to codecov
        - bash <(curl -s https://codecov.io/bash) -f "!*.gcov" -X gcov -e TRAVIS_PYTHON_VERSION -y ci/codecov.yml|| echo "Codecov did not collect coverage reports"

    - <<: *test
      python: 3.7
    - <<: *test
      python: 3.8

    - stage: deploy
      script: ./devel/travis-rebuild-docker-image