.gitlab-ci.yml

# helpful Links:
# https://docs.gitlab.com/ee/ci/variables/predefined_variables.html
# https://www.youtube.com/watch?v=7I6tHw68DMQ

stages:
  - test

test:
  image: $CI_REGISTRY_IMAGE:24032023
  stage: test
  tags:
    - envinf2
  variables:
    RETICULATE_MINICONDA_PATH: "/root/.local/share/r-miniconda/"
    RETICULATE_PYTHON_ENV: "/root/.local/share/r-miniconda/envs/r-reticulate/"
    RENV_CONFIG_EXTERNAL_LIBRARIES: "/usr/local/lib/R/library"
    RENV_PATHS_CACHE: "$CI_PROJECT_DIR/cache"
    RENV_PATHS_LIBRARY: "$CI_PROJECT_DIR/renv/library"
  before_script:
    - R -e "if (!requireNamespace('renv', quietly = TRUE)) install.packages('renv')"
    #- R -e 'renv::restore()' does fail while loading Bioconductor packages
    - R -e 'renv::install()'
    - R -e 'renv::install("bioc::rhdf5")'
  script:
    - R CMD build . --no-build-vignettes --no-manual
    - R CMD check $(ls -1t *.tar.gz | head -n 1) --no-build-vignettes --no-manual
  after_script:
    - R -e 'covr::package_coverage(type = c("tests", "examples"), quiet = F)'
  coverage: '/Coverage: \d+\.\d+\%/'
  cache:
    key: "$CI_COMMIT_REF_SLUG"
    untracked: true
    paths:
      - "$RENV_PATHS_CACHE"
      - "$RENV_PATHS_LIBRARY"
  rules:
    - if: '$CI_PIPELINE_SOURCE == "merge_request_event" || $CI_PIPELINE_SOURCE == "web"'
    - if: '$CI_COMMIT_BRANCH == "master"'