render.yml

name: Quarto Render Chapter for Histopathology Atlas (Patoloji Atlası)

on:
  workflow_dispatch:
  push:

jobs:
  quarto-render-and-deploy:
    # if: "!contains(github.event.head_commit.message, 'WIP') && !contains(github.event.head_commit.message, 'merge') && !contains(github.event.head_commit.message, 'lecture')"
    runs-on: ubuntu-latest
    # continue-on-error: true
    env:
      # RENV_PATHS_ROOT: ~/.local/share/renv
      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}

    steps:
      - name: "actions checkout"
        uses: actions/checkout@v3

      # - name: "Setup pandoc"
      #   uses: r-lib/actions/setup-pandoc@v2

      # - name: Install VIPS
      #   run: sudo apt-get install -y libvips-tools

      # - name: Convert Images
      #   run: |
      #     for file in ./screenshots/*.png; do vips copy "$file" "${file%.png}.jpg"; done

      - name: Set up Quarto
        uses: quarto-dev/quarto-actions/setup@v2
        # with:
          # To install LaTeX to build PDF book
          # tinytex: true
          # uncomment below and fill to pin a version
          #version: 1.3.353


      - name: "render EN"
        run: |
          quarto render


      # - uses: r-lib/actions/setup-tinytex@v2
      # - run: tlmgr --version

      # - name: Install additional LaTeX packages
      #   run: |
      #     tlmgr install titlesec
      #     tlmgr install svg
      #     tlmgr install transparent
      #     tlmgr install tikzfill
      #     tlmgr install sidenotes
      #     tlmgr install marginnote
      #     tlmgr install changepage
      #     tlmgr list --only-installed


      # - uses: actions/setup-python@v2
      #
      # - name: "Install Python deps"
      #   run: |
      #     pip install -r requirements.txt


      # - name: "Install curl for Bioconductor"
      #   run: |
      #     sudo apt-get install libcurl4-openssl-dev
      #     # sudo apt -y install libcurl4-openssl-dev
      #

      # - name: Setup R
      #   uses: r-lib/actions/setup-r@v2

      # - name: Setup renv
      #   uses: r-lib/actions/setup-renv@v2

      - name: Publish to GitHub Pages (and render)
        uses: quarto-dev/quarto-actions/publish@v2
        with:
          target: gh-pages
        env:
          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} # this secret is always available for github actions

      # - uses: r-lib/actions/setup-r-dependencies@v2

      # - name: Restore R package cache
      #   uses: actions/cache@v3
      #   with:
      #     path: ${{ env.R_LIBS_USER }}
      #     key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
      #     restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-

#
#       - name: "Install R Packages: Cache packages"
      #   uses: actions/cache@v3
      #   with:
      #     path: ${{ env.RENV_PATHS_ROOT }}
      #     key: ${{ runner.os }}-renv-${{ hashFiles('**/renv.lock') }}
      #     restore-keys: |
      #       ${{ runner.os }}-renv-


      # - name: Install R dependencies
      #   run: |
      #       if (!requireNamespace("remotes", quietly = TRUE)) {install.packages("remotes", dependencies = TRUE, quiet = TRUE, verbose = FALSE)}
      #       remotes::install_deps(dependencies = TRUE)
      #       if (!requireNamespace("renv", quietly = TRUE)) install.packages("renv", dependencies = TRUE, quiet = TRUE, verbose = FALSE)
      #       renv::restore()
      #       if (!requireNamespace("fs", quietly = TRUE)) install.packages("fs", dependencies = TRUE, quiet = TRUE, verbose = FALSE)
      #       if (!requireNamespace("quarto", quietly = TRUE)) install.packages("quarto", dependencies = TRUE, quiet = TRUE, verbose = FALSE)
      #       if (!requireNamespace("xfun", quietly = TRUE)) {install.packages("xfun", dependencies = TRUE, quiet = TRUE, verbose = FALSE)}
      #       if (!requireNamespace("readxl", quietly = TRUE)) {install.packages("readxl", dependencies = TRUE, quiet = TRUE, verbose = FALSE)}
      #       if (!requireNamespace("tinytex", quietly = TRUE)) {install.packages("tinytex, dependencies = TRUE, quiet = TRUE, verbose = FALSE")}
      #       if (!tinytex::is_tinytex()) {tinytex::install_tinytex()}
      #       saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
      #       writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
      #   shell: Rscript {0}


      # - name: "Install R Packages: Restore packages"
      #   shell: Rscript {0}
      #   run: |
      #     if (!requireNamespace("quarto", quietly = TRUE)) {install.packages("quarto")}
      #     if (!requireNamespace("fs", quietly = TRUE)) {install.packages("fs")}
      #     if (!requireNamespace("renv", quietly = TRUE)) install.packages("renv")
      #     renv::restore()


      # - name: "Setup Quarto"
      #   uses: quarto-dev/quarto-actions/setup@v2

      # - name: "Render Quarto"
      #   uses: quarto-dev/quarto-actions/render@v2

      # - name: "Install Quarto"
      #   # uses: pathologyatlas/quarto-render@main
      #   # uses: pommevilla/quarto-render@main
      #   uses: quarto-dev/quarto-actions/install-quarto@v1


      # - name: "Render Quarto"
      #   uses: quarto-dev/quarto-actions/render@v2


      # - name: "Prepare Render"
      #   shell: Rscript {0}
      #   run: |
      #     folders_to_delete <- fs::dir_ls(path = ".", recurse = FALSE, regexp = "_files$")
      #     fs::dir_delete(folders_to_delete)
      #     if (dir.exists(paths = "./gitlab_atlas/gitlab_atlas")) { fs::dir_delete(path = "./gitlab_atlas/gitlab_atlas") }
      #     if (dir.exists(paths = "./EN")) { fs::dir_delete(path = "./EN") }
      #     if (dir.exists(paths = "./docs")) { fs::dir_delete(path = "./docs") }
      #     if (dir.exists(paths = "./public")) { fs::dir_delete(path = "./public") }
      #     if (dir.exists(paths = "./_freeze")) { fs::dir_delete(path = "./_freeze") }

      # - name: "Prepare Render EN"
      #   shell: Rscript {0}
      #   run: |
      #     # prepare EN
      #     if (dir.exists(paths = "./_freeze_EN")) { fs::dir_copy(path = "./_freeze_EN", new_path = "./_freeze", overwrite = TRUE) }
      #     fs::file_copy(path = "./_quarto_EN.yml", new_path = "./_quarto.yml", overwrite = TRUE)
      #     fs::file_copy(path = "./R/languageEN.R", new_path = "./R/language.R",overwrite = TRUE)
      #     # EN qmd
      #     patolojiatlasi_histopathologyatlas <- readxl::read_excel("./patolojiatlasi_histopathologyatlas.xlsx", sheet = "chapters")
      #     patolojiatlasi_histopathologyatlas <- patolojiatlasi_histopathologyatlas[, c("TR_chapter_qmd", "EN_chapter_qmd")]
      #     TR_chapter_qmd <- paste0("./", patolojiatlasi_histopathologyatlas$TR_chapter_qmd, ".qmd")
      #     EN_chapter_qmd <- paste0("./", patolojiatlasi_histopathologyatlas$EN_chapter_qmd, ".qmd")
      #     subchapter_files <- list.files(path = "./_subchapters", pattern = "*.qmd", recursive = FALSE)
      #     subchapter_files  <- paste0("./_subchapters/", subchapter_files)
      #     subchapter_files_EN <- gsub(pattern = ".qmd", replacement = "_EN.qmd", x = subchapter_files)
      #     TR_chapter_qmd <- c(TR_chapter_qmd, subchapter_files)
      #     EN_chapter_qmd <- c(EN_chapter_qmd, subchapter_files_EN)
      #     fs::file_copy(path = TR_chapter_qmd, new_path = EN_chapter_qmd, overwrite = TRUE)
      #     xfun::gsub_files(files = EN_chapter_qmd, pattern = ".qmd >}}", replacement = "_EN.qmd >}}")

      # - name: "Render Book EN"
      #   shell: Rscript {0}
      #   run: |
      #     # Render EN
      #     quarto::quarto_render(".", as_job = FALSE)

#      - name: "render EN"
#        run: |
#          quarto render

      # - name: "Post Render Book From EN"
      #   shell: Rscript {0}
      #   run: |
      #     # remove unnecessary files and folders
      #     if (dir.exists(paths = "./_freeze")) { fs::dir_copy(path = "./_freeze", new_path = "./_freeze_EN", overwrite = TRUE) }
      #     if (file.exists("./_EN/CNAME")){fs::file_delete(path = "./_EN/CNAME")}
      #     fs::file_copy(path = "./CNAME-histopathologyatlas", new_path = "./_EN/CNAME", overwrite = TRUE)
      #     if (dir.exists(paths = "./_EN/public")) { fs::dir_delete(path = "./_EN/public") }
      #     if (dir.exists(paths = "./_EN/docs")) { fs::dir_delete(path = "./_EN/docs") }
      #     if (dir.exists(paths = "./_EN/gitlab_atlas")) { fs::dir_delete(path = "./_EN/gitlab_atlas") }
      #     if (dir.exists(paths = "./_EN/docs")) { fs::dir_delete(path = "./_EN/docs") }
      #     if (dir.exists(paths = "./_freeze")) { fs::dir_delete(path = "./_freeze") }
      #     # files to delete and revert
      #     patolojiatlasi_histopathologyatlas <- readxl::read_excel("./patolojiatlasi_histopathologyatlas.xlsx", sheet = "chapters")
      #     patolojiatlasi_histopathologyatlas <- patolojiatlasi_histopathologyatlas[, c("TR_chapter_qmd", "EN_chapter_qmd")]
      #     TR_chapter_qmd <- paste0("./", patolojiatlasi_histopathologyatlas$TR_chapter_qmd, ".qmd")
      #     EN_chapter_qmd <- paste0("./", patolojiatlasi_histopathologyatlas$EN_chapter_qmd, ".qmd")
      #     subchapter_files <- list.files(path = "./_subchapters", pattern = "*.qmd", recursive = FALSE)
      #     subchapter_files  <- paste0("./_subchapters/", subchapter_files)
      #     subchapter_files_EN <- gsub(pattern = ".qmd", replacement = "_EN.qmd", x = subchapter_files)
      #     TR_chapter_qmd <- c(TR_chapter_qmd, subchapter_files)
      #     EN_chapter_qmd <- c(EN_chapter_qmd, subchapter_files_EN)
      #     files_to_revert <- EN_chapter_qmd[EN_chapter_qmd %in% TR_chapter_qmd]
      #     xfun::gsub_files(files = files_to_revert, pattern = "_EN.qmd >}}", replacement = ".qmd >}}")
      #     files_to_delete <- list.files(path = "./", pattern = "_EN.qmd", recursive = FALSE)
      #     fs::file_delete(path = files_to_delete)
      #     files_to_delete <- list.files(path = "./_subchapters", pattern = "_EN.qmd", recursive = FALSE)
      #     files_to_delete  <- paste0("./_subchapters/", files_to_delete)
      #     fs::file_delete(path = files_to_delete)

      # - name: "Render Book From TR"
      #   shell: Rscript {0}
      #   run: |
      #     # prepare TR
      #     fs::file_copy(path = "./_quarto_TR.yml", new_path = "./_quarto.yml", overwrite = TRUE)
      #     fs::file_copy(path = "./R/languageTR.R", new_path = "./R/language.R", overwrite = TRUE)
      #     if (dir.exists(paths = "./_freeze")) { fs::dir_delete(path = "./_freeze") }
      #     if (dir.exists(paths = "./_freeze_TR")) { fs::dir_copy(path = "./_freeze_TR", new_path = "./_freeze", overwrite = TRUE) }
      #     if (dir.exists(paths = "./docs")) { fs::dir_delete(path = "./docs") }
      #     if (dir.exists(paths = "./gitlab_atlas/gitlab_atlas")) { fs::dir_delete(path = "./gitlab_atlas/gitlab_atlas") }
      #     # render TR
      #     quarto::quarto_render(".", as_job = FALSE)
      #     # post render TR
      #     if (dir.exists(paths = "./_freeze")) { fs::dir_copy(path = "./_freeze", new_path = "./_freeze_TR", overwrite = TRUE) }
      #     if (dir.exists(paths = "./_freeze")) { fs::dir_delete(path = "./_freeze") }
      #     if (dir.exists(paths = "./_docs/public")) { fs::dir_delete(path = "./_docs/public") }
      #     if (dir.exists(paths = "./_docs/_public")) { fs::dir_delete(path = "./_docs/_public") }
      #     if (dir.exists(paths = "./_docs/EN")) { fs::dir_delete(path = "./_docs/EN") }
      #     if (dir.exists(paths = "./_docs/_EN")) { fs::dir_delete(path = "./_docs/_EN") }
      #     if (dir.exists(paths = "./_docs/_lecture-notes")) { fs::dir_delete(path = "./_docs/_lecture-notes") }
      #     if (dir.exists(paths = "./_docs/lecture-notes")) { fs::dir_delete(path = "./_docs/lecture-notes") }
      #     if (dir.exists(paths = "./_docs/gitlab_atlas")) { fs::dir_delete(path = "./_docs/gitlab_atlas") }
      #     folders_to_delete <- fs::dir_ls(path = "./_docs", recurse = FALSE, regexp = "_files$")
      #     fs::dir_delete(folders_to_delete)
      #     folders_to_delete <- fs::dir_ls(path = "./_docs", recurse = FALSE, regexp = "_pdf_")
      #     fs::dir_delete(folders_to_delete)
      #     folders_to_delete <- fs::dir_ls(path = "./_docs", recurse = FALSE, regexp = "_epub_")
      #     fs::dir_delete(folders_to_delete)
      #     folders_to_delete <- fs::dir_ls(path = "./_docs", recurse = FALSE, regexp = "_freeze")
      #     fs::dir_delete(folders_to_delete)
      #     fs::dir_copy(path = "./_docs", new_path = "./public", overwrite = TRUE)
      #     if (file.exists("./public/CNAME")){ fs::file_delete(path = "./public/CNAME") }
      #     fs::dir_copy(path = "./_docs", new_path = "./gitlab_atlas/public", overwrite = TRUE)
      #     fs::dir_copy(path = "./_docs", new_path = "./docs", overwrite = TRUE)
      #     if (dir.exists(paths = "./_docs")) { fs::dir_delete(path = "./_docs") }
      #     if (dir.exists(paths = "./_EN")) { fs::dir_copy(path = "./_EN", new_path = "./EN", overwrite = TRUE) }
      #     if (dir.exists(paths = "./_EN")) { fs::dir_delete(path = "./_EN") }
      #     folders_to_delete <- fs::dir_ls(path = ".", recurse = FALSE, regexp = "_files$")
      #     fs::dir_delete(folders_to_delete)
      #     if (file.exists("./gitlab_atlas/public/CNAME")){fs::file_delete(path = "./gitlab_atlas/public/CNAME")}
      #     if (dir.exists(paths = "./docs/EN/lecture-notes")) { fs::dir_delete(path = "./docs/EN/lecture-notes") }
      #     if (dir.exists(paths = "./docs/EN")) { fs::dir_delete(path = "./docs/EN") }
      #     if (dir.exists(paths = "./docs/public")) {fs::dir_delete(path = "./docs/public")}
      #     if (dir.exists(paths = "./docs/gitlab_atlas")) {fs::dir_delete(path = "./docs/gitlab_atlas")}
      #     folders_to_delete <- fs::dir_ls(path = "./EN", recurse = FALSE, regexp = "_freeze")
      #     fs::dir_delete(folders_to_delete)
      #     folders_to_delete <- fs::dir_ls(path = "./docs", recurse = FALSE, regexp = "_freeze")
      #     fs::dir_delete(folders_to_delete)
      #     if (dir.exists(paths = "./EN/docs")) {fs::dir_delete(path = "./EN/docs")}
      #     if (dir.exists(paths = "./EN/_docs")) {fs::dir_delete(path = "./EN/_docs")}


#      - name: "render TR"
#        run: |
#          quarto render

#       - name: "Deploy to gh-pages"
#         uses: peaceiris/actions-gh-pages@v3
#         if: github.ref == 'refs/heads/main'
#         with:
#           github_token: ${{ secrets.GITHUB_TOKEN }}
#           publish_dir: ./docs



      - name: Commit results to main branch
        run: |
          git config --local user.email "actions@github.com"
          git config --local user.name "GitHub Actions"
          git add .
          git commit -m "CI added changes `date +'%Y-%m-%d %H:%M:%S'`" || echo "No changes to commit"
          git push origin || echo "No changes to commit"
      - name: Push changes # push the output folder to your repo
        uses: ad-m/github-push-action@master
        with:
          branch: main
          github_token: ${{ secrets.GITHUB_TOKEN }}
          # WORKFLOW_GITHUB_TOKEN
          force: true

      # - name: Pushes to patolojiatlasi EN
      #   uses: cpina/github-action-push-to-another-repository@main
      #   env:
      #     API_TOKEN_GITHUB: ${{ secrets.API_TOKEN_GITHUB }}
      #   with:
      #     source-directory: 'EN'
      #     destination-github-username: 'patolojiatlasi'
      #     destination-repository-name: 'EN'
      #     user-email: drserdarbalci@gmail.com
      #     target-branch: main



      # - name: Pushes to histopathologyatlas
      #   uses: cpina/github-action-push-to-another-repository@main
      #   env:
      #     API_TOKEN_GITHUB: ${{ secrets.API_TOKEN_GITHUB }}
      #   with:
      #     source-directory: 'EN'
      #     destination-github-username: 'histopathologyatlas'
      #     destination-repository-name: 'histopathologyatlas.github.io'
      #     user-email: drserdarbalci@gmail.com
      #     target-branch: main



      # - name: Pushes to atlas
      #   uses: cpina/github-action-push-to-another-repository@main
      #   env:
      #     API_TOKEN_GITHUB: ${{ secrets.API_TOKEN_GITHUB }}
      #   with:
      #      source-directory: 'gitlab_atlas'
      #      destination-github-username: 'sbalci'
      #      destination-repository-name: 'atlas'
      #      user-email: drserdarbalci@gmail.com
      #      target-branch: main

      # - name: Pushes to pathologyatlas EN2
      #   uses: cpina/github-action-push-to-another-repository@main
      #   env:
      #     API_TOKEN_GITHUB: ${{ secrets.API_TOKEN_GITHUB }}
      #   with:
      #     source-directory: 'EN'
      #     destination-github-username: 'pathologyatlas'
      #     destination-repository-name: 'EN2'
      #     user-email: drserdarbalci@gmail.com
      #     target-branch: main


  # send-tweet:
  #   if: "!contains(github.event.head_commit.message, 'WIP') && !contains(github.event.head_commit.message, 'merge')   && !contains(github.event.head_commit.message, 'notweet')"
  #   runs-on: ubuntu-latest
  #   steps:
  #     - uses: actions/checkout@v3
  #     - name: "Tweet"
  #       id: date
  #       run: echo "::set-output name=date::$(date +'%Y-%m-%d')"
  #     - uses: ethomson/send-tweet-action@v1
  #       with:
  #         status: '#Patoloji atlası güncellendi ${{ steps.date.outputs.date }} ${{github.event.head_commit.message}}. #dijitalpatoloji #WSI #preparat #memorialpatoloji #memorialsaglik https://www.patolojiatlasi.com/'
  #         consumer-key: ${{ secrets.API_KEY }}
  #         consumer-secret: ${{ secrets.API_SECRET_KEY }}
  #         access-token: ${{ secrets.ACCESS_TOKEN }}
  #         access-token-secret: ${{ secrets.ACCESS_TOKEN_SECRET }}


  # send-tweet-EN:
  #   if: "!contains(github.event.head_commit.message, 'WIP') && !contains(github.event.head_commit.message, 'merge')  && !contains(github.event.head_commit.message, 'notweet')"
  #   runs-on: ubuntu-latest
  #   steps:
  #     - uses: actions/checkout@v3
  #     - name: "Tweet-EN"
  #       id: date
  #       run: echo "::set-output name=date::$(date +'%Y-%m-%d')"
  #     - uses: ethomson/send-tweet-action@v1
  #       with:
  #         status: '#Pathology #atlas is updated ${{ steps.date.outputs.date }} ${{github.event.head_commit.message}}. #digitalpathology #WSI #slides https://www.patolojiatlasi.com/EN/'
  #         consumer-key: ${{ secrets.API_KEY }}
  #         consumer-secret: ${{ secrets.API_SECRET_KEY }}
  #         access-token: ${{ secrets.ACCESS_TOKEN }}
  #         access-token-secret: ${{ secrets.ACCESS_TOKEN_SECRET }}


  # lecture-notes:
  #   if: "contains(github.event.head_commit.message, 'lecture')"
  #   needs: quarto-render-and-deploy
  #   runs-on: ubuntu-latest
  #   env:
  #     RENV_PATHS_ROOT: ~/.local/share/renv
  #     GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
  #   steps:
  #     - name: "actions checkout"
  #       uses: actions/checkout@v3
  #
  #     - name: "Setup Quarto"
  #       uses: quarto-dev/quarto-actions/setup@v2
  #
  #     - name: "Install curl for Bioconductor"
  #       run: |
  #         sudo apt -y install libcurl4-openssl-dev
  #
  #     - uses: r-lib/actions/setup-r@v2
  #
  #     - uses: r-lib/actions/setup-renv@v2
  #
  #
  #
  #     - name: Restore R package cache
  #       uses: actions/cache@v3
  #       with:
  #         path: ${{ env.R_LIBS_USER }}
  #         key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
  #         restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
  #
  #
  #     - name: Install R dependencies
  #       run: |
  #           if (!requireNamespace("remotes", quietly = TRUE)) {install.packages("remotes", dependencies = TRUE, quiet = TRUE, verbose = FALSE)}
  #           remotes::install_deps(dependencies = TRUE)
  #           if (!requireNamespace("renv", quietly = TRUE)) install.packages("renv", dependencies = TRUE, quiet = TRUE, verbose = FALSE)
  #           renv::restore()
  #           if (!requireNamespace("fs", quietly = TRUE)) install.packages("fs", dependencies = TRUE, quiet = TRUE, verbose = FALSE)
  #           if (!requireNamespace("quarto", quietly = TRUE)) install.packages("quarto", dependencies = TRUE, quiet = TRUE, verbose = FALSE)
  #           saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
  #           writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
  #       shell: Rscript {0}
  #
  #
  #     - name: "Render patoloji-ders-notlari"
  #       shell: Rscript {0}
  #       run: |
  #         filestorender <- list.files(path = "./lecture-notes/", pattern = ".qmd", full.names = TRUE, recursive = TRUE)
  #         purrr::map(.x = filestorender, .f= quarto::quarto_render)
  #         # quarto::quarto_render(input = "./lecture-notes/*.qmd")
  #
  #
  #     - name: Commit results to main branch
  #       run: |
  #         git config --local user.email "actions@github.com"
  #         git config --local user.name "GitHub Actions"
  #         git add .
  #         git commit -m "CI added changes `date +'%Y-%m-%d %H:%M:%S'`" || echo "No changes to commit"
  #         git push origin || echo "No changes to commit"
  #
  #     - name: Push changes # push the output folder to your repo
  #       uses: ad-m/github-push-action@master
  #       with:
  #         branch: main
  #         github_token: ${{ secrets.GITHUB_TOKEN }}
  #         # WORKFLOW_GITHUB_TOKEN
  #         force: true
  #
  #     - name: Pushes to patoloji-ders-notlari
  #       uses: cpina/github-action-push-to-another-repository@main
  #       env:
  #         API_TOKEN_GITHUB: ${{ secrets.API_TOKEN_GITHUB }}
  #       with:
  #         source-directory: 'lecture-notes'
  #         destination-github-username: 'sbalci'
  #         destination-repository-name: 'patoloji-ders-notlari'
  #         user-email: drserdarbalci@gmail.com
  #         target-branch: main

  # build-to-gitlab:
  #   needs: quarto-render-and-deploy
  #   runs-on: ubuntu-latest
  #   steps:
  #   - uses: actions/checkout@v3
  #     with:
  #       fetch-depth: 0
  #   - name: Mirror + trigger CI
  #     uses: SvanBoxel/gitlab-mirror-and-ci-action@master
  #     with:
  #       args: "https://gitlab.com/patolojiatlasi/tr"
  #     env:
  #       FORCE_PUSH: "true"
  #       GITLAB_HOSTNAME: "gitlab.com"
  #       GITLAB_USERNAME: "patolojiatlasi"
  #       GITLAB_PASSWORD: ${{ secrets.GITLAB_PASSWORD }} # // Generate here: https://gitlab.com/profile/personal_access_tokens
  #       GITLAB_PROJECT_ID: "36540563" # // https://gitlab.com/<namespace>/<repository>/edit
  #       GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} # // https://docs.github.com/en/actions/reference/authentication-in-a-workflow#about-the-github_token-secret


  # push-to-gitlab:
  #   needs: quarto-render-and-deploy
  #   runs-on: ubuntu-latest
  #   steps:
  #   - name: Checkout repository
  #     uses: actions/checkout@v3
  #     with:
  #       lfs: true
  #
  #
  #   - name: Setup Git LFS
  #     run: |
  #       sudo apt-get install git-lfs
  #       git lfs install
  #
  #   - name: Push LFS objects to GitLab
  #     run: |
  #       git lfs push --all "https://oauth2:${{ secrets.GITLAB_PASSWORD }}@gitlab.com/patolojiatlasi/patolojiatlasi.gitlab.io.git"
  #
  #
  #
  #   - name: Push to GitLab
  #     run: |
  #       git config --global user.name "GitHub Action"
  #       git config --global user.email "action@github.com"
  #       git remote add gitlab "https://oauth2:${{ secrets.GITLAB_PASSWORD }}@gitlab.com/patolojiatlasi/patolojiatlasi.gitlab.io.git"
  #       git fetch --unshallow
  #       git push --force gitlab main --no-tags


#
  # build-to-gitlab2:
  #   needs: quarto-render-and-deploy
  #   runs-on: ubuntu-latest
  #   steps:
  #   - uses: actions/checkout@v1
  #   - name: Mirror + trigger CI
  #     uses: SvanBoxel/gitlab-mirror-and-ci-action@master
  #     with:
  #       args: "https://gitlab.com/patolojiatlasi/patolojiatlasi.gitlab.io"
  #     env:
  #       FORCE_PUSH: "true"
  #       GITLAB_HOSTNAME: "gitlab.com"
  #       GITLAB_USERNAME: "PatolojiAtlasi"
  #       GITLAB_PASSWORD: ${{ secrets.GITLAB_PASSWORD }} # // Generate here: https://gitlab.com/profile/personal_access_tokens
  #       GITLAB_PROJECT_ID: "48371083" # // https://gitlab.com/<namespace>/<repository>/edit
  #       GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} # // https://docs.github.com/en/actions/reference/authentication-in-a-workflow#about-the-github_token-secret




  # build-to-gitlab3:
  #   needs: quarto-render-and-deploy
  #   runs-on: ubuntu-latest
  #   steps:
  #   - uses: actions/checkout@v1
  #   - name: Mirror + trigger CI
  #     uses: SvanBoxel/gitlab-mirror-and-ci-action@master
  #     with:
  #       args: "https://gitlab.com/patolojiatlasi/patolojiatlasi2"
  #     env:
  #       FORCE_PUSH: "true"
  #       GITLAB_HOSTNAME: "gitlab.com"
  #       GITLAB_USERNAME: "PatolojiAtlasi"
  #       GITLAB_PASSWORD: ${{ secrets.GITLAB_PASSWORD }} # // Generate here: https://gitlab.com/profile/personal_access_tokens
  #       GITLAB_PROJECT_ID: "48375788" # // https://gitlab.com/<namespace>/<repository>/edit
  #       GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} # // https://docs.github.com/en/actions/reference/authentication-in-a-workflow#about-the-github_token-secret




  # quartopub:
  #   needs: quarto-render-and-deploy
  #   runs-on: ubuntu-latest
  #   steps:
  #     - name: Check out repository
  #       uses: actions/checkout@v3
  #
  #     - name: Set up Quarto
  #       uses: quarto-dev/quarto-actions/setup@v2
  #
  #     - name: Render and Publish
  #       uses: quarto-dev/quarto-actions/publish@v2
  #       with:
  #         target: quarto-pub
  #         path: docs
  #         render: false
  #         QUARTO_PUB_AUTH_TOKEN: ${{ secrets.QUARTO_PUB_AUTH_TOKEN }}
  #         GITHUB_EMAIL: drserdarbalci@gmail.com
  #         GITHUB_USERNAME: sbalci