.travis.yml

language: java
git:
    depth: 9999999
jdk:
    - oraclejdk8

env:
    matrix:
    ## shadow runs the shadowJar with some commands for test the uber-jar jar
    - TYPE=shadow
    ## test runs all the unit/integration tests
    - TYPE=test
    ## test the documentation page
    - TYPE=jekyll
    ## test the documentation generation
    - TYPE=docgen
    global:
    # disable gradle daemon
    - GRADLE_OPTS="-Dorg.gradle.daemon=false"
    # test verbosity to minimal
    - TEST_VERBOSITY=minimal
    # speed up testing the documentation with Nokogiri
    - NOKOGIRI_USE_SYSTEM_LIBRARIES=true

# gradle cache
before_cache:
    - rm -f  $HOME/.gradle/caches/modules-2/modules-2.lock
    - rm -fr $HOME/.gradle/caches/*/plugin-resolution/
cache:
    directories:
        - $HOME/.gradle/caches/
        - $HOME/.gradle/wrapper/

install:
    - ./gradlew assemble installDist
    # check also for data integrity (tests and documentation may fail if this is not changed)
    - ./scripts/walkthrough_data_integrity.sh

before_script:
    ## set the branch name for testing hte documentation
    - if [ -z $TRAVIS_PULL_REQUEST_BRANCH ]; then
        BRANCH_NAME=$TRAVIS_BRANCH;
      else
        BRANCH_NAME=$TRAVIS_PULL_REQUEST_BRANCH;
      fi

script:
    - if [[ $TYPE == shadow ]]; then
          ./gradlew shadowJar &&
          java -jar ./build/libs/ReadTools.jar --version &&
          java -jar ./build/libs/ReadTools.jar StandardizeReads --version &&
          java -jar ./build/libs/ReadTools.jar StandardizeReads --verbosity ERROR --input docs/walkthrough/data/legacy.single_index.SE.fq --output ./tmp/test.sam;
      elif [[ $TYPE == test ]]; then
          ./gradlew jacocoTestReport;
      elif [[ $TYPE == jekyll ]]; then
          rvm use 2.5.1 --install --binary --fuzzy &&
          bundle install --gemfile docs/Gemfile &&
          ./scripts/test_documentation.sh ${BRANCH_NAME};
      elif [[ $TYPE == docgen ]]; then
          ./gradlew javadoc readtoolsDoc;
      else
          echo "Test type not recognized $TYPE";
          exit 1;
      fi

after_success:
    - if [[ $TYPE == test ]]; then bash <(curl -s https://codecov.io/bash) -X gcov -X coveragepy; fi