.travis.yml

language: python

matrix:
  include:
    - python: 2.7
      env:
        - TO_TEST=CONDA
        - ENV_BRANCH=master
        - CARD=broadstreet-v2.0.1.tar.gz
    - python: 2.7
      env: TO_TEST=DOCKER
    - python: 2.7
      env: TO_TEST=BASH

sudo: required
services:
  - docker

before_install:
  - sudo apt-get update
  # Check Python version.
  - python --version
  # Turn off O_NONBLOCK. See https://github.com/travis-ci/travis-ci/issues/4704#issuecomment-348435959
  - python -c 'import os,sys,fcntl; flags = fcntl.fcntl(sys.stdout, fcntl.F_GETFL); fcntl.fcntl(sys.stdout, fcntl.F_SETFL, flags&~os.O_NONBLOCK);'
  # Increase workers for NODE DNS resolution. https://stackoverflow.com/questions/35387264/node-js-request-module-getting-etimedout-and-esockettimedout
  - export UV_THREADPOOL_SIZE=16
  #### miniconda install:
  - if [ "$TO_TEST" = "CONDA" ]; then
      wget https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh -O miniconda.sh;
      bash miniconda.sh -b -p $HOME/miniconda;
      export PATH="$HOME/miniconda/bin:$PATH";
      hash -r;
      conda config --set always_yes yes --set changeps1 no;
      conda config --add channels bioconda;
      conda config --add channels conda-forge;
      conda update -q conda;
      conda info -a;
    fi
  - if [ "$TO_TEST" = "DOCKER" ]; then
      docker-compose up -d;
      docker ps -a;
      docker-compose logs webserver;
      ls;
    fi
install:
  - if [ "$TO_TEST" = "CONDA" ] || [ "$TO_TEST" = "DOCKER" ]; then
      cd app/;
    fi
  #### Recreate our Conda env for testing
  - if [ "$TO_TEST" = "CONDA" ]; then
      wget https://raw.githubusercontent.com/superphy/docker-flask-conda/$ENV_BRANCH/app/environment.yml;
      conda env create -q -f environment.yml -n backend;
      source activate backend;
      wget https://raw.githubusercontent.com/superphy/docker-flask-conda/webserver/app/environment.yml -O environment-webserver.yml;
      conda env update -q -f environment-webserver.yml;
      wget https://raw.githubusercontent.com/superphy/docker-flask-conda/$ENV_BRANCH/app/requirements.txt;
      pip install -r requirements.txt;
    fi
  # Additional setup for conda.
  - if [ "$TO_TEST" = "CONDA" ]; then
      wget https://card.mcmaster.ca/download/0/$CARD;
      tar -xf $CARD;
      rgi load --afile card.json;
    fi
  # Install pytest and any additional requirements for tests.
  - if [ "$TO_TEST" = "CONDA" ] || [ "$TO_TEST" = "DOCKER" ]; then
      pip install pytest;
      pip install -r tests/test_requirements.txt; 
    fi
script:
  #### Run Pytest
  - if [ "$TO_TEST" = "CONDA" ]; then
      python -m pytest -v --ignore modules/ectyper/ecoli_serotyping --ignore tests/docker/;
    fi
  - if [ "$TO_TEST" = "DOCKER" ]; then
      python -m pytest -v tests/docker/;
    fi
  - if [ "$TO_TEST" = "BASH" ]; then
      bash production.sh;
    fi
after_failure:
  - if [ "$TO_TEST" = "CONDA" ]; then
      rgi -h;
      ectyper -h;
    fi
  # Check the logs if tests fail.
  - if [ "$TO_TEST" = "DOCKER" ]; then
      docker-compose logs webserver;
      docker-compose logs blazegraph;
    fi
notifications:
  email: false