mirror of https://github.com/msberends/AMR.git
88 lines
3.4 KiB
YAML
88 lines
3.4 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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# from https://stackoverflow.com/questions/51866926
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# and https://github.com/jangorecki/r.gitlab.ci
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# and https://docs.gitlab.com/ce/ci/yaml/README.html
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# how the Docker+R images work: https://hub.docker.com/r/rocker/r-ver/
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stages:
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- build
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- test
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- deploy
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image: debian:buster-slim
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before_script:
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- apt-get update
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# install dependencies for package
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- apt-get -y install libxml2-dev libssl-dev libcurl4-openssl-dev zlib1g-dev pandoc r-base
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- Rscript -e 'install.packages(c("devtools", "rlang"), repos = "https://cran.rstudio.com")'
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- Rscript -e 'devtools::install_dev_deps(repos = "https://cran.rstudio.com")'
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cache:
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key: "$CI_COMMIT_REF_SLUG"
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paths:
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- /usr/local/lib/R/*
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- /usr/lib/R/*
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R 3:
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stage: build
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allow_failure: true
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script:
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# remove vignettes folder and get VignetteBuilder field out of DESCRIPTION file
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- rm -rf vignettes
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- Rscript -e 'd <- read.dcf("DESCRIPTION"); d[, colnames(d) == "VignetteBuilder"] <- NA; write.dcf(d, "DESCRIPTION")'
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# build package
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- R CMD build . --no-build-vignettes --no-manual
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- PKG_FILE_NAME=$(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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- Rscript -e 'print(.libPaths())'
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artifacts:
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paths:
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- '*.Rcheck/*'
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name: 'Rcheck log'
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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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- 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 "install.packages('pkgdown', repos = 'https://cran.rstudio.com')"
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- Rscript -e "devtools::install(build = TRUE, upgrade = FALSE)"
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- R -e "pkgdown::build_site(examples = FALSE, override = list(destination = 'public'))"
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artifacts:
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paths:
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- public
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