Handbook v2.5 jp

.Rhistory

@@ -1,4 +1,3 @@
-############
 learnr,   # interactive tutorials in RStudio Tutorial pane
 swirl,    # interactive tutorials in R console
 # project and file management
@@ -510,3 +509,4 @@ bookdown::render_book(
 output_format = 'bookdown::bs4_book',
 config_file = "_bookdown.yml")
 renv::status()
+here("data", "linelists", "linelist_raw.xlsx")

.github/workflows/create_pr_on_pr.yml

@@ -36,7 +36,11 @@ jobs:
           for lang in "${LANGS[@]}"; do
             TRANSLATION_BRANCH="handbook_${VERSION_SUFFIX/_en/_$lang}"
 
-            # Check if the translation branch exists
+
+            # Ensure we have all history
+            git fetch --all            
+
+            #! Check if the translation branch exists
             if git ls-remote --exit-code --heads origin "${TRANSLATION_BRANCH}"; then
               echo "Branch ${TRANSLATION_BRANCH} exists. Checking out and rebasing with ${EN_BRANCH}"
               git fetch --prune
@@ -55,74 +59,87 @@ jobs:
               git pull origin "${EN_BRANCH#refs/heads/}"
             fi
 
-            # Force push the changes to the remote repository
+            #! Force push the changes to the remote repository
             git push origin "${TRANSLATION_BRANCH}" --force
+
+            #! Get the list of changed .qmd files: COMPARED WITH main branch
+            changed_files=$(git diff --name-only origin/main "${TRANSLATION_BRANCH}" | grep -E '\.qmd$' | grep -Ev '\.[a-z]{2}\.qmd$')
+
+            if [ -z "$changed_files" ]; then
+              echo "No .qmd file changes to include in PR for ${TRANSLATION_BRANCH}"
+              continue
+            fi
+
+            echo "Changed files: $changed_files"
 
 
-            # Get the date of the latest commit on the english branch
+            #! Get the date of the latest commit on the english branch
             latest_commit_date=$(git show -s --format=%ci ${EN_BRANCH})
 
             echo "Commits on the English branch that were made after the latest commit on the translation branch at $latest_commit_date"
             latest_commit_en_branch=$(git show --format=%H -s ${EN_BRANCH})
             latest_commit_info=$(git log ${EN_BRANCH} --since="$latest_commit_date" --format="%H %s" --reverse)
             commit_messages=$(echo "$latest_commit_info" | cut -d' ' -f2-)
             latest_commit_master=$(git show --format=%H -s origin/master)
+
 
             echo $latest_commit_en_branch
             echo $latest_commit_master
             echo $latest_commit_info
 
-            # Check if there are new commits
-            if [ "$latest_commit_en_branch" == "$latest_commit_master" ]; then
+
+            #! Check if there are new commits
+            if [ "$latest_commit_en_branch" == "$latest_commit_main" ]; then
               echo "No new commits to include in PR for ${TRANSLATION_BRANCH}"
               continue
             fi
 
-            # Check if a PR already exists for this branch
+            #! Check if a PR already exists for this branch
             PR_EXISTS=$(gh pr list --head "${TRANSLATION_BRANCH}" --state open --json number --jq length)
             if [ "$PR_EXISTS" -eq 0 ]; then
               echo "Creating new PR for ${TRANSLATION_BRANCH}"
               PR_URL=$(gh pr create --base deploy-preview --head "$TRANSLATION_BRANCH" --title "Handbook ${VERSION_SUFFIX/_en/} $lang" --body "Automated pull request for $lang handbook version ${VERSION_SUFFIX/_en/}")
               PR_NUMBER=$(echo "$PR_URL" | grep -oE '[0-9]+$')
             else
-              # Get the PR number for the translation branch
+              #! Get the PR number for the translation branch
               echo "PR already exists for ${TRANSLATION_BRANCH}"
               PR_NUMBER=$(gh pr list --head "${TRANSLATION_BRANCH}" --state open --json number --jq ".[0].number")
             fi
 
             echo "Pull Request Number: $PR_NUMBER"
+
+            #! Initialize new PR body
+            new_pr_body="# Automated pull request for $lang handbook version ${VERSION_SUFFIX/_en/}"$'\n\n'
+
+            #! Mention a user in the PR description
+            case "$lang" in
+              "vn") new_pr_body+="@ntluong95, please review changes and check the box when you finish"$'\n' ;;
+              "fr") new_pr_body+="@oliviabboyd, please review changes and check the box when you finish"$'\n' ;;
+              "es") new_pr_body+="@amateo250, please review changes and check the box when you finish"$'\n' ;;
+              "jp") new_pr_body+="@hitomik723, please review changes and check the box when you finish"$'\n' ;;
+              "tr") new_pr_body+="@ntluong95, please review changes and check the box when you finish"$'\n' ;;
+              "pt") new_pr_body+="@Luccan97, please review changes and check the box when you finish"$'\n' ;;
+              "ru") new_pr_body+="@ntluong95, please review changes and check the box when you finish"$'\n' ;;
+            esac
 
-            # Add new commits as checkboxes to the PR description
+            #! Add new commits as checkboxes to the PR description
+            IFS=$'\n' # Change the Internal Field Separator to newline for correct iteration over lines
             checkboxes=""
-            for commit in $latest_commit_en_branch; do
-              checkboxes="$checkboxes- [ ] [$commit_messages](https://github.com/${{ github.repository }}/commit/$commit)"
+            for file in $changed_files; do
+              #! List only new commits compared with the main branch, tail -n +2 to skip the first line of output from git log, the latest commit will not be added into the message
+              list_commits=$(git log origin/main..${TRANSLATION_BRANCH} --follow --pretty=format:"%H" -- $file | tail -n +2 | paste -sd, - | sed 's/,/, /g')
+              for commit in $latest_commit_en_branch; do
+                checkboxes="$checkboxes- [ ] Chapter [\`$file\`](https://github.com/${{ github.repository }}/pull/$PR_NUMBER/files?file-filters%5B%5D=.qmd&show-viewed-files=true) has changes in the following commit(s): $list_commits. "
+                checkboxes="$checkboxes"$'\n'"$checkbox"
+
+              done
             done
 
-
-            # Mention a user in the PR description
-            if [ "$lang" = "vn" ]; then
-              checkboxes="$checkboxes @ntluong95, please check the box when you finish"
-            elif [ "$lang" = "fr" ]; then
-              checkboxes="$checkboxes @nsbatra, please check the box when you finish"
-            elif [ "$lang" = "es" ]; then
-              checkboxes="$checkboxes @robcrystalornelas, please check the box when you finish"
-            elif [ "$lang" = "jp" ]; then
-              checkboxes="$checkboxes @ntluong95, please check the box when you finish"
-            elif [ "$lang" = "tr" ]; then
-              checkboxes="$checkboxes @ntluong95, please check the box when you finish"
-            elif [ "$lang" = "pt" ]; then
-              checkboxes="$checkboxes @ntluong95, please check the box when you finish"
-            elif [ "$lang" = "ru" ]; then
-              checkboxes="$checkboxes @ntluong95, please check the box when you finish"
+            if [ -n "$checkboxes" ]; then
+              # Append the checkboxes to the new PR body
+              new_pr_body="$new_pr_body"$'\n'"$checkboxes"
             fi
 
-
-            # Retrieve the current PR description
-            current_pr_body=$(gh pr view $PR_NUMBER --json body --jq '.body')
-
-            # Append checkboxes to the current PR description
-            new_pr_body=$(printf "%s\n%s" "$current_pr_body" "$checkboxes")
-
             # gh api repos/${{ github.repository }}/issues/$PR_NUMBER --method PATCH --field body="$checkboxes"
             gh api repos/${{ github.repository }}/issues/$PR_NUMBER --method PATCH --field body="$new_pr_body"
 

_quarto.yml

@@ -57,7 +57,7 @@ book:
   title: "The Epidemiologist R Handbook"
   search:
     type: textbox
-  repo-url: https://github.com/appliedepi/epihandbook_eng
+  repo-url: https://github.com/appliedepi/epiRhandbook_eng
   # site-url: https://epirhandbook.com
   sharing: ["twitter", "facebook", "linkedin"]
   sidebar:
@@ -66,7 +66,7 @@ book:
       - icon: twitter
         href: "https://twitter.com/appliedepi"
       - icon: linkedin
-        href: "https://www.linkedin.com/company/appliedepi/"
+        href: "https://www.linkedin.com/company/appliedepi"
       # - icon: github
       #   menu:
       #     - text: Source Code
@@ -206,6 +206,7 @@ book:
     - new_pages/reportfactory.qmd #done
     - new_pages/flexdashboard.qmd #done
     - new_pages/shiny_basics.qmd #done
+    - new_pages/quarto.qmd #done
 
   # MISCELLANEOUS
   - part: "Miscellaneous"

banner.html

@@ -9,8 +9,8 @@
 
 <div class="alert alert-info alert-dismissible">
   <!-- <a href="#" class="close" data-dismiss="alert" aria-label="close">&times;</a>
-  <strong>Need help learning R?</strong> Enroll in Applied Epi's <a href="https://www.appliedepi.org/live/"
-    class="alert-link">intro R course</a>, try our <a href="https://www.appliedepi.org/tutorial/"
+  <strong>Need help learning R?</strong> Enroll in Applied Epi's <a href="https://www.appliedepi.org/training/public-courses"
+    class="alert-link">intro R course</a>, try our <a href="https://www.appliedepi.org/resources/tutorials"
     class="alert-link">free R tutorials</a>, post in our <a href="https://community.appliedepi.org/"
     class="alert-link">Community Q&A forum</a>, or ask about our <a href="mailto:[email protected]"
     class="alert-link">R Help Desk service</a>. -->
@@ -36,14 +36,14 @@
 
   // Translations for the content
   const translations = {
-    en: '<strong>Need help learning R?</strong> Enroll in Applied Epi\'s <a href="https://www.appliedepi.org/live/" class="alert-link">intro R course</a>, try our <a href="https://www.appliedepi.org/tutorial/" class="alert-link">free R tutorials</a>, post in our <a href="https://community.appliedepi.org/" class="alert-link">Community Q&A forum</a>, or ask about our <a href="mailto:[email protected]" class="alert-link">R Help Desk service</a>.',
-    fr: '<strong>Besoin d\'aide pour apprendre R ?</strong> Inscrivez-vous au <a href="https://www.appliedepi.org/live/" class="alert-link">cours d\'introduction à R</a> d\'Applied Epi, essayez nos <a href="https://www.appliedepi.org/tutorial/" class="alert-link">tutoriels R gratuits</a>, postez dans notre forum de <a href="https://community.appliedepi.org/" class="alert-link">questions-réponses communautaires</a>, ou demandez-nous des informations sur <a href="mailto:[email protected]" class="alert-link"> notre service d\'assistance R</a>.',
-    es: '<strong>¿Necesitas ayuda para aprender R?</strong> Inscríbete en el <a href="https://www.appliedepi.org/live/" class="alert-link">Curso de introducción a R</a> de Applied Epi, prueba nuestros <a href="https://www.appliedepi.org/tutorial/" class="alert-link">Tutoriales gratuitos de R</a>, escribe en nuestro <a href="https://community.appliedepi.org/" class="alert-link">Foro de preguntas y respuestas,</a> o pregunta por nuestra <a href="mailto:[email protected]" class="alert-link">Asistencia técnica para R</a>.',
-    vn: '<strong>Bạn cần giúp đỡ trong việc học R?</strong> Hãy đăng ký khóa học R cơ bản của Applied Epi tại <a href="https://www.appliedepi.org/live/" class="alert-link">đây</a>, hoặc thử các <a href="https://www.appliedepi.org/tutorial/" class="alert-link">hướng dẫn R miễn phí</a>, đăng bài trong <a href="https://community.appliedepi.org/" class="alert-link">diễn đàn cộng đồng</a>, hoặc gửi câu hỏi tới <a href="mailto:[email protected]" class="alert-link">dịch vụ Trợ giúp R</a> của chúng tôi.',
-    jp: '<strong>Rの学習について助けが必要ですか？</strong>Applied Epiの<a href="https://www.appliedepi.org/live/" class="alert-link">R入門コース</a>に登録するか、<a href="https://www.appliedepi.org/tutorial/" class="alert-link">無料Rチュートリアル</a>を試すか、<a href="https://community.appliedepi.org/" class="alert-link">コミュニティQ＆Aフォーラム</a>に投稿するか、<a href="mailto:[email protected]" class="alert-link">Rヘルプデスクサービス</a>についてお問い合わせください。',
-    pt: '<strong>Você precisa de ajuda para aprender R??</strong> Inscreva-se no curso de <a href="https://www.appliedepi.org/live/" class="alert-link">introdução ao R da Applied Epi</a>, experimente nossos <a href="https://www.appliedepi.org/tutorial/" class="alert-link">tutoriais gratuitos sobre o R</a>, publique em nosso <a href="https://community.appliedepi.org/" class="alert-link">fórum de perguntas e respostas</a>, ou solicite nosso <a href="mailto:[email protected]" class="alert-link">suporte ao R</a>.',
-    tr: '<strong>R öğrenmekte yardıma mı ihtiyacınız var?</strong> Applied Epi\'\nin <a href="https://www.appliedepi.org/live/" class="alert-link">R\'ye giriş kursuna</a> kaydolun, <a href="https://www.appliedepi.org/tutorial/" class="alert-link">ücretsiz R derslerimizi</a> deneyin, <a href="https://community.appliedepi.org/" class="alert-link">Topluluk Q&A forumunda</a> soru paylaşın, ya da <a href="mailto:[email protected]" class="alert-link">R Yardım Masası hizmetimiz</a> hakkında sorun.',
-    ru: '<strong>Нужна помощь в изучении R?</strong> Запишитесь на <a href="https://www.appliedepi.org/live/" class="alert-link">вводный курс по R</a> от Applied Epi, попробуйте наши <a href="https://www.appliedepi.org/tutorial/" class="alert-link">бесплатные учебные материалы по R</a>, задайте вопрос в нашем <a href="https://community.appliedepi.org/" class="alert-link">форуме вопросов и ответов сообщества</a>, или спросите о нашей услуге <a href="mailto:[email protected]" class="alert-link">Службы поддержки по R</a>.'
+    en: '<strong>Need help learning R?</strong> Enroll in Applied Epi\'s <a href="https://www.appliedepi.org/training/public-courses" class="alert-link">intro R course</a>, try our <a href="https://www.appliedepi.org/resources/tutorials" class="alert-link">free R tutorials</a>, post in our <a href="https://community.appliedepi.org/" class="alert-link">Community Q&A forum</a>, or ask about our <a href="mailto:[email protected]" class="alert-link">R Help Desk service</a>.',
+    fr: '<strong>Besoin d\'aide pour apprendre R ?</strong> Inscrivez-vous au <a href="https://www.appliedepi.org/training/public-courses" class="alert-link">cours d\'introduction à R</a> d\'Applied Epi, essayez nos <a href="https://www.appliedepi.org/resources/tutorials" class="alert-link">tutoriels R gratuits</a>, postez dans notre forum de <a href="https://community.appliedepi.org/" class="alert-link">questions-réponses communautaires</a>, ou demandez-nous des informations sur <a href="mailto:[email protected]" class="alert-link"> notre service d\'assistance R</a>.',
+    es: '<strong>¿Necesitas ayuda para aprender R?</strong> Inscríbete en el <a href="https://www.appliedepi.org/training/public-courses" class="alert-link">Curso de introducción a R</a> de Applied Epi, prueba nuestros <a href="https://www.appliedepi.org/resources/tutorials" class="alert-link">Tutoriales gratuitos de R</a>, escribe en nuestro <a href="https://community.appliedepi.org/" class="alert-link">Foro de preguntas y respuestas,</a> o pregunta por nuestra <a href="mailto:[email protected]" class="alert-link">Asistencia técnica para R</a>.',
+    vn: '<strong>Bạn cần giúp đỡ trong việc học R?</strong> Hãy đăng ký khóa học R cơ bản của Applied Epi tại <a href="https://www.appliedepi.org/training/public-courses" class="alert-link">đây</a>, hoặc thử các <a href="https://www.appliedepi.org/resources/tutorials" class="alert-link">hướng dẫn R miễn phí</a>, đăng bài trong <a href="https://community.appliedepi.org/" class="alert-link">diễn đàn cộng đồng</a>, hoặc gửi câu hỏi tới <a href="mailto:[email protected]" class="alert-link">dịch vụ Trợ giúp R</a> của chúng tôi.',
+    jp: '<strong>Rの学習について助けが必要ですか？</strong>Applied Epiの<a href="https://www.appliedepi.org/training/public-courses" class="alert-link">R入門コース</a>に登録するか、<a href="https://www.appliedepi.org/resources/tutorials" class="alert-link">無料Rチュートリアル</a>を試すか、<a href="https://community.appliedepi.org/" class="alert-link">コミュニティQ＆Aフォーラム</a>に投稿するか、<a href="mailto:[email protected]" class="alert-link">Rヘルプデスクサービス</a>についてお問い合わせください。',
+    pt: '<strong>Você precisa de ajuda para aprender R??</strong> Inscreva-se no curso de <a href="https://www.appliedepi.org/training/public-courses" class="alert-link">introdução ao R da Applied Epi</a>, experimente nossos <a href="https://www.appliedepi.org/resources/tutorials" class="alert-link">tutoriais gratuitos sobre o R</a>, publique em nosso <a href="https://community.appliedepi.org/" class="alert-link">fórum de perguntas e respostas</a>, ou solicite nosso <a href="mailto:[email protected]" class="alert-link">suporte ao R</a>.',
+    tr: '<strong>R öğrenmekte yardıma mı ihtiyacınız var?</strong> Applied Epi\'\nin <a href="https://www.appliedepi.org/training/public-courses" class="alert-link">R\'ye giriş kursuna</a> kaydolun, <a href="https://www.appliedepi.org/resources/tutorials" class="alert-link">ücretsiz R derslerimizi</a> deneyin, <a href="https://community.appliedepi.org/" class="alert-link">Topluluk Q&A forumunda</a> soru paylaşın, ya da <a href="mailto:[email protected]" class="alert-link">R Yardım Masası hizmetimiz</a> hakkında sorun.',
+    ru: '<strong>Нужна помощь в изучении R?</strong> Запишитесь на <a href="https://www.appliedepi.org/training/public-courses" class="alert-link">вводный курс по R</a> от Applied Epi, попробуйте наши <a href="https://www.appliedepi.org/resources/tutorials" class="alert-link">бесплатные учебные материалы по R</a>, задайте вопрос в нашем <a href="https://community.appliedepi.org/" class="alert-link">форуме вопросов и ответов сообщества</a>, или спросите о нашей услуге <a href="mailto:[email protected]" class="alert-link">Службы поддержки по R</a>.'
   };
 
   // Default to English if the detected language is not supported