mirror of https://github.com/msberends/AMR.git
103 lines
3.9 KiB
YAML
103 lines
3.9 KiB
YAML
# ==================================================================== #
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# TITLE #
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# Antimicrobial Resistance (AMR) Analysis #
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# #
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# SOURCE #
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# https://gitlab.com/msberends/AMR #
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# #
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# LICENCE #
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# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
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# #
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# This R package is free software; you can freely use and distribute #
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# it for both personal and commercial purposes under the terms of the #
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# GNU General Public License version 2.0 (GNU GPL-2), as published by #
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# the Free Software Foundation. #
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# #
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# This R package was created for academic research and was publicly #
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# released in the hope that it will be useful, but it comes WITHOUT #
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# ANY WARRANTY OR LIABILITY. #
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# Visit our website for more info: https://msberends.gitab.io/AMR. #
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# ==================================================================== #
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stages:
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- build
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- test
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- deploy
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# debian stretch only contains R 3.3...
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image: debian:buster-slim
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before_script:
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- apt-get update -qq
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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 r-base > /dev/null
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# recent pandoc
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- wget --quiet https://github.com/jgm/pandoc/releases/download/2.6/pandoc-2.6-1-amd64.deb
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- dpkg -i pandoc*.deb
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- rm pandoc*.deb
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# set R system language
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- echo "LC_ALL=en_US.UTF-8" >> /etc/environment
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- echo "en_US.UTF-8 UTF-8" >> /etc/locale.gen
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- echo "LANG=en_US.UTF-8" > /etc/locale.conf
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- locale-gen
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# cache R packages
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- mkdir -p installed_deps
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- echo 'R_LIBS="installed_deps"' > .Renviron
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- echo 'R_LIBS_USER="installed_deps"' >> .Renviron
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- 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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- Rscript -e 'sessionInfo()'
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# 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)'
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cache:
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key: "$CI_COMMIT_REF_SLUG"
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paths:
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- installed_deps/
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R:
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stage: build
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allow_failure: false
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variables:
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WARNINGS_ARE_ERRORS: 1
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script:
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- export WARNINGS_ARE_ERRORS=1
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# remove vignettes folder and get VignetteBuilder field out of DESCRIPTION file
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- rm -rf vignettes
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- Rscript -e 'd <- read.dcf("DESCRIPTION"); d[, colnames(d) == "VignetteBuilder"] <- NA; write.dcf(d, "DESCRIPTION")'
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# build package
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- R CMD build . --no-build-vignettes --no-manual
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- PKG_FILE_NAME=$(ls -1t *.tar.gz | head -n 1)
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- R CMD check "${PKG_FILE_NAME}" --no-build-vignettes --no-manual --as-cran
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artifacts:
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paths:
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- '*.Rcheck/*'
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expire_in: '1 month'
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coverage:
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stage: test
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allow_failure: true
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when: on_success
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only:
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- premaster
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- master
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script:
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- apt-get install --yes git
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- Rscript -e 'cc <- covr::package_coverage(); covr::codecov(coverage = cc, token = "50ffa0aa-fee0-4f8b-a11d-8c7edc6d32ca"); cat("Code coverage:", covr::percent_coverage(cc))'
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coverage: '/Code coverage: \d+\.\d+/'
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pages:
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stage: deploy
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when: always
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only:
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- master
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script:
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- Rscript -e "devtools::install(build = TRUE, upgrade = FALSE)"
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- R -e "pkgdown::build_site(examples = FALSE, lazy = TRUE, override = list(destination = 'public'))"
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artifacts:
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paths:
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- public
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