.travis.yml

language: python


matrix:
  include:
    - name: "ubuntu bionic"
      os: linux
      dist: bionic

python:
  - "3.6"
  - "3.7"

addons:
    apt_packages:
        - parallel

install:
  - sudo apt-get update
  # miniconda install
  - if [[ "$TRAVIS_PYTHON_VERSION" == "2.7" ]]; then
      wget https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh -O miniconda.sh;
    else
      wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh;
    fi
  - bash miniconda.sh -b -p $HOME/miniconda
  - source "$HOME/miniconda/etc/profile.d/conda.sh"
  # miniconda setup
  - hash -r
  - conda config --set always_yes yes --set changeps1 no
  - conda update -y -q conda
  - conda config --add channels defaults
  - conda config --add channels conda-forge
  - conda config --add channels bioconda
  - conda info -a
  # conda env setup
  - conda create -n traitar3 python=$TRAVIS_PYTHON_VERSION bioconda::hmmer scipy pandas numpy matplotlib pytest
  - conda activate traitar3
  # traitar install
  - python setup.py build
  - python setup.py install
  - conda list

script:
  - traitar -h
  - traitar pfam -h
  - traitar phenotype -h
  - traitar pfam db
  - traitar phenotype --overwrite db traitar/data/sample_data/ traitar/data/sample_data/samples.txt from_genes tmp 
  - traitar phenotype --cpus 2 --overwrite db traitar/data/sample_data/ traitar/data/sample_data/samples.txt from_genes tmp