Merge branch 'main' into 501-have-urls-periodically-checked

jhudsl · Feb 29, 2024 · cff4724 · cff4724
2 parents b8775cb + cc497be
commit cff4724
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Showing 45 changed files with 299 additions and 299 deletions.
diff --git a/.github/sync.yml b/.github/sync.yml
@@ -37,7 +37,7 @@ group:
       jhudsl/Machine_Learning_for_Cancer_Informatics
       jhudsl/Cancer_Informatics_Data_Visualization
       jhudsl/Cancer_Genome_Informatics
-      jhudsl/Cancer-Imaging-Informatics
+      fhdsl/Cancer_Imaging_Informatics
       datatrail-jhu/DataTrail_Template
       abyzovlab/CNVpytor-course
       opencasestudies/OCS_Guide
@@ -56,11 +56,13 @@ group:
       griffithlab/CIVIC_SVI_Course
       PracticalGenomics/cogaps-on-sciserver
       fhdsl/AI_for_software
+      fhdsl/AI_for_Decision_Makers
       griffithlab/Immuno_Workflow_Course
       fhdsl/S1_Intro_to_R
       fhdsl/S1_Intro_to_Command_Line
       fhdsl/S1_Intro_to_Git_GitHub
       fhdsl/WDL_Workflows_Guide
+      fhdsl/S2-Collaborative-Git-GitHub
 
 ###ADD NEW REPO HERE following the format above#
 

diff --git a/.github/workflows/delete-preview.yml b/.github/workflows/delete-preview.yml
@@ -18,7 +18,7 @@ jobs:
 
       # Check out current repository
       - name: checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           fetch-depth: 0
 

diff --git a/.github/workflows/docker-build.yml b/.github/workflows/docker-build.yml
@@ -20,7 +20,7 @@ jobs:
 
     steps:
       - name: checkout repo
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Login as jhudsl-robot
         run: |

diff --git a/.github/workflows/docker-test.yml b/.github/workflows/docker-test.yml
@@ -33,10 +33,10 @@ jobs:
 
     steps:
       - name: checkout repo
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Verify Dockerfiles changed?
-        uses: tj-actions/verify-changed-files@v8.8
+        uses: tj-actions/verify-changed-files@v17
         id: verify-changed-files
         with:
           files: |

diff --git a/.github/workflows/pull_request.yml b/.github/workflows/pull_request.yml
@@ -14,9 +14,10 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           fetch-depth: 0
+          token: ${{ secrets.GH_PAT }}
 
         # Use the yaml-env-action action.
       - name: Load environment from YAML
@@ -41,6 +42,7 @@ jobs:
           git push --set-upstream origin $branch_name || echo echo branch exists remotely
         shell: bash
 
+
     outputs:
       toggle_spell_check: "${{ env.SPELL_CHECK }}"
       toggle_style_code: "${{ env.STYLE_CODE }}"
@@ -59,6 +61,7 @@ jobs:
       check_type: spelling
       error_min: 3
       gh_pat: secrets.GH_PAT
+      branch_name: ${GITHUB_HEAD_REF}
 
   url-check:
     name: Check URLs
@@ -69,6 +72,7 @@ jobs:
       check_type: urls
       error_min: 0
       gh_pat: secrets.GH_PAT
+      branch_name: ${GITHUB_HEAD_REF}
 
   quiz-check:
     name: Check quiz formatting
@@ -79,6 +83,7 @@ jobs:
       check_type: quiz_format
       error_min: 0
       gh_pat: secrets.GH_PAT
+      branch_name: ${GITHUB_HEAD_REF}
 
 ############################# Style the code ###################################
   style-code:
@@ -91,7 +96,7 @@ jobs:
 
     steps:
       - name: Checkout files
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           fetch-depth: 0
 
@@ -117,7 +122,7 @@ jobs:
 
     steps:
       - name: Checkout files
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           fetch-depth: 0
 

diff --git a/.github/workflows/render-all.yml b/.github/workflows/render-all.yml
@@ -19,7 +19,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
         # Use the yaml-env-action action.
       - name: Load environment from YAML
@@ -44,7 +44,7 @@ jobs:
 
     steps:
       - name: checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           fetch-depth: 0
           token: ${{ secrets.GH_PAT }}
@@ -96,7 +96,7 @@ jobs:
 
     steps:
       - name: checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           fetch-depth: 0
           token: ${{ secrets.GH_PAT }}
@@ -135,7 +135,7 @@ jobs:
 
     steps:
       - name: checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           fetch-depth: 0
           token: ${{ secrets.GH_PAT }}
@@ -211,7 +211,7 @@ jobs:
 
     steps:
       - name: checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           fetch-depth: 0
           token: ${{ secrets.GH_PAT }}
@@ -229,12 +229,16 @@ jobs:
         run: Rscript -e "ottrpal::convert_coursera_quizzes()"
 
       # Commit the rendered bookdown files
+      # Only commit coursera quizzes if the directory is present
       - name: Commit rendered Coursera files
         env:
           GH_PAT: ${{ secrets.GH_PAT }}
         run: |
           git remote set-url origin https://${GH_PAT}@github.com/${GITHUB_REPOSITORY}
           git fetch origin
+          if [ -d 'coursera_quizzes' ]; then
+            git add --force coursera_quizzes/*
+          fi
           git add --force manuscript/*
           git add --force resources/*
           git add --force docs/*

diff --git a/.github/workflows/send-updates.yml b/.github/workflows/send-updates.yml
@@ -18,7 +18,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout Repository
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Login as jhudsl-robot
         run: |

diff --git a/.github/workflows/starting-course.yml b/.github/workflows/starting-course.yml
@@ -16,7 +16,7 @@ jobs:
     if: github.event.repository.name != 'OTTR_Template'
     steps:
       - name: checkout repo
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Login as jhudsl-robot
         run: |

diff --git a/.github/workflows/transfer-rendered-files.yml b/.github/workflows/transfer-rendered-files.yml
@@ -21,7 +21,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
         # Use the yaml-env-action action.
       - name: Load environment from YAML
@@ -42,31 +42,33 @@ jobs:
     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: ${{ secrets.GH_PAT }}
         run: |
-          sudo apt-get install subversion
-
           # What's the Quizzes repository's name?
           QUIZ_REPO=$(echo ${GITHUB_REPOSITORY} | sed "s/_Bookdown/ /g" | sed "s/_Template/ /g" | awk '{print $1"_Quizzes"}')
           echo $QUIZ_REPO
 
-          # Get repo check script
-          svn export --force https://github.com/${GITHUB_REPOSITORY}.git/branches/${GITHUB_REF#refs/heads/}/scripts/git_repo_check.R git_repo_check.R
-
           # Run repo check script
-          results=$(Rscript --vanilla git_repo_check.R --repo "$GITHUB_REPOSITORY" --git_pat "$GH_PAT")
+          results=$(Rscript --vanilla bookdown/scripts/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@v3
+        uses: actions/checkout@v4
         with:
+          path: quizzes
           repository: ${{ steps.git_repo_check.outputs.leanpub_repo }}
           token: ${{ secrets.GH_PAT }}
 
@@ -76,17 +78,19 @@ jobs:
         env:
           GH_PAT: ${{ secrets.GH_PAT }}
         run: |
-          # Copy over images folder
-          svn export --force https://github.com/${GITHUB_REPOSITORY}.git/branches/${GITHUB_REF#refs/heads/}/resources/chapt_screen_images resources/chapt_screen_images
-
-          # Copy over _bookdown.yml
-          svn export --force https://github.com/${GITHUB_REPOSITORY}.git/branches/${GITHUB_REF#refs/heads/}/_bookdown.yml _bookdown.yml
+          # 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

diff --git a/02-chapter_of_course.Rmd b/02-chapter_of_course.Rmd
@@ -98,14 +98,6 @@ knitr::include_url("https://www.youtube.com/embed/VOCYL-FNbr0")
 
 <iframe src="https://www.youtube.com/embed/VOCYL-FNbr0" width="672" height="400px"></iframe>
 
-## File examples
-
-You can again use simple markdown syntax to just include a link to a file like so:
-
-[A file](https://www.bgsu.edu/content/dam/BGSU/center-for-faculty-excellence/docs/TLGuides/TLGuide-Learning-Objectives.pdf).
-
-Alternatively you can embed files like PDFs.
-
 ### Using `knitr`
 
 ```{r, fig.align="center", echo=FALSE, out.width="100%"}
@@ -243,6 +235,15 @@ reflection text
 </div>
 
 
+Here is a `<div class = "wip">` box:
+
+<div class = "wip">
+
+Work in Progress text
+
+</div>
+
+
 ## Dropdown summaries
 
 <details><summary> You can hide additional information in a dropdown menu </summary>

diff --git a/assets/box_images/under_construction.png b/assets/box_images/under_construction.png
diff --git a/assets/style.css b/assets/style.css
@@ -250,7 +250,7 @@ li.appendix span, li.part span { /* for TOC part names */
 /* Sidebar formating --------------------------------------------*/
 /* from r-pkgs.org*/
 
-div.notice, div.warning, div.github, div.dictionary, div.reflection {
+div.notice, div.warning, div.github, div.dictionary, div.reflection, div.wip {
   padding: 1em;
   margin: 1em 0;
   padding-left: 100px;
@@ -304,6 +304,14 @@ div.reflection{
   background-image: url("../assets/box_images/thinking_face.png");
 }
 
+div.wip{
+  border: 4px #000000;
+  border-style: solid;
+  background-size: 70px;
+  background-position: 15px center;
+  background-color: #f4d03f;
+  background-image: url("../assets/box_images/under_construction.png");
+}
 
 /* .book .book-body .page-wrapper .page-inner section.normal is needed
    to override the styles produced by gitbook, which are ridiculously

diff --git a/docs/01-intro.md b/docs/01-intro.md
@@ -32,7 +32,7 @@ devtools::session_info()
 ##  collate  en_US.UTF-8                 
 ##  ctype    en_US.UTF-8                 
 ##  tz       Etc/UTC                     
-##  date     2023-05-24                  
+##  date     2024-01-16                  
 ## 
 ## ─ Packages ───────────────────────────────────────────────────────────────────
 ##  package     * version date       lib source                            

diff --git a/docs/02-chapter_of_course.md b/docs/02-chapter_of_course.md
@@ -130,14 +130,6 @@ Note that you should use `echo=FALSE` in the code chunk because we don't want th
 
 <iframe src="https://www.youtube.com/embed/VOCYL-FNbr0" width="672" height="400px"></iframe>
 
-## File examples
-
-You can again use simple markdown syntax to just include a link to a file like so:
-
-[A file](https://www.bgsu.edu/content/dam/BGSU/center-for-faculty-excellence/docs/TLGuides/TLGuide-Learning-Objectives.pdf).
-
-Alternatively you can embed files like PDFs.
-
 ### Using `knitr`
 
 <iframe src="https://drive.google.com/file/d/1mm72K4V7fqpgAfWkr6b7HTZrc3f-T6AV/preview" width="100%" height="400px"></iframe>
@@ -271,6 +263,15 @@ reflection text
 </div>
 
 
+Here is a `<div class = "wip">` box:
+
+<div class = "wip">
+
+Work in Progress text
+
+</div>
+
+
 ## Dropdown summaries
 
 <details><summary> You can hide additional information in a dropdown menu </summary>
@@ -297,7 +298,7 @@ devtools::session_info()
 ##  collate  en_US.UTF-8                 
 ##  ctype    en_US.UTF-8                 
 ##  tz       Etc/UTC                     
-##  date     2023-05-24                  
+##  date     2024-01-16                  
 ## 
 ## ─ Packages ───────────────────────────────────────────────────────────────────
 ##  package     * version date       lib source