.travis.yml

dist: xenial
language: python            # this works for Linux but is an error on macOS or Windows
jobs:
  include:
    - name: "Python 3.6 on Xenial Linux"
      python: 3.6           # this works for Linux but is ignored on macOS or Windows
    - name: "Python 3.6 on macOS"
      os: osx
      language: shell       # 'language: python' is an error on Travis CI macOS
      python: 3.6

install:

  - if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then MINICONDA_OS=Linux; else MINICONDA_OS=MacOSX; fi
  - wget https://repo.anaconda.com/miniconda/Miniconda3-latest-$MINICONDA_OS-x86_64.sh -O miniconda.sh
  - bash miniconda.sh -b -p "$HOME"/miniconda
  - source "$HOME/miniconda/etc/profile.d/conda.sh"
  - hash -r
  - conda config --set always_yes yes --set changeps1 no
  - conda update -q conda
  - conda info -a
  - conda env create -f environment.yml
  - conda activate artic
  - python setup.py install

script:
  # run the unit tests
  - pytest -s artic/*_unit_test.py

  # run the pipeline test for the medaka pipeline variant
  - ./test-runner.sh medaka

  # run the pipeline test for the nanopolish pipeline variant
  - ./test-runner.sh nanopolish

  # run some of the variant set validation functional tests (will download test data)
  - pytest -s artic/minion_validator.py --workFlow nanopolish --numValidations 1
  - pytest -s artic/minion_validator.py --workFlow medaka --numValidations 2