Merge pull request #410 from appliedepi/handbook_v2.5_en

Handbook v2.5 en

.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 @oliviabboyd, please check the box when you finish"
-            elif [ "$lang" = "es" ]; then
-              checkboxes="$checkboxes @amateo250, 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 @Luccan97, 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

@@ -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:contact@appliedepi.org"
     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:contact@appliedepi.org" 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:contact@appliedepi.org" 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:contact@appliedepi.org" 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:contact@appliedepi.org" 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:contact@appliedepi.org" 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:contact@appliedepi.org" 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:contact@appliedepi.org" 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:contact@appliedepi.org" 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:contact@appliedepi.org" 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:contact@appliedepi.org" 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:contact@appliedepi.org" 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:contact@appliedepi.org" 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:contact@appliedepi.org" 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:contact@appliedepi.org" 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:contact@appliedepi.org" 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:contact@appliedepi.org" class="alert-link">Службы поддержки по R</a>.'
   };
 
   // Default to English if the detected language is not supported

contribution_guide_05-02-2021.qmd

@@ -111,7 +111,7 @@ In your code, please maintain [tidyverse style](https://style.tidyverse.org/) as
   * Bullets are nice and easy to read  
 * Explanations should not rely on websites - users may be offline; links can be included but should not be required viewing  
 * Prioritize using packages and functions that are *stable*, *commonly-used*, and do not require additional downloads  
-* Use lots of `# comments` to explain the code to a beginner - be concise and previse please!  
+* Use lots of `# comments` to explain the code to a beginner - be concise and precise please!  
 * When using a function for the first time in a page, indicate its package in the accompanying text, or in code like `dplyr::mutate()`  
 * Make use of magrittr pipes and dplyr verbs whenever practical  
 * When making assignments, use `<-`, NOT `=`  
@@ -216,7 +216,7 @@ knitr::include_graphics(here::here("images", "Git_console.png"))
 ```  
 Please note the buttons circled as they will be referenced later (from left to right):  
 
-* Button to begin "commiting" your changes to your branch (will open a new window)  
+* Button to begin "committing" your changes to your branch (will open a new window)  
 * Arrows to PULL (update your local version of the branch with any changes to made your branch by others) and to PUSH (send any completed commits stored in your local version of the branch to the remote/Github version of your branch)  
 * The Git tab in RStudio  
 * Button to create a NEW branch of whichever version is listed to the right. **You almost always want to branch off of the master (after you PULL to update the master first)**.