mirror of https://github.com/msberends/AMR.git
74 lines
3.1 KiB
YAML
74 lines
3.1 KiB
YAML
# ==================================================================== #
|
|
# TITLE #
|
|
# Antimicrobial Resistance (AMR) Analysis #
|
|
# #
|
|
# AUTHORS #
|
|
# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
|
|
# #
|
|
# LICENCE #
|
|
# This package is free software; you can redistribute it and/or modify #
|
|
# it under the terms of the GNU General Public License version 2.0, #
|
|
# as published by the Free Software Foundation. #
|
|
# #
|
|
# This R package is distributed in the hope that it will be useful, #
|
|
# but WITHOUT ANY WARRANTY; without even the implied warranty of #
|
|
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
|
|
# GNU General Public License version 2.0 for more details. #
|
|
# ==================================================================== #
|
|
|
|
# from https://stackoverflow.com/questions/51866926
|
|
# and https://github.com/jangorecki/r.gitlab.ci
|
|
# and https://docs.gitlab.com/ce/ci/yaml/README.html
|
|
# how the Docker+R images work: https://hub.docker.com/r/rocker/r-ver/
|
|
|
|
stages:
|
|
- build
|
|
- deploy
|
|
|
|
image: debian:buster-slim
|
|
|
|
before_script:
|
|
- apt-get update
|
|
# install dependencies for package
|
|
- apt-get -y install libxml2-dev libssl-dev libcurl4-openssl-dev zlib1g-dev pandoc r-base
|
|
- Rscript -e 'install.packages(c("devtools", "rlang"), repos = "https://cran.rstudio.com")'
|
|
- Rscript -e 'devtools::install_dev_deps(repos = "https://cran.rstudio.com")'
|
|
|
|
R 3:
|
|
stage: build
|
|
allow_failure: true
|
|
script:
|
|
# 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
|
|
# code coverage
|
|
- apt-get install --yes git
|
|
- Rscript -e 'cc <- covr::package_coverage(); covr::codecov(coverage = cc, token = "50ffa0aa-fee0-4f8b-a11d-8c7edc6d32ca"); cat("Code coverage:", covr::percent_coverage(cc))'
|
|
coverage: '/Code coverage: \d+\.\d+/'
|
|
artifacts:
|
|
paths:
|
|
- '*.Rcheck/*.log'
|
|
- '*.Rcheck/*.out'
|
|
# - '*.Rcheck/*.fail'
|
|
- '*.Rcheck/*.Rout'
|
|
name: 'Rcheck log'
|
|
expire_in: '1 month'
|
|
|
|
pages:
|
|
stage: deploy
|
|
script:
|
|
- Rscript -e "install.packages('pkgdown', repos = 'https://cran.rstudio.com')"
|
|
- Rscript -e "devtools::install(build = TRUE, upgrade = FALSE)"
|
|
# - R -e "pkgdown::build_favicon()"
|
|
- R -e "pkgdown::build_site(examples = FALSE, override = list(destination = 'public'))"
|
|
when: always
|
|
artifacts:
|
|
paths:
|
|
- public
|
|
only:
|
|
- master
|