.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-benchmarks

test:
  image: $CI_REGISTRY_IMAGE:09092022
  stage: test
  tags:
    - envinf2
  variables:
    R_LIBS_USER: "$CI_PROJECT_DIR/ci/lib/"
    RETICULATE_MINICONDA_PATH: "/root/.local/share/r-miniconda/" #default path
    RETICULATE_PYTHON_ENV: "/root/.local/share/r-miniconda/envs/r-reticulate/"
  script:
    - if [ ! -d "$R_LIBS_USER" ]; then mkdir -p "$R_LIBS_USER"; fi
    - R -e 'withr::with_libpaths(new = Sys.getenv("R_LIBS_USER"), devtools::install_deps(dependencies = T))'
    # checks if the packages from the Imports, Suggests, LinkinTo field
    # are already installed in the cache
    - R -e '.libPaths(new = Sys.getenv("R_LIBS_USER"))'
    - R -e 'withr::with_libpaths(new = Sys.getenv("R_LIBS_USER"), {install.packages("BiocManager"); BiocManager::install("rhdf5")})'
    # Build and Check r2ogs6
    - 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:
      - "$R_LIBS_USER"
  rules:
    - if: '$CI_PIPELINE_SOURCE == "merge_request_event" || $CI_PIPELINE_SOURCE == "web"'
    - if: '$CI_COMMIT_BRANCH == "master"'

benchmark:ref:
  stage: test-benchmarks
  tags:
    - envinf3-shell
  variables:
    DOCKER_TAG: "$CI_PROJECT_NAME-$CI_COMMIT_BRANCH-ref-$OGS_VERSION"
    OGS_VERSION: "6.4.1"
  rules:
    - if: '$CI_PIPELINE_SOURCE == "web"'
    - when: on_success
  script:
    - docker login -u $CI_REGISTRY_USER -p $CI_REGISTRY_PASSWORD $CI_REGISTRY
    # in case remove old container
    - docker ps -q --filter name=$DOCKER_TAG | grep -q . && docker rm $DOCKER_TAG -f
    # create and start container
    - docker container create --privileged -e OGS_VERSION=$OGS_VERSION --env-file $CI_PROJECT_DIR/ci/env.list --name $DOCKER_TAG $CI_REGISTRY_IMAGE:09092022
    - docker container start $DOCKER_TAG
    # configure R and start bm-script
    - docker cp $CI_PROJECT_DIR $DOCKER_TAG:/root/r2ogs6
    - docker exec $DOCKER_TAG bash -c 'if [ ! -d "$R_LIBS_USER" ]; then mkdir -p "$R_LIBS_USER"; fi'
    - docker exec $DOCKER_TAG bash -c 'echo $R_LIBS_USER && ls $R_LIBS_USER'
    - docker exec $DOCKER_TAG bash -c 'cd /root/r2ogs6 && R -e "devtools::install_deps(dependencies = T)"'
    - docker exec $DOCKER_TAG bash -c 'cd /root/r2ogs6 && R -e "install.packages(\"BiocManager\"); BiocManager::install(\"rhdf5\")"'
    - docker exec $DOCKER_TAG bash -c 'cd /root/r2ogs6 && Rscript ci/test_bm_script.R "$OGS_VERSION" "ref"'
    - docker exec $DOCKER_TAG bash -c 'cd /root/r2ogs6 && Rscript ci/test_bm_script.R "$OGS_VERSION" "r2ogs6"'
    - docker exec $DOCKER_TAG bash -c 'cd /root/r2ogs6 && Rscript ci/test_bm_script.R "$OGS_VERSION" "test"'
  after_script:
    - docker container rm $DOCKER_TAG -f