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AMR/.gitlab-ci.yml

142 lines
5.4 KiB
YAML

# ==================================================================== #
# TITLE #
# Antimicrobial Resistance (AMR) Analysis #
# #
# SOURCE #
# https://gitlab.com/msberends/AMR #
# #
# LICENCE #
# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
# #
# This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the #
# GNU General Public License version 2.0 (GNU GPL-2), as published by #
# the Free Software Foundation. #
# #
# This R package was created for academic research and was publicly #
# released in the hope that it will be useful, but it comes WITHOUT #
# ANY WARRANTY OR LIABILITY. #
# Visit our website for more info: https://msberends.gitlab.io/AMR. #
# ==================================================================== #
# to check with R-Hub:
# rhub::check_for_cran(devtools::build(args = c('--no-build-vignettes')))
stages:
- build
- test
- deploy
image: rocker/r-base
before_script:
- apt-get update -qq
# install dependencies for packages
- apt-get install -y wget locales libxml2-dev libssl-dev libcurl4-openssl-dev zlib1g-dev > /dev/null
# recent pandoc
- wget --quiet https://github.com/jgm/pandoc/releases/download/2.7.2/pandoc-2.7.2-1-amd64.deb
- dpkg -i pandoc*.deb
- rm pandoc*.deb
# set R system language
- echo "LC_ALL=en_US.UTF-8" >> /etc/environment
- echo "en_US.UTF-8 UTF-8" >> /etc/locale.gen
- echo "LANG=en_US.UTF-8" > /etc/locale.conf
- locale-gen
# cache R packages
- mkdir -p installed_deps
- echo 'R_LIBS="installed_deps"' > .Renviron
- echo 'R_LIBS_USER="installed_deps"' >> .Renviron
- echo 'R_LIBS_SITE="installed_deps"' >> .Renviron
# set language
- echo 'LANGUAGE="en_US.utf8"' >> .Renviron
- echo 'LANG="en_US.utf8"' >> .Renviron
- echo 'LANGUAGE="en_US.utf8"' > ~/.Renviron
R-release:
stage: build
allow_failure: false
script:
- Rscript -e 'sessionInfo()'
# install missing and outdated packages
- Rscript -e 'source(".gitlab-ci.R"); gl_update_pkg_all(repos = "https://cran.rstudio.com", quiet = TRUE, install_pkgdown = TRUE)'
# remove vignettes folder and get VignetteBuilder field out of DESCRIPTION file
- rm -rf vignettes
- Rscript -e 'd <- read.dcf("DESCRIPTION"); d[, colnames(d) == "VignetteBuilder"] <- NA; write.dcf(d, "DESCRIPTION")'
# build package
- R CMD build . --no-build-vignettes --no-manual
- PKG_FILE_NAME=$(ls -1t *.tar.gz | head -n 1)
- R CMD check "${PKG_FILE_NAME}" --no-build-vignettes --no-manual --as-cran
artifacts:
when: always
paths:
- '*.Rcheck/*'
expire_in: '1 month'
cache:
key: r350
paths:
- installed_deps/
R-devel:
stage: build
image: rocker/r-devel
allow_failure: true
script:
- Rscriptdevel -e 'sessionInfo()'
# install missing and outdated packages
- Rscriptdevel -e 'source(".gitlab-ci.R"); gl_update_pkg_all(repos = "https://cran.rstudio.com", quiet = TRUE, install_pkgdown = TRUE)'
# remove vignettes folder and get VignetteBuilder field out of DESCRIPTION file
- rm -rf vignettes
- Rscriptdevel -e 'd <- read.dcf("DESCRIPTION"); d[, colnames(d) == "VignetteBuilder"] <- NA; write.dcf(d, "DESCRIPTION")'
# build package
- Rdevel CMD build . --no-build-vignettes --no-manual
- PKG_FILE_NAME=$(ls -1t *.tar.gz | head -n 1)
- Rdevel CMD check "${PKG_FILE_NAME}" --no-build-vignettes --no-manual --as-cran
artifacts:
when: always
paths:
- '*.Rcheck/*'
expire_in: '1 month'
cache:
key: r360
paths:
- installed_deps/
coverage:
stage: test
allow_failure: true
when: on_success
cache:
key: r350
paths:
- installed_deps/
policy: pull # no uploading after run
only:
- premaster
- master
script:
- apt-get install --yes git
# install missing and outdated packages
- Rscript -e 'source(".gitlab-ci.R"); gl_update_pkg_all(repos = "https://cran.rstudio.com", quiet = TRUE, install_pkgdown = TRUE)'
# codecov token is set in https://gitlab.com/msberends/AMR/settings/ci_cd
- Rscript -e "cc <- covr::package_coverage(); covr::codecov(coverage = cc, token = '$codecov', exclusions = c('R/atc_online.R', 'R/mo_source.R')); cat('Code coverage:', covr::percent_coverage(cc))"
coverage: '/Code coverage: \d+\.\d+/'
pages:
stage: deploy
when: always
#cache:
# key: "$CI_COMMIT_REF_SLUG"
# paths:
# - installed_deps/
only:
- master
script:
- mv docs public
# install missing and outdated packages
#- Rscript -e 'source(".gitlab-ci.R"); gl_update_pkg_all(repos = "https://cran.rstudio.com", quiet = TRUE, install_pkgdown = TRUE)'
#- Rscript -e "devtools::install(build = TRUE, upgrade = FALSE)"
#- R -e "pkgdown::build_site(examples = FALSE, lazy = TRUE, override = list(destination = 'public'))"
artifacts:
paths:
- public