circle.yml

version: 2.0

references:

  install_pips: &install_pips
    run:
      name: Install PyPI dependences
      command: |
        sudo apt-get update
        sudo apt-get install tk-dev pkg-config python-dev python-tk
        sudo pip install --upgrade pip setuptools
        sudo pip install -r ./tests/requirements.txt
        sudo pip install -U backports.functools_lru_cache  # required for matplotlib @py2
        pip install -r requirements.txt --user
        pip list

  test_coverage: &test_coverage
    run:
      name: Testing and Formating
      command: |
        unset DISPLAY
        coverage run --source imsegm -m py.test imsegm tests -v --doctest-modules --junitxml=test-reports/pytest_junit.xml
        python setup.py check -m -s
        flake8 . --ignore=E402,E731 --max-line-length=100

  build_project: &build_project
   run:
     name: Building project
     command: |
       mkdir libs && mkdir output && mkdir results && mkdir test-reports
       gcc --version ; python --version ; pwd ; ls -l
       pip --version ; pip freeze
       python setup.py build_ext --inplace

  make_docs: &make_docs
   run:
     name: Make Documentation
     command: |
       sudo apt-get install pandoc
       sudo pip install -r docs/requirements.txt
       # sphinx-apidoc -o ./docs/source ./imsegm ./tests/* --force --follow-links
       cd docs; make html

jobs:
  Py2:
    docker:
      - image: circleci/python:2.7
    steps: &steps
      - checkout
      # INSTALLATION
      - *install_pips
      # BUILDING
      - *build_project
      # TESTING
      - *test_coverage
      # DOCUMENTATION
      - *make_docs

      # ANNOTATION section
      - run: bash handling_annotations/test_annotations.sh
      # SEGMENTATION section
      - run: bash experiments_segmentation/test_segmentations.sh
      # CENTER DETECT. section
      - run: bash experiments_ovary_centres/test_ovary_centers.sh
      # REGION GROWING section
      - run: bash experiments_ovary_detect/test_ovary_detect.sh

      # PASSING
      - run:
          name: Finalise
          command: |
            python setup.py install --user
            coverage report && coverage xml -o test-reports/coverage.xml

      - store_test_results:
          path: test-reports
      - store_artifacts:
          path: test-reports

  Py3:
    docker:
      - image: circleci/python:3.6
    steps: *steps

workflows:
  version: 2
  build:
    jobs:
      - Py2
      - Py3