AMR/.gitlab-ci.yml

# ==================================================================== #
# TITLE                                                                #
# Antimicrobial Resistance (AMR) Analysis                              #
#                                                                      #
# AUTHORS                                                              #
# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl)           #
#                                                                      #
# LICENCE                                                              #
# This package is free software; you can redistribute it and/or modify #
# it under the terms of the GNU General Public License version 2.0,    #
# as published by the Free Software Foundation.                        #
#                                                                      #
# This R package is distributed in the hope that it will be useful,    #
# but WITHOUT ANY WARRANTY; without even the implied warranty of       #
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the        #
# GNU General Public License version 2.0 for more details.             #
# ==================================================================== #

# https://r-posts.com/gitlab-ci-for-r-package-development/

image: rocker/r-base
before_script:
  - apt-get update
  # install dependencies for package
  - apt-get -y install libxml2-dev libssl-dev libcurl4-openssl-dev zlib1g-dev

stages:
  - setup
  - test
  - deploy

cache:
  # Ommit key to use the same cache across all pipelines and branches
  key: "$CI_COMMIT_REF_SLUG"
  paths:
    - packrat/lib/

setup:
  stage: setup
  script:
    - R -e 'source("ci.R"); ci_setup()'

check:
  stage: test
  dependencies:
    - setup
  when: on_success
  script:
    - R -e 'source("ci.R"); ci_check()'

coverage:
  stage: test
  dependencies:
    - setup
  when: on_success
  only:
    - master
  script:
    - R -e 'source("ci.R"); ci_coverage()'
  coverage: '/Code coverage: \d+\.\d+/'

pages:
  stage: deploy
  dependencies:
    - setup
  when: always
  only:
    - master
  script:
    - R -e 'source("ci.R"); ci_pages()'
  artifacts:
    paths:
      - public