.gitlab-ci.yml

image: rocker/r-ver:4.4.0

stages:
  - build
  - document
  - check
  - sonar
  - publish
  - deploy

variables:
  APT_DEPS: "git libssl-dev libcurl4-openssl-dev  libcurl4-openssl-dev libssl-dev  libfreetype6-dev libfribidi-dev libharfbuzz-dev git libxml2-dev libfontconfig1-dev libgit2-dev libssl-dev pandoc libicu-dev libz-dev libcurl4-openssl-dev libjpeg-dev libpng-dev libtiff-dev make zlib1g-dev  git libgit2-dev libssl-dev libcurl4-openssl-dev  git  libicu-dev pandoc make  make zlib1g-dev  libssl-dev libcurl4-openssl-dev  pandoc  libssl-dev  libfreetype6-dev libfribidi-dev libharfbuzz-dev libxml2-dev libfontconfig1-dev libssl-dev pandoc libicu-dev libcurl4-openssl-dev libjpeg-dev libpng-dev libtiff-dev make  libfreetype6-dev libfribidi-dev libharfbuzz-dev libfontconfig1-dev libjpeg-dev libpng-dev libtiff-dev  libxml2-dev libicu-dev pandoc make  libxml2-dev libcurl4-openssl-dev libssl-dev  libicu-dev  libfontconfig1-dev libfreetype6-dev  libfreetype6-dev libfribidi-dev libharfbuzz-dev libfontconfig1-dev  git libgit2-dev libssl-dev libcurl4-openssl-dev make  libxml2-dev"
  IMAGE: dockerhub.sbgenomics.com/$CI_PROJECT_NAME
  RENV_PATHS_CACHE: ${CI_PROJECT_DIR}/cache
  RENV_PATHS_LIBRARY: ${CI_PROJECT_DIR}/renv/library
  RENV_CONFIG_REPOS_OVERRIDE: http://cran.r-project.org
  LIBRARY_NAME: examplePackage

cache:
  key: $CI_JOB_NAME
  paths:
    - ${RENV_PATHS_CACHE}
    - ${RENV_PATHS_LIBRARY}

before_script:
  - mkdir -p ${RENV_PATHS_CACHE} ${RENV_PATHS_LIBRARY}
  - apt-get -qq update;
  - apt-get -y install ${APT_DEPS}
  - apt-get install -y nodejs
  - apt-get install -y npm
  - R -e "install.packages(c('remotes', 'devtools', 'covr'), repos = 'http://cran.r-project.org')"
  - R -e "if (!requireNamespace('renv', quietly = TRUE)) remotes::install_version('renv', version = '1.0.7')"
  - R -e "renv::restore(lockfile = 'renv.lock')"

buildbinary:
  stage: build
  script:
    - R -e 'devtools::build(binary = TRUE, vignettes = FALSE)'

documentation:
  stage: document
  script:
    - R -e 'devtools::document()'

lintr:
  stage: check
  script:
    # redirect lintr stdout and stderr to file
    - R -e "install.packages('lintr')"
    - CI="" Rscript -e "lintr::lint_package()" &> lint_output.txt
    # fail if file is not empty
    - if [ -s "lint_output.txt" ]; then exit 1; fi
  artifacts:
    when: on_failure
    paths:
      - lint_output.txt

coverage:
  stage: check
  rules:
    - when: always
  script:
    - Rscript -e "devtools::install(dependencies = FALSE)"
    - Rscript run_cov.R
  artifacts:
    paths:
      - covr_sonarqube.xml

sonar:
  stage: sonar
  dependencies:
     - coverage
  image: emeraldsquad/sonar-scanner:2.2.0
  before_script: []
  script:
    - infinity sonar scanner
  allow_failure: true
  only:
    - merge_requests
    - master
    - develop

pages:
  stage: deploy
  script:
  - apt-get update && apt-get install -y pandoc
  - R -e 'devtools::build(binary = TRUE, vignettes = FALSE)'
  - R -e "install.packages('pkgdown')"
  - R -e "pkgdown::build_site()"
  artifacts:
    paths:
    - public