.gitlab-ci.yml

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

stages:
  - test
  - production

variables:
    # RETICULATE_MINICONDA_PATH: "/root/.local/share/r-miniconda/"
    # RETICULATE_PYTHON_ENV: "/root/.local/share/r-miniconda/envs/r-reticulate/"
    RUN_PYTHON_CONFIG_TESTS: "true"

.before_script_templ: &before_script_templ
  - apt-get update && apt-get upgrade -y
  - apt-get install -y git
  # Packages to build Python and R packages
  - |
    apt-get install -y build-essential libssl-dev zlib1g-dev libbz2-dev \
    libreadline-dev libsqlite3-dev curl libncursesw5-dev xz-utils tk-dev \
    libxml2-dev libxmlsec1-dev libffi-dev liblzma-dev \
    libharfbuzz-dev libfribidi-dev libcurl4-openssl-dev \
    libfreetype6-dev libpng-dev libtiff5-dev libjpeg-dev
  - apt-get install -y python3.10-venv python3-pip

test:
  image: rocker/r-ver:4.4.1
  stage: test
  tags:
    - docker
  variables:
    RENV_CONFIG_EXTERNAL_LIBRARIES: "/usr/local/lib/R/library"
    RENV_PATHS_CACHE: "/root/.cache/R/renv/cache" #"$CI_PROJECT_DIR/cache"
    RENV_PATHS_LIBRARY: "/root/.cache/R/renv/library" #"$CI_PROJECT_DIR/renv/library"
    R_LIBS: "/usr/local/lib/R/site-library:/usr/local/lib/R/library:$RENV_PATHS_LIBRARY"
  before_script:
    - *before_script_templ
    - R -e "install.packages('renv', repos = c(CRAN = 'https://cloud.r-project.org'))"
    - R -e "renv::restore()"
    # Setup python and fix python virtual environment
    - R -e 'reticulate::virtualenv_create(envname="r2ogs6", python="/usr/bin/python3", packages = c("numpy==1.26.4", "vtk==9.3.1"))'
    - echo "RETICULATE_PYTHON=/root/.virtualenvs/r2ogs6/bin/python" > .Renviron
    - R -e 'reticulate::py_config()'
    #- R -e 'renv::status()'
    # - R -e 'renv::install()'
    # - R -e 'renv::install("bioc::rhdf5")'
  script:
    - R -e "devtools::test()"
    - R -e "devtools::check(vignettes=FALSE)"
    # - R CMD build . --no-manual --no-build-vignettes
    # - R CMD check $(ls -1t *.tar.gz | head -n 1) --no-manual --no-build-vignettes
  after_script:
    - R -e "install.packages('covr', repos = c(CRAN = 'https://cloud.r-project.org'))"
    - R -e 'covr::package_coverage(type = c("tests", "examples"), quiet = F)'
  coverage: '/Coverage: \d+\.\d+\%/'
  # Omit cache for now, ci always crashed the second time, dunno why
  # cache:
  #   key: "$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"'

test_install:
  image: rocker/r-ver:4.4.1
  stage: production
  tags:
    - docker
  before_script:
    - *before_script_templ
    - mkdir ../test_r2ogs6 && cd ../test_r2ogs6 && ls . -ahl
  script:
    # Install r2ogs6
    - R -e 'install.packages(c("remotes", "BiocManager"))'
    - R -e "remotes::install_local(path=\"$CI_PROJECT_DIR\", dependencies='Imports', repos=BiocManager::repositories())"
    - R -e 'reticulate::virtualenv_create(envname="r2ogs6", python="/usr/bin/python3", packages = c("numpy==1.26.4", "vtk==9.3.1"))'
    #- R -e 'reticulate::use_virtualenv(virtualenv="r2ogs6")'
    - echo "RETICULATE_PYTHON=/root/.virtualenvs/r2ogs6/bin/python" > .Renviron
    - R -e 'reticulate::py_config()'
    - R -e 'r2ogs6::install_ogs(ogs_version = "6.5.2", envname = "r2ogs6")'
    - R -e 'reticulate::py_module_available("ogs")'
    # Run benchmark
    - |
      R -e '
      library(r2ogs6)
      set_ogs6_bin_path();
      prj_path <- system.file("extdata/benchmarks/flow_no_strain/flow_no_strain.prj", package = "r2ogs6");
      sim_path <- tempdir();
      exit_code <- r2ogs6:::run_benchmark(prj_path=prj_path, sim_path=sim_path);
      assertthat::are_equal(exit_code, 0)
      '
  rules:
    - if: '$CI_PIPELINE_SOURCE == "merge_request_event" || $CI_PIPELINE_SOURCE == "web"'
    - if: '$CI_COMMIT_BRANCH == "master"'