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| name: Quarto Render Bilingual Book Push Other Repos GitLab | |
| 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: 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 | |
| # - 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 | |
| # - uses: r-lib/actions/setup-r-dependencies@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 | |
| - 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 = "./public")) { fs::dir_delete(path = "./public") } | |
| if (dir.exists(paths = "./EN")) { fs::dir_delete(path = "./EN") } | |
| if (dir.exists(paths = "./docs")) { fs::dir_delete(path = "./docs") } | |
| 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") | |
| patolojiatlasi_histopathologyatlas <- patolojiatlasi_histopathologyatlas[, c("TR_chapter_qmd", "EN_chapter_qmd")] | |
| patolojiatlasi_histopathologyatlas$TR_chapter_qmd <- paste0(patolojiatlasi_histopathologyatlas$TR_chapter_qmd, ".qmd") | |
| patolojiatlasi_histopathologyatlas$EN_chapter_qmd <- paste0(patolojiatlasi_histopathologyatlas$EN_chapter_qmd, ".qmd") | |
| fs::file_copy(path = patolojiatlasi_histopathologyatlas$TR_chapter_qmd, | |
| new_path = patolojiatlasi_histopathologyatlas$EN_chapter_qmd, | |
| overwrite = TRUE) | |
| - 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: | | |
| 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")} | |
| patolojiatlasi_histopathologyatlas <- readxl::read_excel("./patolojiatlasi_histopathologyatlas.xlsx") | |
| patolojiatlasi_histopathologyatlas <- patolojiatlasi_histopathologyatlas[, c("TR_chapter_qmd", "EN_chapter_qmd")] | |
| `%>%` <- magrittr::`%>%` | |
| patolojiatlasi_histopathologyatlas <- patolojiatlasi_histopathologyatlas %>% | |
| dplyr::distinct() %>% dplyr::filter(TR_chapter_qmd != EN_chapter_qmd) | |
| patolojiatlasi_histopathologyatlas$EN_chapter_qmd <- paste0(patolojiatlasi_histopathologyatlas$EN_chapter_qmd, ".qmd") | |
| fs::file_delete(path = patolojiatlasi_histopathologyatlas$EN_chapter_qmd) | |
| - name: "Render Book From TR" | |
| shell: Rscript {0} | |
| run: | | |
| # prepare TR | |
| 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) } | |
| 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) | |
| # render TR | |
| quarto::quarto_render(".", as_job = FALSE) | |
| 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/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") } | |
| fs::dir_copy(path = "./_docs", new_path = "./public", overwrite = TRUE) | |
| fs::dir_copy(path = "./_docs", new_path = "./docs", overwrite = TRUE) | |
| if (dir.exists(paths = "./_docs")) { fs::dir_delete(path = "./_docs") } | |
| fs::dir_copy(path = "./_EN", new_path = "./EN", overwrite = TRUE) | |
| if (dir.exists(paths = "./_EN")) { fs::dir_delete(path = "./_EN") } | |
| if (file.exists("./public/CNAME")){fs::file_delete(path = "./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")} | |
| folders_to_delete <- fs::dir_ls(path = ".", recurse = FALSE, regexp = "_files$") | |
| fs::dir_delete(folders_to_delete) | |
| # - 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 "[email protected]" | |
| 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: [email protected] | |
| 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: [email protected] | |
| 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: 'public' | |
| destination-github-username: 'sbalci' | |
| destination-repository-name: 'atlas' | |
| user-email: [email protected] | |
| target-branch: main | |
| # - name: Pushes to pathologyatlas EN2 | |
| # uses: cpina/github-action-push-to-another-repository@main | |
| # env: | |
| # API_TOKEN_GITHUB: ${{ secrets.API_TOKEN_GITHUB }} | |
| # with: | |
| # source-directory: 'EN' | |
| # destination-github-username: 'pathologyatlas' | |
| # destination-repository-name: 'EN2' | |
| # user-email: [email protected] | |
| # target-branch: main | |
| # send-tweet: | |
| # if: "!contains(github.event.head_commit.message, 'WIP') && !contains(github.event.head_commit.message, 'merge') && !contains(github.event.head_commit.message, 'notweet')" | |
| # runs-on: ubuntu-latest | |
| # steps: | |
| # - uses: actions/checkout@v3 | |
| # - name: "Tweet" | |
| # id: date | |
| # run: echo "::set-output name=date::$(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 "[email protected]" | |
| # 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: [email protected] | |
| # target-branch: main | |
| build-to-gitlab: | |
| 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/tr" | |
| env: | |
| 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 | |
| # 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: [email protected] | |
| # GITHUB_USERNAME: sbalci |