Upload Johans updated slides #162
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| name: build | |
| on: | |
| push: | |
| branches-ignore: | |
| - gh-pages | |
| env: | |
| REGISTRY: ghcr.io | |
| ORG: nbisweden | |
| IMAGE: workshop-rnaseq:latest | |
| jobs: | |
| rmd-render-job: | |
| runs-on: ubuntu-22.04 | |
| steps: | |
| - name: Set time zone | |
| uses: szenius/set-timezone@v1.0 | |
| with: | |
| timezoneLinux: "Europe/Stockholm" | |
| timezoneMacos: "Europe/Stockholm" | |
| timezoneWindows: "W. Europe Standard Time" | |
| - name: Checkout | |
| uses: actions/checkout@v3 | |
| - 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" >> $GITHUB_ENV | |
| echo "REPO=$(basename ${GITHUB_REPOSITORY})" >> $GITHUB_ENV | |
| - name: Check docker and variables | |
| run: | | |
| 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: Render site, pull repo, copy folder, create index, push repo | |
| run: | | |
| # Add git info | |
| git config --global user.email "do_not_email@example.com" | |
| git config --global user.name "gh_action" | |
| # Render website | |
| echo "Rendering Rmd files ..." | |
| 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 | |
| echo "Removing lab and slide links from schedule for canvas ..." | |
| 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 ..." | |
| 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; yaml::write_yaml(y,"_site.yml");' | |
| ls -lh | |
| cat _site.yml | |
| echo "Rendering Rmd files for canvas ..." | |
| docker run --rm -u $(id -u ${USER}):$(id -g ${USER}) -v ${PWD}:/rmd ${{ env.REGISTRY }}/${{ env.ORG }}/${{ env.IMAGE }} | |
| 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 | |
| echo "Number of links to be corrected:" | |
| grep -E '(<a href="[^#][^(https?)&^(www)?].+html.*">)([^(a>).]+)(<\/a>)' *.html | \ | |
| grep -E '(<a href="[^#][-a-zA-Z0-9@:%._\+~#=/?&]+")(>)' | wc -l | |
| echo "List of links to be corrected:" | |
| grep -E '(<a href="[^#][^(https?)&^(www)?].+html.*">)([^(a>).]+)(<\/a>)' *.html | \ | |
| grep -E '(<a href="[^#][-a-zA-Z0-9@:%._\+~#=/?&]+")(>)' | |
| echo "Fixing bad links ..." | |
| for i in *.html; do | |
| sed -E 's/<h1 class="title toc-ignore">[^>.]*<\/h1>//g' $i | \ | |
| sed -E 's/<h3 class="subtitle">[^>.]*<\/h3>//g' | \ | |
| sed -E 's/<h4 class="author">[^>.]*<\/h4>//g' | \ | |
| sed -E 's/(<a href="[^#][^(https?)&^(www)?].+(html|pdf).*">)([^(a>).]+)(<\/a>)/[link removed]/g' | \ | |
| sed -E 's/(<a href="[^#][-a-zA-Z0-9@:%._\+~#=/?&]+")(>)/\1 target="_blank">/g' > temp | |
| cat temp > $i | |
| rm -rf temp | |
| done | |
| echo "Generating PDFs for HTML slides ..." | |
| 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)) {cat(paste('Running',l[i],'\n')); 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} | |
| # 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." | |
| 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." | |
| fi | |
| cd ${PATH_REPO} | |
| cp -r ${PATH_EXPORT} tmprepo/ | |
| cp -r ${PATH_EXPORT_CANVAS} tmprepo/ | |
| cd tmprepo | |
| echo "Folder contents at $(pwd):" | |
| ls -lh | |
| # create index file | |
| printf "<div class='wrapper-logo'><img class='logo' src='assets/logo.svg'></div>" > index.md | |
| printf "The current and all previous instances of this workshop are listed below.\n" >> index.md | |
| printf "<hr>\n" >> index.md | |
| printf "<div class='workshop-list'>\n" >> index.md | |
| dirs=$(ls -d [0-9]*[0-9]/ | sed 's/\///' | tac) | |
| for i in ${dirs[@]} | |
| do | |
| if [ ${i:2:2} -lt 1 ] || [ ${i:2:2} -gt 12 ] | |
| then echo "Month: ${i:2:2}. Last 2 values in output_dir must be a month between 01 and 12." | |
| fi | |
| # This code works for year 2000 and later | |
| printf -v thedate '2000-01-01 +%s years +%s months -1 day' "${i:0:2}" "${i:2}" | |
| dt=$(date -d "$thedate" +'%Y %b') | |
| echo $dt | |
| printf "<h3><a href='https://${GITHUB_REPOSITORY_OWNER}.github.io/${REPO}/${i}/'>$dt</a></h3>" >> index.md | |
| done | |
| printf "</div>\n" >> index.md | |
| # printf "<hr>\n" >> index.md | |
| # printf "$(date +'%Y') • NBIS\n" >> index.md | |
| echo "Folder contents at $(pwd):" | |
| ls -lh | |
| # Push changes back | |
| git add . | |
| git commit -m "Updated contents at $(date +%Y%m%d-%H%M%S)" | |
| git push origin |