🔄 Synced file(s) with jhudsl/OTTR_Template

.github/ISSUE_TEMPLATE/course-content-add.md

@@ -0,0 +1,17 @@
+---
+name: New content idea
+about: Suggest an idea for the course
+title: ''
+labels: ''
+assignees:
+
+---
+
+## Describe the your scope of your content idea
+<!-- What will this cover and how does it relate to the current course material? -->
+
+## Describe the learning objectives for your content idea
+<!-- What will users learn from this new content? -->
+
+## Additional context or resources
+<!-- Add any other context or related resources we should know about? -->

.github/ISSUE_TEMPLATE/course-problem-report.md

@@ -0,0 +1,28 @@
+---
+name: Course Problem Report
+about: Create a report to help improve the course
+title: [Problem]
+labels: bug
+assignees:
+
+---
+
+## Describe what is not working with the course
+<!-- A clear and concise description of what the bug is. -->
+
+## Steps to Reproduce
+<!-- Steps to reproduce the behavior:
+1. Go to '...'
+2. Click on '....'
+3. Scroll down to '....'
+4. See error
+-->
+
+## Expected behavior
+<!-- A clear and concise description of what you expected to happen. -->
+
+## Screenshots
+<!-- If applicable, add screenshots to help explain your problem. -->
+
+## Additional context
+<!-- Add any other context about the problem here. -->

.github/ISSUE_TEMPLATE/url-error.md

@@ -0,0 +1,8 @@
+---
+title: Broken URLs found in the course!
+labels: url-error
+---
+URL's in this course were just checked and some broken URLs were found.
+
+**Number of errors:** {{ env.ERROR_NUM }}  
+**File where errors are:** [url checks file here]({{ env.FILE_URL }})

.github/workflows/render-all.yml

@@ -200,7 +200,7 @@ jobs:
           git push -u origin main || echo "No changes to push"
 
       - name: Run ottrpal::bookdown_to_embed_leanpub
-        if: needs.yaml-check.outputs.toggle_quiz_check == 'no'
+        if: ${{ needs.yaml-check.outputs.toggle_quiz_check == 'no'}}
         run: |
           echo needs.yaml-check.outputs.toggle_make_book_txt == 'yes'
           echo needs.yaml-check.outputs.toggle_make_book_txt
@@ -211,7 +211,7 @@ jobs:
             quiz_dir = NULL)"
 
       - name: Run ottrpal::bookdown_to_embed_leanpub
-        if: needs.yaml-check.outputs.toggle_quiz_check == 'yes'
+        if: ${{ needs.yaml-check.outputs.toggle_quiz_check == 'yes'}}
         run: |
           Rscript -e "ottrpal::bookdown_to_embed_leanpub(
             render = FALSE, \

.github/workflows/transfer-rendered-files.yml

@@ -0,0 +1,117 @@
+# This code was adapted from code written by Josh Shapiro
+# for the Childhood Cancer Data Lab, an initiative of Alexs Lemonade Stand Foundation.
+# https://github.com/AlexsLemonade/exercise-notebook-answers
+
+# Adapted for this jhudsl repository by Candace Savonen Apr 2021
+
+name: Copy over from main template to _Quizzes repo
+
+on:
+  workflow_dispatch:
+  workflow_run:
+    workflows: [ "Render all output courses" ]
+    branches: [ main, staging ]
+    types:
+      - completed
+
+jobs:
+
+  yaml-check:
+    name: Load user automation choices
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+        # Use the yaml-env-action action.
+      - name: Load environment from YAML
+        uses: doughepi/[email protected]
+        with:
+            files: config_automation.yml # Pass a space-separated list of configuration files. Rightmost files take precedence.
+    outputs:
+      toggle_coursera: "${{ env.RENDER_COURSERA }}"
+      toggle_leanpub: "${{ env.RENDER_LEANPUB }}"
+
+
+  file-quizzes-pr:
+    name: File _Quizzes Transfer PR
+    runs-on: ubuntu-latest
+    container:
+      image: jhudsl/ottrpal:main
+    needs: [yaml-check]
+    if: ${{needs.yaml-check.outputs.toggle_coursera == 'yes' || needs.yaml-check.outputs.toggle_leanpub == 'yes'}}
+
+    steps:
+      - name: Checkout from Bookdown Repo
+        uses: actions/checkout@v4
+        with:
+          path: bookdown
+          token: ${{ secrets.GH_PAT }}
+
+      - name: Run git repo check
+        id: git_repo_check
+        env:
+          GH_PAT: ${{ secrets.GH_PAT }}
+        run: |
+          # What's the Quizzes repository's name?
+          QUIZ_REPO=$(echo ${GITHUB_REPOSITORY} | sed "s/_Bookdown/ /g" | sed "s/_Template/ /g" | awk '{print $1"_Quizzes"}')
+          echo $QUIZ_REPO
+
+          # Run repo check script
+          curl -o git_repo_check.R https://raw.githubusercontent.com/jhudsl/ottr-reports/main/scripts/git_repo_check.R
+          results=$(Rscript --vanilla git_repo_check.R --repo "$GITHUB_REPOSITORY" --git_pat "$GH_PAT")
+          echo $QUIZ_REPO exists: $results
+
+          echo "git_results=$results" >> $GITHUB_OUTPUT
+          echo "leanpub_repo=$QUIZ_REPO" >> $GITHUB_OUTPUT
+
+      - name: Checkout code from Leanpub repo
+        if: ${{ steps.git_repo_check.outputs.git_results == 'TRUE' }}
+        uses: actions/checkout@v4
+        with:
+          path: quizzes
+          repository: ${{ steps.git_repo_check.outputs.leanpub_repo }}
+          token: ${{ secrets.GH_PAT }}
+
+      - name: Get files from Bookdown repo
+        if: ${{ steps.git_repo_check.outputs.git_results == 'TRUE' }}
+        shell: bash
+        env:
+          GH_PAT: ${{ secrets.GH_PAT }}
+        run: |
+          # Copy over images folder (from bookdown to quizzes repo)
+          mkdir -p quizzes/resources/chapt_screen_images
+          cp bookdown/resources/chapt_screen_images/* quizzes/resources/chapt_screen_images
+
+          # Copy over _bookdown.yml (from bookdown to quizzes repo)
+          cp bookdown/_bookdown.yml quizzes/_bookdown.yml
+
+      - name: Create PR with resources files
+        if: ${{ steps.git_repo_check.outputs.git_results == 'TRUE' }}
+        uses: peter-evans/create-pull-request@v3
+        id: cpr
+        with:
+          path: quizzes # Must create the PR in the Quizzes Repo
+          token: ${{ secrets.GH_PAT }}
+          commit-message: Copy files from Bookdown repository
+          signoff: false
+          branch: auto_copy_rendered_files
+          delete-branch: true
+          title: 'GHA: Automated transfer of ottrpal-needed files from Bookdown repository'
+          body: |
+            ### Description:
+             This PR was initiated by transfer-rendered.yml in the Bookdown repository.
+             It copies over the ottrpal-needed folder (for the `bookdown_to_embed_leanpub(render = FALSE)` function
+             to run properly.
+               - resources/chapt_screen_images/*
+               - _bookdown.yml
+          labels: |
+            automated
+          reviewers: $GITHUB_ACTOR
+
+      # Write out PR info
+      - name: Check outputs
+        if: ${{ steps.git_repo_check.outputs.git_results == 'TRUE' }}
+        run: |
+          echo "Pull Request Number - ${{ steps.cpr.outputs.pull-request-number }}"
+          echo "Pull Request URL - ${{ steps.cpr.outputs.pull-request-url }}"

config_automation.yml

@@ -12,15 +12,19 @@ spell-check: yes
 style-code: yes
 # Test build the docker image if any docker-relevant files have been changed
 docker-test: no
-# Do we need to make the book txt file automatically? 
-make_book_txt: yes
+# Should URLs be tested periodically?
+url-check-periodically: yes
 
 ##### Renderings run upon merge to main branch #####
 # Rendering each platform's content
-render-website: quarto
+render-website: rmd
 render-leanpub: yes
 render-coursera: no
 
+## Automate the creation of Book.txt file? yes/no
+## This is only relevant if render-leanpub is yes, otherwise it will be ignored
+make-book-txt: yes
+
 # What docker image should be used for rendering?
-# The default is jhudsl/base_ottr:latest
-rendering-docker-image: 'jhudsl/ottr_quarto:main'
+# The default is jhudsl/base_ottr:main
+rendering-docker-image: 'jhudsl/base_ottr:main'

resources/exclude_files.txt

@@ -0,0 +1,8 @@
+About.Rmd
+docs/*
+style-sets/*
+manuscript/*
+CONTRIBUTING.md
+LICENSE.md
+code_of_conduct.md
+README.md

style-sets/data-trail/_output.yml

@@ -0,0 +1,18 @@
+bookdown::gitbook:
+  css: assets/style_DataTrail.css
+  includes:
+    before_body: assets/big-image-DataTrail.html
+    after_body: assets/footer.html
+  highlight: tango
+  config:
+    toc:
+      collapse: section
+      before: |
+       <a href="https://www.datatrail.org/"><img src="assets/DataTrail_logo.jpg" style="padding-left: 0px; padding-top: 8px;"</a>
+      after: |
+       <p style="text-align:center;"> <a href="https://www.ottrproject.org/" target="blank" > This content was published with</a> <a href="https://bookdown.org/" target="blank"> bookdown using</a> </p>
+       <p style="text-align:center;"> <a href="https://github.com/jhudsl/OTTR_Template"> The OTTR Template by:</a></p>
+       <p style="text-align:center;"> <a href="http://jhudatascience.org/"> The Johns Hopkins Data Science Lab </a></p>
+       <a href="http://jhudatascience.org/"><img src="https://jhudatascience.org/images/dasl.png" style=" width: 80%; filter: grayscale(100%); padding-left: 40px; padding-top: 8px; vertical-align: top "</a>
+       <p style="text-align:center; font-size: 12px;"> <a href="https://github.com/rstudio4edu/rstudio4edu-book/"> Style adapted from: rstudio4edu-book </a> <a href ="https://creativecommons.org/licenses/by/2.0/"> (CC-BY 2.0) </a></p>
+       <p style="padding-left: 40px;"><div class="trapezoid" style = "padding-left: 40px;"><span>  <a href="https://forms.gle/VWaJYc3zATe3qxYC9"> Click here to provide feedback</a> <img src="assets/itcr_arrow.png" style=" width: 10%" ></span></div></p>

style-sets/data-trail/copy-to-assets/big-image-DataTrail.html

@@ -0,0 +1,12 @@
+<head>
+  <meta name="viewport" content="width=device-width,minimum-scale=1.0,maximum-scale=1.0,initial-scale=1.0">
+  <!--script src="https://kit.fontawesome.com/6a26f47516.js"></script-->
+  <!--<script src="assets/hideOutput.js"></script>-->
+  <link href="assets/style_DataTrail.css" rel="stylesheet">
+</head>
+
+
+
+<div class="hero-image-container"> 
+  <img class= "hero-image" src="assets/DataTrail.jpg">
+</div>