AMR/.gitlab-ci.yml

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# ==================================================================== #
# TITLE #
# Antimicrobial Resistance (AMR) Analysis #
# #
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# SOURCE #
# https://gitlab.com/msberends/AMR #
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# #
# LICENCE #
# (c) 2018-2020 Berends MS, Luz CF et al. #
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# #
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# 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. #
# #
# We created this package for both routine data analysis and academic #
# research and it was publicly released in the hope that it will be #
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
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# Visit our website for more info: https://msberends.gitlab.io/AMR. #
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# ==================================================================== #
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# to do a full CRAN check with R-Hub:
# chck <- rhub::check(devtools::build(), platform = rhub::platforms()[!is.na(rhub::platforms()$`cran-name`), 'name'])
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stages:
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- test
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- check
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- lint
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- website
- coverage
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image: rocker/r-base
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before_script:
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- apt-get update -qq --allow-releaseinfo-change
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# install dependencies for packages
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- apt-get install -y wget locales libxml2-dev libssl-dev libcurl4-openssl-dev zlib1g-dev > /dev/null
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# recent pandoc
- wget --quiet https://github.com/jgm/pandoc/releases/download/2.9.2.1/pandoc-2.9.2.1-1-amd64.deb
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- dpkg -i pandoc*.deb
- rm pandoc*.deb
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# 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
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- locale-gen
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# 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
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# set language
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- echo 'LANGUAGE="en_US.utf8"' >> .Renviron
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- echo 'LANG="en_US.utf8"' >> .Renviron
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- echo 'LANGUAGE="en_US.utf8"' > ~/.Renviron
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# ---- TEST
R-release:
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stage: test
when: always
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, install_lintr = TRUE)'
- Rscript -e 'devtools::test(stop_on_failure = FALSE)'
cache:
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key: release
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paths:
- installed_deps/
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R-devel:
stage: test
when: always
image: rocker/r-devel
allow_failure: false
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, install_lintr = TRUE)'
- Rscriptdevel -e 'devtools::test(stop_on_failure = FALSE)'
cache:
key: devel
paths:
- installed_deps/
# ---- CHECK
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R-release:
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stage: check
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when: on_success
allow_failure: true
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script:
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- Rscript -e 'sessionInfo()'
# install missing and outdated packages
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- Rscript -e 'source(".gitlab-ci.R"); gl_update_pkg_all(repos = "https://cran.rstudio.com", quiet = TRUE, install_pkgdown = TRUE, install_lintr = TRUE)'
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# 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)
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- Rscript -e 'Sys.setenv(NOT_CRAN = "true")'
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- R CMD check "${PKG_FILE_NAME}" --no-build-vignettes --no-manual --as-cran
artifacts:
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when: always
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paths:
- '*.Rcheck/*'
expire_in: '1 month'
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cache:
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key: release
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paths:
- installed_deps/
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R-devel:
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stage: check
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when: on_success
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image: rocker/r-devel
allow_failure: true
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script:
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- Rscriptdevel -e 'sessionInfo()'
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# install missing and outdated packages
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- Rscriptdevel -e 'source(".gitlab-ci.R"); gl_update_pkg_all(repos = "https://cran.rstudio.com", quiet = TRUE)'
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# remove vignettes folder and get VignetteBuilder field out of DESCRIPTION file
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- rm -rf vignettes
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- Rscriptdevel -e 'd <- read.dcf("DESCRIPTION"); d[, colnames(d) == "VignetteBuilder"] <- NA; write.dcf(d, "DESCRIPTION")'
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# build package
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- Rdevel CMD build . --no-build-vignettes --no-manual
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- PKG_FILE_NAME=$(ls -1t *.tar.gz | head -n 1)
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- Rscript -e 'Sys.setenv(NOT_CRAN = "true")'
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- Rdevel CMD check "${PKG_FILE_NAME}" --no-build-vignettes --no-manual --as-cran
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artifacts:
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when: always
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paths:
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- '*.Rcheck/*'
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expire_in: '1 month'
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cache:
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key: devel
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paths:
- installed_deps/
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# ---- OTHER
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lintr:
stage: lint
allow_failure: true
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when: always
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only:
- premaster
- master
script:
# check all syntax with lintr
- Rscript -e 'lintr::lint_package()'
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cache:
key: release
paths:
- installed_deps/
policy: pull # no uploading after run
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pages:
stage: website
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allow_failure: true
when: always
only:
- master
script:
- mv docs public
artifacts:
paths:
- public
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codecovr:
stage: coverage
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allow_failure: true
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when: always
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only:
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- premaster
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- master
script:
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- apt-get install --yes git
# codecov token is set in https://gitlab.com/msberends/AMR/settings/ci_cd
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# Sys.setenv(NOT_CRAN = 'true'), because otherwise skip_on_cran() will be applied on Covr too, resulting in extremely low coverage percentages
- Rscript -e "Sys.setenv(NOT_CRAN = 'true'); cc <- covr::package_coverage(line_exclusions = list('R/atc_online.R', 'R/mo_history.R', 'R/mo_source.R', 'R/resistance_predict.R')); covr::codecov(coverage = cc, token = '$codecov'); cat('Code coverage:', covr::percent_coverage(cc))"
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coverage: '/Code coverage: \d+\.\d+/'
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cache:
key: release
paths:
- installed_deps/
policy: pull # no uploading after run