Merge remote-tracking branch 'upstream/release_18.05' into release_18.09

# Python CircleCI 2.0 configuration file

version: 2

variables:

  restore_repo_cache: &restore_repo_cache

    restore_cache:

      keys:

        - v1-repo-{{ .Environment.CIRCLE_SHA1 }}

  restore_yarn_cache: &restore_yarn_cache

    restore_cache:

      keys:

        - v1-repo-{{ .Environment.CIRCLE_SHA1 }}

        - yarn-packages-{{ checksum "client/yarn.lock" }}

  save_yarn_cache: &save_yarn_cache

    save_cache:

      key: yarn-packages-{{ checksum "client/yarn.lock" }}

      paths:

        - ~/.cache/yarn

  install_tox: &install_tox

    run: sudo pip install tox

  set_workdir: &set_workdir

    working_directory: ~/repo

  requires_get_code: &requires_get_code

    requires:

      - get_code

jobs:

  get_code:

    docker:

      - image: circleci/python:2.7.15

    <<: *set_workdir

    steps:

      # Replace standard code checkout with shallow clone to speed things up.

      - run:

          name: Checkout code

          command: |-

              # Add github.com to known hosts

              mkdir -p ~/.ssh

              echo 'github.com ssh-rsa AAAAB3NzaC1yc2EAAAABIwAAAQEAq2A7hRGmdnm9tUDbO9IDSwBK6TbQa+PXYPCPy6rbTrTtw7PHkccKrpp0yVhp5HdEIcKr6pLlVDBfOLX9QUsyCOV0wzfjIJNlGEYsdlLJizHhbn2mUjvSAHQqZETYP81eFzLQNnPHt4EVVUh7VfDESU84KezmD5QlWpXLmvU31/yMf+Se8xhHTvKSCZIFImWwoG6mbUoWf9nzpIoaSjB+weqqUUmpaaasXVal72J+UX2B+2RPW3RcT0eOzQgqlJL3RKrTJvdsjE3JEAvGq3lGHSZXy28G3skua2SmVi/w4yCE6gbODqnTWlg7+wC604ydGXA8VJiS5ap43JXiUFFAaQ==

              ' >> ~/.ssh/known_hosts

              # Add the user ssh key and set correct perms

              (umask 077; touch ~/.ssh/id_rsa)

              chmod 0600 ~/.ssh/id_rsa

              echo "$CHECKOUT_KEY" > ~/.ssh/id_rsa

              # Use git+ssh instead of https

              git config --global url."ssh://git@github.com".insteadOf "https://github.com" || true

              git config --global gc.auto 0 || true

              # Shallow clone

              git clone --depth=1 "${CIRCLE_REPOSITORY_URL}" .

              if [[ -n "${CIRCLE_PR_NUMBER}" ]]; then

                  # Update PR refs for testing.

                  FETCH_REFS="${FETCH_REFS} +refs/pull/${CIRCLE_PR_NUMBER}/head:pr/${CIRCLE_PR_NUMBER}/head"

                  FETCH_REFS="${FETCH_REFS} +refs/pull/${CIRCLE_PR_NUMBER}/merge:pr/${CIRCLE_PR_NUMBER}/merge"

                  # Retrieve the refs

                  git fetch --force origin ${FETCH_REFS}

                  # Checkout PR merge ref.

                  git checkout -f "pr/${CIRCLE_PR_NUMBER}/merge"

                  # Test for *some* merge conflicts.

                  git branch --merged | grep "pr/${CIRCLE_PR_NUMBER}/head" > /dev/null

              else

                  if [ -n "$CIRCLE_TAG" ]; then

                      git fetch --depth=1 --force origin "refs/tags/${CIRCLE_TAG}"

                  else

                      git fetch --depth=1 --force origin "$CIRCLE_BRANCH:remotes/origin/$CIRCLE_BRANCH"

                  fi

                  if [ -n "$CIRCLE_TAG" ]; then

                      git reset --hard "$CIRCLE_SHA1"

                      git checkout "$CIRCLE_TAG"

                  elif [ -n "$CIRCLE_BRANCH" ]; then

                      git reset --hard "$CIRCLE_SHA1"

                      git checkout -B "$CIRCLE_BRANCH"

                  fi

                  git reset --hard "${CIRCLE_SHA1}"

              fi

      - save_cache:

          key: v1-repo-{{ .Environment.CIRCLE_SHA1 }}

          paths:

            - ~/repo

  py27_lint:

    docker:

      - image: circleci/python:2.7.15

    <<: *set_workdir

    steps:

      - *restore_repo_cache

      - *install_tox

      - run: tox -e py27-lint

  py27_unit:

    docker:

      - image: circleci/python:2.7.15

    <<: *set_workdir

    steps:

      - *restore_repo_cache

      - *install_tox

      - run: tox -e py27-unit

  py27_docstring:

    docker:

      - image: circleci/python:2.7.15

    <<: *set_workdir

    steps:

      - *restore_repo_cache

      - *install_tox

      - run: tox -e py27-lint_docstring_include_list

  py27_first_startup:

    docker:

      - image: circleci/python:2.7.15

    <<: *set_workdir

    steps:

      - *restore_repo_cache

      - run: sh scripts/common_startup.sh

      - run: wget -q https://github.com/jmchilton/galaxy-downloads/raw/master/db_gx_rev_0127.sqlite

      - run: mv db_gx_rev_0127.sqlite database/universe.sqlite

      - run: sh manage_db.sh -c ./config/galaxy.yml.sample upgrade

      - *install_tox

      - run: tox -e py27-first_startup

  py35_lint:

    docker:

      - image: circleci/python:3.5

    <<: *set_workdir

    steps:

      - *restore_repo_cache

      - *install_tox

      - run: tox -e py35-lint

  py35_unit:

    docker:

      - image: circleci/python:3.5

    <<: *set_workdir

    steps:

      - *restore_repo_cache

      - *install_tox

      - run: tox -e py35-unit

  py35_first_startup:

    docker:

      - image: circleci/python:3.5

    <<: *set_workdir

    steps:

      - *restore_repo_cache

      - *install_tox

      - run: sudo apt-get update

      # For uwsgi

      - run: sudo apt-get install -y libpython3.5-dev

      - run: tox -e py35-first_startup

  validate_test_tools:

    docker:

      - image: circleci/python:2.7.15

    <<: *set_workdir

    steps:

      - *restore_repo_cache

      - run: sudo apt-get update

      - run: sudo apt-get install -y libxml2-utils

      - *install_tox

      - run: tox -e validate_test_tools

  check_py3_compatibility:

    docker:

      - image: circleci/python:2.7.15

    <<: *set_workdir

    steps:

      - *restore_repo_cache

      - run: sudo apt-get update

      - run: sudo apt-get install -y ack-grep

      - *install_tox

      - run: tox -e check_py3_compatibility

  js_unit:

    docker:

      - image: circleci/node:9-browsers

    <<: *set_workdir

    steps:

      - *restore_yarn_cache

      - run: cd client && yarn install --frozen-lockfile

      - *save_yarn_cache

      - run: cd client && yarn run build

      - run: cd client && yarn run test

workflows:

  version: 2

  get_code_and_test:

    jobs:

      - get_code

      - py27_lint:

          <<: *requires_get_code

      - py27_unit:

          <<: *requires_get_code

      - py27_first_startup:

          <<: *requires_get_code

      - py27_docstring:

          <<: *requires_get_code

      - py35_lint:

          <<: *requires_get_code

      - py35_unit:

          <<: *requires_get_code

      - py35_first_startup:

          <<: *requires_get_code

      - validate_test_tools:

          <<: *requires_get_code

      - check_py3_compatibility:

          <<: *requires_get_code

      - js_unit:

          <<: *requires_get_code