diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index 9180235f..1cd6ad02 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -3,14 +3,14 @@ on: push: branches-ignore: - gh-pages +env: + REGISTRY: ghcr.io + ORG: nbisweden + IMAGE: workshop-r:latest + jobs: rmd-render-job: - strategy: - fail-fast: false - matrix: - config: - - {os: ubuntu-22.04, r: '4.2'} - runs-on: ${{ matrix.config.os }} + runs-on: ubuntu-22.04 steps: - name: Set time zone uses: szenius/set-timezone@v1.0 @@ -18,67 +18,32 @@ jobs: timezoneLinux: "Europe/Stockholm" timezoneMacos: "Europe/Stockholm" timezoneWindows: "W. Europe Standard Time" - - uses: actions/checkout@v3 - - uses: r-lib/actions/setup-r@v2 - with: - r-version: ${{ matrix.config.r }} - - uses: r-lib/actions/setup-pandoc@v2 - - name: Install linux dependencies - run: | - sudo apt-get update - sudo apt-get install libxml2-dev libssl-dev libcurl4-openssl-dev libudunits2-dev libopenblas-base libgdal-dev libfreetype6-dev libpng-dev libtiff5-dev libjpeg-dev libfontconfig1-dev libharfbuzz-dev libfribidi-dev - wget https://dl.google.com/linux/direct/google-chrome-stable_current_amd64.deb - sudo apt install ./google-chrome-stable_current_amd64.deb - rm -rf google-chrome-stable_current_amd64.deb + - name: Checkout + uses: actions/checkout@v2 + - name: Pull image + run: docker pull ${{ env.REGISTRY }}/${{ env.ORG }}/${{ env.IMAGE }} - name: Define variables run: | - echo "path_repo=$(pwd)" >> $GITHUB_ENV - echo "path_export=$(grep -E '^output_dir' _site.yml | sed 's/^output_dir://' | xargs)" >> $GITHUB_ENV - echo "path_export_canvas=$(grep -E '^output_dir' _site.yml | sed 's/^output_dir://' | xargs)-canvas" >> $GITHUB_ENV - echo "repo=$(echo $GITHUB_REPOSITORY | sed 's/.*\///')" >> $GITHUB_ENV - - name: Check R installation and variables + echo "PATH_REPO=$(pwd)" >> $GITHUB_ENV + echo "PATH_EXPORT=$(grep -E '^output_dir' _site.yml | sed 's/^output_dir://' | xargs)" >> $GITHUB_ENV + echo "PATH_EXPORT_CANVAS=$(grep -E '^output_dir' _site.yml | sed 's/^output_dir://' | xargs)-canvas" >> $GITHUB_ENV + echo "REPO=$(basename ${GITHUB_REPOSITORY})" >> $GITHUB_ENV + - name: Check docker and variables run: | - Rscript -e "print('R installation works!')" - echo "Github actor: ${GITHUB_ACTOR}" - echo "Github repository: ${GITHUB_REPOSITORY}" - echo "Github repo: ${repo}" - echo "Path repo: ${path_repo}" - echo "Path export: ${path_export}" - echo "Path export canvas: ${path_export_canvas}" + docker run --rm -u $(id -u ${USER}):$(id -g ${USER}) -v ${PWD}:/rmd ${{ env.REGISTRY }}/${{ env.ORG }}/${{ env.IMAGE }} Rscript -e "print('R in docker works!')" + echo "GITHUB_ACTOR: ${GITHUB_ACTOR}" + echo "GITHUB_REPOSITORY: ${GITHUB_REPOSITORY}" + echo "REPO: ${REPO}" + echo "env.PATH_REPO: ${{ env.PATH_REPO }}" + echo "PATH_EXPORT: ${PATH_EXPORT}" + echo "PATH_EXPORT_CANVAS: ${PATH_EXPORT_CANVAS}" + echo "GITHUB_REPOSITORY_OWNER: ${GITHUB_REPOSITORY_OWNER}" echo "---------------------------------------------------------------------------------------------" echo "Folder contents at $(pwd):" ls -lh echo "---------------------------------------------------------------------------------------------" printenv sed --version - - name: Print R packages - run: | - # parse r packages from Rmd and md files - # grep -Eroh "(^library\([A-Za-z0-9]+\))|(^require\([A-Za-z0-9]+\))" *md | sed 's/library\|(\|)//g' | sort | uniq > r-packages.txt - # parse r packages from _site.yml - awk '/^[^ ]/{ f=/^packages:/; next } f{ if (sub(/:$/,"")) pkg=$2; else print pkg, $2 }' _site.yml | uniq | sort > r-packages.txt - cat r-packages.txt - - name: Cache R packages - id: cache-rp - uses: actions/cache@v3 - with: - path: ${{ env.R_LIBS_USER }} - key: ${{ runner.os }}-${{ matrix.config.r }}-${{ hashFiles('r-packages.txt') }} - - name: Install R dependencies - if: steps.cache-rp.outputs.cache-hit != 'true' - env: - GITHUB_PAT: ${{ secrets.PAT }} - run: | - Rscript -e 'install.packages(c("yaml","pagedown"))' - Rscript -e 'if(!is.null(yaml::read_yaml("_site.yml")$packages$packages_cran_repo)) install.packages(yaml::read_yaml("_site.yml")$packages$packages_cran_repo)' - Rscript -e 'if(!is.null(yaml::read_yaml("_site.yml")$packages$packages_cran_student)) install.packages(yaml::read_yaml("_site.yml")$packages$packages_cran_student)' - Rscript -e 'if(!is.null(yaml::read_yaml("_site.yml")$packages$packages_bioc_repo)) BiocManager::install(as.character(yaml::read_yaml("_site.yml")$packages$packages_bioc_repo))' - Rscript -e 'if(!is.null(yaml::read_yaml("_site.yml")$packages$packages_bioc_student)) BiocManager::install(as.character(yaml::read_yaml("_site.yml")$packages$packages_bioc_student))' - Rscript -e 'if(!is.null(yaml::read_yaml("_site.yml")$packages$packages_github_repo)) remotes::install_github(yaml::read_yaml("_site.yml")$packages$packages_github_repo)' - Rscript -e 'if(!is.null(yaml::read_yaml("_site.yml")$packages$packages_github_student)) remotes::install_github(yaml::read_yaml("_site.yml")$packages$packages_github_student)' - Rscript -e 'rownames(installed.packages())' - echo "R directory size:" - du -sh ${{ env.R_LIBS_USER }} - name: Render site, pull repo, copy folder, create index, push repo run: | # Add git info @@ -87,34 +52,32 @@ jobs: # Render website echo "Rendering Rmd files ..." - Rscript -e "rmarkdown::render_site()" + docker run --rm -u $(id -u ${USER}):$(id -g ${USER}) -v ${PWD}:/rmd ${{ env.REGISTRY }}/${{ env.ORG }}/${{ env.IMAGE }} + # Generate PDFs + cd ${PATH_EXPORT} + echo "Generating PDFs ..." + docker run --rm -u $(id -u ${USER}):$(id -g ${USER}) -v ${PWD}:/rmd ${{ env.REGISTRY }}/${{ env.ORG }}/${{ env.IMAGE }} Rscript -e "l <- list.files('.',pattern='slide.+html');if(length(l)!=0) {for(i in 1:length(l)) pagedown::chrome_print(l[i],extra_args=c('--no-sandbox','--disable-dev-shm-usage','--disable-gpu'))};" + cd .. # Render canvas version of website by changing _site.yml # suffixes output directory with -canvas # adds current output directory to be ignored # renames navbar block to remove menu # removes footer - #sed 's/\(output_dir:\)\s*\([0-9]*\)/\1 \2-canvas/' _site.yml | \ - #sed "/^exclude/s/\]$/,\"${path_export}\"]/" | \ - #sed 's/navbar:/unused:/' | \ - #sed 's/include://' | \ - #sed 's/after_body: assets\/footer-lab.html//' > _site.yml echo "Removing lab and slide links from schedule for canvas ..." - Rscript -e 'x <- read.csv("schedule.csv",sep=";",header=T,stringsAsFactors=F);x$link_youtube <- x$link_lab <- x$link_slide <- NA;write.table(x,"schedule.csv",sep=";",col.names=T,row.names=F,quote=FALSE,na="")' + docker run --rm -u $(id -u ${USER}):$(id -g ${USER}) -v ${PWD}:/rmd ${{ env.REGISTRY }}/${{ env.ORG }}/${{ env.IMAGE }} Rscript -e 'x <- read.csv("schedule.csv",sep=";",header=T,stringsAsFactors=F);x$link_youtube <- x$link_lab <- x$link_slide <- NA;write.table(x,"schedule.csv",sep=";",col.names=T,row.names=F,quote=FALSE,na="")' echo "Fixing _site.yml for canvas ..." - Rscript -e 'y <- yaml::read_yaml("_site.yml"); y$exclude <- append(y$exclude,y$output_dir); y$output_dir <- paste0(y$output_dir,"-canvas"); y$navbar <- NULL; yaml::write_yaml(y,"_site.yml");' + docker run --rm -u $(id -u ${USER}):$(id -g ${USER}) -v ${PWD}:/rmd ${{ env.REGISTRY }}/${{ env.ORG }}/${{ env.IMAGE }} Rscript -e 'y <- yaml::read_yaml("_site.yml"); y$exclude <- append(y$exclude,y$output_dir); y$output_dir <- paste0(y$output_dir,"-canvas"); y$navbar <- NULL; y$output$`bookdown::html_document2`$include <- NULL; yaml::write_yaml(y,"_site.yml");' ls -lh cat _site.yml echo "Rendering Rmd files for canvas ..." - Rscript -e "rmarkdown::render_site()" + docker run --rm -u $(id -u ${USER}):$(id -g ${USER}) -v ${PWD}:/rmd ${{ env.REGISTRY }}/${{ env.ORG }}/${{ env.IMAGE }} - # Modify links and generate PDFs - cd ${path_export} - Rscript -e "l <- list.files('.',pattern='slide.+html');if(length(l)!=0) {for(i in 1:length(l)) pagedown::chrome_print(l[i])};" - cd .. - cd ${path_export_canvas} + cd ${PATH_EXPORT_CANVAS} + + # Fix links # all links (except those starting with #) in all html files are set to open in new tab # all links (those pointing within website and ends with html) in all html files are removed # display links to be fixed @@ -135,45 +98,38 @@ jobs: rm -rf temp done echo "Generating PDFs for HTML slides ..." - Rscript -e "l <- list.files('.',pattern='slide.+html');if(length(l)!=0) {for(i in 1:length(l)) pagedown::chrome_print(l[i])};" + docker run --rm -u $(id -u ${USER}):$(id -g ${USER}) -v ${PWD}:/rmd ${{ env.REGISTRY }}/${{ env.ORG }}/${{ env.IMAGE }} Rscript -e "l <- list.files('.',pattern='slide.+html');if(length(l)!=0) {for(i in 1:length(l)) pagedown::chrome_print(l[i],extra_args=c('--no-sandbox','--disable-dev-shm-usage','--disable-gpu'))};" cd .. # List folder contents echo "Folder contents at $(pwd):" ls -lh - echo "Folder contents at ${path_repo}/${path_export}:" - ls -lh ${path_repo}/${path_export} - echo "Folder contents at ${path_repo}/${path_export_canvas}:" - ls -lh ${path_repo}/${path_export_canvas} + echo "Folder contents at ${PATH_REPO}/${PATH_EXPORT}:" + ls -lh ${PATH_REPO}/${PATH_EXPORT} + echo "Folder contents at ${PATH_REPO}/${PATH_EXPORT_CANVAS}:" + ls -lh ${PATH_REPO}/${PATH_EXPORT_CANVAS} # Clone gh-pages branch and remove old directories with same name git clone --single-branch --branch gh-pages "https://${{ secrets.TOKEN }}@github.com/${GITHUB_REPOSITORY}.git" tmprepo cd tmprepo - if [ -d $path_export ]; then - echo "Directory ${path_export} already exists. Removing the directory." - git rm -r $path_export - git commit -m "Old directory ${path_export} deleted." + if [ -d ${PATH_EXPORT} ]; then + echo "Directory ${PATH_EXPORT} already exists. Removing the directory." + git rm -r ${PATH_EXPORT} + git commit -m "Old directory ${PATH_EXPORT} deleted." fi - if [ -d $path_export_canvas ]; then - echo "Directory ${path_export_canvas} already exists. Removing the directory." - git rm -r $path_export_canvas - git commit -m "Old directory ${path_export_canvas} deleted." + if [ -d ${PATH_EXPORT}_canvas ]; then + echo "Directory ${PATH_EXPORT_CANVAS} already exists. Removing the directory." + git rm -r ${PATH_EXPORT}_canvas + git commit -m "Old directory ${PATH_EXPORT_CANVAS} deleted." fi - cd ${path_repo} - cp -r $path_export tmprepo/ - cp -r $path_export_canvas tmprepo/ + cd ${PATH_REPO} + cp -r ${PATH_EXPORT} tmprepo/ + cp -r ${PATH_EXPORT_CANVAS} tmprepo/ cd tmprepo echo "Folder contents at $(pwd):" ls -lh - # Create index file - echo "Full repo: ${GITHUB_REPOSITORY}" - str_user=$(dirname ${GITHUB_REPOSITORY}) - echo "User: $str_user" - repo=$(basename ${GITHUB_REPOSITORY}) - echo "Repo: $repo" - # create index file printf "" > index.md printf "The current and all previous instances of this workshop are listed below.\n" >> index.md @@ -189,7 +145,7 @@ jobs: printf -v thedate '2000-01-01 +%s years +%s months -1 day' "${i:0:2}" "${i:2}" dt=$(date -d "$thedate" +'%Y %b') echo $dt - printf "

$dt

" >> index.md + printf "

$dt

" >> index.md done printf "\n" >> index.md # printf "
\n" >> index.md