Merge branch 'V2310' #71
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| name: build | |
| on: | |
| push: | |
| branches-ignore: | |
| - gh-pages | |
| jobs: | |
| rmd-render-job: | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| config: | |
| - {os: ubuntu-20.04, r: '4.2'} | |
| runs-on: ${{ matrix.config.os }} | |
| steps: | |
| - name: Set time zone | |
| uses: szenius/[email protected] | |
| with: | |
| 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: ${{ matrix.config.r }} | |
| - uses: r-lib/actions/setup-pandoc@v2 | |
| - name: Install linux dependencies | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get install libxml2-dev libssl-dev libcurl4-openssl-dev libudunits2-dev libopenblas-base libgdal-dev libfreetype6-dev libpng-dev libtiff5-dev libjpeg-dev libfontconfig1-dev libharfbuzz-dev libfribidi-dev | |
| wget https://dl.google.com/linux/direct/google-chrome-stable_current_amd64.deb | |
| sudo apt install ./google-chrome-stable_current_amd64.deb | |
| rm -rf google-chrome-stable_current_amd64.deb | |
| - name: Define variables | |
| run: | | |
| echo "path_repo=$(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 | |
| 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}" | |
| 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 | |
| git config --global user.email "[email protected]" | |
| git config --global user.name "gh_action" | |
| # Render website | |
| echo "Rendering Rmd files ..." | |
| Rscript -e "rmarkdown::render_site()" | |
| # 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$link_slide <- NA;write.table(x,"schedule.csv",sep=";",col.names=T,row.names=F,quote=FALSE,na="")' | |
| echo "Fixing _site.yml for canvas ..." | |
| Rscript -e 'y <- yaml::read_yaml("_site.yml"); y$exclude <- append(y$exclude,y$output_dir); y$output_dir <- paste0(y$output_dir,"-canvas"); y$navbar <- NULL; yaml::write_yaml(y,"_site.yml");' | |
| ls -lh | |
| cat _site.yml | |
| echo "Rendering Rmd files for canvas ..." | |
| Rscript -e "rmarkdown::render_site()" | |
| # 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} | |
| # 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 ..." | |
| Rscript -e "l <- list.files('.',pattern='slide.+html');if(length(l)!=0) {for(i in 1:length(l)) pagedown::chrome_print(l[i])};" | |
| 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 | |
| echo "Full repo: ${GITHUB_REPOSITORY}" | |
| str_user=$(dirname ${GITHUB_REPOSITORY}) | |
| echo "User: $str_user" | |
| repo=$(basename ${GITHUB_REPOSITORY}) | |
| echo "Repo: $repo" | |
| # create index file | |
| printf "<div class='wrapper-logo'><img class='logo' src='assets/logo.svg'></div>" > index.md | |
| printf "The current and all previous instances of this workshop are listed below.\n" >> index.md | |
| printf "<hr>\n" >> index.md | |
| printf "<div class='workshop-list'>\n" >> index.md | |
| dirs=$(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 |