mirror of https://github.com/msberends/AMR.git
191 lines
6.6 KiB
YAML
191 lines
6.6 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) 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 #
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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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# We created this package for both routine data analysis and academic #
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# research and it was publicly released in the hope that it will be #
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# 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:
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# 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
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- 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
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- 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
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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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# ---- TEST
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R-release_test:
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stage: test
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when: always
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allow_failure: false
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script:
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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, install_lintr = TRUE)'
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- Rscript -e 'devtools::test(stop_on_failure = FALSE)'
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cache:
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key: release
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paths:
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- installed_deps/
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R-devel_test:
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stage: test
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when: always
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image: rocker/r-devel
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allow_failure: false
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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, install_pkgdown = TRUE, install_lintr = TRUE)'
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- Rscriptdevel -e 'devtools::test(stop_on_failure = FALSE)'
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cache:
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key: devel
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paths:
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- installed_deps/
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# ---- CHECK
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R-release:
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stage: check
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when: on_success
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allow_failure: true
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script:
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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, install_lintr = 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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- 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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- Rscript -e 'Sys.setenv(NOT_CRAN = "true")'
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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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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: release
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paths:
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- 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
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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:
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- installed_deps/
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# ---- OTHER
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lintr:
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stage: lint
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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
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script:
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# check all syntax with lintr
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- Rscript -e 'lintr::lint_package(exclusions = list("R/aa_helper_functions_dplyr.R"))'
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cache:
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key: release
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paths:
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- installed_deps/
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policy: pull # no uploading after run
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pages:
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stage: website
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allow_failure: true
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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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- mv docs public
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artifacts:
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paths:
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- public
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codecovr:
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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
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script:
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- apt-get install --yes git
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# 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
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- 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:
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key: release
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paths:
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- installed_deps/
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policy: pull # no uploading after run
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