.gitlab-ci.yml

# -----------------------------------Set Up------------------------------------
variables:
    PY_VERSION: 3
    PRIVATE: 0
    TMPDIR: ./tmp
    VENV: pysitk-test-py${PY_VERSION}
    ITK_DIR: /mnt/shared/mebner/environment/ITK/ITK_NiftyMIC-python${PY_VERSION}-build
    FSL_DIR: /mnt/shared/mebner/environment/FSL/fsl
    NIFTYREG_INSTALL: /mnt/shared/mebner/environment/NiftyReg/NiftyReg-master-install
    CONVERT3D_INSTALL: /mnt/shared/mebner/environment/Convert3D/c3d-git-install

before_script:
    # add NiftyReg to PATH
    - export PATH="${NIFTYREG_INSTALL}/bin:$PATH"

    # add FSL
    - PATH=${FSL_DIR}/bin:${PATH}
    - export PATH="${FSL_INSTALL}/bin:$PATH"
    - export FSLOUTPUTTYPE=NIFTI_GZ

    # add Convert3D to PATH
    - export PATH="${CONVERT3D_INSTALL}/bin:$PATH"

    # save current folder path
    - cwd_dir=$(pwd)

    # create virtual environment
    - rm -rf ${VENV}
    - mypython=$(which python${PY_VERSION})
    - virtualenv -p $mypython ${VENV}
    - cd ${VENV}
    - venv_dir=$(pwd)
    - source bin/activate
    
    # print Python version to CI output
    - which python
    - python --version

    # copy ITK_NiftyMIC-build WrapITK to site-packages of python venv
    - py_sitepkg=${venv_dir}/lib/python*/site-packages
    - cp -v ${ITK_DIR}/Wrapping/Generators/Python/WrapITK.pth ${py_sitepkg}

    - cd $cwd_dir
    # If cmiclab is used:
    # add CI_JOB_TOKEN for cloning dependent repositories in requirements.txt
    # (https://docs.gitlab.com/ee/user/project/new_ci_build_permissions_model.html#dependent-repositories)
    - >
      (if [ ${PRIVATE} == 1 ];
      then sed -i -- "s#github.com/gift-surg#gitlab-ci-token:${CI_JOB_TOKEN}@cmiclab.cs.ucl.ac.uk/GIFT-Surg#g" requirements.txt;
      fi);
    # install requirements
    - pip install -r requirements.txt

    # run installation
    - pip install .

after_script:
    # delete tmp-directory
    - rm -rfv ${TMPDIR}

# ----------------------------------Test Jobs----------------------------------
builddocs:
  # only:
  #   - master
  script:
    - cd doc
    - doxygen doxyfile
  tags:
    - gift-adelie

installation:
  # only:
  #   - master
  script:
    - python -m nose tests/installation_test.py
  tags:
    - gift-adelie

applications:
  # only:
  #   - master
  script:
    - python -m nose tests/application_test.py
  tags:
    - gift-adelie