.travis.yml

language: python
python:
  - "3.6"
# command to install dependencies
install:
  - sudo apt-get update
  # We do this conditionally because it saves us some downloading if the
  # version is the same.
  - 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
  
  - sudo apt install libgfortran3
  - 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
  # Useful for debugging any issues with conda
  - conda info -a
  - conda config --add channels defaults
  - conda config --add channels bioconda
  - conda config --add channels conda-forge

  # Replace dep1 dep2 ... with your dependencies
  - conda create -q -n test-environment python=$TRAVIS_PYTHON_VERSION  
      pandas tzlocal rpy2 biopython ReportLab pytest-cov bioconductor-deseq2 
      codecov
  - source activate test-environment
  - pip install .
  # install deseq2
  - Rscript setup.R


# command to run tests
script:
  - coverage run -m pytest

after_success:
    - bash <(curl -s https://codecov.io/bash)