circle.yml

dependencies:
  cache_directories:
    - "~/.apt-cache"
  pre:
    # Let CircleCI cache the apt archive
    - sudo rm -rf /var/cache/apt/archives && sudo ln -s ~/.apt-cache /var/cache/apt/archives && mkdir -p ~/.apt-cache/partial
    - bash <(wget -q -O- http://neuro.debian.net/_files/neurodebian-travis.sh)
    - wget http://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh -O miniconda.sh; bash ./miniconda.sh -b
    
  override:
    # Install apt packages
    - sudo apt-get install -y fsl-core fsl-atlases fsl-mni152-templates fsl-first-data
    - echo 'source /etc/fsl/fsl.sh' >> $HOME/.profile
    - echo 'export PATH=~/miniconda2/bin:$PATH' >> $HOME/.profile
    - source $HOME/.profile; conda config --add channels conda-forge
    - source $HOME/.profile; conda env create -f environment.yml
    - echo 'source activate bh_demo' >> $HOME/.profile
    - source $HOME/.profile; pip install https://github.com/satra/prov/archive/enh/rdf-1.x.zip

machine:
  environment:
    FSLOUTPUTTYPE: NIFTI_GZ
test:
  override:
    - source $HOME/.profile; python run_demo_workflow.py --key 11an55u9t2TAf0EV2pHN0vOd8Ww2Gie-tHp9xGULh_dA -n 2 :
       timeout: 4000
    - source $HOME/.profile; python check_output.py | tee ~/log.txt
    - cat ~/log.txt && if grep -q "MATCH" ~/log.txt; then true; else false; fi

general:
  artifacts:
    - "~/log.txt"
    - "~/simple_workflow/ActualOutput.csv"
    - "~/simple_workflow/Difference.csv"
    - "~/simple_workflow/ExpectedOutput.csv"