config.yml

version: 2.1

commands:
  check-for-built-images:
    steps:
      - run:
          name: "Checking for locally built images"
          command: |
            if [[ ! -f cpac-docker-image.tar.gz || ! -f cpac-singularity-image.simg ]]
            then
              circleci step halt
            fi
  set-python-version:
    steps:
      - run:
          name: "Setting Python Version"
          command: |
            pyenv install 3.6.3
            pyenv global 3.6.3
  install-singularity-requirements:
    steps:
      - run:
          name: "Installing Singularity requirements"
          command: |
           sudo apt-get update && sudo apt-get install flawfinder squashfs-tools uuid-dev libuuid1 libffi-dev libssl-dev libssl1.0.0 libarchive-dev libgpgme11-dev libseccomp-dev -y
  set-up-singularity:
    steps:
      - run:
         name: "Setting up Singularity"
         command: |
           cd singularity
           ./autogen.sh
           ./configure --prefix=/usr/local --sysconfdir=/etc
           make
           sudo make install
           cd ..
  build-images:
    steps:
      - run:
          name: "Building Docker image"
          command: |
            docker build -t fcpindi/c-pac:${CIRCLE_BRANCH//\//_} .
            docker save fcpindi/c-pac:${CIRCLE_BRANCH//\//_} | gzip > cpac-docker-image.tar.gz
          no_output_timeout: 5h
          # Persist the specified paths (workspace/echo-output) into the workspace for use in downstream job.
      - run:
          name: "Starting local registry"
          command: docker run -d -p 5000:5000 --restart=always --name registry registry:2
      - install-singularity-requirements
      - run: 
          name: "Cloning Singularity 2.5.2"
          command: git clone -b 2.5.2 https://github.com/sylabs/singularity
      - set-up-singularity
      - run:
          name: "Building Singularity image from Docker image"
          command: |
            docker load < cpac-docker-image.tar.gz
            docker tag fcpindi/c-pac:${CIRCLE_BRANCH//\//_} localhost:5000/fcpindi/c-pac:${CIRCLE_BRANCH//\//_}
            docker push localhost:5000/fcpindi/c-pac:${CIRCLE_BRANCH//\//_}
            SINGULARITY_NOHTTPS=1 singularity build C-PAC-CI.simg docker://localhost:5000/fcpindi/c-pac:${CIRCLE_BRANCH//\//_}
          no_output_timeout: 5h
      - store_artifacts:
          path: cpac-docker-image.tar.gz
      - store_artifacts:
          path: C-PAC-CI.simg
          destination: cpac-singularity-image.simg
      - persist_to_workspace:
          # Must be an absolute path, or relative path from working_directory. This is a directory on the container which is
          # taken to be the root directory of the workspace.
          root: /home/circleci/
          # Must be relative path from root
          paths: project
  configure-git-user:
    steps:
      - add_ssh_keys:
          fingerprints:
            - "12:bc:f2:e4:31:cc:72:54:54:bc:f5:5b:89:e6:d8:ee"
      - run:
          name: "Configuring git user"
          command: |
            git config --global user.email "${CIRCLE_USERNAME}@users.noreply.github.com"
            git config --global user.name "${CIRCLE_USERNAME} @ CircleCI"

jobs:
  pytest-docker:
    machine: true
    steps:
      - attach_workspace:
          # Must be absolute path or relative path from working_directory
          at: /home/circleci/
      - check-for-built-images
      - set-python-version
      - run:
          name: Getting Sample BIDS Data
          command: git clone https://github.com/bids-standard/bids-examples.git
      - run:
          name: Running pytest on Docker image
          command: |
            docker load < cpac-docker-image.tar.gz
            docker run -dit -P -v /home/circleci/project/test-results:/code/test-results -v /home/circleci/project/htmlcov:/code/htmlcov --entrypoint=/bin/bash --name docker_test fcpindi/c-pac:${CIRCLE_BRANCH//\//_}
            docker exec docker_test /bin/bash ./code/dev/circleci_data/test_in_image.sh
      - store_test_results:
          path: test-results
      - store_artifacts:
          path: test-results
      - store_artifacts:
          path: htmlcov
          no_output_timeout: 5h
  pytest-singularity:
    machine: true
    steps:
      - attach_workspace:
          # Must be absolute path or relative path from working_directory
          at: /home/circleci/
      - check-for-built-images
      - set-python-version
      - install-singularity-requirements
      - set-up-singularity
      - run:
          name: Testing Singularity installation
          command: |
            pip install -r dev/circleci_data/requirements.txt
            coverage run -m pytest --junitxml=test-results/junit.xml --continue-on-collection-errors  dev/circleci_data/test_install.py
  build:
    machine: true
    steps:
      - checkout
      - set-python-version
      - configure-git-user
      - run:
          name: "Checking if version needs updated"
          # update version if version needs updated, otherwise just move on
          command: |
            if [[ ! $(git log -1 --pretty=%B) == *"Update version to"* ]]
            then
              cd $HOME/project/CPAC
              VERSION=$(python -c "from info import __version__; print(__version__)")
              cd ..
              echo "v${VERSION}" > version
              find ./CPAC/resources/configs -name "*.yml" -exec sed -i -r "s/^(# [Vv]ersion ).*$/# Version ${VERSION}/g" {} \;
              git add version CPAC/resources/configs
              if [[ ! -z $(git diff origin/${CIRCLE_BRANCH}) ]]
              then
                git commit -m ":bookmark: Update version to ${VERSION}"
                git push origin HEAD:${CIRCLE_BRANCH} || true
                circleci step halt
              fi
              cd ..
            fi
      - build-images

workflows:
  version: 2
  build-and-test:
    jobs:
      - build
      - pytest-docker:
          requires:
            - build
      - pytest-singularity:
          requires:
            - build