circle.yml

dependencies:
  cache_directories:
    - "~/examples/"
    - "~/afni/"
    - "~/fsl/"
  override:
    - pip install --upgrade pip
    - pip install numpy
    - pip install lockfile
    - pip install -e .
    - if [[ ! -d ~/fsl ]]; then wget "http://fsl.fmrib.ox.ac.uk/fsldownloads/fsl-5.0.9-centos6_64.tar.gz"; tar zxvf fsl-5.0.9-centos6_64.tar.gz; mv fsl ~/fsl; fi
    - if [[ ! -d ~/afni ]]; then wget "http://afni.nimh.nih.gov/pub/dist/tgz/linux_openmp_64.tgz"; tar zxvf linux_openmp_64.tgz; mv linux_openmp_64 ~/afni; fi
    - if [[ ! -d ~/examples/ds003_downsampled ]]; then wget -O ds003_downsampled.tar "https://osf.io/7zb25/?action=download"; mkdir -p ~/examples; tar xvf ds003_downsampled.tar -C ~/examples; fi
test:
  override:
    # First test only on one subject
    - echo "sub-01" > inclusion_file && python scripts/qap_sublist_generator.py --include inclusion_file --BIDS ~/examples/ds003_downsampled/ ~/bids_sub-01.yml
    - FSLDIR=~/fsl/ PATH=~/afni:~/fsl/bin:$PATH LD_LIBRARY_PATH=~/fsl/lib FSLOUTPUTTYPE="NIFTI_GZ" python scripts/qap_measures_pipeline.py ~/bids_sub-01.yml configs/qap_config_ds003.yml
    # Second test on multiple subjects, two subjects at once (qap_config_ds003_ms.yml)
    - python scripts/qap_sublist_generator.py --BIDS ~/examples/ds003_downsampled/ ~/bids_list.yml
    - FSLDIR=~/fsl/ PATH=~/afni:~/fsl/bin:$PATH LD_LIBRARY_PATH=~/fsl/lib FSLOUTPUTTYPE="NIFTI_GZ" python scripts/qap_measures_pipeline.py ~/bids_list.yml configs/qap_config_ds003_ms.yml
general:
  artifacts:
    - "/tmp/output"
    - "/tmp/workdir"
    - "/tmp/output_ms"
    - "/tmp/workdir_ms"
    - "~/bids_sub-01.yml"
    - "~/bids_list.yml"