Merge branch 'main' of https://github.com/patolojiatlasi/patolojiatla… #274
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| 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 |