config.yml

# This is a CircleCI configuration that you can add to your Github repository,
# and connect to CircleCI to build a PDF paper! If you don't
# define any custom variables, your paper will be generated and available
# as an artifact. 

# Variables you can customize
# OPENBASES_CONTAINER: is the container that will be used, see default section
# OPENBASES_PYTHON: is the openbases/openbases python container for testing
# OPENBASES_PAPER_ARGS: are any special arguments to pass to the openbases-pdf container
# OPENBASES_VALIDATE_ARGS: additional arguments to pass to openbases (ob-validate)

# The following variables are optional and will give you
# additional deployments / functionality.

# GITHUB_USER
# GITHUB_EMAIL if defined, you can deploy your paper back to Github pages.

# PAPER_VERSION
# will be first 10 characters of commit, or you can define for a custom

################################################################################
# Functions
################################################################################

# Defaults
defaults: &defaults
  docker:
    - image: docker:18.01.0-ce-git
  working_directory: /tmp/src

# Installation
install: &install
    name: Install parallel gzip, gettext, python3, openbases, and jq
    command: |
        apk add --no-cache pigz python3 gettext jq

# Environment
sourceenv: &sourceenv
    name: Source environment variables from the BASH_ENV
    command: source $BASH_ENV 

pdfenv: &pdfenv
    name: Define container and open bases names
    command: |
        # If not set, define OPENBASES_CONTAINER
        if [ ! -n "${OPENBASES_CONTAINER:-}" ]; then
            OPENBASES_CONTAINER="openbases/openbases-pdf"
        fi
        echo "Open Bases builder is ${OPENBASES_CONTAINER}"
        if [ ! -n "${OPENBASES_PYTHON:-}" ]; then
            OPENBASES_PYTHON="openbases/openbases"
        fi
        echo "Open Bases python container is ${OPENBASES_PYTHON}"
        # If not set, define PAPER_VERSION (akin to commit version)
        if [ ! -n "${PAPER_VERSION:-}" ]; then
            PAPER_VERSION=$(echo "${CIRCLE_SHA1}" | cut -c1-10)
        fi
        # export to bash environment
        echo "export OPENBASES_CONTAINER=${OPENBASES_CONTAINER}" >> ${BASH_ENV}
        echo "export OPENBASES_PYTHON=${OPENBASES_PYTHON}" >> ${BASH_ENV}
        echo "export PAPER_VERSION=${PAPER_VERSION}" >> ${BASH_ENV}
        cat ${BASH_ENV}

githubsetup: &githubsetup
    name: Prepare Github account credentials
    command: |
        # Only proceed if we minimally have a Github email
        if [[ -n "${GITHUB_EMAIL:-}" ]];
            then
                echo "Preparing Github account credentials"
                git config --global user.email $GITHUB_EMAIL
                # If username is defined, use it (otherwuse use circle project)
                if [[ -n "${GITHUB_USER:-}" ]];
                    then
                    git config --global user.name $GITHUB_USER
                else
                    git config --global user.name $CIRCLE_PROJECT_USERNAME
                fi
        fi


test: &test
    name: use openbases/openbases python docker container to test the paper
    command: |
        source ${BASH_ENV}
        cd /tmp/src
        echo "1. Starting OpenBases Python Container!"
        echo "docker run --name openbases --entrypoint bash -dt ${OPENBASES_PYTHON}"
        docker run --name openbases --entrypoint bash -dt "${OPENBASES_PYTHON}"
        echo "2. Copying paper stuffs for Open Bases PDF..."
        echo "docker cp ./paper/. openbases:/data/"
        docker cp ./paper/. openbases:/data/
        echo "3. Validating paper and bibliography"
        echo "docker exec openbases ob-validate paper --infile /data/paper.md"
        docker exec openbases ob-validate paper --infile /data/paper.md "${OPENBASES_VALIDATE_ARGS}"
        echo "4. Stopping openbases validator..."
        docker stop openbases

pdf: &pdf
    name: use openbases/openbases-pdf docker container to generate pdf
    command: |
        source ${BASH_ENV}
        cd /tmp/src
        echo "1. Starting OpenBases PDF Builder bot!"
        echo "docker run --name openbases-pdf  --entrypoint bash -dt ${OPENBASES_CONTAINER}"
        docker run --name openbases-pdf  --entrypoint bash -dt "${OPENBASES_CONTAINER}"
        echo "2. Getting JOSS logo..."
        wget $(docker run openbases/openbases icons --regexp joss) -O ./paper/logo.png
        echo "3. Copying paper stuffs for Open Bases PDF..."
        echo "docker cp ./paper/. openbases-pdf:/data/"
        docker cp ./paper/. openbases-pdf:/data/
        echo "4. Go Robot Go, generate the PDF!"
        echo "docker exec openbases-pdf /bin/bash /code/entrypoint.sh pdf"
        docker exec openbases-pdf /bin/bash /code/entrypoint.sh pdf /data/paper.md "${OPENBASES_PAPER_ARGS}"
        echo "5. Obtaining finished paper.pdf"
        mkdir -p /tmp/paper
        echo "docker cp openbases-pdf:/data/. /tmp/paper"
        docker cp openbases-pdf:/data/. /tmp/paper/
        echo "6. Creating archive."
        echo "tar czf paper.tar.gz /tmp/paper"
        tar czf paper.tar.gz /tmp/paper
        mv paper.tar.gz /tmp/paper
        echo "7. Stopping openbases-pdf..."
        docker stop openbases-pdf
        echo "Contents of /tmp"
        ls /tmp
        echo "Contents of /tmp/paper"
        ls /tmp/paper

################################################################################
# Jobs
################################################################################


version: 2
jobs:
  setup:
    <<: *defaults
    steps:
      - run: *pdfenv
      - run: *install
      - run: *githubsetup

  build:
    <<: *defaults
    steps:
      - run: *install
      - setup_remote_docker
      - checkout
      - run: *pdfenv
      - run: *test
      - run: *pdf
      - persist_to_workspace:
          root: /tmp
          paths:
            - src
            - paper

  manifest:
    <<: *defaults
    steps:
      - attach_workspace:
          at: /tmp
      - run: *pdfenv
      - run: *githubsetup
      - run: *install
      - run:
          name: Generate Paper Manifest
          no_output_timeout: 40m
          command: |
            source ${BASH_ENV}
            ls /tmp
            ls /tmp/paper
            mkdir -p ${HOME}/.ssh
            if [[ -n "${GITHUB_EMAIL:-}" ]];
                then
                    echo "=== Deploying paper to Github Pages ==="
                    echo "1. Checking out Github pages branch"
                    ssh-keyscan -H github.com >> ~/.ssh/known_hosts
                    git clone "git@github.com:${CIRCLE_PROJECT_USERNAME}/${CIRCLE_PROJECT_REPONAME}.git" out
                    cd out
                    # either checkout github pages, or create orphan
                    git checkout gh-pages || git checkout --orphan gh-pages
                    # Save all previous tags, so we don't pull and re-generate
                    mkdir -p ../out-old
                    for ext in tar.gz pdf
                        do
                        if /bin/bash -c "ls *.${ext}" 1> /dev/null 2>&1; then
                                /bin/bash -c "cp *.${ext} ../out-old/" 
                        fi
                    done                    
                    git rm -rf .
                    # ensure that github pages are ignored
                    mkdir -p .circleci && cp -a ../.circleci/. .circleci/.
                    # Copy back previous files
                    for ext in tar.gz pdf
                        do
                           if /bin/bash -c "ls ../out-old/*.${ext}" 1> /dev/null 2>&1; then
                               /bin/bash -c "cp ../out-old/*.${ext} ${PWD}"
                        fi
                    done
                    echo "2. Preparing template..."
                    cp .circleci/template.html template.html
                    cp -R .circleci/assets/ ${PWD}
                    # replace container name in index.html
                    envsubst < template.html > index.html
                    echo "3. Generating paper and archive for latest..."

                    # Need to keep latest also as tag
                    cp /tmp/paper/paper.pdf paper-latest.pdf
                    cp /tmp/paper/paper.tar.gz paper-latest.tar.gz
                    cp /tmp/paper/paper.pdf "paper-${PAPER_VERSION}.pdf"
                    cp /tmp/paper/paper.tar.gz paper-latest.tar.gz

                    git add -A;
                    git commit -m "Automated deployment to GitHub Pages ${CIRCLE_SHA1}" --allow-empty
                    git push origin gh-pages
            else
                echo "GITHUB_EMAIL not set, skipping manifest deploy to Github pages"
            fi


################################################################################
# Workflows
################################################################################


workflows:
  version: 2
  build_deploy:
    jobs:
      - build:
          filters:
            branches:
              ignore: 
                - gh-pages
                - docs/*
            tags:
              ignore: 
                - docs/*
              only: /.*/

      # Push the manifest back to Github pages
      - manifest:
          requires:
            - build
          filters:
            branches:
              only: master
            tags:
              only: /.*/